Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008958.1 Hibiscus syriacus cultivar Beakdansim tig00112289_pilon, 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: 2490255
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1468600 original size:23 final size:23
Alignment explanation
Indices: 1468569--1468652 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
1468559 CACCACAGCT
* ** *
1468569 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGGAGTACCA
*
1468592 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGGAGTACCA
*
1468615 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGGAGTACCA
*
1468638 CATAGAATTGCACCG
1 CGTAGAATTGCACCG
1468653 TAGTGCCATA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTACCA
Found at i:1469250 original size:64 final size:63
Alignment explanation
Indices: 1469168--1469286 Score: 141
Period size: 64 Copynumber: 1.9 Consensus size: 63
1469158 CATAAATCCT
** *
1469168 ATTCGATGTTTGTATTT-AATGGGGTGCATCGATGCACTCCTTATGCATCGATGCATCGATGGC
1 ATTCGATGTTTGTATTTAAAT-GAATGCATCGATGCACTCCATATGCATCGATGCATCGATGGC
* * * * *
1469231 ATTCGATGTTTTTCTTTTAAATTAATGCATCGATGCACTTCATGTGCATCGATGCA
1 ATTCGATGTTTGT-ATTTAAATGAATGCATCGATGCACTCCATATGCATCGATGCA
1469287 CCTTAAACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 12 0.26
64 31 0.67
65 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (63 bp):
ATTCGATGTTTGTATTTAAATGAATGCATCGATGCACTCCATATGCATCGATGCATCGATGGC
Found at i:1472622 original size:30 final size:29
Alignment explanation
Indices: 1472583--1472641 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1472573 GAGAATTAAC
* *
1472583 ATGAACTACGTGATTACATGTATATGTGA
1 ATGAACTACGAGATTACATGAATATGTGA
* *
1472612 ATGAAGCTACGAGCTTATATGAATATGTGA
1 ATGAA-CTACGAGATTACATGAATATGTGA
1472642 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (29 bp):
ATGAACTACGAGATTACATGAATATGTGA
Found at i:1472926 original size:104 final size:104
Alignment explanation
Indices: 1472739--1472960 Score: 264
Period size: 104 Copynumber: 2.1 Consensus size: 104
1472729 GAGTCGAGGG
* * * *
1472739 TCTACGCGGTCCTTCGGGATATATAGGTATCCTATGGAATATCTATGAGGTCCTTTGCGACACAT
1 TCTACGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACAT
* *
1472804 ATTTGGTCCTTAGCATATGTATATGATTCTTAAGGAATT
66 ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATT
* * * * * * * *
1472843 TCTACGTGGTCCTTCGGGACGTATATGTATTCTTTGGAGCATGTATGAGGTCTTTTGAGACACTT
1 TCTACGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACAT
* * * *
1472908 ACTTGATCCTTGGTATATGTATATGGTTCTTAAGGTATT
66 ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATT
* *
1472947 TATATGTGGTCCTT
1 TCTACGTGGTCCTT
1472961 ATAGACAATC
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
104 98 1.00
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.40
Consensus pattern (104 bp):
TCTACGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACAT
ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATT
Found at i:1475733 original size:15 final size:16
Alignment explanation
Indices: 1475713--1475743 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1475703 CAACATGAAA
1475713 ATATTAT-AAGGCATG
1 ATATTATAAAGGCATG
1475728 ATATTATAAAGGCATG
1 ATATTATAAAGGCATG
1475744 CAGTGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (16 bp):
ATATTATAAAGGCATG
Found at i:1478094 original size:47 final size:47
Alignment explanation
Indices: 1478036--1478131 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
1478026 CCTATGGAAC
1478036 ATCTATAAGGTCCTTTGCGACACATATTTGGTCCTCAGCATATGTAT
1 ATCTATAAGGTCCTTTGCGACACATATTTGGTCCTCAGCATATGTAT
* *
1478083 ATCTATGAGGTCCTTTGCGACACATATTTGGTCCTTAGCATATGTAT
1 ATCTATAAGGTCCTTTGCGACACATATTTGGTCCTCAGCATATGTAT
1478130 AT
1 AT
1478132 GATTCTTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (47 bp):
ATCTATAAGGTCCTTTGCGACACATATTTGGTCCTCAGCATATGTAT
Found at i:1478327 original size:23 final size:24
Alignment explanation
Indices: 1478280--1478327 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1478270 ACAATCTTAT
*
1478280 ATGGCACTACGGTGTAAATTCTAC
1 ATGGCACTACGGTGTAAATTATAC
* *
1478304 ATGGCACTTCGGTG-CAATTATAC
1 ATGGCACTACGGTGTAAATTATAC
1478327 A
1 A
1478328 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
ATGGCACTACGGTGTAAATTATAC
Found at i:1481496 original size:18 final size:21
Alignment explanation
Indices: 1481455--1481497 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1481445 TTTTAGTGGT
*
1481455 TTTCCCAGGCTTATATTTCTC
1 TTTCCCAGGCCTATATTTCTC
1481476 TTTCCCA-GCCTAT-TTTC-C
1 TTTCCCAGGCCTATATTTCTC
1481494 TTTC
1 TTTC
1481498 ACTTATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 5 0.24
21 7 0.33
ACGTcount: A:0.12, C:0.33, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTCCCAGGCCTATATTTCTC
Found at i:1499114 original size:19 final size:21
Alignment explanation
Indices: 1499077--1499119 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1499067 TAACTTTTTC
1499077 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
1499097 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
1499117 TTT
1 TTT
1499120 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:1499125 original size:19 final size:20
Alignment explanation
Indices: 1499076--1499125 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1499066 TTAACTTTTT
*
1499076 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
1499096 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
1499115 CTTTTACCTTT
1 CTTTTACCTTT
1499126 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:1505595 original size:21 final size:21
Alignment explanation
Indices: 1505571--1505624 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1505561 AATAAATTAC
1505571 TGGAATTTGAATTACTGGAAT
1 TGGAATTTGAATTACTGGAAT
**
1505592 TGGAAAATGAATTACTGGAAT
1 TGGAATTTGAATTACTGGAAT
*
1505613 TTGAATTCTGAA
1 TGGAATT-TGAA
1505625 AAATAAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (21 bp):
TGGAATTTGAATTACTGGAAT
Found at i:1505659 original size:14 final size:14
Alignment explanation
Indices: 1505637--1505667 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1505627 ATAAATTACA
*
1505637 TTTCTGGAAAACAT
1 TTTCCGGAAAACAT
1505651 TTTCCGGAAAACAT
1 TTTCCGGAAAACAT
1505665 TTT
1 TTT
1505668 TCATAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (14 bp):
TTTCCGGAAAACAT
Found at i:1505888 original size:48 final size:49
Alignment explanation
Indices: 1505765--1505889 Score: 112
Period size: 48 Copynumber: 2.5 Consensus size: 49
1505755 TTGAAAAGTT
* *
1505765 TTTTAAAAATTATTTATTATAAATATT-AAATGTAATAAATAATATTATTTA
1 TTTT-AAAATTATTT-TTAT-AATTTTAAAATATAATAAATAATATTATTTA
* * * * * *
1505816 TCATTAAACTTAATATTATTATTTTAAAATATTA-AAATAAT-TTATTTA
1 T-TTTAAAATTATTTTTATAATTTTAAAATATAATAAATAATATTATTTA
1505864 TTTTAAATATTATTTTTATAATTTTA
1 TTTTAAA-ATTATTTTTATAATTTTA
1505890 TTAATAAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
47 5 0.09
48 22 0.38
49 11 0.19
50 10 0.17
51 8 0.14
52 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (49 bp):
TTTTAAAATTATTTTTATAATTTTAAAATATAATAAATAATATTATTTA
Found at i:1505900 original size:29 final size:31
Alignment explanation
Indices: 1505868--1505937 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
1505858 TATTTATTTT
*
1505868 AAATATTATTTTTATA-ATTTTA-T-TAATAA
1 AAATATTATTTTTATATATTTTAGTGAAAT-A
* *
1505897 AAATAATAATTTTTGTATATTTTAGTGAAATA
1 AAAT-ATTATTTTTATATATTTTAGTGAAATA
1505929 AAATATTAT
1 AAATATTAT
1505938 AAATTATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 4 0.12
30 10 0.30
31 10 0.30
32 6 0.18
33 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (31 bp):
AAATATTATTTTTATATATTTTAGTGAAATA
Found at i:1506027 original size:23 final size:23
Alignment explanation
Indices: 1505978--1506040 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1505968 GTGTTATATT
* **
1505978 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
1506001 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
1506024 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
1506041 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:1506068 original size:19 final size:20
Alignment explanation
Indices: 1506016--1506068 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1506006 TTAAATATCT
1506016 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1506035 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
1506056 TTATTAAATATAT
1 TTATTAAATATAT
1506069 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1506081 original size:30 final size:29
Alignment explanation
Indices: 1506024--1506179 Score: 100
Period size: 30 Copynumber: 5.5 Consensus size: 29
1506014 CTTTATTAAA
1506024 ATATTATTTAAATATATAAA-TAATATTAT
1 ATATTA-TTAAATATATAAATTAATATTAT
**
1506053 -TCATTATTAAATATATAAATTTTTTATTAT
1 AT-ATTATTAAATATATAAA-TTAATATTAT
*
1506083 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATATATAAAT-TAATAT-TAT
