Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015532.1 Corchorus capsularis cultivar CVL-1 contig15553, 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: 43425
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:597 original size:16 final size:17
Alignment explanation
Indices: 567--602 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
557 AATAAGAGAG
*
567 CTCACCCCTTCCTACCC
1 CTCACCCCTTCCTACAC
584 CTCACCCC-TCCTACAC
1 CTCACCCCTTCCTACAC
600 CTC
1 CTC
603 CAACCAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.14, C:0.64, G:0.00, T:0.22
Consensus pattern (17 bp):
CTCACCCCTTCCTACAC
Found at i:4281 original size:2 final size:2
Alignment explanation
Indices: 4274--4301 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4264 AACAACAATA
4274 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4302 CAACATGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:8608 original size:8 final size:8
Alignment explanation
Indices: 8595--8619 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
8585 CAAACAACAG
8595 AATTCAGA
1 AATTCAGA
8603 AATTCAGA
1 AATTCAGA
8611 AATTCAGA
1 AATTCAGA
8619 A
1 A
8620 CAGAATTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (8 bp):
AATTCAGA
Found at i:9704 original size:26 final size:26
Alignment explanation
Indices: 9675--9761 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
9665 TTGTAATATG
9675 CCAAATTAATGAACTCCAGTAAGAAA
1 CCAAATTAATGAACTCCAGTAAGAAA
* * * * *
9701 CCAAATTCA-CAAGT-CTGTCAACTTAATA
1 CCAAATTAATGAACTCCAGT-AA--GAA-A
*
9729 CCAAGTTAATGAACTCCAGTAAGAAA
1 CCAAATTAATGAACTCCAGTAAGAAA
9755 CCAAATT
1 CCAAATT
9762 CAAAAGTCTG
Statistics
Matches: 43, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
24 3 0.07
25 5 0.12
26 15 0.35
27 4 0.09
28 8 0.19
29 5 0.12
30 3 0.07
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (26 bp):
CCAAATTAATGAACTCCAGTAAGAAA
Found at i:9752 original size:54 final size:54
Alignment explanation
Indices: 9675--9784 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
9665 TTGTAATATG
*
9675 CCAAATTAATGAACTCCAGTAAGAAACCAAATTCACAAGTCTGTCAACTTAATA
1 CCAAATTAATGAACTCCAGTAAGAAACCAAATTCAAAAGTCTGTCAACTTAATA
*
9729 CCAAGTTAATGAACTCCAGTAAGAAACCAAATTCAAAAGTCTGTCAACTTAATA
1 CCAAATTAATGAACTCCAGTAAGAAACCAAATTCAAAAGTCTGTCAACTTAATA
9783 CC
1 CC
9785 TAGAATGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.24
Consensus pattern (54 bp):
CCAAATTAATGAACTCCAGTAAGAAACCAAATTCAAAAGTCTGTCAACTTAATA
Found at i:20664 original size:107 final size:106
Alignment explanation
Indices: 20451--20711 Score: 416
Period size: 107 Copynumber: 2.5 Consensus size: 106
20441 ATCTCCAACA
* * *
20451 AGTCAAAAGGGCAAGCAATTGT-AAAATTAGCTCTATACTTGACCTCAAGACCAAAGTTAATTGG
1 AGTCAAAAGGGCGAGCAATCGTAAAAATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTGG
20515 CGAGCGATTGATTTCACTATCCTCGACCCAATAAAAGCACG
66 CGAGCGATTGATTTCACTATCCTCGACCCAATAAAAGCACG
* *
20556 AGTCAAAAGGGCGAGCAATCGTAAAAATTAGCTCTATACTTGACCTCAGGACCAATGCTAATTGG
1 AGTCAAAAGGGCGAGCAATCGTAAAAATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTGG
* * *
20621 ACGGGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
66 -CGAGCGATTGATTTCACTATCCTCGACCCAATAAAAGCACG
* *
20663 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTTTATACTTGACCTCAA
1 AGTCAAAAGGGCGAGCAATCGTAAAAATTAGCTCTATACTTGACCTCAA
20712 AACTAAGGAT
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
105 20 0.14
106 39 0.27
107 84 0.59
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (106 bp):
AGTCAAAAGGGCGAGCAATCGTAAAAATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTGG
CGAGCGATTGATTTCACTATCCTCGACCCAATAAAAGCACG
Found at i:20882 original size:24 final size:24
Alignment explanation
Indices: 20855--20900 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
20845 ATGACCATCT
*
20855 CCAACAAGTCAAAAGGGTGAGCGA
1 CCAACAAGTCAAAAGGGCGAGCGA
