Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014887.1 Corchorus capsularis cultivar CVL-1 contig14908, 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: 44222
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:110 original size:30 final size:28
Alignment explanation
Indices: 40--118 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 28
30 GAACTTACAC
*
40 AAAACGGCCAAATAAGCCCCCTGAACTCT
1 AAAAAGGCCAAATAAG-CCCCTGAACTCT
*
69 AATTACA-GCCAAATAAGCCCCTGAACTCTTT
1 AA--AAAGGCCAAATAAGCCCCTGAACTC--T
100 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
119 TTTTCTGATG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
29 15 0.36
30 23 0.55
31 4 0.10
ACGTcount: A:0.41, C:0.30, G:0.13, T:0.16
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:2292 original size:19 final size:20
Alignment explanation
Indices: 2246--2293 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
2236 TGTGGCACGC
*
2246 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
2268 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
2287 CACATGT
1 CACATGT
2294 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:2298 original size:53 final size:53
Alignment explanation
Indices: 2213--2315 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
2203 GACGTGGCAC
* **
2213 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* *
2266 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
2316 GACACGTGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:4033 original size:3 final size:3
Alignment explanation
Indices: 4025--4053 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4015 ATTTATGTAA
4025 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4054 ATATACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18629 original size:2 final size:2
Alignment explanation
Indices: 18624--18653 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18614 ACGTGTGTTC
18624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18654 TTCAATACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18958 original size:29 final size:30
Alignment explanation
Indices: 18925--18985 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
18915 ACTTATACCA
** *
18925 TTTGGACACTTTGCTCCATGAACT-TCAAT
1 TTTGGACAAATTGCCCCATGAACTGTCAAT
*
18954 TTTGGACAAATTGCCCCCTGAACTGTCAAT
1 TTTGGACAAATTGCCCCATGAACTGTCAAT
18984 TT
1 TT
18986 CAACCTCCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (30 bp):
TTTGGACAAATTGCCCCATGAACTGTCAAT
Found at i:19136 original size:29 final size:30
Alignment explanation
Indices: 19099--19169 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
19089 ACATGTACTA
* * * *
19099 TTTGGACATTTTGCCCCTTGAACT-TTAAT
1 TTTGGACATTTTACCCCCTAAACTCTCAAT
19128 TTTGGACATTTTACCCCCTAAACTCTCAAT
1 TTTGGACATTTTACCCCCTAAACTCTCAAT
*
19158 TTTGGACTTTTT
1 TTTGGACATTTT
19170 TCCCATCCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (30 bp):
TTTGGACATTTTACCCCCTAAACTCTCAAT
Found at i:19549 original size:29 final size:30
Alignment explanation
Indices: 19490--19560 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
19480 GAAAGGGGTT
* * *
19490 AAAATGTCCAAAATTGAGAGTTTAGGGGGC
1 AAAACGTCCAAAATTGAAAGTTCAGGGGGC
*
19520 AAAACGTCCAAAATT-AAAGTTCATGGGGC
1 AAAACGTCCAAAATTGAAAGTTCAGGGGGC
*
19549 AAAACGTTCAAA
1 AAAACGTCCAAA
19561 CCGTACAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (30 bp):
AAAACGTCCAAAATTGAAAGTTCAGGGGGC
Found at i:19951 original size:32 final size:32
