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 100 of 126
Found at i:30379247 original size:87 final size:88
Alignment explanation
Indices: 30379146--30379331 Score: 241
Period size: 87 Copynumber: 2.1 Consensus size: 88
30379136 CGAGCTTCTT
* * ** *
30379146 AAAAATTACATTTTTGCCCTTAAACTTCCAAAAATCACATTTTGACCC-CAAACTTCTCAAAAAT
1 AAAAATCACATTTTTACCCCCAAACTTCCAAAAATAACATTTT-ACCCTCAAACTTCTCAAAAAT
*
30379210 TACA-TTTTTGTCCCAAAACTTCC
65 TACATTTTTTATCCCAAAACTTCC
* **
30379233 AAAAATCACGTTTTTACCCCCAAACTTCCAAAAATAACATTTTACCCTTGAACTTCTCAAAAATT
1 AAAAATCACATTTTTACCCCCAAACTTCCAAAAATAACATTTTACCCTCAAACTTCTCAAAAATT
* **
30379298 ATATTTTTTATCCCCTAACTTCC
66 ACATTTTTTATCCCAAAACTTCC
30379321 AAAAATCACAT
1 AAAAATCACAT
30379332 CCAAAAATCA
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
86 4 0.05
87 54 0.64
88 26 0.31
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (88 bp):
AAAAATCACATTTTTACCCCCAAACTTCCAAAAATAACATTTTACCCTCAAACTTCTCAAAAATT
ACATTTTTTATCCCAAAACTTCC
Found at i:30379336 original size:13 final size:13
Alignment explanation
Indices: 30379318--30379344 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30379308 TCCCCTAACT
30379318 TCCAAAAATCACA
1 TCCAAAAATCACA
30379331 TCCAAAAATCACA
1 TCCAAAAATCACA
30379344 T
1 T
30379345 TTTTGCCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.19
Consensus pattern (13 bp):
TCCAAAAATCACA
Found at i:30379346 original size:72 final size:71
Alignment explanation
Indices: 30379259--30379397 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 71
30379249 CCCCCAAACT
* *
30379259 TCCAAAAATAACA-TTTTACCCTTGAACTTCTCAAAAATTATATTTTTTATCCCCT-AACTTCCA
1 TCCAAAAATAACATTTTTACCCTTGAACTTCTCAAAAATTACA-TTATTAT--CCTAAACTTCCA
30379322 AAAATCACA
63 AAAATCACA
* *
30379331 TCCAAAAATCACATTTTTGCCCTTGAACTTCTCAAAAATTACATTATTATCCTAAACTTCCAAAA
1 TCCAAAAATAACATTTTTACCCTTGAACTTCTCAAAAATTACATTATTATCCTAAACTTCCAAAA
30379396 AT
66 AT
30379398 TATGTTTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
70 3 0.05
71 13 0.21
72 18 0.30
73 27 0.44
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (71 bp):
TCCAAAAATAACATTTTTACCCTTGAACTTCTCAAAAATTACATTATTATCCTAAACTTCCAAAA
ATCACA
Found at i:30379425 original size:101 final size:101
Alignment explanation
Indices: 30379230--30379414 Score: 234
Period size: 101 Copynumber: 1.9 Consensus size: 101
30379220 TCCCAAAACT
* *
30379230 TCCAAAAATCACGTTTTTACCCCCAAACTTCCAAAAATAACATTTTACCCTTGAACTTCTCAAAA
1 TCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATAACATTTTACCCTTAAACTTCTCAAAA
* *
30379295 ATTATATTTTTTATCCCCTAACTTCCAAAAATCACA
66 ATTATAGTTTTTATCCCCAAACTTCCAAAAATCACA
* *** * *
30379331 TCCAAAAATCACATTTTTGCCCTTGAACTTCTCAAAAATTACATTATTATCC-TAAACTTC-CAA
1 TCCAAAAATCACATTTTTACCCCCAAACTTC-CAAAAATAACATT-TTACCCTTAAACTTCTCAA
30379394 AAATTAT-GTTTTTA-CCCCAAA
64 AAATTATAGTTTTTATCCCCAAA
30379415 TTATCCCAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
99 6 0.08
100 6 0.08
101 36 0.50
102 19 0.26
103 5 0.07
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (101 bp):
TCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATAACATTTTACCCTTAAACTTCTCAAAA
ATTATAGTTTTTATCCCCAAACTTCCAAAAATCACA
Found at i:30387605 original size:23 final size:23
Alignment explanation
Indices: 30387575--30387677 Score: 79
Period size: 23 Copynumber: 4.5 Consensus size: 23
30387565 ACATTAGAAC
*
30387575 GCTCTCTGTTTAGCAC-GTCTTGT
1 GCTCTCTGTTTAGCACTGT-GTGT
*
30387598 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
30387621 GCTCTCTGTTGCTCAGCACT-TATGT
1 GCTCTCTGTT--T-AGCACTGTGTGT
* * *
30387646 GCTCTTTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTGTGTGT
*
30387667 ACTCTCTGTTT
1 GCTCTCTGTTT
30387678 GTTCCGTATA
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
21 13 0.20
22 4 0.06
23 27 0.42
24 3 0.05
25 12 0.18
26 6 0.09
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:30388584 original size:49 final size:49
Alignment explanation
Indices: 30388477--30389016 Score: 410
Period size: 49 Copynumber: 10.9 Consensus size: 49
30388467 CAGGTTTGAC
* * * * * * *
30388477 AGGGAAAGATTGAGGCCACGAA-GGCAAATCCAGTACCTTAAAAGATGTGA
1 AGGGAAAGGTTGAGGCCGC-AACGGCGAACCCAGTACCAT-GAAGATATGA
* * * * *
30388527 TGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACTATGAAGATACGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGA
* *
30388576 AGGGAAAGGTTGAGGCTGCAACGGCGAACCCAGTACCATGAAGAGATGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGA
* * * * * * * * *
30388625 AGGGAATGATTGAGGCCGCGACGGTGAATCTAGTAACTTAGAAGATGTGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCAT-GAAGATATGA
*
30388675 CA-GGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGAGATGA
1 -AGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGA
* * * ** * *
30388724 AAGG-AAGGATTGAGGCCGCAACGACGAATCTGGTACCTTAGAAGATGTGA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCAGTACCAT-GAAGATATGA
* * * * * * *
30388774 TGGGAAAGGTTGAGGCCGCAATGACGAACTCGGTACCTAAGAAGATGTGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACC-ATGAAGATATGA
* *
30388824 TA-GGAAAGGTTGAGGCCGCAACGGCAAACCCAGTACCATGAAGATACGA
1 -AGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGA
* * * * * * *
30388873 AGGGAAAGGTT-ATGGCCGCAATGGCAAACTCGGTACCACGGAGATATAA
1 AGGGAAAGGTTGA-GGCCGCAACGGCGAACCCAGTACCATGAAGATATGA
* * * * *
30388922 AAGGAAAGGTTGAGGCTGCAACGGCGAACCCAATACCTTAGAAGATA-CA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCAT-GAAGATATGA
* * * * *
30388971 ATGGGAATGATTGAGGTCGCAACAGCGAATCC-GATACCATGAAGAT
1 A-GGGAAAGGTTGAGGCCGCAACGGCGAACCCAG-TACCATGAAGAT
30389017 TGATAAGTGC
Statistics
Matches: 385, Mismatches: 90, Indels: 31
0.76 0.18 0.06
Matches are distributed among these distances:
48 7 0.02
49 199 0.52
50 174 0.45
51 5 0.01
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (49 bp):
AGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGA
Found at i:30388669 original size:99 final size:98
Alignment explanation
Indices: 30388529--30389015 Score: 405
Period size: 99 Copynumber: 4.9 Consensus size: 98
30388519 AGATGTGATG
* * * **
30388529 GGAAAGGTTGAGGCCGCAATGGCGAACCCGGTA-C-TATGAAGATACGAAGGGAAAGGTTGAGGC
1 GGAAAGATTGAGGCCGCAACGGCGAATCTAGTACCTTA-GAAGATACGAAGGGAAAGGTTGAGGC
*
30388592 TGCAACGGCGAACCCAGTACCATGAAGAGATGAA
65 CGCAACGGCGAACCCAGTACCATGAAGAGATGAA
* * * * **
30388626 GGGAATGATTGAGGCCGCGACGGTGAATCTAGTAACTTAGAAGATGTGACA-GGAAAGGTTGAGG
1 -GGAAAGATTGAGGCCGCAACGGCGAATCTAGTACCTTAGAAGATACGA-AGGGAAAGGTTGAGG
30388690 CCGCAACGGCGAACCCAGTACCATGAAGAGATGAAA
64 CCGCAACGGCGAACCCAGTACCATGAAGAGATG-AA
* * * ** *
30388726 GGAAGGATTGAGGCCGCAACGACGAATCTGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCC
1 GGAAAGATTGAGGCCGCAACGGCGAATCTAGTACCTTAGAAGATACGAAGGGAAAGGTTGAGGCC
* * * * *
30388791 GCAATGACGAACTCGGTACCTAAGAAGATG-TGATA
66 GCAACGGCGAACCCAGTACC-ATGAAGA-GATGA-A
* * * * *
30388826 GGAAAGGTTGAGGCCGCAACGGCAAACCCAGTACCAT-GAAGATACGAAGGGAAAGGTT-ATGGC
1 GGAAAGATTGAGGCCGCAACGGCGAATCTAGTACCTTAGAAGATACGAAGGGAAAGGTTGA-GGC
* * * * * * * *
30388889 CGCAATGGCAAACTCGGTACCACGGAGATATAAAA
65 CGCAACGGCGAACCCAGTACCATGAAGAGAT-GAA
* * * * * * * *
30388924 GGAAAGGTTGAGGCTGCAACGGCGAACCCAATACCTTAGAAGATAC-AATGGGAATGATTGAGGT
1 GGAAAGATTGAGGCCGCAACGGCGAATCTAGTACCTTAGAAGATACGAA-GGGAAAGGTTGAGGC
* *
30388988 CGCAACAGCGAATCC-GATACCATGAAGA
65 CGCAACGGCGAACCCAG-TACCATGAAGA
30389016 TTGATAAGTG
Statistics
Matches: 320, Mismatches: 54, Indels: 29
0.79 0.13 0.07
Matches are distributed among these distances:
98 69 0.22
99 206 0.64
100 44 0.14
101 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (98 bp):
GGAAAGATTGAGGCCGCAACGGCGAATCTAGTACCTTAGAAGATACGAAGGGAAAGGTTGAGGCC
GCAACGGCGAACCCAGTACCATGAAGAGATGAA
Found at i:30388908 original size:149 final size:148
Alignment explanation
Indices: 30388477--30389016 Score: 484
Period size: 148 Copynumber: 3.6 Consensus size: 148
30388467 CAGGTTTGAC
* * * * *
30388477 AGGGAAAGATTGAGGCCACGAA-GGCAAATCCAGTACCTTAA-AAGATGTGATGGGAAAGGTTGA
1 AGGGAAAGATTGAGGCCGC-AACGACGAATCTAGTACC-TAAGAAGATGTGATAGGAAAGGTTGA
* * * *
30388540 GGCCGCAATGGCGAACCCGGTACTATGAAGATACGAAGGGAAAGGTTGAGGCTGCAACGGCGAAC
64 GGCCGCAACGGCGAACCCAGTACCATGAAGATACGAAGGGAAAGGTTGAGGCCGCAACGGCGAAC
* *
30388605 CCAGTACCATGAAGAGATGA
129 TCGGTACCATGAAGAGATGA
* * ** * * *
30388625 AGGGAATGATTGAGGCCGCGACGGTGAATCTAGTAACTTAGAAGATGTGACAGGAAAGGTTGAGG
1 AGGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCTAAGAAGATGTGATAGGAAAGGTTGAGG
* * * *
30388690 CCGCAACGGCGAACCCAGTACCATGAAGAGATGAAAGG-AAGGATTGAGGCCGCAACGACGAA-T
66 CCGCAACGGCGAACCCAGTACCATGAAGATACGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACT
*
30388753 CTGGTACCTTAGAAGATG-TGA
130 C-GGTACCAT-GAAGA-GATGA
* * * *
30388774 TGGGAAAGGTTGAGGCCGCAATGACGAA-CTCGGTACCTAAGAAGATGTGATAGGAAAGGTTGAG
1 AGGGAAAGATTGAGGCCGCAACGACGAATCT-AGTACCTAAGAAGATGTGATAGGAAAGGTTGAG
* * *
30388838 GCCGCAACGGCAAACCCAGTACCATGAAGATACGAAGGGAAAGGTT-ATGGCCGCAATGGCAAAC
65 GCCGCAACGGCGAACCCAGTACCATGAAGATACGAAGGGAAAGGTTGA-GGCCGCAACGGCGAAC
* * * *
30388902 TCGGTACCACGGAGATATAA
129 TCGGTACCATGAAGAGATGA
* * * * * * * * *** * * *
30388922 AAGGAAAGGTTGAGGCTGCAACGGCGAACCCAATACCTTAGAAGATACAATGGGAATGATTGAGG
1 AGGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCTAAGAAGATGTGATAGGAAAGGTTGAGG
* * *
30388987 TCGCAACAGCGAATCC-GATACCATGAAGAT
66 CCGCAACGGCGAACCCAG-TACCATGAAGAT
30389017 TGATAAGTGC
Statistics
Matches: 316, Mismatches: 63, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
147 9 0.03
148 186 0.59
149 114 0.36
150 7 0.02
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (148 bp):
