Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 131 of 427
Found at i:35209348 original size:39 final size:39
Alignment explanation
Indices: 35209231--35209431 Score: 255
Period size: 39 Copynumber: 5.4 Consensus size: 39
35209221 GCGAGTCATC
35209231 GCTAAG-CCCGAAGGCATTTGTGCGAGTTAC--TATCCGG
1 GCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATATCCGG
35209268 GCTAAGTCCCGAAGGCATTTGTGC--G---CTATATCC--
1 GCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATATCCGG
35209301 GCTAAGTCCCGAAGGCATTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTGTGCGAGTTACTATATCCGG
35209340 GCTAAGTCCCGAAGGCATTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTGTGCGAGTTACTATATCCGG
* *
35209379 GCTATGTCCCGAAGGCATTGAGCGAG-TAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTGTGCGAGTTA-CTATATCCGG
* *
35209417 GTTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
35209432 TACTTGGCTT
Statistics
Matches: 148, Mismatches: 5, Indels: 21
0.85 0.03 0.12
Matches are distributed among these distances:
32 6 0.04
33 18 0.12
34 1 0.01
35 5 0.03
36 1 0.01
37 14 0.09
38 32 0.22
39 71 0.48
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (39 bp):
GCTAAGTCCCGAAGGCATTGTGCGAGTTACTATATCCGG
Found at i:35219770 original size:27 final size:27
Alignment explanation
Indices: 35219732--35219785 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
35219722 AACTATACTT
35219732 GTCTTGGTGAGCAAAGATCAAGGAAAA
1 GTCTTGGTGAGCAAAGATCAAGGAAAA
35219759 GTCTTGGTGAGCAAAGATCAAGGAAAA
1 GTCTTGGTGAGCAAAGATCAAGGAAAA
35219786 ATTCAAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.19
Consensus pattern (27 bp):
GTCTTGGTGAGCAAAGATCAAGGAAAA
Found at i:35237301 original size:24 final size:24
Alignment explanation
Indices: 35237247--35237302 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
35237237 GTCACGCACA
* *
35237247 GCCTCGCACATGGCCTACCACACG
1 GCCTGGCACAAGGCCTACCACACG
* *
35237271 ACATGGCACAAGGCCTACCACACG
1 GCCTGGCACAAGGCCTACCACACG
35237295 GCCTGGCA
1 GCCTGGCA
35237303 GACTACCATG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.41, G:0.23, T:0.11
Consensus pattern (24 bp):
GCCTGGCACAAGGCCTACCACACG
Found at i:35238865 original size:20 final size:20
Alignment explanation
Indices: 35238818--35238866 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
35238808 AATTATAGTA
*
35238818 AATTATT-ATATTTTTAAAT
1 AATTATTAAAATTTTTAAAT
*
35238837 AATTTTTAAAATTTTTAAAT
1 AATTATTAAAATTTTTAAAT
**
35238857 GCTTATTAAA
1 AATTATTAAA
35238867 TATGCTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AATTATTAAAATTTTTAAAT
Found at i:35239004 original size:17 final size:17
Alignment explanation
Indices: 35238982--35239017 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35238972 CGACCATGAC
35238982 ATCATTTAACAGTATAA
1 ATCATTTAACAGTATAA
35238999 ATCATTTAACAGTATAA
1 ATCATTTAACAGTATAA
35239016 AT
1 AT
35239018 GGATTGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (17 bp):
ATCATTTAACAGTATAA
Found at i:35241883 original size:2 final size:2
Alignment explanation
Indices: 35241876--35241911 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
35241866 CAACATCACT
35241876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35241912 GTGAAAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35246536 original size:45 final size:45
Alignment explanation
Indices: 35246436--35246560 Score: 143
Period size: 45 Copynumber: 2.8 Consensus size: 45
35246426 TTTTCTCAAA
* *
35246436 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
35246478 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
35246522 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAA
35246561 CAATCAAGTC
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
42 11 0.15
43 14 0.19
44 8 0.11
45 38 0.53
46 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:35246952 original size:43 final size:43
Alignment explanation
Indices: 35246891--35247002 Score: 215
Period size: 43 Copynumber: 2.6 Consensus size: 43
35246881 CTGGCATTAC
35246891 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
35246934 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
35246977 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
35247003 TAATACCAGC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:35247061 original size:38 final size:38
Alignment explanation
Indices: 35246995--35247078 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
35246985 GGCACGAAGG
* * * *
35246995 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAACACGAAGCCTGCGGGATTTAA
* *
35247033 CCCGGATATAATACCAACACGAATCCTGCGGGATTTAA
1 CCCGAATATAATACCAACACGAAGCCTGCGGGATTTAA
35247071 CCCGAATA
1 CCCGAATA
35247079 CACATCAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.21
Consensus pattern (38 bp):
CCCGAATATAATACCAACACGAAGCCTGCGGGATTTAA
Found at i:35262529 original size:15 final size:15
Alignment explanation
Indices: 35262511--35262541 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35262501 TGTTCCTGGT
35262511 TTTCTTGTAGCAAGA
1 TTTCTTGTAGCAAGA
35262526 TTTCTTGTAGCAAGA
1 TTTCTTGTAGCAAGA
35262541 T
1 T
35262542 CCTCTGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (15 bp):
TTTCTTGTAGCAAGA
Found at i:35266847 original size:40 final size:40
Alignment explanation
Indices: 35266803--35266990 Score: 326
Period size: 40 Copynumber: 4.7 Consensus size: 40
35266793 GCTACTTGCT
35266803 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
35266843 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
35266883 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
35266923 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
35266962 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
35266991 CATCCGAATA
Statistics
Matches: 141, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
38 1 0.01
39 34 0.24
40 105 0.74
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:35266989 original size:79 final size:80
Alignment explanation
Indices: 35266780--35266990 Score: 331
Period size: 80 Copynumber: 2.7 Consensus size: 80
35266770 CCTTCAGAAT
* *
35266780 TTAG-CCGGATATAGCT-ACTTGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 TTAGCCCGGATATAG-TAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
35266843 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
* *
35266859 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
1 TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
35266924 AAATGCCTTCGGG-C
66 AAATGCCTTCGGGAC
*
35266938 TTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 TTAGCCCGGATA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
35266991 CATCCGAATA
Statistics
Matches: 123, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
78 1 0.01
79 54 0.44
80 68 0.55
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (80 bp):
TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
AAATGCCTTCGGGAC
Found at i:35270187 original size:27 final size:27
Alignment explanation
Indices: 35270157--35270275 Score: 184
Period size: 27 Copynumber: 4.4 Consensus size: 27
35270147 ATTACCAAAG
*
35270157 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
35270184 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
35270211 TACCCTCGATTTACAGAATTATCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
35270238 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
35270265 TACCCCCGATT
1 TACCCTCGATT
35270276 GTGAAAATAC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:35270204 original size:54 final size:54
Alignment explanation
Indices: 35270132--35270260 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
35270122 TACTGAAATG
* * * *
35270132 CCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCAAAGTACCCTCGATTTACAAAATTACCATTTTA
***** * *
35270186 CCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTACAGAATTATCATTTTA
1 CCCTCGATTTATAGAATTACCAAAGTACCCTCGATTTACAAAATTACCATTTTA
*
35270240 CCCTCGATTTACAGAATTACC
1 CCCTCGATTTATAGAATTACC
35270261 GTTTTACCCC
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (54 bp):
CCCTCGATTTATAGAATTACCAAAGTACCCTCGATTTACAAAATTACCATTTTA
Found at i:35270318 original size:27 final size:27
Alignment explanation
Indices: 35270288--35270406 Score: 89
Period size: 27 Copynumber: 4.4 Consensus size: 27
35270278 GAAAATACTG
* *
35270288 AAATACCTCT-GTAGGGTAGAATTACCA
1 AAATACCCCTAGT-GGGTAAAATTACCA
**
35270315 AAATACCCCTAGTTTGTAAAATTACCA
1 AAATACCCCTAGTGGGTAAAATTACCA
* * ** * *
35270342 AAATACCACTGGTTTGTGAAATTACCG
1 AAATACCCCTAGTGGGTAAAATTACCA
* **
35270369 AAATA-CCCTCAATTTGTAAAATTACCA
1 AAATACCCCT-AGTGGGTAAAATTACCA
35270396 AAATACCCCTA
1 AAATACCCCTA
35270407 ATTTACAAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
26 3 0.04
27 67 0.88
28 6 0.08
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (27 bp):
AAATACCCCTAGTGGGTAAAATTACCA
Found at i:35270409 original size:27 final size:27
Alignment explanation
Indices: 35270307--35270429 Score: 142
Period size: 27 Copynumber: 4.6 Consensus size: 27
35270297 TGTAGGGTAG
*
35270307 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
* ** *
35270334 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAATTTGTAA
*
35270361 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AATTTGTAA
