Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 179 of 279
Found at i:58819066 original size:39 final size:39
Alignment explanation
Indices: 58819019--58819096 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
58819009 TAAATTACAT
*
58819019 AACTTACATAACTCATATAACTCACATAACTTACATAAC
1 AACTTACATAACTCACATAACTCACATAACTTACATAAC
* *
58819058 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTCACATAACTTACATAAC
58819097 TCACATAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTCACATAACTTACATAAC
Found at i:58819070 original size:48 final size:48
Alignment explanation
Indices: 58819013--58819105 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
58819003 CTTAAATAAA
* * *
58819013 TTACATAACTTACATAACTCATATAACTCACATAACTTACATAACAAC
1 TTACATAACTCACATAACTCACATAACTCACATAACTCACATAACAAC
* * *
58819061 TTACATAACTCACATAACTTACATAATTTACATAACTCACATAAC
1 TTACATAACTCACATAACTCACATAACTCACATAACTCACATAAC
58819106 GTACATAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (48 bp):
TTACATAACTCACATAACTCACATAACTCACATAACTCACATAACAAC
Found at i:58819096 original size:57 final size:57
Alignment explanation
Indices: 58819015--58819126 Score: 188
Period size: 57 Copynumber: 2.0 Consensus size: 57
58819005 TAAATAAATT
* *
58819015 ACATAACTTACATAACTCATATAACTCACATAACTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
58819072 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAAC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAAC
58819127 CTAACTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:58819110 original size:27 final size:27
Alignment explanation
Indices: 58819015--58819114 Score: 137
Period size: 27 Copynumber: 3.6 Consensus size: 27
58819005 TAAATAAATT
* *
58819015 ACATAACTTACATAACTCATATAACTC
1 ACATAACTTACATAACTTACATAACTC
58819042 ACATAACTTACATAACAACTTACATAACTC
1 ACATAACTTACAT---AACTTACATAACTC
*
58819072 ACATAACTTACATAATTTACATAACTC
1 ACATAACTTACATAACTTACATAACTC
*
58819099 ACATAACGTACATAAC
1 ACATAACTTACATAAC
58819115 AACTTACATA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
27 40 0.62
30 25 0.38
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (27 bp):
ACATAACTTACATAACTTACATAACTC
Found at i:58827347 original size:31 final size:33
Alignment explanation
Indices: 58827281--58827348 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
58827271 TTAGAATTAA
* *
58827281 TGTTTTTGGTTGTATTTTTTTATACTAAATTTGT
1 TGTTTTTGGCTGCATTTTTTTATA-TAAATTTGT
*
58827315 TGTTTTTGGCTGCA-TTTTTTAT-TATATTTGT
1 TGTTTTTGGCTGCATTTTTTTATATAAATTTGT
58827346 TGT
1 TGT
58827349 ATTTAGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.35
33 8 0.26
34 12 0.39
ACGTcount: A:0.15, C:0.04, G:0.16, T:0.65
Consensus pattern (33 bp):
TGTTTTTGGCTGCATTTTTTTATATAAATTTGT
Found at i:58827476 original size:18 final size:18
Alignment explanation
Indices: 58827450--58827484 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58827440 GCCGCTAAAA
58827450 GCCGCGACTTTTAGCGGT
1 GCCGCGACTTTTAGCGGT
*
58827468 GCCGTGACTTTTAGCGG
1 GCCGCGACTTTTAGCGG
58827485 CGCTTTTCCC
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:0.11, C:0.26, G:0.34, T:0.29
Consensus pattern (18 bp):
GCCGCGACTTTTAGCGGT
Found at i:58827533 original size:43 final size:43
Alignment explanation
Indices: 58827472--58827657 Score: 268
Period size: 43 Copynumber: 4.3 Consensus size: 43
58827462 AGCGGTGCCG
58827472 TGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCT-AAAAGCCA
1 TGACTTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAAAGCCA
* * * *
58827515 TGACTTTTAGCGGCGCTTTCTCTCAAGCGCCGCTAAAAAGCCT
1 TGACTTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAAAGCCA
* *
58827558 TGACTTTTAGCGGCGCTTTCCCTCAAACGCCGCTAAAAAGCCT
1 TGACTTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAAAGCCA
* *
58827601 TGACTTTTAGCGGCACTTTTCCCAAAAACGCCGCT-AAAAGCCA
1 TGACTTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAAAGCCA
58827644 TGACTTTTAGCGGC
1 TGACTTTTAGCGGC
58827658 TTTTTTTTCA
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
42 15 0.11
43 100 0.76
44 16 0.12
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (43 bp):
TGACTTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAAAGCCA
Found at i:58835878 original size:260 final size:260
Alignment explanation
Indices: 58835417--58835931 Score: 960
Period size: 260 Copynumber: 2.0 Consensus size: 260
58835407 TTTAAACAAA
* *
58835417 AGGACCCGCGTGTCGACCCGACTCGGCCAAAGGATCAGCGTGTTTTTTGTTATTGGGCTGATTGC
1 AGGACCCGCGTGTCGACCCGACTCGGCCAAAGGATCAGCGTGTTTTTAGTTATTGGGCTAATTGC
58835482 CCAATTGGTCCTTCCGCATTTTTATCCTTTAAAATTAGGTTTATTTTATCTTTTAATTTTGCTCA
66 CCAATTGGTCCTTCCGCATTTTTATCCTTTAAAATTAGGTTTATTTTATCTTTTAATTTTGCTCA
* *
58835547 AATATTTTGTTTTTATTTTAATTTGGTCCTTGGGCTCTTTTAATAAAGAAAGCGCATAAACGATG
131 AATATTTTGTTTTTATTTTAATTTGGTCCTTGGGCTCTTGTAAAAAAGAAAGCGCATAAACGATG
58835612 TCGTTCTAAAAGGGGATATTTTCCGTTTTAATCCCCCTCCTTGTGCGCACATTTTAATTTTTTTT
196 TCGTTCTAAAAGGGGATATTTTCCGTTTTAATCCCCCTCCTTGTGCGCACATTTTAATTTTTTTT
* *
58835677 AGGACCCGCGTGTCGACCCGACTCGGCCAAAGGATCCGCGTGTTTTCTAG-TATTGGGCTAATTT
1 AGGACCCGCGTGTCGACCCGACTCGGCCAAAGGATCAGCGTGTTTT-TAGTTATTGGGCTAATTG
58835741 CCCAATTGGTCCTTCCGCATTTTTATCCTTTAAAATTAGGTTTATTTTATCTTTTAATTTTGCTC
65 CCCAATTGGTCCTTCCGCATTTTTATCCTTTAAAATTAGGTTTATTTTATCTTTTAATTTTGCTC
58835806 AAATATTTTGTTTTTATTTTAATTTGGTCCTTGGGCTCTTGTAAAAAAGAAAGCGCATAAACGAT
130 AAATATTTTGTTTTTATTTTAATTTGGTCCTTGGGCTCTTGTAAAAAAGAAAGCGCATAAACGAT
58835871 GTCGTTCTAAAAGGGGATATTTTCCGTTTTAATCCCCCTCCTTGTGCGCACATTTTAATTT
195 GTCGTTCTAAAAGGGGATATTTTCCGTTTTAATCCCCCTCCTTGTGCGCACATTTTAATTT
58835932 GACCCTTTTT
Statistics
Matches: 248, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
260 246 0.99
261 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (260 bp):
AGGACCCGCGTGTCGACCCGACTCGGCCAAAGGATCAGCGTGTTTTTAGTTATTGGGCTAATTGC
CCAATTGGTCCTTCCGCATTTTTATCCTTTAAAATTAGGTTTATTTTATCTTTTAATTTTGCTCA
AATATTTTGTTTTTATTTTAATTTGGTCCTTGGGCTCTTGTAAAAAAGAAAGCGCATAAACGATG
TCGTTCTAAAAGGGGATATTTTCCGTTTTAATCCCCCTCCTTGTGCGCACATTTTAATTTTTTTT
Found at i:58838188 original size:20 final size:18
Alignment explanation
Indices: 58838159--58838229 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 18
58838149 TAATGGTTAT
*
58838159 ATTTAAATATTTAAAATATA
1 ATTTATATATTT-AAATA-A
*
58838179 ATTTATATATTCTAATTAA
1 ATTTATATATT-TAAATAA
**
58838198 ATTT-TATAAATAAATAA
1 ATTTATATATTTAAATAA
58838215 TATTTAT-TATTTAAA
1 -ATTTATATATTTAAA
58838230 ATATTTAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
17 6 0.15
18 14 0.34
19 6 0.15
20 14 0.34
21 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTATATATTTAAATAA
Found at i:58838247 original size:22 final size:22
Alignment explanation
Indices: 58838216--58838261 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
58838206 AATAAATAAT
58838216 ATTTATTATTTAAAATATTTAAA
1 ATTTATTATTTAAAATA-TTAAA
* *
58838239 ATTTA-TATTTCATATATTAAA
1 ATTTATTATTTAAAATATTAAA
58838260 AT
1 AT
58838262 ATTAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTATTTAAAATATTAAA
Found at i:58839415 original size:24 final size:24
Alignment explanation
Indices: 58839363--58839412 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 24
58839353 ATTAATTACT
58839363 TTAAATAATTTAATTAAATTTAAA
1 TTAAATAATTTAATTAAATTTAAA
58839387 TTAAATAATTTAAATTAAATTTAAA
1 TTAAATAATTT-AATTAAATTTAAA
58839412 T
1 T
58839413 AAAGTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAAATAATTTAATTAAATTTAAA
Found at i:58839421 original size:10 final size:10
Alignment explanation
Indices: 58839362--58839434 Score: 58
Period size: 10 Copynumber: 6.8 Consensus size: 10
58839352 AATTAATTAC
58839362 TTTAAAT-AA
1 TTTAAATAAA
*
58839371 TTTAATTAAA
1 TTTAAATAAA
58839381 TTTAAATTAAATAA
1 TTTAAA-T--A-AA
58839395 TTTAAATTAAA
1 TTTAAA-TAAA
58839406 TTTAAATAAA
1 TTTAAATAAA
* *
58839416 GTTAAAAAAA
1 TTTAAATAAA
58839426 TATTAAATA
1 T-TTAAATA
58839435 TACATAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
9 6 0.12
10 19 0.37
11 15 0.29
12 1 0.02
13 1 0.02
14 10 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:58839431 original size:21 final size:22
Alignment explanation
Indices: 58839386--58839434 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
58839376 TTAAATTTAA
* *
58839386 ATTAAAT-AATTTAAATTAAAT
1 ATTAAATAAAGTTAAATAAAAT
58839407 -TTAAATAAAGTTAAA-AAAAT
1 ATTAAATAAAGTTAAATAAAAT
58839427 ATTAAATA
1 ATTAAATA
58839435 TACATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATTAAATAAAGTTAAATAAAAT
Found at i:58842392 original size:23 final size:23
Alignment explanation
Indices: 58842366--58842411 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
58842356 CTGTATCAAA
*
58842366 CCCAGAGGAGTTCATTCTGTCGG
1 CCCAGAGGAGATCATTCTGTCGG
58842389 CCCAGAGGAGATCATTCTGTCGG
