Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 191 of 378
Found at i:56183970 original size:43 final size:44
Alignment explanation
Indices: 56183904--56183988 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 44
56183894 TCACCAAGCC
* * *
56183904 TTAAACCCCTAAGCGGTAAGGTAACAGG-TTAAATTTACAGACT
1 TTAAACCCCTAAGCAGTAAGGTAACAGGCTAAAAATTACAGACT
* * *
56183947 TTAACCCCCTAAGCAGTAGGGTAATAGGCTAAAAATTACAGA
1 TTAAACCCCTAAGCAGTAAGGTAACAGGCTAAAAATTACAGA
56183989 TCTTGTCTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
43 24 0.69
44 11 0.31
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (44 bp):
TTAAACCCCTAAGCAGTAAGGTAACAGGCTAAAAATTACAGACT
Found at i:56186480 original size:3 final size:3
Alignment explanation
Indices: 56186472--56186534 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
56186462 TTTTGCATCT
56186472 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
56186520 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
56186535 CCATTTTTTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56186642 original size:2 final size:2
Alignment explanation
Indices: 56186598--56186633 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
56186588 TCGTTATCAT
56186598 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
56186634 GGTATATATT
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:56186740 original size:20 final size:21
Alignment explanation
Indices: 56186712--56186750 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
56186702 TCCTTTTTAT
*
56186712 TACTATTACTAC-ATTATTTC
1 TACTATTACAACTATTATTTC
*
56186732 TACTTTTACAACTATTATT
1 TACTATTACAACTATTATT
56186751 ATTATCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (21 bp):
TACTATTACAACTATTATTTC
Found at i:56186935 original size:25 final size:24
Alignment explanation
Indices: 56186906--56186968 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
56186896 TCCTTTTTAC
56186906 TTATTCTTATTATTCTTGT-TTATTT
1 TTATTCTTATTATT-TT-TATTATTT
*
56186931 TTATTCTTATCATTTTTATTATTT
1 TTATTCTTATTATTTTTATTATTT
56186955 TTA-TC-TATTATTTT
1 TTATTCTTATTATTTT
56186969 CCTCTTAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 8 0.23
23 3 0.09
24 11 0.31
25 13 0.37
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (24 bp):
TTATTCTTATTATTTTTATTATTT
Found at i:56189870 original size:26 final size:26
Alignment explanation
Indices: 56189840--56189895 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
56189830 TGAAATGCCC
56189840 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
56189866 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
56189892 ATCA
1 ATCA
56189896 ATTTTTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:56192839 original size:15 final size:17
Alignment explanation
Indices: 56192809--56192841 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
56192799 TTCTCTTTTA
56192809 TCATCTTTATACACTAT
1 TCATCTTTATACACTAT
56192826 TCAT-TTTA-ACACTAT
1 TCATCTTTATACACTAT
56192841 T
1 T
56192842 TTTATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TCATCTTTATACACTAT
Found at i:56198687 original size:2 final size:2
Alignment explanation
Indices: 56198675--56198710 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
56198665 GTTGATGAGC
* *
56198675 TA TA TA AA TA TA TA TA TG 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
56198711 GATTTGATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:56199923 original size:39 final size:39
Alignment explanation
Indices: 56199862--56199952 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
56199852 TTTATAAGAT
* *
56199862 TGGAAATATATCCAGACATGAGGTCTGCAGGCTATATGC
1 TGGAAATATATCCAGACATGAGGTCCGCAGGCTACATGC
** * *
56199901 TGGAAATATATCTGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAATATATCCAGACATGAGGTCCGCAGGCTACATGC
*
56199940 TGGAAAAATATCC
1 TGGAAATATATCC
56199953 GGGTTAAAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (39 bp):
TGGAAATATATCCAGACATGAGGTCCGCAGGCTACATGC
Found at i:56206391 original size:23 final size:22
Alignment explanation
Indices: 56206363--56206470 Score: 72
Period size: 23 Copynumber: 4.5 Consensus size: 22
56206353 TAATATTCCG
*
56206363 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGG-AGGATATTCT
56206386 GGTGTGTTTGGGAGGATTATATGATACT
1 GGTGTGTTTGGGAGG---ATAT--T-CT
* *
56206414 GGTGTGTTTTGGAGGATTATACT
1 GGTGTGTTTGGGAGGA-TATTCT
** * *
56206437 GGTGTGTTTTGGTTGGACATTTT
1 GGTGTG-TTTGGGAGGATATTCT
56206460 GGTGTGTTTGG
1 GGTGTGTTTGG
56206471 ATGGAATCCG
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
22 7 0.10
23 29 0.43
24 7 0.10
25 5 0.07
26 3 0.04
27 1 0.01
28 16 0.24
ACGTcount: A:0.13, C:0.04, G:0.38, T:0.45
Consensus pattern (22 bp):
GGTGTGTTTGGGAGGATATTCT
Found at i:56206440 original size:51 final size:52
Alignment explanation
Indices: 56206325--56206445 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 52
56206315 GGGAGGATAT
* *
56206325 GATATACTGGTGTGTTATGGAGGATTTATAATATTCCGGGTGTGTTTGGGTTG
1 GATATACTGGTGTGTT-TGGAGGATTTATAATATTACGGGTGTGTTTGGGTAG
* * *
56206378 GATATTCTGGTGTGTTTGGGAGGA-TTAT-ATGA-TACTGGTGTGTTTTGG-AG
1 GATATACTGGTGTGTTT-GGAGGATTTATAAT-ATTACGGGTGTGTTTGGGTAG
56206428 GATTATACTGGTGTGTTT
1 GA-TATACTGGTGTGTTT
56206446 TGGTTGGACA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
50 3 0.05
51 29 0.49
52 6 0.10
53 21 0.36
ACGTcount: A:0.18, C:0.05, G:0.34, T:0.43
Consensus pattern (52 bp):
GATATACTGGTGTGTTTGGAGGATTTATAATATTACGGGTGTGTTTGGGTAG
Found at i:56206688 original size:21 final size:21
Alignment explanation
Indices: 56206638--56206724 Score: 95
Period size: 21 Copynumber: 4.1 Consensus size: 21
56206628 GGCTATACTG
*
56206638 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
* *
56206659 ATTTTAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTATGTGTCGT
**
56206682 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
56206703 TTCAGGCA-CTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
56206723 AT
1 AT
56206725 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 11 0.20
21 26 0.47
23 18 0.33
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (21 bp):
ATCAGGCACCTTATGTGTCGT
Found at i:56206903 original size:17 final size:19
Alignment explanation
Indices: 56206881--56206920 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
56206871 ATTGAAAGTG
56206881 TGAAAA-AAATG-GAATTA
1 TGAAAAGAAATGTGAATTA
*
56206898 TGAAAAGAAATGTGAATTG
1 TGAAAAGAAATGTGAATTA
56206917 TGAA
1 TGAA
56206921 TTGAAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.25
Consensus pattern (19 bp):
TGAAAAGAAATGTGAATTA
Found at i:56207856 original size:46 final size:46
Alignment explanation
Indices: 56207806--56207991 Score: 142
Period size: 46 Copynumber: 3.8 Consensus size: 46
56207796 TGGTTGGACC
56207806 ATGGCATCAATGTGATATGTGATCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAATGTGATATGTGATCTGTGTAAGACCATAGCTGGGCT
* * ** * * *
56207852 ATGGCATCAGAGATATGTGATTACGTGCTTCCATATAAGACCATATCTGGGAT
1 ATGGCATC----A-ATGTGA-TATGTG-ATCTGTGTAAGACCATAGCTGGGCT
* *
56207905 ATGGCATCAGTGTGATATGTGAT-TCGTGTAAGACCATGGCTGGGCT
1 ATGGCATCAATGTGATATGTGATCT-GTGTAAGACCATAGCTGGGCT
** * *
56207951 ATGGC-TACGGTGTGTATATGTGACTATGTGCAAGACCATAG
1 ATGGCAT-CAATGTG-ATATGTGA-TCTGTGTAAGACCATAG
56207992 TTTTACTATG
Statistics
Matches: 109, Mismatches: 19, Indels: 22
0.73 0.13 0.15
Matches are distributed among these distances:
45 1 0.01
46 36 0.33
47 13 0.12
48 18 0.17
49 2 0.02
50 1 0.01
51 6 0.06
52 5 0.05
53 27 0.25
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (46 bp):
ATGGCATCAATGTGATATGTGATCTGTGTAAGACCATAGCTGGGCT
Found at i:56214417 original size:12 final size:12
Alignment explanation
Indices: 56214400--56214424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56214390 GTTAATGTGA
56214400 TTTTTATGAAAT
1 TTTTTATGAAAT
56214412 TTTTTATGAAAT
1 TTTTTATGAAAT
56214424 T
1 T
56214425 AAATTGATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTTTATGAAAT
Found at i:56215823 original size:43 final size:43
Alignment explanation
Indices: 56215776--56215941 Score: 244
Period size: 43 Copynumber: 3.9 Consensus size: 43
56215766 TGAATAATAT
* *
56215776 TATCGGGCTACGGGCCTAGCAGGCTATAATGCCGGTGAGATAA
1 TATCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAA
*
56215819 TATCGGGCTTCGAGCCTAGTAGGCTATAATGCCGGTGAGATAA
1 TATCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAA
* * *
56215862 TATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAATGA
1 TATCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAA
* * *
56215905 TATCGGGCTTCAAGACTAGCAGGCGA-AATGCCGGTGA
1 TATCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
56215942 ATGAGTTCAG
Statistics
Matches: 112, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 11 0.10
43 101 0.90
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.22
Consensus pattern (43 bp):
TATCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAA
Found at i:56215965 original size:41 final size:43
Alignment explanation
Indices: 56215791--56215969 Score: 121
Period size: 43 Copynumber: 4.2 Consensus size: 43
56215781 GGCTACGGGC
* * * * * ** *
56215791 CTAGCAGGCTATAATGCCGGTGAGATAATATCGGGCTTCGAGC
1 CTAGCAGGCGATAATGCCGGTGAAATGATATCAGACTTAAAGA
* * * * * * *** *
