Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015299.1 Kokia drynarioides strain JFW-HI SEQ_130344, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1333876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 300 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:665455 original size:16 final size:16
Alignment explanation
Indices: 665436--665466 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
665426 ATAATGCAAA
*
665436 GAATGAATAATTATAC
1 GAATGAATAAATATAC
665452 GAATGAATAAATATA
1 GAATGAATAAATATA
665467 TGAAAATAAG
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:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (16 bp):
GAATGAATAAATATAC
Found at i:665744 original size:59 final size:61
Alignment explanation
Indices: 665632--665764 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 61
665622 ATTTGGTGTC
* * *
665632 AAAATGCGA-TTTTGGGAAAGTTTGAGGGTCAAAATGTGATTTTTAAGGAGTTCGAGGACT-
1 AAAATGTGATTTTTGGGAAAGTTTGAGGGTCAAAATGTAATTTTTAAGAAGTTCGAGG-CTA
* * ** *
665692 AAAATGTGATTTTTGTG-AAGTTTG-GGGTTAAAATGTAATTTTTGTGAAGTTCGAGGGTA
1 AAAATGTGATTTTTGGGAAAGTTTGAGGGTCAAAATGTAATTTTTAAGAAGTTCGAGGCTA
*
665751 AAAATGTAATTTTT
1 AAAATGTGATTTTT
665765 TTTACAGAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
58 1 0.02
59 40 0.65
60 15 0.24
61 6 0.10
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.38
Consensus pattern (61 bp):
AAAATGTGATTTTTGGGAAAGTTTGAGGGTCAAAATGTAATTTTTAAGAAGTTCGAGGCTA
Found at i:665826 original size:30 final size:30
Alignment explanation
Indices: 665649--665867 Score: 156
Period size: 30 Copynumber: 7.3 Consensus size: 30
665639 GATTTTGGGA
* * * *
665649 AAGTTTGAGGGTCAAAATGTGATTTTTAAG
1 AAGTTTGGGGGTTAAAATGTAATTTTTACG
* * * ** * **
665679 GAGTTCGAGGACTAAAATGTGATTTTTGTG
1 AAGTTTGGGGGTTAAAATGTAATTTTTACG
**
665709 AAGTTT-GGGGTTAAAATGTAATTTTTGTG
1 AAGTTTGGGGGTTAAAATGTAATTTTTACG
* * *
665738 AAGTTCGAGGGTAAAAATGTAATTTTTTTTAC-
1 AAGTTTGGGGGTTAAAATGTAA---TTTTTACG
* * *
665770 AGAGTTTAGGGGCTAAAATGT-GTTTTTACG
1 A-AGTTTGGGGGTTAAAATGTAATTTTTACG
*
665800 AAATTTGGGGGTTAAAATGTAATTTTTACG
1 AAGTTTGGGGGTTAAAATGTAATTTTTACG
* * * *
665830 TAGTTTGGTGGTCAAAATGTAATTTTTGCG
1 AAGTTTGGGGGTTAAAATGTAATTTTTACG
665860 AAGTTTGG
1 AAGTTTGG
665868 AGGCCTTTTA
Statistics
Matches: 148, Mismatches: 34, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
29 47 0.32
30 81 0.55
32 1 0.01
33 19 0.13
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (30 bp):
AAGTTTGGGGGTTAAAATGTAATTTTTACG
Found at i:666861 original size:3 final size:3
Alignment explanation
Indices: 666853--666887 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
666843 CTTTATTTAT
666853 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
666888 TTAAAATCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:668237 original size:209 final size:208
Alignment explanation
Indices: 667869--668370 Score: 675
Period size: 209 Copynumber: 2.4 Consensus size: 208
667859 ACCTCTCTAT
* * * *
667869 ATCTCATCAGGAAGATGACCACTTCATTACTTCGACCCACTTCTTTGTATCTCATC-AGAAAGAT
1 ATCTCATTAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAAG-AAGAT
* * *
667933 AGGGGTTTGAAGTTTCACTCGCATTAAGTTTTGCTTTACTGAATTGGTCTACTTCTCTGTATCTC
65 -GGGGTTTGAAGTTTCACTCGCATTAAGCTTCGCTTCACTGAATTGGTCTACTTCTCTGTATCTC
* * * * * *
667998 ATCAAGAATATGACCGCTTCATTGTTTTAATCTACTTCTCTGTATCTCATCAGGAAGATGAATTT
129 ATCAAGAAGATGACCACTTCATTGTTTTAATCCACTTCTCTATATCTAATCAGGAAGACGAATTT
*
668063 GGTTCACTTCTCTGC
194 GGTTCAATTCTCTGC
* * *
668078 ATCTCGTTAGGAAGATGAACACTTTATTGCTTCGACCCATTTCTCTGTATCTCATCAAGAAGATG
1 ATCTCATTAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATG
* * * * *
668143 GGGTCTGGAAGTTTCACT-GACATTGAGCTTCGCTTCATTGAATTTGTCTACTTCTTTGTATCTC
66 GGGT-TTGAAGTTTCACTCG-CATTAAGCTTCGCTTCACTGAATTGGTCTACTTCTCTGTATCTC
* * * *
668207 ATTAGGAAGATGACCACTTCATTGTTTTAATCCACTTCTCTATATCTAATTAGGAAGACGGATTT
129 ATCAAGAAGATGACCACTTCATTGTTTTAATCCACTTCTCTATATCTAATCAGGAAGACGAATTT
668272 GGTTCAATTCTCTGC
194 GGTTCAATTCTCTGC
* * *
668287 ATCTCATTAAGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATTAGGAAGATG
1 ATCTCATTAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATG
*
668352 GGGTTTTGAATTTTCACTC
66 GGG-TTTGAAGTTTCACTC
668371 TTTCCTATGT
Statistics
Matches: 254, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
208 6 0.02
209 245 0.96
210 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (208 bp):
ATCTCATTAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATG
GGGTTTGAAGTTTCACTCGCATTAAGCTTCGCTTCACTGAATTGGTCTACTTCTCTGTATCTCAT
CAAGAAGATGACCACTTCATTGTTTTAATCCACTTCTCTATATCTAATCAGGAAGACGAATTTGG
TTCAATTCTCTGC
Found at i:668553 original size:39 final size:38
Alignment explanation
Indices: 668505--668643 Score: 95
Period size: 39 Copynumber: 3.6 Consensus size: 38
668495 GCTGACAATG
*
668505 ATCTACCCCATGATCGGGGTAAAAGGTCGAATGGCTACA
1 ATCTGCCCCATGATCGGGGTAAAAGGT-GAATGGCTACA
* * * **
668544 ATCTGCCCCAGGCTCGGGGT--AAGG-GATTGGCTGATGGTG
1 ATCTGCCCCATGATCGGGGTAAAAGGTGAATGGCT-A---CA
* * *
668583 ATCTGCCCCATGATCGGGGTAAAAGATAGAATGGTTGCA
1 ATCTGCCCCATGATCGGGGTAAAAGGT-GAATGGCTACA
* * *
668622 ATTTGCCCCAAGCTCGGGGTAA
1 ATCTGCCCCATGATCGGGGTAA
668644 GAGATTGGCT
Statistics
Matches: 75, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
35 7 0.09
36 1 0.01
37 4 0.05
39 54 0.72
41 3 0.04
43 6 0.08
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (38 bp):
ATCTGCCCCATGATCGGGGTAAAAGGTGAATGGCTACA
Found at i:668593 original size:78 final size:78
Alignment explanation
Indices: 668463--668732 Score: 317
Period size: 78 Copynumber: 3.5 Consensus size: 78
668453 ATTGGATGTT
* * * *** *
668463 TGCAATCTGCCCCTGTCAC-GGGTAAGAGATTGGCTGACAATGATCTACCCCATGATCGGGGTAA
1 TGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAA
*
668527 AAGGTCGAATGGC
66 AAGATCGAATGGC
* *
668540 TACAATCTGCCCCAGGCTCGGGGTAAGGGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAA
1 TGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAA
* *
668605 AAGATAGAATGGT
66 AAGATCGAATGGC
* * * * * **
668618 TGCAATTTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTAATCTGCCCCAGGCTCAAGGTAA
1 TGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAA
*
668683 AAGATCGAATGAC
66 AAGATCGAATGGC
* ** *
668696 TGCAATCTACCTTAGGCTTGGGGTAAGAGATTGGCTG
1 TGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTG
668733 GTCAGAATGA
Statistics
Matches: 162, Mismatches: 30, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
77 15 0.09
78 147 0.91
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (78 bp):
TGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAA
AAGATCGAATGGC
Found at i:668668 original size:39 final size:39
Alignment explanation
Indices: 668543--668675 Score: 149
Period size: 39 Copynumber: 3.4 Consensus size: 39
668533 GAATGGCTAC
*
668543 AATCTGCCCCAGGCTCGGGGTAAGGGATTGGCTGATGGT
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGT
* * * * * ** * * *
668582 GATCTGCCCCATGATCGGGGTAAAAGATAGAATGGTTGC
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGT
* *
668621 AATTTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGT
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGT
668660 AATCTGCCCCAGGCTC
1 AATCTGCCCCAGGCTC
668676 AAGGTAAAAG
Statistics
Matches: 70, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (39 bp):
AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGT
Found at i:671794 original size:23 final size:23
Alignment explanation
Indices: 671764--671811 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
671754 CTTGAATAGG
671764 TATGGTTCATTCCAATGATACTT
1 TATGGTTCATTCCAATGATACTT
671787 TATGGTTCATTCCAATGATACTT
1 TATGGTTCATTCCAATGATACTT
671810 TA
1 TA
671812 CAGCATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (23 bp):
TATGGTTCATTCCAATGATACTT
Found at i:678082 original size:99 final size:99
Alignment explanation
Indices: 677911--678106 Score: 365
Period size: 99 Copynumber: 2.0 Consensus size: 99
677901 AAGTTAAATA
677911 AACAAGCAGACAACGGAAGTTGCTTGAGGCTAAGAAGGAATTTTGGCCACTTATTCTTAAGTGCA
1 AACAAGCAGACAACGGAAGTTGCTTGAGGCTAAGAAGGAATTTTGGCCACTTATTCTTAAGTGCA
*
677976 AGACATTACCAGCAATGAAAGGTGTGGTAGTTTC
66 AGACATTACCAGCAACGAAAGGTGTGGTAGTTTC
678010 AACAAGCAGACAACGGAAGTTGCTTGAGGCTAAGAAGGAATTTTGGCCACTTATTCTTAAGTGCA
1 AACAAGCAGACAACGGAAGTTGCTTGAGGCTAAGAAGGAATTTTGGCCACTTATTCTTAAGTGCA
* *
678075 GGACATTACCAGTAACGAAAGGTGTGGTAGTT
66 AGACATTACCAGCAACGAAAGGTGTGGTAGTT
678107 ACTCGCATTT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (99 bp):
AACAAGCAGACAACGGAAGTTGCTTGAGGCTAAGAAGGAATTTTGGCCACTTATTCTTAAGTGCA
AGACATTACCAGCAACGAAAGGTGTGGTAGTTTC
Found at i:680162 original size:88 final size:88
Alignment explanation
Indices: 680013--680190 Score: 311
Period size: 88 Copynumber: 2.0 Consensus size: 88
680003 AACCACAAGC
680013 TCGAATACCACCATAACAAAATGCAATGCCAAATATTCAAGGACAACATCAACAACAACAACAAC
1 TCGAATACCACCATAACAAAATGCAATGCCAAATATTCAAGGACAACATCAACAACAACAACAAC
*
680078 AATATTCTCAACCAAAGATCATA
66 AATATTCTCAACCAAAGAGCATA
* * *
680101 TCGAATACCACCATAACAGAATGCAATGCCAAATATTCAAGGACAACATCAACAACGACAACAAG
1 TCGAATACCACCATAACAAAATGCAATGCCAAATATTCAAGGACAACATCAACAACAACAACAAC
*
680166 AATATTCTTAACCAAAGAGCATA
66 AATATTCTCAACCAAAGAGCATA
680189 TC
1 TC
680191 TGTTGGCTAC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.17
Consensus pattern (88 bp):
TCGAATACCACCATAACAAAATGCAATGCCAAATATTCAAGGACAACATCAACAACAACAACAAC
AATATTCTCAACCAAAGAGCATA
Found at i:686637 original size:17 final size:18
Alignment explanation
Indices: 686594--686637 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
686584 ATGCATATCA
* *
686594 TTTAGTTGTGATTGCATT
