Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 118 of 126
Found at i:35379350 original size:15 final size:16
Alignment explanation
Indices: 35379330--35379362 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
35379320 AAAACCCAAT
*
35379330 AAAAAGTAA-AAAAGG
1 AAAAAGAAAGAAAAGG
35379345 AAAAAGAAAGAAAAGG
1 AAAAAGAAAGAAAAGG
35379361 AA
1 AA
35379363 GAAAAAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAGAAAAGG
Found at i:35380269 original size:14 final size:14
Alignment explanation
Indices: 35380250--35380317 Score: 84
Period size: 14 Copynumber: 4.9 Consensus size: 14
35380240 TAAAAAATAA
35380250 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
*
35380264 AAAAAAAGCAAAAG
1 AAAAAAAGAAAAAG
35380278 AAAAAAAGAAAAA-
1 AAAAAAAGAAAAAG
* * *
35380291 ACAAAAACAAAAAC
1 AAAAAAAGAAAAAG
*
35380305 AAAAATAGAAAAA
1 AAAAAAAGAAAAA
35380318 ATGAGAAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
13 11 0.24
14 35 0.76
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:35380278 original size:20 final size:20
Alignment explanation
Indices: 35380248--35380309 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
35380238 TATAAAAAAT
35380248 AAAAA-AAAAGAAAAAGAA-A
1 AAAAACAAAAGAAAAA-AAGA
*
35380267 AAAAGCAAAAGAAAAAAAGA
1 AAAAACAAAAGAAAAAAAGA
* *
35380287 AAAAACAAAA-ACAAAAACA
1 AAAAACAAAAGAAAAAAAGA
35380306 AAAA
1 AAAA
35380310 TAGAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.00
Consensus pattern (20 bp):
AAAAACAAAAGAAAAAAAGA
Found at i:35380289 original size:27 final size:25
Alignment explanation
Indices: 35380248--35380318 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 25
35380238 TATAAAAAAT
*
35380248 AAAAAAAAAGAAAAAGAAAAAAAGCAA
1 AAAAAAAAAGAAAAA-ACAAAAA-CAA
35380275 AAGAAAAAAAGAAAAAACAAAAACAA
1 AA-AAAAAAAGAAAAAACAAAAACAA
35380301 AAACAAAAATAGAAAAAA
1 AAA-AAAAA-AGAAAAAA
35380319 TGAGAAAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 1 0.03
26 10 0.25
27 16 0.40
28 13 0.32
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.01
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAACAAAAACAA
Found at i:35380290 original size:35 final size:35
Alignment explanation
Indices: 35380242--35380328 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 35
35380232 AATATATATA
* *
35380242 AAAAATAAAAAAAAAGAAAAAGAAAAA-AAGCAAA-AG
1 AAAAA-AAGAAAAAAGAAAAACAAAAACAA--AAATAG
*
35380278 AAAAAAAGAAAAAACAAAAACAAAAACAAAAATAG
1 AAAAAAAGAAAAAAGAAAAACAAAAACAAAAATAG
* *
35380313 AAAAAATGAGAAAAGA
1 AAAAAAAGAAAAAAGA
35380329 GGAGAGGTCG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 3 0.07
35 33 0.77
36 7 0.16
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (35 bp):
AAAAAAAGAAAAAAGAAAAACAAAAACAAAAATAG
Found at i:35380316 original size:20 final size:19
Alignment explanation
Indices: 35380251--35380318 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
35380241 AAAAAATAAA
35380251 AAAAAAGAAAAAGAAAAAAAG
1 AAAAAA-AAAAAG-AAAAAAG
*
35380272 CAAAAGAAAAAAAGAAAAAAC
1 -AAAA-AAAAAAAGAAAAAAG
* *
35380293 AAAAACAAAAACAAAAATAG
1 AAAAAAAAAAAGAAAAA-AG
35380313 AAAAAA
1 AAAAAA
35380319 TGAGAAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.28
20 10 0.26
21 6 0.15
22 10 0.26
23 2 0.05
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (19 bp):
AAAAAAAAAAAGAAAAAAG
Found at i:35381456 original size:99 final size:99
Alignment explanation
Indices: 35381253--35382175 Score: 417
Period size: 98 Copynumber: 9.4 Consensus size: 99
35381243 AAGATGAAAT
* *
35381253 GGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGCAGATATTATGGGAAGGATTGAGGC
1 GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGCAGATATTGTGGGAAGGATTGAGGC
* ** ** * *
35381318 CGCGACGGTAAATCCGGCT-CCGTGAGGAAGAAAT--A
66 CGCAACGGCGAATCTAG-TACC---ACGAAGATATGGA
* * *
35381353 -GGAAAGGTTGAGGTCGCAACGACGAACTCGGTGCCTTAGCAGATATTGTGGGAAGGATTGAGGC
1 GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGCAGATATTGTGGGAAGGATTGAGGC
* *
35381417 TGCAACGACGAATCTAGTACCACGAAGATATGGA
66 CGCAACGGCGAATCTAGTACCACGAAGATATGGA
* * * * *
35381451 GGGAAAGGTTTAAGTCACAACGGCGAACCCGGTACCTTAGCAGATATTGTGGAAAGGATTGAGAC
1 GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGCAGATATTGTGGGAAGGATTGAGGC
* * * *
35381516 CACAACGGCGAATCTAGTAGCATGAAGATTTGGA
66 CGCAACGGCGAATCTAGTACCACGAAGATATGGA
* * * * * * * * * * *
35381550 GGGTAAGGATT-AAGTCGCAATGGCAAACCTTGG-ACCTCAG-AAACA-TGAAGGGAAAGATTTA
1 GGGAAAGG-TTGAGGTCGCAACGGCGAACC-CGGTACCTTAGCAGATATTG-TGGGAAGGATTGA
* * * * *
35381611 AGCCGCAACAGCGAATCCAGTACCATGAAGATATAGA
63 GGCCGCAACGGCGAATCTAGTACCACGAAGATATGGA
* * * * ** * * * * * * *
35381648 GGGAAAGGTTTAAGTCACAATGGCGAACCTTGTACCTCAG-AAACA-TGAAGGGAAAGATTTAAG
1 GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGCAGATATTG-TGGGAAGGATTGAGG
* * * *
35381711 CCGCAACGGCGAATCCAATACGACGAAGATTTGGA
65 CCGCAACGGCGAATCTAGTACCACGAAGATATGGA
* * ** ** * * * * * * *
35381746 GGGAAAGGTTTAAGTCGCAGTGGCGAACCTTGTACCTCAGAAG-CA-TGAAGGGAAAGATTTAAG
1 GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGCAGATATTG-TGGGAAGGATTGAGG
* * * *
35381809 TCGTAACGGCGAATCTAGTACCATGAAGATTTGGA
65 CCGCAACGGCGAATCTAGTACCACGAAGATATGGA
* * * * ** * * * * * *
35381844 GGGTAAGGTTTAAGTCGCAACAGCGAAGCTTGG-ACCTTAG-AAACA-TGAAGGGAAAGATTTAA
1 GGGAAAGGTTGAGGTCGCAACGGCGAA-CCCGGTACCTTAGCAGATATTG-TGGGAAGGATTGAG
* * *
35381906 GCCGCAACAGCGAATCCAGTACCACGAAGATATAGA
64 GCCGCAACGGCGAATCTAGTACCACGAAGATATGGA
* * * ** * * * ** * * *
35381942 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAG-AAACA-TGAAAGGAAAGATTTAAG
1 GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGCAGATATTG-TGGGAAGGATTGAGG
* * * * * * * *
35382005 TCACAACGACGAATCCAATACTACAAAGATTTGGA
65 CCGCAACGGCGAATCTAGTACCACGAAGATATGGA
* * * * ** * * * * * * *
35382040 GGGAAATGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAG-CA-TGAAGGGAAAGATTTAAG
1 GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGCAGATATTG-TGGGAAGGATTGAGG
* * * * *
35382103 TCGCAACGGCAAATCTAGCACCACGAAGATTTGAA
65 CCGCAACGGCGAATCTAGTACCACGAAGATATGGA
* * * *
35382138 GGGAAAGGTTTAAGTCGCAATGACGAACCCGGTACCTT
1 GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTT
35382176 GGAAACATGA
Statistics
Matches: 690, Mismatches: 119, Indels: 30
0.82 0.14 0.04
Matches are distributed among these distances:
96 8 0.01
97 10 0.01
98 480 0.70
99 188 0.27
100 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (99 bp):
GGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGCAGATATTGTGGGAAGGATTGAGGC
CGCAACGGCGAATCTAGTACCACGAAGATATGGA
Found at i:35381521 original size:50 final size:50
Alignment explanation
Indices: 35381254--35381527 Score: 186
Period size: 50 Copynumber: 5.5 Consensus size: 50
35381244 AGATGAAATG
*
35381254 GGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCTTAGCAGATATTAT
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAGCAGATATTGT
* * ** * * * * *
35381303 GGGAAGGATTGAGGCCGCGACGGTAAATCCGGCT-CCGTGAGGAAGA-AAT-A
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGG-TACC-TTA-GCAGATATTGT
* * * *
35381353 GGAAAGG-TTGAGGTCGCAACGACGAACTCGGTGCCTTAGCAGATATTGT
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAGCAGATATTGT
* * * * ** * * *
35381402 GGGAAGGATTGAGGCTGCAACGACGAATCTAGTACC--ACGAAGATATGGAG
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTA-GCAGATATTG-T
* * * *
35381452 GGAAAGG-TTTAAGTCACAACGGCGAACCCGGTACCTTAGCAGATATTGT
1 GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAGCAGATATTGT
* *
35381501 GGAAAGGATTGAGACCACAACGGCGAA
1 GGAAAGGATTGAGGCCGCAACGGCGAA
35381528 TCTAGTAGCA
Statistics
Matches: 163, Mismatches: 49, Indels: 25
0.69 0.21 0.11
Matches are distributed among these distances:
47 4 0.02
48 6 0.04
49 65 0.40
50 78 0.48
51 6 0.04
52 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.32, T:0.18
Consensus pattern (50 bp):
GGAAAGGATTGAGGCCGCAACGGCGAACCCGGTACCTTAGCAGATATTGT
Found at i:35381650 original size:98 final size:98
Alignment explanation
Indices: 35381418--35382185 Score: 912
Period size: 98 Copynumber: 7.8 Consensus size: 98
35381408 GATTGAGGCT
* * * * * **
35381418 GCAACGACGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGCGAACCCGG
1 GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
* * * * *
35381483 TACCTTAGCAGATATTG--TGGAAAGGA-TTGAGACC
66 TACCTCAG-AAACA-TGAAGGGAAA-GATTTAAG-CC
* * * * * * *
35381517 ACAACGGCGAATCTAGTAGCATGAAGATTTGGAGGGTAAGGATTAAGTCGCAATGGCAAACCTTG
1 GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
*
35381582 GACCTCAGAAACATGAAGGGAAAGATTTAAGCC
66 TACCTCAGAAACATGAAGGGAAAGATTTAAGCC
* * * * *
35381615 GCAACAGCGAATCCAGTACCATGAAGATATAGAGGGAAAGGTTTAAGTCACAATGGCGAACCTTG
1 GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
35381680 TACCTCAGAAACATGAAGGGAAAGATTTAAGCC
66 TACCTCAGAAACATGAAGGGAAAGATTTAAGCC
* * *
35381713 GCAACGGCGAATCCAATACGACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAGTGGCGAACCTTG
1 GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
* *
35381778 TACCTCAGAAGCATGAAGGGAAAGATTTAAGTC
66 TACCTCAGAAACATGAAGGGAAAGATTTAAGCC
* * * * ** *
35381811 GTAACGGCGAATCTAGTACCATGAAGATTTGGAGGGTAAGGTTTAAGTCGCAACAGCGAAGCTTG
1 GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
* *
35381876 GACCTTAGAAACATGAAGGGAAAGATTTAAGCC
66 TACCTCAGAAACATGAAGGGAAAGATTTAAGCC
* * *
35381909 GCAACAGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
1 GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
* *
35381974 TACCTCAGAAACATGAAAGGAAAGATTTAAGTC
66 TACCTCAGAAACATGAAGGGAAAGATTTAAGCC
* * * * * * * *
35382007 ACAACGACGAATCCAATACTACAAAGATTTGGAGGGAAATGTTTAAGTCACAACGGCGAACCTTG
1 GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
* *
35382072 TACCTCAGAAGCATGAAGGGAAAGATTTAAGTC
66 TACCTCAGAAACATGAAGGGAAAGATTTAAGCC
* * * * * **
35382105 GCAACGGCAAATCTAGCACCACGAAGATTTGAAGGGAAAGGTTTAAGTCGCAATGACGAACCCGG
1 GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
**
35382170 TACCTTGGAAACATGA
66 TACCTCAGAAACATGA
35382186 CGAGAAAGGT
Statistics
Matches: 568, Mismatches: 98, Indels: 7
0.84 0.15 0.01
Matches are distributed among these distances:
97 2 0.00
98 498 0.88
99 68 0.12
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.19
Consensus pattern (98 bp):
GCAACGGCGAATCCAGTACCACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTG
TACCTCAGAAACATGAAGGGAAAGATTTAAGCC
Found at i:35382183 original size:294 final size:293
Alignment explanation
Indices: 35381419--35382185 Score: 1083
Period size: 294 Copynumber: 2.6 Consensus size: 293
35381409 ATTGAGGCTG
* * * **
35381419 CAACGACGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGCGAACCCGGT
1 CAACGACGAATCCAATACCACGAAGATTTGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGT
* * * * * * *
35381484 ACCTTAGCAG-AT-ATTGTGGAAAGGA-TTGAGACCACAACGGCGAATCTAGTAGCATGAAGATT
66 ACCTCAGAAGCATGA-AG-GGAAA-GATTTAAG-TCGCAACGGCGAATCTAGTACCATGAAGATT
* * * *
35381546 TGGAGGGTAAGGATTAAGTCGCAATGGCAAACCTTGGACCTCAGAAACATGAAGGGAAAGATTTA
127 TGGAGGGTAAGGTTTAAGTCGCAATGACGAACC-TGGACCTTAGAAACATGAAGGGAAAGATTTA
*
35381611 AGCCGCAACAGCGAATCCAGTACCATGAAGATATAGAGGGAAAGGTTTAAGTCACAATGGCGAAC
191 AGCCGCAACAGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAGTCACAATGGCGAAC
* *
35381676 CTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGCCG
256 CTTGTACCTCAGAAACATGAAAGGAAAGATTTAAGCCA
* * * **
35381714 CAACGGCGAATCCAATACGACGAAGATTTGGAGGGAAAGGTTTAAGTCGCAGTGGCGAACCTTGT
