Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 195 of 208
Found at i:59367207 original size:20 final size:20
Alignment explanation
Indices: 59367176--59367248 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
59367166 CTCTCACAAC
59367176 AAAAATTACAAAATAATTATA
1 AAAAATT-CAAAATAATTATA
*
59367197 AAAAATTCAAAATAATT-TT
1 AAAAATTCAAAATAATTATA
* * * *
59367216 TAAATTTTAAAATATTTATA
1 AAAAATTCAAAATAATTATA
*
59367236 AAAATTTCAAAAT
1 AAAAATTCAAAAT
59367249 TTATATTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 14 0.33
20 22 0.51
21 7 0.16
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTCAAAATAATTATA
Found at i:59367258 original size:25 final size:25
Alignment explanation
Indices: 59367230--59367279 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
59367220 TTTTAAAATA
* * * *
59367230 TTTATAAAAATTTCAAAATTTATAT
1 TTTAAAAAAAATTAAAAATATATAT
59367255 TTTAAAAAAAATTAAAAATATATAT
1 TTTAAAAAAAATTAAAAATATATAT
59367280 ATAAAAAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
TTTAAAAAAAATTAAAAATATATAT
Found at i:59370942 original size:11 final size:12
Alignment explanation
Indices: 59370928--59370964 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
59370918 TAGCAACTCA
59370928 ATTTT-ATAACT
1 ATTTTGATAACT
59370939 ATTTTGATAA-T
1 ATTTTGATAACT
*
59370950 ATTTTGATTACT
1 ATTTTGATAACT
59370962 ATT
1 ATT
59370965 ATTCCACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (12 bp):
ATTTTGATAACT
Found at i:59378103 original size:9 final size:9
Alignment explanation
Indices: 59378089--59378114 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
59378079 GCATTTCCTT
59378089 TTTATTTTA
1 TTTATTTTA
59378098 TTTATTTTA
1 TTTATTTTA
59378107 TTTATTTT
1 TTTATTTT
59378115 GTATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:59378985 original size:17 final size:16
Alignment explanation
Indices: 59378948--59378988 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
59378938 ATTACATAGG
59378948 TTTTATTTATTCATCT
1 TTTTATTTATTCATCT
59378964 TTTTATTTGATTC-TCT
1 TTTTATTT-ATTCATCT
59378980 TATTTATTT
1 T-TTTATTT
59378989 TAACCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTATTTATTCATCT
Found at i:59379044 original size:24 final size:27
Alignment explanation
Indices: 59379007--59379056 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
59378997 ATTATTGCAA
59379007 TATTGTTCAAGCA-TTT-AATATTTGT
1 TATTGTTCAAGCATTTTCAATATTTGT
*
59379032 TATT-TTCATGCATTTTCAATATTTG
1 TATTGTTCAAGCATTTTCAATATTTG
59379057 GATCTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 7 0.32
26 8 0.36
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (27 bp):
TATTGTTCAAGCATTTTCAATATTTGT
Found at i:59383293 original size:20 final size:20
Alignment explanation
Indices: 59383249--59383294 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
59383239 CAAAAAGCAA
* * *
59383249 AAAAAAATCAAAATCAAAGT
1 AAAAAAATAAAAATAAAAAT
*
59383269 CAAAAAATAAAAATAAAAAT
1 AAAAAAATAAAAATAAAAAT
59383289 AAAAAA
1 AAAAAA
59383295 GAGGAGAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (20 bp):
AAAAAAATAAAAATAAAAAT
Found at i:59384198 original size:13 final size:14
Alignment explanation
Indices: 59384164--59384196 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
59384154 CTTTGAGTCA
*
59384164 AAAAAATGAAAGTG
1 AAAAAATGAAAATG
59384178 AAAAAATGAAAATG
1 AAAAAATGAAAATG
59384192 AAAAA
1 AAAAA
59384197 TGGAGAGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAAAATGAAAATG
Found at i:59385603 original size:88 final size:88
Alignment explanation
Indices: 59385440--59385748 Score: 429
Period size: 88 Copynumber: 3.5 Consensus size: 88
59385430 AACAGATCAA
* * * * *
59385440 TGAAGACAACAGATCTTGCCTTCATACATTGACAGGGAAGCAAATCAAAAACACAAACCTTGCCT
1 TGAAGACAACAGATCTTACCTTCATGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCT
*
59385505 CTCTCTGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * * *
59385528 TGAAGACAACAGATATTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTACCT
1 TGAAGACAACAGATCTTACCTTCATGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCT
*
59385593 TTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
** * *
59385616 CAAAGACAATAGATCTTACCTTCATGCCTTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCT
1 TGAAGACAACAGATCTTACCTTCATGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCT
59385681 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* ** * *
59385704 TGAAGATAACAGATCTTACCTTCCCGCATTGACATCGGAGCAGAT
1 TGAAGACAACAGATCTTACCTTCATGCATTGACAGCGAAGCAGAT
59385749 TGAAGCTAGT
Statistics
Matches: 192, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 192 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (88 bp):
TGAAGACAACAGATCTTACCTTCATGCATTGACAGCGAAGCAGATCAAAGACACAAACCTTGCCT
CTCTCGGTTGTAGTGGAGCTGGT
Found at i:59387679 original size:17 final size:16
Alignment explanation
Indices: 59387642--59387682 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
59387632 ATTACATAGG
59387642 TTTTATTTATTCGTCT
1 TTTTATTTATTCGTCT
59387658 TTTTATTTGATTC-TCT
1 TTTTATTT-ATTCGTCT
59387674 TATTTATTT
1 T-TTTATTT
59387683 TAACCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTTATTTATTCGTCT
Found at i:59387738 original size:24 final size:27
Alignment explanation
Indices: 59387701--59387750 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
59387691 ATTATTGCAA
59387701 TATTGTTCAAGCA-TTT-AATATTTGT
1 TATTGTTCAAGCATTTTCAATATTTGT
*
59387726 TATT-TTCATGCATTTTCAATATTTG
1 TATTGTTCAAGCATTTTCAATATTTG
59387751 GATCTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 7 0.32
26 8 0.36
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (27 bp):
TATTGTTCAAGCATTTTCAATATTTGT
Found at i:59389009 original size:16 final size:16
Alignment explanation
Indices: 59388988--59389029 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
59388978 ATATCATCTG
*
59388988 GCTCGCTACTCCGCTA
1 GCTCGCCACTCCGCTA
* *
59389004 GCTCGCCACTCCTCTT
1 GCTCGCCACTCCGCTA
59389020 GCTCGCCACT
1 GCTCGCCACT
59389030 TCCCCAACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.10, C:0.48, G:0.17, T:0.26
Consensus pattern (16 bp):
GCTCGCCACTCCGCTA
Found at i:59390941 original size:54 final size:54
Alignment explanation
Indices: 59390874--59391819 Score: 824
Period size: 54 Copynumber: 17.5 Consensus size: 54
59390864 CTCAATTTAC
* * * ***
59390874 TACTTACAGGATTTTTCGAATCTTGCAGTTTGCCGATTTAAGATTATAACCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* * * * *
59390928 TACTTACAAGATTTTTCGAATCTTGCAGCTCGTCAATTTAATATCACAACCTTG
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
** * * *
59390982 TACTTACAAGATTTTTCGAATCTTGTGGCTCACCGATTTAAGATCACAGCCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* * * * * * *
59391036 TACTTATAAGATTTTTTGAATGTTGCAGTTGGTCGATTTAAAATCGCAACCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* ** * *
59391090 TACTTACAAGATTTTTCGAATCTTGC-GACTCACTAATTTAATATCGCAGCCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAG-CTCGCCGATTTAAGATCGCAACCTTA
* * * * * * ** *
59391144 TACTTACAGGATTTTTCGACTCTTGCAACTCACCGATTTTAGATCACATGCTTG
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* * * * * *
59391198 TACTTACACGATTTTTTGAATCTTAG-GGCTCGTCGATTTAAAATCGCAGCCTTA
1 TACTTACAAGATTTTTCGAATCTT-GCAGCTCGCCGATTTAAGATCGCAACCTTA
* * **
59391252 TACTTACAAGATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATTGCAGTCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* *** * * *
59391306 TACTTACAAGATTTTTCAAATCTTATGGCTCGCCGATTTAATATTGCAGCCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* * ** * * * * * *
59391360 TACTTATAAGATTTTTTGAATCTTGTGGTTGGCCAATTTAGGATCTCAAACTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* * * * *
59391414 TACTTACAAGATTTTTTGAATCTTGCAACTTGCCGATTTAGGATC-AAACCCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAA-CCTTA
* * * * * * *
59391468 TACTTATAGGATTTTTCAAATCTTGCAGTTTGTCGATTTAAGATTGCAACCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
59391522 TACTTACAAGACTTTTT-GAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
1 TACTTACAAGA-TTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* * * * * *
59391576 TACTTATAAGA-TTTTCTGAATCTTGCGGTTGGCCAATTTAATATCGCAACCTTA
1 TACTTACAAGATTTTTC-GAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* * * * * *
59391630 TACTTACAATA-TTTTCTAAATCTTGCGGCTCACCAATTTAAGATCGCAGCCTTA
1 TACTTACAAGATTTTTC-GAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
** * * ** * ** * * *
59391684 TACTTGTAGGATTTTCCGAATCTTGCAATTTGCATATTTAAGACCACAATCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* * ** * *
59391738 TACTTACAAGATTTTTTGAATCTTGCGGCTCATCGATTTAAGATCTCAGCCTTA
1 TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
* *
59391792 TACTTACAAGATTTCTAGAATCTTGCAG
1 TACTTACAAGATTTTTCGAATCTTGCAG
59391820 TTGTTGGTTT
Statistics
Matches: 717, Mismatches: 165, Indels: 20
0.79 0.18 0.02
Matches are distributed among these distances:
52 4 0.01
53 4 0.01
54 697 0.97
55 12 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (54 bp):
TACTTACAAGATTTTTCGAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTA
Found at i:59391063 original size:108 final size:108
Alignment explanation
Indices: 59390874--59391821 Score: 907
Period size: 108 Copynumber: 8.8 Consensus size: 108
59390864 CTCAATTTAC
* * * * *** * *
59390874 TACTTACAGGATTTTTCGAATCTTGCAGTTTGCCGATTTAAGATTATAACCTTATACTTACAAGA
1 TACTTACAAGATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAGA
* * * * *
59390939 TTTTTCGAATCTTGCAGCTCGTCAATTTAATATCACAACCTTG
66 TTTTTCGAATCTTGCAGTTCGCCAATTTAAGATCGCAACCTTA
* * *
59390982 TACTTACAAGATTTTTCGAATCTTGTGGCTCACCGATTTAAGATCACAGCCTTATACTTATAAGA
1 TACTTACAAGATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAGA
* * * * * *
59391047 TTTTTTGAATGTTGCAGTTGGTCGATTTAAAATCGCAACCTTA
66 TTTTTCGAATCTTGCAGTTCGCCAATTTAAGATCGCAACCTTA
* * ** * * *