1 CCCAGAGGAGATCATTCTGTCGG
58842412 TTTTGGTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.24
Consensus pattern (23 bp):
CCCAGAGGAGATCATTCTGTCGG
Found at i:58844658 original size:31 final size:31
Alignment explanation
Indices: 58844591--58844656 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
58844581 ATAATAAAGG
* *
58844591 TAAAATTGTATTTTAGTCTTTCTAAAAATGA
1 TAAAATTGTAATTTAATCTTTCTAAAAATGA
* *
58844622 TAAAATTTTAATTTAATCTTT-TAAAAATTA
1 TAAAATTGTAATTTAATCTTTCTAAAAATGA
58844652 TAAAA
1 TAAAA
58844657 ATATAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (31 bp):
TAAAATTGTAATTTAATCTTTCTAAAAATGA
Found at i:58844668 original size:30 final size:31
Alignment explanation
Indices: 58844607--58844668 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
58844597 TGTATTTTAG
* * *
58844607 TCTTTCTAAAAATGATAAAATTTTAATTTAA
1 TCTTTCTAAAAATGATAAAAATATAAATTAA
*
58844638 TCTTT-TAAAAATTATAAAAATATAAATTAA
1 TCTTTCTAAAAATGATAAAAATATAAATTAA
58844668 T
1 T
58844669 TAAATAGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (31 bp):
TCTTTCTAAAAATGATAAAAATATAAATTAA
Found at i:58850328 original size:40 final size:41
Alignment explanation
Indices: 58850261--58850354 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 41
58850251 GTCGGTATCA
*
58850261 CACACTTAGTGCC-TTATATAGTCGAAGCTAT-TCCAACTCG
1 CACACTTAGTGCCATTATATAGTCGAAGCTATATCAAAC-CG
* * *
58850301 TACACTTAGTGCCATT-TGTAG-CTGAAGCTATATTAAACCG
1 CACACTTAGTGCCATTATATAGTC-GAAGCTATATCAAACCG
58850341 CACACTTAGTGCCA
1 CACACTTAGTGCCA
58850355 AGCATAGTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
39 1 0.02
40 39 0.85
41 6 0.13
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (41 bp):
CACACTTAGTGCCATTATATAGTCGAAGCTATATCAAACCG
Found at i:58857747 original size:31 final size:31
Alignment explanation
Indices: 58857710--58857775 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
58857700 TTTTGAACTA
* *
58857710 AATTTGACCTTCAACCTTTTAAAAAGAGTAG
1 AATTTGACCATCAACCTTTCAAAAAGAGTAG
* *
58857741 AATTTGACCATCAATCTTTCAAAAAGAGTTG
1 AATTTGACCATCAACCTTTCAAAAAGAGTAG
58857772 AATT
1 AATT
58857776 GTTTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (31 bp):
AATTTGACCATCAACCTTTCAAAAAGAGTAG
Found at i:58865493 original size:16 final size:16
Alignment explanation
Indices: 58865472--58865502 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58865462 CCGCTCGGTT
58865472 CCTCCTTCGTCTGTTG
1 CCTCCTTCGTCTGTTG
58865488 CCTCCTTCGTCTGTT
1 CCTCCTTCGTCTGTT
58865503 ATTCAATGTT
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:0.00, C:0.39, G:0.16, T:0.45
Consensus pattern (16 bp):
CCTCCTTCGTCTGTTG
Found at i:58865968 original size:6 final size:7
Alignment explanation
Indices: 58865948--58865976 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
58865938 TTTTAGCCTC
58865948 TTCTTTT
1 TTCTTTT
58865955 TTCTTTT
1 TTCTTTT
58865962 TTCTTTT
1 TTCTTTT
58865969 TTCTTTT
1 TTCTTTT
58865976 T
1 T
58865977 ATAATATGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTCTTTT
Found at i:58866376 original size:19 final size:19
Alignment explanation
Indices: 58866329--58866388 Score: 88
Period size: 17 Copynumber: 3.2 Consensus size: 19
58866319 AATCTTTAAG
58866329 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
58866348 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
58866365 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
58866386 GAT
1 GAT
58866389 CTTGTAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 17 0.46
19 11 0.30
21 9 0.24
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:58866400 original size:22 final size:21
Alignment explanation
Indices: 58866329--58866405 Score: 85
Period size: 17 Copynumber: 3.9 Consensus size: 21
58866319 AATCTTTAAG
58866329 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
58866348 GATA--CAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
58866365 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
* *
58866386 GATCTTGTAATCTTGAAGAT
1 GAT-ATGCAATCTTGAAGAT
58866406 TTAATTTGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
17 17 0.33
19 11 0.22
21 9 0.18
22 14 0.27
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:58869327 original size:15 final size:15
Alignment explanation
Indices: 58869307--58869337 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58869297 AAAATACAAT
58869307 TCAAGTTACACTAAC
1 TCAAGTTACACTAAC
58869322 TCAAGTTACACTAAC
1 TCAAGTTACACTAAC
58869337 T
1 T
58869338 TACCTCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (15 bp):
TCAAGTTACACTAAC
Found at i:58871356 original size:28 final size:30
Alignment explanation
Indices: 58871299--58871366 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
58871289 CCACCCTTAA
* * *
58871299 AATATTTGCACTATTAGTCCTTCAACTTTT
1 AATATTTACACTATTAGTCCCTCAAATTTT
*
58871329 CATATTTACACT-TTA-TCCCTCAAATTTT
1 AATATTTACACTATTAGTCCCTCAAATTTT
58871357 AAGTATTTAC
1 AA-TATTTAC
58871367 TCTTGGGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 12 0.38
29 10 0.31
30 10 0.31
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (30 bp):
AATATTTACACTATTAGTCCCTCAAATTTT
Found at i:58871675 original size:27 final size:27
Alignment explanation
Indices: 58871635--58871689 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
58871625 CGAGATGACG
* *
58871635 GCGGTTTTGTTTACCTGCTTGTCCACT
1 GCGGTTTTGCTTACCGGCTTGTCCACT
*
58871662 GCGGTTTTGCTTACCGGCTTGTCGACT
1 GCGGTTTTGCTTACCGGCTTGTCCACT
58871689 G
1 G
58871690 AGTTTGATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.07, C:0.25, G:0.27, T:0.40
Consensus pattern (27 bp):
GCGGTTTTGCTTACCGGCTTGTCCACT
Found at i:58875004 original size:40 final size:39
Alignment explanation
Indices: 58874973--58875182 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
58874963 GGACTAAGAT
* *
58874973 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
58875013 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
58875053 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
58875093 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
58875133 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
58875172 CCGAAGGCATT
1 CCGAAGGCATT
58875183 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:58875136 original size:120 final size:120
Alignment explanation
Indices: 58874920--58875182 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
58874910 TTGAATGCTG
* *
58874920 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
58874984 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
58875040 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
58875103 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
58875159 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
58875183 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:58875202 original size:79 final size:80
Alignment explanation
Indices: 58874973--58875217 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
58874963 GGACTAAGAT
* * * * * * * ** *
58874973 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
58875036 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
58875053 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
58875118 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
58875133 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
58875197 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
58875211 CCGAAGG
1 CCGAAGG
58875218 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:58880108 original size:25 final size:25
Alignment explanation
Indices: 58880080--58880131 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
58880070 TTAATTTTTC
*
58880080 TTGTGTATTTGAAATTGTGGCATCA
1 TTGTGTATTTGAAAATGTGGCATCA
58880105 TTGTGTATTTGAAAATGTGGCATCA
1 TTGTGTATTTGAAAATGTGGCATCA
58880130 TT
1 TT
58880132 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (25 bp):
TTGTGTATTTGAAAATGTGGCATCA
Found at i:58881929 original size:21 final size:21
Alignment explanation
Indices: 58881894--58881936 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58881884 ACTTTTTTAA
**
58881894 AAGTTAAAATTCAAAATAATT
1 AAGTTAAAAGACAAAATAATT
*
58881915 AAGTTAAAAGACAAAATTATT
1 AAGTTAAAAGACAAAATAATT
58881936 A
1 A
58881937 TATTGTTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (21 bp):
AAGTTAAAAGACAAAATAATT
Found at i:58883437 original size:23 final size:24
Alignment explanation
Indices: 58883411--58883456 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
58883401 TTATATTAAA
58883411 ATTAAAAAT-AAAATATAAATATG
1 ATTAAAAATAAAAATATAAATATG
*
58883434 ATTAAAAATAAAAATATATATAT
1 ATTAAAAATAAAAATATAAATAT
58883457 TTAGTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTAAAAATAAAAATATAAATATG
Found at i:58884060 original size:5 final size:5
