Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 32 of 143
Found at i:9413681 original size:13 final size:12
Alignment explanation
Indices: 9413659--9413701 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
9413649 CAATTATATA
9413659 TATTTATAATTT
1 TATTTATAATTT
9413671 TATTATATAATTT
1 TATT-TATAATTT
*
9413684 TATTT-TTATTT
1 TATTTATAATTT
9413695 T-TTTATA
1 TATTTATA
9413702 TTTATAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.11
11 7 0.26
12 5 0.19
13 12 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTATAATTT
Found at i:9421328 original size:13 final size:12
Alignment explanation
Indices: 9421297--9421331 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
9421287 TTTATATCTA
9421297 TATTATA-TTTT
1 TATTATATTTTT
9421308 TATTATATTTTT
1 TATTATATTTTT
9421320 TATTAATATTTT
1 TATT-ATATTTT
9421332 CTGAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 8 0.36
13 7 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTATATTTTT
Found at i:9421928 original size:289 final size:288
Alignment explanation
Indices: 9421338--9422187 Score: 1388
Period size: 289 Copynumber: 3.0 Consensus size: 288
9421328 TTTTCTGAAA
* *
9421338 ATATTTTTTTACAAAAAAAAATTAATTCGTGTTCTAATAATGGTCAGTTCTCTAATCCGTCACGA
1 ATATTTTTTTACAAAAAAAAA-TAATTCGTGTTCTAATAATGGTCGGTTCTCTAATCCGTCATGA
* *
9421403 TGACAAGCATATTTTCACCACTCAATTGCAAATGATAAGAATATTTTTCAATAAATTTCAATTTT
65 TGACAAGCATATTTCCGCCACTCAATTGCAAATGATAAGAATATTTTTCAATAAATTTCAATTTT
*
9421468 -TTTAATTTTTTATTTAATTTTTATATTTTAACTTAATATTTTGTATA-TTTTTTT-CGTAAATA
130 GTTTAATTTTTTATTTCATTTTTATATTTTAACTTAATATTTTGTATATTTTTTTTACGTAAATA
* * *
9421530 GGCGGAAGATCGAATTTTGCAATGTTATATTCGTAATCTACCCGCTCCTCTATCACTGTTGATCG
195 GGCGGAAGATCGAATTTTGCAATGCTATATTCGTAATCTACCCGCTCCTCCATCACCGTTGATCG
*
9421595 AACCGTACTTGAGGGAAGCCGGTTTTTGT
260 AACCGTACTTGAGGGAAGCCGGTATTTGT
**
9421624 ATATTTTTTTACAAAAAAAAATAATTCGTGTTCTAATAATGGTCGGTTCTCTAATTTGTCATGAT
1 ATATTTTTTTACAAAAAAAAATAATTCGTGTTCTAATAATGGTCGGTTCTCTAATCCGTCATGAT
* *
9421689 GACAAACATATTTCCGCCACTTAATTGCAAATGATAAGAATATTTTTCAATAAATTTCAATTTTG
66 GACAAGCATATTTCCGCCACTCAATTGCAAATGATAAGAATATTTTTCAATAAATTTCAATTTTG
9421754 TTTAATTTTTTTATTTCATTTTTATATTTTAACTTAATATTTTGTATATTTTTTTTACGTAAATA
131 TTTAA-TTTTTTATTTCATTTTTATATTTTAACTTAATATTTTGTATATTTTTTTTACGTAAATA
* *
9421819 GGCGGAAGATCGAATTTTTCAATGCTATATTTGTAATCTACCCGCTCCTCCATCACCGTTGATCG
195 GGCGGAAGATCGAATTTTGCAATGCTATATTCGTAATCTACCCGCTCCTCCATCACCGTTGATCG
*
9421884 AACCGTACTTGAGGGAAGTCGGTATTTGT
260 AACCGTACTTGAGGGAAGCCGGTATTTGT
* * * *
9421913 ATTTTTTTTTACAAAAAAAATTAATTTGTGTTCTAATAATGGCCGGTTCTCTAATCCGTCATGAT
1 ATATTTTTTTACAAAAAAAAATAATTCGTGTTCTAATAATGGTCGGTTCTCTAATCCGTCATGAT
* * * *
9421978 GACAAGCATGTTTCTGCCACTCAATCGCAAATGATAAGACTATTTTTCAATAAATTTCAATTTTG
66 GACAAGCATATTTCCGCCACTCAATTGCAAATGATAAGAATATTTTTCAATAAATTTCAATTTTG
*
9422043 TTTAA-TTTTTATTTCATTTTTATATTTTAACTTAATATTTTG--TATTTTTTTTACGTAAATGG
131 TTTAATTTTTTATTTCATTTTTATATTTTAACTTAATATTTTGTATATTTTTTTTACGTAAATAG
* * *
9422105 GAGGAAGATCGAATTTTGCAATGCTATATTCGTAATCTACCCGCTTCTCCATCACCGTTGATTGA
196 GCGGAAGATCGAATTTTGCAATGCTATATTCGTAATCTACCCGCTCCTCCATCACCGTTGATCGA
9422170 ACCGTACTTGAGGGAAGC
261 ACCGTACTTGAGGGAAGC
9422188 AGGTTTTTAG
Statistics
Matches: 525, Mismatches: 35, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
285 196 0.37
286 26 0.05
287 78 0.15
288 7 0.01
289 218 0.42
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (288 bp):
ATATTTTTTTACAAAAAAAAATAATTCGTGTTCTAATAATGGTCGGTTCTCTAATCCGTCATGAT
GACAAGCATATTTCCGCCACTCAATTGCAAATGATAAGAATATTTTTCAATAAATTTCAATTTTG
TTTAATTTTTTATTTCATTTTTATATTTTAACTTAATATTTTGTATATTTTTTTTACGTAAATAG
GCGGAAGATCGAATTTTGCAATGCTATATTCGTAATCTACCCGCTCCTCCATCACCGTTGATCGA
ACCGTACTTGAGGGAAGCCGGTATTTGT
Found at i:9424036 original size:6 final size:6
Alignment explanation
Indices: 9424025--9424051 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9424015 AGATACCGAG
9424025 ACCCCA ACCCCA ACCCCA ACCCCA ACC
1 ACCCCA ACCCCA ACCCCA ACCCCA ACC
9424052 AGAGGCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCA
Found at i:9425297 original size:39 final size:39
Alignment explanation
Indices: 9425256--9425827 Score: 284
Period size: 39 Copynumber: 14.7 Consensus size: 39
9425246 TGAAGATTCG
* *
9425256 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATCA
*** ** * * * *
9425295 ATCTCTTACCCCGATTATAAGGTAGATTG-CAGCTATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAAT-CA
* * *** *
9425334 ATCTCTTATCCCGAGCCTGGGGTAGATCACCATCAGT-A
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATCA
* * * * * * *
9425372 ATTCTCTTACCCCGATCATGAGGCAGATTAT-AGCCATCTG
1 A-TCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATC-A
* * ** *
9425412 ATCTCTTACCCCGAGCTTGGGGCAAATCATCATC-AGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATC-A
* * * * *
9425451 ATCTCTTACCCCGAGCCTAGTGCAGATTG-CAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAAT-CA
* ** * *
9425490 ATCTTTTACCTTGAGCTTGGGGCAGATTGTCATCAATAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATCA
* ** * * * *
9425529 ATCTCTTACCCCGAGCTTAAGGCAAATTG-CAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAAT-CA
* * * * *
9425568 ATCTCTTACCCTGAGCCTGGGGCAGATCGTCATTAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATCA
* * *
9425607 ATCTCTTA-CCCGAGCCTGGGGCAGATTGT-AGCTATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATC-AATCA
* ** * ** * *
9425645 ATCTCTTACTCTAAGCTTGGGATAGATTATCATC-AGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATC-A
* * * *
9425684 ATCTCTTACCCCGAGCCTAGGGCAGATT-ACAACCATCTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATC-A
* *
9425723 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATC-AGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATC-A
* * *** **
9425762 ATCTCTTACCTCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATCA
* *
9425801 ATCTCTTACCCCGATCATGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
9425828 AGCAATCATT
Statistics
Matches: 389, Mismatches: 126, Indels: 36
0.71 0.23 0.07
Matches are distributed among these distances:
37 1 0.00
38 50 0.13
39 316 0.81
40 22 0.06
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGTCATCAATCA
Found at i:9425464 original size:117 final size:118
Alignment explanation
Indices: 9425334--9425814 Score: 371
Period size: 117 Copynumber: 4.1 Consensus size: 118
9425324 CAGCTATCCG
* * * * * *
9425334 ATCTCTTATCCCGAGCCTGGGGTAGA-T-CACCATCAGTAATTCTCTTACCCCGATCATGAGGCA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTACACCATCAGTAA-TCTCTTACCCCGAGCCTGGGGCA
* ** *
9425397 GATTAT-AGCCATCTGATCTCTTACCCCGAGCTTGGGGCAAATCATCATCAGCAA
65 GATTGTCAGCCAT-AAATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAGCAA
* * * * ** *
9425451 ATCTCTTACCCCGAGCCTAGTGCAGATTGCAGCCATCCG--ATCTTTTACCTTGAGCTTGGGGCA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTACA-CCATCAGTAATCTCTTACCCCGAGCCTGGGGCA
* * ** *
9425514 GATTGTCATCAATAAATCTCTTACCCCGAGCTTAAGGCAAATTGCAGCCATC--C-G
65 GATTGTCAGCCATAAATCTCTTACCCCGAGCTTGGGGCAAA-T-CA-CCATCAGCAA
* * ** *
9425568 ATCTCTTACCCTGAGCCTGGGGCAGA-T-CGTCATTAGTAAATCTCTTA-CCCGAGCCTGGGGCA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTACACCATCAGT-AATCTCTTACCCCGAGCCTGGGGCA
* ** * ** ** * * *
9425630 GATTGT-AGCTATTCGATCTCTTACTCTAAGCTTGGGATAGATTATCATCAGCAA
65 GATTGTCAGCCA-TAAATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAGCAA
9425684 ATCTCTTACCCCGAGCCTAGGGCAGATTACAACCATC--TAATCTCTTACCCCGAGCCTGGGGCA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTAC-ACCATCAGTAATCTCTTACCCCGAGCCTGGGGCA
* * * * * *
9425747 GATCGTCA-TCAGCAAATCTCTTACCTCGAGCTTGGGGCAGATCACCATCAGCCA
65 GATTGTCAGCCA-TAAATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAGCAA
9425801 ATCTCTTACCCCGA
1 ATCTCTTACCCCGA
9425815 TCATGGGGCA
Statistics
Matches: 278, Mismatches: 67, Indels: 38
0.73 0.17 0.10
Matches are distributed among these distances:
113 4 0.01
114 5 0.02
115 6 0.02
116 71 0.26
117 165 0.59
118 10 0.04
119 7 0.03
120 10 0.04
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (118 bp):
ATCTCTTACCCCGAGCCTAGGGCAGATTACACCATCAGTAATCTCTTACCCCGAGCCTGGGGCAG
ATTGTCAGCCATAAATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAGCAA
Found at i:9425777 original size:78 final size:78
Alignment explanation
Indices: 9425254--9425827 Score: 539
Period size: 78 Copynumber: 7.4 Consensus size: 78
9425244 ATTGAAGATT
* * *** * *
9425254 CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATC-GATCTCTTACCCCGATTATAAGGT
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATC-AGCAAATCTCTTACCCCGAGCCTAGGGC
*
9425318 AGATTGCAGCTATC
65 AGATTGCAGCCATC
* * ** * * * *
9425332 CGATCTCTTATCCCGAGCCTGGGGTAGATCACCATCAGTAATTCTCTTACCCCGATCAT-GAGGC
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCCCGAGCCTAG-GGC
**
9425396 AGATTATAGCCATC
65 AGATTGCAGCCATC
* * * * *
9425410 TGATCTCTTACCCCGAGCTTGGGGCAAATCATCATCAGCAAATCTCTTACCCCGAGCCTAGTGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCCCGAGCCTAGGGCA
9425475 GATTGCAGCCATC
66 GATTGCAGCCATC
* ** * * ** * *
9425488 CGATCTTTTACCTTGAGCTTGGGGCAGATTGTCATCAATAAATCTCTTACCCCGAGCTTAAGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCCCGAGCCTAGGGCA
*
9425553 AATTGCAGCCATC
66 GATTGCAGCCATC
* * * *
9425566 CGATCTCTTACCCTGAGCCTGGGGCAGATCGTCATTAGTAAATCTCTTA-CCCGAGCCTGGGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCCCGAGCCTAGGGCA
* * *
9425630 GATTGTAGCTATT
66 GATTGCAGCCATC
* ** * ** **
9425643 CGATCTCTTACTCTAAGCTTGGGATAGATTATCATCAGCAAATCTCTTACCCCGAGCCTAGGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCCCGAGCCTAGGGCA
* *
9425708 GATTACAACCATC
66 GATTGCAGCCATC
** * * *
9425721 TAATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCTCGAGCTTGGGGCA
1 CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCCCGAGCCTAGGGCA
9425786 GA-T-CA-CCATCAGC
66 GATTGCAGCCAT---C
* * *
9425799 CAATCTCTTACCCCGATCATGGGGCAGAT
1 CGATCTCTTACCCCGAGCCTGGGGCAGAT
9425828 AGCAATCATT
Statistics
Matches: 405, Mismatches: 84, Indels: 14
0.81 0.17 0.03
Matches are distributed among these distances:
75 4 0.01
76 2 0.00
77 63 0.16
78 335 0.83
79 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.26
Consensus pattern (78 bp):
CGATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCCCGAGCCTAGGGCA
GATTGCAGCCATC
Found at i:9426255 original size:17 final size:17
Alignment explanation
Indices: 9426235--9426307 Score: 85
Period size: 17 Copynumber: 4.3 Consensus size: 17
9426225 TCAAAACCCA
9426235 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAACTT
* *
9426252 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAACTT
9426269 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAACTT
* * *
9426286 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTT
9426303 ATTTT
1 ATTTT
9426308 GGATTTAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.12
17 43 0.88
