Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 54 of 75
Found at i:17243304 original size:109 final size:109
Alignment explanation
Indices: 17243113--17243367 Score: 343
Period size: 109 Copynumber: 2.3 Consensus size: 109
17243103 TGTCTAACCG
* *
17243113 AACCTTTTTAAGGTTGCCTTAGATGGGTATATCCCAACCTTTTTAATGTTGCCTTAGATAAGGTC
1 AACCTTTTTAAGGTTGCCTTAGATGGGTTTATCCCAACCTTTTTAAGGTTGCCTTAGATAAGGTC
* **
17243178 TATCCCAACTTTATTTAAAGGTTGCCTTAAACACGGCCTATCCC
66 TATCACAACTTTATTTAAAGGTTGCCTTAAACAAAGCCTATCCC
* * * * * *
17243222 AACCTTTCTAAGGTTGTCTTAGACGGGTTTATCTCAACCTTTTATAAGGTTGTCTTAGAT-GGGT
1 AACCTTTTTAAGGTTGCCTTAGATGGGTTTATCCCAACCTTTT-TAAGGTTGCCTTAGATAAGGT
* * *
17243286 CTATCACAACCTTT-TTTAAAGGTTGTCTTAGACAAAGTCTATCCC
65 CTATCACAA-CTTTATTTAAAGGTTGCCTTAAACAAAGCCTATCCC
*
17243331 AACCTTTTTAAGGTTGCCTCAGATGGGTTTATCCCAA
1 AACCTTTTTAAGGTTGCCTTAGATGGGTTTATCCCAA
17243368 TGTTTTTTAA
Statistics
Matches: 125, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
109 107 0.86
110 18 0.14
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (109 bp):
AACCTTTTTAAGGTTGCCTTAGATGGGTTTATCCCAACCTTTTTAAGGTTGCCTTAGATAAGGTC
TATCACAACTTTATTTAAAGGTTGCCTTAAACAAAGCCTATCCC
Found at i:17243378 original size:73 final size:71
Alignment explanation
Indices: 17243104--17243367 Score: 287
Period size: 73 Copynumber: 3.6 Consensus size: 71
17243094 CCTTAGATGT
* * * * *
17243104 GTCTAACCGAACCTTTTTAAGGTTGCCTTAGATGGGTATATCCCAACCTTTTTAATGTTGCCTTA
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGATGGGTCTATCCCAACCTTTTTAAGGTTGTCTTA
*
17243169 GATAAG
66 GACAAG
* * ** * *
17243175 GTCTATCCCAACTTTATTTAAAGGTTGCCTTAAACACGGCCTATCCCAACCTTTCTAAGGTTGTC
1 GTCTATCCCAACCTT-TTT-AAGGTTGCCTTAGA-TGGGTCTATCCCAACCTTTTTAAGGTTGTC
*
17243240 TTAGAC-GG
63 TTAGACAAG
* * * *
17243248 GTTTATCTCAACCTTTTATAAGGTTGTCTTAGATGGGTCTATCACAACCTTTTTTAAAGGTTGTC
1 GTCTATCCCAACCTTTT-TAAGGTTGCCTTAGATGGGTCTATCCCAACC-TTTTT-AAGGTTGTC
*
17243313 TTAGACAAA
63 TTAGACAAG
* *
17243322 GTCTATCCCAACCTTTTTAAGGTTGCCTCAGATGGGTTTATCCCAA
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGATGGGTCTATCCCAA
17243368 TGTTTTTTAA
Statistics
Matches: 155, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
71 24 0.15
72 21 0.14
73 67 0.43
74 43 0.28
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (71 bp):
GTCTATCCCAACCTTTTTAAGGTTGCCTTAGATGGGTCTATCCCAACCTTTTTAAGGTTGTCTTA
GACAAG
Found at i:17271755 original size:13 final size:13
Alignment explanation
Indices: 17271737--17271761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17271727 AATGCTAGGT
17271737 TGGGCACAAAAAG
1 TGGGCACAAAAAG
17271750 TGGGCACAAAAA
1 TGGGCACAAAAA
17271762 CTGAGACAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (13 bp):
TGGGCACAAAAAG
Found at i:17273365 original size:39 final size:41
Alignment explanation
Indices: 17273320--17273425 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 41
17273310 TTTCCTTATG
17273320 CTATTACATCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACATCTCTATTCCATTCAACCAAACACAAGAATTAC
* * *
17273360 C-ATTACGCCTCTATTCCATTCCATTCAACCAAACAGAAGAATTAC
1 CTATTA--CATC---TCTATTCCATTCAACCAAACACAAGAATTAC
**
17273405 CTATTACGCCTCTATTCCATT
1 CTATTACATCTCTATTCCATT
17273426 ACACATCTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
39 4 0.08
40 1 0.02
41 13 0.25
44 27 0.51
45 4 0.08
46 4 0.08
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (41 bp):
CTATTACATCTCTATTCCATTCAACCAAACACAAGAATTAC
Found at i:17273400 original size:44 final size:46
Alignment explanation
Indices: 17273333--17273425 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
17273323 TTACATCTCT
17273333 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACCTATTACGCCTCTATTCC
*
17273377 ATTCCATTCAACCAAACAGAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACCTATTACGCCTCTATTCC
17273423 ATT
1 ATT
17273426 ACACATCTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 23 0.50
45 4 0.09
46 19 0.41
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.28
Consensus pattern (46 bp):
ATTCCATTCAACCAAACACAAGAATTACCTATTACGCCTCTATTCC
Found at i:17273434 original size:16 final size:16
Alignment explanation
Indices: 17273415--17273460 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
17273405 CTATTACGCC
17273415 TCTATTCCATTACACA
1 TCTATTCCATTACACA
17273431 TCTATTCCATTACACA
1 TCTATTCCATTACACA
17273447 TCTATTCCATTACA
1 TCTATTCCATTACA
17273461 GCGAACCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (16 bp):
TCTATTCCATTACACA
Found at i:17275908 original size:50 final size:50
Alignment explanation
Indices: 17275846--17275983 Score: 231
Period size: 50 Copynumber: 2.8 Consensus size: 50
17275836 TGATAATAAC
*
17275846 ATGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTAG
1 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTAG
* *
17275896 ATGCCAATGCCATGTCCTAGACGTGGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTAG
* *
17275946 GTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
17275984 TCTCATTCCC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTAG
Found at i:17292951 original size:396 final size:396
Alignment explanation
Indices: 17292177--17292972 Score: 1321
Period size: 395 Copynumber: 2.0 Consensus size: 396
17292167 AAGACATTTG
* * *
17292177 CCAAGAAACATCGAGATTATACTATTACAAGACTTACCGAAAAGAACATAGTAGAAAGGTACACA
1 CCAAGAAACATCAAGATTATACTATCACAAGACTTACCGAAAAGAACACAGTAGAAAGGTACACA
* *
17292242 AAAAGAGACGAATTGGAAAAAAAAATAACACCAAAAAAAACAAGAGTATCGCCCTTTAGATTCGA
66 AAAAGAGACGAATTGGAAAAAAAAATAACACCAAAAAAAACAAGAGGATCACCCTTTAGATTCGA
*
17292307 ATCCAAAAAGATACGGAAGAAAAGAAAATTGAACAGAGGAGAAGAGGGAGCAGAAACGTCAAAAA
131 ATCCAAAAAGATACGGAAGAAAAGAAAATTGAACAGAGGAAAAGAGGGAGCAGAAACGTCAAAAA
* *
17292372 AGAAAAGAGAAATTTTTGGGAAAACAAAATAAAAGATAAAATAAATTTTGTTTAATTTACTAAAA
196 AGAAAAGAAAAATTTTTGGGAAAACAAAATAAAAGATAAAATAAAATTTGTTTAATTTACTAAAA
* *
17292437 TTTTACTAATATCCTAACTCCCCACTAACCCCCTAACCAACAACTTAACCTCAGAATTTCAACTC
261 TTCTACTAATATCCTAACTCCCCACTAACACCCTAACCAACAACTTAACCTCAGAATTTCAACTC
* *
17292502 CACCAAAACTCTCTCGTGCAACTAAGCAAAAATAACGTCCACGCTCGCGCAGGGATTTGAACACA
326 CACCAAAACTCTCTCGTGCAACTAAGCAAAAATAACGTCCACACTCACGCAGGGATTTGAACACA
17292567 GGACCT
391 GGACCT
* **
17292573 CCAAGAAACATCAAGATTATACTATCACAAGACTTACCGAACAGAATGCAGTCA-AAAGGTACAC
1 CCAAGAAACATCAAGATTATACTATCACAAGACTTACCGAAAAGAACACAGT-AGAAAGGTACAC
*
17292637 AAAAAGAGACGAATTGG-AAAAAAAATAACACCAAAAAAACCAAGAGGATCACCCTTTAGATTCG
65 AAAAAGAGACGAATTGGAAAAAAAAATAACACCAAAAAAAACAAGAGGATCACCCTTTAGATTCG
* *
17292701 AA-CTCGAAAAGATGA-GGAAGAAAAGAAAATTGAATAGAGGAAAAGAGGGAGCAGAAACGTCAA
130 AATC-CAAAAAGAT-ACGGAAGAAAAGAAAATTGAACAGAGGAAAAGAGGGAGCAGAAACGTCAA
17292764 AAAAGAAAAGAAAAATTTTTGGGAAAACAAAATAAAAGATAAAATAAAATTTGTTTAATTTACTA
193 AAAAGAAAAGAAAAATTTTTGGGAAAACAAAATAAAAGATAAAATAAAATTTGTTTAATTTACTA
* *
17292829 AAATTCTACTAATATCCTGACTCCCCACTAACACCCTAACCAACAACTTGACCATCAGAATTTCA
258 AAATTCTACTAATATCCTAACTCCCCACTAACACCCTAACCAACAACTTAACC-TCAGAATTTCA
** *
17292894 ACTCCACTGAAACTCTCTTGTGCAACTAAGCAAAAATAACGTCCACACTCACGCAGGGATTTGAA
322 ACTCCACCAAAACTCTCTCGTGCAACTAAGCAAAAATAACGTCCACACTCACGCAGGGATTTGAA
17292959 CACAGGACCT
387 CACAGGACCT
17292969 CCAA
1 CCAA
17292973 CACCCCACCT
Statistics
Matches: 373, Mismatches: 23, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
394 1 0.00
395 212 0.57
396 159 0.43
397 1 0.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.19
Consensus pattern (396 bp):
CCAAGAAACATCAAGATTATACTATCACAAGACTTACCGAAAAGAACACAGTAGAAAGGTACACA
AAAAGAGACGAATTGGAAAAAAAAATAACACCAAAAAAAACAAGAGGATCACCCTTTAGATTCGA
ATCCAAAAAGATACGGAAGAAAAGAAAATTGAACAGAGGAAAAGAGGGAGCAGAAACGTCAAAAA
AGAAAAGAAAAATTTTTGGGAAAACAAAATAAAAGATAAAATAAAATTTGTTTAATTTACTAAAA
TTCTACTAATATCCTAACTCCCCACTAACACCCTAACCAACAACTTAACCTCAGAATTTCAACTC
CACCAAAACTCTCTCGTGCAACTAAGCAAAAATAACGTCCACACTCACGCAGGGATTTGAACACA
GGACCT
Found at i:17300337 original size:8 final size:8
Alignment explanation
Indices: 17300324--17300350 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17300314 ATATTATTGA
17300324 ATTTTATT
1 ATTTTATT
17300332 ATTTTATT
1 ATTTTATT
17300340 ATTTTATT
1 ATTTTATT
17300348 ATT
1 ATT
17300351 ATAATTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTATT
Found at i:17302580 original size:45 final size:45
Alignment explanation
Indices: 17302516--17302608 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
17302506 ACAGATACTC
* *
17302516 GGTGGATTCAGCACATAGCAACCACATTATTAATCAATGATGTCT
1 GGTGGAATCAGCACATAGCAACCACATTACTAATCAATGATGTCT
* *
17302561 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTT
1 GGTGGAATCAGCACATAGCAACCACATTACTAATCAATGATGTCT
17302606 GGT
1 GGT
17302609 TCACATAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACATTACTAATCAATGATGTCT
Found at i:17310893 original size:64 final size:64
Alignment explanation
Indices: 17310786--17310956 Score: 198
Period size: 64 Copynumber: 2.7 Consensus size: 64
17310776 TGTTCTTCTT
* * * * * ** **
17310786 ATACTAAAACCCCGTTCTCATCCACCAAACCTCTGCAAAGCCATAATTTACTGCATGATATTTG
1 ATACTGAAACCCCATTCTCATCCACCGAACCTTTGCAAAGCCATAATTTACTGAACAATATTCA
* * *
17310850 ATATTGAAACCCCATTCTCATCCACCGAACCTTTGTAAAGCCATAATTTACTTAACAATATTCA
1 ATACTGAAACCCCATTCTCATCCACCGAACCTTTGCAAAGCCATAATTTACTGAACAATATTCA
* * * *
17310914 ATACTGAAACACCATTCTAATCTACCGAACCTTCGCAAAGCCA
1 ATACTGAAACCCCATTCTCATCCACCGAACCTTTGCAAAGCCA
17310957 AAGTTTCCAC
Statistics
Matches: 89, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 89 1.00
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.27
Consensus pattern (64 bp):
ATACTGAAACCCCATTCTCATCCACCGAACCTTTGCAAAGCCATAATTTACTGAACAATATTCA
Found at i:17317773 original size:13 final size:13
Alignment explanation
Indices: 17317757--17317791 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
17317747 TTTAAACAAA
*
17317757 TTAATTAACTTAT
1 TTAATTAACTAAT
17317770 TTAATTAACTAAT
