Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 164 of 222
Found at i:52429274 original size:106 final size:106
Alignment explanation
Indices: 52429088--52429346 Score: 340
Period size: 106 Copynumber: 2.4 Consensus size: 106
52429078 ACTAAATTTC
* * * * **
52429088 CTCATATGAT-TCCATAACCCACCAATTATGGTTTTACATGATATGGGCTTCTTCCCATATGATG
1 CTCATATGATGT-CATAACCCACCAGTTACGATCTTACATGATATGGTATTCTTCCCATATGATG
* * *
52429152 CCATAACCCACCAGTTATAGTTTTACATGATATGGTTTTCTT
65 CCATAACCCACCAGTTACAGTCTTACATGATATGGTCTTCTT
* * *
52429194 CTCATATGATGTCATGACCCACCAGTTACGATCTTACACGATATGGTATTCTTTCCATATGATGC
1 CTCATATGATGTCATAACCCACCAGTTACGATCTTACATGATATGGTATTCTTCCCATATGATGC
* * *
52429259 CATAACCGACTAGTTACGGTCTTACATGATATGGTCTTCTT
66 CATAACCCACCAGTTACAGTCTTACATGATATGGTCTTCTT
* * *
52429300 CCCTTATGATGTCATAACTCACCAGTTACGATCTTACATGATATGGT
1 CTCATATGATGTCATAACCCACCAGTTACGATCTTACATGATATGGT
52429347 CCTTAAATGT
Statistics
Matches: 132, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
106 131 0.99
107 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (106 bp):
CTCATATGATGTCATAACCCACCAGTTACGATCTTACATGATATGGTATTCTTCCCATATGATGC
CATAACCCACCAGTTACAGTCTTACATGATATGGTCTTCTT
Found at i:52431709 original size:15 final size:15
Alignment explanation
Indices: 52431689--52431738 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
52431679 CCGCTTCCTC
52431689 CATTCAATTGTTTAT
1 CATTCAATTGTTTAT
*
52431704 CATTC-A--GTTTCCT
1 CATTCAATTGTTT-AT
52431717 CCATTCAATTGTTTAT
1 -CATTCAATTGTTTAT
52431733 CATTCA
1 CATTCA
52431739 TTATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
12 4 0.14
13 1 0.04
14 6 0.21
15 12 0.43
16 1 0.04
17 4 0.14
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (15 bp):
CATTCAATTGTTTAT
Found at i:52431725 original size:29 final size:29
Alignment explanation
Indices: 52431683--52431738 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
52431673 CTTCTTCCGC
52431683 TTCCTCCATTCAATTGTTTATCATTCAGT
1 TTCCTCCATTCAATTGTTTATCATTCAGT
52431712 TTCCTCCATTCAATTGTTTATCATTCA
1 TTCCTCCATTCAATTGTTTATCATTCA
52431739 TTATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.05, T:0.48
Consensus pattern (29 bp):
TTCCTCCATTCAATTGTTTATCATTCAGT
Found at i:52437478 original size:30 final size:30
Alignment explanation
Indices: 52437444--52437504 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
52437434 TCTCAACACA
52437444 TTATATCATTCAGTCAAACATTCTCATATC
1 TTATATCATTCAGTCAAACATTCTCATATC
52437474 TTATATCATTCAGTCAAACATTCTCATATC
1 TTATATCATTCAGTCAAACATTCTCATATC
52437504 T
1 T
52437505 CATAACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (30 bp):
TTATATCATTCAGTCAAACATTCTCATATC
Found at i:52439264 original size:33 final size:33
Alignment explanation
Indices: 52439227--52439503 Score: 137
Period size: 33 Copynumber: 8.3 Consensus size: 33
52439217 TGGCCCTGTC
* *
52439227 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAATGCCATAACCCAGCT
** * * *
52439260 ATGGTCTTACCATCAGAATGTCATAGCCCAGCT
1 ATGGTCTTACGTTCATAATGCCATAACCCAGCT
** *** * *
52439293 ATGGTCTTATATAT-ATACACTGCCATGGTCCAACC
1 ATGGTCTTACGT-TCATA-A-TGCCATAACCCAGCT
* * * *
52439328 ATGGTCTTACGTTTATAGTGCCATAACCCGGTT
1 ATGGTCTTACGTTCATAATGCCATAACCCAGCT
* * *
52439361 ATGGTCTTAC-TATCAGAATGTCATAGCCCAGCT
1 ATGGTCTTACGT-TCATAATGCCATAACCCAGCT
** * ** * *
52439394 ATGGTCTTATATAT-ATACACTGCCATGATGCAACC
1 ATGGTCTTACGT-TCATA-A-TGCCATAACCCAGCT
* * ** *
52439429 ATGGTCTTATGTTCATAGTGCCATAACCTGGTT
1 ATGGTCTTACGTTCATAATGCCATAACCCAGCT
** * *
52439462 ATGGTCTTACCATCAGAATGCCATAGCCCAGCT
1 ATGGTCTTACGTTCATAATGCCATAACCCAGCT
52439495 ATGGTCTTA
1 ATGGTCTTA
52439504 TATAAATGAA
Statistics
Matches: 174, Mismatches: 61, Indels: 18
0.69 0.24 0.07
Matches are distributed among these distances:
32 1 0.01
33 120 0.69
34 8 0.05
35 45 0.26
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (33 bp):
ATGGTCTTACGTTCATAATGCCATAACCCAGCT
Found at i:52439387 original size:101 final size:101
Alignment explanation
Indices: 52439226--52439507 Score: 492
Period size: 101 Copynumber: 2.8 Consensus size: 101
52439216 ATGGCCCTGT
*
52439226 CATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTACCATCAGAATGTCATAGCCCAG
1 CATGGTCTTACGTTCATAGTGCCATAACCCGGTTATGGTCTTACCATCAGAATGTCATAGCCCAG
*
52439291 CTATGGTCTTATATATATACACTGCCATGGTCCAAC
66 CTATGGTCTTATATATATACACTGCCATGATCCAAC
* *
52439327 CATGGTCTTACGTTTATAGTGCCATAACCCGGTTATGGTCTTACTATCAGAATGTCATAGCCCAG
1 CATGGTCTTACGTTCATAGTGCCATAACCCGGTTATGGTCTTACCATCAGAATGTCATAGCCCAG
*
52439392 CTATGGTCTTATATATATACACTGCCATGATGCAAC
66 CTATGGTCTTATATATATACACTGCCATGATCCAAC
* * *
52439428 CATGGTCTTATGTTCATAGTGCCATAACCTGGTTATGGTCTTACCATCAGAATGCCATAGCCCAG
1 CATGGTCTTACGTTCATAGTGCCATAACCCGGTTATGGTCTTACCATCAGAATGTCATAGCCCAG
52439493 CTATGGTCTTATATA
66 CTATGGTCTTATATA
52439508 AATGAAAACA
Statistics
Matches: 171, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 171 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (101 bp):
CATGGTCTTACGTTCATAGTGCCATAACCCGGTTATGGTCTTACCATCAGAATGTCATAGCCCAG
CTATGGTCTTATATATATACACTGCCATGATCCAAC
Found at i:52441045 original size:13 final size:13
Alignment explanation
Indices: 52441029--52441053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52441019 CCCTTTATGT
52441029 TTCTCCTTAAATG
1 TTCTCCTTAAATG
52441042 TTCTCCTTAAAT
1 TTCTCCTTAAAT
52441054 AACAAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.48
Consensus pattern (13 bp):
TTCTCCTTAAATG
Found at i:52442448 original size:21 final size:21
Alignment explanation
Indices: 52442407--52442449 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
52442397 TATGGTCAAG
*
52442407 TATCGATACTAAATGCTAAAA
1 TATCGATACTAAATGCCAAAA
*
52442428 TATCGATACCT-AATTCCAAAA
1 TATCGATA-CTAAATGCCAAAA
52442449 T
1 T
52442450 GGAAAAACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (21 bp):
TATCGATACTAAATGCCAAAA
Found at i:52443234 original size:45 final size:44
Alignment explanation
Indices: 52443163--52443292 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 44
52443153 TAATTCATCG
* * * * *
52443163 TTCCAAAG-AATGTCATGGCATTTTTCAACCATGGTCTTATGCAT
1 TTCCAAAGTAGTGTCATAGTATCTTTCAACTATGGTCTTAT-CAT
52443207 TTCCAAAGTAGTGTCATAGTATCTTTCAACTATGGTCTTGATCAT
1 TTCCAAAGTAGTGTCATAGTATCTTTCAACTATGGTCTT-ATCAT
* * * * *
52443252 TACCGATGT-GATGCCATAATATCTTTCAACTATGGTCTTAT
1 TTCCAAAGTAG-TGTCATAGTATCTTTCAACTATGGTCTTAT
52443293 TTGTATCAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 11 0.15
45 60 0.82
46 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (44 bp):
TTCCAAAGTAGTGTCATAGTATCTTTCAACTATGGTCTTATCAT
Found at i:52443315 original size:45 final size:44
Alignment explanation
Indices: 52443185--52443337 Score: 141
Period size: 45 Copynumber: 3.4 Consensus size: 44
52443175 TCATGGCATT
* * * * *
52443185 TTTCAACCATGGTCTTATGCATTTCCA-AAGTAGTGTCATAGTATC
1 TTTCAACTATGGTCTTAT-CA-TTACAGATGTAATGTCATAATATC
* * *
52443230 TTTCAACTATGGTCTTGATCATTACCGATGTGATGCCATAATATC
1 TTTCAACTATGGTCTT-ATCATTACAGATGTAATGTCATAATATC
*
52443275 TTTCAACTATGGTCTTAT-TTGTATCAGAT-TCAATGTCATAATATC
1 TTTCAACTATGGTCTTATCAT-TA-CAGATGT-AATGTCATAATATC
*
52443320 TTTCAACTATAGTCTTAT
1 TTTCAACTATGGTCTTAT
52443338 ATAGTTTTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
43 1 0.01
44 8 0.09
45 79 0.88
46 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (44 bp):
TTTCAACTATGGTCTTATCATTACAGATGTAATGTCATAATATC
Found at i:52467290 original size:21 final size:21
Alignment explanation
Indices: 52467266--52467305 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52467256 AAGAAAAAAC
52467266 AAAA-AGCAACAGAAAAAGAGA
1 AAAATAGC-ACAGAAAAAGAGA
*
52467287 AAAATAGCAGAGAAAAAGA
1 AAAATAGCACAGAAAAAGA
52467306 TATTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.70, C:0.07, G:0.20, T:0.03
Consensus pattern (21 bp):
AAAATAGCACAGAAAAAGAGA
Found at i:52471867 original size:21 final size:22
Alignment explanation
Indices: 52471841--52471881 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
52471831 ATAAAACTCA
52471841 AAAAAAAGTT-TAAAT-TATTTC
1 AAAAAAA-TTATAAATATATTTC
52471862 AAAAAAATTATAAATATATT
1 AAAAAAATTATAAATATATT
52471882 CAACTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.67
22 4 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAAAAATTATAAATATATTTC
Found at i:52477244 original size:18 final size:18
Alignment explanation
Indices: 52477212--52477246 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52477202 TTGTTTATGG
**
52477212 CTCCAAAAGTGCTTTTGT
1 CTCCAAAAGAACTTTTGT
52477230 CTCCAAAAGAACTTTTG
1 CTCCAAAAGAACTTTTG
52477247 AAACGCAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (18 bp):
CTCCAAAAGAACTTTTGT
Found at i:52482203 original size:11 final size:11
Alignment explanation
Indices: 52482183--52482214 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
52482173 TGAAATTTCA
52482183 CATCATCCTCG
1 CATCATCCTCG
*
52482194 CATTATCCTCG
1 CATCATCCTCG
52482205 CATCATCCTC
1 CATCATCCTC
52482215 ATTAACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (11 bp):
CATCATCCTCG
Found at i:52496524 original size:54 final size:54
Alignment explanation
Indices: 52496461--52496620 Score: 254
Period size: 54 Copynumber: 3.0 Consensus size: 54
52496451 ACCAAAGTAT
*
52496461 TATCGTACATCAATATTCGTTAAATAATCCAAAAATAAGGAATAAAGAGAAAAA
1 TATCGTACATCAATATTCGTTAAATAATCCAAAAACAAGGAATAAAGAGAAAAA
*
52496515 TATCGTACATCAATATTCGTTAAGTAATCCAAAAACAAGGAAT-AA-AGAAAAA
1 TATCGTACATCAATATTCGTTAAATAATCCAAAAACAAGGAATAAAGAGAAAAA
* *
52496567 TATAGTACATCAATATTCGTTATATAATCCACAAAACAAGGAA-AAAGAGAAAAA
1 TATCGTACATCAATATTCGTTAAATAATCCA-AAAACAAGGAATAAAGAGAAAAA
52496621 ATATACTTGG
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
52 35 0.36
53 15 0.15
54 48 0.49
ACGTcount: A:0.53, C:0.12, G:0.11, T:0.23
Consensus pattern (54 bp):
TATCGTACATCAATATTCGTTAAATAATCCAAAAACAAGGAATAAAGAGAAAAA
Found at i:52498041 original size:35 final size:36
Alignment explanation
