Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024780.1 Corchorus olitorius cultivar O-4 contig24813, 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: 16497
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:633 original size:18 final size:18
Alignment explanation
Indices: 610--645 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
600 TATAATAATT
610 TTATTAATTGTAAATAAA
1 TTATTAATTGTAAATAAA
628 TTATTAATTGTAAATAAA
1 TTATTAATTGTAAATAAA
646 AAAAGAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTATTAATTGTAAATAAA
Found at i:777 original size:29 final size:29
Alignment explanation
Indices: 719--777 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
709 AAAAGAGCGT
*** *
719 ATTTATCTTAATTTATATTTTTTTGGATA
1 ATTTATCTTAATTTATATTTAGATGAATA
748 ATTTATCTTAATTTATATTTAGATGAATA
1 ATTTATCTTAATTTATATTTAGATGAATA
777 A
1 A
778 AAATAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (29 bp):
ATTTATCTTAATTTATATTTAGATGAATA
Found at i:2583 original size:19 final size:19
Alignment explanation
Indices: 2559--2595 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2549 AGCTTAGGAC
2559 ATAATGCAATAAAGTTTAA
1 ATAATGCAATAAAGTTTAA
*
2578 ATAATGCAATGAAGTTTA
1 ATAATGCAATAAAGTTTA
2596 GGCAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (19 bp):
ATAATGCAATAAAGTTTAA
Found at i:4269 original size:15 final size:16
Alignment explanation
Indices: 4243--4272 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4233 CCTTTTCTGG
4243 TTAAATTAAATTAATT
1 TTAAATTAAATTAATT
4259 TTAAA-TAAATTAAT
1 TTAAATTAAATTAAT
4273 ATTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTAAATTAATT
Found at i:6445 original size:25 final size:25
Alignment explanation
Indices: 6411--6459 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
6401 CCAAACAATC
*
6411 TTGAGTACTCTCACTCGGTCTCTAT
1 TTGAGCACTCTCACTCGGTCTCTAT
*
6436 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCACTCGGTCTCTA
6460 CAAACCAATC
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:0.14, C:0.31, G:0.18, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCACTCGGTCTCTAT
Found at i:8540 original size:32 final size:32
Alignment explanation
Indices: 8494--8571 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
8484 AAAAGTAAAC
8494 GACCCGAGACCCGAATAACCTGCAACCCAGAT
1 GACCCGAGACCCGAATAACCTGCAACCCAGAT
* * *
8526 GACCTGAGACCCGAATGACCTGTAACCCAGAT
1 GACCCGAGACCCGAATAACCTGCAACCCAGAT
*
8558 GACCCGAAACCCGA
1 GACCCGAGACCCGA
8572 GTGACTCGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.33, C:0.36, G:0.21, T:0.10
Consensus pattern (32 bp):
GACCCGAGACCCGAATAACCTGCAACCCAGAT
Found at i:8576 original size:16 final size:16
Alignment explanation
Indices: 8494--8649 Score: 73
Period size: 16 Copynumber: 9.3 Consensus size: 16
8484 AAAAGTAAAC
*
8494 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
* * *
8510 AACCTGCAACCC-AGAT
1 GACCCGAAACCCGA-AT
* *
8526 GACCTGAGACCCGAAT
1 GACCCGAAACCCGAAT
* *
8542 GACCTGTAACCC-AGAT
1 GACCCGAAACCCGA-AT
*
8558 GACCCGAAACCCGAGT
1 GACCCGAAACCCGAAT
* *
8574 GACTCGAGACCCGAATGACTTAT
1 GACCCGAAACCC----GA---AT
* *
8597 GACCCGAGACCCGTAT
1 GACCCGAAACCCGAAT
*
8613 GACCCGAAACCCGTAT
1 GACCCGAAACCCGAAT
*
8629 GACCCGAAATCCGAAT
1 GACCCGAAACCCGAAT
*
8645 AACCC
1 GACCC
8650 AAGAAGTTAA
Statistics
Matches: 108, Mismatches: 21, Indels: 22
0.72 0.14 0.15
Matches are distributed among these distances:
15 2 0.02
16 89 0.82
17 2 0.02
19 1 0.01
20 2 0.02
23 12 0.11
ACGTcount: A:0.32, C:0.35, G:0.21, T:0.13
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:8607 original size:7 final size:8
Alignment explanation
Indices: 8518--8635 Score: 52
Period size: 7 Copynumber: 14.8 Consensus size: 8
8508 ATAACCTGCA
8518 ACCCAGATG
