Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2
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: 5794061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 68655 characters in sequence are not A, C, G, or T
File 36 of 38
Found at i:5508347 original size:22 final size:22
Alignment explanation
Indices: 5508290--5508351 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
5508280 ATAATAAATT
* * **
5508290 TAATATATATCATATTTAAATTT
1 TAATTTATATTATATTT-AATGA
*
5508313 TAATTT-TAATATATTTAATGA
1 TAATTTATATTATATTTAATGA
5508334 TAATTTATATTATATTTA
1 TAATTTATATTATATTTA
5508352 CAACATAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 9 0.28
22 18 0.56
23 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TAATTTATATTATATTTAATGA
Found at i:5509233 original size:7 final size:7
Alignment explanation
Indices: 5509221--5509310 Score: 55
Period size: 7 Copynumber: 13.0 Consensus size: 7
5509211 TTATGTTTAA
5509221 AAATTTT
1 AAATTTT
5509228 AAA-TTT
1 AAATTTT
5509234 AAA-TTT
1 AAATTTT
5509240 AAA-TTT
1 AAATTTT
*
5509246 GAATTTT
1 AAATTTT
*
5509253 GAATTTT
1 AAATTTT
* *
5509260 -TATCTTA
1 AAAT-TTT
*
5509267 AAATTTA
1 AAATTTT
5509274 AAATTTT
1 AAATTTT
*
5509281 ATGATTTTT
1 A--AATTTT
5509290 AAATTTAT
1 AAATTT-T
5509298 AAA-TTT
1 AAATTTT
5509304 AAATTTT
1 AAATTTT
5509311 GTATCTGAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
6 23 0.33
7 34 0.49
8 6 0.09
9 6 0.09
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:5513052 original size:127 final size:121
Alignment explanation
Indices: 5512895--5513263 Score: 476
Period size: 123 Copynumber: 3.0 Consensus size: 121
5512885 CGTTAAGAAA
* * * * *
5512895 TTTTTCTTAAATTAAATTATTGACTCATCTTTATTTATTATTTTT-T-AA-CCTTGAAGTCCTTA
1 TTTTTATTACATTAAAATATTAACTAATCTTTATTTATTATTTTTATAAATCC-TGAAGTCCTTA
*
5512957 TT-ATATAAACTTTTCTTAATTAATATATTTTAACTAATTTTTAATCTAAGTTTTTATTAATGAT
65 TTAATATAAA-TTGTC-T-A-T-A-ATA--TTAACT-ATTTTTAATCTAAGTTTTTATTAATGAT
5513021 T
121 T
*
5513022 TTTTTATTACATTAAAATATTAACTAATCTTTATTTATTATTTTTTTATAAATCCTGAAGTCTTT
1 TTTTTATTACATTAAAATATTAACTAATCTTTATTTATTA--TTTTTATAAATCCTGAAGTCCTT
* *
5513087 ATTAATCTAAATTGTCTATAATATTAACTATTTTTTATCTAAGTTTTTATTAATGATT
64 ATTAATATAAATTGTCTATAATATTAACTATTTTTAATCTAAGTTTTTATTAATGATT
*
5513145 TTTTTATTACATTAAAATATTAACTAATCTTTATTTATTATTTTCTTATAAATCCTGAAGTCTTT
1 TTTTTATTACATTAAAATATTAACTAATCTTTATTTATTA-TTT-TTATAAATCCTGAAGTCCTT
* *
5513210 ATTAATCTGAATTGTCTATAATATTAACTATTTTTAATCTAAGTTTTTATTAAT
64 ATTAATATAAATTGTCTATAATATTAACTATTTTTAATCTAAGTTTTTATTAAT
5513264 TAACAAATCT
Statistics
Matches: 224, Mismatches: 11, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
122 4 0.02
123 140 0.62
124 6 0.03
126 3 0.01
127 36 0.16
128 1 0.00
129 6 0.03
130 2 0.01
131 18 0.08
132 8 0.04
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (121 bp):
TTTTTATTACATTAAAATATTAACTAATCTTTATTTATTATTTTTATAAATCCTGAAGTCCTTAT
TAATATAAATTGTCTATAATATTAACTATTTTTAATCTAAGTTTTTATTAATGATT
Found at i:5513110 original size:69 final size:69
Alignment explanation
Indices: 5513037--5513239 Score: 213
Period size: 69 Copynumber: 3.2 Consensus size: 69
5513027 ATTACATTAA
5513037 AATATTAACTAATCTTTATTTATTATTTTTTTATAAATCCTGAAGTCTTTATTAATCTAAATTGT
1 AATATTAACTAATCTTTATTTATTATTTTTTTATAAATCCTGAAGTCTTTATTAATCTAAATTGT
5513102 CTAT
66 CTAT
** * * *
5513106 AATATTAACT-A--TTT-TTTATCTAAGTTTTTATTAA---TG-A-T-TTT-TTTAT-TACA---
1 AATATTAACTAATCTTTATTTAT-TATTTTTTTATAAATCCTGAAGTCTTTATTAATCTAAATTG
*
5513156 T-TAA
65 TCTAT
* *
5513160 AATATTAACTAATCTTTATTTATTATTTTCTTATAAATCCTGAAGTCTTTATTAATCTGAATTGT
1 AATATTAACTAATCTTTATTTATTATTTTTTTATAAATCCTGAAGTCTTTATTAATCTAAATTGT
5513225 CTAT
66 CTAT
5513229 AATATTAACTA
1 AATATTAACTA
5513240 TTTTTAATCT
Statistics
Matches: 103, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
54 12 0.12
55 2 0.02
57 13 0.13
58 8 0.08
59 4 0.04
60 5 0.05
61 2 0.02
62 2 0.02
63 5 0.05
64 4 0.04
65 7 0.07
66 14 0.14
68 2 0.02
69 23 0.22
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.52
Consensus pattern (69 bp):
AATATTAACTAATCTTTATTTATTATTTTTTTATAAATCCTGAAGTCTTTATTAATCTAAATTGT
CTAT
Found at i:5513141 original size:123 final size:123
Alignment explanation
Indices: 5512986--5513263 Score: 520
Period size: 123 Copynumber: 2.3 Consensus size: 123
5512976 TTAATATATT
5512986 TTAACTAATTTTTAATCTAAGTTTTTATTAATGATTTTTTTATTACATTAAAATATTAACTAATC
1 TTAACT-ATTTTTAATCTAAGTTTTTATTAATGATTTTTTTATTACATTAAAATATTAACTAATC
*
5513051 TTTATTTATTATTTTTTTATAAATCCTGAAGTCTTTATTAATCTAAATTGTCTATAATA
65 TTTATTTATTATTTTCTTATAAATCCTGAAGTCTTTATTAATCTAAATTGTCTATAATA
*
5513110 TTAACTATTTTTTATCTAAGTTTTTATTAATGATTTTTTTATTACATTAAAATATTAACTAATCT
1 TTAACTATTTTTAATCTAAGTTTTTATTAATGATTTTTTTATTACATTAAAATATTAACTAATCT
*
5513175 TTATTTATTATTTTCTTATAAATCCTGAAGTCTTTATTAATCTGAATTGTCTATAATA
66 TTATTTATTATTTTCTTATAAATCCTGAAGTCTTTATTAATCTAAATTGTCTATAATA
5513233 TTAACTATTTTTAATCTAAGTTTTTATTAAT
1 TTAACTATTTTTAATCTAAGTTTTTATTAAT
5513264 TAACAAATCT
Statistics
Matches: 150, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
123 144 0.96
124 6 0.04
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.54
Consensus pattern (123 bp):
TTAACTATTTTTAATCTAAGTTTTTATTAATGATTTTTTTATTACATTAAAATATTAACTAATCT
TTATTTATTATTTTCTTATAAATCCTGAAGTCTTTATTAATCTAAATTGTCTATAATA
Found at i:5513278 original size:18 final size:18
Alignment explanation
Indices: 5513255--5513301 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5513245 AATCTAAGTT
*
5513255 TTTATTAATTAACAAATC
1 TTTATTTATTAACAAATC
* *
5513273 TTTATTTATTAGCTAATC
1 TTTATTTATTAACAAATC
5513291 TTTATTTATTA
1 TTTATTTATTA
5513302 TTTTCTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTATTTATTAACAAATC
Found at i:5518980 original size:22 final size:21
Alignment explanation
Indices: 5518954--5519010 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
5518944 TATAAAAATT
*
5518954 TATTTTTATATTAATATTTATA
1 TATTTTTATATTAA-ATTTAAA
5518976 TATTTTTATAATTAAATTTAAA
1 TATTTTTAT-ATTAAATTTAAA
5518998 TAATTTTT-TATTA
1 T-ATTTTTATATTA
5519011 CTTAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.12
22 17 0.53
23 11 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTATATTAAATTTAAA
Found at i:5520036 original size:20 final size:20
Alignment explanation
Indices: 5520011--5520055 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5520001 TTATGAGATA
*
5520011 AATCTATTCAAATATCAATT
1 AATCTATTCAAAAATCAATT
* *
5520031 AATCTATTTAAAAATTAATT
1 AATCTATTCAAAAATCAATT
5520051 AATCT
1 AATCT
5520056 CTAGTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
AATCTATTCAAAAATCAATT
Found at i:5520337 original size:22 final size:22
Alignment explanation
Indices: 5520314--5520380 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
5520304 CTCGATCAAT
*
5520314 AAAATTTATTAAAT-TTAATTATA
1 AAAATATA-TAAATATTAA-TATA
5520337 AAAATATATAAATATTAATATA
1 AAAATATATAAATATTAATATA
* *
5520359 AACATATTTAAATGATATAATA
1 AAAATATATAAAT-AT-TAATA
5520381 GACTTTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 20 0.53
23 13 0.34
24 5 0.13
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (22 bp):
AAAATATATAAATATTAATATA
Found at i:5523917 original size:25 final size:27
Alignment explanation
Indices: 5523889--5523939 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5523879 TATACAAAAA
5523889 ATTA-TATTAA-ATTAATATAAAATTT
1 ATTATTATTAATATTAATATAAAATTT
*
5523914 ATTATTTTTAATATTAATATAAAATT
1 ATTATTATTAATATTAATATAAAATT
5523940 AAATTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 5 0.22
27 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTATTATTAATATTAATATAAAATTT
Found at i:5524261 original size:2 final size:2
Alignment explanation
Indices: 5524254--5524283 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5524244 TCTATGCTTT
5524254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5524284 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5524288 original size:2 final size:2
Alignment explanation
Indices: 5524283--5524309 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5524273 ATATATATAT
5524283 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
5524310 TTAATGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5524807 original size:6 final size:6
Alignment explanation
Indices: 5524796--5524821 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5524786 GTTTTTGTCC
5524796 TTGCCT TTGCCT TTGCCT TTGCCT TT
1 TTGCCT TTGCCT TTGCCT TTGCCT TT
5524822 ACCGGCCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.15, T:0.54
Consensus pattern (6 bp):
TTGCCT
Found at i:5528161 original size:18 final size:19
Alignment explanation
Indices: 5528123--5528166 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5528113 TAATAAAATA
5528123 ATTTATAAATTTATATCAT
1 ATTTATAAATTTATATCAT
* *
5528142 ATTTATATATTT-TGTCAT
1 ATTTATAAATTTATATCAT
5528160 A-TTATAA
1 ATTTATAA
5528167 TCGTACTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 11 0.50