Indices: 52497994--52498079 Score: 156
Period size: 35 Copynumber: 2.4 Consensus size: 36
52497984 CCGTTTACGG
52497994 ACTATTCACGTATACGGCACTATTCACGTATACAGT
1 ACTATTCACGTATACGGCACTATTCACGTATACAGT
52498030 ACTATT-ACGTATACGGCACTATTCACGTATACAGT
1 ACTATTCACGTATACGGCACTATTCACGTATACAGT
*
52498065 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
52498080 AGTAGTTGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 34 0.71
36 14 0.29
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (36 bp):
ACTATTCACGTATACGGCACTATTCACGTATACAGT
Found at i:52498080 original size:18 final size:18
Alignment explanation
Indices: 52497994--52498083 Score: 128
Period size: 18 Copynumber: 5.1 Consensus size: 18
52497984 CCGTTTACGG
* *
52497994 ACTATTCACGTATACGGC
1 ACTATTCACGTATACAGT
52498012 ACTATTCACGTATACAGT
1 ACTATTCACGTATACAGT
* *
52498030 ACTATT-ACGTATACGGC
1 ACTATTCACGTATACAGT
52498047 ACTATTCACGTATACAGT
1 ACTATTCACGTATACAGT
*
52498065 ACTGTTCACGTATACAGT
1 ACTATTCACGTATACAGT
52498083 A
1 A
52498084 GTTGGGATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
17 15 0.23
18 49 0.77
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (18 bp):
ACTATTCACGTATACAGT
Found at i:52503593 original size:18 final size:18
Alignment explanation
Indices: 52503536--52503595 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
52503526 CCTGAGGATC
*
52503536 TCCAAGGTTTCAGAGAAA
1 TCCAAGGTTTCGGAGAAA
* * *
52503554 TCCAATGTCTCAGG-GAAG
1 TCCAAGGTTTC-GGAGAAA
*
52503572 TCCAAGGTTTCGGAAAAA
1 TCCAAGGTTTCGGAGAAA
52503590 TCCAAG
1 TCCAAG
52503596 TCGAACATCT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 2 0.06
18 29 0.91
19 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (18 bp):
TCCAAGGTTTCGGAGAAA
Found at i:52512141 original size:15 final size:15
Alignment explanation
Indices: 52512121--52512192 Score: 58
Period size: 15 Copynumber: 4.8 Consensus size: 15
52512111 TTATGGAAAG
*
52512121 TCAAATATATGGTTA
1 TCAAATATATGGATA
*
52512136 TCAAATA-ATGGAAA
1 TCAAATATATGGATA
* *
52512150 GTCAAAGATATGGGTA
1 -TCAAATATATGGATA
*
52512166 TCAAATAT-TGGAAAA
1 TCAAATATATGG-ATA
*
52512181 TCAAAGATATGG
1 TCAAATATATGG
52512193 GTATTGAGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
14 8 0.18
15 28 0.64
16 8 0.18
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (15 bp):
TCAAATATATGGATA
Found at i:52512149 original size:30 final size:30
Alignment explanation
Indices: 52512113--52512196 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
52512103 ATCCGTATTT
* *
52512113 ATGGAAAGTCAAATATATGGTTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
52512143 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
52512173 TTGGAAAATCAAAGATATGGGTAT
1 ATGGAAAGTCAAAGATATGGGTAT
52512197 TGAGATATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:52518501 original size:35 final size:35
Alignment explanation
Indices: 52518419--52518487 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
52518409 GCGCTGGCCG
* * *
52518419 GTAATATCGACAATAAATATGTCTAGCACTAGTCA
1 GTAAAATCGACAATAAACATGTCCAGCACTAGTCA
*
52518454 GTAAAATCGACAATAAACGTGTCCAGCACTAGTC
1 GTAAAATCGACAATAAACATGTCCAGCACTAGTC
52518488 GGTATAACTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (35 bp):
GTAAAATCGACAATAAACATGTCCAGCACTAGTCA
Found at i:52521216 original size:16 final size:16
Alignment explanation
Indices: 52521195--52521225 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52521185 TTTTTTATTA
*
52521195 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
52521211 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
52521226 ACATTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:52536802 original size:21 final size:22
Alignment explanation
Indices: 52536776--52536816 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
52536766 ATAAAACTCA
52536776 AAAAAAAGTT-TAAAT-TATTTC
1 AAAAAAA-TTATAAATATATTTC
52536797 AAAAAAATTATAAATATATT
1 AAAAAAATTATAAATATATT
52536817 CAACTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.67
22 4 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAAAAATTATAAATATATTTC
Found at i:52542163 original size:18 final size:18
Alignment explanation
Indices: 52542131--52542165 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52542121 TTGTTTATGG
**
52542131 CTCCAAAAGTGCTTTTGT
1 CTCCAAAAGAACTTTTGT
52542149 CTCCAAAAGAACTTTTG
1 CTCCAAAAGAACTTTTG
52542166 AAACGCAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (18 bp):
CTCCAAAAGAACTTTTGT
Found at i:52547104 original size:11 final size:11
Alignment explanation
Indices: 52547084--52547115 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
52547074 TGAAATTTCA
52547084 CATCATCCTCG
1 CATCATCCTCG
*
52547095 CATTATCCTCG
1 CATCATCCTCG
52547106 CATCATCCTC
1 CATCATCCTC
52547116 ATTAACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (11 bp):
CATCATCCTCG
Found at i:52552179 original size:33 final size:33
Alignment explanation
Indices: 52552137--52552221 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
52552127 TGCTCTATGT
* *
52552137 TTGGCGTGTTGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCGTATGAGCA
** * *
52552170 TTGGTGTGTTGGAGGGATTGGCTCGTGTGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCGTATGAGCA
52552203 TCTGGTGTGTTTGGTTGGA
1 T-TGGTGTG-TTGGTTGGA
52552222 ATGATGATGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 28 0.67
34 7 0.17
35 7 0.17
ACGTcount: A:0.12, C:0.09, G:0.40, T:0.39
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGATTAGCTCGTATGAGCA
Found at i:52555729 original size:20 final size:22
Alignment explanation
Indices: 52555692--52555731 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52555682 TAGAAGGTTT
*
52555692 TTAAAAATATTTTAAAGTTTCG
1 TTAAAAATATCTTAAAGTTTCG
52555714 TTAAAAAT-TCTT-AAGTTT
1 TTAAAAATATCTTAAAGTTT
52555732 TAATGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (22 bp):
TTAAAAATATCTTAAAGTTTCG
Found at i:52556843 original size:39 final size:39
Alignment explanation
Indices: 52556800--52556898 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
52556790 AACATGTTTT
* * **
52556800 TGAGTATTGCAATATATGCTTGAACGTTATGTGATTATA
1 TGAGTATTGCGATATATGCTTGAACATTATGCAATTATA
* * *
52556839 TGAGTATTGCGGTTTGTGCTTGAACATTATGCAATTATA
1 TGAGTATTGCGATATATGCTTGAACATTATGCAATTATA
* * *
52556878 TGTGTAATGTGATATATGCTT
1 TGAGTATTGCGATATATGCTT
52556899 AAAAGTGAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.42
Consensus pattern (39 bp):
TGAGTATTGCGATATATGCTTGAACATTATGCAATTATA
Found at i:52564189 original size:28 final size:28
Alignment explanation
Indices: 52564126--52564276 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
52564116 ATATTAAGTC
*
52564126 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
52564153 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
52564181 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
52564209 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * * *
52564237 CGCACACTTAGTGTTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
52564266 CGCACACTTAG
1 CGCACACTTAG
52564277 CGCCAATCTC
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 76 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:52564743 original size:12 final size:12
Alignment explanation
Indices: 52564726--52564752 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52564716 TGGGCATACT
52564726 TATGTATATATA
1 TATGTATATATA
52564738 TATGTATATATA
1 TATGTATATATA
52564750 TAT
1 TAT
52564753 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:52572536 original size:28 final size:28
Alignment explanation
Indices: 52572473--52572623 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
52572463 ATATTAAGTC
*
52572473 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
52572500 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
52572528 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
52572556 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
52572584 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
52572613 CGCACACTTAG
1 CGCACACTTAG
52572624 CGCCAATCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 77 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:52573090 original size:12 final size:12
Alignment explanation
Indices: 52573073--52573099 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52573063 TGGGCATACT
52573073 TATGTATATATA
1 TATGTATATATA
52573085 TATGTATATATA
1 TATGTATATATA
52573097 TAT
1 TAT
52573100 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:52574760 original size:36 final size:36
Alignment explanation
Indices: 52574704--52574831 Score: 107
Period size: 36 Copynumber: 3.5 Consensus size: 36
52574694 ACATTGATAT
* * *
52574704 TCCAACCAAAACACATCAGATGCTTATACGAGCTAA
1 TCCAACCGAAACACACCAGATGCTTATAAGAGCTAA
* * * *
52574740 TCCATCCGAAACACACCAGATGCTCATATGAGAC-AG
1 TCCAACCGAAACACACCAGATGCTTATAAGAG-CTAA
* **
52574776 TCCACCCGATAACACACCA-ATGGCTTCGAAGAGCTAA
1 TCCAACCGA-AACACACCAGAT-GCTTATAAGAGCTAA
*
52574813 TCTAACCGAAGACACACCA
1 TCCAACCGAA-ACACACCA
52574832 AAGCAAGAAG
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
36 40 0.55
37 33 0.45
ACGTcount: A:0.38, C:0.31, G:0.14, T:0.16
Consensus pattern (36 bp):
TCCAACCGAAACACACCAGATGCTTATAAGAGCTAA
Found at i:52578356 original size:28 final size:28
Alignment explanation
Indices: 52578324--52578400 Score: 127
Period size: 28 Copynumber: 2.8 Consensus size: 28
52578314 AGTACAATGA
*
52578324 GGGCCTTAGCCCAATTCAGTAGCAGTGT
1 GGGCCTTAGCCCAATACAGTAGCAGTGT
* *
52578352 GGGCCTTAGCCCAATACAATATCAGTGT
1 GGGCCTTAGCCCAATACAGTAGCAGTGT
52578380 GGGCCTTAGCCCAATACAGTA
1 GGGCCTTAGCCCAATACAGTA
52578401 ACATTACATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (28 bp):
GGGCCTTAGCCCAATACAGTAGCAGTGT
Found at i:52578802 original size:27 final size:27
Alignment explanation
Indices: 52578771--52579074 Score: 344
Period size: 27 Copynumber: 11.3 Consensus size: 27
