Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008656.1 Hibiscus syriacus cultivar Beakdansim tig00111650_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: 2456495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:1056579 original size:15 final size:15
Alignment explanation
Indices: 1056561--1056616 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1056551 TAACCGGTTT
1056561 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
1056576 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
1056593 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
1056608 CGATTTTAA
1 CGGTTTTAA
1056617 TATTCCATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:1056589 original size:17 final size:17
Alignment explanation
Indices: 1056564--1056614 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1056554 CCGGTTTCGG
1056564 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
1056581 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
1056596 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
1056613 TT
1 TT
1056615 AATATTCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:1056809 original size:21 final size:21
Alignment explanation
Indices: 1056785--1056837 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1056775 ACACTTAGGG
1056785 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
1056806 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
1056827 TACCGATTCCC
1 AACCGATTCCC
1056838 CCATGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:1057054 original size:13 final size:13
Alignment explanation
Indices: 1057033--1057087 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1057023 AAGTTCGATA
*
1057033 AATTCAAATACTT
1 AATTGAAATACTT
1057046 AATTGAAATACTT
1 AATTGAAATACTT
* *
1057059 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1057073 AATTGAAATACTT
1 AATTGAAATACTT
1057086 AA
1 AA
1057088 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1057169 original size:32 final size:33
Alignment explanation
Indices: 1057073--1057171 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1057063 AACTCAACAT
* * *
1057073 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1057106 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1057139 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1057171 A
1 A
1057172 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1057190 original size:21 final size:21
Alignment explanation
Indices: 1057166--1057205 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1057156 ACTTCAAGTT
1057166 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1057187 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
1057206 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1059511 original size:12 final size:12
Alignment explanation
Indices: 1059494--1059539 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1059484 TTCGGATAAA
1059494 AACCGGTTTTTT
1 AACCGGTTTTTT
1059506 AACCGGTTTTTTT
1 AACCGG-TTTTTT
1059519 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
1059533 ATCCGGT
1 AACCGGT
1059540 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:1059524 original size:15 final size:14
Alignment explanation
Indices: 1059493--1059532 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1059483 TTTCGGATAA
1059493 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
1059506 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
1059519 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
1059533 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:1060002 original size:42 final size:41
Alignment explanation
Indices: 1059935--1060026 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 41
1059925 AAACAATATA
*
1059935 ATTAAATTATAATATAATATAATATTTGATTAAGAAATAAT
1 ATTAAATTATAATATAAAATAATATTTGATTAAGAAATAAT
* *
1059976 ATTAAATTATAATTATAAAATAATATTTGATTGAGAGATAAT
1 ATTAAATTATAA-TATAAAATAATATTTGATTAAGAAATAAT
*
1060018 ATTCAATTA
1 ATTAAATTA
1060027 CATAAGGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 12 0.26
42 34 0.74
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (41 bp):
ATTAAATTATAATATAAAATAATATTTGATTAAGAAATAAT
Found at i:1061505 original size:16 final size:17
Alignment explanation
Indices: 1061457--1061508 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
1061447 ACAAAAAATG
1061457 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
1061474 GA-TTG-AA-TTACGAGT
1 AATTTGAAAGTTA-GAGT
1061489 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
1061505 AATT
1 AATT
1061509 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 7 0.24
16 13 0.45
17 3 0.10
18 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:1065054 original size:448 final size:446
Alignment explanation
Indices: 1064216--1065113 Score: 1291
Period size: 448 Copynumber: 2.0 Consensus size: 446
1064206 GATGATATAT
* *
1064216 TGATAGATTCGAAACATAAAGAAGAGATTAGAAAGGTGAAAACACAACTTAACAAGGAGTTTAAG
1 TGATAGATGCGAAACATAAAAAAGAGATTAGAAAGGTGAAAACACAACTTAACAAGGAGTTTAAG
* * * *
1064281 ATGAAAGATCTAGGTCATACGAAGAAGATATTTGGAATATAGATCGAAAGAAACTGAAAAACATA
66 ATGAAAGATCCAGGTCATACAAAAAAGATACTTGGAATATAGATCGAAAGAAACTGAAAAACATA
* * * * *
1064346 TAAATTGTACCTAAGTTAAAGGGATATATTGAAAAGTTTCTTTGTAGGTTTAATATGAAGAGTGC
131 TAAATTATACCTAAGTTAAAGAGATACACTGAAAAGTTTCTTTGTAGGTTTAATATGAAGAATGC
* * * *
1064411 GAAGTCTGTGAGCACTCCTCTGGCAGTTCATTTAAGTATTTCATTGGATTGTTCGCCAAAATCAG
196 GAAGTCTATGAGCACTCCTCTGGCAGCTCACTTAAGTATTTCATTAGATTGTTCGCCAAAATCAG
* * *
1064476 ATACAGAGGTAGAGTACATGTCACGTGTTCCATATACTAGTGCATTGTAATCTTTAATGTATGAT
261 ATACAGAGGTAGAGTACATGTCACATGTTCCATATACCAGTGCATTGTAATCTCTAATGTATGAT
* * *
1064541 ATGGTTTGTACGCATCCAAACGTAGCGTACGTAGTTAGTTAAGAGAATAGGTACATGGAAGATCC
326 ATGGTTTGTACGCATCCAAACGTAGCGTACGTAGTCAGTTAAGAGAATAGATAAATGGAAGATCC
* *
1064606 TGGTAAAAAACATTGGAAAGCTATCAAGTGGATTTTCTTGGTATCTTTCCGGTACTAG
391 TGGTAAAAAACATTGGAAAGCTATCAAATGGATTTTC--AGTATCTTTCCGGTACTAG
* *
1064664 TGATAGATGCGAAACATAAAAAAGAGATTAGACAGGTGAAAACATAACTTAACAAGGAGTTTGAA
1 TGATAGATGCGAAACATAAAAAAGAGATTAGAAAGGTGAAAACACAACTTAACAAGGAGTTT-AA
* * * *
1064729 -ATGAAAGATCCAGGTCCTGCAAAAAAGATACTTGGAATATAGATCGGAAGAAACTG-AAAGCAT
65 GATGAAAGATCCAGGTCATACAAAAAAGATACTTGGAATATAGATCGAAAGAAACTGAAAAACAT
* *
1064792 ATAAATTATACCTAAGTTAAAAGAGATACACTGAAAAGTTTCTTTTTAGGTTTAATATGGAGAAT
130 ATAAATTATACCTAAGTT-AAAGAGATACACTGAAAAGTTTCTTTGTAGGTTTAATATGAAGAAT
* *
1064857 GCGAAGTCTATGTGCACTCCTCTGGCAGCTCACTTAAGTATTTCATTAGATTGTTTGCCAAAATC
194 GCGAAGTCTATGAGCACTCCTCTGGCAGCTCACTTAAGTATTTCATTAGATTGTTCGCCAAAATC
** * * *
1064922 AGATGTATAGGTAGTGTACATGTCACATGTTCCATATACCAGTGTATTGTAATCTCTAATGTATG
259 AGATACAGAGGTAGAGTACATGTCACATGTTCCATATACCAGTGCATTGTAATCTCTAATGTATG
* * * *
1064987 ATATGGTTTGTACGTATCCAAACTTAGCGTATGTAGTCAGTTCAA-AGAGTAGATAAAT-GATAG
324 ATATGGTTTGTACGCATCCAAACGTAGCGTACGTAGTCAGTT-AAGAGAATAGATAAATGGA-AG
* * * * *
1065050 ATCCTGGTAAAAAATATTGGAAAGTTGTCAAATGGATTTTCAGTATCTTTGCGGTATTAG
387 ATCCTGGTAAAAAACATTGGAAAGCTATCAAATGGATTTTCAGTATCTTTCCGGTACTAG
1065110 TGAT
1 TGAT
1065114 GTTTACTTAT
Statistics
Matches: 399, Mismatches: 47, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
446 20 0.05
447 25 0.06
448 350 0.88
449 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (446 bp):
TGATAGATGCGAAACATAAAAAAGAGATTAGAAAGGTGAAAACACAACTTAACAAGGAGTTTAAG
ATGAAAGATCCAGGTCATACAAAAAAGATACTTGGAATATAGATCGAAAGAAACTGAAAAACATA
TAAATTATACCTAAGTTAAAGAGATACACTGAAAAGTTTCTTTGTAGGTTTAATATGAAGAATGC
GAAGTCTATGAGCACTCCTCTGGCAGCTCACTTAAGTATTTCATTAGATTGTTCGCCAAAATCAG
ATACAGAGGTAGAGTACATGTCACATGTTCCATATACCAGTGCATTGTAATCTCTAATGTATGAT
ATGGTTTGTACGCATCCAAACGTAGCGTACGTAGTCAGTTAAGAGAATAGATAAATGGAAGATCC
TGGTAAAAAACATTGGAAAGCTATCAAATGGATTTTCAGTATCTTTCCGGTACTAG
Found at i:1075852 original size:23 final size:22
Alignment explanation
Indices: 1075818--1075886 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
1075808 GGAATCGATA
1075818 CCCCTTGAAGGGGAACCGATTC
1 CCCCTTGAAGGGGAACCGATTC
*
1075840 CCCCTTTGAAGGGGAATCGATT-
1 CCCC-TTGAAGGGGAACCGATTC
* *
1075862 CCCCTT--AGGGGAATCGATAC
1 CCCCTTGAAGGGGAACCGATTC
1075882 CCCCT
1 CCCCT
1075887 GGGGTTCTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.28
20 5 0.12
21 2 0.05
22 8 0.19
23 16 0.37
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.22
Consensus pattern (22 bp):
CCCCTTGAAGGGGAACCGATTC
Found at i:1075885 original size:42 final size:44
Alignment explanation
Indices: 1075802--1075886 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 44
1075792 GAATTATAGG
*
1075802 GAAGAGGGAATCGATACCCCTTGAAGGGGAACCGATTCCCCCTTT
1 GAAGAGGGAATCGATACCCCTT-AAGGGGAACCGATACCCCCTTT
* *
1075847 GAAG-GGGAATCGATTCCCCTT-AGGGGAATCGATACCCCCT
1 GAAGAGGGAATCGATACCCCTTAAGGGGAACCGATACCCCCT
1075887 GGGGTTCTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 17 0.46
44 16 0.43
45 4 0.11
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (44 bp):
GAAGAGGGAATCGATACCCCTTAAGGGGAACCGATACCCCCTTT
Found at i:1079328 original size:3 final size:3
Alignment explanation
Indices: 1079312--1079373 Score: 65
Period size: 3 Copynumber: 19.7 Consensus size: 3
1079302 TTTTACTTTA
1079312 ATT ATT ACTT -TT ATT ATT ATT ATT ATT ATT ATTT ATAT ATAT ATT A-T
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T AT-T ATT ATT
1079359 ATGT ATT ATT ATT AT
1 AT-T ATT ATT ATT AT
1079374 AAATAAATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.08
3 34 0.64
4 15 0.28
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1080327 original size:26 final size:24
Alignment explanation
Indices: 1080295--1080372 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 24
1080285 TACAAGTTTT
*
1080295 ATTATTATATTTTTACTATAGTTTGA
1 ATTATTATATTTTTA-TAT-GTTTAA
1080321 ATTATTAT-TGTTTTAGTTATTGTTTAA
1 ATTATTATAT-TTTTA--TA-TGTTTAA
*
1080348 ATATATTTTATTTTTATATGTTTAA
1 AT-TATTATATTTTTATATGTTTAA
1080373 TATTTTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
25 8 0.18
26 15 0.34
27 9 0.20
28 11 0.25
29 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.08, T:0.62
Consensus pattern (24 bp):
ATTATTATATTTTTATATGTTTAA
Found at i:1080459 original size:16 final size:16
Alignment explanation
Indices: 1080440--1080470 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1080430 ATTTTTATTA
1080440 ATATATATTATTTTAT
1 ATATATATTATTTTAT
1080456 ATATATATTATTTTA
1 ATATATATTATTTTA
1080471 AACATGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATATATTATTTTAT
Found at i:1082857 original size:8 final size:8
Alignment explanation
Indices: 1082844--1082882 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
1082834 TTATATTTAC
1082844 ATTTGCAT
1 ATTTGCAT
1082852 ATTTGCAT
1 ATTTGCAT
1082860 ATTTGCAT
1 ATTTGCAT
1082868 -TTTGCAT
1 ATTTGCAT
*
1082875 CTTTGCAT
1 ATTTGCAT
