Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024802.1 Corchorus olitorius cultivar O-4 contig24835, 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: 47868
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:4208 original size:21 final size:19
Alignment explanation
Indices: 4183--4240 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
4173 GCTGCTCTAA
4183 TAATCTCATATGTACAGTACC
1 TAATCTCATATGTACAGT--C
* * *
4204 TAATCTAATCTGTACAGTG
1 TAATCTCATATGTACAGTC
4223 TAATCTCATATGTACAGT
1 TAATCTCATATGTACAGT
4241 TGCTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATATGTACAGTC
Found at i:5549 original size:34 final size:34
Alignment explanation
Indices: 5490--5555 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
5480 AAATTTCTGT
* * *
5490 GGTTATCAAATTTTCATAGGGAGGTTTTTAAAGA
1 GGTTATCAAAATTTCATAGGAAGGTTATTAAAGA
* *
5524 GGTTATTAAAATTTCATAGTAAGGTTATTAAA
1 GGTTATCAAAATTTCATAGGAAGGTTATTAAA
5556 ATTAAATAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (34 bp):
GGTTATCAAAATTTCATAGGAAGGTTATTAAAGA
Found at i:5598 original size:22 final size:22
Alignment explanation
Indices: 5522--5732 Score: 121
Period size: 22 Copynumber: 9.7 Consensus size: 22
5512 GGTTTTTAAA
*
5522 GAGGTTATTAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * **
5544 AAGGTTATTAAAATTAAATAG-
1 GAGGTTATCAAAATTTCATAGT
*
5565 G-GGAATTGTCAAAATTTCATAGT
1 GAGG--TTATCAAAATTTCATAGT
* * *
5588 GTGGTTATCAAAGTTTCATAGG
1 GAGGTTATCAAAATTTCATAGT
* *
5610 GA-G-TACCAAACTTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* * * *
5630 GTGGTT-TCAAATTTTCACAAT
1 GAGGTTATCAAAATTTCATAGT
* * * *
5651 GAGGTTATCGAATTTTAATAGA
1 GAGGTTATCAAAATTTCATAGT
* * *
5673 GAGGTTATCGAAATTGCGTAGT
1 GAGGTTATCAAAATTTCATAGT
*
5695 -AAGTCTATCAAAATTTCATAGT
1 GAGGT-TATCAAAATTTCATAGT
*
5717 -ATGATTATCAAAATTT
1 GA-GGTTATCAAAATTT
5733 TATTAAGAGG
Statistics
Matches: 143, Mismatches: 37, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
20 17 0.12
21 21 0.15
22 101 0.71
23 2 0.01
24 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:5645 original size:21 final size:21
Alignment explanation
Indices: 5573--5646 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
5563 AGGGGAATTG
5573 TCAAAATTTCATAGTGTGGTT
1 TCAAAATTTCATAGTGTGGTT
* *
5594 ATCAAAGTTTCATAG-G-GAGTA
1 -TCAAAATTTCATAGTGTG-GTT
* *
5615 CCAAACTTTCATAGTGTGGTT
1 TCAAAATTTCATAGTGTGGTT
*
5636 TCAAATTTTCA
1 TCAAAATTTCA
5647 CAATGAGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
20 13 0.31
21 15 0.36
22 14 0.33
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (21 bp):
TCAAAATTTCATAGTGTGGTT
Found at i:6001 original size:42 final size:43
