Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 137 of 295
Found at i:42188683 original size:17 final size:18
Alignment explanation
Indices: 42188652--42188685 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42188642 TATTCTCCAT
*
42188652 TTTAATTTTCGCAATTTA
1 TTTAATTTTCACAATTTA
42188670 TTTAA-TTTCACAATTT
1 TTTAATTTTCACAATTT
42188686 CAATTCGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAATTTTCACAATTTA
Found at i:42193734 original size:38 final size:39
Alignment explanation
Indices: 42193614--42193740 Score: 147
Period size: 39 Copynumber: 3.4 Consensus size: 39
42193604 GGTGTTAAAA
* *
42193614 AACCTTTTTT-AAATGTTGCCTTAGACAAGGTCTATCCC
1 AACCTTTTTTAAAAGGTTGACTTAGACAAGGTCTATCCC
** **
42193652 AACC-TTTTT--AAGGTTGACTTAGATGA-CCCTATCCC
1 AACCTTTTTTAAAAGGTTGACTTAGACAAGGTCTATCCC
* *
42193687 AACCTTTTTTAAAAGGTTGAATTACACAAGGTCTATCCC
1 AACCTTTTTTAAAAGGTTGACTTAGACAAGGTCTATCCC
42193726 AACCTTTTTTAAAAG
1 AACCTTTTTTAAAAG
42193741 TCGGCTTATG
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
35 11 0.15
36 18 0.25
37 5 0.07
38 17 0.23
39 22 0.30
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (39 bp):
AACCTTTTTTAAAAGGTTGACTTAGACAAGGTCTATCCC
Found at i:42193740 original size:39 final size:38
Alignment explanation
Indices: 42193614--42193738 Score: 148
Period size: 38 Copynumber: 3.3 Consensus size: 38
42193604 GGTGTTAAAA
* *
42193614 AACCTTTTTTAAATGTTGCCTTAGACAAGGTCTATCCC
1 AACCTTTTTTAAAGGTTGACTTAGACAAGGTCTATCCC
** **
42193652 AACC-TTTTT-AAGGTTGACTTAGATGA-CCCTATCCC
1 AACCTTTTTTAAAGGTTGACTTAGACAAGGTCTATCCC
* *
42193687 AACCTTTTTTAAAAGGTTGAATTACACAAGGTCTATCCC
1 AACCTTTTTT-AAAGGTTGACTTAGACAAGGTCTATCCC
42193726 AACCTTTTTTAAA
1 AACCTTTTTTAAA
42193739 AGTCGGCTTA
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
35 11 0.15
36 18 0.25
37 5 0.07
38 20 0.28
39 17 0.24
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (38 bp):
AACCTTTTTTAAAGGTTGACTTAGACAAGGTCTATCCC
Found at i:42195093 original size:18 final size:18
Alignment explanation
Indices: 42195070--42195107 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42195060 TATTATCATT
42195070 TTATTAATAAAATTATTG
1 TTATTAATAAAATTATTG
42195088 TTATTAATAAAATTATTG
1 TTATTAATAAAATTATTG
42195106 TT
1 TT
42195108 TGATATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATTAATAAAATTATTG
Found at i:42195115 original size:18 final size:18
Alignment explanation
Indices: 42195070--42195116 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
42195060 TATTATCATT
*
42195070 TTATTAATAAAATTATTG
1 TTATGAATAAAATTATTG
*
42195088 TTATTAATAAAATTATTG
1 TTATGAATAAAATTATTG
42195106 TT-TGATATAAA
1 TTATGA-ATAAA
42195117 TATAATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
TTATGAATAAAATTATTG
Found at i:42198337 original size:71 final size:71
Alignment explanation
Indices: 42198221--42198362 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
42198211 AAAATAAAAT
*
42198221 ATTATTTATTTCATTTTCACATCTTTCCATATTTCATTATTCAACTCTTAATAGTAAGTTAATTC
1 ATTATTTATTTCATTTTCACATCTTTCCATATCTCATTATTCAACTCTTAATAGTAAGTTAATTC
42198286 CGTTTC
66 CGTTTC
*
42198292 ATTATTTATTTCATTTTCAGATCTTTCCATATCTCATTATTCAACTCTTAATAGTAAGTTAATTC
1 ATTATTTATTTCATTTTCACATCTTTCCATATCTCATTATTCAACTCTTAATAGTAAGTTAATTC
42198357 CGTTTC
66 CGTTTC
42198363 TTTCTTCCGC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (71 bp):
ATTATTTATTTCATTTTCACATCTTTCCATATCTCATTATTCAACTCTTAATAGTAAGTTAATTC
CGTTTC
Found at i:42201699 original size:10 final size:10
Alignment explanation
Indices: 42201686--42201715 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
42201676 TAAATATATA
42201686 TATGTGTGTG
1 TATGTGTGTG
42201696 TATGTGTGTG
1 TATGTGTGTG
*
42201706 TGTGTGTGTG
1 TATGTGTGTG
42201716 AATGAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (10 bp):
TATGTGTGTG
Found at i:42201917 original size:19 final size:15
Alignment explanation
Indices: 42201871--42201912 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
42201861 TATCTGTTTT
42201871 ATTGAATTTATATTG
1 ATTGAATTTATATTG
42201886 ATTGAATTTATATTG
1 ATTGAATTTATATTG
42201901 ATTGAA-TTATAT
1 ATTGAATTTATAT
42201913 AATATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:42202314 original size:23 final size:23
Alignment explanation
Indices: 42202284--42202370 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
42202274 GCTTTATCGA
* *
42202284 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
42202307 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
42202328 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
42202350 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
42202371 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:42206584 original size:14 final size:14
Alignment explanation
Indices: 42206565--42206594 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42206555 TGGCTGAAAC
42206565 TGATATGCACTAAA
1 TGATATGCACTAAA
*
42206579 TGATATGCACTGAA
1 TGATATGCACTAAA
42206593 TG
1 TG
42206595 GTAACTGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (14 bp):
TGATATGCACTAAA
Found at i:42209403 original size:7 final size:7
Alignment explanation
Indices: 42209386--42209417 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
42209376 ATTTAAATGT
42209386 AAAAATAA
1 AAAAAT-A
42209394 AAAAATA
1 AAAAATA
42209401 AAAAATA
1 AAAAATA
42209408 AAAAATA
1 AAAAATA
42209415 AAA
1 AAA
42209418 CCTTAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:42209573 original size:21 final size:21
Alignment explanation
Indices: 42209547--42209596 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
42209537 CTGTGAGACT
*
42209547 TTTTAGTTGGTATACTAACAA
1 TTTTAGTCGGTATACTAACAA
42209568 TTTTAGTCGGTATACTAACAA
1 TTTTAGTCGGTATACTAACAA
42209589 TTTTAGTC
1 TTTTAGTC
42209597 CTTAGCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (21 bp):
TTTTAGTCGGTATACTAACAA
Found at i:42215041 original size:68 final size:68
Alignment explanation
Indices: 42214964--42215097 Score: 164
Period size: 68 Copynumber: 2.0 Consensus size: 68
42214954 TTTTAATAGT
* * * ** *
42214964 TTAATATTAAATTTAATTTAATACCTATCTTA-AT-AGTATTTTATTAATTTAATATTAAAGTGA
1 TTAATATTAAA-TTAATCTAATACCTATC-AAGATAAATATTAGATTAATTTAATATTAAAATGA
42215027 TTATC
64 TTATC
**
42215032 TTAATATTAAATTAATCTAATATTTATCAAGATAAATATTAGATTAATTTAATATTAAAATGATT
1 TTAATATTAAATTAATCTAATACCTATCAAGATAAATATTAGATTAATTTAATATTAAAATGATT
42215097 A
66 A
42215098 AGTTTAATCA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
66 1 0.02
67 16 0.29
68 39 0.70
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (68 bp):
TTAATATTAAATTAATCTAATACCTATCAAGATAAATATTAGATTAATTTAATATTAAAATGATT
ATC
Found at i:42215098 original size:20 final size:20
Alignment explanation
Indices: 42215006--42215105 Score: 58
Period size: 20 Copynumber: 4.5 Consensus size: 20
42214996 ATAGTATTTT
*
42215006 ATTAATTTAATATTAAAGTG
1 ATTAATTTAATATTAAAATG
* *
42215026 ATT-ATCTTAATATTAAATTA
1 ATTAAT-TTAATATTAAAATG
* *
42215046 ATCTAATATTTATCAAGATAAATATTAG
1 AT-TAAT-TTAAT--A-TTAAA-A-T-G
42215074 ATTAATTTAATATTAAAATG
1 ATTAATTTAATATTAAAATG
42215094 ATTAAGTTTAAT
1 ATTAA-TTTAAT
42215106 CATAGTTGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
19 2 0.03
20 23 0.38
21 8 0.13
22 7 0.11
23 4 0.07
24 2 0.03
25 4 0.07
26 4 0.07
27 5 0.08
28 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (20 bp):
ATTAATTTAATATTAAAATG
Found at i:42220477 original size:20 final size:18
Alignment explanation
Indices: 42220427--42220478 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
42220417 CTACAAAATA
42220427 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
42220444 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
42220464 AATATTAAATTAATA
1 AATATTAAATTAATA
42220479 AAATATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:42224912 original size:40 final size:40
Alignment explanation
Indices: 42224814--42225156 Score: 476
Period size: 40 Copynumber: 8.6 Consensus size: 40
42224804 TCCTCGTTCA
* * * * *
42224814 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42224853 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42224893 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42224933 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42224973 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42225013 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42225053 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
42225093 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
42225133 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42225157 CAGCATTCAA
Statistics
Matches: 280, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 37 0.13
40 235 0.84
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42232983 original size:40 final size:40
Alignment explanation
Indices: 42232840--42233181 Score: 467
Period size: 40 Copynumber: 8.6 Consensus size: 40
42232830 TCCTCGTTCA
* * * * *
42232840 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42232879 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42232919 AATGCCTTC-GGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42232958 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42232998 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42233038 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42233078 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
42233118 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
42233158 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42233182 CAGCATTCAA
Statistics
Matches: 278, Mismatches: 20, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
39 75 0.27
40 195 0.70
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42234999 original size:46 final size:46
Alignment explanation
Indices: 42234946--42235045 Score: 155
Period size: 46 Copynumber: 2.2 Consensus size: 46
42234936 TATATATACA
* *
42234946 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
* * *
42234992 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
42235038 CATCTCAT
1 CATCTCAT
42235046 CCATGCTAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.26, C:0.32, G:0.07, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
Found at i:42235113 original size:47 final size:47
Alignment explanation
Indices: 42235054--42235521 Score: 792
Period size: 47 Copynumber: 10.0 Consensus size: 47
42235044 ATCCATGCTA
* *
42235054 GCCATTCTGCCTTATCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
42235101 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
42235148 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
*
42235195 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCGCATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
* *
42235242 GCCATTCGGCCTTATCACACAGATGCATGTTCACATTCATCGCATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
* * *
42235289 GCCATTGGGCCTTATCACATATATGCATGTTCACATTCATCGCATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
* *
42235336 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACGTTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
*
42235383 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
42235430 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
* * * **
42235477 GCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACAT
42235522 AAAATCCTAA
Statistics
Matches: 404, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 404 1.00
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
Found at i:42235166 original size:22 final size:22
Alignment explanation
Indices: 42235092--42235213 Score: 58
Period size: 23 Copynumber: 5.3 Consensus size: 22
42235082 GTTCACATTC
42235092 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
42235114 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
42235138 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* *