1 CAACGACGAATCCAATACCACGAAGATTTGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGT
*
35381779 ACCTCAGAAGCATGAAGGGAAAGATTTAAGTCGTAACGGCGAATCTAGTACCATGAAGATTTGGA
66 ACCTCAGAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCATGAAGATTTGGA
* *
35381844 GGGTAAGGTTTAAGTCGCAA-CAGCGAAGCTTGGACCTTAGAAACATGAAGGGAAAGATTTAAGC
131 GGGTAAGGTTTAAGTCGCAATGA-CGAA-CCTGGACCTTAGAAACATGAAGGGAAAGATTTAAGC
*
35381908 CGCAACAGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTT
194 CGCAACAGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAGTCACAATGGCGAACCTT
*
35381973 GTACCTCAGAAACATGAAAGGAAAGATTTAAGTCA
259 GTACCTCAGAAACATGAAAGGAAAGATTTAAGCCA
* * *
35382008 CAACGACGAATCCAATACTACAAAGATTTGGAGGGAAATGTTTAAGTCACAACGGCGAACCTTGT
1 CAACGACGAATCCAATACCACGAAGATTTGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGT
* * * *
35382073 ACCTCAGAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCAAATCTAGCACCACGAAGATTTGAA
66 ACCTCAGAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCATGAAGATTTGGA
* * *
35382138 GGGAAAGGTTTAAGTCGCAATGACGAACCCGGTACCTTGGAAACATGA
131 GGGTAAGGTTTAAGTCGCAATGACGAACCTGG-ACCTTAGAAACATGA
35382186 CGAGAAAGGT
Statistics
Matches: 419, Mismatches: 46, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
293 3 0.01
294 338 0.81
295 74 0.18
296 3 0.01
297 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (293 bp):
CAACGACGAATCCAATACCACGAAGATTTGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGT
ACCTCAGAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCATGAAGATTTGGA
GGGTAAGGTTTAAGTCGCAATGACGAACCTGGACCTTAGAAACATGAAGGGAAAGATTTAAGCCG
CAACAGCGAATCCAGTACCACGAAGATATAGAGGGAAAGGTTTAAGTCACAATGGCGAACCTTGT
ACCTCAGAAACATGAAAGGAAAGATTTAAGCCA
Found at i:35382436 original size:51 final size:50
Alignment explanation
Indices: 35382267--35382439 Score: 129
Period size: 51 Copynumber: 3.4 Consensus size: 50
35382257 GACAAGTCGT
*
35382267 TATCTT-TCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAATTCC
1 TATCTTCT-TGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAA-GTCAAATCC
* * *** * *** * * *
35382318 TATCCTCTTGAAGTTGTAGTAA-AGTTGGATTAA-AAACAAATAAACAGGTCTT
1 TATCTTCTTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAAGTCAA-A--TC-C
35382370 TATC-TCTTTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAATGTCAAATCC
1 TATCTTC-TTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAA-GTCAAATCC
35382421 TATCTTCTTGAAGTTGCAG
1 TATCTTCTTGAAGTTGCAG
35382440 CGAAGTTGGA
Statistics
Matches: 88, Mismatches: 24, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
48 3 0.03
49 3 0.03
50 7 0.08
51 38 0.43
52 23 0.26
53 7 0.08
54 4 0.05
55 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (50 bp):
TATCTTCTTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAAGTCAAATCC
Found at i:35382446 original size:103 final size:103
Alignment explanation
Indices: 35382266--35382455 Score: 310
Period size: 103 Copynumber: 1.8 Consensus size: 103
35382256 TGACAAGTCG
*
35382266 TTATCTTTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAATTCCTATCCTCTTGAAG
1 TTATCTTTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAG
* *
35382331 TTGTAGTAAAGTTGGATTAAAAACAAATAAACAGGTCT
66 TTGCAGCAAAGTTGGATTAAAAACAAATAAACAGGTCT
* *
35382369 TTATCTCTT-TGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAATGTCAAATCCTATCTTCTTGAA
1 TTATCT-TTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAA
*
35382433 GTTGCAGCGAAGTTGGATTAAAA
65 GTTGCAGCAAAGTTGGATTAAAA
35382456 CTACAACATC
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 78 0.98
104 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (103 bp):
TTATCTTTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAG
TTGCAGCAAAGTTGGATTAAAAACAAATAAACAGGTCT
Found at i:35382487 original size:103 final size:102
Alignment explanation
Indices: 35382277--35382492 Score: 265
Period size: 103 Copynumber: 2.1 Consensus size: 102
35382267 TATCTTTCTG
* * *
35382277 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAATTCCTATCCTCTTGAAGTTGTAGTAAAG
1 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGCAAAG
* ** *
35382342 TTGGATTAAAAACAAATAAACAGGTCTTTATCTCTTTG
66 TTGGATTAAAAACAAATAAACA-GTCTTAATCTCCCTA
* * *
35382380 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAATGTCAAATCCTATCTTCTTGAAGTTGCAGCGAAG
1 AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGCAAAG
** *
35382445 TTGGATTAAAACTACAACATCGA-A-TCTTAATTTCCCTA
66 TTGGATTAAAA--ACAA-ATAAACAGTCTTAATCTCCCTA
35382483 AAGTTGCAGT
1 AAGTTGCAGT
35382493 GGAATAAAGT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
103 89 0.92
105 5 0.05
106 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (102 bp):
AAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGCAAAG
TTGGATTAAAAACAAATAAACAGTCTTAATCTCCCTA
Found at i:35382582 original size:39 final size:38
Alignment explanation
Indices: 35382525--35382666 Score: 131
Period size: 39 Copynumber: 3.6 Consensus size: 38
35382515 TCAACCAATT
* *
35382525 TTTTACCGCGAGCTTGGGGCAGATTGAAGCCATTTGATC
1 TTTTACCCCGAGCCTGGGGCAGATTGAA-CCATTTGATC
* * * * ****
35382564 TTTTACCCTGAGCCTGGGGCAGATCATCATCAACCAAATC
1 TTTTACCCCGAGCCTGGGGCAGAT--TGAACCATTTGATC
*
35382604 TCTTACCCCGAGCCTGGGGCAGATTGCAACCATTTGATC
1 TTTTACCCCGAGCCTGGGGCAGATTG-AACCATTTGATC
**
35382643 TTTTACCCCGAGTTTGGGGCAGAT
1 TTTTACCCCGAGCCTGGGGCAGAT
35382667 CATCGTCAAC
Statistics
Matches: 78, Mismatches: 22, Indels: 6
0.74 0.21 0.06
Matches are distributed among these distances:
38 1 0.01
39 48 0.62
40 27 0.35
41 2 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (38 bp):
TTTTACCCCGAGCCTGGGGCAGATTGAACCATTTGATC
Found at i:35382688 original size:39 final size:39
Alignment explanation
Indices: 35382561--35382860 Score: 160
Period size: 39 Copynumber: 7.7 Consensus size: 39
35382551 AAGCCATTTG
* * *
35382561 ATCTTTTACCCTGAGCCTGGGGCAGATCATCATCAACCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCGTCAACC-A
35382601 ATCTCTTACCCCGAGCCTGGGGCAGAT--T-G-CAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCGTCAACCA
* **
35382636 TTTGATCTTTTACCCCGAGTTTGGGGCAGATCATCGTCAACCA
1 ----ATCTCTTACCCCGAGCCTGGGGCAGATCATCGTCAACCA
* ** * *
35382679 ATCTCTTACCCTGAGCCTAAGGTA-A--ATTG-CAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCGTCAACCA
* ** *
35382714 TTTGATCTTTTACCCTAAGCTTGGGGCAGATCATCGTCAACCA
1 ----ATCTCTTACCCCGAGCCTGGGGCAGATCATCGTCAACCA
* * *
35382757 ATCTCTTACCTCGAACCTAGGGCAGAT--T-G-CAACC-
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCGTCAACCA
* * * *
35382791 ATCTGACCTTTTACCTCGAG-CTTGGGCAGATCACCATCAACCA
1 ATCT---C--TTACCCCGAGCCTGGGGCAGATCATCGTCAACCA
* *
35382834 ATCTCCTACCCCGAGCTTGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
35382861 TGTAGTTATC
Statistics
Matches: 197, Mismatches: 36, Indels: 55
0.68 0.12 0.19
Matches are distributed among these distances:
34 4 0.02
35 12 0.06
36 9 0.05
37 2 0.01
38 20 0.10
39 97 0.49
40 27 0.14
41 1 0.01
42 9 0.05
43 16 0.08
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCGTCAACCA
Found at i:35382725 original size:78 final size:78
Alignment explanation
Indices: 35382510--35382862 Score: 440
Period size: 78 Copynumber: 4.5 Consensus size: 78
35382500 AGTGAAGTTA
* * * * * *
35382510 CATCATCAACCAATTTTTTACCGCGAGCTTGGGGCAGATTG-AAGCCATTTGATCTTTTACCCTG
1 CATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAA-CCATTTGATCTTTTACCCCG
*
35382574 AGCCTGGGGCAGAT
65 AGCTTGGGGCAGAT
*
35382588 CATCATCAACCAAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTTGATCTTTTACCCCG
1 CATCATCAACC-AATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATTTGATCTTTTACCCCG
*
35382653 AGTTTGGGGCAGAT
65 AGCTTGGGGCAGAT
* * * * * **
35382667 CATCGTCAACCAATCTCTTACCCTGAGCCTAAGGTAAATTGCAACCATTTGATCTTTTACCCTAA
1 CATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATTTGATCTTTTACCCCGA
35382732 GCTTGGGGCAGAT
66 GCTTGGGGCAGAT
* * * * * *
35382745 CATCGTCAACCAATCTCTTACCTCGAACCTAGGGCAGATTGCAACCATCTGACCTTTTACCTCGA
1 CATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATTTGATCTTTTACCCCGA
35382810 GCTT-GGGCAGAT
66 GCTTGGGGCAGAT
* * * *
35382822 CACCATCAACCAATCTCCTACCCCGAGCTTGGGGCAGATTG
1 CATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTG
35382863 TAGTTATCCA
Statistics
Matches: 239, Mismatches: 34, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
77 42 0.18
78 128 0.54
79 67 0.28
80 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (78 bp):
CATCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATTTGATCTTTTACCCCGA
GCTTGGGGCAGAT
Found at i:35383245 original size:6 final size:6
Alignment explanation
Indices: 35383234--35383321 Score: 62
Period size: 6 Copynumber: 15.2 Consensus size: 6
35383224 GGGCCCAACA
* * *
35383234 AAATTT AAATTT -ATTTT GAAATTT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT
* *
35383281 --ATTGA AAATTT AAATTT --ATTAT AAATTT AAATTC AAATTT A
1 AAATT-T AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT A
35383322 TTTAAATAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
4 6 0.09
5 9 0.14
6 39 0.61
7 10 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:35383274 original size:17 final size:17
Alignment explanation
Indices: 35383234--35383313 Score: 115
Period size: 17 Copynumber: 4.6 Consensus size: 17
35383224 GGGCCCAACA
35383234 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
*
35383251 GAAATTTAAGTTTATTTT
1 -AAATTTAAATTTATTTT
**
35383269 AAATTTAAATTTATTGA
1 AAATTTAAATTTATTTT
*
35383286 AAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
35383303 AAATTTAAATT
1 AAATTTAAATT
35383314 CAAATTTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
17 40 0.71
18 16 0.29
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:35383312 original size:23 final size:22
Alignment explanation
Indices: 35383286--35383328 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
35383276 AATTTATTGA
*
35383286 AAATTTAAATTTATTATAAATTT
1 AAATTCAAATTTATT-TAAATTT
35383309 AAATTCAAATTTATTTAAAT
1 AAATTCAAATTTATTTAAAT
35383329 AATGTCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTCAAATTTATTTAAATTT
Found at i:35383946 original size:17 final size:19
Alignment explanation
Indices: 35383912--35383947 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
35383902 TATTGTACCC
35383912 ATTTATTAATATATAATAA
1 ATTTATTAATATATAATAA
35383931 ATTT-TTAATA-ATAATAA
1 ATTTATTAATATATAATAA
35383948 TAATAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATTAATATATAATAA
Found at i:35383978 original size:13 final size:13
Alignment explanation
Indices: 35383936--35384017 Score: 73
Period size: 13 Copynumber: 6.5 Consensus size: 13
35383926 AATAAATTTT
*
35383936 TAAT-AATAATAA
1 TAATAAATAGTAA
35383948 TAATAACAT--TAA
1 TAATAA-ATAGTAA
*
35383960 TAATAAATAGTAG
1 TAATAAATAGTAA
* *
35383973 TAATAAATAGCAT
1 TAATAAATAGTAA
*
35383986 TAATAAATATTAA
1 TAATAAATAGTAA
*
35383999 TAA-AAATATTAA
1 TAATAAATAGTAA
35384011 TAATAAA
1 TAATAAA
35384018 GTGATAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
11 2 0.03
12 25 0.42
13 30 0.51
14 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (13 bp):
TAATAAATAGTAA
Found at i:35385211 original size:30 final size:30
Alignment explanation
Indices: 35385166--35385304 Score: 110
Period size: 30 Copynumber: 4.7 Consensus size: 30
35385156 GCTCAAAAGG
*
35385166 TCCCTGAACTGTCCAAAAATCATATTTTGA
1 TCCCTGAACTTTCCAAAAATCATATTTTGA