52578761 GGGTATAAAA
52578771 ATCATTTTACCCTAT-GGGGGTATTTCG
1 ATCATTTTACCCT-TCGGGGGTATTTCG
* *
52578798 GTCATTTTACCCTTC-GGGGTATTT-T
1 ATCATTTTACCCTTCGGGGGTATTTCG
* *
52578823 AGTTATTTTACCCTTCAGGGGTATTTCG
1 A-TCATTTTACCCTTCGGGGGTATTTCG
* * *
52578851 GTCATTTTACCCTTCGAGGGTATTTTG
1 ATCATTTTACCCTTCGGGGGTATTTCG
* *
52578878 ATCATTTTATCCTTCGAGGGTATTTCG
1 ATCATTTTACCCTTCGGGGGTATTTCG
* *
52578905 ATCATTTTACCCTTTGGAGGTATTTCG
1 ATCATTTTACCCTTCGGGGGTATTTCG
* * *
52578932 GTCATTTTACCCTTTGAGGGTATTTCG
1 ATCATTTTACCCTTCGGGGGTATTTCG
* *
52578959 ATCATTTTACCCTTCGAGGGTATTTTG
1 ATCATTTTACCCTTCGGGGGTATTTCG
* ** *
52578986 GTCATTTTACCCTTCAAGGATATTTCG
1 ATCATTTTACCCTTCGGGGGTATTTCG
* *
52579013 ATCATTTTACCCTTCAGGGGTATTTTG
1 ATCATTTTACCCTTCGGGGGTATTTCG
* * *
52579040 TTCATTTTGCGCTTCGGGGGTATTTCG
1 ATCATTTTACCCTTCGGGGGTATTTCG
52579067 ATCATTTT
1 ATCATTTT
52579075 TTCCATAAAT
Statistics
Matches: 236, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
26 23 0.10
27 213 0.90
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (27 bp):
ATCATTTTACCCTTCGGGGGTATTTCG
Found at i:52582280 original size:195 final size:195
Alignment explanation
Indices: 52581948--52582338 Score: 764
Period size: 195 Copynumber: 2.0 Consensus size: 195
52581938 TATTATATAT
52581948 ATAACACAAAAATCCATTAATATATATTATATATAAAATAAAGCCCATGTATATATTTTATAGGT
1 ATAACACAAAAATCCATTAATATATATTATATATAAAATAAAGCCCATGTATATATTTTATAGGT
*
52582013 TTATGCATTTTGCACTTTTAAAATCGCATAGTGTATATACTCAACGATTCAACCAAAATTGTAAG
66 TTATGCATTTTGCACTATTAAAATCGCATAGTGTATATACTCAACGATTCAACCAAAATTGTAAG
*
52582078 GATTTGCACAAGGAAGAGCTCGCAAGACACACTTCGACTTTTTAGATTTCGCAATTCATGCTAAA
131 GATTTGCACAAGGAAGAGCTCGCAAGACACACTTCGACTCTTTAGATTTCGCAATTCATGCTAAA
52582143 ATAACACAAAAATCCATTAATATATATTATATATAAAATAAAGCCCATGTATATATTTTATAGGT
1 ATAACACAAAAATCCATTAATATATATTATATATAAAATAAAGCCCATGTATATATTTTATAGGT
52582208 TTATGCATTTTGCACTATTAAAATCGCATAGTGTATATACTCAACGATTCAACCAAAATTGTAAG
66 TTATGCATTTTGCACTATTAAAATCGCATAGTGTATATACTCAACGATTCAACCAAAATTGTAAG
52582273 GATTTGCACAAGGAAGAGCTCGCAAGACACACTTCGACTCTTTAGATTTCGCAATTCATGCTAAA
131 GATTTGCACAAGGAAGAGCTCGCAAGACACACTTCGACTCTTTAGATTTCGCAATTCATGCTAAA
52582338 A
1 A
52582339 CATGGCATAC
Statistics
Matches: 194, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
195 194 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (195 bp):
ATAACACAAAAATCCATTAATATATATTATATATAAAATAAAGCCCATGTATATATTTTATAGGT
TTATGCATTTTGCACTATTAAAATCGCATAGTGTATATACTCAACGATTCAACCAAAATTGTAAG
GATTTGCACAAGGAAGAGCTCGCAAGACACACTTCGACTCTTTAGATTTCGCAATTCATGCTAAA
Found at i:52583468 original size:26 final size:25
Alignment explanation
Indices: 52583409--52583468 Score: 59
Period size: 27 Copynumber: 2.3 Consensus size: 25
52583399 ATACCATAAT
*
52583409 TATTTAATTTAATTATTATTTTTAC
1 TATTTAATCTAATTATTATTTTTAC
*
52583434 TATTATTAA-CTAATTATTTATTTTATCC
1 TA-T-TTAATCTAATTA-TTATTTT-TAC
52583462 TATTTAA
1 TATTTAA
52583469 ATTCCTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
25 2 0.07
26 11 0.38
27 12 0.41
28 4 0.14
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTTAATCTAATTATTATTTTTAC
Found at i:52583799 original size:13 final size:13
Alignment explanation
Indices: 52583781--52583806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52583771 AATCCGAGTC
52583781 AAAAAAATATTTT
1 AAAAAAATATTTT
52583794 AAAAAAATATTTT
1 AAAAAAATATTTT
52583807 CTGTGTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAAAAATATTTT
Found at i:52588822 original size:5 final size:5
Alignment explanation
Indices: 52588812--52588836 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52588802 GATATATTTA
52588812 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
52588837 TAATACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:52590822 original size:33 final size:33
Alignment explanation
Indices: 52590780--52590925 Score: 105
Period size: 33 Copynumber: 4.4 Consensus size: 33
52590770 TGTATATATA
*
52590780 TAAGACCATAGCTGGGCTATGACATTCTAATGT
1 TAAGACCATAGCTGGGCTATGGCATTCTAATGT
* * * * * ***
52590813 TAAGACCATAACCGGGTTATGGCACTATAAACA
1 TAAGACCATAGCTGGGCTATGGCATTCTAATGT
* * * * *
52590846 TAAGACCAT-GATTGGACTATGGCAGTGTATATAT
1 TAAGACCATAG-CTGGGCTATGGCATTCTA-ATGT
* * *
52590880 ATAAGACCATAGCTTGTCTATGGCATTCTAATGG
1 -TAAGACCATAGCTGGGCTATGGCATTCTAATGT
52590914 TAAGACCATAGC
1 TAAGACCATAGC
52590926 CGAGTTATGG
Statistics
Matches: 83, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
33 57 0.69
34 3 0.04
35 22 0.27
36 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCTATGGCATTCTAATGT
Found at i:52590890 original size:101 final size:99
Alignment explanation
Indices: 52590709--52591046 Score: 370
Period size: 101 Copynumber: 3.5 Consensus size: 99
52590699 ATAACGTAGT
* * * * * * * *
52590709 TGGTATGACCAAAACAGGGTTGTGACATTATGAACATAAGACCATGGTTGGACCATGGTAATGTA
1 TGGTAAGACCATAACCGGGTTATGGCACTATGAACATAAGACCAT-GTTGGA-CATGGCAGTGTA
* *
52590774 TATATATAAGACCATAGCTGGGCTATGACATTCTAA
64 TATATATAAGACCATAGCTAGGCTATGGCATTCTAA
* *
52590810 TGTTAAGACCATAACCGGGTTATGGCACTATAAACATAAGACCATGATTGGACTATGGCAGTGTA
1 TGGTAAGACCATAACCGGGTTATGGCACTATGAACATAAGACCATG-TTGGAC-ATGGCAGTGTA
* *
52590875 TATATATAAGACCATAGCTTGTCTATGGCATTCTAA
64 TATATATAAGACCATAGCTAGGCTATGGCATTCTAA
* * *
52590911 TGGTAAGACCATAGCCGAGTTATGGCACTATGAACGTAAGA-C--------CATGGCAGTGTATA
1 TGGTAAGACCATAACCGGGTTATGGCACTATGAACATAAGACCATGTTGGACATGGCAGTGTATA
**
52590967 TATATAAGACCATAGCTAGGCTATGGCATTCTGG
66 TATATAAGACCATAGCTAGGCTATGGCATTCTAA
* * * *
52591001 TGGTAAGACCATAATCAGGTTATGACACTATGAACGTAAGACCATG
1 TGGTAAGACCATAACCGGGTTATGGCACTATGAACATAAGACCATG
52591047 GCAGGGCCAT
Statistics
Matches: 204, Mismatches: 27, Indels: 19
0.82 0.11 0.08
Matches are distributed among these distances:
90 79 0.39
91 2 0.01
100 3 0.01
101 120 0.59
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (99 bp):
TGGTAAGACCATAACCGGGTTATGGCACTATGAACATAAGACCATGTTGGACATGGCAGTGTATA
TATATAAGACCATAGCTAGGCTATGGCATTCTAA
Found at i:52591023 original size:90 final size:90
Alignment explanation
Indices: 52590864--52591050 Score: 295
Period size: 90 Copynumber: 2.1 Consensus size: 90
52590854 TGATTGGACT
* * *
52590864 ATGGCAGTGTATATATATAAGACCATAGCTTGTCTATGGCATTCTAATGGTAAGACCATAGCCGA
1 ATGGCAGTGTATATATATAAGACCATAGCTAGGCTATGGCATTCTAATGGTAAGACCATAGCAGA
*
52590929 GTTATGGCACTATGAACGTAAGACC
66 GTTATGACACTATGAACGTAAGACC
** *
52590954 ATGGCAGTGTATATATATAAGACCATAGCTAGGCTATGGCATTCTGGTGGTAAGACCATAATCAG
1 ATGGCAGTGTATATATATAAGACCATAGCTAGGCTATGGCATTCTAATGGTAAGACCAT-AGCAG
52591019 -GTTATGACACTATGAACGTAAGACC
65 AGTTATGACACTATGAACGTAAGACC
52591044 ATGGCAG
1 ATGGCAG
52591051 GGCCATGACA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
90 86 0.97
91 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (90 bp):
ATGGCAGTGTATATATATAAGACCATAGCTAGGCTATGGCATTCTAATGGTAAGACCATAGCAGA
GTTATGACACTATGAACGTAAGACC
Found at i:52593996 original size:12 final size:12
Alignment explanation
Indices: 52593967--52594009 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
52593957 TGAAGATGAA
52593967 TCATTTCTCATTT
1 TCATTTCT-ATTT
52593980 TCATTTCTATTT
1 TCATTTCTATTT
* *
52593992 CCATTTCCATTT
1 TCATTTCTATTT
52594004 TCATTT
1 TCATTT
52594010 TGAGAAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCTATTT
Found at i:52597252 original size:19 final size:20
Alignment explanation
Indices: 52597211--52597263 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
52597201 TCATATTAGT
* * *
52597211 TTTTCTTAATTTTCTATATA
1 TTTTCTTAATTTTTTAAAAA
52597231 TTTT-TTAATTTTTTAAAAA
1 TTTTCTTAATTTTTTAAAAA
*
52597250 TTTTCTTACTTTTT
1 TTTTCTTAATTTTT
52597264 AATTTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTCTTAATTTTTTAAAAA
Found at i:52610905 original size:41 final size:41
Alignment explanation
Indices: 52610860--52611011 Score: 223
Period size: 41 Copynumber: 3.7 Consensus size: 41
52610850 CATTGAATGT
* * *
52610860 AAGGGGTTGCTAAGTGCAGATTACCTGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAAACACTGATCAAA
* *
52610901 AAGGGGTTGCTAAGTGTAGATTCCCCGAAAAACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAAACACTGATCAAA
* * *
52610942 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATAAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAAACACTGATCAAA
*
52610983 AAGGGGTTGCTAAGTGCTGATTCCCCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAA
52611012 TTATTAATTC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAAACACTGATCAAA
Found at i:52611027 original size:41 final size:41
Alignment explanation
Indices: 52610860--52611048 Score: 206
Period size: 41 Copynumber: 4.6 Consensus size: 41
52610850 CATTGAATGT
* * * *
52610860 AAGGGGTTGCTAAGTGCAGATTACCTGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATAACTGATCAAA
*
52610901 AAGGGGTTGCTAAGTG-TAGATTCCCCGAAAAACTGATCAAA
1 AAGGGGTTGCTAAGTGCT-GATTCCCCGAATAACTGATCAAA
* *
52610942 AAGGGGTTGCTAAGTGCAGATTCCCC-AA-AACTCTGATAAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATAA--CTGATCAAA
* * * *
52610983 AAGGGGTTGCTAAGTGCTGATTCCCCGAATTATTAATTC-TA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATAACTGA-TCAAA
52611024 AAGGTGGTTGCTAAGTGCTGATTCC
1 AAGG-GGTTGCTAAGTGCTGATTCC
52611049 ACTGTATCCT
Statistics
Matches: 127, Mismatches: 13, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 99 0.78
42 23 0.18
43 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATAACTGATCAAA
Found at i:52611027 original size:82 final size:82
Alignment explanation
Indices: 52610860--52611048 Score: 229
Period size: 82 Copynumber: 2.3 Consensus size: 82
52610850 CATTGAATGT
* ** * *
52610860 AAGGGGTTGCTAAGTGCAGATTACCTGAATCACTGATCAAAAAGGGGTTGCTAAGTGTAGATTCC
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACACTGATAAAAAAGGGGTTGCTAAGTGTAGATTCC
*
52610925 CCGAAAAACTGATCAAA
66 CCGAAAAACTAATCAAA
*
52610942 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATAAAAAAGGGGTTGCTAAGTGCT-GATTC
