Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013539.1 Corchorus capsularis cultivar CVL-1 contig13560, 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: 95406
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2476 original size:32 final size:32
Alignment explanation
Indices: 2440--2502 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
2430 CAACTTCAAT
*
2440 TTTTTTTATTACCATGTCTAATTTAATACTTC
1 TTTTTTTATTACCATGTCTAATCTAATACTTC
* *
2472 TTTTTTTGTTTCCATGTCTAATCTAATACTT
1 TTTTTTTATTACCATGTCTAATCTAATACTT
2503 GTAATTCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.05, T:0.57
Consensus pattern (32 bp):
TTTTTTTATTACCATGTCTAATCTAATACTTC
Found at i:20475 original size:2 final size:2
Alignment explanation
Indices: 20468--20499 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20458 GATATAAGAG
*
20468 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20500 TTATTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:21231 original size:11 final size:11
Alignment explanation
Indices: 21217--21254 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
21207 ATTCATAACA
21217 AATTTATAATT
1 AATTTATAATT
21228 AATTTATAATT
1 AATTTATAATT
21239 -ATTTGATAATT
1 AATTT-ATAATT
*
21250 TATTT
1 AATTT
21255 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:22793 original size:16 final size:16
Alignment explanation
Indices: 22772--22806 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
22762 ACAATTCAGA
22772 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
22788 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
22804 AAG
1 AAG
22807 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:23010 original size:91 final size:91
Alignment explanation
Indices: 22855--23074 Score: 336
Period size: 91 Copynumber: 2.4 Consensus size: 91
22845 AAGAAGATTG
* *
22855 AAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAGAAGACTCAATTATTGGAGAATTACTG
1 AAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATTACTG
*
22920 AAGACCCAGTTATTTGGG-AGTTATTA
66 AAGACCCAGTTA-TTGGGAAATTATTA
* *
22946 AAAGAAGATCCATGTATGTGGAGTATTCTTCTTTCAAAGAAGA-TCCAATTATTGCAGAATTACT
1 AAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACT-CAATTATTGCAGAATTACT
*
23010 GAAGACCCAGTTATTGGGAAATTATTG
65 GAAGACCCAGTTATTGGGAAATTATTA
* *
23037 AAAGAAAATCCACGTATGTGGAGGATTCTTCTTTCAAA
1 AAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA
23075 TTATCAAAGA
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
90 6 0.05
91 112 0.95
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (91 bp):
AAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATTACTG
AAGACCCAGTTATTGGGAAATTATTA
Found at i:59309 original size:15 final size:15
Alignment explanation
Indices: 59291--59320 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59281 TTTTAAACTT
*
59291 GTAATTAATTTCATA
1 GTAATTAATTCCATA
59306 GTAATTAATTCCATA
1 GTAATTAATTCCATA
59321 ATTAAAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTAATTCCATA
Found at i:61121 original size:18 final size:19
Alignment explanation
Indices: 61100--61135 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
61090 TATTACTTCT
*
61100 ATTG-ATTTTATTTTTAAA
1 ATTGTATTTCATTTTTAAA
61118 ATTGTATTTCATTTTTAA
1 ATTGTATTTCATTTTTAA
61136 TTTTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (19 bp):
ATTGTATTTCATTTTTAAA
Found at i:63179 original size:15 final size:15
Alignment explanation
Indices: 63144--63173 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
63134 ACTTCCGTCC
63144 CAAATTATCTAGTGA
1 CAAATTATCTAGTGA
63159 CAAATTATCTAGTGA
1 CAAATTATCTAGTGA
63174 ATAATTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
CAAATTATCTAGTGA
Found at i:64194 original size:6 final size:6
Alignment explanation
Indices: 64183--64217 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
64173 CTAAACTGTC
64183 TTTTCT TTTTCT TTTTC- TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
64218 CTCCCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:64197 original size:11 final size:11
Alignment explanation
Indices: 64183--64214 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
64173 CTAAACTGTC
64183 TTTTCTTTTTCT
1 TTTTC-TTTTCT
64195 TTTTCTTTTCT
1 TTTTCTTTTCT
64206 TTTTCTTTT
1 TTTTCTTTT
64215 TCTCTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:64203 original size:17 final size:17
Alignment explanation
