Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019523.1 Corchorus olitorius cultivar O-4 contig19556, 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: 86656
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4062 original size:32 final size:32
Alignment explanation
Indices: 4023--4100 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
4013 GTTTTTTTTT
* * ** * *
4023 AAGTAACAAGCACTGTTTTTTTTTTTTCCAAC
1 AAGTAACAAGCACGGTTTATTAGTGTTACAAC
*
4055 AAGTAACAAGCACGGTTTATTAGTGTTATAAC
1 AAGTAACAAGCACGGTTTATTAGTGTTACAAC
4087 AAGTAACAAGCACG
1 AAGTAACAAGCACG
4101 CAACTCACCG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (32 bp):
AAGTAACAAGCACGGTTTATTAGTGTTACAAC
Found at i:6709 original size:52 final size:52
Alignment explanation
Indices: 6627--6729 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
6617 CATTTCTTGG
* *
6627 AGAGATTGGGATTACAAACGCACCCTAACAAACAAACCCAGTGAAATCTCAA
1 AGAGATTGGAATTACAAACGCACCCCAACAAACAAACCCAGTGAAATCTCAA
6679 AGAGATTGGAATTACAAACGCACCCCAACAAACAAACCCAGTGAAATCTCA
1 AGAGATTGGAATTACAAACGCACCCCAACAAACAAACCCAGTGAAATCTCA
6730 TTACAATTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.45, C:0.26, G:0.15, T:0.15
Consensus pattern (52 bp):
AGAGATTGGAATTACAAACGCACCCCAACAAACAAACCCAGTGAAATCTCAA
Found at i:7332 original size:6 final size:6
Alignment explanation
Indices: 7321--7356 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
7311 AACCCTACCA
7321 TCATTC TCATTC TCATTC TCATTC TCATTC TCATTC
1 TCATTC TCATTC TCATTC TCATTC TCATTC TCATTC
7357 ATATTCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATTC
Found at i:12786 original size:27 final size:27
Alignment explanation
Indices: 12756--12809 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12746 CTTATGATTT
12756 ATCAGGAATTTAGCTATAATTAGCTAA
1 ATCAGGAATTTAGCTATAATTAGCTAA
12783 ATCAGGAATTTAGCTATAATTAGCTAA
1 ATCAGGAATTTAGCTATAATTAGCTAA
12810 TAACCTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (27 bp):
ATCAGGAATTTAGCTATAATTAGCTAA
Found at i:15746 original size:13 final size:13
Alignment explanation
Indices: 15728--15753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15718 ACAGCAAATT
15728 GCAGTAATTTATA
1 GCAGTAATTTATA
15741 GCAGTAATTTATA
1 GCAGTAATTTATA
15754 TCATATAAAA
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:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
GCAGTAATTTATA
Found at i:19376 original size:30 final size:30
Alignment explanation
Indices: 19320--19376 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
19310 GATTATCAAT
** **
19320 AAGTATATACTTATATTTTTTTTTTTGAAA
1 AAGTATATACTTATATTAATCATTTTGAAA
19350 AAGTATATACTTATATTAATCATTTTG
1 AAGTATATACTTATATTAATCATTTTG
19377 TTTTGGAGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (30 bp):
AAGTATATACTTATATTAATCATTTTGAAA
Found at i:19803 original size:17 final size:18
Alignment explanation
Indices: 19781--19814 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19771 TGATAAGGAA
19781 AAATAA-AAAAGAAAATC
1 AAATAATAAAAGAAAATC
*
19798 AAATAATAATAGAAAAT
1 AAATAATAAAAGAAAAT
19815 GTAGGCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (18 bp):
AAATAATAAAAGAAAATC
Found at i:36727 original size:31 final size:31
Alignment explanation
Indices: 36686--36750 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
36676 TAACCATTCA
36686 TTTAACCACCAATATTCAATACCTAGACCAC
1 TTTAACCACCAATATTCAATACCTAGACCAC
* *
36717 TTTAATCACCAATATTCAATCCCTAGACCAC
1 TTTAACCACCAATATTCAATACCTAGACCAC
36748 TTT
1 TTT
36751 CCATTTCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (31 bp):
TTTAACCACCAATATTCAATACCTAGACCAC
Found at i:37208 original size:33 final size:33
Alignment explanation
Indices: 37171--37247 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
37161 TTCAAAATCA
37171 ATCAAATTCAAAATATTGCAATTGACCTAAACT
1 ATCAAATTCAAAATATTGCAATTGACCTAAACT
37204 ATCAAATTCAAAATATTGCAATTGACCTAAACT
1 ATCAAATTCAAAATATTGCAATTGACCTAAACT
37237 ATCAAATTCAA
1 ATCAAATTCAA
37248 CACAATTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (33 bp):
ATCAAATTCAAAATATTGCAATTGACCTAAACT
Found at i:39697 original size:7 final size:7
Alignment explanation
Indices: 39685--39709 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39675 TATAAAGAAA
39685 AATAAAT
1 AATAAAT
39692 AATAAAT
1 AATAAAT
39699 AATAAAT
1 AATAAAT
39706 AATA
1 AATA
39710 TGTACTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:58095 original size:18 final size:19
Alignment explanation
Indices: 58058--58094 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
58048 TCAATTATAC
58058 TCTAATTAATGTTTTTTTT
1 TCTAATTAATGTTTTTTTT
58077 TCTAA-TAAT-TTTTTTTT
1 TCTAATTAATGTTTTTTTT
58094 T
1 T
58095 TACATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 4 0.22
19 5 0.28
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (19 bp):
TCTAATTAATGTTTTTTTT
Found at i:58149 original size:2 final size:2
Alignment explanation
Indices: 58142--58183 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
58132 GATACCATTC
58142 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
58184 CATTTTTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59595 original size:12 final size:12
Alignment explanation
Indices: 59578--59618 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
59568 TAATACATAT
59578 ATATATATATAA
1 ATATATATATAA
*
59590 ATATATATATTA
1 ATATATATATAA
59602 ATAT-TATA-AA
1 ATATATATATAA
*
59612 ATCTATA
1 ATATATA
59619 ATTCGAGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
10 4 0.16
11 6 0.24
12 15 0.60
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATATATATAA
Found at i:59595 original size:16 final size:16
Alignment explanation
Indices: 59531--59599 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
59521 CCCCCCCCCC
59531 ATATA-ATATAAATACT
1 ATATATATATAAATA-T
*
59547 ATATA-ATATAATTA-
1 ATATATATATAAATAT
* *
59561 ATGA-ATGTAATACATAT
1 AT-ATATAT-ATAAATAT
59578 ATATATATATAAATAT
1 ATATATATATAAATAT
59594 ATATAT
1 ATATAT
59600 TAATATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
14 3 0.07
15 2 0.05
16 32 0.76
17 5 0.12
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (16 bp):
ATATATATATAAATAT
Found at i:60400 original size:2 final size:2
Alignment explanation
Indices: 60393--60420 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60383 ATTGAGTCAA
60393 AT 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 AT
60421 TCATATGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62537 original size:2 final size:2
Alignment explanation
Indices: 62525--62559 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
62515 GCAGTCTCAA
62525 AT AT AT A- AT 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 AT AT AT AT AT
62560 TGGAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85869 original size:45 final size:45
Alignment explanation
Indices: 85805--85906 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
85795 TTGTGCACTC
85805 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
1 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
*
85850 GGCAATCATGGGGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
1 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
*
85895 GGCAGTCATGGA
1 GGCAATCATGGA
85907 TTCTAACTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (45 bp):
GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
Done.