Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004159.1 Hibiscus syriacus cultivar Beakdansim tig00009097_pilon, 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: 74043
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:278 original size:21 final size:21
Alignment explanation
Indices: 252--292 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
242 AGTCGAGGGT
*
252 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCATTCGGGACAA
273 TACAGTGGTCATTCGGGACA
1 TACAGTGGTCATTCGGGACA
293 TAGTGGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
TACAGTGGTCATTCGGGACAA
Found at i:4880 original size:24 final size:24
Alignment explanation
Indices: 4830--4881 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4820 CGTTTAAATG
* *
4830 ATAAACAAGCACAAATGATCAACC
1 ATAAACAAGCACAAATGAACAAAC
4854 ATAAACAA-CACAAATGAACAAAAC
1 ATAAACAAGCACAAATGAAC-AAAC
4878 ATAA
1 ATAA
4882 TGAACGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.62, C:0.21, G:0.06, T:0.12
Consensus pattern (24 bp):
ATAAACAAGCACAAATGAACAAAC
Found at i:15707 original size:17 final size:18
Alignment explanation
Indices: 15685--15731 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
15675 TATGGAATTG
*
15685 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
15702 GATTCCAAGTCCTTCACA
1 GATTCCAATTCCTTCACA
15720 GATTCCAATTCC
1 GATTCCAATTCC
15732 CTCATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.30
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:16262 original size:24 final size:24
Alignment explanation
Indices: 16230--16305 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
16220 TCATGAACTC
* *
16230 TAAATGAACACGTTTGTGAACATA
1 TAAATGAACACATTCGTGAACATA
16254 TAAATGAACACATTCGTGAACATA
1 TAAATGAACACATTCGTGAACATA
16278 CT-AATGAACACATTCGTGAACATA
1 -TAAATGAACACATTCGTGAACATA
16302 TAAA
1 TAAA
16306 CGAATACGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.02
24 46 0.96
25 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (24 bp):
TAAATGAACACATTCGTGAACATA
Found at i:16323 original size:48 final size:48
Alignment explanation
Indices: 16207--16324 Score: 141
Period size: 48 Copynumber: 2.5 Consensus size: 48
16197 AAACAAACGC
* * *
16207 TAAACGAACATGTTCATGAAC-TCTAAATGAACACGTTTGTGAACATA
1 TAAACGAACACGTTCATGAACATCTAAATGAACACATTCGTGAACATA
* * *
16254 TAAATGAACACATTCGTGAACATACT-AATGAACACATTCGTGAACATA
1 TAAACGAACACGTTCATGAACAT-CTAAATGAACACATTCGTGAACATA
* *
16302 TAAACGAATACGTTCACGAACAT
1 TAAACGAACACGTTCATGAACAT
16325 GAACACGTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
47 17 0.29
48 39 0.67
49 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (48 bp):
TAAACGAACACGTTCATGAACATCTAAATGAACACATTCGTGAACATA
Found at i:18587 original size:16 final size:16
Alignment explanation
Indices: 18563--18602 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
18553 TAAAATATTT
*
18563 TATTACGTTGCGTTAA
1 TATTGCGTTGCGTTAA
18579 TATTGCGTTGCGTTAA
1 TATTGCGTTGCGTTAA
18595 TATTGCGT
1 TATTGCGT
18603 CACGGTGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (16 bp):
TATTGCGTTGCGTTAA
Found at i:36618 original size:37 final size:37
Alignment explanation
Indices: 36568--36641 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
36558 TCGCAATTCC
*
36568 CTGGTATGATCATTGATTAACCAATTAGGTTTTCATA
1 CTGGTATGATCATTGATCAACCAATTAGGTTTTCATA
36605 CTGGTATGATCATTGATCAACCAATTAGGTTTTCATA
1 CTGGTATGATCATTGATCAACCAATTAGGTTTTCATA
36642 TAAACTTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (37 bp):
CTGGTATGATCATTGATCAACCAATTAGGTTTTCATA
Found at i:37581 original size:27 final size:26
Alignment explanation
Indices: 37528--37581 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
37518 TATGTAAAAG
* *
37528 TTTATCAAAAATAAAATAATTATTTA
1 TTTATCAAAAATAAAAAAATTAATTA
37554 TTTAT-AAAAATAATAAGAAATTAATTA
1 TTTATCAAAAATAA-AA-AAATTAATTA
37581 T
1 T
37582 AATATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 7 0.29
