Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 40 of 106
Found at i:15247094 original size:42 final size:41
Alignment explanation
Indices: 15247035--15247154 Score: 177
Period size: 42 Copynumber: 2.9 Consensus size: 41
15247025 TGTTGATGTG
*
15247035 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTACT
1 GACCCGACTATGTGCGAGT-GGAGTGCGCATAAGCCGTTACT
* *
15247077 GACCCGGCTATGTGCGAGTGAGAGTGCGCATAAGCCGTTGCT
1 GACCCGACTATGTGCGAGTG-GAGTGCGCATAAGCCGTTACT
*
15247119 GACCTGACTATGTGCGAGTGGGAGTGCGCATAAGCC
1 GACCCGACTATGTGCGAGT-GGAGTGCGCATAAGCC
15247155 ATTGCATATG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
41 1 0.01
42 69 0.97
43 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (41 bp):
GACCCGACTATGTGCGAGTGGAGTGCGCATAAGCCGTTACT
Found at i:15257685 original size:2 final size:2
Alignment explanation
Indices: 15257678--15257702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15257668 TGTTTTCTTT
15257678 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15257703 CATCTTCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15265288 original size:382 final size:382
Alignment explanation
Indices: 15264596--15265335 Score: 1071
Period size: 382 Copynumber: 1.9 Consensus size: 382
15264586 GTTTTTAGGG
* * *
15264596 AACAACCATGTGTGGTATCGACTATAATTCTATCCAAGAGTGGGAAGAGGATTATATCAACTATC
1 AACAACCATGTGTGGTACCGACTACAATTCTATCCAAGAGTAGGAAGAGGATTATATCAACTATC
* *
15264661 CAGTTCAAGAAAGAAGAACCCTCATAGATGGTCATGCTCATCTACAAAGGCGGAGATAGTACAAT
66 CAGTTCAAGAAAGAAGAACCCTCATAGATGGTCATGCCCATCTACAAAGGCGGAGATAGTACAAA
* * *
15264726 TCCAATATCTGAGGGAGTGAAGCTAGTTTTGGAAGAATTTCAGGATATGATGCCAGAACAACTAC
131 TCCAATATCTGAGGGAGTGAAGCTAATTTTAGAAGAATTTCAAGATATGATGCCAGAACAACTAC
* **
15264791 CTAAGGCTTTACCACCTAGACAAGCTATTGATCATGAGATAGAATTACTCCCAAATGTTAAGCCA
196 ATAAGGCTTTACCACCTAGACAAGCTATTGATCATGAGATAGAATTACTCCCAAACATTAAGCCA
*
15264856 CCTGCAAAAAGGCCATACAGGATGGCTCCTCTAAGAGTGGGAAGAGGATTATATTAGCTATCTAA
261 CCTGCAAAAAGGCCATACAGGATGGCTCCTCTAAGAGTGGGAAGAGGATTATATTAACTATCTAA
*
15264921 TTCAAGAAAAG-AGAACCCTCTTATATGGTCATGCCTATTTGTATAATGTTCTCAAGA
326 TTCAAG-AAAGCAGAACCCTCCTATATGGTCATGCCTATTTGTATAATGTTCTCAAGA
* * *
15264978 AACAACCATGTGTGGTACCTACTACAATTCTA-CCTAATAGTAGGAAGAGGATTATATCAATTAT
1 AACAACCATGTGTGGTACCGACTACAATTCTATCC-AAGAGTAGGAAGAGGATTATATCAACTAT
* * * * * *
15265042 CTAGTTCAAGAGAGGAA-AACCTTTC-TATG-TGGTCATGCCCATTTATAAAGGTGGAGATAGTA
65 CCAGTTCAAGA-AAGAAGAACC-CTCATA-GATGGTCATGCCCATCTACAAAGGCGGAGATAGTA
*
15265104 CAAATCCAATATCTGAGGGAGTGAAGCTAATTTTAGAA-AATTTTCAAGATATGATGCTAGAACA
127 CAAATCCAATATCTGAGGGAGTGAAGCTAATTTTAGAAGAA-TTTCAAGATATGATGCCAGAACA
* * * *
15265168 ACTATATAAGG-TTCTACCACCTTGACAAGCTGTTGATCATGAGATAGAATTACTCCCAAGCATT
191 ACTACATAAGGCTT-TACCACCTAGACAAGCTATTGATCATGAGATAGAATTACTCCCAAACATT
* * *
15265232 AAGCCACTTGCAATAAGGCCATACAGGATGGCTCTTCTAAGAGTGGGAAGAGGATTATATTAACT
255 AAGCCACCTGCAAAAAGGCCATACAGGATGGCTCCTCTAAGAGTGGGAAGAGGATTATATTAACT
* * *
15265297 ATCTAGTTCAAGAAAGCATAACCCTCCTATGTGGTCATG
320 ATCTAATTCAAGAAAGCAGAACCCTCCTATATGGTCATG
15265336 GCCATCTACA
Statistics
Matches: 318, Mismatches: 33, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
381 10 0.03
382 301 0.95
383 7 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (382 bp):
AACAACCATGTGTGGTACCGACTACAATTCTATCCAAGAGTAGGAAGAGGATTATATCAACTATC
CAGTTCAAGAAAGAAGAACCCTCATAGATGGTCATGCCCATCTACAAAGGCGGAGATAGTACAAA
TCCAATATCTGAGGGAGTGAAGCTAATTTTAGAAGAATTTCAAGATATGATGCCAGAACAACTAC
ATAAGGCTTTACCACCTAGACAAGCTATTGATCATGAGATAGAATTACTCCCAAACATTAAGCCA
CCTGCAAAAAGGCCATACAGGATGGCTCCTCTAAGAGTGGGAAGAGGATTATATTAACTATCTAA
TTCAAGAAAGCAGAACCCTCCTATATGGTCATGCCTATTTGTATAATGTTCTCAAGA
Found at i:15265476 original size:257 final size:257
Alignment explanation
Indices: 15265011--15265522 Score: 697
Period size: 257 Copynumber: 2.0 Consensus size: 257
15265001 ACAATTCTAC
* * * * * *
15265011 CTAATAGTAGGAAGAGGATTATATCAATTATCTAGTTCAAGAGAGGAAAACCTTTCTATGTGGTC
1 CTAAGAGTAGGAAGAGGATTATATCAACTATCTAGTTCAAGAAAGCAAAACCCTCCTATGTGGTC
* * * * *
15265076 ATGCCCATTTATAAAGGTGGAGATAGTACAAATCCAATATCTGAGGGAGTGAAGCTAATTTTAGA
66 ATGCCCATCTACAAAGATGAAAATAGTACAAATCCAATATCTGAGGGAGTGAAGCTAATTTTAGA
* *
15265141 AAATTTTCAAGATATGATGCTAGAACAACTATATAAGGTTCTACCACCTTGACAAGCTGTTGATC
131 AAATTTTCAAGATATGATGCTAGAACAACTATATAAGGTTCTACCACCTTAACAAGCTATTGATC
* * **
15265206 ATGAGATAGAATTACTCCCAAGCATTAAGCCACTTGCAATAAGGCCATACAGGATGGCTCTT
196 ATGAGATAGAATTACTCCCAAGCATTAAGCCACCTGCAAAAAGGCCATACAAAATGGCTCTT
* * *
15265268 CTAAGAGTGGGAAGAGGATTATATTAACTATCTAGTTCAAGAAAGCATAACCCTCCTATGTGGTC
1 CTAAGAGTAGGAAGAGGATTATATCAACTATCTAGTTCAAGAAAGCAAAACCCTCCTATGTGGTC
* * * * * *
15265333 ATGGCCATCTACAAATATGAAAATATTACAAATCTAATAT-TCGAGGGAGTGAAGCTAGTTTTGG
66 ATGCCCATCTACAAAGATGAAAATAGTACAAATCCAATATCT-GAGGGAGTGAAGCTAATTTTAG
*
15265397 AAGAA-TTTCAGGATATGATGCTAGAACAACTACT-TAAGGTTCTACCACCTTAACAAGCTATTG
130 AA-AATTTTCAAGATATGATGCTAGAACAACTA-TATAAGGTTCTACCACCTTAACAAGCTATTG
* * * *
15265460 ATCATGAGATAGAATTACTCTCAAGCGTTAAGCCACCTGTAAAAATGCCATACAAAATGGCTC
193 ATCATGAGATAGAATTACTCCCAAGCATTAAGCCACCTGCAAAAAGGCCATACAAAATGGCTC
15265523 CCTCAAAGTT
Statistics
Matches: 221, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
256 1 0.00
257 217 0.98
258 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (257 bp):
CTAAGAGTAGGAAGAGGATTATATCAACTATCTAGTTCAAGAAAGCAAAACCCTCCTATGTGGTC
ATGCCCATCTACAAAGATGAAAATAGTACAAATCCAATATCTGAGGGAGTGAAGCTAATTTTAGA
AAATTTTCAAGATATGATGCTAGAACAACTATATAAGGTTCTACCACCTTAACAAGCTATTGATC
ATGAGATAGAATTACTCCCAAGCATTAAGCCACCTGCAAAAAGGCCATACAAAATGGCTCTT
Found at i:15268340 original size:70 final size:70
Alignment explanation
Indices: 15268266--15268435 Score: 164
Period size: 73 Copynumber: 2.4 Consensus size: 70
15268256 GAAGATGGCC
* **
15268266 AGTTCAGAAACAGAACCAACTTAATCTAAGA-GATATTGTTAGTCAACTAAGTGCTTACTGCCAG
1 AGTTCAGAAACAGAACCAACTTAATCTAAGAGGA-ATCGTTAGTCAACTAAAAGCTTACTGCCAG
*
15268330 AAGC-G
65 AAACTG
* * * * *
15268335 AAGTTCAGAAATAAAATCGACTTAATCGACTAAGAGGAATCGTTAGTCGACTAAAAGCTTACTGC
1 -AGTTCAGAAACAGAACCAACTTAAT---CTAAGAGGAATCGTTAGTCAACTAAAAGCTTACTGC
**
15268400 TTGAAACTG
62 CAGAAACTG
*
15268409 AGATCAGAAGACAGAACCAACTTAATC
1 AGTTCAGAA-ACAGAACCAACTTAATC
15268436 GACTAAGAAG
Statistics
Matches: 78, Mismatches: 16, Indels: 11
0.74 0.15 0.10
Matches are distributed among these distances:
70 21 0.27
71 1 0.01
73 41 0.53
74 15 0.19
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (70 bp):
AGTTCAGAAACAGAACCAACTTAATCTAAGAGGAATCGTTAGTCAACTAAAAGCTTACTGCCAGA
AACTG
Found at i:15272051 original size:19 final size:19
Alignment explanation
Indices: 15272029--15272066 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
15272019 CCATTTGACT
15272029 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
15272048 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
15272067 GTTGAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:15274274 original size:22 final size:23
Alignment explanation
Indices: 15274231--15274275 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
15274221 AGCTTTTACG
15274231 CTATAAAAATTATTTACGTATAACT
1 CTATAAAAATTATTTA--TATAACT
*
15274256 CTATAAATATTATTT-TATAA
1 CTATAAAAATTATTTATATAA
15274276 GAAAATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
25 14 0.74
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
CTATAAAAATTATTTATATAACT
Found at i:15275045 original size:36 final size:36
Alignment explanation
Indices: 15274963--15275068 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
15274953 TGTATGGAGG
* *
15274963 AAGCCCATGCCCAAAACTTAATAAAAGAAAAGAAAT
1 AAGCCCATGCCCAAAACTTATTAAAAGAAAAGAAAC
* ** * *
15274999 AGGCTTATGCCTATAACTTATTAAAAGAAAAGAAAC
1 AAGCCCATGCCCAAAACTTATTAAAAGAAAAGAAAC
*
15275035 AAGCCCATGCCCAAAACTTGTTAAAAGAAAAGAA
1 AAGCCCATGCCCAAAACTTATTAAAAGAAAAGAA
15275069 GCAGCTCAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (36 bp):
AAGCCCATGCCCAAAACTTATTAAAAGAAAAGAAAC
Found at i:15275600 original size:2 final size:2
Alignment explanation
Indices: 15275593--15275617 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15275583 TGTTTTCTTC
15275593 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15275618 TCTTCCNTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15275725 original size:128 final size:127
Alignment explanation
Indices: 15275496--15275743 Score: 487
Period size: 128 Copynumber: 1.9 Consensus size: 127
15275486 GAATGAGCTT
15275496 CTTTGTATAAAGACACTTCTAACTCTAGCAATCTCACTTAGATTGTGTGTTTTCTTAGGAAAATG
1 CTTTGTATAAAGACACTTCTAACTCTAGCAATCTCACTTAGATTGTGTGTTTTCTTAGGAAAATG
15275561 CTAAGCTTAGAGACCCATACCCTGTTTTCTTCTATATATATATATATATATATATATTCTTC
66 CTAAGCTTAGAGACCCATACCCTGTTTTCTTCTATATATATATATATATATATATATTCTTC
15275623 CNTTTGTATAAAGACACTTCTAACTCTAGCAATCTCACTTAGATTGTGTGTTTTCTTAGGAAAAT
1 C-TTTGTATAAAGACACTTCTAACTCTAGCAATCTCACTTAGATTGTGTGTTTTCTTAGGAAAAT
15275688 GCTAAGCTTAGAGACCCATACCCTGTTTTCTTCTATATATATATATATATATATAT
65 GCTAAGCTTAGAGACCCATACCCTGTTTTCTTCTATATATATATATATATATATAT
15275744 TCTTCCCATA
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 1 0.01
128 119 0.99
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.40
Consensus pattern (127 bp):
CTTTGTATAAAGACACTTCTAACTCTAGCAATCTCACTTAGATTGTGTGTTTTCTTAGGAAAATG
CTAAGCTTAGAGACCCATACCCTGTTTTCTTCTATATATATATATATATATATATATTCTTC
Found at i:15278846 original size:28 final size:28
Alignment explanation
Indices: 15278814--15278877 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
15278804 GTATAATTTT
*
15278814 ACCCA-CAAGAAAGCAGATGGATAACTTA
1 ACCCATCAA-AAAGCAGATGAATAACTTA
**
15278842 ACCCATCAAAAAGTGGATGAATAACTTA
1 ACCCATCAAAAAGCAGATGAATAACTTA
15278870 ACCCATCA
1 ACCCATCA
15278878 GGAAGTGGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.17
Consensus pattern (28 bp):
ACCCATCAAAAAGCAGATGAATAACTTA
Found at i:15278883 original size:28 final size:27
Alignment explanation
Indices: 15278833--15278914 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 27
15278823 AAAGCAGATG
15278833 GATAACTTAACCCATCAAAAAGTGGAT