1082883 TTATACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (8 bp):
ATTTGCAT
Found at i:1082873 original size:15 final size:15
Alignment explanation
Indices: 1082844--1082884 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1082834 TTATATTTAC
1082844 ATTTGCATATTTGCAT
1 ATTTGCAT-TTTGCAT
1082860 ATTTGCATTTTGCAT
1 ATTTGCATTTTGCAT
*
1082875 CTTTGCATTT
1 ATTTGCATTT
1082885 ATACTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.54
Consensus pattern (15 bp):
ATTTGCATTTTGCAT
Found at i:1082992 original size:35 final size:34
Alignment explanation
Indices: 1082937--1083004 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
1082927 ATTCGCATAT
*
1082937 TTACATTTGCATTTGCATTTTGCATTTTTGCATTC
1 TTACATTTGCATTTACATTTT-CATTTTTGCATTC
* *
1082972 TTACGTTTGTATTTACATTTTCATTTTTGCATT
1 TTACATTTGCATTTACATTTTCATTTTTGCATT
1083005 TCCATATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.57
Consensus pattern (34 bp):
TTACATTTGCATTTACATTTTCATTTTTGCATTC
Found at i:1083015 original size:34 final size:32
Alignment explanation
Indices: 1082941--1083032 Score: 87
Period size: 35 Copynumber: 2.7 Consensus size: 32
1082931 GCATATTTAC
* * *
1082941 ATTTGCATTTGCATTTTGCATTTTTGCATTCTT
1 ATTTGTATTTACATTTT-CATTTTTGCATTCAT
1082974 ACGTTTGTATTTACATTTTCATTTTTGCATTTCCAT
1 A--TTTGTATTTACATTTTCATTTTTGCA-TT-CAT
1083010 ATTTGTATAATTACATTTT-ATTT
1 ATTTGTAT--TTACATTTTCATTT
1083033 CAAACTATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
33 1 0.02
34 17 0.34
35 20 0.40
36 12 0.24
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.58
Consensus pattern (32 bp):
ATTTGTATTTACATTTTCATTTTTGCATTCAT
Found at i:1085527 original size:8 final size:8
Alignment explanation
Indices: 1085516--1085568 Score: 99
Period size: 8 Copynumber: 6.8 Consensus size: 8
1085506 AAAACAAAAA
1085516 AAAAAAGG
1 AAAAAAGG
1085524 -AAAAAGG
1 AAAAAAGG
1085531 AAAAAAGG
1 AAAAAAGG
1085539 AAAAAAGG
1 AAAAAAGG
1085547 AAAAAAGG
1 AAAAAAGG
1085555 AAAAAAGG
1 AAAAAAGG
1085563 AAAAAA
1 AAAAAA
1085569 TTGAATCATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.16
8 37 0.84
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1090029 original size:52 final size:53
Alignment explanation
Indices: 1089968--1090087 Score: 172
Period size: 52 Copynumber: 2.3 Consensus size: 53
1089958 AGAAAAAGAG
* *
1089968 GAATGTGTTGTCAAAAGTTTTATGAACATCT-AGGCAGAAACCACATGAGAT-T
1 GAATGTGTTGTCAAAAGTTTTATGAACATCTGA-GCAGAAACCACAAGAAATAT
* *
1090020 GAATGTGTTGTCAAAAGTTTTATGAGCATCTGAGCAGAAGCCACAAGAAATGAT
1 GAATGTGTTGTCAAAAGTTTTATGAACATCTGAGCAGAAACCACAAGAAAT-AT
1090074 GAATGTGTTGTCAA
1 GAATGTGTTGTCAA
1090088 GTGTTTTAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
52 45 0.74
53 1 0.02
54 15 0.25
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (53 bp):
GAATGTGTTGTCAAAAGTTTTATGAACATCTGAGCAGAAACCACAAGAAATAT
Found at i:1092751 original size:73 final size:73
Alignment explanation
Indices: 1092659--1093124 Score: 824
Period size: 73 Copynumber: 6.4 Consensus size: 73
1092649 CTATTTCCAA
* *
1092659 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1092724 CTCAGGGT
66 CTCAGGGT
*
1092732 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGT
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1092797 CTCAGGGT
66 CTCAGGGT
1092805 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
*
1092870 CTTAGGGT
66 CTCAGGGT
* * *
1092878 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCTGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1092943 CTCAGGGT
66 CTCAGGGT
* *
1092951 CATCTATAAGACCTACAGTGTATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1093016 CTCAGGGT
66 CTCAGGGT
*
1093024 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAAGCCTTAGGGAGCTTTTTGATTTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATTTTAAAG
1093089 CCTCAGGGT
65 CCTCAGGGT
*
1093098 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
1093125 ATAAGACCTC
Statistics
Matches: 374, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
73 308 0.82
74 66 0.18
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGT
Found at i:1094771 original size:32 final size:32
Alignment explanation
Indices: 1094721--1094783 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1094711 TAAATATAGT
* *
1094721 TTATTTTTATATGTTTAATATTT-TAAATTAAA
1 TTATTATTATATGATTAAT-TTTATAAATTAAA
*
1094753 TTATTATTATTTGATTAATTTTATAAATTAA
1 TTATTATTATATGATTAATTTTATAAATTAA
1094784 TAATAATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (32 bp):
TTATTATTATATGATTAATTTTATAAATTAAA
Found at i:1094781 original size:27 final size:28
Alignment explanation
Indices: 1094747--1094819 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
1094737 AATATTTTAA
1094747 ATTAAATTATTATTATTTGATTAATTTT
1 ATTAAATTATTATTATTTGATTAATTTT
* * * * *
1094775 A-TAAATTAATAATAATTGTTTATTTTT
1 ATTAAATTATTATTATTTGATTAATTTT
1094802 ATTAATATATATTATTAT
1 ATTAA-AT-TATTATTAT
1094820 ATATATATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
27 22 0.65
28 4 0.12
29 2 0.06
30 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
ATTAAATTATTATTATTTGATTAATTTT
Found at i:1099216 original size:17 final size:17
Alignment explanation
Indices: 1099194--1099251 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 17
1099184 GTTGAACAAG
1099194 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
1099211 TTCTTCTCCCTCTATTGGATGAC
1 TTCTTCT-CAT-TA-T-GA--AC
1099234 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
1099251 T
1 T
1099252 CTCCATTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 10 0.30
18 2 0.06
19 4 0.12
20 2 0.06
21 4 0.12
22 2 0.06
23 9 0.27
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:1099342 original size:136 final size:128
Alignment explanation
Indices: 1099154--1099398 Score: 339
Period size: 136 Copynumber: 1.9 Consensus size: 128
1099144 GAGGTATTGC
* * *
1099154 TGATTCGAAATGTCGTGAATCAAGCAATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 TGATTCGAAATGTCATGAATCAAGCAATAGGCTGAACAAGTTCTTCTCATTATGAAATTC--CTC
1099219 CCTCTATTGGATGACTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATACCTTAAGCGAGG
64 CCTC-A---GATGACTTC-T-TCATTATGAACTCTCCATTGGAAATGTTAATACCTTAAGCGAGG
1099284 TGTTAT
123 TGTTAT
*
1099290 TGATTCGAAATGTCATGAATCAAGCAATAGGCCT-AACAAGTTCTTCTCATTATGAAATTCCTCT
1 TGATTCGAAATGTCATGAATCAAGCAATAGG-CTGAACAAGTTCTTCTCATTATGAAATTCCTCC
* * *
1099354 GTCAGATGAGTTCTTCATTATGAACTCTCTATTGGAAATGTTAAT
65 CTCAGATGACTTCTTCATTATGAACTCTCCATTGGAAATGTTAAT
1099399 TGGTTTACCA
Statistics
Matches: 101, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
128 30 0.30
129 1 0.01
130 8 0.08
133 1 0.01
134 5 0.05
136 55 0.54
137 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (128 bp):
TGATTCGAAATGTCATGAATCAAGCAATAGGCTGAACAAGTTCTTCTCATTATGAAATTCCTCCC
TCAGATGACTTCTTCATTATGAACTCTCCATTGGAAATGTTAATACCTTAAGCGAGGTGTTAT
Found at i:1100420 original size:13 final size:13
Alignment explanation
Indices: 1100399--1100437 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1100389 TGAACCTCTC
1100399 TTTTT-CTTTTCT
1 TTTTTCCTTTTCT
1100411 TTTTTCCTTTTCT
1 TTTTTCCTTTTCT
*
1100424 TTTTTCTTTTTCT
1 TTTTTCCTTTTCT
1100437 T
1 T
1100438 AGGCGTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTCCTTTTCT
Found at i:1106925 original size:31 final size:31
Alignment explanation
Indices: 1106890--1106961 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
1106880 GTTCCGGAGA
* * *
1106890 ACATAGGTAATCTGTCCATATGT-TCTAAATG
1 ACATAGGTAAACTATCCATATGTCTCGAAA-G
1106921 ACATAGGTAAACTATCCATATGTCTCGAAAG
1 ACATAGGTAAACTATCCATATGTCTCGAAAG
1106952 ACATAGGTAA
1 ACATAGGTAA
1106962 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (31 bp):
ACATAGGTAAACTATCCATATGTCTCGAAAG
Found at i:1108666 original size:17 final size:17
Alignment explanation
Indices: 1108644--1108677 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1108634 TCCAAGTCAG
1108644 TAAAATAGGGCTTCTTT
1 TAAAATAGGGCTTCTTT
1108661 TAAAATAGGGCTTCTTT
1 TAAAATAGGGCTTCTTT
1108678 GACCCTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
TAAAATAGGGCTTCTTT
Found at i:1110971 original size:56 final size:56
Alignment explanation
Indices: 1110885--1110998 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
1110875 ATCTGAGAAA
1110885 CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCAGATTTTTTCTCTCAAAAG
1 CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCAGATTTTTTCTCTCAAAAG
1110941 CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCAGATTTTTTCTCTCAAAAG
1 CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCAGATTTTTTCTCTCAAAAG
1110997 CT
1 CT
1110999 CGACCTCAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.21, C:0.29, G:0.05, T:0.45
Consensus pattern (56 bp):
CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCAGATTTTTTCTCTCAAAAG
Found at i:1116260 original size:28 final size:29
Alignment explanation
Indices: 1116214--1116268 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
1116204 AAAAATTGAC
1116214 TACAATCCAAGTTTGATGTTAACTTGTAT
1 TACAATCCAAGTTTGATGTTAACTTGTAT
*
1116243 TACAATCCGA-TTTGATGTTAACTTGT
1 TACAATCCAAGTTTGATGTTAACTTGT
1116269 TTATGGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (29 bp):
TACAATCCAAGTTTGATGTTAACTTGTAT
Found at i:1116338 original size:26 final size:26
Alignment explanation
Indices: 1116309--1116360 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1116299 AGATCATATT
*
1116309 TTATCATATCTCAGTCATCAAGTTAA
1 TTATCATATCTCAGTCAGCAAGTTAA
1116335 TTATCATATCTCAGTCAGCAAGTTAA
1 TTATCATATCTCAGTCAGCAAGTTAA
1116361 CATCCAGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (26 bp):
TTATCATATCTCAGTCAGCAAGTTAA
Found at i:1116960 original size:6 final size:6
Alignment explanation
Indices: 1116949--1116974 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1116939 AAACCCAAAT
1116949 AGGGAA AGGGAA AGGGAA AGGGAA AG
1 AGGGAA AGGGAA AGGGAA AGGGAA AG
1116975 CCACTTAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:1117241 original size:3 final size:3
Alignment explanation
Indices: 1117233--1117261 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1117223 TTTTCAACTA
1117233 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1117262 CAAATAAATA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1121368 original size:81 final size:80
Alignment explanation
Indices: 1121283--1121477 Score: 216
Period size: 80 Copynumber: 2.4 Consensus size: 80
1121273 TAAAATGATA
* *
1121283 ACTTTAGCGGTGTTTTTATACAAATGCCACTATA-GGTTCATC-AGTAGTGGCATTTTTCAACAA
1 ACTTTAGAGGCGTTTTTATACAAATGCCACTATAGGGTTCATCTA-TAGTGGCA-TTTT-AACAA
* * *
1121346 ACGTCATGATAGAGTAGT
63 ACATCATAACAGAGTAGT
* * * *
1121364 ACTTTAGAAGCGTTTATATAAAAATGCCA-TAATAGGGTTCATCTATAGTGGTATTTTAACAAAC
