Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018898.1 Corchorus olitorius cultivar O-4 contig18931, 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: 86874
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:92 original size:29 final size:29
Alignment explanation
Indices: 51--118 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
41 TTTTAATTAT
51 TAATT-ATAATTAAT-AATAACAATTTAAA
1 TAATTAATAATTAATGAATAACAA-TTAAA
* * *
79 TCATTAATAATTAATGATTAATAATTAAA
1 TAATTAATAATTAATGAATAACAATTAAA
108 TAATTAATAAT
1 TAATTAATAAT
119 AATTAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.12
29 24 0.71
30 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (29 bp):
TAATTAATAATTAATGAATAACAATTAAA
Found at i:100 original size:14 final size:15
Alignment explanation
Indices: 51--118 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
41 TTTTAATTAT
51 TAATT-ATAATT-AA
1 TAATTAATAATTAAA
*
64 TAA-TAACAATTTAAA
1 TAATTAATAA-TTAAA
*
79 TCATTAATAATT-AA
1 TAATTAATAATTAAA
*
93 TGATTAATAATTAAA
1 TAATTAATAATTAAA
108 TAATTAATAAT
1 TAATTAATAAT
119 AATTAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
12 1 0.02
13 6 0.13
14 15 0.33
15 18 0.40
16 5 0.11
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
TAATTAATAATTAAA
Found at i:116 original size:7 final size:7
Alignment explanation
Indices: 44--118 Score: 73
Period size: 7 Copynumber: 10.6 Consensus size: 7
34 TTTTGTTTTT
*
44 TAATTAT
1 TAATTAA
51 TAATT-A
1 TAATTAA
57 TAATTAA
1 TAATTAA
64 TAA-TAA
1 TAATTAA
*
70 CAATTTAAA
1 TAA-TT-AA
*
79 TCATTAA
1 TAATTAA
86 TAATTAA
1 TAATTAA
*
93 TGATTAA
1 TAATTAA
100 TAATTAAA
1 TAATT-AA
108 TAATTAA
1 TAATTAA
115 TAAT
1 TAAT
119 AATTAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
6 10 0.18
7 33 0.59
8 10 0.18
9 3 0.05
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (7 bp):
TAATTAA
Found at i:130 original size:29 final size:30
Alignment explanation
Indices: 49--131 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 30
39 TTTTTTAATT
* * *
49 ATTAATTATAATTAATAATAACAATTTAAATC
1 ATTAATAATAATTAA-AA-AATAATTTAAATA
* **
81 ATTAATAATTAA-TGATTAATAA-TTAAATA
1 ATTAATAA-TAATTAAAAAATAATTTAAATA
110 ATTAATAATAATTAAAAAATAA
1 ATTAATAATAATTAAAAAATAA
132 AAAAAATAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
28 3 0.08
29 21 0.52
30 4 0.10
32 9 0.22
33 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (30 bp):
ATTAATAATAATTAAAAAATAATTTAAATA
Found at i:8543 original size:24 final size:23
Alignment explanation
Indices: 8512--8557 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
8502 TTCGTGAGAG
*
8512 TGATGAAGAAGGAAGAGCAGAAAA
1 TGATGAAGAAAGAAGAG-AGAAAA
8536 TGATGAAGAAAGAAGAGAGAAA
1 TGATGAAGAAAGAAGAGAGAAA
8558 TGAGAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.57, C:0.02, G:0.33, T:0.09
Consensus pattern (23 bp):
TGATGAAGAAAGAAGAGAGAAAA
Found at i:9367 original size:6 final size:6
Alignment explanation
Indices: 9352--9397 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
9342 TCATTTTCGA
*
9352 TTTTTG -TTTTG TTTTTTG TTTTTG -TTTGG TTTTTG -TTTTG TTTTTG
1 TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
9398 CTGCGTTGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 14 0.41
6 15 0.44
7 5 0.15
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (6 bp):
TTTTTG
Found at i:13376 original size:10 final size:10
Alignment explanation
Indices: 13361--13392 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
13351 TGGTTAACCT
13361 AACCAAATAC
1 AACCAAATAC
13371 AACCAAATAC
1 AACCAAATAC
*
13381 AACCAAACAC
1 AACCAAATAC
13391 AA
1 AA
13393 ACACCACGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.06
Consensus pattern (10 bp):
AACCAAATAC
Found at i:16503 original size:88 final size:88
Alignment explanation
Indices: 16349--16514 Score: 314
Period size: 88 Copynumber: 1.9 Consensus size: 88
16339 TTTCATCGGA
16349 TATGCTTGATATGTTCAAGGTACTTATTGGTGTGCGATATGTAAGTATTTTTGTAAGGCCTTTAT
1 TATGCTTGATATGTTCAAGGTACTTATTGGTGTGCGATATGTAAGTATTTTTGTAAGGCCTTTAT
16414 GAGACTTGTGGTAACGTTTTAGC
66 GAGACTTGTGGTAACGTTTTAGC
* *
16437 TATGTTTGATATGTTCAAGGTACTTATTGGTGTGTGATATGTAAGTATTTTTGTAAGGCCTTTAT
1 TATGCTTGATATGTTCAAGGTACTTATTGGTGTGCGATATGTAAGTATTTTTGTAAGGCCTTTAT
16502 GAGACTTGTGGTA
66 GAGACTTGTGGTA
16515 TCTTGATCTT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 76 1.00
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.43
Consensus pattern (88 bp):
TATGCTTGATATGTTCAAGGTACTTATTGGTGTGCGATATGTAAGTATTTTTGTAAGGCCTTTAT
GAGACTTGTGGTAACGTTTTAGC
Found at i:22218 original size:27 final size:29