27 9 0.38
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
TTTATCAAAAATAAAAAAATTAATTA
Found at i:41690 original size:37 final size:35
Alignment explanation
Indices: 41569--41700 Score: 142
Period size: 37 Copynumber: 3.7 Consensus size: 35
41559 GTCCTACTAG
* *
41569 GATTTAAATTCCTAAAAATAGGATAGAATTT-TAA
1 GATTCAAACTCCTAAAAATAGGATAGAATTTCTAA
41603 GATTCAAACTCCTAAAAATAGGATA-ACATTTTGCTAA
1 GATTCAAACTCCTAAAAATAGGATAGA-A-TTT-CTAA
*
41640 GATTCAAACTCCTAAAAATAGGATAGAGTTCTACTAA
1 GATTCAAACTCCTAAAAATAGGATAGAATT-T-CTAA
* * * *
41677 TATTTAAATTCCTAAAGATAGGAT
1 GATTCAAACTCCTAAAAATAGGAT
41701 CCACAAGCAC
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
33 1 0.01
34 24 0.29
35 3 0.04
36 2 0.02
37 53 0.63
38 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (35 bp):
GATTCAAACTCCTAAAAATAGGATAGAATTTCTAA
Found at i:42399 original size:4 final size:4
Alignment explanation
Indices: 42390--42483 Score: 61
Period size: 4 Copynumber: 22.2 Consensus size: 4
42380 TTTTCTATGC
*
42390 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTTA TTTTA TTTTA TTT- CTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA -TTTA TTTA TTTA
*
42438 TTTA TTT- TGGTTGAA TTTA TTTA TTTA TTTTA TTTTA TTTT TTTA T
1 TTTA TTTA T--TT--A TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA T
42484 ATCTAACATG
Statistics
Matches: 77, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
3 8 0.10
4 42 0.55
5 24 0.31
6 2 0.03
8 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:42424 original size:5 final size:5
Alignment explanation
Indices: 42390--42478 Score: 66
Period size: 5 Copynumber: 18.6 Consensus size: 5
42380 TTTTCTATGC
42390 TTTA- TTTA- TTTA- TTTA- TTTATT TATTAT TTTAT TTTAT TTTAT TTCT-T
1 TTTAT TTTAT TTTAT TTTAT TTTA-T T-TTAT TTTAT TTTAT TTTAT TT-TAT
** * *
42438 TTTAT TTTGG TTGAA TTTA- TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
42479 TTTATATCTA
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
4 25 0.34
5 41 0.56
6 4 0.05
7 3 0.04
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:45506 original size:8 final size:8
Alignment explanation
Indices: 45493--45574 Score: 60
Period size: 8 Copynumber: 10.1 Consensus size: 8
45483 TCCAATCAAG
45493 AAGAAAAA
1 AAGAAAAA
*
45501 AAGAAAAG
1 AAGAAAAA
45509 AAGCAAAAA
1 AAG-AAAAA
* *
45518 AACAAAGA
1 AAGAAAAA
*
45526 AA-AAACA
1 AAGAAAAA
45533 AAG-AAAA
1 AAGAAAAA
*
45540 AAGAGAAAC
1 AAGA-AAAA
45549 AAGAACAAA
1 AAGAA-AAA
*
45558 AGGAAAAA
1 AAGAAAAA
*
45566 AGGAAAAA
1 AAGAAAAA
45574 A
1 A
45575 CAAGAATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
7 12 0.20
8 29 0.48
9 19 0.32
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:45528 original size:10 final size:11
Alignment explanation
Indices: 45514--45541 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
45504 AAAAGAAGCA
45514 AAAAAACAAAG
1 AAAAAACAAAG
45525 AAAAAACAAAG
1 AAAAAACAAAG
45536 AAAAAA
1 AAAAAA
45542 GAGAAACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAG
Found at i:45552 original size:27 final size:28
Alignment explanation
Indices: 45489--45591 Score: 95
Period size: 28 Copynumber: 3.6 Consensus size: 28
45479 AAGATCCAAT
*
45489 CAAGAAGAAAAAAAGAAAAGAAGCAAAAAAA
1 CAAGAA-AAAAAAAGAAAA-AAG-GAAAAAA
*
45520 CAAAGAAAAAACAAAGAAAAAA-G-AGAAA
1 C-AAGAAAAAA-AAAGAAAAAAGGAAAAAA
* *
45548 CAAG-AACAAAAGGAAAAAAGGAAAAAA
1 CAAGAAAAAAAAAGAAAAAAGGAAAAAA
*
45575 CAAGAATAAAAAAGAAA
1 CAAGAAAAAAAAAGAAA
45592 GAGGAATAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
25 9 0.15
26 5 0.08
27 11 0.19
28 14 0.24
31 7 0.12
32 13 0.22
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.01
Consensus pattern (28 bp):
CAAGAAAAAAAAAGAAAAAAGGAAAAAA
Found at i:45589 original size:10 final size:9
Alignment explanation
Indices: 45496--45591 Score: 54
Period size: 9 Copynumber: 10.2 Consensus size: 9
45486 AATCAAGAAG
45496 AAAAAAAGA
1 AAAAAAAGA
45505 AAAGAAGCAA-A
1 AAA-AA--AAGA
45516 AAAACAAAGA
