Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019223.1 Corchorus olitorius cultivar O-4 contig19256, 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: 108060
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:819 original size:320 final size:319
Alignment explanation
Indices: 119--913 Score: 1013
Period size: 320 Copynumber: 2.5 Consensus size: 319
109 TGTGATGATT
* * *
119 AGTACACGATTTCGGCTAAAATTTTGC-AGAACGTAACCT-GAAAAAGTTTTCCGCAATTTTTGG
1 AGTACACGATTTCGGCTAAAATTTTGCAAAAAC-TAACCTCGAAAAAATTTTCCTCAATTTTTGG
* * *
182 CCATAATACTCGTAAAAAATATATAATTGAATGCCAAAAAGAATGAAGGGCTTTT-ATCA-CATA
65 CCACAATACTCGTAAAAAATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCA--AGC-TT
* * * * *
245 TAATATCATATTTGCTATTTTTTTACGAATTAATTTCTAATTAAATTGAAACATGATTCAGATGC
127 TAATATCGTATTTCCTA-TTTTTTCCGAATTAATTTCGAATTAAATCGAAACATGATTCAGATGC
* *
310 TCGTAAAACAAAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCT
191 TCGTAAAACAAAAATCCTTAAATCCAATGTGGCTAAGATTTAGTTAGATGAATATAGATATTTCA
* * *
375 GTAAGTCTTGTCGGCAAAAATCATGCAAAACTGAGTCGGGGACCAGGAACGCGTTTTTAGCAAA
256 GTAAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGAGGACCAGGAACGCGTTTTTAGCAAA
** * * * *
439 AGTACACGATTTCAACTAAATTTTTGCAAAAACTGACC-CGAAAAAATTTTCTTTAATTTTTGGC
1 AGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCTCGAAAAAATTTTCCTCAATTTTTGGC
* * * *
503 CACAATACCCATAAAAGATATATAATTCAATGCCAAAAAGAATGAATGGCTTTTCAAGCTTCTAA
66 CACAATACTCGTAAAAAATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCAAGCTT-TAA
* ** *
568 TCTCGTATTTCCTATTTTTTCCGAATTAATTTCGGCTTAAATCGAAA-ATGAGTT-AGATGCTTG
130 TATCGTATTTCCTATTTTTTCCGAATTAATTTCGAATTAAATCGAAACATGA-TTCAGATGCTCG
* * *
631 TAAAA-ACAAAATCCTTAAATCCAATGTGGCTAATATTTGGTTAGATGAATATAGATTTTTCAGT
194 TAAAACA-AAAATCCTTAAATCCAATGTGGCTAAGATTTAGTTAGATGAATATAGATATTTCAGT
* * *
695 GA-TACTTGGCGCCGAAAATCATGCAAAACTGAGTCGAGGCCTCA-GAACGCGTTTTTAGCTAAA
258 AAGT-CTTGGCGCCAAAAATCATGCAAAACTGAGTCGAGGAC-CAGGAACGCGTTTTTAGC--AA
758 A
319 A
*
759 ACTGT-C-TGATTTCGGCTAAAATTTTGCAAAAACT-ACCTCGAAAAAATTTTCCTCAATTTTTG
1 A--GTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCTCGAAAAAATTTTCCTCAATTTTTG
*
821 GCCACAATACTCGTAAAAAAATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCACGCTTT
64 GCCACAATACTCGT-AAAAAATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCAAGCTTT
886 CAATATCGTATTTCCTATTTTTTCCGAA
128 -AATATCGTATTTCCTATTTTTTCCGAA
914 ATATGATTTA
Statistics
Matches: 411, Mismatches: 48, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
317 2 0.00
318 117 0.28
319 37 0.09
320 175 0.43
321 78 0.19
322 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (319 bp):
AGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCTCGAAAAAATTTTCCTCAATTTTTGGC
CACAATACTCGTAAAAAATATATAATTCAATGCCAAAAAGAATGAAGGGCTTTTCAAGCTTTAAT
ATCGTATTTCCTATTTTTTCCGAATTAATTTCGAATTAAATCGAAACATGATTCAGATGCTCGTA
AAACAAAAATCCTTAAATCCAATGTGGCTAAGATTTAGTTAGATGAATATAGATATTTCAGTAAG
TCTTGGCGCCAAAAATCATGCAAAACTGAGTCGAGGACCAGGAACGCGTTTTTAGCAAA
Found at i:2939 original size:32 final size:32
Alignment explanation
Indices: 2898--2961 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2888 GAAGAAAAAC
2898 TAGAAGAACGTGAAGATATGGTGTCCTAATGT
1 TAGAAGAACGTGAAGATATGGTGTCCTAATGT
2930 TAGAAGAACGTGAAGATATGGTGTCCTAATGT
1 TAGAAGAACGTGAAGATATGGTGTCCTAATGT
2962 ATTGTCATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (32 bp):
TAGAAGAACGTGAAGATATGGTGTCCTAATGT
Found at i:6753 original size:1 final size:1
Alignment explanation
Indices: 6749--6776 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
6739 CCTCCCCCTC
6749 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
6777 CAATATCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12641 original size:9 final size:9