Alignment explanation
Indices: 58884052--58884077 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
58884042 TTTAAAACAA
58884052 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
58884078 GTAAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:58888502 original size:27 final size:27
Alignment explanation
Indices: 58888464--58888519 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
58888454 AAAATAAAAT
* * *
58888464 ACTGTTCTTGCCTTTGTCAGAGGCGGC
1 ACTGGTCTTGCCTCTGCCAGAGGCGGC
*
58888491 ACTGGTCTTGCCTCTGCCATAGGCGGC
1 ACTGGTCTTGCCTCTGCCAGAGGCGGC
58888518 AC
1 AC
58888520 CAGTTGATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.12, C:0.30, G:0.29, T:0.29
Consensus pattern (27 bp):
ACTGGTCTTGCCTCTGCCAGAGGCGGC
Found at i:58891839 original size:63 final size:64
Alignment explanation
Indices: 58891719--58891870 Score: 288
Period size: 63 Copynumber: 2.4 Consensus size: 64
58891709 AATTGAGCTT
*
58891719 ATGTTGTAATGTATTTAATTTATATAAAAAAAATTATATTGCAAAGTTTGTTCCAATTTGATTA
1 ATGTTGTAATGTATTTAATTTATATAAAAAAAATTATATTGCAAAGTTTGTTCCAATTAGATTA
58891783 ATGTTGTAATGTATTTAATTTATAT-AAAAAAATTATATTGCAAAGTTTGTTCCAATTAGATTA
1 ATGTTGTAATGTATTTAATTTATATAAAAAAAATTATATTGCAAAGTTTGTTCCAATTAGATTA
58891846 ATGTTGTAATGTATTTAATTTATAT
1 ATGTTGTAATGTATTTAATTTATAT
58891871 TAGTATACTA
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
63 62 0.71
64 25 0.29
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (64 bp):
ATGTTGTAATGTATTTAATTTATATAAAAAAAATTATATTGCAAAGTTTGTTCCAATTAGATTA
Found at i:58892507 original size:72 final size:72
Alignment explanation
Indices: 58892373--58892512 Score: 203
Period size: 72 Copynumber: 1.9 Consensus size: 72
58892363 ATCCGCCCCC
* * * *
58892373 TGACGAGCCCGGGAAATAGTCATTGCTCGGCAAATTCGGATGATAAGAAGTATCGACTGAATGTG
1 TGACGAGCCCGGGAAATAGTCATTACTCGGCAAATCCGGATGATAAGAAGTATAGACCGAATGTG
58892438 AATGTGA
66 AATGTGA
*
58892445 TGACGAGCCCGGTAAATAGTCATTACTCTGG-AAATCCGGATGATAAGAAGTATTAG-CCGAATG
1 TGACGAGCCCGGGAAATAGTCATTACTC-GGCAAATCCGGATGATAAGAAGTA-TAGACCGAATG
58892508 TGAAT
64 TGAAT
58892513 ACGATTGCTC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
72 57 0.93
73 4 0.07
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (72 bp):
TGACGAGCCCGGGAAATAGTCATTACTCGGCAAATCCGGATGATAAGAAGTATAGACCGAATGTG
AATGTGA
Found at i:58896292 original size:44 final size:44
Alignment explanation
Indices: 58896241--58896329 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
58896231 GTACACCCCC
*
58896241 TATGATATGCATAATGTACGCTTGAGCTGCGCACACCAACTCTT
1 TATGATATGCATAATGTACGCTTGAGCTGCACACACCAACTCTT
58896285 TATGATATGCATAATGTACGCTTGAGCTGCACACACCAACTCTT
1 TATGATATGCATAATGTACGCTTGAGCTGCACACACCAACTCTT
58896329 T
1 T
58896330 TTCAGTGGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
TATGATATGCATAATGTACGCTTGAGCTGCACACACCAACTCTT
Found at i:58897470 original size:137 final size:136
Alignment explanation
Indices: 58897304--58897636 Score: 524
Period size: 137 Copynumber: 2.4 Consensus size: 136
58897294 CTAATTTTTT
* * * * *
58897304 TAAAATTTTCAGATTCTATTTTTTAAAATATATTATTTTCATATTTTATTTTTATCTTATTTTAG
1 TAAAATTTTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTATTTTAG
* *
58897369 TACATAATGTTTCAAATGTATTATTTTAGTGTTTTTAAAATAACCTTGATTTTGTCTCTTTGTTT
66 TACATAATGTTTCAAATGTATTATTTTAGTGTTTTTAAAATAACC-TAATTTTGTCCCTTTGTTT
*
58897434 GTATTTC
130 ATATTTC
*
58897441 TAAAATATTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTTATCTTATTTTA
1 TAAAATTTTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTA-TTTTTATCTTATTTTA
*
58897506 GTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCTAATTTTGTCCCTTTGTTT
65 GTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTAAAATAACCTAATTTTGTCCCTTTGTTT
*
58897571 ATATTTT
130 ATATTTC
* *
58897578 TAAAATTTTTGGATTTT-ATTTTTAAAATATACTATTTTCGTATTTTATTTTTATATTAT
1 TAAAATTTTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTAT
58897637 GTTTCGTATT
Statistics
Matches: 181, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
135 11 0.06
136 30 0.17
137 79 0.44
138 61 0.34
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (136 bp):
TAAAATTTTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTATTTTAG
TACATAATGTTTCAAATGTATTATTTTAGTGTTTTTAAAATAACCTAATTTTGTCCCTTTGTTTA
TATTTC
Found at i:58897647 original size:25 final size:24
Alignment explanation
Indices: 58897605--58897651 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
58897595 ATTTTTAAAA
58897605 TATACTATTTTCGTATTTTATTTT
1 TATACTATTTTCGTATTTTATTTT
*
58897629 TATATTATGTTTCGTATTTTATT
1 TATACTAT-TTTCGTATTTTATT
58897652 CTATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.66
Consensus pattern (24 bp):
TATACTATTTTCGTATTTTATTTT
Found at i:58897684 original size:17 final size:16
Alignment explanation
Indices: 58897648--58897716 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
58897638 TTTCGTATTT
58897648 TATTCTATTTTTTTCA
1 TATTCTATTTTTTTCA
*
58897664 TATTCTATTTCTTTTCG
1 TATTCTATTT-TTTTCA
*
58897681 TATTTTA-TTTTTTCA
1 TATTCTATTTTTTTCA
* * *
58897696 TTAATATATTTGTTTCA
1 -TATTCTATTTTTTTCA
58897713 TATT
1 TATT
58897717 TTCTTTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 5 0.12
16 20 0.47
17 18 0.42
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (16 bp):
TATTCTATTTTTTTCA
Found at i:58897690 original size:33 final size:33
Alignment explanation
Indices: 58897612--58897725 Score: 89
Period size: 33 Copynumber: 3.6 Consensus size: 33
58897602 AAATATACTA
*
58897612 TTTTCGTATTTTA--TTTTTATATTATGTTTCG
1 TTTTCGTATTTTATTTTTTTATATTATATTTCG
* *
58897643 TATTT--TATTCTATTTTTTTCATATTCTATTTC-
1 T-TTTCGTATTTTATTTTTTT-ATATTATATTTCG
* *
58897675 TTTTCGTATTTTATTTTTTCATTAATATATTT-G
1 TTTTCGTATTTTATTTTTTTA-TATTATATTTCG
* *
58897708 -TTTCATATTTTCTTTTTT
1 TTTTCGTATTTTATTTTTT
58897726 ATACTATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
30 6 0.09
31 4 0.06
32 26 0.39
33 30 0.45
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.69
Consensus pattern (33 bp):
TTTTCGTATTTTATTTTTTTATATTATATTTCG
Found at i:58898404 original size:19 final size:19
Alignment explanation
Indices: 58898380--58898418 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58898370 AAGTATGCAT
*
58898380 TATTAAAATAA-AATTAAAA
1 TATT-AAATAAGAAATAAAA
58898399 TATTAAATAAGAAATAAAA
1 TATTAAATAAGAAATAAAA
58898418 T
1 T
58898419 TATAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
TATTAAATAAGAAATAAAA
Found at i:58898520 original size:212 final size:211
Alignment explanation
Indices: 58898151--58898739 Score: 1052
Period size: 212 Copynumber: 2.8 Consensus size: 211
58898141 CCTACTGCTA
58898151 CCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
1 CCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
58898216 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTAGATATAAGTATTTA
66 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTAG-TATAAGTATTTA
*
58898281 AAATTTTGTTTTTGTAATGTGATACATGCGTAAATCTATATATATATAATCATATAAGTGAATCT
130 AAATTTTGTTTTTGTAATGTGATACATGCGTAAATATATATATATATAATCATATAAGTGAATCT
*
58898346 ACTAATACATACTTTAT
195 ACTAATACATACTTCAT
** *
58898363 TTGGATAAAGTATGCATTATTAAAATAAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
1 CCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
*
58898428 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTATGTATAAGTATTTT
66 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTA-GTATAAGTATTTA
* * * *
58898493 AATTTTTATTTTTGTAATGTGATACATGCGTAAATATCTATATATATAATCATATTAGTGAATCT
130 AAATTTTGTTTTTGTAATGTGATACATGCGTAAATATATATATATATAATCATATAAGTGAATCT
*
58898558 GCTAATACATACTTCAT
195 ACTAATACATACTTCAT
58898575 CCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
1 CCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
58898640 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTAGGTATAAGTATTTA
66 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTA-GTATAAGTATTTA
58898705 AAATTTTGTTTTTGTAATGTGATACATGCGTAAAT
130 AAATTTTGTTTTTGTAATGTGATACATGCGTAAAT
58898740 NNNNNNNNNN
Statistics
Matches: 358, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
212 357 1.00
213 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (211 bp):
CCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTAGTATAAGTATTTAA
AATTTTGTTTTTGTAATGTGATACATGCGTAAATATATATATATATAATCATATAAGTGAATCTA
CTAATACATACTTCAT
Found at i:58916294 original size:44 final size:44
Alignment explanation
Indices: 58916243--58916331 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
58916233 GTACACCCCC
*
58916243 TATGATATGCATAATGTACGCTTGAGCTGCGCACACCAACTCTT
1 TATGATATGCATAATGTACGCTTGAGCTGCACACACCAACTCTT
58916287 TATGATATGCATAATGTACGCTTGAGCTGCACACACCAACTCTT
1 TATGATATGCATAATGTACGCTTGAGCTGCACACACCAACTCTT
58916331 T
1 T