56215834 CTAGTAGGCTATAATGCCGGTGAGATAATATCGGGCTTCGGGC
1 CTAGCAGGCGATAATGCCGGTGAAATGATATCAGACTTAAAGA
* * * *
56215877 CTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTCAAGA
1 CTAGCAGGCGATAATGCCGGTGAAATGATATCAGACTTAAAGA
*
56215920 CTAGCAGGCGA-AATGCCGGTG-AATGAGT-TCAGACTTAAAGT
1 CTAGCAGGCGATAATGCCGGTGAAATGA-TATCAGACTTAAAGA
56215961 CTAGCAGGC
1 CTAGCAGGC
56215970 TTCGTGCTGG
Statistics
Matches: 122, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
41 23 0.19
42 11 0.09
43 88 0.72
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (43 bp):
CTAGCAGGCGATAATGCCGGTGAAATGATATCAGACTTAAAGA
Found at i:56223188 original size:11 final size:11
Alignment explanation
Indices: 56223152--56223207 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
56223142 CATGGTATGT
56223152 ATGATATGCAC
1 ATGATATGCAC
* *
56223163 ATGACATG--T
1 ATGATATGCAC
56223172 ATGATATGCAC
1 ATGATATGCAC
*
56223183 ATGATATG--T
1 ATGATATGCAC
56223192 ATGATATGCAC
1 ATGATATGCAC
56223203 ATGAT
1 ATGAT
56223208 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:56223207 original size:20 final size:20
Alignment explanation
Indices: 56223141--56223207 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
56223131 ATTTTGATAA
*
56223141 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
56223161 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
56223181 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
56223201 ACATGAT
1 ACATGAT
56223208 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:56223316 original size:22 final size:23
Alignment explanation
Indices: 56223258--56223394 Score: 208
Period size: 23 Copynumber: 6.0 Consensus size: 23
56223248 AGGAAGTGAA
56223258 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
56223281 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
56223304 AAAGGG-TTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
56223326 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
56223348 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
*
56223372 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTATGCC-CCAGTTAT
56223395 ATGATAAAGC
Statistics
Matches: 106, Mismatches: 3, Indels: 9
0.90 0.03 0.08
Matches are distributed among these distances:
22 32 0.30
23 53 0.50
24 21 0.20
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:56223323 original size:45 final size:47
Alignment explanation
Indices: 56223257--56223394 Score: 212
Period size: 45 Copynumber: 3.0 Consensus size: 47
56223247 GAGGAAGTGA
56223257 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
56223304 -AAAGGG-TTATGCCCCAGTTATTAAAGGGCTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
* *
56223348 AAAAGGGCTTTTGCCCCAGTTATTAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAG-GGCTTATGCC-CCAGTTAT
56223395 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 2, Indels: 9
0.88 0.02 0.09
Matches are distributed among these distances:
44 10 0.12
45 34 0.40
46 28 0.33
47 4 0.05
48 8 0.10
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:56223632 original size:29 final size:30
Alignment explanation
Indices: 56223587--56223644 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
56223577 CGTTTACAGT
56223587 AAAGGCTTCGGCCCAGTAATATGAAATATA
1 AAAGGCTTCGGCCCAGTAATATGAAATATA
**
56223617 AAAGGCTTCGG-CCAGTGTTATGAAATAT
1 AAAGGCTTCGGCCCAGTAATATGAAATAT
56223645 GAAATATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATA
Found at i:56231281 original size:11 final size:11
Alignment explanation
Indices: 56231245--56231300 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
56231235 CATGGTATGT
56231245 ATGATATGCAC
1 ATGATATGCAC
* *
56231256 ATGACATG--T
1 ATGATATGCAC
56231265 ATGATATGCAC
1 ATGATATGCAC
*
56231276 ATGATATG--T
1 ATGATATGCAC
56231285 ATGATATGCAC
1 ATGATATGCAC
56231296 ATGAT
1 ATGAT
56231301 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:56231300 original size:20 final size:20
Alignment explanation
Indices: 56231234--56231300 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
56231224 ATTTTGATAA
*
56231234 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
56231254 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
56231274 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
56231294 ACATGAT
1 ACATGAT
56231301 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:56231429 original size:24 final size:23
Alignment explanation
Indices: 56231351--56231467 Score: 146
Period size: 23 Copynumber: 5.0 Consensus size: 23
56231341 AGGAAGTGAA
56231351 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
56231374 AAAGGGGTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
56231397 AAAGGGCTTATGACCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
56231420 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
*
56231444 CAAAGAGGC-TAGGCCTCCAGTTAT
1 -AAAG-GGCTTATGCC-CCAGTTAT
56231468 ATGATAAAGC
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 42 0.52
24 28 0.35
25 11 0.14
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:56231696 original size:31 final size:31
Alignment explanation
Indices: 56231661--56231720 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
56231651 CGTTTACAGT
56231661 AAAGGCTTCGGCCCAGTAATATGAAATATAA
1 AAAGGCTTCGGCCCAGTAATATGAAATATAA
* **
56231692 AAAGGCTTCGGGCCAGTGTTATGAAATAT
1 AAAGGCTTCGGCCCAGTAATATGAAATAT
56231721 GAAATATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATAA
Found at i:56236166 original size:40 final size:39
Alignment explanation
Indices: 56236119--56236272 Score: 204
Period size: 38 Copynumber: 4.0 Consensus size: 39
56236109 GAATCCAGTC
* ** *
56236119 ACCAGCACAAAGCCTGCGGGACTTTAAGCTTGGATATAAT
1 ACCAGCACGAAGCCTGCGGGACTTTAA-CCCGGATATATT
* *
56236159 ACCAGCACTAAGCCTGCGAGACTTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGACTTTAACCCGGATATATT
* * *
56236198 ACCAACACGAAGCCCGTGGGAC-TTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGACTTTAACCCGGATATATT
56236236 ACCAGCACGAAGCCTGCGGGAC-TTAACCCGGATATAT
1 ACCAGCACGAAGCCTGCGGGACTTTAACCCGGATATAT
56236273 ATCGAGTGCT
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 50 0.50
39 26 0.26
40 25 0.25
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (39 bp):
ACCAGCACGAAGCCTGCGGGACTTTAACCCGGATATATT
Found at i:56244403 original size:38 final size:38
Alignment explanation
Indices: 56244286--56244477 Score: 222
Period size: 38 Copynumber: 5.0 Consensus size: 38
56244276 GAATCCAGTC
* * * *
56244286 ACCAGTACAAAGCCTGCGGGACTTTAAGCTCGGATATAAT
1 ACCAGCACGAAGCCTGCGGGA-TTTAA-CCCGGATATATT
* * * *
56244326 ACCAGTACTAAGCCTGCGAGACTTTAACCCGGATGTATT
1 ACCAGCACGAAGCCTGCGGGA-TTTAACCCGGATATATT
*
56244365 ACCAGCATGAAGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
* **
56244403 ACCAGCACGAAGCCTGCGGGACTTAACCTAGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
* * *
56244441 ACCAGCACGAAGCCTGCGAGACTTAACCCTGATATAT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAT
56244478 ATCGAGTGCT
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
38 84 0.62
39 26 0.19
40 25 0.19
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (38 bp):
ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
Found at i:56257055 original size:30 final size:30
Alignment explanation
Indices: 56257019--56257083 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
56257009 CAACTTAATA
*
56257019 AACAAATGTCTCTAAAATAATAAAAAAATT
1 AACAAATGCCTCTAAAATAATAAAAAAATT
* *
56257049 AACAAATGCCTTTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAAAAAAATT
56257079 AACAA
1 AACAA
56257084 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAAAAAAATT
Found at i:56264186 original size:43 final size:43
Alignment explanation
Indices: 56264138--56264221 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
56264128 AAAATACATC
*
56264138 CACTAATATAGCTAAAGATCTTAGAATA-CGATTCCTTTAATCA
1 CACTAATATAGCTAAAGATCCTAGAATATC-ATTCCTTTAATCA
*
56264181 CACTAATATAGCTAAAGATCCTAGATTATCATTCCTTTAAT
1 CACTAATATAGCTAAAGATCCTAGAATATCATTCCTTTAAT
56264222 TGTTGCACTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (43 bp):
CACTAATATAGCTAAAGATCCTAGAATATCATTCCTTTAATCA
Found at i:56275185 original size:55 final size:53
Alignment explanation
Indices: 56275077--56275284 Score: 204
Period size: 55 Copynumber: 3.8 Consensus size: 53
56275067 ATTAGGGTTT
* ** *
56275077 AAGGATACCATGTAAGACCATGCCAAGACATGAAAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATG-GCATTGATAA-G-TTCATAAGGC
* * *
56275132 AAGGATACCATGTAGGATCATGTCAATACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-C-ATAAGGC
* * * * *
56275187 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCATAAGGC
* * * *
56275240 AAGGATACCATGTAAGACCATGTCGAGACATAGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT
56275285 TCAAAAGGAT
Statistics
Matches: 126, Mismatches: 22, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
52 6 0.05
53 42 0.33
54 8 0.06
55 66 0.52
56 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCATAAGGC
Found at i:56275283 original size:108 final size:110
Alignment explanation
Indices: 56275084--56275284 Score: 273
Period size: 108 Copynumber: 1.8 Consensus size: 110
56275074 TTTAAGGATA
*
56275084 CCATGTAAGACCATGCCAAGACATGAAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAGGA
1 CCATGTAAGACCATGCCAAGACATGAAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
* * * *
56275149 TCATGTCAATACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATAGCAATGATAAGTTACTATAAGGCAAAGGTC
* ** *
56275194 CCATGTAAGACCATGCCAAGGCATG-GCATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGACATGAAAATTGGTAAGGTTTC-TAAGGCAAGGATACCATGTAAG
* *
56275256 ACCATGTCGAGACATAGCAATGGTAAGTT
65 ACCATGTCAAGACATAGCAATGATAAGTT
56275285 TCAAAAGGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 3 0.04
108 45 0.57
109 7 0.09
110 24 0.30
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGACATGAAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACATAGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:56275544 original size:16 final size:16
Alignment explanation
Indices: 56275523--56275553 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56275513 ATAAATTTGA
56275523 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
56275539 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
56275554 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:56279829 original size:42 final size:43
Alignment explanation
Indices: 56279737--56279901 Score: 160
Period size: 43 Copynumber: 3.8 Consensus size: 43
56279727 CAATGCCAAC
* * *
56279737 GTCCTAGACATGGTCTTACATGTAATCAAATATCGATGCCATT
1 GTCCTAGACAGGGTCTTACACGAAATCAAATATCGATGCCATT
56279780 GTCCTAGACAGGGT-TTCACACGAAATCAAATA-CGATGCCGA-T
1 GTCCTAGACAGGGTCTT-ACACGAAATCAAATATCGATGCC-ATT
* * * *
56279822 GTCCTAGACATGGTCTTACACATAAATCTCAA-ATCGATGCCAAT
1 GTCCTAGACAGGGTCTTACAC-GAAATC-AAATATCGATGCCATT
* * *
56279866 GTCCCAGA-TGTGGTCTTACACGAAATCACATATCGA
1 GTCCTAGACAG-GGTCTTACACGAAATCAAATATCGA
56279902 AAATCCTATG
Statistics
Matches: 101, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 28 0.28
43 46 0.46
44 27 0.27
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
GTCCTAGACAGGGTCTTACACGAAATCAAATATCGATGCCATT
Found at i:56279868 original size:44 final size:44
Alignment explanation
Indices: 56279729--56279886 Score: 148
Period size: 44 Copynumber: 3.7 Consensus size: 44
56279719 AGCTCGTACA
* ** *
56279729 ATGCCAACGTCCTAGACATGGTCTTACATGT-AATC-AAATATCG
1 ATGCCAATGTCCTAGACATGGTCTTACACATAAATCTCAA-ATCG
* * *
56279772 ATGCCATTGTCCTAGACAGGGT-TT-CACACGAAA--TCAAATACG
1 ATGCCAATGTCCTAGACATGGTCTTACACA-TAAATCTCAAAT-CG
*
56279814 ATGCCGATGTCCTAGACATGGTCTTACACATAAATCTCAAATCG
1 ATGCCAATGTCCTAGACATGGTCTTACACATAAATCTCAAATCG
* **
56279858 ATGCCAATGTCCCAGATGTGGTCTTACAC
1 ATGCCAATGTCCTAGACATGGTCTTACAC
56279887 GAAATCACAT
Statistics
Matches: 92, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
41 4 0.04
42 25 0.27
43 26 0.28
44 31 0.34
45 6 0.07
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (44 bp):
ATGCCAATGTCCTAGACATGGTCTTACACATAAATCTCAAATCG
Found at i:56280227 original size:26 final size:26
Alignment explanation
Indices: 56280194--56280251 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
56280184 TTATTGAATC
56280194 TCACATTCATTCAAATCAATCCATAT
1 TCACATTCATTCAAATCAATCCATAT
56280220 TCACATTCATTCAAATCAATCCATAT
1 TCACATTCATTCAAATCAATCCATAT
*
56280246 ACACAT
1 TCACAT
56280252 ATTTAGGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (26 bp):
TCACATTCATTCAAATCAATCCATAT
Found at i:56286274 original size:29 final size:29
Alignment explanation
Indices: 56286235--56286314 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
56286225 CTTAATAATC
*
56286235 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
56286265 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
56286294 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
56286315 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:56294094 original size:2 final size:2
Alignment explanation
Indices: 56294087--56294111 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56294077 TTGATAGAAA
56294087 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 A
56294112 GTGGGTTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56294181 original size:29 final size:29
Alignment explanation
Indices: 56294142--56294221 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
56294132 CTTAATAATC
*
56294142 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
56294172 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
56294201 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
56294222 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:56299734 original size:80 final size:80
Alignment explanation
Indices: 56299650--56299798 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
56299640 TATGGTAACC
* * * *
56299650 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
56299714 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
56299730 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
56299795 CCGG
66 CCGG
56299799 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:56299740 original size:40 final size:38
Alignment explanation
Indices: 56299691--56299798 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
56299681 ATCACGATTT
*
56299691 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
56299731 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
56299771 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
56299799 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:56303735 original size:40 final size:40
Alignment explanation
Indices: 56303661--56303880 Score: 239
Period size: 40 Copynumber: 5.5 Consensus size: 40
56303651 AAGTATCTTT
* *
56303661 GGGATTTAG-CCGGATATAG-CAACTTGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTC
* **
56303700 GGGTCTTAGCCCGGATATAGTCACTAGCATGAATGCCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
* * *
56303740 GGGACCTAGCCCGGATATAGTCACTAGCACAATTACCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
* * *
56303780 GGGACTTAGCCCGGGTATAG-CAACTACTCATACAAATGCTTTC
1 GGGACTTAGCCCGGATATAGTC-ACTA-GC--ACAAATGCCTTC
* **
56303823 GGGACTTAGCCCGGATATAGTAACTTTCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
*
56303863 GGGACTTAGCCCAGATAT
1 GGGACTTAGCCCGGATAT
56303881 CATCCGAATA
Statistics
Matches: 152, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
39 8 0.05
40 109 0.72
41 2 0.01
42 2 0.01
43 31 0.20
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (40 bp):
GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
Found at i:56303854 original size:83 final size:80
Alignment explanation
Indices: 56303657--56303880 Score: 265
Period size: 83 Copynumber: 2.8 Consensus size: 80
56303647 ACCCAAGTAT
* * *
56303657 CTTT-GGGATTTAG-CCGGATATAGCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
56303720 TCACTAGCATGAATG
66 TCACTAGCATAAATG
* * * * * * *
56303735 CCTTCGGGACCTAGCCCGGATATAGTCACTAGCACAATTACCTTCGGGACTTAGCCCGGGTATAG
1 CTTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
56303800 -CAACTACTCATACAAATG
66 TC-ACTA-GCAT--AAATG
* *
56303818 CTTTCGGGACTTAGCCCGGATATAGTAACTTTCACAAATGCCTTCGGGACTTAGCCCAGATAT
1 CTTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
56303881 CATCCGAATA
Statistics
Matches: 119, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
78 3 0.03
79 8 0.07
80 47 0.39
81 3 0.03
83 58 0.49
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (80 bp):
CTTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCACTAGCATAAATG
Found at i:56304982 original size:13 final size:13
Alignment explanation
Indices: 56304964--56304993 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
56304954 TACTCATGAA
56304964 CATTAGAATTTAT
1 CATTAGAATTTAT
56304977 CATTAGAATTTAT
1 CATTAGAATTTAT
56304990 CATT
1 CATT
56304994 TGACAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (13 bp):
CATTAGAATTTAT
Found at i:56318605 original size:24 final size:24
Alignment explanation
Indices: 56318578--56318740 Score: 290
Period size: 24 Copynumber: 6.8 Consensus size: 24
56318568 GCTGGAAATA
**
56318578 TATGGCACTATGTGTGCGATCCAC
1 TATGGCACTATGTGTGCGATTTAC
56318602 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
56318626 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
56318650 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
56318674 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
**
56318698 TATGGCACTATGTGTGCGATTCGC
1 TATGGCACTATGTGTGCGATTTAC
56318722 TATGGCACTATGTGTGCGA
1 TATGGCACTATGTGTGCGA
56318741 ACATAATAAG
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 135 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:56318754 original size:48 final size:48
Alignment explanation
Indices: 56318578--56318762 Score: 239
Period size: 48 Copynumber: 3.9 Consensus size: 48
56318568 GCTGGAAATA
* *
56318578 TATGGCACTATGTGTGCGATC-CACTATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGA-CATAATATGGCACTATGTGTGCGATTTAC
** *
56318626 TATGGCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGACATAATATGGCACTATGTGTGCGATTTAC
** * **
56318674 TATGGCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTCGC
1 TATGGCACTATGTGTGCGACATAATATGGCACTATGTGTGCGATTTAC
*
56318722 TATGGCACTATGTGTGCGAACATAATA-AGCACTATGTGTGC
1 TATGGCACTATGTGTGCG-ACATAATATGGCACTATGTGTGC
56318763 CACATTCGGT
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
48 122 0.96
49 5 0.04
