Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020024.1 Corchorus olitorius cultivar O-4 contig20057, 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: 98137
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:325 original size:17 final size:17
Alignment explanation
Indices: 305--356 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
295 AAAATAAAGT
305 AAAGGGCAAAATAGTCC
1 AAAGGGCAAAATAGTCC
*
322 AAAGGG--GAA-AGT--
1 AAAGGGCAAAATAGTCC
334 AAAGGGCAAAATAGTCC
1 AAAGGGCAAAATAGTCC
351 AAAGGG
1 AAAGGG
357 GGGCGGTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
12 6 0.21
14 5 0.18
15 5 0.18
17 12 0.43
ACGTcount: A:0.48, C:0.12, G:0.31, T:0.10
Consensus pattern (17 bp):
AAAGGGCAAAATAGTCC
Found at i:342 original size:29 final size:29
Alignment explanation
Indices: 300--357 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
290 TGAAGAAAAT
300 AAAGTAAAGGGCAAAATAGTCCAAAGGGG
1 AAAGTAAAGGGCAAAATAGTCCAAAGGGG
329 AAAGTAAAGGGCAAAATAGTCCAAAGGGG
1 AAAGTAAAGGGCAAAATAGTCCAAAGGGG
358 GGCGGTGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.31, T:0.10
Consensus pattern (29 bp):
AAAGTAAAGGGCAAAATAGTCCAAAGGGG
Found at i:886 original size:93 final size:93
Alignment explanation
Indices: 727--913 Score: 331
Period size: 93 Copynumber: 2.0 Consensus size: 93
717 TTGTTATTAT
*
727 ATCTTCTATACTAATTATAAAGTCAAGTCCTGAGTTTGTGTCACAAGTTAACTCGGACACAAACT
1 ATCTTCTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACAAGTTAACTCGGACACAAACT
*
792 CATTTTTTAAAAAATTCAAAACAAAATA
66 CAGTTTTTAAAAAATTCAAAACAAAATA
*
820 ATCTTCTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGAA-TCGGACACAAAC
1 ATCTTCTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACAAGTT-AACTCGGACACAAAC
884 TCAGTTTTTAAAAAATTCAAAACAAAATA
65 TCAGTTTTTAAAAAATTCAAAACAAAATA
913 A
1 A
914 AAACTACCGA
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 88 0.98
94 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (93 bp):
ATCTTCTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACAAGTTAACTCGGACACAAACT
CAGTTTTTAAAAAATTCAAAACAAAATA
Found at i:1691 original size:14 final size:14
Alignment explanation
Indices: 1662--1706 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1652 TAGAGGATTG
1662 TACTTATTATATTAC
1 TACTTATTA-ATTAC
*
1677 TACTAATTAATTAC
1 TACTTATTAATTAC
* *
1691 TAATTACTAATTAC
1 TACTTATTAATTAC
1705 TA
1 TA
1707 TATAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (14 bp):
TACTTATTAATTAC
Found at i:4060 original size:121 final size:126
Alignment explanation
Indices: 3930--4181 Score: 327
Period size: 121 Copynumber: 2.0 Consensus size: 126
3920 ATTTAAGAAA
* *
3930 TATATTTAAAAAATTCTAATAT-TCTAAGTTGTTAAATTAAATTAGTAAAATGATAAAAATAAAA
1 TATATTT-AAAAATTCTAATATATATAAGTTGTTAAATTAAAATAGTAAAATGATAAAAATAAAA
* *
3994 TAGATATAAGGATATT-A-AA-T-A-AAAAATAGATTTTTTAGTTGAGTAAAACTATAAAAG
65 TAGATATAAGAATATTAATAATTAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
* * * *
4051 TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAAT
1 TATATTTAAAAATTCTAATATATATAAGTTGTTAAATTAAAATAGTAAAATGATAAAAATAAAAT
* *
4116 AGTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAG
66 AGATATAAGAATATTA-A--TAATT-AATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
4181 T
1 T
4182 TTAAAAAATG
Statistics
Matches: 111, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
120 14 0.13
121 57 0.51
123 1 0.01
126 2 0.02
127 1 0.01
129 1 0.01
130 35 0.32
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.38
Consensus pattern (126 bp):
TATATTTAAAAATTCTAATATATATAAGTTGTTAAATTAAAATAGTAAAATGATAAAAATAAAAT
AGATATAAGAATATTAATAATTAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:9331 original size:19 final size:19
Alignment explanation
Indices: 9307--9347 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
9297 TTTTTAACTT
9307 AATTTGTTAAAAAAATTTA
1 AATTTGTTAAAAAAATTTA
9326 AATTTGTTAAAAAAATTTA
1 AATTTGTTAAAAAAATTTA
9345 AAT
1 AAT
9348 AGTTAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AATTTGTTAAAAAAATTTA
Found at i:9352 original size:18 final size:19
Alignment explanation
Indices: 9307--9353 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
9297 TTTTTAACTT
*
9307 AATTTGTTAAAAAAATTTA
1 AATTAGTTAAAAAAATTTA
*
9326 AATTTGTTAAAAAAATTTA
1 AATTAGTTAAAAAAATTTA
9345 AA-TAGTTAA
1 AATTAGTTAA
9354 TGATTAGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
AATTAGTTAAAAAAATTTA
