Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 90 of 185
Found at i:28543746 original size:13 final size:12
Alignment explanation
Indices: 28543728--28543793 Score: 68
Period size: 13 Copynumber: 5.6 Consensus size: 12
28543718 TAGATTTTTC
28543728 CTAAATATTATCA
1 CTAAATA-TATCA
28543741 CTAAATA-ATC-
1 CTAAATATATCA
28543751 CTAAATATAATCA
1 CTAAATAT-ATCA
*
28543764 CTAAATA-AT-T
1 CTAAATATATCA
28543774 CTAAATATTATCA
1 CTAAATA-TATCA
28543787 CTAAATA
1 CTAAATA
28543794 ATTTAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
10 14 0.31
11 5 0.11
12 5 0.11
13 21 0.47
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
CTAAATATATCA
Found at i:28543753 original size:23 final size:23
Alignment explanation
Indices: 28543726--28543795 Score: 122
Period size: 23 Copynumber: 3.0 Consensus size: 23
28543716 GCTAGATTTT
28543726 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
28543749 TCCTAAATATAATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
28543772 TTCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
28543795 T
1 T
28543796 TTAAAATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:28548006 original size:23 final size:23
Alignment explanation
Indices: 28547979--28548054 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
28547969 AGTGTTATTG
28547979 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28548002 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28548025 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28548048 ATCAGTG
1 ATCAGTG
28548055 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28551917 original size:13 final size:13
Alignment explanation
Indices: 28551899--28551964 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
28551889 TAGATTTTTC
28551899 CTAAATATTATCA
1 CTAAATATTATCA
28551912 CTAAATA-T-TC-
1 CTAAATATTATCA
* *
28551922 CTAACTATAATCA
1 CTAAATATTATCA
*
28551935 CTAAATA--AT-T
1 CTAAATATTATCA
*
28551945 CTAAATGTTATCA
1 CTAAATATTATCA
28551958 CTAAATA
1 CTAAATA
28551965 ATTCAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
10 12 0.30
11 4 0.10
12 5 0.12
13 19 0.47
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:28551965 original size:23 final size:23
Alignment explanation
Indices: 28551899--28551973 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
28551889 TAGATTTTTC
28551899 CTAAATATTATCACTAAAT-ATT
1 CTAAATATTATCACTAAATAATT
* *
28551921 CCTAACTATAATCACTAAATAATT
1 -CTAAATATTATCACTAAATAATT
*
28551945 CTAAATGTTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
28551968 CAAAAT
1 CTAAAT
28551974 TTAAAAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:28553939 original size:15 final size:16
Alignment explanation
Indices: 28553915--28553947 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28553905 TTTGTATAAC
28553915 TTAATATA-TTTAATT
1 TTAATATATTTTAATT
*
28553930 TTAATTTATTTTAATT
1 TTAATATATTTTAATT
28553946 TT
1 TT
28553948 TATAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATATATTTTAATT
Found at i:28554060 original size:14 final size:14
Alignment explanation
Indices: 28554041--28554067 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28554031 TTATTTTTTA
28554041 TATTTAAATGTATT
1 TATTTAAATGTATT
28554055 TATTTAAATGTAT
1 TATTTAAATGTAT
28554068 ACAATTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
TATTTAAATGTATT
Found at i:28556088 original size:43 final size:44
Alignment explanation
Indices: 28556029--28556121 Score: 170
Period size: 43 Copynumber: 2.1 Consensus size: 44
28556019 ACATGCATAT
28556029 TTTTATTTTTATTTTTTATATATATACGTACCTATATATTTTTA
1 TTTTATTTTTATTTTTTATATATATACGTACCTATATATTTTTA
*
28556073 TTTTATTTTTA-TTTTTATATATATACGTACTTATATATTTTTA
1 TTTTATTTTTATTTTTTATATATATACGTACCTATATATTTTTA
28556116 TTTTAT
1 TTTTAT
28556122 AATATTTACA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 37 0.77
44 11 0.23
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (44 bp):
TTTTATTTTTATTTTTTATATATATACGTACCTATATATTTTTA
Found at i:28556615 original size:20 final size:20
Alignment explanation
Indices: 28556578--28556621 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
28556568 GTTTTGCTCG
**
28556578 TGTTATTTTACTTACATTAT
1 TGTTATTTTACACACATTAT
* *
28556598 TGTTATTTTACACCCATTTT
1 TGTTATTTTACACACATTAT
28556618 TGTT
1 TGTT
28556622 CAGATTTCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (20 bp):
TGTTATTTTACACACATTAT
Found at i:28558549 original size:19 final size:19
Alignment explanation
Indices: 28558525--28558571 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
28558515 TCTTTTTCTT
28558525 TTTGCATT-CATTCCATGCA
1 TTTGCATTACATTCCAT-CA
*
28558544 TTTGCATTACATTGCATCA
1 TTTGCATTACATTCCATCA
*
28558563 TATGCATTA
1 TTTGCATTA
28558572 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCATCA
Found at i:28561084 original size:7 final size:7
Alignment explanation
Indices: 28561072--28561120 Score: 80
Period size: 7 Copynumber: 6.7 Consensus size: 7
28561062 AAAAAAGGGC
28561072 AAAAAAG
1 AAAAAAG
28561079 AAAAAAAG
1 -AAAAAAG
28561087 AAAAAAG
1 AAAAAAG
28561094 AAAAAAG
1 AAAAAAG
28561101 AAAAAAG
1 AAAAAAG
28561108 AAAAGAAG
1 AAAA-AAG
28561116 AAAAA
1 AAAAA
28561121 GGAGAGGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 26 0.65
8 14 0.35
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:28561090 original size:15 final size:15
Alignment explanation
Indices: 28561072--28561120 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
28561062 AAAAAAGGGC
28561072 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
28561087 AAAAAAG-AAAAAAG
1 AAAAAAGAAAAAAAG
*
28561101 AAAAAAGAAAAGAAG
1 AAAAAAGAAAAAAAG
28561116 AAAAA
1 AAAAA
28561121 GGAGAGGCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 14 0.44
15 18 0.56
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:28561097 original size:22 final size:22
Alignment explanation
Indices: 28561072--28561120 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
28561062 AAAAAAGGGC
28561072 AAAAAAGAAAAAAAGAAAA-AAG
1 AAAAAAG-AAAAAAGAAAAGAAG
28561094 AAAAAAGAAAAAAGAAAAGAAG
1 AAAAAAGAAAAAAGAAAAGAAG
28561116 AAAAA
1 AAAAA
28561121 GGAGAGGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAAGAAAAGAAG
Found at i:28561751 original size:108 final size:106
Alignment explanation
Indices: 28561443--28561753 Score: 372
Period size: 108 Copynumber: 2.9 Consensus size: 106
28561433 TTTATTCTCA
* * ** *
28561443 TCGTAACTTAGCAAATTTGTTATCTTGATTATTTATTTATTGCGAGCTTTGTTCTCAATAAAATT
1 TCGTATCTTAGCAAATTTGCTATCTTGATTATTTATTTATTTAGAGCCTTGTTCTCAATAAAATT
* * *
28561508 CCATCTTGTCCATTGTGATAATCCTTTTCATCTTATTCATT
66 TCATCTTGTCCATTGTGATAATCTTTTTCATCTTATTCAGT
* * * * * * *
28561549 TTGAATCTTAGCATAATTCGCTATCCTGCTTAATTTATTTGTTTAGAG-CTCTGCTCTCAATAAA
1 TCGTATCTTAGCA-AATTTGCTATCTTGATT-ATTTATTTATTTAGAGCCT-TGTTCTCAATAAA
* *
28561613 ATTTCATCTTATCCACTGTGATAATCTTTTTCATCTTATTCAGT
63 ATTTCATCTTGTCCATTGTGATAATCTTTTTCATCTTATTCAGT
* * *
28561657 TCGTATCTTAGTAAGATTTGCTATCTTGATTGATTTATTCATTTTGAGCCTTGTTCTCAATAAAA
1 TCGTATCTTAGCAA-ATTTGCTATCTTGATT-ATTTATTTATTTAGAGCCTTGTTCTCAATAAAA
* *
28561722 TTTCATCTTGTCCATTTTGATAATATTTTTCA
64 TTTCATCTTGTCCATTGTGATAATCTTTTTCA
28561754 AGCAGTTTTC
Statistics
Matches: 168, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
106 10 0.06
107 15 0.09
108 141 0.84
109 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.48
Consensus pattern (106 bp):
TCGTATCTTAGCAAATTTGCTATCTTGATTATTTATTTATTTAGAGCCTTGTTCTCAATAAAATT
TCATCTTGTCCATTGTGATAATCTTTTTCATCTTATTCAGT
Found at i:28564311 original size:46 final size:46
Alignment explanation
Indices: 28562633--28564305 Score: 2321
Period size: 46 Copynumber: 36.4 Consensus size: 46
28562623 AATGGACTAA
* * * * *
28562633 AAGATAACAGATCTTATCTTCCTGTATTTGGCAGCAGAGTAAATCT
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
28562679 AAGATATAGCAG--CTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCG
1 AAG--ATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
28562725 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
28562771 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
28562817 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
28562863 AAGATAGCAGATCTTGTCTTCCTGTATTTGGAAGCAGAGCAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
28562909 AAAATAGTAGATCTTGTCTTCTTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
28562955 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
28563001 AAGATAGCAGATCTTGTCTTTCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* *
28563047 AAG-CAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* *
28563092 AAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
28563138 AAGATAGCGGATCTTGTCTTCCTG-ATTTGGCAGCAGAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
28563183 AAGATAGCAGATCTTGTCTTCCTGTATTTGGTAGTGGAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28563229 AATATAGTAGATCTTGTTTTCCTGTATTTGGCAGCAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
28563275 AAGATAGCAGATCTTGTTTTCCTGTATCTCGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
28563321 AAGATAGAAGATCTTGTCTTCCTGTATTTGACAGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28563367 AAGATAGCATATCTTATCTTCCTGTATTTGGCAGCAGAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
28563413 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28563459 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
28563505 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28563551 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
28563597 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28563643 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
28563689 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28563735 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
28563781 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28563827 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
28563873 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28563919 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
28563965 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28564011 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
28564057 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCA
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
28564103 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
28564149 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
28564195 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGT-GATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * **
28564240 AAGTTAGCAGATCTTGTCTTCTTGTATTTGGCAGTAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
28564286 AAGATTGCAGATCTTGTCTT
1 AAGATAGCAGATCTTGTCTT
28564306 TTTGTACTAG
Statistics
Matches: 1429, Mismatches: 191, Indels: 14
0.87 0.12 0.01
Matches are distributed among these distances:
44 7 0.00
45 127 0.09
46 1289 0.90
48 6 0.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (46 bp):
AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
Found at i:28564489 original size:44 final size:44
Alignment explanation
Indices: 28564430--28564535 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
28564420 GACGGCAAAT
* * *
28564430 CTTATCTTCCT-AAGTTGCAGTGGGGCAGGTTGAAATCACTAAC
1 CTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAATCACTAAC
* * * * **
28564473 CTTATCTCCCTGAAGTTACAATGGAGCATATTGAAATTACTAGT
1 CTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAATCACTAAC
*
28564517 CGTATCTTCCTGAAGTTGC
1 CTTATCTTCCTGAAGTTGC
28564536 GTTGAAGCGG
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
43 10 0.20
44 40 0.80
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (44 bp):
CTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAATCACTAAC
Found at i:28565734 original size:13 final size:13
Alignment explanation
Indices: 28565713--28565743 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28565703 GGCACTACAG
*
28565713 CGGCGACCACGGC
1 CGGCAACCACGGC
28565726 CGGCAACCACGGC
1 CGGCAACCACGGC
28565739 CGGCA
1 CGGCA
28565744 GCCATGGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.45, G:0.35, T:0.00
Consensus pattern (13 bp):
CGGCAACCACGGC
Found at i:28566391 original size:30 final size:29
Alignment explanation
Indices: 28566355--28566431 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 29
28566345 AATATATATG
*
28566355 TATATATACACATGCATATTTTTATTTTTA
1 TATATATACACATACATATTTTTA-TTTTA
* *
28566385 TATATATACGTACTTATATATTTTTATTTTA
1 TATATATAC--ACATACATATTTTTATTTTA
*
28566416 TAATATTTACACATAC
1 T-ATATATACACATAC
28566432 CTACATACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
30 13 0.34
31 6 0.16
32 19 0.50
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (29 bp):
TATATATACACATACATATTTTTATTTTA
Found at i:28566705 original size:2 final size:2
Alignment explanation
Indices: 28566698--28566728 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28566688 TTTCATAATT
*
28566698 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28566729 TTTTTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28566922 original size:20 final size:20
Alignment explanation
Indices: 28566885--28566928 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
28566875 GTTTTGCTCG
**
28566885 TGTTATTTTACTTACATTAT
1 TGTTATTTTACACACATTAT
* *
28566905 TGTTATTTTACACCCATTTT
1 TGTTATTTTACACACATTAT
28566925 TGTT
1 TGTT
28566929 TAGATTTCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (20 bp):
TGTTATTTTACACACATTAT
Found at i:28569746 original size:22 final size:23
Alignment explanation
Indices: 28569708--28569754 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
28569698 GATTTGCTAA
28569708 TTTAATTATAAATAATT-TTAAT
1 TTTAATTATAAATAATTATTAAT
*
28569730 TTTAATTAT-ATTAAATTATTAAT
1 TTTAATTATAAAT-AATTATTAAT
28569753 TT
1 TT
28569755 CATATGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 13 0.59
23 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAATTATAAATAATTATTAAT
Found at i:28570388 original size:35 final size:35
Alignment explanation
Indices: 28570349--28570416 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
28570339 AAGTTTAGGG
*
28570349 TAGA-CCATTCTATGCCAACCTTAAAAAGGTTGGAA
1 TAGACCCA-TCTAAGCCAACCTTAAAAAGGTTGGAA
*
28570384 TAGACCCATCTAAGGCAACCTTAAAAAGGTTGG
1 TAGACCCATCTAAGCCAACCTTAAAAAGGTTGG
28570417 GATAAACGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (35 bp):
TAGACCCATCTAAGCCAACCTTAAAAAGGTTGGAA
Found at i:28579527 original size:22 final size:20
Alignment explanation
Indices: 28579488--28579545 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
28579478 TACATAATGT
*
28579488 AAAAAAAAAATTAGAATGCACACG
1 AAAAATAAAA-TA-AATGCA-A-G
28579512 AAAAATAAAATAAATGCAAG
1 AAAAATAAAATAAATGCAAG
*
28579532 ATAAATAAAA-AAAT
1 AAAAATAAAATAAAT
28579546 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.12
20 10 0.31
21 1 0.03
22 6 0.19
23 2 0.06
24 9 0.28
ACGTcount: A:0.69, C:0.07, G:0.09, T:0.16
Consensus pattern (20 bp):
AAAAATAAAATAAATGCAAG
Found at i:28580093 original size:23 final size:23
Alignment explanation
Indices: 28580067--28580136 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
28580057 AATTAATAGC
*
28580067 ATAATTATTTATATAATATTTAT
1 ATAATTATTTATATAATAATTAT
**
28580090 ATAATTACATATATAAATAATTAT
1 ATAATTATTTATAT-AATAATTAT
*
28580114 AT--TTATTTAATATAA-AAATAT
1 ATAATTATTT-ATATAATAATTAT
28580135 AT
1 AT
28580137 TGATGTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.18
22 6 0.15
23 16 0.41
24 10 0.26
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATTATTTATATAATAATTAT
Found at i:28581496 original size:29 final size:30
Alignment explanation
Indices: 28581448--28581506 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
28581438 GAACTGGATT
*
28581448 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
* * *
28581478 AAATC-AAAGTTCATTTATACAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
28581507 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:28591637 original size:45 final size:45
Alignment explanation
Indices: 28591544--28591648 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
28591534 AGGAGGAAGA
* * * *
28591544 ATTGGTGGCTTCGTCCACAACCTACATGGTAGTTTGTATGCAAAT
1 ATTGGTGGCTTTGTCCACAACCTACATGGCAGCTAGTATGCAAAT
* ** *
28591589 ATTGGTGGCTTTGTCCACAACCTACATGGCAGCTAGTCTGTGAGT
1 ATTGGTGGCTTTGTCCACAACCTACATGGCAGCTAGTATGCAAAT
28591634 ATTGGTGGCTTTGTC
1 ATTGGTGGCTTTGTC
28591649 TACATTAGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (45 bp):
ATTGGTGGCTTTGTCCACAACCTACATGGCAGCTAGTATGCAAAT
Found at i:28597531 original size:109 final size:109
Alignment explanation
Indices: 28597297--28597787 Score: 642
Period size: 109 Copynumber: 4.5 Consensus size: 109
28597287 GCTTTGACCA
** * * *
28597297 GCTCACGATGCTGCTCACACAAGCTACAGAGAATCCGCAAGAAATGCAGGATCTCAAGCCATCAT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTC-AGCCATCAC
* * *
28597362 TACGGTCTGTATCACCCATACATAGTACTTGCTAAATAATCACCA
65 TACGGTCTGTATCACCCACACATAGTACCTGCTAAATAATCACCG
* *
28597407 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCATT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAGCCATCACT
* * **
28597472 ACGGTCTATATCACCCATACATAGTACCTGCTAAATAATCATTG
66 ACGGTCTGTATCACCCACACATAGTACCTGCTAAATAATCACCG
* * * * * * *
28597516 GCTCACGTTGTTGCTCACACAAGATGTAGAGAATCTGCAACAGATGCAAGATCTTAGCCATCGCT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAGCCATCACT
*
28597581 ACGGTCTGTATCA-CCAGCACGTAGTACCTGCTAAATAATCACCG
66 ACGGTCTGTATCACCCA-CACATAGTACCTGCTAAATAATCACCG
* * * * * * *
28597625 GCTCAAGACGCTACTCACACAAGTTGTAGAGAATTCGCAACAGATGCAGGGTCTCAGCCATCGCT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAGCCATCACT
*** *
28597690 ACGGTCTGTATCACTGGCACATAGTACCTGCTAAATAATCACTG
66 ACGGTCTGTATCACCCACACATAGTACCTGCTAAATAATCACCG
* *
28597734 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCTGCAATAGATGCAGGATCT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCT
28597788 ATTAAAGCCT
Statistics
Matches: 333, Mismatches: 46, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
108 3 0.01
109 278 0.83
110 52 0.16
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (109 bp):
GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAGCCATCACT
ACGGTCTGTATCACCCACACATAGTACCTGCTAAATAATCACCG
Found at i:28604210 original size:7 final size:7
Alignment explanation
Indices: 28604198--28604227 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
28604188 GTTGATAAAT
28604198 AAAATAA
1 AAAATAA
28604205 AAAATAA
1 AAAATAA
28604212 AAAATAA
1 AAAATAA
28604219 AAAATAA
1 AAAATAA
28604226 AA
1 AA
28604228 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:28604218 original size:19 final size:19
Alignment explanation
Indices: 28604194--28604233 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
28604184 TTTAGTTGAT
28604194 AAATAAAATAA-AAAATAAA
1 AAATAAAA-AATAAAATAAA
28604213 AAATAAAAAATAAAATAAA
1 AAATAAAAAATAAAATAAA
28604232 AA
1 AA
28604234 TAGAATTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATAAAAAATAAAATAAA
Found at i:28617471 original size:16 final size:16
Alignment explanation
Indices: 28617450--28617483 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28617440 TCTACTTTCA
28617450 ATGGACTCTGACATAG
1 ATGGACTCTGACATAG
28617466 ATGGACTCTGACATAG
1 ATGGACTCTGACATAG
28617482 AT
1 AT
28617484 AGATGTTGAA
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:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (16 bp):
ATGGACTCTGACATAG
Found at i:28618081 original size:23 final size:22
Alignment explanation
Indices: 28618027--28618081 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
28618017 TACAGAATAC
*
28618027 GCCACACAAGCATCACAAAATAT
1 GCCACA-AAGCATCACAAAACAT
* * *
28618050 GCTATAAAGCATTTACAAAACAT
1 GCCACAAAGCA-TCACAAAACAT
28618073 GCCACAAAG
1 GCCACAAAG
28618082 AGCTTACAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.47, C:0.25, G:0.11, T:0.16
Consensus pattern (22 bp):
GCCACAAAGCATCACAAAACAT
Found at i:28620148 original size:45 final size:45
Alignment explanation
Indices: 28620085--28620229 Score: 184
Period size: 45 Copynumber: 3.2 Consensus size: 45
28620075 GGAGAATAAA
*
28620085 TAAGACCATGACTGAAAGACGTTATGGCATCATGATTCTATCGAG
1 TAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAG
* *
28620130 TAAGACCATGACTTAAAGATGTTATGGCATCACGATTCTATCGAG
1 TAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAG
* * * * * * *
28620175 TAAGGCCAT-AGCTGAAAGACGCTATGACATCACGAATCAAACGAA
1 TAAGACCATGA-CTGAAAGACGTTATGGCATCACGATTCTATCGAG
28620220 TAAGACCATG
1 TAAGACCATG
28620230 GTTGAAAAAC
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.01
45 84 0.99
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (45 bp):
TAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAG
Found at i:28620236 original size:45 final size:45
Alignment explanation
Indices: 28620083--28620294 Score: 149
Period size: 45 Copynumber: 4.7 Consensus size: 45
28620073 CCGGAGAATA
** * * * *
28620083 AATAAGACCATGACTGAAAGACGTTATGGCATCATGATTCTATCG
1 AATAAGACCATGGTTGAAAGACGCTATGGCATCACGATTCAAACG
* * * * * *
28620128 AGTAAGACCATGACTT-AAAGATGTTATGGCATCACGATTCTATCG
1 AATAAGACCATG-GTTGAAAGACGCTATGGCATCACGATTCAAACG
* * * * * *
28620173 AGTAAGGCCATAGCTGAAAGACGCTATGACATCACGAATCAAACG
1 AATAAGACCATGGTTGAAAGACGCTATGGCATCACGATTCAAACG
* * * *** *
28620218 AATAAGACCATGGTTGAAAAACACTATGGCAACACGACGGAAAATG
1 AATAAGACCATGGTTGAAAGACGCTATGGCATCACGA-TTCAAACG
* *
28620264 AAAAAGACCATGGTTGAAAGACAC-ATGGCAT
1 AATAAGACCATGGTTGAAAGACGCTATGGCAT
28620295 TAAGACAACA
Statistics
Matches: 134, Mismatches: 30, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
44 1 0.01
45 106 0.79
46 27 0.20
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (45 bp):
AATAAGACCATGGTTGAAAGACGCTATGGCATCACGATTCAAACG
Found at i:28628631 original size:20 final size:20
Alignment explanation
Indices: 28628608--28628661 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
