Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002143.1 Hibiscus syriacus cultivar Beakdansim tig00004382_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: 103223
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:11419 original size:38 final size:38
Alignment explanation
Indices: 11362--11437 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
11352 TTAGATGATG
*
11362 ACACTTGTAATCATCTGATTGGATAGAAATAAACAAAA
1 ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
* *
11400 ACACGTGTAATCATTTGATTGGATAGAAATTAACAAAA
1 ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
11438 GAAGAAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (38 bp):
ACACGTGTAATCATCTGATTGGATAGAAATAAACAAAA
Found at i:22005 original size:36 final size:35
Alignment explanation
Indices: 21965--22037 Score: 92
Period size: 36 Copynumber: 2.1 Consensus size: 35
21955 AAAAATTTAA
* * * *
21965 GAGCTCAATTGAAGCTCGAGACTCGAGCTCGATTTT
1 GAGCTCAATTCAAGCTCGA-ACTCAAACTCGAATTT
*
22001 GAGCTCGATTCAAGCTCGAACTCAAACTCGAATTT
1 GAGCTCAATTCAAGCTCGAACTCAAACTCGAATTT
22036 GA
1 GA
22038 ACCTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
35 15 0.47
36 17 0.53
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (35 bp):
GAGCTCAATTCAAGCTCGAACTCAAACTCGAATTT
Found at i:24219 original size:3 final size:3
Alignment explanation
Indices: 24213--24237 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24203 TGATGATTTT
24213 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
24238 AAGAAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:37697 original size:3 final size:3
Alignment explanation
Indices: 37689--37723 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
37679 ATAAATGAAC
*
37689 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
37724 GTTTGATATA
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:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:56265 original size:21 final size:21
Alignment explanation
Indices: 56241--56283 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
56231 CTTGCTCCAG
*
56241 CCTTTGC-TTGCGCTGCTTCTT
1 CCTTTGCTTTGCGCAGC-TCTT
56262 CCTTTGCTTTGCGCAGCTCTT
1 CCTTTGCTTTGCGCAGCTCTT
56283 C
1 C
56284 ACAAGCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.02, C:0.35, G:0.19, T:0.44
Consensus pattern (21 bp):
CCTTTGCTTTGCGCAGCTCTT
Found at i:61206 original size:25 final size:26
Alignment explanation
Indices: 61178--61240 Score: 65
Period size: 31 Copynumber: 2.3 Consensus size: 26
61168 ATTAATGTCA
61178 ATATTTTT-AAATAAAAATAAAATAT
1 ATATTTTTAAAATAAAAATAAAATAT
*
61203 ATATGTTAAGTTAAAAATAAGAATAAAATAT
1 ATAT-TT---TT-AAAATAAAAATAAAATAT
61234 ATATTTT
1 ATATTTT
61241 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
25 4 0.13
26 2 0.06
27 1 0.03
29 2 0.06
30 2 0.06
31 20 0.65
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (26 bp):
ATATTTTTAAAATAAAAATAAAATAT
Found at i:61252 original size:30 final size:30
Alignment explanation
Indices: 61186--61417 Score: 156
Period size: 30 Copynumber: 7.8 Consensus size: 30
61176 CAATATTTTT
* *
61186 AAATAAAAATAAAATATATATGTTAAGTTAA
1 AAATAAGAATAAAATATATATTTTAAGTT-A
*
61217 AAATAAGAATAAAATATATATTTTAATTTA
1 AAATAAGAATAAAATATATATTTTAAGTTA
* * * *
61247 AAATAAGGAT--AATTTATATTCAATAATTTA
1 AAATAAGAATAAAATATATATT--TTAAGTTA
* * * **
61277 AGATAAGAATATAATATATGTAATAAGTTA
1 AAATAAGAATAAAATATATATTTTAAGTTA
* **
61307 AAATAAAAATAAGCTATAT-TTTTAAAAGTTA
1 AAATAAGAATAAAATATATATTTT--AAGTTA
* *
61338 AGATACA-AATAAAATATAT-TTTAAAGTTA
1 AAATA-AGAATAAAATATATATTTTAAGTTA
** *
61367 TGATAAG-ATTAAA-ATATATTTTAAGTTA
