Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014092.1 Corchorus olitorius cultivar O-4 contig14125, 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: 21923
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Found at i:561 original size:14 final size:14
Alignment explanation
Indices: 542--571 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
532 ATAGATGCAA
542 TTGAGCATATATAT
1 TTGAGCATATATAT
556 TTGAGCATATATAT
1 TTGAGCATATATAT
570 TT
1 TT
572 TAGGTGCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
TTGAGCATATATAT
Found at i:8013 original size:54 final size:53
Alignment explanation
Indices: 7952--8118 Score: 141
Period size: 54 Copynumber: 3.2 Consensus size: 53
7942 TGAGATTGTA
7952 ACAAGATCCAAGAAGATGCCATTTGATCCATTGAGTATGCCATTGGGTCTTATG
1 ACAAGAT-CAAGAAGATGCCATTTGATCCATTGAGTATGCCATTGGGTCTTATG
* *** * * ** * * * * *
8006 ACAAGATC---AAGA-GCTAAAAGGTTCAAGGAGATAT--CAATGAG-ATTGTA
1 ACAAGATCAAGAAGATGCCATTTGATCCATTGAG-TATGCCATTGGGTCTTATG
8053 ACAAGATCCAAGAAGATGCCATTTGATCCATTGAGTATGCCATTGGGTCTTATG
1 ACAAGAT-CAAGAAGATGCCATTTGATCCATTGAGTATGCCATTGGGTCTTATG
8107 ACAAGATCAAGA
1 ACAAGATCAAGA
8119 GCTAAAAGGT
Statistics
Matches: 78, Mismatches: 26, Indels: 19
0.63 0.21 0.15
Matches are distributed among these distances:
47 10 0.13
48 6 0.08
49 10 0.13
50 7 0.09
51 7 0.09
52 10 0.13
53 11 0.14
54 17 0.22
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (53 bp):
ACAAGATCAAGAAGATGCCATTTGATCCATTGAGTATGCCATTGGGTCTTATG
Found at i:8102 original size:101 final size:101
Alignment explanation
Indices: 7927--8135 Score: 418
Period size: 101 Copynumber: 2.1 Consensus size: 101
7917 TGCATGGAGA
7927 TCAAGGAGATATCAATGAGATTGTAACAAGATCCAAGAAGATGCCATTTGATCCATTGAGTATGC
1 TCAAGGAGATATCAATGAGATTGTAACAAGATCCAAGAAGATGCCATTTGATCCATTGAGTATGC
7992 CATTGGGTCTTATGACAAGATCAAGAGCTAAAAGGT
66 CATTGGGTCTTATGACAAGATCAAGAGCTAAAAGGT
8028 TCAAGGAGATATCAATGAGATTGTAACAAGATCCAAGAAGATGCCATTTGATCCATTGAGTATGC
1 TCAAGGAGATATCAATGAGATTGTAACAAGATCCAAGAAGATGCCATTTGATCCATTGAGTATGC
8093 CATTGGGTCTTATGACAAGATCAAGAGCTAAAAGGT
66 CATTGGGTCTTATGACAAGATCAAGAGCTAAAAGGT
8129 TCAAGGA
1 TCAAGGA
8136 TGCACTTATG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 108 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (101 bp):
TCAAGGAGATATCAATGAGATTGTAACAAGATCCAAGAAGATGCCATTTGATCCATTGAGTATGC
CATTGGGTCTTATGACAAGATCAAGAGCTAAAAGGT
Found at i:9264 original size:26 final size:26
Alignment explanation
Indices: 9224--9273 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
9214 AAAAATTGGC
9224 GGTTTTGGAGGTTATTTGGGGATTAG
1 GGTTTTGGAGGTTATTTGGGGATTAG
*
9250 GGTTTTGGAGTTTATTTGGGGATT
1 GGTTTTGGAGGTTATTTGGGGATT
9274 TCTTGATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.40, T:0.46
Consensus pattern (26 bp):
GGTTTTGGAGGTTATTTGGGGATTAG
Found at i:9774 original size:2 final size:2
Alignment explanation
Indices: 9767--9837 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
9757 TGGTAAACAA
9767 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
* *
9809 GT GT GT GT GT GT GT GT GT TT GT GT TT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