**
35270388 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATACCCCTAATTTGTAA
35270415 AATTA-CAGAAATACC
1 AATTACCA-AAATACC
35270430 TTTGACTTTC
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.06
27 73 0.89
28 4 0.05
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAATTTGTAA
Found at i:35270582 original size:27 final size:27
Alignment explanation
Indices: 35270552--35270635 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
35270542 TAGGTAAAAA
35270552 GACCGTAAAGCCCTTGTAGGGTAAAGT
1 GACCGTAAAGCCCTTGTAGGGTAAAGT
*
35270579 GACCGTAAAGCCCCTGTAGGGTAAAGT
1 GACCGTAAAGCCCTTGTAGGGTAAAGT
* *
35270606 GACCGTAATA-CCCTTGTATGGTAAAAT
1 GACCGTAA-AGCCCTTGTAGGGTAAAGT
35270633 GAC
1 GAC
35270636 AAATATGCCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 51 0.98
28 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (27 bp):
GACCGTAAAGCCCTTGTAGGGTAAAGT
Found at i:35271483 original size:16 final size:15
Alignment explanation
Indices: 35271462--35271509 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
35271452 GATGTGAATA
35271462 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
35271478 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
35271493 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
35271509 A
1 A
35271510 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:35271485 original size:24 final size:24
Alignment explanation
Indices: 35271458--35271513 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
35271448 TAATGATGTG
*
35271458 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
35271482 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
35271506 AATAATAA
1 AATAATAA
35271514 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:35271492 original size:8 final size:8
Alignment explanation
Indices: 35271458--35271509 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
35271448 TAATGATGTG
*
35271458 AATAATAA
1 AATATTAA
35271466 AATATATAA
1 AATAT-TAA
35271475 AATA-TAA
1 AATATTAA
35271482 AATATTAA
1 AATATTAA
*
35271490 AATATCAA
1 AATATTAA
*
35271498 AATATTAG
1 AATATTAA
35271506 AATA
1 AATA
35271510 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:35271683 original size:20 final size:21
Alignment explanation
Indices: 35271627--35271685 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
35271617 ATACTACATC
35271627 AATATGTACAT-ATATAAAAA
1 AATATGTACATAATATAAAAA
** *
35271647 AATAAATACGGATAATAT-TAAA
1 AATATGTAC--ATAATATAAAAA
35271669 AATATGTACATAATATA
1 AATATGTACATAATATA
35271686 GTGTTAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 14 0.47
22 12 0.40
23 4 0.13
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.31
Consensus pattern (21 bp):
AATATGTACATAATATAAAAA
Found at i:35271727 original size:22 final size:24
Alignment explanation
Indices: 35271664--35271728 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
35271654 ACGGATAATA
*
35271664 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
35271689 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
35271712 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
35271729 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:35271806 original size:27 final size:27
Alignment explanation
Indices: 35271744--35271809 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 27
35271734 CATGTAGAAA
*
35271744 AAAATATATATATAAATAATATAATAT
1 AAAATATATATATAAATAAAATAATAT
* * * *
35271771 -TAA-AGATATATACATAAAATAGTAT
1 AAAATATATATATAAATAAAATAATAT
35271796 AAAATATATATATA
1 AAAATATATATATA
35271810 TACGTAATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
25 18 0.60
26 4 0.13
27 8 0.27
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAATATATATATAAATAAAATAATAT
Found at i:35271884 original size:23 final size:25
Alignment explanation
Indices: 35271841--35271886 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35271831 TATACCTAAT
35271841 ATATTAAAAGAATATATATAATACA
1 ATATTAAAAGAATATATATAATACA
*
35271866 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
35271887 ACAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATACA
Found at i:35272417 original size:30 final size:30
Alignment explanation
Indices: 35272381--35272489 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 30
35272371 CAAGTGGTGG
*
35272381 TGGAGCAAGTGTGGTTAGTGGAGTAGGTAA
1 TGGAGCAAGTGTGGCTAGTGGAGTAGGTAA
* * **
35272411 TGGAGCAAGTGTGGCTAGTGGATTTGGTGG
1 TGGAGCAAGTGTGGCTAGTGGAGTAGGTAA
* **
35272441 TGGAG-AAGGTGTGGCTAGTGGAGTTGGTGG
1 TGGAGCAA-GTGTGGCTAGTGGAGTAGGTAA
**
35272471 TGGAAAAAGTGTGGCTAGT
1 TGGAGCAAGTGTGGCTAGT
35272490 TGAGAAAAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
29 2 0.03
30 66 0.94
31 2 0.03
ACGTcount: A:0.22, C:0.05, G:0.46, T:0.28
Consensus pattern (30 bp):
TGGAGCAAGTGTGGCTAGTGGAGTAGGTAA
Found at i:35272481 original size:60 final size:60
Alignment explanation
Indices: 35272375--35272489 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
35272365 TAGGTACAAG
* **
35272375 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGTAGGTAATGGAGCAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGTAGGTAATGGAAAAAGTGTGGCTAGTGGATT
* **
35272435 TGGTGGTGGAG-AAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGTGTGGCTAGT
1 TGGTGGTGGAGCAA-GTGTGGCTAGTGGAGTAGGTAATGGAAAAAGTGTGGCTAGT
35272490 TGAGAAAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.28
Consensus pattern (60 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGTAGGTAATGGAAAAAGTGTGGCTAGTGGATT
Found at i:35273256 original size:14 final size:14
Alignment explanation
Indices: 35273237--35273286 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
35273227 GAGTTGATTT
* *
35273237 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
35273251 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
35273266 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
35273280 TT-AAAAA
1 TTGAAAAA
35273287 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:35273473 original size:74 final size:73
Alignment explanation
Indices: 35273266--35273726 Score: 429
Period size: 74 Copynumber: 6.0 Consensus size: 73
35273256 AAAACAGAAA
* * * **
35273266 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGTCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGT-CCT-GAGGCTCAACTCACCTCTCGCAATAT
*
35273331 GAGTTAATTT
64 GAGTTGATTT
* * * * *
35273341 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
35273406 GTTGATTT
66 GTTGATTT
35273414 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
35273479 AGTTGATTTTT
65 AGTTGA--TTT
* ** * ** * * * * * *
35273490 TTTACGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAG-CATGTGAGCTGAGGCTCAACT
1 TTGAAAAACAGAAATT-AA-AA-A-TACCT---CAG-CGT--GTCCTGAG-GCTCA-ACTC----
* *
35273554 CACCTCTCGTAATATGAGTTAATTT
50 -ACCTCTCGCAATATGAGTTGATTT
* * * * *
35273579 TTGACAAATAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
35273644 ATTGATTT
66 GTTGATTT
35273652 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
35273717 AGTTGATTT
65 AGTTGATTT
35273726 T
1 T
35273727 CCTTGAAAAG
Statistics
Matches: 310, Mismatches: 54, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
73 80 0.26
74 108 0.35
75 30 0.10
76 16 0.05
77 2 0.01
78 4 0.01
79 7 0.02
80 3 0.01
81 2 0.01
82 4 0.01
83 2 0.01
84 4 0.01
85 7 0.02
86 3 0.01
87 2 0.01
88 1 0.00
89 16 0.05
91 19 0.06
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (73 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:35273514 original size:14 final size:14
Alignment explanation
Indices: 35273495--35273522 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35273485 TTTTTTTTAC
35273495 GAACAGAAATTGAA
1 GAACAGAAATTGAA
35273509 GAACAGAAATTGAA
1 GAACAGAAATTGAA
35273523 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:35273568 original size:91 final size:90
Alignment explanation
Indices: 35273414--35273580 Score: 246
Period size: 91 Copynumber: 1.8 Consensus size: 90
35273404 GAGTTGATTT
* *
35273414 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
*
35273479 AGTTGATTTTTTTTACGAACAGAAA
66 AGTTAATTTTTTTTACGAACAGAAA
* * * *
35273504 TTGAAGAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCGTAATA
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATA
35273568 TGAGTTAATTTTT
64 TGAGTTAATTTTT
35273581 GACAAATAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
89 14 0.21
90 13 0.19
91 41 0.60
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (90 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTTTTTTTACGAACAGAAA
Found at i:35273641 original size:164 final size:163
Alignment explanation
Indices: 35273347--35273653 Score: 463
Period size: 164 Copynumber: 1.9 Consensus size: 163
35273337 ATTTTTGACA
** * * *
35273347 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAAGACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAAT
*
35273412 TTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
66 TTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
*
35273477 TGAGTTGATTTTTTTTACGAACAGAAATTGAAG
131 TGAATTGATTTTTTTTACGAACAGAAATTGAAG
* * *
35273510 AACAGAAATTGAAAAGACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCGTAATATGAGTTA
1 AACAGAAATTGAAAAGACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTA
* * * *
35273575 ATTTTTGACAAATAGAAA-TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
64 ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
35273639 TATGAATTGATTTTT
129 TATGAATTGATTTTT
35273654 GAAAAACAGA
Statistics
Matches: 128, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
163 22 0.17
164 57 0.45
165 49 0.38
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (163 bp):
AACAGAAATTGAAAAGACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAAT
TTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
TGAATTGATTTTTTTTACGAACAGAAATTGAAG
Found at i:35273676 original size:238 final size:238
Alignment explanation
Indices: 35273258--35273726 Score: 861
Period size: 238 Copynumber: 2.0 Consensus size: 238
35273248 AAATTGAAAA
35273258 AACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGTCGAGGCTCAACTCACCTCT
1 AACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGTCGAGGCTCAACTCACCTCT
35273323 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
66 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
* *
35273388 TCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTG
131 TCACCTCTCGCAATATGAATTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTG
35273453 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
196 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
*
35273496 AACAGAAATTGAAGAA-CAGAAATTGAAAAGACCTCAGCATGTGAG-CTGAGGCTCAACTCACCT
1 AACAGAAATTGAA-AAGCAGAAATTAAAAAGACCTCAGCATGTGAGTC-GAGGCTCAACTCACCT
* *
35273559 CTCGTAATATGAGTTAATTTTTGACAAATAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCA
64 CTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCA
35273624 ACTCACCTCTCGCAATATGAATTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC
129 ACTCACCTCTCGCAATATGAATTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC
35273689 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
194 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
35273727 CCTTGAAAAG
Statistics
Matches: 224, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
237 1 0.00
238 221 0.99
239 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (238 bp):
AACAGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGTCGAGGCTCAACTCACCTCT
CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
TCACCTCTCGCAATATGAATTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTG
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
Found at i:35285625 original size:22 final size:24
Alignment explanation
Indices: 35285562--35285626 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
35285552 CGTGATAATA
*
35285562 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
35285587 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
35285610 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
35285627 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:35285683 original size:25 final size:25
Alignment explanation
Indices: 35285647--35285784 Score: 67
Period size: 23 Copynumber: 5.6 Consensus size: 25
35285637 AGAAAAAAAT
*
35285647 ATATATAAATAATATAATATTAAAG
1 ATATATACATAATATAATATTAAAG
* *
35285672 ATATATACATAAAATAGTATAATATATATAT
1 ATATATACAT---A-A-TATAATAT-TAAAG
* *
35285703 ATATATACGTAATATAGA-ATTTAA-
1 ATATATACATAATATA-ATATTAAAG
* *
35285727 A-ATATACTTAATAT-AT-TAAAAG
1 ATATATACATAATATAATATTAAAG
* *
35285749 A-ATATATATAATACAATATT-AAG
1 ATATATACATAATATAATATTAAAG
*
35285772 AAATATA-ATAATA
1 ATATATACATAATA
35285785 ACAAAAAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 26
0.69 0.10 0.20
Matches are distributed among these distances:
21 4 0.05
22 11 0.12
23 24 0.27
24 7 0.08
25 11 0.12
26 6 0.07
27 2 0.02
28 2 0.02
29 1 0.01
30 8 0.09
31 12 0.14
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATAATATTAAAG
Found at i:35285782 original size:23 final size:25
Alignment explanation
Indices: 35285739--35285784 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35285729 TATACTTAAT
35285739 ATATTAAAAGAATATATATAATACA
1 ATATTAAAAGAATATATATAATACA
*
35285764 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
35285785 ACAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATACA
Found at i:35286372 original size:30 final size:30
Alignment explanation
Indices: 35286275--35286374 Score: 130
Period size: 30 Copynumber: 3.3 Consensus size: 30
35286265 TAGGTACAAG
*
35286275 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* ** *
35286305 AGGTAATGGAGCAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
35286335 TGGTGGTGGAG-AAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAA-GTGTGGCTAGTGGAGT
*
35286365 TGATGGTGGA
1 TGGTGGTGGA
35286375 AAAGGTGTCG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 57 0.97
ACGTcount: A:0.20, C:0.04, G:0.48, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:35286380 original size:30 final size:30
Alignment explanation
Indices: 35286319--35286389 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
35286309 AATGGAGCAA
* * *
35286319 GTGTGGCTAGTGGATTTGGTGGTGGAGAAG
1 GTGTGGCTAGTGGAGTTGATGGTGGAAAAG
35286349 GTGTGGCTAGTGGAGTTGATGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGATGGTGGAAAAG
*
35286379 GTGTCGCTAGT
1 GTGTGGCTAGT
35286390 TGAGAAAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.18, C:0.06, G:0.46, T:0.30
Consensus pattern (30 bp):
GTGTGGCTAGTGGAGTTGATGGTGGAAAAG
Found at i:35286388 original size:60 final size:60
Alignment explanation
Indices: 35286275--35286389 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
35286265 TAGGTACAAG
* * * *
35286275 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGTAGGTAATGGAGCAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGTAGATAATGGAGAAAGTGTCGCTAGTGGATT
* **
35286335 TGGTGGTGGAG-AAGGTGTGGCTAGTGGAGTTGATGGTGGA-AAAGGTGTCGCTAGT
1 TGGTGGTGGAGCAA-GTGTGGCTAGTGGAGTAGATAATGGAGAAA-GTGTCGCTAGT
35286390 TGAGAAAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.21, C:0.05, G:0.46, T:0.28
Consensus pattern (60 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGTAGATAATGGAGAAAGTGTCGCTAGTGGATT
Found at i:35286995 original size:27 final size:27
Alignment explanation
Indices: 35286954--35287011 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
35286944 ATATGTAAAA
35286954 GCCCCTAGGGCGTTAAATGACTGTTTT
1 GCCCCTAGGGCGTTAAATGACTGTTTT
*
35286981 GCCCCTAGGGTGTTAAATGACTGTTTT
1 GCCCCTAGGGCGTTAAATGACTGTTTT
35287008 GCCC
1 GCCC
35287012 TTGTGGGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (27 bp):
GCCCCTAGGGCGTTAAATGACTGTTTT
Found at i:35288359 original size:42 final size:41
Alignment explanation
Indices: 35288227--35288388 Score: 171
Period size: 42 Copynumber: 3.9 Consensus size: 41
35288217 ACACTCGGTA
35288227 CCATACCAATGCCATATCCCAGATATGGTCTTACATGTAATC
1 CCATACCAATGCCATATCCCAGATATGGTCTTACATG-AATC
*** * * * * *
35288269 TTGTATCGATGCCAATAGCCCAGCTATGGTCTTACACGAAATC
1 CCATACCAATGCC-ATATCCCAGATATGGTCTTACATG-AATC
* *
35288312 TCATACCAATGCCATATCCCAGATATGGTCTTATATGAAGTC
1 CCATACCAATGCCATATCCCAGATATGGTCTTACATGAA-TC
* * *
35288354 CCATACCGATGCCATATCCCAGTTACGGTCTTACA
1 CCATACCAATGCCATATCCCAGATATGGTCTTACA
35288389 CGTAATCTCA
Statistics
Matches: 96, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
41 2 0.02
42 60 0.62
43 34 0.35
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (41 bp):
CCATACCAATGCCATATCCCAGATATGGTCTTACATGAATC
Found at i:35288364 original size:85 final size:84
Alignment explanation
Indices: 35288228--35288398 Score: 236
Period size: 85 Copynumber: 2.0 Consensus size: 84
35288218 CACTCGGTAC
*** *
35288228 CATACCAATGCCATATCCCAGATATGGTCTTACATGTAATCTTGTATCGATGCCAATAGCCCAGC
1 CATACCAATGCCATATCCCAGATATGGTCTTACATGTAATCCCATACCGATGCC-ATAGCCCAGC
*
35288293 TATGGTCTTACACGAAATCT
65 TACGGTCTTACACGAAATCT
* * *
35288313 CATACCAATGCCATATCCCAGATATGGTCTTATATG-AAGTCCCATACCGATGCCATATCCCAGT
1 CATACCAATGCCATATCCCAGATATGGTCTTACATGTAA-TCCCATACCGATGCCATAGCCCAGC
*
35288377 TACGGTCTTACACGTAATCT
65 TACGGTCTTACACGAAATCT
35288397 CA
1 CA
35288399 GTAACCCTAA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
84 30 0.39
85 46 0.61
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (84 bp):
CATACCAATGCCATATCCCAGATATGGTCTTACATGTAATCCCATACCGATGCCATAGCCCAGCT
ACGGTCTTACACGAAATCT
Found at i:35294951 original size:50 final size:50
Alignment explanation
Indices: 35294889--35294996 Score: 171
Period size: 50 Copynumber: 2.2 Consensus size: 50
35294879 ACTCATTTAG
* * *
35294889 CCGAATACACAAGATCAAATATAACATCACATATGTACATACCTATGTGA
1 CCGAATATACAAGATCAAATATAACATCACATATGAACATACCTATCTGA
* *
35294939 CCGAATATACAAGATCAAATATAACATCACATATGAAGATACCTATCTGG
1 CCGAATATACAAGATCAAATATAACATCACATATGAACATACCTATCTGA
35294989 CCGAATAT
1 CCGAATAT
35294997 GGATGGTCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (50 bp):
CCGAATATACAAGATCAAATATAACATCACATATGAACATACCTATCTGA
Found at i:35297395 original size:51 final size:51
Alignment explanation
Indices: 35297313--35297485 Score: 170
Period size: 51 Copynumber: 3.4 Consensus size: 51
35297303 ATGCCCGGTG
*
35297313 GCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTATCTTCTT-CACAAAGTA
1 GCCTGCACATAGTACCACACTTGTGA-TCAAAGCTATCTT-TTACACAAAGTA
* * * * *
35297364 GCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTTACTCATAGTG
1 GCCTGCACATAGTACCACACTTGTGATCAAAGCTATCTTTTACACAAAGTA
* * * *** * *
35297415 GCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGGTACGCATAGTA
1 GCCTGCACATAGTACCACACTTGTGATCAAAGCTATCTTTTACACAAAGTA
* *
35297466 GCCTGCACTTAGTACTACAC
1 GCCTGCACATAGTACCACAC
35297486 ATACGACCTA
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 2 0.02
51 100 0.97
52 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (51 bp):
GCCTGCACATAGTACCACACTTGTGATCAAAGCTATCTTTTACACAAAGTA
Found at i:35301520 original size:31 final size:31
Alignment explanation
Indices: 35301482--35301560 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
35301472 TTTAACAGTT
35301482 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
*
35301513 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
35301544 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
35301561 ACTGTAAACG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCAAATC
Found at i:35301631 original size:42 final size:42
Alignment explanation
Indices: 35301584--35301675 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
35301574 TGGCCCATAG
* *
35301584 GCCCATTTCAATATCACATGTAATATCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
35301626 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
35301668 GCCCATTT
1 GCCCATTT
35301676 AGGGAGACTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:35301906 original size:26 final size:24
Alignment explanation
Indices: 35301823--35301917 Score: 120
Period size: 25 Copynumber: 3.8 Consensus size: 24
35301813 CTCTTTTAAT
*
35301823 AACTAGGGCAAAGCCC-TTTGGATA
1 AACTGGGGCAAAGCCCTTTTGG-TA
*
35301847 AACTGGGGCAAAAGCCCTTTTGATA
1 AACTGGGGC-AAAGCCCTTTTGGTA
35301872 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTT-GGTA
*
35301898 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
35301918 AGCACTTCCT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
24 8 0.12
25 40 0.62
26 16 0.25
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (24 bp):
AACTGGGGCAAAGCCCTTTTGGTA
Found at i:35302789 original size:27 final size:26
Alignment explanation
Indices: 35302730--35302804 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
35302720 GCATATTTGA
35302730 CATTTTACCATACGGGGTATTACGGT
1 CATTTTACCATACGGGGTATTACGGT
* *
35302756 CACTTTACCCTACAGGGGCT-TTACGGT
1 CATTTTACCATAC-GGGG-TATTACGGT
*
35302783 CTTTTTACCTATTA-GGGGTATT
1 CATTTTACC-A-TACGGGGTATT
35302805 TTAGTCATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
26 12 0.31
27 24 0.62
28 1 0.03
29 2 0.05
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (26 bp):
CATTTTACCATACGGGGTATTACGGT
Found at i:35302875 original size:27 final size:27
Alignment explanation
Indices: 35302845--35302951 Score: 85
Period size: 27 Copynumber: 3.9 Consensus size: 27
35302835 GTAAATCTAC
35302845 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
35302872 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* **
35302898 GAAAGTTC-AGGGTATTTTTGTAATTTTGT
1 -AAA--CCAAGGGTATTTCAGTAATTTTGT
* * **
35302927 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
35302952 ACAAATTGAG
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
26 3 0.05
27 42 0.64
28 19 0.29
29 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:35302911 original size:28 final size:27
Alignment explanation
Indices: 35302880--35302978 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
35302870 GTAAACCAAT
35302880 GGTATTTCTATAATTTTTGAAAGTTCAG
1 GGTATTTCTATAATTTTTGAAA-TTCAG
* *
35302908 GGTATTTTTGTAA-TTTTGTAAA-TCAGG
1 GGTATTTCTATAATTTTTG-AAATTCA-G
* ** *
35302935 GGTATTT-TGGTAATTTTACAAATTGAG
1 GGTATTTCT-ATAATTTTTGAAATTCAG
*
35302962 GGTATTTCGATAATTTT
1 GGTATTTCTATAATTTT
35302979 AAAAAACAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
26 4 0.07
27 35 0.60
28 19 0.33
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.47
Consensus pattern (27 bp):
GGTATTTCTATAATTTTTGAAATTCAG
Found at i:35302949 original size:55 final size:54
Alignment explanation
Indices: 35302851--35303029 Score: 150
Period size: 55 Copynumber: 3.3 Consensus size: 54
35302841 CTACAAACCA
* * * * **
35302851 AGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTTGAAAGTTC
1 AGGGTATTTTAGTAATTTTGTAAAACAGTGGTATTT-TGGTAATTTTACAAA-TTC
* * * *
35302906 AGGGTATTTTTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTAGTAATTTTGTAAAACAGTGGTATTTTGGTAATTTTACAAATTC
* ** * *
35302960 AGGGTA-TTTCGATAATTTTAAAAAACAGTGGTATTTTGGT-ATTCTACAAACT-
1 AGGGTATTTTAG-TAATTTTGTAAAACAGTGGTATTTTGGTAATTTTACAAATTC
*
35303012 AGGGGTATTTTGGTAATT
1 A-GGGTATTTTAGTAATT
35303030 CTACCCTGCA
Statistics
Matches: 103, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
52 1 0.01
53 24 0.23
54 37 0.36
55 41 0.40
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTGTAAAACAGTGGTATTTTGGTAATTTTACAAATTC
Found at i:35302957 original size:27 final size:27
Alignment explanation
Indices: 35302907--35303029 Score: 117
Period size: 27 Copynumber: 4.6 Consensus size: 27
35302897 TGAAAGTTCA
* **
35302907 GGGTATTTTTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
*
35302934 GGGTATTTTGGTAATTTTACAAAT-TG
1 GGGTATTTTGGTAATTTTACAAATCAG
* * * *
35302960 AGGGTATTTCGATAATTTTAAAAAACAG
1 -GGGTATTTTGGTAATTTTACAAATCAG
* *
35302988 TGGTATTTTGGT-ATTCTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AG
35303014 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
35303030 CTACCCTGCA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.01
26 22 0.29
27 53 0.69
28 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:35303098 original size:27 final size:27
Alignment explanation
Indices: 35303067--35303448 Score: 460
Period size: 27 Copynumber: 14.1 Consensus size: 27
35303057 TCACAATTAA
35303067 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
35303094 GGTAAAACGATAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* ** * **
35303121 GGTATAATAGTAATTCTATAAATTAAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* * * *
35303148 GATAAAATGGTAATTCTATAAATCGGG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* * **
35303175 GGTAAAACGGTAATTTTATAAATTAAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
35303202 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* **
35303229 GGTAAAACGGTAATTTTGTAAATTAAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* *
35303256 GGTAAAACGATAATTTTGTAAATCGA-
1 GGTAAAACGGTAATTCTGTAAATCGAG
* *
35303282 GGAAGAAACGGTAATTCTATAAATCGAG
1 GGTA-AAACGGTAATTCTGTAAATCGAG
* * * *
35303310 TGTAAAACGGTAATTTTATAAATTGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* *
35303337 GGTAAAATGGTAATTTTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
** *
35303364 GGTAAAATAGTAATTCTATAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
35303391 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
35303418 GGTAAAATGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
35303445 GGTA
1 GGTA
35303449 CTTTGGTAAT
Statistics
Matches: 304, Mismatches: 49, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 3 0.01
27 299 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (27 bp):
GGTAAAACGGTAATTCTGTAAATCGAG
Found at i:35306131 original size:46 final size:46
Alignment explanation
Indices: 35306080--35306183 Score: 138
Period size: 46 Copynumber: 2.3 Consensus size: 46
35306070 ATGGTTTTCC
*
35306080 AAAATT-AGAATAAGGGATTCTAAAATCATTCTGACTCTATCTCACA
1 AAAATTCA-AATAAGGGATTCCAAAATCATTCTGACTCTATCTCACA
* * * *
35306126 AAAATTCAAATAAGGGATTCCGAAATCATTTTGATTCTGTCTCACA
1 AAAATTCAAATAAGGGATTCCAAAATCATTCTGACTCTATCTCACA
*
35306172 AAGATTCAAATA
1 AAAATTCAAATA
35306184 TCTCATAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
46 50 0.98
47 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (46 bp):
AAAATTCAAATAAGGGATTCCAAAATCATTCTGACTCTATCTCACA
Found at i:35308106 original size:55 final size:53
Alignment explanation
Indices: 35307981--35308169 Score: 218
Period size: 55 Copynumber: 3.5 Consensus size: 53
35307971 AACTTACCAT
** * *
35307981 TGCCATGTTTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* *
35308034 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * * * *
35308089 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
* *
35308143 TGCCATGCCTTGGCACGGTCTTACATG
1 TGCCATGCCTTGACATGGTCTTACATG
35308170 ATATCCTTAT
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
52 2 0.02
53 34 0.29
54 34 0.29
55 44 0.38
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
Found at i:35308215 original size:47 final size:47
Alignment explanation
Indices: 35308159--35308277 Score: 202
Period size: 47 Copynumber: 2.5 Consensus size: 47
35308149 GCCTTGGCAC
*
35308159 GGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACAT
1 GGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAACAT
* * *
35308206 TGTCTTACATGGTATCATTGTCTTACCAAATGCCATGTTCCAAACAT
1 GGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAACAT
35308253 GGTCTTACATGGTATCCTTATCTTA
1 GGTCTTACATGGTATCCTTATCTTA
35308278 GTGCCAATGT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (47 bp):
GGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAACAT
Found at i:35313794 original size:43 final size:44
Alignment explanation
Indices: 35313745--35313915 Score: 163
