Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021991.1 Corchorus olitorius cultivar O-4 contig22024, 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: 4371
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:1453 original size:76 final size:75
Alignment explanation
Indices: 1318--1463 Score: 186
Period size: 76 Copynumber: 1.9 Consensus size: 75
1308 TTATCTGGAT
* * * * *
1318 TGTGAGCAAAGGAATGATGAGTTTTAATTGAAAAGTTTTCAAAAATCAGTTTTTATCAAAACTAT
1 TGTGAGCAAAGGAATGAAGAGTTTTAATTCAAAAGTGTTCAAAAATCAGTTTTGATCAAAACGAT
1383 GATTTCGAGC
66 GATTTCGAGC
* * * *
1393 TGTGAGCAAAGGAATGACAGTGTTTTAA-TCAAAAGATGTTCCAAAATCAGTTTTGGTCAAAGCG
1 TGTGAGCAAAGGAATGA-AGAGTTTTAATTCAAAAG-TGTTCAAAAATCAGTTTTGATCAAAACG
1457 ATGATTT
64 ATGATTT
1464 TAAGGTGACT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
75 23 0.38
76 37 0.62
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (75 bp):
TGTGAGCAAAGGAATGAAGAGTTTTAATTCAAAAGTGTTCAAAAATCAGTTTTGATCAAAACGAT
GATTTCGAGC
Found at i:2290 original size:14 final size:15
Alignment explanation
Indices: 2262--2292 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2252 CCACTCAATC
2262 AAGAAATTAAAAAAA
1 AAGAAATTAAAAAAA
2277 AAGAAATTAAAAAAA
1 AAGAAATTAAAAAAA
2292 A
1 A
2293 TCAAAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (15 bp):
AAGAAATTAAAAAAA
Found at i:2298 original size:22 final size:22
Alignment explanation
Indices: 2284--2328 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
2274 AAAAAGAAAT
2284 TAAAAAAAATCAAAAAATCAAA
1 TAAAAAAAATCAAAAAATCAAA
*
2306 TCAAAAAAATCAAAAAAATCAAA
1 TAAAAAAAATC-AAAAAATCAAA
2329 ATCAAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (22 bp):
TAAAAAAAATCAAAAAATCAAA
Found at i:2298 original size:23 final size:22
Alignment explanation
Indices: 2272--2328 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
2262 AAGAAATTAA
*
2272 AAAAAAAGAAATTAAAAAAAATC
1 AAAAAAACAAA-TAAAAAAAATC
* *
2295 AAAAAATCAAATCAAAAAAATC
1 AAAAAAACAAATAAAAAAAATC
2317 AAAAAAATCAAA
1 AAAAAAA-CAAA
2329 ATCAAAAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.12
Consensus pattern (22 bp):
AAAAAAACAAATAAAAAAAATC
Found at i:2300 original size:9 final size:9
Alignment explanation
Indices: 2286--2329 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
2276 AAAGAAATTA
2286 AAAAAAATC
1 AAAAAAATC
2295 -AAAAAATC
1 AAAAAAATC
2303 ---A-AATC
1 AAAAAAATC
2308 AAAAAAATC
1 AAAAAAATC
2317 AAAAAAATC
1 AAAAAAATC
2326 AAAA
1 AAAA
2330 TCAAAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.13
6 1 0.03
8 9 0.29
9 17 0.55
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:2306 original size:13 final size:14
Alignment explanation
Indices: 2290--2319 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2280 AAATTAAAAA
2290 AAATC-AAAAAATC
1 AAATCAAAAAAATC
2303 AAATCAAAAAAATC
1 AAATCAAAAAAATC
2317 AAA
1 AAA
2320 AAAATCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (14 bp):
AAATCAAAAAAATC
Found at i:2335 original size:22 final size:21
Alignment explanation
Indices: 2287--2335 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 21
2277 AAGAAATTAA
2287 AAAAAATCAAAAAATCAAATC
1 AAAAAATCAAAAAATCAAATC
2308 AAAAAAATCAAAAAAATCAAAATC
1 -AAAAAATC-AAAAAATC-AAATC
2332 AAAA
1 AAAA
2336 GAGAATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.32
23 12 0.48
24 5 0.20
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAAATCAAAAAATCAAATC
Found at i:2335 original size:23 final size:22
Alignment explanation
Indices: 2286--2335 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
2276 AAAGAAATTA
2286 AAAAAAATCAAAAAATCAAATC
1 AAAAAAATCAAAAAATCAAATC
2308 AAAAAAATCAAAAAAATCAAAATC
1 AAAAAAATC-AAAAAATC-AAATC
2332 AAAA
1 AAAA
2336 GAGAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 9 0.35
23 8 0.31
24 9 0.35
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (22 bp):
AAAAAAATCAAAAAATCAAATC
Found at i:3043 original size:49 final size:50
Alignment explanation
Indices: 2951--3099 Score: 246
Period size: 49 Copynumber: 3.0 Consensus size: 50
2941 AGTTTTGCAA
*
2951 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
3001 TAAAATTGCTTTCCATTTGTGA-TTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
3050 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
3100 GACATTGAAG
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
49 46 0.50
50 46 0.50
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:3678 original size:91 final size:88
Alignment explanation
Indices: 3515--3716 Score: 289
Period size: 91 Copynumber: 2.3 Consensus size: 88
3505 TTTTAATCAT
*
3515 AACATCAGACTCAGAGTTATTCTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
1 AACATCAGACTCAGAGTTATTTTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
*
3580 TCAATCAAGAAGTTTTCAGCTAC
66 TCAATCAAGAAGTTTCCAGCTAC
* * *
3603 AACATCAGACTCAGAGTTATTTTTCAAGTTGTTTTTC-AAGTTGACCGCACATTGGTCCTTTTTC
1 AACATCAGACTCAGAGTTATTTTTCAA---G-TTATCAAAATTGACCGCAAATTGGTCCTTTTTC
*
3667 ATCATCAATCAAGAAGTTTCCAGTTAC
62 ATCATCAATCAAGAAGTTTCCAGCTAC
* *
3694 AACATCAGAATTAGAGTTATTTT
1 AACATCAGACTCAGAGTTATTTT
3717 CCAAAGGTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
88 26 0.25
91 72 0.71
92 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (88 bp):
AACATCAGACTCAGAGTTATTTTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
TCAATCAAGAAGTTTCCAGCTAC
Found at i:3871 original size:50 final size:50
Alignment explanation
Indices: 3796--4143 Score: 570
Period size: 50 Copynumber: 6.9 Consensus size: 50
3786 CCATCCGAAT
3796 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
3846 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
*
3896 ACATAGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
*
3946 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
*
3996 ACATAGGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
* * *
4046 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCGTACGAGTCGACTATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAT-CA
* * *
4097 AGCCACGTAGGCTTTTCCAGAAGCCTAACTCGTTTCCTTACGAGTCA
1 A--CA--TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
4144 GTTCAAACAT
Statistics
Matches: 280, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
50 239 0.85
51 3 0.01
53 2 0.01
55 36 0.13
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (50 bp):
ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCA
Done.