Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold200
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 649609
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:326582 original size:10 final size:10
Alignment explanation
Indices: 326537--326594 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
326527 GGCTAAAAGA
326537 AAACAAAAAC
1 AAACAAAAAC
**
326547 AAGTAAAAAC
1 AAACAAAAAC
*
326557 AAA-AAACAAA
1 AAACAAA-AAC
326567 AAACAAAAAC
1 AAACAAAAAC
*
326577 AAACAAAAGC
1 AAACAAAAAC
326587 AAA-AAAAA
1 AAACAAAAA
326595 AAGTGGAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 7 0.18
10 29 0.74
11 3 0.08
ACGTcount: A:0.81, C:0.14, G:0.03, T:0.02
Consensus pattern (10 bp):
AAACAAAAAC
Found at i:327744 original size:10 final size:10
Alignment explanation
Indices: 327729--327774 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
327719 GTAGAAACTA
327729 AAAAAAAAAG
1 AAAAAAAAAG
*
327739 -AAAAAAAGG
1 AAAAAAAAAG
327748 AAAAAAAAAG
1 AAAAAAAAAG
**
327758 AAAGCAAAAG
1 AAAAAAAAAG
327768 AAAAAAA
1 AAAAAAA
327775 TGGATTTTCC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:327753 original size:19 final size:19
Alignment explanation
Indices: 327729--327774 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
327719 GTAGAAACTA
327729 AAAAAAAAAGAAA-AAAAGG
1 AAAAAAAAAGAAACAAAA-G
327748 AAAAAAAAAGAAAGCAAAAG
1 AAAAAAAAAGAAA-CAAAAG
327768 AAAAAAA
1 AAAAAAA
327775 TGGATTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.52
20 8 0.32
21 4 0.16
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAACAAAAG
Found at i:333647 original size:21 final size:21
Alignment explanation
Indices: 333614--333658 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
333604 TTGCAAGTTG
*
333614 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
333636 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
333656 AAA
1 AAA
333659 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:337535 original size:20 final size:20
Alignment explanation
Indices: 337509--337586 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
337499 AATGTCCAAA
337509 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
337529 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
*
337554 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
337574 TTGTATCGATACA
1 ATGTATCGATACA
337587 GGGTGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:337734 original size:21 final size:21
Alignment explanation
Indices: 337710--337756 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
337700 AAATCTTTTG
337710 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
337731 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
337751 CAAAAT
1 CAAAAT
337757 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:337753 original size:20 final size:19
Alignment explanation
Indices: 337712--337754 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
337702 ATCTTTTGCA
337712 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
337732 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
337752 AAA
1 AAA
337755 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:340158 original size:13 final size:13
Alignment explanation
Indices: 340140--340165 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
340130 TACAGCAAGT
340140 ATGTATCGATACA
1 ATGTATCGATACA
340153 ATGTATCGATACA
1 ATGTATCGATACA
340166 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:343503 original size:124 final size:124
Alignment explanation
Indices: 343283--343530 Score: 433
Period size: 124 Copynumber: 2.0 Consensus size: 124
343273 TTGATTGTCC
* *
343283 AATGTTGAAAATGCAGAACACGAACAAACTAAGGAAGAAAGCAATGGTGGCCATGTGGAGTGACA
1 AATGTTGAAAACGCAGAACACGAACAAACTAAGGAAGAAAGCAATGGTAGCCATGTGGAGTGACA
343348 GTGACACATCCGATGATGATGATTATGTGGCCAACTTATGTCGTATGGCTCATGATGAG
66 GTGACACATCCGATGATGATGATTATGTGGCCAACTTATGTCGTATGGCTCATGATGAG
* * * *
343407 AATGTTGAAACCGCAGAACACGAACCAACTGAGGAAGAAAGTAATGGTAGCCATGTGGAGTGACA
1 AATGTTGAAAACGCAGAACACGAACAAACTAAGGAAGAAAGCAATGGTAGCCATGTGGAGTGACA
*
343472 GTGACACATCCGATGATGATGATTATGTGGCCAACTTATGTCTTATGGCTCATGATGAG
66 GTGACACATCCGATGATGATGATTATGTGGCCAACTTATGTCGTATGGCTCATGATGAG
343531 CCCAAGGTAG
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 117 1.00
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (124 bp):
AATGTTGAAAACGCAGAACACGAACAAACTAAGGAAGAAAGCAATGGTAGCCATGTGGAGTGACA
GTGACACATCCGATGATGATGATTATGTGGCCAACTTATGTCGTATGGCTCATGATGAG
Found at i:343727 original size:21 final size:21
Alignment explanation
Indices: 343698--343749 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
343688 AAAGGAAAGT
* * *
343698 TAATAAATTAGAAAA-GAACA
1 TAATGAATTACAAAATGAAAA
*
343718 TAAATGAATTTCAAAATGAAAA
1 T-AATGAATTACAAAATGAAAA
343740 TAATGAATTA
1 TAATGAATTA
343750 ACTAAGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.27
Consensus pattern (21 bp):
TAATGAATTACAAAATGAAAA
Found at i:344864 original size:19 final size:19
Alignment explanation
Indices: 344840--344876 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
344830 TAATGCAAAG
*
344840 AAATTGTATCGATACATTA
1 AAATTGTATCAATACATTA
344859 AAATTGTATCAATACATT
1 AAATTGTATCAATACATT
344877 TTGACTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (19 bp):
AAATTGTATCAATACATTA
Found at i:347398 original size:13 final size:13
Alignment explanation
Indices: 347380--347404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
347370 ATATTGCTTA
347380 GTATCAATACATT
1 GTATCAATACATT
347393 GTATCAATACAT
1 GTATCAATACAT
347405 GTTGTTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
GTATCAATACATT
Found at i:348025 original size:34 final size:35
Alignment explanation
Indices: 347935--348028 Score: 111
Period size: 34 Copynumber: 2.7 Consensus size: 35
347925 TGAGACGTTT
*
347935 TATCTTAGCTTTTGAAAAGAATTAGGGAGAAAAGGTTC
1 TATCTTAGCTTGTGAAAAG-A-TA-GGAGAAAAGGTTC
* *
347973 CATCTT-GCTTGTGAAAAGATAGG-GAAGAGGTTC
1 TATCTTAGCTTGTGAAAAGATAGGAGAAAAGGTTC
*
348006 TATCTTAGCCTGTGAAAAGATAG
1 TATCTTAGCTTGTGAAAAGATAG
348029 TATTGTAAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 14 0.28
34 17 0.34
35 2 0.04
36 1 0.02
37 11 0.22
38 5 0.10
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (35 bp):
TATCTTAGCTTGTGAAAAGATAGGAGAAAAGGTTC
Found at i:348588 original size:21 final size:24
Alignment explanation
Indices: 348550--348607 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 24
348540 CCTACATCAA
*
348550 AAAATCCA-CAAAATTAAACA-T-
1 AAAATACACCAAAATTAAACAGTG
*
348571 AAAATACACCAAAA-TAAAGAGTG
1 AAAATACACCAAAATTAAACAGTG
*
348594 AAAACACACCAAAA
1 AAAATACACCAAAA
348608 ATTCATTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 12 0.39
22 6 0.19
23 13 0.42
ACGTcount: A:0.64, C:0.19, G:0.05, T:0.12
Consensus pattern (24 bp):
AAAATACACCAAAATTAAACAGTG
Found at i:349474 original size:34 final size:33
Alignment explanation
Indices: 349436--349531 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
349426 GTGTTGGTGC
* *
349436 TTGCTTGCTTCAGCTACTGTCGTTGCTAGTGCTG
1 TTGCTTGCTTCAGCTA-TTTCGTTGCTAGTACTG
*
349470 TTGCTTGCTTCAGCTATTTCGTTGCT-GCTATTG
1 TTGCTTGCTTCAGCTATTTCGTTGCTAG-TACTG
* *
349503 CTGCTTGCTTTAGCTATTTCGTTGCTAGT
1 TTGCTTGCTTCAGCTATTTCGTTGCTAGT
349532 TTGTTGTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 37 0.67
34 17 0.31
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TTGCTTGCTTCAGCTATTTCGTTGCTAGTACTG
Found at i:349691 original size:35 final size:34
Alignment explanation
Indices: 349636--349727 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 34
349626 CATTTCTTGC
* * *
349636 TTTCTTTTTTTCTTATTTTGAGTTGCTGTTTTGT
1 TTTCTTTTTTTCTTACTTTGAGCTACTGTTTTGT
* **
349670 TTTCTTTTTATTCTTCCTTTGAGCTACTG-TTTCA
1 TTTCTTTTT-TTCTTACTTTGAGCTACTGTTTTGT
* *
349704 TTT-TTTTATTCTTTCTTTGAGCTA
1 TTTCTTTTTTTCTTACTTTGAGCTA
349728 TTGTCGGTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
32 15 0.31
33 4 0.08
34 15 0.31
35 15 0.31
ACGTcount: A:0.10, C:0.14, G:0.11, T:0.65
Consensus pattern (34 bp):
TTTCTTTTTTTCTTACTTTGAGCTACTGTTTTGT
Found at i:349738 original size:36 final size:32
Alignment explanation
Indices: 349671--349746 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 32
349661 CTGTTTTGTT
*
349671 TTCTTTTTATTCTTCCTTTGAGCTACTGTTTC
1 TTCTTTTTATTCTTCCTTTGAGCTACGGTTTC
*
349703 ATT-TTTTTATTCTTTCTTTGAGCTATTGTCGGTTTC
1 -TTCTTTTTATTCTTCCTTTGAGCTA----CGGTTTC
349739 TTCTTTTT
1 TTCTTTTT
349747 CTTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
32 21 0.58
33 2 0.06
35 2 0.06
36 11 0.31
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.63
Consensus pattern (32 bp):
TTCTTTTTATTCTTCCTTTGAGCTACGGTTTC
Found at i:349801 original size:39 final size:39
Alignment explanation
Indices: 349753--349832 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
349743 TTTTCTTTTT
*
349753 TTTTTCAGCAACTTAATTACTTTTTG-TCTGTTTTCCTTC
1 TTTTCCAGCAACTTAATTACTTTTTGTTC-GTTTTCCTTC
* *
349792 TTTTCCAGCAGCTTAATTGCTTTTTGTTCGTTTTCCTTC
1 TTTTCCAGCAACTTAATTACTTTTTGTTCGTTTTCCTTC
349831 TT
1 TT
349833 CTTCTTGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.12, C:0.21, G:0.10, T:0.56
Consensus pattern (39 bp):
TTTTCCAGCAACTTAATTACTTTTTGTTCGTTTTCCTTC
Found at i:351037 original size:14 final size:15
Alignment explanation
Indices: 351007--351038 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
350997 GAATTTTTTA
351007 TTTTCGAGGGAATTT
1 TTTTCGAGGGAATTT
351022 TTTTCGAGGGAATTT
1 TTTTCGAGGGAATTT
351037 TT
1 TT
351039 CTTAGTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (15 bp):
TTTTCGAGGGAATTT
Found at i:351117 original size:125 final size:124
Alignment explanation
Indices: 350893--351123 Score: 270
Period size: 125 Copynumber: 1.9 Consensus size: 124
350883 TCAACTCCGT
** * * *
350893 AATTTTTTTGAGGGGTTTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATACTATTATTTATT
1 AATTTTTTTGAGGGAATTTTTCTTAGTTTTCAATTTTTAAAATTCATCAAATACTATCATTTATT
* * * ** *
350958 TTATATTAAATTAGTTTTCAAAAAATTACCCATTTTCATGAATTTTTTATTTTCGAGGG
66 TCATATTAAATCAATTTAAAAAAAATAACCCATTTTCATGAATTTTTTATTTTCGAGGG
**
351017 AATTTTTTTCGAGGGAATTTTTCTTAGTTTTCAATTTTTAAAATTCATCGGGCAT-C-ATCATTT
1 AATTTTTTT-GAGGGAATTTTTCTTAGTTTTCAATTTTTAAAATTCATC--AAATACTATCATTT
**
351080 GA-TTCATATTAAATCAATTTAAAAAAAATAATTCATTTTCATGA
63 -ATTTCATATTAAATCAATTTAAAAAAAATAACCCATTTTCATGA
351124 GTTTGGATTT
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
124 9 0.10
125 75 0.85
126 2 0.02
127 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (124 bp):
AATTTTTTTGAGGGAATTTTTCTTAGTTTTCAATTTTTAAAATTCATCAAATACTATCATTTATT
TCATATTAAATCAATTTAAAAAAAATAACCCATTTTCATGAATTTTTTATTTTCGAGGG
Found at i:351221 original size:23 final size:23
Alignment explanation
Indices: 351190--351239 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
351180 CTTGGTTTAG
* *
351190 AATTTTTAAA-ACCCATATAATAC
1 AATTATTAAACACCCATAAAAT-C
*
351213 AATTATTAAACTCCCATAAAATC
1 AATTATTAAACACCCATAAAATC
351236 AATT
1 AATT
351240 TTGCAAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (23 bp):
AATTATTAAACACCCATAAAATC
Found at i:352956 original size:13 final size:13
Alignment explanation
Indices: 352938--352963 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
352928 CAATTTTTTG
352938 TGTATCGATACAT
1 TGTATCGATACAT
352951 TGTATCGATACAT
1 TGTATCGATACAT
352964 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:352974 original size:32 final size:33
Alignment explanation
Indices: 352918--352981 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
352908 TACAAGCCAA
*
352918 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
*
352951 TGTATCGATAC-ATATTTTGTGTATTGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
352982 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:353086 original size:20 final size:20
Alignment explanation
Indices: 353033--353088 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
353023 ACATCTTTTT
*
353033 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
353053 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
353072 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
353089 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:357628 original size:15 final size:15
Alignment explanation
Indices: 357608--357638 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
357598 ATTTCGTTTG
*
357608 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
357623 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
357638 G
1 G
357639 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:361733 original size:13 final size:13
Alignment explanation
Indices: 361715--361740 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
361705 CAATTTTTTG
361715 TGTATCGATACAT
1 TGTATCGATACAT
361728 TGTATCGATACAT
1 TGTATCGATACAT
361741 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:361751 original size:32 final size:33
Alignment explanation
Indices: 361695--361758 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
361685 TACAAGCCAA
*
361695 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
361728 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
361759 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:361752 original size:19 final size:19
Alignment explanation
Indices: 361695--361758 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
361685 TACAAGCCAA
*
361695 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
361715 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
361728 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
361747 TGTATCGATACA
1 TGTATCGATACA
361759 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:363569 original size:155 final size:153
Alignment explanation
Indices: 363163--364272 Score: 726
Period size: 156 Copynumber: 7.2 Consensus size: 153
363153 GTCCACTAGA
* * * * **
363163 GGTATCAGGTACTTTTACGTTGAAA-GTATCCCCTA-AGGGCATTTTCATAATTT-TTTGAAATA
1 GGTATCAGGTACTTCTACG-TCAAAGGTATCCCCTAGA-GGCATTTTCGTAATTTCTTAGAACCA
** ** *** *
363225 ACTCCTATATCATCGTCGGGTCCGCTTTTATGCTGAAGGTTAATATTTAGGATAGGTTCATCCTT
64 ACTCCTAGGTCATCACCGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCC-A
* *
363290 TCTATAATTCTTTTAAAGTCTTTTAG
128 TCTATAATTCTTTTTAAGTCCTTTAG
