Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024732.1 Corchorus olitorius cultivar O-4 contig24765, 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: 94067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7435 original size:93 final size:93
Alignment explanation
Indices: 7355--7534 Score: 297
Period size: 93 Copynumber: 1.9 Consensus size: 93
7345 TTAATTAAAT
* * *
7355 TAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTTGATTTAATTAAATAAAAATAGAGTTT
1 TAGTAAAATCGTAAAAATAAAATAAGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
*
7420 TTAGTTGAGTAAAACTATAAAAGTATAA
66 TTAGTTGACTAAAACTATAAAAGTATAA
* * *
7448 TAGTAAAATGGTAAAAATAAAATAATTATAAGGATATTAGATTTAATTTAATAAAAATAGAGTTT
1 TAGTAAAATCGTAAAAATAAAATAAGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
7513 TTAGTTGACTAAAACTATAAAA
66 TTAGTTGACTAAAACTATAAAA
7535 ATTTAAAATA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (93 bp):
TAGTAAAATCGTAAAAATAAAATAAGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
TTAGTTGACTAAAACTATAAAAGTATAA
Found at i:12171 original size:331 final size:330
Alignment explanation
Indices: 11549--12710 Score: 1399
Period size: 332 Copynumber: 3.5 Consensus size: 330
11539 AATTAGATTC
* * * *
11549 AATTCGGAAAAAAGGTAGGAAAAGCAATATTAGAAGCATGAAAAGCCCTTCAGTCTTTTTGGCAT
1 AATTCGGAAAAAA--TAGGAAAAACAATATTAGAAGCATGAAAAGCCTTTCAATCTTTTTGGCGT
* * * * * *
11614 TGAGTTATATATTTTTTATTAGTATTGTGACCCAAAATTGATGAGAAATT-TCTT-GGGTCAATT
64 TGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCT-TTCGGGTCAATT
* * * * *
11677 TTTGCAAGATTTTAGCTGAAATCGTGTATTAACCATCACGGTTTTTGAC-AAAAACGCGTTCCGG
128 TTTACAAAATTTTA-CCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTT-TGG
* ** * *
11741 AACGTCGCCTCAGTTTTGCATGATTTTTGGCACCAAGTCTCATTGAAATATCTATATCCATCTAA
191 -GCCCCGCTTCAGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATCTAA
* * * * *
11806 CCAAACCTTACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATCATGTTTCG-TTT
255 CAAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTT
*
11870 CAATTAGGAATT
320 -AATTAGAAATT
* * * * *
11882 AATACGGAAAAAATAGGAAAAACGATATTAGAAGCATGAATAGCCTTTCAATCTTTTTAGTGTTG
1 AATTCGGAAAAAATAGGAAAAACAATATTAGAAGCATGAAAAGCCTTTCAATCTTTTTGGCGTTG
* * *
11947 AATTATATATTTTTTATGAGTATCATGGCCAAAAATTTAGGA-AAATTCTTTCAGGTCAATTTTT
66 AATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCTTTCGGGTCAATTTTT
* * * * * *
12011 ATAAAATTTTATTCGAAATCATGTACTAACTATCACGGTGTTTGGCTAAAAACGCGTTATGGGCC
131 ACAAAATTTTA-CCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTT-TGGGCC
* * * **
12076 CCGGTTCAGTTTTGTATGATTTTTGGCGCCAA-TACTCATTGGAATATCTATATTTATCTAACAA
194 CCGCTTCAGTTTTGCATGATTTTTGGCGCCAAGT-CTCATTGAAATATCTATATCCATCTAACAA
* * *
12140 AATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTCAATTCA-GTTTCGATTTAA
258 AATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA-TCATGTTTCGATTTAA
12204 TTAGAAATT
322 TTAGAAATT
* * * * * *
12213 AATTCGAAAAAAATTGAAAAAATCAATATTAGAAGCGTGAGAAGCCTTTCAATCTTTTTGGCGTA
1 AATTCGGAAAAAATAGGAAAAA-CAATATTAGAAGCATGAAAAGCCTTTCAATCTTTTTGGCGTT
* * * ** * *
12278 GAGTTATATATTTTTTATGAATATGGTGGCCGGAAATTGAGGAGAAA-TGTTTCGTGTCAATTTT
65 GAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCTTTCGGGTCAATTTT
* * *
12342 TACAAAATTTTAGCCGAAATCGTATACTAACCATCACAGTTTTTGACTAAAAACGTGTTTCGGGA
