Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009584.1 Hibiscus syriacus cultivar Beakdansim tig00116961_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: 2003061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1347645 original size:32 final size:30
Alignment explanation
Indices: 1347597--1347664 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1347587 CTTTTGGTAT
*
1347597 TCGGATCGGATATTTTTTAAAAAAATTTCGGGA
1 TCGG-TCGGA-ATTTTTT-AAAAAATTTCAGGA
* *
1347630 TCGGTCGGATTTTTTTAAAAAATTTCAGGT
1 TCGGTCGGAATTTTTTAAAAAATTTCAGGA
1347660 TCGGT
1 TCGGT
1347665 TCGGGTTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.53
31 6 0.19
32 5 0.16
33 4 0.12
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (30 bp):
TCGGTCGGAATTTTTTAAAAAATTTCAGGA
Found at i:1347736 original size:44 final size:39
Alignment explanation
Indices: 1347698--1347781 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
1347688 GATATTCGGG
* * *
1347698 TCGGGTCGGGGTCTGGTCGGGTTTTTTTAAGCGTGATAT
1 TCGGGTCTGGGTCGGGTCGGGTTTTTTTAAGTGTGATAT
* *
1347737 TCAGGTCTGGTTCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCTGGGTCGGGTCGGGTTTTTTTAAGTGTGATAT
1347776 TCGGGT
1 TCGGGT
1347782 AGGATTCGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.11, C:0.12, G:0.37, T:0.40
Consensus pattern (39 bp):
TCGGGTCTGGGTCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:1347790 original size:39 final size:39
Alignment explanation
Indices: 1347712--1347792 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
1347702 GTCGGGGTCT
*
1347712 GGTCGGGTTTTTTTAAGCGTGATATTCAGGTCTGGTTCG
1 GGTCGGGTTTTTTTAAGCGTGATATTCAGGTCAGGTTCG
* *
1347751 GGTCGGGTTTTTTTAAGTGTGATATTCGGGT-AGGATTCG
1 GGTCGGGTTTTTTTAAGCGTGATATTCAGGTCAGG-TTCG
1347790 GGT
1 GGT
1347793 TTAGGGTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.05
39 36 0.95
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.41
Consensus pattern (39 bp):
GGTCGGGTTTTTTTAAGCGTGATATTCAGGTCAGGTTCG
Found at i:1347975 original size:26 final size:26
Alignment explanation
Indices: 1347946--1348002 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
1347936 TATTTCGGGT
1347946 CGGGTTTCTAATTCATATATTCAGGC
1 CGGGTTTCTAATTCATATATTCAGGC
* *
1347972 CGGGTTTCTAATTCATATATTCGGGT
1 CGGGTTTCTAATTCATATATTCAGGC
1347998 CGGGT
1 CGGGT
1348003 CGGGTCGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (26 bp):
CGGGTTTCTAATTCATATATTCAGGC
Found at i:1348748 original size:2 final size:2
Alignment explanation
Indices: 1348741--1348769 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1348731 TATTGCTTAC
1348741 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 T
1348770 TGAATTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1350535 original size:13 final size:13
Alignment explanation
Indices: 1350517--1350542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1350507 CCTGGGGTAA
1350517 CTCCTCACATCTC
1 CTCCTCACATCTC
1350530 CTCCTCACATCTC
1 CTCCTCACATCTC
1350543 ATCTCGATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (13 bp):
CTCCTCACATCTC
Found at i:1355412 original size:10 final size:10
Alignment explanation
Indices: 1355406--1355434 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1355396 ATAAGAGTAT
1355406 TTGAGAGAAG
1 TTGAGAGAAG
1355416 TTGAGAGAAG
1 TTGAGAGAAG
1355426 TTGAGAGAA
1 TTGAGAGAA
1355435 TTTGGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:1356484 original size:16 final size:16
Alignment explanation
Indices: 1356465--1356510 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1356455 CACATATTGA
1356465 TATATTTTCAAAAAAT
1 TATATTTTCAAAAAAT
*
1356481 TATATTTTAAAAAAAT
1 TATATTTTCAAAAAAT
*
1356497 TACA-TTTCAAAAAA
1 TATATTTTCAAAAAA
1356511 GAACAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (16 bp):
TATATTTTCAAAAAAT
Found at i:1358749 original size:14 final size:15
Alignment explanation
Indices: 1358722--1358763 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 15
1358712 AAAAATAGTG
1358722 AATAAATCAATAAAGA
1 AATAAAT-AATAAAGA
1358738 AA-AAATAATAAAGA
1 AATAAATAATAAAGA
1358752 AATAAGATAATA
1 AATAA-ATAATA
1358764 CTGCAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.42
15 6 0.25
16 8 0.33
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (15 bp):
AATAAATAATAAAGA
Found at i:1362925 original size:19 final size:22
Alignment explanation
Indices: 1362877--1362930 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1362867 TACTACCATT
*
1362877 AGGGTACCGATACCTCTATACT
1 AGGGTACCGATACCTCTATACC
1362899 AGGGTACCGATACC-CTAT-CC
1 AGGGTACCGATACCTCTATACC
1362919 A-GGTACCGATAC
1 AGGGTACCGATAC
1362931 AAAAATTAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 11 0.35
20 2 0.06
21 4 0.13
22 14 0.45
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (22 bp):
AGGGTACCGATACCTCTATACC
Found at i:1362981 original size:21 final size:22
Alignment explanation
Indices: 1362955--1363008 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
1362945 AAGTTCCCTG
1362955 GGTATCGATACCC-TCCACATA-
1 GGTATCGATACCCATCC-CATAT
*
1362976 GGTATCGATACCCATTCCATAT
1 GGTATCGATACCCATCCCATAT
1362998 GGTATCGATAC
1 GGTATCGATAC
1363009 TGTTCATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (22 bp):
GGTATCGATACCCATCCCATAT
Found at i:1366119 original size:3 final size:3
Alignment explanation
Indices: 1366113--1366147 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1366103 TTATTTTAAT
*
1366113 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1366148 TTAATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1367922 original size:21 final size:22
Alignment explanation
Indices: 1367875--1367915 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1367865 TTTATGCATG
1367875 TATTGTAAATATTCTTATTTAA
1 TATTGTAAATATTCTTATTTAA
1367897 TATTGTAAATATT-TTATTT
1 TATTGTAAATATTCTTATTT
1367916 GTCATTGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (22 bp):
TATTGTAAATATTCTTATTTAA
Found at i:1371678 original size:20 final size:20
Alignment explanation
Indices: 1371648--1371715 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 20
1371638 AATAAAGAGA
1371648 AAAGAAGCAAAGAAAAAAAAC
1 AAAG-AGCAAAGAAAAAAAAC
1371669 AAAGAGCAAAGAAAAGAAAA-
1 AAAGAGCAAAGAAAA-AAAAC
**
1371689 AAAGAAAAAAGAAAGCAAAAAC
1 AAAGAGCAAAGAAA--AAAAAC
1371711 AAAGA
1 AAAGA
1371716 AAATAGCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 23 0.56
21 12 0.29
22 6 0.15
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAGAGCAAAGAAAAAAAAC
Found at i:1371708 original size:25 final size:25
Alignment explanation
Indices: 1371636--1371708 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
1371626 AGAAAACACA
*
1371636 AAAATAAAGAGAAAAG-AAGC-AAAG
1 AAAA-AAAGAAAAAAGAAAGCAAAAG
*
1371660 AAAAAAA-ACAAAGAGCAAAG-AAAAG
1 AAAAAAAGA-AAAAAG-AAAGCAAAAG
1371685 AAAAAAAGAAAAAAGAAAGCAAAA
1 AAAAAAAGAAAAAAGAAAGCAAAA
1371709 ACAAAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
22 1 0.03
23 7 0.17
24 8 0.20
25 23 0.57
26 1 0.03
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.01
Consensus pattern (25 bp):
AAAAAAAGAAAAAAGAAAGCAAAAG
Found at i:1371718 original size:20 final size:20
Alignment explanation
Indices: 1371663--1371718 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 20
1371653 AGCAAAGAAA
1371663 AAAAACAAAGAGCAAAGAAAAG
1 AAAAACAAAGA--AAAGAAAAG
*
1371685 -AAAA-AAAGAAAAAAGAAAG
1 AAAAACAAAGAAAAGA-AAAG
1371704 CAAAAACAAAGAAAA
1 -AAAAACAAAGAAAA
1371719 TAGCAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 5 0.17
21 8 0.28
22 8 0.28
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAACAAAGAAAAGAAAAG
Found at i:1371728 original size:20 final size:18
Alignment explanation
Indices: 1371645--1371732 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 18
1371635 AAAAATAAAG
*
1371645 AGAAAAGAAGCAAAGAAAA
1 AGAAAA-AAACAAAGAAAA
1371664 A-AAACAAAGAGCAAAG-AAA
1 AGAAA-AAA-A-CAAAGAAAA
* *
1371683 AGAAAAAAAGAAAAAAGAA
1 AGAAAAAAACAAAGAA-AA
*
1371702 AG-CAAAAACAAAGAAAA
1 AGAAAAAAACAAAGAAAA
*
1371719 TAGCAAAAAACAAA
1 -AGAAAAAAACAAA
1371733 AAGATGACAA
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
17 5 0.09
18 19 0.35
19 22 0.41
20 8 0.15
ACGTcount: A:0.76, C:0.08, G:0.15, T:0.01
Consensus pattern (18 bp):
AGAAAAAAACAAAGAAAA
Found at i:1373473 original size:36 final size:34
Alignment explanation
Indices: 1373433--1373548 Score: 133
Period size: 36 Copynumber: 3.2 Consensus size: 34
1373423 GTTGATTTCA
* *
1373433 CTTGAGATCGCTTTCTTAAAAACAACCTTTGTCTCG
1 CTTGAGA-CGATTTCTTAAAAACAA-ATTTGTCTCG
* *
1373469 CTTGAGACAATTTTTCTAAAAACAAAATTTTGTCTCG
1 CTTGAGACGATTTCT-TAAAAAC-AAA-TTTGTCTCG
1373506 CTTGAGACGATTTCTTGAAAAACAAATTTCGTCTCG
1 CTTGAGACGATTTCTT-AAAAACAAATTT-GTCTCG
1373542 CTTGAGA
1 CTTGAGA
1373549 TATTTTTCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
35 8 0.12
36 31 0.45
37 30 0.43
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (34 bp):
CTTGAGACGATTTCTTAAAAACAAATTTGTCTCG
Found at i:1373501 original size:37 final size:36
Alignment explanation
Indices: 1373450--1373556 Score: 128
Period size: 37 Copynumber: 3.0 Consensus size: 36
1373440 TCGCTTTCTT
** *
1373450 AAAAACAACCTTTGTCTCGCTTGAGACAATTTTTCT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATTTTTCG
*
1373486 AAAAACAAAATTTTGTCTCGCTTGAGACGATTTCTT-G
1 AAAAAC-AAATTTTGTCTCGCTTGAGACAATTT-TTCG
* *
1373523 AAAAACAAATTTCGTCTCGCTTGAGA-TATTTTTC
1 AAAAACAAATTTTGTCTCGCTTGAGACAATTTTTC
