Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 109 of 172
Found at i:31370411 original size:20 final size:19
Alignment explanation
Indices: 31370386--31370431 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
31370376 AATTTTAAAT
**
31370386 TTTTTTTTCTAATTTTTAC
1 TTTTTTTTAGAATTTTTAC
*
31370405 TTATTTTTTAGAATTTTTCC
1 TT-TTTTTTAGAATTTTTAC
31370425 TTTTTTT
1 TTTTTTT
31370432 GGATTGATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTTTAGAATTTTTAC
Found at i:31385467 original size:14 final size:14
Alignment explanation
Indices: 31385429--31385467 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
31385419 TTCAAAAAAT
* *
31385429 AAATTATTTTCCAG
1 AAATTATTTTTCAA
31385443 AAATTATTTTTCAA
1 AAATTATTTTTCAA
31385457 AAATTATTTTT
1 AAATTATTTTT
31385468 AATCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (14 bp):
AAATTATTTTTCAA
Found at i:31390468 original size:44 final size:44
Alignment explanation
Indices: 31390418--31390506 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
31390408 CAATCTTTAG
31390418 CCAAAAGTTTAAAGCTTTAAGCCCTAAATTTCTTCTTTTTTCTT
1 CCAAAAGTTTAAAGCTTTAAGCCCTAAATTTCTTCTTTTTTCTT
31390462 CCAAAAGTTTAAAGCTTTAAGCCCTAAATTTCTTCTTTTTTCTT
1 CCAAAAGTTTAAAGCTTTAAGCCCTAAATTTCTTCTTTTTTCTT
31390506 C
1 C
31390507 GGTTGAAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.45
Consensus pattern (44 bp):
CCAAAAGTTTAAAGCTTTAAGCCCTAAATTTCTTCTTTTTTCTT
Found at i:31397995 original size:20 final size:20
Alignment explanation
Indices: 31397967--31398032 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
31397957 AAAAAAAAAG
*
31397967 AAATCCAAAATAATTTTTTA
1 AAATTCAAAATAATTTTTTA
* *
31397987 AAATTCAAAAT-ATTTATAA
1 AAATTCAAAATAATTTTTTA
31398006 AAATTCCAAAATTGATATTTTTTA
1 AAATT-CAAAA-T-A-ATTTTTTA
31398030 AAA
1 AAA
31398033 AATTATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 11 0.31
20 15 0.42
21 1 0.03
24 9 0.25
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATTCAAAATAATTTTTTA
Found at i:31399269 original size:21 final size:19
Alignment explanation
Indices: 31399223--31399269 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
31399213 TAAAATTTTT
31399223 ATAAATTTTTAATAATTGA
1 ATAAATTTTTAATAATTGA
*
31399242 ATCAATTAATTTAATAAATTG-
1 ATAAATT--TTTAAT-AATTGA
31399263 ATAAATT
1 ATAAATT
31399270 GACTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
21 12 0.52
22 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (19 bp):
ATAAATTTTTAATAATTGA
Found at i:31405892 original size:4 final size:4
Alignment explanation
Indices: 31405883--31405907 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31405873 AAACGATCTT
31405883 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
31405908 ATTTCAAATA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:31407800 original size:30 final size:31
Alignment explanation
Indices: 31407766--31407825 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
31407756 AAACCTTTTA
*
31407766 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
31407796 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
31407826 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:31408478 original size:5 final size:5
Alignment explanation
Indices: 31408468--31408519 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
31408458 GAACAAATAT
* *
31408468 ATTCG ATTCG ATTCG ATTCG ATTCG AATTCC ATCTC- ACTCG ATTCG ATTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG ATTCG
31408519 A
1 A
31408520 GAAAACTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.05
5 33 0.80
6 6 0.15
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (5 bp):
ATTCG
Found at i:31409178 original size:42 final size:42
Alignment explanation
Indices: 31409092--31409188 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
31409082 AGGTTGCAAG
* ***
31409092 TCAGTGAGTTACACGGCCTAACACAAGGGCGTGTGGGGCAAC
1 TCAGAGAGTTACACGGCCTAACACAAGGGCGTGTGACCCAAC
* ** * *
31409134 TCAGATAGTTACACGGCCTGGCACACGGGCGTGTGACCCTAC
1 TCAGAGAGTTACACGGCCTAACACAAGGGCGTGTGACCCAAC
31409176 TCAGAGAGTTACA
1 TCAGAGAGTTACA
31409189 TGGGTGAGGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.19
Consensus pattern (42 bp):
TCAGAGAGTTACACGGCCTAACACAAGGGCGTGTGACCCAAC
Found at i:31410264 original size:7 final size:7
Alignment explanation
Indices: 31410252--31410276 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31410242 ATCAATCTTA
31410252 CAAATAT
1 CAAATAT
31410259 CAAATAT
1 CAAATAT
31410266 CAAATAT
1 CAAATAT
31410273 CAAA
1 CAAA
31410277 GTCACACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (7 bp):
CAAATAT
Found at i:31413263 original size:20 final size:20
Alignment explanation
Indices: 31413212--31413250 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31413202 TACTTTGCTT
31413212 AAAGTATCGATATCTTTATC
1 AAAGTATCGATATCTTTATC
*
31413232 AAAGTGTCGATATCTTTAT
1 AAAGTATCGATATCTTTAT
31413251 TATGGTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
AAAGTATCGATATCTTTATC
Found at i:31421022 original size:13 final size:14
Alignment explanation
Indices: 31421006--31421035 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31420996 ATTTGAATCT
31421006 ATTAAA-AATTCAA
1 ATTAAATAATTCAA
31421019 ATTAAATAATTCAA
1 ATTAAATAATTCAA
31421033 ATT
1 ATT
31421036 TTTTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTAAATAATTCAA
Found at i:31438504 original size:11 final size:10
Alignment explanation
Indices: 31438487--31438520 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
31438477 TTATTTTAAA
31438487 ATTAAAAATT
1 ATTAAAAATT
31438497 ATTAAAAATAT
1 ATTAAAAAT-T
*
31438508 ATAAAAAATT
1 ATTAAAAATT
31438518 ATT
1 ATT
31438521 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:31446746 original size:16 final size:16
Alignment explanation
Indices: 31446725--31446760 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31446715 CTATTTGTAT
31446725 ATATTTATACACATAC
1 ATATTTATACACATAC
* *
31446741 ATATTTTTACACATAT
1 ATATTTATACACATAC
31446757 ATAT
1 ATAT
31446761 ACGTATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATTTATACACATAC
Found at i:31447902 original size:212 final size:207
Alignment explanation
Indices: 31447442--31447960 Score: 833
Period size: 212 Copynumber: 2.5 Consensus size: 207
31447432 TCATACTTTG
* * * *
31447442 AAGTTTTAAGAGGGTATTTGGCTATTTTGGTCGAACGAGAAATC-AAAGCCCAACACGTTAGGGC
1 AAGTTTAAAAAGGATATTTGGCTA-TTTGGTCGAACGAGAAATCGAAA-CCCAGCACGTTAGGGC
*
31447506 ACGTTCTCTCAAATTTCCAAACGCAAATATTGCCTCACTTTGAAATTTTAAAAGGATATTTGGCT
64 ACGTTTTCTCAAATTTCCAAACGCAAATATTGCCTCACTTTGAAATTTTAAAAGGATATTTGGCT
* *
31447571 ATTTGGTCAAACGAGAAGTCGAAACACGTTAGGGCACGTTTCCTCGATTTTCCAAACGCGAAATA
129 ATTTGGTCAAACAAGAAGTCGAAACACGTTAGGGCACGTTTCCTCGATTTTCCAAACGCAAAATA
31447636 TTGCCTTATTTTAA
194 TTGCCTTATTTTAA
31447650 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* *
31447715 ATTTTCTCAAATTTCTAAACGCAAATATTGCCTCACTTTGAAATTTTAAAAGGATATTTGGCTAT
66 GTTTTCTCAAATTTCCAAACGCAAATATTGCCTCACTTTGAAATTTTAAAAGGATATTTGGCTAT
*
31447780 TTGGTCAAACAAGAAGTCGAAACCCAACACGTTAGGGCACGTTTCCTCGATTTTTCAAACGCAAA
131 TTGGTCAAACAAGAAGTCG--A---AACACGTTAGGGCACGTTTCCTCGATTTTCCAAACGCAAA
31447845 ATATTGCCTTATTTTAA
191 ATATTGCCTTATTTTAA
* *
31447862 AAGTTTAAAAATGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* *
31447927 GTTTTCTCGATTTTCCAAACGCGAAATATTGCCT
66 GTTTTCTCAAATTTCCAAACGC-AAATATTGCCT
31447961 TATTTAGAAA
Statistics
Matches: 288, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
207 116 0.40
208 24 0.08
209 1 0.00
212 136 0.47
213 11 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (207 bp):
AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
GTTTTCTCAAATTTCCAAACGCAAATATTGCCTCACTTTGAAATTTTAAAAGGATATTTGGCTAT
TTGGTCAAACAAGAAGTCGAAACACGTTAGGGCACGTTTCCTCGATTTTCCAAACGCAAAATATT
GCCTTATTTTAA
Found at i:31447910 original size:107 final size:105
Alignment explanation
Indices: 31447456--31447965 Score: 665
Period size: 107 Copynumber: 4.8 Consensus size: 105
31447446 TTTAAGAGGG
* *
31447456 TATTTGGCTATTTTGGTCGAACGAGAAATC-AAAGCCCAACACGTTAGGGCACG-TTCTCTCAAA
1 TATTTGGCTA-TTTGGTCGAACGAGAAATCGAAA-CCCAACACGTTAGGGCACGTTTC-CTCGAT
* * * *
31447519 TTTCCAAACGCAAATATTGCCTCACTTTGAAATTTTAAAAGGA
63 TTTCCAAACGCAAATATTGCCTTATTTTAAAATTTAAAAAGGA
* *
31447562 TATTTGGCTATTTGGTCAAACGAGAAGTCG--A---AACACGTTAGGGCACGTTTCCTCGATTTT
1 TATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTCCTCGATTTT
31447622 CCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAGGA
66 CCAAACGC-AAATATTGCCTTATTTTAAAA-TTTAAAAAGGA
* * * * *
31447664 TATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCAAATTT
1 TATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTCCTCGATTTT
* * * * *
31447729 CTAAACGCAAATATTGCCTCACTTTGAAATTTTAAAAGGA
66 CCAAACGCAAATATTGCCTTATTTTAAAATTTAAAAAGGA
* * *
31447769 TATTTGGCTATTTGGTCAAACAAGAAGTCGAAACCCAACACGTTAGGGCACGTTTCCTCGATTTT
1 TATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTCCTCGATTTT
* *
31447834 TCAAACGCAAAATATTGCCTTATTTTAAAAGTTTAAAAATGA
66 CCAAACGC-AAATATTGCCTTATTTTAAAA-TTTAAAAAGGA
* * *
31447876 TATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGATTTT
1 TATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTCCTCGATTTT
31447941 CCAAACGCGAAATATTGCCTTATTT
66 CCAAACGC-AAATATTGCCTTATTT
31447966 AGAAAAACCT
Statistics
Matches: 350, Mismatches: 43, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
100 31 0.09
101 21 0.06
102 38 0.11
104 2 0.01
105 90 0.26
106 46 0.13
107 122 0.35
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (105 bp):
TATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTCCTCGATTTT
CCAAACGCAAATATTGCCTTATTTTAAAATTTAAAAAGGA
Found at i:31448435 original size:22 final size:23
Alignment explanation
Indices: 31448375--31448435 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
31448365 AAATTGTAAT
*
31448375 AATAT-AAGAATATATGTATGTG