** *
1506112 ATATTATTATAATATAATTGATT-ATTTTAT
1 ATATTATTA-AATAT-ATAAATTAATATTAT
*
1506142 ATAATATTAAA-A-AT--ATT-ATATTAT
1 ATATTATTAAATATATAAATTAATATTAT
1506166 ATTATTA-TAAATAT
1 A-TATTATTAAATAT
1506180 TAATAAATAA
Statistics
Matches: 102, Mismatches: 12, Indels: 29
0.71 0.08 0.20
Matches are distributed among these distances:
24 14 0.14
25 5 0.05
26 2 0.02
28 16 0.16
29 27 0.26
30 31 0.30
31 4 0.04
32 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
ATATTATTAAATATATAAATTAATATTAT
Found at i:1506432 original size:41 final size:42
Alignment explanation
Indices: 1506380--1506493 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
1506370 TTACATTCTA
* * *
1506380 GAAAACCAATTACGTT-AAACAAACATG-GAAAACATTTTCCG
1 GAAAACGAATTAC-TTAAAACAAACACGAAAAAACATTTTCCG
* *
1506421 GAAAACGAATTACTTGAAACAAACACGAAAAAACATTTTCTG
1 GAAAACGAATTACTTAAAACAAACACGAAAAAACATTTTCCG
* * *
1506463 AAAAATGAATTACTTAAAACAAATACGAAAA
1 GAAAACGAATTACTTAAAACAAACACGAAAA
1506494 TTCGAAGAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 2 0.03
41 22 0.35
42 39 0.62
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.21
Consensus pattern (42 bp):
GAAAACGAATTACTTAAAACAAACACGAAAAAACATTTTCCG
Found at i:1507693 original size:2 final size:2
Alignment explanation
Indices: 1507686--1507716 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1507676 CAACATAAAC
1507686 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 T
1507717 CTGTGTGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1509594 original size:3 final size:3
Alignment explanation
Indices: 1509581--1509613 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1509571 CTATTAACCA
1509581 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1509614 TAGTGTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1510776 original size:16 final size:16
Alignment explanation
Indices: 1510755--1510790 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1510745 TTTTATGATA
1510755 TTTATAAATCCTTCTT
1 TTTATAAATCCTTCTT
1510771 TTTATAAATCCTTCTT
1 TTTATAAATCCTTCTT
1510787 TTTA
1 TTTA
1510791 GAGTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATAAATCCTTCTT
Found at i:1516724 original size:32 final size:31
Alignment explanation
Indices: 1516651--1516748 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 31
1516641 CAAAAGCTAG
* * **
1516651 AAAATAGTCATTAAACCTCCCAAA-TAGTTAC
1 AAAATAATCATTAAACTTATCAAAGTA-TTAC
*
1516682 AGAATAATCATTAAACTTTATCAAAGTATTAC
1 AAAATAATCATTAAAC-TTATCAAAGTATTAC
* * * *
1516714 AAAATGATCATTAAACTTGTCAAATTAGTAC
1 AAAATAATCATTAAACTTATCAAAGTATTAC
1516745 AAAA
1 AAAA
1516749 GGGTCCTTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 30 0.55
32 23 0.42
33 2 0.04
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (31 bp):
AAAATAATCATTAAACTTATCAAAGTATTAC
Found at i:1516746 original size:31 final size:31
Alignment explanation
Indices: 1516671--1516748 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
1516661 TTAAACCTCC
*
1516671 CAAATAGTTACAGAATAATCATTAAACTTTAT
1 CAAATAG-TACAAAATAATCATTAAACTTTAT
* * *
1516703 CAAAGTATTACAAAATGATCATTAAAC-TTGT
1 CAAA-TAGTACAAAATAATCATTAAACTTTAT
1516734 CAAATTAGTACAAAA
1 CAAA-TAGTACAAAA
1516749 GGGTCCTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
31 16 0.41
32 21 0.54
33 2 0.05
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (31 bp):
CAAATAGTACAAAATAATCATTAAACTTTAT
Found at i:1516759 original size:31 final size:31
Alignment explanation
Indices: 1516688--1516768 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
1516678 TTACAGAATA
* *
1516688 ATCATTAAACTTTATCAAAGTATTACAAAATG
1 ATCATTAAAC-TTATCAAAGTAGTACAAAAGG
* *
1516720 ATCATTAAACTTGTCAAATTAGTACAAAAGG
1 ATCATTAAACTTATCAAAGTAGTACAAAAGG
* * *
1516751 GTCCTTAAACTCATCAAA
1 ATCATTAAACTTATCAAA
1516769 ATTTATCACT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 31 0.76
32 10 0.24
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (31 bp):
ATCATTAAACTTATCAAAGTAGTACAAAAGG
Found at i:1517783 original size:60 final size:60
Alignment explanation
Indices: 1517686--1517836 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 60
1517676 TTTGAGGATC
* * * *
1517686 AATTTAGAATGAG-GTCATAGTTTG-GAAATGAAATTGGAACATTCAG-AAGTATAAAGACT
1 AATTTAAAATGAGAATCATAGTTTGAG-GATGTAATTGGAACATT-AGAAAGTATAAAGACT
* * * *
1517745 AATTTAAAATGAGAATCATAGTTTGAGGATGTAATTGGAAGATTTGAAAGTATGAATACT
1 AATTTAAAATGAGAATCATAGTTTGAGGATGTAATTGGAACATTAGAAAGTATAAAGACT
* * *
1517805 AATTTAAAATAAGAATCATAATTTAAGGATGT
1 AATTTAAAATGAGAATCATAGTTTGAGGATGT
1517837 GTGATGTAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 13 0.17
60 64 0.82
61 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (60 bp):
AATTTAAAATGAGAATCATAGTTTGAGGATGTAATTGGAACATTAGAAAGTATAAAGACT
Found at i:1526105 original size:24 final size:23
Alignment explanation
Indices: 1526070--1526114 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1526060 TTATTTATAA
*
1526070 TATTAACTAAATTATAATATTATT
1 TATTAACTAAA-TATAACATTATT
1526094 TATTAAAC-AAATATAACATTA
1 TATT-AACTAAATATAACATTA
1526115 GAACATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 7 0.37
25 3 0.16
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (23 bp):
TATTAACTAAATATAACATTATT
Found at i:1527455 original size:21 final size:21
Alignment explanation
Indices: 1527431--1527543 Score: 122
Period size: 21 Copynumber: 5.5 Consensus size: 21
1527421 GTTGCATTTA
1527431 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAGTTGAAAATC
* ** **
1527452 GCGTTGCGAT-TTTCCATTTC
1 GCGTTGCGATAGTTGAAAATC
1527472 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAGTTGAAAATC
* ** **
1527493 GCGTTGCGAT-TTTCCATTTC
1 GCGTTGCGATAGTTGAAAATC
1527513 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAGTTGAAAATC
1527534 GCGTTGCGAT
1 GCGTTGCGAT
1527544 TTTCCATTTC
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
20 30 0.43
21 40 0.57
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (21 bp):
GCGTTGCGATAGTTGAAAATC
Found at i:1527475 original size:20 final size:20
Alignment explanation
Indices: 1527450--1527561 Score: 116
Period size: 20 Copynumber: 5.5 Consensus size: 20
1527440 TAGTTGAAAA
1527450 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
1527470 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
1527491 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
1527511 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
1527532 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1527552 TCGCGTTGCG
1 TCGCGTTGCG
1527562 GTAGTCTACA
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
20 40 0.57
21 30 0.43
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1527476 original size:41 final size:41
Alignment explanation
Indices: 1527425--1527590 Score: 273
Period size: 41 Copynumber: 4.0 Consensus size: 41
1527415 ATTCGCGTTG
*
1527425 CATTTAGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1527466 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1527507 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
1527548 CATTTCGCGTTGCGGTAGTCT-ACAAT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
1527589 CA
1 CA
1527591 AATTCATTGC
Statistics
Matches: 120, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
40 1 0.01
41 118 0.98
42 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1528783 original size:55 final size:55
Alignment explanation
Indices: 1528686--1528796 Score: 150
Period size: 55 Copynumber: 2.0 Consensus size: 55
1528676 AATTACCAAG
* * **
1528686 ATTTCTACACCACTTTTATAAGGTATTGATACCTAAAAAATAATACTAATACAAA
1 ATTTCTACACCACATTTATAAGATATCAATACCTAAAAAATAATACTAATACAAA
* * * *
1528741 ATTTCTATACCACATTTATATGATATCAATACTTAAAGAATAATACTAATACAAA
1 ATTTCTACACCACATTTATAAGATATCAATACCTAAAAAATAATACTAATACAAA
1528796 A
1 A
1528797 GCAAAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (55 bp):
ATTTCTACACCACATTTATAAGATATCAATACCTAAAAAATAATACTAATACAAA
Found at i:1532329 original size:6 final size:6
Alignment explanation
Indices: 1532318--1532342 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1532308 TATTCATAAT
1532318 AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA A
1532343 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:1534483 original size:40 final size:40
Alignment explanation
Indices: 1534416--1534495 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
1534406 TCAACATTAG
*
1534416 AGGATGGAAGCTAAACCAGCTACTAAGGAGCTAAAAGCTA
1 AGGATGGAAGCTAAACAAGCTACTAAGGAGCTAAAAGCTA
* * *
1534456 AGGATGGGAGCTAAAACAAGCT-GTAAGGAGCTTAAAGCTA
1 AGGATGGAAGCT-AAACAAGCTACTAAGGAGCTAAAAGCTA
1534496 GGAATTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 27 0.77
41 8 0.23
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.16
Consensus pattern (40 bp):
AGGATGGAAGCTAAACAAGCTACTAAGGAGCTAAAAGCTA
Found at i:1535534 original size:22 final size:23