1373557 CTTTGAGATA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
34 2 0.03
35 4 0.06
36 25 0.40
37 29 0.47
38 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCGCTTGAGACAATTTTTCG
Found at i:1373611 original size:175 final size:176
Alignment explanation
Indices: 1373312--1373708 Score: 559
Period size: 175 Copynumber: 2.2 Consensus size: 176
1373302 GTTTCCTTTG
* * * *
1373312 AAACAAAATTTTGTCTCATTTGAGACAGTTTACGTCG-AAAACAAATTGCTTCTTGCTTGAGATA
1 AAACAAAATTTTGTCTCGTTTGAGACA-TTT-C-TTGAAAAACAAATTGCGTCTCGCTTGAGATA
* *
1373376 TTTTCCCTTTGAGATACAAATGTTAAATTTGCTTCACATTAAACAAAGTTGATTTCACTTGAGAT
63 TTTTCCCTTTGAGATACAAATGTTAAATTTGCTTCACACTAAACAAAGTTGATCTCACTTGAGAT
* *
1373441 CGCTTTCTT-AAAAA-CAACCTTTGTCTCGCTTGAGACAATTTTTCTAA
128 CGCTTTCTTAAAAAACCAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
* *
1373488 AAACAAAATTTTGTCTCGCTTGAGACGATTTCTTGAAAAACAAATTTCGTCTCGCTTGAGATATT
1 AAACAAAATTTTGTCTCGTTTGAGAC-ATTTCTTGAAAAACAAATTGCGTCTCGCTTGAGATATT
* * * *
1373553 TTTCCTTTGAGATACAAATTTTGAATTTGTTTCACACTAAACAAAGTTGATCTCACTTGAGATCG
65 TTCCCTTTGAGATACAAATGTTAAATTTGCTTCACACTAAACAAAGTTGATCTCACTTGAGATCG
*
1373618 TTTTCTTAAAAAACCAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
130 CTTTCTTAAAAAACCAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
* * *
1373665 AAA-TAATTTTTGTCTCGTTTGAGACAATTTCTTTAAAAACAAAT
1 AAACAAAATTTTGTCTCGTTTGAGAC-ATTTCTTGAAAAACAAAT
1373709 GTTGTTTCAC
Statistics
Matches: 197, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
174 2 0.01
175 92 0.47
176 68 0.35
177 35 0.18
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (176 bp):
AAACAAAATTTTGTCTCGTTTGAGACATTTCTTGAAAAACAAATTGCGTCTCGCTTGAGATATTT
TCCCTTTGAGATACAAATGTTAAATTTGCTTCACACTAAACAAAGTTGATCTCACTTGAGATCGC
TTTCTTAAAAAACCAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
Found at i:1373687 original size:36 final size:36
Alignment explanation
Indices: 1373626--1373730 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
1373616 CGTTTTCTTA
*
1373626 AAAAACCAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAA-CAAATTTTGTCTCGCTTGAGACAATTTCTCT
* * * *
1373663 AAAAATAATTTTTGTCTCGTTTGAGACAATTTCTTT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCT
* * *
1373699 AAAAACAAATGTTGTTTCACTTGAGACAATTT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATTT
1373731 TCCAAATTAT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
36 52 0.91
37 5 0.09
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.38
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCT
Found at i:1373804 original size:30 final size:31
Alignment explanation
Indices: 1373768--1373826 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1373758 AACAAACATC
*
1373768 ATCTTTGAGTC-ATTTCTTTTGAAACAAAGT
1 ATCTTTGAGTCTATCTCTTTTGAAACAAAGT
1373798 ATCTTTGAGTCTATCTCTTTTGAAACAAA
1 ATCTTTGAGTCTATCTCTTTTGAAACAAA
1373827 ACTTTGTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (31 bp):
ATCTTTGAGTCTATCTCTTTTGAAACAAAGT
Found at i:1374062 original size:66 final size:64
Alignment explanation
Indices: 1373893--1374110 Score: 233
Period size: 64 Copynumber: 3.3 Consensus size: 64
1373883 AAACAAAAAT
* * * *
1373893 AAAAAATCTTTCAGTTTGTTTATTTGATAACAAAATTCTGTCTCTTTTGAGAAAGTTTCTTTTG
1 AAAAAATCTTTGAGTTTGTTTATTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTG
* * * *
1373957 AAAGAATCTTTGAATTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAG-TTCATTTTG
1 AAAAAATCTTTGAGTTTGTTTATTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTTC-TTTTG
* * *
1374021 AAGAAAAATCTTTGAGTTTGTTT-TTATGAAAACAAAGTTTTGTATCTTTTGAGACAATTTCTCT
1 -A-AAAAATCTTTGAGTTTGTTTATT-TGAAAACAAAATTTTGTCTCTTTTGAGACAGTTTCT-T
**
1374085 TAA
62 TTG
*
1374088 AACAAACATCTTTGAGATTGTTT
1 AA-AAA-ATCTTTGAGTTTGTTT
1374111 CCCTTGAAAC
Statistics
Matches: 129, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
63 3 0.02
64 52 0.40
65 4 0.03
66 50 0.39
67 20 0.16
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (64 bp):
AAAAAATCTTTGAGTTTGTTTATTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTG
Found at i:1374121 original size:30 final size:31
Alignment explanation
Indices: 1374078--1374240 Score: 116
Period size: 29 Copynumber: 5.5 Consensus size: 31
1374068 TTTGAGACAA
*
1374078 TTTCTCTTAAAACAAAC-ATCTTTGAGAT-TG
1 TTTCTCTTGAAACAAACAATCTTTGAG-TCTG
*
1374108 TTTCCCTTGAAACAAAACATATCTTTGAGTCTG
1 TTTCTCTTGAAAC-AAACA-ATCTTTGAGTCTG
*
1374141 TTTCTCTTGAAACAAA-AGT-TTGTGAGT-TG
1 TTTCTCTTGAAACAAACAATCTT-TGAGTCTG
* * * *
1374170 TTTCTTTTAAAATAAA-AATATTTGAGT-TG
1 TTTCTCTTGAAACAAACAATCTTTGAGTCTG
*
1374199 TTT-TTTTG--A-AAAC-ATCTTTGAGTCTG
1 TTTCTCTTGAAACAAACAATCTTTGAGTCTG
* *
1374225 TTTATTTTGAAACAAA
1 TTTCTCTTGAAACAAA
1374241 GTTTTGTCTC
Statistics
Matches: 111, Mismatches: 10, Indels: 24
0.77 0.07 0.17
Matches are distributed among these distances:
25 12 0.11
26 6 0.05
27 5 0.05
28 4 0.04
29 30 0.27
30 22 0.20
31 5 0.05
32 4 0.04
33 23 0.21
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTCTCTTGAAACAAACAATCTTTGAGTCTG
Found at i:1374134 original size:33 final size:33
Alignment explanation
Indices: 1374095--1374157 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1374085 TAAAACAAAC
1374095 ATCTTTGAGAT-TGTTTCCCTTGAAACAAAACAT
1 ATCTTTGAG-TCTGTTTCCCTTGAAACAAAACAT
*
1374128 ATCTTTGAGTCTGTTTCTCTTGAAACAAAA
1 ATCTTTGAGTCTGTTTCCCTTGAAACAAAA
1374158 GTTTGTGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (33 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAT
Found at i:1374315 original size:29 final size:29
Alignment explanation
Indices: 1374283--1374363 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
1374273 AAAATCCTCA
*
1374283 AGTCGTTTCTTTTGGAACAAAAATCTTTG
1 AGTCGTTTCTTTTGAAACAAAAATCTTTG
* * ***
1374312 AGTCATTTCTTCTGAAACACCTATCTTTG
1 AGTCGTTTCTTTTGAAACAAAAATCTTTG
* *
1374341 AGTTTGTTTCCTTTGAAACAAAA
1 AG-TCGTTTCTTTTGAAACAAAA
1374364 TTTTGTCTCT
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (29 bp):
AGTCGTTTCTTTTGAAACAAAAATCTTTG
Found at i:1374424 original size:63 final size:64
Alignment explanation
Indices: 1374355--1374494 Score: 174
Period size: 65 Copynumber: 2.2 Consensus size: 64
1374345 TGTTTCCTTT
* * *
1374355 GAAACAAAATTTTGTCTCTCTCGAGGCAATTTCTTTT-GAAAAATCATTGAATATGTTTATTTG
1 GAAACAAAATTTTGTCCCTCTCAAGACAATTTCTTTTAGAAAAATCATTGAATATGTTTATTTG
* * * * * * *
1374418 GAAACAAAATTTTGTCCCTTTTAAGATAGTTTCTTTTAAGAAAAATCTTTGAGTATGTTTCTTTG
1 GAAACAAAATTTTGTCCCTCTCAAGACAATTTCTTTT-AGAAAAATCATTGAATATGTTTATTTG
1374483 GAAACAAAATTT
1 GAAACAAAATTT
1374495 ACCATCTTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 30 0.46
65 35 0.54
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (64 bp):
GAAACAAAATTTTGTCCCTCTCAAGACAATTTCTTTTAGAAAAATCATTGAATATGTTTATTTG
Found at i:1374487 original size:65 final size:63
Alignment explanation
Indices: 1374334--1374494 Score: 189
Period size: 63 Copynumber: 2.5 Consensus size: 63
1374324 TGAAACACCT
* * * *
1374334 ATCTTTGAGTTTGTTTCCTTT-GAAACAAAATTTTGTCTCTCTCGAGGCAATTTCTTTTGAAAA
1 ATCTTTGAGTATGTTT-CTTTGGAAACAAAATTTTGTCCCTCTCAAGACAATTTCTTTTGAAAA
* * * * * * *
1374397 ATCATTGAATATGTTTATTTGGAAACAAAATTTTGTCCCTTTTAAGATAGTTTCTTTTAAGAAAA
1 ATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCCCTCTCAAGACAATTTCTTTT--GAAAA
1374462 ATCTTTGAGTATGTTTCTTTGGAAACAAAATTT
1 ATCTTTGAGTATGTTTCTTTGGAAACAAAATTT
1374495 ACCATCTTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
62 3 0.04
63 43 0.53
65 35 0.43
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCCCTCTCAAGACAATTTCTTTTGAAAA
Found at i:1374593 original size:70 final size:72
Alignment explanation
Indices: 1374459--1374594 Score: 179
Period size: 74 Copynumber: 1.9 Consensus size: 72
1374449 TCTTTTAAGA
*
1374459 AAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTACCATCTTTGAGTTTGTTACCCTTGAAAC
1 AAAATCTTTGAGTATGTTTCTTTGGAAACAAAA--TACCATCTTTGAGTTTGTTACCCTCGAAAC
1374524 AAAGCAAAC
64 AAAGCAAAC
* * * *
1374533 AAAATCTTTGAGTATGTTT-TTCTTGAAATAAAA-A-CATCTTTGAGTTTGTTTCTCTCGAAACA
1 AAAATCTTTGAGTATGTTTCTT-TGGAAACAAAATACCATCTTTGAGTTTGTTACCCTCGAAACA
1374595 CCGATCTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
70 25 0.45
71 1 0.02
73 2 0.04
74 28 0.50
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (72 bp):
AAAATCTTTGAGTATGTTTCTTTGGAAACAAAATACCATCTTTGAGTTTGTTACCCTCGAAACAA
AGCAAAC
Found at i:1374763 original size:28 final size:26
Alignment explanation
Indices: 1374714--1374794 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 26
1374704 GAGACAATTG
*
1374714 CTTTTGAAACACATCACGTTTGAGTATGTT
1 CTTTTGAAACAAAT--C-TTTGAGTAT-TT
*
1374744 TTTCTTGAAACAAATCTTTGAGCCTATTT
1 CTT-TTGAAACAAATCTTTGAG--TATTT
1374773 CTTTTGAAACAAATCTTTGAGT
1 CTTTTGAAACAAATCTTTGAGT
1374795 CGGTTTCCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 1 0.02
28 24 0.53
29 5 0.11
30 5 0.11
31 10 0.22
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (26 bp):
CTTTTGAAACAAATCTTTGAGTATTT
Found at i:1374801 original size:28 final size:28
Alignment explanation
Indices: 1374747--1374810 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
1374737 GTATGTTTTT
* *
1374747 CTTGAAACAAATCTTTGAGCCTATTTCT
1 CTTGAAACAAATCTTTGAGCCGATTTCC
* * *
1374775 TTTGAAACAAATCTTTGAGTCGGTTTCC
1 CTTGAAACAAATCTTTGAGCCGATTTCC
1374803 CTTGAAAC
1 CTTGAAAC
1374811 CATAATCACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (28 bp):
CTTGAAACAAATCTTTGAGCCGATTTCC
