Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold168
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: 938898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 20427 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:296361 original size:27 final size:27
Alignment explanation
Indices: 295515--296361 Score: 763
Period size: 27 Copynumber: 31.2 Consensus size: 27
295505 GGGTATAACA
* *
295515 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCG
* *
295542 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * * **
295569 ATCATTTTACCCCATAAGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * * *
295596 ATAATT-TGACCCCATAGGGGTATTTCG
1 GTCATTCT-ACCCTATGGGGGTATTTCG
* * * *
295623 ATAATT-TGA-CCTCATAGGGGCATTTCG
1 GTCATTCT-ACCCT-ATGGGGGTATTTCG
* *
295650 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * * **
295677 ATCATTTTACCCTATAGGGGTATTTTA
1 GTCATTCTACCCTATGGGGGTATTTCG
* * **
295704 GTCATTTTACCCTATGAGGGTATTTTA
1 GTCATTCTACCCTATGGGGGTATTTCG
*
295731 GTCATTCTACCCTAT-GGGGTATTTCA
1 GTCATTCTACCCTATGGGGGTATTTCG
* *
295757 GTCATTCTACTCTATGAGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
*
295784 GTCATTCTACCCTATGGGGGTATTTCA
1 GTCATTCTACCCTATGGGGGTATTTCG
*
295811 ATCATTCTACCCTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * *
295838 ATCATTTTACGCTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
** * *
295865 GTCATTCTACCCTATGATGGTACTTCA
1 GTCATTCTACCCTATGGGGGTATTTCG
* *
295892 ATCATTCTACCCTATGGGGGT-TTTCA
1 GTCATTCTACCCTATGGGGGTATTTCG
* *
295918 ATCATTCTACACTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* ** *
295945 GTCATTTTACCCTATGGACGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * * ** *
295972 ATTATTCTACTCTATGACGATATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * * *
295999 ATCATTCTACTCTATGAGGATATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* *
296026 GTCATTCTACTCTATGAGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* **
296053 ATCATTCTACCCTATTAGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
296080 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* *
296107 ATCATTCTAACCTA-GGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * * *
296133 ATCATTTTACCCTATGAGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCG
* **
296160 GTCATTCTACCCTATGAGGGTATTTTA
1 GTCATTCTACCCTATGGGGGTATTTCG
296187 GTCATTCTACCCTATGGGGGTATGTATTTCG
1 GTCATTCTACCCTAT-GGGG---GTATTTCG
* *
296218 TTCATTTTACCCTATGGGGGTATGTATTTCG
1 GTCATTCTACCCTAT-GGGG---GTATTTCG
* * *
296249 GCCATTTTACCCTATGGGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCG
*
296276 GTCACTT-TACCCTATGAGGGTATTTCG
1 GTCA-TTCTACCCTATGGGGGTATTTCG
* * * *
296303 ATCATTTTACCTTATGGTGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* ** *
296330 ATCATTCTACCCTATAAGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCG
296357 GTCAT
1 GTCAT
296362 AATAGTGTAA
Statistics
Matches: 703, Mismatches: 104, Indels: 26
0.84 0.12 0.03
Matches are distributed among these distances:
26 76 0.11
27 566 0.81
28 9 0.01
30 4 0.01
31 48 0.07
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (27 bp):
GTCATTCTACCCTATGGGGGTATTTCG
Found at i:303230 original size:29 final size:29
Alignment explanation
Indices: 303182--303259 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
303172 TGTATCTGAT
*
303182 ATGGGC-CAGGGCCCAAACTGATTCTGTG
1 ATGGGCACAGGCCCCAAACTGATTCTGTG
303210 ATGGGCACAGGCCCCAAACTGATTCTGTG
1 ATGGGCACAGGCCCCAAACTGATTCTGTG
303239 ATGGGCACAGGCCCCAAACTG
1 ATGGGCACAGGCCCCAAACTG
303260 TATCTAACCG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 6 0.12
29 42 0.88
ACGTcount: A:0.24, C:0.28, G:0.29, T:0.18
Consensus pattern (29 bp):
ATGGGCACAGGCCCCAAACTGATTCTGTG
Found at i:308383 original size:11 final size:11
Alignment explanation
Indices: 308356--308385 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
308346 AAAATAAAAA
*
308356 TAAAAGTATTT
1 TAAAATTATTT
308367 TAAAATTATTT
1 TAAAATTATTT
308378 TAAAATTA
1 TAAAATTA
308386 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:310765 original size:55 final size:54
Alignment explanation
Indices: 310676--310806 Score: 183
Period size: 55 Copynumber: 2.4 Consensus size: 54
310666 TATGTCCAAC
* *
310676 CCCGTGTAACTCACTGACTTGGGTTACACGGCCAACCACA-CACATGTGTAACTAG
1 CCCGTGTAACTCACTGACTTGGGTCACACAGCCAACCACAGCACATGTG--ACTAG
* *
310731 CCCGTGTAACTCACTAACTTGGGTCACACAGCCAACCACATGCCCATGTGACTAG
1 CCCGTGTAACTCACTGACTTGGGTCACACAGCCAACCACA-GCACATGTGACTAG
*
310786 CCCGTGTAACTCGCTGACTTG
1 CCCGTGTAACTCACTGACTTG
310807 CTTTCATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
55 61 0.90
57 7 0.10
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (54 bp):
CCCGTGTAACTCACTGACTTGGGTCACACAGCCAACCACAGCACATGTGACTAG
Found at i:312602 original size:61 final size:63
Alignment explanation
Indices: 312537--312670 Score: 152
Period size: 65 Copynumber: 2.1 Consensus size: 63
312527 TTAACTTAAG
*
312537 TAAATGAACTAAAACAT-ATGCATCAAT-TATTCC-AGCAACTAG-TTAATTAAATAAGCAT-AA
1 TAAATGAACT-AAAC-TCATGCATCAATATAATCCTAGCAACTAGATTAATTAAA-AAGCATCAA
312597 T
63 T
* * *
312598 TAAATGAACTTAACTCATGCATCAATAAATAATCCTAGGAACTAGATTAATTAAAAAGCATCTAT
1 TAAATGAACTAAACTCATGCATCAAT--ATAATCCTAGCAACTAGATTAATTAAAAAGCATCAAT
312663 TAAATGAA
1 TAAATGAA
312671 GTTCAATAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
59 1 0.02
60 13 0.21
61 10 0.16
63 5 0.08
64 14 0.23
65 19 0.31
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (63 bp):
TAAATGAACTAAACTCATGCATCAATATAATCCTAGCAACTAGATTAATTAAAAAGCATCAAT
Found at i:312761 original size:17 final size:17
Alignment explanation
Indices: 312731--312789 Score: 73
Period size: 19 Copynumber: 3.3 Consensus size: 17
312721 AGCAACTCAT
312731 TTATTAATCTAAGATGAG
1 TTATTAA-CTAAGATGAG
*
312749 TTATTAACTAAGATGAAC
1 TTATTAACTAAGATG-AG
*
312767 TCAATTAACTAAGATGAG
1 T-TATTAACTAAGATGAG
312785 TTATT
1 TTATT
312790 TATTCACGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 11 0.31
18 11 0.31
19 13 0.37
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (17 bp):
TTATTAACTAAGATGAG
Found at i:317570 original size:20 final size:20
Alignment explanation
Indices: 317520--317576 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
317510 AAGCTTATGC
* * *
317520 TAAGTAAATGAAATGGAATG
1 TAAGTAAATGGAATGGTAGG
317540 TAAGTAAATGGAATGGTAGG
1 TAAGTAAATGGAATGGTAGG
*
317560 TAAGTAAATGGAGTGGT
1 TAAGTAAATGGAATGGT
317577 TCATAATCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (20 bp):
TAAGTAAATGGAATGGTAGG
Found at i:328841 original size:50 final size:50
Alignment explanation
Indices: 328778--328968 Score: 247
Period size: 50 Copynumber: 3.8 Consensus size: 50
328768 TTAAGAGGAT
* * * * *
328778 GAGGTCCCATGTAAGACCATGTATGGGACATGGCTTTGGCACCAAGATCA
1 GAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGA
* *
328828 GAGGACCCATGTAAGACCATATTTGGGACATGGCATTGGCACCGAGATGA
1 GAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGA
** * * *
328878 GAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGA
1 GAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGA
** *
328928 GAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 GAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
328969 GTACAAGAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 121 1.00
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
GAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGA
Found at i:329002 original size:49 final size:49
Alignment explanation
Indices: 328782--329006 Score: 172
Period size: 50 Copynumber: 4.5 Consensus size: 49
328772 GAGGATGAGG
* * * *
328782 TCCCATGTAAGACCATGTATGGGACATGGCTTTGGCACCAAGATC-AGAGGA-
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--GA-CAAGAGAAC
* * * * * **
328833 -CCCATGTAAGACCATATTTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CGACAAGAGAAC
** * *
328882 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CGACAAGAGAAC
* * *
328932 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACG-ACAAGAGAAC
*
328980 ATCCCATGTAATACCATGTCTGGGACA
1 -TCCCATGTAAGACCATGTCTGGGACA
329007 AGGCTTTGGC
Statistics
Matches: 144, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
48 9 0.06
49 27 0.19
50 108 0.75
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.21
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACGACAAGAGAAC
Found at i:331235 original size:20 final size:19
Alignment explanation
Indices: 331206--331252 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
331196 CGAAAAATGA
331206 TTTCTAGAAAATGATTTACT
1 TTTCTAG-AAATGATTTACT
*
331226 TTTCTGGAAATGATTTACT
1 TTTCTAGAAATGATTTACT
331245 TTTCTAGA
1 TTTCTAGA
331253 GTTTTGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.47
Consensus pattern (19 bp):
TTTCTAGAAATGATTTACT
Found at i:336158 original size:17 final size:17
Alignment explanation
Indices: 336136--336177 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
336126 CATATATGTG
336136 AATGTATGTATGAAT-T
1 AATGTATGTATGAATAT
*
336152 CAATGTATGTATGTATAT
1 -AATGTATGTATGAATAT
336170 AATGTATG
1 AATGTATG
336178 ATGCCCTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (17 bp):
AATGTATGTATGAATAT
Found at i:340183 original size:46 final size:46
Alignment explanation
Indices: 340133--340222 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
340123 TTTATTGCAA
* *
340133 TAAGAGTTTTAGTTTTATTTATTTTCTTTATTAT-TTCAGGTTTTAT
1 TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATT-AGGTTTTAT
340179 TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTT
1 TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTT
340223 TATTTCCTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 39 0.95
47 2 0.05
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61
Consensus pattern (46 bp):
TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTTAT
Found at i:341296 original size:19 final size:19
Alignment explanation
Indices: 341272--341320 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
341262 GGAGGGGGAT
341272 GAACAACGGAACCAACAAG
1 GAACAACGGAACCAACAAG
341291 GAACAACGGAACCAACAAG
1 GAACAACGGAACCAACAAG
341310 GAACAACGGAA
1 GAACAACGGAA
341321 AAATAGGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.53, C:0.24, G:0.22, T:0.00
Consensus pattern (19 bp):
GAACAACGGAACCAACAAG
Found at i:341312 original size:11 final size:11
Alignment explanation
Indices: 341273--341313 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
341263 GAGGGGGATG
341273 AACAACGGAACC
1 AACAA-GGAACC
341285 AACAAGGAA-C
1 AACAAGGAACC
341295 AAC--GGAACC
1 AACAAGGAACC
341304 AACAAGGAAC
1 AACAAGGAAC
341314 AACGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.15
9 4 0.15
10 4 0.15
11 9 0.35
12 5 0.19
ACGTcount: A:0.54, C:0.27, G:0.20, T:0.00
Consensus pattern (11 bp):
AACAAGGAACC
Found at i:341498 original size:15 final size:15
Alignment explanation
Indices: 341478--341514 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
341468 AAGGCAAGCA
341478 AGATGATGATGAGGT
1 AGATGATGATGAGGT
341493 AGATGATGATGAGGT
1 AGATGATGATGAGGT
341508 AGATGAT
1 AGATGAT
341515 TTTAAATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (15 bp):
AGATGATGATGAGGT
Found at i:343063 original size:28 final size:28
Alignment explanation
Indices: 343007--343059 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
342997 AATAATTACA
**
343007 CAAAATATTTAAAATAATTTTTAAAATT
1 CAAAATATTTAAAATAATTTAAAAAATT
*
343035 CAAAATATTTATAA-AATTTAAAAAA
1 CAAAATATTTAAAATAATTTAAAAAA
343060 ATTCTAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (28 bp):
CAAAATATTTAAAATAATTTAAAAAATT
Found at i:343067 original size:18 final size:18
Alignment explanation
Indices: 343013--343109 Score: 61
Period size: 18 Copynumber: 5.1 Consensus size: 18
343003 TACACAAAAT
*
343013 ATTTAAAATAATTTTTAAA
1 ATTTAAAA-AATTTCTAAA
* * *
343032 ATTCAAAATATTTATAAA
1 ATTTAAAAAATTTCTAAA
*
343050 ATTTAAAAAAATTCTAAAGA
1 ATTTAAAAAATTTCT-AA-A
