Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015558.1 Corchorus olitorius cultivar O-4 contig15591, 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: 40567
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7921 original size:26 final size:29
Alignment explanation
Indices: 7881--7941 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
7871 TTTTTTTTTC
7881 AAAT-ATATTTCTAAAT-TGTC-ATTATT-
1 AAATAATATTTCTAAATAT-TCAATTATTA
7907 AAATAATATTT-TAAATATTCAATTATTA
1 AAATAATATTTCTAAATATTCAATTATTA
7935 AAATAAT
1 AAATAAT
7942 GGAAATTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 11 0.35
27 13 0.42
28 7 0.23
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (29 bp):
AAATAATATTTCTAAATATTCAATTATTA
Found at i:10091 original size:12 final size:12
Alignment explanation
Indices: 10074--10134 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
10064 CAATCTCTTG
10074 AATCATCCTTTA
1 AATCATCCTTTA
*
10086 AATCATCCTTTG
1 AATCATCCTTTA
*
10098 TATCA-CCTTTTA
1 AATCATCC-TTTA
*
10110 AATGAT-CTTTA
1 AATCATCCTTTA
*
10121 GAATCATCTTTTA
1 -AATCATCCTTTA
10134 A
1 A
10135 TTAACAATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
11 6 0.16
12 28 0.74
13 4 0.11
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (12 bp):
AATCATCCTTTA
Found at i:10102 original size:24 final size:24
Alignment explanation
Indices: 10073--10134 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
10063 ACAATCTCTT
10073 GAATCATCCTTTAAATCATCCTTT-
1 GAATCATCCTTTAAATCAT-CTTTA
* *
10097 GTATCA-CCTTTTAAATGATCTTTA
1 GAATCATCC-TTTAAATCATCTTTA
*
10121 GAATCATCTTTTAA
1 GAATCATCCTTTAA
10135 TTAACAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 6 0.19
24 24 0.77
25 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (24 bp):
GAATCATCCTTTAAATCATCTTTA
Found at i:16543 original size:21 final size:21
Alignment explanation
Indices: 16519--16585 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
16509 AATTCTCTGT
16519 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
16540 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
16561 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
16582 AAAT
1 AAAT
16586 CATAATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:16565 original size:42 final size:42
Alignment explanation
Indices: 16506--16589 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
16496 GCTAAGTCTT
16506 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
16548 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
16590 ATCCTTAGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:16752 original size:56 final size:57
Alignment explanation
Indices: 16652--16762 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 57
16642 TTTATTTTGT
16652 AGAATAATTAAATAGAAATAGGGGGGATATGATTTATTATAACATTTATTGTGTGGA
1 AGAATAATTAAATAGAAATAGGGGGGATATGATTTATTATAACATTTATTGTGTGGA
*
16709 AGAATAATTAAGTAGAAATA-GGGGGATATGATTTATTATAACATTTATTGTGTG
1 AGAATAATTAAATAGAAATAGGGGGGATATGATTTATTATAACATTTATTGTGTG
16763 AAAGGAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
56 34 0.64
57 19 0.36
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (57 bp):
AGAATAATTAAATAGAAATAGGGGGGATATGATTTATTATAACATTTATTGTGTGGA
Found at i:18213 original size:16 final size:17
Alignment explanation
Indices: 18192--18223 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18182 GCTCTGCTAT
18192 ATGATTTAT-TCCATGA
1 ATGATTTATCTCCATGA
18208 ATGATTTATCTCCATG
1 ATGATTTATCTCCATG
18224 GTTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (17 bp):
ATGATTTATCTCCATGA
Found at i:22492 original size:37 final size:37
Alignment explanation