Found at i:10277 original size:16 final size:17
Alignment explanation
Indices: 10249--10285 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
10239 GTACTTTTAT
10249 ATATAGTATAGATATAG
1 ATATAGTATAGATATAG
*
10266 ATATAG-ATAGATTTAG
1 ATATAGTATAGATATAG
10282 ATAT
1 ATAT
10286 CGTGTATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (17 bp):
ATATAGTATAGATATAG
Found at i:11906 original size:33 final size:33
Alignment explanation
Indices: 11864--11935 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
11854 GCGGGACGCA
11864 CCCTACCGTGGTTGGGCGCCTCCTGGGGATGCC
1 CCCTACCGTGGTTGGGCGCCTCCTGGGGATGCC
11897 CCCTACCGTGGTTGGGCGCCTCCTGGGGATGCC
1 CCCTACCGTGGTTGGGCGCCTCCTGGGGATGCC
11930 CCCTAC
1 CCCTAC
11936 GCGGAGGCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.07, C:0.39, G:0.33, T:0.21
Consensus pattern (33 bp):
CCCTACCGTGGTTGGGCGCCTCCTGGGGATGCC
Found at i:14286 original size:32 final size:30
Alignment explanation
Indices: 14250--14339 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 30
14240 ATCGAGGGGT
*
14250 AAAATGTCTTAAATTTGGAAAGTTCATGGGAC
1 AAAATGTCCT-AATTTGG-AAGTTCATGGGAC
* * **
14282 AAAATGTCCCCAATTTGGAAGTTCAGGGGGT
1 AAAATGT-CCTAATTTGGAAGTTCATGGGAC
*
14313 AAAACGTCCTAATTT-GAAGTTCATGGG
1 AAAATGTCCTAATTTGGAAGTTCATGGG
14340 TAAAAACGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 11 0.22
30 7 0.14
31 16 0.33
32 14 0.29
33 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (30 bp):
AAAATGTCCTAATTTGGAAGTTCATGGGAC
Found at i:14334 original size:29 final size:30
Alignment explanation
Indices: 14244--14351 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 30
14234 CCCTTCATCG
* *
14244 AGGGGT-AAAATGTCTTAAATTTGGAAAGTTC
1 AGGGGTAAAAACGTCCT-AATTTGG-AAGTTC
* * *
14275 ATGGG-ACAAAATGTCCCCAATTTGGAAGTTC
1 AGGGGTA-AAAACGT-CCTAATTTGGAAGTTC
14306 AGGGGGT-AAAACGTCCTAATTT-GAAGTTC
1 A-GGGGTAAAAACGTCCTAATTTGGAAGTTC
*
14335 ATGGGTAAAAACGTCCT
1 AGGGGTAAAAACGTCCT
14352 TGACGCAATA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
28 4 0.06
29 18 0.28
30 7 0.11
31 17 0.27
32 17 0.27
33 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
AGGGGTAAAAACGTCCTAATTTGGAAGTTC
Found at i:14702 original size:24 final size:25
Alignment explanation
Indices: 14649--14703 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
14639 ATTTATCAAG
* *
14649 TCGAACTCGAGCTCGAACTTGATGT
1 TCGAATTCGAGCTCGAACTCGATGT
14674 T-GAATTCGAGCTC-AAGCTCGA-GT
1 TCGAATTCGAGCTCGAA-CTCGATGT
14697 TCGAATT
1 TCGAATT
14704 TGAACTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 20 0.77
25 1 0.04
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (25 bp):
TCGAATTCGAGCTCGAACTCGATGT
Found at i:20751 original size:34 final size:34
Alignment explanation
Indices: 20708--20780 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
20698 TTTAGGGTCC
* *
20708 TCGTTAGCTTTGCTGGAGCTGTTATTAAGGACGA
1 TCGTTAGCTTTGCTGGAGCTGTCAGTAAGGACGA
*
20742 TCGTTAGCTTTGCTGGAGTTGTCAGTAAGGACGA
1 TCGTTAGCTTTGCTGGAGCTGTCAGTAAGGACGA
20776 TCGTT
1 TCGTT
20781 CTTCAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.36
Consensus pattern (34 bp):
TCGTTAGCTTTGCTGGAGCTGTCAGTAAGGACGA
Found at i:28408 original size:30 final size:30
Alignment explanation
Indices: 28374--28440 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
28364 CAAACAAGCT
28374 TCAAATTGCAGAAATCAAGT-ATATCCAGTC
1 TCAAATTGCAGAAATCAAGTAATAT-CAGTC
* ** *
28404 TCAAATAGCATCAATCCAGTAATATCAGTC
1 TCAAATTGCAGAAATCAAGTAATATCAGTC
28434 TCAAATT
1 TCAAATT
28441 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.28
Consensus pattern (30 bp):
TCAAATTGCAGAAATCAAGTAATATCAGTC
Found at i:30740 original size:28 final size:27
Alignment explanation
Indices: 30646--30745 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
30636 GTGATCCTAG
* *
30646 AATGACCAAAATGCCCCTGAACATGCA
1 AATGACCAAAATGCCCCTGGATATGCA
* *
30673 AATGACCAAAATGCCCCTGGATGTGCG
1 AATGACCAAAATGCCCCTGGATATGCA
* *
30700 AATGACCAAAATGCCCCTGGATTTTGAA
1 AATGACCAAAATGCCCCTGGA-TATGCA
30728 AATGACCAAAATGCCCCT
1 AATGACCAAAATGCCCCT
30746 AGATGACCCT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 44 0.68
28 21 0.32
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTGGATATGCA
Found at i:31412 original size:27 final size:27
Alignment explanation
Indices: 31381--31454 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 27
31371 AGGATCAACT
* *