20879 CCAACAAGTCAAAAGGGCGAGC
1 CCAACAAGTCAAAAGGGCGAGC
20901 AATTGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.28, T:0.07
Consensus pattern (24 bp):
CCAACAAGTCAAAAGGGCGAGCGA
Found at i:21495 original size:119 final size:119
Alignment explanation
Indices: 21241--22245 Score: 1407
Period size: 119 Copynumber: 8.5 Consensus size: 119
21231 CGCATGATGA
* * *
21241 CCAATCGCGCGGGTGAAGAATGCTTAATGAAGAGCACCGGATGCTCCCCTGAACACGTGCAACT-
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* * *
21305 CCCCAAGCACGTGAAATCACCAATGCGGGAAAGAAGAGCGCTCAATGAAGAGTG
66 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
* *
21359 ACAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACATGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* * *
21424 CTCGAAGCACGTGCAATCACCAATGTGCGAAAGAAGAGTGCTCAATGAAGAGTG
66 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
* * * * * *
21478 CCAACCGCGTGAATGAAGACTGATTAATGAAGAGAACCGAATGCTCCTCTGAACACGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
*
21543 CCCCAAGCACGTGCAATCACAAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
66 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
* * * *
21597 CCAACCGCGCGAATGAAGAATGTTTAATGAAGAGCATCGAATGCTCCTCTGAACACGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* * * * **
21662 CTCTAAGCACGTGCAATTACCAACGCGCGAAAGAAGAGTGCTCAATTTAGAGTG
66 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
* *
21716 CCGACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACATGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* * *
21781 CTCGAAGCACGTGCAATCACCAATGTGCGAAAGAAGAGTGCTCAATGAAGAGTG
66 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
* * *
21835 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCTCTGAACATGTGCAACAC
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* * * * **
21900 CCCTAAGCACGTGCAATTACCAACGCGCAAAAGAAGAGTGCTCAATTTAGAGTG
66 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
* * *
21954 CCGACCGCGCGAGTGAAGACTGATTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
22019 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
66 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
* * * ** *
22073 CCAACCGCGCGAGTGAAGCATGCTTAATGAAGAGCACCAAATGCTTCTTTGAACATGTGCAACTC
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
* * * * * **
22138 CCCTAAGCAGGTGCAATTACCAACGCGCGAAAGAAGAGTACTCAATTTAGAGTG
66 CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
* *
22192 CCGACCGTGCGAGTGAAGAATGC----T----AGCACCGAATGCTCCCCTGAACACGTGCAA
1 CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAA
22246 TCACCAATTT
Statistics
Matches: 792, Mismatches: 94, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
111 25 0.03
115 1 0.00
118 59 0.07
119 707 0.89
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (119 bp):
CCAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC
CCCCAAGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTG
Found at i:21664 original size:19 final size:19
Alignment explanation
Indices: 21640--21677 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
21630 GCATCGAATG
21640 CTCCTCTGAA-CACGTGCAA
1 CTCCTCT-AAGCACGTGCAA
21659 CTCCTCTAAGCACGTGCAA
1 CTCCTCTAAGCACGTGCAA
21678 TTACCAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (19 bp):
CTCCTCTAAGCACGTGCAA
Found at i:21694 original size:238 final size:238
Alignment explanation
Indices: 21246--22213 Score: 1551
Period size: 238 Copynumber: 4.1 Consensus size: 238
21236 GATGACCAAT
* * *
21246 CGCGCGGGTGAAGAATGCTTAATGAAGAGCACCGGATGCTCCCCTGAACACGTGCAACT-CCCCA
1 CGCGCGAGTGAAGAATGATTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTCCCCCA
* * * *
21310 AGCACGTGAAATCACCAATGCGGGAAAGAAGAGCGCTCAATGAAGAGTGACAACCGCGCGAGTGA
66 AGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGA
* * *
21375 AGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACATGTGCAACTCCTCGAAGCACGTGCAA