**
343070 ATATATAAAAAAAGT-TAAA
1 AT-T-TAAAAAATTTCTAAA
*
343089 ATTTTAAAAATTTTCTAAA
1 A-TTTAAAAAATTTCTAAA
343108 AT
1 AT
343110 AATAATTTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
18 27 0.44
19 17 0.28
20 6 0.10
21 2 0.03
22 9 0.15
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTTAAAAAATTTCTAAA
Found at i:343342 original size:163 final size:164
Alignment explanation
Indices: 343084--343411 Score: 649
Period size: 163 Copynumber: 2.0 Consensus size: 164
343074 ATAAAAAAAG
343084 TTAAAATTTTAAAAATTTTCTAAAATAATAATTTTGAAATCTTAAATAAGTATTAATGATTCAAG
1 TTAAAATTTTAAAAATTTTCTAAAATAATAATTTTGAAATCTTAAATAAGTATTAATGATTCAAG
343149 TTTATCATGCTAAAATATCTTAATTTTTATTATTATTTTACTTTGAAAAAGTTTTCAAATATATA
66 TTTATCATGCTAAAATATCTTAATTTTTATTATTATTTTACTTTGAAAAAGTTTTCAAATATATA
343214 TATGGTTTCAAATTTATATGTTATAACATGTAAT
131 TATGGTTTCAAATTTATATGTTATAACATGTAAT
343248 TTAAAATTTT-AAAATTTTCTAAAATAATAATTTTGAAATCTTAAATAAGTATTAATGATTCAAG
1 TTAAAATTTTAAAAATTTTCTAAAATAATAATTTTGAAATCTTAAATAAGTATTAATGATTCAAG
343312 TTTATCATGCTAAAATATCTTAATTTTTATTATTATTTTACTTTGAAAAAGTTTTCAAATATATA
66 TTTATCATGCTAAAATATCTTAATTTTTATTATTATTTTACTTTGAAAAAGTTTTCAAATATATA
343377 TATGGTTTCAAATTTATATGTTATAACATGTAAT
131 TATGGTTTCAAATTTATATGTTATAACATGTAAT
343411 T
1 T
343412 AGTTATACTG
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
163 154 0.94
164 10 0.06
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.47
Consensus pattern (164 bp):
TTAAAATTTTAAAAATTTTCTAAAATAATAATTTTGAAATCTTAAATAAGTATTAATGATTCAAG
TTTATCATGCTAAAATATCTTAATTTTTATTATTATTTTACTTTGAAAAAGTTTTCAAATATATA
TATGGTTTCAAATTTATATGTTATAACATGTAAT
Found at i:344735 original size:20 final size:21
Alignment explanation
Indices: 344700--344749 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
344690 TTTTAAAAAA
* *
344700 TTAAAAATCATTAAAATTA-T
1 TTAAAAATCATAAAAAATACT
*
344720 TTAAAAATTATAAAAAATACTT
1 TTAAAAATCATAAAAAATAC-T
344742 TTAAAAAT
1 TTAAAAAT
344750 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.64
22 9 0.36
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAAAATCATAAAAAATACT
Found at i:344777 original size:20 final size:20
Alignment explanation
Indices: 344740--344778 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
344730 TAAAAAATAC
*
344740 TTTTAAAAATATTTTTAAAA
1 TTTTAAAAATATTATTAAAA
344760 TTTTAAAAA-ATTAATTAAA
1 TTTTAAAAATATT-ATTAAA
344779 TGTTATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAAAAATATTATTAAAA
Found at i:344996 original size:20 final size:20
Alignment explanation
Indices: 344959--344997 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
344949 TAAAAAATAC
*
344959 TTTTAAAAATATTTTTAAAA
1 TTTTAAAAATATTATTAAAA
344979 TTTTAAAAA-ATTAATTAAA
1 TTTTAAAAATATT-ATTAAA
344998 TGTTATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAAAAATATTATTAAAA
Found at i:345083 original size:219 final size:220
Alignment explanation
Indices: 344692--345131 Score: 864
Period size: 219 Copynumber: 2.0 Consensus size: 220
344682 AAGAACTATT
344692 TTAAAAAATTAAAAATCATTAAAATTATTTAAAAATTATAAAAAATACTTTTAAAAATATTTTTA
1 TTAAAAAATT-AAAATCATTAAAATTATTTAAAAATTATAAAAAATACTTTTAAAAATATTTTTA
344757 AAATTTTAAAAAATTAATTAAATGTTATGTGTCATAGACCACTTGAAGAGTGTTGGTTTATATTT
65 AAATTTTAAAAAATTAATTAAATGTTATGTGTCATAGACCACTTGAAGAGTGTTGGTTTATATTT
344822 TCCATCAACAATGACAAAATTTATTATGATATTATAGTTGCTTTCCATCTTGTTGGAAAGGTGTT
130 TCCATCAACAATGACAAAATTTATTATGATATTATAGTTGCTTTCCATCTTGTTGGAAAGGTGTT
344887 GGTCATAAACACATACATTCCATTTC
195 GGTCATAAACACATACATTCCATTTC
344913 TTAAAAAATT-AAATCATTAAAATTATTTAAAAATTATAAAAAATACTTTTAAAAATATTTTTAA
1 TTAAAAAATTAAAATCATTAAAATTATTTAAAAATTATAAAAAATACTTTTAAAAATATTTTTAA
344977 AATTTTAAAAAATTAATTAAATGTTATGTGTCATAGACCACTTGAAGAGTGTTGGTTTATATTTT
66 AATTTTAAAAAATTAATTAAATGTTATGTGTCATAGACCACTTGAAGAGTGTTGGTTTATATTTT
345042 CCATCAACAATGACAAAATTTATTATGATATTATAGTTGCTTTCCATCTTGTTGGAAAGGTGTTG
131 CCATCAACAATGACAAAATTTATTATGATATTATAGTTGCTTTCCATCTTGTTGGAAAGGTGTTG
345107 GTCATAAACACATACATTCCATTTC
196 GTCATAAACACATACATTCCATTTC
345132 ACAAGTAGGG
Statistics
Matches: 219, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
219 209 0.95
221 10 0.05
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (220 bp):
TTAAAAAATTAAAATCATTAAAATTATTTAAAAATTATAAAAAATACTTTTAAAAATATTTTTAA
AATTTTAAAAAATTAATTAAATGTTATGTGTCATAGACCACTTGAAGAGTGTTGGTTTATATTTT
CCATCAACAATGACAAAATTTATTATGATATTATAGTTGCTTTCCATCTTGTTGGAAAGGTGTTG
GTCATAAACACATACATTCCATTTC
Found at i:349407 original size:26 final size:26
Alignment explanation
Indices: 349371--349431 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
349361 GGCATACATA
*
349371 ACATCAAAACATGTTCTTCAATAGAC
1 ACATCAAAACATGTTCTTAAATAGAC
349397 ACATCAAAACATGTTCTTAAATAGAC
1 ACATCAAAACATGTTCTTAAATAGAC
349423 ACATCAAAA
1 ACATCAAAA
349432 GCTATTCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.25
Consensus pattern (26 bp):
ACATCAAAACATGTTCTTAAATAGAC
Found at i:350024 original size:49 final size:49
Alignment explanation
Indices: 349964--350148 Score: 162
Period size: 50 Copynumber: 3.7 Consensus size: 49
349954 GACAATAACA
* * *
349964 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTTCATATACG
* * *
350013 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAG-TTCTTATACCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTTCATATA-C-G
* * ** * * *
350063 TGTCC-ATGTCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCT-CGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTTCATATAC-G
*
350113 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
350149 CCCTCTCATA
Statistics
Matches: 109, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
47 6 0.06
48 2 0.02
49 36 0.33
50 59 0.54
51 2 0.02
52 4 0.04
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTTCATATACG
Found at i:350610 original size:30 final size:30
Alignment explanation
Indices: 350554--350610 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
350544 TCGAACTTTG
**
350554 GCATAATTACAATTTTGCCCTTAAACTATT
1 GCATAATTACAATTTTGCCCCAAAACTATT
* *
350584 GCATATTTACACTTTTGCCCCAAAACT
1 GCATAATTACAATTTTGCCCCAAAACT
350611 CAAAAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
GCATAATTACAATTTTGCCCCAAAACTATT
Found at i:352676 original size:26 final size:26
Alignment explanation
Indices: 352640--352735 Score: 97
Period size: 26 Copynumber: 3.7 Consensus size: 26
352630 ATTTATAGTC
*
352640 CTCCAACCAACTCAAACTTAAGGGTT
1 CTCCGACCAACTCAAACTTAAGGGTT
*
352666 CTCCGACCAACTCAAACTCAAGGG-T
1 CTCCGACCAACTCAAACTTAAGGGTT
** * *
352691 CTTTAGACCCACTCAAACTTAA-GGTAC
1 C-TCCGACCAACTCAAACTTAAGGGT-T
*
352718 CTCTGACCAACTCAAACT
1 CTCCGACCAACTCAAACT
352736 GCTCCGACGC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
25 4 0.07
26 52 0.91
27 1 0.02
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.22
Consensus pattern (26 bp):
CTCCGACCAACTCAAACTTAAGGGTT
Found at i:353325 original size:30 final size:29
Alignment explanation
Indices: 353301--353357 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
353291 GCGGCACCAA
*
353301 GCTTGAAGG-GCACATGTCTGGCGGCACTC
1 GCTTGAAGGACCAC-TGTCTGGCGGCACTC
*
353330 GCTTGGAGGACCACTGTCTGGCGGCACT
1 GCTTGAAGGACCACTGTCTGGCGGCACT
353358 AGTTGGAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.21
Consensus pattern (29 bp):
GCTTGAAGGACCACTGTCTGGCGGCACTC
Found at i:354808 original size:36 final size:35
Alignment explanation
Indices: 354763--354872 Score: 87
Period size: 36 Copynumber: 3.1 Consensus size: 35
354753 GCGCCTTGAG
*
354763 CTAGCTGGTAAAACCAATAAATGAGTGTGCCCAGCA
1 CTAGTTGGTAAAACCAA-AAATGAGTGTGCCCAGCA
* * * * * *
354799 CTAGTTGGTATAAGCGAAAAATAAATGTGCCCTGCG
1 CTAGTTGGTA-AAACCAAAAATGAGTGTGCCCAGCA
* * *
354835 CT-GATCGGTAAAACCGACAAATGAGTGTGTCCAGCA
1 CTAG-TTGGTAAAACC-AAAAATGAGTGTGCCCAGCA
354871 CT
1 CT
354873 GGTCAATATA
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
35 4 0.07
36 46 0.84
37 5 0.09
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (35 bp):
CTAGTTGGTAAAACCAAAAATGAGTGTGCCCAGCA
Found at i:354858 original size:72 final size:72
Alignment explanation
Indices: 354769--354934 Score: 183
Period size: 72 Copynumber: 2.3 Consensus size: 72
354759 TGAGCTAGCT
*** * **
354769 GGTAAAACC-AATAAATGAGTGTGCCCAGCACTAGTTGGTATAAGCGAA-AAATAAATGTGCCCT
1 GGTAAAACCGAA-AAATGAGTGTGCCCAGCACTAGTCAATATAA-CCAACAAATAAATGCACCCT
**
354832 GCGCTGATC
64 AAGCTGATC
* * *
354841 GGTAAAACCGACAAATGAGTGTGTCCAGCACTGGTCAATATAACCAACAAATAAATGCACCCTAA
1 GGTAAAACCGAAAAATGAGTGTGCCCAGCACTAGTCAATATAACCAACAAATAAATGCACCCTAA
*
354906 GCTGGTC
66 GCTGATC
*
354913 AGTAAAACCGAAAAATGAGTGT
1 GGTAAAACCGAAAAATGAGTGT
354935 TTATTCATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
71 3 0.04
72 74 0.95
73 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (72 bp):
GGTAAAACCGAAAAATGAGTGTGCCCAGCACTAGTCAATATAACCAACAAATAAATGCACCCTAA
GCTGATC
Found at i:355460 original size:106 final size:104
Alignment explanation
Indices: 355322--355527 Score: 331
Period size: 106 Copynumber: 2.0 Consensus size: 104
355312 AGATATAATC
*
355322 AGCTTTAGAAAAACACTTATTCGCCTATAATATCAGCATTAAAATCGACATAAACACTTATTCAA
1 AGCTTTAGAAAAAAACTTATTCGCCTATAATATCAGCATTAAAATCGACATAAACACTTATTCAA
355387 TCCTAACATTTAATTTAACATAAACATAATAGAAATGTCT
66 TCCTAACATTTAA-TTAACATAAACATAATAGAAATGTCT
* * ** * *
355427 AGCTTTGGAAAAAAAACTTATTTGCCTATAATATCAGCATTAAAATTTACATAATCACTTATTTA
1 AGCTTTAG-AAAAAAACTTATTCGCCTATAATATCAGCATTAAAATCGACATAAACACTTATTCA
355492 ATCCTAACATTTAATTAACATAAACATAATAGAAAT
65 ATCCTAACATTTAATTAACATAAACATAATAGAAAT
355528 ATCCTCAAAT
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 29 0.31
106 64 0.69
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (104 bp):
AGCTTTAGAAAAAAACTTATTCGCCTATAATATCAGCATTAAAATCGACATAAACACTTATTCAA
TCCTAACATTTAATTAACATAAACATAATAGAAATGTCT
Found at i:359513 original size:72 final size:72
Alignment explanation
Indices: 359437--359588 Score: 187
Period size: 72 Copynumber: 2.1 Consensus size: 72
359427 TAAAACTGAC
* *** * * *
359437 AAATGAGTGTGCCCAGCACTAGTTGGTATAACCGACAAATAAATGCGCCCTGCGTTGGTCAGTAA
1 AAATGAGTGTACCCAGCACTAGTCAATATAACCAACAAATAAATGCGCCCTGCATTGATCAGTAA
*
359502 AATCAAA
66 AACCAAA
* * * *
359509 AAATGAGTGTACCCAGCATTGGTCAATATAACCAACGAATAAATGCGCCCTGCATTGATCGGTAA
1 AAATGAGTGTACCCAGCACTAGTCAATATAACCAACAAATAAATGCGCCCTGCATTGATCAGTAA
*
359574 AACCAAC
66 AACCAAA
359581 AAATGAGT
1 AAATGAGT
359589 TTTCATTCAT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (72 bp):
AAATGAGTGTACCCAGCACTAGTCAATATAACCAACAAATAAATGCGCCCTGCATTGATCAGTAA
AACCAAA
Found at i:359564 original size:36 final size:36
Alignment explanation
Indices: 359463--359584 Score: 100
Period size: 36 Copynumber: 3.4 Consensus size: 36
359453 CACTAGTTGG
* * *
359463 TATAACCGACAAATAAATGCGCCCTGCGTTGGTCAG
1 TATAACCAACAAATAAATGCGCCCTGCATTGGTCAA
* * * * * ** *
359499 TAAAATCAAAAAATGAGTGTACCCAGCATTGGTCAA
1 TATAACCAACAAATAAATGCGCCCTGCATTGGTCAA
* * **
359535 TATAACCAACGAATAAATGCGCCCTGCATTGATCGG
1 TATAACCAACAAATAAATGCGCCCTGCATTGGTCAA
*
359571 TAAAACCAACAAAT
1 TATAACCAACAAAT
359585 GAGTTTTCAT
Statistics
Matches: 61, Mismatches: 25, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (36 bp):
TATAACCAACAAATAAATGCGCCCTGCATTGGTCAA
Found at i:360191 original size:109 final size:109
Alignment explanation
Indices: 360000--360210 Score: 359
Period size: 109 Copynumber: 1.9 Consensus size: 109
359990 CCAGCTTTAG
* *
360000 AAAAACACTTATTCACCTATAATATCAGTATTAAAATCGACATAAACAATTATTTAATCCTAACA
1 AAAAACACTTATTCACCTATAATATCAGCATTAAAATCGACATAAACAATTATTTAATCCCAACA
360065 TTTAATTTAACATAAACATAATAGAAATGTCTAGCTTTGGAAAA
66 TTTAATTTAACATAAACATAATAGAAATGTCTAGCTTTGGAAAA
* * ** *
360109 AAAAACACTTATTCGCCTATAATATTAGCATTAAAATTTACATAAACACTTATTTAATCCCAACA
1 AAAAACACTTATTCACCTATAATATCAGCATTAAAATCGACATAAACAATTATTTAATCCCAACA
360174 TTTAATTTAACATAAACATAATAGAAATGTCTAGCTT
66 TTTAATTTAACATAAACATAATAGAAATGTCTAGCTT
360211 GGACAACACT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 95 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (109 bp):
