Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016494.1 Corchorus olitorius cultivar O-4 contig16527, 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: 28645
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:166 original size:29 final size:30
Alignment explanation
Indices: 124--197 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
114 CTCATTTTTG
* *
124 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
* *
153 AAACATAAGAGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
184 AAACATAAGGGATT
1 AAACATAAGGGATT
198 TTTTTTTGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 24 0.63
31 14 0.37
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:1820 original size:2 final size:2
Alignment explanation
Indices: 1780--1811 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1770 AAACTACTAA
1780 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1812 ACTTATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2119 original size:31 final size:30
Alignment explanation
Indices: 2048--2119 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
2038 GTCTATCAGC
*
2048 TTTTAATTTGTTTAATTTAAGACTTTCATT
1 TTTTAATTTGTTTAATTTAAGACTTACATT
*
2078 TTAATT-ATTTGTTTAATTTAATG-CTTAGATT
1 TT--TTAATTTGTTTAATTTAA-GACTTACATT
2109 GTTTTAATTTG
1 -TTTTAATTTG
2120 CAATAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
30 4 0.11
31 26 0.74
32 5 0.14
ACGTcount: A:0.26, C:0.04, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTTAATTTGTTTAATTTAAGACTTACATT
Found at i:2408 original size:13 final size:12
Alignment explanation
Indices: 2372--2418 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
2362 TCAATCTTTA
*
2372 TATATATTGATAA
1 TATATATT-ATAT
*
2385 TA-ATGTTATAT
1 TATATATTATAT
2396 TATATTATTATAT
1 TATA-TATTATAT
2409 TATATATTAT
1 TATATATTAT
2419 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:2567 original size:17 final size:17
Alignment explanation
Indices: 2545--2608 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
2535 TCGAAATCAA
2545 ACCCGAGCCCGAACCCG
1 ACCCGAGCCCGAACCCG
2562 ACCCGAGCCCGAACCCG
1 ACCCGAGCCCGAACCCG
*
2579 A----A-CCCGAACCCT
1 ACCCGAGCCCGAACCCG
*
2591 ACCCGAGACCGAACCCG
1 ACCCGAGCCCGAACCCG
2608 A
1 A
2609 AAATACCCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.26
13 1 0.03
16 1 0.03
17 27 0.69
ACGTcount: A:0.28, C:0.50, G:0.20, T:0.02
Consensus pattern (17 bp):
ACCCGAGCCCGAACCCG
Found at i:2572 original size:23 final size:22
Alignment explanation
Indices: 2545--2608 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
2535 TCGAAATCAA
2545 ACCCGAGCCCGAACCCGACCCG
1 ACCCGAGCCCGAACCCGACCCG
* *
2567 AGCCCGAACCCGAACCCGAACCCT
1 A-CCCGAGCCCGAACCCG-ACCCG
*
2591 ACCCGAGACCGAACCCGA
1 ACCCGAGCCCGAACCCGA
2609 AAATACCCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.06
23 29 0.81
24 5 0.14
ACGTcount: A:0.28, C:0.50, G:0.20, T:0.02
Consensus pattern (22 bp):
ACCCGAGCCCGAACCCGACCCG
Found at i:2586 original size:29 final size:29
Alignment explanation
Indices: 2544--2609 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
2534 ATCGAAATCA
* *
2544 AACCCGAGCCCGAACCCGACCCGAGCCCG
1 AACCCGAACCCGAACCCGACCCGAGACCG
*
2573 AACCCGAACCCGAACCCTACCCGAGACCG
1 AACCCGAACCCGAACCCGACCCGAGACCG
2602 AACCCGAA
1 AACCCGAA
2610 AATACCCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.30, C:0.48, G:0.20, T:0.02
Consensus pattern (29 bp):
AACCCGAACCCGAACCCGACCCGAGACCG
Found at i:2620 original size:16 final size:16
Alignment explanation
Indices: 2599--2702 Score: 115
Period size: 16 Copynumber: 6.6 Consensus size: 16
2589 CTACCCGAGA
2599 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
2615 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
*
2631 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
**
2647 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
*
2663 CCGAATCCGAAAATAC
1 CCGAACCCGAAAATAC
*
2679 CCGAACCC-AAAGTAC
1 CCGAACCCGAAAATAC
2694 CCGAACCCG
1 CCGAACCCG
2703 CCCAAGCCCG
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
15 19 0.26
16 48 0.67
17 5 0.07
ACGTcount: A:0.38, C:0.40, G:0.14, T:0.08
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:2624 original size:6 final size:6
Alignment explanation
Indices: 2544--2609 Score: 75
Period size: 6 Copynumber: 11.3 Consensus size: 6
2534 ATCGAAATCA
* *
2544 AACCCG AGCCCG AACCCG -ACCCG AGCCCG AACCCG AACCCG AACCC-
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
*
2590 TACCCG AGA-CCG AACCCG AA
1 AACCCG A-ACCCG AACCCG AA
2610 AATACCCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 10 0.20
6 39 0.78
7 1 0.02
ACGTcount: A:0.30, C:0.48, G:0.20, T:0.02
Consensus pattern (6 bp):
AACCCG
Found at i:2645 original size:32 final size:32
Alignment explanation
Indices: 2599--2702 Score: 149
Period size: 32 Copynumber: 3.3 Consensus size: 32
2589 CTACCCGAGA
2599 CCGAACCCGAAAATACCCGAACCCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* *
