Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014061.1 Corchorus capsularis cultivar CVL-1 contig14082, 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: 18578
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:2952 original size:15 final size:16
Alignment explanation
Indices: 2932--2961 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2922 TGTAAGTTAA
2932 TCAAAA-ATCAATTTT
1 TCAAAAGATCAATTTT
2947 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
2962 GAATTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:11589 original size:13 final size:13
Alignment explanation
Indices: 11568--11608 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
11558 TGATTTTTAA
11568 TTATT-ATTTGCT
1 TTATTAATTTGCT
11580 TTATTAATTTGCT
1 TTATTAATTTGCT
*
11593 TTATTAATCTGCT
1 TTATTAATTTGCT
11606 TTA
1 TTA
11609 GATTTAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 5 0.19
13 22 0.81
ACGTcount: A:0.22, C:0.10, G:0.07, T:0.61
Consensus pattern (13 bp):
TTATTAATTTGCT
Found at i:11616 original size:6 final size:6
Alignment explanation
Indices: 11605--11631 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11595 ATTAATCTGC
11605 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
11632 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:13074 original size:21 final size:22
Alignment explanation
Indices: 13033--13074 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
13023 TGTCATTATT
* *
13033 ACACTATGAAATTTTGGTAAGG
1 ACACTATGAAATTCTGATAAGG
13055 ACACT-TGAAATTCTGATAAG
1 ACACTATGAAATTCTGATAAG
13075 CTCACTCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (22 bp):
ACACTATGAAATTCTGATAAGG
Found at i:13187 original size:22 final size:22
Alignment explanation
Indices: 13112--13324 Score: 157
Period size: 22 Copynumber: 9.8 Consensus size: 22
13102 ATAAGCACAC
* * *
13112 TATGTAATTTTAATAATCTTCC-
1 TATGAAATTTTGATAA-CCTCCT
** *
13134 TATGAAATTTTGATTTCCTCCA
1 TATGAAATTTTGATAACCTCCT
* *
13156 TAT-AATATTTTGATAATCGCCT
1 TATGAA-ATTTTGATAACCTCCT
* *
13178 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCT
****
13200 TATGAAATTTTGATAACCAGAG
1 TATGAAATTTTGATAACCTCCT
* * *
13222 TATGAAATTTAG-TAATCTCTT
1 TATGAAATTTTGATAACCTCCT
*
13243 TGTGAAATTTTGATAACCTTCC-
1 TATGAAATTTTGATAACC-TCCT
** **
13265 CGTG-AATTTCAATAACCTCCT
1 TATGAAATTTTGATAACCTCCT
*
13286 TATGAAATTTTGATAACATCCT
1 TATGAAATTTTGATAACCTCCT
13308 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
13325 ATCCCATGAA
Statistics
Matches: 147, Mismatches: 37, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
20 3 0.02
21 33 0.22
22 107 0.73
23 4 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCT
Found at i:13342 original size:21 final size:22
Alignment explanation
Indices: 13245--13345 Score: 91
Period size: 22 Copynumber: 4.7 Consensus size: 22
13235 AATCTCTTTG
* *
13245 TGAAATTTTGATAACCTTCC-CG
1 TGAAATTTTGATAA-CATCCTCA
** * *
13267 TG-AATTTCAATAACCTCCTTA
1 TGAAATTTTGATAACATCCTCA
*
13288 TGAAATTTTGATAACATCCTTA
1 TGAAATTTTGATAACATCCTCA
13310 TGAAATTTTGATAACATCC-CA
1 TGAAATTTTGATAACATCCTCA
* *
13331 TGAACTTGTGATAAC
1 TGAAATTTTGATAAC
13346 TACACTAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
20 4 0.06
21 25 0.38
22 37 0.56
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACATCCTCA
Found at i:13345 original size:65 final size:63
Alignment explanation
Indices: 13162--13345 Score: 165
Period size: 65 Copynumber: 2.8 Consensus size: 63