1 GATAACTTAACCCATCAAAAAGTGGAT
**
15278860 GAATAACTTAACCCATCAGGAAGTGGATT
1 G-ATAACTTAACCCATCAAAAAGTGGA-T
* *
15278889 GATAACTTAATCCA-CCAAAAGTGGAT
1 GATAACTTAACCCATCAAAAAGTGGAT
15278915 AACCCACCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
26 1 0.02
27 9 0.19
28 35 0.74
29 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.23
Consensus pattern (27 bp):
GATAACTTAACCCATCAAAAAGTGGAT
Found at i:15278954 original size:28 final size:28
Alignment explanation
Indices: 15278914--15278989 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
15278904 CAAAAGTGGA
*
15278914 TAACCCACCAAAAGTAGATGGATACCTT
1 TAACCCACCAAAAGTAGATGCATACCTT
**
15278942 TAACCCACCAAAAGTAGATGCATATTTT
1 TAACCCACCAAAAGTAGATGCATACCTT
* * *
15278970 TAATCCACAAAAAGTGGATG
1 TAACCCACCAAAAGTAGATG
15278990 AATAATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (28 bp):
TAACCCACCAAAAGTAGATGCATACCTT
Found at i:15285596 original size:31 final size:29
Alignment explanation
Indices: 15285559--15285652 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 29
15285549 AAATATTAAT
15285559 TATAAAAATTTATTTAATTAAAAATAAAAA
1 TATAAAAATTT-TTTAATTAAAAATAAAAA
* * *
15285589 TATTAAAACTTTTTTTATTTAAAATAAAAA
1 TA-TAAAAATTTTTTAATTAAAAATAAAAA
* * * *
15285619 TACAAAAATTTGTTTAAAT-ATAATAAAAG
1 TATAAAAATTT-TTTAATTAAAAATAAAAA
15285648 TATAA
1 TATAA
15285653 GAGCTATTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 19 0.37
30 25 0.48
31 8 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
TATAAAAATTTTTTAATTAAAAATAAAAA
Found at i:15293465 original size:18 final size:18
Alignment explanation
Indices: 15293444--15293482 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
15293434 TACTTAATCC
15293444 TGTTATCGTGTTTAAACG
1 TGTTATCGTGTTTAAACG
15293462 TGTTATCGTGTTTAAACG
1 TGTTATCGTGTTTAAACG
15293480 TGT
1 TGT
15293483 ATACATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (18 bp):
TGTTATCGTGTTTAAACG
Found at i:15293762 original size:20 final size:20
Alignment explanation
Indices: 15293737--15293774 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
15293727 TTATATTTGA
*
15293737 TGTTATTATTATTTTTATTT
1 TGTTATAATTATTTTTATTT
15293757 TGTTATAATTATTTTTAT
1 TGTTATAATTATTTTTAT
15293775 AATTATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
TGTTATAATTATTTTTATTT
Found at i:15293854 original size:18 final size:18
Alignment explanation
Indices: 15293831--15293869 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
15293821 ATATTTTTAT
15293831 TTAATCATGTTAAACGTG
1 TTAATCATGTTAAACGTG
* *
15293849 TTAATCGTGTTAAATGTG
1 TTAATCATGTTAAACGTG
15293867 TTA
1 TTA
15293870 TTAATCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (18 bp):
TTAATCATGTTAAACGTG
Found at i:15294421 original size:27 final size:28
Alignment explanation
Indices: 15294391--15294449 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
15294381 ATTATGTGGA
15294391 AATAGAATAAAGTGA-TTTGTGG-AATAG
1 AATAGAATAAA-TGATTTTGTGGAAATAG
* *
15294418 AATA-AATTAATTATTTTGTGGAAATAG
1 AATAGAATAAATGATTTTGTGGAAATAG
15294445 AATAG
1 AATAG
15294450 GATATAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.07
26 12 0.44
27 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (28 bp):
AATAGAATAAATGATTTTGTGGAAATAG
Found at i:15294443 original size:22 final size:22
Alignment explanation
Indices: 15294367--15294443 Score: 57
Period size: 26 Copynumber: 3.3 Consensus size: 22
15294357 AAAATAGAAT
* *
15294367 GAAATAAAATAATTATTATGTG
1 GAAATAAATTAATTATTTTGTG
* *
15294389 GAAATAGAATAAAGTGA-TTTGTG
1 GAAATA-AATTAA-TTATTTTGTG
15294412 GAATAGAATAAATTAATTATTTTGTG
1 G---A-AATAAATTAATTATTTTGTG
15294438 GAAATA
1 GAAATA
15294444 GAATAGGATA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
22 10 0.24
23 11 0.26
24 2 0.05
25 2 0.05
26 13 0.31
27 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (22 bp):
GAAATAAATTAATTATTTTGTG
Found at i:15301718 original size:28 final size:29
Alignment explanation
Indices: 15301670--15301733 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
15301660 GTAAATTTTT
**
15301670 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAAGTG
**
15301699 AAAAATTACA-TTTTTGCCCCAAAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAAGTG
15301727 AAAAATT
1 AAAAATT
15301734 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 21 0.68
29 10 0.32
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAAGTG
Found at i:15308216 original size:9 final size:9
Alignment explanation
Indices: 15308199--15308285 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
15308189 AATGGTCCCG
15308199 AAGATCCAA
1 AAGATCCAA
*
15308208 AAGACCCAA
1 AAGATCCAA
* *
15308217 AAG-GCGTAA
1 AAGATC-CAA
15308226 AAGATCCAA
1 AAGATCCAA
*
15308235 AAGGTCCAA
1 AAGATCCAA
*
15308244 AAGATCTAGA
1 AAGATCCA-A
*
15308254 AA-A-CTTAA
1 AAGATC-CAA
15308262 AAGATCCAA
1 AAGATCCAA
* *
15308271 AAGGTCTAA
1 AAGATCCAA
15308280 AAGATC
1 AAGATC
15308286 AAGATTCAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
8 5 0.08
9 50 0.83
10 5 0.08
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14
Consensus pattern (9 bp):
AAGATCCAA
Found at i:15308245 original size:18 final size:18
Alignment explanation
Indices: 15308206--15308285 Score: 83
Period size: 18 Copynumber: 4.4 Consensus size: 18
15308196 CCGAAGATCC
*
15308206 AAAAGACCCAAAAGG-CGT
1 AAAAGATCCAAAAGGTC-T
*
15308224 AAAAGATCCAAAAGGTCC
1 AAAAGATCCAAAAGGTCT
* **
15308242 AAAAGATCTAGAAAACT-T
1 AAAAGATCCA-AAAGGTCT
15308260 AAAAGATCCAAAAGGTCT
1 AAAAGATCCAAAAGGTCT
15308278 AAAAGATC
1 AAAAGATC
15308286 AAGATTCAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
17 4 0.08
18 41 0.82
19 5 0.10
ACGTcount: A:0.53, C:0.17, G:0.16, T:0.14
Consensus pattern (18 bp):
AAAAGATCCAAAAGGTCT
Found at i:15309070 original size:41 final size:41
Alignment explanation
Indices: 15309025--15309108 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
15309015 ATTGCTTGAG
*
15309025 TTAGTAAGGGTAGAGGTGTGCTCTTTAATTTAGAGCTTTTA
1 TTAGTAAGGATAGAGGTGTGCTCTTTAATTTAGAGCTTTTA
* *
15309066 TTAGTGAGGATGGAGGTGTGCTCTTTAATTTAGAGCTTTTA
1 TTAGTAAGGATAGAGGTGTGCTCTTTAATTTAGAGCTTTTA
15309107 TT
1 TT
15309109 GACTTGATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (41 bp):
TTAGTAAGGATAGAGGTGTGCTCTTTAATTTAGAGCTTTTA
Found at i:15314032 original size:19 final size:19
Alignment explanation
Indices: 15313989--15314034 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
15313979 AAAATTTTAG
** *
15313989 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
15314008 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
*
15314027 ATTAAAAT
1 AATAAAAT
15314035 TTTATTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:15314984 original size:23 final size:22
Alignment explanation
Indices: 15314941--15315007 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 22
15314931 GCCCATAACT
15314941 AAGAAGAAAAGAGAAAGGAAAGGA
1 AAGAA-AAAAGA-AAAGGAAAGGA
15314965 AAGAAAAAAGAAAAGAGAAAGGA
1 AAGAAAAAAGAAAAG-GAAAGGA
*
15314988 AAGGAAAGAAAAAAAAGGAA
1 AA-GAAA-AAAGAAAAGGAA
15315008 GGCAAGGCTC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
22 4 0.10
23 15 0.38
24 12 0.31
25 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAGAAAAGGAAAGGA
Found at i:15315009 original size:23 final size:23
Alignment explanation
Indices: 15314941--15315014 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 23
15314931 GCCCATAACT
* *
15314941 AAGAAGAAAAGAGAAAGGAAAGGA
1 AAGAA-AAAAAAGGAAGGAAAGGA
15314965 AAGAAAAAAGAAAAGAGAAAGGAAAGGA
1 AAG--AAAA-AAAAG-G-AAGGAAAGGA
*
15314993 AAGAAAAAAAAGGAAGGCAAGG
1 AAGAAAAAAAAGGAAGGAAAGG
15315015 CTCGATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
23 8 0.19
24 4 0.10
25 7 0.17
26 10 0.24
28 13 0.31
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (23 bp):
AAGAAAAAAAAGGAAGGAAAGGA
Found at i:15315014 original size:28 final size:28
Alignment explanation
Indices: 15314944--15315001 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
15314934 CATAACTAAG
15314944 AAGAAAAGAGAAAGGAAAGGAAAGAAAA
1 AAGAAAAGAGAAAGGAAAGGAAAGAAAA
15314972 AAGAAAAGAGAAAGGAAAGGAAAGAAAA
1 AAGAAAAGAGAAAGGAAAGGAAAGAAAA
15315000 AA
1 AA
15315002 AAGGAAGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (28 bp):
AAGAAAAGAGAAAGGAAAGGAAAGAAAA
Found at i:15316375 original size:2 final size:2
Alignment explanation
Indices: 15316368--15316413 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
15316358 TTCCCTTAAT
15316368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
15316410 TA TA
1 TA TA
15316414 CGTGATGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15319083 original size:42 final size:42
Alignment explanation
Indices: 15319024--15319148 Score: 196
Period size: 42 Copynumber: 3.0 Consensus size: 42
15319014 TGTTGATGTG
15319024 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* *
15319066 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCATTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* * * *
15319108 GACCCGACTATATGCGAGTGGGAGTACGCATAAGCCGTTGC
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
15319149 ATATGAGATG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.21
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
Found at i:15320871 original size:21 final size:21
Alignment explanation
Indices: 15320845--15320972 Score: 69
Period size: 21 Copynumber: 5.6 Consensus size: 21
15320835 ACTTCACTTA
15320845 TTGTCTTAATTAAGACAAGAG
1 TTGTCTTAATTAAGACAAGAG
* *
15320866 TTGTCTCAATTTAGACAAGATGCATATG
1 TTGTCTTAATTAAGAC-A-A-G---A-G
*
15320894 TTGTCTTAATTAAGACAAGAA
1 TTGTCTTAATTAAGACAAGAG
*
15320915 TTG-CTTTAATTTAGACAAGAGTG
1 TTGTC-TTAATTAAGACAAGA--G
* * *
15320938 TATGTATTCATTTAAGACAAGGG
1 T-TGTCTT-AATTAAGACAAGAG
*
15320961 ATGTCTTAATTA
1 TTGTCTTAATTA
15320973 TATTTTTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 26
0.67 0.12 0.22
Matches are distributed among these distances:
20 1 0.01
21 35 0.44
22 7 0.09
23 3 0.04
24 5 0.06
25 11 0.14
26 1 0.01
27 2 0.03
28 15 0.19
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
