Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018492.1 Corchorus olitorius cultivar O-4 contig18525, 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: 55036
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:546 original size:23 final size:24
Alignment explanation
Indices: 510--561 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
500 ATATATACTA
510 TAAAAGGGAGAAAA-AAGAAAAGAG
1 TAAAAGGGAGAAAACAA-AAAAGAG
534 -AAAA-GGAGTAAAACAAAAAAGAG
1 TAAAAGGGAG-AAAACAAAAAAGAG
557 TAAAA
1 TAAAA
562 CCTTTCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 4 0.16
23 15 0.60
24 6 0.24
ACGTcount: A:0.69, C:0.02, G:0.23, T:0.06
Consensus pattern (24 bp):
TAAAAGGGAGAAAACAAAAAAGAG
Found at i:9269 original size:6 final size:6
Alignment explanation
Indices: 9253--9285 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
9243 CTTTTATTTC
9253 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
9286 TCCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:9440 original size:35 final size:35
Alignment explanation
Indices: 9391--9458 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
9381 AGGGGCCCAA
* *
9391 GCCTGGCCTAGGCGCTGGCCCGTGCTGGCCCGCAC
1 GCCTAGCCTAGGCGCTGGCCCGCGCTGGCCCGCAC
* **
9426 GCCTAGCCTGGGCGCTGGGTCGCGCTGGCCCGC
1 GCCTAGCCTAGGCGCTGGCCCGCGCTGGCCCGC
9459 GTGCTTGGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.04, C:0.41, G:0.40, T:0.15
Consensus pattern (35 bp):
GCCTAGCCTAGGCGCTGGCCCGCGCTGGCCCGCAC
Found at i:9562 original size:12 final size:11
Alignment explanation
Indices: 9515--9564 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
9505 TCTTTTCCTT
9515 TTTTTTTC-TC
1 TTTTTTTCTTC
* *
9525 TCTTCTTCTTC
1 TTTTTTTCTTC
9536 TTCTTTTTCTTC
1 TT-TTTTTCTTC
9548 TTTTTATTCTTC
1 TTTTT-TTCTTC
9560 TTTTT
1 TTTTT
9565 CCGGTAACCG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 6 0.18
11 6 0.18
12 21 0.64
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:16216 original size:21 final size:20
Alignment explanation
Indices: 16173--16216 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
16163 ATAAATGCAC
* *
16173 AGAGAAAATGAAATAAGGGA
1 AGAGAAAAGGAAAAAAGGGA
*
16193 AGAGAAAAGGACAAAAATGGA
1 AGAGAAAAGGA-AAAAAGGGA
16214 AGA
1 AGA
16217 ACATAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.61, C:0.02, G:0.30, T:0.07
Consensus pattern (20 bp):
AGAGAAAAGGAAAAAAGGGA
Found at i:22389 original size:21 final size:20
Alignment explanation
Indices: 22365--22423 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
22355 TTTATTATGT
* *
22365 TCTTCCATTTTTGTCCTTTTC
1 TCTTCCATTATT-TCATTTTC
*
22386 TCTTCCCTTATTTCATTTTC
1 TCTTCCATTATTTCATTTTC
*
22406 TCTGTGCATTTATTTCAT
1 TCT-TCCA-TTATTTCAT
22424 GGAAATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 10 0.32
21 12 0.39
22 9 0.29
ACGTcount: A:0.10, C:0.25, G:0.05, T:0.59
Consensus pattern (20 bp):
TCTTCCATTATTTCATTTTC
Found at i:25121 original size:2 final size:2
Alignment explanation
Indices: 25114--25139 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25104 GAATCAGAAA
25114 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
25140 GGTGAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27866 original size:17 final size:16
Alignment explanation