** * * * *
363316 GG-ATACTAGGATACTT-TCACGTTGAAGGTATACCATAGGGGCATTTTGGTAATTTCTTAGAAC
1 GGTAT-C-AGG-TACTTCT-ACGTCAAAGGTATCCCCTAGAGGCATTTTCGTAATTTCTTAGAAC
* * * * ** * * *
363379 TAATTCATAGGTCTTCACCAAGTCCGCTTTTATGCCGAAGGCGGGTATTTAGGATAAGTTCATTC
62 CAACTCCTAGGTCATCACCGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCA-TC
363444 CATCTATAATTCTTTTTAAGTCCTTTAG
126 CATCTATAATTCTTTTTAAGTCCTTTAG
* * *
363472 AGGTATCGGGTACTTCTACGTCAAAGGTATCCCCTAGAGGCATTTTCGTAATTTCCTGGAACCAA
1 -GGTATCAGGTACTTCTACGTCAAAGGTATCCCCTAGAGGCATTTTCGTAATTTCTTAGAACCAA
* * *
363537 CTCCTAGGTCATCACCGGGGCCGCTTTTATGCCGAAGGTCGGTATTTAGGATAGGTTCATCC--C
65 CTCCTAGGTCATCACCGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCATC
* *
363600 ----A--GTTTGTAA-TCCTTTAG
130 TATAATTCTTTTTAAGTCCTTTAG
* * * * * * * * *
363617 GGATATAAAGCACTTCTACGTTGAAA--AATCCTCTAG-GAGCATTTTAGTAA-TTATTAGAATC
1 GG-TATCAGGTACTTCTACG-TCAAAGGTATCCCCTAGAG-GCATTTTCGTAATTTCTTAGAACC
*** * ** * * * * *
363678 GTGTCCTAAGTTGTCACCAGGTTCGCTTTTATGCTGAAGGTAGATATTTAGGATTGGTTCATCTC
63 AACTCCTAGGTCATCACCGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATC-C
* * *
363743 TTTTATAATCCTTTTTAAGTCCTTTAAG
127 ATCTATAATTCTTTTTAAGTCCTTT-AG
* * * * * * *
363771 GATAAT-GGGATAC-TCTTACATCGAAGGTATACCCATAGGGGCATTTTGGTAATTTCTTAGAAC
1 GGT-ATCAGG-TACTTC-TACGTCAAAGGTAT-CCCCTAGAGGCATTTTCGTAATTTCTTAGAAC
* * * ** * *
363834 CAATTTCTAGGTCGTCACTAGGTCCGCTTTTATGCTGAAGATGGGTATTTAGGATAGGGTCATCC
62 CAACTCCTAGGTCATCACCGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCAT-C
363899 CATCTATAATTCTTTTTAAGTCCTTTAGG
126 CATCTATAATTCTTTTTAAGTCCTTTA-G
* * * * * * * *
363928 GGTATCGGGTACTTCAACGTCACAA-GTAT-TCCAAGGGGTATTTTTGTAATTT-TGTAGAAACA
1 GGTATCAGGTACTTCTACGTCA-AAGGTATCCCCTAGAGGCATTTTCGTAATTTCT-TAGAACCA
* * *
363990 ACTCCTAGGTCGA-CACCGGGTCCACTTTTATGCTGAAGGTGGGTATTTAAGATATGTTCATCCC
64 ACTCCTAGGTC-ATCACCGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCAT-CC
* * * *
364054 AGTTTGTAATGCTTTTTAAATCCTTTAG
127 A-TCTATAATTCTTTTTAAGTCCTTTAG
* * * * * * *
364082 GAATATCAAGCACTTCTACGTTAAAGATATCCCCTA-AGGGCATTTT-GATAATTTTTTAGAATC
1 G-GTATCAGGTACTTCTACGTCAAAGGTATCCCCTAGA-GGCATTTTCG-TAATTTCTTAGAACC
* * ** * *** * * * * *
364145 GAGTCCTAGGTTGTCACCGAGTCTATTTTTATGTTGAAGATTGGTATTTAAGATAGGTTCGTCCT
63 AACTCCTAGGTCATCACCGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCC-
* *
364210 ATTTATAA-TCCTTTTAAGTCCTTTAGG
127 ATCTATAATTCTTTTTAAGTCCTTTA-G
* *
364237 GGTATCAGGTACTTCGACGTCGAAGGTATCCCCTAG
1 GGTATCAGGTACTTCTACGTCAAAGGTATCCCCTAG
364273 GGGTTTTTAA
Statistics
Matches: 742, Mismatches: 164, Indels: 100
0.74 0.16 0.10
Matches are distributed among these distances:
143 58 0.08
144 22 0.03
145 21 0.03
146 10 0.01
148 1 0.00
150 1 0.00
152 9 0.01
153 17 0.02
154 144 0.19
155 176 0.24
156 181 0.24
157 99 0.13
158 3 0.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (153 bp):
GGTATCAGGTACTTCTACGTCAAAGGTATCCCCTAGAGGCATTTTCGTAATTTCTTAGAACCAAC
TCCTAGGTCATCACCGGGTCCGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCATCT
ATAATTCTTTTTAAGTCCTTTAG
Found at i:364033 original size:154 final size:153
Alignment explanation
Indices: 363703--364275 Score: 483
Period size: 154 Copynumber: 3.7 Consensus size: 153
363693 ACCAGGTTCG
* * * * * * * *
363703 CTTTTATGCTGAAGGTAGATATTTAGGATTGGTTCATCTCTTTTATAATCCTTTTTAAGTCCTTT
1 CTTTTATGCTGAAGATGGGTATTTAAGATAGGTTCATCCCATTTATAATTCTTTTTAAGTCCTTT
* * * * *
363768 AAGGATAAT-GGGATAC-TCTTACATCGAAGGTATACCCATAGGGGCATTTTGGTAATTTCTTAG
66 AGGGAT-ATCAGG-TACTTC-TACGTC-AAAGTATACCCA-AGGGGCATTTTTGTAATTT-TTAG
* * * ** *
363831 AACCAATTTCTAGGTCGTCACTAGGTCCG
125 AAACAACTCCTAGGTCGTCACCGGGTCCA
* * *
363860 CTTTTATGCTGAAGATGGGTATTTAGGATAGGGTCATCCCATCTATAATTCTTTTTAAGTCCTTT
1 CTTTTATGCTGAAGATGGGTATTTAAGATAGGTTCATCCCATTTATAATTCTTTTTAAGTCCTTT
* * * * *
363925 AGGGGTATCGGGTACTTCAACGTCACAAGTAT-TCCAAGGGGTATTTTTGTAATTTTGTAGAAAC
66 AGGGATATCAGGTACTTCTACGTCA-AAGTATACCCAAGGGGCATTTTTGTAATTTT-TAGAAAC
*
363989 AACTCCTAGGTCGACACCGGGTCCA
129 AACTCCTAGGTCGTCACCGGGTCCA
* * * * *
364014 CTTTTATGCTGAAGGTGGGTATTTAAGATATGTTCATCCCAGTTTGTAATGCTTTTTAAATCCTT
1 CTTTTATGCTGAAGATGGGTATTTAAGATAGGTTCATCCCA-TTTATAATTCTTTTTAAGTCCTT
* * * * *
364079 TAGGAATATCAAGCACTTCTACGTTAAAGATATCCCCTAA-GGGCA-TTTTGATAATTTTTTAGA
65 TAGGGATATCAGGTACTTCTACGTCAAAG-TATACCC-AAGGGGCATTTTTG-TAA-TTTTTAGA
* * * * * *
364142 ATCGAGTCCTAGGTTGTCACCGAGTCTA
126 AACAACTCCTAGGTCGTCACCGGGTCCA
* * * * * *
364170 TTTTTATGTTGAAGATTGGTATTTAAGATAGGTTCGTCCTATTTATAA-TCCTTTTAAGTCCTTT
1 CTTTTATGCTGAAGATGGGTATTTAAGATAGGTTCATCCCATTTATAATTCTTTTTAAGTCCTTT
* * * * *
364234 AGGGGTATCAGGTACTTCGACGTCGAAGGTATCCCCTAGGGG
66 AGGGATATCAGGTACTTCTACGTC-AAAGTATACCCAAGGGG
364276 TTTTTAAACT
Statistics
Matches: 337, Mismatches: 67, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
153 2 0.01
154 123 0.36
155 59 0.18
156 82 0.24
157 71 0.21
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (153 bp):
CTTTTATGCTGAAGATGGGTATTTAAGATAGGTTCATCCCATTTATAATTCTTTTTAAGTCCTTT
AGGGATATCAGGTACTTCTACGTCAAAGTATACCCAAGGGGCATTTTTGTAATTTTTAGAAACAA
CTCCTAGGTCGTCACCGGGTCCA
Found at i:364051 original size:454 final size:454
Alignment explanation
Indices: 363247--364068 Score: 1199
Period size: 454 Copynumber: 1.8 Consensus size: 454
363237 TCGTCGGGTC
* *
363247 CGCTTTTATGCTGAAGGTTAATATTTAGGATAGGTTCATCCTTTCTATAATTCTTTTAAAGTCTT
1 CGCTTTTATGCTGAAGGTTAATATTTAGGATAGGTTCATCCTTTCTATAATCCTTTTAAAGTCCT
* * * *
363312 TTAGGGATACTAGGATACTTTCACGTTGAAGGTATACCATAGGGGCATTTTGGTAATTTCTTAGA
66 TTAAGGATAATAGGATACTTTCACATCGAAGGTATACCATAGGGGCATTTTGGTAATTTCTTAGA
* * * *
363377 ACTAATTCATAGGTCTTCACCAAGTCCGCTTTTATGCCGAAGGCGGGTATTTAGGATAAGTTCAT
131 ACCAATTCATAGGTCGTCACCAAGTCCGCTTTTATGCCGAAGACGGGTATTTAGGATAAGGTCAT
* * *
363442 TCCATCTATAATTCTTTTTAAGTCCTTTAGAGGTATCGGGTACTTCTACGTCAAAGGTATCCCCT
196 CCCATCTATAATTCTTTTTAAGTCCTTTAGAGGTATCGGGTACTTCAACGTCAAAGGTATCCCCA
* * *
363507 AGAGGCATTTTCGTAATTTCCTGGAACCAACTCCTAGGTCATCACCGGGGCCGCTTTTATGCCGA
261 AGAGGCATTTTCGTAATTTCCTAGAAACAACTCCTAGGTCATCACCGGGGCCACTTTTATGCCGA
*
363572 AGGTCGGTATTTAGGATAGGTTCATCCCAGTTTGTAATCCTTTAGGGATATAAAGCACTTCTACG
326 AGGTCGGTATTTAAGATAGGTTCATCCCAGTTTGTAATCCTTTAGGGATATAAAGCACTTCTACG
363637 TTGAAAAATCCTCTAGGAGCATTTTAGTAATTATTAGAATCGTGTCCTAAGTTGTCACCAGGTT
391 TTGAAAAATCCTCTAGGAGCATTTTAGTAATTATTAGAATCGTGTCCTAAGTTGTCACCAGGTT
* *
363701 CGCTTTTATGCTGAAGG-TAGATATTTAGGATTGGTTCATCTCTTT-TATAATCCTTTTTAAGTC
1 CGCTTTTATGCTGAAGGTTA-ATATTTAGGATAGGTTCATC-CTTTCTATAATCCTTTTAAAGTC
*
363764 CTTTAAGGATAATGGGATACTCTT-ACATCGAAGGTATACCCATAGGGGCATTTTGGTAATTTCT
64 CTTTAAGGATAATAGGATACT-TTCACATCGAAGGTATA-CCATAGGGGCATTTTGGTAATTTCT
* * * * *
363828 TAGAACCAATTTC-TAGGTCGTCACTAGGTCCGCTTTTATGCTGAAGATGGGTATTTAGGATAGG
127 TAGAACCAA-TTCATAGGTCGTCACCAAGTCCGCTTTTATGCCGAAGACGGGTATTTAGGATAAG
*
363892 GTCATCCCATCTATAATTCTTTTTAAGTCCTTTAGGGGTATCGGGTACTTCAACGTCACAA-GTA
191 GTCATCCCATCTATAATTCTTTTTAAGTCCTTTAGAGGTATCGGGTACTTCAACGTCA-AAGGTA
* * * * ** *
363956 T-TCCAAGGGGTATTTTTGTAATTTTGTAGAAACAACTCCTAGGTCGA-CACCGGGTCCACTTTT
255 TCCCCAAGAGGCATTTTCGTAATTTCCTAGAAACAACTCCTAGGTC-ATCACCGGGGCCACTTTT
* * * *
364019 ATGCTGAAGGTGGGTATTTAAGATATGTTCATCCCAGTTTGTAATGCTTT
319 ATGCCGAAGGTCGGTATTTAAGATAGGTTCATCCCAGTTTGTAATCCTTT
364069 TTAAATCCTT
Statistics
Matches: 324, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
453 2 0.01
454 175 0.54
455 142 0.44
456 5 0.02
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (454 bp):
CGCTTTTATGCTGAAGGTTAATATTTAGGATAGGTTCATCCTTTCTATAATCCTTTTAAAGTCCT
TTAAGGATAATAGGATACTTTCACATCGAAGGTATACCATAGGGGCATTTTGGTAATTTCTTAGA
ACCAATTCATAGGTCGTCACCAAGTCCGCTTTTATGCCGAAGACGGGTATTTAGGATAAGGTCAT
CCCATCTATAATTCTTTTTAAGTCCTTTAGAGGTATCGGGTACTTCAACGTCAAAGGTATCCCCA
AGAGGCATTTTCGTAATTTCCTAGAAACAACTCCTAGGTCATCACCGGGGCCACTTTTATGCCGA
AGGTCGGTATTTAAGATAGGTTCATCCCAGTTTGTAATCCTTTAGGGATATAAAGCACTTCTACG
TTGAAAAATCCTCTAGGAGCATTTTAGTAATTATTAGAATCGTGTCCTAAGTTGTCACCAGGTT
Found at i:364969 original size:13 final size:13
Alignment explanation
Indices: 364951--364975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
364941 ATATTGCTTA
364951 GTATCGATACATT
1 GTATCGATACATT
364964 GTATCGATACAT
1 GTATCGATACAT
364976 GTTCTTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:364972 original size:33 final size:32
Alignment explanation
Indices: 364930--364993 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
364920 CACACCCAAA
364930 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATT-CTTAGTATCGATACAT
* * *
364963 TGTATCGATACATGTTCTTGGTATTGATACA
1 TGTATCGATACATATTCTTAGTATCGATACA
364994 CACTGAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATATTCTTAGTATCGATACAT
Found at i:372568 original size:17 final size:16
Alignment explanation
Indices: 372529--372592 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
372519 TCCTCTACAT
372529 AACAAACAACAAAAAAA
1 AACAAA-AACAAAAAAA
*
372546 GA-AAAAACAAAACAAA
1 AACAAAAACAAAA-AAA
372562 AACAAAAACAAAAAAA
1 AACAAAAACAAAAAAA
372578 AA-AGGAAAACAAAAA
1 AACA--AAAACAAAAA
372593 GGAAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 8 0.20
16 12 0.29
17 21 0.51
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (16 bp):
AACAAAAACAAAAAAA
Found at i:372586 original size:12 final size:11
Alignment explanation
Indices: 372539--372652 Score: 77
Period size: 12 Copynumber: 9.8 Consensus size: 11
372529 AACAAACAAC
372539 AAAAAAAGAAA
1 AAAAAAAGAAA
*
372550 AAACAAAACAAA
1 AAA-AAAAGAAA
*
372562 AACAAAAACAAA
1 AA-AAAAAGAAA
372574 AAAAAAAGGAAA
1 AAAAAAA-GAAA
* *
372586 ACAAAAAGGAA
1 AAAAAAAGAAA
*
372597 AAAAATA-AAA
1 AAAAAAAGAAA
*
372607 AGAAAAAGAAA
1 AAAAAAAGAAA
***
372618 GTGCAAAAGAAA
1 -AAAAAAAGAAA
372630 AAGAAAAATGAAA
1 AA-AAAAA-GAAA
372643 GAAAAAAAGA
1 -AAAAAAAGA
372653 TGAGGAAATA
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
10 7 0.09
11 19 0.23
12 43 0.53
13 10 0.12
14 2 0.02
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:372614 original size:21 final size:21
Alignment explanation
Indices: 372574--372614 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
372564 CAAAAACAAA
*
372574 AAAAAAAGGAAAACAAAAAGG
1 AAAAAAAGAAAAACAAAAAGG
* *
372595 AAAAAAATAAAAAGAAAAAG
1 AAAAAAAGAAAAACAAAAAG
372615 AAAGTGCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAACAAAAAGG
Found at i:372630 original size:5 final size:6
Alignment explanation
Indices: 372541--372652 Score: 68
Period size: 6 Copynumber: 18.2 Consensus size: 6
372531 CAAACAACAA
* * * * *
372541 AAAAAG AAAAA- ACAAAAC AAAAAC AAAAAC AAAAA- AAAAAG GAAAAC
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* ** *
372588 AAAAAGG AAAAAAAT AAAAAG AAAAAG AAAGTG CAAAAG AAAAAG AAAAATG
1 AAAAA-G --AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G
372640 AAAGAA- AAAAAG A
1 AAA-AAG AAAAAG A
372653 TGAGGAAATA
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
5 8 0.09
6 65 0.76
7 5 0.06
8 2 0.02
9 5 0.06
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:372643 original size:17 final size:17
Alignment explanation
Indices: 372598--372648 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
372588 AAAAAGGAAA
*
372598 AAAATAAAAAGAAAAAG
1 AAAATGAAAAGAAAAAG
*
372615 AAAGTGCAAAAGAAAAAG
1 AAAATG-AAAAGAAAAAG
372633 AAAAATG-AAAGAAAAA
1 -AAAATGAAAAGAAAAA
372649 AAGATGAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 13 0.45
18 11 0.38
19 5 0.17
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (17 bp):
AAAATGAAAAGAAAAAG
Found at i:372921 original size:19 final size:19
Alignment explanation
Indices: 372879--372915 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
372869 GGAAAGGTTG
*
372879 TGAAAGAGAAGAAAAAAAA
1 TGAAAAAGAAGAAAAAAAA
372898 TGAAAAAGAAGAAAAAAA
1 TGAAAAAGAAGAAAAAAA
372916 GAGAAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (19 bp):
TGAAAAAGAAGAAAAAAAA
Found at i:373392 original size:112 final size:112
Alignment explanation
Indices: 373195--373491 Score: 246
Period size: 112 Copynumber: 2.7 Consensus size: 112
373185 AACTTGGAAG
* **
373195 AACATCAAATTTGTTTAATTTTCAAAGAAATTCATGTTTTATACATCTTGATCCATTCGTGCCTA
1 AACATCAAATTTGCTTAATTTTCAAAGAAATTCATACTTTATACATCTTGATCCATTCGTGCCTA
* * * * *
373260 GGAAAATGGGCACGTGTCTTATTAGTTTTGATCTTTTTGAGCCTCAC
66 GGAAAATGAGCACCTATCTTATCAATTTTGATCTTTTTGAGCCTCAC
* * * ** *
373307 AACATCAAATTTGCTTGATTTTTAGAGAAATTCATACTTTATATGT-TTCGATCCATTCGCT-CT
1 AACATCAAATTTGCTTAATTTTCAAAGAAATTCATACTTTATACATCTT-GATCCATTCG-TGCC
****
373370 TAGG-AAATAGAGCACCTATCTTATCAATTTTGAAAACTTTGAGCCT-AGC
64 TAGGAAAAT-GAGCACCTATCTTATCAATTTTGATCTTTTTGAGCCTCA-C
* * * * * * ** * *
373419 AATATTAAATTTG-TTGGATTTTGAAAGAAACTCATA-TGTCATATGTTTTGACCCATTCGTGCC
1 AACATCAAATTTGCTT-AATTTTCAAAGAAATTCATACT-TTATACATCTTGATCCATTCGTGCC
373482 TAGGAAAATG
64 TAGGAAAATG
373492 GGGCATGCAC
Statistics
Matches: 150, Mismatches: 26, Indels: 18
0.77 0.13 0.09
Matches are distributed among these distances:
111 11 0.07
112 132 0.88
113 7 0.05
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (112 bp):
AACATCAAATTTGCTTAATTTTCAAAGAAATTCATACTTTATACATCTTGATCCATTCGTGCCTA
GGAAAATGAGCACCTATCTTATCAATTTTGATCTTTTTGAGCCTCAC
Found at i:373879 original size:87 final size:88
Alignment explanation
Indices: 373775--373976 Score: 246
Period size: 87 Copynumber: 2.3 Consensus size: 88
373765 TTGTCTTCCT
* * * * *
373775 ATTGATGCTTGCATTTGCATCATTTCACTTGCATCTGCATTTTAGATAACATTGGTATTTGGATT
1 ATTGATGCTTGCATTTGCATCATTTCACATACATCTGCACTTTAGATAACATTGGTATTTGCATC
*
373840 AT-TCCATATCCATTT-GCCCTTC
66 ATCT-CATATCCATTTGGCACTTC
* * * **
373862 ATTGATGTTTGCATTTGCATTATTTCACATACATCTGCACTTTAGATGATGTTGGTATTTGCATC
1 ATTGATGCTTGCATTTGCATCATTTCACATACATCTGCACTTTAGATAACATTGGTATTTGCATC
* * *
373927 ATCTCATATGCATTTGGCATTTT
66 ATCTCATATCCATTTGGCACTTC
*
373950 ATTGATGCTTGCATTTACATCATTTCA
1 ATTGATGCTTGCATTTGCATCATTTCA
373977 TGCACATCTA
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
87 67 0.70
88 29 0.30
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (88 bp):
ATTGATGCTTGCATTTGCATCATTTCACATACATCTGCACTTTAGATAACATTGGTATTTGCATC
ATCTCATATCCATTTGGCACTTC
Found at i:373922 original size:44 final size:44
Alignment explanation
Indices: 373787--373925 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 44
373777 TGATGCTTGC
* * * * * **
373787 ATTTGCATCATTTCACTTGCATCTGCATTTTAGATAACATTGGT