31381 AAGGGCATTTCGGTTATTTTCAAAATCC
1 AAGGGCATTTCGGTCATTTGCAAAAT-C
* * * *
31409 AGGGGCATTTTGGTCATTTGCACATTC
1 AAGGGCATTTCGGTCATTTGCAAAATC
**
31436 AAGGGCATTTTAGTCATTT
1 AAGGGCATTTCGGTCATTT
31455 TAAGTCCACT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 18 0.47
28 20 0.53
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (27 bp):
AAGGGCATTTCGGTCATTTGCAAAATC
Found at i:33179 original size:1 final size:1
Alignment explanation
Indices: 33173--33200 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
33163 ATCTGACCAG
33173 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
33201 CTAACCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39497 original size:34 final size:34
Alignment explanation
Indices: 39454--39538 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
39444 CTGCTCATTA
39454 GAACCATTAGCAGTCTCTCGCCAACAAAAAAAAT
1 GAACCATTAGCAGTCTCTCGCCAACAAAAAAAAT
*
39488 GAACCATTAGCAGTCTCTCGCCAACAAAAACAAT
1 GAACCATTAGCAGTCTCTCGCCAACAAAAAAAAT
39522 GAACCATTAGCAGTCTC
1 GAACCATTAGCAGTCTC
39539 CTCTGATCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (34 bp):
GAACCATTAGCAGTCTCTCGCCAACAAAAAAAAT
Found at i:43192 original size:26 final size:26
Alignment explanation
Indices: 43139--43192 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
43129 AAAAGTCACC
**
43139 CAGGGGCATTTCGGTCATTTTTGCTT
1 CAGGGGCATTTCGGTCATTTTTAATT
*
43165 CAGGGGCACTTT-TGTCATTTTTAATT
1 CAGGGGCA-TTTCGGTCATTTTTAATT
43191 CA
1 CA
43193 TTGCTAGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.43
Consensus pattern (26 bp):
CAGGGGCATTTCGGTCATTTTTAATT
Found at i:45198 original size:2 final size:2
Alignment explanation
Indices: 45191--45219 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45181 GCACTGGGAG
45191 TA TA TA 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 T
45220 GCAATAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46166 original size:51 final size:51
Alignment explanation
Indices: 46122--46352 Score: 392
Period size: 51 Copynumber: 4.5 Consensus size: 51
46112 TAAAGGCTTA
*
46122 ATTTTTAAGTGAAAAATTGAAGCTTTTAAATAATTTGTAAATAAAGATTGG
1 ATTTTTAAGTGAAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGG
46173 ATTTTTAAGTGAAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGG
1 ATTTTTAAGTGAAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGG
*
46224 ATTTTCAAGTGAAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGG
1 ATTTTTAAGTGAAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGG
* * *
46275 ATTTTTAAGTGAAACATTTAAGCTTTTAAGTAATTTGTGAATAAAGATTGG
1 ATTTTTAAGTGAAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGG
* *
46326 ATTTTTAAGTGAAAGATT-AATCTTTTA
1 ATTTTTAAGTGAAAAATTGAAGCTTTTA
46353 TCTAAAGTTT
Statistics
Matches: 172, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 8 0.05
51 164 0.95
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.40
Consensus pattern (51 bp):
ATTTTTAAGTGAAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGG
Found at i:47425 original size:47 final size:47
Alignment explanation
Indices: 47354--47835 Score: 614
Period size: 47 Copynumber: 10.7 Consensus size: 47
47344 CTGTTTTCTT
47354 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
* *
47401 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA----A--TT-
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
* *
47441 CCTAGTTTGCCCTTACCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
*
47488 CCCAGTTTGCCCTTCCCCA-CTGGAAGGTGTTGTTTAA----A--TT-
1 CCCAGTTTGCCCTTCCCCATC-GGAAGGTGTTGTCTAAGTCTACTTTA
47528 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
*
47575 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG-CTTAA----A--TT-
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTC-TAAGTCTACTTTA
47615 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
* *
47662 CCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTACTTTA
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
* *
47709 CCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTACTTTA
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
* * * *
47756 CCCAATTTGCCCTTCCCCATCGGAAGGTATTGTTTGAGTCTACTTTA
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
* * * * *
47803 CCCAATTTGTCATTCCTCATCGGAAGGCGTTGT
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGT
47836 TCATATTCCC
Statistics
Matches: 389, Mismatches: 21, Indels: 50