58916332 TTCAGTGGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
TATGATATGCATAATGTACGCTTGAGCTGCACACACCAACTCTT
Found at i:58917472 original size:137 final size:136
Alignment explanation
Indices: 58917306--58917638 Score: 524
Period size: 137 Copynumber: 2.4 Consensus size: 136
58917296 CTAATTTTTT
* * * * *
58917306 TAAAATTTTCAGATTCTATTTTTTAAAATATATTATTTTCATATTTTATTTTTATCTTATTTTAG
1 TAAAATTTTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTATTTTAG
* *
58917371 TACATAATGTTTCAAATGTATTATTTTAGTGTTTTTAAAATAACCTTGATTTTGTCTCTTTGTTT
66 TACATAATGTTTCAAATGTATTATTTTAGTGTTTTTAAAATAACC-TAATTTTGTCCCTTTGTTT
*
58917436 GTATTTC
130 ATATTTC
*
58917443 TAAAATATTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTTATCTTATTTTA
1 TAAAATTTTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTA-TTTTTATCTTATTTTA
*
58917508 GTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCTAATTTTGTCCCTTTGTTT
65 GTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTAAAATAACCTAATTTTGTCCCTTTGTTT
*
58917573 ATATTTT
130 ATATTTC
* *
58917580 TAAAATTTTTGGATTTT-ATTTTTAAAATATACTATTTTCGTATTTTATTTTTATATTAT
1 TAAAATTTTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTAT
58917639 GTTTCGTATT
Statistics
Matches: 181, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
135 11 0.06
136 30 0.17
137 79 0.44
138 61 0.34
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (136 bp):
TAAAATTTTCGGATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTTATCTTATTTTAG
TACATAATGTTTCAAATGTATTATTTTAGTGTTTTTAAAATAACCTAATTTTGTCCCTTTGTTTA
TATTTC
Found at i:58917649 original size:25 final size:24
Alignment explanation
Indices: 58917607--58917653 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
58917597 ATTTTTAAAA
58917607 TATACTATTTTCGTATTTTATTTT
1 TATACTATTTTCGTATTTTATTTT
*
58917631 TATATTATGTTTCGTATTTTATT
1 TATACTAT-TTTCGTATTTTATT
58917654 CTATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.66
Consensus pattern (24 bp):
TATACTATTTTCGTATTTTATTTT
Found at i:58917686 original size:17 final size:16
Alignment explanation
Indices: 58917650--58917718 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
58917640 TTTCGTATTT
58917650 TATTCTATTTTTTTCA
1 TATTCTATTTTTTTCA
*
58917666 TATTCTATTTCTTTTCG
1 TATTCTATTT-TTTTCA
*
58917683 TATTTTA-TTTTTTCA
1 TATTCTATTTTTTTCA
* * *
58917698 TTAATATATTTGTTTCA
1 -TATTCTATTTTTTTCA
58917715 TATT
1 TATT
58917719 TTCTTTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 5 0.12
16 20 0.47
17 18 0.42
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (16 bp):
TATTCTATTTTTTTCA
Found at i:58917692 original size:33 final size:33
Alignment explanation
Indices: 58917614--58917727 Score: 89
Period size: 33 Copynumber: 3.6 Consensus size: 33
58917604 AAATATACTA
*
58917614 TTTTCGTATTTTA--TTTTTATATTATGTTTCG
1 TTTTCGTATTTTATTTTTTTATATTATATTTCG
* *
58917645 TATTT--TATTCTATTTTTTTCATATTCTATTTC-
1 T-TTTCGTATTTTATTTTTTT-ATATTATATTTCG
* *
58917677 TTTTCGTATTTTATTTTTTCATTAATATATTT-G
1 TTTTCGTATTTTATTTTTTTA-TATTATATTTCG
* *
58917710 -TTTCATATTTTCTTTTTT
1 TTTTCGTATTTTATTTTTT
58917728 ATACTATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
30 6 0.09
31 4 0.06
32 26 0.39
33 30 0.45
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.69
Consensus pattern (33 bp):
TTTTCGTATTTTATTTTTTTATATTATATTTCG
Found at i:58918406 original size:19 final size:19
Alignment explanation
Indices: 58918382--58918420 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58918372 AAGTATGCAT
*
58918382 TATTAAAATAA-AATTAAAA
1 TATT-AAATAAGAAATAAAA
58918401 TATTAAATAAGAAATAAAA
1 TATTAAATAAGAAATAAAA
58918420 T
1 T
58918421 TATAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
TATTAAATAAGAAATAAAA
Found at i:58918522 original size:212 final size:212
Alignment explanation
Indices: 58918153--58918602 Score: 785
Period size: 212 Copynumber: 2.1 Consensus size: 212
58918143 CCTACTGCTA
*
58918153 CCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
1 CCGGATAAAGTATGCATTATTAAAATAAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
58918218 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTAGATATAAGTATTTA
66 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTAGATATAAGTATTTA
* *
58918283 AAATTTTGTTTTTGTAATGTGATACATGCGTAAATCTATATATATATAATCATATAAGTGAATCT
131 AAATTTTATTTTTGTAATGTGATACATGCGTAAATATATATATATATAATCATATAAGTGAATCT
*
58918348 ACTAATACATACTTTAT
196 ACTAATACATACTTCAT
**
58918365 TTGGATAAAGTATGCATTATTAAAATAAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
1 CCGGATAAAGTATGCATTATTAAAATAAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
58918430 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTATG-TATAAGTATTT
66 ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTA-GATATAAGTATTT
* * * *
58918494 TAATTTTTATTTTTGTAATGTGATACATGCGTAAATATCTATATATATAATCATATTAGTGAATC
130 AAAATTTTATTTTTGTAATGTGATACATGCGTAAATATATATATATATAATCATATAAGTGAATC
*
58918559 TGCTAATACATACTTCAT
195 TACTAATACATACTTCAT
58918577 CCGGATAAAGTATGCATTATTAAAAT
1 CCGGATAAAGTATGCATTATTAAAAT
58918603 TAATGGTTTG
Statistics
Matches: 224, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
212 223 1.00
213 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.40
Consensus pattern (212 bp):
CCGGATAAAGTATGCATTATTAAAATAAAATTAAAATATTAAATAAGAAATAAAATTATAAAACA
ATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACATGTTTTATTAGATATAAGTATTTA
AAATTTTATTTTTGTAATGTGATACATGCGTAAATATATATATATATAATCATATAAGTGAATCT
ACTAATACATACTTCAT
Found at i:58919265 original size:18 final size:19
Alignment explanation
Indices: 58919238--58919275 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
58919228 TTGCTCCTTC
*
58919238 TTCTTCTTCTCTTCTTTCT
1 TTCTTCTTCTCTCCTTTCT
58919257 TTCTT-TTCTCTCCTTTCT
1 TTCTTCTTCTCTCCTTTCT
58919275 T
1 T
58919276 CCCCAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTCTTCTCTCCTTTCT
Found at i:58919491 original size:12 final size:12
Alignment explanation
Indices: 58919474--58919501 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
58919464 CAGTCAGCTT
58919474 TTTTTTTAACTA
1 TTTTTTTAACTA
58919486 TTTTTTTAACTA
1 TTTTTTTAACTA
58919498 TTTT
1 TTTT
58919502 GTGTTAGAGA
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:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTTAACTA
Found at i:58935500 original size:58 final size:57
Alignment explanation
Indices: 58935418--58935533 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 57
58935408 AAATTTGTGC
* * *
58935418 TAGTTGTTTTTTTATTTTATGTCTATCTATTGTGATACATATGAAATAAATGAGTTT
1 TAGTTGTTTTTTTATTATATGTCTAACTATTGTAATACATATGAAATAAATGAGTTT
58935475 TAGTTGTTTTTTTTATTATATGTCTAACTATTGTAATACATATGAAATAAATGAGTTT
1 TAGTTG-TTTTTTTATTATATGTCTAACTATTGTAATACATATGAAATAAATGAGTTT
58935533 T
1 T
58935534 TTTCCTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 6 0.11
58 49 0.89
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.52
Consensus pattern (57 bp):
TAGTTGTTTTTTTATTATATGTCTAACTATTGTAATACATATGAAATAAATGAGTTT
Found at i:58936241 original size:18 final size:17
Alignment explanation
Indices: 58936219--58936257 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
58936209 CCTTTATACT
58936219 ATTTTTT-TATTTTATGA
1 ATTTTTTATATTTTAT-A
58936236 ATTTTTTATATTTTATA
1 ATTTTTTATATTTTATA
58936253 ATTTT
1 ATTTT
58936258 AATTTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
ATTTTTTATATTTTATA
Found at i:58936265 original size:25 final size:26
Alignment explanation
Indices: 58936235--58936285 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
58936225 TTATTTTATG
58936235 AATTTTTT--ATATTTTAT-AATTTT
1 AATTTTTTGAATATTTTATAAATTTT
58936258 AATTTTTTGAATATTTTATAAATTTT
1 AATTTTTTGAATATTTTATAAATTTT
58936284 AA
1 AA
58936286 ATTATTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 8 0.32
25 9 0.36
26 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
AATTTTTTGAATATTTTATAAATTTT
Found at i:58937583 original size:10 final size:10
Alignment explanation
Indices: 58937568--58937611 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
58937558 CTAATTTTTT
58937568 AAATTATAAA
1 AAATTATAAA
58937578 AAATTA-AAA
1 AAATTATAAA
58937587 AAA-TATAAA
1 AAATTATAAA
*
58937596 AAA-TAT-TA
1 AAATTATAAA
58937604 AAATTATA
1 AAATTATA
58937612 TATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
8 6 0.20
9 18 0.60
10 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAATTATAAA
Found at i:58937587 original size:9 final size:9
Alignment explanation
Indices: 58937568--58937606 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 9
58937558 CTAATTTTTT
58937568 AAATTATAAA
1 AAATTA-AAA
58937578 AAATTAAAA
1 AAATTAAAA
58937587 AAATATAAAA
1 AAAT-TAAAA
58937597 AATATTAAAA
1 AA-ATTAAAA
58937607 TTATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.26
