Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 15 of 25
Found at i:2085044 original size:10 final size:11
Alignment explanation
Indices: 2085020--2085053 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
2085010 TTGCACTTTC
2085020 TTTTTCATTTATT
1 TTTTTC-TTT-TT
2085033 TTTTTCTTTTT
1 TTTTTCTTTTT
2085044 TTTTTCTTTT
1 TTTTTCTTTT
2085054 CTTATTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 3 0.14
13 6 0.29
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:2085417 original size:18 final size:18
Alignment explanation
Indices: 2085382--2085424 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2085372 AAGCATCTGA
* *
2085382 ATTTTCTTTCTTTTTTCT
1 ATTTTTTTTCTTTCTTCT
*
2085400 ATTTTTTTTGTTTCTTCT
1 ATTTTTTTTCTTTCTTCT
2085418 -TTTTTTT
1 ATTTTTTT
2085425 GGTTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (18 bp):
ATTTTTTTTCTTTCTTCT
Found at i:2086315 original size:13 final size:13
Alignment explanation
Indices: 2086297--2086322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2086287 ACACCAAATT
2086297 ATGTATCGATACA
1 ATGTATCGATACA
2086310 ATGTATCGATACA
1 ATGTATCGATACA
2086323 CAAAAAATTA
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:2086337 original size:33 final size:32
Alignment explanation
Indices: 2086278--2086342 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
2086268 TAGCCAAACT
*
2086278 TGTATCGATACACCAAATTATGTATCGATACAA
1 TGTATCGATACACAAAATTA-GTATCGATACAA
2086311 TGTATCGATACACAAAAAATTA-TATCGATACA
1 TGTATCGATACAC--AAAATTAGTATCGATACA
2086343 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 23 0.79
35 6 0.21
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAATTAGTATCGATACAA
Found at i:2092727 original size:8 final size:9
Alignment explanation
Indices: 2092712--2092736 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2092702 AAGAAGAAAG
2092712 GAAAAAAAA
1 GAAAAAAAA
2092721 GAAAAAAAA
1 GAAAAAAAA
2092730 GAAAAAA
1 GAAAAAA
2092737 CTTATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:2096574 original size:24 final size:25
Alignment explanation
Indices: 2096528--2096578 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
2096518 ATATAATTAA
*
2096528 AAGCATTAAACATAGTTACAAACAC
1 AAGCATTAAACATAATTACAAACAC
* *
2096553 AAGCA-TAAGCATAATTATAAACAC
1 AAGCATTAAACATAATTACAAACAC
2096577 AA
1 AA
2096579 CAGTGGGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.55, C:0.18, G:0.08, T:0.20
Consensus pattern (25 bp):
AAGCATTAAACATAATTACAAACAC
Found at i:2099805 original size:24 final size:24
Alignment explanation
Indices: 2099775--2099823 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2099765 TTTGATTTGA
*
2099775 TTCTGCTTTTGTTTTGATTCTGCT
1 TTCTGCTTTTGGTTTGATTCTGCT
2099799 TTCTGCTTTTGGTTTGATTCTGCT
1 TTCTGCTTTTGGTTTGATTCTGCT
2099823 T
1 T
2099824 CTGGTTGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.16, G:0.18, T:0.61
Consensus pattern (24 bp):
TTCTGCTTTTGGTTTGATTCTGCT
Found at i:2099819 original size:17 final size:17
Alignment explanation
Indices: 2099758--2099800 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2099748 CTATTACAAC
*
2099758 TTCTGCCTTTGATTTGA
1 TTCTGCTTTTGATTTGA
*
2099775 TTCTGCTTTTGTTTTGA
1 TTCTGCTTTTGATTTGA
2099792 TTCTGCTTT
1 TTCTGCTTT
2099801 CTGCTTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.07, C:0.16, G:0.16, T:0.60
Consensus pattern (17 bp):
TTCTGCTTTTGATTTGA
Found at i:2099882 original size:32 final size:31
Alignment explanation
Indices: 2099814--2099899 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 31
2099804 CTTTTGGTTT
*
2099814 GATTCTGCTTCTGGTTGAT-ATTGTTATTGTC
1 GATT-TGCTTCTGGTTGCTGATTGTTATTGTC
2099845 GATTTGCTTCTGGTTGCTGATCTGTT-TCTGTC
1 GATTTGCTTCTGGTTGCTGAT-TGTTAT-TGTC
*
2099877 GATTTGCTTCTTGTTGCTG-TTGT
1 GATTTGCTTCTGGTTGCTGATTGT
2099900 CAATCTGCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
30 16 0.32
31 8 0.16
32 26 0.52
ACGTcount: A:0.08, C:0.15, G:0.24, T:0.52
Consensus pattern (31 bp):
GATTTGCTTCTGGTTGCTGATTGTTATTGTC
Found at i:2099980 original size:57 final size:57
Alignment explanation
Indices: 2099912--2100021 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
2099902 ATCTGCTTCT
* *
2099912 AATTGTTGTTGCCAATTATTG-CATT-TACTATTAGGTTTAGTAGTTTAGTTGCTTTCC
1 AATTATTGTTGCCAATTATTGTCATTGT--TATTAAGTTTAGTAGTTTAGTTGCTTTCC
** *
2099969 AATTATTGTTGCTGATTATTGTCGTTGTTATTAAGTTTAGTAGTTTAGTTGCT
1 AATTATTGTTGCCAATTATTGTCATTGTTATTAAGTTTAGTAGTTTAGTTGCT
2100022 GTTAGTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 42 0.91
58 3 0.07
59 1 0.02
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (57 bp):
AATTATTGTTGCCAATTATTGTCATTGTTATTAAGTTTAGTAGTTTAGTTGCTTTCC
Found at i:2100134 original size:45 final size:45
Alignment explanation
Indices: 2100085--2100170 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
2100075 TTTTAAAATG
*
2100085 GGTTTTAATTGGGTTT-GAGTTTAAGTTTATATATATTTTTAATTA
1 GGTTTTAATTGGGTTTAG-GTTTAAGTTTATATAGATTTTTAATTA
2100130 GGTTTTAATTGGGTTTAGGTTTAAGTTTATATAGATTTTTA
1 GGTTTTAATTGGGTTTAGGTTTAAGTTTATATAGATTTTTA
2100171 GTTTTTGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.55
Consensus pattern (45 bp):
GGTTTTAATTGGGTTTAGGTTTAAGTTTATATAGATTTTTAATTA
Found at i:2102693 original size:11 final size:11
Alignment explanation
Indices: 2102677--2102701 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2102667 TATTTTTTAG
2102677 TTTTTTCATTT
1 TTTTTTCATTT
2102688 TTTTTTCATTT
1 TTTTTTCATTT
2102699 TTT
1 TTT
2102702 CCCTCCCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:2103634 original size:17 final size:18
Alignment explanation
Indices: 2103609--2103644 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2103599 CTTTCTAAAA
2103609 TATAATTTTAAAT-ATTT
1 TATAATTTTAAATAATTT
*
2103626 TATATTTTTAAATAATTT
1 TATAATTTTAAATAATTT
2103644 T
1 T
2103645 GTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATAATTTTAAATAATTT
Found at i:2106158 original size:21 final size:22
Alignment explanation
Indices: 2106134--2106175 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2106124 AATAAAAAAA
*
2106134 CTCAAATTTCTT-TTATTTTCT
1 CTCAAATCTCTTATTATTTTCT
*
2106155 CTCAAATCTCTTATTTTTTTC
1 CTCAAATCTCTTATTATTTTC
2106176 ACAGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60
Consensus pattern (22 bp):
CTCAAATCTCTTATTATTTTCT
Found at i:2106225 original size:13 final size:14
Alignment explanation
Indices: 2106208--2106240 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2106198 TATATGTAAC
2106208 ATAAATATTATTTT
1 ATAAATATTATTTT
*
2106222 -TAAAAATTATTTT
1 ATAAATATTATTTT
2106235 ATAAAT
1 ATAAAT
2106241 TATATGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 2
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTATTTT
Found at i:2108379 original size:2 final size:2
Alignment explanation
Indices: 2108374--2108408 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2108364 GTATATAGGC
* *
2108374 AT AT AT AT AT AT AT TT AT AT TT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2108409 CACCTAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2121473 original size:50 final size:51
Alignment explanation
Indices: 2121361--2121477 Score: 166
Period size: 50 Copynumber: 2.3 Consensus size: 51
2121351 ATTTACTTGC
* * *
2121361 ATGTATCAATACATTGAATAATGTATCGATACATTTGGGTAAAATACCCAA
1 ATGTATCGATACAATGAATAATGTATCGATACATTTGGGTAAAAAACCCAA
* *
2121412 ATGTATCGATACAATG-ATCAATGTATCGATATATTT-GGTAAAAAATCCAA
1 ATGTATCGATACAATGAAT-AATGTATCGATACATTTGGGTAAAAAACCCAA
2121462 ATGTATCGATACAATG
1 ATGTATCGATACAATG
2121478 TATCGATACA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
50 30 0.50
51 30 0.50
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACAATGAATAATGTATCGATACATTTGGGTAAAAAACCCAA
Found at i:2121479 original size:13 final size:13
Alignment explanation
Indices: 2121461--2121487 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2121451 AAAAAATCCA
2121461 AATGTATCGATAC
1 AATGTATCGATAC
2121474 AATGTATCGATAC
1 AATGTATCGATAC
2121487 A
1 A
2121488 TTTATTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2121576 original size:19 final size:20
Alignment explanation
Indices: 2121548--2121601 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
2121538 ATCGATACAT
*
2121548 TGTATTGATACAAAACT-TA
1 TGTATCGATACAAAACTATA
** *
2121567 TGTATCGATACATTTACTATT
1 TGTATCGATACA-AAACTATA
2121588 TGTATCGATACAAA
1 TGTATCGATACAAA
2121602 TTGTTGAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 13 0.48
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
TGTATCGATACAAAACTATA
Found at i:2122309 original size:61 final size:61
Alignment explanation
Indices: 2122214--2122360 Score: 165
Period size: 61 Copynumber: 2.4 Consensus size: 61
2122204 AAACATGATG
* * * * *
2122214 AAGATAAGAAGAGTGATAAA-GATGCCAATATGCTGATTC-AGGACCAGTGATACTAGACTTA
1 AAGATGAGAAGAATGATAAATG-TGCTAACATGCTGATTCAAGG-CCAATGATACTAGACTTA
* * *
2122275 AAGATGAGAAGAATGATAAATGTGCTAACATGCTGATTCAAGGCCAATGATATTGGGCTTA
1 AAGATGAGAAGAATGATAAATGTGCTAACATGCTGATTCAAGGCCAATGATACTAGACTTA
