Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013551.1 Corchorus olitorius cultivar O-4 contig13584, 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: 106820
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:973 original size:14 final size:14
Alignment explanation
Indices: 927--975 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
917 TGTTGGGTTT
927 AGTCAGTTTT-TTG
1 AGTCAGTTTTGTTG
**
940 AGTCAGTTCAGTT-
1 AGTCAGTTTTGTTG
953 AGTTCAGTTTTGTTG
1 AG-TCAGTTTTGTTG
968 AGTCAGTT
1 AGTCAGTT
976 AGTTTGAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 10 0.34
14 17 0.59
15 2 0.07
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.47
Consensus pattern (14 bp):
AGTCAGTTTTGTTG
Found at i:973 original size:28 final size:25
Alignment explanation
Indices: 925--979 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
915 TCTGTTGGGT
925 TTAGTCAGTTTTTTGAGTCAGTTCAG
1 TTAGTCAGTTTTTTGAGTCAGTT-AG
951 TTAGTTCAGTTTTGTTGAGTCAGTTAG
1 TTAG-TCAGTTTT-TTGAGTCAGTTAG
978 TT
1 TT
980 TGAGTCTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 4 0.15
27 12 0.44
28 11 0.41
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.49
Consensus pattern (25 bp):
TTAGTCAGTTTTTTGAGTCAGTTAG
Found at i:9349 original size:13 final size:14
Alignment explanation
Indices: 9329--9364 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
9319 TAGTAATTAT
9329 TTAG-ACTAAATA-
1 TTAGTACTAAATAC
9341 TTAGTACTAAATAC
1 TTAGTACTAAATAC
9355 TTA-TACTAAA
1 TTAGTACTAAA
9365 AAAATTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 15 0.68
14 3 0.14
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (14 bp):
TTAGTACTAAATAC
Found at i:12467 original size:21 final size:21
Alignment explanation
Indices: 12442--12483 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12432 TTAAAATTTT
12442 TTTATACAA-AAATGATATATA
1 TTTATA-AATAAATGATATATA
*
12463 TTTATAAATAAATTATATATA
1 TTTATAAATAAATGATATATA
12484 ATTTTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTATAAATAAATGATATATA
Found at i:40116 original size:17 final size:16
Alignment explanation
Indices: 40096--40135 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
40086 TAGGTATAAA
40096 ATAATATAATATAATAT
1 ATAATATAAT-TAATAT
*
40113 ATAATTATAATTATTAT
1 ATAA-TATAATTAATAT
40130 ATAATA
1 ATAATA
40136 ATATGTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 13 0.62
18 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATATAATTAATAT
Found at i:41450 original size:7 final size:7
Alignment explanation
Indices: 41438--41515 Score: 63
Period size: 7 Copynumber: 11.1 Consensus size: 7
41428 ATCACTAAAA
*
41438 ATAATAC
1 ATAATAT
41445 ATAATAT
1 ATAATAT
41452 AT-ATAT
1 ATAATAT
41458 ATAATAT
1 ATAATAT
*
41465 AATAACAAT
1 -ATAA-TAT
41474 ATAATA-
1 ATAATAT
41480 ATAATAT
1 ATAATAT
* *
41487 AATGATAA
1 -ATAATAT
*
41495 ATAATAA
1 ATAATAT
41502 ATAATA-
1 ATAATAT
41508 ATAATAT
1 ATAATAT
41515 A
1 A
41516 AGCCCCTCGA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
6 18 0.31
7 26 0.44
8 13 0.22
9 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (7 bp):
ATAATAT
Found at i:41480 original size:3 final size:3
Alignment explanation
Indices: 41437--41513 Score: 63
Period size: 3 Copynumber: 25.3 Consensus size: 3
41427 AATCACTAAA
*
41437 AAT AAT ACAT AAT -AT ATAT ATAT AAT -AT AAT AAC AAT -AT AAT AAT
1 AAT AAT A-AT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
*
41482 AAT -AT AAT GAT AAAT AAT AAAT AAT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT A
41514 TAAGCCCCTC
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
2 8 0.13
3 39 0.63
4 15 0.24
