Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017922.1 Corchorus olitorius cultivar O-4 contig17955, 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: 11564
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:845 original size:3 final size:3
Alignment explanation
Indices: 830--906 Score: 66
Period size: 3 Copynumber: 25.7 Consensus size: 3
820 AAGTGATGGC
* * * *
830 GAT GAT GAG GAT GAT GAC GAG GAT GAT GAT GAT GAT GACG GA- GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA-T GAT GAT
* * * *
875 GAC AAT GAG GAT GAT GAT GAT GAT GGT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
907 CCATGAGGAG
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.34, C:0.04, G:0.39, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:888 original size:30 final size:29
Alignment explanation
Indices: 830--915 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
820 AAGTGATGGC
* * *
830 GATGATGAGGATGATGACGAGGATGATGAT
1 GATGATGAGGA-GATGACAATGAGGATGAT
860 GATGATGACGGAGATGACAATGAGGATGAT
1 GATGATGA-GGAGATGACAATGAGGATGAT
* *
890 GATGATGATGGTGATGACCATGAGGA
1 GATGATGA-GGAGATGACAATGAGGA
916 GATTTAGCTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 46 0.94
31 3 0.06
ACGTcount: A:0.34, C:0.06, G:0.38, T:0.22
Consensus pattern (29 bp):
GATGATGAGGAGATGACAATGAGGATGAT
Found at i:2161 original size:45 final size:45
Alignment explanation
Indices: 2107--2210 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
2097 AGGCAGCCTC
* * * **
2107 TTATTTTGTATAGGTC-CTTAATTTGCCATTATCTAGACGAGGCAT
1 TTATTTTGTATAGGTCAC-TAACTTGCAATGATCTAGAAAAGGCAT
* *
2152 TTATTTTGTATAGATCACTAACTTGCAATGATCTAGAAAAGGCCT
1 TTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCAT
2197 TTATTTTGTATAGG
1 TTATTTTGTATAGG
2211 GTTTAGTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (45 bp):
TTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCAT
Found at i:2516 original size:24 final size:24
Alignment explanation
Indices: 2484--2533 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2474 TCATAGATAG
*
2484 AATTCCGTTTTTGATTCTATTGCA
1 AATTCCGTTTTTGATTCCATTGCA
* *
2508 AATTTCGTTTTTGATTCCGTTGCA
1 AATTCCGTTTTTGATTCCATTGCA
2532 AA
1 AA
2534 GTACTCAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (24 bp):
AATTCCGTTTTTGATTCCATTGCA
Found at i:3519 original size:22 final size:23
Alignment explanation
Indices: 3494--3540 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
3484 AATATATTAC
*
3494 AAGAAATAAAATTATAA-TAAAA
1 AAGAAATAAAATTAAAATTAAAA
3516 AAGAAATAAAATTAAAATTAAAA
1 AAGAAATAAAATTAAAATTAAAA
3539 AA
1 AA
3541 TAAAATTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (23 bp):
AAGAAATAAAATTAAAATTAAAA
Found at i:3611 original size:22 final size:20
Alignment explanation
Indices: 3576--3616 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
3566 GAAAAAATTC
3576 AATTATGAAAAATAATAAAA
1 AATTATGAAAAATAATAAAA
3596 AATTGATGAAAAAATAATAAA
1 AATT-ATG-AAAAATAATAAA
3617 TTTAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AATTATGAAAAATAATAAAA
Found at i:7159 original size:48 final size:48
Alignment explanation
Indices: 7095--7502 Score: 375
Period size: 48 Copynumber: 8.4 Consensus size: 48
7085 AAGAACAAGT
**
7095 CCTTCCGATGGGGAAGGGCAAAACGGGAATAAAGCATTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACGGGAATAAAGCATTGAAAACAACA
* * * **
7143 CCTTCTGACTGGGAAGGGCAAAA-GAGGAAAAAAAATATTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACG-GG-AATAAAGCATTGAAAACAACA
