Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 136 of 170
Found at i:41245169 original size:29 final size:30
Alignment explanation
Indices: 41245107--41245169 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
41245097 TAAATTTCAT
* *
41245107 TTTTTTAAGAAAATTTTAAAATTTTTTATT
1 TTTTTTAAGAAAATTTTAAAATTTTTAATA
*
41245137 TTTTTTAA-ATAATTTTAAAATTTTTAATA
1 TTTTTTAAGAAAATTTTAAAATTTTTAATA
41245166 TTTT
1 TTTT
41245170 CAACAATGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTTTTAAGAAAATTTTAAAATTTTTAATA
Found at i:41245314 original size:24 final size:23
Alignment explanation
Indices: 41245259--41245314 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
41245249 TAAATTTTAA
*
41245259 ATTTTTTTAAGATATTTTTATTT
1 ATTTTTTTAAGATATTTTTATAT
41245282 ATGTATTTTT-AGATATTTATTAATAT
1 AT-T-TTTTTAAGATATTT-TT-ATAT
41245308 ATTTTTT
1 ATTTTTT
41245315 GTTATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
ATTTTTTTAAGATATTTTTATAT
Found at i:41247432 original size:28 final size:28
Alignment explanation
Indices: 41247400--41247953 Score: 453
Period size: 28 Copynumber: 20.4 Consensus size: 28
41247390 TAAAAACCCT
41247400 AACCCTAACCTAACCTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
41247428 AACCCTAACCT-A-C---TTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
**
41247451 AACCCTAACCTAATTTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
**
41247479 AACCCTAACCTAATTTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
41247507 AACCCTAACCCTAACCTAACCTACTTAAATTAAA
1 AACCCTAA-CCTAACCT-A---A-TTAAATTAAA
* **
41247541 AACCCTAACCTTATTTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
*
41247569 AACCCTAACCT--GC---TTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
* **
41247592 AACCCTAACCTTATTTAATTAAATTAAAAA
1 AACCCTAACCTAACCTAATTAAATT--AAA
41247622 CCCTAACCCTAACCTAACCTAATTAAATTAAA
1 ----AACCCTAACCTAACCTAATTAAATTAAA
41247654 AACCCTAACCTAA--T--TT-AATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
41247677 AACCCTAACCTAA--T--TT-AATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
* **
41247700 AACCCTAACCTTATTTAATTAAATTATAAA
1 AACCCTAACCTAACCTAATTAAA-T-TAAA
*
41247730 CCCTAACCCTAACCTAACCTAATTCAATTAAA
1 ----AACCCTAACCTAACCTAATTAAATTAAA
41247762 AACCCTAACCTAA--T--TT-AATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
** *
41247785 AACCCTAACCTAATTTAATTAAA--AACCCT
1 AACCCTAACCTAACCTAATTAAATTAA---A
*
41247814 AACCCTAACCTAACCTACTTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
* * **
41247842 AACTCTAACCTTATTTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
41247870 AA--C---CCTAACCTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
41247893 AACCCTAACCTAA--T--TT-AATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
41247916 AACCCTAACCTAACCTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
41247944 AACCCTAACC
1 AACCCTAACC
41247954 CTATTTAATT
Statistics
Matches: 442, Mismatches: 31, Indels: 106
0.76 0.05 0.18
Matches are distributed among these distances:
23 143 0.32
24 7 0.02
25 4 0.01
26 7 0.02
27 7 0.02
28 162 0.37
29 28 0.06
30 8 0.02
31 2 0.00
32 8 0.02
33 7 0.02
34 59 0.13
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (28 bp):
AACCCTAACCTAACCTAATTAAATTAAA
Found at i:41247435 original size:23 final size:23
Alignment explanation
Indices: 41247408--41247974 Score: 209
Period size: 23 Copynumber: 21.2 Consensus size: 23
41247398 CTAACCCTAA
41247408 CCTAACCTAATTAAATTAAAAAC
1 CCTAACCTAATTAAATTAAAAAC
*
41247431 CCTAACCTACTTAAATTAAAAAC
1 CCTAACCTAATTAAATTAAAAAC
41247454 CCTAACCTAATTTAATTAAATTAAAAAC
1 CCTAACC-----TAATTAAATTAAAAAC
41247482 CCTAACCTAATTTAATTAAATTAAAAAC
1 CCTAACC-----TAATTAAATTAAAAAC
*
41247510 CCTAACCCTAACCTAACCTACTTAAATTAAAAAC
1 CCTAA-CCTAA-TTAA---A-TT-----AAAAAC
41247544 CCTAACCTTATTTAATTAAATTAAAAAC
1 CCTAACC-----TAATTAAATTAAAAAC
**
41247572 CCTAACCTGCTTAAATTAAAAAC
1 CCTAACCTAATTAAATTAAAAAC
41247595 CCTAACCTTATTTAATTAAATTAAAAAC
1 CCTAACC-----TAATTAAATTAAAAAC
*
41247623 CCTAACCCTAACCTAACCTAATTAAATTAAAAAC
1 CCTAA-CCTAA--TTA---AATT--A---AAAAC
*
41247657 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTAAATTAAAAAC
*
41247680 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTAAATTAAAAAC
*
41247703 CCTAACCTTATTTAATTAAATTATAAAC
1 CCTAACC-----TAATTAAATTAAAAAC
* ** **
41247731 CCTAACCCTAACCTAACCTAATTCAATT
1 CCTAA-CCTAA-TTAAATTAA---AAAC
*** *
41247759 AAAAACCCTAACCTAATTTAATTAAAAAC
1 CCTAA-CCT-----AATTAAATTAAAAAC
*
41247788 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTAATTAAATTAAAAAC
*
41247811 CCTAACCCTAACCTAACCTACTTAAATTAAAAAC
1 CCTAA-CCTAA-TTAA---A-TT-----AAAAAC
*
41247845 TCTAACCTTATTTAATTAAATTAAAAAC
1 CCTAACC-----TAATTAAATTAAAAAC
41247873 CCTAACCTAATTAAATTAAAAAC
1 CCTAACCTAATTAAATTAAAAAC
*
41247896 CCTAACCTAATTTAATTAAAAACCC
1 CCTAACCTAATTAAATTAAAAA--C
41247921 TAACCTAACCTAATTAAATTAAAAAC
1 ---CCTAACCTAATTAAATTAAAAAC
*
41247947 CCTAACCCT-ATTTAATTAAAAAC
1 CCTAA-CCTAATTAAATTAAAAAC
41247970 CCTAA
1 CCTAA
41247975 TTAAATTGTA
Statistics
Matches: 431, Mismatches: 39, Indels: 148
0.70 0.06 0.24
Matches are distributed among these distances:
23 165 0.38
24 17 0.04
25 11 0.03
26 4 0.01
28 149 0.35
29 18 0.04
31 2 0.00
32 5 0.01
33 15 0.03
34 33 0.08
37 6 0.01
38 6 0.01
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (23 bp):
CCTAACCTAATTAAATTAAAAAC
Found at i:41247630 original size:34 final size:34
Alignment explanation
Indices: 41247592--41247663 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
41247582 TTAAATTAAA
* **
41247592 AACCCTAACCTTATTTAATTAAATTAAAAACCCT
1 AACCCTAACCTAACCTAATTAAATTAAAAACCCT
41247626 AACCCTAACCTAACCTAATTAAATTAAAAACCCT
1 AACCCTAACCTAACCTAATTAAATTAAAAACCCT
41247660 AACC
1 AACC
41247664 TAATTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (34 bp):
AACCCTAACCTAACCTAATTAAATTAAAAACCCT
Found at i:41247674 original size:108 final size:108
Alignment explanation
Indices: 41247387--41247956 Score: 783
Period size: 108 Copynumber: 5.2 Consensus size: 108
41247377 AACCCTACTT
*
41247387 AATTAAAAACCCTAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTACTTAAATTAAAA
1 AATTAAAAACCCTAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAA
*
41247452 ACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCTAATTTAATTA
66 ACCCTAACCTAA--T--TT-AATTAAAAACCCTAACCTTATTTAATTA
*
41247500 AATTAAAAACCCTAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCTTATTTAATTAAAT
1 AATTAAAAACCCTAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACC-----TAATTAAAT
** *
41247565 TAAAAACCCTAACCTGCTTAAATTAAAAACCCTAACCTTATTTAATTA
61 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTATTTAATTA
*
41247613 AATTAAAAACCCTAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAA
1 AATTAAAAACCCTAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAA
41247678 ACCCTAACCTAATTTAATTAAAAACCCTAACCTTATTTAATTA
66 ACCCTAACCTAATTTAATTAAAAACCCTAACCTTATTTAATTA
* * *
41247721 AATTATAAACCCTAACCCTAACCTAACCTAATTCAATTAAAAACCCTAACCTAATTTAATTAAAA
1 AATTAAAAACCCTAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAA
** *
41247786 ACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACCTACTTA
66 ACCCTAACCTAATTTAATTAAAAACCCTAA-CCT----T-ATTTAATTA
* **
41247835 AATTAAAAA--CT----CTAACCTTATTTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAA
1 AATTAAAAACCCTAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAA
* **
41247894 ACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTA
66 ACCCTAACCTAATTTAATTAAAAACCCTAACCTTATTTAATTA
41247937 AATTAAAAACCCTAACCCTA
1 AATTAAAAACCCTAACCCTA
41247957 TTTAATTAAA
Statistics
Matches: 416, Mismatches: 24, Indels: 39
0.87 0.05 0.08
Matches are distributed among these distances:
102 17 0.04
104 2 0.00
107 3 0.01
108 222 0.53
109 3 0.01
112 2 0.00
113 128 0.31
114 15 0.04
116 1 0.00
118 23 0.06
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (108 bp):
AATTAAAAACCCTAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAA
ACCCTAACCTAATTTAATTAAAAACCCTAACCTTATTTAATTA
Found at i:41247743 original size:34 final size:34
Alignment explanation
Indices: 41247700--41247771 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
41247690 TTTAATTAAA
* ** *
41247700 AACCCTAACCTTATTTAATTAAATTATAAACCCT
1 AACCCTAACCTAACCTAATTAAATTAAAAACCCT
*
41247734 AACCCTAACCTAACCTAATTCAATTAAAAACCCT
1 AACCCTAACCTAACCTAATTAAATTAAAAACCCT
41247768 AACC
1 AACC
41247772 TAATTTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.28
Consensus pattern (34 bp):
AACCCTAACCTAACCTAATTAAATTAAAAACCCT
Found at i:41251272 original size:84 final size:85
Alignment explanation
Indices: 41251071--41251275 Score: 367
Period size: 84 Copynumber: 2.4 Consensus size: 85
41251061 CAAACTTGCT
*
41251071 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAACCGTCAAAAAAA
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTC-AAAAAA
41251136 AAATTATTTCCTACATGACCA
65 AAATTATTTCCTACATGACCA
*
41251157 ACTGTAGCGAAATCGCGTCCACGAGGTCGCGATTTGACACTATTTGCTCAGAAACGTC-AAAAAA
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
41251221 AATTATTTCCTACATGACCA
66 AATTATTTCCTACATGACCA
*
41251241 ACTGTAGCGAAATTGCGTCCACGAGGGCGCGATTT
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTT
41251276 CACAATTTCT
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
84 59 0.51
86 56 0.49
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (85 bp):
ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
AATTATTTCCTACATGACCA
Found at i:41251405 original size:124 final size:124
Alignment explanation
Indices: 41251185--41251464 Score: 377
Period size: 124 Copynumber: 2.3 Consensus size: 124
41251175 CCACGAGGTC
* * *
41251185 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTCACACTATTTACTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTATAGCG
* * * * * **
41251250 AAATTGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* *
41251309 GCGATTTTATACTATTTACTCAGAAAACGTCAAAAAAAATTATTT-CTCACATGACC-ACTATAG
1 GCGATTTCACACTATTTACTCAG-AAACGTCAAAAAAAATTATTTCCT-ACATGACCAACTATAG
* *
41251372 CGAAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
64 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
*
41251433 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTCACACTATTT-ACTCAGAAACGTCAA
41251465 CTCAAAAAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
123 9 0.07
124 97 0.71
125 31 0.23
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (124 bp):
GCGATTTCACACTATTTACTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTATAGCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:41254330 original size:18 final size:18
