Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022630.1 Corchorus olitorius cultivar O-4 contig22663, 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: 79689
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:559 original size:16 final size:17
Alignment explanation
Indices: 530--574 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
520 TCGGGTTGAA
530 CGGGTTCTGGTCATTTT
1 CGGGTTCTGGTCATTTT
547 -GGGTT-TGGATCATTTT
1 CGGGTTCTGG-TCATTTT
*
563 CGGGTTCGGGTC
1 CGGGTTCTGGTC
575 GTTTGGATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 7 0.29
18 2 0.08
ACGTcount: A:0.07, C:0.16, G:0.36, T:0.42
Consensus pattern (17 bp):
CGGGTTCTGGTCATTTT
Found at i:603 original size:16 final size:16
Alignment explanation
Indices: 560--628 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
550 TTTGGATCAT
* *
560 TTTCGGGTTCGGGTCG
1 TTTCGAGTTCGGGTCA
* *
576 TTTGGA-TTCGGGTAA
1 TTTCGAGTTCGGGTCA
591 TTTCGAGTTCGGGTCA
1 TTTCGAGTTCGGGTCA
*
607 TTTCTGGGTT-GGGTCA
1 TTTC-GAGTTCGGGTCA
623 GTTTCG
1 -TTTCG
629 GTTTCGGTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 12 0.28
16 23 0.53
17 8 0.19
ACGTcount: A:0.09, C:0.14, G:0.36, T:0.41
Consensus pattern (16 bp):
TTTCGAGTTCGGGTCA
Found at i:2265 original size:34 final size:34
Alignment explanation
Indices: 2223--2439 Score: 156
Period size: 34 Copynumber: 6.3 Consensus size: 34
2213 ATATAGTGCT
*
2223 CATTGCTGGAAGGTCCATTGCCGAGCAAACATGT
1 CATTGCTGGAAGGTCCATTGCCGAGCAAACATGC
* **
2257 CATTGCTGGAAGGTCAATTGCCGAGGCGACGTGCATGC
1 CATTGCTGGAAGGTCCATTGCCGA-GC-A--AACATGC
* *
2295 CATTGTTGGAAGGTCCATTGCCGAGCCAAC--GC
1 CATTGCTGGAAGGTCCATTGCCGAGCAAACATGC
* * * * *
2327 TTTATTGCTAGG-AGTTCCATTGCTGAACAAACGTGC
1 --CATTGCT-GGAAGGTCCATTGCCGAGCAAACATGC
* * * * * *
2363 CATTGCCGTG-AGGTCAATTACCGAGCCAACGTAC
1 CATTGCTG-GAAGGTCCATTGCCGAGCAAACATGC
*
2397 CATTGCTGGAAGGT-CATTTGCCGAGCAAACTTGC
1 CATTGCTGGAAGGTCCA-TTGCCGAGCAAACATGC
2431 CATTGCTGG
1 CATTGCTGG
2440 GAGCCCATTG
Statistics
Matches: 141, Mismatches: 30, Indels: 24
0.72 0.15 0.12
Matches are distributed among these distances:
32 2 0.01
33 3 0.02
34 101 0.72
35 4 0.03
36 3 0.02
37 2 0.01
38 26 0.18
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (34 bp):
CATTGCTGGAAGGTCCATTGCCGAGCAAACATGC
Found at i:5380 original size:16 final size:19
Alignment explanation
Indices: 5359--5401 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
5349 CAAGGAAATC
5359 AGAAGAACAAA-AC-A-AA
1 AGAAGAACAAACACAACAA
5375 AGAAGAAACAAACACAACAA
1 AGAAG-AACAAACACAACAA
5395 AGAAGAA
1 AGAAGAA
5402 GAACACAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 6 0.26
18 2 0.09
19 3 0.13
20 7 0.30
ACGTcount: A:0.72, C:0.14, G:0.14, T:0.00
Consensus pattern (19 bp):
AGAAGAACAAACACAACAA
Found at i:7583 original size:19 final size:18
Alignment explanation