* * *
35385196 TCCCTAAACTTTCCAAAAATCACATTTTTA
1 TCCCTGAACTTTCCAAAAATCATATTTTGA
* * *
35385226 -CTCCTAAAC-TTCACAAATATTATATTTT--
1 TC-CCTGAACTTTC-CAAAAATCATATTTTGA
*
35385254 TGCCCATGAACTTTCCAAAATTCCAT-TTTTGA
1 T-CCC-TGAACTTTCCAAAAAT-CATATTTTGA
*
35385286 -CCCTGAACCTTCCAAAAAT
1 TCCCTGAACTTTCCAAAAAT
35385305 TACCATTTTA
Statistics
Matches: 87, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
29 20 0.23
30 62 0.71
31 5 0.06
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (30 bp):
TCCCTGAACTTTCCAAAAATCATATTTTGA
Found at i:35385284 original size:29 final size:31
Alignment explanation
Indices: 35385167--35385665 Score: 191
Period size: 29 Copynumber: 16.9 Consensus size: 31
35385157 CTCAAAAGGT
35385167 CCCTGAA-CTGTCCAAAAA-T--CATATTTTGA
1 CCCTGAACCT-TCCAAAAATTACCAT-TTTTGA
* * *
35385196 TCCCTAAACTTTCCAAAAATCA-CATTTTT-A
1 -CCCTGAACCTTCCAAAAATTACCATTTTTGA
* * *
35385226 CTCCT-AAACTTCACAAATATTA-TATTTTTG-
1 C-CCTGAACCTTC-CAAAAATTACCATTTTTGA
*
35385256 CCCATGAACTTTCC-AAAATT-CCATTTTTGA
1 CCC-TGAACCTTCCAAAAATTACCATTTTTGA
35385286 CCCTGAACCTTCCAAAAATTACCA-TTTT-A
1 CCCTGAACCTTCCAAAAATTACCATTTTTGA
* *
35385315 CCCTCGGA--TGTCCAAAAATT-CCATTTTTAA
1 CCCT-GAACCT-TCCAAAAATTACCATTTTTGA
** * * *
35385345 CCCCAAAACTTTCAAAAATTGCCA-TTTT-A
1 CCCTGAACCTTCCAAAAATTACCATTTTTGA
*
35385374 CCCCTCAGA--TTCCAAAAATT-CCATTTTTGA
1 -CCCTGA-ACCTTCCAAAAATTACCATTTTTGA
* * *
35385404 -CCTCGAAACTTTCAAAAATTACCATTTTT-C
1 CCCT-GAACCTTCCAAAAATTACCATTTTTGA
* * * *
35385434 CCCCGGA--TGTCTAAAAATT-CCATTTTTAA
1 CCCTGAACCT-TCCAAAAATTACCATTTTTGA
**
35385463 CCCCAAACCTTCCAAAAATTACCA-TTTT-A
1 CCCTGAACCTTCCAAAAATTACCATTTTTGA
* * * * *
35385492 CTCT--CCCATGTCTAAAAATT-CTA-TTTTAA
1 CCCTGAACC-T-TCCAAAAATTACCATTTTTGA
* *
35385521 CCCCGAACCTTTC-AAAATTACCA-TTTT-A
1 CCCTGAACCTTCCAAAAATTACCATTTTTGA
**
35385549 CCCCTGAA--TGTGTAAAAATT-CCATTTTTGA
1 -CCCTGAACCT-TCCAAAAATTACCATTTTTGA
*
35385579 CCATGAACCTTCCAAAAATTACCA-TTTT-A
1 CCCTGAACCTTCCAAAAATTACCATTTTTGA
** * * *
35385608 CCCCCAA-ATGGCTAAAAATT-CCATTTTTGA
1 CCCTGAACCT-TCCAAAAATTACCATTTTTGA
*
35385638 CCATGAACCTTCCAAAAATTACCATTTT
1 CCCTGAACCTTCCAAAAATTACCATTTT
35385666 ACCCCCCGAG
Statistics
Matches: 356, Mismatches: 61, Indels: 103
0.68 0.12 0.20
Matches are distributed among these distances:
27 3 0.01
28 42 0.12
29 139 0.39
30 123 0.35
31 46 0.13
32 3 0.01
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (31 bp):
CCCTGAACCTTCCAAAAATTACCATTTTTGA
Found at i:35385363 original size:30 final size:30
Alignment explanation
Indices: 35385201--35385670 Score: 134
Period size: 30 Copynumber: 16.0 Consensus size: 30
35385191 TTTGATCCCT
* * *
35385201 AAACTTTCCAAAAATCA-CATTTTTACTCCT
1 AAACTTT-CAAAAATTACCATTTTTACCCCA
* *
35385231 AAAC-TTCACAAATATTA-TATTTTT-GCCCA
1 AAACTTTCA-AAA-ATTACCATTTTTACCCCA
* * **
35385260 TGAACTTTCCAAAATT-CCATTTTTGACCCTG
1 -AAACTTTCAAAAATTACCATTTTT-ACCCCA
* *
35385291 AACCTTCCAAAAATTACCA-TTTTACCCTC-
1 AAACTTTCAAAAATTACCATTTTTACCC-CA
** *
35385320 GGA-TGTCCAAAAATT-CCATTTTTAACCCCA
1 AAACT-TTCAAAAATTACCATTTTT-ACCCCA
* *
35385350 AAACTTTCAAAAATTGCCA-TTTTACCCCTC
1 AAACTTTCAAAAATTACCATTTTTACCCC-A
* * * *
35385380 AGA-TTCCAAAAATT-CCATTTTTGACCTCG
1 AAACTTTCAAAAATTACCATTTTT-ACCCCA
*
35385409 AAACTTTCAAAAATTACCATTTTT-CCCCC
1 AAACTTTCAAAAATTACCATTTTTACCCCA
** *
35385438 GGA-TGTCTAAAAATT-CCATTTTTAACCCCA
1 AAACTTTC-AAAAATTACCATTTTT-ACCCCA
* *
35385468 AACCTTCCAAAAATTACCA-TTTTACTCTCC-
1 AAACTTTCAAAAATTACCATTTTTAC-C-CCA
* * * * *
35385498 -CA-TGTCTAAAAATT-CTATTTTAACCCCG
1 AAACTTTC-AAAAATTACCATTTTTACCCCA
* *
35385526 AACCTTTC-AAAATTACCA-TTTTACCCCT
1 AAACTTTCAAAAATTACCATTTTTACCCCA
* ***
35385554 GAA-TGTGT-AAAAATT-CCATTTTTGACCATG
1 AAACT-T-TCAAAAATTACCATTTTT-ACCCCA
* * *
35385584 AACCTTCCAAAAATTACCA-TTTTACCCCC
1 AAACTTTCAAAAATTACCATTTTTACCCCA
** ***
35385613 AAA-TGGCTAAAAATT-CCATTTTTGACCATG
1 AAACTTTC-AAAAATTACCATTTTT-ACCCCA
* *
35385643 AACCTTCCAAAAATTACCA-TTTTACCCC
1 AAACTTTCAAAAATTACCATTTTTACCCC
35385671 CCGAGTGACC
Statistics
Matches: 320, Mismatches: 74, Indels: 93
0.66 0.15 0.19
Matches are distributed among these distances:
27 3 0.01
28 49 0.15
29 113 0.35
30 119 0.37
31 36 0.11
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (30 bp):
AAACTTTCAAAAATTACCATTTTTACCCCA
Found at i:35385605 original size:175 final size:177
Alignment explanation
Indices: 35385270--35385669 Score: 565
Period size: 175 Copynumber: 2.3 Consensus size: 177
35385260 TGAACTTTCC
**
35385270 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCTCGGATGTCCAAAAATT
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCTCCCATGTCCAAAAATT
*
35385335 CCATTTTTAACCCCAAAACTTTCAAAAATTGCCATTTTACCCCTCAGATTCCAAAAATTCCATTT
66 CCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCCTCAGATTCCAAAAATTCCATTT
* * ** *
35385400 TTGACCTCGAAACTTTCAAAAATTACCATTTTTCCCCCGGATGTCTA
131 TTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAATGGCTA
* ** * *
35385447 AAAATTCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACTCTCCCATGTCTAAAAATT
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCTCCCATGTCCAAAAATT
* * * * **
35385512 CTA-TTTTAACCCCGAACCTTTC-AAAATTACCATTTTACCCCTGA-ATGTGTAAAAATTCCATT
66 CCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCCTCAGAT-TCCAAAAATTCCATT
*
35385574 TTTGACCAT-GAACCTTCCAAAAATTACCATTTTACCCCCAAATGGCTA
130 TTTGACC-TCGAAACTTCCAAAAATTACCATTTTACCCCCAAATGGCTA
*
35385622 AAAATTCCATTTTTGACCATGAACCTTCCAAAAATTACCATTTTACCC
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCC
35385670 CCCGAGTGAC
Statistics
Matches: 196, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
174 2 0.01
175 116 0.59
176 18 0.09
177 60 0.31
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (177 bp):
AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCTCCCATGTCCAAAAATT
CCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTACCCCTCAGATTCCAAAAATTCCATTT
TTGACCTCGAAACTTCCAAAAATTACCATTTTACCCCCAAATGGCTA
Found at i:35385670 original size:59 final size:59
Alignment explanation
Indices: 35385270--35385671 Score: 474
Period size: 59 Copynumber: 6.8 Consensus size: 59
35385260 TGAACTTTCC
* *
35385270 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCTCGGATGTCCA
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
* ** * * * * *
35385329 AAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTGCCATTTTACCCCTCAGAT-TCCA
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCC-CGGATGTCTA
* * *
35385388 AAAATTCCATTTTTGA-CCTCGAAACTTTCAAAAATTACCATTTTTCCCCCGGATGTCTA
1 AAAATTCCATTTTTGACCCT-GAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
* **
35385447 AAAATTCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACTCTCCC--ATGTCTA
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTAC-C-CCCGGATGTCTA
* * * * * * *
35385506 AAAATTCTA-TTTTAACCCCGAACCTTTC-AAAATTACCATTTTACCCCTGAATGTGTA
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
* ** *
35385563 AAAATTCCATTTTTGACCATGAACCTTCCAAAAATTACCATTTTACCCCCAAATGGCTA
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
*
35385622 AAAATTCCATTTTTGACCATGAACCTTCCAAAAATTACCATTTTACCCCC
1 AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCCC
35385672 CGAGTGACCA
Statistics
Matches: 298, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
55 2 0.01
56 1 0.00
57 30 0.10
58 38 0.13
59 217 0.73
60 7 0.02
61 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCCTGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
Found at i:35385715 original size:30 final size:31
Alignment explanation
Indices: 35385648--35385723 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 31
35385638 CCATGAACCT
* *
35385648 TCCAAAAATTACCATTTTACCCCCCGAGTGA
1 TCCAAAAATTACCATTTTACCCCCCCAGTCA
* *
35385679 -CC-AAAATTACCGTTTTACCCCCCCCG-CA
1 TCCAAAAATTACCATTTTACCCCCCCAGTCA
*
35385707 TCCAAAAATCA-CATTTT
1 TCCAAAAATTACCATTTT
35385724 TGACTCCATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 28 0.76
30 8 0.22
ACGTcount: A:0.32, C:0.36, G:0.07, T:0.26
Consensus pattern (31 bp):
TCCAAAAATTACCATTTTACCCCCCCAGTCA
Found at i:35395880 original size:22 final size:22
Alignment explanation
Indices: 35395844--35395886 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35395834 AAAAAAATTA
* * *
35395844 TTTTCTCATTGTTTTGTTGTTG
1 TTTTCTCACTATTTTGCTGTTG
35395866 TTTTCTCACTATTTTGCTGTT
1 TTTTCTCACTATTTTGCTGTT
35395887 TTTCACCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.14, G:0.14, T:0.65
Consensus pattern (22 bp):
TTTTCTCACTATTTTGCTGTTG
Found at i:35395954 original size:31 final size:31
Alignment explanation
Indices: 35395896--35395954 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
35395886 TTTTCACCAT
35395896 GATATTGCTACTATTTTATTGTTATTTTTTG
1 GATATTGCTACTATTTTATTGTTATTTTTTG
* *
35395927 GATATTG-TATTATTTTATTGTTAATTTT
1 GATATTGCTACTATTTTATTGTTATTTTT
35395955 GCAATTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.63
Consensus pattern (31 bp):
GATATTGCTACTATTTTATTGTTATTTTTTG
Found at i:35401277 original size:19 final size:20
Alignment explanation
Indices: 35401255--35401301 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
35401245 TGTCTTTTTC
35401255 TTCTCTTTTT-TTTTC-AATT
1 TTCT-TTTTTGTTTTCAAATT
35401274 TTCTTTTTTGTTTTCAAATT
1 TTCTTTTTTGTTTTCAAATT
35401294 TTCTTTTT
1 TTCTTTTT
35401302 GACTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 12 0.46
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.74
Consensus pattern (20 bp):
TTCTTTTTTGTTTTCAAATT
Found at i:35401302 original size:19 final size:18
Alignment explanation
Indices: 35401258--35401302 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
35401248 CTTTTTCTTC
35401258 TCTTTTT-TTTTCAATTT
1 TCTTTTTGTTTTCAATTT
35401275 TCTTTTTTGTTTTCAAATTT
1 TC-TTTTTGTTTTC-AATTT
35401295 TCTTTTTG
1 TCTTTTTG
35401303 ACTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 5 0.20
19 11 0.44
20 7 0.28
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.73
Consensus pattern (18 bp):
TCTTTTTGTTTTCAATTT
Found at i:35405553 original size:25 final size:25
Alignment explanation
Indices: 35405500--35405545 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
35405490 GTTAGATCCA
35405500 AATTAAATTCTAAAAAAATAATTAC
1 AATTAAATTCTAAAAAAATAATTAC
*
35405525 AATTAAA-TCT-AAATAATAATT
1 AATTAAATTCTAAAAAAATAATT
35405546 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAAATTCTAAAAAAATAATTAC
Found at i:35409179 original size:3 final size:3
Alignment explanation
Indices: 35409171--35409195 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35409161 GCTCTGTGAG
35409171 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
35409196 GTTGTCTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:35423032 original size:28 final size:27
Alignment explanation
Indices: 35422988--35423046 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
35422978 ATATAATGAT
* * * *
35422988 AAAATTATATTTTAATTTTTTTTTAAA
1 AAAATTATAATTCAATTCTATTTTAAA
*
35423015 AAAACTTATAATTCAATTCTATTTTCAA
1 AAAA-TTATAATTCAATTCTATTTTAAA
35423043 AAAA
1 AAAA
35423047 GATTTGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (27 bp):
AAAATTATAATTCAATTCTATTTTAAA
Found at i:35427014 original size:23 final size:22
Alignment explanation
Indices: 35426987--35427107 Score: 134
Period size: 23 Copynumber: 5.2 Consensus size: 22
35426977 ACACTAGCGC
35426987 GCTCTCTGATTAGCACTATGTGT