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTATAAATTTATATCAT
Found at i:5528202 original size:17 final size:17
Alignment explanation
Indices: 5528180--5528234 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5528170 TACTTAAAAT
5528180 ATTTTATATTATTATAA
1 ATTTTATATTATTATAA
5528197 ATTTTA-ATATATTA-ACA
1 ATTTTATAT-TATTATA-A
*
5528214 A-TTCATATTA-TATAA
1 ATTTTATATTATTATAA
5528229 ATTTTA
1 ATTTTA
5528235 AAAATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
15 4 0.13
16 12 0.39
17 15 0.48
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTATATTATTATAA
Found at i:5528838 original size:2 final size:2
Alignment explanation
Indices: 5528827--5528872 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5528817 TAAGCTTGAG
5528827 TA TA -A TA TA TA TA TA TA TA TA TA TA TA 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
5528868 TA TA T
1 TA TA T
5528873 GATAGATTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5536775 original size:1 final size:1
Alignment explanation
Indices: 5536769--5536797 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
5536759 ATCCAAACTT
5536769 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5536798 GAAGAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5539538 original size:24 final size:25
Alignment explanation
Indices: 5539491--5539542 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
5539481 AAAATAGTAA
**
5539491 TAATATTATAATAATATTTCATACT
1 TAATATTATAATAATATTAAATACT
*
5539516 TAATATTATAGT-ATATTAAATACT
1 TAATATTATAATAATATTAAATACT
5539540 TAA
1 TAA
5539543 AGTGATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (25 bp):
TAATATTATAATAATATTAAATACT
Found at i:5539881 original size:23 final size:24
Alignment explanation
Indices: 5539826--5539884 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
5539816 GTTACATTAT
*
5539826 TAATTTATTATTAAAATAAATAATA
1 TAATTTATT-TTAAAAGAAATAATA
*
5539851 TAACTTTATTTTAAAAGATATAATA
1 TAA-TTTATTTTAAAAGAAATAATA
5539876 T-ATTTATTT
1 TAATTTATTT
5539885 ATTAGCATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 7 0.23
24 1 0.03
25 17 0.55
26 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TAATTTATTTTAAAAGAAATAATA
Found at i:5544378 original size:15 final size:15
Alignment explanation
Indices: 5544355--5544385 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5544345 AACTATAATA
5544355 TACCCTACAATGACC
1 TACCCTACAATGACC
*
5544370 TACCTTACAATGACC
1 TACCCTACAATGACC
5544385 T
1 T
5544386 GAGAACATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.26
Consensus pattern (15 bp):
TACCCTACAATGACC
Found at i:5550463 original size:2 final size:2
Alignment explanation
Indices: 5550458--5550505 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
5550448 AGTGTGTGTG
* *
5550458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5550500 TG TA TA
1 TA TA TA
5550506 ACTCAATTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5554545 original size:368 final size:368
Alignment explanation
Indices: 5553868--5554607 Score: 1471
Period size: 368 Copynumber: 2.0 Consensus size: 368
5553858 ATAATTGCAA
5553868 TATTGAAGCTTCATAAACCTTGAAATGACCAGTGAGCACCAGAAGAAATGAATAAAGAATTGGTT
1 TATTGAAGCTTCATAAACCTTGAAATGACCAGTGAGCACCAGAAGAAATGAATAAAGAATTGGTT
5553933 ACTTAACGGATCTATGGAAGCCTAGTGCCTCGATAATTACACTTGAACCCAGTAACAAGATAATC
66 ACTTAACGGATCTATGGAAGCCTAGTGCCTCGATAATTACACTTGAACCCAGTAACAAGATAATC
5553998 AAGAATATCAGTTGGCATTGAAAATGTCATCAAAAGGAACCAGTTGGTTAACGGACAGAGTCCAA
131 AAGAATATCAGTTGGCATTGAAAATGTCATCAAAAGGAACCAGTTGGTTAACGGACAGAGTCCAA
5554063 GATGTTTAAGTACCCAACTGATAATATAAAAGCCGAAATGCTCTTTGTGCTATATTGTTCGAAAA
196 GATGTTTAAGTACCCAACTGATAATATAAAAGCCGAAATGCTCTTTGTGCTATATTGTTCGAAAA
5554128 TAGTCTTATACAATAATTATCAGAACTAAATATCCCATCAATTTAGTAGCCTAATATGCAGATAA
261 TAGTCTTATACAATAATTATCAGAACTAAATATCCCATCAATTTAGTAGCCTAATATGCAGATAA
*
5554193 AAGGTAGGTCTGTAAAACGCCTGGAACAGCCATTGCAAATTTG
326 AAGGTAGGTCTGTAAAACGCCTGGAACAACCATTGCAAATTTG
5554236 TATTGAAGCTTCATAAACCTTGAAATGACCAGTGAGCACCAGAAGAAATGAATAAAGAATTGGTT
1 TATTGAAGCTTCATAAACCTTGAAATGACCAGTGAGCACCAGAAGAAATGAATAAAGAATTGGTT
5554301 ACTTAACGGATCTATGGAAGCCTAGTGCCTCGATAATTACACTTGAACCCAGTAACAAGATAATC
66 ACTTAACGGATCTATGGAAGCCTAGTGCCTCGATAATTACACTTGAACCCAGTAACAAGATAATC
5554366 AAGAATATCAGTTGGCATTGAAAATGTCATCAAAAGGAACCAGTTGGTTAACGGACAGAGTCCAA
131 AAGAATATCAGTTGGCATTGAAAATGTCATCAAAAGGAACCAGTTGGTTAACGGACAGAGTCCAA
5554431 GATGTTTAAGTACCCAACTGATAATATAAAAGCCGAAATGCTCTTTGTGCTATATTGTTCGAAAA
196 GATGTTTAAGTACCCAACTGATAATATAAAAGCCGAAATGCTCTTTGTGCTATATTGTTCGAAAA
5554496 TAGTCTTATACAATAATTATCAGAACTAAATATCCCATCAATTTAGTAGCCTAATATGCAGATAA
261 TAGTCTTATACAATAATTATCAGAACTAAATATCCCATCAATTTAGTAGCCTAATATGCAGATAA
5554561 AAGGTAGGTCTGTAAAACGCCTGGAACAACCATTGCAAATTTG
326 AAGGTAGGTCTGTAAAACGCCTGGAACAACCATTGCAAATTTG
5554604 TATT
1 TATT
5554608 CTTATGGTTT
Statistics
Matches: 371, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
368 371 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (368 bp):
TATTGAAGCTTCATAAACCTTGAAATGACCAGTGAGCACCAGAAGAAATGAATAAAGAATTGGTT
ACTTAACGGATCTATGGAAGCCTAGTGCCTCGATAATTACACTTGAACCCAGTAACAAGATAATC
AAGAATATCAGTTGGCATTGAAAATGTCATCAAAAGGAACCAGTTGGTTAACGGACAGAGTCCAA
GATGTTTAAGTACCCAACTGATAATATAAAAGCCGAAATGCTCTTTGTGCTATATTGTTCGAAAA
TAGTCTTATACAATAATTATCAGAACTAAATATCCCATCAATTTAGTAGCCTAATATGCAGATAA
AAGGTAGGTCTGTAAAACGCCTGGAACAACCATTGCAAATTTG
Found at i:5556639 original size:97 final size:98
Alignment explanation
Indices: 5556538--5556731 Score: 329
Period size: 97 Copynumber: 2.0 Consensus size: 98
5556528 GAAAATTGAC
*
5556538 AACTGAAAAGGAAAAACAAACTCGATAAAGATTTAAGAAATAAGGTGGATTAAGGATTTC-GATG
1 AACTGAAAAGGAAAAACAAACTCGATAAAGATTTAAGAAATAAGGTGGATTAAGGATTACTGATG
5556602 TTTGGTTGCCAAGGAAAA-GGAGGAAAGCAACAG
66 TTTGGTTGCCAA-GAAAATGGAGGAAAGCAACAG
* *
5556635 AACTGAAAAGGAAAAACAAACTGGATAAAGATTTAAGAAATAGGGTGGATTAAGGATTACTGATG
1 AACTGAAAAGGAAAAACAAACTCGATAAAGATTTAAGAAATAAGGTGGATTAAGGATTACTGATG
*
5556700 TTTGGTTGCCCAGAAAATGGAGGAAAGCAACA
66 TTTGGTTGCCAAGAAAATGGAGGAAAGCAACA
5556732 ATAGAAAAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
97 62 0.68
98 29 0.32
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.20
Consensus pattern (98 bp):
AACTGAAAAGGAAAAACAAACTCGATAAAGATTTAAGAAATAAGGTGGATTAAGGATTACTGATG
TTTGGTTGCCAAGAAAATGGAGGAAAGCAACAG
Found at i:5557729 original size:19 final size:19
Alignment explanation
Indices: 5557689--5557728 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5557679 TAAGGTGAAA
5557689 TTTATTATTAATATTAAAT
1 TTTATTATTAATATTAAAT
5557708 TTTATTATGT-AT-TTAAAT
1 TTTATTAT-TAATATTAAAT
5557726 TTT
1 TTT
5557729 TTTAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 10 0.50
20 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTATTATTAATATTAAAT
Found at i:5557879 original size:21 final size:22
Alignment explanation
Indices: 5557853--5557898 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5557843 GAAATTAAAA
5557853 TATGAAAAT-AAATATTTTGTT
1 TATGAAAATAAAATATTTTGTT
*
5557874 TATGAAAATAAAATTTTTTGTT
1 TATGAAAATAAAATATTTTGTT
5557896 TAT
1 TAT
5557899 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (22 bp):
TATGAAAATAAAATATTTTGTT
Found at i:5558509 original size:2 final size:2
Alignment explanation
Indices: 5558502--5558535 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5558492 AGAGGAAATG
5558502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5558536 TGGGTCTCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5559059 original size:17 final size:17
Alignment explanation
Indices: 5559017--5559064 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
5559007 TATATATTAG
* *
5559017 ATATTTATACTAAAATT
1 ATATTTATATTATAATT
5559034 ATA--TATATTATAATT
1 ATATTTATATTATAATT
5559049 ATATTTATATTTATAA
1 ATATTTATA-TTATAA
5559065 ATTAATTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 13 0.50
17 7 0.27
18 6 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTTATATTATAATT
Found at i:5559435 original size:29 final size:31
Alignment explanation
Indices: 5559386--5559445 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
5559376 TGTGTCAAGT
5559386 AATATCAATTTAATTAGTAAAAAT-ATAAAA
1 AATATCAATTTAATTAGTAAAAATAATAAAA
*
5559416 AATAT-AATTATAA-TATTAAAAATAATAAAA
1 AATATCAATT-TAATTAGTAAAAATAATAAAA
5559446 TTATAAGTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (31 bp):
AATATCAATTTAATTAGTAAAAATAATAAAA
Found at i:5559865 original size:15 final size:16
Alignment explanation
Indices: 5559845--5559874 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5559835 TTGAGATTGA
5559845 TTTTGAATTT-TTTTT
1 TTTTGAATTTGTTTTT
5559860 TTTTGAATTTGTTTT
1 TTTTGAATTTGTTTT
5559875 CTAATGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (16 bp):
TTTTGAATTTGTTTTT
Found at i:5560174 original size:19 final size:21
Alignment explanation
Indices: 5560143--5560181 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5560133 ATTATTGACT
