Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022090.1 Corchorus olitorius cultivar O-4 contig22123, 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: 23827
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Found at i:317 original size:21 final size:21
Alignment explanation
Indices: 293--365 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
283 GGCTTGGAAT
293 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
* * **
314 GGTGGTGGCACGGGCTTAACC
1 GGTGATGGCACGGGCATGGCC
* *
335 GGTGGTGGCACGGTGAATGGCC
1 GGTGATGGCACGG-GCATGGCC
*
357 GGTAATGGC
1 GGTGATGGC
366 TTGGTAGTGT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 30 0.73
22 11 0.27
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (21 bp):
GGTGATGGCACGGGCATGGCC
Found at i:3649 original size:19 final size:20
Alignment explanation
Indices: 3621--3659 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3611 TTTTAGAAAA
3621 ACGCAAAAAC-TTTTTTTTG
1 ACGCAAAAACATTTTTTTTG
*
3640 ACGCAGAAACAATTTTTTTT
1 ACGCAAAAAC-ATTTTTTTT
3660 TATATGACGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
ACGCAAAAACATTTTTTTTG
Found at i:3657 original size:23 final size:23
Alignment explanation
Indices: 3631--3698 Score: 91
Period size: 25 Copynumber: 2.8 Consensus size: 23
3621 ACGCAAAAAC
3631 TTTTTTTTGACGCAGAAACAATTT
1 TTTTTTTTGACGCA-AAACAATTT
*
3655 TTTTTTATATGACGCAAAAAAATTT
1 TTTTTT-T-TGACGCAAAACAATTT
*
3680 TTTTTTTCGACGCAAAACA
1 TTTTTTTTGACGCAAAACA
3699 CAAAACAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 10 0.26
24 7 0.18
25 15 0.38
26 7 0.18
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (23 bp):
TTTTTTTTGACGCAAAACAATTT
Found at i:3885 original size:29 final size:29
Alignment explanation
Indices: 3833--3904 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
3823 AGTCTATTTT
*
3833 CCTTCCCCTGGAAAAAACCAGAAAAAAATC
1 CCTTCCCC-GGCAAAAACCAGAAAAAAATC
* **
3863 CCTTCCCCGGCAAATACCAGAAAAAGTTC
1 CCTTCCCCGGCAAAAACCAGAAAAAAATC
3892 CCTTCCCCGGCAA
1 CCTTCCCCGGCAA
3905 CGGCGCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 30 0.79
30 8 0.21
ACGTcount: A:0.36, C:0.36, G:0.12, T:0.15
Consensus pattern (29 bp):
CCTTCCCCGGCAAAAACCAGAAAAAAATC
Found at i:4113 original size:16 final size:15
Alignment explanation
Indices: 4075--4116 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
4065 ACAGAGATTG
*
4075 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
4090 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
4105 ACTAGAAAACAA
1 AC-AGAAAACAA
4117 AGCAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:11580 original size:12 final size:12
Alignment explanation
Indices: 11563--11598 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
11553 TAAAAGACTC
11563 AAAACCTTTTTG
1 AAAACCTTTTTG
11575 AAAACCTATTTTTG
1 AAAACC--TTTTTG
11589 AAAACCTTTT
1 AAAACCTTTT
11599 CACGAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (12 bp):
AAAACCTTTTTG
Found at i:13091 original size:13 final size:13
Alignment explanation
Indices: 13073--13097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13063 AACATACTTA
13073 AAAACACTTTTGG