2631 CCGAGCCCGAAAATACCCGAACCCGACTTAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* *
2663 CCGAATCCGAAAATACCCGAACCC-AAAGT-AC
1 CCGAACCCGAAAATACCCGAACCCGACA-TAAC
2694 CCGAACCCG
1 CCGAACCCG
2703 CCCAAGCCCG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
31 11 0.17
32 53 0.83
ACGTcount: A:0.38, C:0.40, G:0.14, T:0.08
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:3499 original size:18 final size:17
Alignment explanation
Indices: 3476--3515 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
3466 CCGGAAGGTC
3476 CCTCCTGTTGAACATATT
1 CCTCCTG-TGAACATATT
3494 CCTCC--TGAACATATT
1 CCTCCTGTGAACATATT
3509 CCTCCTG
1 CCTCCTG
3516 GACGTAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 15 0.75
18 5 0.25
ACGTcount: A:0.20, C:0.35, G:0.10, T:0.35
Consensus pattern (17 bp):
CCTCCTGTGAACATATT
Found at i:3502 original size:15 final size:15
Alignment explanation
Indices: 3484--3515 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3474 TCCCTCCTGT
3484 TGAACATATTCCTCC
1 TGAACATATTCCTCC
3499 TGAACATATTCCTCC
1 TGAACATATTCCTCC
3514 TG
1 TG
3516 GACGTAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.34
Consensus pattern (15 bp):
TGAACATATTCCTCC
Found at i:3526 original size:15 final size:15
Alignment explanation
Indices: 3484--3526 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3474 TCCCTCCTGT
*
3484 TGAACATATTCCTCC
1 TGAACATAATCCTCC
*
3499 TGAACATATTCCTCC
1 TGAACATAATCCTCC
* *
3514 TGGACGTAATCCT
1 TGAACATAATCCT
3527 GATTTGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.33
Consensus pattern (15 bp):
TGAACATAATCCTCC
Found at i:13458 original size:18 final size:20
Alignment explanation
Indices: 13413--13460 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
13403 GCTTAATCAA
13413 ATTCATATTATTATTATAATT
1 ATTCAT-TTATTATTATAATT
13434 ATT-ATTTATTATT-TAA-T
1 ATTCATTTATTATTATAATT
13451 ATTCATTTAT
1 ATTCATTTAT
13461 ATATATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.15
18 9 0.35
19 8 0.31
20 2 0.08
21 3 0.12
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTCATTTATTATTATAATT
Found at i:16965 original size:13 final size:13
Alignment explanation
Indices: 16947--17002 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
16937 CTTCTCTTCA
16947 AGATATATATAAC
1 AGATATATATAAC
16960 AGATATATATAAC
1 AGATATATATAAC
* *
16973 AGATAT-CATCA-
1 AGATATATATAAC
16984 AGATATATATAAC
1 AGATATATATAAC
16997 AGATAT
1 AGATAT
17003 CAGTTTGATC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 6 0.16
12 6 0.16
13 25 0.68
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (13 bp):
AGATATATATAAC
Found at i:19571 original size:16 final size:16
Alignment explanation
Indices: 19550--19581 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19540 ATAGTGAAAT
19550 ATCATTTAGTAGTATC
1 ATCATTTAGTAGTATC
19566 ATCATTTAGTAGTATC
1 ATCATTTAGTAGTATC
19582 CGAGGACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
ATCATTTAGTAGTATC
Found at i:19749 original size:24 final size:22
Alignment explanation
Indices: 19722--19769 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 22
19712 TCCTTCTTAA
19722 ATTTTGATTACAATAAAAAAAATT
1 ATTTTG-TTACAAT-AAAAAAATT
**
19746 A-TTTGTTTTAATAAAAAAATT
1 ATTTTGTTACAATAAAAAAATT
19767 ATT
1 ATT
19770 AAACTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
21 10 0.48
22 6 0.29
23 4 0.19
24 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
ATTTTGTTACAATAAAAAAATT
Found at i:21065 original size:16 final size:16
Alignment explanation
Indices: 21041--21074 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21031 AGTTTTCACA
21041 ATCTAAAATCTAAAAC
1 ATCTAAAATCTAAAAC
*
21057 ATCTGAAATCTAAAAC
1 ATCTAAAATCTAAAAC
21073 AT
1 AT
21075 ATAGAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (16 bp):
ATCTAAAATCTAAAAC
Found at i:21345 original size:24 final size:23
Alignment explanation
Indices: 21308--21352 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
21298 TTGACTGCAA
*
21308 ATACAACTAGTAAAATGAATACAT
1 ATACAACTACTAAAA-GAATACAT
*
21332 ATACAAGTACTAAAAGAATAC
1 ATACAACTACTAAAAGAATAC
21353 CATTAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.56, C:0.13, G:0.09, T:0.22
Consensus pattern (23 bp):
ATACAACTACTAAAAGAATACAT
Found at i:25677 original size:27 final size:26
Alignment explanation
Indices: 25647--25742 Score: 79
Period size: 27 Copynumber: 3.6 Consensus size: 26
25637 GTGGACTTAA
25647 AATGACCAAAATGCCCCTGGATGTGCC
1 AATGACCAAAATGCCCCTGGATGTG-C
* *
25674 AATGACCAGAAT-ACCCTGGAATGTGC
1 AATGACCAAAATGCCCCTGG-ATGTGC
* * * **
25700 ATATGACCAGAATGCCCTTAG-TGTAAA
1 A-ATGACCAAAATGCCCCTGGATGT-GC
25727 AATGACCAAAATGCCC
1 AATGACCAAAATGCCC
25743 TTATGTGACC
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
26 25 0.44
27 28 0.49
28 4 0.07
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (26 bp):
AATGACCAAAATGCCCCTGGATGTGC
Done.