Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009492.1 Corchorus olitorius cultivar O-4 contig09524, 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: 2430
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Found at i:394 original size:48 final size:47
Alignment explanation
Indices: 323--862 Score: 562
Period size: 48 Copynumber: 11.6 Consensus size: 47
313 ACGAAGAACT
**
323 CCTTCCGATGGGGAAGGGCAAAACGAGAATAAAACATTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAAC-AGAATAAAACATTGAAAACAACA
* *
371 CCTTCCGACCGAGAAGGGCAAAAC---AT--GA-A-TGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACAGAATAAAACATTGAAAACAACA
* *
411 CCTTCCCACCGGGAAGGGCAAAACAG-----GA-A-TGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACAGAATAAAACATTGAAAACAACA
* * *
451 ACTTACGACCGGGAAGGGCAAAAAAGGAATGAAAACATTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACA-GAAT-AAAACATTGAAAACAACA
* * *
500 CCTTCC-ACTGGGGAAGGGCAGAACGGGAATAAAACATTGAAAACAACA
1 CCTTCCGAC-CGGGAAGGGCAAAAC-AGAATAAAACATTGAAAACAACA
*
548 CCTTCCGACCGGGAAGGGCAAAATAGGAATAAAACATTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACA-GAATAAAACATTGAAAACAACA
* ** * *
596 CCTTCCGACCGGG-ATGATAAAACAAGAATAAAATAATGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAAC-AGAATAAAACATTGAAAACAACA
*
643 CCTTCCGACCAGGAAGGGCAAAACAGAAATAAAACATTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACAG-AATAAAACATTGAAAACAACA
* * *
691 CCTTCCGACCGGGAATGGCGAAACAGGAATAAAATATTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACA-GAATAAAACATTGAAAACAACA
* * * *
739 CCTTCCTACCGAGAAAAGGGCAAAACAAGAATAAAATATTGTAAACAACA
1 CCTTCCGACCG-G-GAAGGGCAAAAC-AGAATAAAACATTGAAAACAACA
* **
789 CCTTCCGGCCGGGAAGGGCAAAAC---A-AAAATGTTGAAAACAACA
1 CCTTCCGACCGGGAAGGGCAAAACAGAATAAAACATTGAAAACAACA
832 CCTTCCGACCGGGAAGGGCAAAACAGGAATA
1 CCTTCCGACCGGGAAGGGCAAAACA-GAATA
863 TTGAAGAAAA
Statistics
Matches: 417, Mismatches: 48, Indels: 54
0.80 0.09 0.10
Matches are distributed among these distances:
40 68 0.16
41 2 0.00
42 1 0.00
43 39 0.09
44 3 0.01
47 42 0.10
48 186 0.45
49 36 0.09
50 39 0.09
51 1 0.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (47 bp):
CCTTCCGACCGGGAAGGGCAAAACAGAATAAAACATTGAAAACAACA
Found at i:406 original size:40 final size:40
Alignment explanation
Indices: 360--487 Score: 202
Period size: 40 Copynumber: 3.2 Consensus size: 40
350 AATAAAACAT
* *
360 TGAAAACAACACCTTCCGACCGAGAAGGGCAAAACATGAA
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAA
*
400 TGAAAACAACACCTTCCCACCGGGAAGGGCAAAACAGGAA
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAA
* * *
440 TGAAAACAACAACTTACGACCGGGAAGGGCAAAAAAGGAA
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAA
480 TGAAAACA
1 TGAAAACA
488 TTGAAAACAA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.47, C:0.23, G:0.22, T:0.09
Consensus pattern (40 bp):
TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAA
Found at i:647 original size:95 final size:96
Alignment explanation
Indices: 440--862 Score: 545
Period size: 95 Copynumber: 4.4 Consensus size: 96
430 AAAACAGGAA
* * *