* *
2122336 AAGATGCGAAGAATG-TCAATGTGCT
1 AAGATGAGAAGAATGATAAATGTGCT
2122361 GATTCACGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
60 9 0.12
61 61 0.82
62 4 0.05
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (61 bp):
AAGATGAGAAGAATGATAAATGTGCTAACATGCTGATTCAAGGCCAATGATACTAGACTTA
Found at i:2122770 original size:99 final size:98
Alignment explanation
Indices: 2122305--2123127 Score: 1007
Period size: 99 Copynumber: 8.3 Consensus size: 98
2122295 TGTGCTAACA
** * * * * *
2122305 TGCTGATTCAAGGCCAATGATATTGGGCTTAAAGATGCGAAGAATGTCAATGTGCTGATTCACGG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--GAAG-GTGCCAATGTGCTGATTCAAGG
* * * * *
2122370 TCAGCGACATGGGACTTGAAGATGAGAAGAATGCCAATG
63 CCAGCGACATTGGACTTAAAGAT--GAAG-GTGTCAATG
* * * * ** * *
2122409 TGCTGATTCAAGGCCAGTGACATTGGGCTTAGGAATGTTAAAGAAGCCAATATGTTGATTCAAGG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-GATGAAGGTGCCAATGTGCTGATTCAAGG
* * ** * *
2122474 CCAGTGATATTAAACTTAAAGATGAAAGTGCCAATG
63 CCAGCGACATTGGACTTAAAGATGAAGGTGTCAATG
* * * * *
2122510 TACTGATTCAAGGCCAGTGACATTGGACTTAAAGATAAATGTGCCAATGTACTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* *
2122575 ACGACATTGGACTTAAAGATGAAGGTGCCAATG
66 GCGACATTGGACTTAAAGATGAAGGTGTCAATG
* * *
2122608 TCCTGATTTAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* *
2122673 GTGACATTGGACTTAAAGATGAAAGTGTCAATG
66 GCGACATTGGACTTAAAGATGAAGGTGTCAATG
* * * * *
2122706 TGTTGATTCAAGGCTAGCGACGTTAGGACTTAAAGATGAAGGTGCCAATGTACTGATTAAAGGCC
1 TGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
*
2122771 AGCGACATTGGACTTAAATATGAAGGTGTCAATG
65 AGCGACATTGGACTTAAAGATGAAGGTGTCAATG
* * *
2122805 TGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTAAAGGCTA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
*
2122870 GCGACGTTAGGACTTAAAGATGAAGGTGTCAATG
66 GCGACATT-GGACTTAAAGATGAAGGTGTCAATG
* * *
2122904 TGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTAAAGGCTA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* *
2122969 GCGACGTTAGGACTTAAAGATGAAAGTGTCAATG
66 GCGACATT-GGACTTAAAGATGAAGGTGTCAATG
* * *
2123003 TGCTGATTCAAGGCTAGCAACATTGGACTTAAAGATGAAGGTGTCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
*
2123068 GCGACATTGGACTTAAAGATGAAGGTGCCAATG
66 GCGACATTGGACTTAAAGATGAAGGTGTCAATG
* *
2123101 TGCTGATTCAAGACCAGCGACGTTGGA
1 TGCTGATTCAAGGCCAGCGACATTGGA
2123128 ACGAAAGATG
Statistics
Matches: 637, Mismatches: 77, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
98 249 0.39
99 279 0.44
101 37 0.06
102 3 0.00
104 62 0.10
105 3 0.00
106 2 0.00
107 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (98 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGACTTAAAGATGAAGGTGTCAATG
Found at i:2122795 original size:148 final size:147
Alignment explanation
Indices: 2122305--2123127 Score: 1036
Period size: 148 Copynumber: 5.5 Consensus size: 147
2122295 TGTGCTAACA
** * * * * *
2122305 TGCTGATTCAAGGCCAATGATATTGGGCTTAAAGATGCGAAGAATGTCAATGTGCTGATTCACGG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--GAAG-GTGCCAATGTGCTGATTCAAGG
* * * * *
2122370 TCAGCGACATGGGACTTGAAGATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAGTGACATTGG
63 CCAGCGACATTGGACTTAAAGATGA-AAG--TGCCAATGTGCTGATTCAAGGCTAGCGACATTGG
* * * ** *
2122435 GCTTAGGAATGTTAAAGAAGCCAATA
125 ACTTA--AA-GATGAAGGTGCCAATG
* * * ** * *
2122461 TGTTGATTCAAGGCCAGTGATATTAAACTTAAAGATGAAAGTGCCAATGTACTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * * *
2122526 GTGACATTGGACTTAAAGAT-AAATGTGCCAATGTACTGATTCAAGGCCAACGACATTGGACTTA
66 GCGACATTGGACTTAAAGATGAAA-GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTA
2122590 AAGATGAAGGTGCCAATG
130 AAGATGAAGGTGCCAATG
* * *
2122608 TCCTGATTTAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * * *
2122673 GTGACATTGGACTTAAAGATGAAAGTGTCAATGTGTTGATTCAAGGCTAGCGACGTTAGGACTTA
66 GCGACATTGGACTTAAAGATGAAAGTGCCAATGTGCTGATTCAAGGCTAGCGACATT-GGACTTA
2122738 AAGATGAAGGTGCCAATG
130 AAGATGAAGGTGCCAATG
* * * *
2122756 TACTGATTAAAGGCCAGCGACATTGGACTTAAATATGAAGGTGTCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * * *
2122821 ACGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTAAAGGCTAGCGACGTTAGGACTTA
66 GCGACATTGGACTTAAAGATGAAAGTGCCAATGTGCTGATTCAAGGCTAGCGACATT-GGACTTA
*
2122886 AAGATGAAGGTGTCAATG
130 AAGATGAAGGTGCCAATG
* * *
2122904 TGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTAAAGGCTA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * *
2122969 GCGACGTTAGGACTTAAAGATGAAAGTGTCAATGTGCTGATTCAAGGCTAGCAACATTGGACTTA
66 GCGACATT-GGACTTAAAGATGAAAGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTA
*
2123034 AAGATGAAGGTGTCAATG
130 AAGATGAAGGTGCCAATG
*
2123052 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGACCA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
*
2123117 GCGACGTTGGA
66 GCGACATTGGA
2123128 ACGAAAGATG
Statistics
Matches: 594, Mismatches: 69, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
147 116 0.20
148 324 0.55
149 44 0.07
150 35 0.06
151 2 0.00
152 2 0.00
153 37 0.06
154 3 0.01
156 31 0.05
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (147 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGACTTAAAGATGAAAGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAA
AGATGAAGGTGCCAATG
Found at i:2123138 original size:49 final size:49
Alignment explanation
Indices: 2122305--2123127 Score: 1007
Period size: 49 Copynumber: 16.6 Consensus size: 49
2122295 TGTGCTAACA
** * * * *
2122305 TGCTGATTCAAGGCCAATGATATTGGGCTTAAAGATGCGAAGAATGTCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--GAAG-GTGCCAATG
* * * * *
2122357 TGCTGATTCACGGTCAGCGACATGGGACTTGAAGATGAGAAGAATGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--GAAG-GTGCCAATG
* * * * ** *
2122409 TGCTGATTCAAGGCCAGTGACATTGGGCTTAGGAATGTTAAAGAAGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-GATGAAGGTGCCAATG
* * * ** *
2122461 TGTTGATTCAAGGCCAGTGATATTAAACTTAAAGATGAAAGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
* * * *
2122510 TACTGATTCAAGGCCAGTGACATTGGACTTAAAGATAAATGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
* *
2122559 TACTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
* * *
2122608 TCCTGATTTAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
* * *
2122657 TGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGAAAGTGTCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
* * *
2122706 TGTTGATTCAAGGCTAGCGACGTTAGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAAGGTGCCAATG
* * * *
2122756 TACTGATTAAAGGCCAGCGACATTGGACTTAAATATGAAGGTGTCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
*
2122805 TGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
* * * *
2122854 TGCTGATTAAAGGCTAGCGACGTTAGGACTTAAAGATGAAGGTGTCAATG
1 TGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAAGGTGCCAATG
*
2122904 TGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
* * * * *
2122953 TGCTGATTAAAGGCTAGCGACGTTAGGACTTAAAGATGAAAGTGTCAATG
1 TGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAAGGTGCCAATG
* * *
2123003 TGCTGATTCAAGGCTAGCAACATTGGACTTAAAGATGAAGGTGTCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
2123052 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
* *
2123101 TGCTGATTCAAGACCAGCGACGTTGGA
1 TGCTGATTCAAGGCCAGCGACATTGGA
2123128 ACGAAAGATG
Statistics
Matches: 672, Mismatches: 93, Indels: 15
0.86 0.12 0.02
Matches are distributed among these distances:
49 433 0.64
50 132 0.20
52 100 0.15
53 3 0.00
54 2 0.00
55 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATG
Found at i:2124946 original size:1 final size:1
Alignment explanation
Indices: 2124940--2124996 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
2124930 TCCTTCATAC
* * * ** * *
2124940 AAAAAAACAAAAAAATAAAAAAAACAAAAAACCAAGAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2124997 CAGAAAATGG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:2124951 original size:8 final size:8
Alignment explanation
Indices: 2124938--2125003 Score: 62
Period size: 8 Copynumber: 7.9 Consensus size: 8
2124928 CGTCCTTCAT
2124938 ACAAAAAA
1 ACAAAAAA
2124946 ACAAAAAA
1 ACAAAAAA
*
2124954 ATAAAAAAA
1 A-CAAAAAA
2124963 ACAAAAAA
1 ACAAAAAA
*
2124971 CCAAGAAAA
1 ACAA-AAAA
2124980 A-AAAACAA
1 ACAAAA-AA
*
2124988 AAAAAAAA
1 ACAAAAAA
2124996 ACAGAAAA
1 ACA-AAAA
2125004 TGGTCCAGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
7 2 0.04
8 27 0.56
9 19 0.40
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.02
Consensus pattern (8 bp):
ACAAAAAA
Found at i:2124983 original size:13 final size:13
Alignment explanation
Indices: 2124940--2124997 Score: 61
Period size: 12 Copynumber: 4.6 Consensus size: 13
2124930 TCCTTCATAC
2124940 AAAAAAA-CAAAA
1 AAAAAAACCAAAA
2124952 AAATAAAA--AAAA
1 AAA-AAAACCAAAA
*
2124964 CAAAAAACCAAGAA
1 AAAAAAACCAA-AA
2124978 AAAAAAA-CAAAA
1 AAAAAAACCAAAA
2124990 AAAAAAAC
1 AAAAAAAC
2124998 AGAAAATGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 4 0.10
12 18 0.46
13 9 0.23
14 8 0.21
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (13 bp):