5560143 GTATTTATTTAACAT-TAAAA
1 GTATTTATTTAACATCTAAAA
5560163 GTATTT-TTTAACATCTAAA
1 GTATTTATTTAACATCTAAA
5560182 TTATTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (21 bp):
GTATTTATTTAACATCTAAAA
Found at i:5561274 original size:18 final size:18
Alignment explanation
Indices: 5561243--5561280 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5561233 TGATTTTGAA
* *
5561243 TAATTTATTTAATTATTT
1 TAATTAATTAAATTATTT
5561261 TAATTAATTAAATTATTT
1 TAATTAATTAAATTATTT
5561279 TA
1 TA
5561281 TTAGAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATTAATTAAATTATTT
Found at i:5561328 original size:20 final size:20
Alignment explanation
Indices: 5561289--5561329 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5561279 TATTAGAATT
*
5561289 AAAATAATTTTATATATTAA
1 AAAATAATTTTAAATATTAA
* *
5561309 AAAATTATTTTAAATGTTAA
1 AAAATAATTTTAAATATTAA
5561329 A
1 A
5561330 TAAGTAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AAAATAATTTTAAATATTAA
Found at i:5566844 original size:20 final size:19
Alignment explanation
Indices: 5566819--5566903 Score: 56
Period size: 21 Copynumber: 4.5 Consensus size: 19
5566809 TATTAAAATA
5566819 TAAAAATATTATAATTTAAT
1 TAAAAATATTATAA-TTAAT
* *
5566839 TAAAAA-ATAAATAAATAAAAT
1 TAAAAATAT-TAT-AAT-TAAT
5566860 TAAAAAT-TTATAA-TAAT
1 TAAAAATATTATAATTAAT
5566877 T-AAAATA-TA-AATTAAT
1 TAAAAATATTATAATTAAT
5566893 ATAATAAATAT
1 -TAA-AAATAT
5566904 AAAATAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
15 2 0.04
16 11 0.22
17 5 0.10
18 1 0.02
19 9 0.18
20 11 0.22
21 12 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATATTATAATTAAT
Found at i:5566845 original size:43 final size:39
Alignment explanation
Indices: 5566797--5566896 Score: 105
Period size: 38 Copynumber: 2.5 Consensus size: 39
5566787 TATAACTATA
*
5566797 AAAAAATAAAAGT-ATTAAAATATAAAAATATTATAATTTAATT
1 AAAAAATAAAA-TAAATAAAAT-TAAAAAT-TTATAA--TAATT
5566840 AAAAAAT-AAATAAATAAAATTAAAAATTTATAATAATT
1 AAAAAATAAAATAAATAAAATTAAAAATTTATAATAATT
* *
5566878 AAAATATAAATTAATATAA
1 AAAAAATAAAATAA-ATAA
5566897 TAAATATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
38 11 0.22
39 5 0.10
40 10 0.20
41 8 0.16
42 10 0.20
43 7 0.14
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (39 bp):
AAAAAATAAAATAAATAAAATTAAAAATTTATAATAATT
Found at i:5566872 original size:24 final size:23
Alignment explanation
Indices: 5566844--5566902 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
5566834 TTAATTAAAA
5566844 AATAAATAAATAAAATTAAAAATT
1 AATAAATAAATAAAA-TAAAAATT
* * *
5566868 TAT-AATAATTAAAATATAAATT
1 AATAAATAAATAAAATAAAAATT
5566890 AATATAATAAATA
1 AATA-AATAAATA
5566903 TAAAATAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 9 0.32
23 10 0.36
24 9 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AATAAATAAATAAAATAAAAATT
Found at i:5566892 original size:19 final size:19
Alignment explanation
Indices: 5566835--5566917 Score: 55
Period size: 19 Copynumber: 4.3 Consensus size: 19
5566825 TATTATAATT
* *
5566835 TAATTAAAAAATAAATAAA
1 TAATTAAAATATAAATTAA
**
5566854 TAAAATTAAAA-ATTTA-TAA
1 T--AATTAAAATATAAATTAA
5566873 TAATTAAAATATAAATTAA
1 TAATTAAAATATAAATTAA
* *
5566892 T-ATAATAAATATAAAATAA
1 TAATTA-AAATATAAATTAA
5566911 TATATTA
1 TA-ATTA
5566918 TTAATATCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
17 8 0.16
18 6 0.12
19 21 0.43
20 3 0.06
21 11 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATTAAAATATAAATTAA
Found at i:5566907 original size:43 final size:41
Alignment explanation
Indices: 5566812--5566907 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 41
5566802 ATAAAAGTAT
5566812 TAAAATATAAAAATATTATAATTTAATTAAAAAATAAATAAA
1 TAAAATATAAAAATATTATAA-TTAATTAAAAAATAAATAAA
*
5566854 TAAAAT-TAAAAAT-TTATAA-TAATTAAAATATAAATTAATA
1 TAAAATATAAAAATATTATAATTAATTAAAAAATAAA-TAA-A
5566894 TAATAAATATAAAA
1 T-A-AAATATAAAA
5566908 TAATATATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
38 14 0.29
39 3 0.06
40 8 0.17
41 8 0.17
42 10 0.21
43 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (41 bp):
TAAAATATAAAAATATTATAATTAATTAAAAAATAAATAAA
Found at i:5569850 original size:2 final size:2
Alignment explanation
Indices: 5569843--5569869 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5569833 TTTAATGTCA
5569843 AT AT AT 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 A
5569870 AATTTCCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5571766 original size:78 final size:78
Alignment explanation
Indices: 5571637--5571793 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
5571627 AACACCATGG
5571637 TGAACTTTCCAAATCTTGAACTCCTTGAGTTGCACCTAGGCAGTGGAATTAATTGATCATGCCTC
1 TGAACTTTCCAAATCTTGAACTCCTTGAGTTGCACCTAGGCAGTGGAATTAATTGATCATGCCTC
5571702 TTATCATTCTGGT
66 TTATCATTCTGGT
5571715 TGAACTTTCCAAATCTTGAACTCCTTGAGTTGCACCTAGGCAGTGGAATTAATTGATCATGCCTC
1 TGAACTTTCCAAATCTTGAACTCCTTGAGTTGCACCTAGGCAGTGGAATTAATTGATCATGCCTC
5571780 TTATCATTCTGGT
66 TTATCATTCTGGT
5571793 T
1 T
5571794 TTGTTTTAGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (78 bp):
TGAACTTTCCAAATCTTGAACTCCTTGAGTTGCACCTAGGCAGTGGAATTAATTGATCATGCCTC
TTATCATTCTGGT
Found at i:5573608 original size:3 final size:3
Alignment explanation
Indices: 5573600--5573634 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5573590 AACCATCAAA
5573600 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
5573635 AGTTAACTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:5582062 original size:52 final size:51
Alignment explanation
Indices: 5581984--5582132 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
5581974 CGAAATATGA
5581984 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
5582036 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
5582088 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
5582133 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:5582139 original size:13 final size:13
Alignment explanation
Indices: 5582121--5582145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5582111 CAAAGATCAG
5582121 TGTATCGATACAA
1 TGTATCGATACAA
5582134 TGTATCGATACA
1 TGTATCGATACA
5582146 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5582225 original size:13 final size:13
Alignment explanation
Indices: 5582207--5582231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5582197 ACAAAAAATA
5582207 TGTATCGATACAT
1 TGTATCGATACAT
5582220 TGTATCGATACA
1 TGTATCGATACA
5582232 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5582227 original size:32 final size:33
Alignment explanation
Indices: 5582186--5582251 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
5582176 AGTAGCTTAA
5582186 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
5582218 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
5582251 A
1 A
5582252 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:5583195 original size:52 final size:51
Alignment explanation
Indices: 5583063--5583274 Score: 179
Period size: 52 Copynumber: 4.2 Consensus size: 51
5583053 GAAAAGTGAT
* * * * * * * *
5583063 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* *
5583117 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAA-G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
5583170 AAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G-
1 AAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
5583217 ---GTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGGA
1 AAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
5583265 AAAGGTGCCA
1 AAA-GTGCCA
5583275 CCGATTTGTG
Statistics
Matches: 129, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
43 35 0.27
44 2 0.02
45 1 0.01
47 1 0.01
48 1 0.01
50 1 0.01
51 2 0.02
52 40 0.31
53 5 0.04
54 4 0.03
55 37 0.29
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (51 bp):
AAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:5583235 original size:43 final size:43
Alignment explanation
Indices: 5583174--5583259 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
5583164 GATGGAAAAT
*
5583174 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * *
5583217 GTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
5583260 ATGGAAAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
Found at i:5583391 original size:30 final size:30
Alignment explanation
Indices: 5583263--5583704 Score: 326
Period size: 30 Copynumber: 15.1 Consensus size: 30
5583253 CTTAAAGATG
* * **
5583263 GAAAA-GGTGCCACCGATTTGTGGGCTTCA
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
* *
5583292 AAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
5583321 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
5583349 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
* *
5583377 GAACAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
5583407 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
***
5583435 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
