Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014078.1 Corchorus capsularis cultivar CVL-1 contig14099, 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: 46321
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:74 original size:33 final size:33
Alignment explanation
Indices: 30--181 Score: 218
Period size: 33 Copynumber: 4.6 Consensus size: 33
20 TTTAGTATCG
* * ** *
30 GTGCCGCCCCAGGGGGGCGGTCTATCCATGGCA
1 GTGCCGCCCCAGGAGGGCGGCCTGGCCATGGTA
**
63 AAGCCGCCCCAGG-GAGGCGGCCTGGCCATGGTA
1 GTGCCGCCCCAGGAG-GGCGGCCTGGCCATGGTA
96 GTGCCGCCCCAGGAGGGCGGCCTGGCCATGGTA
1 GTGCCGCCCCAGGAGGGCGGCCTGGCCATGGTA
129 GTGCCGCCCCAGGAGGGCGGCCTGGCCATGGTA
1 GTGCCGCCCCAGGAGGGCGGCCTGGCCATGGTA
162 GTGCCG-CCCAGGAGGGCGGC
1 GTGCCGCCCCAGGAGGGCGGC
182 ATGAGCAATT
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
32 15 0.14
33 93 0.85
34 1 0.01
ACGTcount: A:0.13, C:0.34, G:0.42, T:0.11
Consensus pattern (33 bp):
GTGCCGCCCCAGGAGGGCGGCCTGGCCATGGTA
Found at i:1396 original size:13 final size:15
Alignment explanation
Indices: 1365--1399 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1355 GGGCTGCTCA
*
1365 TTTTTCGGTGTTGGT
1 TTTTTCGGTGTCGGT
1380 TTTTTCGGT-TCGGT
1 TTTTTCGGTGTCGGT
1394 TTTTTC
1 TTTTTC
1400 AGTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.00, C:0.11, G:0.26, T:0.63
Consensus pattern (15 bp):
TTTTTCGGTGTCGGT
Found at i:1496 original size:12 final size:12
Alignment explanation
Indices: 1470--1506 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
1460 GTTCGGTTTG
1470 TCGGTTTTTGG-
1 TCGGTTTTTGGT
1481 TCGGTTTTTGGT
1 TCGGTTTTTGGT
1493 TCGGTTTTTCGGT
1 TCGGTTTTT-GGT
1506 T
1 T
1507 TTTCGGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 9 0.38
13 4 0.17
ACGTcount: A:0.00, C:0.11, G:0.32, T:0.57
Consensus pattern (12 bp):
TCGGTTTTTGGT
Found at i:2265 original size:8 final size:8
Alignment explanation
Indices: 2252--2283 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
2242 TATACCATAC
*
2252 AAGAAAGA
1 AAGAAAAA
2260 AAGAAAAA
1 AAGAAAAA
2268 AAGAAAAA
1 AAGAAAAA
2276 AAGAAAAA
1 AAGAAAAA
2284 GGTAAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:2906 original size:14 final size:15
Alignment explanation
Indices: 2887--2916 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2877 AATTCCTTTT
2887 AAAAAAAAAC-AAGA
1 AAAAAAAAACGAAGA
2901 AAAAAAAAACGAAGA
1 AAAAAAAAACGAAGA
2916 A
1 A
2917 CTTGCGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAACGAAGA
Found at i:5786 original size:19 final size:20
Alignment explanation
Indices: 5746--5782 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5736 CCTAACATGC
*
5746 AATTATTTTATTTGACTTAT
1 AATTAATTTATTTGACTTAT
5766 AATTAATTT-TTTG-CTTA
1 AATTAATTTATTTGACTTA
5783 ATAAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 4 0.25
20 8 0.50
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTAATTTATTTGACTTAT
Found at i:13458 original size:23 final size:23
Alignment explanation
Indices: 13430--13475 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
13420 AATTTTACCA
13430 AAATATATATAGTATTAATTGTG
1 AAATATATATAGTATTAATTGTG
* *
13453 AAATATATCTATTATTAATTGTG
1 AAATATATATAGTATTAATTGTG
13476 GAATTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (23 bp):
AAATATATATAGTATTAATTGTG
Found at i:23075 original size:21 final size:19
Alignment explanation
Indices: 23046--23088 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
23036 AAATATTAAA
23046 AAATAGAATTTGTAAATCTCC
1 AAATAGAATTTGT-AAT-TCC
*
23067 AAATGGAATTTGTAATTCC
1 AAATAGAATTTGTAATTCC
23086 AAA
1 AAA
23089 CCACTCTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 12 0.57
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (19 bp):
AAATAGAATTTGTAATTCC
Found at i:23822 original size:7 final size:6
Alignment explanation
Indices: 23787--23845 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
23777 AGGGAGGAAG
* *