10 18 0.67
11 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAATTAAAA
Found at i:58938014 original size:14 final size:14
Alignment explanation
Indices: 58937995--58938024 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
58937985 AAGAAATTGA
58937995 TGAATTCTTTACAT
1 TGAATTCTTTACAT
58938009 TGAATTCTTTACAT
1 TGAATTCTTTACAT
58938023 TG
1 TG
58938025 CAAGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (14 bp):
TGAATTCTTTACAT
Found at i:58939428 original size:18 final size:18
Alignment explanation
Indices: 58939405--58939473 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
58939395 CATTTATGGA
58939405 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGT
* *
58939423 ACTATTTATGTATACGGT
1 ACTATTCACGTATACGGT
* * *
58939441 ACTATTTACATATACAGT
1 ACTATTCACGTATACGGT
*
58939459 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
58939474 AGTAGTTGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (18 bp):
ACTATTCACGTATACGGT
Found at i:58949378 original size:3 final size:3
Alignment explanation
Indices: 58949370--58949419 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
58949360 ATTCAAACAC
58949370 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58949418 TA
1 TA
58949420 CCACCATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:58949447 original size:15 final size:15
Alignment explanation
Indices: 58949370--58949448 Score: 86
Period size: 15 Copynumber: 5.3 Consensus size: 15
58949360 ATTCAAACAC
*
58949370 TATTATTATTATTAT
1 TATTATTACTATTAT
*
58949385 TATTATTATTATTAT
1 TATTATTACTATTAT
*
58949400 TATTATTATTATTAT
1 TATTATTACTATTAT
** * *
58949415 TATTACCACCATTTT
1 TATTATTACTATTAT
*
58949430 TATTTTTACTATTAT
1 TATTATTACTATTAT
58949445 TATT
1 TATT
58949449 GTCTTAGTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:58949567 original size:7 final size:7
Alignment explanation
Indices: 58949512--58949584 Score: 69
Period size: 7 Copynumber: 10.3 Consensus size: 7
58949502 CTTTTTTTTC
58949512 ATTTATTT
1 ATTTA-TT
58949520 ATTTATT
1 ATTTATT
58949527 ACTTTATT
1 A-TTTATT
*
58949535 ATTAATT
1 ATTTATT
*
58949542 AATTTAGT
1 -ATTTATT
*
58949550 A-CTATT
1 ATTTATT
*
58949556 GTTTATT
1 ATTTATT
58949563 ATTTATT
1 ATTTATT
58949570 ATTTATT
1 ATTTATT
58949577 A-TTATT
1 ATTTATT
58949583 AT
1 AT
58949585 CCTTATTAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
6 9 0.17
7 27 0.51
8 17 0.32
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (7 bp):
ATTTATT
Found at i:58949832 original size:21 final size:21
Alignment explanation
Indices: 58949814--58949902 Score: 67
Period size: 21 Copynumber: 4.4 Consensus size: 21
58949804 TTTACTATCT
*
58949814 CTATTTTTTTTATCACTATTA
1 CTATTATTTTTATCACTATTA
58949835 CTATTATTTTTA--ACTA-TA
1 CTATTATTTTTATCACTATTA
* * * *
58949853 TTATTATTATTATTATTATTA
1 CTATTATTTTTATCACTATTA
* * * *
58949874 TTATTATTATTATTATTATTA
1 CTATTATTTTTATCACTATTA
*
58949895 TTATTATT
1 CTATTATT
58949903 ACCGCCAGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
18 12 0.20
19 4 0.07
20 3 0.05
21 42 0.69
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (21 bp):
CTATTATTTTTATCACTATTA
Found at i:58949842 original size:3 final size:3
Alignment explanation
Indices: 58949830--58950239 Score: 174
Period size: 3 Copynumber: 139.7 Consensus size: 3
58949820 TTTTTATCAC
* * *
58949830 TAT TAC TAT TAT TTT TAAC TAT -AT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *** * *
58949875 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC CGC CAG TAT TAT T-T TCAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
* * *
58949923 TAT TAT TAT TACT TAGT TA- TAT TAC TAT AAT TGT TA- TAT TAT TAT
1 TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
58949968 TAT TAT TAT TAC TAT TAT TAT TAT TAC TAC AAT TAT TAT TAC TAT GAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * ** *** *
58950016 TA- TAT T-T TCT TTT TAT GCT TAT T-T GCC TAT TAT TAT TA- CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
58950060 TA- TAT CAT TAAT T-T TA- TAT TGT TAT CAT TA- TAA TAGT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * * * * * *
58950103 CAT TACT T-T TAT TGT TA- TGT TCT T-T T-T TTT CTAT GTTT TAT TAC
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT
* * * * *
58950147 TAT TAT TAT TAT CAT TAT TAC TAT TAT TTT TAT TTT TAT TTT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
58950194 TAT TAC TAT TAT CT-T T-T TAT TAT TAC TAC TAC TAT TAT TCT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58950238 TA
1 TA
58950240 ACATATTATC
Statistics
Matches: 304, Mismatches: 78, Indels: 50
0.70 0.18 0.12
Matches are distributed among these distances:
2 34 0.11
3 249 0.82
4 21 0.07
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:58952219 original size:39 final size:39
Alignment explanation
Indices: 58952165--58952382 Score: 346
Period size: 39 Copynumber: 5.6 Consensus size: 39
58952155 GCTCTAATGA
*
58952165 GCTTCAATTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
58952204 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
58952243 GCTTCAGTTAGCCTTCGAGCTTCCATTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* **
58952282 GCTTCAATTAGCCTTCGACCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
58952321 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
58952360 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
58952383 AGATCACGAT
Statistics
Matches: 166, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 166 1.00
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:58954860 original size:8 final size:8
Alignment explanation
Indices: 58954838--58954867 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
58954828 AAATTCTTTT
58954838 AATTCACC
1 AATTCACC
58954846 AAATTCACC
1 -AATTCACC
58954855 AATTCACC
1 AATTCACC
58954863 AATTC
1 AATTC
58954868 TTCTAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (8 bp):
AATTCACC
Found at i:58959191 original size:16 final size:17
Alignment explanation
Indices: 58959160--58959192 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58959150 GCTATGTGGG
*
58959160 TAGGCTTTGTTGGGTTT
1 TAGGCTTAGTTGGGTTT
58959177 TAGGCTTAG-TGGGTTT
1 TAGGCTTAGTTGGGTTT
58959193 AGTGGGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.06, G:0.36, T:0.48
Consensus pattern (17 bp):
TAGGCTTAGTTGGGTTT
Found at i:58961665 original size:10 final size:9
Alignment explanation
Indices: 58961644--58961695 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
58961634 TTAATTTTTT
*
58961644 AAATTTTAA
1 AAATTATAA
58961653 AAATTCATAA
1 AAATT-ATAA
58961663 AAATTATAA
1 AAATTATAA
* * *
58961672 ATTATTTTTA
1 A-AATTATAA
58961682 AAATTATAA
1 AAATTATAA
58961691 AAATT
1 AAATT
58961696 TAACTAAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
9 20 0.59
10 14 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATTATAA
Found at i:58965525 original size:25 final size:24
Alignment explanation
Indices: 58965497--58965588 Score: 71
Period size: 25 Copynumber: 3.8 Consensus size: 24
58965487 CTTATGAACA
58965497 TCCCGATATATGGCTCTCTATAGCT
1 TCCCGATATATGGCTCT-TATAGCT
* * * * **
58965522 TCCCGTTACATGGTTATTGCGAGCT
1 TCCCGATATATGGCTCTT-ATAGCT
*
58965547 TCCCG-TTTATGGCTCTTATGAGCT
1 TCCCGATATATGGCTCTTAT-AGCT
58965571 TCCCGATA-ATTGGCTCTT
1 TCCCGATATA-TGGCTCTT
58965589 TGGCGCTTCT
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
24 19 0.38
25 31 0.62
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (24 bp):
TCCCGATATATGGCTCTTATAGCT
Found at i:58965621 original size:25 final size:25
Alignment explanation
Indices: 58965542--58965623 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
58965532 TGGTTATTGC
* * *
58965542 GAGCTTCCCGTTTA-TGGCTCTTAT
1 GAGCTTCCCGATAACTGACTCTTAT
* *
58965566 GAGCTTCCCGATAATTGGCTCTT-T
1 GAGCTTCCCGATAACTGACTCTTAT
* *
58965590 GGCGCTTCTCGATAACTGACTCTTAT
1 -GAGCTTCCCGATAACTGACTCTTAT
58965616 GAGCTTCC
1 GAGCTTCC
58965624 TAACTTAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
24 13 0.28
25 33 0.70
26 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.37
Consensus pattern (25 bp):
GAGCTTCCCGATAACTGACTCTTAT
Found at i:58967135 original size:10 final size:10
Alignment explanation
Indices: 58967120--58967148 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
58967110 TATAAGGGAC
58967120 AATATGATTG
1 AATATGATTG
58967130 AATATGATTG
1 AATATGATTG
58967140 AATATGATT
1 AATATGATT
58967149 CATTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (10 bp):
AATATGATTG
Found at i:58967988 original size:6 final size:6
Alignment explanation
Indices: 58967979--58968006 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
58967969 TATTTTATTT
58967979 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