1 TTAATTAACTAAT
*
17317783 TTAACTAAC
1 TTAATTAAC
17317792 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:17320272 original size:48 final size:48
Alignment explanation
Indices: 17320184--17320449 Score: 343
Period size: 48 Copynumber: 5.5 Consensus size: 48
17320174 CAGATTTCTC
* * * * ** * * * *
17320184 GGTGGCCTACACACAGTCCGTACCACCTTTGTGTAATAATAGACTCTC
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
* * *
17320232 GGTGGCCTGCACATAGTCCGTGCCACCCTTGTATTTTAATAGAATATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
* * * *
17320280 GGTGGTCTGCAAACAGTCCGTTCCACCCTTGTATTTTAACAGAATATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
*
17320328 GGTGGCGTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
*
17320376 GGTGGCCTGCACACAGTCCATGCCACCCTTGTATCTTAACAGAATATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
* *
17320424 GGTGGCCTACACACAGTCCATGCCAC
1 GGTGGCCTGCACACAGTCCGTGCCAC
17320450 ATATGCAGCC
Statistics
Matches: 195, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 195 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (48 bp):
GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
Found at i:17322554 original size:23 final size:23
Alignment explanation
Indices: 17322527--17322593 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
17322517 CCTCAAGGTC
17322527 AAATGATTATTTTGTCTGTGGTT-
1 AAATGATTA-TTTGTCTGTGGTTG
*
17322550 AAATGACTTATTTGTCTGTGTTTG
1 AAATGA-TTATTTGTCTGTGGTTG
**
17322574 GTATGATTAATTTGTCTGTG
1 AAATGATT-ATTTGTCTGTG
17322594 ATTTGAATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.51
Consensus pattern (23 bp):
AAATGATTATTTGTCTGTGGTTG
Found at i:17322603 original size:24 final size:23
Alignment explanation
Indices: 17322528--17322603 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 23
17322518 CTCAAGGTCA
* * *
17322528 AATGATTATTTTGTCTGTGGTTA
1 AATGATTAATTTGTCTGTGTTTG
17322551 AATGACTT-ATTTGTCTGTGTTTGG
1 AATGA-TTAATTTGTCTGTGTTT-G
*
17322575 TATGATTAATTTGTCTGTGATTTG
1 AATGATTAATTTGTCTGTG-TTTG
17322599 AATGA
1 AATGA
17322604 CTGATTCTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 19 0.43
24 22 0.50
25 3 0.07
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.50
Consensus pattern (23 bp):
AATGATTAATTTGTCTGTGTTTG
Found at i:17322754 original size:26 final size:26
Alignment explanation
Indices: 17322725--17322774 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
17322715 TTAGCCACAT
* *
17322725 ATACTATTACTGGTAGTTTTACTGTG
1 ATACTATTACTGGCAGCTTTACTGTG
*
17322751 ATACTATTGCTGGCAGCTTTACTG
1 ATACTATTACTGGCAGCTTTACTG
17322775 CGATGCTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTACTGTG
Found at i:17322823 original size:32 final size:31
Alignment explanation
Indices: 17322781--17322860 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
17322771 ACTGCGATGC
* *
17322781 TACTGCTGGCTTTGTGTTGATCATAGTACCAT
1 TACTGATGGCTTTGTGAT-ATCATAGTACCAT
* *
17322813 TACTGATGGCTTTGTACATATCATATTACCAT
1 TACTGATGGCTTTGT-GATATCATAGTACCAT
* *
17322845 TACCGATGGCTGTGTG
1 TACTGATGGCTTTGTG
17322861 CCGATCATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 39 0.98
33 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (31 bp):
TACTGATGGCTTTGTGATATCATAGTACCAT
Found at i:17322868 original size:32 final size:32
Alignment explanation
Indices: 17322799--17323014 Score: 148
Period size: 32 Copynumber: 6.8 Consensus size: 32
17322789 GCTTTGTGTT
* * * *
17322799 GATCATAGTACCATTACTGATGGCTTTGTACA
1 GATCATATTACCGTTACTGATGGCTGTGTACC
* * * *
17322831 TATCATATTACCATTACCGATGGCTGTGTGCC
1 GATCATATTACCGTTACTGATGGCTGTGTACC
* * * * *
17322863 GATCAT-TTCACTGTTACTGATGGTTGTATGCA
1 GATCATATT-ACCGTTACTGATGGCTGTGTACC
* * * *
17322895 AATCATATCACCGCTACTGATGGCTTTGTACC
1 GATCATATTACCGTTACTGATGGCTGTGTACC
* * *
17322927 GGTCATGTTACCGTTACTGATGGTTGTGTACC
1 GATCATATTACCGTTACTGATGGCTGTGTACC
* * * * *
17322959 GATCATATCACTGCTACTGATGGCTTTGTGCC
1 GATCATATTACCGTTACTGATGGCTGTGTACC
* * * *
17322991 AATCACATTACTG-TACTTATGGCT
1 GATCATATTACCGTTACTGATGGCT
17323015 TGCCGTCATT
Statistics
Matches: 141, Mismatches: 41, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
31 12 0.09
32 128 0.91
33 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (32 bp):
GATCATATTACCGTTACTGATGGCTGTGTACC
Found at i:17322964 original size:64 final size:63
Alignment explanation
Indices: 17322779--17322987 Score: 195
Period size: 64 Copynumber: 3.3 Consensus size: 63
17322769 TTACTGCGAT
* *** * * * *
17322779 GCTACTGCTGGCTTTGTGTTGATCATAGTACCATTACTGATGGCTT-TGTACATATCATATTACC
1 GCTACTGATGGCTTTGTACCGATCAT-TTACCGTTACTGATGG-TTGTGTACAAATCATATCACC
** * * * * * *
17322843 ATTACCGATGGCTGTGTGCCGATCATTTCACTGTTACTGATGGTTGTATGCAAATCATATCACC
1 GCTACTGATGGCTTTGTACCGATCATTT-ACCGTTACTGATGGTTGTGTACAAATCATATCACC
* ** *
17322907 GCTACTGATGGCTTTGTACCGGTCATGTTACCGTTACTGATGGTTGTGTACCGATCATATCACT
1 GCTACTGATGGCTTTGTACCGATCAT-TTACCGTTACTGATGGTTGTGTACAAATCATATCACC
17322971 GCTACTGATGGCTTTGT
1 GCTACTGATGGCTTTGT
17322988 GCCAATCACA
Statistics
Matches: 116, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
63 3 0.03
64 111 0.96
65 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (63 bp):
GCTACTGATGGCTTTGTACCGATCATTTACCGTTACTGATGGTTGTGTACAAATCATATCACC
Found at i:17322995 original size:96 final size:96
Alignment explanation
Indices: 17322778--17322995 Score: 242
Period size: 96 Copynumber: 2.3 Consensus size: 96
17322768 TTTACTGCGA
* *** * *
17322778 TGCTACTGCTGGCTTTGTGTTGATCATAGTACCATTACTGATGGCTTTGTACATATCATATTACC
1 TGCTACTGATGGCTTTGTGCAAATCATAGTACCACTACTGATGGCTTTGTACAGATCATATTACC
* *
17322843 ATTACCGATGGCTGTGTGCCGATCATTTCAC
66 ATTACCGATGGCTGTGTACCGATCATATCAC
* * * * * *
17322874 TGTTACTGATGG-TTGTATGCAAATCATA-TCACCGCTACTGATGGCTTTGTACCGGTCATGTTA
1 TGCTACTGATGGCTT-TGTGCAAATCATAGT-ACCACTACTGATGGCTTTGTACAGATCATATTA
* * *
17322937 CCGTTACTGATGGTTGTGTACCGATCATATCAC
64 CCATTACCGATGGCTGTGTACCGATCATATCAC
*
17322970 TGCTACTGATGGCTTTGTGCCAATCA
1 TGCTACTGATGGCTTTGTGCAAATCA
17322996 CATTACTGTA
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
95 3 0.03
96 94 0.95
97 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (96 bp):
TGCTACTGATGGCTTTGTGCAAATCATAGTACCACTACTGATGGCTTTGTACAGATCATATTACC
ATTACCGATGGCTGTGTACCGATCATATCAC
Found at i:17323240 original size:28 final size:28
Alignment explanation
Indices: 17323207--17323260 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
17323197 TATACTGATA
*
17323207 CTGTATCGGGCTTAGGCCCACACTGTTT
1 CTGTATCGGGCTAAGGCCCACACTGTTT
*
17323235 CTGTATTGGGCTAAGGCCCACACTGT
1 CTGTATCGGGCTAAGGCCCACACTGT
17323261 ACTGTTCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.30
Consensus pattern (28 bp):
CTGTATCGGGCTAAGGCCCACACTGTTT
Found at i:17329563 original size:20 final size:20
Alignment explanation
Indices: 17329527--17329564 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17329517 ATAAAAGAAA
*
17329527 ATAAAATTAATCTAAAACCT
1 ATAAAATTAATCGAAAACCT
17329547 ATAAAATGTAAT-GAAAAC
1 ATAAAAT-TAATCGAAAAC
17329565 TAACCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (20 bp):
ATAAAATTAATCGAAAACCT
Found at i:17334240 original size:50 final size:50
Alignment explanation
Indices: 17334141--17334285 Score: 166
Period size: 50 Copynumber: 2.9 Consensus size: 50
17334131 TTTTCTGTGC
* * * * *
17334141 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGA-GTCTCATATCGG
1 TGCCAACGCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * ** *
17334190 TGCCCATGTCATGTCCAAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
17334240 TTCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAACGCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATA
17334286 ATCTCAATGA
Statistics
Matches: 78, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
49 30 0.38
50 48 0.62
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:17336598 original size:25 final size:26
Alignment explanation
Indices: 17336556--17336607 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
17336546 AGTTGTAAAT
17336556 TAGAAAAATATCTCTAG-AAATTTTC
1 TAGAAAAATATCTCTAGAAAATTTTC
* * *
17336581 TAGAATAATCTCTTTAGAAAATTTTC
1 TAGAAAAATATCTCTAGAAAATTTTC
17336607 T
1 T
17336608 CTCTACAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (26 bp):
TAGAAAAATATCTCTAGAAAATTTTC
Found at i:17340068 original size:15 final size:15
Alignment explanation
Indices: 17340048--17340104 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
17340038 GTTACAACTT
17340048 TAATATTAATTAATA
1 TAATATTAATTAATA
* * *
17340063 TAATATTTATCAAGA
1 TAATATTAATTAATA
*
17340078 TAAATATTAGATTAAATT
1 T-AATATTA-ATT-AATA
17340096 TAATATTAA
1 TAATATTAA
17340105 ATCTTATTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 13 0.41
16 7 0.22
17 9 0.28
18 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (15 bp):
TAATATTAATTAATA
Found at i:17355666 original size:29 final size:28
Alignment explanation
Indices: 17355603--17355667 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
17355593 TCGTAAAAGG
* *
17355603 ATGCCTTTGTGGCTATCTTAGTTAAAAG
1 ATGCCTTAGTGGCTATCTTAGTTAAAAA
*
17355631 TTAGCCTTAGTGGCTATCTCTA-TTAAATAA
1 AT-GCCTTAGTGGCTATCT-TAGTTAAA-AA
17355661 ATGCCTT
1 ATGCCTT
17355668 TGTAGCAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.03
29 25 0.83
30 4 0.13
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (28 bp):
ATGCCTTAGTGGCTATCTTAGTTAAAAA
Found at i:17355806 original size:28 final size:29
Alignment explanation
Indices: 17355718--17355816 Score: 128
Period size: 28 Copynumber: 3.4 Consensus size: 29
17355708 TTAAAATAAT
** * *
17355718 AGCCTTTGCAGCGATCTCTGTTAAAATAGA
1 AGCCTTTGTGGCGACCTCTGTT-AAATGGA
* *
17355748 AGTCTTTGTGGCGACCTTTGTTAAATGGA
1 AGCCTTTGTGGCGACCTCTGTTAAATGGA
17355777 AGCCTTTGTGGCG-CCTCTGTTAAATGGA
1 AGCCTTTGTGGCGACCTCTGTTAAATGGA
17355805 AGCCTTTGTGGC
1 AGCCTTTGTGGC
