Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015603.1 Corchorus olitorius cultivar O-4 contig15636, 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: 15956
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:5214 original size:77 final size:77
Alignment explanation
Indices: 5026--5215 Score: 179
Period size: 77 Copynumber: 2.5 Consensus size: 77
5016 TTCAAAGTTG
* * * *
5026 AATAGGGGGGCCACTCTTGGCCTTCAGCCATTCGAACGAGGAAATCTCCTGGCGAGACGAACGTC
1 AATA-GGGCGCCACTCTTGGCGTTCAGCCATCCAAACGAGGAAATCTCCTGGCGAGACGAACGTC
*
5091 CTCGTACAACTAA
65 CTCATACAACTAA
* * * * * * **
5104 AATAGGGCGTCACTCTAGGCGCTT-AGCCGTCCAAACGAGGTAGTCTCGTGGCGAGACGTGCGTC
1 AATAGGGCGCCACTCTTGGCG-TTCAGCCATCCAAACGAGGAAATCTCCTGGCGAGACGAACGTC
* *
5168 CTCAT-CTGATTAA
65 CTCATAC-AACTAA
*
5181 ACA-AGGGCGCCACTCTTGGCGTTCAACCATCCAAA
1 A-ATAGGGCGCCACTCTTGGCGTTCAGCCATCCAAA
5216 TTGACAGGGG
Statistics
Matches: 89, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
76 3 0.03
77 79 0.89
78 7 0.08
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (77 bp):
AATAGGGCGCCACTCTTGGCGTTCAGCCATCCAAACGAGGAAATCTCCTGGCGAGACGAACGTCC
TCATACAACTAA
Found at i:5822 original size:39 final size:39
Alignment explanation
Indices: 5762--5871 Score: 123
Period size: 39 Copynumber: 2.8 Consensus size: 39
5752 AAGTTACACG
* * *
5762 GGGGCGCTACTCTCAGTGCTCAGCCATCCAAATTAAACA
1 GGGGCGCCACTCTTAGCGCTCAGCCATCCAAATTAAACA
* **
5801 GGGGCGCCACTCTTAGCGCTCAGCCGTCTGAATTAAACA
1 GGGGCGCCACTCTTAGCGCTCAGCCATCCAAATTAAACA
** *
5840 GGGGATCCACTC-TAGGCCCTCAGCCATCCAAA
1 GGGGCGCCACTCTTA-GCGCTCAGCCATCCAAA
5872 CGAGAGAGTC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
38 2 0.03
39 56 0.97
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (39 bp):
GGGGCGCCACTCTTAGCGCTCAGCCATCCAAATTAAACA
Found at i:6033 original size:152 final size:155
Alignment explanation
Indices: 5661--6057 Score: 444
Period size: 152 Copynumber: 2.6 Consensus size: 155
5651 CGCCTCTTTT
* * * * * * * * * *
5661 GCTCAGCCGTCCGAATTAAATAGGGTG-GCTACTCTTGACCCTCAGCCGTCCAAACGCGGGAGTT
1 GCTCAGCCGTCCGAAGTAAACAGGG-GATCCACTCTAGGCACTCAACCGTCCAAACGAGGGAGTC
*
5725 TCGTGGCGAGACGTGCGTCCTTGTGCAAAGTTACACGGGGGCGCTACTCTCAGTGCTCAGCCATC
65 TCGTGGCGAGACGTGCGTCCTCGTGCAAAGTTACACGGGGGCGCTACTCTCAG-GC-CAGCCATC
*
5790 CAAATTAAACAGGGGCGCCACTCTTAGC
128 CAAATTAAACAGGGGCGCCACACTTAGC
* * * * * *
5818 GCTCAGCCGTCTGAATTAAACAGGGGATCCACTCTAGGCCCTCAGCCATCCAAACGAGAGAGTCT
1 GCTCAGCCGTCCGAAGTAAACAGGGGATCCACTCTAGGCACTCAACCGTCCAAACGAGGGAGTCT
* * * **
