Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012547.1 Corchorus olitorius cultivar O-4 contig12580, 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: 16345
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Found at i:1432 original size:22 final size:21
Alignment explanation
Indices: 1407--1632 Score: 105
Period size: 22 Copynumber: 10.3 Consensus size: 21
1397 ACCAAAAATA
*
1407 CATAGGAAGGTTATCAATATTT
1 CATAGG-AGGTTATCAAAATTT
* *
1429 CATAGTGTGGTTACCAAAATTT
1 CATAG-GAGGTTATCAAAATTT
* *
1451 CATATGGAGGTTATCGAAACTT
1 CATA-GGAGGTTATCAAAATTT
1473 CATAGTGTA-GTTATCAAAATTT
1 CATAG-G-AGGTTATCAAAATTT
* * **
1495 TATATAGAAATTA-CAAAAATTT
1 CATA-GGAGGTTATC-AAAATTT
** *
1517 CATAAAAAGATTATCAAAATTT
1 CAT-AGGAGGTTATCAAAATTT
* * * *
1539 CTTAGAGATGTTAACAACATTT
1 CATAG-GAGGTTATCAAAATTT
* * *
1561 CATACGAAGGTTATCGACATTT
1 CATA-GGAGGTTATCAAAATTT
* * *
1583 TATAGTGTGATTATCAAAATTT
1 CATAG-GAGGTTATCAAAATTT
* * *
1605 TATAAGGATGTTAACAAAATTT
1 CAT-AGGAGGTTATCAAAATTT
1627 CATAGG
1 CATAGG
1633 GAGGGATGTT
Statistics
Matches: 153, Mismatches: 38, Indels: 27
0.70 0.17 0.12
Matches are distributed among these distances:
21 8 0.05
22 137 0.90
23 8 0.05
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (21 bp):
CATAGGAGGTTATCAAAATTT
Found at i:1462 original size:44 final size:45
Alignment explanation
Indices: 1397--1499 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 45
1387 TGACAATTAA
* * * *
1397 ACCAAAAATACATA-GGAAGGTTATC-AATATTTCATAGTGTGGTT
1 ACCAAAATTTCATATGGAAGGTTATCGAA-ACTTCATAGTGTAGTT
1441 ACCAAAATTTCATATGG-AGGTTATCGAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATATGGAAGGTTATCGAAACTTCATAGTGTAGTT
* *
1485 ATCAAAATTTTATAT
1 ACCAAAATTTCATAT
1500 AGAAATTACA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 47 0.92
45 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (45 bp):
ACCAAAATTTCATATGGAAGGTTATCGAAACTTCATAGTGTAGTT
Found at i:1997 original size:66 final size:66
Alignment explanation
Indices: 1784--2040 Score: 234
Period size: 66 Copynumber: 3.9 Consensus size: 66
1774 ATTTCATGGT
* * * * *
1784 GTGATTA-CAAAATTTTATGAG-GAGGTTATCAAATTTTTCATAGTGTGGTTA-CCAATTTTTAT
1 GTGATTATCAAAATTTCAT-AGTGAGGTTATCAAA-ATTTCACAGTGTGGTTATCAAATTTTCAT
1846 -AG
64 AAG
* * * * * * * *
1848 TGTGATTATCAAAATTTAATAGGGAGATTATCACAATTTCACACTGAGGTAATCAAAATTTCATA
1 -GTGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCACAGTGTGGTTATCAAATTTTCATA
*
1913 AT
65 AG
* * * *
1915 GCGCTTGTCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTGTGGTTATCAAATTTTCATAA
1 GTGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCACAGTGTGGTTATCAAATTTTCATAA
1980 G
66 G
* * * * * *
1981 GTGGTTATCTAGATTTCATAATGAGGTTATCAAATTTTCACAGTGTGATTATCAATATTT
1 GTGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCACAGTGTGGTTATCAA-ATTT
2041 CTACGTTGGA
Statistics
Matches: 153, Mismatches: 34, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
65 21 0.14
66 127 0.83
67 5 0.03
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (66 bp):
GTGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCACAGTGTGGTTATCAAATTTTCATAA
G
Found at i:2041 original size:22 final size:22
Alignment explanation
Indices: 1764--2041 Score: 204
Period size: 22 Copynumber: 12.7 Consensus size: 22
1754 CTCATATGGA
* *
1764 GGTTATCGAAATTTCATGGTGT
1 GGTTATCAAAATTTCATAGTGT
* * *
1786 GATTA-CAAAATTTTATGAG-GA
1 GGTTATCAAAATTTCAT-AGTGT
*
1807 GGTTATCAAATTTTTCATAGTGT
1 GGTTATCAAA-ATTTCATAGTGT
* * *
1830 GGTTA-CCAATTTTTATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * * *
1851 GATTATCAAAATTTAATAGGGA
1 GGTTATCAAAATTTCATAGTGT
* * * * *
1873 GATTATCACAATTTCACACTGA
1 GGTTATCAAAATTTCATAGTGT
* * *
1895 GGTAATCAAAATTTCATAATGC
1 GGTTATCAAAATTTCATAGTGT
* *
1917 GCTTGTCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
1939 GGTTATCAAAATTTCACAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
1961 GGTTATCAAATTTTCATAAG-GT
1 GGTTATCAAAATTTCAT-AGTGT
* * * *
1983 GGTTATCTAGATTTCATAATGA
1 GGTTATCAAAATTTCATAGTGT
* *
2005 GGTTATCAAATTTTCACAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
2027 GATTATCAATATTTC
1 GGTTATCAAAATTTC
2042 TACGTTGGAG
Statistics
Matches: 197, Mismatches: 52, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
21 30 0.15
22 154 0.78
23 13 0.07
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:5185 original size:21 final size:21
Alignment explanation
Indices: 5154--5193 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5144 TTATTACCTC
*
5154 TTTCTACTCTTCTTTATTTTTT
1 TTTCTACTCTT-TTAATTTTTT
5176 TTTCT-CTCTTTTAATTTT
1 TTTCTACTCTTTTAATTTT
5194 ATCCTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTCTACTCTTTTAATTTTTT
Found at i:16273 original size:50 final size:49
Alignment explanation
Indices: 16173--16273 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 49
16163 GTTCTTCATA
* **
16173 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTG
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTG
*
16222 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTG
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTG
16272 TT
1 TT
16274 CTTCATTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
49 7 0.16
50 37 0.82
51 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (49 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTG
Done.