59391090 TACTTACAAGATTTTTCGAATCTTGCGACTCACTAATTTAATATCGCAGCCTTATACTTACAGGA
1 TACTTACAAGATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAGA
* ** * * * * ** *
59391155 TTTTTCGACTCTTGCAACTCACCGATTTTAGATCACATGCTTG
66 TTTTTCGAATCTTGCAGTTCGCCAATTTAAGATCGCAACCTTA
* * * * *
59391198 TACTTACACGATTTTTTGAATCTTAG-GGCTCGTCGATTTAAAATCGCAGCCTTATACTTACAAG
1 TACTTACAAGATTTTTCGAATCTT-GCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAG
* * * * **
59391262 ATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATTGCAGTCTTA
65 ATTTTTCGAATCTTGCAGTTCGCCAATTTAAGATCGCAACCTTA
* ** * *
59391306 TACTTACAAGATTTTTCAAATCTTATGGCTCGCCGATTTAATATTGCAGCCTTATACTTATAAGA
1 TACTTACAAGATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAGA
* ** * * * *
59391371 TTTTTTGAATCTTGTGGTTGGCCAATTTAGGATCTCAAACTTA
66 TTTTTCGAATCTTGCAGTTCGCCAATTTAAGATCGCAACCTTA
* ** * * ** * *
59391414 TACTTACAAGATTTTTTGAATCTTGCAACTTGCCGATTTAGGATCAAACCCTTATACTTATAGGA
1 TACTTACAAGATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAGA
* * * * *
59391479 TTTTTCAAATCTTGCAGTTTGTCGATTTAAGATTGCAACCTTA
66 TTTTTCGAATCTTGCAGTTCGCCAATTTAAGATCGCAACCTTA
* *
59391522 TACTTACAAGACTTTTT-GAATCTTGCAGCTCGCCGATTTAAGATCGCAACCTTATACTTATAAG
1 TACTTACAAGA-TTTTTCGAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAG
* * *
59391586 A-TTTTCTGAATCTTGCGGTTGGCCAATTTAATATCGCAACCTTA
65 ATTTTTC-GAATCTTGCAGTTCGCCAATTTAAGATCGCAACCTTA
* * * * * *
59391630 TACTTACAATA-TTTTCTAAATCTTGCGGCTCACCAATTTAAGATCGCAGCCTTATACTTGTAGG
1 TACTTACAAGATTTTTC-GAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAG
* * * * * *
59391694 ATTTTCCGAATCTTGCAATTTG-CATATTTAAGACCACAATCTTA
65 ATTTTTCGAATCTTGCAGTTCGCCA-ATTTAAGATCGCAACCTTA
* ** * *
59391738 TACTTACAAGATTTTTTGAATCTTGCGGCTCATCGATTTAAGATCTCAGCCTTATACTTACAAGA
1 TACTTACAAGATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAGA
* *
59391803 TTTCTAGAATCTTGCAGTT
66 TTTTTCGAATCTTGCAGTT
59391822 GTTGGTTTAA
Statistics
Matches: 686, Mismatches: 145, Indels: 18
0.81 0.17 0.02
Matches are distributed among these distances:
106 4 0.01
107 7 0.01
108 661 0.96
109 14 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (108 bp):
TACTTACAAGATTTTTCGAATCTTGCGGCTCGCCGATTTAAGATCGCAGCCTTATACTTATAAGA
TTTTTCGAATCTTGCAGTTCGCCAATTTAAGATCGCAACCTTA
Found at i:59391913 original size:68 final size:68
Alignment explanation
Indices: 59391799--59391936 Score: 186
Period size: 68 Copynumber: 2.0 Consensus size: 68
59391789 TTATACTTAC
* * **** *
59391799 AAGATTTCTAGAATCTTGCAGTTGTTGGTTTAAGATCACAATTTTCTCATGCAATTGATTTCAAC
1 AAGATTTCCAAAATCTTGCAGTTGCCAATTTAAGATCACAACTTTCTCATGCAATTGATTTCAAC
59391864 TTT
66 TTT
* * *
59391867 AAGATTTCCAAAATCTTGCAGTTGCCAATTTAAGATCGCAACTTTCTCATGCAGTTGATTTCAAT
1 AAGATTTCCAAAATCTTGCAGTTGCCAATTTAAGATCACAACTTTCTCATGCAATTGATTTCAAC
59391932 TTT
66 TTT
59391935 AA
1 AA
59391937 AGTAGCAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (68 bp):
AAGATTTCCAAAATCTTGCAGTTGCCAATTTAAGATCACAACTTTCTCATGCAATTGATTTCAAC
TTT
Found at i:59392623 original size:32 final size:31
Alignment explanation
Indices: 59392571--59392672 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 31
59392561 TTTTTAGATG
59392571 TTGATTAGTAC-AATCCTTGAAAATATTGGGA
1 TTGATTAGTACAAATCCTTGAAAA-ATTGGGA
59392602 TTGATTAGTACAAATCCTTGAAAAAATTGGGA
1 TTGATTAGTACAAATCCTTG-AAAAATTGGGA
* * *
59392634 TTGATTAATACAAACCCTTGAAGAAATTAGGA
1 TTGATTAGTACAAATCCTTGAA-AAATTGGGA
59392666 TTGATTA
1 TTGATTA
59392673 AAAATTTAAC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
31 13 0.20
32 48 0.74
33 4 0.06
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (31 bp):
TTGATTAGTACAAATCCTTGAAAAATTGGGA
Found at i:59394361 original size:20 final size:20
Alignment explanation
Indices: 59394338--59394377 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
59394328 TTGAGTTTCG
59394338 ATTAAAT-TTTAATTTTAAAA
1 ATTAAATATTTAA-TTTAAAA
59394358 ATTAAATATTTAATTTAAAA
1 ATTAAATATTTAATTTAAAA
59394378 TAATTGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAAATATTTAATTTAAAA
Found at i:59399153 original size:13 final size:13
Alignment explanation
Indices: 59399137--59399189 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
59399127 TTTAAACCAA
59399137 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
59399150 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
59399163 ACTTTT-ACACAGC
1 ACTTTTCA-AAAGC
59399176 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
59399189 A
1 A
59399190 ATGAAGAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 1 0.03
13 32 0.94
14 1 0.03
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:59399639 original size:11 final size:11
Alignment explanation
Indices: 59399625--59399664 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
59399615 ATTTTGATGA
*
59399625 TATTTTGTTAC
1 TATTTTGCTAC
*
59399636 TATTTTGCTAT
1 TATTTTGCTAC
*
59399647 TATATTGCTAC
1 TATTTTGCTAC
59399658 TATTTTG
1 TATTTTG
59399665 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (11 bp):
TATTTTGCTAC
Found at i:59399671 original size:22 final size:21
Alignment explanation
Indices: 59399595--59399672 Score: 75
Period size: 22 Copynumber: 3.6 Consensus size: 21
59399585 GTTACTGTTG
* *
59399595 TTTTGTTGTTATTTGTTGCCA
1 TTTTGTTGTTATTTGTTACTA
* *
59399616 TTTTGATGATATTTTGTTACTA
1 TTTTGTTGTTA-TTTGTTACTA
* * *
59399638 TTTTGCTATTATATTGCTACTA
1 TTTTGTTGTTAT-TTGTTACTA
59399660 TTTTGTTGTTATT
1 TTTTGTTGTTATT
59399673 GTTTAGATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 11 0.24
22 34 0.76
ACGTcount: A:0.17, C:0.08, G:0.14, T:0.62
Consensus pattern (21 bp):
TTTTGTTGTTATTTGTTACTA
Found at i:59405672 original size:16 final size:16
Alignment explanation
Indices: 59405639--59405668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59405629 ATGTGTCTAT
59405639 TTTTTTAAGATATTTA
1 TTTTTTAAGATATTTA
59405655 TTTTTTAA-ATATTT
1 TTTTTTAAGATATTT
59405669 TATTATACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTTTAAGATATTTA
Found at i:59406274 original size:15 final size:16
Alignment explanation
Indices: 59406249--59406278 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59406239 TCAAAATTAT
59406249 TAAAAATTGTAAAATA
1 TAAAAATTGTAAAATA
59406265 TAAAAA-TGTAAAAT
1 TAAAAATTGTAAAAT
59406279 TTTTTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
TAAAAATTGTAAAATA
Found at i:59406631 original size:27 final size:25
Alignment explanation
Indices: 59406588--59406662 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 25
59406578 TTACATTTTT
*
59406588 TTTAA-ATTATTATAATTTTTATAAC
1 TTTAATATTTTTA-AATTTTTATAAC
*
59406613 TTTAATCATTTTTTAAATTTTTAATGAC
1 TTTAAT-A-TTTTTAAATTTTT-ATAAC
*
59406641 TTTCATATTTTTAAATTATTTA
1 TTTAATATTTTTAAATT-TTTA
59406663 ATTTTTTCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
25 5 0.12
26 11 0.26
27 12 0.29
28 14 0.33
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTAATATTTTTAAATTTTTATAAC
Found at i:59408441 original size:2 final size:2
Alignment explanation
Indices: 59408434--59408466 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59408424 TCCTTTCTCT
59408434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59408467 TAATACATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59415888 original size:16 final size:16
Alignment explanation
Indices: 59415845--59415890 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
59415835 CCTTCCCCAC
* *
59415845 AAAA-AAAAAGAAAAG
1 AAAAGAAAAAGAGACG
59415860 AAAAGAAAAAGAGACG
1 AAAAGAAAAAGAGACG
59415876 AAAAGAAAAAGAGAC
1 AAAAGAAAAAGAGAC
59415891 AAATATTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAGACG
Found at i:59422613 original size:30 final size:28
Alignment explanation
Indices: 59422535--59422663 Score: 91
Period size: 30 Copynumber: 4.4 Consensus size: 28
59422525 TAAATTTTAA
* *
59422535 AATTATACA-TGAATTTTAATTTAATGTGT
1 AATTATATATTGAATTTTAATTTGA--TGT
* *
59422564 ACTTGTATATATGAATTTTAATTTGATGT
1 AATTATATAT-TGAATTTTAATTTGATGT
*
59422593 AATTATATATGTGAAATTTTAATTGTGGT-T
1 AATTATATAT-TG-AATTTTAATT-TGATGT
* * *
59422623 CAAATGTATACTTGAATTTTAATTTTGATTT
1 -AATTATATA-TTGAATTTTAA-TTTGATGT
59422654 AATTATATAT
1 AATTATATAT
59422664 ATTTAAATAA
Statistics
Matches: 79, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
29 20 0.25
30 29 0.37
31 29 0.37
32 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (28 bp):
AATTATATATTGAATTTTAATTTGATGT
Found at i:59424080 original size:20 final size:21
Alignment explanation
Indices: 59424055--59424095 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
59424045 ATATATGTAC
59424055 ATATATA-AGTTAT-AAAATAA
1 ATATATAGA-TTATGAAAATAA
59424075 ATATATAGATTATGAAAATAA
1 ATATATAGATTATGAAAATAA
59424096 TGATTACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
ATATATAGATTATGAAAATAA
Found at i:59424982 original size:19 final size:19
Alignment explanation
Indices: 59424946--59424983 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
59424936 TATTCGTTTG
*
59424946 TAACAAAAAATAATAAATA
1 TAACAAAAAATAACAAATA
59424965 TAACAGAAAAA-AACAAATA
1 TAACA-AAAAATAACAAATA
59424984 AAAATTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.16
Consensus pattern (19 bp):
TAACAAAAAATAACAAATA
Found at i:59426943 original size:2 final size:2
Alignment explanation
Indices: 59426936--59426967 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
59426926 CCTCTATCGC
*
59426936 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59426968 AACCTCCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59442331 original size:6 final size:6
Alignment explanation
Indices: 59442311--59442400 Score: 53
Period size: 6 Copynumber: 15.3 Consensus size: 6
59442301 TATCATTGAG
* * ** *
59442311 TTTATT ATTATT TTT-TA TTT-TT TTTCGT TTTA-T TTTATT TTTATA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * * *
59442356 TTTATC TTTATT TTTAAT TTTGTT TTAATT GCTTT-TT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT --TTTATT TTTATT TT