0.85 0.05 0.11
Matches are distributed among these distances:
40 101 0.26
41 8 0.02
43 3 0.01
44 3 0.01
46 8 0.02
47 266 0.68
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (47 bp):
CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTA
Found at i:47469 original size:87 final size:87
Alignment explanation
Indices: 47352--47790 Score: 716
Period size: 87 Copynumber: 5.0 Consensus size: 87
47342 CCCTGTTTTC
47352 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCTTCC
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCTTCC
47417 CCACCGGAAGGTGTTGTTTAAA
66 CCACCGGAAGGTGTTGTTTAAA
* *
47439 TTCCTAGTTTGCCCTTACCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCTTCC
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCTTCC
*
47504 CCACTGGAAGGTGTTGTTTAAA
66 CCACCGGAAGGTGTTGTTTAAA
47526 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCTTCC
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCTTCC
*
47591 CCACCGGAAGGTGTTGCTTAAA
66 CCACCGGAAGGTGTTGTTTAAA
*
47613 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTTCC
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCTTCC
*
47678 CCATCGGAAGGTGTTGTTTAAGTCTA
66 CCACCGGAAGGTGTTGTTTAA----A
* * *
47704 CTTTACCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTCTACTTTACCCAATTTGCCCT
1 --TT-CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCT
* *
47769 TCCCCATCGGAAGGTATTGTTT
63 TCCCCACCGGAAGGTGTTGTTT
47791 GAGTCTACTT
Statistics
Matches: 332, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
87 250 0.75
91 1 0.00
93 2 0.01
94 79 0.24
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.35
Consensus pattern (87 bp):
TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAGTTTGCCCTTCC
CCACCGGAAGGTGTTGTTTAAA
Found at i:49438 original size:42 final size:43
Alignment explanation
Indices: 49391--49478 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 43
49381 ATTACCTAAA
* *
49391 TCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATAT
1 TCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAATAT
49433 TCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTAATAT
1 TCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTAATAT
49478 T
1 T
49479 AATTGTTGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 4 0.10
45 37 0.90
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (43 bp):
TCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAATAT
Found at i:60889 original size:27 final size:26
Alignment explanation
Indices: 60859--60942 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 26
60849 GTACAGCCAC
60859 CGGTAAGTTCATCT-CAAGTTTTTCCTG
1 CGGTAA-TTCATCTCCAA-TTTTTCCTG
*
60886 CGGTGAATTCATTTCCAATTTTTCCTG
1 CGGT-AATTCATCTCCAATTTTTCCTG
* *
60913 CGGTAATTGATTCTCCAGA-TCTTCCTG
1 CGGTAATTCA-TCTCCA-ATTTTTCCTG
60940 CGG
1 CGG
60943 CTTCCACTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
26 5 0.10
27 38 0.78
28 6 0.12
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (26 bp):
CGGTAATTCATCTCCAATTTTTCCTG
Found at i:65989 original size:19 final size:18
Alignment explanation
Indices: 65962--65997 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
65952 TGGGCTTTAT
65962 ATCAAATTGCATATTTTTC
1 ATCAAATTGCAT-TTTTTC
*
65981 ATCACATTGCATTTTTT
1 ATCAAATTGCATTTTTT
65998 AGTTTATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (18 bp):
ATCAAATTGCATTTTTTC
Found at i:69489 original size:47 final size:48
Alignment explanation
Indices: 69444--70214 Score: 567
Period size: 47 Copynumber: 16.2 Consensus size: 48
69434 AGAGTAAAAG
* *
69444 AAGAAGTAAACATAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAACGT
1 AAGAAG-AAAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATA-GT
* * * * *
69494 AAG-AGAAGAAGAAAAG--AGTTTAATTCCGAGTAATTAAACTAAAAAGT
1 AAGAAG-A-AAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
* * * *
69541 AAG-AGAAGAAGAAAAG--AGTTTAATTCTGGGTAATTAAACTAAAAAAT
1 AAGAAG-A-AAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
* * * * *
69588 AAG-AGAAGAAGAAAAG--AGTTTAATTCTGGGTAATTAGACTAAAGAGC
1 AAGAAG-A-AAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
** * * *
69635 AAG-AGAAGAAGA-AAAC-AATTTAATTCTGGGTAATTAGACTAAAAAGT
1 AAGAAG-A-AAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
* * *
69682 AA-AAG-AAGAAGAGGTTAGTTTAATTCTGGGAAATTAAACTAAATAGT
1 AAGAAGAAAG-ATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
