Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 29
Found at i:2993766 original size:121 final size:122
Alignment explanation
Indices: 2993393--2993792 Score: 517
Period size: 119 Copynumber: 3.3 Consensus size: 122
2993383 CACTCGATGG
* * * *
2993393 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTTATCTAAAGAGGAA-AGAGAAGTTCAT
1 ATCAACATTTCCAGAAG-TGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGA-AGAAGTTCAT
* * ** * *
2993457 AATGAGAAGAACTTGTTCAACCTTTTTC-TCGATTCTATCCCAAAAGAAGATAGATAAGC
64 AATGAGAAGAACTTATTCAACC-TTTTCATCGACTCTATCATAAAAGGAGATAGATCAGC
*
2993516 ACCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGA-G--GAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * * *
2993578 TGAGAATAATTTATTCAACCTTTTGATCGACGCTATCATAGAAGGAGATAGATCAGC
66 TGAGAAGAACTTATTCAACCTTTTCATCGACTCTATCATAAAAGGAGATAGATCAGC
* * *
2993635 ATCAATATTTCCATAAGTGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
2993700 TGAGAAGAACTT-TTCAACCTTTTACAT-GACTCTATCATACAAGGAGATAAATCAGT
66 TGAGAAGAACTTATTCAACCTTTT-CATCGACTCTATCATAAAAGGAGATAGATCAGC
2993756 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACT
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACT
2993793 TGTTCACCCT
Statistics
Matches: 241, Mismatches: 30, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
118 4 0.02
119 96 0.40
120 2 0.01
121 71 0.29
122 53 0.22
123 15 0.06
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTATTCAACCTTTTCATCGACTCTATCATAAAAGGAGATAGATCAGC
Found at i:2994155 original size:137 final size:139
Alignment explanation
Indices: 2993843--2994181 Score: 459
Period size: 137 Copynumber: 2.5 Consensus size: 139
2993833 ATCAGCACAT
*
2993843 AATGAGAA-AAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTA
1 AATGAGAAGAAA-TCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* * * * *
2993907 ACTTGATTAATCACCTATGGAGTTGAATGAAATAATAACCTCTCTTGAGGATCAATATTTTCAGA
65 ACTTAATTAATCACATATGAAGTTGAATGAAATAATAACCTCTCTTAAGGATCAACATTTTCAGA
*
2993972 AAAAGTTCAT
130 AAAAGTTCAC
* **
2993982 AATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGC
1 AATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAA
* * * * * *
2994047 CTTAATTCATCACATATGAAGTTGAAT-CAATGA-CACCTCTTTTAAGGATCAGCATTTTCAGAA
66 CTTAATTAATCACATATGAAGTTGAATGAAATAATAACCTCTCTTAAGGATCAACATTTTCAGAA
*
2994110 AGAGTTCAC
131 AAAGTTCAC
** * *
2994119 AATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAGCCTT
1 AATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
2994182 TTACTCGACT
Statistics
Matches: 177, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
137 90 0.51
138 4 0.02
139 81 0.46
140 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (139 bp):
AATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAA
CTTAATTAATCACATATGAAGTTGAATGAAATAATAACCTCTCTTAAGGATCAACATTTTCAGAA
AAAGTTCAC
Found at i:2994209 original size:28 final size:28
Alignment explanation
Indices: 2994168--2994225 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2994158 AATCTGAAGA
*
2994168 ACTTATTCAGCCTTTTACTCGACTCATC
1 ACTTATTCAACCTTTTACTCGACTCATC
2994196 ACTTATTCAACCTTTTACTCGACTCATC
1 ACTTATTCAACCTTTTACTCGACTCATC
2994224 AC
1 AC
2994226 AGACGGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.24, C:0.33, G:0.05, T:0.38
Consensus pattern (28 bp):
ACTTATTCAACCTTTTACTCGACTCATC
Found at i:2994686 original size:16 final size:16
Alignment explanation
Indices: 2994662--2994701 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2994652 AACAGCAGCC
*
2994662 ATCCAGCCGGTTTCAT
1 ATCCCGCCGGTTTCAT
2994678 ATCCCGCCGGTTTCAT
1 ATCCCGCCGGTTTCAT
2994694 ATCCCGCC
1 ATCCCGCC
2994702 AGCAATGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.15, C:0.40, G:0.17, T:0.28
Consensus pattern (16 bp):
ATCCCGCCGGTTTCAT
Found at i:3003742 original size:11 final size:10
Alignment explanation
Indices: 3003720--3003756 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
3003710 AATTAAATTA
3003720 TGTTTAAA-G
1 TGTTTAAATG
3003729 TGTTTAAAATG
1 TGTTT-AAATG
3003740 TGTTTAAAT-
1 TGTTTAAATG
3003749 TGTTTAAA
1 TGTTTAAA
3003757 ATATGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 13 0.50
10 7 0.27
11 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (10 bp):
TGTTTAAATG
Found at i:3003743 original size:20 final size:20
Alignment explanation
Indices: 3003720--3003758 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3003710 AATTAAATTA
3003720 TGTTTAAAGTGTTTAAAATG
1 TGTTTAAAGTGTTTAAAATG
*
3003740 TGTTTAAATTGTTTAAAAT
1 TGTTTAAAGTGTTTAAAAT
3003759 ATGAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TGTTTAAAGTGTTTAAAATG
Found at i:3007405 original size:7 final size:7
Alignment explanation
Indices: 3007389--3007432 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
3007379 ACATAATTTC
3007389 ATAATAA
1 ATAATAA
*
3007396 ATATTAA
1 ATAATAA
3007403 ATAATAA
1 ATAATAA
3007410 ATAATAA
1 ATAATAA
3007417 ATAATAA
1 ATAATAA
3007424 ATAATAA
1 ATAATAA
3007431 AT
1 AT
3007433 CTTATATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATAATAA
Found at i:3009083 original size:18 final size:17
Alignment explanation
Indices: 3009060--3009102 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3009050 ATATATACAT
3009060 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
3009078 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
3009095 ATAA-AATA
1 ATAATAATA
3009103 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:3009084 original size:45 final size:44
Alignment explanation
Indices: 3008999--3009084 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 44
3008989 TTAAAGAAAT
3008999 ATATATATATAATAATATAGTAAAAAAATAAATGAAAATAATTTA
1 ATATATATATAATAATATAG-AAAAAAATAAATGAAAATAATTTA
* *
3009044 ATATATATAT-ATACATATA-ATAATAATAACATGAATAATAA
1 ATATATATATAATA-ATATAGAAAAAAATAA-ATGAA-AATAA
3009085 AAATAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
43 8 0.22
44 8 0.22
45 20 0.56
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (44 bp):
ATATATATATAATAATATAGAAAAAAATAAATGAAAATAATTTA
Found at i:3009089 original size:51 final size:51
Alignment explanation
Indices: 3008995--3009114 Score: 122
Period size: 51 Copynumber: 2.4 Consensus size: 51
3008985 AATATTAAAG
* * * *
3008995 AAATATATATATATAATAATATAGTAAAAAAATAAATGAAAATAATTTAAT
1 AAATATATACATATAATAATATAGTAAAAAAATAAATAAAAATAAATGAAT
**
3009046 ATATATATATACATATAATAATA-A-TAACATGAAT-AATAAAAATAAATGAAT
1 A-A-ATATATACATATAATAATATAGTAA-AAAAATAAATAAAAATAAATGAAT
*
3009097 AAA-ATATCCATATAATAA
1 AAATATATACATATAATAA
3009115 ATAAAGGGAC
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
48 14 0.24
49 1 0.02
50 1 0.02
51 19 0.32
52 6 0.10
53 18 0.31
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (51 bp):
AAATATATACATATAATAATATAGTAAAAAAATAAATAAAAATAAATGAAT
Found at i:3009509 original size:37 final size:37
Alignment explanation
Indices: 3009459--3009563 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
3009449 GTGCTTGTGG
* * * *
3009459 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
* * *
3009496 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
3009533 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
3009564 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
Found at i:3010410 original size:105 final size:105
Alignment explanation
Indices: 3010106--3010736 Score: 932
Period size: 105 Copynumber: 6.0 Consensus size: 105
3010096 GCATTGTTCC
* * ** *
3010106 GAGTCCAATACCCTCCGTTGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
3010170 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3010212 GAGTCCAATATCCTTCGCTGTGAAGTTTAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
3010272 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3010312 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
3010377 CAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3010417 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
3010482 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3010522 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
3010587 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3010627 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * ** * *
3010692 CCAACCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3010733 GAGT
1 GAGT
3010737 GTCACGATAT
Statistics
Matches: 486, Mismatches: 32, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
100 83 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 307 0.63
106 83 0.17
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3010976 original size:36 final size:36
Alignment explanation
Indices: 3010936--3011011 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
3010926 TGTTTGGAGA
**
3010936 GAAACTGA-CTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAACT-ATCTCAAGAGAGACAAAATTCATTTCAAGG
* *
3010972 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
3011008 GAAA
1 GAAA
3011012 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
Found at i:3011116 original size:104 final size:103
Alignment explanation
Indices: 3010913--3011228 Score: 467
Period size: 104 Copynumber: 3.1 Consensus size: 103
3010903 CGTTAAATTA
* ** * * *
3010913 TTTTCAAAGTTTATGTTTGGAGAGAAACTGACTCAAGAGAGACAAAA---TTTGTTTCAAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
* *
3010975 ACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAATG
66 ACTATCTCAAGAGAGA-AAAAATCATTTCAAGGGAAATG