130 TACAAAATTTTA-CCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTT-GGG-
* * *
12407 TCCCGACTT-TGTTTTGCATGATTTTTAGCGCCAAGTCTCATTGAAATATCTATATCCATCTAAC
192 CCCCG-CTTCAGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATCTAAC
12471 AAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
256 AAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
*
12536 ACTAGAAATT
321 ATTAGAAATT
* * * *
12546 AATTCGGAAAAAATAAGAAAACCGATATTAGAAGCATGAAAAACCTTTCAATCTTTTTGGCGTTG
1 AATTCGGAAAAAATAGGAAAAACAATATTAGAAGCATGAAAAGCCTTTCAATCTTTTTGGCGTTG
* * * *
12611 AATTATATATTTTTTATGAGTATCGTGGCAAAAAATTTAGGA-AAATTCTTTTGGGTAAATTTTT
66 AATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCTTTCGGGTCAATTTTT
* *
12675 GCAAAATTTTAACCGAAATCGTGTATTAACCATCAC
131 ACAAAATTTT-ACCGAAATCGTGTACTAACCATCAC
12711 AATTTTTTGT
Statistics
Matches: 698, Mismatches: 116, Indels: 31
0.83 0.14 0.04
Matches are distributed among these distances:
330 8 0.01
331 259 0.37
332 277 0.40
333 151 0.22
334 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (330 bp):
AATTCGGAAAAAATAGGAAAAACAATATTAGAAGCATGAAAAGCCTTTCAATCTTTTTGGCGTTG
AATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCTTTCGGGTCAATTTTT
ACAAAATTTTACCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTTGGGCCCC
GCTTCAGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCATCTAACAAAAT
CTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAG
AAATT
Found at i:25278 original size:22 final size:22
Alignment explanation
Indices: 25253--25298 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
25243 TTTTCCTTTC
25253 TCCCAATTTGAGAGGAAAACAT
1 TCCCAATTTGAGAGGAAAACAT
25275 TCCCAATTTGAGAGGAAAACAT
1 TCCCAATTTGAGAGGAAAACAT
25297 TC
1 TC
25299 TTTCTCAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (22 bp):
TCCCAATTTGAGAGGAAAACAT
Found at i:30753 original size:7 final size:7
Alignment explanation
Indices: 30743--30776 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
30733 AAATTAATCA
30743 TTATATT
1 TTATATT
30750 TTATATT
1 TTATATT
30757 TTATATT
1 TTATATT
30764 TTATATT
1 TTATATT
30771 TTATAT
1 TTATAT
30777 AATAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:34253 original size:11 final size:10
Alignment explanation
Indices: 34234--34264 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
34224 CCATTATACG
34234 TAAAAAAAAA
1 TAAAAAAAAA
34244 TAATAAAAAAA
1 TAA-AAAAAAA
34255 TAAAAAAAAA
1 TAAAAAAAAA
34265 CTCTCCTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:39219 original size:37 final size:37
Alignment explanation
Indices: 39177--39259 Score: 166
Period size: 37 Copynumber: 2.2 Consensus size: 37
39167 AGATTGCAAG
39177 GACAACTTCTCCAATATCCCATCTTTTATTTGCAGAT
1 GACAACTTCTCCAATATCCCATCTTTTATTTGCAGAT
39214 GACAACTTCTCCAATATCCCATCTTTTATTTGCAGAT
1 GACAACTTCTCCAATATCCCATCTTTTATTTGCAGAT
39251 GACAACTTC
1 GACAACTTC
39260 ATTTTTATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (37 bp):
GACAACTTCTCCAATATCCCATCTTTTATTTGCAGAT
Found at i:41841 original size:21 final size:23
Alignment explanation
Indices: 41789--41842 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
41779 TTGGAGTTGC
41789 TATTTATATTTTTCTTTTCTTAATT
1 TATTT-TA-TTTTCTTTTCTTAATT
*
41814 T-TATTATTTTC-TTTCTT-ATT