Indices: 7550--7585 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7540 TTGAGATAAT
7550 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
7568 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
7586 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:11955 original size:11 final size:11
Alignment explanation
Indices: 11935--11964 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
11925 CTAAGGGTAA
11935 AGGAAAGAGCT
1 AGGAAAGAGCT
*
11946 AGGAAGGAGCT
1 AGGAAAGAGCT
11957 AGGAAAGA
1 AGGAAAGA
11965 TCCTACTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07
Consensus pattern (11 bp):
AGGAAAGAGCT
Found at i:16133 original size:33 final size:33
Alignment explanation
Indices: 16022--16159 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
16012 ATGATCAACC
* ** * *
16022 AAAACAGATTT-GTTTTCATCACAATTAGCATCC
1 AAAACAGATTTAG-TATCATCACAAACAACATCT
*
16055 AAAACAGAATTT-GTTTCATCACAAACAACATCT
1 AAAACAG-ATTTAGTATCATCACAAACAACATCT
*
16088 AAAACAGATTTAGTGTCATCACAAACAACA-CTT
1 AAAACAGATTTAGTATCATCACAAACAACATC-T
** * *
16121 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTATCATCACAAACAACATCT
16154 AAAACA
1 AAAACA
16160 CTCTTTGCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
32 5 0.06
33 78 0.88
34 6 0.07
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACATCT
Found at i:18653 original size:21 final size:21
Alignment explanation
Indices: 18623--18664 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18613 GCATCTTAGG
18623 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
18644 CAACTTCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
18665 TTCTTTGTGC
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:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:27957 original size:10 final size:9
Alignment explanation
Indices: 27914--27971 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
27904 TAAAAGTAAC
27914 TAAGAAAAA
1 TAAGAAAAA
*
27923 TAAACAAAAA
1 T-AAGAAAAA
27933 TAA-AAGAAA
1 TAAGAA-AAA
27942 -AAGAAAAA
1 TAAGAAAAA
27950 TAACGAAAAA
1 TAA-GAAAAA
*
27960 TAA-AAAGA
1 TAAGAAAAA
27968 TAAG
1 TAAG
27972 GGTAAGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
TAAGAAAAA
Found at i:27957 original size:16 final size:17
Alignment explanation
Indices: 27928--27965 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
27918 AAAAATAAAC
27928 AAAAATAAAAGAAAAAG
1 AAAAATAAAAGAAAAAG
* *
27945 AAAAAT-AACGAAAAAT
1 AAAAATAAAAGAAAAAG
27961 AAAAA
1 AAAAA
27966 GATAAGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAATAAAAGAAAAAG
Found at i:32817 original size:10 final size:10
Alignment explanation
Indices: 32802--32835 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
32792 TATGCTCTGA
32802 ATACCAATTG
1 ATACCAATTG
32812 ATACCAATTG
1 ATACCAATTG
32822 ATACCAATTG
1 ATACCAATTG
32832 ATAC
1 ATAC