1 AATATAAAGAATATATGTATGAG
* * *
31448397 AATTATAAAAAAAATAT-TTTGAG
1 AA-TATAAAGAATATATGTATGAG
31448420 AATATAAAGAATATAT
1 AATATAAAGAATATAT
31448436 ATAATGTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 14 0.45
23 9 0.29
24 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (23 bp):
AATATAAAGAATATATGTATGAG
Found at i:31448598 original size:7 final size:7
Alignment explanation
Indices: 31448580--31448619 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
31448570 ATATCTATGT
31448580 ATATGAAA
1 ATATG-AA
31448588 ATATGAA
1 ATATGAA
31448595 ATATGAA
1 ATATGAA
31448602 ATATGAA
1 ATATGAA
*
31448609 ATATAAA
1 ATATGAA
31448616 ATAT
1 ATAT
31448620 AAAAAGTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 26 0.84
8 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (7 bp):
ATATGAA
Found at i:31448744 original size:15 final size:15
Alignment explanation
Indices: 31448721--31448751 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31448711 ATTTTAACAT
31448721 AGATAATAATATATA
1 AGATAATAATATATA
*
31448736 AGATGATAATATATA
1 AGATAATAATATATA
31448751 A
1 A
31448752 ATTTAAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
AGATAATAATATATA
Found at i:31451283 original size:44 final size:45
Alignment explanation
Indices: 31450462--31451291 Score: 188
Period size: 44 Copynumber: 18.8 Consensus size: 45
31450452 AGAACTACTG
* * * * *
31450462 GCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCCACCA
1 GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGAGCTACCA
* * * * * * ***
31450507 TCTTCGATCTGCTCCAC--TACTGCTTAGGGAGATAAGATCTGTAA
1 GCTTCAATCTACTCCACTGTAGT-CTCAGGGAGATAAGAGCTACCA
* * * * * **
31450551 CCTTCAATCTATTCCACTGTTG-CCCAGGGAGATAA-AACTACTG
1 GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGAGCTACCA
* * * * * * * **
31450594 GTTTCAATGTACTCCGCTGTAATCTCAGGGAGGTAAAATCCGCCA
1 GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGAGCTACCA
* * * * * * ***
31450639 TCTTCGATCTGCTCCAC--TACTGCTTAGGGAGATAAGATCTGTAA
1 GCTTCAATCTACTCCACTGTAGT-CTCAGGGAGATAAGAGCTACCA
* * * * * ***
31450683 TCTTCAGTCTATTCTACTGCT-G-CCCAGGGAGAT-AGAGCTATTG
1 GCTTCAATCTACTCCACTG-TAGTCTCAGGGAGATAAGAGCTACCA
* * * * *
31450726 GCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTGCCA
1 GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGAGCTACCA
* * * * * * ***
31450771 TCTTCGATCTGCTCCAC--TACTGCTTAGGGAGATAAGATCTGTAA
1 GCTTCAATCTACTCCACTGTAGT-CTCAGGGAGATAAGAGCTACCA
* * * * **
31450815 TCTTCAGTCTATTCCACTGCT-G-CCCAGGGAGAT-AGAGCTACTG
1 GCTTCAATCTACTCCACTG-TAGTCTCAGGGAGATAAGAGCTACCA
* * * ** *
31450858 GCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAGATCCGCTA
1 GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGAGCTACCA
* * * * * * ***
31450903 TCTTCGATCTGCTCCAC--TACTACTTAGGGAGATAAGATCTGTAA
1 GCTTCAATCTACTCCACTGTAGT-CTCAGGGAGATAAGAGCTACCA
* * * * **
31450947 TCTTCAGTCTATTCCACTGCT-GCCT-AGGGAGAT-AGAGCTACTG
1 GCTTCAATCTACTCCACTG-TAGTCTCAGGGAGATAAGAGCTACCA
* * * * *
31450990 GCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTGCCA
1 GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGAGCTACCA
* * * * * * * ***
31451035 TCTTCGATCTGCTCCAC--TACTGCTTAAGGAGATAAGATCTGTAA
1 GCTTCAATCTACTCCACTGTAGT-CTCAGGGAGATAAGAGCTACCA
* * * * * **
31451079 TCTTCAGTCTATTCCAC--TACTGCCCAGGGAGAT-AGAGCTACTG
1 GCTTCAATCTACTCCACTGTAGT-CTCAGGGAGATAAGAGCTACCA
* * * * *
31451122 GCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTGCCA
1 GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGAGCTACCA
* * * * * * ***
31451167 TCTTCGATCTGCTCCAC--TACTGCTTAGGGAGATAAGATCTGTAA
1 GCTTCAATCTACTCCACTGTAGT-CTCAGGGAGATAAGAGCTACCA
* * * *
31451211 TCTTCAGTCTATTCCACTGCT-G-CCCAGGGAGAT-AGAGCTACCA
1 GCTTCAATCTACTCCACTG-TAGTCTCAGGGAGATAAGAGCTACCA
* *
31451254 GCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAGA
1 GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGA
31451292 TCTGTAACAC
Statistics
Matches: 545, Mismatches: 203, Indels: 74
0.66 0.25 0.09
Matches are distributed among these distances:
42 4 0.01
43 141 0.26
44 288 0.53
45 107 0.20
46 1 0.00
47 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (45 bp):
GCTTCAATCTACTCCACTGTAGTCTCAGGGAGATAAGAGCTACCA
Found at i:31451295 original size:132 final size:132
Alignment explanation
Indices: 31450375--31451295 Score: 1574
Period size: 132 Copynumber: 7.0 Consensus size: 132
31450365 AAGATTTGCT
* * * *
31450375 ATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTTCAC-GT
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
* * **
31450439 TGCCCAGTGAGATAGAACTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCCA
66 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
31450504 CC
131 CC
* * *
31450506 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAACCTTCAATCTATTCCACTGT
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
* * * * * *
31450571 TGCCCAGGGAGATAAAACTACTGGTTTCAATGTACTCCGCTGTAATCTCAGGGAGGTAAAATCCG
66 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
31450636 CC
131 CC
*
31450638 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCTACTGC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
*
31450703 TGCCCAGGGAGATAGAGCTATTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
66 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
31450768 CC
131 CC
31450770 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
* *
31450835 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAGATCCG
66 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
*
31450900 CT
131 CC
*
31450902 ATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
*
31450967 TGCCTAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
66 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
31451032 CC
131 CC
* *
31451034 ATCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTAC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
31451099 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
66 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
31451164 CC
131 CC
31451166 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
** *
31451231 TGCCCAGGGAGATAGAGCTACCAGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAGATCTG
66 TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
31451296 TAACACCCCT
Statistics
Matches: 750, Mismatches: 39, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
131 59 0.08
132 691 0.92
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (132 bp):
ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTATTCCACTGC
TGCCCAGGGAGATAGAGCTACTGGCTTCAATGTACTCCACTGTAGTCTCAGGGAGGTAAAATCTG
CC
Found at i:31453956 original size:32 final size:32
Alignment explanation
Indices: 31453915--31453978 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
31453905 TGCCTAGGGA
31453915 GATAGAGCTACTGGCTTCAATGTACTCCACTG
1 GATAGAGCTACTGGCTTCAATGTACTCCACTG
31453947 GATAGAGCTACTGGCTTCAATGTACTCCACTG
1 GATAGAGCTACTGGCTTCAATGTACTCCACTG
31453979 TAGTCTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (32 bp):
GATAGAGCTACTGGCTTCAATGTACTCCACTG
Found at i:31454128 original size:44 final size:45
Alignment explanation
Indices: 31454004--31454134 Score: 158
Period size: 45 Copynumber: 2.9 Consensus size: 45
31453994 AAAATCCGCC
* *
31454004 ATCTTCAATCTGCTTCGCTGTCAGTATAGGAAGGCAAGATCTGCT
1 ATCTTCGATCTGCTTCACTGTCAGTATAGGAAGGCAAGATCTGCT
* *
31454049 ATCTT-GAGTCTGCTCCACTGTCAGTATAGGAAGGCAAGA-CTGGT
1 ATCTTCGA-TCTGCTTCACTGTCAGTATAGGAAGGCAAGATCTGCT
* * * * *
31454093 GTCTTCGATCCGCTTCACTGCCAGTGTAAGAAGGCAAGATCT
1 ATCTTCGATCTGCTTCACTGTCAGTATAGGAAGGCAAGATCT
31454135 ACAACTTCAT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 35 0.48
45 38 0.52
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.28
Consensus pattern (45 bp):
ATCTTCGATCTGCTTCACTGTCAGTATAGGAAGGCAAGATCTGCT
Found at i:31471167 original size:43 final size:43
Alignment explanation
Indices: 31471049--31471167 Score: 103
Period size: 44 Copynumber: 2.7 Consensus size: 43
31471039 GAAACCATAA
* * * * *
31471049 AGCCTTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAGC
1 AGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGATCAAAAATACC
* * *** * * *
31471092 AGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAATATACC
1 AG-CCTTGTCTCCCTG-AGCAGCAGTGGAGTAGATCAAAAATACC
31471137 AGCCTTGTCTCCCTGAGCAGCAGTGGAGTAG
1 AGCCTTGTCTCCCTGAGCAGCAGTGGAGTAG
31471168 GTTGAAAATA
Statistics
Matches: 55, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
43 14 0.25
44 21 0.38
45 20 0.36
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (43 bp):
AGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGATCAAAAATACC
Found at i:31471215 original size:88 final size:88
Alignment explanation
Indices: 31471049--31471233 Score: 262
Period size: 88 Copynumber: 2.1 Consensus size: 88
31471039 GAAACCATAA
* *
31471049 AGCCTTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACTGG
* **
31471114 CAGTGAAGTAGATCGAATATACC
66 CAGCGAAACAGATCGAATATACC
* * *
31471137 AGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGG
1 AGCCTTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACTGG
* * *
31471202 TAGCGAAACAGATCGAAGACACC
66 CAGCGAAACAGATCGAATATACC
*
31471225 AGTCTTATC
1 AGCCTTATC
31471234 GCCTTGACGT
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (88 bp):
AGCCTTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACTGG
CAGCGAAACAGATCGAATATACC
Found at i:31471419 original size:50 final size:50
Alignment explanation
Indices: 31471362--31471524 Score: 155
Period size: 50 Copynumber: 3.3 Consensus size: 50
31471352 ATTACAGTTA
*
31471362 AACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGG
1 AACAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGG
* * ** *** ** * * **
31471412 AACAGATTGAAGCTACGACGACGAATCTTGTTTCCCCAACATTGCAATTA
1 AACAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGG
* * * *
31471462 AATAGATTGAAGCGACAACGATGAATCTTACTTCCTTGGCGGTGTAGTGG
1 AACAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGG
*
31471512 AATAGATTGAAGC
1 AACAGATTGAAGC
31471525 TACGAAGGCA
Statistics
Matches: 83, Mismatches: 30, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (50 bp):
AACAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGG
Found at i:31471480 original size:100 final size:100
Alignment explanation
Indices: 31471359--31471573 Score: 322
Period size: 100 Copynumber: 2.1 Consensus size: 100
31471349 GGCATTACAG
*
31471359 TTAAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAG
1 TTAAACAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAG
* *
31471424 CTACGACGACGAATCTTGTTTCCCCAACATTGCAA
66 CTACGAAGACAAATCTTGTTTCCCCAACATTGCAA
* * * * *
31471459 TTAAATAGATTGAAGCGACAACGATGAATCTTACTTCCTTGGCGGTGTAGTGGAATAGATTGAAG
1 TTAAACAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAG
* * *
31471524 CTACGAAGGCAAATCTTGTTTCCCCGACATTGCAG
66 CTACGAAGACAAATCTTGTTTCCCCAACATTGCAA
*
31471559 TTAAACAGACTGAAG
1 TTAAACAGATTGAAG
31471574 ATCGCATCCA
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (100 bp):
TTAAACAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAG
CTACGAAGACAAATCTTGTTTCCCCAACATTGCAA
Found at i:31471788 original size:85 final size:85
Alignment explanation
Indices: 31471624--31471781 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
31471614 ACAGAAGAAA
* * * *
31471624 CTAATCCTATTTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGT
1 CTAATCCTATCTCCCTGAAGCTGCAGTAGAGCGGATTAAAACCACAAATCCTATCTCTCTGAAGT
31471689 TGCAGTAGAGCAGATCGTAT
66 TGCAGTAGAGCAGATCGTAT
* * ** *
31471709 CTAATCCTATCTCCCTGAAGCTGTAGTGGAGCGGATTAAAATGACAAATCCTATAC-CTCTTAAG
1 CTAATCCTATCTCCCTGAAGCTGCAGTAGAGCGGATTAAAACCACAAATCCTAT-CTCTCTGAAG
31471773 TTGCAGTAG
65 TTGCAGTAG
31471782 GTCAGATTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 62 0.98
86 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (85 bp):
CTAATCCTATCTCCCTGAAGCTGCAGTAGAGCGGATTAAAACCACAAATCCTATCTCTCTGAAGT
TGCAGTAGAGCAGATCGTAT
Found at i:31473339 original size:6 final size:6
Alignment explanation
Indices: 31473328--31473358 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
31473318 TATTTTATGT
31473328 ACATAC ACATAC ACATAC ACATAC ACATAC A
1 ACATAC ACATAC ACATAC ACATAC ACATAC A
31473359 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ACATAC
Found at i:31474469 original size:18 final size:19
Alignment explanation
Indices: 31474433--31474470 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
31474423 TTAAAGCTTT
*
31474433 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTATTATAC
31474452 ATTTTAAT-TTTATTATAC
1 ATTTTAATATTTATTATAC
31474470 A
1 A
31474471 CATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATATTTATTATAC
Found at i:31474475 original size:20 final size:19
Alignment explanation
Indices: 31474433--31474477 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
31474423 TTAAAGCTTT
*
31474433 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTTTTACAC
31474452 ATTTTAAT-TTTATTATACAC
1 ATTTTAATATTT-TT-TACAC
31474472 ATTTTA
1 ATTTTA
31474478 TTACCTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 10 0.43
20 10 0.43
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTAATATTTTTTACAC
Found at i:31476934 original size:21 final size:21
Alignment explanation
Indices: 31476908--31476947 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
31476898 AATAAAAAAT
31476908 ATAAAAAATAT-TAAATATTAA
1 ATAAAAAATATAT-AATATTAA
31476929 ATAAAAAATATATAATATT
1 ATAAAAAATATATAATATT
31476948 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAAAATATATAATATTAA
Found at i:31478258 original size:3 final size:3
Alignment explanation
Indices: 31478250--31478279 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31478240 AATCACCATC
31478250 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31478280 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31479749 original size:21 final size:21
Alignment explanation
Indices: 31479725--31479766 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
31479715 TAGTATTCGA
31479725 TGTATGAGGTTGGACAATGCC
1 TGTATGAGGTTGGACAATGCC
31479746 TGTATGAGGTTGGACAATGCC
1 TGTATGAGGTTGGACAATGCC
31479767 AAAGGGTAGG
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:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (21 bp):
TGTATGAGGTTGGACAATGCC
Found at i:31484220 original size:17 final size:17
Alignment explanation
Indices: 31484192--31484265 Score: 69
Period size: 17 Copynumber: 4.1 Consensus size: 17
31484182 TTTTTAAAAA
31484192 AATTTT-AAATTTTTTT
1 AATTTTAAAATTTTTTT
31484208 AATTTTAAAATTTTTTT
1 AATTTTAAAATTTTTTT
**
31484225 AAAATACTTTTTTAATTTTTTT
1 ---A-A-TTTTAAAATTTTTTT
*
31484247 AATTTTAAAATATTTTT
1 AATTTTAAAATTTTTTT
31484264 AA
1 AA
31484266 AATACTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
16 6 0.13
17 24 0.51
18 1 0.02
19 1 0.02
20 1 0.02
21 1 0.02
22 13 0.28
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTAAAATTTTTTT
Found at i:31484226 original size:11 final size:11
Alignment explanation
Indices: 31484210--31484284 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 11
31484200 ATTTTTTTAA
31484210 TTTTAAAATTT
1 TTTTAAAATTT
31484221 TTTTAAAATACTT
1 TTTTAAAAT--TT
31484234 TTTT--AATTT
1 TTTTAAAATTT
31484243 TTTT--AA---
1 TTTTAAAATTT
*
31484249 TTTTAAAATAT
1 TTTTAAAATTT
*
31484260 TTTTAAAATACT
1 TTTTAAAAT-TT
31484272 TTTTAAAATTT
1 TTTTAAAATTT
31484283 TT
1 TT
31484285 ATTTTAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
6 4 0.07
8 2 0.04
9 8 0.15
11 24 0.44
12 10 0.19
13 6 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:31484274 original size:28 final size:28
Alignment explanation
Indices: 31484221--31484274 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
31484211 TTTAAAATTT
* **
31484221 TTTTAAAATACTTTTTTAATTTTTTTAA
1 TTTTAAAATACTTTTTAAATACTTTTAA
31484249 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTT-AAATACTTTT
31484275 TAAAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAATACTTTTAA
Found at i:31484282 original size:40 final size:39
Alignment explanation
Indices: 31484159--31484291 Score: 173
Period size: 39 Copynumber: 3.4 Consensus size: 39
31484149 AAATATTTTT
**
31484159 ATTTTTTTAATTTTAAAATACTTTTTTTAAAA-AAATTTTAA
1 ATTTTTTTAATTTTAAAATA---TTTTTAAAATACTTTTTAA
* *
31484200 ATTTTTTTAATTTTAAAATTTTTTTAAAATACTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
31484239 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
*
31484278 A-ATTTTT-ATTTTAA
1 ATTTTTTTAATTTTAA
31484292 TTTTTAAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
37 7 0.08
38 14 0.17
39 44 0.52
41 19 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
Found at i:31484295 original size:21 final size:21
Alignment explanation
Indices: 31484243--31484301 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
31484233 TTTTTAATTT
*
31484243 TTTTAATTTTAAAATATTTTTA
1 TTTTAATTTTTAAA-ATTTTTA
*** *
31484265 AAATACTTTTTAAAATTTTTA
1 TTTTAATTTTTAAAATTTTTA
31484286 TTTTAATTTTTAAAAT
1 TTTTAATTTTTAAAAT
31484302 GAATTTTTGG
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAATTTTTAAAATTTTTA
Found at i:31492366 original size:197 final size:197
Alignment explanation
Indices: 31492006--31492395 Score: 503
Period size: 197 Copynumber: 2.0 Consensus size: 197
31491996 AAAAAGAAAA
* ** *
31492006 AGAAGGAGGTATAAGAGGACGTCACGTGGCAGTGTGCGATTGGCCTGCATTGCCACGTTAACAAA
1 AGAAGGAGGTATAAGAGGACGTCACGTGGCAGCGTGCGATTGGCCAACATTGCCACGTCAACAAA
*
31492071 AAATTAACGTCCTTAGTCTCAGGTATCAATATAGTGGACAAAAAAAAATTCGGGTACCAATCTGG
66 AAATTAACGTCCTTAGTCTCAGGTATCAATATAGTGGACAAAAAAAAATTCGGATACCAATCTGG
*
31492136 AACAAAAAAAAAACCATAAACATCAAATTGGGAGAAGTGGACAAATCCAGGTACCAATTTTATTA
131 AACAAAAAAAAAACCATAAACATCAAATTGGGAGAAGTGAACAAATCCAGGTACCAATTTTATTA
31492201 GG
196 GG
* * * * * *
31492203 AGAATGAGGTATAAGAGGATGTCATGTGGCGGCGTGCGATTGGCCAACATTGTCACGTCAGCAAA
1 AGAAGGAGGTATAAGAGGACGTCACGTGGCAGCGTGCGATTGGCCAACATTGCCACGTCAACAAA
* ** * * * *
31492268 AAATTAATGTTGTTAGTCTTAGGTATCAATATAGTGGATAGAAAAAAAGTTCGGATACTAATCTG
66 AAATTAACGTCCTTAGTCTCAGGTATCAATATAGTGGACA-AAAAAAAATTCGGATACCAATCTG
* *** ** * * * *
31492333 GGAC-AAAAAAAAATTTTAAGTATCAATTTGGGAGAAGTGAACAAATTCGGGTACTAATTTTAT
130 GAACAAAAAAAAAACCATAAACATCAAATTGGGAGAAGTGAACAAATCCAGGTACCAATTTTAT
31492396 ATTTAATCCT
Statistics
Matches: 163, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
197 139 0.85
198 24 0.15
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (197 bp):
AGAAGGAGGTATAAGAGGACGTCACGTGGCAGCGTGCGATTGGCCAACATTGCCACGTCAACAAA
AAATTAACGTCCTTAGTCTCAGGTATCAATATAGTGGACAAAAAAAAATTCGGATACCAATCTGG
AACAAAAAAAAAACCATAAACATCAAATTGGGAGAAGTGAACAAATCCAGGTACCAATTTTATTA
GG
Found at i:31496626 original size:32 final size:31
Alignment explanation
Indices: 31496548--31496626 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
31496538 GTTTGCCCCC
* *
31496548 TGAACTTGTCCAAAAGTATTTAGTTAGTACT
1 TGAACTTGTCAAAAAGTACTTAGTTAGTACT
* * * *
31496579 TGAATTTATCCAAAAAGTACTTAGTTGGTGCT
1 TGAACTTGT-CAAAAAGTACTTAGTTAGTACT
31496611 TGAACTTGTCTAAAAA
1 TGAACTTGTC-AAAAA
31496627 ATTATACTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
31 8 0.21
32 30 0.79
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (31 bp):
TGAACTTGTCAAAAAGTACTTAGTTAGTACT
Found at i:31496677 original size:20 final size:21
Alignment explanation
Indices: 31496634--31496680 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
31496624 AAAATTATAC
31496634 TTTTTAAAATTAATTTAATAT
1 TTTTTAAAATTAATTTAATAT
* *
31496655 TTTTTAAAA-TATTTTTA-AT
1 TTTTTAAAATTAATTTAATAT
31496674 TTTTTAA
1 TTTTTAA
31496681 TTTATATCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.38
20 6 0.25
21 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTAAAATTAATTTAATAT
