Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014899.1 Corchorus olitorius cultivar O-4 contig14932, 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: 39504
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2469 original size:2 final size:2
Alignment explanation
Indices: 2456--2487 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2446 TCTAGGGTTT
*
2456 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2488 AGAAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12609 original size:14 final size:14
Alignment explanation
Indices: 12590--12620 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12580 AATGTGATCT
*
12590 AAAATAACATACCA
1 AAAATAACATAACA
12604 AAAATAACATAACA
1 AAAATAACATAACA
12618 AAA
1 AAA
12621 GAAATTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAACATAACA
Found at i:12947 original size:128 final size:129
Alignment explanation
Indices: 12690--12953 Score: 340
Period size: 128 Copynumber: 2.1 Consensus size: 129
12680 TTTTCACTCA
* * *
12690 TAAT-TATTCTTTTGTACCTAATTATTTTCTTTCTCGCAATTGATGCAACTCTCATTTACATATA
1 TAATATATTCTGTTGTACCTAATTACTTTATTTCTCGCAATTGATGCAACTCTCATTTACA-ATA
* * * *
12754 TTAAACTTAAACCACAAAACATGAAACCTCCTATATAAAATTTTCTTTGATTATACTAACTTTTG
65 TTAAACCTAAACCACAAAACATGAAACCTCCTATATAAAATTTTCATCGATTATAATAACTTTTG
* *
12819 TAATATATTCTGTTGTACCTGATTACTTTATTTCTCGCAATT-ACTGTAACTCTCATTTAC-ATA
1 TAATATATTCTGTTGTACCTAATTACTTTATTTCTCGCAATTGA-TGCAACTCTCATTTACAATA
** * *
12882 TTAAACCTAATTCACAAAACATGGAACCT-C-ATATACAATGATTTCATCGATTATAATAACTTT
65 TTAAACCTAAACCACAAAACATGAAACCTCCTATATAAAAT--TTTCATCGATTATAATAACTTT
12945 TG
128 TG
12947 TAATATA
1 TAATATA
12954 ATTTATTTGG
Statistics
Matches: 118, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
126 8 0.07
127 1 0.01
128 56 0.47
129 5 0.04
130 48 0.41
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.41
Consensus pattern (129 bp):
TAATATATTCTGTTGTACCTAATTACTTTATTTCTCGCAATTGATGCAACTCTCATTTACAATAT
TAAACCTAAACCACAAAACATGAAACCTCCTATATAAAATTTTCATCGATTATAATAACTTTTG
Found at i:15424 original size:22 final size:22
Alignment explanation
Indices: 15395--15450 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
15385 TATTTTTATT
*
15395 AAATTTTGATAATCACACTATG
1 AAATTTTGATAATCACACTATA
* * *
15417 GAATTTTGATAATTACCCTATA
1 AAATTTTGATAATCACACTATA
15439 AAATTTTGATAA
1 AAATTTTGATAA
15451 ACTCCCAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAATCACACTATA
Found at i:15762 original size:22 final size:22
Alignment explanation
Indices: 15657--15843 Score: 116
Period size: 22 Copynumber: 8.5 Consensus size: 22
15647 ACATAGTTTT
* *
15657 ACTATGAAATTTTGATAATCTC
1 ACTATGAAATTTTGATAACCAC
* *
15679 ACTAT-ATTATTTTGATAACCTC
1 ACTATGA-AATTTTGATAACCAC
* * *
15701 -CTTAAGAAATTGTGATAACCTC
1 AC-TATGAAATTTTGATAACCAC
* * * * *
15723 -CTTGTGGAACTTTAATAACTAC
1 AC-TATGAAATTTTGATAACCAC
* *
15745 ACTATGAAATTCTGATAATCATC
1 ACTATGAAATTTTGATAACCA-C
* *
15768 -CTATGAAATTTTGGTCACCAC
1 ACTATGAAATTTTGATAACCAC
*
15789 ACTCTGAAATTTTGATAACCAC
1 ACTATGAAATTTTGATAACCAC
*
15811 AGTAT-AAATTTATGATAACCAC
1 ACTATGAAATTT-TGATAACCAC
15833 TA-TATGAAATT
1 -ACTATGAAATT
15844 AATTTTGATG
Statistics
Matches: 127, Mismatches: 29, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
21 9 0.07
22 109 0.86
23 9 0.07
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCAC
Found at i:15960 original size:22 final size:22
Alignment explanation
Indices: 15912--16100 Score: 105
Period size: 22 Copynumber: 8.5 Consensus size: 22
15902 GATTTGGTAG