32836 AAATCCACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (10 bp):
ATACCAATTG
Found at i:44430 original size:302 final size:302
Alignment explanation
Indices: 43884--44493 Score: 1130
Period size: 302 Copynumber: 2.0 Consensus size: 302
43874 TTCATCGACC
*
43884 AGATGTTAGAGAGGTTAGCATGCAAGGCTTACTATTGTTTTCTGGATGGGTATTCAGGAGACTTC
1 AGATGTTAGAGAGGTTAGCATGCAAGGCCTACTATTGTTTTCTGGATGGGTATTCAGGAGACTTC
43949 CAGATTCCAATTGCACCTGAAGACCAAGAGAAGACCACCTTTACATGCCCTTTCGGTACGTATGC
66 CAGATTCCAATTGCACCTGAAGACCAAGAGAAGACCACCTTTACATGCCCTTTCGGTACGTATGC
* * *
44014 CTATACAAGGATGCCTTTTGGTTTATGCAATGTAGCTGCGACATTTCAAAGGTGTATGATGAGCT
131 CTATACAAGGATGCCTTTTGGTTTATGCAATGCAGCTGCAACATTTCAAAGGTGTATGATGAGCA
*
44079 TCTTTCAAGATTATGTGGGAGATAAGATGGAAGTATTCATGGATGACTTCACTGTCTATGGAGAT
196 TCTTTCAAGATTATGTGGGAGATAAGATGGAAGTATTCATGGATGACTTCACTATCTATGGAGAT
*
44144 AAGTTCAATCAATGCCTTCATAATCTAGAACTCATCTTGAAA
261 AACTTCAATCAATGCCTTCATAATCTAGAACTCATCTTGAAA
*
44186 AGATGTTAGAGAGGTTAGCATGCAAGGCCTACTATTGTTTTCTGGATGGGTATTCAGGATACTTC
1 AGATGTTAGAGAGGTTAGCATGCAAGGCCTACTATTGTTTTCTGGATGGGTATTCAGGAGACTTC
*
44251 CAGATTCTAATTGCACCTGAAGACCAAGAGAAGACCACCTTTACATGCCCTTTCGGTACGTATGC
66 CAGATTCCAATTGCACCTGAAGACCAAGAGAAGACCACCTTTACATGCCCTTTCGGTACGTATGC
*
44316 CTATACAAGGATGCCTTTTGGTTTATGCAATGCAGCTGCAACATTTCAAAGGTGTATGATGATCA
131 CTATACAAGGATGCCTTTTGGTTTATGCAATGCAGCTGCAACATTTCAAAGGTGTATGATGAGCA
44381 TCTTTCAAGATTATGTGGGAGATAAGATGGAAGTATTCATGGATGACTTCACTATCTATGGAGAT
196 TCTTTCAAGATTATGTGGGAGATAAGATGGAAGTATTCATGGATGACTTCACTATCTATGGAGAT
*
44446 AACTTCAATCAATGCCTTCATAATCTAGAACTTATCTTGAAA
261 AACTTCAATCAATGCCTTCATAATCTAGAACTCATCTTGAAA
44488 AGATGT
1 AGATGT
44494 GTTGAAACCA
Statistics
Matches: 298, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
302 298 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (302 bp):
AGATGTTAGAGAGGTTAGCATGCAAGGCCTACTATTGTTTTCTGGATGGGTATTCAGGAGACTTC
CAGATTCCAATTGCACCTGAAGACCAAGAGAAGACCACCTTTACATGCCCTTTCGGTACGTATGC
CTATACAAGGATGCCTTTTGGTTTATGCAATGCAGCTGCAACATTTCAAAGGTGTATGATGAGCA
TCTTTCAAGATTATGTGGGAGATAAGATGGAAGTATTCATGGATGACTTCACTATCTATGGAGAT
AACTTCAATCAATGCCTTCATAATCTAGAACTCATCTTGAAA
Found at i:48790 original size:21 final size:20
Alignment explanation
Indices: 48766--48828 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
48756 ATTTTCGACA
*
48766 AAAATTTTAATTTTTTATGC
1 AAAATTTCAATTTTTTATGC
* *
48786 TAAAATTTCGATTTTTT-TTC
1 -AAAATTTCAATTTTTTATGC
*
48806 AAACTATTTGAATTTTTTATGC
1 AAA--ATTTCAATTTTTTATGC
48828 A
1 A
48829 TATTTTGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 25 0.76
22 3 0.09
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (20 bp):
AAAATTTCAATTTTTTATGC
Found at i:53487 original size:13 final size:13
Alignment explanation
Indices: 53469--53496 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53459 ATATCATTAT
53469 TTACTTATAACTA
