Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009689.1 Kokia drynarioides strain JFW-HI SEQ_124407, whole genome shotgun sequence
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: 355750
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4516 original size:88 final size:88
Alignment explanation
Indices: 4367--4542 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 88
4357 CATAATGCAT
4367 TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTGCTTAATTTCTCTAGACC
1 TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTGCTTAATTTCTCTAGACC
4432 ATGATTACTTTCAACCATGCAAA
66 ATGATTACTTTCAACCATGCAAA
*
4455 TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTTCTTAATTTCTCTAGACC
1 TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTGCTTAATTTCTCTAGACC
* *
4520 ATGATTAGTTTCAAGCATGCAAA
66 ATGATTACTTTCAACCATGCAAA
4543 CCCCATATAC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (88 bp):
TAGCTAAAAATAATTGCACCAGCTATTTCAAAGATTGCAATAAAGCTGCTTAATTTCTCTAGACC
ATGATTACTTTCAACCATGCAAA
Found at i:5852 original size:15 final size:15
Alignment explanation
Indices: 5834--5867 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5824 ATTGATTTTT
*
5834 TTAATGTTAAAATTG
1 TTAATATTAAAATTG
*
5849 TTAATATTAAAATTT
1 TTAATATTAAAATTG
5864 TTAA
1 TTAA
5868 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTAATATTAAAATTG
Found at i:6714 original size:23 final size:23
Alignment explanation
Indices: 6671--6734 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
6661 TAATGTTCAC
*
6671 GAACATGTTCATTTAAC-TT-AAT
1 GAACATGTTCA-TGAACATTAAAT
*
6693 GGAACATATTCATGAACATTAAAT
1 -GAACATGTTCATGAACATTAAAT
*
6717 GAATATGTTCATGAACAT
1 GAACATGTTCATGAACAT
6735 GTTAACGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.11
23 28 0.80
24 3 0.09
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (23 bp):
GAACATGTTCATGAACATTAAAT
Found at i:6736 original size:12 final size:12
Alignment explanation
Indices: 6688--6756 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
6678 TTCATTTAAC
*
6688 TTAATGGAACATA
1 TTAAT-GAACATG
*
6701 TTCATGAACAT-
1 TTAATGAACATG
* *
6712 TAAATGAATATG
1 TTAATGAACATG
*
6724 TTCATGAACATG
1 TTAATGAACATG
*
6736 TTAACGAACAATG
1 TTAATGAAC-ATG
6749 TTAATGAA
1 TTAATGAA
6757 TAATAAACAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 8 0.18
12 22 0.50
13 14 0.32
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (12 bp):
TTAATGAACATG
Found at i:8401 original size:22 final size:22
Alignment explanation
Indices: 8376--8430 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
8366 CTTCCTTAGA
*
8376 TTATACATATGTAATTTATTAC
1 TTATACATATATAATTTATTAC
* *
8398 TTATATATATATAGTTTATT-C
1 TTATACATATATAATTTATTAC
*
8419 GTTATATATATA
1 -TTATACATATA
8431 GTATGTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (22 bp):
TTATACATATATAATTTATTAC
Found at i:8504 original size:33 final size:34
Alignment explanation
Indices: 8403--8510 Score: 100
Period size: 33 Copynumber: 3.2 Consensus size: 34
8393 ATTACTTATA
8403 TATATATAGTTTATTCGTT-ATATATATAGTATG
1 TATATATAGTTTATTCGTTCATATATATAGTATG
* * * * *
8436 TATATATTCA-TCATATACTTTCCT-TAAATTA-TATG
1 TATATA-T-AGT-TTATTCGTTCATATATA-TAGTATG
8471 TATATATAGTTTATTC-TTCATATATATAGTATG
1 TATATATAGTTTATTCGTTCATATATATAGTATG
8504 TATATAT
1 TATATAT
8511 TCGCCATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
32 6 0.10
33 25 0.43
34 4 0.07
35 20 0.34
36 3 0.05
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (34 bp):
TATATATAGTTTATTCGTTCATATATATAGTATG
Found at i:8576 original size:18 final size:18
Alignment explanation
Indices: 8550--8585 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8540 ATAGTATATA
* *
8550 TATATATATATTATTTTG
1 TATAAATATATTAATTTG
8568 TATAAATATATTAATTTG
1 TATAAATATATTAATTTG
8586 ACTACTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TATAAATATATTAATTTG
Found at i:11698 original size:352 final size:352
Alignment explanation
Indices: 11054--11732 Score: 1234
Period size: 352 Copynumber: 1.9 Consensus size: 352
11044 CTAGGTTTCG
*
11054 TTACTAGGGATATGGGGAGTTGTGAGATATGCTCCTTTGTTAGTAGTGAAATAGTATCAATCAAG
1 TTACTAGGGATATAGGGAGTTGTGAGATATGCTCCTTTGTTAGTAGTGAAATAGTATCAATCAAG
11119 ACAGTTTATCCCAATGACTCAGGGTTTGGCTCAGTGTGAGTTTGTATACAATGAGGATAACAATA
66 ACAGTTTATCCCAATGACTCAGGGTTTGGCTCAGTGTGAGTTTGTATACAATGAGGATAACAATA
11184 AGAAAAGAGTTCGAGAAATATCAAATGTCTGGAATCAAGCCCATAAAATGAAGCCATTTGCAGCA
131 AGAAAAGAGTTCGAGAAATATCAAATGTCTGGAATCAAGCCCATAAAATGAAGCCATTTGCAGCA
*
11249 AATCCTATGAAAACATAAGAGTATGACGATTGGAGGAGTAGGAGAATCAATGATAACATCCCCGT
196 AATCCTATGAAAACATAAGAGTATGACGATTAGAGGAGTAGGAGAATCAATGATAACATCCCCGT
* *
11314 GCCAAATCCCGATAATGTTCACCCAGTTGAGGAGCATTTGTAAGTAGTTCCATCGGAATTAGAGC
261 GCCAAATCCCGATAATGTTCACCCAGTTGAGGAGCATTTGTAAGTAGTCCCATCGAAATTAGAGC
11379 TCGACAAGAGGGATACACCTATTCCGA
326 TCGACAAGAGGGATACACCTATTCCGA
11406 TTACTAGGGATATAGGGAGTTGTGAGATATGCTCCTTTGTTAGTAGTGAAATAGTATCAATCAAG
1 TTACTAGGGATATAGGGAGTTGTGAGATATGCTCCTTTGTTAGTAGTGAAATAGTATCAATCAAG
* *
11471 ACAGTTTATCCCAGTGACTCAGGGTTTGGCTCAGTGTGAGTTTGTATACAA-GGGTGATAACAAT
66 ACAGTTTATCCCAATGACTCAGGGTTTGGCTCAGTGTGAGTTTGTATACAATGAG-GATAACAAT
11535 AAGAAAAGAGTTCGAGAAATATCAAATGTCTGGAATCAAGCCCATAAAATGAAGCCATTTGCAGC
130 AAGAAAAGAGTTCGAGAAATATCAAATGTCTGGAATCAAGCCCATAAAATGAAGCCATTTGCAGC
* * ***
11600 AAATCCTATGAAAACATAAGAGTATGACGATTAGAGGAGTATGAGAGTCAATGATAACATTTTCG
195 AAATCCTATGAAAACATAAGAGTATGACGATTAGAGGAGTAGGAGAATCAATGATAACATCCCCG
*
11665 TGCCAAATCCTGATAATGTTCACCCAGTTGAGGAGCATTTGTAAGTAGTCCCATCGAAATTAGAG
260 TGCCAAATCCCGATAATGTTCACCCAGTTGAGGAGCATTTGTAAGTAGTCCCATCGAAATTAGAG
11730 CTC
325 CTC
11733 ATCAAGCAAG
Statistics
Matches: 314, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
351 2 0.01
352 312 0.99
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (352 bp):
TTACTAGGGATATAGGGAGTTGTGAGATATGCTCCTTTGTTAGTAGTGAAATAGTATCAATCAAG
ACAGTTTATCCCAATGACTCAGGGTTTGGCTCAGTGTGAGTTTGTATACAATGAGGATAACAATA
AGAAAAGAGTTCGAGAAATATCAAATGTCTGGAATCAAGCCCATAAAATGAAGCCATTTGCAGCA
AATCCTATGAAAACATAAGAGTATGACGATTAGAGGAGTAGGAGAATCAATGATAACATCCCCGT
GCCAAATCCCGATAATGTTCACCCAGTTGAGGAGCATTTGTAAGTAGTCCCATCGAAATTAGAGC
TCGACAAGAGGGATACACCTATTCCGA
Found at i:12477 original size:32 final size:32
Alignment explanation
Indices: 12437--12505 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
12427 GCCAAAAGTT
12437 AGCA-TGTCTCCTACAAAGGATTAAGACTTTG
1 AGCATTGTCTCCTACAAAGGATTAAGACTTTG
*
12468 AGCATTGTCTCCTTCAAAGGATTAAGACTTTG
1 AGCATTGTCTCCTACAAAGGATTAAGACTTTG
12500 AGCATT
1 AGCATT
12506 AGGGTAAGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (32 bp):
AGCATTGTCTCCTACAAAGGATTAAGACTTTG
Found at i:20734 original size:50 final size:50
Alignment explanation
Indices: 20658--20781 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 50
20648 ATACCATAAC
* * * ** *
20658 CCTAAAGCTATAAAGGAAC-GAATTGAAGCCGTAATAGTAAATCTCATACA
1 CCTAAAGCTATAGAGGGACAG-ATTGAAACCACAATAGCAAATCTCATACA
* * * *
20708 CCTAAAGCTGTAGAGGGACAGATTGAAACCACAATGGCGAATCTCATTCA
1 CCTAAAGCTATAGAGGGACAGATTGAAACCACAATAGCAAATCTCATACA
*
20758 CCTAAAGCTATAGAGGGGCAGATT
1 CCTAAAGCTATAGAGGGACAGATT
20782 AAAGTCACAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 60 0.98
51 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (50 bp):
CCTAAAGCTATAGAGGGACAGATTGAAACCACAATAGCAAATCTCATACA
Found at i:20791 original size:50 final size:50
Alignment explanation
Indices: 20697--20806 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
20687 CGTAATAGTA
*
20697 AATCTCATACACCTAAAGCTGTAGAGGGACAGATTGAAACCACAATGG-CG
1 AATCTCATACACCTAAAGCTATAGAGGGACAGATTGAAACCACAA-GGACG
* * *
20747 AATCTCATTCACCTAAAGCTATAGAGGGGCAGATT-AAAGTCACAAGGACG
1 AATCTCATACACCTAAAGCTATAGAGGGACAGATTGAAA-CCACAAGGACG
*
20797 AATCTTATAC
1 AATCTCATAC
20807 TCTTGAAGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 5 0.10
50 47 0.90
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (50 bp):
AATCTCATACACCTAAAGCTATAGAGGGACAGATTGAAACCACAAGGACG
Found at i:20988 original size:78 final size:79
Alignment explanation
Indices: 20839--21037 Score: 224
Period size: 78 Copynumber: 2.5 Consensus size: 79
20829 GGTTACAACC
* * *
20839 TCCAATCTTTTACCTTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCTCGACCATGAG
1 TCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGAG
* *
20904 GCAGATTGAAGCAA
66 GCAGATTAAAACAA
* * *
20918 TCCAATCTTTTACCCTAACTAAAGGGCA-ATTGGAGACCAT-CAGATCTTTTACCCCTACCAT-A
1 TCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACCATCCA-ATCTCTTACCCCGACCATGA
20980 GGGCAGATTAAAACAA
65 -GGCAGATTAAAACAA
*
20996 TTCAATCTTTTACCTCTAAAACTATAGAGAGGCAGATTGAAG
1 TCCAATCTTTTACC-CT--AACTA-A-AG-GGCAGATTGAAG
21038 CTACATAAGC
Statistics
Matches: 101, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
77 3 0.03
78 52 0.51
79 28 0.28
81 5 0.05
82 1 0.01
83 2 0.02
84 4 0.04
85 6 0.06
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (79 bp):
TCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGAG
GCAGATTAAAACAA
Found at i:21004 original size:39 final size:40
Alignment explanation
Indices: 20839--21009 Score: 122
Period size: 39 Copynumber: 4.3 Consensus size: 40
20829 GGTTACAACC
* * * * *
20839 TCCAATCTTTTA-CCTTAACTAGAGGGCAGATTGAAGACCA
1 TCCAATCTTTTACCCCT-ACCATAGGGCAGATTGAAAACAA
* * * *
20879 TCCAATCTCTTACCTCGACCAT-GAGGCAGATTG-AAGCAA
1 TCCAATCTTTTACCCCTACCATAG-GGCAGATTGAAAACAA
* * * * *
20918 TCCAATCTTTTA-CCCTAACTAAAGGGCA-ATTGGAGACCA
1 TCCAATCTTTTACCCCT-ACCATAGGGCAGATTGAAAACAA
20957 T-CAGATCTTTTACCCCTACCATAGGGCAGATT-AAAACAA
1 TCCA-ATCTTTTACCCCTACCATAGGGCAGATTGAAAACAA
*
20996 TTCAATCTTTTACC
1 TCCAATCTTTTACC
21010 TCTAAAACTA
Statistics
Matches: 100, Mismatches: 22, Indels: 19
0.71 0.16 0.13
Matches are distributed among these distances:
38 8 0.08
39 58 0.58
40 33 0.33
41 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (40 bp):