Found at i:31503968 original size:317 final size:317
Alignment explanation
Indices: 31503333--31504010 Score: 886
Period size: 317 Copynumber: 2.1 Consensus size: 317
31503323 CAACGGTTTT
* *
31503333 CTAATAGGG-AGGCTTTATGCTTATTGGATAATTGTGGCATTGCCGATGTTGTCCATTTAGGTTG
1 CTAATAGGGCA-GCTTTATGCTTATTCGATAATTGTGGCATTGCCGATGTTGTCCATTTAGGTTC
* **
31503397 TTACATTTTATTAAAGAGAGAACATATATTCAGTAATGGAGTCCTTCTGTGGTGGGGGAAGGGCA
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCCATGGTGGGGGAAGGGCA
* * * *
31503462 AGGGCAGTCTACTCGTTGTCAGGTTGCAATAAGAAATGGAAACTAGTCATTGGAGGGAACACAAG
130 AGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGGAAACTAGTCATTGGAGGGAACACAAG
* * * * *
31503527 GCTAGAGGAGAGTGGCTCTGCATAAGAGCCTTACTCTATAGGGTCATTAGAGTGCTGCAGCTAGC
195 GCTAGAGGAGAGTGGCTCCGCATAAGAGCCTTACTCTACAGGGACATTAGAGTGCTACAACTAGC
* *
31503592 ACTTTGAAGCCCGCTGAAAAACCGATGTGCTCTACTAGCGCAATGGTTTGAACCTTTG
260 ACTTTGAAGCCAGCTGAAAAACCGATGTGCTCTACTAGCGCAATGGTTTCAACCTTTG
* * * * *
31503650 CTGATAGGGCAGCTTAATGCTTATTCAATAATTGTGGTATTGCCGGGAT-TT-TCTATTTAGGTT
1 CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCC--GATGTTGTCCATTTAGGTT
31503713 CTTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCCATGGTGGGGGAAGGGC
64 CTTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCCATGGTGGGGGAAGGGC
* ** * *
31503778 AAGGTCAG-C-A-TCCTTGTTGGGTTGAAACAAGAAACGGAAACTAGTCGTTGGAGGGAACACGA
129 AAGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGGAAACTAGTCATTGGAGGGAACACAA
* * * * *
31503840 GGCTTGTGGA-ATGTGGTTCCGCATAAGAGCCTTACTCTACAGGGACGTTAGTGTGCTACAACTA
194 GGCTAGAGGAGA-GTGGCTCCGCATAAGAGCCTTACTCTACAGGGACATTAGAGTGCTACAACTA
* * ** *
31503904 GCACTTTGAAGCCAGCTGAAAAACTGATGCTTGCTATTGGT-GCGCAATGGTTTTCAAGCTTTG
258 GCACTTTGAAGCCAGCTGAAAAACCGATG--TGCT-CTACTAGCGCAATGG-TTTCAACCTTTG
* *
31503967 CTAATAGGGCAGCTTTATGCTTATTTGATAATTGTGCCATTGCC
1 CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCC
31504011 AGCATTTTCC
Statistics
Matches: 311, Mismatches: 42, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
313 1 0.00
314 123 0.40
315 1 0.00
316 14 0.05
317 166 0.53
318 3 0.01
319 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (317 bp):
CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCGATGTTGTCCATTTAGGTTCT
TACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCCATGGTGGGGGAAGGGCAA
GGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGGAAACTAGTCATTGGAGGGAACACAAGG
CTAGAGGAGAGTGGCTCCGCATAAGAGCCTTACTCTACAGGGACATTAGAGTGCTACAACTAGCA
CTTTGAAGCCAGCTGAAAAACCGATGTGCTCTACTAGCGCAATGGTTTCAACCTTTG
Found at i:31505647 original size:14 final size:14
Alignment explanation
Indices: 31505625--31505672 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
31505615 TAAGTTATGG
*
31505625 ATTTAATTTTTTAT
1 ATTTTATTTTTTAT
* *
31505639 ATTTTATTTTGATCT
1 ATTTTATTTT-TTAT
*
31505654 ATTTTAGTTTTTAT
1 ATTTTATTTTTTAT
31505668 ATTTT
1 ATTTT
31505673 TTGAATTGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (14 bp):
ATTTTATTTTTTAT
Found at i:31509419 original size:27 final size:27
Alignment explanation
Indices: 31509389--31509449 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
31509379 GACCAATCAC
*
31509389 ATTGGCGGCACC-AAAGGTGCCAAAGTG
1 ATTGGCGG-ACCAAAAGGTGCCAAAGAG
* *
31509416 ATTGGCCTGACCAAAAGGTGTCAAAGAG
1 ATTGG-CGGACCAAAAGGTGCCAAAGAG
31509444 ATTGGC
1 ATTGGC
31509450 CTAACTGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (27 bp):
ATTGGCGGACCAAAAGGTGCCAAAGAG
Found at i:31509888 original size:27 final size:26
Alignment explanation
Indices: 31509835--31509895 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
31509825 TGTTTTTGGT
* ***
31509835 ATATTTTGGTAAATAAAAAATTTATA
1 ATATTTTGATAAATAAAAAAAAGATA
31509861 ATATTTTGATAAATAAAAAAAAAGATA
1 ATATTTTGATAAAT-AAAAAAAAGATA
*
31509888 ACATTTTG
1 ATATTTTG
31509896 GTTATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (26 bp):
ATATTTTGATAAATAAAAAAAAGATA
Found at i:31515360 original size:17 final size:19
Alignment explanation
Indices: 31515325--31515363 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
31515315 AGTAAAAAGA
*
31515325 TAAAAATACTTTTATATTT
1 TAAAAATACTTTTAAATTT
31515344 TAAAAA-AC-TTTAAATTT
1 TAAAAATACTTTTAAATTT
31515361 TAA
1 TAA
31515364 TATATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAAATACTTTTAAATTT
Found at i:31517934 original size:14 final size:13
Alignment explanation
Indices: 31517915--31517954 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
31517905 TTGATTGCCA
31517915 GTAAAATGTTTTT
1 GTAAAATGTTTTT
31517928 CGTAAAATGATTTTT
1 -GTAAAATG-TTTTT
*
31517943 GGAAAATGTTTT
1 GTAAAATGTTTT
31517955 ACTTTTCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 15 0.62
15 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (13 bp):
GTAAAATGTTTTT
Found at i:31517967 original size:34 final size:34
Alignment explanation
Indices: 31517924--31517989 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
31517914 AGTAAAATGT
* * *
31517924 TTTTCGTAAAATGATTT-TTGGAAAATGTTTTAC
1 TTTTCGTAAAATAATTTACTGGAAAATATTTTAC
31517957 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATAATTTACTGGAAAATATTTT
31517990 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (34 bp):
TTTTCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:31518397 original size:13 final size:13
Alignment explanation
Indices: 31518379--31518406 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31518369 ATTCTTTCTC
31518379 TATTTATGAAGTT
1 TATTTATGAAGTT
31518392 TATTTATGAAGTT
1 TATTTATGAAGTT
31518405 TA
1 TA
31518407 CTTGTACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (13 bp):
TATTTATGAAGTT
Found at i:31530627 original size:31 final size:32
Alignment explanation
Indices: 31530581--31530644 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
31530571 GAATATATAA
31530581 TAAATATATTTTTTTAATTTTAAAAT-ATTTT
1 TAAATATATTTTTTTAATTTTAAAATAATTTT
*
31530612 TAAA-ATACTTTTTTTATTTTTAAAATAATTTT
1 TAAATATA-TTTTTTTAATTTTAAAATAATTTT
31530644 T
1 T
31530645 TGGTGTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 3 0.10
31 21 0.70
32 6 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (32 bp):
TAAATATATTTTTTTAATTTTAAAATAATTTT
Found at i:31530629 original size:20 final size:20
Alignment explanation
Indices: 31530606--31530645 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31530596 AATTTTAAAA
*
31530606 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTT
31530626 TATTTTTAAAATAATTTTTT
1 TATTTTTAAAATAATTTTTT
31530646 GGTGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTT
Found at i:31530653 original size:20 final size:20
Alignment explanation
Indices: 31530610--31530653 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
31530600 TTAAAATATT
* * *
31530610 TTTAAAATACTTTTTTTATT
1 TTTAAAATAATTTTTTGATG
*
31530630 TTTAAAATAATTTTTTGGTG
1 TTTAAAATAATTTTTTGATG
31530650 TTTA
1 TTTA
31530654 TTAAAAAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTAAAATAATTTTTTGATG
Found at i:31534466 original size:33 final size:32
Alignment explanation
Indices: 31534384--31534503 Score: 138
Period size: 32 Copynumber: 3.8 Consensus size: 32
31534374 AAACGCGTGG
31534384 TTTTGTGAAATGATAACAAATATCAACTTTC-A
1 TTTTGTGAAATGATAACAAATATCAAC-TTCAA
**
31534416 TTTTGTGAAATTCTAACAAAT-TACAACTTCAA
1 TTTTGTGAAATGATAACAAATAT-CAACTTCAA
* *
31534448 TTTTTGTAAAATGATAACAAATATCAACTTTAA
1 -TTTTGTGAAATGATAACAAATATCAACTTCAA
* *
31534481 TTTTGTTAAATGATGAC-AATATC
1 TTTTGTGAAATGATAACAAATATC
31534504 CCTCTAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
31 10 0.13
32 39 0.51
33 26 0.34
34 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (32 bp):
TTTTGTGAAATGATAACAAATATCAACTTCAA
Found at i:31535322 original size:32 final size:32
Alignment explanation
Indices: 31535281--31535345 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
31535271 GGATCCTAAA
31535281 CCATGACATGTACTCCGGATCACATGCTAACT
1 CCATGACATGTACTCCGGATCACATGCTAACT
*
31535313 CCATGACATGTACTCTGGATCACATGCTAACT
1 CCATGACATGTACTCCGGATCACATGCTAACT
31535345 C
1 C
31535346 TGGAACGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (32 bp):
CCATGACATGTACTCCGGATCACATGCTAACT
Found at i:31535347 original size:18 final size:18
Alignment explanation
Indices: 31535292--31535349 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 18
31535282 CATGACATGT
*
31535292 ACTCCGGATCACATGCTA
1 ACTCTGGATCACATGCTA
* *
31535310 ACTC--CATGACATG-T-
1 ACTCTGGATCACATGCTA
31535324 ACTCTGGATCACATGCTA
1 ACTCTGGATCACATGCTA
31535342 ACTCTGGA
1 ACTCTGGA
31535350 ACGATAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 4 0.12
15 1 0.03
16 14 0.44
17 1 0.03
18 12 0.38
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (18 bp):
ACTCTGGATCACATGCTA
Found at i:31536905 original size:11 final size:11
Alignment explanation
Indices: 31536882--31536940 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
31536872 ATAAATTTAA
31536882 GAGAGAA-TTT
1 GAGAGAATTTT
31536892 GAGAGAATTTT
1 GAGAGAATTTT
***
31536903 GAGAGTGGTTT
1 GAGAGAATTTT
31536914 --GAGAATTTT
1 GAGAGAATTTT
*
31536923 GAGAGAATATT
1 GAGAGAATTTT
*
31536934 GTGAGAA
1 GAGAGAA
31536941 ATGAGTAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
9 6 0.16
10 7 0.18
11 25 0.66
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (11 bp):
GAGAGAATTTT
Found at i:31540766 original size:37 final size:37
Alignment explanation
Indices: 31540725--31540801 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
31540715 AATCCAAAAA
* *
31540725 TAATA-TTATTTTCATAATTTTAATATTAAATTTAAT-T
1 TAATACTTATCTTCATAATATT-ATATT-AATTTAATAT
* *
31540762 TAATACTTATCTTGATAGTATTATATTAATTTAATAT
1 TAATACTTATCTTCATAATATTATATTAATTTAATAT
31540799 TAA
1 TAA
31540802 AGTGATTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
36 8 0.24
37 14 0.41
38 12 0.35
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (37 bp):