5883 CGTGGCGAGACATGCGTTCTCGTGCAAAGTTATAC-GGGGCGCTACTCTCA-G-CAGCTGTCCAA
66 CGTGGCGAGACGTGCGTCCTCGTGCAAAGTTACACGGGGGCGCTACTCTCAGGCCAGCCATCCAA
* *
5945 ATTAAATAGGGGCGCCACACTTGGC
131 ATTAAACAGGGGCGCCACACTTAGC
* * * * * *
5970 GCTCAGTCGTCCGAAGTGAATAGGGGGA-CCATTCTTGGCACTCAATCGTCCAAACGAGGGAGTC
1 GCTCAGCCGTCCGAAGTAAACA-GGGGATCCACTCTAGGCACTCAACCGTCCAAACGAGGGAGTC
6034 TCGTGGCGAGACGTGCGTCCTCGT
65 TCGTGGCGAGACGTGCGTCCTCGT
6058 CCAATTAAAC
Statistics
Matches: 205, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
152 99 0.48
153 5 0.02
154 1 0.00
156 16 0.08
157 84 0.41
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.21
Consensus pattern (155 bp):
GCTCAGCCGTCCGAAGTAAACAGGGGATCCACTCTAGGCACTCAACCGTCCAAACGAGGGAGTCT
CGTGGCGAGACGTGCGTCCTCGTGCAAAGTTACACGGGGGCGCTACTCTCAGGCCAGCCATCCAA
ATTAAACAGGGGCGCCACACTTAGC
Found at i:6366 original size:79 final size:79
Alignment explanation
Indices: 6183--6444 Score: 298
Period size: 79 Copynumber: 3.4 Consensus size: 79
6173 CCATACATGC
* * ** * * * * * *
6183 GTGCCACTCTAGGCACTCAGCCGTCCAAACGAGGTCGTCTCAT-CTGTGATGAGCGTCCTC--GC
1 GTGCCACTCTTGGCGCTCAGCCGTCCAAACGAGGGAGTCTCGTGGTGAGACGAACATCCTCGTGC
* *
6245 CCAATTAAATAGGG
66 ACAATTAAACAGGG
* * * * *
6259 G-GCTACTCTTGGCCCTCAACCGTCCAAACGAGGGAGTCTCTTGGTGAGACGATCATCCTCGTGC
1 GTGCCACTCTTGGCGCTCAGCCGTCCAAACGAGGGAGTCTCGTGGTGAGACGAACATCCTCGTGC
6323 ACAATTAAACAGGG
66 ACAATTAAACAGGG
*
6337 GTGCCACTCTTGGTGCTCAGCCGTCCAAACGAGGGAGTCTCGTGGTGAGACGAACATCCTCGTGC
1 GTGCCACTCTTGGCGCTCAGCCGTCCAAACGAGGGAGTCTCGTGGTGAGACGAACATCCTCGTGC
*
6402 ACAATTAAACAAGG
66 ACAATTAAACAGGG
* * *
6416 GTGCCACTTTTGGCGTTTAGCCGTCCAAA
1 GTGCCACTCTTGGCGCTCAGCCGTCCAAA
6445 TTAAACAAGG
Statistics
Matches: 157, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
75 34 0.22
76 13 0.08
78 15 0.10
79 95 0.61
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (79 bp):
GTGCCACTCTTGGCGCTCAGCCGTCCAAACGAGGGAGTCTCGTGGTGAGACGAACATCCTCGTGC
ACAATTAAACAGGG
Found at i:6487 original size:79 final size:78
Alignment explanation
Indices: 6404--6563 Score: 205
Period size: 79 Copynumber: 2.0 Consensus size: 78
6394 CCTCGTGCAC
* * * * * *
6404 AATTAAACAAGGGTGCCACT-TTTGGCGTTTAGCCGTCCAAATTAAACAAGGGGGGGCACTTTTG
1 AATTAAACAAGGGCGCCACTCTTT-ACGCTCAGCCATCCAAATTAAAC-AGGGGGGCCACTTTTG
6468 GCCCTCACCCATCCA
64 GCCCTCACCCATCCA
* * *
6483 AATTAAACAGGGGCGCCACTCTTTACGCTCGGCCATCCAAATTAAACTGGGGGGCCACTTTTGGC
1 AATTAAACAAGGGCGCCACTCTTTACGCTCAGCCATCCAAATTAAACAGGGGGGCCACTTTTGGC
*
6548 CCTCAGCCATCCA
66 CCTCACCCATCCA
6561 AAT
1 AAT