1 ACTTTAGAGGCGTTTTTATACAAATGCCACT-ATAGGGTTCATCTATAGTGGCATTTTAACAAAC
*
1121428 ATCGTAACAGAGTAGT
65 ATCATAACAGAGTAGT
* * *
1121444 ACTTTAGTGGCATTTTTATACAAATGCCGCTATA
1 ACTTTAGAGGCGTTTTTATACAAATGCCACTATA
1121478 AACTCATACT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
80 46 0.49
81 32 0.34
82 15 0.16
83 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (80 bp):
ACTTTAGAGGCGTTTTTATACAAATGCCACTATAGGGTTCATCTATAGTGGCATTTTAACAAACA
TCATAACAGAGTAGT
Found at i:1121514 original size:40 final size:40
Alignment explanation
Indices: 1121443--1121582 Score: 145
Period size: 40 Copynumber: 3.4 Consensus size: 40
1121433 AACAGAGTAG
* * *
1121443 TACTTTAGTGGCATTTTTATACAAATGCCGCTATAAACTCA
1 TACTTTAGTGGC-GTTTTATACAAACGCCGCTATAGACTCA
* * *
1121484 TACTTTAATGGCGTTTTATACAAACACCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTATACAAACGCCGCTATAGACTCA
* ** * *
1121524 TATTTTAGTGATGTTTATGTTTAAAAACGCCGCTATAGACTCA
1 TACTTTAGTGGCG-TT-T-TATACAAACGCCGCTATAGACTCA
1121567 TACTTTAGTGGCGTTT
1 TACTTTAGTGGCGTTT
1121583 GTATTTTAAA
Statistics
Matches: 79, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
40 32 0.41
41 14 0.18
42 3 0.04
43 30 0.38
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (40 bp):
TACTTTAGTGGCGTTTTATACAAACGCCGCTATAGACTCA
Found at i:1121594 original size:43 final size:42
Alignment explanation
Indices: 1121470--1121601 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 42
1121460 TATACAAATG
* *
1121470 CCGCTATAAACTCATACTTTAATGGCGTTTTA---TACAAACA
1 CCGCTATAGACTCATACTTTAGTGGCGTTTTATTTTA-AAACA
* * ** *
1121510 CCGCTATAGACTCGTATTTTAGTGATG-TTTATGTTTAAAAACG
1 CCGCTATAGACTCATACTTTAGTGGCGTTTTAT-TTT-AAAACA
1121553 CCGCTATAGACTCATACTTTAGTGGCGTTTGTATTTTAAAACA
1 CCGCTATAGACTCATACTTTAGTGGCGTTT-TATTTTAAAACA
1121596 CCGCTA
1 CCGCTA
1121602 AAGTTTAAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
39 4 0.05
40 21 0.29
43 39 0.53
44 6 0.08
45 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (42 bp):
CCGCTATAGACTCATACTTTAGTGGCGTTTTATTTTAAAACA
Found at i:1132553 original size:28 final size:28
Alignment explanation
Indices: 1132467--1132591 Score: 96
Period size: 28 Copynumber: 4.5 Consensus size: 28
1132457 ATGACTAAAC
* * * *
1132467 ACCTCTGTGCTTCAATTTAGAATCTGGT
1 ACCTCTGTGCTTTAATATAAAATCTGGA
* ** *
1132495 ACCTCTGTGCTTT-CTA-ATGAT-TGAGC
1 ACCTCTGTGCTTTAATATAAAATCTG-GA
* *
1132521 ACCTCTGTGCTTTAATATAAGATTTGGA
1 ACCTCTGTGCTTTAATATAAAATCTGGA
* *
1132549 ACCTCTGTGCTTCAATATAAAATCTGGC
1 ACCTCTGTGCTTTAATATAAAATCTGGA
1132577 ACCT-TAGTGCTTTAA
1 ACCTCT-GTGCTTTAA
1132592 AATTGATTGA
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
25 2 0.03
26 17 0.22
27 4 0.05
28 53 0.68
29 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (28 bp):
ACCTCTGTGCTTTAATATAAAATCTGGA
Found at i:1132555 original size:82 final size:83
Alignment explanation
Indices: 1132467--1132643 Score: 218
Period size: 83 Copynumber: 2.1 Consensus size: 83
1132457 ATGACTAAAC
* * * ** *
1132467 ACCTCTGTGCTTCAATTTAGAATCTGGTACCTCT-GTGCTTTCTAA-TGATTGAGCACCTCTGTG
1 ACCTCTGTGCTTCAATATAAAATCTGGCACCT-TAGTGCTTTAAAATTGATTGAGCACCTCCGTG
* *
1132530 CT-TTAATATA-AGATTTGGA
65 -TATCAATATAGAG-TATGGA
1132549 ACCTCTGTGCTTCAATATAAAATCTGGCACCTTAGTGCTTTAAAATTGATTGAGCACCTCCGTGT
1 ACCTCTGTGCTTCAATATAAAATCTGGCACCTTAGTGCTTTAAAATTGATTGAGCACCTCCGTGT
*
1132614 ATCAATATAGAGTATGGC
66 ATCAATATAGAGTATGGA
1132632 ACCTCTGTGCTT
1 ACCTCTGTGCTT
1132644 TTGATAAACG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
81 1 0.01
82 39 0.48
83 40 0.49
84 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (83 bp):
ACCTCTGTGCTTCAATATAAAATCTGGCACCTTAGTGCTTTAAAATTGATTGAGCACCTCCGTGT
ATCAATATAGAGTATGGA
Found at i:1132641 original size:83 final size:82
Alignment explanation
Indices: 1132466--1132643 Score: 218
Period size: 82 Copynumber: 2.2 Consensus size: 82
1132456 AATGACTAAA
* * * ** *
1132466 CACCTCTGTGCTTCAATTTAGAATCTGGTACCTCTGTGCTTTCTAATGATTGAGCACCTCTGTGC
1 CACCTCTGTGCTTCAATATAAAATCTGGCACCTCTGTGCTTTAAAATGATTGAGCACCTCCGTGC
* *
1132531 TTTAATATAAGATTTGG
66 TTCAATATAAGATATGG
*
1132548 AACCTCTGTGCTTCAATATAAAATCTGGCACCT-TAGTGCTTTAAAATTGATTGAGCACCTCCGT
1 CACCTCTGTGCTTCAATATAAAATCTGGCACCTCT-GTGCTTTAAAA-TGATTGAGCACCTCCGT
1132612 G-TATCAATAT-AGAGTATGG
64 GCT-TCAATATAAGA-TATGG
1132631 CACCTCTGTGCTT
1 CACCTCTGTGCTT
1132644 TTGATAAACG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
81 1 0.01
82 42 0.51
83 39 0.48
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (82 bp):
CACCTCTGTGCTTCAATATAAAATCTGGCACCTCTGTGCTTTAAAATGATTGAGCACCTCCGTGC
TTCAATATAAGATATGG
Found at i:1136124 original size:29 final size:29
Alignment explanation
Indices: 1136092--1136166 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
1136082 ATAATTGACT
1136092 AAAGCAATAAGTGAGGGAAATTATTGAAC
1 AAAGCAATAAGTGAGGGAAATTATTGAAC
1136121 AAAGCAATAAGTGAGGGAAATTATTGAAC
1 AAAGCAATAAGTGAGGGAAATTATTGAAC
1136150 AAAGCAATAAGTGAGGG
1 AAAGCAATAAGTGAGGG
1136167 GTAAGCTTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.48, C:0.07, G:0.27, T:0.19
Consensus pattern (29 bp):
AAAGCAATAAGTGAGGGAAATTATTGAAC
Found at i:1140008 original size:46 final size:46
Alignment explanation
Indices: 1139898--1140052 Score: 225
Period size: 46 Copynumber: 3.5 Consensus size: 46
1139888 TTTATTGGTT
*
1139898 ATTAAATGGTAAG--TA-T-GT-AAATAAGCTTACGAGATTATGGA
1 ATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
* *
1139939 A-T-AATGGAAAATATATTGGTAAAATAAGCTTACGAGCTTATGGA
1 ATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
*
1139983 ATTAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGA
1 ATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
1140029 ATTAAATGGTAAGTATATTGGTAA
1 ATTAAATGGTAAGTATATTGGTAA
1140053 CATCATTTTA
Statistics
Matches: 101, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
39 7 0.07
40 1 0.01
41 3 0.03
42 1 0.01
43 2 0.02
44 23 0.23
45 1 0.01
46 63 0.62
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (46 bp):
ATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
Found at i:1142686 original size:21 final size:20
Alignment explanation
Indices: 1142661--1142699 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1142651 TTATGATAAA
1142661 CTATCA-AAGTATGAGTTTTGG
1 CTATCAGAAGT-TGA-TTTTGG
1142682 CTATCAGAAGTTGATTTT
1 CTATCAGAAGTTGATTTT
1142700 CTTAGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CTATCAGAAGTTGATTTTGG
Found at i:1142792 original size:4 final size:5
Alignment explanation
Indices: 1142738--1142804 Score: 57
Period size: 5 Copynumber: 12.8 Consensus size: 5
1142728 TAAGAGCTAA
* *
1142738 AAAAG AATA- AAAAG AAAAAG AAAACG AAGAAG AAAA- AAAAC AAATAG
1 AAAAG AAAAG AAAAG -AAAAG AAAA-G AA-AAG AAAAG AAAAG AAA-AG
1142785 AGAAAG AAAAG AAAAG AAAA
1 A-AAAG AAAAG AAAAG AAAA
1142805 AGAGAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
4 7 0.13
5 25 0.48
6 16 0.31
7 4 0.08
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:1142808 original size:22 final size:22
Alignment explanation
Indices: 1142747--1142816 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
1142737 AAAAAGAATA
*
1142747 AAAAGAAAAAGAAAACGA-AGAAG
1 AAAAG-AAAAGAAAAAGAGA-AAG
* *
1142770 AAAA-AAAACAAATAGAGAAAG
1 AAAAGAAAAGAAAAAGAGAAAG
*
1142791 AAAAGAAAAGAAAAAGAGAAAA
1 AAAAGAAAAGAAAAAGAGAAAG
1142813 AAAA
1 AAAA
1142817 TTCACTTGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 16 0.41
22 19 0.49
23 4 0.10
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (22 bp):
AAAAGAAAAGAAAAAGAGAAAG
Found at i:1146930 original size:93 final size:90
Alignment explanation
Indices: 1146738--1146965 Score: 352
Period size: 93 Copynumber: 2.5 Consensus size: 90
1146728 GTAAGTATGC
* *
1146738 AAATAAGCTTACGAGCTTATGGAA-T-AATGGCAAGTATATTGGTAAGATAAGCTTACGAGCATA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCATA
1146801 TGGAATAATGGAAAGTATATTGGTA
66 TGGAATAATGGAAAGTATATTGGTA
* *
1146826 AGATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTTGGTAAAATAAGCTTACGAGCTT
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATA-TTGGTAAAATAAGCTTACGAGCAT
*
1146891 ATGGAATTAAATGGTAAGTATATTGGTA
65 ATGGAA-T-AATGGAAAGTATATTGGTA
* *
1146919 AAATAAGCTTACAAGCTTATGGAATTAAATGATAAGTATATTGGTAA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTAA
1146966 CATGATTTTA
Statistics
Matches: 127, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
88 23 0.18
89 1 0.01
90 12 0.09
91 28 0.22
92 8 0.06
93 55 0.43
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCATA
TGGAATAATGGAAAGTATATTGGTA
Found at i:1146936 original size:46 final size:46
Alignment explanation
Indices: 1146738--1146965 Score: 356
Period size: 44 Copynumber: 5.0 Consensus size: 46
1146728 GTAAGTATGC
*
1146738 AAATAAGCTTACGAGCTTATGGAA-T-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
* * *
1146782 AGATAAGCTTACGAGCATATGGAA-T-AATGGAAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
*
1146826 AGATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATA-TTGGTA
1146873 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
* *
1146919 AAATAAGCTTACAAGCTTATGGAATTAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1146965 A
1 A
1146966 CATGATTTTA
Statistics
Matches: 173, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
44 64 0.37
45 1 0.01
46 63 0.36
47 45 0.26
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
Found at i:1147367 original size:22 final size:22
Alignment explanation
Indices: 1147342--1147388 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1147332 TTCCAGAATG
*
1147342 CTACAAGGGTATCGATACCCT-A
1 CTAC-AGGGTACCGATACCCTCA
*
1147364 CTACAGTGTACCGATACCCTCA
1 CTACAGGGTACCGATACCCTCA
1147386 CTA
1 CTA
1147389 TTCACTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (22 bp):
CTACAGGGTACCGATACCCTCA
Found at i:1148811 original size:17 final size:18
Alignment explanation
Indices: 1148779--1148817 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1148769 GAATTCAATT
*
1148779 TAAAGATTACATTTAATA
1 TAAACATTACATTTAATA
*
1148797 TAAACATTA-ATTTAATT
1 TAAACATTACATTTAATA
1148814 TAAA
1 TAAA
1148818 AATAAACTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAACATTACATTTAATA
Found at i:1149153 original size:27 final size:27
Alignment explanation
Indices: 1149123--1149204 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
1149113 ACTTTAACTT
*
1149123 TCTTATCTTCTTCCTCTTCTTTCTTTC
1 TCTTTTCTTCTTCCTCTTCTTTCTTTC
** * *
1149150 TCTTTTC-TCTTATTTCTTCCTCCTTTC
1 TCTTTTCTTCTT-CCTCTTCTTTCTTTC
1149177 TCTTCTTTCTTCTTCC-CTTCTTTCTTTC
1 TC-T-TTTCTTCTTCCTCTTCTTTCTTTC
1149205 ACTCCCGGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
26 4 0.10
27 19 0.45
28 11 0.26
29 4 0.10
30 4 0.10
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (27 bp):
