Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005451.1 Corchorus capsularis cultivar CVL-1 contig05469, 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: 8791
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 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
35 TCTACATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:312 original size:29 final size:29
Alignment explanation
Indices: 267--325 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
257 TTCGATACAT
*
267 GATACCTATCTCGATTTAACAACTATATA
1 GATACCTATCTCAATTTAACAACTATATA
296 GATACCTATCTCAATTTAACAACTATATA
1 GATACCTATCTCAATTTAACAACTATATA
325 G
1 G
326 TGGACAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (29 bp):
GATACCTATCTCAATTTAACAACTATATA
Found at i:452 original size:3 final size:3
Alignment explanation
Indices: 444--515 Score: 90
Period size: 3 Copynumber: 23.3 Consensus size: 3
434 CTATTTAAGT
* * * *
444 TTA TTA TTA GTA GATA TTA TTA TTA GTA GATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
491 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
516 CTTTACAATC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
3 57 0.93
4 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:461 original size:13 final size:15
Alignment explanation
Indices: 444--514 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 15
434 CTATTTAAGT
444 TTATTATTAGTAGATA
1 TTATTATTAGTAGA-A
460 TTATTATTAGTAGATA
1 TTATTATTAGTAGA-A
* **
476 TTATTATTATTATTA
1 TTATTATTAGTAGAA
* **
491 TTATTATTATTATTA
1 TTATTATTAGTAGAA
506 TTATTATTA
1 TTATTATTA
515 TCTTTACAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 25 0.48
16 27 0.52
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
TTATTATTAGTAGAA
Found at i:765 original size:64 final size:65
Alignment explanation
Indices: 687--835 Score: 228
Period size: 64 Copynumber: 2.3 Consensus size: 65
677 GAAATTTTGA
** * *
687 TAACCTTCCAATGAAATTTTAATAATAATACTATGGAATTTCGAGAACCTTTTTATAA-TTTTTT
1 TAACCTTCTTATGAAATTTTAATAACAATACTATGGAATTTCGAGAAACTTTTTATAATTTTTTT
* * *
751 TAATCTTCTTATGAAATTTTAATAACGATACTATGGAATTTTGAGAAACTTTTTATAATTTTTTT
1 TAACCTTCTTATGAAATTTTAATAACAATACTATGGAATTTCGAGAAACTTTTTATAATTTTTTT
816 TAACCTTCTTATGAAATTTT
1 TAACCTTCTTATGAAATTTT
836 GTTAACCTCC
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
64 51 0.67
65 25 0.33
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (65 bp):
TAACCTTCTTATGAAATTTTAATAACAATACTATGGAATTTCGAGAAACTTTTTATAATTTTTTT
Found at i:835 original size:22 final size:22
Alignment explanation
Indices: 743--843 Score: 62
Period size: 22 Copynumber: 4.6 Consensus size: 22
733 ACCTTTTTAT
* *
743 AATTTTTTTAATCTTCTTATGA
1 AATTTTGTTAACCTTCTTATGA
** * * *
765 AATTTTAATAACGATAC-TATGG
1 AATTTTGTTAAC-CTTCTTATGA
** * *
787 AATTTTGAGAAACTTTTTAT-A
1 AATTTTGTTAACCTTCTTATGA
* *
808 ATTTTTTTTAACCTTCTTATGA
1 AATTTTGTTAACCTTCTTATGA
830 AATTTTGTTAACCT
1 AATTTTGTTAACCT
844 CCCTAAGGAA
Statistics
Matches: 55, Mismatches: 21, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
21 15 0.27
22 38 0.69
23 2 0.04