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACACTGATAAAAAAGGGGTTGCTAAGTG-TAGATTC
** * *
52611006 CCCGAATTATTAATTC-TA
65 CCCGAAAAACTAA-TCAAA
*
52611024 AAGGTGGTTGCTAAGTGCTGATTCC
1 AAGG-GGTTGCTAAGTGCAGATTCC
52611049 ACTGTATCCT
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
82 70 0.76
83 22 0.24
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (82 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCAAAACACTGATAAAAAAGGGGTTGCTAAGTGTAGATTCC
CCGAAAAACTAATCAAA
Found at i:52611132 original size:41 final size:40
Alignment explanation
Indices: 52610853--52611137 Score: 166
Period size: 41 Copynumber: 6.9 Consensus size: 40
52610843 TGGGATTCAT
* * * *
52610853 TGAATGTAAGGGGTTGCTAAGTGCAGATTACCTGAATCAC
1 TGAATATAAGGGGTTGCTAAGTGCTGATTCCCCGAATCAC
* **
52610893 TG-ATCAAAAAGGGGTTGCTAAGTG-TAGATTCCCCGAAAAAC
1 TGAAT--ATAAGGGGTTGCTAAGTGCT-GATTCCCCGAATCAC
* * * * *
52610934 TG-ATCAAAAAGGGGTTGCTAAGTGCAGATTCCCCAAAACTC
1 TGAAT--ATAAGGGGTTGCTAAGTGCTGATTCCCCGAATCAC
* * *
52610975 TGATAAAAAAGGGGTTGCTAAGTGCTGATTCCCCGAATTA-
1 TGA-ATATAAGGGGTTGCTAAGTGCTGATTCCCCGAATCAC
* * * *
52611015 TTAATTCTAAAGGTGGTTGCTAAGTGCTGATTCCACTGTATC-C
1 TGAA-TAT-AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATCAC
* * ** * * *
52611058 TTGATTGTGAAAGGATTTGTTATGTGCTGATTCCCCGTATCAC
1 -TGAATAT--AAGGGGTTGCTAAGTGCTGATTCCCCGAATCAC
52611101 TGAATATAAGGTGGTTGCTAAGTGCTGATTCCACCGA
1 TGAATATAAGG-GGTTGCTAAGTGCTGATTCC-CCGA
52611138 GTAACGGTTA
Statistics
Matches: 190, Mismatches: 39, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
39 3 0.02
40 8 0.04
41 114 0.60
42 34 0.18
43 24 0.13
44 7 0.04
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (40 bp):
TGAATATAAGGGGTTGCTAAGTGCTGATTCCCCGAATCAC
Found at i:52620337 original size:46 final size:48
Alignment explanation
Indices: 52620226--52620337 Score: 146
Period size: 46 Copynumber: 2.4 Consensus size: 48
52620216 CATTTCAGAG
52620226 ATGTATGATGTCTATTTTTACTGACATGGTTGAGAAATATTTGGAAGTTT
1 ATGTATGATGTCTA-TTTTACTGACATGGTTGAGAAATATTTGG-AGTTT
*
52620276 -T-TATGGATG-AT-TTTTACTGACATGGTTGAGAAATATTT-G-GTTT
1 ATGTAT-GATGTCTATTTTACTGACATGGTTGAGAAATATTTGGAGTTT
52620319 ATGTATGATGTCTATTTTA
1 ATGTATGATGTCTATTTTA
52620338 TGGATGATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
43 4 0.07
44 5 0.09
45 5 0.09
46 32 0.58
48 4 0.07
49 5 0.09
ACGTcount: A:0.27, C:0.05, G:0.21, T:0.46
Consensus pattern (48 bp):
ATGTATGATGTCTATTTTACTGACATGGTTGAGAAATATTTGGAGTTT
Found at i:52620339 original size:18 final size:18
Alignment explanation
Indices: 52620316--52620350 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52620306 AAATATTTGG
*
52620316 TTTATGTATGATGTCTAT
1 TTTATGGATGATGTCTAT
52620334 TTTATGGATGATGTCTA
1 TTTATGGATGATGTCTA
52620351 GCCAATCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (18 bp):
TTTATGGATGATGTCTAT
Found at i:52623430 original size:16 final size:16
Alignment explanation
Indices: 52623409--52623441 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52623399 AGCTGTTAAT
*
52623409 TTTTACAGAAAAGAGG
1 TTTTACAAAAAAGAGG
52623425 TTTTACAAAAAAGAGG
1 TTTTACAAAAAAGAGG
52623441 T
1 T
52623442 GGTAAGACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (16 bp):
TTTTACAAAAAAGAGG
Found at i:52623527 original size:25 final size:25
Alignment explanation
Indices: 52623475--52623527 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
52623465 ATTTTAATTT
* * *
52623475 ATTATCTAATTTTTTAATTTATTGA
1 ATTATCTAATATTTTAATTAATTAA
52623500 ATTAT-TAATATTTTATATTAATTAA
1 ATTATCTAATATTTTA-ATTAATTAA
52623525 ATT
1 ATT
52623528 TTTGAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTATCTAATATTTTAATTAATTAA
Found at i:52629635 original size:37 final size:37
Alignment explanation
Indices: 52629585--52629663 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
52629575 TTATTACGAA
* *
52629585 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
52629622 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
52629659 GTCTT
1 GTCTT
52629664 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:52629860 original size:47 final size:47
Alignment explanation
Indices: 52629782--52630328 Score: 842
Period size: 47 Copynumber: 11.4 Consensus size: 47
52629772 CCCTTCGGGA
* * * * * * *
52629782 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52629829 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52629876 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52629923 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52629970 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52630017 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52630064 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52630113 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52630160 CTTATCACATATATACACTTTCACATTCATCACATCCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTT--CA--CAT----T-CATCACATCGGCCATTAGGC
52630216 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52630263 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52630310 CTTATCACATATATACACT
1 CTTATCACATATATACACT
52630329 GTCTTGGCTG
Statistics
Matches: 469, Mismatches: 20, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
47 370 0.79
48 1 0.00
49 48 0.10
51 3 0.01
52 3 0.01
54 2 0.00
55 1 0.00
56 41 0.09
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52630241 original size:103 final size:103
Alignment explanation
Indices: 52629990--52630298 Score: 515
Period size: 103 Copynumber: 3.1 Consensus size: 103
52629980 ATATACACTT
* *
52629990 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGG
1 TCACATCCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
*
52630055 CCATTAGGCCTTATCACATATAT--A--TACAC-TT--
66 CCATTAGGCCTTATCACATATATACACTTTCACATTCA
* *
52630086 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATCCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
*
52630151 CTATTAGGCCTTATCACATATATACACTTTCACATTCA
66 CCATTAGGCCTTATCACATATATACACTTTCACATTCA
52630189 TCACATCCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATCCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
52630254 CCATTAGGCCTTATCACATATATACACTTTCACATTCA
66 CCATTAGGCCTTATCACATATATACACTTTCACATTCA
52630292 TCACATC
1 TCACATC
52630299 GGCTATTAGG
Statistics
Matches: 199, Mismatches: 7, Indels: 7
0.93 0.03 0.03
Matches are distributed among these distances:
96 85 0.43
98 1 0.01
100 4 0.02
101 2 0.01
103 107 0.54
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (103 bp):
TCACATCCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
CCATTAGGCCTTATCACATATATACACTTTCACATTCA
Found at i:52630295 original size:150 final size:151
Alignment explanation
Indices: 52630037--52630328 Score: 550
Period size: 150 Copynumber: 1.9 Consensus size: 151
52630027 ATATACACTT
*
52630037 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATC
1 TCACATCCATCACATCGGCCATTAGGCCTTATCACA-ATATATACACTTTCACATTCATCACATC
52630102 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
65 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCA
52630167 CATATATACACTTTCACATTCA
130 CATATATACACTTTCACATTCA
*
52630189 TCACATCCATCACATCGGCTATTAGGCCTTATCAC-ATATATACACTTTCACATTCATCACATCG
1 TCACATCCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCG
52630253 GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC
66 GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC
52630318 ATATATACACT
131 ATATATACACT
52630329 GTCTTGGCTG
Statistics
Matches: 138, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
150 105 0.76
152 33 0.24
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (151 bp):
TCACATCCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCG
GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC
ATATATACACTTTCACATTCA
Found at i:52643172 original size:31 final size:31
Alignment explanation
Indices: 52643134--52643196 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
52643124 AGTTGGTAAG
52643134 TTAATTTACTTATCACATACAAGGCTAGACA
1 TTAATTTACTTATCACATACAAGGCTAGACA
52643165 TTAATTTACTTATCACATACAAGGCTAGACA
1 TTAATTTACTTATCACATACAAGGCTAGACA
52643196 T
1 T
52643197 GGCTTTTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (31 bp):
TTAATTTACTTATCACATACAAGGCTAGACA
Found at i:52655025 original size:16 final size:16
Alignment explanation
Indices: 52655004--52655037 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
52654994 CATCCATTAA
52655004 TTTTCCTTTCTTT-TTT
1 TTTTCCTTT-TTTCTTT
52655020 TTTTCCTTTTTTCTTT
1 TTTTCCTTTTTTCTTT
52655036 TT
1 TT
52655038 GCTCCAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCCTTTTTTCTTT
Found at i:52655416 original size:15 final size:14
Alignment explanation
Indices: 52655375--52655424 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
52655365 ATTTTTAGAA
*
52655375 AAAAAATTT-AATT
1 AAAATATTTAAATT
*
52655388 AAAAT-GTTAAATT
1 AAAATATTTAAATT
52655401 AAAATATTTAAAATT
1 AAAATATTT-AAATT
*
52655416 ATAATATTT
1 AAAATATTT
52655425 TGGTTTCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 13 0.43
14 2 0.07
15 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AAAATATTTAAATT
Found at i:52658973 original size:30 final size:30
Alignment explanation
Indices: 52658937--52658997 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
52658927 TTTAAAGAAT
52658937 TAAATGATAATAAGCTCGGAAGGATGATTA
1 TAAATGATAATAAGCTCGGAAGGATGATTA
*
52658967 TAAATGATAATAAGCTTGGAAGGATGATTA
1 TAAATGATAATAAGCTCGGAAGGATGATTA
52658997 T
1 T
52658998 TCTAACACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.30
Consensus pattern (30 bp):
TAAATGATAATAAGCTCGGAAGGATGATTA
Found at i:52664881 original size:27 final size:27
Alignment explanation
Indices: 52664851--52664907 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
52664841 GAGGAACAAG
* **
52664851 TATAAAAATTTAATTTTGTGGTGAAGT
1 TATAAAAACTTAATTTTGTGAAGAAGT
*
52664878 TATAAAAACTTGATTTTGTGAAGAAGT
1 TATAAAAACTTAATTTTGTGAAGAAGT