42235161 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
42235185 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
42235208 ATCACA
1 ATCACA
42235214 CATATGCATG
Statistics
Matches: 74, Mismatches: 8, Indels: 36
0.63 0.07 0.31
Matches are distributed among these distances:
22 18 0.24
23 22 0.30
24 22 0.30
25 12 0.16
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:42239371 original size:28 final size:28
Alignment explanation
Indices: 42239340--42239439 Score: 128
Period size: 28 Copynumber: 3.5 Consensus size: 28
42239330 CTGACTGATT
*
42239340 TCGCACACATAGCGCTCGATTAAAAAAC
1 TCGCACACATAGTGCTCGATTAAAAAAC
* ** *
42239368 TCGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTG-CTCGATTAAAAAAC
* *
42239397 TCGCACACATAGTGCTCGATTGAAGAAC
1 TCGCACACATAGTGCTCGATTAAAAAAC
42239425 TCGCACACATAGTGC
1 TCGCACACATAGTGC
42239440 CTCAACTACT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 36 0.60
29 24 0.40
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (28 bp):
TCGCACACATAGTGCTCGATTAAAAAAC
Found at i:42239407 original size:57 final size:57
Alignment explanation
Indices: 42239340--42239500 Score: 223
Period size: 57 Copynumber: 2.8 Consensus size: 57
42239330 CTGACTGATT
* * * *
42239340 TCGCACACATAGCGCTCGATTAAAAAACTCGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
** *
42239397 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACTGATT
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
* * * *
42239454 TGGCACACATAGTGCTCGGTTGAAGAACTTGCACACACAGTGCCTCA
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCA
42239501 TAATTCCAGC
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 93 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (57 bp):
TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
Found at i:42239573 original size:40 final size:40
Alignment explanation
Indices: 42239508--42239702 Score: 358
Period size: 40 Copynumber: 4.9 Consensus size: 40
42239498 TCATAATTCC
*
42239508 AGCACGAATGC-CTTCGAGG-TTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCG-GGACTTAGCCCGGATATATCACT
42239547 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
42239587 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
42239627 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
42239667 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
42239703 ATAACTCTCA
Statistics
Matches: 153, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
39 13 0.08
40 140 0.92
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
Found at i:42241235 original size:46 final size:46
Alignment explanation
Indices: 42241182--42241318 Score: 229
Period size: 46 Copynumber: 3.0 Consensus size: 46
42241172 TATATATACA
* * * * *
42241182 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTCATATC
42241228 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTCATATC
42241274 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTCATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTCATAT
42241319 ATACACTTCC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.26, C:0.31, G:0.08, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTCATATC
Found at i:42241692 original size:47 final size:47
Alignment explanation
Indices: 42241332--42241671 Score: 635
Period size: 47 Copynumber: 7.2 Consensus size: 47
42241322 CACTTCCACG
* *
42241332 TTCATCACATTGGCCATTCTGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
42241379 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
42241426 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
42241473 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
* *
42241520 TTCATCAAATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
42241567 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
*
42241614 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
42241661 TTCATCACATT
1 TTCATCACATT
42241672 CCCTATCACA
Statistics
Matches: 286, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 286 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.34
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
Found at i:42245930 original size:18 final size:18
Alignment explanation
Indices: 42245907--42245942 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
42245897 GATATGATAC
42245907 TAAAAT-TATTAAAAAAAT
1 TAAAATATA-TAAAAAAAT
42245925 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
42245943 CATGGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:42246265 original size:17 final size:18
Alignment explanation
Indices: 42246212--42246354 Score: 211
Period size: 17 Copynumber: 7.9 Consensus size: 18
42246202 AATCATATTT
42246212 TCTAAGATTGCATATCATA
1 TCTAAGATTGC-TATCATA
*
42246231 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
42246249 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
42246266 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
42246283 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
42246301 TATAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
42246318 TCTAAGATTGCATATCATA
1 TCTAAGATTGC-TATCATA
42246337 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
42246355 TGAAGATTAT
Statistics
Matches: 115, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
17 48 0.42
18 31 0.27
19 36 0.31
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:42246268 original size:35 final size:35
Alignment explanation
Indices: 42246212--42246346 Score: 200
Period size: 35 Copynumber: 3.8 Consensus size: 35
42246202 AATCATATTT
42246212 TCTAAGATTGCATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGC-TATCATATCTAAGATTG-AATCATA
*
42246249 TCTAAGATTG-TATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCTATCATATCTAAGATTGAATCATA
* * *
42246283 TCTAAGATTGCAATCATATATAAGATTGTATCATA
1 TCTAAGATTGCTATCATATCTAAGATTGAATCATA
42246318 TCTAAGATTGCATATCATATCTAAGATTG
1 TCTAAGATTGC-TATCATATCTAAGATTG
42246347 CATATCATTG
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
34 16 0.18
35 50 0.55
36 15 0.16
37 10 0.11
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGCTATCATATCTAAGATTGAATCATA
Found at i:42246291 original size:52 final size:53
Alignment explanation
Indices: 42246212--42246354 Score: 243
Period size: 52 Copynumber: 2.7 Consensus size: 53
42246202 AATCATATTT
*
42246212 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCAATCATATATAAGATTGTATCATA
42246266 TCTAAGATTG-TATCATATCTAAGATTGCAATCATATATAAGATTGTATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCAATCATATATAAGATTGTATCATA
42246318 TCTAAGATTGCATATCATATCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCATATCTAAGATTGCA-ATCAT
42246355 TGAAGATTAT
Statistics
Matches: 85, Mismatches: 1, Indels: 5
0.93 0.01 0.05
Matches are distributed among these distances:
52 51 0.60
54 29 0.34
55 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (53 bp):
TCTAAGATTGATATCATATCTAAGATTGCAATCATATATAAGATTGTATCATA
Found at i:42246759 original size:45 final size:45
Alignment explanation
Indices: 42246704--42247022 Score: 310
Period size: 45 Copynumber: 7.1 Consensus size: 45
42246694 GGAAGGCGAT
* * * *
42246704 ATCTGCTATCTTTGATCTGCTCCCCATCTAACACAGAG-TCGGCAA
1 ATCTGTTATCTTTGATCTGCTCCCCGTCTAATACAGAGAT-GCCAA
* * *
42246749 ATCTGTTATCTTCGATCTACTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* *
42246794 ATCTGTTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* *
42246839 ATCT-TCT-TCTTTAATCTGCTCCCCGTCTAATACATAGATGCCAA
1 ATCTGT-TATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
42246883 ATCTGTTATCTCTGATTTGTTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * * * *
42246928 ATCTGTCATC-TTGAATCTGCT--TCGATGTAA-ACACATGAAGGTCAG
1 ATCTGTTATCTTTG-ATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAA
* *
42246973 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTG-T-TATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
42247020 ATC
1 ATC
42247023 ATCTTGGCTC
Statistics
Matches: 223, Mismatches: 37, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
43 6 0.03
44 47 0.21
45 140 0.63
46 1 0.00
47 16 0.07
48 7 0.03
49 6 0.03
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (45 bp):
ATCTGTTATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:42246907 original size:89 final size:90
Alignment explanation
Indices: 42246704--42247763 Score: 346
Period size: 78 Copynumber: 12.5 Consensus size: 90
42246694 GGAAGGCGAT
* * * * * *
42246704 ATCTGCTATCTTTGATCTGCTCCCCATCTAACACAGAG-TCGGCAAATCTGTTATCTTCG-ATCT
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGAT-GCCAAATCTGTCATCTT-GAATCT
*
42246767 ACTCCCCGTCTAATACAGAGACGCCAA
64 GCTCCCCGTCTAATACAGAGACGCCAA
* * *
42246794 ATCTGTTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCT-TCTTCTTTAATCTGC
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCTGC
* *
42246858 TCCCCGTCTAATACATAGATGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
* *
42246883 ATCTGTTATC-TCTGATTTGTTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCTG
1 ATCTGTTATCTTC-GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCTG
* * * * * *
42246947 CT--TCGATGTAA-ACACATGAAGGTCAG
65 CTCCCCG-TCTAATACAGA-G-ACGCCAA
* **
42246973 ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGCTCT
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCT
*
42247034 GCT-----TC-AATGA-AG-G--TCC-A
64 GCTCCCCGTCTAAT-ACAGAGACGCCAA
* *
42247051 ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGATCT
1 ATCTGTTA--TCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCT
* * *
42247112 GCT-----TC-AAT---GA-AGGTCAG
64 GCTCCCCGTCTAATACAGAGACGCCAA
* *
42247129 ATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGATCT
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCT
*
42247190 GCT-----TC-AATGA-AG-G--TCC-A
64 GCTCCCCGTCTAAT-ACAGAGACGCCAA
* *
42247207 ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGATCT
1 ATCTGTTA--TCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCT
* *
42247268 GCT-----TC-AATA-A-AG--GTCAG
64 GCTCCCCGTCTAATACAGAGACGCCAA
* *
42247285 ATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGATCT
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCT
* * *
42247346 GCT-----TC-AAT---GA-AGGTCAG
64 GCTCCCCGTCTAATACAGAGACGCCAA
* * * ** * *
42247363 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGT-TTCTTCG-ATT
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTT-GAATC
* * * * * * *
42247426 TGTTCTCTGGC-AGTACAAAGATGCCAA
63 TGCTCCCCGTCTAATACAGAGACGCCAA
* * * * * * * *
42247453 ATTTGCTATCTTTGATATGCTCTCTGAC-AATACAGAGATACCAAATCTG-CTATCTTTG-ATCT
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTC-ATC-TTGAATCT
* * * *
42247515 GCTCTCTG-ATAATACAGAGATGCCAA
64 GCTCCCCGTCTAATACAGAGACGCCAA
* * * * * * * * *
42247541 GTTTGCTATCTTTGATCTGCTCTCTGAC-AATACAGAGACGCCAAATCT-ACTATCTTCG-ATCT
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTC-ATCTT-GAATCT
* * * *
42247603 GCTCTCTGAC-AATACAGAGATGCCAA
64 GCTCCCCGTCTAATACAGAGACGCCAA
* * * * * * *
42247629 ATCTGCTATCTTCGATCTGCTCTCTGAC-AATACAGAGACGCCAAATATG-CTATTTTCG-ATCT
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTC-ATCTT-GAATCT
* * * *
42247691 GCTCTCTGACT-ATACAGAGATGCCAA
64 GCTCCCCGTCTAATACAGAGACGCCAA
* * * * * *
42247717 ATCTGCTATCTTCGATCTGCTCTCTGTTTAATACAAATATGCCAAAT
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAAT
42247764 TTGTTTCTTC
Statistics
Matches: 817, Mismatches: 96, Indels: 115
0.79 0.09 0.11
Matches are distributed among these distances:
75 1 0.00
76 2 0.00
77 8 0.01
78 299 0.37
79 4 0.00
80 2 0.00
81 10 0.01
82 3 0.00
83 2 0.00
84 2 0.00
85 1 0.00
86 3 0.00
87 20 0.02
88 251 0.31
89 99 0.12
90 72 0.09
91 2 0.00
92 34 0.04
93 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (90 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGAATCTGC
TCCCCGTCTAATACAGAGACGCCAA
Found at i:42247091 original size:78 final size:78
Alignment explanation
Indices: 42246962--42247412 Score: 762
