Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 195 of 325
Found at i:60054541 original size:17 final size:18
Alignment explanation
Indices: 60054499--60054547 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
60054489 AGTTGAAAAG
60054499 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
60054518 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
60054535 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
60054548 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:60055436 original size:40 final size:40
Alignment explanation
Indices: 60055370--60055536 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
60055360 AAATTGAATG
* * *
60055370 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
60055409 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
60055449 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
60055489 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
60055529 ATATCCGG
1 ATATCCGG
60055537 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:60057781 original size:22 final size:23
Alignment explanation
Indices: 60057748--60057790 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
60057738 CTGCCGAAAT
60057748 TTATCAAAATTAATCAAAATTTA
1 TTATCAAAATTAATCAAAATTTA
*
60057771 TTAT-AAAATTAATTAAAATT
1 TTATCAAAATTAATCAAAATT
60057791 AAAAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
TTATCAAAATTAATCAAAATTTA
Found at i:60062536 original size:20 final size:20
Alignment explanation
Indices: 60062503--60062555 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
60062493 GGAAGAATAA
60062503 AGAAATGAAAAAAAA-AAAG
1 AGAAATGAAAAAAAACAAAG
*
60062522 AGAATATGAAGAAAAACAAAG
1 AGAA-ATGAAAAAAAACAAAG
60062543 A-AAA-GAAAAAAAA
1 AGAAATGAAAAAAAA
60062556 AGTGTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 8 0.27
19 5 0.17
20 12 0.40
21 5 0.17
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (20 bp):
AGAAATGAAAAAAAACAAAG
Found at i:60063746 original size:29 final size:29
Alignment explanation
Indices: 60063713--60063805 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
60063703 TGACGAGATT
* *
60063713 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
*
60063742 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
* * * *
60063771 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
60063800 GGCACT
1 GGCACT
60063806 GGGTGTGCGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAAAATAA
Found at i:60063818 original size:29 final size:29
Alignment explanation
Indices: 60063713--60063818 Score: 115
Period size: 29 Copynumber: 3.7 Consensus size: 29
60063703 TGACGAGATT
* *
60063713 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGAGCTGGAAAAATAA
*
60063742 GGCACTAAGTGTGC-ATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGA-GCTGGAAAAATAA
* * * *
60063771 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGAGCTGGAAAAATAA
**
60063800 GGCACTGGGTGTGCGAGCT
1 GGCACTAAGTGTGCGAGCT
60063819 CGGAGGGTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 64 0.98
30 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAGCTGGAAAAATAA
Found at i:60068298 original size:27 final size:27
Alignment explanation
Indices: 60068230--60068300 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
60068220 CGACTTGTAA
* *
60068230 AATTACCAAAGTACTCC-CGATTTACAG
1 AATTACCAAAATAC-CCTCAATTTACAG
****
60068257 AATTACCGTTTTACCCTCAATTTACAG
1 AATTACCAAAATACCCTCAATTTACAG
60068284 AATTACCAAAATACCCT
1 AATTACCAAAATACCCT
60068301 TGGTTTATAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTCAATTTACAG
Found at i:60068342 original size:54 final size:53
Alignment explanation
Indices: 60068284--60068406 Score: 192
Period size: 54 Copynumber: 2.3 Consensus size: 53
60068274 CAATTTACAG
* * *
60068284 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
1 AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATA-CCATGGTTTGAAA
* *
60068338 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCATGGTTTGAAA
1 AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCATGGTTTGAAA
60068391 AATTACTAAAATACCC
1 AATTACTAAAATACCC
60068407 CTGTAGGGTA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
53 27 0.42
54 37 0.58
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (53 bp):
AATTACTAAAATACCCTTGGTTTATAAAATCACCAAAATACCATGGTTTGAAA
Found at i:60068393 original size:26 final size:27
Alignment explanation
Indices: 60068284--60068406 Score: 160
Period size: 27 Copynumber: 4.6 Consensus size: 27
60068274 CAATTTACAG
60068284 AATTACCAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * *
60068311 AATCACCAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* *
60068338 AATTACTAAAATACCCTTTGTTTATAA
1 AATTACCAAAATACCCTTGGTTTATAA
*
60068365 AATTACCAAAATA-CCATGGTTTGA-AA
1 AATTACCAAAATACCCTTGGTTT-ATAA
*
60068391 AATTACTAAAATACCC
1 AATTACCAAAATACCC
60068407 CTGTAGGGTA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 21 0.26
27 61 0.74
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTATAA
Found at i:60068419 original size:53 final size:53
Alignment explanation
Indices: 60068284--60068432 Score: 149
Period size: 53 Copynumber: 2.8 Consensus size: 53
60068274 CAATTTACAG
* ** * * *
60068284 AATTACCAAAATACCCT-TGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAA
1 AATTACTAAAATACCCTCT-GTGGATAAAATTACCAAAATA-CCATGGTTTGAAA
* **
60068338 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCATGGTTTGAAA
1 AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCATGGTTTGAAA
* **
60068391 AATTACTAAAATACCC-CTGTAGGGTAAAATTACTGAAATACC
1 AATTACTAAAATACCCTCTGT-GGATAAAATTACCAAAATACC
60068433 CTTGTGGGGT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
52 3 0.04
53 43 0.52
54 36 0.43
55 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (53 bp):
AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCATGGTTTGAAA
Found at i:60068423 original size:27 final size:27
Alignment explanation
Indices: 60068389--60068450 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
60068379 CATGGTTTGA
60068389 AAAATTACTAAAATACCCCTGTAGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
* * *