1 AAATAAGAATAAAATATATATTTTAAGTTA
* *
61395 AAATAAAAATAAAAAATAT-TTTT
1 AAATAAGAATAAAATATATATTTT
61418 GATATAATAT
Statistics
Matches: 160, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.03
28 28 0.17
29 21 0.13
30 50 0.31
31 49 0.31
32 8 0.05
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (30 bp):
AAATAAGAATAAAATATATATTTTAAGTTA
Found at i:61495 original size:23 final size:23
Alignment explanation
Indices: 61446--61507 Score: 61
Period size: 28 Copynumber: 2.5 Consensus size: 23
61436 TAAATTATTT
*
61446 AATATATTTTATAAGATATATAA
1 AATATATTTTATAAGATAAATAA
*
61469 AATATATTTTTAAGTAAAATAAGAATAA
1 AATATA-TTTT-A-TAAGAT-A-AATAA
61497 AATATATTTTA
1 AATATATTTTA
61508 AAGTTAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 6 0.19
24 4 0.12
25 1 0.03
26 6 0.19
27 5 0.16
28 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (23 bp):
AATATATTTTATAAGATAAATAA
Found at i:61498 original size:28 final size:31
Alignment explanation
Indices: 61456--61540 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
61446 AATATATTTT
*
61456 ATAAGATATATAAAATATATTTTTAAG-TAAA
1 ATAAGA-ACATAAAATATATTTTTAAGTTAAA
* *
61487 ATAAG-A-ATAAAATATATTTTAAAGTTAAG
1 ATAAGAACATAAAATATATTTTTAAGTTAAA
*
61516 ATAAGAACAAAAAATATATTTTTAA
1 ATAAGAACATAAAATATATTTTTAA
61541 TGTTTAGATG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 17 0.36
29 9 0.19
30 1 0.02
31 20 0.43
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.35
Consensus pattern (31 bp):
ATAAGAACATAAAATATATTTTTAAGTTAAA
Found at i:61519 original size:23 final size:23
Alignment explanation
Indices: 61446--61519 Score: 60
Period size: 28 Copynumber: 3.0 Consensus size: 23
61436 TAAATTATTT
* *
61446 AATATATTTTATAAGAT-ATATAA
1 AATATATTTTA-AAGTTAAGATAA
*
61469 AATATATTTTTAAGTAAAATAAGAATAA
1 AATATATTTTAAAGT----TAAG-ATAA
61497 AATATATTTTAAAGTTAAGATAA
1 AATATATTTTAAAGTTAAGATAA
61520 GAACAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
22 3 0.07
23 14 0.34
24 4 0.10
26 1 0.02
27 1 0.02
28 18 0.44
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (23 bp):
AATATATTTTAAAGTTAAGATAA
Found at i:61532 original size:29 final size:28
Alignment explanation
Indices: 61467--61537 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
61457 TAAGATATAT
* *
61467 AAAATATATTTTTAAGTAAAATAAGAAT
1 AAAATATATTTTAAAGTAAAATAAGAAC
*
61495 AAAATATATTTTAAAGTTAAGATAAGAAC
1 AAAATATATTTTAAAG-TAAAATAAGAAC
61524 AAAAAATATATTTT
1 --AAAATATATTTT
61538 TAATGTTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.41
29 10 0.27
31 12 0.32
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAATATATTTTAAAGTAAAATAAGAAC
Found at i:61800 original size:47 final size:47
Alignment explanation
Indices: 61731--61835 Score: 183
Period size: 47 Copynumber: 2.2 Consensus size: 47
61721 GTGTCATTTC
61731 ACCCTCTAATTAGTCTGAAATAAAATGATTAAATTAAAATAAACTAA
1 ACCCTCTAATTAGTCTGAAATAAAATGATTAAATTAAAATAAACTAA
* *
61778 ACCCTCTAATTAGTGTGAAATAAAATGATTAAATTAAAATAAATTAA
1 ACCCTCTAATTAGTCTGAAATAAAATGATTAAATTAAAATAAACTAA
*
61825 ACCCTCCAATT
1 ACCCTCTAATT
61836 GATTGGTAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (47 bp):
ACCCTCTAATTAGTCTGAAATAAAATGATTAAATTAAAATAAACTAA
Found at i:62418 original size:24 final size:24
Alignment explanation
Indices: 62386--62443 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
62376 CACCTTATCC
62386 TAATCAAAAAAATATAAATAATTAT
1 TAAT-AAAAAAATATAAATAATTAT
* *
62411 TAATAAAAATATATAATTAATTAT
1 TAATAAAAAAATATAAATAATTAT
62435 TAATAAAAA
1 TAATAAAAA
62444 GTTAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
TAATAAAAAAATATAAATAATTAT
