Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012689.1 Corchorus olitorius cultivar O-4 contig12722, 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: 11590
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Found at i:2276 original size:25 final size:25
Alignment explanation
Indices: 2242--2295 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2232 AAATGAAATG
*
2242 ATACCCGGAG-GATTTATTAGAATTA
1 ATACCCGGAGAG-TTTATCAGAATTA
2267 ATACCCGGAGAGTTTATCAGAATTA
1 ATACCCGGAGAGTTTATCAGAATTA
2292 ATAC
1 ATAC
2296 ATGGAGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (25 bp):
ATACCCGGAGAGTTTATCAGAATTA
Found at i:2301 original size:25 final size:24
Alignment explanation
Indices: 2242--2305 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
2232 AAATGAAATG
* *
2242 ATACCCGGAGGATTTATTAGAATTA
1 ATACACGGAGG-TTTATCAGAATTA
*
2267 ATACCCGGAGAGTTTATCAGAATTA
1 ATACACGGAG-GTTTATCAGAATTA
*
2292 ATACATGGAGGTTT
1 ATACACGGAGGTTT
2306 TTGAAGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.11
25 30 0.86
26 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (24 bp):
ATACACGGAGGTTTATCAGAATTA
Found at i:2433 original size:166 final size:169
Alignment explanation
Indices: 2112--2461 Score: 474
Period size: 166 Copynumber: 2.1 Consensus size: 169
2102 GGGGACTTAA
* * * *
2112 CAGAATTAATACCTGGAGGTTTCTGAAATTGTGCCCGAAGGTCTTAGAAATGCAAACTCGACCTT
1 CAGAATTAATACATGGAGGTTTCTGAAATTGCGCCCGAAGGTCTTACAAATGCAAACTCGACCTA
*
2177 GAACAAGGTTTTGATTTTGAAACTTAAACCCGCAACTTTGATTAAAAACTTGATGAAATGAAATG
66 GAACAAGG--TAGATTTTGAAACTTAAA-CCGCAACTTTGATTAAAAACTTGATGAAATGAAATG
* *
2242 ATACCCGGAGGATTTATTAGAATTAATACCCGGA-GAGTTTAT
128 ATACCCGGAGGATTTATCAGAATTAATACCCAGAGGA-TTTAT
* * * *
2284 CAGAATTAATACATGGAGGTTTTTGAAGTTGCGCCCGGAGGTCTTACAATTGCAAACTCGACCTA
1 CAGAATTAATACATGGAGGTTTCTGAAATTGCGCCCGAAGGTCTTACAAATGCAAACTCGACCTA
** * * *
2349 GTGCATGG-AGTTTTTGAAACTTAAA-TGCAACTTTGATT-AAAACTTGATGAAATGAAATGATA
66 GAACAAGGTAGATTTTGAAACTTAAACCGCAACTTTGATTAAAAACTTGATGAAATGAAATGATA
* *
2411 CCTGGAGGATTTATCCGAATTAATACCCAGAGGATTTAT
131 CCCGGAGGATTTATCAGAATTAATACCCAGAGGATTTAT
2450 CAGAATTAATAC
1 CAGAATTAATAC
2462 CCGGAGATTT
Statistics
Matches: 159, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
166 68 0.43
167 14 0.09
169 15 0.09
172 62 0.39
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (169 bp):
CAGAATTAATACATGGAGGTTTCTGAAATTGCGCCCGAAGGTCTTACAAATGCAAACTCGACCTA
GAACAAGGTAGATTTTGAAACTTAAACCGCAACTTTGATTAAAAACTTGATGAAATGAAATGATA
CCCGGAGGATTTATCAGAATTAATACCCAGAGGATTTAT
Found at i:2443 original size:25 final size:25
Alignment explanation
Indices: 2415--2492 Score: 122
Period size: 25 Copynumber: 3.2 Consensus size: 25
2405 ATGATACCTG
*
2415 GAGGATTTATCCGAATTAATACCCA
1 GAGGATTTATCAGAATTAATACCCA
*
2440 GAGGATTTATCAGAATTAATACCCG
1 GAGGATTTATCAGAATTAATACCCA
*
2465 GA-GATTTATTAGAATTAATACCCA
1 GAGGATTTATCAGAATTAATACCCA
2489 GAGG
1 GAGG
2493 TTTCTGAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 22 0.46
25 26 0.54
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (25 bp):
GAGGATTTATCAGAATTAATACCCA
Found at i:2575 original size:190 final size:192
Alignment explanation
Indices: 2242--2627 Score: 560
Period size: 190 Copynumber: 2.0 Consensus size: 192
2232 AAATGAAATG
* * ** *
2242 ATACCCGGAGGATTTATTAGAATTAATACCCGGAGAGTTTATCAGAATTAATACATGGAGGTTTT
1 ATACCCAGAGGATTTATCAGAATTAATACCCGGAGAGTTTATCAGAATTAATACACAGAGGTTTC
* * * *
2307 TGAAGTTGCGCCCGGAGGTCTTACAATTGCAAACTCGACCTAGTGCATGGAGTTTTTGAAACTTA
66 TGAAATTGCGCCCGGAGATCTTACAAATGCAAACTCGACCTAGTGCAAGGAGTTTTTGAAACTTA
* * **
2372 AATGCAACTTTGATTAA-AACTTGATGAAATGAAATGATACCTGGAGGATTTATCCGAATTA
131 AATGCAACTTTGATTAACAACTTGATAAAATGAAATGATACCCGGAGGATTTATCAAAATTA
* *