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (48 bp):
TATGGCACTATGTGTGCGACATAATATGGCACTATGTGTGCGATTTAC
Found at i:56318754 original size:72 final size:72
Alignment explanation
Indices: 56318578--56318762 Score: 259
Period size: 72 Copynumber: 2.6 Consensus size: 72
56318568 GCTGGAAATA
*
56318578 TATGGCACTATGTGTGCGATCCACT-AT-GGCACTATGTGTGCGATTTACTATGGCACTATGTGT
1 TATGGCACTATGTGTGCGA-ACA-TAATAGGCACTATGTGTGCGATTTACTATGGCACTATGTGT
*
56318641 GCGATTTAC
64 GCGATTCAC
** *
56318650 TATGGCACTATGTGTGCG-ATTTACTATGGCACTATGTGTGCGATTTACTATGGCACTATGTGTG
1 TATGGCACTATGTGTGCGAACATAATA-GGCACTATGTGTGCGATTTACTATGGCACTATGTGTG
*
56318714 CGATTCGC
65 CGATTCAC
*
56318722 TATGGCACTATGTGTGCGAACATAATAAGCACTATGTGTGC
1 TATGGCACTATGTGTGCGAACATAATAGGCACTATGTGTGC
56318763 CACATTCGGT
Statistics
Matches: 99, Mismatches: 10, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
69 1 0.01
70 1 0.01
72 92 0.93
73 5 0.05
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (72 bp):
TATGGCACTATGTGTGCGAACATAATAGGCACTATGTGTGCGATTTACTATGGCACTATGTGTGC
GATTCAC
Found at i:56321930 original size:28 final size:28
Alignment explanation
Indices: 56321887--56321940 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
56321877 CTTTATTAGG
*
56321887 TTGAATAACAATATCTTGTCACCCTAGA
1 TTGAATAACAAAATCTTGTCACCCTAGA
56321915 TTGAATAACAAAATCTTGTCACCCTA
1 TTGAATAACAAAATCTTGTCACCCTA
56321941 TGTCTAGGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.31
Consensus pattern (28 bp):
TTGAATAACAAAATCTTGTCACCCTAGA
Found at i:56333063 original size:40 final size:40
Alignment explanation
Indices: 56333018--56333184 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
56333008 CGGAATATAA
56333018 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
56333058 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
56333098 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
56333138 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
56333177 CCGGATAT
1 CCGGATAT
56333185 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:56333168 original size:80 final size:79
Alignment explanation
Indices: 56333018--56333184 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
56333008 CGGAATATAA
* *
56333018 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
56333083 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
56333098 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
56333160 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
56333177 CCGGATAT
1 CCGGATAT
56333185 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:56334032 original size:17 final size:19
Alignment explanation
Indices: 56334009--56334054 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
56333999 AAGAAGCATG
56334009 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
56334027 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
56334045 AATCATGCTC
1 AATCATGCTC
56334055 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:56341057 original size:40 final size:39
Alignment explanation
Indices: 56341012--56341175 Score: 163
Period size: 40 Copynumber: 4.2 Consensus size: 39
56341002 CGGAATATAA
56341012 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGG-CTTAGC
* * *
56341052 CCGGATAGAAT-ACTCGCACGAATGCCTTC-GGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
** * *
56341089 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-CTTAGC
** * * * *
56341129 CCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
56341168 CCGGATAT
1 CCGGATAT
56341176 CATTCAATTT
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
37 14 0.14
38 18 0.17
39 30 0.29
40 41 0.40
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
Found at i:56341076 original size:39 final size:39
Alignment explanation
Indices: 56341028--56341135 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 39
56341018 ATAATCACGT
* *
56341028 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGA-ATACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAGACACTA
* *
56341067 GCACGAATGCCTTC-GG-CTTAGCCCGGATATAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAGACACTA
*
56341105 GCACAATTGCCTTCGGGTCTTAACCCGGATA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATA
56341136 TAATTTCCAG
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
37 16 0.27
38 16 0.27
39 15 0.25
40 12 0.20
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.23
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAGACACTA
Found at i:56347734 original size:29 final size:29
Alignment explanation
Indices: 56347695--56347774 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
56347685 CTTAATAATC
*
56347695 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
56347725 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
56347754 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
56347775 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:56355553 original size:2 final size:2
Alignment explanation
Indices: 56355546--56355576 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
56355536 ATTGATAGAA
*
56355546 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56355577 GTGGGTTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:56355646 original size:29 final size:29
Alignment explanation
Indices: 56355607--56355686 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
56355597 CTTAATAATC
*
56355607 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
56355637 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
56355666 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
56355687 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:56365471 original size:40 final size:40
Alignment explanation
Indices: 56365344--56365473 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
56365334 ATGCTGGAAA
* *
56365344 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
56365384 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
56365424 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
56365464 TTATATCCGG
1 TTATATCCGG
56365474 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:56368874 original size:21 final size:21
Alignment explanation
Indices: 56368845--56368919 Score: 53
Period size: 21 Copynumber: 3.4 Consensus size: 21
56368835 CTAGAAATTA
56368845 TGTGATCTGAACTCATTGAGT
1 TGTGATCTGAACTCATTGAGT
* ** *
56368866 TGTGGTCTGAGTTCA-TGACAT
1 TGTGATCTGAACTCATTGA-GT
*
56368887 ATGTGACATATGAACTCATTGAGT
1 -TGTG--ATCTGAACTCATTGAGT
*
56368911 TGTGGTCTG
1 TGTGATCTG
56368920 CGTTCATGAT
Statistics
Matches: 38, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
20 3 0.08
21 16 0.42
22 4 0.11
23 4 0.11
24 8 0.21
25 3 0.08
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (21 bp):
TGTGATCTGAACTCATTGAGT
Found at i:56368905 original size:45 final size:45
Alignment explanation
Indices: 56368852--56368939 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
56368842 TTATGTGATC
*
56368852 TGAACTCATTGAGTTGTGGTCTGAGTTCATGACATATGTGACATA
1 TGAACTCATTGAGTTGTGGTCTGAGTTCATGACATATATGACATA
* *
56368897 TGAACTCATTGAGTTGTGGTCTGCGTTCATGATATATATGACA
1 TGAACTCATTGAGTTGTGGTCTGAGTTCATGACATATATGACA
56368940 CATGTTTTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (45 bp):
TGAACTCATTGAGTTGTGGTCTGAGTTCATGACATATATGACATA
Found at i:56371436 original size:48 final size:48
Alignment explanation
Indices: 56371372--56371497 Score: 180
Period size: 48 Copynumber: 2.6 Consensus size: 48
56371362 CAAGGTAAAT
* * *
56371372 ATATATATGTGTGGTAAAGCCGAATGGCTAATATGAGACATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAACATGTATGAG
* *
56371420 ATATGTATATGTGGTAAAGCCAAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAACATGTATGAG
** *
56371468 GGATGTATATTTGGTAAAGCCGAATGGCTA
1 ATATGTATATGTGGTAAAGCCGAATGGCTA
56371498 TTGTGCAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAACATGTATGAG
Found at i:56371523 original size:48 final size:47
Alignment explanation
Indices: 56371383--56371526 Score: 164
Period size: 48 Copynumber: 3.0 Consensus size: 47
56371373 TATATATGTG
* * *
56371383 TGGTAAAGCCGAATGGCTAATATGAGACATGTATGAGATATGTATATG
1 TGGTAAAGCCGAATGGCTAATATGA-ATATGTATGAGATGTGTATATT
* *
56371431 TGGTAAAGCCAAATGGCTAATATGAAATATGTATGAG-GGATGTATATT
1 TGGTAAAGCCGAATGGCTAATATG-AATATGTATGAGATG-TGTATATT
* * * *
56371479 TGGTAAAGCCGAATGGCTATTGTGCAATACGTAGGAGATGTGTATATT
1 TGGTAAAGCCGAATGGCTAATATG-AATATGTATGAGATGTGTATATT
56371527 GTGGCCGAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
48 79 0.98
49 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (47 bp):
TGGTAAAGCCGAATGGCTAATATGAATATGTATGAGATGTGTATATT
Found at i:56371707 original size:37 final size:37
Alignment explanation
Indices: 56371657--56371735 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
56371647 GAAATATATT
* *
56371657 CGGGTAAGACCCGATGACTACGTGTCGAGATTCTGTC
1 CGGGTAAGACCCGATGACCACGTGTCGAGATTCTATC
* *
56371694 CGGGTAAGACCCGATGACCACGTGTGGAGATTTTATC
1 CGGGTAAGACCCGATGACCACGTGTCGAGATTCTATC
56371731 CGGGT
1 CGGGT
56371736 TAAAACCCCG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.24
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACCACGTGTCGAGATTCTATC
Found at i:56376766 original size:42 final size:43
Alignment explanation