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (22 bp):
AATTTTGTTAACCTTCTTATGA
Found at i:1013 original size:22 final size:22
Alignment explanation
Indices: 887--1102 Score: 95
Period size: 22 Copynumber: 9.7 Consensus size: 22
877 TAACTTCCCA
*
887 ATGAAATTTTGATAACCAACACT
1 ATGAAATTTTGATAATC-ACACT
* *
910 ATGAGATGTTGATAACCTC-CA-T
1 ATGAAATTTTGATAA--TCACACT
* * * *
932 GTGATATATTGATAATCACATT
1 ATGAAATTTTGATAATCACACT
* * *
954 ATGAAAATTTAAAAACCTC-CA-T
1 ATGAAATTTTGATAA--TCACACT
976 ATG-AATTGTT-AGTAATCACACT
1 ATGAAATT-TTGA-TAATCACACT
* *
998 CTGAAATTTTGATAATCACAAT
1 ATGAAATTTTGATAATCACACT
* * * *
1020 ATGAAATTGTGATAACCTCGCT
1 ATGAAATTTTGATAATCACACT
*
1042 ATGAAATTTTGATAAATCTTC-CT
1 ATGAAATTTTGAT-AATC-ACACT
* * * *
1065 ATAAAATTTTGATAAACCTCCCT
1 ATGAAATTTTGAT-AATCACACT
*
1088 ATAAAATTTTGATAA
1 ATGAAATTTTGATAA
1103 CTTTCTTATG
Statistics
Matches: 152, Mismatches: 26, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.03
21 8 0.05
22 77 0.51
23 58 0.38
24 4 0.03
25 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAATCACACT
Found at i:1071 original size:23 final size:23
Alignment explanation
Indices: 1023--1102 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
1013 TCACAATATG
* * *
1023 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
1045 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
1068 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
1091 AAATTTTGATAA
1 AAATTTTGATAA
1103 CTTTCTTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 9 0.18
23 41 0.82
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:1306 original size:22 final size:22
Alignment explanation
Indices: 1276--1582 Score: 148
Period size: 22 Copynumber: 13.8 Consensus size: 22
1266 ATCACATTTA
* *
1276 GAAAATTTGATAACCTCTTTAT
1 GAAATTTTGATAACCTCTCTAT
* *
1298 GAAATTTTGATAAACTCTTTAT
1 GAAATTTTGATAACCTCTCTAT
* * * *
1320 AAAATTTTGTTGACCTATCTAT
1 GAAATTTTGATAACCTCTCTAT
* * *
1342 GAAATTCTGATAATCACAT-TAT
1 GAAATTTTGATAACCTC-TCTAT
* *
1364 -ATAATATTGATAACCTCGT-TTT
1 GA-AATTTTGATAACCTC-TCTAT
** *
1386 GAAATTTTGATAACAACACTAT
1 GAAATTTTGATAACCTCTCTAT
*
1408 GAAATTTTGATAATCTCTCTAT
1 GAAATTTTGATAACCTCTCTAT
*
1430 -AAATTCTGATAATCCGATCTCTAT
1 GAAATTTTGATAA-CC--TCTCTAT
* * * *
1454 GAAAGTTCGATAATCACTCTAT
1 GAAATTTTGATAACCTCTCTAT
*
1476 GAGA-TTTGATAACCT-TCTAT
1 GAAATTTTGATAACCTCTCTAT
* *
1496 CAAATTTTGGT-A-CTC-CTTAT
1 GAAATTTTGATAACCTCTC-TAT
* *
1516 GAAATTGGGACTTTTATAACAT-TCATAT
1 GAAA-T-----TTTGATAACCTCTC-TAT
* *
1544 GAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACCTCTCTAT
*
1566 AAAATTTTGATAACCTC
1 GAAATTTTGATAACCTC
1583 CGCATGAAAA
Statistics
Matches: 209, Mismatches: 55, Indels: 42
0.68 0.18 0.14
Matches are distributed among these distances:
19 3 0.01
20 14 0.07
21 26 0.12
22 131 0.63
23 3 0.01
24 8 0.04
25 9 0.04
26 4 0.02
27 2 0.01
28 9 0.04
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTCTAT
Found at i:1364 original size:44 final size:44
Alignment explanation
Indices: 1250--1443 Score: 171
Period size: 44 Copynumber: 4.4 Consensus size: 44
1240 GAAATACCAC