TTGTCTTAATTAAGACAAGAG
Found at i:15322996 original size:19 final size:19
Alignment explanation
Indices: 15322935--15322996 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
15322925 ACAAGGGATG
*
15322935 TTAATTGATGAAAGTGGCC
1 TTAAATGATGAAAGTGGCC
* *
15322954 TTAAAT-CT-ACA-TGGCAC
1 TTAAATGATGAAAGTGGC-C
15322971 ATTAAATGATGAAAGTGGCC
1 -TTAAATGATGAAAGTGGCC
15322991 TTAAAT
1 TTAAAT
15322997 CTAAATGACA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 7 0.21
19 12 0.36
20 3 0.09
21 4 0.12
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (19 bp):
TTAAATGATGAAAGTGGCC
Found at i:15330525 original size:36 final size:36
Alignment explanation
Indices: 15330485--15330578 Score: 143
Period size: 36 Copynumber: 2.6 Consensus size: 36
15330475 TTATGTGTGC
*
15330485 GTGTGTGGTGTGGGAGTGCACATGACGATGATGGTG
1 GTGTGCGGTGTGGGAGTGCACATGACGATGATGGTG
* * *
15330521 GTGTGCGGTGTGGGAGTACACATGACGGTTATGGTG
1 GTGTGCGGTGTGGGAGTGCACATGACGATGATGGTG
*
15330557 GTGTGCGGTGTGGGACTGCACA
1 GTGTGCGGTGTGGGAGTGCACA
15330579 CGCTGATGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.16, C:0.12, G:0.46, T:0.27
Consensus pattern (36 bp):
GTGTGCGGTGTGGGAGTGCACATGACGATGATGGTG
Found at i:15334253 original size:3 final size:3
Alignment explanation
Indices: 15334245--15334276 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
15334235 TAAATATAGT
*
15334245 TAC TAC TAC TAC TAC TAT TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
15334277 AAGATAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (3 bp):
TAC
Found at i:15334764 original size:16 final size:16
Alignment explanation
Indices: 15334735--15334770 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
15334725 TTTTCTTTCA
* *
15334735 TTCAATACTTTTTTTT
1 TTCAACACTATTTTTT
15334751 TTCAACACTATTTTTT
1 TTCAACACTATTTTTT
15334767 TTCA
1 TTCA
15334771 TAATTTTACA
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:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCAACACTATTTTTT
Found at i:15335749 original size:15 final size:15
Alignment explanation
Indices: 15335723--15335770 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
15335713 GTTAATGTAG
15335723 AAATAAATAATAAATA
1 AAATAAA-AATAAATA
*
15335739 AAATAAAAATAATTA
1 AAATAAAAATAAATA
15335754 AAA-ATAAAATAAATA
1 AAATA-AAAATAAATA
15335769 AA
1 AA
15335771 GAAAAAGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 1 0.03
15 21 0.72
16 7 0.24
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAATAAATA
Found at i:15335760 original size:21 final size:22
Alignment explanation
Indices: 15335723--15335766 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
15335713 GTTAATGTAG
15335723 AAATAAATAATAAATAAAATAA
1 AAATAAATAATAAATAAAATAA
*
15335745 AAATAATTAA-AAATAAAATAA
1 AAATAAATAATAAATAAAATAA
15335766 A
1 A
15335767 TAAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATAAATAATAAATAAAATAA
Found at i:15336024 original size:21 final size:21
Alignment explanation
Indices: 15335989--15336030 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
15335979 GGCTTACCAC
*
15335989 TTTTTTTTGAGTTTTTTTGAA
1 TTTTTTTTGAGTTTTTGTGAA
15336010 TTTTTTTTGCA-TTTTTGTGAA
1 TTTTTTTTG-AGTTTTTGTGAA
15336031 CATGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.14, C:0.02, G:0.14, T:0.69
Consensus pattern (21 bp):
TTTTTTTTGAGTTTTTGTGAA
Found at i:15342136 original size:20 final size:19
Alignment explanation
Indices: 15342107--15342149 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
15342097 TACATTGCAT
15342107 AGAT-AAACAAATACACAAA
1 AGATAAAACAAAT-CACAAA
*
15342126 AGATAAAACAAATTACAAA
1 AGATAAAACAAATCACAAA
15342145 AGATA
1 AGATA
15342150 GAAGCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (19 bp):
AGATAAAACAAATCACAAA
Found at i:15353235 original size:117 final size:117
Alignment explanation
Indices: 15353028--15353249 Score: 390
Period size: 117 Copynumber: 1.9 Consensus size: 117
15353018 GAGGTGCACT
* *
15353028 CAAATCCTACCTCAGGAGTTATCCTACGCGCCTCTCCCATCGAGGTAAGCTCAATAATTGGGAAT
1 CAAATCCTACCTCAGGAGTTATCCTACGCGCCTCTCCAATCGAGGTAAGCTCAATAATTGAGAAT
*
15353093 CGTGCCCCTCTAATTAGGCTAGCCCACGGAACCCTCGTCATTGTAGTGCCCA
66 CGTGCCCCTCTAATTAGGCTAGCCCACGGAACCCCCGTCATTGTAGTGCCCA
* *
15353145 CAAATCCTACCTCGGGAGTTATTCTACGCGCCTCTCCAATCGAGGTAAGCTCAATAATTGAGAAT
1 CAAATCCTACCTCAGGAGTTATCCTACGCGCCTCTCCAATCGAGGTAAGCTCAATAATTGAGAAT
*
15353210 CGTGCCCCTCTAATTAGGCTGGCCCACGGAACCCCCGTCA
66 CGTGCCCCTCTAATTAGGCTAGCCCACGGAACCCCCGTCA
15353250 CTACAGTGCC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 99 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (117 bp):
CAAATCCTACCTCAGGAGTTATCCTACGCGCCTCTCCAATCGAGGTAAGCTCAATAATTGAGAAT
CGTGCCCCTCTAATTAGGCTAGCCCACGGAACCCCCGTCATTGTAGTGCCCA
Found at i:15353501 original size:13 final size:13
Alignment explanation
Indices: 15353483--15353507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15353473 TTTTTTAAAA
15353483 ATTTTATAAAATT
1 ATTTTATAAAATT
15353496 ATTTTATAAAAT
1 ATTTTATAAAAT
15353508 CCCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:15365852 original size:38 final size:38
Alignment explanation
Indices: 15365796--15366629 Score: 838
Period size: 38 Copynumber: 21.9 Consensus size: 38
15365786 CAAAAAAGAA
*
15365796 AAAAGGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
1 AAAA-GTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * *
15365835 AGAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * *
15365873 AAAAGTTTCATTGCCTCAATTTTGAAGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * *
15365911 AAAAAAAGTTTCATTGCCTCAATTTTGAAGAGTTCATTTTT
1 ---AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * * * *
15365952 AAAAAAAAAGTCTCGTTACCTCAGCTTTGAGGAATCCA-TTTT
1 -----AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* *
15365994 AAAAGTCTCGTTACCTCAGTTTTGAGGAGTTCATTTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCA-TTTTT
* ** *
15366033 AAAAGTCTCGTTGCCTCAACTTTAAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* **
15366071 -AAAGTCTCGTTGCCTCAACTTTGAGGAGTTCA-TTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* *
15366107 AGAAGTTTCGTTGCCTCAATTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* *
15366145 AAAAGTCTCGTTGCCTCAATTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
*
15366183 AAAAGTCTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* **
15366221 AAAAGTCTT-ATTGCCTCAGTTTTGAGGAGTTCA---AA
1 AAAAGT-TTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* *
15366256 AAAAGTTCCGTTGCCTCAATTTTGAGGAGTTCATTTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCA-TTTTT
**** *
15366295 AAAA-AAAAG-T--CTC-GTTAGTTGAGGAGTTCATTTTAA
1 AAAAGTTTCGTTGCCTCAGTT--TTGAGGAGTTCATTTT-T
* * * *
15366331 AAATAGTCTCATTGCCTCAATTTTGAGGAGTTTA-TTTT
1 AAA-AGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * *
15366369 AAAAATGTCATTGCCTCAGTTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * *
15366407 AAAAGTTTCGTTGCCTTAGTTTTAAGAAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * * *
15366445 AAAAGTCTCATTGCCTCAATTTTGAGGAGTTTA-TTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* **
15366482 AGAAGTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
*
15366520 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCA-TTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* * *
15366557 AAAAG-TCCGTTGCCTTAGCTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
* *
15366594 -AAAGTTTCGTCGCCTCAGCTTTGAGGAGTCTCATTT
1 AAAAGTTTCGTTGCCTCAGTTTTGAGGAGT-TCATTT
15366630 AAAAAAATAA
Statistics
Matches: 686, Mismatches: 80, Indels: 59
0.83 0.10 0.07
Matches are distributed among these distances:
34 3 0.00
35 35 0.05
36 48 0.07
37 184 0.27
38 285 0.42
39 45 0.07
40 11 0.02
41 41 0.06
42 6 0.01
43 28 0.04
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (38 bp):
AAAAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTT
Found at i:15366118 original size:113 final size:114
Alignment explanation
Indices: 15365796--15366629 Score: 864
Period size: 113 Copynumber: 7.3 Consensus size: 114
15365786 CAAAAAAGAA
* * * *
15365796 AAAAGGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAGAAGTTTCATTGCCTCAGCTTTGAG
1 AAAA-GTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAGCTTTGAG
* *
15365861 GAGTTCATTTTTAAAAGTTTCATTGCCTCAATTTTGAAGAGTTCATTTTTAAA
65 GAGTTCA-TTTTAAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTT--T
* * * *
15365914 AAAAGTTTCATTGCCTCAATTTTGAAGAGTTCATTTTTAAAAAAAAAGTCTCGTTACCTCAGCTT
1 AAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTT-----AAAAGTCTCGTTGCCTCAGCTT
* * * * * *
15365979 TGAGGAATCCATTTTAAAAGTCTCGTTACCTCAGTTTTGAGGAGTTCATTTTTT
61 TGAGGAGTTCATTTTAAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTT
* * *
15366033 AAAAGTCTCGTTGCCTCAACTTTAAGGAGTTCATTTTT-AAAGTCTCGTTGCCTCAACTTTGAGG
1 AAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAGCTTTGAGG
* *
15366097 AGTTCATTTTAGAAGTTTCGTTGCCTCAATTTTGAGGAGTTCA-TTTTT
66 AGTTCATTTTAAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTT
* * *
15366145 AAAAGTCTCGTTGCCTCAATTTTGAGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAGTTTTGAGG
1 AAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAGCTTTGAGG
* **
15366210 AGTTCATTTTTAAAAGTCTT-ATTGCCTCAGTTTTGAGGAGTTCA----AA
66 AGTTCA-TTTTAAAAGT-TTCATTGCCTCAATTTTGAGGAGTTCATTTTTT
* *
15366256 AAAAGTTCCGTTGCCTCAATTTTGAGGAGTTCATTTTTTAAAAAAAAGTCTCG-T---T-AG--T
1 AAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCA-TTTTT----AAAAGTCTCGTTGCCTCAGCTT
* *
15366314 TGAGGAGTTCATTTTAAAAATAGTCTCATTGCCTCAATTTTGAGGAGTT--TATTTT
61 TGAGGAGTTCATTTT--AAA-AGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTT
* * * ** * * * * *
15366369 AAAAATGTCATTGCCTCAGTTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTTAGTTTTAAGA
1 AAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAGCTTTGAGG
* *
15366434 AGTTCATTTTTAAAAGTCTCATTGCCTCAATTTTGAGGAGTT--TATTTT
66 AGTTCA-TTTTAAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTT
* *