1 AAAA-AAAGA
45526 AAAAACAA-A
1 AAAAA-AAGA
*
45535 GAAAAAAGA
1 AAAAAAAGA
* *
45544 GAAACAAG-
1 AAAAAAAGA
* *
45552 AACAAAAGG
1 AAAAAAAGA
*
45561 AAAAAAGGA
1 AAAAAAAGA
45570 AAAAACAAGA
1 AAAAA-AAGA
45580 ATAAAAAAGA
1 A-AAAAAAGA
45590 AA
1 AA
45592 GAGGAATAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
8 7 0.10
9 31 0.46
10 19 0.28
11 9 0.13
12 2 0.03
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.01
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:45596 original size:27 final size:26
Alignment explanation
Indices: 45489--45602 Score: 72
Period size: 27 Copynumber: 4.0 Consensus size: 26
45479 AAGATCCAAT
45489 CAAGAAGAAAAAAAGAAAAGAAGCAAAAAAA
1 CAAGAA-AAAAAAAGAAAAG--G--AAAAAA
45520 CAAAGAAAAAACAAAGAAAA--AAGAGAAA
1 C-AAGAAAAAA-AAAGAAAAGGAA-A-AAA
*
45548 CAAGAACAAAAGGAA-AAAAGGAAAAAA
1 CAAGAA-AAAA-AAAGAAAAGGAAAAAA
*
45575 CAAGAATAAAAAAGAAAGAGGAATAAAA
1 CAAGAAAAAAAAAGAAA-AGGAA-AAAA
45603 AGCACATGCA
Statistics
Matches: 69, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
25 2 0.03
26 8 0.12
27 24 0.35
28 15 0.22
29 2 0.03
31 5 0.07
32 13 0.19
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (26 bp):
CAAGAAAAAAAAAGAAAAGGAAAAAA
Found at i:46251 original size:22 final size:22
Alignment explanation
Indices: 46223--46277 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
46213 GCTATCCCAT
46223 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
46245 CAAACCTTTAAGTATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
46267 CAAACCTTTGA
1 CAAACCTTTGA
46278 CCAAACACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:47201 original size:37 final size:36
Alignment explanation
Indices: 47138--47267 Score: 156
Period size: 37 Copynumber: 3.6 Consensus size: 36
47128 ATTGAAAACA
* ** * *
47138 TTTCCCTTGAAATAAATTTCATCTCTCTTGATATAG
1 TTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAG
*
47174 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACGG
1 TTTCCCTTGAAA-AAAATTTTGTCTCTCTTGAGACAG
*
47211 TTTCCCTTGAAATAAATTTTG-C-CTCTTGAGACAG
1 TTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAG
47245 TTTCCCTTGAAACAAAATATTTG
1 TTTCCCTTGAAA-AAAAT-TTTG
47268 AATATGTTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
34 23 0.28
35 5 0.06
36 24 0.29
37 30 0.37
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAG
Found at i:47254 original size:136 final size:136
Alignment explanation
Indices: 47099--47358 Score: 351
Period size: 136 Copynumber: 1.9 Consensus size: 136
47089 TTTTGTCTCC
* *
47099 CTTGAGACAGTTTCTCTTGAAACATAAACA-TTGAAAACATTTCCCTTGAAATAAATTTCATCTC
1 CTTGAGACAGTTTCCCTTGAAACA-AAACATTTGAAAACATTTCCCTTGAAACAAATTTCATCTC
* * *
47163 TCTTGATATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAATAAAT
65 CCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAATAAAT
47228 TTTGCCT
130 TTTGCCT
* * ** * * *
47235 CTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAATTTCGTCTCC
1 CTTGAGACAGTTTCCCTTGAAACAAAACATTTGAAAACATTTCCCTTGAAACAAATTTCATCTCC
** * * *
47300 CTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACGGTTTCCCTTGAAA
66 CTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAA
47359 CAAAATCTTT
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
135 4 0.04
136 102 0.96
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (136 bp):
CTTGAGACAGTTTCCCTTGAAACAAAACATTTGAAAACATTTCCCTTGAAACAAATTTCATCTCC
CTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAATAAATT
TTGCCT
Found at i:47359 original size:102 final size:99
Alignment explanation
Indices: 47168--47423 Score: 314
Period size: 102 Copynumber: 2.5 Consensus size: 99
47158 ATCTCTCTTG
* *
47168 ATATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAATAAATTTTGC
1 ATATA-TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGC
47233 CTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGA
64 CTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGA
* * * * ** * *