TCCAATCTTTTACCCCTACCATAGGGCAGATTGAAAACAA
Found at i:32791 original size:39 final size:39
Alignment explanation
Indices: 32736--32831 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 39
32726 GATGGTAATG
* * * *
32736 AAGGTGGTGAGGGTGAGGATGGTGAGGTTGCTT-GTAGTA
1 AAGGTGGTAAGGGTGAGGATGGTAAGGTTG-TTGGCAATA
* *
32775 TAGGTGGTAAGGGTGAGGGTGGTAAGGTTGTTGGCAATA
1 AAGGTGGTAAGGGTGAGGATGGTAAGGTTGTTGGCAATA
*
32814 AAAGTGGTAAGGGTGAGG
1 AAGGTGGTAAGGGTGAGG
32832 GAGGTGGTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 2 0.04
39 46 0.96
ACGTcount: A:0.24, C:0.02, G:0.48, T:0.26
Consensus pattern (39 bp):
AAGGTGGTAAGGGTGAGGATGGTAAGGTTGTTGGCAATA
Found at i:34635 original size:29 final size:30
Alignment explanation
Indices: 34603--34659 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
34593 TGGTTTAATG
* *
34603 TGTAATTGTATACATG-AATTTTGATTTTA
1 TGTAATTGTAGACATGAAATTTCGATTTTA
*
34632 TGTAATTTTAGACATGAAATTTCGATTT
1 TGTAATTGTAGACATGAAATTTCGATTT
34660 GATTCAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (30 bp):
TGTAATTGTAGACATGAAATTTCGATTTTA
Found at i:35934 original size:17 final size:19
Alignment explanation
Indices: 35898--35936 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
35888 TCACATCAAC
*
35898 AAATGAATTGAAACTTAAA
1 AAATGAATTGAAAATTAAA
35917 AAAT-AATT-AAAATTAAA
1 AAATGAATTGAAAATTAAA
35934 AAA
1 AAA
35937 AACATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 4 0.21
19 4 0.21
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATGAATTGAAAATTAAA
Found at i:43218 original size:30 final size:30
Alignment explanation
Indices: 43143--43219 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 30
43133 ATATTAAAAG
*
43143 TAAAATTACA-TTTTAATCATTTAAAATAA
1 TAAAATTAAATTTTTAATCATTTAAAATAA
*
43172 TAAAA--AAATTGATTTAATC-TCTTAAAATTA
1 TAAAATTAAATT--TTTAATCAT-TTAAAATAA
*
43202 TAAAATTATATTTTTAAT
1 TAAAATTAAATTTTTAAT
43220 ACGATAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
27 2 0.05
28 1 0.03
29 6 0.15
30 26 0.67
32 4 0.10
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (30 bp):
TAAAATTAAATTTTTAATCATTTAAAATAA
Found at i:48384 original size:27 final size:24
Alignment explanation
Indices: 48323--48369 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
48313 TTTGGTGCAG
48323 AATCAGCAGCACTTTCAACAACAC
1 AATCAGCAGCACTTTCAACAACAC
*
48347 AATCAGCAGCATTTTCAACAACA
1 AATCAGCAGCACTTTCAACAACA
48370 ACAACATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.30, G:0.09, T:0.19
Consensus pattern (24 bp):
AATCAGCAGCACTTTCAACAACAC
Found at i:48755 original size:3 final size:3
Alignment explanation
Indices: 48749--48785 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
48739 TGTTATTATT
48749 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
48786 ATAGCTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:57584 original size:22 final size:22
Alignment explanation
Indices: 57556--57600 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
57546 TGCACATAGA
57556 TATGAAAGCCCTTTATGGGTAG
1 TATGAAAGCCCTTTATGGGTAG
57578 TATGAAAGCCCTTTATGGGTAG
1 TATGAAAGCCCTTTATGGGTAG
57600 T
1 T
57601 TTGAGACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (22 bp):
TATGAAAGCCCTTTATGGGTAG
Found at i:57914 original size:28 final size:28
Alignment explanation
Indices: 57872--57926 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
57862 AAAGGGACAA
57872 TCTTGCAAGTAGGAGCCCGTCAAGACTG
1 TCTTGCAAGTAGGAGCCCGTCAAGACTG
* * *
57900 TCTTGTAAGTGGGAGTCCGTCAAGACT
1 TCTTGCAAGTAGGAGCCCGTCAAGACT
57927 AATCTTACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (28 bp):
TCTTGCAAGTAGGAGCCCGTCAAGACTG
Found at i:62973 original size:2 final size:2
Alignment explanation
Indices: 62960--62992 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
62950 CTTCATTGCA
*
62960 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
62993 GATTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:69437 original size:23 final size:23
Alignment explanation
Indices: 69409--69453 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
69399 TAAATTAATT
69409 TTATAATATAAATAAATATTTAG
1 TTATAATATAAATAAATATTTAG
*
69432 TTATAATATAAATAGATATTTA
1 TTATAATATAAATAAATATTTA
69454 CGACTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TTATAATATAAATAAATATTTAG
Found at i:82180 original size:21 final size:22
Alignment explanation
Indices: 82132--82181 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
82122 ATTAATTACC
82132 ATATTATTTAAAAATAGTATTT
1 ATATTATTTAAAAATAGTATTT
82154 AT-TTATTTAAAAA-A-TATTT
1 ATATTATTTAAAAATAGTATTT
82173 AATATTATT
1 -ATATTATT
82182 CGTTTCAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 3 0.12
21 16 0.62
22 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTATTTAAAAATAGTATTT
Found at i:86830 original size:26 final size:25
Alignment explanation
Indices: 86775--86834 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
86765 CATTTGGTTT
*
86775 ATATATATTTGACTTATAAATCTATA
1 ATATATA-TTGACTTATAAATCGATA
*
86801 ATATATATTGAGCTTATATAT-GATA
1 ATATATATTGA-CTTATAAATCGATA
86826 CATAT-TATT
1 -ATATATATT
86835 AATTTTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (25 bp):
ATATATATTGACTTATAAATCGATA
Found at i:89567 original size:12 final size:12
Alignment explanation
Indices: 89546--89595 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
89536 TAACATATCC
89546 ATAT-ACTTTTT
1 ATATAACTTTTT
89557 ATATAACTTTTT
1 ATATAACTTTTT
89569 ATA-AA-TTATTT
1 ATATAACTT-TTT
*
89580 ATTATAACATTTT
1 A-TATAACTTTTT
89593 ATA
1 ATA
89596 ATACATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
10 2 0.06
11 10 0.30
12 14 0.42
13 6 0.18
14 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATAACTTTTT
Found at i:93155 original size:17 final size:18
Alignment explanation
Indices: 93133--93178 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
93123 CTGCTGTTAG
93133 GAAAGCAAA-TATCATTA
1 GAAAGCAAATTATCATTA
93150 GAAAGCAACCAATTATCATTA
1 GAAAGC-A--AATTATCATTA
93171 GAAAGCAA
1 GAAAGCAA
93179 CCAATGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.24
18 2 0.08
20 3 0.12
21 14 0.56
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (18 bp):
GAAAGCAAATTATCATTA
Found at i:93166 original size:21 final size:21
Alignment explanation
Indices: 93142--93183 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
93132 GGAAAGCAAA
93142 TATCATTAGAAAGCAACCAAT
1 TATCATTAGAAAGCAACCAAT
93163 TATCATTAGAAAGCAACCAAT
1 TATCATTAGAAAGCAACCAAT
93184 GGAAAAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (21 bp):
TATCATTAGAAAGCAACCAAT
Found at i:99680 original size:26 final size:24
Alignment explanation
Indices: 99639--99720 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 24
99629 ACCTTAGCGC
99639 GCTCTCCGTTATTTAGCACATATTGT
1 GCTCTCCGTTA-TTAGCACAT-TTGT
* *
99665 GCTCTCCGTTTATTAGCACGTGTAGT
1 GCTCTCCG-TTATTAGCACAT-TTGT
* *
99691 GCTCTTC-AT-TTAGCACATTTGT
1 GCTCTCCGTTATTAGCACATTTGT
99713 GCTCTCCG
1 GCTCTCCG
99721 ATTAGTACCT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
22 9 0.20
23 8 0.17
24 1 0.02
26 25 0.54
27 3 0.07
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (24 bp):
GCTCTCCGTTATTAGCACATTTGT
Found at i:102331 original size:18 final size:16
Alignment explanation
Indices: 102296--102342 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
102286 CAACGTCAGC
* *
102296 AAAAAAATTTAAACTT
1 AAAAAAAATTAAAATT
102312 AAAAACATAATTAAAATT
1 AAAAA-A-AATTAAAATT
102330 AAAAAAAATTAAA
1 AAAAAAAATTAAA
102343 TTTTTTGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 2 0.07
18 13 0.48
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAAAATTAAAATT
Found at i:106918 original size:23 final size:24
Alignment explanation
Indices: 106872--106936 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 24
106862 GACAAAGCTA
106872 AAATTACAA-TTT-CTATCATGTT
1 AAATTACAATTTTACTATCATGTT
*
106894 AAATTACAATTTTACTATTAT-TT
1 AAATTACAATTTTACTATCATGTT
106917 AAATTATTCAATTTTTACTA
1 AAATTA--CAA-TTTTACTA
106937 AACTTTTTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 9 0.24
23 11 0.30
24 6 0.16
25 3 0.08
26 8 0.22
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATTACAATTTTACTATCATGTT
Found at i:113647 original size:17 final size:18
Alignment explanation
Indices: 113620--113653 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
113610 GCTTCAAAGA
113620 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
113638 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
113654 TAATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:116145 original size:10 final size:10
Alignment explanation
Indices: 116132--116235 Score: 61
Period size: 10 Copynumber: 10.5 Consensus size: 10
116122 TTTTTTACGA
116132 TTTTATAAAT
1 TTTTATAAAT
* *
116142 TTTTTTATAT
1 TTTTATAAAT
* *
116152 TTCTATATA-
1 TTTTATAAAT
* *
116161 TTTTACAATTT
1 TTTTATAA-AT
*
116172 TTTTATAAAAA
1 TTTTAT-AAAT
* *
116183 TTTTACAATT
1 TTTTATAAAT
*
116193 TTTTATATAT
1 TTTTATAAAT
*
116203 TTTTA-CAAT
1 TTTTATAAAT
116212 TTTTATAAAT
1 TTTTATAAAT
*
116222 TTTT-TTAAT
1 TTTTATAAAT
116231 TTTTA
1 TTTTA
116236 ATATTTGATT
Statistics
Matches: 68, Mismatches: 21, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
9 20 0.29
10 36 0.53
11 10 0.15
12 2 0.03
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:116178 original size:20 final size:20
Alignment explanation
Indices: 116155--116215 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
116145 TTTATATTTC
116155 TATATATTTTACAATTTTTT
1 TATATATTTTACAATTTTTT
*
116175 TATAAAAATTTTACAA-TTTTT
1 TAT--ATATTTTACAATTTTTT
116196 TATATATTTTTACAATTTTT
1 TATATA-TTTTACAATTTTT
116216 ATAAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 12 0.34
22 10 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATATTTTACAATTTTTT
Found at i:116225 original size:19 final size:19
Alignment explanation
Indices: 116106--116235 Score: 95
Period size: 19 Copynumber: 6.7 Consensus size: 19
116096 AATAACATTC
*
116106 TTTAC-ATTTTGTATAATTT
1 TTTACAATTTT-TATAAATT
*
116125 TTTACGA-TTTTATAAATT
1 TTTACAATTTTTATAAATT
** * *
116143 TTTTTATATTTCTATATA-T
1 TTTACA-ATTTTTATAAATT
*
116162 TTTACAATTTTTTTATAAAAAT
1 TTTACAA--TTTTTAT-AAATT
*
116184 TTTACAATTTTTTATATATT
1 TTTACAA-TTTTTATAAATT
116204 TTTACAATTTTTATAAATT
1 TTTACAATTTTTATAAATT
**
116223 TTTTTAATTTTTA
1 TTTACAATTTTTA
116236 ATATTTGATT
Statistics
Matches: 89, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
18 11 0.12
19 36 0.40
20 24 0.27
21 10 0.11
22 8 0.09
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTACAATTTTTATAAATT
Found at i:116225 original size:20 final size:20
Alignment explanation
Indices: 116106--116235 Score: 87
Period size: 20 Copynumber: 6.7 Consensus size: 20
116096 AATAACATTC
116106 TTTAC-ATTTTGTAT-AATTT
1 TTTACAATTTT-TATAAATTT
*
116125 TTTACGA-TTTTATAAATTTT
1 TTTACAATTTTTATAAA-TTT
* * *
116145 TTTA-TATTTCTAT--ATAT
1 TTTACAATTTTTATAAATTT
**
116162 TTTACAATTTTTTTATAAAAAT
1 TTTACAA--TTTTTATAAATTT
*
116184 TTTACAATTTTT-TATATATT
1 TTTACAATTTTTATAAAT-TT
116204 TTTACAATTTTTATAAATTT
1 TTTACAATTTTTATAAATTT
*
116224 TTT-TAATTTTTA
1 TTTACAATTTTTA
116236 ATATTTGATT
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
17 6 0.07
18 5 0.06
19 22 0.25
20 42 0.47
21 4 0.04
22 10 0.11
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTACAATTTTTATAAATTT
Found at i:130178 original size:26 final size:25
Alignment explanation
Indices: 130130--130178 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
130120 GGATTGATAA
* *
130130 AATTATTTAATTAGGAAATTAATTT
1 AATTATTTAATTAAGAAACTAATTT
*
130155 AATTAATTTAATTAAGTAACTAAT
1 AATT-ATTTAATTAAGAAACTAAT
130179 ATTATTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (25 bp):
AATTATTTAATTAAGAAACTAATTT
Found at i:133002 original size:21 final size:21
Alignment explanation
Indices: 132960--133002 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
132950 TTTAGTAATA
*
132960 TTTTTATCTCAAAAGTATTTT
1 TTTTTATCTCAAAAGTACTTT
*
132981 TTTTTATCTCAAAAGTGCTTT
1 TTTTTATCTCAAAAGTACTTT
133002 T
1 T
133003 AAGAAGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTTATCTCAAAAGTACTTT
Found at i:133062 original size:13 final size:13
Alignment explanation
Indices: 133044--133075 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
133034 AGTTTAACAT
133044 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
133057 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
133070 TGCTTT
1 TGCTTT
133076 GGAAATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.44
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:136848 original size:23 final size:23
Alignment explanation
Indices: 136822--136876 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
136812 AAATTTTCAA
136822 TAAATAAAAAATAATAAA-AATAT
1 TAAATAAAAAATAATAAATAAT-T
** *
136845 TAAATATTAAATATTAAATAATT
1 TAAATAAAAAATAATAAATAATT
136868 TAATATAAA
1 TAA-ATAAA
136877 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATAAAAAATAATAAATAATT
Found at i:136849 original size:7 final size:7
Alignment explanation
Indices: 136839--136880 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
136829 AAAATAATAA
136839 AAATATT
1 AAATATT
136846 AAATATT
1 AAATATT
136853 AAATATT
1 AAATATT
136860 AAATAATT
1 AAAT-ATT
*
136868 TAATA-T
1 AAATATT
136874 AAATATT
1 AAATATT
136881 TTAAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.16
7 20 0.65
8 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATATT
Found at i:136898 original size:23 final size:21
Alignment explanation
Indices: 136830--136898 Score: 57
Period size: 23 Copynumber: 3.1 Consensus size: 21
136820 AATAAATAAA
* *
136830 AAATAATAAAAATATTAAATATT
1 AAATATTAAAAA-ATTAAA-AAT
* * *
136853 AAATATTAAATAATTTAATAT
1 AAATATTAAAAAATTAAAAAT
136874 AAATATTTTAAAAAATTAAAAAT
1 AAATA--TTAAAAAATTAAAAAT
136897 AA
1 AA
136899 TATGGGCAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 6 0.17
22 5 0.14
23 25 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATTAAAAAATTAAAAAT
Found at i:153492 original size:16 final size:15
Alignment explanation
Indices: 153473--153510 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
153463 TTTAATTTAA
153473 TATTTAATATATTTTT
1 TATTTAAT-TATTTTT
153489 TATTT-ATTATTTTT
1 TATTTAATTATTTTT
*
153503 TATATAAT
1 TATTTAAT
153511 CACGTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 4 0.20
16 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTAATTATTTTT
Found at i:153507 original size:23 final size:24
Alignment explanation
Indices: 153449--153500 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
153439 TTTATAAATG
153449 TATTT-ATATTATTTTTTAATTTAA
1 TATTTAATA-TATTTTTTAATTTAA
*
153473 TATTTAATATATTTTTT-ATTTAT
1 TATTTAATATATTTTTTAATTTAA
153496 TATTT
1 TATTT
153501 TTTATATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 13 0.50
25 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTAATATATTTTTTAATTTAA
Found at i:154135 original size:12 final size:12
Alignment explanation
Indices: 154114--154144 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
154104 ATGGCGTCAG
*
154114 GCCCAGGACCAA
1 GCCCAAGACCAA
154126 GCCCAAGACCAA
1 GCCCAAGACCAA
154138 GCCCAAG
1 GCCCAAG
154145 CCCGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.42, G:0.23, T:0.00
Consensus pattern (12 bp):
GCCCAAGACCAA
Found at i:154597 original size:20 final size:21
Alignment explanation
Indices: 154569--154621 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
154559 TTTGGTATCC
*
154569 ATTAGAAATTTTGATATTT-G
1 ATTACAAATTTTGATATTTGG
*
154589 ATTACAAATATTGATATTTGG
1 ATTACAAATTTTGATATTTGG
*
154610 A-TATAAATTTTG
1 ATTACAAATTTTG
154622 GCATCTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (21 bp):
ATTACAAATTTTGATATTTGG
Found at i:154772 original size:17 final size:18
Alignment explanation
Indices: 154731--154767 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
154721 TACTTCTAAT
* *
154731 AAATACTTTTGATACAAA
1 AAATATTTTTGAGACAAA
154749 AAATATTTTTGAGACAAA
1 AAATATTTTTGAGACAAA
154767 A
1 A
154768 GTATTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (18 bp):
AAATATTTTTGAGACAAA
Found at i:155277 original size:32 final size:32
Alignment explanation
Indices: 155228--155299 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
155218 GAGAAACTAC
* * *
155228 GTCAACATCGTTCGTTGATGTGGCAATATC-AT
1 GTCATCATCGTTCGTTGACGTGACAAT-TCTAT
155260 GTCATCATCGATT-GTTGACGTGACAATTCTAT
1 GTCATCATCG-TTCGTTGACGTGACAATTCTAT
155292 GTCATCAT
1 GTCATCAT
155300 TGAAGGCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 2 0.06
32 31 0.89
33 2 0.06
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (32 bp):
GTCATCATCGTTCGTTGACGTGACAATTCTAT
Found at i:155485 original size:26 final size:26
Alignment explanation
Indices: 155452--155513 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
155442 AGATTTATTC
*
155452 TAAAATTATAAAAACATAAAAAATTA
1 TAAAATTATAAAAAAATAAAAAATTA
* *
155478 TAAAATTATAAAAAAATTAAAATTTA
1 TAAAATTATAAAAAAATAAAAAATTA
155504 TAAGAATTAT
1 TAA-AATTAT
155514 TAGAAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
TAAAATTATAAAAAAATAAAAAATTA
Found at i:155504 original size:18 final size:19
Alignment explanation
Indices: 155453--155506 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
155443 GATTTATTCT
**
155453 AAAATTATAAAAACAT-AA
1 AAAATTATAAAATTATAAA
155471 AAAATTATAAAATTATAAA
1 AAAATTATAAAATTATAAA
*
155490 AAAATTA-AAATTTATAA
1 AAAATTATAAAATTATAA
155507 GAATTATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 23 0.72
19 9 0.28
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATTATAAAATTATAAA
Found at i:155670 original size:10 final size:10
Alignment explanation
Indices: 155649--155678 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
155639 CAAAAATAAA
155649 TTAAATATTTT
1 TTAAA-ATTTT
155660 TTAAAATTTT
1 TTAAAATTTT
155670 TTAAAATTT
1 TTAAAATTT
155679 GTTTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTAAAATTTT
Found at i:159262 original size:31 final size:28
Alignment explanation
Indices: 159203--159268 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 28
159193 AAAAGTAGTT
*
159203 TATATAAAAAGAAATGTATAATAGTATA
1 TATATAAAAACAAATGTATAATAGTATA
159231 TATATAAAAACAATATACGTATATATA-TATA
1 TATATAAAAACAA-AT--GTATA-ATAGTATA
159262 TATATAA
1 TATATAA
159269 GGTTTTCGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 12 0.36
29 2 0.06
31 16 0.48
32 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (28 bp):
TATATAAAAACAAATGTATAATAGTATA
Found at i:159691 original size:519 final size:522
Alignment explanation
Indices: 158200--159776 Score: 2559
Period size: 519 Copynumber: 3.0 Consensus size: 522
158190 ATGCCAGAAC
* *
158200 AAGGTTTTCGTAGTAGGGACCCCTAAGTTGGAGACAATCGAGCTTACCTCAATCGCGGAGTTGGT
1 AAGGTTTTCGTAGTAAGGACCCCTAAGTTGGAGACAATCGAGCCTACCTCAATCGCGGAGTTGGT
158265 CGAGATATTCGAATTTAATGGTGTTGGCTAAGAAGTTGAGATCAACAGGACGAGATATTTGAATT
66 CGAGATATTCGAATTTAATGGTGTTGGCTAAGAAGTTGAGATCAACAGGACGAGATATTTGAATT
*
158330 GGATGGGTTGCAAAATAGGTGTTGAATTTTTCGAGAACATCGCTGTCCTCGAAACATTCAAGTAT
131 GGATGGGTTGCAAAATAGGTGTTGAATTTTTCGAGAGCATCGCTGTCCTCGAAACATTCAAGTAT
158395 CGAAGGATGATCTAAGGGATCGAAAGAGGATTCACCTCTAGCGTGTTTAGTGGCTGGACTCTTAC
196 CGAAGGATGATCTAAGGGATCGAAAGAGGATTCACCTCTAGCGTGTTTAGTGGCTGGACTCTTAC
* *
158460 GGGATGTACGGGGAGGCATTTTATCTAAATGAAAAGTTAAACTAAAGGTTAATGAGTCGAGTAAA
261 GGGATGTACGAGGAGGCATTCTATCTAAATGAAAAGTTAAACTAAAGGTTAATGAGTCGAGTAAA
* * *
158525 AATGTATCTATAGAAGCAAACAAGAATACGAACAATTTATATCCCCAATAGCATTAGATGCAATT
326 AATGTATCTGTAGAAGCAAACAAGAATACGAACAATTTATATCTCCAATAGCAGTAGATGCAATT
* *
158590 TTGAAATATGATACGATGATGTTAT-AAAAAAAATATGTCGAAACATATATATATATATATATAT
