Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021430.1 Corchorus olitorius cultivar O-4 contig21463, 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: 26884
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Found at i:1137 original size:103 final size:101
Alignment explanation
Indices: 1020--1258 Score: 345
Period size: 103 Copynumber: 2.4 Consensus size: 101
1010 TTTGGTAAAT
* *
1020 ATTTGTAATTAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTGTAATAAAAA
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTATAATAAAAA
* **
1085 TGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
66 TGTAATCTTTAAACAAAAAGATGAG-ACCTTTGTTTG
1122 ATTTGTAATAAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTATAATAAAA
1 ATTTGTAAT-AAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTATAATAAAA
* *
1187 ATGTGATCTTTAAGCAAAAAGATGAGACCTTTGTTTG
65 ATGTAATCTTTAAACAAAAAGATGAGACCTTTGTTTG
* * * * *
1224 ATTTATGATAAAATTATAATCTTT-AATTAAAAGAT
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGAT
1259 TGAACCTTTT
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
100 10 0.08
101 13 0.10
102 25 0.20
103 76 0.61
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.41
Consensus pattern (101 bp):
ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTGATTTATAATAAAAA
TGTAATCTTTAAACAAAAAGATGAGACCTTTGTTTG
Found at i:1158 original size:52 final size:51
Alignment explanation
Indices: 1020--1258 Score: 347
Period size: 51 Copynumber: 4.7 Consensus size: 51
1010 TTTGGTAAAT
*
1020 ATTTGTAATTAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
1071 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
1122 ATTTGTAATAAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
1 ATTTGTAAT-AAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
* * * * **
1174 ATTTATAATAAAAATGTGATCTTTAAGCAAAAAGATGAG-ACCTTTGTTTG
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
* * * * *
1224 ATTTATGATAAAATTATAATCTTT-AATTAAAAGAT
1 ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGAT
1259 TGAACCTTTT
Statistics
Matches: 173, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
49 8 0.05
50 29 0.17
51 86 0.50
52 50 0.29
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.41
Consensus pattern (51 bp):
ATTTGTAATAAAAATGTAATCTTTAAACTAAAAGATGAGAATTTTTGTTTG
Found at i:1337 original size:50 final size:50
Alignment explanation
Indices: 1245--1375 Score: 219
Period size: 50 Copynumber: 2.6 Consensus size: 50
1235 AATTATAATC
*
1245 TTTAATTAAAAGATTGAACCTTTTAA-ACAATTTGTAAATAAAGGTTGGACT
1 TTTAATTAAAAGATTGAA-CTTTTAAGA-AATTTGTAAATAAAGGTTGAACT
1296 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGAACT
1 TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGAACT
*
1346 TTTAATTAAAAGATTAAACTTTTAAGAAAT
1 TTTAATTAAAAGATTGAACTTTTAAGAAAT
1376 CTATACCTAA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
50 58 0.75
51 19 0.25
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.38
Consensus pattern (50 bp):
TTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGAACT
Found at i:6979 original size:38 final size:36
Alignment explanation
Indices: 6886--7005 Score: 91
Period size: 38 Copynumber: 3.2 Consensus size: 36
6876 CGCCAATAAA
* * *
6886 ATATATAATATTTTTATATTTTATTTTATATATAATAT
1 ATATATAA-GTTTTTA-ATTTTATTTTATTTATAATTT
* **
6924 ATCTA-AAGATTAATAATTTTAGTTTTAATTTATAATTT
1 ATATATAAG-TTTTTAATTTTA-TTTT-ATTTATAATTT
*
6962 ATATATAAGTTTTTAATTTTAATCTTTCA-TAATAATTT
1 ATATATAAGTTTTTAATTTT-AT-TTT-ATTTATAATTT
7000 ATATAT
1 ATATAT
7006 TTATATTTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
36 6 0.09
37 10 0.15
38 41 0.63
39 8 0.12
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (36 bp):
ATATATAAGTTTTTAATTTTATTTTATTTATAATTT
Found at i:7216 original size:11 final size:12
Alignment explanation
Indices: 7200--7230 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
7190 TCTCAAAATT
7200 AAAACCGA-TAA
1 AAAACCGACTAA
7211 AAAACCGACTAA
1 AAAACCGACTAA
7223 AAAACCGA
