Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011113.1 Corchorus capsularis cultivar CVL-1 contig11134, 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: 48740
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:46 original size:21 final size:21
Alignment explanation
Indices: 17--62 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
7 ACAACTCTAG
*
17 TAATTGATAACTCAAAGTGTT
1 TAATCGATAACTCAAAGTGTT
*
38 TAATCGATAACTCGAAGTGTT
1 TAATCGATAACTCAAAGTGTT
59 TAAT
1 TAAT
63 TGTTCAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (21 bp):
TAATCGATAACTCAAAGTGTT
Found at i:1655 original size:12 final size:12
Alignment explanation
Indices: 1638--1662 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1628 GAGAGTTGGG
1638 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1650 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1662 T
1 T
1663 AAATTCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:2483 original size:14 final size:14
Alignment explanation
Indices: 2464--2491 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2454 TGGAGTACTA
2464 TACTTAGTTCCAAT
1 TACTTAGTTCCAAT
2478 TACTTAGTTCCAAT
1 TACTTAGTTCCAAT
2492 GACTATGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
TACTTAGTTCCAAT
Found at i:3649 original size:2 final size:2
Alignment explanation
Indices: 3644--3671 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3634 CTAATGGGGG
3644 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3672 TCAAATACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7043 original size:31 final size:31
Alignment explanation
Indices: 6999--7123 Score: 133
Period size: 31 Copynumber: 4.0 Consensus size: 31
6989 ACGGTGTCCG
* *
6999 ACGTGGCATGTCATATGTACCAAAAAGTGAC
1 ACGTGTCATGTCATGTGTACCAAAAAGTGAC
* *
7030 ACGTGTCACGTCATGTGTACCAAAAAGTTAC
1 ACGTGTCATGTCATGTGTACCAAAAAGTGAC
* * * *
7061 GCATGTCATGTCACGTGTACCAAAGAGTGAC
1 ACGTGTCATGTCATGTGTACCAAAAAGTGAC
* * * * *
7092 ACATGGCATGACACGTGTATCAAAAAGTGAC
1 ACGTGTCATGTCATGTGTACCAAAAAGTGAC
7123 A
1 A
7124 TGCCACATAC
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (31 bp):
ACGTGTCATGTCATGTGTACCAAAAAGTGAC
Found at i:9516 original size:20 final size:20
Alignment explanation
Indices: 9491--9531 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
9481 TAGCCGAGTA
9491 TGGAAGACCGAGGATGTCAT
1 TGGAAGACCGAGGATGTCAT
9511 TGGAAGACCGAGGATGTCAT
1 TGGAAGACCGAGGATGTCAT
9531 T
1 T
9532 CATGTGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (20 bp):
TGGAAGACCGAGGATGTCAT
Found at i:12920 original size:45 final size:45
Alignment explanation
Indices: 12870--12957 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
12860 CTTTAAGTAG
12870 TGGAATTACTAAAAGATCCCTACCCC-GAATTAATGATAAGCTGTA
1 TGGAATTACTAAAAGATCCCTACCCCAG-ATTAATGATAAGCTGTA
* *
12915 TGGAATTACTAAAATATCCCTACCCCAGATTAATGATGAGCTG
1 TGGAATTACTAAAAGATCCCTACCCCAGATTAATGATAAGCTG
12958 GAGAAGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 39 0.98
46 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (45 bp):
TGGAATTACTAAAAGATCCCTACCCCAGATTAATGATAAGCTGTA
Found at i:24208 original size:62 final size:63
Alignment explanation
Indices: 24099--24248 Score: 162
Period size: 62 Copynumber: 2.4 Consensus size: 63
24089 GACGTGGCAT
* ** * * *
24099 GCCATGTGTACCAAAAAGTGACA--TATGACACGCCATGTGTACAAAAAAATGACACGTATCAC