1 TTTAGTTGTCACTGCATT
*
686612 TTTATTTGTCACTGCA-T
1 TTTAGTTGTCACTGCATT
686629 TTTAGTTGT
1 TTTAGTTGT
686638 TAGTACATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.57
Consensus pattern (18 bp):
TTTAGTTGTCACTGCATT
Found at i:690207 original size:26 final size:26
Alignment explanation
Indices: 690147--690210 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
690137 TTGCGCCTAG
* *
690147 AATTGTCGCTACAAGAACTTATTCAG
1 AATTGTCGCTATAAGAACTTATTCAA
* *
690173 AGTTGTCGCTATAGGAACTTATTCAA
1 AATTGTCGCTATAAGAACTTATTCAA
*
690199 AATTATCGCTAT
1 AATTGTCGCTAT
690211 GTGAATATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (26 bp):
AATTGTCGCTATAAGAACTTATTCAA
Found at i:691567 original size:138 final size:138
Alignment explanation
Indices: 691319--691594 Score: 552
Period size: 138 Copynumber: 2.0 Consensus size: 138
691309 TGTTTATTTT
691319 TTGTTTTTGCACTTATTCTTTCTTATCTCACCTTTATTTGTTACTAATTTGTTTTCTTTTGTTAC
1 TTGTTTTTGCACTTATTCTTTCTTATCTCACCTTTATTTGTTACTAATTTGTTTTCTTTTGTTAC
691384 TGCTTTTACATTTTTCTTTTAGGTGTTTTATGACTTGGAGAAATCCTAAATTTATTGTTGGCTTA
66 TGCTTTTACATTTTTCTTTTAGGTGTTTTATGACTTGGAGAAATCCTAAATTTATTGTTGGCTTA
691449 GATCCAAA
131 GATCCAAA
691457 TTGTTTTTGCACTTATTCTTTCTTATCTCACCTTTATTTGTTACTAATTTGTTTTCTTTTGTTAC
1 TTGTTTTTGCACTTATTCTTTCTTATCTCACCTTTATTTGTTACTAATTTGTTTTCTTTTGTTAC
691522 TGCTTTTACATTTTTCTTTTAGGTGTTTTATGACTTGGAGAAATCCTAAATTTATTGTTGGCTTA
66 TGCTTTTACATTTTTCTTTTAGGTGTTTTATGACTTGGAGAAATCCTAAATTTATTGTTGGCTTA
691587 GATCCAAA
131 GATCCAAA
691595 AATCAAACGT
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (138 bp):
TTGTTTTTGCACTTATTCTTTCTTATCTCACCTTTATTTGTTACTAATTTGTTTTCTTTTGTTAC
TGCTTTTACATTTTTCTTTTAGGTGTTTTATGACTTGGAGAAATCCTAAATTTATTGTTGGCTTA
GATCCAAA
Found at i:716858 original size:13 final size:14
Alignment explanation
Indices: 716829--716858 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
716819 TCCAGTACAT
716829 TGACATTTAACCTC
1 TGACATTTAACCTC
716843 TGACATTTAA-CTC
1 TGACATTTAACCTC
716856 TGA
1 TGA
716859 TTGTGTTGAC
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:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:717187 original size:19 final size:18
Alignment explanation
Indices: 717160--717195 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
717150 TTACTTAACT
717160 TTTAGTCTCTATTGATTTG
1 TTTAGTCTCTATT-ATTTG
*
717179 TTTATTCTCTATTATTT
1 TTTAGTCTCTATTATTT
717196 TTTTTCAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.17, C:0.11, G:0.08, T:0.64
Consensus pattern (18 bp):
TTTAGTCTCTATTATTTG
Found at i:722882 original size:50 final size:50
Alignment explanation
Indices: 722807--722906 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
722797 CCTTGCAGAA
722807 ATAAAAATCATAATTTTGTCGAAGCATCGAAGCATGAATTGTCGCACATT
1 ATAAAAATCATAATTTTGTCGAAGCATCGAAGCATGAATTGTCGCACATT
* * *
722857 ATAAAAATCGTATTTTTGTCGAAGCATTGAAGCATGAATTGTCGCACATT
1 ATAAAAATCATAATTTTGTCGAAGCATCGAAGCATGAATTGTCGCACATT
722907 CTGTGATGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (50 bp):
ATAAAAATCATAATTTTGTCGAAGCATCGAAGCATGAATTGTCGCACATT
Found at i:725629 original size:10 final size:10
Alignment explanation
Indices: 725598--725648 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
725588 CAATCATTTG
*
725598 AAAAGAAACA
1 AAAAGAAAGA
* *
725608 AAATGAGA-A
1 AAAAGAAAGA
*
725617 AAAAGGAAGA
1 AAAAGAAAGA
*
725627 AAAAGAAAAA
1 AAAAGAAAGA
725637 AAAAGAAAGA
1 AAAAGAAAGA
725647 AA
1 AA
725649 TTTTTGATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
9 6 0.19
10 26 0.81
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:725642 original size:16 final size:17
Alignment explanation
Indices: 725598--725644 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
725588 CAATCATTTG
*
725598 AAAAGAAACAAAATGAGAA
1 AAAAGAAAGAAAA--AGAA
*
725617 AAAAGGAAGAAAAAGAA
1 AAAAGAAAGAAAAAGAA
725634 AAAA-AAAGAAA
1 AAAAGAAAGAAA
725645 GAAATTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
19 11 0.44
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAAAAAGAA
Found at i:726446 original size:20 final size:19
Alignment explanation
Indices: 726421--726460 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
726411 GTATCTTTCA
*
726421 TTATTTGATCTCTTTTATTC
1 TTATTTAATCT-TTTTATTC
*
726441 TTATTTAATGTTTTTATTC
1 TTATTTAATCTTTTTATTC
726460 T
1 T
726461 GTTTATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (19 bp):
TTATTTAATCTTTTTATTC
Found at i:726864 original size:13 final size:14
Alignment explanation
Indices: 726835--726864 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
726825 TCCAGTACAT
726835 TGACATTTAACCTC
1 TGACATTTAACCTC
726849 TGACATTTAA-CTC
1 TGACATTTAACCTC
726862 TGA
1 TGA
726865 TTGTGTTGAC
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:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:733207 original size:19 final size:19
Alignment explanation
Indices: 733161--733207 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
733151 AAAAATTGTG
733161 AATGAGAAAAAGAAAAGAAA
1 AATGA-AAAAAGAAAAGAAA
*
733181 AAGAGAAAAAGAGAAAAG-AA
1 AA-TGAAAAA-AGAAAAGAAA
733201 AATGAAA
1 AATGAAA
733208 TATTGCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (19 bp):
AATGAAAAAAGAAAAGAAA
Found at i:748798 original size:24 final size:22
Alignment explanation
Indices: 748765--748808 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
748755 ACAGAATATT
748765 TTTTTATTTTTTATTTTTCTCGTA
1 TTTTTA-TTTTT-TTTTTCTCGTA
*
748789 TTTTTCTTTTTTTTTTCTCG
1 TTTTTATTTTTTTTTTCTCG
748809 ACTTTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTTTATTTTTTTTTTCTCGTA
Found at i:752205 original size:24 final size:21
Alignment explanation
Indices: 752161--752200 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
752151 CAAGAGGAAC
*
752161 CTGCTTTTGAGGAGGAAGTTA
1 CTGCTGTTGAGGAGGAAGTTA
752182 CTGCTGTTGAGGAGGAAGT
1 CTGCTGTTGAGGAGGAAGT
752201 CGTTAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.30
Consensus pattern (21 bp):
CTGCTGTTGAGGAGGAAGTTA
Found at i:757720 original size:24 final size:24
Alignment explanation
Indices: 757683--757737 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
757673 GTTAAGAGTA
*
757683 AAAATTGTCAGTGCAAAAGTAATAT
1 AAAA-TGTCAGTGCAAAAGCAATAT
* *
757708 AAAATGTCTGTGCAAATGCAATAT
1 AAAATGTCAGTGCAAAAGCAATAT
757732 AAAATG
1 AAAATG
757738 AATTGATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAATGTCAGTGCAAAAGCAATAT
Found at i:765873 original size:52 final size:52
Alignment explanation
Indices: 765790--766027 Score: 352
Period size: 52 Copynumber: 4.6 Consensus size: 52
765780 ATGCAAAAAG
765790 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
* *
765842 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
* * *
765894 GGTCCGATGACTATGCGTCATCGTGAGTGTATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
* * * * * **
765946 GGTTCGATGACTATGTGTCATCATGAGTGTATGATTCCTTTACGGAA-CAACA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAC-GAATTATGA
765998 GGTCCGATGACTATGTGTCATCGTGAGTAT
1 GGTCCGATGACTATGTGTCATCGTGAGTAT
766028 TAAATGAAAT
Statistics
Matches: 169, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 167 0.99
53 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
Found at i:768167 original size:22 final size:23
Alignment explanation
Indices: 768140--768182 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
768130 AATAGTTAAC
*
768140 ATTGTCAATGTAA-TAAAAGTTA
1 ATTGTCAATGCAACTAAAAGTTA
*
768162 ATTGTCAGTGCAACTAAAAGT
1 ATTGTCAATGCAACTAAAAGT
768183 AAATCAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
ATTGTCAATGCAACTAAAAGTTA
Found at i:778875 original size:20 final size:21
Alignment explanation
Indices: 778838--778877 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
778828 CATTTTTGTT
*
778838 ATTTACTTTTATTTGTTTCAC
1 ATTTACTTTTAGTTGTTTCAC
778859 ATTTACTTTT-GTTGTTTCA
1 ATTTACTTTTAGTTGTTTCA
778878 AATTCCTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.62
Consensus pattern (21 bp):
ATTTACTTTTAGTTGTTTCAC
Found at i:780560 original size:39 final size:39
Alignment explanation
Indices: 780514--780612 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
780504 TTAAATAGGG
780514 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
780553 TTTTAATGTGTCTTATTTTGATACATATTTAATTGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
780592 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
780613 GACAAATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:780694 original size:32 final size:32
Alignment explanation
Indices: 780658--780720 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
780648 AGCCGAAATT
*
780658 AATTAGCTGATTAATGTATTTTAGGTACATGC
1 AATTAGCTGATTAATATATTTTAGGTACATGC
780690 AATTAGCTGATTAATATATTTTAGGTACATG
1 AATTAGCTGATTAATATATTTTAGGTACATG
780721 TATGGATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.41
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTTAGGTACATGC
Found at i:781033 original size:10 final size:10
Alignment explanation
Indices: 781018--781060 Score: 77
Period size: 10 Copynumber: 4.3 Consensus size: 10
781008 TCTAGCCTAG
781018 TCCATTCAGC
1 TCCATTCAGC
781028 TCCATTCAGC
1 TCCATTCAGC
781038 TCCATTCAGC
1 TCCATTCAGC
*
781048 TCCATTCAAC
1 TCCATTCAGC
781058 TCC
1 TCC
781061 TTACTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.21, C:0.42, G:0.07, T:0.30
Consensus pattern (10 bp):
TCCATTCAGC
Found at i:798488 original size:19 final size:19
Alignment explanation
Indices: 798464--798510 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
798454 TTGGTGATGT
798464 AGTTGTGCCAACAAATGGG
1 AGTTGTGCCAACAAATGGG
798483 AGTTGTGCCAACAAATGGG