**
3011014 TTTTCAATGTTTATGTTTCAAGAGAATTTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
3011079 ACTATCTCAAGAGAGAGAAAAATCATTTCAAGGGAAATG
66 ACTATCTCAAGAGAGA-AAAAATCATTTCAAGGGAAATG
*
3011118 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
* *
3011183 ACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAATG
66 ACTATCTCAAGAGAGAAAAAA-TCATTTCAAGGGAAATG
3011222 TTTTCAA
1 TTTTCAA
3011229 GAGAAACTGT
Statistics
Matches: 195, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
101 40 0.21
103 5 0.03
104 150 0.77
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (103 bp):
TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTGTTTCGAGGGAA
ACTATCTCAAGAGAGAAAAAATCATTTCAAGGGAAATG
Found at i:3011185 original size:39 final size:39
Alignment explanation
Indices: 3011131--3011205 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
3011121 TCAATGTTTA
* *
3011131 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
3011170 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
3011206 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:3011446 original size:72 final size:75
Alignment explanation
Indices: 3011299--3011466 Score: 186
Period size: 72 Copynumber: 2.3 Consensus size: 75
3011289 TAAAATCTTC
** * * * *
3011299 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTTAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTAAAATGAAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
3011363 CAAATCTTGTT
65 CAAATCATGTT
*
3011374 TTAAGAAAAACAATCTTGAGTAAAAT-AAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGAC
1 TTAAGAAAAACAATCTTGAGTAAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
3011436 AAAGT-ATGTT
66 AAA-TCATGTT
*
3011446 TTCAGAAAAACAAAT-TTGAGT
1 TTAAGAAAAAC-AATCTTGAGT
3011467 GAGATAATCA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
72 40 0.49
73 15 0.19
75 8 0.10
76 18 0.22
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (75 bp):
TTAAGAAAAACAATCTTGAGTAAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
AAATCATGTT
Found at i:3012922 original size:183 final size:183
Alignment explanation
Indices: 3012614--3013150 Score: 959
Period size: 183 Copynumber: 2.9 Consensus size: 183
3012604 ATCAGGTTTA
*
3012614 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
**
3012679 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAATGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
3012743 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACAAATC
* * *
3012797 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTAACAAAAGCAATGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
3012862 GCCAAGTGTCCGACCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
* *
3012927 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTAAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACAAATC
*
3012980 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
3013045 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
3013110 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
3013151 CGGATTTAAT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 335 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACAAATC
Found at i:3017148 original size:9 final size:9
Alignment explanation
Indices: 3017128--3017157 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3017118 ATACAAGGGA
3017128 AAAATAAAAT
1 AAAAT-AAAT
3017138 AAAATAAAT
1 AAAATAAAT
3017147 AAAATAAAT
1 AAAATAAAT
3017156 AA
1 AA
3017158 GTAAGATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.75
10 5 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:3017267 original size:47 final size:48
Alignment explanation
Indices: 3017172--3017311 Score: 121
Period size: 47 Copynumber: 2.9 Consensus size: 48
3017162 GATAAGAAAA
* * * *
3017172 AAAATACTAAAGTAATA-AT-TATATATAGTAATATTAGAT-TTATAAGT
1 AAAATAATAAAGAAATATATATATATATA-TAATAATA-ATAATATAAGT
*
3017219 AAAATATTAAAGAAATATATATATATATATAATAATAATAATAT-AGT
1 AAAATAATAAAGAAATATATATATATATATAATAATAATAATATAAGT
*
3017266 AAAA-AATAAATGAAAATAATTTAATATATATATACAT-ATAATAATA
1 AAAATAATAAA-G-AAAT-ATAT-ATATATATATA-ATAATAATAATA
3017312 ACATGAATAA
Statistics
Matches: 79, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
46 5 0.06
47 25 0.32
48 16 0.20
49 11 0.14
50 20 0.25
51 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (48 bp):
AAAATAATAAAGAAATATATATATATATATAATAATAATAATATAAGT
Found at i:3017336 original size:17 final size:18
Alignment explanation
Indices: 3017303--3017338 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3017293 ATATATACAT
*
3017303 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
3017321 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
3017338 A
1 A
3017339 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:3017749 original size:37 final size:37
Alignment explanation
Indices: 3017699--3017803 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
3017689 GTGCTTGTGG
* * * *
3017699 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
* * *
3017736 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
3017773 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
3017804 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAATTCT
Found at i:3018799 original size:19 final size:19
Alignment explanation
Indices: 3018771--3018815 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3018761 GAGCCTTCTA
* *
3018771 GAACCAATCCAGTCAGATC
1 GAACCGATCCAGTCAGACC
*
3018790 GAACCGATCCAGTCAGGCC
1 GAACCGATCCAGTCAGACC
3018809 GAACCGA
1 GAACCGA
3018816 GTCAAGCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (19 bp):
GAACCGATCCAGTCAGACC
Found at i:3025921 original size:22 final size:22
Alignment explanation
Indices: 3025895--3025977 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
3025885 TTAGTACAGA
3025895 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* *
3025917 GGGAA-CTGATTCCCCATTTGAAG
1 GGGAATC-GATACCCC-CTTGAAG
* * *
3025940 GGGAACCGATTCCCCCTTGTAG
1 GGGAATCGATACCCCCTTGAAG
*
3025962 GGGAATTGATACCCCC
1 GGGAATCGATACCCCC
3025978 CATGGGGTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.02
22 30 0.59
23 19 0.37
24 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.27, T:0.22
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:3025941 original size:23 final size:22
Alignment explanation
Indices: 3025906--3025977 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
3025896 GGAATCGATA
3025906 CCCCCTTGAAGGGGAACTGATT
1 CCCCCTTGAAGGGGAACTGATT
* *
3025928 CCCCATTTGAAGGGGAACCGATT
1 CCCC-CTTGAAGGGGAACTGATT
* * *
3025951 CCCCCTTGTAGGGGAATTGATA
1 CCCCCTTGAAGGGGAACTGATT
3025973 CCCCC
1 CCCCC
3025978 CATGGGGTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 22 0.52
23 20 0.48
ACGTcount: A:0.22, C:0.31, G:0.25, T:0.22
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACTGATT
Found at i:3027530 original size:18 final size:18
Alignment explanation
Indices: 3027514--3027559 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
3027504 GAACCAGAAT
3027514 AGCATGAGGAACAAGAACG
1 AGCA-GAGGAACAAGAACG
*
3027533 AGCAGAGGAACAAGCAC-
1 AGCAGAGGAACAAGAACG
3027550 AGCCAGAGGA
1 AG-CAGAGGA
3027560 TCAAATGCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 19 0.76
19 4 0.16
ACGTcount: A:0.46, C:0.20, G:0.33, T:0.02
Consensus pattern (18 bp):
AGCAGAGGAACAAGAACG
Found at i:3029397 original size:17 final size:19
Alignment explanation
Indices: 3029364--3029398 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3029354 CAAAATGAAT
3029364 AAATCAACCTCAAATACCA
1 AAATCAACCTCAAATACCA
3029383 AAAT-AACCT-AAATACC
1 AAATCAACCTCAAATACC
3029399 CTCGTGACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATCAACCTCAAATACCA
Found at i:3040911 original size:25 final size:25
Alignment explanation
Indices: 3040879--3040929 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3040869 CTTCATTCCA
3040879 TGGACTTCAAGACATCATCCTATGG
1 TGGACTTCAAGACATCATCCTATGG
*
3040904 TGGACTTCAAGACATCGTCCTATGG
1 TGGACTTCAAGACATCATCCTATGG
3040929 T
1 T
3040930 TGCAACCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (25 bp):
TGGACTTCAAGACATCATCCTATGG
Found at i:3054854 original size:30 final size:30
Alignment explanation
Indices: 3054818--3054887 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
3054808 CTAATAATAG
3054818 CTCCAACATTTTAAGAAATAAGTTAGAATT
1 CTCCAACATTTTAAGAAATAAGTTAGAATT
3054848 CTCCAACATTTTAAGAAATAAGTTAGAATT
1 CTCCAACATTTTAAGAAATAAGTTAGAATT
3054878 CTCCAACATT
1 CTCCAACATT
3054888 AGTCTAGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (30 bp):
CTCCAACATTTTAAGAAATAAGTTAGAATT
Found at i:3055727 original size:31 final size:31
Alignment explanation
Indices: 3055689--3055754 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
3055679 AGGGAGTGTT
**
3055689 GCAGTAGCTTGTGGAGCTATGTTGTGTAGCA
1 GCAGTAGCTTGTGGAGCTATGTCATGTAGCA
3055720 GCAGTAGCTTGTGGAGCTATGTCATGTAGCA
1 GCAGTAGCTTGTGGAGCTATGTCATGTAGCA
3055751 GCAG
1 GCAG
3055755 CAATTAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (31 bp):
GCAGTAGCTTGTGGAGCTATGTCATGTAGCA
Found at i:3056766 original size:33 final size:33
Alignment explanation
Indices: 3056709--3056978 Score: 229
Period size: 33 Copynumber: 7.8 Consensus size: 33
3056699 GTTTAGCACT
* *** *
3056709 AGGTGCCTCCAAGAGTCCCATCTCTTCATTAAA
1 AGGTCCCTCCAAGAGTCGTGTCTCTTCATCAAA
3056742 AGGTCCCTCCAAGAGTCGTGTCTCTTTC-TCAAA
1 AGGTCCCTCCAAGAGTCGTGTCTC-TTCATCAAA
3056775 AGGTTTCTCCAAGATCCCTCCAAGAGTCGTGTCTCTTCATCAAA