1 ATTTGCATTATTTCACATACATCTGCACTTTAGATGATGTTGGT
* * * * * * * * * *
373831 ATTTGGATTATTCCATATCCATTTGCCCTTCA-TTGATGTTTGC
1 ATTTGCATTATTTCACATACATCTGCACTTTAGATGATGTTGGT
373874 ATTTGCATTATTTCACATACATCTGCACTTTAGATGATGTTGGT
1 ATTTGCATTATTTCACATACATCTGCACTTTAGATGATGTTGGT
373918 ATTTGCAT
1 ATTTGCAT
373926 CATCTCATAT
Statistics
Matches: 68, Mismatches: 26, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
43 30 0.44
44 38 0.56
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (44 bp):
ATTTGCATTATTTCACATACATCTGCACTTTAGATGATGTTGGT
Found at i:374624 original size:89 final size:90
Alignment explanation
Indices: 374416--374635 Score: 234
Period size: 89 Copynumber: 2.4 Consensus size: 90
374406 TTTCTTTTTT
* * * *
374416 CTTAACTC-CTAGATGGTATTGATGCGTCACAAAGTCTAATTTCCCTGGGGTAAGGATATCCTAA
1 CTTAAC-CACTAGATGGTATTGATGCATCACAAAGCCTAATTTCCATGGGCTAAGG--ATCCTAA
* ** *
374480 CCCCACATTCTTAATTATATCCCTTTCA
63 CCCCACACTCCCAATCATATCCCTTTCA
* * *
374508 CTTAACCACTAGGTGGTATTGACGCATCACAAAGCCTAATTTCCATGGGCTAAGG-T-GTAACCC
1 CTTAACCACTAGATGGTATTGATGCATCACAAAGCCTAATTTCCATGGGCTAAGGATCCTAACCC
*
374571 ACACACTCCCAATCGTAT-CCTCTTCA
66 -CACACTCCCAATCATATCCCT-TTCA
*
374597 -TCTAACCACTAGATGGTATTGATGCATCGCAAAGCCTAA
1 CT-TAACCACTAGATGGTATTGATGCATCACAAAGCCTAA
374636 CTTCTCTTGA
Statistics
Matches: 109, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
88 10 0.09
89 51 0.47
91 1 0.01
92 47 0.43
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (90 bp):
CTTAACCACTAGATGGTATTGATGCATCACAAAGCCTAATTTCCATGGGCTAAGGATCCTAACCC
CACACTCCCAATCATATCCCTTTCA
Found at i:374989 original size:42 final size:41
Alignment explanation
Indices: 374943--375049 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 41
374933 TTTTCTCGTC
*
374943 AGCTTAAACCCGAGAGACTTCTTTATCTTTTATCTACCCATT
1 AGCTTAGACCCG-GAGACTTCTTTATCTTTTATCTACCCATT
* * * *
374985 AGCTTAGACCCGGGAGACTTTTTTATCTTTTGTTTGCCCATT
1 AGCTTAGACCC-GGAGACTTCTTTATCTTTTATCTACCCATT
*
375027 AGCTCAGACCTCGGAGACTTCTT
1 AGCTTAGACC-CGGAGACTTCTT
375050 CATCAATCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 54 0.96
43 2 0.04
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.37
Consensus pattern (41 bp):
AGCTTAGACCCGGAGACTTCTTTATCTTTTATCTACCCATT
Found at i:375074 original size:42 final size:41
Alignment explanation
Indices: 375019--375153 Score: 117
Period size: 42 Copynumber: 3.2 Consensus size: 41
375009 ATCTTTTGTT
**
375019 TGCCCATTAGCTCAGACCTCGGAGACTTCTTCATCAATCATC
1 TGCCCATCGGCTCA-ACCTCGGAGACTTCTTCATCAATCATC
* * * * **
375061 TGCTCGTCGGCTCAAACTTGGGAGACTTCTTCATCTTTCATC
1 TGCCCATCGGCTC-AACCTCGGAGACTTCTTCATCAATCATC
* * * *
375103 TGCCCATCGGCTTAATCTCGGGAGACTTCCTTTATCAATCATT
1 TGCCCATCGGCTCAACCTC-GGAGACTT-CTTCATCAATCATC
*
375146 TGGCCATC
1 TGCCCATC
375154 AGTTCAGGCT
Statistics
Matches: 71, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
41 3 0.04
42 50 0.70
43 18 0.25
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (41 bp):
TGCCCATCGGCTCAACCTCGGAGACTTCTTCATCAATCATC
Found at i:375438 original size:83 final size:84
Alignment explanation
Indices: 375279--376099 Score: 432
Period size: 83 Copynumber: 9.8 Consensus size: 84
375269 AACTTGTCAA
* * * * * * * *
375279 CTTAGTCTCCAGTCAACCTTCATCCCTTGTTTACCTGTCGGCTCAATCCTCGATAATCCTCTCAT
1 CTTAGTCTCCAGTCAACCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTTAT
* *
375344 -CCTTTGTTGACCTATTAG
66 CCCCTTGGTGACCTATTAG
* * ** *
375362 CTTAGTCTCCGGTCAACCTTAATTTTTTGTTTACCTATCGGCTCAGTCCCCGGTAAACC-CTTAT
1 CTTAGTCTCCAGTCAACCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTTAT
* * **
375426 CCCCTTAGTGACCCATCGG
66 CCCCTTGGTGACCTATTAG
* * * * * * *
375445 TTTAGTC-CTCAGTCAACCTTTTATCCATTATTTACCTATTGGCTTAGTCCCCAGTAAACCTATT
1 CTTAGTCTC-CAGTCAACC-TTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTT
* *
375509 ACCCCCTATGGGGACCTATTAG
64 ATCCCCT-TGGTGACCTATTAG
* * * * * * **
375531 CTTAGTCTCCAATGAACTTTCATCCTTTATTTACCTGTTGACTCAGTCCCAAGTAAACC-CTTAT
1 CTTAGTCTCCAGTCAACCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTTAT
** *
375595 CCCCTTGGTGACC-CGTCG
66 CCCCTTGGTGACCTATTAG
* * * * * * * * * *
375613 ATTAGTCTTCAATCAACCCTTCATCCATTGTTTACCTATTGGCTTAGTCCCTGATAAACCTATTA
1 CTTAGTCTCCAGTCAA-CCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTTA
* *
375678 T--CCTATGGTGACCTGTCAG
65 TCCCCT-TGGTGACCTATTAG
* *** * * * * *
375697 CTCAGTCTTTGGTCAACCTTTATCCTTTATTTACTTGTCGGATCAGTCCCCGATAAACC-CTTAT
1 CTTAGTCTCCAGTCAACCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTTAT
*
375761 CCCTTTGGTGACC-AGTCT-G
66 CCCCTTGGTGACCTA-T-TAG
* * * * * * * *
375780 TTTAGTCCCCAGTCAACCCTTCATCCCTTGTTTACCTATCGACTTAGTCCCCGGCAAACCTATTA
1 CTTAGTCTCCAGTCAA-CCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTTA
* * *
375845 -CCCCATGGTGACCTGTCAG
65 TCCCCTTGGTGACCTATTAG
* * ** * * *
375864 CTGAATCT-TTGATCAACCTTCATCCTTTATTTACCTATCAGCTTAGTCCTCGGTAAACC-CTTA
1 CTTAGTCTCCAG-TCAACCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTTA
* * *
375927 ACCCTTTTGGTGACC-AGTAGG
65 TCCC-CTTGGTGACCTATTA-G
* * * * * ** * * * *
375948 TTTAGTC-CTCAGTCAACCCTTCATCCCTTGTTTACTTGTTAGCTCAGTCCTCGATAAACTTATT
1 CTTAGTCTC-CAGTCAA-CCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTT
* * * *
376012 ATCCCTTTGGTGACCTGTCAA
64 ATCCCCTTGGTGACCTATTAG
* * * * * * * * * *
376033 CTCAATCTTC-GATTAACCTTCATCTCATTGTTTACCTGTCGACTTAGTCCCCAGTAAACCTCTT
1 CTTAGTCTCCAG-TCAACCTTCATC-CTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTT
376097 ATC
64 ATC
376100 TCAATCATCT
Statistics
Matches: 549, Mismatches: 159, Indels: 58
0.72 0.21 0.08
Matches are distributed among these distances:
82 30 0.05
83 220 0.40
84 139 0.25
85 131 0.24
86 28 0.05
87 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (84 bp):
CTTAGTCTCCAGTCAACCTTCATCCTTTATTTACCTATCGGCTCAGTCCCCGGTAAACCTCTTAT
CCCCTTGGTGACCTATTAG
Found at i:375966 original size:335 final size:335
Alignment explanation
Indices: 375280--376052 Score: 851
Period size: 335 Copynumber: 2.3 Consensus size: 335
375270 ACTTGTCAAC
* * * * *
375280 TTAGT-CTCCAGTCAA-CCTTCATCCCTTGTTTACCTGTCGGCTCAATCCTCGATAATCCTCTCA
1 TTAGTCCT-CAGTCAACCCTTCATCCCTTGTTTACCTGTTGGCTCAGTCCTCGATAAACCTATTA
* * * * * ** * *
375343 TCCTTTGTTGACCTATTAGCTTAGTCTCCGGTCAACCTTAATTTTTTGTTTACCTATCGGCTCAG
65 TCCTTTGGTGACCTGTCAGCTCAGTCTTCGGTCAACCTTAATCCTTTATTTACCTATCGGATCAG
* * * *
375408 TCCCCGGTAAACCCTTATCCCCTTAGTGACCCATCGGTTTAGTCCTCAGTCAACCTTTTATCCAT
130 TCCCCGATAAACCCTTATCCCCTTAGTGACCCATCGGTTTAGTCCCCAGTCAACCCTTCATCCAT
* * * * * *
375473 TATTTACCTATTGGCTTAGTCCCCAGTAAACCTATTACCCCCTATGGGGACCTATTAGCTTAGTC
195 TATTTACCTATCGACTTAGTCCCCAGCAAACCTATTACCCCCTATGGGGACCTATCAGCTGAATC
* * * * *
375538 TCCAATGAACTTTCATCCTTTATTTACCTGTTGACTCAGTCCCAAGTAAACCCTTATCCCCTTGG
260 TCCAATCAACCTTCATCCTTTATTTACCTATAGACTCAGTCCCAAGTAAACCCTTAACCCCTTGG
*
375603 TGACCCGTCGA
325 TGACCAGTCGA
* * * * *
375614 TTAGTCTTCAATCAACCCTTCATCCATTGTTTACCTATTGGCTTAGTCC-CTGATAAACCTATTA
1 TTAGTCCTCAGTCAACCCTTCATCCCTTGTTTACCTGTTGGCTCAGTCCTC-GATAAACCTATTA
* * * * *
375678 TCCTATGGTGACCTGTCAGCTCAGTCTTTGGTCAACCTTTATCCTTTATTTACTTGTCGGATCAG
65 TCCTTTGGTGACCTGTCAGCTCAGTCTTCGGTCAACCTTAATCCTTTATTTACCTATCGGATCAG
* * * *
375743 TCCCCGATAAACCCTTATCCCTTTGGTGA-CCAGTCTGTTTAGTCCCCAGTCAACCCTTCATCCC
130 TCCCCGATAAACCCTTATCCCCTTAGTGACCCA-TCGGTTTAGTCCCCAGTCAACCCTTCATCCA
* * * *
375807 TTGTTTACCTATCGACTTAGTCCCCGGCAAACCTATTA-CCCC-ATGGTGACCTGTCAGCTGAAT
194 TTATTTACCTATCGACTTAGTCCCCAGCAAACCTATTACCCCCTATGGGGACCTATCAGCTGAAT
*** * * *
375870 CTTTGATCAACCTTCATCCTTTATTTACCTATCAG-CTTAGTCCTC-GGTAAACCCTTAACCCTT
259 CTCCAATCAACCTTCATCCTTTATTTACCTAT-AGACTCAGTCC-CAAGTAAACCCTTAACCC-C
* *
375933 TTGGTGACCAGTAGGT
321 TTGGTGACCAGT-CGA
* * *
375949 TTAGTCCTCAGTCAACCCTTCATCCCTTGTTTACTTGTTAGCTCAGTCCTCGATAAACTTATTAT
1 TTAGTCCTCAGTCAACCCTTCATCCCTTGTTTACCTGTTGGCTCAGTCCTCGATAAACCTATTAT
* * * *
376014 CCCTTTGGTGACCTGTCAACTCAATCTTCGATTAACCTT
66 -CCTTTGGTGACCTGTCAGCTCAGTCTTCGGTCAACCTT
376053 CATCTCATTG
Statistics
Matches: 359, Mismatches: 70, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
333 63 0.18
334 32 0.09
335 231 0.64
336 33 0.09
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.36
Consensus pattern (335 bp):
TTAGTCCTCAGTCAACCCTTCATCCCTTGTTTACCTGTTGGCTCAGTCCTCGATAAACCTATTAT
CCTTTGGTGACCTGTCAGCTCAGTCTTCGGTCAACCTTAATCCTTTATTTACCTATCGGATCAGT
CCCCGATAAACCCTTATCCCCTTAGTGACCCATCGGTTTAGTCCCCAGTCAACCCTTCATCCATT
ATTTACCTATCGACTTAGTCCCCAGCAAACCTATTACCCCCTATGGGGACCTATCAGCTGAATCT
CCAATCAACCTTCATCCTTTATTTACCTATAGACTCAGTCCCAAGTAAACCCTTAACCCCTTGGT
GACCAGTCGA
Found at i:377745 original size:166 final size:165
Alignment explanation
Indices: 377467--378307 Score: 762
Period size: 165 Copynumber: 5.1 Consensus size: 165
377457 TTCAAGCATC
** * * * *
377467 AAAATTCATTGAATATTATTATTTAATTTC-CATCAAATCAATTTTCAAAAATTAATTCATTTTC
1 AAAATTCATCAAATATTATCATTT-ATTTCATATTAAATTAATTTTCAAAAATTAATTCATTTTC
* * * *
377531 ATGAGTTTTTGATTTTTTTCTTTGAAATTTTATTTTTTTCGAAATACGTTGTTTTGTACTTCGTA
65 ATGAGTTTTTGATTTTTTTCCTTGAAATTCT-TTTTTTTCGAAATACGGTGTTTTCTACTTCGTA
* * *
377596 ATTTTTTTCGAGGAAATTTTTCTTGGTTTTTAATTTT
129 AATTTTTTCGAGGAGATTTTTCTTAGTTTTTAATTTT
* * * *
377633 GAAAATTCATCAAATATTATCATTTATTTTATATTAAATTATTTTTTAAAAATTCATTCATTTTC
1 -AAAATTCATCAAATATTATCATTTATTTCATATTAAATTAATTTTCAAAAATTAATTCATTTTC
* * * *
377698 ATAAGTTTTTGA-TTTTTTCCTTGAAATTCTTCTTTTTTCGAAATACGTTGTTTTTTACTTCATA
65 ATGAGTTTTTGATTTTTTTCCTTGAAATTCTT-TTTTTTCGAAATACGGTGTTTTCTACTTCGTA
*
377762 AATTTTTTC-AAGAGGATTTTTCTTAGTTTTTAATTTT
129 AATTTTTTCGAGGA-GATTTTTCTTAGTTTTTAATTTT
* * * * * *
377799 TAAATTCATGAAATATTATAATTTATTTCATATTCAATTAGTTTTTAAAAATT-ATTCATTTTCA
1 AAAATTCATCAAATATTATCATTTATTTCATATTAAATTAATTTTCAAAAATTAATTCATTTTCA
* * * *
377863 TGAGTTTTTTATTATTTTTCCCTGGAA-T-TTTTTTTT-GAAATACGGTGTTTCCTACTTCGTAA
66 TGAGTTTTTGATT-TTTTTCCTTGAAATTCTTTTTTTTCGAAATACGGTGTTTTCTACTTCGTAA
377925 ATTTTTTCGA-GAGGATTTTTCTTAGTTTTTAACTTTT
130 ATTTTTTCGAGGA-GATTTTTCTTAGTTTTTAA-TTTT
* * * * * *
377962 AAAATTCATAAAATGTTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTTACTCCTTTTCA
1 AAAATTCATCAAATATTATCATTTATTTCATATTAAATTAATTTTCAAAAATTAATTCATTTTCA
* * * ** * *
378027 CT-CGTTTTTTATTTTTTTCCTTGAAA-CCACTTTTTTCTAAAATACGGTGTTTTCTACTCCGT-
66 -TGAGTTTTTGATTTTTTTCCTTGAAATTCTTTTTTTTC-GAAATACGGTGTTTTCTACTTCGTA
* * **** *
378089 AATTTTTTTGAGGGGATTTTTAAGGGTTTTAAATTTTT
129 AATTTTTTCGAGGAGATTTTTCTTAGTTTTTAA-TTTT
* * * ** *
378127 AAAATTCATCAAACATCATCATTTGA-TTCATATTAAATCAATTTAAAAAAATTAATTCATGTTC
1 AAAATTCATCAAATATTATCATTT-ATTTCATATTAAATTAATTTTCAAAAATTAATTCATTTTC
* * ** * * * * *
378191 ATGAGTTTTGGA-TATTTT-GGTGAAATTCCTTTTTTTCGAGAA-ACCGAGTTTTCTTCTCCGTA
65 ATGAGTTTTTGATTTTTTTCCTTGAAATTCTTTTTTTTCGA-AATACGGTGTTTTCTACTTCGT-
* * **
378253 AAATTTTGT-G-GGCAAATTTTTCTTAGTTTAGAATTTTT
128 AAATTTTTTCGAGG-AGATTTTTCTTAGTTTTTAA-TTTT
* *
378291 AAAACTCATCTAATATT
1 AAAATTCATCAAATATT
378308 GTTATTAAAA
Statistics
Matches: 558, Mismatches: 96, Indels: 43
0.80 0.14 0.06
Matches are distributed among these distances:
162 52 0.09
163 93 0.17
164 94 0.17
165 146 0.26
166 113 0.20
167 60 0.11
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (165 bp):
AAAATTCATCAAATATTATCATTTATTTCATATTAAATTAATTTTCAAAAATTAATTCATTTTCA
TGAGTTTTTGATTTTTTTCCTTGAAATTCTTTTTTTTCGAAATACGGTGTTTTCTACTTCGTAAA
TTTTTTCGAGGAGATTTTTCTTAGTTTTTAATTTT
Found at i:378159 original size:328 final size:330
Alignment explanation
Indices: 377501--378208 Score: 824
Period size: 328 Copynumber: 2.1 Consensus size: 330
377491 AATTTCCATC
* **
377501 AAATCAATTTTCAAAAATTAATTCATTTTCATGAGTTTTTGATTTTTTTCTTTGAAATTTTATTT
1 AAATCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTTTTTTCCCTGAAA-TTTATTT
* ** * *
377566 TTTTCGAAATACGTTGTTTTGTACTTCGTAATTTTTTTCGAGGAAATTTTTCTTGGTTTTTAATT
65 TTTTCGAAATACGGTGTTTCCTACTTCGTAAATTTTTTCGAGGAAATTTTTCTTAGTTTTTAATT
* * * * *
377631 TTGAAAATTCATCAAATATTATCATTTATTTTATATTAAATTATTTTTTAAAAATTCATTCATTT
130 TTGAAAATTCATAAAATATTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTCACTCATTT
** * * * *
377696 TCATAAGTTTTTGATTTTTTCCTTGAAATTCTTCTTTTTTCGAAATACGTTGTTTTTTACTTCAT
195 TCATAAGTTTTTGATTTTTTCCTTGAAA-TCCACTTTTTTCAAAATACGGTGTTTTCTACTCCAT
*** * * * *
377761 AAATTTTTTCAAGAGGATTTTTCTTAGTTTTTAATTTTTAAATTCATGAAATATTATAATTTATT
259 AAATTTTTTCAAGAGGATTTTTAAGAGTTTTAAATTTTTAAATTCATCAAACATCATAATTTATT
377826 TCATATT
324 TCATATT
* * * * * *
377833 CAATTAGTTTTTAAAAATT-ATTCATTTTCATGAGTTTTTTATTATTTTTCCCTGGAA-TT-TTT
1 AAATCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATT-TTTTTCCCTGAAATTTATTT
*
377895 TTTT-GAAATACGGTGTTTCCTACTTCGTAAATTTTTTCGA-GAGGATTTTTCTTAGTTTTTAAC
65 TTTTCGAAATACGGTGTTTCCTACTTCGTAAATTTTTTCGAGGA-AATTTTTCTTAGTTTTTAA-
* * *
377958 TTTT-AAAATTCATAAAATGTTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTTACTCCT
128 TTTTGAAAATTCATAAAATATTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTCACTCAT
* *
378022 TTTCACT-CGTTTTTTATTTTTTTCCTTGAAA-CCACTTTTTTCTAAAATACGGTGTTTTCTACT
193 TTTCA-TAAGTTTTTGA-TTTTTTCCTTGAAATCCACTTTTTTC-AAAATACGGTGTTTTCTACT
* ** * * *
378085 CCGT-AATTTTTTTGAGGGGATTTTTAAGGGTTTTAAATTTTTAAAATTCATCAAACATCATCAT
255 CCATAAATTTTTTCAAGAGGATTTTTAAGAGTTTTAAATTTTT-AAATTCATCAAACATCATAAT
378149 TTGA-TTCATATT
319 TT-ATTTCATATT
* * * *
378161 AAATCAATTTAAAAAAATTAATTCATGTTCATGAGTTTTGGATATTTT
1 AAATCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTTTTT
378209 GGTGAAATTC
Statistics
Matches: 315, Mismatches: 52, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
327 41 0.13
328 177 0.56
329 47 0.15
330 2 0.01
331 23 0.07
332 25 0.08
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (330 bp):
AAATCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTTTTTTCCCTGAAATTTATTTT
TTTCGAAATACGGTGTTTCCTACTTCGTAAATTTTTTCGAGGAAATTTTTCTTAGTTTTTAATTT
TGAAAATTCATAAAATATTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTCACTCATTTT
CATAAGTTTTTGATTTTTTCCTTGAAATCCACTTTTTTCAAAATACGGTGTTTTCTACTCCATAA
ATTTTTTCAAGAGGATTTTTAAGAGTTTTAAATTTTTAAATTCATCAAACATCATAATTTATTTC
ATATT
Found at i:378226 original size:328 final size:328
Alignment explanation
Indices: 377501--378299 Score: 814
Period size: 328 Copynumber: 2.4 Consensus size: 328
377491 AATTTCCATC
* * **
377501 AAATCAATTTTCAAAAATTAATTCATTTTCATGAGTTTTTGATTTTTTTCTTTGAAATTTTATTT