Alignment explanation
Indices: 41254281--41254330 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
41254271 AAAAAAAACG
*
41254281 TTTTGAAATTGAATAACA
1 TTTTGAAAATGAATAACA
* * *
41254299 ATTTGTAAATGAATAATA
1 TTTTGAAAATGAATAACA
*
41254317 TTTTGAAAACGAAT
1 TTTTGAAAATGAAT
41254331 GACACGATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTTGAAAATGAATAACA
Found at i:41256316 original size:41 final size:41
Alignment explanation
Indices: 41256271--41256366 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
41256261 GAACACTGGA
* *
41256271 ATTAAGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGC
1 ATTAAGCCTGCTAGACATAAAGTATGAAATATTTCACCAGC
* *
41256312 ATTAAGCCTGTTAGACGTAAAGTATGAAATATTTCACCAGC
1 ATTAAGCCTGCTAGACATAAAGTATGAAATATTTCACCAGC
41256353 ATTAAGCCTGCTAG
1 ATTAAGCCTGCTAG
41256367 GCACAGAGCC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (41 bp):
ATTAAGCCTGCTAGACATAAAGTATGAAATATTTCACCAGC
Found at i:41256764 original size:65 final size:64
Alignment explanation
Indices: 41256578--41256792 Score: 211
Period size: 68 Copynumber: 3.2 Consensus size: 64
41256568 CATGTATAAT
* * *
41256578 TATATATAA-TTACTAACATTAAGTTCAGCTCAAAGGAACTTGTATCT-TACATTCGAACCTCTT
1 TATATATAATTTA-TAACATTAAGTTCAACTCAAA-GAA-TTGTAT-TATACATTCGAACCACAT
41256641 ATA
62 ATA
* * * **
41256644 TATATATATATTTCATAACATTACA-TTCAATTCAAAGACATTGCATCATTTATTCGAACCACAT
1 TATATATA-ATTT-ATAACATTA-AGTTCAACTCAAAGA-ATTGTATTATACATTCGAACCACAT
41256708 ATA
62 ATA
*
41256711 TATATACAATTTATAACATTAAGTTCAACTCAAAGAATTTGTATTATACATTCGAACATCATCAT
1 TATATATAATTTATAACATTAAGTTCAACTCAAAGAA-TTGTATTATACATTCGAAC--CA-CAT
41256776 ATA
62 ATA
*
41256779 TTTATATAATTTAT
1 TATATATAATTTAT
41256793 GCTATTAATT
Statistics
Matches: 122, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
64 2 0.02
65 36 0.30
66 12 0.10
67 32 0.26
68 38 0.31
69 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.39
Consensus pattern (64 bp):
TATATATAATTTATAACATTAAGTTCAACTCAAAGAATTGTATTATACATTCGAACCACATATA
Found at i:41259457 original size:6 final size:6
Alignment explanation
Indices: 41259446--41259481 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
41259436 AATAATTGTA
41259446 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
41259482 CACAATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:41260588 original size:21 final size:21
Alignment explanation
Indices: 41260562--41260602 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
41260552 TCAAAAGCTG
*
41260562 AACAGAAGCTCGTGAGAGTTA
1 AACAGAAGCTCGTAAGAGTTA
41260583 AACAGAAGCTCGTAAGAGTT
1 AACAGAAGCTCGTAAGAGTT
41260603 GATCCACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGTTA
Found at i:41264010 original size:34 final size:34
Alignment explanation
Indices: 41263966--41264033 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
41263956 GCACAGTTGA
* *
41263966 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
41264001 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
41264034 TTAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:41271183 original size:67 final size:67
Alignment explanation
Indices: 41271099--41271256 Score: 280
Period size: 67 Copynumber: 2.4 Consensus size: 67
41271089 TCTGGTTCTA
*
41271099 CCGATGAAGCACTGGGTGCCAAACACACTAATGAGCACTGAGTGCAAACTATTTACCTCGGCATT
1 CCGATGAGGCACTGGGTGCCAAACACACTAATGAGCACTGAGTGCAAACTATTTACCTCGGCATT
41271164 GT
66 GT
*
41271166 CCGATGAGGCACTGGGTGCCAAACACACTAATGATCACTGAGTGCAAACTATTTACCTCGGCATT
1 CCGATGAGGCACTGGGTGCCAAACACACTAATGAGCACTGAGTGCAAACTATTTACCTCGGCATT
41271231 GT
66 GT
* *
41271233 CTGATGAGGCACTGGGTGTCAAAC
1 CCGATGAGGCACTGGGTGCCAAAC
41271257 TAGTGTAATT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 87 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (67 bp):
CCGATGAGGCACTGGGTGCCAAACACACTAATGAGCACTGAGTGCAAACTATTTACCTCGGCATT
GT
Found at i:41273310 original size:14 final size:13
Alignment explanation
Indices: 41273291--41273347 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
41273281 ATTTAGCCGA
41273291 ATATGCATCACCAC
1 ATATGCATCA-CAC
41273305 ATATGCAT-ACAC
1 ATATGCATCACAC
*
41273317 ATAGTTACATCATCAC
1 ATA--TGCATCA-CAC
41273333 ATATGCAT-ACAC
1 ATATGCATCACAC
41273345 ATA
1 ATA
41273348 GCTCACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 12 0.32
13 2 0.05
14 16 0.43
15 1 0.03
16 6 0.16
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (13 bp):
ATATGCATCACAC
Found at i:41276524 original size:5 final size:5
Alignment explanation
Indices: 41276516--41276553 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
41276506 TATAGATACT
41276516 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT- TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
41276554 TTCTCTCGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:41286989 original size:62 final size:59
Alignment explanation
Indices: 41286916--41287032 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
41286906 AGTGATTATC
* * * *
41286916 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTAACTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTCATC-T-T-GATAAATATTATATTAACTTAATAAGAT
*
41286978 TTAATATTAAATTTAATCTAATATTCATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTCATCTTGATAAATATTATATTAACTTAATA
41287033 TTAATATGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.44
60 1 0.02
61 1 0.02
62 26 0.52
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTCATCTTGATAAATATTATATTAACTTAATAAGAT
Found at i:41292074 original size:132 final size:132
Alignment explanation
Indices: 41291910--41293105 Score: 1723
Period size: 132 Copynumber: 9.1 Consensus size: 132
41291900 TGGGGTCTTC
* * * ** * * * *
41291910 GATCTGCTCCATTATTGCCTAGGGAGGTAAGATCTGTAATCTTCAATATATTCCACTGCTGCCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCA
* * *
41291975 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGTCATCC
66 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCC
41292040 TT
131 TT
* * * * * *
41292042 GATCTGCTCCACTACTGCTTAGGGAGACAAGATATAAAATATTTAATCTATTCCACTGCTGCCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCA
* * * * * *
41292107 GGGAAGTAGAATTACTGGCTTCAATGTACTCCTCTATATCCACAGGGAGGTAAAATTCACCATCT
66 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCC
41292172 TT
131 TT
* * * * *
41292174 GATCTGCCCCACTACTGCTTAGGGAGACAATATCTGAAATATTCAATCTATTCCACTGCTGCCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCA
* * * *
41292239 GGGAAGTAGAATTACTGGTTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACTAT-C
66 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCC
41292303 TT
131 TT
*
41292305 CGATTTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC
1 -GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC
* * * * *
41292370 AGGGAAGTAGAATTGCTGGTTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGTCATA
65 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
*
41292435 TTT
130 CTT
* * *
41292438 GACCTGCTCCACTACTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTACTGTCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCA
* * * *
41292503 GGGAAGTAGAATTGCTGGCTTCAATGTATTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCT
66 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCC
41292568 TT
131 TT
* * * * *
41292570 GATCTACTCCACTACTGTTTAGGAAGACAAGATCTGAAATATTCAATCTATTCCGCTGTTGTCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCA
* * *
41292635 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCGGGGAGGTAAAATCCGTCAT-C
66 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCC
41292699 TT
131 TT
41292701 CGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC
1 -GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC
* *
41292766 AGGGAAGTAGAATTGCTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
65 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
*
41292831 TTT
130 CTT
* * *
41292834 GATCTGCTCCACCACTGTTTAGGGAGACAAGATCTGAAATATTCAATCTATTCCGCTGCTGTCCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCA
*
41292899 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT-C
66 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCC
41292963 TT
131 TT
*
41292965 CGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTACTGTCC
1 -GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC
* * **
41293030 AGGAAAGTAGAATTACTGGCTTCAATGTACTCCGCTGTAACCACAGGGAGGTAAAATATGCCATC
65 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
*
41293095 TTT
130 CTT
*
41293098 GATATGCT
1 GATCTGCT
41293106 TCGCTGTTTA
Statistics
Matches: 964, Mismatches: 94, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
131 6 0.01
132 952 0.99
133 6 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (132 bp):
GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCA
GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCC
TT
Found at i:41294490 original size:8 final size:7
Alignment explanation
Indices: 41294446--41294487 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
41294436 TTAGCCTCTC
41294446 CATTTTT
1 CATTTTT
41294453 -ACTTTTT
1 CA-TTTTT
41294460 CATTTTT
1 CATTTTT
41294467 CA-TTTT
1 CATTTTT
41294473 CATCTTTT
1 CAT-TTTT
41294481 CATTTTT
1 CATTTTT
41294488 TCACATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.23
7 16 0.52
8 8 0.26
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:41301154 original size:42 final size:42
Alignment explanation
Indices: 41301107--41301195 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
41301097 AATATGTAAT
*
41301107 TCACTAACACATCTTGCCATATGCAATATCCAATTGGTGAAA
1 TCACTAACACATCTTGCCATATACAATATCCAATTGGTGAAA
41301149 TCACTAACACATCTTGCCATATACAATATCCAATTGGTGAAA
1 TCACTAACACATCTTGCCATATACAATATCCAATTGGTGAAA
41301191 TCACT
1 TCACT
41301196 TAAATGAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (42 bp):
TCACTAACACATCTTGCCATATACAATATCCAATTGGTGAAA
Found at i:41301382 original size:49 final size:49
Alignment explanation
Indices: 41301319--41301451 Score: 203
Period size: 49 Copynumber: 2.7 Consensus size: 49
41301309 TTCTCGATGT
* *
41301319 CATAGTCCAACTATGGTCTTACACGTAATCACATAACATATACCGATAC
1 CATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCGATAC
* **
41301368 CATAGCCTAGCTATGGTCTTACACGTAATCACATAACATATACCGATGT
1 CATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCGATAC
* *
41301417 TATAGCCCAGCTATGGTCTTACACGGAATCACATA
1 CATAGCCCAGCTATGGTCTTACACGTAATCACATA
41301452 TCACTTATTG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (49 bp):
CATAGCCCAGCTATGGTCTTACACGTAATCACATAACATATACCGATAC
Found at i:41302663 original size:23 final size:23