5583465 GAAAAGGGTGCCACTAACTTGTGGGC---T
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
** * * * **
5583492 GAAAATAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GAAAAGGGTGCCACT-GACTTGTGGGCTT----TT
* * * * *
5583526 GAAAAAGAGTGCCACGGAGTTGTGGACTTTG
1 G-AAAAGGGTGCCACTGACTTGTGGGCTTTT
* * *
5583557 GAAAA-GATGCCACCGACTTGTGGGC-TTC
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
* *
5583585 GAAAAAGGGTGCCACTGATTTGTGGAC-TTT
1 G-AAAAGGGTGCCACTGACTTGTGGGCTTTT
* *
5583615 G--AAGGTTGCCACTGACTTGTGGGCTTTC
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
***
5583643 GAAAAAAATGCCACTGACTTGTGGGC-TTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*** *
5583672 GAAAAAAATGCCACTGACTTGTGGACTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
5583702 GAA
1 GAA
5583705 GGGTGATGAA
Statistics
Matches: 336, Mismatches: 54, Indels: 45
0.77 0.12 0.10
Matches are distributed among these distances:
26 1 0.00
27 60 0.18
28 61 0.18
29 51 0.15
30 140 0.42
31 1 0.00
34 1 0.00
35 21 0.06
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (30 bp):
GAAAAGGGTGCCACTGACTTGTGGGCTTTT
Found at i:5583408 original size:58 final size:57
Alignment explanation
Indices: 5583294--5583709 Score: 292
Period size: 58 Copynumber: 7.1 Consensus size: 57
5583284 GGGCTTCAAA
* *
5583294 AAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTT
1 AAAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTT
* * *
5583349 AAAGGTTGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT
1 AAAGGGTGCCACTGACTTGTGGGCTTTTGAA-AGGATGCCACTGACTTGTGGGCTTTT
* **
5583407 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTT
1 AAAGGGTGCCACTGACTTGTGGGCTTTTG-AAAGGATGCCACTGACTTGTGGGCTTTT
* ** * * * **
5583465 GAAAAGGGTGCCACTAACTTGTGGGC---TGAAAATAGTGCTA-TAGAGTTGTGAGCTTACA
1 --AAAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGA-TGCCACT-GACTTGTGGGCTT-TT
* * * * * * **
5583523 AAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAA
1 AAAG-----G-GTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTT--TT
* * * *
5583588 AAAGGGTGCCACTGATTTGTGGAC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTCGA
1 AAAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTT--T
*** ** *
5583645 AAAAAATGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTT
1 AAAGGGTGCCACTGACTTGTGGGCTTTTG-AAAGGATGCCACTGACTTGTGGGCTTTT
*
5583702 GAAGGGTG
1 AAAGGGTG
5583710 ATGAATGTCT
Statistics
Matches: 289, Mismatches: 48, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
55 22 0.08
56 15 0.05
57 68 0.24
58 78 0.27
59 41 0.14
60 23 0.08
61 1 0.00
62 15 0.05
64 15 0.05
65 11 0.04
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (57 bp):
AAAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTT
Found at i:5583577 original size:29 final size:29
Alignment explanation
Indices: 5583526--5583700 Score: 183
Period size: 29 Copynumber: 6.0 Consensus size: 29
5583516 GCTTACAAAA
* *
5583526 GAAAAAGAGTGCCACGGAGTTGTGGACTTT
1 GAAAAAGA-TGCCACTGACTTGTGGACTTT
* * * *
5583556 GGAAAAGATGCCACCGACTTGTGGGCTTC
1 GAAAAAGATGCCACTGACTTGTGGACTTT
* *
5583585 GAAAAAGGGTGCCACTGATTTGTGGACTTT
1 GAAAAA-GATGCCACTGACTTGTGGACTTT
* * *
5583615 G--AAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGACTTT
* *
5583642 CGAAAAAAATGCCACTGACTTGTGGGCTTT
1 -GAAAAAGATGCCACTGACTTGTGGACTTT
*
5583672 GAAAAAAATGCCACTGACTTGTGGACTTT
1 GAAAAAGATGCCACTGACTTGTGGACTTT
5583701 TGAAGGGTGA
Statistics
Matches: 122, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
27 20 0.16
28 3 0.02
29 50 0.41
30 49 0.40
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGACTTT
Found at i:5585141 original size:1 final size:1
Alignment explanation
Indices: 5585135--5585246 Score: 116
Period size: 1 Copynumber: 112.0 Consensus size: 1
5585125 CCGGACCCTC
* * * * * * *
5585135 TTTTTTTTGTTTTTGTTTTTTTTTTGTTTTTTTTTTTGTTTTTGTTTTTTTTTGTTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * ** *
5585200 TTTTTTTGTTGTTTTTTTTTTGGTTTTTTCTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5585247 GGAGGACGCC
Statistics
Matches: 89, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 89 1.00
ACGTcount: A:0.00, C:0.01, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:5585158 original size:11 final size:11
Alignment explanation
Indices: 5585135--5585243 Score: 134
Period size: 11 Copynumber: 9.7 Consensus size: 11
5585125 CCGGACCCTC
5585135 TTTTTTTTGTT
1 TTTTTTTTGTT
5585146 TTTGTTTTT-TT
1 TTT-TTTTTGTT
*
5585157 TTTGTTTTTTTT
1 TTT-TTTTTGTT
5585169 TTTGTTTTTG-T
1 TTT-TTTTTGTT
5585180 TTTTTTTTGTT
1 TTTTTTTTGTT
5585191 TTTTTTTTGTT
1 TTTTTTTTGTT
*
5585202 TTTTTGTTGTT
1 TTTTTTTTGTT
5585213 TTTTTTTTGGTT
1 TTTTTTTT-GTT
5585225 TTTTCTTTT-TT
1 TTTT-TTTTGTT
5585236 TTTTTTTT
1 TTTTTTTT
5585244 TTTGGAGGAC
Statistics
Matches: 90, Mismatches: 3, Indels: 11
0.87 0.03 0.11
Matches are distributed among these distances:
10 10 0.11
11 53 0.59
12 23 0.26
13 4 0.04
ACGTcount: A:0.00, C:0.01, G:0.10, T:0.89
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:5585175 original size:29 final size:29
Alignment explanation
Indices: 5585135--5585246 Score: 147
Period size: 29 Copynumber: 3.8 Consensus size: 29
5585125 CCGGACCCTC
5585135 TTTTTTTTGTTTTTGTTTTTTTTTTGTTT
1 TTTTTTTTGTTTTTGTTTTTTTTTTGTTT
*
5585164 TTTTTTTTGTTTTTGTTTTTTTTTGTTTTT
1 TTTTTTTTGTTTTTGTTTTTTTTT-TGTTT
* *
5585194 TTTTTGTTTTTTTGTTGTTTTTTTTTTGGTT
1 TTTTT-TTTGTTT-TTGTTTTTTTTTTGTTT
*
5585225 TTTTCTTT-TTTTT-TTTTTTTTT
1 TTTTTTTTGTTTTTGTTTTTTTTT
5585247 GGAGGACGCC
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.12
28 2 0.03
29 27 0.36
30 12 0.16
31 13 0.17
32 12 0.16
ACGTcount: A:0.00, C:0.01, G:0.10, T:0.89
Consensus pattern (29 bp):
TTTTTTTTGTTTTTGTTTTTTTTTTGTTT
Found at i:5585219 original size:50 final size:48
Alignment explanation
Indices: 5585135--5585247 Score: 172
Period size: 50 Copynumber: 2.3 Consensus size: 48
5585125 CCGGACCCTC
* * * *
5585135 TTTTTTTTGTTTTTGTTTTTTTTTTGTTTTTTTTTTTGTTTTTGTTTTT
1 TTTTTTTTTTTTTTGTTTTTTTGTTGTTTTTTTTTTGGTTTTT-TCTTT
5585184 TTTTGTTTTTTTTTTGTTTTTTTGTTGTTTTTTTTTTGGTTTTTTCTTT
1 TTTT-TTTTTTTTTTGTTTTTTTGTTGTTTTTTTTTTGGTTTTTTCTTT
5585233 TTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTG
5585248 GAGGACGCCG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
48 11 0.19
49 12 0.20
50 36 0.61
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.88
Consensus pattern (48 bp):
TTTTTTTTTTTTTTGTTTTTTTGTTGTTTTTTTTTTGGTTTTTTCTTT
Found at i:5599200 original size:52 final size:51
Alignment explanation
Indices: 5599122--5599270 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
5599112 CGAAATATGA
5599122 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
5599174 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
5599226 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
5599271 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:5599277 original size:13 final size:13
Alignment explanation
Indices: 5599259--5599283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5599249 CAAAGATCAG
5599259 TGTATCGATACAA
1 TGTATCGATACAA
5599272 TGTATCGATACA
1 TGTATCGATACA
5599284 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5599363 original size:13 final size:13
Alignment explanation
Indices: 5599345--5599369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5599335 ACAAAAAATA
5599345 TGTATCGATACAT
1 TGTATCGATACAT
5599358 TGTATCGATACA
1 TGTATCGATACA
5599370 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5599365 original size:32 final size:33
Alignment explanation
Indices: 5599324--5599389 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
5599314 AGTAGCTTAA
5599324 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
5599356 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
5599389 A
1 A
5599390 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:5601283 original size:14 final size:15
Alignment explanation
Indices: 5601249--5601283 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5601239 TTTCACATAT
5601249 TTTTCATTTCATGCA
1 TTTTCATTTCATGCA
5601264 TTTTCATTTCATGC-
1 TTTTCATTTCATGCA
5601278 TTTTCA
1 TTTTCA
5601284 CGTAACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTTCATTTCATGCA
Found at i:5601321 original size:5 final size:5
Alignment explanation
Indices: 5601311--5601485 Score: 179
Period size: 5 Copynumber: 35.0 Consensus size: 5
5601301 GCATAATTTT
* * * *
5601311 CATTG CATTG CATTT CATTT CATTT CATTG CATTG CATTT CATTG CATTG
1 CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG
* * * * * * *
5601361 CATTT CATTA CATTG CATTT CATTT CATTT CATTG CATTG CATTT CATTA
1 CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG
* * * * * *
5601411 CATTG CATTT CATTT CATTA CATTG CATTT CATTG CATTG CATTT CATTA
1 CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG
* *
5601461 CATTG CATTT CATTT CATTG CATTG
1 CATTG CATTG CATTG CATTG CATTG
5601486 GTTTCATGCA
Statistics