Found at i:62772 original size:27 final size:28
Alignment explanation
Indices: 62709--62772 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
62699 TATCAATCAC
62709 ATAATA-AAAAAATCAAACAATAATAAT
1 ATAATATAAAAAATCAAACAATAATAAT
* * * *
62736 AAAATTTAAAAAAT-ATATAATAATAAT
1 ATAATATAAAAAATCAAACAATAATAAT
*
62763 TTAATATAAA
1 ATAATATAAA
62773 TATAAAGTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (28 bp):
ATAATATAAAAAATCAAACAATAATAAT
Found at i:62773 original size:24 final size:21
Alignment explanation
Indices: 62727--62776 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
62717 AAAATCAAAC
62727 AATA-ATAATAAAATTTAAAA
1 AATATATAATAAAATTTAAAA
62747 AATATATAATAATAATTTAATATA
1 AATATATAATAA-AATTTAA-A-A
62771 AATATA
1 AATATA
62777 AAGTCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 7 0.27
23 1 0.04
24 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATATATAATAAAATTTAAAA
Found at i:63239 original size:41 final size:42
Alignment explanation
Indices: 63192--63282 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
63182 TACGCGCTCG
* *
63192 AATTTGATTTACATGTGACAATAGTTTTT-CAGTAGTTTGAT
1 AATTTGATTTACAGGTGACAATAGTTTTTCCAATAGTTTGAT
* * *
63233 ACTTTGATTTACGGGTGTCAATAGTTTTTCCAATAGTTTGAT
1 AATTTGATTTACAGGTGACAATAGTTTTTCCAATAGTTTGAT
63275 AATTTGAT
1 AATTTGAT
63283 ATACTTTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 25 0.58
42 18 0.42
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (42 bp):
AATTTGATTTACAGGTGACAATAGTTTTTCCAATAGTTTGAT
Found at i:70052 original size:141 final size:141
Alignment explanation
Indices: 69608--70182 Score: 595
Period size: 143 Copynumber: 4.0 Consensus size: 141
69598 TAATAGTTGT
* ** ** * **
69608 TGAATATGATTAAATGACCACTGAAAAGTTGGTGAAATGATGCATTATTTAGCCTATGAGATTTA
1 TGAAGATGATTAAATGACCACTGAAAAGTTTCTGCCATGGTGCATTATTTAGCCTATGAGAAATA
* * *
69673 CACTTTTTTTTATATGAAATAATAATGCACCATTGAAAAATTTTCTTAAATGAGTTGATATATCA
66 CACGTTTTTTTATATGAATTAATAATGCACCATT-AAAAATTTTCTGAAATGAGTTGATATATCA
* *
69738 CTGAAAAGTTGT
130 CTGAAAAATTGA
* * *** * * * **
69750 TGAAAATGATTAATTGGGTACTGAAATGTTTCTACCATGGTGTATTATTT-GATATATGAGAAAT
1 TGAAGATGATTAAATGACCACTGAAAAGTTTCTGCCATGGTGCATTATTTAG-CCTATGAGAAAT
* * *
69814 ACACGTTTTTCTCATATGAATTAATAATGTACCACTTTAAAATTTTCTGAAATGAGTTGATATAT
65 ACACGTTTTT-TTATATGAATTAATAATGCACCA-TTAAAAATTTTCTGAAATGAGTTGATATAT
* *
69879 GACTGAAAAGTTGA
128 CACTGAAAAATTGA
* * *
69893 TGAAGATGATTAAATGACCACTGAAAAGTTTTTGTCATGGTGTATTATTT-GACCTATGAGAAAT
1 TGAAGATGATTAAATGACCACTGAAAAGTTTCTGCCATGGTGCATTATTTAG-CCTATGAGAAAT
* * *
69957 ACACGTTTTTTTATATGAATTGATAATGCACCA-TAAAAAGTATTATGAAATGAGTTGATATATC
65 ACACGTTTTTTTATATGAATTAATAATGCACCATTAAAAA-TTTTCTGAAATGAGTTGATATATC
*
70021 ACTGAAAAATTGC
129 ACTGAAAAATTGA
* * *
70034 CGAAGATGATTAAATGACCACTAAAAAATTTCTGCCATGGTGCATTATTTAGCCTATGAGAAATA
1 TGAAGATGATTAAATGACCACTGAAAAGTTTCTGCCATGGTGCATTATTTAGCCTATGAGAAATA
* * * * * * *
70099 CGA-GTTTTTTTAATTTGAAGTGATAATGCACTATTGAGAAGTGTTT-TGAAATGAATTGATATA
66 C-ACGTTTTTTT-ATATGAATTAATAATGCACCATT-AAAAAT-TTTCTGAAATGAGTTGATATA
*
70162 TCACT-AAAAAGTTGT
127 TCACTGAAAAA-TTGA
70177 TGAAGA
1 TGAAGA
70183 ATGGTGTATT
Statistics
Matches: 362, Mismatches: 60, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
140 5 0.01
141 99 0.27
142 99 0.27
143 152 0.42
144 7 0.02
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (141 bp):
TGAAGATGATTAAATGACCACTGAAAAGTTTCTGCCATGGTGCATTATTTAGCCTATGAGAAATA
CACGTTTTTTTATATGAATTAATAATGCACCATTAAAAATTTTCTGAAATGAGTTGATATATCAC
TGAAAAATTGA
Found at i:70151 original size:284 final size:285
Alignment explanation
