Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009667.1 Corchorus capsularis cultivar CVL-1 contig09688, 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: 16355
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1030 original size:35 final size:35
Alignment explanation
Indices: 984--1275 Score: 403
Period size: 35 Copynumber: 8.3 Consensus size: 35
974 TCAACTCTGT
* *
984 GATCAACTCTGATCATCGGAAATTACTTG-AAATGA
1 GATCAACTCTGATCGTTGGAAATTAC-TGAAAATGA
* * * *
1019 GATCACCTCTGATTGTTGGAAACTACTGAAAATGT
1 GATCAACTCTGATCGTTGGAAATTACTGAAAATGA
* *
1054 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAATTACTGAAAATGA
*
1089 GATCAACTCTGATCGTTGGAAATTACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAATTACTGAAAATGA
*
1124 GATCAACTCTGATCGTTGGAGAA-TACTGAAAATGC
1 GATCAACTCTGATCGTTGGA-AATTACTGAAAATGA
* *
1159 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAATTACTGAAAATGA
*
1194 GATCAACTCTGATCGTTGGAAACTACTGAAAATGA
1 GATCAACTCTGATCGTTGGAAATTACTGAAAATGA
1229 GATCAACTCTGATCGTTGGAAACTT-CTTG-AAATGA
1 GATCAACTCTGATCGTTGGAAA-TTAC-TGAAAATGA
1264 GATCAACTCTGA
1 GATCAACTCTGA
1276 CCTCTGAAAA
Statistics
Matches: 238, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
34 4 0.02
35 229 0.96
36 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (35 bp):
GATCAACTCTGATCGTTGGAAATTACTGAAAATGA
Found at i:1166 original size:105 final size:105
Alignment explanation
Indices: 984--1275 Score: 455
Period size: 105 Copynumber: 2.8 Consensus size: 105
974 TCAACTCTGT
* * * *
984 GATCAACTCTGATCATCGGAAATTACTTG-AAATGAGATCACCTCTGATTGTTGGAAACTACTGA
1 GATCAACTCTGATCGTTGGAAATTAC-TGAAAATGAGATCAACTCTGATCGTTGGAAACTACTGA
*
1048 AAATGTGATCAACTCTGATCGTTGGAAAATACTGAAAATGC
65 AAATGAGATCAACTCTGATCGTTGGAAAATACTGAAAATGC
*
1089 GATCAACTCTGATCGTTGGAAATTACTGAAAATGCGATCAACTCTGATCGTTGGAGAA-TACTGA
1 GATCAACTCTGATCGTTGGAAATTACTGAAAATGAGATCAACTCTGATCGTTGGA-AACTACTGA
*
1153 AAATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGC
65 AAATGAGATCAACTCTGATCGTTGGAAAATACTGAAAATGC
* *
1194 GATCAACTCTGATCGTTGGAAACTACTGAAAATGAGATCAACTCTGATCGTTGGAAACTTCTTG-
1 GATCAACTCTGATCGTTGGAAATTACTGAAAATGAGATCAACTCTGATCGTTGGAAACTAC-TGA
1258 AAATGAGATCAACTCTGA
65 AAATGAGATCAACTCTGA
1276 CCTCTGAAAA
Statistics
Matches: 173, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
104 4 0.02
105 165 0.95
106 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (105 bp):
GATCAACTCTGATCGTTGGAAATTACTGAAAATGAGATCAACTCTGATCGTTGGAAACTACTGAA
AATGAGATCAACTCTGATCGTTGGAAAATACTGAAAATGC
Found at i:1287 original size:35 final size:35
Alignment explanation
Indices: 1188--1902 Score: 819
Period size: 35 Copynumber: 20.1 Consensus size: 35
1178 AAAATACTGA
* * * *
1188 AAATGCGATCAACTCTGATCGT-TGGAAACTAC-TG
1 AAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG
* *
1222 AAAATGAGATCAACTCTGATCGT-TGGAAACTTCTTG
1 -AAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG
1258 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1293 ATATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1328 GAATGAGATCAACTCCGACCTCTGAAAACTTC-T-
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1361 ---TGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1393 AAATGAGATCAACTCTGACCTCTAAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1428 AAATGAGATCAACTCTGATCTCTGAAAACTTCTTTA
1 AAATGAGATCAACTCTGACCTCTGAAAACTTC-TTG
* *
1464 AAATGAGATCAACTCTGATCGTTTG-AAACTTCTTG
1 AAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG
*
1499 GAATGAGATCAACTCTGACCTCTGAAAACTTCTTAATATG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTC----T-TG
*
1539 AAATGAGATCAACTCTGACCTCTGGAAACTTCTTAATATG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTC----T-TG