60068416 AAAATTACTGAAATACCCTTGTGGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
60068443 AAAATTAC
1 AAAATTAC
60068451 CATTTTGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTGTAGGGT
Found at i:60068446 original size:80 final size:81
Alignment explanation
Indices: 60068284--60068452 Score: 202
Period size: 80 Copynumber: 2.1 Consensus size: 81
60068274 CAATTTACAG
* **
60068284 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAAAATTACTAAAA
1 AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTGGTGGGTAAAATTACTAAAA
**
60068349 TACCCTTTGTTTATAA
66 TACCCTTTGTGGATAA
* * *
60068365 AATTACCAAAATA-CCATGGTTTGA-AAAATTACTAAAATACCCCT-GTAGGGTAAAATTACTGA
1 AATTACCAAAATACCCATGGTTT-ATAAAATCACCAAAATACCCCTGGT-GGGTAAAATTACTAA
*
60068427 AATACCC-TTGTGGGGTAA
64 AATACCCTTTGT-GGATAA
60068445 AATTACCA
1 AATTACCA
60068453 TTTTGCCCCT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
79 6 0.08
80 56 0.74
81 14 0.18
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.30
Consensus pattern (81 bp):
AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTGGTGGGTAAAATTACTAAAA
TACCCTTTGTGGATAA
Found at i:60069124 original size:26 final size:28
Alignment explanation
Indices: 60069071--60069165 Score: 135
Period size: 26 Copynumber: 3.5 Consensus size: 28
60069061 GCGTAGATCA
60069071 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
60069099 TGAAATTACCCCT-AA-AGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
60069125 CGAAATTACCCCTAAATAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
60069153 C--AATATACCCCTA
1 CGAAAT-TACCCCTA
60069166 GGGTTTAAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
26 26 0.42
27 12 0.19
28 24 0.39
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.21
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:60072528 original size:29 final size:29
Alignment explanation
Indices: 60072495--60072597 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 29
60072485 GTGACGAGAT
*
60072495 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
60072524 TGGCACTAACTGTGTATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* ** * * ***
60072553 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
60072582 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
60072598 GGCTTAAATT
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:60079239 original size:50 final size:50
Alignment explanation
Indices: 60079159--60079356 Score: 218
Period size: 50 Copynumber: 4.0 Consensus size: 50
60079149 GACCTTGTAT
* * * *
60079159 ATATTCGGCCACATAGGTATGTACATATGTGATGTTACATTGGATTTTGA
1 ATATTCGGCCATATAGGTATGCACATATGTGATGTTATATTTGATTTTGA
* * * * *
60079209 ATATTCGGCCATGA-AGGTATGCACAAATGTGATATTATACTTGAATTTGT
1 ATATTCGGCCAT-ATAGGTATGCACATATGTGATGTTATATTTGATTTTGA
* * * * * * * *
60079259 ATATTCGGCTATATAAGTAAGTACATATTTGATGTTAAATTTGATCTTGC
1 ATATTCGGCCATATAGGTATGCACATATGTGATGTTATATTTGATTTTGA
*
60079309 ATATTCGGCCATATAGGTATGCACATATGTGATCTTATATTTGATTTT
1 ATATTCGGCCATATAGGTATGCACATATGTGATGTTATATTTGATTTT
60079357 CTATAATCGA
Statistics
Matches: 117, Mismatches: 29, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
49 1 0.01
50 115 0.98
51 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.40
Consensus pattern (50 bp):
ATATTCGGCCATATAGGTATGCACATATGTGATGTTATATTTGATTTTGA
Found at i:60079331 original size:100 final size:100
Alignment explanation
Indices: 60079158--60079381 Score: 270
Period size: 100 Copynumber: 2.2 Consensus size: 100
60079148 TGACCTTGTA
* * * *
60079158 TATATTCGGCCACATAGGTATGTACATATGTGATGTTACATTGGATTTTGAATATTCGGCCATGA
1 TATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
*
60079223 AGGTATGCACAAATGTGATATTATACTTGAATTTG
66 AGGTATGCACAAATGTGATATTATACTTGAATTTC
* * * * *
60079258 TATATTCGGCTATATAAGTAAGTACATATTTGATGTTAAATTTGATCTTGCATATTCGGCCAT-A
1 TATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
* * * *
60079322 TAGGTATGCACATATGTGATCTTATATTTGATTTTC
66 -AGGTATGCACAAATGTGATATTATACTTGAATTTC
* * *
60079358 TATAATCGACCAAATAAGTGAAGT
1 TATATTCGGCCACATAAGT-AAGT
60079382 TGGTTTATAA
Statistics
Matches: 104, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
99 1 0.01
100 99 0.95
101 4 0.04
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (100 bp):
TATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
AGGTATGCACAAATGTGATATTATACTTGAATTTC
Found at i:60083163 original size:69 final size:71
Alignment explanation
Indices: 60082914--60083303 Score: 244
Period size: 69 Copynumber: 5.6 Consensus size: 71
60082904 TAAGGTTTGT
* * * ** *
60082914 AGGTTTAATATCACAGCC-CTCAAATAGTTAGTAAGAGTT-AAAAGCT-TCTAGCTGTCATT-TA
1 AGGTTTAATACCGCAGCCTC-CAAACAGTTAGCGAGAGTTAAAAAGCTCTC-AACTGTCATTCTA
** **
60082975 AAACTTGC
64 AGGCTCAC
* ** * * ** *
60082983 AGGTTTAATACCACAATCTCCAAACAGTTAGTGAGAGTT-AAAAGCTCTTAGTTGTCA--CTAAA
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAAGCTCTCAACTGTCATTCTAAG
* **
60083045 ACTCGT
66 GCTCAC
* * * * * *
60083051 AGGTTTAATAACGCAGCCTCCAAACAGTTAAC-AAAATTCAAAAGCTC-CTAATTGTCATTCTAA
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAAGCTCTC-AACTGTCATTCTAA
*
60083114 GGCTCAT
65 GGCTCAC
* * * *
60083121 AGGTTTAATACCGTAGCC-CCAAATAGTTAGCGAGGGTT-AAAAGCTCTCAACTGTCATTTTAAG
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAAGCTCTCAACTGTCATTCTAAG
60083184 GCTCAC
66 GCTCAC
** * * * * * * *
60083190 AAATTTAATCCCACAACCTTCAAATAGTTAGCGAGAGTTAAAAAGCTCTCAACTATCATTTTAAG
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAAGCTCTCAACTGTCATTCTAAG
60083255 GCTCAC
66 GCTCAC
* * * * * * *
60083261 AGTTTTAATATCGTAGCCCCCACACAGCTAACGAGAGTTAAAA
1 AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAA
60083304 GCACCCGACT
Statistics
Matches: 256, Mismatches: 54, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
67 4 0.02
68 49 0.19
69 95 0.37
70 48 0.19
71 60 0.23
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (71 bp):
AGGTTTAATACCGCAGCCTCCAAACAGTTAGCGAGAGTTAAAAAGCTCTCAACTGTCATTCTAAG
GCTCAC
Found at i:60083296 original size:71 final size:71
Alignment explanation
Indices: 60083105--60083303 Score: 222
Period size: 71 Copynumber: 2.8 Consensus size: 71
60083095 CTCCTAATTG
* * * *