AGGGAAAGATTGAGGCCGCAACGACGAATCTAGTACCTAAGAAGATGTGATAGGAAAGGTTGAGG
CCGCAACGGCGAACCCAGTACCATGAAGATACGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTC
GGTACCATGAAGAGATGA
Found at i:30388977 original size:198 final size:198
Alignment explanation
Indices: 30388529--30388993 Score: 453
Period size: 198 Copynumber: 2.4 Consensus size: 198
30388519 AGATGTGATG
*
30388529 GGAAAGGTTGAGGCCGCAATGGCGAACCCGGTA-C-TATGAAGATACGAA-GGGAAAGGTTGAGG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA-GAAGATAC-AATGGGAAAGGTTGAGG
* * * * * ** * *
30388591 CTGCAACGGCGAACCCAGTACCATGAAGAGATGAAGGGAATGATTGAGGCCGCGACGGTGAATCT
64 CCGCAACGACGAACCCAGTACCAAGAAGAGATGAAGGGAAAGATTGAGGCCGCAACGGCAAACCC
* ** * *
30388656 AGTAACTTAGAAGATGTGACAGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGAGA
129 AGTAACATAGAAGATACGACAGGAAAGGTTGAGGCCGCAACGGCAAACCCAGTACCACGAAGAGA
*
30388721 TGAAA
194 TAAAA
* * * ***
30388726 GG-AAGGATTGAGGCCGCAACGACGAATCTGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGC
1 GGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATACAATGGGAAAGGTTGAGGC
* * * *
30388790 CGCAATGACGAACTCGGTACCTAAGAAGATG-TGATA-GGAAAGGTTGAGGCCGCAACGGCAAAC
65 CGCAACGACGAACCCAGTACC-AAGAAGA-GATGA-AGGGAAAGATTGAGGCCGCAACGGCAAAC
* * * * *
30388853 CCAGTACCAT-GAAGATACGA-AGGGAAAGGTT-ATGGCCGCAATGGCAAACTCGGTACCACGGA
127 CCAGTAACATAGAAGATACGACA-GGAAAGGTTGA-GGCCGCAACGGCAAACCCAGTACCACGAA
*
30388915 GATATAAAA
190 GAGATAAAA
* ** * * *
30388924 GGAAAGGTTGAGGCTGCAACGGCGAACCCAATACCTTAGAAGATACAATGGGAATGATTGAGGTC
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATACAATGGGAAAGGTTGAGGCC
30388989 GCAAC
66 GCAAC
30388994 AGCGAATCCG
Statistics
Matches: 213, Mismatches: 45, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
196 4 0.02
197 27 0.13
198 137 0.64
199 43 0.20
200 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (198 bp):
GGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATACAATGGGAAAGGTTGAGGCC
GCAACGACGAACCCAGTACCAAGAAGAGATGAAGGGAAAGATTGAGGCCGCAACGGCAAACCCAG
TAACATAGAAGATACGACAGGAAAGGTTGAGGCCGCAACGGCAAACCCAGTACCACGAAGAGATA
AAA
Found at i:30389896 original size:15 final size:15
Alignment explanation
Indices: 30389859--30389897 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
30389849 TTATGTGTTC
*
30389859 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
30389874 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
30389888 TTAATTCTTG
1 TTAATTCTTG
30389898 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:30392873 original size:30 final size:30
Alignment explanation
Indices: 30392837--30392976 Score: 92
Period size: 30 Copynumber: 4.7 Consensus size: 30
30392827 CTAAACTATC
30392837 CAAAAATCATATTTTGACCCCCAAAATTCT
1 CAAAAATCATATTTTGACCCCCAAAATTCT
* * * *
30392867 CAAAAATTTATATTTTTG-TCCCCGAACTTC-
1 CAAAAA-TCATA-TTTTGACCCCCAAAATTCT
* * **
30392897 CAAAAATCATATTTTTACCCCTAATTTTCT
1 CAAAAATCATATTTTGACCCCCAAAATTCT
* *
30392927 CAAAATAACAT-TTTT-ACCCCAAAAACTT-T
1 CAAAA-ATCATATTTTGACCCCCAAAA-TTCT
* * *
30392956 CCAAAATTATATTTTAACCCC
1 CAAAAATCATATTTTGACCCC
30392977 AAACTCTTTG
Statistics
Matches: 84, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
28 7 0.08
29 27 0.32
30 28 0.33
31 17 0.20
32 5 0.06
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
CAAAAATCATATTTTGACCCCCAAAATTCT
Found at i:30392958 original size:60 final size:61
Alignment explanation
Indices: 30392829--30392976 Score: 144
Period size: 60 Copynumber: 2.5 Consensus size: 61
30392819 GAAGGTCCCT
* * * * *
30392829 AAACTATCCAAAAATCATATTTTGACCCCCAAAATTCTCAAAAATTTATATTTTTGTCCCC
1 AAACTTTCCAAAAATCATATTTTAACCCCCAAAATTCTCAAAAATTAACATTTTTGACCCC
* * * **
30392890 GAAC-TTCCAAAAATCATATTTTTACCCCTAATTTTCTC-AAAA-TAACATTTTT-ACCCC
1 AAACTTTCCAAAAATCATATTTTAACCCCCAAAATTCTCAAAAATTAACATTTTTGACCCC
*
30392947 AAAAACTTTCC-AAAATTATATTTTAACCCC
1 --AAACTTTCCAAAAATCATATTTTAACCCC
30392977 AAACTCTTTG
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
57 4 0.06
58 8 0.11
59 24 0.33
60 33 0.46
61 3 0.04
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (61 bp):
AAACTTTCCAAAAATCATATTTTAACCCCCAAAATTCTCAAAAATTAACATTTTTGACCCC
Found at i:30397112 original size:10 final size:10
Alignment explanation
Indices: 30397097--30397129 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
30397087 AACTATTCTT
*
30397097 TCTCTCTCTC
1 TCTCTCTCAC
30397107 TCTCTCTCAC
1 TCTCTCTCAC
30397117 TCTCTCTCAC
1 TCTCTCTCAC
30397127 TCT
1 TCT
30397130 TTATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.06, C:0.48, G:0.00, T:0.45
Consensus pattern (10 bp):
TCTCTCTCAC
Found at i:30404429 original size:42 final size:42
Alignment explanation
Indices: 30404380--30404463 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
30404370 CAAATATTTT
* *
30404380 TAAACCCAAATATTATTTCATTCTTCAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCT-AAATAACACTCATAAAC
* *
30404422 TAAACCCAAATATAATTTTATTCCTAAATAACACTTATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
30404464 AATTCCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
Found at i:30405050 original size:26 final size:26
Alignment explanation
Indices: 30405019--30405069 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
30405009 GAACAAATAT
*
30405019 ATTCTAT-TCTACTCGATTCGATTCGA
1 ATTCTATCTC-ACTCGACTCGATTCGA
30405045 ATTCTATCTCACTCGACTCGATTCG
1 ATTCTATCTCACTCGACTCGATTCG
30405070 TAAAAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (26 bp):
ATTCTATCTCACTCGACTCGATTCGA
Found at i:30406184 original size:34 final size:34
Alignment explanation
Indices: 30406146--30406218 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
30406136 AGTAAACAAC
*
30406146 ATTTGGATAAGGTAAAAGGA-AAAAAATTAAAAAT
1 ATTTGGATAAGATAAAA-GATAAAAAATTAAAAAT
* *
30406180 ATTTGGGTAAGATAAAATATAAAAAATTAAAAAT
1 ATTTGGATAAGATAAAAGATAAAAAATTAAAAAT
30406214 ATTTG
1 ATTTG
30406219 AGTTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (34 bp):
ATTTGGATAAGATAAAAGATAAAAAATTAAAAAT
Found at i:30407200 original size:32 final size:32
Alignment explanation
Indices: 30407163--30407226 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
30407153 AAGATGAAGA
30407163 CCCTGCACTATCATAAGGTTAATTCTAGAATC
1 CCCTGCACTATCATAAGGTTAATTCTAGAATC
*
30407195 CCCTGCACTATTATAAGGTTAATTCTAGAATC
1 CCCTGCACTATCATAAGGTTAATTCTAGAATC
30407227 ATTCATTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (32 bp):
CCCTGCACTATCATAAGGTTAATTCTAGAATC
Found at i:30409687 original size:10 final size:10
Alignment explanation
Indices: 30409672--30409700 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
30409662 TGGTAGTGAA
30409672 TTTGAGAGAG
1 TTTGAGAGAG
30409682 TTTGAGAGAG
1 TTTGAGAGAG
30409692 -TTGAGAGAG
1 TTTGAGAGAG
30409701 ATAAGACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (10 bp):
TTTGAGAGAG
Found at i:30411461 original size:24 final size:24
Alignment explanation
Indices: 30411424--30411476 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
30411414 TCATTAATAA
* *
30411424 ATAAATTAGTCAATAAACGAGCTT
1 ATAAAATAGCCAATAAACGAGCTT
*
30411448 ATAAAATAGCCAATAAATGAGCTT
1 ATAAAATAGCCAATAAACGAGCTT
*
30411472 TTAAA
1 ATAAA
30411477 CGAGCTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (24 bp):
ATAAAATAGCCAATAAACGAGCTT
Found at i:30414376 original size:59 final size:58
Alignment explanation
Indices: 30414270--30414405 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 58
30414260 GCTATGTGCC
* * *
30414270 TAAT-AGGCTTCGTGTCGGTGAATTCAGACTGTGTGTTTACTAAGCTTTGTGCCGGTG
1 TAATCAGGCTTTGTGTCGGTGAATTCAGACTATGTGTCTACTAAGCTTTGTGCCGGTG
* * * *
30414327 TATTCAGGGCTTTGTGTCGGTGGATTCAGACTATGTGTCTAGTAGGCTTTGTGCCGGTG
1 TAATCA-GGCTTTGTGTCGGTGAATTCAGACTATGTGTCTACTAAGCTTTGTGCCGGTG
* *
30414386 TAATCAGACTTTGTGCCGGT
1 TAATCAGGCTTTGTGTCGGT
30414406 ATAATCAGAC
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 3 0.04
58 13 0.19
59 51 0.76
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.37
Consensus pattern (58 bp):
TAATCAGGCTTTGTGTCGGTGAATTCAGACTATGTGTCTACTAAGCTTTGTGCCGGTG
Found at i:30414433 original size:79 final size:79
Alignment explanation
Indices: 30414314--30414469 Score: 201
Period size: 79 Copynumber: 2.0 Consensus size: 79
30414304 GTTTACTAAG
* * * * *
30414314 CTTTGTGCCGGTGTATTCAGGGCTTTGTGTCGGTGGATTC-AGACTATGTGTC-TAGTAGGCTTT
1 CTTTGTGCCGGTATAATCAGGACTTTGTGCCGGTGCATTCAAG-CTATGTG-CATAGTAGGCTTT
30414377 GTGCCGGTGTAATCAGA
64 GTGCCGGTG-AATCAGA
*
30414394 CTTTGTGCCGGTATAATCA-GACTTTGTGCCGGTGCATTCAAGCTTTGTGCATAGTAGGCTTTGT
1 CTTTGTGCCGGTATAATCAGGACTTTGTGCCGGTGCATTCAAGCTATGTGCATAGTAGGCTTTGT
*
30414458 GCCTGTGAATCA
66 GCCGGTGAATCA
30414470 AGAAGGAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 6 0.09
79 42 0.63
80 19 0.28
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36
Consensus pattern (79 bp):
CTTTGTGCCGGTATAATCAGGACTTTGTGCCGGTGCATTCAAGCTATGTGCATAGTAGGCTTTGT
GCCGGTGAATCAGA
Found at i:30414443 original size:21 final size:21
Alignment explanation
Indices: 30414373--30414427 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
30414363 GTCTAGTAGG
30414373 CTTTGTGCCGGTGTAATCAGA
1 CTTTGTGCCGGTGTAATCAGA
*
30414394 CTTTGTGCCGGTATAATCAGA
1 CTTTGTGCCGGTGTAATCAGA
30414415 CTTTGTGCCGGTG
1 CTTTGTGCCGGTG
30414428 CATTCAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.35
Consensus pattern (21 bp):
CTTTGTGCCGGTGTAATCAGA
Found at i:30420615 original size:37 final size:37
Alignment explanation
Indices: 30420542--30420736 Score: 160
Period size: 37 Copynumber: 5.3 Consensus size: 37
30420532 TGTGCTTAAA
* * * * * * *
30420542 AGGCTTCGTGCCGGTGAATTTAGACTGTGTGTCTAGT