Period size: 43 Copynumber: 4.0 Consensus size: 44
35313735 GGTTATCGAG
*
35313745 ATGTGATTACATGTTAGACCATGTCTGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* ** * * *
35313789 -TGTGATTACGTGTAAGATGATGTCTGGAACATTGGAATCGT-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * *
35313831 ATATGATTTCGTGTAAGA-CACTGTCTGGGACAGTGGCATTG-AT
1 ATGTGATTACATGTAAGACCA-TGTCTGGGACATTGGCATTGTAT
* * * *
35313874 ATGTGATAACATGTAAGACCATATTTGGGATA-TGGCATTGTA
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
35313916 CGAGCTTATG
Statistics
Matches: 101, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
42 10 0.10
43 89 0.88
44 2 0.02
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:35320073 original size:49 final size:50
Alignment explanation
Indices: 35319894--35320079 Score: 230
Period size: 50 Copynumber: 3.7 Consensus size: 50
35319884 ATCTATTGTG
* * ** *
35319894 AGGTCACATGTGTAGTACTAAGTGCAAGCTACTATGCATACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * **
35319945 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
35319995 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
35320045 -GGTCGCATGTGTAGTACTATGTGCAGGCTACTACG
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACG
35320080 CGTGTAACAC
Statistics
Matches: 115, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
49 33 0.29
50 45 0.39
51 37 0.32
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:35320085 original size:101 final size:101
Alignment explanation
Indices: 35319894--35320079 Score: 277
Period size: 101 Copynumber: 1.9 Consensus size: 101
35319884 ATCTATTGTG
* *
35319894 AGGTCACATGTGTAGTACTAAGTGCAAGCTACTATGCATACCCGATAACTTCGATCACGTGTGTA
1 AGGTCACATGTGTAGTACTAAGTGCAAGCTACTACGCATACCCGATAACTTCGATCACATGTGTA
35319959 GTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
66 GTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
* ** * * *
35319995 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCATGTGTA
1 AGGTCACATGTGTAGTACTAAGTGCAAGCTACTACGCATACCCGATAACTTCGATCACATGTGTA
*
35320058 GTACTATGTGCAGGCTACTACG
66 GTACTAAGTGCAGGCTACTACG
35320080 CGTGTAACAC
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
99 31 0.41
100 2 0.03
101 43 0.57
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (101 bp):
AGGTCACATGTGTAGTACTAAGTGCAAGCTACTACGCATACCCGATAACTTCGATCACATGTGTA
GTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
Found at i:35321660 original size:41 final size:40
Alignment explanation
Indices: 35321516--35321673 Score: 208
Period size: 40 Copynumber: 3.9 Consensus size: 40
35321506 CCCAGTTATA
* * *
35321516 GTAATTCGCGCAAATGCCTTCGGGACTTAACCTGGATTTG
1 GTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTG
*
35321556 GTAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTG
1 GTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTG
* *
35321596 GTAACTCGCACAAATTCCTTCGGGACTTAACCCGGATTTA
1 GTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTG
* * * * *
35321636 GTCACTTAGTACAAAAGCCTTCGGGACTTAGCCCGGAT
1 GTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGAT
35321674 ACCATTCGAA
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 77 0.74
41 27 0.26
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
GTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTG
Found at i:35324933 original size:28 final size:28
Alignment explanation
Indices: 35324868--35324968 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
35324858 ATAGTGAATC
*
35324868 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
35324897 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
35324925 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
35324955 CGCACACTTAGTGC
1 CGCACACTTAGTGC
35324969 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:35332878 original size:28 final size:28
Alignment explanation
Indices: 35332813--35332913 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
35332803 ATAGTGAATC
*
35332813 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
35332842 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
35332870 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
35332900 CGCACACTTAGTGC
1 CGCACACTTAGTGC
35332914 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:35340330 original size:46 final size:46
Alignment explanation
Indices: 35340280--35340452 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
35340270 TGGTTGAGCA
* *
35340280 TCCGAACTTGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
35340326 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTGA--GATG-TAACTAGGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T----G
*
35340373 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
35340419 CCCGAGCTCGTTAAGCTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
35340453 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 58 0.54
47 30 0.28
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:35347256 original size:6 final size:6
Alignment explanation
Indices: 35347245--35347270 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
35347235 TAAACACTTT
35347245 TAATTA TAATTA TAATTA TAATTA TA
1 TAATTA TAATTA TAATTA TAATTA TA
35347271 TGTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:35350616 original size:18 final size:18
Alignment explanation
Indices: 35350593--35350631 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
35350583 ATTTCTATAA
35350593 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
*
35350611 TTAGTTTAAATTTGATTT
1 TTAGTTTAAATTTGATCT
35350629 TTA
1 TTA
35350632 AATTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (18 bp):
TTAGTTTAAATTTGATCT
Found at i:35352289 original size:42 final size:43
Alignment explanation
Indices: 35352157--35352423 Score: 294
Period size: 43 Copynumber: 6.3 Consensus size: 43
35352147 CTAATTTTTG
* * * * * * *
35352157 CATGGCCTTTAGCGGTGCTTTTATAAAAAATGCTGCTAATGAA
1 CATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAA
* * *
35352200 TATAACCTTTAGCGGCGC-TTTACCCACAAACGCCGCTAAA-AA
1 CATGACCTTTAGCGGCGCTTTTA-TCACAAACGCCGCTAAAGAA
* * * *
35352242 GCATGACCTTTAGGGGTG-ATTTA-CCCATAACGCCGCTAAAGAA
1 -CATGACCTTTAGCGGCGCTTTTATCACA-AACGCCGCTAAAGAA
35352285 CATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAA
*
35352328 CA-GACCTTTAGCGGCGCTTTTATCACAAACGCCTCTAAAGAA
1 CATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAA
* * *
35352370 CATGACCTTTAACAGCGCTTTTATCACAAACACCGCTAAAGAGA
1 CATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGA-A
35352414 -ATGACCTTTA
1 CATGACCTTTA
35352424 ACGATGCTTT
Statistics
Matches: 191, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
41 3 0.02
42 74 0.39
43 110 0.58
44 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAA
Found at i:35352295 original size:85 final size:86
Alignment explanation
Indices: 35352156--35352423 Score: 285
Period size: 85 Copynumber: 3.1 Consensus size: 86
35352146 GCTAATTTTT
* * * * * * * * * *
35352156 GCATGGCCTTTAGCGGTGCTTTTATAAAAAATGCTGCTAATGAATATAACCTTTAGCGGCGC-TT
1 GCATGACCTTTAGCGGCGCATTTATCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTT
*
35352220 TACCCACAAACGCCGCTAAAAA
66 TA-TCACAAACGCCGCTAAAAA
* * *
35352242 GCATGACCTTTAGGGGTG-ATTTA-CCCATAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT
1 GCATGACCTTTAGCGGCGCATTTATCACA-AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT
35352305 TTATCACAAACGCCGCTAAAGAA
65 TTATCACAAACGCCGCTAAA-AA
* * * *
35352328 -CA-GACCTTTAGCGGCGCTTTTATCACAAACGCCTCTAAAGAACATGACCTTTAACAGCGCTTT
1 GCATGACCTTTAGCGGCGCATTTATCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTT
* *
35352391 TATCACAAACACCGCTAAAGA
66 TATCACAAACGCCGCTAAAAA
*
35352412 GAATGACCTTTA
1 GCATGACCTTTA
35352424 ACGATGCTTT
Statistics
Matches: 153, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
84 14 0.09
85 106 0.69
86 33 0.22
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (86 bp):
GCATGACCTTTAGCGGCGCATTTATCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTT
TATCACAAACGCCGCTAAAAA
Found at i:35352433 original size:43 final size:43
Alignment explanation
Indices: 35352270--35352442 Score: 228
Period size: 43 Copynumber: 4.0 Consensus size: 43
35352260 ATTTACCCAT
* *
35352270 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACA
1 AACGCCGCTAAAGAACATGACCTTTAACGACGCTTTTATCACA
* *
35352313 AACGCCGCTAAAGAACA-GACCTTTAGCGGCGCTTTTATCACA
1 AACGCCGCTAAAGAACATGACCTTTAACGACGCTTTTATCACA
*
35352355 AACGCCTCTAAAGAACATGACCTTTAAC-AGCGCTTTTATCACA
1 AACGCCGCTAAAGAACATGACCTTTAACGA-CGCTTTTATCACA
* *
35352398 AACACCGCTAAAGAGA-ATGACCTTTAACGATGC-TTTATCAACA
1 AACGCCGCTAAAGA-ACATGACCTTTAACGACGCTTTTATC-ACA
35352441 AA
1 AA
35352443 TGCTTCTATA
Statistics
Matches: 119, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
42 47 0.39
43 70 0.59
44 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.23
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGACCTTTAACGACGCTTTTATCACA
Found at i:35352435 original size:85 final size:85
Alignment explanation
Indices: 35352162--35352460 Score: 275
Period size: 85 Copynumber: 3.5 Consensus size: 85
35352152 TTTTGCATGG
* * * * * * * * *
35352162 CCTTTAGCGGTGCTTTTATAAAAAATG-CTGCTAATGAATATAACCTTTAGCGGCGC-TTTACCC
1 CCTTTAGCGGTGC-TTTATCACAAACGCCT-CTAAAGAACATGACCTTTAACAGCGCTTTTA-TC