Alignment explanation
Indices: 41302637--41302735 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
41302627 ATAAGTGCCA
41302637 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
41302660 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41302683 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41302706 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
41302729 CACTGAT
1 CACTGAT
41302736 CATTAACACT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:41304378 original size:19 final size:19
Alignment explanation
Indices: 41304309--41304381 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 19
41304299 ATTTTAAAAT
*
41304309 TTATTAAATTGAACTATAA
1 TTATTAAATTAAACTATAA
* * *
41304328 TTATTAAA-AAAATTAGAA
1 TTATTAAATTAAACTATAA
41304346 TTACATTTAAAAATTAAACTATAA
1 TT--A-TT--AAATTAAACTATAA
41304370 TTATTAAATTAA
1 TTATTAAATTAA
41304382 GTTATTCGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
18 8 0.20
19 15 0.37
20 1 0.02
21 4 0.10
22 1 0.02
23 3 0.07
24 9 0.22
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (19 bp):
TTATTAAATTAAACTATAA
Found at i:41304922 original size:20 final size:22
Alignment explanation
Indices: 41304879--41304937 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 22
41304869 AATTTGTGAG
* *
41304879 ATTATAATTTTATTTTTTGGAA
1 ATTATAATTTTATATTTTGAAA
41304901 ATTATAA-TTTA-ATTTTGAAA
1 ATTATAATTTTATATTTTGAAA
*
41304921 ATT-TGAATTTTAGATTT
1 ATTAT-AATTTTATATTT
41304938 GGATGCCCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.03
20 12 0.38
21 8 0.25
22 11 0.34
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (22 bp):
ATTATAATTTTATATTTTGAAA
Found at i:41314337 original size:35 final size:35
Alignment explanation
Indices: 41314291--41314361 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
41314281 ACACAGATGA
41314291 CACATTATATTTTAAACAGCATCTGAAAGTTAATT
1 CACATTATATTTTAAACAGCATCTGAAAGTTAATT
*
41314326 CACATTATATTTTAAACGGCATCTGAAAGTTAATT
1 CACATTATATTTTAAACAGCATCTGAAAGTTAATT
41314361 C
1 C
41314362 TCAAAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (35 bp):
CACATTATATTTTAAACAGCATCTGAAAGTTAATT
Found at i:41318170 original size:16 final size:17
Alignment explanation
Indices: 41318149--41318181 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
41318139 ATATTTATTT
41318149 TTTTAAAAT-TTTTTAA
1 TTTTAAAATATTTTTAA
41318165 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
41318182 AATACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:41318637 original size:18 final size:18
Alignment explanation
Indices: 41318614--41318651 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41318604 TTTTTTATTT
41318614 AAATCAAAATCAAAATTA
1 AAATCAAAATCAAAATTA
* *
41318632 AAATCAAAATGAAATTTA
1 AAATCAAAATCAAAATTA
41318650 AA
1 AA
41318652 TTTTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATCAAAATCAAAATTA
Found at i:41318913 original size:20 final size:22
Alignment explanation
Indices: 41318865--41318920 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
41318855 TAAATTAAAC
* *
41318865 AATTTTTAAAATAAATTTTTGA
1 AATTCTTAAAATATATTTTTGA
*
41318887 TATTCTTAAAATATA-TTTT-A
1 AATTCTTAAAATATATTTTTGA
41318907 AATTCTTAAAATAT
1 AATTCTTAAAATAT
41318921 TTTCTTAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.47
21 4 0.13
22 12 0.40
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
AATTCTTAAAATATATTTTTGA
Found at i:41319015 original size:17 final size:17
Alignment explanation
Indices: 41318993--41319025 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41318983 ATTGATAACA
41318993 TTAAAAA-AATGTAAATT
1 TTAAAAATAAT-TAAATT
41319010 TTAAAAATAATTAAAT
1 TTAAAAATAATTAAAT
41319026 AAATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAAAAATAATTAAATT
Found at i:41319709 original size:26 final size:27
Alignment explanation
Indices: 41319651--41319712 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
41319641 GAAAAAAATA
*
41319651 TAAATTATTATTTTAATATAATTAAAT
1 TAAATTATTATTTTAATATAATTAAAC
* *
41319678 TGAATTGTT-TTTTAATATAATTAAAC
1 TAAATTATTATTTTAATATAATTAAAC
41319704 TAAATTATT
1 TAAATTATT
41319713 GAGCTAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (27 bp):
TAAATTATTATTTTAATATAATTAAAC
Found at i:41319805 original size:48 final size:48
Alignment explanation
Indices: 41319752--41319856 Score: 167
Period size: 48 Copynumber: 2.2 Consensus size: 48
41319742 TATGTTGAAG
* *
41319752 AAATTAATTTA-TTATGAGTTTATTTATTTTTGTGTCTTTTCTTGGATT
1 AAATTAATGTATTTATGAGTTTATTTATTTTTG-CTCTTTTCTTGGATT
*
41319800 AAATTAATGTATTTATGATTTTATTTATTTTTGCTCTTTTCTTGGATT
1 AAATTAATGTATTTATGAGTTTATTTATTTTTGCTCTTTTCTTGGATT
41319848 AAATTAATG
1 AAATTAATG
41319857 CGTTTATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
48 33 0.62
49 20 0.38
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (48 bp):
AAATTAATGTATTTATGAGTTTATTTATTTTTGCTCTTTTCTTGGATT
Found at i:41319967 original size:26 final size:28
Alignment explanation
Indices: 41319912--41319969 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
41319902 GAAAAAACTA
* **
41319912 AATTATTATTTTAATATAAATTAAGTTG
1 AATTATTATTTTAACATAAATTAAAATG
41319940 AATTATT-TTTTAACAT-AATTAAAATG
1 AATTATTATTTTAACATAAATTAAAATG
41319966 AATT
1 AATT
41319970 GTTGAGCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 12 0.44
27 8 0.30
28 7 0.26
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
AATTATTATTTTAACATAAATTAAAATG
Found at i:41320075 original size:14 final size:15
Alignment explanation
Indices: 41320056--41320084 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41320046 AACGCCCTGA
41320056 TTTCGT-AATTTTAT
1 TTTCGTAAATTTTAT
41320070 TTTCGTAAATTTTAT
1 TTTCGTAAATTTTAT
41320085 CATAAATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTCGTAAATTTTAT
Found at i:41325417 original size:23 final size:23
Alignment explanation
Indices: 41325386--41325436 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
41325376 ACCTACTTTC
* * *
41325386 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
41325409 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
41325432 TTACA
1 TTACA
41325437 TTAATTGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:41326205 original size:28 final size:28
Alignment explanation
Indices: 41326171--41326228 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
41326161 AATCGCCTAA
41326171 GACTGAGGATTACCTGCACAGTTAAGAG
1 GACTGAGGATTACCTGCACAGTTAAGAG
41326199 GACTGAGGATTACCTGCACAGTTAAGAG
1 GACTGAGGATTACCTGCACAGTTAAGAG
41326227 GA
1 GA
41326229 GAGGGTGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (28 bp):
GACTGAGGATTACCTGCACAGTTAAGAG
Found at i:41326367 original size:28 final size:28
Alignment explanation
Indices: 41326334--41326407 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
41326324 AGTACAATGA
** *
41326334 AGGCCTTAGCCCAATTTAGTAGCAGTGT
1 AGGCCTTAGCCCAATACAATAGCAGTGT
* *
41326362 GGGCCTTAGCCCAATACAATATCAGTGT
1 AGGCCTTAGCCCAATACAATAGCAGTGT
41326390 AGGCCTTAGCCCAATACA
1 AGGCCTTAGCCCAATACA
41326408 GTAACATTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (28 bp):
AGGCCTTAGCCCAATACAATAGCAGTGT
Found at i:41326792 original size:27 final size:26
Alignment explanation
Indices: 41326762--41327201 Score: 425
Period size: 27 Copynumber: 16.4 Consensus size: 26
41326752 GGTATAAAAA
41326762 TCATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCT-TAGGGGTATTTCGG
* * *
41326789 TCATTCTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCT-TAGGGGTATTTCGG
* * **
41326816 TCATTTTATCCTTCGGGGGTATTTCTA
1 TCATTTTACCCTT-AGGGGTATTTCGG
* *
41326843 TTATTTTACCCTTTGAGGGTA-TTCAGG
1 TCATTTTACCCTTAG-GGGTATTTC-GG
* *
41326870 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTAG-GGGTATTTCGG
*
41326897 TCATTTTACCCTTCAGGGGTATTTCGA
1 TCATTTTACCCTT-AGGGGTATTTCGG
* * *
41326924 TCATTTTACCCTTCAAGGTTATTTCGA
1 TCATTTTACCCTT-AGGGGTATTTCGG
* *
41326951 TCATTTTACCCTTTGGGGTATTTCAG
1 TCATTTTACCCTTAGGGGTATTTCGG
* * *
41326977 TCATTTTACCTTTGGGGGTATTTTGG
1 TCATTTTACCCTTAGGGGTATTTCGG
**
41327003 TCATTTTACCCTTAGAGGGTATTTCAA
1 TCATTTTACCCTTAG-GGGTATTTCGG
* *
41327030 TCATTTTACCCTTTGAGGGTATTTTGG
1 TCATTTTACCCTTAG-GGGTATTTCGG
*
41327057 TCATTTTATCCTTTAGGGGTATTTCGG
1 TCATTTTA-CCCTTAGGGGTATTTCGG
* *
41327084 TCATTTTACCATTCGAGGGTATTTCGG
1 TCATTTTACCCTTAG-GGGTATTTCGG
* *
41327111 TCATTTTACCCTTTGAGGGTATTTTGG
1 TCATTTTACCCTTAG-GGGTATTTCGG
* * **
41327138 TCATTTTACCCTTCGAGTGTATTTCAT
1 TCATTTTACCCTTAG-GGGTATTTCGG
*
41327165 TCATTTTACCCTTTGGGGGTATTTCGG
1 TCATTTTACCC-TTAGGGGTATTTCGG
41327192 TCA-TTTACCC
1 TCATTTTACCC
41327202 ATAACTCGCA
Statistics
Matches: 352, Mismatches: 52, Indels: 19
0.83 0.12 0.04
Matches are distributed among these distances:
26 60 0.17
27 280 0.80
28 12 0.03
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (26 bp):
TCATTTTACCCTTAGGGGTATTTCGG
Found at i:41326872 original size:81 final size:80
Alignment explanation
Indices: 41326761--41327201 Score: 482
Period size: 81 Copynumber: 5.5 Consensus size: 80
41326751 GGGTATAAAA
* * * *
41326761 ATCATTTTACCCTAT-AGGGGTATTTCGGTCATTCTACCCTATGGGGGTATTTCGATCATTTTAT
1 ATCATTTTACCCTTTGA-GGGTATTTCGGTCATTTTACCCT-TGAGGGTATTTCGATCATTTTAC
*
41326825 CCTTCGGGGGTATTTCT
64 CCTTCGGGGGTATTTCG
*
41326842 ATTATTTTACCCTTTGAGGGTA-TTCAGGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTAC
1 ATCATTTTACCCTTTGAGGGTATTTC-GGTCATTTTACCCTT-GAGGGTATTTCGATCATTTTAC
*
41326906 CCTTCAGGGGTATTTCG
64 CCTTCGGGGGTATTTCG
** * *
41326923 ATCATTTTACCCTTCAAGGTTATTTCGATCATTTTACCCTTTG-GGGTATTTC-AGTCATTTTA-
1 ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC-TTGAGGGTATTTCGA-TCATTTTAC
* *
41326985 CCTTTGGGGGTATTTTG
64 CCTTCGGGGGTATTTCG
* * ** * * *
41327002 GTCATTTTACCCTTAGAGGGTATTTCAATCATTTTACCCTTTGAGGGTATTTTGGTCATTTTATC
1 ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC-TTGAGGGTATTTCGATCATTTTACC
**
41327067 CTTTAGGGGTATTTCG
65 CTTCGGGGGTATTTCG
* * * * *
41327083 GTCATTTTACCATTCGAGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTTGGTCATTTTACC
1 ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC-TTGAGGGTATTTCGATCATTTTACC
* *
41327148 CTTCGAGTGTATTTC-
65 CTTCGGGGGTATTTCG
*
41327163 ATTCATTTTACCCTTTGGGGGTATTTCGGTCA-TTTACCC
1 A-TCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC
41327202 ATAACTCGCA
Statistics
Matches: 313, Mismatches: 37, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
79 53 0.17
80 44 0.14
81 210 0.67
82 6 0.02
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (80 bp):
ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCCTTGAGGGTATTTCGATCATTTTACCC
TTCGGGGGTATTTCG