6564 GAGAGAGTCT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
78 31 0.44
79 36 0.51
80 3 0.04
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (78 bp):
AATTAAACAAGGGCGCCACTCTTTACGCTCAGCCATCCAAATTAAACAGGGGGGCCACTTTTGGC
CCTCACCCATCCA
Found at i:6519 original size:39 final size:39
Alignment explanation
Indices: 6404--6563 Score: 151
Period size: 39 Copynumber: 4.1 Consensus size: 39
6394 CCTCGTGCAC
* * * ** * *
6404 AATTAAACAAGGGTGCCACTTTTGGCGTTTAGCCGTCCA
1 AATTAAACAGGGGCGCCACTTTTGACCCTCAGCCATCCA
* * * *
6443 AATTAAACAAGGGGGGGCACTTTTGGCCCTCACCCATCCA
1 AATTAAAC-AGGGGCGCCACTTTTGACCCTCAGCCATCCA
* *
6483 AATTAAACAGGGGCGCCACTCTTT-ACGCTCGGCCATCCA
1 AATTAAACAGGGGCGCCACT-TTTGACCCTCAGCCATCCA
* * *
6522 AATTAAACTGGGGGGCCACTTTTGGCCCTCAGCCATCCA
1 AATTAAACAGGGGCGCCACTTTTGACCCTCAGCCATCCA
6561 AAT
1 AAT
6564 GAGAGAGTCT
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
38 3 0.03
39 62 0.63
40 34 0.34
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
AATTAAACAGGGGCGCCACTTTTGACCCTCAGCCATCCA
Found at i:6611 original size:276 final size:273
Alignment explanation
Indices: 6247--6759 Score: 679
Period size: 276 Copynumber: 1.9 Consensus size: 273
6237 GTCCTCGCCC
* * * * *
6247 AATTAAATAGGGGGCTACTCTTGGCCCTCAACCGTCCAAACGAGGGAGTCTCTTGGTGAGACGAT
1 AATTAAATAGGGGGCCACTCTTGGCCCTCAACCATCCAAACGAGAGAGTCTCTTAGTGAGACGAA
* * ** *
6312 CATCCTCGTGCACAATTAAACAGGGGTGCCACTCTTGGTGCTCAGCCGTCCAAACGAGGGAGTCT
66 CATCCTCATGCACAATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCGTCAAAACGAGGGAGTCT
* * * *
6377 CGTGGTGAGACGAACATCCTCGTGCACAATTAAACAAGGGTG-CCACTTTTGGCGTTTAGCCGTC
131 CGTGATGAGACGAACATCCTCGTGCACAATTAAA-AA-GGTGACCACTCTTGGCGCTCAGCCGTC
* *
6441 CAAATTAAACAAGGGGGGGC-ACTTTTGGCCCTCACCCATCCAAATTAAACAGGGGCGCCACTCT
194 CAAATTAAA-AA-GGGGGACTACTCTTGGCCCTCACCCATCCAAATTAAACAGGGGCGCCACTCT
6505 TTACGCTCGGCCATCCA
257 TTACGCTCGGCCATCCA
* * * * *
6522 AATTAAACTGGGGGGCCACTTTTGGCCCTCAGCCATCCAAATGAGAGAGTCTTTTAGTGAGACGA
1 AATTAAA-TAGGGGGCCACTCTTGGCCCTCAACCATCCAAACGAGAGAGTCTCTTAGTGAGACGA
* * *
6587 ACATCCTCATTCATAATTAAACAGGGGGGCCACTCTTGGCCCTTAGCCGTCAAAACGAGGGAGTC
65 ACATCCTCATGCACAATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCGTCAAAACGAGGGAGTC
* * * * *
6652 TCTTGATGGGACGAACATCTTCGTGCACAATTAAATAGGTGCACCGCTCTTGGCGCTCAGCCGTC
130 TCGTGATGAGACGAACATCCTCGTGCACAATTAAAAAGGTG-ACCACTCTTGGCGCTCAGCCGTC
* *
6717 CAAATTAAAAAGGGGGACTGCTCTTGGCCCTCAGCCATCCAAA
194 CAAATTAAAAAGGGGGACTACTCTTGGCCCTCACCCATCCAAA
6760 CGAGGGAATC
Statistics
Matches: 203, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