* *
35352225 ACAAACGCCGCTAAAAAGCATGA
63 ACAAACGCCGCTAAAGAGAATGA
* * * * * *
35352248 CCTTTAGGGGTGATTTA-CCCATAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
1 CCTTTAGCGGTGCTTTATCACA-AACGCCTCTAAAGAACATGACCTTTAACAGCGCTTTTATCAC
35352312 AAACGCCGCTAAAGA-ACA-GA
65 AAACGCCGCTAAAGAGA-ATGA
*
35352332 CCTTTAGCGGCGCTTTTATCACAAACGCCTCTAAAGAACATGACCTTTAACAGCGCTTTTATCAC
1 CCTTTAGCGGTGC-TTTATCACAAACGCCTCTAAAGAACATGACCTTTAACAGCGCTTTTATCAC
*
35352397 AAACACCGCTAAAGAGAATGA
65 AAACGCCGCTAAAGAGAATGA
* * * * * *
35352418 CCTTTAACGATGCTTTATCAACAAATGCTTCTATAGAGCATGA
1 CCTTTAGCGGTGCTTTATC-ACAAACGCCTCTAAAGAACATGA
35352461 ATTTTAGTGG
Statistics
Matches: 176, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
84 13 0.07
85 112 0.64
86 51 0.29
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (85 bp):
CCTTTAGCGGTGCTTTATCACAAACGCCTCTAAAGAACATGACCTTTAACAGCGCTTTTATCACA
AACGCCGCTAAAGAGAATGA
Found at i:35353843 original size:15 final size:15
Alignment explanation
Indices: 35353818--35353855 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
35353808 TTCAAGGCTT
35353818 ATATTTTTC-TTAAA
1 ATATTTTTCTTTAAA
35353832 ATATTCTTTCTTTAAA
1 ATATT-TTTCTTTAAA
35353848 ATACTTTT
1 ATA-TTTT
35353856 ATAGTCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.24
15 4 0.19
16 10 0.48
17 2 0.10
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTTTCTTTAAA
Found at i:35358248 original size:14 final size:14
Alignment explanation
Indices: 35358225--35358302 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
35358215 TTAAAATCAG
*
35358225 ACCCTAAACATTAA
1 ACCCTAAACACTAA
*
35358239 ACCCTTAACACTAA
1 ACCCTAAACACTAA
* * *
35358253 ATCATAAACCCTAA
1 ACCCTAAACACTAA
* *
35358267 ACCTTAAACTGC-AA
1 ACCCTAAAC-ACTAA
* *
35358281 ACCATAAAC-CTAC
1 ACCCTAAACACTAA
35358294 ACCCTAAAC
1 ACCCTAAAC
35358303 CGTAAATATA
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
12 1 0.02
13 9 0.18
14 39 0.78
15 1 0.02
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.19
Consensus pattern (14 bp):
ACCCTAAACACTAA
Found at i:35358498 original size:21 final size:22
Alignment explanation
Indices: 35358447--35358498 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
35358437 AACCATGAAC
* *
35358447 AATACTAAAACCCTAACTATAA
1 AATACTAAAACCCAAACTACAA
* *
35358469 AATAATAAACCCCAAACTACAA
1 AATACTAAAACCCAAACTACAA
35358491 AAT-CTAAA
1 AATACTAAA
35358499 TCATAAACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (22 bp):
AATACTAAAACCCAAACTACAA
Found at i:35358499 original size:28 final size:28
Alignment explanation
Indices: 35358468--35358525 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
35358458 CCTAACTATA
35358468 AAATAATAAACCCCAAACTACAAAA-TCT
1 AAATAATAAACCCCAAACT-CAAAACTCT
* *
35358496 AAATCATAAACCCTAAACTCAAAACTCT
1 AAATAATAAACCCCAAACTCAAAACTCT
35358524 AA
1 AA
35358526 TCCCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (28 bp):
AAATAATAAACCCCAAACTCAAAACTCT
Found at i:35359764 original size:17 final size:19
Alignment explanation
Indices: 35359722--35359765 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
35359712 ACGAAATTTT
*
35359722 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
35359741 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
35359759 AA-TATTA
1 AATTATTA
35359766 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:35360415 original size:5 final size:5
Alignment explanation
Indices: 35360405--35360430 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
35360395 GGCGAAATTC
35360405 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
35360431 TCTCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:35365681 original size:113 final size:116
Alignment explanation
Indices: 35365442--35365722 Score: 372
Period size: 113 Copynumber: 2.4 Consensus size: 116
35365432 TTCAACAAAT
* * * ** *
35365442 GCCGCTAATTCTCGATCTATTGCGGTGTTTTTTAAAAAGCTTCGCTAATGCCACTAAAGCTCAGC
1 GCCGCTAATGCTCAATCTATTGCGG-CTTTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAAC
* **
35365507 AACAAAACGAGGTTGTTTTGCTCAACTTTTTTTGCGGCGTTTTCTGAAAAGC
65 AACAAAACGACGTTGTTTTGCTCAACTTTTTTTAAGGCGTTTTCTGAAAAGC
* * *
35365559 ACCGCTAATGCTCAATCTATTGCGGCTTTTTTAAGAAGCGCCGCTAATGCCACTAAAGCTCAACA
1 GCCGCTAATGCTCAATCTATTGCGGCTTTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACA
*
35365624 AC-AAACGACG-TGTTTTGCTTAAC-TTTTTTAAGGCGTTTT-TCGAAAAGC
66 ACAAAACGACGTTGTTTTGCTCAACTTTTTTTAAGGCGTTTTCT-GAAAAGC
* *
35365672 GCCGCTAATGCTCAATCTATTGCGACGTTTTTCAAAAAGCACCGCTAATGC
1 GCCGCTAATGCTCAATCTATTGCGGC-TTTTTTAAAAAGCACCGCTAATGC
35365723 TCGACCTATA
Statistics
Matches: 145, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
112 1 0.01
113 45 0.31
114 33 0.23
115 7 0.05
116 37 0.26
117 22 0.15
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (116 bp):
GCCGCTAATGCTCAATCTATTGCGGCTTTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACA
ACAAAACGACGTTGTTTTGCTCAACTTTTTTTAAGGCGTTTTCTGAAAAGC
Found at i:35365737 original size:40 final size:40
Alignment explanation
Indices: 35365657--35365737 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
35365647 TTTTTTAAGG
* * * *
35365657 CGTTTTTCGAAAAGCGCCGCTAATGCTCAATCTATTGCGA
1 CGTTTTTCAAAAAGCACCGCTAATGCTCAACCTATAGCGA
*
35365697 CGTTTTTCAAAAAGCACCGCTAATGCTCGACCTATAGCGA
1 CGTTTTTCAAAAAGCACCGCTAATGCTCAACCTATAGCGA
35365737 C
1 C
35365738 CTTTGTTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCACCGCTAATGCTCAACCTATAGCGA
Found at i:35365912 original size:19 final size:18
Alignment explanation
Indices: 35365888--35365935 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
35365878 TCATGACTGC
35365888 AAAATAAATTAAGCGAAAT
1 AAAATAAATTAAG-GAAAT
*
35365907 AAAATAAATT-AGTAAAT
1 AAAATAAATTAAGGAAAT
*
35365924 AAAATATATTAA
1 AAAATAAATTAA
35365936 AGTTTAGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 3 0.12
19 10 0.38
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAATAAATTAAGGAAAT
Found at i:35368669 original size:7 final size:7
Alignment explanation
Indices: 35368657--35368688 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
35368647 TTGTGATGCT
35368657 ATTTTTA
1 ATTTTTA
35368664 ATTTTTA
1 ATTTTTA
35368671 ATTTTTA
1 ATTTTTA
35368678 ATTTTTA
1 ATTTTTA
35368685 ATTT
1 ATTT
35368689 AATAACTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:35370215 original size:2 final size:2
Alignment explanation
Indices: 35370208--35370235 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35370198 CATGCATGCA
35370208 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
35370236 TAAATTACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35384496 original size:18 final size:19
Alignment explanation
Indices: 35384456--35384496 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
35384446 ATTATTTGGA
*
35384456 TATTATATAACTCTTGTTT
1 TATTATATAACTCTTGTTC
35384475 TATTAT-TAACT-TTGTTAC
1 TATTATATAACTCTTGTT-C
35384493 TATT
1 TATT
35384497 TTAGAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTATATAACTCTTGTTC
Found at i:35386049 original size:8 final size:8
Alignment explanation
Indices: 35386038--35386063 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
35386028 AAAATATCTA
35386038 AATAAAAT
1 AATAAAAT
35386046 AATAAAAT
1 AATAAAAT
35386054 AATAAAAT
1 AATAAAAT
35386062 AA
1 AA
35386064 ATTAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAAAAT
Found at i:35386680 original size:18 final size:20
Alignment explanation
Indices: 35386647--35386688 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
35386637 CGAAAAAAAA
*
35386647 AGAAAATAAGGTAAAAATTT
1 AGAAAATAAGGTAAAAATGT
35386667 AGAAAATAA-G-AAAAATGT
1 AGAAAATAAGGTAAAAATGT
35386685 AGAA
1 AGAA
35386689 GGATTGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 1 0.05
20 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (20 bp):
AGAAAATAAGGTAAAAATGT
Found at i:35386903 original size:3 final size:3
Alignment explanation
Indices: 35386897--35386973 Score: 111
Period size: 3 Copynumber: 25.7 Consensus size: 3
35386887 ATTTAGTAGT
35386897 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
35386945 TTA TT- TCA TTTA TTT TTA TTT TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
35386974 GGGCTGAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 1 0.02
3 63 0.95
4 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:35389856 original size:16 final size:16
Alignment explanation
Indices: 35389832--35389863 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35389822 ATTTGATTCG
*
35389832 GTCCTTACTTTTGCGA
1 GTCCATACTTTTGCGA
35389848 GTCCATACTTTTGCGA
1 GTCCATACTTTTGCGA
35389864 CTTTTTCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.41
Consensus pattern (16 bp):
GTCCATACTTTTGCGA
Found at i:35394722 original size:5 final size:5
Alignment explanation
Indices: 35394712--35394816 Score: 210
Period size: 5 Copynumber: 21.0 Consensus size: 5
35394702 CTTATAAATA
35394712 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
35394762 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
35394812 TATAT
1 TATAT
35394817 ACAATAAAAC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 100 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:35394908 original size:17 final size:17