AAAAACACTTATTCACCTATAATATCAGCATTAAAATCGACATAAACAATTATTTAATCCCAACA
TTTAATTTAACATAAACATAATAGAAATGTCTAGCTTTGGAAAA
Found at i:365985 original size:30 final size:31
Alignment explanation
Indices: 365959--366017 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
365949 GTAAATACTC
* **
365959 AAAATTTGAGGGATTAA-AGTGTAAATATGA
1 AAAATTTGAAGGACCAATAGTGTAAATATGA
365989 AAAATTTGAAGGACCAATAGTGTAAATAT
1 AAAATTTGAAGGACCAATAGTGTAAATAT
366018 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.29
Consensus pattern (31 bp):
AAAATTTGAAGGACCAATAGTGTAAATATGA
Found at i:377109 original size:22 final size:21
Alignment explanation
Indices: 377066--377110 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
377056 TTGAAAAGTT
* *
377066 ATATTATTTGAAGGTAATTTA
1 ATATTATTTGAAGATAAATTA
*
377087 ATATTAATTTTAAGATAAATTA
1 ATATT-ATTTGAAGATAAATTA
377109 AT
1 AT
377111 TAAAATATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (21 bp):
ATATTATTTGAAGATAAATTA
Found at i:379771 original size:45 final size:45
Alignment explanation
Indices: 379716--379894 Score: 358
Period size: 45 Copynumber: 4.0 Consensus size: 45
379706 AATTTTTTTA
379716 AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATATT
1 AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATATT
379761 AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATATT
1 AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATATT
379806 AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATATT
1 AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATATT
379851 AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATAT
1 AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATAT
379895 GTCTGAATGT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 134 1.00
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.40
Consensus pattern (45 bp):
AAAAAAATTGTTCGTGTATTTAGAAGGTATTTGGGAGATTATATT
Found at i:382321 original size:23 final size:23
Alignment explanation
Indices: 382295--382340 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
382285 TCCCAGCATG
382295 CTACAACCCATATGTGGTTAGCA
1 CTACAACCCATATGTGGTTAGCA
382318 CTACAACCCATATGTGGTTAGCA
1 CTACAACCCATATGTGGTTAGCA
382341 TGGAGCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (23 bp):
CTACAACCCATATGTGGTTAGCA
Found at i:382460 original size:158 final size:158
Alignment explanation
Indices: 382172--382465 Score: 579
Period size: 158 Copynumber: 1.9 Consensus size: 158
382162 AACACTTTGG
*
382172 TGTGGTTAGCATGGAGCAACATGACTTTCCCCAGTGAAAACATCCCTAGGAACCTAGTAAACCCA
1 TGTGGTTAGCATGGAGCAACATGACTTTCCCCAATGAAAACATCCCTAGGAACCTAGTAAACCCA
382237 ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCATGCTACAAC
66 ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCATGCTACAAC
382302 CCATATGTGGTTAGCACTACAACCCATA
131 CCATATGTGGTTAGCACTACAACCCATA
382330 TGTGGTTAGCATGGAGCAACATGACTTTCCCCAATGAAAACATCCCTAGGAACCTAGTAAACCCA
1 TGTGGTTAGCATGGAGCAACATGACTTTCCCCAATGAAAACATCCCTAGGAACCTAGTAAACCCA
382395 ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCATGCTACAAC
66 ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCATGCTACAAC
382460 CCATAT
131 CCATAT
382466 TTGGAAATTT
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 135 1.00
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (158 bp):
TGTGGTTAGCATGGAGCAACATGACTTTCCCCAATGAAAACATCCCTAGGAACCTAGTAAACCCA
ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCATGCTACAAC
CCATATGTGGTTAGCACTACAACCCATA
Found at i:399831 original size:24 final size:24
Alignment explanation
Indices: 399776--399831 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
399766 TATGGTGCTT
399776 CCTGATTAATTGCTCTTCAGAGCTA
1 CCTG-TTAATTGCTCTTCAGAGCTA
* *
399801 CCCGTTAATTGCTC-TCTGGAGCTA
1 CCTGTTAATTGCTCTTC-AGAGCTA
399825 CCTGTTA
1 CCTGTTA
399832 TAGGCTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 22 0.81
25 3 0.11
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (24 bp):
CCTGTTAATTGCTCTTCAGAGCTA
Found at i:411387 original size:494 final size:494
Alignment explanation
Indices: 410460--411449 Score: 1980
Period size: 494 Copynumber: 2.0 Consensus size: 494
410450 ACTTGAGCAG
410460 TATAGGGTGTAGGGTTGATCCCTCAGAGACTGGGTTCACGTAAAATTGTTGCTCTTTCTCGACCA
1 TATAGGGTGTAGGGTTGATCCCTCAGAGACTGGGTTCACGTAAAATTGTTGCTCTTTCTCGACCA
410525 GATTCGTGTCTAGGCAGTTGTCGTGCCCAAGAAATTTGGGGGAGGATAAAAATTAAAAACATTAA
66 GATTCGTGTCTAGGCAGTTGTCGTGCCCAAGAAATTTGGGGGAGGATAAAAATTAAAAACATTAA
410590 ATAAACAAAAAAAATGCGTAAAAAGTAAAAGCTAAAAACAAATAATAAAAACAATTAAATAAATC
131 ATAAACAAAAAAAATGCGTAAAAAGTAAAAGCTAAAAACAAATAATAAAAACAATTAAATAAATC
410655 TGAAGAGAAATCAATTAAACTTAGCTCAGCTTTAGGCACGGGTTTTTTTCTCATCTTTGAACTGA
196 TGAAGAGAAATCAATTAAACTTAGCTCAGCTTTAGGCACGGGTTTTTTTCTCATCTTTGAACTGA
410720 TCCTCGAAATTAAATGAACTCCTCTTTTCCAATAAACTAATTATAGCTACCAAGGATGCCTCGGA
261 TCCTCGAAATTAAATGAACTCCTCTTTTCCAATAAACTAATTATAGCTACCAAGGATGCCTCGGA
410785 CACCAAATCTTTCTTGTGTAAATTAGTTATGGAACATCCTATAACTAACCCTTACCGATTGAACA
326 CACCAAATCTTTCTTGTGTAAATTAGTTATGGAACATCCTATAACTAACCCTTACCGATTGAACA
410850 ACCAATGAAACGTTCGTGGTTTAGAACTCCGGCAGCTTTTTGTTCTAGAAGAGCCTAGCTCAAAC
391 ACCAATGAAACGTTCGTGGTTTAGAACTCCGGCAGCTTTTTGTTCTAGAAGAGCCTAGCTCAAAC
410915 TAATGTCCTCAACTACGTGGGACTTTTAAATCCGGTTAC
456 TAATGTCCTCAACTACGTGGGACTTTTAAATCCGGTTAC
410954 TATAGGGTGTAGGGTTGATCCCTCAGAGACTGGGTTCACGTAAAATTGTTGCTCTTTCTCGACCA
1 TATAGGGTGTAGGGTTGATCCCTCAGAGACTGGGTTCACGTAAAATTGTTGCTCTTTCTCGACCA
411019 GATTCGTGTCTAGGCAGTTGTCGTGCCCAAGAAATTTGGGGGAGGATAAAAATTAAAAACATTAA
66 GATTCGTGTCTAGGCAGTTGTCGTGCCCAAGAAATTTGGGGGAGGATAAAAATTAAAAACATTAA
411084 ATAAACAAAAAAAATGCGTAAAAAGTAAAAGCTAAAAACAAATAATAAAAACAATTAAATAAATC
131 ATAAACAAAAAAAATGCGTAAAAAGTAAAAGCTAAAAACAAATAATAAAAACAATTAAATAAATC
411149 TGAAGAGAAATCAATTAAACTTAGCTCAGCTTTAGGCACGGGTTTTTTTCTCATCTTTGAACTGA
196 TGAAGAGAAATCAATTAAACTTAGCTCAGCTTTAGGCACGGGTTTTTTTCTCATCTTTGAACTGA
411214 TCCTCGAAATTAAATGAACTCCTCTTTTCCAATAAACTAATTATAGCTACCAAGGATGCCTCGGA
261 TCCTCGAAATTAAATGAACTCCTCTTTTCCAATAAACTAATTATAGCTACCAAGGATGCCTCGGA
411279 CACCAAATCTTTCTTGTGTAAATTAGTTATGGAACATCCTATAACTAACCCTTACCGATTGAACA
326 CACCAAATCTTTCTTGTGTAAATTAGTTATGGAACATCCTATAACTAACCCTTACCGATTGAACA
411344 ACCAATGAAACGTTCGTGGTTTAGAACTCCGGCAGCTTTTTGTTCTAGAAGAGCCTAGCTCAAAC
391 ACCAATGAAACGTTCGTGGTTTAGAACTCCGGCAGCTTTTTGTTCTAGAAGAGCCTAGCTCAAAC
411409 TAATGTCCTCAACTACGTGGGACTTTTAAATCCGGTTAC
456 TAATGTCCTCAACTACGTGGGACTTTTAAATCCGGTTAC
411448 TA
1 TA
411450 CTTTCATTGA
Statistics
Matches: 496, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
494 496 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (494 bp):
TATAGGGTGTAGGGTTGATCCCTCAGAGACTGGGTTCACGTAAAATTGTTGCTCTTTCTCGACCA
GATTCGTGTCTAGGCAGTTGTCGTGCCCAAGAAATTTGGGGGAGGATAAAAATTAAAAACATTAA
ATAAACAAAAAAAATGCGTAAAAAGTAAAAGCTAAAAACAAATAATAAAAACAATTAAATAAATC
TGAAGAGAAATCAATTAAACTTAGCTCAGCTTTAGGCACGGGTTTTTTTCTCATCTTTGAACTGA
TCCTCGAAATTAAATGAACTCCTCTTTTCCAATAAACTAATTATAGCTACCAAGGATGCCTCGGA
CACCAAATCTTTCTTGTGTAAATTAGTTATGGAACATCCTATAACTAACCCTTACCGATTGAACA
ACCAATGAAACGTTCGTGGTTTAGAACTCCGGCAGCTTTTTGTTCTAGAAGAGCCTAGCTCAAAC
TAATGTCCTCAACTACGTGGGACTTTTAAATCCGGTTAC
Found at i:414823 original size:533 final size:533
Alignment explanation
Indices: 413817--414882 Score: 2132
Period size: 533 Copynumber: 2.0 Consensus size: 533
413807 GGACTCTACC
413817 AAATAATTTAATTTCAAATTAACTATTCCAAAAAGAATATTGTTTTAATAAATTTAATATTAAAT
1 AAATAATTTAATTTCAAATTAACTATTCCAAAAAGAATATTGTTTTAATAAATTTAATATTAAAT
413882 TTAATTTAATACTTATCTTGATAGTATTTTACTAATTTAATAGATTTAATATTAAATTAATATAA
66 TTAATTTAATACTTATCTTGATAGTATTTTACTAATTTAATAGATTTAATATTAAATTAATATAA
413947 TACTTAATAATATTTATTTTGTTAAGTATTATATTAATTTAATATTAAAGTGATTAAGTTTAATT
131 TACTTAATAATATTTATTTTGTTAAGTATTATATTAATTTAATATTAAAGTGATTAAGTTTAATT
414012 ATAGTTGAACTCTCTAAACTCTCCCTATATAAAGAAAACCTTGGGTCATTATTTTACACACTTAA
196 ATAGTTGAACTCTCTAAACTCTCCCTATATAAAGAAAACCTTGGGTCATTATTTTACACACTTAA
414077 ATTCAAGAGAAAGTTATAAGGAGAAAATTCTTTGAAGAAATTATTTCAGAAAATTTTTAAAGATA
261 ATTCAAGAGAAAGTTATAAGGAGAAAATTCTTTGAAGAAATTATTTCAGAAAATTTTTAAAGATA
414142 TTTTTCTTATTTACAACTTGATCCAGAAGTTTAGAGAAATTGCAAAATTACCCCACTGGTCATTT
326 TTTTTCTTATTTACAACTTGATCCAGAAGTTTAGAGAAATTGCAAAATTACCCCACTGGTCATTT
414207 GTTGGAAAATTTTCTAATTTGAATCGTGTCTACAATCAGCAGACGTGAGCTTGAGATAGCGAAGA
391 GTTGGAAAATTTTCTAATTTGAATCGTGTCTACAATCAGCAGACGTGAGCTTGAGATAGCGAAGA
414272 AGACTACTCGGTCGAAGCATTCATTCTAGATGAATAAAAAAGATACAATTTTGATTAAGTGTTTA
456 AGACTACTCGGTCGAAGCATTCATTCTAGATGAATAAAAAAGATACAATTTTGATTAAGTGTTTA
414337 TTACTTTAGATAT
521 TTACTTTAGATAT
414350 AAATAATTTAATTTCAAATTAACTATTCCAAAAAGAATATTGTTTTAATAAATTTAATATTAAAT
1 AAATAATTTAATTTCAAATTAACTATTCCAAAAAGAATATTGTTTTAATAAATTTAATATTAAAT
414415 TTAATTTAATACTTATCTTGATAGTATTTTACTAATTTAATAGATTTAATATTAAATTAATATAA
66 TTAATTTAATACTTATCTTGATAGTATTTTACTAATTTAATAGATTTAATATTAAATTAATATAA
414480 TACTTAATAATATTTATTTTGTTAAGTATTATATTAATTTAATATTAAAGTGATTAAGTTTAATT
131 TACTTAATAATATTTATTTTGTTAAGTATTATATTAATTTAATATTAAAGTGATTAAGTTTAATT
414545 ATAGTTGAACTCTCTAAACTCTCCCTATATAAAGAAAACCTTGGGTCATTATTTTACACACTTAA
196 ATAGTTGAACTCTCTAAACTCTCCCTATATAAAGAAAACCTTGGGTCATTATTTTACACACTTAA
414610 ATTCAAGAGAAAGTTATAAGGAGAAAATTCTTTGAAGAAATTATTTCAGAAAATTTTTAAAGATA
261 ATTCAAGAGAAAGTTATAAGGAGAAAATTCTTTGAAGAAATTATTTCAGAAAATTTTTAAAGATA
414675 TTTTTCTTATTTACAACTTGATCCAGAAGTTTAGAGAAATTGCAAAATTACCCCACTGGTCATTT
326 TTTTTCTTATTTACAACTTGATCCAGAAGTTTAGAGAAATTGCAAAATTACCCCACTGGTCATTT
414740 GTTGGAAAATTTTCTAATTTGAATCGTGTCTACAATCAGCAGACGTGAGCTTGAGATAGCGAAGA
391 GTTGGAAAATTTTCTAATTTGAATCGTGTCTACAATCAGCAGACGTGAGCTTGAGATAGCGAAGA
414805 AGACTACTCGGTCGAAGCATTCATTCTAGATGAATAAAAAAGATACAATTTTGATTAAGTGTTTA
456 AGACTACTCGGTCGAAGCATTCATTCTAGATGAATAAAAAAGATACAATTTTGATTAAGTGTTTA
414870 TTACTTTAGATAT
521 TTACTTTAGATAT
414883 CACAACCAAG
Statistics
Matches: 533, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
533 533 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (533 bp):
AAATAATTTAATTTCAAATTAACTATTCCAAAAAGAATATTGTTTTAATAAATTTAATATTAAAT
TTAATTTAATACTTATCTTGATAGTATTTTACTAATTTAATAGATTTAATATTAAATTAATATAA
TACTTAATAATATTTATTTTGTTAAGTATTATATTAATTTAATATTAAAGTGATTAAGTTTAATT
ATAGTTGAACTCTCTAAACTCTCCCTATATAAAGAAAACCTTGGGTCATTATTTTACACACTTAA
ATTCAAGAGAAAGTTATAAGGAGAAAATTCTTTGAAGAAATTATTTCAGAAAATTTTTAAAGATA
TTTTTCTTATTTACAACTTGATCCAGAAGTTTAGAGAAATTGCAAAATTACCCCACTGGTCATTT
GTTGGAAAATTTTCTAATTTGAATCGTGTCTACAATCAGCAGACGTGAGCTTGAGATAGCGAAGA
AGACTACTCGGTCGAAGCATTCATTCTAGATGAATAAAAAAGATACAATTTTGATTAAGTGTTTA
TTACTTTAGATAT
Found at i:421480 original size:50 final size:49
Alignment explanation
Indices: 421417--421545 Score: 170
Period size: 50 Copynumber: 2.6 Consensus size: 49
421407 GATGAGACCC
**
421417 CATGTAAGACCATGTCTGGGACATGGCGATGGTG-CCGAGATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGC-ATGG-GACCGAGATGAGAACTCT
* *
421467 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATGGG-ACCGAGATGAGAACTCT
* *
421517 CATGTAAGACCATATCTGGGAAATGGCAT
1 CATGTAAGACCATGTCTGGGACATGGCAT
421546 TTGCAGTACA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 1 0.01
49 4 0.06
50 65 0.93
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (49 bp):
CATGTAAGACCATGTCTGGGACATGGCATGGGACCGAGATGAGAACTCT
Found at i:421582 original size:49 final size:49
Alignment explanation
Indices: 421520--421645 Score: 200
Period size: 49 Copynumber: 2.6 Consensus size: 49
421510 GAACTCTCAT
421520 GTAAGACCATATCTGGGAAATGGCATTTGCAGTACAGGAAACATCCCAC
1 GTAAGACCATATCTGGGAAATGGCATTTGCAGTACAGGAAACATCCCAC
* * *
421569 GTAAGACCATATCTGGGATATGTCATTTGCAGTACAGGAAACATCCCAT
1 GTAAGACCATATCTGGGAAATGGCATTTGCAGTACAGGAAACATCCCAC
* *
421618 GTAAGACCATGTCTGGGACATGGC-TTTG
1 GTAAGACCATATCTGGGAAATGGCATTTG
421646 GCATGTTATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
48 4 0.06
49 67 0.94
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (49 bp):
GTAAGACCATATCTGGGAAATGGCATTTGCAGTACAGGAAACATCCCAC
Found at i:421876 original size:20 final size:20
