Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019058.1 Corchorus olitorius cultivar O-4 contig19091, 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: 18496
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:12392 original size:13 final size:13
Alignment explanation
Indices: 12374--12399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12364 CATTTGGAAG
12374 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
12387 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
12400 TTTGGCCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:12532 original size:17 final size:16
Alignment explanation
Indices: 12506--12540 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
12496 ACATGCTTTC
12506 AAAAGATTTTTCAAAA
1 AAAAGATTTTTCAAAA
12522 AAAATGATTTTTCAAAA
1 AAAA-GATTTTTCAAAA
12539 AA
1 AA
12541 TGGTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAAGATTTTTCAAAA
Found at i:12538 original size:15 final size:15
Alignment explanation
Indices: 12506--12552 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
12496 ACATGCTTTC
12506 AAAA-GATTTTTCAAAA
1 AAAATGATTTTTC--AA
12522 AAAATGATTTTTCAA
1 AAAATGATTTTTCAA
*
12537 AAAATG-GTTTTCAA
1 AAAATGATTTTTCAA
12551 AA
1 AA
12553 TTTGTTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.31
15 8 0.28
16 4 0.14
17 8 0.28
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (15 bp):
AAAATGATTTTTCAA
Found at i:14318 original size:36 final size:35
Alignment explanation
Indices: 14175--14374 Score: 287
Period size: 35 Copynumber: 5.7 Consensus size: 35
14165 AGGGCAGTCC
*
14175 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCT
* * * *
14210 TTCTTCAATTTATTTTAGTTGATCCAGGGCGGTCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCT
* * *
14245 TTCTTCAGTTTATCTAAGTTAATCCC--GGCGATCTT
1 TTCTTCAGTTTATTTCAGTTGA-CCCAGGGCGATC-T
14280 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATC-T
14316 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCT
1 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCT
14351 TTCTTCAGTTTATTTCAGTTGACC
1 TTCTTCAGTTTATTTCAGTTGACC
14375 AAGTGATCGG
Statistics
Matches: 149, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
34 9 0.06
35 95 0.64
36 45 0.30
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.43
Consensus pattern (35 bp):
TTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCT
Found at i:16283 original size:35 final size:35
Alignment explanation
Indices: 16216--16901 Score: 750
Period size: 35 Copynumber: 20.0 Consensus size: 35
16206 GCTCAATCAC
* * *
16216 CCAGGGCGGTCTTTCTTCAATTCATTTAAGTTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
*
16251 CTAGGGCGGTCCTTT-TTCAGTTTATTTCAGTTGAT
1 CCAGGGCGGT-CTTTCTTCAGTTTATTTCAGTTGAT
* * * * *
16286 CCAGGGCGATCTTTTCTTCAATTTATTTTACTTGAC
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGAT
*
16322 CCAGGGCGGTCTTTCTTTAGTTTATTTCAGTTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* * *
16357 CGAGGGCAGTCTTTCTTCAGTTTATTTCAGTTGAC
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
16392 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
*
16427 GCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* *
16462 CCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGAC
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGAT
*
16498 CCAGGACGGTCTTTCTTCAGTTTATTTCAGTTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* *
16533 CGAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGA-
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGAT
*
16568 CCTAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAC
1 CC-AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
*
16604 CCAGGGCGGTCTTTCTTCAGTTGATTTCAGTTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
*
16639 CCAGGGCGG--TTT-TTC-------TTCAATTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* * * *
16664 CCAGGGCGATTTTTTCTTTAGTTTA--T---TTGAC
1 CCAGGGCG-GTCTTTCTTCAGTTTATTTCAGTTGAT
* *
16695 CCAGGGCGGTCTTTCTTCAGGTTATTTTAGTTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* *
16730 CCGGGGCGGTTTTTCTTCAGTTTATTTCAGTTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* * *
16765 CTAGGGCGATCTTTTCTTCAGTTTA--T---TTGAC
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGAT
* * * *
16796 CCATGGCGGTATTTCTTCAGGTTATTTCAATTGAT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* *
16831 CCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGAT
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGAT
* ** *
16867 CCTGGGCAATCTTTTCTGCAGTTTATTTCAGTTGA
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGA
16902 CCGCAAATTG
Statistics
Matches: 551, Mismatches: 71, Indels: 57
0.81 0.10 0.08
Matches are distributed among these distances:
25 17 0.03
28 3 0.01
29 2 0.00
30 24 0.04
31 23 0.04
32 5 0.01
33 3 0.01
34 3 0.01
35 310 0.56
36 161 0.29
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (35 bp):
CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
Found at i:16331 original size:71 final size:70
Alignment explanation
Indices: 16216--16901 Score: 750
Period size: 71 Copynumber: 10.0 Consensus size: 70
16206 GCTCAATCAC
* * * *
16216 CCAGGGCGGTCTTTCTTCAATTCATTTAAGTTGATCTAGGGCGGTCCTTT-TTCAGTTTATTTCA
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGT-CTTTCTTCAGTTTATTTCA
16280 GTTGAT
65 GTTGAT
* * * * * *
16286 CCAGGGCGATCTTTTCTTCAATTTATTTTACTTGACCCAGGGCGGTCTTTCTTTAGTTTATTTCA
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCA
16351 GTTGAT
65 GTTGAT
* * *
16357 CGAGGGCAGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
16422 TTGAT
66 TTGAT
* *
16427 GCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCA
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTC-TTTCTTCAGTTTATTTCA
*
16492 GTTGAC
65 GTTGAT
* * *
16498 CCAGGACGGTCTTTCTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTTCTTCAGTTTATTTCA
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTC-TTTCTTCAGTTTATTTCA
16563 GTTGA-
65 GTTGAT
* *
16568 CCTAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTGATTTCA
1 CC-AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCA
16633 GTTGAT
65 GTTGAT
* * * *
16639 CCAGGGCGG--TTT-TTC-------TTCAATTGATCCAGGGCGATTTTTTCTTTAGTTTA--T--
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG-GTCTTTCTTCAGTTTATTTCA
*
16690 -TTGAC
65 GTTGAT
* * * *
16695 CCAGGGCGGTCTTTCTTCAGGTTATTTTAGTTGATCCGGGGCGGTTTTTCTTCAGTTTATTTCAG
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
16760 TTGAT
66 TTGAT
* * * * * *
16765 CTAGGGCGATCTTTTCTTCAGTTTA--T---TTGACCCATGGCGGTATTTCTTCAGGTTATTTCA
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCA
*
16825 ATTGAT
65 GTTGAT
* * * ** *
16831 CCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCCTGGGCAATCTTTTCTGCAGTTTATTTC
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTC-TTTCTTCAGTTTATTTC
16896 AGTTGA
64 AGTTGA
16902 CCGCAAATTG
Statistics
Matches: 527, Mismatches: 61, Indels: 54
0.82 0.10 0.08
Matches are distributed among these distances:
56 13 0.02
58 3 0.01
59 4 0.01
60 16 0.03
61 12 0.02
65 14 0.03
66 72 0.14
67 4 0.01
68 4 0.01
69 1 0.00
70 154 0.29
71 210 0.40
72 20 0.04
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (70 bp):
CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
TTGAT
Found at i:16399 original size:106 final size:104
Alignment explanation
Indices: 16216--16903 Score: 781
Period size: 106 Copynumber: 6.7 Consensus size: 104
16206 GCTCAATCAC
* * * *
16216 CCAGGGCGGTCTTTCTTCAATTCATTTAAGTTGATCTAGGGCGGTCCTTT-TTCAGTTTATTTCA
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGC-GT-CTTTCTTCAGTTTATTTCA
* * * * * *
16280 GTTGATCCAGGGCGATCTTTTCTTCAATTTATTTTACTTGAC
64 GTTGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGAT
* *
16322 CCAGGGCGGTCTTTCTTTAGTTTATTTCAGTTGATCGAGGGCAGTCTTTCTTCAGTTTATTTCAG
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGC-GTCTTTCTTCAGTTTATTTCAG
16387 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
65 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
*
16427 GCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCA
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG-TC-TTTCTTCAGTTTATTTCA
*
16492 GTTGACCCAGGACGGTCTTTCTTCAGTTTATTTCAGTTGAT
64 GTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* *
16533 CGAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGA-CCTAGGGCGGTCTTTCTTCAGTTTATTTC
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCC-AGGGC-GTCTTTCTTCAGTTTATTTC
*
16597 AGTTGACCCAGGGCGGTCTTTCTTCAGTTGATTTCAGTTGAT
63 AGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
*
16639 CCAGGGCGG--TTT-TTC-------TTCAATTGATCCAGGGCGAT-TTT-TTC--TTTAGTTT-A
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG-TCTTTCTTCAGTTTA-TTTCA
* * *
16689 TTTGACCCAGGGCGGTCTTTCTTCAGGTTATTTTAGTTGAT
64 GTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* * *
16730 CCGGGGCGGTTTTTCTTCAGTTTATTTCAGTTGATCTAGGGCGATCTTTTCTTCAGTTTA--T--
