Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012360.1 Corchorus olitorius cultivar O-4 contig12393, 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: 23949
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:827 original size:336 final size:335
Alignment explanation
Indices: 1--1811 Score: 2937
Period size: 334 Copynumber: 5.4 Consensus size: 335
1 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
* *
66 TATTGTGGCCAAA-AATTATGGAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCTGAAAT
66 TATTGTGG-CAAATAATTGTGGAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCCGAAAT
* ** ***
130 CGTGTACTAACCATCATGGTTTTTGGCTAAAAATATGTTTCTATGCCCTGACTCAGTTTTGCATG
130 CGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCATG
195 ATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGG
195 ATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGG
* *
260 ATTTACGGATTTATTTTTACGAGAATTTGAATCTTGTTTCGATTTAATTAGAAATAAATT---AA
260 ATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAA
322 AAAAATGGAAA
325 AAAAATGGAAA
* *
333 AACTATATTAGAAGCGTG-AAAACCCTAAAATATTTTTGGCATTGAATTATAAGATTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
397 TATTGTGGCAAATAATTGTGGAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCCGAAATC
66 TATTGTGGCAAATAATTGTGGAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCCGAAATC
* * * * *
462 GTGTACTGTTA-CATTACGGTTTTTGGCTAAAAATGCATTTCGGGGCCTTGACTCTGTTTTGCAA
131 GTGTAC--TAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGC-A
526 T-ATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAAT
193 TGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAAT
*
590 GGATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTCATTAGAAATAAATTCTA
258 GGATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-A
*
655 G-AAAAAATGTAAA
322 GAAAAAAATGGAAA
*
668 AACGATATTAGATGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
*
733 TATTGTGGCAAATAATTGTGGAAAAACTTTTCGCATCAGTTTTTTGCAAAATTTTAGCCGAAATC
66 TATTGTGGCAAATAATTGTGGAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCCGAAATC
* * *
798 GTGTACTGTTA-CATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCTTGACTCTGTTTTGCAA
131 GTGTAC--TAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGC-A
862 T-ATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAAT
193 TGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAAT
926 GGATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG
258 GGATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG
991 AAAAAAATGGAAA
323 AAAAAAATGGAAA
*
1004 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
* * ** * *
1069 TATTGTCGCAAAAAATTG-GTGAAAAACTTTTCGGGTTAGTTTTTT-CCAAATTTTAGCCGAAAT
66 TATTGTGGCAAATAATTGTG-GAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCCGAAAT
* * *
1132 CGTATACTAACCATCACGGTTTTGGGCTAAAAATGAGTTTCGGGGCCCTGACTCAGTTTTGCATG
130 CGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCATG
* *
1197 ATTTTTGGCAGAAAGACTTCTCGAAATATCTATACTCATCCAATCAAATCTCTCAGCCACAATGG
195 ATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGG
1262 ATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAA
260 ATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAA
1327 AAAAATGGAAA
325 AAAAATGGAAA
* *
1338 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGAATTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
* * ** *
1403 TATTGTCGCAAAAAATTG-GGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATC
66 TATTGTGGCAAATAATTGTGGAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCCGAAATC
* * * * *
1467 GTATACTAACCGTCACGGTTTTTAGCTAAAAATGTGTTTCGGAGCCCTGACTCAGTTTTGCATGA