Found at i:1375199 original size:135 final size:134
Alignment explanation
Indices: 1374878--1375171 Score: 367
Period size: 134 Copynumber: 2.2 Consensus size: 134
1374868 CCAGACCTTT
* * * * * * *
1374878 TCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTAGGAACCAAGTTG
1 TCATCACGTAGGAGCCGTGTCACCCATACACAACCAGACATCCTCATCGCGTAGGAACCAAGTTA
* * *
1374943 TCACCCTTCCTAAAGATGGCCAGACCTCTTCATCATGTATGAGTCGTGTCATCCACTGACCAGAT
66 TCACCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCACCGACCAGAT
* *
1375008 CTCT
131 ATCC
* * * **
1375012 TCATCACGTAGGAGCCGTGTTACCCATACATAACCAGCCATCCTCATCGCGTAGGAACTGAGTTA
1 TCATCACGTAGGAGCCGTGTCACCCATACACAACCAGACATCCTCATCGCGTAGGAACCAAGTTA
* * *
1375077 TTACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCCCCCGACTAG
66 TCACCCTTCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGTC-GTGTCATCCACCGACCAG
1375141 ATATCC
129 ATATCC
1375147 TCATCACGTAGGAGCAC-TGTCACCC
1 TCATCACGTAGGAGC-CGTGTCACCC
1375172 TTAGACGACC
Statistics
Matches: 139, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
134 77 0.55
135 61 0.44
136 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (134 bp):
TCATCACGTAGGAGCCGTGTCACCCATACACAACCAGACATCCTCATCGCGTAGGAACCAAGTTA
TCACCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCACCGACCAGAT
ATCC
Found at i:1375395 original size:18 final size:17
Alignment explanation
Indices: 1375364--1375405 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
1375354 CGGGTCTTTT
1375364 TTATT-TTAATTTATTA
1 TTATTATTAATTTATTA
1375380 TTATTATTATATTTATTA
1 TTATTATTA-ATTTATTA
1375398 TTATTATT
1 TTATTATT
1375406 GTTGTTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 5 0.21
17 3 0.12
18 16 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATTAATTTATTA
Found at i:1375410 original size:3 final size:3
Alignment explanation
Indices: 1375404--1375432 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1375394 ATTATTATTA
1375404 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1375433 ATTTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1379177 original size:18 final size:18
Alignment explanation
Indices: 1379154--1379188 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1379144 ATAACACATT
1379154 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
1379172 TGTCCCGAAAGACCACT
1 TGTCCCGAAAGACCACT
1379189 CCTTAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:1384929 original size:22 final size:21
Alignment explanation
Indices: 1384901--1384957 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
1384891 GTACTACCCT
*
1384901 TAGGGTACTGATACCTCTATAC
1 TAGGGTACCGATACC-CTATAC
1384923 TAGGGTACCGATACCCTAT-C
1 TAGGGTACCGATACCCTATAC
* *
1384943 CA-GGTATCGATACCC
1 TAGGGTACCGATACCC
1384958 CATGAATCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.38
20 2 0.06
21 4 0.12
22 14 0.44
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (21 bp):
TAGGGTACCGATACCCTATAC
Found at i:1392130 original size:31 final size:31
Alignment explanation
Indices: 1392064--1392131 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1392054 TGGTGTTCCT
***
1392064 AAATTTTAAATAAAATATCATTTTAACTGTT
1 AAATTTTAAATAAAATATCATTTTAACTCCA
* *
1392095 AAATTTTAGAT-AAATATCAATTTTACCTCCA
1 AAATTTTAAATAAAATATC-ATTTTAACTCCA
1392126 AAATTT
1 AAATTT
1392132 AGAGGTCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (31 bp):
AAATTTTAAATAAAATATCATTTTAACTCCA
Found at i:1398693 original size:21 final size:21
Alignment explanation
Indices: 1398667--1398707 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1398657 TTTGAACAGT
1398667 AAAAAAAATAGACCCTTGTTC
1 AAAAAAAATAGACCCTTGTTC
*
1398688 AAAAAAAATAGACTCTTGTT
1 AAAAAAAATAGACCCTTGTT
1398708 TTGTTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (21 bp):
AAAAAAAATAGACCCTTGTTC
Found at i:1401225 original size:19 final size:19
Alignment explanation
Indices: 1401156--1401218 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
1401146 ATGCATTATG
*
1401156 TGCATCGATGCACATACCA
1 TGCATCAATGCACATACCA
1401175 TGCATCAATGCACATACCA
1 TGCATCAATGCACATACCA
* *
1401194 TACATCAATGCACATGCCA
1 TGCATCAATGCACATACCA
1401213 TGCATC
1 TGCATC
1401219 GCTGCACTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.33, C:0.32, G:0.13, T:0.22
Consensus pattern (19 bp):
TGCATCAATGCACATACCA
Found at i:1409941 original size:66 final size:62
Alignment explanation
Indices: 1409862--1410020 Score: 187
Period size: 66 Copynumber: 2.5 Consensus size: 62
1409852 GAATAAATTG
* *
1409862 AACATCGAATGCATTATATGCATCGATGCACATACCATGCATCGATGCACTCAGAAT-TTTATGA
1 AACATCGAATGCATT-TATGCATCGATGCACAGA-CATGCATCAATGCACTCAGAATATTT-T-A
1409926 A
62 A
* *
1409927 ATACATCGAATGCATTTGATGCATCGATGCA-AGACATGTATCAATGCACTCAGACTATTTTAA
1 A-ACATCGAATGCATTT-ATGCATCGATGCACAGACATGCATCAATGCACTCAGAATATTTTAA
* *
1409990 AACATCAAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
1410021 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
62 24 0.29
63 5 0.06
64 20 0.24
65 7 0.08
66 27 0.33
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (62 bp):
AACATCGAATGCATTTATGCATCGATGCACAGACATGCATCAATGCACTCAGAATATTTTAA
Found at i:1410020 original size:17 final size:19
Alignment explanation
Indices: 1409998--1410040 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1409988 AAAACATCAA
1409998 ATGCACT-TCA-TGCATCG
1 ATGCACTCTCAGTGCATCG
*
1410015 ATGCACTCTTAGTGCATCG
1 ATGCACTCTCAGTGCATCG
1410034 ATGCACT
1 ATGCACT
1410041 GAGGGACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 2 0.09
19 14 0.61
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (19 bp):
ATGCACTCTCAGTGCATCG
Found at i:1411494 original size:18 final size:18
Alignment explanation
Indices: 1411456--1411494 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1411446 GCGATGATGG
* * *
1411456 TGATGATGGTGGTGGTCA
1 TGATCATGGTGGTGATAA
1411474 TGATCATGGTGGTGATAA
1 TGATCATGGTGGTGATAA
1411492 TGA
1 TGA
1411495 AGGTACGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.38, T:0.33
Consensus pattern (18 bp):
TGATCATGGTGGTGATAA
Found at i:1414306 original size:24 final size:24
Alignment explanation
Indices: 1414279--1414335 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
1414269 TATATCATAT
* *
1414279 ATCATAACAAAATCCATATAAGAA
1 ATCAGAACAAAATCCAGATAAGAA
* * *
1414303 ATCAGAACAGAATTCAGATCAGAA
1 ATCAGAACAAAATCCAGATAAGAA
1414327 ATCAGAACA
1 ATCAGAACA
1414336 TATTTGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.18
Consensus pattern (24 bp):
ATCAGAACAAAATCCAGATAAGAA
Found at i:1414314 original size:12 final size:12
Alignment explanation
Indices: 1414299--1414335 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1414289 AATCCATATA
1414299 AGAAATCAGAAC
1 AGAAATCAGAAC
* *
1414311 AGAATTCAGATC
1 AGAAATCAGAAC
1414323 AGAAATCAGAAC
1 AGAAATCAGAAC
1414335 A
1 A
1414336 TATTTGAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.16, G:0.16, T:0.14
Consensus pattern (12 bp):
AGAAATCAGAAC
Found at i:1416611 original size:17 final size:17
Alignment explanation
Indices: 1416589--1416632 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1416579 TCAAAGTTCT
1416589 GGTCAACAGTGGTCAAC
1 GGTCAACAGTGGTCAAC
1416606 GGTCAATGCA--GGTCAAC
1 GGTCAA--CAGTGGTCAAC
1416623 GGTCAACAGT
1 GGTCAACAGT
1416633 CGACTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
15 2 0.09
17 19 0.83
19 2 0.09
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTGGTCAAC
Found at i:1418048 original size:129 final size:123
Alignment explanation
Indices: 1417805--1418055 Score: 297
Period size: 129 Copynumber: 2.0 Consensus size: 123
1417795 ACATAACGCT
* *
1417805 TGTTATCAGTAGGTATCGATACATATATACAAGTATCAATACATAAGAAGACAATAGGTTAGAAC
1 TGTTATCAGTAGATATCGATACATATATACAAGTATCAATACATAAGAAGACAACAGGTTAGAAC
* * * * *
1417870 TTAAACAAACCGGTTAAAACTTTATATTTGAGATTGGTTGGACCTGATAACATTTGAA
66 TTAAACAAACCGGTTAAAACTTAACATTTAAGATAGGTTGGACCGGATAACATTTGAA
* ** * *
1417928 TGTTATCGGTAGATA-CTGATACATATATACAAGTATTGATACATAAGAATACAACATGTTGGAC
1 TGTTATCAGTAGATATC-GATACATATATACAAGTATCAATACATAAGAAGACAACAGGTT--A-
* * *
1417992 TTGAAACTTAAACAAACCGGTTGAAACTTAACATTTAAGGTAGGTTGGACCGGATAACTTTTGA
62 --G-AACTTAAACAAACCGGTTAAAACTTAACATTTAAGATAGGTTGGACCGGATAACATTTGA
1418056 GACTATAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
122 1 0.01
123 51 0.48
125 1 0.01
128 1 0.01
129 52 0.49
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (123 bp):
TGTTATCAGTAGATATCGATACATATATACAAGTATCAATACATAAGAAGACAACAGGTTAGAAC
TTAAACAAACCGGTTAAAACTTAACATTTAAGATAGGTTGGACCGGATAACATTTGAA
Found at i:1418128 original size:16 final size:15
Alignment explanation
Indices: 1418095--1418137 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1418085 CACATATCAA
* *
1418095 TATATTTTTAAAATT
1 TATATTTTAAAAAGT
1418110 TATATTTTCAAAAAGT
1 TATATTTT-AAAAAGT
1418126 TATA-TTTAAAAA
1 TATATTTTAAAAA
1418138 AATAGGGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 11 0.44
16 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
TATATTTTAAAAAGT
Found at i:1418136 original size:14 final size:16
Alignment explanation
Indices: 1418095--1418132 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1418085 CACATATCAA
* *
1418095 TATATTTT-TAAAATT
1 TATATTTTCAAAAAGT
1418110 TATATTTTCAAAAAGT
1 TATATTTTCAAAAAGT
1418126 TATATTT
1 TATATTT
1418133 AAAAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTTTCAAAAAGT
Found at i:1418426 original size:30 final size:30
Alignment explanation