131 AGAATGCTTAATGAAGAGCACCGAATGCTCCTCTGAACATGTGCAACTCCCCTAAGCACGTGCAA
* * * ** *
21440 TCACCAATGTGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAAC
196 TTACCAACGCGCGAAAGAAGAGTGCTCAATTTAGAGTGCCGAC
* * * * *
21483 CGCGTGAATGAAGACTGATTAATGAAGAGAACCGAATGCTCCTCTGAACACGTGCAACTCCCCCA
1 CGCGCGAGTGAAGAATGATTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTCCCCCA
* *
21548 AGCACGTGCAATCACAAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAATGA
66 AGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGA
* * * *
21613 AGAATGTTTAATGAAGAGCATCGAATGCTCCTCTGAACACGTGCAACTCCTCTAAGCACGTGCAA
131 AGAATGCTTAATGAAGAGCACCGAATGCTCCTCTGAACATGTGCAACTCCCCTAAGCACGTGCAA
21678 TTACCAACGCGCGAAAGAAGAGTGCTCAATTTAGAGTGCCGAC
196 TTACCAACGCGCGAAAGAAGAGTGCTCAATTTAGAGTGCCGAC
* * * *
21721 CGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACATGTGCAACTCCTCGA
1 CGCGCGAGTGAAGAATGATTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTCCCCCA
*
21786 AGCACGTGCAATCACCAATGTGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGA
66 AGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGA
*
21851 AGAATGCTTAATGAAGAGCACCGAATGCTCCTCTGAACATGTGCAACACCCCTAAGCACGTGCAA
131 AGAATGCTTAATGAAGAGCACCGAATGCTCCTCTGAACATGTGCAACTCCCCTAAGCACGTGCAA
*
21916 TTACCAACGCGCAAAAGAAGAGTGCTCAATTTAGAGTGCCGAC
196 TTACCAACGCGCGAAAGAAGAGTGCTCAATTTAGAGTGCCGAC
*
21959 CGCGCGAGTGAAGACTGATTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTCCCCCA
1 CGCGCGAGTGAAGAATGATTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTCCCCCA
22024 AGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGA
66 AGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGA
* * * * *
22089 AGCATGCTTAATGAAGAGCACCAAATGCTTCTTTGAACATGTGCAACTCCCCTAAGCAGGTGCAA
131 AGAATGCTTAATGAAGAGCACCGAATGCTCCTCTGAACATGTGCAACTCCCCTAAGCACGTGCAA
*
22154 TTACCAACGCGCGAAAGAAGAGTACTCAATTTAGAGTGCCGAC
196 TTACCAACGCGCGAAAGAAGAGTGCTCAATTTAGAGTGCCGAC
*
22197 CGTGCGAGTGAAGAATG
1 CGCGCGAGTGAAGAATG
22214 CTAGCACCGA
Statistics
Matches: 671, Mismatches: 59, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
237 51 0.08
238 620 0.92
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (238 bp):
CGCGCGAGTGAAGAATGATTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTCCCCCA
AGCACGTGCAATCACCAATGCGCGAAAGAAGAGTGCTCAATGAAGAGTGCCAACCGCGCGAGTGA
AGAATGCTTAATGAAGAGCACCGAATGCTCCTCTGAACATGTGCAACTCCCCTAAGCACGTGCAA
TTACCAACGCGCGAAAGAAGAGTGCTCAATTTAGAGTGCCGAC
Found at i:23655 original size:19 final size:21
Alignment explanation
Indices: 23608--23655 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
23598 TGTGGCACGC
*
23608 CACATGTACCAAAAAGTCGTG
1 CACATGTACCAAAAAGTCGTA
23629 CTACATGTACCAAAAAGT-G-A
1 C-ACATGTACCAAAAAGTCGTA
23649 CACATGT
1 CACATGT
23656 CACACCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 2 0.08
22 16 0.64
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (21 bp):
CACATGTACCAAAAAGTCGTA
Found at i:27527 original size:32 final size:31
Alignment explanation
Indices: 27486--27572 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 31
27476 TTTTTTATAT
27486 CTAATTTGAACTAAAACAGAGGATTTCGAAAC
1 CTAATTTGAAC-AAAACAGAGGATTTCGAAAC
*
27518 CTAATTTGAAGACAAAA-AGAGGGTTTTCGAAAC
1 CTAATTTG-A-ACAAAACAGA-GGATTTCGAAAC
*
27551 CTATTTTGAAGCAAAAACAGAG
1 CTAATTTGAA-C-AAAACAGAG
27573 ATATTTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
31 1 0.02
32 13 0.28
33 28 0.60
34 5 0.11
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (31 bp):
CTAATTTGAACAAAACAGAGGATTTCGAAAC
Found at i:31131 original size:3 final size:3
Alignment explanation
Indices: 31118--31149 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31108 TCGTCTCCCG
*
31118 TGA TTA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
31150 CCCATGCGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (3 bp):
TGA
Found at i:31626 original size:16 final size:16