17355817 AATCTCTGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.43
29 18 0.30
30 17 0.28
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (29 bp):
AGCCTTTGTGGCGACCTCTGTTAAATGGA
Found at i:17365825 original size:15 final size:15
Alignment explanation
Indices: 17365807--17365836 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17365797 CCTATTTACT
*
17365807 TTCCCGAAACTTTTA
1 TTCCCAAAACTTTTA
17365822 TTCCCAAAACTTTTA
1 TTCCCAAAACTTTTA
17365837 CTTTTCACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (15 bp):
TTCCCAAAACTTTTA
Found at i:17367067 original size:47 final size:47
Alignment explanation
Indices: 17366992--17367120 Score: 159
Period size: 47 Copynumber: 2.7 Consensus size: 47
17366982 TTGATAGTTT
* * * * **
17366992 ATATTCTCGACCAATAGTTTTATCCACAACATATTTTAGTCGGTAGTC
1 ATATGCTCGACCAGT-GGTTTATCCACAACGTATTTTAGTCGCAAGTC
* *
17367040 ATATGCTCGACCAGTGGTTTATCCACAATGTCTTTTAGTCGCAAGTC
1 ATATGCTCGACCAGTGGTTTATCCACAACGTATTTTAGTCGCAAGTC
* *
17367087 ATATGCACGACCAGTGGTTCATCCACAACGTATT
1 ATATGCTCGACCAGTGGTTTATCCACAACGTATT
17367121 AACAGCTTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 56 0.81
48 13 0.19
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (47 bp):
ATATGCTCGACCAGTGGTTTATCCACAACGTATTTTAGTCGCAAGTC
Found at i:17367190 original size:92 final size:92
Alignment explanation
Indices: 17367094--17367346 Score: 332
Period size: 91 Copynumber: 2.8 Consensus size: 92
17367084 GTCATATGCA
* * *
17367094 CGACCAGTGGTTCATCCACAACGTATTAACAGCTTTTATATGCACTAATAGATGGTTCATCCATC
1 CGACCAGTGGTTCATCCACAAAGTATTAACAGCTTTTATATGCACTAATGGATGGTTCATCCACC
17367159 AATATTTTAGTCAGCAGTTTACCTACT
66 AATATTTTAGTCAGCAGTTTACCTACT
* * * * *
17367186 CGACCAATGGTTCATCCATAATGT-TTAACAGCTTTTATATACACAAATGGATGGTTCATCCACC
1 CGACCAGTGGTTCATCCACAAAGTATTAACAGCTTTTATATGCACTAATGGATGGTTCATCCACC
17367250 AATATTTTAGTCAGCAGTTTACCTACT
66 AATATTTTAGTCAGCAGTTTACCTACT
** * * * * *
17367277 TAACC-GATGGTTCATCCACAAAGTATTAGCAACTTTTATCTGCA-TAGACGGTTGGTTCATCCA
1 CGACCAG-TGGTTCATCCACAAAGTATTAACAGCTTTTATATGCACTA-ATGGATGGTTCATCCA
17367340 CCAATAT
64 CCAATAT
17367347 ATTTTAATAT
Statistics
Matches: 139, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
91 82 0.59
92 57 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (92 bp):
CGACCAGTGGTTCATCCACAAAGTATTAACAGCTTTTATATGCACTAATGGATGGTTCATCCACC
AATATTTTAGTCAGCAGTTTACCTACT
Found at i:17382124 original size:50 final size:48
Alignment explanation
Indices: 17381995--17382132 Score: 154
Period size: 47 Copynumber: 2.8 Consensus size: 48
17381985 GTGGAAGTAT
* *
17381995 GTGGCAGTTTATCTGTAAATTAGTGGTGGCTTGTCCACAAAGTGTTGTA
1 GTGGCAGTTTATCT-AAAAATAGTGGTGGCTTGTCCACAAAGTGTTGTA
* * * * *
17382044 ATGGCAGTATATCTACATAT-GTGGTGGCTTGTCC-CTAAAGTGTTATTA
1 GTGGCAGTTTATCTAAAAATAGTGGTGGCTTGTCCAC-AAAGTGTT-GTA
*
17382092 GTGGCAATTTATCTAAAAATCAGTGGTGGCTTGTCCACAAA
1 GTGGCAGTTTATCTAAAAAT-AGTGGTGGCTTGTCCACAAA
17382133 AGGTGTTTCG
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
46 1 0.01
47 22 0.31
48 19 0.26
49 12 0.17
50 17 0.24
51 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (48 bp):
GTGGCAGTTTATCTAAAAATAGTGGTGGCTTGTCCACAAAGTGTTGTA
Found at i:17391364 original size:76 final size:75
Alignment explanation
Indices: 17391273--17391418 Score: 193
Period size: 76 Copynumber: 1.9 Consensus size: 75
17391263 TAATCTAATT
* * * *
17391273 TCTAAATTAACATCTAATGAAATCTATGAAAACTTCAAATCTAAAATCTACAACTTAAAAATGAA
1 TCTAAACTAAAATCTAATGAAATCTATGAAAACCTAAAATCTAAAATCTACAAC-TAAAAATGAA
17391338 ACAAATCCAAC
65 ACAAATCCAAC
* * * * * *
17391349 TCTAAACTAAAATCTAATTAAATTTATTAAAACCTAAAATCTAAATTCTAGAGCTAAAAATGAAA
1 TCTAAACTAAAATCTAATGAAATCTATGAAAACCTAAAATCTAAAATCTACAACTAAAAATGAAA
17391414 CAAAT
66 CAAAT
17391419 TCGGAATTTC
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 16 0.27
76 44 0.73
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (75 bp):
TCTAAACTAAAATCTAATGAAATCTATGAAAACCTAAAATCTAAAATCTACAACTAAAAATGAAA
CAAATCCAAC
Found at i:17392562 original size:18 final size:19
Alignment explanation
Indices: 17392541--17392593 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
17392531 CTAGAAATTT
*
17392541 AAAAATTAAATTAAA-TAA
1 AAAAATTAAAATAAATTAA
* *
17392559 AAAAACTAAAATAAATTAG
1 AAAAATTAAAATAAATTAA
17392578 AAAAATTAAAAATAAA
1 AAAAATT-AAAATAAA
17392594 AAGGTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 13 0.45
19 8 0.28
20 8 0.28
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATTAAAATAAATTAA
Found at i:17396283 original size:50 final size:50
Alignment explanation
Indices: 17396216--17396355 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
17396206 TTTCTGTGCA
* * **
17396216 GCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCAGATCGGT
1 GCCAATGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCAGATCGGT
* * ** * **
17396266 GCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTTATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCAGATCGGT
**
17396316 GCCAACACCATGTCCCAGACATGGTTTTACATGGGACCTC
1 GCCAATGCCATGTCCCAGACATGGTTTTACATGGGACCTC
17396356 ATAATCTAAT
Statistics
Matches: 73, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCAGATCGGT
Found at i:17401101 original size:5 final size:5
Alignment explanation
Indices: 17401091--17401121 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
17401081 CTTGAAAATT
*
17401091 TTCGA TTCGA TTAGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
17401122 CGAATGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:17404354 original size:50 final size:50
Alignment explanation
Indices: 17404280--17404476 Score: 189
Period size: 50 Copynumber: 3.8 Consensus size: 50
17404270 TTTCCGTGCA
* * * **
17404280 GCCAATGCCATATCCGAGATATGGTCTTACATGGGAGTTCTCATATCGGT
1 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATCGGT
* * * *
17404330 GCCCATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCTAGACATGGTCTTACATG-GGACCTCTCATATCGGT
** * *
17404380 GCCAACACCATGTCCTAGACATGGTTTTACATGGGACCTCTCATAATCTCAATGAT
1 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGT
* *
17404436 GCCAATGCCATGTCCTAGAAATGGTCTTACATGGGATCTCT
1 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCT
17404477 TTACCCAAAT
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
49 1 0.01
50 76 0.64
51 1 0.01
53 2 0.02
56 38 0.32
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
GCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATCGGT
Found at i:17413858 original size:21 final size:21
Alignment explanation
Indices: 17413834--17413896 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
17413824 AGAGCAAAAC
17413834 GACCTTTGATGTTGCAACACT
1 GACCTTTGATGTTGCAACACT
* * ** *
17413855 GACCTTCGGTGTTGTGACATCA
1 GACCTTTGATGTTGCAACA-CT
*
17413877 GA-CTCTGATGTTGCAACACT
1 GACCTTTGATGTTGCAACACT
17413897 ACAGGCCTAT
Statistics
Matches: 30, Mismatches: 11, Indels: 3
0.68 0.25 0.07
Matches are distributed among these distances:
20 1 0.03
21 26 0.87
22 3 0.10
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
GACCTTTGATGTTGCAACACT
Found at i:17417610 original size:9 final size:9
Alignment explanation
Indices: 17417596--17417654 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
17417586 GTAGTGATTC
17417596 AATTCGGTT
1 AATTCGGTT
*
17417605 AATTCGGGT
1 AATTCGGTT
*
17417614 AATTCAGTT
1 AATTCGGTT
17417623 AATTCGGTT
1 AATTCGGTT
17417632 AATTCGGTT
1 AATTCGGTT
*
17417641 AATTCGGGT
1 AATTCGGTT
17417650 AATTC
1 AATTC
17417655 AATTAATTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:17417623 original size:18 final size:18
Alignment explanation
Indices: 17417596--17417662 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
17417586 GTAGTGATTC
*
17417596 AATTCGGTTAATTCGGGT
1 AATTCAGTTAATTCGGGT
*
17417614 AATTCAGTTAATTCGGTT
1 AATTCAGTTAATTCGGGT
*
17417632 AATTCGGTTAATTCGGGT
1 AATTCAGTTAATTCGGGT
*
17417650 AATTCAATTAATT
1 AATTCAGTTAATT
17417663 TGATTAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.42
Consensus pattern (18 bp):
AATTCAGTTAATTCGGGT
Found at i:17417660 original size:27 final size:27
Alignment explanation
Indices: 17417603--17417671 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
17417593 TTCAATTCGG
* * **
17417603 TTAATTCGGGTAATTCAGTTAATTCGG
1 TTAATTCGGTTAATTCAGGTAATTCAA
*
17417630 TTAATTCGGTTAATTCGGGTAATTCAA
1 TTAATTCGGTTAATTCAGGTAATTCAA
* *
17417657 TTAATTTGATTAATT
1 TTAATTCGGTTAATT
17417672 TTTAATCAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (27 bp):
TTAATTCGGTTAATTCAGGTAATTCAA
Found at i:17419457 original size:10 final size:12
Alignment explanation
Indices: 17419441--17419472 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
17419431 GGCTGCCATT
17419441 TTTTTCTCTC-A
1 TTTTTCTCTCAA
17419452 -TTTTCTCTCAA
1 TTTTTCTCTCAA
17419463 TTTTTCTCTC
1 TTTTTCTCTC
17419473 TATGCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.47
11 1 0.05
12 9 0.47
ACGTcount: A:0.09, C:0.28, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTCTCTCAA
Found at i:17423838 original size:32 final size:32
Alignment explanation
Indices: 17423800--17423951 Score: 189
Period size: 32 Copynumber: 4.8 Consensus size: 32
17423790 ATAAGTACAA
* * *
17423800 TAATATGATTGGCATAAAGCCATCAGTAGTAG
1 TAATATGATCGGCACAAAGCCATCAGTAATAG
* * *
17423832 TAATATGATTGGCACACAGCCATTAGTAATAG
1 TAATATGATCGGCACAAAGCCATCAGTAATAG
* * *
17423864 TAGTATGATCGGCATAAAGCCATCAGTAGTAG
1 TAATATGATCGGCACAAAGCCATCAGTAATAG
* *
17423896 TAATATGATCGGCACACAA-CCATCAATAATGG
1 TAATATGATCGGCACA-AAGCCATCAGTAATAG
17423928 TAATATGATCGGCACAAAGCCATC
1 TAATATGATCGGCACAAAGCCATC
17423952 GATAGCATCG
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
31 2 0.02
32 99 0.96
33 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAATAG
Found at i:17423886 original size:64 final size:64
Alignment explanation
Indices: 17423800--17423951 Score: 232