Alignment explanation
Indices: 1535499--1535542 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1535489 CAATTGGTAC
*
1535499 AAAAGAATATAAAAGAAAAGAAA
1 AAAAGAATAAAAAAGAAAAGAAA
*
1535522 AAAAGAA-AAAAAAGTAAAGAA
1 AAAAGAATAAAAAAGAAAAGAA
1535543 TAATTCCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (23 bp):
AAAAGAATAAAAAAGAAAAGAAA
Found at i:1542099 original size:20 final size:20
Alignment explanation
Indices: 1542074--1542116 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1542064 CATGTTTTTT
1542074 GTGGTGGTGTTAAAGTGGAG
1 GTGGTGGTGTTAAAGTGGAG
*
1542094 GTGGTGGTGTTACAGTGGAG
1 GTGGTGGTGTTAAAGTGGAG
1542114 GTG
1 GTG
1542117 CTGATAACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.02, G:0.51, T:0.30
Consensus pattern (20 bp):
GTGGTGGTGTTAAAGTGGAG
Found at i:1545588 original size:10 final size:10
Alignment explanation
Indices: 1545573--1545597 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1545563 CAAATATAAC
1545573 CTAAATGCAA
1 CTAAATGCAA
1545583 CTAAATGCAA
1 CTAAATGCAA
1545593 CTAAA
1 CTAAA
1545598 ATGTTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:1563518 original size:14 final size:14
Alignment explanation
Indices: 1563499--1563526 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1563489 AAAAATTATT
1563499 TAAATAAATTCTAA
1 TAAATAAATTCTAA
1563513 TAAATAAATTCTAA
1 TAAATAAATTCTAA
1563527 CAATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATAAATTCTAA
Found at i:1570369 original size:23 final size:23
Alignment explanation
Indices: 1570339--1570387 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1570329 TTATCTTTTC
1570339 AATTTGGATGAAAATTACAAGTA
1 AATTTGGATGAAAATTACAAGTA
1570362 AATTTGGATGAAAATTACAAGTA
1 AATTTGGATGAAAATTACAAGTA
1570385 AAT
1 AAT
1570388 GTGAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.31
Consensus pattern (23 bp):
AATTTGGATGAAAATTACAAGTA
Found at i:1571737 original size:21 final size:21
Alignment explanation
Indices: 1571712--1571752 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1571702 CCCATAATAC
1571712 ATTCCAAACAAAATAAGTAAT
1 ATTCCAAACAAAATAAGTAAT
1571733 ATTCCAAACAAAATAAGTAA
1 ATTCCAAACAAAATAAGTAA
1571753 AATACTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.05, T:0.22
Consensus pattern (21 bp):
ATTCCAAACAAAATAAGTAAT
Found at i:1572822 original size:33 final size:33
Alignment explanation
Indices: 1572754--1572820 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
1572744 CTTTACAAAC
* *
1572754 TCCTAGTTTTTCACGGGCTAAACTGGAACCTTT
1 TCCTAGTTTTACACGGGCTAAACTAGAACCTTT
* *
1572787 TCCTAGCTTTTACACGGGCTTAGCTAGAACCTTT
1 TCCTAG-TTTTACACGGGCTAAACTAGAACCTTT
1572821 CCCCTTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (33 bp):
TCCTAGTTTTACACGGGCTAAACTAGAACCTTT
Found at i:1573232 original size:20 final size:20
Alignment explanation
Indices: 1573185--1573240 Score: 103
Period size: 21 Copynumber: 2.8 Consensus size: 20
1573175 TTTGAGCCTT
1573185 AGGGTATCGATACTCCTTCA
1 AGGGTATCGATACTCCTTCA
1573205 AGGGGTATCGATACTCCTTCA
1 A-GGGTATCGATACTCCTTCA
1573226 AGGGTATCGATACTC
1 AGGGTATCGATACTC
1573241 ATTTGCACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (20 bp):
AGGGTATCGATACTCCTTCA
Found at i:1584420 original size:12 final size:13
Alignment explanation
Indices: 1584390--1584420 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1584380 TATGTCATAA
1584390 GAAAAAGGTTGAG
1 GAAAAAGGTTGAG
1584403 GAAAAAGGTTGAG
1 GAAAAAGGTTGAG
1584416 GAAAA
1 GAAAA
1584421 TGCTTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.35, T:0.13
Consensus pattern (13 bp):
GAAAAAGGTTGAG
Found at i:1587428 original size:17 final size:16
Alignment explanation
Indices: 1587397--1587430 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1587387 CACGTGAGGA
1587397 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1587413 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1587430 T
1 T
1587431 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1593592 original size:81 final size:80
Alignment explanation
Indices: 1593507--1593731 Score: 215
Period size: 80 Copynumber: 2.8 Consensus size: 80
1593497 ATACATTATA
* * * * * *
1593507 ATTCCTTTCTTCTTTTACCCAA-ATATATTTAGCCTTTCATCTAACTT-GCATATTTGACACTTT
1 ATTCCATTATTCTTTTA-CCAACA-ATATTTAACCGTTCATCTAA-TTGGCATAATTGACACCTT
*
1593570 TCTATCAAATGCAAATCT
63 TCTACCAAATGCAAATCT
* *
1593588 ATTCCATTATTCTTTTACCAACAGTATTTAATCGTTCATCTAATTGGCATAATTGACACCTTTCT
1 ATTCCATTATTCTTTTACCAACAATATTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCT
* * *
1593653 GCCAAATGCACAGCT
66 ACCAAATGCAAATCT
* * ** *
1593668 AGAT-CATTCA-TCTTTTACTAAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTT
1 A-TTCCATT-ATTCTTTTAC-CAACAATATTTAACCGTTCATCTAATTGGCATAATTGACACCTT
1593731 T
63 T
1593732 TTGTCAAATG
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
79 2 0.02
80 61 0.50
81 59 0.48
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (80 bp):
ATTCCATTATTCTTTTACCAACAATATTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCT
ACCAAATGCAAATCT
Found at i:1593630 original size:80 final size:81
Alignment explanation
Indices: 1593532--1593743 Score: 236
Period size: 80 Copynumber: 2.6 Consensus size: 81
1593522 TACCCAAATA
* * * * * *
1593532 TATTTAGCCTTTCATCTAACTTGCATATTTGACACTTTTCTATCAAATGCAAATCTA-TTCCATT
1 TATTTAACCGTTCATCTAACTTGCATAATTGACACTTTTCTGTCAAATGCAAAGCTAGAT-CATT
*
1593596 -ATTCTTTTAC-CAACAG
65 CA-TCTTTTACTAAACAG
* * * *
1593612 TATTTAATCGTTCATCTAA-TTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGATCATT
1 TATTTAACCGTTCATCTAACTT-GCATAATTGACACTTTTCTGTCAAATGCAAAGCTAGATCATT
*
1593676 CATCTTTTACTAAACGG
65 CATCTTTTACTAAACAG
*
1593693 TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTT-TGTCAAATGCA
1 TATTTAACCGTTCATCTAACTTGCATAATTGACA-CTTTTCTGTCAAATGCA
1593744 CAGTTAGGCC
Statistics
Matches: 110, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
79 2 0.02
80 57 0.52
81 46 0.42
82 5 0.05
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (81 bp):
TATTTAACCGTTCATCTAACTTGCATAATTGACACTTTTCTGTCAAATGCAAAGCTAGATCATTC
ATCTTTTACTAAACAG
Found at i:1593740 original size:81 final size:80
Alignment explanation
Indices: 1593532--1593746 Score: 247
Period size: 81 Copynumber: 2.7 Consensus size: 80
1593522 TACCCAAATA
* * * * * * * *
1593532 TATTTAGCCTTTCATCTAACTTGCATATTTGACA-CTTTTCTATCAAATGCAAATCTATTCCATT
1 TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTT-TGTCAAATGCACAGCTAATCCATT
*
1593596 ATTCTTTTACCAACAG
65 ATTCTTTTACAAACAG
* * * *
1593612 TATTTAATCGTTCATCTAATTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGAT-CATT
1 TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAGCTA-ATCCATT
*
1593676 CA-TCTTTTACTAAACGG
65 -ATTCTTTTAC-AAACAG
1593693 TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAG
1 TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAG
1593747 TTAGGCCTCA
Statistics
Matches: 113, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
80 53 0.47
81 60 0.53
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (80 bp):
TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAGCTAATCCATTA
TTCTTTTACAAACAG
Found at i:1593817 original size:68 final size:68
Alignment explanation
Indices: 1593703--1594504 Score: 1194
Period size: 68 Copynumber: 11.8 Consensus size: 68
1593693 TATTTAACCG
* *
1593703 TTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTGG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1593768 CCT
66 CCT
* * * *
1593771 TTCCTCTAACTGGCATAATTGACACCTTTTTGTCAAATGCATAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1593836 CCT
66 CCT
* * * *
1593839 TTCATATAACTGGAATAATTGACACCTTTCTATCAAATGCACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
1593904 TCT
66 CCT
* * * *
1593907 TTCATATAACTGGCATAATTGACACATTTCTGTCAAATACACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1593972 CCT
66 CCT
* * *
1593975 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGAATAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1594040 CCT
66 CCT
* * * *
1594043 TTCATCTAACTGGCATAATTGGCACCTTTCTATCAAATGCACAGTTAGGCATCAAAGGCACTTAT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1594108 CCT
66 CCT
* * * *
1594111 TTCATCTAACTGGTATAATTG-CATCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1594175 CCT
66 CCT
* * * * *
1594178 TTCATCTAACTGGTATAATTGACACATTTCTGTCAAATTCAGAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1594243 CCT
66 CCT
**
1594246 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATTTACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1594311 CCT
66 CCT
*
1594314 TTCATCTAACTGGCATAATTGACACCTTTCTGTAAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1594379 CCT
66 CCT
* * * *
1594382 TTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGTACAGTTAGGCCTTAAA-GAACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1594446 CCT
