Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014062.1 Corchorus olitorius cultivar O-4 contig14095, 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, 770
Length: 1284
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Found at i:489 original size:26 final size:26
Alignment explanation
Indices: 434--489 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
424 TATATATATC
* * **
434 ATTAGTCATTACGTTTTTTTTTAGGA
1 ATTAGTCATTACATTTTTCTTTACCA
460 ATTAGTCATTACATTTTTCTTT-CCA
1 ATTAGTCATTACATTTTTCTTTACCA
485 TATTA
1 -ATTA
490 CGAAAGTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTCATTACATTTTTCTTTACCA
Found at i:703 original size:140 final size:141
Alignment explanation
Indices: 334--732 Score: 653
Period size: 140 Copynumber: 2.8 Consensus size: 141
324 TCCAATCAGA
* * * *
334 TTTTATTTCCATATTAAAAAAGTC-TAAA--ATAATAACAATTATTTTTACATTAAACAACTTAT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATT-TTTTTACATTAAACAACTTAT
396 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTAGGAA
65 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACG-TTTTTTTTAGGAA
*
461 TTAGTCATTACAT
129 TTAATCATTACAT
* *
474 TTTTCTTTCCATATTACGAAAGTCTTAAATGATACTAATAATTTTTTTACGTTAAACAACTTATT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACATTAAACAACTTATT
539 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTAGGAATT
66 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTAGGAATT
*
604 AATCATTACGT
131 AATCATTACAT
*
615 TTTTCTTTCCGTATTACAAAAGTCTTAAATGATACTAATAATTTTTTTAC-TTAAACAACTTATT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACATTAAACAACTTATT
* *
679 ATTATAATTATTAAAATTATTATTAGTTATATATATTATTAGTCACTACGTTTT
66 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTT
733 CCTTTCCATA
Statistics
Matches: 244, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
140 87 0.36
141 76 0.31
142 71 0.29
143 10 0.04
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (141 bp):
TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACATTAAACAACTTATT
ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTAGGAATT
AATCATTACAT
Found at i:738 original size:115 final size:114
Alignment explanation
Indices: 601--823 Score: 324
Period size: 115 Copynumber: 1.9 Consensus size: 114
591 TTTTTTAGGA
* * * *
601 ATTAATCATTACGTTTTTCTTTCCGTATTACAAAAGTCTT-AAATGATACTAATAATTTTTTTAC
1 ATTAATCACTACGTTTTCCTTTCCATATTACAAAAGT-TTAAAATAATACTAA-AATTTTTTTAC
665 -TTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATATT
64 GTTAAACAACTTATTATTATAATTATTAAAATTATTATTA-TTATATATATT
* *
716 ATTAGTCACTACGTTTTCCTTTCCATATTACAAAAGTTTAAAATAATACTAACATTTTTTTACGT
1 ATTAATCACTACGTTTTCCTTTCCATATTACAAAAGTTTAAAATAATACTAAAATTTTTTTACGT
* * *
781 TAAACATCTTCTTATTATAATTATTAAACTTATTATTATTATA
66 TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATA
824 ACAATTATTA
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
114 17 0.18
115 80 0.82
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.48
Consensus pattern (114 bp):
ATTAATCACTACGTTTTCCTTTCCATATTACAAAAGTTTAAAATAATACTAAAATTTTTTTACGT
TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATATATATT
Found at i:818 original size:15 final size:16
Alignment explanation
Indices: 795--842 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
785 CATCTTCTTA
*
795 TTATAATTATTA-AAC
1 TTATTATTATTATAAC
810 TTATTATTATTATAAC
1 TTATTATTATTATAAC
826 AATTATTATTAGTTATA
1 --TTATTATTA-TTATA
843 TGATCACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTATTATTATAAC
Found at i:831 original size:18 final size:17
Alignment explanation
Indices: 792--842 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
782 AAACATCTTC
* *
792 TTATTATAATTATTAAAC
1 TTATTATTATTA-TAAAA
810 TTATTATTATTATAACAA
1 TTATTATTATTATAA-AA
828 TTATTATTAGTTATA
1 TTATTATTA-TTATA
843 TGATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 21 0.72
19 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATTATTATTATAAAA
Done.