1 TTACTTATAACTA
53482 TTACTTATAACTA
1 TTACTTATAACTA
53495 TT
1 TT
53497 TGTATTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (13 bp):
TTACTTATAACTA
Found at i:56417 original size:440 final size:440
Alignment explanation
Indices: 55584--56557 Score: 1517
Period size: 440 Copynumber: 2.2 Consensus size: 440
55574 CCCGCTGTCA
* * * * * * * **
55584 ATAAATAAATAATTTTTTTGTTGG-TTTATTTATCAAATGATTCATATACTTTTATACACTATGC
1 ATAAACAAATATTTTTTTTGCTGGATTT-TTTATCAAATGATCCTTAGACTTTTATGCTTTATGC
** *
55648 TATTTAGTCCCTCACAATTTCTAAGTTGGACGACCGAACGTTTCGACTTTAATTCTTTTATTTTT
65 TATTTAGTCCCTCACAATTTCTGGGTTGGATGACCGAACGTTTCGACTTTAATTCTTTTATTTTT
* * **
55713 TGTTTTGCTTGTCCGATCAACGTGATTCAAGTGTCTATTAAAACGTAATTTCGTGATCTACAACT
130 TCTTTTGCTTGTCCGATCAACGTGATTCAAGTATCTATTAAAACGTAATTTAATGATCTACAACT
* * *
55778 TCCATGAAGGACTTAAAAGCCAATTTTAATGTTTTGATTTTAAAAAATGCTTTTGAAATTTTGTG
195 TCCATGAAGGACTCAAAAGCCAATTTTAATGTTTTCATTTTAAAAAATGCTTTTAAAATTTTGTG
**
55843 GTCTTGATTGCCGGTCTATTTGATATCCTATAATTTTTGTTCCACTTGTCCGATTGAGGTTATTC
260 GTCTTGATTGCCGGTCTATTTGATATCCTATAATTTTTGTTCCACTTGTCCGATTGAGACTATTC
*
55908 AAGTGTCAGTTAAAAGGTTATTGTGTGATCTATGGCTTTCGTCAAGGGCTTCAAAGCTGAATTTG
325 AAGTGTCAGTTAAAAGGTTATTGTGTGATCTACGGCTTTCGTCAAGGGCTTCAAAGCTGAATTTG
55973 ATTAATGAGTTTCGTGGAGAGTTCAAGAGGGAATTTTGATGTTTGGTCTCC
390 ATTAATGAGTTTCGTGGAGAGTTCAAGAGGGAATTTTGATGTTTGGTCTCC
56024 ATAAACAAATATTTTTTTTGCTGGATTTTTTATCAAATGATCCTTAGACTTTTATGCTTTATGCT
1 ATAAACAAATATTTTTTTTGCTGGATTTTTTATCAAATGATCCTTAGACTTTTATGCTTTATGCT
* *
56089 ATTTAGTCCCTCACAATTTCTGGGTTGGATG-CCTGAACGTTTTGGCTTTAATTCTTTTATTTTT
66 ATTTAGTCCCTCACAATTTCTGGGTTGGATGACC-GAACGTTTCGACTTTAATTCTTTTATTTTT
* * *
56153 TCTTTTGCTTGTCCGATCAAGGTGATTCAAGTATCTATTAAAAGGTAATTTAATGATCTACAATT
130 TCTTTTGCTTGTCCGATCAACGTGATTCAAGTATCTATTAAAACGTAATTTAATGATCTACAACT
56218 TCCATGAAGGACTCAAAAGCCAAATTTTAATGTTTTCATTTT-AAAAATGCTTTTAAAATTTTGT
195 TCCATGAAGGACTCAAAAGCC-AATTTTAATGTTTTCATTTTAAAAAATGCTTTTAAAATTTTGT
*
56282 GGTCTTGATTGCCGGTCTATTTGATATCGTATAATTTTT-TGTCCACTTGTCCGATTGAGACTAT
259 GGTCTTGATTGCCGGTCTATTTGATATCCTATAATTTTTGT-TCCACTTGTCCGATTGAGACTAT
** *
56346 TCAAGTGTTGGTTAAAAGGTTATTGTGTGATCTACGGCTTTCGTTAAGGGCTTCAAAGCTGAATT
323 TCAAGTGTCAGTTAAAAGGTTATTGTGTGATCTACGGCTTTCGTCAAGGGCTTCAAAGCTGAATT
* *
56411 TGATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCC
388 TGATTAATGAGTTTCGTGGAGAGTTCAAGAGGGAATTTTGATGTTTGGTCTCC
* * * *
56464 ATAAACAAATATTTTTTTTGCTGGAATATTTATCAAATGATCCTCAGATTTTTATGCTTTATGCT
1 ATAAACAAATATTTTTTTTGCTGGATTTTTTATCAAATGATCCTTAGACTTTTATGCTTTATGCT
* * *
56529 ATTTAATCCCTCATAA-TTATGGGTTGGAT
66 ATTTAGTCCCTCACAATTTCTGGGTTGGAT
56558 CATTTAATGC
Statistics
Matches: 490, Mismatches: 40, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
439 15 0.03
440 453 0.92
441 22 0.04
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.43