66 CCT
* * ** * *
1594449 TTCATATAACTGACATAATTGACATATTTCTGTCAAATTCACAGTTATGCCTCAAA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAA
1594505 TCTTTTATTT
Statistics
Matches: 665, Mismatches: 68, Indels: 3
0.90 0.09 0.00
Matches are distributed among these distances:
67 120 0.18
68 545 0.82
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1594275 original size:271 final size:272
Alignment explanation
Indices: 1593703--1594504 Score: 1241
Period size: 271 Copynumber: 3.0 Consensus size: 272
1593693 TATTTAACCG
* * *
1593703 TTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTGG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGAACAGTTAGGCCTCAAAGGCACTTAG
* * * *
1593768 CCTTTCCTCTAACTGGCATAATTGACACCTTTTTGTCAAATGCATAGTTAGGCCTCAAAGACACT
66 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
* * *
1593833 TAGCCTTTCATATAACTGGAATAATTGACACCTTTCTATCAAATGCACAGTTAGGCTTCAAAGGC
131 TAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGC
*
1593898 ACTTAGT-CTTTCATATAACTGGCATAATTGACACATTTCTGTCAAATACACAGTTAGGCCTCAA
196 ACTTA-TCCTTTCATATAACTGGCATAATTGACACATTTCTGTCAAATTCACAGTTAGGCCTCAA
1593962 AGACACTTAGCCT
260 AGACACTTAGCCT
* *
1593975 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGAATAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGAACAGTTAGGCCTCAAAGGCACTTAG
* * *
1594040 CCTTTCATCTAACTGGCATAATTGGCACCTTTCTATCAAATGCACAGTTAGGCATCAAAGGCACT
66 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
* * * *
1594105 TATCCTTTCATCTAACTGGTATAATTG-CATCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGC
131 TAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGC
* * * *
1594169 ACTTATCCTTTCATCTAACTGGTATAATTGACACATTTCTGTCAAATTCAGAATTAGGCCTCAAA
196 ACTTATCCTTTCATATAACTGGCATAATTGACACATTTCTGTCAAATTCACAGTTAGGCCTCAAA
*
1594234 GGCACTTAGCCT
261 GACACTTAGCCT
**
1594246 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATTTACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGAACAGTTAGGCCTCAAAGGCACTTAG
*
1594311 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTAAAATGCACAGTTAGGCCTCAAAGGCACT
66 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
* * * * *
1594376 TAGCCTTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGTACAGTTAGGCCTTAAA-GA
131 TAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGC
* * * *
1594440 ACTTAGCCTTTCATATAACTGACATAATTGACATATTTCTGTCAAATTCACAGTTATGCCTCAAA
196 ACTTATCCTTTCATATAACTGGCATAATTGACACATTTCTGTCAAATTCACAGTTAGGCCTCAAA
1594505 TCTTTTATTT
Statistics
Matches: 479, Mismatches: 49, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
270 1 0.00
271 306 0.64
272 172 0.36
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (272 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGAACAGTTAGGCCTCAAAGGCACTTAG
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGC
ACTTATCCTTTCATATAACTGGCATAATTGACACATTTCTGTCAAATTCACAGTTAGGCCTCAAA
GACACTTAGCCT
Found at i:1594866 original size:54 final size:54
Alignment explanation
Indices: 1594721--1594866 Score: 213
Period size: 54 Copynumber: 2.7 Consensus size: 54
1594711 CATAGAGAAC
** * *
1594721 TTCATACACTTAGTATGAATTTCTTAGTTCGTACATATAGTACCCATACGAAAA
1 TTCATACACTTAGTATGAATTTCTTAGTTTTTACACAAAGTACCCATACGAAAA
*
1594775 TTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTACCCATACG-AAA
1 TTCATACACTTAGTATGAATTTCTTAGTTTT-TACACAAAGTACCCATACGAAAA
*
1594829 TTCATACACTTAGTATGAATTTTTTAGGTTTTTACACA
1 TTCATACACTTAGTATGAATTTCTTA-GTTTTTACACA
1594867 CTTAGTGCCA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
54 62 0.75
55 21 0.25
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (54 bp):
TTCATACACTTAGTATGAATTTCTTAGTTTTTACACAAAGTACCCATACGAAAA
Found at i:1597774 original size:14 final size:15
Alignment explanation
Indices: 1597737--1597772 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1597727 AGTTCCTTAT
*
1597737 AATTTTTAATCTCAA
1 AATTTTTAACCTCAA
*
1597752 AATTTTTAACCTCGA
1 AATTTTTAACCTCAA
1597767 AATTTT
1 AATTTT
1597773 AAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (15 bp):
AATTTTTAACCTCAA
Found at i:1597781 original size:23 final size:23
Alignment explanation
Indices: 1597750--1597806 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1597740 TTTTAATCTC
*
1597750 AAAATTTTTAACCTCGAAATTTT
1 AAAATTTTTAACCTCAAAATTTT
* *
1597773 AAAAATTTTAACTTCAAAATTTT
1 AAAATTTTTAACCTCAAAATTTT
1597796 AAAATTTTTAA
1 AAAATTTTTAA
1597807 TATTTTTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
AAAATTTTTAACCTCAAAATTTT
Found at i:1600090 original size:11 final size:12
Alignment explanation
Indices: 1600074--1600114 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1600064 AACAAATCTT
1600074 GAAAAAT-AAAA
1 GAAAAATGAAAA
1600085 GAAAAATGAAAA
1 GAAAAATGAAAA
*
1600097 G-AACATGAAAA
1 GAAAAATGAAAA
1600108 GTAAAAA
1 G-AAAAA
1600115 GAGAAAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 17 0.68
12 5 0.20
13 3 0.12
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.10
Consensus pattern (12 bp):
GAAAAATGAAAA
Found at i:1601242 original size:18 final size:18
Alignment explanation
Indices: 1601221--1601263 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1601211 TTCGAACTGC
1601221 TTTTTTTTTTCTTCTTCT
1 TTTTTTTTTTCTTCTTCT
*
1601239 TTTTCTTTTTCTTCTTCT
1 TTTTTTTTTTCTTCTTCT
1601257 TTTTTTT
1 TTTTTTT
1601264 CGATGGAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTCTTCTTCT
Found at i:1602954 original size:17 final size:17
Alignment explanation
Indices: 1602934--1602966 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1602924 TGCTCGGTCG
1602934 AAAAAAAAAAATAAAAC
1 AAAAAAAAAAATAAAAC
*
1602951 AAAAACAAAAATAAAA
1 AAAAAAAAAAATAAAA
1602967 AAATGTAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAAATAAAAC
Found at i:1609708 original size:21 final size:21
Alignment explanation
Indices: 1609670--1609709 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1609660 TTGAGGGTTC
* **
1609670 TACGAGGTCTTTTGAGACATA
1 TACGAGGTCCTTCAAGACATA
1609691 TACGAGGTCCTTCAAGACA
1 TACGAGGTCCTTCAAGACA
1609710 ATTTTATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
TACGAGGTCCTTCAAGACATA
Found at i:1616718 original size:21 final size:21
Alignment explanation
Indices: 1616694--1616765 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
1616684 GGGTTCTACG
* *
1616694 AGGTCCTTCGAGACATATACA
1 AGGTCCTTCGGGGCATATACA
*
1616715 AGGTCCTTTGGGGCATATACA
1 AGGTCCTTCGGGGCATATACA
*
1616736 AGGTCCTTTGGGGCATATACA
1 AGGTCCTTCGGGGCATATACA
1616757 AGGTCCTTC
1 AGGTCCTTC
1616766 AGGACAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (21 bp):
AGGTCCTTCGGGGCATATACA
Found at i:1619905 original size:13 final size:13
Alignment explanation
Indices: 1619887--1619913 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1619877 GATTAAAGTG
1619887 AAAAAAAAGGTAA
1 AAAAAAAAGGTAA
1619900 AAAAAAAAGGTAA
1 AAAAAAAAGGTAA
1619913 A
1 A
1619914 GTAGAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAAAAGGTAA
Found at i:1620845 original size:209 final size:209
Alignment explanation
Indices: 1620454--1620871 Score: 820
Period size: 208 Copynumber: 2.0 Consensus size: 209
1620444 AACCCAAACT
1620454 AAGCTAAGTTAGTTAATGGCTTGGTAAATAACATCTATAATCATTTGTTTAATAGAACCCATAGA
1 AAGCTAAGTTAGTTAATGGCTTGGTAAATAACATCTATAATCATTTGTTTAATAGAACCCATAGA
1620519 AGAAAAGATGAAGAAATAAAGAAAAATTAAAGAAGGAAGAAAACTCTCAAGCCGATAGTTGTCGT
66 AGAAAAGATGAAGAAATAAAGAAAAATTAAAGAAGGAAGAAAACTCTCAAGCCGATAGTTGTCGT
1620584 GAACTACCGTGAACGACCCAAGCGTTGTTGCTTCTCTCAAAGGCCAACAAGTTTTATCCCTTGGA
131 GAACTACCGTGAACGACCCAAGCGTTGTTGCTTCTCTCAAAGGCCAACAAGTTTTATCCCTTGGA
1620649 GCTCCAACAATTGA
196 GCTCCAACAATTGA
1620663 AAGCTAAGTTAGTTAATGGCTTGGT-AATAACATCTATAATCATTTGTTTAATAGAACCCATAGA
1 AAGCTAAGTTAGTTAATGGCTTGGTAAATAACATCTATAATCATTTGTTTAATAGAACCCATAGA
1620727 AGAAAAGATGAAGAAATAAAGAAAAATTAAAGAAGGAAGAAAACTCTCAAGCCGATAGTTGTCGT
66 AGAAAAGATGAAGAAATAAAGAAAAATTAAAGAAGGAAGAAAACTCTCAAGCCGATAGTTGTCGT
1620792 GAACTACCGTGAACGACCCAAAGCGTTGTTGCTTCTCTCAAAGGCCAACAAGTTTTATCCCTTGG
131 GAACTACCGTGAACGACCC-AAGCGTTGTTGCTTCTCTCAAAGGCCAACAAGTTTTATCCCTTGG
1620857 AGCTCCAACAATTGA
195 AGCTCCAACAATTGA
1620872 GGTCACCATG
Statistics
Matches: 208, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
208 123 0.59
209 85 0.41
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (209 bp):
AAGCTAAGTTAGTTAATGGCTTGGTAAATAACATCTATAATCATTTGTTTAATAGAACCCATAGA
AGAAAAGATGAAGAAATAAAGAAAAATTAAAGAAGGAAGAAAACTCTCAAGCCGATAGTTGTCGT
GAACTACCGTGAACGACCCAAGCGTTGTTGCTTCTCTCAAAGGCCAACAAGTTTTATCCCTTGGA
GCTCCAACAATTGA
Found at i:1621452 original size:3 final size:3
Alignment explanation
Indices: 1621439--1621506 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
1621429 TCGTTATAAG
1621439 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1621485 TAT TAT TAT TA- TAT TAT AAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
1621507 ATTGTTACAA
