Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012866.1 Corchorus olitorius cultivar O-4 contig12899, 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: 38952
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:5913 original size:2 final size:2
Alignment explanation
Indices: 5906--5930 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5896 ATTGATTAAA
5906 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5931 AACTGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11657 original size:26 final size:26
Alignment explanation
Indices: 11605--11663 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
11595 CATCAGGTGG
*
11605 TATTATTATTTAATAGTTGTAATATT
1 TATTATTATTTAATAGATGTAATATT
* *
11631 TATTATTATTTATTA-ATGTATTCATT
1 TATTATTATTTAATAGATGTAAT-ATT
11657 TATTATT
1 TATTATT
11664 GCCGCAGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (26 bp):
TATTATTATTTAATAGATGTAATATT
Found at i:14428 original size:31 final size:29
Alignment explanation
Indices: 14328--14499 Score: 184
Period size: 29 Copynumber: 5.9 Consensus size: 29
14318 CCATTCGCAC
* *
14328 ATCCAGGGGCATTTTGGTCATTTTCGCAT
1 ATCCGGGGGCATTTTGGTCATTTTTGCAT
* *
14357 ATTCGGGGGCATTTTGATCATTTTTGCAT
1 ATCCGGGGGCATTTTGGTCATTTTTGCAT
*
14386 ATACGGGGGCATTTTGGTCATTTTTGCAT
1 ATCCGGGGGCATTTTGGTCATTTTTGCAT
* *
14415 ATCCGGGGGGGCATTTTGGTCATTTTTACAC
1 ATCC--GGGGGCATTTTGGTCATTTTTGCAT
* * * * *
14446 ATCCAGGGGCATTTCGGTCATCTTTACAC
1 ATCCGGGGGCATTTTGGTCATTTTTGCAT
* *
14475 A-CTCTGGGGCAGTTTGGTCATTTTT
1 ATC-CGGGGGCATTTTGGTCATTTTT
14500 TTGCATACTC
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
28 1 0.01
29 96 0.77
31 27 0.22
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (29 bp):
ATCCGGGGGCATTTTGGTCATTTTTGCAT
Found at i:14455 original size:60 final size:58
Alignment explanation
Indices: 14325--14466 Score: 194
Period size: 60 Copynumber: 2.4 Consensus size: 58
14315 CAACCATTCG
* *
14325 CACATCCAGGGGCATTTTGGTCATTTTCGCATATTCGGGGGCATTTTGATCATTTTTG
1 CACATCCAGGGGCATTTTGGTCATTTTCGCATATCCGGGGGCATTTTGATCATTTTTA
* * * * *
14383 CATATACGGGGGCATTTTGGTCATTTTTGCATATCCGGGGGGGCATTTTGGTCATTTTTA
1 CACATCCAGGGGCATTTTGGTCATTTTCGCATATCC--GGGGGCATTTTGATCATTTTTA
*
14443 CACATCCAGGGGCATTTCGGTCAT
1 CACATCCAGGGGCATTTTGGTCAT
14467 CTTTACACAC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
58 31 0.44
60 40 0.56
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (58 bp):
CACATCCAGGGGCATTTTGGTCATTTTCGCATATCCGGGGGCATTTTGATCATTTTTA
Found at i:14484 original size:89 final size:89
Alignment explanation
Indices: 14333--14499 Score: 210
Period size: 89 Copynumber: 1.9 Consensus size: 89
14323 CGCACATCCA
* * * * * * * * *
14333 GGGGCATTTTGGTCATTTTCGCATATTCGGGGGCATTTTGATCATTTTTGCATATACGGGGGCAT
1 GGGGCATTTTGGTCATTTTCACACATCCAGGGGCATTTCGATCATCTTTACACATACGGGGGCAG
14398 TTTGGTCATTTTTGCATATCCGGG
66 TTTGGTCATTTTTGCATATCCGGG
* * *
14422 GGGGCATTTTGGTCATTTTTACACATCCAGGGGCATTTCGGTCATCTTTACACACT-CTGGGGCA
1 GGGGCATTTTGGTCATTTTCACACATCCAGGGGCATTTCGATCATCTTTACACA-TACGGGGGCA
14486 GTTTGGTCATTTTT
65 GTTTGGTCATTTTT
14500 TTGCATACTC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
89 64 0.98
90 1 0.02
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (89 bp):
GGGGCATTTTGGTCATTTTCACACATCCAGGGGCATTTCGATCATCTTTACACATACGGGGGCAG
TTTGGTCATTTTTGCATATCCGGG
Found at i:16432 original size:9 final size:8
Alignment explanation
Indices: 16395--16440 Score: 56
Period size: 9 Copynumber: 5.2 Consensus size: 8
16385 TGTTAGTTAG
16395 AAGAAAAA
1 AAGAAAAA
16403 AAGAAAAA
1 AAGAAAAA
16411 GAAGAAAATA
1 -AAGAAAA-A
16421 AAGGAAAAA
1 AA-GAAAAA
16430 AAGACAAAA
1 AAGA-AAAA
16439 AA
1 AA
16441 AAGTTGTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 10 0.29
9 18 0.53
10 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:16580 original size:15 final size:16
Alignment explanation
Indices: 16554--16587 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
16544 GGGAGGAGGT
16554 GGAAGAAAAATTTTGG
1 GGAAGAAAAATTTTGG
16570 GGAAG-AAAATTTTGG
1 GGAAGAAAAATTTTGG
16585 GGA
1 GGA
16588 GAAGGAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (16 bp):
GGAAGAAAAATTTTGG
Found at i:21356 original size:33 final size:33
Alignment explanation