1 AGG----T-------CCCTCCAAGAGTCGTGTCTCTTCATCAAA
3056819 AGGTCCCTCCAAGAGTCGTGTCTCTTTC-TCAAA
1 AGGTCCCTCCAAGAGTCGTGTCTC-TTCATCAAA
** * *
3056852 AGGTTTCTCCAAGAGTCGTTTCTCTTTATCAAA
1 AGGTCCCTCCAAGAGTCGTGTCTCTTCATCAAA
* * * * * *
3056885 AGATACCTCCAAGATTTGTGTCTCTTAACCAAA
1 AGGTCCCTCCAAGAGTCGTGTCTCTTCATCAAA
* * *
3056918 AGGTGCCTCCAAGAATCGTGTCTCTTCACCAAA
1 AGGTCCCTCCAAGAGTCGTGTCTCTTCATCAAA
* *
3056951 AGGTGCCTCCAAGAGTCGTGTCTTTTCA
1 AGGTCCCTCCAAGAGTCGTGTCTCTTCA
3056979 CCAAGAGTTA
Statistics
Matches: 198, Mismatches: 24, Indels: 30
0.79 0.10 0.12
Matches are distributed among these distances:
32 2 0.01
33 157 0.79
34 6 0.03
37 1 0.01
40 1 0.01
43 3 0.02
44 28 0.14
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (33 bp):
AGGTCCCTCCAAGAGTCGTGTCTCTTCATCAAA
Found at i:3056841 original size:77 final size:77
Alignment explanation
Indices: 3056714--3056865 Score: 268
Period size: 77 Copynumber: 2.0 Consensus size: 77
3056704 GCACTAGGTG
*
3056714 CCTCCAAGAGTCCCATCTCTTCATTAAAAGGTCCCTCCAAGAGTCGTGTCTCTTTCTCAAAAGGT
1 CCTCCAAGAGTCCCATCTCTTCATCAAAAGGTCCCTCCAAGAGTCGTGTCTCTTTCTCAAAAGGT
3056779 TTCTCCAAGATC
66 TTCTCCAAGATC
***
3056791 CCTCCAAGAGTCGTGTCTCTTCATCAAAAGGTCCCTCCAAGAGTCGTGTCTCTTTCTCAAAAGGT
1 CCTCCAAGAGTCCCATCTCTTCATCAAAAGGTCCCTCCAAGAGTCGTGTCTCTTTCTCAAAAGGT
3056856 TTCTCCAAGA
66 TTCTCCAAGA
3056866 GTCGTTTCTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (77 bp):
CCTCCAAGAGTCCCATCTCTTCATCAAAAGGTCCCTCCAAGAGTCGTGTCTCTTTCTCAAAAGGT
TTCTCCAAGATC
Found at i:3056961 original size:99 final size:99
Alignment explanation
Indices: 3056785--3056969 Score: 264
Period size: 99 Copynumber: 1.9 Consensus size: 99
3056775 AGGTTTCTCC
* * * * *
3056785 AAGATCCCTCCAAGAGTCGTGTCTCTTCATCAAAAGGTCCCTCCAAGAGTCGTGTCTCTTTCTCA
1 AAGATACCTCCAAGAGTCGTGTCTCTTAACCAAAAGGTCCCTCCAAGAATCGTGTCTCTTTCCCA
**
3056850 AAAGGTTTCTCCAAGAGTCGTTTCTCTTTATCAA
66 AAAGGTGCCTCCAAGAGTCGTTTCTCTTTATCAA
* * *
3056884 AAGATACCTCCAAGATTTGTGTCTCTTAACCAAAAGGTGCCTCCAAGAATCGTGTCTC-TTCACC
1 AAGATACCTCCAAGAGTCGTGTCTCTTAACCAAAAGGTCCCTCCAAGAATCGTGTCTCTTTC-CC
3056948 AAAAGGTGCCTCCAAGAGTCGT
65 AAAAGGTGCCTCCAAGAGTCGT
3056970 GTCTTTTCAC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
98 3 0.04
99 72 0.96
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (99 bp):
AAGATACCTCCAAGAGTCGTGTCTCTTAACCAAAAGGTCCCTCCAAGAATCGTGTCTCTTTCCCA
AAAGGTGCCTCCAAGAGTCGTTTCTCTTTATCAA
Found at i:3056979 original size:33 final size:33
Alignment explanation
Indices: 3056791--3056982 Score: 233
Period size: 33 Copynumber: 5.8 Consensus size: 33
3056781 CTCCAAGATC
* *
3056791 CCTCCAAGAGTCGTGTCTCTTCATCAAAAGGTC
1 CCTCCAAGAGTCGTGTCTCTTCACCAAAAGGTG
* *
3056824 CCTCCAAGAGTCGTGTCTCTTTC-TCAAAAGGTT
1 CCTCCAAGAGTCGTGTCTC-TTCACCAAAAGGTG
* * * * * *
3056857 TCTCCAAGAGTCGTTTCTCTTTATCAAAAGATA
1 CCTCCAAGAGTCGTGTCTCTTCACCAAAAGGTG
* * *
3056890 CCTCCAAGATTTGTGTCTCTTAACCAAAAGGTG
1 CCTCCAAGAGTCGTGTCTCTTCACCAAAAGGTG
*
3056923 CCTCCAAGAATCGTGTCTCTTCACCAAAAGGTG
1 CCTCCAAGAGTCGTGTCTCTTCACCAAAAGGTG
*
3056956 CCTCCAAGAGTCGTGTCTTTTCACCAA
1 CCTCCAAGAGTCGTGTCTCTTCACCAA
3056983 GAGTTATCTG
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
32 2 0.01
33 133 0.96
34 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (33 bp):
CCTCCAAGAGTCGTGTCTCTTCACCAAAAGGTG
Found at i:3061971 original size:16 final size:16
Alignment explanation
Indices: 3061950--3061982 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3061940 TTGATATTGT
*
3061950 GCATTTGTAAACGAGG
1 GCATTTGTAAAAGAGG
3061966 GCATTTGTAAAAGAGG
1 GCATTTGTAAAAGAGG
3061982 G
1 G
3061983 AGCTAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.24
Consensus pattern (16 bp):
GCATTTGTAAAAGAGG
Found at i:3068792 original size:27 final size:27
Alignment explanation
Indices: 3068748--3068913 Score: 172
Period size: 27 Copynumber: 5.9 Consensus size: 27
3068738 TATCCCGATA
3068748 AAGTTGCTCGAATCATGCCCTGCTATC
1 AAGTTGCTCGAATCATGCCCTGCTATC
* * * *
3068775 AAATTTCTCGAATCATGCCTTGTTACCCTGATA
1 AAGTTGCTCGAATCATGCCCTG-----CT-ATC
* *
3068808 AAGTTGATCGAATCATGCTCTGCTA-C
1 AAGTTGCTCGAATCATGCCCTGCTATC
* *
3068834 TTAGTTACTCGAATCATGCCCTGCTATC
1 -AAGTTGCTCGAATCATGCCCTGCTATC
*
3068862 AAGTTGCTCGAACCATGCCCTGCTATC
1 AAGTTGCTCGAATCATGCCCTGCTATC
*
3068889 AAGTTGCTCGAACCATGCCCTGCTA
1 AAGTTGCTCGAATCATGCCCTGCTA
3068914 CCCTGACTCT
Statistics
Matches: 114, Mismatches: 17, Indels: 16
0.78 0.12 0.11
Matches are distributed among these distances:
27 90 0.79
28 3 0.03
32 2 0.02
33 19 0.17
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (27 bp):
AAGTTGCTCGAATCATGCCCTGCTATC
Found at i:3068819 original size:60 final size:59
Alignment explanation
Indices: 3068744--3068919 Score: 193
Period size: 60 Copynumber: 3.0 Consensus size: 59
3068734 CTGCTATCCC
* * *
3068744 GATAAAGTTGCTCGAATCATGCCCTGCTATCAAATTTCTCGAATCATGCCTTGTTACCCT
1 GATAAAGTTGCTCGAATCATGCCCTGCTATCAAGTTACTCGAATCATGCCCTG-TACCCT
* * *
3068804 GATAAAGTTGATCGAATCATGCTCTGCTA-CTTAGTTACTCGAATCATGCCCTG----CT
1 GATAAAGTTGCTCGAATCATGCCCTGCTATC-AAGTTACTCGAATCATGCCCTGTACCCT
* * * *
3068859 -ATCAAGTTGCTCGAACCATGCCCTGCTATCAAGTTGCTCGAACCATGCCCTGCTACCCT
1 GATAAAGTTGCTCGAATCATGCCCTGCTATCAAGTTACTCGAATCATGCCCTG-TACCCT
3068918 GA
1 GA
3068920 CTCTACAAGT
Statistics
Matches: 95, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
54 43 0.45
55 3 0.03
59 3 0.03
60 46 0.48
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.30
Consensus pattern (59 bp):
GATAAAGTTGCTCGAATCATGCCCTGCTATCAAGTTACTCGAATCATGCCCTGTACCCT
Found at i:3068975 original size:144 final size:146
Alignment explanation
Indices: 3068798--3069083 Score: 389
Period size: 150 Copynumber: 1.9 Consensus size: 146
3068788 CATGCCTTGT
* ** * *
3068798 TACCCTGATAAAGTTGATCGAATCATGCTCTGCTACTTAGTTACTCGAATCATGCCCTG-CT-AT
1 TACCCCGATAAAGTTGATCGAATCATGCTCTGCTACCAAATTACTCGAATCATACCCTGCCTAAT
* * *
3068861 CAAGTTGCTCGAACCATGCCCTGCTATCAAGTTGCTCGAACCATGCCCTGCTACCCTGACTCTAC
66 CAAGTTGCTCGAACCATGCCCTGCTACCAAGTTGCTCAAACCATGCCCTGCTACCCTGACACTAC
3068926 AAGTTGTTCTTCCTGC
131 AAGTTGTTCTTCCTGC
* *
3068942 TACCCCGATAAAGTT-ACTCGAATCATGCTCTGCTACCAAATTTCTCGAATCATACCTTGTTACC
1 TACCCCGATAAAGTTGA-TCGAATCATGCTCTGCTACCAAATTACTCGAATCATACCCTG----C
* * *
3069006 CTAATCAAGTTGTTCGAACCATGCCTTGCTACCAAGTTGCTCAAACCATGCCCTTCTACCCTGAC
61 CTAATCAAGTTGCTCGAACCATGCCCTGCTACCAAGTTGCTCAAACCATGCCCTGCTACCCTGAC
3069071 ACTACAAGTTGTT
126 ACTACAAGTTGTT
3069084 GAAGTGTTAG
Statistics
Matches: 122, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
143 1 0.01
144 50 0.41
149 2 0.02
150 69 0.57
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (146 bp):
TACCCCGATAAAGTTGATCGAATCATGCTCTGCTACCAAATTACTCGAATCATACCCTGCCTAAT
CAAGTTGCTCGAACCATGCCCTGCTACCAAGTTGCTCAAACCATGCCCTGCTACCCTGACACTAC
AAGTTGTTCTTCCTGC
Found at i:3069052 original size:27 final size:27
Alignment explanation
Indices: 3069011--3069065 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3069001 TTACCCTAAT
* *
3069011 CAAGTTGTTCGAACCATG-CCTTGCTAC
1 CAAGTTGCTCAAACCATGCCCTT-CTAC
3069038 CAAGTTGCTCAAACCATGCCCTTCTAC
1 CAAGTTGCTCAAACCATGCCCTTCTAC
3069065 C
1 C
3069066 CTGACACTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.27
Consensus pattern (27 bp):
CAAGTTGCTCAAACCATGCCCTTCTAC
Found at i:3069168 original size:33 final size:27
Alignment explanation
Indices: 3069099--3069207 Score: 110
Period size: 27 Copynumber: 3.8 Consensus size: 27
3069089 GTTAGGATAG
3069099 CAGGGCATGGTTCGAGCAACTTGGTAA
1 CAGGGCATGGTTCGAGCAACTTGGTAA
*
3069126 CAGGACATGGTTCGAGCAACTAGATCAGGGTAA
1 CAGGGCATGGTTCGAGCAACT---T---GGTAA
* * * *
3069159 CAGGGCATGGTTCGAGAAATTTGATAG
1 CAGGGCATGGTTCGAGCAACTTGGTAA
*
3069186 CAGGGCATGATTCGAGCAACTT
1 CAGGGCATGGTTCGAGCAACTT
3069208 TATCAGGATA
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
27 42 0.63
30 2 0.03
33 23 0.34
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.22
Consensus pattern (27 bp):
CAGGGCATGGTTCGAGCAACTTGGTAA
Found at i:3078974 original size:19 final size:21
Alignment explanation
Indices: 3078931--3078974 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
3078921 CACTAAAATG
* *
3078931 TTATATGTTCATTTTAATATT
1 TTATATGTTAATTTGAATATT
3078952 TTATAT-TTAATTTGAAT-TT
1 TTATATGTTAATTTGAATATT
3078971 TTAT
1 TTAT
3078975 TTGAAATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
TTATATGTTAATTTGAATATT
Found at i:3080342 original size:18 final size:16
Alignment explanation
Indices: 3080315--3080355 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
3080305 ACTTATAGTC
*
3080315 TATATGTAAATAAAGAT
1 TATATTTAAATAAA-AT
3080332 TGATATTTAAATAAAAT
1 T-ATATTTAAATAAAAT
3080349 TATATTT
1 TATATTT
3080356 TTTCCGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (16 bp):
TATATTTAAATAAAAT
Found at i:3081295 original size:48 final size:48
Alignment explanation
Indices: 3081230--3081581 Score: 314
Period size: 48 Copynumber: 7.6 Consensus size: 48
3081220 TGTAAACTGG
* * *
3081230 TGGTGGCGGGGGTGGAGACTTGTACTTATAAGGATGTTTGGGTGGTGA
1 TGGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTGGGTGGTGA
* *
3081278 TGGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGCTTGGGTGGTGA
1 TGGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTGGGTGGTGA
* *
3081326 TGGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGGTTGGGTGGTGA
1 TGGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTGGGTGGTGA
* * * * *
3081374 TGGTGGTGGTGGTGGTGGGGACTTATACTTGTAAGG-TGGTGGAGGATAGTGCA
1 ---TGGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTG-GG-TGGTG-A