391 TTGAAATATGATACAATGATGTTATAAAAAAAAATAAGTCGAAAC------A-ATATATATATA-
* *
158654 ATAAGTAGTTTATATAAAAAAGAAATGTATAACAGTGTGTATATAAAAACAATATACGTATATAA
448 A-AAGTAGTTTATAT-AAAAAGAAATGTATAACAGTATATATATAAAAACAATATACG-------
158719 AATAAATAAATATATATATATATATGTA
504 ------T--ATATATATATATATA-GTA
* * *
158747 CAAGGTTTTCGTAGTAAGGACCCCTAAGTTAGAGACAATCGAGCCTACCCCAATCACGGAGTTGG
1 -AAGGTTTTCGTAGTAAGGACCCCTAAGTTGGAGACAATCGAGCCTACCTCAATCGCGGAGTTGG
* * * *
158812 TCGAGATATTCGAATTTAATGATGTTGGCTAAGAAGTTTAGATCAACAGGTCGAGATATGTGAAT
65 TCGAGATATTCGAATTTAATGGTGTTGGCTAAGAAGTTGAGATCAACAGGACGAGATATTTGAAT
*
158877 TGGATAGGTTGCAAAATAGGTGTTGAATTTTTCGAGAGCATCGCTGTCCTCGAAACATTCAAGTA
130 TGGATGGGTTGCAAAATAGGTGTTGAATTTTTCGAGAGCATCGCTGTCCTCGAAACATTCAAGTA
*
158942 TCGAAGGATGATCTAAGGGATCGAAAAAGGATTCACCTCTAGCGTGTTTAGTGGCTGGACTCTTA
195 TCGAAGGATGATCTAAGGGATCGAAAGAGGATTCACCTCTAGCGTGTTTAGTGGCTGGACTCTTA
*
159007 CGGGATGTACGAGGAGGTATTCTATCTAAATGAAAAGTTAAACTAAAGGTTAATGAGTCGAGTAA
260 CGGGATGTACGAGGAGGCATTCTATCTAAATGAAAAGTTAAACTAAAGGTTAATGAGTCGAGTAA
* * * *
159072 AAATGTATCTGTAAAAGCAAACAAGAATACGAACAATTTATATCTCTAATAGCAGTAGATACATT
325 AAATGTATCTGTAGAAGCAAACAAGAATACGAACAATTTATATCTCCAATAGCAGTAGATGCAAT
159137 TTTGAAATATGATACAATGATGTTATAAAAAAAAATAAGTCGAAAC-ATATATATATAAAAGTAG
390 TTTGAAATATGATACAATGATGTTATAAAAAAAAATAAGTCGAAACAATATATATATAAAAGTAG
*
159201 TTTATATAAAAAGAAATGTATAATAGTATATATATAAAAACAATATACGTATATATATATATATA
455 TTTATATAAAAAGAAATGTATAACAGTATATATATAAAAACAATATACGTATATATATATATATA
159266 -T-
520 GTA
* *
159267 AAGGTTTTCGTAGTAAGGACCCCTAAGTTGGAGACAATCGAGCCTACCTCAATTGTGGAGTTGGT
1 AAGGTTTTCGTAGTAAGGACCCCTAAGTTGGAGACAATCGAGCCTACCTCAATCGCGGAGTTGGT
*
159332 CGAGATATTCGAATTTAATGGTATTGGCTAAGAAGTTGAGATCAACAGGACGAGATATTTGAATT
66 CGAGATATTCGAATTTAATGGTGTTGGCTAAGAAGTTGAGATCAACAGGACGAGATATTTGAATT
* *
159397 GGATGGGTTGCAAAATAGGTGTTGAATTTTTCTAGAGCATCGTTGTCCTCGAAACATTCAAGTAT
131 GGATGGGTTGCAAAATAGGTGTTGAATTTTTCGAGAGCATCGCTGTCCTCGAAACATTCAAGTAT
*
159462 CGAAGGATGATCTAAGGGATCGAAAGAGGATTCACCTCTAGCGTGTTTAGTGGCTGGACTCTTAG
196 CGAAGGATGATCTAAGGGATCGAAAGAGGATTCACCTCTAGCGTGTTTAGTGGCTGGACTCTTAC
*
159527 GGGATGTACAAGGAGGCATTCTATCTAAATGAAAAGTTAAACTAAAGGTTAATGAGTCGAGTAAA
261 GGGATGTACGAGGAGGCATTCTATCTAAATGAAAAGTTAAACTAAAGGTTAATGAGTCGAGTAAA
159592 AATGTATCTGTAGAAGCAAACAAGAATACGAACAATTTATATCTCCAATAGCAGTAGATGCAATT
326 AATGTATCTGTAGAAGCAAACAAGAATACGAACAATTTATATCTCCAATAGCAGTAGATGCAATT
159657 TTGAAATATGATACAATGATGTTATAAAAAAAAATAAGTCGAAACATATATATATATAAAAGTAG
391 TTGAAATATGATACAATGATGTTATAAAAAAAAATAAGTCGAAACA-ATATATATATAAAAGTAG
*
159722 TTTATATAAAAAGAAATGTATAACAATATATATATAAAAACAATATACGTATATA
455 TTTATATAAAAAGAAATGTATAACAGTATATATATAAAAACAATATACGTATATA
159777 AAATAAATAT
Statistics
Matches: 976, Mismatches: 50, Indels: 33
0.92 0.05 0.03
Matches are distributed among these distances:
519 414 0.42
521 72 0.07
523 15 0.02
525 1 0.00
538 39 0.04
539 13 0.01
540 1 0.00
541 11 0.01
548 392 0.40
549 18 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (522 bp):
AAGGTTTTCGTAGTAAGGACCCCTAAGTTGGAGACAATCGAGCCTACCTCAATCGCGGAGTTGGT
CGAGATATTCGAATTTAATGGTGTTGGCTAAGAAGTTGAGATCAACAGGACGAGATATTTGAATT
GGATGGGTTGCAAAATAGGTGTTGAATTTTTCGAGAGCATCGCTGTCCTCGAAACATTCAAGTAT
CGAAGGATGATCTAAGGGATCGAAAGAGGATTCACCTCTAGCGTGTTTAGTGGCTGGACTCTTAC
GGGATGTACGAGGAGGCATTCTATCTAAATGAAAAGTTAAACTAAAGGTTAATGAGTCGAGTAAA
AATGTATCTGTAGAAGCAAACAAGAATACGAACAATTTATATCTCCAATAGCAGTAGATGCAATT
TTGAAATATGATACAATGATGTTATAAAAAAAAATAAGTCGAAACAATATATATATAAAAGTAGT
TTATATAAAAAGAAATGTATAACAGTATATATATAAAAACAATATACGTATATATATATATATAG
TA
Found at i:159776 original size:19 final size:17
Alignment explanation
Indices: 159743--159809 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
159733 AGAAATGTAT
159743 AACAATATATATATAAA
1 AACAATATATATATAAA
159760 AACAATATACGTATATAAA
1 AACAATATA--TATATAAA
* *
159779 ATA-AATATATACATATA
1 A-ACAATATATATATAAA
*
159796 TAC-ATATATATATA
1 AACAATATATATATA
159810 TGTATATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
16 11 0.26
17 15 0.36
19 15 0.36
20 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.33
Consensus pattern (17 bp):
AACAATATATATATAAA
Found at i:159776 original size:21 final size:21
Alignment explanation
Indices: 159751--159797 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
159741 ATAACAATAT
*
159751 ATATATAAAA-ACA-ATATAC
1 ATATATAAAATAAATATATAC
*
159770 GTATATAAAATAAATATATAC
1 ATATATAAAATAAATATATAC
159791 ATATATA
1 ATATATA
159798 CATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 12 0.52
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (21 bp):
ATATATAAAATAAATATATAC
Found at i:159788 original size:2 final size:2
Alignment explanation
Indices: 159783--159825 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
159773 TATAAAATAA
* * * *
159783 AT AT AT AC AT AT AT AC AT AT AT AT AT AT GT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159825 A
1 A
159826 AAAATAGATA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:162818 original size:20 final size:21
Alignment explanation
Indices: 162775--162827 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
162765 ATAGCACTAG
*
162775 TGTGATCACAT-TTTATAGGAA
1 TGTGATC-CATATCTATAGGAA
162796 TGTGATCCATATCTATA-GAA
1 TGTGATCCATATCTATAGGAA
162816 TGTGATCCATAT
1 TGTGATCCATAT
162828 AAATTCCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTGATCCATATCTATAGGAA
Found at i:171885 original size:12 final size:12
Alignment explanation
Indices: 171870--171927 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
171860 ATTGCTATTT
171870 TTGTTGTTT-TTG
1 TTGTT-TTTGTTG
*
171882 TTG-TTTTGTTA
1 TTGTTTTTGTTG
*
171893 TTATTTTTGTTG
1 TTGTTTTTGTTG
* *
171905 CTGTTTTGGTTG
1 TTGTTTTTGTTG
171917 TTGTTTTTGTT
1 TTGTTTTTGTT
171928 ATTTGGATGC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 3 0.08
11 5 0.14
12 28 0.78
ACGTcount: A:0.03, C:0.02, G:0.22, T:0.72
Consensus pattern (12 bp):
TTGTTTTTGTTG
Found at i:171894 original size:32 final size:29
Alignment explanation
Indices: 171865--171923 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 29
171855 TTTTTATTGC
171865 TATTTTTGTTG-TTTTTGTTGTTTTGTTAT
1 TATTTTTGTTGCTTTTTGTTGTTTT-TTAT
171894 TATTTTTGTTGCTGTTTTGGTTGTTGTTTT
1 TATTTTTGTTGCT-TTTT-GTTGTT-TTTT
171924 TGTTATTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 11 0.42
30 1 0.04
31 4 0.15
32 8 0.31
33 2 0.08
ACGTcount: A:0.05, C:0.02, G:0.20, T:0.73
Consensus pattern (29 bp):
TATTTTTGTTGCTTTTTGTTGTTTTTTAT
Found at i:171902 original size:17 final size:17
Alignment explanation
Indices: 171868--171931 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
171858 TTATTGCTAT
*
171868 TTTTGTTGTTTTTGTTG
1 TTTTGTTATTTTTGTTG
171885 TTTTGTTATTATTT-TTG
1 TTTTGTTATT-TTTGTTG
* *
171902 TTGCTGTT-TTGGTTGTTG
1 TT-TTGTTATT-TTTGTTG
171920 TTTTTGTTATTT
1 -TTTTGTTATTT
171932 GGATGCTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
17 18 0.50
18 14 0.39
19 4 0.11
ACGTcount: A:0.05, C:0.02, G:0.20, T:0.73
Consensus pattern (17 bp):
TTTTGTTATTTTTGTTG
Found at i:172140 original size:49 final size:47
Alignment explanation
Indices: 172061--172153 Score: 123
Period size: 49 Copynumber: 1.9 Consensus size: 47
172051 TATAAAAAAA
** * *
172061 TTTTAATATATTTTTTATTTATTTATTTTTTAATGTTTATTTTAATAT
1 TTTTAATATATTTAATATTTATATATTTTTTAA-ATTTATTTTAATAT
172109 TTTTGAATATATTTAATATATTATATATTTTTTAAATTTATTTTA
1 TTTT-AATATATTTAATAT-TTATATATTTTTTAAATTTATTTTA
172154 TATAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
48 4 0.10
49 21 0.54
50 14 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (47 bp):
TTTTAATATATTTAATATTTATATATTTTTTAAATTTATTTTAATAT
Found at i:172157 original size:22 final size:22
Alignment explanation
Indices: 172074--172157 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 22
172064 TAATATATTT
* *
172074 TTTA-TTTATTTATTTTTTAATG
1 TTTATTTTATATATTTTTTAA-A
*
172096 TTTATTTTA-ATATTTTTGAATATA
1 TTTATTTTATATATTTTT---TAAA
172120 TTTAATATATTATATATTTTTTAAA
1 TTT-AT-T-TTATATATTTTTTAAA
172145 TTTATTTTATATA
1 TTTATTTTATATA
172158 ATAAAATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
22 18 0.36
23 5 0.10
24 5 0.10
25 10 0.20
26 1 0.02
27 3 0.06
28 8 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATTTTATATATTTTTTAAA
Found at i:186443 original size:4 final size:4
Alignment explanation
Indices: 186420--186460 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
186410 TTAATTGAGA
*
186420 AATT AATTT AGTT AATTT AATT AATT AATT AATT AATT AAT
1 AATT AA-TT AATT AA-TT AATT AATT AATT AATT AATT AAT
186461 ATTTATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 26 0.79
5 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (4 bp):
AATT
Found at i:189705 original size:52 final size:52
Alignment explanation
Indices: 189624--189728 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
189614 AATAGGTAAG
*
189624 CAAAAGAGGATTTCACATGATAATTAGCTTTAAAAGTGGGTGATCTAGTGAA
1 CAAAAGAGGATTTCACATGATAATGAGCTTTAAAAGTGGGTGATCTAGTGAA
*
189676 CAAAAGAGGATTTCACATGATAGTGAGCTTTAAAAGTGGGTGATCTAGTGAA
1 CAAAAGAGGATTTCACATGATAATGAGCTTTAAAAGTGGGTGATCTAGTGAA
189728 C
1 C
189729 TTACCTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (52 bp):
CAAAAGAGGATTTCACATGATAATGAGCTTTAAAAGTGGGTGATCTAGTGAA
Found at i:194968 original size:42 final size:41
Alignment explanation
Indices: 194841--194990 Score: 151
Period size: 41 Copynumber: 3.6 Consensus size: 41
194831 GTAAAAATTT
** * * *
194841 TTCCTTTTTAAACGATCTTATGCT-TTACCGAGTCATAAGTC
1 TTCC-TTTTAAATAATCTCATGCTCTTATCGAGACATAAGTC
* * *
194882 TTCCTTTTCAAACAATCTTATTCTC-TATCGAGACATAAGTC
1 TTCCTTTT-AAATAATCTCATGCTCTTATCGAGACATAAGTC
* *
194923 TTCCTTTTAACATAATCTCATGCTCTTTTCGAGACATGAGTC
1 TTCCTTTTAA-ATAATCTCATGCTCTTATCGAGACATAAGTC
*
194965 TTCCTTTAAATATAATCTCATGCTCT
1 TTCCTTTTAA-ATAATCTCATGCTCT