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG-TC-TTTCTTCAGTTTATTTCA
* * * *
16791 -TTGACCCATGGCGGTATTTCTTCAGGTTATTTCAATTGAT
64 GTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
* * * * *
16831 CCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCCTGGGCAATCTTTTCTGCAGTTTATTTC
1 CCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGC-GTC-TTTCTTCAGTTTATTTC
16896 AGTTGACC
63 AGTTGACC
16904 GCAAATTGGT
Statistics
Matches: 508, Mismatches: 43, Indels: 61
0.83 0.07 0.10
Matches are distributed among these distances:
91 50 0.10
92 3 0.01
93 6 0.01
94 7 0.01
95 14 0.03
96 2 0.00
101 61 0.12
102 47 0.09
103 7 0.01
104 5 0.01
105 65 0.13
106 204 0.40
107 36 0.07
108 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (104 bp):
CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGTCTTTCTTCAGTTTATTTCAGT
TGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAT
Found at i:16662 original size:25 final size:25
Alignment explanation
Indices: 16629--16677 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
16619 TTCAGTTGAT
* *
16629 TTCAGTTGATCCAGGGCGGTTTTTC
1 TTCAATTGATCCAGGGCGATTTTTC
16654 TTCAATTGATCCAGGGCGATTTTT
1 TTCAATTGATCCAGGGCGATTTTT
16678 TCTTTAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.41
Consensus pattern (25 bp):
TTCAATTGATCCAGGGCGATTTTTC
Found at i:16737 original size:126 final size:129
Alignment explanation
Indices: 16523--16901 Score: 361
Period size: 126 Copynumber: 2.9 Consensus size: 129
16513 TTCAGTTTAT
* * *
16523 TTCAGTTGATCGAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGACCTAGGGCGGTCTTTCTTCA
1 TTCAATTGATCCAGGGCGATCTTTTCTTCAGTTTA-TT-A-TTGACCCAGGGCGGTCTTTCTTCA
* *
16588 GTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTGATTTCAGTTGATCCAGGGCGGT-TTT
63 GGTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTGATTTCAGTTGATCCAGGGCGATCTTT
16652 TC
128 TC
* *
16654 TTCAATTGATCCAGGGCGATTTTTTCTTTAGTTTA-T-TTGACCCAGGGCGGTCTTTCTTCAGGT
1 TTCAATTGATCCAGGGCGATCTTTTCTTCAGTTTATTATTGACCCAGGGCGGTCTTTCTTCAGGT
* * * * * *
16717 TATTTTAGTTGATCCGGGGCGGTTTTTCTTCAGTTTATTTCAGTTGATCTAGGGCGATCTTTTC
66 TATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTGATTTCAGTTGATCCAGGGCGATCTTTTC
* * * * * * * *
16781 TTCAGTTTATTTGACCCATGGCGGT-ATTTCTTCAGGTTATTTCAATTGATCCAGGGTGATCTTT
1 TTCA----A-TTGATCCAGGGCGATCTTTTCTTCAGTTTA-TT--ATTGACCCAGGGCGGTC-TT
* * * ** * *
16845 TCTTCAGTTTATTTCAGTTGATCCTGGGCAATCTTTTCTGCAGTTTATTTCAGTTGA
57 TCTTCAGGTTATTTCAGTTGACCCAGGGCGGTC-TTTCTTCAGTTGATTTCAGTTGA
16902 CCGCAAATTG
Statistics
Matches: 206, Mismatches: 29, Indels: 19
0.81 0.11 0.07
Matches are distributed among these distances:
126 76 0.37
127 9 0.04
129 1 0.00
131 43 0.21
132 12 0.06
133 1 0.00
136 13 0.06
137 29 0.14
138 22 0.11
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (129 bp):
TTCAATTGATCCAGGGCGATCTTTTCTTCAGTTTATTATTGACCCAGGGCGGTCTTTCTTCAGGT
TATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTGATTTCAGTTGATCCAGGGCGATCTTTTC
Found at i:17479 original size:38 final size:38
Alignment explanation
Indices: 17428--17572 Score: 209
Period size: 38 Copynumber: 3.8 Consensus size: 38
17418 CACTTTGTCA
* *
17428 ATTTCGATCCTGGTTTAGGATCATTGGTTTATCAGTTT
1 ATTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTT
*
17466 ATTTCAATCCTGGTTTAGGATCATTGCTTTATTAGTTT
1 ATTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTT
* * * * *
17504 ATTTCGATCCTAGTTTAGGATCATTCCTTCATCGGTTT
1 ATTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTT
*
17542 ATTTCAATCCTGGTTTAGGATCGTTGCTTTA
1 ATTTCAATCCTGGTTTAGGATCATTGCTTTA
17573 AATTTCATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 93 1.00
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (38 bp):
ATTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTT
Found at i:17520 original size:76 final size:76
Alignment explanation
Indices: 17428--17572 Score: 236
Period size: 76 Copynumber: 1.9 Consensus size: 76
17418 CACTTTGTCA
* ** *
17428 ATTTCGATCCTGGTTTAGGATCATTGGTTTATCAGTTTATTTCAATCCTGGTTTAGGATCATTGC
1 ATTTCGATCCTAGTTTAGGATCATTCCTTCATCAGTTTATTTCAATCCTGGTTTAGGATCATTGC
17493 TTTATTAGTTT
66 TTTATTAGTTT
* *
17504 ATTTCGATCCTAGTTTAGGATCATTCCTTCATCGGTTTATTTCAATCCTGGTTTAGGATCGTTGC
1 ATTTCGATCCTAGTTTAGGATCATTCCTTCATCAGTTTATTTCAATCCTGGTTTAGGATCATTGC
17569 TTTA
66 TTTA
17573 AATTTCATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (76 bp):
ATTTCGATCCTAGTTTAGGATCATTCCTTCATCAGTTTATTTCAATCCTGGTTTAGGATCATTGC
TTTATTAGTTT
Done.