15366482 AGAAGTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAGCTTTGAGG
1 AAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAGCTTTGAGG
* * * **
15366547 AGTTCATTTTAAAAG-TCCGTTGCCTTAGCTTTGAGGAGTTCA-TTTTT
66 AGTTCATTTTAAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTT
* *
15366594 -AAAGTTTCGTCGCCTCAGCTTTGAGGAGTCTCATTT
1 AAAAGTTTCGTTGCCTCAACTTTGAGGAGT-TCATTT
15366630 AAAAAAATAA
Statistics
Matches: 612, Mismatches: 72, Indels: 70
0.81 0.10 0.09
Matches are distributed among these distances:
108 13 0.02
109 13 0.02
110 4 0.01
111 102 0.17
112 72 0.12
113 216 0.35
114 34 0.06
115 13 0.02
116 14 0.02
117 30 0.05
118 4 0.01
119 33 0.05
121 37 0.06
122 27 0.04
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (114 bp):
AAAAGTTTCGTTGCCTCAACTTTGAGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAGCTTTGAGG
AGTTCATTTTAAAAGTTTCATTGCCTCAATTTTGAGGAGTTCATTTTTT
Found at i:15366654 original size:3 final size:3
Alignment explanation
Indices: 15366648--15366694 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
15366638 AAAAAAAACG
*
15366648 AAC AAC AAC AAC AAC AA- AAA AAC AAC AAAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC -AAC AAC AAC AAC AAC AAC
15366693 AA
1 AA
15366695 AAAAACACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:15366678 original size:27 final size:25
Alignment explanation
Indices: 15366638--15366720 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 25
15366628 TTAAAAAAAT
15366638 AAAAAAAACGAACAACAACAACAACA
1 AAAAAAAAC-AACAACAACAACAACA
15366664 AAAAAACAACAAACAACAACAACAACA
1 AAAAAA-AAC-AACAACAACAACAACA
* *
15366691 ACAAAAAAAC-ACAATAAAAACAA-A
1 A-AAAAAAACAACAACAACAACAACA
15366715 AAAAAA
1 AAAAAA
15366721 CATTGGTAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.10
24 2 0.04
25 11 0.21
26 6 0.12
27 23 0.44
28 5 0.10
ACGTcount: A:0.77, C:0.20, G:0.01, T:0.01
Consensus pattern (25 bp):
AAAAAAAACAACAACAACAACAACA
Found at i:15366684 original size:30 final size:31
Alignment explanation
Indices: 15366643--15366701 Score: 111
Period size: 30 Copynumber: 1.9 Consensus size: 31
15366633 AAAATAAAAA
15366643 AAACGAACAACAACAACAACAAAAAAACAAC
1 AAACGAACAACAACAACAACAAAAAAACAAC
15366674 AAAC-AACAACAACAACAACAAAAAAACA
1 AAACGAACAACAACAACAACAAAAAAACA
15366702 CAATAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.73, C:0.25, G:0.02, T:0.00
Consensus pattern (31 bp):
AAACGAACAACAACAACAACAAAAAAACAAC
Found at i:15368079 original size:30 final size:29
Alignment explanation
Indices: 15368037--15368101 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
15368027 GCAAATTTTC
*
15368037 AATTTTGGGGTAAAAATATAATTTATGAAA
1 AATTTGGGGGTAAAAATATAATTT-TGAAA
* * *
15368067 AGTTTGGGGGTAAAAGTGTAATTTTGAAA
1 AATTTGGGGGTAAAAATATAATTTTGAAA
15368096 AATTTG
1 AATTTG
15368102 CTCTACCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (29 bp):
AATTTGGGGGTAAAAATATAATTTTGAAA
Found at i:15379229 original size:15 final size:15
Alignment explanation
Indices: 15379206--15379235 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15379196 AACATAAAAC
15379206 TAAAATAAAACAACT
1 TAAAATAAAACAACT
*
15379221 TAAATTAAAACAACT
1 TAAAATAAAACAACT
15379236 CATCATGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAATAAAACAACT
Found at i:15387741 original size:42 final size:42
Alignment explanation
Indices: 15387682--15387807 Score: 198
Period size: 42 Copynumber: 3.0 Consensus size: 42
15387672 GTAATGATAT
* *
15387682 TGACCCGGCTATGTGCGAGTAGGAGTGTGCATAAGCCGATGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
* **
15387724 TGACCCGGCTATGTGCGAATGGGAGTGCGCATAAGCCGATAT
1 TGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
*
15387766 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGATGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
15387808 ATATGAGCTG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.21
Consensus pattern (42 bp):
TGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
Found at i:15388329 original size:19 final size:19
Alignment explanation
Indices: 15388305--15388341 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15388295 AGGTTTGGTG
15388305 AGAAACCCTCGGCTAGTTA
1 AGAAACCCTCGGCTAGTTA
*
15388324 AGAAACCCTCGGTTAGTT
1 AGAAACCCTCGGCTAGTT
15388342 GATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (19 bp):
AGAAACCCTCGGCTAGTTA
Found at i:15392936 original size:27 final size:27
Alignment explanation
Indices: 15392904--15392964 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
15392894 CCTATAAAAG
* *
15392904 AATAAAACTAAATCAATATTAAACTAA
1 AATAAAACTAAATCAACATAAAACTAA
* * * *
15392931 ACTAAAAGTAATTTAACATAAAACTAA
1 AATAAAACTAAATCAACATAAAACTAA
15392958 AATAAAA
1 AATAAAA
15392965 TAACTTAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.25
Consensus pattern (27 bp):
AATAAAACTAAATCAACATAAAACTAA
Found at i:15392968 original size:21 final size:22
Alignment explanation
Indices: 15392929--15392973 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
15392919 ATATTAAACT
**
15392929 AAACTAAAAGTAATTTAACATA
1 AAACTAAAAGTAAAATAACATA
*
15392951 AAACTAAAA-TAAAATAACTTA
1 AAACTAAAAGTAAAATAACATA
15392972 AA
1 AA
15392974 TTAAAACAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.24
Consensus pattern (22 bp):
AAACTAAAAGTAAAATAACATA
Found at i:15392972 original size:26 final size:27
Alignment explanation
Indices: 15392924--15392980 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
15392914 AATCAATATT
* *
15392924 AAACTAAACTAAAAGTAATTTAACA-TA
1 AAACTAAAATAAAAGTAACTTAA-ATTA
15392951 AAACTAAAATAAAA-TAACTTAAATTA
1 AAACTAAAATAAAAGTAACTTAAATTA
15392977 AAAC
1 AAAC
15392981 AACTCATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 13 0.48
27 13 0.48
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.25
Consensus pattern (27 bp):
AAACTAAAATAAAAGTAACTTAAATTA
Found at i:15395000 original size:30 final size:31
Alignment explanation
Indices: 15394958--15395022 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
15394948 TAAAAGATTT
*
15394958 ATTGGATTCAAAATAAAAGTATAAGAACTTA
1 ATTGGATTCAAAATAAAAATATAAGAACTTA
15394989 ATTGG-TTCAAAATAAAAATATAAGAACTTA
1 ATTGGATTCAAAATAAAAATATAAGAACTTA
15395019 ATTG
1 ATTG
15395023 AACGTAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (31 bp):
ATTGGATTCAAAATAAAAATATAAGAACTTA
Found at i:15395070 original size:19 final size:19
Alignment explanation
Indices: 15395048--15395085 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
15395038 TAAAGACTTA
15395048 TTAAAATTTTTTAAATAAT
1 TTAAAATTTTTTAAATAAT
*
15395067 TTAAAATTTTTTAGATAAT
1 TTAAAATTTTTTAAATAAT
15395086 ATGCCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTAAAATTTTTTAAATAAT
Found at i:15396697 original size:10 final size:11
Alignment explanation
Indices: 15396677--15396701 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15396667 AAGCAAAGAC
15396677 TTTCTTTTTTT
1 TTTCTTTTTTT
15396688 TTTCTTTTTTT
1 TTTCTTTTTTT
15396699 TTT
1 TTT
15396702 GTGTCCCTTA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:15411918 original size:20 final size:20
Alignment explanation
Indices: 15411893--15411930 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15411883 TTTTGTTTAA
15411893 AATGTATCGATACATTTGCC
1 AATGTATCGATACATTTGCC
* *
15411913 AATGTATCTATACTTTTG
1 AATGTATCGATACATTTG
15411931 AGATAGTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTGCC
Found at i:15414859 original size:26 final size:26
Alignment explanation
Indices: 15414803--15414861 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
15414793 GGCCGGCCAT
* *
15414803 AAGGAAAGAACAAGAGAGAAAATAGA
1 AAGGAAAGAACAAAAGAGAAAATACA
* *
15414829 GAGGAAAGGAAGAAAAGAGAAAA-ACA
1 AAGGAAA-GAACAAAAGAGAAAATACA
15414855 AAGGAAA
1 AAGGAAA
15414862 ACTAGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.02
Consensus pattern (26 bp):
AAGGAAAGAACAAAAGAGAAAATACA
Found at i:15417063 original size:15 final size:16
Alignment explanation
Indices: 15417032--15417068 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
15417022 GGTTTTGAAA
*
15417032 AAAGTTTTTGATTTTT
1 AAAGTTTTTGATATTT
15417048 AAAGTTTTTGA-ATTT
1 AAAGTTTTTGATATTT
15417063 AAAGTT
1 AAAGTT
15417069 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (16 bp):
AAAGTTTTTGATATTT
Found at i:15422805 original size:26 final size:26
Alignment explanation
Indices: 15422749--15422807 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
15422739 GGCCGGCCAT
* *
15422749 AAGGAAAGAACAAGAGAGAAAATAGA
1 AAGGAAAGAACAAAAGAGAAAATACA
* *
15422775 GAGGAAAGGAAGAAAAGAGAAAA-ACA
1 AAGGAAA-GAACAAAAGAGAAAATACA
15422801 AAGGAAA
1 AAGGAAA
15422808 ACTAGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.02
Consensus pattern (26 bp):
AAGGAAAGAACAAAAGAGAAAATACA
Found at i:15426890 original size:102 final size:102
Alignment explanation
Indices: 15426714--15426916 Score: 318
Period size: 102 Copynumber: 2.0 Consensus size: 102
15426704 CTACTAGTGA
* * ** * **
15426714 TGAGATAATGCAAGGAGCCAATTATATATCTATGGAGTGTTTGGTCTACAGGCGTACCTTTTTCA
1 TGAGATAATGCAAGGAGCAAATTATAGATCTATAAAGTGTTTGGTCAACAGAAGTACCTTTTTCA
15426779 TCCTTGTCAAGCATTGTTGAAGTGCTCATTGGTGTGG
66 TCCTTGTCAAGCATTGTTGAAGTGCTCATTGGTGTGG
*
15426816 TGAGAT-ATAGCAAGGAGCAAATTATAGATCTATAAAGTTTTTGGTCAACAGAAGTACCTTTTTC
1 TGAGATAAT-GCAAGGAGCAAATTATAGATCTATAAAGTGTTTGGTCAACAGAAGTACCTTTTTC
15426880 ATCCTTGTCAAGCATTGTTGAAGTGCTCATTGGTGTG
65 ATCCTTGTCAAGCATTGTTGAAGTGCTCATTGGTGTG
15426917 TGATATGTTC
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 2 0.02
102 90 0.98
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (102 bp):
TGAGATAATGCAAGGAGCAAATTATAGATCTATAAAGTGTTTGGTCAACAGAAGTACCTTTTTCA
TCCTTGTCAAGCATTGTTGAAGTGCTCATTGGTGTGG
Found at i:15427721 original size:18 final size:18
Alignment explanation
Indices: 15427694--15427732 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
15427684 CATCTAAAGC
15427694 TTCATCAATGTTTTTAGG
1 TTCATCAATGTTTTTAGG
*
15427712 TTCATTAATGTTTTTAGG
1 TTCATCAATGTTTTTAGG
15427730 TTC
1 TTC
15427733 GATTTGTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (18 bp):