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAACTT
Found at i:9426273 original size:34 final size:34
Alignment explanation
Indices: 9426235--9426316 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
9426225 TCAAAACCCA
9426235 ATTTTAAATTTTAAA-TTATTTTAAGTTTAAATTT
1 ATTTTAAA-TTTAAACTTATTTTAAGTTTAAATTT
*
9426269 ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTATTTTAAGTTTAAATTT
**
9426303 ATTTTGGATTTAAA
1 ATTTTAAATTTAAA
9426317 ATTAAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 6 0.14
34 38 0.86
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (34 bp):
ATTTTAAATTTAAACTTATTTTAAGTTTAAATTT
Found at i:9426308 original size:17 final size:17
Alignment explanation
Indices: 9426244--9426307 Score: 94
Period size: 17 Copynumber: 3.8 Consensus size: 17
9426234 AATTTTAAAT
9426244 TTTAAA-TTATTTTAAG
1 TTTAAATTTATTTTAAG
*
9426260 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAG
* *
9426277 TTTAAACTTATTTTGAG
1 TTTAAATTTATTTTAAG
9426294 TTTAAATTTATTTT
1 TTTAAATTTATTTT
9426308 GGATTTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 6 0.14
17 36 0.86
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:9426314 original size:17 final size:16
Alignment explanation
Indices: 9426244--9426316 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 16
9426234 AATTTTAAAT
*
9426244 TTTAAA-TTATTTTAA
1 TTTAAATTTATTTTGA
*
9426259 GTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTT-GA
*
9426277 TTTAAACTTATTTTGA
1 TTTAAATTTATTTTGA
9426293 GTTTAAATTTATTTTGGA
1 -TTTAAATTTATTTT-GA
9426311 TTTAAA
1 TTTAAA
9426317 ATTAAAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
16 7 0.14
17 39 0.78
18 4 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (16 bp):
TTTAAATTTATTTTGA
Found at i:9428119 original size:29 final size:29
Alignment explanation
Indices: 9428027--9428543 Score: 256
Period size: 29 Copynumber: 17.6 Consensus size: 29
9428017 TCCAAGAGGT
* * * *
9428027 CCCTGAACTGTCCAAAAATCATATTTTAA
1 CCCTAAACTTTCCAAAAATCACATTTTTA
** * *
9428056 CCCCTGTACTTTGCAAAAATCATATTTTTA
1 -CCCTAAACTTTCCAAAAATCACATTTTTA
9428086 CCCCTAAACTTTCCAAAAATCACATTTTTA
1 -CCCTAAACTTTCCAAAAATCACATTTTTA
*
9428116 CCCTCAAACTTT-CAAAAATCACATTTTTT
1 CCCT-AAACTTTCCAAAAATCACATTTTTA
* * *
9428145 CCCTCGAGC-TTCCAAAAATCACATTTTTGC
1 CCCT-AAACTTTCCAAAAATCACATTTTT-A
* *
9428175 CCCTGAAC-TTCCAAAAATCACATTTTTG
1 CCCTAAACTTTCCAAAAATCACATTTTTA
* * *
9428203 CCCTTGAAC-TTCCAAAAATTACATTTTTGC
1 CCC-TAAACTTTCCAAAAATCACATTTTT-A
* * ** * *
9428233 CCCCAACCTTT-TGAAAATTACA-TTTTC
1 CCCTAAACTTTCCAAAAATCACATTTTTA
*
9428260 CCCTCCAAACTTTCCAAAAATCACATTTTTTT
1 CCCT--AAACTTTCCAAAAATCACA-TTTTTA
* * * * *
9428292 CTCTCGAACTTT-TAAAATTCATATTTTTA
1 CCCT-AAACTTTCCAAAAATCACATTTTTA
* *
9428321 CCCTTGAAC-TTCTCAAAAATCACATTTTTT
1 CCC-TAAACTTTC-CAAAAATCACATTTTTA
** * * *
9428351 CTCCCGAAC-TTCGAAAAATTACATTTTTGCC
1 C-CCTAAACTTTCCAAAAATCACATTTTT--A
* * *
9428382 CCCTTAAC-TTCTCAAAAATTAC-TTTTATG
1 CCCTAAACTTTC-CAAAAATCACATTTT-TA
* * * *
9428411 CCTCGAGA--TTCTAAAAATCACATTTTTGC
1 CC-CTAAACTTTCCAAAAATCACATTTTT-A
*
9428440 CCCTAAA-TTTCCAAAAATCACGTTTTTA
1 CCCTAAACTTTCCAAAAATCACATTTTTA
* * *
9428468 CCCCAAA-TCTTCCCAAAATGACATTTTTA
1 CCCTAAACT-TTCCAAAAATCACATTTTTA
* *
9428497 CCCCTAAAACTTTCC-AAAATTACATTTTAA
1 -CCCT-AAACTTTCCAAAAATCACATTTTTA
* *
9428527 CCCCAAACTCTCCAAAA
1 CCCTAAACTTTCCAAAA
9428544 CTTCATTTTC
Statistics
Matches: 393, Mismatches: 66, Indels: 57
0.76 0.13 0.11
Matches are distributed among these distances:
27 4 0.01
28 38 0.10
29 181 0.46
30 135 0.34
31 27 0.07
32 8 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATCACATTTTTA
Found at i:9428168 original size:58 final size:58
Alignment explanation
Indices: 9428063--9428499 Score: 284
Period size: 58 Copynumber: 7.4 Consensus size: 58
9428053 TAACCCCTGT
* * *
9428063 ACTTTGCAAAAATCATATTTTTACCC-CTAAACTTTCCAAAAATCACATTTTTACCCTCAA
1 ACTTT-CAAAAATCACATTTTTACCCTC-GAAC-TTCCAAAAATCACATTTTTGCCCTCAA
* * *
9428123 ACTTTCAAAAATCACATTTTTTCCCTCGAGCTTCCAAAAATCACATTTTTGCCC-CTGA
1 ACTTTCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTGCCCTC-AA
* * * * *
9428181 ACTTCCAAAAATCACATTTTTGCCCTTGAACTTCCAAAAATTACATTTTTGCCCCCAA
1 ACTTTCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTGCCCTCAA
* ** * * * * * *
9428239 CCTTTTGAAAATTACA-TTTTCCCCTCCAAACTTTCCAAAAATCACATTTTTTTCTCTCGA
1 ACTTTCAAAAATCACATTTTTACCCT-CGAAC-TTCCAAAAATCACA-TTTTTGCCCTCAA
* * * * * *
9428299 ACTTTTAAAATTCATATTTTTACCCTTGAACTTCTCAAAAATCACATTTTTTCTCC-CGA
1 ACTTTCAAAAATCACATTTTTACCCTCGAACTTC-CAAAAATCACATTTTTGC-CCTCAA
* * * * * *
9428358 AC-TTCGAAAAATTACATTTTTGCCCCCTTAACTTCTCAAAAATTAC-TTTTATG-CCTCGAG
1 ACTTTC-AAAAATCACATTTTTACCCTC-GAACTTC-CAAAAATCACATTTT-TGCCCTC-AA
* * * * *
9428418 A--TTCTAAAAATCACATTTTTGCCC-CTAAATTTCCAAAAATCACGTTTTTACCC-CAA
1 ACTTTC-AAAAATCACATTTTTACCCTC-GAACTTCCAAAAATCACATTTTTGCCCTCAA
* * *
9428474 ATCTTCCCAAAATGACATTTTTACCC
1 A-CTTTCAAAAATCACATTTTTACCC
9428500 CTAAAACTTT
Statistics
Matches: 301, Mismatches: 57, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
56 2 0.01
57 20 0.07
58 120 0.40
59 92 0.31
60 59 0.20
61 8 0.03
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (58 bp):
ACTTTCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTGCCCTCAA
Found at i:9428501 original size:58 final size:57
Alignment explanation
Indices: 9428027--9428543 Score: 335
Period size: 59 Copynumber: 8.8 Consensus size: 57
9428017 TCCAAGAGGT
* * * ** * *
9428027 CCCTGAACTGTCCAAAAATCATATTTTAACCCCTGTACTTTGCAAAAATCATATTTTTAC
1 CCCTAAACT-TCCAAAAATCACATTTTTACCCC-AAAC-TTCCAAAAATCACATTTTTAC
* *
9428087 CCCTAAACTTTCCAAAAATCACATTTTTACCCTCAAACTTTCAAAAATCACATTTTT-T
1 CCCTAAAC-TTCCAAAAATCACATTTTTACCC-CAAACTTCCAAAAATCACATTTTTAC
* * * * *
9428145 CCCTCGAGCTTCCAAAAATCACATTTTTGCCCCTGAACTTCCAAAAATCACATTTTTGC
1 CCCT-AAACTTCCAAAAATCACATTTTTACCCC-AAACTTCCAAAAATCACATTTTTAC
* * * * * *** *
9428204 CCTTGAACTTCCAAAAATTACATTTTTGCCCCCAACCTTTTGAAAATTACA-TTTT-C
1 CCCTAAACTTCCAAAAATCACATTTTT-ACCCCAAACTTCCAAAAATCACATTTTTAC
* * * ** * *
9428260 CCCTCCAAACTTTCCAAAAATCACATTTTTTTCTCTCGAACTTTTAAAATTCATATTTTTAC
1 CCCT--AAAC-TTCCAAAAATCACA-TTTTTAC-CCCAAACTTCCAAAAATCACATTTTTAC
* * * * * * *
9428322 CCTTGAACTTCTCAAAAATCACATTTTTTCTCCCGAACTTCGAAAAATTACATTTTTGCC
1 CCCTAAACTTC-CAAAAATCACATTTTTAC-CCCAAACTTCCAAAAATCACATTTTT-AC
* * * * * * *
9428382 CCCTTAACTTCTCAAAAATTAC-TTTTATGCCTCGAGA-TTCTAAAAATCACATTTTTGC
1 CCCTAAACTTC-CAAAAATCACATTTT-TACC-CCAAACTTCCAAAAATCACATTTTTAC
* * * *
9428440 CCCTAAATTTCCAAAAATCACGTTTTTACCCCAAATCTTCCCAAAATGACATTTTTAC
1 CCCTAAACTTCCAAAAATCACATTTTTACCCCAAA-CTTCCAAAAATCACATTTTTAC
* *
9428498 CCCTAAAACTTTCC-AAAATTACATTTTAACCCCAAACTCTCCAAAA
1 CCCT-AAAC-TTCCAAAAATCACATTTTTACCCCAAACT-TCCAAAA
9428544 CTTCATTTTC
Statistics
Matches: 365, Mismatches: 69, Indels: 47
0.76 0.14 0.10
Matches are distributed among these distances:
56 7 0.02
57 17 0.05
58 120 0.33
59 121 0.33
60 90 0.25
61 6 0.02
62 4 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (57 bp):
CCCTAAACTTCCAAAAATCACATTTTTACCCCAAACTTCCAAAAATCACATTTTTAC
Found at i:9429375 original size:196 final size:196
Alignment explanation
Indices: 9429041--9429434 Score: 734
Period size: 196 Copynumber: 2.0 Consensus size: 196
9429031 GATAGCTCGT
*
9429041 TATTTTCGGATCTCGAAACGTTATGTCCTAACTCACTGGACATGACTTTCTTTCTCGATCACCTC
1 TATTTTCGAATCTCGAAACGTTATGTCCTAACTCACTGGACATGACTTTCTTTCTCGATCACCTC
9429106 AAAATAGCGAGACTTCCAAACAAAAATCGATTTCTTTCTTAAACATGACTTATGCATTTAAGGAT
66 AAAATAGCGAGACTTCCAAACAAAAATCGATTTCTTTCTTAAACATGACTTATGCATTTAAGGAT
* *
9429171 CGTACTTTAAAACTTTATTCGAGTTTTTAAAATTTTACAAACAAGACCCTAAAATAATCAATGTG
131 CGTACTTTAAAACTTTATTCGAGTTTTCAAAATTTTACAAACAAGACCCTAAAATAATCAATATG
9429236 G
196 G
* **
9429237 TATTTTCGAATCTCGAAACGTTATGTCCTAACTTACTGGATGTGACTTTCTTTCTCGATCACCTC
1 TATTTTCGAATCTCGAAACGTTATGTCCTAACTCACTGGACATGACTTTCTTTCTCGATCACCTC
9429302 AAAATAGCGAGACTTCCAAACAAAAATCGATTTCTTTCTTAAACATGACTTATGCATTTAAGGAT
66 AAAATAGCGAGACTTCCAAACAAAAATCGATTTCTTTCTTAAACATGACTTATGCATTTAAGGAT
9429367 CGTACTTTAAAACTTTATTCGAGTTTTCAAAATTTTACAAACAAGACCCTAAAATAATCAATATG
131 CGTACTTTAAAACTTTATTCGAGTTTTCAAAATTTTACAAACAAGACCCTAAAATAATCAATATG
9429432 G
196 G
9429433 TA
1 TA
9429435 CCAATTTTGG
Statistics
Matches: 192, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
196 192 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (196 bp):
TATTTTCGAATCTCGAAACGTTATGTCCTAACTCACTGGACATGACTTTCTTTCTCGATCACCTC
AAAATAGCGAGACTTCCAAACAAAAATCGATTTCTTTCTTAAACATGACTTATGCATTTAAGGAT
CGTACTTTAAAACTTTATTCGAGTTTTCAAAATTTTACAAACAAGACCCTAAAATAATCAATATG
G
Found at i:9430846 original size:15 final size:15
Alignment explanation
Indices: 9430828--9430857 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9430818 GGGTAGGGTA
9430828 TTAGGTTTAAAGAGT
1 TTAGGTTTAAAGAGT
*
9430843 TTAGGTTTGAAGAGT
1 TTAGGTTTAAAGAGT
9430858 ATTAAGTTTT
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:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (15 bp):
TTAGGTTTAAAGAGT
Found at i:9433074 original size:5 final size:5
Alignment explanation
Indices: 9433066--9433252 Score: 112
Period size: 5 Copynumber: 37.4 Consensus size: 5
9433056 AGTCGAGTCT
* * * * *
9433066 AATCG AATCG AATCG AGTCG AATTG AGTCG AATCG AATCG AATTG AAAT-T
1 AATCG AATCG AATCG AATCG AATCG AATCG AATCG AATCG AATCG -AATCG
* * * * * * * *
9433116 AATCG ATTCG AATCG AGTC- AAGTTG AGTAG AATCG ACTCG AATCG AGTCT
1 AATCG AATCG AATCG AATCG AA-TCG AATCG AATCG AATCG AATCG AATCG
* * * * * * **
9433166 AGTC- AAGTTG AGTGG AATCG AGTTG AATCG AATCG AATCG AATAA AATCG
1 AATCG AA-TCG AATCG AATCG AATCG AATCG AATCG AATCG AATCG AATCG
*
9433216 AATCG AATCG AGTC- AAGTCG AATCG AATCG AATCG AA
1 AATCG AATCG AATCG AA-TCG AATCG AATCG AATCG AA
9433253 GCGATTGAAA
Statistics
Matches: 136, Mismatches: 38, Indels: 16
0.72 0.20 0.08
Matches are distributed among these distances:
4 6 0.04
5 123 0.90
6 7 0.05
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (5 bp):
AATCG
Found at i:9433083 original size:20 final size:20
Alignment explanation
Indices: 9433058--9433252 Score: 126
Period size: 20 Copynumber: 9.5 Consensus size: 20
9433048 GAAATTCTAG
*
9433058 TCGAGTCTAATCGAATCGAA
1 TCGAGTCGAATCGAATCGAA
* *
9433078 TCGAGTCGAATTGAGTCGAA
1 TCGAGTCGAATCGAATCGAA
* * *
9433098 TCGAATCGAATTGAAAT-TAA
1 TCGAGTCGAATCG-AATCGAA
* *
9433118 TCGATTCGAATCGAGTC-AA
1 TCGAGTCGAATCGAATCGAA
* * *
9433137 GTTGAGTAGAATCGACTCGAA
1 -TCGAGTCGAATCGAATCGAA
* * *
9433158 TCGAGTCTAGTCAAGTTGAGTGGAA
1 TCGAGTC--G--AA-TCGAATCGAA
*
9433183 TCGAGTTGAATCGAATCGAA
1 TCGAGTCGAATCGAATCGAA
* **
9433203 TCGAATAAAATCGAATCGAA
1 TCGAGTCGAATCGAATCGAA
9433223 TCGAGTC-AAGTCGAATCGAA
1 TCGAGTCGAA-TCGAATCGAA
*
9433243 TCGAATCGAA
1 TCGAGTCGAA
9433253 GCGATTGAAA
Statistics
Matches: 136, Mismatches: 28, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
19 6 0.04
20 105 0.77
21 8 0.06
22 1 0.01
23 1 0.01
24 2 0.01