Indices: 22445--22517 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
22435 GTCGTCTTCT
22445 TTTATCTACTTCTTGAGCAAGGTGCACATTCATGTTC
1 TTTATCTACTTCTTGAGCAAGGTGCACATTCATGTTC
22482 TTTATCTACTTCTTGAGCAAGGTGCACATTCATGTT
1 TTTATCTACTTCTTGAGCAAGGTGCACATTCATGTT
22518 TTATTTACGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTATCTACTTCTTGAGCAAGGTGCACATTCATGTTC
Found at i:30091 original size:17 final size:18
Alignment explanation
Indices: 30071--30116 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
30061 ATGCGACGGA
30071 TGGGGCTCCTATAAAAG-
1 TGGGGCTCCTATAAAAGC
* *
30088 TGGGGCTCCTATAGAGGC
1 TGGGGCTCCTATAAAAGC
30106 TGGGGCTCCTA
1 TGGGGCTCCTA
30117 CTCCTACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.24
Consensus pattern (18 bp):
TGGGGCTCCTATAAAAGC
Found at i:30157 original size:36 final size:35
Alignment explanation
Indices: 30106--30233 Score: 175
Period size: 36 Copynumber: 3.6 Consensus size: 35
30096 CTATAGAGGC
* *
30106 TGGGGCTCCTACTCCTACTAACCGAGAGGCGGCGGA
1 TGGGGCTCCTACTCCTACTCATCGAG-GGCGGCGGA
* *
30142 TGGGGCTCCTGCTCCTACTCATCGAGGAGCAGCGGA
1 TGGGGCTCCTACTCCTACTCATCGAGG-GCGGCGGA
*
30178 TCGGGCTCCTACTCCTACTCATCGAGTGGCGGCGGA
1 TGGGGCTCCTACTCCTACTCATCGAG-GGCGGCGGA
*
30214 TGGGGCTCCTACTTCTACTC
1 TGGGGCTCCTACTCCTACTC
30234 CTCTTCTTGG
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
35 1 0.01
36 79 0.98
37 1 0.01
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (35 bp):
TGGGGCTCCTACTCCTACTCATCGAGGGCGGCGGA
Found at i:30375 original size:33 final size:33
Alignment explanation
Indices: 30333--30412 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
30323 CGACGAAGGG
30333 CTCCTACTTCTACTAATAGAGCGGCGGATGGGA
1 CTCCTACTTCTACTAATAGAGCGGCGGATGGGA
* * *
30366 CTCCTACTTCCACTCATAGAGCGGCGGATGGGG
1 CTCCTACTTCTACTAATAGAGCGGCGGATGGGA
30399 CTCCTACTTCTACT
1 CTCCTACTTCTACT
30413 CCTTCTCTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (33 bp):
CTCCTACTTCTACTAATAGAGCGGCGGATGGGA
Found at i:34511 original size:18 final size:18
Alignment explanation
Indices: 34488--34529 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
34478 CAGGGGATCT
*
34488 AGAATCATCCGAGGAAGA
1 AGAATCATCCGAAGAAGA
*
34506 AGAATCATCGGAAGAAGA
1 AGAATCATCCGAAGAAGA
34524 AGAATC
1 AGAATC
34530 CCAAGAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.26, T:0.12
Consensus pattern (18 bp):
AGAATCATCCGAAGAAGA
Found at i:34566 original size:93 final size:93
Alignment explanation
Indices: 34422--34715 Score: 534
Period size: 93 Copynumber: 3.2 Consensus size: 93
34412 AATCCGACGA
*
34422 GGAAGAAGAAGAATCCCAAGAAGAAACATTCCATATGCTGCGGCGCGGCTTCTTATCAGGGGATC
1 GGAAGAAGAAGAATCCCAAGAAGAAACATTCCATATGCTGCGGCGCAGCTTCTTATCAGGGGATC
34487 TAGAATCATCCGAGGAAGAAGAATCATC
66 TAGAATCATCCGAGGAAGAAGAATCATC
* * * *
34515 GGAAGAAGAAGAATCCCAAGAAGAAACATTCCATATGTTGCGGTGCCGCTTCTTACCAGGGGATC
1 GGAAGAAGAAGAATCCCAAGAAGAAACATTCCATATGCTGCGGCGCAGCTTCTTATCAGGGGATC
34580 TAGAATCATCCGAGGAAGAAGAATCATC
66 TAGAATCATCCGAGGAAGAAGAATCATC
*
34608 GGAAGAAGAAGAATCCCAGGAAGAAACATTCCATATGCTGCGGCGCAGCTTCTTATCAGGGGATC
1 GGAAGAAGAAGAATCCCAAGAAGAAACATTCCATATGCTGCGGCGCAGCTTCTTATCAGGGGATC
34673 TAGAATCATCCGAGGAAGAAGAATCATC
66 TAGAATCATCCGAGGAAGAAGAATCATC
34701 GGAAGAAGAAGAATC
1 GGAAGAAGAAGAATC
34716 AGAATCATCC
Statistics
Matches: 192, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 192 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (93 bp):
GGAAGAAGAAGAATCCCAAGAAGAAACATTCCATATGCTGCGGCGCAGCTTCTTATCAGGGGATC
TAGAATCATCCGAGGAAGAAGAATCATC
Found at i:34604 original size:18 final size:18
Alignment explanation