TTCATCAATGTTTTTAGG
Found at i:15434894 original size:42 final size:42
Alignment explanation
Indices: 15434805--15434981 Score: 201
Period size: 42 Copynumber: 4.2 Consensus size: 42
15434795 AGCCGGGTCA
*
15434805 TCATCATCGGCTTATGCGCACTCCTTACTCGCACATAGTCGGG
1 TCATCATCGGCTTATGCGCACTCC-TACTCGCACATAGCCGGG
* *
15434848 TCATCATCGGCTTATGCGCACTCCTACTAGCACATAGCCAGG
1 TCATCATCGGCTTATGCGCACTCCTACTCGCACATAGCCGGG
* ** * *
15434890 TCATCATTGATTTATGAGCACTCTTACTCGCACATAGCCGGG
1 TCATCATCGGCTTATGCGCACTCCTACTCGCACATAGCCGGG
** * * * * *
15434932 TCATCATTAGCTCATGTGCCCTCCCACATCGCACATAGCTGGG
1 TCATCATCGGCTTATGCGCACTCCTAC-TCGCACATAGCCGGG
15434975 TCATCAT
1 TCATCAT
15434982 TATCACACAA
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
42 69 0.61
43 45 0.39
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.28
Consensus pattern (42 bp):
TCATCATCGGCTTATGCGCACTCCTACTCGCACATAGCCGGG
Found at i:15447488 original size:2 final size:2
Alignment explanation
Indices: 15447481--15447517 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
15447471 ATCTCCATGA
*
15447481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15447518 CTTGCGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15449629 original size:2 final size:2
Alignment explanation
Indices: 15449589--15449618 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15449579 ATCTGCTTGA
15449589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15449619 TGGGAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15450512 original size:21 final size:21
Alignment explanation
Indices: 15450488--15450530 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
15450478 TCTAAACAAT
* * *
15450488 TAAAATTAAAATTAGAACTAA
1 TAAAATAAAAACTAAAACTAA
*
15450509 TAAACTAAAAACTAAAACTAA
1 TAAAATAAAAACTAAAACTAA
15450530 T
1 T
15450531 CTAAAATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAATAAAAACTAAAACTAA
Found at i:15451718 original size:53 final size:54
Alignment explanation
Indices: 15451588--15451742 Score: 240
Period size: 54 Copynumber: 2.9 Consensus size: 54
15451578 ATAAGCACAT
*
15451588 ACACCACCATCTCACCCAGCTTATGTGCATCCCCCCACATCGTGCACATAGCCAG
1 ACACC-CCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
* * *
15451643 ACACCCCGTCTCACCCAGCTCATGTGCATCCCCCCACATCATGCACATAGCCGG
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
* *
15451697 ACACCCC-TCTCACCCAACTCATGTGCATCCCTCCACATCGTGCACA
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACA
15451743 AAATCGGAGT
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 36 0.39
54 52 0.56
55 5 0.05
ACGTcount: A:0.24, C:0.46, G:0.12, T:0.18
Consensus pattern (54 bp):
ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
Found at i:15451845 original size:40 final size:41
Alignment explanation
Indices: 15451757--15451856 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 41
15451747 CGGAGTCACA
**
15451757 GTGTGCATCCCCCCACATCGTGGACAAGCAATATCATCGCT
1 GTGTGCATCCCCCCACATCGTACACAAGCAATATCATCGCT
* * * *
15451798 TTATGCATCCCCCC-GATCGTACACAAGCAATATCATC-AT
1 GTGTGCATCCCCCCACATCGTACACAAGCAATATCATCGCT
15451837 CGTGTGCATCCCCCCACATC
1 -GTGTGCATCCCCCCACATC
15451857 ATGCACACGG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
39 1 0.02
40 32 0.67
41 15 0.31
ACGTcount: A:0.25, C:0.37, G:0.15, T:0.23
Consensus pattern (41 bp):
GTGTGCATCCCCCCACATCGTACACAAGCAATATCATCGCT
Found at i:15451981 original size:2 final size:2
Alignment explanation
Indices: 15451974--15452005 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
15451964 TTATGACATA
*
15451974 AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15452006 CAATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:15458320 original size:2 final size:2
Alignment explanation
Indices: 15458308--15458357 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
15458298 CAAATAGCTC
15458308 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15458350 TA TA TA TA
1 TA TA TA TA
15458358 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.93
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:15458462 original size:2 final size:2
Alignment explanation
Indices: 15458455--15458494 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
15458445 NNNNNNNNNN
*
15458455 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA 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
15458495 AGCATATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:15458585 original size:54 final size:55
Alignment explanation
Indices: 15458502--15458606 Score: 167
Period size: 54 Copynumber: 1.9 Consensus size: 55
15458492 ATAAGCATAT
* *
15458502 ACACCACCATCTCAACCAGCTCATGTGCATCCCCCCACATCATGTACATAGCTGG
1 ACACCACCATCTCAACCAACTCATGTGCATCCCCCCACATCATGCACATAGCTGG
* *
15458557 ACACC-CCATCTCACCCAACTCATGTGCATCCCCCCACATCGTGCACATAG
1 ACACCACCATCTCAACCAACTCATGTGCATCCCCCCACATCATGCACATAG
15458607 TCGGAGTCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 41 0.89
55 5 0.11
ACGTcount: A:0.27, C:0.43, G:0.11, T:0.19
Consensus pattern (55 bp):
ACACCACCATCTCAACCAACTCATGTGCATCCCCCCACATCATGCACATAGCTGG
Found at i:15458668 original size:41 final size:41
Alignment explanation
Indices: 15458581--15458766 Score: 220
Period size: 41 Copynumber: 4.6 Consensus size: 41
15458571 CCAACTCATG
* * *
15458581 TGCATCCCCCCACATCGTGCACATAGTCGGA-GTCATC-ATGTA
1 TGCATCCCCCCACATCGTGCACA-AG-C-AATATCATCGATTTA
*
15458623 --CATCCCCCCACATCGTGCACAAGCAATATCATCGCTTTA
1 TGCATCCCCCCACATCGTGCACAAGCAATATCATCGATTTA
*
15458662 TGCATCCCCCCACATCGTGCACAAGCAATATCATCGTTTTA
1 TGCATCCCCCCACATCGTGCACAAGCAATATCATCGATTTA
* * *
15458703 TGCATCCCCCCATATCGTGCACAAGCGATATCATC-ATCTTG
1 TGCATCCCCCCACATCGTGCACAAGCAATATCATCGAT-TTA
*
15458744 TGCATCCCCCTACATCGTGCACA
1 TGCATCCCCCCACATCGTGCACA
15458767 GCTAATGCCA
Statistics
Matches: 128, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
37 1 0.01
38 6 0.05
39 5 0.04
40 22 0.17
41 94 0.73
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (41 bp):
TGCATCCCCCCACATCGTGCACAAGCAATATCATCGATTTA
Found at i:15460412 original size:36 final size:36
Alignment explanation
Indices: 15460365--15460437 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
15460355 CTCTATTATA
15460365 TACTTGCCATGTCATTCATGTGCTTGATAGGATGTT
1 TACTTGCCATGTCATTCATGTGCTTGATAGGATGTT
15460401 TACTTGCCATGTCATTCATGTGCTTGATAGGATGTT
1 TACTTGCCATGTCATTCATGTGCTTGATAGGATGTT
15460437 T
1 T
15460438 GCATAAGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.42
Consensus pattern (36 bp):
TACTTGCCATGTCATTCATGTGCTTGATAGGATGTT
Found at i:15461108 original size:9 final size:9
Alignment explanation
Indices: 15461094--15461118 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
15461084 AAATTCAAGA
15461094 GAAATTTGT
1 GAAATTTGT
15461103 GAAATTTGT
1 GAAATTTGT
15461112 GAAATTT
1 GAAATTT
15461119 CAAAGGACAA
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:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (9 bp):
GAAATTTGT
Found at i:15470959 original size:20 final size:20
Alignment explanation
Indices: 15470934--15470974 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
15470924 ATAACCCTAG
*
15470934 TTGATTTTTATGAAATGAAA
1 TTGATTTATATGAAATGAAA
*
15470954 TTGATTTATGTGAAATGAAA
1 TTGATTTATATGAAATGAAA
15470974 T
1 T
15470975 GAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (20 bp):
TTGATTTATATGAAATGAAA
Found at i:15470992 original size:25 final size:23
Alignment explanation
Indices: 15470941--15470992 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 23
15470931 TAGTTGATTT
*
15470941 TTATGAAATGAAATTGATTTATG
1 TTATGAAATGAAATAGATTTATG
15470964 ---TGAAATGAAATGAGATTTGATG
1 TTATGAAATGAAAT-AGATTT-ATG
15470986 TTATGAA
1 TTATGAA
15470993 TCATATTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 8
0.72 0.03 0.25
Matches are distributed among these distances:
20 11 0.48
21 5 0.22
22 3 0.13
25 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (23 bp):
TTATGAAATGAAATAGATTTATG
Found at i:15472837 original size:22 final size:23
Alignment explanation
Indices: 15472798--15472844 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
15472788 ATTTCTATGC
15472798 ATTACTACAAAAACTAAGCT-AA
1 ATTACTACAAAAACTAAGCTCAA
*
15472820 ATTACTATC-AAAATTAAGCTCAA
1 ATTACTA-CAAAAACTAAGCTCAA
15472843 AT
1 AT
15472845 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (23 bp):
ATTACTACAAAAACTAAGCTCAA
Found at i:15480157 original size:14 final size:14
Alignment explanation
Indices: 15480122--15480164 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
15480112 TTCAAAGAGC
15480122 TTAATGTTTGAGAA
1 TTAATGTTTGAGAA
15480136 TT-ATGTTTG-GAAA
1 TTAATGTTTGAG-AA
15480149 TTAATGTTT-AGAA
1 TTAATGTTTGAGAA
15480162 TTA
1 TTA
15480165 TTTCTTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.04
13 16 0.62
14 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.47
Consensus pattern (14 bp):
TTAATGTTTGAGAA
Found at i:15482171 original size:2 final size:2
Alignment explanation
Indices: 15482164--15482198 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
15482154 GTATCTAGCT
15482164 TA TA TA TA TA TA TA TA T- TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15482199 GTAATCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:15482186 original size:9 final size:9
Alignment explanation
Indices: 15482163--15482198 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
15482153 CGTATCTAGC
15482163 TTATATATA
1 TTATATATA
15482172 -TATATATA
1 TTATATATA
15482180 TTATATATA
1 TTATATATA
15482189 TTATATATA
1 TTATATATA
15482198 T
1 T
15482199 GTAATCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTATATATA
Found at i:15482499 original size:2 final size:2
Alignment explanation
Indices: 15482492--15482526 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15482482 CGTCTGCTAC
15482492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15482527 GTAATCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15483949 original size:13 final size:12
Alignment explanation