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 6 0.10
3 54 0.90
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1622241 original size:45 final size:45
Alignment explanation
Indices: 1622177--1622278 Score: 188
Period size: 45 Copynumber: 2.3 Consensus size: 45
1622167 AGGAGTGTCG
1622177 ACAGGCTTGTATTATAAGCGTGTTTTCTGATTGAAATCAGAAAAC
1 ACAGGCTTGTATTATAAGCGTGTTTTCTGATTGAAATCAGAAAAC
1622222 ACAGGCTTGTATTATAAGCGTGTTTTCTGATTGAAATCAGAAAAC
1 ACAGGCTTGTATTATAAGCGTGTTTTCTGATTGAAATCAGAAAAC
*
1622267 ACATGCTT-TATT
1 ACAGGCTTGTATT
1622279 TACTTAAAAC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
44 4 0.07
45 52 0.93
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (45 bp):
ACAGGCTTGTATTATAAGCGTGTTTTCTGATTGAAATCAGAAAAC
Found at i:1622962 original size:29 final size:29
Alignment explanation
Indices: 1622894--1622996 Score: 133
Period size: 28 Copynumber: 3.7 Consensus size: 29
1622884 ACCCGACCCA
*
1622894 GTGACATTCTGGGAA-TTTTGTGAAAAAT
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
*
1622922 GTGACATT-TGGGAATTTTTGTGGAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
*
1622950 GTGATATTCTGGGAATTTTTGTGAAAAA-
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
*
1622978 ATGACAATT-TGGGAATTTT
1 GTGAC-ATTCTGGGAATTTT
1622997 CGAATGTGGA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
27 6 0.09
28 39 0.59
29 21 0.32
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (29 bp):
GTGACATTCTGGGAATTTTTGTGAAAAAG
Found at i:1627865 original size:33 final size:34
Alignment explanation
Indices: 1627820--1627886 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
1627810 TTTCACTGAT
1627820 CATAAGAGCTTAAAGTATCTTCTGACTCAGAAGG
1 CATAAGAGCTTAAAGTATCTTCTGACTCAGAAGG
1627854 CATAAG-GCTTAAAGTATCTTCTGACTCAGAAGG
1 CATAAGAGCTTAAAGTATCTTCTGACTCAGAAGG
1627887 AGCTTAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (34 bp):
CATAAGAGCTTAAAGTATCTTCTGACTCAGAAGG
Found at i:1629774 original size:19 final size:19
Alignment explanation
Indices: 1629750--1629797 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1629740 ACCGGTCCAA
*
1629750 ACCGGTCCGAACCGGTTTG
1 ACCGGTCCGAACCGGGTTG
1629769 ACCGGTCCGAACCGGGTTG
1 ACCGGTCCGAACCGGGTTG
1629788 ACCGGTCCGA
1 ACCGGTCCGA
1629798 CCCGACCCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (19 bp):
ACCGGTCCGAACCGGGTTG
Found at i:1629782 original size:10 final size:10
Alignment explanation
Indices: 1629740--1629783 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
1629730 TGGTGTTATG
*
1629740 ACCGGTCCAA
1 ACCGGTCCGA
1629750 ACCGGTCCGA
1 ACCGGTCCGA
**
1629760 ACCGGTTTG-
1 ACCGGTCCGA
1629769 ACCGGTCCGA
1 ACCGGTCCGA
1629779 ACCGG
1 ACCGG
1629784 GTTGACCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.20, C:0.36, G:0.30, T:0.14
Consensus pattern (10 bp):
ACCGGTCCGA
Found at i:1629863 original size:29 final size:29
Alignment explanation
Indices: 1629807--1629863 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1629797 ACCCGACCCA
* *
1629807 GTGACATTCTGGGAATTTTTGTGGAAAAT
1 GTGACATTCTGGGAATTTTTATGAAAAAT
1629836 GTGACATTCTGGGAATTTTTATGAAAAA
1 GTGACATTCTGGGAATTTTTATGAAAAA
1629864 AATGACAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.37
Consensus pattern (29 bp):
GTGACATTCTGGGAATTTTTATGAAAAAT
Found at i:1629869 original size:29 final size:29
Alignment explanation
Indices: 1629808--1629884 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
1629798 CCCGACCCAG
* * **
1629808 TGACATTCTGGGAATTTTTGTGGAAAATG
1 TGACATTCTGGGAATTTTTATGAAAAAAA
1629837 TGACATTCTGGGAATTTTTATGAAAAAAA
1 TGACATTCTGGGAATTTTTATGAAAAAAA
*
1629866 TGACAATT-TGGGAAGTTTT
1 TGAC-ATTCTGGGAATTTTT
1629885 GAATGTGGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 39 0.93
30 3 0.07
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (29 bp):
TGACATTCTGGGAATTTTTATGAAAAAAA
Found at i:1632069 original size:13 final size:13
Alignment explanation
Indices: 1632051--1632075 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1632041 TTTTTATACA
1632051 TTTTAATTTTGTC
1 TTTTAATTTTGTC
1632064 TTTTAATTTTGT
1 TTTTAATTTTGT
1632076 TTATTTTTTA
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:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTAATTTTGTC
Found at i:1639622 original size:24 final size:22
Alignment explanation
Indices: 1639584--1639630 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
1639574 AAATATGATG
*
1639584 TTAAAAATGACATCAATTAAATAT
1 TTAAAAATGAAATCAA--AAATAT
*
1639608 TTAAAAATTAAATCAAAAATAT
1 TTAAAAATGAAATCAAAAATAT
1639630 T
1 T
1639631 GAGGCTCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34
Consensus pattern (22 bp):
TTAAAAATGAAATCAAAAATAT
Found at i:1643783 original size:23 final size:22
Alignment explanation
Indices: 1643753--1643827 Score: 89
Period size: 23 Copynumber: 3.4 Consensus size: 22
1643743 GCATGGCCTT
1643753 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1643775 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1643797 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
1643819 ATGCATCGA
1 GTGCATCGA
1643828 GTATTGTTAG
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
21 15 0.36
22 11 0.26
23 16 0.38
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1643809 original size:21 final size:22
Alignment explanation
Indices: 1643753--1643815 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
1643743 GCATGGCCTT
1643753 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTC-AGGC
* * *
1643776 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGC
*
1643797 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
1643816 AGGATGCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGC
Found at i:1643967 original size:23 final size:22
Alignment explanation
Indices: 1643937--1644013 Score: 93
Period size: 23 Copynumber: 3.5 Consensus size: 22
1643927 GCATGGCCTT
1643937 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1643959 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1643981 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
1644003 ATGCATCGATG
1 GTGCATCGATG
1644014 TATTGTTAGG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.34
22 13 0.30
23 16 0.36
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1643987 original size:184 final size:185
Alignment explanation
Indices: 1643678--1644048 Score: 735
Period size: 184 Copynumber: 2.0 Consensus size: 185
1643668 AGAGAGTTTT
1643678 AAGAGAATTTTAAGAAAATGAGGAAGAAATAGGGTTTTATCCAAAAACTCGATGGATGCATCGAT
1 AAGAGAATTTTAAGAAAATGAGGAAGAAATAGGGTTTTATCCAAAAACTCGATGGATGCATCGAT
1643743 GCATGGCCTTGTGCATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATCGATG
66 GCATGGCCTTGTGCATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATCGATG
1643808 CACATTCAAGGATGCATCGA-GTATTGTTAGGTGTATCGATGCATTAAGCACAAA
131 CACATTCAAGGATGCATCGATGTATTGTTAGGTGTATCGATGCATTAAGCACAAA
1643862 AAGAGAATTTTAAGAAAATGAGGAAGAAATAGGGTTTTATCCAAAAACTCGATGGATGCATCGAT
1 AAGAGAATTTTAAGAAAATGAGGAAGAAATAGGGTTTTATCCAAAAACTCGATGGATGCATCGAT
1643927 GCATGGCCTTGTGCATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATCGATG
66 GCATGGCCTTGTGCATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATCGATG
1643992 CACATTCAAGGATGCATCGATGTATTGTTAGGTGTATCGATGCATTAAGCACAAA
131 CACATTCAAGGATGCATCGATGTATTGTTAGGTGTATCGATGCATTAAGCACAAA
1644047 AA
1 AA
1644049 TGTCAAAAAT
Statistics
Matches: 186, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
184 150 0.81
185 36 0.19
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (185 bp):
AAGAGAATTTTAAGAAAATGAGGAAGAAATAGGGTTTTATCCAAAAACTCGATGGATGCATCGAT
GCATGGCCTTGTGCATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATCGATG
CACATTCAAGGATGCATCGATGTATTGTTAGGTGTATCGATGCATTAAGCACAAA
Found at i:1643993 original size:21 final size:21
Alignment explanation
Indices: 1643937--1644013 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 21
1643927 GCATGGCCTT
1643937 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAA-G
* * *
1643959 CGTGCATCGGTGCACCTTCATG
1 -GTGCATCGATGCACATTCAAG
*
1643981 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
1644002 GATGCATCGATG
1 G-TGCATCGATG
1644014 TATTGTTAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
21 18 0.40
22 10 0.22
23 17 0.38
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (21 bp):
GTGCATCGATGCACATTCAAG
Found at i:1645029 original size:23 final size:23
Alignment explanation
Indices: 1645003--1645058 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1644993 CATCTCATAT
* *
1645003 AATTACACCTAAGTACCACGTAG
1 AATTGCACCGAAGTACCACGTAG
* * *
1645026 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTACCACGTAG
1645049 AATTGCACCG
1 AATTGCACCG
1645059 TAGTGCCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTACCACGTAG
Found at i:1645063 original size:23 final size:23
Alignment explanation