Indices: 1418392--1418449 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
1418382 TTCTTAAATA
*
1418392 AAATATCATTTTAACCAT-TAAATTTTAGAT
1 AAATATCAATTTAACC-TCTAAATTTTAGAT
1418422 AAATATCAATTTAACCTCTAAATTTTAG
1 AAATATCAATTTAACCTCTAAATTTTAG
1418450 GGGCCAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.41
Consensus pattern (30 bp):
AAATATCAATTTAACCTCTAAATTTTAGAT
Found at i:1427990 original size:109 final size:109
Alignment explanation
Indices: 1427856--1428054 Score: 328
Period size: 109 Copynumber: 1.8 Consensus size: 109
1427846 TACTTGCATA
* * *
1427856 TATGTATTGATACCTATCGATAACATTCAAATGTTATTCAGTCCAACCTACCTCAAATGTTAAGG
1 TATGTATTGATACCTACCGATAACATTCAAATGTTATCCAGTCCAACATACCTCAAATGTTAAGG
1427921 TTCAACC-GATTTGTTTAAGTTCCAAGTCCAACTTGATGTATTCT
66 TTCAACCAG-TTTGTTTAAGTTCCAAGTCCAACTTGATGTATTCT
* *
1427965 TATGTATTGATACCTACCGATAACATTCAAATGTTATCCGGTCCAACATACCTCAAATGTTAAGT
1 TATGTATTGATACCTACCGATAACATTCAAATGTTATCCAGTCCAACATACCTCAAATGTTAAGG
*
1428030 TTTAACCAGTTTGTTTAAGTTCCAA
66 TTCAACCAGTTTGTTTAAGTTCCAA
1428055 CCTGTTATCT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
109 82 0.99
110 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (109 bp):
TATGTATTGATACCTACCGATAACATTCAAATGTTATCCAGTCCAACATACCTCAAATGTTAAGG
TTCAACCAGTTTGTTTAAGTTCCAAGTCCAACTTGATGTATTCT
Found at i:1429564 original size:17 final size:16
Alignment explanation
Indices: 1429542--1429613 Score: 83
Period size: 16 Copynumber: 4.4 Consensus size: 16
1429532 TATCTACTCT
1429542 AAATATAAATTTTTTGA
1 AAATATAAA-TTTTTGA
*
1429559 AAATATAACTTTTTGA
1 AAATATAAATTTTTGA
*
1429575 AAATATAACA-TTTTAA
1 AAATATAA-ATTTTTGA
*
1429591 AAATATAAAATTTTGA
1 AAATATAAATTTTTGA
*
1429607 TAATATA
1 AAATATA
1429614 TTGATAAGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.02
16 39 0.81
17 8 0.17
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (16 bp):
AAATATAAATTTTTGA
Found at i:1429573 original size:16 final size:16
Alignment explanation
Indices: 1429553--1429613 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
1429543 AATATAAATT
*
1429553 TTTTGAAAATATAACT
1 TTTTGAAAATATAACA
1429569 TTTTGAAAATATAACA
1 TTTTGAAAATATAACA
* *
1429585 TTTTAAAAATATAAAA
1 TTTTGAAAATATAACA
*
1429601 TTTTGATAATATA
1 TTTTGAAAATATA
1429614 TTGATAAGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (16 bp):
TTTTGAAAATATAACA
Found at i:1429836 original size:20 final size:20
Alignment explanation
Indices: 1429813--1429850 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1429803 ACCTCAAATG
* *
1429813 TTAAGTTTCAACCTGTTTGT
1 TTAAGTTCCAAACTGTTTGT
1429833 TTAAGTTCCAAACTGTTT
1 TTAAGTTCCAAACTGTTT
1429851 TCTTCTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (20 bp):
TTAAGTTCCAAACTGTTTGT
Found at i:1430345 original size:54 final size:54
Alignment explanation
Indices: 1430181--1430382 Score: 178
Period size: 54 Copynumber: 3.7 Consensus size: 54
1430171 ATAGGTTGTG
* * * * * *
1430181 CCTTGTTATTTTTAACCCGTTCCCTTATAAGTAGGATTAACG-TATTCGATTGCA
1 CCTTGTTATTTTTAACCAGTTACCTTATAAGTATGAGTAACGTTAATAGA-TGCA
* * * * * * *
1430235 CCTTATT-TTTCTT-TCTATTGTTTACCTCATACGTAAGAGTAACGTTAATGGATGCA
1 CCTTGTTATTT-TTAACCA--G-TTACCTTATAAGTATGAGTAACGTTAATAGATGCA
*
1430291 CCTTGTTATTTTTAACCAGTTACCTTATAAGTATGAGTAAC-TTAACTAGTTGCA
1 CCTTGTTATTTTTAACCAGTTACCTTATAAGTATGAGTAACGTTAA-TAGATGCA
* *
1430345 CCTTGTTTTTTTTAATCAGTTACCTTATAAGTATGAGT
1 CCTTGTTATTTTTAACCAGTTACCTTATAAGTATGAGT
1430383 CATTAATGTT
Statistics
Matches: 119, Mismatches: 21, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
53 8 0.07
54 69 0.58
55 2 0.02
56 30 0.25
57 10 0.08
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (54 bp):
CCTTGTTATTTTTAACCAGTTACCTTATAAGTATGAGTAACGTTAATAGATGCA
Found at i:1430525 original size:17 final size:16
Alignment explanation
Indices: 1430499--1430545 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
1430489 CTTTTTGTTC
1430499 TTTTTG-AAATATAACT
1 TTTTTGAAAATATAA-T
1430515 TTTTTGAAAATATAAT
1 TTTTTGAAAATATAAT
1430531 TATTTTGAAAATATA
1 T-TTTTGAAAATATA
1430546 TCGAACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (16 bp):
TTTTTGAAAATATAAT
Found at i:1431657 original size:19 final size:19
Alignment explanation
Indices: 1431633--1431684 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1431623 AATGCATTTG
1431633 ATGCATCGATGCACAAGCA
1 ATGCATCGATGCACAAGCA
1431652 ATGCATCGATGCACAAGCA
1 ATGCATCGATGCACAAGCA
1431671 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1431685 CAGGCTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACAAGCA
Found at i:1439194 original size:21 final size:21
Alignment explanation
Indices: 1439152--1439195 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1439142 ACCCCGGGAG
*
1439152 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1439173 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1439194 CT
1 CT
1439196 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1440317 original size:64 final size:64
Alignment explanation
Indices: 1440201--1440406 Score: 213
Period size: 64 Copynumber: 3.2 Consensus size: 64
1440191 ATTCAAGGTG
* * * * * *
1440201 ATGCACCGATGCATCAAACCATGCATCGATGCACCTATGAT-TTAATT-GAACATCGAATGCATT
1 ATGCATCGATGCA-CAAGCAATGCATCGATGCACC-AGGATATT-TTTCAAACATCGAATGCATT
1440264 TC
63 TC
* *** *
1440266 ATGCACCGATGCACTCTCCATGCATCGATGCACTC-GGA-ATATTTTCAAACATCGAATGCATTT
1 ATGCATCGATGCACAAGCAATGCATCGATGCAC-CAGGATAT-TTTTCAAACATCGAATGCATTT
*
1440329 G
64 C
* *
1440330 ATGCATCGATGCACAAGCAATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTC
1440394 ATGCATCGATGCA
1 ATGCATCGATGCA
1440407 TCCTTAGTGC
Statistics
Matches: 121, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 6 0.05
64 99 0.82
65 16 0.13
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCAATGCATCGATGCACCAGGATATTTTTCAAACATCGAATGCATTTC
Found at i:1441628 original size:17 final size:17
Alignment explanation
Indices: 1441600--1441647 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
1441590 GCTTTTTGTT
1441600 CTTTTTTG-AAATATAA
1 CTTTTTTGAAAATATAA
1441616 CTTTTTTGAAAATATAA
1 CTTTTTTGAAAATATAA
*
1441633 C-TTTTTAAAAATATA
1 CTTTTTTGAAAATATA
1441648 TCAATGCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 21 0.70
17 9 0.30
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (17 bp):
CTTTTTTGAAAATATAA
Found at i:1441893 original size:45 final size:45
Alignment explanation
Indices: 1441829--1441917 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
1441819 TCCGGTCTAA
1441829 CCTACCTCAAATGTTAAGTTTCAACCAGTTTGTTTAAGTTCCAAC
1 CCTACCTCAAATGTTAAGTTTCAACCAGTTTGTTTAAGTTCCAAC
* *
1441874 CCTACCTCAAATGTTAAGTTTCAACCGGTTTTTTTAAGTTCCAA
1 CCTACCTCAAATGTTAAGTTTCAACCAGTTTGTTTAAGTTCCAA
1441918 TCTATTGTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (45 bp):
CCTACCTCAAATGTTAAGTTTCAACCAGTTTGTTTAAGTTCCAAC
Found at i:1444117 original size:28 final size:26
Alignment explanation
Indices: 1444080--1444131 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1444070 GTAACCAATA
1444080 AAAAACAAAACAAGGCGCAATAATTAT
1 AAAAACAAAA-AAGGCGCAATAATTAT
*
1444107 AAGAAA-AAAAAAGGCGCAATCATTA
1 AA-AAACAAAAAAGGCGCAATAATTA
1444132 GTTACTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 14 0.61
27 6 0.26
28 3 0.13
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (26 bp):
AAAAACAAAAAAGGCGCAATAATTAT
Found at i:1444924 original size:33 final size:32
Alignment explanation
Indices: 1444866--1444930 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1444856 AACACATATC
* *
1444866 GATATATTTTAAAAAATTTAAATTTTCAAAAA
1 GATATATTTAAAAAAAATTAAATTTTCAAAAA
*
1444898 GATATATTTAAAAAAAAATTATATTTTCAAAAA
1 GATATATTT-AAAAAAAATTAAATTTTCAAAAA
1444931 AGCATGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (32 bp):
GATATATTTAAAAAAAATTAAATTTTCAAAAA
Found at i:1444929 original size:17 final size:17
Alignment explanation
Indices: 1444868--1444931 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 17
1444858 CACATATCGA
*
1444868 TATATTTT-AAAAAATT
1 TATATTTTCAAAAAAAT
* *
1444884 TAAATTTTCAAAAAGA-
1 TATATTTTCAAAAAAAT
**
1444900 TATATTTAAAAAAAAAT
1 TATATTTTCAAAAAAAT
1444917 TATATTTTCAAAAAA
1 TATATTTTCAAAAAA
1444932 GCATGGAAAG
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
16 19 0.51
17 18 0.49
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (17 bp):
TATATTTTCAAAAAAAT
Found at i:1450957 original size:20 final size:21
Alignment explanation
Indices: 1450900--1450958 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1450890 AATAATAAAA
*
1450900 AATTTATCTAAAAATATATAT
1 AATTTATTTAAAAATATATAT
*
1450921 AATTTA--TAAAAGTAATATATT
1 AATTTATTTAAAAAT-ATATA-T
*
1450942 TATTTATTTAAAAATAT
1 AATTTATTTAAAAATAT
1450959 CAGAAAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 12 0.39
22 2 0.06
23 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AATTTATTTAAAAATATATAT
Found at i:1452470 original size:3 final size:3
Alignment explanation
Indices: 1452464--1452540 Score: 84
Period size: 3 Copynumber: 25.3 Consensus size: 3
1452454 TTATATTATT
* * * * *
1452464 TAA TAA TAA TAA TAA TAT TATT TAA TAA TAA TAA TAA TAT TAT TAT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1452510 TAA TAA TAA TAA TAA TAA -AA TTAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA T
1452541 GAAAAAAAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 2 0.03
3 60 0.90
4 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1452484 original size:22 final size:22