Alignment explanation
Indices: 5942--6040 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
5932 ACCGATTTTC
* * ** *
5942 AAATTTCATAGTGTGGTTACCAACGTTTCATAGAG-ATCATCA
1 AAATTTTATAGTATGGTTACCAAAATCTCATAGAGAATCATCA
* *
5984 AAATTTTATAGTATGGTTATCAAAATCTCATAGAGTAATTATCA
1 AAATTTTATAGTATGGTTACCAAAATCTCATAGAG-AATCATCA
6028 AAATTTTCATAGT
1 AAATTTT-ATAGT
6041 TAGGTTATCG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 29 0.62
44 13 0.28
45 5 0.11
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (43 bp):
AAATTTTATAGTATGGTTACCAAAATCTCATAGAGAATCATCA
Found at i:6048 original size:23 final size:23
Alignment explanation
Indices: 5980--6082 Score: 83
Period size: 22 Copynumber: 4.6 Consensus size: 23
5970 CATAGAGATC
5980 ATCAAAATTTT-ATAG-TATGGTT
1 ATCAAAATTTTCATAGTTA-GGTT
* * *
6002 ATCAAAA-TCTCATAGAGTA-ATT
1 ATCAAAATTTTCATAG-TTAGGTT
6024 ATCAAAATTTTCATAGTTAGGTT
1 ATCAAAATTTTCATAGTTAGGTT
* *
6047 ATCGAAA-TTTCGTAGTGT-GGTTT
1 ATCAAAATTTTCATAGT-TAGG-TT
6070 ATCAAAATTTTCA
1 ATCAAAATTTTCA
6083 AAATTAAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
21 2 0.03
22 32 0.50
23 24 0.38
24 6 0.09
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (23 bp):
ATCAAAATTTTCATAGTTAGGTT
Found at i:6048 original size:45 final size:46
Alignment explanation
Indices: 5980--6082 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 46
5970 CATAGAGATC
5980 ATCAAAATTTT-ATAGTATGGTTATCAAAATCTCATAGAGT-AATT
1 ATCAAAATTTTCATAGTATGGTTATCAAAATCTCATAGAGTGAATT
* * * * **
6024 ATCAAAATTTTCATAGT-TAGGTTATCGAAATTTCGTAGTGTGGTTT
1 ATCAAAATTTTCATAGTAT-GGTTATCAAAATCTCATAGAGTGAATT
6070 ATCAAAATTTTCA
1 ATCAAAATTTTCA
6083 AAATTAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 12 0.24
45 23 0.46
46 15 0.30
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (46 bp):
ATCAAAATTTTCATAGTATGGTTATCAAAATCTCATAGAGTGAATT
Found at i:6991 original size:76 final size:76
Alignment explanation
Indices: 6904--7057 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
6894 TAAAAATTTT
6904 TTGTCTAAATTGACAGACATAATTTATTCCCTAAAAACACACAAACAACAAGGTTTATAAAGATA
1 TTGTCTAAATTGACAGACATAATTTATTCCCTAAAAACACACAAACAACAAGGTTTATAAAGATA
6969 AATAAATAAAG
66 AATAAATAAAG
6980 TTGTCTAAATTGACAGACATAATTTATTCCCTAAAAACACACAAACAACAAGGTTTATAAAGATA
1 TTGTCTAAATTGACAGACATAATTTATTCCCTAAAAACACACAAACAACAAGGTTTATAAAGATA
7045 AATAAATAAAG
66 AATAAATAAAG
7056 TT
1 TT
7058 CACAAATTAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.27
Consensus pattern (76 bp):
TTGTCTAAATTGACAGACATAATTTATTCCCTAAAAACACACAAACAACAAGGTTTATAAAGATA
AATAAATAAAG
Found at i:13653 original size:208 final size:208
Alignment explanation
