Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011886.1 Corchorus capsularis cultivar CVL-1 contig11907, 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: 16880
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Found at i:2144 original size:13 final size:13
Alignment explanation
Indices: 2128--2164 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2118 GATAATTCTT
2128 TTTGACCCTCCAA
1 TTTGACCCTCCAA
2141 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
2154 CTTGACCCTCC
1 TTTGACCCTCC
2165 TAATAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.43, G:0.08, T:0.30
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:6548 original size:17 final size:16
Alignment explanation
Indices: 6494--6544 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
6484 ATCACCCCCC
*
6494 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
*
6511 AGATCACCAGTAATGCA
1 AGATCACCAGTGAT-CA
*
6528 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
6544 A
1 A
6545 AGATTACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:7006 original size:21 final size:22
Alignment explanation
Indices: 6982--7028 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
6972 TCGTTCTTGC
6982 TCTGCTTCC-GTGGTTCGAGGG
1 TCTGCTTCCGGTGGTTCGAGGG
*
7003 TCTGCTTCCGGTGGTTCGAGTG
1 TCTGCTTCCGGTGGTTCGAGGG
7025 TCTG
1 TCTG
7029 TTTGACAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.04, C:0.23, G:0.36, T:0.36
Consensus pattern (22 bp):
TCTGCTTCCGGTGGTTCGAGGG
Found at i:7335 original size:17 final size:17
Alignment explanation
Indices: 7309--7362 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
7299 TTTCTTTTTT
7309 AATTAAATTAGGGTTTC
1 AATTAAATTAGGGTTTC
* *
7326 AATTAGATTAGGTTTTC
1 AATTAAATTAGGGTTTC
**
7343 TGTTGTAAATTAGGGTTTC
1 -AAT-TAAATTAGGGTTTC
7362 A
1 A
7363 TATGGAAGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 15 0.54
18 1 0.04
19 12 0.43
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (17 bp):
AATTAAATTAGGGTTTC
Found at i:7416 original size:41 final size:40
Alignment explanation
Indices: 7352--7488 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 40
7342 CTGTTGTAAA
* * *
7352 TTAGGGTTTCAT-ATGGAAGAAATTTTGGGTTTTATGGAAT
1 TTAGGGTTTC-TGATGAAATAAATTTTGGGTTTTATGAAAT
*
7392 TCTAGGGTTTCTGATGAAATAAA-TTTGGGTATTTGTGAAAT
1 T-TAGGGTTTCTGATGAAATAAATTTTGGGT-TTTATGAAAT
* * * *
7433 GTT-GGGTTTCTTATGAAATAAATTTGGGGGTTTATTAAATT
1 -TTAGGGTTTCTGATGAAATAAATTTTGGGTTTTATGAAA-T
*
7474 TTAGGGTTTTTGATG
1 TTAGGGTTTCTGATG
7489 TGATTAATGG
Statistics
Matches: 79, Mismatches: 11, Indels: 13
0.77 0.11 0.13
Matches are distributed among these distances:
40 36 0.46
41 42 0.53
42 1 0.01
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (40 bp):
TTAGGGTTTCTGATGAAATAAATTTTGGGTTTTATGAAAT
Found at i:7421 original size:22 final size:22
Alignment explanation
Indices: 7396--7460 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
7386 TGGAATTCTA
7396 GGGTTTCTGATGAAATAAATTT
1 GGGTTTCTGATGAAATAAATTT
*
7418 GGGTATT-TG-TGAAAT---GTT
1 GGGT-TTCTGATGAAATAAATTT
*
7436 GGGTTTCTTATGAAATAAATTT
1 GGGTTTCTGATGAAATAAATTT
7458 GGG
1 GGG
7461 GGTTTATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
17 2 0.06
18 7 0.21
19 6 0.18
21 6 0.18
22 11 0.32
23 2 0.06
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.42
Consensus pattern (22 bp):
GGGTTTCTGATGAAATAAATTT
Found at i:8586 original size:55 final size:55
Alignment explanation
Indices: 8500--8607 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
8490 TATTATTTAA
* *
8500 TTGTTCATTTTTAGTCAAAATGTTCTCATTTTTTACCATTATTTAGAAGAAAATT
1 TTGTTCACTTTTAGTCAAAATGTTCTAATTTTTTACCATTATTTAGAAGAAAATT
8555 TTGTTCACTTTTAGTCAAAACT-TTCTAATTTTTTACCATTATTTAGAAGAAAA
1 TTGTTCACTTTTAGTCAAAA-TGTTCTAATTTTTTACCATTATTTAGAAGAAAA
8608 ATAGGTAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
55 49 0.98
56 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.47
Consensus pattern (55 bp):
TTGTTCACTTTTAGTCAAAATGTTCTAATTTTTTACCATTATTTAGAAGAAAATT
Found at i:13035 original size:27 final size:27
Alignment explanation