AAAAAAACCAAAA
Found at i:2127725 original size:20 final size:19
Alignment explanation
Indices: 2127687--2127728 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2127677 TATTTTTATC
* *
2127687 TAATATAAGATATTATTAA
1 TAATATAAAATAATATTAA
2127706 TAATATAAAAATAATATTAA
1 TAATAT-AAAATAATATTAA
2127726 TAA
1 TAA
2127729 ATTATTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAATATAAAATAATATTAA
Found at i:2127777 original size:12 final size:12
Alignment explanation
Indices: 2127750--2127791 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2127740 AAAATTTAAT
*
2127750 ATATTCTAATATA
1 ATATTTTAA-ATA
2127763 ATATTTTAAATA
1 ATATTTTAAATA
2127775 ATATTTT-AAT-
1 ATATTTTAAATA
2127785 ATATTTT
1 ATATTTT
2127792 GTTCATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 7 0.25
11 3 0.11
12 10 0.36
13 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATTTTAAATA
Found at i:2127864 original size:29 final size:30
Alignment explanation
Indices: 2127800--2127873 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 30
2127790 TTGTTCATAA
*
2127800 ATATTTATAAATAATAATATAATAATTAAT
1 ATATTTATAAATAATAATATAATAATAAAT
** * *
2127830 AT-TTTATATTTAATGATATATTAA-AAAT
1 ATATTTATAAATAATAATATAATAATAAAT
2127858 ATATTTA-AAAT-ATAAT
1 ATATTTATAAATAATAAT
2127874 TTTTTAAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
27 4 0.11
28 7 0.20
29 22 0.63
30 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
ATATTTATAAATAATAATATAATAATAAAT
Found at i:2129338 original size:2 final size:2
Alignment explanation
Indices: 2129331--2129369 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2129321 GGAATTGGGT
* *
2129331 AG AG AG AG AG AG AG GG AG AG AG CG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2129370 ATGAATTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2129585 original size:12 final size:12
Alignment explanation
Indices: 2129570--2129628 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
2129560 TTAATTTTTT
2129570 TATTTATAAATA
1 TATTTATAAATA
* *
2129582 TATTCATACATA
1 TATTTATAAATA
2129594 -ATTTATAAAATA
1 TATTTAT-AAATA
2129606 TTATTTATAAATA
1 -TATTTATAAATA
*
2129619 TATTTTTAAA
1 TATTTATAAA
2129629 AATTTAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 5 0.13
12 23 0.59
13 5 0.13
14 6 0.15
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (12 bp):
TATTTATAAATA
Found at i:2129613 original size:14 final size:14
Alignment explanation
Indices: 2129594--2129631 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2129584 TTCATACATA
2129594 ATTTATAAAATATT
1 ATTTATAAAATATT
2129608 ATTTATAAATATATT
1 ATTTATAAA-ATATT
2129623 -TTTA-AAAAT
1 ATTTATAAAAT
2129632 TTAATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 3 0.13
14 13 0.57
15 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTATAAAATATT
Found at i:2129906 original size:36 final size:37
Alignment explanation
Indices: 2129832--2129911 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 37
2129822 TTATTCTCTC
* *
2129832 TTTATTTTATTCTCACTAAATAATTATGATAA-TTTT
1 TTTATTTTATTCTCAATAAATAAATATGATAATTTTT
2129868 TTTATTTTATT-TCAATAAATTAAATAT-ACT-ATTATTT
1 TTTATTTTATTCTCAATAAA-TAAATATGA-TAATT-TTT
2129905 TTTATTT
1 TTTATTT
2129912 ACTATGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
35 9 0.24
36 19 0.50
37 10 0.26
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (37 bp):
TTTATTTTATTCTCAATAAATAAATATGATAATTTTT
Found at i:2129994 original size:18 final size:18
Alignment explanation
Indices: 2129960--2129997 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2129950 ATGTTGTAAG
2129960 TTTTTCCTAAACCTAATTT
1 TTTTTCCTAAA-CTAATTT
2129979 TTTTTCTCTAAA-TAATTT
1 TTTTTC-CTAAACTAATTT
2129997 T
1 T
2129998 AAGACTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTCCTAAACTAATTT
Found at i:2134846 original size:12 final size:12
Alignment explanation
Indices: 2134827--2134872 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
2134817 AAATACGATT
2134827 ATATAATATAAA
1 ATATAATATAAA
*
2134839 AAATAATA-AAA
1 ATATAATATAAA
2134850 ATATAATATAAA
1 ATATAATATAAA
2134862 ATATAATATAA
1 ATATAATATAA
2134873 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:2135250 original size:25 final size:26
Alignment explanation
Indices: 2135221--2135288 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 26
2135211 AGTTAAATAG
2135221 TAATTTTAAAAT-TTTAAAATATTT-T
1 TAATTTTAAAATATTT-AAATATTTAT
*
2135246 TAATTTTAAAATATTTAATTATTTAT
1 TAATTTTAAAATATTTAAATATTTAT
2135272 TATATTATTAAAATATT
1 TA-ATT-TTAAAATATT
2135289 ATTTTTTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 19 0.50
26 6 0.16
27 3 0.08
28 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATTTTAAAATATTTAAATATTTAT
Found at i:2135264 original size:15 final size:16
Alignment explanation
Indices: 2135230--2135265 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
2135220 GTAATTTTAA
2135230 AATTTTAAAATATTTTT
1 AATTTTAAAATA-TTTT
2135247 AATTTTAAAATA-TTT
1 AATTTTAAAATATTTT
2135262 AATT
1 AATT
2135266 ATTTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
17 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTTAAAATATTTT
Found at i:2135348 original size:30 final size:30
Alignment explanation
Indices: 2135306--2135362 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
2135296 AATATTTATA
2135306 TATTTTATAATAAAAATAAAAAATTAATTT
1 TATTTTATAATAAAAATAAAAAATTAATTT
* **
2135336 TATTATTA-AATAATAATTTAAAATTAA
1 TATT-TTATAATAAAAATAAAAAATTAA
2135363 ATTAAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.87
31 3 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TATTTTATAATAAAAATAAAAAATTAATTT
Found at i:2135642 original size:7 final size:7
Alignment explanation
Indices: 2135628--2135668 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
2135618 CGTCTATTTT
2135628 TTAT-TA
1 TTATATA
2135634 TTATATA
1 TTATATA
2135641 TTATATA
1 TTATATA
2135648 TTATATA
1 TTATATA
*
2135655 TTACATA
1 TTATATA
*
2135662 TAATATA
1 TTATATA
2135669 AATATAGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (7 bp):
TTATATA
Found at i:2147020 original size:22 final size:22
Alignment explanation
Indices: 2146995--2147047 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
2146985 ATATATAATA
2146995 AAATAATAAT-TTATCAAAAAGT
1 AAATAAT-ATCTTATCAAAAAGT
*
2147017 AAATTATATCTTATCAAAAAGT
1 AAATAATATCTTATCAAAAAGT
*
2147039 AAATTATAT
1 AAATAATAT
2147048 TATGAACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (22 bp):
AAATAATATCTTATCAAAAAGT
Found at i:2147588 original size:20 final size:19
Alignment explanation
Indices: 2147546--2147594 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2147536 AAATAAAGAT
*
2147546 AATATATA-ATTAAAGATA
1 AATATATATATTAAACATA
*
2147564 TATATATATATTAAATCATA
1 AATATATATATTAAA-CATA
2147584 AATATAT-TATT
1 AATATATATATT
2147595 TAGAAAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATATATATTAAACATA
Found at i:2149261 original size:18 final size:18
Alignment explanation
Indices: 2149238--2149272 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2149228 AATTATTTAA
2149238 AAATTAATTTTATATAAC
1 AAATTAATTTTATATAAC
2149256 AAATTAATTTTATATAA
1 AAATTAATTTTATATAA
2149273 ATAAAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTAATTTTATATAAC
Found at i:2149288 original size:16 final size:16
Alignment explanation
Indices: 2149262--2149307 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2149252 TAACAAATTA
2149262 ATTTTATATAAATAAAG
1 ATTTTA-ATAAATAAAG
*
2149279 ATTTTAATAAATAAAT
1 ATTTTAATAAATAAAG
*
2149295 ATATTAA-AAATAA
1 ATTTTAATAAATAA
2149308 CATATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTTTAATAAATAAAG
Found at i:2149312 original size:16 final size:16
Alignment explanation
Indices: 2149269--2149312 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2149259 TTAATTTTAT
* *
2149269 ATAAATAAAGATTTTA
1 ATAAATAAATATATTA
2149285 ATAAATAAATATATTA
1 ATAAATAAATATATTA
2149301 A-AAATAACATAT
1 ATAAATAA-ATAT
2149313 TATAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
ATAAATAAATATATTA
Found at i:2149915 original size:31 final size:32
Alignment explanation
Indices: 2149849--2149915 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 32
2149839 TTAATTTAAA
** *
2149849 TTAATATTTAATAATAAAAATAATATTTTTAT
1 TTAATATTTAATAATAAAAATAATAAATATAT
*
2149881 TTAA-ATTTAATTATAAAAATATATAAATAT-T
1 TTAATATTTAATAATAAAAATA-ATAAATATAT
2149912 TTAA
1 TTAA
2149916 CAAATAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TTAATATTTAATAATAAAAATAATAAATATAT
Found at i:2150008 original size:2 final size:2
Alignment explanation
Indices: 2150003--2150057 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
2149993 TGTACATACG
* * *
2150003 TA TA TA TA AA TA TA TA -A TT TA TA TT TA T- TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2150042 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
2150058 AATGCCTACT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2152004 original size:22 final size:21
Alignment explanation
