Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014449.1 Corchorus olitorius cultivar O-4 contig14482, 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: 34703
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1269 original size:24 final size:24
Alignment explanation
Indices: 1234--1285 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1224 AACTATCTCC
*
1234 TTGG-TTTTGTGAATCTTCTTGGT
1 TTGGTTTTTGTGAATCTTCTTGAT
1257 TTGGTTTTTGTGAATCTTCTTGAT
1 TTGGTTTTTGTGAATCTTCTTGAT
1281 TTGGT
1 TTGGT
1286 GAGGAGTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.10, C:0.08, G:0.25, T:0.58
Consensus pattern (24 bp):
TTGGTTTTTGTGAATCTTCTTGAT
Found at i:1526 original size:30 final size:30
Alignment explanation
Indices: 1490--1911 Score: 502
Period size: 30 Copynumber: 13.8 Consensus size: 30
1480 TACTTACAAA
1490 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* *
1520 TGACACCAGAAGTTGTCATAATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* * *
1550 TGACACCAGAAGTTGTCATGCTCTTGCAAA
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
1580 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
1610 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* * * *
1640 TGACACTAGAGGCTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* *
1670 TGACACCAGAAGCTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* * * *
1700 TGACACAAGAAGCTGTCATGATGTTGAAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
*
1730 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* * *
1760 TGACACCATAAATTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
** * * *
1790 TGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TTT-TGCAAT
*
1822 TGACACCAGAAGTTGTCATGATAAATTTCCAAT
1 TGACACCAGAAGTTGTCATGAT---TTTGCAAT
* ** * * *
1855 AGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TTT-TGCAAT
1887 TGACACCAGAAGTTGTCATGATTTT
1 TGACACCAGAAGTTGTCATGATTTT
1912 ACCTTTCAAA
Statistics
Matches: 339, Mismatches: 46, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
30 264 0.78
31 8 0.02
32 43 0.13
33 21 0.06
34 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATTTTGCAAT
Found at i:1872 original size:33 final size:32
Alignment explanation
Indices: 1786--1892 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 32
1776 CATGATCTTG
** *
1786 CAATTGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAAAATTATC
** *
1818 CAATTGACACCAGAAGTTGTCATGATAAATT-TC
1 CAATTGACACTTGAAGATGTCAT-A-AAATTATC
* ** *
1851 CAATAGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAAAATTATC
1883 CAATTGACAC
1 CAATTGACAC
1893 CAGAAGTTGT
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
31 3 0.05
32 31 0.53
33 21 0.36
34 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
CAATTGACACTTGAAGATGTCATAAAATTATC
Found at i:4006 original size:33 final size:33
Alignment explanation
Indices: 3943--4006 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3933 ATACTGAATA
**
3943 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
* *
3976 ATATTGCCCCTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCATAAACCCATGA
4007 AAAGATCACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
Found at i:13678 original size:31 final size:32
Alignment explanation
Indices: 13619--13681 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
13609 GATTGATGAA
*
13619 GTGTTTTTGATCATTCAAAATAGTTGTATCAT
1 GTGTTTTTGATCATTCAAAATAGCTGTATCAT
* *
13651 GTGTTTTTTATCATTC-TAATAGCTGTATCAT
1 GTGTTTTTGATCATTCAAAATAGCTGTATCAT
13682 TTTTATTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.49
Consensus pattern (32 bp):
GTGTTTTTGATCATTCAAAATAGCTGTATCAT
Found at i:19114 original size:159 final size:159