25 13 0.10
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (20 bp):
TCGAGTCGAATCGAATCGAA
Found at i:9433280 original size:29 final size:29
Alignment explanation
Indices: 9433245--9433300 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
9433235 GAATCGAATC
*
9433245 GAATCGAAGCGATTGAAAGTGTTCGAACT
1 GAATCGAAGCGAGTGAAAGTGTTCGAACT
*
9433274 GAATCGAATCGAGTGAAAGTGTTCGAA
1 GAATCGAAGCGAGTGAAAGTGTTCGAA
9433301 TCAAATTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (29 bp):
GAATCGAAGCGAGTGAAAGTGTTCGAACT
Found at i:9436126 original size:7 final size:7
Alignment explanation
Indices: 9436106--9436176 Score: 67
Period size: 7 Copynumber: 10.0 Consensus size: 7
9436096 AATTGAGGAC
*
9436106 TGAAGAT
1 TGAAAAT
9436113 TGAAAATT
1 TGAAAA-T
9436121 TG-AAAT
1 TGAAAAT
9436127 TGAAAAT
1 TGAAAAT
9436134 TGAAAAT
1 TGAAAAT
9436141 T-AAAATT
1 TGAAAA-T
*
9436148 TGAAGAT
1 TGAAAAT
9436155 TGAAAAT
1 TGAAAAT
9436162 AT-AAAAT
1 -TGAAAAT
9436169 TGGAAAAT
1 T-GAAAAT
9436177 GAGGATTGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
6 8 0.15
7 34 0.63
8 12 0.22
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (7 bp):
TGAAAAT
Found at i:9436128 original size:14 final size:14
Alignment explanation
Indices: 9436106--9436176 Score: 74
Period size: 14 Copynumber: 4.9 Consensus size: 14
9436096 AATTGAGGAC
9436106 TGAAGATTGAAAATT
1 TGAA-ATTGAAAATT
9436121 TGAAATTGAAAA-T
1 TGAAATTGAAAATT
9436134 TGAAAATT-AAAATT
1 TG-AAATTGAAAATT
*
9436148 TGAAGATTGAAAATA
1 TGAA-ATTGAAAATT
*
9436163 TAAAATTGGAAAAT
1 TGAAATT-GAAAAT
9436177 GAGGATTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
13 9 0.18
14 22 0.45
15 18 0.37
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (14 bp):
TGAAATTGAAAATT
Found at i:9436130 original size:21 final size:21
Alignment explanation
Indices: 9436106--9436170 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
9436096 AATTGAGGAC
*
9436106 TGAAGATTGAAAATTTGAAAT
1 TGAAGATTGAAAATTTAAAAT
*
9436127 TGAAAATTGAAAA-TTAAAATT
1 TGAAGATTGAAAATTTAAAA-T
*
9436148 TGAAGATTGAAAATATAAAAT
1 TGAAGATTGAAAATTTAAAAT
9436169 TG
1 TG
9436171 GAAAATGAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.13
21 28 0.74
22 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.32
Consensus pattern (21 bp):
TGAAGATTGAAAATTTAAAAT
Found at i:9437025 original size:23 final size:22
Alignment explanation
Indices: 9436974--9437209 Score: 164
Period size: 23 Copynumber: 10.5 Consensus size: 22
9436964 CGAAGTACTG
* *
9436974 AACAGAGAGCACATAAGTGCTGGGC
1 AACAGAGAGCACACAAGTGCT---A
*
9436999 AACAGAGAGAACACAAGGTGCTA
1 AACAGAGAGCACACAA-GTGCTA
*
9437022 AACAGAGAGTACAC-A-TAG-T-
1 AACAGAGAGCACACAAGT-GCTA
*
9437041 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACAC-AAGTGCTA
*
9437061 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACAC-AAGTGCTA
* *
9437084 ATCAGAGAGCAC-CGAAATGCTAA
1 AACAGAGAGCACAC-AAGTGCT-A
* * *
9437107 TAATAGAGAGCACGAGACGTGCTA
1 -AACAGAGAGCAC-ACAAGTGCTA
*
9437131 AACAGAGAGCACACACAGTGCTG
1 AACAGAGAGCACACA-AGTGCTA
*
9437154 AATAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACA-AGTGCTA
9437177 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACA-AGTGCTA
*
9437200 AACAAAGAGC
1 AACAGAGAGC
9437210 GTGCTAGTGT
Statistics
Matches: 173, Mismatches: 23, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.04
18 4 0.02
19 2 0.01
20 2 0.01
21 2 0.01
22 11 0.06
23 110 0.64
24 11 0.06
25 19 0.11
26 5 0.03
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (22 bp):
AACAGAGAGCACACAAGTGCTA
Found at i:9443371 original size:21 final size:21
Alignment explanation
Indices: 9443347--9443391 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
9443337 GTTGCAGTTG
9443347 TAATCAG-TTGTTATTAGTTTC
1 TAATCAGTTTG-TATTAGTTTC
*
9443368 TAATCAGTTTGTATTATTTTC
1 TAATCAGTTTGTATTAGTTTC
9443389 TAA
1 TAA
9443392 GTATTGAGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (21 bp):
TAATCAGTTTGTATTAGTTTC
Found at i:9443857 original size:16 final size:16
Alignment explanation
Indices: 9443815--9443858 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
9443805 ATTGTGTAAC
9443815 TAATATTATGAT-AAAT
1 TAATATTAT-ATAAAAT
*
9443831 T-ATAGTATATAAAAT
1 TAATATTATATAAAAT
9443846 TAATATTATATAA
1 TAATATTATATAA
9443859 TTAGGGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.08
15 11 0.46
16 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
TAATATTATATAAAAT
Found at i:9443956 original size:17 final size:18
Alignment explanation
Indices: 9443934--9443994 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
9443924 AAATTGATAC
9443934 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
9443951 ATATATTATATACTATATG
1 ATATA-TATAAACTATATA
*
9443970 ATATGATATAACATTATATA
1 ATAT-ATATAA-ACTATATA
9443990 ATATA
1 ATATA
9443995 GTAAGAAGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 10 0.29
20 11 0.31
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:9448550 original size:21 final size:21
Alignment explanation
Indices: 9448522--9448570 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
9448512 CTTGCAAACT
9448522 TCTACCGGTAGAAGTGAGAGC
1 TCTACCGGTAGAAGTGAGAGC
*
9448543 TTTACCGGTAGAAGTGAGAGC
1 TCTACCGGTAGAAGTGAGAGC
9448564 TCTACCG
1 TCTACCG
9448571 AAACAACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (21 bp):
TCTACCGGTAGAAGTGAGAGC
Found at i:9450693 original size:51 final size:51
Alignment explanation
Indices: 9450629--9450754 Score: 234
Period size: 51 Copynumber: 2.5 Consensus size: 51
9450619 ATTTCTCATG
9450629 ATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACA
1 ATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACA
*
9450680 ATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACG
1 ATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACA
*
9450731 ATGACACTTAGTCACCGGACCTTT
1 ATGACACTTAGTCATCGGACCTTT
9450755 CGTTTATAGC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 73 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (51 bp):
ATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACA
Found at i:9456516 original size:22 final size:21
Alignment explanation
Indices: 9456491--9456538 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
9456481 CAAATATTGA
*
9456491 TTAATAATATGATAAAGTAAGG
1 TTAATAAGATGATAAAGTAA-G
* * *
9456513 TTAAAAAGATGATTAATTAAG
1 TTAATAAGATGATAAAGTAAG
9456534 TTAAT
1 TTAAT
9456539 TATGAAAGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGATGATAAAGTAAG
Found at i:9457428 original size:41 final size:41
Alignment explanation
Indices: 9457381--9457534 Score: 209
Period size: 41 Copynumber: 3.8 Consensus size: 41
9457371 TTGTATAAAT
* *
9457381 GGAAGACTCATGTCTCGATATGAGAATGAAATTATGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAA
*
9457422 GAAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAA
* * * *
9457463 GGAAGAGTCATTTCTCGAAATGAGAATGAGATTTTGATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAA
** * *
9457504 GGAAGACTCACATCTCGAGATGAGGATGAGA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGA
9457535 ATACGGTTAA
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAA
Found at i:9463687 original size:22 final size:21
Alignment explanation
Indices: 9463662--9463709 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
9463652 AAAATATTGA
*
9463662 TTAATAATAGGATAAATTAAGG
1 TTAATAAGAGGATAAATTAA-G
* * *
9463684 TTAAAAAGATGATTAATTAAG
1 TTAATAAGAGGATAAATTAAG
9463705 TTAAT
1 TTAAT
9463710 TATGAAAGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGAGGATAAATTAAG
Found at i:9464616 original size:41 final size:41
Alignment explanation
Indices: 9464514--9464711 Score: 222
Period size: 41 Copynumber: 4.8 Consensus size: 41
9464504 GGTGTATAAA
* * *
9464514 AAGGAAGACTCATGTCTCG-GATTGAGCATGAGA-AAGTGTAT
1 AAGGAAGACTCATGTCTCGAGA-TGAGAATGAGATTA-TGAAT
*
9464555 AAATGGAAGACTCATGTCTCGATATGAGAATGAGATTATGAAT
1 -AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* *
9464598 AAGGAAGACTCATATCTCGAGATGAGAATGAGATTATAAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * * * * *
9464639 AAGAAAGACTCATGTCTCAAAATGAGAAGGAGATTTTGATT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
*
9464680 AAGGAAGACTCA-CTCTCGAGATGAGAATGAGA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGA
9464712 ATACGGTTAA
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
40 16 0.12
41 80 0.60
42 4 0.03
43 31 0.23
44 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
Found at i:9472704 original size:39 final size:39
Alignment explanation
Indices: 9472664--9473236 Score: 360
Period size: 39 Copynumber: 14.7 Consensus size: 39
9472654 TGAAGATTCG
* *
9472664 ATCTCTTACCTCGAGCCTGGGGCAGATCGTCATCAATCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATCA
* * * * * *
9472703 ATCTCTTACCCCGATCATAGGGTAGAT--TACAGCTATCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGT-CATCAAT-CA
* * * * *
9472742 ATCTCTTATCCCGAGCCTGGGGTAGATC-ACGATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTC-ATCAATCA
* * * *
9472781 ATCTCTTACCCCGATCATGGGGCAGAT--TACAGCCATCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGT-CATCAAT-CA
* *
9472820 ATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAA-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATC-A
* * * * *
9472859 ATCTCTTACCCCGAGCCTGAGGCAGATTG-CAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAAT-CA
* * * *
9472898 ATCTCTTACCCCAAGCTTGGAGCAGATCGTCATC-AGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATC-A
* * * * * *
9472937 ATCTCTTACCCCGAGCTTGGGGCAAATTG-CAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAAT-CA
* * * * *
9472976 ATCTCTTACCCTGAGCCTGGTGCAGATCATCATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATCA
** * * * * *
9473015 ATCTCTTACCCTAAGCTTGGGGCAGATTGT-AGCTATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAAT-CA
* * ** * * * *
9473054 ATCTCTTACCCTGAGCTTGGGATAAATCATCATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATCA
* * * *
9473093 ATCTCTTACCCCGAGCCTAGGGCAGATTG-CAACCATCTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATC-A
*
9473132 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATC-AGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATC-A
** * **
9473171 ATCTCTTACCTTGAGCCTGGGGCAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATCA
* *
9473210 ATCTCTTACCCCGATCATGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
9473237 GGCAATCATT
Statistics
Matches: 402, Mismatches: 111, Indels: 42
0.72 0.20 0.08
Matches are distributed among these distances:
37 1 0.00
38 24 0.06
39 353 0.88
40 23 0.06
41 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAATCA
Found at i:9472757 original size:78 final size:77
Alignment explanation
Indices: 9472664--9473236 Score: 549
Period size: 78 Copynumber: 7.3 Consensus size: 77
9472654 TGAAGATTCG
* ** * * *
9472664 ATCTCTTACCTCGAGCCTGGGGCAGATCGTCATCAATCGATCTCTTACCCCGATCATAGGGTAGA