Alignment explanation
Indices: 1452456--1452540 Score: 127
Period size: 22 Copynumber: 3.8 Consensus size: 22
1452446 ATAATTATTT
1452456 ATATTATTTAATAATAATAATA
1 ATATTATTTAATAATAATAATA
1452478 ATATTATTTAATAATAATAATA
1 ATATTATTTAATAATAATAATA
1452500 ATATTATTATTAATAATAATAATA
1 ATATTA-T-TTAATAATAATAATA
* *
1452524 ATA-AAATTAATAATAAT
1 ATATTATTTAATAATAAT
1452541 GAAAAAAAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
21 11 0.19
22 28 0.47
23 2 0.03
24 18 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATTATTTAATAATAATAATA
Found at i:1452988 original size:112 final size:111
Alignment explanation
Indices: 1452857--1453208 Score: 411
Period size: 112 Copynumber: 3.0 Consensus size: 111
1452847 TGTGATAGAA
1452857 TCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTT
1452921 CTCATTATGAACTTTCTCTGGAAAAATTGATGCATTGAGTAATGAAT
66 CTCATTATGAACTTTCTCT-GAAAAATTGATGCATTGAGTAATGAAT
* * *
1452968 TCAAACAAAAGGTTAAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCT
* ** * *
1453033 TCTCATTATGAACTTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCTGTGAT-AGAG
65 TCTCATTATGAACTTTCTCT-GAAAAATTGA---TG--C-A-----TTGAGTAATGA-AT
** * * *
1453092 TCATGCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTTTT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTT
* *
1453157 CTCATTATGAACTTTCTCTGAAAAAGTTGATCCATTGAGTAATGTAT
66 CTCATTATGAACTTTCTCTGAAAAA-TTGATGCATTGAGTAATGAAT
1453204 TCAAA
1 TCAAA
1453209 TCTTTTGCTA
Statistics
Matches: 199, Mismatches: 26, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
111 6 0.03
112 49 0.25
113 44 0.22
116 2 0.01
117 1 0.01
118 2 0.01
119 1 0.01
120 1 0.01
122 5 0.03
123 39 0.20
124 49 0.25
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (111 bp):
TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTT
CTCATTATGAACTTTCTCTGAAAAATTGATGCATTGAGTAATGAAT
Found at i:1453073 original size:235 final size:235
Alignment explanation
Indices: 1452772--1453208 Score: 682
Period size: 236 Copynumber: 1.9 Consensus size: 235
1452762 GTTGAACAAA
* *
1452772 TTCTTCTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGCTGATACTGATC
1 TTCTTCTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCCTTCTAGAAAAGCTGATACTGATC
*
1452837 TATCTCATTCTGTGATAGAATCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
66 TATCTCATTCTGTGATAGAATCAAACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
*
1452901 TCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAA-TTGATGCATTGAGTAATG
131 TCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCT-GAAAAAGTTGATCCATTGAGTAATG
1452965 AATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATAAAC
195 AATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATAAAC
* * * **
1453006 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTAGAAAAGTTGATGTTGA
1 TTCTTC-TCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCCT-TCTAGAAAAGCTGATACTGA
* * ** *
1453070 TCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTT
64 TCTATCTCATTCTGTGATAGAATCAAACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
*
1453135 CTTCCTCTTCAGATAAGTTTTTCTCATTATGAACTTTCTCTGAAAAAGTTGATCCATTGAGTAAT
129 CTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGAAAAAGTTGATCCATTGAGTAAT
*
1453200 GTATTCAAA
194 GAATTCAAA
1453209 TCTTTTGCTA
Statistics
Matches: 183, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
234 7 0.04
235 78 0.43
236 98 0.54
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (235 bp):
TTCTTCTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCCTTCTAGAAAAGCTGATACTGATC
TATCTCATTCTGTGATAGAATCAAACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
TCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGAAAAAGTTGATCCATTGAGTAATGA
ATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATAAAC
Found at i:1453627 original size:215 final size:216
Alignment explanation
Indices: 1453255--1453685 Score: 855
Period size: 215 Copynumber: 2.0 Consensus size: 216
1453245 TTAACATGGA
1453255 TAAAATGAATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATAAATGTTAAGTTCAT
1 TAAAATGAATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATAAATGTTAAGTTCAT
1453320 CTTTATTTGATTTTCAAAGTGGTGAACTCGGTCTTTCTTCAATTGTGTAGAAATCCAATAAATCT
66 CTTTATTTGATTTTCAAAGTGGTGAACTCGGTCTTTCTTCAATTGTGTAGAAATCCAATAAATCT
1453385 TTCTTCTTTGAAAAGAGAATTTATCATCTTTGGAGAGTGTAGATGTAGATATGCCTGAATTTTTG
131 TTCTTCTTTGAAAAGAGAATTTATCATCTTTGGAGAGTGTAGATGTAGATATGCCTGAATTTTTG
1453450 TATGATGTCACAAAACCACTT
196 TATGATGTCACAAAACCACTT
1453471 TAAAATGAATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATAAATGTTAAGTTCAT
1 TAAAATGAATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATAAATGTTAAGTTCAT
1453536 CTTTATTTGA-TTTCAAAGTGGTGAACTCGGTCTTTCTTCAATTGTGTAGAAATCCAATAAATCT
66 CTTTATTTGATTTTCAAAGTGGTGAACTCGGTCTTTCTTCAATTGTGTAGAAATCCAATAAATCT
1453600 TTCTTCTTTGAAAAGAGAATTTATCATCTTTGGAGAGTGTAGATGTAGATATGCCTGAATTTTTG
131 TTCTTCTTTGAAAAGAGAATTTATCATCTTTGGAGAGTGTAGATGTAGATATGCCTGAATTTTTG
1453665 TATGATGTCACAAAACCACTT
196 TATGATGTCACAAAACCACTT
1453686 GAGAACAAAA
Statistics
Matches: 215, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
215 140 0.65
216 75 0.35
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (216 bp):
TAAAATGAATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATAAATGTTAAGTTCAT
CTTTATTTGATTTTCAAAGTGGTGAACTCGGTCTTTCTTCAATTGTGTAGAAATCCAATAAATCT
TTCTTCTTTGAAAAGAGAATTTATCATCTTTGGAGAGTGTAGATGTAGATATGCCTGAATTTTTG
TATGATGTCACAAAACCACTT
Found at i:1454782 original size:9 final size:9
Alignment explanation
Indices: 1454768--1454801 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
1454758 CATCATCATT
1454768 TTTTTTTCA
1 TTTTTTTCA
1454777 TTTTTTTTCA
1 -TTTTTTTCA
1454787 TTTTTTTCA
1 TTTTTTTCA
1454796 TTTTTT
1 TTTTTT
1454802 CTTCTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1454785 original size:27 final size:29
Alignment explanation
Indices: 1454733--1454787 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1454723 ATCTTGACCC
1454733 TCATTTTTTCTTTCATTTTTCATTTCATCA
1 TCATTTTTTCTTTCATTTTT-ATTTCATCA
1454763 TCATTTTTT-TTTCATTTTT-TTTCAT
1 TCATTTTTTCTTTCATTTTTATTTCAT
1454788 TTTTTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 6 0.24
29 10 0.40
30 9 0.36
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (29 bp):
TCATTTTTTCTTTCATTTTTATTTCATCA
Found at i:1454801 original size:11 final size:10
Alignment explanation
Indices: 1454767--1454801 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
1454757 TCATCATCAT
1454767 TTTTTTTTCA
1 TTTTTTTTCA
1454777 TTTTTTTTCA
1 TTTTTTTTCA
1454787 -TTTTTTTCA
1 TTTTTTTTCA
1454796 TTTTTT
1 TTTTTT
1454802 CTTCTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:1462119 original size:15 final size:15
Alignment explanation
Indices: 1462099--1462130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1462089 TGCAATGAAT
*
1462099 AATGAATGTGTGCAA
1 AATGAATGTATGCAA
1462114 AATGAATGTATGCAA
1 AATGAATGTATGCAA
1462129 AA
1 AA
1462131 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1465410 original size:24 final size:25
Alignment explanation
Indices: 1465383--1465435 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
1465373 ATACTTGAAA
1465383 AATAAAATA-AAACATTAAT-AAAAT
1 AATAAAATATAAACATT-ATGAAAAT
* *
1465407 AAT-ATATATAAATATTATGAAAAT
1 AATAAAATATAAACATTATGAAAAT
1465431 AATAA
1 AATAA
1465436 GTATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 6 0.25
24 17 0.71
25 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (25 bp):
AATAAAATATAAACATTATGAAAAT
Found at i:1465455 original size:28 final size:27
Alignment explanation
Indices: 1465404--1465457 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
1465394 ACATTAATAA
*
1465404 AATAATATATATAAATATTATGAAAAT
1 AATAATATATATAAAAATTATGAAAAT
*
1465431 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAATTATGAAAA
1465458 GAAAGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AATAATATATATAAAAATTATGAAAAT
Found at i:1465877 original size:20 final size:20
Alignment explanation
Indices: 1465841--1465878 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1465831 ATGATTGGTA
*
1465841 CTTTATTTATTATAATTTGT
1 CTTTATTTATTAAAATTTGT
1465861 CTTTA-TTATTAGAAATTT
1 CTTTATTTATTA-AAATTT
1465879 AAATATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
CTTTATTTATTAAAATTTGT
Found at i:1466251 original size:3 final size:3
Alignment explanation
Indices: 1466245--1466290 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
1466235 ATAGATATTT
* *
1466245 ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATG ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1466291 ATGTATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1466268 original size:15 final size:15
Alignment explanation
Indices: 1466248--1466290 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
1466238 GATATTTATA
1466248 ATAATAATAATAATG
1 ATAATAATAATAATG
1466263 ATAATAATAATAATG
1 ATAATAATAATAATG
1466278 ATAATAATAATAA
1 ATAATAATAATAA
1466291 ATGTATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
ATAATAATAATAATG
Found at i:1466884 original size:17 final size:15
Alignment explanation
Indices: 1466842--1466882 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1466832 AGCCATATTC
*
1466842 TTCATTTTCTCATTT
1 TTCATTCTCTCATTT
1466857 TTCATTCTCTCATTT
1 TTCATTCTCTCATTT
1466872 TTCATTCTCTC
1 TTCATTCTCTC