47269 ATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTC
1 ATATATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTT-GAAATAAATTTTG-C
* *
47334 TCTCTTGAGACGGTTTCCCTTGAAACAAAATCTTTGA
64 -CTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGA
* * * * *
47371 ATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAA
1 ATATATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAA
47424 CACAAAATCT
Statistics
Matches: 130, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
99 26 0.20
100 22 0.17
101 8 0.06
102 74 0.57
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (99 bp):
ATATATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGCCT
CTTGAGACAGTTTCCCTTGAAACAAAATATTTGA
Found at i:47454 original size:67 final size:68
Alignment explanation
Indices: 47327--47493 Score: 223
Period size: 68 Copynumber: 2.5 Consensus size: 68
47317 TGGAACTAAG
* * * **
47327 TTTTGTCTCTCTTGAGACGGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCCTAAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACA
47390 -AA
66 TAA
* *
47392 TTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACA
47457 TAA
66 TAA
* * *
47460 TTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
47494 ACAGATATCT
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 25 0.28
66 2 0.02
67 29 0.33
68 32 0.36
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (68 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACA
TAA
Found at i:48457 original size:100 final size:105
Alignment explanation
Indices: 48129--48548 Score: 582
Period size: 105 Copynumber: 4.0 Consensus size: 105
48119 ATATCGTGAC
* * *
48129 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
* *
48194 AATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTAG
66 AA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * *
48235 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
48299 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
48340 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AA-AA-TT-TC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
**
48401 -ATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
48440 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
** *
48505 GGTTCCAGAGCCAATTTCAACTTCACGACGAAGGATATTGG
66 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
48546 ACT
1 ACT
48549 TGGAACAATG
Statistics
Matches: 284, Mismatches: 23, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
100 83 0.29
101 4 0.01
102 3 0.01
103 4 0.01
104 4 0.01
105 103 0.36
106 83 0.29
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
AATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:49860 original size:23 final size:23
Alignment explanation
Indices: 49808--49860 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
49798 TTATGTGTAT
*
49808 TTTATTTATTTATATATATTACC
1 TTTATTTATTTATATATATTAAC
49831 TTT-TTTATTT-TATAT-TTATAC
1 TTTATTTATTTATATATATTA-AC
49852 TATTATTTA
1 T-TTATTTA
49861 CTATCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 9 0.35
23 7 0.27
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTATTTATATATATTAAC
Found at i:49904 original size:5 final size:5
Alignment explanation
Indices: 49894--49958 Score: 64
Period size: 5 Copynumber: 13.4 Consensus size: 5
49884 TATTTATTTA
** * *
49894 TTATT TTATT TTATT TTATT TCT-TT TTATT TTGGT TGAAT TTA-T TTA-T
1 TTATT TTATT TTATT TTATT T-TATT TTATT TTATT TTATT TTATT TTATT
49942 TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TT
49959 TTTATATCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
4 9 0.18
5 41 0.80
6 1 0.02
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:57270 original size:12 final size:12
Alignment explanation
Indices: 57253--57295 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
57243 TATTTATTAA
57253 AAAATAAATAAT
1 AAAATAAATAAT
** *
57265 AAAATATTTATT
1 AAAATAAATAAT
57277 AAAAATAAATAAT
1 -AAAATAAATAAT
57290 AAAATA
