Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007462.1 Hibiscus syriacus cultivar Beakdansim tig00020467_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: 121552
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1797 original size:29 final size:31
Alignment explanation
Indices: 1758--1816 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
1748 AAGGGTCCTG
1758 TTTTATTTTAAGTCCTTAA-TT-TATTTTTT
1 TTTTATTTTAAGTCCTTAAGTTCTATTTTTT
* * *
1787 TTTTTTTTTAATTCTTTAAGTTCTATTTTT
1 TTTTATTTTAAGTCCTTAAGTTCTATTTTT
1817 GTTATTTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
30 2 0.08
31 7 0.28
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (31 bp):
TTTTATTTTAAGTCCTTAAGTTCTATTTTTT
Found at i:1824 original size:29 final size:29
Alignment explanation
Indices: 1760--1824 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
1750 GGGTCCTGTT
* * *
1760 TTATTTTAAGTCCTTAATTTATTTTTTTT
1 TTATTTTAAGTCCTTAAGTTATATTTTTG
* * * *
1789 TTTTTTTAATTCTTTAAGTTCTATTTTTG
1 TTATTTTAAGTCCTTAAGTTATATTTTTG
1818 TTATTTT
1 TTATTTT
1825 GGATCTTTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.71
Consensus pattern (29 bp):
TTATTTTAAGTCCTTAAGTTATATTTTTG
Found at i:1993 original size:29 final size:29
Alignment explanation
Indices: 1961--2038 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
1951 TTGTTTTGCC
*
1961 ATTTAGTCTTTTAAATTTCATCTTGTGA-T
1 ATTTAGTCTTTTAAATTT-ATATTGTGACT
* ** * *
1990 ATTTGGTCTTCAAAATTTATATTTTTACT
1 ATTTAGTCTTTTAAATTTATATTGTGACT
2019 ATTTAGTCTTTTAAATTTAT
1 ATTTAGTCTTTTAAATTTAT
2039 GTTTGTGTCA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
28 6 0.15
29 33 0.85
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (29 bp):
ATTTAGTCTTTTAAATTTATATTGTGACT
Found at i:2051 original size:29 final size:28
Alignment explanation
Indices: 1952--2062 Score: 82
Period size: 29 Copynumber: 3.8 Consensus size: 28
1942 TTAAAAGTTT
*
1952 TGTTTTGCCATTTAGTCTTTTAAATTTCA
1 TGTTTTGTCATTTAGTCTTTTAAATTT-A
* * * **
1981 TCTTGTGAT-ATTTGGTCTTCAAAATTTA
1 TGTTTTG-TCATTTAGTCTTTTAAATTTA
*
2009 TATTTT-TACTATTTAGTCTTTTAAATTTA
1 TGTTTTGT-C-ATTTAGTCTTTTAAATTTA
*
2038 TGTTTGTGTCATTTTAGTCCTTTAA
1 TGTTT-TGTCA-TTTAGTCTTTTAA
2063 TTTTTTAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
26 1 0.02
28 5 0.08
29 41 0.66
30 14 0.23
31 1 0.02
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.56
Consensus pattern (28 bp):
TGTTTTGTCATTTAGTCTTTTAAATTTA
Found at i:13448 original size:7 final size:7
Alignment explanation
Indices: 13426--13476 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
13416 AAAGAGGAAC
*
13426 AAATAAA
1 AAATGAA
13433 AAGATGAA
1 AA-ATGAA
13441 AAATG-A
1 AAATGAA
13447 AAATGAA
1 AAATGAA
13454 AAATGAA
1 AAATGAA
13461 AAA--AA
1 AAATGAA
13466 GAAATGAA
1 -AAATGAA
13474 AAA
1 AAA
13477 ATAAAAAGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
5 2 0.05
6 9 0.24
7 19 0.50
8 8 0.21
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.12
Consensus pattern (7 bp):
AAATGAA
Found at i:13454 original size:13 final size:13
Alignment explanation
Indices: 13436--13475 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
13426 AAATAAAAAG
13436 ATGAAAAATGAAA
1 ATGAAAAATGAAA
13449 ATGAAAAATGAAA
1 ATGAAAAATGAAA
*
13462 A-AAAGAAATGAAA
1 ATGAA-AAATGAAA
13475 A
1 A
13476 AATAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 2 0.08
13 23 0.92
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:13461 original size:20 final size:20
Alignment explanation
Indices: 13447--13489 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
13437 TGAAAAATGA
13447 AAATGAAAAATGAAAAAAAG
1 AAATGAAAAATGAAAAAAAG
*
13467 AAATGAAAAAAT-AAAAAGAG
1 AAATG-AAAAATGAAAAAAAG
13487 AAA
1 AAA
13490 AAAGAGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AAATGAAAAATGAAAAAAAG
Found at i:13476 original size:13 final size:12
Alignment explanation
Indices: 13439--13492 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
13429 TAAAAAGATG
*
13439 AAAAATGAAAATG
1 AAAAATGAAAA-A
13452 AAAAATGAAAAA
1 AAAAATGAAAAA
13464 AAGAAATGAAAAA
1 AA-AAATGAAAAA
*
13477 ATAAAAAGAGAAAA