1 AAATCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTATTTTCCCTGAAA--TT-TTT
* ** * *
377566 TTTTCGAAATACGTTGTTTTGTACTTCGTAATTTTTTTCGAGGAAATTTTTCTTGGTTTTTAATT
63 TTTTCGAAATACGGTGTTTCCTACTTCGTAAATTTTTTCGAGGAAATTTTTCTTAGTTTTTAATT
* * * * *
377631 TTGAAAATTCATCAAATATTATCATTTATTTTATATTAAATTATTTTTTAAAAATTCATTCATTT
128 TTGAAAATTCATAAAATATTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTCACTCATTT
** * * * *
377696 TCATAAGTTTTTGATTTTTTCCTTGAAATTCTTCTTTTTTCGAAATACGTTGTTTTTTACTTCAT
193 TCATAAGTTTTTGATTTTTTCCTTGAAA-TCCACTTTTTTCAAAATACGGTGTTTTCTACTCCAT
*** * * * *
377761 AAATTTTTTCAAGAGGATTTTTCTTAGTTTTTAATTTTTAAATTCATGAAATATTATAATTTATT
257 AAATTTTTTCAAGAGGATTTTTAAGAGTTTTAAATTTTTAAATTCATCAAACATCATAATTTATT
377826 TCATATT
322 TCATATT
* * * * * *
377833 CAATTAGTTTTTAAAAATT-ATTCATTTTCATGAGTTTTTTATTATTTTTCCCTGGAATTTTTTT
1 AAATCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTA-TTTTCCCTGAAATTTTTTT
*
377897 TT-GAAATACGGTGTTTCCTACTTCGTAAATTTTTTCGA-GAGGATTTTTCTTAGTTTTTAACTT
65 TTCGAAATACGGTGTTTCCTACTTCGTAAATTTTTTCGAGGA-AATTTTTCTTAGTTTTTAA-TT
* * *
377960 TT-AAAATTCATAAAATGTTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTTACTCCTTT
128 TTGAAAATTCATAAAATATTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTCACTCATTT
* *
378024 TCACT-CGTTTTTTATTTTTTTCCTTGAAA-CCACTTTTTTCTAAAATACGGTGTTTTCTACTCC
193 TCA-TAAGTTTTTGA-TTTTTTCCTTGAAATCCACTTTTTTC-AAAATACGGTGTTTTCTACTCC
* ** * * *
378087 GT-AATTTTTTTGAGGGGATTTTTAAGGGTTTTAAATTTTTAAAATTCATCAAACATCATCATTT
255 ATAAATTTTTTCAAGAGGATTTTTAAGAGTTTTAAATTTTT-AAATTCATCAAACATCATAATTT
378151 GA-TTCATATT
319 -ATTTCATATT
* * * **
378161 AAATCAATTTAAAAAAATTAATTCATGTTCATGAGTTTTGGA-TATTTT-GGTGAAATTCCTTTT
1 AAATCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTATTTTCCCTGAAATT--TTTT
* * * * * * **
378224 TTTCGAGAA-ACCGAGTTTTCTTCTCCGTAAAATTTTGT-G-GGCAAATTTTTCTTAGTTTAGAA
64 TTTCGA-AATACGGTGTTTCCTACTTCGT-AAATTTTTTCGAGG-AAATTTTTCTTAGTTTTTAA
* *
378286 TTTTTAAAACTCAT
126 TTTTGAAAATTCAT
378300 CTAATATTGT
Statistics
Matches: 385, Mismatches: 65, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
326 6 0.02
327 45 0.12
328 186 0.48
329 88 0.23
330 13 0.03
331 23 0.06
332 24 0.06
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (328 bp):
AAATCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTATTTTCCCTGAAATTTTTTTT
TCGAAATACGGTGTTTCCTACTTCGTAAATTTTTTCGAGGAAATTTTTCTTAGTTTTTAATTTTG
AAAATTCATAAAATATTATCATTTATTTCATATTAAATTAGTTTTCAAAAATTCACTCATTTTCA
TAAGTTTTTGATTTTTTCCTTGAAATCCACTTTTTTCAAAATACGGTGTTTTCTACTCCATAAAT
TTTTTCAAGAGGATTTTTAAGAGTTTTAAATTTTTAAATTCATCAAACATCATAATTTATTTCAT
ATT
Found at i:378537 original size:14 final size:14
Alignment explanation
Indices: 378520--378573 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 14
378510 ATTTTCAAAC
378520 TTTAATTTTTATAA
1 TTTAATTTTTATAA
*
378534 TTTAATTATTT-TTA
1 TTTAATT-TTTATAA
*
378548 -TTGATTTTTATAA
1 TTTAATTTTTATAA
*
378561 TATAA-TTTTATAA
1 TTTAATTTTTATAA
378574 ATGATACAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
12 3 0.09
13 15 0.47
14 11 0.34
15 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTAATTTTTATAA
Found at i:379174 original size:2 final size:2
Alignment explanation
Indices: 379167--379193 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
379157 TTTCTTGTTA
379167 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
379194 AAATGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:381216 original size:155 final size:153
Alignment explanation
Indices: 380424--381929 Score: 994
Period size: 156 Copynumber: 9.7 Consensus size: 153
380414 TGAAGGAAAA
* * * * * * ** *
380424 TATTTTGGATAGGTCCATCCCTTCTATAATCCTTTTTAAGTCCTTCAAAGATATCGTGATACTT-
1 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAGGGATATCGAG-TACTTC
* * * * * *
380488 TCACGTTGAAGGTATACCCATA-AGGGCATTTTGGTAATATCTTAGAACCAATTCCTAGGTCATC
65 T-ACATCGAAGGTAT-CCC-TAGA-GGCATTTTGGTAAT-TTTTAAAACCAACTCCTAGGTCGTC
**
380552 ACCT-GGTCCGCTTTTATGCCGAAGGTGAA
125 A-CTAGGTCCGCTTTTATGCCGAAGGTGGG
380581 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAGTGG-TATCGAGTACTTC
1 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAG-GGATATCGAGTACTTC
* * * *
380645 TACATCGAAGGTATCCCTCAGAGGCATTTTCGTAATTTTTCAAAACCAACGCTTAGGT-GTTACT
65 TACATCGAAGGTATCCCT-AGAGGCATTTTGGTAATTTTT-AAAACCAACTCCTAGGTCGTCACT
* * **
380709 AGGTCTGCTTTTTTGTTGAAGGTGGG
128 AGGTCCGCTTTTATGCCGAAGGTGGG
* * * ** * * *
380735 TA--TAAGATAGGCTCATCCCAGTTTAT-ATTCCTCGTTAAAT-TCTTTAGGGATATCGAGCATT
1 TATTTAGGATAGGTTCATCCCA-TCTATAATT-CTTTTTAAGTCT-TTTAGGGATATCGAGTACT
** * * * * * * * * *
380796 TCTACATCGAAAATATCTCTTAAAGGTATTTTGGTAATTTTTTAAAATCGAGTCTTAAGTTGTCA
63 TCTACATCGAAGGTATC-CCTAGAGGCATTTTGGTAA-TTTTTAAAACCAACTCCTAGGTCGTCA
* * *
380861 -TCGAGTCCGCTTTTATGCCGAAGGTAGA
126 CTAG-GTCCGCTTTTATGCCGAAGGTGGG
* * * * *
380889 TATTTAGGATAGGTTCATCCCTTCTATAA-TCATTTTTAAGTCTTTAAAGGATATTGGGATAC-T
1 TATTTAGGATAGGTTCATCCCATCTATAATTC-TTTTTAAGTCTTTTAGGGATATCGAG-TACTT
* * * * * *
380952 CTCATATCGAAGGTA-CACCTATAAAGGCATTTTGGTAATTTGTTAGAACAAATTCCTAGCTCGT
64 CT-ACATCGAAGGTATC-CC--TAGAGGCATTTTGGTAATTT-TTAAAACCAACTCCTAGGTCGT
* * *
381016 CAC-CGAGTTCGCTTTTATGCCGAAGGTGAG
124 CACTAG-GTCCGCTTTTATGCCGAAGGTGGG
381046 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAGAGG-TATCGAGTACTTC
1 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAG-GGATATCGAGTACTTC
* * * * * *
381110 TACGTCGAAGGTATCTCCTGGAGGTATTTTTGTAATTTTCTAAAACCAACTCATAGGTCGTTACT
65 TACATCGAAGGTATC-CCTAGAGGCATTTTGGTAATTTT-TAAAACCAACTCCTAGGTCGTCACT
** *
381175 AGGTCTACTTTTTTGCCGAAGGTGGG
128 AGGTCCGCTTTTATGCCGAAGGTGGG
* * * * * *
381201 TATTTAGGATTGGTTCATCCCAGTTTAT-ATTCCTTGTTAAATCCTTTAGGGATATCGAGCACTT
1 TATTTAGGATAGGTTCATCCCA-TCTATAATT-CTTTTTAAGTCTTTTAGGGATATCGAGTACTT
* * * * *** * *
381265 CTATC-TCGAAGATATCCCCTAG-GAGTATTTTGGTAATTTCTTAGAATCGTGTCCTAAGTTGTC
64 CTA-CATCGAAGGTAT-CCCTAGAG-GCATTTTGGTAATTT-TTAAAACCAACTCCTAGGTCGTC
* * * * *
381328 AC-CGAGTCCGCTTTTATGTCAAAGGTAGA
125 ACTAG-GTCCGCTTTTATGCCGAAGGTGGG
* * * * * * * *
381357 TATTTATGATAGGTTTATCCCTTCTATGATCCTTTTTAAGTCCTTAAAGGATATC-AGGATACTT
1 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAGGGATATCGA-G-TACTT
* * * * * *
381421 -TCACATCGAAGGCATACTTATAGGGCATTTTGGTAATTTCTTAGAACCAATTCCTAGGTCGTCA
64 CT-ACATCGAAGGTATCCCTAGA-GGCATTTTGGTAATTT-TTAAAACCAACTCCTAGGTCGTCA
* * *
381485 -TCGGGTCTGCTTTTATGCCTAAGGTGGG
126 CT-AGGTCCGCTTTTATGCCGAAGGTGGG
* *
381513 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCCTTTAGGGGTATC-AGGTACTTC
1 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAGGGATATCGA-GTACTTC
* * ** *
381577 TACGTCGAAGGTATCCCTTAGATGCATTTTCCTAATTTTTCAAAACCAACTCCTAGGTCGTCACC
65 TACATCGAAGGTATCCC-TAGAGGCATTTTGGTAATTTTT-AAAACCAACTCCTAGGTCGTCACT
* * *
381642 AAGTCCACTTTTATGCTGAAGGTGGG
128 AGGTCCGCTTTTATGCCGAAGGTGGG
* * * * * ** * * *
381668 TATTTAGGATATGCTCATCTCAGTTTGTAAACCTTTTTAAATCCTTTAGGGATATCGGGTACTTC
1 TATTTAGGATAGGTTCATCCCA-TCTATAATTCTTTTTAAGTCTTTTAGGGATATCGAGTACTTC
* * ** * * * * * * * *
381733 TACGTTGAAAATATCCCTTAGGGGTATTTTGGTAATTTTTAGAATCGAGTCCTAGGTTGTCAC-C
65 TACATCGAAGGTATCCC-TAGAGGCATTTTGGTAATTTTTAAAACCAACTCCTAGGTCGTCACTA
* ** *
381797 GAGTTCGCTTTTACACTGAAGGTGGG
129 G-GTCCGCTTTTATGCCGAAGGTGGG
* * * * *
381823 TATTTAGGATATGTTCGTCCCATCTATAA-TCCTTTTAAGTGCTTTAAGGG-TAGCGAGTACTTC
1 TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGT-CTTTTAGGGATATCGAGTACTTC
* * * ** * * * *
381886 GATATCGATGGTATCGTTAGGGGTATTTTCGTAATTTTTTAAAC
65 TACATCGAAGGTATCCCTAGAGGCATTTTGGTAATTTTTAAAAC
381930 TTAGCCCTTT
Statistics
Matches: 1051, Mismatches: 242, Indels: 117
0.75 0.17 0.08
Matches are distributed among these distances:
152 45 0.04
153 96 0.09
154 74 0.07
155 314 0.30
156 357 0.34
157 160 0.15
158 5 0.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (153 bp):
TATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAGGGATATCGAGTACTTCT
ACATCGAAGGTATCCCTAGAGGCATTTTGGTAATTTTTAAAACCAACTCCTAGGTCGTCACTAGG
TCCGCTTTTATGCCGAAGGTGGG
Found at i:381655 original size:311 final size:308
Alignment explanation
Indices: 380423--381928 Score: 1046
Period size: 311 Copynumber: 4.9 Consensus size: 308
380413 CTGAAGGAAA
*
380423 ATATTT-TGGATAGGTCCATCCCTTCTATAATCCTTTTTAAGTCCTTCAAA-GATATCGTGATAC
1 ATATTTAT-GATAGGTTCATCCCTTCTATAATCCTTTTTAAGTCCTT-AAAGGATATC--GATAC
* * * * * *
380486 TTTC-ACGTTGAAGGTATACCCATAAGGGCATTTTGGTAATATCTTAGAACCAATTCCTAGGTCA
62 TTTCTACATCGAAGGTATACTCAT-AGGGCATTTTGGTAATTTCTTAAAACCAATTCCTAGGTCG
* * *
380550 TCACCTGGTCCGCTTTTATGCCGAAGGTGAATATTTAGGATAGGTTCATCCCATCTATAATTCTT
126 TCATCGGGTCCGCTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCATCTATAATTCTT
* *
380615 TTTAAGTCTTTTAGTGG-TATCGAGTACTTCTACATCGAAGGTATCCCTCAGAGGCATTTTCGTA
191 TTTAAGTCCTTTAG-GGATATCGAGTACTTCTAC-TCGAAGGTATCCCTTAGAGGCATTTTCGTA
* * * * * * * *
380679 ATTT-TTCAAAACCAACGCTTAGGT-GTTACTAGGTCTGCTTTTTTGTTGAAGGTGG
254 ATTTCTT-AAAACCAACTCCTAGGTCGTCACCAAGTCCGCTTTTATGTCGAAGGT-G
* * * * ** * * * * *
380734 GTA--TAAGATAGGCTCATCCCAGTT-TATATTCCTCGTTAAATTCTTTAGGGATATCGA-GCAT
1 ATATTTATGATAGGTTCATCCC--TTCTATAATCCTTTTTAAGTCCTTAAAGGATATCGATAC-T
** * * * * * * * * * *
380795 TTCTACATCGAAAATAT-CTCTTAAAGGTATTTTGGTAATTTTTTAAAATCGAGTCTTAAGTTGT
63 TTCTACATCGAAGGTATACTCAT-AGGGCATTTTGGTAATTTCTTAAAACCAATTCCTAGGTCGT
* * *
380859 CATCGAGTCCGCTTTTATGCCGAAGGTAGATATTTAGGATAGGTTCATCCCTTCTATAA-TCATT
127 CATCGGGTCCGCTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCATCTATAATTC-TT
* * * *
380923 TTTAAGT-CTTTAAAGGATATTGGGATACTCTCATA-TCGAAGGTA-CACCTATAAAGGCATTTT
191 TTTAAGTCCTTT-AGGGATATCGAG-TACT-TC-TACTCGAAGGTATC-CCT-TAGAGGCATTTT
* * * * * * * * *
380985 GGTAATTTGTTAGAACAAATTCCTAGCTCGTCACCGAGTTCGCTTTTATGCCGAAGGTG
250 CGTAATTTCTTAAAACCAACTCCTAGGTCGTCACCAAGTCCGCTTTTATGTCGAAGGTG
* * * * *
381044 AGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTAGAGG-TATCGAGTAC-
1 A-TATTTATGATAGGTTCATCCCTTCTATAATCCTTTTTAAGTC-CTTAAAGGATATCGA-TACT
* * * * * * *
381107 TTCTACGTCGAAGGTAT-CTCCTGGAGGTATTTTTGTAATTT-TCTAAAACCAACTCATAGGTCG
63 TTCTACATCGAAGGTATACTCATAG-GGCATTTTGGTAATTTCT-TAAAACCAATTCCTAGGTCG
* * ** * * * *
381170 TTA-CTAGGTCTACTTTTTTGCCGAAGGTGGGTATTTAGGATTGGTTCATCCCAGTTTAT-ATTC
126 TCATC-GGGTCCGCTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCA-TCTATAATT-
* * * * * * *
381233 CTTGTTAAATCCTTTAGGGATATCGAGCACTTCTATCTCGAAGATATCCCCTAG-GAGTATTTTG
188 CTTTTTAAGTCCTTTAGGGATATCGAGTACTTCTA-CTCGAAGGTATCCCTTAGAG-GCATTTTC
* * *** * * * *
381297 GTAATTTCTTAGAATCGTGTCCTAAGTTGTCACCGAGTCCGCTTTTATGTCAAAGGTAG
251 GTAATTTCTTAAAACCAACTCCTAGGTCGTCACCAAGTCCGCTTTTATGTCGAAGGT-G
* *
381356 ATATTTATGATAGGTTTATCCCTTCTATGATCCTTTTTAAGTCCTTAAAGGATATCAGGATACTT
1 ATATTTATGATAGGTTCATCCCTTCTATAATCCTTTTTAAGTCCTTAAAGGATATC--GATACTT
* * *
381421 TC-ACATCGAAGGCATACTTATAGGGCATTTTGGTAATTTCTTAGAACCAATTCCTAGGTCGTCA
64 TCTACATCGAAGGTATACTCATAGGGCATTTTGGTAATTTCTTAAAACCAATTCCTAGGTCGTCA
* * *
381485 TCGGGTCTGCTTTTATGCCTAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTT
129 TCGGGTCCGCTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCATCTATAATTCTTTTT
* * *
381550 AAGTCCTTTAGGGGTATC-AGGTACTTCTACGTCGAAGGTATCCCTTAGATGCATTTTCCTAATT
194 AAGTCCTTTAGGGATATCGA-GTACTTCTAC-TCGAAGGTATCCCTTAGAGGCATTTTCGTAATT
*
381614 T-TTCAAAACCAACTCCTAGGTCGTCACCAAGTCCACTTTTATG-CTGAAGGTGG
257 TCTT-AAAACCAACTCCTAGGTCGTCACCAAGTCCGCTTTTATGTC-GAAGGT-G
* * * * * * * * * * *
381667 GTATTTAGGATATGCTCATCTCAGTT-TGTAAACCTTTTTAAATCCTTTAGGGATATCGGGTAC-
1 ATATTTATGATAGGTTCATC-C-CTTCTATAATCCTTTTTAAGTCCTTAAAGGATATC-GATACT
* * ** * * * * * * * *
381730 TTCTACGTTGAAAATAT-CCCTTAGGGGTATTTTGGTAATTT-TTAGAATCGAGTCCTAGGTTGT
63 TTCTACATCGAAGGTATACTCATA-GGGCATTTTGGTAATTTCTTAAAACCAATTCCTAGGTCGT
* * * ** * * * * *
381793 CACCGAGTTCGCTTTTACACTGAAGGTGGGTATTTAGGATATGTTCGTCCCATCTATAA-TCCTT
127 CATCGGGTCCGCTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCATCTATAATTCTTT
* * * * * *
381857 TTAAGTGCTTTAAGGG-TAGCGAGTACTTCGATA-TCGATGGTAT-CGTTAGGGGTATTTTCGTA
192 TTAAGTCCTTT-AGGGATATCGAGTACTTC--TACTCGAAGGTATCCCTTAGAGGCATTTTCGTA
*
381919 ATTTTTTAAA
254 ATTTCTTAAA
381929 CTTAGCCCTT
Statistics
Matches: 929, Mismatches: 209, Indels: 117
0.74 0.17 0.09
Matches are distributed among these distances:
307 8 0.01
308 129 0.14
309 74 0.08
310 145 0.16
311 272 0.29
312 241 0.26
313 54 0.06
314 6 0.01
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (308 bp):
ATATTTATGATAGGTTCATCCCTTCTATAATCCTTTTTAAGTCCTTAAAGGATATCGATACTTTC
TACATCGAAGGTATACTCATAGGGCATTTTGGTAATTTCTTAAAACCAATTCCTAGGTCGTCATC
GGGTCCGCTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAA
GTCCTTTAGGGATATCGAGTACTTCTACTCGAAGGTATCCCTTAGAGGCATTTTCGTAATTTCTT
AAAACCAACTCCTAGGTCGTCACCAAGTCCGCTTTTATGTCGAAGGTG
Found at i:381710 original size:467 final size:466
Alignment explanation
Indices: 380423--381871 Score: 1873
Period size: 467 Copynumber: 3.1 Consensus size: 466
380413 CTGAAGGAAA
*
380423 ATATTT-TGGATAGGTCCATCCCTTCTATAATCCTTTTTAAGTCCTTCAAA-GATATCGTGATAC
1 ATATTTAT-GATAGGTTCATCCCTTCTATAATCCTTTTTAAGTCCTT-AAAGGATATCG-GATAC
* * * * *
380486 TTTCACGTTGAAGGTATACCCATAAGGGCATTTTGGTAATATCTTAGAACCAATTCCTAGGTCAT
63 TTTCACATCGAAGGTATACCTATAAGGGCATTTTGGTAATTTCTTAGAACCAATTCCTAGGTCGT
* * *
380551 CACCTGGTCCGCTTTTATGCCGAAGGTGAATATTTAGGATAGGTTCATCCCATCTATAATTCTTT
128 CACCGGGTCTGCTTTTATGCCGAAGGTGAGTATTTAGGATAGGTTCATCCCATCTATAATTCTTT
* * *
380616 TTAAGTCTTTTAGTGGTATCGAGTACTTCTACATCGAAGGTATCCCTCAGAGGCATTTTCGTAAT
193 TTAAGTCTTTTAGAGGTATCGAGTACTTCTACGTCGAAGGTATCCCTTAGAGGCATTTTCGTAAT
* * * * *
380681 TTTTCAAAACCAACGCTTAGGT-GTTACTAGGTCTGCTTTTTTGTTGAAGGTGGGTA--TAAGAT
258 TTTTCAAAACCAACTCATAGGTCGTTACTAGGTCTACTTTTTTGCTGAAGGTGGGTATTTAGGAT
* * * *
380743 AGGCTCATCCCAGTTTATATTCCTCGTTAAATTCTTTAGGGATATCGAGCATTTCTACATCGAAA
323 ATGCTCATCCCAGTTTATATTCCTTGTTAAATCCTTTAGGGATATCGAGCACTTCTACATCGAAA
* * * * *
380808 ATATCTCTTA-AAGGTATTTTGGTAATTTTTTAAAATCGAGTCTTAAGTTGTCATCGAGTCCGCT
388 ATATCCCTTAGGA-GTATTTTGGTAA-TTTTTAGAATCGAGTCCTAAGTTGTCACCGAGTCCGCT
*
380872 TTTATGCCGAAGGTAG
451 TTTATGCCAAAGGTAG
* * * * *
380888 ATATTTAGGATAGGTTCATCCCTTCTATAATCATTTTTAAGTCTTTAAAGGATATTGGGATACTC
1 ATATTTATGATAGGTTCATCCCTTCTATAATCCTTTTTAAGTCCTTAAAGGATA-TCGGATACTT
* * * * * *
380953 TCATATCGAAGGTACACCTATAAAGGCATTTTGGTAATTTGTTAGAACAAATTCCTAGCTCGTCA
