Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010945.1 Corchorus capsularis cultivar CVL-1 contig10966, 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: 75652
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:42 original size:17 final size:15
Alignment explanation
Indices: 4--36 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1 AAG
4 AAAG-GAAAGAGAGA
1 AAAGTGAAAGAGAGA
*
18 AGAGTGAAAGAGAGA
1 AAAGTGAAAGAGAGA
33 AAAG
1 AAAG
37 GCTGAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
AAAGTGAAAGAGAGA
Found at i:218 original size:23 final size:21
Alignment explanation
Indices: 191--235 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
181 TTTTCAAGTG
*
191 TTTAAATAGTGAGATTAGGGGTT
1 TTTAAATA-T-AGATTAAGGGTT
*
214 TTTAATTATAGATTAAGGGTT
1 TTTAAATATAGATTAAGGGTT
235 T
1 T
236 AAAGTGTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.44
Consensus pattern (21 bp):
TTTAAATATAGATTAAGGGTT
Found at i:1323 original size:81 final size:81
Alignment explanation
Indices: 1171--1324 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
1161 CATGTTGGGG
* * * **
1171 CTGGTGAGGGGTTAAATGAGGAAGTTACTGTGCAAGAAGTGGTTGGTGATGTTTTTTCTGAGTAT
1 CTGGTGAGGGGTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTTGGTGATGTTTTTTCTGACCAT
1236 AATGAAGATGTACGGC
66 AATGAAGATGTACGGC
* *
1252 CTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGG-TGTGTGATGTTTTTTCTGTCCA
1 CTGGTGAGGGGTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTTG-GTGATGTTTTTTCTGACCA
*
1316 TATTGAAGA
65 TAATGAAGA
1325 GTTAAGGTCT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 2 0.03
81 62 0.97
ACGTcount: A:0.27, C:0.07, G:0.34, T:0.32
Consensus pattern (81 bp):
CTGGTGAGGGGTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTTGGTGATGTTTTTTCTGACCAT
AATGAAGATGTACGGC
Found at i:1337 original size:81 final size:81
Alignment explanation
Indices: 1171--1345 Score: 219
Period size: 81 Copynumber: 2.1 Consensus size: 81
1161 CATGTTGGGG
* * * * **
1171 CTGGTGAGGGGTTAAATGAGGAAGTTACTGTGCAAGAAGTGGTTGGTGATGTTTTTTCTGAGTAT
1 CTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTTGGTGATGTTTTTTCTGACCAT
*
1236 AATGAAGATGTACGGC
66 AATGAAGATGTAAGGC
*
1252 CTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGG-TGTGTGATGTTTTTTCTGTCCA
1 CTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTTG-GTGATGTTTTTTCTGACCA
* *
1316 TATTGAAGA-GTTAAGGT
65 TAATGAAGATG-TAAGGC
1333 CTGGTGAAGGGTT
1 CTGGTG-AGGGTT
1346 GGATGATGGT
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
80 3 0.04
81 72 0.89
82 6 0.07
ACGTcount: A:0.26, C:0.07, G:0.35, T:0.33
Consensus pattern (81 bp):
CTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTTGGTGATGTTTTTTCTGACCAT
AATGAAGATGTAAGGC
Found at i:12516 original size:13 final size:13
Alignment explanation
Indices: 12495--12524 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12485 GATCAAGTGT
*
12495 AAAAGTAAAAAGG
1 AAAAATAAAAAGG
12508 AAAAATAAAAAGG
1 AAAAATAAAAAGG
12521 AAAA
1 AAAA
12525 CAAATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (13 bp):
AAAAATAAAAAGG
Found at i:32495 original size:29 final size:29
Alignment explanation
Indices: 32453--32525 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
32443 TGATTAATGA
32453 GAATGGTTCATCTTCCTATAGATGTTATG
1 GAATGGTTCATCTTCCTATAGATGTTATG
*
32482 GAATGGTTCATCTTCCTATGGATGTTATG
1 GAATGGTTCATCTTCCTATAGATGTTATG
*
32511 GAATGATTCATCTTC
1 GAATGGTTCATCTTC
32526 TTGCATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (29 bp):
GAATGGTTCATCTTCCTATAGATGTTATG
Found at i:37785 original size:30 final size:30
