Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013510.1 Corchorus olitorius cultivar O-4 contig13543, 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: 41910
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4767 original size:42 final size:42
Alignment explanation
Indices: 4720--4799 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
4710 AGAGGATCAA
* * * *
4720 TGAGAAAGGTCAATCATCCGAGGAGAGGAAAGATGAGATAGC
1 TGAGAAAGGTCAACCATCAGAAGAGAAGAAAGATGAGATAGC
* *
4762 TGAGAAGGGTCAACCATCAGAAGAGAAGAAGGATGAGA
1 TGAGAAAGGTCAACCATCAGAAGAGAAGAAAGATGAGA
4800 CAGTTGCCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.34, T:0.12
Consensus pattern (42 bp):
TGAGAAAGGTCAACCATCAGAAGAGAAGAAAGATGAGATAGC
Found at i:9177 original size:27 final size:28
Alignment explanation
Indices: 9111--9181 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
9101 TGTGAACTTA
* *
9111 AAATGACCACAATGCCCCTTGAGTGTGC
1 AAATGACCAAAATGCCCCTGGAGTGTGC
*
9139 AAATGACCAAAATGCCCCTGGA-TGTTC
1 AAATGACCAAAATGCCCCTGGAGTGTGC
*
9166 AAATGACTAAAATGCC
1 AAATGACCAAAATGCC
9182 TTTGAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 19 0.49
28 20 0.51
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGAGTGTGC
Found at i:11196 original size:21 final size:21
Alignment explanation
Indices: 11144--11197 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
11134 GGGATTGGAG
* *
11144 TATTTA-TTTATCTTGTTGCT
1 TATTTATTTTATTTTCTTGCT
*
11164 TAATTT-TATTATTTTCTTGCT
1 T-ATTTATTTTATTTTCTTGCT
11185 TATTTATTTTATT
1 TATTTATTTTATT
11198 GTTACACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.69
Consensus pattern (21 bp):
TATTTATTTTATTTTCTTGCT
Found at i:15746 original size:21 final size:20
Alignment explanation
Indices: 15721--15770 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
15711 GGGATTGCAG
*
15721 TATTTATTTATCTTGTTGCT
1 TATTTATTTATCTTCTTGCT
*
15741 TAATTT-TATTATTTTCTTGCT
1 T-ATTTAT-TTATCTTCTTGCT
15762 TATTTATTT
1 TATTTATTT
15771 TGTTGTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (20 bp):
TATTTATTTATCTTCTTGCT
Found at i:22779 original size:67 final size:67
Alignment explanation
Indices: 22649--23143 Score: 698
Period size: 67 Copynumber: 7.4 Consensus size: 67
22639 CCCTTTCACT
* * * * * * * *
22649 GAAATGGTATTTTTGGAAACATAAAATA--GAGCTTATATGCAAGAAGACAAAAACGACCCTTCG
1 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAA-AAGACGAAAATGACCCTTCG
22712 ACC
65 ACC
* *
22715 GAAAGGGTATTTTTAGAAGTAGAAAATACTAAA-TTGAAATGCAAAAGACGAAAATGACCCTTCG
1 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTT-AAATGCAAAAGACGAAAATGACCCTTCG
22779 ACC
65 ACC
* * * * * * *
22782 GAAAAGGTATTCTTGAAAATAGAGAATA--GAGCTTATATGCAAGAAGAC-AAAA-GCAACCCTT
1 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAA-AAGACGAAAATG--ACCCTT
22843 CGACC
63 CGACC
*
22848 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGATGAAAATGACCCTTCGA
1 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCTTCGA
22913 CC
66 CC
* *
22915 GAAAGGGTATTTTTGGAAATAGAAAATACCAAACTTAAATGCAACAGACGAAAATGACCCTTCGA
1 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCTTCGA
22980 CC
66 CC
22982 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCTTCGA
1 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCTTCGA
23047 CC
66 CC
*
23049 GAAAGGGTATTTTTCGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCTTCGA
1 GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCTTCGA
23114 CC
66 CC
*
23116 GAAAGGGTATTTTTCGAAATAGAAAATA
1 GAAAGGGTATTTTTGGAAATAGAAAATA
23144 GAGCTTTACT
Statistics
Matches: 385, Mismatches: 33, Indels: 21
0.88 0.08 0.05
Matches are distributed among these distances:
64 1 0.00
65 12 0.03
66 65 0.17
67 283 0.74
68 23 0.06
69 1 0.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.22
Consensus pattern (67 bp):
GAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCTTCGA
CC
Found at i:26363 original size:194 final size:194
Alignment explanation
Indices: 25901--26484 Score: 1161
Period size: 194 Copynumber: 3.0 Consensus size: 194
25891 AATGGTTGAT
25901 TGATTGGACTACTTTTGTATGCTGAAATGTGCTAAAATGTGTGCTTTTGGAATGCAAATATATCA
1 TGATTGGACTACTTTTGTATGCTGAAATGTGCTAAAATGTGTGCTTTTGGAATGCAAATATATCA
25966 TTGTATGCCAAGTAATCATGCTACAATGCTATGCAATTTTGACTTTGAAGTGTAGTGATGAAGAT
66 TTGTATGCCAAGTAATCATGCTACAATGCTATGCAATTTTGACTTTGAAGTGTAGTGATGAAGAT
26031 GTT-AAAAAAATGCTGATGGATTTACCTACATGTAAATTAAATGTGCTGGAAATTAAATGTCAG
131 GTTAAAAAAAATGCTGATGGATTTACCTACATGTAAATTAAATGTGCTGGAAATTAAATGTCAG
26094 TGATTGGACTACTTTTGTATGCTGAAATGTGCTAAAATGTGTGCTTTTGGAATGCAAATATATCA
1 TGATTGGACTACTTTTGTATGCTGAAATGTGCTAAAATGTGTGCTTTTGGAATGCAAATATATCA
26159 TTGTATGCCAAGTAATCATGCTACAATGCTATGCAATTTTGACTTTGAAGTGTAGTGATGAAGAT
66 TTGTATGCCAAGTAATCATGCTACAATGCTATGCAATTTTGACTTTGAAGTGTAGTGATGAAGAT
26224 GTTAAAAAAAATGCTGATGGATTTACCTACATGTAAATTAAATGTGCTGGAAATTAAATGTCAG
131 GTTAAAAAAAATGCTGATGGATTTACCTACATGTAAATTAAATGTGCTGGAAATTAAATGTCAG
26288 TGATTGGACTACTTTTGTATGCTGAAATGTGCTAAAATGTGTGCTTTTGGAATGCAAATATATCA
1 TGATTGGACTACTTTTGTATGCTGAAATGTGCTAAAATGTGTGCTTTTGGAATGCAAATATATCA
26353 TTGTATGCCAAGTAATCATGCTACAATGCTATGCAATTTTGACTTTGAAGTGTAGTGATGAAGAT
66 TTGTATGCCAAGTAATCATGCTACAATGCTATGCAATTTTGACTTTGAAGTGTAGTGATGAAGAT
26418 GTTAAAAAAAATGCTGATGGATTTACCTACATGTAAATTAAATGTGCTGGAAATTAAATGTCAG
131 GTTAAAAAAAATGCTGATGGATTTACCTACATGTAAATTAAATGTGCTGGAAATTAAATGTCAG
26482 TGA
1 TGA
26485 GGTTGTTTGG
Statistics
Matches: 390, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
193 133 0.34
194 257 0.66
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (194 bp):
TGATTGGACTACTTTTGTATGCTGAAATGTGCTAAAATGTGTGCTTTTGGAATGCAAATATATCA
TTGTATGCCAAGTAATCATGCTACAATGCTATGCAATTTTGACTTTGAAGTGTAGTGATGAAGAT
GTTAAAAAAAATGCTGATGGATTTACCTACATGTAAATTAAATGTGCTGGAAATTAAATGTCAG
Found at i:28613 original size:90 final size:89
Alignment explanation
Indices: 28467--28742 Score: 286
Period size: 90 Copynumber: 3.1 Consensus size: 89
28457 CTGAATCAAA
* * * *
28467 CTGAACTGTTTAAAAATGTGCTGCACCGAGCTCACTGAACCCAATCTTGAAGAAATAATGTACCG
1 CTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCG
28532 CATCAACTTGATTCACCGAATTACC
66 CATCAA-TTGATTCACCGAATTACC
* * * *
28557 CTGAACTGTTTGAAAATGTGATGCACCGAGCTCACCGAATCCGATCTTGACA-AAATATTGCACT
1 CTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCCAATCTTGA-AGAAATAATGCACC
* * *
28621 GTACCAAATTGATTCACCGAATCACC
65 GCATC-AATTGATTCACCGAATTACC
* ** * * * * *
28647 CT-AATCTATTTGAAAACATGCTGCCCCAAGCTCACCAAACTCCAATTTTAAAGAAATAATGCAC
1 CTGAA-CTGTTTGAAAATGTGCTGCACCGAGCTCACCGAA-TCCAATCTTGAAGAAATAATGCAC
* * *
28711 CGCATTAATATGATTCACTGAATTATC
64 CGCATCAAT-TGATTCACCGAATTACC
28738 CTGAA
1 CTGAA
28743 GAAAATGAAT
Statistics
Matches: 150, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
89 2 0.01
90 107 0.71
91 39 0.26
92 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (89 bp):
CTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCG
CATCAATTGATTCACCGAATTACC
Found at i:31983 original size:15 final size:16
Alignment explanation
Indices: 31957--31987 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
31947 ACAGAGGGTT
31957 AAGAAGAACAATTAAA
1 AAGAAGAACAATTAAA
31973 AAGAA-AACAATTAAA
1 AAGAAGAACAATTAAA
31988 CTAGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (16 bp):
AAGAAGAACAATTAAA
Found at i:34076 original size:15 final size:16
Alignment explanation
Indices: 34052--34091 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
34042 AGAGGTTGAA
*
34052 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
34067 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
34083 AGAAAACAA
1 AGAAAACAA
34092 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.