Indices: 2151946--2152000 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2151936 ATATAACTTC
* *
2151946 AAATTATTCATTATATATGAA
1 AAATTTTTCATTATTTATGAA
*
2151967 AATTTTTTCATTATTTATGAA
1 AAATTTTTCATTATTTATGAA
2151988 AAATTTTTCATTA
1 AAATTTTTCATTA
2152001 ATTTTTATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (21 bp):
AAATTTTTCATTATTTATGAA
Found at i:2152613 original size:4 final size:4
Alignment explanation
Indices: 2152606--2152630 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2152596 TTCTTATTTA
2152606 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
2152631 TTGATTGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:2153441 original size:22 final size:20
Alignment explanation
Indices: 2153410--2153451 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
2153400 ATTACATAAA
2153410 TAATTATACATATATAAATTAT
1 TAATTATACA-AT-TAAATTAT
*
2153432 TAATTTTACAATTAAATTAT
1 TAATTATACAATTAAATTAT
2153452 CAAGTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATTATACAATTAAATTAT
Found at i:2156827 original size:18 final size:19
Alignment explanation
Indices: 2156794--2156829 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2156784 ATATTTTTAG
*
2156794 TCGTTATTATCATTATTTT
1 TCGTTATTACCATTATTTT
2156813 TCGTTA-TACCATTATTT
1 TCGTTATTACCATTATTT
2156830 ATTACTGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (19 bp):
TCGTTATTACCATTATTTT
Found at i:2156914 original size:18 final size:18
Alignment explanation
Indices: 2156893--2156930 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2156883 ATTGATATCC
2156893 ATGACAAAAATGATCGTT
1 ATGACAAAAATGATCGTT
2156911 ATGACAAAAATGATCGTT
1 ATGACAAAAATGATCGTT
2156929 AT
1 AT
2156931 CATAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (18 bp):
ATGACAAAAATGATCGTT
Found at i:2156937 original size:18 final size:18
Alignment explanation
Indices: 2156896--2156937 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2156886 GATATCCATG
*
2156896 ACAAAAATGATCGTTATG
1 ACAAAAATGATCGTTATC
2156914 ACAAAAATGATCGTTATC
1 ACAAAAATGATCGTTATC
*
2156932 ATAAAA
1 ACAAAA
2156938 TAATAACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (18 bp):
ACAAAAATGATCGTTATC
Found at i:2158937 original size:67 final size:67
Alignment explanation
Indices: 2158853--2158987 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 67
2158843 TTATCCTATT
* *
2158853 CACCACACTTGATATTCTACACACTAGTCAAGTTGAAGTATTGAATGCAACTC-GTCTAAGATGA
1 CACCACACTTGACATTCTACACACTAGTCAAGTTGAAGTATTGAATGCAAC-CGGTCTAAGAAGA
2158917 GAC
65 GAC
*
2158920 CACCAGACTTGACATTCTACACACTAGTCAAGTTGAAGTATTGAATGCAACCGGTCTAAGAAGAG
1 CACCACACTTGACATTCTACACACTAGTCAAGTTGAAGTATTGAATGCAACCGGTCTAAGAAGAG
2158985 AC
66 AC
2158987 C
1 C
2158988 CTGACCAAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 1 0.02
67 63 0.98
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (67 bp):
CACCACACTTGACATTCTACACACTAGTCAAGTTGAAGTATTGAATGCAACCGGTCTAAGAAGAG
AC
Found at i:2159309 original size:30 final size:30
Alignment explanation
Indices: 2159273--2159354 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
2159263 TAATTACGTC
2159273 TAATATTTATCAAATTTATGAGATTTTATT
1 TAATATTTATCAAATTTATGAGATTTTATT
* * * * *
2159303 TAATATTCACCACATTTAAGAGATTTTGTT
1 TAATATTTATCAAATTTATGAGATTTTATT
* * *
2159333 TAATATATATTAAATATATGAG
1 TAATATTTATCAAATTTATGAG
2159355 TAGTTATGTC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (30 bp):
TAATATTTATCAAATTTATGAGATTTTATT
Found at i:2165962 original size:13 final size:13
Alignment explanation
Indices: 2165946--2165971 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2165936 CAGGGCAACT
2165946 TTGTATCGATACA
1 TTGTATCGATACA
2165959 TTGTATCGATACA
1 TTGTATCGATACA
2165972 ACACTTATGT
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):
TTGTATCGATACA
Found at i:2170903 original size:43 final size:43
Alignment explanation
Indices: 2170855--2170943 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
2170845 TAATTCCTAG
*
2170855 AGAGGTAAACCGTGCAGAAGACTGGATTGCAGTCCATTCAAAA
1 AGAGGTAAACCATGCAGAAGACTGGATTGCAGTCCATTCAAAA
*
2170898 AGAGGTGAACCATGCAGAAGACTGGATTGCAGTCCATTCAAAA
1 AGAGGTAAACCATGCAGAAGACTGGATTGCAGTCCATTCAAAA
2170941 AGA
1 AGA
2170944 ATGATGTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (43 bp):
AGAGGTAAACCATGCAGAAGACTGGATTGCAGTCCATTCAAAA
Found at i:2172735 original size:3 final size:3
Alignment explanation
Indices: 2172727--2172766 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2172717 TATTTCTCCA
2172727 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2172767 CAAATTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2177900 original size:6 final size:6
Alignment explanation
Indices: 2177860--2177899 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
2177850 CCCAATCCCA
*
2177860 TATAAT TATAAT TATAAT TATAAT TATAAT TATATT TATA
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATA
2177900 TATATTATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TATAAT
Found at i:2177940 original size:23 final size:23
Alignment explanation
Indices: 2177914--2177958 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2177904 TTATACACAA
2177914 AATT-TTC-TTTACTATAATATTAC
1 AATTATTCATTTAC-AT-ATATTAC
2177937 AATTATTCATTTACATATATTA
1 AATTATTCATTTACATATATTA
2177959 TATAAACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTATTCATTTACATATATTAC
Found at i:2182328 original size:2 final size:2
Alignment explanation
Indices: 2182323--2182350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2182313 AATAAAAAAT
2182323 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2182351 TACGGATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2182497 original size:6 final size:6
Alignment explanation
Indices: 2182475--2182509 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
2182465 GTATTAGAGG
2182475 TAAAAA TTAATAAA TAAAAA TAAAAA TAAAAA TAA
1 TAAAAA -TAA-AAA TAAAAA TAAAAA TAAAAA TAA
2182510 TAAAAGTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.67
7 6 0.22
8 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
TAAAAA
Found at i:2182503 original size:12 final size:13
Alignment explanation
Indices: 2182475--2182513 Score: 62
Period size: 12 Copynumber: 3.0 Consensus size: 13
2182465 GTATTAGAGG
2182475 TAAAAATTAATAAA
1 TAAAAA-TAATAAA
2182489 TAAAAATAA-AAA
1 TAAAAATAATAAA
2182501 TAAAAATAATAAA
1 TAAAAATAATAAA
2182514 AGTGTGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.50
13 6 0.25
14 6 0.25
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAATAATAAA
Found at i:2184980 original size:22 final size:23
Alignment explanation
Indices: 2184955--2184997 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2184945 AAAAAAAATT
*
2184955 AGGAAAG-AAAACTAAGGTTTGA
1 AGGAAAGAAAAAATAAGGTTTGA
*
2184977 AGGAGAGAAAAAATAAGGTTT
1 AGGAAAGAAAAAATAAGGTTT
2184998 CGAGTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.51, C:0.02, G:0.28, T:0.19
Consensus pattern (23 bp):
AGGAAAGAAAAAATAAGGTTTGA
Found at i:2185705 original size:13 final size:13
Alignment explanation
Indices: 2185687--2185712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2185677 CATTATTCAA
2185687 TGTATCGATACAT
1 TGTATCGATACAT
2185700 TGTATCGATACAT
1 TGTATCGATACAT
2185713 CGATCTTTGT
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:2185815 original size:33 final size:33
Alignment explanation
Indices: 2185769--2185837 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
2185759 TACATTTTGT
**
2185769 ATTGTATTGATACATTGCTCATTGTATCGATAC
1 ATTGTATCAATACATTGCTCATTGTATCGATAC
2185802 ATTGTATCAATACATTGCTCATTGTATCGATAC
1 ATTGTATCAATACATTGCTCATTGTATCGATAC
2185835 ATT
1 ATT
2185838 TTACAATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (33 bp):
ATTGTATCAATACATTGCTCATTGTATCGATAC
Found at i:2185817 original size:53 final size:53
Alignment explanation
Indices: 2185667--2185857 Score: 153
Period size: 53 Copynumber: 3.6 Consensus size: 53
2185657 GCCAAGGAAA
* * * * * *
2185667 TGTATCGATACATTATTCAATGTATCGATACATTGTATCGATACATCGATCTT
1 TGTATCGATACATTCTACAATGTATCGATACATTGTATCAATACATTGCTCAT
* * ** * *
2185720 TGTATCGATACA-TCTAGGAA-GT-T-TACCCAGATGTATCGATACATTTTG-T-AT
1 TGTATCGATACATTCTA-CAATGTATCGATACA-TTGTATCAATACA--TTGCTCAT
* *
2185771 TGTATTGATACATTGCT-CATTGTATCGATACATTGTATCAATACATTGCTCAT
1 TGTATCGATACATT-CTACAATGTATCGATACATTGTATCAATACATTGCTCAT
*
2185824 TGTATCGATACATTTTACAATGTATCGATACATT
1 TGTATCGATACATTCTACAATGTATCGATACATT
2185858 CAGGCATTTT
Statistics
Matches: 106, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
50 3 0.03
51 29 0.27
52 10 0.09
53 61 0.58
54 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (53 bp):
TGTATCGATACATTCTACAATGTATCGATACATTGTATCAATACATTGCTCAT
Found at i:2185837 original size:13 final size:13
Alignment explanation
Indices: 2185788--2185818 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2185778 ATACATTGCT
*
2185788 CATTGTATCGATA
1 CATTGTATCAATA
2185801 CATTGTATCAATA
1 CATTGTATCAATA
2185814 CATTG
1 CATTG