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:41481 original size:39 final size:39
Alignment explanation
Indices: 41437--41516 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
41427 AATCACTAAA
*
41437 AATAAT-ACATAAT-ATATATATATAATATAATAACAATAT
1 AATAATAACATAATGATAAATA-ATAA-ATAATAACAATAT
* *
41476 AATAATAATATAATGATAAATAATAAATAATAATAATAT
1 AATAATAACATAATGATAAATAATAAATAATAACAATAT
41515 AA
1 AA
41517 GCCCCTCGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 20 0.56
40 10 0.28
41 6 0.17
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (39 bp):
AATAATAACATAATGATAAATAATAAATAATAACAATAT
Found at i:41516 original size:11 final size:11
Alignment explanation
Indices: 41438--41513 Score: 82
Period size: 11 Copynumber: 6.5 Consensus size: 11
41428 ATCACTAAAA
41438 ATAATACATAAT
1 ATAATA-ATAAT
41450 ATATATATATAAT
1 ATA-ATA-ATAAT
*
41463 ATAATAACAAT
1 ATAATAATAAT
41474 ATAATAATAAT
1 ATAATAATAAT
*
41485 ATAATGATAA-
1 ATAATAATAAT
41495 ATAATAAATAAT
1 ATAAT-AATAAT
41507 AATAATA
1 -ATAATA
41514 TAAGCCCCTC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
10 5 0.09
11 27 0.49
12 7 0.13
13 16 0.29
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:42686 original size:11 final size:11
Alignment explanation
Indices: 42659--42702 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
42649 ATAATTTGCT
*
42659 TCCCCTTCCCC
1 TCCCCTCCCCC
42670 -CCCCTCCCCC
1 TCCCCTCCCCC
42680 TCCCCTCCCCC
1 TCCCCTCCCCC
42691 TCCCCCTCCCCC
1 T-CCCCTCCCCC
42703 ATTTCTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.30
11 11 0.37
12 10 0.33
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (11 bp):
TCCCCTCCCCC
Found at i:42691 original size:17 final size:16
Alignment explanation
Indices: 42660--42702 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
42650 TAATTTGCTT
*
42660 CCCCTTCCCCCCCCTC
1 CCCCTCCCCCCCCCTC
42676 CCCCTCCCCTCCCCCTC
1 CCCCTCCCC-CCCCCTC
42693 CCCCTCCCCC
1 CCCCTCCCCC
42703 ATTTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.00, C:0.84, G:0.00, T:0.16
Consensus pattern (16 bp):
CCCCTCCCCCCCCCTC
Found at i:42702 original size:6 final size:6
Alignment explanation
Indices: 42669--42702 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
42659 TCCCCTTCCC
42669 CCCCCT CCCCCT -CCCCT CCCCCT CCCCCT CCCCC
1 CCCCCT CCCCCT CCCCCT CCCCCT CCCCCT CCCCC
42703 ATTTCTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCCT
Found at i:43580 original size:13 final size:13
Alignment explanation
Indices: 43562--43587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43552 CATCATCATC
43562 TTTCTTTAATTGG
1 TTTCTTTAATTGG
43575 TTTCTTTAATTGG
1 TTTCTTTAATTGG
43588 AATTACTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
TTTCTTTAATTGG
Found at i:43964 original size:40 final size:40
Alignment explanation
Indices: 43909--43990 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
43899 TTATATATTG
43909 CTTAAATATTGGAGTGTTTGTTGATTGCTTCTTAAGAGCT
1 CTTAAATATTGGAGTGTTTGTTGATTGCTTCTTAAGAGCT
43949 CTTAAATATTGGAGTGTTTGTTGATTGCTTCTTAAGAGCT
1 CTTAAATATTGGAGTGTTTGTTGATTGCTTCTTAAGAGCT
43989 CT
1 CT
43991 GTGGTGTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (40 bp):
CTTAAATATTGGAGTGTTTGTTGATTGCTTCTTAAGAGCT
Found at i:46425 original size:43 final size:43
Alignment explanation
Indices: 46364--46449 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
46354 TCCACAAGGT
46364 TTGTATTGGAATACCTAGACTTCTGTGTTGGATGTGGTCAATC
1 TTGTATTGGAATACCTAGACTTCTGTGTTGGATGTGGTCAATC
*
46407 TTGTATTGGAATACCTAGACTTTTGTGTTGGATGTGGTCAATC
1 TTGTATTGGAATACCTAGACTTCTGTGTTGGATGTGGTCAATC