274 10 0.05
275 31 0.15
276 162 0.80
ACGTcount: A:0.26, C:0.27, G:0.25, T:0.23
Consensus pattern (273 bp):
AATTAAATAGGGGGCCACTCTTGGCCCTCAACCATCCAAACGAGAGAGTCTCTTAGTGAGACGAA
CATCCTCATGCACAATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCGTCAAAACGAGGGAGTCT
CGTGATGAGACGAACATCCTCGTGCACAATTAAAAAGGTGACCACTCTTGGCGCTCAGCCGTCCA
AATTAAAAAGGGGGACTACTCTTGGCCCTCACCCATCCAAATTAAACAGGGGCGCCACTCTTTAC
GCTCGGCCATCCA
Found at i:6665 original size:79 final size:79
Alignment explanation
Indices: 6522--6670 Score: 201
Period size: 79 Copynumber: 1.9 Consensus size: 79
6512 CGGCCATCCA
* * * * *
6522 AATTAAACTGGGGGGCCACTTTTGGCCCTCAGCCATCCAAATGAGAGAGTCTTTTAGTGAGACGA
1 AATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCATCAAAACGAGAGAGTCTTTGAGTGAGACGA
6587 ACATCCTCATTCAT
66 ACATCCTCATTCAT
* * * *
6601 AATTAAACAGGGGGGCCACTCTTGGCCCTTAGCCGTCAAAACGAGGGAGTCTCTTGA-TGGGACG
1 AATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCATCAAAACGAGAGAGTCT-TTGAGTGAGACG
6665 AACATC
65 AACATC
6671 TTCGTGCACA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
79 57 0.95
80 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (79 bp):
AATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCATCAAAACGAGAGAGTCTTTGAGTGAGACGA
ACATCCTCATTCAT
Found at i:6684 original size:79 final size:79
Alignment explanation
Indices: 6522--6713 Score: 197
Period size: 79 Copynumber: 2.4 Consensus size: 79
6512 CGGCCATCCA
* * * * *
6522 AATTAAACTGGGGGGCCACTTTTGGCCCTCAGCCATCCAAATGAGAGAGTCTTTTAGTGAGACGA
1 AATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCATCAAAACGAGAGAGTCTTTGAGTGAGACGA
* *
6587 ACATCCTCATTCAT
66 ACATCCTCATGCAC
* * * *
6601 AATTAAACAGGGGGGCCACTCTTGGCCCTTAGCCGTCAAAACGAGGGAGTCTCTTGA-TGGGACG
1 AATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCATCAAAACGAGAGAGTCT-TTGAGTGAGACG
* *
6665 AACATCTTCGTGCAC
65 AACATCCTCATGCAC
* * ** * *
6680 AATTAAATAGGTGCACCGCTCTTGGCGCTCAGCC
1 AATTAAACAGGGGGGCCACTCTTGGCCCTCAGCC
6714 GTCCAAATTA
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
79 89 0.97
80 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (79 bp):
AATTAAACAGGGGGGCCACTCTTGGCCCTCAGCCATCAAAACGAGAGAGTCTTTGAGTGAGACGA
ACATCCTCATGCAC
Found at i:9293 original size:18 final size:19
Alignment explanation
Indices: 9258--9293 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9248 TGAAAAAAAG
*
9258 TTAAAAATGAAATACAATT
1 TTAAAAATAAAATACAATT
9277 TTAAAAATAAAAT-CAAT
1 TTAAAAATAAAATACAAT
9294 AAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (19 bp):