Indices: 56376652--56376766 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
56376642 GGTTATCGAG
* *
56376652 TTGTGATTACATGTAAGACCATGTCTGGGGCATTGACATTGTA
1 TTGTGATTACGTGTAAGACCATGTCTGGGACATTGACATTGTA
* *
56376695 TTGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATTGTA
1 TTGTGATTACGTGTAAGACCATGTCTGGGACATTGACATTGTA
* *
56376738 TAT-TGATT-CGTGTAAGACCTTGTTTGGGA
1 T-TGTGATTACGTGTAAGACCATGTCTGGGA
56376767 TAGTGGTATC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
42 18 0.28
43 45 0.70
44 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.37
Consensus pattern (43 bp):
TTGTGATTACGTGTAAGACCATGTCTGGGACATTGACATTGTA
Found at i:56391359 original size:13 final size:13
Alignment explanation
Indices: 56391341--56391370 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56391331 CACACGCCTG
56391341 TGTGTCTAGCCCA
1 TGTGTCTAGCCCA
*
56391354 TGTGTCTAGCCCG
1 TGTGTCTAGCCCA
56391367 TGTG
1 TGTG
56391371 CCCTTCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.27, G:0.30, T:0.33
Consensus pattern (13 bp):
TGTGTCTAGCCCA
Found at i:56396206 original size:65 final size:65
Alignment explanation
Indices: 56396130--56396260 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
56396120 GCTTAAGTCA
*
56396130 ACATATGCTAACTTATAGAAACTCAGAACCCAAAAAATAGGGAAGAAGCATTCGGCCAACACCCT
1 ACATATGCTAACTTATAGAAACTCAGAACCCAAAAAATAGGGAAGAAGCATTCGACCAACACCCT
* *
56396195 ACATATGCTAACTTATAGAAACTCAGAACCTAAAAAGTAGGGAAGAAGCATTCGACCAACACCCT
1 ACATATGCTAACTTATAGAAACTCAGAACCCAAAAAATAGGGAAGAAGCATTCGACCAACACCCT
56396260 A
1 A
56396261 TTACGCAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (65 bp):
ACATATGCTAACTTATAGAAACTCAGAACCCAAAAAATAGGGAAGAAGCATTCGACCAACACCCT
Found at i:56396943 original size:12 final size:12
Alignment explanation
Indices: 56396926--56396953 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
56396916 CCTTAATACT
56396926 CTCCTAAAATCC
1 CTCCTAAAATCC
56396938 CTCCTAAAATCC
1 CTCCTAAAATCC
56396950 CTCC
1 CTCC
56396954 AACCGATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.46, G:0.00, T:0.25
Consensus pattern (12 bp):
CTCCTAAAATCC
Found at i:56408287 original size:28 final size:28
Alignment explanation
Indices: 56408255--56408309 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
56408245 CATCAAGTCA
*
56408255 CCTTTCTCTTCTCTTATTCATGACATTG
1 CCTTTCTCTGCTCTTATTCATGACATTG
56408283 CCTTTCTCTGCTCTTATTCATGACATT
1 CCTTTCTCTGCTCTTATTCATGACATT
56408310 ATCCTTGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.15, C:0.29, G:0.07, T:0.49
Consensus pattern (28 bp):
CCTTTCTCTGCTCTTATTCATGACATTG
Found at i:56408325 original size:28 final size:28
Alignment explanation
Indices: 56408255--56408319 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
56408245 CATCAAGTCA
* *
56408255 CCTTTCTCTTCTCTTATTCATGACATTG
1 CCTTGCTCTGCTCTTATTCATGACATTG
* *
56408283 CCTTTCTCTGCTCTTATTCATGACATTAT
1 CCTTGCTCTGCTCTTATTCATGACATT-G
56408312 CCTTGCTC
1 CCTTGCTC
56408320 GTTCTTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 26 0.79
29 7 0.21
ACGTcount: A:0.14, C:0.31, G:0.08, T:0.48
Consensus pattern (28 bp):
CCTTGCTCTGCTCTTATTCATGACATTG
Found at i:56409232 original size:43 final size:43
Alignment explanation
Indices: 56409166--56409248 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
56409156 AAATACATCC
*
56409166 ACTAGTATAGCTAAAGAGCCTAGAATATCATTACTTTAATCGT
1 ACTAATATAGCTAAAGAGCCTAGAATATCATTACTTTAATCGT
* *
56409209 ACTAATATAGCTAAAGATCCTAGAATATCATTCCTTTAAT
1 ACTAATATAGCTAAAGAGCCTAGAATATCATTACTTTAAT
56409249 TGTTGTACTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (43 bp):
ACTAATATAGCTAAAGAGCCTAGAATATCATTACTTTAATCGT
Found at i:56413837 original size:42 final size:42
Alignment explanation
Indices: 56413787--56413871 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
56413777 ATTGTCAAAG
56413787 TTTAGTTGAGACCTAGTTGGAATTGAACTACGGTATTGTTGA
1 TTTAGTTGAGACCTAGTTGGAATTGAACTACGGTATTGTTGA
*
56413829 TTTAGTTGAGACCTAGTTGGAATTGAACTAGGGTATTGTTGA
1 TTTAGTTGAGACCTAGTTGGAATTGAACTACGGTATTGTTGA
56413871 T
1 T
56413872 GATTAGACTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.39
Consensus pattern (42 bp):
TTTAGTTGAGACCTAGTTGGAATTGAACTACGGTATTGTTGA
Found at i:56421524 original size:40 final size:39
Alignment explanation
Indices: 56421473--56421697 Score: 272
Period size: 40 Copynumber: 5.7 Consensus size: 39
56421463 GCCACTAGCT
* *
56421473 CAAATGCCTTCGGGACTTAGCCCGGTTATAATAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
56421513 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
56421552 CAAACGCCTTCGGGACTTAGCCCGAATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCG-GTATAGTAACTCGCA
* *
56421592 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
56421632 CGAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
56421672 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
56421698 TATCATCCGA
Statistics
Matches: 165, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
39 39 0.24
40 126 0.76
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:56427687 original size:46 final size:46
Alignment explanation
Indices: 56427620--56427789 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
56427610 TGTAACCCGC
*
56427620 CCATATGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
*
56427666 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCACAT
* * * * *
56427716 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCTCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
*
56427759 CCATAAGTGAACTCGAACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
56427790 TTTGGATGCC
Statistics
Matches: 103, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 1 0.01
46 56 0.54
47 26 0.25
48 1 0.01
49 1 0.01
50 6 0.06
51 4 0.04
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
Found at i:56427740 original size:93 final size:93
Alignment explanation
Indices: 56427628--56427799 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
56427618 GCCCATATGT
* *
56427628 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTC-AGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGA-ACTCAACTCA
56427692 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
* *
56427721 GAACTCGGACTCAACTCAACGAGTTCGGACATTCTCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGAACTCAACTCAA
* *
56427786 CGAGTTTGGATGCC
66 CGAGCTCGGATGCC
56427800 CAAATATCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 71 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGAACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:56431326 original size:41 final size:41
Alignment explanation
Indices: 56431281--56431398 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
56431271 TGAAAGATAA
56431281 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
56431322 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
56431352 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
56431393 ATGTAG
1 ATGTAG
56431399 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:56431337 original size:71 final size:71
Alignment explanation
Indices: 56431249--56431412 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
56431239 GAGATGTATC
56431249 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
56431314 AGGACA
66 AGGACA
56431320 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
56431385 AGGACA
66 AGGACA
56431391 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
56431413 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:56434087 original size:17 final size:17
Alignment explanation
Indices: 56434065--56434106 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
56434055 ACATGGTTGG
56434065 ACACACGGGCGTGTGTC
1 ACACACGGGCGTGTGTC
*
56434082 ACACACAGGCGTGTGTC
1 ACACACGGGCGTGTGTC
56434099 ACACACGG
1 ACACACGG
56434107 CTCACTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.14
Consensus pattern (17 bp):
ACACACGGGCGTGTGTC
Found at i:56436044 original size:15 final size:17
Alignment explanation
Indices: 56436006--56436045 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
56435996 TTATGTAAAT
56436006 TTAATGTTGTATTGTATG
1 TTAATG-TGTATTGTATG
56436024 -TAATGTG-ATT-TATG
1 TTAATGTGTATTGTATG
56436038 TTAATGTG
1 TTAATGTG
56436046 CCTTACTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 2 0.10
17 5 0.24
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (17 bp):
TTAATGTGTATTGTATG
Found at i:56438744 original size:22 final size:21
Alignment explanation
Indices: 56438691--56438744 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
56438681 TGGCCTGCAG
**
56438691 CACGGGCGTGTCCTAGGGTCA
1 CACGGGCGTGTCCTAGGACCA
* * *
56438712 CACAGGAGTGTCCCTTGGACCA
1 CACGGGCGTGT-CCTAGGACCA
56438734 CACGGGCGTGT
1 CACGGGCGTGT
56438745 GAACCCTATA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.19
Consensus pattern (21 bp):
CACGGGCGTGTCCTAGGACCA
Found at i:56439795 original size:6 final size:6
Alignment explanation
Indices: 56439784--56439809 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56439774 AGTTATGGTG
56439784 GAATAT GAATAT GAATAT GAATAT GA
1 GAATAT GAATAT GAATAT GAATAT GA
56439810 TTGATACGTG
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:0.19, T:0.31
Consensus pattern (6 bp):
GAATAT