Indices: 1645021--1645065 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1645011 CTAAGTACCA
1645021 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
*
1645044 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGGAGTGCC
1645066 ATATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCG
Found at i:1645293 original size:103 final size:103
Alignment explanation
Indices: 1645082--1645400 Score: 581
Period size: 103 Copynumber: 3.1 Consensus size: 103
1645072 TAATGTCCAT
1645082 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTA--TGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1645145 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1645183 AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1645248 GAAC-TCACACATGTTCCAAAGAATACATATATGTCCCG
66 G-ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1645286 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1645351 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1645389 AAGGACCACATA
1 AAGGACCACATA
1645401 GACCCTCTAC
Statistics
Matches: 209, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
101 51 0.24
102 2 0.01
103 154 0.74
104 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1645965 original size:21 final size:21
Alignment explanation
Indices: 1645941--1645983 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1645931 TCATATTCGT
* *
1645941 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATAGATTCCCC
*
1645962 TTGAATGGGTATAGATTCCCC
1 TTGAAGGGGTATAGATTCCCC
1645983 T
1 T
1645984 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATAGATTCCCC
Found at i:1647241 original size:16 final size:16
Alignment explanation
Indices: 1647220--1647252 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1647210 TCATTTACCT
1647220 ATATAATTTAACATCC
1 ATATAATTTAACATCC
1647236 ATATAATTTAACATCC
1 ATATAATTTAACATCC
1647252 A
1 A
1647253 CACATTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAATTTAACATCC
Found at i:1652153 original size:56 final size:57
Alignment explanation
Indices: 1652081--1652192 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
1652071 AAGAGTGCAT
*
1652081 TGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAAAGTGCATCGATGCATGGC
1 TGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCAAAGTGCATCGATGCATGGC
* **
1652137 TGATGCATCAAATGCATTCGATGTTTTCATAAAATCCCTAGTGCATCGATGCATGG
1 TGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAAAGTGCATCGATGCATGG
1652193 TGTGTGCATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 22 0.44
57 25 0.50
58 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (57 bp):
TGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAAAGTGCATCGATGCATGGC
Found at i:1652208 original size:56 final size:55
Alignment explanation
Indices: 1652081--1652209 Score: 154
Period size: 57 Copynumber: 2.3 Consensus size: 55
1652071 AAGAGTGCAT
1652081 TGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAAAGTGCATCGATGCATGGC
1 TGATGCATCAA-TGCATTCGATGTTTCAAAATAGCCAAAGTGCATCGATGCATGGC
* **
1652137 TGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCCTAGTGCATCGATGCATGG-
1 TGATGCATC-AATGCATTCGATG-TTTCA-AAATAGCCAAAGTGCATCGATGCATGGC
* *
1652193 TGTGTGCATCGATGCAT
1 TG-ATGCATCAATGCAT
1652210 GAAATGCATT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
56 28 0.44
57 33 0.52
58 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (55 bp):
TGATGCATCAATGCATTCGATGTTTCAAAATAGCCAAAGTGCATCGATGCATGGC
Found at i:1652846 original size:20 final size:18
Alignment explanation
Indices: 1652799--1652871 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
1652789 ATTGAATATT
* *
1652799 TGTCCCGAATGACCACTA
1 TGTCTCGAAGGACCACTA
1652817 TGTCTCGAAGGACCACTGA
1 TGTCTCGAAGGACCACT-A
* *
1652836 TTGTTTCGAAGAACCACTA
1 -TGTCTCGAAGGACCACTA
*
1652855 TGTCCCGAAGGACCACT
1 TGTCTCGAAGGACCACT
1652872 GATTATCCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 2 0.04
20 15 0.33
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (18 bp):
TGTCTCGAAGGACCACTA
Found at i:1653515 original size:19 final size:19
Alignment explanation
Indices: 1653491--1653542 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1653481 TTTAAGCAGG
*
1653491 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCGTA
1653510 TGCATCGATGCACTCCGTA
1 TGCATCGATGCACTCCGTA
1653529 TGCATCGATGCACT
1 TGCATCGATGCACT
1653543 AATTGCATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTCCGTA
Found at i:1661897 original size:21 final size:22
Alignment explanation
Indices: 1661862--1661904 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1661852 TTCAAAAATT
1661862 AAATATAAATTTTTTTAAAAAA
1 AAATATAAATTTTTTTAAAAAA
*
1661884 AAAT-TAATTTTTTTTAAAAAA
1 AAATATAAATTTTTTTAAAAAA
1661905 TATACATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATATAAATTTTTTTAAAAAA
Found at i:1662457 original size:38 final size:36
Alignment explanation
Indices: 1662415--1662491 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 36
1662405 TATTATCTAT
**
1662415 TATATACATTTGATTTTTTATATTTTCAA-TATTTTTAA
1 TATATACATTCAATTTTTTA-ATTTT-AATTA-TTTTAA
*
1662453 TATATATATTCAATTTTTTAATTTTAATTATTTTAA
1 TATATACATTCAATTTTTTAATTTTAATTATTTTAA
1662489 TAT
1 TAT
1662492 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 11 0.31
37 7 0.20
38 17 0.49
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (36 bp):
TATATACATTCAATTTTTTAATTTTAATTATTTTAA
Found at i:1662464 original size:22 final size:21
Alignment explanation
Indices: 1662433--1662474 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1662423 TTTGATTTTT
*
1662433 TATATTTTCAATATTTTTAATA
1 TATATATTCAAT-TTTTTAATA
1662455 TATATATTCAATTTTTTAAT
1 TATATATTCAATTTTTTAAT
1662475 TTTAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATATTCAATTTTTTAATA
Found at i:1662484 original size:22 final size:23
Alignment explanation
Indices: 1662430--1662493 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 23
1662420 ACATTTGATT
1662430 TTTTATATT-TTCAATATTTTTAA
1 TTTTA-ATTATTCAATATTTTTAA
*
1662453 -TAT-ATATATTCAAT-TTTTTAA
1 TTTTAAT-TATTCAATATTTTTAA
*
1662474 TTTTAATTATTTTAATATTT
1 TTTTAATTA-TTCAATATTT
1662494 AATTTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
20 2 0.06
21 8 0.25
22 12 0.38
23 7 0.22
24 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTAATTATTCAATATTTTTAA
Found at i:1662494 original size:16 final size:15
Alignment explanation
Indices: 1662458--1662527 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 15
1662448 TTTAATATAT
*
1662458 ATATTCAATTTTTTA
1 ATATTTAATTTTTTA
1662473 AT-TTTAATTATTTTA
1 ATATTTAATT-TTTTA
1662488 ATATTTAATTTTTTAA
1 ATATTTAATTTTTT-A
*
1662504 ATATTTGAATAATTTT-
1 ATATTT-AAT-TTTTTA
1662520 ATATTTAA
1 ATATTTAA
1662528 AATTGAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.12
15 15 0.31
16 20 0.42
17 3 0.06
18 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (15 bp):
ATATTTAATTTTTTA
Found at i:1662552 original size:33 final size:32
Alignment explanation
Indices: 1662475--1662552 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 32
1662465 ATTTTTTAAT
** **
1662475 TTTAATTATTTTAATATTTAATTTTTTAAATA
1 TTTAATTATTTTAATATTTAAAATTGAAAATA
*
1662507 TTTGAATAATTTT-ATATTTAAAATTGAAAATAA
1 TTT-AATTATTTTAATATTTAAAATTGAAAAT-A
1662540 CTTTAATTATTTT
1 -TTTAATTATTTT
1662553 TAAAAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
32 17 0.46
33 17 0.46
34 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (32 bp):
TTTAATTATTTTAATATTTAAAATTGAAAATA
Found at i:1667431 original size:29 final size:29
Alignment explanation
Indices: 1667389--1667457 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
1667379 CCATTTCATC
1667389 ATCATCATCATCATAAACAATATATCCAA
1 ATCATCATCATCATAAACAATATATCCAA
1667418 ATCATCATCATCATAAACAATATATCCAA
1 ATCATCATCATCATAAACAATATATCCAA
1667447 ATCATCATCAT
1 ATCATCATCAT
1667458 TCTTCTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (29 bp):
ATCATCATCATCATAAACAATATATCCAA
Found at i:1668048 original size:16 final size:17
Alignment explanation
Indices: 1668027--1668058 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1668017 AAATCAATAT
1668027 TATT-AATTATTTAAAA
1 TATTAAATTATTTAAAA
1668043 TATTAAATTATTTAAA
1 TATTAAATTATTTAAA
1668059 CTTTATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAATTATTTAAAA
Found at i:1668352 original size:20 final size:20
Alignment explanation
Indices: 1668327--1668379 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1668317 TTTTCCAAAT
1668327 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1668347 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1668367 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1668380 CTGACTATCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1668389 original size:20 final size:20
Alignment explanation
Indices: 1668366--1668452 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
1668356 GAATACGTAA
* *
