Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019344.1 Corchorus olitorius cultivar O-4 contig19377, 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: 24476
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:1253 original size:15 final size:15
Alignment explanation
Indices: 1233--1263 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1223 AATTGATAAT
*
1233 ATGCTATATGGAGGA
1 ATGCTAAATGGAGGA
1248 ATGCTAAATGGAGGA
1 ATGCTAAATGGAGGA
1263 A
1 A
1264 CTAAGTCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
ATGCTAAATGGAGGA
Found at i:1583 original size:20 final size:21
Alignment explanation
Indices: 1546--1588 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
1536 ATCTCACACA
1546 AAGATTATCAAAAATCATAGG
1 AAGATTATCAAAAATCATAGG
*
1567 AAGATTA-CAAAATTCATAGG
1 AAGATTATCAAAAATCATAGG
1587 AA
1 AA
1589 AGTTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (21 bp):
AAGATTATCAAAAATCATAGG
Found at i:1675 original size:43 final size:44
Alignment explanation
Indices: 1614--1716 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 44
1604 CATAGTTAGG
* * * * *
1614 TTATCAAAGTTTCTTATGGAGTTTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
*
1657 TTATCAAAATTTCATATGGTGGTTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
1701 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
1717 AAAATATTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 32 0.60
44 21 0.40
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.42
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
Found at i:1683 original size:22 final size:21
Alignment explanation
Indices: 1548--1716 Score: 101
Period size: 22 Copynumber: 7.9 Consensus size: 21
1538 CTCACACAAA
* *
1548 GATTATCAAAA-ATCATAGGAA
1 GATTATCAAAATTTCATAGG-T
*
1569 GATTA-CAAAA-TTCATAGGAAA
1 GATTATCAAAATTTCATAGG--T
* * *
1590 GTTTATTAAAATTTCATAGTT
1 GATTATCAAAATTTCATAGGT
* * * *
1611 AGGTTATCAAAGTTTCTTATGGA
1 -GATTATCAAAATTTCATA-GGT
* * *
1634 GTTTATCACAATTTTATAGGT
1 GATTATCAAAATTTCATAGGT
*
1655 AATTATCAAAATTTCATATGGT
1 GATTATCAAAATTTCATA-GGT
* *
1677 GGTTATCAAAATTTAATAGGGT
1 GATTATCAAAATTTCATA-GGT
*
1699 AATTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
1717 AAAATATTCA
Statistics
Matches: 114, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
20 12 0.11
21 27 0.24
22 67 0.59
23 8 0.07
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (21 bp):
GATTATCAAAATTTCATAGGT
Found at i:1923 original size:13 final size:13
Alignment explanation
Indices: 1905--1929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1895 TCTCATAAAT
1905 ATTTTTATTTATA
1 ATTTTTATTTATA
1918 ATTTTTATTTAT
1 ATTTTTATTTAT
1930 TTATTTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTATA
Found at i:3289 original size:87 final size:88
Alignment explanation
Indices: 3126--3289 Score: 258
Period size: 87 Copynumber: 1.9 Consensus size: 88
3116 CATGCTTGGA
*
3126 TTTTCTTAAAAATTGGGAGATTTGACTTAGTACGTAATTGTTATATGAATTCATGACATGAGGAA
1 TTTTCTTAAAAATTGGAAGATTTGACTTAGTACGTAATTGTTATATGAATTCATGACATGAGGAA
* * **
3191 GATATTTTTTTTAACCGATAACT
66 AACATCATTTTTAACCGATAACT
* *
3214 TTTTCTTAAAGATT-GAAGATTTGACTTAGTACGTAATTGTTATATGAATTCATGACATGAGTAA
1 TTTTCTTAAAAATTGGAAGATTTGACTTAGTACGTAATTGTTATATGAATTCATGACATGAGGAA
3278 AACATCATTTTT
66 AACATCATTTTT
3290 TTAACCCTGC
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 56 0.81
88 13 0.19
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (88 bp):
TTTTCTTAAAAATTGGAAGATTTGACTTAGTACGTAATTGTTATATGAATTCATGACATGAGGAA
AACATCATTTTTAACCGATAACT
Found at i:5556 original size:21 final size:22
Alignment explanation
Indices: 5527--5569 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5517 TAAAAGTGCA
*
5527 AAAGACAGGGAGACGACTCCTG
1 AAAGACAGGAAGACGACTCCTG
*
5549 AAAG-CAGGAAGACGCCTCCTG
1 AAAGACAGGAAGACGACTCCTG
5570 GGCTTCAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.35, C:0.26, G:0.30, T:0.09
Consensus pattern (22 bp):
AAAGACAGGAAGACGACTCCTG
Found at i:16071 original size:22 final size:20
Alignment explanation
Indices: 16036--16086 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
16026 AAATTTATGA
*
16036 AGAGAGATAGTAAGTAGGAGG
1 AGAGAGAAAGTAAGT-GGAGG
* *
16057 AGGAGAGAAATTAAGTGGGGG
1 A-GAGAGAAAGTAAGTGGAGG
16078 AGAGAGAAA
1 AGAGAGAAA
16087 AATGACAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 6 0.23
22 12 0.46
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.12
Consensus pattern (20 bp):
AGAGAGAAAGTAAGTGGAGG
Found at i:17308 original size:6 final size:6
Alignment explanation
Indices: 17297--17345 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
17287 ACAAGACTTG
17297 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA
1 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA
17345 T
1 T
17346 ATTATATAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTATA
Found at i:17525 original size:18 final size:17
Alignment explanation
Indices: 17483--17528 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