Alignment explanation
Indices: 19908--20097 Score: 258
Period size: 32 Copynumber: 5.9 Consensus size: 32
19898 TTTGCCCTTA
19908 GCCAC-GCGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGC-GAGCCTCCCCACTAGGACGGCTCT
*
19940 GCCACGGGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGCGAGCCTCCCCACTAGGACGGCTCT
19972 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGC-GAGCCTCCCCACTAGGACGGCTCT
* * *
20005 GCCACAGCTAGCCGCCCCACTAGGACGGCTCT
1 GCCACGGCGAGCCTCCCCACTAGGACGGCTCT
* *
20037 GCCACGGCTAGCCGT-CCCACTAGGATGGCTCT
1 GCCACGGCGAGCC-TCCCCACTAGGACGGCTCT
* * *
20069 GCCACGGCTAGCCGCCCCACTAGGGCGGC
1 GCCACGGCGAGCCTCCCCACTAGGACGGC
20098 AAGGCTTTTT
Statistics
Matches: 143, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
32 111 0.78
33 32 0.22
ACGTcount: A:0.16, C:0.42, G:0.29, T:0.13
Consensus pattern (32 bp):
GCCACGGCGAGCCTCCCCACTAGGACGGCTCT
Found at i:20023 original size:65 final size:65
Alignment explanation
Indices: 19908--20097 Score: 287
Period size: 65 Copynumber: 3.0 Consensus size: 65
19898 TTTGCCCTTA
** *
19908 GCCAC-GCGGAGCCTCCCCACTAGGACGGCTCTGCCACGGGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCTGCCACGGCTAGCCGCCCCACTAGGACGGCTCT
*
19972 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCTGCCACAGCTAGCCGCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCTGCCACGGCTAGCCGCCCCACTAGGACGGCTCT
* * *
20037 GCCACGGC-TAGCCGT-CCCACTAGGATGGCTCTGCCACGGCTAGCCGCCCCACTAGGGCGGC
1 GCCACGGCGGAGCC-TCCCCACTAGGACGGCTCTGCCACGGCTAGCCGCCCCACTAGGACGGC
20098 AAGGCTTTTT
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
64 52 0.45
65 64 0.55
ACGTcount: A:0.16, C:0.42, G:0.29, T:0.13
Consensus pattern (65 bp):
GCCACGGCGGAGCCTCCCCACTAGGACGGCTCTGCCACGGCTAGCCGCCCCACTAGGACGGCTCT
Found at i:20074 original size:97 final size:96
Alignment explanation
Indices: 19917--20097 Score: 274
Period size: 97 Copynumber: 1.9 Consensus size: 96
19907 AGCCACGCGG
* *
19917 AGCCTCCCCACTAGGACGGCTCTGCCACGGGGAGCCTCCCCACTAGGACGGCTCTGCCACGGCGG
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCGAGCCTCCCCACTAGGACGGCTCTGCCACGGC-G
*
19982 AGCCTCCCCACTAGGACGGCTCTGCCACAGCT
65 AGCCGCCCCACTAGGACGGCTCTGCCACAGCT
* * *
20014 AGCCGCCCCACTAGGACGGCTCTGCCACGGCTAGCCGT-CCCACTAGGATGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCGAGCC-TCCCCACTAGGACGGCTCTGCCACGGCG
*
20078 AGCCGCCCCACTAGGGCGGC
65 AGCCGCCCCACTAGGACGGC
20098 AAGGCTTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
96 18 0.24
97 57 0.75
98 1 0.01
ACGTcount: A:0.16, C:0.42, G:0.29, T:0.13
Consensus pattern (96 bp):
AGCCGCCCCACTAGGACGGCTCTGCCACGGCGAGCCTCCCCACTAGGACGGCTCTGCCACGGCGA
GCCGCCCCACTAGGACGGCTCTGCCACAGCT
Found at i:20211 original size:33 final size:33
Alignment explanation
Indices: 20172--20259 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 33
20162 GGGGGTCTAT
20172 CCATGGTAGGGCCGCCCCAGGGA-AGCGGCCTGG
1 CCATGGTA-GGCCGCCCCAGGGAGAGCGGCCTGG
* *
20205 CCATGGTAGTGCCGCCCCA-GGAGGGCGGCTTGG
1 CCATGGTAG-GCCGCCCCAGGGAGAGCGGCCTGG
20238 CCATGGCTCA-GCCGCCCCAGGG
1 CCATGG-T-AGGCCGCCCCAGGG
20260 GGACGGCACT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
32 4 0.08
33 40 0.83
34 3 0.06
35 1 0.02
ACGTcount: A:0.14, C:0.35, G:0.40, T:0.11
Consensus pattern (33 bp):
CCATGGTAGGCCGCCCCAGGGAGAGCGGCCTGG
Found at i:22487 original size:50 final size:51
Alignment explanation
Indices: 22381--22487 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
22371 TACCTTTGTC
* * *
