Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012130.1 Corchorus capsularis cultivar CVL-1 contig12151, 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: 26035
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:312 original size:22 final size:22
Alignment explanation
Indices: 192--533 Score: 192
Period size: 22 Copynumber: 15.6 Consensus size: 22
182 TTCGGAAGGA
* * *
192 GGTTATCAACATTTCATCGTGT
1 GGTTATCAAAATTTCATAGAGT
214 GGTTA-CTAAAATTTCATATGCA--
1 GGTTATC-AAAATTTCATA-G-AGT
* * * *
236 AGTTATCAAAATTTGATGGTGT
1 GGTTATCAAAATTTCATAGAGT
*
258 GATTAT-AGAAATTTCATA-AG-
1 GGTTATCA-AAATTTCATAGAGT
* *
278 GAAGTT-TTAAAATCTCATAGAGT
1 G--GTTATCAAAATTTCATAGAGT
* *
301 GGTTATCAAAATTTAATATGA-A
1 GGTTATCAAAATTTCATA-GAGT
*
323 GGTTATCAAAATTTTATA-ATGT
1 GGTTATCAAAATTTCATAGA-GT
* * *
345 AGTTATCAAAATTTCACAGTGT
1 GGTTATCAAAATTTCATAGAGT
*
367 GGTTATCAAAAATTTCATATG-GA
1 GGTTATC-AAAATTTCATA-GAGT
* **
390 GGTTA-CAAAATTTCACATTGT
1 GGTTATCAAAATTTCATAGAGT
411 GGTTATCAAAATTTCATAGA-T
1 GGTTATCAAAATTTCATAGAGT
* * *
432 AGTGTAACAAAATTTCATAGAGA
1 GGT-TATCAAAATTTCATAGAGT
* * * *
455 GG-TATTTATAATTTCATTGAGA
1 GGTTA-TCAAAATTTCATAGAGT
*
477 GGTTATCAAAATTTCATTAG-GA
1 GGTTATCAAAATTTCA-TAGAGT
*
499 GG-TATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGAGT
*
520 GATTATCAAAATTT
1 GGTTATCAAAATTT
534 TAGACTATGG
Statistics
Matches: 246, Mismatches: 46, Indels: 56
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.02
21 53 0.22
22 161 0.65
23 26 0.11
24 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGAGT
Found at i:799 original size:22 final size:22
Alignment explanation
Indices: 589--803 Score: 131
Period size: 22 Copynumber: 9.9 Consensus size: 22
579 GCTACTAAAT
* *
589 TAGGAAGGTTATCAAAATTTTA
1 TAGGGAGGTTATCAAAATTTCA
** *
611 CTCTGGA-GTAATCAAAATTTCA
1 -TAGGGAGGTTATCAAAATTTCA
* * * * *
633 CACGGATGTTATTAAAATTTCT
1 TAGGGAGGTTATCAAAATTTCA
* *
655 TATGAAGGTTATCAAAATTTCA
1 TAGGGAGGTTATCAAAATTTCA
**
677 TAGGGAGGTTATTGAAATTTC-
1 TAGGGAGGTTATCAAAATTTCA
** *
698 TCAGTTTA-GTTTTCAAAATTTCA
1 T-AG-GGAGGTTATCAAAATTTCA
*
721 TAGGGA-GTTATCAAAATTCCA
1 TAGGGAGGTTATCAAAATTTCA
* *
742 TAGCGTGG-T-TCAAAATTTCA
1 TAGGGAGGTTATCAAAATTTCA
*
762 TAGTGTGTGG--ATCAAAATTTCA
1 TAG-G-GAGGTTATCAAAATTTCA
*
784 TAGGGAGGTTAACAAAATTT
1 TAGGGAGGTTATCAAAATTT
804 GATAATGAGA
Statistics
Matches: 146, Mismatches: 36, Indels: 21
0.72 0.18 0.10
Matches are distributed among these distances:
20 16 0.11
21 24 0.16
22 101 0.69
23 5 0.03
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (22 bp):
TAGGGAGGTTATCAAAATTTCA
Found at i:817 original size:22 final size:22
Alignment explanation
Indices: 774--822 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
764 GTGTGTGGAT
* *
774 CAAAATTTCATAGGGAGGTTAA
1 CAAAATTTCATAAGGAGATTAA
* *
796 CAAAATTTGATAATGAGATTAA
1 CAAAATTTCATAAGGAGATTAA
*
818 TAAAA
1 CAAAA
823 AAACCATGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (22 bp):
CAAAATTTCATAAGGAGATTAA
Found at i:852 original size:16 final size:16
Alignment explanation
Indices: 833--878 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
823 AAACCATGGG
*
833 TATCAAAATTTGTGGT
1 TATCAAAATTTGAGGT
849 TATCAAAATTTTATGAGGT
1 TATCAAAA--TT-TGAGGT
868 TATCAAAATTT
1 TATCAAAATTT
879 TATAAGAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 2 0.08
19 13 0.50
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (16 bp):
TATCAAAATTTGAGGT
Found at i:919 original size:21 final size:22
Alignment explanation
Indices: 867--928 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
857 TTTTATGAGG
*
867 TTATCAAAATTTTATAAG-AAGGT
1 TTATCAAAAATTTAT-AGTAA-GT
*
890 TTATAAAAAATTTATAGTAA-T
1 TTATCAAAAATTTATAGTAAGT
911 TTATC-AAAATTTCATAGT
1 TTATCAAAAATTT-ATAGT
929 GAGGTCACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.21
21 10 0.29
22 2 0.06
23 15 0.44
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (22 bp):
TTATCAAAAATTTATAGTAAGT
Found at i:3052 original size:15 final size:15
Alignment explanation
Indices: 3029--3058 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3019 ATCGGTTGAA
*
3029 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