59442401 CTTAAACTTA
Statistics
Matches: 64, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
5 16 0.25
6 44 0.69
7 2 0.03
8 2 0.03
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:59442369 original size:28 final size:28
Alignment explanation
Indices: 59442311--59442369 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
59442301 TATCATTGAG
* *
59442311 TTTATTATTATTTTTTATTTTTTTTCGT
1 TTTATTATTATTTTTTATTTTCTTTCAT
59442339 TTTATT-TTATTTTTATATTTATCTTT-AT
1 TTTATTATTATTTTT-TATTT-TCTTTCAT
59442367 TTT
1 TTT
59442370 TAATTTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 15 0.56
29 4 0.15
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (28 bp):
TTTATTATTATTTTTTATTTTCTTTCAT
Found at i:59448887 original size:18 final size:20
Alignment explanation
Indices: 59448866--59448904 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
59448856 ATGTTTTTTT
59448866 ATAGA-GACATAATT-TTCA
1 ATAGAGGACATAATTATTCA
*
59448884 ATAGAGGTCATAATTATTCA
1 ATAGAGGACATAATTATTCA
59448904 A
1 A
59448905 CTAATATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
ATAGAGGACATAATTATTCA
Found at i:59448918 original size:22 final size:22
Alignment explanation
Indices: 59448891--59448933 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59448881 TCAATAGAGG
*
59448891 TCATAATTATTCAACTAATATC
1 TCATAACTATTCAACTAATATC
* *
59448913 TCATAACTATTCGAGTAATAT
1 TCATAACTATTCAACTAATAT
59448934 TATTTGTATA
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:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (22 bp):
TCATAACTATTCAACTAATATC
Found at i:59454204 original size:20 final size:20
Alignment explanation
Indices: 59454182--59454294 Score: 93
Period size: 20 Copynumber: 5.5 Consensus size: 20
59454172 CTTTTTTTTT
*
59454182 TATTCTTTCATAATTTTTGT
1 TATTCTTTCATAATTTTTGG
* *
59454202 TATTTTTTTTTATAA-TTTTGG
1 TA--TTCTTTCATAATTTTTGG
* *
59454223 ATATACTTTCATAATTATTGG
1 -TATTCTTTCATAATTTTTGG
* * *
59454244 TAATCTCTCATAATTTTTAG
1 TATTCTTTCATAATTTTTGG
*
59454264 TATTTTTTTCATAATTTTTGG
1 TA-TTCTTTCATAATTTTTGG
*
59454285 TATGCTTTCA
1 TATTCTTTCA
59454295 AAATAAAATT
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
20 33 0.47
21 26 0.37
22 11 0.16
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.59
Consensus pattern (20 bp):
TATTCTTTCATAATTTTTGG
Found at i:59455087 original size:20 final size:20
Alignment explanation
Indices: 59454964--59455091 Score: 69
Period size: 20 Copynumber: 6.4 Consensus size: 20
59454954 TATGATAGGA
* *
59454964 TACCAAGAATTATAAGAAAG
1 TACCAAAAATTATAAGGAAG
* * *
59454984 TACCAAAATTTATAAAGAAC
1 TACCAAAAATTATAAGGAAG
* * *
59455004 TGCCAAAACTTATGA-GAATG
1 TACCAAAAATTATAAGGAA-G
* * * * *
59455024 AATCAAAATTTATGAGGAAA
1 TACCAAAAATTATAAGGAAG
** * * *
59455044 TACCAAAAAACACAATGAAT
1 TACCAAAAATTATAAGGAAG
*
59455064 TACCAAAAATTATGAGGAAG
1 TACCAAAAATTATAAGGAAG
59455084 TACCAAAA
1 TACCAAAA
59455092 GATGTATAAA
Statistics
Matches: 77, Mismatches: 29, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
19 3 0.04
20 71 0.92
21 3 0.04
ACGTcount: A:0.53, C:0.13, G:0.12, T:0.21
Consensus pattern (20 bp):
TACCAAAAATTATAAGGAAG
Found at i:59455149 original size:20 final size:20
Alignment explanation
Indices: 59455113--59455166 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
59455103 CGTTACAACA
** *
59455113 AAATA-CAAAAAAAATGAGT
1 AAATACCAAAAATTATGAGC
*
59455132 AAGTACCAAAAATTATGAGC
1 AAATACCAAAAATTATGAGC
*
59455152 AAATACTAAAAATTA
1 AAATACCAAAAATTA
59455167 CGAGGGATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (20 bp):
AAATACCAAAAATTATGAGC
Found at i:59455257 original size:21 final size:21
Alignment explanation
Indices: 59455213--59455317 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 21
59455203 TGGATGCACC
* *
59455213 AAAAATTATGA-AGATGTACAA
1 AAAAATTATGAGAGA-ATACTA
59455234 AAAAATTATGAGAGAATACTA
1 AAAAATTATGAGAGAATACTA
59455255 AAAAA-TATGAG-GAAGTAC--
1 AAAAATTATGAGAGAA-TACTA
*
59455273 CAAAATTATGAGAGAATACTA
1 AAAAATTATGAGAGAATACTA
* * *
59455294 TAAAATT-TGAG-GAAAAATA
1 AAAAATTATGAGAGAATACTA
59455313 AAAAA
1 AAAAA
59455318 AAAATGATGA
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.06
19 22 0.31
20 16 0.23
21 26 0.37
22 3 0.04
ACGTcount: A:0.58, C:0.05, G:0.15, T:0.22
Consensus pattern (21 bp):
AAAAATTATGAGAGAATACTA
Found at i:59455264 original size:41 final size:39
Alignment explanation
Indices: 59455213--59455299 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
59455203 TGGATGCACC
* *
59455213 AAAAATTATGAAGATGTACAAAAAAATTATGAGAGAATACT
1 AAAAAATATGAAGAAGTAC--AAAAATTATGAGAGAATACT
* *
59455254 AAAAAATATGAGGAAGTACCAAAATTATGAGAGAATACT
1 AAAAAATATGAAGAAGTACAAAAATTATGAGAGAATACT
*
59455293 ATAAAAT
1 AAAAAAT
59455300 TTGAGGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
39 25 0.61
41 16 0.39
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.23
Consensus pattern (39 bp):
AAAAAATATGAAGAAGTACAAAAATTATGAGAGAATACT
Found at i:59455265 original size:20 final size:19
Alignment explanation
Indices: 59455233--59455371 Score: 75
Period size: 20 Copynumber: 6.9 Consensus size: 19
59455223 AAGATGTACA
59455233 AAAAAATTATGAGAGAATACT
1 AAAAAA-TATGAG-GAATACT
59455254 AAAAAATATGAGGAAGTAC-
1 AAAAAATATGAGGAA-TACT
* *
59455273 CAAAATTATGAGAGAATACT
1 AAAAAATATGAG-GAATACT
* * * *
59455293 ATAAAATTTGAGGAAAAAT
1 AAAAAATATGAGGAATACT
* * * *
59455312 AAAAAAAAAATGATGATGTACC
1 --AAAAAATATGAGGA-ATACT
*
59455334 AAAACATATGAGGAAGTAC-
1 AAAAAATATGAGGAA-TACT
59455353 AAAAAATTATGAGGGAATA
1 AAAAAA-TATGA-GGAATA
59455372 TCAAATACCA
Statistics
Matches: 88, Mismatches: 21, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
19 26 0.30
20 41 0.47
21 20 0.23
22 1 0.01
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (19 bp):
AAAAAATATGAGGAATACT
Found at i:59455278 original size:60 final size:57
Alignment explanation
Indices: 59455195--59455371 Score: 140
Period size: 60 Copynumber: 2.9 Consensus size: 57
59455185 AGGAATTACC
* * * *
59455195 AAAAAATGTGGATGCACCAAAAATTATGAAGATGTACAAAAAAATTATGAGAGAATACTAA
1 AAAAAATGAGGAAGTACC-AAAATTATGAAGA-GTAC-AAAAAATTATGAGAGAATA-AAA
* * * *
59455256 AAAATATGAGGAAGTACCAAAATTATGAGAGAATACTATAAAATT-TGAGGAAAAATAAAA
1 AAAAAATGAGGAAGTACCAAAATTATGA-AGAGTAC-AAAAAATTATGA-G-AGAATAAAA
* * * * *
59455316 AAAAAATGATGATGTACCAAAACATATGAGGAAGTACAAAAAATTATGAGGGAATA
1 AAAAAATGAGGAAGTACCAAAA-TTATGAAG-AGTACAAAAAATTATGAGAGAATA
59455372 TCAAATACCA
Statistics
Matches: 92, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
59 7 0.08
60 51 0.55
61 34 0.37
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.21
Consensus pattern (57 bp):
AAAAAATGAGGAAGTACCAAAATTATGAAGAGTACAAAAAATTATGAGAGAATAAAA
Found at i:59455284 original size:19 final size:20
Alignment explanation
Indices: 59455234--59455304 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
59455224 AGATGTACAA
59455234 AAAAATTATGAGAGAATACT
1 AAAAATTATGAGAGAATACT
*
59455254 AAAAAATATGAG-GAAGTAC-
1 AAAAATTATGAGAGAA-TACT
*
59455273 CAAAATTATGAGAGAATACT
1 AAAAATTATGAGAGAATACT
59455293 ATAAAATT-TGAG
1 A-AAAATTATGAG
59455305 GAAAAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 16 0.37
20 21 0.49
21 6 0.14
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.24
Consensus pattern (20 bp):
AAAAATTATGAGAGAATACT
Found at i:59455758 original size:20 final size:20
Alignment explanation
Indices: 59455702--59455743 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
59455692 CTTGAGTAAA
*
59455702 TATAAAAAA-AATGAGGATG
1 TATAAAAAATGATGAGGATG
59455721 TATAAAAAATGATGAGGATG
1 TATAAAAAATGATGAGGATG
59455741 TAT
1 TAT
59455744 CCAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.26
Consensus pattern (20 bp):
TATAAAAAATGATGAGGATG
Found at i:59459461 original size:75 final size:75
Alignment explanation
Indices: 59459382--59459527 Score: 220
Period size: 75 Copynumber: 1.9 Consensus size: 75
59459372 GGAAATATTG
* ** * *
59459382 AAAGTGAGCCCAGCTCTAGTTGGATAAACCAATAATGTTTGTGCCTAGCGCTAGTCGGATATACC
1 AAAGTGAGCCCAGCTCTAGTTGGATAAACCAACAATGTTTGCACCCAGCGCTAGTCGGATAAACC
59459447 GACGATAATA
66 GACGATAATA
* **
59459457 AAAGTGAGCCCAGCTCTAGTTGGATGAACCAACGGTGTTTGCACCCAGCGCTAGTCGGATAAACC
1 AAAGTGAGCCCAGCTCTAGTTGGATAAACCAACAATGTTTGCACCCAGCGCTAGTCGGATAAACC
59459522 GACGAT
66 GACGAT
59459528 TGTGTACCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (75 bp):
AAAGTGAGCCCAGCTCTAGTTGGATAAACCAACAATGTTTGCACCCAGCGCTAGTCGGATAAACC
GACGATAATA
Found at i:59461530 original size:37 final size:37
Alignment explanation
Indices: 59461480--59461576 Score: 126
Period size: 37 Copynumber: 2.6 Consensus size: 37
59461470 AGTACATCAT
*
59461480 CAACAAAAGCTCATAGAGCT-AGTCCACCCGAACACAC
1 CAACAGAAGCTCATAGAGCTGA-TCCACCCGAACACAC
*
59461517 CAACAGAAGCTCATAGAGCTGATCCACCTGAACACAC
1 CAACAGAAGCTCATAGAGCTGATCCACCCGAACACAC
*
59461554 CAAC-GAAAACTCATAAGAGCTGA
1 CAACAG-AAGCTCAT-AGAGCTGA
59461577 ACAGAAGCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
36 1 0.02
37 44 0.81
38 9 0.17
ACGTcount: A:0.41, C:0.31, G:0.15, T:0.12
Consensus pattern (37 bp):
CAACAGAAGCTCATAGAGCTGATCCACCCGAACACAC
Found at i:59474882 original size:22 final size:22
Alignment explanation
Indices: 59474854--59474896 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
59474844 TCAGAATCGA
59474854 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
59474876 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
59474897 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:59476857 original size:24 final size:24
Alignment explanation
Indices: 59476830--59476880 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
59476820 CTTCACCAGG
59476830 AACTTTGAAACCTTCAGGTTGTTC
1 AACTTTGAAACCTTCAGGTTGTTC
59476854 AACTTTGAAACCTTCAGGTTGTTC
1 AACTTTGAAACCTTCAGGTTGTTC
59476878 AAC
1 AAC
59476881 ATAGATCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (24 bp):