1 ATCTCTTACC-CGAGCCTGGGGCAGATCATCATCAATAAATCTCTTACCCCGAGCATGGGGCAGA
* *
9472729 TTACAGCTATCCA
65 TTGCAGCCATCCA
* * *
9472742 ATCTCTTATCCCGAGCCTGGGGTAGATCA-CGATCAGTAAATCTCTTACCCCGATCATGGGGCAG
1 ATCTCTTA-CCCGAGCCTGGGGCAGATCATC-ATCAATAAATCTCTTACCCCGAGCATGGGGCAG
*
9472806 ATTACAGCCATCCA
64 ATTGCAGCCATCCA
* * * *
9472820 ATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAACAAATCTCTTACCCCGAGCCTGAGGCAGA
1 ATCTCTTA-CCCGAGCCTGGGGCAGATCATCATCAATAAATCTCTTACCCCGAGCATGGGGCAGA
*
9472885 TTGCAGCCATCCG
65 TTGCAGCCATCCA
* * * * ** * *
9472898 ATCTCTTACCCCAAGCTTGGAGCAGATCGTCATCAGCAAATCTCTTACCCCGAGCTTGGGGCAAA
1 ATCTCTTA-CCCGAGCCTGGGGCAGATCATCATCAATAAATCTCTTACCCCGAGCATGGGGCAGA
*
9472963 TTGCAGCCATCCG
65 TTGCAGCCATCCA
* * ** *
9472976 ATCTCTTACCCTGAGCCTGGTGCAGATCATCATCAGTAAATCTCTTACCCTAAGCTTGGGGCAGA
1 ATCTCTTACCC-GAGCCTGGGGCAGATCATCATCAATAAATCTCTTACCCCGAGCATGGGGCAGA
* * *
9473041 TTGTAGCTATCCG
65 TTGCAGCCATCCA
* ** * * * *
9473054 ATCTCTTACCCTGAGCTTGGGATAAATCATCATCAGTAAATCTCTTACCCCGAGCCTAGGGCAGA
1 ATCTCTTACCC-GAGCCTGGGGCAGATCATCATCAATAAATCTCTTACCCCGAGCATGGGGCAGA
* *
9473119 TTGCAACCATCTA
65 TTGCAGCCATCCA
* ** ** *
9473132 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCTTGAGCCTGGGGCAGA
1 ATCTCTTA-CCCGAGCCTGGGGCAGATCATCATCAATAAATCTCTTACCCCGAGCATGGGGCAGA
* *
9473197 TCAT-CA-TCAGCCA
65 T--TGCAGCCATCCA
* *
9473210 ATCTCTTACCCCGATCATGGGGCAGAT
1 ATCTCTTA-CCCGAGCCTGGGGCAGAT
9473237 GGCAATCATT
Statistics
Matches: 423, Mismatches: 65, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
77 4 0.01
78 410 0.97
79 8 0.02
80 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (77 bp):
ATCTCTTACCCGAGCCTGGGGCAGATCATCATCAATAAATCTCTTACCCCGAGCATGGGGCAGAT
TGCAGCCATCCA
Found at i:9473214 original size:156 final size:156
Alignment explanation
Indices: 9472664--9473220 Score: 615
Period size: 156 Copynumber: 3.6 Consensus size: 156
9472654 TGAAGATTCG
* * * * * * * *
9472664 ATCTCTTACCTCGAGCCTGGGGCAGATCGTCATCAATC-GATCTCTTACCCCGATCATAGGGTAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATC-AGCAAATCTCTTACCCCGAGCCTGGGGCAG
* *
9472728 ATTA-CAGCTATCCAATCTCTTATCCCGAGCCTGGGGTAGATCA-CGATCAGTAAATCTCTTACC
65 ATTATCAGCTATCCAATCTCTTA-CCCGAGCTTGGGATAGATCATC-ATCAGTAAATCTCTTACC
* *
9472791 CCGATCATGGGGCAGATTACAGCCATCCA
128 CCGAGCATGGGGCAGATTGCAGCCATCCA
* * *
9472820 ATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAACAAATCTCTTACCCCGAGCCTGAGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
* * * * * * *
9472885 TT-GCAGCCATCCGATCTCTTACCCCAAGCTT-GGAGCAGATCGTCATCAGCAAATCTCTTACCC
66 TTATCAGCTATCCAATCTCTTA-CCCGAGCTTGGGA-TAGATCATCATCAGTAAATCTCTTACCC
* * *
9472948 CGAGCTTGGGGCAAATTGCAGCCATCCG
129 CGAGCATGGGGCAGATTGCAGCCATCCA
* * * ** *
9472976 ATCTCTTACCCTGAGCCTGGTGCAGATCATCATCAGTAAATCTCTTACCCTAAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
* * *
9473041 TTGT-AGCTATCCGATCTCTTACCCTGAGCTTGGGATAAATCATCATCAGTAAATCTCTTACCCC
66 TTATCAGCTATCCAATCTCTTACCC-GAGCTTGGGATAGATCATCATCAGTAAATCTCTTACCCC
* * * *
9473105 GAGCCTAGGGCAGATTGCAACCATCTA
130 GAGCATGGGGCAGATTGCAGCCATCCA
* **
9473132 ATCTCTTACCCCGAGCCTGGGGCAGATCGTCATCAGCAAATCTCTTACCTTGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
* * *
9473197 TCATCATC-AGCCAATCTCTTACCC
66 TTATCAGCTATCCAATCTCTTACCC
9473221 CGATCATGGG
Statistics
Matches: 335, Mismatches: 58, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
155 7 0.02
156 322 0.96
157 6 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (156 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
TTATCAGCTATCCAATCTCTTACCCGAGCTTGGGATAGATCATCATCAGTAAATCTCTTACCCCG
AGCATGGGGCAGATTGCAGCCATCCA
Found at i:9473739 original size:17 final size:16
Alignment explanation
Indices: 9473653--9473742 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 16
9473643 AATTTTAAAT
*
9473653 TTTAAA-TTATTTTAA
1 TTTAAATTTATTTTGA
*
9473668 GTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTT-GA
*
9473686 TTTAAACTTATTTTGA
1 TTTAAATTTATTTTGA
9473702 GTTTAAATTTATTTTGAA
1 -TTTAAATTTATTTTG-A
9473720 TTTAAATTTATTTTTGA
1 TTTAAATTTA-TTTTGA
9473737 TTTAAA
1 TTTAAA
9473743 ATTAAAAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.11
17 51 0.77
18 8 0.12
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTAAATTTATTTTGA
Found at i:9473741 original size:34 final size:33
Alignment explanation
Indices: 9473644--9473742 Score: 137
Period size: 34 Copynumber: 2.9 Consensus size: 33
9473634 TCAAAACGCA
*
9473644 ATTTTAAATTTTAAATTATTTTAAGTTTAAATTT
1 ATTTTAAA-TTTAAATTATTTTGAGTTTAAATTT
9473678 ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAA-TTATTTTGAGTTTAAATTT
*
9473712 ATTTTGAATTTAAATTTATTTTTGA-TTTAAA
1 ATTTTAAATTTAAA-TTA-TTTTGAGTTTAAA
9473743 ATTAAAAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
33 6 0.10
34 48 0.80
35 6 0.10
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (33 bp):
ATTTTAAATTTAAATTATTTTGAGTTTAAATTT
Found at i:9474467 original size:11 final size:11
Alignment explanation
Indices: 9474451--9474475 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9474441 TTCATTAAAT
9474451 AAATAATAATA
1 AAATAATAATA
9474462 AAATAATAATA
1 AAATAATAATA
9474473 AAA
1 AAA
9474476 AGAAACCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAATAATA
Found at i:9475613 original size:30 final size:29
Alignment explanation
Indices: 9475550--9475933 Score: 309
Period size: 29 Copynumber: 13.1 Consensus size: 29
9475540 TCTAGGAGGT
* * *
9475550 CCCTAAACTATCCAAAAATCATA-TTTGAC
1 CCCTGAACT-TCCAAAAATCACATTTTTAC
* *
9475579 CCCTGTACTTCGCAAAAATCATATTTTTAC
1 CCCTGAACTTC-CAAAAATCACATTTTTAC
*
9475609 CCCTGAACTTTCCAAAAATCACATTTTTGC
1 CCCTGAAC-TTCCAAAAATCACATTTTTAC
* *
9475639 CCCTAAACTTCCAAAAATCACATTTTTGC
1 CCCTGAACTTCCAAAAATCACATTTTTAC
* * *
9475668 CCTTGAACTTCCAAAAATTACATTTTT-G
1 CCCTGAACTTCCAAAAATCACATTTTTAC
* **
9475696 CCCTTAACCTTCCAAAAATCACATTTTTTG
1 CCCTGAA-CTTCCAAAAATCACATTTTTAC
* *
9475726 CCCTCGAACTTTCAAAAATCATATTTTTA-
1 CCCT-GAACTTCCAAAAATCACATTTTTAC
9475755 CCCTCGAACTTCTCAAAAATCACATTTTT--
1 CCCT-GAACTTC-CAAAAATCACATTTTTAC
* ** * *
9475784 TCCTGAACTTTTAAAAATTACATTTTTGC
1 CCCTGAACTTCCAAAAATCACATTTTTAC
* * * *
9475813 GTCCTTAACTTCTCAAAAATTAC--TTTTAT
1 -CCCTGAACTTC-CAAAAATCACATTTTTAC
* *
9475842 GCCTCGAGA-TTCCAAAAATCACATTTTTGC
1 CCCT-GA-ACTTCCAAAAATCACATTTTTAC
* *
9475872 CCCTGAATTTTCAAAAATCACATTTTTAC
1 CCCTGAACTTCCAAAAATCACATTTTTAC
* * *
9475901 CCCAT-ATCTTCCTAAAATGACATTTTTAC
1 CCC-TGAACTTCCAAAAATCACATTTTTAC
9475930 CCCT
1 CCCT
9475934 AAAACTTTCT
Statistics
Matches: 296, Mismatches: 42, Indels: 35
0.79 0.11 0.09
Matches are distributed among these distances:
27 14 0.05
28 27 0.09
29 150 0.51
30 91 0.31
31 14 0.05
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (29 bp):
CCCTGAACTTCCAAAAATCACATTTTTAC
Found at i:9475698 original size:58 final size:59
Alignment explanation
Indices: 9475555--9475936 Score: 320
Period size: 59 Copynumber: 6.5 Consensus size: 59
9475545 GAGGTCCCTA
* ** * * * *
9475555 AACTATCCAAAAAT--CATATTTGACCCCTGTACTTCGCAAAAATCATATTTTTACCCCTG
1 AACT-TCCAAAAATCACATTTTTG-CCCCTAAACTTCTCAAAAATCACATTTTTGCCCTTG
9475614 AACTTTCCAAAAATCACATTTTTGCCCCTAAACTTC-CAAAAATCACATTTTTGCCCTTG
1 AAC-TTCCAAAAATCACATTTTTGCCCCTAAACTTCTCAAAAATCACATTTTTGCCCTTG
* * * *
9475673 AACTTCCAAAAATTACATTTTTGCCCTTAACCTTC-CAAAAATCACATTTTTTGCCCTCG
1 AACTTCCAAAAATCACATTTTTGCCCCTAAACTTCTCAAAAATCACA-TTTTTGCCCTTG
* * * * *
9475732 AACTTTCAAAAATCATATTTTT-ACCCTCGAACTTCTCAAAAATCACATTTTT-TCC-TG
1 AACTTCCAAAAATCACATTTTTGCCCCT-AAACTTCTCAAAAATCACATTTTTGCCCTTG
** * * * * *
9475789 AACTTTTAAAAATTACATTTTTGCGTCCTTAACTTCTCAAAAATTAC-TTTTATG-CCTCG
1 AACTTCCAAAAATCACATTTTTGC-CCCTAAACTTCTCAAAAATCACATTTT-TGCCCTTG
* * * *
9475848 AGA-TTCCAAAAATCACATTTTTGCCCCTGAA-TTTTCAAAAATCACATTTTTACCCCAT-
1 A-ACTTCCAAAAATCACATTTTTGCCCCTAAACTTCTCAAAAATCACATTTTT-GCCCTTG
* * * *
9475906 ATCTTCCTAAAATGACATTTTTACCCCTAAA
1 AACTTCCAAAAATCACATTTTTGCCCCTAAA
9475937 ACTTTCTAAA
Statistics
Matches: 265, Mismatches: 42, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
57 37 0.14
58 98 0.37
59 100 0.38
60 23 0.09
61 7 0.03
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (59 bp):
AACTTCCAAAAATCACATTTTTGCCCCTAAACTTCTCAAAAATCACATTTTTGCCCTTG
Found at i:9475724 original size:88 final size:87
Alignment explanation
Indices: 9475550--9475927 Score: 333
Period size: 88 Copynumber: 4.3 Consensus size: 87
9475540 TCTAGGAGGT
* *** * * *
9475550 CCCTAAACTATCCAAAAATCATATTTGACCCCT-GTACTTCGCAAAAATCATATTTTTACCCCTG
1 CCCTAAACT-TCCAAAAATCACATTTTTGCCCTCGAACTTCGCAAAAATCACATTTTT-GCCCTG
9475614 AACTTTCCAAAAATCACATTTTTGC
64 AAC-TTCCAAAAATCACATTTTTGC
* * *
9475639 CCCTAAACTTCCAAAAATCACATTTTTGCCCTTGAACTTC-CAAAAATTACATTTTTGCCCTTAA
1 CCCTAAACTTCCAAAAATCACATTTTTGCCCTCGAACTTCGCAAAAATCACATTTTTGCCCTGAA
9475703 CCTTCCAAAAATCACATTTTTTG-
66 -CTTCCAAAAATCACA-TTTTTGC
* * * * * *
9475726 CCCTCGAACTTTCAAAAATCATATTTTTACCCTCGAACTTCTCAAAAATCACATTTTT-TCCTGA
1 CCCT-AAACTTCCAAAAATCACATTTTTGCCCTCGAACTTCGCAAAAATCACATTTTTGCCCTGA
** *
9475790 ACTTTTAAAAATTACATTTTTGC
65 ACTTCCAAAAATCACATTTTTGC
* * *
9475813 GTCCTTAACTTCTCAAAAATTAC-TTTTATG-CCTCGAGA-TTC-CAAAAATCACATTTTTGCCC
1 -CCCTAAACTTC-CAAAAATCACATTTT-TGCCCTCGA-ACTTCGCAAAAATCACATTTTTG-CC
* * *
9475874 CTGAATTTTCAAAAATCACATTTTTAC
61 CTGAACTTCCAAAAATCACATTTTTGC
* * *
9475901 CCC-ATATCTTCCTAAAATGACATTTTT
1 CCCTA-AACTTCCAAAAATCACATTTTT
9475928 ACCCCTAAAA
Statistics
Matches: 239, Mismatches: 36, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
86 31 0.13
87 65 0.27
88 113 0.47
89 30 0.13
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (87 bp):
CCCTAAACTTCCAAAAATCACATTTTTGCCCTCGAACTTCGCAAAAATCACATTTTTGCCCTGAA
CTTCCAAAAATCACATTTTTGC
Found at i:9476351 original size:96 final size:98
Alignment explanation
Indices: 9476238--9476426 Score: 328
Period size: 96 Copynumber: 1.9 Consensus size: 98
9476228 AAAATATTTA
*
9476238 AAATCGAGGTAATATTCCTTTATTTCGGGTTTTGAAAATTCGTGCCTTAACTTACTAGGCACGA-
1 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTCGTGCCTTAACTTACTAGGCACGAC
9476302 TTTTT-TTCAAATCGGAATAATCGAATACCCAT
66 TTTTTCTTCAAATCGGAATAATCGAATACCCAT
*
9476334 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
1 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTCGTGCCTTAACTTACTAGGCACGAC
* *
9476399 TTTTTCTTTAAATCGGGATAATCGAATA
66 TTTTTCTTCAAATCGGAATAATCGAATA
9476427 ACCTTTTTCA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
96 62 0.71
97 5 0.06
98 20 0.23
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (98 bp):
AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTCGTGCCTTAACTTACTAGGCACGAC
TTTTTCTTCAAATCGGAATAATCGAATACCCAT
Found at i:9480958 original size:10 final size:10
Alignment explanation
Indices: 9480911--9481101 Score: 74
Period size: 10 Copynumber: 19.7 Consensus size: 10
9480901 TAATCGAAAA
*
9480911 GAATCGAGCC
1 GAATCGAGTC
*
9480921 GAATCGAATC
1 GAATCGAGTC
* *