1 GCCACGTGTACCAAAAAGTGACACGTAT-ACACGCCACATATACAAAAAAATGACACATAGCAC
* * * *
24161 GCCACGTGTACAAAAAAGTGACACGTAT-CACGCCACATATACCAAAAAATGACACATGGCAT
1 GCCACGTGTACCAAAAAGTGACACGTATACACGCCACATATACAAAAAAATGACACATAGCAC
* *
24223 GCCACGTGTACCAGAAAGTGGCACGT
1 GCCACGTGTACCAAAAAGTGACACGT
24249 GGCATGCCAT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
62 70 0.96
64 3 0.04
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (63 bp):
GCCACGTGTACCAAAAAGTGACACGTATACACGCCACATATACAAAAAAATGACACATAGCAC
Found at i:24252 original size:31 final size:31
Alignment explanation
Indices: 24090--24257 Score: 147
Period size: 31 Copynumber: 5.4 Consensus size: 31
24080 ACGGTGTCCG
* *
24090 ACGTGGCATGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
** * * * *
24121 ATATGACACGCCATGTGTACAAAAAAATGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
** *
24152 ACGTATCACGCCACGTGTACAAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
** * * *
24183 ACGTATCACGCCACATATACCAAAAAATGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * *
24214 ACATGGCATGCCACGTGTACCAGAAAGTGGC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
24245 ACGTGGCATGCCA
1 ACGTGGCACGCCA
24258 TGTGCATAAA
Statistics
Matches: 111, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 111 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:27531 original size:77 final size:77
Alignment explanation
Indices: 27404--27559 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
27394 AGTTGACAAA
27404 TACCACATCCTATTAGAGATTATAAGTTGATTGAACTATGGTTAAATTAGTTAACAAGTTAGTCA
1 TACCACATCCTATTAGAGATTATAAGTTGATTGAACTATGGTTAAATTAGTTAACAAGTTAGTCA
27469 ATAGAAGCTAGC
66 ATAGAAGCTAGC
27481 TACCACATCCTATTAGAGATTATAAGTTGATTGAACTATGGTTAAATTAGTTAACAAGTTAGTCA
1 TACCACATCCTATTAGAGATTATAAGTTGATTGAACTATGGTTAAATTAGTTAACAAGTTAGTCA
27546 ATAGAAGCTAGC
66 ATAGAAGCTAGC
27558 TA
1 TA
27560 TTAGTTAGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (77 bp):
TACCACATCCTATTAGAGATTATAAGTTGATTGAACTATGGTTAAATTAGTTAACAAGTTAGTCA
ATAGAAGCTAGC
Found at i:28249 original size:16 final size:16
Alignment explanation
Indices: 28228--28283 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
28218 TATAAAAGTA
28228 AATATATATTTATTAT
1 AATATATATTTATTAT
*
28244 AATATATA-TAATTAT
1 AATATATATTTATTAT
28259 AAT-TATAAGTTTA-TAT
1 AATATAT-A-TTTATTAT
*
28275 AATAAATAT
1 AATATATAT
28284 ATATAAAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 3 0.09
15 11 0.33
16 15 0.45
17 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATATATATTTATTAT
Found at i:28259 original size:15 final size:15
Alignment explanation
Indices: 28228--28357 Score: 76
Period size: 15 Copynumber: 8.5 Consensus size: 15
28218 TATAAAAGTA
*
28228 AATATATATTTATTAT
1 AATATATA-TAATTAT
28244 AATATATATAATTAT
1 AATATATATAATTAT
* *
28259 AATTATAAGTTTATATAAT
1 AA-TAT-A-TATA-ATTAT
28278 AAATATATATAA--AGT
1 -AATATATATAATTA-T
28293 AA-ATATATAATTACT
1 AATATATATAATTA-T
*
28308 -TTATATAT-ATTAT
1 AATATATATAATTAT
*
28321 -ATATATATAAAGTA-
1 AATATATAT-AATTAT
*
28335 AATACATATAATTAT
1 AATATATATAATTAT
28350 AATATATA
1 AATATATA
28358 ATTTATATTT
Statistics
Matches: 90, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
13 16 0.18
14 11 0.12
15 34 0.38
16 12 0.13
17 4 0.04
18 4 0.04
19 7 0.08
20 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:28355 original size:41 final size:39