1 AGGCTTTGTGCTGGTGTATTCAGGCTTTGTGCCTAGT
*
30420579 AGGCTTTGTACTGGTGTATTCAGGCTTTGTGCCTAGT
1 AGGCTTTGTGCTGGTGTATTCAGGCTTTGTGCCTAGT
* * * ** * *
30420616 AGGCTTAGTGCCGGTGGATTCATACTGTGTGTCTAGT
1 AGGCTTTGTGCTGGTGTATTCAGGCTTTGTGCCTAGT
* * * *
30420653 AGGCTTTGTG-TCGGTGTAATCGGGTTTTATGCCTAGT
1 AGGCTTTGTGCT-GGTGTATTCAGGCTTTGTGCCTAGT
* **
30420690 AGGCTTCGTGCTTTTGTATTCAGGCTTTGTGCCT-GAT
1 AGGCTTTGTGCTGGTGTATTCAGGCTTTGTGCCTAG-T
30420727 AGGCTTTGTG
1 AGGCTTTGTG
30420737 TCGGTGAATT
Statistics
Matches: 120, Mismatches: 35, Indels: 6
0.75 0.22 0.04
Matches are distributed among these distances:
36 1 0.01
37 118 0.98
38 1 0.01
ACGTcount: A:0.14, C:0.16, G:0.31, T:0.39
Consensus pattern (37 bp):
AGGCTTTGTGCTGGTGTATTCAGGCTTTGTGCCTAGT
Found at i:30420653 original size:74 final size:74
Alignment explanation
Indices: 30420542--30420700 Score: 221
Period size: 74 Copynumber: 2.1 Consensus size: 74
30420532 TGTGCTTAAA
* *
30420542 AGGCTTCGTGCCGGTGAATTTAGACTGTGTGTCTAGTAGGCTTTGTACT-GGTGTATTCAGGCTT
1 AGGCTTCGTGCCGGTGAATTCAGACTGTGTGTCTAGTAGGCTTTGT-CTCGGTGTAATCAGGCTT
*
30420606 TGTGCCTAGT
65 TATGCCTAGT
* * * * * *
30420616 AGGCTTAGTGCCGGTGGATTCATACTGTGTGTCTAGTAGGCTTTGTGTCGGTGTAATCGGGTTTT
1 AGGCTTCGTGCCGGTGAATTCAGACTGTGTGTCTAGTAGGCTTTGTCTCGGTGTAATCAGGCTTT
30420681 ATGCCTAGT
66 ATGCCTAGT
30420690 AGGCTTCGTGC
1 AGGCTTCGTGC
30420701 TTTTGTATTC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 1 0.01
74 73 0.99
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.37
Consensus pattern (74 bp):
AGGCTTCGTGCCGGTGAATTCAGACTGTGTGTCTAGTAGGCTTTGTCTCGGTGTAATCAGGCTTT
ATGCCTAGT
Found at i:30420711 original size:74 final size:74
Alignment explanation
Indices: 30420542--30420742 Score: 217
Period size: 74 Copynumber: 2.7 Consensus size: 74
30420532 TGTGCTTAAA
* * * * *
30420542 AGGCTTCGTGCCGGTGAATTTAGACTGTGTGTCTAGTAGGCTTTGT-ACTGGTGTATTCAGGCTT
1 AGGCTTAGTGCCGGTGGATTCAGACTGTGTGTCTAGTAGGCTTTGTGTC-GGTGTAATCAGGCTT
*
30420606 TGTGCCTAGT
65 TATGCCTAGT
* * *
30420616 AGGCTTAGTGCCGGTGGATTCATACTGTGTGTCTAGTAGGCTTTGTGTCGGTGTAATCGGGTTTT
1 AGGCTTAGTGCCGGTGGATTCAGACTGTGTGTCTAGTAGGCTTTGTGTCGGTGTAATCAGGCTTT
30420681 ATGCCTAGT
66 ATGCCTAGT
* *** * * * *
30420690 AGGCTTCGTGCTTTTGTATTCAGGCTTTGTGCCT-GATAGGCTTTGTGTCGGTG
1 AGGCTTAGTGCCGGTGGATTCAGACTGTGTGTCTAG-TAGGCTTTGTGTCGGTG
30420743 AATTAAGGAA
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
73 1 0.01
74 105 0.98
75 1 0.01
ACGTcount: A:0.13, C:0.16, G:0.32, T:0.39
Consensus pattern (74 bp):
AGGCTTAGTGCCGGTGGATTCAGACTGTGTGTCTAGTAGGCTTTGTGTCGGTGTAATCAGGCTTT
ATGCCTAGT
Found at i:30423408 original size:52 final size:53
Alignment explanation
Indices: 30423232--30423426 Score: 226
Period size: 52 Copynumber: 3.7 Consensus size: 53
30423222 ATGAAAAAAG
* *
30423232 GGTCCGATGAC-TAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT-AGA
1 GGTCCGATGACTTAAGTGTCATAGTGAGTATATGAATCCTTTACGGATTAAGA
*
30423283 GGTCCGATGA-TTAAGTGTCATCA-TGAGTATATGAAATCCTTTTATGGATTTAA-A
1 GGTCCGATGACTTAAGTGTCAT-AGTGAGTATATG-AATCC-TTTACGGA-TTAAGA
* *
30423337 GGTCCGAT-AATTAAGTGTCATAGTGAGTATATGGATCCTTTACGGATTAAGA
1 GGTCCGATGACTTAAGTGTCATAGTGAGTATATGAATCCTTTACGGATTAAGA
* *
30423389 GGTCCGATGACTCT-A-TGTCATCGTGAGTGTATGAATCC
1 GGTCCGATGACT-TAAGTGTCATAGTGAGTATATGAATCC
30423427 CTCGTGGATT
Statistics
Matches: 124, Mismatches: 9, Indels: 21
0.81 0.06 0.14
Matches are distributed among these distances:
51 33 0.27
52 41 0.33
53 16 0.13
54 33 0.27
55 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (53 bp):
GGTCCGATGACTTAAGTGTCATAGTGAGTATATGAATCCTTTACGGATTAAGA
Found at i:30423426 original size:105 final size:105
Alignment explanation
Indices: 30423232--30423423 Score: 280
Period size: 105 Copynumber: 1.8 Consensus size: 105
30423222 ATGAAAAAAG
* *
30423232 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAGAGGTCCGATGATTAA
1 GGTCCGATAACTAAGTGTCATAGTGAGTAAATGAATCCTTTACGGATTAGAGGTCCGATGATTAA
30423297 GTGTCATCATGAGTATATGAAATCCTTTTATGGATTTAAA
66 GTGTCATCATGAGTATATGAAATCCTTTTATGGATTTAAA
* * *
30423337 GGTCCGATAATTAAGTGTCATAGTGAGTATATGGATCCTTTACGGATTAAGAGGTCCGATGACTC
1 GGTCCGATAACTAAGTGTCATAGTGAGTAAATGAATCCTTTACGGATT-AGAGGTCCGATGA-T-
* *
30423402 T-A-TGTCATCGTGAGTGTATGAA
63 TAAGTGTCATCATGAGTATATGAA
30423424 TCCCTCGTGG
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
105 43 0.56
106 31 0.40
107 2 0.03
108 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (105 bp):
GGTCCGATAACTAAGTGTCATAGTGAGTAAATGAATCCTTTACGGATTAGAGGTCCGATGATTAA
GTGTCATCATGAGTATATGAAATCCTTTTATGGATTTAAA
Found at i:30424240 original size:21 final size:21
Alignment explanation
Indices: 30424193--30424247 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
30424183 GCATGACATA
* **
30424193 TATCAGTAGAAATTATACTTG
1 TATCGGTAGAAATTATACAGG
*
30424214 TATCGGTAGAACTTATACAGG
1 TATCGGTAGAAATTATACAGG
*
30424235 TTTCGGTAGAAAT
1 TATCGGTAGAAAT
30424248 CTGCACTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (21 bp):
TATCGGTAGAAATTATACAGG
Found at i:30426163 original size:113 final size:113
Alignment explanation
Indices: 30425965--30426207 Score: 387
Period size: 113 Copynumber: 2.2 Consensus size: 113
30425955 CATGACCAAA
* *
30425965 TAAGCAAATAACATAATAAGGCTATGCACATTTTCTAAATGGCCTCACCTTCATCGGTTGCTTCC
1 TAAGCAAATAACATAAGAAGGCTATGCACATTTTCTAAATGGCCTCACCTTCATCGGTTACTTCC
*
30426030 TGCTCTATCCAAACAAATCTCTCACAACACACTTTCCAGAAATCTAAC
66 TACTCTATCCAAACAAATCTCTCACAACACACTTTCCAGAAATCTAAC
* *
30426078 TAAGCAAATAACATAAGAAGGCTATGCACATTTTCTAAATGGCCTCCCCTTCATCTGTTACTTCC
1 TAAGCAAATAACATAAGAAGGCTATGCACATTTTCTAAATGGCCTCACCTTCATCGGTTACTTCC
* ** * *
30426143 TACTCTATCCAAACAAATCTCTCACAACACATTTTTTAGGAATCTAGC
66 TACTCTATCCAAACAAATCTCTCACAACACACTTTCCAGAAATCTAAC
*
30426191 TAGGCAAATAACATAAG
1 TAAGCAAATAACATAAG
30426208 GCTATACACA
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 119 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (113 bp):
TAAGCAAATAACATAAGAAGGCTATGCACATTTTCTAAATGGCCTCACCTTCATCGGTTACTTCC
TACTCTATCCAAACAAATCTCTCACAACACACTTTCCAGAAATCTAAC
Found at i:30433424 original size:26 final size:25
Alignment explanation
Indices: 30433395--30433474 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
30433385 AAGGTACATA
30433395 AGTGCTAGGGAAACAGAAGCACACAC
1 AGTGCT-GGGAAACAGAAGCACACAC
* *
30433421 AGTGCTGGGTAACAGAAGCACACAA
1 AGTGCTGGGAAACAGAAGCACACAC
* *
30433446 AGTTCT--G-ATCAGAGAGCACACAC
1 AGTGCTGGGAAACAGA-AGCACACAC
30433469 AGTGCT
1 AGTGCT
30433475 AATCAGAGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
22 5 0.11
23 14 0.30
25 22 0.47
26 6 0.13
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.14
Consensus pattern (25 bp):
AGTGCTGGGAAACAGAAGCACACAC
Found at i:30433463 original size:23 final size:23
Alignment explanation
Indices: 30433433--30433485 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
30433423 TGCTGGGTAA
* *
30433433 CAGA-AGCACACAAAGTTCTGAT
1 CAGAGAGCACACAAAGTGCTAAT
*
30433455 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
30433478 CAGAGAGC
1 CAGAGAGC
30433486 GTGCTAGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:30433712 original size:14 final size:14
Alignment explanation
Indices: 30433695--30433734 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
30433685 TTATAATTAA
30433695 ACACATAATATTTC
1 ACACATAATATTTC
30433709 ACACATAATATTTC
1 ACACATAATATTTC
30433723 ACACAT-ATATTT
1 ACACATAATATTT
30433735 TTCTCTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (14 bp):
ACACATAATATTTC
Found at i:30436236 original size:31 final size:31
Alignment explanation
Indices: 30436199--30436264 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
30436189 AGATTTTTAT
* *
30436199 AAAATTT-TAAAATTTATTTTAAAATATATAA
1 AAAATTTAGAAAATTTATTTAAAAAT-TATAA
* *
30436230 AAAATTTAGAAAATTTCTTTAAAAATTGTAA
1 AAAATTTAGAAAATTTATTTAAAAATTATAA
30436261 AAAA
1 AAAA
30436265 AATATTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAATTTAGAAAATTTATTTAAAAATTATAA
Found at i:30437160 original size:17 final size:17
Alignment explanation
Indices: 30437140--30437181 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
30437130 AAAAAAATAA
30437140 AAATCTTTAAAATATAT
1 AAATCTTTAAAATATAT
*
30437157 AAAT-TAATAAAATATAT
1 AAATCT-TTAAAATATAT
30437174 AAATCTTT
1 AAATCTTT
30437182 TTTCACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATCTTTAAAATATAT
Found at i:30437423 original size:17 final size:19
Alignment explanation
Indices: 30437378--30437435 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 19
30437368 TATAATATAT
30437378 AATATATAAATTAATAAAAG
1 AATATA-AAATTAATAAAAG
*
30437398 AATTATAAAATT-ATAACA-
1 AA-TATAAAATTAATAAAAG
30437416 AATAT-AAA-TATATAAAAG
1 AATATAAAATTA-ATAAAAG
30437434 AA
1 AA
30437436 CTAAGAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 1 0.03
16 3 0.09
17 8 0.25
18 4 0.12
19 5 0.16
20 7 0.22
21 4 0.12
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (19 bp):
AATATAAAATTAATAAAAG
Found at i:30438497 original size:28 final size:28
Alignment explanation
Indices: 30438455--30438510 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
30438445 TCGATCGGTT
* *
30438455 AAAAAATCATTAAAAATTAATTAAAATA
1 AAAAAATCATAAAAAATTAATAAAAATA
* *
30438483 AAAAAATTATAAAAAGTTAATAAAAATA
1 AAAAAATCATAAAAAATTAATAAAAATA
30438511 TATTTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAATCATAAAAAATTAATAAAAATA
Found at i:30438505 original size:11 final size:10
Alignment explanation
Indices: 30438465--30438509 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
30438455 AAAAAATCAT
30438465 TAAAAATTAA
1 TAAAAATTAA
*
