Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020037.1 Corchorus olitorius cultivar O-4 contig20070, 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: 68309
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2182 original size:93 final size:93
Alignment explanation
Indices: 2085--2263 Score: 295
Period size: 93 Copynumber: 1.9 Consensus size: 93
2075 TTAATTAAAT
*
2085 TAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
1 TAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
* *
2150 TTAGTTGAGTAAAATTATAAAAGCAAAA
66 TTAGTTGACTAAAACTATAAAAGCAAAA
* * * *
2178 TAGTAAAATGGTAAAAATGAAATAGTTATATGGATATTAGATTTAATTAAATAAAAATAGAGTTT
1 TAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
2243 TTAGTTGACTAAAACTATAAA
66 TTAGTTGACTAAAACTATAAA
2264 TATATTCTAA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (93 bp):
TAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
TTAGTTGACTAAAACTATAAAAGCAAAA
Found at i:2309 original size:31 final size:31
Alignment explanation
Indices: 2271--2333 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2261 AAATATATTC
2271 TAATAAGGGTATAATAGGCGATTCAAAAGTT
1 TAATAAGGGTATAATAGGCGATTCAAAAGTT
2302 TAATAAGGGTATAATAGGCGATTCAAAAGTT
1 TAATAAGGGTATAATAGGCGATTCAAAAGTT
2333 T
1 T
2334 TACAAAACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.30
Consensus pattern (31 bp):
TAATAAGGGTATAATAGGCGATTCAAAAGTT
Found at i:2626 original size:1 final size:1
Alignment explanation
Indices: 2620--2644 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2610 GCCTGTTGTC
2620 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2645 CTATTAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7372 original size:22 final size:22
Alignment explanation
Indices: 7347--7388 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
7337 AACAAACACA
*
7347 TAACCCGAATGACCCGAGAAGT
1 TAACCCAAATGACCCGAGAAGT
*
7369 TAACCCAAATGATCCGAGAA
1 TAACCCAAATGACCCGAGAA
7389 TATTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (22 bp):
TAACCCAAATGACCCGAGAAGT
Found at i:9777 original size:18 final size:18
Alignment explanation
Indices: 9754--9789 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9744 TTCAAGGACT
9754 ATAGTTTTCGGCTGCCCC
1 ATAGTTTTCGGCTGCCCC
9772 ATAGTTTTCGGCTGCCCC
1 ATAGTTTTCGGCTGCCCC
9790 TCTGACAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.22, T:0.33
Consensus pattern (18 bp):
ATAGTTTTCGGCTGCCCC
Found at i:10889 original size:31 final size:31
Alignment explanation
Indices: 10851--10912 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
10841 TATGTTAGAA
* *
10851 AAATAAGGATATAATAGGTATTTCAAAAGTT
1 AAATAAGGATACAATAGGCATTTCAAAAGTT
*
10882 AAATAAGGATACAATAGGCGTTTCAAAAGTT
1 AAATAAGGATACAATAGGCATTTCAAAAGTT
10913 TTACAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (31 bp):
AAATAAGGATACAATAGGCATTTCAAAAGTT
Found at i:17662 original size:29 final size:30
Alignment explanation
Indices: 17630--17706 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
17620 AAATGTAGCG
* * *
17630 TTTGGATGTTTTTCTCTTTGAA-TTTCAAT
1 TTTGGATGTTTTTCCCCTTGAACTCTCAAT
** *
17659 TTTGGACATTTTGCCCCTTGAACTCTCAAT
1 TTTGGATGTTTTTCCCCTTGAACTCTCAAT
* *
17689 TTTGAATGTTTTTTCCCT
1 TTTGGATGTTTTTCCCCT
17707 ATCAAACGAT
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.17, C:0.18, G:0.13, T:0.52
Consensus pattern (30 bp):