Period size: 78 Copynumber: 5.8 Consensus size: 78
42246952 ATGTAAACAC
42246962 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
*
42247027 TGGCTCTGCTTCA
66 TGGATCTGCTTCA
* *
42247040 ATGAAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
42247104 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
*
42247118 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
42247183 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* *
42247196 ATGAAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
42247260 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* *
42247274 ATAAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
42247339 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * **
42247352 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
42247413 TGTTTCTTCG
Statistics
Matches: 350, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
77 4 0.01
78 342 0.98
79 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:42247498 original size:44 final size:44
Alignment explanation
Indices: 42247363--42247807 Score: 543
Period size: 44 Copynumber: 10.1 Consensus size: 44
42247353 TGAAGGTCAG
* * **
42247363 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAA
1 ATCTGCTA--TCTTCGATCTGCTCTCTGAC-AATACAGAGATGCCAA
* * * * * *
42247410 ATCTG-TTTCTTCGATTTGTTCTCTGGCAGTACAAAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * * *
42247453 ATTTGCTATCTTTGATATGCTCTCTGACAATACAGAGATACCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* *
42247497 ATCTGCTATCTTTGATCTGCTCTCTGATAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * * *
42247541 GTTTGCTATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
*
42247585 ATCTACTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
*
42247629 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * *
42247673 ATATGCTATTTTCGATCTGCTCTCTGACTATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
** * *
42247717 ATCTGCTATCTTCGATCTGCTCTCTGTTTAATACAAATATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTG-ACAATACAGAGATGCCAA
* * * *
42247762 ATTTG-TTTCTTCGATTTGTTCTCTGACAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
42247805 ATC
1 ATC
42247808 ATCTTGGATC
Statistics
Matches: 343, Mismatches: 53, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
43 32 0.09
44 288 0.84
45 17 0.05
46 1 0.00
47 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.34
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
Found at i:42257770 original size:18 final size:18
Alignment explanation
Indices: 42257747--42257781 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42257737 GATATGATAC
42257747 TAAAAT-TATTAAAAAAAT
1 TAAAATATA-TAAAAAAAT
42257765 TAAAATATATAAAAAAA
1 TAAAATATATAAAAAAA
42257782 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:42258070 original size:22 final size:21
Alignment explanation
Indices: 42258035--42258110 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 21
42258025 AAAAGGTATC
* *
42258035 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
42258056 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
42258079 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
42258098 TAC-AATCATATCT
1 TACAAATCATATCT
42258111 AAGATTGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 6 0.13
19 10 0.22
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:42258095 original size:19 final size:19
Alignment explanation
Indices: 42258071--42258161 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
42258061 AATCATATCT
42258071 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
42258090 TCTAAGATTACA-ATCATA
1 TCTAAGATTGCATATCATA
42258108 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
42258125 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
42258144 TCTAAGATTTCATATCAT
1 TCTAAGATTGCATATCAT
42258162 TGAAGATTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 15 0.23
19 35 0.53
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:42258125 original size:40 final size:39
Alignment explanation
Indices: 42258048--42258161 Score: 139
Period size: 35 Copynumber: 3.0 Consensus size: 39
42258038 AAATTAAATC
42258048 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-AAATCATA--TTCTAAGATTGCATATCATA
42258090 TCTAAGATTAC-AATCATA-TCTAAGATTG--TATCATA
1 TCTAAGATTACAAATCATATTCTAAGATTGCATATCATA
* * *
42258125 TCTAAGATTGCATATCATA-TCTAAGATTTCATATCAT
1 TCTAAGATTACAAATCATATTCTAAGATTGCATATCAT
42258162 TGAAGATTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
35 17 0.26
36 15 0.23
37 10 0.15
38 6 0.09
40 7 0.11
42 11 0.17
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.38
Consensus pattern (39 bp):
TCTAAGATTACAAATCATATTCTAAGATTGCATATCATA
Found at i:42258318 original size:21 final size:20
Alignment explanation
Indices: 42258280--42258319 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42258270 TTGGACTTCG
**
42258280 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
42258300 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
42258320 TCTGGGCTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:42259361 original size:40 final size:40
Alignment explanation
Indices: 42259231--42259362 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 40
42259221 AATTTGTAGG
*
42259231 CAAGCCACCAATAATGCA-AGCAAGCTGCCAGTAATGTGGT
1 CAAGCCACCAGTAATGCAGA-CAAGCTGCCAGTAATGTGGT
* * * * * ***
42259271 CAAGTCACCATTAGTGCAGACAGGCTGCCAGTATTGCAAAT
1 CAAGCCACCAGTAATGCAGACAAGCTGCCAGTAATG-TGGT
* * * *
42259312 -AAACTACCAGTAATGCAGACAAGTTGCTAGTAATGTGGT
1 CAAGCCACCAGTAATGCAGACAAGCTGCCAGTAATGTGGT
42259351 CAAGCCACCAGT
1 CAAGCCACCAGT
42259363 GTTGCAGATA
Statistics
Matches: 67, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
39 1 0.01
40 64 0.96
41 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (40 bp):
CAAGCCACCAGTAATGCAGACAAGCTGCCAGTAATGTGGT
Found at i:42268573 original size:46 final size:46
Alignment explanation
Indices: 42268424--42268645 Score: 200
Period size: 46 Copynumber: 4.8 Consensus size: 46
42268414 TCACTTGTGT
* * * ** *
42268424 GAGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCACGTTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
* ** **
42268470 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGTATTAAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* *
42268518 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
* * *
42268565 -AGCCAGTGTAAGACATGTCTGGGACATTCATC-GACTACGAGA--T
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGA
* *
42268608 GTGCCAGTGTAAGACCATGTCTGGTACATAGCATCGGC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
42268646 ACAGATATGC
Statistics
Matches: 141, Mismatches: 27, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
44 12 0.09
45 16 0.11
46 63 0.45
47 29 0.21
48 21 0.15
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
Found at i:42275972 original size:47 final size:44
Alignment explanation
Indices: 42275859--42275985 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 44
42275849 TCACTTGTGT
* *
42275859 GAGCTAGTGTAAGACATATCTGGGACATGCATCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTAGGACATGCATCGG-C-CATTATGA
*
42275905 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGG-CATTGA-GA
1 GAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCATT-ATGA
42275950 CGAGTGCTAGTGTAAGACATGTCTAGGACATGCATC
1 -GA--GCTAGTGTAAGACATGTCTAGGACATGCATC
42275986 AACCTTGAGA
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
45 6 0.08
46 21 0.30
47 26 0.37
48 18 0.25
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCATTATGA
Found at i:42276008 original size:46 final size:46
Alignment explanation
Indices: 42275903--42276031 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 46
42275893 GCCACATTAT
**
42275903 GAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGAC
1 GAGAGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCAACATTGAGAC
* * *
42275951 GAGTGCTAGTGTAAGACATGTCTAGGACATGCATCAACCTTGAGAC
1 GAGAGCCAGTGTAAGACATGTCTAGGACATGCATCAACATTGAGAC
* * * *
42275997 GTA-AGCCAGTGTAAGATATGTTTGGGATATGCATC
1 G-AGAGCCAGTGTAAGACATGTCTAGGACATGCATC
42276032 TGCTACGAGA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 40 0.58
47 15 0.22
48 14 0.20
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
GAGAGCCAGTGTAAGACATGTCTAGGACATGCATCAACATTGAGAC
Found at i:42278375 original size:132 final size:132
Alignment explanation
Indices: 42277958--42278896 Score: 842
Period size: 132 Copynumber: 7.1 Consensus size: 132
42277948 TTAATTGGAG
* * * * * * *
42277958 TTAGGTTGC-AGTCTTAAATTAGC-AACCTTAACAATATCAACCGCTATCTTAAATTAGAGAGCT
1 TTAGGTTGCGA-TCTTAAATCAACGAACCTTAACAATATCAGCTGCGATCTTAAATCAGTGAGCT
* * * * * * *
42278021 TTTCGAAGTTGCGATCTAAGATCATCTAACTCAAATAAAATTTGTTCATGTTATTAAAAT-GAAT
65 TTTTGGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTT-AAATCAAAT
42278085 GAAC
129 GAAC
* * * * *
42278089 TTAGGTTGCGATATTAAATCAGC-AACCTTAACAATATTAGCTGTGATAC-TAAATCAGCGAGCT
1 TTAGGTTGCGATCTTAAATCAACGAACCTTAACAATATCAGCTGCGAT-CTTAAATCAGTGAGCT
* ** * * * * *
42278152 GTTTGGAGTTGTTAT-TGAAATGAACTAAGC-CAAATAAATTTTTTTCATGTTCTTAAATCAAAT
65 TTTTGGAGTTGCGATCTGAGATCAACTAA-CTCAAATAAAATTTGTTCATGATCTTAAATCAAAT
*
42278215 AAAC
129 GAAC
* * *
42278219 TTAGGTTGTGATCTTAAATAAACGAACCTTAACAATATCAACTGCGATCTTAAATCAGTGAGCTT
1 TTAGGTTGCGATCTTAAATCAACGAACCTTAACAATATCAGCTGCGATCTTAAATCAGTGAGCTT
** * * * * **
42278284 TTTAAAGTTGCGATCTGAGATCAGCTAACTAAAATAAAATTTGTTCACGGTCTTAAATTGAATGA
66 TTTGGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATGA
42278349 AC
131 AC
* * * * *
42278351 TTAAGTGGCGATCTTAAATCAACGAACTTTAACAATATCAGCTGCGATATTAAATTAGTGAGCTT
1 TTAGGTTGCGATCTTAAATCAACGAACCTTAACAATATCAGCTGCGATCTTAAATCAGTGAGCTT
*** * * * *
42278416 TTCAAAATTGC-AACTTGAAATCAACTAACTCAAATAAAATTTGTTCTTGATCTTAAATCAAATG
66 TTTGGAGTTGCGATC-TGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATG
42278480 AAC
130 AAC
* ** * * * **
42278483 TTAGGTTACGATCTTAAATCAGTGAACCTTAACAATATCAAC-GACGATATTAAATTAGAAAGCT
1 TTAGGTTGCGATCTTAAATCAACGAACCTTAACAATATCAGCTG-CGATCTTAAATCAGTGAGCT
* ** ** * * *
42278547 TTTTGGAGTTGCGATATGAGATCAGTTAACTCAAATAAGTTTTTTTCATTATCATAAATCAAATG
65 TTTTGGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATG
42278612 AAC
130 AAC
* * * * * ** * *
42278615 TTAGGTTGCGATCTTAAATCAACGAACCTTAACAATATTAGTTTCTATCTTAAACCAACGAGATG
1 TTAGGTTGCGATCTTAAATCAACGAACCTTAACAATATCAGCTGCGATCTTAAATCAGTGAGCTT
** * * * * *
42278680 TTCAGAGTTGCGATTTGGGATCAACTAACTCAAATAAAATTTGTCCATGATCTT-GATCGAATGA
66 TTTGGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATGA
*
42278744 AG
131 AC
* ** * ** * *
42278746 TTAGGTTGTGATCTTAAATCAGTGAACCTTAATC-ATATCAGTTATGATATTAAATCAATGAGCT
1 TTAGGTTGCGATCTTAAATCAACGAACCTTAA-CAATATCAGCTGCGATCTTAAATCAGTGAGCT
* **
42278810 TTTTGGAGTTGCGAT-TGGAGA-CTAGCTAACTCAAATAAAATTTGTTCATGATCTTAAATTTAA
65 TTTTGGAGTTGCGATCT-GAGATC-AACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAA
42278873 TGAAC
128 TGAAC
*
42278878 TTAGGTTGCAATCTTAAAT
1 TTAGGTTGCGATCTTAAAT
42278897 ATGTGATCTT
Statistics
Matches: 648, Mismatches: 144, Indels: 31
0.79 0.17 0.04
Matches are distributed among these distances:
129 4 0.01
130 58 0.09
131 214 0.33
132 371 0.57
133 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (132 bp):
TTAGGTTGCGATCTTAAATCAACGAACCTTAACAATATCAGCTGCGATCTTAAATCAGTGAGCTT
TTTGGAGTTGCGATCTGAGATCAACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATGA
AC
Found at i:42278522 original size:264 final size:263
Alignment explanation
Indices: 42277981--42279231 Score: 1032
Period size: 264 Copynumber: 4.8 Consensus size: 263
42277971 TTAAATTAGC
* * * * * * *
42277981 AACCTTAACAATATCAACCGCTATCTTAAATTAGAGAGCTTTTCGAAGTTGCGATCTAAGATCAT
1 AACCTTAACAATATCAACTGCGATATTAAATCAGAGAGCTTTTTGAAGTTGCGATCTGAGATCAG
* * * * *
42278046 CTAACTCAAATAAAATTTGTTCATGTTATTAAAATGAATGAACTTAGGTTGCGATATTAAATCAG