1 TATTTTATTTTCTTTTCTTAATT
41834 TATTTTATT
1 TATTTTATT
41843 GTTGCTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 4 0.15
21 12 0.46
22 5 0.19
23 2 0.08
24 2 0.08
25 1 0.04
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (23 bp):
TATTTTATTTTCTTTTCTTAATT
Found at i:42769 original size:178 final size:177
Alignment explanation
Indices: 42451--42832 Score: 507
Period size: 178 Copynumber: 2.1 Consensus size: 177
42441 GTTTGCTTAC
* * * * *
42451 ACGGTCTATTTAACATTATATAATATTCTCTCCGGTTATCTGATTAAGGTGATTTAAGTGTCTAT
1 ACGGTCTATTTAATATTATATAAT-TTCTCTCCAGATATCTGATCAAGGTGATTCAAGTGTCTAT
*
42516 TGAAAGATTGTTCCATGATCTACAACTTTTATGAAGGACTCGAAAACTAAATTTAATGTTTCAAG
65 TGAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAAG
* * ** *
42581 TATCAAAAATGCTTCCAAAAAATTTGTTGTTTCAGTTAA-CGGGAATAG
130 TATAAAAAATGCATCCAAAAAATTAATTGTTTC-GGTAAGCGGGAATAG
* * * *
42629 ACGGTCCATTTAATATTATATAATTTTTGCTCCAGATATCTGATCGAGGTGATTCAAGTGTCTCT
1 ACGGTCTATTTAATATTATATAATTTCT-CTCCAGATATCTGATCAAGGTGATTCAAGTGTCTAT
* * *
42694 TGAAAGGTTGTTCCATTATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTATTG-TTCAAG
65 TGAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAA-
*
42758 GTATAAAAAATGCATCCAAAGAATTAATTGTTTCGGTAAGCGGGAATAG
129 GTATAAAAAATGCATCCAAAAAATTAATTGTTTCGGTAAGCGGGAATAG
* * * *
42807 ATGATCTACTTAATATTACATAATTT
1 ACGGTCTATTTAATATTATATAATTT
42833 GTACTTATGA
Statistics
Matches: 177, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
177 12 0.07
178 165 0.93
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (177 bp):
ACGGTCTATTTAATATTATATAATTTCTCTCCAGATATCTGATCAAGGTGATTCAAGTGTCTATT
GAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAAGT
ATAAAAAATGCATCCAAAAAATTAATTGTTTCGGTAAGCGGGAATAG
Found at i:46222 original size:6 final size:6
Alignment explanation
Indices: 46211--46237 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46201 AGAGTATATG
46211 AGAAAT AGAAAT AGAAAT AGAAAT AGA
1 AGAAAT AGAAAT AGAAAT AGAAAT AGA
46238 GTACTAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (6 bp):
AGAAAT
Found at i:46638 original size:43 final size:42
Alignment explanation
Indices: 46591--46716 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 42
46581 GTCATTCAAC
* *
46591 TTTTTTTATT-AATTATGAAAATATATTGTAAATCCAATATTTA
1 TTTTTTT-TTAAATTATGAAAATATATTTTAAATCC-ATATTAA
* *
46634 TTTTTCTTTTAAATTATGGAAAA-ATATTTTAAATTCATCTTAA
1 TTTTT-TTTTAAATTAT-GAAAATATATTTTAAATCCATATTAA
* *
46677 TTTTATTTTTGAATTATGAAAATATATTTTAAATCTATAT
1 TTTT-TTTTTAAATTATGAAAATATATTTTAAATCCATAT
46717 ATTAAATTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
42 5 0.07
43 40 0.57
44 20 0.29
45 5 0.07
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (42 bp):
TTTTTTTTTAAATTATGAAAATATATTTTAAATCCATATTAA
Found at i:48429 original size:20 final size:20
Alignment explanation
Indices: 48404--48449 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
48394 TGTTGATACT
*
48404 ATTATAACTT-TTTTATAATC
1 ATTATAACTTCTTTAATAA-C
48424 ATTATAACTTCTTTAATAAC
1 ATTATAACTTCTTTAATAAC
48444 ATTATA
1 ATTATA
48450 TTAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATAACTTCTTTAATAAC
Found at i:49387 original size:31 final size:31
Alignment explanation
Indices: 49352--49438 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