1 AGTTGTGCCAACAAATGGG
798502 AGTTGTGCC
1 AGTTGTGCC
798511 CTGAGATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (19 bp):
AGTTGTGCCAACAAATGGG
Found at i:799445 original size:15 final size:17
Alignment explanation
Indices: 799422--799465 Score: 65
Period size: 15 Copynumber: 2.7 Consensus size: 17
799412 GAAGCCCAGA
799422 AAGGAAGAAAAGAAGAT
1 AAGGAAGAAAAGAAGAT
*
799439 -A-GAAGAATAGAAGAT
1 AAGGAAGAAAAGAAGAT
799454 AAGGAAGAAAAG
1 AAGGAAGAAAAG
799466 CACCATGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.07
Consensus pattern (17 bp):
AAGGAAGAAAAGAAGAT
Found at i:805093 original size:37 final size:37
Alignment explanation
Indices: 805043--805117 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
805033 CATTACTAGA
* *
805043 ACTTAAAATGGCCTTATCAACTTTTAAAAACAGTTTC
1 ACTTAAAATGGCCTTATCAACCTTTAAAAACAATTTC
*
805080 ACTTAAAATGGCCTTATCGACCTTTAAAAACAATTTC
1 ACTTAAAATGGCCTTATCAACCTTTAAAAACAATTTC
805117 A
1 A
805118 ACACCTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (37 bp):
ACTTAAAATGGCCTTATCAACCTTTAAAAACAATTTC
Found at i:817234 original size:52 final size:52
Alignment explanation
Indices: 817150--817331 Score: 274
Period size: 52 Copynumber: 3.5 Consensus size: 52
817140 AAAAAGGGTT
817150 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
* * *
817202 TGATGACTATGTGTCATCATGAGTATACGAATCCTTTACGGATTATGAGGTC
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
* * * ** *
817254 CGATGACTATGTGTCATCGTGATTGTATGATTCCTTTACGGAACAAGAGGTC
1 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
*
817306 CAATGACTATGTGTCATCGTGAGTAT
1 CGATGACTATGTGTCATCGTGAGTAT
817332 TAAATAAAAT
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 115 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (52 bp):
CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC
Found at i:829235 original size:13 final size:13
Alignment explanation
Indices: 829217--829241 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
829207 ATATAAATCA
829217 TATCAACCAATAG
1 TATCAACCAATAG
829230 TATCAACCAATA
1 TATCAACCAATA
829242 TCGCATTTAC
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:0.24, G:0.04, T:0.24
Consensus pattern (13 bp):
TATCAACCAATAG
Found at i:829537 original size:20 final size:20
Alignment explanation
Indices: 829514--829556 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
829504 CTAATAGAGA
* *
829514 CACCGAACTGCTAACAGAAG
1 CACCAAACTGCAAACAGAAG
* *
829534 CACCAAAGTGCAAACAGAGG
1 CACCAAACTGCAAACAGAAG
829554 CAC
1 CAC
829557 TGAAGTGCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.30, G:0.21, T:0.07
Consensus pattern (20 bp):
CACCAAACTGCAAACAGAAG
Found at i:835787 original size:44 final size:44
Alignment explanation
Indices: 835724--835812 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
835714 ATCTGCCCTC
835724 AATAACTGATAGTACTAGAAAGAATAATTGAATTTTCCTTACTT
1 AATAACTGATAGTACTAGAAAGAATAATTGAATTTTCCTTACTT
835768 AATAACTGATAGTACTAGAAAGAATAATTGAATTTTCCTTACTT
1 AATAACTGATAGTACTAGAAAGAATAATTGAATTTTCCTTACTT
835812 A
1 A
835813 TTATTTAAGT
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:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (44 bp):
AATAACTGATAGTACTAGAAAGAATAATTGAATTTTCCTTACTT
Found at i:851901 original size:25 final size:24
Alignment explanation
Indices: 851846--851908 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
851836 TTATTACTAT
851846 TTTTATTTTTATTTATGTTATTAA
1 TTTTATTTTTATTTATGTTATTAA
* * *
851870 TTGTATTATTTA-TTAGTGTTGTTTA
1 TTTTATT-TTTATTTA-TGTTATTAA
851895 TTTTA-TTTTATTTA
1 TTTTATTTTTATTTA
851909 ATTATTCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.12
24 13 0.41
25 15 0.47
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (24 bp):
TTTTATTTTTATTTATGTTATTAA
Found at i:862909 original size:26 final size:26
Alignment explanation
Indices: 862859--862921 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
862849 TAAATTAACC
862859 TAATTATTAATGAAATAATTCATGT-T
1 TAATTATTAA-GAAATAATTCATGTCT
*
862885 TAATTATTAA-AATATAATTTTATGTCT
1 TAATTATTAAGAA-ATAA-TTCATGTCT
*
862912 TAATAATTAA
1 TAATTATTAA
862922 TTATTTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 2 0.06
25 4 0.12
26 16 0.50
27 10 0.31
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (26 bp):
TAATTATTAAGAAATAATTCATGTCT
Found at i:868900 original size:19 final size:19
Alignment explanation
Indices: 868834--868900 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
868824 TAAATAATTA
868834 ATTAAATTACATAATATTT
1 ATTAAATTACATAATATTT
* *
868853 ATTATAATTTATGATATTAATTTT
1 ATTA-AA-TTA-CATAAT-A-TTT
868877 AATTAAATTACATAATATTT
1 -ATTAAATTACATAATATTT
868897 ATTA
1 ATTA
868901 TCAACCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
19 8 0.21
20 5 0.13
21 4 0.11
22 8 0.21
23 4 0.11
24 5 0.13
25 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (19 bp):
ATTAAATTACATAATATTT
Found at i:872990 original size:27 final size:27
Alignment explanation
Indices: 872960--873021 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
872950 TGACACAAAG
*
872960 GAACAAGAATTAAGGTGTGATTTAAGA
1 GAACAAGAATTAAGGCGTGATTTAAGA
* *
872987 GAACAAGATTTAAGGCGTGATTTAAGG
1 GAACAAGAATTAAGGCGTGATTTAAGA
*
873014 GAAAAAGA
1 GAACAAGA
873022 CTTATCAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.45, C:0.05, G:0.27, T:0.23
Consensus pattern (27 bp):
GAACAAGAATTAAGGCGTGATTTAAGA
Found at i:875413 original size:5 final size:5
Alignment explanation
Indices: 875403--875433 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
875393 AATTGATGAC
875403 GGATG GGATG GGATG GGATG GGATG GGATG G
1 GGATG GGATG GGATG GGATG GGATG GGATG G
875434 ATGACCGCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.61, T:0.19
Consensus pattern (5 bp):
GGATG
Found at i:876227 original size:6 final size:7
Alignment explanation
Indices: 876205--876234 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
876195 AAGAAAATAC
*
876205 AAACTTA
1 AAACTAA
876212 AAACTAA
1 AAACTAA
876219 AAACTAA
1 AAACTAA
876226 AAACTAA
1 AAACTAA
876233 AA
1 AA
876235 TCTAGTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACTAA
Found at i:877489 original size:21 final size:22
Alignment explanation
Indices: 877458--877499 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
877448 ATTCACACGT
877458 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
877480 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
877500 ATTTTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:901006 original size:21 final size:21
Alignment explanation
Indices: 900980--901030 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
900970 TCATAAAAGA
900980 AAACTAAACTAAATCTTCAA-G
1 AAACTAAACTAAATCTT-AAGG
901001 AAACTAAACTAAATCTTAAGG
1 AAACTAAACTAAATCTTAAGG
*
901022 AAACAAAAC
1 AAACTAAAC
901031 AAAAATACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.57, C:0.18, G:0.06, T:0.20
Consensus pattern (21 bp):
AAACTAAACTAAATCTTAAGG
Found at i:903637 original size:39 final size:39
Alignment explanation
Indices: 903583--903663 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
903573 TAGTAAGTAT
*
903583 ATATTATTTATTAATATAATAGATTAATCCAAATTAAAA
1 ATATTATTTATTAATATAAGAGATTAATCCAAATTAAAA
* *
903622 ATATTATTTATTAATATAAGAGATTAGTCTAAATTAAAA
1 ATATTATTTATTAATATAAGAGATTAATCCAAATTAAAA
903661 ATA
1 ATA
903664 ATTTAATTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.41
Consensus pattern (39 bp):
ATATTATTTATTAATATAAGAGATTAATCCAAATTAAAA
Found at i:906035 original size:31 final size:31
Alignment explanation
Indices: 905994--906056 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
905984 TGTACCCGAG
*
905994 TTAGATTTTGTTTTCGGGATTTGGTATTGTA
1 TTAGACTTTGTTTTCGGGATTTGGTATTGTA
906025 TTAGACTTTGTTTTCGGGATTTGGTATTGTA
1 TTAGACTTTGTTTTCGGGATTTGGTATTGTA
906056 T
1 T
906057 GTTTAGTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.05, G:0.25, T:0.54
Consensus pattern (31 bp):
TTAGACTTTGTTTTCGGGATTTGGTATTGTA
Found at i:906412 original size:29 final size:30
Alignment explanation
Indices: 906361--906427 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
906351 TCCGTTTGAG
*
906361 AAAATTATAATAAATGTAATAAAATAA-ATTCA
1 AAAATTATAATAAA--TAAT-AAATAATATTAA
906393 AAAATTATAATAAA-AATAAATAATATTAA
1 AAAATTATAATAAATAATAAATAATATTAA
906422 AAAATT
1 AAAATT
906428 GAGTAGGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 6 0.18
29 13 0.39
32 14 0.42
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (30 bp):
AAAATTATAATAAATAATAAATAATATTAA
Found at i:907449 original size:45 final size:48
Alignment explanation
Indices: 907351--907454 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 48
907341 CTACATTAAA
* * * *
907351 GTGACACTGTTCACGATTTTGATTATGTGGCAGTATATCCACGATTTTG
1 GTGACATTGTCCACGATATTGATTATGTGGCAG-ATATCCACGATATTG
**
907400 GTGAC-TTGTCCACGATATTGATTAT-TGGCA-ATATCTGCGATATTG
1 GTGACATTGTCCACGATATTGATTATGTGGCAGATATCCACGATATTG
907445 GTGACATTGT
1 GTGACATTGT
907455 TCACAATTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
45 17 0.35
46 4 0.08
47 5 0.10
48 17 0.35
49 5 0.10
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (48 bp):
GTGACATTGTCCACGATATTGATTATGTGGCAGATATCCACGATATTG
Found at i:908745 original size:12 final size:12
Alignment explanation
Indices: 908723--908754 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
908713 TTAACAAGTA
908723 AGTGAGTTGGCCT
1 AGTG-GTTGGCCT
908736 AGTGGTTGGCCT
1 AGTGGTTGGCCT
908748 AGTGGTT
1 AGTGGTT
908755 AAGTGCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.12, C:0.12, G:0.41, T:0.34
Consensus pattern (12 bp):
AGTGGTTGGCCT
Found at i:926600 original size:26 final size:26
