Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015450.1 Corchorus olitorius cultivar O-4 contig15483, 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: 11960
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Found at i:578 original size:11 final size:11
Alignment explanation
Indices: 557--587 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
547 TAAACTCCAC
557 TAAAAAA-AAA
1 TAAAAAACAAA
567 TAAAAAACAAA
1 TAAAAAACAAA
578 TAAAAAACAA
1 TAAAAAACAA
588 CAAGAGGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (11 bp):
TAAAAAACAAA
Found at i:2440 original size:37 final size:37
Alignment explanation
Indices: 2390--2460 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2380 TGTGGAGGTA
2390 CTTATTGTCAATAATTTTCTTGAAATATTATATTAAC
1 CTTATTGTCAATAATTTTCTTGAAATATTATATTAAC
2427 CTTATTGTCAATAATTTTCTTGAAATATTATATT
1 CTTATTGTCAATAATTTTCTTGAAATATTATATT
2461 GGTTAAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.51
Consensus pattern (37 bp):
CTTATTGTCAATAATTTTCTTGAAATATTATATTAAC
Found at i:7706 original size:33 final size:33
Alignment explanation
Indices: 7667--7946 Score: 533
Period size: 33 Copynumber: 8.5 Consensus size: 33
7657 AATGTGAGTG
*
7667 AAGGCAAGTTCAATGTTGTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
*
7700 AAGGCAAGTTCAATGTTGTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
7733 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
7766 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
7799 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
7832 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
*
7865 AAGGCAAGTTCAATATTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
7898 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
1 AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
7931 AAGGCAAGTTCAATGT
1 AAGGCAAGTTCAATGT
7947 CAATTGGGAA
Statistics
Matches: 244, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 244 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (33 bp):
AAGGCAAGTTCAATGTTTTTGGATGTGAGAATT
Found at i:7981 original size:22 final size:22
Alignment explanation
Indices: 7916--7982 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 22
7906 TTCAATGTTT
7916 TTGGATGTGAGAATTAAGGCAAG
1 TTGGATGTGAGAA-TAAGGCAAG
** * ** *
7939 TTCAATGT--CAATTGGGAAAG
1 TTGGATGTGAGAATAAGGCAAG
7959 TTGGATGTGAGAATAAGGCAAG
1 TTGGATGTGAGAATAAGGCAAG
7981 TT
1 TT
7983 CAATGTCAAT
Statistics
Matches: 30, Mismatches: 12, Indels: 5
0.64 0.26 0.11
Matches are distributed among these distances:
20 12 0.40
21 2 0.07
22 10 0.33
23 6 0.20
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.28
Consensus pattern (22 bp):
TTGGATGTGAGAATAAGGCAAG
Found at i:7988 original size:22 final size:22
Alignment explanation
Indices: 7920--7988 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
7910 ATGTTTTTGG
7920 ATGTGAGAATTAAGGCAAGTTCA
1 ATGTGAGAA-TAAGGCAAGTTCA
* ** * **
7943 ATGT--CAATTGGGAAAGTTGG
1 ATGTGAGAATAAGGCAAGTTCA
7963 ATGTGAGAATAAGGCAAGTTCA
1 ATGTGAGAATAAGGCAAGTTCA
7985 ATGT
1 ATGT
7989 CAATTGGGAA
Statistics
Matches: 32, Mismatches: 12, Indels: 5
0.65 0.24 0.10
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 14 0.44
23 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.28
Consensus pattern (22 bp):
ATGTGAGAATAAGGCAAGTTCA
Found at i:8030 original size:41 final size:41
Alignment explanation
Indices: 7926--8093 Score: 241
Period size: 41 Copynumber: 4.1 Consensus size: 41
7916 TTGGATGTGA
* * *
7926 GAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGGATGT
1 GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
*