1466883 TCTGGCTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (15 bp):
TTCATTCTCTCATTT
Found at i:1467682 original size:3 final size:3
Alignment explanation
Indices: 1467676--1467736 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
1467666 ATTTATTATT
* * * * *
1467676 TAA TAA TAA TAA TAA TAA TAT TAT TAT TAA TAT TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1467724 -AA TTAA TAA TAA T
1 TAA -TAA TAA TAA T
1467737 GAAAAAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:1467688 original size:24 final size:24
Alignment explanation
Indices: 1467658--1467736 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
1467648 CTGTAATATG
1467658 TAATAATTAT-TTATTATTTAATAA
1 TAATAATTATATTATTA-TTAATAA
*
1467682 TAATAATAATAATATTATTATTAATAT
1 TAATAAT--T-ATATTATTATTAATAA
* **
1467709 TAATAATTATAATAAAATTAATAA
1 TAATAATTATATTATTATTAATAA
1467733 TAAT
1 TAAT
1467737 GAAAAAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
24 23 0.50
25 1 0.02
26 1 0.02
27 15 0.33
28 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATAATTATATTATTATTAATAA
Found at i:1470931 original size:29 final size:29
Alignment explanation
Indices: 1470855--1470923 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
1470845 ATGGATTTTA
1470855 AACGTTATTATATATATATGTATCTAAAG
1 AACGTTATTATATATATATGTATCTAAAG
1470884 AACGTTATTATATATATATGTATCTAAAG
1 AACGTTATTATATATATATGTATCTAAAG
1470913 AACGTT-TTATA
1 AACGTTATTATA
1470924 AAATATATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (29 bp):
AACGTTATTATATATATATGTATCTAAAG
Found at i:1473610 original size:18 final size:17
Alignment explanation
Indices: 1473568--1473637 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
1473558 ATATAAAGAG
*
1473568 CTAGTTTAATTAATGAA
1 CTAGTTTAATGAATGAA
* *
1473585 CCAATTTAAATGAATGAA
1 CTAGTTT-AATGAATGAA
*
1473603 CTAGTTTAATTG-GTGAA
1 CTAGTTTAA-TGAATGAA
*
1473620 CTAGCTTTATTGAATGAA
1 CTAG-TTTAATGAATGAA
1473638 AGAGGATACT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
17 17 0.41
18 24 0.59
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (17 bp):
CTAGTTTAATGAATGAA
Found at i:1473775 original size:20 final size:20
Alignment explanation
Indices: 1473737--1473775 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1473727 CAACTTAATG
* *
1473737 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATGAACAC
1473757 TCATGCAAATTCATGAACA
1 TCATGCAAATTCATGAACA
1473776 AATAAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATGAACAC
Found at i:1474910 original size:13 final size:13
Alignment explanation
Indices: 1474892--1474938 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
1474882 GATGTTCTCT
1474892 AAAATCCTACAAC
1 AAAATCCTACAAC
**
1474905 AAAATCCTGTAAC
1 AAAATCCTACAAC
1474918 AAAATCCTACAAC
1 AAAATCCTACAAC
1474931 AAAATCCT
1 AAAATCCT
1474939 TTGACTAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.51, C:0.28, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAATCCTACAAC
Found at i:1479607 original size:31 final size:31
Alignment explanation
Indices: 1479566--1479658 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
1479556 GGAAAAAATC
*
1479566 CCTAACGTTATCGATCCATTCAATTTTAGTA
1 CCTAACGTTATCAATCCATTCAATTTTAGTA
* *
1479597 CCTAATGTTATCAATCCATTCAATTTTAGTC
1 CCTAACGTTATCAATCCATTCAATTTTAGTA
*
1479628 CCTCAACCGTTA--ACTCTCATTCAATTTTAGT
1 CCT-AA-CGTTATCAATC-CATTCAATTTTAGT
1479659 CTCTCAATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 34 0.63
32 16 0.30
33 4 0.07
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.40
Consensus pattern (31 bp):
CCTAACGTTATCAATCCATTCAATTTTAGTA
Found at i:1485754 original size:18 final size:19
Alignment explanation
Indices: 1485731--1485774 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1485721 AGAGCAGGAA
1485731 AAGAAATAT-GAAAAAAAT
1 AAGAAATATGGAAAAAAAT
*
1485749 AAGAAA-ATGGAAAAGAAT
1 AAGAAATATGGAAAAAAAT
1485767 AA-AAATAT
1 AAGAAATAT
1485775 TGGTGTTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (19 bp):
AAGAAATATGGAAAAAAAT
Found at i:1488615 original size:59 final size:59
Alignment explanation
Indices: 1488516--1488652 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 59
1488506 CAGCAGGCTG
** * * *
1488516 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCATGA-CTTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGAGC-TTATGTGT
* ** *
1488575 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGAGCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGAGCTTATGTGT
*
1488634 CATACTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
1488653 CGGTGCTTAT
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
58 1 0.02
59 60 0.97
60 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGAGCTTATGTGT
Found at i:1495952 original size:59 final size:59
Alignment explanation
Indices: 1495853--1495989 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
1495843 CAGCAGGCTG
** * *
1495853 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** *
1495912 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
*
1495971 CATACTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
1495990 CGGTGCTTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:1499890 original size:53 final size:53
Alignment explanation
Indices: 1499828--1499930 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
1499818 TAGTTTCAGC
*
1499828 ACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTTGGT
1 ACTATGTGTGCATCCATGGTATTCACAATGAGTTTGTGAATTACCATTTTGGT
* *
1499881 ACTATGTGTGCATCTATGGTATTCACAATGAGTTTTTGAATTACCATTTT
1 ACTATGTGTGCATCCATGGTATTCACAATGAGTTTGTGAATTACCATTTT
1499931 ATATACCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (53 bp):
ACTATGTGTGCATCCATGGTATTCACAATGAGTTTGTGAATTACCATTTTGGT
Found at i:1502757 original size:20 final size:20
Alignment explanation
Indices: 1502733--1502792 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
1502723 TACTGATACA
*
1502733 GTTCTTCTAGTATTGATATT
1 GTTCTTCTAGTATCGATATT
* *
1502753 TTTCTTTGTCAGTATCGATATT
1 GTTC-TTCT-AGTATCGATATT
* *
1502775 GTTCTTCAAGTACCGATA
1 GTTCTTCTAGTATCGATA
1502793 CTATTCCTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 12 0.39
21 5 0.16
22 14 0.45
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (20 bp):
GTTCTTCTAGTATCGATATT
Found at i:1504667 original size:54 final size:54
Alignment explanation
Indices: 1504242--1504679 Score: 617
Period size: 54 Copynumber: 8.1 Consensus size: 54
1504232 TAACCGAATG
* * *
1504242 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATC
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
1504296 GGCATTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTACGTATA
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * ** *
1504350 GACACTGTGTGTGCAGCCTAA-AAATTTCATAATAAGTTTATGAATTTCAATATC
1 GGCACTGTGTGTGCAACCTAAGAAA-TTCATAATAAGTTTATGAATTTCCGTATT
* * *
1504404 GGCACTGTGGGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCATATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
1504458 GGCACTGTGTGTGCAACCTAAAAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * *
1504512 GGCATTGTGTGTGCAACCTAATAATTTCATAATAAGTTTATGAATTTCCGTATC
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
1504566 GGCATTGTGTGTGCAACCTAAAAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * * *
1504620 GGCACTGTATGTGCAACTTAAGAAATTCATAATGATTTTATGAATTTCCATATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1504674 GGCACT
1 GGCACT
1504680 AGGTATGCAT
Statistics
Matches: 345, Mismatches: 37, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
53 3 0.01
54 339 0.98
55 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:1505429 original size:14 final size:14
Alignment explanation
Indices: 1505407--1505437 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1505397 AAAAATATAC
1505407 ATATCTTTAAAAAT
1 ATATCTTTAAAAAT
*
1505421 ATATTTTTAAAAAT
1 ATATCTTTAAAAAT
1505435 ATA
1 ATA
1505438 ACACTACCCC
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATCTTTAAAAAT
Found at i:1505660 original size:24 final size:24
Alignment explanation
Indices: 1505633--1505709 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
1505623 TCAAACATAT
* *
1505633 ATCAGAACATAATCCATATCAAAA
1 ATCAGAACATAATTCATATCAGAA
*
1505657 ATCAGTACA-AATTCATATCAGAA
1 ATCAGAACATAATTCATATCAGAA
*
1505680 ATCAGAACATAATTCAAATCAGAA
1 ATCAGAACATAATTCATATCAGAA
1505704 ATCAGA
1 ATCAGA
1505710 TAAAACATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 20 0.43
24 27 0.57
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.22
Consensus pattern (24 bp):
ATCAGAACATAATTCATATCAGAA
Found at i:1510110 original size:24 final size:24
Alignment explanation
Indices: 1510083--1510160 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
1510073 TGGAACATAT
*
1510083 ATCATAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATCCAGATCAGAA
* * *
1510107 ATCAGAACATAATTCAGATTAGAA
1 ATCAGAACAGAATCCAGATCAGAA
* *
1510131 ATCAGAACAGAAGT-CAAATCAAAA
1 ATCAGAACAGAA-TCCAGATCAGAA
1510155 ATCAGA
1 ATCAGA
1510161 TAAAACATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 44 0.98
25 1 0.02
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.18
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGATCAGAA
Found at i:1510112 original size:12 final size:12
Alignment explanation
Indices: 1510097--1510161 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
1510087 TAACAGAATC
1510097 CAGATCAGAAAT
1 CAGATCAGAAAT
* * *