9838 AGGATTTTCT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
GT
Found at i:15755 original size:49 final size:49
Alignment explanation
Indices: 15698--16165 Score: 717
Period size: 49 Copynumber: 9.6 Consensus size: 49
15688 ACAGAATTAA
* * * *
15698 CCAAAGTGCCCTTCCTGGTCGGAAGGTATTGTTTTTACTTGTCTTGTTT
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
* *
15747 CCAAAGTGCCCTACCCGGTCGGAAGGTGTTGGTTTTACTTGTCTTATTC
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
*
15796 CCAAAATGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
* *
15845 CCAAACTGCCCTTCCCGGTCGGAAGGTGTTGTTCTTACTTGTCTTATTC
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
* *
15894 CCAAAGTGCCCTTCCTGGTCGGAAGGTGTTGTTGTTACTTGTCTTATTC
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
*
15943 CCAAAGTGTCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
* ** *
15992 CCAAAGTGCCCTTTCTAGACGGAAGGTGTTGTTTTTACTTGTCTTATTC
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
16041 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
* *
16090 CCAAAATGCCCTTCCCGGTCAGAAGGTGTTAG-TTTTA-TT-TCATTATTC
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTGTT-GTTTTTACTTGTC-TTATTC
* *
16138 CCAAAATGCCCTTCCCGGTCGGATGGTG
1 CCAAAGTGCCCTTCCCGGTCGGAAGGTG
16166 CGAGTTTGTC
Statistics
Matches: 387, Mismatches: 30, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
47 2 0.01
48 34 0.09
49 350 0.90
50 1 0.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (49 bp):
CCAAAGTGCCCTTCCCGGTCGGAAGGTGTTGTTTTTACTTGTCTTATTC
Found at i:16355 original size:47 final size:47
Alignment explanation
Indices: 16273--16429 Score: 167
Period size: 47 Copynumber: 3.3 Consensus size: 47
16263 GTTTTTACTT
* * *
16273 TTCCCAAAATGCCCTTTCCAGTC-AAAAGGCGTTAGTTTTACTTCATTA
1 TTCCCAAAATGCCC-TCCCAATCGGAAA-GCGTTAGTTTTACTTCATTA
* * *
16321 CTCCCAAAACGCCCTCCCAATCGGAGAGCGTTAGTTTTACTTGC-TT-
1 TTCCCAAAATGCCCTCCCAATCGGAAAGCGTTAGTTTTACTT-CATTA
* * *
16367 TTCGCAAAATGCCCCTCCTAGTCGGAAAGCGTTAGTTTTACTTCATTA
1 TTCCCAAAATG-CCCTCCCAATCGGAAAGCGTTAGTTTTACTTCATTA
*
16415 TTTCCAAAATGCCCT
1 TTCCCAAAATGCCCT
16430 TCCCGGTCGG
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
46 9 0.10
47 57 0.63
48 24 0.27
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (47 bp):
TTCCCAAAATGCCCTCCCAATCGGAAAGCGTTAGTTTTACTTCATTA
Found at i:16516 original size:94 final size:92
Alignment explanation
Indices: 16039--16664 Score: 344
Period size: 94 Copynumber: 6.7 Consensus size: 92
16029 CTTGTCTTAT
* ** * *
16039 TCCCAAAGTGCCCTTCCCGGTCGGAAGGTG-TTGTTTTTACTTGTCTTATTCCCAAAATGCCCTT
1 TCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAG-TTTT-CTTAT-TT-TT-CCAAAATTCCCTT
* * ** * *
16103 CCCGGTCAGAAGGTGTTAGTTTTATTTCA-TTA
61 CCCAGTCGGAAGGTGCCAGTTTTCTAT-ATTTA
* * *
16135 TTCCCAAAATGCCCTTCCCGGTCGGATGGTGCGAGTTTGTCTTTATTTGTTCCAAAATGCCCTTC
1 -TCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTT-TC-TTATTT-TTCCAAAATTCCCTTC
* * *
16200 TCGGTCGGAAGGTGCCAG-TTT-TA-CTTT-
62 CCAGTCGGAAGGTGCCAGTTTTCTATATTTA
* * * * * * *
16227 TCCCAAGATGCTCTTCCCGGTCGGAAGGTGCCTGTTGTTTTTACTTTTCCCAAAATGCCCTTTCC
1 TCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTT-TTCTTA-TTTTTCCAAAATTCCCTTCCC