60083105 TCATTCTAAGGCTCATAGGTTTAATACCGTAG-CCCCAAATAGTTAGCGAGGGTT-AAAAGCTCT
1 TCATTTTAAGGCTCACAGATTTAATACCGTAGCCCCCAAATAGTTAGCGAGAGTTAAAAAGCTCT
*
60083168 CAACTG
66 CAACTA
* * ** * **
60083174 TCATTTTAAGGCTCACAAATTTAATCCCACAACCTTCAAATAGTTAGCGAGAGTTAAAAAGCTCT
1 TCATTTTAAGGCTCACAGATTTAATACCGTAGCCCCCAAATAGTTAGCGAGAGTTAAAAAGCTCT
60083239 CAACTA
66 CAACTA
* * * * * *
60083245 TCATTTTAAGGCTCACAGTTTTAATATCGTAGCCCCCACACAGCTAACGAGAGTTAAAA
1 TCATTTTAAGGCTCACAGATTTAATACCGTAGCCCCCAAATAGTTAGCGAGAGTTAAAA
60083304 GCACCCGACT
Statistics
Matches: 103, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
69 24 0.23
70 19 0.18
71 60 0.58
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.28
Consensus pattern (71 bp):
TCATTTTAAGGCTCACAGATTTAATACCGTAGCCCCCAAATAGTTAGCGAGAGTTAAAAAGCTCT
CAACTA
Found at i:60087815 original size:25 final size:25
Alignment explanation
Indices: 60087787--60087848 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
60087777 CAGCTCTTAT
60087787 GAGCTTACCGTTATTCAACTCGGAG
1 GAGCTTACCGTTATTCAACTCGGAG
*
60087812 GAGCTTACCATTATTCAACTCGGAG
1 GAGCTTACCGTTATTCAACTCGGAG
60087837 GAGCTTACCGTT
1 GAGCTTACCGTT
60087849 TACAGCTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAACTCGGAG
Found at i:60098075 original size:42 final size:42
Alignment explanation
Indices: 60097922--60098088 Score: 149
Period size: 42 Copynumber: 4.0 Consensus size: 42
60097912 AGTCATACCA
* * * * * *
60097922 ATGCCATATCCCAAATGTGGTTTTACATGTAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAACG
* * * * * *
60097964 ATGCCAATAGCCTAGATATGGTCTTACATG-ATTCTCATATCA
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATAACG
* * * *
60098006 ATGCCGTGTCCTAGACATGGTCTTACACGAAATCTCATAACG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAACG
*
60098048 ATGCCATATCCCGGATATGGTCTTACACGTAAA-CTCATAAC
1 ATGCCATATCCCAGATATGGTCTTACACG-AAATCTCATAAC
60098089 CCTAATGTCA
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
41 19 0.19
42 61 0.60
43 22 0.22
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAACG
Found at i:60101027 original size:40 final size:39
Alignment explanation
Indices: 60100945--60101043 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 39
60100935 GAAATTATAA
* *
60100945 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GCTACAT
*
60100985 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGT-CATTCTAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGC-TAC-AT
60101025 CCGGGCTAAGA-CCGAAGGC
1 CCGGGCTAAGACCCGAAGGC
60101044 GAAGGCATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
38 1 0.02
39 13 0.25
40 39 0.74
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.19
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGCTACAT
Found at i:60109093 original size:40 final size:40
Alignment explanation
Indices: 60109049--60109196 Score: 212
Period size: 40 Copynumber: 3.7 Consensus size: 40
60109039 GAAATTATAA
* * *
60109049 CCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGGC-TAC-AT
1 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGT--CATTCTAT
60109089 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTAT
60109129 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTAT
*
60109169 CCGGGCTAAGACCCGAAGGCATTTGTGC
1 CCGGGCTAAGACCCGAAGGCATTCGTGC
60109197 AAATCGTGAT
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
38 1 0.01
39 5 0.05
40 95 0.94
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTAT
Found at i:60109210 original size:40 final size:39
Alignment explanation
Indices: 60109005--60109228 Score: 175
Period size: 40 Copynumber: 5.6 Consensus size: 39
60108995 AAATTGAATG
* * * *
60109005 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAGTCAT
* * * *
60109045 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGT--CAT
* * *
60109085 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCA-T
* * *
60109125 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCA-T
* * *
60109165 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCAT
* * *
60109204 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
60109229 CTTGGTGCGG
Statistics
Matches: 154, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
37 4 0.03
38 3 0.02
39 3 0.02
40 144 0.94
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTCAT
Found at i:60109210 original size:80 final size:77
Alignment explanation
Indices: 60109006--60109237 Score: 209
Period size: 80 Copynumber: 2.9 Consensus size: 77
60108996 AATTGAATGA
* * * *
60109006 TATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT-TATAACCGGGTTAAGACCCGAAGGCA
1 TATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCTATATCCGGGTTAAGACCCGAAGGC-
*
60109070 ATTGTGCTAGTGGCTAC
62 ATTGTGCGAGT-GCTAC
* * * * *
60109087 -ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTATCCGGGCTAAGACCCGAAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC--TATATCCGGGTTAAGACCCGAAGGCAT
*
60109151 TCGTGCGAGT-CATTC
64 T-GTGCGAGTGC-TAC
* * *
60109166 TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTGATATCCGGGTTAAGTCCCGTAGGCCT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-T-ATATCCGGGTTAAGACCCGAAGGCAT
60109231 TGGTGCG
64 T-GTGCG
60109238 GGTTACCATA
Statistics
Matches: 123, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
77 4 0.03
78 2 0.02
79 9 0.07
80 108 0.88
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (77 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCTATATCCGGGTTAAGACCCGAAGGCATTG
TGCGAGTGCTAC
Found at i:60109253 original size:80 final size:80
Alignment explanation
Indices: 60109089--60109268 Score: 191
Period size: 80 Copynumber: 2.2 Consensus size: 80
60109079 GTGGCTACAT
* * **
60109089 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGATATCCGGGCTAAGACCCGAAGGCATTCG
* *
60109154 TGCGAGTCATTCTAT
66 TGCGAGTCATCCTAA
* * * * * * *
60109169 CCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTGATATCCGGGTTAAGTCCCGTAGGCCTTGG
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGATATCCGGGCTAAGACCCGAAGGCATTCG
* *
60109234 TGCGGGTTA-CCATAA
66 TGCGAGTCATCC-TAA
* *
60109249 CCGGGCTATGTCCCGAAGGC
1 CCGGGCTAAGACCCGAAGGC
60109269 GATTGATCGA
