Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013467.1 Corchorus olitorius cultivar O-4 contig13500, 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: 52161
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:190 original size:45 final size:43
Alignment explanation
Indices: 118--201 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
108 AAAAAACCCC
* * * *
118 TTTCGGTATATATAATACATATTAAATATATAATAAAATTGAT
1 TTTCAGTATATATAAAACATATTAAATAAATAAAAAAATTGAT
*
161 TTTCAGTATATATAAAATATAATTAAAATAAATAAAAAAAT
1 TTTCAGTATATATAAAACAT-ATT-AAATAAATAAAAAAAT
202 CATACCTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 17 0.50
44 3 0.09
45 14 0.41
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.38
Consensus pattern (43 bp):
TTTCAGTATATATAAAACATATTAAATAAATAAAAAAATTGAT
Found at i:2324 original size:15 final size:14
Alignment explanation
Indices: 2304--2355 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 14
2294 GGCCTGGCCC
2304 AAAAGAAGAAAAGAA
1 AAAAGAA-AAAAGAA
2319 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
*
2333 AAAGGAAATAAAGAA
1 AAAAGAAA-AAAGAA
2348 AATAAGAA
1 AA-AAGAA
2356 TTTTGGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 14 0.42
15 15 0.45
16 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:2327 original size:6 final size:7
Alignment explanation
Indices: 2304--2355 Score: 68
Period size: 7 Copynumber: 7.0 Consensus size: 7
2294 GGCCTGGCCC
2304 AAAAGAA
1 AAAAGAA
2311 GAAAAGAA
1 -AAAAGAA
2319 AAAAGAA
1 AAAAGAA
2326 AAAAGAA
1 AAAAGAA
*
2333 AAAGGAA
1 AAAAGAA
2340 ATAAAGAA
1 A-AAAGAA
2348 AATAAGAA
1 AA-AAGAA
2356 TTTTGGAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 22 0.55
8 18 0.45
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:8968 original size:29 final size:29
Alignment explanation
Indices: 8893--8979 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
8883 TTTAAAGGCT
* *
8893 AAAAGTTCAAATAGGGGCCTAACCTTTAGGG
1 AAAAGGTCAAATAAGGGCCTAACCTTTA--G
**
8924 AAAAGGTCATTTAAGGGCCTAACCTTTCA-
1 AAAAGGTCAAATAAGGGCCTAACCTTT-AG
* *
8953 ATAAGGTCAAATAAGGGCCCAACCTTT
1 AAAAGGTCAAATAAGGGCCTAACCTTT
8980 TCGAATTGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 23 0.49
31 23 0.49
32 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (29 bp):
AAAAGGTCAAATAAGGGCCTAACCTTTAG
Found at i:9515 original size:24 final size:24
Alignment explanation
Indices: 9483--9561 Score: 158
Period size: 24 Copynumber: 3.3 Consensus size: 24
9473 TAAATTAGGG
9483 TTTGGGGATTGGGTTTTCGCGAAA
1 TTTGGGGATTGGGTTTTCGCGAAA
9507 TTTGGGGATTGGGTTTTCGCGAAA
1 TTTGGGGATTGGGTTTTCGCGAAA
9531 TTTGGGGATTGGGTTTTCGCGAAA
1 TTTGGGGATTGGGTTTTCGCGAAA
9555 TTTGGGG
1 TTTGGGG
9562 GTTTTGAGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.15, C:0.08, G:0.39, T:0.38
Consensus pattern (24 bp):
TTTGGGGATTGGGTTTTCGCGAAA
Found at i:15377 original size:33 final size:33
Alignment explanation
Indices: 15307--15444 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
15297 ATGATCAACC
** *
15307 AAAACAGATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGATTTAG-TTTCATCACAAACAACA-CCT
* *
15340 AAAACAGAATTGGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
*
15373 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
** * * *
15405 CAAATTAGATTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTTTCATCACAAACAACACCT
15439 AAAACA
1 AAAACA
15445 CTCTTTGCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
32 4 0.05
33 81 0.92
34 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:16042 original size:15 final size:15
Alignment explanation
Indices: 16022--16053 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
16012 AAACTAAGTG
16022 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
16037 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
16052 GA
1 GA
16054 ACCCCCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (15 bp):
GAGCTTGTTGATTTT
Found at i:16886 original size:10 final size:10
Alignment explanation
Indices: 16871--16904 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
16861 TGGTCGAAAA
*
16871 TTTTTTATGT
1 TTTTTTATAT
*
16881 TTTTTTATTT
1 TTTTTTATAT
16891 TTTTTTATAT
1 TTTTTTATAT
16901 TTTT
1 TTTT
16905 CGATTAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:17055 original size:19 final size:17
Alignment explanation
Indices: 17018--17057 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
17008 CTTGAAAATT
*
17018 TGAAAAACTTTGATGGA
1 TGAAAAACTTTGATAGA
17035 TGAAAAACTTGATGATAGA
1 TGAAAAACTT--TGATAGA
17054 TGAA
1 TGAA
17058 TAGAAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
19 10 0.50
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.28
Consensus pattern (17 bp):
TGAAAAACTTTGATAGA
Found at i:25108 original size:22 final size:22
Alignment explanation
Indices: 25080--25125 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