* * * **
3081427 --CTGGAGGTGGTGGAGACTTATACTTGTAA--A--------CCG-GA
1 TGGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTGGGTGGTGA
* * *
3081462 -GGTGGTGGTGGTGGAGATTTGTACTTGTAAGGATGTTTTGGTGGCGA
1 TGGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTGGGTGGTGA
*
3081509 TGGTGGTGGTGGT---GACTTGTACTTGTAAGGATGTTTGGGTGGCGA
1 TGGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTGGGTGGTGA
3081554 TGGTGGTGGTGGT---GACTTGTACTTGTAA
1 TGGTGGTGGTGGTGGAGACTTGTACTTGTAA
3081582 ACTGGAGTTG
Statistics
Matches: 262, Mismatches: 22, Indels: 43
0.80 0.07 0.13
Matches are distributed among these distances:
35 1 0.00
36 26 0.10
37 1 0.00
38 1 0.00
45 58 0.22
46 1 0.00
47 2 0.01
48 130 0.50
50 5 0.02
51 32 0.12
52 4 0.02
53 1 0.00
ACGTcount: A:0.17, C:0.07, G:0.44, T:0.33
Consensus pattern (48 bp):
TGGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTGGGTGGTGA
Found at i:3081505 original size:39 final size:41
Alignment explanation
Indices: 3081462--3081581 Score: 141
Period size: 45 Copynumber: 2.7 Consensus size: 41
3081452 GTAAACCGGA
*
3081462 GGTGGTGGTGGTGGAGATTTGTACTTGTAAGGATGTTTTGGTG
1 GGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATG-TTT-GTG
*
3081505 GCGATGGTGGTGGTGGTGACTTGTACTTGTAAGGATGTTTGGGTG
1 G-G-TGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTT--GTG
*
3081550 GCGATGGTGGTGGTGGTGACTTGTACTTGTAA
1 G-G-TGGTGGTGGTGGAGACTTGTACTTGTAA
3081582 ACTGGAGTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
43 1 0.01
44 4 0.06
45 67 0.93
ACGTcount: A:0.14, C:0.06, G:0.43, T:0.37
Consensus pattern (41 bp):
GGTGGTGGTGGTGGAGACTTGTACTTGTAAGGATGTTTGTG
Found at i:3081580 original size:231 final size:229
Alignment explanation
Indices: 3081102--3081567 Score: 691
Period size: 231 Copynumber: 2.0 Consensus size: 229
3081092 ATGTACTGGC
* *
3081102 GGTGGTGGAGACTTGTACTTGTAAGGATGCTTGGGAGGGGTTGGTGAAGGAGGTGGTGGGGACCT
1 GGTGGTGGAGACTTGTACTTATAAGGATGCTTGGGAGGGGATGGTGAAGGAGGTGGTGGGGACCT
* * *
3081167 GTACTTATAAGGGGGTGGAGGATAGTGCACCGGAGGTGGTGGAGACTTATACTTGTAAACTGGTG
66 ATACTTATAAGGGGGTGGAGGATAGTGCACCGGAGGTGGTGGAGACTTATACTTGTAAACCGGAG
*
3081232 GTGGCGGGGGTGGAGACTTGTACTTATAAGGATGTTTGGGTGGTGATGGTGGTGGTGGTGGAGAC
131 GTGGCGGGGGTGGAGACTTGTACTTATAAGGATGTTTGGGTGGCGATGGTGGTGGTGGT-G-GAC
*
3081297 TTGTACTTATAAGGATGCTTGGGTGGTGATGGTGGT
194 TTGTACTTATAAGGATGCTTGGGTGGCGATGGTGGT
* * * ** * *
3081333 GGTGGTGGAGACTTGTACTTATAAGGATGGTTGGGTGGTGATGGTGGTGGTGGTGGTGGGGACTT
1 GGTGGTGGAGACTTGTACTTATAAGGATGCTTGGGAGGGGATGGTGAAGGAGGTGGTGGGGACCT
* * *
3081398 ATACTTGTAAGGTGGTGGAGGATAGTGCACTGGAGGTGGTGGAGACTTATACTTGTAAACCGGAG
66 ATACTTATAAGGGGGTGGAGGATAGTGCACCGGAGGTGGTGGAGACTTATACTTGTAAACCGGAG
* * * * *
3081463 GTGGTGGTGGTGGAGATTTGTACTTGTAAGGATGTTTTGGTGGCGATGGTGGTGGTGGT-GACTT
131 GTGGCGGGGGTGGAGACTTGTACTTATAAGGATGTTTGGGTGGCGATGGTGGTGGTGGTGGACTT
* *
3081527 GTACTTGTAAGGATGTTTGGGTGGCGATGGTGGT
196 GTACTTATAAGGATGCTTGGGTGGCGATGGTGGT
3081561 GGTGGTG
1 GGTGGTG
3081568 ACTTGTACTT
Statistics
Matches: 211, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
228 43 0.20
231 168 0.80
ACGTcount: A:0.18, C:0.07, G:0.45, T:0.31
Consensus pattern (229 bp):
GGTGGTGGAGACTTGTACTTATAAGGATGCTTGGGAGGGGATGGTGAAGGAGGTGGTGGGGACCT
ATACTTATAAGGGGGTGGAGGATAGTGCACCGGAGGTGGTGGAGACTTATACTTGTAAACCGGAG
GTGGCGGGGGTGGAGACTTGTACTTATAAGGATGTTTGGGTGGCGATGGTGGTGGTGGTGGACTT
GTACTTATAAGGATGCTTGGGTGGCGATGGTGGT
Found at i:3081631 original size:129 final size:129
Alignment explanation
Indices: 3081380--3081631 Score: 289
Period size: 129 Copynumber: 2.0 Consensus size: 129
3081370 GTGATGGTGG
3081380 TGGTGGTGGTGGGGACTTATACTTGTAAGGTGGTGGAGGATAGTGCACTGGAGGTGGTGGAGACT
1 TGGTGGTGGTGGGGACTTATACTTGTAAGGTGGTGGAGGATAGTGCACTGGAGGTGGTGGAGACT
* * * *
3081445 TATACTTGTAAACCGGAGGTGGTGGTGGTGGAGATTTGTACTTGTAAGGATGTTTTGGTGGCGA
66 TATACTTGTAAACCGGAGGGGGTGGTGGAGGAGATTTATACTTGTAAGGATGCTTTGGTGGCGA
* * * * * *
3081509 TGGTGGTGGTGGTGACTTGTACTTGTAAGGATGTTTG-GG-T-G-GCGA-TGGTGGTGGTGGTGA
1 TGGTGGTGGTGGGGACTTATACTTGTAAGG-TGGTGGAGGATAGTGC-ACTGGAGGTGGTGGAGA
* * * * *
3081569 CTTGTACTTGTAAACTGGAGTTGGGGGTGGTGGAGGAGATTTATATTTGTATGGGTGCTTTGG
64 CTTATACTTGTAAACCGGA---GGGGGTGGTGGAGGAGATTTATACTTGTAAGGATGCTTTGG
3081632 CGGAGGTGGG
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
126 32 0.31
127 2 0.02
128 1 0.01
129 64 0.62
130 4 0.04
ACGTcount: A:0.17, C:0.07, G:0.42, T:0.34
Consensus pattern (129 bp):
TGGTGGTGGTGGGGACTTATACTTGTAAGGTGGTGGAGGATAGTGCACTGGAGGTGGTGGAGACT
TATACTTGTAAACCGGAGGGGGTGGTGGAGGAGATTTATACTTGTAAGGATGCTTTGGTGGCGA
Found at i:3081703 original size:33 final size:33
Alignment explanation
Indices: 3081633--3081704 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
3081623 GTGCTTTGGC
* * *
3081633 GGAGGTGGGGGAGACTTGTACTTATAAACCGGG
1 GGAGGAGGAGGAGACTTGTACTTATAAACCGGA
* **
3081666 GGAGGAGGAGGAGACTTGTACTTGTAAGGCGGA
1 GGAGGAGGAGGAGACTTGTACTTATAAACCGGA
3081699 GGAGGA
1 GGAGGA
3081705 TAATGCACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.10, G:0.46, T:0.18
Consensus pattern (33 bp):
GGAGGAGGAGGAGACTTGTACTTATAAACCGGA
Found at i:3083327 original size:17 final size:17
Alignment explanation
Indices: 3083305--3083343 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3083295 CTCTCTAAAA
3083305 ATTTTAAATTTTTTTAT
1 ATTTTAAATTTTTTTAT
* *
3083322 ATTTTAAGTTTTTTTGT
1 ATTTTAAATTTTTTTAT
3083339 ATTTT
1 ATTTT
3083344 TATTGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
ATTTTAAATTTTTTTAT
Found at i:3083993 original size:41 final size:41
Alignment explanation
Indices: 3083883--3083993 Score: 103
Period size: 37 Copynumber: 2.8 Consensus size: 41
3083873 AATATCTAAA
* *
3083883 AATAAAAAATTAATTATACATGTTATTGGATC-AATAATTT
1 AATAAAAAATTAATTATACATGTTATTGGATCAAAGAAATT
* *
3083923 AAAAATAAACACTTAAGTA-A-A--TTA-T--ATCAAAGAAATT
1 AATAA-AAA-A-TTAATTATACATGTTATTGGATCAAAGAAATT
3083960 AATAAAAAATTAATTATACATGTTATTGGATCAA
1 AATAAAAAATTAATTATACATGTTATTGGATCAA
3083994 TATTTTTCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 21
0.67 0.07 0.26
Matches are distributed among these distances:
34 6 0.11
35 2 0.04
36 7 0.13
37 10 0.19
38 4 0.07
39 4 0.07
40 4 0.07
41 9 0.17
42 2 0.04
43 6 0.11
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.34
Consensus pattern (41 bp):
AATAAAAAATTAATTATACATGTTATTGGATCAAAGAAATT
Found at i:3094111 original size:23 final size:23
Alignment explanation
Indices: 3094085--3094136 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
3094075 AGTGTGAGTG
3094085 GAGTGAAATCTGAATTTTCTTTA
1 GAGTGAAATCTGAATTTTCTTTA
*
3094108 GAGTGAAATCTGAATTTTCTTTG
1 GAGTGAAATCTGAATTTTCTTTA
3094131 GAGTGA
1 GAGTGA
3094137 CCAAGTGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (23 bp):
GAGTGAAATCTGAATTTTCTTTA
Found at i:3100764 original size:24 final size:24
Alignment explanation
Indices: 3100730--3100795 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
3100720 TTACAAAAGT
3100730 TTGTGCTTTTGCAGCAGATGAAAC
1 TTGTGCTTTTGCAGCAGATGAAAC
* * *
3100754 TTGTGCATTTGCAACAGATGAAGC
1 TTGTGCTTTTGCAGCAGATGAAAC
3100778 TTGTGCTTTTGCAGCAGA
1 TTGTGCTTTTGCAGCAGA
3100796 CGAGTCTCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (24 bp):
TTGTGCTTTTGCAGCAGATGAAAC
Found at i:3104497 original size:17 final size:15
Alignment explanation
Indices: 3104466--3104501 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
3104456 AAATGAAAAA
3104466 TAAATAAAAAAATAT
1 TAAATAAAAAAATAT
3104481 TAAATTAAAAGAAATAT
1 TAAA-TAAAA-AAATAT
3104498 TAAA
1 TAAA
3104502 GATGGATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 5 0.26
17 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
TAAATAAAAAAATAT
Found at i:3105762 original size:24 final size:23
Alignment explanation
Indices: 3105730--3105828 Score: 82
Period size: 24 Copynumber: 4.4 Consensus size: 23
3105720 AAATCATACA
3105730 ATATGTTTTTAAAATATATATTAC
1 ATATGTTTTTAAAA-ATATATTAC
*
3105754 ATATGTTTTT-CAAA-A-ATT--
1 ATATGTTTTTAAAAATATATTAC
* * *
3105772 ATATGTTTTCAAAATTATATAAC
1 ATATGTTTTTAAAAATATATTAC
*
3105795 AATATGTTTTTAAAAACTATATTAT
1 -ATATGTTTTTAAAAA-TATATTAC
*
3105820 ACATGTTTT
1 ATATGTTTT
3105829 CCAAAAACCA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
18 9 0.16
19 2 0.03
20 4 0.07
21 3 0.05
22 1 0.02
23 2 0.03
24 31 0.53
25 6 0.10
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATGTTTTTAAAAATATATTAC
Found at i:3105779 original size:42 final size:41
Alignment explanation
Indices: 3105730--3105816 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
3105720 AAATCATACA
* * *
3105730 ATATGTTTTTAAAATATATATTAC-ATATGTTTTTCAAAAATT
1 ATATGTTTTCAAAAT-TATATAACAATATGTTTTT-AAAAACT
3105772 ATATGTTTTCAAAATTATATAACAATATGTTTTTAAAAACT
1 ATATGTTTTCAAAATTATATAACAATATGTTTTTAAAAACT
3105813 ATAT
1 ATAT
3105817 TATACATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 17 0.41
42 24 0.59
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.47
Consensus pattern (41 bp):
ATATGTTTTCAAAATTATATAACAATATGTTTTTAAAAACT
Found at i:3105787 original size:16 final size:18
Alignment explanation
Indices: 3105754--3105791 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
3105744 TATATATTAC
3105754 ATATGTTTTTCAAAAATT
1 ATATGTTTTTCAAAAATT
3105772 ATATG-TTTTC-AAAATT
1 ATATGTTTTTCAAAAATT
3105788 ATAT
1 ATAT
3105792 AACAATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 5 0.25
18 5 0.25
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (18 bp):
ATATGTTTTTCAAAAATT