49342 GATTCAACAG
* *
49352 TTTTAGTAGGGTGAATGCTATGAAACTTTGA
1 TTTTAGTAGGGTGAATACTATAAAACTTTGA
* * *
49383 TTTTAAT-GAGGTTAATACTATAAAACTTTTA
1 TTTTAGTAG-GGTGAATACTATAAAACTTTGA
* * *
49414 TTTTAGAAGGGTTAATACTGTAAAA
1 TTTTAGTAGGGTGAATACTATAAAA
49439 TTCCAATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (31 bp):
TTTTAGTAGGGTGAATACTATAAAACTTTGA
Found at i:49973 original size:22 final size:23
Alignment explanation
Indices: 49948--50041 Score: 72
Period size: 22 Copynumber: 4.3 Consensus size: 23
49938 TATATTGAAG
49948 TTTCATAGT-GTGATTACCAAAA
1 TTTCATAGTAGTGATTACCAAAA
* * *
49970 TTTCAAATGGAG-G-TTATCAAAA
1 TTTCATA-GTAGTGATTACCAAAA
* * *
49992 CTTCATAGTATTG-TTATCAAAA
1 TTTCATAGTAGTGATTACCAAAA
* *
50014 TTTCATA-TAGAGGTTACCAAAA
1 TTTCATAGTAGTGATTACCAAAA
50036 TTTCAT
1 TTTCAT
50042 GTATCAAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.09
22 49 0.86
23 2 0.04
24 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (23 bp):
TTTCATAGTAGTGATTACCAAAA
Found at i:50047 original size:37 final size:37
Alignment explanation
Indices: 50006--50078 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
49996 ATAGTATTGT
* *
50006 TATCAAAATTTCATATAGAGGTTACCAAAATTTCATG
1 TATCAAAATTTCATAGAGAGGTTAACAAAATTTCATG
* *
50043 TATCAAAATTTCTTAGGGAGGTTAACAAAATTTCAT
1 TATCAAAATTTCATAGAGAGGTTAACAAAATTTCAT
50079 ACGAAGGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (37 bp):
TATCAAAATTTCATAGAGAGGTTAACAAAATTTCATG
Found at i:50074 original size:22 final size:22
Alignment explanation
Indices: 50046--50151 Score: 104
Period size: 22 Copynumber: 4.8 Consensus size: 22
50036 TTTCATGTAT
*
50046 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGGGAGGTTAA
* * *
50068 CAAAATTTCATACGAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAA
* * * * *
50090 CGAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGGGAGGTTAA
* *
50112 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAGGGAGGTTAA
*
50134 CAAAATATCATAGGGAGG
1 CAAAATTTCATAGGGAGG
50152 GAGATTATCA
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAA
Found at i:50364 original size:20 final size:22
Alignment explanation
Indices: 50324--50384 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
50314 AAATTTTATT
50324 GTTATCAAACTTTTCATAGTGCG
1 GTTATC-AACTTTTCATAGTGCG
*
50347 GTTATCAA-TTTT-ATAGTGTG
1 GTTATCAACTTTTCATAGTGCG
* **
50367 ATTATCAAAATTTCATAG
1 GTTATCAACTTTTCATAG
50385 GGAGATTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 14 0.42
21 7 0.21
22 6 0.18
23 6 0.18
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (22 bp):
GTTATCAACTTTTCATAGTGCG
Found at i:50384 original size:22 final size:22
Alignment explanation
Indices: 50284--50528 Score: 162
Period size: 22 Copynumber: 11.4 Consensus size: 22
50274 CTCAAAAGAA
* * *
50284 GGTTATCGAAATTTCATGGTCT
1 GGTTATCAAAATTTCATAGTGT
50306 GGTTATCAAAATTT--TA-T-T
1 GGTTATCAAAATTTCATAGTGT
* *
50324 -GTTATCAAACTTTTCATAGTGC
1 GGTTATCAAA-ATTTCATAGTGT
*
50346 GGTTATC--AATTTTATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * *
50366 GATTATCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGT
* * * * *
50388 GATTATCAAAATTTTACACTGA
1 GGTTATCAAAATTTCATAGTGT
* * *
50410 AGTTATCAAAATTTCATCGTAT
1 GGTTATCAAAATTTCATAGTGT
*
50432 GGTTATCAAAATTTCACAGTGT
1 GGTTATCAAAATTTCATAGTGT