Alignment explanation
Indices: 31585--31629 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
31575 AAAGAAAAGG
*
31585 TTTTTGTTTTT-GTTT
1 TTTTTGTTTTTCCTTT
31600 TTTTTGGGTTTTTCCTTT
1 TTTTT--GTTTTTCCTTT
31618 TTTTTGTTTTTC
1 TTTTTGTTTTTC
31630 TTTGAAACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 6 0.23
18 8 0.31
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (16 bp):
TTTTTGTTTTTCCTTT
Found at i:35673 original size:2 final size:2
Alignment explanation
Indices: 35662--35799 Score: 50
Period size: 2 Copynumber: 75.5 Consensus size: 2
35652 TAGATATTTT
* *
35662 TA TA TA -A TA TA TA TT TA -A AA TA TA T- TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
35700 T- TA TA TA TG TT TT TA T- TA TA TA TA AA TA AA TA -A AA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
35739 -A AA TA TA T- TA TA AA TA TA T- TT TA TA TA AA TA TA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
35777 AA TA TA T- TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
35800 GTTTTTATTA
Statistics
Matches: 101, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
1 13 0.13
2 88 0.87
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35748 original size:46 final size:46
Alignment explanation
Indices: 35696--35837 Score: 164
Period size: 46 Copynumber: 3.1 Consensus size: 46
35686 TTATATATAT
35696 TATATTATATATGTTTTTATTATATATAAATAAATAAAATTTAAAA
1 TATATTATATATGTTTTTATTATATATAAATAAATAAAATTTAAAA
* * * ** * *
35742 TATATTATAAATATATTTTA-TATA-A-ATATATTTAAAATATATTATA
1 TATATTATATATGT-TTTTATTATATATAAATAAATAAAAT-T-TAAAA
*
35788 TATATTATATATGTTTTTATTATGTATAAATAAATAAAATTTAAAA
1 TATATTATATATGTTTTTATTATATATAAATAAATAAAATTTAAAA
35834 TATA
1 TATA
35838 GTTTAAATAT
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
44 10 0.13
45 7 0.09
46 41 0.55
47 7 0.09
48 10 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (46 bp):
TATATTATATATGTTTTTATTATATATAAATAAATAAAATTTAAAA
Found at i:35775 original size:37 final size:36
Alignment explanation
Indices: 35712--35799 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 36
35702 ATATATGTTT
*
35712 TTAT-TATA-TATAAATAAATAAAATTTAAAATATA
1 TTATATATATTATATATAAATAAAATTTAAAATATA
* *
35746 TTATAAATATATTTTATATAAAT-ATATTTAAAATATA
1 TTAT--ATATATTATATATAAATAAAATTTAAAATATA
35783 TTATATATATTATATAT
1 TTATATATATTATATAT
35800 GTTTTTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.09
35 12 0.26
37 21 0.46
38 9 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (36 bp):
TTATATATATTATATATAAATAAAATTTAAAATATA
Found at i:35816 original size:92 final size:98
Alignment explanation
Indices: 35655--35851 Score: 320
Period size: 92 Copynumber: 2.1 Consensus size: 98
35645 AACCGAATAG
35655 ATAT-TTTTATATAATATATATTTAAAATATATTATATATATTATATTATATATGTTTTTATTAT
1 ATATATTTTATATAATATATATTTAAAATATATTATATATATTATATTATATATGTTTTTATTAT
35719 ATATAAATAAATAAAATTTAAAATATA-TTATAA
66 ATATAAATAAATAAAATTTAAAATATAGTT-TAA
35752 ATATATTTTATATAA-ATATATTT-AAA-ATA-TAT-TATA-TATATTATATATGTTTTTATTAT
1 ATATATTTTATATAATATATATTTAAAATATATTATATATATTATATTATATATGTTTTTATTAT
*
35811 GTATAAATAAATAAAATTTAAAATATAGTTTAA
66 ATATAAATAAATAAAATTTAAAATATAGTTTAA
35844 ATATATTT
1 ATATATTT
35852 AGAGAACCGA
Statistics
Matches: 97, Mismatches: 1, Indels: 9
0.91 0.01 0.08
Matches are distributed among these distances:
92 60 0.62
93 6 0.06
94 3 0.03
95 3 0.03
96 3 0.03
97 12 0.12
98 10 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (98 bp):
ATATATTTTATATAATATATATTTAAAATATATTATATATATTATATTATATATGTTTTTATTAT
ATATAAATAAATAAAATTTAAAATATAGTTTAA
Found at i:38144 original size:6 final size:6
Alignment explanation
Indices: 38135--38164 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
38125 ACATATATAT
38135 ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA
38165 CACAACCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
ATATGA
Done.