28628598 ATACCAAATA
**
28628608 AAAAATATCGATACTTTTAT
1 AAAAATATCGATACTCGTAT
*
28628628 AAAAATATCGATACTCGTGT
1 AAAAATATCGATACTCGTAT
*
28628648 AAAAATATCAATAC
1 AAAAATATCGATAC
28628662 CATGGAGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAAATATCGATACTCGTAT
Found at i:28634770 original size:45 final size:45
Alignment explanation
Indices: 28634721--28634877 Score: 163
Period size: 45 Copynumber: 3.5 Consensus size: 45
28634711 ACCAGAAACG
*
28634721 AGTAAGACCATGATTGAAAGACGTTATGGCATCACGATTCTATCA
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCA
* *
28634766 AGTAAGACCATGACTGAAAGATGTTATGGCATCACGATTCTATCG
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCA
* * *** * * * *
28634811 AGTAAAACCGT-AGCTGAAAGAAACTATCGCATCACGAATCAAACA
1 AGTAAGACCATGA-CTGAAAGACGTTATGGCATCACGATTCTATCA
* **
28634856 AATAAGACCATGGGTGAAAGAC
1 AGTAAGACCATGACTGAAAGAC
28634878 ACCATGGCAC
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
44 1 0.01
45 90 0.99
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCA
Found at i:28641264 original size:75 final size:75
Alignment explanation
Indices: 28641137--28641340 Score: 243
Period size: 75 Copynumber: 2.7 Consensus size: 75
28641127 AAGTGAGCAT
* * * * *
28641137 ATTATCTTATAATGATTAAAAATGATCAAATTCCAAAT-TTAATCATAATAGAGAGACCAAAACT
1 ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTTAA-CATAGTAGAGAGACCAAAACT
*
28641201 ACAATTTGATC
65 ACAATTTAATC
* * **
28641212 ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTGAACATAGTAGAGGGGTCAAAACTA
1 ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTTAACATAGTAGAGAGACCAAAACTA
*
28641277 TAATTTAATC
66 CAATTTAATC
* * * *
28641287 ATCATCTTAT-ACGACTAAAAGGGATTAAATCCCAAATGTTAGCATAGTA-AGAGA
1 ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTTAACATAGTAGAGAGA
28641341 TCGAAATTGA
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
73 3 0.03
74 35 0.32
75 69 0.63
76 3 0.03
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (75 bp):
ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTTAACATAGTAGAGAGACCAAAACTA
CAATTTAATC
Found at i:28641589 original size:16 final size:16
Alignment explanation
Indices: 28641570--28641600 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28641560 AATTAGATTC
*
28641570 AAATTTAAATTAAATA
1 AAATTTAAAATAAATA
28641586 AAATTTAAAATAAAT
1 AAATTTAAAATAAAT
28641601 TTATTACTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTTAAAATAAATA
Found at i:28643031 original size:14 final size:14
Alignment explanation
Indices: 28642996--28643037 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
28642986 TTTTAAAATT
28642996 TTTAAATTA-TAAA
1 TTTAAATTATTAAA
*
28643009 -TT-AACTATTAAA
1 TTTAAATTATTAAA
28643021 TTTAAATTATTAAA
1 TTTAAATTATTAAA
28643035 TTT
1 TTT
28643038 TAAGTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 4 0.17
12 6 0.25
13 2 0.08
14 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAATTATTAAA
Found at i:28648152 original size:6 final size:6
Alignment explanation
Indices: 28648141--28648171 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
28648131 GCATTGATGT
28648141 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA A
28648172 TGGTTTCGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:28649544 original size:22 final size:22
Alignment explanation
Indices: 28649513--28649563 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
28649503 TTTCCTCAAT
28649513 GTTTC-AATTTAGTCTCGAATC
1 GTTTCTAATTTAGTCTCGAATC
28649534 GTTTCTAATTTAGTCTCGAATC
1 GTTTCTAATTTAGTCTCGAATC
*
28649556 ATTTCTAA
1 GTTTCTAA
28649564 GGCCTTGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (22 bp):
GTTTCTAATTTAGTCTCGAATC
Found at i:28654067 original size:306 final size:308
Alignment explanation
Indices: 28653556--28654126 Score: 720
Period size: 306 Copynumber: 1.9 Consensus size: 308
28653546 TACAAAGATA
* *
28653556 TGTTTATAAATAACATACAATAAATAATGAAACGTATGATTTGAAACTAATTAATAATAACACAT
1 TGTTTAAAAATAACATACAATAAAT-ATGAAACATATGATTTGAAACTAATTAATAATAACACAT
* * * * **
28653621 GGAATTTATACGATATTAAAATGAAAATAAATTAGATTAACTTGTGAGTAAAACGAAATTTAATT
65 GAAATATATACGATATTAAAATGAAAAT--ATTAGATTAAATTGTGAGTAAAACAAAATTTAAAC
* * * *
28653686 GCATAAATACATCTGATTAATAATACTAAATCAATACATTTGTTTATCATGATGTTGTCATCAAT
128 GCATAAATACATCTGATTAAGAATACTAAATAAATACAATTGTTTATCATGATGTTGCCATCAAT
* * * ** * *
28653751 CTTGAGTTGGTGTCCATTTAATTTGTGACATCAACTCAATCAACAATATTA-TAATACTAGAAAT
193 CCTAAGTTGGTGTCAAGATAATTTGTGACACCAACTCAATCAACAACATTATTAATACTAGAAAT
28653815 TCTATCACACGTATATGCATCTACAAATCACATATTTAGAACAAAAATGTG
258 TCTATCACACGTATATGCATCTACAAATCACATATTTAGAACAAAAATGTG
* * * * *
28653866 TGTTTAAAAATAGCATATAATAAAT-TTAAACATATGGTTTGAAACTAATTAATAATAACACATT
1 TGTTTAAAAATAACATACAATAAATATGAAACATATGATTTGAAACTAATTAATAATAACACATG
* ** * *
28653930 AAATATGTGTGATATTAAAATGAAACGT-TTATATTAAATTGTGAGTAAAACAAAATTTAAACGC
66 AAATATATACGATATTAAAATGAAA-ATATTAGATTAAATTGTGAGTAAAACAAAATTTAAACGC
* * ** * *
28653994 ATAGATATATC-GTATTGGGAATACTAAATAAATATAATTGTTTATCATGGTGTTGCCAGT-AAT
130 ATAAATACATCTG-ATTAAGAATACTAAATAAATACAATTGTTTATCATGATGTTGCCA-TCAAT
* *
28654057 CCTAAGTTGGTGTCAAGATAATTTGTGACACCAATTCAATCAGCAACATTATTAATACTAGAAAT
193 CCTAAGTTGGTGTCAAGATAATTTGTGACACCAACTCAATCAACAACATTATTAATACTAGAAAT
28654122 TCTAT
258 TCTAT
28654127 TATATGTGTA
Statistics
Matches: 220, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
305 1 0.00
306 122 0.55
307 19 0.09
308 55 0.25
309 1 0.00
310 22 0.10
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (308 bp):
TGTTTAAAAATAACATACAATAAATATGAAACATATGATTTGAAACTAATTAATAATAACACATG
AAATATATACGATATTAAAATGAAAATATTAGATTAAATTGTGAGTAAAACAAAATTTAAACGCA
TAAATACATCTGATTAAGAATACTAAATAAATACAATTGTTTATCATGATGTTGCCATCAATCCT
AAGTTGGTGTCAAGATAATTTGTGACACCAACTCAATCAACAACATTATTAATACTAGAAATTCT
ATCACACGTATATGCATCTACAAATCACATATTTAGAACAAAAATGTG
Found at i:28655974 original size:49 final size:50
Alignment explanation
Indices: 28655914--28656092 Score: 231
Period size: 50 Copynumber: 3.6 Consensus size: 50
28655904 TCATTCGATA
28655914 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTACAATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATT
* * *
28655963 CACGTAGTAGCCTTCACATAGTACTACACACGTGAACAAGTTTTACGACT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATT
* *
28656013 CACGTAGTAGCCTTCAC-TCAGTACTACACACGTGCTCAAGCTTCTT--AGTT
1 CACGTAGTAGCCTTCACAT-AGTACTACACACGTGATCAAG-TT-TTACAATT
* * *
28656063 CACATAGTAGCATTCACTTAGTACTACACA
1 CACGTAGTAGCCTTCACATAGTACTACACA
28656093 TATAACCGTA
Statistics
Matches: 115, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
49 37 0.32
50 73 0.63
51 3 0.03
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATT
Found at i:28656026 original size:50 final size:50
Alignment explanation
Indices: 28655909--28656249 Score: 259
Period size: 51 Copynumber: 6.8 Consensus size: 50
28655899 TTTTATCATT
*
28655909 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* *
28655958 CAATTCACGTAGTAGCCTTCACATAGTACTACACACGTGAACAAGTTTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* *
28656008 CGACTCACGTAGTAGCCTTCAC-TCAGTACTACACACGTGCTCAAGCTTCTTA
1 CGATTCACGTAGTAGCCTTCACAT-AGTACTACACACGTGATCAAG-TT-TTA
* * * ** * * *
28656060 -G-TTCACATAGTAGCATTCACTTAGTACTACACATATAACCGTAG-TTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTA
** * * * * *
28656108 CCGAGACACGTGGTAGCATTCACACAGTACTACACATGTGCTCAAAGCTTCTT-
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TT-TTA
* * * * * * *
28656161 -GGTGCACATAGTAGCCTTCACTTAGTACCACACATGTGA-CCA-TTACTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTT--TTA
* *
28656210 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTG
28656250 TTCATCGATA
Statistics
Matches: 230, Mismatches: 46, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
47 2 0.01
48 6 0.03
49 42 0.18
50 77 0.33
51 97 0.42
52 3 0.01
53 1 0.00
54 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (50 bp):
CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
Found at i:28656219 original size:102 final size:99
Alignment explanation
Indices: 28655909--28656249 Score: 361
Period size: 102 Copynumber: 3.4 Consensus size: 99
28655899 TTTTATCATT
* * * * *
28655909 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AG-TT-TTACAATTCACGTAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTT--AGTGCACATAGT
* * *
28655971 AGCCTTCACATAGTACTACACACGTGAACAAGTT-TTA
64 AGCCTTCACTTAGTACTACACATGTG-ACCA-TTATTA
* *
28656008 CGACT-CACGTAGTAGCCTTCACTCAGTACTACACACGTGCTCAAGCTTCTTAGTTCACATAGTA
1 CGA-TACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTA
* * * *
28656072 GCATTCACTTAGTACTACACATATAACC-GTAGTTTA
65 GCCTTCACTTAGTACTACACATGTGACCATTA--TTA
* * * * *
28656108 CCGAGACACGTGGTAGCATTCACACAGTACTACACATGTGCTCAAAGCTTCTTGGTGCACATAGT
1 -CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTC-AAGCTTCTTAGTGCACATAGT
*
28656173 AGCCTTCACTTAGTACCACACATGTGACCATTACTTA
64 AGCCTTCACTTAGTACTACACATGTGACCATTA-TTA
28656210 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 -CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
28656250 TTCATCGATA
Statistics
Matches: 201, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
97 1 0.00
99 39 0.19
100 37 0.18
101 38 0.19
102 84 0.42
103 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (99 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTAG
CCTTCACTTAGTACTACACATGTGACCATTATTA
Found at i:28663620 original size:50 final size:50
Alignment explanation
Indices: 28663503--28663843 Score: 250
Period size: 51 Copynumber: 6.8 Consensus size: 50
28663493 TTTTATCATT
*
28663503 CGATACACGTAGTAGCCTTCA-TATAGTACTACACACGTGATC-AGTTTTA
1 CGATTCACGTAGTAGCCTTCACT-TAGTACTACACACGTGATCAAGTTTTA
* *
28663552 CAATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGAACAAGTTTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTA
* * * *
28663602 CGACTCACGTAGTAGCCTTCACTCAATACTACACACGTGCTCAAGCTTCTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAG-TT-TTA
* ** * * *
28663654 -G-TTCACATAGTAGCCTTCACTTAGTACTACACATATAACCGTAG-TTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATC-AAGTTTTA
** * * ** * *
28663702 CCGAGACACGTGGTAGCATTCACACAGTACTACACATGTGCTCAAAGCTTCTT-
1 -CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATC-AAG-TT-TTA
* * * * * *
28663755 -GGTGCACATAGTAGCCTTCACTTAGTACCACACATGTGA-CCA-TTACTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTT--TTA
* **
28663804 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 -CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTG
28663844 TTCATCGATA
Statistics
Matches: 227, Mismatches: 50, Indels: 28
0.74 0.16 0.09
Matches are distributed among these distances:
47 2 0.01
48 6 0.03
49 39 0.17
50 79 0.35
51 95 0.42
52 3 0.01
53 1 0.00
54 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (50 bp):
CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTA
Found at i:28663788 original size:102 final size:101
Alignment explanation