194991 GTAACACCCA
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
40 6 0.06
41 50 0.53
42 38 0.40
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.41
Consensus pattern (41 bp):
TTCCTTTTAAATAATCTCATGCTCTTATCGAGACATAAGTC
Found at i:202987 original size:123 final size:123
Alignment explanation
Indices: 202820--203188 Score: 621
Period size: 123 Copynumber: 3.0 Consensus size: 123
202810 TCCCCACATA
* *
202820 GAATCCCGCTTCCTCTTATTTGTAGAAAATTTTTCCTTAATGTCACTTGAATCCAAATTCACAAC
1 GAATCCCTCTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAAATTCACAAC
* * *
202885 ATCATCATCACTATGTGTGCATTCCTTACATTCAAGAGAATCCTCCATGATTGCACTT
66 ATCATCATCACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
* *
202943 GAATCCCTCTTCCTCTTATTTGAAGAAAAATTTTCCTTAATGTCACTTGAATCCAATTTCACAAC
1 GAATCCCTCTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAAATTCACAAC
* *
203008 ATCATCATCACTGTGTGTACATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
66 ATCATCATCACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
** *
203066 GAATCCCTCTTCCTCTTATTTGAAGAATTTTTTTCCTTAATGTCACTTGAATCCAACTTCACAAC
1 GAATCCCTCTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAAATTCACAAC
*
203131 ATCATCATCATTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
66 ATCATCATCACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
203189 TTCACCTCAT
Statistics
Matches: 230, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 230 1.00
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (123 bp):
GAATCCCTCTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAAATTCACAAC
ATCATCATCACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
Found at i:206953 original size:139 final size:138
Alignment explanation
Indices: 206681--206995 Score: 495
Period size: 139 Copynumber: 2.3 Consensus size: 138
206671 AGAATATTAA
* * *
206681 TTTTCATATTTTAATCAAAATTAATTAATATAACTGCTTATATTAATAAATTTGGTAAAATATAT
1 TTTT-ATATTTTAATCGAAATTAATTAATATAACTGTTTATATTAATAAATTTGATAAAATATAT
*
206746 ACAATTAATATTTTGTATGAATCAAATCCATATATTAATTATATTCTTTCCAAAAGAATATTAAT
65 ACAATTAATATTTTGTATGAATAAAATCCATATATTAATTATATTCTTTCCAAAAGAATATTAAT
*
206811 TTTCATTTC
130 TTTCATGTC
* *
206820 TTTTATATTTTAATCGGAATTAATTAATATAATTGTTTATATTAATAAATTTGATAAAATATATA
1 TTTTATATTTTAATCGAAATTAATTAATATAACTGTTTATATTAATAAATTTGATAAAATATATA
** *
206885 CAAATTAATATTTTGTATTTATAAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAAT
66 C-AATTAATATTTTGTATGAATAAAATCCATATATTAATTATATTCTTTCCAAAAGAATATTAAT
206950 TTTCATGTC
130 TTTCATGTC
* * *
206959 TTTTGTATTTTTATCGAAATTAATTAGTATAACTGTT
1 TTTTATATTTTAATCGAAATTAATTAATATAACTGTT
206996 AATAGATAAA
Statistics
Matches: 160, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
138 57 0.36
139 103 0.64
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (138 bp):
TTTTATATTTTAATCGAAATTAATTAATATAACTGTTTATATTAATAAATTTGATAAAATATATA
CAATTAATATTTTGTATGAATAAAATCCATATATTAATTATATTCTTTCCAAAAGAATATTAATT
TTCATGTC
Found at i:211360 original size:15 final size:15
Alignment explanation
Indices: 211340--211369 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
211330 ATTAGATATA
211340 CTATTCATTCAACAT
1 CTATTCATTCAACAT
*
211355 CTATTCATTTAACAT
1 CTATTCATTCAACAT
211370 TCCACATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
CTATTCATTCAACAT
Found at i:215747 original size:42 final size:42
Alignment explanation
Indices: 215643--215831 Score: 245
Period size: 42 Copynumber: 4.5 Consensus size: 42
215633 TGATGTATAA
* * * * *
215643 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGGATTTG-TAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT-T
* *
215685 AAATGGAAGACTCATGTCTCGAGATGAGAATCAGATTATGATT
1 AAA-GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
*
215728 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGTTT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
215770 AAAGGAAGACTCATGTCTTGGGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
215812 AAAGGAAGACTTATGACTCG
1 AAAGGAAGACTCATGTCTCG
215832 TTAGAGCATA
Statistics
Matches: 129, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
42 95 0.74
43 33 0.26
44 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
Found at i:222139 original size:24 final size:24
Alignment explanation
Indices: 222094--222140 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
222084 TGCAAAAACT
*
222094 AAAGAAACAAATTAAAATAAAATA
1 AAAGAAACAAATTAAAAGAAAATA
*
222118 AAAGACAA-AAATTAATAGAAAAT
1 AAAGA-AACAAATTAAAAGAAAAT
222141 TTTTTGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.17
Consensus pattern (24 bp):
AAAGAAACAAATTAAAAGAAAATA
Found at i:230326 original size:25 final size:27
Alignment explanation
Indices: 230293--230343 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
230283 TTAGAAAAGG
230293 AAAATGAGAAAA-AGAAAGAA-AAAAAT
1 AAAATGAGAAAAGA-AAAGAAGAAAAAT
230319 AAAA-GAGAAAAGAAAAGAAGAAAAA
1 AAAATGAGAAAAGAAAAGAAGAAAAA
230344 AATGTTTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (27 bp):
AAAATGAGAAAAGAAAAGAAGAAAAAT
Found at i:230329 original size:12 final size:13
Alignment explanation
Indices: 230285--230342 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
230275 TCAGTCACTT
230285 AGAAAAGGAAAATG-
1 AGAAAA-GAAAA-GA
230299 AGAAAA-AGAAAGA
1 AGAAAAGA-AAAGA
* *
230312 AAAAAATAAAAG-
1 AGAAAAGAAAAGA
230324 AGAAAAGAAAAGA
1 AGAAAAGAAAAGA
230337 AGAAAA
1 AGAAAA
230343 AAATGTTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 12 0.32
13 18 0.49
14 7 0.19
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (13 bp):
AGAAAAGAAAAGA
Found at i:230342 original size:20 final size:19
Alignment explanation
Indices: 230285--230343 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
230275 TCAGTCACTT
230285 AGAAAAGGAAAATG-AGAAAA
1 AGAAAA-GAAAA-GAAGAAAA
* *
230305 AG-AAAGAAAAAAATAAAA
1 AGAAAAGAAAAGAAGAAAA
230323 GAGAAAAGAAAAGAAGAAAA
1 -AGAAAAGAAAAGAAGAAAA
230343 A
1 A
230344 AATGTTTGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
18 10 0.31
19 6 0.19
20 16 0.50
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (19 bp):
AGAAAAGAAAAGAAGAAAA
Found at i:234918 original size:23 final size:22
Alignment explanation
Indices: 234887--234930 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
234877 AAAGAAATAA
*
234887 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
234909 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
234931 AAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:236270 original size:41 final size:41
Alignment explanation
Indices: 236215--236375 Score: 193
Period size: 41 Copynumber: 3.9 Consensus size: 41
236205 TTTCTTTTTC
* *
236215 CATATTCTCATTCTCATCTCGAGACATAAGTCTTCCTTATT
1 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
236256 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
1 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
* *
236297 CATAATCTTATTCTCATC-CTGAGTCATGAGTCTTCCATT-TT
1 CATAATCTCATTCTCATCTC-GAGACATGAGTCTTCC-TTATT
* * * * *
236338 ACA-ATTCTCATGCTTAACCCGAGACATGAGTCTTCCTT
1 -CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTT
236376 TTTATACACC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 3 0.03
41 98 0.92
42 5 0.05
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (41 bp):
CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
Found at i:239032 original size:102 final size:102
Alignment explanation
Indices: 238851--239055 Score: 315
Period size: 102 Copynumber: 2.0 Consensus size: 102
238841 AACTCATTCA
238851 ATGAAGCATCACTTTACACCACAAATTCCTTTCCCATCTCAGGCTACATTAAAACTAGAGCCTCT
1 ATGAAGCATCACTTTACACCACAAATTCCTTTCCCATCTCAGGCTACATTAAAACTAGAGCCTCT
*
238916 GTTAGCATTTTCTTCAATTGATCGAAACTCTATTGAC
66 GTTAGCATTTTCTTCAATCGATCGAAACTCTATTGAC
* * * * *
238953 ATGATGCATCA-TTGTACACCACAAATTCCTTTCCCGTCTCAGGCTGA-GTTAAACCTGGAGCCT
1 ATGAAGCATCACTT-TACACCACAAATTCCTTTCCCATCTCAGGCT-ACATTAAAACTAGAGCCT
*
239016 CTGTTAGCATTTTCTTCAATCGATCGAAACTCTGTTGAC
64 CTGTTAGCATTTTCTTCAATCGATCGAAACTCTATTGAC
239055 A
1 A
239056 CTTTTCGGAC
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
101 2 0.02
102 91 0.97
103 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (102 bp):
ATGAAGCATCACTTTACACCACAAATTCCTTTCCCATCTCAGGCTACATTAAAACTAGAGCCTCT
GTTAGCATTTTCTTCAATCGATCGAAACTCTATTGAC
Found at i:242843 original size:41 final size:41
Alignment explanation
Indices: 242770--242986 Score: 208
Period size: 41 Copynumber: 5.2 Consensus size: 41
242760 TCGAGGTATA
* * * *
242770 AGTCTTCCTTTTTCCATATTCTCAATCTCATCTCGAGACATA
1 AGTCTTCCTTATT-CATAATCTCATTCTCATCTCGAGACATG
* *
242812 AGTC-TCTCTTATACATAATCTCATTCTCATCTCGATACATG
1 AGTCTTC-CTTATTCATAATCTCATTCTCATCTCGAGACATG
* * *
242853 AGTCTTCCTTATTCATAATCTCGTTTTCATCCCGAGACATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATG
* * *
242894 AGTCTTCCTTATTCATATTCTCATGCTCAT-TCCGAGTCATG
1 AGTCTTCCTTATTCATAATCTCATTCTCATCT-CGAGACATG
* ** *
242935 AGTCTTCCATT-TTACA-ATTTCTCAAGCTCAACTCGAGACATG
1 AGTCTTCC-TTATT-CATA-ATCTCATTCTCATCTCGAGACATG
242977 AGTCTTCCTT
1 AGTCTTCCTT
242987 TTTATACACC
Statistics
Matches: 148, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
41 106 0.72
42 41 0.28
43 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (41 bp):
AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATG
Found at i:254809 original size:42 final size:42
Alignment explanation
Indices: 254707--254895 Score: 245
Period size: 42 Copynumber: 4.5 Consensus size: 42
254697 TGATGTATAA
* * * * *
254707 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGGATTTG-TAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT-T
* *
254749 AAATGGAAGACTCGTGTCTCGAGATGAGAATGAGATTATGATT
1 AAA-GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
*
254792 AAAGGAAGACCCATGTCTCGAGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