**
69729 AA-AAG-AAGA-AGATGCTAGTTTAATTCTGAATAATTAAACTAAATAGT
1 AAGAAGAAAGATAG--GCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
*
69776 AA-AAGAAGAGGAT--GCTAGTTTAATTGTGGGTAATTAAACTAAATAGT
1 AAGAAGAA-A-GATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
*
69823 GAAAGAAG-AGGAT--GCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
1 --AAGAAGAAAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
69870 AAAAGAAGAAA-ATA--CTAGTTTAATTCTGGGTAATTAAACTAAATAAGT
1 --AAGAAGAAAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAAT-AGT
* *
69918 AA-AAGAAGAGGAT-GACTAGTTTAATTCTGGGTAAATAAACTAAATAGT
1 AAGAAGAA-A-GATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
*
69966 GAAAGAAG-AGGAT--GCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
1 --AAGAAGAAAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
* * * *
70013 AAAAAGAAGAGGAT--GATGGTTTAATTCTGGGTGATTAAACTAAATAGT
1 AAGAAGAA-A-GATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
* *
70061 AA-AAG-AAGA-AGAGTTTAGTTTAATTCTGGGTGATTAAACTAAATAGT
1 AAGAAGAAAGATAG-G-CTAGTTTAATTCTGGGTAATTAAACTAAATAGT
*
70108 AA-AAG-AAGA-AGAGGTCAGTTTAATTCTGGGTAATTAAACTAAATAGT
1 AAGAAGAAAGATAG-GCT-AGTTTAATTCTGGGTAATTAAACTAAATAGT
* * * * * *
70155 AAAAGAAGTAAGCAGAGACTGGTTTAATTCTGGGTAACTAAACTAAAGAGT
1 --AAGAAGAAAG-ATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
*
70206 AAAAAGAAA
1 AAGAAGAAA
70215 AAGTAAACAG
Statistics
Matches: 626, Mismatches: 55, Indels: 81
0.82 0.07 0.11
Matches are distributed among these distances:
44 5 0.01
45 14 0.02
46 11 0.02
47 418 0.67
48 76 0.12
49 45 0.07
50 19 0.03
51 34 0.05
52 2 0.00
53 2 0.00
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (48 bp):
AAGAAGAAAGATAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT
Found at i:69623 original size:94 final size:94
Alignment explanation
Indices: 69460--70209 Score: 857
Period size: 94 Copynumber: 7.9 Consensus size: 94
69450 TAAACATAGG
* * * * * *
69460 CTAGTTTAATTCTGGGTAATTAAACTAAAAACGTAAGAGAAGAAGAAAAGAGTTTAATTCCGAGT
1 CTAGTTTAATTCTGGGTAATTAAACTAAATA-GTAAAAGAAGAAGAAGATAGTTTAATTCTGGGT
* * *
69525 AATTAAACTAAAAAGTAAGAGAAGAAGAAA
65 AATTAAACTAAATAGTAAAAGAAGAAGAGA
** * * * * *
69555 AGAGTTTAATTCTGGGTAATTAAACTAAAAAATAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTA
1 CTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAGATAGTTTAATTCTGGGTA
* * * * *
69620 ATTAGACTAAAGAGCAAGAGAAGAAGAAAA
66 ATTAAACTAAATAGTAAAAGAAGAAG-AGA
* * * * * *
69650 C-AATTTAATTCTGGGTAATTAGACTAAAAAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGAA
1 CTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAGATAGTTTAATTCTGGGTA
69714 ATTAAACTAAATAGTAAAAGAAGAAGATG-
66 ATTAAACTAAATAGTAAAAGAAGAAGA-GA
** * * * *
69743 CTAGTTTAATTCTGAATAATTAAACTAAATAGTAAAAGAAGAGGATGCTAGTTTAATTGTGGGTA
1 CTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAGATAGTTTAATTCTGGGTA
* *
69808 ATTAAACTAAATAGTGAAAGAAGAGGATG-
66 ATTAAACTAAATAGTAAAAGAAGAAGA-GA
*
69837 CTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAA-AATACTAGTTTAATTCTGGGT
1 CTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAGA-TAGTTTAATTCTGGGT
*
69901 AATTAAACTAAATAAGTAAAAGAAGAGGATGA
65 AATTAAACTAAAT-AGTAAAAGAAGAAGA-GA
* * * * *
69933 CTAGTTTAATTCTGGGTAAATAAACTAAATAGTGAAAGAAGAGGATGCTAGTTTAATTCTGGGTA
1 CTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAGATAGTTTAATTCTGGGTA
*
69998 ATTAAACTAAATAGTAAAAAGAAGAGGATGA
66 ATTAAACTAAATAGT-AAAAGAAGAAGA-GA
* * *
70029 -TGGTTTAATTCTGGGTGATTAAACTAAATAGTAAAAGAAGAAG-AGTTTAGTTTAATTCTGGGT
1 CTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAG-ATAGTTTAATTCTGGGT
*
70092 GATTAAACTAAATAGTAAAAGAAGAAGAG-
65 AATTAAACTAAATAGTAAAAGAAGAAGAGA
* *
70121 GTCAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGTAAGCAGAGACTGGTTTAATTCT
1 CT-AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAG-AAG-A-AGA-TAGTTTAATTCT
* *
70186 GGGTAACTAAACTAAAGAGTAAAA
61 GGGTAATTAAACTAAATAGTAAAA
70210 AGAAAAAGTA
Statistics
Matches: 574, Mismatches: 65, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
93 5 0.01
94 327 0.57
95 123 0.21
96 84 0.15
97 1 0.00
98 34 0.06
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (94 bp):
CTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGAAGATAGTTTAATTCTGGGTA
ATTAAACTAAATAGTAAAAGAAGAAGAGA
Found at i:69676 original size:141 final size:140
Alignment explanation
Indices: 69462--70225 Score: 816