9480931 GAA-CTGAATT
1 GAATC-GAGTC
*
9480941 TAATCGAGTC
1 GAATCGAGTC
9480951 GAATCGAGTC
1 GAATCGAGTC
* *
9480961 -AAGTCAAGTA
1 GAA-TCGAGTC
**
9480971 GAATATA-TC
1 GAATCGAGTC
*
9480980 GAATTGAGTC
1 GAATCGAGTC
* * *
9480990 TAGTCAAGTC
1 GAATCGAGTC
*
9481000 GAGTCGAGTC
1 GAATCGAGTC
9481010 GAATCGAGTC
1 GAATCGAGTC
9481020 GAA-C---T-
1 GAATCGAGTC
*
9481025 GAATCGAGTT
1 GAATCGAGTC
* *
9481035 GAATCGAATT
1 GAATCGAGTC
* *
9481045 GAATCAAATC
1 GAATCGAGTC
* *
9481055 GAATCGAATA
1 GAATCGAGTC
* * *
9481065 AAATCGAATA
1 GAATCGAGTC
*
9481075 AAATCGAGTC
1 GAATCGAGTC
*
9481085 GAATCGAATC
1 GAATCGAGTC
9481095 GAATCGA
1 GAATCGA
9481102 AGCGAGTGAA
Statistics
Matches: 140, Mismatches: 31, Indels: 20
0.73 0.16 0.10
Matches are distributed among these distances:
5 3 0.02
6 2 0.01
9 11 0.08
10 121 0.86
11 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (10 bp):
GAATCGAGTC
Found at i:9480965 original size:15 final size:15
Alignment explanation
Indices: 9480947--9481061 Score: 53
Period size: 15 Copynumber: 7.7 Consensus size: 15
9480937 AATTTAATCG
9480947 AGTCGAATCGAGTCA
1 AGTCGAATCGAGTCA
* *
9480962 AGTC-AAGTAGAAT-A
1 AGTCGAA-TCGAGTCA
* *
9480976 TA-TCGAATTGAGTCT
1 -AGTCGAATCGAGTCA
*
9480991 AGTC-AAGTCGAGTCG
1 AGTCGAA-TCGAGTCA
9481006 AGTCGAATCGAGTCGA
1 AGTCGAATCGAGTC-A
* *
9481022 ACT-GAATCGAGTTGA
1 AGTCGAATCGAG-TCA
* *
9481037 A-TCGAATTGAATCA
1 AGTCGAATCGAGTCA
*
9481051 AATCGAATCGA
1 AGTCGAATCGA
9481062 ATAAAATCGA
Statistics
Matches: 75, Mismatches: 14, Indels: 22
0.68 0.13 0.20
Matches are distributed among these distances:
14 16 0.21
15 54 0.72
16 5 0.07
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (15 bp):
AGTCGAATCGAGTCA
Found at i:9481091 original size:5 final size:5
Alignment explanation
Indices: 9480998--9481182 Score: 92
Period size: 5 Copynumber: 37.2 Consensus size: 5
9480988 TCTAGTCAAG
* * * * * *
9480998 TCGAG TCGAG TCGAA TCGAG TCGAA -CTGAA TCGAG TTGAA TCGAA TTGAA
1 TCGAA TCGAA TCGAA TCGAA TCGAA TC-GAA TCGAA TCGAA TCGAA TCGAA
* ** ** *
9481048 TCAAA TCGAA TCGAA TAAAA TCGAA TAAAA TCGAG TCGAA TCGAA TCGAA
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA
* * * * * * * *
9481098 TCGAA GCGAG T-GAAA GT-G-T TCGAA TCAAA TCGAG TCGAG TCGAA TCTAG
1 TCGAA TCGAA TCG-AA -TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA
* * *
9481147 TC-AA ACTGAA TCGAG TTGAA TCGAA TCGAA TCGAA T
1 TCGAA TC-GAA TCGAA TCGAA TCGAA TCGAA TCGAA T
9481183 GAGTGAAAGT
Statistics
Matches: 132, Mismatches: 40, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
3 1 0.01
4 5 0.04
5 120 0.91
6 6 0.05
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:9482701 original size:23 final size:23
Alignment explanation
Indices: 9482665--9482921 Score: 192
Period size: 23 Copynumber: 11.4 Consensus size: 23
9482655 AGTGTTGGGT
*
9482665 AACAGAGAGAACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
9482688 AATAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
9482707 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
9482727 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * * *
9482750 ATCATAGAGGAC-CGAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
9482773 TAATAGAGAG-A-ACGAGACGTGCTA
1 -AACAGAGAGCACAC-A-AAGTGCTA
* * * * *
9482797 AACAGTGAGCACCCACAGTACTG
1 AACAGAGAGCACACAAAGTGCTA
* * *
9482820 AACAGACAGCACACACAGTGCTG
1 AACAGAGAGCACACAAAGTGCTA
* *
9482843 AACAGACAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
9482866 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
9482889 AACAGAGAGCACACATAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
9482912 AACAGAGAGC
1 AACAGAGAGC
9482922 GTGCTAGTGT
Statistics
Matches: 191, Mismatches: 29, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
16 10 0.05
18 2 0.01
19 1 0.01
20 1 0.01
21 2 0.01
22 9 0.05
23 150 0.79
24 9 0.05
25 7 0.04
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:9489166 original size:23 final size:23
Alignment explanation
Indices: 9489106--9489181 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
9489096 GGAGAGTACC
* *
9489106 AAAGTACTGAACAGAGAGCAC-A
1 AAAGTGCTAAACAGAGAGCACAA
*
9489128 TAAGTGCTAGGCAACAGAGAGCACAA
1 AAAGTGCTA---AACAGAGAGCACAA
* *
9489154 AAAGTGCTAAACAGAGAGTACAC
1 AAAGTGCTAAACAGAGAGCACAA
9489177 AAAGT
1 AAAGT
9489182 ACTGAGCACA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 6 0.14
23 17 0.39
25 12 0.27
26 9 0.20
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (23 bp):
AAAGTGCTAAACAGAGAGCACAA
Found at i:9489200 original size:39 final size:39
Alignment explanation
Indices: 9489146--9489220 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
9489136 AGGCAACAGA
*
9489146 GAGCACAAAAAGTGCTAA-ACAGAGAGTACACAAAGTACT
1 GAGCACAAAAAGTGCTAATA-AGAGAGCACACAAAGTACT
* *
9489185 GAGCACACAAAGTGCTAATAAGAGAGCACACGAAGT
1 GAGCACAAAAAGTGCTAATAAGAGAGCACACAAAGT
9489221 GCTAATCAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 31 0.97
40 1 0.03
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACAAAAAGTGCTAATAAGAGAGCACACAAAGTACT
Found at i:9489215 original size:23 final size:24
Alignment explanation
Indices: 9489185--9489300 Score: 125
Period size: 23 Copynumber: 5.0 Consensus size: 24
9489175 ACAAAGTACT
9489185 GAGCACACAAAGTGCTAATA-AGA
1 GAGCACACAAAGTGCTAATACAGA
*
9489208 GAGCACACGAAGTGCTAAT-CAGA
1 GAGCACACAAAGTGCTAATACAGA
* * *
9489231 GAGCAC-CGAAGTGCTAACAATAGA
1 GAGCACACAAAGTGCTAA-TACAGA
**
9489255 GAGCACACTCAGTGCTAA-ACAGA
1 GAGCACACAAAGTGCTAATACAGA
*
9489278 GAGCACACACAGTGCTAA-ACAGA
1 GAGCACACAAAGTGCTAATACAGA
9489301 AAGCGCGATA
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
22 11 0.13
23 53 0.65
24 9 0.11
25 9 0.11
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (24 bp):
GAGCACACAAAGTGCTAATACAGA
Found at i:9491205 original size:11 final size:11
Alignment explanation
Indices: 9491182--9491236 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
9491172 TACCATTAGA
9491182 TTTTATAACTTT
1 TTTTATAA-TTT
9491194 TTTTATAATTT
1 TTTTATAATTT
*
9491205 TTTT-T-ATAT
1 TTTTATAATTT
*
9491214 TTTTATGATTT
1 TTTTATAATTT
*
9491225 TTTAATAATTT
1 TTTTATAATTT
9491236 T
1 T
9491237 AAATTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 7 0.19
10 2 0.05
11 20 0.54
12 8 0.22
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:9491217 original size:12 final size:12
Alignment explanation
Indices: 9491182--9491217 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
9491172 TACCATTAGA
*
9491182 TTTTATAACTTT
1 TTTTATAATTTT
9491194 TTTTATAATTTT
1 TTTTATAATTTT
9491206 TTTTAT-ATTTT
1 TTTTATAATTTT
9491217 T
1 T
9491218 ATGATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTATAATTTT
Found at i:9491235 original size:20 final size:20
Alignment explanation
Indices: 9491193--9491243 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
9491183 TTTATAACTT
*
9491193 TTTTTATAATTTTTTTTATA
1 TTTTTATAATTTTTTATATA
*
9491213 TTTTTATGATTTTTTA-ATA
1 TTTTTATAATTTTTTATATA
*
9491232 ATTTTA-AATTTT
1 TTTTTATAATTTT
9491244 AAAAGGGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 5 0.19
19 8 0.30
20 14 0.52
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTATAATTTTTTATATA
Found at i:9492006 original size:21 final size:21
Alignment explanation
Indices: 9491982--9492035 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 21
9491972 ATAAATATAA
*
9491982 ATTTTGAAATTTTTTATAAA-T
1 ATTTTG-AATTTTTTAAAAATT
9492003 ATTTTGAA--TTTTAAAAATT
1 ATTTTGAATTTTTTAAAAATT
9492022 ATTTTGTAATTTTT
1 ATTTTG-AATTTTT
9492036 GTTGAGAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.29
19 7 0.25
20 4 0.14
21 6 0.21
22 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (21 bp):
ATTTTGAATTTTTTAAAAATT
Found at i:9492020 original size:18 final size:20
Alignment explanation
Indices: 9491993--9492034 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
9491983 TTTTGAAATT
*
9491993 TTTTATAAA-TATTTTG-AA
1 TTTTAAAAATTATTTTGTAA
9492011 TTTTAAAAATTATTTTGTAA
1 TTTTAAAAATTATTTTGTAA
9492031 TTTT
1 TTTT
9492035 TGTTGAGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGTAA
Found at i:9492784 original size:21 final size:21
Alignment explanation
Indices: 9492760--9492799 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9492750 ATTGCAGGTG
9492760 TAATCAG-TTGTTATTAGTTTT
1 TAATCAGTTTG-TATTAGTTTT
9492781 TAATCAGTTTGTATTAGTT
1 TAATCAGTTTGTATTAGTT
9492800 GCTAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.55
Consensus pattern (21 bp):
TAATCAGTTTGTATTAGTTTT
Found at i:9497814 original size:21 final size:21
Alignment explanation
Indices: 9497785--9497834 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
9497775 CATCTGTTGC
9497785 AGTTG-TAATCAG-TTGTTATT
1 AGTTGCTAATCAGTTTG-TATT
*
9497805 AGTTTCTAATCAGTTTGTATT
1 AGTTGCTAATCAGTTTGTATT
9497826 AGTTGCTAA
1 AGTTGCTAA
9497835 GTATTTAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 19 0.73
22 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (21 bp):
AGTTGCTAATCAGTTTGTATT
Found at i:9498397 original size:17 final size:18
Alignment explanation
Indices: 9498377--9498437 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
9498367 TAATTGATAC
9498377 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
9498394 ATATATTATATACTATATG
1 ATATA-TATAAACTATATA
*
9498413 ATATGATATAACATTATATA
1 ATAT-ATATAA-ACTATATA
9498433 ATATA
1 ATATA
9498438 GTAAGAAGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 10 0.29
20 11 0.31
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:9505800 original size:51 final size:51
Alignment explanation
Indices: 9505726--9505861 Score: 238
Period size: 51 Copynumber: 2.7 Consensus size: 51
9505716 ACTCGCATTT
9505726 ATTT-CTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTC
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTC
*
9505776 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTC
* *
9505827 ATTTACTCACGATGACACTTAGTCACCGAACCTTT
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTT
9505862 CGTTTATAGC
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
50 4 0.05
51 78 0.95
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTC
Found at i:9511598 original size:22 final size:21
Alignment explanation
Indices: 9511573--9511620 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
9511563 CAAATATTGA
*
9511573 TTAATAATAGGATAAATTAAGG
1 TTAATAAGAGGATAAATTAA-G
* * *
9511595 TTAAAAAGATGATTAATTAAG
1 TTAATAAGAGGATAAATTAAG
9511616 TTAAT
1 TTAAT
9511621 TATGAAAGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGAGGATAAATTAAG
Found at i:9512584 original size:41 final size:41
Alignment explanation
Indices: 9512460--9512613 Score: 184
Period size: 41 Copynumber: 3.8 Consensus size: 41
9512450 TTGTATAAAT
* * * *
9512460 GGAAAACTCATGTCTCGATATGAGAACGAAATTATGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAA
* *
9512501 GAAAGACTCATGTCTCGAAATGAGAAAGAGATTATGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAA
* *
9512542 GGAAGAATCATGTCTCGAAATGAGAATGAGACTT-TGATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGA-TTATGAATAA
* ** *
9512583 GGAGGACTCACATCTCGAGATGAGAATGAGA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGA
9512614 ATACGGTTAA
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 96 0.98
42 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.23
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAA
Found at i:9516558 original size:158 final size:158
Alignment explanation
Indices: 9516263--9516586 Score: 422
Period size: 158 Copynumber: 2.1 Consensus size: 158
9516253 ATTTCTGTAC
* * *
9516263 CATATAATGCTCACACGAGCTGTGGAATGGGTCTGCTCACACGAGCTGTGAGTCAAGATGTTAAG
1 CATATAATGCTCACACAAGCTGTGAAATGGGCCTGCTCACACGAGCTGTGAGTCAAGATGTTAAG
* * * *
9516328 TTACACGATACTGCTCACAAGAGCTATGGAAAATCCGCAACATATGCCGGATCTCAACCATCAGT
66 CTACACGATACTACTCACAAGAGCTATGAAAAATCCACAACATATGCCGGATCTCAACCATCAGT
* *
9516393 AGAACATCTATGACCAGTACCCATATAT
131 AGAACATCTATGACCAGCACCAATATAT
* *
9516421 CATGTAATGCTCACACAAGCT-TAGAAATGGGCCTGCTCACACGAGCTGTGGGTCAAGATGTTAA
1 CATATAATGCTCACACAAGCTGT-GAAATGGGCCTGCTCACACGAGCTGTGAGTCAAGATGTTAA
* * * * * * *
9516485 GCTACACGATGCTATTTACATGAGCTGT-AAAGAATCCACAACATATGCTGGATCTCAGCCATC-
65 GCTACACGATACTACTCACAAGAGCTATGAAA-AATCCACAACATATGCCGGATCTCAACCATCA
9516548 GATA-AGACATCTATGACCAGCACCAATATAT
129 G-TAGA-ACATCTATGACCAGCACCAATATAT
9516579 CATATAAT
1 CATATAAT
9516587 CCCGAAATCG
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
157 5 0.03
158 138 0.97
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (158 bp):
CATATAATGCTCACACAAGCTGTGAAATGGGCCTGCTCACACGAGCTGTGAGTCAAGATGTTAAG
CTACACGATACTACTCACAAGAGCTATGAAAAATCCACAACATATGCCGGATCTCAACCATCAGT
AGAACATCTATGACCAGCACCAATATAT
Found at i:9519281 original size:25 final size:26
Alignment explanation
Indices: 9519238--9519289 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
9519228 GGAATAGATC
*
9519238 ATTGTAAATAAAATTATTGTATTCTA
1 ATTGTAAATAAAAATATTGTATTCTA
9519264 ATTGTAAA-AAAAATATTGTATTCTA
1 ATTGTAAATAAAAATATTGTATTCTA
9519289 A
1 A
9519290 AAACAAAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (26 bp):
ATTGTAAATAAAAATATTGTATTCTA
Found at i:9520234 original size:13 final size:14
Alignment explanation
Indices: 9520218--9520250 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
9520208 TATATTTTTC
9520218 TTTATATAT-AATA
1 TTTATATATAAATA
9520231 TTTATATATCAAATA
1 TTTATATAT-AAATA
9520246 TTTAT
1 TTTAT
9520251 TTTCTCCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATATATAAATA
Found at i:9520390 original size:23 final size:22
Alignment explanation
Indices: 9520364--9520421 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
9520354 ATTGTTTTTC
*
9520364 ATATAAAAATTAGAGGATCATAA
1 ATATAAAAATTA-AAGATCATAA
* *
9520387 ATATTATAAAA-TAAAGATTATAC
1 ATA-TA-AAAATTAAAGATCATAA
9520410 ATATAAAAATTA
1 ATATAAAAATTA
9520422 TATTTACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 13 0.45
24 4 0.14
25 4 0.14
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (22 bp):
ATATAAAAATTAAAGATCATAA
Found at i:9523874 original size:21 final size:23
Alignment explanation
Indices: 9523848--9523889 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9523838 AGAAGTACTA
9523848 GTAATAA-AAA-TAAAAATAAAT
1 GTAATAATAAACTAAAAATAAAT
*
9523869 GTAATAATAAACTAAAGATAA
1 GTAATAATAAACTAAAAATAA
9523890 TAAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (23 bp):
GTAATAATAAACTAAAAATAAAT
Found at i:9540202 original size:21 final size:21
Alignment explanation
Indices: 9540155--9540231 Score: 55
Period size: 21 Copynumber: 3.7 Consensus size: 21
9540145 AGTAGTGCAG
** * *
9540155 ACTTCTACCGATACTTGGGAA
1 ACTTCTACCGATACAAGCGTA
* *
9540176 AGTTCTACCGATACAAGTGTA
1 ACTTCTACCGATACAAGCGTA
* * * *
9540197 ACTTCTACGGAAACAAGCCTT
1 ACTTCTACCGATACAAGCGTA
*
9540218 ACTTTTACCGATAC
1 ACTTCTACCGATAC
9540232 TAAAAACTCC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (21 bp):
ACTTCTACCGATACAAGCGTA
Found at i:9541992 original size:2 final size:2
Alignment explanation
Indices: 9541985--9542017 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9541975 TTTTAATTTC
9541985 AT AT AT 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 AT AT AT A
9542018 CTTAATAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9546443 original size:194 final size:195
Alignment explanation
Indices: 9546106--9546551 Score: 567
Period size: 194 Copynumber: 2.3 Consensus size: 195
9546096 ACCAGTACCT
* * * * * * * *
9546106 GATGCTGCTTACACAAGCTGTCGTGGACTCGTAACATATGAGGTACTCCAGCCATCGGTATGATG
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCCCAGCCATCGATATGATA
* ** * * *
9546171 TTTGTTTATATAAATGTCTTCTAACGATGCTGCTCGCACGAGCTGTCAAGAATATGCACTTATGC
66 TCTGTGCATATAAATGTCTCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCACTTACGC
* * * **
9546236 AAAATTTCCAGCCATCGTAGGGCTTGTAATCCATTCTAAGATTCATATCTC-TTTTTCGACTCAC
131 AAAATTCCCAGCCATCGTAGGGCCTGTAATCCATCCTAAGATTCATATCTCATTTCCCGACTCAC
*
9546300 GATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCGGTACCCCAGCCATCGATACTG-T
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCCCAGCCATCGATA-TGAT
* * *
9546364 ATCTGTGCATATAACTGT-TCCCTAACGATGCTGCTCACACGAGTTGTCAAGAATATGTACTTAC
65 ATCTGTGCATATAAATGTCT-CCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCACTTAC
** *
9546428 GCATAAA-TCCCAGCCATCGTAGGGCCTGTAATCCATCCTTGGATTCATTTCTCATTTCCCGACT
129 GCA-AAATTCCCAGCCATCGTAGGGCCTGTAATCCATCCTAAGATTCATATCTCATTTCCCGACT
9546492 CAC
193 CAC
** * *
9546495 GATAATGCTCACACGAGCTGTCGAGGAATCACAACATATGCGGTACCCCAGCCATCG
1 GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCCCAGCCATCG
9546552 CGTCGGTTTC
Statistics
Matches: 217, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
193 1 0.00
194 148 0.68
195 68 0.31
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (195 bp):
GATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCCCAGCCATCGATATGATA
TCTGTGCATATAAATGTCTCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCACTTACGC
AAAATTCCCAGCCATCGTAGGGCCTGTAATCCATCCTAAGATTCATATCTCATTTCCCGACTCAC
Found at i:9550640 original size:21 final size:22
Alignment explanation
Indices: 9550609--9550650 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
9550599 ATAAAACCTC
9550609 TGTCTATTAATTCTTGCAACTG
1 TGTCTATTAATTCTTGCAACTG
*
9550631 TGTCT-TTAATTCTTTCAACT
1 TGTCTATTAATTCTTGCAACT
9550651 CATTCAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (22 bp):
TGTCTATTAATTCTTGCAACTG
Found at i:9553040 original size:21 final size:21
Alignment explanation
Indices: 9553014--9553066 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
9553004 GTTGAGATGG
*
9553014 TTCTACCGATACAA-GTATGTC
1 TTCTACCGATACAATGCATG-C
*
9553035 TTCTACCGAAACAATGCATGC
1 TTCTACCGATACAATGCATGC
*
9553056 TTTTACCGATA
1 TTCTACCGATA
9553067 TTATAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (21 bp):
TTCTACCGATACAATGCATGC
Found at i:9555170 original size:35 final size:35
Alignment explanation
Indices: 9555115--9555190 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
9555105 TTGTGTGACC
* *
9555115 CAAATTCTAAGAGATTGCTTGCAAGTCAAGTTAAA
1 CAAAATCTAAGAGATTGCTTGCAAATCAAGTTAAA
*
9555150 CAAAATCTGAGAGATTGCTTGCAAATCAAGTTAAA
1 CAAAATCTAAGAGATTGCTTGCAAATCAAGTTAAA
9555185 CAAAAT
1 CAAAAT
9555191 ATATTTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (35 bp):
CAAAATCTAAGAGATTGCTTGCAAATCAAGTTAAA
Found at i:9557013 original size:21 final size:20
Alignment explanation
Indices: 9556987--9557039 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
9556977 TTTAATTTTC
* *
9556987 ATATAATATAAATTACAAAAT
1 ATATAATATAAAATA-AAAAA
*
9557008 ATATAAAATAAAATAAAAAA
1 ATATAATATAAAATAAAAAA
*
9557028 ATATATTATAAA
1 ATATAATATAAA
9557040 CTTGAGAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
ATATAATATAAAATAAAAAA
Found at i:9559960 original size:9 final size:9
Alignment explanation
Indices: 9559937--9560018 Score: 65
Period size: 9 Copynumber: 8.7 Consensus size: 9
9559927 ATATTTTTTC
9559937 ATAAAAATA
1 ATAAAAATA
*
9559946 TTTAAAAATA
1 -ATAAAAATA
*
9559956 ATAAAAAATT
1 AT-AAAAATA
9559966 ATAAAAATA
1 ATAAAAATA
* *
9559975 AAAAAAATT
1 ATAAAAATA
9559984 ATAAAAATCA
1 ATAAAAAT-A
*
9559994 AAAAGAAATA
1 ATAA-AAATA
*
9560004 TTAAAAATA
1 ATAAAAATA
*
9560013 TTAAAA
1 ATAAAA
9560019 TTGGTATAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
9 32 0.55
10 22 0.38
11 4 0.07
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (9 bp):
ATAAAAATA
Found at i:9559963 original size:11 final size:10
Alignment explanation
Indices: 9559939--9559990 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
9559929 ATTTTTTCAT
* *
9559939 AAAAATATTT
1 AAAAATAATA
9559949 AAAAATAATA
1 AAAAATAATA
*
9559959 AAAAATTAT-
1 AAAAATAATA
9559968 AAAAATAA-A
1 AAAAATAATA
*
9559977 AAAAATTATA
1 AAAAATAATA
9559987 AAAA
1 AAAA
9559991 TCAAAAAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 14 0.40
10 21 0.60
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAAATAATA
Found at i:9559971 original size:18 final size:19
Alignment explanation
Indices: 9559937--9560018 Score: 91
Period size: 19 Copynumber: 4.3 Consensus size: 19
9559927 ATATTTTTTC
9559937 ATAAAAATATT-TAAAAATA
1 ATAAAAA-ATTATAAAAATA
9559956 ATAAAAAATTATAAAAATA
1 ATAAAAAATTATAAAAATA
9559975 A-AAAAAATTATAAAAATCA
1 ATAAAAAATTATAAAAAT-A
9559994 A-AAAGAAA-TATTAAAAATA
1 ATAAA-AAATTA-TAAAAATA
*
9560013 TTAAAA
1 ATAAAA
9560019 TTGGTATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
18 19 0.33
19 25 0.44
20 13 0.23
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (19 bp):
ATAAAAAATTATAAAAATA
Found at i:9560088 original size:16 final size:17
Alignment explanation
Indices: 9560069--9560102 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9560059 TATCAAAAGT
*
9560069 TATAAATATT-ACAAAA
1 TATAAAAATTAACAAAA
9560085 TATAAAAATTAACAAAA
1 TATAAAAATTAACAAAA
9560102 T
1 T
9560103 CTAGGGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAAAAATTAACAAAA
Found at i:9569015 original size:14 final size:14
Alignment explanation
Indices: 9568996--9569025 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9568986 AATGATTGAA
*
9568996 AAATATTTATATAT
1 AAATATATATATAT
9569010 AAATATATATATAT
1 AAATATATATATAT
9569024 AA
1 AA
9569026 TTGACTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:9575323 original size:6 final size:6
Alignment explanation
Indices: 9575312--9575345 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
9575302 ATTATGTTTT
* *
9575312 AAAATG AAAATG GAAATG GAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
9575346 ATGATACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:9578085 original size:13 final size:14
Alignment explanation
Indices: 9578058--9578087 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9578048 AACAGTTTTA
9578058 AAAATAAGCAAAAT
