Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022199.1 Corchorus olitorius cultivar O-4 contig22232, 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: 9778
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:594 original size:27 final size:27
Alignment explanation
Indices: 559--633 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
549 TGTGAACTTA
559 AAAAATGACCAAAATGCCCCTGAATGC
1 AAAAATGACCAAAATGCCCCTGAATGC
*
586 AAAAATGACCAAAATGCCCCTGAATGT
1 AAAAATGACCAAAATGCCCCTGAATGC
613 AAAAATGACCAAAATGCCCCT
1 AAAAATGACCAAAATGCCCCT
634 AGGTGATCCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGAATGC
Found at i:971 original size:50 final size:50
Alignment explanation
Indices: 911--1680 Score: 1261
Period size: 50 Copynumber: 15.4 Consensus size: 50
901 GATCCTCGAA
* * *
911 TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
* * * * *
961 CTTGGCTTGTGGAAAAGCCTATGTTGATAGTTGACTCGTATAGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
* * * * *
1011 CTTGGCTTGTGGAAAAGTCTATGTTGATAATTGACTTGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
* * *
1061 TTCGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
* *
1111 TTTGGCTTATGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGGG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1161 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1211 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
* *
1261 TTTGGCTTGTGAAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
*
1311 TTTGGCTTATGGAAAACCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
* * *
1361 TTCGGCTTGTGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAATGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
*
1411 TTTGGCTTATCGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
* *
1461 TTTGGCTTGTGGAAAAGCCTGTGTTGATAATTGATTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
*
1511 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGATTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
* *
1561 TTTGGCTTGTGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAATGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
*
1611 TTCGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
1661 TTTGGCTTATGGAAAAGCCT
1 TTTGGCTTATGGAAAAGCCT
1681 ATGTATTCGG
Statistics
Matches: 679, Mismatches: 41, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 679 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (50 bp):
TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
Found at i:1904 original size:80 final size:79
Alignment explanation
Indices: 1764--2038 Score: 379
Period size: 87 Copynumber: 3.4 Consensus size: 79
1754 ATACCTTTGG
* * *
1764 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
1 AAAAAAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGACCAATG
*
1829 TGCGGCCAACTTGA
66 TGCGGTCAACTTGA
1843 AAAAAAACCTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGACCAAT
1 AAAAAAA-CTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGACCAAT
* *
1908 TTGCAGTCAACTTGAAA
65 GTGCGGTCAACTTG--A
*
1925 ACTTGAAGAATAACTCTGAGTCTGATGTTGTAACTAAAAACTTCTTAATTGATGATGAAAAAGGA
1 A----AA-AA-AACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGA
* *
1990 TCGATGTGCGGTCAACTTGA
60 CCAATGTGCGGTCAACTTGA
*
2010 AAAATAACTCTGAGTCTGATGTTGTAACT
1 AAAAAAACTCTGAGTCTGATGTTGTAACT
2039 CGAATCTTTG
Statistics
Matches: 175, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
79 30 0.17
80 67 0.38
81 2 0.01
82 2 0.01
85 2 0.01
86 2 0.01
87 68 0.39
88 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (79 bp):
AAAAAAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAAAAAGGACCAATG
TGCGGTCAACTTGA
Found at i:2569 original size:51 final size:50
Alignment explanation
Indices: 2425--2575 Score: 223
Period size: 50 Copynumber: 3.0 Consensus size: 50
2415 CTTCAATGTC
* *
2425 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
* *
2475 CTTTGAAAAGCAAATTTCGATCTTGGA-TCTACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTC-ACAAATGGAAAGCAATTTTA
* *
2525 CTTTGAAAAGCGAATTTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAA-TTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
2576 TTGTAGAACT
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
49 2 0.02
50 56 0.62
51 30 0.33
52 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
Found at i:3200 original size:5 final size:5
Alignment explanation
Indices: 3184--3248 Score: 64
Period size: 5 Copynumber: 12.6 Consensus size: 5
3174 TCAATTCTCT
3184 TTTGA TTTTGA TTTGA TTTGA TTTTTGA TTTTGA TTTGA TTT-- TTTGA
1 TTTGA -TTTGA TTTGA TTTGA --TTTGA -TTTGA TTTGA TTTGA TTTGA
3231 -TTGA CTTTGA TTTGA TTT
1 TTTGA -TTTGA TTTGA TTT
3249 TTTTAATTCT
Statistics
Matches: 53, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 26 0.49
6 15 0.28
7 5 0.09
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.65
Consensus pattern (5 bp):
TTTGA
Found at i:3209 original size:23 final size:21
Alignment explanation
Indices: 3183--3252 Score: 95
Period size: 23 Copynumber: 3.1 Consensus size: 21
3173 ATCAATTCTC
3183 TTTTGATTTTGATTTGATTTGAT
1 TTTTGATTTTGATTTGATTT--T
3206 TTTTGATTTTGATTTGATTTT
1 TTTTGATTTTGATTTGATTTT
*
3227 TTGATTGACTTTGATTTGATTTT
1 TT--TTGATTTTGATTTGATTTT
3250 TTT
1 TTT
3253 AATTCTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
21 4 0.09
23 40 0.91
ACGTcount: A:0.16, C:0.01, G:0.16, T:0.67
Consensus pattern (21 bp):
TTTTGATTTTGATTTGATTTT
Found at i:3228 original size:13 final size:13
Alignment explanation
Indices: 3212--3251 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3202 TGATTTTTGA
3212 TTTTGATTTGATT
1 TTTTGATTTGATT
3225 TTTTGA-TTGA--
1 TTTTGATTTGATT
*
3235 CTTTGATTTGATT
1 TTTTGATTTGATT
3248 TTTT
1 TTTT
3252 TAATTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 5 0.23
11 4 0.18
12 4 0.18
13 9 0.41
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.68
Consensus pattern (13 bp):
TTTTGATTTGATT
Found at i:3239 original size:18 final size:18
Alignment explanation
Indices: 3189--3243 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
3179 TCTCTTTTGA
3189 TTTTGATTTGATTTGA-T
1 TTTTGATTTGATTTGATT
3206 TTTTGATTTTGATTTGATT
1 TTTTGA-TTTGATTTGATT
3225 TTTTGA-TTGACTTTGATT
1 TTTTGATTTGA-TTTGATT
3243 T
1 T
3244 GATTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.29
18 18 0.51
19 7 0.20
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.65
Consensus pattern (18 bp):
TTTTGATTTGATTTGATT
Found at i:3272 original size:7 final size:7
Alignment explanation
Indices: 3260--3293 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
3250 TTTAATTCTT
3260 TTTTTTG
1 TTTTTTG
3267 TTTTTTG
1 TTTTTTG
3274 -TTTTTG
1 TTTTTTG
3280 TTTTATTG
1 TTTT-TTG
3288 TTTTTT
1 TTTTTT
3294 TTTGAATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (7 bp):
TTTTTTG
Found at i:3277 original size:13 final size:14
Alignment explanation
Indices: 3261--3296 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
3251 TTAATTCTTT
3261 TTTTTGTTTT-TTG
1 TTTTTGTTTTATTG
3274 TTTTTGTTTTATTG
1 TTTTTGTTTTATTG
3288 TTTTT-TTTT
1 TTTTTGTTTT
3297 GAATTTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTATTG
Done.