66 CTAACTCAAATAAAATTTGTTCATGATCTTAAATTGAATGAACTTAGGTTGCGATCTTAAATCAA
* * * ** *
42278111 C-AACCTTAACAATATTAGCTGTGATACTAAATCAGCGAGCTGTTT-GGAGTTGTTATTGAAATG
131 CGAACCTTAACAATATTAGCTGCGATATTAAATCAGCGAGCT-TTTCAGAGTTGCAATTGAAATC
* * * *
42278174 AACTAAGC-CAAATAAATTTTTTTCATGTTCTTAAATCAAATAAACTTAGGTTGTGATCTTAAAT
195 AACTAA-CTCAAATAAAATTTGTTCATGATCTTAAATCAAATGAACTTAGGTTGTGATCTTAAAT
* **
42278238 AAACG
259 CAGTG
* * *
42278243 AACCTTAACAATATCAACTGCGATCTTAAATCAGTGAGCTTTTTAAAGTTGCGATCTGAGATCAG
1 AACCTTAACAATATCAACTGCGATATTAAATCAGAGAGCTTTTTGAAGTTGCGATCTGAGATCAG
* * * * *
42278308 CTAACTAAAATAAAATTTGTTCACGGTCTTAAATTGAATGAACTTAAGTGGCGATCTTAAATCAA
66 CTAACTCAAATAAAATTTGTTCATGATCTTAAATTGAATGAACTTAGGTTGCGATCTTAAATCAA
* * * * * *
42278373 CGAACTTTAACAATATCAGCTGCGATATTAAATTAGTGAGCTTTTCAAAATTGCAACTTGAAATC
131 CGAACCTTAACAATATTAGCTGCGATATTAAATCAGCGAGCTTTTCAGAGTTGCAA-TTGAAATC
* **
42278438 AACTAACTCAAATAAAATTTGTTCTTGATCTTAAATCAAATGAACTTAGGTTACGATCTTAAATC
195 AACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATGAACTTAGGTTGTGATCTTAAATC
42278503 AGTG
260 AGTG
* * * *
42278507 AACCTTAACAATATCAAC-GACGATATTAAATTAGAAAGCTTTTTGGAGTTGCGATATGAGATCA
1 AACCTTAACAATATCAACTG-CGATATTAAATCAGAGAGCTTTTTGAAGTTGCGATCTGAGATCA
* ** * * * **
42278571 GTTAACTCAAATAAGTTTTTTTCATTATCATAAATCAAATGAACTTAGGTTGCGATCTTAAATCA
65 GCTAACTCAAATAAAATTTGTTCATGATCTTAAATTGAATGAACTTAGGTTGCGATCTTAAATCA
* * * * * * * * * **
42278636 ACGAACCTTAACAATATTAGTTTCTATCTTAAACCAACGAGATGTTCAGAGTTGCGATTTGGGAT
130 ACGAACCTTAACAATATTAGCTGCGATATTAAATCAGCGAGCTTTTCAGAGTTGC-AATTGAAAT
* * * *
42278701 CAACTAACTCAAATAAAATTTGTCCATGATCTT-GATCGAATGAAGTTAGGTTGTGATCTTAAAT
194 CAACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATGAACTTAGGTTGTGATCTTAAAT
42278765 CAGTG
259 CAGTG
** ** *
42278770 AACCTTAATC-ATATCAGTTATGATATTAAATCA-ATGAGCTTTTTGGAGTTGCGAT-TGGAGA-
1 AACCTTAA-CAATATCAACTGCGATATTAAATCAGA-GAGCTTTTTGAAGTTGCGATCT-GAGAT
*
42278831 CTAGCTAACTCAAATAAAATTTGTTCATGATCTTAAATTTAATGAACTTAGGTT--G--C---AA
63 C-AGCTAACTCAAATAAAATTTGTTCATGATCTTAAATTGAATGAACTTAGGTTGCGATCTTAAA
* * * * * * *
42278889 T--------CTT-A-AATA-T-G-T--GATCTTGATTTAGCGAGCTTTTTAGAGTTTCGATCTGA
127 TCAACGAACCTTAACAATATTAGCTGCGATATTAAATCAGCGAGCTTTTCAGAGTTGCAAT-TGA
* * ** * * * **
42278939 GATCAACTAATTCAAAT-ATTTTTTTTCATGATCTAAAATCGAATGAACTTAGGTTGCAAT-TCT
191 AATCAACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATGAACTTAGGTTGTGATCT-T
*
42279002 AAATGAGCT-
255 AAATCAG-TG
* ** * * * * *
42279011 AACCTTAACAATAACAACTATGATCTTAAATCAAAAAGATGTTT-AGAGTTGCGATCTGAGAT-A
1 AACCTTAACAATATCAACTGCGATATTAAATCAGAGAGCTTTTTGA-AGTTGCGATCTGAGATCA
* * * *
42279074 TACTAACTCAAATAAAATTTGTTCATGATCTTAAATCGATTGAACTTAGGTT-CTGATATTAAAT
65 -GCTAACTCAAATAAAATTTGTTCATGATCTTAAATTGAATGAACTTAGGTTGC-GATCTTAAAT
** * * * ** * **
42279138 CAGTGAATCTTGAA-AATATTAGCTACGATCTTAAATCAATGAGCTGTTC-GAAGTTGTGATCTG
128 CAACGAACCTT-AACAATATTAGCTGCGATATTAAATCAGCGAGCTTTTCAG-AGTTGCAAT-TG
*
42279201 AAATCAGCTAACTCAAATAAAATTTGTTCAT
190 AAATCAACTAACTCAAATAAAATTTGTTCAT
42279232 AAAATAAAGT
Statistics
Matches: 795, Mismatches: 149, Indels: 88
0.77 0.14 0.09
Matches are distributed among these distances:
240 17 0.02
241 159 0.20
242 3 0.00
243 2 0.00
244 1 0.00
245 1 0.00
246 4 0.01
247 1 0.00
248 6 0.01
256 6 0.01
258 5 0.01
259 2 0.00
260 1 0.00
261 2 0.00
262 121 0.15
263 205 0.26
264 258 0.32
265 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Consensus pattern (263 bp):
AACCTTAACAATATCAACTGCGATATTAAATCAGAGAGCTTTTTGAAGTTGCGATCTGAGATCAG
CTAACTCAAATAAAATTTGTTCATGATCTTAAATTGAATGAACTTAGGTTGCGATCTTAAATCAA
CGAACCTTAACAATATTAGCTGCGATATTAAATCAGCGAGCTTTTCAGAGTTGCAATTGAAATCA
ACTAACTCAAATAAAATTTGTTCATGATCTTAAATCAAATGAACTTAGGTTGTGATCTTAAATCA
GTG
Found at i:42279137 original size:132 final size:132
Alignment explanation
Indices: 42278921--42279231 Score: 316
Period size: 132 Copynumber: 2.4 Consensus size: 132
42278911 TAGCGAGCTT
* * ** *
42278921 TTTAGAGTTTCGATCTGAGATCA-ACTAATTCAAAT-ATTTTTTTTCATGATCTAAAATCGAATG
1 TTTAGAGTTGCGATCTGAGAT-ATACTAACTCAAATAAAATTTGTTCATGATCTAAAATCGAATG
* *
42278984 AACTTAGGTTGCAATTCTAAATGAGCT-AACCTT-AACAATAACAACTATGATCTTAAATCAAAA
65 AACTTAGGTTGCAATTCTAAATCAG-TGAACCTTGAA-AATAACAACTACGATCTTAAATCAAAA
42279047 AGATG
128 AGATG
* *
42279052 TTTAGAGTTGCGATCTGAGATATACTAACTCAAATAAAATTTGTTCATGATCTTAAATCGATTGA
1 TTTAGAGTTGCGATCTGAGATATACTAACTCAAATAAAATTTGTTCATGATCTAAAATCGAATGA
* * ** * **
42279117 ACTTAGGTT-CTGATAT-TAAATCAGTGAATCTTGAAAATATTAGCTACGATCTTAAATCAATGA
66 ACTTAGGTTGC-AAT-TCTAAATCAGTGAACCTTGAAAATAACAACTACGATCTTAAATCAAAAA
*
42279180 GCTG
129 GATG
* *
42279184 -TTCGAAGTTGTGATCTGA-A-ATCAGCTAACTCAAATAAAATTTGTTCAT
1 TTTAG-AGTTGCGATCTGAGATAT-A-CTAACTCAAATAAAATTTGTTCAT
42279232 AAAATAAAGT
Statistics
Matches: 152, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
130 3 0.02
131 38 0.25
132 108 0.71
133 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (132 bp):
TTTAGAGTTGCGATCTGAGATATACTAACTCAAATAAAATTTGTTCATGATCTAAAATCGAATGA
ACTTAGGTTGCAATTCTAAATCAGTGAACCTTGAAAATAACAACTACGATCTTAAATCAAAAAGA
TG
Found at i:42284561 original size:22 final size:22
Alignment explanation
Indices: 42284533--42284578 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
42284523 ATGATATGAT
*
42284533 TACTGTTCATTGATGTGATATC
1 TACTGTTCATTGATGTAATATC
42284555 TACTGTTCATTGATGTAATATC
1 TACTGTTCATTGATGTAATATC
42284577 TA
1 TA
42284579 GGTAGGCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (22 bp):
TACTGTTCATTGATGTAATATC
Found at i:42284836 original size:24 final size:24
Alignment explanation
Indices: 42284809--42284863 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
42284799 TAATAATAAG
* * *
42284809 TAGATTTCAAATTTTAAGTTTAAC
1 TAGATTTCAAATATTAAATTCAAC
* *
42284833 TAGATTTTAAATATTAAATTCAAT
1 TAGATTTCAAATATTAAATTCAAC
42284857 TAGATTT
1 TAGATTT
42284864 AGTTTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (24 bp):
TAGATTTCAAATATTAAATTCAAC
Found at i:42286728 original size:6 final size:7
Alignment explanation
Indices: 42286712--42286739 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
42286702 TTTTAAATCC
42286712 AAAAATA
1 AAAAATA
42286719 AAAAATA
1 AAAAATA
42286726 AAAAATA
1 AAAAATA
42286733 AAAAATA
1 AAAAATA
42286740 CCCCACCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:42290277 original size:43 final size:43
Alignment explanation
Indices: 42290218--42290299 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
42290208 CACGGCATGG
*
42290218 CACACGGGCATTTGTGGCCATAGCCTAGGGCACACGGGCTAGC
1 CACACGGGCATGTGTGGCCATAGCCTAGGGCACACGGGCTAGC
* *
42290261 CACATGGGCATGTGTGGCCATAGCCTGGGGCACACGGGC
1 CACACGGGCATGTGTGGCCATAGCCTAGGGCACACGGGC
42290300 ATGTGTGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.20, C:0.29, G:0.35, T:0.16
Consensus pattern (43 bp):
CACACGGGCATGTGTGGCCATAGCCTAGGGCACACGGGCTAGC
Found at i:42299399 original size:15 final size:15
Alignment explanation
Indices: 42299379--42299412 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42299369 ATTGTGTGAC
42299379 TTGAAATGGT-TGATA
1 TTGAAATGGTATGA-A
42299394 TTGAAATGGTATGAA
1 TTGAAATGGTATGAA
42299409 TTGA
1 TTGA
42299413 GTTTAATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.38
Consensus pattern (15 bp):
TTGAAATGGTATGAA
Found at i:42300935 original size:28 final size:28
Alignment explanation
Indices: 42300902--42301002 Score: 148
Period size: 28 Copynumber: 3.6 Consensus size: 28
42300892 GCCCCTTTAA
* * *
42300902 GCCCAATCTCATTCATATGGCCCATCGG
1 GCCCAATCACATTCATATGGTCCATCAG
42300930 GCCCAATCACATTCATATGGTCCATCAG
1 GCCCAATCACATTCATATGGTCCATCAG
* * *
42300958 CCCCAATCACTTTCATATGGTCCGTCAG
1 GCCCAATCACATTCATATGGTCCATCAG
42300986 GCCCAATCACATTCATA
1 GCCCAATCACATTCATA
42301003 GTCATGCAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.26
Consensus pattern (28 bp):
GCCCAATCACATTCATATGGTCCATCAG
Found at i:42301240 original size:16 final size:16
Alignment explanation
Indices: 42301219--42301252 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
42301209 CTAAACTTCC
42301219 GGCTTTTCGGCATTTT
1 GGCTTTTCGGCATTTT
42301235 GGCTTTTCGGCATTTT
1 GGCTTTTCGGCATTTT
42301251 GG
1 GG
42301253 GATTTGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.29, T:0.47
Consensus pattern (16 bp):
GGCTTTTCGGCATTTT
Found at i:42303474 original size:40 final size:40
Alignment explanation
Indices: 42303378--42303561 Score: 221
Period size: 40 Copynumber: 4.5 Consensus size: 40
42303368 TATTCGGATG
*
42303378 ATATCCGGGCTAATTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC---TAGTTGCT
*
42303421 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTG-CT
* **
42303461 ATATCTGGGCTAAGTCCCGAAGGCATTCATGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTG-CT
* *
42303501 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGCT
* *
42303541 ATAT-CTGGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
42303562 ATACTTGGGT
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 16 0.13
40 77 0.62
41 2 0.02
43 30 0.24
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTGCT
Found at i:42306537 original size:8 final size:8
Alignment explanation
Indices: 42306521--42306652 Score: 52
Period size: 8 Copynumber: 15.4 Consensus size: 8
42306511 AATGGATTTT
*
42306521 AATAAAAA
1 AATATAAA
42306529 AATATAAA
1 AATATAAA
* *
42306537 ATCTTTCAAA
1 A-ATAT-AAA
42306547 AATTATAGAA
1 AA-TATA-AA
42306557 AATATATAAA
1 AAT--ATAAA
*
42306567 AATTTAAA
1 AATATAAA
42306575 AATATATTATA
1 AATATA--A-A
42306586 AA-ATATAA
1 AATATA-AA
42306594 AATATAAA
1 AATATAAA
42306602 AATATAAA
1 AATATAAA
*
42306610 AA-ATATA
1 AATATAAA
*
42306617 TATATAAA
1 AATATAAA
* * *
42306625 GAGAGAAA
1 AATATAAA
42306633 AATAGTAAA
1 AATA-TAAA
* *
42306642 ATTTTAAA
1 AATATAAA
42306650 AAT
1 AAT
42306653 TTTAAACTTT
Statistics
Matches: 93, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
7 5 0.05
8 49 0.53
9 14 0.15
10 19 0.20
11 6 0.06
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (8 bp):
AATATAAA
Found at i:42306558 original size:28 final size:29
Alignment explanation
Indices: 42306527--42306607 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
42306517 TTTTAATAAA
*
42306527 AAAATATAAAATCTTTCAAAAAT-TA-TAG
1 AAAATATAAAATATTT-AAAAATATATTAG
* *
42306555 AAAATATATAAAAATTTAAAAATATATTAT
1 AAAATATA-AAATATTTAAAAATATATTAG
42306585 AAAATATAAAATA--TAAAAATATA
1 AAAATATAAAATATTTAAAAATATA
42306608 AAAAATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 10 0.22
28 14 0.30
29 12 0.26
30 10 0.22
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATATAAAATATTTAAAAATATATTAG
Found at i:42306566 original size:30 final size:30
Alignment explanation
Indices: 42306525--42306618 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 30
42306515 GATTTTAATA
* *
42306525 AAAAAATATAAAATCTTTCAAAAAT-TA-TAG
1 AAAATATATAAAA-ATTT-AAAAATATATTAG
42306555 AAAATATATAAAAATTTAAAAATATATTA-
1 AAAATATATAAAAATTTAAAAATATATTAG
* *
42306584 TAAA-ATAT-AAAATATAAAAATATA--A-
1 AAAATATATAAAAATTTAAAAATATATTAG
42306609 AAAATATATA
1 AAAATATATA
42306619 TATAAAGAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
25 4 0.07
26 4 0.07
27 15 0.27
28 10 0.18
29 8 0.15
30 14 0.25
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (30 bp):
AAAATATATAAAAATTTAAAAATATATTAG
Found at i:42306585 original size:21 final size:20
Alignment explanation
Indices: 42306544--42306618 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 20
42306534 AAAATCTTTC
*
42306544 AAAAATTATAGAAAATATAT
1 AAAAATTATAAAAAATATAT
42306564 AAAAATT-T-AAAAATATATT
1 AAAAATTATAAAAAATATA-T
42306583 ATAAAA-TAT---AAA-ATAT
1 A-AAAATTATAAAAAATATAT
42306599 AAAAA-TATAAAAAATATAT
1 AAAAATTATAAAAAATATAT
42306618 A
1 A
42306619 TATAAAGAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
15 7 0.15
16 2 0.04
17 3 0.06
18 14 0.30
19 9 0.19
20 12 0.26
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (20 bp):