2185819 CTCATTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:2188240 original size:51 final size:52
Alignment explanation
Indices: 2188145--2188285 Score: 130
Period size: 51 Copynumber: 2.8 Consensus size: 52
2188135 AAATTTCTAG
* * *
2188145 ATTTTTCA-TATCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAAACA-TCA
1 ATTTTTCACAATCAGGGATACTCCAACTCCCGATTTCATTTCCAAAACACT-A
** * * * *
2188195 ATTTTTCTTAATTAGGGATACTCCAACT-CCGATTTTATTTTCAAAAGACTA
1 ATTTTTCACAATCAGGGATACTCCAACTCCCGATTTCATTTCCAAAACACTA
*
2188246 ATTTTTCACAATCGGGGATACTCCAAC-CCCGTTATTTCAT
1 ATTTTTCACAATCAGGGATACTCCAACTCCCG--ATTTCAT
2188286 CGGGGATACT
Statistics
Matches: 72, Mismatches: 13, Indels: 9
0.77 0.14 0.10
Matches are distributed among these distances:
50 7 0.10
51 57 0.79
52 2 0.03
53 6 0.08
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (52 bp):
ATTTTTCACAATCAGGGATACTCCAACTCCCGATTTCATTTCCAAAACACTA
Found at i:2188292 original size:28 final size:28
Alignment explanation
Indices: 2188256--2188332 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
2188246 ATTTTTCACA
2188256 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2188284 ATCGGGGATACTCCAACCCCCTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
***
2188312 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2188333 GCTTTATTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:2188391 original size:51 final size:51
Alignment explanation
Indices: 2188318--2188434 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
2188308 TTTCCGAGGG
* *
2188318 GATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATTAGC
1 GATACTCCAACCCCAGCCTTATTTCCAAAATATTGATTTCTCACAATTAGC
* * * * *
2188369 GATACTTCAACCCCAGCCTTATTTCTAAAATATTGATTTCTCATAATTGGG
1 GATACTCCAACCCCAGCCTTATTTCCAAAATATTGATTTCTCACAATTAGC
2188420 GATACTCCAACCCCA
1 GATACTCCAACCCCA
2188435 TTATTTTCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.32
Consensus pattern (51 bp):
GATACTCCAACCCCAGCCTTATTTCCAAAATATTGATTTCTCACAATTAGC
Found at i:2188619 original size:130 final size:130
Alignment explanation
Indices: 2188284--2188620 Score: 394
Period size: 130 Copynumber: 2.6 Consensus size: 130
2188274 CCGTTATTTC
* * * *
2188284 ATCGGGGATACTCCAACCCCCTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGTCTTTATTTCTAAAAT
* * * * *
2188349 ATTGATTTCTCACAATTAGCGATACTTCAACCCCAGCCTTATTTCTAAAATATTGATTTCTCATA
66 ATTAATTTCTCACAATCAGCGACACTTCAACCCCAGCCTTATTTCTAAAATATCGATTTCTCACA
* * * *
2188414 ATTGGGGATACTCCAACCCCATTATTTTC-ACGGGGATACTCCAATCCCGAT-TTTATTTTTGAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGA-GGGGATACTCCAACCCCG-TCTTTATTTCTAAA
* * * * ** *
2188477 ACATCTATTTTCT-ATAATCAGGGACACTTCAACCCTTGCCTTATTTCT-AAATCATCGATTTTT
64 ATAT-TAATTTCTCACAATCAGCGACACTTCAACCCCAGCCTTATTTCTAAAAT-ATCGATTTCT
2188540 CACA
127 CACA
* * *
2188544 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGTCATTATCTCTAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGTCTTTATTTCTAAAAT
2188609 ATTAAATTTCTC
66 ATT-AATTTCTC
2188621 GTTGGGAGAT
Statistics
Matches: 170, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
129 7 0.04
130 156 0.92
131 7 0.04
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (130 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGTCTTTATTTCTAAAAT
ATTAATTTCTCACAATCAGCGACACTTCAACCCCAGCCTTATTTCTAAAATATCGATTTCTCACA
Found at i:2191798 original size:20 final size:19
Alignment explanation
Indices: 2191756--2191798 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
2191746 ATAGTCTTAT
*
2191756 ATAAAAAAATATACATGAA
1 ATAAAAAAATATACAAGAA
2191775 ATAAAAAACATATA-AAGAA
1 ATAAAAAA-ATATACAAGAA
2191794 CATAA
1 -ATAA
2191799 TTTAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.19
Consensus pattern (19 bp):
ATAAAAAAATATACAAGAA
Found at i:2194498 original size:35 final size:35
Alignment explanation
Indices: 2194453--2194522 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2194443 ATCACATTGT
2194453 TTGTTTATTTTCAACCTCAATTACTCATAAAAAAA
1 TTGTTTATTTTCAACCTCAATTACTCATAAAAAAA
2194488 TTGTTTATTTTCAACCTCAATTACTCATAAAAAAA
1 TTGTTTATTTTCAACCTCAATTACTCATAAAAAAA
2194523 GAATAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (35 bp):
TTGTTTATTTTCAACCTCAATTACTCATAAAAAAA
Found at i:2195081 original size:12 final size:12
Alignment explanation
Indices: 2195064--2195106 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2195054 TAAGTTTTAT
*
2195064 TTATTTAAAATA
1 TTATTTTAAATA
*
2195076 TTATTTTTAATA
1 TTATTTTAAATA
*
2195088 TAATTTTAAATA
1 TTATTTTAAATA
2195100 TTATTTT
1 TTATTTT
2195107 TAATTATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTTTAAATA
Found at i:2195096 original size:25 final size:27
Alignment explanation
Indices: 2195067--2195129 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 27
2195057 GTTTTATTTA
2195067 TTTAAAATATTATTTTTAA-TATA-AT
1 TTTAAAATATTATTTTTAATTATACAT
2195092 TTT-AAATATTATTTTTAATTATACAT
1 TTTAAAATATTATTTTTAATTATACAT
*
2195118 TACTAAAATATT
1 T-TTAAAATATT
2195130 TTCAGATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 15 0.45
25 7 0.21
26 3 0.09
27 1 0.03
28 7 0.21
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAAAATATTATTTTTAATTATACAT
Found at i:2197719 original size:40 final size:39
Alignment explanation
Indices: 2197643--2197720 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 39
2197633 GGTAAAAAGA
* * *
2197643 CATAATGTGTCGATACATTGCAGAATATATCAATACATT
1 CATAATGTATCGATACATTGAAAAATATATCAATACATT
* * *
2197682 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCAATACAT
2197721 CAAGGTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCAATACATT
Found at i:2198165 original size:21 final size:21
Alignment explanation
Indices: 2198120--2198167 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2198110 TTTTACTAAT
*
2198120 TTTTCTCTCTTCCTTTCTTCT
1 TTTTCTCTCTTCCTTTCTTCC
2198141 TTTTCTCTCTGT-C-TTCTCTCC
1 TTTTCTCTCT-TCCTTTCT-TCC
2198162 TTTTCT
1 TTTTCT
2198168 TTTTCATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTCTCTCTTCCTTTCTTCC
Found at i:2198837 original size:20 final size:20
Alignment explanation
Indices: 2198811--2198879 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
2198801 TTACCCAGAC
2198811 GTATCGATATATTTTTCAAT
1 GTATCGATATATTTTTCAAT
* * * * *
2198831 ATATCGATACATGTATGAAT
1 GTATCGATATATTTTTCAAT
*
2198851 GTATCGATATATTCTTCAAT
1 GTATCGATATATTTTTCAAT
2198871 GTATCGATA
1 GTATCGATA
2198880 CATTATGTCT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATATATTTTTCAAT
Found at i:2198855 original size:40 final size:39
Alignment explanation
Indices: 2198811--2198886 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 39
2198801 TTACCCAGAC
*
2198811 GTATCGATATATTTTTCAATATATCGATACATGTATGAAT
1 GTATCGATATATTCTTCAATATATCGATACAT-TATGAAT
*
2198851 GTATCGATATATTCTTCAATGTATCGATACATTATG
1 GTATCGATATATTCTTCAATATATCGATACATTATG
2198887 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
GTATCGATATATTCTTCAATATATCGATACATTATGAAT
Found at i:2199844 original size:27 final size:23
Alignment explanation
Indices: 2199793--2199849 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
2199783 AGCCTTTGAC
2199793 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
2199816 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
*
2199839 CATTCATTTTT
1 CATGCATTTTT
2199850 AACATGTCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.65
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:2212881 original size:10 final size:10
Alignment explanation
Indices: 2212866--2212920 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
2212856 TTACACCCAA
2212866 AAAAAAAAAT
1 AAAAAAAAAT
2212876 AAAAAAAAAT
1 AAAAAAAAAT
*
2212886 AAAAACAAA-
1 AAAAAAAAAT
* *
2212895 ACAAAAAAAC
1 AAAAAAAAAT
*
2212905 AAAAAAAAAG
1 AAAAAAAAAT
2212915 AAAAAA
1 AAAAAA
2212921 TAGCAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
9 7 0.18
10 32 0.82
ACGTcount: A:0.89, C:0.05, G:0.02, T:0.04
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:2212894 original size:28 final size:28
Alignment explanation
Indices: 2212863--2212936 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
2212853 CCTTTACACC
*
2212863 CAAAAAAAAAAATAAAAAAAAATAAAAA
1 CAAAAAAAAAAATAAAAAAAAAGAAAAA
*
2212891 CAAAACAAAAAAACAAAAAAAAAGAAAAA
1 CAAAA-AAAAAAATAAAAAAAAAGAAAAA
**
2212920 -ATAGCAAAAAAATAAAA
1 CA-AAAAAAAAAATAAAA
2212937 GGGTCTAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 17 0.44
29 22 0.56
ACGTcount: A:0.85, C:0.07, G:0.03, T:0.05
Consensus pattern (28 bp):
CAAAAAAAAAAATAAAAAAAAAGAAAAA
Found at i:2212900 original size:19 final size:18
Alignment explanation
Indices: 2212864--2212931 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
2212854 CTTTACACCC
*
2212864 AAAAA-AAAAAATAA-AA
1 AAAAACAAAAAAAAACAA
*
2212880 AAAAATAAAAACAAAACAA
1 AAAAACAAAAA-AAAACAA
*
2212899 AAAAACAAAAAAAAAGAA
1 AAAAACAAAAAAAAACAA
2212917 AAAATAGCAAAAAAA
1 AAAA-A-CAAAAAAA
2212932 TAAAAGGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.11
17 5 0.11
18 13 0.30
19 13 0.30
20 8 0.18
ACGTcount: A:0.87, C:0.06, G:0.03, T:0.04