Alignment explanation
Indices: 18898--19222 Score: 650
Period size: 159 Copynumber: 2.0 Consensus size: 159
18888 TCCTGAAGGC
18898 TTATATTGGATGCCCGAATTACCCCTAAAAGTTCTACGAAATAACAAAACAACCATACGCAAAAA
1 TTATATTGGATGCCCGAATTACCCCTAAAAGTTCTACGAAATAACAAAACAACCATACGCAAAAA
18963 GACAAAAAAACCATGCAAATAGTACCCCAAATAAATGTGGTGAGAGAATAAGATTGCCCTTGGTG
66 GACAAAAAAACCATGCAAATAGTACCCCAAATAAATGTGGTGAGAGAATAAGATTGCCCTTGGTG
19028 TAATTCACACTTCAACTATTATTGTTTGT
131 TAATTCACACTTCAACTATTATTGTTTGT
19057 TTATATTGGATGCCCGAATTACCCCTAAAAGTTCTACGAAATAACAAAACAACCATACGCAAAAA
1 TTATATTGGATGCCCGAATTACCCCTAAAAGTTCTACGAAATAACAAAACAACCATACGCAAAAA
19122 GACAAAAAAACCATGCAAATAGTACCCCAAATAAATGTGGTGAGAGAATAAGATTGCCCTTGGTG
66 GACAAAAAAACCATGCAAATAGTACCCCAAATAAATGTGGTGAGAGAATAAGATTGCCCTTGGTG
19187 TAATTCACACTTCAACTATTATTGTTTGT
131 TAATTCACACTTCAACTATTATTGTTTGT
19216 TTATATT
1 TTATATT
19223 TCTTTTTATT
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 166 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (159 bp):
TTATATTGGATGCCCGAATTACCCCTAAAAGTTCTACGAAATAACAAAACAACCATACGCAAAAA
GACAAAAAAACCATGCAAATAGTACCCCAAATAAATGTGGTGAGAGAATAAGATTGCCCTTGGTG
TAATTCACACTTCAACTATTATTGTTTGT
Found at i:20109 original size:34 final size:34
Alignment explanation
Indices: 20066--20133 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
20056 GCTATTAATG
20066 GTTTGGAAAAGAACTCAATATCCAAGAATACAAA
1 GTTTGGAAAAGAACTCAATATCCAAGAATACAAA
20100 GTTTGGAAAAGAACTCAATATCCAAGAATACAAA
1 GTTTGGAAAAGAACTCAATATCCAAGAATACAAA
20134 CTCTTACGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (34 bp):
GTTTGGAAAAGAACTCAATATCCAAGAATACAAA
Found at i:20469 original size:29 final size:29
Alignment explanation
Indices: 20432--20495 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
20422 AAAAATTCCC
*
20432 TATG-TTTTTTTGGGATAAAATAATC-CAT
1 TATGTTTTTTTTGGGACAAAATAATCTC-T
*
20460 TATGTTTTTTTTGGGACAAATTAATCTCT
1 TATGTTTTTTTTGGGACAAAATAATCTCT
20489 TATGTTT
1 TATGTTT
20496 CAAAAGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 4 0.12
29 27 0.84
30 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.52
Consensus pattern (29 bp):
TATGTTTTTTTTGGGACAAAATAATCTCT
Found at i:20656 original size:25 final size:27
Alignment explanation
Indices: 20612--20661 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
20602 ACATGTCAGC
20612 AAATAAAAAAATTAACTAAAATTATTA
1 AAATAAAAAAATTAACTAAAATTATTA
*
20639 AAAT-AAAAAA-TAATTAAAATTAT
1 AAATAAAAAAATTAACTAAAATTAT
20662 AATAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
26 6 0.27
27 4 0.18
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (27 bp):
AAATAAAAAAATTAACTAAAATTATTA
Found at i:20909 original size:22 final size:22
Alignment explanation
Indices: 20884--20926 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20874 TTGAAACGTG
20884 AGGGATTGA-TTTGTCCAAAAAA
1 AGGGATT-ATTTTGTCCAAAAAA
*
20906 AGGGATTATTTTGTCCCAAAA
1 AGGGATTATTTTGTCCAAAAA
20927 GAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (22 bp):
AGGGATTATTTTGTCCAAAAAA
Found at i:25419 original size:20 final size:20
Alignment explanation
Indices: 25394--25431 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25384 GACACACTAT
25394 AATACATA-TATAATATGTGC
1 AATACATATTAT-ATATGTGC
25414 AATACATATTATATATGT
1 AATACATATTATATATGT
25432 ATTAAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (20 bp):
AATACATATTATATATGTGC
Found at i:25816 original size:146 final size:146
Alignment explanation
Indices: 25497--25926 Score: 481
Period size: 146 Copynumber: 2.9 Consensus size: 146
25487 TCAAAATTTT
* * ** * *
25497 TTGGAGATGACAACCAAAATTTTCCAATGGAGGAGGATTATGTTGGTAGCTCTCCCACGGCGAAG