65 TCACATCGAAGGTATACCTATAAGGGCATTTTGGTAATTTCTTAGAACCAATTCCTAGGTCGTCA
*
381018 CCGAGT-TCGCTTTTATGCCGAAGGTGAGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTT
130 CCGGGTCT-GCTTTTATGCCGAAGGTGAGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTT
* * *
381082 TAAGTCTTTTAGAGGTATCGAGTACTTCTACGTCGAAGGTATCTCC-TGGAGGTATTTTTGTAA-
194 TAAGTCTTTTAGAGGTATCGAGTACTTCTACGTCGAAGGTATC-CCTTAGAGGCATTTTCGTAAT
*
381145 TTTTCTAAAACCAACTCATAGGTCGTTACTAGGTCTACTTTTTTGCCGAAGGTGGGTATTTAGGA
258 TTTTC-AAAACCAACTCATAGGTCGTTACTAGGTCTACTTTTTTGCTGAAGGTGGGTATTTAGGA
*
381210 T-TGGTTCATCCCAGTTTATATTCCTTGTTAAATCCTTTAGGGATATCGAGCACTTCTATC-TCG
322 TAT-GCTCATCCCAGTTTATATTCCTTGTTAAATCCTTTAGGGATATCGAGCACTTCTA-CATCG
* * *
381273 AAGATATCCCCTAGGAGTATTTTGGTAATTTCTTAGAATCGTGTCCTAAGTTGTCACCGAGTCCG
385 AAAATATCCCTTAGGAGTATTTTGGTAATTT-TTAGAATCGAGTCCTAAGTTGTCACCGAGTCCG
*
381338 CTTTTATGTCAAAGGTAG
449 CTTTTATGCCAAAGGTAG
* *
381356 ATATTTATGATAGGTTTATCCCTTCTATGATCCTTTTTAAGTCCTTAAAGGATATCAGGATACTT
1 ATATTTATGATAGGTTCATCCCTTCTATAATCCTTTTTAAGTCCTTAAAGGATATC-GGATACTT
* *
381421 TCACATCGAAGGCATACTTAT-AGGGCATTTTGGTAATTTCTTAGAACCAATTCCTAGGTCGTCA
65 TCACATCGAAGGTATACCTATAAGGGCATTTTGGTAATTTCTTAGAACCAATTCCTAGGTCGTCA
* * *
381485 TCGGGTCTGCTTTTATGCCTAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTT
130 CCGGGTCTGCTTTTATGCCGAAGGTGAGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTT
* * * *
381550 AAGTCCTTTAGGGGTATC-AGGTACTTCTACGTCGAAGGTATCCCTTAGATGCATTTTCCTAATT
195 AAGTCTTTTAGAGGTATCGA-GTACTTCTACGTCGAAGGTATCCCTTAGAGGCATTTTCGTAATT
* * * * * *
381614 TTTCAAAACCAACTCCTAGGTCGTCACCAAGTCCACTTTTATGCTGAAGGTGGGTATTTAGGATA
259 TTTCAAAACCAACTCATAGGTCGTTACTAGGTCTACTTTTTTGCTGAAGGTGGGTATTTAGGATA
* * ** * * * * *
381679 TGCTCATCTCAGTTTGTAAACCTTTTTAAATCCTTTAGGGATATCGGGTACTTCTACGTTGAAAA
324 TGCTCATCCCAGTTTATATTCCTTGTTAAATCCTTTAGGGATATCGAGCACTTCTACATCGAAAA
* * *
381744 TATCCCTTAGGGGTATTTTGGTAATTTTTAGAATCGAGTCCTAGGTTGTCACCGAGTTCGCTTTT
389 TATCCCTTAGGAGTATTTTGGTAATTTTTAGAATCGAGTCCTAAGTTGTCACCGAGTCCGCTTTT
** ** *
381809 ACACTGAAGGTGG
454 ATGCCAAAGGTAG
* * * * * * *
381822 GTATTTAGGATATGTTCGTCCCATCTATAATCC-TTTTAAGTGCTTTAAGG
1 ATATTTATGATAGGTTCATCCCTTCTATAATCCTTTTTAAGTCCTTAAAGG
381872 GTAGCGAGTA
Statistics
Matches: 853, Mismatches: 111, Indels: 40
0.85 0.11 0.04
Matches are distributed among these distances:
464 8 0.01
465 248 0.29
466 107 0.13
467 282 0.33
468 206 0.24
469 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (466 bp):
ATATTTATGATAGGTTCATCCCTTCTATAATCCTTTTTAAGTCCTTAAAGGATATCGGATACTTT
CACATCGAAGGTATACCTATAAGGGCATTTTGGTAATTTCTTAGAACCAATTCCTAGGTCGTCAC
CGGGTCTGCTTTTATGCCGAAGGTGAGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTA
AGTCTTTTAGAGGTATCGAGTACTTCTACGTCGAAGGTATCCCTTAGAGGCATTTTCGTAATTTT
TCAAAACCAACTCATAGGTCGTTACTAGGTCTACTTTTTTGCTGAAGGTGGGTATTTAGGATATG
CTCATCCCAGTTTATATTCCTTGTTAAATCCTTTAGGGATATCGAGCACTTCTACATCGAAAATA
TCCCTTAGGAGTATTTTGGTAATTTTTAGAATCGAGTCCTAAGTTGTCACCGAGTCCGCTTTTAT
GCCAAAGGTAG
Found at i:383830 original size:41 final size:41
Alignment explanation
Indices: 383721--383831 Score: 105
Period size: 41 Copynumber: 2.7 Consensus size: 41
383711 GACAAGTAAG
* * *
383721 CAAAAGAGAAAAAAGTCTTTCAAGTCTAAGCCGATGGGCAGA
1 CAAAAGA-AAAAAAGTCTTTCAAGTCAAAACCGATAGGCAGA
* ** * ** * **
383763 CAAAGGTGAAATAGTCTCCCAGGTCAAAATTGATAGGCAGA
1 CAAAAGAAAAAAAGTCTTTCAAGTCAAAACCGATAGGCAGA
383804 CAAAAGAAAAAAAGTCTTTCAAGTCAAA
1 CAAAAGAAAAAAAGTCTTTCAAGTCAAA
383832 GTCGACGGTC
Statistics
Matches: 50, Mismatches: 19, Indels: 1
0.71 0.27 0.01
Matches are distributed among these distances:
41 45 0.90
42 5 0.10
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (41 bp):
CAAAAGAAAAAAAGTCTTTCAAGTCAAAACCGATAGGCAGA
Found at i:383845 original size:41 final size:41
Alignment explanation
Indices: 383729--383923 Score: 135
Period size: 42 Copynumber: 4.7 Consensus size: 41
383719 AGCAAAAGAG
* * * * *
383729 AAAAAAGTCTTTCAAGTCTAAGCCGATGGGCAGACAAAGGT
1 AAAAAAGTCTTTCAAGTCAAAGTCGACGGTCAGACAAAAGT
* * ** * * * * *
383770 GAAATAGTCTCCCAGGTCAAAATTGATAGG-CAGACAAAAGA
1 AAAAAAGTCTTTCAAGTCAAAGTCGA-CGGTCAGACAAAAGT
*
383811 AAAAAAGTCTTTCAAGTCAAAGTCGACGGTCAGACAAAGGGT
1 AAAAAAGTCTTTCAAGTCAAAGTCGACGGTCAGACAAA-AGT
* * *
383853 AAAGAAGTCTCTCAAGTCAAAGTAGACGAGT-AGACAAAGAGT
1 AAAAAAGTCTTTCAAGTCAAAGTCGACG-GTCAGACAAA-AGT
* **
383895 AAATAAGTCTATT-GGGTCAAAGTCGACGG
1 AAAAAAGTCT-TTCAAGTCAAAGTCGACGG
383924 GTAGATAAGG
Statistics
Matches: 118, Mismatches: 31, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
40 2 0.02
41 54 0.46
42 59 0.50
43 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (41 bp):
AAAAAAGTCTTTCAAGTCAAAGTCGACGGTCAGACAAAAGT
Found at i:384551 original size:42 final size:42
Alignment explanation
Indices: 383826--384591 Score: 387
Period size: 42 Copynumber: 18.3 Consensus size: 42
383816 AGTCTTTCAA
* * *
383826 GTCAAAGTCGA-CGGTCAGACAAAGGGTAAAGAAGTCTCTCAA
1 GTCAAAGTCGATGGGT-AGACAAAGGGTAAAGAAGTCTCTTAG
* * * * * * *
383868 GTCAAAGTAGACGAGTAGACAAAGAGTAAATAAGTCTATTGG
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
* * * * **
383910 GTCAAAGTCGACGGGTAGATAAGGGGTTAAGAAGTCTCCCAG
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
** * * *
383952 GTCAAAG-CTGGCGGGTAGACAAAGGGGAAAGAAATCTCTCAG
1 GTCAAAGTC-GATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
* * * *
383994 GTCAAAGTCAACGGGTAGACAAAGGGTGAAGAAGTCTC-TCG
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
* * *
384035 AGTTAAAG-CTGATGGGTAGCCAAAGGGTAAAGAAGT-T-TATCG
1 -GTCAAAGTC-GATGGGTAGACAAAGGGTAAAGAAGTCTCT-TAG
* * *** * * * *
384077 AGTCAAAGCCCACT-AACAAATAAAGGGTGAAGAAGTCTCTTGG
1 -GTCAAAGTCGA-TGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
* * * * * * *
384120 GTCAAAGTTGACGGGCAAACAAAAGGTAAAAAAGTCTCAT-G
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
* * * **
384161 AGTCAAAG-CTGATGGGCCA-AAAAAGGGTGAAGAAGTCTC-CCG
1 -GTCAAAGTC-GATGGG-TAGACAAAGGGTAAAGAAGTCTCTTAG
** * * *
384203 AGTCAAAGTCGATAAGTAGATAAAAGGTAAAGAAGTCTCCTAG
1 -GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
** *
384246 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCCCAA
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
** ** * * * * * *
384288 GTCAAAACCGACAGGCAAAAAAAGGGTGAAGAAATCT-TTCGG
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTT-AG
* * ** * ***
384330 GTCAAAGTCGATGGGCACACAAAAAGTAAAGAAGTTTCCCGG
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
* *
384372 GTCAAAGTCGATGGG-AGACAAAAGGTAAAAAAGTCTCCTTAG
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCT-CTTAG
* * * * * **
384414 ATCAAAGTCGACGGGTAGACGAAA-AGTGAATAAGTCTCTCGG
1 GTCAAAGTCGATGGGTAGAC-AAAGGGTAAAGAAGTCTCTTAG
* * * *
384456 GTCAAAGTTGATGGGTAGAC-AAGCAGTAAA-AAATCT-TTCG
1 GTCAAAGTCGATGGGTAGACAAAG-GGTAAAGAAGTCTCTTAG
* **
384496 AGTCAAAATCGATGGACAGACAAAGGGTAAAGAAGTCTCTTAG
1 -GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
* * * * * *
384539 GTCAAAGCCGATGGGCAGATAAAAGGTAAAGAAGCCTCCTAG
1 GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
*
384581 GTCAAAATCGA
1 GTCAAAGTCGA
384592 CTAGGAGATG
Statistics
Matches: 550, Mismatches: 144, Indels: 60
0.73 0.19 0.08
Matches are distributed among these distances:
40 4 0.01
41 49 0.09
42 464 0.84
43 29 0.05
44 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.18
Consensus pattern (42 bp):
GTCAAAGTCGATGGGTAGACAAAGGGTAAAGAAGTCTCTTAG
Found at i:384606 original size:42 final size:42
Alignment explanation
Indices: 384497--384614 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
384487 AATCTTTCGA
* * * * *
384497 GTCAAAATCGAT-GGACAGACAAAGGGTAAAGAAGTCTCTTAG
1 GTCAAAACCGATAGG-CAGATAAAAGGTAAAGAAGCCTCCTAG
* *
384539 GTCAAAGCCGATGGGCAGATAAAAGGTAAAGAAGCCTCCTAG
1 GTCAAAACCGATAGGCAGATAAAAGGTAAAGAAGCCTCCTAG
* *
384581 GTCAAAATCGACTAGG-AGATGAAAGGTAAAGAAG
1 GTCAAAACCGA-TAGGCAGATAAAAGGTAAAGAAG
384615 ATTCTCGAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 59 0.92
43 5 0.08
ACGTcount: A:0.42, C:0.14, G:0.28, T:0.16
Consensus pattern (42 bp):
GTCAAAACCGATAGGCAGATAAAAGGTAAAGAAGCCTCCTAG
Found at i:384784 original size:42 final size:41
Alignment explanation
Indices: 384670--384811 Score: 142
Period size: 42 Copynumber: 3.4 Consensus size: 41
384660 TGACGAGCAA
* * **
384670 ACAAAGGGTTAAGAAGTCTCTCGGGTCAAAACCAACAGGTAG
1 ACAAAGGGTAAAGAAGTTTCTCGGGTCAAAA-CAATGGGTAG
* * ** * * *
384712 ACAAGGGGTAAAGAAGTTTCCCATGACAAAATCGATGGGCAG
1 ACAAAGGGTAAAGAAGTTTCTCGGGTCAAAA-CAATGGGTAG
384754 ACAAAGGGTAAAGAAGTTTCTCGGGTCAAAACTAATGGGTAG
1 ACAAAGGGTAAAGAAGTTTCTCGGGTCAAAAC-AATGGGTAG
*
384796 AC-AAGGGTGAAGAAGT
1 ACAAAGGGTAAAGAAGT
384812 CTCCTAGGTC
Statistics
Matches: 79, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
41 14 0.18
42 65 0.82
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.18
Consensus pattern (41 bp):
ACAAAGGGTAAAGAAGTTTCTCGGGTCAAAACAATGGGTAG
Found at i:384822 original size:41 final size:42
Alignment explanation
Indices: 384673--384866 Score: 130
Period size: 42 Copynumber: 4.7 Consensus size: 42
384663 CGAGCAAACA
* * * **
384673 AAGGGTTAAGAAGTCT-CTCGGGTCAAAACCAACAGGTAGAC
1 AAGGGTAAAGAAGTCTCCTCAGGTCAAAACTAATGGGTAGAC
* * * * *
384714 AAGGGGTAAAGAAGTTTCC-CATGACAAAA-TCGATGGGCAGAC
1 AA-GGGTAAAGAAGTCTCCTCAGGTCAAAACT-AATGGGTAGAC
* *
384756 AAAGGGTAAAGAAGT-TTCTCGGGTCAAAACTAATGGGTAGAC
1 -AAGGGTAAAGAAGTCTCCTCAGGTCAAAACTAATGGGTAGAC
* * * * *
384798 AAGGGTGAAGAAGTCTCCT-AGGTCAAAGCCAACGGGTAGATA
1 AAGGGTAAAGAAGTCTCCTCAGGTCAAAACTAATGGGTAGA-C
* * *
384840 AATGGAAAAGAAGTCTCC-CAAGTCAAA
1 AAGGGTAAAGAAGTCTCCTCAGGTCAAA
384867 GCCAATGAGC
Statistics
Matches: 117, Mismatches: 27, Indels: 17
0.73 0.17 0.11
Matches are distributed among these distances:
41 34 0.29
42 79 0.68
43 4 0.03
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (42 bp):
AAGGGTAAAGAAGTCTCCTCAGGTCAAAACTAATGGGTAGAC
Found at i:386448 original size:15 final size:14
Alignment explanation
Indices: 386426--386463 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
386416 GTTTTCATCC
386426 ATTTTTTTATTATT
1 ATTTTTTTATTATT
*
386440 TTATTTTTTATTATT
1 AT-TTTTTTATTATT
386455 ATTTTTTTA
1 ATTTTTTTA
386464 CTTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTTTTTATTATT
Found at i:391115 original size:19 final size:19
Alignment explanation
Indices: 391072--391142 Score: 106
Period size: 19 Copynumber: 3.6 Consensus size: 19
391062 TTCAATAATT
**
391072 TGTATCGATACATTTAGTAAA
1 TGTATCGATACA-AAAGT-AA
391093 TGTATCGATACAAAAGTAA
1 TGTATCGATACAAAAGTAA
391112 TGTATCGATACAAAAGTAA
1 TGTATCGATACAAAAGTAA
391131 TGTATCGATACA
1 TGTATCGATACA
391143 GTGTATCGCT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 33 0.69
20 3 0.06
21 12 0.25
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:393664 original size:51 final size:50
Alignment explanation
Indices: 393587--393715 Score: 177
Period size: 51 Copynumber: 2.5 Consensus size: 50
393577 TAAATTTCTA
* * *
393587 GATTTTTCATCTCGAGGATACTCCAACTCTGATTTTATTTCTAAAACACT
1 GATTTTTCATATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACT
* *
393637 TATTTTTCATAATCGGGGATACGCCAACTCCGATTTTATTTCTAAAACACT
1 GATTTTTCAT-ATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACT
* *
393688 GACTTTTCACCATCGGGGATACTCCAAC
1 GATTTTTCA-TATCGGGGATACTCCAAC
393716 CCCGTTATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 9 0.13
51 59 0.87
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (50 bp):
GATTTTTCATATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACT
Found at i:393783 original size:79 final size:78
Alignment explanation
Indices: 393651--393902 Score: 264
Period size: 79 Copynumber: 3.2 Consensus size: 78
393641 TTTCATAATC
* * *
393651 GGGGATACGCCAACTCC-GATTTTATTT-CTAAAACA-CTGACTTTTCACCATCGGGGATACTCC
1 GGGGATACTCCAAC-CCAG-TTTTATTTCCT-AAACATC-GATTTTTCACAATCGGGGATACTCC
393713 AACCCCGTTATTTCTGA
62 AACCCCGTTATTTCTGA
** * * * *
393730 GGGGATACTCCAACCCCTTCTTTATTT-CTAAAACATC-ATTTTTTTATAGTCGGGGATCCTCCA
1 GGGGATACTCCAACCCAGT-TTTATTTCCT-AAACATCGA-TTTTTCACAATCGGGGATACTCCA
393793 ACCCCGTTATTTCTGA
63 ACCCCGTTATTTCTGA
* * *
393809 GGGGATACTCCAATCCCAGTTTTATTTCCTAATCATCGATTTTTCACAACCGGGGATACTCCAAT
1 GGGGATACTCCAA-CCCAGTTTTATTTCCTAAACATCGATTTTTCACAATCGGGGATACTCCAAC
*
393874 CCCGTTATTT-TCAA
65 CCCGTTATTTCT-GA
393888 GGGGATACTCCAACC
1 GGGGATACTCCAACC
393903 TCGTTATTAT
Statistics
Matches: 147, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
78 7 0.05
79 132 0.90
80 8 0.05
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCAGTTTTATTTCCTAAACATCGATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTCTGA
Found at i:400178 original size:61 final size:60
Alignment explanation
Indices: 400078--400631 Score: 634
Period size: 60 Copynumber: 9.3 Consensus size: 60
400068 TAGCCCTTCC
* *
400078 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
** * **
400139 AGTTTTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCA-CTGTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCT-TT
* * *
400200 AGTCCTCAAAGAGCAGGACACTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTCT
1 AGTCCTCAAAGAGCAGGACGC-CTTTTTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
400262 AGTCCTCAAAGAGCATGACG-CTTTTTCTTTTTAAAGCTCACACGAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* *
400322 AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
400382 AGTCCTCAAAAAGCAGGACGCC-TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTT
* * *
400443 TGTCCTCAAAGAGCAAGACG-C-----CTTTTAAAGCCCACACAAGTTGGTAGCACCTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTT
* ** * * *
400498 AGTCCTCAAAGAGCAGGACACCTTTTTCCCTTTTAAATACCACTCTAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTT--CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T
* * *
400561 AGTCCTCAAAGAGTAGGATG-C-----CTTTTAAAGCCCACACAAGTTGGTGGCACCTTAC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T
400616 AGTCCTCAAAGAGCAG
1 AGTCCTCAAAGAGCAG
400632 TTCTTTTTGT
Statistics
Matches: 428, Mismatches: 49, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
55 89 0.21
56 6 0.01
59 8 0.02
60 132 0.31
61 96 0.22
62 49 0.11
63 48 0.11
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:400585 original size:63 final size:63
Alignment explanation
Indices: 400463--400631 Score: 174
Period size: 55 Copynumber: 2.8 Consensus size: 63
