Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006805.1 Corchorus capsularis cultivar CVL-1 contig06826, 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: 15955
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:438 original size:95 final size:97
Alignment explanation
Indices: 313--486 Score: 316
Period size: 95 Copynumber: 1.8 Consensus size: 97
303 TTTTCTGGAT
*
313 ATCTAGTAATTAATTATTTACATATTACATATTAATCC-TTAAAATATAAAATT-AAAATTTTAA
1 ATCTAATAATTAATTATTTACATATTACATATTAATCCATTAAAATATAAAATTGAAAATTTTAA
376 AATTAAAAGGGTATATAAAAGTAATTCTAGAG
66 AATTAAAAGGGTATATAAAAGTAATTCTAGAG
*
408 ATCTAATAATTAATTATTTACATATTACATATTAATCCATTAAAATGTAAAATTGAAAATTTTAA
1 ATCTAATAATTAATTATTTACATATTACATATTAATCCATTAAAATATAAAATTGAAAATTTTAA
473 AATTAAAAGGGTAT
66 AATTAAAAGGGTAT
487 TTTAGATATT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
95 37 0.49
96 14 0.19
97 24 0.32
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (97 bp):
ATCTAATAATTAATTATTTACATATTACATATTAATCCATTAAAATATAAAATTGAAAATTTTAA
AATTAAAAGGGTATATAAAAGTAATTCTAGAG
Found at i:536 original size:2 final size:2
Alignment explanation
Indices: 525--581 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
515 AGTTTAGACT
* *
525 TA TA TA -A TA TA TA TA TA TA TA TA GA TA TA GA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
565 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
582 TTTGGAAGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1169 original size:24 final size:23
Alignment explanation
Indices: 1126--1172 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1116 ATTATGTGCC
* *
1126 AAAAAAAACTATCATTATTATTA
1 AAAAAAAACAATCATCATTATTA
1149 AAAAAAAACAATGCATCATTATTA
1 AAAAAAAACAAT-CATCATTATTA
1173 TTTTATGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAAAACAATCATCATTATTA
Found at i:8795 original size:30 final size:30
Alignment explanation
Indices: 8759--8820 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
8749 AAAAAAAATT
*
8759 AATACAAATGAGAACTTGGGTCAAGTCAAG
1 AATACAAATGAGAACTTGAGTCAAGTCAAG
8789 AATACAAATGAGAACTTGAGTCAAGTCAAG
1 AATACAAATGAGAACTTGAGTCAAGTCAAG
8819 AA
1 AA
8821 ATAAACTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (30 bp):
AATACAAATGAGAACTTGAGTCAAGTCAAG
Found at i:9411 original size:109 final size:109
Alignment explanation
Indices: 9238--9444 Score: 299
Period size: 109 Copynumber: 1.9 Consensus size: 109
9228 ACCATCAGAT
** * * *
9238 CAATTGCAGCTTCATAACTTGATCCTCAATTTTCTACGCTTGAAGAATTTTCCATGAAAATGGTG
1 CAATTGCAGCTT-ATAACTTGATCCAAAATTTTCTACGCTAGAAAAAATTTCCATGAAAATGGTG
* *
9303 TATTAATTGAGTTGATGAAGATATTTGTCTTGTTCACCAACCGAC
65 CATTAATTGAGTTGATGAAGATAGTTGTCTTGTTCACCAACCGAC
* *
9348 CAATTGCAGCTT-TAACTTGATCCAAAAGTTTTCTAGGCTAGAAAAAATTTCCATGAAAGTGGTG
1 CAATTGCAGCTTATAACTTGATCCAAAA-TTTTCTACGCTAGAAAAAATTTCCATGAAAATGGTG
*
9412 CATTAATTGGGTTGATGAAGATAGTTGTCTTGT
65 CATTAATTGAGTTGATGAAGATAGTTGTCTTGT
9445 CCACAAAATG
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
108 13 0.15
109 61 0.71
110 12 0.14
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (109 bp):
CAATTGCAGCTTATAACTTGATCCAAAATTTTCTACGCTAGAAAAAATTTCCATGAAAATGGTGC
ATTAATTGAGTTGATGAAGATAGTTGTCTTGTTCACCAACCGAC
Found at i:9862 original size:17 final size:19
Alignment explanation
Indices: 9832--9868 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9822 TGCCGTGAAA
9832 AAAATGTGCTAAAAA-GAT
1 AAAATGTGCTAAAAATGAT
9850 AAAATGT-CTAAAAATGAT
1 AAAATGTGCTAAAAATGAT
9868 A
1 A
9869 TATTAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (19 bp):
AAAATGTGCTAAAAATGAT
Found at i:15496 original size:72 final size:71
Alignment explanation
Indices: 15420--15931 Score: 192
Period size: 72 Copynumber: 7.1 Consensus size: 71
15410 TTGGTTAAGT
*
15420 TTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAGAT
1 TTCCAATCGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTA-TCAATTCAAGATCGGTAAGAGAT
15485 TTAAGCA
65 TTAAGCA