TCTTTTCTTCTTCCTCTTCTTTCTTTC
Found at i:1149165 original size:20 final size:20
Alignment explanation
Indices: 1149136--1149204 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1149126 TATCTTCTTC
* *
1149136 CTCTTCTTTCTTTCTCTTTT
1 CTCTTCTTTCTTCCTCCTTT
*
1149156 CTCTTATTTCTTCCTCCTTT
1 CTCTTCTTTCTTCCTCCTTT
* *
1149176 CTCTTCTTTCTTCTTCCCTT
1 CTCTTCTTTCTTCCTCCTTT
1149196 CT-TTCTTTC
1 CTCTTCTTTC
1149205 ACTCCCGGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 7 0.16
20 36 0.84
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (20 bp):
CTCTTCTTTCTTCCTCCTTT
Found at i:1150947 original size:3 final size:3
Alignment explanation
Indices: 1150939--1150988 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
1150929 GTTTTTAATA
* * *
1150939 TAT TAT TAT AAT TAT TAT TAT TAA TAT TAT TAT T-T AAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1150985 TAT T
1 TAT T
1150989 TTCTTGTAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 3 0.08
3 36 0.92
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1150976 original size:26 final size:26
Alignment explanation
Indices: 1150933--1150983 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1150923 TGTCCCGTTT
1150933 TTAATATATTATTATAATTATTATTA
1 TTAATATATTATTATAATTATTATTA
1150959 TTAATATTATTATT-TAATTATTATT
1 TTAATA-TATTATTATAATTATTATT
1150984 TTATTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTAATATATTATTATAATTATTATTA
Found at i:1150986 original size:12 final size:12
Alignment explanation
Indices: 1150931--1150986 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 12
1150921 TTTGTCCCGT
1150931 TTTTAATATATTA
1 TTTTAAT-TATTA
*
1150944 TTATAATTATTA
1 TTTTAATTATTA
1150956 TTATTAA-TATTA
1 TT-TTAATTATTA
1150968 TTATTTAATTATTA
1 -T-TTTAATTATTA
1150982 TTTTA
1 TTTTA
1150987 TTTTCTTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 16 0.43
13 15 0.41
14 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAATTATTA
Found at i:1153947 original size:2 final size:2
Alignment explanation
Indices: 1153940--1153975 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1153930 AAATAAATAA
1153940 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
1153976 TTACATGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1155480 original size:3 final size:3
Alignment explanation
Indices: 1155474--1155535 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
1155464 TAATATTTAT
1155474 TAA TAA TAA -AA -AA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1155519 -AA -AA T-A TAAA TAA TAA T
1 TAA TAA TAA T-AA TAA TAA T
1155536 CAAATGAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 12 0.22
3 40 0.74
4 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1155931 original size:123 final size:122
Alignment explanation
Indices: 1155753--1156007 Score: 386
Period size: 123 Copynumber: 2.1 Consensus size: 122
1155743 TAATCTAGCA
1155753 AAAAGTTGATACTGATCTATCTCCTTCTATGATAGAATCAAATAAAGGTTGAACAAGTTCTTCTC
1 AAAAGTTGATACTGATCTATCTCCTTCTATGATAGAATCAAATAAAGGTTGAACAAGTTCTTCTC
* * *
1155818 ATTATGAACTTCTTCTTCCTTTTCAAATAAGTTCTTCTTATTACAAACTTTCTCTGG
66 ATTATGAACTTCTTCTTCATCTTCAAATAAGTTCTTCTTAGTACAAACTTTCTCTGG
** * * *
1155875 AAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCA-AAAGGTTGAACAAGTTCTTC
1 AAAAGTTGATACTGATCTATCTCCTTCTATGATAGAATCA--AATAAAGGTTGAACAAGTTCTTC
* **
1155939 TCATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTTAGTATGAACTTTCTCTGG
64 TCATTATGAACTTCTTCTTCATCTTCAAATAAGTTCTTCTTAGTACAAACTTTCTCTGG
1155998 AAAAGTTGAT
1 AAAAGTTGAT
1156008 CCATCGAGTG
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
122 36 0.30
123 83 0.69
124 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (122 bp):
AAAAGTTGATACTGATCTATCTCCTTCTATGATAGAATCAAATAAAGGTTGAACAAGTTCTTCTC
ATTATGAACTTCTTCTTCATCTTCAAATAAGTTCTTCTTAGTACAAACTTTCTCTGG
Found at i:1156110 original size:112 final size:112
Alignment explanation
Indices: 1155916--1156351 Score: 705
Period size: 112 Copynumber: 3.9 Consensus size: 112
1155906 ATAGAGTCAT
* * *
1155916 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CATCTTCAGATAAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
1155980 AGTATGAACTTTCT-CTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAAC--TCTACTGGAAATGCTGATCCATCGAATGATGAATTCGA
* * *
1156028 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTTCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1156093 ATTATGAACTCTACTGGAAATGTTGATCCATCGAATGATGAATTCGA
66 ATTATGAACTCTACTGGAAATGCTGATCCATCGAATGATGAATTCGA
1156140 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1156205 ATTATGAACTCTACTGGAAATGCTGATCCATCGAATGATGAATTCGA
66 ATTATGAACTCTACTGGAAATGCTGATCCATCGAATGATGAATTCGA
*
1156252 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1156317 ATTATGAACTCTACCTGGCAATGCTGATCCATCGA
66 ATTATGAACTCTA-CTGGAAATGCTGATCCATCGA
1156352 GGGATGGGTT
Statistics
Matches: 306, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
111 3 0.01
112 257 0.84
113 46 0.15
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTACTGGAAATGCTGATCCATCGAATGATGAATTCGA
Found at i:1157940 original size:18 final size:17
Alignment explanation
Indices: 1157905--1157958 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 17
1157895 TTCATTCATT
1157905 TTTTTCTTTTTTCTTTCA-
1 TTTTT-TTTTTTC-TTCAC
1157923 TTTCATTTTTTTTCTTCAC
1 TTT--TTTTTTTTCTTCAC
1157942 TTTTTTTTTCTTCTTCA
1 TTTTTTTTT-TTCTTCA
1157959 AGCATAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.19
18 14 0.44
19 10 0.31
20 2 0.06
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTTTTTCTTCAC
Found at i:1157944 original size:24 final size:24
Alignment explanation
Indices: 1157894--1157944 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1157884 TATTTTATCA
* **
1157894 TTTCATTCATTTTTTTCTTTTTTC
1 TTTCATTCATTTTTTTCTCTTCAC
1157918 TTTCATTTCATTTTTTT-TCTTCAC
1 TTTCA-TTCATTTTTTTCTCTTCAC
1157942 TTT
1 TTT
1157945 TTTTTTCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTCATTCATTTTTTTCTCTTCAC
Found at i:1161478 original size:22 final size:21
Alignment explanation
Indices: 1161434--1161478 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1161424 AATCAGACAT
* **
1161434 ATTTATGAAAGAATATAGTGA
1 ATTTATGAAAAAATATAAAGA
1161455 ATTTATGAAATAAATATAAAGA
1 ATTTATGAAA-AAATATAAAGA
1161477 AT
1 AT
1161479 GGAAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (21 bp):
ATTTATGAAAAAATATAAAGA
Found at i:1164984 original size:38 final size:38
Alignment explanation
Indices: 1164934--1165014 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
1164924 TTTCATAAAT
1164934 TTTTCCAATGGTAGCTTGCTTCATGAGCATATCCTCTA
1 TTTTCCAATGGTAGCTTGCTTCATGAGCATATCCTCTA
*
1164972 TTTTCCAATGGTAGCTTGCTTCCTGAGCATATCCTCTA
1 TTTTCCAATGGTAGCTTGCTTCATGAGCATATCCTCTA
1165010 TTTTC
1 TTTTC
1165015 TGCATCATAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.42
Consensus pattern (38 bp):
TTTTCCAATGGTAGCTTGCTTCATGAGCATATCCTCTA
Found at i:1165314 original size:15 final size:15
Alignment explanation
Indices: 1165294--1165325 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1165284 TGCAATAAAT
1165294 AATGAATGTATGCAA
1 AATGAATGTATGCAA
1165309 AATGAATGTATGCAA
1 AATGAATGTATGCAA
1165324 AA
1 AA
1165326 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1168596 original size:28 final size:26
Alignment explanation
Indices: 1168541--1168598 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
1168531 AATAAAAATA
* *
1168541 AAAATAATATATATATATATATTATG
1 AAAATAATATATATATAAAAATTATG
*
1168567 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TATATATAAAAATTATG
1168595 AAAA
1 AAAA
1168599 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (26 bp):
AAAATAATATATATATAAAAATTATG
Found at i:1169429 original size:2 final size:2
Alignment explanation
Indices: 1169418--1169453 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1169408 AAATAAATAA
1169418 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1169454 CATGACTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1170983 original size:12 final size:12
Alignment explanation
Indices: 1170968--1171027 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
1170958 AAAAGTATAA
1170968 TAATAATAATTT
1 TAATAATAATTT
1170980 TAATAATTTTAATTT
1 TAATAA---TAATTT
* *
1170995 TAATTATAATTA
1 TAATAATAATTT
*
1171007 TAATAA-AATAT
1 TAATAATAATTT
*
1171018 AAATAATAAT
1 TAATAATAAT
1171028 CAAATGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
11 8 0.21
12 19 0.50
15 11 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:1170983 original size:15 final size:15
Alignment explanation
Indices: 1170936--1171004 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
1170926 CCTGTAATAT
*
1170936 ATAATAATATTTATTA
1 ATAATAATAATT-TTA
* * *
1170952 ATAATAAAAAGTATA
1 ATAATAATAATTTTA
1170967 ATAATAATAATTTTA
1 ATAATAATAATTTTA
**
1170982 ATAATTTTAATTTTA
1 ATAATAATAATTTTA
*
1170997 ATTATAAT
1 ATAATAAT
1171005 TATAATAAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
15 32 0.78
16 9 0.22
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (15 bp):
ATAATAATAATTTTA
Found at i:1174148 original size:7 final size:7
Alignment explanation
Indices: 1174136--1174263 Score: 77
Period size: 7 Copynumber: 17.9 Consensus size: 7
1174126 AGATATAGCA
1174136 AAAAAAG
1 AAAAAAG
1174143 AAAAAAG
1 AAAAAAG
1174150 AAAAAAGAG
1 -AAAAA-AG
1174159 AAAAAAG
1 AAAAAAG
1174166 AGAAAGAGAG
1 A-AAA-A-AG
*
1174176 AGAGAAA-
1 A-AAAAAG
1174183 AAAAAAG
1 AAAAAAG
*
1174190 AAATAAG
1 AAAAAAG
1174197 AAAAAAG
1 AAAAAAG
*
1174204 -CAAAA-
1 AAAAAAG
1174209 AAAAAAG
1 AAAAAAG
* *
1174216 AGAATATG
1 A-AAAAAG
*
1174224 TAACAAA-
1 -AAAAAAG
1174231 AAAAAAG
1 AAAAAAG
* *
1174238 -AAACAT
1 AAAAAAG
1174244 AAAAAAG
1 AAAAAAG
1174251 AAAAAAG
1 AAAAAAG
1174258 AAAAAA
1 AAAAAA
1174264 AGAAGAAGAA
Statistics
Matches: 93, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
6 21 0.23
7 41 0.44
8 20 0.22
9 5 0.05
10 6 0.06
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:1174232 original size:47 final size:45
Alignment explanation
Indices: 1174135--1174274 Score: 126
Period size: 47 Copynumber: 3.0 Consensus size: 45
1174125 AAGATATAGC
1174135 AAAAAAAGAAAAAAGAAAAAAGAGAAAAAAGAGAAAGAG-AGAGAG-AA
1 AAAAAAAG-AAAAAGAAAAAAGA-AAAAAA-A-AAAGAGAAGAGAGAAA
* *
1174182 AAAAAAAGAAATAAGAAAAAAGCAAAAAAAAAAGAGAATATGTA-ACAA
1 AAAAAAAGAAA-AAGAAAAAAGAAAAAAAAAAAGAGAAGA-G-AGA-AA
* * *
1174230 AAAAAAAGAAACATAAAAAAGAAAAAAGAAAAAAAGAAGA-AGAAA
1 AAAAAAAGAAAAAGAAAAAAGAAAAAA-AAAAAGAGAAGAGAGAAA
1174275 GATAAAGAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
44 6 0.08
45 6 0.08
46 11 0.14
47 32 0.41
48 23 0.29
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (45 bp):
AAAAAAAGAAAAAGAAAAAAGAAAAAAAAAAAGAGAAGAGAGAAA