Alignment explanation
Indices: 421851--421889 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
421841 TGAGTTATTT
421851 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
421871 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
421890 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:423061 original size:6 final size:6
Alignment explanation
Indices: 423050--423080 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
423040 ATTGATAATA
423050 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
423081 AAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:431247 original size:20 final size:20
Alignment explanation
Indices: 431224--431288 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
431214 ACTTCGGTGT
*
431224 CCCTGTTTGCACAAC-TGTGC
1 CCCTGATTGCAC-ACTTGTGC
431244 CCCTGATTGCACACTTGTGC
1 CCCTGATTGCACACTTGTGC
*
431264 CCCTGATTGCAC-TTTGGTGC
1 CCCTGATTGCACACTT-GTGC
431284 CCCTG
1 CCCTG
431289 TTTTGCATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.10
20 37 0.90
ACGTcount: A:0.12, C:0.35, G:0.22, T:0.31
Consensus pattern (20 bp):
CCCTGATTGCACACTTGTGC
Found at i:431306 original size:22 final size:20
Alignment explanation
Indices: 431240--431311 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
431230 TTGCACAACT
*
431240 GTGCCCCTGATTGCAC-ACTT
1 GTGCCCCTGATTGCACTA-TG
*
431260 GTGCCCCTGATTGCACTTTG
1 GTGCCCCTGATTGCACTATG
*
431280 GTGCCCCTGTTTTGCATCTATG
1 GTGCCCCTG-ATTGCA-CTATG
431302 GTGCCCCTGA
1 GTGCCCCTGA
431312 AAATGAGTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 26 0.59
21 5 0.11
22 13 0.30
ACGTcount: A:0.11, C:0.32, G:0.24, T:0.33
Consensus pattern (20 bp):
GTGCCCCTGATTGCACTATG
Found at i:434660 original size:17 final size:17
Alignment explanation
Indices: 434626--434660 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
434616 CTTGTATTTA
*
434626 AGTGTGAACACTCCTCT
1 AGTGTGAACACACCTCT
*
434643 AGTGTGAACACACTTCT
1 AGTGTGAACACACCTCT
434660 A
1 A
434661 AGACAATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (17 bp):
AGTGTGAACACACCTCT
Found at i:435236 original size:20 final size:18
Alignment explanation
Indices: 435197--435239 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
435187 CCCCCTCTTC
435197 TTCTTCTTCTTCCTTATT
1 TTCTTCTTCTTCCTTATT
435215 TTCTT-TTCTTCTCTTCATT
1 TTCTTCTTCTTC-CTT-ATT
435234 TT-TTCT
1 TTCTTCT
435240 CCTATTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 6 0.27
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.70
Consensus pattern (18 bp):
TTCTTCTTCTTCCTTATT
Found at i:435247 original size:26 final size:26
Alignment explanation
Indices: 435225--435292 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
435215 TTCTTTTCTT
435225 CTCTTCATTTTTTCTCCTATTTTCTCC
1 CTCTTC-TTTTTTCTCCTATTTTCTCC
*
435252 CTCTTCCTTTTTCTCCTATTTTCTCC
1 CTCTTCTTTTTTCTCCTATTTTCTCC
*
435278 CTCTTCCTTTTTCTC
1 CTCTTCTTTTTTCTC
435293 GATCGTGGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 34 0.85
27 6 0.15
ACGTcount: A:0.04, C:0.37, G:0.00, T:0.59
Consensus pattern (26 bp):
CTCTTCTTTTTTCTCCTATTTTCTCC
Found at i:448584 original size:23 final size:22
Alignment explanation
Indices: 448541--448584 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
448531 TTTCAAAATC
* * *
448541 CCCCTGTCGAATGGCCTGTTCT
1 CCCCGGTCGAATGGACAGTTCT
448563 CCCCGGTCGAAATGGACAGTTC
1 CCCCGGTCG-AATGGACAGTTC
448585 AATTCCTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (22 bp):
CCCCGGTCGAATGGACAGTTCT
Found at i:451901 original size:2 final size:2
Alignment explanation
Indices: 451894--451923 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
451884 AAGCTTAAGA
*
451894 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
451924 GCTAGTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:454227 original size:27 final size:27
Alignment explanation
Indices: 454186--454269 Score: 132
Period size: 27 Copynumber: 3.1 Consensus size: 27
454176 TAGTATTGGC
* *
454186 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCACCAATGGTGGT
* *
454213 GCCTATTTGGGAGGCACCAATGGTAGT
1 GCCTATCTGGGAGGCACCAATGGTGGT
454240 GCCTATCTGGGAGGCACCAATGGTGGT
1 GCCTATCTGGGAGGCACCAATGGTGGT
454267 GCC
1 GCC
454270 ATACTGAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.23
Consensus pattern (27 bp):
GCCTATCTGGGAGGCACCAATGGTGGT
Found at i:454281 original size:27 final size:27
Alignment explanation
Indices: 454186--454288 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
454176 TAGTATTGGC
*
454186 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCACCAATGGTGGT
* * *
454213 GCCTATTTGGGAGGCACCAATGGTAGT
1 GCCTATCTGGAAGGCACCAATGGTGGT
*
454240 GCCTATCTGGGAGGCACCAATGGTGGT
1 GCCTATCTGGAAGGCACCAATGGTGGT
* *
454267 GCC-ATACTGAAAGGCGCCAATG
1 GCCTAT-CTGGAAGGCACCAATG
454289 CTGTGATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 2 0.03
27 64 0.97
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.21
Consensus pattern (27 bp):
GCCTATCTGGAAGGCACCAATGGTGGT
Found at i:454382 original size:22 final size:21
Alignment explanation
Indices: 454354--454398 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
454344 CGGAAGAAAG
*
454354 AAGAAGGAAAGAAGCAGAAGAA
1 AAGAAGGAAAGAA-AAGAAGAA
*
454376 AAGAAGGAAGGAAAAGAAGAA
1 AAGAAGGAAAGAAAAGAAGAA
454397 AA
1 AA
454399 AAATTAGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (21 bp):
AAGAAGGAAAGAAAAGAAGAA
Found at i:458006 original size:145 final size:145
Alignment explanation
Indices: 457796--458088 Score: 586
Period size: 145 Copynumber: 2.0 Consensus size: 145
457786 TATTTCAGTA
457796 TTTTTTTTTTCTATACTATTCCTGTAAAACCCTATAAAAACCGTTTTCTCATCTCACTGAAATTC
1 TTTTTTTTTTCTATACTATTCCTGTAAAACCCTATAAAAACCGTTTTCTCATCTCACTGAAATTC
457861 AAAATATTGGGTGGAATGCTTTGAAAGTCCAAAAATAGGGGTAAATATTTTAGCCTTCCAATTCT
66 AAAATATTGGGTGGAATGCTTTGAAAGTCCAAAAATAGGGGTAAATATTTTAGCCTTCCAATTCT
457926 TCTTTTATTATTTAT
131 TCTTTTATTATTTAT
457941 TTTTTTTTTTCTATACTATTCCTGTAAAACCCTATAAAAACCGTTTTCTCATCTCACTGAAATTC
1 TTTTTTTTTTCTATACTATTCCTGTAAAACCCTATAAAAACCGTTTTCTCATCTCACTGAAATTC
458006 AAAATATTGGGTGGAATGCTTTGAAAGTCCAAAAATAGGGGTAAATATTTTAGCCTTCCAATTCT
66 AAAATATTGGGTGGAATGCTTTGAAAGTCCAAAAATAGGGGTAAATATTTTAGCCTTCCAATTCT
458071 TCTTTTATTATTTAT
131 TCTTTTATTATTTAT
458086 TTT
1 TTT
458089 ATTTAATACT
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 148 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (145 bp):
TTTTTTTTTTCTATACTATTCCTGTAAAACCCTATAAAAACCGTTTTCTCATCTCACTGAAATTC
AAAATATTGGGTGGAATGCTTTGAAAGTCCAAAAATAGGGGTAAATATTTTAGCCTTCCAATTCT
TCTTTTATTATTTAT
Found at i:458577 original size:33 final size:33
Alignment explanation
Indices: 458540--458607 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 33
458530 TGTATTTTTT
*
458540 TATTT-TAAAAAACTAATAATATAAATAACTTGA
1 TATTTATAAAAAACTAAAAATATAAA-AACTTGA
* *
458573 TATTTAATAAAAAATTAAAAATATATAAACTTGA
1 TATTT-ATAAAAAACTAAAAATATAAAAACTTGA
458607 T
1 T
458608 TGCATCTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 5 0.17
34 8 0.27
35 17 0.57
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (33 bp):
TATTTATAAAAAACTAAAAATATAAAAACTTGA
Found at i:460454 original size:18 final size:17
Alignment explanation
Indices: 460431--460465 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
460421 AAGCAAAACA
460431 AATCTAAAAAATGGAGTT
1 AATCTAAAAAAT-GAGTT
*
460449 AATCTAAGAAATGAGTT
1 AATCTAAAAAATGAGTT
460466 CAAGCTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (17 bp):
AATCTAAAAAATGAGTT
Found at i:465164 original size:19 final size:19
Alignment explanation
Indices: 465129--465172 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
465119 TGCAAATAAT
* *
465129 TTCTAA-ATATTATTTTAA
1 TTCTAATATAGTACTTTAA
465147 TTCTAATATAGTACTTTAA
1 TTCTAATATAGTACTTTAA
*
465166 TTATAAT
1 TTCTAAT
465173 TTTATTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (19 bp):
TTCTAATATAGTACTTTAA
Found at i:469923 original size:2 final size:2
Alignment explanation
Indices: 469916--469959 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
469906 GAATTGAGAA
469916 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
469958 CT
1 CT
469960 TTTTGCTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:472982 original size:23 final size:23
Alignment explanation
Indices: 472955--473031 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
472945 ATCCCAACGC
472955 TATCATGAAAATGAATTAACAAA
1 TATCATGAAAATGAATTAACAAA
* * * *
472978 TATCA-CAAGATTTGTGAGATCAACATA
1 TATCATGAA-A---ATGA-ATTAACAAA
473005 -ATCATGAAAATGAATTAACAAA
1 TATCATGAAAATGAATTAACAAA
473027 TATCA
1 TATCA
473032 AATTCTAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
22 9 0.23
23 13 0.33
26 8 0.21
27 9 0.23
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (23 bp):
TATCATGAAAATGAATTAACAAA
Found at i:478801 original size:32 final size:31
Alignment explanation
Indices: 478738--478801 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
478728 ACTTGTCCTT
** *
478738 CAAAACTTTTACTCCTTCCCACTTTCTCCCC
1 CAAAACTTTTACTCCTTCCCACTCCCACCCC
478769 CAAAACTTTTACTCCCTTCCC-CTCCCAACCCC
1 CAAAACTTTTACT-CCTTCCCACTCCC-ACCCC
478801 C
1 C
478802 CAATCTAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.20, C:0.50, G:0.00, T:0.30
Consensus pattern (31 bp):
CAAAACTTTTACTCCTTCCCACTCCCACCCC
Found at i:486597 original size:51 final size:50
Alignment explanation
Indices: 486466--486609 Score: 162
Period size: 51 Copynumber: 2.8 Consensus size: 50
486456 TTTAATGCCA
* *
486466 AGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGTC
1 AGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCC
* * * * * * *
486516 AGGGAAACAAGATTTGCTACCTTTAGCTTTAATCTGTTCCACTGTAACGCC
1 A-GGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCC
* * *
486567 TAGGAGATAGGATTCGCTGCCTTCAACTTTAATCCGCTCCACT
1 -AGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACT
486610 TCAGCTTTAA
Statistics
Matches: 74, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
50 1 0.01
51 72 0.97
52 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.30
Consensus pattern (50 bp):
AGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAACGCC
Found at i:486704 original size:123 final size:123
Alignment explanation
Indices: 486485--487210 Score: 522
Period size: 123 Copynumber: 5.7 Consensus size: 123
486475 GATTCGCTGC
* * * *
486485 CTTCAGCTTTAATCTGCTCCGCTGCAACGTCAGGGAAACAAGATTTGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
*
486550 TGTTCCACTGTAACGCCTA-GGAGATAGGATTCGCTGCCTTCAACTTTAATCCGCTCCA
66 TGTTCCACTGCAACGCC-AGGGAGATAGGATTCGCTGCCTTCAACTTTAATCCGCTCCA
* * *
486608 CTTCAGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
* * * *
486673 TATTCCACTGCAACGCCAGGGCA-AT-GAGATTCGCTGACTTCAAATTTAACGCCGGGGAGATAA
66 TGTTCCACTGCAACGCCAGGG-AGATAG-GATTCGCTGCCTTCAACTTTAA-TCC----------
* *
486736 GATTCGCTGC
118 G-CTC-C--A
* * * *
486746 CTTCATCTTTAATCTGCTCCGCTACAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
* * ** * * *
486811 TGTTCCACTGAAATGCCAAAGAGATAGGATTCGCTGCCCTCAGCTTTAATCGGCTCCA
66 TGTTCCACTGCAACGCCAGGGAGATAGGATTCGCTGCCTTCAACTTTAATCCGCTCCA
* * * *
486869 CTTCAGC--TATTCTATTCCACTGCAATGCTAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
* * * ** *
486932 TGTTCC-CTGCAACGCCAGGGA-AGTAAGATTGGTTACTTTCAGTCTTAACACCAGAGAGATAAG
66 TGTTCCACTGCAACGCCAGGGAGA-TAGGATTCG---C--T--GCCTT-----C--A-ACTTTA-
* * *
486995 ATTCGCTGCC
114 ATCCGCTCCA
* * * * * *
487005 CTT-AGCTTTAATCTGCTCCGCTGCAACACCAGGGAAACCAGGTTTGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
* * ** * * * *
487069 TGTTCCACTGTAATGCCAAAGATATAGGATTCACTGCCCTCAACTTTAATCTGCTCCA
66 TGTTCCACTGCAACGCCAGGGAGATAGGATTCGCTGCCTTCAACTTTAATCCGCTCCA
* * * * *
487127 CTTCAGCTATT--TC-ATTCAATTGCAATGCCAGGGAAACAAAATTCGCTACC-TTAGCTTTAAT
1 CTTCAGCT-TTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAAT
*
487188 CTGTTCCACTGTAACGCCAGGGA
65 CTGTTCCACTGCAACGCCAGGGA
487211 AATAAGACTG
Statistics
Matches: 462, Mismatches: 98, Indels: 89