Matches: 148, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 148 1.00
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (5 bp):
CATTG
Found at i:5601328 original size:15 final size:15
Alignment explanation
Indices: 5601311--5601484 Score: 231
Period size: 15 Copynumber: 11.6 Consensus size: 15
5601301 GCATAATTTT
* *
5601311 CATTGCATTGCATTT
1 CATTGCATTTCATTG
*
5601326 CATTTCATTTCATTG
1 CATTGCATTTCATTG
5601341 CATTGCATTTCATTG
1 CATTGCATTTCATTG
*
5601356 CATTGCATTTCATTA
1 CATTGCATTTCATTG
*
5601371 CATTGCATTTCATTT
1 CATTGCATTTCATTG
* *
5601386 CATTTCATTGCATTG
1 CATTGCATTTCATTG
* *
5601401 CATTTCATTACATTG
1 CATTGCATTTCATTG
* *
5601416 CATTTCATTTCATTA
1 CATTGCATTTCATTG
5601431 CATTGCATTTCATTG
1 CATTGCATTTCATTG
*
5601446 CATTGCATTTCATTA
1 CATTGCATTTCATTG
*
5601461 CATTGCATTTCATTT
1 CATTGCATTTCATTG
5601476 CATTGCATT
1 CATTGCATT
5601485 GGTTTCATGC
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 143 1.00
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (15 bp):
CATTGCATTTCATTG
Found at i:5601333 original size:20 final size:20
Alignment explanation
Indices: 5601308--5601485 Score: 230
Period size: 20 Copynumber: 8.7 Consensus size: 20
5601298 CATGCATAAT
5601308 TTTCATTGCATTGCATTTCA
1 TTTCATTGCATTGCATTTCA
* *
5601328 TTTCATTTCATTGCATTGCA
1 TTTCATTGCATTGCATTTCA
5601348 TTTCATTGCATTGCATTTCA
1 TTTCATTGCATTGCATTTCA
* *
5601368 TTACATTGCATTTCATTTCA
1 TTTCATTGCATTGCATTTCA
5601388 TTTCATTGCATTGCATTTCA
1 TTTCATTGCATTGCATTTCA
* *
5601408 TTACATTGCATTTCATTTCA
1 TTTCATTGCATTGCATTTCA
* *
5601428 TTACATTGCATTTCATTGCATTGCA
1 -T---TT-CATTGCATTGCATTTCA
*
5601453 TTTCATTACATTGCATTTCA
1 TTTCATTGCATTGCATTTCA
5601473 TTTCATTGCATTG
1 TTTCATTGCATTG
5601486 GTTTCATGCA
Statistics
Matches: 136, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
20 117 0.86
21 3 0.02
24 2 0.01
25 14 0.10
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTCATTGCATTGCATTTCA
Found at i:5602400 original size:16 final size:15
Alignment explanation
Indices: 5602379--5602409 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5602369 GATTTCCATA
5602379 AAAATAATAACAAAAT
1 AAAATAATAA-AAAAT
5602395 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
5602410 TCTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:5606014 original size:20 final size:20
Alignment explanation
Indices: 5605991--5606029 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5605981 TATTTAAAAA
*
5605991 ATAATTTAAATATTAAATAT
1 ATAATTTAAATAATAAATAT
*
5606011 ATAATTTTAATAATAAATA
1 ATAATTTAAATAATAAATA
5606030 AATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATTTAAATAATAAATAT
Found at i:5606159 original size:10 final size:10
Alignment explanation
Indices: 5606146--5606189 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
5606136 ATCAAATCAC
*
5606146 TTTTAATGATT
1 TTTTAAT-AAT
5606157 TTTTAA-AAT
1 TTTTAATAAT
*
5606166 TTTTACTAAT
1 TTTTAATAAT
5606176 TTTTAATAAT
1 TTTTAATAAT
5606186 TTTT
1 TTTT
5606190 TACTAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 7 0.24
10 16 0.55
11 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:5606189 original size:21 final size:19
Alignment explanation
Indices: 5606156--5606197 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
5606146 TTTTAATGAT
5606156 TTTTTAAAATTTTTACTAA
1 TTTTTAAAATTTTTACTAA
5606175 TTTTTAATAATTTTTTACTAA
1 TTTTTAA-AA-TTTTTACTAA
5606196 TT
1 TT
5606198 CAATTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 2 0.10
21 12 0.57
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAAAATTTTTACTAA
Found at i:5606196 original size:11 final size:11
Alignment explanation
Indices: 5606165--5606197 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5606155 TTTTTTAAAA
5606165 TTTTTACTAA-
1 TTTTTACTAAT
*
5606175 TTTTTAATAAT
1 TTTTTACTAAT
5606186 TTTTTACTAAT
1 TTTTTACTAAT
5606197 T
1 T
5606198 CAATTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTTACTAAT
Found at i:5606222 original size:20 final size:20
Alignment explanation
Indices: 5606165--5606222 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
5606155 TTTTTTAAAA
5606165 TTTTTACTAATTTTTAA-TAAT
1 TTTTTACTAA--TTTAATTAAT
*
5606186 TTTTTACTAATTCAATTAAT
1 TTTTTACTAATTTAATTAAT
* *
5606206 TTTTTATTTATTTAATT
1 TTTTTACTAATTTAATT
5606223 TTTTTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 4 0.12
20 18 0.56
21 10 0.31
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTACTAATTTAATTAAT
Found at i:5606234 original size:16 final size:16
Alignment explanation
Indices: 5606201--5606230 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5606191 ACTAATTCAA
5606201 TTAATTTTTTATTTAT
1 TTAATTTTTTATTTAT
5606217 TTAATTTTTT-TTTA
1 TTAATTTTTTATTTA
5606231 ATTTGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTAATTTTTTATTTAT
Found at i:5606712 original size:26 final size:25
Alignment explanation
Indices: 5606653--5606713 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
5606643 TGTTTTAATC
* * *
5606653 ATTAAATTTAATACTAAAATATTAT
1 ATTATATTAAATACTAAAATAATAT
5606678 ATTAATATTAAATACTTAAAATAATACT
1 ATT-ATATTAAATAC-TAAAATAATA-T
5606706 ATT-TATTA
1 ATTATATTA
5606714 CTAAAACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 3 0.10
26 14 0.47
27 9 0.30
28 4 0.13
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTATATTAAATACTAAAATAATAT
Found at i:5606800 original size:14 final size:14
Alignment explanation
Indices: 5606754--5606810 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
5606744 TATTATTATA
*
5606754 ATTATTAAATTATT
1 ATTATTAAAATATT
*
5606768 ATTTATATCAATATAATT
1 A-TTAT-T-AAAAT-ATT
5606786 ATTATTAAAATATT
1 ATTATTAAAATATT
*
5606800 ATTTTTAAAAT
1 ATTATTAAAAT
5606811 TTTTAAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 14 0.40
15 8 0.23
16 2 0.06
17 7 0.20
18 4 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTATTAAAATATT
Found at i:5606999 original size:25 final size:25
Alignment explanation
Indices: 5606969--5607016 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5606959 AAAATTAATT
5606969 ATATAAAAATT-TTAAAATATTTAAA
1 ATATAAAAATTATTAAAAT-TTTAAA
*
5606994 ATATAATAATTATTAAAATTTTA
1 ATATAAAAATTATTAAAATTTTA
5607017 TTTCTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATAAAAATTATTAAAATTTTAAA
Found at i:5607233 original size:22 final size:22
Alignment explanation
Indices: 5607195--5607238 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5607185 TTATAATTTA
* *
5607195 TTATTAAAATAATAATTTTATT
1 TTATTAAAAGAATAATTATATT
5607217 TTATTAAAAGGAA-AATTATATT
1 TTATTAAAA-GAATAATTATATT
5607239 ACTAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TTATTAAAAGAATAATTATATT
Found at i:5607278 original size:17 final size:16
Alignment explanation
Indices: 5607256--5607302 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
5607246 TATTATGAAA
5607256 AATAAAATTATATTATT
1 AATAAAATTATATTA-T
*
5607273 AATAAAATAATATTAT
1 AATAAAATTATATTAT
5607289 AA-AATAATTATATT
1 AATAA-AATTATATT
5607303 TGTTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 14 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAAAATTATATTAT
Found at i:5608896 original size:2 final size:2
Alignment explanation
Indices: 5608889--5608916 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5608879 ACTACAAATG
5608889 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5608917 ACACACTTTC
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:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5613025 original size:3 final size:3
Alignment explanation
Indices: 5613017--5613045 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5613007 AAGTTTCAAA
5613017 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5613046 AGACAGTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5613907 original size:18 final size:17
Alignment explanation
Indices: 5613877--5613910 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5613867 AAATATTTAA
*
5613877 AATATTATTTTTATATT
1 AATATTATATTTATATT
5613894 AATATTTATATTTATAT
1 AATA-TTATATTTATAT
5613911 AATTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATATTATATTTATATT
Found at i:5614391 original size:24 final size:26
Alignment explanation
Indices: 5614364--5614411 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5614354 GGTTATTTTT
*
5614364 TTATATAAA-AT-TTAAAATTTTACG
1 TTATATAAATATATCAAAATTTTACG
5614388 TTATATAAATATATCAAAATTTTA
1 TTATATAAATATATCAAAATTTTA
5614412 TTAATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 2 0.10
26 10 0.48
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (26 bp):
TTATATAAATATATCAAAATTTTACG
Found at i:5614743 original size:20 final size:20
Alignment explanation
Indices: 5614720--5614812 Score: 123
Period size: 20 Copynumber: 4.6 Consensus size: 20
5614710 ACTCACTATG
*
5614720 TCATATTTGTTATATTATTT
1 TCATATTTATTATATTATTT
* *
5614740 TCATATTTATTAAATATATAT
1 TCATATTTATTATAT-TATTT
* *
5614761 TCATATTTGTTATATCATTT
1 TCATATTTATTATATTATTT
*