Indices: 13295--13711 Score: 789
Period size: 208 Copynumber: 2.0 Consensus size: 208
13285 GCATATGCAC
*
13295 GGTACTTTCCTAATAAGCCTACCATTGCTATAATCCCAATTCCTACGGAGGACCCTTCCGAAGAA
1 GGTACTTTCCTAATAAGCCTACCATTGCTATAATCCCAATTCCTACGGAGGACCCTTCCGAAAAA
* *
13360 GAATGGAAAGTGTTTATGAGAAATCCGGAAGTTGTGCTTCTTCGATGCTTCTGAAACCTCATTTA
66 GAATGGAAAGTGTTTATGAGAAATCCGGAAGCTGTGCTTCTTCGATGCTTCCGAAACCTCATTTA
13425 GGGAGGCTCTAGTTCAATTCTGGAACCTTTTTCTCGGTTCTGATTTTGATTCCGGTTTGGTGAAC
131 GGGAGGCTCTAGTTCAATTCTGGAACCTTTTTCTCGGTTCTGATTTTGATTCCGGTTTGGTGAAC
* *
13490 ACGATTCTGATTT
196 ACAATTCCGATTT
13503 GGTACTTTCCTAATAAGCCTACCATTGCTATAATCCCAATTCCTACGGAGGACCCTTCCGAAAAA
1 GGTACTTTCCTAATAAGCCTACCATTGCTATAATCCCAATTCCTACGGAGGACCCTTCCGAAAAA
13568 GAATGGAAAGTGTTTATGAGAAATCCGGAAGCTGTGCTTCTTCGATGCTTCCGAAACCTCATTTA
66 GAATGGAAAGTGTTTATGAGAAATCCGGAAGCTGTGCTTCTTCGATGCTTCCGAAACCTCATTTA
13633 GGGAGGCTCTAGTTCAATTCTGGAACCTTTTTCTCGGTTCTGATTTTGATTCCGGTTTGGTGAAC
131 GGGAGGCTCTAGTTCAATTCTGGAACCTTTTTCTCGGTTCTGATTTTGATTCCGGTTTGGTGAAC
13698 ACAATTCCGATTT
196 ACAATTCCGATTT
13711 G
1 G
13712 ATTCCATAGT
Statistics
Matches: 204, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
208 204 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (208 bp):
GGTACTTTCCTAATAAGCCTACCATTGCTATAATCCCAATTCCTACGGAGGACCCTTCCGAAAAA
GAATGGAAAGTGTTTATGAGAAATCCGGAAGCTGTGCTTCTTCGATGCTTCCGAAACCTCATTTA
GGGAGGCTCTAGTTCAATTCTGGAACCTTTTTCTCGGTTCTGATTTTGATTCCGGTTTGGTGAAC
ACAATTCCGATTT
Found at i:14242 original size:159 final size:159
Alignment explanation
Indices: 13953--14270 Score: 627
Period size: 159 Copynumber: 2.0 Consensus size: 159
13943 ATGAGAATTT
13953 TACAAATTTGGCATTCGATTAGAATTGATAGGTGTGTTTAACACAGGCTTTTCACAAAGTTATAA
1 TACAAATTTGGCATTCGATTAGAATTGATAGGTGTGTTTAACACAGGCTTTTCACAAAGTTATAA
14018 TCAAATTAGGTGAACTTCCTAACACAATTTTTGTGCAAAAGTTGAAAAATAATTTGTTCATGACC
66 TCAAATTAGGTGAACTTCCTAACACAATTTTTGTGCAAAAGTTGAAAAATAATTTGTTCATGACC
14083 CAACCACTCATGTGTTTTTAATCCAAACA
131 CAACCACTCATGTGTTTTTAATCCAAACA
14112 TACAAATTTGGCATTCGATTAGAATTGATAGGTGTGTTTAACACAGGCTTTTCACAAAGTTATAA
1 TACAAATTTGGCATTCGATTAGAATTGATAGGTGTGTTTAACACAGGCTTTTCACAAAGTTATAA
14177 TCAAATTAGGTGAACTTCCTAACACAATTTTTGTGCAAAAGTTGAAAAATAATTTGTTCATGACC
66 TCAAATTAGGTGAACTTCCTAACACAATTTTTGTGCAAAAGTTGAAAAATAATTTGTTCATGACC
*
14242 CAACTACTCATGTGTTTTTAATCCAAACA
131 CAACCACTCATGTGTTTTTAATCCAAACA
14271 ATAATATATA
Statistics
Matches: 158, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 158 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (159 bp):
TACAAATTTGGCATTCGATTAGAATTGATAGGTGTGTTTAACACAGGCTTTTCACAAAGTTATAA
TCAAATTAGGTGAACTTCCTAACACAATTTTTGTGCAAAAGTTGAAAAATAATTTGTTCATGACC