Indices: 28663507--28663843 Score: 344
Period size: 102 Copynumber: 3.3 Consensus size: 101
28663497 ATCATTCGAT
* * * * * *
28663507 ACACGTAGTAGCCTTCATATAGTACTACACACGTGATC-AG-TT-TTACAATTCACGTAGTAGCC
1 ACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTT--AGTGCACATAGTAGCC
* ** * * *
28663569 TTCACTTAGTACTACACACGTGAACAAGT-TTTA-CGAC
64 TTCACTTAGTACCACACATAT-AACCAGTACTTACCGAG
* * * *
28663606 TCACGTAGTAGCCTTCACTCAATACTACACACGTGCTCAAGCTTCTTAGTTCACATAGTAGCCTT
1 ACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTAGCCTT
* *
28663671 CACTTAGTACTACACATATAACC-GTAGTTTACCGAG
66 CACTTAGTACCACACATATAACCAGTA-CTTACCGAG
* * * *
28663707 ACACGTGGTAGCATTCACACAGTACTACACATGTGCTCAAAGCTTCTTGGTGCACATAGTAGCCT
1 ACACGTAGTAGCCTTCACACAGTACTACACACGTGCTC-AAGCTTCTTAGTGCACATAGTAGCCT
* * * * *
28663772 TCACTTAGTACCACACATGTGACCATTACTTATCGAT
65 TCACTTAGTACCACACATATAACCAGTACTTACCGAG
28663809 ACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 ACACGTAGTAGCCTTCACACAGTACTACACACGTG
28663844 TTCATCGATA
Statistics
Matches: 200, Mismatches: 30, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
98 2 0.01
99 35 0.17
100 39 0.19
101 37 0.19
102 85 0.43
103 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (101 bp):
ACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTAGCCTT
CACTTAGTACCACACATATAACCAGTACTTACCGAG
Found at i:28674565 original size:25 final size:25
Alignment explanation
Indices: 28674527--28674574 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
28674517 TCATATTCAT
28674527 GTATGCTCATACGAGCTATGAATCA
1 GTATGCTCATACGAGCTATGAATCA
28674552 GTATGCTC-TCACGAGCTATGAAT
1 GTATGCTCAT-ACGAGCTATGAAT
28674575 TGGGAAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCA
Found at i:28680200 original size:36 final size:36
Alignment explanation
Indices: 28680160--28680233 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
28680150 GCTGAGAATA
*
28680160 AATTCTCTCTATTTTTCGGAAGAATAATAATATATC
1 AATTCTCTCAATTTTTCGGAAGAATAATAATATATC
* *
28680196 AATTCTCTCAATTTTTCGGTAGAATAATAATATCTC
1 AATTCTCTCAATTTTTCGGAAGAATAATAATATATC
28680232 AA
1 AA
28680234 AAGTCGTCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (36 bp):
AATTCTCTCAATTTTTCGGAAGAATAATAATATATC
Found at i:28687029 original size:28 final size:26
Alignment explanation
Indices: 28686996--28687061 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 26
28686986 TTTTACTCTA
28686996 GTAAAATTTTGACGATTTTAAGCCCTCG
1 GTAAAATTTTGACGATTTTAA-CCCT-G
* *
28687024 GTAAAATTTTGACGATTTTAACTCTT
1 GTAAAATTTTGACGATTTTAACCCTG
28687050 GTAAAATTTTGA
1 GTAAAATTTTGA
28687062 AAAAATTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 12 0.33
27 3 0.08
28 21 0.58
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (26 bp):
GTAAAATTTTGACGATTTTAACCCTG
Found at i:28687234 original size:24 final size:24
Alignment explanation
Indices: 28687201--28687258 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
28687191 GGATTGCAAG
*
28687201 TTTCCATTTTCA-TTTTCATTTCCA
1 TTTCCATTTT-AGTTTTCATTTCAA
*
28687225 TTTCCGTTTTAGTTTTCATTTCAA
1 TTTCCATTTTAGTTTTCATTTCAA
*
28687249 TTTACATTTT
1 TTTCCATTTT
28687259 TGGAAACTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.17, C:0.19, G:0.03, T:0.60
Consensus pattern (24 bp):
TTTCCATTTTAGTTTTCATTTCAA
Found at i:28689444 original size:96 final size:96
Alignment explanation
Indices: 28689275--28689658 Score: 669
Period size: 96 Copynumber: 4.0 Consensus size: 96
28689265 TCGAGCAGAA
* * ** ** * * *
28689275 CAGAAGAGCGCATCAGTCAGAATAGATCTGAAAGGCTACTAAATTGAATAGAGTTTACTCTTTCC
1 CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
28689340 TCTTGTTATTTATTTTAATTATGTTTTCTTT
66 TCTTGTTATTTATTTTAATTATGTTTTCTTT
28689371 CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
1 CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
28689436 TCTTGTTATTTATTTTAATTATGTTTTCTTT
66 TCTTGTTATTTATTTTAATTATGTTTTCTTT
28689467 CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
1 CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
28689532 TCTTGTTATTTATTTTAATTATGTTTTCTTT
66 TCTTGTTATTTATTTTAATTATGTTTTCTTT
28689563 CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
1 CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
* *
28689628 TCTTGTTATTTATTTTAGTTATGTTTGCTTT
66 TCTTGTTATTTATTTTAATTATGTTTTCTTT
28689659 GAGTTTATTA
Statistics
Matches: 277, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 277 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (96 bp):
CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
TCTTGTTATTTATTTTAATTATGTTTTCTTT
Found at i:28695730 original size:33 final size:33
Alignment explanation
Indices: 28695684--28695834 Score: 160
Period size: 33 Copynumber: 4.5 Consensus size: 33
28695674 TACTCTCTAG
*
28695684 TTGGTGTGCTGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
* * *
28695717 TTGTTGTGATGGTTGGTTTAGCTCTTATTAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
*
28695750 TTGGTGTGATGGTTGGATTAGCTATTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
*** * * *
28695783 CCAGTGTGATGGATGGATTGGCT-TGATTGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTA-TGAGCA
*
28695816 TCTGGTGTGTTTGGTTGGA
1 T-TGGTGTG-ATGGTTGGA
28695835 CTAATGATGT
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
32 2 0.02
33 82 0.85
34 5 0.05
35 7 0.07
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (33 bp):
TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
Found at i:28701323 original size:75 final size:75
Alignment explanation
Indices: 28701200--28701349 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
28701190 ATATTACAAG
28701200 CCTAAAATCATACAGACCAAATACACCCCAGCCCAATCGCCTTACAAGCCCAAACCAACTAAATA
1 CCTAAAATCATACAGACCAAATACACCCCAGCCCAATCGCCTTACAAGCCCAAACCAACTAAATA
28701265 CCCTCGGCCC
66 CCCTCGGCCC
28701275 CCTAAAATCATACAGACCAAATACACCCCAGCCCAATCGCCTTACAAGCCCAAACCAACTAAATA
1 CCTAAAATCATACAGACCAAATACACCCCAGCCCAATCGCCTTACAAGCCCAAACCAACTAAATA
*
28701340 CCCTTGGCCC
66 CCCTCGGCCC
28701350 AAAACTGGAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.37, C:0.41, G:0.08, T:0.14
Consensus pattern (75 bp):
CCTAAAATCATACAGACCAAATACACCCCAGCCCAATCGCCTTACAAGCCCAAACCAACTAAATA
CCCTCGGCCC
Found at i:28707245 original size:13 final size:13
Alignment explanation
Indices: 28707229--28707286 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 13
28707219 AAAAAAAATC
28707229 AAAATCAAAATA-A
1 AAAATCAAAA-AGA
28707242 AAAA-CAAAAAGA
1 AAAATCAAAAAGA
***
28707254 AAAATCAAAGTCA
1 AAAATCAAAAAGA
*
28707267 AAAGT-AAAAAGA
1 AAAATCAAAAAGA
28707279 AAAATCAA
1 AAAATCAA
28707287 TCAAAGTCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
11 1 0.03
12 18 0.53
13 15 0.44
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAATCAAAAAGA
Found at i:28707258 original size:31 final size:31
Alignment explanation
Indices: 28707216--28707276 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
28707206 AGCTCGGATT
28707216 CAAAAAAAAAATCAAAATCAAAA-TAAAAAA
1 CAAAAAAAAAATCAAAATCAAAAGTAAAAAA
*
28707246 CAAAAAGAAAAATCAAAGTCAAAAGTAAAAA
1 CAAAAA-AAAAATCAAAATCAAAAGTAAAAA
28707277 GAAAAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 6 0.21
31 16 0.57
32 6 0.21
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (31 bp):
CAAAAAAAAAATCAAAATCAAAAGTAAAAAA
Found at i:28707269 original size:25 final size:24
Alignment explanation
Indices: 28707215--28707286 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
28707205 GAGCTCGGAT
**
28707215 TCAAAAAAAAAATCAAAATCAAAA
1 TCAAAAAAAAAAGAAAAATCAAAA
* *
28707239 TAAAAAACAAAAAGAAAAATCAAAG
1 TCAAAAA-AAAAAGAAAAATCAAAA
*
28707264 TCAAAAGTAAAAAGAAAAATCAA
1 TCAAAA-AAAAAAGAAAAATCAA
28707287 TCAAAGTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 6 0.15
25 34 0.85
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.11
Consensus pattern (24 bp):
TCAAAAAAAAAAGAAAAATCAAAA
Found at i:28708179 original size:6 final size:7
Alignment explanation
Indices: 28708160--28708215 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
28708150 AAAAAAAAGG
28708160 TGAAAAA
1 TGAAAAA
28708167 TGAAAAA
1 TGAAAAA
28708174 TGAAAAA
1 TGAAAAA
28708181 TG-AAAA
1 TGAAAAA
*
28708187 CGAAAAA
1 TGAAAAA
28708194 TG-AAAA
1 TGAAAAA
28708200 TGAAAAA
1 TGAAAAA
28708207 -GTAAAAA
1 TG-AAAAA
28708214 TG
1 TG
28708216 GAGAGGCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 12 0.28
7 30 0.70
8 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.16, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:28708186 original size:20 final size:19
Alignment explanation
Indices: 28708160--28708215 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
28708150 AAAAAAAAGG
28708160 TGAAAAATGAAAAATGAAAAA
1 TGAAAAA-GAAAAATG-AAAA
*
28708181 TGAAAACGAAAAATGAAAA
1 TGAAAAAGAAAAATGAAAA
28708200 TGAAAAAGTAAAAATG
1 TGAAAAAG-AAAAATG
28708216 GAGAGGCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 11 0.34
20 15 0.47
21 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.16, T:0.14
Consensus pattern (19 bp):
TGAAAAAGAAAAATGAAAA
Found at i:28708212 original size:13 final size:13
Alignment explanation
Indices: 28708160--28708206 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
28708150 AAAAAAAAGG
28708160 TGAAAAATGAAAAA
1 TGAAAAATG-AAAA
28708174 TGAAAAATGAAAA
1 TGAAAAATGAAAA
*
28708187 CGAAAAATGAAAA
1 TGAAAAATGAAAA
28708200 TGAAAAA
1 TGAAAAA
28708207 GTAAAAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 22 0.71
14 9 0.29
ACGTcount: A:0.70, C:0.02, G:0.15, T:0.13
Consensus pattern (13 bp):
TGAAAAATGAAAA
Found at i:28708213 original size:14 final size:13
Alignment explanation
Indices: 28708160--28708215 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
28708150 AAAAAAAAGG
28708160 TGAAAAATGAAAAA
1 TGAAAAAT-AAAAA
*
28708174 TGAAAAATGAAAA
1 TGAAAAATAAAAA
* *
28708187 CGAAAAATGAAAA
1 TGAAAAATAAAAA
28708200 TGAAAAAGTAAAAA
1 TGAAAAA-TAAAAA
28708214 TG
1 TG
28708216 GAGAGGCTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
13 22 0.59
14 15 0.41
ACGTcount: A:0.68, C:0.02, G:0.16, T:0.14
Consensus pattern (13 bp):
TGAAAAATAAAAA
Found at i:28709644 original size:44 final size:44
Alignment explanation
Indices: 28709578--28709690 Score: 156
Period size: 44 Copynumber: 2.6 Consensus size: 44
28709568 GGAAATGGTG
*
28709578 AATCTTATCTCCCTGATG-TTACAGTAGAGAAAATTAAAGCTAGA
1 AATCTTATCTCCCTGA-GATTACAGTAGAGAAAATTAAAGCAAGA
* * * * *
28709622 AATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCAAGT
1 AATCTTATCTCCCTGAGATTACAGTAGAGAAAATTAAAGCAAGA
28709666 AATCTTATCTCCCTGAGATTACAGT
1 AATCTTATCTCCCTGAGATTACAGT
28709691 GGAGCGGATT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 60 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTAGAGAAAATTAAAGCAAGA
Found at i:28709715 original size:44 final size:44
Alignment explanation
Indices: 28709578--28709725 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 44
28709568 GGAAATGGTG
* * * ** *