7967 GAGAAT-AAGGCAAGTTCAATGTCAATTGGGAATGTTGAAAGT
1 --GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
8009 GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
1 GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
* * *
8050 GAATCAAGGAAAGTTCAATGTCAATTGGGAA-ATTCAATGT
1 GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
8090 GAAT
1 GAAT
8094 GCGCCGCGTA
Statistics
Matches: 117, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
40 15 0.13
41 65 0.56
42 33 0.28
43 4 0.03
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (41 bp):
GAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGT
Found at i:10343 original size:263 final size:261
Alignment explanation
Indices: 9858--10364 Score: 596
Period size: 263 Copynumber: 1.9 Consensus size: 261
9848 AAATAACTAC
* * * * * *
9858 ATTCATCTAATCGAATCTTAGGCATATTGGTTTTAAGAAATTGTTTTTATGAGCATCCGAAATTG
1 ATTCATCTAACCAAATCTTAGCCATATTGGTATTAAGAAATTGTTTTTACGAGCAACCGAAATTG
* *
9923 GTTTCAATTTATTTAGAAATTGATTCAGAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGC
66 GTTTCAATTTATTTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAGCATCAAAAGC
* * * * * * *
9988 CGTACCATTTTTTTGGCGATAAATTATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAA
131 CCTACAATCTTGTTGGCGATAAATTACATATTTTCATGAGTATTGTGACCAAAAATTGAGGAAAA
* * * *
10053 ATCATTCGGGTCAACTTTTGTAAAATTTTAA-CCGAAATCGTGTATTAACTATATTGAGATATCT
196 ATCATTCAGGTCAACTTTTGCAAAA-TTTAAGCAGAAATCGTGTACTAACTATATTGAGATATCT
10117 AT
260 AT
* * *
10119 ATTCATCTAACCAAATTTTAGCCATATTGG-ATTAA-AAGATTTGTTTTTACGAGCAACTGAATT
1 ATTCATCTAACCAAATCTTAGCCATATTGGTATTAAGAA-A-TTGTTTTTACGAGCAACCGAAAT
* * * *
10182 ATGG-TTCGATTTAATTT-GAAAATTAATTCGGAAAAGAATAGGAAAAACGATATTAGCAGCGTC
64 -TGGTTTCAATTT-ATTTAG-AAATTAATTCAGAAAA-AATAGGAAAAACGATATTAGAAGCATC
* * * *
10245 AAAAGCCCTTCAATCTTGTTGGTGATGAATTACATACTTTTCATGAGTATTGTTACCAAAAATTG
125 AAAAGCCCTACAATCTTGTTGGCGATAAATTACATA-TTTTCATGAGTATTGTGACCAAAAATTG
* *
10310 AGGGAAAAA-C-TTCAGTTCAATTTTTGCAAAATTTAAGCAGAAATCGTGTACTAAC
189 A-GGAAAAATCATTCAGGTCAACTTTTGCAAAATTTAAGCAGAAATCGTGTACTAAC
10365 CATCACACTT
Statistics
Matches: 205, Mismatches: 32, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
259 2 0.01
260 5 0.02
261 53 0.26
262 26 0.13
263 85 0.41
264 27 0.13
265 7 0.03
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (261 bp):
ATTCATCTAACCAAATCTTAGCCATATTGGTATTAAGAAATTGTTTTTACGAGCAACCGAAATTG
GTTTCAATTTATTTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAGCATCAAAAGC
CCTACAATCTTGTTGGCGATAAATTACATATTTTCATGAGTATTGTGACCAAAAATTGAGGAAAA
ATCATTCAGGTCAACTTTTGCAAAATTTAAGCAGAAATCGTGTACTAACTATATTGAGATATCTA
T
Found at i:11776 original size:331 final size:328
Alignment explanation
Indices: 10552--11960 Score: 1274
Period size: 331 Copynumber: 4.3 Consensus size: 328
10542 GAATAAGTTG
* *
10552 TTCCATCTTTTTGGCGATGAATTATATATTTTTTTATTAGTATTGTAGCCAAAAATT-AAGGAAA
1 TTCCATCTTTTTGGCGATGAATTATATA--TTTTTATGAGTATTGTGGCCAAAAATTGAAGG-AA
* * * * *
10616 AATCATTCGAGTCAATTTTTGCAAAATTTAAGCGGAAATTGTGTACTAACCACCACAGTTTTTTC
63 AATCATTCGGGTCAATTTTTGCAAAATTTAA-CCGAAATCGTGTACTAACCATCACAG-TTTTTG
* * * ** *
10681 TCTAAAAACGCATTCCGAGGCCCCGACTTAGTTTTGAATGATTTTTGGCGCCAAGACTCCTTGTA
126 GCTAAAAACGCATTCCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTAATTGAA
* * * * * *
10746 GTATCTATATTCATCTAACCAAATCTCAAGCACATTGGATTTAAGAAATTGTCTTTACTAGCATC
191 ATATCTATATTCATCTAACCAAATCTC-AGAACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * * * *
10811 TGAATTATGTTTCAATTTAATTAGAAATCAATT---------TAGAAAAATGATATTAGAAGCGT
255 AGAATTAGGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATAGAAAAACGATATCAGAAGCAT
** *
10867 GAAAAGTCG