AAAAATTATAAAAAATATAT
Found at i:42310195 original size:21 final size:22
Alignment explanation
Indices: 42310146--42310208 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
42310136 TATGTATCTC
*
42310146 TTTAAAAATTTAATTAATAAAT
1 TTTAAAAATTTATTTAATAAAT
*
42310168 TTT-AAAATTTATTTAAT-ATT
1 TTTAAAAATTTATTTAATAAAT
* *
42310188 TTTAAAAA-ATATTTAAAAAAT
1 TTTAAAAATTTATTTAATAAAT
42310209 ATATAATTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 12 0.35
21 19 0.56
22 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAAAATTTATTTAATAAAT
Found at i:42314054 original size:5 final size:5
Alignment explanation
Indices: 42314044--42314073 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
42314034 TATACTGACA
42314044 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT
42314074 ATGATTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TGTTT
Found at i:42322158 original size:15 final size:15
Alignment explanation
Indices: 42322138--42322181 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
42322128 TCTATTGATC
42322138 GAGAAAAAGAAAAAA
1 GAGAAAAAGAAAAAA
*
42322153 GAGAAAAA-CAAAAA
1 GAGAAAAAGAAAAAA
*
42322167 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
42322182 GAAAGAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 12 0.50
16 4 0.17
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.02
Consensus pattern (15 bp):
GAGAAAAAGAAAAAA
Found at i:42322182 original size:15 final size:14
Alignment explanation
Indices: 42322142--42322193 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
42322132 TTGATCGAGA
*
42322142 AAAAGAAAAAAGAGA
1 AAAAG-AAAAAGAGG
*
42322157 AAAACAAAAAGAGTG
1 AAAAGAAAAAGAG-G
*
42322172 AAAAGAAAAAGAAAG
1 AAAAGAAAAAG-AGG
42322187 AAAAGAA
1 AAAAGAA
42322194 TGAGGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 8 0.26
15 22 0.71
16 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAGAGG
Found at i:42326862 original size:45 final size:46
Alignment explanation
Indices: 42326804--42326891 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
42326794 AGTAGGAAGA
* * *
42326804 TACAAATCCTATA-CCCTGAACTGTAGTGGGATGGATTGAAGATGG
1 TACAAATCCTATACCCCCGAACTGCAGTGGGATGGATGGAAGATGG
* **
42326849 TACAAATCTTATACCCCCGAGTTGCAGTGGGATGGATGGAAGA
1 TACAAATCCTATACCCCCGAACTGCAGTGGGATGGATGGAAGA
42326892 AACCACAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 12 0.33
46 24 0.67
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (46 bp):
TACAAATCCTATACCCCCGAACTGCAGTGGGATGGATGGAAGATGG
Found at i:42326874 original size:80 final size:81
Alignment explanation
Indices: 42326724--42326876 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 81
42326714 TGAAGAAGCC
** * * *
42326724 ACAAACCCTATACCCCTGAGTTGCAGTGGGATGGATTGAAGACGATACAGATCATATGCCCCTGA
1 ACAAACCCTATACCCCTGAACTGCAGTGGGATGGATTGAAGACGATACAAATCATATACCCCCGA
42326789 ATTGCAGTAGGAAGAT
66 ATTGCAGTAGGAAGAT
* * * * *
42326805 ACAAATCCTATA-CCCTGAACTGTAGTGGGATGGATTGAAGATGGTACAAATCTTATACCCCCGA
1 ACAAACCCTATACCCCTGAACTGCAGTGGGATGGATTGAAGACGATACAAATCATATACCCCCGA
*
42326869 GTTGCAGT
66 ATTGCAGT
42326877 GGGATGGATG
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
80 50 0.82
81 11 0.18
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (81 bp):
ACAAACCCTATACCCCTGAACTGCAGTGGGATGGATTGAAGACGATACAAATCATATACCCCCGA
ATTGCAGTAGGAAGAT
Found at i:42327577 original size:143 final size:140
Alignment explanation
Indices: 42327319--42327635 Score: 424
Period size: 143 Copynumber: 2.2 Consensus size: 140
42327309 CAAATGGCAG
* *
42327319 ATCTTATCTTCCTGAAGTTGCAGTGAAGTAGATTGAAGCCACCAGCCTTATCTCGTTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAGCCTTATCTCGCTGAAGTTGC
* * * *
42327384 AGTGGAGCAGACTGAAGACATCGAATCTTATTTCCTTGACGTTGCAGTGGAACAGATTAAAGCTA
66 AGCGGAACAGACTGAAGACATCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTA
*
42327449 TAAATTATGGA-AA
131 -AAA--AT-CACAA
* * *
42327462 ATCTTATCTTCCTAAAGTTGCAGTGGAGCATATTGAAGCCACCAGCCTTATCTTC-CTGAAGTTG
1 ATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAGCCTTATC-TCGCTGAAGTTG
* **
42327526 CAGCGGAACAGACTGACGACAAT-AAATCTTATTTCCCTGACGTTTTAGTGGAACAGATTAAAGC
65 CAGCGGAACAGACTGAAGAC-ATCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGC
42327590 TAAAAATCACAA
129 TAAAAATCACAA
* *
42327602 ATCTTATCTTCGTGAAGTTGCAGTGAAGAAGATT
1 ATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATT
42327636 CAATATACGA
Statistics
Matches: 153, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
139 1 0.01
140 33 0.22
142 3 0.02
143 112 0.73
144 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (140 bp):
ATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGCCACCAGCCTTATCTCGCTGAAGTTGC
AGCGGAACAGACTGAAGACATCAAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTA
AAAATCACAA
Found at i:42327840 original size:45 final size:46
Alignment explanation
Indices: 42327730--42327841 Score: 120
Period size: 46 Copynumber: 2.5 Consensus size: 46
42327720 AACCGAAGCC
* * *
42327730 ACAATCCTTATCTCTCTGAAGTTGCAGTAGAGTAGCATAAAAATAT
1 ACAATTCTTATCTCTTTGAAGTTGCAGTAGAGCAGCATAAAAATAT
* * * * **
42327776 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAG-GTTGAAAT-T
1 ACAATTCTTATCTCTTTGAAGTTGCAGTAGAGCAGCATAAAAATAT
42327820 ACCAATTCTTATCTCTTTGAAG
1 A-CAATTCTTATCTCTTTGAAG
42327842 ATTTAGCGGA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
44 2 0.04
45 23 0.43
46 29 0.54
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (46 bp):
ACAATTCTTATCTCTTTGAAGTTGCAGTAGAGCAGCATAAAAATAT
Found at i:42333310 original size:22 final size:22
Alignment explanation
Indices: 42333284--42333326 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
42333274 AATGTTTTAG
42333284 GGTAATACTGTAACTTATCTTA
1 GGTAATACTGTAACTTATCTTA
42333306 GGTAATACTGTAACTTATCTT
1 GGTAATACTGTAACTTATCTT
42333327 TTTTTAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (22 bp):
GGTAATACTGTAACTTATCTTA
Found at i:42334303 original size:15 final size:15
Alignment explanation
Indices: 42334283--42334312 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42334273 TAATGTATTT
42334283 AATTTATATAACAAA
1 AATTTATATAACAAA
*
42334298 AATTTATATTACAAA
1 AATTTATATAACAAA
42334313 GTTTGTTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTTATATAACAAA
Found at i:42334313 original size:63 final size:63
Alignment explanation
Indices: 42334235--42334360 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
42334225 CAATGTACCT
42334235 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGATGTAATGTATTTAATTTATATAACAAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGATGTAATGTATTTAATTTATATAACAAA
* * *
42334298 AATTTATATTACAAAGTTTGTTCCAATTTTTTATGTTGTAATGTATTTAATTTATATTACAAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGATGTAATGTATTTAATTTATATAACAAA
42334361 GTTTGATCCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (63 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAATGATGTAATGTATTTAATTTATATAACAAA
Found at i:42334365 original size:48 final size:48
Alignment explanation
Indices: 42334298--42334389 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
42334288 ATATAACAAA
* *
42334298 AATTTATATTACAAAGTTTGTTCCAATTTTTTA-TGTTGTAATGTATTT
1 AATTTATATTACAAAGTTTGATCCAA-GTTTTAGTGTTGTAATGTATTT
*
42334346 AATTTATATTACAAAGTTTGATCCAAGTTTTAGTGTTTTAATGT
1 AATTTATATTACAAAGTTTGATCCAAGTTTTAGTGTTGTAATGT
42334390 TATAATGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 5 0.12
48 35 0.88
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (48 bp):
AATTTATATTACAAAGTTTGATCCAAGTTTTAGTGTTGTAATGTATTT
Found at i:42335917 original size:68 final size:68
Alignment explanation
Indices: 42335820--42335990 Score: 209
Period size: 68 Copynumber: 2.5 Consensus size: 68
42335810 TTTTTAAGGG
* * *
42335820 ATTAAAATTAATTTTTAATGAAAACAGTGAAGAAGTGAGCTATTGGAGTATCCTCTAGTTAATAT
1 ATTAAAATTAATTTTTAATGAAAATAGTGAAGAAGTGAGCTATGGGAGTATCCTCTAGTCAATAT
42335885 GAA
66 GAA
* * * * * *
42335888 ATTAAAATTAATCTTTTAATG-AAATAGTGATGGAGTGAGTTATGGGAGTATTCTCTGGTCAATG
1 ATTAAAATTAAT-TTTTAATGAAAATAGTGAAGAAGTGAGCTATGGGAGTATCCTCTAGTCAATA
**
42335952 TGGG
65 TGAA
*
42335956 ATTAAAATTAAAATTTTAATGAAAATAGTGAAGAA
1 ATTAAAATT-AATTTTTAATGAAAATAGTGAAGAA
42335991 ATTGTCACTT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
68 65 0.76
69 21 0.24
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (68 bp):
ATTAAAATTAATTTTTAATGAAAATAGTGAAGAAGTGAGCTATGGGAGTATCCTCTAGTCAATAT
GAA
Found at i:42336359 original size:68 final size:69
Alignment explanation
Indices: 42336256--42336417 Score: 177
Period size: 68 Copynumber: 2.4 Consensus size: 69
42336246 TTTAAGGGAT
* * * * * * ** *
42336256 TAAAATTAA-TTTTTAATGAGAATATTGATCGAAGTGAGCTATGTGAGTATTCTCTAATGAATGT
1 TAAAATTAACTTTTTAATAAAAATAGTGA-AGAAGTGAGCTATGAGAATATTCTCTAACCAATAT
42336320 GAGAC
65 GAGAC
* *
42336325 T-AAATTAACTTTGTT-ATAAAAATAGTGAAGAAGTGAGCTATGAGAATATTCTTTAGCCAATAT
1 TAAAATTAACTTT-TTAATAAAAATAGTGAAGAAGTGAGCTATGAGAATATTCTCTAACCAATAT
*
42336388 GAGAT
65 GAGAC
42336393 TAAAATTAACTTTTTAATAAAAATA
1 TAAAATTAACTTTTTAATAAAAATA
42336418 ATTAAGAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
68 41 0.53
69 34 0.44
70 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (69 bp):
TAAAATTAACTTTTTAATAAAAATAGTGAAGAAGTGAGCTATGAGAATATTCTCTAACCAATATG
AGAC
Found at i:42341758 original size:48 final size:47
Alignment explanation
Indices: 42341666--42341800 Score: 146
Period size: 48 Copynumber: 2.8 Consensus size: 47
42341656 GAATTCATTG
* * * * * *
42341666 ATTTAGCTTCGGGCTATGATATTGGCACATTGAGTGTGAGCTTTATTA
1 ATTTGGCTTCGGGCCATGATATTAGCAC-TTGGGTGCGAACTTTATTA
*
42341714 ATTTGGCTTCGGGCCATGATATCT-GCACTTCGGGTGCGAACTTTATTG
1 ATTTGGCTTCGGGCCATGATAT-TAGCACTT-GGGTGCGAACTTTATTA
**
42341762 ATTTGGCTTTAGGCCATGATATTAGCACTTTGGGTGCGA
1 ATTTGGCTTCGGGCCATGATATTAGCAC-TTGGGTGCGA
42341801 GATACATTGA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
47 3 0.04
48 69 0.92
49 3 0.04
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (47 bp):
ATTTGGCTTCGGGCCATGATATTAGCACTTGGGTGCGAACTTTATTA
Found at i:42341810 original size:48 final size:48
Alignment explanation
Indices: 42341714--42341829 Score: 137
Period size: 48 Copynumber: 2.4 Consensus size: 48
42341704 AGCTTTATTA
* **
42341714 ATTTGGCTTCGGGCCATGATATCTGCACTTCGGGTGCGAACTTTATTG
1 ATTTGGCTTCAGGCCATGATATCTGCACTTCGGGTGCGAACTACATTG
* *
42341762 ATTTGGCTTTAGGCCATGATAT-TAGCACTTTGGGTGCGAGA-TACATTG
1 ATTTGGCTTCAGGCCATGATATCT-GCACTTCGGGTGCGA-ACTACATTG
**
42341810 AGCTGGCTTCAGGCCATGAT
1 ATTTGGCTTCAGGCCATGAT
42341830 TTGAGAACTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 56 0.97
49 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.34
Consensus pattern (48 bp):
ATTTGGCTTCAGGCCATGATATCTGCACTTCGGGTGCGAACTACATTG
Found at i:42347938 original size:28 final size:29
Alignment explanation
Indices: 42347896--42348010 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
42347886 TACCGGTATT
* *
42347896 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
42347924 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
42347953 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
42347982 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
42348010 T
1 T
42348011 TCATGCTCAC
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
28 27 0.35
29 49 0.64
30 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:42348264 original size:15 final size:16
Alignment explanation
Indices: 42348225--42348263 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
42348215 CCAAACTTTT
42348225 GACTTTTTGGCATTTC
1 GACTTTTTGGCATTTC
42348241 GACTTTTTGGCATTTC
1 GACTTTTTGGCATTTC
*
42348257 GGCTTTT
1 GACTTTT
42348264 GCCGATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.18, G:0.21, T:0.51
Consensus pattern (16 bp):
GACTTTTTGGCATTTC
Found at i:42354651 original size:48 final size:48
Alignment explanation
Indices: 42354595--42354734 Score: 199