Found at i:56445205 original size:26 final size:25
Alignment explanation
Indices: 56445131--56445216 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 25
56445121 CAAATAAATA
*
56445131 AAAGAAAAAAAGAAAGAGAAAAAGAAAC
1 AAAGAAAAAAA-AAAGAG--AAAGAAAG
* *
56445159 AAAGTAAAACGAAACAG-GAAAGAAAG
1 AAAG-AAAA-AAAAAAGAGAAAGAAAG
56445185 AAAGAAAAATAAAAAGAGAAAG-AAG
1 AAAGAAAAA-AAAAAGAGAAAGAAAG
56445210 AAAGAAA
1 AAAGAAA
56445217 GCCATGGCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
25 19 0.39
26 16 0.33
28 5 0.10
29 7 0.14
30 2 0.04
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.02
Consensus pattern (25 bp):
AAAGAAAAAAAAAAGAGAAAGAAAG
Found at i:56449230 original size:40 final size:40
Alignment explanation
Indices: 56449185--56449352 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
56449175 CGGAATATAA
56449185 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
56449225 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
56449265 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
56449305 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
56449345 CCGGATAT
1 CCGGATAT
56449353 TATTCGATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:56452505 original size:40 final size:40
Alignment explanation
Indices: 56452460--56452626 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
56452450 CGGAATATAA
56452460 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
56452500 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
56452540 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
56452580 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
56452619 CCGGATAT
1 CCGGATAT
56452627 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:56460515 original size:40 final size:40
Alignment explanation
Indices: 56460470--56460636 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
56460460 CGGAATATAA
56460470 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
56460510 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
56460550 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
56460590 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
56460629 CCGGATAT
1 CCGGATAT
56460637 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:56466155 original size:40 final size:40
Alignment explanation
Indices: 56466100--56466275 Score: 228
Period size: 40 Copynumber: 4.4 Consensus size: 40
56466090 ACCGCACAAG
* * *** *
56466100 TCGGGTCTTAACCCGGATTTGGTAACTTGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCT
*
56466140 TCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCT
1 TCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCT
* *
56466180 TCGGGTCTTAGCTCGGATATAACAACTCGCACGAATGCCT
1 TCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCT
* *
56466220 TCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGCCT
1 TCGGGTCTTAGCCCGGATATAA-CAACTCGCACAAATGCCT
*
56466260 TCGGGACTTAGCCCGG
1 TCGGGTCTTAGCCCGG
56466276 GTATCATTCA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
40 121 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCT
Found at i:56473129 original size:31 final size:31
Alignment explanation
Indices: 56473094--56473156 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
56473084 GGTGTCTGAG
56473094 TCCCATCATGTGCAGTTGTCATGTGTGAGTT
1 TCCCATCATGTGCAGTTGTCATGTGTGAGTT
56473125 TCCCATCATGTGCAGTTGTCATGTGTGAGTT
1 TCCCATCATGTGCAGTTGTCATGTGTGAGTT
56473156 T
1 T
56473157 TAGTCTAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (31 bp):
TCCCATCATGTGCAGTTGTCATGTGTGAGTT
Found at i:56473567 original size:1 final size:1
Alignment explanation
Indices: 56473561--56473612 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
56473551 AGCTAAAGGC
** * * *
56473561 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAGAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
56473613 CCCAAATAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:56475007 original size:13 final size:13
Alignment explanation
Indices: 56474989--56475022 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
56474979 GTAATATTTT
56474989 TCTTTGTTGCTT-C
1 TCTTTGTT-CTTCC
56475002 TCTTTGTTCTTCC
1 TCTTTGTTCTTCC
56475015 TCTTTGTT
1 TCTTTGTT
56475023 ATCAGACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.65
Consensus pattern (13 bp):
TCTTTGTTCTTCC
Found at i:56507902 original size:43 final size:42
Alignment explanation
Indices: 56507849--56508007 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 42
56507839 CCAACATCCT
* * * *
56507849 AGACGTGGTCTTACATGTAATCAAATATCAATGCCACTGTCCC
1 AGACATGGTCTTACACGAAATCAAATATCGATGCCA-TGTCCC
*
56507892 AGACAAGGTCTTACACGAAATCAAATA-CGATGCCGATGTCCC
1 AGACATGGTCTTACACGAAATCAAATATCGATGCC-ATGTCCC
* * *
56507934 AGCCATGGTCTTACACGTAAATCTCAA-ATCGATACCAATGTCCC
1 AGACATGGTCTTACACG-AAATC-AAATATCGATGCC-ATGTCCC
* *
56507978 AGACGTGGTCTTACACGAAATCACATATCG
1 AGACATGGTCTTACACGAAATCAAATATCG
56508008 GAAGTCCTAT
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 28 0.29
43 39 0.40
44 30 0.31
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (42 bp):
AGACATGGTCTTACACGAAATCAAATATCGATGCCATGTCCC
Found at i:56507987 original size:44 final size:43
Alignment explanation
Indices: 56507879--56507999 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 43
56507869 TCAAATATCA
* *
56507879 ATGCCACTGTCCCAGACAAGGTCTTACACGAAA--TCAAATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCTCAAAT-CG
* *
56507921 ATGCCGATGTCCCAGCCATGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AAATCTCAAATCG
* *
56507965 ATACCAATGTCCCAGACGTGGTCTTACACGAAATC
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATC
56508000 ACATATCGGA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
42 26 0.38
43 8 0.12
44 28 0.41
45 6 0.09
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCTCAAATCG
Found at i:56513238 original size:30 final size:31
Alignment explanation
Indices: 56513198--56513258 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
56513188 ATGCATATGT
* *
56513198 ATGAATGAATTTGATTTG-AACAAAATTTTA
1 ATGAACGAATTTGATTTGAAAAAAAATTTTA
56513228 ATGAACGAATTTGATTTGAAAAAAAATTTTA
1 ATGAACGAATTTGATTTGAAAAAAAATTTTA
56513259 TGACCCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (31 bp):
ATGAACGAATTTGATTTGAAAAAAAATTTTA
Found at i:56513269 original size:30 final size:30
Alignment explanation
Indices: 56513205--56513269 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
56513195 TGTATGAATG
* *
56513205 AATTTGATTTGAACAAAATTTTAATGAACG
1 AATTTGATTTGAAAAAAATTTTAATGAACC
*
56513235 AATTTGATTTGAAAAAAAATTTT-ATGACCC
1 AATTTGATTTG-AAAAAAATTTTAATGAACC
56513265 AATTT
1 AATTT
56513270 TGTATGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (30 bp):
AATTTGATTTGAAAAAAATTTTAATGAACC
Found at i:56519944 original size:40 final size:40
Alignment explanation
Indices: 56519889--56520056 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 40
56519879 TGAATGATAC
* *
56519889 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
56519929 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
56519969 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
56520009 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
56520049 CC-GGCTAA
1 CCGGGCTAA
56520057 ATTCCGAAGA
Statistics
Matches: 106, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 6 0.06
40 98 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:56528248 original size:40 final size:40
Alignment explanation
Indices: 56528193--56528360 Score: 171
Period size: 40 Copynumber: 4.2 Consensus size: 40
56528183 TGAATGATAC
* *
56528193 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAA
* * *
56528233 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAA
* * **
56528273 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCA-AA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAA
* * * * *
56528312 TCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 -CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAA
56528353 CC-GGCTAA
1 CCGGGCTAA
56528361 ATTCCGAAGA
Statistics
Matches: 103, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
39 7 0.07
40 93 0.90
41 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAA
Found at i:56528326 original size:80 final size:80
Alignment explanation
Indices: 56528193--56528360 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
56528183 TGAATGATAC
* * **
56528193 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAACCGGGCTAAGACCCGAAGGC-ATTC
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCATAACCGGGCTAAGACCCGAAGGCAATT-
*
56528257 GTGCGAGTTGTTATAT
65 GTGCGAGTGGTTATAT
* * *
56528273 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCA-AATCCGGGTTAAGACCCGAAGGCAATT
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCATAA-CCGGGCTAAGACCCGAAGGCAATT
**
56528337 GTGCTTGTGGTTATAT
65 GTGCGAGTGGTTATAT
56528353 CC-GGCTAA
1 CCGGGCTAA
56528361 ATTCCGAAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
79 8 0.11
80 65 0.86
81 3 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCATAACCGGGCTAAGACCCGAAGGCAATTG
TGCGAGTGGTTATAT
Found at i:56530848 original size:47 final size:45
Alignment explanation
Indices: 56530699--56530970 Score: 162
Period size: 47 Copynumber: 5.9 Consensus size: 45