Alignment explanation
Indices: 37749--37830 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 30
37739 ACATTTTCGT
37749 AACGTTATATCCTGAATTG-TTACTTC-ATCA
1 AACGTTATATCCTGAATTGATT--TTCGATCA
*
37779 AACGTTATATCCTGAATTGGATTTTCGGTCA
1 AACGTTATATCCTGAATT-GATTTTCGATCA
37810 AACGTTATATCCTGAATTGAT
1 AACGTTATATCCTGAATTGAT
37831 CATTTAGCCC
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
30 24 0.50
31 22 0.46
32 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (30 bp):
AACGTTATATCCTGAATTGATTTTCGATCA
Found at i:37814 original size:31 final size:30
Alignment explanation
Indices: 37749--37828 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 30
37739 ACATTTTCGT
37749 AACGTTATATCCTGAATT-GTTACTTCATCA
1 AACGTTATATCCTGAATTGGTTA-TTCATCA
*
37779 AACGTTATATCCTGAATTGGATT-TTCGGTCA
1 AACGTTATATCCTGAATTGG-TTATTC-ATCA
37810 AACGTTATATCCTGAATTG
1 AACGTTATATCCTGAATTG
37829 ATCATTTAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
30 21 0.46
31 23 0.50
32 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (30 bp):
AACGTTATATCCTGAATTGGTTATTCATCA
Found at i:49006 original size:32 final size:33
Alignment explanation
Indices: 48967--49059 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 33
48957 CCGGCCATTG
48967 CTTGGAGAAG-CC-GCGCAACACCGGCCACGCGA
1 CTTGGAGAAGCCCGGC-CAACACCGGCCACGCGA
* **
48999 CTTGGAGATGCCCGGCCATTACCGGCCACGCGA
1 CTTGGAGAAGCCCGGCCAACACCGGCCACGCGA
** * *
49032 CAAGGACATGCCCGGCC-ACAACCGGCCA
1 CTTGGAGAAGCCCGGCCAAC-ACCGGCCA
49060 AACGACTCGG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
32 9 0.18
33 39 0.78
34 2 0.04
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.09
Consensus pattern (33 bp):
CTTGGAGAAGCCCGGCCAACACCGGCCACGCGA
Found at i:49026 original size:33 final size:33
Alignment explanation
Indices: 48986--49093 Score: 117
Period size: 33 Copynumber: 3.3 Consensus size: 33
48976 GCCGCGCAAC
** * **
48986 ACCGGCCACGCGACTTGGAGATGCCCGGCCATT
1 ACCGGCCACGCGACAAGGACATGCCCGGCCACA
49019 ACCGGCCACGCGACAAGGACATGCCCGGCCACA
1 ACCGGCCACGCGACAAGGACATGCCCGGCCACA
** ** * *
49052 ACCGGCCAAACGACTCGGCCATGCTCGGCCACA
1 ACCGGCCACGCGACAAGGACATGCCCGGCCACA
49085 ACCGGCCAC
1 ACCGGCCAC
49094 ATGATACTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACAAGGACATGCCCGGCCACA
Found at i:54914 original size:33 final size:33
Alignment explanation
Indices: 54870--54933 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
54860 CGGCCACAAG
* ** *
54870 ACCGGCCACGCGACTTGGAGATGCCCGGCCATT
1 ACCGACCACGCGACAAGGACATGCCCGGCCATT
54903 ACCGACCACGCGACAAGGACATGCCCGGCCA
1 ACCGACCACGCGACAAGGACATGCCCGGCCA
54934 CAATCGGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.23, C:0.39, G:0.28, T:0.09
Consensus pattern (33 bp):
ACCGACCACGCGACAAGGACATGCCCGGCCATT
Found at i:58370 original size:33 final size:33
Alignment explanation
Indices: 58328--58398 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
58318 GTGTTTTAGA
* * *
58328 TGTTGTTTGCGATGATGCTAAACCTAATTTGAG
1 TGTTGTTTGCAATAATACTAAACCTAATTTGAG
* **
58361 TGTTGTTTGCAATAATACTAAATCTGTTTTGAG
1 TGTTGTTTGCAATAATACTAAACCTAATTTGAG
58394 TGTTG
1 TGTTG
58399 ATAGAGATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGCAATAATACTAAACCTAATTTGAG
Found at i:58513 original size:33 final size:33
Alignment explanation
Indices: 58427--58565 Score: 244
Period size: 33 Copynumber: 4.2 Consensus size: 33
58417 TCTTATTAGA
58427 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
58460 TGCAAATAA-TCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
58492 TGAAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