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
79 1 0.01
80 81 0.99
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGATATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTCATCCTAA
Found at i:60121995 original size:29 final size:29
Alignment explanation
Indices: 60121963--60122104 Score: 121
Period size: 29 Copynumber: 4.9 Consensus size: 29
60121953 CGATCTCCCT
60121963 CACATAGTGCTCGGTTAAAGGAATTCGCA
1 CACATAGTGCTCGGTTAAAGGAATTCGCA
* ** **
60121992 CACACAGTGCCTCAATT-ACTG-ATCTCGCA
1 CACATAGTG-CTCGGTTAAAGGAAT-TCGCA
60122021 CACATAGTGCTCGGTTAAAGGAATTCGCA
1 CACATAGTGCTCGGTTAAAGGAATTCGCA
* * ** **
60122050 CATACAGTGCCTCAATT-ACTG-ATCTCGCA
1 CACATAGTG-CTCGGTTAAAGGAAT-TCGCA
60122079 CACATAGTGCTCGGTTAAAGGAATTC
1 CACATAGTGCTCGGTTAAAGGAATTC
60122105 ATACGGTAAT
Statistics
Matches: 83, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
28 14 0.17
29 55 0.66
30 14 0.17
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (29 bp):
CACATAGTGCTCGGTTAAAGGAATTCGCA
Found at i:60122016 original size:58 final size:58
Alignment explanation
Indices: 60121897--60122104 Score: 337
Period size: 58 Copynumber: 3.6 Consensus size: 58
60121887 CCCACTGACC
** * * *
60121897 GATCTCGCACACATAGTGCTCGGTTGGA-GAACTCGCACACACAGTGCCTCATTTACC
1 GATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATTACT
* *
60121954 GATCTCCCTCACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATTACT
1 GATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATTACT
*
60122012 GATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACATACAGTGCCTCAATTACT
1 GATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATTACT
60122070 GATCTCGCACACATAGTGCTCGGTTAAAGGAATTC
1 GATCTCGCACACATAGTGCTCGGTTAAAGGAATTC
60122105 ATACGGTAAT
Statistics
Matches: 140, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
57 24 0.17
58 116 0.83
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (58 bp):
GATCTCGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATTACT
Found at i:60122209 original size:43 final size:43
Alignment explanation
Indices: 60122148--60122356 Score: 373
Period size: 43 Copynumber: 4.9 Consensus size: 43
60122138 CATCGGCATT
* * *
60122148 AAGCCTGCTAGGCACGAAGACCCAAATACATATCACCGGTACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
*
60122191 AAGCCTGCTAGGCTCGAAGGCCCGAATACATATCACCGGCACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
*
60122234 AAGCCTGCTAGGCTCGAAGGCCCGAATACATATCACCGGCACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
60122277 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
60122320 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACC
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACC
60122357 AGCATAACTG
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 161 1.00
ACGTcount: A:0.33, C:0.32, G:0.22, T:0.13
Consensus pattern (43 bp):
AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
Found at i:60122446 original size:40 final size:43
Alignment explanation
Indices: 60122349--60122511 Score: 142
Period size: 40 Copynumber: 3.9 Consensus size: 43
60122339 GCCCGAATAC
* * * *
60122349 ATATCACCAGCA-TAACTGCTCTTCGGGACCTGGTCCGG--A-T
1 ATATCACCAGCACGAA-TGCTCTTCGGGACTTAGCCCGGATAGT
* * * * *
60122389 ACATCACTAGCATGAATGCTCTTCGAGATTTAGCCCGGAT-GT
1 ATATCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAGT
* * * *
60122431 A-A-CACCAGCACGAATGCTCTACGGGACTTAACCTGGATATT
1 ATATCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAGT
*
60122472 ATATCGCCAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ATATCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
60122512 CATCGTCGAG
Statistics
Matches: 96, Mismatches: 20, Indels: 11
0.76 0.16 0.09
Matches are distributed among these distances:
40 56 0.58
41 5 0.05
42 3 0.03
43 32 0.33
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (43 bp):
ATATCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAGT
Found at i:60125324 original size:2 final size:2
Alignment explanation
Indices: 60125291--60125315 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60125281 TAAGGCATAC
60125291 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
60125316 CCTATATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60131806 original size:16 final size:16
Alignment explanation
Indices: 60131785--60131816 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60131775 TCTGTAACGC
60131785 CCCAAAAATCTCGAAA
1 CCCAAAAATCTCGAAA
*
60131801 CCCAAAAATCTTGAAA
1 CCCAAAAATCTCGAAA
60131817 TCCCGATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (16 bp):
CCCAAAAATCTCGAAA
Found at i:60140447 original size:16 final size:15
Alignment explanation
Indices: 60140421--60140457 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
60140411 TATGTATTGG
*
60140421 CAAAAGCCGAAGAGC
1 CAAAAGCCGAAAAGC
60140436 CAAAATGCCGAAAAGC
1 CAAAA-GCCGAAAAGC
60140452 CAAAAG
1 CAAAAG
60140458 TTTGTCTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.51, C:0.24, G:0.22, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:60140731 original size:29 final size:29
Alignment explanation
Indices: 60140697--60140784 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 29
60140687 AACGAGCAAT
60140697 GTGATTTGGGCCTAATGGGCCATATACAG
1 GTGATTTGGGCCTAATGGGCCATATACAG
*
60140726 GTGATTTGGGCCTAATGGGCCATATGA-AT
1 GTGATTTGGGCCTAATGGGCCATAT-ACAG
* * *
60140755 ATGA-TTGGGCTTAATGGGCCAAATACAG
1 GTGATTTGGGCCTAATGGGCCATATACAG
60140783 GT
1 GT
60140785 ATGTGAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.02
28 20 0.39
29 29 0.57
30 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (29 bp):
GTGATTTGGGCCTAATGGGCCATATACAG
Found at i:60145200 original size:29 final size:29
Alignment explanation
Indices: 60145168--60145250 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 29
60145158 CTAACGGGCG
60145168 ATATAAATGTGATTTGGGCTTAATGGACA
1 ATATAAATGTGATTTGGGCTTAATGGACA
*** * * *
60145197 ATATACGGGTGATTTGGGCCTAATGGCCC
1 ATATAAATGTGATTTGGGCTTAATGGACA
* * *
60145226 ATATGAATATGA-TTGAGCTTAATGG
1 ATATAAATGTGATTTGGGCTTAATGG
60145251 GCCAGATACA
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
28 11 0.27
29 30 0.73