13152 TCCATATAAT
* * * *
13162 ATTTTGATAATCGCCTTATGAAATTTTGTTAACCTCCCTATGAAATTTTGATAACCAGAGTATGA
1 ATTTTGATAATCTCCTTATGAAATTTTGATAACATCCC-ATG-AA-TTTGATAACCACAGTATGA
13227 A
63 A
* * * * * * * **
13228 ATTTAG-TAATCTCTTTGTGAAATTTTGATAACCTTCCCGTGAATTTCAATAACCTCCTTATGAA
1 ATTTTGATAATCTCCTTATGAAATTTTGATAA-CATCCCATGAATTT-GATAACCACAGTATGAA
13292 ATTTTGATAA-CATCCTTATGAAATTTTGATAACATCCCATGAACTTGTGATAAC
1 ATTTTGATAATC-TCCTTATGAAATTTTGATAACATCCCATGAA-TT-TGATAAC
13346 TACACTAAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 13
0.75 0.14 0.10
Matches are distributed among these distances:
63 3 0.03
64 29 0.31
65 51 0.54
66 11 0.12
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (63 bp):
ATTTTGATAATCTCCTTATGAAATTTTGATAACATCCCATGAATTTGATAACCACAGTATGAA
Found at i:13400 original size:22 final size:22
Alignment explanation
Indices: 13370--13450 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
13360 AATATCCTAC
* *
13370 CTATGAAATTTTGGTAACCTCA
1 CTATAAAATTTTGGTAACCACA
13392 CTATAAAATTTTGAG-AACCACA
1 CTATAAAATTTTG-GTAACCACA
* *
13414 CTATAAAATTTTAGTAACTACA
1 CTATAAAATTTTGGTAACCACA
*
13436 CAATAATGAATTTTG
1 CTATAA--AATTTTG
13451 ATACCTCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 41 0.84
23 1 0.02
24 6 0.12
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.35
Consensus pattern (22 bp):
CTATAAAATTTTGGTAACCACA
Found at i:14831 original size:7 final size:7
Alignment explanation
Indices: 14811--14937 Score: 80
Period size: 7 Copynumber: 17.7 Consensus size: 7
14801 TTATCATTTT
14811 TCTTTAC
1 TCTTTAC
**
14818 TGATTAC
1 TCTTTAC
14825 TCTTTAC
1 TCTTTAC
14832 TCTTTAC
1 TCTTTAC
*
14839 -CATTCCAC
1 TC-TT-TAC
*
14847 TTTTTAC
1 TCTTTAC
**
14854 TGATTAC
1 TCTTTAC
14861 TCTTTAC
1 TCTTTAC
14868 TCTTTAC
1 TCTTTAC
14875 -CATTCTAC
1 TC-TT-TAC
14883 TCTTTAC
1 TCTTTAC
**
14890 TGATTAC
1 TCTTTAC
14897 TCTTTAC
1 TCTTTAC
*
14904 TTTTTAC
1 TCTTTAC
14911 -CATTTTAC
1 TC--TTTAC
14919 TCTTTAC
1 TCTTTAC
**
14926 TGATTAC
1 TCTTTAC
14933 TCTTT
1 TCTTT
14938 TACTATTATT
Statistics
Matches: 90, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
6 2 0.02
7 72 0.80
8 14 0.16
9 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.03, T:0.53
Consensus pattern (7 bp):
TCTTTAC
Found at i:14858 original size:36 final size:36
Alignment explanation
Indices: 14811--14937 Score: 218
Period size: 36 Copynumber: 3.5 Consensus size: 36
14801 TTATCATTTT
*
14811 TCTTTACTGATTACTCTTTACTCTTTACCATTCCAC
1 TCTTTACTGATTACTCTTTACTCTTTACCATTCTAC
*
14847 TTTTTACTGATTACTCTTTACTCTTTACCATTCTAC
1 TCTTTACTGATTACTCTTTACTCTTTACCATTCTAC
* *
14883 TCTTTACTGATTACTCTTTACTTTTTACCATTTTAC
1 TCTTTACTGATTACTCTTTACTCTTTACCATTCTAC
14919 TCTTTACTGATTACTCTTT
1 TCTTTACTGATTACTCTTT
14938 TACTATTATT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 86 1.00
ACGTcount: A:0.19, C:0.25, G:0.03, T:0.53
Consensus pattern (36 bp):
TCTTTACTGATTACTCTTTACTCTTTACCATTCTAC
Found at i:14932 original size:22 final size:22
Alignment explanation
Indices: 14893--14957 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
14883 TCTTTACTGA
**
14893 TTACTCTTTACTTTTTACCATT
1 TTACTCTTTACTGATTACCATT
14915 TTACTCTTTACTGATTACTC-TT
1 TTACTCTTTACTGATTAC-CATT
* *
14937 TTACT-ATTATTGATTACCATT
1 TTACTCTTTACTGATTACCATT
14958 ACTTTTTACC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 23 0.62
23 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.03, T:0.55