1 A-AAAATGA-AAAA
13491 AA
1 AA
13493 GAGGGTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 2 0.06
13 28 0.78
14 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (12 bp):
AAAAATGAAAAA
Found at i:14766 original size:19 final size:17
Alignment explanation
Indices: 14741--14794 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
14731 CAATGAAGAG
14741 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
* * *
14758 TCATCATAAAG-GAAAAAG
1 T--TCATAATGAGAAGAAC
14776 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
14793 TT
1 TT
14795 GTTCCTTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 6 0.21
19 7 0.25
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (17 bp):
TTCATAATGAGAAGAAC
Found at i:14938 original size:105 final size:105
Alignment explanation
Indices: 14724--14972 Score: 302
Period size: 105 Copynumber: 2.4 Consensus size: 105
14714 TGAGGGATCG
14724 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAAAAAGTTCATAATGAGAA
1 ACATTTCC--TGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAAAAAGTTCATAATGAGAA
* * * *
14789 GAACTTGTTCCTTTCAAATTCACCACAAATGGAGGTGAACCA
64 AAACATGTTCCTTTCAAATCCACCACAAAAGGAGGTGAACCA
* * * * * *
14831 ACATTTCTTGAAGAGTTCATAATGAGAAGAACTCGTCCTAATGGAGAAAGTTTATAATGAGAAAA
1 ACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAAAAAGTTCATAATGAGAAAA
* * ** * *
14896 ACATGTT-CTTTCTAAGTCCACCGCAAAAGGATTTGGATCA
66 ACATGTTCCTTTC-AAATCCACCACAAAAGGAGGTGAACCA
**
14936 ACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 ACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATC
14973 CACGAGAAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
104 5 0.04
105 109 0.90
107 7 0.06
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (105 bp):
ACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAAAAAGTTCATAATGAGAAAA
ACATGTTCCTTTCAAATCCACCACAAAAGGAGGTGAACCA
Found at i:15159 original size:3 final size:3
Alignment explanation
Indices: 15153--15223 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
15143 ATTATTAAAA
15153 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15201 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
15224 AGTGTGTTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:18229 original size:29 final size:30
Alignment explanation
Indices: 18188--18255 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
18178 AAGGGTCCTG
18188 TTTTATTTATTAAGTCCTTTAA-TT-TATTT
1 TTTTATTTATTAA-TCCTTTAAGTTCTATTT
* * *
18217 TTTTCTTTTTTAATTCTTTAAGTTCTATTT
1 TTTTATTTATTAATCCTTTAAGTTCTATTT
18247 TTGTTATTT
1 TT-TTATTT
18256 TGGATCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.22
29 13 0.41
30 7 0.22
31 5 0.16
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.69
Consensus pattern (30 bp):
TTTTATTTATTAATCCTTTAAGTTCTATTT
Found at i:18328 original size:30 final size:30
Alignment explanation
Indices: 18292--18363 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
18282 ATTTTAGTCA
18292 TTTGAGTTTTTGTTTATT-TTATCTAGGTCC
1 TTTGAGTTTTTGTTT-TTGTTATCTAGGTCC
* * **
18322 TTTGAGTTTCTGTTTTTGTTATTTTTGTCC
1 TTTGAGTTTTTGTTTTTGTTATCTAGGTCC
*
18352 TTTAAGTTTTTG
1 TTTGAGTTTTTG
18364 AAATTATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.06
30 33 0.94
ACGTcount: A:0.11, C:0.08, G:0.17, T:0.64
Consensus pattern (30 bp):
TTTGAGTTTTTGTTTTTGTTATCTAGGTCC
Found at i:18478 original size:30 final size:30
Alignment explanation
Indices: 18402--18525 Score: 85
Period size: 30 Copynumber: 4.2 Consensus size: 30
18392 TGTTTTTGCC
* * *
18402 ATTTTAGTCTTTTAAATTTCATCTTGTGA-T
1 ATTTTAGTCTTTTAAATTT-ATATTTTTACT
* **
18432 A-TTTGGTCTTCAAAATTTATATTTTTACT
1 ATTTTAGTCTTTTAAATTTATATTTTTACT
*
18461 ATTTTAGTCTTTTAAATTTATGTTTGTGT-C-
1 ATTTTAGTCTTTTAAATTTATATTT-T-TACT
* * * * *
18491 ATTTTAGTCCTTTAATTTTTTAATTTTATT
1 ATTTTAGTCTTTTAAATTTATATTTTTACT
18521 ATTTT
1 ATTTT
18526 GATTCTTAAG
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
28 7 0.10
29 17 0.24
30 45 0.62
31 2 0.03
32 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.60
Consensus pattern (30 bp):
ATTTTAGTCTTTTAAATTTATATTTTTACT