Found at i:3105792 original size:18 final size:19
Alignment explanation
Indices: 3105749--3105792 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
3105739 TAAAATATAT
*
3105749 ATTACATATGTTTTTCAAA
1 ATTATATATGTTTTTCAAA
*
3105768 AAT-TATATG-TTTTCAAA
1 ATTATATATGTTTTTCAAA
3105785 ATTATATA
1 ATTATATA
3105793 ACAATATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 10 0.48
18 9 0.43
19 2 0.10
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (19 bp):
ATTATATATGTTTTTCAAA
Found at i:3105900 original size:37 final size:36
Alignment explanation
Indices: 3105800--3105912 Score: 120
Period size: 37 Copynumber: 2.9 Consensus size: 36
3105790 ATAACAATAT
*
3105800 GTTTTTAAAAACTAT-ATTATACATGTTTTCCAAAAACC
1 GTTTTAAAAAACTATAATTAT--ATGTTTT-CAAAAACC
* *
3105838 ATTTTAAAAAATAACTATATATTATATATTTTCAAAAACC
1 GTTTT--AAAA-AACTATA-ATTATATGTTTTCAAAAACC
3105878 GTTTTAAAAAACTATAAATTATATGTTTTCAAAAA
1 GTTTTAAAAAACTAT-AATTATATGTTTTCAAAAA
3105913 TATGTTTTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
37 23 0.36
38 9 0.14
40 15 0.23
41 12 0.19
43 5 0.08
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (36 bp):
GTTTTAAAAAACTATAATTATATGTTTTCAAAAACC
Found at i:3105917 original size:14 final size:14
Alignment explanation
Indices: 3105898--3105924 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3105888 ACTATAAATT
3105898 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
3105912 ATATGTTTTCAAA
1 ATATGTTTTCAAA
3105925 GACTTTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:3108771 original size:2 final size:2
Alignment explanation
Indices: 3108764--3108821 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3108754 AAAATGGATA
3108764 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
3108806 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3108822 GTTAAAGGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3109574 original size:19 final size:20
Alignment explanation
Indices: 3109534--3109575 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3109524 AATTATTAAA
*
3109534 ATTTATAAAATAGTTTTTTT
1 ATTTATAAAATAGTTATTTT
3109554 ATTTATAAAATA-TTATTTT
1 ATTTATAAAATAGTTATTTT
3109573 ATT
1 ATT
3109576 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTATAAAATAGTTATTTT
Found at i:3115305 original size:26 final size:25
Alignment explanation
Indices: 3115269--3115330 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
3115259 AGAATCTATT
3115269 TTTG-CTC-CTTAAAATTATA-TAAG
1 TTTGTCTCTCTTAAAATTATAGT-AG
*
3115292 TTTGTCATCTCTTAAAATTTTAGTAG
1 TTTGTC-TCTCTTAAAATTATAGTAG
3115318 TTTGTCTCT-TTAA
1 TTTGTCTCTCTTAA
3115331 CATAAAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
23 4 0.12
24 5 0.15
25 5 0.15
26 19 0.56
27 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (25 bp):
TTTGTCTCTCTTAAAATTATAGTAG
Found at i:3116291 original size:73 final size:74
Alignment explanation
Indices: 3116203--3116346 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 74
3116193 GAGATTTCTT
3116203 TTTTTAAAAAAAACCCAAAACAAAACAAAGAAATTAGAAGAAGAAATCCATAAACAATACCCACA
1 TTTTTAAAAAAAACCCAAAACAAAACAAAGAAATTAGAAGAAGAAATCCATAAACAATACCCACA
3116268 A-ATTTTTC
66 ATATTTTTC
3116276 TTTTTAAAAAAAACCCAAAACAAAACAAAGAAATTAGAAGAAGAAATCCATAAACAATACCCACA
1 TTTTTAAAAAAAACCCAAAACAAAACAAAGAAATTAGAAGAAGAAATCCATAAACAATACCCACA
3116341 ATATTT
66 ATATTT
3116347 GAATCTTCGT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 66 0.94
74 4 0.06
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20
Consensus pattern (74 bp):
TTTTTAAAAAAAACCCAAAACAAAACAAAGAAATTAGAAGAAGAAATCCATAAACAATACCCACA
ATATTTTTC
Found at i:3116614 original size:2 final size:2
Alignment explanation
Indices: 3116607--3116640 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3116597 AAAACCCTAA
3116607 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
3116641 TTGATGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3117778 original size:4 final size:4
Alignment explanation
Indices: 3117769--3117810 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
3117759 CTAACAATTG
* * *
3117769 TTTA TTTA TTTA TTTG TTTG TTTG TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3117811 CTAATATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3117791 original size:20 final size:20
Alignment explanation
Indices: 3117766--3117803 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3117756 ATTCTAACAA
3117766 TTGTTTATTTATTTATTTGT
1 TTGTTTATTTATTTATTTGT
*
3117786 TTGTTTGTTTATTTATTT
1 TTGTTTATTTATTTATTT
3117804 ATTATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (20 bp):
TTGTTTATTTATTTATTTGT
Found at i:3120886 original size:8 final size:7
Alignment explanation
Indices: 3120862--3120903 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
3120852 TTTTCATACA
3120862 TGCA-TT
1 TGCATTT
3120868 TGCATTT
1 TGCATTT
3120875 TGCATCTT
1 TGCAT-TT
3120883 TGCATTT
1 TGCATTT
* *
3120890 TTCATTG
1 TGCATTT
3120897 TGCATTT
1 TGCATTT
3120904 ATACTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:3120886 original size:15 final size:14
Alignment explanation
Indices: 3120862--3120903 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
3120852 TTTTCATACA
3120862 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
3120875 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
3120890 TTCATTGTGCATTT
1 TGCATTTTGCATTT
3120904 ATACTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:3123673 original size:9 final size:9
Alignment explanation
Indices: 3123658--3123747 Score: 76
Period size: 9 Copynumber: 9.9 Consensus size: 9
3123648 TATTATGCTT
3123658 GAAAAAAAA
1 GAAAAAAAA
*
3123667 -TAAAAAAA
1 GAAAAAAAA
3123675 GAAAAAAAAA
1 G-AAAAAAAA
3123685 GAAGGAAAAAA
1 GAA--AAAAAA
*
3123696 GAAAGAAAA
1 GAAAAAAAA
3123705 GAAAAAAAA
1 GAAAAAAAA
* *
3123714 GGAAAAAAG
1 GAAAAAAAA
**
3123723 GAAAAATGA
1 GAAAAAAAA
*
3123732 G-AAAAAAG
1 GAAAAAAAA
3123740 GAAAAAAA
1 GAAAAAAA
3123748 GGGAAAAAGA
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 12 0.19
9 34 0.54
10 8 0.13
11 9 0.14
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:3123680 original size:17 final size:16
Alignment explanation
Indices: 3123658--3123747 Score: 69
Period size: 17 Copynumber: 5.5 Consensus size: 16
3123648 TATTATGCTT
3123658 GAAAAAAAATAAAAAA-
1 GAAAAAAAA-AAAAAAG
* *
3123674 -AGAAAAAAAAAGAAG
1 GAAAAAAAAAAAAAAG
*
3123689 GAAAAAAGAAAGAAAA-
1 GAAAAAA-AAAAAAAAG
3123705 GAAAAAAAAGGAAAAAAG
1 GAAAAAAAA--AAAAAAG
* *
3123723 GAAAAATGAGAAAAAAG
1 GAAAAA-AAAAAAAAAG
3123740 GAAAAAAA
1 GAAAAAAA
3123748 GGGAAAAAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.09
15 9 0.16
16 13 0.22
17 24 0.41
18 6 0.10
19 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
GAAAAAAAAAAAAAAG
Found at i:3123685 original size:10 final size:10
Alignment explanation
Indices: 3123659--3123721 Score: 67
Period size: 10 Copynumber: 6.4 Consensus size: 10
3123649 ATTATGCTTG
*
3123659 AAAAAAA-AT
1 AAAAAAAGAA
3123668 AAAAAAAGAA
1 AAAAAAAGAA
3123678 AAAAAAAGAA
1 AAAAAAAGAA
*
3123688 GGAAAAAAG-A
1 -AAAAAAAGAA
*
3123698 AAGAAAAGAA
1 AAAAAAAGAA
*
3123708 AAAAAAGGAA
1 AAAAAAAGAA
3123718 AAAA
1 AAAA
3123722 GGAAAAATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
9 13 0.29
10 25 0.56
11 7 0.16
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:3123709 original size:25 final size:24
Alignment explanation
Indices: 3123668--3123746 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
3123658 GAAAAAAAAT
*
3123668 AAAA-AAAGAAAAAAAAAGAAGGAA
1 AAAAGAAAGAAAAGAAAA-AAGGAA
3123692 AAAAGAAAGAAAAGAAAAAAAAGGAA
1 AAAAGAAAGAAAAG--AAAAAAGGAA
*
3123718 AAAAGGAAA-AATGAGAAAAAAGGAA
1 AAAA-GAAAGAA-AAGAAAAAAGGAA
3123743 AAAA
1 AAAA
3123747 AGGGAAAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
24 4 0.08
25 22 0.46
26 12 0.25
27 10 0.21
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (24 bp):
AAAAGAAAGAAAAGAAAAAAGGAA
Found at i:3123737 original size:10 final size:8
Alignment explanation
Indices: 3123668--3123761 Score: 77
Period size: 8 Copynumber: 11.6 Consensus size: 8
3123658 GAAAAAAAAT
*
3123668 AAAAAAAG
1 AAAAAAGG
3123676 AAAAAA--
1 AAAAAAGG
*
3123682 AAAGAAGG
1 AAAAAAGG
*
3123690 AAAAAAGA
1 AAAAAAGG
*
3123698 AAGAAAAGAA
1 AA-AAAAG-G
3123708 AAAAAAGG
1 AAAAAAGG
3123716 AAAAAAGG
1 AAAAAAGG
*
3123724 AAAAATGAG
1 AAAAAAG-G
3123733 AAAAAAGG
1 AAAAAAGG
3123741 AAAAAAAGG
1 -AAAAAAGG
*
3123750 GAAAAA-G
1 AAAAAAGG
3123757 AAAAA
1 AAAAA
3123762 GGGGAGAAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
6 5 0.07
7 5 0.07
8 34 0.47
9 25 0.35
10 3 0.04
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (8 bp):
AAAAAAGG
Found at i:3123739 original size:34 final size:34
Alignment explanation
Indices: 3123681--3123761 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
3123671 AAAAGAAAAA
3123681 AAAAGAAGGAAAAAAGAAAGAAAAGAAAAAAAAGG
1 AAAA-AAGGAAAAAAGAAAGAAAAGAAAAAAAAGG
* *
3123716 AAAAAAGGAAAAATGAGAA-AAAAGGAAAAAAAGG
1 AAAAAAGGAAAAAAGA-AAGAAAAGAAAAAAAAGG
*
3123750 GAAAAA-GAAAAA
1 AAAAAAGGAAAAA
3123762 GGGGAGAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 6 0.14
34 30 0.71
35 6 0.14
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (34 bp):
AAAAAAGGAAAAAAGAAAGAAAAGAAAAAAAAGG
Found at i:3123747 original size:26 final size:25
Alignment explanation
Indices: 3123679--3123761 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 25
3123669 AAAAAAGAAA
*
3123679 AAAAAAGAAGGAAAAAAGAAAGAAAAG