46450 ATTTCATGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.41
Consensus pattern (43 bp):
TTGTATTGGAATACCTAGACTTCTGTGTTGGATGTGGTCAATC
Found at i:49218 original size:20 final size:21
Alignment explanation
Indices: 49195--49236 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
49185 TTTAACTTAT
49195 AATTTAAAAA-AAAAACTACC
1 AATTTAAAAAGAAAAACTACC
*
49215 AATTTAAAAAGGAAAACTACC
1 AATTTAAAAAGAAAAACTACC
49236 A
1 A
49237 TAAATTACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.62, C:0.14, G:0.05, T:0.19
Consensus pattern (21 bp):
AATTTAAAAAGAAAAACTACC
Found at i:54065 original size:21 final size:21
Alignment explanation
Indices: 54041--54087 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
54031 TTCCTGGAAG
* *
54041 CCAGGTTTTGATTTATGCGAA
1 CCAGATTTCGATTTATGCGAA
*
54062 CCAGATTTCGATTTATGTGAA
1 CCAGATTTCGATTTATGCGAA
54083 CCAGA
1 CCAGA
54088 AACCTTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (21 bp):
CCAGATTTCGATTTATGCGAA
Found at i:59010 original size:6 final size:6
Alignment explanation
Indices: 58999--59033 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
58989 ATTAGCACAG
*
58999 AGAGAA AGAGAA AGAGAA AGAGAG AGAGAA AGAGA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGA
59034 GGGGACTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (6 bp):
AGAGAA
Found at i:63634 original size:21 final size:19
Alignment explanation
Indices: 63609--63666 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
63599 GCTGCTCTAA
63609 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
63630 TAATCTAATCTATACAGTG
1 TAATCTCATCTGTACAGTC
*
63649 TAATTTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
63667 TGCTAAACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:73790 original size:64 final size:64
Alignment explanation
Indices: 73711--73830 Score: 222
Period size: 64 Copynumber: 1.9 Consensus size: 64
73701 TACCTTGAAG
*
73711 GAATGGCAGGATTATAGTGCTGCTACCTCAACACAACAGTTCATAATCACTTCAAAGTTCAAAC
1 GAATGGCAGGATTATAATGCTGCTACCTCAACACAACAGTTCATAATCACTTCAAAGTTCAAAC
*
73775 GAATGGCGGGATTATAATGCTGCTACCTCAACACAACAGTTCATAATCACTTCAAA
1 GAATGGCAGGATTATAATGCTGCTACCTCAACACAACAGTTCATAATCACTTCAAA
73831 CATAACAAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (64 bp):
GAATGGCAGGATTATAATGCTGCTACCTCAACACAACAGTTCATAATCACTTCAAAGTTCAAAC
Found at i:85110 original size:82 final size:82
Alignment explanation
Indices: 84990--85155 Score: 305
Period size: 82 Copynumber: 2.0 Consensus size: 82
84980 CTTTTGATCA
*
84990 ATATTACTAAAATTATAATTGAGTATCGATTAATTCAGAGTGAGTTGTTTAAGACTTAAAAACGA
1 ATATTACTAAAATTATAATTGAGTATCGATTAATTCAGAGTGAATTGTTTAAGACTTAAAAACGA
*
85055 TGATATTATTATCTTTT
66 TGACATTATTATCTTTT
*
85072 ATATTACTGAAATTATAATTGAGTATCGATTAATTCAGAGTGAATTGTTTAAGACTTAAAAACGA
1 ATATTACTAAAATTATAATTGAGTATCGATTAATTCAGAGTGAATTGTTTAAGACTTAAAAACGA
85137 TGACATTATTATCTTTT
66 TGACATTATTATCTTTT
85154 AT
1 AT
85156 GTTCTTCTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (82 bp):
ATATTACTAAAATTATAATTGAGTATCGATTAATTCAGAGTGAATTGTTTAAGACTTAAAAACGA
TGACATTATTATCTTTT
Found at i:86267 original size:2 final size:2
Alignment explanation
Indices: 86260--86285 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86250 CCAAATCAAA
86260 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
86286 TAATGGTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87752 original size:3 final size:3
Alignment explanation
Indices: 87744--87774 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
87734 TCTCTGCCTC
*
87744 TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
87775 TATTTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Done.