Period size: 141 Copynumber: 5.4 Consensus size: 140
69452 AACATAGGCT
* * * *
69462 AGTTTAATTCTGGGTAATTAAACTAAAAACGTAAGAGAAGAAGAAAAGAGTTTAATTCCGAGTAA
1 AGTTTAATTCTGGGTAATTAAACTAAAAA-GTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAA
* **** * * *
69527 TTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAAAATAAGA
65 TTAAACTAAATAGTAA-AGAAGAAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAA
69592 GAAGAAGAAAAG
129 GAAGAAGAAAAG
* * * * *
69604 AGTTTAATTCTGGGTAATTAGACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTGGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAAT
* * * *
69669 TAGACTAAAAAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGAAATTAAACTAAATAGTAAAAG
66 TAAACTAAATAGT-AAAGAAGAAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAG
****
69734 AAGAAGATGCT
130 AAGAAGAAAAG
** * * ** *
69745 AGTTTAATTCTGAATAATTAAACTAAATAGTAAAAGAAG-AGGATGCTAGTTTAATTGTGGGTAA
1 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAC-AGTTTAATTCTGGGTAA
* *
69809 TTAAACTAAATAGTGAAAGAAGAGGATGCTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAA
65 TTAAACTAAATAGT-AAAGAAGAAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAA
**
69874 GAAGAA-AATACT
129 GAAGAAGAA-AAG
* **
69886 AGTTTAATTCTGGGTAATTAAACTAAATAAGTAAAAGAAGAGGATGACTAGTTTAATTCTGGGTA
1 AGTTTAATTCTGGGTAATTAAACTAAA-AAGTAAAAGAAGAAGAAAAC-AGTTTAATTCTGGGTA
* * *
69951 AATAAACTAAATAGTGAAAGAAGAGGATGCTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA
64 ATTAAACTAAATAGT-AAAGAAGAAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGT-AA
* * *
70016 AAGAAGAGGATGATG
127 AAGAAGAAGA-AAAG
* * **** *
70031 -GTTTAATTCTGGGTGATTAAACTAAATAGTAAAAGAAGAAGAGTTTAGTTTAATTCTGGGTGAT
1 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAAT
70095 TAAACTAAATAGTAAAAGAAGAAGAGG-TCAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAA
66 TAAACTAAATAGT-AAAGAAGAAGAGGCT-AGTTTAATTCTGGGTAATTAAACTAAATAGTAAAA
* *
70159 GAAGTAAGCAGAG
129 GAAG-AAGAAAAG
* * * *
70172 ACTGGTTTAATTCTGGGTAACTAAACTAAAGAGTAAAAAGAAAAAGTAAACAGT
1 A---GTTTAATTCTGGGTAATTAAACTAAAAAGT-AAAAGAAGAAGAAAACAGT
70226 AATTTCTAAT
Statistics
Matches: 527, Mismatches: 80, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
140 5 0.01
141 240 0.46
142 113 0.21
143 93 0.18
144 34 0.06
145 29 0.06
146 13 0.02
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (140 bp):
AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAAT
TAAACTAAATAGTAAAGAAGAAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGA
AGAAGAAAAG
Found at i:71506 original size:15 final size:16
Alignment explanation
Indices: 71478--71507 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
71468 TGGACACGTT
71478 TTGTACTATTGTAATG
1 TTGTACTATTGTAATG
71494 TTGTACT-TTGTAAT
1 TTGTACTATTGTAAT
71508 CTGTAGTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (16 bp):
TTGTACTATTGTAATG
Found at i:77554 original size:51 final size:51
Alignment explanation
Indices: 77454--77555 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
77444 GTTCTTCATA
* *
77454 TTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGTTT
1 TTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGTTT
* * *
77505 TTTTCTTGTTTCA-ATCTTGTCTCCGGAC-ATAAAAACACTGTATTCGTGTTT
1 TTTTCTTGTTT-AGATCTTGTCTCAGGACAAT-AAAACACTCTATTAGTGTTT
77556 CTCTTTCAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
50 2 0.05
51 41 0.93
52 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.46
Consensus pattern (51 bp):
TTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGTTT
Found at i:83868 original size:46 final size:46
Alignment explanation
Indices: 83808--83908 Score: 195
Period size: 46 Copynumber: 2.2 Consensus size: 46
83798 TTGTCTTTGG
83808 GTTTTATTTCAGCAACTTTGAGGAACTTGTCTCCTCTAATCTTTAT
1 GTTTTATTTCAGCAACTTTGAGGAACTTGTCTCCTCTAATCTTTAT
83854 GTTTTATTTCAGCAACTTTGAGGAACTTGTCTCCTCTAATCTTTAT
1 GTTTTATTTCAGCAACTTTGAGGAACTTGTCTCCTCTAATCTTTAT
83900 G-TTTATTTC
1 GTTTTATTTC
83909 TGATTTAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 8 0.15
46 47 0.85
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.48
Consensus pattern (46 bp):
GTTTTATTTCAGCAACTTTGAGGAACTTGTCTCCTCTAATCTTTAT
Found at i:84316 original size:42 final size:42
Alignment explanation
Indices: 84257--84466 Score: 420
Period size: 42 Copynumber: 5.0 Consensus size: 42
84247 CATACCATAT