254834 AAAGGAAGACTCATATCTCGGGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
254876 AAAGGAAGACTTATGACTCG
1 AAAGGAAGACTCATGTCTCG
254896 TTAGAGCATA
Statistics
Matches: 129, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
42 95 0.74
43 33 0.26
44 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.25
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
Found at i:255513 original size:66 final size:66
Alignment explanation
Indices: 255434--255577 Score: 218
Period size: 66 Copynumber: 2.2 Consensus size: 66
255424 CTAACTTGGA
* *
255434 TTGTATCGATAGTTGCATCTTAAGTTTC-GATAATTTTGTGCATGTTTGTATCGGTAGTTAGAAT
1 TTGTATCGATAGTTGCATCTTAAGTTTCAG-TAATTCTATGCATGTTTGTATCGGTAGTTAGAAT
255498 AC
65 AC
* * * *
255500 TTGTATCGGTAGTTGCATGTTAAGTTTCAGTAGTTCTATGCATGTTTGTGTCGGTAGTTAGAATA
1 TTGTATCGATAGTTGCATCTTAAGTTTCAGTAATTCTATGCATGTTTGTATCGGTAGTTAGAATA
255565 C
66 C
255566 TTGTATCGATAG
1 TTGTATCGATAG
255578 AAGTTGCAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
66 69 0.99
67 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.43
Consensus pattern (66 bp):
TTGTATCGATAGTTGCATCTTAAGTTTCAGTAATTCTATGCATGTTTGTATCGGTAGTTAGAATA
C
Found at i:256478 original size:12 final size:12
Alignment explanation
Indices: 256450--256501 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
256440 GTTGGGCTTG
*
256450 GCCTT-GCCATT
1 GCCTTAGCCTTT
*
256461 GTCCTTAGGCTTT
1 G-CCTTAGCCTTT
*
256474 GCCTTAGCCTTA
1 GCCTTAGCCTTT
256486 GCCTTAGCCTTT
1 GCCTTAGCCTTT
256498 -CCTT
1 GCCTT
256502 TATCCTTGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 5 0.15
12 24 0.71
13 5 0.15
ACGTcount: A:0.10, C:0.33, G:0.17, T:0.40
Consensus pattern (12 bp):
GCCTTAGCCTTT
Found at i:257588 original size:34 final size:34
Alignment explanation
Indices: 257532--257617 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 34
257522 AATTATATTG
*
257532 TTGTTTTGGTG-TGGTTTTTTTACTGTTTTGATTA
1 TTGTTTTCGTGCT-GTTTTTTTACTGTTTTGATTA
* *
257566 TTGCTTTT-GTGCTGTTTTTTTACTGTTTTGGTTG
1 TTG-TTTTCGTGCTGTTTTTTTACTGTTTTGATTA
*
257600 TTGTTTTCGTGTTGTTTT
1 TTGTTTTCGTGCTGTTTT
257618 GCTGTTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 4 0.09
34 37 0.80
35 5 0.11
ACGTcount: A:0.05, C:0.06, G:0.23, T:0.66
Consensus pattern (34 bp):
TTGTTTTCGTGCTGTTTTTTTACTGTTTTGATTA
Found at i:257604 original size:12 final size:11
Alignment explanation
Indices: 257589--257703 Score: 51
Period size: 11 Copynumber: 10.5 Consensus size: 11
257579 GTTTTTTTAC
257589 TGTTTTGGTTGT
1 TGTTTTGG-TGT
*
257601 TGTTTTCGTGT
1 TGTTTTGGTGT
*
257612 TGTTTTGCTGT
1 TGTTTTGGTGT
*
257623 TATTTT--TGT
1 TGTTTTGGTGT
*
257632 TGCTATTT-TTGT
1 TG-T-TTTGGTGT
**
257644 TGTTTTAATGT
1 TGTTTTGGTGT
* *
257655 TGTTTTGCTAT
1 TGTTTTGGTGT
* *
257666 TATTTTTGCTGT
1 T-GTTTTGGTGT
257678 TGTTTTGGTTGT
1 TGTTTTGG-TGT
*
257690 TATTTT--TGT
1 TGTTTTGGTGT
257699 TGTTT
1 TGTTT
257704 GGATGTTATT
Statistics
Matches: 82, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
9 11 0.13
10 4 0.05
11 38 0.46
12 29 0.35
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (11 bp):
TGTTTTGGTGT
Found at i:257623 original size:11 final size:11
Alignment explanation
Indices: 257598--257684 Score: 56
Period size: 11 Copynumber: 7.9 Consensus size: 11
257588 CTGTTTTGGT
257598 TGTTGTTTT-C
1 TGTTGTTTTGC
257608 GTGTTGTTTTGC
1 -TGTTGTTTTGC
*
257620 TGTTATTTT--
1 TGTTGTTTTGC
*
257629 TGTTGCTATTT-T
1 TGTTG-T-TTTGC
**
257641 TGTTGTTTTAA
1 TGTTGTTTTGC
257652 TGTTGTTTTGC
1 TGTTGTTTTGC
* *
257663 TATTATTTTTGC
1 TGTT-GTTTTGC
257675 TGTTGTTTTG
1 TGTTGTTTTG
257685 GTTGTTATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 38 0.62
12 15 0.25
ACGTcount: A:0.07, C:0.06, G:0.21, T:0.67
Consensus pattern (11 bp):
TGTTGTTTTGC
Found at i:257644 original size:43 final size:43
Alignment explanation
Indices: 257597--257716 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
257587 ACTGTTTTGG
** *
257597 TTGTTGTTTTCGTGTTGTTTTGCTGTTATTTTTGTTGCTATTT
1 TTGTTGTTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTATTT
* * *
257640 TTGTTGTTTTAATGTTGTTTTGCTATTATTTTTGCTGTTGTTT
1 TTGTTGTTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTATTT
* ** * *
257683 TGGTTGTTATTTTTGTTGTTTGGATGTTATTTTT
1 TTGTTGTT-TTAATGTTGTTTTGCTGTTATTTTT
257717 TATGCGTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
43 44 0.69
44 20 0.31
ACGTcount: A:0.07, C:0.04, G:0.21, T:0.68
Consensus pattern (43 bp):
TTGTTGTTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTATTT
Found at i:257710 original size:20 final size:21
Alignment explanation
Indices: 257589--257716 Score: 68
Period size: 23 Copynumber: 5.9 Consensus size: 21
257579 GTTTTTTTAC
* *
257589 TGTTTTGGTTGTTGTTTTCGTGT
1 TGTTTTGGATGTTATTTT--TGT
*
257612 TGTTTT-GCTGTTATTTTTGT
1 TGTTTTGGATGTTATTTTTGT
* *
257632 TGCTATTT--TTGTTGTTTTAATGT
1 TG-T-TTTGGATGTTATTTT--TGT
* *
257655 TGTTTT-GCTATTATTTTTGCTGT
1 TGTTTTGGATGTTA-TTTT--TGT
*
257678 TGTTTTGGTTGTTATTTTTGT
1 TGTTTTGGATGTTATTTTTGT
257699 TG-TTTGGATGTTATTTTT
1 TGTTTTGGATGTTATTTTT
257717 TATGCGTTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
20 20 0.23
21 17 0.20
22 16 0.19
23 28 0.33
24 5 0.06
ACGTcount: A:0.07, C:0.04, G:0.22, T:0.67
Consensus pattern (21 bp):
TGTTTTGGATGTTATTTTTGT
Found at i:257726 original size:43 final size:41
Alignment explanation
Indices: 257580--257726 Score: 114
Period size: 43 Copynumber: 3.3 Consensus size: 41
257570 TTTTGTGCTG
*
257580 TTTTTTTACTGTTTTGGTTGTTGTTTTCGTGTTGTTTTGCTGTTA
1 TTTTTTTGC-GTTTTGGTTGTT-TTTT--TGTTGTTTTGCTGTTA
* * ** *
257625 TTTTTGTTGCTATTTTTGTTGTTTTAATGTTGTTTTGCTATTA
1 TTTTT-TTGC-GTTTTGGTTGTTTTTTTGTTGTTTTGCTGTTA
* * * *
257668 TTTTTGCTGTTGTTTTGGTTGTTATTTTTGTTGTTTGGATGTTA
1 TTTTT-TTG-CGTTTTGGTTGTT-TTTTTGTTGTTTTGCTGTTA
257712 TTTTTTATGCGTTTT
1 TTTTTT-TGCGTTTT
257727 TACTATTGTT
Statistics
Matches: 81, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
43 38 0.47
44 22 0.27
45 7 0.09
46 14 0.17
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.67
Consensus pattern (41 bp):
TTTTTTTGCGTTTTGGTTGTTTTTTTGTTGTTTTGCTGTTA
Found at i:262949 original size:13 final size:13
Alignment explanation
Indices: 262931--262956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
262921 ATATTAAGTT
262931 GGTAACCTTAACA
1 GGTAACCTTAACA
262944 GGTAACCTTAACA
1 GGTAACCTTAACA
262957 CATTAAGGGA
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:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
GGTAACCTTAACA
Found at i:263245 original size:138 final size:138
Alignment explanation
Indices: 263065--263429 Score: 561
Period size: 138 Copynumber: 2.6 Consensus size: 138
263055 TAAAAAAAAG
263065 AATTATATTCTTTCCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
* * *
263130 TATAAATATTTATATTAATAAATTTAGTAAAATATATACAATTAATATTTTGTATTAATCAAATT
66 TATAAATGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGAATTAATCAAATT
263195 CATATATT
131 CATATATT
* * * * *
263203 TATTATATTCTTTCCGAAACAATATTAATTTTTATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
* *
263268 TATATATGTTTATATTAATAAATTCCGTAAAATATATACAATTAATATTTTGAATTAATCAAATT
66 TATAAATGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGAATTAATCAAATT
*
263333 CGTATATT
131 CATATATT
* * * * * *
263341 AATTATAATCTTTCCAAAAGAATATTAATTTTCATGTCTTTTCTATCTTAATCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
263406 TATAACA-GTTTATATTAATAAATT
66 TATAA-ATGTTTATATTAATAAATT
263430 AGGTAAAGAA
Statistics
Matches: 204, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
138 203 1.00
139 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAAAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
TATAAATGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGAATTAATCAAATT
CATATATT
Found at i:263442 original size:77 final size:77
Alignment explanation
Indices: 263357--263513 Score: 206
Period size: 77 Copynumber: 2.0 Consensus size: 77
263347 AATCTTTCCA
* * * * * *
263357 AAAGAATATTAATTTTCATGTCTTTTCTATCTTAATCAAAATTAATTAATATAACAGTTTATATT
1 AAAGAATATTAATGTCCACGTCTTTTATATCTTAACCAAAACTAATTAATATAACAGTTTATATT
263422 AATAAATTAGGT
66 AATAAATTAGGT
* * * **
263434 AAAGAATATTAATGTCCACGTCTTTTATATTTTGACCAAAACTAATTAATATTATTGTTTATATT
1 AAAGAATATTAATGTCCACGTCTTTTATATCTTAACCAAAACTAATTAATATAACAGTTTATATT
*
263499 AATAAATTCGGT
66 AATAAATTAGGT
263511 AAA
1 AAA
263514 ATATATACAA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.43
Consensus pattern (77 bp):
AAAGAATATTAATGTCCACGTCTTTTATATCTTAACCAAAACTAATTAATATAACAGTTTATATT
AATAAATTAGGT
Found at i:263482 original size:215 final size:211
Alignment explanation
Indices: 263238--263647 Score: 624
Period size: 211 Copynumber: 1.9 Consensus size: 211
263228 TAATTTTTAT
* *
263238 GTCTTTTATATTTTGACCGAAATTAATTAATA-TATATGTTTATATTAATAAATTCCGTAAAATA
1 GTCTTTTATATTTTGACCAAAACTAATTAATATTAT-TGTTTATATTAATAAATTCCGTAAAATA
* *
263302 TATACAATTAATATTTTGAATTAATCAAATTCGTATATTAATTATAATCTTTCCAAAAGAATATT
65 TATACAATT-A-A-TTTGAATTAATAAAATTCATATATTAATTAT-ATCTTTCCAAAAGAATATT
* *
263367 AATTTTCATGTCTTTTCTATCTTAATCAAAATTAATTAATATAACAGTTTATATTAATAAATTAG
126 AATTTTCATATCTTTTATATCTTAATCAAAATTAATTAATATAACAGTTTATATTAATAAATTAG
263432 GTAAAGAATATTAATGTCCAC
191 GTAAAGAATATTAATGTCCAC
*
263453 GTCTTTTATATTTTGACCAAAACTAATTAATATTATTGTTTATATTAATAAATTCGGTAAAATAT
1 GTCTTTTATATTTTGACCAAAACTAATTAATATTATTGTTTATATTAATAAATTCCGTAAAATAT
* * *
263518 ATACAATTAATTTGTATTAATAAAATTCATATATTAATTATATTTTTTCAAAAGAATATTAATTT
66 ATACAATTAATTTGAATTAATAAAATTCATATATTAATTATATCTTTCCAAAAGAATATTAATTT
* * * ** *
263583 TCATATCTTTTATATTTTGATCGAAATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAA
131 TCATATCTTTTATATCTTAATCAAAATTAATTAATATAACAGTTTATATTAATAAATTAGGTAAA
263648 ATATATACAA
Statistics
Matches: 178, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 79 0.44
212 28 0.16
213 1 0.01
214 1 0.01
215 66 0.37
216 3 0.02