** * *
50454 GGTTATCAATCTTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGT
* * * *
50476 GCTTATCGAAATTTCATAATGA
1 GGTTATCAAAATTTCATAGTGT
* * * *
50498 GGTTATTAAATTTTCACAATGT
1 GGTTATCAAAATTTCATAGTGT
50520 GGTTATCAA
1 GGTTATCAA
50529 CAGTTCTACG
Statistics
Matches: 170, Mismatches: 45, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
17 9 0.05
18 4 0.02
19 1 0.01
20 18 0.11
21 2 0.01
22 130 0.76
23 6 0.04
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:52136 original size:2 final size:2
Alignment explanation
Indices: 52129--52153 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52119 CGTGGCAAAG
52129 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 T
52154 TCCTAGTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52972 original size:2 final size:2
Alignment explanation
Indices: 52965--53006 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
52955 TGTCTTTTAG
52965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53007 AAAGCATTTC
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):
TA
Found at i:59050 original size:16 final size:16
Alignment explanation
Indices: 59029--59060 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59019 TTAATTATTT
*
59029 TTTTCTATTTTAATTA
1 TTTTCTAGTTTAATTA
59045 TTTTCTAGTTTAATTA
1 TTTTCTAGTTTAATTA
59061 GGATGGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTTCTAGTTTAATTA
Found at i:59397 original size:22 final size:22
Alignment explanation
Indices: 59354--59405 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
59344 ACCTTTTTAT
* * * *
59354 AAATTTTTTTAACCTTCTTAAG
1 AAATTTTGTTAACATCCCTAAG
59376 AAATTTTGTTAACATCCCTAAG
1 AAATTTTGTTAACATCCCTAAG
*
59398 GAATTTTG
1 AAATTTTG
59406 AAGACCTTAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (22 bp):
AAATTTTGTTAACATCCCTAAG
Found at i:59565 original size:22 final size:22
Alignment explanation
Indices: 59527--59586 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
59517 AAAACCTCAA
* *
59527 TATG-AATTGTTAGTAATCGCAC
1 TATGAAATTGTGA-TAATCACAC
* *
59549 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
59571 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
59587 CCTCGCTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:59595 original size:22 final size:22
Alignment explanation
Indices: 59553--59805 Score: 121
Period size: 22 Copynumber: 11.7 Consensus size: 22
59543 TCGCACTCTG
* * *
59553 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTCACTATA
* *
59575 AAATTGTGATAACCTCGCTATA
1 AAATTTTGATAACCTCACTATA
* *
59597 AAATTTTGACAAACCTCCCTATA
1 AAATTTTGA-TAACCTCACTATA
*
59620 AAATTTTGATAACCTC-CTTATG
1 AAATTTTGATAACCTCAC-TATA
* *
59642 TAATCTTGATAA-CT-AC----
1 AAATTTTGATAACCTCACTATA
* * *
59658 AAATTTCGATAACCTCTCTATG
1 AAATTTTGATAACCTCACTATA
** * *
59680 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCACTATA
* * * *
59702 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCACTATA
* * *
59724 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCACTATA
* * * *
59746 AAATTTT-AAAAACTAAACTATG
1 AAATTTTGATAACCT-CACTATA
*
59768 AAATTTTGATAACCTTCA-TATG
1 AAATTTTGATAACC-TCACTATA
*
59790 AAATTTTGATATCCTC
1 AAATTTTGATAACCTC
59806 CCTGAAATTT
Statistics
Matches: 177, Mismatches: 40, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