* * *
1579 AAATGAGAGAAATGAAATC-AACTCTGACCTCTGAAAACTTCTTG
1 AAAT--GAG--ATCAACTCTGAC-C-----TCTGAAAACTTCTTG
1623 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1658 AAATGAGATCAACTCCGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1693 ATATGAGATCAACTTTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* *
1728 AAATGAGATCAACTCTAACCTCTGTAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1763 ATATGAGATCAACTCTGACCTCTGAAAACTTCTTG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
* * * *
1798 AAATGAGATCAACTATGACCTTTGAAATCTTCTTC
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1833 AAATGAGATCAACTCTGACCTTTGAAAA---C-TG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
*
1864 ATATGAGATCAACTCTGACCTCTGAAAACTTCTATG
1 AAATGAGATCAACTCTGACCTCTGAAAACTTCT-TG
1900 AAA
1 AAA
1903 GACCACACAT
Statistics
Matches: 598, Mismatches: 51, Indels: 61
0.84 0.07 0.09
Matches are distributed among these distances:
30 28 0.05
31 28 0.05
32 1 0.00
34 8 0.01
35 410 0.69
36 33 0.06
37 3 0.01
39 1 0.00
40 51 0.09
41 2 0.00
42 6 0.01
43 2 0.00
44 13 0.02
45 1 0.00
49 11 0.02
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (35 bp):
AAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
Found at i:1287 original size:70 final size:71
Alignment explanation
Indices: 984--1902 Score: 753
Period size: 70 Copynumber: 13.0 Consensus size: 71
974 TCAACTCTGT
* * * ** *
984 GATCAACTCTGATCATC-GGAAA-TTACTTGAAATGAGATCACCTCTGATTGT-TGGAAACTAC-
1 GATCAACTCTGA-CCTCTGAAAACTT-CTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTCT
*
1045 TGAAAATGT
64 TG-AAATGA
* * * *
1054 GATCAACTCTGATCGT-TGGAAAA-TAC-TGAAAATGCGATCAACTCTGATCGT-TGGAAA-TTA
1 GATCAACTCTGA-CCTCT-GAAAACTTCTTG-AAATGAGATCAACTCTGATCCTCTGGAAACTT-
*
1114 C-TGAAAATGC
62 CTTG-AAATGA
* * * * * * *
1124 GATCAACTCTGATCGT-TGGAGAA-TAC-TGAAAATGCGATCAACTCTGATCGT-TGGAAAATAC
1 GATCAACTCTGA-CCTCT-GAAAACTTCTTG-AAATGAGATCAACTCTGATCCTCTGGAAACTTC
*
1185 -TGAAAATGC
63 TTG-AAATGA
* * * *
1194 GATCAACTCTGATCGT-TGGAAACTAC-TGAAAATGAGATCAACTCTGATCGT-TGGAAACTTCT
1 GATCAACTCTGA-CCTCTGAAAACTTCTTG-AAATGAGATCAACTCTGATCCTCTGGAAACTTCT
1256 TGAAATGA
64 TGAAATGA
* *
1264 GATCAACTCTGACCTCTGAAAACTTCTTGATATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTCTTG
*
1328 GAATGA
66 AAATGA
* *
1334 GATCAACTCCGACCTCTGAAAACTTC-T----TGAGATCAACTCTGA-CCTCTGAAAACTTCTTG
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTCTTG
1393 AAATGA
66 AAATGA
* *
1399 GATCAACTCTGACCTCTAAAAACTTCTTGAAATGAGATCAACTCTGAT-CTCTGAAAACTTCTTT
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTC-TT
*
1463 AAAATGA
65 GAAATGA
* * * *
1470 GATCAACTCTGATCGTTTG-AAACTTCTTGGAATGAGATCAACTCTGA-CCTCTGAAAACTTCTT
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTC--
1533 AATATGAAATGA
63 --T-TGAAATGA
* * * *
1545 GATCAACTCTGACCTCTGGAAACTTCTTAATATGAAATGAGAGAAATGAAATCAACT-CTGACCT
1 GATCAACTCTGACCTCTGAAAACTTC----T-TGAAAT--GAG--AT-CAA-C-TCTGAT--CCT
*
1609 CTGAAAACTTCTTGAAATGA
52 CTGGAAACTTCTTGAAATGA
* *
1629 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCCGA-CCTCTGAAAACTTCTTG
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTCTTG
*
1693 ATATGA
66 AAATGA
* * *
1699 GATCAACTTTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCT-AACCTCTGTAAACTTCTTG
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTCTTG
*
1763 ATATGA
66 AAATGA
* *
1769 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTATGA-CCT-TTGAAATCTTCTT
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAA-CTTCTT
*
1832 CAAATGA
65 GAAATGA
* * *
1839 GATCAACTCTGACCTTTGAAAA---C-TGATATGAGATCAACTCTGA-CCTCTGAAAACTTCTAT