1 AAAATA
57296 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:57271 original size:26 final size:26
Alignment explanation
Indices: 57242--57304 Score: 119
Period size: 25 Copynumber: 2.5 Consensus size: 26
57232 TGATGATATG
57242 ATATTTATTAAAAAATAAATAATAAA
1 ATATTTATTAAAAAATAAATAATAAA
57268 ATATTTATT-AAAAATAAATAATAAA
1 ATATTTATTAAAAAATAAATAATAAA
57293 ATATTTATTAAA
1 ATATTTATTAAA
57305 TACAACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 25 0.69
26 11 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATTTATTAAAAAATAAATAATAAA
Found at i:57438 original size:44 final size:45
Alignment explanation
Indices: 57349--57441 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 45
57339 ATCATTTAAT
* *
57349 TTTACTGAAATAAATAATAAAATTTTAAAAACTTTGATCGTTACA
1 TTTACTGAAATAAATAATAAAATTTAAAAAACTCTGATCGTTACA
57394 TTTACTGAAATAAATAATAAAA-TTAAAAAACTCTGATCGTTACA
1 TTTACTGAAATAAATAATAAAATTTAAAAAACTCTGATCGTTACA
57438 TTTA
1 TTTA
57442 ATAAATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 24 0.52
45 22 0.48
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (45 bp):
TTTACTGAAATAAATAATAAAATTTAAAAAACTCTGATCGTTACA
Found at i:58729 original size:13 final size:13
Alignment explanation
Indices: 58711--58736 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58701 ACATAGTTAA
58711 ACAGTCTTCATAT
1 ACAGTCTTCATAT
58724 ACAGTCTTCATAT
1 ACAGTCTTCATAT
58737 GCGCGTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:60043 original size:11 final size:11
Alignment explanation
Indices: 60022--60057 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
60012 ATATTTATTG
60022 TTATT-ATAAA
1 TTATTAATAAA
60032 TTATTAATAAA
1 TTATTAATAAA
*
60043 TTATTAATATA
1 TTATTAATAAA
60054 TTAT
1 TTAT
60058 ATATCAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTATTAATAAA
Found at i:60956 original size:33 final size:33
Alignment explanation
Indices: 60914--61068 Score: 175
Period size: 33 Copynumber: 4.5 Consensus size: 33
60904 CAAAATCGCA
60914 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
60947 TTGCGATTTTCATTTTGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** * *
60980 TTGCGATAGTCATTTCGCGTTGCAATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
61013 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTATCTCG
1 TTGCGATTTTCATTT-CGCGTTGCGA--TTC----TCTCG
61053 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
61069 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
33 73 0.71
34 9 0.09
36 3 0.03
39 1 0.01
40 17 0.17
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:61045 original size:20 final size:20
Alignment explanation
Indices: 61022--61068 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
61012 ATTGCGATAG
61022 TCATTTCCGCGTTGCGATTT
1 TCATTTCCGCGTTGCGATTT
*
61042 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTT
61062 TCATTTC
1 TCATTTC
61069 AACCAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTT
Found at i:62469 original size:19 final size:20
Alignment explanation
Indices: 62454--62491 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62444 GTTGCGATTT
62454 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCATTGCGATAG
*
62473 TCATTTCCGCGTTGCGATA
1 TCATTTCCGCATTGCGATA
62492 TACATTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (20 bp):
TCATTTCCGCATTGCGATAG
Found at i:62489 original size:20 final size:19
Alignment explanation
Indices: 62443--62491 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
62433 GCGATTCTCT
**
62443 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
62462 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
62482 CGTTGCGATA
1 CGTTGCGATA
62492 TACATTAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:62497 original size:20 final size:18
Alignment explanation
Indices: 62443--62497 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
62433 GCGATTCTCT
*
62443 CGTTGCGATTTTCATTTCG
1 CGTTGCGA-TATCATTTCG
*