440 TGAAAACAACAACTTACGACCGGGAAGGGCAAAAAAGGAATGAAAACATTGAAAACAACACCTTC
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAAT-AAAACATTGAAAACAACACCTTC
* * * *
505 C-ACTGGGGAAGGGCAGAACGGGAATAAAACAT
65 CGAC-CGGGAAGGGCAAAACAGGAATAAAATAT
*
537 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAATAGGAATAAAACATTGAAAACAACACCTTCC
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCC
* ** * *
602 GACCGGG-ATGATAAAACAAGAATAAAATAA
66 GACCGGGAAGGGCAAAACAGGAATAAAATAT
* *
632 TGAAAACAACACCTTCCGACCAGGAAGGGCAAAACAGAAATAAAACATTGAAAACAACACCTTCC
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCC
* *
697 GACCGGGAATGGCGAAACAGGAATAAAATAT
66 GACCGGGAAGGGCAAAACAGGAATAAAATAT
* * * * *
728 TGAAAACAACACCTTCCTACCGAGAAAAGGGCAAAACAAGAATAAAATATTGTAAACAACACCTT
1 TGAAAACAACACCTTCCGACCG-G-GAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTT
* *
793 CCGGCCGGGAAGGGCAAAAC----A-AAAATGT
64 CCGACCGGGAAGGGCAAAACAGGAATAAAATAT
821 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATA
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATA
863 TTGAAGAAAA
Statistics
Matches: 288, Mismatches: 34, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
91 17 0.06
92 1 0.00
93 27 0.09
94 1 0.00
95 84 0.29
96 65 0.23
97 41 0.14
98 52 0.18
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.13
Consensus pattern (96 bp):
TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACATTGAAAACAACACCTTCC
GACCGGGAAGGGCAAAACAGGAATAAAATAT
Found at i:682 original size:143 final size:141
Alignment explanation
Indices: 440--862 Score: 532
Period size: 143 Copynumber: 3.0 Consensus size: 141
430 AAAACAGGAA
* * *
440 TGAAAACAACAACTTACGACCGGGAAGGGCAAAA-AAGGAATGAAAACATTGAAAACAACACCTT
1 TGAAAACAACACCTTCCGACCGGG-AGGGCAAAACAA-GAAT-AAAATATTGAAAACAACACCTT
* *
504 CC-ACTGGGGAAGGGCAGAACGGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCA
63 CCGAC-CGGGAAGGGCAAAAC--GAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCA
*
568 AAATAGGAATAAAACAT
125 AAACAGGAATAAAACAT
* ** *
585 TGAAAACAACACCTTCCGACCGGGATGATAAAACAAGAATAAAATAATGAAAACAACACCTTCCG
1 TGAAAACAACACCTTCCGACCGGGAGGGCAAAACAAGAATAAAATATTGAAAACAACACCTTCCG
* * *
650 ACCAGGAAGGGCAAAACAGAAATAAAACATTGAAAACAACACCTTCCGACCGGGAATGGCGAAAC
66 ACCGGGAAGGGCAAAAC-G-AATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC
*
715 AGGAATAAAATAT
129 AGGAATAAAACAT
* * *
728 TGAAAACAACACCTTCCTACCGAGAAAAGGGCAAAACAAGAATAAAATATTGTAAACAACACCTT
1 TGAAAACAACACCTTCCGACCG-G--GAGGGCAAAACAAGAATAAAATATTGAAAACAACACCTT
* **
793 CCGGCCGGGAAGGGCAAAAC--A-AAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAA
63 CCGACCGGGAAGGGCAAAACGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAA
855 CAGGAATA
128 CAGGAATA
863 TTGAAGAAAA
Statistics
Matches: 244, Mismatches: 28, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
141 45 0.18
142 2 0.01
143 109 0.45
144 13 0.05
145 24 0.10
146 51 0.21
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.13
Consensus pattern (141 bp):
TGAAAACAACACCTTCCGACCGGGAGGGCAAAACAAGAATAAAATATTGAAAACAACACCTTCCG
ACCGGGAAGGGCAAAACGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAG
GAATAAAACAT