52664905 TAT
1 TAT
52664908 CTGTAGGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.42
Consensus pattern (27 bp):
TATAAAAACTTAATTTTGTGAAGAAGT
Found at i:52665040 original size:184 final size:184
Alignment explanation
Indices: 52664721--52665087 Score: 698
Period size: 184 Copynumber: 2.0 Consensus size: 184
52664711 ACTACATGAA
52664721 TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
1 TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
*
52664786 GCCTTGCCACATGTGACCATAGGGTGTGTATTAGTTGGTATAGAAATTGGACTTTGAGGAACAAG
66 GCCTTGCCACATGTGACCATAGGGTGTGTATTAGTTGGTATAGAAATAGGACTTTGAGGAACAAG
52664851 TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAGT
131 TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAGT
* *
52664905 TATCTGTAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAATAATACCT
1 TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
*
52664970 GCCTTGCCACATGTGACCATAGGGTGTGTATTAGTTGGTATAGAAATAGGACTTTGAGGAACAGG
66 GCCTTGCCACATGTGACCATAGGGTGTGTATTAGTTGGTATAGAAATAGGACTTTGAGGAACAAG
52665035 TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAG
131 TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAG
52665088 GTATAGAATA
Statistics
Matches: 179, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 179 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (184 bp):
TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
GCCTTGCCACATGTGACCATAGGGTGTGTATTAGTTGGTATAGAAATAGGACTTTGAGGAACAAG
TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAGT
Found at i:52665168 original size:27 final size:27
Alignment explanation
Indices: 52665032--52665181 Score: 169
Period size: 27 Copynumber: 5.6 Consensus size: 27
52665022 TTTGAGGAAC
* * * *
52665032 AGGTATAAAAATTTAATTTTGTGGTGA
1 AGGTATAGAAACTTGATTTTGTGATGA
* * *
52665059 AGTTATAAAAACTTGATTTTGTGAAGA
1 AGGTATAGAAACTTGATTTTGTGATGA
52665086 AGGTATAGAATA-TTGATTTTGTGATGA
1 AGGTATAGAA-ACTTGATTTTGTGATGA
* * *
52665113 AGGTATGGAAAATTGATTTTGTGAAGA
1 AGGTATAGAAACTTGATTTTGTGATGA
*
52665140 AGGTATAGAAACTTGAGTTTGT-AGTGA
1 AGGTATAGAAACTTGATTTTGTGA-TGA
52665167 AGGTATAGAAACTTG
1 AGGTATAGAAACTTG
52665182 TGAAGGCAAC
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.02
27 103 0.97
28 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (27 bp):
AGGTATAGAAACTTGATTTTGTGATGA
Found at i:52669294 original size:45 final size:45
Alignment explanation
Indices: 52669210--52669361 Score: 164
Period size: 45 Copynumber: 3.4 Consensus size: 45
52669200 TATGGTATTA
* ** *
52669210 AGCTATGGTCTTACTCAT-TTCTATCAG-GATGGCAAAGCATCTTTC
1 AGCTATGGTCTTACTCATCTT-TAT-GGTGATACCATAGCATCTTTC
* * * *
52669255 AACTATGGTTTTACTCATCTTTATGGTGATGCCATAGCATCTTTT
1 AGCTATGGTCTTACTCATCTTTATGGTGATACCATAGCATCTTTC
* * *
52669300 AGCTATGGTCTTACACATTTTTATGGTGATACCATAGCATTTTTC
1 AGCTATGGTCTTACTCATCTTTATGGTGATACCATAGCATCTTTC
*
52669345 AGCTAAGGTCTTACTCA
1 AGCTATGGTCTTACTCA
52669362 ATTTAAACGT
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
44 1 0.01
45 87 0.97
46 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
AGCTATGGTCTTACTCATCTTTATGGTGATACCATAGCATCTTTC
Found at i:52671038 original size:43 final size:42
Alignment explanation
Indices: 52670931--52671040 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
52670921 GATTTGAGAT
52670931 TTACATGTAAGACCATGTCTGGGACATCGGCATCGTATACGA
1 TTACATGTAAGACCATGTCTGGGACATCGGCATCGTATACGA
* * * *
52670973 TTTCGTGTAAGACTC-TGTCTGGGATAGT-GGCATCG-ATAGTTGA
1 TTACATGTAAGAC-CATGTCTGGGACA-TCGGCATCGTATA--CGA
*
52671016 TTACATGTAAGACCACGTCTGGGAC
1 TTACATGTAAGACCATGTCTGGGAC
52671041 GTTGGCATTG
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
41 3 0.05
42 29 0.53
43 23 0.42
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGGGACATCGGCATCGTATACGA
Found at i:52675484 original size:43 final size:44
Alignment explanation
Indices: 52675431--52675513 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
52675421 ACATGGTTTT
*
52675431 CGACAAGATCGTGTGACGC-T-ATTTCGAATTGCACACGGTCTAG
1 CGACAAGATCGTGTGAC-CTTAATTTCAAATTGCACACGGTCTAG
* *
52675474 CGACACGATCGTGTGACCTTAATTTCAAATTGTACACGGT
1 CGACAAGATCGTGTGACCTTAATTTCAAATTGCACACGGT
52675514 TTGGCCACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 1 0.03
43 17 0.49
44 17 0.49
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (44 bp):
CGACAAGATCGTGTGACCTTAATTTCAAATTGCACACGGTCTAG
Found at i:52679142 original size:3 final size:3
Alignment explanation
Indices: 52679134--52679212 Score: 97
Period size: 3 Copynumber: 26.3 Consensus size: 3
52679124 TTTCTATCAT
* * * * *
52679134 TTC TTC TTC TTC TAC TAC TTC TAC TTC TAC TT- TGTC TTC TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC
52679179 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
52679213 CAAAGAGCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.02
3 64 0.97
4 1 0.02
ACGTcount: A:0.05, C:0.30, G:0.01, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:52685938 original size:15 final size:14
Alignment explanation
Indices: 52685917--52685952 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
52685907 ATAATTCTTA
*
52685917 ATAATTATCTTAAT
1 ATAATTATCCTAAT
52685931 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
52685946 ATAATTA
1 ATAATTA
52685953 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:52687961 original size:18 final size:18
Alignment explanation
Indices: 52687938--52687972 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52687928 ACGATGTGTC
52687938 AAACTATATTCATGCTTG
1 AAACTATATTCATGCTTG
* *
52687956 AAACTATTTTGATGCTT
1 AAACTATATTCATGCTT
52687973 ACAGTTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
AAACTATATTCATGCTTG
Found at i:52688127 original size:55 final size:55
Alignment explanation
Indices: 52688063--52688284 Score: 194
Period size: 55 Copynumber: 3.9 Consensus size: 55
52688053 CGTGCTACGT
* * *
52688063 AACAATCGATTTAAACATATAAAAAATCAATTCAAAATAAGTAGTA-TTCTAACAT
1 AACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGTAGTATTTC-AACAG
* ** * *
52688118 AATAATCGATTTAAATGTATAAACAATCGATTCAAAAGCAGTAGTATTTCAACAG
1 AACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGTAGTATTTCAACAG
** * * * * *
52688173 AACAATAAATTTAAACATATAAAAAATTGATTCAAAAGAAGAAGAAGAAGAAGTATTCCACCAT
1 AACAATCGATTTAAACATATAAAAAATCGATTC--------AA-AAGAAGTAGTATTTCAACAG
* *
52688237 AACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGTAATATT
1 AACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGTAGTATT
52688285 CCACAAATTA
Statistics
Matches: 131, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
55 80 0.61
56 5 0.04
63 2 0.02
64 44 0.34
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (55 bp):
AACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGTAGTATTTCAACAG
Found at i:52704856 original size:19 final size:19
Alignment explanation
Indices: 52704832--52704871 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
52704822 ATGTTAAAAG
*
52704832 ATACATATAGTATATATCT
1 ATACATATAGTATACATCT
52704851 ATACATATAGTATACATCT
1 ATACATATAGTATACATCT
52704870 AT
1 AT
52704872 GTGGCTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (19 bp):
ATACATATAGTATACATCT
Found at i:52706373 original size:20 final size:20
Alignment explanation
Indices: 52706348--52706388 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52706338 ATCCTTCAAC
* *
52706348 TTAATCTTATTCAGCTTTGT
1 TTAATCTCATTCAACTTTGT
52706368 TTAATCTCATTCAACTTTGT
1 TTAATCTCATTCAACTTTGT
52706388 T
1 T
52706389 CTATTTTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (20 bp):
TTAATCTCATTCAACTTTGT
Found at i:52711162 original size:17 final size:17
Alignment explanation
Indices: 52711135--52711167 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52711125 TCACTATATT
52711135 TTTATTTCACATATTCAC
1 TTTATTTCACA-ATTCAC
52711153 TTTA-TTCACAATTCA
1 TTTATTTCACAATTCA
52711168 TAAAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCACAATTCAC
Found at i:52711414 original size:51 final size:51
Alignment explanation
Indices: 52711357--52711457 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
52711347 TTACTTTTCT
52711357 AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATTC
1 AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATTC
52711408 AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATT
1 AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATT
52711458 TTGTAACACC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.42
Consensus pattern (51 bp):
AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATTC
Found at i:52712552 original size:39 final size:39
Alignment explanation
Indices: 52712509--52712601 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
52712499 CACATTCAAT
** *
52712509 TTTAAGCATATATCACGTTACACATGTAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
52712548 TTTAAGCATATATCACAATACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
52712587 TTCAAGCATACATCA
1 TTTAAGCATATATCA
52712602 TCGTACTCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:52712601 original size:22 final size:21
Alignment explanation
Indices: 52712535--52712601 Score: 54
Period size: 22 Copynumber: 3.3 Consensus size: 21
52712525 GTTACACATG
*
52712535 TAATCACATAACATTTAAGCA
1 TAATCACATAACATTCAAGCA
*
52712556 TATATCACA-ATACA--C-A-TA
1 TA-ATCACATA-ACATTCAAGCA
52712574 TAATCACATAACATTCAAGCA
1 TAATCACATAACATTCAAGCA
52712595 TACATCA
1 TA-ATCA
52712602 TCGTACTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 15
0.66 0.06 0.28
Matches are distributed among these distances:
17 9 0.26
18 4 0.11
19 2 0.06
20 1 0.03
21 6 0.17
22 13 0.37
ACGTcount: A:0.48, C:0.22, G:0.03, T:0.27
Consensus pattern (21 bp):
TAATCACATAACATTCAAGCA
Found at i:52714866 original size:33 final size:34
Alignment explanation
Indices: 52714820--52714894 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
52714810 GCATGGGAGA
*
52714820 TTTCTTTTCTTTTT-TCCATATTTTTCATTTTCCT