84257 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
1 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
84299 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
1 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
84341 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
1 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
84383 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
1 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
84425 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
1 GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
84467 ATATATCTTT
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 168 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (42 bp):
GAATTCATTTGTGTAAAAAGATTAGTTTCAAAGATATTTTCC
Found at i:85202 original size:22 final size:22
Alignment explanation
Indices: 85160--85216 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
85150 GTTCTGGTTT
*
85160 GAAACCGAAACCGTATAGAATC
1 GAAACCGAAACCGTACAGAATC
* *
85182 GAAACCGAAACCGTACGGAATT
1 GAAACCGAAACCGTACAGAATC
* *
85204 GGAACCGGAACCG
1 GAAACCGAAACCG
85217 AAACCTTACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.11
Consensus pattern (22 bp):
GAAACCGAAACCGTACAGAATC
Found at i:85992 original size:119 final size:119
Alignment explanation
Indices: 85781--86023 Score: 486
Period size: 119 Copynumber: 2.0 Consensus size: 119
85771 ATACTATATA
85781 TACTACTACATATTATTTGAAACACCCAATAAAATTACTAAACACCCCTTTTGAGGATCGATAAG
1 TACTACTACATATTATTTGAAACACCCAATAAAATTACTAAACACCCCTTTTGAGGATCGATAAG
85846 GAGGCTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCATTTGCCAAAT
66 GAGGCTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCATTTGCCAAAT
85900 TACTACTACATATTATTTGAAACACCCAATAAAATTACTAAACACCCCTTTTGAGGATCGATAAG
1 TACTACTACATATTATTTGAAACACCCAATAAAATTACTAAACACCCCTTTTGAGGATCGATAAG
85965 GAGGCTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCATTTGCCAAAT
66 GAGGCTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCATTTGCCAAAT
86019 TACTA
1 TACTA
86024 AGAAGACCCT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 124 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (119 bp):
TACTACTACATATTATTTGAAACACCCAATAAAATTACTAAACACCCCTTTTGAGGATCGATAAG
GAGGCTCCATTTGAACTTTTTTTGTCCTTTTCTGTCTTTTCTCATTTGCCAAAT
Found at i:86260 original size:42 final size:42
Alignment explanation
Indices: 86213--86293 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
86203 TAAGGATCAG
86213 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
86255 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTC
86294 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (42 bp):
GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:87050 original size:22 final size:22
Alignment explanation
Indices: 87022--87063 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
87012 TCCACTTGTA
87022 TAAATGAAGGTTAATTAACACC
1 TAAATGAAGGTTAATTAACACC
87044 TAAATGAAGGTTAATTAACA
1 TAAATGAAGGTTAATTAACA
87064 GTTTTAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (22 bp):
TAAATGAAGGTTAATTAACACC
Found at i:87305 original size:156 final size:157
Alignment explanation
Indices: 87020--87328 Score: 557
Period size: 156 Copynumber: 2.0 Consensus size: 157
87010 GATCCACTTG
* * *
87020 TATAAATGAAGGTTAATTAACACCTAAATGAAGGTTAATTAACAGTTTTAACAAATCAGGATCAA
1 TATAAATGAAGGTTAATTAACACCAAAACGAAGGTTAATTAACAGCTTTAACAAATCAGGATCAA
87085 ATTTCCAAAAGATATTAACCAAAAAGAATACCAATATAAGTTATAACTACTAACCAGTGTAACGA
66 ATTTCCAAAAGATATTAACCAAAAAGAATACCAATATAAGTTATAACTACTAACCAGTGTAACGA
87150 ATTATGGATCAACTCTCCCAAATACTA
131 ATTATGGATCAACTCTCCCAAATACTA
*
87177 TATAAATGAAGGTTAATTAACACCAAAACGAAGGTTAATTAACA-CTTTAACAAATTAGGATCAA
1 TATAAATGAAGGTTAATTAACACCAAAACGAAGGTTAATTAACAGCTTTAACAAATCAGGATCAA
* *
87241 ATTTCCTAAAGATATTAACCAAAAAGAATACTAATATAAGTTATAACTACTAACCAGTGTAACGA
66 ATTTCCAAAAGATATTAACCAAAAAGAATACCAATATAAGTTATAACTACTAACCAGTGTAACGA
87306 ATTATGGATCAACTCTCCCAAAT
131 ATTATGGATCAACTCTCCCAAAT
87329 TAAAGATTTT
Statistics
Matches: 146, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
156 104 0.71
157 42 0.29
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.28
Consensus pattern (157 bp):
TATAAATGAAGGTTAATTAACACCAAAACGAAGGTTAATTAACAGCTTTAACAAATCAGGATCAA
ATTTCCAAAAGATATTAACCAAAAAGAATACCAATATAAGTTATAACTACTAACCAGTGTAACGA
ATTATGGATCAACTCTCCCAAATACTA
Found at i:90938 original size:44 final size:44