Found at i:1174235 original size:27 final size:25
Alignment explanation
Indices: 1174180--1174270 Score: 76
Period size: 26 Copynumber: 3.5 Consensus size: 25
1174170 AGAGAGAGAG
1174180 AAAAAAAAAGAAATAAGAAAAAAGCA
1 AAAAAAAAAGAAATAAGAAAAAA-CA
*
1174206 AAAAAAAAAGAGAATATGTAACAAAA-A
1 AAAAAAAAAGA-AATAAG-AA-AAAACA
* * * *
1174233 AAAAGAAACATAAAAAAGAAAAAAGA
1 AAAA-AAAAAGAAATAAGAAAAAACA
*
1174259 AAAAAAGAAGAA
1 AAAAAAAAAGAA
1174271 GAAAGATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
25 9 0.17
26 18 0.35
27 14 0.27
28 7 0.13
29 4 0.08
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.05
Consensus pattern (25 bp):
AAAAAAAAAGAAATAAGAAAAAACA
Found at i:1174272 original size:14 final size:15
Alignment explanation
Indices: 1174135--1174285 Score: 87
Period size: 14 Copynumber: 9.8 Consensus size: 15
1174125 AAGATATAGC
1174135 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
1174150 AAAAAAGAGAAAAAAG
1 AAAAAA-AGAAAAAAG
* * *
1174166 AGAAAGAGAGAGAGAA-
1 A-AAA-AAAGAAAAAAG
*
1174182 AAAAAAAGAAATAAG
1 AAAAAAAGAAAAAAG
*
1174197 -AAAAAAGCAAAAA-
1 AAAAAAAGAAAAAAG
* * *
1174210 AAAAAGAGAATATGTAAC
1 AAAAAAAGAA-A--AAAG
* *
1174228 AAAAAAA-AAGAAAC
1 AAAAAAAGAAAAAAG
1174242 ATAAAAAAGAAAAAAG
1 A-AAAAAAGAAAAAAG
*
1174258 AAAAAAAG-AAGAAG
1 AAAAAAAGAAAAAAG
1174272 AAAGATAAAGAAAA
1 AAA-A-AAAGAAAA
1174286 CCAATCAAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
14 37 0.36
15 24 0.23
16 21 0.20
17 15 0.14
18 7 0.07
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:1174284 original size:10 final size:8
Alignment explanation
Indices: 1174135--1174267 Score: 62
Period size: 9 Copynumber: 15.2 Consensus size: 8
1174125 AAGATATAGC
1174135 AAAAAAAG
1 AAAAAAAG
1174143 -AAAAAAG
1 AAAAAAAG
1174150 AAAAAAGAG
1 AAAAAA-AG
1174159 AAAAAAGAG
1 AAAAAA-AG
1174168 AAAGAGAGAGAG
1 AAA-A-A-A-AG
1174180 AAAAAAA-
1 AAAAAAAG
1174187 AAGAAATAAG
1 AA-AAA-AAG
1174197 -AAAAAAG
1 AAAAAAAG
1174204 CAAAAAAA-
1 -AAAAAAAG
1174212 AAAGAGAATATG
1 AAA-A-AA-A-G
1174224 TAACAAAAA-
1 -AA-AAAAAG
*
1174233 AAAAGAAAC
1 AAAA-AAAG
1174242 ATAAAAAAG
1 A-AAAAAAG
1174251 -AAAAAAG
1 AAAAAAAG
1174258 AAAAAAAG
1 AAAAAAAG
1174266 AA
1 AA
1174268 GAAGAAAGAT
Statistics
Matches: 103, Mismatches: 1, Indels: 42
0.71 0.01 0.29
Matches are distributed among these distances:
7 24 0.23
8 27 0.26
9 30 0.29
10 6 0.06
11 3 0.03
12 9 0.09
13 3 0.03
14 1 0.01
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1175663 original size:22 final size:22
Alignment explanation
Indices: 1175610--1175664 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1175600 TATTCAAAGG
*
1175610 GTATCGATA-CATGGTTAGGTA
1 GTATCGATACCATAGTTAGGTA
* *
1175631 GTATTGGTACCATAGTATA-GTA
1 GTATCGATACCATAGT-TAGGTA
1175653 GTATCGATACCA
1 GTATCGATACCA
1175665 GGTTAAAGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 7 0.26
22 18 0.67
23 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.33
Consensus pattern (22 bp):
GTATCGATACCATAGTTAGGTA
Found at i:1176351 original size:18 final size:18
Alignment explanation
Indices: 1176328--1176368 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1176318 AAGGGTTATC
* *
1176328 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGAGACAA
1176346 AGTGGTCCTTCGAGACAA
1 AGTGGTCCTTCGAGACAA
1176364 AGTGG
1 AGTGG
1176369 CCATTTAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAA
Found at i:1178372 original size:24 final size:24
Alignment explanation
Indices: 1178340--1178392 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
1178330 ATTAGTAGTA
1178340 AGTTAGTGAGGGAATTGAACATTC
1 AGTTAGTGAGGGAATTGAACATTC
1178364 AGTTAGTGAGGGAATTGAACATTC
1 AGTTAGTGAGGGAATTGAACATTC
1178388 AGTTA
1 AGTTA
1178393 TAAACTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (24 bp):
AGTTAGTGAGGGAATTGAACATTC
Found at i:1183246 original size:18 final size:18
Alignment explanation
Indices: 1183223--1183275 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1183213 GAGGGTTATC
1183223 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTTGGGACAT
*
1183241 AGTGGT-CTTTCGAGACAT
1 AGTGGTCCTTT-GGGACAT
** *
1183259 AGTAATCCTTCGGGACA
1 AGTGGTCCTTTGGGACA
1183276 ATGTAGTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 4 0.14
18 21 0.75
19 3 0.11
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTTGGGACAT
Found at i:1185575 original size:20 final size:20
Alignment explanation
Indices: 1185550--1185627 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
1185540 TTTCTTGATG
1185550 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGGCCATC
* * *
1185570 AGTAAGTCTTTCGAG-CATG
1 AGTAAGTCCTTCGGGCCATC
1185589 ATGCTTAAGTCCTTCGGGCCATCC
1 A-G--TAAGTCCTTCGGGCCAT-C
*
1185613 A-TAAGACCTTCGGGC
1 AGTAAGTCCTTCGGGC
1185628 AAGATGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.09
20 27 0.59
22 11 0.24
23 3 0.07
24 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (20 bp):
AGTAAGTCCTTCGGGCCATC
Found at i:1185860 original size:144 final size:144
Alignment explanation
Indices: 1185607--1185876 Score: 400
Period size: 144 Copynumber: 1.9 Consensus size: 144
1185597 GTCCTTCGGG
* ** *
1185607 CCATCCATAAGACCTTCGGGCAAGATGTTTTCAGTATTTCCTTTGCTTGATTCACAACACTTAGA
1 CCATCCATAAGACCTTCAGGCAAGATGTTTTCAACATTTCCTTTGCTCGATTCACAACACTTAGA
* * * *
1185672 ATCAGCAATGCCCCATCAGAGGGGTTAACATTTTATTTTCTCGATTCACAACACTTTGAATAAGC
66 ATCAGCAACGCCCCATCAGAGGGGTTAAAATTTTATTGTCTCGATTCACAACACTTGGAATAAGC
1185737 TTAAGTTTTTCAAT
131 TTAAGTTTTTCAAT
* * * *
1185751 CCATCCATAAGACCTTCAGGTAGGATGTTTTCAACATTTCCTTTGCTCGATTCACAACATTTCGA
1 CCATCCATAAGACCTTCAGGCAAGATGTTTTCAACATTTCCTTTGCTCGATTCACAACACTTAGA
1185816 ATCAGCAACGCCCCATCAGAGGGGTTAAAAGTTCTT-TTGT-TCGATTCACAACACTTGGAAT
66 ATCAGCAACGCCCCATCAGAGGGGTTAAAA-TT-TTATTGTCTCGATTCACAACACTTGGAAT
1185877 CAATAACACC
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
144 105 0.94
145 5 0.04
146 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (144 bp):
CCATCCATAAGACCTTCAGGCAAGATGTTTTCAACATTTCCTTTGCTCGATTCACAACACTTAGA
ATCAGCAACGCCCCATCAGAGGGGTTAAAATTTTATTGTCTCGATTCACAACACTTGGAATAAGC
TTAAGTTTTTCAAT
Found at i:1185928 original size:60 final size:59
Alignment explanation
Indices: 1185783--1185936 Score: 166
Period size: 59 Copynumber: 2.6 Consensus size: 59
1185773 GGATGTTTTC
* * * * * * *
1185783 AACATTTCCTTTGCTCGATTCACAACATTTCGAATCAGCAACGCCCCATCAGAGGGGTT
1 AACATTTCCTTTGCTTGATTCACAACACTTCGAATCAACAACACCCCACCAGAAGGATT
* * * * * *
1185842 AAAAGTTCTTTTG-TTCGATTCACAACACTTGGAATCAATAACACCCCACCATAAGGATT
1 AACATTTCCTTTGCTT-GATTCACAACACTTCGAATCAACAACACCCCACCAGAAGGATT
1185901 AACATTTCCTATTGCTTGATTCACAACACTTCGAAT
1 AACATTTCCT-TTGCTTGATTCACAACACTTCGAAT
1185937 TAGCATAAGT
Statistics
Matches: 75, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
58 1 0.01
59 51 0.68
60 21 0.28
61 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (59 bp):
AACATTTCCTTTGCTTGATTCACAACACTTCGAATCAACAACACCCCACCAGAAGGATT
Found at i:1186337 original size:54 final size:56
Alignment explanation
Indices: 1186244--1186354 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 56
1186234 TTTTTATAAA
** *
1186244 CTAAACTTAATTTTTAGGGGTTTCATGATGTTTTAAAATGAAT-TTTATGAAAGAAG
1 CTAAACTTAATTTTTAGGGGTTTCATGATACTGTAAAATGAATCTTTATGAAA-AAG
* *
1186300 CTAAAC-TAA-TTTTAGGGGTTTCTTGATAACTGT-AAATGAATCTTTTTGAAAAAG
1 CTAAACTTAATTTTTAGGGGTTTCATGAT-ACTGTAAAATGAATCTTTATGAAAAAG
1186354 C
1 C
1186355 AAAATTTACC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
54 29 0.60
55 13 0.27
56 6 0.12
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (56 bp):
CTAAACTTAATTTTTAGGGGTTTCATGATACTGTAAAATGAATCTTTATGAAAAAG
Found at i:1187566 original size:138 final size:139
Alignment explanation
Indices: 1187070--1187833 Score: 889
Period size: 139 Copynumber: 5.6 Consensus size: 139
1187060 GGGAAAACCA
* * * *
1187070 ATCAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAAATTCA
1 ATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCAGAT-GAGGGAGAAGAAGTTCA
* ** * * * * *
1187135 TAATGAGAAGAGCTTGTTTGACCTATCACTCGATTCA-C-GATAT---TTTGAATCAGTGAC-CC
65 TAATGAGAAGAACTTGTTCAACCT-TAACTCAATTCATCACATATGGAGTTGAATCAGTAACACC
** *
1187194 TTGCTTGAGGG
129 TCACTCGAGGG
* * *
1187205 AAT-AACATTTCAAAT-GTAGAATTCATAGTGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
1 -ATCAACATTTCAAATAG-AGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTC
* ** * ** * *
1187268 ATAATGAGAAGAGCTTGTTTGACCTATCACTCGTTTCA-CGACAT-T----TCGAATCAGTGATC
64 ATAATGAGAAGAACTTGTTCAACCT-TAACTCAATTCATC-ACATATGGAGTTGAATCAGT-AAC
* *
1187327 A--TCGCTTGAGGG
126 ACCTCACTCGAGGG
* *
1187339 ATCAACATTTCAAAT-GTAAAGTTCATAGTGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCA
1 ATCAACATTTCAAATAG-AGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCA
* *
1187403 TAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATCAGCAACACCT
65 TAATGAGAAGAACTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAGTAACACCT
1187468 CACTCGAGGG
130 CACTCGAGGG
* * *
1187478 ATCAATATTTCAAATAGAGAGTTTATAATGAGAAGAACTCATCAGATGA-GGAGAAGAAGTTAAT
1 ATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCAT
*
1187542 ATTGAGAAGAACTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAGTAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAGTAACACCTC
*
1187607 ACTTGAGGG
131 ACTCGAGGG
* * * * *
1187616 ATCAATATTTCAAATAGAGAGTTCATAATGAGAATAACACATCCGATGAGGGAGAAGAAGATCAT
1 ATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCAT
*
1187681 AATGAGAAGATCTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAGTAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAGTAACACCTC
1187746 ACTCGAGGG
131 ACTCGAGGG
* * * * * *
1187755 ATCAACATTTCCATTAGAGAGTTCATAATGAGAAGAACTAATCTGATAAAGGAGAAGAAGTTCAT
1 ATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCAT
1187820 AATGAGAAGAACTT
66 AATGAGAAGAACTT
1187834 TAGCTTGTTT
Statistics
Matches: 557, Mismatches: 55, Indels: 29
0.87 0.09 0.05
Matches are distributed among these distances:
133 14 0.03
134 154 0.28
135 40 0.07
136 4 0.01
137 3 0.01
138 137 0.25
139 204 0.37
140 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (139 bp):
ATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAGTAACACCTC
ACTCGAGGG
Found at i:1187666 original size:277 final size:270
Alignment explanation
Indices: 1187070--1187833 Score: 884
Period size: 277 Copynumber: 2.8 Consensus size: 270
1187060 GGGAAAACCA
* * *
1187070 ATCAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAAATTCA
1 ATCAACATTT-CAAATGAGAGTTCATAATGAGAAGAACTCATCAGAT-GAGGGAGAAGAAGTTCA
* ** * * * *
1187135 TAATGAGAAGAGCTTGTTTGACCTATCACTCGATTCA-C-GATAT---TTTGAATCAGTGAC-CC
64 TAATGAGAAGAACTTGTTCAACCT-T-ACTCAATTCATCACATATGGAGTTGAATCAGTAACACC
** * * * *
1187194 TTGCTTGAGGGAAT-AACATTTCAAAT-GTAGAATTCATAGTGAGAAGAACTCATCCGATGAGGG