Alignment explanation
Indices: 926544--926600 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
926534 GTTTTGGGCG
* *
926544 CAATTCTGGACATGATTATACAGCGA
1 CAATTCTGGACATGATTACACAACGA
926570 CAATTCTGGACAT-ATTCACACAACGA
1 CAATTCTGGACATGATT-ACACAACGA
*
926596 TAATT
1 CAATT
926601 TTGAACAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (26 bp):
CAATTCTGGACATGATTACACAACGA
Found at i:926681 original size:38 final size:37
Alignment explanation
Indices: 926639--926725 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 37
926629 AGGCATGCTT
* * *
926639 ATGCAGTGACAATTTTGGGCGTAATTCTAGACATCG-TC
1 ATGCAGTGACAATTCTGGGCGCAATTCT-GA-ATAGATC
926677 ATGCAGTGACAATTCTGGGCGCAATTCTGAATAGACTC
1 ATGCAGTGACAATTCTGGGCGCAATTCTGAATAGA-TC
926715 ATGCAGTGACA
1 ATGCAGTGACA
926726 TTAATAGTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 3 0.07
37 2 0.05
38 39 0.89
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (37 bp):
ATGCAGTGACAATTCTGGGCGCAATTCTGAATAGATC
Found at i:932821 original size:17 final size:17
Alignment explanation
Indices: 932801--932839 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
932791 GAAAATGTAG
932801 ATGCAACAACAATAAAA
1 ATGCAACAACAATAAAA
***
932818 ATGCAGTGACAATAAAA
1 ATGCAACAACAATAAAA
932835 ATGCA
1 ATGCA
932840 GGGATAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (17 bp):
ATGCAACAACAATAAAA
Found at i:936074 original size:38 final size:37
Alignment explanation
Indices: 936024--936102 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 37
936014 CATTCCTGGG
*
936024 TGCAATTGAAGAATACTTATGCAGTGAAAGTTTTAGA
1 TGCAATTGAAGAATACTTATGCAGTGAAAGTCTTAGA
* * * *
936061 TGCAATTTGAAGAATATTTATGCGGTGACAGTCTTAGG
1 TGCAA-TTGAAGAATACTTATGCAGTGAAAGTCTTAGA
936099 TGCA
1 TGCA
936103 TTTCAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 5 0.14
38 31 0.86
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (37 bp):
TGCAATTGAAGAATACTTATGCAGTGAAAGTCTTAGA
Found at i:936115 original size:37 final size:38
Alignment explanation
Indices: 936035--936115 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 38
936025 GCAATTGAAG
* * * *
936035 AATACTTATGCAGTGAAAGTTTTAGATGCAATTTGAAG
1 AATATTTATGCAGTGAAAGTCTTAGATGCAATTTCAAA
* * *
936073 AATATTTATGCGGTGACAGTCTTAGGTGC-ATTTCAAA
1 AATATTTATGCAGTGAAAGTCTTAGATGCAATTTCAAA
936110 AATATT
1 AATATT
936116 CCTACAGCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 12 0.33
38 24 0.67
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (38 bp):
AATATTTATGCAGTGAAAGTCTTAGATGCAATTTCAAA
Found at i:937735 original size:21 final size:21
Alignment explanation
Indices: 937694--937736 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
937684 TCAGCATCTT
* *
937694 TTTTCTTCATCTTTTTCTTCC
1 TTTTCTTCAACTTTGTCTTCC
937715 TTTTCTTCAACTTGTGT-TTCC
1 TTTTCTTCAACTT-TGTCTTCC
937736 T
1 T
937737 CCCCTTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.07, C:0.26, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTCTTCAACTTTGTCTTCC
Found at i:939805 original size:38 final size:39
Alignment explanation
Indices: 939710--939807 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 39
939700 CTTACAGCGA
* * *
939710 CAATTCTGGGCAT-GTTCATGTAGTGACAATTTTGGACG
1 CAATTCTAGACATAGTTCATGCAGTGACAATTTTGGACG
* * *
939748 TAATTCTAGACATCG-TCATGCAGTGACAATTTTGGGCG
1 CAATTCTAGACATAGTTCATGCAGTGACAATTTTGGACG
939786 CAATTCTA-A-ATAGATTCATGCA
1 CAATTCTAGACATAG-TTCATGCA
939808 ACGACATTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
36 3 0.06
37 1 0.02
38 45 0.90
39 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (39 bp):
CAATTCTAGACATAGTTCATGCAGTGACAATTTTGGACG
Found at i:947388 original size:31 final size:30
Alignment explanation
Indices: 947323--947398 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
947313 AATATAACGT
* *
947323 TTGGTACGTAAACTTGACATTTTTCCTAAT
1 TTGGTACCTAAACTTGACATTTTTCCTAAG
**
947353 TTGGTACCTAAACTTGACATTTTTTTTTAAG
1 TTGGTACCTAAACTTGACA-TTTTTCCTAAG
*
947384 TTGGTACTTAAACTT
1 TTGGTACCTAAACTT
947399 TTTTGGGGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 18 0.45
31 22 0.55
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.46
Consensus pattern (30 bp):
TTGGTACCTAAACTTGACATTTTTCCTAAG
Found at i:947668 original size:32 final size:30
Alignment explanation
Indices: 947599--947705 Score: 85
Period size: 32 Copynumber: 3.5 Consensus size: 30
947589 ATTTAATACA
947599 TTTAGGTACCAAATTGAATCTAAAAAAAAAAG
1 TTTAGGTACCAAATTGAA--TAAAAAAAAAAG
* *
947631 CTTAGGTACCAAATTAGAA-AAAAAATACCAAG
1 TTTAGGTACCAAATT-GAATAAAAAA-A-AAAG
* * **
947663 TTTAGGTATCAAATTGAGT--CCAAAAAAG
1 TTTAGGTACCAAATTGAATAAAAAAAAAAG
*
947691 TTTAAGTACCAAATT
1 TTTAGGTACCAAATT
947706 AGGAAAACGT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
28 16 0.26
29 1 0.02
30 8 0.13
31 3 0.05
32 30 0.49
33 3 0.05
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (30 bp):
TTTAGGTACCAAATTGAATAAAAAAAAAAG
Found at i:948076 original size:59 final size:59
Alignment explanation
Indices: 947960--948151 Score: 215
Period size: 59 Copynumber: 3.2 Consensus size: 59
947950 ATTTAATAAA
* * * * *
947960 TTTAGGTACCAAATTGAATCTAAAAAAAGCTTAGGTACCAAACTAAGAAAATATGTCAAG
1 TTTAGGTACCAAATTGAGTC-AAAAAAAGTTTAAGTACCAAATTAAGAAAATGTGTCAAG
* *
948020 TTTAGGTACCAAATTGAGTCCAAAAAAGTTTAAGTACCAAATTAGGAAAATGTGTCAA-
1 TTTAGGTACCAAATTGAGTCAAAAAAAGTTTAAGTACCAAATTAAGAAAATGTGTCAAG
* * * ** * *
948078 TTTCAAGTATCAAATTGGGTCAAAAAAAGTTTAAGTACTTACTTAAGAAAAAGTGTCAAG
1 TTT-AGGTACCAAATTGAGTCAAAAAAAGTTTAAGTACCAAATTAAGAAAATGTGTCAAG
* *
948138 TTCATGTACCAAAT
1 TTTAGGTACCAAAT
948152 GTTATATTAA
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
58 3 0.03
59 87 0.78
60 21 0.19
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (59 bp):
TTTAGGTACCAAATTGAGTCAAAAAAAGTTTAAGTACCAAATTAAGAAAATGTGTCAAG
Found at i:948077 original size:357 final size:364
Alignment explanation
Indices: 947387--948118 Score: 1093
Period size: 357 Copynumber: 2.0 Consensus size: 364
947377 TTTTAAGTTG
* *
947387 GTACTTAAACTTTTTTGGGGTCTAATTTAGTATCAGAACTTGACTCTTTTTCTTAATTTAGTACC
1 GTACTTAAACTTTTTTGGGATCTAATTTAGTACCAGAACTTGACTCTTTTTCTTAATTTAGTACC
*
947452 TAATCTTTTTTTAAAATTAATTTGTTAAGCATAGCTCAATACCTATTTTTAACATGAATTTTCTT
66 TAATCTTTTTTTAAAATTAATTCGTTAAGCATAGCTCAATACCTATTTTTAACATGAA-TTTC-T
* * * * *
947517 TAAAACTGAAAATATTTTTGTAGCATAACAAAAGAAATTAATACCGTTATTGTTTTACATAATTT
129 TAAAACTGAAAATATTTGTGTAGCATAACAAAAAAAAGTAACACCGTTAATGTTTTACATAATTT
* *
947582 TTATAATATTTAATACATTTAGGTACCAAATTGAATCTAAAAAAAAAAGCTTAGGTACCAAATTA
194 TTATAATATTTAATAAATTTAGGTACCAAATTGAATCT--AAAAAAAAGCTTAGGTACCAAACTA
*
947647 GAAAAAAAATACCAAGTTTAGGTATCAAATTGAGTCCAAAAAAGTTTAAGTACCAAATTAGGAAA
257 GAAAAAAAATACCAAGTTTAGGTACCAAATTGAGTCCAAAAAAGTTTAAGTACCAAATTAGGAAA
*
947712 ACGTGTCAAGTTCAAGTACCAAATTGGGTC-AAAAAAGTTTAT
322 ACGTGTCAAGTTCAAGTACCAAATTGGGTCAAAAAAAGTTTAA
* * *
947754 GTACTTAAAC-TTTTTGGGATCTAATTTGGTACCTGAACTTGACTCTTTTTCTTAATTTGGTACC
1 GTACTTAAACTTTTTTGGGATCTAATTTAGTACCAGAACTTGACTCTTTTTCTTAATTTAGTACC
* * *
947818 TAATC-TTTTTTAATATTAATTCGTTTAGTATAGCTCAATACCTA-TTTTAACATGAA-TTC-TA
66 TAATCTTTTTTTAAAATTAATTCGTTAAGCATAGCTCAATACCTATTTTTAACATGAATTTCTTA
* * ***
947879 AAACTGACAATATTTGTGTAGCATAACAAAAAAAAAGTAACACTGTTAATGTTTTGTGTAATTTT
131 AAACTGAAAATATTTGTGTAGCATAAC-AAAAAAAAGTAACACCGTTAATGTTTTACATAATTTT
*
947944 TATAATATTTAATAAATTTAGGTACCAAATTGAATCT-AAAAAAAGCTTAGGTACCAAACTA-AG
195 TATAATATTTAATAAATTTAGGTACCAAATTGAATCTAAAAAAAAGCTTAGGTACCAAACTAGAA
* ** *
948007 AAAATATGTCAAGTTTAGGTACCAAATTGAGTCCAAAAAAGTTTAAGTACCAAATTAGGAAAATG
260 AAAAAATACCAAGTTTAGGTACCAAATTGAGTCCAAAAAAGTTTAAGTACCAAATTAGGAAAACG
* *
948072 TGTCAATTTCAAGTATCAAATTGGGTCAAAAAAAGTTTAA
325 TGTCAAGTTCAAGTACCAAATTGGGTCAAAAAAAGTTTAA
948112 GTACTTA
1 GTACTTA
948119 CTTAAGAAAA
Statistics
Matches: 333, Mismatches: 30, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
357 86 0.26
358 41 0.12
360 27 0.08
361 65 0.20
362 3 0.01
364 12 0.04
365 35 0.11
366 54 0.16
367 10 0.03
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (364 bp):
GTACTTAAACTTTTTTGGGATCTAATTTAGTACCAGAACTTGACTCTTTTTCTTAATTTAGTACC
TAATCTTTTTTTAAAATTAATTCGTTAAGCATAGCTCAATACCTATTTTTAACATGAATTTCTTA
AAACTGAAAATATTTGTGTAGCATAACAAAAAAAAGTAACACCGTTAATGTTTTACATAATTTTT
ATAATATTTAATAAATTTAGGTACCAAATTGAATCTAAAAAAAAGCTTAGGTACCAAACTAGAAA
AAAAATACCAAGTTTAGGTACCAAATTGAGTCCAAAAAAGTTTAAGTACCAAATTAGGAAAACGT
GTCAAGTTCAAGTACCAAATTGGGTCAAAAAAAGTTTAA
Found at i:956768 original size:81 final size:80
Alignment explanation
Indices: 956590--956791 Score: 291
Period size: 81 Copynumber: 2.5 Consensus size: 80
956580 TATCTTTTTT
* *
956590 ATAATTGAAAGTGGAGACAGAGGTTGAT-TGGGATTGAACCAAGTACAACCTGTTGCCCTAGGCA
1 ATAATTGGAAGTGGAGAAAGAGGTTG-TGTGGGATTGAACCAAGTACAACCTGTTGCCCTAGGCA
956654 AATAAATCGTAGAATC
65 AATAAATCGTAGAATC
* * *
956670 ATAAATGGAAGTGGAGAAAGGGGTTGTGTGGGATTGAAGCAAGTACAACCTGTGTTG-CCTAGGC
1 ATAATTGGAAGTGGAGAAAGAGGTTGTGTGGGATTGAACCAAGTACAACC--TGTTGCCCTAGGC
*
956734 TAATAAATCGTAGAATC
64 AAATAAATCGTAGAATC
* *
956751 ATAATTGGAAGTAGAGAAAGAGGTTGTGTGGGATTCAACCA
1 ATAATTGGAAGTGGAGAAAGAGGTTGTGTGGGATTGAACCA
956792 GAGCTTTAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
79 1 0.01
80 43 0.40
81 59 0.55
82 5 0.05
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (80 bp):
ATAATTGGAAGTGGAGAAAGAGGTTGTGTGGGATTGAACCAAGTACAACCTGTTGCCCTAGGCAA
ATAAATCGTAGAATC
Found at i:961517 original size:255 final size:255
Alignment explanation
Indices: 961064--961578 Score: 994
Period size: 255 Copynumber: 2.0 Consensus size: 255
961054 AATCACAATA
961064 TTTTAAGCATAGTCTATTAATAATTTCAGATATATTTATTTTCATATAGACGTGATCCAAATAAT