3044 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
3059 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:12792 original size:42 final size:43
Alignment explanation
Indices: 12721--12803 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
12711 CTTAAACGTG
*
12721 TTAATCGTGTCTTGACACAATTAGGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACAATTAGGACACGAAACACGATAATC
* *
12764 TTAATCGTGTC-CGACACGATTTA-GACACGAGACACGATAA
1 TTAATCGTGTCTCGACAC-AATTAGGACACGAAACACGATAA
12804 ACCAAAACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 21 0.58
43 15 0.42
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACAATTAGGACACGAAACACGATAATC
Found at i:13296 original size:114 final size:116
Alignment explanation
Indices: 13096--13327 Score: 398
Period size: 114 Copynumber: 2.0 Consensus size: 116
13086 AACTTTCAAG
13096 AACACAGGTTTTGTGTGTGTGTGTGTTTTTAGAGTAATAAAGAGAAAATCCGAATAGAATCAATT
1 AACACAGGTTTTGTGTGTGTGTGTGTTTTTAGAGTAATAAAGAGAAAATCCGAATAGAATCAATT
*
13161 AAGAAAAAAGAAACTAAACAAGCA-TT-TTTTTTTTTGGGGTGGATATGCA
66 AAGAAAAAAGAAACTAAACAAGCATTTATTTTTTTTTGAGGTGGATATGCA
13210 AACACAGGTTTATGTGTGTGTGTGT-TTTTTAGAGTAATAAAGAGAAAATCCGAATAGAATCAAT
1 AACACAGGTTT-TGTGTGTGTGTGTGTTTTTAGAGTAATAAAGAGAAAATCCGAATAGAATCAAT
* *
13274 TAAGAAAAAAGAAACTTAACAAGCATTTGATTTTTTTTTTAGGTGGATATGCA
65 TAAGAAAAAAGAAACTAAACAAGCATTT-ATTTTTTTTTGAGGTGGATATGCA
13327 A
1 A
13328 TGCAAGAAAT
Statistics
Matches: 111, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
114 74 0.67
115 15 0.14
117 22 0.20
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (116 bp):
AACACAGGTTTTGTGTGTGTGTGTGTTTTTAGAGTAATAAAGAGAAAATCCGAATAGAATCAATT
AAGAAAAAAGAAACTAAACAAGCATTTATTTTTTTTTGAGGTGGATATGCA
Found at i:13619 original size:2 final size:2
Alignment explanation
Indices: 13606--13647 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
13596 TCTTCCATAG
13606 AT AT AT AGT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13647 A
1 A
13648 AAATTGCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13630 original size:19 final size:18
Alignment explanation
Indices: 13606--13647 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
13596 TCTTCCATAG
13606 ATATATAGTATATATATA
1 ATATATAGTATATATATA
*
13624 TATATATATTATATATATA
1 -ATATATAGTATATATATA
13643 ATATA
1 ATATA
13648 AAATTGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATATAGTATATATATA
Found at i:14204 original size:2 final size:2
Alignment explanation
Indices: 14197--14239 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
14187 TTACGTACAT
* * *
14197 TA TA TA TA TA TG TA TC TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14239 T
1 T
14240 TCATCTGTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16267 original size:19 final size:21
Alignment explanation
Indices: 16231--16272 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
16221 TTTCTTCTAT
16231 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
16251 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
16271 TT
1 TT
16273 CATATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:22880 original size:19 final size:21
Alignment explanation
Indices: 22844--22885 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
22834 TTTCTTCTAT
22844 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
22864 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
22884 TT
1 TT
22886 CATATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:24490 original size:13 final size:14
Alignment explanation
Indices: 24466--24497 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
24456 GAATTATAAT
24466 TAAATCTAACTAAG
1 TAAATCTAACTAAG
24480 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
24493 -AAATC
1 TAAATC
24498 AATCAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (14 bp):
TAAATCTAACTAAG
Found at i:25809 original size:19 final size:18
Alignment explanation
Indices: 25776--25811 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25766 TTGAAATAAT
25776 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
25794 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
25812 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.