TTTGGATGTTTTTCCCCTTGAACTCTCAAT
Found at i:24362 original size:3 final size:3
Alignment explanation
Indices: 24354--24412 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
24344 AACAAATTAT
*
24354 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24402 ATA ATA TATA A
1 ATA ATA -ATA A
24413 AGATAATTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28232 original size:19 final size:18
Alignment explanation
Indices: 28195--28242 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
28185 CTGAAATTAT
28195 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
* *
28213 TAATTATTT-TT-CAGAA
1 TAATTATTTATTAAATAA
28229 TAATTA-TTATTAAA
1 TAATTATTTATTAAA
28243 ATTACCTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 11 0.44
17 3 0.12
18 9 0.36
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:31192 original size:45 final size:45
Alignment explanation
Indices: 31128--31214 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
31118 AGCAACAATT
*
31128 AATATTAGCTTTATTTTGATGAATTATATAGAGATGGAGTAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGTAGTAG
*
31173 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGTAG
31215 AATTTAGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACATAGAGATGGAGTAGTAG
Found at i:45902 original size:7 final size:7
Alignment explanation
Indices: 45892--45918 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
45882 GGTTTTTATT
45892 TTTTTTA
1 TTTTTTA
45899 TTTTTTA
1 TTTTTTA
45906 TTTTTTA
1 TTTTTTA
45913 TTTTTT
1 TTTTTT
45919 GGTGAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:45929 original size:23 final size:23
Alignment explanation
Indices: 45903--45956 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
45893 TTTTTATTTT
45903 TTATTTTTTATTTTTTGGTG-AA-A
1 TTATTTTTTATTTTTT--TGAAACA
45926 TTA-TTTTTATTTTTTTGAAACA
1 TTATTTTTTATTTTTTTGAAACA
45948 TTATTTTTT
1 TTATTTTTT
45957 TAATGATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 16 0.57
23 8 0.29
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (23 bp):
TTATTTTTTATTTTTTTGAAACA
Found at i:47898 original size:429 final size:420
Alignment explanation
Indices: 47026--48011 Score: 1043
Period size: 429 Copynumber: 2.3 Consensus size: 420
47016 TTTGTTCTAT
*
47026 AATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCGTGATCTACAACTTTCAT
1 AATTTGTCCGATTAAGGTGATTC-AGTGTCTATT--AAGGTAATTTCATGATCTACAACTTTCAT
* * *
47091 GAAGGACTGAAAAAGCCAATTTTTATGTTTCAATTCAAAAAAAAAAAGCTTCTAAAATTTGGTGG
63 GAAGGACT-CAAAAGCCAATTTTTATGTTTCAATT---AAAAAAAATGCTTCCAAAATTTGGTGG
* * *
47156 TTTCGATTGCCAGTCTAATTAATATCATATAATTTTCAATCCACATATCCGATTAAAGTTATTCA
124 TTTCAATTGCCAGTCTAATTAATACCATATAATTTGCAATCCACATATCCGATTAAAGTTATTCA
* *
47221 AGTGTCGGTTAAAAGGTTATTGCATGATCTACAACTTTCATGAAGGACCCAAAAGTTAAATTTGA
189 AGTGTC------AAGG-T-TTGCATGATCTACAACTTTCATAAAGGACCCAAAAGTAAAATTTGA
** * * * * *
47286 TCTATTAGTTTCATTAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATCAACAAATAT
246 TCTACAAGCTTCATGAAGGGTTCAAAAGGAAATTTTGATGTTTCAAGATCTCCATCAACAAACAT
* * * * * * *
47351 TTTCTTATTTTGATTGTTTATCAAATGAACCTTATATTTTTCTACTTTATACTAAGTTCTTTACT
311 TTTCTTATTTGGATTATTTATCAAATGAACCTCATACTTTTCTACTTTATACTAACTTCTCTACA
* ** *
47416 CATTCTATCTTAATCAATATAACGCTTCATGGTTTTTTTTTTAATC
376 AATTCTATCTTAATCAATATAACGCTTCATCCTTTTTTTTGT-ATC
* * *