1 AAAACACTTTTGG
13086 AAAACACTTTTG
1 AAAACACTTTTG
13098 ATTTTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
AAAACACTTTTGG
Found at i:16678 original size:29 final size:28
Alignment explanation
Indices: 16644--16966 Score: 364
Period size: 29 Copynumber: 11.3 Consensus size: 28
16634 CTAAAGCATT
* *
16644 CAAAATGACCATAATGCCCCTGGGTGTG
1 CAAAATGACCAAAATGCCCCTGGATGTG
*
16672 CAGAAATGACCATAATGCCCCTGGATGTG
1 CA-AAATGACCAAAATGCCCCTGGATGTG
* *
16701 CAAAGATAACCAAAATGCCCCTGGTTGTG
1 CAAA-ATGACCAAAATGCCCCTGGATGTG
* * *
16730 CAAAGATGATCGAAATGCCCCTGGATATG
1 CAAA-ATGACCAAAATGCCCCTGGATGTG
* *
16759 TAAAAATGACCATAATGCCCCTGGATGTG
1 -CAAAATGACCAAAATGCCCCTGGATGTG
**
16788 CAAAGATGACCAAAATGCCCCTGGATACG
1 CAAA-ATGACCAAAATGCCCCTGGATGTG
16817 CAAAAATGACCAAAATGCCCCTGGATGTG
1 C-AAAATGACCAAAATGCCCCTGGATGTG
* *
16846 CAAAGATGATCAAAATGCCCCTGGATATG
1 CAAA-ATGACCAAAATGCCCCTGGATGTG
*
16875 CAAAACTGACCATAATGCCCCTGGATGTG
1 CAAAA-TGACCAAAATGCCCCTGGATGTG
** *
16904 CAAAAATGACCAAAACACCCCTGGACGTG
1 C-AAAATGACCAAAATGCCCCTGGATGTG
*
16933 C-AAATGACCAAAATGCCTCTGCG-TGTG
1 CAAAATGACCAAAATGCCCCTG-GATGTG
16960 -AAAATGA
1 CAAAATGA
16967 TTAATTAAGA
Statistics
Matches: 252, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
27 26 0.10
28 12 0.05
29 204 0.81
30 10 0.04
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (28 bp):
CAAAATGACCAAAATGCCCCTGGATGTG
Found at i:17287 original size:59 final size:59
Alignment explanation
Indices: 17200--17671 Score: 553
Period size: 59 Copynumber: 8.0 Consensus size: 59
17190 GAGGTATAGG
* * * * *
17200 CTCT-CAATCAGAGATCTCGAACAAGATTTAAAAAAAAAGATAAGATTTTGTATTGAAAA
1 CTCTCCAA-CAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
* *
17259 CTCTCCAACAGAGACCTCAAACAGGATTTTAAAAACAAGATGAGATTTTGAATTGAAAA
1 CTCTCCAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
* * * *
17318 CTCTCTAACAGAGACCTCAAACA-G---TTAAAAGCAGGATAAGATTTTGAATTGAAAAAAAAAA
1 CTCTCCAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTG------AAAA
* * * **
17379 CTCGCTAACAGAGACCTCGAACAGGA--TTAAAAACAATATTTGATTTTGAATTGAAAAA
1 CTCTCCAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTG-AAAA
* *
17437 CTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAGGATAAGATTTTGAATTGAAAA
1 CTCTCCAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
* * * *
17496 CTCTCCAAGAGAGACCTCGAACAGGGTTTTAAAAACAAGATAGGGTTTTGAATTGAAAA
1 CTCTCCAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
* * * *
17555 CTCTCTAACAAAGACCTCGAACAGGATTTTAAAAACAGGATAAGATTTTGCATTGAAAA
1 CTCTCCAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
* * * *
17614 CTCTCCAACAGAGACCTCGAACAGGGTTTTAAAAACAGGATAGGATTTTGATTTGAAA
1 CTCTCCAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
17672 CTGAAACTCA
Statistics
Matches: 359, Mismatches: 43, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
55 24 0.07
58 31 0.09
59 230 0.64
60 26 0.07
61 25 0.07
62 1 0.00
63 22 0.06
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (59 bp):
CTCTCCAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
Found at i:17650 original size:237 final size:232
