Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012892.1 Corchorus olitorius cultivar O-4 contig12925, 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: 9057
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:463 original size:27 final size:27
Alignment explanation
Indices: 425--495 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
415 AAAGTGCTTA
* *
425 AAATGACCAAAATGCCCATGGACATGC
1 AAATGACTAAAATGCCCATGAACATGC
* *
452 AAATGACTAAAATGCCCCTGAACGTGC
1 AAATGACTAAAATGCCCATGAACATGC
* *
479 AAACGACTATAATGCCC
1 AAATGACTAAAATGCCC
496 CCTGAATAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACTAAAATGCCCATGAACATGC
Found at i:833 original size:52 final size:51
Alignment explanation
Indices: 795--999 Score: 331
Period size: 50 Copynumber: 4.0 Consensus size: 51
785 ACTCTAATAG
*
795 ATTAAAGGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-T
1 ATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATT
*
845 CTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATT
1 ATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATT
* *
896 CTATAAAAGGACTGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT
1 AT-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA--TT
*
950 ATAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAAT
1 ATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAAT
1000 CTTAAAAAAA
Statistics
Matches: 145, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
50 47 0.32
51 4 0.03
52 46 0.32
53 45 0.31
54 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (51 bp):
ATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATT
Found at i:945 original size:102 final size:103
Alignment explanation
Indices: 796--1006 Score: 365
Period size: 102 Copynumber: 2.1 Consensus size: 103
786 CTCTAATAGA
*
796 TTAAAGGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC-T-T-AAAAGGACCG
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTATAAAAAGGACCG
858 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC
66 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TC
*
897 TATAAAAGGACTGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTATAAAAAGGACC
1 T-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTATAAAAAGGACC
962 GTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
65 GTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1001 TTAAAA
1 TTAAAA
1007 AAAAGGTAAT
Statistics
Matches: 104, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
101 1 0.01
102 47 0.45
103 6 0.06
104 4 0.04
105 46 0.44
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (103 bp):
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTATAAAAAGGACCG
TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
Found at i:980 original size:53 final size:52
Alignment explanation
Indices: 797--1008 Score: 358
Period size: 52 Copynumber: 4.1 Consensus size: 52
787 TCTAATAGAT
*
797 TAAAGGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC-T-
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
847 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAAT-TCTA
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT-TA
*
899 TAAAAGGACTGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
951 TAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
1 T-AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
*
1004 AAAAA
1 TAAAA
1009 AAGGTAATGC
Statistics
Matches: 153, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
50 47 0.31
51 1 0.01
52 54 0.35
53 51 0.33
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (52 bp):
TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
Found at i:1126 original size:50 final size:50
Alignment explanation
Indices: 1064--1453 Score: 681
Period size: 50 Copynumber: 7.8 Consensus size: 50
1054 AGGTTTGAAA
*
1064 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
1114 TGACTTGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
1164 TGACTCGTATGGAAACGAGTTTGACTTGTGGAGAAGCCCATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
1214 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAATGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
1264 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGTCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1314 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
1364 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAACCCATGTTGATATT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
1414 TAACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1454 ATCATTCGAA
Statistics
Matches: 321, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 321 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:1677 original size:91 final size:90
Alignment explanation
Indices: 1536--1828 Score: 405
Period size: 91 Copynumber: 3.3 Consensus size: 90
1526 ATACCTTTGG
* *
1536 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTAATTGATGATGAGAAAGGACCAATG
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGA-AAAGGACCAATG
**
1601 TGTGGTCAACTTGAAAAACAACTTGA
65 TGCAGTCAACTTGAAAAACAACTTGA
* *
1627 ACAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAA-AGGACCAATG
1692 TGCAGTCAACTTGAAAAACAACTTGA
65 TGCAGTCAACTTGAAAAACAACTTGA
* *
1718 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGAAGATGAAAAAGGACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATG-AAAAGGACCAATG
* * * *
1783 TCCTGTCAATTTTG----ATAACTTGA
65 TGCAGTCAA-CTTGAAAAACAACTTGA
*
1806 AGAATAACTCTGAGTCTGATGTT
1 AAAATAACTCTGAGTCTGATGTT
1829 ATGATTAAAA
Statistics
Matches: 186, Mismatches: 13, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
88 30 0.16
90 2 0.01
91 148 0.80
92 6 0.03
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (90 bp):
AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGACCAATGT
GCAGTCAACTTGAAAAACAACTTGA
Found at i:1918 original size:26 final size:25
Alignment explanation
Indices: 1866--1924 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
1856 CGAAACTTTT
1866 CTTTCTTGACTTTGCTTCATTTCTG
1 CTTTCTTGACTTTGCTTCATTTCTG
*
1891 CTCTTCTTGA-TTTGTCCTTGATTT-TG
1 CT-TTCTTGACTTTG--CTTCATTTCTG
1917 CTTTCTTG
1 CTTTCTTG
1925 TTCATGCTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 12 0.40
26 11 0.37
27 7 0.23
ACGTcount: A:0.07, C:0.22, G:0.14, T:0.58
Consensus pattern (25 bp):
CTTTCTTGACTTTGCTTCATTTCTG
Found at i:2301 original size:50 final size:50
Alignment explanation
Indices: 2247--2441 Score: 327
Period size: 50 Copynumber: 3.9 Consensus size: 50
2237 TAAATGCCCT
2247 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAC
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAC
* * * *
2297 TTTGAAAAGCGAATTTTGACCTTGAACTCACAAATGGAAAGCAATTTTAC
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAC
*
2347 TTTGAAAAGCGAATTTTGATCTTGGCCTCACAAATGGAATGCAATCTTAC
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAC
* *
2397 TTTGAAAAGTGAATTTTGATCTTGGGCTCACAAATGGAATGCAAT
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAAT
2442 ATTATTCTAA
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAC
Found at i:3053 original size:7 final size:7
Alignment explanation
Indices: 3029--3073 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
3019 ATCAATTGTC
3029 TTTTGA-
1 TTTTGAT
3035 TTTTGA-
1 TTTTGAT
3041 TTTTGAT
1 TTTTGAT
3048 TTTTGAT
1 TTTTGAT
*
3055 TTTTGCT
1 TTTTGAT
3062 TTTTGAAT
1 TTTTG-AT
3070 TTTT
1 TTTT
3074 TTTTGAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 12 0.34
7 18 0.51
8 5 0.14
ACGTcount: A:0.13, C:0.02, G:0.13, T:0.71
Consensus pattern (7 bp):
TTTTGAT
Found at i:3462 original size:14 final size:14
Alignment explanation
Indices: 3443--3482 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3433 AAGTGCCTTT
*
3443 ATTTTCCTTTTTTC
1 ATTTTCATTTTTTC
3457 ATTTTCATTTTTTC
1 ATTTTCATTTTTTC
3471 AAATTTTCATTT
1 --ATTTTCATTT
3483 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTCATTTTTTC
Done.