Indices: 64181--64217 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
64171 AACTAAACTG
64181 TCTTTTCTTTTTCTTTT
1 TCTTTTCTTTTTCTTTT
64198 TCTTTTCTTTTTCTTTT
1 TCTTTTCTTTTTCTTTT
64215 TCT
1 TCT
64218 CTCCCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TCTTTTCTTTTTCTTTT
Found at i:67241 original size:16 final size:16
Alignment explanation
Indices: 67220--67252 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
67210 TGGATTCAGT
67220 TATCTTCAGGTTCGGG
1 TATCTTCAGGTTCGGG
*
67236 TATCTTCGGGTTCGGG
1 TATCTTCAGGTTCGGG
67252 T
1 T
67253 TTCGGGCGAG
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:0.09, C:0.18, G:0.33, T:0.39
Consensus pattern (16 bp):
TATCTTCAGGTTCGGG
Found at i:70867 original size:25 final size:25
Alignment explanation
Indices: 70826--70876 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
70816 CTTCAATTTA
*
70826 ATCACATCTAAGCCCATATATGGTT
1 ATCACATCGAAGCCCATATATGGTT
*
70851 ATCACATCGAAGGCCATATATGGTT
1 ATCACATCGAAGCCCATATATGGTT
70876 A
1 A
70877 GTAGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (25 bp):
ATCACATCGAAGCCCATATATGGTT
Found at i:87287 original size:38 final size:38
Alignment explanation
Indices: 87245--87323 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
87235 TATTGATTAT
87245 TACAAGTATGCATATATATAAATCAAGATAAAAAAAAG
1 TACAAGTATGCATATATATAAATCAAGATAAAAAAAAG
87283 TACAAGTATGCATATATATAAATCAAGATAAAAAAAAG
1 TACAAGTATGCATATATATAAATCAAGATAAAAAAAAG
87321 TAC
1 TAC
87324 TTTTTATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (38 bp):
TACAAGTATGCATATATATAAATCAAGATAAAAAAAAG
Found at i:89881 original size:31 final size:32
Alignment explanation
Indices: 89836--89902 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
89826 AACTTTAAAT
*
89836 TTTCCGATTATACCCTTATTTT-TAAAACATA
1 TTTCCAATTATACCCTTATTTTCTAAAACATA
* *
89867 TTTCCAATTGTACCCTTTTTTTCTAAAACATA
1 TTTCCAATTATACCCTTATTTTCTAAAACATA
89899 TTTC
1 TTTC
89903 TAAATTGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.48
Consensus pattern (32 bp):
TTTCCAATTATACCCTTATTTTCTAAAACATA
Found at i:90285 original size:169 final size:167
Alignment explanation
Indices: 90107--90418 Score: 434
Period size: 171 Copynumber: 1.8 Consensus size: 167
90097 TGTCTTTATC
* * *
90107 TCCGATTGCAC-CCT-TTTTTTTCAAATATATTTCTAAATTGACATTATTAAAATTTATTATTTA
1 TCCGATTGCACTCATCTTTTTTCCAAATATATTTCTAAATTGACATTATTAAAATTTAGTA---A
90170 AA-AATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTTGTAAAATTGATTTTCA-TTG
63 AATAATTAATTA-AAAATTTCAATTTAGACCGAATTATAAG-TTTGTAAAATTGATTTT-AGTTG
90233 ATGAACATGCAAATTTCTACGAATAATAGGAAACTTTATGTTT
125 ATGAACATGCAAATTTCTACGAATAATAGGAAACTTTATGTTT
* ** *
90276 TCCGATTGCACTGATCTTTTTTCCAAATATATTTCTAAATTTCCGTTATTAAAATTTAGTAAAAT
1 TCCGATTGCACTCATCTTTTTTCCAAATATATTTCTAAATTGACATTATTAAAATTTAGTAAAA-
* *
90341 TTTATTAATTAAAAATTTCAATTTAGACCGAATTATAAGTTTGTCAAATTGATTTTAGTTGATGA
65 -TAATTAATTAAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTAGTTGATGA
*
90406 ACATGTAAATTTC
129 ACATGCAAATTTC
90419 CTTTACTATT
Statistics
Matches: 127, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
168 4 0.03
169 46 0.36
170 29 0.23
171 48 0.38
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (167 bp):
TCCGATTGCACTCATCTTTTTTCCAAATATATTTCTAAATTGACATTATTAAAATTTAGTAAAAT
AATTAATTAAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTAGTTGATGAAC
ATGCAAATTTCTACGAATAATAGGAAACTTTATGTTT
Found at i:90788 original size:22 final size:21
Alignment explanation
Indices: 90763--90811 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
90753 TTCCTTAGGG
*
90763 AGGTTAACAAAATTTCATAAGA
1 AGGTTAA-AAAATTTCATAAAA
*
90785 AGGTTTAAAAAATTTTATAAAA
1 AGG-TTAAAAAATTTCATAAAA
90807 AGGTT
1 AGGTT
90812 CTCGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 18 0.75
23 4 0.17
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (21 bp):
AGGTTAAAAAATTTCATAAAA
Found at i:93501 original size:31 final size:30
Alignment explanation
Indices: 93441--93501 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
93431 GTGATTAGAT
* **
93441 AAAAAGAATGGCAAAGATCTGGCCAAAAAA
1 AAAAAGAATGGCAAAGATATAACCAAAAAA
93471 AAAAAGGAATGGCAAAGATATAAACCAAAAA
1 AAAAA-GAATGGCAAAGATAT-AACCAAAAA
93502 GAGCAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 14 0.54
32 7 0.27
ACGTcount: A:0.61, C:0.11, G:0.18, T:0.10
Consensus pattern (30 bp):
AAAAAGAATGGCAAAGATATAACCAAAAAA
Done.