5614781 TCATATTTATTATAATATTT
1 TCATATTTATTATATTATTT
5614801 TCATATTTATTA
1 TCATATTTATTA
5614813 AATATATTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.59
Consensus pattern (20 bp):
TCATATTTATTATATTATTT
Found at i:5614767 original size:41 final size:40
Alignment explanation
Indices: 5614720--5614808 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 40
5614710 ACTCACTATG
*
5614720 TCATATTTGTTATATTATTTTCATATTTATTA-AATATATAT
1 TCATATTTGTTATATCATTTTCATATTTATTATAATAT-T-T
5614761 TCATATTTGTTATATCATTTTCATATTTATTATAATATTT
1 TCATATTTGTTATATCATTTTCATATTTATTATAATATTT
5614801 TCATATTT
1 TCATATTT
5614809 ATTAAATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 9 0.20
41 32 0.70
42 5 0.11
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (40 bp):
TCATATTTGTTATATCATTTTCATATTTATTATAATATTT
Found at i:5614821 original size:13 final size:13
Alignment explanation
Indices: 5614803--5614856 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
5614793 TAATATTTTC
5614803 ATATTTATTAAAT
1 ATATTTATTAAAT
5614816 ATATTTATTAAAT
1 ATATTTATTAAAT
*
5614829 ATA--TATTAAAA
1 ATATTTATTAAAT
*
5614840 ATGTTTATTAAAT
1 ATATTTATTAAAT
5614853 ATAT
1 ATAT
5614857 ATTCATGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 9 0.26
13 26 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
ATATTTATTAAAT
Found at i:5614830 original size:24 final size:24
Alignment explanation
Indices: 5614803--5614859 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
5614793 TAATATTTTC
* *
5614803 ATATTTATTAAATATATTTATTAA
1 ATATATATTAAAAATATTTATTAA
*
5614827 ATATATATTAAAAATGTTTATTAA
1 ATATATATTAAAAATATTTATTAA
5614851 ATATATATT
1 ATATATATT
5614860 CATGTCTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATATATTAAAAATATTTATTAA
Found at i:5619199 original size:15 final size:16
Alignment explanation
Indices: 5619171--5619200 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5619161 CTTTCTTTCA
5619171 AACAAAACCAAAAAAT
1 AACAAAACCAAAAAAT
5619187 AACAAAA-CAAAAAA
1 AACAAAACCAAAAAA
5619201 CAAAGCCTTG
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:0.80, C:0.17, G:0.00, T:0.03
Consensus pattern (16 bp):
AACAAAACCAAAAAAT
Found at i:5621145 original size:22 final size:21
Alignment explanation
Indices: 5621115--5621169 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
5621105 ATTATTTTTT
5621115 TTTAT-TATTTAAATTTAATAA
1 TTTATATATTTAAATTTAA-AA
** *
5621136 TTTATATATTTATTTTTAAAT
1 TTTATATATTTAAATTTAAAA
5621157 TATTATATATTTA
1 T-TTATATATTTA
5621170 TATAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATATATTTAAATTTAAAA
Found at i:5621153 original size:28 final size:31
Alignment explanation
Indices: 5621115--5621173 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
5621105 ATTATTTTTT
5621115 TTTATTATTTAAATT-TAATA-ATTTATATA
1 TTTATTATTTAAATTATAATATATTTATATA
*
5621144 TTTATT-TTTAAATTATTATATATTTATATA
1 TTTATTATTTAAATTATAATATATTTATATA
5621174 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.30
29 10 0.37
30 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTATTATTTAAATTATAATATATTTATATA
Found at i:5621175 original size:20 final size:20
Alignment explanation
Indices: 5621118--5621222 Score: 58
Period size: 20 Copynumber: 5.8 Consensus size: 20
5621108 ATTTTTTTTT
*
5621118 ATTATT-TAAATTTA-ATAA
1 ATTATTATATATTTATATAA
* *
5621136 TTTATATATTTATTT-T-TAA
1 ATTAT-TATATATTTATATAA
5621155 ATTATTATATATTTATATAA
1 ATTATTATATATTTATATAA
5621175 ATT-TTA-A-A---ATATAA
1 ATTATTATATATTTATATAA
*
5621189 ATAATT-T-TA-TTATATAA
1 ATTATTATATATTTATATAA
5621206 ATT-TTGATATATTTATA
1 ATTATT-ATATATTTATA
5621223 AAAAAATTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 26
0.67 0.07 0.26
Matches are distributed among these distances:
14 8 0.12
15 3 0.05
16 2 0.03
17 9 0.14
18 14 0.21
19 14 0.21
20 16 0.24
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
ATTATTATATATTTATATAA
Found at i:5621178 original size:28 final size:27
Alignment explanation
Indices: 5621122--5621210 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 27
5621112 TTTTTTATTA
*
5621122 TTTAAATTTAATAATTTATATATTTATT
1 TTTAAATTTAATAATTTATATA-TAATT
*
5621150 TTTAAATTATTATATATTTATATA-AATT
1 TTTAAATT-TAATA-ATTTATATATAATT
* * *
5621178 TTAAAATATAAATAATTTTATTATATAAAT
1 TTTAAAT-TTAATAA-TTTA-TATATAATT
5621208 TTT
1 TTT
5621211 GATATATTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.02
28 24 0.50
29 9 0.19
30 14 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTAAATTTAATAATTTATATATAATT
Found at i:5621178 original size:40 final size:36
Alignment explanation
Indices: 5621100--5621174 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 36
5621090 AACAAGTTTT
*
5621100 TTTATATTATTTTTTTTTATTATTTAAATTTAATAA
1 TTTATATTATTTTTTTTAATTATTTAAATTTAATAA
*
5621136 TTTATA-TATTTATTTTTAAATTATTATATATTTATATAA
1 TTTATATTATTT-TTTTT-AATTATT-TAAATTTA-ATAA
5621175 ATTTTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 5 0.15
36 11 0.33
37 6 0.18
38 7 0.21
39 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (36 bp):
TTTATATTATTTTTTTTAATTATTTAAATTTAATAA
Found at i:5621196 original size:17 final size:17
Alignment explanation
Indices: 5621174--5621207 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5621164 TATTTATATA
5621174 AATTTTAAAATATAAAT
1 AATTTTAAAATATAAAT
**
5621191 AATTTTATTATATAAAT
1 AATTTTAAAATATAAAT
5621208 TTTGATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTAAAATATAAAT
Found at i:5621216 original size:51 final size:52
Alignment explanation
Indices: 5621144--5621248 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 52
5621134 AATTTATATA
* *
5621144 TTTATTTTTAAATTATTATATATTTAT-ATAAATTT-TAAA-ATATAAATAAT
1 TTTATTTATAAATTATTATATATTTATAAAAAATTTATAAATATATAAA-AAT
5621194 TTTATTATATAAATT-TTGATATATTTATAAAAAAATTTATAAATATATAAAAAT
1 TTTATT-TATAAATTATT-ATATATTTAT-AAAAAATTTATAAATATATAAAAAT
5621248 T
1 T
5621249 AAAACTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
50 8 0.17
51 17 0.36
53 7 0.15
54 8 0.17
55 7 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (52 bp):
TTTATTTATAAATTATTATATATTTATAAAAAATTTATAAATATATAAAAAT
Found at i:5621673 original size:1 final size:1
Alignment explanation
Indices: 5621667--5621697 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
5621657 GGAAACTATC
*
5621667 TTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5621698 GCCAATAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:5623008 original size:50 final size:50
Alignment explanation
Indices: 5622954--5623049 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
5622944 GTTCTATCAG
*
5622954 GATCCCAAGATGCAGAATCTTCTGGCTAATAACTGAAACACCAAAAAAAA
1 GATCCAAAGATGCAGAATCTTCTGGCTAATAACTGAAACACCAAAAAAAA
* *
5623004 GATCCAAAGATGCGGAATCTTCTGGCTAATAATTGAAACACCAAAA
1 GATCCAAAGATGCAGAATCTTCTGGCTAATAACTGAAACACCAAAA
5623050 TTAGAGGCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.20
Consensus pattern (50 bp):
GATCCAAAGATGCAGAATCTTCTGGCTAATAACTGAAACACCAAAAAAAA
Found at i:5626314 original size:2 final size:2
Alignment explanation
Indices: 5626307--5626331 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5626297 CCAAATCTTA
5626307 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5626332 ACATGTCATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5627121 original size:2 final size:2
Alignment explanation
Indices: 5627105--5627151 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
5627095 ATAATGCAAT
* *
5627105 TA TA TA CA TA CA TA TA TA TA TA TA TA TA 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
5627147 TA TA T
1 TA TA T
5627152 CAAAACAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5631186 original size:23 final size:24
Alignment explanation
Indices: 5631130--5631186 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
5631120 TTATTATTAA
*
5631130 ATAATATAAAATTAACTAAAAAATT
1 ATAA-ATAAAATTAAATAAAAAATT
*
5631155 ATAAA-AAAATTAAAT-AATAATT
1 ATAAATAAAATTAAATAAAAAATT
*
5631177 TTAAATAAAA
1 ATAAATAAAA
5631187 ACTAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.36
23 13 0.46
24 1 0.04
25 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAAATAAAATTAAATAAAAAATT
Found at i:5631245 original size:31 final size:32
Alignment explanation
Indices: 5631200--5631259 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
5631190 AAATTTAAAA
5631200 TATTTATATTTTTATTTAAAATAA-TAATTAAC
1 TATTTATATTTTTATTTAAAA-AATTAATTAAC
5631232 TATTTA-ATTTTTATTTAAAAAATTAATT
1 TATTTATATTTTTATTTAAAAAATTAATT
5631260 TTTATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 2 0.07
31 19 0.70
32 6 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
TATTTATATTTTTATTTAAAAAATTAATTAAC
Found at i:5631271 original size:20 final size:19
Alignment explanation
Indices: 5631235--5631286 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
5631225 AATTAACTAT
5631235 TTAATTTTTATTTAAAAAA
1 TTAATTTTTATTTAAAAAA
5631254 TTAATTTTTATTTAAAAAA