1510109 CAGAACATAATT
1 CAGATCAGAAAT
*
1510121 CAGATTAGAAAT
1 CAGATCAGAAAT
* *
1510133 CAGAACAGAAGT
1 CAGATCAGAAAT
* *
1510145 CAAATCAAAAAT
1 CAGATCAGAAAT
1510157 CAGAT
1 CAGAT
1510162 AAAACATTCA
Statistics
Matches: 38, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.52, C:0.15, G:0.14, T:0.18
Consensus pattern (12 bp):
CAGATCAGAAAT
Found at i:1514688 original size:24 final size:24
Alignment explanation
Indices: 1514661--1514720 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
1514651 CGAAACATAT
1514661 ATCAGAACAGAATCCAGATAAGAA
1 ATCAGAACAGAATCCAGATAAGAA
* * * * *
1514685 ATCATAACATAATTCATATCAGAA
1 ATCAGAACAGAATCCAGATAAGAA
**
1514709 ATTGGAACAGAA
1 ATCAGAACAGAA
1514721 ATCATATAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGATAAGAA
Found at i:1519277 original size:12 final size:11
Alignment explanation
Indices: 1519235--1519361 Score: 51
Period size: 12 Copynumber: 10.6 Consensus size: 11
1519225 AGATATCAGA
*
1519235 AATCAAAACAG
1 AATCAGAACAG
*
1519246 AATTTAGAACAG
1 AA-TCAGAACAG
1519258 ATATCAGAACAG
1 A-ATCAGAACAG
* *
1519270 AATCCAGACCAAA
1 AAT-CAGAAC-AG
* *
1519283 AATCATAATAG
1 AATCAGAACAG
* *
1519294 AATCCAGATAAAA
1 AAT-CAGA-ACAG
*
1519307 AATCAGAACAA
1 AATCAGAACAG
1519318 AATTCAGATA-AG
1 AA-TCAGA-ACAG
1519330 AAATCAGAACAG
1 -AATCAGAACAG
1519342 AAGTCA-AATCAG
1 AA-TCAGAA-CAG
1519354 AAATCAGA
1 -AATCAGA
1519362 TAAAATATTC
Statistics
Matches: 88, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
11 18 0.20
12 54 0.61
13 16 0.18
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.16
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:1519287 original size:24 final size:23
Alignment explanation
Indices: 1519260--1519343 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 23
1519250 TAGAACAGAT
*
1519260 ATCAGAACAGAATCCAGACCAAAA
1 ATCAGAACAGAATCCAGA-AAAAA
* *
1519284 ATCATAATAGAATCCAGATAAAAA
1 ATCAGAACAGAATCCAGA-AAAAA
* * *
1519308 ATCAGAACAAAATTCAGATAAGAA
1 ATCAGAACAGAATCCAGA-AAAAA
1519332 ATCAGAACAGAA
1 ATCAGAACAGAA
1519344 GTCAAATCAG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.14
Consensus pattern (23 bp):
ATCAGAACAGAATCCAGAAAAAA
Found at i:1519355 original size:24 final size:24
Alignment explanation
Indices: 1519301--1519361 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1519291 TAGAATCCAG
* * *
1519301 ATAAAAAATCAGAACAAAATTCAG
1 ATAAGAAATCAGAACAAAAGTCAA
*
1519325 ATAAGAAATCAGAACAGAAGTCAA
1 ATAAGAAATCAGAACAAAAGTCAA
*
1519349 ATCAGAAATCAGA
1 ATAAGAAATCAGA
1519362 TAAAATATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (24 bp):
ATAAGAAATCAGAACAAAAGTCAA
Found at i:1528093 original size:54 final size:54
Alignment explanation
Indices: 1528002--1528438 Score: 547
Period size: 54 Copynumber: 8.1 Consensus size: 54
1527992 TTATCGAATG
* * *
1528002 GGCACTATGTGTGCAACCTAAG-AATTTATAATAAGTTTATGAATTTTCGTAAT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
1528055 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTTCTGTATC
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATT
* * *
1528109 GACACTCTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * * * * * *
1528163 GACACTATGTGAGCAAACTAAGAAATTTATAATATGCTTATGAATTTTCATATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * ** * * *
1528217 GGCACCGAGTGTGCAACCTAAGGGATTCATAATAAATTTATGAATTTCCGTATC
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
1528271 GGCACTGTGTGTGCAGCCTAAGAAATTCATAAAAAGTTTATGAATTTTCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
1528325 GGCATTGTGTGTGCAACGTAAGAAATTCATAATAAGTTTATGAA-TTTCTGCATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATT
* * * *
1528379 GGCACTATATGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
1528433 AGCACT
1 GGCACT
1528439 AGGGATGCAT
Statistics
Matches: 327, Mismatches: 52, Indels: 9
0.84 0.13 0.02
Matches are distributed among these distances:
53 29 0.09
54 291 0.89
55 7 0.02
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
Found at i:1540319 original size:23 final size:23
Alignment explanation
Indices: 1540284--1540334 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1540274 AATAATGAAG
*
1540284 GAAATAGAGTGAGTGGATG-GTT
1 GAAATAGAGTGAGTGGATGAGGT
* *
1540306 GAAATTGATGTGAGTTGATGAGGT
1 GAAATAGA-GTGAGTGGATGAGGT
1540330 GAAAT
1 GAAAT
1540335 GGGTAGGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 10 0.42
24 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.29
Consensus pattern (23 bp):
GAAATAGAGTGAGTGGATGAGGT
Found at i:1546629 original size:50 final size:50
Alignment explanation
Indices: 1546570--1546671 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1546560 GTCTCACTTC
1546570 TATGTTTTACTTGCATGGCATAGTTTACTAAAGGTGCCCTATGCAATCTA
1 TATGTTTTACTTGCATGGCATAGTTTACTAAAGGTGCCCTATGCAATCTA
1546620 TATGTTTTACTTGCATGGCATAGTTTACTAAAGGTGCCCTATGCAATCTA
1 TATGTTTTACTTGCATGGCATAGTTTACTAAAGGTGCCCTATGCAATCTA
1546670 TA
1 TA
1546672 GTCAAGAATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (50 bp):
TATGTTTTACTTGCATGGCATAGTTTACTAAAGGTGCCCTATGCAATCTA
Found at i:1552835 original size:13 final size:13
Alignment explanation
Indices: 1552819--1552852 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1552809 GCAATGAGCA
1552819 TCATAAATGCGCG
1 TCATAAATGCGCG
*
1552832 TCATAAATGCGTG
1 TCATAAATGCGCG
1552845 TCATAAAT
1 TCATAAAT
1552853 TTTTGTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:1555933 original size:23 final size:24
Alignment explanation
Indices: 1555903--1555947 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1555893 AATTTCTAAA
1555903 TAAAAATAAT-AAAATAAAATATC
1 TAAAAATAATAAAAATAAAATATC
*
1555926 TAAAAATATTAAAAATAAAATA
1 TAAAAATAATAAAAATAAAATA
1555948 AAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAAATAATAAAAATAAAATATC
Found at i:1558511 original size:10 final size:10
Alignment explanation
Indices: 1558496--1558521 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1558486 AAATAAATCA
1558496 TTTTTTCTAT
1 TTTTTTCTAT
1558506 TTTTTTCTAT
1 TTTTTTCTAT
1558516 TTTTTT
1 TTTTTT
1558522 GTTTCCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTAT
Found at i:1564146 original size:2 final size:2
Alignment explanation
Indices: 1564139--1564196 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1564129 AATGTTTTTA
1564139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1564181 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1564197 TTCTGACATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1565822 original size:45 final size:45
Alignment explanation
Indices: 1565773--1565991 Score: 330
Period size: 45 Copynumber: 4.9 Consensus size: 45
1565763 CATACTTATT
* * * * * *
1565773 ATACACCATTATGCATTTAAATCATGGCATCATTTCATGCCGATA
1 ATACACTATTATACATTTCATTTATGGCATCCTTTCATGCCGATA
*
1565818 ATACACTATTATACATTTCATTTACGGCATCCTTTCATGCCGATA
1 ATACACTATTATACATTTCATTTATGGCATCCTTTCATGCCGATA
*
1565863 TTACACTATTATACATTTCATTTATGGCATCCTTTCATGCCGATA
1 ATACACTATTATACATTTCATTTATGGCATCCTTTCATGCCGATA
*
1565908 TTACACTATTATACATTTCATTTATGGCATCCTTTCATGCCGATA
1 ATACACTATTATACATTTCATTTATGGCATCCTTTCATGCCGATA
* * *
1565953 TTACACTATTATACATTTCATTTATTGCATCATTTCATG
1 ATACACTATTATACATTTCATTTATGGCATCCTTTCATG
1565992 TCGTTTATAC
Statistics
Matches: 163, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 163 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.41
Consensus pattern (45 bp):
ATACACTATTATACATTTCATTTATGGCATCCTTTCATGCCGATA
Found at i:1566143 original size:81 final size:81
Alignment explanation
Indices: 1566028--1566357 Score: 475
Period size: 81 Copynumber: 4.1 Consensus size: 81
1566018 ATACATCTAG
* * *
1566028 TCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTTTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGC
1566093 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * **
1566109 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATGATTGACACTTTTTTCTCAAATTT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGC
*
1566174 AGAGCTAGG-CATTTAA
66 ACAGCTAGGCCA-TTAA
* * *
1566190 TCTTTTACTCAAAGGTATCTAATCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGC
1566255 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
1566271 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATGATTGACACATTTTTGTC-AATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGC
* * *
1566335 ACAGTTAGACCTTTAA
66 ACAGCTAGGCCATTAA
1566351 TCTTTTA
1 TCTTTTA
1566358 TTTTAGAATA
Statistics
Matches: 221, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
80 27 0.12
81 192 0.87
82 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGC
ACAGCTAGGCCATTAA
Found at i:1566993 original size:19 final size:19
Alignment explanation
Indices: 1566953--1566993 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1566943 ATATTGATAC
*
1566953 TACTATACTATGGTACCGA
1 TACTATACTATGGTACCAA
* *
1566972 TACTCTACTATGGTATCAA
1 TACTATACTATGGTACCAA
1566991 TAC
1 TAC
1566994 CATTTTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (19 bp):
TACTATACTATGGTACCAA
Found at i:1567042 original size:20 final size:20
Alignment explanation
Indices: 1567017--1567088 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1567007 TGTTTCAGAT
*
1567017 GGTATCGATAC-CTTCCCTTC
1 GGTATCGATACTC-CCCCTTC
*
1567037 GGTATCGGTACTCCCCCTTC
1 GGTATCGATACTCCCCCTTC
*
1567057 GGTATCGGTACTCCCCCTTC
1 GGTATCGATACTCCCCCTTC
*
1567077 GATATCGATACT
1 GGTATCGATACT