30438475 TTAAAA-TAA
1 TAAAAATTAA
30438484 -AAAAATT-A
1 TAAAAATTAA
30438492 TAAAAAGTTAA
1 TAAAAA-TTAA
30438503 TAAAAAT
1 TAAAAAT
30438510 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.17
9 9 0.31
10 8 0.28
11 7 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:30438686 original size:20 final size:19
Alignment explanation
Indices: 30438661--30438712 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
30438651 TTTTTACCAT
30438661 TTTTAATATTTTTAAATGAA
1 TTTTAATATTTTTAAAT-AA
* *
30438681 TTTTAAAATTCTCTAAATAA
1 TTTTAATATT-TTTAAATAA
30438701 TTTT-ATATTTTT
1 TTTTAATATTTTT
30438713 GCAAGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 4 0.15
20 15 0.56
21 6 0.22
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTAATATTTTTAAATAA
Found at i:30439815 original size:18 final size:16
Alignment explanation
Indices: 30439791--30439839 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 16
30439781 AATATATAAT
30439791 ATATAAATTAATAACAA
1 ATATAAATT-ATAACAA
30439808 ATTATAAAATTATAACAA
1 A-TAT-AAATTATAACAA
30439826 ATATAAATATATAA
1 ATATAAAT-TATAA
30439840 AAGAACTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.14
17 9 0.31
18 11 0.38
19 5 0.17
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAATTATAACAA
Found at i:30443846 original size:20 final size:19
Alignment explanation
Indices: 30443821--30443863 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
30443811 TATTTTCTGA
* *
30443821 ATTTTTAGTTATTTATTTCC
1 ATTTTTAATT-TTTATTTAC
30443841 ATTTTTAATTTTTATTTAC
1 ATTTTTAATTTTTATTTAC
30443860 ATTT
1 ATTT
30443864 GATAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTAATTTTTATTTAC
Found at i:30445046 original size:20 final size:19
Alignment explanation
Indices: 30445017--30445056 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
30445007 ATAAAAACGC
*
30445017 ATAAAAAAATAACATCCAA
1 ATAAAAAAATAACAACCAA
30445036 ATAATAAAAATAACAACCAA
1 ATAA-AAAAATAACAACCAA
30445056 A
1 A
30445057 ACAGCAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (19 bp):
ATAAAAAAATAACAACCAA
Found at i:30445104 original size:44 final size:43
Alignment explanation
Indices: 30444987--30445110 Score: 101
Period size: 44 Copynumber: 2.8 Consensus size: 43
30444977 AATAATATTA
* *
30444987 AAAACAACAGCAAAACAATAATAAAA-ACGCATAAAAAAATAACATC
1 AAAACAACA--AAAACAACAATAAAACA-GCAT-AAAAAATAACAGC
* * * * *
30445033 CAAATAATAAAAATAACAACCAAAACAGCAGT-AAAAATAACAGC
1 AAAACAACAAAAACAACAA-TAAAACAGCA-TAAAAAATAACAGC
30445077 AAAACAACAAAAACAACAATAATAACAGCA-AAAA
1 AAAACAACAAAAACAACAATAA-AACAGCATAAAA
30445111 CATCAAAACA
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
43 5 0.08
44 41 0.67
45 7 0.11
46 8 0.13
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.10
Consensus pattern (43 bp):
AAAACAACAAAAACAACAATAAAACAGCATAAAAAATAACAGC
Found at i:30445108 original size:29 final size:29
Alignment explanation
Indices: 30445068--30445124 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
30445058 CAGCAGTAAA
30445068 AATAACAGC-AAAACAACAAAAACAACAAT
1 AATAACAGCAAAAACAAC-AAAACAACAAT
*
30445097 AATAACAGCAAAAACATCAAAACAACAA
1 AATAACAGCAAAAACAACAAAACAACAA
30445125 CAAAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.68, C:0.21, G:0.04, T:0.07
Consensus pattern (29 bp):
AATAACAGCAAAAACAACAAAACAACAAT
Found at i:30445133 original size:21 final size:21
Alignment explanation
Indices: 30445079--30445130 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
30445069 ATAACAGCAA
*
30445079 AACAACAAAAACAACAATAAT
1 AACAACAAAAACAACAATAAC
* *
30445100 AACAGCAAAAACATCAA-AAC
1 AACAACAAAAACAACAATAAC
30445120 AACAACAAAAA
1 AACAACAAAAA
30445131 ACAAGAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.71, C:0.21, G:0.02, T:0.06
Consensus pattern (21 bp):
AACAACAAAAACAACAATAAC
Found at i:30445736 original size:12 final size:12
Alignment explanation
Indices: 30445721--30445753 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
30445711 TTAAGAATTT
30445721 AATTTTTTTTAG
1 AATTTTTTTTAG
30445733 AA--TTTTTTAG
1 AATTTTTTTTAG
30445743 AATTTTTTTTA
1 AATTTTTTTTA
30445754 AAAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.53
12 9 0.47
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (12 bp):
AATTTTTTTTAG
Found at i:30445772 original size:15 final size:14
Alignment explanation
Indices: 30445748--30445787 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
30445738 TTTAGAATTT
30445748 TTTTTAAAAATATATA
1 TTTTT-AAAATATA-A
30445764 TTTTTAAAATATAA
1 TTTTTAAAATATAA
*
30445778 ATTTTAAAAT
1 TTTTTAAAAT
30445788 TTTTATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 8 0.35
16 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTAAAATATAA
Found at i:30445796 original size:18 final size:19
Alignment explanation
Indices: 30445773--30445808 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30445763 ATTTTTAAAA
30445773 TATAAAT-TTTAAAATTTT
1 TATAAATATTTAAAATTTT
*
30445791 TATAAATATTTTAAATTT
1 TATAAATATTTAAAATTT
30445809 ATTTTGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATAAATATTTAAAATTTT
Found at i:30448287 original size:14 final size:14
Alignment explanation
Indices: 30448268--30448300 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30448258 TAAATAAATG
30448268 TTGAAG-AAGATGTC
1 TTGAAGAAAGAT-TC
30448282 TTGAAGAAAGATTC
1 TTGAAGAAAGATTC
30448296 TTGAA
1 TTGAA
30448301 TAGCCCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.30
Consensus pattern (14 bp):
TTGAAGAAAGATTC
Found at i:30451738 original size:17 final size:17
Alignment explanation
Indices: 30451718--30451758 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
30451708 TTTTTTATTT
30451718 ATATTATA-TAAAATTAA
1 ATATTATAGTAAAA-TAA
*
30451735 ATA-TATAGTAATATAA
1 ATATTATAGTAAAATAA
30451751 ATATTATA
1 ATATTATA
30451759 AAATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATATTATAGTAAAATAA
Found at i:30451763 original size:16 final size:15
Alignment explanation
Indices: 30451722--30451765 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
30451712 TTATTTATAT
30451722 TATATAAAAT-TAAA
1 TATATAAAATATAAA
*
30451736 TATATAGTAATATAAA
1 TATATA-AAATATAAA
30451752 TATTATAAAATATA
1 TA-TATAAAATATA
30451766 TTAAGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.24
15 3 0.12
16 12 0.48
17 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TATATAAAATATAAA
Found at i:30452251 original size:41 final size:41
Alignment explanation
Indices: 30452174--30452283 Score: 107
Period size: 41 Copynumber: 2.7 Consensus size: 41
30452164 TAATGTAGTA
** **
30452174 ACCCAAAACCCTAAATCTTAAGTCATAAACTTTAAATCTCAT
1 ACCCAAAA-CCTAAATCTTAAACCATAAACCCTAAATCTCAT
* * *
30452216 ACCCAAAACCTAAATCTTAAACCTTTAACCCTAAATCTTAT
1 ACCCAAAACCTAAATCTTAAACCATAAACCCTAAATCTCAT
* * *
30452257 ACCCCAAACATAAA-CATAAA-CATAAAC
1 ACCCAAAACCTAAATCTTAAACCATAAAC
30452284 ATAAGCATAA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 5 0.09
40 5 0.09
41 38 0.68
42 8 0.14
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (41 bp):
ACCCAAAACCTAAATCTTAAACCATAAACCCTAAATCTCAT
Found at i:30452273 original size:6 final size:6
Alignment explanation
Indices: 30452262--30452331 Score: 63
Period size: 6 Copynumber: 11.3 Consensus size: 6
30452252 CTTATACCCC
* * *
30452262 AAACAT AAACAT AAACAT AAACAT AAGCAT AAATAT AATTA-AT TAA-AT
1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AA--ACAT AAACAT
30452310 GCAAACAT AAACAT AAACAT AA
1 --AAACAT AAACAT AAACAT AA
30452332 TTAATTCCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
5 3 0.06
6 43 0.80
7 5 0.09
8 3 0.06
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.21
Consensus pattern (6 bp):
AAACAT
Found at i:30455410 original size:28 final size:27
Alignment explanation
Indices: 30455362--30455442 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 27
30455352 CATTTAATCA
* *
30455362 AAAATTAAATTATAACAAACAATATTTTT
1 AAAATTAAATTAAAACAAACAA-A-ATTT
30455391 AAAA-TAAATTAAAATC-AACAAAATTT
1 AAAATTAAATTAAAA-CAAACAAAATTT
30455417 AAAATTTAAATTAAAACAAAACAAAA
1 AAAA-TTAAATTAAAAC-AAACAAAA
30455443 CCCTAAACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
26 7 0.16
27 2 0.04
28 24 0.53
29 12 0.27
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAATTAAATTAAAACAAACAAAATTT
Found at i:30456172 original size:20 final size:21
Alignment explanation
Indices: 30456133--30456170 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
30456123 TCTCTCGTAT
30456133 TTTTTCATTTATTCAATTTGA
1 TTTTTCATTTATTCAATTTGA
30456154 TTTTT-ATTTA-TCAATTT
1 TTTTTCATTTATTCAATTT
30456171 TGTGTCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTTTCATTTATTCAATTTGA
Found at i:30458157 original size:21 final size:22
Alignment explanation
Indices: 30458109--30458157 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
30458099 AAGTTTAATT
* *
30458109 CATTTTTTAATTATTTTGTTAA
1 CATTTGTTAATTATTTTATTAA
*
30458131 CA-TTGTTAATTTTTTTATTAA
1 CATTTGTTAATTATTTTATTAA
30458152 -ATTTGT
1 CATTTGT
30458158 AGATGTCACC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (22 bp):
CATTTGTTAATTATTTTATTAA
Found at i:30468904 original size:33 final size:33
Alignment explanation
Indices: 30468867--30468934 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
30468857 GTTTAATGAA
30468867 AGCAGCACTCATGCTTAGTTTAAACAAATACAC
1 AGCAGCACTCATGCTTAGTTTAAACAAATACAC
30468900 AGCAGCACTCATGCTTAGTTTAAACAAATACAC
1 AGCAGCACTCATGCTTAGTTTAAACAAATACAC
30468933 AG
1 AG
30468935 TACATTTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (33 bp):
AGCAGCACTCATGCTTAGTTTAAACAAATACAC