62462 CATTGCGATAGTCATTTCCG
1 CGTTGCGATA-TCATTT-CG
62482 CGTTGCGATATACATT
1 CGTTGCGATAT-CATT
62498 AAGATGATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 15 0.50
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (18 bp):
CGTTGCGATATCATTTCG
Found at i:64821 original size:12 final size:12
Alignment explanation
Indices: 64804--64828 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64794 TCTTCGGGGA
64804 CTTTTTCTTCTT
1 CTTTTTCTTCTT
64816 CTTTTTCTTCTT
1 CTTTTTCTTCTT
64828 C
1 C
64829 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:65037 original size:24 final size:24
Alignment explanation
Indices: 65003--65056 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
64993 CTGAAACATC
65003 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
* *
65027 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
65051 ATCAAA
1 ATCAAA
65057 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAT
Found at i:65635 original size:12 final size:12
Alignment explanation
Indices: 65611--65644 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
65601 TGCCGGATGG
*
65611 GGAA-GGATGTA
1 GGAACGGATATA
65622 GGAACGGATATA
1 GGAACGGATATA
65634 GGAACGGATAT
1 GGAACGGATAT
65645 CGCCGGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.38, C:0.06, G:0.38, T:0.18
Consensus pattern (12 bp):
GGAACGGATATA
Found at i:65824 original size:20 final size:20
Alignment explanation
Indices: 65803--65910 Score: 162
Period size: 20 Copynumber: 5.4 Consensus size: 20
65793 TGTATTATCT
* *
65803 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
65823 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
65843 CGGTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
65863 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
* *
65883 CGTTGCGAAAGTCAGTATCT
1 CGTTGCGAAAGTCAGAATCG
65903 CGTTGCGA
1 CGTTGCGA
65911 TTTTGTATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:65944 original size:20 final size:20
Alignment explanation
Indices: 65798--65944 Score: 161
Period size: 20 Copynumber: 7.3 Consensus size: 20
65788 GATTCTGTAT
* *
65798 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
65818 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
65838 AATCGCGGTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
65858 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
65878 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
65898 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
65919 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
65939 TATCGC
1 TATCGC
65945 ATTACGATTT
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 93 0.84
21 13 0.12
22 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:65953 original size:41 final size:41
Alignment explanation
Indices: 65878--65955 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
65868 CGAAAGTCAG
* * *
65878 TATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCATTACGATTTTGTAT
*
65919 TATCGCGTTGCGATAGTCAGTATCGCATTACGATTTT
1 TATCGCGTTGCGAAAGTCAGTATCGCATTACGATTTT
65956 CCAAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCGCATTACGATTTTGTAT
Found at i:65986 original size:21 final size:21
Alignment explanation
Indices: 65962--66011 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
65952 TTTTCCAAAT
65962 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATT-GGAAAA
**
65983 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCGAAATTGGAAAA
66004 TCGCATTG
1 TCGCATTG
66012 TGATAGTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (21 bp):
TCGCATTGCGAAATTGGAAAA
Found at i:66517 original size:20 final size:20
Alignment explanation
Indices: 66489--66530 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
66479 GGAATTATTT
*
66489 TAATATTTTAAAATTAATAA
1 TAATATTTTAAAATAAATAA
* *
66509 TAATTTTTTATAATAAATAA
1 TAATATTTTAAAATAAATAA
66529 TA
1 TA
66531 TTAATTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTTTAAAATAAATAA
Found at i:66547 original size:22 final size:22
Alignment explanation
Indices: 66516--66559 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
66506 TAATAATTTT
66516 TTATAATAAAT-AATATTAATTA
1 TTATAATAAATAAATA-TAATTA
*
66538 TTATATTAAATAAATATAATTA
1 TTATAATAAATAAATATAATTA
66560 ATCATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATAATAAATAAATATAATTA
Found at i:66574 original size:26 final size:26
Alignment explanation
Indices: 66499--66589 Score: 71
Period size: 26 Copynumber: 3.5 Consensus size: 26
66489 TAATATTTTA
* *
66499 AAAT-TAA-TAATAATTTTTTATAAT
1 AAATATAATTAATAATTTTATAAAAT
* * *
66523 AAATA-ATATTAATTATTATATTAAAT
1 AAATATA-ATTAATAATTTTATAAAAT
*
66549 AAATATAATTAATCATTTTATAAAATT
1 AAATATAATTAATAATTTTATAAAA-T
*
66576 ACAATATAAATAAT
1 A-AATATAATTAAT
66590 TTATATAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 5 0.10
25 1 0.02
26 32 0.62
27 3 0.06
28 11 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATATAATTAATAATTTTATAAAAT
Found at i:70020 original size:117 final size:117
Alignment explanation
Indices: 69750--70409 Score: 925
Period size: 117 Copynumber: 5.7 Consensus size: 117
69740 ACTATTCACA
* * * *
69750 TGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTAATTTGTCAGATAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGAGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * *
69815 TTATATCACTCATGT-CCCTCGGGGTACTATTCATGTCAGTACCCAAAGTGG
66 TTATGTCACTCATGTCCCCCCGGAGAACTATTCATGTCAGTACCCAAAGTGG
* * * *
69866 TGAAAGCGCGTTCCCGGGGGGGCACCTTCCATTATTTTGTCAGATAATATGTTACCATTGCCCTA
1 TGAAAGCGCGTTCCCGAGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
69931 TTATGTCACTCATGTCCCCCCGAAGAACTATTTATGTCAGTACCCAAAGTGG
66 TTATGTCACTCATGTCCCCCCGGAGAACTATTCATGTCAGTACCCAAAGTGG
* ** * * *
69983 TGAAAGCGCGTTCTCGAGGGGGCGCCTTTTATCATTTTGTCAGAGAATATGTTATCATTGTCATA
1 TGAAAGCGCGTTCCCGAGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* ** * * *
70048 TTATATCACTCATGT-CCCTTGGGGAACTATTCATGTTAATACCCAAAGTGG
66 TTATGTCACTCATGTCCCCCCGGAGAACTATTCATGTCAGTACCCAAAGTGG
70099 TGAAAGCGCGTTCCCGA-GGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGAGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
70163 TTATGTCACTCATGTCCCCCCGAAGAACTATTTATGTCAGTACCCAAAGTGG
66 TTATGTCACTCATGTCCCCCCGGAGAACTATTCATGTCAGTACCCAAAGTGG
* ** * *
70215 TGAAAGCGCGTTCTCGAGGGGGCGCCTTTTATCATTTTGTCAGAGAATATGTTATCATTGTCCTA
1 TGAAAGCGCGTTCCCGAGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * * *
70280 TTATGTCACTCATGTCCCTCGGGTGCACTATTCATGTCAGTACCCAAAGTAG
66 TTATGTCACTCATGTCCCCCCGGAGAACTATTCATGTCAGTACCCAAAGTGG
* *
70332 TGAAAGCGCG-TCCCCA-GGGGCGCCTTCCATTATTTTGTCAGAGAATATGCTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGAGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
70395 TTATGTCACTCATGT
66 TTATGTCACTCATGT
70410 GAAATTGGAT
Statistics
Matches: 480, Mismatches: 61, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
115 113 0.24
116 169 0.35
117 198 0.41
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (117 bp):
TGAAAGCGCGTTCCCGAGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCCCCGGAGAACTATTCATGTCAGTACCCAAAGTGG
Found at i:70226 original size:232 final size:232
Alignment explanation
Indices: 69750--70409 Score: 1088
Period size: 232 Copynumber: 2.8 Consensus size: 232
69740 ACTATTCACA
* * * ** * * * *
69750 TGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTAATTTGTCAGATAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCTCGAGGGGGCGCCTTTTATCATTTTGTCAGAGAATATGTTATCATTGTCCTA
*
69815 TTATATCACTCATGTCCCTCGGGGTACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCC
66 TTATATCACTCATGTCCCTCGGGGAACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCC
* * * *
69880 CGGGGGGGCACCTTCCATTATTTTGTCAGATAATATGTTACCATTGCCCTATTATGTCACTCATG
131 C-GAGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
69945 TCCCCCCGAAGAACTATTTATGTCAGTACCCAAAGTGG