1567089 GATTGCATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 46 0.98
21 1 0.02
ACGTcount: A:0.15, C:0.35, G:0.18, T:0.32
Consensus pattern (20 bp):
GGTATCGATACTCCCCCTTC
Found at i:1570312 original size:28 final size:28
Alignment explanation
Indices: 1570263--1570320 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1570253 TAATATCCCC
* *
1570263 TAAAAATAATATTCTTTAAATT-TTTGAA
1 TAAAAATAATAATATTTAAATTATTT-AA
1570291 TAAAACATAATAATATTT-AATTATTTAA
1 TAAAA-ATAATAATATTTAAATTATTTAA
1570319 TA
1 TA
1570321 TCGAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
TAAAAATAATAATATTTAAATTATTTAA
Found at i:1571133 original size:10 final size:10
Alignment explanation
Indices: 1571120--1571148 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1571110 ATGAACTAAC
1571120 ATGCAAAAAA
1 ATGCAAAAAA
1571130 ATGCAAAAAA
1 ATGCAAAAAA
1571140 ATGCAAAAA
1 ATGCAAAAA
1571149 TAAAAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.10
Consensus pattern (10 bp):
ATGCAAAAAA
Found at i:1572578 original size:3 final size:3
Alignment explanation
Indices: 1572566--1572665 Score: 76
Period size: 3 Copynumber: 33.0 Consensus size: 3
1572556 GTTTGCATCT
* * * * * *
1572566 ATA A-A ATA ATA ATTA AAA ATA ATG TTA ATA TTA ATA ATA TTA TTA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
1572611 TTA ATA ATA ATA GTA ATA ATA ATG ATG ATA ATA ATA ATA ATA TTAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
1572657 ATA ATA ATA
1 ATA ATA ATA
1572666 GGGGGTGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.03
3 71 0.91
4 5 0.06
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:1581772 original size:134 final size:133
Alignment explanation
Indices: 1581400--1582102 Score: 808
Period size: 134 Copynumber: 5.3 Consensus size: 133
1581390 ACCTGGGAAC
* *
1581400 GTTGATTCATTCCACTGTCACTCACGGAAGATTGAATCGAGGTAGAATTGTTCCACTATTACTCA
1 GTTGATTTATTCCACTGTCACTCA-GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCA
* * * *
1581465 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTACGCTTCTTCTTGAGGGAAAATTAATTCTAG
65 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTTCACTTCTTCTTGAGGGAAAATCAAATCTAG
*
1581530 AGAT
130 GGAT
* * ** *
1581534 GTTGATTTATTCCACTATCACT--GGAAGATTGAATTGAGGTAGACTTGTTCCACTGCTACTTAG
1 GTTGATTTATTCCACTGTCACTCAGGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAG
* * * *
1581597 GGAATATCAAATCTTGAAATAAAGGGATCTATTTCGCTTCTTCTTGAGGGAAAATCAAATCTAGG
66 GGAATATCAAATCTTGAAATAGAGGGATTTGTTTCACTTCTTCTTGAGGGAAAATCAAATCTAGG
1581662 GAT
131 GAT
* * * *
1581665 GTTGATTTATTCGATTGTCACTCAGAGAAGATTGAATCGAGGCAGACTTTTTCCACTATTACTCA
1 GTTGATTTATTCCACTGTCACTCAG-GAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCA
* * * *
1581730 GGGAATATCAAATCTTGAAAGAGAGGGGTTTGTTTCATTTCTTCTTGA-GGAAAATCACATATGT
65 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTTCACTTCTTCTTGAGGGAAAATCA-A-ATCT
*
1581794 A--GAC
128 AGGGAT
* * * *
1581798 GTTGATTTATTCCACTGTCACTCAGGGAAGATTGAATTGAGGAAGACTTGATCCACTATTGCTCA
1 GTTGATTTATTCCACTGTCACTCA-GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCA
* * * * * *
1581863 GGGAATATAAAATCTTGAAAGATAGGTATATGTTTCACTTCTTCTTGAGGGAAAATCAGATCTAG
65 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTTCACTTCTTCTTGAGGGAAAATCAAATCTAG
*
1581928 GTAT
130 GGAT
* * * * * *
1581932 GTTGAGTCATTCTACTATCACTCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTGTTACTCA
1 GTTGATTTATTCCACTGTCACTCA-GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCA
* * * * *
1581997 GAGAATATTAAATCTTGAAATAGAGGGATTTG-TTCTGCTTCTTCTTGAGGGAAAATCAAATATG
65 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTTC-ACTTCTTCTTGAGGGAAAATCAAATCTA
*
1582061 GGGAC
129 GGGAT
* * * *
1582066 GTT-TTTTCATTTCACTTTCACTAAAGGAAGATTGAAT
1 GTTGATTT-ATTCCACTGTCACT-CAGGAAGATTGAAT
1582103 TGAGTTTGAT
Statistics
Matches: 479, Mismatches: 78, Indels: 24
0.82 0.13 0.04
Matches are distributed among these distances:
131 116 0.24
132 4 0.01
133 114 0.24
134 240 0.50
135 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (133 bp):
GTTGATTTATTCCACTGTCACTCAGGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAG
GGAATATCAAATCTTGAAATAGAGGGATTTGTTTCACTTCTTCTTGAGGGAAAATCAAATCTAGG
GAT
Found at i:1581936 original size:267 final size:263
Alignment explanation
Indices: 1581400--1582106 Score: 866
Period size: 267 Copynumber: 2.6 Consensus size: 263
1581390 ACCTGGGAAC
*
1581400 GTTGATTCATTCCACTGTCACTCACGGAAGATTGAATCGAGGTAGAATTGTTCCACTATTACTCA
1 GTTGATTCATTCCACTGTCACTCA-GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCA
* * * *
1581465 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTACGCTTCTTCTTGAGGGAAAATTAAT-TCTA
65 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTTC-TTTCTTCTTGAGGGAAAATCAATATGT-
* * * *
1581529 GAGATGTTGATTTATTCCACTATCACT-GGAAGATTGAATTGAGGTAGACTTGTTCCACTGCTAC
128 -AGACGTTGATTTATTCCACTATCACTAGGAAGATTGAATTGAGGAAGACTTGATCCACTACTAC
* * * * *
1581593 TTAGGGAATATCAAATCTTGAAATAAAGGGATCTATTTCGCTTCTTCTTGAGGGAAAATCAAATC
192 TCAGGGAATATAAAATCTTGAAAGAAAGGGATATATTTCACTTCTTCTTGAGGGAAAATCAAATC
1581658 TAGGGAT
257 TAGGGAT
* * * * *
1581665 GTTGATTTATTCGATTGTCACTCAGAGAAGATTGAATCGAGGCAGACTTTTTCCACTATTACTCA
1 GTTGATTCATTCCACTGTCACTCAG-GAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCA
* *
1581730 GGGAATATCAAATCTTGAAAGAGAGGGGTTTGTTTCATTTCTTCTTGA-GGAAAATCACATATGT
65 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTTC-TTTCTTCTTGAGGGAAAATCA-ATATGT
* * *
1581794 AGACGTTGATTTATTCCACTGTCACTCAGGGAAGATTGAATTGAGGAAGACTTGATCCACTATTG
128 AGACGTTGATTTATTCCACTATCACT-A-GGAAGATTGAATTGAGGAAGACTTGATCCACTACTA
* * * *
1581859 CTCAGGGAATATAAAATCTTGAAAGATAGGTATATGTTTCACTTCTTCTTGAGGGAAAATCAGAT
191 CTCAGGGAATATAAAATCTTGAAAGAAAGGGATATATTTCACTTCTTCTTGAGGGAAAATCAAAT
*
1581924 CTAGGTAT
256 CTAGGGAT
* * * * *
1581932 GTTGAGTCATTCTACTATCACTCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTGTTACTCA
1 GTTGATTCATTCCACTGTCACTCA-GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCA
* *
1581997 GAGAATATTAAATCTTGAAATAGAGGGATTTG-TTCTGCTTCTTCTTGAGGGAAAATCAAATATG
65 GGGAATATCAAATCTTGAAATAGAGGGATTTGTTTCT--TTCTTCTTGAGGGAAAATC-AATATG
** * * *
1582061 GGGACGTT-TTTTCATTTCACTTTCACTAAAGGAAGATTGAATTGAG
127 TAGACGTTGATTT-ATTCCACTATCACT--AGGAAGATTGAATTGAG
1582107 TTTGATTCAT
Statistics
Matches: 380, Mismatches: 49, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
264 33 0.09
265 103 0.27
266 5 0.01
267 189 0.50
268 48 0.13
269 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (263 bp):
GTTGATTCATTCCACTGTCACTCAGGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAG
GGAATATCAAATCTTGAAATAGAGGGATTTGTTTCTTTCTTCTTGAGGGAAAATCAATATGTAGA
CGTTGATTTATTCCACTATCACTAGGAAGATTGAATTGAGGAAGACTTGATCCACTACTACTCAG
GGAATATAAAATCTTGAAAGAAAGGGATATATTTCACTTCTTCTTGAGGGAAAATCAAATCTAGG
GAT
Found at i:1583384 original size:2 final size:2
Alignment explanation
Indices: 1583371--1583413 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1583361 TGTATGTATG
*
1583371 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1583412 TA
1 TA
1583414 ATCGCCTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1590020 original size:17 final size:18
Alignment explanation
Indices: 1589988--1590022 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1589978 AATCTATCGA
1589988 AAAACAAATGAAAAAAAT
1 AAAACAAATGAAAAAAAT
1590006 AAAACAAAT-AAAAAAAT
1 AAAACAAATGAAAAAAAT
1590023 TTATCAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAACAAATGAAAAAAAT
Found at i:1593938 original size:15 final size:15
Alignment explanation
Indices: 1593920--1593949 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1593910 ATTAAATTGT
1593920 TAATAATAATAACAA
1 TAATAATAATAACAA
1593935 TAATAATAATAACAA
1 TAATAATAATAACAA
1593950 GAACCTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATAATAATAACAA
Found at i:1594378 original size:137 final size:136
Alignment explanation
Indices: 1594132--1594544 Score: 461
Period size: 137 Copynumber: 3.0 Consensus size: 136
1594122 TTATGTATAC
* * * * * *
1594132 TGGAGATAATATGCTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGAAACTG-CTCCTAC
1 TGGAGATAACACGGTTCCTACGTGATAAGGAAGTCTGGTTATCTAAGGGTGACAC-GACTCCTAC
* * * *
1594196 GTGATGAGGAAATCTGGTCAGTAGATTACACAGTTCCTACGTGATGAGGATGGTTGGCCATCTTT
65 GTGATAAGGAAATCTGGTCAGTGGATGACACGGTTCCTACGTGATGAGGA-GGTTGGCCATCTTT
1594261 AGGGATAA
129 AGGGATAA
* * *
1594269 TGGAGATAACACGGTTTCTACGTGATAAGGAAGTCTGGTTATATAAGGGTGACACGACTTCTACG
1 TGGAGATAACACGGTTCCTACGTGATAAGGAAGTCTGGTTATCTAAGGGTGACACGACTCCTACG
* * ** * * * *
1594334 TGACAAGGAGATCCAGTCAGTGGATGACGCGGTTCCTACGTGATGTGGACGTGTGGCCATCTTCA
66 TGATAAGGAAATCTGGTCAGTGGATGACACGGTTCCTACGTGATGAGGAGGT-TGGCCATCTTTA
1594399 GGGATAAA
130 GGGAT-AA
* * * * * * *
1594407 TGGTGATAACATGGTTCCTACGTGATAAAGATAGT-TGGTTATCTAAGGTTGACTCAACTCCTAT
1 TGGAGATAACACGGTTCCTACGTGATAAGGA-AGTCTGGTTATCTAAGGGTGACACGACTCCTAC
* * * *
1594471 GTGATAAGGACATCTGGTCAGTGGATGACATGATTCCTACGTGATGAGGACGGCTGGCCATCTTT
65 GTGATAAGGAAATCTGGTCAGTGGATGACACGGTTCCTACGTGATGAGGA-GGTTGGCCATCTTT
*
1594536 AGAGATAA
129 AGGGATAA
1594544 T
1 T
1594545 TATTTCAAGA
Statistics
Matches: 228, Mismatches: 43, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
136 3 0.01
137 112 0.49
138 109 0.48
139 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (136 bp):
TGGAGATAACACGGTTCCTACGTGATAAGGAAGTCTGGTTATCTAAGGGTGACACGACTCCTACG
TGATAAGGAAATCTGGTCAGTGGATGACACGGTTCCTACGTGATGAGGAGGTTGGCCATCTTTAG
GGATAA
Done.