** * **
16292 AGTCAAAAGGCGTTAGTTTTACT-TCA-TTA
64 AGTCGGAAGGTGCCAGTTTT-CTAT-ATTTA
* ** * ** * *
16321 CTCCCAAAACGCCC-TCCCAATCGGAGAGCGT--TAGTTTTACTTGCTTTTCGCAAAATGCCCCT
1 -TCCCAAAATGCCCTTCCCGGTCGGA-AG-GTGCCAGTTTT-CTTATTTTTC-CAAAATTCCCTT
* * * **
16383 CCTAGTCGGAAAGCGTTAGTTTTACT-TCA-TTA
61 CCCAGTCGGAAGGTGCCAGTTTT-CTAT-ATTTA
* *
16415 TTTCCAAAATGCCCTTCCCGGTCGGAAGTTGCCAGTTTTTCTTTATTTGTTCCAAAATTCCCTTC
1 -TCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAG-TTTTC-TTATTT-TTCCAAAATTCCCTTC
* *
16480 CCAGTTGGAAGGTGCCGGTTTTC-ATATTTA
62 CCAGTCGGAAGGTGCCAGTTTTCTATATTTA
* * * ** *
16510 TCCCAAAATACCCTTCCCGGTCGGGAGGTGCCAGTTTTCCTTCTTTATTCCCAAAACACTCTTCC
1 TCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTT-CTTATTT-TT-CCAAAATTCCCTTCC
* * *
16575 CGGTCGGAAGGTGCCAGTTTTCTTTATTTG
63 CAGTCGGAAGGTGCCAGTTTTCTATATTTA
* * * * * * *
16605 TTCCAAAATGTCCTTCCCAGTCAGAAGGTGTCAGTTTTCTTATTTTTCCCAAATTGCCTT
1 TCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTATTTTTCCAAAATTCCCTT
16665 TCTCGGTCGG
Statistics
Matches: 411, Mismatches: 90, Indels: 61
0.73 0.16 0.11
Matches are distributed among these distances:
90 28 0.07
91 38 0.09
92 9 0.02
93 25 0.06
94 135 0.33
95 68 0.17
96 64 0.16
97 39 0.09
98 5 0.01
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (92 bp):
TCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTATTTTTCCAAAATTCCCTTCCCAG
TCGGAAGGTGCCAGTTTTCTATATTTA
Found at i:16621 original size:47 final size:46
Alignment explanation
Indices: 15744--16680 Score: 405
Period size: 49 Copynumber: 19.7 Consensus size: 46
15734 ACTTGTCTTG
* * *** *
15744 TTTCCAAAGTGCCCTACCCGGTCGGAAGGTGTTGGTTTTACTTGTCTT
1 TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTT-CTT-TATT
* ** *
15792 ATTCCCAAAATGCCCTTCCCGGTCGGAAGGTG-TTGTTTTTACTTGTCTT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAG-TTTT-CTT-TATT
* * ** *
15841 ATTCCCAAACTGCCCTTCCCGGTCGGAAGGTG-TTGTTCTTACTTGTCTT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTT-TT-CTT-TATT
* * * ** *
15890 ATTCCCAAAGTGCCCTTCCTGGTCGGAAGGTG-TTGTTGTTACTTGTCTT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTT-TT-CTT-TATT
* * * ** *
15939 ATTCCCAAAGTGTCCTTCCCGGTCGGAAGGTG-TTGTTTTTACTTGTCTT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAG-TTTT-CTT-TATT
* * * ** * ** *
15988 ATTCCCAAAGTGCCCTTTCTAGACGGAAGGTG-TTGTTTTTACTTGTCTT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAG-TTTT-CTT-TATT
* * ** *
16037 ATTCCCAAAGTGCCCTTCCCGGTCGGAAGGTG-TTGTTTTTACTTGTCTT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAG-TTTT-CTT-TATT
* * ** *
16086 ATTCCCAAAATGCCCTTCCCGGTCAGAAGGTGTTAGTTTTATTTCATT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTT-ATT
* * *
16134 ATTCCCAAAATGCCCTTCCCGGTCGGATGGTGCGAGTTTGTCTTTATT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTT-TCTTTATT
*
16182 TGTTCCAAAATGCCCTTCTCGGTCGGAAGGTGCCAG---T-TTTACTT
1 T-TTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTA-TT
* * * *
16226 TTCCCAAGATGCTCTTCCCGGTCGGAAGGTGCCTGTTGTT-TTTACTT
1 TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTT-TTCTTTA-TT
* * * ** * ** *
16273 TTCCCAAAATGCCCTTTCCAGTCAAAAGGCGTTAGTTTTACTTCATT