28709578 AATCTTATCTCCCTGATG-TTACAGTAGAGAAAATTAAAGCTAGA
1 AATCTTATCTCCCTGA-GATTACAGCAGAGCAGATTAAAGAAAGT
* *
28709622 AATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCAAGT
1 AATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGAAAGT
** * *
28709666 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGCAGAGCAGATT-AAAGAAAGT
* *
28709710 GATCTTATCTCTCTGA
1 AATCTTATCTCCCTGA
28709726 AGTTACAATA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.01
44 82 0.93
45 5 0.06
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGAAAGT
Found at i:28709881 original size:50 final size:50
Alignment explanation
Indices: 28709827--28710392 Score: 353
Period size: 50 Copynumber: 11.3 Consensus size: 50
28709817 GCAGTGGAGC
*
28709827 AGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * ** **
28709877 AGATTAAAGCCACAAC-GACGAATCTTACTTCTCTGGCGA-TGCAGTGGAGC
1 AGATTAAAGCCACAACAG-TGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAA
* * * * * *
28709927 AGATTAAGGCCACATCGGCGAATCTCGCTTCCCCGAGATTGCAGTTAAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTT-AAAA
* * * * * * * * ** **
28709978 AAATTAAAGCTAAAACAGTGAATCTTACCTCCCTGGCGA-TGCAATGGAGC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAA
* * *
28710028 AGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAACATTGCAATTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * **
28710078 AGGTTAAAGCCACAGCGGCGAATCTTACTTCTCTGGCGA-TGCAG-TAGAGC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGAC-ATTGCAGTTA-AAA
*** *
28710128 AGATTAAAGCCACATTGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * *** *
28710178 AGATTAATGCTACAACAGTGAATCTTAC-TCCCCAGGCGA-TGCAGCGGAAC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCC-GAC-ATTGCAGTTAAAA
* *
28710228 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * *
28710278 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAGGCGA-TGCAG-CAGAACA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCC-GAC-ATTGCAGTTA-AA-A
* * * *
28710329 A-ATTAAAGCCACGACGGTGTATCTTGCTTCCTCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* *
28710378 AGATTGAAGCTACAA
1 AGATTAAAGCCACAA
28710393 GCTACGAATC
Statistics
Matches: 376, Mismatches: 117, Indels: 46
0.70 0.22 0.09
Matches are distributed among these distances:
49 21 0.06
50 305 0.81
51 49 0.13
52 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:28709971 original size:100 final size:100
Alignment explanation
Indices: 28709798--28710392 Score: 753
Period size: 100 Copynumber: 5.9 Consensus size: 100
28709788 AGAATTACAG
* ** * *
28709798 ATCTTACCTCCCAAGCGGTGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
*
28709863 CATTGCAGTTAAAAAGATTAAAGCCACAAC-GACGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAG-CGA
* * * *
28709898 ATCTTACTTCTCTGGCGATGCAGTGGAGCAGATTAAGGCCACATCGGCGAATCTCGCTTCCCCGA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
* * * *
28709963 GATTGCAGTTAAAAAAAATTAAAGCTAAAACAGTGA
66 CATTGCAGTT-AAAAAGATTAAAGCTACAACAGCGA
* * * *
28709999 ATCTTACCTCCCTGGCGATGCAATGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
* * * * *
28710064 CATTGCAATTAAAAAGGTTAAAGCCACAGCGGCGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
* * * *
28710099 ATCTTACTTCTCTGGCGATGCAGTAGAGCAGATTAAAGCCACATTGGTGAATCTCGCTTCCCCGA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
* *
28710164 CATTGCAGTTAAAAAGATTAATGCTACAACAGTGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
* * * * * *
28710199 ATCTTACTCCCCAGGCGATGCAGCGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCAA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
28710264 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
* * ** * * * *
28710299 ATCTTACTCCCCAGGCGATGCAGCAGAACAAATTAAAGCCACGA-CGGTGTATCTTGCTTCCTCG
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCCG
*
28710363 ACATTGCAGTTAAAAAGATTGAAGCTACAA
65 ACATTGCAGTTAAAAAGATTAAAGCTACAA
28710393 GCTACGAATC
Statistics
Matches: 428, Mismatches: 64, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
100 342 0.80
101 85 0.20
102 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
Found at i:28710153 original size:201 final size:201
Alignment explanation
Indices: 28709798--28710378 Score: 835
Period size: 200 Copynumber: 2.9 Consensus size: 201
28709788 AGAATTACAG
* * *
28709798 ATCTTACCTCCCAAGCGGTGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGA
1 ATCTTACCTCCCAGGCGATGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
* *
28709863 CATTGCAGTTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCTCTGGCGATGCAGTGGAGCA
66 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGCA
* * *
28709928 GATTAAGGCCACATCGGCGAATCTCGCTTCCCCGAGATTGCAGTTAAAAAAAATTAAAGCTAAAA
131 GATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAAAAATTAAAGCTAAAA
28709993 CAGTGA
196 CAGTGA
* *
28709999 ATCTTACCTCCCTGGCGATGCAATGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
1 ATCTTACCTCCCAGGCGATGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
* * *
28710064 CATTGCAATTAAAAAGGTTAAAGCCACAGCGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGCA
66 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGCA
* * * *
28710129 GATTAAAGCCACATTGGTGAATCTCGCTTCCCCGACATTGCAGTT-AAAAAGATTAATGCTACAA
131 GATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAAAAATTAAAGCTAAAA
28710193 CAGTGA
196 CAGTGA
* * * *
28710199 ATCTTA-CTCCCCAGGCGATGCAGCGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCA
1 ATCTTACCT-CCCAGGCGATGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCA
* * * * * * *
28710263 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGATGCAGCAGAAC
65 ACATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGC
* * * *
28710328 AAATTAAAGCCACGA-CGGTGTATCTTGCTTCCTCGACATTGCAGTTAAAAA
130 AGATTAAAGCCAC-ATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAA
28710379 GATTGAAGCT
Statistics
Matches: 339, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
199 2 0.01
200 171 0.50
201 166 0.49
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (201 bp):
ATCTTACCTCCCAGGCGATGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGCA
GATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAAAAATTAAAGCTAAAA
CAGTGA
Found at i:28710977 original size:7 final size:7
Alignment explanation
Indices: 28710943--28710997 Score: 56
Period size: 8 Copynumber: 7.3 Consensus size: 7
28710933 ACAAAAGAAC
*
28710943 AAAAAGG
1 AAAAAAG
28710950 AAGAAAAG
1 AA-AAAAG
*
28710958 AAAACAG
1 AAAAAAG
28710965 AAAAAAGAG
1 -AAAAA-AG
28710974 AAAAAAG
1 AAAAAAG
28710981 AAAGAAAG
1 AAA-AAAG
28710989 AAAAAAG
1 AAAAAAG
28710996 AA
1 AA
28710998 CAGAAAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
7 17 0.41
8 22 0.54
9 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:28710977 original size:16 final size:16
Alignment explanation
Indices: 28710943--28711003 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
28710933 ACAAAAGAAC
*
28710943 AAAAAGGAAGAAA-AG
1 AAAAAGAAAGAAAGAG
28710958 AAAACAGAAA-AAAGAG
1 AAAA-AGAAAGAAAGAG
28710974 AAAAAAGAAAGAAAGA-
1 -AAAAAGAAAGAAAGAG
28710990 AAAAAGAACAGAAA
1 AAAAAGAA-AGAAA
28711004 AGAGGACGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
15 15 0.38
16 16 0.40
17 9 0.22
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAGAG
Found at i:28710980 original size:9 final size:8
Alignment explanation
Indices: 28710935--28710994 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 8
28710925 CGCAGCACAC
28710935 AAAAGAACA
1 AAAAGAA-A
*
28710944 AAAAGGAAG
1 AAAA-GAAA
28710953 AAAAG-AA
1 AAAAGAAA
*
28710960 AACAG-AA
1 AAAAGAAA
28710967 AAAAGAGAA
1 AAAAGA-AA
28710976 AAAAGAAA
1 AAAAGAAA
*
28710984 GAAAGAAA
1 AAAAGAAA
28710992 AAA
1 AAA
28710995 GAACAGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 11 0.26
8 12 0.29
9 16 0.38
10 3 0.07
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:28710989 original size:31 final size:32
Alignment explanation
Indices: 28710935--28710997 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
28710925 CGCAGCACAC
* *
28710935 AAAAGAACAAAAAGGAAGAAAAGAAAACAGAA
1 AAAAGAACAAAAAGAAAGAAAAGAAAAAAGAA
28710967 AAAAGAGA-AAAAAGAAAG-AAAGAAAAAAGAA
1 AAAAGA-ACAAAAAGAAAGAAAAGAAAAAAGAA
28710998 CAGAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 12 0.43
32 15 0.54
33 1 0.04
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (32 bp):
AAAAGAACAAAAAGAAAGAAAAGAAAAAAGAA
Found at i:28710990 original size:24 final size:24
Alignment explanation
Indices: 28710943--28711006 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 24
28710933 ACAAAAGAAC
*
28710943 AAAAAG-GAAGAAAAGAAAACAGA
1 AAAAAGAGAAGAAAAGAAAAAAGA
28710966 AAAAAGAGAA-AAAAGAAAGAAAGA
1 AAAAAGAGAAGAAAAGAAA-AAAGA
28710990 AAAAAGA-ACAGAAAAGA
1 AAAAAGAGA-AGAAAAGA
28711007 GGACGATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 15 0.42
24 15 0.42
25 6 0.17
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAGAGAAGAAAAGAAAAAAGA
Found at i:28711767 original size:23 final size:22
Alignment explanation
Indices: 28711740--28711788 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
28711730 ACTTCAGTCC
28711740 TTAGT-TTTGAATTGATTGTAAAT
1 TTAGTCTTTGAA-TG-TTGTAAAT
*
28711763 TTAGTCCTTTGAATGTTGTAATT
1 TTAGT-CTTTGAATGTTGTAAAT
28711786 TTA
1 TTA
28711789 ATGCGATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 15 0.65
24 2 0.09
25 6 0.26
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (22 bp):
TTAGTCTTTGAATGTTGTAAAT
Found at i:28712197 original size:16 final size:16
Alignment explanation
Indices: 28712172--28712206 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28712162 TATCATATAC
*
28712172 ATTCTTTAATATTTTT
1 ATTCTATAATATTTTT
28712188 ATTCTATAATATTTTT
1 ATTCTATAATATTTTT
28712204 ATT
1 ATT
28712207 TAATTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTCTATAATATTTTT
Found at i:28716514 original size:48 final size:48
Alignment explanation
Indices: 28716474--28716595 Score: 190
Period size: 48 Copynumber: 2.5 Consensus size: 48
28716464 ACAGACTCTC
*
28716474 GGTGGCCTGCACATAGTCCGTGCCACCCTTATATCTTAACAGAATATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTATATCTTAACAGAATATT
* * *
28716522 GGTGGCCTGCACACAATCCGTGCCACCCTTGTATCTTAAAAGAATATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTATATCTTAACAGAATATT
* *
28716570 GGTGGCCTACACACAGCCCGTGCCAC
1 GGTGGCCTGCACACAGTCCGTGCCAC
28716596 ATATGCGACC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (48 bp):
GGTGGCCTGCACACAGTCCGTGCCACCCTTATATCTTAACAGAATATT
Found at i:28744076 original size:87 final size:86
Alignment explanation
Indices: 28743981--28744139 Score: 239
Period size: 87 Copynumber: 1.8 Consensus size: 86
28743971 TTAAGTTCAA
* *
28743981 TGAATTCATCAAGTCCATCTCAATAA-GACCACCCGAAATCTGAGATATGAACTCATTAACCGTA
1 TGAATTCATCAAGTCCATCTCAA-AAGGACCACCCAAAATCTGAGATATGAACTCATTAACAGTA
28744045 ATAAACTCAACCTCTCAAGTTGG
65 A-AAACTCAACCTCTCAAGTTGG
* * * *
28744068 TGAATTCATCAAGTCCATCTCAAAAGGACCACCCAAAATCTGGGCTATGAATTCATTAAGAGTAA