TAATACTTATCTTCATAATATTATATTAATTTAATAT
Found at i:31550179 original size:31 final size:31
Alignment explanation
Indices: 31550131--31550199 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
31550121 AATTAAAAGG
*
31550131 TGAA-AGATCGATCGAATAAACAAATGGATA
1 TGAATAGATCAATCGAATAAACAAATGGATA
* *
31550161 TGAATAGATCAATTGAATAAATAAATGGATA
1 TGAATAGATCAATCGAATAAACAAATGGATA
31550192 TGAATAGA
1 TGAATAGA
31550200 AGATAACCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.25
Consensus pattern (31 bp):
TGAATAGATCAATCGAATAAACAAATGGATA
Found at i:31551883 original size:15 final size:16
Alignment explanation
Indices: 31551856--31551885 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31551846 ATATAAAAGT
31551856 AAAAAAATAGAAAATA
1 AAAAAAATAGAAAATA
31551872 AAAAAAAT-GAAAAT
1 AAAAAAATAGAAAAT
31551886 GTATGTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAAAAATAGAAAATA
Found at i:31552183 original size:3 final size:3
Alignment explanation
Indices: 31552155--31552224 Score: 58
Period size: 3 Copynumber: 24.3 Consensus size: 3
31552145 AATGCGGCAG
* * * **
31552155 TAA TAA TGA TAG TAA GTAA T-A TAA TAA TAC TAA TAA TGG T-A TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31552199 TAA TAA TAA -AA TAA TAA TAA -AA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
31552225 TGAAAAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 7 0.13
3 43 0.81
4 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31552211 original size:11 final size:11
Alignment explanation
Indices: 31552197--31552224 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31552187 ATAATGGTAT
31552197 AATAATAATAA
1 AATAATAATAA
31552208 AATAATAATAA
1 AATAATAATAA
31552219 AATAAT
1 AATAAT
31552225 TGAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:31558021 original size:10 final size:11
Alignment explanation
Indices: 31557996--31558022 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31557986 TTTTTAATGA
31557996 AAAAATAAATT
1 AAAAATAAATT
31558007 AAAAATAAATT
1 AAAAATAAATT
31558018 AAAAA
1 AAAAA
31558023 AAGAATAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAATAAATT
Found at i:31558175 original size:15 final size:14
Alignment explanation
Indices: 31558155--31558187 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
31558145 ATATTAGAGA
31558155 AAAATAAAAATAAC
1 AAAATAAAAATAAC
31558169 TAAAATAAAAATAAC
1 -AAAATAAAAATAAC
31558184 AAAA
1 AAAA
31558188 CTATCTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATAAAAATAAC
Found at i:31561692 original size:4 final size:4
Alignment explanation
Indices: 31561683--31561710 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31561673 TATACATATG
31561683 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
31561711 TATTCAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:31563724 original size:23 final size:27
Alignment explanation
Indices: 31563675--31563727 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
31563665 TATATGATAT
31563675 AAATAATATAATATATAAACCAAATGAA
1 AAATAATATAATATATAAACC-AATGAA
31563703 AAATAATAT-AT-TATAAA-C-ATGAA
1 AAATAATATAATATATAAACCAATGAA
31563726 AA
1 AA
31563728 CAAGTCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.28
25 1 0.04
26 6 0.24
27 2 0.08
28 9 0.36
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
AAATAATATAATATATAAACCAATGAA
Found at i:31566342 original size:24 final size:26
Alignment explanation
Indices: 31566315--31566362 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
31566305 TTATAAAGCG
*
31566315 TAAAAACATG-A-GTATGTATATATC
1 TAAAAACATGTAGGTATATATATATC
*
31566339 TAAAAATATGTAGGTATATATATA
1 TAAAAACATGTAGGTATATATATA
31566363 AATTATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 1 0.05
26 10 0.50
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.35
Consensus pattern (26 bp):
TAAAAACATGTAGGTATATATATATC
Found at i:31566515 original size:18 final size:18
Alignment explanation
Indices: 31566494--31566533 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
31566484 CATATATGTG
31566494 TATGTAAATTA-ATATATA
1 TATGTAAA-TAGATATATA
*
31566512 TATGTATATAGATATATA
1 TATGTAAATAGATATATA
31566530 TATG
1 TATG
31566534 AATTATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (18 bp):
TATGTAAATAGATATATA
Found at i:31566546 original size:18 final size:18
Alignment explanation
Indices: 31566507--31566548 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31566497 GTAAATTAAT
* *
31566507 ATATATATGTATATAGAT
1 ATATATATGAATATAGAA
31566525 ATATATATGAAT-TATGAA
1 ATATATATGAATATA-GAA
31566543 ATATAT
1 ATATAT
31566549 GTAAGTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (18 bp):
ATATATATGAATATAGAA
Found at i:31566726 original size:24 final size:24
Alignment explanation
Indices: 31566680--31566728 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31566670 ATATGTACGG
* * *
31566680 ATTATAAAATATGTGCATGTATAT
1 ATTATAAAAGATATGCATATATAT
*
31566704 ATTATAAAAGATATGTATATATAT
1 ATTATAAAAGATATGCATATATAT
31566728 A
1 A
31566729 ATAAAACTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (24 bp):
ATTATAAAAGATATGCATATATAT
Found at i:31569160 original size:19 final size:16
Alignment explanation
Indices: 31569136--31569178 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 16
31569126 ACTTTCTTTA
31569136 AAATTTTTAAAATTATTAT
1 AAATTTTTAAAA--A-TAT
31569155 AAATTTTTTAAAAATAT
1 AAA-TTTTTAAAAATAT
31569172 AAATTTT
1 AAATTTT
31569179 GGATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 6 0.26
18 1 0.04
19 3 0.13
20 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTTTTAAAAATAT
Found at i:31569204 original size:20 final size:21
Alignment explanation
Indices: 31569139--31569231 Score: 68
Period size: 24 Copynumber: 4.4 Consensus size: 21
31569129 TTCTTTAAAA
* *
31569139 TTTTTA-AAATTATTATAAAT
1 TTTTTATAAATTATTTTGAAT
* *
31569159 TTTTTAAAAATATAAATTTTGGAT
1 TTTTTATAAAT-T--ATTTTGAAT
31569183 TTTTTATAAATGT-TTTT-AA-
1 TTTTTATAAAT-TATTTTGAAT
* *
31569202 TTTTGAAAAATTATTTTGAAT
1 TTTTTATAAATTATTTTGAAT
31569223 TTTTTATAA
1 TTTTTATAA
31569232 TTTTTGTTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
18 1 0.02
19 13 0.23
20 9 0.16
21 15 0.27
22 1 0.02
24 17 0.30
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTTATAAATTATTTTGAAT
Found at i:31569233 original size:20 final size:20
Alignment explanation
Indices: 31569174--31569233 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
31569164 AAAAATATAA
* *
31569174 ATTTTGGATTTTTTATAAAT
1 ATTTTGAATTTTTTATAATT
* * ** *
31569194 GTTTTTAATTTTGAAAAATT
1 ATTTTGAATTTTTTATAATT
31569214 ATTTTGAATTTTTTATAATT
1 ATTTTGAATTTTTTATAATT
31569234 TTTGTTGTGA
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
ATTTTGAATTTTTTATAATT
Found at i:31571365 original size:18 final size:18
Alignment explanation
Indices: 31571338--31571377 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31571328 GATAGAAATT
*
31571338 AAAAATAAAAAATAAAAA
1 AAAAACAAAAAATAAAAA
**
31571356 AAAAACAAAATTTAAAAA
1 AAAAACAAAAAATAAAAA
31571374 AAAA
1 AAAA
31571378 TAAAGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAACAAAAAATAAAAA
Found at i:31573116 original size:12 final size:12
Alignment explanation
Indices: 31573099--31573133 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
31573089 TGTTTGATTC
31573099 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
31573111 TTTTCTTTTTTT
1 TTTTCTTTTCTT
31573123 TTTTCATTTTC
1 TTTTC-TTTTC
31573134 ATTTATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:31577505 original size:6 final size:6
Alignment explanation
Indices: 31577494--31577529 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
31577484 ATATGATTAA
31577494 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
31577530 AAAGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
GAAAAT
Found at i:31579266 original size:20 final size:21
Alignment explanation
Indices: 31579227--31579266 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31579217 ACTTGGATTG
31579227 AATTGAATGTAAATTGTACTA
1 AATTGAATGTAAATTGTACTA
31579248 AATTG-ATGTTAAATT-TACT
1 AATTGAATG-TAAATTGTACT
31579267 CGTATAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (21 bp):
AATTGAATGTAAATTGTACTA
Found at i:31579846 original size:24 final size:24
Alignment explanation
Indices: 31579813--31579871 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
31579803 GCTATCTGGT
* *
31579813 GCTACTCGTTAATTTCTCTTCAGA
1 GCTACCCGTTAATTGCTCTTCAGA
**
31579837 GCTACCCGTTAATTGCTCTTTGGA
1 GCTACCCGTTAATTGCTCTTCAGA
31579861 GCTACCCGTTA
1 GCTACCCGTTA
31579872 TAAGCTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (24 bp):
GCTACCCGTTAATTGCTCTTCAGA
Found at i:31579878 original size:24 final size:26
Alignment explanation
Indices: 31579835--31579899 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 26
31579825 TTTCTCTTCA
*
31579835 GAGCTACCCGTTA-ATTGCTCTTTG-
1 GAGCTACCCGTTATATAGCTCTTTGT
31579859 GAGCTACCCGTTATA-AGCTCTTTGT
1 GAGCTACCCGTTATATAGCTCTTTGT
* *
31579884 GAGCTTCCCTTTATAT
1 GAGCTACCCGTTATAT
31579900 TTCCCGAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 21 0.60
25 14 0.40
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (26 bp):
GAGCTACCCGTTATATAGCTCTTTGT
Found at i:31580905 original size:42 final size:42
Alignment explanation
Indices: 31580846--31580930 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
31580836 TTGTTGCAAC
31580846 TAAGAACCTCTAACTTTTCCCTTTTATGTTATCTTTGATGAA
1 TAAGAACCTCTAACTTTTCCCTTTTATGTTATCTTTGATGAA
31580888 TAAGAACCTCTAACTTTTCCCTTTTATGTTATCTTTGATGAA
1 TAAGAACCTCTAACTTTTCCCTTTTATGTTATCTTTGATGAA
31580930 T
1 T
31580931 CATATGAGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (42 bp):
TAAGAACCTCTAACTTTTCCCTTTTATGTTATCTTTGATGAA
Found at i:31597936 original size:28 final size:29
Alignment explanation