TTAAAAATAAAATACAATT
Found at i:14177 original size:67 final size:66
Alignment explanation
Indices: 14106--14326 Score: 164
Period size: 67 Copynumber: 3.3 Consensus size: 66
14096 GCGCCATTTA
*
14106 TTTGGTTGCGAATAATTTTTAAAAACGACAAAATGTTGTTGTCAAAATGTTTACACAACAAAATT
1 TTTGGTTGCAAATAATTTTT-AAAACGACAAAATGTTGTTGTCAAAATGTTTACACAACAAAATT
14171 AT
65 AT
* * * * * * * * ** * **
14173 TTTGGTTGTAAATACTTTTCGACAAC-A-ATATTTTCTGGTTATGT-AAAGT-TTTTTATAATGA
1 TTTGGTTGCAAATAATTTT-TAAAACGACAAAATGT-T-G-T-TGTCAAAATGTTTACACAACAA
*
14234 TATT-T
61 AATTAT
* *
14239 AGTTGGTTGCAAATAAATTTTTAAAATGACAAAATGTTGTTGTCAAAATGTTTACACAACAAAAT
1 -TTTGGTTGCAAAT-AATTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACACAACAAAAT
14304 TAT
64 TAT
* *
14307 TTTGGTTGTAAATACTTTTT
1 TTTGGTTGCAAATAATTTTT
14327 GACAACAATA
Statistics
Matches: 108, Mismatches: 34, Indels: 25
0.65 0.20 0.15
Matches are distributed among these distances:
65 7 0.06
66 14 0.13
67 67 0.62
68 13 0.12
69 7 0.06
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.42
Consensus pattern (66 bp):
TTTGGTTGCAAATAATTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACACAACAAAATTA
T
Found at i:14239 original size:134 final size:133
Alignment explanation
Indices: 14101--14433 Score: 474
Period size: 134 Copynumber: 2.5 Consensus size: 133
14091 ACGTGGCGCC
* *
14101 ATTTATTTGGTTGCGAATAATTTTTAAAAACGACAAAATGTTGTTGTCAAAATGTTTACACAACA
1 ATTTAGTTGGTTGCAAATAATTTTT-AAAACGACAAAATGTTGTTGTCAAAATGTTTACACAACA
* * * *
14166 AAATTATTTTGGTTGTAAATACTTTTCGACAACAATA-TTTTCTGGTTATGTAA-AGTTTTTTAT
65 AAATTATTTTGGTTGTAAATACTTTTCGACAACAATATTTTTC-GGTTACGTAATA-ATATTTAC
*
14229 AATGAT
128 AACGAT
*
14235 ATTTAGTTGGTTGCAAATAAATTTTTAAAATGACAAAATGTTGTTGTCAAAATGTTTACACAACA
1 ATTTAGTTGGTTGCAAAT-AATTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACACAACA
*
14300 AAATTATTTTGGTTGTAAATACTTTTTGACAACAATATTTTTCGGTTACGTAATAATATTTACAA
65 AAATTATTTTGGTTGTAAATACTTTTCGACAACAATATTTTTCGGTTACGTAATAATATTTACAA
14365 CGAT
130 CGAT
* * * *
14369 ATCTAGTTGGTTACAAATAACTTTTTAAAACGGA-AAAATGTTGTTGCCAAAATGCTTACACAAC
1 ATTTAGTTGGTTGCAAATAA-TTTTTAAAAC-GACAAAATGTTGTTGTCAAAATGTTTACACAAC
14433 A
64 A
14434 TTTTCACAAC
Statistics
Matches: 180, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
133 2 0.01
134 163 0.91
135 15 0.08
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (133 bp):
ATTTAGTTGGTTGCAAATAATTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACACAACAA
AATTATTTTGGTTGTAAATACTTTTCGACAACAATATTTTTCGGTTACGTAATAATATTTACAAC
GAT
Done.