400453 GAGCAAGACG
* **
400463 CCTTTTAAAGCCCACACAAGTTGGTAGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTC
1 CCTTTTAAAGACCACACAAGTTGGTAGCACCTTCCAGTCCTCAAAGAGCAGGACACCTTTTTC
* * * * * *
400526 CCTTTTAAATACCACTCTAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGG--A------TG
1 CCTTTTAAAGACCACACAAGTTGGTAGCACCTTCCAGTCCTCAAAGAGCAGGACACCTTTTTC
* * *
400581 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTACAGTCCTCAAAGAGCAG
1 CCTTTTAAAGACCACACAAGTTGGTAGCACCTTCCAGTCCTCAAAGAGCAG
400632 TTCTTTTTGT
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
55 46 0.51
61 1 0.01
63 44 0.48
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (63 bp):
CCTTTTAAAGACCACACAAGTTGGTAGCACCTTCCAGTCCTCAAAGAGCAGGACACCTTTTTC
Found at i:400585 original size:118 final size:113
Alignment explanation
Indices: 400230--400631 Score: 475
Period size: 118 Copynumber: 3.4 Consensus size: 113
400220 CTTTTTTTCT
* * * *
400230 TTTTAAAGCCCACACAAGTTGGTGGCACCTCTAGTCCTCAAAGAGCATGACGCTTTTTCTTTTTA
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACCCTTTTTCCTTTTA
* * *
400295 AAGCTCACACGAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACACCTTTTCC
66 AAAC-CACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGG--A----TGCC
*
400350 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAAAGCAGGACGCC-TTTT-CTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGAC-CCTTTTTCCTTTT
* * * *
400413 CAAAGCCCACACAAGTTGGTGGCACCTTTTTGTCCTCAAAGAGCAAGACGCC
65 -AAA-ACCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAGAGCAGGATGCC
*
400465 TTTTAAAGCCCACACAAGTTGGTAGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCCCTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAGAGCAGGAC-CCTTTTT-CCTT
* * * *
400530 TTAAATACCACTCTAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATGCC
63 TTAAA-ACCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGATGCC
*
400583 TTTTAAAGCCCACACAAGTTGGTGGCACCTTACAGTCCTCAAAGAGCAG
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAG
400632 TTCTTTTTGT
Statistics
Matches: 247, Mismatches: 25, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
115 30 0.12
116 23 0.09
117 8 0.03
118 83 0.34
119 10 0.04
120 73 0.30
121 20 0.08
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (113 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACCCTTTTTCCTTTTA
AAACCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCC
Found at i:400922 original size:57 final size:57
Alignment explanation
Indices: 400828--400942 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
400818 AGATGAATGG
* * * * *
400828 GGTTGGAGTATCCCCGACAATAATAATTTGGAGAAAATAAGACTTGAATTTCGATGA
1 GGTTAGAGTATCCCCAACAATAATAATTTAGACAAAATAAGACTTAAATTTCGATGA
* *
400885 GGTTAGAGTATCCCCAACAATGATAATTTAGACAAAATAAGACTTAAATTTTGATGA
1 GGTTAGAGTATCCCCAACAATAATAATTTAGACAAAATAAGACTTAAATTTCGATGA
400942 G
1 G
400943 TTTAAAAACG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (57 bp):
GGTTAGAGTATCCCCAACAATAATAATTTAGACAAAATAAGACTTAAATTTCGATGA
Found at i:401092 original size:97 final size:96
Alignment explanation
Indices: 400893--401092 Score: 231
Period size: 97 Copynumber: 2.1 Consensus size: 96
400883 GAGGTTAGAG
* *
400893 TATCCCCAACAATGATAATTTAGACAAAATAAGACTTAAATTTTGATGAGTTTAAAAACGAGGCT
1 TATCCCCAACAATGACAATTTAGACAAAATAAGACTTAAATTTTGATAAGTTTAAAAACGAGGCT
* * *
400958 AGAGTATCTCCTCGAAAGACTGGGGTTGGAG
66 AGAGTATCCCCTCGAAAGAATGGGGTTGGAC
* ** * * *
400989 TGTCCCCAATGATGACAATTTA-ACCGAAAATAAGATTTAAATTTTGATAAGTTTAAAAGCGGGG
1 TATCCCCAACAATGACAATTTAGA-C-AAAATAAGACTTAAATTTTGATAAGTTTAAAAACGAGG
* * * * *
401053 TTGGAGTATCCCCTCGGAGGAATGGGGTTGGTC
64 CTAGAGTATCCCCTCGAAAGAATGGGGTTGGAC
401086 TATCCCC
1 TATCCCC
401093 GATAAACAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
95 1 0.01
96 19 0.22
97 65 0.76
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (96 bp):
TATCCCCAACAATGACAATTTAGACAAAATAAGACTTAAATTTTGATAAGTTTAAAAACGAGGCT
AGAGTATCCCCTCGAAAGAATGGGGTTGGAC
Found at i:403359 original size:69 final size:69
Alignment explanation
Indices: 403248--403464 Score: 362
Period size: 69 Copynumber: 3.1 Consensus size: 69
403238 CTTTGAGGGG
403248 ATACTCCAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCTAAATTATCATTGTC
1 ATACTCCAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCTAAATTATCATTGTC
403313 GGGA
66 GGGA
403317 ATACTCCAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCTAAATTATCATTGTC
1 ATACTCCAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCTAAATTATCATTGTC
403382 GGGA
66 GGGA
* * * * ** *
403386 ATACTCCAACCCCGTTTTTAAAGTCATCAAAATTTAAGTCTTGTTTTGTCTAAATTATTGTTGTT
1 ATACTCCAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCTAAATTATCATTGTC
*
403451 GGGG
66 GGGA
403455 ATACTCCAAC
1 ATACTCCAAC
403465 TCTATTCCTC
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 140 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (69 bp):
ATACTCCAACCCCGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCTAAATTATCATTGTC
GGGA
Found at i:407378 original size:52 final size:52
Alignment explanation
Indices: 407308--407448 Score: 239
Period size: 52 Copynumber: 2.7 Consensus size: 52
407298 GAAAATTTAT
407308 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
407360 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
407412 CTGCATGTATCGATACA-TTGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
407449 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
51 4 0.05
52 80 0.95
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:407455 original size:13 final size:13
Alignment explanation
Indices: 407437--407461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
407427 CATTGATCAG
407437 TGTATCGATACAA
1 TGTATCGATACAA
407450 TGTATCGATACA
1 TGTATCGATACA
407462 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:407544 original size:13 final size:13
Alignment explanation
Indices: 407526--407550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
407516 CAAAAAAATA
407526 TGTATCGATACAT
1 TGTATCGATACAT
407539 TGTATCGATACA
1 TGTATCGATACA
407551 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:407546 original size:33 final size:33
Alignment explanation
Indices: 407504--407570 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
407494 AGTAGCTTAA
407504 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
407537 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
407570 A
1 A
407571 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:408549 original size:171 final size:171
Alignment explanation
Indices: 408359--408753 Score: 682
Period size: 171 Copynumber: 2.3 Consensus size: 171
408349 TTTTAGAGAT
*
408359 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
408424 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTGAAGATGAGAAAAAAGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGA
408489 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* * * *
408530 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAGA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
408595 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGA
408660 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
408701 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
408754 GTGCCAATGT
Statistics
Matches: 211, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
171 167 0.79
172 4 0.02
174 40 0.19
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:408754 original size:22 final size:22
Alignment explanation
Indices: 408729--408797 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
408719 ATGCTGATTC
408729 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * * *
408751 AAGGTGCCA-ATGTGTT-GA-TTC
1 AA-G-GCCAGCTATATTGGACTTA
*
408772 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
408794 AAGG
1 AAGG
408798 TGAAGGTGCC
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.18
22 10 0.30
23 5 0.15
24 4 0.12
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:408807 original size:49 final size:49
Alignment explanation
Indices: 408667--409478 Score: 1002
Period size: 49 Copynumber: 16.7 Consensus size: 49
408657 GGATGTCAAC
* * *
408667 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-G--AAGGTGCCAAT
* *
408719 ATGCTGATTCAAGGCCAGCTATATTGGACTT--A----AAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
*
408762 GTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * * *
408811 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * * *
408860 ATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * *
408909 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGATGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * *
408958 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * * *
409007 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * * *
409056 ATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * * *
409105 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * * *
409154 ATGTTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * * *
409203 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * *
409252 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * * *
409301 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* * *
409350 ATGCTGATTCAAGGCCAGCGATATTGGACTT--A----AAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* *
409393 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAA-
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
* *
409441 GATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 G-TGCTGATTCAAGGCCAGCTACATTGGACTTA-AAGG
409479 GTTGCCACCG
Statistics
Matches: 647, Mismatches: 99, Indels: 30
0.83 0.13 0.04
Matches are distributed among these distances:
43 75 0.12
45 2 0.00
47 1 0.00
48 1 0.00
49 536 0.83
50 4 0.01
52 28 0.04
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (49 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAAT
Found at i:408902 original size:98 final size:98
Alignment explanation
Indices: 408668--409478 Score: 1295
Period size: 98 Copynumber: 8.4 Consensus size: 98
408658 GATGTCAACG
* * * * * * *
408668 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT-G--AAGGTGCCAATGTGCTGAGTCAAGG
* *
408733 CCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
63 CCAGCTACATTGGACTTAAAGATGATGATGCCAATA
* * *
408763 TGTTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
408828 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
*
408861 TGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
*
408926 GCTACATTGGACTTAAAGGTGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
408959 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
409024 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
*
409057 TGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
409122 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
* * *
409155 TGTTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
409220 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
409253 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
409318 GCTACATTGGACTTAAAGATGATGATGCCAATA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
*
409351 TGCTGATTCAAGGCCAGCGATATTGGACTT--A----AAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
* *
409410 GCTACATTGGACTTAAAGATGAAGATGCCAAGA
66 GCTACATTGGACTTAAAGATGATGATGCCAATA
* *
409443 TGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGG
409479 GTTGCCACCG
Statistics
Matches: 679, Mismatches: 26, Indels: 20
0.94 0.04 0.03
Matches are distributed among these distances:
92 124 0.18
93 2 0.00
94 2 0.00
95 35 0.05
96 1 0.00
97 1 0.00
98 514 0.76
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (98 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCA
GCTACATTGGACTTAAAGATGATGATGCCAATA
Found at i:409517 original size:33 final size:35
Alignment explanation
Indices: 409473--409542 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
409463 TATTGGGCTT
409473 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
409507 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
409541 AG
1 AG
409543 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:409579 original size:34 final size:34
Alignment explanation
Indices: 409547--409683 Score: 159
Period size: 35 Copynumber: 3.9 Consensus size: 34
409537 AGGAAGGGAG
*
409547 AAAGATGCCACGGAGTTATGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTTATGGACTTAAAAGGAAA
* * *
409581 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
1 AAAGA-TGCCACGGAGTTATGGAC-TTAAAAG-GAAA
* * *
409618 AAAGGTGCCACGGAGTTATGGACTCAAAGATGAAA
1 AAAGATGCCACGGAGTTATGGACTTAAA-AGGAAA
*
409653 AAAG-TGCCACGGAGTTATGGGCTTAAAAGGA
1 AAAGATGCCACGGAGTTATGGACTTAAAAGGA
409684 TGCCACGGAG
Statistics
Matches: 86, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
33 3 0.03
34 26 0.30
35 27 0.31
36 24 0.28
37 6 0.07
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (34 bp):
AAAGATGCCACGGAGTTATGGACTTAAAAGGAAA
Found at i:409688 original size:27 final size:27
Alignment explanation
Indices: 409657--409710 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
409647 ATGAAAAAAG
409657 TGCCACGGAGTTATGGGCTTAAAAGGA
1 TGCCACGGAGTTATGGGCTTAAAAGGA
* *
409684 TGCCACGGAGTTGTGGGCTTAGAAGGA
1 TGCCACGGAGTTATGGGCTTAAAAGGA
409711 AAAAGAGTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (27 bp):
TGCCACGGAGTTATGGGCTTAAAAGGA
Found at i:409692 original size:61 final size:60
Alignment explanation
Indices: 409617--409738 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 60
409607 TAAAAGAAAA
*
409617 AAAAGGTGCCACGGAGTTATGGACTCA-AAGATGAAAAA-AGTGCCACGGAGTTATGGGCTT
1 AAAAGGTGCCACGGAGTTATGGACTCAGAAG--GAAAAAGAGTGCCACAGAGTTATGGGCTT
* * * *
409677 AAAAGGATGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGG-TGCCACGGAGTTATGGACTCAGAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT
409738 A
1 A
409739 GGAGGAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 12 0.22
61 39 0.72
62 3 0.06
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.20
Consensus pattern (60 bp):
AAAAGGTGCCACGGAGTTATGGACTCAGAAGGAAAAAGAGTGCCACAGAGTTATGGGCTT
Found at i:409700 original size:97 final size:98
Alignment explanation
Indices: 409579--409906 Score: 314