1 TTGGAGATGGCAAACAAAATTTTCCAATGGAGGAGGATTATGTCCGTAGCTCTCCTAAGGCGAAG
* * * * * * * * * *
25562 GTATGACTGGTA-ACTG---TTTTTCTATTTTCTTGAAATATATAAAGTTTATAACTAATATAAG
66 GTATGATTGGTATA-TGTTTTTTTTTTGTTTTATTCAAATATATAATGTTTACAAGTAGTACAAG
* * *
25623 TATTTAATAGGTTGTCG
130 TATTTAATAGGGTATCC
* * * *
25640 ATGGAGATGGCAAGCAACATTTTCCCATGGAGGAGGATTATGTCCGTAGCTCTCCTAAGGCGAAG
1 TTGGAGATGGCAAACAAAATTTTCCAATGGAGGAGGATTATGTCCGTAGCTCTCCTAAGGCGAAG
25705 GTATGATTGGTATATGTTTTTTTTTTGTTTTATTCAAATATATAATGTTTACAAGTAGTACAAGT
66 GTATGATTGGTATATGTTTTTTTTTTGTTTTATTCAAATATATAATGTTTACAAGTAGTACAAGT
*
25770 ATTTTATAGGGTATCC
131 ATTTAATAGGGTATCC
* * * ** *
25786 TTGGAGATGGCAAAAAAAATTGTCCAATGGAGGAGAATTATGTCCGTAGCTCTCCTAACTCTAAG
1 TTGGAGATGGCAAACAAAATTTTCCAATGGAGGAGGATTATGTCCGTAGCTCTCCTAAGGCGAAG
* * *
25851 TTATGATTGATATATGTTTTTTTTTCCTTTTGTTTTATTCAAATCTATAATGTTTACAAGTAGTA
66 GTATGATTGGTATATG---TTTTTT--TTTTGTTTTATTCAAATATATAATGTTTACAAGTAGTA
25916 CAAGTATTTAA
126 CAAGTATTTAA
25927 CAGTATTTAA
Statistics
Matches: 241, Mismatches: 37, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
143 69 0.29
144 1 0.00
146 118 0.49
149 6 0.02
151 47 0.20
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (146 bp):
TTGGAGATGGCAAACAAAATTTTCCAATGGAGGAGGATTATGTCCGTAGCTCTCCTAAGGCGAAG
GTATGATTGGTATATGTTTTTTTTTTGTTTTATTCAAATATATAATGTTTACAAGTAGTACAAGT
ATTTAATAGGGTATCC
Found at i:27271 original size:13 final size:13
Alignment explanation
Indices: 27229--27275 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
27219 TCATGCACCC
*
27229 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
27243 AAAACCATTT-AT
1 AAAACAATTTAAT
27255 AAAACAATTTAAT
1 AAAACAATTTAAT
27268 AAAACAAT
1 AAAACAAT
27276 AATAAAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 10 0.34
13 10 0.34
14 9 0.31
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:27470 original size:13 final size:13
Alignment explanation
Indices: 27452--27494 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
27442 GTATCATAAT
*
27452 CAAAGTCATAAAC
1 CAAAGTAATAAAC
*
27465 CAAAGTAATAAAT
1 CAAAGTAATAAAC
27478 CAGAA-TAATAAAC
1 CA-AAGTAATAAAC
27491 CAAA
1 CAAA
27495 CAGTCAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.16
Consensus pattern (13 bp):
CAAAGTAATAAAC
Found at i:32893 original size:2 final size:2
Alignment explanation
Indices: 32888--32925 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
32878 TACTATGGTT
*
32888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32926 CACACACACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33930 original size:22 final size:21
Alignment explanation
Indices: 33793--33939 Score: 84
Period size: 22 Copynumber: 6.8 Consensus size: 21
33783 TCATAAGAAG
*
33793 GTTA-CAAAA-TTCATAGGAAA
1 GTTATCAAAATTTCATAGG-TA
* *
33813 GTTTATTAAAATTTCATAGTTA
1 G-TTATCAAAATTTCATAGGTA
* * *
33835 GGTTATCAAAGTCTCTTATGG-A
1 -GTTATCAAAATTTCATA-GGTA
* *
33857 GTTTATCACAATTTTATAGGTA
1 G-TTATCAAAATTTCATAGGTA
* * *
33879 ATTATCAAAATTTCATATGATG
1 GTTATCAAAATTTCATA-GGTA
*
33901 GTTATCAAAATTTGATAGGGTA
1 GTTATCAAAATTTCATA-GGTA
* *
33923 GTTTTCAATATTTCATA
1 GTTATCAAAATTTCATA
33940 AAAATATCCA
Statistics
Matches: 93, Mismatches: 26, Indels: 14
0.70 0.20 0.11
Matches are distributed among these distances:
20 1 0.01
21 20 0.22
22 63 0.68
23 9 0.10
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGTA
Found at i:34005 original size:2 final size:2
Alignment explanation
Indices: 33998--34030 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
33988 CTAAAACTAG
*
33998 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34031 CAAGGGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Done.