47462 TATTTGTCGGATTAAGGTGATTCAGTTGTCTATT-AGGTAATTTCATAATCTACAACTTTCATGA
1 AATTTGTCCGATTAAGGTGATTCAG-TGTCTATTAAGGTAATTTCATGATCTACAACTTTCATGA
* *
47526 AGGACTCAAAAGCCAATTTTTATGTTTCACTTAAAAAAAATGCTTCCCAAATTTGGTGGTTTCAA
65 AGGACTCAAAAGCCAATTTTTATGTTTCAATTAAAAAAAATGCTTCCAAAATTTGGTGGTTTCAA
* * * * * *
47591 TTTCCGGTCTATTTAATACCATATAATTTGCGATCCACATGTCCGATTAAAGTTGTTCAAGTGTC
130 TTGCCAGTCTAATTAATACCATATAATTTGCAATCCACATATCCGATTAAAGTTATTCAAGTGTC
* ** *
47656 -A-G-TTGCATGATCTACGACTTTCATAAAGGACCTGAAAGTAAAATTTGATCTACAAGCTTCCT
195 AAGGTTTGCATGATCTACAACTTTCATAAAGGACCCAAAAGTAAAATTTGATCTACAAGCTTCAT
* * *
47718 GAAGGGTTCAAAATGAAATTTTGATGTTTCAAGTTCTCCATCAACAAACATTTTTTTTAATTTGG
260 GAAGGGTTCAAAAGGAAATTTTGATGTTTCAAGATCTCCATCAACAAACA-TTTTCTT-ATTTGG
* *
47783 ATTATTTATCAAATATTTATAAAATGAGCCTCATACTTTTCTATTTTATACT-ACTTGCTCTACA
323 ATTATTTATC-----------AAATGAACCTCATACTTTTCTACTTTATACTAACTT-CTCTACA
* ** *
47847 AATTCTACTTTTAATTGATTTAACGCTTCA-CCTTTTTTTTGT-TC
376 AATTCTA-TCTTAATCAATATAACGCTTCATCCTTTTTTTTGTATC
* * * * *
47891 AATTTGTCCAATTAAGGTAATTCAGATATCTATTAAAAGATAATTTCATGCTCTACAACTTTCAT
1 AATTTGTCCGATTAAGGTGATTCAG-TGTCTATT--AAGGTAATTTCATGATCTACAACTTTCAT
* * * **
47956 GAATGACTCAAATA-CTAAATTTTATGTTTCAATTCTAAAAAATGCTTCCAAAATTT
63 GAAGGACTCAAA-AGCCAATTTTTATGTTTCAATTAAAAAAAATGCTTCCAAAATTT
48012 TGTAGATTCG
Statistics
Matches: 463, Mismatches: 67, Indels: 44
0.81 0.12 0.08
Matches are distributed among these distances:
418 95 0.21
419 6 0.01
420 14 0.03
421 1 0.00
422 1 0.00
429 116 0.25
430 3 0.01
431 47 0.10
432 114 0.25
433 35 0.08
435 2 0.00
436 29 0.06
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (420 bp):
AATTTGTCCGATTAAGGTGATTCAGTGTCTATTAAGGTAATTTCATGATCTACAACTTTCATGAA
GGACTCAAAAGCCAATTTTTATGTTTCAATTAAAAAAAATGCTTCCAAAATTTGGTGGTTTCAAT
TGCCAGTCTAATTAATACCATATAATTTGCAATCCACATATCCGATTAAAGTTATTCAAGTGTCA
AGGTTTGCATGATCTACAACTTTCATAAAGGACCCAAAAGTAAAATTTGATCTACAAGCTTCATG
AAGGGTTCAAAAGGAAATTTTGATGTTTCAAGATCTCCATCAACAAACATTTTCTTATTTGGATT
ATTTATCAAATGAACCTCATACTTTTCTACTTTATACTAACTTCTCTACAAATTCTATCTTAATC
AATATAACGCTTCATCCTTTTTTTTGTATC
Found at i:48034 original size:432 final size:423
Alignment explanation
Indices: 47026--48034 Score: 1068
Period size: 432 Copynumber: 2.3 Consensus size: 423
47016 TTTGTTCTAT
*
47026 AATTTGTCCGATTAAGGTGATTCA-AGTGTCTATTAAAAGGTAATTTCGTGATCTACAACTTTCA
1 AATTTGTCCGATTAAGGTGATTCAGA-TGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCA
* * *
47090 TGAAGGACTGAAAAAGCCAATTTTTATGTTTCAATTCAAAAAAAAAAAGCTTCTAAAATTTGGTG
65 TGAAGGACT-CAAAAGCCAATTTTTATGTTTCAATTC---AAAAAAATGCTTCCAAAATTTGGTG
* * * *
47155 GTTTCGATTGCCAGTCTAATTAATATCATATAATTTTCAATCCACATATCCGATTAAAGTTATTC
126 GTTTCGATTGCCGGTCTATTTAATACCATATAATTTGCAATCCACATATCCGATTAAAGTTATTC
* *
47220 AAGTGTCGGTTAAAAGGTTATTGCATGATCTACAACTTTCATGAAGGACCCAAAAGTTAAATTTG
191 AAGTGTC------AAGG-T-TTGCATGATCTACAACTTTCATAAAGGACCCAAAAGTAAAATTTG
** * * * * *
47285 ATCTATTAGTTTCATTAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATCAACAAATA
248 ATCTACAAGCTTCATGAAGGGTTCAAAAGGAAATTTTGATGTTTCAAGATCTCCATCAACAAACA
* * * * * *
47350 TTTTCTTATTTTGATTGTTTATCAAATGAACCTTATATTTTTCTACTTTATACTAAGTTCTTTAC
313 TTTTCTTATTTGGATTATTTATCAAATGAACCTCATACTTTTCTACTTTATACTAACTTCTCTAC
** ** *
47415 TCATTCTATCTTAATCAATATAACGCTTCATGGTTTTTTTTTTAATC
378 AAATTCTATCTTAATCAATATAACGCTTCATCCTTTTTTTTGT-ATC
* * * *