Found at i:21216 original size:22 final size:22
Alignment explanation
Indices: 21170--21224 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
21160 AGTGCTATAA
*
21170 CACTTTTGTATCAGTGTGAATG
1 CACTTTTGTATCAGTGTGAAGG
21192 CACTTTTGTATCAGTGTTG-AGG
1 CACTTTTGTATCAGTG-TGAAGG
*
21214 CACTTTAGTAT
1 CACTTTTGTAT
21225 TAATGATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (22 bp):
CACTTTTGTATCAGTGTGAAGG
Found at i:24482 original size:140 final size:140
Alignment explanation
Indices: 24282--24564 Score: 566
Period size: 140 Copynumber: 2.0 Consensus size: 140
24272 GTTCTAAAAA
24282 CTCTTAATCATTTGACAATGAAATCTCAAATTTAAAATGGGATAGTTATGTTTTTACATGTAAAA
1 CTCTTAATCATTTGACAATGAAATCTCAAATTTAAAATGGGATAGTTATGTTTTTACATGTAAAA
24347 CCTCATGCACTCGATTACTTACCTTTGTAACTGTTTAGGGACATGCACATGATTTACATCATGGG
66 CCTCATGCACTCGATTACTTACCTTTGTAACTGTTTAGGGACATGCACATGATTTACATCATGGG
24412 CAAACTAGAG
131 CAAACTAGAG
24422 CTCTTAATCATTTGACAATGAAATCTCAAATTTAAAATGGGATAGTTATGTTTTTACATGTAAAA
1 CTCTTAATCATTTGACAATGAAATCTCAAATTTAAAATGGGATAGTTATGTTTTTACATGTAAAA
24487 CCTCATGCACTCGATTACTTACCTTTGTAACTGTTTAGGGACATGCACATGATTTACATCATGGG
66 CCTCATGCACTCGATTACTTACCTTTGTAACTGTTTAGGGACATGCACATGATTTACATCATGGG
24552 CAAACTAGAG
131 CAAACTAGAG
24562 CTC
1 CTC
24565 ATAAAATTCT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 143 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (140 bp):
CTCTTAATCATTTGACAATGAAATCTCAAATTTAAAATGGGATAGTTATGTTTTTACATGTAAAA
CCTCATGCACTCGATTACTTACCTTTGTAACTGTTTAGGGACATGCACATGATTTACATCATGGG
CAAACTAGAG
Found at i:26196 original size:139 final size:139
Alignment explanation
Indices: 25946--26211 Score: 523
Period size: 139 Copynumber: 1.9 Consensus size: 139
25936 AATGTTAGAA
25946 GGATCAAGTCTGTATCCATATTGTTGTTACTTTGCTGTCAGCTATTCAGGTGGGTTTGAAATGAA
1 GGATCAAGTCTGTATCCATATTGTTGTTACTTTGCTGTCAGCTATTCAGGTGGGTTTGAAATGAA
26011 TGACTTAAGGTTGTACTTGTACCTTTTGTTATTGTCCATTTTGTTATTGTTGCCGGATGGTTTTG
66 TGACTTAAGGTTGTACTTGTACCTTTTGTTATTGTCCATTTTGTTATTGTTGCCGGATGGTTTTG
26076 TACTTTGCC
131 TACTTTGCC
*
26085 GGATCAAGTCTGTATCCATATTGTTGTTACTTTGCTGTCAGCTTTTCAGGTGGGTTTGAAATGAA
1 GGATCAAGTCTGTATCCATATTGTTGTTACTTTGCTGTCAGCTATTCAGGTGGGTTTGAAATGAA
26150 TGACTTAAGGTTGTACTTGTACCTTTTGTTATTGTCCATTTTGTTATTGTTGCCGGATGGTT
66 TGACTTAAGGTTGTACTTGTACCTTTTGTTATTGTCCATTTTGTTATTGTTGCCGGATGGTT
26212 CTGTTGCAAG
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 126 1.00
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (139 bp):
GGATCAAGTCTGTATCCATATTGTTGTTACTTTGCTGTCAGCTATTCAGGTGGGTTTGAAATGAA
TGACTTAAGGTTGTACTTGTACCTTTTGTTATTGTCCATTTTGTTATTGTTGCCGGATGGTTTTG
TACTTTGCC
Found at i:44356 original size:18 final size:18
Alignment explanation
Indices: 44323--44359 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44313 GAGAGTCCCC
*
44323 AGCCTGCTGAATCTGAAG
1 AGCCTGCTGAAGCTGAAG
*
44341 AGCCTGCTGACGCTGAAG
1 AGCCTGCTGAAGCTGAAG
44359 A
1 A
44360 TCCCAAAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (18 bp):
AGCCTGCTGAAGCTGAAG
Found at i:46184 original size:24 final size:25
Alignment explanation
Indices: 46152--46200 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
46142 AATCCAATCC
46152 GATCCAAAAAA-ATAACCGAAAACT
1 GATCCAAAAAACATAACCGAAAACT
46176 GATCCAAAAAATCGATAACCGAAAA
1 GATCCAAAAAA-C-ATAACCGAAAA
46201 AAACCGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.50
27 11 0.50
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.12
Consensus pattern (25 bp):
GATCCAAAAAACATAACCGAAAACT
Found at i:51675 original size:3 final size:3
Alignment explanation
Indices: 51667--51701 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
51657 ATATATATAT
*
51667 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
51702 TAAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:53121 original size:3 final size:3
Alignment explanation
Indices: 53113--53164 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
53103 TGTAATTATT
*
53113 TAA TAA TAA TAA TAA -AA TAAA TAA -AA TAA TAA TAA T-A TATT TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA-A TAA
53157 TAA TAA TA
1 TAA TAA TA