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.33
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCTTAATGGACA
Found at i:60148380 original size:46 final size:46
Alignment explanation
Indices: 60148311--60148441 Score: 208
Period size: 46 Copynumber: 2.8 Consensus size: 46
60148301 GATATTTGGG
* *
60148311 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGTGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** *
60148357 TGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*
60148403 CACCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
60148442 GCGGGTTACA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (46 bp):
CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:60151470 original size:26 final size:26
Alignment explanation
Indices: 60151441--60151521 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
60151431 AGCTATCTGG
60151441 TACACATAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
* * * *
60151467 TACACACA-T-GACCT-CAC-CATCTAA
1 TACACATAGTAG-CCTGCACTTA-GTAC
*
60151491 TACACGTAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
60151517 TACAC
1 TACAC
60151522 GTGATCACAG
Statistics
Matches: 40, Mismatches: 9, Indels: 12
0.66 0.15 0.20
Matches are distributed among these distances:
23 1 0.03
24 12 0.30
25 8 0.20
26 18 0.45
27 1 0.03
ACGTcount: A:0.32, C:0.31, G:0.12, T:0.25
Consensus pattern (26 bp):
TACACATAGTAGCCTGCACTTAGTAC
Found at i:60162125 original size:43 final size:42
Alignment explanation
Indices: 60162077--60162225 Score: 190
Period size: 43 Copynumber: 3.7 Consensus size: 42
60162067 ATCTCATATT
*
60162077 GATGCCAATGTCCCATACATGGTCTTATACGAAATCATATAAC
1 GATGCCAATGTCCCA-ACATGGTCTTACACGAAATCATATAAC
60162120 GATGCCAATGTCCCAAACATGGTCTTACACGAAATCATAT-A-
1 GATGCCAATGTCCC-AACATGGTCTTACACGAAATCATATAAC
60162161 -ATG---ATG--CC-ACATGGTCTTACACGAAATCATATAAC
1 GATGCCAATGTCCCAACATGGTCTTACACGAAATCATATAAC
*
60162196 GATGCCAATGTCCCAGACATGGCCTTACAC
1 GATGCCAATGTCCCA-ACATGGTCTTACAC
60162226 ATAATCACAA
Statistics
Matches: 93, Mismatches: 2, Indels: 22
0.79 0.02 0.19
Matches are distributed among these distances:
33 24 0.26
34 1 0.01
35 2 0.02
36 3 0.03
37 3 0.03
39 3 0.03
40 3 0.03
41 2 0.02
42 1 0.01
43 50 0.54
44 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (42 bp):
GATGCCAATGTCCCAACATGGTCTTACACGAAATCATATAAC
Found at i:60162178 original size:33 final size:33
Alignment explanation
Indices: 60162136--60162202 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
60162126 AATGTCCCAA
*
60162136 ACATGGTCTTACACGAAATCATATAATGATGCC
1 ACATGGTCTTACACGAAATCATATAACGATGCC
60162169 ACATGGTCTTACACGAAATCATATAACGATGCC
1 ACATGGTCTTACACGAAATCATATAACGATGCC
60162202 A
1 A
60162203 ATGTCCCAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (33 bp):
ACATGGTCTTACACGAAATCATATAACGATGCC
Found at i:60164993 original size:29 final size:29
Alignment explanation
Indices: 60164951--60165032 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
60164941 TGCCGTATTT
**
60164951 TTTCCAGCTTGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
60164980 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
60165009 TTTCCAGCACGCACACTTAGTGCC
1 TTTCCAGCACGCACACTTAGTGCC
60165033 GATCTTGTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCATATA
Found at i:60168077 original size:28 final size:28
Alignment explanation
Indices: 60168037--60168115 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
60168027 GCAATCAAAT
* * *
60168037 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGAACTTAGTGTGCGAAATATTGAGA
* *
60168065 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGAACTTAGTGTGCGAAATATTGAGA
* *
60168093 ATGAAACTTAGTGTGCAAAATAT
1 ATGGAACTTAGTGTGCGAAATAT
60168116 CGAATGATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGAACTTAGTGTGCGAAATATTGAGA
Found at i:60170437 original size:41 final size:41
Alignment explanation
Indices: 60170379--60170526 Score: 176
Period size: 41 Copynumber: 3.6 Consensus size: 41
60170369 GAGCTTGGTC
60170379 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * *
60170420 TCGAAGGGCTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
60170460 CCGAAGGGCCTTCGAGCCAGTGGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
60170501 TCGAAGGGCTTTTGAGCCAGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
60170527 GAATCGGGCT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
39 4 0.04
40 35 0.39
41 48 0.53
43 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:60176806 original size:24 final size:24
Alignment explanation
Indices: 60176766--60176827 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
60176756 GATTATGTAG
60176766 AAAGAATAAAGAAATGAA-AAAAAA
1 AAAGAA-AAAGAAATGAAGAAAAAA
* *
60176790 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAGAAAAAA
*
60176815 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
60176828 AAAAAAAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 5 0.16
24 12 0.38
25 15 0.47
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAGAAAAAA
Found at i:60178026 original size:29 final size:29
Alignment explanation
Indices: 60177993--60178123 Score: 147
Period size: 29 Copynumber: 4.6 Consensus size: 29
60177983 GTGACGAGAT
60177993 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
60178022 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* *
60178051 TGGCACTAA-TGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** * * ***
60178079 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
60178108 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
60178124 GGCTTAAATT
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 24 0.28
29 63 0.72
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:60178072 original size:28 final size:29
Alignment explanation
Indices: 60177993--60178085 Score: 152
Period size: 29 Copynumber: 3.2 Consensus size: 29
60177983 GTGACGAGAT
*
60177993 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
60178022 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
60178051 TGGCACTAA-TGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
60178079 CGGCACT
1 TGGCACT
