Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017178.1 Corchorus olitorius cultivar O-4 contig17211, 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: 39263
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1152 original size:16 final size:17
Alignment explanation
Indices: 1120--1152 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1110 GATTAAACGA
1120 AATAAAATAAAAGATAG
1 AATAAAATAAAAGATAG
*
1137 AATAAATTAAAA-ATAG
1 AATAAAATAAAAGATAG
1153 TAATTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
AATAAAATAAAAGATAG
Found at i:7510 original size:21 final size:23
Alignment explanation
Indices: 7462--7510 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
7452 AGTTTACCAA
7462 GTAAAACGTAATCAAATAATTAT
1 GTAAAACGTAATCAAATAATTAT
7485 GTAAAA-GTAATCAAAT-ATTAT
1 GTAAAACGTAATCAAATAATTAT
*
7506 TTAAA
1 GTAAA
7511 TGAGATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.36
22 10 0.40
23 6 0.24
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (23 bp):
GTAAAACGTAATCAAATAATTAT
Found at i:17097 original size:22 final size:21
Alignment explanation
Indices: 17045--17098 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
17035 TGCTTCTTGA
17045 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
17066 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
17085 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
17099 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:27009 original size:23 final size:24
Alignment explanation
Indices: 26965--27012 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
26955 TAATTAAAGT
26965 AAAACTCCATTTCTTTTTTCCAGC
1 AAAACTCCATTTCTTTTTTCCAGC
26989 AAAACTCCATTTC-TTTTTCCAGC
1 AAAACTCCATTTCTTTTTTCCAGC
27012 A
1 A
27013 GATAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.40
Consensus pattern (24 bp):
AAAACTCCATTTCTTTTTTCCAGC
Found at i:27267 original size:20 final size:20
Alignment explanation
Indices: 27239--27277 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27229 GAAATTCCCT
* *
27239 TAAATAAACTAATTATAAAC
1 TAAACAAACAAATTATAAAC
27259 TAAACAAACAAATTATAAA
1 TAAACAAACAAATTATAAA
27278 GACAAAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAACAAACAAATTATAAAC
Found at i:32224 original size:15 final size:14
Alignment explanation
Indices: 32184--32234 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
32174 CCTATTTTTA
*
32184 TTTTATATATTATA
1 TTTTATATATTATT
*
32198 TTATATCATATTATT
1 TTTTAT-ATATTATT
32213 TTTTATATTATTATT
1 TTTTATA-TATTATT
32228 TTATTAT
1 TT-TTAT
32235 TATAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 6 0.19
15 21 0.68
16 4 0.13
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATATATTATT
Found at i:32244 original size:33 final size:34
Alignment explanation
Indices: 32178--32244 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
32168 ATACTTCCTA
* *
32178 TTTTTATTTTATATATTATATTATATCATATTAT
1 TTTTTATATTATATATTATATTATATCAAATTAT
*
32212 TTTTTATATTAT-TATTTTATTATTAT-AAATTAT
1 TTTTTATATTATATATTATATTA-TATCAAATTAT
32245 AAAAGTAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (34 bp):
TTTTTATATTATATATTATATTATATCAAATTAT
Found at i:33004 original size:22 final size:22
Alignment explanation
Indices: 32989--33058 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 22
32979 AGTTATTACG
*
32989 ATTTCATAGTTTAGTTATCAAA
1 ATTTCATAGTTTAGTTATAAAA
*
33011 ATTTCATAGTTTGGTTATAAAA
1 ATTTCATAGTTTAGTTATAAAA
* * *
33033 ATTTCATAGTGTGGTTACAAAA
1 ATTTCATAGTTTAGTTATAAAA