Alignment explanation
Indices: 17200--17638 Score: 614
Period size: 237 Copynumber: 1.9 Consensus size: 232
17190 GAGGTATAGG
* *
17200 CTCTCAATCAGAGATCTCGAACAAGATTTAAAAAAAAAGATAAGATTTTGTATTGAAAACTCTCC
1 CTCTCAATCAGAGACCTCGAACAAGATTTAAAAAAAAAGATAAGATTTTGAATTGAAAACTCTCC
*
17265 AACAGAGACCTCAAACAGGATTTTAAAAACAAGATGAGATTTTGAATTGAAAACTCTCTAACAGA
66 AACAGAGACCTCAAACAGGATTTTAAAAACAAGATGAGATTTTGAATTGAAAACTCTCTAACAAA
* *
17330 GACCTCAAACAGTTAAAAGCAGGATAAGATTTTGAATTGAAAAAAAAAACTCGCTAACAGAGACC
131 GACCTCAAACAGTTAAAAACAGGATAAGATTTTGAATTG-----AAAAACTCGCCAACAGAGACC
17395 TCGAACAGGATTAAAAACAATATTTGATTTTGAATTGAAAAA
191 TCGAACAGGATTAAAAACAATATTTGATTTTGAATTGAAAAA
* * * *
17437 CTCTCTAA-CAGAGACCTCGAACAGGATTTTAAAAACAGGATAAGATTTTGAATTGAAAACTCTC
1 CTCTC-AATCAGAGACCTCGAACAAGATTTAAAAAAAAAGATAAGATTTTGAATTGAAAACTCTC
* * * *
17501 CAAGAGAGACCTCGAACAGGGTTTTAAAAACAAGAT-AGGGTTTTGAATTGAAAACTCTCTAACA
65 CAACAGAGACCTCAAACAGGATTTTAAAAACAAGATGA-GATTTTGAATTGAAAACTCTCTAACA
* * *
17565 AAGACCTCGAACAGGATTTTAAAAACAGGATAAGATTTTGCATTG-AAAACTCTCCAACAGAGAC
129 AAGACCTCAAACA-G---TTAAAAACAGGATAAGATTTTGAATTGAAAAACTCGCCAACAGAGAC
17629 CTCGAACAGG
190 CTCGAACAGG
17639 GTTTTAAAAA
Statistics
Matches: 180, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
235 27 0.15
236 1 0.01
237 124 0.69
238 3 0.02
241 25 0.14
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (232 bp):
CTCTCAATCAGAGACCTCGAACAAGATTTAAAAAAAAAGATAAGATTTTGAATTGAAAACTCTCC
AACAGAGACCTCAAACAGGATTTTAAAAACAAGATGAGATTTTGAATTGAAAACTCTCTAACAAA
GACCTCAAACAGTTAAAAACAGGATAAGATTTTGAATTGAAAAACTCGCCAACAGAGACCTCGAA
CAGGATTAAAAACAATATTTGATTTTGAATTGAAAAA
Found at i:18565 original size:18 final size:18
Alignment explanation
Indices: 18544--18600 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
18534 CCTCTTTCTA
18544 TTTTAGGTCCTGTTTTTG
1 TTTTAGGTCCTGTTTTTG
** * * *
18562 TTTTTCGACCTCTTTCTG
1 TTTTAGGTCCTGTTTTTG
*
18580 TTTTAGGTCCAGTTTTT-
1 TTTTAGGTCCTGTTTTTG
18597 TTTT
1 TTTT
18601 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 11, Indels: 1
0.70 0.28 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.07, C:0.16, G:0.16, T:0.61
Consensus pattern (18 bp):
TTTTAGGTCCTGTTTTTG
Found at i:18598 original size:1 final size:1
Alignment explanation
Indices: 18592--18620 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
18582 TTAGGTCCAG
18592 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18621 ATTAGCTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18603 original size:37 final size:37
Alignment explanation
Indices: 18495--18603 Score: 141
Period size: 36 Copynumber: 3.0 Consensus size: 37
18485 ATTTTTATAT
* *
18495 GACCTCTCTT-TGTTTTAGGTCCAATTTTTTCTTTTCC
1 GACCTCT-TTCTGTTTTAGGTCCAGTTTTTTCTTTTTC
* * *
18532 GACCTCTTTCTATTTTAGGTCCTG-TTTTTGTTTTTC
1 GACCTCTTTCTGTTTTAGGTCCAGTTTTTTCTTTTTC
*
18568 GACCTCTTTCTGTTTTAGGTCCAGTTTTTTTTTTTT
1 GACCTCTTTCTGTTTTAGGTCCAGTTTTTTCTTTTT
18604 TTTTTTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 34 0.55
37 28 0.45
ACGTcount: A:0.09, C:0.20, G:0.13, T:0.58
Consensus pattern (37 bp):
GACCTCTTTCTGTTTTAGGTCCAGTTTTTTCTTTTTC
Done.