0.71 0.15 0.14
Matches are distributed among these distances:
119 1 0.00
120 49 0.11
121 81 0.18
122 13 0.03
123 111 0.24
124 6 0.01
125 2 0.00
126 3 0.01
127 4 0.01
131 3 0.01
132 1 0.00
133 1 0.00
134 2 0.00
135 8 0.02
136 10 0.02
137 54 0.12
138 111 0.24
139 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (123 bp):
CTTCAGCTTTAATCTACTCCACTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
TGTTCCACTGCAACGCCAGGGAGATAGGATTCGCTGCCTTCAACTTTAATCCGCTCCA
Found at i:486721 original size:51 final size:51
Alignment explanation
Indices: 486615--486721 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
486605 CCACTTCAGC
* **
486615 TTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTTAGC
1 TTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTCAAA
* ** *
486666 TTTAATCTATTCCACTGCAACGCCAGGGCAATGAGATTCGCTGA-CTTCAAA
1 TTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCT-ATCTTCAAA
486717 TTTAA
1 TTTAA
486722 CGCCGGGGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (51 bp):
TTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTCAAA
Found at i:487059 original size:258 final size:257
Alignment explanation
Indices: 486468--487230 Score: 1077
Period size: 258 Copynumber: 2.9 Consensus size: 257
486458 TAATGCCAAG
*
486468 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGTCAGGGAAACAAGATTTGC
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAAACAAGATTTGC
* * * *
486533 TACCTTTAGCTTTAATCTGTTCCACTGTAACGCCTAGGAGATAGGATTCGCTGCCTTCAACTTTA
66 TACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCTCAACTTTA
* * * *
486598 ATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTT
131 ATCCGCTCCACTTCAGC--TATTCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTTT
* * * * *
486663 AGCTTTAATCTATTCCACTGCAACGCCAGGGCAATGAGATTCGCTGACTTCAAATTTAACGCCGG
194 AGCTTTAATCTGTTCCACTGCAACGCCAGGG-AATAAGATT-GGTGACTTCAAATTTAACACCAG
*
486728 G
257 A
* * *
486729 GAGATAAGATTCGCTGCCTTCATCTTTAATCTGCTCCGCTACAACGCCAGGGAAACAAGATTCGC
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAAACAAGATTTGC
* *
486794 TACCTTTAGCTTTAATCTGTTCCACTGAAATGCCAAAGAGATAGGATTCGCTGCCCTCAGCTTTA
66 TACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCTCAACTTTA
* *
486859 ATCGGCTCCACTTCAGCTATTCTATTCCACTGCAATGCTAGGGAAACAAGATTCGCTACCTTTAG
131 ATCCGCTCCACTTCAGCTATTCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTTTAG
* *
486924 CTTTAATCTGTTCC-CTGCAACGCCAGGGAAGTAAGATTGGTTACTTTC-AGTCTTAACACCAGA
196 CTTTAATCTGTTCCACTGCAACGCCAGGGAA-TAAGATTGGTGAC-TTCAAAT-TTAACACCAGA
* * *
486987 GAGATAAGATTCGCTGCCCTT-AGCTTTAATCTGCTCCGCTGCAACACCAGGGAAACCAGGTTTG
1 GAGATAAGATTCGCTG-CCTTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAAACAAGATTTG
* *
487051 CTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGATATAGGATTCACTGCCCTCAACTTT
65 CTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCTCAACTTT
* * * *
487116 AATCTGCTCCACTTCAGCTATT-TCATTCAATTGCAATGCCAGGGAAACAAAATTCGCTACC-TT
130 AATCCGCTCCACTTCAGCTATTCT-ATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTTT
* * *
487179 AGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGACTGGTGTCTTCAA
194 AGCTTTAATCTGTTCCACTGCAACGCCAGGG-AATAAGATTGGTGACTTCAA
487231 TCCACTCCAC
Statistics
Matches: 451, Mismatches: 43, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
257 30 0.07
258 223 0.49
259 62 0.14
261 136 0.30
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (257 bp):
GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAAACAAGATTTGC
TACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCTCAACTTTA
ATCCGCTCCACTTCAGCTATTCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTTTAG
CTTTAATCTGTTCCACTGCAACGCCAGGGAATAAGATTGGTGACTTCAAATTTAACACCAGA
Found at i:489549 original size:7 final size:8
Alignment explanation
Indices: 489532--489571 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
489522 TGTTTCATCA
*
489532 TTTTCATT
1 TTTTGATT
489540 TTTTGATT
1 TTTTGATT
489548 TTTTGATTT
1 TTTTGA-TT
489557 TTTTGA-T
1 TTTTGATT
489564 TTTTGATT
1 TTTTGATT
489572 GAATCTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.24
8 14 0.48
9 8 0.28
ACGTcount: A:0.12, C:0.03, G:0.10, T:0.75
Consensus pattern (8 bp):
TTTTGATT
Found at i:489550 original size:9 final size:9
Alignment explanation
Indices: 489538--489567 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
489528 ATCATTTTCA
489538 TTTTTTGA-
1 TTTTTTGAT
489546 TTTTTTGAT
1 TTTTTTGAT
489555 TTTTTTGAT
1 TTTTTTGAT
489564 TTTT
1 TTTT
489568 GATTGAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (9 bp):
TTTTTTGAT
Found at i:492599 original size:30 final size:29
Alignment explanation
Indices: 492564--492620 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
492554 CCTCGACTCT
492564 AACTTTGT-CAAAATTACGATTTTGCCCCTA
1 AACTTT-TACAAAATTAC-ATTTTGCCCCTA
* *
492594 AACTTTTACATAATTACATTTTTCCCC
1 AACTTTTACAAAATTACATTTTGCCCC
492621 AAGGCTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTGCCCCTA
Found at i:496269 original size:67 final size:68
Alignment explanation
Indices: 496175--496309 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 68
496165 TAAATGGTTT
496175 GTGATACGACCCCGGTTTAGTAGTTAAATCCGAGTCGTTGTTGTGCCCGATCGTGAATTGGAGTA
1 GTGATACGACCCCGGTTTAGTAGTTAAATCCGAGTCGTTGTTGTGCCCGATCGTGAATTGGAGTA
496240 ATA
66 ATA
496243 GTGATACGA-CCCGGTTTAGTAGTTAAATCCGAGTCGTTGTTGTGCCCGATCGTGAATTGGAGTA
1 GTGATACGACCCCGGTTTAGTAGTTAAATCCGAGTCGTTGTTGTGCCCGATCGTGAATTGGAGTA
496307 ATA
66 ATA
496310 TTAAGGTTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 58 0.87
68 9 0.13
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (68 bp):
GTGATACGACCCCGGTTTAGTAGTTAAATCCGAGTCGTTGTTGTGCCCGATCGTGAATTGGAGTA
ATA
Found at i:499020 original size:16 final size:18
Alignment explanation
Indices: 498989--499021 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
498979 ACTCTTCAAT
498989 CCATCATCCAAATCAAAG
1 CCATCATCCAAATCAAAG
499007 CCATCA-CC-AATCAAA
1 CCATCATCCAAATCAAA
499022 AATTGATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.45, C:0.36, G:0.03, T:0.15
Consensus pattern (18 bp):
CCATCATCCAAATCAAAG
Found at i:499718 original size:15 final size:17
Alignment explanation
Indices: 499698--499740 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
499688 TTTTGATATC
499698 TCATTTTCATC-TT-TT
1 TCATTTTCATCATTCTT
*
499713 TCATTTTCTTCATTTCTT
1 TCATTTTCATCA-TTCTT
499731 TCATTTTCAT
1 TCATTTTCAT
499741 TTTCTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 10 0.43
17 2 0.09
18 11 0.48
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (17 bp):
TCATTTTCATCATTCTT
Found at i:499727 original size:24 final size:24
Alignment explanation
Indices: 499702--499746 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
499692 GATATCTCAT
*
499702 TTTC-ATCTTTTTCATTTTCTTCA
1 TTTCTATCATTTTCATTTTCTTCA
*
499725 TTTCTTTCATTTTCATTTTCTT
1 TTTCTATCATTTTCATTTTCTT
499747 TGTTCTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTCTATCATTTTCATTTTCTTCA
Found at i:499756 original size:24 final size:23
Alignment explanation
Indices: 499710--499754 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
499700 ATTTTCATCT
499710 TTTTCATTTTCTTCATTTCTTTCA
1 TTTTCATTTTCTT-ATTTCTTTCA
499734 TTTTCATTTTCTT-TGTTCTTT
1 TTTTCATTTTCTTAT-TTCTTT
499755 TCTCGCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 6 0.30
24 13 0.65
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTCATTTTCTTATTTCTTTCA
Found at i:500656 original size:14 final size:13
Alignment explanation
Indices: 500637--500681 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
500627 GAATACAAAC
500637 TTTTTTTATTCGAA
1 TTTTTTT-TTCGAA
500651 -TTTTTTTTCGAA
1 TTTTTTTTTCGAA
*
500663 --TTTTTTTCGAC
1 TTTTTTTTTCGAA
500674 TTTTTTTT
1 TTTTTTTT
500682 ACAATCTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.36
12 6 0.21
13 12 0.43
ACGTcount: A:0.13, C:0.09, G:0.07, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:500660 original size:12 final size:12
Alignment explanation
Indices: 500638--500681 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
500628 AATACAAACT
500638 TTTTTTATTCGAA
1 TTTTTT-TTCGAA
500651 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
500663 -TTTTTTTCGAC
1 TTTTTTTTCGAA
500674 TTTTTTTT
1 TTTTTTTT
500682 ACAATCTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 10 0.34
12 13 0.45
13 6 0.21
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:500668 original size:10 final size:11
Alignment explanation
Indices: 500639--500680 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
500629 ATACAAACTT
500639 TTTTTATTCGAA
1 TTTTT-TTCGAA
500651 TTTTTTTTCGAA
1 -TTTTTTTCGAA
*
500663 TTTTTTTCGAC
1 TTTTTTTCGAA
500674 TTTTTTT
1 TTTTTTT
500681 TACAATCTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 17 0.61
12 6 0.21
13 5 0.18
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:508207 original size:25 final size:25
Alignment explanation
Indices: 508162--508376 Score: 100
Period size: 26 Copynumber: 8.3 Consensus size: 25
508152 TTTTAGTAAT
** *
508162 TTTACCCTTCAGAGGAAATTCGATAG
1 TTTACCCTTC-GAGGGTATTCGATAA
* *
508188 TTTTCCCATT-GAGGGTATTCTAGTAA
1 TTTACCC-TTCGAGGGTATTCGA-TAA
508214 TTTACCCTTCGAGGGTATTTCGATAA
1 TTTACCCTTCGAGGGTA-TTCGATAA
* * **
508240 TTTAACCATATAGGGTATTTC-AGTAA
1 TTTACCCTTCGAGGGTA-TTCGA-TAA
* *
508266 TTTA-CCTATCGAGGGTATTTCGGTAC
1 TTTACCCT-TCGAGGGTA-TTCGATAA
* *
508292 TTTACCCATT-GAAGGTATTTCAATAA
1 TTTACCC-TTCGAGGGTA-TTCGATAA
* * *
508318 TGTA-CCTATTGAGGGTATTTCGGTAA
1 TTTACCCT-TCGAGGGTA-TTCGATAA
* *
508344 TTTACCCGTT-GAGTGTATTTCGGTAA
1 TTTACCC-TTCGAGGGTA-TTCGATAA
508370 TTTACCC
1 TTTACCC
508377 ATTAAGACGC
Statistics
Matches: 150, Mismatches: 26, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
24 1 0.01
25 17 0.11
26 118 0.79
27 12 0.08
28 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (25 bp):
TTTACCCTTCGAGGGTATTCGATAA
Found at i:508227 original size:26 final size:25
Alignment explanation
Indices: 508198--508376 Score: 105
Period size: 26 Copynumber: 6.9 Consensus size: 25
508188 TTTTCCCATT
508198 GAGGGTATTCTAGTAATTTACCCTTC
1 GAGGGTATT-TAGTAATTTACCCTTC
* * * *
508224 GAGGGTATTTCGATAATTTAACCATA
1 GAGGGTATTTAG-TAATTTACCCTTC
*
508250 TAGGGTATTTCAGTAATTTA-CCTATC
1 GAGGGTATTT-AGTAATTTACCCT-TC
* *
508276 GAGGGTATTTCGGTACTTTACCCATT-
1 GAGGGTATTT-AGTAATTTACCC-TTC
* * * *
508302 GAAGGTATTTCAATAATGTA-CCTATT
1 GAGGGTATTT-AGTAATTTACCCT-TC
*
508328 GAGGGTATTTCGGTAATTTACCCGTT-
1 GAGGGTATTT-AGTAATTTACCC-TTC
* *
508354 GAGTGTATTTCGGTAATTTACCC
1 GAGGGTATTT-AGTAATTTACCC
508377 ATTAAGACGC
Statistics
Matches: 123, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
24 1 0.01
25 7 0.06
26 106 0.86
27 7 0.06
28 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (25 bp):
GAGGGTATTTAGTAATTTACCCTTC
Found at i:508237 original size:52 final size:53
Alignment explanation
Indices: 508147--508376 Score: 231
Period size: 52 Copynumber: 4.4 Consensus size: 53
508137 TACCCTTTAG
* * * * *
508147 GGGTATTTTAGTAATTTTACCCT-TC-AGAGGAAATTCGATAGTTTTCCCATTGA
1 GGGTATTTCAGTAA-TTTACCCTATCGAG-GGTATTTCGATAATTTACCCATTGA
*
508200 GGGTA-TTCTAGTAATTTACCCT-TCGAGGGTATTTCGATAATTTAACCATAT-A
1 GGGTATTTC-AGTAATTTACCCTATCGAGGGTATTTCGATAATTTACCCAT-TGA
* *
508252 GGGTATTTCAGTAATTTA-CCTATCGAGGGTATTTCGGTACTTTACCCATTGA
1 GGGTATTTCAGTAATTTACCCTATCGAGGGTATTTCGATAATTTACCCATTGA
* * * * * *
508304 AGGTATTTCAATAATGTA-CCTATTGAGGGTATTTCGGTAATTTACCCGTTGA
1 GGGTATTTCAGTAATTTACCCTATCGAGGGTATTTCGATAATTTACCCATTGA
* *
508356 GTGTATTTCGGTAATTTACCC
1 GGGTATTTCAGTAATTTACCC
508377 ATTAAGACGC
Statistics
Matches: 150, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
51 4 0.03
52 128 0.85
53 18 0.12
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (53 bp):
GGGTATTTCAGTAATTTACCCTATCGAGGGTATTTCGATAATTTACCCATTGA
Found at i:508309 original size:78 final size:79
Alignment explanation
Indices: 508192--508379 Score: 215