Alignment explanation
Indices: 35394896--35394931 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
35394886 AGAGAAGGAA
35394896 AGAAAGAAAAGAAAAAG
1 AGAAAGAAAAGAAAAAG
35394913 AGAAAGAAAGGAGAAAAAG
1 AGAAAGAAA--AGAAAAAG
35394932 CTAGGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAGAAAAAG
Found at i:35394916 original size:25 final size:24
Alignment explanation
Indices: 35394850--35394929 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
35394840 ATAAATAAAT
* *
35394850 AGAAATAGAAAAAGAG-AGCCAAAGT
1 AGAAA-AGAAAAAGAGAAG-GAAAGA
* *
35394875 AGAAATGAAACAGAGAAGGAAAGAA
1 AGAAAAGAAAAAGAGAAGGAAAG-A
* *
35394900 AGAAAAGAAAAAGAGAAAGAAAGG
1 AGAAAAGAAAAAGAGAAGGAAAGA
35394924 AGAAAA
1 AGAAAA
35394930 AGCTAGGGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
24 18 0.40
25 27 0.60
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.04
Consensus pattern (24 bp):
AGAAAAGAAAAAGAGAAGGAAAGA
Found at i:35404645 original size:61 final size:61
Alignment explanation
Indices: 35404550--35404673 Score: 176
Period size: 61 Copynumber: 2.0 Consensus size: 61
35404540 GGTTTTGAAC
** * **
35404550 ACCTCTTAGAAATCCATGTGAATATTGGAGTATTGTTAGAGTGTTACAATATGTGGTTCTT
1 ACCTCTTAGAAATCCACATGAATATCGGAGTATTGCCAGAGTGTTACAATATGTGGTTCTT
** *
35404611 ACCTCTTAGTGATCCACATGAATATCGGAGTATTGCCAGAGTGTTACAATATGTGTTTCTT
1 ACCTCTTAGAAATCCACATGAATATCGGAGTATTGCCAGAGTGTTACAATATGTGGTTCTT
35404672 AC
1 AC
35404674 TCTACCTGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (61 bp):
ACCTCTTAGAAATCCACATGAATATCGGAGTATTGCCAGAGTGTTACAATATGTGGTTCTT
Found at i:35406244 original size:20 final size:19
Alignment explanation
Indices: 35406221--35406272 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
35406211 AAATCCTTTT
35406221 AAAATTTAAAAATTATTAAA
1 AAAATTTAAAAATTA-TAAA
**
35406241 AAAACATAAAAATTATAAA
1 AAAATTTAAAAATTATAAA
*
35406260 CAAATTTATAAAA
1 AAAATTTA-AAAA
35406273 AATTATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATTTAAAAATTATAAA
Found at i:35406280 original size:10 final size:10
Alignment explanation
Indices: 35406228--35406280 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
35406218 TTTAAAATTT
35406228 AAAAATTATTA
1 AAAAATTA-TA
**
35406239 AAAAAACAT-
1 AAAAATTATA
35406248 AAAAATTATA
1 AAAAATTATA
35406258 AACAAATTTATA
1 AA-AAA-TTATA
35406270 AAAAATTATA
1 AAAAATTATA
35406280 A
1 A
35406281 TTATAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 7 0.20
10 9 0.26
11 12 0.34
12 7 0.20
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:35408996 original size:6 final size:6
Alignment explanation
Indices: 35408987--35409014 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35408977 TTCACTTTCA
35408987 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
35409015 AATAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:35409514 original size:17 final size:18
Alignment explanation
Indices: 35409483--35409531 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
35409473 ATCACTTATT
* *
35409483 TTTTTAAAATTAAATTTA-
1 TTTTTAAAA-AAAATTGAG
35409501 TTTTTAAAAAAAATTGAG
1 TTTTTAAAAAAAATTGAG
35409519 TTTTTACAAAAAA
1 TTTTTA-AAAAAA
35409532 CATAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 15 0.56
19 6 0.22
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (18 bp):
TTTTTAAAAAAAATTGAG
Found at i:35423276 original size:21 final size:21
Alignment explanation
Indices: 35423250--35423294 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35423240 CTATCTACTT
* *
35423250 AAAAAAGTTGTAACATTATAA
1 AAAAAAATTATAACATTATAA
* *
35423271 AAAAAAATTATAATATTTTAA
1 AAAAAAATTATAACATTATAA
35423292 AAA
1 AAA
35423295 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAAAATTATAACATTATAA
Found at i:35424511 original size:34 final size:31
Alignment explanation
Indices: 35424444--35424511 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
35424434 TTTAGCTAAA
* * *
35424444 TGGGCTCACATGCCCATATGGTTTGCCCGTG
1 TGGGCCCACATGCCCACATGGTTAGCCCGTG
35424475 TGGGCCCACATGCCCACATTGGCCTTAGCCCGTG
1 TGGGCCCACATGCCCACA-TGG--TTAGCCCGTG
35424509 TGG
1 TGG
35424512 ATCACACGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 16 0.52
32 3 0.10
34 12 0.39
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.25
Consensus pattern (31 bp):
TGGGCCCACATGCCCACATGGTTAGCCCGTG
Found at i:35426004 original size:40 final size:40
Alignment explanation
Indices: 35425960--35426144 Score: 205
Period size: 39 Copynumber: 4.7 Consensus size: 40
35425950 GTTCAAAACA
* * ***
35425960 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
* * *
35426000 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
* * * *
35426040 CCTTCGGG-CTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
* ** *
35426079 CCTTCAGG-CTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
35426118 CCTTCGGG-CTTAGCCCGGATATCACAA
1 CCTTCGGGACTTAGCCCGGATATCACAA
35426145 TTCGCACATT
Statistics
Matches: 129, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 89 0.69
40 40 0.31
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
Found at i:35426071 original size:39 final size:39
Alignment explanation
Indices: 35425990--35426152 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
35425980 TATGGTAACC
* *
35425990 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
35426030 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
35426069 CGCACAATTGCCTTCAGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
35426108 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
35426147 CGCACA
1 CGCACA
35426153 TTCATTCACA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:35428634 original size:74 final size:74
Alignment explanation
Indices: 35428511--35428656 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 74
35428501 AAACGTTAAT
*
35428511 TTCTTTTCTAAGAGAGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
1 TTCTTTTCTAAAAGAGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
35428576 CACTACCTC
66 CACTACCTC
* *
35428585 TTCTTTTCTAAAAGGGAGAGGAAAACAAAACTAATCAGATATTCTAAAATCCTCTTAATTCTCTC
1 TTCTTTTCTAAAAGAGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
*
35428650 CATTACC
66 CACTACC
35428657 GCACTCTTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (74 bp):
TTCTTTTCTAAAAGAGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
CACTACCTC
Found at i:35429235 original size:15 final size:16
Alignment explanation
Indices: 35429207--35429247 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
35429197 TATTAATATA
35429207 TAATTTTT--TTATTT
1 TAATTTTTAATTATTT
35429221 T-ATTTTTAATTATTT
1 TAATTTTTAATTATTT
35429236 TAAATTTTTAAT
1 T-AATTTTTAAT
35429248 ATAACTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 1 0.04
15 7 0.30
17 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TAATTTTTAATTATTT
Found at i:35429327 original size:12 final size:12
Alignment explanation
Indices: 35429312--35429340 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
35429302 GTATTATTTT
35429312 TATTTATTTTAA
1 TATTTATTTTAA
35429324 TATTTATTTTAA
1 TATTTATTTTAA
35429336 TATTT
1 TATTT
35429341 TTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTATTTTAA
Found at i:35429327 original size:21 final size:20
Alignment explanation
Indices: 35429304--35429383 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 20
35429294 TTGTTTTAGT
35429304 ATTATTTTTATTTATTTTAA
1 ATTATTTTTATTTATTTTAA
* *
35429324 TATTTATTTTAATAT-TTTTAA
1 -A-TTATTTTTATTTATTTTAA
35429345 ATATATTTGATTTATTATATTTTTAA
1 AT-TA-TT--TTTATT-TA-TTTTAA
35429371 ATT-TTTTTATTTA
1 ATTATTTTTATTTA
35429384 ATGAAATAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
19 1 0.02
20 5 0.11
21 15 0.32
22 10 0.21
23 6 0.13
24 1 0.02
25 1 0.02
26 8 0.17
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (20 bp):
ATTATTTTTATTTATTTTAA
Found at i:35429350 original size:24 final size:25
Alignment explanation
Indices: 35429323--35429383 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
35429313 ATTTATTTTA
35429323 ATATTTATTT-TAATATTTTTAAAT
1 ATATTTATTTATAATATTTTTAAAT
*
35429347 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTTATAATATTTTTAAAT
* *
35429373 TTTTTTATTTA
1 ATATTTATTTA
35429384 ATGAAATAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 9 0.28
26 17 0.53
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
ATATTTATTTATAATATTTTTAAAT
Found at i:35432651 original size:142 final size:142
Alignment explanation
Indices: 35432395--35432680 Score: 509
Period size: 142 Copynumber: 2.0 Consensus size: 142
35432385 TTGGTCTCGC
*
35432395 AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAACTTAACCACCAAACCAGTAGGCC
1 AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAACTTAACCACCAAACCAGTAGACC
* * *
35432460 CATTCTGATATGATTTTACAAATAATTTAATATAAACCCACTGAGCAAGTATAACGCTTAAGTTA
66 CATTCTAATATGATTTTACAAATAATTTAATATAAACCCACCGAGCAAGTATAACGCTTAAGTCA
35432525 GAAAAATACCAA
131 GAAAAATACCAA
* *
35432537 AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAATTTAACCACCAAACCAGTTGACC
1 AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAACTTAACCACCAAACCAGTAGACC
*
35432602 CATTCTAATATGATTTTGCAAATAATTTAATATAAACCCACCGAGCAAGTATAACGCTTAAGTCA
66 CATTCTAATATGATTTTACAAATAATTTAATATAAACCCACCGAGCAAGTATAACGCTTAAGTCA