1 AAAACCGA
7231 AAACCGACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.61, C:0.23, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAACCGACTAA
Found at i:10768 original size:51 final size:50
Alignment explanation
Indices: 10603--10928 Score: 408
Period size: 50 Copynumber: 6.5 Consensus size: 50
10593 CAAACACTAG
* * *
10603 TTTGTAAATAAAGGTTGTACTTTTAATTAAAAGATTGAACTTTTAAGAAA
1 TTTGTAAATAAAGATTGGACTTTTAATTAAAAGATTGAACTTTTAAGTAA
* *
10653 TTTGTAAATAAAGGTTGGACTTTTAATTAAAAGATTGAACTTTTAAGAAA
1 TTTGTAAATAAAGATTGGACTTTTAATTAAAAGATTGAACTTTTAAGTAA
* *
10703 TTGGTAAATAAAGATTGGACTTTTAATTAAAAGATTGAAGCTTTTAAGTAG
1 TTTGTAAATAAAGATTGGACTTTTAATTAAAAGATTGAA-CTTTTAAGTAA
* **
10754 TTTGTAAATAAAGATTGG-GTTTTAGATTAAAAGATCAAACTTTTAAGTAA
1 TTTGTAAATAAAGATTGGACTTTTA-ATTAAAAGATTGAACTTTTAAGTAA
* *
10804 TTTGTAAATAAAGATTGGATTTTTAATGAAAAG-TTGAAACCTTTTAAGTAA
1 TTTGTAAATAAAGATTGGACTTTTAATTAAAAGATTG-AA-CTTTTAAGTAA
* * * * *
10855 TTTGTAAATAAA-AATGAAATCTTTAAGTTAAAATATTGAACTTTTAACTAA
1 TTTGTAAATAAAGATTGGACT-TTTAA-TTAAAAGATTGAACTTTTAAGTAA
*
10906 TTTGTAAATAAAGA-TGGAATTTT
1 TTTGTAAATAAAGATTGGACTTTT
10929 TGATGGGCTT
Statistics
Matches: 246, Mismatches: 21, Indels: 18
0.86 0.07 0.06
Matches are distributed among these distances:
49 1 0.00
50 136 0.55
51 98 0.40
52 8 0.03
53 3 0.01
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (50 bp):
TTTGTAAATAAAGATTGGACTTTTAATTAAAAGATTGAACTTTTAAGTAA
Found at i:10795 original size:101 final size:100
Alignment explanation
Indices: 10606--10928 Score: 366
Period size: 101 Copynumber: 3.2 Consensus size: 100
10596 ACACTAGTTT
* * * *
10606 GTAAATAAAGGTTGTACTTTTAATTAAAAGATTGAACTTTTAAGAAATTTGTAAATAAAGGTTGG
1 GTAAATAAAGATTGGACTTTTAATTAAAAGATTGAACTTTTAAGTAATTTGTAAATAAAGATTGG
**
10671 ACTTTTAATTAAAAGATTGAACTTTTAAGAAATTG
66 ACTTTTAATTAAAAGATCAAACTTTTAAGAAATTG
*
10706 GTAAATAAAGATTGGACTTTTAATTAAAAGATTGAAGCTTTTAAGTAGTTTGTAAATAAAGATTG
1 GTAAATAAAGATTGGACTTTTAATTAAAAGATTGAA-CTTTTAAGTAATTTGTAAATAAAGATTG
* * *
10771 G-GTTTTAGATTAAAAGATCAAACTTTTAAGTAATTT
65 GACTTTTA-ATTAAAAGATCAAACTTTTAAGAAATTG
* * *
10807 GTAAATAAAGATTGGATTTTTAATGAAAAG-TTGAAACCTTTTAAGTAATTTGTAAATAAA-AAT
1 GTAAATAAAGATTGGACTTTTAATTAAAAGATTG-AA-CTTTTAAGTAATTTGTAAATAAAGATT
* * * ** ** *
10870 GAAATCTTTAAGTTAAAATATTGAACTTTTAACTAATTT
64 GGACT-TTTAA-TTAAAAGATCAAACTTTTAAGAAATTG
*
10909 GTAAATAAAGA-TGGAATTTT
1 GTAAATAAAGATTGGACTTTT
10929 TGATGGGCTT
Statistics
Matches: 195, Mismatches: 22, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
100 45 0.23
101 112 0.57
102 38 0.19
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (100 bp):
GTAAATAAAGATTGGACTTTTAATTAAAAGATTGAACTTTTAAGTAATTTGTAAATAAAGATTGG
ACTTTTAATTAAAAGATCAAACTTTTAAGAAATTG
Found at i:11562 original size:48 final size:48
Alignment explanation
Indices: 11556--12016 Score: 582
Period size: 48 Copynumber: 9.4 Consensus size: 48
11546 TATTTCATTC
* *
11556 ACATTTTATTCCCGTTTTGCCCTTCCCAGTCAGAAGGTGTTGTTTTCA
1 ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
* * ** * *
11604 ATATTTTATTCCCGTTTTGCCCTTCCTGGTCGGAAGGTGTTCTTTCCA
1 ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
** * **
11652 ACATTTTATTCCCATTTCGCCCTTCCTGGTCGGAAGGTGTTGTTTTCA
1 ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
* *
11700 ACATTTTATTCCTGTTTTGCCATTCCTAGTCGGAAGGTGTTGTTTTCA
1 ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
* *
11748 ACATTGTATTCCCGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
1 ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
* *
11796 ACGTTTTATTCCTCTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
1 ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
* * *
11844 ACACTTTATTCCTGTTTTACCCTTCTCAGTCGGAAGGTGTTGTTTTCA
1 ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
*
11892 ACATTGTATT-CTCGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATATTTCA
1 ACATTTTATTCCT-GTTTTGCCCTTCCCAGTCGGAAGGTGTTG-------T-TTTCA
*
11948 TTCACATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCA
1 ---ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
*
11999 ACATTTTATTCCTATTTT
1 ACATTTTATTCCTGTTTT
12017 CATTGTTTTA
Statistics
Matches: 364, Mismatches: 36, Indels: 26
0.85 0.08 0.06
Matches are distributed among these distances:
47 2 0.01
48 311 0.85
51 5 0.01
52 1 0.00
55 1 0.00
56 5 0.01
59 37 0.10
60 2 0.01
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (48 bp):
ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCA
Found at i:12016 original size:59 final size:59
Alignment explanation
Indices: 11892--12009 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 59
11882 GTTGTTTTCA
* *
11892 ACATTGTATT-CTCGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATATTTCATTC
1 ACATTTTATTCCT-GTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAACATTTCATTC
* *
11951 ACATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTC
1 ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAACATTTCATTC
12010 CTATTTTCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 52 0.96
60 2 0.04
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (59 bp):
ACATTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAACATTTCATTC
Found at i:12063 original size:68 final size:68
Alignment explanation
Indices: 11954--12086 Score: 185
Period size: 68 Copynumber: 2.0 Consensus size: 68
11944 TTCATTCACA
** *
11954 TTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCTATTTTCA
1 TTTTATTCCAATTTTGCCATTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCTATTTTCA
12019 TTG
66 TTG
* * ** * *
12022 TTTTATTCCAATTTTGTCATTCCCGGTCGGGAGGTGTTGTTTTCAATGTTTTATTCTTGTTTTCA
1 TTTTATTCCAATTTTGCCATTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCTATTTTCA
12087 ATGTCTTGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.14, C:0.18, G:0.17, T:0.51
Consensus pattern (68 bp):
TTTTATTCCAATTTTGCCATTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCTATTTTCA
TTG
Found at i:12083 original size:20 final size:20
Alignment explanation
Indices: 12058--12117 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
12048 TCGGGAGGTG
12058 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATGTTTTATTC
* *
12078 TTGTTTTCAATGTCTTGTTC
1 TTGTTTTCAATGTTTTATTC
*
12098 TTGTCTTCAATGTTTTATTC
1 TTGTTTTCAATGTTTTATTC
12118 CCGTTTGCCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.13, C:0.13, G:0.12, T:0.62
Consensus pattern (20 bp):
TTGTTTTCAATGTTTTATTC
Found at i:12174 original size:20 final size:20
Alignment explanation
Indices: 12145--12184 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12135 TCGGAAGGTG
* *
12145 TTGTTTTCAATCTTTTATTC
1 TTGTTCTCAACCTTTTATTC
12165 TTGTTCTCAACCTTTTATTC
1 TTGTTCTCAACCTTTTATTC
12185 CCGCTTTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.20, G:0.05, T:0.60
Consensus pattern (20 bp):
TTGTTCTCAACCTTTTATTC
Found at i:18461 original size:86 final size:86
Alignment explanation
Indices: 18316--18503 Score: 376
Period size: 86 Copynumber: 2.2 Consensus size: 86
18306 CCATCAGTCC
18316 CACCACCCCAACCTTTTATTCCCAAACCACCAACGGTACACTTCCATCACACCTGCAAAAGTCAC
1 CACCACCCCAACCTTTTATTCCCAAACCACCAACGGTACACTTCCATCACACCTGCAAAAGTCAC
18381 CGGTGGCATCTTTGATTATAA
66 CGGTGGCATCTTTGATTATAA
18402 CACCACCCCAACCTTTTATTCCCAAACCACCAACGGTACACTTCCATCACACCTGCAAAAGTCAC
1 CACCACCCCAACCTTTTATTCCCAAACCACCAACGGTACACTTCCATCACACCTGCAAAAGTCAC
18467 CGGTGGCATCTTTGATTATAA
66 CGGTGGCATCTTTGATTATAA
18488 CACCACCCCAACCTTT
1 CACCACCCCAACCTTT
18504 CCCTTATAAG
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 102 1.00
ACGTcount: A:0.30, C:0.38, G:0.10, T:0.23
Consensus pattern (86 bp):
CACCACCCCAACCTTTTATTCCCAAACCACCAACGGTACACTTCCATCACACCTGCAAAAGTCAC
CGGTGGCATCTTTGATTATAA
Found at i:23694 original size:1 final size:1
Alignment explanation
Indices: 23654--23680 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
23644 CAGATGCAGT
23654 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
23681 CTCGGCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.