Found at i:41333939 original size:15 final size:14
Alignment explanation
Indices: 41333918--41333953 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
41333908 ATAATCTTTA
41333918 ATAATTATCTCAAT
1 ATAATTATCTCAAT
*
41333932 ATTAATTATCTTAAT
1 A-TAATTATCTCAAT
41333947 ATAATTA
1 ATAATTA
41333954 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCTCAAT
Found at i:41335595 original size:10 final size:10
Alignment explanation
Indices: 41335554--41335612 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
41335544 ATAAGTAATA
*
41335554 AATAATAAAG
1 AATAATAAAT
41335564 AA-AATAAAGT
1 AATAATAAA-T
*
41335574 AA-AGAAAAAT
1 AATA-ATAAAT
41335584 AATAATAAAT
1 AATAATAAAT
41335594 AATAATAAAT
1 AATAATAAAT
*
41335604 AAAAATAAA
1 AATAATAAA
41335613 AATTGGGTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 6 0.14
10 31 0.74
11 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (10 bp):
AATAATAAAT
Found at i:41342044 original size:15 final size:14
Alignment explanation
Indices: 41342023--41342058 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
41342013 ATAATCTTTA
41342023 ATAATTATCTCAAT
1 ATAATTATCTCAAT
*
41342037 ATTAATTATCTTAAT
1 A-TAATTATCTCAAT
41342052 ATAATTA
1 ATAATTA
41342059 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCTCAAT
Found at i:41343010 original size:20 final size:21
Alignment explanation
Indices: 41342974--41343014 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
41342964 CTTACATGCC
*
41342974 AAAGTGAAAAAATTGATTTTT
1 AAAGTGAAAAAAGTGATTTTT
41342995 AAAGTG-AAAAAGTGATTTTT
1 AAAGTGAAAAAAGTGATTTTT
41343015 GGTCATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
AAAGTGAAAAAAGTGATTTTT
Found at i:41343127 original size:47 final size:47
Alignment explanation
Indices: 41343058--41343217 Score: 214
Period size: 47 Copynumber: 3.4 Consensus size: 47
41343048 AATGAGGAAG
* * * *
41343058 AAGTGGAAGTTTATTTGCAAAAGTGGTAACTTGTCCACAATATTATA
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATATTATA
* *
41343105 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATTTTATT
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATATTATA
* * **
41343152 AAGTGGCAGTTCATCTACAAAAGTGGTGGTTTGTCCATAATATTATTA
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATATTA-TA
41343200 AA-TGGCAGTTTATCTGCA
1 AAGTGGCAGTTTATCTGCA
41343218 TTACTGTGAC
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
47 95 0.97
48 3 0.03
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (47 bp):
AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCATAATATTATA
Found at i:41344387 original size:21 final size:21
Alignment explanation
Indices: 41344362--41344403 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41344352 ATACATGGTA
*
41344362 AAAGGTATTGATAATTTTTGT
1 AAAGGTATCGATAATTTTTGT
*
41344383 AAAGGTATCGATACTTTTTGT
1 AAAGGTATCGATAATTTTTGT
41344404 GTAAATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (21 bp):
AAAGGTATCGATAATTTTTGT
Found at i:41344638 original size:22 final size:24
Alignment explanation
Indices: 41344613--41344656 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
41344603 ATTTTGTTCA
41344613 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
41344635 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
41344657 GATATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:41348374 original size:3 final size:3
Alignment explanation
Indices: 41348366--41348427 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
41348356 TTTCATTTTC
*
41348366 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TAT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
41348414 TC- TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT
41348428 ATTGCCCAGG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:41348844 original size:57 final size:56
Alignment explanation
Indices: 41348688--41348854 Score: 176
Period size: 57 Copynumber: 2.9 Consensus size: 56
41348678 GTTGGGTTAG
* * * * * *
41348688 TGGTGGAAAAGAATAAAGAAAAAAAAGTGGTGGGCCATGGTCATT-ATGAAGGGCTTG
1 TGGTGGAAAAGAATAAAG-ATAAATAGTGGTGGGCGAAGG-CATTAATGAAGGGCATA
* * * *
41348745 TGGTGGAAAGGAA-AAAAATAAATAAGTGGTGGGCGAATGCATTAATGAAGTGCATA
1 TGGTGGAAAAGAATAAAGATAAAT-AGTGGTGGGCGAAGGCATTAATGAAGGGCATA
* *
41348801 TGGTGGAAAAGAATAATGATGAAATAGTGGTGGGCGAAGGCATTAAAGAAGGGC
1 TGGTGGAAAAGAATAAAGAT-AAATAGTGGTGGGCGAAGGCATTAATGAAGGGC
41348855 CTGTTGAACG
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
55 8 0.09
56 36 0.40
57 42 0.47
58 4 0.04
ACGTcount: A:0.40, C:0.06, G:0.34, T:0.20
Consensus pattern (56 bp):
TGGTGGAAAAGAATAAAGATAAATAGTGGTGGGCGAAGGCATTAATGAAGGGCATA
Found at i:41348902 original size:30 final size:30
Alignment explanation
Indices: 41348868--41348925 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
41348858 TTGAACGGTC
*
41348868 AAATGGGTTGCTAAGAAATGAAATTGGGTT
1 AAATGGGTTACTAAGAAATGAAATTGGGTT
*
41348898 AAATGGGTTATTAAGAAATGAAATTGGG
1 AAATGGGTTACTAAGAAATGAAATTGGG
41348926 CAAGATCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.29, T:0.29
Consensus pattern (30 bp):
AAATGGGTTACTAAGAAATGAAATTGGGTT
Found at i:41349510 original size:15 final size:15
Alignment explanation
Indices: 41349490--41349519 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41349480 TTAGTGGAGA
41349490 AAAAGCAGATTCGAT
1 AAAAGCAGATTCGAT
41349505 AAAAGCAGATTCGAT
1 AAAAGCAGATTCGAT
41349520 TATCGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
AAAAGCAGATTCGAT
Found at i:41354393 original size:22 final size:22
Alignment explanation
Indices: 41354365--41354410 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
41354355 GGAAATCATT
41354365 TCCACTTCATTCAACCACTTGG
1 TCCACTTCATTCAACCACTTGG
41354387 TCCACTTCATTCAACCACTTGG
1 TCCACTTCATTCAACCACTTGG
41354409 TC
1 TC
41354411 TGAATTGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.37, G:0.09, T:0.33
Consensus pattern (22 bp):
TCCACTTCATTCAACCACTTGG
Found at i:41356881 original size:17 final size:17
Alignment explanation
Indices: 41356847--41356890 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41356837 GAAATTATTA
* *
41356847 AAATAAGTTTTTATATT
1 AAATAAGTTATTAAATT
41356864 AAATAAGTTATTAAATT
1 AAATAAGTTATTAAATT
*
41356881 -ATTAAGTTAT
1 AAATAAGTTAT
41356891 ATTATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (17 bp):
AAATAAGTTATTAAATT
Found at i:41357980 original size:103 final size:102
Alignment explanation
Indices: 41357783--41358003 Score: 302
Period size: 103 Copynumber: 2.1 Consensus size: 102
41357773 AGAGTACGAG
***
41357783 AAAAAGT-AAAAAAAAAAATTGGTGGTAGCCTGGCAATGGCCGGCACCACCTTTTAAAATTTTTT
1 AAAAAGTAAAAAAAAAAAATTGGTGGTAGCCTGGCAATGGCCGGCACCACCTTTTAAAA--TAAA
* * * *
41357847 TTTTACTTTTTTTGTGTTAGATAAGATATCAGTATACAA
64 ATTTACTTTTTTCGTGTCAAATAAGATATCAGTATACAA
* *
41357886 AAAAAGTAAAAAAAAAAAATTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTTAAAA-AAA
1 AAAAAGTAAAAAAAAAAAA--TTGGTGGTAGCCTGGCAATGGCCGGCACCACCTTTTAAAATAAA
*
41357950 ATTTACTTTTTTCGTGTCAAATAAGATATCAGTATACGA
64 ATTTACTTTTTTCGTGTCAAATAAGATATCAGTATACAA
41357989 AAAAAGTAAAAAAAA
1 AAAAAGTAAAAAAAA
41358004 TTACTTTTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
103 56 0.53
104 11 0.10
106 38 0.36
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (102 bp):
AAAAAGTAAAAAAAAAAAATTGGTGGTAGCCTGGCAATGGCCGGCACCACCTTTTAAAATAAAAT
TTACTTTTTTCGTGTCAAATAAGATATCAGTATACAA
Found at i:41358001 original size:52 final size:52
Alignment explanation
Indices: 41357942--41358055 Score: 201
Period size: 52 Copynumber: 2.2 Consensus size: 52
41357932 CACCACCTTT
41357942 TAAAAAAAATTTACTTTTTTCGTGTCAAATAAGATATCAGTATACGAAAAAAG
1 TAAAAAAAA-TTACTTTTTTCGTGTCAAATAAGATATCAGTATACGAAAAAAG
* *
41357995 TAAAAAAAATTACTTTTTTCGTGTCAGATAAGCTATCAGTATACGAAAAAAG
1 TAAAAAAAATTACTTTTTTCGTGTCAAATAAGATATCAGTATACGAAAAAAG
41358047 TAAAAAAAA
1 TAAAAAAAA
41358056 ATTTGGTGGT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 50 0.85
53 9 0.15
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (52 bp):
TAAAAAAAATTACTTTTTTCGTGTCAAATAAGATATCAGTATACGAAAAAAG
Found at i:41360449 original size:17 final size:18
Alignment explanation
Indices: 41360429--41360465 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
41360419 TTTTTTAAAA
41360429 AAAAAACTG-TTTTTT-T
1 AAAAAACTGCTTTTTTCT
*
41360445 TAAAAACTGCTTTTTTCT
1 AAAAAACTGCTTTTTTCT
41360463 AAA
1 AAA
41360466 CAGAGGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.47
17 6 0.35
18 3 0.18
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
AAAAAACTGCTTTTTTCT
Found at i:41360451 original size:16 final size:17
Alignment explanation
Indices: 41360430--41360465 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
41360420 TTTTTAAAAA
*
41360430 AAAAACTG-TTTTTTTT
1 AAAAACTGCTTTTTTCT
41360446 AAAAACTGCTTTTTTCT
1 AAAAACTGCTTTTTTCT
41360463 AAA
1 AAA
41360466 CAGAGGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (17 bp):
AAAAACTGCTTTTTTCT
Found at i:41360720 original size:98 final size:99
Alignment explanation
Indices: 41360523--41360978 Score: 519
Period size: 98 Copynumber: 4.5 Consensus size: 99
41360513 CCTATATATA
* * * *
41360523 TTTTAAAAAAGGTGGTGTCGGCCATTGGCAGGCCACCACTAATTTTTTTTTTAACTTTTTTCGTA
1 TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCAC-AAATTTTTTTTTAACTTTTTTCGTA
* * *
41360588 TACTGATAGCTTATCTGATACGAAAAAAGTAATTT
65 TACTGATATCTTATCTGACACGAAAAAAGAAATTT
* * *
41360623 TTTTTAAAAAGGTGATGCCGGCCATTGGCAGGCCACCACAAATTTTTTTTT-ACTTTTTTTGTAT
1 TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTAACTTTTTTCGTAT
* *
41360687 ACTGATACCTTATTTGACACGAAAAAAGAAATTTT
66 ACTGATATCTTATCTGACACGAAAAAAGAAA-TTT
* * *
41360722 TTTTTAAAAAAAGGTGGCGCTGGCCATTGCCAGGCCACCACAAAAAAAAATAAATTTTTTTT-AT
1 TTTTT--AAAAAGGTGGTGCCGGCCATTGCCAGGCCACCAC------AAAT---TTTTTTTTAAC
* * **
41360786 TTTTTTCGTATACTGATATCTTATCTGAAACGAAAAAATTAAAAAT
55 TTTTTTCGTATACTGATATCTTATCTGACACGAAAAAA-GAAATTT
* * *
41360832 TTTTT--AAAGGTGGTGCCGGCTATTTCCAGGCCACCACGAATTTTTTTTTAACTTTTTTCGTAT
1 TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTAACTTTTTTCGTAT
*
41360895 ACTGATATCTTATCTGACACGAAAAAAGTAATTT
66 ACTGATATCTTATCTGACACGAAAAAAGAAATTT
*
41360929 TTTTT--AAAGGTGGTGCCGGCCATTTCCAGGCCACCACCAAATTTTTTTTT
1 TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCA-CAAATTTTTTTTT
41360979 TTTTACTTTT
Statistics
Matches: 307, Mismatches: 34, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
97 46 0.15
98 89 0.29
99 19 0.06
100 39 0.13
101 30 0.10
106 28 0.09
107 4 0.01
110 49 0.16
111 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (99 bp):
TTTTTAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTAACTTTTTTCGTAT
ACTGATATCTTATCTGACACGAAAAAAGAAATTT
Found at i:41360821 original size:208 final size:204
Alignment explanation
Indices: 41360567--41360965 Score: 552
Period size: 208 Copynumber: 1.9 Consensus size: 204
41360557 ACCACTAATT
* **
41360567 TTTTTTTTAACTTTTTTCGTATACTGATAGCTTATCTGATACGAAAAAAGT-AATTTTTTTTAAA
1 TTTTTTTTAACTTTTTTCGTATACTGATAGCTTATCTGAAACGAAAAAAGTAAAAATTTTTT--A
* *
41360631 AAGGTGATGCCGGCCATTGGCAGGCCACCACAAATTTTTTTTT-ACTTTTTTTGTATACTGATAC
64 AAGGTGATGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTAACTTTTTTCGTATACTGATAC
* *
41360695 CTTATTTGACACGAAAAAAGAAATTTTTTTTTAAAAAAAGGTGGCGCTGGCCATTGCCAGGCCAC
129 CTTATCTGACACGAAAAAAGAAA-TTTTTTTT----AAAGGTGGCGCCGGCCATTGCCAGGCCAC
41360760 CACAAAAAAAAATAAA
189 CACAAAAAAAAATAAA
* * *
41360776 TTTTTTTT-ATTTTTTTCGTATACTGATATCTTATCTGAAACGAAAAAATTAAAAATTTTTTAAA
1 TTTTTTTTAACTTTTTTCGTATACTGATAGCTTATCTGAAACGAAAAAAGTAAAAATTTTTTAAA
* * * * *
41360840 GGTGGTGCCGGCTATTTCCAGGCCACCACGAATTTTTTTTTAACTTTTTTCGTATACTGATATCT
66 GGTGATGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTAACTTTTTTCGTATACTGATACCT
* * *
41360905 TATCTGACACGAAAAAAGTAATTTTTTTTAAAGGTGGTGCCGGCCATTTCCAGGCCACCAC
131 TATCTGACACGAAAAAAGAAATTTTTTTTAAAGGTGGCGCCGGCCATTGCCAGGCCACCAC
41360966 CAAATTTTTT
Statistics
Matches: 170, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
203 29 0.17
207 47 0.28
208 78 0.46
209 16 0.09
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (204 bp):
TTTTTTTTAACTTTTTTCGTATACTGATAGCTTATCTGAAACGAAAAAAGTAAAAATTTTTTAAA
GGTGATGCCGGCCATTGCCAGGCCACCACAAATTTTTTTTTAACTTTTTTCGTATACTGATACCT
TATCTGACACGAAAAAAGAAATTTTTTTTAAAGGTGGCGCCGGCCATTGCCAGGCCACCACAAAA
AAAAATAAA
Found at i:41360880 original size:97 final size:96
Alignment explanation
Indices: 41360773--41360982 Score: 323
Period size: 97 Copynumber: 2.2 Consensus size: 96
41360763 AAAAAAAAAT
*
41360773 AAATTTTTTTTATTTTTTTCGTATACTGATATCTTATCTGAAACGAAAAAATTAAAAATTTTTTA
1 AAATTTTTTTTATTTTTTTCGTATACTGATATCTTATCTGAAACGAAAAAAGT-AAAATTTTTTA
* *
41360838 AAGGTGGTGCCGGCTATTTCCAGGCCACCACG
65 AAGGTGGTGCCGGCCATTTCCAGGCCACCACC
* * * **
41360870 AATTTTTTTTTAACTTTTTTCGTATACTGATATCTTATCTGACACGAAAAAAGTAATTTTTTTTA
1 AAATTTTTTTT-ATTTTTTTCGTATACTGATATCTTATCTGAAACGAAAAAAGTAAAATTTTTTA
41360935 AAGGTGGTGCCGGCCATTTCCAGGCCACCACC
65 AAGGTGGTGCCGGCCATTTCCAGGCCACCACC
41360967 AAATTTTTTTT-TTTTT
1 AAATTTTTTTTATTTTT
41360983 ACTTTTTCTC
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
95 4 0.04
97 59 0.58
98 39 0.38
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (96 bp):
AAATTTTTTTTATTTTTTTCGTATACTGATATCTTATCTGAAACGAAAAAAGTAAAATTTTTTAA
AGGTGGTGCCGGCCATTTCCAGGCCACCACC
Found at i:41363985 original size:16 final size:16
Alignment explanation
Indices: 41363964--41363994 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41363954 CATATTAGAG
41363964 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
41363980 CATATATATTTGAAA
1 CATATAAATTTGAAA
41363995 ACTTTTTCAA
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:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:41364987 original size:5 final size:5
Alignment explanation
Indices: 41364946--41364970 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41364936 GAGGAGTTAG
41364946 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
41364971 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:41366624 original size:15 final size:15
Alignment explanation
Indices: 41366604--41366643 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
41366594 ACAATAGGTG
41366604 GTTCGCAT-TCAATTA
1 GTTCGCATATC-ATTA
41366619 GTTCGCATATCATTA
1 GTTCGCATATCATTA
*
41366634 GTTCACATAT
1 GTTCGCATAT
41366644 AACAAACCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (15 bp):
GTTCGCATATCATTA
Found at i:41368833 original size:8 final size:8
Alignment explanation
Indices: 41368816--41368876 Score: 70
Period size: 8 Copynumber: 7.5 Consensus size: 8
41368806 AATACATAAA
41368816 TTTT-CTT
1 TTTTCCTT
41368823 TTTTCCTT
1 TTTTCCTT
41368831 TTTTCCTT
1 TTTTCCTT
*
41368839 TTTCCCTT
1 TTTTCCTT
41368847 TCTTTCCTT
1 T-TTTCCTT
**
41368856 TTATTATTT
1 TT-TTCCTT
41368865 TTTTCCTT
1 TTTTCCTT
41368873 TTTT
1 TTTT
41368877 TTTCTTTTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
7 4 0.09
8 28 0.62
9 13 0.29
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTCCTT
Found at i:41368865 original size:25 final size:24
Alignment explanation
Indices: 41368820--41368876 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
41368810 CATAAATTTT
*
41368820 CTTTTTTCCTTTTTTCCTTTTTCC
1 CTTTTTTCCTTTTTTCATTTTTCC
*
41368844 CTTTCTTTCCTTTTATT-ATTTTTTTC
1 CTTT-TTTCCTTTT-TTCA-TTTTTCC
41368870 CTTTTTT
1 CTTTTTT
41368877 TTTCTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 4 0.14
25 12 0.43
26 12 0.43
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.74
Consensus pattern (24 bp):
CTTTTTTCCTTTTTTCATTTTTCC
Found at i:41370822 original size:17 final size:18
Alignment explanation
Indices: 41370798--41370841 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
41370788 TTGGGTTGAG
41370798 GAAA-TAATTTAATTAA-
1 GAAATTAATTTAATTAAT
*
41370814 GAAATTAATTTAGTTAAT
1 GAAATTAATTTAATTAAT
*
41370832 TAAATTAATT
1 GAAATTAATT
41370842 GATTAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 11 0.46
18 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (18 bp):
GAAATTAATTTAATTAAT
Found at i:41385277 original size:43 final size:43
Alignment explanation
Indices: 41385216--41385339 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
41385206 ATTTCCGAAA
*
41385216 TGTGTTTTCATGTAAGACCACGTCTGGGATGTTGGCATCAACT
1 TGTGTTTACATGTAAGACCACGTCTGGGATGTTGGCATCAACT
* * * *
41385259 TGTGTTTACGTGTAAGACC-CTGTCTGGGATAG-TGGCGTCGATT
1 TGTGTTTACATGTAAGACCAC-GTCTGGGAT-GTTGGCATCAACT
* * *
41385302 TGTGATCACATGTAAGACCACGTTTGGGATGTTGGCAT
1 TGTGTTTACATGTAAGACCACGTCTGGGATGTTGGCAT
41385340 TGTACGAGCT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 2 0.03
43 63 0.94
44 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (43 bp):
TGTGTTTACATGTAAGACCACGTCTGGGATGTTGGCATCAACT
Found at i:41386727 original size:6 final size:6
Alignment explanation
Indices: 41386713--41386742 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
41386703 TTTTTTAATG
*
41386713 ATATAT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT
41386743 TTTGGTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:41393328 original size:43 final size:43
Alignment explanation
Indices: 41393275--41393388 Score: 115
Period size: 43 Copynumber: 2.7 Consensus size: 43
41393265 TTTCGATATT
*
41393275 TGTTTTCGTGTAAGACCACGTCTGGGACA-TCGGCAAAGACTTG
1 TGTTTACGTGTAAGACCACGTCTGGGACAGT-GGCAAAGACTTG
* *** *
41393318 TGTTTACGTGTAAGACC-CTGTCTGGGATAGTGGCGTCGATTTG
1 TGTTTACGTGTAAGACCAC-GTCTGGGACAGTGGCAAAGACTTG
* * *
41393361 TGATCACATGTAAGACCACGTCTGGGAC
1 TGTTTACGTGTAAGACCACGTCTGGGAC
41393389 GTTGGCATTG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 1 0.02
43 55 0.95
44 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (43 bp):
TGTTTACGTGTAAGACCACGTCTGGGACAGTGGCAAAGACTTG
Found at i:41403052 original size:38 final size:38
Alignment explanation
Indices: 41402990--41403208 Score: 147
Period size: 38 Copynumber: 5.8 Consensus size: 38
41402980 ATCACATAGC
*
41402990 ACGCCACACAGGCTTCATCGAATACGCCATTACAGAAT
1 ACGCCACACAGGCTTCACCGAATACGCCATTACAGAAT
* * * *
41403028 ATGCCATACGGGCTTCACCAAATACG-CATTACAGAAT
1 ACGCCACACAGGCTTCACCGAATACGCCATTACAGAAT
* ** ** ** *
41403065 ACGCCACACAGGCTTTACTAAATATACTGTTATAGAAT
1 ACGCCACACAGGCTTCACCGAATACGCCATTACAGAAT
* * * * ** *
41403103 ATGCCACACAAGCTTCACTGAATATGTTATTACAAAAT
1 ACGCCACACAGGCTTCACCGAATACGCCATTACAGAAT
* *
41403141 ACGCCATAC-GAGCTTCACCGAATA-GACCATTACATAAT
1 ACGCCACACAG-GCTTCACCGAATACG-CCATTACAGAAT
* * * ***
41403179 ACTCGACACGGGCTTTGTCGAATACGCCAT
1 ACGCCACACAGGCTTCACCGAATACGCCAT
41403209 GAAGGTCTTA
Statistics
Matches: 139, Mismatches: 37, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
37 31 0.22
38 106 0.76
39 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (38 bp):
ACGCCACACAGGCTTCACCGAATACGCCATTACAGAAT
Found at i:41404718 original size:26 final size:26
Alignment explanation
Indices: 41404688--41404758 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 26
41404678 GAATTTTTTT
41404688 AAAATTTTATTGGGGGTAAAATCGTC
1 AAAATTTTATTGGGGGTAAAATCGTC
* *
41404714 AAAATTTTATCGGGGGTAAAATTGTC
1 AAAATTTTATTGGGGGTAAAATCGTC
*
41404740 AAAATTTTACT-GGGGTAAA
1 AAAATTTTATTGGGGGTAAA
41404759 TTTGGGGTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 8 0.20
26 33 0.80
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.34
Consensus pattern (26 bp):
AAAATTTTATTGGGGGTAAAATCGTC
Found at i:41422292 original size:18 final size:19
Alignment explanation
Indices: 41422257--41422292 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41422247 ATCAAACTAC
*
41422257 AAAAAAAATCATTTTTTAG
1 AAAAAAAATCATTATTTAG
41422276 AAAAAAAAT-ATTATTTA
1 AAAAAAAATCATTATTTA
41422293 TCATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAAAAAATCATTATTTAG
Found at i:41436696 original size:7 final size:7
Alignment explanation
Indices: 41436684--41436708 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41436674 TAGTCGATTC
41436684 GTATTTA
1 GTATTTA
41436691 GTATTTA
1 GTATTTA
41436698 GTATTTA
1 GTATTTA
41436705 GTAT
1 GTAT
41436709 ATAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTTA
Found at i:41439163 original size:127 final size:127
Alignment explanation
Indices: 41439011--41439430 Score: 666
Period size: 126 Copynumber: 3.3 Consensus size: 127
41439001 GCCAAATAGG
*
41439011 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGTTGACATTGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACATTGCATCC
* * *
41439076 TACTTGAAGCATTTTTGACATTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
* * * *
41439138 AACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTAACATTGCTTCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACATTGCATCC
*
41439203 TGCTTGAAGCGTTTTTGACACTATTTTCTCAGAAACATCTTCTCAAAATT-TTTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
* * * *
41439264 AACAACTGTAGTAAAACAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAATGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACATTGCATCC
* *
41439329 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTA-TTTTTTCAGG
66 TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
* *
41439390 AACTATTGTAGCAAAAGAGCGTCCATGTGGGAGCTT-TTTTA
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTA
41439431 AATTAACAAA
Statistics