60178086 GGGTGTGCGA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
28 24 0.39
29 37 0.61
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:60178110 original size:57 final size:57
Alignment explanation
Indices: 60177989--60178119 Score: 142
Period size: 57 Copynumber: 2.3 Consensus size: 57
60177979 TACGGTGACG
* * * *
60177989 AGAT-TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAA-TGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
* **
60178046 ATATATGGCACTAATGTGCATGCTGGAAAAATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAATGTGCATGCTGGAAAAATACGGCACTAAGTGTGC-ATGCTCGAA
* *
60178103 GGGTATGGCACT-ATGTG
1 AGATATGGCACTAATGTG
60178120 TGCGGGCTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
56 5 0.08
57 47 0.76
58 10 0.16
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.25
Consensus pattern (57 bp):
AGATATGGCACTAATGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
Found at i:60184679 original size:26 final size:25
Alignment explanation
Indices: 60184645--60184706 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 25
60184635 GAAAGAATAA
60184645 AGAAATGAAAAAAAAAAAAAAAAAG
1 AGAAATGAAAAAAAAAAAAAAAAAG
* * *
60184670 AGAATATGAAGAAAAACAAAGAAAAG
1 AGAA-ATGAAAAAAAAAAAAAAAAAG
60184696 -GAAA--AAAAAAA
1 AGAAATGAAAAAAA
60184707 GTGTTCATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 6 0.19
24 1 0.03
25 7 0.22
26 18 0.56
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.05
Consensus pattern (25 bp):
AGAAATGAAAAAAAAAAAAAAAAAG
Found at i:60184703 original size:19 final size:21
Alignment explanation
Indices: 60184657--60184706 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
60184647 AAATGAAAAA
*
60184657 AAAAAAAAAAAAGAGAATATG
1 AAAAAAAAAAAAGAGAATAGG
* *
60184678 AAGAAAAACAAAGA-AA-AGG
1 AAAAAAAAAAAAGAGAATAGG
60184697 AAAAAAAAAA
1 AAAAAAAAAA
60184707 GTGTTCATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 10 0.42
20 2 0.08
21 12 0.50
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAAAGAGAATAGG
Found at i:60190018 original size:11 final size:11
Alignment explanation
Indices: 60190002--60190026 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60189992 TTATATATAC
60190002 TAATAAAATAA
1 TAATAAAATAA
60190013 TAATAAAATAA
1 TAATAAAATAA
60190024 TAA
1 TAA
60190027 AATATCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:60193888 original size:28 final size:28
Alignment explanation
Indices: 60193817--60193890 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
60193807 GTAATAAGCC
* *
60193817 CGCACACTTAGTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTAT-ATAATCAAACT
60193845 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
60193873 TGCACACTTAGTGCTATA
1 CGCACACTTAGTGCTATA
60193891 CCATTTGAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 41 0.98
29 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:60194036 original size:2 final size:2
Alignment explanation
Indices: 60194029--60194053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60194019 TACATACATG
60194029 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
60194054 TTATCATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60206433 original size:40 final size:40
Alignment explanation
Indices: 60206388--60206469 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
60206378 TATGAAATTG
* *
60206388 CCTTAGATTATGAATTAGAAGGTATTGGAGAGCAATTTTC
1 CCTTAGATTAAGAATTAGAAAGTATTGGAGAGCAATTTTC
*
60206428 CCTTAGATTAAGAATTAGAAAGTCTTGGAGAGCAATTTTC
1 CCTTAGATTAAGAATTAGAAAGTATTGGAGAGCAATTTTC
60206468 CC
1 CC
60206470 AAATTCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (40 bp):
CCTTAGATTAAGAATTAGAAAGTATTGGAGAGCAATTTTC
Found at i:60212016 original size:46 final size:46
Alignment explanation
Indices: 60211966--60212141 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
60211956 TATTTGGGCA
60211966 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
60212012 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
60212059 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
60212105 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
60212142 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:60212121 original size:93 final size:93
Alignment explanation
Indices: 60211962--60212133 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
60211952 TGGATATTTG
* *
60211962 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
60212027 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
60212055 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
60212120 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
60212134 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:60215091 original size:15 final size:15
Alignment explanation
Indices: 60215052--60215130 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
60215042 GTATCTTGGG
*
60215052 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
60215067 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
60215082 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
60215096 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
60215111 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
60215125 TTTCTT
1 TTTCTT
60215131 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:60215115 original size:29 final size:29
Alignment explanation
Indices: 60215043--60215129 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
60215033 CATAGTATCG
* * * *
60215043 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
60215073 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
60215102 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
60215130 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:60217100 original size:45 final size:45
Alignment explanation
Indices: 60217049--60217221 Score: 226
Period size: 45 Copynumber: 3.8 Consensus size: 45
60217039 TATTTGGGCA
60217049 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAGCG
* * * *
60217094 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATG---CGA-GCG
*
60217141 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAGCG
*
60217187 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG
60217222 GGCGGGTTAC
Statistics
Matches: 111, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
43 4 0.04
44 3 0.03
45 62 0.56
46 3 0.03
47 33 0.30
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAGCG
Found at i:60217202 original size:92 final size:92
Alignment explanation
Indices: 60217045--60217214 Score: 306
Period size: 92 Copynumber: 1.8 Consensus size: 92
60217035 GGGATATTTG
*
60217045 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAGCGTCCGAACTCGTTGAGT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGTCCGAACTCGTTGAGT
60217110 TGAGTCCGAGTTCGTGAGATGTAACTA
66 TGAGTCCGAGTTCGTGAGATGTAACTA
*
60217137 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAACGTCCGAACTCGTTGAG
60217201 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
60217215 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 66 0.88
93 9 0.12
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:60227539 original size:43 final size:43
Alignment explanation
Indices: 60227491--60227648 Score: 194
Period size: 43 Copynumber: 3.7 Consensus size: 43
60227481 CAATGCCATA
* * *
60227491 CCCAGATATGGTCTTACATGTTATCTCATATCGATGCCAATGT
1 CCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGT
* *
60227534 CCCAGACATGGTCTTACACGAAATCAT-ATAACGATGCCAATGT
1 CCCAGACATGGTCTTACACGTAATC-TCATATCGATGCCAATGT
* * * *
60227577 CCCAAACATGGTCTTATACGTAATCACA-ATACAATGCCAATGT
1 CCCAGACATGGTCTTACACGTAATCTCATAT-CGATGCCAATGT
*
60227620 CCCAGACATGGTCTTACATGTAATCTCAT
1 CCCAGACATGGTCTTACACGTAATCTCAT
60227649 GTCGGTAATC
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.01
43 94 0.98
44 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (43 bp):
CCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGT
Found at i:60242403 original size:24 final size:25
Alignment explanation
Indices: 60242345--60242405 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
60242335 AGGCCTACCT
*
60242345 CTTTTAAT-AACTGGGGCAAAAGCC
1 CTTTTGATAAACTGGGGCAAAAGCC
60242369 CTTTTGATAAACTGGGGC-AAAG-C
1 CTTTTGATAAACTGGGGCAAAAGCC
*
60242392 CTTTTCGGTAAACT
1 CTTTT-GATAAACT
60242406 AGGGTATAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 6 0.18
24 18 0.55
25 9 0.27
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (25 bp):
CTTTTGATAAACTGGGGCAAAAGCC
Found at i:60242488 original size:20 final size:20
Alignment explanation
Indices: 60242465--60242551 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
60242455 TTATGAATAC
60242465 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
60242485 ATCATATGCATATCACACAT
1 ATCATGTGCATATCATACAT
*
60242505 ATCATGAGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
60242525 ACCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
60242545 ATCATGT
1 ATCATGT
60242552 ATACCAAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 56 0.97
21 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:60242494 original size:40 final size:41
Alignment explanation
Indices: 60242450--60242539 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 41
60242440 ACCCAACCCA
* * * *
60242450 ATGCATTATGA-ATACATCATGTGCATATCATACATATCAT
1 ATGCATTATCACACACATCATGAGCATATCATACATACCAT
*
60242490 ATGCA-TATCACACATATCATGAGCATATCATACATACCAT
1 ATGCATTATCACACACATCATGAGCATATCATACATACCAT
*
60242530 GTGCA-TATCA
1 ATGCATTATCA
60242540 TATCAATCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (41 bp):
ATGCATTATCACACACATCATGAGCATATCATACATACCAT
Found at i:60242496 original size:11 final size:10
Alignment explanation
Indices: 60242472--60242541 Score: 65
Period size: 9 Copynumber: 7.0 Consensus size: 10
60242462 TACATCATGT
60242472 GCATATCATA
1 GCATATCATA
60242482 -CATATCATA
1 GCATATCATA
*
60242491 TGCATATCACA
1 -GCATATCATA
60242502 -CATATCATGA
1 GCATATCAT-A
60242512 GCATATCATA
1 GCATATCATA
* *
60242522 -CATACCATGT
1 GCATATCAT-A
60242532 GCATATCATA
1 GCATATCATA
60242542 TCAATCATGT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
9 23 0.48
10 2 0.04
11 23 0.48
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (10 bp):
GCATATCATA
Found at i:60246058 original size:40 final size:40
Alignment explanation
Indices: 60245996--60246253 Score: 342
Period size: 40 Copynumber: 6.5 Consensus size: 40
60245986 AAGCCAAGTA
* * * *
60245996 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
60246035 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
60246075 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
60246115 CCTTCGGGACTTAACCCGGATATAGTAACTCGGACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
60246155 CCTTCGGGACTTAACCCGGATATAGTAATTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
60246195 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
60246235 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
60246254 TTATCATCCG
Statistics
Matches: 197, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.07
40 184 0.93
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:60254156 original size:40 final size:40
Alignment explanation
Indices: 60254094--60254350 Score: 394
Period size: 40 Copynumber: 6.5 Consensus size: 40
60254084 AAGCCAAGTA
* * * *
60254094 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
60254133 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
60254173 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
60254213 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
60254253 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
60254293 CCTTCGGGACTTAGCCCGGA-ATAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
60254332 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
60254351 TTATCATCCG
Statistics
Matches: 204, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
39 47 0.23
40 157 0.77
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:60261682 original size:31 final size:31
Alignment explanation
Indices: 60261644--60261707 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
60261634 CCTTTACATA
*
60261644 TTTCATATTTCATAACCCTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
** *
60261675 TTTCATATTTCATATTATTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
60261706 TT
1 TT