CAACCACTCATGTGTTTTTAATCCAAACA
Found at i:14384 original size:31 final size:31
Alignment explanation
Indices: 14296--14393 Score: 114
Period size: 31 Copynumber: 3.2 Consensus size: 31
14286 ATAAATATTA
14296 TTGAGCATTTTGGCAAACGTTAGGCCCTTAT
1 TTGAGCATTTTGGCAAACGTTAGGCCCTTAT
** * *
14327 TTG-GTCAAATT---AAAAGATCAGGCCCTTAT
1 TTGAG-CATTTTGGCAAACG-TTAGGCCCTTAT
14356 TTGAGCATTTTGGCAAACGTTAGGCCCTTAT
1 TTGAGCATTTTGGCAAACGTTAGGCCCTTAT
14387 TTGAGCA
1 TTGAGCA
14394 ATTAGCCTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
28 4 0.08
29 18 0.34
30 2 0.04
31 25 0.47
32 4 0.08
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (31 bp):
TTGAGCATTTTGGCAAACGTTAGGCCCTTAT
Found at i:14824 original size:36 final size:36
Alignment explanation
Indices: 14777--14846 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
14767 GAGATTTTGG
* *
14777 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
14813 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
14847 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:17993 original size:22 final size:22
Alignment explanation
Indices: 17963--18006 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17953 TAAAACACTT
*
17963 TTGTCAATACTAAGATAAATTA
1 TTGTAAATACTAAGATAAATTA
17985 TTGTAAATACTAAGATAAATTA
1 TTGTAAATACTAAGATAAATTA
18007 ATGACCCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (22 bp):
TTGTAAATACTAAGATAAATTA
Found at i:36230 original size:51 final size:50
Alignment explanation
Indices: 36081--36230 Score: 113
Period size: 51 Copynumber: 3.1 Consensus size: 50
36071 TTGTTCTACT
*
36081 ACTAATTGCCTGGTAAATGTAGTGTTATAATTTGCAAAACAAGAGGAAACA
1 ACTAATTGCCTAGTAAATG-AGTGTTATAATTTGCAAAACAAGAGGAAACA
** * * ** *
36132 ACTAAAAAG--TAGT-AA--AG-GTTATCA-CT-C-AAAC-AGATTAATAACT
1 ACT-AATTGCCTAGTAAATGAGTGTTATAATTTGCAAAACAAGA-GGA-AACA
36175 ACTAATTGCCTAGTAAATGCAGTGTTATAATTTGCAAAACAAGAGGAAACA
1 ACTAATTGCCTAGTAAATG-AGTGTTATAATTTGCAAAACAAGAGGAAACA
36226 ACTAA
1 ACTAA
36231 AAAGTAGTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 28
0.62 0.13 0.25
Matches are distributed among these distances:
41 3 0.04
42 8 0.11
43 7 0.10
44 5 0.07
45 8 0.11
46 2 0.03
48 2 0.03
49 8 0.11
50 4 0.06
51 12 0.17
52 8 0.11
53 3 0.04
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (50 bp):
ACTAATTGCCTAGTAAATGAGTGTTATAATTTGCAAAACAAGAGGAAACA
Found at i:36239 original size:94 final size:95
Alignment explanation
Indices: 36078--36264 Score: 349
Period size: 94 Copynumber: 2.0 Consensus size: 95
36068 CACTTGTTCT
* *
36078 ACTACTAATTGCCTGGTAAATGTAGTGTTATAATTTGCAAAACAAGAGGAAACAACTAAAAAGTA