Period size: 64 Copynumber: 2.4 Consensus size: 64
17423790 ATAAGTACAA
* * * * *
17423800 TAATATGATTGGCATAAAGCCATCAGTAGTAGTAATATGATTGGCACACAGCCATTAGTAATAG
1 TAATATGATCGGCATAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAATAATAG
* *
17423864 TAGTATGATCGGCATAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAATAATGG
1 TAATATGATCGGCATAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAATAATAG
*
17423928 TAATATGATCGGCACAAAGCCATC
1 TAATATGATCGGCATAAAGCCATC
17423952 GATAGCATCG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (64 bp):
TAATATGATCGGCATAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAATAATAG
Found at i:17424007 original size:26 final size:26
Alignment explanation
Indices: 17423946--17424011 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
17423936 TCGGCACAAA
* * *
17423946 GCCATCGATAGCATCGCAGCAAAGTT
1 GCCATCAATAGTATCGCAGCAAAGCT
17423972 GCCATCAATAGTATCGCAGCAAAGCT
1 GCCATCAATAGTATCGCAGCAAAGCT
17423998 GCCAGT-AATAGTAT
1 GCCA-TCAATAGTAT
17424012 ATGTCACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 35 0.97
27 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (26 bp):
GCCATCAATAGTATCGCAGCAAAGCT
Found at i:17424156 original size:24 final size:24
Alignment explanation
Indices: 17424127--17424236 Score: 123
Period size: 24 Copynumber: 4.6 Consensus size: 24
17424117 CCATGCACAG
17424127 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
17424151 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* * *
17424175 AATC-GATCATTTACATCTCGGACA
1 AATCAG-TCATTTAAATCACAGACA
* * * * *
17424199 AGTCATTTATTTACATCACAGGCA
1 AATCAGTCATTTAAATCACAGACA
*
17424223 AATCAATCATTTAA
1 AATCAGTCATTTAA
17424237 CCCCGAGGGG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
23 1 0.01
24 70 0.99
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:17424272 original size:27 final size:27
Alignment explanation
Indices: 17424255--17424480 Score: 120
Period size: 27 Copynumber: 8.4 Consensus size: 27
17424245 GGTAAAATAG
* *
17424255 TCATTTTACCCTACAGGGGCATTACGT
1 TCATTTTACCCTACAGGGGAAATACGT
* *
17424282 TCATTTTACCCTACAGGGGCACTACAGT
1 TCATTTTACCCTACAGGGGAAATAC-GT
* * * *
17424310 T-ATTTTACCCT--AGAGGCATTACGG
1 TCATTTTACCCTACAGGGGAAATACGT
* * * * *
17424334 TCATTGTATCCTACAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGAAATACGT
* * * * *
17424361 TCATTTTACCATACAAGGGCATTACGG
1 TCATTTTACCCTACAGGGGAAATACGT
* * *
17424388 TCATTTTACCCTATAGGGGAATTACGA
1 TCATTTTACCCTACAGGGGAAATACGT
* * * * * *
17424415 CCATTTCACCTTACAGGGG-CATCATGG
1 TCATTTTACCCTACAGGGGAAAT-ACGT
* * *
17424442 TCATTTTACCCTATAGGGG-CATCACGA
1 TCATTTTACCCTACAGGGGAAAT-ACGT
17424469 TCATTTTACCCT
1 TCATTTTACCCT
17424481 TCGATGGTAT
Statistics
Matches: 162, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
24 2 0.01
25 17 0.10
26 1 0.01
27 139 0.86
28 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGAAATACGT
Found at i:17424300 original size:54 final size:54
Alignment explanation
Indices: 17424255--17424480 Score: 226
Period size: 54 Copynumber: 4.2 Consensus size: 54
17424245 GGTAAAATAG
* * *
17424255 TCATTTTACCCTACAGGGGCATTACGTTCATTTTACCCTACAGGGGCACTAC-A
1 TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGAAATACGA
* * * * * *
17424308 GTTATTTTACCCT--AGAGGCATTACGGTCATTGTATCCTACAGGGGCATTACGA
1 -TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGAAATACGA
* * * *
17424361 TCATTTTACCATACAAGGGCATTACGGTCATTTTACCCTATAGGGGAATTACGA
1 TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGAAATACGA
* * * * * * *
17424415 CCATTTCACCTTACAGGGGCATCATGGTCATTTTACCCTATAGGGG-CATCACGA
1 TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGAAAT-ACGA
17424469 TCATTTTACCCT
1 TCATTTTACCCT
17424481 TCGATGGTAT
Statistics
Matches: 143, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
52 43 0.30
53 2 0.01
54 98 0.69
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (54 bp):
TCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGGAAATACGA
Found at i:17424348 original size:79 final size:78
Alignment explanation
Indices: 17424254--17424479 Score: 224
Period size: 81 Copynumber: 2.8 Consensus size: 78
17424244 GGGTAAAATA
* *
17424254 GTCATTTTACCCTACAGGGGCATTACGTTCATTTTACCCTACAGGGGCACTACAGTTATTTTACC
1 GTCA-TTTA-CCTACAGGGGCATTACGATCATTTTACCCTACAGGGGCACTACAGTCATTTTACC
*
17424319 C-TAGAGGCATTACG
64 CATAGAGGAATTACG
* * * *
17424333 GTCATTGTATCCTACAGGGGCATTACGATCATTTTACCATACAAGGGCATTACGGTCATTTTACC
1 GTCATT-TA-CCTACAGGGGCATTACGATCATTTTACCCTACAGGGGCACTACAGTCATTTTACC
*
17424398 CTATAGGGGAATTACG
64 C-ATAGAGGAATTACG
** * * * *
17424414 ACCATTTCACCTTACAGGGGCATCATGGTCATTTTACCCTATAGGGGCA-T-CACGATCATTTTA
1 GTCATTT-ACC-TACAGGGGCATTACGATCATTTTACCCTACAGGGGCACTACA-G-TCATTTTA
17424477 CCC
62 CCC
17424480 TTCGATGGTA
Statistics
Matches: 122, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
78 2 0.02
79 57 0.47
80 5 0.04
81 58 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (78 bp):
GTCATTTACCTACAGGGGCATTACGATCATTTTACCCTACAGGGGCACTACAGTCATTTTACCCA
TAGAGGAATTACG
Found at i:17424745 original size:18 final size:17
Alignment explanation
Indices: 17424707--17424745 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
17424697 TCCGTGTGGG
*
17424707 GCCCACAAGCCCATTGA
1 GCCCACAAGCCCATTCA
*
17424724 GCCCACACAGCCCATTCC
1 GCCCACA-AGCCCATTCA
17424742 GCCC
1 GCCC
17424746 CACGTGGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.23, C:0.51, G:0.15, T:0.10
Consensus pattern (17 bp):
GCCCACAAGCCCATTCA
Found at i:17425250 original size:20 final size:20
Alignment explanation
Indices: 17425225--17425267 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
17425215 GGCAGTATTT
17425225 CACTCCAACTCTACCACTTA
1 CACTCCAACTCTACCACTTA
*
17425245 CACTCCAACTCTGCCACTTA
1 CACTCCAACTCTACCACTTA
17425265 CAC
1 CAC
17425268 GGCTCAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.47, G:0.02, T:0.23
Consensus pattern (20 bp):
CACTCCAACTCTACCACTTA
Found at i:17426347 original size:25 final size:25
Alignment explanation
Indices: 17426283--17426333 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
17426273 GAAAACCATT
17426283 TTCAAACCAAATTTTTTCCAACACG
1 TTCAAACCAAATTTTTTCCAACACG
17426308 TTCAAACCAAATTTTTTCCAACACG
1 TTCAAACCAAATTTTTTCCAACACG
17426333 T
1 T
17426334 CACCCATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (25 bp):
TTCAAACCAAATTTTTTCCAACACG
Found at i:17426516 original size:37 final size:37
Alignment explanation
Indices: 17426413--17426516 Score: 95
Period size: 37 Copynumber: 2.8 Consensus size: 37
17426403 GTATCGATTT
* **
17426413 TAGTA-TGGTGGTATGCTTAACATGTAGTT-AGTAAAA
1 TAGTATTGGTGGTATGCTTTACATGTA-TTCAACAAAA
* * * * **
17426449 CAATATTAGTGGTATGCTTTGCATACATTCAACAAAA
1 TAGTATTGGTGGTATGCTTTACATGTATTCAACAAAA
*
17426486 TAGTATTGGTGGCATGCTTTACATGTATTCA
1 TAGTATTGGTGGTATGCTTTACATGTATTCA
17426517 GTAAGAACAC
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
36 5 0.10
37 45 0.90
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (37 bp):
TAGTATTGGTGGTATGCTTTACATGTATTCAACAAAA
Found at i:17442666 original size:329 final size:331
Alignment explanation
Indices: 17442033--17442678 Score: 1188
Period size: 329 Copynumber: 2.0 Consensus size: 331
17442023 GGGTGTTACA
*
17442033 AATATCTTTTCCAAAAGGATATTAATTTCCATATATATATATTTTATGTCTGACTGAAATAAATT
1 AATATCCTTTCCAAAAGGATATTAATTTCCA-ATATATATATTTTATGTCTGACTGAAATAAATT
17442098 ATTATAATACTTTATTTTAATAATTTCGGTATACAAATCAGAATTAATATTTTATATAAATCAAA
65 ATTATAATACTTTATTTTAATAATTTCGGTATACAAATCAGAATTAATATTTTATATAAATCAAA
17442163 GTCGTACATTTATTTTAATTATGTTCTCTATTCTTGTACAACTAATTTGTACATATATTGTGTGT
130 GTCGTACATTTATTTTAATTATGTTCTCTATTCTTGTACAACTAATTTGTACATATATTGTGTGT
*
17442228 ATTATTTAATTGTCAAATTAAATTAATTCAGTAATTAATTCCAACTGTGTTTAGTTGGTATTAAA
195 ATTATTTAACTGTCAAATTAAATTAATTCAGTAATTAATTCCAACTGTGTTTAGTTGGTATTAAA
* *
17442293 TTAAACTAATTCTCGAGACAGTTAAATTTGACACCAATTGTGTTTAGTTTCTATTCGAAAATATC
260 TTAAACTAATTCTCGAGACAGTTAAATTTAACACCAACTGTGTTTAGTTTCTATTCGAAAATATC
17442358 ACACTGT
325 ACACTGT
17442365 AATATCCTTTCCAAAAGGATATTAATTTCC-ATATATATATTTTATGTCTGACTGAAATAAATTA
1 AATATCCTTTCCAAAAGGATATTAATTTCCAATATATATATTTTATGTCTGACTGAAATAAATTA
17442429 TTATAATACTTTATTTTAATAATTT-GGTATACAAATCAGAATTAATATTTTATATAAATCAAAG
66 TTATAATACTTTATTTTAATAATTTCGGTATACAAATCAGAATTAATATTTTATATAAATCAAAG
*
17442493 TCGTACATTTATTTTAATTATGTTCTCTATTCTTGTACAACTAATTTGTACATATATTGTGTTTA
131 TCGTACATTTATTTTAATTATGTTCTCTATTCTTGTACAACTAATTTGTACATATATTGTGTGTA
*
17442558 TTATTTAACTGTCAAATTAAATTAATTCAGTAATTAATTCCAACTGTGTTTAGTTGGTATTAGAT
196 TTATTTAACTGTCAAATTAAATTAATTCAGTAATTAATTCCAACTGTGTTTAGTTGGTATTAAAT
* * *
17442623 TAAATTAATTCTCGAGATAGTTAAATTTAATACCAACTGTGTTTAGTTTCTATTCG
261 TAAACTAATTCTCGAGACAGTTAAATTTAACACCAACTGTGTTTAGTTTCTATTCG
17442679 TTTCAACCAT
Statistics
Matches: 305, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
329 217 0.71
330 59 0.19
332 29 0.10
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (331 bp):
AATATCCTTTCCAAAAGGATATTAATTTCCAATATATATATTTTATGTCTGACTGAAATAAATTA
TTATAATACTTTATTTTAATAATTTCGGTATACAAATCAGAATTAATATTTTATATAAATCAAAG
TCGTACATTTATTTTAATTATGTTCTCTATTCTTGTACAACTAATTTGTACATATATTGTGTGTA
TTATTTAACTGTCAAATTAAATTAATTCAGTAATTAATTCCAACTGTGTTTAGTTGGTATTAAAT
TAAACTAATTCTCGAGACAGTTAAATTTAACACCAACTGTGTTTAGTTTCTATTCGAAAATATCA
CACTGT
Found at i:17443353 original size:17 final size:17
Alignment explanation
Indices: 17443333--17443383 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
17443323 TTTGACATCC
*
17443333 CTATGTTAATGACAACA
1 CTATGTCAATGACAACA
17443350 CTATGTCAATGACAACA
1 CTATGTCAATGACAACA
*
17443367 CTTTGTCAATGACAACA
1 CTATGTCAATGACAACA
17443384 ATTTGTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (17 bp):
CTATGTCAATGACAACA
Found at i:17443388 original size:17 final size:17
Alignment explanation
Indices: 17443340--17443391 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