1 TTTTAAGCATAGTCTATTAATAATTTCAGATATATTTATTTTCATATAGACGTGATCCAAATAAT
*
961129 GATATCTAGTTATCTCTCTCAGGTATACTGGAAAGCTACCCCCAAGTTCTCTTTTTAGGAACAGA
66 GATATCTAGTTATCTCTCTCAGGTATACTGGAAAGCTACCCCCAAGTTCTCTCTTTAGGAACAGA
961194 TAATGAAAATTTCCTGGATTCTCATGAAAGAGAACATCAAGGTGATATTCTTTTCTCCACTCTCT
131 TAATGAAAATTTCCTGGATTCTCATGAAAGAGAACATCAAGGTGATATTCTTTTCTCCACTCTCT
*
961259 CCCCGCCCAAACTTTTATTCGTTGATTTGTTAGCTGTGATTTACAAAGAGCAAGATATTT
196 CCCCGCCCAAACTTTTATTCGTTGATTTGTTAGATGTGATTTACAAAGAGCAAGATATTT
961319 TTTTAAGCATAGTCTATTAATAATTTCAGATATATTTATTTTCATATAGACGTGATCCAAATAAT
1 TTTTAAGCATAGTCTATTAATAATTTCAGATATATTTATTTTCATATAGACGTGATCCAAATAAT
*
961384 GATATCTAGTTATCTCTCTCAGGTATACTGGAAAGCTACCCCCGAGTTCTCTCTTTAGGAACAGA
66 GATATCTAGTTATCTCTCTCAGGTATACTGGAAAGCTACCCCCAAGTTCTCTCTTTAGGAACAGA
*
961449 TAATGAAAATTTCCTGGATTCTCATGAAAGAGAACATCAAGGTGATATTCTTTTCTCCACTGTCT
131 TAATGAAAATTTCCTGGATTCTCATGAAAGAGAACATCAAGGTGATATTCTTTTCTCCACTCTCT
961514 CCCCGCCCAAACTTTTATTCGTTGATTTGTTAGATGTGATTTACAAAGAGCAAGATATTT
196 CCCCGCCCAAACTTTTATTCGTTGATTTGTTAGATGTGATTTACAAAGAGCAAGATATTT
961574 TTTTA
1 TTTTA
961579 TCTGTGGATT
Statistics
Matches: 256, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
255 256 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (255 bp):
TTTTAAGCATAGTCTATTAATAATTTCAGATATATTTATTTTCATATAGACGTGATCCAAATAAT
GATATCTAGTTATCTCTCTCAGGTATACTGGAAAGCTACCCCCAAGTTCTCTCTTTAGGAACAGA
TAATGAAAATTTCCTGGATTCTCATGAAAGAGAACATCAAGGTGATATTCTTTTCTCCACTCTCT
CCCCGCCCAAACTTTTATTCGTTGATTTGTTAGATGTGATTTACAAAGAGCAAGATATTT
Found at i:969143 original size:23 final size:24
Alignment explanation
Indices: 969109--969154 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
969099 TACTCTTGCC
969109 TTTTTGTGTTTTT-ACTTATTTTT
1 TTTTTGTGTTTTTCACTTATTTTT
*
969132 TTTTTGTTTTTTTCACTTATTTT
1 TTTTTGTGTTTTTCACTTATTTT
969155 CCTCTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTTGTGTTTTTCACTTATTTTT
Found at i:969144 original size:24 final size:23
Alignment explanation
Indices: 969109--969154 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
969099 TACTCTTGCC
*
969109 TTTTTGTGTTTTTACTTATTTTT
1 TTTTTGTGTTTTCACTTATTTTT
*
969132 TTTTTGTTTTTTTCACTTATTTT
1 TTTTTG-TGTTTTCACTTATTTT
969155 CCTCTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.78
Consensus pattern (23 bp):
TTTTTGTGTTTTCACTTATTTTT
Found at i:972353 original size:13 final size:12
Alignment explanation
Indices: 972333--972391 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
972323 ATAGAAAACA
972333 TTTT-TTTTCTTC
1 TTTTCTTTTC-TC
972345 TTTTCTTTTCTC
1 TTTTCTTTTCTC
972357 TTTTCTTTT-TC
1 TTTTCTTTTCTC
*
972368 TTATTTTTTTCTC
1 TT-TTCTTTTCTC
972381 ATTTTCCTTTT
1 -TTTT-CTTTT
972392 TCAAGTGACT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 4 0.10
12 21 0.52
13 9 0.22
14 6 0.15
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTCTC
Found at i:972367 original size:26 final size:26
Alignment explanation
Indices: 972336--972393 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
972326 GAAAACATTT
*
972336 TTTTTCTTCTTTTCTTTTCTC-TTTT-C
1 TTTTTCTT-ATTT-TTTTCTCATTTTCC
972362 TTTTTCTTATTTTTTTCTCATTTTCC
1 TTTTTCTTATTTTTTTCTCATTTTCC
972388 TTTTTC
1 TTTTTC
972394 AAGTGACTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 7 0.24
25 7 0.24
26 15 0.52
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTCTTATTTTTTTCTCATTTTCC
Found at i:973045 original size:41 final size:41
Alignment explanation
Indices: 973000--973136 Score: 118
Period size: 40 Copynumber: 3.3 Consensus size: 41
972990 GCATTTTTAA
*
973000 CGGCGTTTGGGCAGAAAACGCCGCAAAAGGTAAAGCAATAG
1 CGGCGTTTGGGCAGAAAACGCCGCAAAAGGTAGAGCAATAG
*** * *
973041 CGGCGTTTTTACA-TAAACGCCGCAAAAGATAGAGCAATAG
1 CGGCGTTTGGGCAGAAAACGCCGCAAAAGGTAGAGCAATAG
* ** **
973081 CGGCACTTAAGG--GAAAGTGCCGCAAAAGGTCAGAGCAATAG
1 CGGC-GTTTGGGCAGAAAACGCCGCAAAAGGT-AGAGCAATAG
973122 CGGCGCTTATGGGCA
1 CGGCG-TT-TGGGCA
973137 AGCGCCACTA
Statistics
Matches: 71, Mismatches: 18, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
40 41 0.58
41 28 0.39
42 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.30, T:0.15
Consensus pattern (41 bp):
CGGCGTTTGGGCAGAAAACGCCGCAAAAGGTAGAGCAATAG
Found at i:973154 original size:41 final size:41
Alignment explanation
Indices: 973058--973507 Score: 503
Period size: 41 Copynumber: 11.0 Consensus size: 41
973048 TTTACATAAA
* * * *
973058 CGCCGCAAAAGAT-AGAGCAATAGCGGCACTTAAGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * *
973098 TGCCGCAAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * ** *
973139 CGCCACTAAAAGTCAGAGCAATAGCGATGCTTATGGGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* *
973180 CGCTGCTAAAGGTCAGAGCAATAGTGGCGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * *
973221 CGCCACTAAAGGTTAGAGCAATAGCGACGCTTAT-GGACAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGA-AAG
973262 CGCCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
1 CG-CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * *
973304 CGCCGCTAAAGGTCAGAGCAATAGCAGTGCTTTTGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * * *
973345 CGCCGTTAAAGGTCAGAGCAATAACGACGCTTATAGGTAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * * *
973386 CCCCGCTAAAGGCCAGAGCATTAGCGACG-TTCATGTGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT-ATGGGAAAG
* *
973427 CGCCAG-TAAAGGTCAGAGCAATAACGGCGCTTATGGGCAAG
1 CGCC-GCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * * *
973468 CGCCACTAAAGGTCAGAGCATTGGCGACGCTTATGTGAAA
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAA
973508 AATGCCGCTA
Statistics
Matches: 343, Mismatches: 59, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
40 16 0.05
41 287 0.84
42 37 0.11
43 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.30, T:0.17
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
Found at i:973428 original size:206 final size:205
Alignment explanation
Indices: 973071--973507 Score: 561
Period size: 206 Copynumber: 2.1 Consensus size: 205
973061 CGCAAAAGAT
* * * * *
973071 AGAGCAATAGCGGCACTTAAGGGAAAGTGCCGCAAAAGGTCAGAGCAATAGCGGCGCTTATGGGC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCAAAAGGTCAGAGCAATAGCAGCGCTTATGGGA
* * * * * *
973136 AAGCGCCACTAAAAGTCAGAGCAATAGCGATGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAA
66 AAGCGCCACTAAAAGTCAGAGCAATAACGACGCTTATAGGCAAGCCCCGCTAAAGGCCAGAGCAA
* * * *
973201 TAGTGGCGCTTATGGGAAAGCGCCACTAAAGGTTAGAGCAATAGCGACGCTTATGGACAAGCGCC
131 TAGCGACGCTTATGGGAAAGCGCCACTAAAGGTCAGAGCAATAACGACGCTTATGGACAAGCG-C
*
973266 CGCTAAAGGTC
195 CACTAAAGGTC
* * *
973277 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCAGTGCTTTTGGGA
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCAAAAGGTCAGAGCAATAGCAGCGCTTATGGGA
** * * *
973342 AAGCGCCGTTAAAGGTCAGAGCAATAACGACGCTTATAGGTAAGCCCCGCTAAAGGCCAGAGCAT
66 AAGCGCCACTAAAAGTCAGAGCAATAACGACGCTTATAGGCAAGCCCCGCTAAAGGCCAGAGCAA
* * * *
973407 TAGCGACG-TTCATGTGAAAGCGCCAGTAAAGGTCAGAGCAATAACGGCGCTTATGGGCAAGCGC
131 TAGCGACGCTT-ATGGGAAAGCGCCACTAAAGGTCAGAGCAATAACGACGCTTATGGACAAGCGC
973471 CACTAAAGGTC
195 CACTAAAGGTC
* * * *
973482 AGAGCATTGGCGACGCTTATGTGAAA
1 AGAGCAATAGCGGCGCTTATGGGAAA
973508 AATGCCGCTA
Statistics
Matches: 198, Mismatches: 32, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
205 35 0.18
206 163 0.82
ACGTcount: A:0.32, C:0.21, G:0.30, T:0.17
Consensus pattern (205 bp):
AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCAAAAGGTCAGAGCAATAGCAGCGCTTATGGGA
AAGCGCCACTAAAAGTCAGAGCAATAACGACGCTTATAGGCAAGCCCCGCTAAAGGCCAGAGCAA
TAGCGACGCTTATGGGAAAGCGCCACTAAAGGTCAGAGCAATAACGACGCTTATGGACAAGCGCC
ACTAAAGGTC
Found at i:979280 original size:43 final size:42
Alignment explanation
Indices: 979138--979282 Score: 114
Period size: 43 Copynumber: 3.4 Consensus size: 42
979128 TTTGTTAATG
* * *
979138 TTAGTGGCATTTGTGGGAAAAATG-CTGCTAAAG-ACTTTGTTCT
1 TTAGCGGCATTTGTGGG-AAAATGTC-GCTAAAGAAC-ATGATCT
* * ** * * *
979181 TTAGTGGCGTTTACGGGAAAATCGTCGCTAAATATCATGGTCT
1 TTAGCGGCATTTGTGGGAAAAT-GTCGCTAAAGAACATGATCT
* *
979224 TTAACTGCATTTGTGGGAAAAGTGTCGCTAAAGAACATGATCT
1 TTAGCGGCATTTGTGGGAAAA-TGTCGCTAAAGAACATGATCT
*
979267 TTAGCGGCGTTTGTGG
1 TTAGCGGCATTTGTGG
979283 AATCCGTTAC
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
42 5 0.06
43 71 0.90
44 3 0.04
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.34
Consensus pattern (42 bp):
TTAGCGGCATTTGTGGGAAAATGTCGCTAAAGAACATGATCT
Found at i:982918 original size:100 final size:100
Alignment explanation
Indices: 982745--982944 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
982735 TTCTTCTTTC
982745 ATTTTCTCATTAAGTTTTCTTTGTTGCTCAATTGATTGCTTCCCTTCATCTTCTAGCCTTATCTT
1 ATTTTCTCATTAAGTTTTCTTTGTTGCTCAATTGATTGCTTCCCTTCATCTTCTAGCCTTATCTT
982810 ATGCATGCAAAAAGAGGGGCTGATGCCTTTGATAT
66 ATGCATGCAAAAAGAGGGGCTGATGCCTTTGATAT
982845 ATTTTCTCATTAAGTTTTCTTTGTTGCTCAATTGATTGCTTCCCTTCATCTTCTAGCCTTATCTT
1 ATTTTCTCATTAAGTTTTCTTTGTTGCTCAATTGATTGCTTCCCTTCATCTTCTAGCCTTATCTT
982910 ATGCATGCAAAAAGAGGGGCTGATGCCTTTGATAT
66 ATGCATGCAAAAAGAGGGGCTGATGCCTTTGATAT
982945 CTACAATGCT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (100 bp):
ATTTTCTCATTAAGTTTTCTTTGTTGCTCAATTGATTGCTTCCCTTCATCTTCTAGCCTTATCTT
ATGCATGCAAAAAGAGGGGCTGATGCCTTTGATAT
Found at i:985993 original size:13 final size:14
Alignment explanation
Indices: 985975--986004 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
985965 GTCAACGCAA
985975 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
985988 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
986002 TCA
1 TCA
986005 AAGTATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:995938 original size:106 final size:106
