Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014660.1 Corchorus capsularis cultivar CVL-1 contig14681, 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: 30740
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:3443 original size:25 final size:27
Alignment explanation
Indices: 3391--3443 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3381 TTACTAAACT
**
3391 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
3418 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
3443 A
1 A
3444 TCTAATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:11088 original size:28 final size:27
Alignment explanation
Indices: 11007--11088 Score: 65
Period size: 33 Copynumber: 2.8 Consensus size: 27
10997 TTTTCTAACC
*
11007 GTTTATTAGACATCCATTTTTTCAATT
1 GTTTATTAGACATCTATTTTTTCAATT
** *
11034 GTTCTCATGATTTACCATTCTAGTTTTTCAATCT
1 GTT-T-AT--TAGA-CA-TCTATTTTTTCAAT-T
11068 GTTTATTAGACATCTATTTTT
1 GTTTATTAGACATCTATTTTT
11089 CTAGTTGTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 13
0.67 0.11 0.21
Matches are distributed among these distances:
27 3 0.07
28 9 0.22
29 4 0.10
30 2 0.05
31 2 0.05
32 4 0.10
33 13 0.32
34 4 0.10
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (27 bp):
GTTTATTAGACATCTATTTTTTCAATT
Found at i:11138 original size:145 final size:145
Alignment explanation
Indices: 10866--11185 Score: 498
Period size: 145 Copynumber: 2.2 Consensus size: 145
10856 CCTCAAACAC
10866 ATTAGACATCCATTTTTTCAATTGTTCTCATGATTTACCATTCTATATTTTCAATCCATTTATTA
1 ATTAGACATCCATTTTTTCAATTGTTCTCATGATTTACCATTCTATATTTTCAATCCATTTATTA
* *
10931 GACATCTATTTTTCCAGTTATTCTCTTAATAGATTCAATTGTTCTCTTTATTGTATATCATTCTA
66 GACATCTATTTTTCCAGTTATTCTCTTAATAGATTCAATTGTTCTCTTTATTATATACCATTCTA
10996 TTTTTCTAACCGTTT
131 TTTTTCTAACCGTTT
**
11011 ATTAGACATCCATTTTTTCAATTGTTCTCATGATTTACCATTCTAGT-TTTTCAATCTGTTTATT
1 ATTAGACATCCATTTTTTCAATTGTTCTCATGATTTACCATTCTA-TATTTTCAATCCATTTATT
* * * *
11075 AGACATCTATTTTTCTAGTTGTTCTCTTTATAGATTCAATTGTTCTCTTTATTATTTACCATTCT
65 AGACATCTATTTTTCCAGTTATTCTCTTAATAGATTCAATTGTTCTCTTTATTATATACCATTCT
**
11140 ATTTTTCTATTCGTTT
130 ATTTTTCTAACCGTTT
* * *
11156 ATCAGACGTCTATTTTTTCAAATTGTTCTC
1 ATTAGACATCCATTTTTTC-AATTGTTCTC
11186 TTCTCTTAAT
Statistics
Matches: 160, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
145 149 0.93
146 11 0.07
ACGTcount: A:0.23, C:0.17, G:0.07, T:0.52
Consensus pattern (145 bp):
ATTAGACATCCATTTTTTCAATTGTTCTCATGATTTACCATTCTATATTTTCAATCCATTTATTA
GACATCTATTTTTCCAGTTATTCTCTTAATAGATTCAATTGTTCTCTTTATTATATACCATTCTA
TTTTTCTAACCGTTT
Found at i:11168 original size:84 final size:83
Alignment explanation
Indices: 11027--11187 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 83
11017 CATCCATTTT
* *
11027 TTCAATTGTTCTCATGATTTACCATTCTAGTTTTTCAATCTGTTTATTAGACATCTA-TTTTTCT
1 TTCAATTGTTCTCATGATTTACCATTCTAGTTTTTCAATCTGTTTATCAGACATCTATTTTTTCA
*
11091 AGTTGTTCTCTTTATAGA
66 AATTGTTCTCTTTATAGA
* * *
11109 TTCAATTGTTCTCTTTATTATTTACCATTCTA-TTTTTCTAT-TCGTTTATCAGACGTCTATTTT
1 TTCAATTGTTCTC---ATGATTTACCATTCTAGTTTTTCAATCT-GTTTATCAGACATCTATTTT
11172 TTCAAATTGTTCTCTT
62 TTCAAATTGTTCTCTT
11188 CTCTTAATCG
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
82 13 0.19
83 1 0.01
84 22 0.32
85 32 0.47
ACGTcount: A:0.20, C:0.17, G:0.08, T:0.55
Consensus pattern (83 bp):
TTCAATTGTTCTCATGATTTACCATTCTAGTTTTTCAATCTGTTTATCAGACATCTATTTTTTCA
AATTGTTCTCTTTATAGA
Found at i:12632 original size:2 final size:2
Alignment explanation
Indices: 12625--12665 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
12615 CAATAAAGTG
12625 TA TA TA TA TA TA TA TA TA TA T- TA TGA -A TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
12665 T
1 T
12666 TTCGGGCCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 31 0.89
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14089 original size:41 final size:40
Alignment explanation
Indices: 14042--14269 Score: 183
Period size: 41 Copynumber: 5.5 Consensus size: 40
14032 AAATTACCCT
* *
14042 TGTGTTATAATTGTGTTTAGGGACTTT-AGCATGGATGCCTC
1 TGTGTTATAAATGTGTTT-GGGACTTTGA-TATGGATGCCTC
* *
14083 TGTGTTATAAATGTGTTTGAGGACTTTTAGAGA-AGATTGCC-C
1 TGTGTTATAAATGTGTTTG-GGAC-TTT-GATATGGA-TGCCTC
* * *
14125 TTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGTCTC
1 -TGTGTTATAAATGTGTTT-GGGACTTTGATATGGATGCCTC
* * * * *
14167 TGTGTTATAAATGTGCTTGAGAACTTTGAAATAGAGGTGCCCC
1 TGTGTTATAAATGTGTTTG-GGACTTTGATAT-G-GATGCCTC
* * * *
14210 TGTGTTATAATTGTGCTTGGGGACTTTGATATGGGTGTCTC
1 TGTGTTATAAATGTG-TTTGGGACTTTGATATGGATGCCTC
14251 TGTGTTATAAATGTGTTTG
1 TGTGTTATAAATGTGTTTG
14270 AGAATTTTAG
Statistics
Matches: 151, Mismatches: 23, Indels: 27
0.75 0.11 0.13
Matches are distributed among these distances:
40 5 0.03
41 73 0.48
42 14 0.09
43 55 0.36
44 4 0.03
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (40 bp):
TGTGTTATAAATGTGTTTGGGACTTTGATATGGATGCCTC
Found at i:14140 original size:84 final size:85
Alignment explanation
Indices: 14038--14321 Score: 362
Period size: 84 Copynumber: 3.4 Consensus size: 85
14028 ATAGAAATTA
* * *
14038 CCCTTGTGTTATAATTGTGTTTAGGGACTTT-AGCATGGATGCCTCTGTGTTATAAATGTGTTTG
1 CCCTTGTGTTATAATTGTGTTTGGGGACTTTGA-TATGGATGTCTCTGTGTTATAAATGTGTTTG
*
14102 AGGACTTTTAGAGA-AGATTG
65 AGGACTTTTAGAAAGAGATTG
* *
14122 CCCTTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGTCTCTGTGTTATAAATGTGCTTGA
1 CCCTTGTGTTATAATTGTGTTTGGGGACTTTGATATGGATGTCTCTGTGTTATAAATGTGTTTGA
* * *
14187 GAAC-TTT-GAAATAGAGGTG
66 GGACTTTTAGAAAGAGA-TTG
* * *
14206 CCCCTGTGTTATAATTGTGCTTGGGGACTTTGATATGGGTGTCTCTGTGTTATAAATGTGTTTGA
1 CCCTTGTGTTATAATTGTGTTTGGGGACTTTGATATGGATGTCTCTGTGTTATAAATGTGTTTGA
*
14271 -GAATTTTAGAAAGAGAATTG
66 GGACTTTTAGAAAGAG-ATTG
* * *
14291 TCTTTGTGTTATAAATGTGTTTGGGGACTTT
1 CCCTTGTGTTATAATTGTGTTTGGGGACTTT
14322 AGGGAGAGAG
Statistics
Matches: 172, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
82 3 0.02
83 7 0.04
84 126 0.73
85 35 0.20
86 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (85 bp):
CCCTTGTGTTATAATTGTGTTTGGGGACTTTGATATGGATGTCTCTGTGTTATAAATGTGTTTGA
GGACTTTTAGAAAGAGATTG
Found at i:23254 original size:2 final size:2
Alignment explanation
Indices: 23242--23276 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
23232 ATTATTATTA
23242 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23277 GAGTTTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24217 original size:3 final size:3
Alignment explanation
Indices: 24211--24236 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
24201 TATATAATAA
24211 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
24237 ATATATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:24355 original size:22 final size:21
Alignment explanation
Indices: 24325--24393 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
24315 TTAGTTATAA
24325 TAAACTAATAATCTATCTTAT
1 TAAACTAATAATCTATCTTAT
* * *
24346 TATAACTAAT-ATATATGATGAT
1 TA-AACTAATAATCTAT-CTTAT
*
24368 TAAACTAATAATCTAACTTA-
1 TAAACTAATAATCTATCTTAT
24388 TAAACT
1 TAAACT
24394 CTAAACCGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
20 6 0.16
21 16 0.42
22 16 0.42
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (21 bp):
TAAACTAATAATCTATCTTAT
Found at i:26254 original size:2 final size:2
Alignment explanation
Indices: 26249--26275 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26239 TAATATATGT
26249 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 T
26276 TAGATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27151 original size:2 final size:2
Alignment explanation
Indices: 27144--27177 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
27134 TTAGGATCAA
27144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27178 GTTATAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27830 original size:19 final size:18
Alignment explanation
Indices: 27801--27842 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
27791 GAGTAGATTT
* *
27801 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
27819 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
27838 TTAAA
1 TTAAA
27843 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:27846 original size:19 final size:19
Alignment explanation
Indices: 27806--27842 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27796 GATTTTTAAG
*
27806 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
27825 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
27843 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Done.