1 TTAATTTTTATTTAAAAAA
*
5631273 -TAACTTTTCATTTA
1 TTAA-TTTTTATTTA
5631287 TTTATTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 3 0.10
19 28 0.90
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATTTTTATTTAAAAAA
Found at i:5631355 original size:14 final size:14
Alignment explanation
Indices: 5631317--5631354 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5631307 TTTTTCTTAA
*
5631317 AATTTTTAATATAT
1 AATTTTTAAAATAT
*
5631331 CATTTTTAAAATAT
1 AATTTTTAAAATAT
5631345 AA-TTTTAAAA
1 AATTTTTAAAA
5631355 AAAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTTTAAAATAT
Found at i:5633542 original size:39 final size:39
Alignment explanation
Indices: 5633487--5633563 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
5633477 AAGAATAAGC
* *
5633487 GCAAAATTCTTTGCACTAAATTGCATTGAACATTATTTA
1 GCAAAATTCTTAGCACTAAATGGCATTGAACATTATTTA
* *
5633526 GCAAAATTCTTAGCACTAAATGGCGTTTAACATTATTT
1 GCAAAATTCTTAGCACTAAATGGCATTGAACATTATTT
5633564 TACCATTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (39 bp):
GCAAAATTCTTAGCACTAAATGGCATTGAACATTATTTA
Found at i:5633652 original size:15 final size:15
Alignment explanation
Indices: 5633634--5633663 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5633624 CAAAAATAAT
*
5633634 AAAAATGACAAAAGA
1 AAAAATGAAAAAAGA
5633649 AAAAATGAAAAAAGA
1 AAAAATGAAAAAAGA
5633664 TTATTTGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (15 bp):
AAAAATGAAAAAAGA
Found at i:5641886 original size:13 final size:13
Alignment explanation
Indices: 5641868--5641924 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
5641858 CATAAAGTAT
5641868 TGTATCGATACAA
1 TGTATCGATACAA
5641881 TGTATCGATACATAA
1 TGTATCGATAC--AA
5641896 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
5641913 TGTATCGATACA
1 TGTATCGATACA
5641925 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5641905 original size:19 final size:18
Alignment explanation
Indices: 5641846--5641943 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
5641836 ATTTCAACGA
*
5641846 TTTGTCTCGATACATAAAG
1 TTTGTATCGATACAT-AAG
5641865 TATTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
5641881 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5641897 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
5641913 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5641929 TTTTGTATCGATACA
1 -TTTGTATCGATACA
5641944 ATATAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 24 0.37
20 11 0.17
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:5641908 original size:32 final size:32
Alignment explanation
Indices: 5641852--5641945 Score: 161
Period size: 32 Copynumber: 2.9 Consensus size: 32
5641842 ACGATTTGTC
5641852 TCGATACATAAAGTATTGTATCGATACAATGTA
1 TCGATACAT-AAGTATTGTATCGATACAATGTA
*
5641885 TCGATACATAAGTGTTGTATCGATACAATGTA
1 TCGATACATAAGTATTGTATCGATACAATGTA
*
5641917 TCGATACATAAGTTTTGTATCGATACAAT
1 TCGATACATAAGTATTGTATCGATACAAT
5641946 ATAAGCTACT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.85
33 9 0.15
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TCGATACATAAGTATTGTATCGATACAATGTA
Found at i:5642004 original size:13 final size:13
Alignment explanation
Indices: 5641986--5642010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5641976 ATTACTCAAA
5641986 TGTATCGATACAT
1 TGTATCGATACAT
5641999 TGTATCGATACA
1 TGTATCGATACA
5642011 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5649234 original size:17 final size:16
Alignment explanation
Indices: 5649211--5649264 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
5649201 GTTCTTTTCC
5649211 AAAAAAAAGAAACAAA
1 AAAAAAAAGAAACAAA
*
5649227 ACAAAAAAGGAAA-AAA
1 A-AAAAAAAGAAACAAA
* *
5649243 AAGAAGAAATAAACAAA
1 AA-AAAAAAGAAACAAA
5649260 AAAAA
1 AAAAA
5649265 GAAGGAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.03
16 14 0.47
17 15 0.50
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.02
Consensus pattern (16 bp):
AAAAAAAAGAAACAAA
Found at i:5649263 original size:29 final size:26
Alignment explanation
Indices: 5649211--5649262 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
5649201 GTTCTTTTCC
*
5649211 AAAAAAAAGAAACAAAACAAAAAAGG
1 AAAAAAAAGAAAAAAAACAAAAAAGG
5649237 AAAAAAAAGAAGAAATAAACAAAAAA
1 AAAAAAAAGAA-AAA-AAACAAAAAA
5649263 AAGAAGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.48
27 2 0.09
28 10 0.43
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.02
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAAACAAAAAAGG
Found at i:5650253 original size:31 final size:31
Alignment explanation
Indices: 5650210--5650365 Score: 169
Period size: 31 Copynumber: 5.1 Consensus size: 31
5650200 TTCAAATACC
5650210 TTCTT-AAAGTCCACGACTCCA-TGGCACCTT
1 TTCTTCAAAGTCCACGACT-CAGTGGCACCTT
5650240 CTT-TTCAAAGTCCACGACTCAGTGGCATCCTT
1 -TTCTTCAAAGTCCACGACTCAGTGGCA-CCTT
* *
5650272 TTCTTTAAAGTCCACGATTCAGTGGCA--TT
1 TTCTTCAAAGTCCACGACTCAGTGGCACCTT
* **
5650301 TTGTCTCAAAGTCCACGACTCAGTGGCATTTT
1 TTCT-TCAAAGTCCACGACTCAGTGGCACCTT
* * *
5650333 TTCTTCAAAGCCCACAACTCCGTGGCACCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCACCTT
5650364 TT
1 TT
5650366 TCTTTTTAAA
Statistics
Matches: 107, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
29 5 0.05
30 25 0.23
31 46 0.43
32 31 0.29
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (31 bp):
TTCTTCAAAGTCCACGACTCAGTGGCACCTT
Found at i:5650380 original size:34 final size:34
Alignment explanation
Indices: 5650339--5650497 Score: 156
Period size: 34 Copynumber: 4.8 Consensus size: 34
5650329 TTTTTTCTTC
5650339 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
5650373 AAAGCCCACAACTCCGTGGCA-CTTTTTTTTCTTCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTT-TT-T
*
5650408 AAA-TCCACAACTCCGTGGCACC-----C-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
5650435 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* * * *
5650471 -AAGTCCACAATTCCATGGTACCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTT
5650498 AAGTCCATAA
Statistics
Matches: 105, Mismatches: 8, Indels: 24
0.77 0.06 0.18
Matches are distributed among these distances:
27 4 0.04
28 19 0.18
29 2 0.02
33 8 0.08
34 45 0.43
35 23 0.22
36 4 0.04
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.34
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
Found at i:5650441 original size:62 final size:63
Alignment explanation
Indices: 5650329--5650524 Score: 191
Period size: 62 Copynumber: 3.0 Consensus size: 63
5650319 CTCAGTGGCA
*
5650329 TTTTTTCTTC-AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGC
1 TTTTTTCTTCTAAA-TCCACAACTCCGTGGCACC-----C-TTTTAAAGCCCACAACTCCGTGGC
5650393 ACT-T
59 ACTCT
5650397 TTTTTTCTTCTAAATCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACTCT
1 TTTTTTCTTCTAAATCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACTCT
** * * * * * * * * * *
5650460 TTTTCCCTTTTAAGTCCACAATTCCATGGTA-CCTTTTTAAGTCCATAACTCCGTGGTACCCT
1 TTTTTTCTTCTAAATCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACTCT
5650522 TTT
1 TTT
5650525 AAGTCCACAA
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
62 56 0.50
63 26 0.23
68 28 0.25
69 3 0.03
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (63 bp):
TTTTTTCTTCTAAATCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACTCT
Found at i:5650468 original size:36 final size:34
Alignment explanation
Indices: 5650428--5650497 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
5650418 CTCCGTGGCA
*
5650428 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTT-AAGCCCACAACTCCATGGCAC-CTTTTT
* * *
5650464 CCCTTTTAAGTCCACAATTCCATGGTACCTTTTT
1 CCCTTTTAAGCCCACAACTCCATGGCACCTTTTT
5650498 AAGTCCATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 6 0.20
35 17 0.57
36 7 0.23
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (34 bp):
CCCTTTTAAGCCCACAACTCCATGGCACCTTTTT
Found at i:5650539 original size:27 final size:27
Alignment explanation
Indices: 5650464--5650542 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
5650454 CACTCTTTTT
* *
5650464 CCCTTTTAAGTCCACAATTCCATGGTA
1 CCCTTTTAAGTCCACAACTCCGTGGTA
* *
5650491 CCTTTTTAAGTCCATAACTCCGTGGTA
1 CCCTTTTAAGTCCACAACTCCGTGGTA
5650518 CCCTTTTAAGTCCACAACTCCGTGG
1 CCCTTTTAAGTCCACAACTCCGTGG
5650543 CATCTTTCTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCGTGGTA
Found at i:5650597 original size:33 final size:33
Alignment explanation
Indices: 5650560--5650851 Score: 443
Period size: 33 Copynumber: 8.9 Consensus size: 33
5650550 CTCCTTTTCA
*
5650560 AAAGCCCACACAAGTTGGTGGCAACCCTTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCT
*
5650593 AAAGCCCACATAAGTCGGTGGCAACCCTTCTC-
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCT
* *
5650625 AAAGCCCGCACAAGTTGGTGGCAACCAC-TCTCT
1 AAAGCCCACACAAGTCGGTGGCAACC-CTTCTCT
*
5650658 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCT
5650691 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC-TCT