Alignment explanation
Indices: 995753--995965 Score: 390
Period size: 106 Copynumber: 2.0 Consensus size: 106
995743 ATACTATCGG
* *
995753 GACGCGTTGACAGCAAATAGCTTCTTGTCAGGCAATGCGTCAACAATTTGGAATGTATTTCCATC
1 GACGCGTCGACAGCAAATAGCTTCTCGTCAGGCAATGCGTCAACAATTTGGAATGTATTTCCATC
995818 TTCACTTCCTACTTCCATACGAGACAAATGATCTACTACTT
66 TTCACTTCCTACTTCCATACGAGACAAATGATCTACTACTT
995859 GACGCGTCGACAGCAAATAGCTTCTCGTCAGGCAATGCGTCAACAATTTGGAATGTATTTCCATC
1 GACGCGTCGACAGCAAATAGCTTCTCGTCAGGCAATGCGTCAACAATTTGGAATGTATTTCCATC
* *
995924 TTCACTTCCTACTTCCATATGAGATAAATGATCTACTACTT
66 TTCACTTCCTACTTCCATACGAGACAAATGATCTACTACTT
995965 G
1 G
995966 GTTCTTCGAT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (106 bp):
GACGCGTCGACAGCAAATAGCTTCTCGTCAGGCAATGCGTCAACAATTTGGAATGTATTTCCATC
TTCACTTCCTACTTCCATACGAGACAAATGATCTACTACTT
Found at i:1001735 original size:36 final size:36
Alignment explanation
Indices: 1001695--1001774 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
1001685 GGTCAATAGA
1001695 GAGTAAAATAAGCATAATGACC-TTCGAGTCAAC-AAG
1 GAGTAAAATAAGCATAATGACCATT-GAGTC-ACTAAG
* * * *
1001731 GAGTAAAATGAGTATCATGACCATTGAGTCACTAGG
1 GAGTAAAATAAGCATAATGACCATTGAGTCACTAAG
1001767 GAGTAAAA
1 GAGTAAAA
1001775 CGAATAACGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 2 0.05
36 34 0.89
37 2 0.05
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (36 bp):
GAGTAAAATAAGCATAATGACCATTGAGTCACTAAG
Found at i:1010246 original size:80 final size:78
Alignment explanation
Indices: 1010113--1010314 Score: 278
Period size: 80 Copynumber: 2.5 Consensus size: 78
1010103 CATGGTACCT
* * * *
1010113 AGTGCCTAGCGGATAAACTTCAAATGTGAGCCCAGCTCTAGTTGTATTAACCAACAATTATTCGT
1 AGTGCCTAGCGGATAAACTGC-AATGTGAG-CCAGCTCTAGTTGGATTAACCAACAATTATCCAT
1010178 CAAATCCTAGCACCC
64 CAAATCCTAGCACCC
1010193 AGTGCCTAGCGGATAAACTGCACATGTGAGCCTAGCTCTAGTTGGATTAACCAACAATTATCCAT
1 AGTGCCTAGCGGATAAACTGCA-ATGTGAGCC-AGCTCTAGTTGGATTAACCAACAATTATCCAT
*
1010258 CAAATCCTGGCACCC
64 CAAATCCTAGCACCC
* * *
1010273 AATGCCTAGCAGATAAACTGCGAAAGTGAGTCCAGCTCTAGT
1 AGTGCCTAGCGGATAAACTGC-AATGTGAG-CCAGCTCTAGT
1010315 CAATTAAACC
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
79 3 0.03
80 104 0.95
81 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (78 bp):
AGTGCCTAGCGGATAAACTGCAATGTGAGCCAGCTCTAGTTGGATTAACCAACAATTATCCATCA
AATCCTAGCACCC
Found at i:1010391 original size:16 final size:16
Alignment explanation
Indices: 1010370--1010403 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1010360 ATTCACAATT
*
1010370 TACATGTAGCAACTTA
1 TACATGGAGCAACTTA
1010386 TACATGGAGCAACTTA
1 TACATGGAGCAACTTA
1010402 TA
1 TA
1010404 ACTATCAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (16 bp):
TACATGGAGCAACTTA
Found at i:1011932 original size:36 final size:36
Alignment explanation
Indices: 1011885--1012056 Score: 245
Period size: 36 Copynumber: 4.8 Consensus size: 36
1011875 AGTAACAGGC
*
1011885 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGGATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
*
1011921 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGGATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* *
1011957 ATGACCTTTGGGTCAACAAGGAGTAAAATGAACATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* * * *
1011993 ATGACCTTCGGGTCAAGAAGGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* * *
1012029 ATGACCATTGAGTCAATAGGGAGTAAAA
1 ATGACCTTTGGGTCAACAGGGAGTAAAA
1012057 CGAATAACGA
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 124 1.00
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
Found at i:1015152 original size:43 final size:43
Alignment explanation
Indices: 1015104--1015387 Score: 288
Period size: 43 Copynumber: 6.5 Consensus size: 43
1015094 TAATGATTAA
* * *
1015104 TTATGTCTCGGGTAGAGCATAAGATTGATTATAAATGGAATAC
1 TTATGTCTCAGTTAGAGCATAAGATTGATTATAAATGGAAGAC
* *
1015147 TTATGTCTCAGTTGGAGCATTAGATTGATTATAAATGGAAGAC
1 TTATGTCTCAGTTAGAGCATAAGATTGATTATAAATGGAAGAC
* *
1015190 TTATGTCTCGGTT-GAAGCATAAAATTGATTATAAATGGAAGAC
1 TTATGTCTCAGTTAG-AGCATAAGATTGATTATAAATGGAAGAC
*
1015233 TTATGTCTC-GATT-GAAGCATAAAATT-ATTTATGAAATGGAAGAC
1 TTATGTCTCAG-TTAG-AGCATAAGATTGA-TTAT-AAATGGAAGAC
* * * *
1015277 TTATGTCTCGGTTTGAGCATAAGATTGTTTATGAAATGGAGGAC
1 TTATGTCTCAGTTAGAGCATAAGATTGATTAT-AAATGGAAGAC
* * * * * * *
1015321 TTATTTCCCAGCTAGAGCATAAGGTTAATTGTAAATGGAATAAC
1 TTATGTCTCAGTTAGAGCATAAGATTGATTATAAATGGAA-GAC
* *
1015365 TTATGACTCAATTAGAGCATAAG
1 TTATGTCTCAGTTAGAGCATAAG
1015388 GTTAAATGTG
Statistics
Matches: 206, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
42 3 0.01
43 111 0.54
44 90 0.44
45 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (43 bp):
TTATGTCTCAGTTAGAGCATAAGATTGATTATAAATGGAAGAC
Found at i:1021429 original size:44 final size:43
Alignment explanation
Indices: 1021306--1021513 Score: 244
Period size: 44 Copynumber: 4.8 Consensus size: 43
1021296 CTATTTGAAC
**
1021306 AAATGGAAGACTTATGTCTCGGGCAGAGCATAAGATTGATTAT-
1 AAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTG-TTATG
*
1021349 AAATGGAAGACTTATGT-TTGGTT-GCAGCATAAGATTGTGTATG
1 AAATGGAAGACTTATGTCTCGGTTAG-AGCATAAGATTGT-TATG
*
1021392 AAATGGAAGACTTATGTCTCGGTTGGAGCATAAGATTGTTTATG
1 AAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTG-TTATG
* **
1021436 AAATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTAAT-TG
1 AAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTATG
* * *
1021478 TAAATGGAAGAAATTATGACTCGATTAGAGCATAAG
1 -AAATGGAAG-ACTTATGTCTCGGTTAGAGCATAAG
1021514 GTTAAATGTG
Statistics
Matches: 145, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.01
42 20 0.14
43 44 0.30
44 77 0.53
45 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (43 bp):
AAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTATG
Found at i:1022202 original size:18 final size:18
Alignment explanation
Indices: 1022179--1022215 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1022169 GATGACACAT
1022179 AGTCTAGCCCACAATTTA
1 AGTCTAGCCCACAATTTA
1022197 AGTCTAGCCCACAATTTA
1 AGTCTAGCCCACAATTTA
1022215 A
1 A
1022216 CACATAGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (18 bp):
AGTCTAGCCCACAATTTA
Found at i:1031178 original size:23 final size:24
Alignment explanation
Indices: 1031151--1031199 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1031141 CACAACAATT
* *
1031151 CATTTTCTATTA-ATTTGCTTTGA
1 CATTTTATATTATATTTGCGTTGA
*
1031174 CATTTTATGTTATATTTGCGTTGA
1 CATTTTATATTATATTTGCGTTGA
1031198 CA
1 CA
1031200 GAATTAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (24 bp):
CATTTTATATTATATTTGCGTTGA
Found at i:1041207 original size:37 final size:37
Alignment explanation
Indices: 1041166--1041276 Score: 222
Period size: 37 Copynumber: 3.0 Consensus size: 37
1041156 ATTTGCTCTA
1041166 ACATTTTATGTTATAATTACGTTGACAGAGTTAACTC
1 ACATTTTATGTTATAATTACGTTGACAGAGTTAACTC
1041203 ACATTTTATGTTATAATTACGTTGACAGAGTTAACTC
1 ACATTTTATGTTATAATTACGTTGACAGAGTTAACTC
1041240 ACATTTTATGTTATAATTACGTTGACAGAGTTAACTC
1 ACATTTTATGTTATAATTACGTTGACAGAGTTAACTC
1041277 TTTGATTTGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ACATTTTATGTTATAATTACGTTGACAGAGTTAACTC
Found at i:1052816 original size:81 final size:81
Alignment explanation
Indices: 1052681--1052848 Score: 327
Period size: 81 Copynumber: 2.1 Consensus size: 81
1052671 TTTCAATCTT
*
1052681 CAAAAGTATGAAAATAATTCAATCTGCTAGGTACAAAACCAGCAGACCAGATGCATATGAAAATG
1 CAAAACTATGAAAATAATTCAATCTGCTAGGTACAAAACCAGCAGACCAGATGCATATGAAAATG
1052746 CCCAAGTTCATAAAGA
66 CCCAAGTTCATAAAGA
1052762 CAAAACTATGAAAATAATTCAATCTGCTAGGTACAAAACCAGCAGACCAGATGCATATGAAAATG
1 CAAAACTATGAAAATAATTCAATCTGCTAGGTACAAAACCAGCAGACCAGATGCATATGAAAATG
1052827 CCCAAGTTCATAAAGA
66 CCCAAGTTCATAAAGA
1052843 CAAAAC
1 CAAAAC
1052849 AAAGGTGTTT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.19
Consensus pattern (81 bp):
CAAAACTATGAAAATAATTCAATCTGCTAGGTACAAAACCAGCAGACCAGATGCATATGAAAATG
CCCAAGTTCATAAAGA
Found at i:1055195 original size:12 final size:12
Alignment explanation
Indices: 1055178--1055227 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
1055168 ATTTTCGTTA
1055178 TTTTATT-TTGAT
1 TTTTATTATT-AT
1055190 TTTTATTATTAT
1 TTTTATTATTAT
1055202 TTTTATTATTAT
1 TTTTATTATTAT
*
1055214 TATTATTATTAT
1 TTTTATTATTAT
1055226 TT
1 TT
1055228 AGGCTATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 33 0.94
13 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:1055200 original size:3 final size:3
Alignment explanation
Indices: 1055175--1055226 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1055165 ATGATTTTCG
* *
1055175 TTA TT- TTA TT- TTGA TTT TTA TTA TTA TTT TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1055219 TTA TTA TT
1 TTA TTA TT
1055227 TAGGCTATAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 36 0.86
4 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:1060081 original size:40 final size:40
Alignment explanation
Indices: 1060006--1060081 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
1059996 ACTCTGCGTT
* *
1060006 CTTCGTTGCAACATAGCATGTCTATGTTGCAACAAAACCC
1 CTTCGTTGCAACATAGCATGTCTACGTCGCAACAAAACCC
** *
1060046 CTTCGTTGTGACATAGCATGTCTACGTCGCGACAAA
1 CTTCGTTGCAACATAGCATGTCTACGTCGCAACAAA
1060082 CCCTTGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (40 bp):
CTTCGTTGCAACATAGCATGTCTACGTCGCAACAAAACCC
Found at i:1063184 original size:45 final size:45
Alignment explanation
Indices: 1063120--1063253 Score: 180
Period size: 45 Copynumber: 3.0 Consensus size: 45
1063110 ATAGCTCATT
*