22381 ATATATAGCTCGATTAATTTTGAATTTGTCGGGGATTCAATGTTTCTAAAT
1 ATATATAGCTCAATTAATTTCGAATTTATCGGGGATTCAATGTTTCTAAAT
*
22432 ATATATAGCTCAATTAATTTCGAATTTATC-GGGATTCAATGTTTCTAGAT
1 ATATATAGCTCAATTAATTTCGAATTTATCGGGGATTCAATGTTTCTAAAT
22482 ATATAT
1 ATATAT
22488 TGATAATTGA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 25 0.48
51 27 0.52
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (51 bp):
ATATATAGCTCAATTAATTTCGAATTTATCGGGGATTCAATGTTTCTAAAT
Found at i:23505 original size:16 final size:16
Alignment explanation
Indices: 23484--23516 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
23474 TTCTCTTCGG
23484 TTTTCTCTAGTTTTTT
1 TTTTCTCTAGTTTTTT
*
23500 TTTTCTTTAGTTTTTT
1 TTTTCTCTAGTTTTTT
23516 T
1 T
23517 GTTTTGCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTCTCTAGTTTTTT
Found at i:28846 original size:21 final size:22
Alignment explanation
Indices: 28822--28866 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
28812 TATTTTTGAA
28822 TTGCTAAACACCGCCCCA-TTT
1 TTGCTAAACACCGCCCCACTTT
** *
28843 TTGCTATTCACCGTCCCACTTT
1 TTGCTAAACACCGCCCCACTTT
28865 TT
1 TT
28867 ACACTTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCACTTT
Found at i:29241 original size:33 final size:33
Alignment explanation
Indices: 29172--29241 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
29162 GCTGTGCCGT
* * * * *
29172 GGCAAAGCCTTGGCAAGGCCGCCCTAGTGGGTC
1 GGCAAAGCCGTGGCAAGGCCACCCCAGGGGGGC
29205 GGCAAAGCCGTGGCTAA-GCCACCCCAGGGGGGC
1 GGCAAAGCCGTGGC-AAGGCCACCCCAGGGGGGC
29238 GGCA
1 GGCA
29242 TGAGCCATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.20, C:0.31, G:0.39, T:0.10
Consensus pattern (33 bp):
GGCAAAGCCGTGGCAAGGCCACCCCAGGGGGGC
Found at i:37145 original size:25 final size:27
Alignment explanation
Indices: 37117--37172 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
37107 CTAAAATTAA
*
37117 TTTTCA-GTACTTTAATGTCTTTCTTTT
1 TTTTCAGGAACTTTAATGTCTTTC-TTT
*
37144 TTTTGAGGGAACTTTAATGTCTTTCTTT
1 TTTTCA-GGAACTTTAATGTCTTTCTTT
37172 T
1 T
37173 CTTTATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 4 0.16
29 16 0.64
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (27 bp):
TTTTCAGGAACTTTAATGTCTTTCTTT
Found at i:37920 original size:14 final size:14
Alignment explanation
Indices: 37903--37945 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
37893 TCCTCTGTTG
37903 CTTTTTAATTGTCC
1 CTTTTTAATTGTCC
** *
37917 C-TTTCCATTGTTC
1 CTTTTTAATTGTCC
37930 CTTTTTAATTGTCC
1 CTTTTTAATTGTCC
37944 CT
1 CT
37946 CATATTTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.12, C:0.26, G:0.07, T:0.56
Consensus pattern (14 bp):
CTTTTTAATTGTCC
Found at i:38849 original size:26 final size:25
Alignment explanation
Indices: 38810--38861 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
38800 GTGGGCTTTA
38810 TGCCCTTTTATGTGGGATTAATTAG
1 TGCCCTTTTATGTGGGATTAATTAG
*
38835 TGCCCTTTTTATGTGGGATTAGTTAG
1 TGCCC-TTTTATGTGGGATTAATTAG
38861 T
1 T
38862 TTGTTGCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (25 bp):
TGCCCTTTTATGTGGGATTAATTAG
Found at i:42817 original size:33 final size:33
Alignment explanation
Indices: 42775--42839 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
42765 TGCTCTTTGT
42775 ATTACTCCATGCAAATTGAAAGATGGGCATATA
1 ATTACTCCATGCAAATTGAAAGATGGGCATATA
42808 ATTACTCCATGCAAATTGAAAGATGGGCATAT
1 ATTACTCCATGCAAATTGAAAGATGGGCATAT
42840 GCTTATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
ATTACTCCATGCAAATTGAAAGATGGGCATATA
Done.