23787 AAAGAA AGAA-AA AAAGGAA AAAGAA AAAGAA CAAAGAA GACGAGA AAA-AA
1 AAAGAA A-AAGAA AAA-GAA AAAGAA AAAGAA -AAAGAA AAAGA-A AAAGAA
23837 AAAGAA AAA
1 AAAGAA AAA
23846 AAGATATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
5 6 0.14
6 22 0.51
7 15 0.35
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:28875 original size:101 final size:99
Alignment explanation
Indices: 28716--28905 Score: 281
Period size: 101 Copynumber: 1.9 Consensus size: 99
28706 TATATTTTAT
* *
28716 TTCTAAAATCCTATAACAATATTAATAATTATGGAATTTACCCATAAAATAAAAATAAAATTTTA
1 TTCTAAAACCCTATAACAATATTAATAATTATGAAATTTACCCATAAAATAAAAATAAAATTTTA
*
28781 ATTTGGGGCTAAACTTAGTGAAATCAGTTTTGTA
66 ATTTAGGGCTAAACTTAGTGAAATCAGTTTTGTA
* * * * *
28815 TTCTAAAACCCTATATCAATAAATTATTAATTTTGAAATTTACCCTTAAATTAAAAATAAAATTT
1 TTCTAAAACCCTATAACAAT--ATTAATAATTATGAAATTTACCCATAAAATAAAAATAAAATTT
*
28880 TAATTTAGTGCTAAACTTAGTGAAAT
64 TAATTTAGGGCTAAACTTAGTGAAAT
28906 TAAGGCTAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 18 0.22
101 62 0.77
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.38
Consensus pattern (99 bp):
TTCTAAAACCCTATAACAATATTAATAATTATGAAATTTACCCATAAAATAAAAATAAAATTTTA
ATTTAGGGCTAAACTTAGTGAAATCAGTTTTGTA
Found at i:30459 original size:19 final size:20
Alignment explanation
Indices: 30432--30469 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
30422 TACTATTATT
30432 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
30452 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
30470 AATGTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:30661 original size:22 final size:22
Alignment explanation
Indices: 30633--30773 Score: 124
Period size: 22 Copynumber: 6.3 Consensus size: 22
30623 TGTCTCTATG
*
30633 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
30655 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
30678 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
30699 TGGTTAACCAAAATTTCATAGGA
1 TGGTT-ATCAAAATTTCATAGGA
* * *
30722 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
30746 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
30768 TGGTTA
1 TGGTTA
30774 ATTATCACAA
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
21 2 0.02
22 60 0.62
23 17 0.18
24 14 0.14
25 4 0.04
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:30739 original size:69 final size:67
Alignment explanation
Indices: 30631--30774 Score: 166
Period size: 69 Copynumber: 2.1 Consensus size: 67
30621 CTTGTCTCTA
* *
30631 TGTGGTT-ATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 TGTGGTTAACCAAAATTTCATAAGATGGTTATTAAAATTTC-TGAGGTAGGTTATCAAAATTCCA
30694 TAG
65 TAG
* * * ** *
30697 TGTGGTTAACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGTTGGTTATTGAAATTTC
1 TGTGGTTAACCAAAATTTCATAAGAT--GGTTATTAAAATTTCTGAGGTAGGTTATCAAAATTCC
30762 ATAG
64 ATAG
*
30766 GGTGGTTAA
1 TGTGGTTAA
30775 TTATCACAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
66 7 0.11
67 16 0.25
68 4 0.06
69 38 0.58
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (67 bp):
TGTGGTTAACCAAAATTTCATAAGATGGTTATTAAAATTTCTGAGGTAGGTTATCAAAATTCCAT
AG
Found at i:30847 original size:22 final size:20
Alignment explanation
Indices: 30809--30948 Score: 84
Period size: 22 Copynumber: 6.4 Consensus size: 20
30799 ATCAAAGAGA
30809 TTATCAAAATGTT-ATAGCGAGG
1 TTAT-AAAAT-TTCATAG-GAGG
*
30831 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAG-GAGG
*
30853 TTAACAAAATTTCATTAGGAGG
1 TT-ATAAAATTTCA-TAGGAGG
* *
30875 TTACTAATATTTCATGGGGAGG
1 TTA-TAAAATTTCAT-AGGAGG
* *
30897 TTATCAAAATTTTATAGAGTGG
1 TTAT-AAAATTTCATAG-GAGG
* *
30919 TTATCGAAATTTCATATGAAGG
1 TTAT-AAAATTTCATA-GGAGG
30941 TTATAAAA
1 TTATAAAA
30949 GTCTCAATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
21 11 0.12
22 75 0.81
23 7 0.08
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (20 bp):
TTATAAAATTTCATAGGAGG
Found at i:30921 original size:44 final size:43