53165 TAAAAAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 6 0.14
3 31 0.74
4 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:53142 original size:20 final size:21
Alignment explanation
Indices: 53113--53169 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
53103 TGTAATTATT
53113 TAATAATAATAATAAAATAAA
1 TAATAATAATAATAAAATAAA
* **
53134 TAA-AATAATAATAATATATT
1 TAATAATAATAATAAAATAAA
53154 TAATAATAAT-ATAAAA
1 TAATAATAATAATAAAA
53170 AAACAAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAATAATAATAAAATAAA
Found at i:53167 original size:23 final size:24
Alignment explanation
Indices: 53113--53164 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
53103 TGTAATTATT
53113 TAATAATAATAATAAAATAAATAA
1 TAATAATAATAATAAAATAAATAA
* * *
53137 -AATAATAATAATATATTTAATAA
1 TAATAATAATAATAAAATAAATAA
53160 TAATA
1 TAATA
53165 TAAAAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TAATAATAATAATAAAATAAATAA
Found at i:53616 original size:121 final size:113
Alignment explanation
Indices: 53524--54203 Score: 941
Period size: 113 Copynumber: 6.0 Consensus size: 113
53514 GAATCAAATT
* * * * * *
53524 AAGGTTGAACAAGTTATTTTTATTATGAACTTCTT-TTCATTTTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
53588 TGAAC-ACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCAGTGATAGAA-TCAA-ACA
66 TGAACTTCTTCTGGAAA-----ATGTTGATCCA--T-C--AAGTGAT-GAATTCAACA-A
* * *
53645 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTATTCC-TCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
53709 TGAAC-TCTTCTGG-AAATGTTGATCCATCGAGTGATGAATTCAAGCAA
66 TGAACTTCTTCTGGAAAATGTTGATCCATCAAGTGATGAATTCAA-CAA
53756 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
53821 TGAACTTCTTCTGGAAAA-GTTGATCCATCAAGTGATGAATTCAAGCAA
66 TGAACTTCTTCTGGAAAATGTTGATCCATCAAGTGATGAATTCAA-CAA
*
53869 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAAGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
53934 TGAACTTCTTCTGGAAAA-GTTGATCCATCAAGTGATGAATTCAAGCAT
66 TGAACTTCTTCTGGAAAATGTTGATCCATCAAGTGATGAATTCAA-CAA
*
53982 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
54047 TGAACTTCTTCTGGAAAA-GTTGATCCATCAAGTGACGAATTCAAGCAA
66 TGAACTTCTTCTGGAAAATGTTGATCCATCAAGTGATGAATTCAA-CAA
* * *
54095 AAGGTTAAACATGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCATATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
54160 TGAACTCCTTATGGAAAA-GTTGATCCATCAAGTGATGAATTCAA
66 TGAACTTCTTCTGGAAAATGTTGATCCATCAAGTGATGAATTCAA
54204 ATCTTTGCTA
Statistics
Matches: 530, Mismatches: 22, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
109 3 0.01
110 10 0.02
111 38 0.07
112 31 0.06
113 362 0.68
114 3 0.01
115 10 0.02
120 2 0.00
121 68 0.13
122 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTCTTCTGGAAAATGTTGATCCATCAAGTGATGAATTCAACAA
Found at i:53867 original size:113 final size:113
Alignment explanation
Indices: 53628--54203 Score: 980
Period size: 113 Copynumber: 5.1 Consensus size: 113
53618 TATCTCCTTC
* * * *
53628 AGTGATAGAA-TCAAAC-AAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTATTCC-TCTTC
1 AGTGAT-GAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
53690 AGATGAGTTCTTCTCATTATGAAC-TCTTCTGGAAATGTTGATCCATCG
65 AGATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
53738 AGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 AGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
53803 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
66 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
53851 AGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 AGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
53916 GAAGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
66 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
* *
53964 AGTGATGAATTCAAGCATAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCA
1 AGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
54029 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
66 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
* * *
54077 AGTGACGAATTCAAGCAAAAGGTTAAACATGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCA
1 AGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * *
54142 TATGAGTTCTTCTCATTATGAACTCCTTATGGAAAAGTTGATCCATCA
66 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
54190 AGTGATGAATTCAA
1 AGTGATGAATTCAA
54204 ATCTTTGCTA
Statistics
Matches: 445, Mismatches: 17, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
109 3 0.01
110 11 0.02
111 38 0.09
112 29 0.07
113 364 0.82
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATCCATCA
Found at i:55779 original size:21 final size:21
Alignment explanation
Indices: 55755--55794 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55745 TTTTCATCAT
*
55755 TTTCATTTTTTTTTCTTTTCA
1 TTTCATTTTTTTTTATTTTCA
55776 TTTCATTTTTTTTTATTTT
1 TTTCATTTTTTTTTATTTT
55795 TTCATCATTT
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:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTCATTTTTTTTTATTTTCA
Found at i:55802 original size:21 final size:21
Alignment explanation
Indices: 55744--55808 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 21
55734 TCTACATATA
*
55744 TTTTTCATCATTTTCATTTTTTTT
1 TTTTTCATCA-TTT--TTTTTTAT
55768 TCTTTTCATTTCATTTTTTTTTAT
1 T-TTTTCA--TCATTTTTTTTTAT
55792 TTTTTCATCATTTTTTT
1 TTTTTCATCATTTTTTT
55809 CTTCTTCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 10 0.27
23 6 0.16
24 9 0.24
25 6 0.16
26 3 0.08
27 3 0.08
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTCATCATTTTTTTTTAT
Found at i:63106 original size:14 final size:16
Alignment explanation
Indices: 63089--63120 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
63079 ATTATTTTTT
63089 TGAAT-TTTAT-TTAA
1 TGAATGTTTATCTTAA
63103 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
63119 TG
1 TG
63121 TAAAATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:66465 original size:25 final size:25
Alignment explanation
Indices: 66437--66494 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
66427 TTTAATAACT
66437 GAAAATAAAACTAAAAACATTAATA
1 GAAAATAAAACTAAAAACATTAATA
66462 GAAAATAAAACTAAAAACATTAATA
1 GAAAATAAAACTAAAAACATTAATA
*
66487 AAAAATAA
1 GAAAATAA
66495 TATATATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.71, C:0.07, G:0.03, T:0.19
Consensus pattern (25 bp):
GAAAATAAAACTAAAAACATTAATA
Found at i:66541 original size:27 final size:25
Alignment explanation
Indices: 66485--66543 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
66475 AAAACATTAA
*
66485 TAAAAAATAATATATATAAATATAT
1 TAAAAAATAATATATATAAAAATAT
* *
66510 GAAAATAATAAGTATATATAAAAATTT
1 TAAAA-AATAA-TATATATAAAAATAT
66537 TAAAAAA
1 TAAAAAA
66544 AAGAAGTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.14
26 7 0.25
27 17 0.61
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (25 bp):
TAAAAAATAATATATATAAAAATAT
Found at i:67051 original size:15 final size:15
Alignment explanation
Indices: 67033--67083 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
67023 TAACCGGTTT
67033 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
67048 CGG--TT-AAAAAAC
1 CGGTTTTAAAAAAAC
* *
67060 CGGTTATAAAAAAAT
1 CGGTTTTAAAAAAAC
*
67075 CGATTTTAA
1 CGGTTTTAA
67084 TATTATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 10 0.34
13 2 0.07
14 1 0.03
15 16 0.55
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:67056 original size:13 final size:13
Alignment explanation
Indices: 67038--67072 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
67028 GGTTTCGGTT
67038 TTAAAAAAACCGG
1 TTAAAAAAACCGG
67051 TT-AAAAAACCGG
1 TTAAAAAAACCGG
67063 TTATAAAAAA
1 TTA-AAAAAA
67073 ATCGATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.60
13 2 0.10
14 6 0.30
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (13 bp):
TTAAAAAAACCGG
Found at i:68307 original size:21 final size:21
Alignment explanation
Indices: 68283--68324 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
68273 ACTTCAAGTT
68283 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
68304 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
68325 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:71588 original size:15 final size:15