127 TCACTCGAGGG-ATCAACATTTCAAATAG-AGAGTTCATAATGAGAAGAACTCATCAGATGA-GG
* ** * **
1187257 AGAAGAAGTTCATAATGAGAAGAGCTTGTTTGACCTATCACTCGTTTCACGACATTTCGAATCAG
189 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTATAACTCAATTCACGACATTTCGAATCAG
* *
1187322 TGATCATCGCTTGAGGG
254 TGAACATCACTTGAGGG
* *
1187339 ATCAACATTTCAAATGTAAAGTTCATAGTGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCAAATG-AGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCAT
*
1187404 AATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATCAGCAACACCTC
65 AATGAGAAGAACTTGTTCAACCTTA-CTCAATTCATCACATATGGAGTTGAATCAGTAACACCTC
* *
1187469 ACTCGAGGGATCAATATTTCAAATAGAGAGTTTATAATGAGAAGAACTCATCAGATGAGGAGAAG
129 ACTCGAGGGATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCAGATGAGGAGAAG
* * *
1187534 AAGTTAATATTGAGAAGAACTTGTTCAACCT-TAACTCAATTCATC-ACATATGGAGTTGAATCA
194 AAGTTCATAATGAGAAGAACTTGTTCAACCTATAACTCAATTCA-CGACAT-T----TCGAATCA
1187597 GT-AACACCTCACTTGAGGG
253 GTGAACA--TCACTTGAGGG
* * * * *
1187616 ATCAATATTTCAAATAGAGAGTTCATAATGAGAATAACACATCCGATGAGGGAGAAGAAGATCAT
1 ATCAACATTTCAAAT-GAGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCAT
*
1187681 AATGAGAAGATCTTGTTCAACCTTAACTCAATTCATCACATATGGAGTTGAATCAGTAACACCTC
65 AATGAGAAGAACTTGTTCAACCTT-ACTCAATTCATCACATATGGAGTTGAATCAGTAACACCTC
* * * * *
1187746 ACTCGAGGGATCAACATTTCCATTAGAGAGTTCATAATGAGAAGAACTAATCTGATAAAGGAGAA
129 ACTCGAGGGATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCAGAT-GAGGAGAA
1187811 GAAGTTCATAATGAGAAGAACTT
193 GAAGTTCATAATGAGAAGAACTT
1187834 TAGCTTGTTT
Statistics
Matches: 424, Mismatches: 50, Indels: 33
0.84 0.10 0.07
Matches are distributed among these distances:
266 1 0.00
267 9 0.02
268 43 0.10
269 41 0.10
271 13 0.03
272 48 0.11
273 49 0.12
274 1 0.00
275 3 0.01
276 9 0.02
277 177 0.42
278 30 0.07
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (270 bp):
ATCAACATTTCAAATGAGAGTTCATAATGAGAAGAACTCATCAGATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTACTCAATTCATCACATATGGAGTTGAATCAGTAACACCTCAC
TCGAGGGATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCAGATGAGGAGAAGAA
GTTCATAATGAGAAGAACTTGTTCAACCTATAACTCAATTCACGACATTTCGAATCAGTGAACAT
CACTTGAGGG
Found at i:1197096 original size:67 final size:64
Alignment explanation
Indices: 1196956--1197098 Score: 232
Period size: 67 Copynumber: 2.2 Consensus size: 64
1196946 TTGCTTAGCA
1196956 GTGTTGGTTTATGATATTCCTAATTTCCATAGGGTGGAGTGATAGGTTTTATAGTTGTGTTTTT
1 GTGTTGGTTTATGATATTCCTAATTTCCATAGGGTGGAGTGATAGGTTTTATAGTTGTGTTTTT
* * *
1197020 GTGTTGGTTTATGATATTCCTAATTTCCATAGGGTGGTGGTGTGGTAGGTTTTGTAGTTGTGTTT
1 GTGTTGGTTTATGATATTCCTAATTTCCATA--G-GGTGGAGTGATAGGTTTTATAGTTGTGTTT
1197085 TT
63 TT
1197087 GTGTTGGTTTAT
1 GTGTTGGTTTAT
1197099 TATGGTGACA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
64 31 0.42
66 1 0.01
67 41 0.56
ACGTcount: A:0.15, C:0.06, G:0.29, T:0.50
Consensus pattern (64 bp):
GTGTTGGTTTATGATATTCCTAATTTCCATAGGGTGGAGTGATAGGTTTTATAGTTGTGTTTTT
Found at i:1197621 original size:23 final size:23
Alignment explanation
Indices: 1197589--1197632 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1197579 TGTTCGTGTT
*
1197589 TGTTTATTTATTGATTGCGAATA
1 TGTTTATTTAATGATTGCGAATA
* *
1197612 TGTTTGTTTAATGTTTGCGAA
1 TGTTTATTTAATGATTGCGAA
1197633 CGTGTTCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (23 bp):
TGTTTATTTAATGATTGCGAATA
Found at i:1197638 original size:23 final size:23
Alignment explanation
Indices: 1197589--1197644 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
1197579 TGTTCGTGTT
* *
1197589 TGTTTATTTATTGATTGCGAATA
1 TGTTTATTTAATGATTGCGAACA
* * *
1197612 TGTTTGTTTAATGTTTGCGAACG
1 TGTTTATTTAATGATTGCGAACA
*
1197635 TGTTCATTTA
1 TGTTTATTTA
1197645 TATGTTCTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.20, T:0.52
Consensus pattern (23 bp):
TGTTTATTTAATGATTGCGAACA
Found at i:1199752 original size:3 final size:3
Alignment explanation
Indices: 1199744--1199797 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1199734 TTTGGGTTTG
1199744 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1199792 TAA TAA
1 TAA TAA
1199798 AGGGTCGGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1200272 original size:116 final size:118
Alignment explanation
Indices: 1200080--1200335 Score: 338
Period size: 117 Copynumber: 2.2 Consensus size: 118
1200070 ATATTGGTGC
* * * *
1200080 TAATCCAACTCCTTATGTGAT-GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
1 TAATCCAACTCATTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * *
1200144 TTCTTCCTCATCGGATGAGTTCTTCTCATTATGAACTC-TCCACTGAAAATGT
66 TTATCCCTCATCGGATGAGTTCTTCTCATTACGAACCCTTCCACTGAAAATGT
* * *
1200196 TAATCCACCTCTTTCTGTGATGGAATCGAACCAAGGTTGAATAAGTTCTTCTCATTA-GAACTTC
1 TAATCCAACTCATTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * *
1200260 TTATCCCTCATCGGATGAGTTCTTCTCATTACGATCCCTTTCATTGGAAATGT
66 TTATCCCTCATCGGATGAGTTCTTCTCATTACGAACCCTTCCACTGAAAATGT
* *
1200313 TGATCCATCTCATTCTGTGATGG
1 TAATCCAACTCATTCTGTGATGG
1200336 GATCTAGTGA
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
116 58 0.48
117 63 0.52
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (118 bp):
TAATCCAACTCATTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
TTATCCCTCATCGGATGAGTTCTTCTCATTACGAACCCTTCCACTGAAAATGT
Found at i:1200567 original size:321 final size:320
Alignment explanation
Indices: 1199918--1200954 Score: 1261
Period size: 321 Copynumber: 3.2 Consensus size: 320
1199908 CTTGAGCTAC
* * * * * *
1199918 AAGTTCTTCTCATTATGAAC-TCTTCA-CTCTCCTCGAATGAGTTCTTCTTATTATGAACTC-TC
1 AAGTTCTTCTCATTATGAACTTCTT-ATCCCTCATCGGATGAGTTCTTCTCATTACGAACCCTTC
* * * * *
1199980 CACTGGAAATGTTGATCCACCT-ATTTCTATGATGAAATCAAGAGAAAAGGCGATGTTGATCCAA
65 CATTGGAAATGTTGATCCATCTCA-TTCTATGATGAGATCAAGTGAAATGGCGATGTTGATCCAA
* * * *
1200044 CTTTTTATATGATGGAATCGAGCAAAATATTGGTGCTAATCCAACTCCTTATGTGATGAATCGAG
129 CTTCTTATATGATGGAATCGAGCAAAGTGTTGGTGCTGATCCAACTCCTTATGTGATGAATCGAG
*
1200109 CTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-TCCTCATCGGATGAGTTCTTCTCAT
194 CTAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCT-CTCATCGGATGAGTTCTTCTCAT
* * * * *
1200173 TATGAACTCTCCACTGAAAATGTTAATCCACCTCTTTCTGTGATGGAATCGAACCAAGGTTGAAT
258 TATGAACTCCCCACTG-AAATGTTGATCTACCTC-TTCTGTGATGGAATCGAGCTAAGGTTGAAT
* *
1200238 AAGTTCTTCTCATTA-GAACTTCTTATCCCTCATCGGATGAGTTCTTCTCATTACGATCCCTTTC
1 AAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCTCATTACGAACCCTTCC
* * * * *
1200302 ATTGGAAATGTTGATCCATCTCATTCTGTGATGGGATCTAGTGAAATGGTGATGCTGATCCAACT
66 ATTGGAAATGTTGATCCATCTCATTCTATGATGAGATCAAGTGAAATGGCGATGTTGATCCAACT
* *
1200367 TCTTATATGATGGAATCGAGCAAAGTGTTAGTGCTGATCCAACTCCTTATATGATGAATCGAGCT
131 TCTTATATGATGGAATCGAGCAAAGTGTTGGTGCTGATCCAACTCCTTATGTGATGAATCGAGCT
* * *
1200432 GAGGTTGAACAAGTTATTCTCATTATGAACTTATTCTCTCTCATCGGATGAGTTCTTCTCGTTAT
196 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCTCTCATCGGATGAGTTCTTCTCATTAT
* *
1200497 GAACTCCCCACTAGAATTGTCGATCTACCTCATTCTGTGATGGAATCGAGCTAAGGTTGAAT
261 GAACTCCCCACT-GAAATGTTGATCTACCTC-TTCTGTGATGGAATCGAGCTAAGGTTGAAT
* * * * *
1200559 AGGTTCTTCTCATAATGAACTTCTTCTCCCTTATCGGATGAGTTCTTTTC--TACGAACCCTTCC
1 AAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCTCATTACGAACCCTTCC
* * * * * *
1200622 ATTGGAAATGTTGATCC-TCCCGCTTCTATGATGTGATCGAGTGAAATAGCGATGTTGATCCTAC
66 ATTGGAAATGTTGATCCATCTC-ATTCTATGATGAGATCAAGTGAAATGGCGATGTTGATCCAAC
* * * * *
1200686 TTCTCATATGATGGAATAGAGCAAAGTGTCGGTGTTGATCCAACTTCTTATGTGATGAATCGAGC
130 TTCTTATATGATGGAATCGAGCAAAGTGTTGGTGCTGATCCAACTCCTTATGTGATGAATCGAGC
* * * * * * *
1200751 TAAGGATGAACAA-CTACTTCTCCTTATGAACTTCTTCTCCCTCATCAGATGATTTATTCTCATT
195 TAAGGTTGAACAAGTTA-TTCTCATTATGAACTTCTTCTCTCTCATCGGATGAGTTCTTCTCATT
* * *
1200815 ATGAACTCCTCATTGGAAATGTTGAT-TCACCTCTTCTGTGATGGAATCGAGCTAAGGTTGAAC
259 ATGAACTCCCCACT-GAAATGTTGATCT-ACCTCTTCTGTGATGGAATCGAGCTAAGGTTGAAT
* * * * * * *
1200878 AAGTTCTTCTTATTATGAACTTTTTCTCCCTTATCAGG-TAATTTCTTCTCATTATGAACCCTTC
1 AAGTTCTTCTCATTATGAACTTCTTATCCCTCATC-GGATGAGTTCTTCTCATTACGAACCCTTC
*
1200942 CATTGGGAATGTT
65 CATTGGAAATGTT
1200955 AAATGGTTTA
Statistics
Matches: 620, Mismatches: 84, Indels: 25
0.85 0.12 0.03
Matches are distributed among these distances:
319 80 0.13
320 245 0.40
321 261 0.42
322 34 0.05
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (320 bp):
AAGTTCTTCTCATTATGAACTTCTTATCCCTCATCGGATGAGTTCTTCTCATTACGAACCCTTCC
ATTGGAAATGTTGATCCATCTCATTCTATGATGAGATCAAGTGAAATGGCGATGTTGATCCAACT
TCTTATATGATGGAATCGAGCAAAGTGTTGGTGCTGATCCAACTCCTTATGTGATGAATCGAGCT
AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCTCTCATCGGATGAGTTCTTCTCATTAT
GAACTCCCCACTGAAATGTTGATCTACCTCTTCTGTGATGGAATCGAGCTAAGGTTGAAT
Found at i:1200927 original size:116 final size:116
Alignment explanation
Indices: 1200731--1200954 Score: 308
Period size: 116 Copynumber: 1.9 Consensus size: 116
1200721 TGATCCAACT
*
1200731 TCTTATGTGATGAATCGAGCTAAGGATGAACAACTACTTCTCCTTATGAACTTCTTCTCCCTCAT
1 TCTTATGTGATGAATCGAGCTAAGGATGAACAACTACTTCTCATTATGAACTTCTTCTCCCTCAT
*
1200796 CAGATGATTTATTCTCATTATGAACTCC-T-CATTGGAAATGTTGATTCACC
66 CAGATAATTTATTCTCATTATGAAC-CCTTCCATTGGAAATGTTGATTCACC
* * * * * * *
1200846 TCTTCTGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTTTTCTCCCTTA
1 TCTTATGTGAT-GAATCGAGCTAAGGATGAACAACTACTTCTCATTATGAACTTCTTCTCCCTCA
* * *
1200911 TCAGGTAATTTCTTCTCATTATGAACCCTTCCATTGGGAATGTT
65 TCAGATAATTTATTCTCATTATGAACCCTTCCATTGGAAATGTT
1200955 AAATGGTTTA
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
115 12 0.13
116 70 0.74
117 12 0.13
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (116 bp):
TCTTATGTGATGAATCGAGCTAAGGATGAACAACTACTTCTCATTATGAACTTCTTCTCCCTCAT
CAGATAATTTATTCTCATTATGAACCCTTCCATTGGAAATGTTGATTCACC
Found at i:1205486 original size:53 final size:53
Alignment explanation
Indices: 1205418--1205728 Score: 250
Period size: 53 Copynumber: 5.8 Consensus size: 53
1205408 GAAATCCTAA
* *
1205418 AAAATTAGGCTTAGCTTCTTTAAAAATCATTTGAAAACATAAAAAAAACCCTG
1 AAAATCAGGCTTAGCTTCTTTAAAAATCATTTGAAAACATCAAAAAAACCCTG
* * *
1205471 AAAATCAAGCTTAGCTTCTTTAAAAATTCATTAGAAAACATC-AAGAAACCCTTG
1 AAAATCAGGCTTAGCTTCTTTAAAAA-TCATTTGAAAACATCAAAAAAACCC-TG
* * * * ** * * * * *
1205525 AAAATGAGGTTTAGTTTTTTTCTAAATCCATTTGTAGACATCAAGAAACCCCTA
1 AAAATCAGGCTTAGCTTCTTTAAAAAT-CATTTGAAAACATCAAAAAAACCCTG
* * * * *
1205579 AAAAT-AGGCTTAGCTCCTTTAAAAACCCATTTGAAAAGATCAAGAAACCCCTG
1 AAAATCAGGCTTAGCTTCTTTAAAAA-TCATTTGAAAACATCAAAAAAACCCTG
* * * * * *
1205632 AAAATCATGCTTAGCTTCTTTCAAAATTCATTTGAAGTGATCATC-AAGAACCCCTA
1 AAAATCAGGCTTAGCTTCTTT-AAAAATCATTTGAA---AACATCAAAAAAACCCTG
* * *
1205688 AAAATTAGGCTTAGTTTCTTAAAAAATTCATTTGAAAACAT
1 AAAATCAGGCTTAGCTTCTTTAAAAA-TCATTTGAAAACAT
1205729 TATATTGTTT