17443330 TCCCTATGTT
*
17443340 AATGACAACACTATGTC
1 AATGACAACACTTTGTC
17443357 AATGACAACACTTTGTC
1 AATGACAACACTTTGTC
*
17443374 AATGACAACAATTTGTC
1 AATGACAACACTTTGTC
17443391 A
1 A
17443392 TCAATCAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (17 bp):
AATGACAACACTTTGTC
Found at i:17449550 original size:31 final size:31
Alignment explanation
Indices: 17449515--17449579 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
17449505 GCCGTTGTCA
* *
17449515 GGCTGTGTGGGCCACACAGTCTGGTCAATTG
1 GGCTGTGTAGGCCACACAATCTGGTCAATTG
*
17449546 GGCTGTGTAGGCCACACAATCTGGTGAATTG
1 GGCTGTGTAGGCCACACAATCTGGTCAATTG
17449577 GGC
1 GGC
17449580 GAACGATTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.18, C:0.22, G:0.35, T:0.25
Consensus pattern (31 bp):
GGCTGTGTAGGCCACACAATCTGGTCAATTG
Found at i:17450990 original size:20 final size:21
Alignment explanation
Indices: 17450960--17451004 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
17450950 ATATCCCTCT
17450960 ACATAGATTGTGGTATATCCA
1 ACATAGATTGTGGTATATCCA
17450981 ACAT-GATTGTGGTATATCCA
1 ACATAGATTGTGGTATATCCA
17451001 ACAT
1 ACAT
17451005 CAGCCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (21 bp):
ACATAGATTGTGGTATATCCA
Found at i:17451793 original size:19 final size:19
Alignment explanation
Indices: 17451769--17451862 Score: 143
Period size: 19 Copynumber: 4.8 Consensus size: 19
17451759 AATTTTTGAG
17451769 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
17451788 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
*
17451807 GATATATGCATTCTTAGATAT
1 G--ATATGCAATCTTAGATAT
17451828 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
17451847 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
17451863 ATATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 51 0.76
21 16 0.24
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:17451814 original size:40 final size:38
Alignment explanation
Indices: 17451769--17451869 Score: 143
Period size: 40 Copynumber: 2.7 Consensus size: 38
17451759 AATTTTTGAG
17451769 GATATGCAATCTTAGATATGATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCAAGATAT
* **
17451807 GATATATGCATTCTTAGATATGATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCCAAGATAT
17451847 GATATGCAATCTTAGA-AT-ATATG
1 GATATGCAATCTTAGATATGATATG
17451870 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
36 5 0.09
37 2 0.04
38 15 0.26
40 35 0.61
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCAAGATAT
Found at i:17458530 original size:20 final size:20
Alignment explanation
Indices: 17458502--17458542 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
17458492 GCTGATAGAA
*
17458502 AGCTAAATTGAGCTCGAATG
1 AGCTAAATTGAGCTCAAATG
*
17458522 AGCTGAATTGAGCTCAAATG
1 AGCTAAATTGAGCTCAAATG
17458542 A
1 A
17458543 TCTTATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (20 bp):
AGCTAAATTGAGCTCAAATG
Found at i:17468466 original size:17 final size:17
Alignment explanation
Indices: 17468446--17468479 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17468436 TTTGACATCT
17468446 CTATGTCAATGACAACA
1 CTATGTCAATGACAACA
17468463 CTATGTCAATGACAACA
1 CTATGTCAATGACAACA
17468480 ATTTGTCATC
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:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
CTATGTCAATGACAACA
Found at i:17468486 original size:17 final size:17
Alignment explanation
Indices: 17468447--17468487 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
17468437 TTGACATCTC
*
17468447 TATGTCAATGACAACAC
1 TATGTCAATGACAACAA
17468464 TATGTCAATGACAACAA
1 TATGTCAATGACAACAA
*
17468481 TTTGTCA
1 TATGTCA
17468488 TCAATCAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (17 bp):
TATGTCAATGACAACAA
Found at i:17476434 original size:46 final size:46
Alignment explanation
Indices: 17476380--17476474 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
17476370 TCTCTTTTCT
17476380 TTTAATTAGGAGATTAGATGATAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGATAAAGTTTAGGAGATAATATTTTGG
*
17476426 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGATAAAGTTTAGGAGATAATATTTTGG
17476472 TTT
1 TTT
17476475 CTATCTTTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGATAAAGTTTAGGAGATAATATTTTGG
Found at i:17484270 original size:42 final size:43
Alignment explanation
Indices: 17484223--17484310 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 43
17484213 GTAATACTTA
* *
17484223 TTCACTATCTTGTAATAGTGA-TTTTTTACTTTAAAATAAGTT
1 TTCACTATATTGTAATAGCGATTTTTTTACTTTAAAATAAGTT
*
17484265 TTCACTATATTGTAATAGCGATTTTTTTTGCTTTAAAATAAGTT
1 TTCACTATATTGTAATAGCGA-TTTTTTTACTTTAAAATAAGTT
17484309 TT
1 TT
17484311 AAGAATTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 19 0.46
44 22 0.54
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (43 bp):
TTCACTATATTGTAATAGCGATTTTTTTACTTTAAAATAAGTT
Found at i:17485966 original size:22 final size:21
Alignment explanation
Indices: 17485938--17486017 Score: 56
Period size: 22 Copynumber: 3.8 Consensus size: 21
17485928 AGTATTTGCA
*
17485938 GATAAACTACCAGAAATATGTG
1 GATAAACCACCA-AAATATGTG
* *
17485960 GATAAACCACTAAAAT-TGTA
1 GATAAACCACCAAAATATGTG
** * *
17485980 GATAAAGTGA-AAGAAATATATG
1 GATAAA-CCACCA-AAATATGTG
17486002 GATAAACCACCAAAAT
1 GATAAACCACCAAAAT
17486018 TACAGATAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 9
0.68 0.17 0.14
Matches are distributed among these distances:
20 10 0.23
21 14 0.33
22 19 0.44
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.21
Consensus pattern (21 bp):
GATAAACCACCAAAATATGTG
Found at i:17485984 original size:42 final size:42
Alignment explanation
Indices: 17485936--17486037 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
17485926 CAAGTATTTG
* * *
17485936 CAGATAAACTACCAGAAATATGTGGATAAACCACTAAAATTG
1 CAGATAAACTACCAGAAATATATGGATAAACCACCAAAATTA
* * *
17485978 TAGATAAAGTGA-AAGAAATATATGGATAAACCACCAAAATTA
1 CAGATAAACT-ACCAGAAATATATGGATAAACCACCAAAATTA
17486020 CAGATAAACTACCA-AAAT
1 CAGATAAACTACCAGAAAT
17486038 CTTTCTCCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
41 5 0.10
42 43 0.88
43 1 0.02
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.21
Consensus pattern (42 bp):
CAGATAAACTACCAGAAATATATGGATAAACCACCAAAATTA
Found at i:17485985 original size:20 final size:22
Alignment explanation
Indices: 17485937--17485985 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
17485927 AAGTATTTGC
*
17485937 AGATAAACTACCAGAAATATGT
1 AGATAAACCACCAGAAATATGT
* *
17485959 GGATAAACCACTA-AAAT-TGT
1 AGATAAACCACCAGAAATATGT
17485979 AGATAAA
1 AGATAAA
17485986 GTGAAAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.39
21 4 0.17
22 10 0.43
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.22
Consensus pattern (22 bp):
AGATAAACCACCAGAAATATGT
Found at i:17493644 original size:5 final size:6
Alignment explanation
Indices: 17493610--17493664 Score: 65
Period size: 6 Copynumber: 8.5 Consensus size: 6
17493600 TCAGTTTTTG
*
17493610 TTTATT TTTATAT TTAATATT TTTATT TTTATT TTTATT TTTCTT GTTTATT
1 TTTATT TTTAT-T TT--TATT TTTATT TTTATT TTTATT TTTATT -TTTATT
17493662 TTT
1 TTT
17493665 CGTGATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 29 0.67
7 8 0.19
8 3 0.07
9 3 0.07
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:17520655 original size:17 final size:18
Alignment explanation
Indices: 17520618--17520666 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
17520608 GGTTTCCATT
*
17520618 AAAAAAGAAAAAAAAGGGA
1 AAAAAAGAAAGAAAA-GGA
17520637 AAAAAAGAAAGAAAA-GA
1 AAAAAAGAAAGAAAAGGA
* *
17520654 AAAGAATAAAGAA
1 AAAAAAGAAAGAA
17520667 GAATAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
19 14 0.52
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAGGA
Found at i:17520659 original size:10 final size:9
Alignment explanation
Indices: 17520618--17520656 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
17520608 GGTTTCCATT
17520618 AAAAAAGAA
1 AAAAAAGAA
*
17520627 AAAAAAGGGA
1 AAAAAA-GAA
17520637 AAAAAAGAA
1 AAAAAAGAA
*
17520646 AGAAAAGAA
1 AAAAAAGAA
17520655 AA
1 AA
17520657 GAATAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:17529981 original size:23 final size:23
Alignment explanation
Indices: 17529955--17530027 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
17529945 AAATTAAAAG
*
17529955 AAAAGAAAGAAAAAGTGAAAGAA
1 AAAAGAAAGAAAAAGAGAAAGAA
** *
17529978 AAAAGATTGAAAAAGAGAAATAA
1 AAAAGAAAGAAAAAGAGAAAGAA
*
17530001 AAGAA-AAACGATAAAA-AGAAAGGA
1 AA-AAGAAA-GA-AAAAGAGAAAGAA
17530025 AAA
1 AAA
17530028 GGTGAGGGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
23 23 0.59
24 12 0.31
25 4 0.10
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (23 bp):
AAAAGAAAGAAAAAGAGAAAGAA
Found at i:17532551 original size:12 final size:10
Alignment explanation
Indices: 17532514--17532545 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
17532504 ATTATGCTTA
*
17532514 TTTAGTGTGT
1 TTTAATGTGT
17532524 TTTAATGTGT
1 TTTAATGTGT
17532534 TTTAATGTGT
1 TTTAATGTGT
17532544 TT
1 TT
17532546 GTTAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (10 bp):
TTTAATGTGT
Found at i:17535408 original size:4 final size:4
Alignment explanation
Indices: 17535399--17535423 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17535389 TGTACTTTTA
17535399 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
17535424 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:17545362 original size:25 final size:25
Alignment explanation
Indices: 17545329--17545392 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
17545319 TTAGCCATCT
17545329 CAAGCTTCCCGTTATATTGTTCTTA
1 CAAGCTTCCCGTTATATTGTTCTTA
*
17545354 CAAGATTCCCGTTATATTGTTCTTA
1 CAAGCTTCCCGTTATATTGTTCTTA
*
17545379 CAAGCTTTCCGTTA
1 CAAGCTTCCCGTTA
17545393 ATAGCTCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.42