Alignment explanation
Indices: 71568--71596 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
71558 ATTATGTTTG
71568 ATTAAAATCATAATT
1 ATTAAAATCATAATT
71583 ATTAAAATCATAAT
1 ATTAAAATCATAAT
71597 GGCTAATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAATCATAATT
Found at i:75346 original size:43 final size:43
Alignment explanation
Indices: 75297--75396 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
75287 AACTTTAAAT
* *
75297 GCCGCTAAAGGTTATGCTTTTTAGCGGCGTTTGTTTTACAAAC
1 GCCGCTAAAGGTTATGCTTTTTAGCGGCATTTATTTTACAAAC
* *
75340 GCCGCTAAAGGTTATGTTTTTTTGCGGCATTTATTTTACAAAC
1 GCCGCTAAAGGTTATGCTTTTTAGCGGCATTTATTTTACAAAC
75383 GCCGC-AATAGGTTA
1 GCCGCTAA-AGGTTA
75397 GGTCATTTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 2 0.04
43 50 0.96
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
GCCGCTAAAGGTTATGCTTTTTAGCGGCATTTATTTTACAAAC
Found at i:75616 original size:96 final size:97
Alignment explanation
Indices: 75433--75665 Score: 414
Period size: 96 Copynumber: 2.4 Consensus size: 97
75423 AATTTCACCC
*
75433 AAACGTCTCTAAGGCATGTTATAACCAAATGTTAAGTAATCATTTTTCACCCAAACGTCGTTAAT
1 AAACGCCTCTAAGGCATGTTATAACCAAATGTTAAGTAATCATTTTTCACCCAAACGTCGTTAAT
75498 AGTCATGACTTGTCGTGGCATTTTTATTCACA
66 AGTCATGACTTGTCGTGGCATTTTTATTCACA
* *
75530 AAACGCCTCTAAGGCATGTTATAAACAAATGTTAAGTAATCA-TTTTCACCCAAACGTTGTTAAT
1 AAACGCCTCTAAGGCATGTTATAACCAAATGTTAAGTAATCATTTTTCACCCAAACGTCGTTAAT
75594 AGTCATGACTTGTCGTGGCATTTTTATTCACA
66 AGTCATGACTTGTCGTGGCATTTTTATTCACA
* *
75626 AAATGCCTCTAAGGCATGTTCTAACCAAATGTTAAGTAAT
1 AAACGCCTCTAAGGCATGTTATAACCAAATGTTAAGTAAT
75666 TATGTTATCT
Statistics
Matches: 130, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
96 90 0.69
97 40 0.31
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (97 bp):
AAACGCCTCTAAGGCATGTTATAACCAAATGTTAAGTAATCATTTTTCACCCAAACGTCGTTAAT
AGTCATGACTTGTCGTGGCATTTTTATTCACA
Found at i:77827 original size:41 final size:42
Alignment explanation
Indices: 77768--77979 Score: 209
Period size: 42 Copynumber: 5.2 Consensus size: 42
77758 GTGTATGACT
* *
77768 AAACGCCACTAAAGTGCATGACTATTGCGACGTTTATTCCAA
1 AAACGCCACTAAAGTGCATGACTATTGCAACGTTTATTACAA
*
77810 AAACGCCAC-AAAGTGCATGACTATTGCAACGTTTA-TAAAA
1 AAACGCCACTAAAGTGCATGACTATTGCAACGTTTATTACAA
* * * * ***
77850 AAACGCCACAAAAGTACAAGATTATTGTGGCGTTTA-T--AA
1 AAACGCCACTAAAGTGCATGACTATTGCAACGTTTATTACAA
*** * *
77889 AAACGATGCTAAAGTGCATGACTATTGCAACATTTGTTACAA
1 AAACGCCACTAAAGTGCATGACTATTGCAACGTTTATTACAA
* * * * *
77931 AAACACCGCTAAGGTGCATGACTACTGCAGCGTTTATTACAA
1 AAACGCCACTAAAGTGCATGACTATTGCAACGTTTATTACAA
77973 AAACGCC
1 AAACGCC
77980 GCCTTGTAAG
Statistics
Matches: 136, Mismatches: 30, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
39 26 0.19
40 13 0.10
41 46 0.34
42 51 0.38
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (42 bp):
AAACGCCACTAAAGTGCATGACTATTGCAACGTTTATTACAA
Found at i:77891 original size:40 final size:40
Alignment explanation
Indices: 77768--77891 Score: 122
Period size: 41 Copynumber: 3.0 Consensus size: 40
77758 GTGTATGACT
* * * **
77768 AAACGCCACTAAAGTGCATGACTATTGCGACGTTTATTCCAA
1 AAACGCCAC-AAAGTACAAGACTATTGCAACGTTTA-TAAAA
* *
77810 AAACGCCACAAAGTGCATGACTATTGCAACGTTTATAAAA
1 AAACGCCACAAAGTACAAGACTATTGCAACGTTTATAAAA
* ***
77850 AAACGCCACAAAAGTACAAGATTATTGTGGCGTTTATAAAA
1 AAACGCCAC-AAAGTACAAGACTATTGCAACGTTTATAAAA
77891 A
1 A
77892 CGATGCTAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
40 12 0.17
41 51 0.71
42 9 0.12
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.24
Consensus pattern (40 bp):
AAACGCCACAAAGTACAAGACTATTGCAACGTTTATAAAA
Found at i:78551 original size:20 final size:20
Alignment explanation
Indices: 78528--78593 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
78518 ATTTCTTTTC
78528 CGCAACGCGAATATGTAATT
1 CGCAACGCGAATATGTAATT
*
78548 CGCAACACGAATATGTAAATT
1 CGCAACGCGAATATGT-AATT
*
78569 -GCAACGCTG-ATTTGTAATT
1 CGCAACGC-GAATATGTAATT
78588 CGCAAC
1 CGCAAC
78594 ACATAAGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.10
20 31 0.77
21 5 0.12
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (20 bp):