Consensus pattern (18 bp):
AAAAACAAAAAAAAACAA
Found at i:2212931 original size:1 final size:1
Alignment explanation
Indices: 2212864--2212920 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
2212854 CTTTACACCC
* * * * * *
2212864 AAAAAAAAAAATAAAAAAAAATAAAAACAAAACAAAAAAACAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2212921 TAGCAAAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.89, C:0.05, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:2214275 original size:28 final size:28
Alignment explanation
Indices: 2214142--2215391 Score: 1484
Period size: 28 Copynumber: 43.9 Consensus size: 28
2214132 GAATGTTCAT
2214142 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2214170 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2214199 CTCTTTTAAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2214228 CTCTTTTTAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2214257 CCATTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
2214285 CCCTTGCGAAGCCCATAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2214313 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2214341 CCCTTTCAAAGCCCACAAGTTAGTGGTA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2214369 CCCTTTCGAAGCCCATAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2214397 CCCTTGT-GAAGCCCACAATTCAGTGGCA
1 CCCTT-TCAAAGCCCACAAGTCAGTGGCA
* *
2214425 CTCTTTCAAAGCCCTCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
2214453 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
*
2214483 CTCCTATT-AGAGCCCACAAGTCAGTGGCA
1 C-CCT-TTCAAAGCCCACAAGTCAGTGGCA
*
2214512 CCATTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2214540 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
2214568 CTCTTGCGAAGCCCACAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2214596 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
2214624 CCCTTTCAAAGCCCACATAAGTCAGTGGCA
1 CCCTTTCAAAGCCCAC--AAGTCAGTGGCA
* *
2214654 CTCCTTTTAGAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
**
2214683 CCCTTTTGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
2214711 CCCTTGCGAAGCCCACAATTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2214739 CTCTTTTAAAGCCTACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
2214767 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
*
2214797 CTCCTTTTAAAGCCCATGCAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
2214828 CCTTTTCAAAGCCCA-AGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACA-AGTCAGTGGCA
* *
2214856 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2214884 CCTTTTC-AAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2214911 CCCTTTCAAAGCCCACACAAGTTAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* * *
2214941 CTCCTTTTAAAGCCCACGCAAATCAGTGGTA
1 C-CCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
2214972 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2215000 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2215028 CCCTTTC-AAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2215055 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2215083 CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2215111 TCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2215139 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
2215167 CCCTTGCGAAGCCCGCAATTCAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2215195 CTCTTTCAAAGCTCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2215223 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
2215251 CTTTTTTCAAAGCCCACGAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2215280 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
2215308 TCCTTTCAAAGCTCACGAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
**
2215336 TTCTTTCAAAGCCCACGTAAGTCAGTGGCA
1 CCCTTTCAAAGCCCAC--AAGTCAGTGGCA
*
2215366 CCCTTTTAAAGCCCACGCAAGTCAGT
1 CCCTTTCAAAGCCCA--CAAGTCAGT
2215392 AACATTCTTT
Statistics
Matches: 1069, Mismatches: 123, Indels: 58
0.86 0.10 0.05
Matches are distributed among these distances:
27 56 0.05
28 683 0.64
29 148 0.14
30 117 0.11
31 62 0.06
32 3 0.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:2216047 original size:20 final size:19
Alignment explanation
Indices: 2216022--2216079 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
2216012 TTTTACCCAG
2216022 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TATGA
* * *
2216042 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATT-ATGA
2216062 ATGTATCGATACATTATG
1 ATGTATCGATACATTATG
2216080 TCTTTTTACC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:2218435 original size:28 final size:28
Alignment explanation
Indices: 2218402--2218459 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2218392 ATGAAAATAA
2218402 TAAAAAA-ATACAAA-AAGAATCAAAATTT
1 TAAAAAACATA-AAAGAA-AATCAAAATTT
*
2218430 TAAAAAACATAAAAGAAAATGAAAATTT
1 TAAAAAACATAAAAGAAAATCAAAATTT
2218458 TA
1 TA
2218460 GAGAAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.22
Consensus pattern (28 bp):
TAAAAAACATAAAAGAAAATCAAAATTT
Found at i:2227885 original size:23 final size:23
Alignment explanation
Indices: 2227855--2227902 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2227845 TTTAAAAAAT
*
2227855 ATATATACGTAATTAAATAAGAA
1 ATATATACATAATTAAATAAGAA
* *
2227878 ATATATACATATTTAAATAATAA
1 ATATATACATAATTAAATAAGAA
2227901 AT
1 AT
2227903 TTTTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATATACATAATTAAATAAGAA
Found at i:2228307 original size:2 final size:2
Alignment explanation
Indices: 2228300--2228330 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2228290 GGAAAGTAAG
*
2228300 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2228331 AATTAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2228628 original size:44 final size:43
Alignment explanation
Indices: 2228551--2228679 Score: 183
Period size: 44 Copynumber: 3.0 Consensus size: 43
2228541 TTTCTTCCAA
*
2228551 AGCCCAAATTGTC-AGTGATGCGTATGGAAAAAGGCAAAGCAG
1 AGCCCAAATTGTCAAGTAATGCGTATGGAAAAAGGCAAAGCAG
2228593 AGCCCAAATTGTCAAGTAATGCCGTATGGAAAAAGGCAAAGCAG
1 AGCCCAAATTGTCAAGTAATG-CGTATGGAAAAAGGCAAAGCAG
* * * *
2228637 AGCCCAAATTGTCAAATAACGCGTAAGGAATAAGG--AAGCAG
1 AGCCCAAATTGTCAAGTAATGCGTATGGAAAAAGGCAAAGCAG
2228678 AG
1 AG
2228680 TACACGCTGT
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
41 8 0.10
42 13 0.16
43 18 0.22
44 41 0.51
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.16
Consensus pattern (43 bp):
AGCCCAAATTGTCAAGTAATGCGTATGGAAAAAGGCAAAGCAG
Found at i:2228823 original size:13 final size:13
Alignment explanation
Indices: 2228807--2228831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2228797 TTAAGCATTT
2228807 AATTTAATAAAAA
1 AATTTAATAAAAA
2228820 AATTTAATAAAA
1 AATTTAATAAAA
2228832 TATAAGATAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTTAATAAAAA
Found at i:2230563 original size:13 final size:13
Alignment explanation
Indices: 2230545--2230570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2230535 ACATCTTGTA
2230545 TGTATCGATACAT
1 TGTATCGATACAT
2230558 TGTATCGATACAT
1 TGTATCGATACAT
2230571 GACCAAATGT
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:2238965 original size:32 final size:33
Alignment explanation
Indices: 2238904--2238965 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
2238894 AGGGGTTAGA
*
2238904 GTATTGATACATAATGCACAGTATCGATACATT
1 GTATTGATACATAATCCACAGTATCGATACATT
* *
2238937 GTATTGATACATGA-CCACTGTATCGATAC
1 GTATTGATACATAATCCACAGTATCGATAC
2238966 TTGCAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (33 bp):
GTATTGATACATAATCCACAGTATCGATACATT
Found at i:2239058 original size:32 final size:33
Alignment explanation
Indices: 2239017--2239080 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
2239007 CCTTAACTGT
2239017 TTGTATCGATACAT-A-CAAGATGTATCGATACG
1 TTGTATCGATACATGACCAA-ATGTATCGATACG
2239049 TTGTATCGATACATGACCAAATGTATCGATAC
1 TTGTATCGATACATGACCAAATGTATCGATAC
2239081 ATGACCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 13 0.43
34 3 0.10
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACG
Found at i:2239075 original size:20 final size:20
Alignment explanation
Indices: 2239050--2239102 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
2239040 ATCGATACGT
2239050 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
2239070 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
2239090 TGTATCGATACAT
1 TGTATCGATACAT
2239103 TGGCTTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:2242683 original size:23 final size:22
Alignment explanation
Indices: 2242669--2242716 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
2242659 TTAATGATAT
*
2242669 AAATTAATGTATTTTATTAATTA
1 AAATTAAT-TATTTTAATAATTA
2242692 AAATTAATTATTTTGAATAAATTA
1 AAATTAATTATTTT-AAT-AATTA
2242716 A
1 A
2242717 TTAGAGCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 10 0.45
24 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
AAATTAATTATTTTAATAATTA
Found at i:2249075 original size:23 final size:24