**** * * * * * ** * ** *
15492 TTCCAATCTCTTCAGGTATTGACCCAGAAAGCTTATT--T-TCAA-AGAGGTAAAGAGT-AGACA
1 TTCCAATCGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTATCAATTCAAG-ATCG-GTAAGA-G
* *
15552 ATTTGGTTAG-G
63 A-TT--TAAGCA
* *
15563 TGTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTAGTCAATTTAAGATCGGTAAGAGA
1 T-TCCAATCGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTA-TCAATTCAAGATCGGTAAGAGA
15628 TTTAAGCA
64 TTTAAGCA
**** * * * * * * * * * *
15636 TTCCAATCTCTTCAGGTATTGACCCAAAAAG-CTGATTTGTATGAAGGTAAAGA---GT-AGACA
1 TTCCAATCGAGGCAGGGATTGAGCCAGAGAGATTG-TTGGTATCAA-TTCAAGATCGGTAAGA-G
* **
15696 ATTTGGTTAGGT
63 A-TT--TAAGCA
* *
15708 TTCCAATAGAGGTAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAGAT
1 TTCCAATCGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTA-TCAATTCAAGATCGGTAAGAGAT
15773 TTAAGCA
65 TTAAGCA
**** * * * * * * * * *
15780 TTCCAATCTCTTCAGGTATTGACCCAGAAAG-CTGATTTGTATGAAGGTAAAGA---GT-AGACA
1 TTCCAATCGAGGCAGGGATTGAGCCAGAGAGATTG-TTGGTATCAA-TTCAAGATCGGTAAGA-G
* **
15840 ATTTGGTTAGGT
63 A-TT--TAAGCA
*
15852 TTCCAATAGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAGAT
1 TTCCAATCGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTA-TCAATTCAAGATCGGTAAGAGAT
15917 TTAAGCA
65 TTAAGCA
*
15924 TCCCAATC
1 TTCCAATC
15932 TCTTCAGGTA
Statistics
Matches: 292, Mismatches: 110, Indels: 76
0.61 0.23 0.16
Matches are distributed among these distances:
67 2 0.01
68 15 0.05
69 9 0.03
70 7 0.02
71 11 0.04
72 204 0.70
73 11 0.04
74 7 0.02
75 9 0.03
76 15 0.05
77 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (71 bp):
TTCCAATCGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTATCAATTCAAGATCGGTAAGAGATT
TAAGCA
Found at i:15540 original size:144 final size:144
Alignment explanation
Indices: 15274--15954 Score: 1105
Period size: 144 Copynumber: 4.7 Consensus size: 144
15264 GACTCGTCAA
* * * * *
15274 GTTTCCAATGGAGGCGGGGATTAAGCCAAAGAGATTGTTGGTACTCAATTCAAGATGGGTAACAG
1 GTTTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
* * * * **
15339 ATCTAAGCATCCCAATCTCTTTAGGTATTGACCCAGAAAGTTGATTTGTTTGAAGGTAAAGAGTA
66 ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAGAAAGCTGATTTGTAAGAAGGTAAAGAGTA
* *
15404 TACAATTTGGTTAA
131 GACAATTTGGTTAG
15418 GTTTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
1 GTTTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
*
15483 ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAGAAAGCTTATTT-TCAA-AGAGGTAAAGAG
66 ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAGAAAGCTGATTTGT-AAGA-AGGTAAAGAG
15546 TAGACAATTTGGTTAG
129 TAGACAATTTGGTTAG
* * *
15562 GTGTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTAGTCAATTTAAGATCGGTAAGAG
1 GTTTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
* *
15627 ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAAAAAGCTGATTTGTATGAAGGTAAAGAGTA
66 ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAGAAAGCTGATTTGTAAGAAGGTAAAGAGTA
15692 GACAATTTGGTTAG
131 GACAATTTGGTTAG
* *
15706 GTTTCCAATAGAGGTAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
1 GTTTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
*
15771 ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAGAAAGCTGATTTGTATGAAGGTAAAGAGTA
66 ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAGAAAGCTGATTTGTAAGAAGGTAAAGAGTA
15836 GACAATTTGGTTAG
131 GACAATTTGGTTAG
*
15850 GTTTCCAATAGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
1 GTTTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
* *
15915 ATTTAAGCATCCCAATCTCTTCAGGTATTGACGCAGAAAG
66 ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAGAAAG
15955 T
Statistics
Matches: 504, Mismatches: 29, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
143 2 0.00
144 500 0.99
145 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (144 bp):
GTTTCCAATGGAGGCAGGGATTGAGCCAGAGAGATTGTTGGTACTCAATTCAAGATCGGTAAGAG
ATTTAAGCATTCCAATCTCTTCAGGTATTGACCCAGAAAGCTGATTTGTAAGAAGGTAAAGAGTA
GACAATTTGGTTAG
Done.