Alignment explanation
Indices: 12627--12654 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12617 AAGTAAGCAT
12627 GCTCAAATG
1 GCTCAAATG
12636 GCTCAAATG
1 GCTCAAATG
12645 GCTCAAATG
1 GCTCAAATG
12654 G
1 G
12655 TTATACTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (9 bp):
GCTCAAATG
Found at i:12903 original size:36 final size:37
Alignment explanation
Indices: 12853--12972 Score: 119
Period size: 37 Copynumber: 3.4 Consensus size: 37
12843 TGGCTAATGC
*
12853 TTTAATTTATGCATATACATAATAGTAAATATGGCAT
1 TTTAATGTATGCATATACATAATAGTAAATATGGCAT
* * * **
12890 TTTAATGT-TGCATA-ATAGAA-CGTGGATAAT-GC--
1 TTTAATGTATGCATATACATAATAGTAAAT-ATGGCAT
*
12922 TTTAATTTATGCATATACATAATAGTAAATATGGCAT
1 TTTAATGTATGCATATACATAATAGTAAATATGGCAT
12959 TTTAATGT-TGCATA
1 TTTAATGTATGCATA
12973 ATAATCGAGA
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
32 7 0.11
33 6 0.10
34 12 0.19
35 12 0.19
36 12 0.19
37 14 0.22
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTAATGTATGCATATACATAATAGTAAATATGGCAT
Found at i:12949 original size:69 final size:69
Alignment explanation
Indices: 12838--12975 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
12828 AAGGTTCGAC
*
12838 GAACGTGGCTAATGCTTTAATTTATGCATATACATAATAGTAAATATGGCATTTTAATGTTGCAT
1 GAACGTGGATAATGCTTTAATTTATGCATATACATAATAGTAAATATGGCATTTTAATGTTGCAT
12903 AATA
66 AATA
12907 GAACGTGGATAATGCTTTAATTTATGCATATACATAATAGTAAATATGGCATTTTAATGTTGCAT
1 GAACGTGGATAATGCTTTAATTTATGCATATACATAATAGTAAATATGGCATTTTAATGTTGCAT
12972 AATA
66 AATA
12976 ATCGAGACAG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (69 bp):
GAACGTGGATAATGCTTTAATTTATGCATATACATAATAGTAAATATGGCATTTTAATGTTGCAT
AATA
Found at i:13953 original size:10 final size:10
Alignment explanation
Indices: 13915--13961 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
13905 TGATCTCACA
13915 TAATAGAGCT
1 TAATAGAGCT
*
13925 TAACTAGAGTAT
1 TAA-TAGAG-CT
13937 ATAATAGAGCT
1 -TAATAGAGCT
13948 TAATAGAGCT
1 TAATAGAGCT
13958 TAAT
1 TAAT
13962 TCACATCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 17 0.53
11 6 0.19
12 6 0.19
13 3 0.09
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32
Consensus pattern (10 bp):
TAATAGAGCT
Found at i:29516 original size:152 final size:149
Alignment explanation
Indices: 29227--29528 Score: 550
Period size: 152 Copynumber: 2.0 Consensus size: 149
29217 TTTTTTTTTG
29227 AGAGTGGGATTGAATTTGGGCTAATTATTTCTGCAACTTTAATATGAACTCAAATCAGGGTGGAA
1 AGAGTGGGATTGAATTTGGGCTAATTATTTCTGCAACTTTAATATGAACTCAAATCAGGGTGGAA
29292 ATGTGAAGAGTTTGGGCTCATTCTCGGCCCAATTCATTAATAACATCTCTTGTCATTTTGTGCAC
66 ATGTGAAGAGTTTGGGCTCATTCTCGGCCCAATTCATTAATAACATCTCTTGTCATTTTGTGCAC
29357 AATTTAATCTTAGGTGAAC
131 AATTTAATCTTAGGTGAAC
* * *
29376 AGAGTGGGATTGAATTTGGGCTTATTGTTTCTGCAACTTTAATATGAACTCAAATCGGGGTGGAA
1 AGAGTGGGATTGAATTTGGGCTAATTATTTCTGCAACTTTAATATGAACTCAAATCAGGGTGGAA
29441 ATGTGAAATTGAGTTTGGGCTCATTCTCGGCCCAATTCATTAATAACATCTCTTGTCATTTTGTG
66 ATGTG-AA--GAGTTTGGGCTCATTCTCGGCCCAATTCATTAATAACATCTCTTGTCATTTTGTG
29506 CACAATTTAATCTTAGGTGAAC
128 CACAATTTAATCTTAGGTGAAC
29528 A
1 A
29529 TCATAAGAAC
Statistics
Matches: 147, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 67 0.46
150 2 0.01
152 78 0.53
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (149 bp):
AGAGTGGGATTGAATTTGGGCTAATTATTTCTGCAACTTTAATATGAACTCAAATCAGGGTGGAA
ATGTGAAGAGTTTGGGCTCATTCTCGGCCCAATTCATTAATAACATCTCTTGTCATTTTGTGCAC
AATTTAATCTTAGGTGAAC
Found at i:47343 original size:21 final size:21
Alignment explanation
Indices: 47317--47356 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
47307 TGCCACGAAG
*
47317 AAAGAAGAA-GGAAGGAAAAGA
1 AAAGAAAAATGGAA-GAAAAGA
47338 AAAGAAAAATGGAAGAAAA