Period size: 78 Copynumber: 2.4 Consensus size: 79
508182 CGATAGTTTT
* * * * *
508192 CCCATTGAGGGTA-TTCTAGTAATTTACCC-TTCGAGGGTATTTCGATAATTTAACC-ATAT-AG
1 CCCATCGAGGGTATTTC-GGTAATTTACCCATTCGAAGGTATTTCAATAATGT-ACCTAT-TGAG
508253 GGTATTTCAGTAATTTA
63 GGTATTTCAGTAATTTA
* *
508270 CCTATCGAGGGTATTTCGGTACTTTACCCATT-GAAGGTATTTCAATAATGTACCTATTGAGGGT
1 CCCATCGAGGGTATTTCGGTAATTTACCCATTCGAAGGTATTTCAATAATGTACCTATTGAGGGT
*
508334 ATTTCGGTAATTTA
66 ATTTCAGTAATTTA
* * *
508348 CCCGTTGAGTGTATTTCGGTAATTTACCCATT
1 CCCATCGAGGGTATTTCGGTAATTTACCCATT
508380 AAGACGCATA
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
77 4 0.04
78 84 0.90
79 5 0.05
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (79 bp):
CCCATCGAGGGTATTTCGGTAATTTACCCATTCGAAGGTATTTCAATAATGTACCTATTGAGGGT
ATTTCAGTAATTTA
Found at i:509043 original size:18 final size:18
Alignment explanation
Indices: 509020--509055 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
509010 AAGAAAGCTG
509020 GGAGTAGCCTTTGATCAC
1 GGAGTAGCCTTTGATCAC
509038 GGAGTAGCCTTTGATCAC
1 GGAGTAGCCTTTGATCAC
509056 TTACCGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAGTAGCCTTTGATCAC
Found at i:519928 original size:20 final size:19
Alignment explanation
Indices: 519903--519944 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
519893 TTCAAAATTG
*
519903 AAAATACGTGTTTGTTGTGA
1 AAAATA-GTATTTGTTGTGA
519923 AAAATAGTATTTGTTGTGA
1 AAAATAGTATTTGTTGTGA
519942 AAA
1 AAA
519945 CTTATTTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (19 bp):
AAAATAGTATTTGTTGTGA
Found at i:519952 original size:17 final size:18
Alignment explanation
Indices: 519913--519953 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
519903 AAAATACGTG
519913 TTTGTTGTGAAAAATAGTA
1 TTTGTTGTGAAAAATA-TA
*
519932 TTTGTTGTGAAAACT-TA
1 TTTGTTGTGAAAAATATA
519949 TTTGT
1 TTTGT
519954 GTTCGTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
19 14 0.67
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTGTTGTGAAAAATATA
Found at i:520737 original size:27 final size:26
Alignment explanation
Indices: 520706--521001 Score: 170
Period size: 26 Copynumber: 11.3 Consensus size: 26
520696 TATAACGGTC
* *
520706 ATTCTATCCTTCAGGTGTATTTTAGTA
1 ATTCTACCCTTCAGG-GTATTTCAGTA
*
520733 GTTCTACCCTTCAAGGGTATTTCAGTA
1 ATTCTACCCTTC-AGGGTATTTCAGTA
520760 ATTCTACCCTTCAGGGGTATTTC-GATA
1 ATTCTACCCTTCA-GGGTATTTCAG-TA
* * * **
520787 GTT-TCCCCATTGAGGGTATTTTGGTA
1 ATTCTACCC-TTCAGGGTATTTCAGTA
520813 ATT-TA-CCTTCGAGGGTATTTC-GATA
1 ATTCTACCCTTC-AGGGTATTTCAG-TA
*
520838 ATT-TA-CCTATCAAGGGTATTT-TGATA
1 ATTCTACCCT-TC-AGGGTATTTCAG-TA
* *
520864 ATT-TACCCATCGAGAGTATTTCAGTA
1 ATTCTACCCTTC-AGGGTATTTCAGTA
* **
520890 ATT-TACCCATTGAGGGTATTTTGGTA
1 ATTCTACCC-TTCAGGGTATTTCAGTA
* *
520916 ATT-TACCCATTGAGGTTATTTCAGTA
1 ATTCTACCC-TTCAGGGTATTTCAGTA
* * *
520942 ATT-TACCCATTGAGGATATTTCTGTA
1 ATTCTACCC-TTCAGGGTATTTCAGTA
* *
520968 ATT-TACCCATTGAGGGTATTTCTGTA
1 ATTCTACCC-TTCAGGGTATTTCAGTA
520994 ATT-TACCC
1 ATTCTACCC
521002 ATTGAGACCC
Statistics
Matches: 229, Mismatches: 28, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
24 3 0.01
25 21 0.09
26 150 0.66
27 52 0.23
28 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (26 bp):
ATTCTACCCTTCAGGGTATTTCAGTA
Found at i:520789 original size:54 final size:52
Alignment explanation
Indices: 520706--520858 Score: 145
Period size: 51 Copynumber: 2.9 Consensus size: 52
520696 TATAACGGTC
* *
520706 ATTCTATCCTTCAGGTGTATTT-TAGTAGTTCTACCCTTCAAGGGTATTTCAGTA
1 ATTCTA-CCTTCAGGGGTATTTCGA-TAGTT-TACCCTTCAAGGGTATTTCAGTA
* * **
520760 ATTCTACCCTTCAGGGGTATTTCGATAGTTTCCCCATT-GAGGGTATTTTGGTA
1 ATTCTA-CCTTCAGGGGTATTTCGATAGTTTACCC-TTCAAGGGTATTTCAGTA
*
520813 ATT-TACCTTC-GAGGGTATTTCGATAATTTA-CCTATCAAGGGTATTT
1 ATTCTACCTTCAG-GGGTATTTCGATAGTTTACCCT-TCAAGGGTATTT
520859 TGATAATTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
49 1 0.01
50 4 0.05
51 30 0.36
52 2 0.02
53 19 0.23
54 27 0.32
55 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (52 bp):
ATTCTACCTTCAGGGGTATTTCGATAGTTTACCCTTCAAGGGTATTTCAGTA
Found at i:520863 original size:26 final size:26
Alignment explanation
Indices: 520774--521007 Score: 246
Period size: 26 Copynumber: 9.0 Consensus size: 26
520764 TACCCTTCAG
* * *
520774 GGGTATTTCGATAGTTTCCCCATTGA
1 GGGTATTTTGATAATTTACCCATTGA
*
520800 GGGTATTTTGGTAATTTA-CC-TTCGA
1 GGGTATTTTGATAATTTACCCATT-GA
* * **
520825 GGGTATTTCGATAATTTACCTATCAA
1 GGGTATTTTGATAATTTACCCATTGA
*
520851 GGGTATTTTGATAATTTACCCATCGA
1 GGGTATTTTGATAATTTACCCATTGA
* *
520877 GAGTA-TTTCAGTAATTTACCCATTGA
1 GGGTATTTTGA-TAATTTACCCATTGA
*
520903 GGGTATTTTGGTAATTTACCCATTGA
1 GGGTATTTTGATAATTTACCCATTGA
* *
520929 GGTTA-TTTCAGTAATTTACCCATTGA
1 GGGTATTTTGA-TAATTTACCCATTGA
*
520955 GGATATTTCTG-TAATTTACCCATTGA
1 GGGTATTT-TGATAATTTACCCATTGA
520981 GGGTATTTCTG-TAATTTACCCATTGA
1 GGGTATTT-TGATAATTTACCCATTGA
521007 G
1 G
521008 ACCCATAACG
Statistics
Matches: 176, Mismatches: 24, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.01
25 27 0.15
26 140 0.80
27 6 0.03
28 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (26 bp):
GGGTATTTTGATAATTTACCCATTGA
Found at i:520895 original size:52 final size:52
Alignment explanation
Indices: 520746--521007 Score: 300
Period size: 52 Copynumber: 5.0 Consensus size: 52
520736 CTACCCTTCA
** * * *
520746 AGGGTATTTCAGTAATTCTACCCTTC-AGGGGTATTTC-GATAGTTTCCCCATTG
1 AGGGTATTTTGGTAATT-TACCCATCGA-GGGTATTTCAG-TAATTTACCCATTG
* * **
520799 AGGGTATTTTGGTAATTTA-CCTTCGAGGGTATTTC-GATAATTTACCTATCA
1 AGGGTATTTTGGTAATTTACCCATCGAGGGTATTTCAG-TAATTTACCCATTG
* *
520850 AGGGTATTTTGATAATTTACCCATCGAGAGTATTTCAGTAATTTACCCATTG
1 AGGGTATTTTGGTAATTTACCCATCGAGGGTATTTCAGTAATTTACCCATTG
* *
520902 AGGGTATTTTGGTAATTTACCCATTGAGGTTATTTCAGTAATTTACCCATTG
1 AGGGTATTTTGGTAATTTACCCATCGAGGGTATTTCAGTAATTTACCCATTG
* * *
520954 AGGATATTTCT-GTAATTTACCCATTGAGGGTATTTCTGTAATTTACCCATTG
1 AGGGTATTT-TGGTAATTTACCCATCGAGGGTATTTCAGTAATTTACCCATTG
521006 AG
1 AG
521008 ACCCATAACG
Statistics
Matches: 185, Mismatches: 20, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
51 43 0.23
52 125 0.68
53 17 0.09
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (52 bp):
AGGGTATTTTGGTAATTTACCCATCGAGGGTATTTCAGTAATTTACCCATTG
Found at i:521002 original size:78 final size:78
Alignment explanation
Indices: 520746--521007 Score: 288
Period size: 78 Copynumber: 3.4 Consensus size: 78
520736 CTACCCTTCA
* * * * *
520746 AGGGTATTTCAGTAATTCTACCC-TTCAGGGGTATTTCGATAGTTTCCCCATTGAGGGTATTT-T
1 AGGGTATTTCTGTAATT-TACCCATTGA-GGGTATTTCGATAATTTACCCATTGAGGATATTTCT
520809 GGTAATTTA-CC-TTCG
64 -GTAATTTACCCATT-G
* ** * * *
520824 AGGGTATTTC-GATAATTTACCTATCAAGGGTATTTTGATAATTTACCCATCGA-GAGTATTTCA
1 AGGGTATTTCTG-TAATTTACCCATTGAGGGTATTTCGATAATTTACCCATTGAGGA-TATTTCT
520887 GTAATTTACCCATTG
64 GTAATTTACCCATTG
*
520902 AGGGTATTT-TGGTAATTTACCCATTGAGGTTATTTC-AGTAATTTACCCATTGAGGATATTTCT
1 AGGGTATTTCT-GTAATTTACCCATTGAGGGTATTTCGA-TAATTTACCCATTGAGGATATTTCT
520965 GTAATTTACCCATTG
64 GTAATTTACCCATTG
520980 AGGGTATTTCTGTAATTTACCCATTGAG
1 AGGGTATTTCTGTAATTTACCCATTGAG
521008 ACCCATAACG
Statistics
Matches: 157, Mismatches: 16, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
76 1 0.01
77 41 0.26
78 109 0.69
79 6 0.04
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (78 bp):
AGGGTATTTCTGTAATTTACCCATTGAGGGTATTTCGATAATTTACCCATTGAGGATATTTCTGT
AATTTACCCATTG
Found at i:526174 original size:67 final size:66
Alignment explanation
Indices: 526103--526451 Score: 169
Period size: 67 Copynumber: 5.1 Consensus size: 66
526093 TTGATTCATA
526103 CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTCG
1 CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTC-
526168 GT
65 GT
** * ** * * * * ** *
526170 CAAAATA-TAAAAG-ACATGGACATTAAT--ATTCTTTTGGAAGAATATAATTAATATATGAACT
1 CAAAATATTAATTGTATAT--ATTTTACTGAATT-TATT--AA-TATA-AACTGTTATATTAAC-
* *
526231 TGA-TTCCT
58 TAATTTCGT
526239 ACAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTC
1 -CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTC
526304 AGT
65 -GT
** * ** * * * * * ** * *
526307 CAAAATA-TAAAAG-ACATGGAAATTAAT-ATTCTTCCA-AAAGAATATAATTAATATATGAATT
1 CAAAATATTAATTGTATAT--ATTTTACTGAAT-TT--ATTAA-TATA-AACTGTTATATTAA-C
* *
526368 TGA-TTCCT
58 TAATTTCGT
526376 ACAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTC
1 -CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTC
526441 AGT
65 -GT
526444 CAAAATAT
1 CAAAATAT
526452 AAAAGACATG
Statistics
Matches: 192, Mismatches: 60, Indels: 60
0.62 0.19 0.19
Matches are distributed among these distances:
65 9 0.05
66 17 0.09
67 61 0.32
68 13 0.07
69 13 0.07
70 53 0.28
71 17 0.09
72 9 0.05
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.41
Consensus pattern (66 bp):
CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTCG
T
Found at i:526273 original size:137 final size:138
Alignment explanation
Indices: 525936--527302 Score: 1765
Period size: 138 Copynumber: 10.0 Consensus size: 138
525926 AAGAACATAG
* * * *
525936 ATATAATTAATATATGAAATTCATTCATACAAAATATTAAATGTATATATTTTACTGAATTTGTT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* * *
526001 AATATAAA-TAGTTACATTAATTAATTTCGTTCAAAATATAAAAGACATGAAAATTAATATTCTT
66 AATATAAACT-GTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
*
526065 TTGGAAATA
130 TTGGAAAGA
*
526074 ATATAATTAATATATGAAATTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* *
526139 AATATAAACTGTTATATTAACTAATTTCGGTCAAAATATAAAAGACATGGACATTAATATTCTTT
66 AATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
526204 TGG-AAGA
131 TGGAAAGA
* *
526211 ATATAATTAATATATGAACTTGATTCCTACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* *
526276 AATATAAACTGTTATATTAACTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTC-TT
66 AATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
***
526340 CCAAAAGA
131 TGGAAAGA
*
526348 ATATAATTAATATATGAATTTGATTCCTACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* *
526413 AATATAAACTGTTATATTAACTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTC-TT
66 AATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
***
526477 CCAAAAGA
131 TGGAAAGA
* * **
526485 ATATAATTAATATATGAATTTGATTTATACAAAATATTCATTGTATATA---TACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* ** * * * *
526547 AATGTAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATCTTCCTT
66 AATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
*
526612 TCGAAAGA
131 TGGAAAGA
* * * * * *
526620 ATATAATTAATATATGAATTTAACTCATACAAAATATTAATTATATACATTTTACCGATTTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
** * *
526685 AATATAAAAAGTTATATTAACTAATTTCGGTC-AAATATAAAAGAGATGG--A--AA-ATTC-TT
66 AATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
526743 TGGAAAGA
131 TGGAAAGA
* * *
526751 ATATAATTAATATATGAATTTGATTCATATAAAATATTAATTGTATATGTTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* * * * * *
526816 AA-A-CAA---TTATATTAATTAATTTTGGCCAAAATATAAAAGATATTGAAATTAATATTCTCT
66 AATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
*
526876 TGGAAACA
131 TGGAAAGA
* * * *
526884 ATATAATTAATTTATCAAATTGATTCATACAAAATATTAATTATATATATTTTACTGAA-TTAGT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTA-T
** * ** * *
526948 TAATATAAACAATTATATTAATTATTTTCTATCAAAATATTAAAGACATGAAAATTAATATTCTT
65 TAATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
527013 TTGGAAAGA
130 TTGGAAAGA
* * * *
527022 ATATAATTAACAAATGAATTTGATTCATACAAAATATTAATTGTATATATTTGACCGAA-TTACT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTA-T
* ** * * *
527086 TAATATAAGCAATTATATTAATTAATTTCGATCAAACTATAAAAGACATGGAAATTAAT-TGTCC
65 TAATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATAT-TCT
527150 TTTGGAAAGA
129 TTTGGAAAGA
* *
527160 ATATAATTAATATATGAATTTAATTCATATAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* * * *
527225 AATATAAA-TAGTTTTCTTAATTAATTTCGATCAAAGTATAAAAGACAT-GAAATTAATATTCTT