1 TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTT-CTTTATT
* * * ** * **
16320 ACTCCCAAAACGCCC-TCCCAATCGGAGAGCGT--TAGTTTTAC-TTGCT
1 -TTTCCAAAATGCCCTTCCCGGTCGGA-AG-GTGCCAGTTTT-CTTTATT
* ** * * ** *
16366 TTTCGCAAAATGCCCCTCCTAGTCGGAAAGCGTTAGTTTTACTTCATT
1 TTTC-CAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTT-CTTTATT
*
16414 ATTTCCAAAATGCCCTTCCCGGTCGGAAGTTGCCAGTTTTTCTTTATT
1 -TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAG-TTTTCTTTATT
* * * * *
16462 TGTTCCAAAATTCCCTTCCCAGTTGGAAGGTGCCGGTTTTC-ATATT
1 T-TTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTATT
* * * * *
16508 TATCCCAAAATACCCTTCCCGGTCGGGAGGTGCCAGTTTTCCTTCTT
1 T-TTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTATT
** *
16555 TATTCCCAAAACACTCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTATT
1 T-TT-CCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTATT
* * * *
16603 TGTTCCAAAATGTCCTTCCCAGTCAGAAGGTGTCAGTTTTC-TTATT
1 T-TTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTATT
* * * *
16649 TTTCCCAAATTGCCTTTCTCGGTCGGGAGGTG
1 TTT-CCAAAATGCCCTTCCCGGTCGGAAGGTG
16681 TGACCGGTCG
Statistics
Matches: 746, Mismatches: 114, Indels: 59
0.81 0.12 0.06
Matches are distributed among these distances:
43 33 0.04
44 4 0.01
45 5 0.01
46 79 0.11
47 115 0.15
48 194 0.26
49 312 0.42
50 4 0.01
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (46 bp):
TTTCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTATT
Found at i:16706 original size:141 final size:142
Alignment explanation
Indices: 16428--16706 Score: 319
Period size: 141 Copynumber: 2.0 Consensus size: 142
16418 CCAAAATGCC
* **
16428 CTTCCCGGTCGGAAGTTGCCAGTTTTTCTTTATTTGTTCCAAAATTCCCTTCCCAGTTGGAAGGT
1 CTTCCCGGTCGGAAGGTGCCAGTTTTTCTTTATTTGTTCCAAAATTCCCTTCCCAGTCAGAAGGT
* **** **** *
16493 GCCGGTTTTCATATTTATCCCAAAATACCCTTCCCGGTCGGGAGGTGCCAGTTTTCCTTCTTTAT
66 GCCAGTTTTCATATTTATCCCAAAATACCCTTCCCGGTCGGGAGGTGCCACCGGTCCTTAGCAAA
*
16558 TCCCAAAACACT
131 TCACAAAACACT
16570 CTTCCCGGTCGGAAGGTGCCAG-TTTTCTTTATTTGTTCCAAAATGT-CCTTCCCAGTCAGAAGG
1 CTTCCCGGTCGGAAGGTGCCAGTTTTTCTTTATTTGTTCCAAAAT-TCCCTTCCCAGTCAGAAGG
* * * * * * * ** *
16633 TGTCAGTTTTCTTATTTTTCCCAAATTGCCTTTCTCGGTCGGGAGGTGTGACCGGTCGTTAGCAA
65 TGCCAGTTTTCATATTTATCCCAAAATACCCTTCCCGGTCGGGAGGTGCCACCGGTCCTTAGCAA
16698 ATCACAAAA
130 ATCACAAAA
16707 TAATCCCCAC
Statistics
Matches: 112, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
141 90 0.80
142 22 0.20
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (142 bp):
CTTCCCGGTCGGAAGGTGCCAGTTTTTCTTTATTTGTTCCAAAATTCCCTTCCCAGTCAGAAGGT
GCCAGTTTTCATATTTATCCCAAAATACCCTTCCCGGTCGGGAGGTGCCACCGGTCCTTAGCAAA
TCACAAAACACT
Found at i:19781 original size:16 final size:15
Alignment explanation
Indices: 19760--19806 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
19750 GGGAATAAGC
19760 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
19775 TAATCAATCAAAGCAA
1 -AATCAATCAAAGCAA
19791 AA-CAATACAAAG-AA
1 AATCAAT-CAAAGCAA
19805 AA
1 AA
19807 AGTAAATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 15 0.50
ACGTcount: A:0.64, C:0.17, G:0.06, T:0.13
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Done.