1 TGAATTCATCAAGTCCATCTCAAAAGGACCACCCAAAATCTGAGATATGAACTCATTAACAGTAA
28744133 AAACTCA
66 AAACTCA
28744140 TCCTTATGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
86 9 0.14
87 56 0.86
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (86 bp):
TGAATTCATCAAGTCCATCTCAAAAGGACCACCCAAAATCTGAGATATGAACTCATTAACAGTAA
AAACTCAACCTCTCAAGTTGG
Found at i:28747221 original size:21 final size:21
Alignment explanation
Indices: 28747197--28747236 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28747187 AACCACATGT
28747197 CCACAAAAT-CTTCAACAACCC
1 CCACAAAATCCTT-AACAACCC
*
28747218 CCACTAAATCCTTAACAAC
1 CCACAAAATCCTTAACAAC
28747237 TTTACATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.17
Consensus pattern (21 bp):
CCACAAAATCCTTAACAACCC
Found at i:28750543 original size:29 final size:28
Alignment explanation
Indices: 28750508--28750585 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
28750498 TCATGAGATT
28750508 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
28750538 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
28750565 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
28750586 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:28758120 original size:30 final size:30
Alignment explanation
Indices: 28758085--28758153 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
28758075 ATACAAAGAG
*
28758085 CACACGATCGTGTCACATGCCCGTGTGTGA
1 CACACGACCGTGTCACATGCCCGTGTGTGA
28758115 CACACGACCGTGTCACATGCCCGTGTGTGA
1 CACACGACCGTGTCACATGCCCGTGTGTGA
28758145 CACACGACC
1 CACACGACC
28758154 ATGTGTCAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.19
Consensus pattern (30 bp):
CACACGACCGTGTCACATGCCCGTGTGTGA
Found at i:28758125 original size:17 final size:17
Alignment explanation
Indices: 28758105--28758159 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
28758095 TGTCACATGC
28758105 CCGTGTGTGACACACGA
1 CCGTGTGTGACACACGA
* *
28758122 CC--GTGT--CACATGC
1 CCGTGTGTGACACACGA
28758135 CCGTGTGTGACACACGA
1 CCGTGTGTGACACACGA
*
28758152 CCATGTGT
1 CCGTGTGT
28758160 CAGCCTGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
13 7 0.24
15 8 0.28
17 14 0.48
ACGTcount: A:0.20, C:0.31, G:0.27, T:0.22
Consensus pattern (17 bp):
CCGTGTGTGACACACGA
Found at i:28759835 original size:17 final size:16
Alignment explanation
Indices: 28759804--28759842 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
28759794 TTTTGAGTTA
*
28759804 TTTTTAAATTTTTTAG
1 TTTTTAAATTATTTAG
28759820 TTTTTAATATTATTTAG
1 TTTTTAA-ATTATTTAG
28759837 TCTTTT
1 T-TTTT
28759843 TATAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTTTAAATTATTTAG
Found at i:28770474 original size:83 final size:83
Alignment explanation
Indices: 28770372--28770550 Score: 286
Period size: 83 Copynumber: 2.2 Consensus size: 83
28770362 TTCAGTTAAT
* ** * *
28770372 GGTTAATTCGGTTTGAAATCGATTAATTAACTGAACTTAATAAATAATATTATATATTATATGCA
1 GGTTAATTCAGTTCAAAATCGATTAATTAACCGAACTTAATAAATAATAGTATATATTATATGCA
*
28770437 TTAGGCTATTCCTAGTTC
66 TTAGGCTATTACTAGTTC
*
28770455 GGTTAATTCAGTTCAAAATCGATTAATTAACCGAATTTAATAAATAATAGTATATATTATATGCA
1 GGTTAATTCAGTTCAAAATCGATTAATTAACCGAACTTAATAAATAATAGTATATATTATATGCA
28770520 TTAGGCTATTACTAGTTC
66 TTAGGCTATTACTAGTTC
*
28770538 GGTTAATTTAGTT
1 GGTTAATTCAGTT
28770551 AATCCGATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 88 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (83 bp):
GGTTAATTCAGTTCAAAATCGATTAATTAACCGAACTTAATAAATAATAGTATATATTATATGCA
TTAGGCTATTACTAGTTC
Found at i:28771786 original size:3 final size:3
Alignment explanation
Indices: 28771778--28771803 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28771768 GATGAAGTTT
28771778 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
28771804 AATTCTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:28790381 original size:19 final size:19
Alignment explanation
Indices: 28790359--28790398 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28790349 ATTAATTTTG
* *
28790359 ATCAAGTAAATTTAAATTA
1 ATCAAATAAATTAAAATTA
*
28790378 ATCAAATCAATTAAAATTA
1 ATCAAATAAATTAAAATTA
28790397 AT
1 AT
28790399 ATGATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:28795370 original size:84 final size:84
Alignment explanation
Indices: 28795279--28795782 Score: 1008
Period size: 84 Copynumber: 6.0 Consensus size: 84
28795269 AGATCTTGTT
28795279 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
1 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
28795344 TTTTTCCAACATGCTTGCC
66 TTTTTCCAACATGCTTGCC
28795363 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
1 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
28795428 TTTTTCCAACATGCTTGCC
66 TTTTTCCAACATGCTTGCC
28795447 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
1 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
28795512 TTTTTCCAACATGCTTGCC
66 TTTTTCCAACATGCTTGCC
28795531 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
1 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
28795596 TTTTTCCAACATGCTTGCC
66 TTTTTCCAACATGCTTGCC
28795615 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
1 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
28795680 TTTTTCCAACATGCTTGCC
66 TTTTTCCAACATGCTTGCC
28795699 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
1 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
28795764 TTTTTCCAACATGCTTGCC
66 TTTTTCCAACATGCTTGCC
28795783 ACAACAAGAC
Statistics
Matches: 420, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 420 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (84 bp):
TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
TTTTTCCAACATGCTTGCC
Found at i:28798141 original size:125 final size:125
Alignment explanation
Indices: 28797919--28798144 Score: 452
Period size: 125 Copynumber: 1.8 Consensus size: 125
28797909 AAAGGTATAT
28797919 TTTCTTGTCCATAGTTTTGTGAATCGGTTTCTTGTCCATAGTTAGAAAGATTTTGGCCCCTATTT
1 TTTCTTGTCCATAGTTTTGTGAATCGGTTTCTTGTCCATAGTTAGAAAGATTTTGGCCCCTATTT
28797984 ATGCTGAATGTCACCTTTGCTGTCACTGATCTGTGCGGGTTAGTTCCTTTATGTTATTGG
66 ATGCTGAATGTCACCTTTGCTGTCACTGATCTGTGCGGGTTAGTTCCTTTATGTTATTGG
28798044 TTTCTTGTCCATAGTTTTGTGAATCGGTTTCTTGTCCATAGTTAGAAAGATTTTGGCCCCTATTT
1 TTTCTTGTCCATAGTTTTGTGAATCGGTTTCTTGTCCATAGTTAGAAAGATTTTGGCCCCTATTT
28798109 ATGCTGAATGTCACCTTTGCTGTCACTGATCTGTGC
66 ATGCTGAATGTCACCTTTGCTGTCACTGATCTGTGC
28798145 CTACAGTCTT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 101 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (125 bp):
TTTCTTGTCCATAGTTTTGTGAATCGGTTTCTTGTCCATAGTTAGAAAGATTTTGGCCCCTATTT
ATGCTGAATGTCACCTTTGCTGTCACTGATCTGTGCGGGTTAGTTCCTTTATGTTATTGG
Found at i:28806153 original size:22 final size:22
Alignment explanation
Indices: 28806127--28806168 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28806117 TAATTAAATT
28806127 TATATTTTTCAATATTTTTATA
1 TATATTTTTCAATATTTTTATA
*
28806149 TATATTTTTCTATATTTTTA
1 TATATTTTTCAATATTTTTA
28806169 ACGTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (22 bp):
TATATTTTTCAATATTTTTATA
Found at i:28806166 original size:50 final size:50
Alignment explanation
Indices: 28806075--28806169 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
28806065 TATTTTCTAT
* *
28806075 TTTATAATTTTTTAATATTTTTAACATTTTTTTCTAAATTTTTAATTAAA
1 TTTATAATTTTTCAATATTTTTAACATATTTTTCTAAATTTTTAATTAAA
* *
28806125 TTTAT-ATTTTTCAATATTTTTATATATATTTTTCTATATTTTTAA
1 TTTATAATTTTTCAATATTTTTA-ACATATTTTTCTAAATTTTTAA
28806170 CGTTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 16 0.40
50 24 0.60
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (50 bp):
TTTATAATTTTTCAATATTTTTAACATATTTTTCTAAATTTTTAATTAAA
Found at i:28806178 original size:49 final size:46
Alignment explanation
Indices: 28806074--28806193 Score: 125
Period size: 49 Copynumber: 2.5 Consensus size: 46
28806064 ATATTTTCTA
*
28806074 TTTTATAATTTTTTAATATTTTTAACATTTTTTTCTAAATTTTTAAT
1 TTTTAT-ATTTTTTAATATTTTTAACATATTTTTCTAAATTTTTAAT
* * *
28806121 TAAATTTATATTTTTCAATATTTTTATATATATTTTTCTATATTTTTAACGT
1 T---TTTATATTTTTTAATATTTTTA-ACATATTTTTCTAAATTTTTAA--T
28806173 TTTTAT-TTATTTTAATATTTT
1 TTTTATATT-TTTTAATATTTT
28806194 ATCTTTTTGC
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
47 1 0.02
48 2 0.03
49 32 0.52
50 24 0.39
52 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (46 bp):
TTTTATATTTTTTAATATTTTTAACATATTTTTCTAAATTTTTAAT
Found at i:28812654 original size:50 final size:51
Alignment explanation
Indices: 28812593--28812774 Score: 208
Period size: 51 Copynumber: 3.6 Consensus size: 51
28812583 TGAAAGTGAT
*
28812593 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-ATA
* * * ** * *
28812643 GGTCGCATGTGTAGTATTATGTGCAGGCTACTATGCATACCGGATAGTTTC
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATA
* * * *
28812694 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-ATA
*
28812746 -GTCACATGTATAGTACTATGTGCAGGCTA
1 GGTCACATGTGTAGTACTATGTGCAGGCTA
28812775 TTATGTGAAC
Statistics
Matches: 107, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
50 38 0.36
51 67 0.63
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATA
Found at i:28812837 original size:45 final size:45
Alignment explanation
Indices: 28812783--28812877 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
28812773 TATTATGTGA
* *
28812783 ACCGAACATCATTAATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
28812828 ACCGGACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCC
28812873 ACCGA
1 ACCGA
28812878 GTATCTGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:28814427 original size:21 final size:20
Alignment explanation
Indices: 28814377--28814432 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 20
28814367 ATTAAATGGA
28814377 AATTGCAAATGATATGATTTG
1 AATTG-AAATGATATGATTTG
*
28814398 AATT-AAATGA-ATTATTGTG
1 AATTGAAATGATATGATT-TG
28814417 ATATTGAAATGTATAT
1 A-ATTGAAATG-ATAT
28814433 TGGATTGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 9 0.31
20 3 0.10
21 9 0.31
22 1 0.03
23 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (20 bp):
AATTGAAATGATATGATTTG
Found at i:28832241 original size:46 final size:46
Alignment explanation
Indices: 28832167--28833157 Score: 1869
Period size: 46 Copynumber: 21.6 Consensus size: 46
28832157 TACGTATGAT
* * * * *
28832167 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832211 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832257 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832303 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832349 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832395 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832441 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832487 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832533 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832579 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832625 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832671 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832717 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832763 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832809 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832855 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832901 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832947 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28832993 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