5650724 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC-
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCT
*
5650756 AAAGCCCACACAAGTCGGTGACAACCC-TCAT-T
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC-TCT
* *
5650788 AAAGCCCACACAAGTTGGTGGCAACCATTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCT
5650821 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
5650852 AAGCCCAATA
Statistics
Matches: 235, Mismatches: 15, Indels: 18
0.88 0.06 0.07
Matches are distributed among these distances:
31 2 0.01
32 83 0.35
33 145 0.62
34 5 0.02
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.19
Consensus pattern (33 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTCT
Found at i:5650637 original size:65 final size:66
Alignment explanation
Indices: 5650560--5650851 Score: 443
Period size: 65 Copynumber: 4.5 Consensus size: 66
5650550 CTCCTTTTCA
* *
5650560 AAAGCCCACACAAGTTGGTGGCAACCCTTCTCTAAAGCCCACATAAGTCGGTGGCAACCCTTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC
5650625 -
66 T
* * *
5650625 AAAGCCCGCACAAGTTGGTGGCAACCAC-TCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACC-CTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
5650689 CT
65 CT
5650691 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
5650755 C-
65 CT
* * *
5650756 AAAGCCCACACAAGTCGGTGACAACCC-TCAT-TAAAGCCCACACAAGTTGGTGGCAACCATTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
5650819 CT
65 CT
5650821 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
5650852 AAGCCCAATA
Statistics
Matches: 209, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
64 32 0.15
65 116 0.56
66 61 0.29
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.19
Consensus pattern (66 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC
T
Found at i:5650831 original size:163 final size:163
Alignment explanation
Indices: 5650552--5650851 Score: 496
Period size: 163 Copynumber: 1.8 Consensus size: 163
5650542 GCATCTTTCT
* * *
5650552 CCTTTTCAAAAGCCCACACAAGTTGGTGGCAACCCTTCTCTAAAGCCCACATAAGTCGGTGGCAA
1 CCTTTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGACAA
*
5650617 CCCTTCTCAAAGCCCGCACAAGTTGGTGGCAACCACTCTCTAAAGCCCACACAAGTCGGTGGCAA
66 CCCTTCTCAAAGCCCACACAAGTTGGTGGCAACCACTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
5650682 CCTTTCTCTAAAGCCCACACAAGTCGGTGGCAA
131 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
5650715 CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC-AAAGCCCACACAAGTCGGTGACA
1 CCTT-TTCAAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGACA
* *
5650779 ACCC-TCATTAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGC
65 ACCCTTC-TCAAAGCCCACACAAGTTGGTGGCAACCACTCTCTAAAGCCCACACAAGTCGGTGGC
5650843 AACCCTTCT
129 AACCCTTCT
5650852 AAGCCCAATA
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
162 2 0.02
163 91 0.72
164 34 0.27
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (163 bp):
CCTTTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGACAA
CCCTTCTCAAAGCCCACACAAGTTGGTGGCAACCACTCTCTAAAGCCCACACAAGTCGGTGGCAA
CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:5650960 original size:43 final size:43
Alignment explanation
Indices: 5650897--5651173 Score: 293
Period size: 43 Copynumber: 6.1 Consensus size: 43
5650887 GCACCTTCAT
*
5650897 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
5650940 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-G-------CAC
* * *
5650992 CTTTAAGTCCAATGTCGCTGGTCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
5651035 CTTTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
5651082 TTCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
5651127 CTTTAAGTCTAATATAGTTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
5651170 CTTT
1 CTTT
5651174 TCCATCTTTA
Statistics
Matches: 197, Mismatches: 22, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
43 116 0.59
44 1 0.01
45 2 0.01
47 1 0.01
49 38 0.19
50 1 0.01
51 1 0.01
52 37 0.19
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:5651012 original size:95 final size:92
Alignment explanation
Indices: 5650846--5651226 Score: 573
Period size: 95 Copynumber: 4.1 Consensus size: 92
5650836 CGGTGGCAAC
* *
5650846 CCTTCTAAGCCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
5650911 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
5650939 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTTTCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC---TTCATCTTTAAGTCCAA
* *
5651004 TGTCGCTGGTCTTGAATCAGCACATTGGCA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
5651034 CCTTTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
5651099 AGCTGGCCTTAAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
5651126 CCTTTAAGTCTAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
*
5651191 TGTAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
5651221 TCCTTT
1 -CCTTT
5651227 TTCTTATCTT
Statistics
Matches: 261, Mismatches: 20, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
92 122 0.47
93 4 0.02
94 2 0.01
95 128 0.49
96 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:5651182 original size:187 final size:188
Alignment explanation
Indices: 5650846--5651226 Score: 622
Period size: 187 Copynumber: 2.0 Consensus size: 188
5650836 CGGTGGCAAC
5650846 CCTTCTAAGCCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGCCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
5650911 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
65 TAGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
* * * * *
5650976 TTGGCGCCTTTTTCATCTTTAAGTCCAATGTCGCTGGTCTTGAATCAGCACATTGGCA-
130 TTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAT
* *
5651034 CCTTTAAGTCCAATATA-ACTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
1 CCTTTAAGCCCAATATAGA-TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
5651098 TAGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCTAATATAGTTGGCCTTGAATCAGCATA
65 TAGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
*
5651163 TTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACAT
130 TTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAT
5651222 CCTTT
1 CCTTT
5651227 TTCTTATCTT
Statistics
Matches: 179, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
186 1 0.01
187 169 0.94
188 9 0.05
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (188 bp):
CCTTTAAGCCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAT
Found at i:5651340 original size:67 final size:67
Alignment explanation
Indices: 5651228--5651356 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 67
5651218 ACATCCTTTT
* * * *
5651228 TCTTATCTTTAAGCCCAATATCGTTGGTCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCT
1 TCTTATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCT
5651292 CA
66 CA
* * * *
5651294 TCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCTT-ATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
5651357 AAAACCCAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 4 0.08
67 45 0.85
68 4 0.08
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.40
Consensus pattern (67 bp):
TCTTATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCT
CA
Found at i:5652193 original size:19 final size:18
Alignment explanation
Indices: 5652134--5652231 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
5652124 ATTTCAACGA
*
5652134 TTTGCATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
5652153 TGTTGTATCGATA-A-AA-
1 T-TTGTATCGATACATAAG
5652169 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5652185 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
5652201 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5652217 TTTTGTATCGATACA
1 -TTTGTATCGATACA
5652232 ATATAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 21 0.32
14 1 0.02
15 4 0.06
17 4 0.06
19 25 0.38
20 10 0.15
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:5652211 original size:13 final size:13
Alignment explanation
Indices: 5652156--5652212 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
5652146 CATAAAGTGT
*
5652156 TGTATCGATAAAA
1 TGTATCGATACAA
5652169 TGTATCGATACATAA
1 TGTATCGATAC--AA
5652184 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
5652201 TGTATCGATACA
1 TGTATCGATACA
5652213 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5652230 original size:32 final size:32
Alignment explanation
Indices: 5652139--5652233 Score: 163
Period size: 32 Copynumber: 2.9 Consensus size: 32
5652129 AACGATTTGC
*
5652139 ATCGATACATAAAGTGTTGTATCGATAAAATGT
1 ATCGATACAT-AAGTGTTGTATCGATACAATGT
5652172 ATCGATACATAAGTGTTGTATCGATACAATGT
1 ATCGATACATAAGTGTTGTATCGATACAATGT
*
5652204 ATCGATACATAAGTTTTGTATCGATACAAT
1 ATCGATACATAAGTGTTGTATCGATACAAT
5652234 ATAAGCTACT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.83
33 10 0.17
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (32 bp):
ATCGATACATAAGTGTTGTATCGATACAATGT
Done.