1 AAAAAA-AAGGAAAAAAGGAA-AAAAG
*
3123706 AAAAAAAAGGAAAAAAGGAAAAATG
1 AAAAAAAAGGAAAAAAGGAAAAAAG
* *
3123731 AGAAAAAAGGAAAAAAAGGGAAAAAG
1 AAAAAAAAGG-AAAAAAGGAAAAAAG
3123757 AAAAA
1 AAAAA
3123762 GGGGAGAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
25 13 0.27
26 30 0.61
27 6 0.12
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (25 bp):
AAAAAAAAGGAAAAAAGGAAAAAAG
Found at i:3123754 original size:17 final size:17
Alignment explanation
Indices: 3123681--3123761 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
3123671 AAAAGAAAAA
*
3123681 AAAAGAAGG-AAAAAAGA
1 AAAA-AAGGAAAAAAAGG
*
3123698 AAGAAAAGAAAAAAAAGG
1 AA-AAAAGGAAAAAAAGG
*
3123716 AAAAAAGG-AAAAATGAG
1 AAAAAAGGAAAAAAAG-G
3123733 AAAAAAGGAAAAAAAGG
1 AAAAAAGGAAAAAAAGG
*
3123750 GAAAAA-GAAAAA
1 AAAAAAGGAAAAA
3123762 GGGGAGAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 12 0.22
17 25 0.46
18 17 0.31
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (17 bp):
AAAAAAGGAAAAAAAGG
Found at i:3126121 original size:114 final size:114
Alignment explanation
Indices: 3125921--3126148 Score: 447
Period size: 114 Copynumber: 2.0 Consensus size: 114
3125911 GTGCCACGTT
*
3125921 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAG
3125986 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
3126035 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAG
3126100 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
3126149 ATGATAGTCT
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAG
GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
Found at i:3128734 original size:22 final size:22
Alignment explanation
Indices: 3128684--3128735 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3128674 TACATTCTTC
* *
3128684 AAAGATAATAAATTTTCTTTTT
1 AAAGATGATAAATTCTCTTTTT
*
3128706 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAAATTCTCTTTTT
*
3128728 GAAGATGA
1 AAAGATGA
3128736 AAGCTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.42
Consensus pattern (22 bp):
AAAGATGATAAATTCTCTTTTT
Found at i:3129497 original size:76 final size:76
Alignment explanation
Indices: 3129415--3129798 Score: 696
Period size: 76 Copynumber: 5.1 Consensus size: 76
3129405 CTATTTCTCA
*
3129415 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAACGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3129480 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3129491 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3129556 AGCCTTAGGGT
66 AGCCTTAGGGT
3129567 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3129632 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3129643 CATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3129708 AGCCTTAGGGT
66 AGCCTTAGGGT
*
3129719 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
3129784 AACCTTCGGGT
66 AGCCTTAGGGT
3129795 CATC
1 CATC
3129799 AGCATTTTCA
Statistics
Matches: 298, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 298 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:3129943 original size:113 final size:114
Alignment explanation
Indices: 3129808--3130223 Score: 597
Period size: 113 Copynumber: 3.7 Consensus size: 114
3129798 CAGCATTTTC
* *
3129808 AGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
** * *
3129873 TGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTCTTCCAG
66 TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAACTCTTCCAG
*
3129922 AGAA-AGTTCATAATGAGAAGAACTAATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
* * * *
3129986 TGTTTAACCTTTTGCTTGAATTTATCACTTGATGGATTAACTCTTCCAA
66 TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAACTCTTCCAG
* * * *
3130035 AG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGGAAGAAATTCATAATGAGAA-AATT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA-C
* * * *
3130098 TTGTTCAACTTTTTGTTTGAATTCATCACTCGATGGATCAACTTTTCCAG
65 TTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAACTCTTCCAG
* * *
3130148 AGAAGAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAATT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
3130212 TGTTCAACCTTT
66 TGTTCAACCTTT
3130224 GTTTGACTCT
Statistics
Matches: 268, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
112 3 0.01
113 229 0.85
114 36 0.13
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (114 bp):
AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAACTCTTCCAG
Found at i:3130563 original size:3 final size:3
Alignment explanation
Indices: 3130555--3130598 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
3130545 TTTGTTTTAT
*
3130555 TTA TTA TTA TTA TTT TGTA TTA TTA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3130599 AATAATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3130569 original size:13 final size:13
Alignment explanation
Indices: 3130551--3130598 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
3130541 TTCATTTGTT
3130551 TTATTTATTATTA
1 TTATTTATTATTA
3130564 TTATTT-TGTATTA
1 TTATTTAT-TATTA
3130577 TTATTATATTA-TA
1 TTATT-TATTATTA
3130590 TTA-TTATTA
1 TTATTTATTA
3130599 AATAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.16
12 2 0.06
13 21 0.66
14 3 0.09
15 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:3130577 original size:16 final size:16
Alignment explanation
Indices: 3130552--3130598 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
3130542 TCATTTGTTT
3130552 TATT-TATTATTATTA
1 TATTATATTATTATTA
* *
3130567 TTTTGTATTATTATTA
1 TATTATATTATTATTA
3130583 TATTATATTATTATTA
1 TATTATATTATTATTA
3130599 AATAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 3 0.11
16 25 0.89
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTATATTATTATTA
Found at i:3131955 original size:3 final size:3
Alignment explanation
Indices: 3131942--3132010 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
3131932 TTATTTGCAA
* *
3131942 TAT TAT T-T TAT TAT TAT TAT TAT TATT TAT TGCT T-T AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT T-AT TAT TAT TAT TAT
* *
3131987 T-T CAT TAT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3132011 TATATATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.07
3 45 0.83
4 5 0.09
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3132306 original size:117 final size:118
Alignment explanation
Indices: 3132086--3132307 Score: 274
Period size: 117 Copynumber: 1.9 Consensus size: 118
3132076 ATCCTATATT
* * *
3132086 TCATAAATTACTTTTAATAATCATATTTTAATTTATTTTTCAATATTAAAAAAATGACTGTTTTA
1 TCATAAATTACTTTTAATAA-CATATTTTAATTTATTTTT-AATATCAAAAAAATGAATGTCTTA
* * * *
3132151 AAGCACCTAGAAGTCCGTTTTCTGATATTTTCAGTAAATATCATACTTTTATAAA
64 AAGCACCTAGAAGTCCCTTTTATGATATTTTAAATAAATATCATACTTTTATAAA
* *
3132206 TCATATATTAACTTTTAATAA-ATGTTTT-ATTTATTTTT-ATATCAAAGAAAA-GAGATGTCTT
1 TCATAAATT-ACTTTTAATAACATATTTTAATTTATTTTTAATATCAAA-AAAATGA-ATGTCTT
3132267 AAAGCACCTAGAAG-CCCTTTTATGATATTTCTAAATAAATA
63 AAAGCACCTAGAAGTCCCTTTTATGATATTT-TAAATAAATA
3132308 AATATCTTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
116 23 0.26
117 31 0.35
118 10 0.11
119 6 0.07
120 8 0.09
121 11 0.12
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (118 bp):
TCATAAATTACTTTTAATAACATATTTTAATTTATTTTTAATATCAAAAAAATGAATGTCTTAAA
GCACCTAGAAGTCCCTTTTATGATATTTTAAATAAATATCATACTTTTATAAA
Found at i:3133220 original size:13 final size:14
Alignment explanation
Indices: 3133189--3133221 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3133179 AAGCCAAATG
3133189 TAAACAAACATAAC
1 TAAACAAACATAAC
*
3133203 AAAACAAA-ATAAC
1 TAAACAAACATAAC
3133216 TAAACA
1 TAAACA
3133222 TCAGAGACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (14 bp):
TAAACAAACATAAC
Found at i:3138829 original size:20 final size:21
Alignment explanation
Indices: 3138804--3138842 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3138794 CAATAGGAAT
*
3138804 AAGAAGAAAGTAAT-GTGAGG
1 AAGAAGAAACTAATAGTGAGG
3138824 AAGAAGAAACTAATAGTGA
1 AAGAAGAAACTAATAGTGA
3138843 AGAAAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.03, G:0.28, T:0.15
Consensus pattern (21 bp):
AAGAAGAAACTAATAGTGAGG
Found at i:3139801 original size:70 final size:68
Alignment explanation
Indices: 3139710--3139848 Score: 233
Period size: 70 Copynumber: 2.0 Consensus size: 68
3139700 TCATTGTCAA
* *
3139710 TACCAATAAATAAACATTGCCTTGATAATTAAGAAACTATGATGCATGATTTTGAAAAAAGATTT
1 TACCAATAAATAAACATTGCCTTGATAATTAAGAAAATATGATCCA-GATTTTG-AAAAAGATTT
3139775 CAATT
64 CAATT
*
3139780 TACCAATAAATAAACATTGCCTTGATAATTAAGAAAATATGATCCAGATTTTGAAAAAGATTTCG
1 TACCAATAAATAAACATTGCCTTGATAATTAAGAAAATATGATCCAGATTTTGAAAAAGATTTCA
3139845 ATT
66 ATT
3139848 T
1 T
3139849 TACTTCGGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 15 0.23
69 7 0.11
70 44 0.67
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (68 bp):
TACCAATAAATAAACATTGCCTTGATAATTAAGAAAATATGATCCAGATTTTGAAAAAGATTTCA
ATT
Found at i:3146254 original size:14 final size:14
Alignment explanation
Indices: 3146235--3146282 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
3146225 TCGACCTGAC
*
3146235 CTGTTGATCGTTGA
1 CTGTTGATCATTGA
3146249 CTGTTGATCATTGA
1 CTGTTGATCATTGA
* *
3146263 CTATTGA-CTTTGA
1 CTGTTGATCATTGA
*
3146276 TTGTTGA
1 CTGTTGA
3146283 CTTGACCCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (14 bp):
CTGTTGATCATTGA
Found at i:3147777 original size:3 final size:3
Alignment explanation
Indices: 3147769--3147794 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3147759 TGTTATTTCA