2433 ATACCCAGAGGATTTATCAGAATTAATACCCGGAGA-TTTATTAGAATTAATACCCAGAGGTTTC
1 ATACCCAGAGGATTTATCAGAATTAATACCCGGAGAGTTTATCAGAATTAATACACAGAGGTTTC
* * * **
2497 TGAAATTGTGCCCGGAGATTTTACAAATGCAAACTCGACCTTGTGCAAGGTTTTTTTGAAACTTA
66 TGAAATTGCGCCCGGAGATCTTACAAATGCAAACTCGACCTAGTGCAAGGAGTTTTTGAAACTTA
* *
2562 AATGCATCTTTGATTAACAACTTGATAAAATGAAGTGATACCCGGAGGATTTATCAAAATTA
131 AATGCAACTTTGATTAACAACTTGATAAAATGAAATGATACCCGGAGGATTTATCAAAATTA
2624 ATAC
1 ATAC
2628 TCGGAGGTTT
Statistics
Matches: 172, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
190 95 0.55
191 77 0.45
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (192 bp):
ATACCCAGAGGATTTATCAGAATTAATACCCGGAGAGTTTATCAGAATTAATACACAGAGGTTTC
TGAAATTGCGCCCGGAGATCTTACAAATGCAAACTCGACCTAGTGCAAGGAGTTTTTGAAACTTA
AATGCAACTTTGATTAACAACTTGATAAAATGAAATGATACCCGGAGGATTTATCAAAATTA
Found at i:2766 original size:143 final size:141
Alignment explanation
Indices: 2458--2847 Score: 559
Period size: 143 Copynumber: 2.8 Consensus size: 141
2448 ATCAGAATTA
* * * *
2458 ATACCCGG-AGATTTATTAGAATTAATACCCAGAGGTTTCTGAAATTGTGCCCGGAGATTTTACA
1 ATACCCGGAAGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
* *
2522 AATGCAAACTCGACCTTGTGCAAGGTTTTTTTGAAACTTAAATGCATCTTTGATTAACAACTTGA
66 AATGCAAACTCGACCTTGTGCAAGG-TTTTTTGAAACTTAAATGCAACATTGATTAACAACTTGA
2587 TAAAATGAAGTG
130 TAAAATGAAGTG
* * *
2599 ATACCCGGAGGATTTATCAAAATTAATACTCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
1 ATACCCGGAAGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
* *
2664 AATGCAAACTCAACATTGTGCAAGGTTTTCCTTGAAACTTAAATGCAACATTGATTAACAACTTG
66 AATGCAAACTCGACCTTGTGCAAGGTTTT--TTGAAACTTAAATGCAACATTGATTAACAACTTG
* *
2729 ATGAAATGAGGTG
129 ATAAAATGAAGTG
* ** *
2742 ATACCCGGAAGATTTATCAGAATTAATACCCGGAGGTTTCTAAAATCATGCCCGGACGTCTTACA
1 ATACCCGGAAGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
* *
2807 AATGCTAAACTCGACCTTGAGTAAGG-TTTTTGAAACTTAAA
66 AATGC-AAACTCGACCTTGTGCAAGGTTTTTTGAAACTTAAA
2848 CACAACTTTG
Statistics
Matches: 221, Mismatches: 24, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
141 24 0.11
142 72 0.33
143 109 0.49
144 16 0.07
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (141 bp):
ATACCCGGAAGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACA
AATGCAAACTCGACCTTGTGCAAGGTTTTTTGAAACTTAAATGCAACATTGATTAACAACTTGAT
AAAATGAAGTG
Found at i:7977 original size:27 final size:27
Alignment explanation
Indices: 7943--8004 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
7933 CATTTCTTAA
7943 TTGG-CATTAGGT-CATATAGGGGCATT
1 TTGGTCATT-GGTGCATATAGGGGCATT
**
7969 TTGGTCATTTTTGCATATAGGGGCATT
1 TTGGTCATTGGTGCATATAGGGGCATT
7996 TTGGTCATT
1 TTGGTCATT
8005 TTGTAGGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.42
Consensus pattern (27 bp):
TTGGTCATTGGTGCATATAGGGGCATT
Found at i:8005 original size:27 final size:27
Alignment explanation
Indices: 7955--8006 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
7945 GGCATTAGGT
7955 CATATAGGGGCATTTTGGTCATTTTTG
1 CATATAGGGGCATTTTGGTCATTTTTG
7982 CATATAGGGGCATTTTGGTCATTTT
1 CATATAGGGGCATTTTGGTCATTTT
8007 GTAGGTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (27 bp):
CATATAGGGGCATTTTGGTCATTTTTG
Found at i:8033 original size:28 final size:27
Alignment explanation
Indices: 7960--8046 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
7950 TAGGTCATAT
* * **
7960 AGGGGCATTTTGGTCATTTTTGCAT-A
1 AGGGGCATTATAGTCATTTTTGGTTCA
* *
7986 TAGGGGCATTTTGGTCATTTTGTAGGTTC-
1 -AGGGGCATTATAGTCATTTT-T-GGTTCA
*
8015 AGGGGCATTATAGTTATTTTTGGTTCA
1 AGGGGCATTATAGTCATTTTTGGTTCA
8042 AGGGG
1 AGGGG
8047 GGCATTGTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 5 0.10
27 26 0.51
28 18 0.35
29 2 0.04
ACGTcount: A:0.18, C:0.09, G:0.31, T:0.41
Consensus pattern (27 bp):
AGGGGCATTATAGTCATTTTTGGTTCA
Done.