1 AAAGAAAAATGGAAGAAAA
47357 TTGACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (21 bp):
AAAGAAAAATGGAAGAAAAGA
Found at i:60362 original size:1 final size:1
Alignment explanation
Indices: 60351--60423 Score: 110
Period size: 1 Copynumber: 73.0 Consensus size: 1
60341 TTAGAGTTTG
* ** *
60351 TTTTATTTTTTTTTTAATTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
60416 TTTTTTTT
1 TTTTTTTT
60424 CTGGTGGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:62969 original size:2 final size:2
Alignment explanation
Indices: 62962--63001 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
62952 ACCCTAAATA
* *
62962 AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63002 TAAGAGTGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:62984 original size:14 final size:14
Alignment explanation
Indices: 62965--63001 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
62955 CTAAATAATA
62965 TATATATATATATT
1 TATATATATATATT
62979 TATATATATATATT
1 TATATATATATATT
62993 TATATATAT
1 TATATATAT
63002 TAAGAGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATATATATATT
Found at i:69163 original size:101 final size:101
Alignment explanation
Indices: 68977--69190 Score: 329
Period size: 101 Copynumber: 2.1 Consensus size: 101
68967 ACATAAACTT
* * * *
68977 AATAATTTCCATCTAACATTTGGTCTAATGACAGAGTACTAAACCCTCAGTTTATTGAATGATCA
1 AATAA-TTACATCTAACATCTGATCTAATAACAGAGTACTAAACCCTCAGTTTATTGAATGATCA
69042 AAGTTCGATCTCTAACAATTTCAAGTAAAATAAAATC
65 AAGTTCGATCTCTAACAATTTCAAGTAAAATAAAATC
* * * * *
69079 AATAATTACATCTGACATCTGATCTAATAAGAGAGTATTAAACCCTCAGTTTGTTGAATGATTAA
1 AATAATTACATCTAACATCTGATCTAATAACAGAGTACTAAACCCTCAGTTTATTGAATGATCAA
*
69144 AGTTCGATCTCTAATAATTTCAAGTAAAATAAAATC
66 AGTTCGATCTCTAACAATTTCAAGTAAAATAAAATC
69180 AATAATTACAT
1 AATAATTACAT
69191 TAGGAAAAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 97 0.95
102 5 0.05
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (101 bp):
AATAATTACATCTAACATCTGATCTAATAACAGAGTACTAAACCCTCAGTTTATTGAATGATCAA
AGTTCGATCTCTAACAATTTCAAGTAAAATAAAATC
Found at i:71001 original size:2 final size:2
Alignment explanation
Indices: 70994--71058 Score: 64
Period size: 2 Copynumber: 32.0 Consensus size: 2
70984 TATCTTACTA
*
70994 AT AT AT AT AT AT AGT AC AT -T AT AT AT AT AT AT AT AT AT -T CAT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
71036 AT AT AT AGT CAT -T AT AT AT AT AT
1 AT AT AT A-T -AT AT AT AT AT AT AT
71059 TCATATTCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
1 3 0.06
2 45 0.83
3 5 0.09
4 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80193 original size:32 final size:32
Alignment explanation
Indices: 80152--80213 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
80142 TTCTTCTCTT
*
80152 CTGTCAAAGTTAACAGTTAACAGACCTGTTAA
1 CTGTCAAAGTTAAAAGTTAACAGACCTGTTAA
80184 CTGTCAAAGTTAAAAGTTAACAGACCTGTT
1 CTGTCAAAGTTAAAAGTTAACAGACCTGTT
80214 TGAATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (32 bp):
CTGTCAAAGTTAAAAGTTAACAGACCTGTTAA
Found at i:89922 original size:2 final size:2
Alignment explanation
Indices: 89917--89941 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89907 GTAAAAAAAA
89917 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
89942 AATATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:97268 original size:16 final size:16
Alignment explanation
Indices: 97247--97281 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
97237 TCTACTAGGC
97247 TATTCAAGTTTGTGTA
1 TATTCAAGTTTGTGTA
97263 TATTCAAGTTTGTGTA
1 TATTCAAGTTTGTGTA
97279 TAT
1 TAT
97282 ATATAGTATT
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:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (16 bp):
TATTCAAGTTTGTGTA
Done.