Matches: 267, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
125 5 0.02
126 156 0.58
127 106 0.40
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (127 bp):
AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACATTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTTCAGA
Found at i:41439758 original size:97 final size:96
Alignment explanation
Indices: 41439462--41439891 Score: 517
Period size: 97 Copynumber: 4.4 Consensus size: 96
41439452 AATAACCCTA
* * *
41439462 AACCTTAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCAAAACCCAAAACACTAAATCCTA
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAAC-CT-AAT-CT-
* *
41439526 ATCTATTTTTTTAAAATTTATAATTAATTTACTCAAAT
62 A---ATTTTTTAAAAATTTATAATTAATTTACTCAAGT
* * *
41439564 AACCCCAAACCCTAATTTATTTGATTTTTTCCTTAAAAATCCTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAA-CCTAATCTAAT
* *
41439629 TTTTT-TAAATTTATAATTAATTTATTCAAGT
65 TTTTTAAAAATTTATAATTAATTTACTCAAGT
*
41439660 AACCCTAAACCCTAATTTATTTGATTTTTTTCTTAAAAACCCTAAACCCTAAACTCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAAC-CTAATCTAAT
*
41439725 TTTTTAAAAATTTATAATTAATTTTCTCAAGT
65 TTTTTAAAAATTTATAATTAATTTACTCAAGT
* * * * * *
41439757 AAACTTAAACCTTAATTTATTTCATTTTTTCCTTAAAAACCATAAACGCTAAACCTTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAACC-TAATCTAAT
** *
41439822 TTTTTAAAAATTTATAATTAACCTAAACTCTA--
65 TTTTTAAAAATTTATAATTAA--TTTACTCAAGT
* *
41439854 AACCCTAAACCCTTATTTATTTAATTTTTTCCTTAAAA
1 AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAA
41439892 CCTTAAAATC
Statistics
Matches: 289, Mismatches: 32, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
95 1 0.00
96 88 0.30
97 140 0.48
99 5 0.02
100 1 0.00
101 2 0.01
102 25 0.09
103 26 0.09
104 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCTAAACCCTAAACCTAATCTAATT
TTTTAAAAATTTATAATTAATTTACTCAAGT
Found at i:41439811 original size:193 final size:197
Alignment explanation
Indices: 41439461--41439891 Score: 554
Period size: 193 Copynumber: 2.2 Consensus size: 197
41439451 AAATAACCCT
*
41439461 AAACCTTAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCAAAACCCAAAACACTAAATCCT
1 AAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCAAAACCCAAAACACTAAATCCT
* * *
41439525 AATCTATTTTTTTAAAATTTATAATTAATTTACTCAAATAACCCCAAACCCTAATTTATTTGATT
66 AA--TATTTTTTAAAAATTTATAATTAATTTACTCAAATAAACCCAAACCCTAATTTATTTCATT
* **
41439590 TTTTCCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTTT-TAAATTTATAATTAA-TTTA
129 TTTTCCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAACTAAA
*
41439653 TTCA
194 CTCA
* * * *
41439657 AGTAACCCTAAACCCTAATTTATTTGATTTTTTTCTTAAAAACCCTAAACCCTAAACTCT-AAT-
1 A--AACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCAAAACCCAAAACACTAAATC
* * ** *
41439720 CT-A-ATTTTTTAAAAATTTATAATTAATTTTCTCAAGTAAACTTAAACCTTAATTTATTTCATT
64 CTAATATTTTTTAAAAATTTATAATTAATTTACTCAAATAAACCCAAACCCTAATTTATTTCATT
* *
41439783 TTTTCCTTAAAAA-CCATAAACGCTAAACCTTAATCTAATTTTTTAAAAATTTATAATTAACCTA
129 TTTTCCTTAAAAATCC-TAAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAA-CTA
*
41439847 AACTCT
192 AACTCA
* *
41439853 AAACCCTAAACCCTTATTTATTTAATTTTTTCCTTAAAA
1 AAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAA
41439892 CCTTAAAATC
Statistics
Matches: 205, Mismatches: 23, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
192 2 0.01
193 91 0.44
194 49 0.24
196 7 0.03
197 2 0.01
198 26 0.13
199 28 0.14
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (197 bp):
AAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCCAAAACCCAAAACACTAAATCCT
AATATTTTTTAAAAATTTATAATTAATTTACTCAAATAAACCCAAACCCTAATTTATTTCATTTT
TTCCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTTTAAAAATTTATAATTAACTAAACT
CA
Found at i:41440484 original size:10 final size:11
Alignment explanation
Indices: 41440462--41440496 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
41440452 AACAAATCCT
41440462 CTCTCGTAATTC
1 CTCTCG-AATTC
41440474 CTCTC-AATTC
1 CTCTCGAATTC
41440484 CTCTCGAATTC
1 CTCTCGAATTC
41440495 CT
1 CT
41440497 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 7 0.32
12 5 0.23
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (11 bp):
CTCTCGAATTC
Found at i:41440509 original size:22 final size:22
Alignment explanation
Indices: 41440479--41440534 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
41440469 AATTCCTCTC
41440479 AATTCCTCTCGAA-TTCCTTCCAA
1 AATT-CTCTC-AATTTCCTTCCAA
*
41440502 AATTCTCTCAATTTTCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
41440524 AATTCTCTCAA
1 AATTCTCTCAA
41440535 ATCTATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 2 0.06
22 25 0.81
23 4 0.13
ACGTcount: A:0.29, C:0.30, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:41440563 original size:51 final size:51
Alignment explanation
Indices: 41440506--41440621 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
41440496 TTCCAAAATT
* * * *
41440506 CTCTCAATTTTCTTCCAAAATTCTCTCAAATCTATATTTAATTTTAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
41440557 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
*
41440608 TTCTCAATTTCCTT
1 CTCTCAATTTCCTT
41440622 TTTTAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.47
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
Found at i:41442056 original size:23 final size:23
Alignment explanation
Indices: 41441998--41442066 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
41441988 TCCAGTGGAT
*
41441998 CCTAATTTAATTAAAAGCCCTAAA
1 CCTAATTTAATTAAAAACCCT-AA
* * *
41442022 CC---CTTAAATAAAATCCCTAA
1 CCTAATTTAATTAAAAACCCTAA
41442042 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
41442065 CC
1 CC
41442067 CTAACCTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
20 4 0.11
21 13 0.36
23 17 0.47
24 2 0.06
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (23 bp):
CCTAATTTAATTAAAAACCCTAA
Found at i:41442076 original size:24 final size:23
Alignment explanation
Indices: 41442030--41442077 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
41442020 AACCCTTAAA
* **
41442030 TAAAATCCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAACCTAAT
41442053 TAAAAACCCTAACCCTAACCTAAT
1 TAAAAACCCTAA-CCTAACCTAAT
41442077 T
1 T
41442078 CATTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAAACCCTAACCTAACCTAAT
Found at i:41444959 original size:125 final size:124
Alignment explanation
Indices: 41444660--41445027 Score: 452
Period size: 125 Copynumber: 3.0 Consensus size: 124
41444650 CCCAAACATG
* * * * *
41444660 CTACTGTAGAAAAATCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *** *
41444725 TATAAGCGATTTTATATTATTTGCAT-AGAAACGTCAAAAAAAATTATAGATTAAAAGAC
66 TAAAAGCGATTTTATATTATTTGC-TCAGAAACGTCAAAAAAAATTATTTCTTCAAAGAC
* * * * *
41444784 CTACTGTAGCAAAAGCGCG-CTGATGAGGCCGCAATTTCACAAATTGTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* * ***
41444848 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTCTGTGAC
65 CTAAAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAA-AATTATTTCTTCAAAGAC
* *
41444909 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** **
41444974 TAAAAGCGATTTTATATTATTTTATCAGAAACGTCAACTCAAAATTATTTCTTC
66 TAAAAGCGATTTTATATTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTC
41445028 CAGGACCTTA
Statistics
Matches: 207, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
123 2 0.01
124 90 0.43
125 112 0.54
126 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAAAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCAAAGAC
Found at i:41448115 original size:22 final size:22
Alignment explanation
Indices: 41448066--41448130 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
41448056 GCTTAATATT
41448066 ATTTTAAATTTA-T-TATTAAC
1 ATTTTAAATTTATTGTATTAAC
*
41448086 ATTGTTTAAATTTATTGTATTACC
1 A-T-TTTAAATTTATTGTATTAAC
*
41448110 ATTTTAATTTTATATGTATTA
1 ATTTTAAATTTAT-TGTATTA
41448131 TTTTTCTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 20 0.53
23 9 0.24
24 7 0.18
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTTTAAATTTATTGTATTAAC
Found at i:41448325 original size:18 final size:17
Alignment explanation
Indices: 41448302--41448345 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41448292 TTATGTAGTA
41448302 TTTATTTTTAACTATATT
1 TTTATTTTTAA-TATATT
* *
41448320 TTTATTTATTTATTTATT
1 TTTATTT-TTAATATATT
41448338 TTTATTTT
1 TTTATTTT
41448346 CCAAATTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.83
19 3 0.13
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTTAATATATT
Found at i:41450301 original size:29 final size:30
Alignment explanation
Indices: 41450242--41450299 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41450232 TCCGAGCCTT
*
41450242 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
41450272 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
41450300 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:41450538 original size:13 final size:14
Alignment explanation
Indices: 41450512--41450544 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
41450502 TTTCCAGCAA
41450512 TTATGAATTTTATT
1 TTATGAATTTTATT
41450526 TTATGAA-TTTATT
1 TTATGAATTTTATT
*
41450539 TGATGA
1 TTATGA
41450545 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (14 bp):
TTATGAATTTTATT
Found at i:41450752 original size:50 final size:50
Alignment explanation
Indices: 41450639--41450880 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
41450629 ATTTGGGTAA
* * *
41450639 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
41450695 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41450745 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41450795 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
41450845 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
41450881 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:41450828 original size:100 final size:103
Alignment explanation
Indices: 41450639--41450888 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
41450629 ATTTGGGTAA
41450639 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
41450704 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
41450745 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
41450807 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
41450845 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
41450889 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:41457826 original size:31 final size:32
Alignment explanation
Indices: 41457791--41457851 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
41457781 TCCGAGCCTT
*