Period size: 97 Copynumber: 3.3 Consensus size: 98
409569 CTTAAAAGGG
*
409579 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAAAGGTGCCACGGAGTTATGGACTCA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAAA-GTGCCACAGAGTTATGGACT-A
* *
409644 AAGATGAAAAA-AGTGCCACGGAGTTATGGGC-TT
64 AAGAGGAAAAAGAGTGCCACAGAGTTATGGGCTTT
* * * * * * * *
409677 AAAAGGA-TGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAAAGTGCCACAGAGTTATGGACTAAA
*
409740 GAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
66 GAGGAAAAAGAGTGCCACAGAGTTATGGGCTTT
* * * * *
409773 AAAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAG--AAGAAGGTGCCACAGAGTTGTGGGCTTT
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAAAGTGCCACAGAGTTATGGAC--T
* *
409836 GAAA-A-GAAGAAG-GTGCCACAGAGTTGTGGGCTTT
63 -AAAGAGGAAAAAGAGTGCCACAGAGTTATGGGCTTT
*
409870 GAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTAAA
1 --AAA-AAG-A-GTGCCACGGAGTTGTGGGCTTTAAA
409907 GAGTGCCACG
Statistics
Matches: 194, Mismatches: 23, Indels: 23
0.81 0.10 0.10
Matches are distributed among these distances:
94 9 0.05
95 35 0.18
96 20 0.10
97 79 0.41
98 14 0.07
99 9 0.05
100 4 0.02
101 4 0.02
102 20 0.10
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (98 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAAAGTGCCACAGAGTTATGGACTAAA
GAGGAAAAAGAGTGCCACAGAGTTATGGGCTTT
Found at i:409722 original size:34 final size:33
Alignment explanation
Indices: 409547--410215 Score: 417
Period size: 34 Copynumber: 20.9 Consensus size: 33
409537 AGGAAGGGAG
* *
409547 AAAGA-TGCCACGGAGTTATGGACTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAA--GAA
409581 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAG-AA
* * * *
409616 AAAAAGGTGCCACGGAGTTATGGACTCAAAGATGAA
1 AAAGA-GTGCCACGGAGTTGTGGGCTTAAA-A-GAA
*
409652 AAA-AGTGCCACGGAGTTATGGGCTTAAAAG--
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
*
409682 ---GA-TGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTA-AAAGAA
* * *
409712 AAAGAGTGCCACAGAGTTGTGGGCTTAGGAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTA-AAAGAA
* *
409746 AAAGAGTGCCACAGAGTTGTGGGCTT----TAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
*
409775 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGAA
* *
409810 GAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGAA
* *
409844 GAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGAA
* * *
409878 GAAG-GTGCCACAGAGTTGTGGGCTT------T
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
* *
409904 AAAGAGTGCCACGGAATCGTGGGCTTTGAAAAGAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT--AAA-AGAA
409941 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAA-AGAA
*
409976 AAAG-GTGCCACGGAGTTGTGGGCTT---TG--
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
* *
410003 -AAGAGTGCCACGGAGTCGTGGGCTT---TG--
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
*
410030 -AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT--AAA-AGAA
410066 AAAGAGTGCCACGGAGTTGTGGGCTT-AAAG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
** *
410097 TGAG-GTGCCACGGAATTGTGGGCTGTAAAAG--
1 AAAGAGTGCCACGGAGTTGTGGGCT-TAAAAGAA
*
410128 ---G-GTGCCACGGAGTTGTGGACTT-AAAG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
** * *
410155 TGAG-GTGCCACGGAATTGTGGGCTTTAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
* * *
410187 AAA-A-TGCCACTGAGTCGTGGACGTTAAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAA
410216 AGGTATTTGA
Statistics
Matches: 537, Mismatches: 46, Indels: 106
0.78 0.07 0.15
Matches are distributed among these distances:
26 10 0.02
27 82 0.15
28 27 0.05
29 25 0.05
30 41 0.08
31 22 0.04
32 14 0.03
33 9 0.02
34 185 0.34
35 43 0.08
36 31 0.06
37 48 0.09
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (33 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAA
Found at i:409981 original size:98 final size:97
Alignment explanation
Indices: 409743--410120 Score: 376
Period size: 98 Copynumber: 3.9 Consensus size: 97
409733 GGCTTAGGAG
* *
409743 GAAAAAGAGTGCCACAGAGTTGTGGGCTTT---AA-AAAGA-GTGCCACGGAGTCGTGGGCTTTG
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-
* * *
409803 AAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAA
65 ---A-AAG-AGGTGCCACGGAATCGTGGGCTTTGAAAA
* * *
409841 GAAGAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTA
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
409905 AAGA-GTGCCACGGAATCGTGGGCTTTGAAAAGA
66 AAGAGGTGCCACGGAATCGTGGGCTTTG-AAA-A
*
409938 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTT
* *
410002 GAAGA-GTGCCACGGAGTCGTGGGCTTT-----
65 AAAGAGGTGCCACGGAATCGTGGGCTTTGAAAA
* *
410029 G---AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCT
1 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTG-AAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCT
* *
410091 TAAAGATGAGGTGCCACGGAATTGTGGGCT
63 TTAA-A-GAGGTGCCACGGAATCGTGGGCT
410121 GTAAAAGGGT
Statistics
Matches: 245, Mismatches: 20, Indels: 34
0.82 0.07 0.11
Matches are distributed among these distances:
88 25 0.10
90 11 0.04
91 23 0.09
92 1 0.00
93 2 0.01
94 18 0.07
95 20 0.08
96 4 0.02
97 35 0.14
98 81 0.33
100 2 0.01
101 3 0.01
102 20 0.08
ACGTcount: A:0.30, C:0.14, G:0.36, T:0.21
Consensus pattern (97 bp):
GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
AAGAGGTGCCACGGAATCGTGGGCTTTGAAAA
Found at i:410018 original size:27 final size:27
Alignment explanation
Indices: 409980--410058 Score: 149
Period size: 27 Copynumber: 2.9 Consensus size: 27
409970 ACAGAAAAAG
*
409980 GTGCCACGGAGTTGTGGGCTTTGAAGA
1 GTGCCACGGAGTCGTGGGCTTTGAAGA
410007 GTGCCACGGAGTCGTGGGCTTTGAAGA
1 GTGCCACGGAGTCGTGGGCTTTGAAGA
410034 GTGCCACGGAGTCGTGGGCTTTGAA
1 GTGCCACGGAGTCGTGGGCTTTGAA
410059 AAGAGAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.18, C:0.18, G:0.41, T:0.24
Consensus pattern (27 bp):
GTGCCACGGAGTCGTGGGCTTTGAAGA
Found at i:410072 original size:27 final size:27
Alignment explanation
Indices: 410015--410072 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
410005 GAGTGCCACG
* * ** **
410015 GAGTCGTGGGCTTTGAAGAGTGCCACG
1 GAGTCGTGGGCTTTGAAAAGAGAAAAA
410042 GAGTCGTGGGCTTTGAAAAGAGAAAAA
1 GAGTCGTGGGCTTTGAAAAGAGAAAAA
410069 GAGT
1 GAGT
410073 GCCACGGAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.38, T:0.21
Consensus pattern (27 bp):
GAGTCGTGGGCTTTGAAAAGAGAAAAA
Found at i:410107 original size:30 final size:30
Alignment explanation
Indices: 410071--410185 Score: 164
Period size: 30 Copynumber: 3.9 Consensus size: 30
410061 GAGAAAAAGA
*
410071 GTGCCACGGAGTTGTGGGCTTAAAGATGAG
1 GTGCCACGGAATTGTGGGCTTAAAGATGAG
410101 GTGCCACGGAATTGTGGGCTGTAAA-A-G-G
1 GTGCCACGGAATTGTGGGCT-TAAAGATGAG
* *
410129 GTGCCACGGAGTTGTGGACTTAAAGATGAG
1 GTGCCACGGAATTGTGGGCTTAAAGATGAG
410159 GTGCCACGGAATTGTGGGCTTTAAAGA
1 GTGCCACGGAATTGTGGGC-TTAAAGA
410186 AAAAATGCCA
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.05
28 20 0.27
29 2 0.03
30 38 0.51
31 11 0.15
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.23
Consensus pattern (30 bp):
GTGCCACGGAATTGTGGGCTTAAAGATGAG
Found at i:410155 original size:58 final size:58
Alignment explanation
Indices: 410065--410183 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
410055 TGAAAAGAGA
*
410065 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAGATGAGGTGCCACGGAATTGTGGGCTGT
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAGATGAGGTGCCACGGAATTGTGGGCTGT
* *
410123 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAGGTGCCACGGAATTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAGATGAGGTGCCACGGAATTGTGGGCTGT
410181 AAA
1 AAA
410184 GAAAAAATGC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.28, C:0.13, G:0.36, T:0.23
Consensus pattern (58 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAGATGAGGTGCCACGGAATTGTGGGCTGT
Found at i:410163 original size:125 final size:125
Alignment explanation
Indices: 409745--410180 Score: 510
Period size: 125 Copynumber: 3.4 Consensus size: 125
409735 CTTAGGAGGA
*
409745 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGGCTTTG-AAA-AG
1 AAAAGAGTGCCACAGAGTTGTGGGC-TTAAAAAGAGTGCCACGGAATCGTGGGCTTTGAAAAGAG
* * *
409808 AAGAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGA
65 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAG-AGGTGCCACGGAGTTGTGGGC--TG-
*
409872 A
125 T
*
409873 AAGAAGAAGGTGCCACAGAGTTGTGGGCTT-TAAAGAGTGCCACGGAATCGTGGGCTTTGAAAAG
1 AA-AAG-A-GTGCCACAGAGTTGTGGGCTTAAAAAGAGTGCCACGGAATCGTGGGCTTTGAAAAG
*
409937 AGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCT-T
63 AGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG-AAGAGGTGCCACGGAGTTGTGGGCTGT
** * * ** *
410001 TGAAGAGTGCCACGGAGTCGTGGGCTT-TGAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAAAGAGTGCCACGGAATCGTGGGCTTTGAAAAGAGA
* *
410065 AAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAGATGAGGTGCCACGGAATTGTGGGCTGT
66 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAGGTGCCACGGAGTTGTGGGCTGT
* * * * *
410123 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAGGTGCCACGGAATTGTGGGCTTT
1 AAAAGAGTGCCACAGAGTTGTGGGCTTAAA-AAGA-GTGCCACGGAATCGTGGGCTTT
410181 AAAGAAAAAA
Statistics
Matches: 270, Mismatches: 26, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
121 22 0.08
122 25 0.09
123 2 0.01
124 5 0.02
125 99 0.37
126 1 0.00
127 3 0.01
128 2 0.01
129 30 0.11
130 7 0.03
131 29 0.11
132 43 0.16
133 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (125 bp):
AAAAGAGTGCCACAGAGTTGTGGGCTTAAAAAGAGTGCCACGGAATCGTGGGCTTTGAAAAGAGA
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAGGTGCCACGGAGTTGTGGGCTGT
Found at i:411172 original size:15 final size:16
Alignment explanation
Indices: 411148--411187 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
411138 TGAAAAGGGG
*
411148 TTTTTCTTTTTTTTC-
1 TTTTTTTTTTTTTTCA
411163 TTTTTTTTTTTTTTCA
1 TTTTTTTTTTTTTTCA
411179 TCTTTTTTT
1 T-TTTTTTT
411188 GTGAAGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTTTTTCA
Found at i:411175 original size:18 final size:18
Alignment explanation
Indices: 411148--411187 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
411138 TGAAAAGGGG
**
411148 TTTTTCTTTTTTTTCTTT
1 TTTTTCTTTTTCATCTTT
*
411166 TTTTTTTTTTTCATCTTT
1 TTTTTCTTTTTCATCTTT
411184 TTTT
1 TTTT
411188 GTGAAGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTCTTTTTCATCTTT
Found at i:418503 original size:52 final size:52
Alignment explanation
Indices: 418433--418573 Score: 239
Period size: 52 Copynumber: 2.7 Consensus size: 52
418423 GAAAATTTAT
418433 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
418485 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
418537 CTGCATGTATCGATACA-TTGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
418574 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
51 4 0.05
52 80 0.95
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:418580 original size:13 final size:13
Alignment explanation
Indices: 418562--418586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
418552 CATTGATCAG
418562 TGTATCGATACAA
1 TGTATCGATACAA
418575 TGTATCGATACA
1 TGTATCGATACA
418587 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:418669 original size:13 final size:13
Alignment explanation
Indices: 418651--418675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
418641 CAAAAAAATA
418651 TGTATCGATACAT
1 TGTATCGATACAT
418664 TGTATCGATACA
1 TGTATCGATACA
418676 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:418671 original size:33 final size:33
Alignment explanation
Indices: 418629--418695 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
418619 AGTAGCTTAA
418629 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
418662 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
418695 A
1 A
418696 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:421537 original size:51 final size:51
Alignment explanation
Indices: 421461--421573 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
421451 CAAAGATAAC
* *
421461 GGGGTTGGAGTATCTCCTATGGTAGAAAATTGGTGTTTTAGAAATAAAACT
1 GGGGTTGGAGTATCTCCCATCGTAGAAAATTGGTGTTTTAGAAATAAAACT
421512 GGGGTTGGAGTATCTCCCATCGTAGAAAATTGGTGTTTTAGAAATAAAACT
1 GGGGTTGGAGTATCTCCCATCGTAGAAAATTGGTGTTTTAGAAATAAAACT
421563 GGGGTTGGAGT
1 GGGGTTGGAGT
421574 GTCCCCTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.09, G:0.30, T:0.32
Consensus pattern (51 bp):
GGGGTTGGAGTATCTCCCATCGTAGAAAATTGGTGTTTTAGAAATAAAACT
Found at i:421649 original size:79 final size:78
Alignment explanation
Indices: 421514--422112 Score: 537
Period size: 79 Copynumber: 7.6 Consensus size: 78
421504 ATAAAACTGG
* * ** *
421514 GGTTGGAGTATCTCCC-ATCGTAGAAAATTGGTGTTTTAGAAATAAAACTGGGGTTGGAGTGTCC
1 GGTTGGAGTATC-CCCGATGGTGGAAAATT-GTGTTTTAGAAATAAAACCAGGGTTGGAGTATCC
*
421578 CCTAAAAAATAACAA
64 CCTAAAAAATAACGA
* ** * * *
421593 GCTTGGAGTATCCCTAATGGTGGAAAATTAGTGTTTTAGAAATAAAACTAGAGTTGGAGTATCCA
1 GGTTGGAGTATCCCCGATGGTGGAAAATT-GTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCC
421658 CTAAAAAATAACGA
65 CTAAAAAATAACGA
* * * * *
421672 GGTTGGAGTATCCCCGATGATGAAAAATTGATGTTGTAGAAATAAAACC-GAAGTTAGAGTATCC
1 GGTTGGAGTATCCCCGATGGTGGAAAATTG-TGTTTTAGAAATAAAACCAG-GGTTGGAGTATCC
* * *
421736 CCTCAAAAATAATGGG
64 CCTAAAAAATAA-CGA
* * ** *
421752 GGTTGGAGTATCCCCGATGGTAGAAAATTGATATTTTAGAAATAAAA-CAGGGATTAAAGTGTCC
1 GGTTGGAGTATCCCCGATGGTGGAAAATTG-TGTTTTAGAAATAAAACCAGGG-TTGGAGTATCC
*
421816 CCTTAAAAATAACG-
64 CCTAAAAAATAACGA
* * *
421830 GAGTTGGAGTAT-CCCGATGGTAGAAAATTGGTGTTTTAGAAATAAAACCAGGGTTGGGGTATTC
1 G-GTTGGAGTATCCCCGATGGTGGAAAATT-GTGTTTTAGAAATAAAACCAGGGTTGGAGTATCC
**
421894 CCTCGAAAATAACCG-
64 CCTAAAAAATAA-CGA
* *** * * * * * **
421909 GGTTGGAGTATCCCCGACGGCATAAAATCGATGTTTTAAAAATAAAACCGGGGTTAGAATATTTC
1 GGTTGGAGTATCCCCGATGGTGGAAAATTG-TGTTTTAGAAATAAAACCAGGGTTGGAGTATCCC
*
421974 CTAAAAAATAACGG
65 CTAAAAAATAACGA
* * * *
421988 GGTTAGAGTATCCCTGATGGTGGAAAATCCGTGTTTTAGAAATAAAGCCAGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATGGTGGAAAAT-TGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCC
*
422053 CTAAAAAATAACCA
65 CTAAAAAATAACGA
* * * ** *
422067 AGTTAGAGTAT-CCCAATGGTGGAAAATCAATATTTTAGAAATAAAA
1 GGTTGGAGTATCCCCGATGGTGGAAAAT-TGTGTTTTAGAAATAAAA
422113 TTGAGTTTAG
Statistics