320 GAAAAACCC
* * * *
10876 TTCCATTTTTTTTGGCGATGAATTCCT-T-TTTTTATGAGTATTGTTGCCAAAAATTGAGGGAAA
1 TTCCA-TCTTTTTGGCGATGAATT-ATATATTTTTATGAGTATTGTGGCCAAAAATTGAAGGAAA
* * * *
10939 ATCATTCGGATCAATTTCTGCAAAAATTTAACCGAAATCATGTACTAACCATCACAGTTTTTGAC
64 ATCATTCGGGTCAATTTTTGC-AAAATTTAACCGAAATCGTGTACTAACCATCACAGTTTTTGGC
* * * * * * * * * * *
11004 TCAAAACGCGTTCTGGGGCCCCGGCTTAGTTTTGCATGATTTTTTGCTCCTACAGTAATTGAAAT
128 TAAAAACGCATTCCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTAATTGAAAT
* * * *
11069 ATCTATATTCATCTAATCGAATCTCAGACACATTGGATTTAAGGATTCGTTTTTACGAACATCAG
193 ATCTATATTCATCTAACCAAATCTCAGA-ACATTGGATTTAAGGATTTGTTTTTACGAGCATCAG
* * * * * * *
11134 AA-AACGGTTTCAGTTTTATTAGAAATTAATTCATAAAATATAGGAAAAACGATATCACATGCAT
257 AATTA-GGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATA-GAAAAACGATATCAGAAGCAT
*
11198 -AAAAAGTCC
320 GAAAAA-CCC
* * * *
11207 TTCCATTTTTTTGGCGATGAATTATATATTTTTAAGAGAATTGTGGCAAAAAATT-AAGGAAAAA
1 TTCCATCTTTTTGGCGATGAATTATATATTTTTATGAGTATTGTGGCCAAAAATTGAAGG-AAAA
* * * * * * ** *
11271 TCATTCGGGTCACTTTTTGGAAAA-TTGA-GGAAAAC-----CGAA--ATCATTGTTTTTAGCTA
65 TCATTCGGGTCAATTTTTGCAAAATTTAACCGAAATCGTGTACTAACCATCACAGTTTTTGGCTA
* * * **
11327 AAAATGCATTCCGAGG-CCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTTATTCTAATAT
130 AAAACGCATTCCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTAATTGAAATAT
* * * * * * * *
11391 CTATATTCTTCAAACCAAATATCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGTATCTGAA
195 CTATATTCATCTAACCAAATCTCAG-AACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAA
** * * * * *
11456 TTATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAA
259 TTAGGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATA-GAAAAACGATATCAGAAGCATGAA
11521 AAACCC
323 AAACCC
* * * *
11527 TTCAATCTTTTTGTG-GATGAATTATATACATATTATGAGTATTGTGGCCAAAAATTGAGGGAGA
1 TTCCATCTTTTTG-GCGATGAATTATATA-TTTTTATGAGTATTGTGGCCAAAAATTGAAGGA-A
* * **
11591 AA-CTTTCGGTTCAATTTTTGCAAAATTTAACCCGAAATCGTGTACT-ACCATCATGGTTTTTGG
63 AATCATTCGGGTCAATTTTTGCAAAATTTAA-CCGAAATCGTGTACTAACCATCACAGTTTTTGG
* * * * * * *
11654 TTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCTAGAGTAATTGAAA
127 CTAAAAACGCATTCCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTAATTGAAA
* * *
11719 TATCTATATTCATCTAGCCGAATCTCAAGAACATTGGATTTAAGGATTTGTTTTTACGAGCGTCA
192 TATCTATATTCATCTAACCAAATCTC-AGAACATTGGATTTAAGGATTTGTTTTTACGAGCATCA
*** * *
11784 GAAAGCGGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATAGAAAAATGAAATCAGAAGCATG
256 GAATTAGGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATAGAAAAACGATATCAGAAGCATG
* *
11849 AAAAGCCG
321 AAAAACCC
* * *
11857 TTCCATTTTTTTGGCGATGAATTATATATTTTTTTATGATTATTGTGGCCAAAAATAG-AGGAAA
1 TTCCATCTTTTTGGCGATGAATTATATA--TTTTTATGAGTATTGTGGCCAAAAATTGAAGG-AA
* * * *
11921 AATTAATCGGGTCAACTTTTGTAAAATTTTAACCGAAATC
63 AATCATTCGGGTCAATTTTTGCAAAA-TTTAACCGAAATC
Statistics
Matches: 861, Mismatches: 180, Indels: 81
0.77 0.16 0.07
Matches are distributed among these distances:
320 165 0.19
321 205 0.24
322 77 0.09
323 15 0.02
324 10 0.01
325 18 0.02
326 1 0.00
328 6 0.01
329 6 0.01
330 111 0.13
331 240 0.28
332 7 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (328 bp):
TTCCATCTTTTTGGCGATGAATTATATATTTTTATGAGTATTGTGGCCAAAAATTGAAGGAAAAT
CATTCGGGTCAATTTTTGCAAAATTTAACCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAA
AAACGCATTCCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTAATTGAAATATC
TATATTCATCTAACCAAATCTCAGAACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAATT
AGGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATAGAAAAACGATATCAGAAGCATGAAAAA
CCC
Done.