Consensus pattern (25 bp):
CAAGCTTCCCGTTATATTGTTCTTA
Found at i:17548711 original size:11 final size:10
Alignment explanation
Indices: 17548694--17548721 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
17548684 TGTGTGTTGT
17548694 ATTTTTTTCA
1 ATTTTTTTCA
17548704 ATTTTTTTCA
1 ATTTTTTTCA
17548714 ATTTTTTT
1 ATTTTTTT
17548722 GTTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (10 bp):
ATTTTTTTCA
Found at i:17549593 original size:6 final size:6
Alignment explanation
Indices: 17549582--17549610 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17549572 TGCCGAGCAG
17549582 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
17549611 ATGACATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:17551024 original size:16 final size:17
Alignment explanation
Indices: 17550998--17551031 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17550988 CACTTTTTTT
*
17550998 TTAATTTTTAAAATTAA
1 TTAATTTTTAAAAATAA
17551015 TTAA-TTTTAAAAATAA
1 TTAATTTTTAAAAATAA
17551031 T
1 T
17551032 CATGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTTTTAAAAATAA
Found at i:17554979 original size:13 final size:13
Alignment explanation
Indices: 17554961--17554987 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17554951 GGCACATGGG
17554961 CGTGTGGCCACCC
1 CGTGTGGCCACCC
17554974 CGTGTGGCCACCC
1 CGTGTGGCCACCC
17554987 C
1 C
17554988 ATATGGAAAT
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:0.07, C:0.48, G:0.30, T:0.15
Consensus pattern (13 bp):
CGTGTGGCCACCC
Found at i:17559630 original size:9 final size:9
Alignment explanation
Indices: 17559617--17559658 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
17559607 TTTATTCAAG
17559617 TTATTATAA
1 TTATTATAA
*
17559626 ATATTAT-A
1 TTATTATAA
17559634 TCTA-TATAA
1 T-TATTATAA
17559643 TTATTATAA
1 TTATTATAA
17559652 TTATTAT
1 TTATTAT
17559659 TATTTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
TTATTATAA
Found at i:17560231 original size:3 final size:3
Alignment explanation
Indices: 17560223--17560257 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17560213 GTGAGGTAAG
17560223 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17560258 GTGAGAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:17567117 original size:34 final size:34
Alignment explanation
Indices: 17567069--17567134 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
17567059 GGGAGAATGC
* *
17567069 ATGTGAATAAGACTGAATGATATGCTTGTGATGT
1 ATGTAAATAAGACTGAATGATATGCTTCTGATGT
17567103 ATGTAAATAAGACTGAATGATATGCTTCTGAT
1 ATGTAAATAAGACTGAATGATATGCTTCTGAT
17567135 TCTAAATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (34 bp):
ATGTAAATAAGACTGAATGATATGCTTCTGATGT
Found at i:17570952 original size:11 final size:12
Alignment explanation
Indices: 17570924--17570956 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17570914 ATTTTAAATT
17570924 AAAATTGAATAGA
1 AAAATT-AATAGA
17570937 AAAATTAATA-A
1 AAAATTAATAGA
17570948 AAAATTAAT
1 AAAATTAAT
17570957 TTAGTGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 4 0.20
13 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (12 bp):
AAAATTAATAGA
Found at i:17580645 original size:27 final size:29
Alignment explanation
Indices: 17580586--17580645 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 29
17580576 GATTATATCG
* * *
17580586 CATTATTTTTTATTCGGCAGTTTTACTGA
1 CATTATTTGTTATTCGGCAATTTTACTCA
17580615 -ATTA-TTGTTATTCGGCAATTTTAC-CA
1 CATTATTTGTTATTCGGCAATTTTACTCA
17580641 CATTA
1 CATTA
17580646 AGTTATGCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 1 0.04
27 22 0.81
28 4 0.15
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (29 bp):
CATTATTTGTTATTCGGCAATTTTACTCA
Found at i:17587660 original size:15 final size:14
Alignment explanation
Indices: 17587640--17587719 Score: 53
Period size: 15 Copynumber: 5.7 Consensus size: 14
17587630 AATACAAAAG
17587640 AAAAGAAAAATGAGA
1 AAAAGAAAAA-GAGA
17587655 AAAAG--AAAG-GA
1 AAAAGAAAAAGAGA
*
17587666 AAAATAATAAA-AGA
1 AAAAGAA-AAAGAGA
**
17587680 AAGTG-AAAAGATGA
1 AAAAGAAAAAGA-GA
17587694 GAAAAGAAAAAGATGA
1 -AAAAGAAAAAGA-GA
17587710 AAAAGAAAAA
1 AAAAGAAAAA
17587720 CAATGCGAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
11 6 0.12
12 4 0.08
13 5 0.10
14 9 0.18
15 18 0.35
16 9 0.18
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (14 bp):
AAAAGAAAAAGAGA
Found at i:17587662 original size:41 final size:43
Alignment explanation
Indices: 17587605--17587712 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 43
17587595 TCTGTAGATC
17587605 AAATGAGAGAAAAGAAAAGAATGAAAAT-ACAAAAGAAA-AGAA
1 AAATGAGA-AAAAGAAAAGAATGAAAATAACAAAAGAAAGAGAA
* * *
17587647 AAATGAGAAAAAG-AAAGGA--AAAATAATAAAAGAAAGTGAA
1 AAATGAGAAAAAGAAAAGAATGAAAATAACAAAAGAAAGAGAA
17587687 AAGATGAG-AAAAGAAAA-AGATGAAAA
1 AA-ATGAGAAAAAGAAAAGA-ATGAAAA
17587713 AGAAAAACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
38 5 0.09
39 9 0.16
40 15 0.27
41 14 0.25
42 8 0.15
43 4 0.07
ACGTcount: A:0.70, C:0.01, G:0.20, T:0.08
Consensus pattern (43 bp):
AAATGAGAAAAAGAAAAGAATGAAAATAACAAAAGAAAGAGAA
Found at i:17587663 original size:19 final size:20
Alignment explanation
Indices: 17587635--17587702 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
17587625 ATGAAAATAC
*
17587635 AAAAGAAAAGAAAAATGAGA
1 AAAAGAAAGGAAAAATGAGA
17587655 AAAAGAAAGGAAAAAT-A-A
1 AAAAGAAAGGAAAAATGAGA
17587673 TAAAAGAAAGTGAAAAGATGAG-
1 -AAAAGAAAG-GAAAA-ATGAGA
17587695 AAAAGAAA
1 AAAAGAAA
17587703 AAGATGAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 1 0.02
19 10 0.24
20 20 0.48
21 10 0.24
22 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (20 bp):
AAAAGAAAGGAAAAATGAGA
Found at i:17587704 original size:16 final size:15
Alignment explanation
Indices: 17587685--17587719 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
17587675 AAAGAAAGTG
17587685 AAAAGATGAGAAAAGA
1 AAAAGATGA-AAAAGA
17587701 AAAAGATGAAAAAGA
1 AAAAGATGAAAAAGA
17587716 AAAA
1 AAAA
17587720 CAATGCGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (15 bp):
AAAAGATGAAAAAGA
Found at i:17587718 original size:20 final size:20
Alignment explanation
Indices: 17587614--17587718 Score: 59
Period size: 19 Copynumber: 5.5 Consensus size: 20
17587604 CAAATGAGAG
17587614 AAAAGAAAAGAATGAAA-AT-A
1 AAAAGAAAAGAA--AAAGATGA
17587634 CAAAAGAAAAGAAAAATGA-GA
1 -AAAAGAAAAGAAAAA-GATGA
* *
17587655 AAAAG-AAAGGAAAA-ATAA
1 AAAAGAAAAGAAAAAGATGA
*
17587673 TAAAAG-AAAGTGAAAAGATG-
1 -AAAAGAAAAG-AAAAAGATGA
17587693 ---AGAAAAGAAAAAGATGA
1 AAAAGAAAAGAAAAAGATGA
17587710 AAAAGAAAA
1 AAAAGAAAA
17587719 ACAATGCGAG
Statistics
Matches: 68, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
16 10 0.15
17 5 0.07
18 1 0.01
19 20 0.29
20 16 0.24
21 16 0.24
ACGTcount: A:0.72, C:0.01, G:0.19, T:0.08
Consensus pattern (20 bp):
AAAAGAAAAGAAAAAGATGA
Found at i:17590578 original size:28 final size:28
Alignment explanation
Indices: 17590543--17590613 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
17590533 TATTTTCATG
17590543 CATGCATTTAATATGTCTTAG-TTAGTA
1 CATGCATTTAATATGTCTTAGCTTAGTA
* * *
17590570 CATGACA-TTAATTTGTTTTAGCTTATTA
1 CATG-CATTTAATATGTCTTAGCTTAGTA
17590598 CAT-CATTTTAATATGT
1 CATGCA-TTTAATATGT
17590614 TTGTACAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
26 2 0.06
27 16 0.44
28 18 0.50
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (28 bp):
CATGCATTTAATATGTCTTAGCTTAGTA
Found at i:17590704 original size:24 final size:24
Alignment explanation
Indices: 17590677--17590723 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
17590667 ACATAACCCA
17590677 AACAAACTAAACCCAATCAGCCCC
1 AACAAACTAAACCCAATCAGCCCC
*
17590701 AACAAACTAAACCCAATTAGCCC
1 AACAAACTAAACCCAATCAGCCC
17590724 ATTTACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.38, G:0.04, T:0.11
Consensus pattern (24 bp):
AACAAACTAAACCCAATCAGCCCC
Found at i:17591860 original size:3 final size:3
Alignment explanation
Indices: 17591842--17591886 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
17591832 GTTATTTTTG
* * *
17591842 TAT TAT GAT AAT TAT TAT TAT TAT TAT TAT TAT TAAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
17591887 GTTTTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:17592260 original size:15 final size:12
Alignment explanation
Indices: 17592226--17592284 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
17592216 TTATATTCTT
17592226 TATATTTTATAA
1 TATATTTTATAA
17592238 TATATTTTATACA
1 TATATTTTATA-A
17592251 TAGGTATTTTAT-A
1 TA--TATTTTATAA
17592264 TATA---TAT-A
1 TATATTTTATAA
17592272 TATATTTTATAA
1 TATATTTTATAA
17592284 T
1 T
17592285 TCACATATGC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
8 8 0.20
11 5 0.12
12 13 0.32
13 6 0.15
15 8 0.20
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATTTTATAA
Found at i:17597243 original size:9 final size:9
Alignment explanation
Indices: 17597229--17597278 Score: 93
Period size: 9 Copynumber: 5.7 Consensus size: 9
17597219 TCAGACTCAA
17597229 AAAAAAATC
1 AAAAAAATC
17597238 AAAAAAATC
1 AAAAAAATC
17597247 AAAAAAATC
1 AAAAAAATC
17597256 AAAAAAATC
1 AAAAAAATC
17597265 -AAAAAATC
1 AAAAAAATC
17597273 AAAAAA
1 AAAAAA
17597279 GAAAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.20
9 32 0.80
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:17597295 original size:26 final size:26
Alignment explanation
Indices: 17597230--17597298 Score: 61
Period size: 27 Copynumber: 2.6 Consensus size: 26
17597220 CAGACTCAAA
* *
17597230 AAAAAATCAAAAAAATCAAAAAAATC
1 AAAAAATCAAAAAAATAAAAAAAAAC
17597256 AAAAAAATC-AAAAAATCAAAAAAGAAA-
1 -AAAAAATCAAAAAAAT-AAAAAA-AAAC
*
17597283 AACAAAAACAAAAAAA
1 AA-AAAATCAAAAAAA
17597299 AATCAAAGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 9 0.26
27 18 0.51
28 8 0.23
ACGTcount: A:0.81, C:0.10, G:0.01, T:0.07