28833039 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
* * *
28833085 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
* * *
28833131 CACTTATCACTTTATCTCTTAATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
28833158 AGTACTCAAA
Statistics
Matches: 934, Mismatches: 11, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
44 10 0.01
45 5 0.01
46 919 0.98
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAAAGTTAA
Found at i:28844894 original size:46 final size:45
Alignment explanation
Indices: 28844823--28844914 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 45
28844813 AAAAGCAAAG
28844823 AACATGTGAACCAGTTCAGACTTTTATCACCTACCCCTTAACATC
1 AACATGTGAACCAGTTCAGACTTTTATCACCTACCCCTTAACATC
*
28844868 AACATGTGAACCCAGTTCAGAGTTTTATCACCTACCCCTTAACATC
1 AACATGTGAA-CCAGTTCAGACTTTTATCACCTACCCCTTAACATC
28844914 A
1 A
28844915 TGAGTTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 10 0.22
46 35 0.78
ACGTcount: A:0.32, C:0.30, G:0.10, T:0.28
Consensus pattern (45 bp):
AACATGTGAACCAGTTCAGACTTTTATCACCTACCCCTTAACATC
Found at i:28845225 original size:24 final size:24
Alignment explanation
Indices: 28845198--28845246 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
28845188 CAATTTTATT
*
28845198 TTATATAATATACATAATTCATAC
1 TTATATAATATACATAATCCATAC
*
28845222 TTATATAATATACATGATCCATAC
1 TTATATAATATACATAATCCATAC
28845246 T
1 T
28845247 AAAAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (24 bp):
TTATATAATATACATAATCCATAC
Found at i:28850821 original size:41 final size:41
Alignment explanation
Indices: 28850743--28850840 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
28850733 ATAAAGCCTA
*
28850743 CTAGGCATAAAGCCTGATAATATACACCGACACGAAGCCCG
1 CTAGGCACAAAGCCTGATAATATACACCGACACGAAGCCCG
* ** * * **
28850784 CTAGGCACAAAGCCTGATAATCTACATTGGCATGAAGCTTG
1 CTAGGCACAAAGCCTGATAATATACACCGACACGAAGCCCG
28850825 CTAGGCACAAAGCCTG
1 CTAGGCACAAAGCCTG
28850841 CTAGGTACAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (41 bp):
CTAGGCACAAAGCCTGATAATATACACCGACACGAAGCCCG
Found at i:28850837 original size:16 final size:16
Alignment explanation
Indices: 28850818--28850856 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28850808 CATTGGCATG
*
28850818 AAGCTTGCTAGGCACA
1 AAGCCTGCTAGGCACA
*
28850834 AAGCCTGCTAGGTACA
1 AAGCCTGCTAGGCACA
28850850 AAGCCTG
1 AAGCCTG
28850857 GTAATATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.18
Consensus pattern (16 bp):
AAGCCTGCTAGGCACA
Found at i:28855547 original size:41 final size:41
Alignment explanation
Indices: 28855490--28855646 Score: 188
Period size: 41 Copynumber: 3.8 Consensus size: 41
28855480 TTTTGTAAGT
* *
28855490 TCAGGCTTTGTGCCTAGCAGGCTTTATGCCAGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
**
28855531 TCAGGCTTTATGCCTAGCAGGCTTTATATCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* * * * * * *
28855572 TCAGACTTTATGTCTAGCAGGCTTTGTTCTGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* * *
28855613 TCGGGCTTTGTGCCTAGTAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
28855647 TTTTATACAA
Statistics
Matches: 96, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
Found at i:28856450 original size:18 final size:17
Alignment explanation
Indices: 28856422--28856458 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
28856412 TTCGAAAGTA
28856422 ATATGTGTATTATATAT
1 ATATGTGTATTATATAT
*
28856439 ATATGATGTATTATGTAT
1 ATATG-TGTATTATATAT
28856457 AT
1 AT
28856459 GCTGCCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (17 bp):
ATATGTGTATTATATAT
Found at i:28856526 original size:69 final size:69
Alignment explanation
Indices: 28856450--28856909 Score: 740
Period size: 69 Copynumber: 6.7 Consensus size: 69
28856440 TATGATGTAT
* * * * *
28856450 TATGTATATGCTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
1 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
28856515 TTGG
66 TTGG
* * * * *
28856519 TATGTATATGTTGCCTATTTGTTGTATATATGCTATTAAATTTTGGTGTAAAAATGCTGCTCAAT
1 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
28856584 TTGG
66 TTGG
*
28856588 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCAGTTAAAT
1 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
28856653 TTGG
66 TTGG
*
28856657 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCAGTTAAAT
1 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
28856722 TTGG
66 TTGG
*
28856726 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGTTGTTAAAT
1 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
28856791 TTGG
66 TTGG
** *
28856795 TATGTATATACTGCCTATTTGCTGTATATATGCTATTAAATTTTGGTGTAAAAGTGCTGTTAAAT
1 TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
28856860 TTGG
66 TTGG
* * *
28856864 TATGTATATGCTGCCTATTTGCTGTATATAAGCTGTCCAAATTTTG
1 TATGTATATGTTGCCTATTTGCTGTATATATGCTGT-TAAATTTTG
28856910 TTCTATAAAT
Statistics
Matches: 372, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
69 364 0.98
70 8 0.02
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (69 bp):
TATGTATATGTTGCCTATTTGCTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
TTGG
Found at i:28858677 original size:20 final size:20
Alignment explanation
Indices: 28858652--28858691 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28858642 AATATTTTCC
*
28858652 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28858672 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28858692 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28858697 original size:34 final size:35
Alignment explanation
Indices: 28858640--28858706 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28858630 CAAACACCAC
*
28858640 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28858675 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28858707 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28858698 original size:14 final size:14
Alignment explanation
Indices: 28858675--28858714 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28858665 ACAGAAAAGT
*
28858675 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
28858689 AAATCATTTTACGG
1 AAAACATTTTACAG
28858703 AAAACATTTTAC
1 AAAACATTTTAC
28858715 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28867333 original size:41 final size:41
Alignment explanation
Indices: 28867275--28868275 Score: 1824
Period size: 41 Copynumber: 24.4 Consensus size: 41
28867265 ACCTAATATA
* * * * * *
28867275 ATACACTGGCACAAAGCCTGCTAGACTCAATGCCTAATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
* *
28867316 ATACACCGACTCGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
* * * * *
28867357 CTACACCAGCACGAAGCCTGCAAGGCACAAAGGCTAATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
* *
28867398 ATACACTGGCACGAAGCCTGCTAGGCACAAAGCCTAATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867439 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867480 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867521 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867562 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867603 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867644 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867685 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867726 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867767 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867808 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867849 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867890 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867931 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28867972 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28868013 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28868054 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28868095 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28868136 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
28868177 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
**
28868218 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTG-TGAGG
1 ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGAT-AAT
*
28868259 ATACATCGGCACGAAGC
1 ATACACCGGCACGAAGC
28868276 TTTTTGGACT
Statistics
Matches: 934, Mismatches: 25, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
40 1 0.00
41 933 1.00
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (41 bp):
ATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGATAAT
Found at i:28901188 original size:18 final size:17
Alignment explanation
Indices: 28901161--28901196 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
28901151 AATAAGTAGC
*
28901161 AAAAATTTTAAAATGAAA
1 AAAAAATTTAAAAT-AAA
28901179 AAAAAATTTAAAATAAA
1 AAAAAATTTAAAATAAA
28901196 A
1 A
28901197 TGCAAAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAAAATTTAAAATAAA
Found at i:28902354 original size:13 final size:13
Alignment explanation
Indices: 28902336--28902376 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
28902326 CAAAGCACGG
28902336 TTAAAAGATATTA
1 TTAAAAGATATTA
28902349 TTAAAAGATATTA
1 TTAAAAGATATTA
*
28902362 TT-AAAGATATGA
1 TTAAAAGATATTA
28902374 TTA
1 TTA
28902377 TGGGTTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (13 bp):
TTAAAAGATATTA
Found at i:28902369 original size:12 final size:12
Alignment explanation
Indices: 28902339--28902376 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
28902329 AGCACGGTTA
28902339 AAAGATATTATT
1 AAAGATATTATT
28902351 AAAAGATATTATT
1 -AAAGATATTATT
*
28902364 AAAGATATGATT
1 AAAGATATTATT
28902376 A
1 A
28902377 TGGGTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (12 bp):
AAAGATATTATT
Found at i:28902887 original size:5 final size:4
Alignment explanation
Indices: 28902857--28902896 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
28902847 AAGTCAAACA
28902857 AAAT AAAT AAAT AAGAT AAAT AAAT AGAAT -AAT AAAT AAA
1 AAAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT AAAT AAA
28902897 AGATTAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 23 0.70
5 7 0.21
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:28902892 original size:12 final size:13
Alignment explanation
Indices: 28902859--28902895 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
28902849 GTCAAACAAA
28902859 ATAAATAAATAAG
1 ATAAATAAATAAG
28902872 ATAAATAAAT-AG
1 ATAAATAAATAAG
28902884 A-ATAATAAATAA
1 ATA-AATAAATAA