Found at i:1577 original size:50 final size:50
Alignment explanation
Indices: 1494--1998 Score: 704
Period size: 50 Copynumber: 10.1 Consensus size: 50
1484 ATATTTCCTT
* * * *
1494 TTTATTTACAAAATGCTTAGAAGGTTTAATCTTTTAATAAAAAATCCAATC
1 TTTATTTACAAATTGCTTA-AAAGTTCAATCTTTTAATTAAAAATCCAATC
* * * * ** * *
1545 TTTATTCATAAATTACTTAAGAGTTTGATCTTTTGATCAAAAATCCAATC
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
* * ** *
1595 CTTATTTACAAATTGCTTAAAGGTTTGATCTTTTAATTAAAAATACAATC
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
* * *
1645 TTTATTCACAAATTACTTAAAAGTTCAATCTTTTAATTAAAAATACAATC
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
* *
1695 TTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATG
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
* * * *
1745 TTTATTTACGAATTGCTTAAAGGTTCAATCTTTTAATTAAAAGTCCAACC
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
* * *
1795 TTTATTTACAATTTGCTTAAAGGTTCAATCTTTTAATTAAAGATCCAATC
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
* *
1845 TTTATTTACAAATTCCTTAAAAGTTCAATGTTTTAATTAAAAATCCAATC
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
1895 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
* *
1945 TTTATTTACAAATTTCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATT
1 TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
1995 TTTA
1 TTTA
1999 ACTCAAAGGT
Statistics
Matches: 406, Mismatches: 48, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
50 391 0.96
51 15 0.04
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (50 bp):
TTTATTTACAAATTGCTTAAAAGTTCAATCTTTTAATTAAAAATCCAATC
Found at i:1674 original size:30 final size:29
Alignment explanation
Indices: 1631--1727 Score: 77
Period size: 30 Copynumber: 3.6 Consensus size: 29
1621 GATCTTTTAA
*
1631 TTAAAAATACAATCTTTATTCACAAATTAC
1 TTAAAAGTACAATCTTTATT-ACAAATTAC
*
1661 TTAAAAGTTCAATC-TT-TT---AATTA-
1 TTAAAAGTACAATCTTTATTACAAATTAC
*
1684 --AAAA-TACAATCTTTATTTACAAATTTC
1 TTAAAAGTACAATCTTTA-TTACAAATTAC
*
1711 TTAAAAGTTCAATCTTT
1 TTAAAAGTACAATCTTT
1728 TAATTAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
20 6 0.12
21 6 0.12
23 2 0.04
24 5 0.10
26 4 0.08
28 2 0.04
29 6 0.12
30 21 0.40
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.42
Consensus pattern (29 bp):
TTAAAAGTACAATCTTTATTACAAATTAC
Found at i:1924 original size:30 final size:29
Alignment explanation
Indices: 1881--1977 Score: 77
Period size: 30 Copynumber: 3.6 Consensus size: 29
1871 AATGTTTTAA
1881 TTAAAAATCCAATCTTTATTTACAAATTGC
1 TTAAAAATCCAATCTTTATTTACAAATT-C
* *
1911 TTAAAAGTTCAATC--T-TTT---AA---
1 TTAAAAATCCAATCTTTATTTACAAATTC
1931 TTAAAAATCCAATCTTTATTTACAAATTTC
1 TTAAAAATCCAATCTTTATTTACAAA-TTC
* *
1961 TTAAAAGTTCAATCTTT
1 TTAAAAATCCAATCTTT
1978 TAATTAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 20
0.66 0.08 0.26
Matches are distributed among these distances:
20 12 0.24
22 1 0.02
23 3 0.06
24 2 0.04
26 2 0.04
27 3 0.06
28 1 0.02
30 27 0.53
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.43
Consensus pattern (29 bp):
TTAAAAATCCAATCTTTATTTACAAATTC
Done.