58525 TGCAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
58558 TGAAAATA
1 TGAAAATA
58566 GGACTGTTTC
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
32 31 0.31
33 68 0.69
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:58531 original size:65 final size:66
Alignment explanation
Indices: 58427--58565 Score: 262
Period size: 65 Copynumber: 2.1 Consensus size: 66
58417 TCTTATTAGA
58427 TGAAAATAATTCTGTTTTGGTTGATCATAGCATTGCAAATAA-TCTGTTTTGGTTGATCATAGCA
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCATTGCAAATAATTCTGTTTTGGTTGATCATAGCA
58491 T
66 T
*
58492 TGAAAATAATTTTGTTTTGGTTGATCATAGCATTGCAAATAATTCTGTTTTGGTTGATCATAGCA
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCATTGCAAATAATTCTGTTTTGGTTGATCATAGCA
58557 T
66 T
58558 TGAAAATA
1 TGAAAATA
58566 GGACTGTTTC
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 41 0.57
66 31 0.43
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (66 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCATTGCAAATAATTCTGTTTTGGTTGATCATAGCA
T
Found at i:58991 original size:30 final size:30
Alignment explanation
Indices: 58955--59013 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
58945 CAAGGGGGAG
58955 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
*
58985 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
59014 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:63097 original size:8 final size:8
Alignment explanation
Indices: 63084--63117 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
63074 CACCTTCTTG
63084 AAAAATTC
1 AAAAATTC
63092 AAAAATTC
1 AAAAATTC
*
63100 AGAAACTTC
1 A-AAAATTC
63109 AAAAATTC
1 AAAAATTC
63117 A
1 A
63118 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:63214 original size:15 final size:16
Alignment explanation
Indices: 63190--63219 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
63180 AGTTATATCG
63190 AAAAATATAAAAAAAT
1 AAAAATATAAAAAAAT
63206 AAAAA-ATAAAAAAA
1 AAAAATATAAAAAAA
63220 ATTTCGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAATATAAAAAAAT
Found at i:63217 original size:16 final size:17
Alignment explanation
Indices: 63190--63221 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
63180 AGTTATATCG
63190 AAAAATATAAAAAAATA
1 AAAAATATAAAAAAATA
63207 AAAAATA-AAAAAAAT
1 AAAAATATAAAAAAAT
63222 TTCGACCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAATATAAAAAAATA
Found at i:64727 original size:33 final size:33
Alignment explanation
Indices: 64690--64777 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 33
64680 AATTGTGATG
64690 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
** *
64723 AAAACAATTCTGTTTTGGTTGATTATAGCATTG
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
* * *
64756 CAAATAATCCTGTTTTGGTTGA
1 AAAACAATTCTGTTTTGGTTGA
64778 TAGCATTGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (33 bp):
AAAACAATTCTGTTTTGGTTGAACATAGCATTA
Found at i:64783 original size:30 final size:31
Alignment explanation
Indices: 64688--64792 Score: 113
Period size: 33 Copynumber: 3.3 Consensus size: 31
64678 CTAATTGTGA
* *
64688 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAATCCTGTTTTGGTTG-A-ATAGCAT
* * *
64721 TAAAAACAATTCTGTTTTGGTTGATTATAGCAT
1 TGAAAATAATCCTGTTTTGGTTGA--ATAGCAT
*
64754 TGCAAATAATCCTGTTTTGGTTG-ATAGCAT
1 TGAAAATAATCCTGTTTTGGTTGAATAGCAT
64784 TGAAAATAA
1 TGAAAATAA
64793 ATCTGATTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
30 15 0.23
32 1 0.02
33 48 0.75
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (31 bp):
TGAAAATAATCCTGTTTTGGTTGAATAGCAT
Done.