1 GCTCTCTGATTAGCACT-TGTGT
* * *
35427010 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTTGT-GT
*
35427033 GCTCTTTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACT-TGTGT
*
35427058 GCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTT-GTGT
35427081 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
35427104 GCTC
1 GCTC
35427108 AGTACTTTGT
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
22 3 0.04
23 60 0.73
24 2 0.02
25 15 0.18
26 2 0.02
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTGTGT
Found at i:35427057 original size:48 final size:46
Alignment explanation
Indices: 35426987--35427107 Score: 154
Period size: 48 Copynumber: 2.6 Consensus size: 46
35426977 ACACTAGCGC
* *
35426987 GCTCTCTGATTAGCACTATGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTATGTGTGCTCTCCGATTAGCACGTCGT-GT
* * *
35427033 GCTCTTTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTATGTGTGCTCTCCGATTAGCACGTCGTGT
*
35427081 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTATGTGTGCTC
35427108 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
46 25 0.38
48 39 0.60
49 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTATGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:35427136 original size:39 final size:39
Alignment explanation
Indices: 35427072--35427146 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
35427062 TCCGATTAGC
*
35427072 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
35427111 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
35427147 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:35427141 original size:23 final size:23
Alignment explanation
Indices: 35427106--35427199 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
35427096 CTTTGTGTGC
*
35427106 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
35427129 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
35427152 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
35427177 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
35427199 T
1 T
35427200 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:35428249 original size:23 final size:24
Alignment explanation
Indices: 35428223--35428277 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
35428213 TTAAATTTAT
*
35428223 TTTAAAATTAAGTT-T-ATTTTAAA
1 TTTAAAATTAA-TTATAAGTTTAAA
*
35428246 TTT-AAATTTATTATAAGTTTAAA
1 TTTAAAATTAATTATAAGTTTAAA
35428269 TTTAAAATT
1 TTTAAAATT
35428278 TATTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.07
22 7 0.26
23 13 0.48
24 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTAAAATTAATTATAAGTTTAAA
Found at i:35428286 original size:17 final size:17
Alignment explanation
Indices: 35428210--35428272 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
35428200 GGCCCAACAG
35428210 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
35428227 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
35428244 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
35428261 AGTTTAAATTTA
1 AATTTAAATTTA
35428273 AAATTTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:35428908 original size:3 final size:3
Alignment explanation
Indices: 35428900--35428954 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
35428890 TTTAAACGGT
* *
35428900 TAA TAA TAA TAA CAA TAA TAA TGA TAA TAA -ATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
35428945 TAA TAA TAA T
1 TAA TAA TAA T
35428955 TGTCAAAACC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35430211 original size:30 final size:30
Alignment explanation
Indices: 35430175--35430336 Score: 124
Period size: 29 Copynumber: 5.5 Consensus size: 30
35430165 ATCCGAGGGT
35430175 AAAATGGTAA-TTTTGAAAGTTTCAAGGTCA
1 AAAAT-GTAATTTTTGAAAGTTTCAAGGTCA
* *
35430205 AAAATGGAATTTTTGAAAG-TTCGGAGG-CA
1 AAAATGTAATTTTTGAAAGTTTC-AAGGTCA
* * *
35430234 AAAATGAAATTTTTGGAAGTTTCATGGTCA
1 AAAATGTAATTTTTGAAAGTTTCAAGGTCA
* *
35430264 AAAATGTAA-TTTTCAGAAGTTT-AGGGGT-A
1 AAAATGTAATTTTTGA-AAGTTTCA-AGGTCA
* ** *
35430293 AAAAAGTAATTTTAAAAAGTTT-AGGGGT-A
1 AAAATGTAATTTTTGAAAGTTTCA-AGGTCA
35430322 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
35430337 GATAATTTAG
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
29 66 0.61
30 43 0.39
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTTGAAAGTTTCAAGGTCA
Found at i:35430296 original size:59 final size:59
Alignment explanation
Indices: 35430185--35430314 Score: 138
Period size: 59 Copynumber: 2.2 Consensus size: 59
35430175 AAAATGGTAA
* * *
35430185 TTTTGAAAGTTTCAAGGTCAAAAATGGAATTTTTGAAAGTTCGGAGGCAAAAATGAAAT
1 TTTTGAAAGTTTCAAGGTCAAAAATGGAATTTTAGAAAGTTAGGAGGCAAAAAAGAAAT
* * * * *
35430244 TTTTGGAAGTTTCATGGTCAAAAATGTAATTTTCAG-AAGTTTAGG-GGTAAAAAAGTAAT
1 TTTTGAAAGTTTCAAGGTCAAAAATGGAATTTT-AGAAAG-TTAGGAGGCAAAAAAGAAAT
**
35430303 TTTAAAAAGTTT
1 TTTTGAAAGTTT
35430315 AGGGGTAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
59 53 0.91
60 5 0.09
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (59 bp):
TTTTGAAAGTTTCAAGGTCAAAAATGGAATTTTAGAAAGTTAGGAGGCAAAAAAGAAAT
Found at i:35431385 original size:18 final size:17
Alignment explanation
Indices: 35431362--35431421 Score: 79
Period size: 18 Copynumber: 3.5 Consensus size: 17
35431352 TCTTCTTTTT
35431362 TTATTAATACTATTATTA
1 TTATTAATA-TATTATTA
35431380 TTATT-AT-TATTATTA
1 TTATTAATATATTATTA
*
35431395 TTATTAATATGATTAATA
1 TTATTAATAT-ATTATTA
35431413 TTATTAATA
1 TTATTAATA
35431422 AATGCTATCA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
15 13 0.34
16 2 0.05
17 3 0.08
18 20 0.53
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATTAATATATTATTA
Found at i:35431437 original size:3 final size:3
Alignment explanation
Indices: 35431362--35431418 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
35431352 TCTTCTTTTT
* * * *
35431362 TTA TTA ATA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
35431410 ATA TTA TTA
1 TTA TTA TTA
35431419 ATAAATGCTA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:35432150 original size:6 final size:6
Alignment explanation
Indices: 35432124--35432226 Score: 81
Period size: 6 Copynumber: 17.8 Consensus size: 6
35432114 TATTCCTTAT
* * * *
35432124 TTTAAA TTTATAA --TAAT TTTAAA TTTAAA -ATAAA TTTAAA CTCAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
35432170 TTTAAA ATTAAT TTTAAA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
35432217 -ATAAA TTTAA
1 TTTAAA TTTAA
35432227 TCTTAAAACA
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
4 1 0.01
5 14 0.19
6 57 0.77
7 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:35432150 original size:23 final size:23
Alignment explanation
Indices: 35432141--35432216 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
35432131 TTATAATAAT
*
35432141 TTTAAATTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAATTTTAAA
* *
35432164 CTCAAATTTAAAATTAATTTTAAA
1 TTTAAATTTAAAA-TAATTTTAAA
* *
35432188 TTTAAATTTAAAATAAATCTAAA
1 TTTAAATTTAAAATAATTTTAAA
35432211 TTTAAA
1 TTTAAA
35432217 ATAAATTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 25 0.56
24 20 0.44
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTAAATTTAAAATAATTTTAAA
Found at i:35432172 original size:12 final size:12
Alignment explanation
Indices: 35432142--35432245 Score: 83
Period size: 12 Copynumber: 9.0 Consensus size: 12
35432132 TATAATAATT
35432142 TTAAATTTAAAA
1 TTAAATTTAAAA
*
35432154 -TAAATTTAAAC
1 TTAAATTTAAAA
*
35432165 TCAAATTTAAAA
1 TTAAATTTAAAA
* *
35432177 TTAATTTTAAAT
1 TTAAATTTAAAA
35432189 TTAAATTTAAAA
1 TTAAATTTAAAA
* *
35432201 -TAAATCTAAAT
1 TTAAATTTAAAA
*
35432212 TTAAA-AT-AAA
1 TTAAATTTAAAA
*
35432222 TTTAATCTTAAAA
1 TTAAAT-TTAAAA
*
35432235 -CAAATTTAAAA
1 TTAAATTTAAAA
35432246 GGGCCCAGTC
Statistics
Matches: 71, Mismatches: 16, Indels: 11
0.72 0.16 0.11
Matches are distributed among these distances:
10 6 0.08
11 26 0.37
12 36 0.51
13 3 0.04
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (12 bp):
TTAAATTTAAAA
Found at i:35432204 original size:17 final size:17
Alignment explanation
Indices: 35432124--35432244 Score: 110
Period size: 17 Copynumber: 7.4 Consensus size: 17
35432114 TATTCCTTAT
* *
35432124 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
35432141 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* * *
35432158 TTTAAACTCAAATTTAAA
1 TTTAAATTTAAA-ATAAA
*
35432176 ATT-AATTT----TAAA
1 TTTAAATTTAAAATAAA
35432188 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
35432205 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
35432222 TTT-AATCTTAAAACAAA
1 TTTAAAT-TTAAAATAAA
35432239 TTTAAA
1 TTTAAA
35432245 AGGGCCCAGT
Statistics
Matches: 84, Mismatches: 12, Indels: 15
0.76 0.11 0.14
Matches are distributed among these distances:
12 6 0.07
13 5 0.06
16 3 0.04
17 62 0.74
18 8 0.10
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:35433435 original size:30 final size:30
Alignment explanation
Indices: 35433395--35433548 Score: 156
Period size: 30 Copynumber: 5.1 Consensus size: 30
35433385 ACCTAAGAGG
* *
35433395 CCCTCAAACTTTGCAAAAATCACATTTTGA
1 CCCTCAAACTTTCCAAAAATTACATTTTGA
35433425 CTCC-CAAACTTTCCAAAAATTACATTTTGA
1 C-CCTCAAACTTTCCAAAAATTACATTTTGA
* *
35433455 CCCTCAAACTTTCCAATAATTACATTTTAA
1 CCCTCAAACTTTCCAAAAATTACATTTTGA
* *
35433485 CCC-CTATA-TGTCCAAAAA-TACCATTTTTGA
1 CCCTC-AAACTTTCCAAAAATTA-CA-TTTTGA
* *
35433515 -CCTCAAAGTTTCCAAAAATTACCATTTTGC
1 CCCTCAAACTTTCCAAAAATTA-CATTTTGA
35433545 CCCT
1 CCCT
35433549 GAAGTGTCCA
Statistics
Matches: 104, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
28 2 0.02
29 17 0.16
30 75 0.72
31 10 0.10
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAAATTACATTTTGA
Found at i:35433480 original size:60 final size:60
Alignment explanation
Indices: 35433395--35433571 Score: 193
Period size: 60 Copynumber: 3.0 Consensus size: 60
35433385 ACCTAAGAGG
* * *
35433395 CCCTCAAACTTTGCAAAAATCACATTTTGACTCCC-AAACTTTCCAAAAATTA-CA-TTTTGA
1 CCCTCAAACTTTCCAAAAATTACATTTTGAC-CCCTAAA-TGTCCAAAAA-TACCATTTTTGA
* * *
35433455 CCCTCAAACTTTCCAATAATTACATTTTAACCCCTATATGTCCAAAAATACCATTTTTGA
1 CCCTCAAACTTTCCAAAAATTACATTTTGACCCCTAAATGTCCAAAAATACCATTTTTGA
* * *
35433515 -CCTCAAAGTTTCCAAAAATTACCATTTTG-CCCCTGAAGTGTCCAAAATTACCATTTT
1 CCCTCAAACTTTCCAAAAATTA-CATTTTGACCCCT-AAATGTCCAAAAATACCATTTT
35433572 GCTCTCGAGC
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
58 2 0.02
59 38 0.38
60 60 0.60
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (60 bp):
CCCTCAAACTTTCCAAAAATTACATTTTGACCCCTAAATGTCCAAAAATACCATTTTTGA
Found at i:35433559 original size:30 final size:31
Alignment explanation
Indices: 35433436--35433573 Score: 121
Period size: 30 Copynumber: 4.6 Consensus size: 31
35433426 TCCCAAACTT
* * *
35433436 TCCAAAAATTA-CATTTTGACCCTCAAACTT
1 TCCAAAAATTACCATTTTGCCCCTCAAAGTG
* * *
35433466 TCCAATAATTA-CATTTTAACCCCT-ATA-TG
1 TCCAAAAATTACCATTTT-GCCCCTCAAAGTG
* *
35433495 TCCAAAAA-TACCATTTTTG-ACCTCAAAGTT
1 TCCAAAAATTACCA-TTTTGCCCCTCAAAGTG
*
35433525 TCCAAAAATTACCATTTTGCCCCT-GAAGTG
1 TCCAAAAATTACCATTTTGCCCCTCAAAGTG
35433555 TCC-AAAATTACCATTTTGC
1 TCCAAAAATTACCATTTTGC
35433574 TCTCGAGCAT
Statistics
Matches: 88, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
28 5 0.06
29 28 0.32
30 43 0.49
31 12 0.14
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (31 bp):
TCCAAAAATTACCATTTTGCCCCTCAAAGTG