Indices: 21309--21400 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
21299 TTCCGGCGGT
21309 GCCG-CCCCAGGGGGGCGCCACCGCCATGCCT-AC
1 GCCGCCCCCA-GGGGGCGCCACCGCCATG-CTGAC
* *
21342 GCCGCCCCCAGGGGGCGCCACCGCTATGGTGAC
1 GCCGCCCCCAGGGGGCGCCACCGCCATGCTGAC
** *
21375 GCCGCCCCC-CTGGGCGCCACTGCCAT
1 GCCGCCCCCAGGGGGCGCCACCGCCAT
21401 TTTTTCTAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 14 0.27
33 32 0.63
34 5 0.10
ACGTcount: A:0.11, C:0.48, G:0.33, T:0.09
Consensus pattern (33 bp):
GCCGCCCCCAGGGGGCGCCACCGCCATGCTGAC
Found at i:22476 original size:15 final size:17
Alignment explanation
Indices: 22440--22477 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
22430 AACCGAAAAC
22440 GACCC-AACCCAGAATG
1 GACCCGAACCCAGAATG
22456 GACCCGAACCC-GAAT-
1 GACCCGAACCCAGAATG
22471 GACCCGA
1 GACCCGA
22478 CATTGAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 9 0.43
17 5 0.24
ACGTcount: A:0.34, C:0.39, G:0.21, T:0.05
Consensus pattern (17 bp):
GACCCGAACCCAGAATG
Found at i:24000 original size:13 final size:13
Alignment explanation
Indices: 23962--24015 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 13
23952 AAAGAAAGGA
23962 GGAAAGG-AAAA-
1 GGAAAGGAAAAAG
23973 GGAATAGGGAAAAAAG
1 GGAA-A-GG-AAAAAG
23989 GGAAAAGGAAAAAG
1 GG-AAAGGAAAAAG
24003 GGAAAGGAAAAAG
1 GGAAAGGAAAAAG
24016 AAAAAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
11 4 0.11
12 1 0.03
13 13 0.35
14 8 0.22
15 6 0.16
16 3 0.08
17 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (13 bp):
GGAAAGGAAAAAG
Found at i:24738 original size:18 final size:18
Alignment explanation
Indices: 24715--24749 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24705 TGGAGAAAAA
24715 GACAAGA-AGATTGCCAAT
1 GACAAGACAGATT-CCAAT
24733 GACAAGACAGATTCCAA
1 GACAAGACAGATTCCAA
24750 GGTACAGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (18 bp):
GACAAGACAGATTCCAAT
Found at i:26160 original size:21 final size:22
Alignment explanation
Indices: 26116--26168 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
26106 CCACCATCAG
* *
26116 GCCACTACCGGCCATCCACCGT
1 GCCACCACCAGCCATCCACCGT
*
26138 GCCACCACCAGCCATGC-CCGT
1 GCCACCACCAGCCATCCACCGT
*
26159 GCCATCACCA
1 GCCACCACCA
26169 TTCCGCGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.21, C:0.51, G:0.17, T:0.11
Consensus pattern (22 bp):
GCCACCACCAGCCATCCACCGT
Found at i:27072 original size:17 final size:18
Alignment explanation
Indices: 27050--27085 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27040 AAGGGTAGTT
*
27050 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
27067 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
27085 T
1 T
27086 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:27996 original size:18 final size:19
Alignment explanation
Indices: 27962--28001 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
27952 TTGAAGATTT
27962 ATTGAAGATAAATTGAAGA
1 ATTGAAGATAAATTGAAGA
*
27981 ATTGAAGAT-GATTGAAGA
1 ATTGAAGATAAATTGAAGA
27999 ATT
1 ATT
28002 ATTTCAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (19 bp):
ATTGAAGATAAATTGAAGA
Found at i:30805 original size:27 final size:25
Alignment explanation
Indices: 30756--30811 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
30746 CTTACCTTTA
30756 TCTTTTTATTTTTTTTCGTTATTTT
1 TCTTTTTATTTTTTTTCGTTATTTT
* *
30781 TCTTTTTCTTTTATTTTTGTTTATTTT
1 TCTTTTTATTTT-TTTTCG-TTATTTT
30808 TCTT
1 TCTT
30812 AGTCACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 11 0.41
26 5 0.19
27 11 0.41
ACGTcount: A:0.07, C:0.09, G:0.04, T:0.80
Consensus pattern (25 bp):
TCTTTTTATTTTTTTTCGTTATTTT
Found at i:31977 original size:21 final size:21
Alignment explanation
Indices: 31938--31986 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
31928 TTAATGCTTT
**
31938 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
31960 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
31981 A-GAAGC
1 AGGAAGC
31987 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:36725 original size:3 final size:3
Alignment explanation
Indices: 36717--36759 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
36707 ATATATATAT
36717 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
36760 GGTTAGTAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.