Statistics
Matches: 202, Mismatches: 45, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
53 78 0.39
54 72 0.36
55 14 0.07
56 34 0.17
57 4 0.02
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (53 bp):
AAAATCAGGCTTAGCTTCTTTAAAAATCATTTGAAAACATCAAAAAAACCCTG
Found at i:1205527 original size:54 final size:54
Alignment explanation
Indices: 1205375--1205728 Score: 329
Period size: 54 Copynumber: 6.5 Consensus size: 54
1205365 TCAAACTTGT
* * * * *
1205375 CTTCTTTAAAAATTCATTTACTGATATCATCAAGAAA-TCCTAAAAAATTAGGCTTAG
1 CTTCTTTAAAAATTCA-TT--TGAAAACATCAAGAAACCCCT-GAAAATCAGGCTTAG
* * * *
1205432 CTTCTTTAAAAA-TCATTTGAAAACATAAAAAAAACCCTGAAAATCAAGCTTAG
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * * *
1205485 CTTCTTTAAAAATTCATTAGAAAACATCAAGAAACCCTTGAAAATGAGGTTTAG
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * ** * * * *
1205539 TTTTTTTCTAAATCCATTTGTAGACATCAAGAAACCCCTAAAAAT-AGGCTTAG
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* ** * *
1205592 CTCCTTTAAAAACCCATTTGAAAAGATCAAGAAACCCCTGAAAATCATGCTTAG
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * * *
1205646 CTTCTTTCAAAATTCATTTGAAGTGATCATCAAG-AACCCCTAAAAATTAGGCTTAG
1 CTTCTTTAAAAATTCATTTGAA---AACATCAAGAAACCCCTGAAAATCAGGCTTAG
* *
1205702 TTTCTTAAAAAATTCATTTGAAAACAT
1 CTTCTTTAAAAATTCATTTGAAAACAT
1205729 TATATTGTTT
Statistics
Matches: 240, Mismatches: 51, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
53 82 0.34
54 96 0.40
55 2 0.01
56 41 0.17
57 19 0.08
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (54 bp):
CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAGGCTTAG
Found at i:1205590 original size:107 final size:106
Alignment explanation
Indices: 1205375--1205728 Score: 350
Period size: 107 Copynumber: 3.3 Consensus size: 106
1205365 TCAAACTTGT
* * * ** * *
1205375 CTTCTTTAAAAATTCATTTACTGATATCATCAAGAAATCCTAAAAAATTAGGCTTAGCTTCTTTA
1 CTTCTTTAAAAATTCA-TTA--GAAAACATCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTTC
* * * * * *
1205440 AAAATCATTTGAAAACATAAAAAAAACCCTGAAAATCAAGCTTAG
63 AAAATCATTTGAAGACATCAAGAAACCCCTAAAAAT-AGGCTTAG
* * * * *
1205485 CTTCTTTAAAAATTCATTAGAAAACATCAAGAAACCCTTGAAAATGAGGTTTAGTTTTTTTCTAA
1 CTTCTTTAAAAATTCATTAGAAAACATCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTTCAAA
*
1205550 ATCCATTTGTAGACATCAAGAAACCCCTAAAAATAGGCTTAG
66 AT-CATTTGAAGACATCAAGAAACCCCTAAAAATAGGCTTAG
* ** * * * *
1205592 CTCCTTTAAAAACCCATTTGAAAAGATCAAGAAACCCCTGAAAATCATGCTTAGCTTCTTTCAAA
1 CTTCTTTAAAAATTCATTAGAAAACATCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTTCAAA
1205657 ATTCATTTGAAGTGATCATCAAG-AACCCCTAAAAATTAGGCTTAG
66 A-TCATTTGAA--GA-CATCAAGAAACCCCTAAAAA-TAGGCTTAG
* * *
1205702 TTTCTTAAAAAATTCATTTGAAAACAT
1 CTTCTTTAAAAATTCATTAGAAAACAT
1205729 TATATTGTTT
Statistics
Matches: 201, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
107 105 0.52
108 26 0.13
109 17 0.08
110 53 0.26
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (106 bp):
CTTCTTTAAAAATTCATTAGAAAACATCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTTCAAA
ATCATTTGAAGACATCAAGAAACCCCTAAAAATAGGCTTAG
Found at i:1207094 original size:27 final size:28
Alignment explanation
Indices: 1207035--1207100 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
1207025 GAAGGTAGAG
**
1207035 TGTTTCAGGTTAATTTGGGGAGGTAATG
1 TGTTTCAGGTTAATTTGGGGAGGTAAAA
* *
1207063 CGTTTAAGGTTAATTT-GGGAGGTAAAA
1 TGTTTCAGGTTAATTTGGGGAGGTAAAA
1207090 TGTTTCAGGTT
1 TGTTTCAGGTT
1207101 GGTTTCTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.24, C:0.05, G:0.32, T:0.39
Consensus pattern (28 bp):
TGTTTCAGGTTAATTTGGGGAGGTAAAA
Found at i:1214265 original size:22 final size:22
Alignment explanation
Indices: 1214218--1214282 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
1214208 CCCTCCTGAT
*
1214218 GGGGAACTGATTCCCCCTTTGAA
1 GGGGAACCGATTCCCCC-TTGAA
*
1214241 GGGGAACCGATTCCCCCTTGTA
1 GGGGAACCGATTCCCCCTTGAA
* *
1214263 GGGGAATCGATACCCCCTTG
1 GGGGAACCGATTCCCCCTTG
1214283 GGGTTCTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
22 22 0.58
23 16 0.42
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (22 bp):
GGGGAACCGATTCCCCCTTGAA
Found at i:1220908 original size:18 final size:17
Alignment explanation
Indices: 1220887--1220953 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 17
1220877 TATTAGTTAC
*
1220887 AATAATATAATTAAAGTA
1 AATAATATAAATAAA-TA
*
1220905 AATAATTTAAATAAATA
1 AATAATATAAATAAATA
*
1220922 AATTAAGA-AAATAAGATA
1 AA-TAATATAAATAA-ATA
*
1220940 AATTAAAATAAATA
1 AA-TAATATAAATA
1220954 GATGTAATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.24
18 26 0.63
19 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
AATAATATAAATAAATA
Found at i:1220956 original size:18 final size:18
Alignment explanation
Indices: 1220912--1220956 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1220902 GTAAATAATT
* *
1220912 TAAATAAATAAATTAAGA
1 TAAATAGATAAATTAAAA
1220930 -AAATAAGATAAATTAAAA
1 TAAAT-AGATAAATTAAAA
1220948 TAAATAGAT
1 TAAATAGAT
1220957 GTAATGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (18 bp):
TAAATAGATAAATTAAAA
Found at i:1222393 original size:3 final size:3
Alignment explanation
Indices: 1222385--1222414 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1222375 TTTGGGTTTG
1222385 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1222415 AGGGATTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1222699 original size:60 final size:60
Alignment explanation
Indices: 1222623--1222772 Score: 207
Period size: 60 Copynumber: 2.5 Consensus size: 60
1222613 TTCAAACTCT
* *
1222623 ACTTTTAAACATTCTAATTTCATCCCCAAAT-TATGACTCTCATTT-TAAATTAGTCCTTAA
1 ACTTTTAAATATTCTAATTTCATCCCCAAATATATGACCCTC-TTTCTAAATTAGTCC-TAA
* * *
1222683 ACTTTTAAATAATCTAATTTCAT-CCCTAATATATGACCCTCTTTCTAAATTGGTCCTAA
1 ACTTTTAAATATTCTAATTTCATCCCCAAATATATGACCCTCTTTCTAAATTAGTCCTAA
*
1222742 ACTTTTAAATATTCCAATTTCATCCCCAAAT
1 ACTTTTAAATATTCTAATTTCATCCCCAAAT
1222773 CCATCAAACA
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
59 33 0.42
60 46 0.58
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (60 bp):
ACTTTTAAATATTCTAATTTCATCCCCAAATATATGACCCTCTTTCTAAATTAGTCCTAA
Found at i:1222984 original size:60 final size:60
Alignment explanation
Indices: 1222888--1223003 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
1222878 AGTATATACA
* *
1222888 TATAGTTTGAGATGAAATTGAAATGTTCAAAAAGTTTG-GAGACTAATTTAGAATGAATGT
1 TATAGTTTGAGATAAAATTGAAATATTCAAAAAGTTTGAG-GACTAATTTAGAATGAATGT
* *
1222948 TATAGTTTGGGGATAAAATTGAAATATTC-AAAAGTTTGAGGATTAATTTAGAATGA
1 TATAGTTT-GAGATAAAATTGAAATATTCAAAAAGTTTGAGGACTAATTTAGAATGA
1223004 GAGTCATAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 32 0.64
61 18 0.36
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (60 bp):
TATAGTTTGAGATAAAATTGAAATATTCAAAAAGTTTGAGGACTAATTTAGAATGAATGT
Found at i:1223027 original size:60 final size:62
Alignment explanation
Indices: 1222889--1223028 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 62
1222879 GTATATACAT
* * *
1222889 ATAGTTTG-AG-ATGAAATTGAAATGTTCAAAAAGTTTGGAGACTAATTTAGAATGAATGTT
1 ATAGTTTGAAGAAAGAAATTGAAATATTCAAAAAGTTTGGAGACTAATTTAGAATGAATGTC
** * *
1222949 ATAGTTTGGGGATA-AAATTGAAATATTC-AAAAGTTT-GAGGATTAATTTAGAATGAGA-GTC
1 ATAGTTTGAAGAAAGAAATTGAAATATTCAAAAAGTTTGGA-GACTAATTTAGAATGA-ATGTC
1223009 ATAGTTT-AAGAAAGAAATTG
1 ATAGTTTGAAGAAAGAAATTG
1223029 GACATTTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
59 5 0.08
60 46 0.70
61 15 0.23
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (62 bp):
ATAGTTTGAAGAAAGAAATTGAAATATTCAAAAAGTTTGGAGACTAATTTAGAATGAATGTC
Found at i:1224076 original size:35 final size:37
Alignment explanation
Indices: 1224030--1224098 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
1224020 ATGAAAACGG
1224030 TTGCCAAT-AAAAATGTT-AAAAATTAACATTTTCGA
1 TTGCCAATAAAAAATGTTAAAAAATTAACATTTTCGA
1224065 TTGCCAATAAAAAATGTTAAAAAATTAACATTTT
1 TTGCCAATAAAAAATGTTAAAAAATTAACATTTT
1224099 AGGTTGTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 8 0.25
36 9 0.28
37 15 0.47
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (37 bp):
TTGCCAATAAAAAATGTTAAAAAATTAACATTTTCGA
Found at i:1228672 original size:9 final size:9
Alignment explanation
Indices: 1228660--1228718 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
1228650 AATATTTTAT
1228660 ATATAATTA
1 ATATAATTA
**
1228669 ATATAAAAAA
1 ATAT-AATTA
1228679 ATATAA--A
1 ATATAATTA
*
1228686 ATATTA-TA
1 ATATAATTA
1228694 TATATAATTA
1 -ATATAATTA
1228704 ATATAATTA
1 ATATAATTA
1228713 ATATAA
1 ATATAA
1228719 AAAATATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.14
8 1 0.02
9 26 0.62
10 9 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATAATTA
Found at i:1228735 original size:43 final size:44
Alignment explanation
Indices: 1228660--1228742 Score: 159
Period size: 43 Copynumber: 1.9 Consensus size: 44
1228650 AATATTTTAT
1228660 ATATAATTAATATAAAAAAATATAAAATATTATATATATAATTA
1 ATATAATTAATATAAAAAAATATAAAATATTATATATATAATTA
1228704 ATATAATTAATAT-AAAAAATATAAAATATTATATATATA
1 ATATAATTAATATAAAAAAATATAAAATATTATATATATA
1228743 TATATCGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
43 26 0.67
44 13 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (44 bp):
ATATAATTAATATAAAAAAATATAAAATATTATATATATAATTA
Found at i:1230080 original size:26 final size:26
Alignment explanation
Indices: 1230037--1230089 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1230027 AGAAGGCGCG
* * *
1230037 CTGAGTAGATCTTCTAGAAACCGCCA
1 CTGACTAGACCTTATAGAAACCGCCA
*
1230063 CTGACTAGACCTTATAGAAACTGCCA
1 CTGACTAGACCTTATAGAAACCGCCA
1230089 C
1 C
1230090 GTTAGACCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (26 bp):
CTGACTAGACCTTATAGAAACCGCCA
Found at i:1230908 original size:14 final size:15
Alignment explanation
Indices: 1230876--1230912 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1230866 TTTCGAACAA
1230876 CTTT-TTTTCTCTTT
1 CTTTCTTTTCTCTTT
*
1230890 TTTTCTTTT-TCTTT
1 CTTTCTTTTCTCTTT
1230904 CTTTCTTTT
1 CTTTCTTTT
1230913 GATCTATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
CTTTCTTTTCTCTTT
Found at i:1239960 original size:14 final size:14
Alignment explanation
Indices: 1239944--1239991 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
1239934 TCGGCTAGTT
*
1239944 GTAGCAATATCGTT
1 GTAGCAATATCGTC
1239958 GTAGCAATATCGTC
1 GTAGCAATATCGTC
1239972 GTAGCAATATCGTC
1 GTAGCAATATCGTC
1239986 GTAGCA
1 GTAGCA
1239992 CCCTCGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (14 bp):
GTAGCAATATCGTC
Found at i:1243074 original size:139 final size:138
Alignment explanation
Indices: 1242792--1243190 Score: 563
Period size: 139 Copynumber: 2.9 Consensus size: 138
1242782 GAAACGATGA