Found at i:35433572 original size:29 final size:30
Alignment explanation
Indices: 35433493--35433573 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
35433483 AACCCCTATA
*
35433493 TGTCCAAAAATACCATTTTTG-ACCTCAAAG
1 TGTCCAAAATTACCA-TTTTGCACCTCAAAG
* * *
35433523 TTTCCAAAAATTACCATTTTGCCCCT-GAAG
1 TGTCC-AAAATTACCATTTTGCACCTCAAAG
35433553 TGTCCAAAATTACCATTTTGC
1 TGTCCAAAATTACCATTTTGC
35433574 TCTCGAGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 16 0.36
30 16 0.36
31 12 0.27
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (30 bp):
TGTCCAAAATTACCATTTTGCACCTCAAAG
Found at i:35436731 original size:2 final size:2
Alignment explanation
Indices: 35436724--35436750 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35436714 GCTCAAACAT
35436724 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35436751 TCAATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35457262 original size:16 final size:14
Alignment explanation
Indices: 35457226--35457263 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
35457216 TATCTAAAAC
35457226 ATTAATATAAATAT
1 ATTAATATAAATAT
35457240 -TTAATATAAATAAT
1 ATTAATATAAAT-AT
35457254 ATTATATATA
1 ATTA-ATATA
35457264 TTATATGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 11 0.52
14 2 0.10
15 3 0.14
16 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAATATAAATAT
Found at i:35459511 original size:3 final size:3
Alignment explanation
Indices: 35459503--35459535 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
35459493 ATACATACAA
*
35459503 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35459536 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35459813 original size:14 final size:14
Alignment explanation
Indices: 35459794--35459847 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
35459784 TTGAATCGAA
35459794 TTTTTTAAATTATT
1 TTTTTTAAATTATT
*
35459808 TTTTTTAAATTAAT
1 TTTTTTAAATTATT
** *
35459822 TTTAATAAATAATT
1 TTTTTTAAATTATT
35459836 TTTTTCTAAATT
1 TTTTT-TAAATT
35459848 TAAATTGCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 26 0.84
15 5 0.16
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTAAATTATT
Found at i:35462288 original size:3 final size:3
Alignment explanation
Indices: 35462280--35462305 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35462270 AAATTAGCCT
35462280 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
35462306 TTATGAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:35477022 original size:20 final size:20
Alignment explanation
Indices: 35476997--35477039 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
35476987 TGGTAAATTC
*
35476997 AAAATATTA-ATTATTTTGGT
1 AAAATATTAGA-TATTTTAGT
35477017 AAAATATTAGATATTTTAGT
1 AAAATATTAGATATTTTAGT
35477037 AAA
1 AAA
35477040 TTCAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (20 bp):
AAAATATTAGATATTTTAGT
Found at i:35477147 original size:41 final size:41
Alignment explanation
Indices: 35477102--35477214 Score: 126
Period size: 41 Copynumber: 2.8 Consensus size: 41
35477092 ATAAATTCAA
* *
35477102 AGAAATATTGGTAAATTCGTATAAATTTTGGTTAAATTA-TT
1 AGAAATATTGGTAAAGTCATATAAATTTTGGTTAAA-TAGTT
* * *
35477143 AGAAATATCGGTAAAGTCACATAAATTTTAG-TAAATAGTT
1 AGAAATATTGGTAAAGTCATATAAATTTTGGTTAAATAGTT
35477183 AGAAATTATT-GTAAAGTCATA-AAAGTTTTGGT
1 AGAAA-TATTGGTAAAGTCATATAAA-TTTTGGT
35477215 AATTGTTAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
39 5 0.08
40 26 0.43
41 29 0.48
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (41 bp):
AGAAATATTGGTAAAGTCATATAAATTTTGGTTAAATAGTT
Found at i:35477148 original size:21 final size:20
Alignment explanation
Indices: 35477102--35477157 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
35477092 ATAAATTCAA
*
35477102 AGAAATATTGGTAAATTCGT
1 AGAAATATTGGTAAATTAGT
* * *
35477122 ATAAATTTTGGTTAAATTATT
1 AGAAATATTGG-TAAATTAGT
*
35477143 AGAAATATCGGTAAA
1 AGAAATATTGGTAAA
35477158 GTCACATAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.38
Consensus pattern (20 bp):
AGAAATATTGGTAAATTAGT
Found at i:35477273 original size:20 final size:19
Alignment explanation
Indices: 35477250--35477358 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 19
35477240 AGAAATTTTG
35477250 GAAATATTGGTAAAATCTTA
1 GAAATATTGGT-AAATCTTA
* *
35477270 GAAA-ATTTGATAAAATCTCA
1 GAAATA-TTGGT-AAATCTTA
* * *
35477290 TAAATATTAGTAAATTTATA
1 GAAATATTGGTAAATCT-TA
* *
35477310 GAAATTTTGGTAAATCATGA
1 GAAATATTGGTAAATC-TTA
* * *
35477330 GATATATCGGTAAGTCCTTA
1 GAAATATTGGTAAAT-CTTA
35477350 GAAATATTG
1 GAAATATTG
35477359 AAAAATCGTC
Statistics
Matches: 65, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
19 6 0.09
20 56 0.86
21 3 0.05
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (19 bp):
GAAATATTGGTAAATCTTA
Found at i:35491050 original size:68 final size:69
Alignment explanation
Indices: 35490924--35491061 Score: 188
Period size: 68 Copynumber: 2.0 Consensus size: 69
35490914 TTCCACCTTT
* ** * *
35490924 TCTTTTAAATGGCATCAAAACATTTCCAAAAAACCAATCAAGTCCAAGAGAAATCAACCAATAAG
1 TCTTTCAAATGGCATCAAAACATAGCCAAAAAACCAATCAAGTCCAACAGAAAACAACCAATAAG
35490989 CCAA
66 CCAA
* * * *
35490993 TCTTTCAAATGGCATCAAAAC-TAGCCAATATACTAGTCAAGTCCAACAGAAAACAACCAATAAG
1 TCTTTCAAATGGCATCAAAACATAGCCAAAAAACCAATCAAGTCCAACAGAAAACAACCAATAAG
35491057 CCAA
66 CCAA
35491061 T
1 T
35491062 AGTCTGTTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
68 40 0.67
69 20 0.33
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.20
Consensus pattern (69 bp):
TCTTTCAAATGGCATCAAAACATAGCCAAAAAACCAATCAAGTCCAACAGAAAACAACCAATAAG
CCAA
Found at i:35493527 original size:23 final size:21
Alignment explanation
Indices: 35493477--35493519 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
35493467 AACCAAATTA
*
35493477 TTATTTAAAAGTTTTTATTTG
1 TTATTCAAAAGTTTTTATTTG
35493498 TAATATTCAAAAGTTTTTATTT
1 T--TATTCAAAAGTTTTTATTT
35493520 AAGTTATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
23 18 0.95
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (21 bp):
TTATTCAAAAGTTTTTATTTG
Found at i:35513171 original size:22 final size:23
Alignment explanation
Indices: 35513129--35513173 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35513119 AGATATGATT
*
35513129 AAAATCTATAGTGAAATTATTAA
1 AAAATCTATAGTGAAAGTATTAA
*
35513152 AAAATTTATAGT-AAAGTATTAA
1 AAAATCTATAGTGAAAGTATTAA
35513174 TTAAAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (23 bp):
AAAATCTATAGTGAAAGTATTAA
Found at i:35515778 original size:25 final size:26
Alignment explanation
Indices: 35515750--35515803 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
35515740 AAAGTTCATC
35515750 TTTCCT-TCACCCAAGTGCTCTGTTT
1 TTTCCTCTCACCCAAGTGCTCTGTTT
*
35515775 TTT-CTCTCACCTAAGTGCTCTGTTT
1 TTTCCTCTCACCCAAGTGCTCTGTTT
35515800 TTTC
1 TTTC
35515804 TCATCATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.11, C:0.30, G:0.11, T:0.48
Consensus pattern (26 bp):
TTTCCTCTCACCCAAGTGCTCTGTTT
Found at i:35515806 original size:23 final size:25
Alignment explanation
Indices: 35515756--35515805 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
35515746 CATCTTTCCT
35515756 TCACCCAAGTGCTCTGTTTTTTCTC
1 TCACCCAAGTGCTCTGTTTTTTCTC
*
35515781 TCACCTAAGTGCTCTGTTTTTTCTC
1 TCACCCAAGTGCTCTGTTTTTTCTC
35515806 ATCATCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.30, G:0.12, T:0.46
Consensus pattern (25 bp):
TCACCCAAGTGCTCTGTTTTTTCTC
Found at i:35519279 original size:17 final size:18
Alignment explanation
Indices: 35519259--35519292 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35519249 TCAACTTTTA
35519259 AAAAAATTTAA-AAAATG
1 AAAAAATTTAAGAAAATG
*
35519276 AAAAATTTTAAGAAAAT
1 AAAAAATTTAAGAAAAT
35519293 ATATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAAAATTTAAGAAAATG
Found at i:35519302 original size:28 final size:27
Alignment explanation
Indices: 35519254--35519315 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
35519244 AAAAGTCAAC
*
35519254 TTTTAAAAAAATTTAAAAAATGAAAAA
1 TTTTAAAAAAATATAAAAAATGAAAAA
* *
35519281 TTTTAAGAAAATATATAAAAAT-TAAAA
1 TTTTAAAAAAATATA-AAAAATGAAAAA
*
35519308 TTATAAAA
1 TTTTAAAA
35519316 CAAAAAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (27 bp):
TTTTAAAAAAATATAAAAAATGAAAAA
Found at i:35519647 original size:6 final size:6
Alignment explanation
Indices: 35519627--35519687 Score: 51
Period size: 6 Copynumber: 11.0 Consensus size: 6
35519617 ATCAAACCAT
* **
35519627 TTTAAA TTT-AT TTTAAA TTTAAA TTT--A -TTAAA TTTAAA TTTGGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
35519671 TTT-AA TATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
35519688 GTTATTATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
3 2 0.05
4 1 0.02
5 8 0.19
6 32 0.74
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:35519659 original size:15 final size:16
Alignment explanation
Indices: 35519627--35519685 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 16
35519617 ATCAAACCAT
35519627 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
35519644 TTTAAATTTA-TTAAA
1 TTTAAATTTATTTAAA
35519659 TTTAAATTTGGATTT-AA
1 TTTAAATTT--ATTTAAA
*
35519676 TATAAATTTA
1 TTTAAATTTA
35519686 AAGTTATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 15 0.39
17 21 0.55
18 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:35519662 original size:21 final size:23
Alignment explanation
Indices: 35519638--35519687 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
35519628 TTAAATTTAT
35519638 TTTAAATTTAAATTT-AT-TAAA
1 TTTAAATTTAAATTTAATATAAA
**
35519659 TTTAAATTTGGATTTAATATAAA
1 TTTAAATTTAAATTTAATATAAA
35519682 TTTAAA
1 TTTAAA
35519688 GTTATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.52
22 2 0.08
23 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATATAAA
Found at i:35520510 original size:24 final size:25
Alignment explanation
Indices: 35520481--35520537 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
35520471 GATTTAATAA
35520481 TAATAATAATAATAAT-AAGTGTTT
1 TAATAATAATAATAATAAAGTGTTT
* *
35520505 TAATAATATTAATAATAAATTGTTT
1 TAATAATAATAATAATAAAGTGTTT
*
35520530 AAATAATA
1 TAATAATA
35520538 TTTATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (25 bp):
TAATAATAATAATAATAAAGTGTTT
Found at i:35521644 original size:30 final size:29
Alignment explanation
Indices: 35521581--35521809 Score: 239
Period size: 30 Copynumber: 7.7 Consensus size: 29
35521571 TGGACTATTC
* *
35521581 AAAAATTATATTTTGACCCCAAAA-TTTTCT
1 AAAAATTATATTTT-AACCTAAAACTTTT-T
35521611 AAAAAATTATATTTTAACCTAAAACTTTTT
1 -AAAAATTATATTTTAACCTAAAACTTTTT
* *
35521641 AAAAATTACATTTTGACCCTAAAACTTTTT
1 AAAAATTATATTTT-AACCTAAAACTTTTT
* *
35521671 AAAAATTATATTTTAGCCCTAAAACTTTTC
1 AAAAATTATATTTTA-ACCTAAAACTTTTT
* *
35521701 CAAAATTATATTTTAACCCTAAAACTTTCT
1 AAAAATTATATTTTAA-CCTAAAACTTTTT
35521731 AAAAATTATATTTTAACCTTAAAACTTTTT
1 AAAAATTATATTTTAACC-TAAAACTTTTT
* * *
35521761 -GAAATTATATTTTAACCCTTAAATTTTTCT
1 AAAAATTATATTTTAA-CCTAAAACTTTT-T
*
35521791 AAAATTTCAT-TTTTAACCT
1 AAAAATT-ATATTTTAACCT
35521810 CGATTTTGCC
Statistics
Matches: 172, Mismatches: 17, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
29 38 0.22
30 104 0.60
31 28 0.16
32 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (29 bp):
AAAAATTATATTTTAACCTAAAACTTTTT
Found at i:35521674 original size:60 final size:60