1668366 ATCGCAATGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
1668386 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
1668406 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1668426 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1668446 ATCGCAA
1 ATCGCAA
1668453 TACTGAATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1668390 original size:40 final size:39
Alignment explanation
Indices: 1668286--1668439 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 39
1668276 GTTTCCAGAT
* ** * *
1668286 TCGCAATGCGATTCTGACTATCGCATTGCGATTTTCCAAA
1 TCGCAATGCGAATCTGACTATCGCAACGCGA-TTACGAAA
* * *
1668326 TTCGCAATGCGAATAC-GTA-AATCGCAATGCGAATACGTAAA
1 -TCGCAATGCGAAT-CTG-ACTATCGCAACGCGATTACG-AAA
* *
1668367 TCGCAATGCGAATCTGACTATCGCAACGCGATTATGACTA
1 TCGCAATGCGAATCTGACTATCGCAACGCGATTACGA-AA
* * *
1668407 TCGCAACGAGATTCTGACTATCGCAACGCGATT
1 TCGCAATGCGAATCTGACTATCGCAACGCGATT
1668440 CTGACTATCG
Statistics
Matches: 93, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
39 3 0.03
40 61 0.66
41 27 0.29
42 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (39 bp):
TCGCAATGCGAATCTGACTATCGCAACGCGATTACGAAA
Found at i:1669321 original size:24 final size:24
Alignment explanation
Indices: 1669294--1669347 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1669284 GTATTTGAAA
1669294 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1669318 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1669342 TTTGAT
1 TTTGAT
1669348 GATTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1671773 original size:20 final size:18
Alignment explanation
Indices: 1671748--1671841 Score: 82
Period size: 20 Copynumber: 4.8 Consensus size: 18
1671738 GACATTCATT
1671748 TGACTATCGCAACGTCAATA
1 TGACTATCGCAACG-CAA-A
*
1671768 TGACTATCGCAATACGGAAA
1 TGACTATCGC-A-ACGCAAA
1671788 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGC--AAA
*
1671808 TAACTATCGCAACGCGGAAA
1 TGACTATCGCAACGC--AAA
1671828 T-ATCTATCGCAACG
1 TGA-CTATCGCAACG
1671842 AGAGAATCGC
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
18 3 0.05
19 2 0.03
20 55 0.83
21 3 0.05
22 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (18 bp):
TGACTATCGCAACGCAAA
Found at i:1671814 original size:40 final size:40
Alignment explanation
Indices: 1671748--1671841 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
1671738 GACATTCATT
* *
1671748 TGACTATCGCAACGTCAATATGACTATCGCAATACGGAAA
1 TGACTATCGCAACGTCAATATAACTATCGCAACACGGAAA
*
1671788 TGACTATCGCAACG-CGGAA-ATAACTATCGCAACGCGGAAA
1 TGACTATCGCAACGTC--AATATAACTATCGCAACACGGAAA
1671828 T-ATCTATCGCAACG
1 TGA-CTATCGCAACG
1671842 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.04
40 44 0.92
41 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (40 bp):
TGACTATCGCAACGTCAATATAACTATCGCAACACGGAAA
Found at i:1671872 original size:33 final size:34
Alignment explanation
Indices: 1671833--1671908 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
1671823 GGAAATATCT
1671833 ATCGCAACGAGAGAATCGCAATG-CAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGACAAAATGAAA
*
1671866 ATCGCAACGAGAGAATCGCAATGAGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGACAAAATGAAA
*
1671900 ATCACAACG
1 ATCGCAACG
1671909 CGAATTTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 23 0.57
34 17 0.43
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGACAAAATGAAA
Found at i:1671980 original size:33 final size:34
Alignment explanation
Indices: 1671923--1671998 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 34
1671913 TTTAGTTTCG
1671923 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1671957 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1671990 CGTTGCGAT
1 CGTTGCGAT
1671999 AGACATTACC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 28 0.67
34 14 0.33
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:1671997 original size:14 final size:14
Alignment explanation
Indices: 1671945--1671998 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1671935 CATTTTCGCA
1671945 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1671959 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1671976 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1671992 TTGCGAT
1 TTGCGAT
1671999 AGACATTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1672143 original size:14 final size:14
Alignment explanation
Indices: 1672124--1672160 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1672114 TATCAATTAA
1672124 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1672138 ACAAATCATCTTTT
1 ACAAATCAACATTT
1672152 ACAAATCAA
1 ACAAATCAA
1672161 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1673597 original size:42 final size:42
Alignment explanation
Indices: 1673530--1673621 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1673520 GTGAATCGGG
* * *
1673530 CTCTAGAATGTTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* ** *
1673572 CTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
1673614 CTCTTGAA
1 CTCTTGAA
1673622 CGATAGGGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:1674155 original size:20 final size:20
Alignment explanation
Indices: 1674132--1674238 Score: 153
Period size: 20 Copynumber: 5.3 Consensus size: 20
1674122 GAAACTTAAA
1674132 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
1674152 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
1674172 ATCGTAATGCCAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
1674192 ATCGCAATGC-AAATTTGACT
1 ATCGCAATGCGAAA-ATGACT
**
1674212 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
1674232 ATCGCAA
1 ATCGCAA
1674239 CGAGAGAATC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 3 0.04
20 75 0.94
21 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1674304 original size:34 final size:34
Alignment explanation
Indices: 1674263--1674418 Score: 154
Period size: 34 Copynumber: 4.4 Consensus size: 34
1674253 TGCGATTTTT
1674263 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
1674297 AATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCA
1 ATTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCA
* * * **
1674337 TTTTCGCGTTGCGATT-TTGTTGTTGCGATTTTC-
1 ATTTCGCATTGCGATTCTT-TCGTTGCGATAGTCA
* *
1674370 ATTTCGCATTGCAATTCTCTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
1674404 TTTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
1674419 AGTCATTTTC
Statistics
Matches: 97, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
33 24 0.25
34 37 0.38
35 2 0.02
36 4 0.04
38 6 0.06
40 24 0.25
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
Found at i:1674310 original size:20 final size:20
Alignment explanation
Indices: 1674285--1674441 Score: 144
Period size: 20 Copynumber: 8.5 Consensus size: 20
1674275 GATTCTTTCG
**
1674285 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1674305 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1674325 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1674345 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
1674359 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1674378 TTGC-A-ATTC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
1674392 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1674412 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1674432 TTGCGATAGT
1 TTGCGATAGT
1674442 AAACTATTCT
Statistics
Matches: 116, Mismatches: 7, Indels: 28
0.77 0.05 0.19
Matches are distributed among these distances:
14 11 0.09
15 1 0.01
16 13 0.11
17 7 0.06
18 6 0.05
19 4 0.03
20 74 0.64
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1676393 original size:39 final size:39
Alignment explanation
Indices: 1676333--1676472 Score: 157
Period size: 39 Copynumber: 3.7 Consensus size: 39
1676323 GAAACTTAAA
*
1676333 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACT
*
1676373 ATCGCAACGCGACATGAAAATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACT
* ** *
1676412 ATCGCAACGCGAATTTGACTATCGC-A-ACG-CAA-GA--
1 ATCGCAACGCGAA-ATGAAAATCGCAACACGAAAATGACT
*
1676446 ATCGTAACGCGAAATGAAAATCGCAAC
1 ATCGCAACGCGAAATGAAAATCGCAAC
1676473 GACAGAATCG
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
33 8 0.09
34 13 0.15
36 2 0.02
37 2 0.02
38 3 0.03
39 40 0.47
40 18 0.21
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (39 bp):
ATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACT
Found at i:1676430 original size:20 final size:20
Alignment explanation
Indices: 1676333--1676441 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
1676323 GAAACTTAAA
* **
1676333 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
1676353 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1676373 ATCGCAACGCG-ACATGAAA
1 ATCGCAACGCGAAAATGACT
*
1676392 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1676412 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1676432 ATCGCAACGC