58968007 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:58968108 original size:31 final size:31
Alignment explanation
Indices: 58968073--58968142 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
58968063 GTGGGTGACC
* *
58968073 AAAATGAAAAT-GATTTTTAATGGCAATGCCT
1 AAAATGAAAATAG-TTTTTAATGACAATACCT
58968104 AAAATGAAAATAGTTTTTAATGACAATACCT
1 AAAATGAAAATAGTTTTTAATGACAATACCT
58968135 AAAATGAA
1 AAAATGAA
58968143 TTTTTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.30
Consensus pattern (31 bp):
AAAATGAAAATAGTTTTTAATGACAATACCT
Found at i:58969599 original size:22 final size:21
Alignment explanation
Indices: 58969574--58969620 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
58969564 AAATAAAGCG
58969574 TAAA-AACTATTTAAAAAGATAA
1 TAAATAACT-TTTAAAAAGA-AA
* *
58969596 TAAATAAGTTTTAAAAATAAA
1 TAAATAACTTTTAAAAAGAAA
58969617 TAAA
1 TAAA
58969621 GTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 13 0.59
23 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAATAACTTTTAAAAAGAAA
Found at i:58971636 original size:15 final size:15
Alignment explanation
Indices: 58971616--58971646 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58971606 TTATAACTTT
58971616 TTTAAAATTTAGTGA
1 TTTAAAATTTAGTGA
58971631 TTTAAAATTTAGTGA
1 TTTAAAATTTAGTGA
58971646 T
1 T
58971647 CAAAACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (15 bp):
TTTAAAATTTAGTGA
Found at i:58974041 original size:77 final size:78
Alignment explanation
Indices: 58973900--58974056 Score: 262
Period size: 77 Copynumber: 2.0 Consensus size: 78
58973890 GATACCATAA
* *
58973900 ATTAATTATCGATACCATTATTTTACAAAAAAAATAATTAAATTTTAGTATCGATTTTCAGAAAG
1 ATTAATTATCGATACCATTATTTTACAAAAAAAATAATTAAACTTTAGTATCAATTTTCAGAAAG
*
58973965 GTATTGATTTAGT
66 ATATTGATTTAGT
* *
58973978 ATTAATTATCGATACCATTATTTTA-TAAAAAAATAATTAAACTTTGGTATCAATTTTCAGAAAG
1 ATTAATTATCGATACCATTATTTTACAAAAAAAATAATTAAACTTTAGTATCAATTTTCAGAAAG
58974042 ATATTGATTTAGT
66 ATATTGATTTAGT
58974055 AT
1 AT
58974057 CAATACCTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 49 0.66
78 25 0.34
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (78 bp):
ATTAATTATCGATACCATTATTTTACAAAAAAAATAATTAAACTTTAGTATCAATTTTCAGAAAG
ATATTGATTTAGT
Found at i:58974343 original size:3 final size:3
Alignment explanation
Indices: 58974335--58974366 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
58974325 ACAAAAACAA
58974335 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58974367 ATGGGTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:58975577 original size:25 final size:25
Alignment explanation
Indices: 58975543--58975593 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
58975533 TATAATGCTC
58975543 TCGAATTTATTTCAAAAATTACTTT
1 TCGAATTTATTTCAAAAATTACTTT
58975568 TCGAATTTATTTCAAAAATTACTTT
1 TCGAATTTATTTCAAAAATTACTTT
58975593 T
1 T
58975594 GAACATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.49
Consensus pattern (25 bp):
TCGAATTTATTTCAAAAATTACTTT
Found at i:58976172 original size:40 final size:36
Alignment explanation
Indices: 58976097--58976176 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 36
58976087 GCCTACCTGG
*
58976097 GAAAAAAATAAAAAAATAGAATTAAAAGTTATGATTT
1 GAAAAAAATAAAAAAATAAAATTAAAAGTTATGA-TT
*
58976134 GAAAAAAATAAAATAAAATTAAAATTAAAAGTTTTGATT
1 GAAAAAAAT-AAA-AAAA-TAAAATTAAAAGTTATGATT
58976173 GAAA
1 GAAA
58976177 TTTCGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 9 0.24
38 3 0.08
39 10 0.26
40 16 0.42
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (36 bp):
GAAAAAAATAAAAAAATAAAATTAAAAGTTATGATT
Found at i:58976931 original size:10 final size:10
Alignment explanation
Indices: 58976904--58976942 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
58976894 TTAAATTCTA
58976904 AAAGATAAAT
1 AAAGATAAAT
58976914 ATAA-ATAAAT
1 A-AAGATAAAT
*
58976924 AAAGATAATT
1 AAAGATAAAT
58976934 AAAGATAAA
1 AAAGATAAA
58976943 AGCTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:58977725 original size:95 final size:96
Alignment explanation
Indices: 58977561--58977756 Score: 286
Period size: 95 Copynumber: 2.1 Consensus size: 96
58977551 TTAATACATC
* * *
58977561 TTTTTTTTTTACTTAAGAATATATTGAACCTTTTGACGAGAAGAGAGATGACAGCCAAGCACCCC
1 TTTTTATTTTACTTAAGAACATATTGAACATTTTGACGAGAAGAGAGATGACAGCCAAGCACCCC
* *
58977626 ACCCCGGTTACTCAGCCCAACATACTCCTAA
66 ACCCCGGTTACTCAGCCCAACACAATCCTAA
* * * *
58977657 TTTTTATTTT-CTTAAGAACATATTGAACATTTTGATGCGAAGAGGGATGACAGCCAAGCACCTC
1 TTTTTATTTTACTTAAGAACATATTGAACATTTTGACGAGAAGAGAGATGACAGCCAAGCACCCC
* *
58977721 ACCCCGGTTACTTAGCCCAATACAATCCTAA
66 ACCCCGGTTACTCAGCCCAACACAATCCTAA
58977752 TTTTT
1 TTTTT
58977757 TAAAAATAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 80 0.90
96 9 0.10
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (96 bp):
TTTTTATTTTACTTAAGAACATATTGAACATTTTGACGAGAAGAGAGATGACAGCCAAGCACCCC
ACCCCGGTTACTCAGCCCAACACAATCCTAA
Found at i:58978866 original size:8 final size:8
Alignment explanation
Indices: 58978849--58978909 Score: 63
Period size: 8 Copynumber: 7.8 Consensus size: 8
58978839 TATTAATATT
58978849 TAAAAAAA
1 TAAAAAAA
*
58978857 TAAAATAA
1 TAAAAAAA
*
58978865 T-AAATAA
1 TAAAAAAA
58978872 TAAAAAAA
1 TAAAAAAA
58978880 TAAAAAGAA
1 TAAAAA-AA
* *
58978889 -AGAATAA
1 TAAAAAAA
58978896 TAAAAAAA
1 TAAAAAAA
58978904 TAAAAA
1 TAAAAA
58978910 TTGGGTTGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
7 9 0.20
8 33 0.75
9 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:58978885 original size:24 final size:24
Alignment explanation
Indices: 58978849--58978910 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
58978839 TATTAATATT
58978849 TAAAAAAAT-AAAATAATA-AATAA
1 TAAAAAAATAAAAATAA-AGAATAA
*
58978872 TAAAAAAATAAAAAGAAAGAATAA
1 TAAAAAAATAAAAATAAAGAATAA
58978896 TAAAAAAATAAAAAT
1 TAAAAAAATAAAAAT
58978911 TGGGTTGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 10 0.29
24 25 0.71
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (24 bp):
TAAAAAAATAAAAATAAAGAATAA
Found at i:58982735 original size:10 final size:10
Alignment explanation
Indices: 58982708--58982746 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
58982698 TTAAATTCTA
58982708 AAAGATAAAT
1 AAAGATAAAT
58982718 ACAA-ATAAAT
1 A-AAGATAAAT
*
58982728 AAAGATAATT
1 AAAGATAAAT
58982738 AAAGATAAA
1 AAAGATAAA
58982747 AGCTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:58985772 original size:16 final size:15
Alignment explanation
Indices: 58985743--58985773 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58985733 ATTACGAAGG
58985743 TTTTTGTATTAAAAA
1 TTTTTGTATTAAAAA
*
58985758 TTTTTTTATTAAAAA
1 TTTTTGTATTAAAAA
58985773 T
1 T
58985774 ATTACAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTTGTATTAAAAA
Found at i:59000259 original size:18 final size:20
Alignment explanation
Indices: 59000233--59000277 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
59000223 AGACCACCAA
*
59000233 TGATTAATTTTAA-A-TATT
1 TGATCAATTTTAAGAGTATT
59000251 TGATCAA-TTTAAGAGTATT
1 TGATCAATTTTAAGAGTATT
59000270 T-ATCAATT
1 TGATCAATT
59000278 ATGCATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 12 0.52
19 6 0.26
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (20 bp):
TGATCAATTTTAAGAGTATT
Found at i:59001549 original size:5 final size:5
Alignment explanation
Indices: 59001539--59001569 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
59001529 TTATGTTTTA
59001539 ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
59001570 AAACTAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:59001744 original size:9 final size:9
Alignment explanation
Indices: 59001730--59001755 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
59001720 AATTTTGATA
59001730 TTTTAGAAG
1 TTTTAGAAG
59001739 TTTTAGAAG
1 TTTTAGAAG
59001748 TTTTAGAA
1 TTTTAGAA
59001756 CAAAGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (9 bp):
TTTTAGAAG
Found at i:59002918 original size:18 final size:19
Alignment explanation
Indices: 59002895--59002933 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
59002885 ATATATAGAT
59002895 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
59002913 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
59002932 AT
1 AT
59002934 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:59004831 original size:22 final size:23
Alignment explanation
Indices: 59004788--59004841 Score: 83
Period size: 22 Copynumber: 2.3 Consensus size: 23
59004778 GAAATAAATA
*
59004788 TAATAAATTATTATAAATTTAGAT
1 TAATAAA-TATAATAAATTTAGAT
59004812 TAATAAATATAAT-AATTTAGAT
1 TAATAAATATAATAAATTTAGAT
59004834 TAATAAAT
1 TAATAAAT
59004842 TCATAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 17 0.59
23 5 0.17
24 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TAATAAATATAATAAATTTAGAT