Alignment explanation
Indices: 35521581--35521809 Score: 288
Period size: 60 Copynumber: 3.8 Consensus size: 60
35521571 TGGACTATTC
* *
35521581 AAAAATTATATTTTGACCCCAAAA-TTTTCTAAAAAATTATATTTTAACCTAAAACTTTTT
1 AAAAATTATATTTTAACCCTAAAACTTTTCT-AAAAATTATATTTTAACCTAAAACTTTTT
* * * *
35521641 AAAAATTACATTTTGACCCTAAAACTTTT-TAAAAATTATATTTTAGCCCTAAAACTTTTC
1 AAAAATTATATTTTAACCCTAAAACTTTTCTAAAAATTATATTTTA-ACCTAAAACTTTTT
*
35521701 CAAAATTATATTTTAACCCTAAAAC-TTTCTAAAAATTATATTTTAACCTTAAAACTTTTT
1 AAAAATTATATTTTAACCCTAAAACTTTTCTAAAAATTATATTTTAACC-TAAAACTTTTT
* * * *
35521761 -GAAATTATATTTTAACCCTTAAATTTTTCTAAAATTTCAT-TTTTAACCT
1 AAAAATTATATTTTAACCCTAAAACTTTTCTAAAAATT-ATATTTTAACCT
35521810 CGATTTTGCC
Statistics
Matches: 150, Mismatches: 13, Indels: 13
0.85 0.07 0.07
Matches are distributed among these distances:
59 42 0.28
60 102 0.68
61 6 0.04
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (60 bp):
AAAAATTATATTTTAACCCTAAAACTTTTCTAAAAATTATATTTTAACCTAAAACTTTTT
Found at i:35521808 original size:90 final size:90
Alignment explanation
Indices: 35521581--35521796 Score: 285
Period size: 90 Copynumber: 2.4 Consensus size: 90
35521571 TGGACTATTC
* * *
35521581 AAAAATTATATTTTGACCC-CAAAATTTTCTAAAAAATTATATTTTAA-CCTAAAACTTTTTAAA
1 AAAAATTATATTTTAACCCTAAAAATTTTCT--AAAATTATATTTTAACCCTAAAACTTTCTAAA
*
35521644 AATTACATTTTGACCCTAAAACTTTTT
64 AATTACATTTTAACCCTAAAACTTTTT
* * *
35521671 AAAAATTATATTTTAGCCCTAAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTCTAAAAA
1 AAAAATTATATTTTAACCCTAAAAATTTTCTAAAATTATATTTTAACCCTAAAACTTTCTAAAAA
* *
35521736 TTATATTTTAACCTTAAAACTTTTT
66 TTACATTTTAACCCTAAAACTTTTT
* * *
35521761 -GAAATTATATTTTAACCCTTAAATTTTTCTAAAATT
1 AAAAATTATATTTTAACCCTAAAAATTTTCTAAAATT
35521797 TCATTTTTAA
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
89 46 0.42
90 56 0.51
91 8 0.07
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (90 bp):
AAAAATTATATTTTAACCCTAAAAATTTTCTAAAATTATATTTTAACCCTAAAACTTTCTAAAAA
TTACATTTTAACCCTAAAACTTTTT
Found at i:35533566 original size:51 final size:51
Alignment explanation
Indices: 35533497--35533994 Score: 168
Period size: 50 Copynumber: 9.9 Consensus size: 51
35533487 AAATACAAAA
* * * * * *
35533497 GAAAAATCTAAGACCGCAATTGCATATCTAGTACCGCAAAAAACACAA-AGG
1 GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGC-AAAAACACAACAGG
*
35533548 GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCATAAACACAACAGG
1 GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCAAAAACACAACAGG
* ** * * * *
35533599 GAAAGGTCTAAG-TCGCAACAGCGGA-CCATGTACC-TAAGAAGCACAA-AGG
1 GAAAGATCTAAGATCGCAATGGCAGATCCA-ATACCGCAA-AAACACAACAGG
* * ** * * * * *
35533648 GAAAGATCTAATACCATAATTGCGGATCCAGTACCGCAAAGATACTAA-AGG
1 GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCAAAAACAC-AACAGG
* * * * * * * * *
35533699 GAAAGGTCTAAG-TCGCAACGACGGA-CCATGTACCTCAGAAACACGAC-GA
1 GAAAGATCTAAGATCGCAATGGCAGATCCA-ATACCGCAAAAACACAACAGG
** * * * * *
35533748 GAAAGATCTAAGGCCGCAATGACGGATCCAATATCGCAAAGATACTAA-AGG
1 GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCAAAAACAC-AACAGG
** * * * ** * * *
35533799 GAAAGGCCTAAG-TCGTAACGGCGGA-CCGTGTACCTCAGAAACACGAC-GG
1 GAAAGATCTAAGATCGCAATGGCAGATCC-AATACCGCAAAAACACAACAGG
* * * *
35533848 GAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATC-CTAA-AGG
1 GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCAAA-AACAC-AACAGG
* * * ** ** * *
35533899 GAAAGGTCTAAG-TCGCAACGGCGGA-CCGTGTACCTTAGAAACACGAC-GG
1 GAAAGATCTAAGATCGCAATGGCAGATCC-AATACCGCAAAAACACAACAGG
* * * * * *
35533948 GAAAGATCTAAGACCACAATGACGGATCTAGTACCGCAAAAACACAA
1 GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCAAAAACACAA
35533995 AAAGGGAAGG
Statistics
Matches: 327, Mismatches: 95, Indels: 51
0.69 0.20 0.11
Matches are distributed among these distances:
49 66 0.20
50 162 0.50
51 99 0.30
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (51 bp):
GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCAAAAACACAACAGG
Found at i:35533713 original size:100 final size:100
Alignment explanation
Indices: 35533537--35534143 Score: 664
Period size: 100 Copynumber: 6.0 Consensus size: 100
35533527 GTACCGCAAA
* * * *
35533537 AAACACAAAGGGAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCATAA-ACAC-AACAGGG
1 AAACACAAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCA-AAGATACTAA-AGGG
*
35533600 AAAGGTCTAAGTCGCAACAGCGGACCATGTACCTAAG
64 AAAGGTCTAAGTCGCAACGGCGGACCATGTACCTAAG
* * ** *
35533637 AAGCACAAAGGGAAAGATCTAATACCATAATTGCGGATCCAGTACCGCAAAGATACTAAAGGGAA
1 AAACACAAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACTAAAGGGAA
* *
35533702 AGGTCTAAGTCGCAACGACGGACCATGTACCTCAG
66 AGGTCTAAGTCGCAACGGCGGACCATGTACCTAAG
* * * * * * *
35533737 AAACACGACGAGAAAGATCTAAGGCCGCAATGACGGATCCAATATCGCAAAGATACTAAAGGGAA
1 AAACACAAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACTAAAGGGAA
* * * *
35533802 AGGCCTAAGTCGTAACGGCGGACCGTGTACCTCAG
66 AGGTCTAAGTCGCAACGGCGGACCATGTACCTAAG
* * *
35533837 AAACACGACGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATCCTAAAGGGAA
1 AAACACAAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACTAAAGGGAA
* *
35533902 AGGTCTAAGTCGCAACGGCGGACCGTGTACCTTAG
66 AGGTCTAAGTCGCAACGGCGGACCATGTACCTAAG
* * * * * * * *
35533937 AAACACGACGGGAAAGATCTAAGACCACAATGACGGATCTAGTACCGCAAAAACACAAAAAGGG-
1 AAACACAAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATAC-TAAAGGGA
* *
35534001 AAGGTCTAAGTCGTAACGGCGGACTATGTACCTCAA-
65 AAGGTCTAAGTCGCAACGGCGGACCATGTACCT-AAG
* * * ** * * *
35534037 AAGCATGAAAGGGAATGATCTAAGACCGCAATGGCAAATCCAGTACCACAAAGATGCAAAAAGGG
1 AAACA-CAAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATAC-TAAAGGG
* * * ** *
35534102 AAAGGTTTAAGTCGCAACGACGAACCCGGTACCTTAG
64 AAAGGTCTAAGTCGCAACGGCGGACCATGTACCTAAG
35534139 AAACA
1 AAACA
35534144 TGAAAGGTCA
Statistics
Matches: 429, Mismatches: 71, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
99 2 0.00
100 341 0.79
101 56 0.13
102 30 0.07
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.14
Consensus pattern (100 bp):
AAACACAAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACTAAAGGGAA
AGGTCTAAGTCGCAACGGCGGACCATGTACCTAAG
Found at i:35533772 original size:50 final size:49
Alignment explanation
Indices: 35533697--35533973 Score: 177
Period size: 50 Copynumber: 5.6 Consensus size: 49
35533687 AGATACTAAA
* *
35533697 GGGAAAGGTCTAAGTCGCAACGACGGACCATGTACCTCAGAAACACGAC
1 GGGAAAGATCTAAGCCGCAACGACGGACCATGTACCTCAGAAACACGAC
* * * * * * * *
35533746 GAGAAAGATCTAAGGCCGCAATGACGGATCCA-ATATCGCA-AAGATACTAAA
1 GGGAAAGATCTAA-GCCGCAACGACGGA-CCATGTACCTCAGAA-ACAC-GAC
** * * * *
35533797 GGGAAAGGCCTAAGTCGTAACGGCGGACCGTGTACCTCAGAAACACGAC
1 GGGAAAGATCTAAGCCGCAACGACGGACCATGTACCTCAGAAACACGAC
* * * * *
35533846 GGGAAAGATCTAAGACCGCAATGGCGGATCCA-GTACCGCA-AAGATC-CTAAA
1 GGGAAAGATCTAAG-CCGCAACGACGGA-CCATGTACCTCAGAA-A-CAC-GAC
* * * * *
35533897 GGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTTAGAAACACGAC
1 GGGAAAGATCTAAGCCGCAACGACGGACCATGTACCTCAGAAACACGAC
* *
35533946 GGGAAAGATCTAAGACCACAATGACGGA
1 GGGAAAGATCTAAG-CCGCAACGACGGA
35533974 TCTAGTACCG
Statistics
Matches: 167, Mismatches: 46, Indels: 29
0.69 0.19 0.12
Matches are distributed among these distances:
49 47 0.28
50 85 0.51
51 35 0.21
ACGTcount: A:0.36, C:0.23, G:0.27, T:0.13
Consensus pattern (49 bp):
GGGAAAGATCTAAGCCGCAACGACGGACCATGTACCTCAGAAACACGAC
Found at i:35533898 original size:200 final size:198
Alignment explanation
Indices: 35533548--35534143 Score: 746
Period size: 200 Copynumber: 3.0 Consensus size: 198
35533538 AACACAAAGG
* * *
35533548 GAAAGATCTAAGATCGCAATGGCAGATCCAATACCGCATAAACACAACAGGGAAAGGTCTAAGTC
1 GAAAGATCTAAGACCGCAATGACGGATCCAATACCGCA-AAACACAA-AGGGAAAGGTCTAAGTC
* * * * * * ** *
35533613 GCAACAGCGGACCATGTACCTAAGAAGCACAAAGGGAAAGATCTAATACCATAATTGCGGATCCA
64 GTAACGGCGGACCATGTACCTCAGAAACACGAAGGGAAAGATCTAAGACCGCAATGGCGGATCCA
* *
35533678 GTACCGCAAAGATACTAAAGGGAAAGGTCTAAGTCGCAACGACGGACCATGTACCTCAGAAACAC
129 GTACCGCAAAGATCCTAAAGGGAAAGGTCTAAGTCGCAACGACGGACCATGTACCTTAGAAACAC
35533743 GACGA
194 GACGA
* * * *
35533748 GAAAGATCTAAGGCCGCAATGACGGATCCAATATCGCAAAGATACTAAAGGGAAAGGCCTAAGTC
1 GAAAGATCTAAGACCGCAATGACGGATCCAATACCGCAAA-ACAC-AAAGGGAAAGGTCTAAGTC
* *
35533813 GTAACGGCGGACCGTGTACCTCAGAAACACGACGGGAAAGATCTAAGACCGCAATGGCGGATCCA
64 GTAACGGCGGACCATGTACCTCAGAAACACGAAGGGAAAGATCTAAGACCGCAATGGCGGATCCA
* *
35533878 GTACCGCAAAGATCCTAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTTAGAAACAC
129 GTACCGCAAAGATCCTAAAGGGAAAGGTCTAAGTCGCAACGACGGACCATGTACCTTAGAAACAC
*
35533943 GACGG
194 GACGA
* * *
35533948 GAAAGATCTAAGACCACAATGACGGATCTAGTACCGCAAAAACACAAAAAGGG-AAGGTCTAAGT
1 GAAAGATCTAAGACCGCAATGACGGATCCAATACCGC-AAAACAC--AAAGGGAAAGGTCTAAGT
* * * **
35534012 CGTAACGGCGGACTATGTACCTCA-AAAGCATGAAAGGGAATGATCTAAGACCGCAATGGCAAAT
63 CGTAACGGCGGACCATGTACCTCAGAAA-CACG-AAGGGAAAGATCTAAGACCGCAATGGCGGAT
* ** * * **
35534076 CCAGTACCACAAAGATGCAAAAAGGGAAAGGTTTAAGTCGCAACGACGAACCCGGTACCTTAGAA
126 CCAGTACCGCAAAGAT-CCTAAAGGGAAAGGTCTAAGTCGCAACGACGGACCATGTACCTTAGAA
35534141 ACA
190 ACA
35534144 TGAAAGGTCA
Statistics
Matches: 343, Mismatches: 46, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
199 5 0.01
200 241 0.70
201 53 0.15
202 44 0.13
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.14
Consensus pattern (198 bp):
GAAAGATCTAAGACCGCAATGACGGATCCAATACCGCAAAACACAAAGGGAAAGGTCTAAGTCGT
AACGGCGGACCATGTACCTCAGAAACACGAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGT
ACCGCAAAGATCCTAAAGGGAAAGGTCTAAGTCGCAACGACGGACCATGTACCTTAGAAACACGA
CGA
Found at i:35534532 original size:17 final size:17
Alignment explanation
Indices: 35534509--35534613 Score: 117
Period size: 17 Copynumber: 6.3 Consensus size: 17
35534499 ACCAAGCCAT
35534509 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
35534527 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
35534543 TTTAAATTTA--TTAAA
1 TTTAAATTTATTTTAAA
*
35534558 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
** * *
35534575 TTTGGATTTAATATAAA
1 TTTAAATTTATTTTAAA
* *
35534592 TTTAAAGTTATTATAAA
1 TTTAAATTTATTTTAAA
35534609 TTTAA
1 TTTAA
35534614 TAAATGTCCA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
15 15 0.19
16 3 0.04
17 59 0.77
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:35534541 original size:11 final size:11
Alignment explanation
Indices: 35534527--35534614 Score: 67
Period size: 11 Copynumber: 8.0 Consensus size: 11
35534517 TATTTTCAAA
*
35534527 TTAAATTTATT
1 TTAAATTTAAT
35534538 TTAAATTTAAAT
1 TTAAATTT-AAT
*
35534550 TT--ATTAAAT
1 TTAAATTTAAT
35534559 TTAAATTTAAT
1 TTAAATTTAAT
*
35534570 TTAAATTTGGAT
1 TTAAATTT-AAT
*
35534582 TT-AATATAAAT
1 TTAAAT-TTAAT
*
35534593 TTAAAGTT-AT
1 TTAAATTTAAT
35534603 TATAAATTTAAT
1 T-TAAATTTAAT
35534615 AAATGTCCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
9 5 0.08
10 6 0.10
11 36 0.60
12 13 0.22
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:35534548 original size:6 final size:6
Alignment explanation
Indices: 35534509--35534597 Score: 68
Period size: 6 Copynumber: 16.0 Consensus size: 6
35534499 ACCAAGCCAT
* *
35534509 TTTAAA TTT-AT TTTCAAA -TTAAA TTT-AT TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
35534553 -TTAAA TTTAAA TTT-AA TTTAAA TTTGGA TTT-AA TATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