AACTTTGAAACCTTCAGGTTGTTC
Found at i:59477943 original size:20 final size:21
Alignment explanation
Indices: 59477918--59477956 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59477908 AATTAAAAGT
*
59477918 TTAATTG-AATTGAAATTGCG
1 TTAATTGAAATTAAAATTGCG
59477938 TTAATTGAAATTAAAATTG
1 TTAATTGAAATTAAAATTG
59477957 TAAAGATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (21 bp):
TTAATTGAAATTAAAATTGCG
Found at i:59480336 original size:13 final size:12
Alignment explanation
Indices: 59480317--59480361 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
59480307 GAAAATAAAG
59480317 AAAATATAAAAT
1 AAAATATAAAAT
59480329 ATAAATATAAATAT
1 A-AAATATAAA-AT
*
59480343 AAAAAAATAAAAT
1 -AAAATATAAAAT
59480356 AAAATA
1 AAAATA
59480362 AAATTGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 6 0.21
13 11 0.39
14 10 0.36
15 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATATAAAAT
Found at i:59480342 original size:19 final size:18
Alignment explanation
Indices: 59480318--59480365 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
59480308 AAAATAAAGA
59480318 AAATATAAAATATAAATAT
1 AAATATAAAATATAAA-AT
*
59480337 AAATATAAAAAAATAAAAT
1 AAATAT-AAAATATAAAAT
59480356 AAA-ATAAAAT
1 AAATATAAAAT
59480366 TGTGTTGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 2 0.08
19 11 0.42
20 9 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATATAAAATATAAAAT
Found at i:59480356 original size:5 final size:5
Alignment explanation
Indices: 59480308--59480365 Score: 57
Period size: 5 Copynumber: 11.0 Consensus size: 5
59480298 AATATGTAAG
59480308 AAAAT AAAGA- AAATAT AAAAT ATAAAT ATAAAT ATAAA- AAAAT AAAAT
1 AAAAT AAA-AT AAA-AT AAAAT A-AAAT A-AAAT A-AAAT AAAAT AAAAT
59480356 AAAAT AAAAT
1 AAAAT AAAAT
59480366 TGTGTTGCCT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
4 3 0.06
5 26 0.54
6 19 0.40
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:59484504 original size:21 final size:21
Alignment explanation
Indices: 59484475--59484529 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
59484465 TTCTCTCAAA
*
59484475 CATCTAGCATCTAGCCATATC
1 CATCAAGCATCTAGCCATATC
*
59484496 CATCAAGCATCTGGCCATATC
1 CATCAAGCATCTAGCCATATC
*
59484517 CATCAAGCTTCTA
1 CATCAAGCATCTA
59484530 TTCTTTCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.27
Consensus pattern (21 bp):
CATCAAGCATCTAGCCATATC
Found at i:59485673 original size:35 final size:35
Alignment explanation
Indices: 59485633--59485703 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
59485623 ATAATTTGCC
*
59485633 TCTGGATCGCTAAGTCTTCTACAATGTGAGCAAGG
1 TCTGGATCGCTAAGCCTTCTACAATGTGAGCAAGG
59485668 TCTGGATCGCTAAGCCTTCTACAATGTGAGCAAGG
1 TCTGGATCGCTAAGCCTTCTACAATGTGAGCAAGG
59485703 T
1 T
59485704 GGATATCTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (35 bp):
TCTGGATCGCTAAGCCTTCTACAATGTGAGCAAGG
Found at i:59486886 original size:20 final size:21
Alignment explanation
Indices: 59486861--59486905 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
59486851 CTTAGTTCAT
59486861 ATCTAACT-AAGTAACAAAAC
1 ATCTAACTGAAGTAACAAAAC
*
59486881 ATCTAATTGAAGTAACAAAAC
1 ATCTAACTGAAGTAACAAAAC
59486902 ATCT
1 ATCT
59486906 GCATGATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (21 bp):
ATCTAACTGAAGTAACAAAAC
Found at i:59489118 original size:16 final size:15
Alignment explanation
Indices: 59489092--59489134 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
59489082 AATATGTGAC
59489092 ATATAAAAAAATTAT
1 ATATAAAAAAATTAT
59489107 ATATAAAGAAAATTAT
1 ATATAAA-AAAATTAT
*
59489123 AT-CAAAAAAATT
1 ATATAAAAAAATT
59489135 GGTTGATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.23
15 10 0.38
16 10 0.38
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
ATATAAAAAAATTAT
Found at i:59489132 original size:14 final size:13
Alignment explanation
Indices: 59489092--59489134 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 13
59489082 AATATGTGAC
59489092 ATATAAAAAAATTAT
1 ATATAAAAAAA-T-T
59489107 ATATAAAGAAAATT
1 ATATAAA-AAAATT
59489121 ATATCAAAAAAATT
1 ATAT-AAAAAAATT
59489135 GGTTGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.42
15 11 0.42
16 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (13 bp):
ATATAAAAAAATT
Found at i:59492416 original size:19 final size:20
Alignment explanation
Indices: 59492392--59492432 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
59492382 GAATTTAGGC
*
59492392 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
59492411 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
59492431 AA
1 AA
59492433 TTGTGTTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:59499044 original size:19 final size:20
Alignment explanation
Indices: 59499020--59499060 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
59499010 GAATTTAGGC
*
59499020 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
59499039 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
59499059 AA
1 AA
59499061 TTGCGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:59502959 original size:11 final size:11
Alignment explanation
Indices: 59502943--59502967 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59502933 TGATTCTTCA
59502943 TTTTTTTTATT
1 TTTTTTTTATT
59502954 TTTTTTTTATT
1 TTTTTTTTATT
59502965 TTT
1 TTT
59502968 GATGAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:59503657 original size:25 final size:25
Alignment explanation
Indices: 59503623--59503699 Score: 154
Period size: 25 Copynumber: 3.1 Consensus size: 25
59503613 TAGGATAACA
59503623 ATAATGTCATCCATGACCAGGTGAG
1 ATAATGTCATCCATGACCAGGTGAG
59503648 ATAATGTCATCCATGACCAGGTGAG
1 ATAATGTCATCCATGACCAGGTGAG
59503673 ATAATGTCATCCATGACCAGGTGAG
1 ATAATGTCATCCATGACCAGGTGAG
59503698 AT
1 AT
59503700 CAACTGTGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (25 bp):
ATAATGTCATCCATGACCAGGTGAG
Found at i:59508197 original size:2 final size:2
Alignment explanation
Indices: 59508190--59508239 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
59508180 GATGGATGGA
* * *
59508190 TG TG TG TG TG TG TG TG TG TG TA TG TG TA TG TG TA TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
59508232 TG TG TG TG
1 TG TG TG TG
59508240 GTACCATTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (2 bp):
TG
Found at i:59511858 original size:22 final size:22
Alignment explanation
Indices: 59511830--59511874 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
59511820 GAAGAAAAAG
59511830 AAAGTTTTCAAAATGCTGTCCT
1 AAAGTTTTCAAAATGCTGTCCT
59511852 AAAGTTTTCAAAATGCTGTCCT
1 AAAGTTTTCAAAATGCTGTCCT
59511874 A
1 A
59511875 CCCATAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (22 bp):
AAAGTTTTCAAAATGCTGTCCT
Found at i:59517334 original size:27 final size:27
Alignment explanation
Indices: 59517300--59517357 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
59517290 GTTATTTTTC
59517300 AAAATATCATACCAATAAATTTAATAA
1 AAAATATCATACCAATAAATTTAATAA
* * *
59517327 AAAATATCCTATCAATAAATTTAGTAA
1 AAAATATCATACCAATAAATTTAATAA
59517354 AAAA
1 AAAA
59517358 AATTAACAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (27 bp):
AAAATATCATACCAATAAATTTAATAA
Found at i:59517520 original size:19 final size:19
Alignment explanation
Indices: 59517493--59517533 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
59517483 ATTAACCTAC
* *
59517493 TTTCTTTTATCTGTTTTCT
1 TTTCCTTTAACTGTTTTCT
*
59517512 TTTCCTTTAACTGTTTTGT
1 TTTCCTTTAACTGTTTTCT
59517531 TTT
1 TTT
59517534 TATTTTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.71
Consensus pattern (19 bp):
TTTCCTTTAACTGTTTTCT
Found at i:59518473 original size:22 final size:24
Alignment explanation
Indices: 59518431--59518475 Score: 67
Period size: 22 Copynumber: 1.9 Consensus size: 24
59518421 ATAAATAATA
59518431 TTATTAATATTTTGTTGAAAATATT
1 TTATTAATA-TTTGTTGAAAATATT
59518456 TTATTAATA-TT-TTGAAAATA
1 TTATTAATATTTGTTGAAAATA
59518476 AATGTATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 2 0.10
25 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
TTATTAATATTTGTTGAAAATATT
Found at i:59521277 original size:12 final size:14
Alignment explanation
Indices: 59521260--59521292 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
59521250 TAATGGTCAC
59521260 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
59521272 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
59521286 ATGTGTA
1 ATGTGTA
59521293 CCGGATGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 1 0.05
14 11 0.58
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.39
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:59521286 original size:51 final size:51
Alignment explanation
Indices: 59521210--59521430 Score: 259
Period size: 51 Copynumber: 4.4 Consensus size: 51
59521200 TATGAACACG
* * *
59521210 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATAGATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GACAATGGTCACA
* * **
59521261 TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGATGACCTTGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGACAATGGTCACA
* * * * *
59521312 TGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGA-AAGC-TTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGA-CAATGGTCACA
* *
59521362 TGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATGACAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGACAATGGTCACA
* *
59521413 TGGGTGGTACTATGTGCA
1 TGTGTAGTACTATGTGCA
59521431 AACCACCAAA
Statistics
Matches: 143, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
50 43 0.30
51 97 0.68
52 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGACAATGGTCACA
Found at i:59521393 original size:101 final size:101
Alignment explanation
Indices: 59521210--59521430 Score: 300
Period size: 101 Copynumber: 2.2 Consensus size: 101
59521200 TATGAACACG
* * * * *