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTCT-T
1899 GAAA
65 GAAA
1903 GACCACACAT
Statistics
Matches: 743, Mismatches: 61, Indels: 93
0.83 0.07 0.10
Matches are distributed among these distances:
65 61 0.08
66 27 0.04
67 9 0.01
69 16 0.02
70 445 0.60
71 71 0.10
72 4 0.01
73 1 0.00
74 7 0.01
75 28 0.04
77 3 0.00
79 7 0.01
80 6 0.01
82 3 0.00
84 35 0.05
85 3 0.00
86 1 0.00
87 2 0.00
89 14 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (71 bp):
GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCCTCTGGAAACTTCTTG
AAATGA
Found at i:2040 original size:22 final size:22
Alignment explanation
Indices: 2012--2059 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2002 GGCACCTATA
*
2012 CTTGAC-TCTTCATCTACCCTTT
1 CTTGACTTCTTC-TCTACCCATT
*
2034 CTTGACTTCTTCTTTACCCATT
1 CTTGACTTCTTCTCTACCCATT
2056 CTTG
1 CTTG
2060 GCTACTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.12, C:0.33, G:0.06, T:0.48
Consensus pattern (22 bp):
CTTGACTTCTTCTCTACCCATT
Found at i:3001 original size:13 final size:13
Alignment explanation
Indices: 2983--3015 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2973 ATCATTTCCC
2983 TTTTTTCCCTCTT
1 TTTTTTCCCTCTT
*
2996 TTTTTTCTCTCTT
1 TTTTTTCCCTCTT
3009 TTTTTTC
1 TTTTTTC
3016 ACCATGCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTCCCTCTT
Found at i:4319 original size:17 final size:17
Alignment explanation
Indices: 4297--4330 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4287 AAAAACATCC
* *
4297 TTTTATTTCGAAAACAA
1 TTTTATTCCAAAAACAA
4314 TTTTATTCCAAAAACAA
1 TTTTATTCCAAAAACAA
4331 CCCTTTCACT
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:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTTATTCCAAAAACAA
Found at i:8555 original size:87 final size:87
Alignment explanation
Indices: 8242--8552 Score: 493
Period size: 87 Copynumber: 3.6 Consensus size: 87
8232 TTATATCTTA
* * *
8242 TAAATCTCCCACAATTTGGCAAGATTTA-AAAAATATTCTCATTATTA-TTATATCTTTATAATT
1 TAAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTTA-ATCTTTATTATT
*
8305 TATTTATTTACTTAAAATATCTCG
65 TATTTATTT-CTTAAAATATCTCC
* *
8329 TAAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCCTTATTATTT
1 TAAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTTAATCTTTATTATTT
*
8394 ATTTATTTCTTAAAATACCTCC
66 ATTTATTTCTTAAAATATCTCC
*
8416 TAAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCACTACTATTTAATCTTTATTATTT
1 TAAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTTAATCTTTATTATTT
8481 ATTTATTTCTTAAAATATCTCC
66 ATTTATTTCTTAAAATATCTCC
* *
8503 TAAATCTCCCACAATTTGGAAAGATTTAGA-AAATATTCTCATTATTATTT
1 TAAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTT
8553 TAACAATTTT
Statistics
Matches: 208, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
86 18 0.09
87 152 0.73
88 36 0.17
89 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (87 bp):
TAAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTTAATCTTTATTATTT
ATTTATTTCTTAAAATATCTCC
Found at i:10063 original size:2 final size:2
Alignment explanation
Indices: 10056--10085 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10046 TTTATATTGC
10056 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
10086 TATGCATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13566 original size:30 final size:30
Alignment explanation
Indices: 13532--13589 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
13522 AAATTCTACA
13532 AACCAACTAACTTCAAACTAATTACTTTAG
1 AACCAACTAACTTCAAACTAATTACTTTAG
13562 AACCAACTAACTTCAAACTAATTACTTT
1 AACCAACTAACTTCAAACTAATTACTTT
13590 GGTTGAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (30 bp):
AACCAACTAACTTCAAACTAATTACTTTAG
Done.