1063120 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCATCGCAATACTA
1 AAGCCAAGGATATCAGCCTCAGTTTGACAAGCCATCGCAATACTA
* *
1063165 AAGCCAAGGATATCAGCCTCAGTTTGACAAGCCA-CTGTAATACTC
1 AAGCCAAGGATATCAGCCTCAGTTTGACAAGCCATC-GCAATACTA
** * * *
1063210 AAGGGAAAGATATCAGGCTGAGTTTGACAAGCCATCGCAATACT
1 AAGCCAAGGATATCAGCCTCAGTTTGACAAGCCATCGCAATACT
1063254 TTACTCCTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
44 1 0.01
45 76 0.97
46 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (45 bp):
AAGCCAAGGATATCAGCCTCAGTTTGACAAGCCATCGCAATACTA
Found at i:1063544 original size:20 final size:20
Alignment explanation
Indices: 1063521--1063569 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1063511 AAACCAATAC
*
1063521 CCTAGACCCTAAACGTGAAA
1 CCTAAACCCTAAACGTGAAA
*
1063541 CCTAAACCCTAAACTTGAAA
1 CCTAAACCCTAAACGTGAAA
1063561 CCTTAAACC
1 CC-TAAACC
1063570 TTAACCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.41, C:0.33, G:0.08, T:0.18
Consensus pattern (20 bp):
CCTAAACCCTAAACGTGAAA
Found at i:1064233 original size:11 final size:11
Alignment explanation
Indices: 1064217--1064247 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
1064207 TTTTGACTTT
1064217 GAAAAATTATA
1 GAAAAATTATA
1064228 GAAAAA-TATA
1 GAAAAATTATA
1064238 GAAAAATTAT
1 GAAAAATTAT
1064248 TAGAGACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:1074964 original size:59 final size:59
Alignment explanation
Indices: 1074897--1075013 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
1074887 ATAGTTTAAA
* *
1074897 TTATAAATTTTATATAAGTTGTTTTAAATTTGCGATTTTTGTATTTGTTTTAATATTTG
1 TTATAAATTTTATATAAGTTGTTTTAAATTAGCGATTTTGGTATTTGTTTTAATATTTG
* *
1074956 TTATAAATTTTATATAAGTTGTTTTAAATTAGGGATTTTGGTATTTGTTTTAGTATTT
1 TTATAAATTTTATATAAGTTGTTTTAAATTAGCGATTTTGGTATTTGTTTTAATATTT
1075014 AAACAAATAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (59 bp):
TTATAAATTTTATATAAGTTGTTTTAAATTAGCGATTTTGGTATTTGTTTTAATATTTG
Found at i:1076328 original size:13 final size:13
Alignment explanation
Indices: 1076310--1076366 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
1076300 TGTTAAGGTT
1076310 GGTTTGGGTTTAA
1 GGTTTGGGTTTAA
1076323 GGTTTGGG-TTAA
1 GGTTTGGGTTTAA
*
1076335 ---ATGGGTTTAAA
1 GGTTTGGGTTT-AA
*
1076346 GGTTTGGGTTTAG
1 GGTTTGGGTTTAA
1076359 GGTTTGGG
1 GGTTTGGG
1076367 CTTAGGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
9 4 0.11
10 2 0.06
11 2 0.06
12 4 0.11
13 17 0.47
14 7 0.19
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (13 bp):
GGTTTGGGTTTAA
Found at i:1085821 original size:29 final size:29
Alignment explanation
Indices: 1085788--1085846 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1085778 TCCACCTTGA
* * *
1085788 CACGAATTCTCAACAAACCAGTTCTTCAC
1 CACGAACTCTCAACAAACAAGTTCTCCAC
*
1085817 CACGAACTCTCAACGAACAAGTTCTCCAC
1 CACGAACTCTCAACAAACAAGTTCTCCAC
1085846 C
1 C
1085847 TCTTCCACGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.37, G:0.08, T:0.20
Consensus pattern (29 bp):
CACGAACTCTCAACAAACAAGTTCTCCAC
Found at i:1089244 original size:170 final size:169
Alignment explanation
Indices: 1088908--1089249 Score: 578
Period size: 170 Copynumber: 2.0 Consensus size: 169
1088898 CAACTAGGAG
*
1088908 TTCACCATCACTGTAGTCTTCTACTACATCAGCTTCACTAGATTGTTCTGGTTGTTTTCCCTTTT
1 TTCACCATCACTGTAGTCTTCTACTACATCAGCTTCACCAGATTGTTCTGGTTGTTTTCCCTTTT
*
1088973 GATTCTCTGCCTCCCTTTTGGTTTTATTTTGCAACTTGTAGCACTCTTTCTTAATGTGCTCTTTC
66 GATTCTCTGCCTCCCTTTTGGTTTTATTTTGCAACTTGTAGCACTCTTTCTTAATGTGCCCTTTC
*
1089038 TTCTTGCAGAACTTACAATTTTTACTTCTGTTTGAAGAT
131 TTCTTGCAGAACTTACAATTTTTACTTCTATTTGAAGAT
*
1089077 TTCACCATCACTGTAGTCTTCTACTACATTAGCTTCACCAGATTGTTCTGGTTGTTTTCCCTTTT
1 TTCACCATCACTGTAGTCTTCTACTACATCAGCTTCACCAGATTGTTCTGGTTGTTTTCCCTTTT
* ** *
1089142 GATTCTCTGCCT-TCTTTTTTTATCTTATTTTGCAACTTGTATCACTCTTTCTTAATGTGCCCTT
66 GATTCTCTGCCTCCCTTTTGGT-T-TTATTTTGCAACTTGTAGCACTCTTTCTTAATGTGCCCTT
*
1089206 TCTTCTTTCAGAACTTACAATTTTTACTTCTATTTGAAGAT
129 TCTTCTTGCAGAACTTACAATTTTTACTTCTATTTGAAGAT
1089247 TTC
1 TTC
1089250 TATCTACCTT
Statistics
Matches: 162, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
168 6 0.04
169 76 0.47
170 80 0.49
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (169 bp):
TTCACCATCACTGTAGTCTTCTACTACATCAGCTTCACCAGATTGTTCTGGTTGTTTTCCCTTTT
GATTCTCTGCCTCCCTTTTGGTTTTATTTTGCAACTTGTAGCACTCTTTCTTAATGTGCCCTTTC
TTCTTGCAGAACTTACAATTTTTACTTCTATTTGAAGAT
Found at i:1089988 original size:375 final size:375
Alignment explanation
Indices: 1089290--1090028 Score: 1176
Period size: 375 Copynumber: 2.0 Consensus size: 375
1089280 GATTCTTGTG
* * *
1089290 TCCTCCCATGATTATCATCAATATTTAGTTCTTGTCTCCCACGAGCAGTGAAACCCTCTCCCTGA
1 TCCTCCCATGATTATCATCAATATTTAGTTCTTATCTCCCACGAACAGTGAAACACTCTCCCTGA
* * * *
1089355 TAGTCAGATCTAGCCACAAGATGCCTCATCTTGTCATACGAGGCTAAGAAAGCATAGACTTCATC
66 GAGTCAGATCCAGCCACAAGATGCCTAATCTTATCATACGAGGCTAAGAAAGCATAGACTTCATC
* * *
1089420 CATTGTCAGAGATTCGCGACTATACAAGATTATATCTCTAAAGGTTAAATAAGACGGTGGCAACA
131 CATTGTCAAAGATTCACGACTATACAAGATTATATATCTAAAGGTTAAATAAGACGGTGGCAACA
* *
1089485 AACAAAGGAGAATTAACCCTAAGAACCTCCATGGCCTCCGAATTTGAGATAATTTCTTTAAACAC
196 AACAAAGGAGAATTAACCCTAAGAACCTCCATGGCCTCCAAATTTGAGACAATTTCTTTAAACAC
* * * *
1089550 ATTCAAGTGTTCGTGTACAGAAGCACCTTCCTCCAAATGATGAGAATAAAGATGCTGCTTCATAT
261 ATTCAAGTGTTCGTGTACAGAAGCACCTTCCTCCAAACGATAAGAATAAAGACGCTACTTCATAT
* *
1089615 GTAATTTGCTGGTTAGGGTTTTTAACATACATAGTTGCTTCATTCCTATA
326 GTAATTTGCTGGTTAGGGTTTTCAACATACATAGCTGCTTCATTCCTATA
* * *
1089665 TCCTCCCATGATTATCATCAGTATTTCGTTCTTATCTCCCACGAACAGTGAGAA-ACTCTCCTTG
1 TCCTCCCATGATTATCATCAATATTTAGTTCTTATCTCCCACGAACAGTGA-AACACTCTCCCTG
* * *
1089729 AGAGTTAGATCCAGCCACAAGGTGTCTAATCTTATCATACGAGGCTAAGGAAA-CATAGACTTCA
65 AGAGTCAGATCCAGCCACAAGATGCCTAATCTTATCATACGAGGCTAA-GAAAGCATAGACTTCA
* * *
1089793 TCCATTGTTAAAGATTCATGACTATACAAGATTGTATATCTAAAGGTTAAATAAGACGGTGGCAA
129 TCCATTGTCAAAGATTCACGACTATACAAGATTATATATCTAAAGGTTAAATAAGACGGTGGCAA
* *
1089858 CGAACAAAGGAGAATTAACCCTAAGAACCTCCATGGCCTTCAAATTTGAGACAATTTCTTTAAAC
194 CAAACAAAGGAGAATTAACCCTAAGAACCTCCATGGCCTCCAAATTTGAGACAATTTCTTTAAAC
1089923 ACATTCAAGTGTTCGTGTACAGAAGCACCTTCCTCCAAACGATAAGAATAAAGACGCTACTTCAT
259 ACATTCAAGTGTTCGTGTACAGAAGCACCTTCCTCCAAACGATAAGAATAAAGACGCTACTTCAT
*
1089988 ATGTAATTTGCTGGTTAGGGTTTTCGACATACATAGCTGCT
324 ATGTAATTTGCTGGTTAGGGTTTTCAACATACATAGCTGCT
1090029 ACAGTTTTGC
Statistics
Matches: 332, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
375 326 0.98
376 6 0.02
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (375 bp):
TCCTCCCATGATTATCATCAATATTTAGTTCTTATCTCCCACGAACAGTGAAACACTCTCCCTGA
GAGTCAGATCCAGCCACAAGATGCCTAATCTTATCATACGAGGCTAAGAAAGCATAGACTTCATC
CATTGTCAAAGATTCACGACTATACAAGATTATATATCTAAAGGTTAAATAAGACGGTGGCAACA
AACAAAGGAGAATTAACCCTAAGAACCTCCATGGCCTCCAAATTTGAGACAATTTCTTTAAACAC
ATTCAAGTGTTCGTGTACAGAAGCACCTTCCTCCAAACGATAAGAATAAAGACGCTACTTCATAT
GTAATTTGCTGGTTAGGGTTTTCAACATACATAGCTGCTTCATTCCTATA
Found at i:1102763 original size:18 final size:18
Alignment explanation
Indices: 1102740--1102805 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
1102730 AAGTAATGTA
*
1102740 ATACTGTCTCGTTTGAGC
1 ATACTGGCTCGTTTGAGC
1102758 ATACTGGCTCGTTTGAGC
1 ATACTGGCTCGTTTGAGC
* *
1102776 ATACTGGTTCGTTAGAGC
1 ATACTGGCTCGTTTGAGC
1102794 ATACTGGCTCGT
1 ATACTGGCTCGT
1102806 AAGAGCGTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
ATACTGGCTCGTTTGAGC
Found at i:1109335 original size:18 final size:18
Alignment explanation
Indices: 1109309--1109407 Score: 117
Period size: 18 Copynumber: 5.4 Consensus size: 18
1109299 AATGTAATAT
1109309 TGGCTCGTTTGAGCATAC
1 TGGCTCGTTTGAGCATAC
* * *
1109327 TGACTCGTTTGAGTATAT
1 TGGCTCGTTTGAGCATAC
**
1109345 TGGCTCGTAAGAGCATTAC
1 TGGCTCGTTTGAGCA-TAC
* *
1109364 TGGCTCATTGGAGCATAC
1 TGGCTCGTTTGAGCATAC
1109382 TGGCTCGTTTGAGCATAC
1 TGGCTCGTTTGAGCATAC
*
1109400 TAGCTCGT
1 TGGCTCGT
1109408 AAGAGAGTTA
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
18 52 0.79
19 14 0.21
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (18 bp):
TGGCTCGTTTGAGCATAC
Found at i:1109386 original size:37 final size:36
Alignment explanation
Indices: 1109309--1109400 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 36
1109299 AATGTAATAT
** * * * *
1109309 TGGCTCGTTTGAGCATACTGACTCGTTTGAGTATAT
1 TGGCTCGTAAGAGCATACTGACTCATTGGAGCATAC
*
1109345 TGGCTCGTAAGAGCATTACTGGCTCATTGGAGCATAC
1 TGGCTCGTAAGAGCA-TACTGACTCATTGGAGCATAC
**
1109382 TGGCTCGTTTGAGCATACT
1 TGGCTCGTAAGAGCATACT
1109401 AGCTCGTAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
36 17 0.37
37 29 0.63
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (36 bp):
TGGCTCGTAAGAGCATACTGACTCATTGGAGCATAC
Found at i:1109393 original size:55 final size:55
Alignment explanation
Indices: 1109309--1109424 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 55
1109299 AATGTAATAT
* * * * *
1109309 TGGCTCGTTTGAGCATACTGACTCGTTTGAGTATATTGGCTCGTAAGAGCA-TTAC
1 TGGCTCATTGGAGCATACTGACTCGTTTGAGCATACTAGCTCGTAAGAG-AGTTAC
*
1109364 TGGCTCATTGGAGCATACTGGCTCGTTTGAGCATACTAGCTCGTAAGAGAGTTAC
1 TGGCTCATTGGAGCATACTGACTCGTTTGAGCATACTAGCTCGTAAGAGAGTTAC
1109419 TGGCTC
1 TGGCTC
1109425 GTGAGGGCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 1 0.02
55 53 0.98
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (55 bp):
TGGCTCATTGGAGCATACTGACTCGTTTGAGCATACTAGCTCGTAAGAGAGTTAC
Found at i:1127066 original size:23 final size:23
Alignment explanation
Indices: 1127036--1127081 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1127026 TCCTTAGTAG
1127036 GATTATTTCCTTAGTAAGCCTTT
1 GATTATTTCCTTAGTAAGCCTTT
*
1127059 GATTATTTCCTTAGTAAGTCTTT
1 GATTATTTCCTTAGTAAGCCTTT