59521210 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCACATGTGTAGTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAGAT-ATGATCACATGTGTAGTACTATG
* **
59521275 TGTAGGCTACTATGTGTACCGGATGACCTTGGTCACA
65 TGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
* *
59521312 TGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGCT-TGATCACGTGTGTAGTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGAACC-GAAAGATATGATCACATGTGTAGTACTATG
*
59521376 TGTAGGCTACTACGTGTATCGGATGACAATGGTCACA
65 TGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
* *
59521413 TGGGTGGTACTATGTGCA
1 TGTGTAGTACTATGTGCA
59521431 AACCACCAAA
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
101 69 0.66
102 31 0.30
103 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (101 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAGATATGATCACATGTGTAGTACTATGT
GTAGGCTACTACGTGTACCGGATGACAATGGTCACA
Found at i:59530351 original size:21 final size:20
Alignment explanation
Indices: 59530326--59530377 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
59530316 CCAAAAAATG
*
59530326 TTTTATAGACATCTAATCTAT
1 TTTTATAGAAATC-AATCTAT
* *
59530347 TTTTAGAAAAATCAATCTAT
1 TTTTATAGAAATCAATCTAT
59530367 TTTT-TAGAAAT
1 TTTTATAGAAAT
59530378 TATTTTCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 5 0.19
20 11 0.42
21 10 0.38
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (20 bp):
TTTTATAGAAATCAATCTAT
Found at i:59533636 original size:24 final size:25
Alignment explanation
Indices: 59533607--59533661 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
59533597 GTATAACAGA
*
59533607 AAGCTCATAAGAGCCA-TAATTAGG
1 AAGCTCATAAGAGCCATTAATCAGG
**
59533631 AAGCTCATGCGAGCCATTAATCAGG
1 AAGCTCATAAGAGCCATTAATCAGG
59533656 AAGCTC
1 AAGCTC
59533662 CAGATAGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (25 bp):
AAGCTCATAAGAGCCATTAATCAGG
Found at i:59533657 original size:25 final size:24
Alignment explanation
Indices: 59533599--59533661 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
59533589 TCCGGGTTGT
*
59533599 ATAA-CAGAAAGCTCATAAGAGCC
1 ATAATCAGGAAGCTCATAAGAGCC
* **
59533622 ATAATTAGGAAGCTCATGCGAGCC
1 ATAATCAGGAAGCTCATAAGAGCC
59533646 ATTAATCAGGAAGCTC
1 A-TAATCAGGAAGCTC
59533662 CAGATAGCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 4 0.12
24 16 0.48
25 13 0.39
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (24 bp):
ATAATCAGGAAGCTCATAAGAGCC
Found at i:59533682 original size:25 final size:25
Alignment explanation
Indices: 59533654--59533735 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 25
59533644 CCATTAATCA
* *
59533654 GGAAGCTCCAGATAGCCATATATTG
1 GGAAGCTCAAGATAGCCATATATCG
* *
59533679 GGAAGTTCAAGTTAGCC--ATATCG
1 GGAAGCTCAAGATAGCCATATATCG
** *
59533702 GGAAGCTCTGGAGAGCCATATATCG
1 GGAAGCTCAAGATAGCCATATATCG
*
59533727 GGACGCTCA
1 GGAAGCTCA
59533736 TAAGAGTTGT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
23 17 0.39
25 27 0.61
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (25 bp):
GGAAGCTCAAGATAGCCATATATCG
Found at i:59550035 original size:5 final size:5
Alignment explanation
Indices: 59550027--59550053 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
59550017 AAAGGAAAGA
59550027 AAATC AAATC AAATC AAATC AAATC AA
1 AAATC AAATC AAATC AAATC AAATC AA
59550054 GCAGATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:59550260 original size:28 final size:28
Alignment explanation
Indices: 59550219--59550273 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
59550209 CAAGGTTGAT
* *
59550219 AGTTATTTCTTTATCT-TTGTTAATCTAC
1 AGTTATTTCATTATATGTTGTT-ATCTAC
59550247 AGTTATTTCATTATATGTTGTTATCTA
1 AGTTATTTCATTATATGTTGTTATCTA
59550274 TATGCTACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (28 bp):
AGTTATTTCATTATATGTTGTTATCTAC
Found at i:59551061 original size:20 final size:19
Alignment explanation
Indices: 59551009--59551061 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
59550999 TAGTAATTTC
*
59551009 TTATTATTTTTTAATGTAA
1 TTATTATTTTTTCATGTAA
* *
59551028 TTATTATTTTTTTCATTTAT
1 TTATTA-TTTTTTCATGTAA
59551048 TTATTTATTTTTTC
1 TTA-TTATTTTTTC
59551062 CTTTTTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.21
20 20 0.69
21 3 0.10
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATTATTTTTTCATGTAA
Found at i:59563363 original size:44 final size:44
Alignment explanation
Indices: 59563300--59563842 Score: 286
Period size: 44 Copynumber: 12.6 Consensus size: 44
59563290 GCTAATGATA
* * *
59563300 TTATCTCCCTAAAGTTGCAGTGGAGCTGATTAAAACCACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGATC
* * * * *
59563344 TTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCACATC-TAG-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGATC
* *
59563384 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-AG-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCATAGATC
* * * *** *
59563428 CTATCGT-CCTGAAGTTGCAGT-GAGATAGACTGAAGATGGA-AAATC
1 TTATC-TCCCTGAAGTTGCAGTGGAG-CAGA-TTAA-AACCATAGATC
* * * *
59563473 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAGAGCTGATA-ATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC-CATAGATC
* * * * * *
59563517 CTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAAACTTGGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGATC
* * * *** *
59563561 TTATCTCTCTGAAGTTGCAG-AGAGCATA-TCGCATC-TAG-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGATC
* *
59563601 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCA-AG-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCATAGATC
* ** * * * **
59563645 CTATCTTTCTGAAGTTGCAGTGAAGTAGACTGAAGATGGCA-A-ATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-A-ACCATAGATC
* *
59563690 TTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGATA-ATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-ATAGATC
* * * *
59563734 CTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGATC
* * * * * * * *
59563778 TTATTTCTCTAAAATTGCAG-AGAGCAGA-TCACATC-TAG-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGATC
59563818 TTATCTCCCTGAAGTTGCAGTGGAG
1 TTATCTCCCTGAAGTTGCAGTGGAG
59563843 TCTTATCCTC
Statistics
Matches: 380, Mismatches: 93, Indels: 55
0.72 0.18 0.10
Matches are distributed among these distances:
40 60 0.16
41 23 0.06
42 16 0.04
43 27 0.07
44 194 0.51
45 57 0.15
46 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCATAGATC
Found at i:59563676 original size:217 final size:217
Alignment explanation
Indices: 59563301--59564265 Score: 1268
Period size: 217 Copynumber: 4.5 Consensus size: 217
59563291 CTAATGATAT
* ***
59563301 TATCTCCCTAAAGTTGCAGTGGAGCTGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
*
59563366 AGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCTA
66 AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCTA
* * * *
59563431 TCGTCCTGAAGTTGCAGTG-AGATAGACTGAAGATGGAAAATCTTATCTCCCTAAAGTTGCAGTG
131 TCCTCCTGAAGTTGCAGTGAAG-CAGACTGAAGATGGCAAACCTTATCTCCCTAAAGTTGCAGTG
* *
59563495 GAGCAGATTAGAGCTGATAATCC
195 GAGCAGATTAAAGCCGATAATCC
* * *
59563518 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAAACTTGGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
* *
59563583 AGCATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCCTA
66 AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCTA
* * * * * *
59563648 TCTTTCTGAAGTTGCAGTGAAGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTAG
131 TCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGGCAAACCTTATCTCCCTAAAGTTGCAGTGG
59563713 AGCAGATTAAAGCCGATAATCC
196 AGCAGATTAAAGCCGATAATCC
* * * * * *
59563735 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATTTCTCTAAAATTGCAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
*
59563800 AGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGT---G--G----AGT---C---T--TA
66 AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCTA
** * *
59563848 TCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCTCTAAAGTTGTAGTGG
131 TCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGGCAAACCTTATCTCCCTAAAGTTGCAGTGG
* *
59563913 AGCAGGTTAAATCCGATAATCC
196 AGCAGATTAAAGCCGATAATCC
* * *
59563935 TATCTCCCTAAAGTTGTAGTGGAACGGATTAAAATCTTGGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
* * * *
59564000 AACAGATTGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
66 AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCTA
* * * *
59564065 TCCTCCTGAAGTTGTAGT-AGGGCAGACTGAAGATGGCAAACCTTATCTCCTTGAAGTTGCAGTG
131 TCCTCCTGAAGTTGCAGTGA-AGCAGACTGAAGATGGCAAACCTTATCTCCCTAAAGTTGCAGTG
* *
59564129 GAGCAGGTTAAAGCCGATAGTCC
195 GAGCAGATTAAAGCCGATAATCC
* * * * *
59564152 TATCTCCCTAAAGTTACAGTGCAGTGGATTAAAATCTTGGATCTTATCTCTCTGAAGTTGCAAAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
* *
59564217 AGCAGATCGCAACTAGTCTTATCTCCCTGACA-TTGCAGTGGAGTAGACT
66 AGCAGATCGCATCTAGTCTTATCTCCCTGA-AGTTGCAGTGGAGCAGACT
59564266 GCAGCACTAG
Statistics
Matches: 657, Mismatches: 71, Indels: 40
0.86 0.09 0.05
Matches are distributed among these distances:
200 168 0.26
202 1 0.00
203 1 0.00
205 2 0.00
208 2 0.00
209 3 0.00
212 2 0.00
214 1 0.00
215 1 0.00
217 473 0.72
218 3 0.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (217 bp):
TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCTA
TCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGGCAAACCTTATCTCCCTAAAGTTGCAGTGG
AGCAGATTAAAGCCGATAATCC
Found at i:59563855 original size:27 final size:27
Alignment explanation
Indices: 59563814--59563867 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
59563804 GATCACATCT
59563814 AGTCTTATCTCCCTGAAGTTGCAGTGG
1 AGTCTTATCTCCCTGAAGTTGCAGTGG
59563841 AGTCTTATC-CTCCTGAAGTTGCAGTGG
1 AGTCTTATCTC-CCTGAAGTTGCAGTGG
59563868 GGCAGACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (27 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGG
Found at i:59564073 original size:44 final size:44