Period size: 48 Copynumber: 2.9 Consensus size: 48
42354585 CATTAAGGAA
*
42354595 TTCATTGATTTGGCTTCGGGACATGATATTGGCACTTCGGGTGCAAGC
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCAAGC
* * * ***
42354643 TTTATTGATTTGGCTTCGGGCCATGATATCGGTACTTCGGGTATGAGC
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCAAGC
* *
42354691 TTCATTGATTTGGCTTCGGGCCATGATATTAGCAGTTCGGGTGC
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGC
42354735 GAGATAATTG
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36
Consensus pattern (48 bp):
TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCAAGC
Found at i:42356990 original size:16 final size:16
Alignment explanation
Indices: 42356952--42356984 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42356942 CCAAACGTTT
*
42356952 GACTTTTTGGCATTTC
1 GACTTTTCGGCATTTC
42356968 GACTTTTCGGCATTTC
1 GACTTTTCGGCATTTC
42356984 G
1 G
42356985 GGTTTTACCG
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:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (16 bp):
GACTTTTCGGCATTTC
Found at i:42361255 original size:29 final size:28
Alignment explanation
Indices: 42361198--42361282 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
42361188 TACCTGTATT
*
42361198 TGGCCCATTAGGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
*
42361226 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTCATA
* * *
42361255 TGTCCCGTTAGGCCCATTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
42361283 ATCATACTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 26 0.52
29 24 0.48
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:42362814 original size:16 final size:16
Alignment explanation
Indices: 42362793--42362824 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42362783 AAGTTCAGGA
*
42362793 TTTCAGGATTTTTGGG
1 TTTCAGAATTTTTGGG
42362809 TTTCAGAATTTTTGGG
1 TTTCAGAATTTTTGGG
42362825 GCGTTACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
TTTCAGAATTTTTGGG
Found at i:42364042 original size:160 final size:162
Alignment explanation
Indices: 42363838--42364140 Score: 423
Period size: 160 Copynumber: 1.9 Consensus size: 162
42363828 TGAGTTATAG
* *
42363838 GAGTCTTTTCTAGTCAATATGGAATTAAATTTAACTTTTTAATGAAAATAATGAAAAACTAAGCT
1 GAGTCTTTTCTAGTCAATATAGAATTAAATTTAACTTTTTAATGAAAATAATGAAAAAATAAGCT
* * * * *
42363903 ATGAGAGTATTCTCTAGTCATTGTGGGATTAAAATAAACTTTTTAATAAAAATAGTGAA-AATTT
66 ATGAGAATATTCTCTAGTCAATGCGGGATTAAAATAAACATTTTAATAAAAATAGTGAAGAAATT
*
42363967 GTCATTTATTTATTAGAAAAAGTGAGATATTA
131 GTCACTTATTTATTAGAAAAAGTGAGATATTA
* * * * **
42363999 GAGTGTTTTCTAGTCAATATAG-ATTCGAA-TTAACTTTTTAATGAAAATTATGAAAAAATGATT
1 GAGTCTTTTCTAGTCAATATAGAATT-AAATTTAACTTTTTAATGAAAATAATGAAAAAATAAGC
* * *
42364062 TATGAGAATATTCTCTAGTCAATGCGGGATTAAAATTATCATTTTAATGAAAATAGTGAAGAAAT
65 TATGAGAATATTCTCTAGTCAATGCGGGATTAAAATAAACATTTTAATAAAAATAGTGAAGAAAT
42364127 TGTCACTTATTTAT
130 TGTCACTTATTTAT
42364141 AACTTAAATG
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
160 85 0.69
161 38 0.31
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (162 bp):
GAGTCTTTTCTAGTCAATATAGAATTAAATTTAACTTTTTAATGAAAATAATGAAAAAATAAGCT
ATGAGAATATTCTCTAGTCAATGCGGGATTAAAATAAACATTTTAATAAAAATAGTGAAGAAATT
GTCACTTATTTATTAGAAAAAGTGAGATATTA
Found at i:42365548 original size:24 final size:24
Alignment explanation
Indices: 42365482--42365556 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
42365472 CTTGGGTGGC
* *
42365482 GGCGGTGGTGCTGGTGGTGGAGTT
1 GGCGGTGGAGCTGGTGGTGGTGTT
* * *
42365506 GGAGGTGGAG-TCGGAGGTGCTGTT
1 GGCGGTGGAGCT-GGTGGTGGTGTT
42365530 GGCGGTGGAGCTGGTGGTGGTGTT
1 GGCGGTGGAGCTGGTGGTGGTGTT
42365554 GGC
1 GGC
42365557 ACTGGTGTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.02
24 39 0.95
25 1 0.02
ACGTcount: A:0.07, C:0.09, G:0.57, T:0.27
Consensus pattern (24 bp):
GGCGGTGGAGCTGGTGGTGGTGTT
Found at i:42372508 original size:21 final size:23
Alignment explanation
Indices: 42372469--42372525 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
42372459 GTTTTAAAAT
* *
42372469 TTGGGCTCAGGTAGTTTTA-GG-A
1 TTGGGCT-AGGTTGGTTTAGGGTA
42372491 TTGGGCTAGGTTGGTTTAGGGTA
1 TTGGGCTAGGTTGGTTTAGGGTA
42372514 TTGGGCTAGGTT
1 TTGGGCTAGGTT
42372526 AGTTGGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 9 0.29
22 9 0.29
23 13 0.42
ACGTcount: A:0.14, C:0.07, G:0.40, T:0.39
Consensus pattern (23 bp):
TTGGGCTAGGTTGGTTTAGGGTA
Found at i:42373125 original size:95 final size:95
Alignment explanation
Indices: 42372962--42373147 Score: 336
Period size: 95 Copynumber: 2.0 Consensus size: 95
42372952 TGCTCTTCAC
** *
42372962 TCTATTCCACTGTTGAATGCAGGGAGATAGAGTTATTGGCTTCAATGTACTCCACTGTAGTCAGG
1 TCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGG
*
42373027 GAGGTAAAATCTGCCATCTTTGATCTCCAA
66 GAGGTAAAATCTGCCATCTTCGATCTCCAA
42373057 TCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGG
1 TCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGG
42373122 GAGGTAAAATCTGCCATCTTCGATCT
66 GAGGTAAAATCTGCCATCTTCGATCT
42373148 GCTTCGCTGC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (95 bp):
TCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGG
GAGGTAAAATCTGCCATCTTCGATCTCCAA
Found at i:42373232 original size:44 final size:43
Alignment explanation
Indices: 42373130--42373675 Score: 443
Period size: 44 Copynumber: 12.4 Consensus size: 43
42373120 GGGAGGTAAA
* * * **
42373130 ATCTGCCATCTTCGATCTGCTTCGCTGCCAACTACAGGAAGGTAAG
1 ATCTGCTATCTTCGATCTACTTC-C-ACCAA-TACAGGAAGACAAG
* * * * *
42373176 ATCTACAATCTTCGATCTACTTCACGCCAATACATGAAGATAAG
1 ATCTGCTATCTTCGATCTACTTC-CACCAATACAGGAAGACAAG
* * **
42373220 ATCTGCTTTCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTAC-TT-CCACCAATACAGGAAGACAAG
* * * *
42373265 ATCTGC-ATCGTCGATCCACTTCCTACCAATATAGGAAGACAGG
1 ATCTGCTATCTTCGATCTACTTCC-ACCAATACAGGAAGACAAG
* * *
42373308 ACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CACCAATACAGGAAGACAAG
* * * *
42373352 ATCTGC-ATCGTCGATCCACTTCCTACCAATATAGGAAGACAGG
1 ATCTGCTATCTTCGATCTACTTCC-ACCAATACAGGAAGACAAG
* * *
42373395 ACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CACCAATACAGGAAGACAAG
* * **
42373439 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTT--CCACCAATACAGGAAGACAAG
* * * * *
42373484 ATCTGC-ATCGTCGATCCACCTCCTACCAATATAGGAAGATAAG
1 ATCTGCTATCTTCGATCTACTTCC-ACCAATACAGGAAGACAAG
* * * * *
42373527 ACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CACCAATACAGGAAGACAAG
* * * * * *
42373571 ATCTGCTTTCTGCGATCTACTTTACGCCAATACATGAAGATAAG
1 ATCTGCTATCTTCGATCTAC-TTCCACCAATACAGGAAGACAAG
* * * *
42373615 ATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCC-ACCAATACAGGAAGACAAG
*
42373658 ATCTGATATCTTCGATCT
1 ATCTGCTATCTTCGATCT
42373676 GTTCTCTGGG
Statistics
Matches: 401, Mismatches: 83, Indels: 34
0.77 0.16 0.07
Matches are distributed among these distances:
42 8 0.02
43 108 0.27
44 208 0.52
45 54 0.13
46 23 0.06
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (43 bp):
ATCTGCTATCTTCGATCTACTTCCACCAATACAGGAAGACAAG
Found at i:42373340 original size:132 final size:131
Alignment explanation
Indices: 42373132--42373675 Score: 617
Period size: 132 Copynumber: 4.1 Consensus size: 131
42373122 GAGGTAAAAT
* * * * ** * * *
42373132 CTGCCATCTTCGATCTGCTTCGCTGCCAACTACAGGAAGGTAAGATCTACAATCTTCGATCTACT
1 CTGCTATCTTCGATCTACTTCAC-GCCAA-TACATGAAGACAAGATCTGCTATCTGCGATCTACT
* * * * * *
42373197 TCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTTGCC-ACCAGTATGGGAAGA
64 TCACGCCAATACATGAAGACAAGATCTGC-ATCGTCGATCCAC-TT-CCTACCAATATAGGAAGA
*
42373261 CAAGAT
126 CAAGAC
* * * * * * * *
42373267 CTGC-ATCGTCGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTT
1 CTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTATCTGCGATCTACTT
*
42373330 CACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACAGG
65 CACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACAAG
42373395 AC
130 AC
*
42373397 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTGCGATCTACTTC
* * *** * *
42373462 GCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACCTCCTACCAATATAGGAAGATAAG
66 -ACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACAAG
42373527 AC
130 AC
* * * *
42373529 CTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTT
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTGCGATCTACTTC
* * * *
42373594 ACGCCAATACATGAAGATAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGA
66 ACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACAAGA
*
42373659 T
131 C
*
42373660 CTGATATCTTCGATCT
1 CTGCTATCTTCGATCT
42373676 GTTCTCTGGG
Statistics
Matches: 353, Mismatches: 52, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
129 2 0.01
130 23 0.07
131 128 0.36
132 177 0.50
133 6 0.02
134 13 0.04
135 4 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (131 bp):
CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTGCGATCTACTTC
ACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACAAGA
C
Found at i:42373374 original size:87 final size:87
Alignment explanation
Indices: 42373130--42373675 Score: 492
Period size: 87 Copynumber: 6.2 Consensus size: 87
42373120 GGGAGGTAAA
* * * * ** * * *
42373130 ATCTGCCATCTTCGATCTGCTTCGCTGCCAACTACAGGAAGGTAAGATCTACAATCTTCGATCTA
1 ATCTGCTATCTTCGATCTACTTCAC-GCCAA-TACATGAAGACAAGATCTGC-ATCGTCGATCCA
* * * * *
42373195 CTTCAC-GCCAATACATGAAGATAAG
63 CTTC-CTACCAATATAGGAAGACAGG
* * * ***
42373220 ATCTGCTTTCTTCGATCTACTTTGC-CACCAGTATGGGAAGACAAGATCTGCATCGTCGATCCAC
1 ATCTGCTATCTTCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCAC
42373284 TTCCTACCAATATAGGAAGACAGG
64 TTCCTACCAATATAGGAAGACAGG
*
42373308 ACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTT
42373373 CCTACCAATATAGGAAGACAGG
66 CCTACCAATATAGGAAGACAGG
* * *
42373395 ACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC-TGCGATCTAC
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC-ATCGT-CGATCCAC
* * *
42373459 TTCGCCACCAATATGGGAAGACAAG
64 TTC-CTACCAATATAGGAAGACAGG
* * * * * * * * * * * *
42373484 ATCTGC-ATCGTCGATCCACCTC-CTACCAATATAGGAAGATAAGACCTACTATCTTTGATCTAC
1 ATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGC-ATCGTCGATCCAC
* * * *
42373547 TTCAC-GCCAATACATGAAGACAAG
64 TTC-CTACCAATATAGGAAGACAGG
* * * * *
42373571 ATCTGCTTTCTGCGATCTACTTTACGCCAATACATGAAGATAAGATCTGCATCTTCGATCCACTT
1 ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTT
*
42373636 CCTACCAATATAGGAAGATAGG
66 CCTACCAATATAGGAAGACAGG
*
42373658 ATCTGATATCTTCGATCT
1 ATCTGCTATCTTCGATCT
42373676 GTTCTCTGGG
Statistics
Matches: 377, Mismatches: 67, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
86 2 0.01
87 177 0.47
88 134 0.36
89 40 0.11
90 20 0.05
91 3 0.01
92 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (87 bp):
ATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCATCGTCGATCCACTT
CCTACCAATATAGGAAGACAGG
Found at i:42373627 original size:219 final size:219
Alignment explanation
Indices: 42373156--42373636 Score: 709
Period size: 219 Copynumber: 2.2 Consensus size: 219
42373146 CTGCTTCGCT
* * *
42373156 GCCAACTACAGGAAGGTAAGATCTACAATCTTCGATCTACTTCACGCCAATACATGAAGATAAGA
1 GCCAA-TACAGGAAGATAAGATCTGCAATCTTCGATCTACTTCACGCCAATACATGAAGACAAGA
* * * *
42373221 TCTGCTTTCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCATCGTCGATCCACTT
65 TCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACCT
* *
42373286 CCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
130 CCTACCAATATAGGAAGACAAGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
42373351 GATCTGCATCGTCGATCCACTTCCTA
195 GATCTGCATCGTCGATCCACTT-CTA
* * * * *
42373377 -CCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
1 GCCAATACAGGAAGATAAGATCTGCAATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
42373441 CTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACCTC
66 CTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACCTC
* *