Indices: 31597905--31597960 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
31597895 TATTATTATT
*
31597905 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
31597933 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
31597961 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:31598723 original size:3 final size:3
Alignment explanation
Indices: 31598715--31598743 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
31598705 GTGAGGTAAG
31598715 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31598744 GAGTGGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:31598926 original size:24 final size:25
Alignment explanation
Indices: 31598894--31598953 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
31598884 CGGATTAATT
31598894 ATTG-ATTGAAAG-GTGGAAAAA-TG
1 ATTGAATTGAAAGTGT-GAAAAAGTG
31598917 ATTGAATTGAAAGTGTGAAAAAGTGTG
1 ATTGAATTGAAAGTGTGAAAAA--GTG
31598944 ATTGAATTGA
1 ATTGAATTGA
31598954 GAATATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.12
24 14 0.44
25 2 0.06
27 12 0.38
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (25 bp):
ATTGAATTGAAAGTGTGAAAAAGTG
Found at i:31599156 original size:37 final size:39
Alignment explanation
Indices: 31599097--31599192 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
31599087 CGGATAGATT
* * * *
31599097 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
31599134 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
31599173 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
31599193 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:31599947 original size:12 final size:12
Alignment explanation
Indices: 31599930--31599954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31599920 AAATTTTTAT
31599930 AAAAAAAAATGA
1 AAAAAAAAATGA
31599942 AAAAAAAAATGA
1 AAAAAAAAATGA
31599954 A
1 A
31599955 GTCATTTGGT
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:31610028 original size:46 final size:44
Alignment explanation
Indices: 31609961--31610290 Score: 204
Period size: 46 Copynumber: 7.6 Consensus size: 44
31609951 ATAATACAGG
*
31609961 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* *
31610007 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * *
31610051 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * * *
31610090 TCGTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
*
31610131 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
31610177 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * * *
31610221 TCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCA-GA
*
31610264 TCCTATCTCCCTGA-AGTTACAGTGGAA
1 TCTTATCTCCCTGAGA-TTACAGTGGAA
31610291 TGGATTAAAA
Statistics
Matches: 222, Mismatches: 45, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.10
40 1 0.00
41 27 0.12
42 5 0.02
43 24 0.11
44 69 0.31
45 1 0.00
46 70 0.32
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
Found at i:31611923 original size:3 final size:3
Alignment explanation
Indices: 31611917--31611963 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
31611907 TTTAGCCACT
*
31611917 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA CTTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
31611962 TT
1 TT
31611964 TGTTTATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:31612521 original size:16 final size:16
Alignment explanation
Indices: 31612502--31612532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31612492 TACACCCATA
*
31612502 TATATGTACATATTTT
1 TATATATACATATTTT
31612518 TATATATACATATTT
1 TATATATACATATTT
31612533 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:31617389 original size:20 final size:21
Alignment explanation
Indices: 31617366--31617409 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
31617356 AACTCTTCAG
31617366 AAAAA-TAGAA-ATAAATATAT
1 AAAAATTAGAATA-AAATATAT
31617386 AAAAATTTAGAATAAAATATAT
1 AAAAA-TTAGAATAAAATATAT
31617408 AA
1 AA
31617410 TCTAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
22 15 0.71
23 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAATTAGAATAAAATATAT
Found at i:31624341 original size:19 final size:20
Alignment explanation
Indices: 31624306--31624349 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
31624296 GCTTCTTTTC
*
31624306 GCATT-CATTTCATTCATCT
1 GCATTACATTTCATTCATAT
31624325 GCATTACATTTCA-TCATAT
1 GCATTACATTTCATTCATAT
31624344 GCATTA
1 GCATTA
31624350 AGATTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (20 bp):
GCATTACATTTCATTCATAT
Found at i:31630077 original size:189 final size:189
Alignment explanation
Indices: 31629751--31630125 Score: 588
Period size: 189 Copynumber: 2.0 Consensus size: 189
31629741 TATGTTGTGA
* * *
31629751 CTACTGAAGAATGCGCTCAAGAATGACATCTTTGGAAACTAAATTTTAACGAAGCTTCAAACGCT
1 CTACTGAAGAATGCGCTCAAGAAGGACATCCTTAGAAACTAAATTTTAACGAAGCTTCAAACGCT
* * *
31629816 ATGGGTAACGGAATCGGGGCAGTCCTAGTATCCCTAAACGGAGATCATTATCCCTTTACTAGCAA
66 ATAGGTAACAGAATCGAGGCAGTCCTAGTATCCCTAAACGGAGATCATTATCCCTTTACTAGCAA
* *
31629881 TTTGGATTTTTATTACACGAATAATGTGGAAAAATATGAAGCATGCATCATGGGCACCC
131 ATTGGATTTTTATTACACGAATAATATGGAAAAATATGAAGCATGCATCATGGGCACCC
* *
31629940 CTACTGAAGAATGTGCTCAAGAAGGACATCCTTAGAAACTAAATTTTAACGGAGCTTCAAACGCT
1 CTACTGAAGAATGCGCTCAAGAAGGACATCCTTAGAAACTAAATTTTAACGAAGCTTCAAACGCT
* * * * *
31630005 ATAGGTAACAGAATCGAGGCAGTCCTGGTATCCCTAAATGGGGGTCATTATCCCTTTACTAGTAA
66 ATAGGTAACAGAATCGAGGCAGTCCTAGTATCCCTAAACGGAGATCATTATCCCTTTACTAGCAA
* * *
31630070 ATTGGATTTTTATTGCATGAATAATATGGCAAAATATGAAGCATGCATCATGGGCA
131 ATTGGATTTTTATTACACGAATAATATGGAAAAATATGAAGCATGCATCATGGGCA
31630126 TCTGTGCAGC
Statistics
Matches: 168, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
189 168 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (189 bp):
CTACTGAAGAATGCGCTCAAGAAGGACATCCTTAGAAACTAAATTTTAACGAAGCTTCAAACGCT
ATAGGTAACAGAATCGAGGCAGTCCTAGTATCCCTAAACGGAGATCATTATCCCTTTACTAGCAA
ATTGGATTTTTATTACACGAATAATATGGAAAAATATGAAGCATGCATCATGGGCACCC
Found at i:31630475 original size:9 final size:9
Alignment explanation
Indices: 31630461--31630491 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31630451 GTTAAACGAA
31630461 TCGAGTTAT
1 TCGAGTTAT
*
31630470 TCGAGTTAA
1 TCGAGTTAT
31630479 TCGAGTTAT
1 TCGAGTTAT
31630488 TCGA
1 TCGA
31630492 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:31633247 original size:50 final size:50
Alignment explanation
Indices: 31633070--31633249 Score: 171
Period size: 50 Copynumber: 3.5 Consensus size: 50
31633060 GGGAATGAGA
* * **
31633070 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATAATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGC---A--CCGA-TATGAGAGG
* * * * * *
31633126 TCCCATGTAAGACCATGCCTGAGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGATATGAGAGG
** **
31633176 TCCCCCGTAAGACCATGTCTGGGACATGACATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGATATGAGAGG
*
31633226 TCCCATGTAAGACCATATCTGGGA
1 TCCCATGTAAGACCATGTCTGGGA
31633250 TATGGCATTG
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
50 69 0.66
51 2 0.02
53 1 0.01
56 33 0.31
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGATATGAGAGG
Found at i:31633527 original size:12 final size:12
Alignment explanation
Indices: 31633510--31633548 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
31633500 ATGAGTTATT
31633510 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
31633522 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
31633534 TAAGTGAGTAAG
1 TAAGTAAGCAAG
31633546 TAA
1 TAA
31633549 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:31636235 original size:501 final size:500
Alignment explanation
Indices: 31635292--31636283 Score: 1551
Period size: 501 Copynumber: 2.0 Consensus size: 500
31635282 AAGGCAGCCA
*
31635292 ATAAGAACATTAAGAAGATCGTCTGGAAAATGACTGAGACTTATAAAGATTGGCATGAGAAGTTA
1 ATAAGAACATTAAGAAGATCGTCGGGAAAATGACTGAGACTTATAAAGATTGGCATGAGAAGTTA
* * *
31635357 CCATTTGCCTTCTATGCTTATCAAACGTTTATTAGAACCTCCACCGAGGCAACTCCTTTCTCATT
66 CCATTTGCCCTCTATGCTTATCAAACGTCTATTAGAACCTCCACCGAGGCAACGCCTTTCTCATT
* *
31635422 GGTTTAAGGAATAGAGGCGATTTTGCCCATGAAGTCGAGATTCGTTCTCTCTGAGTTTTGTTAGA
131 GGTTTAAGGAATAGAGGCGATTTTGCCCATGAAGTCGAGATTCATTCTCTCTGAGTTTTGTCAGA
* * * *
31635487 TTTGAAGTTAGATGAAATAGAATGGATCCAATCCTGATATGATCAGCTGAACTTGATTGAAAAGA
196 GTTGAAGTTAGACGAAACAGAATAGATCCAATCCTGATATGATCAGCTGAACTTGATTGAAAAGA
*
31635552 AGAGGTTGAAAGCTATCCGTCATGGTCAGATGTACTAAAAATGAATGATGTGAGCTTATGACAAA
261 AGAGGTTGAAAGCTATCCGTCATGGTCAGATGTACTAAAAACGAATGATGTGAGCTTATGACAAA
* * * * *
31635617 AAGATTCGCCCAAGAGAATTTCATGAGGGGAACCTGGTATTGAGAAATATCATTCCCATACAAAA
326 AAGATTCCCCCAAGAAAATTTCATGAGGGGAACCTGGAATTGAAAAAGATCATTCCCATACAAAA
*
31635682 GGAATTCAAAAAAAAGTAGATGCCAAACTGGAAAGGACCTTATGTGATAAAGAAGGCCTTTTCTA
391 GGAATTCAAAAAAAAGTAGATGCCAAACTGGAAAGGACCTTATGTAATAAAGAAGGCCTTTTCTA
** * *
31635747 GAGGAGTGCTGATTTTGACCTAGATGGATGGTAAAAGCCTGCCTG
456 GAGGAGCACTGATTTTGACCGAGATAGATGGTAAAAGCCTGCCTG
*
31635792 ATAAGAACATTAAGAAGATCGTGGGGAAAATGACTGAGACTTATAAAGATTGGCATGAGAAGTTA
1 ATAAGAACATTAAGAAGATCGTCGGGAAAATGACTGAGACTTATAAAGATTGGCATGAGAAGTTA
* * *
31635857 CCATTTTCCCTCTATGCTTATCGAATGTCTATTAGAACCTCCACCGAGGCAACGCCTTTCTCATT
66 CCATTTGCCCTCTATGCTTATCAAACGTCTATTAGAACCTCCACCGAGGCAACGCCTTTCTCATT
*
31635922 GGTTTATA-GAATGGAGGCGATTTTGCCCATTGAAGTCGAGATTCATTCTCTCTGAGTTTTGTCA
131 GGTTTA-AGGAATAGAGGCGATTTTGCCCA-TGAAGTCGAGATTCATTCTCTCTGAGTTTTGTCA
* *
31635986 GAGTTGAAGTTAGACGAAGCAGAATAGATCCAATCCTGATATGATCAGCTGAACTTGATTGAAGA
194 GAGTTGAAGTTAGACGAAACAGAATAGATCCAATCCTGATATGATCAGCTGAACTTGATTGAAAA
* *
31636051 GAAGAGGTTGAAAGTTATCCGTCATGGTTAGATGTACTAAAAACGAATGATGTGAGCTTATGACA
259 GAAGAGGTTGAAAGCTATCCGTCATGGTCAGATGTACTAAAAACGAATGATGTGAGCTTATGACA
* *
31636116 AAAAGGTTCACCCCAA-AAAATTTGATGAGTGGG-ACCTGGAATTGAAAAAGATTC-TTCCCATA
324 AAAAGATTC-CCCCAAGAAAATTTCATGAG-GGGAACCTGGAATTGAAAAAGA-TCATTCCCATA
* * * ** * *