1 ACTACTAATTGCCTAGTAAATGCAGTGTTATAATTTGCAAAACAAGAGGAAACAACTAAAAAGTA
36143 GTAAAGGTTATCACTC-AAACAGATTAATA
66 GTAAAGGTTATCACTCAAAACAGATTAATA
36172 ACTACTAATTGCCTAGTAAATGCAGTGTTATAATTTGCAAAACAAGAGGAAACAACTAAAAAGTA
1 ACTACTAATTGCCTAGTAAATGCAGTGTTATAATTTGCAAAACAAGAGGAAACAACTAAAAAGTA
36237 GTAAAGGTTATCACTCAAAACAGATTAA
66 GTAAAGGTTATCACTCAAAACAGATTAA
36265 CAATACCTAG
Statistics
Matches: 90, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 79 0.88
95 11 0.12
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (95 bp):
ACTACTAATTGCCTAGTAAATGCAGTGTTATAATTTGCAAAACAAGAGGAAACAACTAAAAAGTA
GTAAAGGTTATCACTCAAAACAGATTAATA
Found at i:40456 original size:10 final size:9
Alignment explanation
Indices: 40422--40448 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40412 TTAAAATTAG
40422 CTTTTTTTT
1 CTTTTTTTT
40431 CTTTTTTTT
1 CTTTTTTTT
40440 CTTTTTTTT
1 CTTTTTTTT
40449 ACGTTTTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:42192 original size:14 final size:14
Alignment explanation
Indices: 42170--42203 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42160 GATAATCAAT
42170 ATATATGTATGTAC
1 ATATATGTATGTAC
* *
42184 ATATGTGTATGTGC
1 ATATATGTATGTAC
42198 ATATAT
1 ATATAT
42204 TTTTACCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (14 bp):
ATATATGTATGTAC
Found at i:46151 original size:15 final size:15
Alignment explanation
Indices: 46131--46162 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
46121 CATGTACTAA
46131 TTTTCGACAAACTTG
1 TTTTCGACAAACTTG
46146 TTTTCGACAAACTTG
1 TTTTCGACAAACTTG
46161 TT
1 TT
46163 AATTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (15 bp):
TTTTCGACAAACTTG
Found at i:46638 original size:120 final size:121
Alignment explanation
Indices: 46437--46672 Score: 411
Period size: 120 Copynumber: 2.0 Consensus size: 121
46427 CTTTAGGAAA
*
46437 TATTTTTGAATTTTAAATACAAAATTAATTAAAAAAATGAGACATATGTCAACACCTTAACTCGC
1 TATTTTTGAATTTTAAATACAAAATTAA-TAAAAAAATGAGACATATGTCAACACCTTAACCCGC
* *
46502 TTGTGGAGCCCAGAATTTACACCGATAATGTATTGTATGATCATCCTTTATCCTAAT
65 TTATGGAGCCCAGAATTTACACCGACAATGTATTGTATGATCATCCTTTATCCTAAT
*
46559 TATTTTTGAATTTTAAATACAAAATTAA-GAAAAAATGAGACATATGTCAACACCTTAACCCGCT
1 TATTTTTGAATTTTAAATACAAAATTAATAAAAAAATGAGACATATGTCAACACCTTAACCCGCT
*
46623 TATGGAGCCCAGAATTTATACCGACAATGTATTGTATGATCATCCTTTAT
66 TATGGAGCCCAGAATTTACACCGACAATGTATTGTATGATCATCCTTTAT
46673 ATATATCTTT
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
120 81 0.74
122 28 0.26
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (121 bp):
TATTTTTGAATTTTAAATACAAAATTAATAAAAAAATGAGACATATGTCAACACCTTAACCCGCT
TATGGAGCCCAGAATTTACACCGACAATGTATTGTATGATCATCCTTTATCCTAAT
Done.