42373506 CTACCAATATAGGAAGATAAGACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAG
131 CTACCAATATAGGAAGACAAGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
* *
42373571 ATCTGCTTTC-TGCGATCTACTT-TA
196 ATCTGC-ATCGT-CGATCCACTTCTA
* *
42373595 CGCCAATACATGAAGATAAGATCTGC-ATCTTCGATCCACTTC
1 -GCCAATACAGGAAGATAAGATCTGCAATCTTCGATCTACTTC
42373637 CTACCAATAT
Statistics
Matches: 232, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
218 2 0.01
219 196 0.84
220 34 0.15
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (219 bp):
GCCAATACAGGAAGATAAGATCTGCAATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
CTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACCTC
CTACCAATATAGGAAGACAAGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
ATCTGCATCGTCGATCCACTTCTA
Found at i:42386920 original size:21 final size:23
Alignment explanation
Indices: 42386881--42386937 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
42386871 GTTTTAAAAT
* *
42386881 TTGGGCTCAGGTAGTTTTA-GG-A
1 TTGGGCT-AGGTTGGTTTAGGGTA
42386903 TTGGGCTAGGTTGGTTTAGGGTA
1 TTGGGCTAGGTTGGTTTAGGGTA
42386926 TTGGGCTAGGTT
1 TTGGGCTAGGTT
42386938 AGTTGGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 9 0.29
22 9 0.29
23 13 0.42
ACGTcount: A:0.14, C:0.07, G:0.40, T:0.39
Consensus pattern (23 bp):
TTGGGCTAGGTTGGTTTAGGGTA
Found at i:42396074 original size:17 final size:17
Alignment explanation
Indices: 42396052--42396085 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42396042 AAAGTTGCTG
42396052 ATTAGTCCCTAAAATTT
1 ATTAGTCCCTAAAATTT
42396069 ATTAGTCCCTAAAATTT
1 ATTAGTCCCTAAAATTT
42396086 TGCTATCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTAGTCCCTAAAATTT
Found at i:42397389 original size:19 final size:19
Alignment explanation
Indices: 42397361--42397399 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
42397351 AGAGCGAAAG
42397361 AAACGAG-AAACGGGCCAA
1 AAACGAGAAAACGGGCCAA
*
42397379 AAACAGAGAAAATGGGCCAA
1 AAAC-GAGAAAACGGGCCAA
42397399 A
1 A
42397400 GTACGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 3 0.17
20 11 0.61
ACGTcount: A:0.54, C:0.18, G:0.26, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAACGGGCCAA
Found at i:42414514 original size:27 final size:27
Alignment explanation
Indices: 42414480--42414630 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
42414470 TAAATTGTAC
* *
42414480 AGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42414506 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
42414534 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
42414562 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
42414589 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
42414616 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42414631 GACTCAATAT
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 84 0.78
28 23 0.21
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:42414577 original size:55 final size:54
Alignment explanation
Indices: 42414479--42414630 Score: 171
Period size: 55 Copynumber: 2.8 Consensus size: 54
42414469 TTAAATTGTA
** *
42414479 CAGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATG
1 CAGCACTAAGTGTGCGAGTTGAATATGTA-GCACTAAGTGTGCGAATTGACCACG
* * * **
42414533 CGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG
1 CAGCACTAAGTGTGCGAG-TTGAATATGTAGCACTAAGTGTGCGAATTGACCACG
* * * *
42414588 TAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 CAGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
42414631 GACTCAATAT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 38 0.46
55 44 0.53
56 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (54 bp):
CAGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAATTGACCACG
Found at i:42414621 original size:82 final size:82
Alignment explanation
Indices: 42414480--42414630 Score: 187
Period size: 82 Copynumber: 1.8 Consensus size: 82
42414470 TAAATTGTAC
* * *
42414480 AGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTG
1 AGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGCGAATTGACCATACAGCACTAAGTG
42414545 TGCGAGTTTGACTATGT
66 TGCGAGTTTGACTATGT
** * * ** * *
42414562 AGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGT
1 AGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGTGTGCGAATTGACCATACAGCACTAAGT
42414626 GTGCG
65 GTGCG
42414631 GACTCAATAT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 1 0.02
82 56 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGCGAATTGACCATACAGCACTAAGTG
TGCGAGTTTGACTATGT
Found at i:42419595 original size:40 final size:40
Alignment explanation
Indices: 42419558--42419689 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
42419548 GCTACTCGTT
* *
42419558 CAAATGCCTTCGGGACATAGCTCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
* *
42419598 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * *
42419638 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
42419677 CAAATGCCTTCGG
1 CAAATGCCTTCGG
42419690 ATCTTAGTTC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.41
40 46 0.56
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:42419679 original size:39 final size:40
Alignment explanation
Indices: 42419586--42419689 Score: 156
Period size: 39 Copynumber: 2.6 Consensus size: 40
42419576 AGCTCGGTTA
* * *
42419586 TAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
*
42419626 TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCAGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
*
42419665 TAGTATCTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
42419690 ATCTTAGTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 34 0.58
40 25 0.42
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAAT
Found at i:42419703 original size:79 final size:80
Alignment explanation
Indices: 42419586--42419739 Score: 188
Period size: 79 Copynumber: 1.9 Consensus size: 80
42419576 AGCTCGGTTA
* * *
42419586 TAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCACAAATGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTTAGCACAAA-GCCTTCG
42419650 GG-CTTAGCCCAGAAT
65 GGACTTAGCCCAGAAT
* *** * *
42419665 TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTTCGGATATGGTCACTTAGCACAAAGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCG
42419729 GGACTTAGCCC
65 GGACTTAGCCC
42419740 GGACATCATT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
78 3 0.05
79 44 0.70
80 16 0.25
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGG
GACTTAGCCCAGAAT
Found at i:42427532 original size:39 final size:40
Alignment explanation
Indices: 42427410--42427591 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 40
42427400 GCTACTCGTT
*
42427410 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
42427450 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
42427490 CAAATGCCTTCGGG-CTTAGTCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
42427529 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
42427570 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
42427592 AGACATCATT
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 75 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42435573 original size:18 final size:19
Alignment explanation
Indices: 42435550--42435586 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
42435540 GAGTAAAAAG
*
42435550 AACGAG-AAATGGGCCAAA
1 AACGAGAAAATAGGCCAAA
42435568 AACGAGAAAATAGGCCAAA
1 AACGAGAAAATAGGCCAAA
42435587 GTACAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.16, G:0.24, T:0.05
Consensus pattern (19 bp):
AACGAGAAAATAGGCCAAA
Found at i:42443202 original size:27 final size:25
Alignment explanation
Indices: 42443170--42443228 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
42443160 ATAAAACTTC
**
42443170 AAAATAACTTAAAATACTTAATAATT
1 AAAATAACTTAAAATAAATAATAA-T
* *
42443196 ATAAATAATTTAGAATAAATAATAAT
1 A-AAATAACTTAAAATAAATAATAAT
42443222 AAAATAA
1 AAAATAA
42443229 TAAGAGATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 19 0.68
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATAACTTAAAATAAATAATAAT
Found at i:42443285 original size:33 final size:33
Alignment explanation
Indices: 42443243--42443310 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
42443233 AGATGATAAA
42443243 TACAATATTGGGATCATATAGTAAAATTAAGCC
1 TACAATATTGGGATCATATAGTAAAATTAAGCC
*
42443276 TACAATATTGGGATCATATATTAAAATTAAGCC
1 TACAATATTGGGATCATATAGTAAAATTAAGCC
42443309 TA
1 TA
42443311 AAACCTGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (33 bp):
TACAATATTGGGATCATATAGTAAAATTAAGCC
Found at i:42454524 original size:37 final size:37
Alignment explanation
Indices: 42454474--42454552 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42454464 TTATTACGAA
* * *
42454474 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
42454511 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
42454548 GTCTT
1 GTCTT
42454553 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:42454747 original size:49 final size:47
Alignment explanation
Indices: 42454670--42454778 Score: 164
Period size: 49 Copynumber: 2.3 Consensus size: 47
42454660 GCCCTTCGGG
42454670 ACTTATCACATTCATCACATCAGCCATTAGGCCCGATCACATATATATAC
1 ACTT-TCACATTCATCACATCAGCCATTAGGCCCGATCAC--ATATATAC
* **
42454720 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCAGCCATTAGGCCCGATCACATATATAC
42454767 ACTTTCACATTC
1 ACTTTCACATTC
42454779 TCAAAGTAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 20 0.36
49 32 0.57
50 4 0.07
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCAGCCATTAGGCCCGATCACATATATAC
Found at i:42471067 original size:39 final size:39
Alignment explanation
Indices: 42470995--42471208 Score: 193
Period size: 40 Copynumber: 5.4 Consensus size: 39
42470985 ACCCAATTAT
* **
42470995 CTTCGGGATTTAG-CCGGATATAACCACTCGCACAAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAGGC
* * * * *
42471033 CATT-GGGTCTTAGTCCGGATATGGTCACTAGCACAAATGC
1 C-TTCGGGACTTAGCCCGGATATAGTCACTCGCAC-AAGGC
* *
42471073 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTCGCAC-AAGGC
* * *
42471113 CTTCGGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATA-TAGTCACTCGCAC-AAGGC
* *
42471153 CTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATA-TAGTCACTCGCAC-AAGGC
*
42471193 CTTGGGGACTTAGCCC
1 CTTCGGGACTTAGCCC
42471209 AGAATTAATC
Statistics
Matches: 156, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
38 8 0.05
39 21 0.13
40 127 0.81
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.23
Consensus pattern (39 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAGGC
Found at i:42471093 original size:40 final size:40
Alignment explanation
Indices: 42471063--42471244 Score: 276
Period size: 40 Copynumber: 4.5 Consensus size: 40
42471053 ATGGTCACTA
42471063 GCACAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTC
*
42471103 GCACAAATGCCTTCGGGGCTTAGCCCGGAATTAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
42471143 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
* * * * *
42471183 GCACAAATGCCTTGGGGACTTAGCCCAGAATTAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
* *
42471223 GCAGAAATGTCTTCGGGACTTA
1 GCACAAATGCCTTCGGGACTTA
42471245 ACCCCGTTAG
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 129 0.98
41 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTC
Found at i:42471151 original size:80 final size:79
Alignment explanation
Indices: 42470995--42471244 Score: 301
Period size: 80 Copynumber: 3.2 Consensus size: 79
42470985 ACCCAATTAT
* *** * * * *
42470995 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGCCATTGGGTCTTAGTCCGG-ATATGG
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCC-TTGGGGCTTAGCCCGGAAT-TAG
42471057 TCACTAGCACAAATGC
64 TCACTAGCACAAATGC
42471073 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGGCTTAGCCCGGAATTAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTT-GGGGCTTAGCCCGGAATTAGT