Alignment explanation
Indices: 28228--28365 Score: 115
Period size: 41 Copynumber: 3.4 Consensus size: 39
28218 TATAAAAGTA
*
28228 AATATATATT-TAT-TATAATATA-TATAAT-TATAATTAT
1 AATATATATTATATATAT-ATAAAGTA-AATATATAATTAT
* *
28265 AAGTTTATATAATAAATATATATAAAGTAAATATATAATTACTT
1 AA---TATATATTATATATATATAAAGTAAATATATAATTA--T
*
28309 TATATATATTATATATATATAAAGTAAATACATATAATTAT
1 AATATATATTATATATATATAAAGTAAAT--ATATAATTAT
28350 AATATATAATT-TATAT
1 AATATAT-ATTATATAT
28366 TTATTATTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
37 2 0.02
40 7 0.09
41 46 0.56
42 16 0.20
43 9 0.11
44 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (39 bp):
AATATATATTATATATATATAAAGTAAATATATAATTAT
Found at i:28365 original size:11 final size:13
Alignment explanation
Indices: 28247--28360 Score: 64
Period size: 13 Copynumber: 8.8 Consensus size: 13
28237 TTATTATAAT
28247 ATATATAATTATA
1 ATATATAATTATA
28260 AT-TATAAGTT-T-
1 ATATATAA-TTATA
*
28271 ATATAATAAATAT-
1 ATAT-ATAATTATA
*
28284 ATATA-AAGTA-A
1 ATATATAATTATA
28295 ATATATAATTACT-
1 ATATATAATTA-TA
*
28308 TTATATATATTATA
1 ATATATA-ATTATA
*
28322 TATATATAAAGTA-A
1 -ATATAT-AATTATA
28336 ATACATATAATTATA
1 AT--ATATAATTATA
28351 ATATATAATT
1 ATATATAATT
28361 TATATTTATT
Statistics
Matches: 79, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
11 11 0.14
12 13 0.16
13 30 0.38
14 9 0.11
15 15 0.19
16 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:31265 original size:12 final size:12
Alignment explanation
Indices: 31248--31273 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31238 TAGAGGAGGG
31248 AACTCCTAGAAT
1 AACTCCTAGAAT
31260 AACTCCTAGAAT
1 AACTCCTAGAAT
31272 AA
1 AA
31274 ATAACAGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (12 bp):
AACTCCTAGAAT
Found at i:44289 original size:3 final size:3
Alignment explanation
Indices: 44281--44313 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
44271 ATATTACAAT
*
44281 ATA ATA AT- ATA ATA ATA ATA ATG ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44314 CTTAGTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46717 original size:21 final size:21
Alignment explanation
Indices: 46691--46734 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
46681 TTATACTGGA
*
46691 TTGCTAAAT-ACCGTCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
46712 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
46733 TT
1 TT
46735 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:47106 original size:19 final size:19
Alignment explanation
Indices: 47082--47119 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
47072 AGGGCGGCCT
47082 GCCGTGGCGAAGCCGCCCC
1 GCCGTGGCGAAGCCGCCCC
47101 GCCGTGGCGAAGCCGCCCC
1 GCCGTGGCGAAGCCGCCCC
47120 AGTGGGGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.47, G:0.37, T:0.05
Consensus pattern (19 bp):
GCCGTGGCGAAGCCGCCCC
Found at i:47136 original size:33 final size:33
Alignment explanation
Indices: 47099--47165 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
47089 CGAAGCCGCC
*
47099 CCGCCGTGGC-GAAGCCGCCCCAGTGGGGAGGCT
1 CCGCCGTGGCTG-AGCCGCCCCAGCGGGGAGGCT
* *
47132 CCGCCGTGGCTGAGCCGTCCTAGCGGGGAGGCT
1 CCGCCGTGGCTGAGCCGCCCCAGCGGGGAGGCT
47165 C
1 C
47166 AGTGTAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.10, C:0.36, G:0.42, T:0.12
Consensus pattern (33 bp):
CCGCCGTGGCTGAGCCGCCCCAGCGGGGAGGCT
Done.