Alignment explanation
Indices: 22150--22218 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
22140 TACAGCTTGC
* * * *
22150 GAGTACATAGATTAAATTGATCGCTTTTT
1 GAGTATATAGATGAAATTGAACGATTTTT
*
22179 GAGTATATGGATGAAATTGAAC-ATTTTT
1 GAGTATATAGATGAAATTGAACGATTTTT
*
22207 GTGT-TATAGATG
1 GAGTATATAGATG
22219 GACCTACCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
27 7 0.21
28 8 0.24
29 18 0.55
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.41
Consensus pattern (29 bp):
GAGTATATAGATGAAATTGAACGATTTTT
Found at i:31579 original size:13 final size:13
Alignment explanation
Indices: 31561--31590 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31551 TTCAACTTTA
*
31561 ATATATGTTATGT
1 ATATATGTCATGT
31574 ATATATGTCATGT
1 ATATATGTCATGT
31587 ATAT
1 ATAT
31591 GTAATAGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATATATGTCATGT
Found at i:32251 original size:38 final size:38
Alignment explanation
Indices: 32204--32286 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
32194 TTATTTATCA
32204 TTTCTTATTACACAAGTAATATTTAATTTAAGTTTGTCT
1 TTTC-TATTACACAAGTAATATTTAATTTAAGTTTGTCT
32243 TTTCTATTACACAAGTAATATTTAATTTAAGTTTGTCT
1 TTTCTATTACACAAGTAATATTTAATTTAAGTTTGTCT
32281 TTTCTA
1 TTTCTA
32287 ACTCATAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 40 0.91
39 4 0.09
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (38 bp):
TTTCTATTACACAAGTAATATTTAATTTAAGTTTGTCT
Found at i:32768 original size:30 final size:30
Alignment explanation
Indices: 32732--32792 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
32722 TAGTAAAGAT
* *
32732 ATTAAAATTCGAGGGTATAAGAGGAAAGTC
1 ATTAAAATTCGAAGGTATAAAAGGAAAGTC
*
32762 ATTAAAATTTGAAGGTATAAAAGGAAAGTC
1 ATTAAAATTCGAAGGTATAAAAGGAAAGTC
32792 A
1 A
32793 AGATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.23, T:0.25
Consensus pattern (30 bp):
ATTAAAATTCGAAGGTATAAAAGGAAAGTC
Found at i:43337 original size:31 final size:30
Alignment explanation
Indices: 43301--43375 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 30
43291 GTCCAAAATA
43301 AGCCCAATTTGGTGCAATTTGCTAAAGTTT
1 AGCCCAATTTGGTGCAATTTGCTAAAGTTT
*
43331 ATGCCCAATTTGGTGCAATTTGTTAAAGTTT
1 A-GCCCAATTTGGTGCAATTTGCTAAAGTTT
43362 AGACCCAATTTGGT
1 AG-CCCAATTTGGT
43376 CCTGTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 2 0.05
31 40 0.95
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (30 bp):
AGCCCAATTTGGTGCAATTTGCTAAAGTTT
Found at i:79020 original size:22 final size:22
Alignment explanation
Indices: 78995--79061 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
78985 GACACACTTA
78995 TAAAACCAATACAATTTGTAAT
1 TAAAACCAATACAATTTGTAAT
79017 TAAAACCAATACAATTTGTAAT
1 TAAAACCAATACAATTTGTAAT
79039 TAAAACCAATACAATTTGTAAT
1 TAAAACCAATACAATTTGTAAT
79061 T
1 T
79062 TTTTCCATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.33
Consensus pattern (22 bp):
TAAAACCAATACAATTTGTAAT
Found at i:79538 original size:102 final size:102
Alignment explanation
Indices: 79413--79600 Score: 342
Period size: 103 Copynumber: 1.8 Consensus size: 102
79403 AATCAGTTAG
79413 GTTTAGCCCAAATTATATAAAAAATATTTTAAGGGTATGTT-TTGAATTTAAAATATTTATTTAT
1 GTTTAGCCCAAATTATATAAAAAATATTTTAAGGGTAT-TTCTTGAATTTAAAATATTTATTTAT
79477 AGGGTTTTAGAATTTTAGTTGAGCCTCAAATTACTAGT
65 AGGGTTTTAGAATTTTAGTTGAGCCTCAAATTACTAGT
*
79515 GTTTAGCCCCAAATTATATAAAAAATATTTTAAGGGTATTTCTTGAATTTAAAATATTTATTTCT
1 GTTTAG-CCCAAATTATATAAAAAATATTTTAAGGGTATTTCTTGAATTTAAAATATTTATTTAT
79580 AGGGTTTTAGAATTTTAGTTG
65 AGGGTTTTAGAATTTTAGTTG
79601 GACCCGAAAG
Statistics
Matches: 83, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
102 8 0.10
103 75 0.90
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (102 bp):
GTTTAGCCCAAATTATATAAAAAATATTTTAAGGGTATTTCTTGAATTTAAAATATTTATTTATA
GGGTTTTAGAATTTTAGTTGAGCCTCAAATTACTAGT
Found at i:83019 original size:2 final size:2
Alignment explanation
Indices: 83012--83043 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
83002 AAATTGTTAT
83012 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83044 AATCCCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:86481 original size:15 final size:16
Alignment explanation
Indices: 86448--86482 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
86438 TTACTTTGCT
86448 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
86464 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
86479 TTGT
1 TTGT
86483 GATTCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.17, C:0.06, G:0.14, T:0.63
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Done.