Indices: 69602--70182 Score: 672
Period size: 284 Copynumber: 2.0 Consensus size: 285
69592 ACATAATAAT
*
69602 AGTTGTTGAATATGATTAAATGACCACTGAAAAGTTGGTGAAATGATGCATTATTTAGCCTATGA
1 AGTTGTTGAAGATGATTAAATGACCACTGAAAAGTTGGTGAAATGATGCATTATTTAGCCTATGA
** * * * *
69667 GATTTACACTTTTTTTTATATGAAATAATAATGCACCATTGAAAAATTTTCTTAAATGAGTTGAT
66 GAAATACACGTTTTTTTATATGAAATAATAATGCACCATTGAAAAATATTATGAAATGAGTTGAT
* ** * *** * ** *
69732 ATATCACTGAAAAGTTGTTGAAAATGATTAATTGGGTACTGAAATGTTTCTACCATGGTGTATTA
131 ATATCACTGAAAAATTGCCGAAAATGATTAAATGACCACTAAAAAATTTCTACCATGGTGCATTA
* * * * *
69797 TTTGATATATGAGAAATACACGTTTTTCTCATATGAATTAATAATGTACCACTTTAAAATTTTCT
196 TTTGACATATGAGAAATACACGTTTTTCTAATATGAAGTAATAATGCACCACTTGAAAATTTTCT
* * *
69862 GAAATGAGTTGATATATGACTGAAA
261 GAAATGAATTGATATATCACTAAAA
* ** ** * *
69887 AGTTGATGAAGATGATTAAATGACCACTGAAAAGTTTTTGTCATGGTGTATTATTT-GACCTATG
1 AGTTGTTGAAGATGATTAAATGACCACTGAAAAGTTGGTGAAATGATGCATTATTTAG-CCTATG
* *
69951 AGAAATACACGTTTTTTTATATGAATTGATAATGCACCA-T-AAAAAGTATTATGAAATGAGTTG
65 AGAAATACACGTTTTTTTATATGAAATAATAATGCACCATTGAAAAA-TATTATGAAATGAGTTG
* *
70014 ATATATCACTGAAAAATTGCCGAAGATGATTAAATGACCACTAAAAAATTTCTGCCATGGTGCAT
129 ATATATCACTGAAAAATTGCCGAAAATGATTAAATGACCACTAAAAAATTTCTACCATGGTGCAT
* * * * * *
70079 TATTT-AGCCTATGAGAAATACGA-GTTTTTTTAATTTGAAGTGATAATGCACTA-TTGAGAAGT
194 TATTTGA-CATATGAGAAATAC-ACGTTTTTCTAATATGAAGTAATAATGCACCACTTGA-AAAT
70141 GTTT-TGAAATGAATTGATATATCACTAAAA
256 -TTTCTGAAATGAATTGATATATCACTAAAA
70171 AGTTGTTGAAGA
1 AGTTGTTGAAGA
70183 ATGGTGTATT
Statistics
Matches: 246, Mismatches: 44, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
283 9 0.04
284 145 0.59
285 92 0.37
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (285 bp):
AGTTGTTGAAGATGATTAAATGACCACTGAAAAGTTGGTGAAATGATGCATTATTTAGCCTATGA
GAAATACACGTTTTTTTATATGAAATAATAATGCACCATTGAAAAATATTATGAAATGAGTTGAT
ATATCACTGAAAAATTGCCGAAAATGATTAAATGACCACTAAAAAATTTCTACCATGGTGCATTA
TTTGACATATGAGAAATACACGTTTTTCTAATATGAAGTAATAATGCACCACTTGAAAATTTTCT
GAAATGAATTGATATATCACTAAAA
Found at i:77938 original size:21 final size:21
Alignment explanation
Indices: 77912--77965 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
77902 TTACATATGC
77912 TTTTAATTATGCGTCTGCATG
1 TTTTAATTATGCGTCTGCATG
*
77933 TTTTAATTACGCGTCTGCATG
1 TTTTAATTATGCGTCTGCATG
77954 TTTTAATTATGC
1 TTTTAATTATGC
77966 TAACCCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (21 bp):
TTTTAATTATGCGTCTGCATG
Found at i:80462 original size:21 final size:21
Alignment explanation
Indices: 80417--80462 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
80407 AAATAGCATT
* * **
80417 GCGATTTTCCAAGTTCGCATT
1 GCGATTTTCCAAATTCACAAC
80438 GCGATTTTCCAAATTCACAAC
1 GCGATTTTCCAAATTCACAAC
80459 GCGA
1 GCGA
80463 ATCTGTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
GCGATTTTCCAAATTCACAAC
Found at i:80491 original size:40 final size:41
Alignment explanation
Indices: 80447--80551 Score: 137
Period size: 40 Copynumber: 2.6 Consensus size: 41
80437 TGCGATTTTC
* * *
80447 CAAATTCACAACGCGAAT-CTGTAAAT-CGCAACACAGAAGT
1 CAAATTCGCAACGCGAATAGT-TAAATCCGCAACACAAAAGT
80487 CAAATTCGCAACGCG-ATAGTTAAATCCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATAGTTAAATCCGCAACACAAAAGT
*
80527 CAAATTCGCAACGCGAA-AGTCAAAT
1 CAAATTCGCAACGCGAATAGTTAAAT
80552 TTGCAACGCG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
39 7 0.12
40 50 0.86
41 1 0.02
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (41 bp):
CAAATTCGCAACGCGAATAGTTAAATCCGCAACACAAAAGT
Found at i:80495 original size:20 final size:19
Alignment explanation
Indices: 80472--80663 Score: 163