1127082 CTATTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (23 bp):
GATTATTTCCTTAGTAAGCCTTT
Found at i:1143412 original size:27 final size:28
Alignment explanation
Indices: 1143382--1143451 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 28
1143372 TAACCCTATA
*
1143382 ACCCAAAACCATAAACCC-AAACCTAAT-
1 ACCC-AAACCATAAACCCAAAACCAAATC
1143409 ACCCTAAA--ATCAAACCCAAAACCAAATC
1 ACCC-AAACCAT-AAACCCAAAACCAAATC
*
1143437 ACCCAAACCTTAAAC
1 ACCCAAACCATAAAC
1143452 ACAATTCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
25 2 0.06
26 6 0.17
27 18 0.51
28 8 0.23
29 1 0.03
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.11
Consensus pattern (28 bp):
ACCCAAACCATAAACCCAAAACCAAATC
Found at i:1143516 original size:27 final size:27
Alignment explanation
Indices: 1143483--1143558 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
1143473 GTTGACCGAT
*
1143483 CCATTGACTTGAGTTGATCGACTCGAC
1 CCATTGACTCGAGTTGATCGACTCGAC
* * * * *
1143510 CCGTTGACCCAAGTTGACCAACTCGAC
1 CCATTGACTCGAGTTGATCGACTCGAC
*
1143537 CTATTGACTCGAGTTGATCGAC
1 CCATTGACTCGAGTTGATCGAC
1143559 CTGTTGACTT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (27 bp):
CCATTGACTCGAGTTGATCGACTCGAC
Found at i:1146542 original size:80 final size:80
Alignment explanation
Indices: 1146402--1146556 Score: 238
Period size: 80 Copynumber: 1.9 Consensus size: 80
1146392 GTGCAAACCA
* * * ** **
1146402 TTGGTTAATCCAACTAGAGTTGGGCTCACTTATCGCGGTTTATCTGCTAAGCACTGGGTGCCATG
1 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATCACGGTTTAACCACTAAGCACCAGGTGCCATG
1146467 AATTGACGGACTGTG
66 AATTGACGGACTGTG
*
1146482 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATCACGGTTTAACCACTAGGCACCAGGTGCCATG
1 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATCACGGTTTAACCACTAAGCACCAGGTGCCATG
1146547 AATTGACGGA
66 AATTGACGGA
1146557 AATTATAAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (80 bp):
TTGGTTAATCCAACTAGAGCTGGGCTCACTTATCACGGTTTAACCACTAAGCACCAGGTGCCATG
AATTGACGGACTGTG
Found at i:1148304 original size:21 final size:21
Alignment explanation
Indices: 1148280--1148324 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1148270 TAAATTTTAC
1148280 TATTTCGAAATTAGGTATCGA
1 TATTTCGAAATTAGGTATCGA
** *
1148301 TATTTCGGCATTTGGTATCGA
1 TATTTCGAAATTAGGTATCGA
1148322 TAT
1 TAT
1148325 CATCTATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (21 bp):
TATTTCGAAATTAGGTATCGA
Found at i:1157669 original size:2 final size:2
Alignment explanation
Indices: 1157662--1157691 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1157652 AAAATATGAA
1157662 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1157692 GCAAAACCTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1158390 original size:16 final size:16
Alignment explanation
Indices: 1158369--1158416 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
1158359 TTGAGATGAG
1158369 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
1158385 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
* *
1158399 ATTGAAATTTTAAATTA
1 AAT-AAATTTTTAATTA
1158416 A
1 A
1158417 TTACAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 10 0.37
15 3 0.11
16 6 0.22
17 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:1158424 original size:17 final size:15
Alignment explanation
Indices: 1158371--1158424 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 15
1158361 GAGATGAGAA
*
1158371 TAAATTTTTAATTAAA
1 TAAA-TTTTAATTAAT
1158387 TAAA-TTTAATTAAT
1 TAAATTTTAATTAAT
1158401 TGAAATTTTAAATTAAT
1 T-AAATTTT-AATTAAT
1158418 TACAATT
1 TA-AATT
1158425 GAAAAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 10 0.30
15 3 0.09
16 8 0.24
17 12 0.36
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TAAATTTTAATTAAT
Found at i:1158824 original size:29 final size:30
Alignment explanation
Indices: 1158787--1158845 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1158777 TATGGTTTAA
* *
1158787 TGTGTAATTGTATATATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
1158816 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
1158846 GATCCAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:1159222 original size:26 final size:26
Alignment explanation
Indices: 1159172--1159225 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1159162 TTGAAATTTT
* *
1159172 TTCGAATCAAGTCGAGTGAAATGAAA
1 TTCGAATCAAGTCGAATCAAATGAAA
* *
1159198 TTCGAGTCAAGTCGAATCAAGTGAAA
1 TTCGAATCAAGTCGAATCAAATGAAA
1159224 TT
1 TT
1159226 AAAATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (26 bp):
TTCGAATCAAGTCGAATCAAATGAAA
Found at i:1159573 original size:15 final size:15
Alignment explanation
Indices: 1159524--1159574 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1159514 ATTTATTTTG
*
1159524 TTTTGAAAACTTAAA
1 TTTTGGAAACTTAAA
* **
1159539 TTTTTGAAAAAT-AA
1 TTTTGGAAACTTAAA
1159553 -TTTGGAAACTTAAA
1 TTTTGGAAACTTAAA
1159567 TTTTGGAA
1 TTTTGGAA
1159575 GATAGCAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
13 8 0.30
14 4 0.15
15 15 0.56
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (15 bp):
TTTTGGAAACTTAAA
Found at i:1159584 original size:17 final size:15
Alignment explanation
Indices: 1159564--1159602 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1159554 TTGGAAACTT
*
1159564 AAATTTTGGAAGATAGC
1 AAATTTTGG-AGA-AAC
1159581 AAATTTTGGAGAAAC
1 AAATTTTGGAGAAAC
1159596 AAATTTT
1 AAATTTT
1159603 TTATATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 3 0.14
17 9 0.43
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (15 bp):
AAATTTTGGAGAAAC
Found at i:1159824 original size:23 final size:23
Alignment explanation
Indices: 1159798--1159859 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1159788 ATTACAATAG
1159798 AATATTCACTGTTCATGCCAGAA
1 AATATTCACTGTTCATGCCAGAA
* *
1159821 AATATTCACTATTCATGCCAGAG
1 AATATTCACTGTTCATGCCAGAA
* *
1159844 AATCTTCATTGTTCAT
1 AATATTCACTGTTCAT
1159860 TCATTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (23 bp):
AATATTCACTGTTCATGCCAGAA
Found at i:1162037 original size:66 final size:66
Alignment explanation
Indices: 1161955--1162086 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
1161945 CAATGATTTG
1161955 ATTTGGGAATTTATTGTAAAATTCTATGACCTTTTTATTGGAGTAATGGTTCCTTAGGTAATGTA
1 ATTTGGGAATTTATTGTAAAATTCTATGACCTTTTTATTGGAGTAATGGTTCCTTAGGTAATGTA
1162020 A
66 A
*
1162021 ATTTGGGAATTTATTGTAAAATTCTATGACCTTTTTATTGGGGTAATGGTTCCTTAGGTAATGTA
1 ATTTGGGAATTTATTGTAAAATTCTATGACCTTTTTATTGGAGTAATGGTTCCTTAGGTAATGTA
1162086 A
66 A
1162087 TGACCTAGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (66 bp):
ATTTGGGAATTTATTGTAAAATTCTATGACCTTTTTATTGGAGTAATGGTTCCTTAGGTAATGTA
A
Found at i:1165478 original size:24 final size:25
Alignment explanation
Indices: 1165451--1165500 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1165441 ATAATATTCC
1165451 TAAAA-AATACTT-TCTTTTTTATTT
1 TAAAATAAT-CTTCTCTTTTTTATTT
*
1165475 TAAAATAATCTTCTCTTTTTTTTTT
1 TAAAATAATCTTCTCTTTTTTATTT
1165500 T
1 T
1165501 TTGCTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (25 bp):
TAAAATAATCTTCTCTTTTTTATTT
Found at i:1165488 original size:23 final size:23
Alignment explanation
Indices: 1165454--1165499 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1165444 ATATTCCTAA
*
1165454 AAAATACTTTCT-TTTTTATTTT
1 AAAATAATTTCTCTTTTTATTTT
*
1165476 AAAATAATCTTCTCTTTTTTTTTT
1 AAAATAAT-TTCTCTTTTTATTTT
1165500 TTTGCTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (23 bp):
AAAATAATTTCTCTTTTTATTTT
Found at i:1166376 original size:39 final size:40
Alignment explanation
Indices: 1166294--1166386 Score: 152
Period size: 39 Copynumber: 2.4 Consensus size: 40
1166284 AGGTCTCTTC
**
1166294 CAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGACTTTT
1 CAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGACTCAT
*
1166334 CAAAAGGTGTCCATCCAATATG-AAATGGTTGTGACTCAT
1 CAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGACTCAT
1166373 CAAAAGGTGTCCAT
1 CAAAAGGTGTCCAT
1166387 TGAGTGCATA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
39 28 0.56
40 22 0.44
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (40 bp):
CAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGACTCAT
Found at i:1168116 original size:17 final size:17
Alignment explanation
Indices: 1168094--1168129 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1168084 TATGGAAAAA
1168094 AATGGTTATATCAATCT
1 AATGGTTATATCAATCT
1168111 AATGGTTATATCAATCT
1 AATGGTTATATCAATCT
1168128 AA
1 AA
1168130 GTAATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (17 bp):
AATGGTTATATCAATCT
Found at i:1171333 original size:39 final size:39
Alignment explanation
Indices: 1171250--1171341 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 39
1171240 AGTCTCTTCG
1171250 AAAAGGTGTCCATCCAATATGAAAAAGGTTGTGACTTTTC
1 AAAAGGTGTCCATCCAATATG-AAAAGGTTGTGACTTTTC
1171290 AAAAGGTGTCCATCCAATATG-AAAGGTTTGTGACTCTTT-
1 AAAAGGTGTCCATCCAATATGAAAAGG-TTGTGACT-TTTC
1171329 AAAAGGTGTCCAT
1 AAAAGGTGTCCAT
1171342 TGAGTGCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
38 5 0.10
39 21 0.42
40 24 0.48
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (39 bp):
AAAAGGTGTCCATCCAATATGAAAAGGTTGTGACTTTTC
Found at i:1179644 original size:19 final size:18
Alignment explanation
Indices: 1179607--1179650 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1179597 AAACATAATG
* *
1179607 AATAAAATTAAAATTAAA
1 AATAAAATAAAAATGAAA
1179625 AATAACAATAAAAATGAAA
1 AATAA-AATAAAAATGAAA
1179644 AATAAAA
1 AATAAAA
1179651 ATTTCAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAAAATAAAAATGAAA
Done.