Found at i:30474077 original size:17 final size:17
Alignment explanation
Indices: 30474049--30474127 Score: 86
Period size: 17 Copynumber: 4.6 Consensus size: 17
30474039 CTAACTTTTA
*
30474049 ATTTTAAAATTTTAATTT
1 ATTTT-AAATTTAAATTT
*
30474067 ATTTTAAATTTAAATTC
1 ATTTTAAATTTAAATTT
***
30474084 ATTTTGGGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
30474101 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
*
30474118 ATTTTGAATT
1 ATTTTAAATT
30474128 AAAAATTGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
17 45 0.90
18 5 0.10
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:30474858 original size:26 final size:26
Alignment explanation
Indices: 30474820--30474886 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
30474810 CCATTTATTG
** *
30474820 TATTATATAATTAATAGGTGTATTAAA
1 TATTAT-TAATTAATAAATATATTAAA
30474847 TATTATTAATTAATAAATATATTAAA
1 TATTATTAATTAATAAATATATTAAA
30474873 TATTATT--TTAATAA
1 TATTATTAATTAATAA
30474887 TTAATATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.19
26 24 0.65
27 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
TATTATTAATTAATAAATATATTAAA
Found at i:30476160 original size:28 final size:28
Alignment explanation
Indices: 30476103--30476327 Score: 175
Period size: 28 Copynumber: 7.8 Consensus size: 28
30476093 TTTTGACCCC
*
30476103 GAAACTTTCC-AAAATTCCATTTTAACCTT
1 GAAAC-TTCCAAAAATTACATTTTAACC-T
*
30476132 GAAACTTCCAAAAATTACATTTTAACTT
1 GAAACTTCCAAAAATTACATTTTAACCT
* * *
30476160 GAAACTTTCAAAACTTACATTTTACCCCT
1 GAAACTTCCAAAAATTACATTTTA-ACCT
* * *
30476189 -AAACTTCCAAAAATTATATTTTGACCCC
1 GAAACTTCCAAAAATTACATTTT-AACCT
* * * * *
30476217 AAAACTTTCAAAAAATACATTTTTTACCCC
1 GAAACTTCCAAAAATTACA--TTTTAACCT
* * * *
30476247 AAAACTTCCTAAAATTACATTTTTACCC
1 GAAACTTCCAAAAATTACATTTTAACCT
* * *
30476275 CAAAATTCCAAAAATTCCATTTTTAACCCT
1 GAAACTTCCAAAAATTACA-TTTTAA-CCT
*
30476305 GAAACTTCCCAAAATTACATTTT
1 GAAACTTCCAAAAATTACATTTT
30476328 TGCCCCCAGA
Statistics
Matches: 160, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
28 71 0.44
29 47 0.29
30 38 0.24
31 4 0.03
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (28 bp):
GAAACTTCCAAAAATTACATTTTAACCT
Found at i:30476246 original size:30 final size:29
Alignment explanation
Indices: 30476092--30476386 Score: 247
Period size: 29 Copynumber: 10.2 Consensus size: 29
30476082 TAAAAACTGT
* * *
30476092 ATTTTGACCCCGAAACTTTCC-AAAATTCC
1 ATTTTTACCCCAAAAC-TTCCAAAAATTAC
* ***
30476121 ATTTTAACCTTGAAACTTCCAAAAATTAC
1 ATTTTTACCCCAAAACTTCCAAAAATTAC
* *** * *
30476150 A-TTTTAACTTGAAACTTTCAAAACTTAC
1 ATTTTTACCCCAAAACTTCCAAAAATTAC
* *
30476178 A-TTTTACCCCTAAACTTCCAAAAATTAT
1 ATTTTTACCCCAAAACTTCCAAAAATTAC
* * *
30476206 ATTTTGACCCCAAAACTTTCAAAAAATAC
1 ATTTTTACCCCAAAACTTCCAAAAATTAC
*
30476235 ATTTTTTACCCCAAAACTTCCTAAAATTAC
1 A-TTTTTACCCCAAAACTTCCAAAAATTAC
*
30476265 ATTTTTACCCCAAAA-TTCCAAAAATTCC
1 ATTTTTACCCCAAAACTTCCAAAAATTAC
** *
30476293 ATTTTTAACCCTGAAACTTCCCAAAATTAC
1 ATTTTT-ACCCCAAAACTTCCAAAAATTAC
* * * *
30476323 ATTTTTGCCCCCAGACTTCCAAAAATTCC
1 ATTTTTACCCCAAAACTTCCAAAAATTAC
* * * * *
30476352 ATTTTTTCCTCTAAACTTCTAAAAATTCC
1 ATTTTTACCCCAAAACTTCCAAAAATTAC
30476381 ATTTTT
1 ATTTTT
30476387 GACACCGGGA
Statistics
Matches: 220, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
28 66 0.30
29 112 0.51
30 42 0.19
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTTTTACCCCAAAACTTCCAAAAATTAC
Found at i:30476733 original size:146 final size:145
Alignment explanation
Indices: 30476403--30476723 Score: 365
Period size: 146 Copynumber: 2.2 Consensus size: 145
30476393 GGGACTCTCG
* * *
30476403 AAATTACCATTTTACCCCCGGATATCCAAAAATCTCGTTTTTGATACTGATTTTTCTAAAAAATA
1 AAATTACCATTTTACCCCCGGGTATCCAAAAATCTCGTTTTTGATACCGAATTTTCTAAAAAATA
* * * * * * * ** *
30476468 CTATTTTGCTCTCAAGTGTCTAAAATATCATTTTTAACCCTAAATTTTTTTAAAATTATCATTTT
66 CCATGTTGATCCCAAATGTCTAAAATATCATCTTTAACCCAAAATTTTTCCAAAATTACCATTTT
*
30476533 ACCCTCAAGAGACCA
131 ACCCTCAAAAGACCA
* * * * ** * * *
30476548 AAATTACAATTTTGCCCACGGGCATAAAAAAATCTCGTTTTTGATCCCGAAATTTTGTAAAAATT
1 AAATTACCATTTTACCCCCGGGTATCCAAAAATCTCGTTTTTGATACCG-AATTTTCTAAAAAAT
*
30476613 ACCATGTT-ATCCCAAAATGTCTAAAATGTCATCTTTAACCCAAAATTTTTCCAAAATTACCATT
65 ACCATGTTGATCCC-AAATGTCTAAAATATCATCTTTAACCCAAAATTTTTCCAAAATTACCATT
** * *
30476677 TTGTCCTCAAAAGTCTA
129 TTACCCTCAAAAGACCA
30476694 AAATTACCATTTTACCCCCGGGTATCCAAA
1 AAATTACCATTTTACCCCCGGGTATCCAAA
30476724 GGTCCCGTTT
Statistics
Matches: 140, Mismatches: 34, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
145 43 0.31
146 97 0.69
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (145 bp):
AAATTACCATTTTACCCCCGGGTATCCAAAAATCTCGTTTTTGATACCGAATTTTCTAAAAAATA
CCATGTTGATCCCAAATGTCTAAAATATCATCTTTAACCCAAAATTTTTCCAAAATTACCATTTT
ACCCTCAAAAGACCA
Found at i:30487683 original size:14 final size:17
Alignment explanation
Indices: 30487650--30487688 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 17
30487640 TATGTGGAAC
30487650 AAATTATATTAAGAATT
1 AAATTATATTAAGAATT
30487667 AAATTATA-T-AG-ATT
1 AAATTATATTAAGAATT
30487681 AAATTATA
1 AAATTATA
30487689 AATTTAAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.50
15 2 0.09
16 1 0.05
17 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AAATTATATTAAGAATT
Found at i:30488242 original size:36 final size:33
Alignment explanation
Indices: 30488202--30488269 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 33
30488192 TTTAAAATAT
30488202 AAATGTA-TATTTAAAAGTTATATATAATAAATAATG
1 AAATGTATTATTTAAAA-TTA-AT-TAAT-AATAATG
30488238 AAATGTATTATTTAAAATTAATTAATAATAAT
1 AAATGTATTATTTAAAATTAATTAATAATAAT
30488270 ATATAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 6 0.19
34 4 0.13
35 2 0.06
36 10 0.32
37 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (33 bp):
AAATGTATTATTTAAAATTAATTAATAATAATG
Found at i:30489830 original size:21 final size:21
Alignment explanation
Indices: 30489804--30489843 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
30489794 AAAAATTTAT
30489804 AAAATATAATAC-AATAAAATA
1 AAAATAT-ATACTAATAAAATA
30489825 AAAATATATACTAATAAAA
1 AAAATATATACTAATAAAA
30489844 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAATATATACTAATAAAATA
Found at i:30493825 original size:22 final size:22
Alignment explanation
Indices: 30493792--30493845 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
30493782 GTGTGTGCAA
*
30493792 ACCCAAAACCTTAAAAACCCAAT-
1 ACCC-AAACCTT-AAAACCAAATC
30493815 ACCCAAACCTTAAAACCAAATC
1 ACCCAAACCTTAAAACCAAATC
30493837 ACCCAAACC
1 ACCCAAACC
30493846 CTAGACCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 9 0.31
22 16 0.55
23 4 0.14
ACGTcount: A:0.50, C:0.39, G:0.00, T:0.11
Consensus pattern (22 bp):
ACCCAAACCTTAAAACCAAATC
Found at i:30493915 original size:14 final size:14
Alignment explanation
Indices: 30493896--30493944 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
30493886 GACCAGAACC
*
30493896 CGTTGATCATTGAT
1 CGTTGACCATTGAT
30493910 CGTTGACCATTGA-
1 CGTTGACCATTGAT
*
30493923 CTGTTGACCGTTGAT
1 C-GTTGACCATTGAT
*
30493938 CATTGAC
1 CGTTGAC
30493945 TTTTTGGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (14 bp):
CGTTGACCATTGAT
Found at i:30493929 original size:21 final size:21
Alignment explanation
Indices: 30493905--30493945 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30493895 CCGTTGATCA
*
30493905 TTGATCGTTGACCATTGACTG
1 TTGACCGTTGACCATTGACTG
*
30493926 TTGACCGTTGATCATTGACT
1 TTGACCGTTGACCATTGACT
30493946 TTTTGGATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (21 bp):
TTGACCGTTGACCATTGACTG
Found at i:30500473 original size:21 final size:21
Alignment explanation
Indices: 30500448--30500487 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
30500438 CAACCAAAAC
30500448 CCGTTGATC-GTTGATCGTTGG
1 CCGTTGA-CAGTTGATCGTTGG
30500469 CCGTTGACAGTTGATCGTT
1 CCGTTGACAGTTGATCGTT
30500488 AACCTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.12, C:0.20, G:0.30, T:0.38
Consensus pattern (21 bp):
CCGTTGACAGTTGATCGTTGG
Found at i:30500502 original size:21 final size:20
Alignment explanation
Indices: 30500478--30500516 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
30500468 GCCGTTGACA
30500478 GTTGATCGTTAACCTTTTTAG
1 GTTGATCGTTAA-CTTTTTAG
*
30500499 GTTGATCGTTGACTTTTT
1 GTTGATCGTTAACTTTTT
30500517 CTGAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
GTTGATCGTTAACTTTTTAG
Found at i:30502954 original size:17 final size:19
Alignment explanation
Indices: 30502913--30502970 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
30502903 AAGATTAAAG
*
30502913 ATTTTTCATTAATCATAATT
1 ATTTTT-ATAAATCATAATT
30502933 ATTTTTATAAAT-ATAA-T
1 ATTTTTATAAATCATAATT
*
30502950 ATTTTTAAAAAATCAT-ATT
1 ATTTTT-ATAAATCATAATT
30502969 AT
1 AT
30502971 CGAAACCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 7 0.21
18 10 0.30
19 10 0.30
20 6 0.18
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTATAAATCATAATT
Found at i:30502962 original size:18 final size:18
Alignment explanation
Indices: 30502927--30502960 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30502917 TTCATTAATC
*
30502927 ATAATTATTTTTATAAAT
1 ATAATTATTTTTAAAAAT
30502945 ATAA-TATTTTTAAAAA
1 ATAATTATTTTTAAAAA
30502961 ATCATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAATTATTTTTAAAAAT
Found at i:30502967 original size:16 final size:17
Alignment explanation
Indices: 30502927--30502968 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
30502917 TTCATTAATC
*
30502927 ATAATTATTTTTATAAAT
1 ATAA-TATTTTTATAAAA
30502945 ATAATATTTTTA-AAAA
1 ATAATATTTTTATAAAA