* *
7192 CCTTCCGACCGGGAAGGGCAAAATGGGAATAGAATG--TTGAAAGCAACA
1 CCTTCCGACCGGGAAGGGCAAAACGGGAATA-AA-GCATTGAAAACAACA
* *
7240 CCTTCCGACCGGGAAGGGCAAAACAGGAATGAAA-TATTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACGGGAAT-AAAGCATTGAAAACAACA
* * ** *
7288 CCTTCCGACCGGGAAGGGCAAGATGGGAATAGAATG--TTGAATGCAATA
1 CCTTCCGACCGGGAAGGGCAAAACGGGAATA-AA-GCATTGAAAACAACA
* * *
7336 CCTTCTGACCGGGAAGGGCAAAACGGGAATGAAA-TATTGAAAACAAAA
1 CCTTCCGACCGGGAAGGGCAAAACGGGAAT-AAAGCATTGAAAACAACA
*
7384 CCTTCCGACCGGGAAGGGCAAAACGGGAATTAAAGCATTGAAAACTGTA-A
1 CCTTCCGACCGGGAAGGGCAAAACGGGAA-TAAAGCATTGAAAAC--AACA
* * * ***
7434 CCTTCCGACTGGGAAGGGGCAACACAGTGAAT-AAGACATTGAAAACTGGGA
1 CCTTCCGACCGGGAA-GGGCAAAAC-GGGAATAAAG-CATTGAAAAC-AACA
*
7485 CCTTCCGACTGGGAAGGG
1 CCTTCCGACCGGGAAGGG
7503 GCATTTTTGG
Statistics
Matches: 303, Mismatches: 35, Indels: 42
0.80 0.09 0.11
Matches are distributed among these distances:
47 2 0.01
48 184 0.61
49 55 0.18
50 22 0.07
51 36 0.12
52 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (48 bp):
CCTTCCGACCGGGAAGGGCAAAACGGGAATAAAGCATTGAAAACAACA
Found at i:7314 original size:96 final size:96
Alignment explanation
Indices: 7095--7413 Score: 462
Period size: 96 Copynumber: 3.3 Consensus size: 96
7085 AAGAACAAGT
** * *
7095 CCTTCCGATGGGGAAGGGCAAAACGGGAATA-AA-GCATTGAAAACAACACCTTCTGACTGGGAA
1 CCTTCCGACCGGGAAGGGCAAAACGGGAATAGAATG--TTGAAAGCAACACCTTCTGACCGGGAA
* **
7158 GGGCAAAAGAGGAAAAAAAATATTGAAAACAACA
64 GGGCAAAACAGG-AATGAAATATTGAAAACAACA
* *
7192 CCTTCCGACCGGGAAGGGCAAAATGGGAATAGAATGTTGAAAGCAACACCTTCCGACCGGGAAGG
1 CCTTCCGACCGGGAAGGGCAAAACGGGAATAGAATGTTGAAAGCAACACCTTCTGACCGGGAAGG
7257 GCAAAACAGGAATGAAATATTGAAAACAACA
66 GCAAAACAGGAATGAAATATTGAAAACAACA
* * * *
7288 CCTTCCGACCGGGAAGGGCAAGATGGGAATAGAATGTTGAATGCAATACCTTCTGACCGGGAAGG
1 CCTTCCGACCGGGAAGGGCAAAACGGGAATAGAATGTTGAAAGCAACACCTTCTGACCGGGAAGG
* *
7353 GCAAAACGGGAATGAAATATTGAAAACAAAA
66 GCAAAACAGGAATGAAATATTGAAAACAACA
7384 CCTTCCGACCGGGAAGGGCAAAACGGGAAT
1 CCTTCCGACCGGGAAGGGCAAAACGGGAAT
7414 TAAAGCATTG
Statistics
Matches: 203, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
96 137 0.67
97 63 0.31
98 2 0.01
99 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.14
Consensus pattern (96 bp):
CCTTCCGACCGGGAAGGGCAAAACGGGAATAGAATGTTGAAAGCAACACCTTCTGACCGGGAAGG
GCAAAACAGGAATGAAATATTGAAAACAACA
Found at i:7392 original size:144 final size:144
Alignment explanation
Indices: 7095--7451 Score: 452
Period size: 144 Copynumber: 2.5 Consensus size: 144
7085 AAGAACAAGT
** *
7095 CCTTCCGATGGGGAAGGGCAAAACGGGAATAAAGCATTGAAAACAACACCTTCTGACTGGGAAGG
1 CCTTCCGACCGGGAAGGGCAAAACGGGAATAAAGCATTGAAAACAACACCTTCCGACTGGGAAGG
*
7160 GCAAAAGAGGAAAAAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAATGGGAATAGA
66 GC-AAAGAGGAAAAAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAGA
* * *
7225 ATGTTGAAAGCAACA
130 ATATTGAAAACAAAA
* * *
7240 CCTTCCGACCGGGAAGGGCAAAACAGGAATGAAA-TATTGAAAACAACACCTTCCGACCGGGAAG
1 CCTTCCGACCGGGAAGGGCAAAACGGGAAT-AAAGCATTGAAAACAACACCTTCCGACTGGGAAG
* * * * ** * *
7304 GGC-AAGATGGGAATAGAATGTTGAATGCAATACCTTCTGACCGGGAAGGGCAAAACGGGAAT-G
65 GGCAAAGA-GGAAAAAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAG
7367 AAATATTGAAAACAAAA
129 -AATATTGAAAACAAAA
*
7384 CCTTCCGACCGGGAAGGGCAAAACGGGAATTAAAGCATTGAAAACTGTA-ACCTTCCGACTGGGA
1 CCTTCCGACCGGGAAGGGCAAAACGGGAA-TAAAGCATTGAAAAC--AACACCTTCCGACTGGGA
7448 AGGG
63 AGGG
7452 GCAACACAGT