66 AATATAAACT-GTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
*
527288 TTGAAAAGA
130 TTGGAAAGA
527297 ATATAA
1 ATATAA
527303 ATCTTTTTTT
Statistics
Matches: 1093, Mismatches: 113, Indels: 47
0.87 0.09 0.04
Matches are distributed among these distances:
126 18 0.02
127 15 0.01
129 3 0.00
130 1 0.00
131 71 0.06
132 10 0.01
133 66 0.06
134 66 0.06
135 54 0.05
136 2 0.00
137 354 0.32
138 429 0.39
139 4 0.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
AATATAAACTGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
TGGAAAGA
Found at i:527160 original size:540 final size:542
Alignment explanation
Indices: 525936--527302 Score: 1831
Period size: 540 Copynumber: 2.5 Consensus size: 542
525926 AAGAACATAG
* * * * *
525936 ATATAATTAATATATGAAATTCATTCATACAAAATATTAAATGTATATATTTTACTGAATTTGTT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATA-TTTACCGAA-TTATT
* * * * *
526001 AATATAAATAGTTACATTAATTAATTTCGTTCAAAATATAAAAGACATGAAAATTAATATTCTTT
64 AATATAAACAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCCTT
* * *
526066 TGGAAATAATATAATTAATATATGAAATTGATTCATACAAAATATTAATTGTATATATTTTACTG
129 TGGAAAGAATATAATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACTG
**
526131 AATTTATTAATATAAACTGTTATATTAACTAATTTCGGTCAAAATATAAAAGACATGGACATTAA
194 AATTTATTAATATAAAAAGTTATATTAACTAATTTCGGTC-AAATATAAAAGACATGGA-A-TAA
*
526196 TATTCTTTTGGAAGAATATAATTAATATATGAACTTGATTCCTACAAAATATTAATTGTATATAT
256 TATTCTTTTGGAAGAATATAATTAATATATGAACTTGATTCATACAAAATATTAATTGTATATAT
* *
526261 TTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTCAGTCAAAATATAAAAGACATGG
321 TTTACCGAATTTATTAATATAAAC--TTATATTAACTAATTTCAGCCAAAATATAAAAGACATGG
* * * * *
526326 AAATTAATATTCTTCCAAAAGAATATAATTAATATATGAATTTGATTCCTACAAAATATTAATTG
384 AAATTAATATTCTTCCAAAACAATATAATTAATATATCAAATTGATTCATACAAAATATTAATTA
**
526391 TATATATTTTACTGAATTTATTAATATAAACTGTTATATTAACTAATTTCAGTCAAAATATAAAA
449 TATATATTTTACTGAATTTATTAATATAAACAATTATATTAACTAATTTCAGTCAAAATATAAAA
*
526456 GACATGGAAATTAATATTCTTCCAAAAGA
514 GACATGAAAATTAATATTCTTCCAAAAGA
* * *
526485 ATATAATTAATATATGAATTTGATTTATACAAAATATTCATTGTATATA--TACCAAATTTATTA
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTACCGAA-TTATTA
* * * *
526548 ATGTAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATCTTCCTTT
65 ATATAAACAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCCTTT
* * * * *
526613 CGAAAGAATATAATTAATATATGAATTTAACTCATACAAAATATTAATTATATACATTTTACCGA
130 GGAAAGAATATAATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACTGA
* *
526678 TTTTATTAATATAAAAAGTTATATTAACTAATTTCGGTCAAATATAAAAGAGATGG-A-AA-ATT
195 ATTTATTAATATAAAAAGTTATATTAACTAATTTCGGTCAAATATAAAAGACATGGAATAATATT
* * *
526740 C-TTTGGAAAGAATATAATTAATATATGAATTTGATTCATATAAAATATTAATTGTATATGTTTT
260 CTTTTGG-AAGAATATAATTAATATATGAACTTGATTCATACAAAATATTAATTGTATATATTTT
* * ** * *
526804 ACCGAATTTATTAA-A-CAA-TTATATTAATTAATTTTGGCCAAAATATAAAAGATATTGAAATT
324 ACCGAATTTATTAATATAAACTTATATTAACTAATTTCAGCCAAAATATAAAAGACATGGAAATT
*** *
526866 AATATTCTCTTGGAAACAATATAATTAATTTATCAAATTGATTCATACAAAATATTAATTATATA
389 AATATTCT-TCCAAAACAATATAATTAATATATCAAATTGATTCATACAAAATATTAATTATATA
* * *
526931 TATTTTACTGAA-TTAGTTAATATAAACAATTATATTAATTATTTTCTA-TCAAAATATTAAAGA
453 TATTTTACTGAATTTA-TTAATATAAACAATTATATTAACTAATTTC-AGTCAAAATATAAAAGA
***
526994 CATGAAAATTAATATTCTTTTGGAAAGA
516 CATGAAAATTAATATTC-TTCCAAAAGA
* *
527022 ATATAATTAACAAATGAATTTGATTCATACAAAATATTAATTGTATATATTTGACCGAATTACTT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTT-ACCGAATTA-TT
* * *
527087 AATATAAGCAATTATATTAATTAATTTCGATCAAACTATAAAAGACATGGAAATTAAT-TGTCCT
64 AATATAAACAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATAT-TCCT
*
527151 TTGGAAAGAATATAATTAATATATGAATTTAATTCATATAAAATATTAATTGTATATATTTTACT
128 TTGGAAAGAATATAATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACT
* * * * * *
527216 GAATTTATTAATATAAATAGTTTTCTTAATTAATTTCGATCAAAGTATAAAAGACATGAAATTAA
193 GAATTTATTAATATAAAAAGTTATATTAACTAATTTCGGTCAAA-TATAAAAGACATGGAA-TAA
*
527281 TATTCTTTTGAAAAGAATATAA
256 TATTCTTTTG-GAAGAATATAA
527303 ATCTTTTTTT
Statistics
Matches: 717, Mismatches: 84, Indels: 37
0.86 0.10 0.04
Matches are distributed among these distances:
535 49 0.07
536 115 0.16
537 53 0.07
538 2 0.00
539 11 0.02
540 230 0.32
541 14 0.02
542 1 0.00
543 1 0.00
544 2 0.00
545 20 0.03
546 175 0.24
549 44 0.06
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (542 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTACCGAATTATTAA
TATAAACAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCCTTTG
GAAAGAATATAATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACTGAA
TTTATTAATATAAAAAGTTATATTAACTAATTTCGGTCAAATATAAAAGACATGGAATAATATTC
TTTTGGAAGAATATAATTAATATATGAACTTGATTCATACAAAATATTAATTGTATATATTTTAC
CGAATTTATTAATATAAACTTATATTAACTAATTTCAGCCAAAATATAAAAGACATGGAAATTAA
TATTCTTCCAAAACAATATAATTAATATATCAAATTGATTCATACAAAATATTAATTATATATAT
TTTACTGAATTTATTAATATAAACAATTATATTAACTAATTTCAGTCAAAATATAAAAGACATGA
AAATTAATATTCTTCCAAAAGA
Found at i:536086 original size:13 final size:13
Alignment explanation
Indices: 536047--536097 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
536037 AGTTCTTCTT
536047 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
536060 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
*
536073 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
536086 TGCTTTTGAAAA
1 TGCTTTTGAAAA
536098 ACTTAAGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:536427 original size:20 final size:21
Alignment explanation
Indices: 536394--536432 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
536384 TTGTAATTAG
536394 TATTTTAAAAAAT-ATTTTTT
1 TATTTTAAAAAATAATTTTTT
**
536414 TATTTTAATTAATAATTTT
1 TATTTTAAAAAATAATTTT
536433 AACACATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTAAAAAATAATTTTTT
Found at i:538613 original size:14 final size:14
Alignment explanation
Indices: 538596--538628 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
538586 TAATAAATTT
538596 TAGAACTAAAATGC
1 TAGAACTAAAATGC
538610 TAGAACTAAAATGC
1 TAGAACTAAAATGC
*
538624 CAGAA
1 TAGAA
538629 ATTGTTCGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (14 bp):
TAGAACTAAAATGC
Found at i:541163 original size:24 final size:24
Alignment explanation
Indices: 541115--541161 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
541105 ACTGGTCATA
*
541115 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
541139 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
541162 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:541878 original size:27 final size:27
Alignment explanation
Indices: 541829--542392 Score: 396
Period size: 27 Copynumber: 21.1 Consensus size: 27
541819 TTGATATCTG
541829 GACCGAAATACCCCCGA-AGGGTAAAAT
1 GACCGAAATACCCCC-ATAGGGTAAAAT
* *
541856 GACTGAAATACCCCCATAAGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* *
541883 GACCGAAATACCCCCTTAGGGTAGAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
*
541910 -ACCGAAATA-CCCCAGAAGGGTAAAAT
1 GACCGAAATACCCCCA-TAGGGTAAAAT
* * *
541936 AACTGAAATACCCCCGTAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* *
541963 GACTGAGATACCCCCATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
**
541990 -ACCGAAATACCCCTGTAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* * ***
542016 GACCGTAATGCCCTTGTAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* * ** *
542043 GACCGTAATGCCCCTGTAGGGTAAAAC
1 GACCGAAATACCCCCATAGGGTAAAAT
* * *
542070 GACCGTAAA-ACCCCTATAGAGTAAAAA
1 GACCG-AAATACCCCCATAGGGTAAAAT
* * *
542097 GACCGTAATGCCCCTATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* ***
542124 GACC-ATAATGCCCATGTAGGGTAAAAT
1 GACCGA-AATACCCCCATAGGGTAAAAT
* *
542151 G-GC-TAATACCCCCATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* * ** *
542176 GACCGTAATGCCCCTGTAGAGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* ***
542203 GACCGTAATACCCTTGTAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
*
542230 GACC-ATAATACCCCCATTGGGTAAAAT
1 GACCGA-AATACCCCCATAGGGTAAAAT
* * **
542257 AACCGTAATACCCCTGTAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* ** **
542284 GATCGTTATA-CCGTATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* * ** *
542310 GACAGTAATACCCTTATAGAGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
* * **
542337 GACAGTAATACCCCTGTTA-GGTAAAAT
1 GACCGAAATACCCC-CATAGGGTAAAAT
* * * *
542364 GACCGTAATACTCCTAGAGGGT-AAAT
1 GACCGAAATACCCCCATAGGGTAAAAT
542390 GAC
1 GAC
542393 TAGTTTGCCC
Statistics
Matches: 443, Mismatches: 79, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
25 22 0.05
26 74 0.17
27 339 0.77
28 8 0.02
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (27 bp):
GACCGAAATACCCCCATAGGGTAAAAT
Found at i:542109 original size:81 final size:81
Alignment explanation
Indices: 541829--542392 Score: 531
Period size: 80 Copynumber: 7.0 Consensus size: 81
541819 TTGATATCTG
* * * * * ** * *
541829 GACCGAAATACCCCCGA-AGGGTAAAATGACTGAAATACCCCCATAAGGTAAAATGACCGAAATA
1 GACCGTAATA-CCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATA
*
541893 CCCCCT-TAGGGTAGAAT
65 -CCCCTGTAGGGTAAAAT
* * * * * * * *
541910 -ACCGAAATACCCC-AGAAGGGTAAAATAACTGAAATACCCCCGTAGGGTAAAATGACTG-AGAT
1 GACCGTAATACCCCTA-TAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTA-AT
**
541972 ACCCCCATAGGGTAAAAT
64 ACCCCTGTAGGGTAAAAT
* * * *
541990 -ACCGAAATACCCCTGTAGGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGACCGTAATGC
1 GACCGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATAC
*
542054 CCCTGTAGGGTAAAAC
66 CCCTGTAGGGTAAAAT
* * * * * *
542070 GACCGTAAAACCCCTATAGAGTAAAAAGACCGTAATGCCCCTATAGGGTAAAATGACCATAATGC
1 GACCGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATAC
*
542135 CCATGTAGGGTAAAAT
66 CCCTGTAGGGTAAAAT
* * *
542151 G-GC-TAATACCCCCATAGGGTAAAATGACCGTAATGCCCCTGTAGAGTAAAATGACCGTAATAC
1 GACCGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATAC
*
542214 CCTTGTAGGGTAAAAT
66 CCCTGTAGGGTAAAAT
* * * * * * *
542230 GACCATAATACCCCCATTGGGTAAAATAACCGTAATACCCCTGTAGGGTAAAATGATCGTTATA-
1 GACCGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATAC
* *
542294 CCGTATAGGGTAAAAT
66 CCCTGTAGGGTAAAAT
* * * * *
542310 GACAGTAATACCCTTATAGAGTAAAATGACAGTAATACCCCTGTTA-GGTAAAATGACCGTAATA
1 GACCGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTG-TAGGGTAAAATGACCGTAATA
*
542374 CTCCTAG-AGGGT-AAAT
65 CCCCT-GTAGGGTAAAAT
542390 GAC
1 GAC
542393 TAGTTTGCCC
Statistics
Matches: 410, Mismatches: 61, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.00
79 77 0.19
80 198 0.48
81 134 0.33
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (81 bp):
GACCGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATAC
CCCTGTAGGGTAAAAT
Found at i:542438 original size:23 final size:23
Alignment explanation
Indices: 542408--542451 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
542398 TGCCCCTCGA
*
542408 GGTTAAATGATTGATTTGTCTGG
1 GGTTAAATGACTGATTTGTCTGG
542431 GGTTAAATGACTGATTTGTCT
1 GGTTAAATGACTGATTTGTCT
542452 ATGTTTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (23 bp):
GGTTAAATGACTGATTTGTCTGG
Found at i:542482 original size:24 final size:23
Alignment explanation
Indices: 542413--542493 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
542403 CTCGAGGTTA
* ** * *
542413 AATGATTGATTTGTCTGGGGTTA
1 AATGACTGATTTGTCTATGTTTG
542436 AATGACTGATTTGTCTATGTTTGG
1 AATGACTGATTTGTCTATGTTT-G
* * *
542460 TATGACTGATTT-TTTGTGATTTG
1 AATGACTGATTTGTCTATG-TTTG
542483 AATGACTGATT
1 AATGACTGATT
542494 CTGAGCATGG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 33 0.70
24 14 0.30
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.47
Consensus pattern (23 bp):
AATGACTGATTTGTCTATGTTTG
Found at i:542674 original size:26 final size:26
Alignment explanation
Indices: 542619--542674 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
542609 ATCTTATTAC
* * *
542619 TGGCAGATTTGCTACGATACTGTTGC
1 TGGCAGATTTACTACGATACTATTGA