1 AAAATAAGCAAAAT
9578072 AAAATAAG-AAAAT
1 AAAATAAGCAAAAT
9578085 AAA
1 AAA
9578088 TATTAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAATAAGCAAAAT
Found at i:9579549 original size:23 final size:21
Alignment explanation
Indices: 9579519--9579572 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
9579509 TATATATATA
*
9579519 TATATTTTCTTTTCTTCTTTTTC
1 TATATTTT-TTCTCTT-TTTTTC
*
9579542 TATATTTTTTCTCTTTTTTTT
1 TATATTTTTTCTCTTTTTTTC
*
9579563 TAAATTTTTT
1 TATATTTTTT
9579573 GAGACACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 14 0.50
22 6 0.21
23 8 0.29
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (21 bp):
TATATTTTTTCTCTTTTTTTC
Found at i:9584839 original size:22 final size:22
Alignment explanation
Indices: 9584809--9584861 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
9584799 AGCTTACTCT
*
9584809 AGCTGTACAAGTTGGTTATACC
1 AGCTATACAAGTTGGTTATACC
9584831 AGCTATACAAGTTGGTTATACC
1 AGCTATACAAGTTGGTTATACC
9584853 AGCTATACA
1 AGCTATACA
9584862 CTTATGCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (22 bp):
AGCTATACAAGTTGGTTATACC
Found at i:9585120 original size:20 final size:21
Alignment explanation
Indices: 9585082--9585121 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9585072 TAAACCAAGC
*
9585082 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
9585103 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
9585122 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:9585341 original size:20 final size:21
Alignment explanation
Indices: 9585303--9585342 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9585293 TAAACCAAGC
*
9585303 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
9585324 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
9585343 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:9585351 original size:221 final size:220
Alignment explanation
Indices: 9584968--9585629 Score: 1207
Period size: 221 Copynumber: 3.0 Consensus size: 220
9584958 CCTTTATGCG
*
9584968 TTGATCTTTCAGGACAGATTCCTGCACTGATATCTTTGGATGCAATACTAAACAACTAATTATGG
1 TTGATCTTTCAGGACAGATTCCTGCACTGACATCTTTGGATGCAATACTAAACAACTAATTATGG
* *
9585033 CGACATTAGTAGCAAAAATAAGATAAAATTAAAGAAAATTAAACCAAGCATCACTGAGTTAGAAA
66 CGACATTAGTAGCAAAAACAGGAT-AAATTAAAGAAAATTAAACCAAGCATCACTGAGTTAGAAA
*
9585098 ATGCAATCACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAAATAATAAAATGGGAACAAATTA
130 ATGCAATCACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAAATGATAAAATGGGAACAAATTA
9585163 TACCCTAAGCAAGGAGAAATTAATGA
195 TACCCTAAGCAAGGAGAAATTAATGA
*
9585189 TTGATCTTTCAGGACAGATTCCTGCATTGACATCTTTGGATGCAATACTAAACAACTAATTATGG
1 TTGATCTTTCAGGACAGATTCCTGCACTGACATCTTTGGATGCAATACTAAACAACTAATTATGG
9585254 CGACATTAGTAGCAAAAACAGGATAACATTAAAGAAAATTAAACCAAGCATCACTGAGTTAGAAA
66 CGACATTAGTAGCAAAAACAGGATAA-ATTAAAGAAAATTAAACCAAGCATCACTGAGTTAGAAA
9585319 ATGCAATCACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAAATGATAAAATGGGAACAAATTA
130 ATGCAATCACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAAATGATAAAATGGGAACAAATTA
9585384 TACCCTAAGCAAGGAGAAATTAAATGA
195 TACCCTAAGCAAGGAGAAATT-AATGA
* * * *
9585411 CTGATCTTTTATGACAGATTCCTGCACTGACATCTTTGGATGCAATACTAAACAACTAATTGTGG
1 TTGATCTTTCAGGACAGATTCCTGCACTGACATCTTTGGATGCAATACTAAACAACTAATTATGG
*
9585476 CGACATTAGTAGCAAAAACAGGATAAATTAAAGAAAATTAAACCAAGTATCACTGAGTTAGAAAA
66 CGACATTAGTAGCAAAAACAGGATAAATTAAAGAAAATTAAACCAAGCATCACTGAGTTAGAAAA
9585541 TGCAATCACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAAATGATAAAATGGGAACAAATTAT
131 TGCAATCACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAAATGATAAAATGGGAACAAATTAT
9585606 ACCCTAAGCAAGGAGAAATTAATG
196 ACCCTAAGCAAGGAGAAATTAATG
9585630 GTCTTTTCTA
Statistics
Matches: 428, Mismatches: 11, Indels: 5
0.96 0.02 0.01
Matches are distributed among these distances:
220 6 0.01
221 331 0.77
222 91 0.21
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.25
Consensus pattern (220 bp):
TTGATCTTTCAGGACAGATTCCTGCACTGACATCTTTGGATGCAATACTAAACAACTAATTATGG
CGACATTAGTAGCAAAAACAGGATAAATTAAAGAAAATTAAACCAAGCATCACTGAGTTAGAAAA
TGCAATCACTAAGTTAAAAATGCTAAAAATGCATGCTAAAAAATGATAAAATGGGAACAAATTAT
ACCCTAAGCAAGGAGAAATTAATGA
Found at i:9585562 original size:20 final size:21
Alignment explanation
Indices: 9585524--9585563 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9585514 TAAACCAAGT
*
9585524 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
9585545 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
9585564 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:9586532 original size:17 final size:17
Alignment explanation
Indices: 9586476--9586533 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
9586466 AATATATATG
* *
9586476 GAAATGCAAAGACAAAT
1 GAAATGCAGAGACAAAA
*
9586493 GAAGATGCAGTGACAATAA
1 GAA-ATGCAGAGACAA-AA
*
9586512 -AAATGCAGGGACAAAA
1 GAAATGCAGAGACAAAA
9586528 GAAATG
1 GAAATG
9586534 TGATGACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 2 0.06
17 19 0.56
18 12 0.35
19 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.24, T:0.12
Consensus pattern (17 bp):
GAAATGCAGAGACAAAA
Found at i:9587029 original size:12 final size:12
Alignment explanation
Indices: 9586972--9587031 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
9586962 CAAGTTCTGC
*
9586972 TCTTCTTTCTTCT
1 TCTT-TTTCCTCT
9586985 TCTTTTTCCT-T
1 TCTTTTTCCTCT
* *
9586996 CTCTTTGTCATCT
1 -TCTTTTTCCTCT
9587009 TCTTTTTCCTCT
1 TCTTTTTCCTCT
9587021 TCTTTTTCCTC
1 TCTTTTTCCTC
9587032 ATCTATCTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 1 0.03
12 34 0.85
13 5 0.12
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.65
Consensus pattern (12 bp):
TCTTTTTCCTCT
Found at i:9598404 original size:26 final size:26
Alignment explanation
Indices: 9598356--9598420 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
9598346 GATCCTTGGC
9598356 CTTTCACCTACT-AAAAACTCTTGAT
1 CTTTCACCTACTAAAAAACTCTTGAT
* *
9598381 CTTTTATCTACTAAAAAACTCTTGAT
1 CTTTCACCTACTAAAAAACTCTTGAT
9598407 CTTTCACCTACTAA
1 CTTTCACCTACTAA
9598421 CTACTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 10 0.29
26 25 0.71
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.38
Consensus pattern (26 bp):
CTTTCACCTACTAAAAAACTCTTGAT
Found at i:9601859 original size:26 final size:26
Alignment explanation
Indices: 9601811--9601875 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
9601801 GACCCTTGGC
9601811 CTTTCACCTACT-AAAAACTCTTGAT
1 CTTTCACCTACTAAAAAACTCTTGAT
*
9601836 CTTTCATCTACTAAAAAACTCTTGAT
1 CTTTCACCTACTAAAAAACTCTTGAT
9601862 CTTTCACCTACTAA
1 CTTTCACCTACTAA
9601876 CTACTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
25 11 0.30
26 26 0.70
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (26 bp):
CTTTCACCTACTAAAAAACTCTTGAT
Found at i:9605349 original size:6 final size:6
Alignment explanation
Indices: 9605338--9605373 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
9605328 TATAAGAAAC
* *
9605338 ATCATT ATCATT ATCATT ATCATT AGCATT AGCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
9605374 TTTCTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (6 bp):
ATCATT
Found at i:9611717 original size:12 final size:12
Alignment explanation
Indices: 9611700--9611727 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9611690 TATTTATTGG
9611700 AAGGGCCTTTCC
1 AAGGGCCTTTCC
9611712 AAGGGCCTTTCC
1 AAGGGCCTTTCC
9611724 AAGG
1 AAGG
9611728 ACATTAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (12 bp):
AAGGGCCTTTCC
Found at i:9614661 original size:26 final size:26
Alignment explanation
Indices: 9614632--9614687 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
9614622 AATGAGTTCT
*
9614632 TGCAACGACAATTCTGGGCATGC-TCA
1 TGCAACGACAATTCTGGACAT-CATCA
*
9614658 TGCAACGACATTTCTGGACATCATCA
1 TGCAACGACAATTCTGGACATCATCA
9614684 TGCA
1 TGCA
9614688 GTGGCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.25
Consensus pattern (26 bp):
TGCAACGACAATTCTGGACATCATCA
Found at i:9615799 original size:17 final size:17
Alignment explanation
Indices: 9615777--9615810 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9615767 CATTAACACT
*
9615777 AAAATGCAATGACAATG
1 AAAATGCAACGACAATG
9615794 AAAATGCAACGACAATG
1 AAAATGCAACGACAATG
9615811 CTTACTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATG
Found at i:9616281 original size:21 final size:21
Alignment explanation
Indices: 9616240--9616282 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
9616230 TCAGCATCTT
* *
9616240 TTTTCTTCATCTTTTTCTTCC
1 TTTTCTTCAACTTTGTCTTCC
9616261 TTTTCTTCAACTTGTGT-TTCC
1 TTTTCTTCAACTT-TGTCTTCC
9616282 T
1 T
9616283 CCCTTTCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.07, C:0.26, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTCTTCAACTTTGTCTTCC
Found at i:9618272 original size:26 final size:26
Alignment explanation
Indices: 9618220--9618273 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
9618210 AACGACTTCC
* **
9618220 TGCAGCAACAATTCTGGGCATGCTCA
1 TGCAGCAACAATTCTGGACATAATCA
* *
9618246 TGCAGCGACATTTCTGGACATAATCA
1 TGCAGCAACAATTCTGGACATAATCA
9618272 TG
1 TG
9618274 TAGTGACAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (26 bp):
TGCAGCAACAATTCTGGACATAATCA
Found at i:9631040 original size:20 final size:20
Alignment explanation
Indices: 9631015--9631064 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
9631005 GTATGGGTTA
* *
9631015 AATTAAGAG-TAAATATATTT
1 AATTAA-AGTTAAAAATAGTT
9631035 AATTAAAGTTAAAAATAGTT
1 AATTAAAGTTAAAAATAGTT
9631055 AATTAAAGTT
1 AATTAAAGTT
9631065 TAATGATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
AATTAAAGTTAAAAATAGTT
Found at i:9632054 original size:51 final size:51
Alignment explanation
Indices: 9631925--9632092 Score: 228
Period size: 51 Copynumber: 3.3 Consensus size: 51
9631915 TAAACAAAAG
*
9631925 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* *
9631976 GGTCCGATGATTAAGTGCCATCGTGAGTAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* ** * * **
9632027 GGTCCGATGACTATGTGTCATCGTGAGTTTATGGATTCCTATATGGAACAAGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAAT-GAATCCTTTATGGATTAA-A
9632080 GGTCCGATGACTA
1 GGTCCGATGACTA
9632093 TATATCATCA
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 75 0.73
52 14 0.14
53 14 0.14
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
Found at i:9632654 original size:21 final size:21
Alignment explanation
Indices: 9632627--9632686 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
9632617 TAGATGCATG
9632627 ACATGTACCGGTAGAAATTAT
1 ACATGTACCGGTAGAAATTAT
* * * *
9632648 ACTTGTATCGGTAGAACTTGT
1 ACATGTACCGGTAGAAATTAT
* *
9632669 ACAAGTACCAGTAGAAAT
1 ACATGTACCGGTAGAAAT
9632687 CTGCACTATT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (21 bp):
ACATGTACCGGTAGAAATTAT
Found at i:9646614 original size:29 final size:29
Alignment explanation
Indices: 9646580--9646682 Score: 140