17473 ATGTAATTTC
17483 ATTTATCAATTAAATTAA
1 ATTTAT-AATTAAATTAA
* *
17501 ATATATAATTATATTAAA
1 ATTTATAATTAAATT-AA
17519 ATTTATAATT
1 ATTTATAATT
17529 TCTTTTACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTATAATTAAATTAA
Found at i:17625 original size:39 final size:40
Alignment explanation
Indices: 17569--17649 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
17559 TTTAATTCCT
17569 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
17609 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
17648 AT
1 AT
17650 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:18103 original size:202 final size:203
Alignment explanation
Indices: 17757--18166 Score: 761
Period size: 202 Copynumber: 2.0 Consensus size: 203
17747 TTCCTTAATA
*
17757 ATAAATAAATTGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
17822 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAGT
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAAT
17887 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAA-AATTAATAACATT
131 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAGAATTAATAACATT
17951 CACCATTG
196 CACCATTG
17959 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
18024 AATTTAATAATTCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTT-TAATATATAATAA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCT-ATATATAATAA
*
18088 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATTTTAGACTTAAAGAATTAATAACAT
130 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAGAATTAATAACAT
18153 TCACCATTG
195 TCACCATTG
18162 ATAAA
1 ATAAA
18167 GTTATTAAGC
Statistics
Matches: 202, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
201 1 0.00
202 175 0.87
203 26 0.13
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAAT
AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAGAATTAATAACATT
CACCATTG
Found at i:18735 original size:18 final size:17
Alignment explanation
Indices: 18693--18738 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
18683 ATGTAATTTC
18693 ATTTATCAATTAAATTAA
1 ATTTAT-AATTAAATTAA
* *
18711 ATATATAATTATATTAAA
1 ATTTATAATTAAATT-AA
18729 ATTTATAATT
1 ATTTATAATT
18739 TCTTTTACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTATAATTAAATTAA
Found at i:18835 original size:39 final size:40
Alignment explanation
Indices: 18779--18859 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
18769 TTTAATTCCT
18779 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
18819 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
18858 AT
1 AT
18860 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:19288 original size:202 final size:202
Alignment explanation
Indices: 18942--19350 Score: 766
Period size: 202 Copynumber: 2.0 Consensus size: 202
18932 TTCCTTAATA
*
18942 ATAAATAAATTGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
19007 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAGTA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
19072 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
19137 ACCATTG
196 ACCATTG
19144 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
19209 AATTTAATAATTCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-TAATATATAATAAT
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCT-ATATATAATAAT
*
19273 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAGAATTAATAACATT
130 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
19338 CACCATTG
195 CACCATTG
19346 ATAAA
1 ATAAA
19351 GTTATTAAGC
Statistics
Matches: 202, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
201 1 0.00
202 201 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG
Found at i:19912 original size:36 final size:36
Alignment explanation
Indices: 19865--19934 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
19855 GAGATTTTGG
** *
19865 AGAAATATGATAGTCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
19901 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
19935 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:20667 original size:58 final size:58
Alignment explanation
Indices: 20577--20686 Score: 175
Period size: 58 Copynumber: 1.9 Consensus size: 58
20567 ATCATGCCTC
* *
20577 GGTCCTAAAACGTCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTA
1 GGTCCGAAAACATCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTA
* * *
20635 GGTCCGAAAACATCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GGTCCGAAAACATCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
20687 TTTGATTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (58 bp):
GGTCCGAAAACATCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTA
Found at i:22706 original size:12 final size:12
Alignment explanation
Indices: 22689--22718 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
22679 TTTAAAGTAA
22689 AGAATTATTAAT
1 AGAATTATTAAT
22701 AGAATTATTAAT
1 AGAATTATTAAT
*
22713 ATAATT
1 AGAATT
22719 GAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
AGAATTATTAAT
Done.