Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011284.1 Corchorus capsularis cultivar CVL-1 contig11305, 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: 33021
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:6678 original size:2 final size:2
Alignment explanation
Indices: 6673--6721 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
6663 GTATACAAAT
* *
6673 TA TA TA TA GA TA GTA TA TA TA TA CA TA T- TA TA TA 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
6715 TA TA TA T
1 TA TA TA T
6722 TAAAAGCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6693 original size:15 final size:14
Alignment explanation
Indices: 6664--6721 Score: 66
Period size: 13 Copynumber: 4.2 Consensus size: 14
6654 TTTTTTGGGG
*
6664 TATACAAAT-TATA
1 TATACATATATATA
*
6677 TATAGATAGTATATA
1 TATACATA-TATATA
6692 TATACATAT-TATA
1 TATACATATATATA
*
6705 TATATATATATATA
1 TATACATATATATA
6719 TAT
1 TAT
6722 TAAAAGCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
13 18 0.47
14 9 0.24
15 11 0.29
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (14 bp):
TATACATATATATA
Found at i:13576 original size:20 final size:19
Alignment explanation
Indices: 13551--13592 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13541 GATCTGTCGG
13551 GTTTAGTCAATTTTGAGTCA
1 GTTTAGT-AATTTTGAGTCA
**
13571 GTTTAGTTTTTTTGAGTCA
1 GTTTAGTAATTTTGAGTCA
13590 GTT
1 GTT
13593 AGTTTGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.52
Consensus pattern (19 bp):
GTTTAGTAATTTTGAGTCA
Found at i:13594 original size:18 final size:19
Alignment explanation
Indices: 13561--13597 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13551 GTTTAGTCAA
13561 TTTTGAGTCAGTTTAGTTT
1 TTTTGAGTCAGTTTAGTTT
13580 TTTTGAGTCAG-TTAGTTT
1 TTTTGAGTCAGTTTAGTTT
13598 GAGTCTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.57
Consensus pattern (19 bp):
TTTTGAGTCAGTTTAGTTT
Found at i:17120 original size:2 final size:2
Alignment explanation
Indices: 17113--17144 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17103 TTTCCGGAAC
17113 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17145 GGATTTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18871 original size:3 final size:3
Alignment explanation
Indices: 18863--18902 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
18853 TATATTATAC
18863 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
18903 CTTATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19905 original size:17 final size:18
Alignment explanation
Indices: 19861--19906 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
19851 GAAATTTTGA
*
19861 GAAATTATCAAAACAAGT
1 GAAATTATAAAAACAAGT
* *
19879 TAAAAT-TAAAAACAA-T
1 GAAATTATAAAAACAAGT
19895 GAAATTATAAAA
1 GAAATTATAAAA
19907 GCAGGGAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (18 bp):
GAAATTATAAAAACAAGT
Found at i:19906 original size:16 final size:17
Alignment explanation
Indices: 19861--19906 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 17
19851 GAAATTTTGA
19861 GAAATTATCAAAACAAGTT
1 GAAATTAT-AAAACAAG-T
*
19880 AAAATTA-AAAACAA-T
1 GAAATTATAAAACAAGT
19895 GAAATTATAAAA
1 GAAATTATAAAA
19907 GCAGGGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 7 0.29
16 4 0.17
17 7 0.29
19 6 0.25
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (17 bp):
GAAATTATAAAACAAGT
Found at i:26939 original size:18 final size:18
Alignment explanation
Indices: 26916--26956 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
26906 TATTGGGATA
26916 GAGTTTTAGAAAATTGAT
1 GAGTTTTAGAAAATTGAT
26934 GAGTTTTAGAAAATTGAT
1 GAGTTTTAGAAAATTGAT
26952 GAGTT
1 GAGTT
26957 GTCTTCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (18 bp):
GAGTTTTAGAAAATTGAT
Found at i:27544 original size:28 final size:28
Alignment explanation
Indices: 27504--27561 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
27494 TCCCTGCCCC
27504 TACATAATTTTTACTATAGTTTTTAATA
1 TACATAATTTTTACTATAGTTTTTAATA
27532 TACATAATTTTTACTATAGTTTTTAATA
1 TACATAATTTTTACTATAGTTTTTAATA
27560 TA
1 TA
27562 TTTGTTGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.53
Consensus pattern (28 bp):
TACATAATTTTTACTATAGTTTTTAATA
Found at i:27776 original size:22 final size:22
Alignment explanation
Indices: 27735--27776 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27725 AATGCTTTGG
*
27735 ACATATATAATAACATAATGTC
1 ACATATATAATAACACAATGTC
*
27757 ACATATATAATAAGACAATG
1 ACATATATAATAACACAATG
27777 AGCTATACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (22 bp):
ACATATATAATAACACAATGTC
Found at i:28012 original size:2 final size:2
Alignment explanation
Indices: 28005--28043 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
27995 TAGTTTATGG
*
28005 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28044 ATTAGTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29196 original size:13 final size:13
Alignment explanation
Indices: 29178--29205 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29168 ACTTATGAAA
29178 TTTATTGAAAAAT
1 TTTATTGAAAAAT
29191 TTTATTGAAAAAT
1 TTTATTGAAAAAT
29204 TT
1 TT
29206 CGATTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTATTGAAAAAT
Found at i:32218 original size:6 final size:6
Alignment explanation
Indices: 32209--32241 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
32199 AAAGCAAAGC
32209 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
32242 GCAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:32253 original size:12 final size:13
Alignment explanation
Indices: 32238--32282 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
32228 AATCTAAATC
32238 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
32250 TAAAGCAAATTAA
1 TAAAGCAGATTAA
32263 TAAAGCAGATTAA
1 TAAAGCAGATTAA
32276 TAAAGCA
1 TAAAGCA
32283 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:32289 original size:25 final size:25
Alignment explanation
Indices: 32238--32290 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
32228 AATCTAAATC
*
32238 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
32263 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
32288 TAA
1 TAA
32291 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Done.