41457791 GGGGCAA-AAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAGAAAATGTAATTATGAAAAAGTTTA
* * *
41457822 GGGGCAAGTAATTGTAATTTTGAAAAAGTT
1 GGGGCAAGAAAATGTAATTATGAAAAAGTT
41457852 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (32 bp):
GGGGCAAGAAAATGTAATTATGAAAAAGTTTA
Found at i:41458083 original size:13 final size:13
Alignment explanation
Indices: 41458065--41458096 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41458055 TTTCCAGCAA
41458065 TTATGAATTTATT
1 TTATGAATTTATT
41458078 TTATGAATTTATT
1 TTATGAATTTATT
*
41458091 TGATGA
1 TTATGA
41458097 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:41458291 original size:58 final size:50
Alignment explanation
Indices: 41458191--41458438 Score: 247
Period size: 50 Copynumber: 4.9 Consensus size: 50
41458181 ATTTGGGTAA
* *
41458191 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TGG-GCA-CC--AAGA-C--G
* *
41458249 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* ** *
41458299 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC---GCCA-TGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* **
41458345 AGAGGTCACC--GATAAGACCATGACTGGGACATGGCATGGGCACCATCACG
1 AGAGGTC-CCATG-TAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
41458395 AGAAATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACC
41458439 TTTATCATCA
Statistics
Matches: 164, Mismatches: 18, Indels: 24
0.80 0.09 0.12
Matches are distributed among these distances:
45 1 0.01
46 34 0.21
47 5 0.03
49 5 0.03
50 73 0.45
51 1 0.01
52 1 0.01
53 3 0.02
55 2 0.01
56 2 0.01
57 3 0.02
58 34 0.21
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:41458361 original size:96 final size:96
Alignment explanation
Indices: 41458246--41458429 Score: 291
Period size: 96 Copynumber: 1.9 Consensus size: 96
41458236 CCTTAAGATC
* * * **
41458246 ATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACGAGAGGTCCCAT
1 ATGAGAGGTCACCTGTAAGACCATGACTGGGACATGGCATGGGCACC-ATCACGAGAAATCCCAT
41458310 GTAAGACCATGTCTGGGACATGGCGCCATGAG
65 GTAAGACCATGTCTGGGACATGGCGCCATGAG
41458342 ATGAGAGGTCACC-GATAAGACCATGACTGGGACATGGCATGGGCACCATCACGAGAAATCCCAT
1 ATGAGAGGTCACCTG-TAAGACCATGACTGGGACATGGCATGGGCACCATCACGAGAAATCCCAT
41458406 GTAAGACCATGTCTGGGACATGGC
65 GTAAGACCATGTCTGGGACATGGC
41458430 ATGGGCACCT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
95 2 0.02
96 79 0.98
ACGTcount: A:0.28, C:0.24, G:0.31, T:0.17
Consensus pattern (96 bp):
ATGAGAGGTCACCTGTAAGACCATGACTGGGACATGGCATGGGCACCATCACGAGAAATCCCATG
TAAGACCATGTCTGGGACATGGCGCCATGAG
Found at i:41458365 original size:46 final size:47
Alignment explanation
Indices: 41458246--41458380 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 47
41458236 CCTTAAGATC
*
41458246 ATGAGAGGTCCCCTG-TAAGACCATGTCTGGGACATGGCATGGGCACCGAG
1 ATGAGAGGT-CCC-GATAAGACCATGTCTGGGACATGGCA--GCCACCGAG
* *
41458296 ACGAGAGGTCCC-ATGTAAGACCATGTCTGGGACATGGC-GCCA-TGAG
1 ATGAGAGGTCCCGA--TAAGACCATGTCTGGGACATGGCAGCCACCGAG
*
41458342 ATGAGAGGTCACCGATAAGACCATGACTGGGACATGGCA
1 ATGAGAGGTC-CCGATAAGACCATGTCTGGGACATGGCA
41458381 TGGGCACCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
46 34 0.46
47 5 0.07
48 1 0.01
49 3 0.04
50 31 0.42
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.17
Consensus pattern (47 bp):
ATGAGAGGTCCCGATAAGACCATGTCTGGGACATGGCAGCCACCGAG
Found at i:41463171 original size:13 final size:13
Alignment explanation
Indices: 41463149--41463191 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
41463139 TCAAGAAATC
*
41463149 AAAATCAAAAAAG
1 AAAATGAAAAAAG
41463162 AAAATGAAAAAAG
1 AAAATGAAAAAAG
* *
41463175 AAAAAGAACAAA-
1 AAAATGAAAAAAG
41463187 AAAAT
1 AAAAT
41463192 AACAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.79, C:0.05, G:0.09, T:0.07
Consensus pattern (13 bp):
AAAATGAAAAAAG
Found at i:41467506 original size:21 final size:21
Alignment explanation
Indices: 41467456--41467502 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
41467446 AACTTAACGT
* *
41467456 AAATAATAATAATATATATAG
1 AAATAATAAAAATATAAATAG
*
41467477 TAATAATAAAAATATAAAT-G
1 AAATAATAAAAATATAAATAG
41467497 AAATAA
1 AAATAA
41467503 ATAATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (21 bp):
AAATAATAAAAATATAAATAG
Found at i:41478576 original size:32 final size:32
Alignment explanation
Indices: 41478540--41478600 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
41478530 AAATAAACAC
41478540 ATAATTATTCATTT-AATA-TTATAACTATTCAA
1 ATAA-TATT-ATTTAAATAGTTATAACTATTCAA
*
41478572 ATAATATTATTTAAATAGTTATAATTATT
1 ATAATATTATTTAAATAGTTATAACTATT
41478601 TTTCAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATATTATTTAAATAGTTATAACTATTCAA
Found at i:41478762 original size:32 final size:32
Alignment explanation
Indices: 41478720--41478780 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
41478710 TTTTTTGAAA
41478720 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
41478752 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
41478781 GTGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:41478773 original size:20 final size:20
Alignment explanation
Indices: 41478739--41478780 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41478729 AACTATTTAA
** *
41478739 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
41478759 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
41478779 AT
1 AT
41478781 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:41478909 original size:25 final size:25
Alignment explanation
Indices: 41478878--41478930 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
41478868 GGAATGAAAT
41478878 TTCATCTAGAAAACACACCAACAAA
1 TTCATCTAGAAAACACACCAACAAA
41478903 TTCATCTAGAAAACACACCAACAAA
1 TTCATCTAGAAAACACACCAACAAA
41478928 TTC
1 TTC
41478931 TAATATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.28, G:0.04, T:0.19
Consensus pattern (25 bp):
TTCATCTAGAAAACACACCAACAAA
Found at i:41480884 original size:15 final size:16
Alignment explanation
Indices: 41480859--41480892 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
41480849 AAGATGAAGC
41480859 GTTTGATAAATTTAAA
1 GTTTGATAAATTTAAA
*
41480875 GTTT-ATAAATTTGAA
1 GTTTGATAAATTTAAA
41480890 GTT
1 GTT
41480893 GAACTTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
GTTTGATAAATTTAAA
Found at i:41483316 original size:27 final size:27
Alignment explanation
Indices: 41482968--41483328 Score: 404
Period size: 27 Copynumber: 13.4 Consensus size: 27
41482958 AGGTATAATA
* *
41482968 ATCATTTTACCCTATGAGGGTATTTAG
1 ATCATTTTACCCTATGGGGGTATTTCG
*
41482995 GTCATTTTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
41483022 ATCATTCTACCCTATGGGGGTATATCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* * * * *
41483049 GTTACTTTACCCTATGAGGGTATTT-T
1 ATCATTTTACCCTATGGGGGTATTTCG
* ** *
41483075 AGTCATTTTATCCTAT-AAGATATTTCG
1 A-TCATTTTACCCTATGGGGGTATTTCG
* *
41483102 GTCATTTTATCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* * *
41483129 GTTATTCTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
*
41483156 ATCATTTTACCCTATAGGGGTATTTC-
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
41483182 AGTCATTCTATCCTATGGGGGTATTTCG
1 A-TCATTTTACCCTATGGGGGTATTTCG
* * * * *
41483210 GTCATTCTATCGTATAGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
* *
41483237 ATCATTCTACCCTATAGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
41483264 ATCATTTTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
*
41483291 ATCATTCTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATGGGGGTATTTCG
*
41483318 ATTATTTTACC
1 ATCATTTTACC
41483329 TATTTTAGGG
Statistics
Matches: 284, Mismatches: 45, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
26 22 0.08
27 262 0.92
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
ATCATTTTACCCTATGGGGGTATTTCG
Found at i:41487459 original size:23 final size:22
Alignment explanation
Indices: 41487416--41487459 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
41487406 TTCTAAGTCG
41487416 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
41487439 ATATTCACTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
41487460 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:41490421 original size:20 final size:20
Alignment explanation
Indices: 41490387--41490428 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41490377 AACTATTTAA
** *
41490387 ATAATATTAGTTGAATAGTT
1 ATAATATTAAATGAATAATT
41490407 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
41490427 AT
1 AT
41490429 GTGTTTATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:41491990 original size:32 final size:32
Alignment explanation
Indices: 41491929--41492163 Score: 269
Period size: 32 Copynumber: 7.4 Consensus size: 32
41491919 GAATGTCTAC
** *
41491929 AAGCCATAAGT-ACAATAATATGATTGGCACA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
* * *
41491960 AAGCCATAAGTAGCAGTGATATGATCGGCACA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
* *
41491992 CAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
41492024 AAGCCATCAA-TAACGGTAATATGATCGGCACA
1 AAGCCAT-AAGTAACGGTAATATGATCGGCACA
* * *
41492056 AAGCCATCAA-TAATGGTAATATGACCGGTACA
1 AAGCCAT-AAGTAACGGTAATATGATCGGCACA
* **
41492088 AAGCCATTAGTAACGGTAATATGATCGATACA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
* * *
41492120 AAGCCATCAGTAACGGTAATATGATCGGTATA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
*
41492152 AAGCCATCAGTA
1 AAGCCATAAGTA
41492164 GCATCGCAGC
Statistics
Matches: 180, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
31 12 0.07
32 167 0.93
33 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (32 bp):
AAGCCATAAGTAACGGTAATATGATCGGCACA
Found at i:41492183 original size:26 final size:26
Alignment explanation
Indices: 41492154--41492210 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
41492144 TCGGTATAAA
* *
41492154 GCCATCAGTAGCATCGCAGCAAAACT
1 GCCAGCAGAAGCATCGCAGCAAAACT
* * *
41492180 GCCAGCAGAAGTATTGCAGCAAAGCT
1 GCCAGCAGAAGCATCGCAGCAAAACT
41492206 GCCAG
1 GCCAG
41492211 TAATAGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.25, T:0.14
Consensus pattern (26 bp):
GCCAGCAGAAGCATCGCAGCAAAACT
Found at i:41492362 original size:24 final size:24
Alignment explanation
Indices: 41492335--41492392 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
41492325 CCATGCTCAG
* *
41492335 AATCAGTCA-ATCAAATCACAGACA
1 AATCAGTCATACCAAA-CACAGAAA
41492359 AATCAGTCATACCAAACACAGAAA
1 AATCAGTCATACCAAACACAGAAA
41492383 AATCAGTCAT
1 AATCAGTCAT
41492393 TTAACCACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.17
Consensus pattern (24 bp):
AATCAGTCATACCAAACACAGAAA