Consensus pattern (26 bp):
AAAAAATCAAAAAAATAAAAAAAAAC
Found at i:17597321 original size:38 final size:37
Alignment explanation
Indices: 17597256--17597339 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 37
17597246 CAAAAAAATC
*
17597256 AAAAAAATCAAAAAATCAAAAAAGAAAAACAAA-AACAA
1 AAAAAAATC-AAAAATCAAAAAAGAAAAA-AAAGAAAAA
*
17597294 AAAAAAATC-AAAGTCAAAAATAGGAAAAAAAAGAAAAA
1 AAAAAAATCAAAAATCAAAAA-A-GAAAAAAAAGAAAAA
17597332 AGAAAAAA
1 A-AAAAAA
17597340 GAAAAAGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 10 0.25
37 4 0.10
38 20 0.50
39 6 0.15
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.06
Consensus pattern (37 bp):
AAAAAAATCAAAAATCAAAAAAGAAAAAAAAGAAAAA
Found at i:17597330 original size:6 final size:6
Alignment explanation
Indices: 17597321--17597357 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
17597311 AAATAGGAAA
17597321 AAAAAG AAAAAAG AAAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG -AAAAAG -AAAAAG AAAAAG AAAAAG AAAAA
17597358 TGAGAGGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:17597332 original size:7 final size:7
Alignment explanation
Indices: 17597320--17597357 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
17597310 AAAATAGGAA
17597320 AAAAAAG
1 AAAAAAG
17597327 AAAAAAG
1 AAAAAAG
17597334 AAAAAAG
1 AAAAAAG
17597341 -AAAAAG
1 AAAAAAG
17597347 -AAAAAG
1 AAAAAAG
17597353 AAAAA
1 AAAAA
17597358 TGAGAGGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:17597344 original size:19 final size:18
Alignment explanation
Indices: 17597318--17597357 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 18
17597308 CAAAAATAGG
17597318 AAAAAAAAGAAAAAAGAAA
1 AAAAAAAAG-AAAAAGAAA
17597337 AAAGAAAAAGAAAAAGAAA
1 AAA-AAAAAGAAAAAGAAA
17597356 AA
1 AA
17597358 TGAGAGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAGAAA
Found at i:17599582 original size:85 final size:84
Alignment explanation
Indices: 17599482--17599767 Score: 265
Period size: 85 Copynumber: 3.4 Consensus size: 84
17599472 CTAGTAATCC
* * * *
17599482 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAACCAATGATCATATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAACAGATTAAAATCAA-GATCTTATCTCTCTGAAGTTACAGTA
* * *
17599547 GAGTAAATCGCGTCAGGTCT
65 GAGTAGATCGAGTCAGATCT
* ** *
17599567 TATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTC-AGATCTTATCTCCCTG-AGATTAC
1 TATCTCCCTGAGATTACAGTGGAACAGA-TTAA-AA--TCAAGATCTTATCTCTCTGAAG-TTAC
** * * *
17599630 AGCGGAGCAGATTGAAGT-A-ATCC
61 AGTAGAGTAGATCG-AGTCAGATCT
** * *
17599653 TATCTCCCTGAGATTACAGTGGAATGGATTAAAATAAAGGATCTTTTCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAACAGATTAAAATCAA-GATCTTATCTCTCTGAAGTTACAGTA
*
17599718 GAGTAGATCGTGTCAGATCT
65 GAGTAGATCGAGTCAGATCT
* *
17599738 TATCTCCCTGAGATTACAGCGGAGCAGATT
1 TATCTCCCTGAGATTACAGTGGAACAGATT
17599768 GAAGATAGTA
Statistics
Matches: 156, Mismatches: 34, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
82 1 0.01
83 3 0.02
84 30 0.19
85 58 0.37
86 31 0.20
87 29 0.19
88 3 0.02
89 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (84 bp):
TATCTCCCTGAGATTACAGTGGAACAGATTAAAATCAAGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCGAGTCAGATCT
Found at i:17599748 original size:171 final size:173
Alignment explanation
Indices: 17599389--17599805 Score: 576
Period size: 171 Copynumber: 2.4 Consensus size: 173
17599379 ATTATACAGG
* *
17599389 TCTTATTCTCCCTGAG-TTACAGTGGAGCAGACTGAAGAATTGCAGATCTTATCTTCCTGAGATT
1 TCTTA-TCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATT
* *
17599453 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACC
65 ACAGCGGAGCAGATTGAA-C-AGTAATCCTATCTCCCTGAGATTACAGTGGAACGGATTAAAACA
* *
17599518 AATGATCATATCTCTCTGAAGTTACAGTAGAGTAAATCGCGTCAGG
128 AAGGATCATATCTCTCTGAAGTTACAGTAGAGTAAATCGCGTCAGA
* * *
17599564 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATTA
* *
17599629 CAGCGGAGCAGATTG-A-AGTAATCCTATCTCCCTGAGATTACAGTGGAATGGATTAAAATAAAG
66 CAGCGGAGCAGATTGAACAGTAATCCTATCTCCCTGAGATTACAGTGGAACGGATTAAAACAAAG
* * * *
17599692 GATCTTTTCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGA
131 GATCATATCTCTCTGAAGTTACAGTAGAGTAAATCGCGTCAGA
* * * *
17599735 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-ATAGT-A-ATCCTATCTCCCTGAGATT
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAAT-TTCAGATCTTATCTCCCTGAGATT
*
17599797 ACAGTGGAG
65 ACAGCGGAG
17599806 TGGATTAAAA
Statistics
Matches: 217, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
169 26 0.12
170 3 0.01
171 113 0.52
174 10 0.05
175 65 0.30
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (173 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATTA
CAGCGGAGCAGATTGAACAGTAATCCTATCTCCCTGAGATTACAGTGGAACGGATTAAAACAAAG
GATCATATCTCTCTGAAGTTACAGTAGAGTAAATCGCGTCAGA
Found at i:17599832 original size:129 final size:127
Alignment explanation
Indices: 17599605--17599931 Score: 478
Period size: 129 Copynumber: 2.5 Consensus size: 127
17599595 CCGAAGAATT
17599605 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATT--GAAGTAATCCTATCTCCCTGAGATT
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAGAAGTAATCCTATCTCCCTGAGATT
* * *
17599668 ACAGTGGAATGGATTAAAATAAAGGATCTTTTCTCTCTGAAGTTACAGTAGAGTAGATCGTG
66 ACAGTGGAATGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCG
17599730 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATT-AAGA-AGTAATCCTATCTCCCTGAGA
* *
17599795 TTACAGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCG
64 TTACAGTGGAATGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCG
* * * * ** *
17599859 TCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAATGTCAGATCTTATCTCCCTGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TTAAGAA-GT-A-ATCCTATCTCCCTGA
17599924 GATTACAG
62 GATTACAG
17599932 AAGAGCAGAT
Statistics
Matches: 182, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
125 38 0.21
128 3 0.02
129 118 0.65
130 1 0.01
131 22 0.12
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (127 bp):
TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAGAAGTAATCCTATCTCCCTGAGATT
ACAGTGGAATGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCG
Found at i:17600005 original size:44 final size:43
Alignment explanation
Indices: 17599389--17600029 Score: 253
Period size: 44 Copynumber: 14.7 Consensus size: 43
17599379 ATTATACAGG
* *
17599389 TCTTATTCTCCCTGAG-TTACAGTGGAGCAGACTGAAGAAT-TGCAGA
1 TCTTA-TCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AATAAG--GA
* * ** *
17599435 TCTTATCTTCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAG-GA
* * * *
17599479 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACCAATGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAA-TAAGGA
* * * * * **** *
17599523 TCATATCTCTCTGA-AGTTACAGTAGAGTA-AATCGCGTCAGG-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAGGA
* * ** *
17599564 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCA-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA--TAAGGA
* * *
17599610 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGT-A--A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAGGA
* ***
17599650 TCCTATCTCCCTGAGATTACAGTGGAATGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAGGA
* * * * **** *
17599694 TCTTTTCTCTCTGA-AGTTACAGTAGAGTAGA-TCGTGTCA-GA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAGGA
* * *
17599735 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAG-GA
* **
17599779 TCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATGAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAGGA
* ** * **** *
17599823 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGCGTCAGG-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAGGA
* * ** *
17599864 TCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATGTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA-ATAAG---GA
** *
17599910 TCTTATCTCCCTGAGATTACAGAAGAGCAGATCAAAGAT--GGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA-ATAAGG--A
* *
17599954 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AAGGA
* * *
17599998 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGAT
17600030 CGCATCAGGT
Statistics
Matches: 435, Mismatches: 121, Indels: 80
0.68 0.19 0.13
Matches are distributed among these distances:
40 32 0.07
41 71 0.16
42 16 0.04
43 19 0.04
44 191 0.44
45 19 0.04
46 87 0.20
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAGGA
Found at i:17600329 original size:5 final size:5
Alignment explanation
Indices: 17600319--17600350 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
17600309 GAAAGGTAGT
17600319 AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AG
1 AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AG
17600351 CGAGAAGCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGAGA
Found at i:17601093 original size:13 final size:13
Alignment explanation
Indices: 17601075--17601099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17601065 TCACCGTGAC
17601075 GGAGTTTCAAATT
1 GGAGTTTCAAATT
17601088 GGAGTTTCAAAT
1 GGAGTTTCAAAT
17601100 GCCGATCCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
GGAGTTTCAAATT
Found at i:17601722 original size:3 final size:3
Alignment explanation
Indices: 17601716--17601749 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
17601706 AATAATAATA
*
17601716 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
17601750 AATGTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:17602133 original size:15 final size:12
Alignment explanation
Indices: 17602099--17602157 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
17602089 TTATATTCTT
17602099 TATATTTTATAA
1 TATATTTTATAA
17602111 TATATTTTATACA
1 TATATTTTATA-A
17602124 TAGGTATTTTAT-A
1 TA--TATTTTATAA
17602137 TATA---TAT-A
1 TATATTTTATAA
17602145 TATATTTTATAA
1 TATATTTTATAA
17602157 T
1 T