** *
1250 CTATGAAATTTTTTTAATCACATT-TAGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATA-AAATTTTGATAACCTCT
* * * * * * *
1294 TTATGAAATTTTGATAAACTCTTTATAAAATTTTGTTGACCTAT
1 CTATGAAATTTTGATAATCACATTATAAAATTTTGATAACCTCT
* * *
1338 CTATGAAATTCTGATAATCACATTATATAATATTGATAACCTCGT
1 CTATGAAATTTTGATAATCACATTATAAAATTTTGATAACCTC-T
* * * *
1383 -TTTGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCTCT
1 CTATGAAATTTTGATAATC-ACATTATAAAATTTTGATAACCTCT
*
1426 CTAT-AAATTCTGATAATC
1 CTATGAAATTTTGATAATC
1444 CGATCTCTAT
Statistics
Matches: 116, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
43 13 0.11
44 100 0.86
45 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATAAAATTTTGATAACCTCT
Found at i:1413 original size:88 final size:87
Alignment explanation
Indices: 1250--1443 Score: 216
Period size: 88 Copynumber: 2.2 Consensus size: 87
1240 GAAATACCAC
* ** *
1250 CTATGAAATTTTTTTAATCACATTTAGAAAATTTGATAACCTCTTTATGAAATTTTGATAAACTC
1 CTATGAAATTCTGATAATCACATTTAGAAAATTTGATAACCTCTTTATGAAATTTTGATAAACAC
* *
1315 TTTATAAAATTTTGTTGACCTAT
66 -TTATAAAATTTTGATAACCTAT
* *
1338 CTATGAAATTCTGATAATCACA-TTATATAATATTGATAACCTCGTTT-TGAAATTTTGATAACA
1 CTATGAAATTCTGATAATCACATTTAGAAAAT-TTGATAACCTC-TTTATGAAATTTTGAT-A-A
* * *
1401 ACAC-TATGAAATTTTGATAATCTCT
62 ACACTTATAAAATTTTGATAACCTAT
1426 CTAT-AAATTCTGATAATC
1 CTATGAAATTCTGATAATC
1444 CGATCTCTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
87 21 0.23
88 62 0.68
89 4 0.04
90 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (87 bp):
CTATGAAATTCTGATAATCACATTTAGAAAATTTGATAACCTCTTTATGAAATTTTGATAAACAC
TTATAAAATTTTGATAACCTAT
Found at i:1751 original size:22 final size:21
Alignment explanation
Indices: 1724--1811 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 21
1714 ATAACCTGAT
*
1724 CCTATGAAATTTTGGTAACCA
1 CCTATGAAATTTTGATAACCA
*
1745 CACTATGAAATTTTGATAACCT
1 C-CTATGAAATTTTGATAACCA
* * * *
1767 CCTCATGAAATTATAATGATCA
1 CCT-ATGAAATTTTGATAACCA
*
1789 TCTTATGAAATTTTGATAACCA
1 -CCTATGAAATTTTGATAACCA
1811 C
1 C
1812 ATAGAGATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
21 4 0.08
22 46 0.88
23 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (21 bp):
CCTATGAAATTTTGATAACCA
Found at i:2888 original size:19 final size:19
Alignment explanation
Indices: 2864--2900 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2854 ATATTATTTT
*
2864 AATAGTAAACTAATTAAAA
1 AATAGTAAAATAATTAAAA
2883 AATAGTAAAATAATTAAA
1 AATAGTAAAATAATTAAA
2901 CTATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (19 bp):
AATAGTAAAATAATTAAAA
Found at i:3220 original size:31 final size:31
Alignment explanation
Indices: 3175--3248 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
3165 TTTAGTAATG
* *
3175 ACAATTTAGAAATATGATTTTTAAAA-AAGGGT
1 ACAATTGA-AAATATG-TTTTAAAAATAAGGGT
3207 ACAATTGAAAATATGTTTTAAAAATAAGGGT
1 ACAATTGAAAATATGTTTTAAAAATAAGGGT
*
3238 ACAATCGAAAA
1 ACAATTGAAAA
3249 ACATAAAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.21
31 23 0.61
32 7 0.18
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (31 bp):
ACAATTGAAAATATGTTTTAAAAATAAGGGT
Done.