* * * * *
1242792 TGCTGATCCAACTCCTTATGCGATGGAAACAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAAC
1 TGCTGATTCAACTCCATATGCGA-CGAATCAAGCTAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
1242857 TTCTTCTCCCTT-ATCGAATGAGTTCTTCTCATTATGAACTCTCCACTAGTAATGTTGATCCCTC
65 TTCTTCT-CCTTCATCGGATGAGTTCTTCT-ATTATGAACTCTCCATTAGAAATGTTGATCCCTC
1242921 GAGTGAGGTAT
128 GAGTGAGGTAT
** * * *
1242932 TGCTGATTCAACTCTTTATGTGACGAATCGAGCTAAGGTTGAACAAATTCTTCTCATTATAAACT
1 TGCTGATTCAACTCCATATGCGACGAATCAAGCTAAGGTTGAACAAATTCTTCTCATTATGAACT
1242997 TCTTCTCCTTCATCGGATGAGTTCTTCTTATTATGAACTCTCCATTAGAAATGTTGATCCCTCGA
66 TCTTCTCCTTCATCGGATGAGTTCTTC-TATTATGAACTCTCCATTAGAAATGTTGATCCCTCGA
*
1243062 GTGAGGTGT
130 GTGAGGTAT
* *
1243071 TGCTGATTCAACTCCATATGCGATGAATCAAGCTAAGGTCGAACAAGA-TCTTCTCATTATGAAC
1 TGCTGATTCAACTCCATATGCGACGAATCAAGCTAAGGTTGAACAA-ATTCTTCTCATTATGAAC
* *
1243135 TTCTTCTACTTCATCGGATGAGTTC-TC-ATTATGAACTCTCCATTTGAAATGTTGAT
65 TTCTTCTCCTTCATCGGATGAGTTCTTCTATTATGAACTCTCCATTAGAAATGTTGAT
1243191 TGGTTCATCT
Statistics
Matches: 235, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
136 28 0.12
138 6 0.03
139 179 0.76
140 22 0.09
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (138 bp):
TGCTGATTCAACTCCATATGCGACGAATCAAGCTAAGGTTGAACAAATTCTTCTCATTATGAACT
TCTTCTCCTTCATCGGATGAGTTCTTCTATTATGAACTCTCCATTAGAAATGTTGATCCCTCGAG
TGAGGTAT
Found at i:1243871 original size:41 final size:41
Alignment explanation
Indices: 1243809--1243939 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 41
1243799 CATTTGAAAA
* * *
1243809 CATCCTGCTCGAAGGTCTTATAGATGGTCCGAAGGACTTAT
1 CATCATGCTCGAAAGACTTATAGATGGTCCGAAGGACTTAT
* * ** * * *
1243850 CATCTTGCTCGAAAGACTTATAGTTGACCCGAAAGATTTAAG
1 CATCATGCTCGAAAGACTTATAGATGGTCCGAAGGACTT-AT
* *
1243892 CATCACGCTCGAAAGACTTATTGAT-GTCCCCGAAGGACTTACT
1 CATCATGCTCGAAAGACTTATAGATGGT--CCGAAGGACTTA-T
1243935 CATCA
1 CATCA
1243940 AGAAACCCTT
Statistics
Matches: 68, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
41 31 0.46
42 23 0.34
43 14 0.21
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAGATGGTCCGAAGGACTTAT
Found at i:1244213 original size:42 final size:41
Alignment explanation
Indices: 1244113--1244213 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
1244103 ATGGATGTCA
* *
1244113 CGAAGGACTTATCATCTTGCTTGAAAGACTTATAGATGACC
1 CGAAGGACTTATCATCATGCTCGAAAGACTTATAGATGACC
* * *
1244154 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACT-GATGGCC
1 CGAAGGACTT-ATCATCATGCTCGAAAGACTTA-TAGATGACC
*
1244196 CGAAAGACTTATTCATCA
1 CGAAGGACTTA-TCATCA
1244214 AGAAACCCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
41 10 0.20
42 38 0.78
43 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (41 bp):
CGAAGGACTTATCATCATGCTCGAAAGACTTATAGATGACC
Found at i:1244555 original size:55 final size:55
Alignment explanation
Indices: 1244266--1244627 Score: 382
Period size: 54 Copynumber: 6.7 Consensus size: 55
1244256 TTTTTCAGTT
* * * * * *
1244266 ATCATAAAGAAACTCCTAAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTGAAA
1 ATCATCAAGAAACCCCTGAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAA
* * *
1244321 AT-ATCAAGAAACCACTGAAAATTAGGCTTCA-TTTCTTTGAAAATTCATTTGAAA
1 ATCATCAAGAAACCCCTGAAAATCAGACTT-AGTTTCTTTGAAAATTCATTTGAAA
*
1244375 A-CATCAAGAAACCCCT-AAAATTCAGACTTAATTTCTTTGAAAATTCATTTGAAA
1 ATCATCAAGAAACCCCTGAAAA-TCAGACTTAGTTTCTTTGAAAATTCATTTGAAA
* * * *
1244429 A-CATCCAA-AAACCCCTAAAAATTAGGCTTAGCTTCTTT-AAAATTCATTTGAAA
1 ATCAT-CAAGAAACCCCTGAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAA
** *
1244482 A-CATCAAGAAACCCCTGAAAATCAGACTTAGTTTCTTTGAAAGGTCATTTAAAA
1 ATCATCAAGAAACCCCTGAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAA
** * *
1244536 ATCATCAAGAAACTTCTGAAAATCAGACTTAGTTCCTTT-AAAAGCTCATTTGAAA
1 ATCATCAAGAAACCCCTGAAAATCAGACTTAGTTTCTTTGAAAA-TTCATTTGAAA
** ** * *
1244591 ATTGTCAAGAAACTTCTGAAAATCAAACTTAATTTCT
1 ATCATCAAGAAACCCCTGAAAATCAGACTTAGTTTCT
1244628 AAAAAAACAC
Statistics
Matches: 267, Mismatches: 30, Indels: 20
0.84 0.09 0.06
Matches are distributed among these distances:
52 3 0.01
53 50 0.19
54 129 0.48
55 85 0.32
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (55 bp):
ATCATCAAGAAACCCCTGAAAATCAGACTTAGTTTCTTTGAAAATTCATTTGAAA
Found at i:1245938 original size:28 final size:26
Alignment explanation
Indices: 1245873--1245944 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 26
1245863 TTAGGGTTCC
* *
1245873 TTGGGAAGGTAATGTGTTTCGTTAAT
1 TTGGGGAGGTAATGTGTTTCGTCAAT
*
1245899 TTGGGGAAGTAATGTGTTTCAGGTCAAT
1 TTGGGGAGGTAATGTGTTTC--GTCAAT
*
1245927 TTGGGGAGGTAATATGTT
1 TTGGGGAGGTAATGTGTT
1245945 CCGGGTTGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 18 0.46
28 21 0.54
ACGTcount: A:0.24, C:0.04, G:0.33, T:0.39
Consensus pattern (26 bp):
TTGGGGAGGTAATGTGTTTCGTCAAT
Found at i:1246618 original size:7 final size:7
Alignment explanation
Indices: 1246580--1246680 Score: 57
Period size: 7 Copynumber: 14.4 Consensus size: 7
1246570 GATATGTCTA
*
1246580 TTTCTAT
1 TTTCTCT
1246587 TTTCTTCT
1 TTTC-TCT
* *
1246595 TTTTTTT
1 TTTCTCT
* *
1246602 TTTTTTT
1 TTTCTCT
1246609 TTTCTCTT
1 TTTCTC-T
*
1246617 TTTCTGT
1 TTTCTCT
1246624 TTTCTC-
1 TTTCTCT
1246630 TTTCT-T
1 TTTCTCT
*
1246636 TCTTCTTT
1 T-TTCTCT
1246644 TTTCTCT
1 TTTCTCT
*
1246651 TTTTTCT
1 TTTCTCT
*
1246658 GTTTTTCT
1 -TTTCTCT
1246666 TTT-T-T
1 TTTCTCT
1246671 TTTCTCT
1 TTTCTCT
1246678 TTT
1 TTT
1246681 TTTCTGTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
5 4 0.05
6 8 0.10
7 45 0.58
8 20 0.26
ACGTcount: A:0.01, C:0.17, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTCTCT
Found at i:1246618 original size:8 final size:8
Alignment explanation
Indices: 1246586--1246691 Score: 57
Period size: 8 Copynumber: 13.5 Consensus size: 8
1246576 TCTATTTCTA
1246586 TTTTCTTCT
1 TTTTC-TCT
1246595 TTTT-T-T
1 TTTTCTCT
*
1246601 TTTT-TTT
1 TTTTCTCT
1246608 TTTTCTCT
1 TTTTCTCT
*
1246616 TTTTCT-G
1 TTTTCTCT
1246623 TTTTCTCTT
1 TTTTCTC-T
1246632 TCTTTCTTCTT
1 T-TTTC-TC-T
1246643 TTTTCTCT
1 TTTTCTCT
1246651 TTTT-TCT
1 TTTTCTCT
1246658 GTTTT-TCT
1 -TTTTCTCT
1246666 TTTT-T-T
1 TTTTCTCT
* *
1246672 TTCTCTTT
1 TTTTCTCT
*
1246680 TTTTCTGT
1 TTTTCTCT
1246688 TTTT
1 TTTT
1246692 ACTTTCCTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 19
0.77 0.06 0.18
Matches are distributed among these distances:
6 10 0.12
7 21 0.26
8 31 0.38
9 7 0.09
10 8 0.10
11 5 0.06
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (8 bp):
TTTTCTCT
Found at i:1246645 original size:27 final size:27
Alignment explanation
Indices: 1246604--1246691 Score: 97
Period size: 27 Copynumber: 3.2 Consensus size: 27
1246594 TTTTTTTTTT
* *
1246604 TTTTTTTTCTCTTTTTCTGTTTTCTCT-
1 TTTTTCTTCT-TTTTTCTCTTTTCTCTG
*
1246631 TTCTTTCTTCTTTTTTCTCTTTTTTCTG
1 TT-TTTCTTCTTTTTTCTCTTTTCTCTG
* *
1246659 TTTTTCTTTTTTTTTCTCTTTTTTTCTG
1 TTTTTCTTCTTTTTTCTC-TTTTCTCTG
1246687 TTTTT
1 TTTTT
1246692 ACTTTCCTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 31 0.57
28 23 0.43
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (27 bp):
TTTTTCTTCTTTTTTCTCTTTTCTCTG
Found at i:1246645 original size:37 final size:35
Alignment explanation
Indices: 1246580--1246691 Score: 136
Period size: 37 Copynumber: 3.1 Consensus size: 35
1246570 GATATGTCTA
* *
1246580 TTTCTATTTTCTTCTTTTTTTTTTTTTTTTTTCTCTT
1 TTTCTGTTTTC-TCTTTTTTTTTCTTTTTTTTCT-TT
* *
1246617 TTTCTGTTTTCTCTTTCTTTCTTCTTTTTTCTCTTT
1 TTTCTGTTTTCTCTTT-TTTTTTCTTTTTTTTCTTT
1246653 TTTCTGTTTT-TCTTTTTTTTTCTCTTTTTTTCTGTT
1 TTTCTGTTTTCTCTTTTTTTTTCT-TTTTTTTCT-TT
1246689 TTT
1 TTT
1246692 ACTTTCCTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
34 7 0.11
35 13 0.20
36 22 0.33
37 24 0.36
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.80
Consensus pattern (35 bp):
TTTCTGTTTTCTCTTTTTTTTTCTTTTTTTTCTTT
Found at i:1246645 original size:44 final size:43
Alignment explanation
Indices: 1246587--1246691 Score: 114
Period size: 44 Copynumber: 2.6 Consensus size: 43
1246577 CTATTTCTAT
* * *
1246587 TTTCTTCTTTTTTTTTTTTTTTTTTCTCTTTTTCTGTTTTCTC
1 TTTCTTCTTCTTTTTTCTCTTTTTTCTCTTTTTCTGTTTTCTC
*
1246630 TTTCTTTCTTCTTTTTTCTCTTTTTTCTGTTTTTCT-TTTT-T-
1 TTTC-TTCTTCTTTTTTCTCTTTTTTCTCTTTTTCTGTTTTCTC
*
1246671 TTTC-TC-T-TTTTTTCTGTTTTT
1 TTTCTTCTTCTTTTTTCTCTTTTT
1246692 ACTTTCCTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
37 13 0.23
38 1 0.02
39 2 0.04
41 4 0.07
42 1 0.02
43 8 0.14
44 27 0.48
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (43 bp):
TTTCTTCTTCTTTTTTCTCTTTTTTCTCTTTTTCTGTTTTCTC
Found at i:1246674 original size:47 final size:47
Alignment explanation
Indices: 1246587--1246685 Score: 125
Period size: 47 Copynumber: 2.1 Consensus size: 47
1246577 CTATTTCTAT
1246587 TTTCTTCTTTTTTTTTTTTTTTTTTCTCTTTTTCTGTTTTCTCTTTC
1 TTTCTTCTTTTTTTTTTTTTTTTTTCTCTTTTTCTGTTTTCTCTTTC
*
1246634 TTTCTTCTTTTTTCTCTTTTTTCTGTTTT-TC-TTTT-T-TTTTCTCTTTT
1 TTTCTTCTTTTTT-T-TTTTTT-T-TTTTCTCTTTTTCTGTTTTCTCTTTC
1246681 TTTCT
1 TTTCT
1246686 GTTTTTACTT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
47 28 0.60
48 2 0.04
49 10 0.21
50 3 0.06
51 4 0.09
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (47 bp):
TTTCTTCTTTTTTTTTTTTTTTTTTCTCTTTTTCTGTTTTCTCTTTC
Found at i:1246691 original size:36 final size:34
Alignment explanation
Indices: 1246591--1246691 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 34
1246581 TTCTATTTTC
*
1246591 TTCTTTTTTTTTTTTTTTTTTCTCTTTTTCTGTTT
1 TTCTTTTTTTTTCTTTTTTTTCT-TTTTTCTGTTT
* *
1246626 TCTCTTTCTTTCTTCTTTTTTCTCTTTTTTCTGTTT
1 T-TCTTT-TTTTTTCTTTTTTTTCTTTTTTCTGTTT
1246662 TTCTTTTTTTTTCTCTTTTTTTCTGTTTTT
1 TTCTTTTTTTTTCT-TTTTTTTCT-TTTTT
1246692 ACTTTCCTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 7 0.12
35 14 0.25
36 22 0.39
37 14 0.25
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (34 bp):
TTCTTTTTTTTTCTTTTTTTTCTTTTTTCTGTTT
Found at i:1246966 original size:2 final size:2
Alignment explanation
Indices: 1246959--1247205 Score: 361
Period size: 2 Copynumber: 124.0 Consensus size: 2
1246949 ACAACAAGGG
1246959 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
* *
1247001 AT AT AT AT AT AT AT AT AT GT AT GT 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
*
1247043 AT AT -T AT AT AT AT GT 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
* * * *
1247084 AT AT AT AT AC AT AT AT AT AT AT AT GT AT AT GT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1247126 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1247168 AT AT AT AT GT AT AT AT GT AT AT AT AT AC AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1247206 TTTTTAAAAG
Statistics
Matches: 216, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
1 1 0.00
2 215 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Done.