Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012987.1 Corchorus olitorius cultivar O-4 contig13020, 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: 53611
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:5111 original size:77 final size:77
Alignment explanation
Indices: 4984--5137 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
4974 TACCGACTGC
* *
4984 TCACCCCCCTCAATATAGCTAAACAAACTTTAGAGCTATGACATCAACAACGATTCATGTGCTTG
1 TCACCCCCCTCAATATAGCTAAACAAACTTTAGAGCTATGACACCAACAACCATTCATGTGCTTG
5049 AAATGGGGACAA
66 AAATGGGGACAA
*
5061 TCACCCCCCTCAATATAGCTAAACAAACTTTAGAGTTATGACACCAACAACCATTCATGTGCTTG
1 TCACCCCCCTCAATATAGCTAAACAAACTTTAGAGCTATGACACCAACAACCATTCATGTGCTTG
5126 AAATGGGGACAA
66 AAATGGGGACAA
5138 ATATACTAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.23
Consensus pattern (77 bp):
TCACCCCCCTCAATATAGCTAAACAAACTTTAGAGCTATGACACCAACAACCATTCATGTGCTTG
AAATGGGGACAA
Found at i:10895 original size:63 final size:63
Alignment explanation
Indices: 10818--10943 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
10808 TGCTCTTAAA
*
10818 CCTAGTTTCTCTTAAACTCATGGTCCAGGTATGCTGGAACTAAGAGTTCAGTACTCTACCACC
1 CCTAGTTTCTCTTAAACTCATGGTCCAGGTATGCTGGAACTAAGAGTCCAGTACTCTACCACC
10881 CCTAGTTTCTCTTAAACTCATGGTCCAGGTATGCTGGAACTAAGAGTCCAGTACTCTACCACC
1 CCTAGTTTCTCTTAAACTCATGGTCCAGGTATGCTGGAACTAAGAGTCCAGTACTCTACCACC
10944 AGACCAAATG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (63 bp):
CCTAGTTTCTCTTAAACTCATGGTCCAGGTATGCTGGAACTAAGAGTCCAGTACTCTACCACC
Found at i:11982 original size:7 final size:7
Alignment explanation
Indices: 11970--11999 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
11960 AACAAAACAT
11970 TAACAAC
1 TAACAAC
11977 TAACAAC
1 TAACAAC
*
11984 TAACAGC
1 TAACAAC
11991 TAACAAC
1 TAACAAC
11998 TA
1 TA
12000 TGTGAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.53, C:0.27, G:0.03, T:0.17
Consensus pattern (7 bp):
TAACAAC
Found at i:20397 original size:25 final size:25
Alignment explanation
Indices: 20363--20412 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20353 AAGGAACAAC
20363 ATGATTAATGAAATAAATCAGATTT
1 ATGATTAATGAAATAAATCAGATTT
20388 ATGATTAATGAAATAAATCAGATTT
1 ATGATTAATGAAATAAATCAGATTT
20413 CATATTCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (25 bp):
ATGATTAATGAAATAAATCAGATTT
Found at i:22972 original size:19 final size:18
Alignment explanation
Indices: 22948--22983 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22938 TGAAGATTTA
22948 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
22967 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
22984 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:24575 original size:42 final size:42
Alignment explanation
Indices: 24528--24610 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
24518 TAAATTCTAG
*
24528 TACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTC
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
24570 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
24611 AATTGTTGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (42 bp):
TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
Found at i:25797 original size:12 final size:13
Alignment explanation
Indices: 25780--25808 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25770 ATTGCGTTAA
25780 TTTTTC-TTTTTC
1 TTTTTCTTTTTTC
25792 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
25805 TTTT
1 TTTT
25809 CCTATTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:28831 original size:18 final size:18
Alignment explanation
Indices: 28810--28845 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28800 GGTAATTACA
*
28810 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
28828 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
28846 GATAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:29723 original size:19 final size:18
Alignment explanation
Indices: 29699--29734 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29689 TGAAGATTTA
29699 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
29718 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
29735 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:31635 original size:9 final size:9
Alignment explanation
Indices: 31621--31654 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
31611 CCGCCCAAAT
31621 TGCAATTTG
1 TGCAATTTG
31630 TGCAATTT-
1 TGCAATTTG
*
31638 AGCAATTTG
1 TGCAATTTG
31647 TGCAATTT
1 TGCAATTT
31655 AGGCCGCGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (9 bp):
TGCAATTTG
Found at i:31644 original size:17 final size:17
Alignment explanation
Indices: 31622--31656 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
31612 CGCCCAAATT
31622 GCAATTTGTGCAATTTA
1 GCAATTTGTGCAATTTA
31639 GCAATTTGTGCAATTTA
1 GCAATTTGTGCAATTTA
31656 G
1 G
31657 GCCGCGGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (17 bp):
GCAATTTGTGCAATTTA
Found at i:53293 original size:29 final size:28
Alignment explanation
Indices: 53222--53412 Score: 161
Period size: 29 Copynumber: 6.6 Consensus size: 28
53212 GATCACCTAA
* *
53222 GGGCATTTTGGTCATTTT-CAAAAGATCCAG
1 GGGCATTTTGGTCATTTTGC---ACATTCAG
* *
53252 GGGCATTTCGGTCATTTTTCACATTCAGG
1 GGGCATTTTGGTCATTTTGCACATTCA-G
*
53281 GGGCATTTTGGTCATTTCTGCACACTCAG
1 GGGCATTTTGGTCATTT-TGCACATTCAG
* * * *
53310 GGACATTGTGGTCATTTTCGCATATTCAA
1 GGGCATTTTGGTCATTTT-GCACATTCAG
** *
53339 GGGCATTTTGGTCATTTTTTTACATACAG
1 GGGCATTTTGGTCA-TTTTGCACATTCAG
* * **
53368 GGGCATTTTGG-AAATTTGCATGTTCAG
1 GGGCATTTTGGTCATTTTGCACATTCAG
53395 GGGCATTTTGGTCATTTT
1 GGGCATTTTGGTCATTTT
53413 AGGATCACTT
Statistics
Matches: 128, Mismatches: 27, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
27 19 0.15
28 11 0.09
29 68 0.53
30 29 0.23
31 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTGCACATTCAG
Done.