56530689 GTGTATAAGT
* * **
56530699 GCTGATGAATGTCCCAGACATGTCTTACACTAGCACGAAACT-TA-
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCAC-TCACTCTAC
* * *
56530743 G-TCGATGCATGTCCTAGACATGTCTTACACTGGCTAACATCA-TCGAG
1 GCT-GATGCATGTCCCAGACATGTCTTACACTGGC--AC-TCACTCTAC
*
56530790 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCACCTCTAC
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCACTCA-CTCTAC
* * * * *
56530836 GCTGATGCCATGTCCCAAACGTGGTCTTACACGGGCTA-TCA-TGATGC
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ACTCACT-CTAC
* * * * * * *
56530883 GGCTGATGCATG-CTCTAGACACGTCTTACACTAGCCCTCGTCTCAAT
1 -GCTGATGCATGTC-CCAGACATGTCTTACACTGGCACTC-ACTCTAC
* *
56530930 GCTGATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCA
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCA
56530971 TATAACCCCA
Statistics
Matches: 173, Mismatches: 35, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
43 1 0.01
44 32 0.18
45 3 0.02
46 35 0.20
47 63 0.36
48 38 0.22
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (45 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTGGCACTCACTCTAC
Found at i:56530909 original size:94 final size:95
Alignment explanation
Indices: 56530702--56530958 Score: 240
Period size: 94 Copynumber: 2.8 Consensus size: 95
56530692 TATAAGTGCT
* * ** * * * *
56530702 GATGAATGTCCCAGACATGTCTTACACTAGCACGAAACT-TA-G-TCGATG-CATGTCCTAGACA
1 GATGCATGTCCCAGACACGTCTTACACTAGCACTCACCTCAACGCT-GATGCCATGTCCCAAACA
*
56530763 T-GTCTTACACTGGCTAACATCATCGAGGCC
65 TGGTCTTACACGGGCTAACATCATCGAGGCC
* * * *
56530793 GATGCATGTCCCAGACATGTCTTACACTGGCACTCACCTCTACGCTGATGCCATGTCCCAAACGT
1 GATGCATGTCCCAGACACGTCTTACACTAGCACTCACCTCAACGCTGATGCCATGTCCCAAACAT
* * * *
56530858 GGTCTTACACGGGCTATCATGAT-GCGGCT
66 GGTCTTACACGGGCTAACATCATCGAGGCC
* * ** * *
56530887 GATGCATG-CTCTAGACACGTCTTACACTAGCCCTCGTCTCAATGCTGATGCCATGTCCCAGACA
1 GATGCATGTC-CCAGACACGTCTTACACTAGCACTCACCTCAACGCTGATGCCATGTCCCAAACA
56530951 TGGTCTTA
65 TGGTCTTA
56530959 TACTGGCTCT
Statistics
Matches: 137, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
91 34 0.25
92 2 0.01
93 6 0.04
94 76 0.55
95 19 0.14
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (95 bp):
GATGCATGTCCCAGACACGTCTTACACTAGCACTCACCTCAACGCTGATGCCATGTCCCAAACAT
GGTCTTACACGGGCTAACATCATCGAGGCC
Found at i:56533667 original size:29 final size:29
Alignment explanation
Indices: 56533577--56533736 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
56533567 ACTCGATTTC
* * **
56533577 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
56533606 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
56533634 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
56533664 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
56533693 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
56533722 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
56533737 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:56537449 original size:46 final size:46
Alignment explanation
Indices: 56537396--56537565 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
56537386 GGCATTCGAG
56537396 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAA
* * * * *
56537442 CTCGTTGAGTTGAGTCTGAGTTCA-TGAAATGTA-GC-TAGGCATCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGAATGC--CCGAA
* * *
56537489 CTCGTTGAGTTGAGTCCGATTTCACTTATGGATGCGAATGCCTGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAA
*
56537535 CTCGTTGAGTTGAGTCCAAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56537566 GCAGGTTACA
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
45 4 0.04
46 61 0.60
47 33 0.32
48 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAA
Found at i:56537557 original size:93 final size:93
Alignment explanation
Indices: 56537384--56537558 Score: 287
Period size: 93 Copynumber: 1.9 Consensus size: 93
56537374 TTTAGATATT
* *
56537384 TAGGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTG
1 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTG
**
56537449 AGTTGAGTCTGAGTTCATGAAATGTAGC
66 AGTTGAGTCCAAGTTCATGAAATGTAGC
* * *
56537477 TAGGCATCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATGCGAATGCCTGAGCTCGTTG
1 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTG
56537542 AGTTGAGTCCAAGTTCA
66 AGTTGAGTCCAAGTTCA
56537559 CTTATGGGCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTG
AGTTGAGTCCAAGTTCATGAAATGTAGC
Found at i:56543980 original size:28 final size:28
Alignment explanation
Indices: 56543948--56544003 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
56543938 TCAAAAGTAA
56543948 GTATAAACTGGACTTACTCATTACCATC
1 GTATAAACTGGACTTACTCATTACCATC
56543976 GTATAAACTGGACTTACTCATTACCATC
1 GTATAAACTGGACTTACTCATTACCATC
56544004 AACTCAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (28 bp):
GTATAAACTGGACTTACTCATTACCATC
Found at i:56546188 original size:51 final size:52
Alignment explanation
Indices: 56546127--56546237 Score: 163
Period size: 51 Copynumber: 2.2 Consensus size: 52
56546117 ATTTCCAAGT
* *
56546127 CATTTTCATTTTGGAGAAAAACACATTCATTTCCAAAT-TATT-CTATTTCTC
1 CATTTTCATTTTGGAGAAAAACACAATCATTTCCAAATGT-TTCCTATTTCAC
* *
56546178 CATTTTCATTTTGGAGAAAATCATAATCATTTCCAAATGTTTCCTATTTCAC
1 CATTTTCATTTTGGAGAAAAACACAATCATTTCCAAATGTTTCCTATTTCAC
56546230 CATTTTCA
1 CATTTTCA
56546238 CCATTTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
51 37 0.69
52 17 0.31
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (52 bp):
CATTTTCATTTTGGAGAAAAACACAATCATTTCCAAATGTTTCCTATTTCAC
Found at i:56552801 original size:91 final size:92
Alignment explanation
Indices: 56552627--56552807 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 92
56552617 CGTGTGAGAC
* * *
56552627 ACATGGCCTTGCCACACAGGCATGTGTCCCCTGTTTCAAGAAAAAAATTCAAAGTTTTGTAAAAG
1 ACATGACCTGGCCACACAGGCATGTGTCCCCTGTTTCAAGAAAAAAATTCAAAGTTTCGTAAAAG
*
56552692 TTTCTTGAGTTATTGGTTTAGTCCCGA
66 TTTCTTGAGTTATCGGTTTAGTCCCGA
* ** *
56552719 ACATGACCTGGCCACACAGTCATGTGTCCCCTGTTTTGAG-AAAAAATTCAAAGTTTCGTGAAAG
1 ACATGACCTGGCCACACAGGCATGTGTCCCCTGTTTCAAGAAAAAAATTCAAAGTTTCGTAAAAG
56552783 TTTCTTGAGTTATCGGTTTAGTCCC
66 TTTCTTGAGTTATCGGTTTAGTCCC
56552808 AAACCACTCC
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 46 0.57
92 35 0.43
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (92 bp):
ACATGACCTGGCCACACAGGCATGTGTCCCCTGTTTCAAGAAAAAAATTCAAAGTTTCGTAAAAG
TTTCTTGAGTTATCGGTTTAGTCCCGA
Found at i:56553352 original size:31 final size:30
Alignment explanation
Indices: 56553317--56553562 Score: 142
Period size: 31 Copynumber: 8.3 Consensus size: 30
56553307 TCATAGGTTA
*
56553317 GCCACAAAGGCACCCTTTTCAATTAGTACT
1 GCCACAAAGGCATCCTTTTCAATTAGTACT
* * *
56553347 CGCCACAAAGGTATCCTTTTCAGTTAGTACCA
1 -GCCACAAAGGCATCCTTTTCAATTAGTA-CT
** * * *
56553379 GCCATGAAGGCTTTCC-ATTC-A-GAGATA-T
1 GCCACAAAGGC-ATCCTTTTCAATTAG-TACT
*
56553407 GCCACAAAGGCATGCTTTTCAATTAGTACTT
1 GCCACAAAGGCATCCTTTTCAATTAGTAC-T
*
56553438 GCCACAAAGGCTTTCC-TTTCAA--A-TA-T
1 GCCACAAAGGC-ATCCTTTTCAATTAGTACT
* * *
56553464 TCTACAAAGGCATCTTTTTCAATTAGTACTT
1 GCCACAAAGGCATCCTTTTCAATTAGTAC-T
*
56553495 GCCACAAAGGCTTTCC-TTTCAA--A-TA-T
1 GCCACAAAGGC-ATCCTTTTCAATTAGTACT
* * *
56553521 GCTACAAAGGCATCCCTTTTCAATCAATACT
1 GCCACAAAGGCAT-CCTTTTCAATTAGTACT
56553552 CGCCACAAAGG
1 -GCCACAAAGG
56553563 ATTTTCTTTC
Statistics
Matches: 161, Mismatches: 31, Indels: 45
0.68 0.13 0.19
Matches are distributed among these distances:
25 3 0.02
26 29 0.18
27 8 0.05
28 17 0.11
29 10 0.06
30 6 0.04
31 71 0.44
32 17 0.11
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (30 bp):
GCCACAAAGGCATCCTTTTCAATTAGTACT
Found at i:56553470 original size:26 final size:26
Alignment explanation
Indices: 56553441--56553531 Score: 87
Period size: 26 Copynumber: 3.3 Consensus size: 26
56553431 AGTACTTGCC
56553441 ACAAAGGCTTTCCTTTCAAATATTCT
1 ACAAAGGCTTTCCTTTCAAATATTCT
*
56553467 ACAAAGGCATCTT--TTTCAATTAGTACTTGCC
1 ACAAAGGC-T-TTCCTTTCAA--A-TA-TT-CT
*
56553498 ACAAAGGCTTTCCTTTCAAATATGCT
1 ACAAAGGCTTTCCTTTCAAATATTCT
56553524 ACAAAGGC
1 ACAAAGGC
56553532 ATCCCTTTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
26 23 0.43
27 2 0.04
28 5 0.09
29 5 0.09
30 3 0.06
31 15 0.28
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (26 bp):
ACAAAGGCTTTCCTTTCAAATATTCT
Found at i:56553572 original size:58 final size:57
Alignment explanation
Indices: 56553351--56553599 Score: 284
Period size: 57 Copynumber: 4.3 Consensus size: 57
56553341 AGTACTCGCC
* * ** ** * *
56553351 ACAAAGGTATCCTTTTCAGTTAGTACCAGCCATGAAGGCTTTCCATTCAGAGATATGCC
1 ACAAAGGCATCCTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCA-A-ATATGCT
* *
56553410 ACAAAGGCATGCTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCAAATATTCT
1 ACAAAGGCATCCTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCAAATATGCT
*
56553467 ACAAAGGCATCTTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCAAATATGCT
1 ACAAAGGCATCCTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCAAATATGCT
* * * * * *
56553524 ACAAAGGCATCCCTTTTCAATCAATACTCGCCACAAAGGATTTTCTTTCAAATACGCT
1 ACAAAGGCAT-CCTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCAAATATGCT
*
56553582 ATGAAA-GCATCCCTTTTC
1 A-CAAAGGCAT-CCTTTTC
56553600 TAACGTGTTT
Statistics