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (211 bp):
GTCTTTTATATTTTGACCAAAACTAATTAATATTATTGTTTATATTAATAAATTCCGTAAAATAT
ATACAATTAATTTGAATTAATAAAATTCATATATTAATTATATCTTTCCAAAAGAATATTAATTT
TCATATCTTTTATATCTTAATCAAAATTAATTAATATAACAGTTTATATTAATAAATTAGGTAAA
GAATATTAATGTCCAC
Found at i:263728 original size:349 final size:352
Alignment explanation
Indices: 263081--263790 Score: 1025
Period size: 349 Copynumber: 2.0 Consensus size: 352
263071 ATTCTTTCCA
* * * * * *
263081 AAAAAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAATATAAATATTTATATT
1 AAAAAATATTAATGTCCACGTCTTTTATATTTTGACCAAAACTAATTAATATAAATATTTATATT
* * *
263146 AATAAATTTAGTAAAATATATACAATTAATATTTTGTATTAATCAAATTCATATATTTATTATAT
66 AATAAATTCAGTAAAATATATACAATTAATATTTTGTATTAATAAAATTCATATATTAATTATAT
* * *
263211 TCTTTCCGAAACAATATTAATTTTTATGTCTTTTATATTTTGACCGAAATTAATTAATATATATG
131 TCTTTCCAAAACAATATTAATTTTCATATCTTTTATATTTTGACCGAAATTAATTAATATATATG
* **
263276 TTTATATTAATAAATTCCGTAAAATATATACAATTAATATTTTGAATTAATCAAATTCGTATATT
196 TTTATATTAATAAATTCCGTAAAATATATACAATTAATATTTTGAATGAATCAAATTCACATATT
* * * *
263341 AATTATAATCTTTCCAAAAGAATATTAATTTTCATGTCTTTTCTATCTTAATCAAAATTAATTAA
261 AATGATAATCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATCTTAACCAAAATTAATCAA
*
263406 TATAACAGTTTATATTAATAAATTAGGT
326 TATAA-AGTTTATATTAATAAACTAGGT
* * * *
263434 AAAGAATATTAATGTCCACGTCTTTTATATTTTGACCAAAACTAATTAATATTATTGTTTATATT
1 AAAAAATATTAATGTCCACGTCTTTTATATTTTGACCAAAACTAATTAATATAAATATTTATATT
*
263499 AATAAATTCGGTAAAATATATACAATT-A-A-TTTGTATTAATAAAATTCATATATTAATTATAT
66 AATAAATTCAGTAAAATATATACAATTAATATTTTGTATTAATAAAATTCATATATTAATTATAT
* * *
263561 T-TTTTCAAAAGAATATTAATTTTCATATCTTTTATATTTTGATCGAAATTAATTAATATA-ATT
131 TCTTTCCAAAACAATATTAATTTTCATATCTTTTATATTTTGACCGAAATTAATTAATATATA-T
* ** *
263624 GTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTTTATGAATCAAATTTACATAT
195 GTTTATATTAATAAATTCCGTAAAATATATACAATTAATATTTTGAATGAATCAAATTCACATAT
* * * *
263689 TAATGATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATCA
260 TAATGATAATCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATCTTAACCAAAATTAATCA
* *
263754 ATATAATGTTTATATTAATAAACTCGGT
325 ATATAAAGTTTATATTAATAAACTAGGT
263782 AAAAAATAT
1 AAAAAATAT
263791 AAAATTAATA
Statistics
Matches: 317, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
348 28 0.09
349 175 0.55
350 32 0.10
351 1 0.00
352 1 0.00
353 80 0.25
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (352 bp):
AAAAAATATTAATGTCCACGTCTTTTATATTTTGACCAAAACTAATTAATATAAATATTTATATT
AATAAATTCAGTAAAATATATACAATTAATATTTTGTATTAATAAAATTCATATATTAATTATAT
TCTTTCCAAAACAATATTAATTTTCATATCTTTTATATTTTGACCGAAATTAATTAATATATATG
TTTATATTAATAAATTCCGTAAAATATATACAATTAATATTTTGAATGAATCAAATTCACATATT
AATGATAATCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATCTTAACCAAAATTAATCAA
TATAAAGTTTATATTAATAAACTAGGT
Found at i:263757 original size:138 final size:136
Alignment explanation
Indices: 263434--263829 Score: 573
Period size: 137 Copynumber: 2.9 Consensus size: 136
263424 TAAATTAGGT
* * * * * *
263434 AAAGAATATTAATGTCCACGTCTTTTATATTTTGACCAAAACTAATTAATATTATTGTTTATATT
1 AAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTTTATATT
* * *
263499 AATAAATTCGGTAAAATATATACAATT-A-ATTTGTATTAATAAAATTCATATATTAATTATATT
66 AATAAATTCGGTAAAATATATACAATTAATATTTGTATGAATCAAATTCATATATTAATGATATT
*
263562 TTTTCA
131 TTTCCA
* *
263568 AAAGAATATTAATTTTCATATCTTTTATATTTTGATCGAAATTAATTAATATAATTGTTTATATT
1 AAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTTTATATT
* * *
263633 AATAAATTCGGTAAAATATATACAATTAATATTTTTTATGAATCAAATTTACATATTAATGATAT
66 AATAAATTCGGTAAAATATATACAATTAATA-TTTGTATGAATCAAATTCATATATTAATGATAT
263698 TCTTTCCA
130 T-TTTCCA
*
263706 AAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATCAATATAA-TGTTTATATT
1 AAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTTTATATT
* * *
263770 AATAAACTCGGTAAAAAATATAAAATTAATAATTTGTATGAATCAAATTCATATATTAAT
66 AATAAATTCGGTAAAATATATACAATTAAT-ATTTGTATGAATCAAATTCATATATTAAT
263830 TTTATCTATG
Statistics
Matches: 233, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
134 84 0.36
135 1 0.00
136 1 0.00
137 90 0.39
138 57 0.24
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (136 bp):
AAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTTTATATT
AATAAATTCGGTAAAATATATACAATTAATATTTGTATGAATCAAATTCATATATTAATGATATT
TTTCCA
Found at i:269048 original size:21 final size:24
Alignment explanation
Indices: 268998--269054 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 24
268988 TAAGCATGCA
268998 AACTACCGATACTTCTATACATAC
1 AACTACCGATACTTCTATACATAC
**
269022 AACTACCGATAC-TC-ATA-ATTT
1 AACTACCGATACTTCTATACATAC
269043 AACTACCGATAC
1 AACTACCGATAC
269055 AGCTCAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 14 0.45
22 3 0.10
23 2 0.06
24 12 0.39
ACGTcount: A:0.39, C:0.28, G:0.05, T:0.28
Consensus pattern (24 bp):
AACTACCGATACTTCTATACATAC
Found at i:269741 original size:51 final size:51
Alignment explanation
Indices: 269663--269897 Score: 326
Period size: 51 Copynumber: 4.6 Consensus size: 51
269653 AGTATAGAAG
* * * * * * **
269663 TTCATATACTCACGATGACGCTGAGTCATTGGACCTTTAATTCATCATTGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGA
** * *
269714 TTCATTTACTCAAAATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGA
* *
269765 TTCATTTACTCACGATGACACTTAGTCACCGGACCTTTAATCCGTAAAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGA
* *
269816 TTCATTTACTCACGATGACACTTAGTCACCGAACCTTTAATCCATAAAGGA
1 TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGA
269867 TTCATTTACTCACGATGACACTTAGTCATCG
1 TTCATTTACTCACGATGACACTTAGTCATCG
269898 AACTCTTTCG
Statistics
Matches: 165, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 165 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGA
Found at i:273595 original size:51 final size:51
Alignment explanation
Indices: 273512--273652 Score: 149
Period size: 51 Copynumber: 2.7 Consensus size: 51
273502 TGTTCTGTAT
* * * ** *
273512 AGAAGTTCATATACTCACGATTAC-GTTGAGTCATCGGACCTGTAATTTGTCA
1 AGAA-TTCATTTACTCACGATGACACTT-AGTCATCGGACCTGTAATCCGTAA
* * * * * *
273564 TGGATTCATTTACTCATGATGACACTTAGTCACCAGACCTTTAATCCGTAA
1 AGAATTCATTTACTCACGATGACACTTAGTCATCGGACCTGTAATCCGTAA
273615 AGAATTCATTTACTCACGATGACACTTAGTCATCGGAC
1 AGAATTCATTTACTCACGATGACACTTAGTCATCGGAC
273653 AGACTCTTTC
Statistics
Matches: 71, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
51 67 0.94
52 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (51 bp):
AGAATTCATTTACTCACGATGACACTTAGTCATCGGACCTGTAATCCGTAA
Found at i:279804 original size:2 final size:2
Alignment explanation
Indices: 279797--279830 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
279787 CACTGCAATA
279797 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
279831 GAGGCACCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:282906 original size:37 final size:36
Alignment explanation
Indices: 282861--282930 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
282851 TGACGAGTAT
*
282861 AAATTAAAAATATTTAAAAATAAATA-AATTAATAAA
1 AAATTAAAAAAATTT-AAAATAAATATAATTAATAAA
**
282897 AAATATAAAAAAATTTCCAATAAATATAATTAAT
1 AAAT-TAAAAAAATTTAAAATAAATATAATTAAT
282931 TTATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 12 0.41
37 17 0.59
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (36 bp):
AAATTAAAAAAATTTAAAATAAATATAATTAATAAA
Found at i:283663 original size:31 final size:31
Alignment explanation
Indices: 283619--283696 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 31
283609 CAATAATTCT
283619 AAAAAAATT-TAAAAATC-TTAAAATAAATA
1 AAAAAAATTATAAAAATCATTAAAATAAATA
**
283648 AATAAAAATTATAAAAATCATTAAAATTTATA
1 AA-AAAAATTATAAAAATCATTAAAATAAATA
283680 AAAAAAA-TATTAAAAAT
1 AAAAAAATTA-TAAAAAT
283697 TCTAAGAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 2 0.05
30 9 0.21
31 20 0.47
32 12 0.28
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (31 bp):
AAAAAAATTATAAAAATCATTAAAATAAATA
Found at i:284631 original size:34 final size:34
Alignment explanation
Indices: 284588--284656 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
284578 TCATTTCCGA
* *
284588 TACAAAATCGACTAAAAACCTAGTTACATGCCAT
1 TACAAAATCGACTAAAAACCAAATTACATGCCAT
*
284622 TACAAAATCGGCTAAAAACCAAATTACATGCCAT
1 TACAAAATCGACTAAAAACCAAATTACATGCCAT
284656 T
1 T
284657 TATTGAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (34 bp):
TACAAAATCGACTAAAAACCAAATTACATGCCAT
Found at i:285772 original size:22 final size:23
Alignment explanation
Indices: 285745--285796 Score: 97
Period size: 22 Copynumber: 2.3 Consensus size: 23
285735 GTATATGCAT
285745 ATAAATAGTATGATCTTGAATC-
1 ATAAATAGTATGATCTTGAATCA
285767 ATAAATAGTATGATCTTGAATCA
1 ATAAATAGTATGATCTTGAATCA
285790 ATAAATA
1 ATAAATA
285797 AAACAATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (23 bp):
ATAAATAGTATGATCTTGAATCA
Found at i:287444 original size:18 final size:20
Alignment explanation
Indices: 287406--287446 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
287396 AGTAATTGTT
*
287406 ATTTTATATTTAACTATTTA
1 ATTTTATATTTAACGATTTA
287426 ATTTTATATTT-A-GATTTA
1 ATTTTATATTTAACGATTTA
287444 ATT
1 ATT
287447 AATATAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTATATTTAACGATTTA
Found at i:289091 original size:11 final size:11
Alignment explanation
Indices: 289071--289099 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
289061 GAAAAAATTC
289071 AAAG-TAAAGA
1 AAAGTTAAAGA
289081 AAAGTTAAAGA
1 AAAGTTAAAGA
289092 AAAGTTAA
1 AAAGTTAA
289100 TCCTGCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (11 bp):
AAAGTTAAAGA
Found at i:292567 original size:12 final size:12
Alignment explanation
Indices: 292550--292574 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
292540 ATGTGTTTTT
292550 TTGTTGTATTGG
1 TTGTTGTATTGG
292562 TTGTTGTATTGG