Found at i:59005009 original size:17 final size:18
Alignment explanation
Indices: 59004971--59005009 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
59004961 CTCAAATTTT
* *
59004971 AATTTTTTTAGTTAATAA
1 AATTATTTTAATTAATAA
59004989 AATTATTTTAATTAA-AA
1 AATTATTTTAATTAATAA
59005006 AATT
1 AATT
59005010 TAGGATAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTATTTTAATTAATAA
Found at i:59007549 original size:25 final size:22
Alignment explanation
Indices: 59007504--59007569 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 22
59007494 GAAACAAGGT
*
59007504 AAAGTAATATATAAAATAGTTC
1 AAAGTAATATATAAAACAGTTC
*
59007526 AAAGTAATATGTATTAAAACAGTTT
1 AAAGTAATA--TA-TAAAACAGTTC
*
59007551 AAAATGAATACTATAAAAC
1 AAAGT-AATA-TATAAAAC
59007570 TTAAAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 9 0.25
24 8 0.22
25 15 0.42
26 4 0.11
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAGTAATATATAAAACAGTTC
Found at i:59007934 original size:3 final size:3
Alignment explanation
Indices: 59007928--59008099 Score: 150
Period size: 3 Copynumber: 55.3 Consensus size: 3
59007918 AAAAGGAAAA
* * *
59007928 AAT AAT AAT AAT AAT AAT AAT AAGC AAA AAA AAT AGACT AAT AAAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT A-A-T AAT -AAT AAT
* * * *
59007976 AAT AAT AAT AAT AAT AGT AAT AAT GAG GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
59008024 AAT AAT AAT AAT AAGT AAT AAT AAT ACGTT AAGT TAT AAT AGT AA- AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT A--AT AA-T AAT AAT AAT AAT AAT
* *
59008072 AAT AAT AAT AGT GAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
59008100 CGATAAAAAT
Statistics
Matches: 140, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
2 4 0.03
3 120 0.86
4 12 0.09
5 4 0.03
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:59009834 original size:15 final size:15
Alignment explanation
Indices: 59009803--59009854 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
59009793 GTGCAAAATT
*
59009803 AATAAAATA-ATTCAA
1 AATAATATATATT-AA
59009818 AATAATATATATTAA
1 AATAATATATATTAA
59009833 AATAATATATATAATAA
1 AATAATATATAT--TAA
59009850 AATAA
1 AATAA
59009855 AATAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 22 0.67
16 3 0.09
17 8 0.24
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATATATATTAA
Found at i:59009844 original size:17 final size:17
Alignment explanation
Indices: 59009816--59009854 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
59009806 AAAATAATTC
59009816 AAAATAATATATAT--T
1 AAAATAATATATATAAT
59009831 AAAATAATATATATAAT
1 AAAATAATATATATAAT
59009848 AAAATAA
1 AAAATAA
59009855 AATAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.64
17 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATATATATAAT
Found at i:59011914 original size:9 final size:9
Alignment explanation
Indices: 59011900--59011939 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
59011890 AGTAGATTCG
59011900 AAAAGAAAA
1 AAAAGAAAA
59011909 AAAAGAAAA
1 AAAAGAAAA
*
59011918 AAAATAAAAA
1 AAAA-GAAAA
59011928 AGAAAGAAAA
1 A-AAAGAAAA
59011938 AA
1 AA
59011940 GGAAAATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 14 0.52
10 10 0.37
11 3 0.11
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.03
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:59011926 original size:16 final size:17
Alignment explanation
Indices: 59011907--59011938 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
59011897 TCGAAAAGAA
59011907 AAAAAAGAAA-AAAAAT
1 AAAAAAGAAAGAAAAAT
59011923 AAAAAAGAAAGAAAAA
1 AAAAAAGAAAGAAAAA
59011939 AGGAAAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAGAAAAAT
Found at i:59023075 original size:26 final size:24
Alignment explanation
Indices: 59023044--59023096 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
59023034 ATAATTTTTT
*
59023044 AAAAATCTAAAACTATTAAAAATAAA
1 AAAAATAT-AAACTATTAAAAA-AAA
* *
59023070 AAAAATATAAATTTTTAAAAAAAA
1 AAAAATATAAACTATTAAAAAAAA
59023094 AAA
1 AAA
59023097 TTCAATGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 11 0.46
26 7 0.29
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATATAAACTATTAAAAAAAA
Found at i:59024019 original size:17 final size:15
Alignment explanation
Indices: 59023972--59024019 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 15
59023962 TTTAATAATA
*
59023972 AATTTTTAAAATATT
1 AATTTTAAAAATATT
59023987 AATTTTAAATAATATT
1 AATTTTAAA-AATATT
59024003 ATATTATTAAAAATATT
1 A-ATT-TTAAAAATATT
59024020 CAATATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.28
16 7 0.24
17 9 0.31
18 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTTAAAAATATT
Found at i:59024024 original size:24 final size:24
Alignment explanation
Indices: 59023997--59024042 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
59023987 AATTTTAAAT
59023997 AATATT-ATATTATTAAAAATATTC
1 AATATTAATATT-TTAAAAATATTC
*
59024021 AATATTAATATTTTAATAATAT
1 AATATTAATATTTTAAAAATAT
59024043 ATATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AATATTAATATTTTAAAAATATTC
Found at i:59024028 original size:16 final size:15
Alignment explanation
Indices: 59023979--59024028 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
59023969 ATAAATTTTT
*
59023979 AAAATATTAATTTTA
1 AAAATATTAATATTA
59023994 AATAATATTATATTATTA
1 AA-AATATTA-A-TATTA
59024012 AAAATATTCAATATTA
1 AAAATATT-AATATTA
59024028 A
1 A
59024029 TATTTTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 2 0.07
16 13 0.43
17 8 0.27
18 7 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATATTAATATTA
Found at i:59024065 original size:40 final size:40
Alignment explanation
Indices: 59023980--59024071 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 40
59023970 TAAATTTTTA
59023980 AAATATTAATTTTAAATAATATTATATTATTAAAAATATT
1 AAATATTAATTTTAAATAATATTATATTATTAAAAATATT
* * * * *
59024020 CAATATTAATATTTTAATAATA-TATATTTATTACAATTATA
1 AAATATTAAT-TTTAAATAATATTATA-TTATTAAAAATATT
59024061 AATATATTAAT
1 AA-ATATTAAT
59024072 AATAAAGAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
40 13 0.30
41 22 0.51
42 8 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (40 bp):
AAATATTAATTTTAAATAATATTATATTATTAAAAATATT
Found at i:59033150 original size:19 final size:19
Alignment explanation
Indices: 59033113--59033151 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
59033103 TAAAAATGTA
*
59033113 AGGAATAATATATATATAT
1 AGGAATAATATATACATAT
59033132 AGGAA-AATATATAACATAT
1 AGGAATAATATAT-ACATAT
59033151 A
1 A
59033152 ATAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (19 bp):
AGGAATAATATATACATAT
Found at i:59033184 original size:21 final size:21
Alignment explanation
Indices: 59033160--59033213 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
59033150 TAATAAAATT
59033160 TATAAATAAAATG-TATAATAA
1 TATAAATAAAATGATA-AATAA
*
59033181 TATAAATAATATGATAAATAA
1 TATAAATAAAATGATAAATAA
59033202 TATATAA-AAAAT
1 TATA-AATAAAAT
59033214 AATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
TATAAATAAAATGATAAATAA
Found at i:59033189 original size:12 final size:11
Alignment explanation
Indices: 59033174--59033219 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
59033164 AATAAAATGT
59033174 ATAATAATATAA
1 ATAAT-ATATAA
59033186 ATAATATGATAA
1 ATAATAT-ATAA
59033198 ATAATATATAA
1 ATAATATATAA
*
59033209 AAAATAATATA
1 ATAAT-ATATA
59033220 TATACAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
ATAATATATAA
Found at i:59036260 original size:25 final size:24
Alignment explanation
Indices: 59036186--59036267 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 24
59036176 TTTTAAGTGA
*
59036186 TATTATTGTGTTTTGTATGCATTTGTAT
1 TATTATTGTGATTTG-ATGC-TTT-T-T
59036214 ATATTATTGTGATATT-AT--TTTTT
1 -TATTATTGTGAT-TTGATGCTTTTT
*
59036237 TATTATTGTGATTTGCATGCTTTTG
1 TATTATTGTGATTTG-ATGCTTTTT
59036262 TATTAT
1 TATTAT
59036268 ATTTATGTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
21 2 0.04
22 12 0.26
23 3 0.07
24 1 0.02
25 13 0.28
28 2 0.04
29 11 0.24
30 2 0.04
ACGTcount: A:0.21, C:0.04, G:0.15, T:0.61
Consensus pattern (24 bp):
TATTATTGTGATTTGATGCTTTTT
Found at i:59042927 original size:37 final size:37
Alignment explanation
Indices: 59042866--59043011 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
59042856 TACGTATGAT
* *
59042866 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
59042901 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
59042938 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
59042975 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
59043012 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:59043028 original size:46 final size:46
Alignment explanation