Indices: 15483915--15483951 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
15483905 CAAATCACCC
*
15483915 TTTTTATTTATT
1 TTTTTATTTTTT
*
15483927 TTTTTATTTTAT
1 TTTTTATTTTTT
15483939 TTTTTATTTTTT
1 TTTTTATTTTTT
15483951 T
1 T
15483952 ATTCCTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTATTTTTT
Found at i:15494506 original size:29 final size:28
Alignment explanation
Indices: 15494402--15494580 Score: 173
Period size: 29 Copynumber: 6.3 Consensus size: 28
15494392 ATAAAGAGAG
* * ** *
15494402 AACATGTTATGTTGTCTAAATTGTGGCA
1 AACATGTTTTCTTGTCTAAATTAAGACA
* *
15494430 AACATGTTTTCTTGTCTAGATCAAGACAA
1 AACATGTTTTCTTGTCTAAATTAAGAC-A
*
15494459 AACATATTTTTCTTGTCTTAAATTAAGACA
1 AACAT-GTTTTCTTGTC-TAAATTAAGACA
* * * *
15494489 AACATGTTTTCTTATCT-TATTAAAAAA
1 AACATGTTTTCTTGTCTAAATTAAGACA
* *
15494516 AACATATTTTCTTATCTAAATTAAGACA
1 AACATGTTTTCTTGTCTAAATTAAGACA
15494544 TAACATGTCTTT-TTGTCTAAATTAAGACA
1 -AACATGT-TTTCTTGTCTAAATTAAGACA
15494573 AACATGTT
1 AACATGTT
15494581 AAAGTTGCTA
Statistics
Matches: 124, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
27 24 0.19
28 35 0.28
29 37 0.30
30 19 0.15
31 9 0.07
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (28 bp):
AACATGTTTTCTTGTCTAAATTAAGACA
Found at i:15494518 original size:27 final size:27
Alignment explanation
Indices: 15494429--15494532 Score: 82
Period size: 27 Copynumber: 3.7 Consensus size: 27
15494419 AAATTGTGGC
* * * *
15494429 AAACATGTTTTCTTGTCTAGATCAAGACA
1 AAACATGTTTTCTTATCT-TATTAA-AAA
* * * *
15494458 AAACATATTTTTCTTGTCTTAAATTAAGAC
1 AAACAT-GTTTTCTTATCTT--ATTAAAAA
15494488 AAACATGTTTTCTTATCTTATTAAAAA
1 AAACATGTTTTCTTATCTTATTAAAAA
*
15494515 AAACATATTTTCTTATCT
1 AAACATGTTTTCTTATCT
15494533 AAATTAAGAC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
27 23 0.38
29 17 0.28
30 17 0.28
31 4 0.07
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (27 bp):
AAACATGTTTTCTTATCTTATTAAAAA
Found at i:15495889 original size:560 final size:559
Alignment explanation
Indices: 15494825--15495948 Score: 2086
Period size: 560 Copynumber: 2.0 Consensus size: 559
15494815 TGTTTCAATA
15494825 CTTGATATTAATTATTAGTTATCCAATTGCAAACCTTACATTGAGAACCCACATAACCATCTAAT
1 CTTGATATTAATTATTAGTTATCCAATTGCAAACCTTACATTGAGAACCCACATAACCATCTAAT
*
15494890 GACAAAAAGTGAAATTACCATTTTACCCATTATATCAATTTTGTCCTCTTATCTTATTTCATTCA
66 GACAAAAAGTGAAATTACCATTTTACCCATTATATCAATTTTGTCCTCTTATCTTATTTCATCCA
15494955 ATTAGTGATTCAATACTCTAGATCTAATCTCTTTTGAGTATCCAGATGTGATAAGTAGCTAATTC
131 ATTAGTGATTCAATACTCTAGATCTAATCTCTTTTGAGTATCCAGATGTGATAAGTAGCTAATTC
*
15495020 ATTAATCCACTAGGCCCAGATTAATGATAAACATCCTGAAATCACTAGAAGTGATGTTAATGCTA
196 ATTAATCCACTAGGCCCAGATTAATGACAAACATCCTGAAATCACTAGAAGTGATGTTAATGCTA
15495085 TGAACTCTACTATTTGGATATATGTTCCTAAATGTTTATCTCGATTATAATCCCGACAAACAAAG
261 TGAACTCTACTATTTGGATATATGTTCCTAAATGTTTATCTCGATTATAATCCCGACAAACAAAG
15495150 TCTACATCAACACTTTATGATGATCATGCTCATGGTATATCAAAGATTATAAAGAGATTAAATAC
326 TCTACATCAACACTTTATGATGATCATGCTCATGGTATATCAAAGATTATAAAGAGATTAAATAC
* * *
15495215 GAGTCCACTATGCATCAAGATTTCGGTTCTACTATAAGCAAATGTATAAGTGTGAGATTAAGATT
391 AAGTCCACTATGCATCAAGATTTCGATTCTACTATAAGCAAATGTATAAGTGTGAGATTAAAATT
*
15495280 TAAGTAACGGTTAAACTTAAATTTGATTTTCACATGATTCTATTTTATGTTATAGTATCATTACT
456 TAAGTAACGGTTAAACTTAAATTTGATTTTCACATGATTCTAGTTTATGTTATAGTATCATTACT
15495345 CGAAGTTAACCATTGCGATGATTTGACATTCATTATTTC
521 CGAAGTTAACCATTGCGATGATTTGACATTCATTATTTC
* * *
15495384 CTTGATATTAATTATTAGTTGTCCAATTGCAAACCTTATATTGAGAACCCACATAACTATCTAAT
1 CTTGATATTAATTATTAGTTATCCAATTGCAAACCTTACATTGAGAACCCACATAACCATCTAAT
* *
15495449 GATAAAAAGTGAAATTACCATTTTACCCATTATATCAATTTTGTCCTCTTGTCTTATTTCATCCA
66 GACAAAAAGTGAAATTACCATTTTACCCATTATATCAATTTTGTCCTCTTATCTTATTTCATCCA
* *
15495514 ATTAGTGATTCAATACTCTAGATCTAATCTCTTTTGAGTATCCAGATGTGATGAGTAGCTACTTC
131 ATTAGTGATTCAATACTCTAGATCTAATCTCTTTTGAGTATCCAGATGTGATAAGTAGCTAATTC
**
15495579 ATTAATCCACTAGGCCCAGATTAATGACAAATTGTCCTGAAATCACTAGAAGTGATGTTAATGCT
196 ATTAATCCACTAGGCCCAGATTAATGACAAA-CATCCTGAAATCACTAGAAGTGATGTTAATGCT
*
15495644 ATGAACTCTACTATTTGGATATATGTTCCTAGATGTTTATCTCGATTATAATCCCGACAAACAAA
260 ATGAACTCTACTATTTGGATATATGTTCCTAAATGTTTATCTCGATTATAATCCCGACAAACAAA
*
15495709 GTCTACATCAACACTTTATGATGATTATGCTCATGGTATATCAAAGATTATAAAGAGATTAAATA
325 GTCTACATCAACACTTTATGATGATCATGCTCATGGTATATCAAAGATTATAAAGAGATTAAATA
15495774 CAAGTCCACTATGCATCAAGATTTCGATTCTACTATAAGCAAATGTATAAGTGTGAGATTAAAAT
390 CAAGTCCACTATGCATCAAGATTTCGATTCTACTATAAGCAAATGTATAAGTGTGAGATTAAAAT
15495839 TTAAGTAACGGTTAAACTTAAATTTGATTTTCACATGATTCTAGTTTATGTTATAGTATCATTAC
455 TTAAGTAACGGTTAAACTTAAATTTGATTTTCACATGATTCTAGTTTATGTTATAGTATCATTAC
15495904 TCGAAGTTAACCATTGCGATGATTTGACATTCATTATTTC
520 TCGAAGTTAACCATTGCGATGATTTGACATTCATTATTTC
15495944 CTTGA
1 CTTGA
15495949 AGTGAATCAT
Statistics
Matches: 547, Mismatches: 17, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
559 217 0.40
560 330 0.60
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (559 bp):
CTTGATATTAATTATTAGTTATCCAATTGCAAACCTTACATTGAGAACCCACATAACCATCTAAT
GACAAAAAGTGAAATTACCATTTTACCCATTATATCAATTTTGTCCTCTTATCTTATTTCATCCA
ATTAGTGATTCAATACTCTAGATCTAATCTCTTTTGAGTATCCAGATGTGATAAGTAGCTAATTC
ATTAATCCACTAGGCCCAGATTAATGACAAACATCCTGAAATCACTAGAAGTGATGTTAATGCTA
TGAACTCTACTATTTGGATATATGTTCCTAAATGTTTATCTCGATTATAATCCCGACAAACAAAG
TCTACATCAACACTTTATGATGATCATGCTCATGGTATATCAAAGATTATAAAGAGATTAAATAC
AAGTCCACTATGCATCAAGATTTCGATTCTACTATAAGCAAATGTATAAGTGTGAGATTAAAATT
TAAGTAACGGTTAAACTTAAATTTGATTTTCACATGATTCTAGTTTATGTTATAGTATCATTACT
CGAAGTTAACCATTGCGATGATTTGACATTCATTATTTC
Found at i:15498138 original size:99 final size:98
Alignment explanation
Indices: 15498011--15498208 Score: 351
Period size: 99 Copynumber: 2.0 Consensus size: 98
15498001 TATAAAATTT
* * *
15498011 GGCCAAAGATGGTTGTTGAAGGGCATGTGATTTTCTTACTTGTTTTTCATTCCAAACATCATTAA
1 GGCCAAAGAGGGTTGTTGAAGGGCATGTGATTTTCTTACTTGTTTTTCATGCCAAACATCATCAA
15498076 ACAACTAAAAACACTAAGATATCATGAAATCTA
66 ACAACTAAAAACACTAAGATATCATGAAATCTA
*
15498109 GNGCCAAAGAGGGTTGTTGAAGGGCATGTGATTTTCTTGCTTGTTTTTCATGCCAAACATCATCA
1 G-GCCAAAGAGGGTTGTTGAAGGGCATGTGATTTTCTTACTTGTTTTTCATGCCAAACATCATCA
15498174 AACAACTAAAAACACTAAGATATCATGAAATCTA
65 AACAACTAAAAACACTAAGATATCATGAAATCTA
15498208 G
1 G
15498209 CAAAATCCAC
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
98 1 0.01
99 94 0.99
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (98 bp):
GGCCAAAGAGGGTTGTTGAAGGGCATGTGATTTTCTTACTTGTTTTTCATGCCAAACATCATCAA
ACAACTAAAAACACTAAGATATCATGAAATCTA
Found at i:15506760 original size:20 final size:21
Alignment explanation
Indices: 15506720--15506766 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
15506710 AGATATCTAA
*
15506720 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
15506741 TATAATTGTTT-AAATAAAAT
1 AATAATTATTTGAAATAAAAT
15506761 AATAAT
1 AATAAT
15506767 ATTCTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:15507731 original size:13 final size:13
Alignment explanation
Indices: 15507713--15507737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15507703 TTCCAGAAAA
15507713 TTTATAAAATCAT
1 TTTATAAAATCAT
15507726 TTTATAAAATCA
1 TTTATAAAATCA
15507738 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:15516904 original size:27 final size:26
Alignment explanation
Indices: 15516849--15516905 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
15516839 ATTTTATTTT
*
15516849 ATTT-TTTAAATATTAATAATTGGTA
1 ATTTATTTAAATATTAATAATTGATA
*
15516874 ATTTATTTAAAATATTAATAATTGATC
1 ATTTATTT-AAATATTAATAATTGATA
15516901 ATTTA
1 ATTTA
15516906 ATTTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 3 0.11
27 21 0.75
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGATA
Found at i:15516993 original size:7 final size:7
Alignment explanation
Indices: 15516981--15517051 Score: 58
Period size: 7 Copynumber: 10.1 Consensus size: 7
15516971 TTAAATTGTA
15516981 ATAATTT
1 ATAATTT
15516988 ATAATTT
1 ATAATTT
15516995 ATAATTT
1 ATAATTT
* *
15517002 ATTTTATTA
1 A--TAATTT
*
15517011 ATAATTG
1 ATAATTT
15517018 ATAATTT
1 ATAATTT
*
15517025 A-AATAT
1 ATAATTT
15517031 -TAATATT
1 ATAAT-TT
15517038 -TAATTT
1 ATAATTT
15517044 ATAATTT
1 ATAATTT
15517051 A
1 A
15517052 ATTTTTAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
6 9 0.17
7 38 0.73
9 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (7 bp):
ATAATTT
Found at i:15517025 original size:120 final size:115
Alignment explanation
Indices: 15516793--15517052 Score: 294
Period size: 120 Copynumber: 2.2 Consensus size: 115
15516783 NNNNNNNNNN
* *
15516793 ATATTAATATTTTATT-TTATTTAAATATTATTATGATTAATTTTTCATTTTATTTTATTTTTTA
1 ATATTAATATTTTATTATAATTTAAATATTATTATGATTAATTTTTCAATTTATTTTATTTTTTA
* *
15516857 AATATTAATAATTGGTAATTTATTTAAAATATTAATAATTGATCATTTAA
66 AATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAATTTAA
* * * *
15516907 TTTTTAATATTTTATATATAATTTAAATGTTATTATGCTTATTTATTTTT-AATTTATTTTA-TT
1 ATATTAATATTTTAT-TATAATTTAAATATTATTATG---ATTAATTTTTCAATTTATTTTATTT
* ***
15516970 TTTAAAT-TGTAATAATTTATAATTTATAATTTATTTTATTAATAATTGATAATTTAA
62 TTTAAATAT-TAATAATTGATAA-TT-T-ATTTAAAATATTAATAATTGATAATTTAA
*
15517027 ATATTAATATTTAATTTATAATTTAA
1 ATATTAATATTTTA-TTATAATTTAA
15517053 TTTTTAATAT
Statistics
Matches: 121, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
114 13 0.11
115 1 0.01
116 18 0.15
117 20 0.17
118 12 0.10
119 10 0.08
120 46 0.38
121 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (115 bp):
ATATTAATATTTTATTATAATTTAAATATTATTATGATTAATTTTTCAATTTATTTTATTTTTTA
AATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAATTTAA
Found at i:15517047 original size:26 final size:26
Alignment explanation
Indices: 15517012--15517066 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
15517002 ATTTTATTAA
15517012 TAATTGATAATTTAAATATTAATATT
1 TAATTGATAATTTAAATATTAATATT
* * *
15517038 TAATTTATAATTTAATTTTTAATATT
1 TAATTGATAATTTAAATATTAATATT
15517064 TAA
1 TAA
15517067 ACTAGTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TAATTGATAATTTAAATATTAATATT