17602158 TCACATATGC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
8 8 0.20
11 5 0.12
12 13 0.32
13 6 0.15
15 8 0.20
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATTTTATAA
Found at i:17606027 original size:15 final size:16
Alignment explanation
Indices: 17606007--17606036 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17605997 TTAGAATTTA
17606007 TATTAAAAT-TAAATT
1 TATTAAAATATAAATT
17606022 TATTAAAATATAAAT
1 TATTAAAATATAAAT
17606037 ATGACTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAAAATATAAATT
Found at i:17606316 original size:16 final size:17
Alignment explanation
Indices: 17606285--17606322 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
17606275 CCTACAATTT
*
17606285 TATATTTATTCTTAATA
1 TATATTTATACTTAATA
17606302 TATATTTA-ACTTAATA
1 TATATTTATACTTAATA
17606318 T-TATT
1 TATATT
17606323 ATTTACATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTATACTTAATA
Found at i:17611165 original size:17 final size:17
Alignment explanation
Indices: 17611112--17611165 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
17611102 CTAAATAGAT
17611112 TAAATATTAAAATAAT--
1 TAAA-ATTAAAATAATAC
* *
17611128 TACAATTAAAATAATAG
1 TAAAATTAAAATAATAC
17611145 TAAAATTAACAATAA-AC
1 TAAAATTAA-AATAATAC
17611162 TAAA
1 TAAA
17611166 TTAGGCGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 11 0.34
16 3 0.09
17 13 0.41
18 5 0.16
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAATTAAAATAATAC
Found at i:17613525 original size:31 final size:30
Alignment explanation
Indices: 17613467--17613525 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
17613457 TAAAATAAAC
*
17613467 TATTTAACCAATGTGAAAATCCAATTAAGCA
1 TATTTAACCAATGT-AAAATACAATTAAGCA
17613498 TATTTAACCAATG-ATAAATACATATTAA
1 TATTTAACCAATGTA-AAATACA-ATTAA
17613526 TTGAATACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 1 0.04
30 6 0.24
31 18 0.72
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (30 bp):
TATTTAACCAATGTAAAATACAATTAAGCA
Found at i:17613734 original size:29 final size:29
Alignment explanation
Indices: 17613701--17613756 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
17613691 CTGAATGTAA
*
17613701 CATTAGTCTAAACAAGCTATGGTTCATAG
1 CATTAGTCTAAACAAGCTATGATTCATAG
17613730 CATTAGTCTAAACAAGCTATGATTCAT
1 CATTAGTCTAAACAAGCTATGATTCAT
17613757 GAAGGTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (29 bp):
CATTAGTCTAAACAAGCTATGATTCATAG
Found at i:17613765 original size:29 final size:29
Alignment explanation
Indices: 17613704--17613765 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
17613694 AATGTAACAT
* * *
17613704 TAGTCTAAACAAGCTATGGTTCATAGCAT
1 TAGTCTAAACAAGCTATGATTCATAGAAG
17613733 TAGTCTAAACAAGCTATGATTCAT-GAAGG
1 TAGTCTAAACAAGCTATGATTCATAGAA-G
17613762 TAGT
1 TAGT
17613766 AAGATTAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (29 bp):
TAGTCTAAACAAGCTATGATTCATAGAAG
Found at i:17622973 original size:18 final size:18
Alignment explanation
Indices: 17622939--17622973 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17622929 TCAAAAGCCA
* *
17622939 AACCAAATGGCCTTATTC
1 AACCAAATGACCCTATTC
17622957 AACCAAATGACCCTATT
1 AACCAAATGACCCTATT
17622974 TACAATCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.26
Consensus pattern (18 bp):
AACCAAATGACCCTATTC
Found at i:17623271 original size:41 final size:41
Alignment explanation
Indices: 17623205--17623530 Score: 311
Period size: 41 Copynumber: 8.0 Consensus size: 41
17623195 TTGTGTTTTA
* * * * * *
17623205 GGGGCTTTAGTGGCATTTTTCAAAAAGCGTCGCTAAGGCAT
1 GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT
*
17623246 GGGGATTTAGCGGCGTTTTTGAAAAAGAGCCGCTAATGCAT
1 GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT
*
17623287 GGGGATTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCAT
1 GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT
* *
17623328 GGGGATTTAGCGGTGTTTTTGAAAAAGCACCGCTAATGC-T
1 GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT
* * * * *
17623368 CGGGGCTTTAGCGACGTTTTTGAAAAAGTGTCGCTGATGC-T
1 -GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT
* * **
17623409 CGGGGCTTTAGCGGCGTTTTTGAAGAAGCGTTGCTAATGC-T
1 -GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT
***** *
17623450 CTATTTTTAGCGGCGTCTTTT-AAAAAGCGCCGCTAGTGC-T
1 GGGGATTTAGCGGCGT-TTTTGAAAAAGCGCCGCTAATGCAT
** * *
17623490 CGAGGTCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGC
1 -G-GGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
17623531 TCTATTTTAG
Statistics
Matches: 240, Mismatches: 40, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
40 27 0.11
41 186 0.77
42 27 0.11
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (41 bp):
GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCAT
Found at i:17623478 original size:40 final size:40
Alignment explanation
Indices: 17623251--17623562 Score: 216
Period size: 41 Copynumber: 7.7 Consensus size: 40
17623241 GGCATGGGGA
* *****
17623251 TTTAGCGGCGTTTTTGAAAAAGAGCCGCTAATGCATGGGGA
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-TCTATT
* *****
17623292 TTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCATGGGGA
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-TCTATT
* * ****
17623333 TTTAGCGGTGTTTTTGAAAAAGCACCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-TATT
* * * * ****
17623374 TTTAGCGACGTTTTTGAAAAAGTGTCGCTGATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-TATT
* **
17623415 TTTAGCGGCGTTTTTGAAGAAGCGTTGCTAATGCTCTATT
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATT
* * *
17623455 TTTAGCGGCGTCTTTT-AAAAAGCGCCGCTAGTGCTCGAGGTC
1 TTTAGCGGCGT-TTTTGAAAAAGCGCCGCTAATGCTCTA--TT
* *
17623497 TTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCTA-T
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATT
* *
17623536 TTTAGCGACG-TTTTCAAAAAGCGCCGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGC
17623563 AAAAAATATT
Statistics
Matches: 229, Mismatches: 37, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
38 15 0.07
39 8 0.03
40 29 0.13
41 147 0.64
42 30 0.13
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATT
Found at i:17623953 original size:22 final size:23
Alignment explanation
Indices: 17623903--17623981 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 23
17623893 ATATTGTTTA
17623903 GAGTTTAAGGTTTA-GGAGTTACT
1 GAGTTTAAGGTTTATGGAGTTA-T
*
17623926 -ATTTTAAGGTTTATGGA-TTAT
1 GAGTTTAAGGTTTATGGAGTTAT
* * *
17623947 GAGTTTAGGGGTTAT-GATTTAT
1 GAGTTTAAGGTTTATGGAGTTAT
*
17623969 G-GTTTATGGTTTA
1 GAGTTTAAGGTTTA
17623982 AAGGCTGGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 13 0.28
22 31 0.66
23 3 0.06
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.47
Consensus pattern (23 bp):
GAGTTTAAGGTTTATGGAGTTAT
Found at i:17623974 original size:7 final size:7
Alignment explanation
Indices: 17623928--17623981 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
17623918 GAGTTACTAT
*
17623928 TTTAAGG
1 TTTATGG
17623935 TTTATGG
1 TTTATGG
*
17623942 ATTATGAG
1 TTTATG-G
*
17623950 TTTAGGG
1 TTTATGG
* *
17623957 GTTATGA
1 TTTATGG
17623964 TTTATGG
1 TTTATGG
17623971 TTTATGG
1 TTTATGG
17623978 TTTA
1 TTTA
17623982 AAGGCTGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:17624022 original size:29 final size:27
Alignment explanation
Indices: 17623989--17624052 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
17623979 TTAAAGGCTG
17623989 GGGTTTAAGGTTTAGAGGTTATGTGTTAA
1 GGGTTTAAGGTTTA-AGGTTATG-GTTAA
* * *
17624018 GGGTTTTAGGGTTTAAGTTTATGGTTTA
1 GGG-TTTAAGGTTTAAGGTTATGGTTAA
17624046 GGGTTTA
1 GGGTTTA
17624053 GATTAACTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 7 0.23
29 10 0.32
30 10 0.32
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.45
Consensus pattern (27 bp):
GGGTTTAAGGTTTAAGGTTATGGTTAA
Found at i:17624051 original size:14 final size:14
Alignment explanation
Indices: 17623870--17624052 Score: 70
Period size: 14 Copynumber: 12.9 Consensus size: 14
17623860 TATCACTATA
* *
17623870 GTTTAAGGTTTTTG
1 GTTTAGGGTTTATG
* *
17623884 GTTTAGGGTATATT
1 GTTTAGGGTTTATG
* *
17623898 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
17623912 GTTTAGGAGTTACTAT-
1 GTTTAGG-GTT--TATG
*
17623928 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
* * *
17623941 GATTATGAGTTTAGG
1 GTTTA-GGGTTTATG
* * *
17623956 GGTTATGATTTATG
1 GTTTAGGGTTTATG
* *
17623970 GTTTATGGTTTAAAG
1 GTTTAGGGTTT-ATG
* * *
17623985 G-CTGGGGTTTAAG
1 GTTTAGGGTTTATG
17623998 GTTTAGAGG-TTATG
1 GTTTAG-GGTTTATG
* *
17624012 TGTTAAGGGTTTTAGG
1 -GTTTAGGG-TTTATG
*
17624028 GTTTA-AGTTTATG
1 GTTTAGGGTTTATG
17624041 GTTTAGGGTTTA
1 GTTTAGGGTTTA
17624053 GATTAACTAG
Statistics
Matches: 121, Mismatches: 35, Indels: 26
0.66 0.19 0.14
Matches are distributed among these distances:
12 3 0.02
13 14 0.12
14 66 0.55
15 32 0.26
16 4 0.03
17 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:17647662 original size:87 final size:86
Alignment explanation
Indices: 17647514--17647705 Score: 285
Period size: 87 Copynumber: 2.2 Consensus size: 86
17647504 TCCTTCTACT
* * * ** *
17647514 TTATAAAAGTTGAAAATTTGGTCTGGTTGTTGATGAATGCATGAACTTGAACTGTTGATTTTTTT
1 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGATAAATGCATGAACTTGAACCATTGA-TTTTTG
17647579 CTAATTTGTTGCACATAAGTTG
65 CTAATTTGTTGCACATAAGTTG
* *
17647601 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTTATTTTTGC
1 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGATAAATGCATGAACTTGAACCATTGATTTTTGC
*
17647666 TAATTTGTTGCATATAAGTTG
66 TAATTTGTTGCACATAAGTTG
*
17647687 TTATAAATATTGAAAATTT
1 TTATAAAAATTGAAAATTT
17647706 TCTTTTTTAG
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 44 0.46
87 51 0.54
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (86 bp):
TTATAAAAATTGAAAATTTAGTCTGGTTGTTGATAAATGCATGAACTTGAACCATTGATTTTTGC
TAATTTGTTGCACATAAGTTG
Done.