Found at i:41492496 original size:27 final size:27
Alignment explanation
Indices: 41492452--41492609 Score: 174
Period size: 27 Copynumber: 5.9 Consensus size: 27
41492442 TTCACCCACT
* *
41492452 AGGGCATTACGATCATTTTACCTTACA
1 AGGGCATTACGGTCATTTTACCCTACA
* *
41492479 AGGGTATTACGGTTATTTTACCCTACA
1 AGGGCATTACGGTCATTTTACCCTACA
* *
41492506 GGGGCATTACGATCATTTTACCCTACA
1 AGGGCATTACGGTCATTTTACCCTACA
* * *
41492533 TGGGTATTACGTTCATTTTA-CCTCACA
1 AGGGCATTACGGTCATTTTACCCT-ACA
*
41492560 AGGGCATTACGGTCATTTTACCCTATA
1 AGGGCATTACGGTCATTTTACCCTACA
* ***
41492587 AGGGTATTTTAGTCATTTTACCC
1 AGGGCATTACGGTCATTTTACCC
41492610 ATCGAGGGTA
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
26 3 0.03
27 104 0.95
28 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (27 bp):
AGGGCATTACGGTCATTTTACCCTACA
Found at i:41492518 original size:54 final size:54
Alignment explanation
Indices: 41492452--41492594 Score: 209
Period size: 54 Copynumber: 2.6 Consensus size: 54
41492442 TTCACCCACT
*
41492452 AGGGCATTACGATCATTTTACCTTACAAGGGTATTACGGTT-ATTTTACC-CTACA
1 AGGGCATTACGATCATTTTACCCTACAAGGGTATTAC-GTTCATTTTACCTC-ACA
* *
41492506 GGGGCATTACGATCATTTTACCCTACATGGGTATTACGTTCATTTTACCTCACA
1 AGGGCATTACGATCATTTTACCCTACAAGGGTATTACGTTCATTTTACCTCACA
* *
41492560 AGGGCATTACGGTCATTTTACCCTATAAGGGTATT
1 AGGGCATTACGATCATTTTACCCTACAAGGGTATT
41492595 TTAGTCATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
53 3 0.04
54 76 0.95
55 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (54 bp):
AGGGCATTACGATCATTTTACCCTACAAGGGTATTACGTTCATTTTACCTCACA
Found at i:41492617 original size:27 final size:27
Alignment explanation
Indices: 41492571--41492650 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
41492561 GGGCATTACG
*
41492571 GTCATTTTACCCTAT-AAGGGTATTTTA
1 GTCATTTTACCC-ATCGAGGGTATTTTA
**
41492598 GTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTA
* * *
41492625 GTTATTCTACCCTTCGAGGGTATTTT
1 GTCATTTTACCCATCGAGGGTATTTT
41492651 GGTCTAGATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.04
27 43 0.96
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTTA
Found at i:41492636 original size:54 final size:54
Alignment explanation
Indices: 41492452--41492650 Score: 149
Period size: 54 Copynumber: 3.7 Consensus size: 54
41492442 TTCACCCACT
* * *** *
41492452 AGGGCATTACGATCATTTTA-CCTTACAAGGGTATTACGGTTATTTTACC-CTACA
1 AGGGCATTACGGTCATTCTACCCTT-CAAGGGTATTTTAGTCATTTTACCTC-ACA
* * * * *
41492506 GGGGCATTACGATCATTTTACCCTACATGGGTA--TTACGTTCATTTTACCTCACA
1 AGGGCATTACGGTCATTCTACCCTTCAAGGGTATTTTA-G-TCATTTTACCTCACA
* *
41492560 AGGGCATTACGGTCATTTTACCCTAT-AAGGGTATTTTAGTCATTTTACC-CATCG
1 AGGGCATTACGGTCATTCTACCCT-TCAAGGGTATTTTAGTCATTTTACCTCA-CA
* * * *
41492614 AGGGTATTTCGGTTATTCTACCCTTCGAGGGTATTTT
1 AGGGCATTACGGTCATTCTACCCTTCAAGGGTATTTT
41492651 GGTCTAGATA
Statistics
Matches: 119, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
53 4 0.03
54 107 0.90
55 5 0.04
56 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (54 bp):
AGGGCATTACGGTCATTCTACCCTTCAAGGGTATTTTAGTCATTTTACCTCACA
Found at i:41500318 original size:16 final size:16
Alignment explanation
Indices: 41500287--41500323 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
41500277 AAGTGAAGAA
41500287 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
41500303 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
41500319 TATTA
1 TATTA
41500324 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:41500407 original size:26 final size:25
Alignment explanation
Indices: 41500335--41500409 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 25
41500325 AATAAAATTG
*
41500335 AAATATTAAAT-ATTAAAT-TATATT
1 AAATA-TAAATAATTAAATATATACT
* * *
41500359 AATTATACTAATAATTTATTATATGACT
1 AAATATA--AATAATTAAATATAT-ACT
41500387 AAATATAAATAATTAAATATATA
1 AAATATAAATAATTAAATATATA
41500410 TGTTTAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
23 2 0.05
24 4 0.10
25 4 0.10
26 18 0.46
27 3 0.08
28 8 0.21
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
AAATATAAATAATTAAATATATACT
Found at i:41500478 original size:5 final size:6
Alignment explanation
Indices: 41500462--41500486 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41500452 TTAATATTTT
41500462 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
41500487 TATTATCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:41509297 original size:20 final size:21
Alignment explanation
Indices: 41509261--41509303 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
41509251 GTTATTAAAT
41509261 ATTATGTTATTATAAAA-TAA
1 ATTATGTTATTATAAAACTAA
*
41509281 ATTATGTT-TTGTCAAAACTAA
1 ATTATGTTATTAT-AAAACTAA
41509302 AT
1 AT
41509304 GCTACTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 12 0.60
21 5 0.25
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (21 bp):
ATTATGTTATTATAAAACTAA
Found at i:41513083 original size:16 final size:19
Alignment explanation
Indices: 41513062--41513101 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 19
41513052 TTTATGAACA
41513062 AATTTTTA-CTT-AGTT-T
1 AATTTTTACCTTCAGTTGT
41513078 AA-TTTTACCTTCAGTTGT
1 AATTTTTACCTTCAGTTGT
41513096 AATTTT
1 AATTTT
41513102 GATTTCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.25
16 5 0.25
17 4 0.20
18 3 0.15
19 3 0.15
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (19 bp):
AATTTTTACCTTCAGTTGT
Found at i:41513116 original size:23 final size:23
Alignment explanation
Indices: 41513090--41513135 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41513080 TTTTACCTTC
*
41513090 AGTTGTAATTTTGATTTCCTTTT
1 AGTTATAATTTTGATTTCCTTTT
* * *
41513113 AGTTATAGTTTTTATTTCGTTTT
1 AGTTATAATTTTGATTTCCTTTT
41513136 TTCTATTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.17, C:0.07, G:0.13, T:0.63
Consensus pattern (23 bp):
AGTTATAATTTTGATTTCCTTTT
Found at i:41517189 original size:15 final size:14
Alignment explanation
Indices: 41517146--41517190 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
41517136 TAATTCTATT
41517146 TTTATTTTTATTTA
1 TTTATTTTTATTTA
*
41517160 TTATATATTTATTTA
1 TT-TATTTTTATTTA
*
41517175 CTTTATTTTTCTTTA
1 -TTTATTTTTATTTA
41517190 T
1 T
41517191 CAACTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 3 0.12
15 21 0.81
16 2 0.08
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:41526454 original size:23 final size:23
Alignment explanation
Indices: 41526422--41526923 Score: 369
Period size: 23 Copynumber: 21.5 Consensus size: 23
41526412 ACACCAAAAT
* *
41526422 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
* * * *
41526445 TTGGGTAGCATTTATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * *
41526468 CTAGGCAGCATATATACAAAAAA
1 TTGGGCAGCATATATACAACAAA
* * * *
41526491 TTGAGCAGCATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
*
41526516 TTGGACAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * *
41526539 TTGGGCAGAATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
41526562 TTGAGCCGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* * *
41526586 TTGGACAGCATATATACAACCAT
1 TTGGGCAGCATATATACAACAAA
*
41526609 TTGGGCAGCATAAATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
41526632 TTGAGTAGCATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
*
41526657 TTGGACAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
41526680 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
41526703 TTGAGCCGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
41526727 TTGGACAGCATATATACTACAAA
1 TTGGGCAGCATATATACAACAAA
* *
41526750 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
41526773 TTGAGCCGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
41526797 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
*
41526820 TTGGGCAGCATAAATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * *
41526843 TTGAGCAGCACT-TTTACACCAAAAA
1 TTGGGCAGCA-TATATACA--ACAAA
* * *
41526868 TTGGACAGCCTATATGCAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
41526891 TTGAGCAGTATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
41526914 TT-GGCAGCAT
1 TTGGGCAGCAT
41526924 TTAAGCATCA
Statistics
Matches: 357, Mismatches: 111, Indels: 23
0.73 0.23 0.05
Matches are distributed among these distances:
22 6 0.02
23 248 0.69
24 52 0.15
25 51 0.14
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (23 bp):
TTGGGCAGCATATATACAACAAA
Found at i:41526477 original size:71 final size:71
Alignment explanation
Indices: 41526285--41526478 Score: 300
Period size: 75 Copynumber: 2.7 Consensus size: 71
41526275 AACTATACTA
** *
41526285 CATAT-TACAACAATTTGGACAGCATTTATATACCAAACTAGACATCATTTTCACACCAAAATTT
1 CATATATACAACAATTTGGGTAGCATTTATATACCAAACTAGACAGCATTTTCACACCAAAATTT
41526349 GGACAG
66 GGACAG
*
41526355 CATATATATATACAACAATTTGGGTAGCATTTATATACCTAACTAGACAGCATTTTCACACCAAA
1 C----ATATATACAACAATTTGGGTAGCATTTATATACCAAACTAGACAGCATTTTCACACCAAA
41526420 ATTTGGACAG
62 ATTTGGACAG
*
41526430 CATATATACAACAATTTGGGTAGCATTTATATACCAAACTAGGCAGCAT
1 CATATATACAACAATTTGGGTAGCATTTATATACCAAACTAGACAGCAT
41526479 ATATACAAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
70 1 0.01
71 46 0.41
74 4 0.04
75 62 0.55
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (71 bp):
CATATATACAACAATTTGGGTAGCATTTATATACCAAACTAGACAGCATTTTCACACCAAAATTT
GGACAG
Found at i:41526617 original size:141 final size:141
Alignment explanation
Indices: 41526471--41526925 Score: 689
Period size: 141 Copynumber: 3.2 Consensus size: 141
41526461 TACCAAACTA
*
41526471 GGCAGCATATATACAAAAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
*
41526536 AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
66 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
* *
41526601 ACAACCATTTG
131 ACAACAAATTG
* *
41526612 GGCAGCATAAATACAACAAATTGAGTAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
41526677 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
66 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
*
41526742 ACTACAAATTG
131 ACAACAAATTG
* * * *
41526753 GGCAGCATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
* * * * * * * *
41526817 AATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGCCTATA
66 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATA
*
41526882 TGCAACAAATTG
130 TACAACAAATTG
* *
41526894 AGCAGTATATATACAACAAATTG-GCAGCATTT
1 GGCAGCATATATACAACAAATTGAGCAGCATTT
41526926 AAGCATCAAA
Statistics
Matches: 285, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
140 71 0.25
141 214 0.75
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (141 bp):
GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
ACAACAAATTG
Done.