Found at i:15517050 original size:12 final size:12
Alignment explanation
Indices: 15516989--15517060 Score: 60
Period size: 12 Copynumber: 5.9 Consensus size: 12
15516979 TAATAATTTA
15516989 TAATTTATAATT
1 TAATTTATAATT
*
15517001 TATTTTATTAA--
1 TAATTTA-TAATT
*
15517012 TAATTGATAATT
1 TAATTTATAATT
15517024 TAAATATTA-ATATT
1 T-AAT-TTATA-ATT
15517038 TAATTTATAATT
1 TAATTTATAATT
*
15517050 TAATTTTTAAT
1 TAATTTATAAT
15517061 ATTTAAACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
10 3 0.06
11 5 0.10
12 23 0.48
13 11 0.23
14 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (12 bp):
TAATTTATAATT
Found at i:15517076 original size:41 final size:39
Alignment explanation
Indices: 15517021--15517128 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 39
15517011 ATAATTGATA
* *
15517021 ATTTAAATATTAATATTTAATTTATAATTTAATTTTTAAT
1 ATTTAAATAGTAATATTTAATTTATAATTTAA-TATTAAT
*
15517061 ATTTAAACTAGTAATATTTTATTTATAATTTAATATTAAT
1 ATTTAAA-TAGTAATATTTAATTTATAATTTAATATTAAT
* *
15517101 ATTTTGAAATATTAATATTTTA-TTATAA
1 A-TTT-AAATAGTAATATTTAATTTATAA
15517129 GTTGGAATCA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
40 20 0.33
41 38 0.62
42 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (39 bp):
ATTTAAATAGTAATATTTAATTTATAATTTAATATTAAT
Found at i:15519568 original size:5 final size:5
Alignment explanation
Indices: 15519544--15519614 Score: 85
Period size: 5 Copynumber: 14.6 Consensus size: 5
15519534 GCCATGCCCA
* * *
15519544 TTTTC CTTTC TTGTTA TTTTC TTTTC CTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
15519595 TTTTC -TTTC -TTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTT
15519615 CTTCCACCGT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
4 12 0.21
5 42 0.72
6 4 0.07
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:15521269 original size:21 final size:18
Alignment explanation
Indices: 15521245--15521289 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
15521235 GTTTAAATTA
15521245 TAAAATATTATGTTTTTCAAT
1 TAAAATATT-T-TTTTT-AAT
15521266 TAAAATATTTTTTTTAAT
1 TAAAATATTTTTTTTAAT
*
15521284 AAAAAT
1 TAAAAT
15521290 GAGATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 1 0.04
21 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TAAAATATTTTTTTTAAT
Found at i:15521288 original size:18 final size:21
Alignment explanation
Indices: 15521246--15521289 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
15521236 TTTAAATTAT
*
15521246 AAAATATTATGTTTTTCAATT
1 AAAATATTATGTTTTTCAATA
15521267 AAAATATT-T-TTTTT-AATA
1 AAAATATTATGTTTTTCAATA
15521285 AAAAT
1 AAAAT
15521290 GAGATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 5 0.23
20 1 0.05
21 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
AAAATATTATGTTTTTCAATA
Found at i:15529012 original size:16 final size:16
Alignment explanation
Indices: 15528988--15529021 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15528978 TAAAACAGAT
* *
15528988 ATGATGTGGGAATAGA
1 ATGAAGTGGAAATAGA
15529004 ATGAAGTGGAAATAGA
1 ATGAAGTGGAAATAGA
15529020 AT
1 AT
15529022 AGAATAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (16 bp):
ATGAAGTGGAAATAGA
Found at i:15529311 original size:22 final size:22
Alignment explanation
Indices: 15529286--15529523 Score: 62
Period size: 22 Copynumber: 10.3 Consensus size: 22
15529276 TTTTTATTTT
15529286 TTTATTTTTTAAATATTAATAA
1 TTTATTTTTTAAATATTAATAA
* *
15529308 TTTATATTTTCTTTATAATACTAATAT
1 -TT-TA-TTT-TTTA-AATATTAATAA
** **
15529335 TTTATCATTTAAATATTAATTT
1 TTTATTTTTTAAATATTAATAA
**
15529357 TTTA-TTGGT-AA-ATTAACT-A
1 TTTATTTTTTAAATATTAA-TAA
15529376 -TTATTTTTTACAATATTAATATTTTA
1 TTTATTTTTTA-AATATTAATA----A
* * * *
15529402 TTTATATTTTAAATGTT-GTTA
1 TTTATTTTTTAAATATTAATAA
**
15529423 TGATTATTTATTTTTAT-TTAAT--
1 T--TTATTT-TTTAAATATTAATAA
* *
15529445 TTTATCTTTTAAATATTAGTAA
1 TTTATTTTTTAAATATTAATAA
15529467 TTTATATTTTTATTTAAAATATTAATAA
1 -TT-TA--TTT-TTT-AAATATTAATAA
* * *
15529495 TTGATTATTTAAATATTAATAT
1 TTTATTTTTTAAATATTAATAA
15529517 TTTATTT
1 TTTATTT
15529524 ATAATTTAAT
Statistics
Matches: 155, Mismatches: 32, Indels: 57
0.64 0.13 0.23
Matches are distributed among these distances:
18 3 0.02
19 13 0.08
20 12 0.08
21 6 0.04
22 35 0.23
23 18 0.12
24 13 0.08
25 6 0.04
26 15 0.10
27 23 0.15
28 11 0.07
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (22 bp):
TTTATTTTTTAAATATTAATAA
Found at i:15529338 original size:27 final size:27
Alignment explanation
Indices: 15529293--15529344 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
15529283 TTTTTTATTT
*
15529293 TTTAAATATTAATAATTTAT-ATTTTC
1 TTTAAATACTAATAATTTATCATTTTC
*
15529319 TTTATAATACTAATATTTTATCATTT
1 TTTA-AATACTAATAATTTATCATTT
15529345 AAATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 14 0.64
28 4 0.18
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAAATACTAATAATTTATCATTTTC
Found at i:15529437 original size:157 final size:159
Alignment explanation
Indices: 15529184--15529522 Score: 443
Period size: 157 Copynumber: 2.1 Consensus size: 159
15529174 TATTTTATTT
** * ** * *
15529184 TTTAAATATTAATATTTTATTTATAATTTAA-TCATTAACATTGTAAAATACTAATATTTTATTT
1 TTTAAATATTAATATTTTATTGGTAAATTAACT-ATT-ATTTTTTACAATACTAATATTTTATTT
*
15529248 ATAATTTAAATGTTATTATGATTATCTTTTTTTATTT-TTTTATTTTTTAAATATTAATAATTTA
64 ATAATTTAAATGTTATTATGATTATCTTTTTTTATTTATTTTATCTTTTAAATATTAATAATTTA
* * * *
15529312 TA-TTTTCTTTATAATACTAATATTTTATCA
129 TATTTTTATTTAAAATACTAATAATTGATCA
* *
15529342 TTTAAATATTAATTTTTTATTGGTAAATTAACTATTATTTTTTACAATATTAATATTTTATTTAT
1 TTTAAATATTAATATTTTATTGGTAAATTAACTATTATTTTTTACAATACTAATATTTTATTTAT
* * *
15529407 ATTTTAAATGTTGTTATGATTAT-TTATTTTTATTTAATTTTATCTTTTAAATATTAGTAATTTA
66 AATTTAAATGTTATTATGATTATCTT-TTTTTATTT-ATTTTATCTTTTAAATATTAATAATTTA
* *
15529471 TATTTTTATTTAAAATATTAATAATTGATTA
129 TATTTTTATTTAAAATACTAATAATTGATCA
15529502 TTTAAATATTAATATTTTATT
1 TTTAAATATTAATATTTTATT
15529523 TATAATTTAA
Statistics
Matches: 156, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
156 2 0.01
157 54 0.35
158 30 0.19
159 28 0.18
160 42 0.27
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (159 bp):
TTTAAATATTAATATTTTATTGGTAAATTAACTATTATTTTTTACAATACTAATATTTTATTTAT
AATTTAAATGTTATTATGATTATCTTTTTTTATTTATTTTATCTTTTAAATATTAATAATTTATA
TTTTTATTTAAAATACTAATAATTGATCA
Found at i:15529470 original size:28 final size:28
Alignment explanation
Indices: 15529438--15529496 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
15529428 ATTTATTTTT
* * *
15529438 ATTTA-ATTTTATCTTTTAAATATTAGTA
1 ATTTATATTTT-TATTTAAAATATTAATA
15529466 ATTTATATTTTTATTTAAAATATTAATA
1 ATTTATATTTTTATTTAAAATATTAATA
15529494 ATT
1 ATT
15529497 GATTATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTATATTTTTATTTAAAATATTAATA
Found at i:15529941 original size:16 final size:16
Alignment explanation
Indices: 15529905--15529946 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
15529895 ATATTTTCAC
*
15529905 TTAATAATTTAAAAAA
1 TTAATATTTTAAAAAA
*
15529921 -CAATATTTTAAAAAA
1 TTAATATTTTAAAAAA
15529936 TTAATATTTTA
1 TTAATATTTTA
15529947 TTTATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAATATTTTAAAAAA
Found at i:15529961 original size:20 final size:17
Alignment explanation
Indices: 15529934--15529978 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
15529924 TATTTTAAAA
* *
15529934 AATTAATATTTTATTTAT
1 AATTAAAATATTA-TTAT
15529952 AATTAAAATA-TATTAT
1 AATTAAAATATTATTAT
15529968 AATTAAAATAT
1 AATTAAAATAT
15529979 GAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 14 0.58
17 2 0.08
18 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAAAATATTATTAT
Found at i:15529969 original size:16 final size:16
Alignment explanation
Indices: 15529948--15529978 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
15529938 AATATTTTAT
15529948 TTATAATTAAAATATA
1 TTATAATTAAAATATA
15529964 TTATAATTAAAATAT
1 TTATAATTAAAATAT
15529979 GAAAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATAATTAAAATATA
Found at i:15530008 original size:19 final size:19
Alignment explanation
Indices: 15529984--15530022 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
15529974 AATATGAAAA
* *
15529984 TATTAATAATTTTTTAATT
1 TATTAATAACTTATTAATT
15530003 TATTAATAACTTATTAATT
1 TATTAATAACTTATTAATT
15530022 T
1 T
15530023 TATAAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTAATAACTTATTAATT
Found at i:15532469 original size:30 final size:30
Alignment explanation
Indices: 15532408--15532469 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
15532398 AATTTTAAAT
* **
15532408 TTTGTTTTGTTATATTTGATGTTATTGTTA
1 TTTGTTTTGTTATAATTGATGTTATAATTA
* *
15532438 TTTGTTTTGTTATAATTGTTTTTATAATTA
1 TTTGTTTTGTTATAATTGATGTTATAATTA
15532468 TT
1 TT
15532470 GATTTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (30 bp):
TTTGTTTTGTTATAATTGATGTTATAATTA
Found at i:15532536 original size:9 final size:9
Alignment explanation
Indices: 15532519--15532548 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
15532509 ATATTTTTAT
15532519 TTAATCGTG
1 TTAATCGTG
*
15532528 TTAAACGTG
1 TTAATCGTG
15532537 TTAATCGTG
1 TTAATCGTG
15532546 TTA
1 TTA
15532549 TTAATCGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
TTAATCGTG
Found at i:15533540 original size:41 final size:39
Alignment explanation
Indices: 15533473--15533596 Score: 146
Period size: 39 Copynumber: 3.2 Consensus size: 39
15533463 GGACTGTATG
*
15533473 AACTACC-ACAAAACCAAATC-AAGGGTAGGACCATGTC
1 AACTACCAACGAAACCAAATCAAAGGGTAGGACCATGTC
* ** *
15533510 AACTACCAAAC-ACAATCATCTCAAAGGGGTAGGACCTTGTC
1 AACTACC-AACGA-AACCAAATCAAA-GGGTAGGACCATGTC
*
15533551 AACTACCAACGAAACCAAATCAAAGGGTAGGATCATGTC
1 AACTACCAACGAAACCAAATCAAAGGGTAGGACCATGTC
15533590 AACTACC
1 AACTACC
15533597 TAATCAAGCT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
37 7 0.10
38 1 0.01
39 28 0.39
40 14 0.19
41 22 0.31
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (39 bp):
AACTACCAACGAAACCAAATCAAAGGGTAGGACCATGTC
Found at i:15549567 original size:251 final size:250
Alignment explanation