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCATT
Found at i:14996 original size:36 final size:36
Alignment explanation
Indices: 14947--15083 Score: 125
Period size: 36 Copynumber: 3.6 Consensus size: 36
14937 TTACTATTAT
*
14947 TGATTAC-CATTACTTTTTACCATCTTACTTTTTAC
1 TGATTACTCTTTACTTTTTACCATCTTACTTTTTAC
* *
14982 TGATTGCCCTTTACTACTCTTTACCATTTTACTTTTTACTTTTTAC
1 TGATTACTCTTTACT--T-TTTACCA---T-C---TTACTTTTTAC
* *
15028 TGATTACTCTTTACTTTTTACTATTTTACTTTTTAC
1 TGATTACTCTTTACTTTTTACCATCTTACTTTTTAC
15064 TGATTACTC-TTACTTTTTAC
1 TGATTACTCTTTACTTTTTAC
15084 TCTTTTTAAC
Statistics
Matches: 85, Mismatches: 6, Indels: 22
0.75 0.05 0.19
Matches are distributed among these distances:
35 17 0.20
36 26 0.31
38 1 0.01
39 7 0.08
40 1 0.01
42 1 0.01
43 7 0.08
44 1 0.01
46 24 0.28
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (36 bp):
TGATTACTCTTTACTTTTTACCATCTTACTTTTTAC
Found at i:15020 original size:7 final size:7
Alignment explanation
Indices: 15008--15089 Score: 85
Period size: 7 Copynumber: 11.6 Consensus size: 7
14998 CTCTTTACCA
15008 TTTTACT
1 TTTTACT
15015 TTTTACT
1 TTTTACT
15022 TTTTACT
1 TTTTACT
**
15029 GATTACT
1 TTTTACT
*
15036 CTTTACT
1 TTTTACT
15043 TTTTACT
1 TTTTACT
15050 ATTTTACT
1 -TTTTACT
15058 TTTTACT
1 TTTTACT
**
15065 GATTAC-
1 TTTTACT
*
15071 TCTTACT
1 TTTTACT
15078 TTTTACT
1 TTTTACT
15085 CTTTT
1 -TTTT
15090 TAACTTAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
6 4 0.06
7 47 0.76
8 11 0.18
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (7 bp):
TTTTACT
Found at i:15091 original size:36 final size:37
Alignment explanation
Indices: 14996--15327 Score: 147
Period size: 36 Copynumber: 9.4 Consensus size: 37
14986 TGCCCTTTAC
*
14996 TACTCTTTACCATTTTA--CTTTTTACTTTTTACTGAT
1 TACTCTTTA-CTTTTTACTCTTTTTACTTTTTACTGAT
*
15032 TACTCTTTACTTTTTACT-ATTTTACTTTTTACTGAT
1 TACTCTTTACTTTTTACTCTTTTTACTTTTTACTGAT
* * *
15068 TACTC-TTACTTTTTACTCTTTTTAACTTAATTACTAAA
1 TACTCTTTACTTTTTACTCTTTTT-ACTT-TTTACTGAT
* * * * *
15106 TAC-C-AT-CTTTTGAC-CTTAATTACTTATTAC-CAT
1 TACTCTTTACTTTTTACTCTT-TTTACTTTTTACTGAT
* ** * *
15139 TACTTTTTACTGATTA--CTTTTTACTCTTTAC-CATT
1 TACTCTTTACTTTTTACTCTTTTTACTTTTTACTGA-T
** * *
15174 CTACTCTTTACTGATTACTC--TTTACTCTTTAC-CATT
1 -TACTCTTTACTTTTTACTCTTTTTACTTTTTACTGA-T
* *
15210 CTACTCTTTACTTTTTACT-ATTTTAC-CTTT--T--T
1 -TACTCTTTACTTTTTACTCTTTTTACTTTTTACTGAT
** **
15242 TACTCTTTACTGATTACT-TTTTTAC-GATTACTGAT
1 TACTCTTTACTTTTTACTCTTTTTACTTTTTACTGAT
* * *
15277 TAC-CATTACTTTTTAC-CATCTTACTTTTTACTGAT
1 TACTCTTTACTTTTTACTCTTTTTACTTTTTACTGAT
*
15312 TACCCTTTACTCTTTT
1 TACTCTTTACT-TTTT
15328 TAACTTAATT
Statistics
Matches: 237, Mismatches: 35, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
31 24 0.10
32 1 0.00
33 5 0.02
34 31 0.13
35 45 0.19
36 106 0.45
37 15 0.06
38 10 0.04
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (37 bp):
TACTCTTTACTTTTTACTCTTTTTACTTTTTACTGAT
Found at i:15123 original size:27 final size:27
Alignment explanation
Indices: 15084--15138 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
15074 TACTTTTTAC
*
15084 TCTTTTTAACTTAATTACTAAATACCA
1 TCTTTTGAACTTAATTACTAAATACCA
* * *
15111 TCTTTTGACCTTAATTACTTATTACCA
1 TCTTTTGAACTTAATTACTAAATACCA
15138 T
1 T
15139 TACTTTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.02, T:0.47
Consensus pattern (27 bp):
TCTTTTGAACTTAATTACTAAATACCA
Found at i:15156 original size:14 final size:14
Alignment explanation