Indices: 27824--27867 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
27814 AAGCCTAAGC
27824 CTTCTTCTTCCTCGCA
1 CTTCTTCTTCCTCGCA
27840 CTTCTCTCTTCCTCG-A
1 CTTCT-TCTTCCTCGCA
27856 CTCATCTTCTTC
1 CT--TCTTCTTC
27868 GACAGAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 14 0.56
18 3 0.12
ACGTcount: A:0.07, C:0.43, G:0.05, T:0.45
Consensus pattern (16 bp):
CTTCTTCTTCCTCGCA
Found at i:44234 original size:35 final size:35
Alignment explanation
Indices: 44188--44323 Score: 218
Period size: 35 Copynumber: 3.9 Consensus size: 35
44178 GGCTGATTTC
*
44188 TTGGTCATCAACTTAATTCGGTGTAATTAAGTAAA
1 TTGGTAATCAACTTAATTCGGTGTAATTAAGTAAA
*
44223 TTGGTAATCAACTTAATTCGGCGTAATTAAGTAAA
1 TTGGTAATCAACTTAATTCGGTGTAATTAAGTAAA
* *
44258 TTGGTAATCAACTTAATCCGGTGTAACTAAGTAAA
1 TTGGTAATCAACTTAATTCGGTGTAATTAAGTAAA
**
44293 TCAGTAATCAACTTAATTCGGTGTAATTAAG
1 TTGGTAATCAACTTAATTCGGTGTAATTAAG
44324 AATCAAGGAA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 92 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (35 bp):
TTGGTAATCAACTTAATTCGGTGTAATTAAGTAAA
Found at i:44240 original size:16 final size:16
Alignment explanation
Indices: 44188--44274 Score: 57
Period size: 16 Copynumber: 5.1 Consensus size: 16
44178 GGCTGATTTC
*
44188 TTGGTCATCAACTTAA
1 TTGGTAATCAACTTAA
* * *
44204 TTCGGTGTAATTAAGTAAA
1 TT--G-GTAATCAACTTAA
44223 TTGGTAATCAACTTAA
1 TTGGTAATCAACTTAA
* * *
44239 TTCGGCGTAATTAAGTAAA
1 TT--G-GTAATCAACTTAA
44258 TTGGTAATCAACTTAA
1 TTGGTAATCAACTTAA
44274 T
1 T
44275 CCGGTGTAAC
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
16 25 0.48
17 2 0.04
18 2 0.04
19 23 0.44
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (16 bp):
TTGGTAATCAACTTAA
Found at i:44259 original size:19 final size:18
Alignment explanation
Indices: 44202--44323 Score: 58
Period size: 16 Copynumber: 6.9 Consensus size: 18
44192 TCATCAACTT
44202 AATTCGGTGTAATTAAGTA
1 AATTCGG-GTAATTAAGTA
* * *
44221 AATT--GGTAATCAACTT
1 AATTCGGGTAATTAAGTA
44237 AATTCGGCGTAATTAAGTA
1 AATTCGG-GTAATTAAGTA
* * *
44256 AATT--GGTAATCAACTT
1 AATTCGGGTAATTAAGTA
* *
44272 AATCCGGTGTAACTAAGTA
1 AATTCGG-GTAATTAAGTA
* * * *
44291 AA-TC-AGTAATCAACTT
1 AATTCGGGTAATTAAGTA
44307 AATTCGGTGTAATTAAG
1 AATTCGG-GTAATTAAG
44324 AATCAAGGAA
Statistics
Matches: 71, Mismatches: 23, Indels: 18
0.63 0.21 0.16
Matches are distributed among these distances:
16 32 0.45
17 4 0.06
18 3 0.04
19 32 0.45
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (18 bp):
AATTCGGGTAATTAAGTA
Found at i:51603 original size:18 final size:19
Alignment explanation
Indices: 51570--51606 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
51560 GAAGTTCGTG
*
51570 TTTGAAGATTTATTGAAGA
1 TTTGAAGATCTATTGAAGA
51589 TTTGAAGA-CTATTGAAGA
1 TTTGAAGATCTATTGAAGA
51607 ATTATCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (19 bp):
TTTGAAGATCTATTGAAGA
Found at i:52229 original size:18 final size:18
Alignment explanation
Indices: 52206--52242 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52196 TTCTCTTCTT
52206 TTTTTCTTCAAGTTCTAG
1 TTTTTCTTCAAGTTCTAG
* *
52224 TTTTTCTTCTAGTTTTAG
1 TTTTTCTTCAAGTTCTAG
52242 T
1 T
52243 GTTAGGGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.62
Consensus pattern (18 bp):
TTTTTCTTCAAGTTCTAG
Done.