*
30502961 ATCATATT
1 ATAATATT
30502969 ATCGAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
17 8 0.36
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAATATTTTTATAAAA
Found at i:30503826 original size:30 final size:30
Alignment explanation
Indices: 30503745--30504014 Score: 212
Period size: 30 Copynumber: 9.0 Consensus size: 30
30503735 AAAATCGAAA
* * *
30503745 CAAATTTGAATTTTTGG-AAACTTCAGGAGT
1 CAAATTAGAATTTTTGGAAAATTTGAGG-GT
* * * *
30503775 CAAATAAAAAATTTTGAAAAATTTGAGGGT
1 CAAATTAGAATTTTTGGAAAATTTGAGGGT
* * *
30503805 CAAATTGGAATTTTTAGAAAATTCGAGGGT
1 CAAATTAGAATTTTTGGAAAATTTGAGGGT
* **
30503835 CAAATTCA-AATTTTTGGAAAGTTCAAGGGT
1 CAAATT-AGAATTTTTGGAAAATTTGAGGGT
* * *
30503865 CAATTTTGAATTTTTGGAAAATTTAAGGGT
1 CAAATTAGAATTTTTGGAAAATTTGAGGGT
* *
30503895 CAAATTTGAATTTTTGGAAAGTTT-AGGGGT
1 CAAATTAGAATTTTTGGAAAATTTGA-GGGT
*
30503925 CAAATTAGAATTTTTGGAAAGTTTG-GTGGT
1 CAAATTAGAATTTTTGGAAAATTTGAG-GGT
**
30503955 CAAATTCA-AATTTTTAAAAAATTT-AGAGGT
1 CAAATT-AGAATTTTTGGAAAATTTGAG-GGT
* * *
30503985 CAAAATATAATTTTT-GAATAGTTTGAGGGT
1 CAAATTAGAATTTTTGGAA-AATTTGAGGGT
30504015 AAAAGAATAA
Statistics
Matches: 197, Mismatches: 32, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
29 5 0.03
30 181 0.92
31 11 0.06
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (30 bp):
CAAATTAGAATTTTTGGAAAATTTGAGGGT
Found at i:30503956 original size:90 final size:88
Alignment explanation
Indices: 30503753--30504013 Score: 244
Period size: 90 Copynumber: 2.9 Consensus size: 88
30503743 AACAAATTTG
* ** * *
30503753 AATTTTTGGAAACTTC-AGGAGTCAAATAAAAAATTTTGAAAAATTTGAGGGTCAAATTGGAATT
1 AATTTTTGGAAAGTTCAAGG-GTCAAATTCAAATTTTTGAAAAATTT-AGGGTCAAATTTGAATT
* *
30503817 TTTAGAAA-ATTCGAGGGTCAAATTCA
64 TTT-GAAAGTTTAG-GGGTCAAATTCA
* ** *
30503843 AATTTTTGGAAAGTTCAAGGGTCAATTTTGAATTTTTGGAAAATTTAAGGGTCAAATTTGAATTT
1 AATTTTTGGAAAGTTCAAGGGTCAAATTCAAATTTTTGAAAAATTT-AGGGTCAAATTTGAATTT
30503908 TTGGAAAGTTTAGGGGTCAAATT-A
65 TT-GAAAGTTTAGGGGTCAAATTCA
** * *
30503932 GAATTTTTGGAAAGTT-TGGTGGTCAAATTCAAATTTTTAAAAAATTTAGAGGTCAAAATAT-AA
1 -AATTTTTGGAAAGTTCAAG-GGTCAAATTCAAATTTTTGAAAAATTTAG-GGTC-AAATTTGAA
30503995 TTTTTGAATAGTTTGAGGG
62 TTTTTGAA-AGTTT-AGGG
30504014 TAAAAGAATA
Statistics
Matches: 143, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
89 7 0.05
90 121 0.85
91 15 0.10
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (88 bp):
AATTTTTGGAAAGTTCAAGGGTCAAATTCAAATTTTTGAAAAATTTAGGGTCAAATTTGAATTTT
TGAAAGTTTAGGGGTCAAATTCA
Found at i:30505289 original size:4 final size:4
Alignment explanation
Indices: 30505282--30505322 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
30505272 GTATTTATTT
* *
30505282 ATAA AT-A ATAA ATAA ATAA AAAA ATAA ATGA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
30505323 TTGGGCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:30505290 original size:21 final size:21
Alignment explanation
Indices: 30505252--30505291 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30505242 GAGTTCTTAT
***
30505252 TATTTATTTATTTTTAATATG
1 TATTTATTTATAAATAATATG
30505273 TATTTATTTATAAATAATA
1 TATTTATTTATAAATAATA
30505292 AATAAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TATTTATTTATAAATAATATG
Found at i:30506126 original size:40 final size:40
Alignment explanation
Indices: 30506059--30506200 Score: 146
Period size: 39 Copynumber: 3.6 Consensus size: 40
30506049 ATAGCTTTAA
* * * *
30506059 GGGTAAAAGATTGAATTG-CTTAAATCTGCCCCATGGTCG
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGGTCG
* * **
30506098 GGGTAAGAGATCGGATGGTCTTCAATCTGCCCTC-TAGTTA
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCC-CATGGTCG
* * * *
30506138 GGGTAAAAGATTTGATTG-CTTCAATCTGTCCCATGGTCG
1 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGGTCG
30506177 GGGTAAGAGATTGGATGGTCTTCA
1 GGGTAAGAGATTGGATGGTCTTCA
30506201 CTCCATTTCA
Statistics
Matches: 80, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
38 1 0.01
39 44 0.55
40 34 0.43
41 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (40 bp):
GGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATGGTCG
Found at i:30506358 original size:50 final size:50
Alignment explanation
Indices: 30506220--30506373 Score: 152
Period size: 50 Copynumber: 3.1 Consensus size: 50
30506210 AACTTCAGGA
* * * * *
30506220 GTATAAGATTCGTCC-TTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGT
1 GTATGAGATTCG-CCATTGCGGCTTCAATCCGTCCCTCTATAGCTTTAGGT
** *
30506270 CAATGAGATTCGCCATTGCAGCTTCAAT-C-TACCTCTCTATAGCTTTAGGT
1 GTATGAGATTCGCCATTGCGGCTTCAATCCGT-CC-CTCTATAGCTTTAGGT
** * *
30506320 GTATGAGATTTTCCATTGCGGCTTCAATCCGTTCCTCTATAGCTTTAGGG
1 GTATGAGATTCGCCATTGCGGCTTCAATCCGTCCCTCTATAGCTTTAGGT
30506370 GTAT
1 GTAT
30506374 AGGACTTGTC
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
49 4 0.05
50 77 0.92
51 2 0.02
52 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (50 bp):
GTATGAGATTCGCCATTGCGGCTTCAATCCGTCCCTCTATAGCTTTAGGT
Found at i:30517972 original size:30 final size:30
Alignment explanation
Indices: 30517938--30518135 Score: 158
Period size: 30 Copynumber: 6.7 Consensus size: 30
30517928 TTAAAACCAA
** *
30517938 GTCAAATTTGAATTTTTAGAAACTTTAGGG
1 GTCAAATTCAAATTTTTAGAAAATTTAGGG
30517968 GTCAAA-TCAAATTTTT-GTAAAATTTTA--G
1 GTCAAATTCAAATTTTTAG-AAAA-TTTAGGG
** *
30517996 GTCAAATTGGAATTTTTGGAAAATTTAGGG
1 GTCAAATTCAAATTTTTAGAAAATTTAGGG
* *
30518026 GTCAAATTCAAATTTTT-GAAAAGTTCAAGG
1 GTCAAATTCAAATTTTTAGAAAA-TTTAGGG
* * * **
30518056 GTCAAATTCAAATTTCTAGAAAGTTCAATG
1 GTCAAATTCAAATTTTTAGAAAATTTAGGG
** *
30518086 GTCAAATTTGAATTTTTGGAAAATTTAGGG
1 GTCAAATTCAAATTTTTAGAAAATTTAGGG
30518116 GTCGAAA--CATAATTTTTAGA
1 GTC-AAATTCA-AATTTTTAGA
30518136 TAGTTTGAGG
Statistics
Matches: 135, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
28 12 0.09
29 28 0.21
30 88 0.65
31 7 0.05
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (30 bp):
GTCAAATTCAAATTTTTAGAAAATTTAGGG
Found at i:30518009 original size:58 final size:58
Alignment explanation
Indices: 30517938--30518111 Score: 179
Period size: 60 Copynumber: 2.9 Consensus size: 58
30517928 TTAAAACCAA
* *
30517938 GTCAAATTTGAATTTTTAGAAACTTTAGGGGTCAAA-TCAAATTTTTGTAAAATTTTAG
1 GTCAAATTGGAATTTTTAGAAAATTTAGGGGTCAAATTCAAATTTTTG-AAAATTTTAG
* **
30517996 GTCAAATTGGAATTTTTGGAAAATTTAGGGGTCAAATTCAAATTTTTGAAAAGTTCAAGG
1 GTCAAATTGGAATTTTTAGAAAATTTAGGGGTCAAATTCAAATTTTTGAAAA-TTTTA-G
** * * * ** **
30518056 GTCAAATTCAAATTTCTAGAAAGTTCAATGGTCAAATTTGAATTTTTGGAAAATTT
1 GTCAAATTGGAATTTTTAGAAAATTTAGGGGTCAAATTCAAATTTTT-GAAAATTT
30518112 AGGGGTCGAA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
58 37 0.39
59 14 0.15
60 40 0.42
61 5 0.05
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (58 bp):
GTCAAATTGGAATTTTTAGAAAATTTAGGGGTCAAATTCAAATTTTTGAAAATTTTAG
Found at i:30519436 original size:4 final size:4
Alignment explanation
Indices: 30519429--30519469 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
30519419 TTATTTTTAT
*
30519429 ATAA AT-A ATAA ATAA ATAA A-AA ATTAA ATGA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA A-TAA ATAA ATAA ATAA AT
30519470 TTGGACCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 6 0.19
4 23 0.72
5 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:30519833 original size:17 final size:17
Alignment explanation
Indices: 30519813--30519846 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
30519803 AATTTATGCT
30519813 TTTATTTTTTTAATTAA
1 TTTATTTTTTTAATTAA
30519830 TTTATTTTTTTAATTAA
1 TTTATTTTTTTAATTAA
30519847 ATAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTTTTAATTAA
Found at i:30523209 original size:61 final size:62
Alignment explanation
Indices: 30523082--30523209 Score: 134
Period size: 61 Copynumber: 2.1 Consensus size: 62
30523072 TCCTAAATAT
* * * * * * * * *
30523082 AAAAAAATTCAATAAGTTTACCCTTAACGTTTACAAAAAAATTTCATTTTAGTTTTCATTCT
1 AAAAAAATTCAATAAATTTACCCTCAACATTTACAAAAAAATGTCAATTTAGTTCTAACTCA
* *
30523144 AAAAAAATT-AATAAATTTGTCCCTCAACATTTAC-AAAATATGTCAATTTAGTTCTAACTCA
1 AAAAAAATTCAATAAATTT-ACCCTCAACATTTACAAAAAAATGTCAATTTAGTTCTAACTCA
30523205 AAAAA
1 AAAAA
30523210 TTAATTCTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
61 33 0.61
62 21 0.39
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.36
Consensus pattern (62 bp):
AAAAAAATTCAATAAATTTACCCTCAACATTTACAAAAAAATGTCAATTTAGTTCTAACTCA
Found at i:30523227 original size:80 final size:81
Alignment explanation
Indices: 30523141--30523294 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
30523131 TAGTTTTCAT
* *
30523141 TCTAAAAAAA-TTAATAAATTTGTCCCTCAACATTTACAAAATATGTCAATTTAGTTCTAACTCA
1 TCTAAAAAAATTTAATAAATTTGACCCTCAACATTTACAAAATATGTCAATTTAGTACTAACTCA
30523205 AAAAATTAATTCTAAC
66 AAAAATTAATTCTAAC
* * * * * *
30523221 TCTAAAAAAATTTAATAAATTTGACCCTCAATATTTATAAATTTTTTCAATTTAGTACTAACTCT
1 TCTAAAAAAATTTAATAAATTTGACCCTCAACATTTACAAAATATGTCAATTTAGTACTAACTCA
*
30523286 AAAATTTAA
66 AAAAATTAA
30523295 AAAGTATTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
80 10 0.16
81 54 0.84
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.38
Consensus pattern (81 bp):
TCTAAAAAAATTTAATAAATTTGACCCTCAACATTTACAAAATATGTCAATTTAGTACTAACTCA
AAAAATTAATTCTAAC
Found at i:30523235 original size:22 final size:20
Alignment explanation
Indices: 30523188--30523236 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
30523178 AAAATATGTC
*
30523188 AATTTAGTTCTAACTCAAAA
1 AATTTAATTCTAACTCAAAA
30523208 AA-TTAATTCTAACTCTAAAAA
1 AATTTAATTCTAACTC--AAAA
30523229 AATTTAAT
1 AATTTAAT
30523237 AAATTTGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 12 0.48