33055 ATTT
1 ATTT
33059 TCAAGAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (22 bp):
ATTTCATAGTTTAGTTATAAAA
Found at i:33357 original size:13 final size:13
Alignment explanation
Indices: 33339--33364 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33329 TAGTTTCATT
33339 TCATCAATATTAA
1 TCATCAATATTAA
33352 TCATCAATATTAA
1 TCATCAATATTAA
33365 AGGTATTAAA
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TCATCAATATTAA
Found at i:33463 original size:56 final size:56
Alignment explanation
Indices: 33402--33507 Score: 167
Period size: 56 Copynumber: 1.9 Consensus size: 56
33392 ACTAAAAAGC
* *
33402 TTTAGATTTTAGATTAAATGTTACGATACCAAATTTACATTTTTAGTCATTTTAGT
1 TTTAGATTTTAGATTAAATGTTACGAAACCAAACTTACATTTTTAGTCATTTTAGT
***
33458 TTTAGATTTTAGATTAAATGTTACGAAAGTTAACTTACATTTTTAGTCAT
1 TTTAGATTTTAGATTAAATGTTACGAAACCAAACTTACATTTTTAGTCAT
33508 CTAAATCCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.47
Consensus pattern (56 bp):
TTTAGATTTTAGATTAAATGTTACGAAACCAAACTTACATTTTTAGTCATTTTAGT
Found at i:33941 original size:31 final size:31
Alignment explanation
Indices: 33821--33943 Score: 131
Period size: 31 Copynumber: 4.0 Consensus size: 31
33811 TTAGGTACTA
* * *
33821 ATTTAAGCCAATTTTGCAACGTTAGGGACTG
1 ATTTTAGCCGATTTTGCAACGTTATGGACTG
* * *
33852 ATTTGAGCCGATCTTGCAATGTTA-GGAACTG
1 ATTTTAGCCGATTTTGCAACGTTATGG-ACTG
* * * *
33883 ATTTTAGTCGATTTTGCAACATCATGGATTG
1 ATTTTAGCCGATTTTGCAACGTTATGGACTG
*
33914 ATTTTAGCCGATTTTGCAATGTTATGGACT
1 ATTTTAGCCGATTTTGCAACGTTATGGACT
33944 TAATGAACCA
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
30 2 0.03
31 70 0.95
32 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (31 bp):
ATTTTAGCCGATTTTGCAACGTTATGGACTG
Found at i:34588 original size:23 final size:23
Alignment explanation
Indices: 34554--34597 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
34544 ATTTTCACAT
34554 CTAATAAACTTACTAAAAAAAAC
1 CTAATAAACTTACTAAAAAAAAC
*
34577 CTAATAAGCTTACTAAAAAAA
1 CTAATAAACTTACTAAAAAAA
34598 CTATAGAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.23
Consensus pattern (23 bp):
CTAATAAACTTACTAAAAAAAAC
Found at i:34702 original size:28 final size:27
Alignment explanation
Indices: 34650--34702 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
34640 TAATAACTTC
* **
34650 TAAATCTTTTTAATTTATTTTTTTAAA
1 TAAAGCTTTTTAATTTATTAGTTTAAA
34677 TAAAGCTTTTTAACTTTATTAGTTTA
1 TAAAGCTTTTTAA-TTTATTAGTTTA
34703 TTTAACTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (27 bp):
TAAAGCTTTTTAATTTATTAGTTTAAA
Found at i:36722 original size:30 final size:30
Alignment explanation
Indices: 36688--36750 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
36678 AACTTGGCAG
* * *
36688 TAATAGTGAAAATCTTTTTTTTTTTTTAGA
1 TAATAGTGAAAATCATTTGTTTTTTCTAGA
36718 TAATAGTGAAAATCATTTGTTTTTTCTAGA
1 TAATAGTGAAAATCATTTGTTTTTTCTAGA
36748 TAA
1 TAA
36751 AGAAAAACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (30 bp):
TAATAGTGAAAATCATTTGTTTTTTCTAGA
Found at i:37906 original size:49 final size:47
Alignment explanation
Indices: 37805--37946 Score: 169
Period size: 49 Copynumber: 3.0 Consensus size: 47
37795 GAGCGTGCCA
* * * *
37805 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
37852 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
37901 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
37947 GGATTGCTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.34
49 42 0.51
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Done.