CGCAACGCGAATATGTAATT
Found at i:78787 original size:22 final size:22
Alignment explanation
Indices: 78756--78810 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
78746 TCTCTCACTC
78756 TCTCCGGCGACATCCGTCCCCA
1 TCTCCGGCGACATCCGTCCCCA
* *
78778 TCTCCCGCGACATCCGTTCCCA
1 TCTCCGGCGACATCCGTCCCCA
*
78800 TATCCGGCGAC
1 TCTCCGGCGAC
78811 CCCCCTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.15, C:0.47, G:0.18, T:0.20
Consensus pattern (22 bp):
TCTCCGGCGACATCCGTCCCCA
Found at i:79163 original size:20 final size:20
Alignment explanation
Indices: 79140--79190 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
79130 TTTGAAACTT
79140 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
79160 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
79180 AAAATCGCAAC
1 AAATTCGCAAC
79191 GCGATTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:79244 original size:20 final size:20
Alignment explanation
Indices: 79194--79244 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
79184 TCGCAACGCG
* *
79194 ATTTAAGCTTCGCTTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
* * *
79214 TTTTCATTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
79234 ATTTAAGTTTC
1 ATTTAAGTTTC
79245 AAAAACTACT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTGCGA
Found at i:79465 original size:18 final size:18
Alignment explanation
Indices: 79442--79477 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
79432 AAGCCGGTTG
79442 TGATTGAAATTTTGATTT
1 TGATTGAAATTTTGATTT
**
79460 TGATTGCGATTTTGATTT
1 TGATTGAAATTTTGATTT
79478 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (18 bp):
TGATTGAAATTTTGATTT
Found at i:81768 original size:24 final size:24
Alignment explanation
Indices: 81741--81787 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
81731 ATCATAAAAA
81741 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
81765 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
81788 TTTCGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:81801 original size:24 final size:24
Alignment explanation
Indices: 81741--81801 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
81731 ATCATAAAAA
* *
81741 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAATACTGACCAAGATCAAAG
** * *
81765 TCCGGGTATTGACCAAGATCAAAT
1 TCCGAATACTGACCAAGATCAAAG
*
81789 TTCGAATACTGAC
1 TCCGAATACTGAC
81802 TAGTACTCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (24 bp):
TCCGAATACTGACCAAGATCAAAG
Found at i:82580 original size:25 final size:25
Alignment explanation
Indices: 82552--82619 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 25
82542 AAATAAAATT
82552 ATGTCGTCGGAGAGAGTGGTAAAGG
1 ATGTCGTCGGAGAGAGTGGTAAAGG
* * * *
82577 ATGTCGTTGGATATA--GG-AACGG
1 ATGTCGTCGGAGAGAGTGGTAAAGG
*
82599 ATGTTGTCGGAGAGAGTGGTA
1 ATGTCGTCGGAGAGAGTGGTA
82620 GATGGAGATG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 15 0.47
23 2 0.06
24 2 0.06
25 13 0.41
ACGTcount: A:0.26, C:0.07, G:0.41, T:0.25
Consensus pattern (25 bp):
ATGTCGTCGGAGAGAGTGGTAAAGG
Found at i:82746 original size:20 final size:20
Alignment explanation
Indices: 82720--82887 Score: 70
Period size: 20 Copynumber: 8.4 Consensus size: 20
82710 AAATAAAAGT
82720 TGTTGCGAATTCGAAAATCG
1 TGTTGCGAATTCGAAAATCG
* **
82740 AGTTGCGAAAAC-AAAATCCG
1 TGTTGCGAATTCGAAAAT-CG
* * *
82760 TGTTGCGATTTAGAAAATCT
1 TGTTGCGAATTCGAAAATCG
*** * *
82780 TGTTGCGAAAAGGAAACTTG
1 TGTTGCGAATTCGAAAATCG
*** *
82800 TGTTGCGAAAAAGAAATTCG
1 TGTTGCGAATTCGAAAATCG
** ***
82820 CATTGCGAAAAAG-AAATCG
1 TGTTGCGAATTCGAAAATCG
* * *
82839 AGTTGCGAATTTGAAATTTCG
1 TGTTGCGAATTCGAAA-ATCG
* *
82860 TGTTGCGAATTTGGAAATCG
1 TGTTGCGAATTCGAAAATCG
*
82880 CGTTGCGA
1 TGTTGCGA
82888 TTGCAGAAGC
Statistics
Matches: 112, Mismatches: 32, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
19 18 0.16
20 72 0.64
21 22 0.20
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (20 bp):
TGTTGCGAATTCGAAAATCG
Found at i:82866 original size:40 final size:39
Alignment explanation
Indices: 82720--82868 Score: 122
Period size: 40 Copynumber: 3.7 Consensus size: 39