Indices: 15124--15314 Score: 77
Period size: 14 Copynumber: 13.4 Consensus size: 14
15114 TTTGACCTTA
*
15124 ATTACTTATTAC-C
1 ATTACTTTTTACTC
*
15137 ATTACTTTTTACTG
1 ATTACTTTTTACTC
15151 ATTACTTTTTACTC
1 ATTACTTTTTACTC
* * *
15165 TTTACCATTCTACTC
1 ATTA-CTTTTTACTC
* **
15180 TTTACTGATTACTC
1 ATTACTTTTTACTC
* *
15194 TTTACTCTTTAC-C
1 ATTACTTTTTACTC
* *
15207 ATTCTACTCTTTACTT
1 A-T-TACTTTTTACTC
* *
15223 TTTACTATTTTACCTTT
1 ATTACT-TTTTA-C-TC
* * *
15240 TTTACTCTTTACTG
1 ATTACTTTTTACTC
*
15254 ATTACTTTTTTAC-G
1 ATTAC-TTTTTACTC
**
15268 ATTACTGATTAC-C
1 ATTACTTTTTACTC
15281 ATTACTTTTTAC-C
1 ATTACTTTTTACTC
*
15294 ATCTTACTTTTTACTG
1 A--TTACTTTTTACTC
15310 ATTAC
1 ATTAC
15315 CCTTTACTCT
Statistics
Matches: 140, Mismatches: 26, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
13 29 0.21
14 52 0.37
15 45 0.32
16 6 0.04
17 8 0.06
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTACTTTTTACTC
Found at i:15178 original size:15 final size:15
Alignment explanation
Indices: 15160--15220 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 15
15150 GATTACTTTT
15160 TACTCTTTACCATTC
1 TACTCTTTACCATTC
*
15175 TACTCTTTACTGATTACTC
1 TACTCTTTAC-CA-T--TC
15194 TTTACTCTTTACCATTC
1 --TACTCTTTACCATTC
15211 TACTCTTTAC
1 TACTCTTTAC
15221 TTTTTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 20 0.53
16 1 0.03
17 3 0.08
19 3 0.08
20 1 0.03
21 10 0.26
ACGTcount: A:0.20, C:0.30, G:0.02, T:0.49
Consensus pattern (15 bp):
TACTCTTTACCATTC
Found at i:15217 original size:22 final size:22
Alignment explanation
Indices: 15189--15251 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
15179 CTTTACTGAT
15189 TACTCTTTACTCTTTACCATTC
1 TACTCTTTACTCTTTACCATTC
* * *
15211 TACTCTTTACTTTTTACTATTT
1 TACTCTTTACTCTTTACCATTC
*
15233 TACCTTTTTTACTCTTTAC
1 TA-C-TCTTTACTCTTTAC
15252 TGATTACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 21 0.62
23 1 0.03
24 12 0.35
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (22 bp):
TACTCTTTACTCTTTACCATTC
Found at i:15235 original size:8 final size:7
Alignment explanation
Indices: 15138--15263 Score: 63
Period size: 7 Copynumber: 17.3 Consensus size: 7
15128 CTTATTACCA
15138 TTACTTT
1 TTACTTT
**
15145 TTACTGA
1 TTACTTT
15152 TTACTTT
1 TTACTTT
*
15159 TTACTCT
1 TTACTTT
*
15166 TTACCATT
1 TTA-CTTT
* *
15174 CTACTCT
1 TTACTTT
**
15181 TTACTGA
1 TTACTTT
*
15188 TTACTCT
1 TTACTTT
*
15195 TTACTCT
1 TTACTTT
*
15202 TTACCATT
1 TTA-CTTT
* *
15210 CTACTCT
1 TTACTTT
15217 TTACTTT
1 TTACTTT
15224 TTACTATT
1 TTACT-TT
15232 TTACCTTTT
1 TTA-C-TTT
*
15241 TTACTCT
1 TTACTTT
**
15248 TTACTGA
1 TTACTTT
15255 TTACTTT
1 TTACTTT
15262 TT
1 TT
15264 TACGATTACT
Statistics
Matches: 87, Mismatches: 27, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
7 66 0.76
8 14 0.16
9 6 0.07
10 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.57
Consensus pattern (7 bp):
TTACTTT
Found at i:15353 original size:27 final size:28
Alignment explanation
Indices: 15322--15385 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
15312 TACCCTTTAC
15322 TCTTTTTAACTTAATTACTAAATACCA-
1 TCTTTTTAACTTAATTACTAAATACCAT
* * * *
15349 TCTTTTGACCTTAATTACTGATTACCAT
1 TCTTTTTAACTTAATTACTAAATACCAT
15377 TACTTTTTA
1 T-CTTTTTA
15386 CCAAACTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.77
28 1 0.03
29 6 0.20
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.48
Consensus pattern (28 bp):
TCTTTTTAACTTAATTACTAAATACCAT
Done.