Alignment explanation
Indices: 2249049--2249095 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2249039 TTATCTAAGT
*
2249049 GAATAAAATTAATAATT-TAATTA
1 GAATAAAATTAAGAATTCTAATTA
* *
2249072 GAATTAGATTAAGAATTCTAATTA
1 GAATAAAATTAAGAATTCTAATTA
2249096 AACTCTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (24 bp):
GAATAAAATTAAGAATTCTAATTA
Found at i:2253331 original size:33 final size:33
Alignment explanation
Indices: 2253263--2253540 Score: 342
Period size: 33 Copynumber: 8.4 Consensus size: 33
2253253 CCAATTTAAC
* * * *
2253263 TTAAGTCCACAACTTCGTGGTATCTTTTTCTTT
1 TTAAGTCCACAACTCCGTGGCACCTTTTTCCTT
2253296 TTAAAGTCCACAACTCCGTGGCA-CTTTTTCCTT
1 TT-AAGTCCACAACTCCGTGGCACCTTTTTCCTT
* *
2253329 TTAAGTCCACGACTCCATGGCACCCTTTTTCCCTT
1 TTAAGTCCACAACTCCGTGGCA-CCTTTTT-CCTT
* * *
2253364 TTAAGCCCACACCTCCGTGGCACCTTGTTCCTT
1 TTAAGTCCACAACTCCGTGGCACCTTTTTCCTT
* * *
2253397 TTAAGTCCACAACTCTGTGGCATCTCTTTCCTT
1 TTAAGTCCACAACTCCGTGGCACCTTTTTCCTT
* *
2253430 TTAAGTCCACAACTTCGTGGCACCTTGTTCCTT
1 TTAAGTCCACAACTCCGTGGCACCTTTTTCCTT
* *
2253463 TTAAGTCCACAACTTCGTGGCACCTTGTTCCTT
1 TTAAGTCCACAACTCCGTGGCACCTTTTTCCTT
* * *
2253496 TTAAGTCCACAACTCCATGGCATCTTTCTCCTT
1 TTAAGTCCACAACTCCGTGGCACCTTTTTCCTT
*
2253529 TTAAGCCCACAA
1 TTAAGTCCACAA
2253541 GTCAGTGACA
Statistics
Matches: 214, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
32 18 0.08
33 144 0.67
34 30 0.14
35 22 0.10
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (33 bp):
TTAAGTCCACAACTCCGTGGCACCTTTTTCCTT
Found at i:2253579 original size:27 final size:30
Alignment explanation
Indices: 2253531--2253591 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
2253521 TTCTCCTTTT
*
2253531 AAGCCCACAAGTCAGTGACAA-CC-TTCAA
1 AAGCACACAAGTCAGTGACAACCCTTTCAA
*
2253559 AAGCACACAAGTTAGTG-CAACCCTTTCAA
1 AAGCACACAAGTCAGTGACAACCCTTTCAA
2253588 AAGC
1 AAGC
2253592 CCATACAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 3 0.10
28 17 0.59
29 9 0.31
ACGTcount: A:0.39, C:0.30, G:0.15, T:0.16
Consensus pattern (30 bp):
AAGCACACAAGTCAGTGACAACCCTTTCAA
Found at i:2253732 original size:39 final size:39
Alignment explanation
Indices: 2253667--2253830 Score: 175
Period size: 39 Copynumber: 4.0 Consensus size: 39
2253657 CCTTTATCTT
* *
2253667 TAAGACTAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
2253706 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
2253745 CCTTGTCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCA
1 ---------TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
2253793 TAAGACCAATATTGCTGGCCTTGAATCAGCATATTGGC
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGC
2253831 GCCTTGTCTC
Statistics
Matches: 106, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
39 71 0.67
48 35 0.33
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
Found at i:2253788 original size:87 final size:87
Alignment explanation
Indices: 2253618--2253878 Score: 423
Period size: 87 Copynumber: 3.0 Consensus size: 87
2253608 CGTCTTCTGC
* * * *
2253618 TAAGTCCAATATCGCTGGCCTAGAATCAGCATATTGGCACCTTTATCTTTAAGACTAATGTCGCT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGTCGCT
2253683 GGCCTTGAATCAGCACATTGGCA
65 GGCCTTGAATCAGCACATTGGCA
* *
2253706 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTTGCTG
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
2253771 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * *
2253793 TAAGACCAATATTGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCTCTAAGACCAATGTCGCTG
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
*
2253858 GCCTTGAATCAGCATATTGGC
66 GCCTTGAATCAGCACATTGGC
2253879 GCCTTCGTCA
Statistics
Matches: 162, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 123 0.76
88 39 0.24
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (87 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
GCCTTGAATCAGCACATTGGCA
Found at i:2253929 original size:52 final size:52
Alignment explanation
Indices: 2253806--2254377 Score: 681
Period size: 52 Copynumber: 11.3 Consensus size: 52
2253796 GACCAATATT
*
2253806 GCTGGCCTTGAATCAGCATATTGGCGCCTT-GTC-TC--TAAGACCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
*
2253854 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCTAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
* * * * *
2253906 GCTGGCCTTGAATCAGCACATT-G-G-CATCTTCATCTTTAAATCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
* *
2253955 GCTGGCATTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGTCCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
* * * * * * *
2254007 GCTGGCCTTGAATCAGCACATT---GTCATCTTCATATTTAAATCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
*
2254056 GCTGGCCTTAAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
* **** * *
2254108 GCTGGCCTTGAATCAGCACATTGGTATATT--T-ATCTTTAAATCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
* *
2254157 GCTGGCCTTGAATCAGCATATTGGCACATTCGTCATCTTTAAGTCCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
* * * * *
2254209 GTTGGCTTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
* *
2254258 GCTGGCCTTGAATCAGCATATTGACGCCTTCGTCATCTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
* **
2254310 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGCCATCTTTAAAACCCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTT-AAGTCCAATGTC
**
2254363 ATTGGCCTTGAATCA
1 GCTGGCCTTGAATCA
2254378 ACACATTGAC
Statistics
Matches: 445, Mismatches: 62, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
48 30 0.07
49 168 0.38
50 6 0.01
51 3 0.01
52 216 0.49
53 22 0.05
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (52 bp):
GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
Found at i:2253985 original size:101 final size:101
Alignment explanation
Indices: 2253806--2254496 Score: 850
Period size: 101 Copynumber: 6.8 Consensus size: 101
2253796 GACCAATATT
* ** * * *
2253806 GCTGGCCTTGAATCAGCATATTGGCGCCTT-GTCTCTAAGA-CCAATGTCGCTGGCCTTGAATCA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAA-ATCCAATATCGCTGGCCTTGAATCA
* *
2253869 GCATATTGGCGCCTTCGTCATCTTTAAGTCTAATGTC
65 GCATATTGGCACCTTCGTCATCTTTAAGTCCAATGTC
*
2253906 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAATCCAATATCGCTGGCATTGAATCAG
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAATCCAATATCGCTGGCCTTGAATCAG
2253971 CATATTGGCACCTTCGTCATCTTTAAGTCCAATGTC
66 CATATTGGCACCTTCGTCATCTTTAAGTCCAATGTC
* * *
2254007 GCTGGCCTTGAATCAGCACATTGTCATCTTCATATTTAAATCCAATATCGCTGGCCTTAAATCAG
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAATCCAATATCGCTGGCCTTGAATCAG
*
2254072 CATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTC
66 CATATTGGCACCTTCGTCATCTTTAAGTCCAATGTC
* * *
2254108 GCTGGCCTTGAATCAGCACATTGGTATATTTATCTTTAAATCCAATATCGCTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAATCCAATATCGCTGGCCTTGAATCAG
*
2254173 CATATTGGCACATTCGTCATCTTTAAGTCCAATGTC
66 CATATTGGCACCTTCGTCATCTTTAAGTCCAATGTC
* * * *
2254209 GTTGGCTTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAATCCAATATCGCTGGCCTTGAATCAG
* * *
2254274 CATATTGACGCCTTCGTCATCTTTAAGTCCAATATC
66 CATATTGGCACCTTCGTCATCTTTAAGTCCAATGTC
* ** * * **
2254310 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGCCATCTTTAAAACCCAATGTCATTGGCCTTGAA
1 GCTGGCCTTGAATCAGCACATTGGCATCTT---CATCTTT-AAATCCAATATCGCTGGCCTTGAA
* * * * * * *
2254375 TCAACACATTGACATTCTTC-TCATCTTCAAGACTAATGTC
62 TCAGCATATTGGCA-CCTTCGTCATCTTTAAGTCCAATGTC
* * * ** * * *
2254415 GCT-GACTGTGAATCAGCACATTGACATTCTTTACATCTCTAAGCCCAATATCACTGGTCATGAA
1 GCTGGCCT-TGAATCAGCACATTGGCA-TC-TT-CATCTTTAAATCCAATATCGCTGGCCTTGAA
2254479 TCAGCATATTGGCACCTT
62 TCAGCATATTGGCACCTT
2254497 TATCACTCTT
Statistics
Matches: 515, Mismatches: 66, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
100 28 0.05
101 367 0.71
103 3 0.01
104 40 0.08
105 70 0.14
106 5 0.01
107 2 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (101 bp):
GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAATCCAATATCGCTGGCCTTGAATCAG
CATATTGGCACCTTCGTCATCTTTAAGTCCAATGTC
Found at i:2254479 original size:157 final size:152
Alignment explanation
Indices: 2253794--2254496 Score: 538
Period size: 153 Copynumber: 4.6 Consensus size: 152
2253784 ACATTGGCAT
* * * * * * *
2253794 AAGACCAATATTGCTGGCCTTGAATCAGCATATTGGCGCCTT-G---TCTCTAAGACCAATGTCG
1 AAGACCAATATCGCTGGACTTGAATCAGCACATTGAC-CATTCGTCATCTCTAAGCCCAATATCG
* * ** * **
2253855 CTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCTAATGTCGCTGGCCTTGAATC
65 CTGGCCTTGAATCAGCATATTGGCACCTTCGCCATCTTTAAACCCAATGTCATTGGCCTTGAATC
* * * *
2253920 AGCACATTGGCATCTTCATCTTT
130 AACACATTGACACCTTCATCTTC
* * * *
2253943 AA-ATCCAATATCGCTGG-CATTGAATCAGCATATTGGCACC-TTCGTCATCTTTAAGTCCAATG
1 AAGA-CCAATATCGCTGGAC-TTGAATCAGCACATT-G-ACCATTCGTCATCTCTAAGCCCAATA
* * * * * * ** *
2254005 TCGCTGGCCTTGAATCAGCACATTGTCATCTT---CATATTTAAATCCAATATCGCTGGCCTTAA
62 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCGCCATCTTTAAACCCAATGTCATTGGCCTTGA
* * * * *
2254067 ATCAGCATATTGGCGCCTTCGTCATCTTT
127 ATCAACACATTGACACC-T--TCATCTTC