* *
42471138 AACTCGCACAAATGC
65 CACTAGCACAAATGC
* *
42471153 CTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTGGGGACTTAGCCCAGAATTAA
1 CTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTGGGG-CTTAGCCCGGAATTAG
* *
42471217 TCACTAGCAGAAATGT
64 TCACTAGCACAAATGC
42471233 CTTCGGGACTTA
1 CTTCGGGACTTA
42471245 ACCCCGTTAG
Statistics
Matches: 150, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
78 12 0.08
79 24 0.16
80 112 0.75
81 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.24
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTGGGGCTTAGCCCGGAATTAGTC
ACTAGCACAAATGC
Found at i:42479156 original size:37 final size:39
Alignment explanation
Indices: 42479085--42479195 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 39
42479075 GCACAAGCCT
*
42479085 GGGACTTAGCCCGGATATAG-AA-T-ACACAAATGCCTTC
1 GGGACTTAGCCCGGA-ATAGTAACTCGCACAAATGCCTTC
42479122 GGG-CTTAGCCCGGAA-AGTAACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTC
42479159 GGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCC
1 GGGACTTAGCCCGGAA-TAGTAACTCGCACAAATGCC
42479196 ACTTCGGCNN
Statistics
Matches: 67, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
34 2 0.03
35 3 0.04
36 12 0.18
37 19 0.28
38 12 0.18
40 19 0.28
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (39 bp):
GGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTC
Found at i:42493397 original size:14 final size:14
Alignment explanation
Indices: 42493375--42493419 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
42493365 TTAAAGAAGC
42493375 AACTCATTAAATTA
1 AACTCATTAAATTA
*
42493389 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
42493402 AACTCATTTAATTA
1 AACTCATTAAATTA
42493416 AACT
1 AACT
42493420 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:42493457 original size:22 final size:22
Alignment explanation
Indices: 42493431--42493500 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
42493421 AGATGAGTTG
42493431 TATTAATGACCAGCAACTCATT
1 TATTAATGACCAGCAACTCATT
* *
42493453 TATTAA--ACTA--AGA-TGAGTT
1 TATTAATGACCAGCA-ACTCA-TT
42493472 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACCAGCAACTCATT
42493495 TATTAA
1 TATTAA
42493501 ACTAAGAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 9 0.25
22 15 0.42
23 3 0.08
24 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
TATTAATGACCAGCAACTCATT
Found at i:42493463 original size:42 final size:42
Alignment explanation
Indices: 42493402--42493507 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
42493392 TCATTAAATA
42493402 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
42493445 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
42493487 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
42493508 GGCTTAAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 54 0.86
43 9 0.14
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:42498541 original size:34 final size:31
Alignment explanation
Indices: 42498503--42498581 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 31
42498493 CAATTTCCTT
42498503 CTCTTTTTTTTTTTCTTTACTGATTTTCTTTTC
1 CTCTTTTTTTTTTTCTTTACTGA-TTT-TTTTC
* *
42498536 ACTCTTTTTATTTTTCTTTTCTGATTTTTTTC
1 -CTCTTTTTTTTTTTCTTTACTGATTTTTTTC
*
42498568 CTCTTTTATTTTTT
1 CTCTTTTTTTTTTT
42498582 ACAATCTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 12 0.29
32 5 0.12
33 3 0.07
34 21 0.51
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (31 bp):
CTCTTTTTTTTTTTCTTTACTGATTTTTTTC
Found at i:42506225 original size:15 final size:14
Alignment explanation
Indices: 42506189--42506243 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
42506179 TCTATTGATC
42506189 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
42506203 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
42506217 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
42506232 GAAAGAAAAGAA
1 GAGA-AAAAGAA
42506244 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:42519301 original size:40 final size:40
Alignment explanation
Indices: 42519247--42519458 Score: 297
Period size: 40 Copynumber: 5.3 Consensus size: 40
42519237 CTCGCACAAG
* * * *
42519247 GCCTTCGGGTCTTAGTCCGG-ATATGGTCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTAGCACAAAT
42519287 GCCTTCGGGACTTAGCCCGG-ATATAGTAACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTAGCACAAAT
*
42519327 GCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAAT
*
42519366 GCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAAT
* *
42519406 GCCTTCGGGACTTAGCCCGGAATTAATCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAAT
*
42519446 GTCTTC-GGACTTA
1 GCCTTCGGGACTTA
42519459 ACCCCGTTAG
Statistics
Matches: 161, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 42 0.26
40 119 0.74
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAAT
Found at i:42519346 original size:79 final size:80
Alignment explanation
Indices: 42519247--42519458 Score: 306
Period size: 79 Copynumber: 2.7 Consensus size: 80
42519237 CTCGCACAAG
* * *
42519247 GCCTTCGGGTCTTAGTCCGG-ATATGGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG-ATA
1 GCCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT-
42519310 TAGTAACTAGCACAAAT
64 TAGTAACTAGCACAAAT
* *
42519327 GCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
1 GCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
*
42519391 GTAACTCGCACAAAT
66 GTAACTAGCACAAAT
* *
42519406 GCCTTCGGGACTTAGCCCGGAATTAATCACTAGCACAAATGTCTTC-GGACTTA
1 GCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTA
42519459 ACCCCGTTAG
Statistics
Matches: 120, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
79 75 0.62
80 45 0.38
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
GTAACTAGCACAAAT
Found at i:42527093 original size:44 final size:43
Alignment explanation
Indices: 42527041--42527125 Score: 143
Period size: 44 Copynumber: 2.0 Consensus size: 43
42527031 CGTAAGTTAG
*
42527041 ACTAGTTGCTTTAAAATTTAAACCCCTCCAGCAAAGTTCAAGAA
1 ACTAGTTGCTTTAAAATTTAAA-CCATCCAGCAAAGTTCAAGAA
*
42527085 ACTAGTTGCTTTAAAATTTTAACCATCCAGCAAAGTTCAAG
1 ACTAGTTGCTTTAAAATTTAAACCATCCAGCAAAGTTCAAG
42527126 GAAAGTGGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 18 0.46
44 21 0.54
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (43 bp):
ACTAGTTGCTTTAAAATTTAAACCATCCAGCAAAGTTCAAGAA
Found at i:42531036 original size:47 final size:47
Alignment explanation
Indices: 42530961--42531129 Score: 193
Period size: 47 Copynumber: 3.6 Consensus size: 47
42530951 ATTTACAAGT
42530961 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
* * * * * * ***
42531008 GAACTCAGACTTAACTTAACGAGTTCGGACATTCGC-A--TCCATAAGT-
1 GAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTTACATCTCTC
42531054 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
*
42531101 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGCTCGGA
42531130 CATTCGCATC
Statistics
Matches: 96, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 29 0.30
47 57 0.59
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:42531075 original size:93 final size:93
Alignment explanation
Indices: 42530923--42531178 Score: 422
Period size: 93 Copynumber: 2.8 Consensus size: 93
42530913 GCTAACTCGA
* * * ** *
42530923 ACTCAACTCAACGAGCTCGGGCATTCTCATTTACAAGTGAACTCGGACTCAACTCAACGAGCTCG
1 ACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
42530988 GATGCCTAGTTACATCTCTCGAACTCAG
66 GATGCCTAGTTACATCTCTCGAACTCAG
* *
42531016 ACTTAACTTAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
1 ACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
*
42531081 GATGCCTAGTTACATCTCTCGAACTCGG
66 GATGCCTAGTTACATCTCTCGAACTCAG
*
42531109 ACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 ACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
42531174 GATGC
66 GATGC
42531179 TCAAATATCC
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 151 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (93 bp):
ACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCG
GATGCCTAGTTACATCTCTCGAACTCAG
Found at i:42531175 original size:46 final size:45
Alignment explanation
Indices: 42530907--42531175 Score: 206
Period size: 46 Copynumber: 5.8 Consensus size: 45
42530897 TGTAACCCGC
* *
42530907 CCATAAGCT-AACTCGAACTCAACTCAACGAGCTCGGGCATTCTCAT
1 CCATAAG-TGAACTCGGACTCAACTCAACGAGCTCGGACATTC-CAT
** * *
42530953 TTACAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCC-A--T
* *** * * * *
42530999 ACATCTCTCGAACTCAGACTTAACTTAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTC-CAT
*
42531046 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCC-A--T
* *** *
42531092 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTC-CAT
*
42531139 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
42531176 TGCTCAAATA
Statistics
Matches: 173, Mismatches: 35, Indels: 30
0.73 0.15 0.13
Matches are distributed among these distances:
43 2 0.01
44 8 0.05
45 1 0.01
46 91 0.53
47 61 0.35
49 8 0.05
50 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCCAT
Found at i:42536710 original size:47 final size:47
Alignment explanation
Indices: 42536651--42536869 Score: 204
Period size: 47 Copynumber: 4.7 Consensus size: 47
42536641 ATCCACAAGT
* * *
42536651 GAACTCGGACTCAATTCAATGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCTC
* * * *
42536698 GAACTCGGACTCAACTCAACGAGTTC-GA--AC-A-TTCGCATCTATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTCT---C
42536744 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCTC
* * ***
42536791 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCATAAGT-
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTTACATCTCTC
42536837 GAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC
42536870 CAAATATCCT
Statistics
Matches: 143, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.01
43 8 0.06
44 4 0.03
46 56 0.39
47 58 0.41
49 5 0.03
50 8 0.06
51 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCTC
Found at i:42536720 original size:93 final size:93
Alignment explanation
Indices: 42536605--42536869 Score: 440
Period size: 93 Copynumber: 2.8 Consensus size: 93
42536595 ATCCACAAGT
* * * * * *
42536605 GAACTCGGACTCAACCCAACGAGCTCGGGCGTTCGCATCCACAAGTGAACTCGGACTCAATTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
42536670 TGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGTTCGGATGCCTAGTTACATCTCTC
* *
42536698 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCTATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42536763 CGAGTTCGGATGCCTAGTTACATCTCTC
66 CGAGTTCGGATGCCTAGTTACATCTCTC
42536791 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42536856 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
42536870 CAAATATCCT
Statistics
Matches: 160, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 160 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCTC
Found at i:42536865 original size:46 final size:46
Alignment explanation
Indices: 42536551--42536865 Score: 282
Period size: 46 Copynumber: 6.8 Consensus size: 46
42536541 TGTAACCCGC
* * * * *
42536551 CCATAAGCGAACTCGGACTCAACCCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * * * *
42536597 CCACAAGTGAACTCGGACTCAACCCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * * * *
42536643 CCACAAGTGAACTCGGACTCAATTCAATGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* *** *
42536689 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
42536736 CTATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* ***
42536782 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
42536829 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42536866 TGCCCAAATA
Statistics
Matches: 221, Mismatches: 34, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
43 2 0.01
44 7 0.03
46 141 0.64
47 61 0.28
49 8 0.04
50 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.