Statistics
Matches: 183, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
143 5 0.03
144 89 0.49
145 67 0.37
146 21 0.11
147 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (144 bp):
CCTTCCGACCGGGAAGGGCAAAACGGGAATAAAGCATTGAAAACAACACCTTCCGACTGGGAAGG
GCAAAGAGGAAAAAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAGAA
TATTGAAAACAAAA
Found at i:7539 original size:50 final size:50
Alignment explanation
Indices: 7419--7763 Score: 473
Period size: 50 Copynumber: 6.9 Consensus size: 50
7409 GGAATTAAAG
** *****
7419 CATTGAAAACTGTAACCTTCCGACTGGGAAGGGGCAACACAGTGAATA-AGA
1 CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTG-GAA-AGAGA
7470 CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAGAGA
1 CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAGAGA
*
7520 CATTGGAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAATA-AGA
1 CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAA-AGAGA
*
7570 CATTGAAAACTGGGACCTTCTGACTGGGAAGGGGCATTTTTGGAAAGAGA
1 CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAGAGA
* * * * * *
7620 CATTGGAAACT-GGACTTTCCGACCGGGAATGGGCATTTTT-GTAATAGA
1 CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAGAGA
*
7668 CATTGAAAACTGGGACATTCCGACTGGGAAGGGGCATTTTTGGAAAGAGA
1 CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAGAGA
* *
7718 CATTGAAAACTGGGACTTTCCGACCGGGAAGGGGCATTTTTGGAAA
1 CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAA
7764 AGTTGTTCGA
Statistics
Matches: 264, Mismatches: 25, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
48 16 0.06
49 53 0.20
50 159 0.60
51 36 0.14
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (50 bp):
CATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAGAGA
Found at i:7703 original size:148 final size:150
Alignment explanation
Indices: 7467--7763 Score: 465
Period size: 148 Copynumber: 2.0 Consensus size: 150
7457 ACAGTGAATA
* *
7467 AGACATTGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAGAGACATTGGAAACTG
1 AGACATTGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAAAGAGACATTGAAAACTG
* * *
7532 GGACCTTCCGACTGGGAAGGGGCATTTTTGGAATA-AGACATTGAAAACTGGGACCTTCTGACTG
66 GGACATTCCGACTGGGAAGGGGCATTTTTGGAA-AGAGACATTGAAAACTGGGACCTTCCGACCG
7596 GGAAGGGGCATTTTTGGAAAG
130 GGAAGGGGCATTTTTGGAAAG
* * * * *
7617 AGACATTGGAAACT-GGACTTTCCGACCGGGAATGGGCATTTTT-GTAATAGACATTGAAAACTG
1 AGACATTGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAAAGAGACATTGAAAACTG
*
7680 GGACATTCCGACTGGGAAGGGGCATTTTTGGAAAGAGACATTGAAAACTGGGACTTTCCGACCGG
66 GGACATTCCGACTGGGAAGGGGCATTTTTGGAAAGAGACATTGAAAACTGGGACCTTCCGACCGG
7745 GAAGGGGCATTTTTGGAAA
131 GAAGGGGCATTTTTGGAAA
7764 AGTTGTTCGA
Statistics
Matches: 135, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
147 1 0.01
148 95 0.70
149 26 0.19
150 13 0.10
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (150 bp):
AGACATTGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAAAGAGACATTGAAAACTG
GGACATTCCGACTGGGAAGGGGCATTTTTGGAAAGAGACATTGAAAACTGGGACCTTCCGACCGG
GAAGGGGCATTTTTGGAAAG
Found at i:8676 original size:20 final size:20
Alignment explanation
Indices: 8651--8705 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
8641 CACATTATTC
*
8651 AAAGATTTC-ATCTTTTACTT
1 AAAGA-TTCAATCTTTCACTT
8671 AAAGATTCAATCTTTCACTT
1 AAAGATTCAATCTTTCACTT
*
8691 AAAAATTCAATCTTT
1 AAAGATTCAATCTTT
8706 ATTTACAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (20 bp):
AAAGATTCAATCTTTCACTT
Done.