35534598 GTTATTATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
5 20 0.31
6 41 0.63
7 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:35535425 original size:24 final size:24
Alignment explanation
Indices: 35535398--35535465 Score: 91
Period size: 25 Copynumber: 2.8 Consensus size: 24
35535388 ATAATAATAA
*
35535398 TAATAATAATAATAATAAGTGTTT
1 TAATAATATTAATAATAAGTGTTT
*
35535422 TAATAATATTAATAATAAATTGTTT
1 TAATAATATTAATAAT-AAGTGTTT
*
35535447 AAATAATATTTAATAATAA
1 TAATAATA-TTAATAATAA
35535466 TAAATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 15 0.38
25 16 0.41
26 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TAATAATATTAATAATAAGTGTTT
Found at i:35535429 original size:3 final size:3
Alignment explanation
Indices: 35535383--35535415 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
35535373 TTGATAGATT
35535383 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35535416 GTGTTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35536428 original size:31 final size:29
Alignment explanation
Indices: 35536369--35536462 Score: 73
Period size: 31 Copynumber: 3.1 Consensus size: 29
35536359 AAACTATTCG
* *
35536369 AAAATTATATTTTGGCCCTAAAATTTTTTAA
1 AAAATTATATTTT-ACCCCAAAA-TTTTTAA
*
35536400 AAAATTATATTTTAACCCCCAAAATTTTT-T
1 AAAATTATATTTT-A-CCCCAAAATTTTTAA
* * *
35536430 GAAATTACATTTTGACCCCTAAATTTTCTAA
1 AAAATTATATTTT-ACCCCAAAATTTT-TAA
35536461 AA
1 AA
35536463 TTTTATTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
29 11 0.22
30 13 0.26
31 19 0.38
32 7 0.14
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.41
Consensus pattern (29 bp):
AAAATTATATTTTACCCCAAAATTTTTAA
Found at i:35542786 original size:6 final size:6
Alignment explanation
Indices: 35542777--35542807 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
35542767 GAATAAAGAG
*
35542777 AAAGGA AAAGGA AAAGGA AAAGGC AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA A
35542808 TGCTTAGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:35547148 original size:20 final size:19
Alignment explanation
Indices: 35547123--35547160 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
35547113 TTAAGTGTCA
35547123 ATGTTTGTCTCGAAAAAAAT
1 ATGTTTGTCTC-AAAAAAAT
35547143 ATGTTTGTCTCAAAAAAA
1 ATGTTTGTCTCAAAAAAA
35547161 CTAAGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (19 bp):
ATGTTTGTCTCAAAAAAAT
Found at i:35547896 original size:25 final size:24
Alignment explanation
Indices: 35547854--35547902 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
35547844 TAGATTTTAA
*
35547854 ATATTTTTTAAAAATAATTATATT
1 ATATTTTTTAAAAATAATAATATT
* *
35547878 ATATTATTTTAATATTAATAATATT
1 ATATT-TTTTAAAAATAATAATATT
35547903 TTTTTTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATTTTTTAAAAATAATAATATT
Found at i:35560207 original size:23 final size:23
Alignment explanation
Indices: 35560161--35560207 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
35560151 GTTTATTTAA
* * **
35560161 ATTAAATGAACATGTTCATGAAT
1 ATTAAACGAACATGATCACAAAT
35560184 ATTAAACGAACATGATCACAAAT
1 ATTAAACGAACATGATCACAAAT
35560207 A
1 A
35560208 ACGTTTATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.28
Consensus pattern (23 bp):
ATTAAACGAACATGATCACAAAT
Found at i:35562239 original size:15 final size:16
Alignment explanation
Indices: 35562219--35562252 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
35562209 AATCTTTTAG
35562219 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
35562234 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
35562250 AAA
1 AAA
35562253 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:35562888 original size:18 final size:17
Alignment explanation
Indices: 35562840--35562888 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
35562830 ATGTCAAATA
*
35562840 AAATAAATATTTGTATT
1 AAATAAATATTTTTATT
* *
35562857 TAATTAA-ATTTTTATT
1 AAATAAATATTTTTATT
35562873 AAATAAATAGTTTTTA
1 AAATAAATA-TTTTTA
35562889 AATATTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 13 0.52
17 6 0.24
18 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
AAATAAATATTTTTATT
Found at i:35562915 original size:36 final size:36
Alignment explanation
Indices: 35562804--35562933 Score: 98
Period size: 36 Copynumber: 3.7 Consensus size: 36
35562794 TATTTTTATT
* *
35562804 AAATAGATAATTT-TTAAATATTACTTATGTCAAATA
1 AAATAAAT-ATTTATTAAATATTATTTATGTCAAATA
* * *
35562840 AAATAAATATTTGTATTTAAT-TAAATTT-T-T---ATT
1 AAATAAATA-TT-TATTAAATAT-TATTTATGTCAAATA
35562873 AAATAAATAGTTT-TTAAATATTATTTATGTCAAATA
1 AAATAAATA-TTTATTAAATATTATTTATGTCAAATA
*
35562909 AAATAAATATTTATT-TATATTATTT
1 AAATAAATATTTATTAAATATTATTT
35562934 TACTAAATAA
Statistics
Matches: 73, Mismatches: 10, Indels: 23
0.69 0.09 0.22
Matches are distributed among these distances:
31 9 0.12
32 3 0.04
33 14 0.19
35 13 0.18
36 23 0.32
37 3 0.04
38 8 0.11
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (36 bp):
AAATAAATATTTATTAAATATTATTTATGTCAAATA
Found at i:35564179 original size:29 final size:31
Alignment explanation
Indices: 35564146--35564229 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
35564136 TTGATTTAAT
35564146 GTGCAATTGTATACAT-AAACTTTAATT-TG
1 GTGCAATTGTATACATGAAACTTTAATTGTG
* *
35564175 GTGCAATTATATACGTGAAACTTTAATTGTG
1 GTGCAATTGTATACATGAAACTTTAATTGTG
* * **
35564206 GTTCAAATGTATATTTGAAACTTT
1 GTGCAATTGTATACATGAAACTTT
35564230 TGTTTTGATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
29 14 0.30
30 11 0.24
31 21 0.46
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (31 bp):
GTGCAATTGTATACATGAAACTTTAATTGTG
Found at i:35564198 original size:30 final size:30
Alignment explanation
Indices: 35564146--35564207 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
35564136 TTGATTTAAT
*
35564146 GTGCAATTGTATACATAAACTTTAATT-TG
1 GTGCAATTATATACATAAACTTTAATTGTG
*
35564175 GTGCAATTATATACGTGAAACTTTAATTGTG
1 GTGCAATTATATACAT-AAACTTTAATTGTG
35564206 GT
1 GT
35564208 TCAAATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 14 0.48
30 11 0.38
31 4 0.14
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (30 bp):
GTGCAATTATATACATAAACTTTAATTGTG
Found at i:35570500 original size:8 final size:8
Alignment explanation
Indices: 35570487--35570549 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 8
35570477 AAAATTTTAA
35570487 ATTTATAT
1 ATTTATAT
35570495 ATTTATAT
1 ATTTATAT
*
35570503 -TTTTTA-
1 ATTTATAT
35570509 ATTTA-AT
1 ATTTATAT
35570516 ATTTAATAT
1 ATTT-ATAT
*
35570525 TTTTATAT
1 ATTTATAT
* *
35570533 ATTGAAAT
1 ATTTATAT
35570541 -TTTATAT
1 ATTTATAT
35570548 AT
1 AT
35570550 AGTCATCTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
6 1 0.02
7 17 0.40
8 19 0.45
9 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
ATTTATAT
Found at i:35570511 original size:22 final size:22
Alignment explanation
Indices: 35570481--35570529 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
35570471 ATTTACAAAA
35570481 TTTTAAATTTATATATTT-ATAT
1 TTTTAAATTTA-ATATTTAATAT
*
35570503 TTTTTAATTTAATATTTAATAT
1 TTTTAAATTTAATATTTAATAT
35570525 TTTTA
1 TTTTA
35570530 TATATTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTAAATTTAATATTTAATAT
Found at i:35570529 original size:21 final size:21
Alignment explanation
Indices: 35570480--35570529 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
35570470 TATTTACAAA
*
35570480 ATTTTAAATTTATATATTTAT
1 ATTTTTAATTTATATATTTAT
35570501 ATTTTTTAATTTA-ATATTTAAT
1 A-TTTTTAATTTATATATTT-AT
35570523 ATTTTTA
1 ATTTTTA
35570530 TATATTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTAATTTATATATTTAT
Found at i:35570542 original size:30 final size:29
Alignment explanation
Indices: 35570482--35570547 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 29
35570472 TTTACAAAAT
* **
35570482 TTTAA-ATTTATATATTTATATTTTTTAA
1 TTTAATATTTATATATTTATATATTGAAA
*
35570510 TTTAATATTTAATATTTTTATATATTGAAA
1 TTTAATATTT-ATATATTTATATATTGAAA
*
35570540 TTTTATAT
1 TTTAATAT
35570548 ATAGTCATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 5 0.16
29 4 0.13
30 22 0.71
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTAATATTTATATATTTATATATTGAAA
Found at i:35581861 original size:31 final size:31
Alignment explanation
Indices: 35581826--35581889 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
35581816 GATTTAACTA
35581826 AAAAAGTTACAATTT-GATCATTAAATTATTC
1 AAAAAGTTAC-ATTTCGATCATTAAATTATTC
* * * *
35581857 AAAAATTTTCATTTCGATTATTGAATTATTC
1 AAAAAGTTACATTTCGATCATTAAATTATTC
35581888 AA
1 AA
35581890 CTATTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (31 bp):
AAAAAGTTACATTTCGATCATTAAATTATTC
Found at i:35582291 original size:30 final size:30
Alignment explanation
Indices: 35582255--35582311 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
35582245 TAAAAATAAA
35582255 AATTTACCCATAAT-T-TAATGATGATGGTGT
1 AATTTACCCA-AATATATAATG-TGATGGTGT
35582285 AATTTACCCAAATATATAATGTGATGG
1 AATTTACCCAAATATATAATGTGATGG
35582312 GTCATGGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 3 0.12
30 17 0.68
31 5 0.20
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (30 bp):
AATTTACCCAAATATATAATGTGATGGTGT
Found at i:35585170 original size:31 final size:30
Alignment explanation
Indices: 35585134--35585196 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
35585124 TAGTAATGGT
* *
35585134 AAAATTACATTTTAGCCCTCTAAAAATAATA
1 AAAATTACA-TTTAACCCTATAAAAATAATA
** *
35585165 AAAATTTGATTTAACCCTATAAAAATTATA
1 AAAATTACATTTAACCCTATAAAAATAATA
35585195 AA
1 AA
35585197 TATATAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAATTACATTTAACCCTATAAAAATAATA
Found at i:35591521 original size:18 final size:18
Alignment explanation
Indices: 35591498--35591535 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
35591488 TGAATTTTAC
35591498 AATTCAAATAACTCGAAT
1 AATTCAAATAACTCGAAT
*
35591516 AATTCAAATAATTCGAAT
1 AATTCAAATAACTCGAAT
35591534 AA
1 AA
35591536 CAGACTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (18 bp):
AATTCAAATAACTCGAAT
Found at i:35591649 original size:20 final size:20
Alignment explanation
Indices: 35591620--35591672 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
35591610 TTACAAAAAA
* *
35591620 GAAAAATCAAAATAATTTTT
1 GAAAATTCAAAATAATTTAT
*
35591640 GAAAATTC-AAATTATTTAT
1 GAAAATTCAAAATAATTTAT
*
35591659 AAAAATTCCAAAAT
1 GAAAATT-CAAAAT
35591673 TTATATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 15 0.56
20 8 0.30
21 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (20 bp):
GAAAATTCAAAATAATTTAT
Found at i:35591651 original size:19 final size:19
Alignment explanation
Indices: 35591629--35591677 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
35591619 AGAAAAATCA
* *
35591629 AAATAATTTTTGAAAATTC
1 AAATAATTTATAAAAATTC
*
35591648 AAATTATTTATAAAAATTC
1 AAATAATTTATAAAAATTC
*
35591667 CAA-AATTTATA
1 AAATAATTTATA
35591678 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATAATTTATAAAAATTC
Found at i:35591953 original size:21 final size:21
Alignment explanation
Indices: 35591929--35591976 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
35591919 TTTTTAATTT
*
35591929 AATTCGATTTGATTCGACTTG
1 AATTCGATTTGACTCGACTTG
*
35591950 AATTTC-ATTTTACTCGACTTG
1 AA-TTCGATTTGACTCGACTTG
35591971 -ATTCGA
1 AATTCGA
35591977 AAAAATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 3 0.13
20 2 0.09
21 15 0.65
22 3 0.13