28902896 AAGATTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 10 0.45
13 11 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (13 bp):
ATAAATAAATAAG
Found at i:28905818 original size:17 final size:18
Alignment explanation
Indices: 28905791--28905827 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28905781 AATTAAAACC
28905791 AAAATTTAAATAATAATT
1 AAAATTTAAATAATAATT
*
28905809 AAAA-TTAAATATTAATT
1 AAAATTTAAATAATAATT
28905826 AA
1 AA
28905828 CACATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTTAAATAATAATT
Found at i:28908049 original size:28 final size:27
Alignment explanation
Indices: 28907962--28908061 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 27
28907952 GAAAACTAGT
* * *
28907962 GTGCTTATCGTATTATTTCGCACTTCA
1 GTGCTTATCTTATTATTTTGCACTTCG
** * *
28907989 GTGCTTATCGTTGTAAAAATTTGCACTTTG
1 GTGCTTATC--T-TATTATTTTGCACTTCG
28908019 GTGCTTATCATTATTATTTTGCACTTCG
1 GTGCTTATC-TTATTATTTTGCACTTCG
28908047 GTGCTTATCGTTATT
1 GTGCTTATC-TTATT
28908062 TGCACTTTGT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
27 9 0.16
28 27 0.47
29 1 0.02
30 20 0.35
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (27 bp):
GTGCTTATCTTATTATTTTGCACTTCG
Found at i:28908067 original size:52 final size:53
Alignment explanation
Indices: 28907961--28908075 Score: 137
Period size: 58 Copynumber: 2.1 Consensus size: 53
28907951 AGAAAACTAG
28907961 TGTGCTTATCGTATTATTTCGCACTTCAGTGCTTATCGTTGTAAAAATTTGCACTT
1 TGTGCTTATCGTATTATTTCGCACTTCAGTGCTTATCGTTGT---AATTTGCACTT
* * *
28908017 TGGTGCTTATCATTATTATTTTGCACTTCGGTGCTTATCG-T-T-ATTTGCACTT
1 T-GTGCTTATC-GTATTATTTCGCACTTCAGTGCTTATCGTTGTAATTTGCACTT
28908069 TGTGCTT
1 TGTGCTT
28908076 GGTGATATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
51 6 0.11
52 11 0.20
56 2 0.04
57 10 0.19
58 25 0.46
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (53 bp):
TGTGCTTATCGTATTATTTCGCACTTCAGTGCTTATCGTTGTAATTTGCACTT
Found at i:28935622 original size:30 final size:30
Alignment explanation
Indices: 28935541--28935713 Score: 220
Period size: 30 Copynumber: 5.7 Consensus size: 30
28935531 ATCCAATGCT
* * *
28935541 CAAATCAATTCAGCAATATATATCCATATA
1 CAAATCAATTCGGCAATGTATATCTATATA
* * *
28935571 CGAACCAAATTCGGTAATGTATATCTATATA
1 CAAATC-AATTCGGCAATGTATATCTATATA
*
28935602 CAAATCAATTTGGCAATGTATATCTATATA
1 CAAATCAATTCGGCAATGTATATCTATATA
* * *
28935632 CAAATAAATTCGACAATGTATATCTTTATA
1 CAAATCAATTCGGCAATGTATATCTATATA
* *
28935662 CAAATCAATTCGGCAATGTATATCTTTGTA
1 CAAATCAATTCGGCAATGTATATCTATATA
*
28935692 CAAATCAATTCGGAAATGTATA
1 CAAATCAATTCGGCAATGTATA
28935714 AAACATATAC
Statistics
Matches: 124, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
30 100 0.81
31 24 0.19
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATATCTATATA
Found at i:28939748 original size:85 final size:85
Alignment explanation
Indices: 28939605--28940595 Score: 1710
Period size: 85 Copynumber: 11.7 Consensus size: 85
28939595 TTTTTATCTC
28939605 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28939670 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
28939690 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28939755 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
28939775 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28939840 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
28939860 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28939925 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
28939945 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28940010 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
28940030 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28940095 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
28940115 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28940180 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
28940200 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28940265 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
28940285 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
28940350 CTTTAGTAGCGCTTTCCCTG
66 CTTTAGTAGCGCTTTCCCTG
*
28940370 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTT-TGACCACAAACACCACTAAAG-ACCTAT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTAT-ACCACAAACGCCACTAAAGAACCTAT
** *
28940433 TCTTTAGCGGCGCTTTCCCCTC
65 TCTTTAGTAGCGCTTT-CCCTG
* * * * *
28940455 AAACGCCGCAATAGACTCTAATCTGTAGCGGCGCTT-TATCACAAACGCCGCTAAAG-ACC-ATG
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTAT-
* *
28940517 ATCTTTAGTGGCGCTTTTTCCAT-
65 -TCTTTAGTAGCGC--TTTCCCTG
* * * * *
28940540 AAATGCCGCTAA-AGACCCTTATTTTTAGCGGCGCTT-TGACCAAAAACGCCACTAAA
1 AAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTAT-ACCACAAACGCCACTAAA
28940596 AAGAAAATGC
Statistics
Matches: 878, Mismatches: 20, Indels: 15
0.96 0.02 0.02
Matches are distributed among these distances:
83 2 0.00
84 40 0.05
85 813 0.93
86 20 0.02
87 3 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (85 bp):
AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTATACCACAAACGCCACTAAAGAACCTATT
CTTTAGTAGCGCTTTCCCTG
Found at i:28940992 original size:21 final size:21
Alignment explanation
Indices: 28940920--28941011 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 21
28940910 TTTGATGCTG
**
28940920 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
28940941 CTCTGCTTCCCTCGCTACAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
28940962 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
28940983 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
28941004 ATCTGCTT
1 CTCTGCTT
28941012 TAAGCTGCTG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.05, C:0.42, G:0.16, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:28941072 original size:66 final size:66
Alignment explanation
Indices: 28940982--28941147 Score: 201
Period size: 66 Copynumber: 2.5 Consensus size: 66
28940972 CTCGCTGCCG
* * * *
28940982 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTGTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
28941045 GAA
64 GAA
* * *
28941048 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
28941113 A
66 A
* * * *
28941114 CCTTAGCTTCTCTCGATGTTGCATCCGCTTTAAG
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAG
28941148 TTGTGTAATT
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 81 0.94
67 4 0.05
ACGTcount: A:0.13, C:0.27, G:0.19, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:28946644 original size:25 final size:26
Alignment explanation
Indices: 28946594--28946650 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
28946584 TAAGTTATGC
* *
28946594 ATTATGTAAGTTATTTTATTATGAAA
1 ATTATGTAAGTTAGTGTATTATGAAA
28946620 ATTATGTAAGTT-GTGTATTATGAAA
1 ATTATGTAAGTTAGTGTATTATGAAA
*
28946645 AGTATG
1 ATTATG
28946651 CTATGTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.46
Consensus pattern (26 bp):
ATTATGTAAGTTAGTGTATTATGAAA
Found at i:28946664 original size:9 final size:9
Alignment explanation
Indices: 28946652--28946784 Score: 86
Period size: 9 Copynumber: 15.7 Consensus size: 9
28946642 AAAAGTATGC
28946652 TATGTAAGT
1 TATGTAAGT
28946661 TATGTAAGT
1 TATGTAAGT
** *
28946670 CGTATAAGT
1 TATGTAAGT
28946679 TATGTAAG-
1 TATGTAAGT
28946687 T-TGTAAGT
1 TATGTAAGT
28946695 TATGTAAGT
1 TATGTAAGT
*
28946704 TAT-TTA-T
1 TATGTAAGT
* *
28946711 TATGAAAAT
1 TATGTAAGT
*
28946720 TAAGTAAGT
1 TATGTAAGT
*
28946729 TATGTAATT
1 TATGTAAGT
*
28946738 TACG-AA-T
1 TATGTAAGT
* **
28946745 AAT-TAAAAA
1 TATGT-AAGT
28946754 TATGTAAGT
1 TATGTAAGT
28946763 TATGTAAG-
1 TATGTAAGT
28946771 T-TGTAAGT
1 TATGTAAGT
28946779 TATGTA
1 TATGTA
28946785 TAATATTAAA
Statistics
Matches: 93, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
7 18 0.19
8 11 0.12
9 63 0.68
10 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (9 bp):
TATGTAAGT
Found at i:28946679 original size:18 final size:16
Alignment explanation
Indices: 28946656--28946706 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
28946646 GTATGCTATG
28946656 TAAGTTATGTAAGTCGTA
1 TAAGTTATGTAAGT--TA
*
28946674 TAAGTTATGTAAGTTG
1 TAAGTTATGTAAGTTA
28946690 TAAGTTATGTAAGTTA
1 TAAGTTATGTAAGTTA
28946706 T
1 T
28946707 TTATTATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 17 0.55
18 14 0.45
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (16 bp):
TAAGTTATGTAAGTTA
Found at i:28946727 original size:34 final size:34
Alignment explanation
Indices: 28946689--28946772 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 34
28946679 TATGTAAGTT
*** * *
28946689 GTAAGTTATGTAAGTTATTTATTATGAAAATTAA
1 GTAAGTTATGTAAGTTACGAATAATGAAAAATAA
* * *
28946723 GTAAGTTATGTAATTTACGAATAATTAAAAATAT
1 GTAAGTTATGTAAGTTACGAATAATGAAAAATAA
28946757 GTAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTT
28946773 GTAAGTTATG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (34 bp):
GTAAGTTATGTAAGTTACGAATAATGAAAAATAA
Found at i:28946777 original size:50 final size:50
Alignment explanation
Indices: 28946723--28946940 Score: 178
Period size: 50 Copynumber: 4.2 Consensus size: 50
28946713 TGAAAATTAA
28946723 GTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTAAGTT
1 GTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTAAGTT
* ** * *
28946773 GTAAGTTATGTATAATATTA--AATAACT-AAGTTATGTAATTTATGTATAATATTAAT
1 GTAAGTTATG--TAAT-TTACGAATAATTAAAAATATGTAAGTTATG--T-A-AGT--T
* * * * * * *
28946829 GTATGTTATGTAATTTATGTAT-ATTAACTAATAT-TTA-TTATGAAAATT
1 GTAAGTTATGTAATTTACGAATAATTAA-AAATATGTAAGTTATGTAAGTT
28946877 AAGTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTAAGTT
1 --GTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTAAGTT
28946929 GTAAGTTATGTA
1 GTAAGTTATGTA
28946941 TAATATTAAA
Statistics
Matches: 129, Mismatches: 21, Indels: 36
0.69 0.11 0.19
Matches are distributed among these distances:
48 1 0.01
50 62 0.48
51 14 0.11
52 14 0.11
53 7 0.05
54 13 0.10
55 5 0.04
56 13 0.10
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (50 bp):
GTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTAAGTT
Found at i:28946782 original size:25 final size:25
Alignment explanation
Indices: 28946652--28946784 Score: 71
Period size: 25 Copynumber: 5.2 Consensus size: 25
28946642 AAAAGTATGC
*
28946652 TATGTAAGTTATGTAAGTCGTATAAGT
1 TATGTAAGTTATGTAAGT--TGTAAGT
28946679 TATGTAAG-T-TGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAG-T-TGTAAGT
* * *
28946704 TAT-TTA-TTATGAAAATTAAGTAAGT
1 TATGTAAGTTATGTAAGTT--GTAAGT
* * * **
28946729 TATGTAATTTACGAATAA-TT-AAAAA
1 TATGTAAGTTATG--TAAGTTGTAAGT
28946754 TATGTAAGTTATGTAAGTTGTAAGT
1 TATGTAAGTTATGTAAGTTGTAAGT
28946779 TATGTA
1 TATGTA
28946785 TAATATTAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 24
0.66 0.13 0.20
Matches are distributed among these distances:
23 4 0.05
24 6 0.08
25 49 0.62
26 4 0.05
27 12 0.15
28 2 0.03
29 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (25 bp):
TATGTAAGTTATGTAAGTTGTAAGT
Done.