3147769 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3147795 CGATGATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3164274 original size:171 final size:170
Alignment explanation
Indices: 3163985--3164326 Score: 395
Period size: 171 Copynumber: 2.0 Consensus size: 170
3163975 TGCACAATTA
* * * **
3163985 TTTGCAAGGCCCACTTTAATCACATCCTCCACCACTTTGATTCTACTCGACCATCCAACATGGGG
1 TTTGAAAGGCCCACTTGAATCACATCCTCCACCACTTTGACTCTAAACGACCATCCAACATGGGG
* ** *
3164050 AAATTTGTAAAATAATCCTTCGAACCCTCATAAGCACGTGCAGACTCACAACTTTTCCTATTAAC
66 AAATTTATAAAATAATCCTTCGAACCCTCATAAGCACGTGCAGACAAACAACTTTCCCTATTAAC
* * * *
3164115 ATCTTCTGCCTTTCTCTCCATGTGAACCAACACTACCTCG
131 ATCTACTGCCTCTCTCTCCACGTGAACCAACACTAACTCG
* * **
3164155 TTTGAAAGGCCCA-TATGAATCCCATCCTCCACCTCGTTTGACTCTAAACGACCATCCAGGAT-G
1 TTTGAAAGGCCCACT-TGAATCACATCCTCCACCAC-TTTGACTCTAAACGACCATCCAACATGG
* * *
3164218 GGAAATTCTATTAAATAATCCTTC-ATCCCCTCATTAA-CACGTGCAGACAAACAACTTTCCCTT
64 GGAAATT-TATAAAATAATCCTTCGA-ACCCTCA-TAAGCACGTGCAGACAAACAACTTTCCCTA
** **
3164281 TTGTCATCTACTGCCTCTCTCTCTGCGTGAACCAACACTAACTCG
126 TTAACATCTACTGCCTCTCTCTCCACGTGAACCAACACTAACTCG
3164326 T
1 T
3164327 GTTCCCCCAC
Statistics
Matches: 143, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
169 1 0.01
170 38 0.27
171 101 0.71
172 3 0.02
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (170 bp):
TTTGAAAGGCCCACTTGAATCACATCCTCCACCACTTTGACTCTAAACGACCATCCAACATGGGG
AAATTTATAAAATAATCCTTCGAACCCTCATAAGCACGTGCAGACAAACAACTTTCCCTATTAAC
ATCTACTGCCTCTCTCTCCACGTGAACCAACACTAACTCG
Found at i:3165957 original size:142 final size:144
Alignment explanation
Indices: 3165698--3166085 Score: 418
Period size: 142 Copynumber: 2.7 Consensus size: 144
3165688 GACCTTCCTC
* * * * *
3165698 AAGTACCTACCTATATTGAAATCATATCTAACACTTTGATGTTATGAATTGTAACCTCGTTTGGT
1 AAGTAACTACCTATATTGAAATCATATCTAACAC-TTAATGTTATGAACTGTAACCTCGTTAGAT
** * * *
3165763 TCTCGGGTTAAGGTTTATTCAATGATTATTAAGTGAATATTCTTGCAATACTCTAA-CTATTTT-
65 TCTCAAGTTAAGGTTTATTCAATGATTATTAAGTGAATACTCCTCCAATACTC-AAGCTATTTTC
3165826 CATTT-GTT-CCCCTA
129 CATTTAGTTCCCCCTA
* *
3165840 AAGTAATTACCTACATTGAAATCATATCTAGA-ACTTCAATGTTATGAACTGTAACCTCGTTAGA
1 AAGTAACTACCTATATTGAAATCATATCTA-ACACTT-AATGTTATGAACTGTAACCTCGTTAGA
* * * **
3165904 TTCTCAAGTTAAGGCTTATTCGATGATTATTAAGTCAATACTCCTCCGTTACTCAAGCTATTTTC
64 TTCTCAAGTTAAGGTTTATTCAATGATTATTAAGTGAATACTCCTCCAATACTCAAGCTATTTTC
* *
3165969 CTTTTATTTCCCCCTA
129 CATTTAGTTCCCCCTA
* * * * * *
3165985 GAGTAACTACCTATATCGAAATCATATGTAACACTTAA-ATT-T--CCTGTAACCTCG-TAGCTT
1 AAGTAACTACCTATATTGAAATCATATCTAACACTTAATGTTATGAACTGTAACCTCGTTAGATT
* * *
3166045 CTCAAATTAAGGTTTATTCAATGATTAGTGAGTGAATACTC
66 CTCAAGTTAAGGTTTATTCAATGATTATTAAGTGAATACTC
3166086 GTGTTGTTTC
Statistics
Matches: 206, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
139 40 0.19
140 11 0.05
141 4 0.02
142 104 0.50
143 7 0.03
144 5 0.02
145 35 0.17
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (144 bp):
AAGTAACTACCTATATTGAAATCATATCTAACACTTAATGTTATGAACTGTAACCTCGTTAGATT
CTCAAGTTAAGGTTTATTCAATGATTATTAAGTGAATACTCCTCCAATACTCAAGCTATTTTCCA
TTTAGTTCCCCCTA
Found at i:3180508 original size:24 final size:24
Alignment explanation
Indices: 3180464--3180510 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3180454 ATAAAGAACC
*
3180464 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3180488 AAAATAAAGTTCAAACA-ACCATT
1 AAAATAAACTT-AAACATACCATT
3180511 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3187867 original size:24 final size:24
Alignment explanation
Indices: 3187835--3187883 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3187825 GCAACTTACT
3187835 CAATGAAGAACAAAATTCTGTTGC
1 CAATGAAGAACAAAATTCTGTTGC
3187859 CAATGAAGAACAAAATTCTGTTGC
1 CAATGAAGAACAAAATTCTGTTGC
3187883 C
1 C
3187884 GTGGAAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (24 bp):
CAATGAAGAACAAAATTCTGTTGC
Found at i:3190742 original size:24 final size:24
Alignment explanation
Indices: 3190698--3190744 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3190688 ATAAAGAACC
* *
3190698 AAAATAAACTTAAATATACCATTA
1 AAAATAAAATTAAACATACCATTA
3190722 AAAATAAAATTCAAACA-ACCATT
1 AAAATAAAATT-AAACATACCATT
3190745 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATAAAATTAAACATACCATTA
Found at i:3199789 original size:16 final size:16
Alignment explanation
Indices: 3199768--3199800 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3199758 TTACTTTTAA
3199768 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
3199784 ATTTATTTATAATATT
1 ATTTATTTATAATATT
3199800 A
1 A
3199801 ATTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:3199828 original size:17 final size:17
Alignment explanation
Indices: 3199806--3199839 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3199796 TATTAATTTG
3199806 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
3199823 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
3199840 ATCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:3199860 original size:2 final size:2
Alignment explanation
Indices: 3199853--3199894 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3199843 ACATAAATAA
3199853 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
3199895 TTTAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3200102 original size:27 final size:27
Alignment explanation
Indices: 3200072--3200126 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3200062 ATATTTTTAA
3200072 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTTATAAATAT
* * *
3200099 ATAAATTAATATTTTTTTTATAATTAT
1 ATAAATAAATATTTTATTTATAAATAT
3200126 A
1 A
3200127 ATTTCGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATAAATAAATATTTTATTTATAAATAT
Found at i:3209426 original size:54 final size:53
Alignment explanation
Indices: 3209337--3209439 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 53
3209327 TGATTGAGAA
* * *
3209337 ATCTTGGCATAAGCCACAAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTTAGCAGAAGCCACAAAAAGGATGAAAGTGTTGTCAAATGCTTTACGAAC
* *
3209390 ATCTTAGCAGAAGCCACAGAAAAGGAT-AAAGATGTTGTCAAGTGTTTTAC
1 ATCTTAGCAGAAGCCACA-AAAAGGATGAAAG-TGTTGTCAAATGCTTTAC
3209440 ATCTCGACAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 19 0.44
54 24 0.56
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (53 bp):
ATCTTAGCAGAAGCCACAAAAAGGATGAAAGTGTTGTCAAATGCTTTACGAAC
Found at i:3210505 original size:112 final size:113
Alignment explanation
Indices: 3210339--3210975 Score: 985
Period size: 113 Copynumber: 5.7 Consensus size: 113
3210329 TGTCAGTTAG
*
3210339 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * * * ** *
3210403 AACTTTTTACTTGAATTCATCATTTGATGGATCAACAGTGT-CAGTTAG
66 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGC-TTTTCCAGAAAA
*
3210451 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
3210515 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
66 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
* *
3210563 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
3210628 AACTTTTTCCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
66 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
* *
3210676 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
3210741 AACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
66 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
* * * *
3210789 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTTAGAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * *
3210854 AACCTTTTGCTTGAATTCATCACTCGATGGATCAGCTTTTCCAGAAAA
66 AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
3210902 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
3210966 AACTTTTTGC
66 AACTTTTTGC
3210976 ATGACTCTAT
Statistics
Matches: 493, Mismatches: 30, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
111 2 0.00
112 168 0.34
113 323 0.66
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAA
Found at i:3212439 original size:16 final size:16
Alignment explanation
Indices: 3212418--3212450 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3212408 TTACTTTTAA
3212418 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
3212434 ATTTATTTATAATATT
1 ATTTATTTATAATATT
3212450 A
1 A
3212451 ATTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:3212744 original size:27 final size:27
Alignment explanation
Indices: 3212714--3212768 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3212704 ATATTTTTAA
3212714 ATAAATAAATATT-TTATTTATAAATAT
1 ATAAATAAATATTGTT-TTTATAAATAT
* *
3212741 ATAAATTAATATTGTTTTTATAATTAT
1 ATAAATAAATATTGTTTTTATAAATAT
3212768 A
1 A
3212769 ATTTCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
ATAAATAAATATTGTTTTTATAAATAT
Found at i:3220901 original size:18 final size:16
Alignment explanation
Indices: 3220843--3221028 Score: 125
Period size: 18 Copynumber: 11.0 Consensus size: 16
3220833 TTAATCCATA
3220843 ATTTATTATTAGTATT-T
1 ATTTATTA-TA-TATTAT
3220860 -TTTATTATATATTAGT
1 ATTTATTATATATTA-T
3220876 ATTTATTATATA-TAT
1 ATTTATTATATATTAT
* *
3220891 ATATATTAT-TA-GA-
1 ATTTATTATATATTAT
3220904 ATTTATTATATATTAAAT
1 ATTTATTATATATT--AT
3220922 ATATTATTAGTATTTATATCAT
1 AT-TTATTA-TA--TAT-T-AT
3220944 ATTTA-TATATATTAGT
1 ATTTATTATATATTA-T
3220960 ATTGTATTATATATTAGT
1 ATT-TATTATATATTA-T
*
3220978 ATTTCATTACATATTAGT
1 ATTT-ATTATATATTA-T
*
3220996 ATTTCATTACATATTAT
1 ATTT-ATTATATATTAT
*
3221013 ATTTATTATCTATTAT
1 ATTTATTATATATTAT