18 1 0.01
20 2 0.01
21 7 0.04
22 128 0.72
23 27 0.15
24 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATA
Found at i:59618 original size:23 final size:22
Alignment explanation
Indices: 59570--59636 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
59560 GATAATCACA
* * * *
59570 CTATGAAATTGTGATAACCTCG
1 CTATAAAATTTTGAAAACCTCC
59592 CTATAAAATTTTGACAAACCTCC
1 CTATAAAATTTTGA-AAACCTCC
*
59615 CTATAAAATTTTGATAACCTCC
1 CTATAAAATTTTGAAAACCTCC
59637 TTATGTAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.49
23 20 0.51
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (22 bp):
CTATAAAATTTTGAAAACCTCC
Found at i:59884 original size:22 final size:21
Alignment explanation
Indices: 59853--59966 Score: 56
Period size: 22 Copynumber: 5.2 Consensus size: 21
59843 AGCTTCCTAA
59853 TTTAGTAACCATACTATGAAAT
1 TTTA-TAACCATACTATGAAAT
59875 TTTGATAACC-TCCAC-ATGAAAT
1 TTT-ATAACCAT--ACTATGAAAT
* *
59897 ATTAGTAA-CAT-CGTTATGAATT
1 TTTA-TAACCATAC--TATGAAAT
* *
59919 TTTGTTAACCACACTATGAAAT
1 TTT-ATAACCATACTATGAAAT
* * *
59941 TCTTATAACCTTGCTATGACAT
1 T-TTATAACCATACTATGAAAT
59963 TTTA
1 TTTA
59967 ATAATCTCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 25
0.66 0.10 0.24
Matches are distributed among these distances:
19 1 0.01
21 6 0.09
22 54 0.78
23 7 0.10
24 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTATAACCATACTATGAAAT
Found at i:60075 original size:68 final size:65
Alignment explanation
Indices: 59989--60148 Score: 167
Period size: 68 Copynumber: 2.4 Consensus size: 65
59979 ATAACCTTTT
* * * * *
59989 CTATAAAATTGTGATAACCACATTATAAAATTTCAATAACCTTTCTAAAAAATTTTAATAACCTG
1 CTATGAAATTTTGGTAACCACACTATAAAATTTCAATAACCTTTCCAAAAAATTTTAATAA-CT-
60054 ATC
64 -TC
* *** ** *
60057 CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCTTTCCATGAAATTTTGATAACTTC
1 CTATGAAATTTTGGTAACCACACTATAAAATTTCAATAACCTTTCCAAAAAATTTTAATAACTTC
*
60122 CATATGAAATTTAGGTAACCACACTAT
1 C-TATGAAATTTTGGTAACCACACTAT
60149 GGAATTTTGA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
65 3 0.04
66 24 0.31
67 2 0.03
68 49 0.63
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.36
Consensus pattern (65 bp):
CTATGAAATTTTGGTAACCACACTATAAAATTTCAATAACCTTTCCAAAAAATTTTAATAACTTC
Found at i:60085 original size:22 final size:22
Alignment explanation
Indices: 60057--60211 Score: 120
Period size: 22 Copynumber: 7.0 Consensus size: 22
60047 TAACCTGATC
*
60057 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* ***
60079 CTATGAAATTTTGGTAACCTTT
1 CTATGAAATTTTGATAACCACA
*
60101 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* *
60124 -TATGAAATTTAGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
60145 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
60166 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
* *
60189 TTATGAAATTTTTATAACCACA
1 CTATGAAATTTTGATAACCACA
60211 C
1 C
60212 AGAGACAAGA
Statistics
Matches: 104, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 95 0.91
23 2 0.02
24 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:60124 original size:20 final size:22
Alignment explanation
Indices: 60024--60118 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
60014 TAAAATTTCA
* ** *
60024 ATAACCTTTCTAAAAAATTTTA
1 ATAACCTTTCCATGAAATTTTG