Alignment explanation
Indices: 30809--30948 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 43
30799 ATCAAAGAGA
* * *
30809 TTATCAAAATGTTATAGCGAGGTTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTTATAG-GAGGTTATAAGAATTTCATAGGGAGG
* * * *
30853 TTAACAAAATTTCATTAGGAGGTTACTAA-TATTTCATGGGGAGG
1 TTATCAAAATTTTA-TAGGAGGTTA-TAAGAATTTCATAGGGAGG
* * * *
30897 TTATCAAAATTTTATAGAGTGGTTAT-CGAAATTTCATATGAAGG
1 TTATCAAAATTTTATAG-GAGGTTATAAG-AATTTCATAGGGAGG
30941 TTAT-AAAA
1 TTATCAAAA
30949 GTCTCAATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
43 8 0.11
44 62 0.82
45 6 0.08
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTTATAGGAGGTTATAAGAATTTCATAGGGAGG
Found at i:31023 original size:22 final size:22
Alignment explanation
Indices: 30971--31138 Score: 107
Period size: 22 Copynumber: 7.6 Consensus size: 22
30961 TAAGGAGTAC
* *
30971 CAAAATTTGATAGAA-GGTTAT
1 CAAAATTTCATAGAATGATTAT
* *
30992 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAATGATTAT
*
31013 CGAAATTTCATAGAAATTGGATTAT
1 CAAAATTTCATAG-AA-T-GATTAT
*
31038 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAATGATTAT
*
31059 CAAAATTTCATACTG-TTG-TTAT
1 CAAAATTTCATA--GAATGATTAT
* * * *
31081 CAAAATTCCAAAGCGA-GTTTAT
1 CAAAATTTCATAG-AATGATTAT
*
31103 CAAAATTACATA-ATATGATTAT
1 CAAAATTTCATAGA-ATGATTAT
*
31125 CAGAATTTCATAGA
1 CAAAATTTCATAGA
31139 GAGGTCAACA
Statistics
Matches: 114, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
20 11 0.10
21 23 0.20
22 56 0.49
23 5 0.04
24 6 0.05
25 13 0.11
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGAATGATTAT
Found at i:31058 original size:21 final size:22
Alignment explanation
Indices: 30971--31070 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 22
30961 TAAGGAGTAC
* *
30971 CAAAATTTGATAG-AAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* **
30992 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAAAGATTAT
*
31013 CGAAATTTCATAGAAATTGGATTAT
1 CAAAATTTCATAGAAA---GATTAT
31038 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAAAGATTAT
31059 CAAAATTTCATA
1 CAAAATTTCATA
31071 CTGTTGTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 9 0.14
21 21 0.33
22 14 0.22
24 7 0.11
25 13 0.20
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGATTAT
Found at i:31172 original size:22 final size:22
Alignment explanation
Indices: 31121--31176 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
31111 CATAATATGA
* * *
31121 TTATCAGAATTTCATAGAGAGG
1 TTATCAAAATTTTATAAAGAGG
* *
31143 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTTATAAAGAGG
31165 TTATC-AAATTTT
1 TTATCAAAATTTT
31177 CAAAATGTGA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTTATAAAGAGG
Found at i:31331 original size:22 final size:22
Alignment explanation
Indices: 31256--31466 Score: 112
Period size: 22 Copynumber: 9.7 Consensus size: 22
31246 ACAAATTAGA
* * *
31256 AAGGTTATTAAACTTTTATTATG
1 AAGGTTATCAAAATTTCA-TATG
* *
31279 AA-GTAATCAAAATTTC--AGG
1 AAGGTTATCAAAATTTCATATG
* *
31298 GAGGATATCAAAATTTCATATG
1 AAGGTTATCAAAATTTCATATG
*
31320 AAGGTTATCAAAATTTCATAGTT
1 AAGGTTATCAAAATTTCATA-TG
* * *
31343 TA-GTT-TAAAAATTTCATAAG
1 AAGGTTATCAAAATTTCATATG
*
31363 AGGGTTATCAAAATTTCATA-G
1 AAGGTTATCAAAATTTCATATG
* * * * *
31384 TATGTAGATCAAAATTTCACAGG
1 AAGGT-TATCAAAATTTCATATG
* * *
31407 GAGATTAACAAAATTTCATAATG
1 AAGGTTATCAAAATTTCAT-ATG
** *
31430 -AGGTTATCAAAAAATCATAGG
1 AAGGTTATCAAAATTTCATATG
* *
31451 GAGATTATCAAAATTT
1 AAGGTTATCAAAATTT
31467 GTAGTTATCA
Statistics
Matches: 139, Mismatches: 39, Indels: 21
0.70 0.20 0.11
Matches are distributed among these distances:
19 3 0.02
20 12 0.09
21 20 0.14
22 95 0.68
23 9 0.06
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
AAGGTTATCAAAATTTCATATG
Found at i:31592 original size:22 final size:22
Alignment explanation
Indices: 31560--31606 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