Indices: 34581--34622 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
34571 CAGGGGATCT
*
34581 AGAATCATCCGAGGAAGA
1 AGAATCATCCGAAGAAGA
*
34599 AGAATCATCGGAAGAAGA
1 AGAATCATCCGAAGAAGA
34617 AGAATC
1 AGAATC
34623 CCAGGAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.26, T:0.12
Consensus pattern (18 bp):
AGAATCATCCGAAGAAGA
Found at i:34629 original size:18 final size:18
Alignment explanation
Indices: 34581--34632 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
34571 CAGGGGATCT
*
34581 AGAATCATCC-GAGGAAGA
1 AGAATCA-CCGGAAGAAGA
*
34599 AGAATCATCGGAAGAAGA
1 AGAATCACCGGAAGAAGA
34617 AGAATC-CCAGGAAGAA
1 AGAATCACC-GGAAGAA
34633 ACATTCCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.48, C:0.15, G:0.27, T:0.10
Consensus pattern (18 bp):
AGAATCACCGGAAGAAGA
Found at i:34697 original size:18 final size:18
Alignment explanation
Indices: 34674--34716 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
34664 CAGGGGATCT
*
34674 AGAATCATCCGAGGAAGA
1 AGAATCATCCGAAGAAGA
*
34692 AGAATCATCGGAAGAAGA
1 AGAATCATCCGAAGAAGA
34710 AGAATCA
1 AGAATCA
34717 GAATCATCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.26, T:0.12
Consensus pattern (18 bp):
AGAATCATCCGAAGAAGA
Found at i:34713 original size:21 final size:21
Alignment explanation
Indices: 34674--34746 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 21
34664 CAGGGGATCT
34674 AGAATCATCCG-AG--GAAGA
1 AGAATCATCCGAAGAAGAAGA
*
34692 AGAATCATCGGAAGAAGAAGAA
1 AGAATCATCCGAAGAAGAAG-A
*
34714 TCAGAATCATCCGATGAAGAAGA
1 --AGAATCATCCGAAGAAGAAGA
*
34737 AGAAACATCC
1 AGAATCATCC
34747 CAAATGTTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
18 10 0.22
19 2 0.04
21 13 0.29
22 1 0.02
23 1 0.02
24 18 0.40
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.12
Consensus pattern (21 bp):
AGAATCATCCGAAGAAGAAGA
Found at i:34721 original size:24 final size:24
Alignment explanation
Indices: 34692--34737 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
34682 CCGAGGAAGA
*
34692 AGAATCATCGGAAGAAGAAGAATC
1 AGAATCATCCGAAGAAGAAGAATC
*
34716 AGAATCATCCGATGAAGAAGAA
1 AGAATCATCCGAAGAAGAAGAA
34738 GAAACATCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.13, G:0.24, T:0.13
Consensus pattern (24 bp):
AGAATCATCCGAAGAAGAAGAATC
Found at i:35541 original size:18 final size:18
Alignment explanation
Indices: 35518--35553 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35508 CACAACCTGC
35518 TTGTGGAGTCCAAAATTT
1 TTGTGGAGTCCAAAATTT
35536 TTGTGGAGTCCAAAATTT
1 TTGTGGAGTCCAAAATTT
35554 ACACCGCCGG
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:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (18 bp):
TTGTGGAGTCCAAAATTT
Found at i:36312 original size:29 final size:30
Alignment explanation
Indices: 36270--36327 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
36260 TTTGAAGGAA
36270 TTAACTAAAAATCTCTAGTG-ATTTTTTTC
1 TTAACTAAAAATCTCTAGTGAATTTTTTTC
36299 TTAACTAAAAATCTCTAGTGAATTTTTTT
1 TTAACTAAAAATCTCTAGTGAATTTTTTT
36328 TTTCAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (30 bp):
TTAACTAAAAATCTCTAGTGAATTTTTTTC
Found at i:36597 original size:40 final size:40
Alignment explanation
Indices: 36542--36622 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
36532 TCCCTCTATG
36542 TTTGACCTCATTTCCAATTTATAATCATCTTATAATATCA
1 TTTGACCTCATTTCCAATTTATAATCATCTTATAATATCA
36582 TTTGACCTCATTTCCAATTTATAATCATCTTATAATATCA
1 TTTGACCTCATTTCCAATTTATAATCATCTTATAATATCA
36622 T
1 T
36623 ATGTAGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.02, T:0.46
Consensus pattern (40 bp):
TTTGACCTCATTTCCAATTTATAATCATCTTATAATATCA
Found at i:36971 original size:23 final size:24