Period size: 20 Copynumber: 9.6 Consensus size: 19
80462 AATCTGTAAA
*
80472 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
*
80492 TCGCAACGCGATAGTTAAAT
1 TCGCAACGCGA-AGTCAAAT
* * *
80512 CCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
80532 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCG-AAGTCAAAT
*
80552 TTGCAACGCGAATTTGT-AAA-
1 TCGCAACGCGAA---GTCAAAT
* *
80572 TCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
* *
80592 TCGCAGCGCGATAGCCAAAT
1 TCGCAACGCGA-AGTCAAAT
* *
80612 TCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
80632 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
80652 TCGCAACGCGAA
1 TCGCAACGCGAA
80664 ACACAATATT
Statistics
Matches: 137, Mismatches: 23, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.01
19 10 0.07
20 116 0.85
21 7 0.05
22 2 0.01
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (19 bp):
TCGCAACGCGAAGTCAAAT
Found at i:80547 original size:60 final size:58
Alignment explanation
Indices: 80483--80664 Score: 211
Period size: 60 Copynumber: 3.0 Consensus size: 58
80473 CGCAACACAG
80483 AAGTCAAATTCGCAACGCGATAGTTAAATCCGCAACACAAAAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA-AGTTAAAT-CGCAACACAAAAGTCAAATTCGCAACGCGA
* * *
80543 AAGTCAAATTTGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAGCGCGA
1 AAGTCAAATTCGCAACGCGAA-GT-TAAATCGCAACACAAAAGTCAAATTCGCAACGCGA
* * * * * * * *
80603 TAGCCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGC-GAAGTTAAA-TCGCAACACAAAAGTCAAATTCGCAACGCGA
80663 AA
1 AA
80665 CACAATATTA
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
59 4 0.04
60 92 0.89
61 7 0.07
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (58 bp):
AAGTCAAATTCGCAACGCGAAGTTAAATCGCAACACAAAAGTCAAATTCGCAACGCGA
Found at i:80558 original size:40 final size:40
Alignment explanation
Indices: 80484--80664 Score: 195
Period size: 40 Copynumber: 4.5 Consensus size: 40
80474 GCAACACAGA
* * * * *
80484 AGTCAAATTCGCAACGCGATAGTTAAATCCGCAACACAAA
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAT
*
80524 AGTCAAATTCGCAACGCGAAAGTCAAATTTGCAACGCGAATT
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGC-AA-T
* * * * *
80566 TGT-AAA-TCGCAACACAAAAGTCAAATTCGCAGCGCGAT
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAT
* * * *
80604 AGCCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAT
80644 AGTCAAATTCGCAACGCGAAA
1 AGTCAAATTCGCAACGCGAAA
80665 CACAATATTA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.02
39 4 0.03
40 106 0.89
41 5 0.04
42 2 0.02
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (40 bp):
AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAT
Found at i:80570 original size:100 final size:100
Alignment explanation
Indices: 80447--80663 Score: 353
Period size: 100 Copynumber: 2.2 Consensus size: 100
80437 TGCGATTTTC
* * **
80447 CAAATTCACAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTTAAAT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGCCAAAT
80512 CCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
66 CCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
* * *
80547 CAAATTTGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAGCGCGATAGCCAAAT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGCCAAAT
* *
80612 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGT
66 CCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
80647 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
80664 ACACAATATT
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 107 1.00
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.18