47462 TATTTGTCGGATTAAGGTGATTCAGTTGTCTATT---AGGTAATTTCATAATCTACAACTTTCAT
1 AATTTGTCCGATTAAGGTGATTCAGATGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCAT
* * *
47524 GAAGGACTCAAAAGCCAATTTTTATGTTTCACTTAAAAAAAATGCTTCCCAAATTTGGTGGTTTC
66 GAAGGACTCAAAAGCCAATTTTTATGTTTCAATTCAAAAAAATGCTTCCAAAATTTGGTGGTTTC
* * * * *
47589 AATTTCCGGTCTATTTAATACCATATAATTTGCGATCCACATGTCCGATTAAAGTTGTTCAAGTG
131 GATTGCCGGTCTATTTAATACCATATAATTTGCAATCCACATATCCGATTAAAGTTATTCAAGTG
* **
47654 TC-A-G-TTGCATGATCTACGACTTTCATAAAGGACCTGAAAGTAAAATTTGATCTACAAGCTTC
196 TCAAGGTTTGCATGATCTACAACTTTCATAAAGGACCCAAAAGTAAAATTTGATCTACAAGCTTC
* * * *
47716 CTGAAGGGTTCAAAATGAAATTTTGATGTTTCAAGTTCTCCATCAACAAACATTTTTTTTAATTT
261 ATGAAGGGTTCAAAAGGAAATTTTGATGTTTCAAGATCTCCATCAACAAACA-TTTTCTT-ATTT
* *
47781 GGATTATTTATCAAATATTTATAAAATGAGCCTCATACTTTTCTATTTTATACT-ACTTGCTCTA
324 GGATTATTTATC-----------AAATGAACCTCATACTTTTCTACTTTATACTAACTT-CTCTA
* ** *
47845 CAAATTCTACTTTTAATTGATTTAACGCTTCA-CCTTTTTTTTGT-TC
377 CAAATTCTA-TCTTAATCAATATAACGCTTCATCCTTTTTTTTGTATC
* * * * *
47891 AATTTGTCCAATTAAGGTAATTCAGATATCTATTAAAAGATAATTTCATGCTCTACAACTTTCAT
1 AATTTGTCCGATTAAGGTGATTCAGATGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCAT
* * * * * * *
47956 GAATGACTCAAATA-CTAAATTTTATGTTTCAATTCTAAAAAATGCTTCCAAAATTTTGTAGATT
66 GAAGGACTCAAA-AGCCAATTTTTATGTTTCAATTCAAAAAAATGCTTCCAAAATTTGGTGGTTT
**
48020 CGATTGATGGTCTAT
130 CGATTGCCGGTCTAT
48035 CCAAGATTAA
Statistics
Matches: 477, Mismatches: 76, Indels: 44
0.80 0.13 0.07
Matches are distributed among these distances:
418 95 0.20
419 6 0.01
420 14 0.03
421 1 0.00
422 1 0.00
429 115 0.24
430 3 0.01
431 47 0.10
432 130 0.27
433 35 0.07
436 30 0.06
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (423 bp):
AATTTGTCCGATTAAGGTGATTCAGATGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCAT
GAAGGACTCAAAAGCCAATTTTTATGTTTCAATTCAAAAAAATGCTTCCAAAATTTGGTGGTTTC
GATTGCCGGTCTATTTAATACCATATAATTTGCAATCCACATATCCGATTAAAGTTATTCAAGTG
TCAAGGTTTGCATGATCTACAACTTTCATAAAGGACCCAAAAGTAAAATTTGATCTACAAGCTTC
ATGAAGGGTTCAAAAGGAAATTTTGATGTTTCAAGATCTCCATCAACAAACATTTTCTTATTTGG
ATTATTTATCAAATGAACCTCATACTTTTCTACTTTATACTAACTTCTCTACAAATTCTATCTTA
ATCAATATAACGCTTCATCCTTTTTTTTGTATC
Found at i:54349 original size:24 final size:24
Alignment explanation
Indices: 54322--54369 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
54312 AGAAGCTTTG
54322 CTTGATGATATTAAGAATCTTATT
1 CTTGATGATATTAAGAATCTTATT
54346 CTTGATGATATTAAGAATCTTATT
1 CTTGATGATATTAAGAATCTTATT
54370 GAAGGGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.46
Consensus pattern (24 bp):
CTTGATGATATTAAGAATCTTATT
Found at i:57673 original size:11 final size:11
Alignment explanation
Indices: 57657--57682 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57647 CCTTGCCTAA
57657 AAAACTAGAAG
1 AAAACTAGAAG
57668 AAAACTAGAAG
1 AAAACTAGAAG
57679 AAAA
1 AAAA
57683 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:63448 original size:29 final size:28
Alignment explanation
Indices: 63407--63464 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
63397 AACAAAAATT
*
63407 AAAAACACAAAAATCTAATT-TTTTTTAG
1 AAAAACACAAAAATAT-ATTATTTTTTAG
*
63435 AAAAACGCAGAAAATATATTATTTTTTAG
1 AAAAACACA-AAAATATATTATTTTTTAG
63464 A
1 A
63465 TTAAAAAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (28 bp):
AAAAACACAAAAATATATTATTTTTTAG
Done.