Alignment explanation
Indices: 36926--36976 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 24
36916 GGGTCTCGTC
36926 TCATCCATATAATGATGGACTTCAA
1 TCATCCATATAA-GATGGACTTCAA
*
36951 TCATCCATATAA-CTGGACTTCAA
1 TCATCCATATAAGATGGACTTCAA
36974 TCA
1 TCA
36977 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 13 0.52
25 12 0.48
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (24 bp):
TCATCCATATAAGATGGACTTCAA
Found at i:37703 original size:24 final size:24
Alignment explanation
Indices: 37676--37816 Score: 110
Period size: 24 Copynumber: 5.6 Consensus size: 24
37666 GCTGCTCCTC
37676 GAATCATCCGAATCCGAGGAAGAA
1 GAATCATCCGAATCCGAGGAAGAA
37700 GAATCATCCGAATCCGAGGAAG-A
1 GAATCATCCGAATCCGAGGAAGAA
**
37723 GAAAGAATCCGAAGAATCCGAAGGAGAAGAA
1 G-AATCATCC---GAATCCG-A-G-GAAGAA
*
37754 GAATCATCCGAA---GGGGAAGAA
1 GAATCATCCGAATCCGAGGAAGAA
* *
37775 GAATCATCCGAATCGTCCGAAGAGGAA
1 GAATCATCCGAA---TCCGAGGAAGAA
*
37802 GAATAATCCGAATCC
1 GAATCATCCGAATCC
37817 TCCTCAGAAT
Statistics
Matches: 94, Mismatches: 9, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
21 18 0.19
22 1 0.01
23 2 0.02
24 32 0.34
27 27 0.29
28 1 0.01
29 1 0.01
30 10 0.11
31 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.12
Consensus pattern (24 bp):
GAATCATCCGAATCCGAGGAAGAA
Found at i:37756 original size:18 final size:18
Alignment explanation
Indices: 37733--37779 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
37723 GAAAGAATCC
37733 GAAGAATCCGAAGGAGAA
1 GAAGAATCCGAAGGAGAA
*
37751 GAAGAATCATCCGAAGGGGAA
1 GAAG-A--ATCCGAAGGAGAA
37772 GAAGAATC
1 GAAGAATC
37780 ATCCGAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
19 1 0.04
20 1 0.04
21 16 0.64
ACGTcount: A:0.47, C:0.13, G:0.32, T:0.09
Consensus pattern (18 bp):
GAAGAATCCGAAGGAGAA
Found at i:37762 original size:21 final size:21
Alignment explanation
Indices: 37738--37786 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
37728 AATCCGAAGA
37738 ATCCGAAGGAGAAGAAGAATC
1 ATCCGAAGGAGAAGAAGAATC
*
37759 ATCCGAAGGGGAAGAAGAATC
1 ATCCGAAGGAGAAGAAGAATC
37780 ATCCGAA
1 ATCCGAA
37787 TCGTCCGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.16, G:0.29, T:0.10
Consensus pattern (21 bp):
ATCCGAAGGAGAAGAAGAATC
Found at i:37873 original size:30 final size:30
Alignment explanation
Indices: 37754--37874 Score: 95
Period size: 30 Copynumber: 3.8 Consensus size: 30
37744 AGGAGAAGAA
* * *
37754 GAATCATCCGAAGGGGAAGAAGAATCATCC
1 GAATCCTCCGAAGAGGAAGAATAATCATCC
*
37784 GAATCGTCCGAAGAGGAAGAAT-A--ATCC
1 GAATCCTCCGAAGAGGAAGAATAATCATCC
37811 GAATCCTCCTCAGAATCCGAAGGAGAAGAATAATCATCC
1 GAATCCT-C-C-GAA---G-A-G-GAAGAATAATCATCC
*
37850 GAATCCTCCGAAGAGGAACAATAAT
1 GAATCCTCCGAAGAGGAAGAATAAT
37875 GCCGCTCCTT
Statistics
Matches: 74, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
27 10 0.14
28 1 0.01
29 2 0.03
30 31 0.42
31 1 0.01
32 1 0.01
33 2 0.03
34 1 0.01
35 1 0.01
36 10 0.14
37 2 0.03
38 1 0.01
39 11 0.15
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.16
Consensus pattern (30 bp):
GAATCCTCCGAAGAGGAAGAATAATCATCC
Found at i:39006 original size:27 final size:28
Alignment explanation
Indices: 38960--39029 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
38950 GGAAACCTTT
* * *
38960 GAGAAACTACAATTCTTTTTTTTTTTTG
1 GAGAAACTACTATTCTTTTTTTTTTATA
*
38988 GATAAACTACTATTC-TTTTTTTTTATA
1 GAGAAACTACTATTCTTTTTTTTTTATA
*
39015 TAGAAACTACTATTC
1 GAGAAACTACTATTC
39030 AGTTTAACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 23 0.64
28 13 0.36
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (28 bp):
GAGAAACTACTATTCTTTTTTTTTTATA
Done.