Consensus pattern (100 bp):
CAAATTCGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGCCAAAT
CCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
Found at i:80800 original size:22 final size:22
Alignment explanation
Indices: 80774--80824 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
80764 CTACGGCGAC
*
80774 ATCCGTCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
80796 ATCCGTCCCCATCTCCGATGAA
1 ATCCGTCCCCATCTCCGACGAA
80818 ATCCGTC
1 ATCCGTC
80825 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:81253 original size:20 final size:20
Alignment explanation
Indices: 81210--81258 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
81200 AAAATCGCAA
*
81210 CGCGATTTT-AGTTTCGCGT
1 CGCGATTTTCAGTTTCACGT
*
81229 CGCGATTTTCATTTTCACGT
1 CGCGATTTTCAGTTTCACGT
*
81249 TGCGATTTTC
1 CGCGATTTTC
81259 TCGTTGCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (20 bp):
CGCGATTTTCAGTTTCACGT
Found at i:83441 original size:24 final size:24
Alignment explanation
Indices: 83409--83462 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 24
83399 GCCCGATGCA
*
83409 CCTATCATTATTCAAGAGTCGCTT
1 CCTATCATTATTCAAGAGGCGCTT
83433 CCTATC---ATTCAAGAGGCGCTT
1 CCTATCATTATTCAAGAGGCGCTT
83454 CCTATCATT
1 CCTATCATT
83463 CAAGAGGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 20 0.77
24 6 0.23
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (24 bp):
CCTATCATTATTCAAGAGGCGCTT
Found at i:83444 original size:21 final size:21
Alignment explanation
Indices: 83418--83470 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
83408 ACCTATCATT
*
83418 ATTCAAGAGTCGCTTCCTATC
1 ATTCAAGAGGCGCTTCCTATC
83439 ATTCAAGAGGCGCTTCCTATC
1 ATTCAAGAGGCGCTTCCTATC
83460 ATTCAAGAGGC
1 ATTCAAGAGGC
83471 CCCTCCCATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
ATTCAAGAGGCGCTTCCTATC
Found at i:83481 original size:21 final size:21
Alignment explanation
Indices: 83418--83532 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
83408 ACCTATCATT
* * * *
83418 ATTCAAGAGTCGCTTCCTATC
1 ATTCAAGAGGCCCCTCCCATC
* * *
83439 ATTCAAGAGGCGCTTCCTATC
1 ATTCAAGAGGCCCCTCCCATC
83460 ATTCAAGAGGCCCCTCCCATC
1 ATTCAAGAGGCCCCTCCCATC
* * *
83481 A-TCGAAGAAGCCCCTTCCACC
1 ATTC-AAGAGGCCCCTCCCATC
* **
83502 GTTCAAGAGGCCCCTGTCATC
1 ATTCAAGAGGCCCCTCCCATC
*
83523 GTTCAAGAGG
1 ATTCAAGAGG
83533 TCCTGTCCGC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
20 2 0.03
21 76 0.95
22 2 0.03
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.23
Consensus pattern (21 bp):
ATTCAAGAGGCCCCTCCCATC
Found at i:83482 original size:42 final size:41
Alignment explanation
Indices: 83418--83532 Score: 97
Period size: 42 Copynumber: 2.8 Consensus size: 41
83408 ACCTATCATT
* * * * * *
83418 ATTCAAGAGTCGCTTCCTATCATTCAAGAGGCGCTTCCTATC
1 ATTCAAGAGGCCCCTCCCATCATTCAAGAGGCCCTTCC-ACC
*
83460 ATTCAAGAGGCCCCTCCCATCA-TCGAAGAAGCCCCTTCCACC
1 ATTCAAGAGGCCCCTCCCATCATTC-AAG-AGGCCCTTCCACC
* ** *
83502 GTTCAAGAGGCCCCTGTCATCGTTCAAGAGG
1 ATTCAAGAGGCCCCTCCCATCATTCAAGAGG
83533 TCCTGTCCGC
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
41 4 0.07
42 44 0.76
43 10 0.17
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.23
Consensus pattern (41 bp):
ATTCAAGAGGCCCCTCCCATCATTCAAGAGGCCCTTCCACC
Found at i:83546 original size:21 final size:21
Alignment explanation
Indices: 83485--83549 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
83475 CCCATCATCG
*
83485 AAGAAGCCCCT-TCCACCGTTC
1 AAGAGGCCCCTGT-CACCGTTC
*
83506 AAGAGGCCCCTGTCATCGTTC
1 AAGAGGCCCCTGTCACCGTTC
* *
83527 AAGAGG-TCCTGTCCGCCGTTC