31636178 CAAAAGGACTTTAGAGGAAAGTGGATGCCAAACTGGGAAGGACCTTATGTAATAAAGAAGGCCTT
386 CAAAAGGAATTCAAAAAAAAGTAGATGCCAAACTGGAAAGGACCTTATGTAATAAAGAAGGCCTT
*
31636243 TTTTAGAGGAGCACTGATTTTGACCGAGATAGATGGTAAAA
451 TTCTAGAGGAGCACTGATTTTGACCGAGATAGATGGTAAAA
31636284 ACCTACCTAA
Statistics
Matches: 447, Mismatches: 40, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
500 148 0.33
501 289 0.65
502 10 0.02
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (500 bp):
ATAAGAACATTAAGAAGATCGTCGGGAAAATGACTGAGACTTATAAAGATTGGCATGAGAAGTTA
CCATTTGCCCTCTATGCTTATCAAACGTCTATTAGAACCTCCACCGAGGCAACGCCTTTCTCATT
GGTTTAAGGAATAGAGGCGATTTTGCCCATGAAGTCGAGATTCATTCTCTCTGAGTTTTGTCAGA
GTTGAAGTTAGACGAAACAGAATAGATCCAATCCTGATATGATCAGCTGAACTTGATTGAAAAGA
AGAGGTTGAAAGCTATCCGTCATGGTCAGATGTACTAAAAACGAATGATGTGAGCTTATGACAAA
AAGATTCCCCCAAGAAAATTTCATGAGGGGAACCTGGAATTGAAAAAGATCATTCCCATACAAAA
GGAATTCAAAAAAAAGTAGATGCCAAACTGGAAAGGACCTTATGTAATAAAGAAGGCCTTTTCTA
GAGGAGCACTGATTTTGACCGAGATAGATGGTAAAAGCCTGCCTG
Found at i:31637286 original size:44 final size:46
Alignment explanation
Indices: 31637223--31637730 Score: 234
Period size: 44 Copynumber: 11.1 Consensus size: 46
31637213 TTAAAGCTAT
* *
31637223 AAGTTACAAAGT-TTATCTCCCTGAAGAG-T-CAGTGGAGCATACTG
1 AAGTTACAAA-TCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
* *
31637267 AAGTTACAAATCTTATCTCCTTG--GAGTTACAGTGAAGCAGATTG
1 AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
*
31637311 AAGTTACAAATCTTATCTCCCT-AA-AGTTACAGTGGAGCAAATTG
1 AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
* * * *
31637355 AAGCTACAAATCTTTTCACCCTG--GAGTTGCAGTGGAGCAGATTG
1 AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
* * * * * *
31637399 AAGCTACAAATCTTATTTCCTTG-A-AGTTGCAGTAGAACAGATTAAAG
1 AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATT---G
** * * * *
31637446 CTACAAGTTATGAATCTTATCTCCTTG-A-AGTTGCAGTGGAGCAAATTA
1 ----AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
** * * * ** * *
31637494 AAACTACAAAACTTATTTCCTTG-A-AGTTGTAGTGGAACAAATTAAAG
1 AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATT---G
** * * *
31637541 CTACAAGTTATGAATCTTATCTCCTTG-A-AGTTGCAGTGGAGCTGATTG
1 ----AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
** * * *
31637589 AAACTACAAATCTTATTTCCCTG-A-AGTTGCAGTGGAACAGATTAAAG
1 AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATT---G
** *
31637636 CTACAAGTTATGAATCTTATCTCCCTG-A-AGTTGCAGTGGAGCAGATTG
1 ----AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
* * * *
31637684 AAGTTACAAGTCTCATCTCCCTG-A-AGTTGCATTGGAGCAGATTG
1 AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
31637728 AAG
1 AAG
31637731 CGTCAAACCC
Statistics
Matches: 371, Mismatches: 64, Indels: 58
0.75 0.13 0.12
Matches are distributed among these distances:
42 3 0.01
43 2 0.01
44 256 0.69
47 2 0.01
48 2 0.01
51 106 0.29
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (46 bp):
AAGTTACAAATCTTATCTCCCTGAAGAGTTACAGTGGAGCAGATTG
Found at i:31637380 original size:88 final size:87
Alignment explanation
Indices: 31637223--31637731 Score: 257
Period size: 95 Copynumber: 5.5 Consensus size: 87
31637213 TTAAAGCTAT
* * * *
31637223 AAGTTACAAAGT-TTATCTCCCTGAAGAG-TCAGTGGAGCATACTGAAGTTACAAATCTTATCTC
1 AAGTTACAAA-TCTTATCTCCCT-AA-AGTTCAGTGGAGCAAATTGAAGCTACAAATCTTATCAC
*
31637286 CTTGGAGTTACAGTGAAGCAGATTG
63 CCTGGAGTTACAGTGAAGCAGATTG
*
31637311 AAGTTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAAATTGAAGCTACAAATCTTTTCACCC
1 AAGTTACAAATCTTATCTCCCTAAAGTT-CAGTGGAGCAAATTGAAGCTACAAATCTTATCACCC
* *
31637376 TGGAGTTGCAGTGGAGCAGATTG
65 TGGAGTTACAGTGAAGCAGATTG
* * * * * * * *
31637399 AAGCTACAAATCTTATTTCCTTGAAGTTGCAGTAGAACAGATTAAAGCTACAAGTTATGAATCTT
1 AAGTTACAAATCTTATCTCCCTAAAGTT-CAGTGGAGCAAATTGAAGCTAC-----A--AATCTT
* * * * * * *
31637464 ATCTCCTTGAAGTTGCAGTGGAGCAAATTA
58 ATCACCCTGGAGTTACAGTGAAGCAGATTG
** * * * * * * *
31637494 AAACTACAAAACTTATTTCCTTGAAGTTGTAGTGGAACAAATTAAAGCTACAAGTTATGAATCTT
1 AAGTTACAAATCTTATCTCCCTAAAGTT-CAGTGGAGCAAATTGAAGCTAC-----A--AATCTT
* * * * * *
31637559 ATCTCCTTGAAGTTGCAGTGGAGCTGATTG
58 ATCACCCTGGAGTTACAGTGAAGCAGATTG
** * * * * *
31637589 AAACTACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTATGAATCTT
1 AAGTTACAAATCTTATCTCCCTAAAGTT-CAGTGGAGCAAATTGAAGCTAC-----A--AATCTT
* * * *
31637654 ATCTCCCTGAAGTTGCAGTGGAGCAGATTG
58 ATCACCCTGGAGTTACAGTGAAGCAGATTG
* * * * *
31637684 AAGTTACAAGTCTCATCTCCCTGAAGTTGCATTGGAGCAGATTGAAGC
1 AAGTTACAAATCTTATCTCCCTAAAGTT-CAGTGGAGCAAATTGAAGC
31637732 GTCAAACCCT
Statistics
Matches: 366, Mismatches: 45, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
86 2 0.01
87 4 0.01
88 113 0.31
93 1 0.00
95 246 0.67
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (87 bp):
AAGTTACAAATCTTATCTCCCTAAAGTTCAGTGGAGCAAATTGAAGCTACAAATCTTATCACCCT
GGAGTTACAGTGAAGCAGATTG
Found at i:31637494 original size:51 final size:51
Alignment explanation
Indices: 31637407--31637694 Score: 318
Period size: 51 Copynumber: 5.9 Consensus size: 51
31637397 TGAAGCTACA
* *
31637407 AATCTTATTTCCTTGAAGTTGCAGTAGAACAGATTAAAGCTACAAGTTATG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTATG
* * *
31637458 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAATTAAAACTAC-A---A--
1 AATCTTATCTCCTTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTATG
* * *
31637503 AA-CTTATTTCCTTGAAGTTGTAGTGGAACAAATTAAAGCTACAAGTTATG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTATG
* *
31637553 AATCTTATCTCCTTGAAGTTGCAGTGGAGCTGATTGAAA-CTAC-----A--
1 AATCTTATCTCCTTGAAGTTGCAGTGGAACAGATT-AAAGCTACAAGTTATG
* *
31637597 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTATG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTATG
* * * *
31637648 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGT
1 AATCTTATCTCCTTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGT
31637695 CTCATCTCCC
Statistics
Matches: 199, Mismatches: 22, Indels: 32
0.79 0.09 0.13
Matches are distributed among these distances:
43 3 0.02
44 71 0.36
45 3 0.02
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 3 0.02
51 112 0.56
52 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (51 bp):
AATCTTATCTCCTTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTATG
Found at i:31637501 original size:95 final size:95
Alignment explanation
Indices: 31637275--31637731 Score: 559
Period size: 95 Copynumber: 4.9 Consensus size: 95
31637265 TGAAGTTACA
* * * ** * * *
31637275 AATCTTATCTCCTTGGAGTTACAGTGAAGCAGATTGAAGTTACAAATCTTATCTCCCTAAAGTTA
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTACAAATCTTATTTCCCTGAAGTTG
* * *
31637340 CAGTGGAGCAAATTGAAGCTAC-----A--
66 CAGTGGAACAGATTAAAGCTACAAGTTATG
* * * * * *
31637363 AATCTTTTCACCCTGGAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATTTCCTTGAAGTTG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTACAAATCTTATTTCCCTGAAGTTG
*
31637428 CAGTAGAACAGATTAAAGCTACAAGTTATG
66 CAGTGGAACAGATTAAAGCTACAAGTTATG
* * * *
31637458 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAATTAAAACTACAAAACTTATTTCCTTGAAGTTG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTACAAATCTTATTTCCCTGAAGTTG
* *
31637523 TAGTGGAACAAATTAAAGCTACAAGTTATG
66 CAGTGGAACAGATTAAAGCTACAAGTTATG
*
31637553 AATCTTATCTCCTTGAAGTTGCAGTGGAGCTGATTGAAACTACAAATCTTATTTCCCTGAAGTTG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTACAAATCTTATTTCCCTGAAGTTG
31637618 CAGTGGAACAGATTAAAGCTACAAGTTATG
66 CAGTGGAACAGATTAAAGCTACAAGTTATG
* ** * * *
31637648 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTCATCTCCCTGAAGTTG
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTACAAATCTTATTTCCCTGAAGTTG
* * *
31637713 CATTGGAGCAGATTGAAGC
66 CAGTGGAACAGATTAAAGC
31637732 GTCAAACCCT
Statistics
Matches: 320, Mismatches: 42, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
88 73 0.23
93 1 0.00
95 246 0.77
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (95 bp):
AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACTACAAATCTTATTTCCCTGAAGTTG
CAGTGGAACAGATTAAAGCTACAAGTTATG
Found at i:31637720 original size:139 final size:133
Alignment explanation
Indices: 31637172--31637729 Score: 469
Period size: 139 Copynumber: 4.0 Consensus size: 133
31637162 CATATCAATA
* * *
31637172 AAACTACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAGTTACAAAGT-T
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGC-------TACAAAATCT
* * * * * *
31637236 TATCTCCCTGAAG-AGTCAGTGGAGCATACTGAAGTTACAAATCTTATCTCCTTGGAGTTACAGT
59 TATCTCCCTGAAGTTG-CAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCTTGAAGTTGCAGT
*
31637300 GAAGCAGATTG
123 GGAGCAGATTG
** * * * * * *
31637311 AAGTTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAAATTGAAGCTAC-AAATCTTTTCACC
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAAATCTTATCTCC
* * * *
31637375 CTGGAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATTTCCTTGAAGTTGCAGTAGAACAGA
66 CTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGA
31637440 TT-
131 TTG
* * *
31637442 AAAGCTACAAGTTATGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAATTAAAACTACAAAA-C
1 AAA-CTAC-----A--AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAAATC
* * * * * *
31637506 TTATTTCCTTGAAGTTGTAGTGGAACAAATTAAAGCTACAAGTTATGAATCTTATCTCCTTGAAG
58 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC-----A--AATCTTATCTCCTTGAAG
*
31637571 TTGCAGTGGAGCTGATTG
116 TTGCAGTGGAGCAGATTG
* *
31637589 AAACTACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTATGAATCTT
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTAC-A---A--AATCTT
* * * * *
31637654 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTCATCTCCCTGAAGTTGCATTGG
60 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCTTGAAGTTGCAGTGG
31637719 AGCAGATTG
125 AGCAGATTG
31637728 AA
1 AA
31637730 GCGTCAAACC
Statistics
Matches: 334, Mismatches: 59, Indels: 52
0.75 0.13 0.12