131 GTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCATGA
* * * *
1532 TTTTTGGCAGTAAGACTTCTCGAAATATCTATATTCGTCTAATCAAATCTTTCAACCACAATGGA
196 TTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGA
* *
1597 TTTACAGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTCATTAGAAATAAATTCAGAAA
261 TTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAA
1662 AAAATGGAAA
326 AAAATGGAAA
1672 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
1 AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
* * *
1737 TATTGTGGCAAATAATTGTGGAAAAACTTTTCGCATTAGTTTTTTACAAAATTTTAGACGAAATC
66 TATTGTGGCAAATAATTGTGGAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCCGAAATC
1802 GTGTACTAAC
131 GTGTACTAAC
1812 ATTAATTCAA
Statistics
Matches: 1395, Mismatches: 69, Indels: 27
0.94 0.05 0.02
Matches are distributed among these distances:
330 4 0.00
331 109 0.08
332 180 0.13
333 32 0.02
334 558 0.40
335 103 0.07
336 409 0.29
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (335 bp):
AACGATATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATAAGATTTTTCTGAG
TATTGTGGCAAATAATTGTGGAAAAACTTTTCGCATAAGTTTTTTGCAAAATTTTAGCCGAAATC
GTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCATGA
TTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGA
TTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAA
AAAATGGAAA
Found at i:1971 original size:62 final size:64
Alignment explanation
Indices: 1900--2026 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
1890 TTTCAAAATT
* * *
1900 AACATTGACATTATATTACAC-A-ATATGCAACTTAAAATATGTTTCAAACAAAACTTCAACCC
1 AACACTGACATTATATTACACAATATATACAACTTAAAATATATTTCAAACAAAACTTCAACCC
*
1962 AACACTGACATTATATTACACAATATATATAACTTAAAATATATTTCAAACAAAACTTCAACCC
1 AACACTGACATTATATTACACAATATATACAACTTAAAATATATTTCAAACAAAACTTCAACCC
2026 A
1 A
2027 TGTGTGGAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 20 0.34
63 1 0.02
64 38 0.64
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.29
Consensus pattern (64 bp):
AACACTGACATTATATTACACAATATATACAACTTAAAATATATTTCAAACAAAACTTCAACCC
Found at i:2060 original size:2 final size:2
Alignment explanation
Indices: 2053--2082 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2043 CAAATTACTA
2053 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2083 AAGTTGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4647 original size:73 final size:73
Alignment explanation
Indices: 4504--4648 Score: 213
Period size: 73 Copynumber: 2.0 Consensus size: 73
4494 CTCCTGTTAC
* * *
4504 TACTTGATGAATACACACATATTTATTAAAAAAAAAGTAATTGATATATATGGTGCCACTTATCA
1 TACTCGATGAATACACACATATTTATTAAAAAAAAAG-AAGTAATATATATGGTGCCACTTATCA
4569 ATTATATAT
65 ATTATATAT
4578 TACTCGATGAATACACACATATTTATATAAAAAAAAAG-AGTAATATATATGGTGCCA-TATATC
1 TACTCGATGAATACACACATATTTAT-TAAAAAAAAAGAAGTAATATATATGGTGCCACT-TATC
*
4641 AGTTATAT
64 AATTATAT
4649 CATGCTACAT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
72 1 0.02
73 28 0.43
74 25 0.38
75 11 0.17
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (73 bp):
TACTCGATGAATACACACATATTTATTAAAAAAAAAGAAGTAATATATATGGTGCCACTTATCAA
TTATATAT
Found at i:5302 original size:20 final size:21
Alignment explanation
Indices: 5274--5317 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5264 TTGTTAACAC
5274 TAAACAAAAA-AATTATAGCT
1 TAAACAAAAATAATTATAGCT
*
5294 TAAATAAAAATAATTATAGCT
1 TAAACAAAAATAATTATAGCT
5315 TAA
1 TAA
5318 TTATTGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAACAAAAATAATTATAGCT
Found at i:7095 original size:21 final size:20
Alignment explanation
Indices: 7071--7109 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