1 AAGAGGCCCCTGT-CACCGTTC
83548 AA
1 AA
83550 AAGCCCGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.14
21 31 0.84
22 1 0.03
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.22
Consensus pattern (21 bp):
AAGAGGCCCCTGTCACCGTTC
Found at i:85009 original size:14 final size:14
Alignment explanation
Indices: 84963--84999 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
84953 GCTTGTTTAA
*
84963 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
84977 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
84991 TTGATTTGT
1 TTGATTTGT
85000 TTAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:85055 original size:80 final size:78
Alignment explanation
Indices: 84909--85065 Score: 269
Period size: 80 Copynumber: 2.0 Consensus size: 78
84899 TTTTACATTG
84909 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTATAA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTATAA
84974 AAGTTGATTTGTA
66 AAGTTGATTTGTA
* * *
84987 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTAT
85052 AAAAGTTGATTTGT
64 AAAAGTTGATTTGT
85066 TGTTTTAAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
78 17 0.23
79 19 0.26
80 38 0.51
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (78 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTATAA
AAGTTGATTTGTA
Found at i:85508 original size:18 final size:18
Alignment explanation
Indices: 85485--85520 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
85475 AAGCCGGTTG
*
85485 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
85503 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
85521 CTTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:87816 original size:24 final size:24
Alignment explanation
Indices: 87782--87835 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
87772 CCATCACATC
87782 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
87806 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
87830 ATCAAA
1 ATCAAA
87836 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:87849 original size:24 final size:24
Alignment explanation
Indices: 87782--87849 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
87772 CCATCACATC
* * *
87782 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
87806 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
87830 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
87850 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:93445 original size:37 final size:37
Alignment explanation
Indices: 93403--93511 Score: 170
Period size: 35 Copynumber: 3.0 Consensus size: 37
93393 ATATTTCAAC
* *
93403 AAACATCTATCAAACTTTGAAAAGCCATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAGCCATTTTTCAAAG
93440 AAACATTTACCAAACTTTGAAAAG-CA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAGCCATTTTTCAAAG
93475 AAACATTTACCAAACTTTGAAAA-CCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAGCCA-TTTTTCAAAG
93512 TTTGTTGCCA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
35 34 0.51
36 2 0.03
37 31 0.46
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.30
Consensus pattern (37 bp):
AAACATTTACCAAACTTTGAAAAGCCATTTTTCAAAG
Found at i:93467 original size:21 final size:20
Alignment explanation
Indices: 93440--93503 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
93430 TTTTTCAAAG
93440 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
93460 AAAGCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
93475 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
93495 AAACCATTT
1 AAA-CATTT
93504 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Done.