35432667 GAAAAATACCAA
131 GAAAAATACCAA
35432679 AA
1 AA
35432681 CTTACCAGAG
Statistics
Matches: 137, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 137 1.00
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.22
Consensus pattern (142 bp):
AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAACTTAACCACCAAACCAGTAGACC
CATTCTAATATGATTTTACAAATAATTTAATATAAACCCACCGAGCAAGTATAACGCTTAAGTCA
GAAAAATACCAA
Found at i:35434150 original size:2 final size:2
Alignment explanation
Indices: 35434143--35434171 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35434133 ATTTTGTTAA
35434143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35434172 ATAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35436087 original size:29 final size:29
Alignment explanation
Indices: 35436040--35436109 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
35436030 TTAAAATATT
* *
35436040 AAAAT-AATTTTTATTATTTTTATTTTTA
1 AAAATAAATTTATAATATTTTTATTTTTA
35436068 AAAATAAATTTATAATATTTTTATTTTTA
1 AAAATAAATTTATAATATTTTTATTTTTA
35436097 AAAATAAATTTAT
1 AAAATAAATTTAT
35436110 GTATGCAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
AAAATAAATTTATAATATTTTTATTTTTA
Found at i:35436279 original size:18 final size:16
Alignment explanation
Indices: 35436256--35436290 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
35436246 TTTTAAAATT
35436256 AATATAAATATATAAAAA
1 AATATAAA-A-ATAAAAA
35436274 AATATAAAAATAAAAA
1 AATATAAAAATAAAAA
35436290 A
1 A
35436291 TAAGTTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATATAAAAATAAAAA
Found at i:35436407 original size:27 final size:26
Alignment explanation
Indices: 35436351--35436408 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
35436341 ACAATTTAAT
* *
35436351 AATTATTGATAAAATGAAATGTAAAT
1 AATTATTAATAAAATGAAATGTAAAA
*
35436377 AATTATTAATAAAAATTAAATG-AGAAA
1 AATTATTAAT-AAAATGAAATGTA-AAA
35436404 AATTA
1 AATTA
35436409 CTGAACATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (26 bp):
AATTATTAATAAAATGAAATGTAAAA
Found at i:35439930 original size:20 final size:20
Alignment explanation
Indices: 35439901--35439945 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35439891 AGCACATATA
* *
35439901 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
35439921 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
35439941 TTCAT
1 TTCAT
35439946 TTTAGTCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:35443604 original size:3 final size:3
Alignment explanation
Indices: 35443591--35443641 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
35443581 AATGCTAAAA
35443591 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35443637 AAT AA
1 AAT AA
35443642 ACTAATAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35443754 original size:2 final size:2
Alignment explanation
Indices: 35443747--35443775 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35443737 AGTAGGTGTA
35443747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35443776 GATAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35443801 original size:20 final size:20
Alignment explanation
Indices: 35443776--35443824 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
35443766 TATATATATA
35443776 GATAATAAAAAAATAATAAT
1 GATAATAAAAAAATAATAAT
** *
35443796 GATAATAAAATGATGATAAT
1 GATAATAAAAAAATAATAAT
*
35443816 AATAATAAA
1 GATAATAAA
35443825 GACACAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (20 bp):
GATAATAAAAAAATAATAAT
Found at i:35443805 original size:17 final size:17
Alignment explanation
Indices: 35443777--35443820 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
35443767 ATATATATAG
*
35443777 ATAATAAAAAAATAATA
1 ATAATAATAAAATAATA
* * *
35443794 ATGATAATAAAATGATG
1 ATAATAATAAAATAATA
35443811 ATAATAATAA
1 ATAATAATAA
35443821 TAAAGACACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (17 bp):
ATAATAATAAAATAATA
Found at i:35446871 original size:47 final size:47
Alignment explanation
Indices: 35446762--35446872 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
35446752 CCGGGATAAG
* * *
35446762 CACATAGTGCTTTATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTATAGTA
* * * *
35446809 CACAAAGTACTTCATCGGAACAAATCTAGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTA-TAGTA
35446856 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
35446873 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 1 0.02
47 50 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTATAGTA
Found at i:35447643 original size:4 final size:4
Alignment explanation
Indices: 35447634--35447722 Score: 88
Period size: 4 Copynumber: 21.8 Consensus size: 4
35447624 CCCTTTTCTA
** *
35447634 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TCAC GTTTGC TCTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC
* * ** *
35447684 TGTA ACTC TTTC TATC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
35447723 TTAACTTACT
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
4 65 0.94
5 3 0.04
6 1 0.01
ACGTcount: A:0.04, C:0.26, G:0.03, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:35454119 original size:47 final size:47
Alignment explanation
Indices: 35454010--35454120 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
35454000 CCGGGATAAG
* * *
35454010 CACATAGTGCTTTATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTATAGTA
* * * *
35454057 CACAAAGTACTTCATCGGAACAAATCTAGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTA-TAGTA
35454104 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
35454121 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 1 0.02
47 50 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCAGAACTTTAACAGTATAGTA
Found at i:35454890 original size:4 final size:4
Alignment explanation
Indices: 35454881--35454909 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
35454871 CCCTTTTCTA
35454881 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
35454910 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:35457207 original size:192 final size:192
Alignment explanation
Indices: 35456860--35457265 Score: 618
Period size: 192 Copynumber: 2.1 Consensus size: 192
35456850 CAATTATTAA
*
35456860 AATTCCATGTACATGTAACAATTATACTGTATATCCTTATATCATATATATATATATGAACCATT
1 AATTCC-TGTACATGTAACAATTATACCGTATATCCTTATATC--A-ATATATATATGAACCATT
* *
35456925 TCCATGTAAGTACCTATACTAGTTCGTATTGAACTTATATAATCTCATAATAACACTATGCCCAT
62 TCCATGTAAATACCTATACTAGTTCGTATTGAACTTATACAATCTCATAATAACACTATGCCCAT
*
35456990 TGAACCACTTAGAATCACGTTAGATACATG-GGTAGTACAAACGAGGTGTACTGAACTGTAATCT
127 TGAACCACTTAGAATCACGTTAGAT--ATGCGGTAGTACAAACAAGGTGTACTGAACTGTAATCT
35457054 GTC
190 GTC
* *
35457057 AATTCCTGTACATGTAACATTTATACCGTATATCCTTATATC-ATATATATATGAACTATTTCCA
1 AATTCCTGTACATGTAACAATTATACCGTATATCCTTATATCAATATATATATGAACCATTTCCA
* * *
35457121 TGTAAATACTTGTACTAGTTCGTATTGAACTTATACAATCTCATAATAACACTATGCCCGTTGAA
66 TGTAAATACCTATACTAGTTCGTATTGAACTTATACAATCTCATAATAACACTATGCCCATTGAA
*** *
35457186 CCACTTAGAATCTTTTTAGATATGCTGGTAGTACACACAAGGTGTACTGAACTGTAATCTGTC
131 CCACTTAGAATCACGTTAGATATGC-GGTAGTACAAACAAGGTGTACTGAACTGTAATCTGTC
35457249 AATTCCTGTACATGTAA
1 AATTCCTGTACATGTAA
35457266 GCTCATACAA
Statistics
Matches: 194, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
190 3 0.02
192 151 0.78
196 34 0.18
197 6 0.03
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (192 bp):
AATTCCTGTACATGTAACAATTATACCGTATATCCTTATATCAATATATATATGAACCATTTCCA
TGTAAATACCTATACTAGTTCGTATTGAACTTATACAATCTCATAATAACACTATGCCCATTGAA
CCACTTAGAATCACGTTAGATATGCGGTAGTACAAACAAGGTGTACTGAACTGTAATCTGTC
Found at i:35471004 original size:14 final size:14
Alignment explanation
Indices: 35470981--35471011 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35470971 TTAAGGTGAA
*
35470981 TTTTCTATTTTTAT
1 TTTTCAATTTTTAT
35470995 TTTTCAATTTTTAT
1 TTTTCAATTTTTAT
35471009 TTT
1 TTT
35471012 CAAATCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCAATTTTTAT
Found at i:35471693 original size:3 final size:3
Alignment explanation
Indices: 35471676--35471730 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
35471666 AATACTCTTG
*
35471676 TTA TTG TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35471723 TTTA TTA T
1 -TTA TTA T
35471731 GCATTAGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35472066 original size:25 final size:25
Alignment explanation
Indices: 35472036--35472095 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
35472026 ATATTTTACA
35472036 TATATATTATCATGTATATACTTTTT
1 TATATATTATCATGTATATA-TTTTT
* * *
35472062 T-TATATCATTATTTATATATTTTT
1 TATATATTATCATGTATATATTTTT
*
35472086 TATACATTAT
1 TATATATTAT
35472096 TTCGTGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 6 0.21
25 21 0.75
26 1 0.04
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (25 bp):
TATATATTATCATGTATATATTTTT
Found at i:35472078 original size:12 final size:12
Alignment explanation
Indices: 35472061--35472097 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
35472051 ATATACTTTT
35472061 TTTATATCATTA
1 TTTATATCATTA
*
35472073 TTTATAT-ATTT
1 TTTATATCATTA
35472084 TTTATA-CATTA
1 TTTATATCATTA
35472095 TTT
1 TTT
35472098 CGTGAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATATCATTA
Done.