Matches are distributed among these distances:
131 5 0.01
132 66 0.20
133 1 0.00
137 1 0.00
139 180 0.54
140 4 0.01
141 2 0.01
143 1 0.00
144 1 0.00
145 2 0.01
146 68 0.20
147 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (133 bp):
AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAAATCTTATCTCC
CTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGA
TTG
Found at i:31639107 original size:12 final size:12
Alignment explanation
Indices: 31639092--31639119 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31639082 TTATAAGTTG
31639092 TTTTATTTATTA
1 TTTTATTTATTA
31639104 TTTTATTTATTA
1 TTTTATTTATTA
31639116 TTTT
1 TTTT
31639120 TCAACCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:31639188 original size:3 final size:3
Alignment explanation
Indices: 31639176--31639230 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
31639166 TGTGCTTTTA
* ** * *
31639176 TAT T-T TAT TAT TAT TGT CCT TGT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31639223 TAT TAT TA
1 TAT TAT TA
31639231 GTGATATGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:31644130 original size:16 final size:16
Alignment explanation
Indices: 31644093--31644132 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
31644083 TTGATAAAAT
* *
31644093 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
31644109 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
31644125 TAAAATTA
1 TAAAATTA
31644133 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:31644193 original size:66 final size:59
Alignment explanation
Indices: 31644135--31644250 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
31644125 TAAAATTATC
* * *
31644135 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
31644193 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGT
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGT
31644251 TTACATTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 7 0.13
59 47 0.87
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:31644552 original size:31 final size:30
Alignment explanation
Indices: 31644509--31644574 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 30
31644499 AAAAGAAGAG
31644509 TAAA-TGTCGGGGAAATGAAATTGAAAACT
1 TAAACTGTCGGGGAAATGAAATTGAAAACT
31644538 TAAACTGTCAGGGGAAATGAAATTGAAAACT
1 TAAACTGTC-GGGGAAATGAAATTGAAAACT
*
31644569 AAAACT
1 TAAACT
31644575 AAAAATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 4 0.12
30 4 0.12
31 26 0.76
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (30 bp):
TAAACTGTCGGGGAAATGAAATTGAAAACT
Found at i:31657390 original size:21 final size:21
Alignment explanation
Indices: 31657364--31657404 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31657354 AGACGAGCAA
* *
31657364 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
31657385 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
31657405 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:31660088 original size:23 final size:23
Alignment explanation
Indices: 31660044--31660111 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 23
31660034 ATATATGGAC
* *
31660044 TATAT-ATTAAAT-ATTGAAATA
1 TATATAATTACATAATTCAAATA
31660065 TA-ATAATTACA-AATTCAAATA
1 TATATAATTACATAATTCAAATA
** *
31660086 TATATTGTTACATATTTCAAATA
1 TATATAATTACATAATTCAAATA
31660109 TAT
1 TAT
31660112 TTTGAGAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.05
21 17 0.45
22 7 0.18
23 12 0.32
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (23 bp):
TATATAATTACATAATTCAAATA
Found at i:31661721 original size:17 final size:18
Alignment explanation
Indices: 31661699--31661741 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31661689 AATTCAACAG
31661699 TTGTATTTA-AAAAATAA
1 TTGTATTTATAAAAATAA
* *
31661716 TTGTATTTATTAATATAA
1 TTGTATTTATAAAAATAA
31661734 TTGTATTT
1 TTGTATTT
31661742 GTAATGCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (18 bp):
TTGTATTTATAAAAATAA
Found at i:31661801 original size:31 final size:31
Alignment explanation
Indices: 31661759--31661819 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
31661749 ATCTAAAATT
* *
31661759 TTAAATAAAAACTTCTGAATAGTTTAATAAC
1 TTAAATAAAAACTTCTAAATAGTTCAATAAC
* *
31661790 TTAAATGAAAACTTTTAAATAGTTCAATAA
1 TTAAATAAAAACTTCTAAATAGTTCAATAA
31661820 TCATTTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (31 bp):
TTAAATAAAAACTTCTAAATAGTTCAATAAC
Found at i:31671848 original size:20 final size:20
Alignment explanation
Indices: 31671825--31671865 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31671815 TAATAATGAG
31671825 AATACCAATTTTATAATAAT
1 AATACCAATTTTATAATAAT
*
31671845 AATATCAATTTTATAATAAT
1 AATACCAATTTTATAATAAT
31671865 A
1 A
31671866 TCAATAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
AATACCAATTTTATAATAAT
Found at i:31679499 original size:22 final size:23
Alignment explanation
Indices: 31679442--31679499 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
31679432 GTGATTATGT
* **
31679442 TTTATTTCTATTTCCACGGGGTAG
1 TTTAGTTCTA-TTCCACAAGGTAG
*
31679466 GTTAGTTC-ATTCCACAAGGTAG
1 TTTAGTTCTATTCCACAAGGTAG
31679488 TTTA-TTCTATTC
1 TTTAGTTCTATTC
31679500 TGTGACTGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 3 0.11
22 18 0.64
23 1 0.04
24 6 0.21
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (23 bp):
TTTAGTTCTATTCCACAAGGTAG
Found at i:31687228 original size:21 final size:20
Alignment explanation
Indices: 31687204--31687250 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
31687194 AAATTAAATT
31687204 TTAAAATTTGAAATATAAAAA
1 TTAAAATTTGAAA-ATAAAAA
*
31687225 TTAAAAATTTTAAAATAAAAA
1 TT-AAAATTTGAAAATAAAAA
31687246 -TAAAA
1 TTAAAA
31687251 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 9 0.38
22 10 0.42
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAAATTTGAAAATAAAAA
Found at i:31687251 original size:21 final size:22
Alignment explanation
Indices: 31687206--31687252 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
31687196 ATTAAATTTT
*
31687206 AAAATTTGAAATATAAAAATTA
1 AAAATTTGAAATATAAAAATAA
*
31687228 AAAATTTTAAA-ATAAAAATAA
1 AAAATTTGAAATATAAAAATAA
31687249 AAAA
1 AAAA
31687253 AAATAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAATTTGAAATATAAAAATAA
Found at i:31690516 original size:52 final size:52
Alignment explanation
Indices: 31690451--31690647 Score: 326
Period size: 52 Copynumber: 3.8 Consensus size: 52
31690441 AGTTACAAAT
*
31690451 TTTATAACAGTATATTAAAATAGTATATTACATTAAAAATTAAGGTGTAGTA
1 TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAAGGTGTAGTA
* *
31690503 TTTATAATAGTATATTAAAACAGTATATTACATTAAAAAATAAGGTGTAGTA
1 TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAAGGTGTAGTA
* *
31690555 TTT-T-ACAATATATTAAAACAATATATTACATTAAAAATTAAGGTGTAGTA
1 TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAAGGTGTAGTA
*
31690605 TTTATAACAGTATATTAAAACAGTATATTACCTTAAAAATTAA
1 TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAA
31690648 TGGTTTAATC
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
50 45 0.34
51 2 0.02
52 86 0.65
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (52 bp):
TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAAGGTGTAGTA
Found at i:31690628 original size:13 final size:13
Alignment explanation
Indices: 31690601--31690634 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
31690591 ATTAAGGTGT
*
31690601 AGTAT-TTATAAC
1 AGTATATTAAAAC
31690613 AGTATATTAAAAC
1 AGTATATTAAAAC
31690626 AGTATATTA
1 AGTATATTA
31690635 CCTTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:31690688 original size:13 final size:13
Alignment explanation
Indices: 31690662--31690714 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
31690652 TTAATCAAAA
* *
31690662 AATTAACAATATT
1 AATTAATAACATT
*
31690675 AATTATTTAA-ATT
1 AATTA-ATAACATT
31690688 AATTAATAACATT
1 AATTAATAACATT
*
31690701 AATTAATAATATT
1 AATTAATAACATT
31690714 A
1 A
31690715 TAGAAGTGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 29 0.85
14 2 0.06
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTAATAACATT
Found at i:31690714 original size:26 final size:26
Alignment explanation
Indices: 31690662--31690714 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
31690652 TTAATCAAAA
* *
31690662 AATTAACAATATTAATTATTTAAATT
1 AATTAACAACATTAATTATATAAATT
*
31690688 AATTAATAACATTAATTA-ATAATATT
1 AATTAACAACATTAATTATATAA-ATT
31690714 A
1 A
31690715 TAGAAGTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTAACAACATTAATTATATAAATT
Found at i:31697221 original size:19 final size:17
Alignment explanation
Indices: 31697187--31697221 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
31697177 CTAAAATAGT
31697187 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
31697204 AACAAGAATTATACAATA
1 AACAA-AATTA-ACAATA
31697222 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:31704199 original size:27 final size:27
Alignment explanation
Indices: 31704161--31704240 Score: 151
Period size: 27 Copynumber: 3.0 Consensus size: 27
31704151 AACTATGTCG
*
31704161 TTGTATACTATTGTCTTAATTTTTTCC
1 TTGTATACTATTGTCTTAATTTTTTCA
31704188 TTGTATACTATTGTCTTAATTTTTTCA
1 TTGTATACTATTGTCTTAATTTTTTCA
31704215 TTGTATACTATTGTCTTAATTTTTTC
1 TTGTATACTATTGTCTTAATTTTTTC
31704241 TTTCATCTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.60
Consensus pattern (27 bp):
TTGTATACTATTGTCTTAATTTTTTCA
Found at i:31704351 original size:27 final size:28
Alignment explanation
Indices: 31704309--31704362 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
31704299 ATGATAATTT
31704309 TATATTGCATTAATTAAATAACAAAATCC
1 TATATTG-ATTAATTAAATAACAAAATCC
*
31704338 TATATTG-TTAATTAAATAACTAAAT
1 TATATTGATTAATTAAATAACAAAAT
31704363 AATTAAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 17 0.71
29 7 0.29
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (28 bp):
TATATTGATTAATTAAATAACAAAATCC
Done.