* * **
15912 ACTATGAAATTTGGATAATCAA
1 ACTATGAAATTTTGATAACCTC
15934 ACTATGAAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCTC
* * * * *
15956 CCTATGGAATGTTAATAACTTC
1 ACTATGAAATTTTGATAACCTC
* * *
15978 CCTAT-AGAATTTAGTGTTAATCTC
1 ACTATGA-AATTT--TGATAACCTC
* * *
16002 ACCATGAAATTTTGATAAACAC
1 ACTATGAAATTTTGATAACCTC
* * * *
16024 AATTTGAAACTTTGATTACCT-
1 ACTATGAAATTTTGATAACCTC
* *
16045 TCTATGAAATTTTTG-TAACCAC
1 ACTATGAAA-TTTTGATAACCTC
* * *
16067 ATTATGAAATTTTGATAGCCAC
1 ACTATGAAATTTTGATAACCTC
16089 ACTATGAAATTT
1 ACTATGAAATTT
16101 CAATAATCTA
Statistics
Matches: 123, Mismatches: 37, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
21 15 0.12
22 93 0.76
24 14 0.11
25 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCTC
Found at i:18751 original size:17 final size:17
Alignment explanation
Indices: 18729--18762 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18719 AACTAAAAAG
18729 AGTAACTTAAATGAGAA
1 AGTAACTTAAATGAGAA
18746 AGTAACTTAAATGAGAA
1 AGTAACTTAAATGAGAA
18763 CTGATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
AGTAACTTAAATGAGAA
Found at i:23663 original size:14 final size:14
Alignment explanation
Indices: 23644--23670 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23634 CATGATTTGA
23644 GAAAAAACCTTTTT
1 GAAAAAACCTTTTT
23658 GAAAAAACCTTTT
1 GAAAAAACCTTTT
23671 ATTACCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (14 bp):
GAAAAAACCTTTTT
Found at i:25027 original size:60 final size:60
Alignment explanation
Indices: 24940--25099 Score: 277
Period size: 60 Copynumber: 2.6 Consensus size: 60
24930 GCTAATTGTT
*
24940 CAAATAAGGGCCTAATGTTTTGCCAAAATGCTCAAATAAGGG-CCGAATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACG-TTTGCCAAAATGCTCAAATAAGGGTCCG-ATCTTTTAATTTGAC
*
25001 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGAC
25061 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAG
25100 AGCCTGACAT
Statistics
Matches: 96, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
60 77 0.80
61 19 0.20
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGAC
Found at i:25070 original size:29 final size:28
Alignment explanation
Indices: 24972--25072 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 28
24962 CCAAAATGCT
*
24972 CAAATAAGGGCCGAATCTTTTAATTTGAC
1 CAAATAAGGGCCG-ATCTTTTAATTTGGC
* * * **
25001 CAAATAAGGGCCTAACGTTTGCCAAAAT-GC
1 CAAATAAGGGCCGATC-TTT--TAATTTGGC
25031 TCAAATAAGGGTCCGATCTTTTAATTTGGC
1 -CAAATAAGGG-CCGATCTTTTAATTTGGC
25061 CAAATAAGGGCC
1 CAAATAAGGGCC
25073 TAACGTTTGC
Statistics
Matches: 55, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
28 4 0.07
29 28 0.51
30 3 0.05
31 16 0.29
32 4 0.07
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (28 bp):
CAAATAAGGGCCGATCTTTTAATTTGGC
Found at i:25240 original size:60 final size:58
Alignment explanation
Indices: 25144--25305 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 58
25134 ACTGATGACG
* * *
25144 GGCCCTTATTTGAGTATTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGACCC
1 GGCCCTTATTTGAGCATTT-TCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGACCA
* *
25203 GGCCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCA
1 GGCCCTTATTTGAGCATTTTC-A-AACGTTAGGCCCTTATTTAGCCAAATTAAAAGACCA
*
25263 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTA
1 GGCCCTTATTTGAGCATTTT--CAAACGTTAGGCCCTTATTTA
25306 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
58 1 0.01
59 19 0.21
60 70 0.76
61 1 0.01
62 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (58 bp):
GGCCCTTATTTGAGCATTTTCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGACCA
Found at i:25241 original size:31 final size:30
Alignment explanation
Indices: 25144--25309 Score: 96
Period size: 29 Copynumber: 5.5 Consensus size: 30
25134 ACTGATGACG
* *
25144 GGCCCTTATTTGAGTATTTGGC-AAACGTTA
1 GGCCCTTATTTGAGCATTT-TCAAAACGTTA
** ***
25174 GGCCCTTATTT-AGCCAAATT-AAAA-GACCC
1 GGCCCTTATTTGAG-CATTTTCAAAACG-TTA
25203 GGCCCTTATTTGAGCATTTTCAATAACGTTA
1 GGCCCTTATTTGAGCATTTTCAA-AACGTTA
** *
25234 GGCCCTTATTTG-GCCAAATT-AAAA-GATCA
1 GGCCCTTATTTGAG-CATTTTCAAAACG-TTA
*
25263 GACCCTTATTTGAGCATTTTGGC-AAACGTTA
1 GGCCCTTATTTGAGCATTTT--CAAAACGTTA
*
25294 GGCCCTTATTTAAGCA
1 GGCCCTTATTTGAGCA
25310 ATTAGCCAGC
Statistics
Matches: 101, Mismatches: 21, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
28 2 0.02
29 39 0.39
30 21 0.21
31 37 0.37
32 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (30 bp):
GGCCCTTATTTGAGCATTTTCAAAACGTTA
Found at i:28170 original size:27 final size:27
Alignment explanation
Indices: 28149--28201 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
28139 GCCCCTGAAT
*
28149 GTGCAACTGACTAAAATACCCCTAGAC
1 GTGCAAATGACTAAAATACCCCTAGAC
*
28176 GTGCAAATGACTAAAATGCCCCTAGA
1 GTGCAAATGACTAAAATACCCCTAGA
28202 TGACCCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (27 bp):
GTGCAAATGACTAAAATACCCCTAGAC
Found at i:36058 original size:21 final size:21
Alignment explanation
Indices: 36029--36079 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
36019 ATGACACTGC
* *
36029 CCACTTGGGTGATCAAACAAA
1 CCACATGGGTCATCAAACAAA
* *
36050 CCACATGGGTCTTCAGACAAA
1 CCACATGGGTCATCAAACAAA
*
36071 CCATATGGG
1 CCACATGGG
36080 CGCCCAAGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (21 bp):
CCACATGGGTCATCAAACAAA
Found at i:37463 original size:46 final size:46
Alignment explanation
Indices: 37407--37523 Score: 148
Period size: 45 Copynumber: 2.5 Consensus size: 46
37397 TCCATTTTAA
*
37407 TAAAGCCCATTTCCTCATTAGTTTCATTCAAAGTCCATTACCATTT
1 TAAAGCCCATTTCCTTATTAGTTTCATTCAAAGTCCATTACCATTT
* * * **
37453 TAGAGCCCATTTCCTTATTTAG--TAATTCAAAGTCCATTTCTTTTT
1 TAAAGCCCATTTCCTTA-TTAGTTTCATTCAAAGTCCATTACCATTT
37498 TAAAGACCCATTTCCTTATTAGTTTC
1 TAAAG-CCCATTTCCTTATTAGTTTC
37524 TCAAAATGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 27 0.46
46 27 0.46
47 5 0.08
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (46 bp):
TAAAGCCCATTTCCTTATTAGTTTCATTCAAAGTCCATTACCATTT
Found at i:37488 original size:45 final size:46
Alignment explanation
Indices: 37407--37521 Score: 137
Period size: 46 Copynumber: 2.5 Consensus size: 46
37397 TCCATTTTAA
* *
37407 TAAAGCCCATTTCCTCA-TTAGTTTCATTCAAAGTCCATTACCATTT
1 TAAAGCCCATTTCCTTATTTAG-TTAATTCAAAGTCCATTACCATTT
* * **
37453 TAGAGCCCATTTCCTTATTTAG-TAATTCAAAGTCCATTTCTTTTT
1 TAAAGCCCATTTCCTTATTTAGTTAATTCAAAGTCCATTACCATTT
37498 TAAAGACCCATTTCCTTA-TTAGTT
1 TAAAG-CCCATTTCCTTATTTAGTT
37522 TCTCAAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 27 0.46
46 28 0.47
47 4 0.07
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.43
Consensus pattern (46 bp):
TAAAGCCCATTTCCTTATTTAGTTAATTCAAAGTCCATTACCATTT
Found at i:37589 original size:13 final size:15
Alignment explanation
Indices: 37562--37593 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
37552 GTCTTCTCCT
37562 TTTTTTCCTTCTTTC
1 TTTTTTCCTTCTTTC
37577 TTTTTT-CTT-TTTC
1 TTTTTTCCTTCTTTC
37590 TTTT
1 TTTT
37594 CTTTTGGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTCCTTCTTTC
Done.