1 TTGTTGTATTGG
292574 T
1 T
292575 GTTATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.32, T:0.60
Consensus pattern (12 bp):
TTGTTGTATTGG
Found at i:292580 original size:21 final size:21
Alignment explanation
Indices: 292556--292601 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
292546 TTTTTTGTTG
*
292556 TATTGGTTGTTGTATTGGTGT
1 TATTGGTTGTTATATTGGTGT
** *
292577 TATTTTTTGTTATTTTGGTGT
1 TATTGGTTGTTATATTGGTGT
292598 TATT
1 TATT
292602 TTTACTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.00, G:0.24, T:0.65
Consensus pattern (21 bp):
TATTGGTTGTTATATTGGTGT
Found at i:292600 original size:11 final size:11
Alignment explanation
Indices: 292570--292603 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
292560 GGTTGTTGTA
292570 TTGGTGTTATT
1 TTGGTGTTATT
*
292581 TT-TTGTTATT
1 TTGGTGTTATT
292591 TTGGTGTTATT
1 TTGGTGTTATT
292602 TT
1 TT
292604 TACTATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.09, C:0.00, G:0.21, T:0.71
Consensus pattern (11 bp):
TTGGTGTTATT
Found at i:292610 original size:20 final size:20
Alignment explanation
Indices: 292570--292627 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
292560 GGTTGTTGTA
**
292570 TTGGTGTTATTTTTTGTTATT
1 TTGGTGTTA-TTTTTACTATT
292591 TTGGTGTTATTTTTACTATT
1 TTGGTGTTATTTTTACTATT
* *
292611 TTGGTGCTACTTTTACT
1 TTGGTGTTATTTTTACT
292628 GTTATTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.64
Consensus pattern (20 bp):
TTGGTGTTATTTTTACTATT
Found at i:292648 original size:24 final size:24
Alignment explanation
Indices: 292621--292709 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 24
292611 TTGGTGCTAC
292621 TTTTACTGTTATTTTTGTCGTTGT
1 TTTTACTGTTATTTTTGTCGTTGT
* *
292645 TTTTTCAGTTATTTTTGTCGTTG-
1 TTTTACTGTTATTTTTGTCGTTGT
* *
292668 TTTTGCTGTTATTTTTG-CTGCTGT
1 TTTTACTGTTATTTTTGTC-GTTGT
*
292692 TTTTATTGTTATTTTTGT
1 TTTTACTGTTATTTTTGT
292710 TGTTTGAATG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
22 1 0.02
23 18 0.33
24 36 0.65
ACGTcount: A:0.08, C:0.08, G:0.17, T:0.67
Consensus pattern (24 bp):
TTTTACTGTTATTTTTGTCGTTGT
Found at i:292712 original size:12 final size:12
Alignment explanation
Indices: 292627--292713 Score: 61
Period size: 12 Copynumber: 7.3 Consensus size: 12
292617 CTACTTTTAC
292627 TGTTATTTTTGT
1 TGTTATTTTTGT
* *
292639 CGTTGTTTTT-T
1 TGTTATTTTTGT
*
292650 CAGTTATTTTTGT
1 -TGTTATTTTTGT
* * *
292663 CGTT-GTTTTGC
1 TGTTATTTTTGT
*
292674 TGTTATTTTTGC
1 TGTTATTTTTGT
* * *
292686 TGCTGTTTTTAT
1 TGTTATTTTTGT
292698 TGTTATTTTTGT
1 TGTTATTTTTGT
292710 TGTT
1 TGTT
292714 TGAATGTTAT
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
11 9 0.16
12 46 0.82
13 1 0.02
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:292926 original size:39 final size:38
Alignment explanation
Indices: 292843--292927 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
292833 ATATAAAGAA
* * * * *
292843 TTTTTAATGTATTTTAAATTTGTTTATTTTTTAATGTT
1 TTTTTAATGTATTTTAAATGTATTTATATATTAATATT
292881 TGTTTTAATGT-TTTTAAATGTATTTGATATATTATATATT
1 T-TTTTAATGTATTTTAAATGTATTT-ATATATTA-ATATT
292921 TTTTTAA
1 TTTTTAA
292928 ATTTGTTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
38 13 0.33
39 21 0.54
40 5 0.13
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (38 bp):
TTTTTAATGTATTTTAAATGTATTTATATATTAATATT
Found at i:293533 original size:42 final size:42
Alignment explanation
Indices: 293474--293556 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
293464 TAAAAATCAG
*
293474 CCTCTTTATAATAAATTTTGAATTTGTGGGTATAGATGACAA
1 CCTCTTTATAATAAATTTTGAATTTGTGAGTATAGATGACAA
293516 CCTCTTTATAATAAATTTTGAATTTGTGAGTATAGATGACA
1 CCTCTTTATAATAAATTTTGAATTTGTGAGTATAGATGACA
293557 TGTCATTAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.41
Consensus pattern (42 bp):
CCTCTTTATAATAAATTTTGAATTTGTGAGTATAGATGACAA
Found at i:293846 original size:114 final size:114
Alignment explanation
Indices: 293629--293854 Score: 267
Period size: 114 Copynumber: 2.0 Consensus size: 114
293619 AATATTACTT
* * **
293629 TTTTGAATCGATTGTTTATATGTTTGAATCGACTGTCATGTTGGAATATTATTTCTTTTCAACCA
1 TTTTGAATCGATTGTTTATATGTTTGAATCGACTATCATATTGGAATACCA--TCTTTTCAACCA
* * * *
293694 ATTGTTTATATGTTTAAATTGATTATTATGATGAAATATTGTTTCTTCTTC
64 ATTATTTATATGTTTAAATCGATTATTATGATAAAATATTGCTTCTTCTTC
* * * * * *
293745 TTTTGAATCGATTTTTTTATATGTTTGAATCGATTATTATATTGGAATACCA-CTTTTGAATCGA
1 TTTTGAATCGA-TTGTTTATATGTTTGAATCGACTATCATATTGGAATACCATCTTTTCAACCAA
*
293809 TTATTTATATGTTTAAATCGATTGTTAT-ATTAAAATATTGCTTCTT
65 TTATTTATATGTTTAAATCGATTATTATGA-TAAAATATTGCTTCTT
293855 TTGAATCTAG
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
113 1 0.01
114 48 0.52
116 11 0.12
117 33 0.35
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (114 bp):
TTTTGAATCGATTGTTTATATGTTTGAATCGACTATCATATTGGAATACCATCTTTTCAACCAAT
TATTTATATGTTTAAATCGATTATTATGATAAAATATTGCTTCTTCTTC
Found at i:296598 original size:21 final size:21
Alignment explanation
Indices: 296574--296623 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
296564 CCTATGACAA
* * *
296574 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
296595 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
296616 TTCTACCG
1 TTCTACCG
296624 GTACTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:297381 original size:28 final size:28
Alignment explanation
Indices: 297341--297423 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
297331 GATATCTGAT
297341 TTACTCCCTATTGACCCAAAGGTCATGC
1 TTACTCCCTATTGACCCAAAGGTCATGC
*
297369 TTACTCCCTATTGACCCAAAGGTTATGC
1 TTACTCCCTATTGACCCAAAGGTCATGC
*
297397 TTACTCCCTGTTGACCCAAAGGTCATG
1 TTACTCCCTATTGACCCAAAGGTCATG
297424 ATGCTCATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAGGTCATGC
Found at i:297453 original size:36 final size:36
Alignment explanation
Indices: 297397--297495 Score: 171
Period size: 36 Copynumber: 2.8 Consensus size: 36
297387 AAGGTTATGC
297397 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
* * *
297433 TTACCCCCTGTTGACTCAAAGGTTATGATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
297469 TTACTCCCTGTTGACCCAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
297496 CCTGTTACCA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.33
Consensus pattern (36 bp):
TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
Found at i:312469 original size:15 final size:15
Alignment explanation
Indices: 312449--312494 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
312439 ACTACTTCCT
312449 CCTGGGCAGTATCCA
1 CCTGGGCAGTATCCA
*
312464 CCTGGGCAATATCCA
1 CCTGGGCAGTATCCA
312479 CCTGGGCAGTATCCA
1 CCTGGGCAGTATCCA
312494 C
1 C
312495 AAGGACAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.20
Consensus pattern (15 bp):
CCTGGGCAGTATCCA
Found at i:312640 original size:18 final size:17
Alignment explanation
Indices: 312613--312646 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
312603 CTGGGCATCC
312613 ACTACCTCCTCCAGGTT
1 ACTACCTCCTCCAGGTT
*
312630 ACTATCCTCCTGCAGGT
1 ACTA-CCTCCTCCAGGT
312647 CAAGGTCAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.38, G:0.15, T:0.29
Consensus pattern (17 bp):
ACTACCTCCTCCAGGTT
Found at i:313373 original size:18 final size:19
Alignment explanation
Indices: 313333--313375 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
313323 AAAATTTAAA
**
313333 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTAC
313352 AAAATTCAAAAT-ATTTAC
1 AAAATTCAAAATAATTTAC
313370 AAAATT
1 AAAATT
313376 TTCAGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAC
Found at i:319274 original size:3 final size:3
Alignment explanation
Indices: 319266--319291 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
319256 AAATTGGGCC
319266 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
319292 AAGCTTCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:322744 original size:40 final size:40
Alignment explanation
Indices: 322678--322900 Score: 234
Period size: 40 Copynumber: 5.6 Consensus size: 40
322668 GAACGTTTAT
* *
322678 AACTGGCAGTGACACTATAAACACTGCGATAATATTACTG
1 AACTGGCAGTGACACTGTAAACACTGCGATATTATTACTG
* * * * ** *
322718 AACTGGAAGTGACATTGTAAAAACTGCAATGCTATCACTG
1 AACTGGCAGTGACACTGTAAACACTGCGATATTATTACTG
* *
322758 AACTGGCAGTGACACTGTAAACACTGCGATATTACTACTA
1 AACTGGCAGTGACACTGTAAACACTGCGATATTATTACTG
* * * *
322798 AACTGGC-GATGACACTGTAAATATTGTGATATTACTACTG
1 AACTGGCAG-TGACACTGTAAACACTGCGATATTATTACTG
* * *
322838 AACTGGTAGTGACACTGTAAACACTGCAATATTATTACCG
1 AACTGGCAGTGACACTGTAAACACTGCGATATTATTACTG
* *
322878 AACTAGCCA-TGACACTATAAACA
1 AACT-GGCAGTGACACTGTAAACA
322901 TTGCTAGATT
Statistics
Matches: 149, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 145 0.97
41 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (40 bp):
AACTGGCAGTGACACTGTAAACACTGCGATATTATTACTG
Found at i:322891 original size:120 final size:120
Alignment explanation
Indices: 322678--322900 Score: 279
Period size: 120 Copynumber: 1.9 Consensus size: 120
322668 GAACGTTTAT
* *
322678 AACTGGCAGTGACACTATAAACACTGCGATAATATTACTGAACTGGAAGTGACATTGTAAAAACT
1 AACTGGCAGTGACACTATAAACACTGCGATAATACTACTGAACTGGAAGTGACACTGTAAAAACT
* * * *
322743 GCAATGCTATCACTGAACTGGCAGTGACACTGTAAACACTGCGATATTACTACTA
66 GCAATACTATCACCGAACTGCCAGTGACACTATAAACACTGCGATATTACTACTA
* * * * * * *
322798 AACTGGC-GATGACACTGTAAATATTGTGATATTACTACTGAACTGGTAGTGACACTGTAAACAC
1 AACTGGCAG-TGACACTATAAACACTGCGATAATACTACTGAACTGGAAGTGACACTGTAAAAAC
* *
322862 TGCAATATTATTACCGAACTAGCCA-TGACACTATAAACA
65 TGCAATACTATCACCGAACT-GCCAGTGACACTATAAACA
322901 TTGCTAGATT
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
119 1 0.01
120 82 0.95
121 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (120 bp):
AACTGGCAGTGACACTATAAACACTGCGATAATACTACTGAACTGGAAGTGACACTGTAAAAACT
GCAATACTATCACCGAACTGCCAGTGACACTATAAACACTGCGATATTACTACTA
Done.