25070 CTGCTTGTTG
25080 TTTACCATACCTGAACTTAAAC
1 TTTACCATACCTGAACTTAAAC
* * *
25102 TTTACCATGCCTGATCTTGAAC
1 TTTACCATACCTGAACTTAAAC
25124 TT
1 TT
25126 GGTCGTCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTACCATACCTGAACTTAAAC
Found at i:35870 original size:21 final size:20
Alignment explanation
Indices: 35846--35884 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35836 AGACAAAATT
*
35846 TACTTACTCTAAGACACTTAA
1 TACTTACCCT-AGACACTTAA
*
35867 TACTTCCCCTAGACACTT
1 TACTTACCCTAGACACTT
35885 CAACATTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (20 bp):
TACTTACCCTAGACACTTAA
Found at i:38389 original size:16 final size:16
Alignment explanation
Indices: 38370--38413 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
38360 ACCCGCCCGA
*
38370 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
38386 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
38402 ACCCGAACCCGA
1 ACCCGAACCCGA
38414 CTCGAGCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.39, C:0.41, G:0.14, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:38445 original size:16 final size:17
Alignment explanation
Indices: 38403--38446 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
38393 CCCGAAAATA
38403 CCCGAACCCGACTCGAG
1 CCCGAACCCGACTCGAG
38420 CCC-AATCCCGAC-CGAG
1 CCCGAA-CCCGACTCGAG
38436 CCCGAACCCGA
1 CCCGAACCCGA
38447 AATAATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.25, C:0.50, G:0.20, T:0.05
Consensus pattern (17 bp):
CCCGAACCCGACTCGAG
Found at i:38960 original size:31 final size:31
Alignment explanation
Indices: 38889--38960 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
38879 GTCTATCAGC
*
38889 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
38920 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
38950 GTTTTAATTTG
1 -TTTTAATTTG
38961 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:39242 original size:8 final size:8
Alignment explanation
Indices: 39229--39278 Score: 93
Period size: 8 Copynumber: 6.4 Consensus size: 8
39219 AATAATGTTA
39229 TATTATAT
1 TATTATAT
39237 TATTATAT
1 TATTATAT
39245 TATTATAT
1 TATTATAT
39253 TATTATAT
1 TATTATAT
39261 TATTATAT
1 TATTATAT
39269 TA-TATAT
1 TATTATAT
39276 TAT
1 TAT
39279 CAATAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.17
8 34 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATAT
Found at i:39425 original size:8 final size:8
Alignment explanation
Indices: 39412--39438 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
39402 AATAATGTTA
39412 TATTATAT
1 TATTATAT
39420 TATTATAT
1 TATTATAT
39428 TATTATAT
1 TATTATAT
39436 TAT
1 TAT
39439 CTATTATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTATAT
Found at i:39598 original size:23 final size:23
Alignment explanation
Indices: 39572--39629 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
39562 CGAAATCAAA
*
39572 CTCGAGCCCGAACCCGACCCGAG
1 CTCGAACCCGAACCCGACCCGAG
*
39595 CTCGAACCCGAACCCTACCCGAG
1 CTCGAACCCGAACCCGACCCGAG
39618 AC-CGAACCCGAA
1 -CTCGAACCCGAA
39630 AATACCCGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.28, C:0.47, G:0.21, T:0.05
Consensus pattern (23 bp):
CTCGAACCCGAACCCGACCCGAG
Found at i:39640 original size:16 final size:16
Alignment explanation
Indices: 39619--39703 Score: 136
Period size: 16 Copynumber: 5.3 Consensus size: 16
39609 CTACCCGAGA
39619 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
39635 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
39651 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
39667 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
39683 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
39699 CCGAA
1 CCGAA
39704 GTACCCGAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
15 3 0.05
16 57 0.90
17 3 0.05
ACGTcount: A:0.41, C:0.39, G:0.14, T:0.06
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:41196 original size:14 final size:15
Alignment explanation
Indices: 41177--41205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41167 AGATGAGGGA
41177 ATTTTA-TTTTTTTT
1 ATTTTACTTTTTTTT
41191 ATTTTACTTTTTTTT
1 ATTTTACTTTTTTTT
41206 GTATATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
ATTTTACTTTTTTTT
Found at i:51868 original size:33 final size:31
Alignment explanation
Indices: 51795--51940 Score: 123
Period size: 33 Copynumber: 4.5 Consensus size: 31
51785 GCTATGATCA
** *
51795 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
51827 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
51860 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * *
51893 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC
*
51926 ATCTAAAACAGATTT
1 A-CCAAAACAGATTT
51941 AGAATTACTC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
32 7 0.07
33 79 0.84
34 8 0.09
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Done.