195 TCCCCCCGAAGAACTATTTATGTCAGTACCCAAAGTGG
*
69983 TGAAAGCGCGTTCTCGAGGGGGCGCCTTTTATCATTTTGTCAGAGAATATGTTATCATTGTCATA
1 TGAAAGCGCGTTCTCGAGGGGGCGCCTTTTATCATTTTGTCAGAGAATATGTTATCATTGTCCTA
* * *
70048 TTATATCACTCATGTCCCTTGGGGAACTATTCATGTTAATACCCAAAGTGGTGAAAGCGCGTTCC
66 TTATATCACTCATGTCCCTCGGGGAACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCC
70113 CGAGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
131 CGAGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
70178 CCCCCCGAAGAACTATTTATGTCAGTACCCAAAGTGG
196 CCCCCCGAAGAACTATTTATGTCAGTACCCAAAGTGG
70215 TGAAAGCGCGTTCTCGAGGGGGCGCCTTTTATCATTTTGTCAGAGAATATGTTATCATTGTCCTA
1 TGAAAGCGCGTTCTCGAGGGGGCGCCTTTTATCATTTTGTCAGAGAATATGTTATCATTGTCCTA
* * *
70280 TTATGTCACTCATGTCCCTCGGGTGCACTATTCATGTCAGTACCCAAAGTAGTGAAAGCGCG-TC
66 TTATATCACTCATGTCCCTCGGG-GAACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTC
* *
70344 CCCAGGGGCGCCTTCCATTATTTTGTCAGAGAATATGCTATCATTGCCCTATTATGTCACTCATG
130 CCGAGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
70409 T
195 T
70410 GAAATTGGAT
Statistics
Matches: 399, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
232 248 0.62
233 151 0.38
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (232 bp):
TGAAAGCGCGTTCTCGAGGGGGCGCCTTTTATCATTTTGTCAGAGAATATGTTATCATTGTCCTA
TTATATCACTCATGTCCCTCGGGGAACTATTCATGTCAGTACCCAAAGTGGTGAAAGCGCGTTCC
CGAGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
CCCCCCGAAGAACTATTTATGTCAGTACCCAAAGTGG
Found at i:70482 original size:21 final size:23
Alignment explanation
Indices: 70458--70508 Score: 88
Period size: 21 Copynumber: 2.3 Consensus size: 23
70448 GGAAGTTTGA
70458 ATAAATTGGATAAAATG-TAT-G
1 ATAAATTGGATAAAATGTTATGG
70479 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
70502 ATAAATT
1 ATAAATT
70509 AAATAAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.61
22 3 0.11
23 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (23 bp):
ATAAATTGGATAAAATGTTATGG
Found at i:70518 original size:22 final size:22
Alignment explanation
Indices: 70458--70515 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
70448 GGAAGTTTGA
**
70458 ATAAATTGGATAAAATG-TATG
1 ATAAATTAAATAAAATGTTATG
**
70479 ATAAATTGGATAAAATGTTATGG
1 ATAAATTAAATAAAATGTTAT-G
70502 ATAAATTAAATAAA
1 ATAAATTAAATAAA
70516 TGTGAAGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 17 0.52
22 3 0.09
23 13 0.39
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.33
Consensus pattern (22 bp):
ATAAATTAAATAAAATGTTATG
Found at i:70683 original size:14 final size:14
Alignment explanation
Indices: 70664--70708 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
70654 TGATAAGTTG
70664 GTTTTAATGTATAT
1 GTTTTAATGTATAT
70678 GTTTTAATGTATAT
1 GTTTTAATGTATAT
*
70692 GTTTCAATGTATAT
1 GTTTTAATGTATAT
70706 GTT
1 GTT
70709 ATCAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.56
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:73138 original size:16 final size:16
Alignment explanation
Indices: 73117--73175 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
73107 ATTACTAATT
73117 TAAATAAATAATTATA
1 TAAATAAATAATTATA
* *
73133 TAAATATAT-TTTA-A
1 TAAATAAATAATTATA
* *
73147 TAAAAAAATATTTATA
1 TAAATAAATAATTATA
73163 TAAATATAATAAT
1 TAAATA-AATAAT
73176 AAAAAATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.24
15 7 0.21
16 14 0.41
17 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATAAATAATTATA
Found at i:73156 original size:30 final size:28
Alignment explanation
Indices: 73117--73186 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 28
73107 ATTACTAATT
* *
73117 TAAATAAATAATTATATAAATATATTTTAA
1 TAAAAAAATAATTATATAAATATA--ATAA
*
73147 TAAAAAAATATTTATATAAATATAATAA
1 TAAAAAAATAATTATATAAATATAATAA
73175 TAAAAAATATAA
1 TAAAAAA-ATAA
73187 CAACTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.29
29 3 0.09
30 22 0.63
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
TAAAAAAATAATTATATAAATATAATAA
Done.