82710 AAATAAAAGT
* *
82720 TGTTGCGAATTCGAAAATCGAGTTGCGAAAACA-AAATCCG
1 TGTTGCGAATTTGAAAATCGTGTTGCGAAAA-AGAAAT-CG
* * *
82760 TGTTGCG-ATTTAGAAAATCTTGTTGCGAAAAGGAAACTTG
1 TGTTGCGAATTT-GAAAATCGTGTTGCGAAAAAGAAA-TCG
*** * **
82800 TGTTGCGAAAAAGAAATTCGCATTGCGAAAAAGAAATCG
1 TGTTGCGAATTTGAAAATCGTGTTGCGAAAAAGAAATCG
* *
82839 AGTTGCGAATTTGAAATTTCGTGTTGCGAA
1 TGTTGCGAATTTGAAA-ATCGTGTTGCGAA
82869 TTTGGAAATC
Statistics
Matches: 84, Mismatches: 20, Indels: 10
0.74 0.18 0.09
Matches are distributed among these distances:
39 17 0.20
40 65 0.77
41 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (39 bp):
TGTTGCGAATTTGAAAATCGTGTTGCGAAAAAGAAATCG
Found at i:85514 original size:22 final size:22
Alignment explanation
Indices: 85486--85528 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
85476 TACTTACCCT
85486 TCAATCTTACTTGATAAACTAC
1 TCAATCTTACTTGATAAACTAC
85508 TCAATCTTACTTGATAAACTA
1 TCAATCTTACTTGATAAACTA
85529 TCTATGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (22 bp):
TCAATCTTACTTGATAAACTAC
Found at i:108069 original size:18 final size:18
Alignment explanation
Indices: 108046--108105 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
108036 GCGTAGAATT
108046 TGTCCCATAAGACCACTA
1 TGTCCCATAAGACCACTA
* *
108064 TGTCCCGA-AGGACCACTG
1 TGTCCC-ATAAGACCACTA
108082 TGT-CC-TGAAGGACCACTA
1 TGTCCCAT-AA-GACCACTA
108100 TGTCCC
1 TGTCCC
108106 GAAGTACCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
17 3 0.09
18 27 0.82
19 3 0.09
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (18 bp):
TGTCCCATAAGACCACTA
Found at i:108109 original size:18 final size:18
Alignment explanation
Indices: 108056--108116 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
108046 TGTCCCATAA
108056 GACCACTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
* *
108074 GACCACTGTGTCCTGAAG
1 GACCACTATGTCCCGAAG
108092 GACCACTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
*
108110 TACCACT
1 GACCACT
108117 GTTAATCCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.20
Consensus pattern (18 bp):
GACCACTATGTCCCGAAG
Found at i:108187 original size:16 final size:16
Alignment explanation
Indices: 108166--108214 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
108156 TAGCTCTCAT
108166 AACACATGACATGGGC
1 AACACATGACATGGGC
108182 AACACATGACATGGGC
1 AACACATGACATGGGC
108198 AACACATGACATGGGC
1 AACACATGACATGGGC
108214 A
1 A
108215 TTACCTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12
Consensus pattern (16 bp):
AACACATGACATGGGC
Found at i:108956 original size:24 final size:24
Alignment explanation
Indices: 108924--108984 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
108914 ACATTTTACA
*
108924 GTGCATCGATGTATTCCTTAACAT
1 GTGCATCGATGCATTCCTTAACAT
108948 GTGCATCGATGCATTCCTTAACAT
1 GTGCATCGATGCATTCCTTAACAT
108972 GTGCATCGATGCA
1 GTGCATCGATGCA
108985 CTATCCATGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (24 bp):
GTGCATCGATGCATTCCTTAACAT
Found at i:109499 original size:10 final size:10
Alignment explanation
Indices: 109484--109517 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
109474 CTTGGTGTTT
109484 TAAGCTTACA
1 TAAGCTTACA
*
109494 TAAGCTTTACT
1 TAAGC-TTACA
109505 TAAGCTTACA
1 TAAGCTTACA
109515 TAA
1 TAA
109518 CACCCAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (10 bp):
TAAGCTTACA
Found at i:116272 original size:25 final size:25
Alignment explanation
Indices: 116227--116274 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
116217 GAGTTCGTTC
*
116227 TATTTTTTTAAAAATTTAAAAATTT
1 TATTTTTTTAAAAATTAAAAAATTT
*
116252 TATTTTTTT-TAAATTCAAAAAAT
1 TATTTTTTTAAAAATT-AAAAAAT
116275 ATTTTTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTTTTTTAAAAATTAAAAAATTT
Found at i:119863 original size:12 final size:12
Alignment explanation
Indices: 119846--119871 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
119836 ACTAGACCAC
119846 AAAGAGAGAGAG
1 AAAGAGAGAGAG
119858 AAAGAGAGAGAG
1 AAAGAGAGAGAG
119870 AA
1 AA
119872 CATTATCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
AAAGAGAGAGAG
Done.