1 ACCC-GATG
*
8527 ACCTGA-G
1 ACCCGATG
8534 ACCCGAATG
1 ACCCG-ATG
* *
8543 ACCTG-TA
1 ACCCGATG
8550 ACCCAGATG
1 ACCC-GATG
*
8559 ACCCGA-A
1 ACCCGATG
8566 ACCCGAGTG
1 ACCCGA-TG
*
8575 ACTCGA-G
1 ACCCGATG
8582 ACCCGAATG
1 ACCCG-ATG
**
8591 A-CTTATG
1 ACCCGATG
8598 ACCCGA-G
1 ACCCGATG
8605 ACCCGTATG
1 ACCCG-ATG
*
8614 ACCCGA-A
1 ACCCGATG
8621 ACCCGTATG
1 ACCCG-ATG
8630 ACCCGA
1 ACCCGA
8636 AATCCGAATA
Statistics
Matches: 80, Mismatches: 16, Indels: 27
0.65 0.13 0.22
Matches are distributed among these distances:
7 35 0.44
8 14 0.17
9 31 0.39
ACGTcount: A:0.31, C:0.34, G:0.22, T:0.14
Consensus pattern (8 bp):
ACCCGATG
Found at i:8625 original size:39 final size:39
Alignment explanation
Indices: 8556--8631 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
8546 TGTAACCCAG
* *
8556 ATGACCCGAAACCCGAGTGACTCGAGACCCGAATGACTT
1 ATGACCCGAAACCCGAGTGACCCGAAACCCGAATGACTT
* *
8595 ATGACCCGAGACCCGTA-TGACCCGAAACCCGTATGAC
1 ATGACCCGAAACCCG-AGTGACCCGAAACCCGAATGAC
8632 CCGAAATCCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 31 0.97
40 1 0.03
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.14
Consensus pattern (39 bp):
ATGACCCGAAACCCGAGTGACCCGAAACCCGAATGACTT
Found at i:9515 original size:16 final size:16
Alignment explanation
Indices: 9496--9614 Score: 120
Period size: 16 Copynumber: 7.6 Consensus size: 16
9486 AGACTCGGTA
9496 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
9512 GACCCG-GAATCCGAAT
1 GACCCGAG-ACCCGAAT
* *
9528 GACCCGAAACCCGTAT
1 GACCCGAGACCCGAAT
*
9544 GACTCGAGACCCGAAT
1 GACCCGAGACCCGAAT
* *
9560 GACCTGAAACCCGAAT
1 GACCCGAGACCCGAAT
*
9576 AACCCGA-ACCC-AGAT
1 GACCCGAGACCCGA-AT
*
9591 GACCCGAAACCCGAAT
1 GACCCGAGACCCGAAT
9607 GA-CCGAGA
1 GACCCGAGA
9615 AAACTGCTTG
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
14 1 0.01
15 18 0.21
16 64 0.76
17 1 0.01
ACGTcount: A:0.34, C:0.34, G:0.22, T:0.09
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:9554 original size:48 final size:47
Alignment explanation
Indices: 9496--9610 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 47
9486 AGACTCGGTA
* * *
9496 GACCCGAGACCCGAATGACCCGGAATCCGAATGACCCGAAACCC-GTAT
1 GACCCGAGACCCGAATGACCCGAAACCCGAATAACCCG-AACCCAG-AT
* *
9544 GACTCGAGACCCGAATGACCTGAAACCCGAATAACCCGAACCCAGAT
1 GACCCGAGACCCGAATGACCCGAAACCCGAATAACCCGAACCCAGAT
*
9591 GACCCGAAACCCGAATGACC
1 GACCCGAGACCCGAATGACC
9611 GAGAAAACTG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
47 25 0.42
48 34 0.58
ACGTcount: A:0.34, C:0.36, G:0.21, T:0.10
Consensus pattern (47 bp):
GACCCGAGACCCGAATGACCCGAAACCCGAATAACCCGAACCCAGAT
Found at i:12211 original size:28 final size:28
Alignment explanation
Indices: 12171--12265 Score: 154
Period size: 28 Copynumber: 3.4 Consensus size: 28
12161 CAATTTATGA
12171 CTCAACCTTTCGATTGGTCGAATCAAGG
1 CTCAACCTTTCGATTGGTCGAATCAAGG
*
12199 CTCAACCTTTCGATTGGTCGAATCAAGA
1 CTCAACCTTTCGATTGGTCGAATCAAGG
*
12227 CTTAACCTTTCGATTGGTCGAATCAAGG
1 CTCAACCTTTCGATTGGTCGAATCAAGG
* *
12255 CTTAACATTTC
1 CTCAACCTTTC
12266 AATTTTAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (28 bp):
CTCAACCTTTCGATTGGTCGAATCAAGG
Found at i:16441 original size:29 final size:29
Alignment explanation
Indices: 16408--16497 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 29
16398 GCTAATTGCT
16408 CAAATAAGGGCCTAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATCTTTTAATTTGGC
* **
16437 CAAATAAGGGCCTAA-CGTTTGCCAAAAT-GC
1 CAAATAAGGGCCTAATC-TTT--TAATTTGGC
*
16467 TCAAATAAGGGCCTGATCTTTTAATTTGGC
1 -CAAATAAGGGCCTAATCTTTTAATTTGGC
16497 C
1 C
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
28 1 0.02
29 22 0.46
30 4 0.08
31 20 0.42
32 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGCCTAATCTTTTAATTTGGC
Done.