Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001496.1 Corchorus olitorius cultivar O-4 contig01496, 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: 2489
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Found at i:306 original size:22 final size:22
Alignment explanation
Indices: 265--858 Score: 260
Period size: 22 Copynumber: 26.4 Consensus size: 22
255 ACAATCAAAC
*
265 CAAAATTACATAG-GAAGGTTAT
1 CAAAATTTCATAGTG-AGGTTAT
* *
287 CAAAATTTCATAGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
* * *
309 CGAAATTTCA-AATGGAGATTAT
1 CAAAATTTCATAGT-GAGGTTAT
*
331 C-AAACTTCATAGTGTA-GTTAT
1 CAAAATTTCATAGTG-AGGTTAT
** *
352 CAAAATTTCATACAGATGTTA-
1 CAAAATTTCATAGTGAGGTTAT
* * *
373 CTAATATTTCATAAAATTAAAGGTTAT
1 C-AAAATTTCAT---AGT-GAGGTTAT
* * *
400 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGTGAGGTTAT
*
422 CAAAATTTCATACG-AAGGTTAT
1 CAAAATTTCATA-GTGAGGTTAT
** * *
444 TGAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
*
466 CAAAATTTCATAAG-AAGGTTA-
1 CAAAATTTCAT-AGTGAGGTTAT
* *
487 CAAAAATTTCATAGGAAGGAGGTCAT
1 C-AAAATTTCATA-G--TGAGGTTAT
* * *
513 CAAAATTTTATAGAGTGGTTAAT
1 CAAAATTTCATAGTGAGGTT-AT
*
536 -AAAATTTCATAGGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
557 GAAAATTTTATGGAGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
579 CAAAATTATATATAGAGAGGATAT
1 CAAAATT-T-CATAGTGAGGTTAT
* * *
603 CACAGTTTCATTCTTATAGGGAGGTTAT
1 CA-A----AATT-TCATAGTGAGGTTAT
* **
631 CGAAATTTCAGGGT-ATGGTTAT
1 CAAAATTTCATAGTGA-GGTTAT
*
653 CAAAATTTACATAGTGCGGTTA-
1 CAAAATTT-CATAGTGAGGTTAT
* * *
675 CCAAATTT-ATAGTGCGATTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
696 CAAAATTTCATAGGGAGATTAT
1 CAAAATTTCATAGTGAGGTTAT
*** *
718 CAAAATTTCACCTTAAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
740 AAAAATTTAATAGTGTGTTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
762 CAAAATTTTACAATGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
784 CAAATTTTCATAGGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
806 CAAAATTTCATAATGAAGTTAT
1 CAAAATTTCATAGTGAGGTTAT
** * *
828 CAATTTTTCATAATGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
850 -AAATATTTC
1 CAAA-ATTTC
859 TACGTTAGAG
Statistics
Matches: 429, Mismatches: 107, Indels: 72
0.71 0.18 0.12
Matches are distributed among these distances:
20 11 0.03
21 32 0.07
22 301 0.70
23 20 0.05
24 15 0.03
25 17 0.04
26 14 0.03
27 2 0.00
28 13 0.03
29 4 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAT
Found at i:517 original size:113 final size:113
Alignment explanation
Indices: 339--585 Score: 277
Period size: 113 Copynumber: 2.2 Consensus size: 113
329 ATCAAACTTC
* * * * *
339 ATAGTGTAGTTATCAAAATTTCATACAGATGTTACTAATATTTCATAAAATTAAAGGTTATCAAA
1 ATAGTGTGGTTATCAAAATTTCATACAGAGGTTACAAAAATTTCATAAAA-TAAAGGTCATCAAA
*
404 ATTTCT-TAGGGAGGTTAACAAAATTTCATACGAAGGTTATTG-AAATTTT
65 ATTT-TATAGAGAGGTTAACAAAATTTCATACGAAGGTTA-TGAAAATTTT
* **
453 ATAGTGTGGTTATCAAAATTTCATA-AGAAGGTTACAAAAATTTCATAGGAA-GGAGGTCATCAA
1 ATAGTGTGGTTATCAAAATTTCATACAG-AGGTTACAAAAATTTCATA-AAATAAAGGTCATCAA
* * * *
516 AATTTTATAGAGTGGTTAATAAAATTTCATAGGGAGGTTATGAAAATTTT
64 AATTTTATAGAGAGGTTAACAAAATTTCATACGAAGGTTATGAAAATTTT
* * *
566 ATGGAGAGGTTATCAAAATT
1 ATAGTGTGGTTATCAAAATT
586 ATATATAGAG
Statistics
Matches: 113, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
112 3 0.03
113 68 0.60
114 40 0.35
115 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (113 bp):
ATAGTGTGGTTATCAAAATTTCATACAGAGGTTACAAAAATTTCATAAAATAAAGGTCATCAAAA
TTTTATAGAGAGGTTAACAAAATTTCATACGAAGGTTATGAAAATTTT
Found at i:1727 original size:8 final size:8
Alignment explanation
Indices: 1703--1737 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
1693 CAAATGCTTT
1703 TTTTTTTG
1 TTTTTTTG
1711 TTTTGTTTTG
1 -TTT-TTTTG
1721 TTTTTTTG
1 TTTTTTTG
1729 TTTTTTTG
1 TTTTTTTG
1737 T
1 T
1738 GAAACCAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 14 0.56
9 6 0.24
10 5 0.20
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:2307 original size:43 final size:43
Alignment explanation
Indices: 2259--2345 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
2249 AATCTTGTTG
2259 TCATGAAATCGACAGTGCAGCCTTTACCAAGGCACATCTGAAT
1 TCATGAAATCGACAGTGCAGCCTTTACCAAGGCACATCTGAAT
2302 TCATGAAATCGACAGTGCAGCCTTTACCAAGGCACATCTGAAT
1 TCATGAAATCGACAGTGCAGCCTTTACCAAGGCACATCTGAAT
2345 T
1 T
2346 GATCAATCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
TCATGAAATCGACAGTGCAGCCTTTACCAAGGCACATCTGAAT
Done.