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (21 bp):
AATTCGATTTGACTCGACTTG
Found at i:35602192 original size:103 final size:103
Alignment explanation
Indices: 35602013--35602224 Score: 415
Period size: 103 Copynumber: 2.1 Consensus size: 103
35602003 ATCATCAACA
35602013 ATATTCATCTCAAAACCGAATGAAATAATTACTTGATAAAACTTGTGGTACCATTGACGGGAAGC
1 ATATTCATCTCAAAACCGAATGAAATAATTACTTGATAAAACTTGTGGTACCATTGACGGGAAGC
35602078 TTGTTTGAGTCCATATGGATTTTTTTAATTTGCAAACC
66 TTGTTTGAGTCCATATGGATTTTTTTAATTTGCAAACC
*
35602116 ATATTCATCTCAAAACCGAATGAAATAATTACTTGATGAAACTTGTGGTACCATTGACGGGAAGC
1 ATATTCATCTCAAAACCGAATGAAATAATTACTTGATAAAACTTGTGGTACCATTGACGGGAAGC
35602181 TTGTTTGAGTCCATATGGATTTTTTTAATTTGCAAACC
66 TTGTTTGAGTCCATATGGATTTTTTTAATTTGCAAACC
35602219 ATATTC
1 ATATTC
35602225 TTTAGGTCTT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (103 bp):
ATATTCATCTCAAAACCGAATGAAATAATTACTTGATAAAACTTGTGGTACCATTGACGGGAAGC
TTGTTTGAGTCCATATGGATTTTTTTAATTTGCAAACC
Found at i:35618728 original size:29 final size:27
Alignment explanation
Indices: 35618698--35618884 Score: 132
Period size: 28 Copynumber: 6.5 Consensus size: 27
35618688 TTCAAGGTTA
35618698 AAAATGGAATTTTGGAAAGTTTGGGAGT
1 AAAATGGAATTTTGGAAAGTTTGGG-GT
* *
35618726 AAAATGGTAATTTTTGGTGAAA--TAGTGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTTG-GGGT
35618756 AAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGAAAGTTT-GGGGT
* *
35618784 AAAATGGTATTTTGGGTGAAA--TCGGGGTT
1 AAAATGGAATTTT--G-GAAAGTTTGGGG-T
35618813 AAAAATGGAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGAATTTTGGAAAGTTT-GGGGT
*
35618842 AAAATGGTAATTTTTGG-AAGTTTCAGGGT
1 AAAATGG-AA-TTTTGGAAAGTTT-GGGGT
*
35618871 CAAAATGTAATTTT
1 -AAAATGGAATTTT
35618885 TTGAAGTTTT
Statistics
Matches: 129, Mismatches: 11, Indels: 38
0.72 0.06 0.21
Matches are distributed among these distances:
26 4 0.03
27 5 0.04
28 43 0.33
29 23 0.18
30 43 0.33
31 7 0.05
32 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAAGTTTGGGGT
Found at i:35618761 original size:58 final size:58
Alignment explanation
Indices: 35618693--35618858 Score: 264
Period size: 58 Copynumber: 2.8 Consensus size: 58
35618683 GAAAATTCAA
*
35618693 GGTTAAAAATGGAATTTTGGAAAGTTTGGGAGTAAAATGGTAATTTTTGGTGAAATAGT
1 GGTTAAAAATGGAATTTTGGAAAGTTTGGG-GTAAAATGGTAATTTTTGGTGAAATAGG
* *
35618752 GGTT-AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGT-ATTTTGGGTGAAATCGG
1 GGTTAAAAATGGAATTTTGGAAAGTTT-GGGGTAAAATGGTAATTTTTGGTGAAATAGG
35618809 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGG
1 GGTTAAAAATGGAATTTTGGAAAGTTT-GGGGTAAAATGGTAATTTTTGG
35618859 AAGTTTCAGG
Statistics
Matches: 99, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
57 18 0.18
58 67 0.68
59 14 0.14
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.35
Consensus pattern (58 bp):
GGTTAAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGGTGAAATAGG
Found at i:35618876 original size:58 final size:56
Alignment explanation
Indices: 35618696--35618884 Score: 222
Period size: 58 Copynumber: 3.3 Consensus size: 56
35618686 AATTCAAGGT
35618696 TAAAAATGGAATTTTGGAAAGTTTGGGAGTAAAATGGTAATTTTTGGTGAAAT-AGTGG
1 TAAAAATGGAATTTTGGAAAGTTTGGG-GTAAAATGGTAATTTTT-GTGAAATCAG-GG
* * *
35618754 TTAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGT-ATTTTGGGTGAAATCGGGG
1 TAAAAATGGAATTTTGGAAAGTTT-GGGGTAAAATGGTAATTTT-TGTGAAATCAGGG
*
35618811 TTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTG-GAAGTTTCAGGG
1 -TAAAAATGGAATTTTGGAAAGTTT-GGGGTAAAATGGTAATTTTTGTGAA--ATCAGGG
* *
35618870 TCAAAATGTAATTTT
1 TAAAAATGGAATTTT
35618885 TTGAAGTTTT
Statistics
Matches: 114, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
57 17 0.15
58 84 0.74
59 13 0.11
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (56 bp):
TAAAAATGGAATTTTGGAAAGTTTGGGGTAAAATGGTAATTTTTGTGAAATCAGGG
Found at i:35618885 original size:29 final size:28
Alignment explanation
Indices: 35618814--35618893 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
35618804 ATCGGGGTTA
*
35618814 AAAATGGAA-TTTTGGAAAGTTTAGGGGT
1 AAAATGTAATTTTTGG-AAGTTTAGGGGT
35618842 AAAATGGTAATTTTTGGAAGTTTCA-GGGT
1 AAAAT-GTAATTTTTGGAAGTTT-AGGGGT
*
35618871 CAAAATGTAATTTTTTGAAGTTT
1 -AAAATGTAATTTTTGGAAGTTT
35618894 TGAGATAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
28 5 0.11
29 29 0.63
30 12 0.26
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTAGGGGT
Found at i:35619254 original size:32 final size:33
Alignment explanation
Indices: 35619193--35619256 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
35619183 TTACTGGGCC
* *
35619193 AAATTAAAAATAATTAAAATTATGAAAAGGACT
1 AAATTAAAAACAATTAAAAATATGAAAAGGACT
35619226 AAATT-AAAACAATTAAAAAATATG-AAAGGAC
1 AAATTAAAAACAATT-AAAAATATGAAAAGGAC
35619257 CAAACGCGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.23
Consensus pattern (33 bp):
AAATTAAAAACAATTAAAAATATGAAAAGGACT
Found at i:35619923 original size:22 final size:20
Alignment explanation
Indices: 35619886--35619928 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
35619876 TTCATTTTTT
*
35619886 TTATTTTATTATTATAAATA
1 TTATTTTATTACTATAAATA
35619906 TTATTATTAATTACTATAAATA
1 TTATT-TT-ATTACTATAAATA
35619928 T
1 T
35619929 CAACAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTTTATTACTATAAATA
Found at i:35620696 original size:14 final size:14
Alignment explanation
Indices: 35620675--35620744 Score: 76
Period size: 13 Copynumber: 5.1 Consensus size: 14
35620665 CATTGGGCCT
35620675 ATTTGGGCCATTGTA
1 ATTTGGGCC-TTGTA
*
35620690 A-TTGGGCCTT-CA
1 ATTTGGGCCTTGTA
35620702 ATTTGGGCCTTTGTA
1 ATTTGGGCC-TTGTA
35620717 A-TTGGGCCTT-TA
1 ATTTGGGCCTTGTA
35620729 ATTTGGGCCTTTGTA
1 ATTTGGGCC-TTGTA
35620744 A
1 A
35620745 ATGGACTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.11
13 18 0.38
14 18 0.38
15 6 0.13
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (14 bp):
ATTTGGGCCTTGTA
Found at i:35620710 original size:27 final size:27
Alignment explanation
Indices: 35620675--35620744 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
35620665 CATTGGGCCT
*
35620675 ATTTGGGCCATTGTAATTGGGCCTTCA
1 ATTTGGGCCTTTGTAATTGGGCCTTCA
*
35620702 ATTTGGGCCTTTGTAATTGGGCCTTTA
1 ATTTGGGCCTTTGTAATTGGGCCTTCA
35620729 ATTTGGGCCTTTGTAA
1 ATTTGGGCCTTTGTAA
35620745 ATGGACTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (27 bp):
ATTTGGGCCTTTGTAATTGGGCCTTCA
Found at i:35620831 original size:17 final size:18
Alignment explanation
Indices: 35620809--35620849 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
35620799 TTTCAAATAT
*
35620809 TTTAAATTTAA-AATGAA
1 TTTAAATTTAATAATAAA
35620826 TTTAAATTTAATAATAAA
1 TTTAAATTTAATAATAAA
35620844 TTTAAA
1 TTTAAA
35620850 CCTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:35621590 original size:200 final size:201
Alignment explanation
Indices: 35621205--35621837 Score: 974
Period size: 200 Copynumber: 3.2 Consensus size: 201
35621195 GTCTTCTTCC
* * *
35621205 CTCTGT-T-TCATCAGGAAGATGACCGCAATC-ATCTGTTTTAATTCGCTTCTCTAGATCTCCTC
1 CTCTGTATCTCATCAGGAAGATGACCGCCATCGCT-TGTTTTAATTCGCTTCTCTGGATCTCCTC
* * * *
35621267 AGGAAGACAAATTTGGTCCACTTCTCTGTATCTCATCAAGAAACTAACCATGTTATTGTTTCGAC
65 AGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGAC
* * *
35621332 CTGCTTCTTAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCACTTTGAGCGTTGATTTGG
130 CTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGG
35621397 TATTCTT
195 TATTCTT
* *
35621404 CTCTGTGTCTCATCAGGAAAATGACCGCCA-CGCTTGTTTTAATTCGCTTCTCTGGATCTCCTCA
1 CTCTGTATCTCATCAGGAAGATGACCGCCATCGCTTGTTTTAATTCGCTTCTCTGGATCTCCTCA
* *
35621468 AGAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACC
66 GGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACC
*
35621533 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTAAGCGTTGAGTTGGT
131 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGT
35621598 ATTCTT
196 ATTCTT
* * * *
35621604 CTCTGTATCTCATCAGGAAGATAACCG-CATCACTTGTTTTAATTCACTTCTCTGGATCTCCTTA
1 CTCTGTATCTCATCAGGAAGATGACCGCCATCGCTTGTTTTAATTCGCTTCTCTGGATCTCCTCA
*
35621668 GGAAGATGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACC
66 GGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACC
* * * *
35621733 TGCTTCTCAGTGTCTCACCAAGAAGCTGGGTACGAAGAATGGCTCG-TGTTGAGCGTTGAGTTGG
131 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCT-TTGAGCGTTGAGTTGG
35621797 TATTCTT
195 TATTCTT
*
35621804 CTCTGTATCTCATCAGGAAGATGATCGCC-TCGCT
1 CTCTGTATCTCATCAGGAAGATGACCGCCATCGCT
35621838 GTCTTGTTGA
Statistics
Matches: 397, Mismatches: 31, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
199 9 0.02
200 367 0.92
201 21 0.05
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (201 bp):
CTCTGTATCTCATCAGGAAGATGACCGCCATCGCTTGTTTTAATTCGCTTCTCTGGATCTCCTCA
GGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACC
TGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGT
ATTCTT
Found at i:35633131 original size:29 final size:28
Alignment explanation
Indices: 35633063--35633221 Score: 94
Period size: 29 Copynumber: 5.5 Consensus size: 28
35633053 CTCGATGGCA
* * *
35633063 AAAATGTAATTTCGGGAAAATTT-GGGGTT
1 AAAATGGAATTT-TGGAAAGTTTAGGGG-T
*
35633092 AAAATGGAATTTTGGAAAGTTTAGGAGT
1 AAAATGGAATTTTGGAAAGTTTAGGGGT
*
35633120 AAAATGGTAATTTTTGGTGAAA---TCGGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTTAGGGG-T
*
35633150 AAAAATGGAATTTTGGAAAGTTTGGGGGT
1 -AAAATGGAATTTTGGAAAGTTTAGGGGT
* * *
35633179 AAAACGGTAATTTT-TAGAAGTTTCGGGGT
1 AAAATGG-AATTTTGGA-AAGTTTAGGGGT
*
35633208 CAAAATGTAATTTT
1 -AAAATGGAATTTT
35633222 TTGAAGTTTT
Statistics
Matches: 105, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
27 4 0.04
28 24 0.23
29 48 0.46
30 17 0.16
31 8 0.08
32 4 0.04
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:35633178 original size:88 final size:88
Alignment explanation
Indices: 35633062--35633222 Score: 195
Period size: 88 Copynumber: 1.8 Consensus size: 88
35633052 TCTCGATGGC
* *
35633062 AAAAATGTAATTTCGGGAAAATTTGGGGTTAAAATGG-AATTTTG-GAAAGTTTAGGAGT-AAAA
1 AAAAATGGAATTTCGGGAAAATTTGGGG-TAAAACGGTAATTTTGAG-AAGTTTAGGAGTCAAAA
35633124 TGGTAATTTTTGGTGAAATCGGGGTT
64 T-GTAATTTTTGGTGAAATCGGGGTT
* * * * *
35633150 AAAAATGGAATTT-TGGAAAGTTTGGGGGTAAAACGGTAATTTTTAGAAGTTTCGGGGTCAAAAT
1 AAAAATGGAATTTCGGGAAAATTT-GGGGTAAAACGGTAATTTTGAGAAGTTTAGGAGTCAAAAT
35633214 GTAATTTTT
65 GTAATTTTT
35633223 TGAAGTTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
87 15 0.24
88 41 0.66
89 6 0.10
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (88 bp):
AAAAATGGAATTTCGGGAAAATTTGGGGTAAAACGGTAATTTTGAGAAGTTTAGGAGTCAAAATG
TAATTTTTGGTGAAATCGGGGTT
Found at i:35633205 original size:59 final size:57
Alignment explanation
Indices: 35633086--35633221 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 57
35633076 GGGAAAATTT
* *
35633086 GGGGTTAAAATGGAATTTTGGAAAGTTTAGGAGTAAAATGGTAATTTTTGGTGAAATC
1 GGGGTTAAAATGGAATTTTGGAAAGTTTAGGAGTAAAACGGTAATTTTT-GAGAAATC
* * *
35633144 GGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAACGGTAATTTTT-AGAAGTTTC
1 GGGGTT-AAAATGGAATTTTGGAAAGTTTAGGAGTAAAACGGTAATTTTTGAGAA--ATC
* *
35633203 GGGGTCAAAATGTAATTTT
1 GGGGTTAAAATGGAATTTT
35633222 TTGAAGTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 3 0.04
58 18 0.26
59 47 0.69
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (57 bp):
GGGGTTAAAATGGAATTTTGGAAAGTTTAGGAGTAAAACGGTAATTTTTGAGAAATC
Done.