20 2 0.08
21 6 0.24
22 5 0.20
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (20 bp):
AATTTAATTCTAACTCAAAA
Found at i:30524183 original size:19 final size:19
Alignment explanation
Indices: 30524159--30524196 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
30524149 TTAACTTTAT
30524159 TTTTATGATGTAAAA-AATA
1 TTTTAT-ATGTAAAATAATA
*
30524178 TTTTATATTTAAAATAATA
1 TTTTATATGTAAAATAATA
30524197 AAATTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TTTTATATGTAAAATAATA
Found at i:30524933 original size:22 final size:22
Alignment explanation
Indices: 30524891--30524933 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30524881 ATATTTCAAT
* **
30524891 TTTTTTAATAATTTATTATTTA
1 TTTTTTAAAAATTTAAAATTTA
30524913 TTTTTTAAAAATTTAAAATTT
1 TTTTTTAAAAATTTAAAATTT
30524934 TTTGGATGGA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTTAAAAATTTAAAATTTA
Found at i:30525023 original size:18 final size:18
Alignment explanation
Indices: 30525002--30525037 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30524992 ATTATATAAT
30525002 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
*
30525020 ATTTAAATATATATTTTA
1 ATTTAAATATATAGTTTA
30525038 TTTTTGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:30526003 original size:16 final size:16
Alignment explanation
Indices: 30525982--30526012 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30525972 TAGGCCTTTG
30525982 TATAAACCAAATTATT
1 TATAAACCAAATTATT
*
30525998 TATAAACTAAATTAT
1 TATAAACCAAATTAT
30526013 ATAGTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAAACCAAATTATT
Found at i:30528076 original size:86 final size:86
Alignment explanation
Indices: 30527959--30528121 Score: 247
Period size: 87 Copynumber: 1.9 Consensus size: 86
30527949 GACATGCTTA
* *
30527959 AGGTTGAGTTCTTACTCTTAATGAATTCATATACCAGAGTTT-GGTGGTCCTATTGAGACGAACT
1 AGGTTGAGTTCTGACTCTTAATGAATTCATATACCAGAGTTTGGGTGATCCTATTGAGACGAACT
30528023 TGATGAATTCACCGGCATGTG
66 TGATGAATTCACCGGCATGTG
* * * * *
30528044 AGGTTGAGTTTCTGGCTCTTAATGAGTTCATATCCCAGAGTTTGGGTGATCCTATTGAGTCGGAC
1 AGGTTGAG-TTCTGACTCTTAATGAATTCATATACCAGAGTTTGGGTGATCCTATTGAGACGAAC
30528109 TTGATGAATTCAC
65 TTGATGAATTCAC
30528122 TGAACTTAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 8 0.12
86 30 0.43
87 31 0.45
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (86 bp):
AGGTTGAGTTCTGACTCTTAATGAATTCATATACCAGAGTTTGGGTGATCCTATTGAGACGAACT
TGATGAATTCACCGGCATGTG
Found at i:30532746 original size:23 final size:23
Alignment explanation
Indices: 30532715--30532792 Score: 101
Period size: 23 Copynumber: 3.6 Consensus size: 23
30532705 CATAAGACAG
*
30532715 AAGCATGCCACAAGGTAGAGGAA
1 AAGCGTGCCACAAGGTAGAGGAA
*
30532738 AAGCGTGCCACAAGGTAGAGAAA
1 AAGCGTGCCACAAGGTAGAGGAA
*
30532761 AAGCGTGCTACAA---A-AGGAA
1 AAGCGTGCCACAAGGTAGAGGAA
30532780 AAGCGTGCCACAA
1 AAGCGTGCCACAA
30532793 AAGCAGATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 16 0.32
20 1 0.02
23 33 0.66
ACGTcount: A:0.44, C:0.19, G:0.28, T:0.09
Consensus pattern (23 bp):
AAGCGTGCCACAAGGTAGAGGAA
Found at i:30532783 original size:19 final size:19
Alignment explanation
Indices: 30532733--30532795 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 19
30532723 CACAAGGTAG
30532733 AGGAAAAGCGTGCCACAAGGTA
1 AGGAAAAGCGTGCCACAA---A
* *
30532755 GAGAAAAAGCGTGCTACAAA
1 -AGGAAAAGCGTGCCACAAA
30532775 AGGAAAAGCGTGCCACAAA
1 AGGAAAAGCGTGCCACAAA
30532794 AG
1 AG
30532796 CAGATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 19 0.53
20 1 0.03
23 16 0.44
ACGTcount: A:0.46, C:0.17, G:0.29, T:0.08
Consensus pattern (19 bp):
AGGAAAAGCGTGCCACAAA
Found at i:30534056 original size:18 final size:18
Alignment explanation
Indices: 30534035--30534087 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
30534025 TAATTTTTTT
30534035 ATTTAAAATGTAT-TTAAA
1 ATTTAAAAT-TATATTAAA
*
30534053 ATTTATAATTATATTAAA
1 ATTTAAAATTATATTAAA
30534071 TTATTTAAATATTATAT
1 --ATTTAAA-ATTATAT
30534088 AACTCAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 3 0.10
18 13 0.45
20 6 0.21
21 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTTAAAATTATATTAAA
Found at i:30538971 original size:26 final size:26
Alignment explanation
Indices: 30538933--30538991 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
30538923 CAAAATATTG
* *
30538933 TTTTTTAATTTTTAAGGGCCTCAATT
1 TTTTTTAACTTTTAAGGGCCTAAATT
*
30538959 TTTTTTTACTTTTAAGGGCCTAAATT
1 TTTTTTAACTTTTAAGGGCCTAAATT
30538985 TTTTTTA
1 TTTTTTA
30538992 CCAACTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.58
Consensus pattern (26 bp):
TTTTTTAACTTTTAAGGGCCTAAATT
Found at i:30557007 original size:15 final size:14
Alignment explanation
Indices: 30556981--30557025 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
30556971 AAAGATAACT
*
30556981 AATAAAATTTAAAA
1 AATAAAAATTAAAA
*
30556995 GATAAAAAATTAAAA
1 AAT-AAAAATTAAAA
*
30557010 AATGAAAATTAAAA
1 AATAAAAATTAAAA
30557024 AA
1 AA
30557026 AGAGTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AATAAAAATTAAAA
Found at i:30559145 original size:17 final size:18
Alignment explanation
Indices: 30559088--30559145 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
30559078 ACACAATTAA
30559088 AAATAATAAAAA-ATACA-
1 AAATAATAAAAATATA-AT
*
30559105 AAAT-TTAAAAATATAAT
1 AAATAATAAAAATATAAT
* *
30559122 ATATAATAAAATTAT-AT
1 AAATAATAAAAATATAAT
30559139 AAATAAT
1 AAATAAT
30559146 TTAATATTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.21
17 18 0.55
18 8 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAATAAAAATATAAT
Found at i:30560159 original size:5 final size:5
Alignment explanation
Indices: 30560144--30560188 Score: 72
Period size: 5 Copynumber: 8.8 Consensus size: 5
30560134 AGTTAAATAA
*
30560144 ATATAT ATATT ATATT ACATT ATATT ATATT ATATT ATATT ATAT
1 ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
30560189 ATCTAAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:30563991 original size:23 final size:22
Alignment explanation
Indices: 30563961--30564087 Score: 87
Period size: 23 Copynumber: 5.6 Consensus size: 22
30563951 GAATGCTAGC
*
30563961 GTGCTTACTGTTTCGCACTTTGT
1 GTGCCTACTGTTT-GCACTTTGT
* * *
30563984 GTGCTTACTATTTCGCACTTCGT
1 GTGCCTACTGTTT-GCACTTTGT
* * *
30564007 GTGCCTATTGATTTGCGCTATGT
1 GTGCCTACTG-TTTGCACTTTGT
* *
30564030 GCT-CCTACTGATTGCACTGTGT
1 G-TGCCTACTGTTTGCACTTTGT
*
30564052 GTGCCTACTGGATTGCA-TTGTGT
1 GTGCCTACT-GTTTGCACTT-TGT
*
30564075 GTGCTTACTGTTT
1 GTGCCTACTGTTT
30564088 CCCCGGCACT
Statistics
Matches: 84, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.01
22 20 0.24
23 59 0.70
24 4 0.05
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (22 bp):
GTGCCTACTGTTTGCACTTTGT
Found at i:30564601 original size:20 final size:21
Alignment explanation
Indices: 30564563--30564601 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
30564553 TTGTACTAAA
**
30564563 AAATCATATTTTATTTCTTTT
1 AAATCATATTTTAAGTCTTTT
30564584 AAATCA-ATTTTAAGTCTT
1 AAATCATATTTTAAGTCTT
30564602 GATCTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (21 bp):
AAATCATATTTTAAGTCTTTT
Found at i:30569723 original size:15 final size:15
Alignment explanation
Indices: 30569687--30569725 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
30569677 GGAAATAGAC
*
30569687 AAGAAAGAAAGATGA
1 AAGAAAGAAACATGA
*
30569702 AACAAAGAAACATGA
1 AAGAAAGAAACATGA
*
30569717 AGGAAAGAA
1 AAGAAAGAA
30569726 TAAAGAGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.05, G:0.23, T:0.05
Consensus pattern (15 bp):
AAGAAAGAAACATGA
Found at i:30572905 original size:21 final size:21
Alignment explanation
Indices: 30572881--30572934 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
30572871 ACTCTGAATA
*
30572881 TCGAATCTTAAACTTTGAACC
1 TCGAATCTTAAACTTTAAACC
* * *
30572902 TCGAACCTAAAATTTTAAACC
1 TCGAATCTTAAACTTTAAACC
*
30572923 -CTAATCTTAAAC
1 TCGAATCTTAAAC
30572935 CTCAAACCCC
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (21 bp):
TCGAATCTTAAACTTTAAACC
Found at i:30575538 original size:73 final size:73
Alignment explanation
Indices: 30575419--30575565 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
30575409 ACTTTAGTCG
30575419 ATGGAATTGGTAGCATGATGCTACGGTGAGTCAAGGATAAAAGGCACGACAAAGGTGAGAGTGTT
1 ATGGAATTGGTAGCATGATGCTACGGTGAGTCAAGGATAAAAGGCACGACAAAGGTGAGAGTGTT
30575484 AATGGTGT
66 AATGGTGT
30575492 ATGGAATTGGTAGCATGATGCTACGGTGAGTCAAGGATAAAAGGCACGACAAAGGTGAGAGTGTT
1 ATGGAATTGGTAGCATGATGCTACGGTGAGTCAAGGATAAAAGGCACGACAAAGGTGAGAGTGTT
30575557 AATGGTGT
66 AATGGTGT
30575565 A
1 A
30575566 GTTGGGTGAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.33, C:0.10, G:0.34, T:0.23
Consensus pattern (73 bp):
ATGGAATTGGTAGCATGATGCTACGGTGAGTCAAGGATAAAAGGCACGACAAAGGTGAGAGTGTT
AATGGTGT
Found at i:30575874 original size:3 final size:3
Alignment explanation
Indices: 30575866--30575893 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30575856 GTCATTTTCC
30575866 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
30575894 CTAAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:30577712 original size:87 final size:87
Alignment explanation
Indices: 30577598--30577775 Score: 338
Period size: 87 Copynumber: 2.0 Consensus size: 87
30577588 TTTAACATAT
*
30577598 AAATCCTTTAAAGTTGTATTGTCTTTGAATGTGAGTCCAACCTACAATATGATGTACAAACGAAA
1 AAATCCTTTAAAGTTGTATTGTCTTTGAATGTGAGTCCAACCTACAATATGATGCACAAACGAAA
30577663 ATTATGACAATATCAATTCATC
66 ATTATGACAATATCAATTCATC
*
30577685 AAATCCTTTAAAGTTGTATTGTTTTTGAATGTGAGTCCAACCTACAATATGATGCACAAACGAAA