3221029 TATTACTTAT
Statistics
Matches: 144, Mismatches: 8, Indels: 35
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.06
14 9 0.06
15 12 0.08
16 25 0.17
17 23 0.16
18 44 0.31
19 8 0.06
20 4 0.03
21 3 0.02
22 7 0.05
23 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.56
Consensus pattern (16 bp):
ATTTATTATATATTAT
Found at i:3220948 original size:11 final size:10
Alignment explanation
Indices: 3220875--3220956 Score: 59
Period size: 10 Copynumber: 8.4 Consensus size: 10
3220865 TATATATTAG
3220875 TATTTAT-TA
1 TATTTATATA
*
3220884 TATATATATA
1 TATTTATATA
3220894 TA-TTAT-TA
1 TATTTATATA
*
3220902 GAATTTAT-TA
1 -TATTTATATA
*
3220912 TATATTAAATA
1 TAT-TTATATA
3220923 TA-TTAT-TA
1 TATTTATATA
3220931 GTATTTATATCA
1 -TATTTATAT-A
3220943 TATTTATATA
1 TATTTATATA
3220953 TATT
1 TATT
3220957 AGTATTGTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
8 4 0.07
9 17 0.29
10 22 0.38
11 14 0.24
12 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (10 bp):
TATTTATATA
Found at i:3220951 original size:57 final size:56
Alignment explanation
Indices: 3220865--3220975 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 56
3220855 TATTTTTTAT
3220865 TATATATTAGTATTTATTATATATATATATATTATTAGAATT-TATTATATATTAAA
1 TATATATTAGTATTTATTATATATATATATA-TATTAGAATTGTATTATATATTAAA
* *
3220921 TATATTATTAGTATTTA-TATCATATTTATATATATTAGTATTGTATTATATATTA
1 TATA-TATTAGTATTTATTAT-ATATATATATATATTAGAATTGTATTATATATTA
3220976 GTATTTCATT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
56 16 0.32
57 34 0.68
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.55
Consensus pattern (56 bp):
TATATATTAGTATTTATTATATATATATATATATTAGAATTGTATTATATATTAAA
Found at i:3220974 original size:28 final size:28
Alignment explanation
Indices: 3220860--3220974 Score: 146
Period size: 28 Copynumber: 4.1 Consensus size: 28
3220850 ATTAGTATTT
3220860 TTTAT-TATATATTAGTATTTATTATATA
1 TTTATATAT-TATTAGTATTTATTATATA
* *
3220888 TATATATATTATTAGAATTTATTATATA
1 TTTATATATTATTAGTATTTATTATATA
*
3220916 TTAAATATATTATTAGTATTTA-TATCATA
1 TT-TATATATTATTAGTATTTATTAT-ATA
3220945 TTTATATA-TATTAGTATTGTATTATATA
1 TTTATATATTATTAGTATT-TATTATATA
3220973 TT
1 TT
3220975 AGTATTTCAT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
27 10 0.13
28 38 0.50
29 28 0.37
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTATATATTATTAGTATTTATTATATA
Found at i:3230574 original size:17 final size:17
Alignment explanation
Indices: 3230552--3230585 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3230542 GTGTCGATCC
*
3230552 TCCAAGTTCCATGTTCA
1 TCCAAGTGCCATGTTCA
3230569 TCCAAGTGCCATGTTCA
1 TCCAAGTGCCATGTTCA
3230586 GGACGCCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (17 bp):
TCCAAGTGCCATGTTCA
Found at i:3231915 original size:19 final size:19
Alignment explanation
Indices: 3231891--3231930 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3231881 GTTAACGGTA
*
3231891 AGGTCAAAGTCAACGGTTC
1 AGGTCAAAGTCAACGGGTC
*
3231910 AGGTCAAGGTCAACGGGTC
1 AGGTCAAAGTCAACGGGTC
3231929 AG
1 AG
3231931 ACCAGTTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.33, T:0.17
Consensus pattern (19 bp):
AGGTCAAAGTCAACGGGTC
Found at i:3232683 original size:2 final size:2
Alignment explanation
Indices: 3232672--3232703 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3232662 CAAACCAAAT
3232672 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3232704 TACTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3235210 original size:13 final size:13
Alignment explanation
Indices: 3235192--3235216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3235182 TTGACTTTTT
3235192 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
3235205 GGTCAAAGTCAA
1 GGTCAAAGTCAA
3235217 AGTCAATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:3245913 original size:20 final size:19
Alignment explanation
Indices: 3245890--3245937 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
3245880 CTCAAAAACA
*
3245890 TTTTTCAAATTTTTATTTTG
1 TTTTTCAAATTTGT-TTTTG
3245910 TTTTTCAAAATTTGTTTTTG
1 TTTTTC-AAATTTGTTTTTG
3245930 -TTTTCAAA
1 TTTTTCAAA
3245938 AGAAAATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 11 0.42
21 7 0.27
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTTCAAATTTGTTTTTG
Found at i:3245927 original size:19 final size:18
Alignment explanation
Indices: 3245890--3245938 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3245880 CTCAAAAACA
*
3245890 TTTTTCAAATTTTTATTTT
1 TTTTTCAAA-ATTTATTTT
*
3245909 GTTTTTCAAAATTTGTTTT
1 -TTTTTCAAAATTTATTTT
3245928 TGTTTTCAAAA
1 T-TTTTCAAAA
3245939 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTTCAAAATTTATTTT
Found at i:3259396 original size:59 final size:59
Alignment explanation
Indices: 3259323--3259443 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
3259313 AATAGATGAA
* *
3259323 TAAGTGTCCCATCGAACCCTCCTAGTCGCAATGGAAAGCCAAACTCGATAATATGGCTC
1 TAAGTGTCCCATCGAACCCTCCTAGTCGCAATGAAAAGCAAAACTCGATAATATGGCTC
* * *
3259382 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACTTGATAATATGGCTC
1 TAAGTGTCCCATCGAACCCTCCTAGTCGCAATGAAAAGCAAAACTCGATAATATGGCTC
3259441 TAA
1 TAA
3259444 CCAACCCTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (59 bp):
TAAGTGTCCCATCGAACCCTCCTAGTCGCAATGAAAAGCAAAACTCGATAATATGGCTC
Found at i:3263892 original size:59 final size:59
Alignment explanation
Indices: 3263798--3263918 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
3263788 AATAGATGGA
*
3263798 TAAGTGTCATATCGAACCCTCCTAGTCGCATTGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
* * *
3263857 TAAGTGTCCTATCGAACCCTCCTAGTCGTAATGAAAAGGCAAACTTGATAATATGGCTC
1 TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
3263916 TAA
1 TAA
3263919 CCGACCCTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (59 bp):
TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
Found at i:3264859 original size:27 final size:27
Alignment explanation
Indices: 3264821--3264886 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
3264811 TTTAAAAGTG
*
3264821 TTGAGATCCTCTGTTATATATTTAGTA
1 TTGAGATCCTCTATTATATATTTAGTA
3264848 TTGAGATCCTCTATTATATATTTAGTA
1 TTGAGATCCTCTATTATATATTTAGTA
3264875 TTGAGATGCCTC
1 TTGAGAT-CCTC
3264887 CATTCTAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (27 bp):
TTGAGATCCTCTATTATATATTTAGTA
Found at i:3270925 original size:16 final size:15
Alignment explanation
Indices: 3270900--3270930 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3270890 TTTAAGATAA
3270900 CAAAAATTAAATTAT
1 CAAAAATTAAATTAT
3270915 CAAATAATTAAATTAT
1 CAAA-AATTAAATTAT
3270931 TTTTTATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
CAAAAATTAAATTAT
Found at i:3276667 original size:78 final size:78
Alignment explanation
Indices: 3276578--3276734 Score: 278
Period size: 78 Copynumber: 2.0 Consensus size: 78
3276568 GAAAATGAAA
3276578 AAAAGAAAGTATTTGTATTAATCTTCGTATTATTTTAAATGTGTTTAAAGTATTCAAATATGTAT
1 AAAAGAAAGTATTTGTATTAATCTTCGTATTATTTTAAATGTGTTTAAAGTATTCAAATATGTAT
3276643 ATTATTGTACATG
66 ATTATTGTACATG
* * * *
3276656 AAAAGACAGTATTTGTGTTAATCTTCGTATTGTTTTTAATGTGTTTAAAGTATTCAAATATGTAT
1 AAAAGAAAGTATTTGTATTAATCTTCGTATTATTTTAAATGTGTTTAAAGTATTCAAATATGTAT
3276721 ATTATTGTACATG
66 ATTATTGTACATG
3276734 A
1 A
3276735 GTAATGATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (78 bp):
AAAAGAAAGTATTTGTATTAATCTTCGTATTATTTTAAATGTGTTTAAAGTATTCAAATATGTAT
ATTATTGTACATG
Found at i:3276814 original size:31 final size:32
Alignment explanation
Indices: 3276753--3276819 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
3276743 TTATTCGGTG
*
3276753 AAAATATTGTTTTATCAAGTCTTTCTATTA-T
1 AAAATATTATTTTATCAAGTCTTTCTATTATT
* *
3276784 AAAATATTATTTTATTAAGT-TTTGTAATTATT
1 AAAATATTATTTTATCAAGTCTTTCT-ATTATT
3276816 AAAA
1 AAAA
3276820 GTTAGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 22 0.71
32 5 0.16
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (32 bp):
AAAATATTATTTTATCAAGTCTTTCTATTATT
Found at i:3278938 original size:17 final size:19
Alignment explanation
Indices: 3278918--3278966 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 19
3278908 TTAATAAATA
3278918 TAAAATATTAAAT-CAAC-
1 TAAAATATTAAATACAACG
3278935 TAAAATA-TAAATACAACG
1 TAAAATATTAAATACAACG
3278953 TTAAAATAATTAAA
1 -TAAAAT-ATTAAA
3278967 AAGATAACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.19
17 11 0.41
19 6 0.22
20 1 0.04
21 4 0.15
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (19 bp):
TAAAATATTAAATACAACG
Found at i:3281188 original size:19 final size:19
Alignment explanation
Indices: 3281166--3281213 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3281156 GGAATGATAT
**
3281166 TTTATTTATATTTTAAATA
1 TTTATTTATATTGAAAATA
*
3281185 TTTATATAATATTGAAAATA
1 TTTAT-TTATATTGAAAATA
3281205 -TTATTTATA
1 TTTATTTATA
3281214 AAAATGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.17
19 9 0.38
20 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTATTTATATTGAAAATA
Found at i:3283343 original size:31 final size:31
Alignment explanation
Indices: 3283308--3283368 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3283298 TGACCGGTCA
* *
3283308 TAACCTGACCCGACTCGTTTACCCAACCCGT
1 TAACCTGACCCGACCCGTTGACCCAACCCGT
*
3283339 TAACCTGACCCGACCCGTTGACCCGACCCG
1 TAACCTGACCCGACCCGTTGACCCAACCCG
3283369 ACCCGTTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.18
Consensus pattern (31 bp):
TAACCTGACCCGACCCGTTGACCCAACCCGT
Done.