Indices: 13005--13064 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
12995 ATTTTGGCTA
**
13005 GTTGCGACAGTTTTGCAATCTCGGGTT
1 GTTGCGACAACTTTGCAATCTCGGGTT
* * *
13032 GTTGCGGCAACTTTGCAATTTTGGGTT
1 GTTGCGACAACTTTGCAATCTCGGGTT
*
13059 GATGCG
1 GTTGCG
13065 GTATCTTTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.17, G:0.32, T:0.37
Consensus pattern (27 bp):
GTTGCGACAACTTTGCAATCTCGGGTT
Found at i:13100 original size:47 final size:47
Alignment explanation
Indices: 13032--13173 Score: 130
Period size: 47 Copynumber: 3.1 Consensus size: 47
13022 ATCTCGGGTT
* * * * *
13032 GTTGCGGCAACTTT-GCAATTTTGGGTTGATGCGGTATCTTTGGCTA
1 GTTGTGGCAACTTTGGCTATTTTGGGTTGATACGGCAACTTTGGCTA
* * * *
13078 GTTGTGGCAATTTTGGCTATTTTGAGTTGCTACGGCAACTTTTGCTA
1 GTTGTGGCAACTTTGGCTATTTTGGGTTGATACGGCAACTTTGGCTA
* * * *
13125 GTTGTGGCAACTGTGG-TAATTTTGGGTT-TTGCGGCGA-TTTGGCTA
1 GTTGTGGCAACTTTGGCT-ATTTTGGGTTGATACGGCAACTTTGGCTA
13170 GTTG
1 GTTG
13174 CGGGTTTGCT
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
45 11 0.14
46 19 0.24
47 48 0.62
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (47 bp):
GTTGTGGCAACTTTGGCTATTTTGGGTTGATACGGCAACTTTGGCTA
Found at i:15784 original size:24 final size:26
Alignment explanation
Indices: 15757--15809 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
15747 TGACATGTGG
15757 CACGCCACATGTACCAAAAAGTGACAC
1 CACGCCACATGTACCAAAAAGTGA-AC
*
15784 GTCACGCCACGTGTACCAAAAAGTGA
1 --CACGCCACATGTACCAAAAAGTGA
15810 CACGTGGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.30, G:0.19, T:0.13
Consensus pattern (26 bp):
CACGCCACATGTACCAAAAAGTGAAC
Found at i:15799 original size:29 final size:30
Alignment explanation
Indices: 15689--15855 Score: 174
Period size: 31 Copynumber: 5.4 Consensus size: 30
15679 ACGGTGCCCG
* *
15689 ACGTGGCATGCCACATGTACCAAAAAGTAAC
1 ACGT-GCACGCCACATGTACCAAAAAGTGAC
* * * *
15720 ACATGTCACACCACGTATACCAAAAAGTGAC
1 ACGTG-CACGCCACATGTACCAAAAAGTGAC
*
15751 ATGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGT-GCACGCCACATGTACCAAAAAGTGAC
*
15782 ACGT-CACGCCACGTGTACCAAAAAGTGAC
1 ACGTGCACGCCACATGTACCAAAAAGTGAC
** *
15811 ACGTGGCACGCCACATGTTTCAAAAAGTGGC
1 ACGT-GCACGCCACATGTACCAAAAAGTGAC
*
15842 ACGTGGCATGCCAC
1 ACGT-GCACGCCAC
15856 GTGCACAAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
29 28 0.25
30 1 0.01
31 84 0.74
32 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (30 bp):
ACGTGCACGCCACATGTACCAAAAAGTGAC
Found at i:15810 original size:60 final size:60
Alignment explanation
Indices: 15689--15845 Score: 224
Period size: 60 Copynumber: 2.6 Consensus size: 60
15679 ACGGTGCCCG
* *
15689 ACGTGGCATGCCACATGTACCAAAAAGTAACACATGTCACACCACGTATACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGACAC--GTCACACCACGTATACCAAAAAGTGAC
* * *
15751 ATGTGGCACGCCACATGTACCAAAAAGTGACACGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGACACGTCACACCACGTATACCAAAAAGTGAC
** *
15811 ACGTGGCACGCCACATGTTTCAAAAAGTGGCACGT
1 ACGTGGCACGCCACATGTACCAAAAAGTGACACGT
15846 GGCATGCCAC
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 56 0.65
62 30 0.35
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (60 bp):
ACGTGGCACGCCACATGTACCAAAAAGTGACACGTCACACCACGTATACCAAAAAGTGAC
Found at i:15866 original size:60 final size:60
Alignment explanation
Indices: 15689--15865 Score: 212
Period size: 60 Copynumber: 2.9 Consensus size: 60
15679 ACGGTGCCCG
* * * **
15689 ACGTGGCATGCCACATGTACCAAAAAGTAACACATGTCACACCACGTATACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGACAC--GTCACGCCACGTGCACCAAAAAGTGAC
* *
15751 ATGTGGCACGCCACATGTACCAAAAAGTGACACGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGACACGTCACGCCACGTGCACCAAAAAGTGAC
** * *
15811 ACGTGGCACGCCACATGTTTCAAAAAGTGGCACGTGGCATGCCACGTGCA-CAAAA
1 ACGTGGCACGCCACATGTACCAAAAAGTGACACGT--CACGCCACGTGCACCAAAA
15866 GGATATCTGC
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
60 56 0.55
61 5 0.05
62 41 0.40
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (60 bp):
ACGTGGCACGCCACATGTACCAAAAAGTGACACGTCACGCCACGTGCACCAAAAAGTGAC
Done.