Alignment explanation
Indices: 59564014--59564134 Score: 140
Period size: 44 Copynumber: 2.7 Consensus size: 44
59564004 GATTGCATCT
59564014 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCA
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCA
* * *
59564058 AGTCTTATCCTCCTGAAGTTGTAGTAGG-GCAGACTGAAGATGGCA
1 AATCTTAT-CTCCTGAAGTTGCAGT-GGAGCAGACTGAAGATAGCA
*
59564103 AACCTTATCTCCTTGAAGTTGCAGTGGAGCAG
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAG
59564135 GTTAAAGCCG
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
44 33 0.51
45 31 0.48
46 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (44 bp):
AATCTTATCTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
Found at i:59564221 original size:417 final size:417
Alignment explanation
Indices: 59563424--59564260 Score: 1219
Period size: 417 Copynumber: 2.0 Consensus size: 417
59563414 TAAGTAAGCA
* * *
59563424 AGTCCTATCGTCCTGAAGTTGCAGTGAGATAGACTGAAGATGGAAAATCTTATCTCCCTAAAGTT
1 AGTCCTATCCTCCTGAAGTTGCAGTGAGACAGACTGAAGATGGAAAACCTTATCTCCCTAAAGTT
* * * *
59563489 GCAGTGGAGCAGATTAGAGCTGATAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAAAC
66 GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTAGAACGGATTAAAAAC
* * *
59563554 TTGGATCTTATCTCTCTGAAGTTGCAGAGAGCATATCGCATCTAGTCTTATCTCCCTGAAGTTGC
131 TTGGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCTAATCTTATCTCCCTGAAGTTGC
* * *
59563619 AGTGGAGCAGACTAAGCAAGCAAGTCCTATCTTTCTGAAGTTGCAGTGAAGTAGACTGAAGATGG
196 AGTGGAGCAGACTAAGCAAGCAAGTCCTATCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGG
* * *
59563684 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGATAATCCTATCTCCTTGAAGT
261 CAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGT
* * * * *
59563749 TGCAGTGGAGCGGATTAAAACCTTAGATCTTATTTCTCTAAAATTGCAGAGAGCAGATCACATCT
326 TACAGTGCAGCGGATTAAAACCTTAGATCTTATCTCTCTAAAATTGCAAAGAGCAGATCACAACT
59563814 AGTCTTATCTCCCTGA-AGTTGCAGTGG
391 AGTCTTATCTCCCTGACA-TTGCAGTGG
* * * * *
59563841 AGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCTCTAAAGTT
1 AGTCCTATCCTCCTGAAGTTGCAGTGAGACAGACTGAAGATGGAAAACCTTATCTCCCTAAAGTT
* * * * * *
59563906 GTAGTGGAGCAGGTTAAATCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAACGGATTAAAATC
66 GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTAGAACGGATTAAAAAC
*
59563971 TTGGATCTTATCTCTCTGAAGTTGCAGAGAACAGATTGCATCTAATCTTATCTCCCTGAAGTTGC
131 TTGGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCTAATCTTATCTCCCTGAAGTTGC
* * * *
59564036 AGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGTAGT-AGGGCAGACTGAAGATG
196 AGTGGAGCAGACTAAGCAAGCAAGTCCTATCCTCCTGAAGTTGCAGTGA-AGCAGACTGAAGATG
* * * *
59564100 GCAAACCTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTAAAGCCGATAGTCCTATCTCCCTAAAG
260 GCAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAG
* * * * * *
59564165 TTACAGTGCAGTGGATTAAAATCTTGGATCTTATCTCTCTGAAGTTGCAAAGAGCAGATCGCAAC
325 TTACAGTGCAGCGGATTAAAACCTTAGATCTTATCTCTCTAAAATTGCAAAGAGCAGATCACAAC
59564230 TAGTCTTATCTCCCTGACATTGCAGTGG
390 TAGTCTTATCTCCCTGACATTGCAGTGG
59564258 AGT
1 AGT
59564261 AGACTGCAGC
Statistics
Matches: 371, Mismatches: 47, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
416 1 0.00
417 369 0.99
418 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (417 bp):
AGTCCTATCCTCCTGAAGTTGCAGTGAGACAGACTGAAGATGGAAAACCTTATCTCCCTAAAGTT
GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTAGAACGGATTAAAAAC
TTGGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCTAATCTTATCTCCCTGAAGTTGC
AGTGGAGCAGACTAAGCAAGCAAGTCCTATCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGG
CAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGT
TACAGTGCAGCGGATTAAAACCTTAGATCTTATCTCTCTAAAATTGCAAAGAGCAGATCACAACT
AGTCTTATCTCCCTGACATTGCAGTGG
Found at i:59564622 original size:5 final size:5
Alignment explanation
Indices: 59564614--59564640 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
59564604 AAAGGAAAGA
59564614 AAATC AAATC AAATC AAATC AAATC AA
1 AAATC AAATC AAATC AAATC AAATC AA
59564641 GCAGATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:59564859 original size:28 final size:28
Alignment explanation
Indices: 59564806--59564860 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
59564796 CAAGGTTGAT
* *
59564806 AGTTATTTCTTTATATTTGTTAATCTAC
1 AGTTATTTCATTACATTTGTTAATCTAC
59564834 AGTTATTTCATTACATGTTGTT-ATCTA
1 AGTTATTTCATTACAT-TTGTTAATCTA
59564861 TATGCTACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (28 bp):
AGTTATTTCATTACATTTGTTAATCTAC
Found at i:59565969 original size:37 final size:37
Alignment explanation
Indices: 59565904--59566012 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
59565894 TACGTATGAT
* *
59565904 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
59565939 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
59565976 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
59566013 TAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:59566055 original size:52 final size:52
Alignment explanation
Indices: 59565976--59566244 Score: 406
Period size: 52 Copynumber: 5.2 Consensus size: 52
59565966 TAAGTGTAGC
* * **
59565976 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
59566029 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
59566081 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
59566127 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
59566179 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACCTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
59566231 CACTTTGTCACTTG
1 CACTTT-TCACTTG
59566245 ATCAGAAGTA
Statistics
Matches: 200, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
46 44 0.22
49 1 0.00
52 140 0.70
53 15 0.08
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:59566086 original size:98 final size:98
Alignment explanation
Indices: 59565976--59566244 Score: 421
Period size: 98 Copynumber: 2.7 Consensus size: 98
59565966 TAAGTGTAGC
* **
59565976 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTT
59566041 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
59566074 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTT
59566139 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
59566172 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACCTATCACTTT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
59566237 GTCACTTG
60 -TCACTTG
59566245 ATCAGAAGTA
Statistics
Matches: 156, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
98 103 0.66
100 1 0.01
104 46 0.29
105 6 0.04
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:59570382 original size:33 final size:32
Alignment explanation
Indices: 59570345--59570443 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 32
59570335 AATGGTTGGC
* *
59570345 TGTCCATTGAGATGCCCGAACAGTCATGTGCTG
1 TGTCCATTGAG-TGCACGAACAGCCATGTGCTG
* *
59570378 TGTCCATTGGTGTGCACGAACAGCCTTGTGCTG
1 TGTCCATT-GAGTGCACGAACAGCCATGTGCTG
* *
59570411 TGTCCATTGATGTGCACGAACAGCTATGAGCTG
1 TGTCCATTGA-GTGCACGAACAGCCATGTGCTG
59570444 AGTAAGCTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.02
33 53 0.95
34 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.28
Consensus pattern (32 bp):
TGTCCATTGAGTGCACGAACAGCCATGTGCTG
Found at i:59574529 original size:44 final size:42
Alignment explanation
Indices: 59574466--59574581 Score: 148
Period size: 43 Copynumber: 2.7 Consensus size: 42
59574456 ATGAGTATTT
59574466 GTGTAAGACCACGTCTGGGACGTTGGCATCGA-TTTGAGGTTTAC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTT---GTTTAC
59574510 GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGACGTTTGTTTAC
1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAC-TTTGTTTAC
*
59574553 ATGTAAGACCACGTCTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
59574582 TGTACGAGCT
Statistics
Matches: 65, Mismatches: 1, Indels: 13
0.82 0.01 0.16
Matches are distributed among these distances:
42 1 0.02
43 31 0.48
44 29 0.45
45 1 0.02
46 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTTGTTTAC
Found at i:59574890 original size:24 final size:24
Alignment explanation
Indices: 59574863--59574912 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
59574853 GATTTATTTT
59574863 CTATGACTTACTAAGCGTTTTAAG
1 CTATGACTTACTAAGCGTTTTAAG
*
59574887 CTATGACTTACTAAGCTTTTTAAG
1 CTATGACTTACTAAGCGTTTTAAG
59574911 CT
1 CT
59574913 TACTTTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (24 bp):
CTATGACTTACTAAGCGTTTTAAG
Found at i:59575458 original size:23 final size:23
Alignment explanation
Indices: 59575415--59575460 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
59575405 GTTAATTATA
* *
59575415 GACTTATAGATTGACGTATAATT
1 GACTTATAAATAGACGTATAATT
59575438 GACTTATAAATAGA-GTGATAATT
1 GACTTATAAATAGACGT-ATAATT
59575461 AGTAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
GACTTATAAATAGACGTATAATT
Found at i:59583950 original size:38 final size:38
Alignment explanation
Indices: 59583908--59583984 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
59583898 TTCAGATATA
59583908 TCATTATATCAAGAAAAAAAAGAATTGCATTGCTTCTT
1 TCATTATATCAAGAAAAAAAAGAATTGCATTGCTTCTT
59583946 TCATTATATCAAGAAAAAAAAGAATTGCATTGCTTCTT
1 TCATTATATCAAGAAAAAAAAGAATTGCATTGCTTCTT
59583984 T
1 T
59583985 TGACGTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (38 bp):
TCATTATATCAAGAAAAAAAAGAATTGCATTGCTTCTT
Found at i:59591210 original size:15 final size:15
Alignment explanation
Indices: 59591190--59591224 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
59591180 ACAGATCGGG
*
59591190 TCAGTTTTTGGTTTC
1 TCAGTTTTTGGTTGC
*
59591205 TCAGTTTTTTGTTGC
1 TCAGTTTTTGGTTGC
59591220 TCAGT
1 TCAGT
59591225 CCTACTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.14, G:0.20, T:0.57
Consensus pattern (15 bp):
TCAGTTTTTGGTTGC
Found at i:59592795 original size:17 final size:18
Alignment explanation