Alignment explanation
Indices: 90870--90954 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
90860 AGAAAACTTC
* *
90870 ACCATGCCCTGTCTATCTCGAATCACCATTCCAAGGTCAGCGAA
1 ACCATGCCCTGTCTATCTCAAATCACCATTCCAAGGCCAGCGAA
90914 ACCATGCCCTGTCTATCTCAAATCACCATTCCAAGGCCAGC
1 ACCATGCCCTGTCTATCTCAAATCACCATTCCAAGGCCAGC
90955 TTCGCCCTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.22
Consensus pattern (44 bp):
ACCATGCCCTGTCTATCTCAAATCACCATTCCAAGGCCAGCGAA
Found at i:91637 original size:29 final size:30
Alignment explanation
Indices: 91561--91639 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
91551 GGCTAAATAT
* *
91561 CCAAATTGGGCCTAAACCTTTCACGATCTGC
1 CCAAATTGAGCCTAAACCTTTCAC-ATCAGC
* *
91592 TCAATTTGAGCCTAAACCTTT-AC-TCAGC
1 CCAAATTGAGCCTAAACCTTTCACATCAGC
91620 ACCAAATTGAGCCTAAACCT
1 -CCAAATTGAGCCTAAACCT
91640 ATTCGGGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.10
29 17 0.41
30 2 0.05
31 18 0.44
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (30 bp):
CCAAATTGAGCCTAAACCTTTCACATCAGC
Found at i:92767 original size:17 final size:16
Alignment explanation
Indices: 92743--92788 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
92733 TAGGTGTTTG
*
92743 GGGAAGAAGCAGCGCT
1 GGGAAGAAGAAGCGCT
*
92759 GGAGAAGAAGAAGCGTT
1 GG-GAAGAAGAAGCGCT
92776 GGGAAGAAAGAAG
1 GGGAAG-AAGAAG
92789 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.41, C:0.09, G:0.43, T:0.07
Consensus pattern (16 bp):
GGGAAGAAGAAGCGCT
Found at i:92817 original size:31 final size:30
Alignment explanation
Indices: 92776--92835 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
92766 AAGAAGCGTT
* *
92776 GGGAAGAAAGAAGAAAATAAA-AATAAGAAAA
1 GGGAAAAAAGAA-AAAAGAAAGAAT-AGAAAA
92807 GGGAAAAAAGAAAAAAGAAAGAATAGAAA
1 GGGAAAAAAGAAAAAAGAAAGAATAGAAA
92836 TTAAGGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (30 bp):
GGGAAAAAAGAAAAAAGAAAGAATAGAAAA
Found at i:93552 original size:34 final size:33
Alignment explanation
Indices: 93450--93652 Score: 192
Period size: 34 Copynumber: 5.7 Consensus size: 33
93440 AAAGCTTTTG
*
93450 GTGGGAACTTTCCCAATTTGAAAACTAAAACCGAGAAT
1 GTGGGAACTTTCCCAATTTGAAAACTAAAA-C----TT
* *
93488 GAGGGAACTTTCCCTAAATTGAAAACTAAAACTTT
1 GTGGGAACTTTCCC-AATTTGAAAACTAAAAC-TT
*
93523 GTGGGAACTTTCCCAATTTGAAAATTAAAACTT
1 GTGGGAACTTTCCCAATTTGAAAACTAAAACTT
*
93556 GATGGGAACTTTCCCAATTTAAAAACTTTTAAAAAC-T
1 G-TGGGAACTTTCCCAATTTGAAAAC---T-AAAACTT
* *
93593 GAATGGGAACTTTCCTAATTTGAAAACATAAAACTA
1 G--TGGGAACTTTCCCAATTTGAAAAC-TAAAACTT
*
93629 GTGGGAACTTTCCCAATTTTAAAA
1 GTGGGAACTTTCCCAATTTGAAAA
93653 AAACTTGATG
Statistics
Matches: 142, Mismatches: 15, Indels: 20
0.80 0.08 0.11
Matches are distributed among these distances:
33 3 0.02
34 58 0.41
35 19 0.13
36 2 0.01
37 3 0.02
38 42 0.30
39 15 0.11
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (33 bp):
GTGGGAACTTTCCCAATTTGAAAACTAAAACTT
Found at i:94415 original size:62 final size:60
Alignment explanation
Indices: 94262--94419 Score: 178
Period size: 61 Copynumber: 2.5 Consensus size: 60
94252 ATTAAGTACA
**
94262 AAGCCCAAAT-TCAAAAGAAGCCCATAAGGCCCAATCAACTCAACAAATATATAACATATTT
1 AAGCCCAAATAT-AAAAGAAG-CCATAAGGCCCAATCAACAAAACAAATATATAACATATTT
* * *
94323 AAGCCCAAATTTAAAAGGAAAACCATAAGGCCCAA-CCACAAAACAAATATATAACA-AGTTT
1 AAGCCCAAATATAAAA-G-AAGCCATAAGGCCCAATCAACAAAACAAATATATAACATA-TTT
94384 AAGCCCACACATATAAAAGAAGCCAATAAGGCCCAA
1 AAGCCCA-A-ATATAAAAGAAGCC-ATAAGGCCCAA
94420 ATAGTTAAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 13
0.82 0.06 0.13
Matches are distributed among these distances:
60 1 0.01
61 46 0.55
62 28 0.33
63 9 0.11
ACGTcount: A:0.50, C:0.24, G:0.10, T:0.16
Consensus pattern (60 bp):
AAGCCCAAATATAAAAGAAGCCATAAGGCCCAATCAACAAAACAAATATATAACATATTT
Found at i:95928 original size:2 final size:2
Alignment explanation
Indices: 95923--95947 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
95913 ACTACTGTTG
95923 TA 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 T
95948 GCTTGTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97154 original size:16 final size:15
Alignment explanation
Indices: 97118--97159 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
97108 ACAGAGGTTG
97118 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
*
97133 ACAGAAAACAATTTA
1 ACAGAAAACAATTAA
97148 ACTAGAAAACAA
1 AC-AGAAAACAA
97160 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.