Matches: 432, Mismatches: 74, Indels: 29
0.81 0.14 0.05
Matches are distributed among these distances:
78 95 0.22
79 271 0.63
80 66 0.15
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (78 bp):
GGTTGGAGTATCCCCGATGGTGGAAAATTGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCCC
TAAAAAATAACGA
Found at i:422843 original size:61 final size:61
Alignment explanation
Indices: 422660--423008 Score: 431
Period size: 59 Copynumber: 5.8 Consensus size: 61
422650 ATCATGAACC
* * * * *
422660 TGTGTGAGCTTTAAAAGGAAAATG--TCTTACTGTTTGAGGACTGAAAGGTGCCACCAACC
1 TGTGTGGGCTTTAAAAGGAAAATGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACT
* * * * *
422719 TATGTGGCCTTTCAAAGGAAAATG--TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACC
1 TGTGTGGGCTTTAAAAGGAAAATGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACT
* * * * * * *
422778 TGTGTAGCCTTCAAAAGTAAAAGGCATCCTGCTCTTTGAGGACTGAAAGCTGCCACTAACT
1 TGTGTGGGCTTTAAAAGGAAAATGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACT
*
422839 TGTGTGGGCTTTAAAAGGAAAATG--TCCTGCTCTTTGAGGACTGAACGGTGCCACCAACT
1 TGTGTGGGCTTTAAAAGGAAAATGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACT
* * *
422898 TCTGTGGGCTTTAAAAGGAAAATGCATCCTACTCTTTGAGGACTGAAATGTGCCACCAACT
1 TGTGTGGGCTTTAAAAGGAAAATGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACT
* * * *
422959 TGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTTTTTAAAGACTGAAAGG
1 TGTGTGGGCTTTAAAAGGAAAATGCATCCTGCTCTTTGAGGACTGAAAGG
423009 ATAAAAGGTT
Statistics
Matches: 251, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
59 126 0.50
61 125 0.50
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (61 bp):
TGTGTGGGCTTTAAAAGGAAAATGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACT
Found at i:422856 original size:120 final size:119
Alignment explanation
Indices: 422687--422980 Score: 417
Period size: 120 Copynumber: 2.4 Consensus size: 119
422677 GAAAATGTCT
* * * * *
422687 TACTGTTTGAGGACTGAAAGGTGCCACCAACCTATGTGGCCTTTCAAAGGAAAATGTCCTACTCT
1 TACTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGTCCTACTCT
* *
422752 TTGAGGACTGAAAGGTGCCACCAACCTGTGTAGCCTTCAAAAGTAAAAGGCATCC
65 TTGAGGACTGAAAGGTGCCACCAACCTCTGTAGCCTTCAAAAGGAAAAGGCATCC
* * *
422807 TGCTCTTTGAGGACTGAAAGCTGCCACTAACTTGTGTGGGCTTTAAAAGGAAAATGTCCTGCTCT
1 TACTCTTTGAGGACTGAAAG-TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGTCCTACTCT
* * * * * *
422872 TTGAGGACTGAACGGTGCCACCAACTTCTGTGGGCTTTAAAAGGAAAATGCATCC
65 TTGAGGACTGAAAGGTGCCACCAACCTCTGTAGCCTTCAAAAGGAAAAGGCATCC
422927 TACTCTTTGAGGACTGAAATGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
1 TACTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
422981 GGCATCCTGC
Statistics
Matches: 154, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
119 1 0.01
120 152 0.99
121 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (119 bp):
TACTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGTCCTACTCTT
TGAGGACTGAAAGGTGCCACCAACCTCTGTAGCCTTCAAAAGGAAAAGGCATCC
Found at i:423956 original size:63 final size:63
Alignment explanation
Indices: 423857--424040 Score: 212
Period size: 63 Copynumber: 2.9 Consensus size: 63
423847 GTCGAACACA
* * * *
423857 TTTGGAGAGGGGAGGGTCGAATGC-TGGGCAAGGACTCGTTGCACACGCTTGGCCTTCTGCATG
1 TTTGGAGGGGGGAGGGACGAATGCTTGGG-AGGGACTCGTTGCACACGCTTGGCCTTCCGCATG
**
423920 TTTGGAGGGGGGAGGGACGAATGCTTAAGAGGGACTCGTTGC-CAACGCTTGGGCC-TCCGCATG
1 TTTGGAGGGGGGAGGGACGAATGCTTGGGAGGGACTCGTTGCAC-ACGCTT-GGCCTTCCGCATG
* * ** *
423983 TTTGGAGGGGGGAGGGACGGATACTTGGGAGGGACTTATTGCACACGCATGGGCCTTC
1 TTTGGAGGGGGGAGGGACGAATGCTTGGGAGGGACTCGTTGCACACGC-TTGGCCTTC
424041 GTATGTGCTA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 91 0.89
64 10 0.10
ACGTcount: A:0.18, C:0.20, G:0.40, T:0.22
Consensus pattern (63 bp):
TTTGGAGGGGGGAGGGACGAATGCTTGGGAGGGACTCGTTGCACACGCTTGGCCTTCCGCATG
Found at i:426331 original size:13 final size:13
Alignment explanation
Indices: 426313--426338 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
426303 AATTTTTTTG
426313 TGTATCGATACAT
1 TGTATCGATACAT
426326 TGTATCGATACAT
1 TGTATCGATACAT
426339 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:427077 original size:21 final size:21
Alignment explanation
Indices: 427036--427079 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
427026 CTCCCCTTTA
* *
427036 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
427057 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
427078 TC
1 TC
427080 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:428901 original size:13 final size:13
Alignment explanation
Indices: 428883--428908 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
428873 ATAATCACCC
428883 TGTATCGATACAA
1 TGTATCGATACAA
428896 TGTATCGATACAA
1 TGTATCGATACAA
428909 AGAAAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:431006 original size:15 final size:15
Alignment explanation
Indices: 430986--431016 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
430976 ATTTCGTTTG
*
430986 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
431001 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
431016 G
1 G
431017 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:432862 original size:21 final size:21
Alignment explanation
Indices: 432833--432877 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
432823 AAGTTTTCAT
*
432833 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
432853 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
432875 TTT
1 TTT
432878 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:435124 original size:13 final size:13
Alignment explanation
Indices: 435106--435131 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
435096 AATTTTTTTG
435106 TGTATCGATACAT
1 TGTATCGATACAT
435119 TGTATCGATACAT
1 TGTATCGATACAT
435132 ACTTGGTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:435215 original size:20 final size:20
Alignment explanation
Indices: 435170--435242 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
435160 CTGCCAAGAA
***
435170 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
435191 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
435211 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
435231 ATGTATCGATAC
1 ATGTATCGATAC
435243 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:435243 original size:20 final size:20
Alignment explanation
Indices: 435190--435245 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
435180 ACATCTTTTT
*
435190 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
435210 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
435229 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
435246 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:446573 original size:79 final size:79
Alignment explanation
Indices: 446442--446890 Score: 359
Period size: 79 Copynumber: 5.7 Consensus size: 79
446432 GAATGTTCTT
* * * ** *
446442 TCAAAGATAACGGGGTTGGAGTATTCC-CGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAA
1 TCAAAAATAACGAGGTTGGAGTA-TCCTCAATGGTAAAAAATCAATGTTTTAGAAATAAAATCAA
*
446506 GGTTGGAGTATCCCC
65 GGTTAGAGTATCCCC
* * * * ***
446521 TCAAAAATAACAAGGTTGGAGTAACCCCAATGGTAAAAAAAT-TATGTTTTAGAAATAAAATTGG
1 TCAAAAATAACGAGGTTGGAGTATCCTCAATGGT-AAAAAATCAATGTTTTAGAAATAAAATCAA
** * *
446585 GGTGGGACTATCTCC
65 GGTTAGAGTATCCCC
* * * *
446600 TCGAAAATAATG-GGATTGGAGTATCCTCAATGTTGAAAAATCAATGTTTTAGAAATAAAA-CTA
1 TCAAAAATAACGAGG-TTGGAGTATCCTCAATGGTAAAAAATCAATGTTTTAGAAATAAAATC-A
* *
446663 AGGTTAAAGTATCACC
64 AGGTTAGAGTATCCCC
* * * * ** * *
446679 TCGAAATTAACGAGGTTGGAGTATCCTCGATGGTAGAAAATCGGTGTTTTAGAAATAAAACCGAG
1 TCAAAAATAACGAGGTTGGAGTATCCTCAATGGTAAAAAATCAATGTTTTAGAAATAAAATCAAG
446744 GTTAGAGTATCCCC
66 GTTAGAGTATCCCC
* * * * * ** * *
446758 TCAAAAGTAACGGGGTTGGAGTATCCTCGATGGTGAAAATTTGATATTTTAGAAACAAAA-CAAG
1 TCAAAAATAACGAGGTTGGAGTATCCTCAATGGTAAAAAATCAATGTTTTAGAAATAAAATCAAG
* *
446822 AGTTAGAGTGTTCCC
66 -GTTAGAGTATCCCC
** * * * * **
446837 TTGAAAATAACGAGGCTAGAGTATCCTCAATGGTAGAAATTCGGTGTTTTAGAA
1 TCAAAAATAACGAGGTTGGAGTATCCTCAATGGTAAAAAATCAATGTTTTAGAA
446891 GTAGAACATC
Statistics
Matches: 296, Mismatches: 66, Indels: 16
0.78 0.17 0.04
Matches are distributed among these distances:
78 13 0.04
79 275 0.93
80 8 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (79 bp):
TCAAAAATAACGAGGTTGGAGTATCCTCAATGGTAAAAAATCAATGTTTTAGAAATAAAATCAAG
GTTAGAGTATCCCC
Found at i:452702 original size:67 final size:69
Alignment explanation
Indices: 452594--452732 Score: 255
Period size: 67 Copynumber: 2.0 Consensus size: 69
452584 CATTCGGCCA
452594 TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTCAGCCCAACATTG-A-TTGAGTGCAATTA
1 TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTCAGCCCAACATTGAATTTGAGTGCAATTA
452657 AAAT
66 AAAT
*
452661 TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTTAGCCCAACATTGAATTTGAGTGCAATTA
1 TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTCAGCCCAACATTGAATTTGAGTGCAATTA
452726 AAAT
66 AAAT
452730 TAT
1 TAT
452733 TATACCACTT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 48 0.70
68 1 0.01
69 20 0.29
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (69 bp):
TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTCAGCCCAACATTGAATTTGAGTGCAATTA
AAAT
Found at i:453129 original size:48 final size:46
Alignment explanation
Indices: 453045--453147 Score: 127
Period size: 48 Copynumber: 2.2 Consensus size: 46
453035 CATTTGCTAA
* ** *
453045 TAGTGTTTTAGGTTGTACCCTTCAGATGTCCTGATAGGAATATCGC
1 TAGTATTTTAGGTTGTACCCCCCAGATGTCCTGATAGGAATACCGC
*
453091 TAGTACTTTTAGGTTGTACTCCCCCAGATGT-CTCGATAGGAATGCCGC
1 TAGTA-TTTTAGGTTGTAC-CCCCCAGATGTCCT-GATAGGAATACCGC
453139 TAGTATTTT
1 TAGTATTTT
453148 CTTAGTGCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
46 4 0.08
47 19 0.39
48 26 0.53
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (46 bp):
TAGTATTTTAGGTTGTACCCCCCAGATGTCCTGATAGGAATACCGC
Found at i:457992 original size:154 final size:156
Alignment explanation
Indices: 457653--458153 Score: 378
Period size: 154 Copynumber: 3.2 Consensus size: 156
457643 AAATACTCAA
* * * * **
457653 TAATCCTAAAGAACATGAAAATATTATAAAAGGATGAACTTATCCTAAACATATACCTACGGTAT
1 TAATCCTAAAGGACATGAAAATATTATAAAAGGATGAACCTATCCTAAACATATATCTTCGACAT
** * * * * ** * * * *
457718 -AAAA-GCGATCCTCCGACTACCTAGGATTTAATTTTAAGGAAAATTACCAAAATGTGCC--T-C
66 AAAAATGC-AT-CGGCAACTACCTAGGACTTAGTTCTAAAAAAAAATACTAAAATGCGCCTTTAA
** * * * ***
457778 GGTACGCTTTTGATGTAAAAGTACCCGG
129 GGTATACCTTTGAAGTGAAAGTACTTAG
* * ** * * * *
457806 TAATCCTAAAAGATACAAAAACATTATAAAAAGGATGAACCTCTCCTAAACATAT-TCCTTTGGC
1 TAATCCTAAAGGACATGAAAATATTAT-AAAAGGATGAACCTATCCTAAACATATAT-CTTCGAC
* * * *
457870 ATAAAAGCA-GCAT-GGTAACTACTTAGGA-TTTGATTCTAAAAAAAAAATACTAAAATGC-TC-
64 ATAAAA--ATGCATCGGCAACTACCTAGGACTTAG-TTCT-AAAAAAAAATACTAAAATGCGCCT
* * *
457930 TTAGGGTATACTTTTGAAGTGAGAGTAC-TAG
125 TTAAGGTATACCTTTGAAGTGAAAGTACTTAG
* * *
457961 TAATCTTAAAGGACATGAAAATATTATAAAAGGATAAACCTATCCTAAGCATATATCTTCGACAT
1 TAATCCTAAAGGACATGAAAATATTATAAAAGGATGAACCTATCCTAAACATATATCTTCGACAT
** * **
458026 AAAAATGGTTCGGCAACTACCTAGGACTTAGTTCTAAAGAAATTTACTAAAATGCGCCTTTAAGG
66 AAAAATGCATCGGCAACTACCTAGGACTTAGTTCTAAAAAAAAATACTAAAATGCGCCTTTAAGG
* *
458091 TATACCTTTGACGTGAAAGTGCTTAG
131 TATACCTTTGAAGTGAAAGTACTTAG
*
458117 TAATCCTAAAGGACATGAAAATATTATAAAATGATGA
1 TAATCCTAAAGGACATGAAAATATTATAAAAGGATGA
458154 CTTTGACCCT
Statistics
Matches: 270, Mismatches: 62, Indels: 29
0.75 0.17 0.08
Matches are distributed among these distances:
152 1 0.00
153 42 0.16
154 98 0.36
155 68 0.25
156 58 0.21
157 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (156 bp):
TAATCCTAAAGGACATGAAAATATTATAAAAGGATGAACCTATCCTAAACATATATCTTCGACAT
AAAAATGCATCGGCAACTACCTAGGACTTAGTTCTAAAAAAAAATACTAAAATGCGCCTTTAAGG
TATACCTTTGAAGTGAAAGTACTTAG
Found at i:458358 original size:17 final size:18
Alignment explanation
Indices: 458340--458373 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
458330 TAAAGGAAAT
458340 TTTAT-TATAT-ATTTTA
1 TTTATATATATAATTTTA
458356 TTTATATATATAATTTTA
1 TTTATATATATAATTTTA
458374 AAAGTGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATATATATAATTTTA
Found at i:459291 original size:27 final size:26
Alignment explanation
Indices: 459240--459291 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
459230 TTCTAACAAG
*
459240 ACATAAATATTATCAAATAATATCAAA
1 ACATAAATATTAT-AAATAAAATCAAA
459267 ACATAAATTATTAT-AATGAAAATCA
1 ACATAAA-TATTATAAAT-AAAATCA
459292 GCACAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 3 0.14
27 13 0.59
28 6 0.27
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (26 bp):
ACATAAATATTATAAATAAAATCAAA
Found at i:461535 original size:28 final size:27
Alignment explanation
Indices: 461523--461575 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
461513 TCCCCTTAGA
461523 AATAACGGGGTTGGAGTATCCCCGATG
1 AATAACGGGGTTGGAGTATCCCCGATG
*
461550 ATTAACGGGGTTGGAGTATCCCCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
461576 TGTGAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTATCCCCGATG
Found at i:464062 original size:33 final size:33
Alignment explanation
Indices: 464024--464090 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
464014 AAAATTTCCA
***
464024 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
464057 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
464090 A
1 A
464091 TTTCCTTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:464063 original size:13 final size:13
Alignment explanation
Indices: 464045--464070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464035 ACAAAGATCC
464045 ATGTATCGATACA
1 ATGTATCGATACA
464058 ATGTATCGATACA
1 ATGTATCGATACA
464071 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:464134 original size:19 final size:18
Alignment explanation
Indices: 464110--464177 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
464100 AAGTAGCTAA
464110 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
464129 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
464144 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
464161 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
464178 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Done.