Matches: 167, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
57 69 0.41
58 54 0.32
59 44 0.26
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.32
Consensus pattern (57 bp):
ACAAAGGCATCCTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCAAATATGCT
Found at i:56553592 original size:115 final size:116
Alignment explanation
Indices: 56553351--56553582 Score: 288
Period size: 115 Copynumber: 2.0 Consensus size: 116
56553341 AGTACTCGCC
* * * ** **
56553351 ACAAAGGTATCCTTTTCAGTTAGTACCAGCCATGAAGGCTTTCCATTCAGAGATATGCCACAAAG
1 ACAAAGGCATCTTTTTCAATTAGTACTTGCCACAAAGGCTTTCCATTCAGAGATATGCCACAAAG
* * * * * **
56553416 GCATGCTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCAAATATTCT
66 GCATCCTTTTCAATCAATACTCGCCACAAAGGATTTCCTTTCAAATACGCT
* *
56553467 ACAAAGGCATCTTTTTCAATTAGTACTTGCCACAAAGGCTTTCCTTTCA-A-ATATGCTACAAAG
1 ACAAAGGCATCTTTTTCAATTAGTACTTGCCACAAAGGCTTTCCATTCAGAGATATGCCACAAAG
*
56553530 GCATCCCTTTTCAATCAATACTCGCCACAAAGGATTTTCTTTCAAATACGCT
66 GCAT-CCTTTTCAATCAATACTCGCCACAAAGGATTTCCTTTCAAATACGCT
56553582 A
1 A
56553583 TGAAAGCATC
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
114 16 0.16
115 41 0.42
116 41 0.42
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (116 bp):
ACAAAGGCATCTTTTTCAATTAGTACTTGCCACAAAGGCTTTCCATTCAGAGATATGCCACAAAG
GCATCCTTTTCAATCAATACTCGCCACAAAGGATTTCCTTTCAAATACGCT
Found at i:56558936 original size:55 final size:54
Alignment explanation
Indices: 56558848--56559103 Score: 244
Period size: 55 Copynumber: 4.8 Consensus size: 54
56558838 CATTAGGGTT
* *
56558848 TAAGGATACCATGTAAGGCCATGCCAAGGCATGGAAATTGGTAATGTTTCA-AAGG
1 TAAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAA-GTTTCATAAGG
* * * * *
56558903 TGAGGATATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTTCTATAAGG
1 TAAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTC-ATAAGG
* * * * *
56558958 CAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGG
1 -TAAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCATAAGG
*
56559011 TAAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC--AA--
1 TAAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAGTTTCATAAGG
* * *
56559061 -AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 TAAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAG
56559104 GTACCCATGT
Statistics
Matches: 171, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
49 40 0.23
52 6 0.04
53 42 0.25
54 15 0.09
55 65 0.38
56 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.23
Consensus pattern (54 bp):
TAAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCATAAGG
Found at i:56559055 original size:108 final size:110
Alignment explanation
Indices: 56558856--56559058 Score: 313
Period size: 108 Copynumber: 1.9 Consensus size: 110
56558846 TTTAAGGATA
* * *
56558856 CCATGTAAGGCCATGCCAAGGCATGGAAATTGGTAATGTTTCAAAGGTGAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAATGTTTCAAAGGTAAGGATACCATGTAAGA
*
56558921 CCATGTCAAGACATGGCATTGATAAGTTTCTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTTCTATAAGGCAAAGGTC
* *
56558966 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGTAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAATGTTTCA-AAGGTAAGGATACCATGTAAG
*
56559028 ACCATGTCAAGACATGGCAATGGTAAGTTTC
65 ACCATGTCAAGACATGGCAATGATAAGTTTC
56559059 AAAAGGATAC
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 4 0.05
108 49 0.58
109 7 0.08
110 25 0.29
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAATGTTTCAAAGGTAAGGATACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTTCTATAAGGCAAAGGTC
Found at i:56559317 original size:16 final size:16
Alignment explanation
Indices: 56559296--56559326 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56559286 ATAAATTTGA
56559296 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
56559312 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
56559327 AGTAAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:56564629 original size:20 final size:20
Alignment explanation
Indices: 56564591--56564629 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56564581 TGATTGGTTG
* *
56564591 TGATTGAATTATATTTGAAT
1 TGATTAAATTATATGTGAAT
*
56564611 TGATTAAATTGTATGTGAA
1 TGATTAAATTATATGTGAA
56564630 ATGTATGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
TGATTAAATTATATGTGAAT
Found at i:56570815 original size:40 final size:40
Alignment explanation
Indices: 56570770--56570899 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
56570760 CGGAATATAA
56570770 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* *** * *
56570810 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
56570850 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
56570890 CCGGATATAA
1 CCGGATATAA
56570900 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:56570914 original size:40 final size:40
Alignment explanation
Indices: 56570786--56570936 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
56570776 ATAACCACGT
* * *
56570786 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
56570826 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
56570866 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* * *
56570906 GCATAATTGTCTT-GGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
56570937 CATTCAATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 18 0.20
40 70 0.78
41 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:56578939 original size:80 final size:80
Alignment explanation
Indices: 56578855--56579003 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
56578845 TATGGTAACC
* * * *
56578855 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
56578919 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
56578935 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
56579000 CCGG
66 CCGG
56579004 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:56578945 original size:40 final size:38
Alignment explanation
Indices: 56578896--56579003 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
56578886 ATCACGATTT
*
56578896 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
56578936 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
56578976 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
56579004 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:56585250 original size:16 final size:16
Alignment explanation
Indices: 56585211--56585251 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
56585201 TAACCCAAAT
56585211 TAAATTAGATTAAATTA
1 TAAATTA-ATTAAATTA
*
56585228 -AAATTAATTATATTA
1 TAAATTAATTAAATTA
56585243 TAAATTAAT
1 TAAATTAAT
56585252 ACACATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAATTAATTAAATTA
Found at i:56588301 original size:25 final size:26
Alignment explanation
Indices: 56588272--56588327 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
56588262 TTAATCAGTA
*
56588272 TAAAATATTAA-TAATTCAAT-AAAT
1 TAAAATATTAATTAATTAAATAAAAT
56588296 TGAAAA-ATTAATTAATTAAATAAAAT
1 T-AAAATATTAATTAATTAAATAAAAT
56588322 TAAAAT
1 TAAAAT
56588328 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 6 0.22
25 16 0.59
26 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAAATATTAATTAATTAAATAAAAT
Found at i:56589136 original size:30 final size:29
Alignment explanation
Indices: 56589079--56589139 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
56589069 GCCTTTTGAA
**
56589079 AATATTTATATAAAAGACATTAAATTTTT
1 AATATTTATATAAAAGACACCAAATTTTT
56589108 AATATTTATA-AAAAGAGCAACCAAATTTTT
1 AATATTTATATAAAAGA-C-ACCAAATTTTT
56589138 AA
1 AA
56589140 AATAATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.21
29 11 0.39
30 11 0.39
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.38
Consensus pattern (29 bp):
AATATTTATATAAAAGACACCAAATTTTT
Found at i:56597615 original size:29 final size:27
Alignment explanation
Indices: 56597581--56597683 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
56597571 TACTCAATCA
*
56597581 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
56597610 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
56597639 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
56597668 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
56597684 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:56605404 original size:29 final size:27
Alignment explanation
Indices: 56605370--56605472 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
56605360 TACTCAATCA
*
56605370 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
56605399 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
56605428 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
56605457 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
56605473 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:56611814 original size:29 final size:29
Alignment explanation
Indices: 56611723--56611793 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
56611713 GACGAGATCA
56611723 GCACTAAGTGTGCGTGCTGGAAATATATG
1 GCACTAAGTGTGCGTGCTGGAAATATATG
56611752 GCACTAAGTGTGCGTGCTGGAAATATATG
1 GCACTAAGTGTGCGTGCTGGAAATATATG
56611781 GCACTAAGTGTGC
1 GCACTAAGTGTGC
56611794 AAGTTGGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (29 bp):
GCACTAAGTGTGCGTGCTGGAAATATATG
Done.