1 TTTCTTTTCTTTTTCTCCATATTTTTC-TTTCCCT
* *
52714854 TTTC-TTTCTTTTTCTCCTTCTTTTTCTTTCCCT
1 TTTCTTTTCTTTTTCTCCATATTTTTCTTTCCCT
*
52714887 TTTATTTT
1 TTTCTTTT
52714895 TTGATGACCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 18 0.51
34 17 0.49
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (34 bp):
TTTCTTTTCTTTTTCTCCATATTTTTCTTTCCCT
Found at i:52717960 original size:21 final size:19
Alignment explanation
Indices: 52717914--52717967 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
52717904 CAAATCAGGT
*
52717914 AAAAGAAAGAG-AAATGAA
1 AAAAGAAAGAGAAAAGGAA
*
52717932 AAATGAAAGAGAACAAGGAAA
1 AAAAGAAAGAGAA-AAGG-AA
52717953 AAAAGAAAGAGAAAA
1 AAAAGAAAGAGAAAA
52717968 ATTAAAAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.33
19 1 0.03
20 5 0.17
21 14 0.47
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (19 bp):
AAAAGAAAGAGAAAAGGAA
Found at i:52717974 original size:21 final size:20
Alignment explanation
Indices: 52717914--52717974 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 20
52717904 CAAATCAGGT
*
52717914 AAAAGAAAGAG--AAATGAA
1 AAAAGAAAGAGAAAAATAAA
* **
52717932 AAATGAAAGAGAACAAGGAAA
1 AAAAGAAAGAGAA-AAATAAA
*
52717953 AAAAGAAAGAGAAAAATTAA
1 AAAAGAAAGAGAAAAATAAA
52717973 AA
1 AA
52717975 GGAAATGAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 10 0.31
20 6 0.19
21 16 0.50
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.07
Consensus pattern (20 bp):
AAAAGAAAGAGAAAAATAAA
Found at i:52720284 original size:32 final size:30
Alignment explanation
Indices: 52720224--52720337 Score: 97
Period size: 32 Copynumber: 3.6 Consensus size: 30
52720214 GGTTGGTGCA
*
52720224 TATATAATATAA-ATATGTGTGCATGTTTTTGT
1 TATAT-ATATAATATATATG-GCATG-TTTTGT
*
52720256 TATATATATAATATATATGCGCAAGTTTTGT
1 TATATATATAATATATATG-GCATGTTTTGT
* * *
52720287 GT-TATATGTAATATATATAGGCGTGGCTTTGT
1 -TATATATATAATATATAT-GGCAT-GTTTTGT
*
52720319 TATATAGATAATATATATG
1 TATATATATAATATATATG
52720338 TGTGTTGGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
31 31 0.46
32 37 0.54
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (30 bp):
TATATATATAATATATATGGCATGTTTTGT
Found at i:52720452 original size:22 final size:22
Alignment explanation
Indices: 52720421--52720472 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
52720411 ATACATATAT
52720421 TATATTATATG-AGTGGGTCTTAC
1 TATA-TATATGCA-TGGGTCTTAC
*
52720444 TATATATATGCATGGGTCTTAT
1 TATATATATGCATGGGTCTTAC
52720466 TATATAT
1 TATATAT
52720473 TATAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (22 bp):
TATATATATGCATGGGTCTTAC
Found at i:52721630 original size:51 final size:51
Alignment explanation
Indices: 52721563--52721671 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
52721553 TATGATGGAG
* * * *
52721563 TATGAATTGTTATTTTGCATAAACTATTATTCGGTATGAACTGATATTTCA
1 TATGAACTATTATTTTGCATAAACTATCATTCGGTATGAACTGATATTTAA
* * * * *
52721614 TGTGAACTATTATTTTGCATGAGCTATCATTTGGTATGAACTGTTATTTAA
1 TATGAACTATTATTTTGCATAAACTATCATTCGGTATGAACTGATATTTAA
52721665 TATGAAC
1 TATGAAC
52721672 AAATGTTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (51 bp):
TATGAACTATTATTTTGCATAAACTATCATTCGGTATGAACTGATATTTAA
Found at i:52721662 original size:17 final size:17
Alignment explanation
Indices: 52721584--52721662 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 17
52721574 ATTTTGCATA
*
52721584 AACTATTATTCGGTATG
1 AACTATTATTTGGTATG
** *
52721601 AACTGA-TATTTCATGTG
1 AACT-ATTATTTGGTATG
* *
52721618 AACTATTATTTTGCATG
1 AACTATTATTTGGTATG
* *
52721635 AGCTATCATTTGGTATG
1 AACTATTATTTGGTATG
*
52721652 AACTGTTATTT
1 AACTATTATTT
52721663 AATATGAACA
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
16 1 0.02
17 43 0.96
18 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.44
Consensus pattern (17 bp):
AACTATTATTTGGTATG
Found at i:52723351 original size:101 final size:101
Alignment explanation
Indices: 52723129--52723332 Score: 329
Period size: 101 Copynumber: 2.0 Consensus size: 101
52723119 ATGCATTTGT
*
52723129 ATCATTCAAGAGCATATGCATGTAGTTATTTTAGTCACGAAACTATAATCATATTTTATTGATAT
1 ATCATTCCAGAGCATATGCATGTAGTTATTTTAGTCACGAAACTATAATCATATTTTATTGATAT
* *
52723194 CGTAATAACATTTGCAGTTGTTTATGAAGCATTCGC
66 CATAATAACATTTGCAGCTGTTTATGAAGCATTCGC
* * *
52723230 ATCATTCCAGAGCATATGCATGTGGTTATTTTAGTCATGAAACTATAATCATATTTTATTGTTAT
1 ATCATTCCAGAGCATATGCATGTAGTTATTTTAGTCACGAAACTATAATCATATTTTATTGATAT
*
52723295 CATAATAACATTTGCA-CTGCTTTATGAAGCATTTGC
66 CATAATAACATTTGCAGCTG-TTTATGAAGCATTCGC
52723331 AT
1 AT
52723333 TATCTTGGAT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 2 0.02
101 93 0.98
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (101 bp):
ATCATTCCAGAGCATATGCATGTAGTTATTTTAGTCACGAAACTATAATCATATTTTATTGATAT
CATAATAACATTTGCAGCTGTTTATGAAGCATTCGC
Found at i:52723825 original size:90 final size:89
Alignment explanation
Indices: 52723607--52723898 Score: 261
Period size: 90 Copynumber: 3.2 Consensus size: 89
52723597 TCCTGGGTTC
* * * *
52723607 GCCTAGTAAGTCCTTTCAAATTCTGGTTCCACCCAAGTTCATTTCGAGATTTATAGTTTCT-CCG
1 GCCTAGTAAGTCCTTTCAAATTCTGGTTTCACCCAGGTTC-TTTCGAAATTTATAGTTT-TGCCC
* *
52723671 AAGTCCATTATCAAAGTTATGGTTTCAT
64 AAGTCCATTGTCGAAGTTATGGTTT--T
* * *
52723699 -CC-AGTAAGTCCTTTCAAATTCTTG-TTCGGCCCAGGTT-TGTTCTGAAAGTTATAGTTTTGCC
1 GCCTAGTAAGTCCTTTCAAATTCTGGTTTC-ACCCAGGTTCT-TTC-GAAATTTATAGTTTTGCC
*
52723760 CAAGTCCATTGTCGAAGTTCTGGTTTT
63 CAAGTCCATTGTCGAAGTTATGGTTTT
** * * * * * *
52723787 GCCTAGTAAGTCCTTTCAAATTCTGGTTTCTTCTAGGTTCTTTCCAATATTTCTGGTTCTGCCTA
1 GCCTAGTAAGTCCTTTCAAATTCTGGTTTCACCCAGGTTCTTTCGAA-ATTTATAGTTTTGCCCA
* * * *
52723852 GGTCCGTTGTTGAAGTTTTGGTTTT
65 AGTCCATTGTCGAAGTTATGGTTTT
* *
52723877 GCGTAGTAAGTCCTTTGAAATT
1 GCCTAGTAAGTCCTTTCAAATT
52723899 TTGATTTCGC
Statistics
Matches: 165, Mismatches: 26, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
88 2 0.01
89 10 0.06
90 147 0.89
91 6 0.04
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (89 bp):
GCCTAGTAAGTCCTTTCAAATTCTGGTTTCACCCAGGTTCTTTCGAAATTTATAGTTTTGCCCAA
GTCCATTGTCGAAGTTATGGTTTT
Found at i:52723996 original size:30 final size:30
Alignment explanation
Indices: 52723917--52724002 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 30
52723907 GCTCACTTCT
* **
52723917 ATTGTCGAAGTTCTGGTTTCACCCAGGTCC
1 ATTGTCGAAGTTTTGGTTTTGCCCAGGTCC
*
52723947 ATTGTCGAAGTTTTGGTTTTGTCCAGGTCC
1 ATTGTCGAAGTTTTGGTTTTGCCCAGGTCC
*
52723977 ATTGTTGAAGTTTTGGTTTTGCCCAG
1 ATTGTCGAAGTTTTGGTTTTGCCCAG
52724003 TAACTCCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.41
Consensus pattern (30 bp):
ATTGTCGAAGTTTTGGTTTTGCCCAGGTCC
Found at i:52724114 original size:30 final size:30
Alignment explanation
Indices: 52724074--52724144 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
52724064 TTAATTCTCG
52724074 AATTTCTGGTTTTAC-CCAGGTCCA-TTGTCA
1 AATTT-TGGTTTT-CGCCAGGTCCATTTGTCA
* *
52724104 AAGTTTTGG-TTTCGCCAGGTCTATTTTTCA
1 AA-TTTTGGTTTTCGCCAGGTCCATTTGTCA
52724134 AATTTTGGTTT
1 AATTTTGGTTT
52724145 CGTCCAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
28 1 0.03
29 17 0.49
30 14 0.40
31 3 0.09
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.46
Consensus pattern (30 bp):
AATTTTGGTTTTCGCCAGGTCCATTTGTCA
Found at i:52724123 original size:29 final size:30
Alignment explanation
Indices: 52724089--52724151 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
52724079 CTGGTTTTAC
52724089 CCAGGTCCA-TTGTCAAAGTTTTGGTTTCG-
1 CCAGGTCCATTTGTCAAA-TTTTGGTTTCGT
* *
52724118 CCAGGTCTATTTTTCAAATTTTGGTTTCGT
1 CCAGGTCCATTTGTCAAATTTTGGTTTCGT
52724148 CCAG
1 CCAG
52724152 TAAGTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (30 bp):
CCAGGTCCATTTGTCAAATTTTGGTTTCGT
Found at i:52724498 original size:78 final size:78
Alignment explanation
Indices: 52724410--52724553 Score: 191
Period size: 78 Copynumber: 1.8 Consensus size: 78
52724400 GTCAAACTTG
* * * * **
52724410 TTTTCAAAAATAGGTTGAGCCTGGGGATTGTTATTGAGGTCCTTTTAGTGTTTTTTCA-TTTTAT
1 TTTTCAAAAATAGGTTGAACCTCGAGATTGTCATCAAGGTCCTTTTAGT-TTTTTTCATTTTTAT
52724474 TAGGGTTGAATTCA
65 TAGGGTTGAATTCA
* * *
52724488 TTTTCGAAAATGGGTTGAACCTCGAGATTGTCGTCAAGGTCCTTTTAGTTTTTTTCATTTTTATT
1 TTTTCAAAAATAGGTTGAACCTCGAGATTGTCATCAAGGTCCTTTTAGTTTTTTTCATTTTTATT
52724553 A
66 A
52724554 AAAGTTAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 8 0.14
78 48 0.86
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.47
Consensus pattern (78 bp):
TTTTCAAAAATAGGTTGAACCTCGAGATTGTCATCAAGGTCCTTTTAGTTTTTTTCATTTTTATT
AGGGTTGAATTCA
Found at i:52724610 original size:79 final size:77
Alignment explanation
Indices: 52724446--52724617 Score: 202
Period size: 79 Copynumber: 2.2 Consensus size: 77
52724436 ATTGTTATTG
** * * * * * *
52724446 AGGTCCTTTTAGTGTTTTTTCATTTTATTAGGGTTGAATTCATTTTCGAAAATGGGTTGAACCTC
1 AGGTCCTTTTAGT-TTTTTTCATTTTATTAAAGTTAAATCCATTTCCAAAAATGGATTCAACCTC
52724511 GAGATTGTCGTCA
65 GAGATTGTCGTCA
*
52724524 AGGTCCTTTTAGTTTTTTTCATTTTTATTAAAAGTTAAATCCATTTCCAAAAATGGATTCAGCCT
1 AGGTCCTTTTAGTTTTTTTCA-TTTTATT-AAAGTTAAATCCATTTCCAAAAATGGATTCAACCT
*
52724589 CGAGATTG-CGGTCG
64 CGAGATTGTC-GTCA
*
52724603 AGTTCCTTTTAGTTT
1 AGGTCCTTTTAGTTT
52724618 GATTTTGTCA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
77 8 0.10
78 21 0.26
79 51 0.64
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (77 bp):
AGGTCCTTTTAGTTTTTTTCATTTTATTAAAGTTAAATCCATTTCCAAAAATGGATTCAACCTCG
AGATTGTCGTCA
Found at i:52727596 original size:32 final size:32
Alignment explanation
Indices: 52727555--52727619 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
52727545 AAACTTCATA
*
52727555 ATCTGCAAGGGAGAGGGAAAGAGAGATTTCTT
1 ATCTGCAAGGGAGAGGAAAAGAGAGATTTCTT
52727587 ATCTGCAAGGGAGAGGAAAAGAGAGATTTCTT
1 ATCTGCAAGGGAGAGGAAAAGAGAGATTTCTT
52727619 A
1 A
52727620 CCTGAGTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.09, G:0.32, T:0.22
Consensus pattern (32 bp):
ATCTGCAAGGGAGAGGAAAAGAGAGATTTCTT
Found at i:52727970 original size:19 final size:17