1 ATCGCAACGC
1676442 AAGAATCGTA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
19 15 0.20
20 60 0.80
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1676431 original size:59 final size:59
Alignment explanation
Indices: 1676330--1676472 Score: 181
Period size: 59 Copynumber: 2.5 Consensus size: 59
1676320 TCTGAAACTT
1676330 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGACATG
1 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGACATG
** * **
1676389 AAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGC-A-A-G
1 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGACATG
* *
1676445 --AATCGTAACGCG-AAATGAAAATCGCAAC
1 AAAATCGCAACACGAAAATGAAAATCGCAAC
1676473 GACAGAATCG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
53 14 0.19
54 10 0.13
56 1 0.01
57 1 0.01
58 1 0.01
59 48 0.64
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (59 bp):
AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGACATG
Found at i:1676871 original size:22 final size:22
Alignment explanation
Indices: 1676809--1676874 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
1676799 TGACAGTGAA
* * *
1676809 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCAGAGATGGGGAC
*
1676831 TGATATCGTCAGAGATGGGGAC
1 TGATTTCGTCAGAGATGGGGAC
*
1676853 TGATTTCGTCTGAGATGGGGAC
1 TGATTTCGTCAGAGATGGGGAC
1676875 AGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCAGAGATGGGGAC
Found at i:1677094 original size:20 final size:20
Alignment explanation
Indices: 1677071--1677139 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
1677061 CGATAGTCAG
*
1677071 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1677091 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1677111 ATTTGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
1677131 ATTCGCATT
1 ATTCGCATT
1677140 TCAAATTAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1677601 original size:19 final size:19
Alignment explanation
Indices: 1677577--1677632 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
1677567 TTATTCTTGT
1677577 ATTTATGTTTTGGTCACTC
1 ATTTATGTTTTGGTCACTC
*
1677596 ATTTA--TTCTGG-CA-TC
1 ATTTATGTTTTGGTCACTC
1677611 ---TATGTTTTGGTCACTC
1 ATTTATGTTTTGGTCACTC
1677627 ATTTAT
1 ATTTAT
1677633 TCTGGCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 2 0.07
14 5 0.18
15 4 0.14
16 4 0.14
17 5 0.18
19 8 0.29
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (19 bp):
ATTTATGTTTTGGTCACTC
Found at i:1677615 original size:31 final size:31
Alignment explanation
Indices: 1677523--1677656 Score: 169
Period size: 31 Copynumber: 4.3 Consensus size: 31
1677513 AAAATTCATA
* *** * *
1677523 TTTGGTCAATCATTTATTCTCATATTTATAT
1 TTTGGTCACTCATTTATTCTGGCATCTATGT
* * * * *
1677554 TATGATCACTCATTTATTCTTGTATTTATGT
1 TTTGGTCACTCATTTATTCTGGCATCTATGT
1677585 TTTGGTCACTCATTTATTCTGGCATCTATGT
1 TTTGGTCACTCATTTATTCTGGCATCTATGT
1677616 TTTGGTCACTCATTTATTCTGGCATCTATGT
1 TTTGGTCACTCATTTATTCTGGCATCTATGT
1677647 TTTGGTCACT
1 TTTGGTCACT
1677657 AAAATATTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 92 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.51
Consensus pattern (31 bp):
TTTGGTCACTCATTTATTCTGGCATCTATGT
Found at i:1677890 original size:11 final size:11
Alignment explanation
Indices: 1677866--1677904 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1677856 ATTCTTATTT
1677866 TAATTTAA-AA
1 TAATTTAATAA
*
1677876 TAATTTATTAA
1 TAATTTAATAA
1677887 TAATTTAATAA
1 TAATTTAATAA
*
1677898 TAGTTTA
1 TAATTTA
1677905 GTGGTCCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (11 bp):
TAATTTAATAA
Found at i:1678964 original size:17 final size:18
Alignment explanation
Indices: 1678937--1678975 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
1678927 ATTTTTTATT
1678937 ATTATTTAAAAATAAAAA
1 ATTATTTAAAAATAAAAA
1678955 ATTA-TTAAAAATAAAAA
1 ATTATTTAAAAATAAAAA
1678972 ATTA
1 ATTA
1678976 AATTCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTATTTAAAAATAAAAA
Found at i:1680866 original size:5 final size:5
Alignment explanation
Indices: 1680856--1680932 Score: 62
Period size: 4 Copynumber: 16.4 Consensus size: 5
1680846 TTTAGTATGC
1680856 TTTTA TTTTA TTTTA -TTTA -TTTA -TTTA -TTTA TTTTTA TTTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
*
1680902 -TTTA -TTTA CTTCTTA TTAT- TTTTA TTTTA TT
1 TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA TT
1680933 ACTCTATTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
4 31 0.48
5 23 0.36
6 7 0.11
7 3 0.05
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:1680876 original size:4 final size:4
Alignment explanation
Indices: 1680857--1680909 Score: 65
Period size: 4 Copynumber: 13.0 Consensus size: 4
1680847 TTAGTATGCT
1680857 TTTA TTTTA TTTTA TTTA TTTA TTTA TTTA -TT- TTTA TTTTA TTTA TTTA
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
1680906 TTTA
1 TTTA
1680910 CTTCTTATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.09
4 28 0.62
5 13 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1680899 original size:27 final size:27
Alignment explanation
Indices: 1680857--1680928 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
1680847 TTAGTATGCT
1680857 TTTA-TTTTATTTTATTTATTTATTTA
1 TTTATTTTTATTTTATTTATTTATTTA
1680883 TTTATTTTTATTTTATTTATTTATTTA
1 TTTATTTTTATTTTATTTATTTATTTA
* * *
1680910 CTTCTTATTATTTTTATTT
1 TTTATTTTTA-TTTTATTT
1680929 TATTACTCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.10
27 29 0.71
28 8 0.20
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTATTTTTATTTTATTTATTTATTTA
Found at i:1680901 original size:23 final size:23
Alignment explanation
Indices: 1680857--1680928 Score: 87
Period size: 23 Copynumber: 3.1 Consensus size: 23
1680847 TTAGTATGCT
1680857 TTTATTT-TATTTTA-TTTATTTA
1 TTTATTTAT-TTTTATTTTATTTA
1680879 TTTATTTATTTTTATTTTATTTA
1 TTTATTTATTTTTATTTTATTTA
*
1680902 TTTATTTACTTCTTATTATT-TTTA
1 TTTATTTA-TTTTTATT-TTATTTA
1680926 TTT
1 TTT
1680929 TATTACTCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
22 12 0.27
23 17 0.38
24 14 0.31
25 2 0.04
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTATTTATTTTTATTTTATTTA
Found at i:1680917 original size:19 final size:17
Alignment explanation
Indices: 1680857--1680932 Score: 83
Period size: 15 Copynumber: 4.6 Consensus size: 17
1680847 TTAGTATGCT
1680857 TTTATTTTATTTTATTTA
1 TTTATTTTA-TTTATTTA
1680875 TTTA-TTTATTTA-TT-
1 TTTATTTTATTTATTTA
1680889 TTTATTTTATTTATTTA
1 TTTATTTTATTTATTTA
1680906 TTTACTTCTTA-TTA-TT-
1 TTTA-TT-TTATTTATTTA
1680922 TTTATTTTATT
1 TTTATTTTATT
1680933 ACTCTATTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.13
15 13 0.25
16 10 0.19
17 10 0.19
18 9 0.17
19 3 0.06
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTATTTA
Found at i:1681006 original size:16 final size:16
Alignment explanation
Indices: 1680987--1681017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1680977 TATTTTTCCT
1680987 TTTTTCATTTGATTTA
1 TTTTTCATTTGATTTA
*
1681003 TTTTTCCTTTGATTT
1 TTTTTCATTTGATTT
1681018 TTTCCTTTGA
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:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTTCATTTGATTTA
Found at i:1681007 original size:83 final size:81
Alignment explanation
Indices: 1680878--1681133 Score: 211
Period size: 83 Copynumber: 3.1 Consensus size: 81
1680868 TTATTTATTT
* * * * *
1680878 ATTTATTT-ATTTTTATTTTATTTATTTATTTAC-TTCTTA-TTATTTTTATTTTATTACTCTAT
1 ATTTATTTAATATTTA-TTTATTTATTTATTTTCATT-TGAGTTATTTTTATTTTATTATTTTAT
1680940 TTAACTTTTTTCCCTTTG
64 TTAACTTTTTTCCCTTTG
* * * * *
1680958 ATTTATTTAATATTTTTTTTATTT-TTCCTTTTTTCATTTGATTTATTTTTCCTTTGATT-TTTT
1 ATTTATTTAATA-TTTATTTATTTATT--TATTTTCATTTGAGTTATTTTT-ATTTTATTATTTT
* * *
1681021 CCTTTGA-TTTTTTCCTTTTG
62 -ATTTAACTTTTTTCCCTTTG
* *
1681041 ATTTATTTAATATTTATTTATTTATTTATTTTCCTTTGAGTTATTTAATATTTT-TTATTTTTAT
1 ATTTATTTAATATTTATTTATTTATTTATTTTCATTTGAGTTATTT-TTATTTTATTA-TTTTA-
* *
1681105 TTGTATCTTTTTTTCCTTTG
63 TT-TAACTTTTTTCCCTTTG
1681125 ATTTATTTA
1 ATTTATTTA
1681134 TTTTTCTTTT
Statistics
Matches: 137, Mismatches: 24, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
80 12 0.09
81 29 0.21
82 27 0.20
83 39 0.28
84 30 0.22
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.70
Consensus pattern (81 bp):
ATTTATTTAATATTTATTTATTTATTTATTTTCATTTGAGTTATTTTTATTTTATTATTTTATTT
AACTTTTTTCCCTTTG
Found at i:1681021 original size:13 final size:13
Alignment explanation
Indices: 1681003--1681044 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1680993 ATTTGATTTA
1681003 TTTTTCCTTTGAT
1 TTTTTCCTTTGAT
1681016 TTTTTCCTTTGAT
1 TTTTTCCTTTGAT
1681029 TTTTTCCTTTTGAT
1 TTTTTCC-TTTGAT
1681043 TT
1 TT
1681045 ATTTAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 20 0.71
14 8 0.29
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.71
Consensus pattern (13 bp):
TTTTTCCTTTGAT
Done.