* *
542645 TGGCAGCTTTACTACGATGCTATTGA
1 TGGCAGATTTACTACGATACTATTGA
542671 TGGC
1 TGGC
542675 TTTGAGCCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (26 bp):
TGGCAGATTTACTACGATACTATTGA
Found at i:542716 original size:32 final size:32
Alignment explanation
Indices: 542668--542867 Score: 224
Period size: 32 Copynumber: 6.3 Consensus size: 32
542658 ACGATGCTAT
*
542668 TGATGGCTTTGAGCCGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
*
542700 TAATGGCTTTGTGCCGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * *
542732 TGATGCCTTTGTGCCGATTATATTACCATTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* ** *
542764 TGATGGCTGTGTATCGATCATATTATCGTTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * * *
542796 TGATGGCTGTGTGCCGATCATATCACTGCTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * *
542828 T-AGTGGCTTTATGCCAATCATATTACAG-TAC
1 TGA-TGGCTTTGTGCCGATCATATTACCGTTAC
*
542859 TTATGGCTT
1 TGATGGCTT
542868 GTAGCCATTC
Statistics
Matches: 142, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.08
32 131 0.92
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATTACCGTTAC
Found at i:545376 original size:3 final size:3
Alignment explanation
Indices: 545368--545419 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
545358 TTTAATTAGT
* * * *
545368 TTA TTA TTA TTG TTA TTA TTA -CA TTA TTA TTA TCA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
545415 TTA TT
1 TTA TT
545420 CATATGAGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 1 0.03
3 39 0.98
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:550404 original size:16 final size:17
Alignment explanation
Indices: 550379--550412 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
550369 ACTCAAGCAT
550379 TCATGAGGCA-ATATGG
1 TCATGAGGCAGATATGG
*
550395 TCATGTGGCAGATATGG
1 TCATGAGGCAGATATGG
550412 T
1 T
550413 TCCTGATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (17 bp):
TCATGAGGCAGATATGG
Found at i:560129 original size:15 final size:15
Alignment explanation
Indices: 560105--560136 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
560095 TATGCATGCA
*
560105 AAATATAAAAGACAT
1 AAATACAAAAGACAT
560120 AAATACAAAAGACAT
1 AAATACAAAAGACAT
560135 AA
1 AA
560137 TAGTGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:566761 original size:39 final size:40
Alignment explanation
Indices: 566667--566830 Score: 204
Period size: 40 Copynumber: 4.1 Consensus size: 40
566657 TGTTTGGATA
*
566667 AAAAACGCCGCTATAGATCGAGCATTAGCGACGCTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* *
566707 AAAAACGTCGCTATAGATCGCGCATTAGCGGCGCTTTTT-
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* * *
566746 AAAAACGCCGCTATAGGTCGAGCTTTAGTGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* * * * ** *
566786 AAAAATGCCGCTATAGGTTGACCATTAGCACCACTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
566826 AAAAA
1 AAAAA
566831 TTAAGCATAA
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
39 34 0.32
40 73 0.68
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
Found at i:566823 original size:79 final size:80
Alignment explanation
Indices: 566667--566830 Score: 206
Period size: 79 Copynumber: 2.1 Consensus size: 80
566657 TGTTTGGATA
*
566667 AAAAACGCCGCTATAGATCGAGCATTAGCGACGCTTTTTGAAAAACGTCGCTATAGATCGCGCAT
1 AAAAACGCCGCTATAGATCGAGCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGATCGCGCAT
** *
566732 TAGCGGCGCTTTTT-
66 TAGCACCACTTTTTG
* * * * * * *
566746 AAAAACGCCGCTATAGGTCGAGCTTTAGTGGCGCTTTTTGAAAAATGCCGCTATAGGTTGAC-CA
1 AAAAACGCCGCTATAGATCGAGCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGATCG-CGCA
566810 TTAGCACCACTTTTTG
65 TTAGCACCACTTTTTG
566826 AAAAA
1 AAAAA
566831 TTAAGCATAA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 66 0.92
80 6 0.08
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (80 bp):
AAAAACGCCGCTATAGATCGAGCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGATCGCGCAT
TAGCACCACTTTTTG
Found at i:567248 original size:7 final size:7
Alignment explanation
Indices: 567234--567423 Score: 57
Period size: 7 Copynumber: 26.6 Consensus size: 7
567224 TCATTACAAA
567234 TTAGGGT
1 TTAGGGT
*
567241 TTATGGT
1 TTAGGGT
567248 TTAGGGT
1 TTAGGGT
* *
567255 ATATGGT
1 TTAGGGT
567262 TTAGGGT
1 TTAGGGT
*
567269 TTAAGGT
1 TTAGGGT
**
567276 TTAAAAGT
1 TT-AGGGT
*
567284 TACTA--TT
1 T--TAGGGT
*
567291 TTAAGGT
1 TTAGGGT
* *
567298 TTATGGA
1 TTAGGGT
567305 TTATGGGT
1 TTA-GGGT
*
567313 TTAGGGA
1 TTAGGGT
567320 TTATGGGT
1 TTA-GGGT
*
567328 TAAGGG-
1 TTAGGGT
567334 TT-GGAGT
1 TTAGG-GT
*
567341 TTAAGGT
1 TTAGGGT
567348 TTAAGGGT
1 TT-AGGGT
* *
567356 TAAGGGC
1 TTAGGGT
567363 TTAGGGT
1 TTAGGGT
** *
567370 TTTTGTT
1 TTAGGGT
* *
567377 TTATGAT
1 TTAGGGT
567384 TTAGGGT
1 TTAGGGT
*
567391 TTAAAGG-
1 TT-AGGGT
567398 TTAGGGGT
1 TTA-GGGT
*
567406 TAAGGGT
1 TTAGGGT
*
567413 TTAAGGT
1 TTAGGGT
567420 TTAG
1 TTAG
567424 ATTAATTAGT
Statistics
Matches: 132, Mismatches: 37, Indels: 28
0.67 0.19 0.14
Matches are distributed among these distances:
5 4 0.03
6 3 0.02
7 97 0.73
8 26 0.20
9 1 0.01
10 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.33, T:0.43
Consensus pattern (7 bp):
TTAGGGT
Found at i:567253 original size:14 final size:14
Alignment explanation
Indices: 567234--567278 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
567224 TCATTACAAA
567234 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
567248 TTAGGGTATATGGT
1 TTAGGGTTTATGGT
*
567262 TTAGGGTTTAAGGT
1 TTAGGGTTTATGGT
567276 TTA
1 TTA
567279 AAAGTTACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:567313 original size:15 final size:15
Alignment explanation
Indices: 567295--567333 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
567285 ACTATTTTAA
*
567295 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
567310 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
*
567325 GGTTAAGGG
1 GGTTTAGGG
567334 TTGGAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:567315 original size:22 final size:22
Alignment explanation
Indices: 567290--567335 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
567280 AAGTTACTAT
* *
567290 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAAGGG
* *
567312 TTTAGGGATTATGGGTTAAGGG
1 TTTAAGGATTATGGATTAAGGG
567334 TT
1 TT
567336 GGAGTTTAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (22 bp):
TTTAAGGATTATGGATTAAGGG
Found at i:567596 original size:15 final size:15
Alignment explanation
Indices: 567578--567616 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
567568 ACTATTTTAA
*
567578 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
567593 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
*
567608 GGTTAAGGG
1 GGTTTAGGG
567617 TTGGAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:567598 original size:22 final size:22
Alignment explanation
Indices: 567573--567618 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
567563 AAGTTACTAT
* *
567573 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAAGGG
* *
567595 TTTAGGGATTATGGGTTAAGGG
1 TTTAAGGATTATGGATTAAGGG
567617 TT
1 TT
567619 GGAGTTTAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (22 bp):
TTTAAGGATTATGGATTAAGGG
Found at i:567707 original size:283 final size:283
Alignment explanation
Indices: 567200--567743 Score: 1027
Period size: 283 Copynumber: 1.9 Consensus size: 283
567190 ATTAAGTACT
* *
567200 AATTTTAAAATATTAAATTAATTATCATTACAAATTAGGGTTTATGGTTTAGGGTATATGGTTTA
1 AATTTTAAAATATTAAATTAATTATCATTACAAATTAGGGATTATGGGTTAGGGTATATGGTTTA
567265 GGGTTTAAGGTTTAAAAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATTATGGGTTA
66 GGGTTTAAGGTTTAAAAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATTATGGGTTA
567330 AGGGTTGGAGTTTAAGGTTTAAGGGTTAAGGGCTTAGGGTTTTTGTTTTATGATTTAGGGTTTAA
131 AGGGTTGGAGTTTAAGGTTTAAGGGTTAAGGGCTTAGGGTTTTTGTTTTATGATTTAGGGTTTAA
567395 AGGTTAGGGGTTAAGGGTTTAAGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAT
196 AGGTTAGGGGTTAAGGGTTTAAGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAT
567460 TTCTTATATAATTGTAAAAGAGA
261 TTCTTATATAATTGTAAAAGAGA
* **
567483 AATTTTAAAATATTAAATTAATTATCATTATAGTTTAGGGAATTA-GGGTTAGGGTATATGGTTT
1 AATTTTAAAATATTAAATTAATTATCATTACAAATTAGGG-ATTATGGGTTAGGGTATATGGTTT
567547 AGGGTTTAAGGTTTAAAAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATTATGGGTT
65 AGGGTTTAAGGTTTAAAAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATTATGGGTT
567612 AAGGGTTGGAGTTTAAGGTTTAAGGGTTAAGGGCTTAGGGTTTTTGTTTTATGATTTAGGGTTTA
130 AAGGGTTGGAGTTTAAGGTTTAAGGGTTAAGGGCTTAGGGTTTTTGTTTTATGATTTAGGGTTTA
567677 AAGGTTAGGGGTTAAGGGTTTAAGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAA
195 AAGGTTAGGGGTTAAGGGTTTAAGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAA
567742 TT
260 TT
567744 GTAAAAGAGA
Statistics
Matches: 255, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
283 252 0.99
284 3 0.01
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.44
Consensus pattern (283 bp):
AATTTTAAAATATTAAATTAATTATCATTACAAATTAGGGATTATGGGTTAGGGTATATGGTTTA
GGGTTTAAGGTTTAAAAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATTATGGGTTA
AGGGTTGGAGTTTAAGGTTTAAGGGTTAAGGGCTTAGGGTTTTTGTTTTATGATTTAGGGTTTAA
AGGTTAGGGGTTAAGGGTTTAAGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAT
TTCTTATATAATTGTAAAAGAGA
Found at i:569165 original size:16 final size:16
Alignment explanation
Indices: 569146--569176 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
569136 ATATTAAATA
569146 ATTTCAAATTTTAAAG
1 ATTTCAAATTTTAAAG
569162 ATTTCAAATTTTAAA
1 ATTTCAAATTTTAAA
569177 TAATTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTTCAAATTTTAAAG
Found at i:569241 original size:22 final size:22
Alignment explanation
Indices: 569216--569261 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
569206 TTCTTTTAAA
**
569216 TATTAATTAAAATTTAAAAAAT
1 TATTAATTAAAATGAAAAAAAT
* *
569238 TATTTATTTAAATGAAAAAAAT
1 TATTAATTAAAATGAAAAAAAT
569260 TA
1 TA
569262 AACTATTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TATTAATTAAAATGAAAAAAAT
Found at i:569482 original size:14 final size:14
Alignment explanation
Indices: 569463--569489 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
569453 CGTTCGTAAT
569463 ATGAAAATCCAACG
1 ATGAAAATCCAACG
569477 ATGAAAATCCAAC
1 ATGAAAATCCAAC
569490 ACAAAGCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.22, G:0.11, T:0.15
Consensus pattern (14 bp):
ATGAAAATCCAACG
Found at i:570242 original size:12 final size:12
Alignment explanation
Indices: 570225--570252 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
570215 GCTATCCATG
570225 ATGTTACTATTA
1 ATGTTACTATTA
570237 ATGTTACTATTA
1 ATGTTACTATTA
570249 ATGT
1 ATGT
570253 CATTAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (12 bp):
ATGTTACTATTA
Found at i:570378 original size:10 final size:9
Alignment explanation
Indices: 570353--570377 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
570343 TAGGTATATA
570353 TTTTTTTCT
1 TTTTTTTCT
570362 TTTTTTTCT
1 TTTTTTTCT
570371 TTTTTTT
1 TTTTTTT
570378 TAAAGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:573104 original size:43 final size:43
Alignment explanation
Indices: 573036--573170 Score: 200
Period size: 43 Copynumber: 3.1 Consensus size: 43
573026 TTTTTTACGA
* * *
573036 TCTTTAGCAGTGTTTTTGGTA-AAAGCGCCGCTAAAAGTCATGT
1 TCTTTAGCAGCGTTTGTGG-AGAAAGCGCCGCTAAAGGTCATGT
573079 TCTTTAGCAGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGT
1 TCTTTAGCAGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGT
* *
573122 TCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGT
1 TCTTTAGCAGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGT
*
573165 TTTTTA
1 TCTTTA
573171 CCGGCGTTCT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
42 1 0.01
43 84 0.99
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TCTTTAGCAGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGT
Done.