Indices: 15548685--15550483 Score: 2250
Period size: 251 Copynumber: 7.2 Consensus size: 250
15548675 TATTATTATC
* * * * * * *
15548685 ACTTATTACGTTAATTCTCACACATTTACGTTAAGATTTTAAATTTACTTATTTCACTTTTACAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* ** * ** * *
15548750 GATTTTATATCAATTCTTACAACTTTACGTCAA-ACTTTTTCAATAGT-AACTTTT-AACTATAA
66 GTTTTTACGTCAATTGTTACAGTTTTACGTCAAGTC-TTTTCTAT-GTCAA-TTTTGAACTATAA
** * * * * * *
15548812 TTATCGTTATCTTTATTATTTTTTATTT-AAAATAAAAATTTAAATATTGTTACATACTTTTA-T
128 TTATTTTTATC-TTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGT
* * * * * *
15548875 CTCGATAATATAAATATAAATGTTTATTTTTCATTAAAATTAGATTTTTCTTACTTAATTA
192 -TTGAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTT-TTACTTAATTG
* ** * * *
15548936 ACTTATTGTGTTAACTCTAATACATTTACGTTAAGATTTAAAATTTAGTTATTCCACATTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * *
15549001 GTTTTTATGTCAATTGTTACAGTTTTACGTTAAGGCTTATT-TATGTCAATTTTGAACTATAATT
66 GTTTTTACGTCAATTGTTACAGTTTTACGTCAAGTCTT-TTCTATGTCAATTTTGAACTATAATT
* * * *
15549065 ATTATTATTATTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGCTC
130 ATTTTTA-TCTTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTTT
* * *
15549130 GAGAATATCAATTTAAATATTTATTTTTTACTAAAATTAAATTTTTTTTACTTAATTG
194 GAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGA-TTTTTTTACTTAATTG
15549188 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * * *
15549253 GTTTTTCCGTCAATTGTTGCAGTTTTATGTCAAGGT-TTATCTATGTCAATTTTGAATTATAATT
66 GTTTTTACGTCAATTGTTACAGTTTTACGTCAA-GTCTTTTCTATGTCAATTTTGAACTATAATT
* * ** * *
15549317 ATTTTTATCCTTATTATTCTTTGTTTAAAAATTAAAATTCGTATATCGTTAAATATTTTTAGTTT
130 ATTTTTAT-CTTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTTT
15549382 GAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTG
194 GAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTG
* * * *
15549439 ACTTGTTACATTAATTCTCACATATTTATGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * *
15549504 GGTTTTACGTCAATTCTTACAATTTTACATCAAGTCTTTTCTATGTCAATTTTGAACTATAATTA
66 GTTTTTACGTCAATTGTTACAGTTTTACGTCAAGTCTTTTCTATGTCAATTTTGAACTATAATTA
* * * *
15549569 TTTTTATCATATTATTCTTTATTTAAAAATTTAAATTTGTATATCGTTAAACACTTTTA-TTTCG
131 TTTTTATCTTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTTT-G
15549633 AGAATATAAATTTAAATATTTATTTTTCACTAAAA-TAGATTTTTTTTTACTTAATTG
195 AGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGA--TTTTTTTACTTAATTG
* * * * * *
15549690 ACTTGTTATGTTAACTCTCGCATATTTACGTTAAGATTTAAAATTTTGTTATTCTACTTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * * * *
15549755 ATTTTTTCATCAATTGTTACAGTTTTATGTCAAGGCTTATT-TATGTAAATTTTGAACTATAATT
66 GTTTTTACGTCAATTGTTACAGTTTTACGTCAAGTCTT-TTCTATGTCAATTTTGAACTATAATT
* * *
15549819 ATTTTTA--TTATTATTATTTATTTAAAAATTAAAATTTATATATTGTTAAACACTTGTAGTCTG
130 ATTTTTATCTTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTTTG
* *
15549882 AGAATATAAATTTAAATATTTATTTTTAACTAAAATTATATTTTTTTACTTAATTG
195 AGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTG
* * *
15549938 ACTTGTTACATTAATTCTCACATATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * * *
15550003 GGTTTTATGTTAATTCTTACAGTTTTACGTCAAGTCTTTTCTATATCAATTTTGAACTATAATTA
66 GTTTTTACGTCAATTGTTACAGTTTTACGTCAAGTCTTTTCTATGTCAATTTTGAACTATAATTA
* * * * * * *
15550068 TTTTCATCCTATTATTTTTTATTT-AAAATTAAAATTTGTTTATCTTTAAACACTTTTA-TTCCG
131 TTTTTATCTTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTT-TG
* *
15550131 AGAGTATAAATTTAAATATTTGTTTTTCACT-AAATTAGATTTTTTTACTTAATTG
195 AGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTG
* * * * *
15550186 ATTTGTTATGTTAACTCTCACACATTTACGTTCATATTTAAAATTTTGTTATTCCACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* ** *
15550251 GTTTTTTCGTCAATTGTTACAGTTTTACGTCAACACTTATCTATGTCAATTTTGAACTATAATTA
66 GTTTTTACGTCAATTGTTACAGTTTTACGTCAAGTCTTTTCTATGTCAATTTTGAACTATAATTA
* *
15550316 TTATTA--TTATTATTA-TTATTTAAAAATTAAAATTTATATATTGTTAAACACTTTTAGTCTT-
131 TTTTTATCTTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGT-TTG
*
15550377 AGAATATAAATTTTAATATTTATTTTTCACTAAAATTAGATTTTTTTTACTTAATTG
195 AGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGA-TTTTTTTACTTAATTG
* **
15550434 ACTTGTTATGTTAACTCTCACACATTTACACTAAGATTTAAAATTTAGTT
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTT
15550484 GTCAAGCTAA
Statistics
Matches: 1345, Mismatches: 176, Indels: 57
0.85 0.11 0.04
Matches are distributed among these distances:
245 6 0.00
246 65 0.05
247 11 0.01
248 332 0.25
249 145 0.11
250 109 0.08
251 388 0.29
252 283 0.21
253 6 0.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (250 bp):
ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
GTTTTTACGTCAATTGTTACAGTTTTACGTCAAGTCTTTTCTATGTCAATTTTGAACTATAATTA
TTTTTATCTTATTATTATTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTTTGA
GAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTG
Found at i:15560036 original size:2 final size:2
Alignment explanation
Indices: 15560029--15560055 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15560019 ACGTAATAAC
15560029 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15560056 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15560171 original size:2 final size:2
Alignment explanation
Indices: 15560164--15560198 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15560154 ACGTAATAAC
15560164 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15560199 TTAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15565706 original size:89 final size:88
Alignment explanation
Indices: 15565556--15565727 Score: 217
Period size: 89 Copynumber: 1.9 Consensus size: 88
15565546 TTTTAGTATT
* * * *
15565556 ATATGTTGTTTTATGTTAACTTGTTTAATTTTTGTATTTTTACGACCATGTACTTGCATCATGCA
1 ATATGTTGTTTTATGTTAACTAGTTTAATTTTTGTACTTTTACAACCATGCACTTGCATCATGCA
15565621 TCAATC-ATATAGGGATATCTACC
66 TCAATCAAT-TAGGGATATCTACC
*
15565644 ATATGTTGTTTTGTAT-TTATACTAGTTTAATTTTTGT-CTTTTACAATCATGCA-TTCGCATCA
1 ATATGTTG-TTT-TATGTTA-ACTAGTTTAATTTTTGTACTTTTACAACCATGCACTT-GCATCA
*
15565706 TGCATCCATCAATTAGGGATAT
62 TGCATCAATCAATTAGGGATAT
15565728 TTGCCACGTC
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
88 10 0.14
89 42 0.58
90 21 0.29
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (88 bp):
ATATGTTGTTTTATGTTAACTAGTTTAATTTTTGTACTTTTACAACCATGCACTTGCATCATGCA
TCAATCAATTAGGGATATCTACC
Found at i:15568260 original size:15 final size:16
Alignment explanation
Indices: 15568224--15568263 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
15568214 ACAAACAAGC
* *
15568224 AAAATTAAAGACACTG
1 AAAATTAAAAAAACTG
15568240 AAAATTAAAAAAACT-
1 AAAATTAAAAAAACTG
15568255 AAAATTAAA
1 AAAATTAAA
15568264 CTAGAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (16 bp):
AAAATTAAAAAAACTG
Found at i:15568839 original size:13 final size:13
Alignment explanation
Indices: 15568800--15568840 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
15568790 TATAAATATT
15568800 AAAACTAAACAAG
1 AAAACTAAACAAG
* *
15568813 -AAAGTATA-AAG
1 AAAACTAAACAAG
15568824 AAAACTAAACAAG
1 AAAACTAAACAAG
15568837 AAAA
1 AAAA
15568841 GAACTCCAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 3 0.14
12 12 0.55
13 7 0.32
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (13 bp):
AAAACTAAACAAG
Found at i:15573079 original size:4 final size:4
Alignment explanation
Indices: 15573070--15573100 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
15573060 ATTAATGAAC
15573070 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
15573101 CAAGAGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:15574204 original size:12 final size:12
Alignment explanation
Indices: 15574173--15574215 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
15574163 CCATAACATT
* *
15574173 TTTTTCAGCATC
1 TTTTTCAACTTC
*
15574185 TTTCTCAACTTC
1 TTTTTCAACTTC
*
15574197 TTTTTCAATTTC
1 TTTTTCAACTTC
15574209 TTTTTCA
1 TTTTTCA
15574216 GCAAGCTTAA
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:0.16, C:0.23, G:0.02, T:0.58
Consensus pattern (12 bp):
TTTTTCAACTTC
Found at i:15575218 original size:20 final size:20
Alignment explanation
Indices: 15575195--15575232 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15575185 TTTGGGAGAC
15575195 AGAAAAGACTTAGTCGACCA
1 AGAAAAGACTTAGTCGACCA
* *
15575215 AGAAATGAGTTAGTCGAC
1 AGAAAAGACTTAGTCGAC
15575233 TAAGTGCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
AGAAAAGACTTAGTCGACCA
Found at i:15575773 original size:35 final size:33
Alignment explanation
Indices: 15575734--15575862 Score: 120
Period size: 32 Copynumber: 3.8 Consensus size: 33
15575724 GTTGATCCCG
15575734 TGAAAAACCATTGTTGTAGGTTATGGTTGAGCCTT
1 TGAAAAACCATT-TTG-AGGTTATGGTTGAGCCTT
* * *
15575769 TGAAAAATCACTTTG-GGTTTTGGTTGAG-CTT
1 TGAAAAACCATTTTGAGGTTATGGTTGAGCCTT
* *
15575800 GTGAAAAACCATTATGAAAGGTTGTGGTTGAGCCTT
1 -TGAAAAACCATTTTG--AGGTTATGGTTGAGCCTT
* * *
15575836 TGAAAATCCACTTTG-GGTTTTGGTTGA
1 TGAAAAACCATTTTGAGGTTATGGTTGA
15575863 TCCGGTAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
31 3 0.04
32 35 0.45
34 3 0.04
35 34 0.44
36 3 0.04
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (33 bp):
TGAAAAACCATTTTGAGGTTATGGTTGAGCCTT
Found at i:15575805 original size:32 final size:32
Alignment explanation
Indices: 15575714--15575862 Score: 140
Period size: 35 Copynumber: 4.5 Consensus size: 32
15575704 AAGTTAGTTG
* ** *
15575714 TTGGGTTTTGGTTGATCCCGTGAAAAACCATT
1 TTGGGTTTTGGTTGAGCCTTTGAAAAACCACT
* *
15575746 GTTGTAGGTTATGGTTGAGCCTTTGAAAAATCACT
1 -TTG--GGTTTTGGTTGAGCCTTTGAAAAACCACT
15575781 TTGGGTTTTGGTTGAG-CTTGTGAAAAACCA-T
1 TTGGGTTTTGGTTGAGCCTT-TGAAAAACCACT
* *
15575812 TATGAAAGGTTGTGGTTGAGCCTTTGAAAATCCACT
1 T-TG---GGTTTTGGTTGAGCCTTTGAAAAACCACT
15575848 TTGGGTTTTGGTTGA
1 TTGGGTTTTGGTTGA
15575863 TCCGGTAAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
31 5 0.05
32 34 0.35
33 3 0.03
34 3 0.03
35 46 0.48
36 5 0.05
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (32 bp):
TTGGGTTTTGGTTGAGCCTTTGAAAAACCACT
Done.