Indices: 59592773--59592806 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59592763 CAACCGCGAT
59592773 AAACGCAAT-GCGACCGA
1 AAACGCAATCGCGACCGA
*
59592790 AAACGCGATCGCGACCG
1 AAACGCAATCGCGACCG
59592807 CAATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.32, G:0.26, T:0.06
Consensus pattern (18 bp):
AAACGCAATCGCGACCGA
Found at i:59604366 original size:165 final size:166
Alignment explanation
Indices: 59604062--59604394 Score: 501
Period size: 165 Copynumber: 2.0 Consensus size: 166
59604052 GGGGACAATC
* *
59604062 AAATATTTATGTACAAAGCTACTATTCATAAAATTAACGTTCTTAGTAGACTCTATGCATATGTT
1 AAATATTTATGTACAAAGCTACTATTCATAAAATTAACGTTCTTAGTAAACTCTATGCA-ATGCT
* * *
59604127 GGATACGTGTACTACTCTGAGCTGCTTGCTAGATGCTTCTTGGGCATATGCAAGCAAAGACCGCG
65 GGATACGTGTACTACTCTGAGCTGCTTGCTAGATGCTCCTTGGGCATATGCAAGCAAAGACCACA
* *
59604192 AGCTCCCTTTGCGAACACCCTATGATGTGTGCGGCTG
130 AGATCCCTTTGCGAACAACCTATGATGTGTGCGGCTG
*
59604229 AAATATTTATGTACAAAGCTACTATTCA-AAGAATTGACGTTCTTAGTAAACTCTATGC-ATGCT
1 AAATATTTATGTACAAAGCTACTATTCATAA-AATTAACGTTCTTAGTAAACTCTATGCAATGCT
* * *
59604292 GGATACGTGTACTGCTCT-AGGCTGCTTGCTGGATGCTCCTTGGGCATATGCGAGCAAAGACCAC
65 GGATACGTGTACTACTCTGA-GCTGCTTGCTAGATGCTCCTTGGGCATATGCAAGCAAAGACCAC
* *
59604356 AAGATCCCTTTGTGAACAACCTCTGATGTGTGCGGCTG
129 AAGATCCCTTTGCGAACAACCTATGATGTGTGCGGCTG
59604394 A
1 A
59604395 GTCCGCGAGC
Statistics
Matches: 151, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
164 1 0.01
165 95 0.63
166 2 0.01
167 53 0.35
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (166 bp):
AAATATTTATGTACAAAGCTACTATTCATAAAATTAACGTTCTTAGTAAACTCTATGCAATGCTG
GATACGTGTACTACTCTGAGCTGCTTGCTAGATGCTCCTTGGGCATATGCAAGCAAAGACCACAA
GATCCCTTTGCGAACAACCTATGATGTGTGCGGCTG
Found at i:59604531 original size:2 final size:2
Alignment explanation
Indices: 59604520--59604577 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
59604510 TCATAAGTAC
59604520 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59604561 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
59604578 AATTTAATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59608200 original size:44 final size:43
Alignment explanation
Indices: 59608012--59608154 Score: 254
Period size: 41 Copynumber: 3.3 Consensus size: 43
59608002 CGGATCACAT
59608012 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCAC
59608056 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCAC
59608099 TTATCACTTG-C-CTGATCAGATAAGTGTAGCTAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCAC
*
59608140 TTATCACTTGCCACT
1 TTATCACTTGTCACT
59608155 TGTCATTGAT
Statistics
Matches: 97, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
41 40 0.41
42 2 0.02
43 22 0.23
44 33 0.34
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (43 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCAC
Found at i:59613298 original size:13 final size:13
Alignment explanation
Indices: 59613280--59613304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59613270 TCCAGCAACT
59613280 ATGAATTTATTTC
1 ATGAATTTATTTC
59613293 ATGAATTTATTT
1 ATGAATTTATTT
59613305 GATGTTGATT
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:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:59613512 original size:50 final size:50
Alignment explanation
Indices: 59613404--59613652 Score: 293
Period size: 50 Copynumber: 4.8 Consensus size: 50
59613394 ATTTGGGTAA
* *
59613404 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTCTTGAGATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--C-CGAG---ACG
* *
59613460 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGAATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
59613510 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * *
59613560 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGC-TTGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATT-GGCACCGAGACG
** * *
59613610 AGAACATTCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
59613653 TGTTTTTACC
Statistics
Matches: 174, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
49 2 0.01
50 95 0.55
51 32 0.18
52 2 0.01
53 3 0.02
54 1 0.01
56 39 0.22
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:59617283 original size:10 final size:10
Alignment explanation
Indices: 59617268--59617292 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59617258 ATTTTTCTAT
59617268 AATAATAATA
1 AATAATAATA
59617278 AATAATAATA
1 AATAATAATA
59617288 AATAA
1 AATAA
59617293 AACACTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAATAATA
Found at i:59617323 original size:2 final size:2
Alignment explanation
Indices: 59617316--59617365 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
59617306 ACCTCTAATA
59617316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59617358 AT AT AT AT
1 AT AT AT AT
59617366 CCAAGCATGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59619600 original size:17 final size:18
Alignment explanation
Indices: 59619578--59619623 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
59619568 CGATGTAAAA
59619578 TAATATTATATAAATT-T
1 TAATATTATATAAATTGT
*
59619595 TAATA-TATAT-ATTTGT
1 TAATATTATATAAATTGT
*
59619611 TAGTATTATATAA
1 TAATATTATATAA
59619624 GTATATGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 10 0.42
18 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
TAATATTATATAAATTGT
Found at i:59635339 original size:18 final size:18
Alignment explanation
Indices: 59635308--59635342 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59635298 AATAATTTCT
* *
59635308 AAAAATATGTATATGTAA
1 AAAAAAATGCATATGTAA
59635326 AAAAAAATGCATATGTA
1 AAAAAAATGCATATGTA
59635343 TTATAAAATG
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:0.57, C:0.03, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAAAAATGCATATGTAA
Found at i:59635377 original size:2 final size:2
Alignment explanation
Indices: 59635372--59635409 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
59635362 ACACACACAC
*
59635372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59635410 TTATTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:59639392 original size:132 final size:132
Alignment explanation
Indices: 59637350--59639383 Score: 3226
Period size: 132 Copynumber: 15.4 Consensus size: 132
59637340 GCCGACTAGA
* * * *
59637350 GAGATAGAATTACTGGCTTCAATATATTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* * * * ** *
59637415 GATCTACTCCACTACTGCCTAGGGAAATAAGATCTATAATCTTCAATCTATTCCACTATTGGCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59637480 GG
131 GG
* * *
59637482 GAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAAGTAAAATCCGCCATCATT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
**
59637547 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGTTCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59637612 GG
131 GG
* * * *
59637614 GAGATAGAATTACTGGCTTCAATGTGCTCCACTGTAATCTCAGGGAGGTAAAATCCGTCATCCTT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* * *
59637679 GATCTGCTCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCAACTGTTGCCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59637744 GG
131 GG
*
59637746 GAGATAGAATTACTGGCTTCAATAG-ACTCCACTGTAACCTCAGGGAGATAAAATCCGCCATCTT
1 GAGATAGAATTACTGGCTTCAAT-GTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
*
59637810 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATCTTCAATCTATTCCACTGCTGCCC
65 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
59637875 AGG
130 AGG
* *
59637878 GAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
*
59637943 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGAATCTTCAATCTATTCCACTGCTGCCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59638008 GG
131 GG
* ***
59638010 GAGATAGAATTACTGGTTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCATTATCTTT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* * *
59638075 GATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCTA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59638140 GG
131 GG
* *
59638142 GAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* *
59638207 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59638272 GG
131 GG
* * * *
59638274 GAGATAGAATTACTGGCTTCAATATATTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* * * * ** *
59638339 GATCTACTCCACTACTGCCTAGGGAAATAAGATCTATAATCTTCAATCTATTCCACTATTGGCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59638404 GG
131 GG
* * * *
59638406 GAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAAGTAAAATCTGCCATCATT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
59638471 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59638536 GG
131 GG
* * * *
59638538 GAGATAGAATTACTGGCTTCAATGTGCTCCACTGTAATCTCAGGGAGGTAAAATCCGTCATCCTT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* * *
59638603 GATCTGCTCCACTACTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCAACTGTTGCCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59638668 GG
131 GG
*
59638670 GAGATAGAATTACTGGCTTCAATAG-ACTCCACTGTAACCTCAGGGAGATAAAATCCGCCATCTT
1 GAGATAGAATTACTGGCTTCAAT-GTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
*
59638734 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATCTTCAATCTATTCCACTGCTGCCC
65 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
59638799 AGG
130 AGG
* * *
59638802 GAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATCTTC
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
*
59638867 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGAATCTTCAATCTATTCCACTGCTGCCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59638932 GG
131 GG
* ***
59638934 GAGATAGAATTACTGGTTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCATTATCTTT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* * * *