Consensus pattern (440 bp):
ATAAACAAATATTTTTTTTGCTGGATTTTTTATCAAATGATCCTTAGACTTTTATGCTTTATGCT
ATTTAGTCCCTCACAATTTCTGGGTTGGATGACCGAACGTTTCGACTTTAATTCTTTTATTTTTT
CTTTTGCTTGTCCGATCAACGTGATTCAAGTATCTATTAAAACGTAATTTAATGATCTACAACTT
CCATGAAGGACTCAAAAGCCAATTTTAATGTTTTCATTTTAAAAAATGCTTTTAAAATTTTGTGG
TCTTGATTGCCGGTCTATTTGATATCCTATAATTTTTGTTCCACTTGTCCGATTGAGACTATTCA
AGTGTCAGTTAAAAGGTTATTGTGTGATCTACGGCTTTCGTCAAGGGCTTCAAAGCTGAATTTGA
TTAATGAGTTTCGTGGAGAGTTCAAGAGGGAATTTTGATGTTTGGTCTCC
Found at i:58943 original size:18 final size:18
Alignment explanation
Indices: 58903--58947 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
58893 ACTAGAAATT
*
58903 TAATAATAATTATTCAAA
1 TAATAATTATTATTCAAA
* * *
58921 AAATAATTATTATTTAAC
1 TAATAATTATTATTCAAA
58939 TAATAATTA
1 TAATAATTA
58948 ATTAATTTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATTATTATTCAAA
Found at i:60725 original size:6 final size:6
Alignment explanation
Indices: 60714--60774 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
60704 TATATACCTG
* * ** *
60714 TCGAGC TCGAGC TCGAGC TCGAAC TCG-GTA TCGAAT TCGAGC TCGAAC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAG-C TCGAGC TCGAGC TCGAGC
60762 TCGAGC TCGAGC T
1 TCGAGC TCGAGC T
60775 TGAATTTTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (6 bp):
TCGAGC
Found at i:60731 original size:12 final size:12
Alignment explanation
Indices: 60714--60771 Score: 73
Period size: 12 Copynumber: 4.8 Consensus size: 12
60704 TATATACCTG
*
60714 TCGAGCTCGAGC
1 TCGAGCTCGAAC
60726 TCGAGCTCGAAC
1 TCGAGCTCGAAC
* *
60738 TCG-GTATCGAAT
1 TCGAG-CTCGAAC
60750 TCGAGCTCGAAC
1 TCGAGCTCGAAC
60762 TCGAGCTCGA
1 TCGAGCTCGA
60772 GCTTGAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
11 1 0.03
12 37 0.95
13 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.21
Consensus pattern (12 bp):
TCGAGCTCGAAC
Found at i:76890 original size:2 final size:2
Alignment explanation
Indices: 76879--76942 Score: 50
Period size: 2 Copynumber: 34.5 Consensus size: 2
76869 AACGTGGGAC
*
76879 AT AT -T AT AT AT AT AT AT A- AT AT A- AT AC AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
76916 -T AT AT AT AT AT AC AC ACT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT A
76943 ACAAATACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
1 6 0.12
2 44 0.86
3 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:78236 original size:38 final size:38
Alignment explanation
Indices: 78185--78260 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
78175 CGAACCAGTC
*
78185 AAACCGTGGATAAAATGTCTAAAAAGGTACTGTACTAA
1 AAACCATGGATAAAATGTCTAAAAAGGTACTGTACTAA
*
78223 AAACCATGGATAAAATGTCTAAAAAGGTATTGTACTAA
1 AAACCATGGATAAAATGTCTAAAAAGGTACTGTACTAA
78261 TTAAAATAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (38 bp):
AAACCATGGATAAAATGTCTAAAAAGGTACTGTACTAA
Done.