1 AAATCCTTTAAAGTTGTATTGTCTTTGAATGTGAGTCCAACCTACAATATGATGCACAAACGAAA
30577750 ATTATGACAATATCAATTCATC
66 ATTATGACAATATCAATTCATC
30577772 AAAT
1 AAAT
30577776 TTAGAGTTTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (87 bp):
AAATCCTTTAAAGTTGTATTGTCTTTGAATGTGAGTCCAACCTACAATATGATGCACAAACGAAA
ATTATGACAATATCAATTCATC
Found at i:30581726 original size:167 final size:167
Alignment explanation
Indices: 30581538--30581867 Score: 660
Period size: 167 Copynumber: 2.0 Consensus size: 167
30581528 TATATGAGAT
30581538 TCCTTACATCTTGACGGAGTTATAATGTTTAGATTAATTAATACAAATCATTAAAAAATTATGAT
1 TCCTTACATCTTGACGGAGTTATAATGTTTAGATTAATTAATACAAATCATTAAAAAATTATGAT
30581603 TAATTATATTTATGATTTTGAATTTTTTGAATATTGACTAGAAATTTAATATTTTTATTAAAAAC
66 TAATTATATTTATGATTTTGAATTTTTTGAATATTGACTAGAAATTTAATATTTTTATTAAAAAC
30581668 TAGTTGTTGCTAGTGTAATTATTATAAATATTTTTTG
131 TAGTTGTTGCTAGTGTAATTATTATAAATATTTTTTG
30581705 TCCTTACATCTTGACGGAGTTATAATGTTTAGATTAATTAATACAAATCATTAAAAAATTATGAT
1 TCCTTACATCTTGACGGAGTTATAATGTTTAGATTAATTAATACAAATCATTAAAAAATTATGAT
30581770 TAATTATATTTATGATTTTGAATTTTTTGAATATTGACTAGAAATTTAATATTTTTATTAAAAAC
66 TAATTATATTTATGATTTTGAATTTTTTGAATATTGACTAGAAATTTAATATTTTTATTAAAAAC
30581835 TAGTTGTTGCTAGTGTAATTATTATAAATATTT
131 TAGTTGTTGCTAGTGTAATTATTATAAATATTT
30581868 ACAAAAACCT
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 163 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (167 bp):
TCCTTACATCTTGACGGAGTTATAATGTTTAGATTAATTAATACAAATCATTAAAAAATTATGAT
TAATTATATTTATGATTTTGAATTTTTTGAATATTGACTAGAAATTTAATATTTTTATTAAAAAC
TAGTTGTTGCTAGTGTAATTATTATAAATATTTTTTG
Found at i:30588651 original size:41 final size:41
Alignment explanation
Indices: 30588594--30588687 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
30588584 ATTTTATTTG
*
30588594 AACAAGAATTCTAGTCACCTAATTCTAACAATCTCCACCTT
1 AACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTT
30588635 AACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTT
1 AACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTT
*
30588676 GACAAGAATTCT
1 AACAAGAATTCT
30588688 CTATAAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.28
Consensus pattern (41 bp):
AACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTT
Found at i:30592649 original size:5 final size:5
Alignment explanation
Indices: 30592639--30592676 Score: 58
Period size: 5 Copynumber: 7.2 Consensus size: 5
30592629 ATGAAAACCC
30592639 AAAAT AAAAT AAAAT AAAAGAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT -AAA-AT AAAAT AAAAT AAAAT A
30592677 TATATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 23 0.74
6 6 0.19
7 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:30592662 original size:17 final size:17
Alignment explanation
Indices: 30592642--30592674 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30592632 AAAACCCAAA
30592642 ATAAAATAAAATAAAAG
1 ATAAAATAAAATAAAAG
30592659 ATAAAATAAAATAAAA
1 ATAAAATAAAATAAAA
30592675 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
ATAAAATAAAATAAAAG
Found at i:30598412 original size:21 final size:23
Alignment explanation
Indices: 30598388--30598429 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30598378 TCAATTTATC
*
30598388 TTTTAT-T-CATTTGCTCTGACA
1 TTTTATATACATTTGCACTGACA
30598409 TTTTATATACATTTGCACTGA
1 TTTTATATACATTTGCACTGA
30598430 TAGATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.50
Consensus pattern (23 bp):
TTTTATATACATTTGCACTGACA
Found at i:30603600 original size:21 final size:21
Alignment explanation
Indices: 30603576--30603625 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
30603566 CTTTCAGTAC
* *
30603576 CGGTAGAAGCATGATTTGTTT
1 CGGTAGAAGCATGACTTGTAT
* * *
30603597 CGGTAAAAGCTTTACTTGTAT
1 CGGTAGAAGCATGACTTGTAT
30603618 CGGTAGAA
1 CGGTAGAA
30603626 CTGTCATAGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (21 bp):
CGGTAGAAGCATGACTTGTAT
Found at i:30607703 original size:23 final size:22
Alignment explanation
Indices: 30607659--30607708 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
30607649 TCAATTCATC
* *
30607659 TTTTA-TTCATTTGCTCTCACA
1 TTTTATTTCATTTGCACTAACA
30607680 TTTTATTTACATTTGCACTAACA
1 TTTTATTT-CATTTGCACTAACA
*
30607703 TATTAT
1 TTTTAT
30607709 AATCTTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 2 0.08
23 17 0.71
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTTATTTCATTTGCACTAACA
Found at i:30611602 original size:21 final size:21
Alignment explanation
Indices: 30611562--30611629 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
30611552 TGGTTTACTT
30611562 GGTTTAGG-TCAAAA-GGTTTG
1 GGTTT-GGTTCAAAAGGGTTTG
30611582 GGTTTGGTTCAAAAGGGTTTG
1 GGTTTGGTTCAAAAGGGTTTG
* *
30611603 AGTTTGGTTCATAAGGGTTTG
1 GGTTTGGTTCAAAAGGGTTTG
30611624 GGTTTG
1 GGTTTG
30611630 ATGTTGATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.05
20 11 0.26
21 30 0.70
ACGTcount: A:0.19, C:0.04, G:0.37, T:0.40
Consensus pattern (21 bp):
GGTTTGGTTCAAAAGGGTTTG
Found at i:30613930 original size:28 final size:28
Alignment explanation
Indices: 30613890--30614001 Score: 143
Period size: 28 Copynumber: 4.0 Consensus size: 28
30613880 ACACGAGACT
* * *
30613890 AATTTGCTCACACAAGTTATAAAATTCG
1 AATTTGCTCACACAAGTTATGATATTTG
** *
30613918 AATTTGCTCACACGTGTTATGGTATTTG
1 AATTTGCTCACACAAGTTATGATATTTG
* * *
30613946 AATTTGCTCGCACAAGCTGTGATATTTG
1 AATTTGCTCACACAAGTTATGATATTTG
30613974 AATTTGCTCACACAAGTTATGATATTTG
1 AATTTGCTCACACAAGTTATGATATTTG
30614002 GGATGCTCAT
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (28 bp):
AATTTGCTCACACAAGTTATGATATTTG
Found at i:30621604 original size:25 final size:25
Alignment explanation
Indices: 30621558--30621606 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
30621548 ATGATATTAA
30621558 TTTAAATGGCTATGAATATAATATT
1 TTTAAATGGCTATGAATATAATATT
* *
30621583 TTTAATATGGTTATG-ATTTAATAT
1 TTTAA-ATGGCTATGAATATAATAT
30621607 AAATATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (25 bp):
TTTAAATGGCTATGAATATAATATT
Found at i:30635857 original size:16 final size:16
Alignment explanation
Indices: 30635834--30635905 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
30635824 CGTTTGGTTC
30635834 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
30635850 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
30635866 GGTGTAATGGAATATA
1 GCTGTAATGGAATAGA
30635882 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
30635898 GCTGTAAT
1 GCTGTAAT
30635906 CAGTAATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.36, C:0.04, G:0.32, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:30636142 original size:58 final size:55
Alignment explanation
Indices: 30636075--30636220 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 55
30636065 AATTTTAATG
*
30636075 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
30636133 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
30636191 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
30636221 TATAATATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
57 3 0.04
58 40 0.52
59 17 0.22
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (55 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:30639830 original size:15 final size:14
Alignment explanation
Indices: 30639802--30639889 Score: 54
Period size: 15 Copynumber: 6.0 Consensus size: 14
30639792 TTAATTTATT
*
30639802 TAATTATATTTTAACA
1 TAATTAT-TATTAA-A
30639818 TAATTATTATTAAA
1 TAATTATTATTAAA
* *
30639832 TACAATT-TAATAAAA
1 T--AATTATTATTAAA
* *
30639847 TAATATATAATTTAA
1 TAAT-TATTATTAAA
*
30639862 TAA-TATTTTTAATA
1 TAATTATTATTAA-A
30639876 TAATTATTATTAAA
1 TAATTATTATTAAA
30639890 ATATGAATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
13 9 0.16
14 8 0.14
15 29 0.51
16 11 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATTATTATTAAA
Found at i:30639831 original size:57 final size:57
Alignment explanation
Indices: 30639763--30639889 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 57
30639753 TATTTTAATG
* * *
30639763 ATTATTATTAAATATAATGTAA-AAAAT-T-TTTAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATACAATGTAATAAAATATATATAATTTA-ATAA-TAT-TTTTAACATA
* *
30639820 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATACAATGTAATAAAAT-ATATATAATTTAATAATATTTTTAACATA
30639878 ATTATTATTAAA
1 ATTATTATTAAA
30639890 ATATGAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
57 20 0.33
58 26 0.43
59 3 0.05
60 4 0.07
61 8 0.13
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (57 bp):
ATTATTATTAAATACAATGTAATAAAATATATATAATTTAATAATATTTTTAACATA
Found at i:30644340 original size:40 final size:39
Alignment explanation
Indices: 30644285--30644362 Score: 138
Period size: 40 Copynumber: 2.0 Consensus size: 39
30644275 CAACTCTCTT
30644285 AAAACGGAATCTATTCCAAACAAATATGCCATGGTTCCTC
1 AAAACGGAATCTATTCCAAACAAA-ATGCCATGGTTCCTC
*
30644325 AAAACGGAATCTATTCCAAACATAATGCCATGGTTCCT
1 AAAACGGAATCTATTCCAAACAAAATGCCATGGTTCCT
30644363 TACTTCGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 14 0.38
40 23 0.62
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (39 bp):
AAAACGGAATCTATTCCAAACAAAATGCCATGGTTCCTC
Found at i:30647048 original size:5 final size:5
Alignment explanation
Indices: 30647038--30647077 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
30647028 CTTACAACCC
*
30647038 AAATA AAATA AAAGGTA AAATA AAATA AAACA AAATA AAA
1 AAATA AAATA AAA--TA AAATA AAATA AAATA AAATA AAA
30647078 AGTTTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 26 0.84
7 5 0.16
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (5 bp):
AAATA
Done.