7061 TTTAGTCACT
*
7071 AAACCTTTAATTTGCTTTAAA
1 AAACCCTTAATTTG-TTTAAA
7092 AAACCCTTAATTTGTTTA
1 AAACCCTTAATTTGTTTA
7110 GATGGCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (20 bp):
AAACCCTTAATTTGTTTAAA
Found at i:10071 original size:16 final size:15
Alignment explanation
Indices: 10046--10075 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10036 TTTATTTATC
10046 TATATATATGATATT
1 TATATATATGATATT
10061 TATATTATATGATAT
1 TATA-TATATGATAT
10076 ATAATGGTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TATATATATGATATT
Found at i:13745 original size:22 final size:23
Alignment explanation
Indices: 13697--13747 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
13687 TAATATATAT
** * *
13697 ATATATAGCAGTTTTTTTTTAAT
1 ATATATAGCAGTTAGTTTTCAAA
13720 ATATATAGCA-TTAGTTTTCAAA
1 ATATATAGCAGTTAGTTTTCAAA
13742 ATATAT
1 ATATAT
13748 TTTTGGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (23 bp):
ATATATAGCAGTTAGTTTTCAAA
Found at i:20359 original size:11 final size:11
Alignment explanation
Indices: 20343--20367 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20333 AATTAGAATC
20343 TCAAGTTCTAA
1 TCAAGTTCTAA
20354 TCAAGTTCTAA
1 TCAAGTTCTAA
20365 TCA
1 TCA
20368 CGAAAGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (11 bp):
TCAAGTTCTAA
Found at i:21713 original size:60 final size:60
Alignment explanation
Indices: 21555--21714 Score: 194
Period size: 60 Copynumber: 2.7 Consensus size: 60
21545 GTGTCTGTTT
* * * ** ** * *
21555 AAATAAGGACCTAACGTTTACCAAAATGCTCAAATAAGAATTTGATCTTTTAATTTGGTC
1 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCCGACCTTTTAATTTGGCC
* * *
21615 AAATAAGGGTCTAATTTTTGCAAAAATGCTCAAATAAGGGTCCGACCTTTTAATTTGGCC
1 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCCGACCTTTTAATTTGGCC
* *
21675 AAATAAGGGCCTAATGTTTGCCAAAATGTTAAAATAAGGG
1 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGG
21715 CCTGGCGTTG
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 83 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (60 bp):
AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCCGACCTTTTAATTTGGCC
Found at i:21834 original size:60 final size:60
Alignment explanation
Indices: 21759--21896 Score: 204
Period size: 60 Copynumber: 2.3 Consensus size: 60
21749 TGACGCCAAG
* *
21759 CCCTTATTTGAGCATTTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAAA
1 CCCTTATTTGAGCATTTTTGATAACGTTAAGCCCTTATTTGACCAAATTAAAAGATCAAA
* * * *
21819 CCCTTATTTGAGCATTTTTTATAACGTTAAGCTCTTATTTGATCAAATTAAAAGTTCAAA
1 CCCTTATTTGAGCATTTTTGATAACGTTAAGCCCTTATTTGACCAAATTAAAAGATCAAA
* *
21879 CCTTTATTTAAGCATTTT
1 CCCTTATTTGAGCATTTT
21897 GACAAACATT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTTGATAACGTTAAGCCCTTATTTGACCAAATTAAAAGATCAAA
Found at i:21914 original size:60 final size:60
Alignment explanation
Indices: 21759--21920 Score: 175
Period size: 60 Copynumber: 2.7 Consensus size: 60
21749 TGACGCCAAG
* * * * * *
21759 CCCTTATTTGAGCATTTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAAA
1 CCCTTATTTAAGCATTTTTGAAAACATTAAGCTCTTATTTGACCAAATTAAAAGATCAAA
* * * * * *
21819 CCCTTATTTGAGCATTTTTTATAACGTTAAGCTCTTATTTGATCAAATTAAAAGTTCAAA
1 CCCTTATTTAAGCATTTTTGAAAACATTAAGCTCTTATTTGACCAAATTAAAAGATCAAA
*
21879 CCTTTATTTAAGCA-TTTTGACAAACATT-AGACTCTTATTTGA
1 CCCTTATTTAAGCATTTTTGA-AAACATTAAG-CTCTTATTTGA
21921 GCAATTAGCA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
59 7 0.08
60 82 0.92
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.40
Consensus pattern (60 bp):
CCCTTATTTAAGCATTTTTGAAAACATTAAGCTCTTATTTGACCAAATTAAAAGATCAAA
Done.