59638999 GATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAATCTATTCCAGTGCTGCCTA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59639064 GG
131 GG
* *
59639066 GAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* *
59639131 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
59639196 GG
131 GG
* * * *
59639198 GAGATAGAATTGCTGGCTGCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCATT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
* * * *
59639263 GATCTGCTCCACTATTGCTTATGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCACA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
*
59639328 TG
131 GG
* *
59639330 GAGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAAT
1 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAAT
59639384 TCACCATCAA
Statistics
Matches: 1755, Mismatches: 143, Indels: 8
0.92 0.08 0.00
Matches are distributed among these distances:
131 2 0.00
132 1751 1.00
133 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTT
GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCA
GG
Found at i:59640209 original size:13 final size:13
Alignment explanation
Indices: 59640191--59640215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59640181 AAATTGTCGA
59640191 GGATAACAAAGAT
1 GGATAACAAAGAT
59640204 GGATAACAAAGA
1 GGATAACAAAGA
59640216 AATTGATTTA
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:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:59649382 original size:21 final size:21
Alignment explanation
Indices: 59649356--59649398 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
59649346 CATGACATTC
59649356 TCCCTCA-CCCATTCTTGCGAA
1 TCCCTCATCCCATTCTTG-GAA
*
59649377 TCCCTCATCGCATTCTTGGAA
1 TCCCTCATCCCATTCTTGGAA
59649398 T
1 T
59649399 GACGCTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.19, C:0.37, G:0.12, T:0.33
Consensus pattern (21 bp):
TCCCTCATCCCATTCTTGGAA
Found at i:59655844 original size:26 final size:27
Alignment explanation
Indices: 59655809--59655877 Score: 113
Period size: 26 Copynumber: 2.5 Consensus size: 27
59655799 TTGTTGTGTG
59655809 ATATATAATATATTAATGCTCTAGT-T
1 ATATATAATATATTAATGCTCTAGTAT
59655835 ATATATAATATATTAATGCTCTAGTGAT
1 ATATATAATATATTAATGCTCTAGT-AT
59655863 ATATGATAATATATT
1 ATAT-ATAATATATT
59655878 GATATTTGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
26 25 0.62
28 5 0.12
29 10 0.25
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (27 bp):
ATATATAATATATTAATGCTCTAGTAT
Found at i:59666497 original size:18 final size:18
Alignment explanation
Indices: 59666474--59666516 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
59666464 AATATTTATC
59666474 TTGATGTTGTTAGTATTT
1 TTGATGTTGTTAGTATTT
*
59666492 TTGATGTTGTTGGTATTT
1 TTGATGTTGTTAGTATTT
59666510 TTGATGT
1 TTGATGT
59666517 ATTATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (18 bp):
TTGATGTTGTTAGTATTT
Found at i:59669583 original size:19 final size:19
Alignment explanation
Indices: 59669561--59669597 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
59669551 AATTAAAATT
59669561 AATTATAAA-AATTATTTTA
1 AATTA-AAATAATTATTTTA
59669580 AATTAAAATAATTATTTT
1 AATTAAAATAATTATTTT
59669598 TATTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAAAATAATTATTTTA
Found at i:59674581 original size:25 final size:26
Alignment explanation
Indices: 59674538--59674593 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
59674528 AACTATAGTG
59674538 ATAAATTTAAATTATATTAATATT-AA
1 ATAAATTTAAATTATATTAA-ATTAAA
59674564 ATAAATTT-AATTATATTAAATTAAA
1 ATAAATTTAAATTATATTAAATTAAA
59674589 ATAAA
1 ATAAA
59674594 AATCTACCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 3 0.10
25 18 0.62
26 8 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAATTTAAATTATATTAAATTAAA
Found at i:59676278 original size:21 final size:22
Alignment explanation
Indices: 59676238--59676278 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
59676228 CATATATATG
* *
59676238 CTTTTTTATTTGAAATTATTTT
1 CTTTTTTATTTCAAAATATTTT
59676260 CTTTTTT-TTTCAAAATATT
1 CTTTTTTATTTCAAAATATT
59676279 ATATACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (22 bp):
CTTTTTTATTTCAAAATATTTT
Found at i:59691000 original size:23 final size:22
Alignment explanation
Indices: 59690964--59691033 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
59690954 TTAACGATGA
59690964 TAAAA-ATATAATTTTATTATTT
1 TAAAAGAT-TAATTTTATTATTT
* *
59690986 TAATAGATTATATTTTTATAATTTT
1 TAAAAGATTA-A-TTTTATTA-TTT
*
59691011 TAAAAGATTAAATTTATT-TTT
1 TAAAAGATTAATTTTATTATTT
59691032 TA
1 TA
59691034 TTATTTTGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.13
22 6 0.15
23 8 0.21
24 8 0.21
25 12 0.31
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TAAAAGATTAATTTTATTATTT
Found at i:59691002 original size:24 final size:25
Alignment explanation
Indices: 59690970--59691025 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
59690960 ATGATAAAAA
* * *
59690970 TATAATTTTATTA-TTTTAATAGAT
1 TATATTTTTATAATTTTTAAAAGAT
59690994 TATATTTTTATAATTTTTAAAAGAT
1 TATATTTTTATAATTTTTAAAAGAT
*
59691019 TAAATTT
1 TATATTT
59691026 ATTTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATTTTTATAATTTTTAAAAGAT
Found at i:59694355 original size:16 final size:17
Alignment explanation
Indices: 59694334--59694369 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
59694324 GTTTACTCAT
59694334 TTTCATTTTTT-TTTAA
1 TTTCATTTTTTGTTTAA
59694350 TTTCATTTTTTGTTTAA
1 TTTCATTTTTTGTTTAA
59694367 TTT
1 TTT
59694370 AATGTTTCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTCATTTTTTGTTTAA
Found at i:59694359 original size:17 final size:16
Alignment explanation
Indices: 59694334--59694369 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
59694324 GTTTACTCAT
*
59694334 TTTCATTTTTTTTTAA
1 TTTCATTTTTGTTTAA
59694350 TTTCATTTTTTGTTTAA
1 TTTCA-TTTTTGTTTAA
59694367 TTT
1 TTT
59694370 AATGTTTCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTCATTTTTGTTTAA
Found at i:59695094 original size:16 final size:16
Alignment explanation
Indices: 59695070--59695111 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
59695060 GAAAATTGGA
*
59695070 AAGAT-GAAAAATTG-
1 AAGATAGAAAAATAGC
59695084 AAGAATAGAAAAATAGC
1 AAG-ATAGAAAAATAGC
59695101 AAGATAGAAAA
1 AAGATAGAAAA
59695112 TATATTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 2 0.08
16 16 0.67
17 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.19, T:0.14
Consensus pattern (16 bp):
AAGATAGAAAAATAGC
Found at i:59696062 original size:21 final size:21
Alignment explanation
Indices: 59696038--59696077 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59696028 CTTTAGTTAA
59696038 TGATGATAATCCTTT-TTTCAC
1 TGATG-TAATCCTTTATTTCAC
*
59696059 TGATGTGATCCTTTATTTC
1 TGATGTAATCCTTTATTTC
59696078 TGCACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.50
Consensus pattern (21 bp):
TGATGTAATCCTTTATTTCAC
Found at i:59696272 original size:33 final size:33
Alignment explanation
Indices: 59696230--59696299 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
59696220 AAGCTGAAGA
59696230 TGTTGGATAGACTATCTATCTTGTTTCACACAT
1 TGTTGGATAGACTATCTATCTTGTTTCACACAT
59696263 TGTTGGATAGACTATCTATCTTGTTTCACACAT
1 TGTTGGATAGACTATCTATCTTGTTTCACACAT
59696296 TGTT
1 TGTT
59696300 TTTGATTCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTTGGATAGACTATCTATCTTGTTTCACACAT
Found at i:59698627 original size:51 final size:51
Alignment explanation
Indices: 59698546--59698644 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
59698536 GATGCTAGGT
* *
59698546 TGGATCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATATCTGGGAGAAGTG
1 TGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTGGGAGAAGTG
* *
59698597 TGGAGCAGGCTGCTGATTCAAGAAACGAAGTTGGAATAACTGGGAGAA
1 TGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTGGGAGAA
59698645 ATTTAGAGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.20
Consensus pattern (51 bp):
TGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTGGGAGAAGTG
Found at i:59698700 original size:60 final size:60
Alignment explanation
Indices: 59698606--59698773 Score: 196
Period size: 60 Copynumber: 2.8 Consensus size: 60
59698596 GTGGAGCAGG
* * * * * **
59698606 CTGCTGATTCAAGAAACGAAGTTGGAATAACTGGGAGAAATTTAGAGCCAAGTCAACTTA
1 CTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAGAAATTTAGAGCCAAGCCAACCGA
* *
59698666 CTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGA-AGAGTTTAGAGCCAAGCCAACCGG
1 CTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAGA-AATTTAGAGCCAAGCCAACCGA
* * *
59698726 CTGCTGAATCTAGAAAAGAAGCTGGAATAG-TCGGGAGAACTTTGGAGC
1 CTGCTGAATCTAGAAAAGAAGTTGGAATAGCT-GGGAGAAATTTAGAGC
59698774 AGGGAGCTGA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.02
60 90 0.97
61 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (60 bp):
CTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAGAAATTTAGAGCCAAGCCAACCGA
Found at i:59703919 original size:30 final size:26
Alignment explanation
Indices: 59703859--59703919 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 26
59703849 CTCTCAAAAC
* *
59703859 TAAATAAAATATTTTATAATTATATT
1 TAAATAAAATATTTTATAAATATAGT
59703885 TAAATAAAATATATTTATTAAATAGTAAGT
1 TAAATAAAATAT-TTTA-TAAATA-T-AGT
59703915 TAAAT
1 TAAAT
59703920 TTGAGTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 12 0.41
27 4 0.14
28 5 0.17
29 1 0.03
30 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (26 bp):
TAAATAAAATATTTTATAAATATAGT
Found at i:59704125 original size:31 final size:31
Alignment explanation
Indices: 59704090--59704150 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
59704080 CTGGTCATTG
59704090 AACTATTCCAAAGTTTTCATATAAGTCACTA
1 AACTATTCCAAAGTTTTCATATAAGTCACTA
** * * *
59704121 AACTATTTGAAATTTTTTATTTAAGTCACT
1 AACTATTCCAAAGTTTTCATATAAGTCACT
59704151 GAGATGTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (31 bp):
AACTATTCCAAAGTTTTCATATAAGTCACTA
Done.