* * * * * **
2254096 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTA-TATT--T-ATCTTTAAATCCAATATC
1 AAGACCAATATCGCTGGACTTGAATCAGCACATT-G-ACCATTCGTCATCTCTAAGCCCAATATC
* * ** * *
2254157 GCTGGCCTTGAATCAGCATATTGGCACATTCGTCATCTTTAAGTCCAATGTCGTTGGCTTTGAAT
64 GCTGGCCTTGAATCAGCATATTGGCACCTTCGCCATCTTTAAACCCAATGTCATTGGCCTTGAAT
* * *
2254222 CAGCACATTGGCACCTTCATCTTT
129 CAACACATTGACACCTTCATCTTC
* * * * * *
2254246 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACGCCTTCGTCATCTTTAAGTCCAATATCG
1 AAGACCAATATCGCTGGACTTGAATCAGCACATTGAC-CATTCGTCATCTCTAAGCCCAATATCG
*
2254311 CTGGCCTTGAATCAGCATATTGGCGCCTTCGCCATCTTTAAAACCCAATGTCATTGGCCTTGAAT
65 CTGGCCTTGAATCAGCATATTGGCACCTTCGCCATCTTT-AAACCCAATGTCATTGGCCTTGAAT
*
2254376 CAACACATTGACATTCTTCTCATCTTC
129 CAACACATTGACA--CCT-TCATCTTC
* * *
2254403 AAGACTAATGTCGCT-GACTGTGAATCAGCACATTGA-CATTCTTTACATCTCTAAGCCCAATAT
1 AAGACCAATATCGCTGGACT-TGAATCAGCACATTGACCATTC-GT-CATCTCTAAGCCCAATAT
* * *
2254466 CACTGGTCATGAATCAGCATATTGGCACCTT
63 CGCTGGCCTTGAATCAGCATATTGGCACCTT
2254497 TATCACTCTT
Statistics
Matches: 461, Mismatches: 64, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
148 3 0.01
149 32 0.07
150 126 0.27
151 3 0.01
152 2 0.00
153 175 0.38
154 33 0.07
155 4 0.01
156 6 0.01
157 77 0.17
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (152 bp):
AAGACCAATATCGCTGGACTTGAATCAGCACATTGACCATTCGTCATCTCTAAGCCCAATATCGC
TGGCCTTGAATCAGCATATTGGCACCTTCGCCATCTTTAAACCCAATGTCATTGGCCTTGAATCA
ACACATTGACACCTTCATCTTC
Found at i:2255140 original size:32 final size:32
Alignment explanation
Indices: 2255099--2255176 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
2255089 ACAAACAGTA
*
2255099 AATGTATCGATACATAAGTTTTATATCGATAC
1 AATGTATCGATACATAAGTGTTATATCGATAC
*
2255131 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTATATCGATAC
*
2255163 AATGTATCGCTACA
1 AATGTATCGATACA
2255177 AACTACTGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTATATCGATAC
Found at i:2255157 original size:19 final size:18
Alignment explanation
Indices: 2255074--2255163 Score: 66
Period size: 19 Copynumber: 5.1 Consensus size: 18
2255064 TTGAATTTTA
2255074 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
2255091 AAACAGTAAATGTATCGATAC
1 ATA-AGT--TTGTATCGATAC
*
2255112 ATAAGTTTTATATCGATAC
1 ATAAG-TTTGTATCGATAC
2255131 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
2255144 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
2255163 A
1 A
2255164 ATGTATCGCT
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
13 10 0.18
15 2 0.04
17 4 0.07
18 1 0.02
19 23 0.41
20 2 0.04
21 14 0.25
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:2259962 original size:13 final size:13
Alignment explanation
Indices: 2259944--2259972 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2259934 CAATTCTTCA
2259944 TGTATCGATACAT
1 TGTATCGATACAT
2259957 TGTATCGATACAT
1 TGTATCGATACAT
2259970 TGT
1 TGT
2259973 GCCATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2260062 original size:19 final size:19
Alignment explanation
Indices: 2260019--2260071 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2260009 TGCTAGTTTT
* **
2260019 ATGTATCGATACATTTGTTC
1 ATGTATCGATACA-ATGAAC
2260039 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
2260058 ATGTATCGATACAA
1 ATGTATCGATACAA
2260072 AGCATAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:2260903 original size:18 final size:18
Alignment explanation
Indices: 2260882--2260922 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2260872 TACGACTACT
2260882 CCTAAAATTAAGACTAAA
1 CCTAAAATTAAGACTAAA
2260900 CCTAAAATTAAGACTAAA
1 CCTAAAATTAAGACTAAA
2260918 CCTAA
1 CCTAA
2260923 GACTCATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.54, C:0.20, G:0.05, T:0.22
Consensus pattern (18 bp):
CCTAAAATTAAGACTAAA
Found at i:2262572 original size:20 final size:20
Alignment explanation
Indices: 2262547--2262631 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
2262537 TAGTAACCCA
*
2262547 TGTATCAATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
2262567 TGTATCGATAC-----A-A-
1 TGTATCGATACAAAGAACAT
* *
2262580 TGTATTGATACAAAAAACAT
1 TGTATCGATACAAAGAACAT
2262600 TGTATCGATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
2262620 TGTATCGATACA
1 TGTATCGATACA
2262632 TCTGGGTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
13 10 0.19
14 1 0.02
15 1 0.02
18 1 0.02
19 1 0.02
20 40 0.74
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (20 bp):
TGTATCGATACAAAGAACAT
Found at i:2262658 original size:27 final size:26
Alignment explanation
Indices: 2262620--2262706 Score: 78
Period size: 27 Copynumber: 3.5 Consensus size: 26
2262610 CAAAGAACAT
2262620 TGTATCGATACATCTGGGTTTTCTAGA
1 TGTATCGATACATCT-GGTTTTCTAGA
***
2262647 TGTATCGATACAT-T-GAAAT-T---
1 TGTATCGATACATCTGGTTTTCTAGA
*
2262667 TGTATCGATACATCTAGGTTTTCCAGA
1 TGTATCGATACATCT-GGTTTTCTAGA
2262694 TGTATCGATACAT
1 TGTATCGATACAT
2262707 TGAAATATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
20 13 0.28
21 1 0.02
23 3 0.07
24 2 0.04
26 1 0.02
27 26 0.57
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (26 bp):
TGTATCGATACATCTGGTTTTCTAGA
Found at i:2262670 original size:47 final size:47
Alignment explanation
Indices: 2262600--2262731 Score: 194
Period size: 47 Copynumber: 2.8 Consensus size: 47
2262590 CAAAAAACAT
** *
2262600 TGTATCGATACAAAGAACA-TTGTATCGATACATCTGGGTTTTCTAGA
1 TGTATCGATACATTGAA-ATTTGTATCGATACATCTGGGTTTTCCAGA
*
2262647 TGTATCGATACATTGAAATTTGTATCGATACATCTAGGTTTTCCAGA
1 TGTATCGATACATTGAAATTTGTATCGATACATCTGGGTTTTCCAGA
*
2262694 TGTATCGATACATTGAAATATGTATCGATACATTCTGG
1 TGTATCGATACATTGAAATTTGTATCGATACA-TCTGG
2262732 AAAATTTCCA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.01
47 72 0.94
48 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (47 bp):
TGTATCGATACATTGAAATTTGTATCGATACATCTGGGTTTTCCAGA
Found at i:2267175 original size:3 final size:3
Alignment explanation
Indices: 2267167--2267200 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2267157 TCCGAGTCAA
* *
2267167 CAT CAT CAT CAT CAT CAT CAC CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
2267201 GTCTTTGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:2268830 original size:13 final size:13
Alignment explanation
Indices: 2268812--2268838 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2268802 CAATTCTTTA
2268812 TGTATCGATACAT
1 TGTATCGATACAT
2268825 TGTATCGATACAT
1 TGTATCGATACAT
2268838 T
1 T
2268839 ATGCCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2270687 original size:15 final size:15
Alignment explanation
Indices: 2270667--2270695 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2270657 CTAAATAATT
2270667 TTTTTATTTTTTAAG
1 TTTTTATTTTTTAAG
2270682 TTTTTATTTTTTAA
1 TTTTTATTTTTTAA
2270696 AAAAGCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTATTTTTTAAG
Found at i:2270864 original size:2 final size:2
Alignment explanation
Indices: 2270857--2270914 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
2270847 TATAAAAATT
*
2270857 TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA TC T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2270896 CTA AA TA TA AA AA TA TA TA
1 -TA TA TA TA TA TA TA TA TA
2270915 AAAAAATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2270865 original size:20 final size:20
Alignment explanation
Indices: 2270825--2270885 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
2270815 TATAACTTTA
* *
2270825 ATATATAAAACTTTTTA-AT
1 ATATATAAAAATTTATATAT
*
2270844 ATGTATAAAAATTTATATAT
1 ATATATAAAAATTTATATAT
* * *
2270864 ATATATATATATTAATATAT
1 ATATATAAAAATTTATATAT
2270884 AT
1 AT
2270886 CTTATATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATATAAAAATTTATATAT
Found at i:2270868 original size:18 final size:19
Alignment explanation
Indices: 2270825--2270870 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2270815 TATAACTTTA
* *
2270825 ATATATAAAACTTTTTAAT
1 ATATATAAAAATTTATAAT
*
2270844 ATGTATAAAAATTTATATAT
1 ATATATAAAAATTTATA-AT
2270864 ATATATA
1 ATATATA
2270871 TATATTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATATAAAAATTTATAAT
Found at i:2270915 original size:10 final size:10
Alignment explanation
Indices: 2270898--2270945 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
2270888 TATATATACT
2270898 AAATATAAAA
1 AAATATAAAA
*
2270908 ATATATAAAA
1 AAATATAAAA
*
2270918 AAATATTTAAA
1 AAATA-TAAAA
2270929 AAA-ATAAAA
1 AAATATAAAA
*
2270938 TAATATAA
1 AAATATAA
2270946 TATTGATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 6 0.19
10 18 0.58
11 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATATAAAA
Found at i:2270921 original size:12 final size:12
Alignment explanation
Indices: 2270904--2270934 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2270894 TACTAAATAT
2270904 AAAAATATATAA
1 AAAAATATATAA
*
2270916 AAAAATATTTAA
1 AAAAATATATAA
2270928 AAAAATA
1 AAAAATA
2270935 AAATAATATA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATATATAA
Done.