31550 ATTAGCGAGG
*
31560 TTATCACAATTTCACAGTGTGA
1 TTATCAAAATTTCACAGTGTGA
*
31582 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCACAGTGTGA
31604 TTA
1 TTA
31607 CTAACAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCACAGTGTGA
Found at i:31617 original size:22 final size:23
Alignment explanation
Indices: 31560--31615 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
31550 ATTAGCGAGG
31560 TTATC-ACAATTTCACAGTGTGA
1 TTATCAACAATTTCACAGTGTGA
*
31582 TTATCAA-AATTTCAGAGTGTGA
1 TTATCAACAATTTCACAGTGTGA
31604 TTA-CTAACAATT
1 TTATC-AACAATT
31616 CATATGGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.03
22 24 0.80
23 5 0.17
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATCAACAATTTCACAGTGTGA
Found at i:31781 original size:22 final size:22
Alignment explanation
Indices: 31756--31804 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31746 ATCCTTAGGG
* ** *
31756 AGGTTAATAAAATTTTATAAGA
1 AGGTTAAAAAAAAATTATAAAA
31778 AGGTTAAAAAAAAATTATAAAA
1 AGGTTAAAAAAAAATTATAAAA
31800 AGGTT
1 AGGTT
31805 CTCGAAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (22 bp):
AGGTTAAAAAAAAATTATAAAA
Found at i:36198 original size:139 final size:139
Alignment explanation
Indices: 35948--36231 Score: 541
Period size: 139 Copynumber: 2.0 Consensus size: 139
35938 ACTTGTAAAA
35948 CTTTTGAATCGCCTATTATACCCTTATTTGTCAAATATATTTCTAAATTGCCATTGTTTAGGTTT
1 CTTTTGAATCGCCTATTATACCCTTATTTGTCAAATATATTTCTAAATTGCCATTGTTTAGGTTT
*
36013 TTATAGTTTTACTCCACTAAAAACTCTATTTTTATTTAATTAAATATAATATATTTATAACTATT
66 TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATTTATAACTATT
36078 ATATTTTAC
131 ATATTTTAC
*
36087 CTTTTGAATCGCCTATTATACCCTTATTTGTCAAATATATTTCTAAATTGCCATTGTTTAGTTTT
1 CTTTTGAATCGCCTATTATACCCTTATTTGTCAAATATATTTCTAAATTGCCATTGTTTAGGTTT
36152 TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATTTATAACTATT
66 TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATTTATAACTATT
36217 ATATTTTAC
131 ATATTTTAC
36226 CATTTT
1 C-TTTT
36232 ACTATTTTAC
Statistics
Matches: 142, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
139 138 0.97
140 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (139 bp):
CTTTTGAATCGCCTATTATACCCTTATTTGTCAAATATATTTCTAAATTGCCATTGTTTAGGTTT
TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATTTATAACTATT
ATATTTTAC
Found at i:36232 original size:78 final size:78
Alignment explanation
Indices: 36150--36318 Score: 252
Period size: 78 Copynumber: 2.2 Consensus size: 78
36140 TTGTTTAGTT
* *
36150 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATA-TTTATAAC
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATA-ACCTTATAAC
36213 TATTATATTTTACCA
64 TATTATATTTTACCA
* *
36228 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTATTAACCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTA
**
36293 TTATATTTTAATA
66 TTATATTTTACCA
36306 TTTTACTATTTTA
1 TTTTACTATTTTA
36319 ATTAAAAAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
77 1 0.01
78 80 0.96
79 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTA
TTATATTTTACCA
Found at i:37068 original size:31 final size:31
Alignment explanation
Indices: 37020--37078 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
37010 TCAAAAACGA
** *
37020 TCAATTTAGTCTTTGTACTAATAAGATTAGG
1 TCAATTTAGTCACTGTACTAACAAGATTAGG
*
37051 TCAATTTAGTCACTGTACTCACAAGATT
1 TCAATTTAGTCACTGTACTAACAAGATT
37079 GGCTAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (31 bp):
TCAATTTAGTCACTGTACTAACAAGATTAGG
Found at i:44286 original size:22 final size:23
Alignment explanation
Indices: 44259--44301 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
44249 CATGTTAGAC
44259 TCTAACATGTGATA-ACATGTGA
1 TCTAACATGTGATAGACATGTGA
*
44281 TCTAACGTGTGATAGACATGT
1 TCTAACATGTGATAGACATGT
44302 TAGGAGGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (23 bp):
TCTAACATGTGATAGACATGTGA
Done.