Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017670.1 Corchorus olitorius cultivar O-4 contig17703, 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: 41613
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1093 original size:13 final size:12
Alignment explanation
Indices: 1075--1119 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
1065 ATTTTATTAC
1075 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
1088 TGTTTTATAAAT
1 TGTTTTATAAAT
*
1100 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
1114 TGTTTT
1 TGTTTT
1120 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:3295 original size:21 final size:21
Alignment explanation
Indices: 3271--3425 Score: 242
Period size: 21 Copynumber: 7.4 Consensus size: 21
3261 CTTAGGCAAT
*
3271 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
3292 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
3313 TCCAATGAGTTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
3334 TCCAATGAGTTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
3355 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
3376 TCCAATGAGTTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
3397 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
3418 TCCAATGA
1 TCCAATGA
3426 ACTCCTAGCA
Statistics
Matches: 128, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
20 3 0.02
21 125 0.98
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:6123 original size:17 final size:17
Alignment explanation
Indices: 6101--6134 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6091 ATAGTGAATA
* *
6101 TAAAATTTCATCTATAT
1 TAAAATTCCATCCATAT
6118 TAAAATTCCATCCATAT
1 TAAAATTCCATCCATAT
6135 ATATACTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATTCCATCCATAT
Found at i:9635 original size:19 final size:19
Alignment explanation
Indices: 9611--9652 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
9601 AACTTTAAAA
9611 CCTTTGGCTCAATAAATTT
1 CCTTTGGCTCAATAAATTT
9630 CCTTTGGCTCAATAAATTT
1 CCTTTGGCTCAATAAATTT
9649 CCTT
1 CCTT
9653 CAATCTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (19 bp):
CCTTTGGCTCAATAAATTT
Found at i:11188 original size:2 final size:2
Alignment explanation
Indices: 11175--11213 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
11165 GAATCGAAAT
*
11175 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11214 GTATTCTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12725 original size:18 final size:18
Alignment explanation
Indices: 12702--12737 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12692 TGTTGCTGAA
12702 TGTCCATAGGAAGTATAC
1 TGTCCATAGGAAGTATAC
*
12720 TGTCCATATGAAGTATAC
1 TGTCCATAGGAAGTATAC
12738 GACCTCGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (18 bp):
TGTCCATAGGAAGTATAC
Found at i:13626 original size:20 final size:20
Alignment explanation
Indices: 13601--13644 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
13591 CCTTTAATTA
13601 TTAATATGTTAAGTGGGTTT
1 TTAATATGTTAAGTGGGTTT
13621 TTAATATGTTAAGTGGGTTT
1 TTAATATGTTAAGTGGGTTT
13641 TTAA
1 TTAA
13645 GACATCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (20 bp):
TTAATATGTTAAGTGGGTTT
Found at i:14491 original size:96 final size:100
Alignment explanation
Indices: 14274--14526 Score: 306
Period size: 108 Copynumber: 2.5 Consensus size: 100
14264 TATTATAGAA
14274 TTTTAGAAATAAAATATAAAACTAATTTCAC-ATAGTTTAGCCCCAAATTAAAATTTTATTTTTA
1 TTTTAGAAATAAAATATAAAACTAATTTCACTA-AGTTTAGCCCCAAATT---A----ATTTTTA
*
14338 TTTTAAGGGTAAATTTCAAAATCAATAATTTATTGTTTATAGGG
58 TTTTAAGGGTAAATTTCAAAATCAATAA-TTATTGTCTATAGGG
* *
14382 TTTTAGAAATAAAATACAAAACTAATTTTACTAAGTTTAGCCCCAAATTAA-TTTT-TTTTAAGG
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAATTTTTATTTTAAGG
* *
14445 GTAAA-TTCTATAATTAATAA-TATTG-CTATAGGG
66 GTAAATTTC-AAAATCAATAATTATTGTCTATAGGG
*
14478 TTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAG-CCCAAATTAA
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAA
14527 AATTAAAATT
Statistics
Matches: 135, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
94 10 0.07
95 13 0.10
96 30 0.22
97 5 0.04
98 3 0.02
99 22 0.16
100 4 0.03
101 1 0.01
105 1 0.01
108 45 0.33
109 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (100 bp):
TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAATTTTTATTTTAAGG
GTAAATTTCAAAATCAATAATTATTGTCTATAGGG
Found at i:16651 original size:27 final size:27
Alignment explanation
Indices: 16597--16654 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
16587 TTTGCTACTC
* * **
16597 AACTTTTCCTACTCCTTTACATTACCA
1 AACTGTTCCTACTCCTTAACAACACCA
*
16624 AACTGTTCCTACTCCTTAACAACGCCA
1 AACTGTTCCTACTCCTTAACAACACCA
16651 AACT
1 AACT
16655 ACACCAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.33
Consensus pattern (27 bp):
AACTGTTCCTACTCCTTAACAACACCA
Found at i:18252 original size:9 final size:9
Alignment explanation
Indices: 18227--18260 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
18217 AATCCAATGC
18227 ATATATATT
1 ATATATATT
18236 ATACATATATT
1 AT--ATATATT
18247 ATATATATT
1 ATATATATT
18256 ATATA
1 ATATA
18261 AAAACAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (9 bp):
ATATATATT
Found at i:26081 original size:23 final size:23
Alignment explanation
Indices: 26042--26086 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
26032 CCACCAAGAC
*
26042 ACATGCATATACAATACATATAG
1 ACATGCACATACAATACATATAG
26065 ACATGACACATAC-ATACATATA
1 ACATG-CACATACAATACATATA
26087 TACAATCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (23 bp):
ACATGCACATACAATACATATAG
Found at i:27649 original size:2 final size:2
Alignment explanation
Indices: 27644--27668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27634 TAAAAAACAA
27644 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27669 CTAAATACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28878 original size:22 final size:19
Alignment explanation
Indices: 28850--28891 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
28840 TCTATAGTAA
28850 TCTCTCTCTCTAACTGAGAGCT
1 TCTCTCTC-CTAAC-G-GAGCT
28872 TCTCTCTCCTAACGGAGCT
1 TCTCTCTCCTAACGGAGCT
28891 T
1 T
28892 GTCGGAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 1 0.05
21 5 0.25
22 8 0.40
ACGTcount: A:0.17, C:0.33, G:0.14, T:0.36
Consensus pattern (19 bp):
TCTCTCTCCTAACGGAGCT
Found at i:39810 original size:13 final size:13
Alignment explanation
Indices: 39794--39829 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
39784 TCAACCTCAA
39794 TTTTAAAAAGCAC
1 TTTTAAAAAGCAC
*
39807 TTTTCAAAAGCAC
1 TTTTAAAAAGCAC
39820 TTCTTAAAAA
1 TT-TTAAAAA
39830 CCAAGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (13 bp):
TTTTAAAAAGCAC
Found at i:41021 original size:2 final size:2
Alignment explanation
Indices: 41016--41049 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
41006 GAATATTTCA
*
41016 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41050 GCAATGATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41254 original size:2 final size:2
Alignment explanation
Indices: 41247--41284 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41237 ATAATTACCC
41247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41285 CACAAAAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.