Alignment explanation
Indices: 52727931--52727973 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
52727921 ACCTAAAAAT
*
52727931 TAAATATAATTAAAATAA
1 TAAA-ATAATAAAAATAA
52727949 TAAAATAATAAAAAGTATA
1 TAAAATAATAAAAA-TA-A
52727968 TAAAAT
1 TAAAAT
52727974 TGGGTCTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAATAATAAAAATAA
Found at i:52728402 original size:16 final size:15
Alignment explanation
Indices: 52728377--52728411 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
52728367 TCTGATGTGA
52728377 GAAAAGTACAGTGTT
1 GAAAAGTACAGTGTT
52728392 GAAATAGTACAGTGTT
1 GAAA-AGTACAGTGTT
52728408 GAAA
1 GAAA
52728412 CAAGCACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (15 bp):
GAAAAGTACAGTGTT
Found at i:52736264 original size:10 final size:9
Alignment explanation
Indices: 52736246--52736288 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
52736236 GTTAGTGAAC
52736246 AAAATAAAT
1 AAAATAAAT
52736255 AAATATAAAT
1 AAA-ATAAAT
*
52736265 AAACATATAT
1 AAA-ATAAAT
52736275 AAAATAAAAT
1 AAAAT-AAAT
52736285 AAAA
1 AAAA
52736289 ATAGAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAATAAAT
Found at i:52737543 original size:725 final size:729
Alignment explanation
Indices: 52736104--52737562 Score: 2554
Period size: 725 Copynumber: 2.0 Consensus size: 729
52736094 AAGTGTATCT
*
52736104 AGGGTTGAGTGGTCAACAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
1 AGGGTTGAATGGTCAACAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
* * *
52736169 TGCAGACTTAGAGACATAATTTTTCCTATTCAATTTTTTTTTATATTTTCTTTGTTGGACAAAAC
66 TACAGACTTAGAGACATAATTTTTCCTATTCAA--TGTTTTTATATTTTCTTTGTTGGAAAAAAC
* * *
52736234 ACGTTAGTGAACAAAATAAATAAATATAAATAAACATATATAAAATAAAATAAAAATAGAATAAT
129 ACATTAGCGAACAAAATAAATAAATAAAAATAAACATATATAAAATAAAATAAAAATAGAATAAT
* *
52736299 TTATATTTAATTTTTCAAATACGAAAAACAATCAAAACCGTAATAAAAGTTGAAATCAAAAGGGA
194 TTATATTTAATTTTTCAAATACGAAAAACAATCAAAACCATAACAAAAGTTGAAATCAAAAGGGA
*
52736364 GAATAGAGATTTTACTAAATGTTTAGGCCTGTTAAAAACAATTTCCTTAAGACATATTCATTCAC
259 GAATAAAGATTTTACTAAATGTTTAGGCCTGTTAAAAACAATTTCCTTAAGACATATTCATTCAC
*
52736429 TCCTATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAGGATACAACAAGAACAATGACCAAA
324 TCCTATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAAGATACAACAAGAACAATGACCAAA
* ** *
52736494 GCAGTAGCACCTCTGCAGCGATTTACGAACAAACGATGTCTTTTTCTATCATCGGAACATTTGAA
389 GCAGTAGCACCTCTACAGCGATCAACGAACAAACGACGTCTTTTTCTATCATCGGAACATTTGAA
*
52736559 AAATATAGAGAGGAAAAGAAAATTTTTGAGAGAAACAAAATTTCGGTGTGAAAGAATATTAGAGT
454 AAATATAGAGAGGAAAAGAAAAGTTTTGAGAGAAACAAAATTTCGGTGTGAAAGAATATTAGAGT
52736624 GTCTAATACTACAGAATTTGTAGCCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTTC
519 GTCTAATACTACAGAATTTGTAGCCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTTC
52736689 CACAAAATCTGCCATTAATGAACAAATAAATCAAATTTGATTTAAAGATTAAATCAAATTTATTG
584 CACAAAATCTGCCATTAATGAACAAATAAATCAAATTTGATTTAAAGATTAAATCAAATTTATTG
* *
52736754 GAATCAAATAAATAAGATAAATGTCCTTATATAAACAGATTATGTAGGAAAAGTAATTTTGTGTT
649 GAATCAAATAAATAAGATAAATGTCATTATATAAACAGATTATGTAGGAAAAATAATTTTGTGTT
52736819 GAGCTAAAATATCCGC
714 GAGCTAAAATATCCGC
*
52736835 AGGGTTGAATGGTCACCAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
1 AGGGTTGAATGGTCAACAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
*
52736900 TACAGACTTAGAGACATAATTTTTCCTATTC-A-GTTTTT-T-TTTTCTTTGTTGGAAAAAATAC
66 TACAGACTTAGAGACATAATTTTTCCTATTCAATGTTTTTATATTTTCTTTGTTGGAAAAAACAC
52736961 ATTAGCGAACAAAATAAATAAATAAAAATAAACATATATAAAAT-AAATAAAAATAGAATAATTT
131 ATTAGCGAACAAAATAAATAAATAAAAATAAACATATATAAAATAAAATAAAAATAGAATAATTT
52737025 ATATTTAATTTTTCAAATACGAAAAACAATCAAAACCATAACAAAAGTTGAAATCAAAAGGGAGA
196 ATATTTAATTTTTCAAATACGAAAAACAATCAAAACCATAACAAAAGTTGAAATCAAAAGGGAGA
52737090 ATAAAGATTTTACTAAATGTTTAGGCCTGTTAAAAACAATTTCCTTAAGACATATTCATTCACTC
261 ATAAAGATTTTACTAAATGTTTAGGCCTGTTAAAAACAATTTCCTTAAGACATATTCATTCACTC
52737155 CTATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAAGATACAACAAGAACAATGACCAAAGC
326 CTATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAAGATACAACAAGAACAATGACCAAAGC
52737220 AGTAGCACCTCTACAGCGATCAACGAACAAACGACGTCTTTTTCTATCA-CTGGAACATTT-AAC
391 AGTAGCACCTCTACAGCGATCAACGAACAAACGACGTCTTTTTCTATCATC-GGAACATTTGAA-
* *
52737283 AAATATAGAGAGGAAAAAGAAAAGTTTTGAGAGAAACAGAATTTTGGTGTGAAAGAATATTAGAG
454 AAATATAGAGAGG-AAAAGAAAAGTTTTGAGAGAAACAAAATTTCGGTGTGAAAGAATATTAGAG
* *
52737348 TGTCTAATACTGCAGAATTTGTAGTCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTT
518 TGTCTAATACTACAGAATTTGTAGCCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTT
* * *
52737413 CCACAAAATCTGTCATTAATGAGCAAATAAATCAAATTTGATTTAAAGATTAAATCAATTTTATT
583 CCACAAAATCTGCCATTAATGAACAAATAAATCAAATTTGATTTAAAGATTAAATCAAATTTATT
* *
52737478 GGAATCAAATAAATAAGATAAATGTCATTATATAAATAGATTATGTATGAAAAATAATTTTGTGT
648 GGAATCAAATAAATAAGATAAATGTCATTATATAAACAGATTATGTAGGAAAAATAATTTTGTGT
*
52737543 TGAGCTAAAATATCTGC
713 TGAGCTAAAATATCCGC
52737560 AGG
1 AGG
52737563 TCCACTCTAG
Statistics
Matches: 695, Mismatches: 30, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
723 3 0.00
724 278 0.40
725 314 0.45
726 1 0.00
727 5 0.01
730 1 0.00
731 93 0.13
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (729 bp):
AGGGTTGAATGGTCAACAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
TACAGACTTAGAGACATAATTTTTCCTATTCAATGTTTTTATATTTTCTTTGTTGGAAAAAACAC
ATTAGCGAACAAAATAAATAAATAAAAATAAACATATATAAAATAAAATAAAAATAGAATAATTT
ATATTTAATTTTTCAAATACGAAAAACAATCAAAACCATAACAAAAGTTGAAATCAAAAGGGAGA
ATAAAGATTTTACTAAATGTTTAGGCCTGTTAAAAACAATTTCCTTAAGACATATTCATTCACTC
CTATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAAGATACAACAAGAACAATGACCAAAGC
AGTAGCACCTCTACAGCGATCAACGAACAAACGACGTCTTTTTCTATCATCGGAACATTTGAAAA
ATATAGAGAGGAAAAGAAAAGTTTTGAGAGAAACAAAATTTCGGTGTGAAAGAATATTAGAGTGT
CTAATACTACAGAATTTGTAGCCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTTCCA
CAAAATCTGCCATTAATGAACAAATAAATCAAATTTGATTTAAAGATTAAATCAAATTTATTGGA
ATCAAATAAATAAGATAAATGTCATTATATAAACAGATTATGTAGGAAAAATAATTTTGTGTTGA
GCTAAAATATCCGC
Found at i:52746359 original size:28 final size:29
Alignment explanation
Indices: 52746290--52746362 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 29
52746280 TAGTAGTAGT
*
52746290 GTGTGGGCCATAGCCCAATACAGTAACAGA
1 GTGTGGGCCTTAGCCCAATACAGTAACA-A
52746320 GTGTGGGCCTTAGCCCAATACAGTAAC-A
1 GTGTGGGCCTTAGCCCAATACAGTAACAA
*
52746348 GTGTGGGTCTTAGCC
1 GTGTGGGCCTTAGCC
52746363 TAAAATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 15 0.37
30 26 0.63
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (29 bp):
GTGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:52746508 original size:26 final size:25
Alignment explanation
Indices: 52746479--52746534 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
52746469 GCCAACACAT
* *
52746479 CGTAGCAAAGTTTCCAGTAATAATAA
1 CGTAGCAAAGTTGCCAG-AACAATAA
*
52746505 CGTAGCAAAGTTGCCAGAACAGTAA
1 CGTAGCAAAGTTGCCAGAACAATAA
52746530 CGTAG
1 CGTAG
52746535 TAGAGCTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (25 bp):
CGTAGCAAAGTTGCCAGAACAATAA
Found at i:52746772 original size:27 final size:27
Alignment explanation
Indices: 52746742--52746829 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 27
52746732 TCAATTCCTA
52746742 GGGGTATAACAGTCATTTTACCCTAT-G
1 GGGGTATAACAGTCATTTTACCCT-TCG
** *
52746769 GGGGTATTTCGGTCATTTTACCCTTCG
1 GGGGTATAACAGTCATTTTACCCTTCG
** * *
52746796 GGGGTATTTCGGTCATTTTAACCTTCG
1 GGGGTATAACAGTCATTTTACCCTTCG
*
52746823 AGGGTAT
1 GGGGTAT
52746830 TTTGATCATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.02
27 54 0.98
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (27 bp):
GGGGTATAACAGTCATTTTACCCTTCG
Found at i:52746830 original size:27 final size:27
Alignment explanation
Indices: 52746753--52746969 Score: 250
Period size: 27 Copynumber: 8.2 Consensus size: 27
52746743 GGGTATAACA
52746753 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
52746780 GTCATTTTACCCT-TCGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* * *
52746807 GTCATTTTAACCT-TCGAGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* ** *
52746834 ATCATTTTACCCT-TCAAGGGTATTTCT
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* *
52746861 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
52746888 G----TTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
52746911 GTTATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
52746938 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
52746965 GTCAT
1 GTCAT
52746970 ATATCGACTT
Statistics
Matches: 167, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
23 22 0.13
26 1 0.01
27 143 0.86
28 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:52753381 original size:47 final size:47
Alignment explanation
Indices: 52753236--52753509 Score: 422
Period size: 47 Copynumber: 5.7 Consensus size: 47
52753226 ATTTGGATAA
52753236 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
52753285 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
52753334 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
52753381 ATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
52753428 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
52753475 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
52753510 TCCCGAAGGG
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
47 142 0.67
49 69 0.33
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:52755795 original size:40 final size:40
Alignment explanation
Indices: 52755730--52756050 Score: 439
Period size: 40 Copynumber: 8.1 Consensus size: 40
52755720 AGGTCTCGAC
*
52755730 GATG-ATCTGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
52755769 GATGTATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52755809 GATGTACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
52755849 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