Indices: 59042975--59043243 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
59042965 TAAGTGTAGC
* **
59042975 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
59043021 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
59043067 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
59043119 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
59043165 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
59043217 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
59043244 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:59043094 original size:52 final size:52
Alignment explanation
Indices: 59043018--59043237 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
59043008 TAGCTAAAGC
* *
59043018 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
59043071 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
59043123 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
59043169 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
59043221 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
59043238 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:59043140 original size:98 final size:98
Alignment explanation
Indices: 59042975--59043243 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
59042965 TAAGTGTAGC
* * *
59042975 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
59043040 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
59043074 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
59043139 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
59043172 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
59043237 GATCAGA
66 GATCAGA
59043244 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:59046599 original size:31 final size:31
Alignment explanation
Indices: 59046543--59046610 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
59046533 GAAAAAAAAT
* *
59046543 TTCAAGCCCCAATGTAGGAATAATTGTCTAG
1 TTCAAGCCCCAATGTAGGAACAATTGTCAAG
* * *
59046574 TTCATGCCCTAATGTGGGAACAATTGTCAAG
1 TTCAAGCCCCAATGTAGGAACAATTGTCAAG
59046605 TTCAAG
1 TTCAAG
59046611 GACTAACTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (31 bp):
TTCAAGCCCCAATGTAGGAACAATTGTCAAG
Found at i:59046674 original size:91 final size:89
Alignment explanation
Indices: 59046493--59046761 Score: 337
Period size: 91 Copynumber: 3.0 Consensus size: 89
59046483 CAAGTTTAAA
* * * *
59046493 CCTAATATGAGAACAAATT-CCAAGTTCGAGGACTAACTT--AGAAAAAAAATTTCAAGCCCCAA
1 CCTAATATGGGAAC-AATTGCCAAGTTCAAGGACTAACTTGGACAAAAAAAATTTTAAGCCCCAA
* *
59046555 TGTAGGAATAATTGTCTAGTTCATGC
65 TGTA-GAACAATTGTCTAGTTCAGGC
* * *
59046581 CCTAATGTGGGAACAATTGTCAAGTTCAAGGACTAACTTGGACAAAAAAAATGTTTAAGCCACAA
1 CCTAATATGGGAACAATTGCCAAGTTCAAGGACTAACTTGGACAAAAAAAAT-TTTAAGCCCCAA
* *
59046646 TGTGAGAACAATTGTTTAGTTCGGGC
65 TGT-AGAACAATTGTCTAGTTCAGGC
* * *
59046672 CCTAATATGGGAACAATTGCCAAGCTCAAGGACTAACTTGGATAAAAAAAATTCTAAGCCCCAAT
1 CCTAATATGGGAACAATTGCCAAGTTCAAGGACTAACTTGGACAAAAAAAATTTTAAGCCCCAAT
*
59046737 GTAGAAACAATTGCCTAGTTCAGGC
66 GTAG-AACAATTGTCTAGTTCAGGC
59046762 TTTAATGTAA
Statistics
Matches: 155, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
87 4 0.03
88 30 0.19
89 2 0.01
90 40 0.26
91 78 0.50
92 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (89 bp):
CCTAATATGGGAACAATTGCCAAGTTCAAGGACTAACTTGGACAAAAAAAATTTTAAGCCCCAAT
GTAGAACAATTGTCTAGTTCAGGC
Found at i:59048069 original size:49 final size:49
Alignment explanation
Indices: 59047997--59048184 Score: 259
Period size: 49 Copynumber: 3.8 Consensus size: 49
59047987 TGAGGTCACG
59047997 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * * * * * *
59048046 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGACAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCA
* *
59048097 TGTGTAGTACTAAGTGCAGGATACTACGTGTACCGAATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* *
59048146 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATA
59048185 GCTTTGGCTA
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 75 0.64
50 4 0.03
51 38 0.32
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
Found at i:59048165 original size:100 final size:100
Alignment explanation
Indices: 59047992--59048179 Score: 349
Period size: 100 Copynumber: 1.9 Consensus size: 100
59047982 TATTGTGAGG
* *
59047992 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACT
59048057 AAGTGCAGGCTACTATGCGTACCTGACAACTTCGA
66 AAGTGCAGGCTACTATGCGTACCTGACAACTTCGA
59048092 TCACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACT
*
59048157 AAGTGCAGGCTACTATGTGTACC
66 AAGTGCAGGCTACTATGCGTACC
59048180 AGATAGCTTT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCTGACAACTTCGA
Found at i:59049385 original size:18 final size:18
Alignment explanation
Indices: 59049362--59049404 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
59049352 GAACGATTAT
* *
59049362 TTATTCAATAACAGTCAG
1 TTATTCAATAACAATCAA
**
59049380 TTATTCGGTAACAATCAA
1 TTATTCAATAACAATCAA
59049398 TTATTCA
1 TTATTCA
59049405 GGAATAATCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (18 bp):
TTATTCAATAACAATCAA
Found at i:59049527 original size:47 final size:47
Alignment explanation
Indices: 59049471--59049657 Score: 266
Period size: 47 Copynumber: 4.0 Consensus size: 47
59049461 TAGCAATACG
*
59049471 GTACACAGAGTACCTCATCGGAACAAATCTGGAACAGTAACAGTAAA
1 GTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAAA
* * * * * * **
59049518 GTATACAGAGTACCTCATCGGAACAAATCAGTAATAGTAGCAATACG
1 GTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAAA
*
59049565 GTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTACA
1 GTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAAA
* *
59049612 GTACACAGAGTAACTCATCGGAACAAATCCGAAACAGTAACAGTAA
1 GTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAA
59049658 CAATATCCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 122 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (47 bp):
GTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAAA
Found at i:59049620 original size:94 final size:94
Alignment explanation
Indices: 59049452--59049650 Score: 335
Period size: 94 Copynumber: 2.1 Consensus size: 94
59049442 GAAACAGTAA
*
59049452 CAGTAACAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCTGGAACAGTAACAGTAA
1 CAGTAACAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAA
* *
59049517 AGTATACAGAGTACCTCATCGGAACAAAT
66 AGTACACAGAGTAACTCATCGGAACAAAT
* *
59049546 CAGTAATAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAC
1 CAGTAACAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAA
59049611 AGTACACAGAGTAACTCATCGGAACAAAT
66 AGTACACAGAGTAACTCATCGGAACAAAT
* *
59049640 CCGAAACAGTA
1 CAGTAACAGTA
59049651 ACAGTAACAA
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (94 bp):
CAGTAACAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCCGGAACAGTAACAGTAA
AGTACACAGAGTAACTCATCGGAACAAAT
Found at i:59049702 original size:12 final size:12
Alignment explanation
Indices: 59049685--59049709 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59049675 AGTGCCGAAT
59049685 CGGTAACAGTAA
1 CGGTAACAGTAA
59049697 CGGTAACAGTAA
1 CGGTAACAGTAA
59049709 C
1 C
59049710 AGTAGTCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:59049883 original size:20 final size:20
Alignment explanation
Indices: 59049835--59049883 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
59049825 CACTTTTCAG
59049835 TTTTCAATTAATTCATATTT
1 TTTTCAATTAATTCATATTT
*
59049855 TAATT-AATTAATT-ATATATT
1 T-TTTCAATTAATTCATAT-TT
59049875 TTTTCAATT
1 TTTTCAATT
59049884 CAATATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 6 0.25
20 16 0.67
21 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTCAATTAATTCATATTT
Found at i:59053904 original size:20 final size:19
Alignment explanation
Indices: 59053866--59053916 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
59053856 ACTATTAAGT
* *
59053866 AAATATTTTTTTTATTTTA
1 AAATATTTTTTTGAATTTA
59053885 AAATATTATTTTTGAATTTA
1 AAATATT-TTTTTGAATTTA
59053905 ATAA-ATTTTTTT
1 A-AATATTTTTTT
59053917 AGTAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.43
20 14 0.50
21 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
AAATATTTTTTTGAATTTA
Found at i:59053910 original size:22 final size:20
Alignment explanation
Indices: 59053860--59053930 Score: 56
Period size: 22 Copynumber: 3.4 Consensus size: 20
59053850 TATATGACTA
*
59053860 TTAAGTAAATATTTTTTTTAT
1 TTAA-TAAATATTTTTTTAAT
*
59053881 TTTA-AAATATTATTTTTGAAT
1 TTAATAAATATT-TTTTT-AAT
59053902 TTAATAAAT-TTTTTTAGTAATT
1 TTAATAAATATTTTTT--TAA-T
59053924 TTAATAA
1 TTAATAA
59053931 TTAAACATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
19 7 0.17
20 9 0.22
21 12 0.29
22 13 0.32
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTAATAAATATTTTTTTAAT
Done.