*
60046 ATAACCTGATCCTATGAAATTTTG
1 ATAACCT-TTCC-ATGAAATTTTG
* *** *
60070 GTAACCACACTATGAAATTTTG
1 ATAACCTTTCCATGAAATTTTG
*
60092 GTAACCTTTCCATGAAATTTTG
1 ATAACCTTTCCATGAAATTTTG
60114 ATAAC
1 ATAAC
60119 TTCCATATGA
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
22 40 0.71
23 3 0.05
24 13 0.23
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
ATAACCTTTCCATGAAATTTTG
Found at i:60199 original size:44 final size:43
Alignment explanation
Indices: 60038--60207 Score: 148
Period size: 44 Copynumber: 3.8 Consensus size: 43
60028 CCTTTCTAAA
* *
60038 AAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTATG
1 AAATTTTAATAACC--ATCCTATGAAATTTTGATAACCTC-CTATG
** * *
60084 AAATTTTGGTAACCTTTCC-ATGAAATTTTGATAACTTCCATATG
1 AAATTTTAATAACC-ATCCTATGAAATTTTGATAACCTCC-TATG
* *
60128 AAA-TTTAGGTAACCA-CACTATGGAATTTTGATAACCTCCTCATG
1 AAATTTTA-ATAACCATC-CTATGAAATTTTGATAACCTCCT-ATG
* * *
60172 AAATTATAATAACCATCTTATGAAATTTTTATAACC
1 AAATTTTAATAACCATCCTATGAAATTTTGATAACC
60208 ACACAGAGAC
Statistics
Matches: 101, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
42 1 0.01
43 6 0.06
44 75 0.74
45 7 0.07
46 12 0.12
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (43 bp):
AAATTTTAATAACCATCCTATGAAATTTTGATAACCTCCTATG
Found at i:60207 original size:66 final size:66
Alignment explanation
Indices: 60038--60211 Score: 199
Period size: 66 Copynumber: 2.6 Consensus size: 66
60028 CCTTTCTAAA
* * *
60038 AAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCTTTCC
1 AAATTTTAATAACC--ATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCTCC
60103 ATG
64 ATG
* * * *
60106 AAATTTTGATAA-CTTCCATATGAAATTTAGGTAACCACACTATGGAATTTTGATAACCTC-CTC
1 AAATTTTAATAACCAT-CATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCTC-C
60169 ATG
64 ATG
* * **
60172 AAATTATAATAACCATCTTATGAAATTTTTATAACCACAC
1 AAATTTTAATAACCATCATATGAAATTTTGGTAACCACAC
60212 AGAGACAAGA
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
65 2 0.02
66 73 0.82
67 3 0.03
68 11 0.12
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (66 bp):
AAATTTTAATAACCATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCTCCAT
G
Found at i:62347 original size:37 final size:37
Alignment explanation
Indices: 62302--62372 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
62292 CTTGATCAAT
* *
62302 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
62339 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
62373 AAAATTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:66149 original size:26 final size:25
Alignment explanation
Indices: 66111--66162 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
66101 TTTCTTACAA
66111 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * * *
66137 AAATCATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
66162 A
1 A
66163 TCTCATTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Found at i:78252 original size:42 final size:43
Alignment explanation
Indices: 78201--78294 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
78191 AGTGCGTTAC
* *
78201 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
78242 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
*
78287 TTAATATT
1 CTAATATT
78295 AATTATTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Done.