52755889 GATGTATCCGGACTAAGTCCCGAAGAGTATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
52755929 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * * *
52755969 AATATATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCC-CGAAGAGCATTCATGCTAGT
* * * * *
52756009 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
52756049 GA
1 GA
52756051 CGTGTATTCG
Statistics
Matches: 250, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 5 0.02
40 243 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:52759688 original size:49 final size:47
Alignment explanation
Indices: 52759455--52759916 Score: 739
Period size: 47 Copynumber: 9.7 Consensus size: 47
52759445 ATTTGGATAA
52759455 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG-CG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
52759503 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
52759550 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
52759596 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
52759643 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
52759692 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
52759741 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
52759788 ATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
52759835 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
52759882 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
52759917 TCCCGAAGGG
Statistics
Matches: 392, Mismatches: 18, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
46 69 0.18
47 209 0.53
48 20 0.05
49 94 0.24
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:52762588 original size:16 final size:16
Alignment explanation
Indices: 52762550--52762600 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
52762540 TGAATTATTG
* * *
52762550 ATTACAACTCTGTTCT
1 ATTACAGCTCTATTCC
52762566 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* *
52762582 ATTACAGCTATATTTC
1 ATTACAGCTCTATTCC
52762598 ATT
1 ATT
52762601 CCCCCCAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:52763961 original size:3 final size:3
Alignment explanation
Indices: 52763953--52763989 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
52763943 TATTTTCATT
52763953 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
52763990 ACGGGATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:52764152 original size:15 final size:14
Alignment explanation
Indices: 52764115--52764148 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
52764105 AACTTTAAAT
*
52764115 TATTTTTA-CAAAA
1 TATTTTTATAAAAA
52764128 TATTTTTATAAAAA
1 TATTTTTATAAAAA
52764142 TATTTTT
1 TATTTTT
52764149 TATATAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTTTATAAAAA
Found at i:52765560 original size:14 final size:15
Alignment explanation
Indices: 52765530--52765570 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
52765520 TAAATAATGC
52765530 TAAAAATA-ATTTCTA
1 TAAAAATATA-TTCTA
52765545 TAAAAATATATT-TA
1 TAAAAATATATTCTA
*
52765559 TAAAAATTTATT
1 TAAAAATATATT
52765571 AATCAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 10 0.42
16 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAAATATATTCTA
Found at i:52769011 original size:14 final size:14
Alignment explanation
Indices: 52768994--52769034 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
52768984 CTTAGCCGCC
52768994 TATATTAATTTTTT
1 TATATTAATTTTTT
52769008 TATATT-ATTATTTT
1 TATATTAATT-TTTT
52769022 TATA-TAATTTTTT
1 TATATTAATTTTTT
52769035 AAAAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATATTAATTTTTT
Found at i:52798888 original size:26 final size:25
Alignment explanation
Indices: 52798859--52798920 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
52798849 AAATAAAACT
*
52798859 AAAAGAAAAAAATATACTCTAAAAA-G
1 AAAAGAAAAAAATA-A-ACTAAAAATG
**
52798885 AAAAGAGAAAACCTAAACTAAAAATG
1 AAAAGA-AAAAAATAAACTAAAAATG
52798911 AAAAGAAAAA
1 AAAAGAAAAA
52798921 GAAAAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 11 0.35
26 14 0.45
27 6 0.19
ACGTcount: A:0.71, C:0.08, G:0.10, T:0.11
Consensus pattern (25 bp):
AAAAGAAAAAAATAAACTAAAAATG
Found at i:52799355 original size:10 final size:10
Alignment explanation
Indices: 52799327--52799370 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
52799317 AGACAAGTAT
52799327 TTTTATTAAG
1 TTTTATTAAG
*
52799337 TTTTAATTATG
1 TTTT-ATTAAG
52799348 TTTTATTAAG
1 TTTTATTAAG
*
52799358 TTCTATTTAAG
1 TTTTA-TTAAG
52799369 TT
1 TT
52799371 AATAAAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 13 0.45
11 16 0.55
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (10 bp):
TTTTATTAAG
Found at i:52805675 original size:21 final size:21
Alignment explanation
Indices: 52805626--52805678 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
52805616 ACCACCTACT
52805626 CTTGAGACTTAGGATCTAAGC
1 CTTGAGACTTAGGATCTAAGC
* *
52805647 CTTAAGACTTATGG-TCTAAGT
1 CTTGAGACTTA-GGATCTAAGC
*
52805668 TTTGAGACTTA
1 CTTGAGACTTA
52805679 CTCCATTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (21 bp):
CTTGAGACTTAGGATCTAAGC
Found at i:52813112 original size:15 final size:15
Alignment explanation
Indices: 52813092--52813124 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52813082 ACTGAACTTA
52813092 CAACTGCACCTAAAT
1 CAACTGCACCTAAAT
*
52813107 CAACTGCACCTATAT
1 CAACTGCACCTAAAT
52813122 CAA
1 CAA
52813125 AGCAAGATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.21
Consensus pattern (15 bp):
CAACTGCACCTAAAT
Found at i:52824251 original size:5 final size:5
Alignment explanation
Indices: 52824243--52824271 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
52824233 TTGATTATCT
52824243 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
52824272 TTCAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:52836892 original size:16 final size:16
Alignment explanation
Indices: 52836871--52836938 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
52836861 TTTGGTTCGC
52836871 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
52836887 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
52836903 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52836919 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52836935 TGTA
1 TGTA
52836939 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:52837191 original size:16 final size:16
Alignment explanation
Indices: 52837154--52837195 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52837144 TTAATCATAT
*
52837154 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
52837170 TT-AAATATATTATAA
1 TTAAAATATATTATAA
52837185 TTAAAATATAT
1 TTAAAATATAT
52837196 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:52837202 original size:14 final size:15
Alignment explanation
Indices: 52837163--52837204 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52837153 TTTAAACATA
*
52837163 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52837178 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52837192 A-TATAATTTAATA
1 ATTATAATTAAATA
52837205 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:52837399 original size:26 final size:28
Alignment explanation
Indices: 52837370--52837430 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
52837360 CATGAATTTG
*
52837370 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
52837396 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
52837424 TAAAATT
1 TATAATT
52837431 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:52845183 original size:25 final size:27
Alignment explanation
Indices: 52845123--52845193 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 27
52845113 AATACTCTTA
*
52845123 CGAGCACATA-AATAGGAAGCTCTCTCT
1 CGAGC-CATATAACAGGAAGCTCTCTCT
* *
52845150 CGAGTCATATAACAGGAAGCTCT-TGT
1 CGAGCCATATAACAGGAAGCTCTCTCT
*
52845176 -GAGCCATATAACGGGAAG
1 CGAGCCATATAACAGGAAG
52845194 TTTATCCGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
25 16 0.42
26 6 0.16
27 16 0.42
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (27 bp):
CGAGCCATATAACAGGAAGCTCTCTCT
Found at i:52845380 original size:26 final size:26
Alignment explanation
Indices: 52845338--52845403 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
52845328 CCCATATCGG
52845338 GAAGCTCT-GAAGAGCCATTAATCAA
1 GAAGCTCTCGAAGAGCCATTAATCAA
* *
52845363 GAAGCTCTCAAAGAGCCATTAATCGA
1 GAAGCTCTCGAAGAGCCATTAATCAA
52845389 GAAGCTC-CGAAGAGC
1 GAAGCTCTCGAAGAGC
52845404 TACGGTGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 15 0.41
26 22 0.59
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
GAAGCTCTCGAAGAGCCATTAATCAA
Found at i:52847788 original size:30 final size:30
Alignment explanation
Indices: 52847748--52847854 Score: 115
Period size: 30 Copynumber: 3.6 Consensus size: 30
52847738 TCTGGGCCTG
* * *
52847748 AGCCCTATACAGTAGCAGTGTATAGGCCAT
1 AGCCCAATACAGTAACAGAGTATAGGCCAT
* * *
52847778 AGCTCAATACAGTAACAGAGTGTAGGCCTT
1 AGCCCAATACAGTAACAGAGTATAGGCCAT
* * * *
52847808 AGCCCAATACAGTAACAGAGTGTTGGTCTT
1 AGCCCAATACAGTAACAGAGTATAGGCCAT
*
52847838 AGCCCAATACAATAACA
1 AGCCCAATACAGTAACA
52847855 TTGCAAATGC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (30 bp):
AGCCCAATACAGTAACAGAGTATAGGCCAT
Found at i:52847992 original size:26 final size:26
Alignment explanation
Indices: 52847964--52848091 Score: 114
Period size: 26 Copynumber: 4.9 Consensus size: 26
52847954 CACCAATATC
* *
52847964 GCAGCAAAGCTACCAGTAATAGTAAC
1 GCAGCAAAGCTGCCAGTAATAGTAAT
* *
52847990 GCAGTAAAGCTGCCAGTAACAGTAAT
1 GCAGCAAAGCTGCCAGTAATAGTAAT
* * * *
52848016 ACAGCAGAGCCGCCAGTAACAGTAAT
1 GCAGCAAAGCTGCCAGTAATAGTAAT
*
52848042 GCAGCAGAGCTGCCAGT-ATCAGTAAT
1 GCAGCAAAGCTGCCAGTAAT-AGTAAT
* ** * *
52848068 GTAAAAAAGCTACCAATAATAGTA
1 GCAGCAAAGCTGCCAGTAATAGTA
52848092 TTTGTGGCAA
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
25 1 0.01
26 80 0.96
27 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAATAGTAAT
Done.