Period size: 29 Copynumber: 3.6 Consensus size: 29
9646570 TTGGAGATAG
9646580 CCACAAAGGCTTCCTTTAACAGAATTTTT
1 CCACAAAGGCTTCCTTTAACAGAATTTTT
* **
9646609 CCACAAAGGCTTCCTTTCATC-GAGA--TAG
1 CCACAAAGGCTTCCTTT-AACAGA-ATTTTT
9646637 CCACAAAGGCTTCCTTTAACAGAATTTTT
1 CCACAAAGGCTTCCTTTAACAGAATTTTT
9646666 CCACAAAGGCTTCCTTT
1 CCACAAAGGCTTCCTTT
9646683 CATCGAGATA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
27 3 0.05
28 20 0.32
29 37 0.59
30 3 0.05
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (29 bp):
CCACAAAGGCTTCCTTTAACAGAATTTTT
Found at i:9646636 original size:57 final size:57
Alignment explanation
Indices: 9646573--9646705 Score: 266
Period size: 57 Copynumber: 2.3 Consensus size: 57
9646563 TACTCTTTTG
9646573 GAGATAGCCACAAAGGCTTCCTTTAACAGAATTTTTCCACAAAGGCTTCCTTTCATC
1 GAGATAGCCACAAAGGCTTCCTTTAACAGAATTTTTCCACAAAGGCTTCCTTTCATC
9646630 GAGATAGCCACAAAGGCTTCCTTTAACAGAATTTTTCCACAAAGGCTTCCTTTCATC
1 GAGATAGCCACAAAGGCTTCCTTTAACAGAATTTTTCCACAAAGGCTTCCTTTCATC
9646687 GAGATAGCCACAAAGGCTT
1 GAGATAGCCACAAAGGCTT
9646706 TCCCATCGTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 76 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (57 bp):
GAGATAGCCACAAAGGCTTCCTTTAACAGAATTTTTCCACAAAGGCTTCCTTTCATC
Found at i:9646708 original size:29 final size:28
Alignment explanation
Indices: 9646573--9646705 Score: 130
Period size: 29 Copynumber: 4.7 Consensus size: 28
9646563 TACTCTTTTG
*
9646573 GAGATAGCCACAAAGGCTTCCTTT-AAC
1 GAGATAGCCACAAAGGCTTCCTTTCATC
**
9646600 -AGAATTTTTCCACAAAGGCTTCCTTTCATC
1 GAG-A--TAGCCACAAAGGCTTCCTTTCATC
*
9646630 GAGATAGCCACAAAGGCTTCCTTT-AAC
1 GAGATAGCCACAAAGGCTTCCTTTCATC
**
9646657 -AGAATTTTTCCACAAAGGCTTCCTTTCATC
1 GAG-A--TAGCCACAAAGGCTTCCTTTCATC
9646687 GAGATAGCCACAAAGGCTT
1 GAGATAGCCACAAAGGCTT
9646706 TCCCATCGTT
Statistics
Matches: 85, Mismatches: 11, Indels: 19
0.74 0.10 0.17
Matches are distributed among these distances:
26 4 0.05
27 4 0.05
28 31 0.36
29 36 0.42
30 6 0.07
31 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (28 bp):
GAGATAGCCACAAAGGCTTCCTTTCATC
Found at i:9649657 original size:2 final size:2
Alignment explanation
Indices: 9649652--9649698 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
9649642 TTTTATACGC
* **
9649652 AT AT AT AT AT AT AT AT AT AT -T AT AC GC 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 AT AT AT AT
9649693 AT AT AT
1 AT AT AT
9649699 GTTTGTTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9649681 original size:27 final size:27
Alignment explanation
Indices: 9649644--9649698 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
9649634 GTTTATTTTT
9649644 TTATACGCATATATATATATATATATA
1 TTATACGCATATATATATATATATATA
9649671 TTATACGCATATATATATATATATATA
1 TTATACGCATATATATATATATATATA
9649698 T
1 T
9649699 GTTTGTTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (27 bp):
TTATACGCATATATATATATATATATA
Found at i:9650506 original size:29 final size:28
Alignment explanation
Indices: 9650422--9650551 Score: 109
Period size: 29 Copynumber: 4.4 Consensus size: 28
9650412 AAAAATTTAG
*
9650422 TTTTGACCCTTAAACTTTCCCAAAATCACA
1 TTTTGACCC-T-AACTTTCCAAAAATCACA
* * *
9650452 TTTTAACCCCCAAACTTTCCCAAAATCACA
1 TTTTGA--CCCTAACTTTCCAAAAATCACA
*
9650482 TTTTGACCTCTAACTTTCCAAAAATTACA
1 TTTTGACC-CTAACTTTCCAAAAATCACA
* * * *
9650511 CTTTGACCCTTAAATTT-TATAAAATTACA
1 TTTTGACCC-TAACTTTCCA-AAAATCACA
9650540 TTTTGACCCTAA
1 TTTTGACCCTAA
9650552 ATTCTTCGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
28 7 0.08
29 47 0.55
30 28 0.33
32 3 0.04
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
TTTTGACCCTAACTTTCCAAAAATCACA
Found at i:9659150 original size:14 final size:14
Alignment explanation
Indices: 9659131--9659164 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9659121 AGAGTGATGT
*
9659131 TATATACATATATA
1 TATATACATAGATA
*
9659145 TATATAGATAGATA
1 TATATACATAGATA
9659159 TATATA
1 TATATA
9659165 TAGTGGCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (14 bp):
TATATACATAGATA
Found at i:9663070 original size:12 final size:12
Alignment explanation
Indices: 9663055--9663087 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
9663045 GGAAAAGCAT
*
9663055 AAAATAAAGTAG
1 AAAATAAAATAG
9663067 AAAATAAAATAG
1 AAAATAAAATAG
9663079 AAAATAAAA
1 AAAATAAAA
9663088 GCAAGATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAG
Found at i:9664699 original size:23 final size:25
Alignment explanation
Indices: 9664673--9664719 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
9664663 TCCCACTCTA
*
9664673 TCTCACC-TCCTTATTTC-TCCTTC
1 TCTCACCTTCCTTATCTCTTCCTTC
9664696 TCTCACCTTCCTTATCTCTTCCTT
1 TCTCACCTTCCTTATCTCTTCCTT
9664720 TTCAGGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 9 0.43
25 5 0.24
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.49
Consensus pattern (25 bp):
TCTCACCTTCCTTATCTCTTCCTTC
Found at i:9668349 original size:27 final size:27
Alignment explanation
Indices: 9668285--9668360 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
9668275 TTTTTTTTGG
9668285 GACCCCTTAAAAGTTGGAAAAAAAAATTT
1 GACCCCTTAAAAGTT--AAAAAAAAATTT
*
9668314 GA-CCTTTAAAAGTTAAAAAAAAA-TT
1 GACCCCTTAAAAGTTAAAAAAAAATTT
9668339 GAACCCCTTAAAA-TCTAAAAAA
1 G-ACCCCTTAAAAGT-TAAAAAA
9668361 TAATATTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 3 0.07
26 11 0.26
27 15 0.36
28 11 0.26
29 2 0.05
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (27 bp):
GACCCCTTAAAAGTTAAAAAAAAATTT
Found at i:9668821 original size:14 final size:16
Alignment explanation
Indices: 9668802--9668834 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
9668792 GATGAGGAAA
9668802 ATATTAAAT-TA-TGT
1 ATATTAAATATATTGT
9668816 ATATTAAATATATTGT
1 ATATTAAATATATTGT
9668832 ATA
1 ATA
9668835 GGGTAAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
ATATTAAATATATTGT
Found at i:9672281 original size:7 final size:7
Alignment explanation
Indices: 9672269--9672302 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
9672259 CTCAATTCAT
9672269 CCCTAAA
1 CCCTAAA
9672276 CCCTAAA
1 CCCTAAA
9672283 CCCTAAA
1 CCCTAAA
9672290 CCCTAAA
1 CCCTAAA
9672297 CTCCTA
1 C-CCTA
9672303 GTAGTCAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (7 bp):
CCCTAAA
Found at i:9676200 original size:6 final size:6
Alignment explanation
Indices: 9676189--9676226 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
9676179 TTTGAACATT
9676189 CGAGCC CGAGCC CGAGCC CGAGCC CGAGCC CGA-CC CGA
1 CGAGCC CGAGCC CGAGCC CGAGCC CGAGCC CGAGCC CGA
9676227 TCCATTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.18, C:0.50, G:0.32, T:0.00
Consensus pattern (6 bp):
CGAGCC
Found at i:9676413 original size:21 final size:21
Alignment explanation
Indices: 9676387--9676429 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9676377 TAAAAAATGT
* *
9676387 ATAAAATTATTAAATATTAAA
1 ATAAAATAAATAAATATTAAA
*
9676408 ATAAAATAAATAAATTTTAAA
1 ATAAAATAAATAAATATTAAA
9676429 A
1 A
9676430 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAATAAATAAATATTAAA
Found at i:9677109 original size:24 final size:23
Alignment explanation
Indices: 9677081--9677125 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
9677071 CCTGAGAAAT
9677081 AAGGAGAAATAAGGAAGGTGAGAG
1 AAGGAGAAATAA-GAAGGTGAGAG
*
9677105 AAGGAGAAATAAGACGGTGAG
1 AAGGAGAAATAAGAAGGTGAG
9677126 CGGGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.49, C:0.02, G:0.40, T:0.09
Consensus pattern (23 bp):
AAGGAGAAATAAGAAGGTGAGAG
Found at i:9678749 original size:17 final size:17
Alignment explanation
Indices: 9678727--9678777 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
9678717 TTAACATTCG
9678727 AAAAAAGAAAAAAAATA
1 AAAAAAGAAAAAAAATA
***
9678744 AAAAAAGAAATTTGAA-A
1 AAAAAAGAAA-AAAAATA
9678761 AAAAAAGAAAAAAAATA
1 AAAAAAGAAAAAAAATA
9678778 TAGGCATCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (17 bp):
AAAAAAGAAAAAAAATA
Found at i:9685414 original size:15 final size:15
Alignment explanation
Indices: 9685396--9685434 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
9685386 GTGTTGCAAG
9685396 CACTAATGCTACAAA
1 CACTAATGCTACAAA
* *
9685411 CACTGATGCTACGAA
1 CACTAATGCTACAAA
9685426 CACTAATGC
1 CACTAATGC
9685435 CGTGAGCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (15 bp):
CACTAATGCTACAAA
Found at i:9689254 original size:24 final size:23
Alignment explanation
Indices: 9689205--9689248 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
9689195 TTTATTTCTC
9689205 AAGAAGAAATAGCAAGAAAATATA
1 AAGAAGAAATA-CAAGAAAATATA
*
9689229 AAGAAGAAAT-CAATAAAATA
1 AAGAAGAAATACAAGAAAATA
9689249 AATAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
24 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (23 bp):
AAGAAGAAATACAAGAAAATATA
Found at i:9691964 original size:23 final size:23
Alignment explanation
Indices: 9691945--9692058 Score: 158
Period size: 23 Copynumber: 5.0 Consensus size: 23
9691935 TCCATTTACA
*
9691945 CATAAATCATATTACTATTTAAG
1 CATAAATCATATTAATATTTAAG
*
9691968 CATAAATCACATTAATATTTAAG
1 CATAAATCATATTAATATTTAAG
* * *
9691991 CACAACTCACATTAATATTTAAG
1 CATAAATCATATTAATATTTAAG
*
9692014 CATAAATCATATTAACATTTAAG
1 CATAAATCATATTAATATTTAAG
9692037 CATAAATCACT-TTAATATTTAA
1 CATAAATCA-TATTAATATTTAA
9692059 CACATTTAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
23 80 0.99
24 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.36
Consensus pattern (23 bp):
CATAAATCATATTAATATTTAAG
Found at i:9695701 original size:21 final size:21
Alignment explanation
Indices: 9695663--9695702 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9695653 GGTTCTATTT
*
9695663 CTTCCTTCTCTTCTTCCTTTC
1 CTTCCTTCTCTTCATCCTTTC
* *
9695684 CTTCCTTGTCTTGATCCTT
1 CTTCCTTCTCTTCATCCTT
9695703 CTCTTGATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.38, G:0.05, T:0.55
Consensus pattern (21 bp):
CTTCCTTCTCTTCATCCTTTC
Found at i:9713309 original size:22 final size:22
Alignment explanation
Indices: 9713215--9713297 Score: 105
Period size: 22 Copynumber: 3.8 Consensus size: 22
9713205 CCTAATAGAA
*
9713215 CACTAGGCACCAAAGTGCAAAT
1 CACTAAGCACCAAAGTGCAAAT
* *
9713237 CACTAAACACC-GAGATGCAAAT
1 CACTAAGCACCAAAG-TGCAAAT
*
9713259 CATTAAGCACCAAAGTGCAAAT
1 CACTAAGCACCAAAGTGCAAAT
*
9713281 CACTAAGCACCGAAGTG
1 CACTAAGCACCAAAGTG
9713298 TGAAACAGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 2 0.04
22 47 0.92
23 2 0.04
ACGTcount: A:0.42, C:0.27, G:0.17, T:0.14
Consensus pattern (22 bp):
CACTAAGCACCAAAGTGCAAAT
Found at i:9713848 original size:19 final size:19
Alignment explanation
Indices: 9713811--9713849 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9713801 AGACTACAAA
*
9713811 TTTCATATATTCTTGTATT
1 TTTCATATATGCTTGTATT
9713830 TTTCACTATATGCTT-TATT
1 TTTCA-TATATGCTTGTATT
9713849 T
1 T
9713850 ATCAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTCATATATGCTTGTATT
Done.