60261708 ACTGTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:60261954 original size:24 final size:24
Alignment explanation
Indices: 60261916--60261997 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
60261906 CTAGAGGCCT
60261916 AGCCTCTTTTAAT-AACTAGGGCAAA
1 AGCC-CTTTTAATAAACTAGGGC-AA
* *
60261941 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTAATAAACTAGGGCAA
* *
60261965 AG-CCTTTTCAGTAAACTAGGGCAT
1 AGCCCTTTT-AATAAACTAGGGCAA
60261989 AGCCCTTTT
1 AGCCCTTTT
60261998 TGCACTTCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
23 6 0.12
24 24 0.50
25 18 0.38
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTAGGGCAA
Found at i:60262064 original size:20 final size:20
Alignment explanation
Indices: 60262041--60262087 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
60262031 TTATGGATAC
60262041 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
60262060 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
60262081 ATCATGT
1 ATCATGT
60262088 ATACCAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:60267978 original size:47 final size:47
Alignment explanation
Indices: 60267909--60268001 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
60267899 AATGAGTTAG
60267909 GTGGAGAGTAATTTGAACAAGAAGTTCAACAAGGATAACCCATTACT
1 GTGGAGAGTAATTTGAACAAGAAGTTCAACAAGGATAACCCATTACT
60267956 GTGGAGAGTAATTTGAACAAGAAGTTCAACAAGGATAACCCATTAC
1 GTGGAGAGTAATTTGAACAAGAAGTTCAACAAGGATAACCCATTAC
60268002 AAGTTAACTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.23
Consensus pattern (47 bp):
GTGGAGAGTAATTTGAACAAGAAGTTCAACAAGGATAACCCATTACT
Found at i:60270509 original size:49 final size:49
Alignment explanation
Indices: 60270420--60270541 Score: 148
Period size: 49 Copynumber: 2.6 Consensus size: 49
60270410 TCCAAATAGA
*
60270420 ACTACACTTCATTTATTT--TATT--TTAGAATAAGGTTCTTCAACCTT
1 ACTACACTTCATCTATTTGATATTGATTAGAATAAGGTTCTTCAACCTT
*
60270465 ATTACACTTCATCTATTTGATATTGATTAGAATAAGGTGT-TTCAACCTT
1 ACTACACTTCATCTATTTGATATTGATTAGAATAAGGT-TCTTCAACCTT
* *
60270514 ACTACACTCCTTCTATTTGA-ATATGATT
1 ACTACACTTCATCTATTTGATAT-TGATT
60270542 TTACAAGCTA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
45 16 0.24
47 4 0.06
48 2 0.03
49 43 0.65
50 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (49 bp):
ACTACACTTCATCTATTTGATATTGATTAGAATAAGGTTCTTCAACCTT
Found at i:60271457 original size:42 final size:42
Alignment explanation
Indices: 60271394--60271476 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
60271384 AAAATCGTAA
* * *
60271394 TGCTGATGATAGTTATAGAAGGATAGAGGAAAGAAATCCTCG
1 TGCTGATGATAGTAATAGAAGGACACAGGAAAGAAATCCTCG
* *
60271436 TGCTGATGAT-GATAATGGAAGGACACAGGAACGAAATCCTC
1 TGCTGATGATAG-TAATAGAAGGACACAGGAAAGAAATCCTC
60271477 ACGGTAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (42 bp):
TGCTGATGATAGTAATAGAAGGACACAGGAAAGAAATCCTCG
Found at i:60273077 original size:40 final size:40
Alignment explanation
Indices: 60273009--60273099 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
60272999 GTCGGTATCT
* * *
60273009 CACACTTAGTGCGCTCTATAACTGAAGCTATGCCAACTCG
1 CACACTTAGTGCGCTCTATAACTAAAGCTATACCAAATCG
* * **
60273049 CACACTTAGTGC-CATTTATAGCTAAAGCTATATTAAATCG
1 CACACTTAGTGCGC-TCTATAACTAAAGCTATACCAAATCG
60273089 CACACTTAGTG
1 CACACTTAGTG
60273100 GCAATCATAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (40 bp):
CACACTTAGTGCGCTCTATAACTAAAGCTATACCAAATCG
Found at i:60280492 original size:24 final size:24
Alignment explanation
Indices: 60280456--60280519 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
60280446 TCTTACTTAT
* **
60280456 TCGCACACT-TAGTGCTACGTTTTC
1 TCGCACA-TATAGTGCCACGTAATC
*
60280480 TCGCACATATAGTGCCATGTAATC
1 TCGCACATATAGTGCCACGTAATC
*
60280504 TCGCACACATAGTGCC
1 TCGCACATATAGTGCC
60280520 GTATAGCCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (24 bp):
TCGCACATATAGTGCCACGTAATC
Found at i:60281833 original size:20 final size:21
Alignment explanation
Indices: 60281808--60281846 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
60281798 TAATTTCTTC
*
60281808 TTTTATTCCTATT-TTTATTT
1 TTTTATTCATATTGTTTATTT
60281828 TTTTATTCATATTGTTTAT
1 TTTTATTCATATTGTTTAT
60281847 GATATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTATTCATATTGTTTATTT
Found at i:60297661 original size:15 final size:17
Alignment explanation
Indices: 60297643--60297674 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
60297633 TAGCATAATT
60297643 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
60297658 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
60297675 CAAGTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:60303264 original size:20 final size:19
Alignment explanation
Indices: 60303235--60303273 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
60303225 TTTGAGAGTA
*
60303235 AAGGGTGAAAAATAAAAGTT
1 AAGGGGGAAAAA-AAAAGTT
*
60303255 AAGGGGGAAATAAAAAGTT
1 AAGGGGGAAAAAAAAAGTT
60303274 TTGAGGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.28, T:0.18
Consensus pattern (19 bp):
AAGGGGGAAAAAAAAAGTT
Found at i:60309626 original size:37 final size:36
Alignment explanation
Indices: 60309576--60309662 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
60309566 TACGAAGTCT
60309576 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
60309612 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
60309649 TCACCCGGAACATA
1 T-ACCCGG-ACATA
60309663 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:60309800 original size:49 final size:49
Alignment explanation
Indices: 60309731--60310090 Score: 569
Period size: 49 Copynumber: 7.4 Consensus size: 49
60309721 TTTACCACAT
*
60309731 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
60309780 ATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
60309829 ATATACATATACTTTCACATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
60309878 ATATACATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
60309927 ATATACATATACTTTC-CATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * * *
60309975 ATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * *
60310024 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
60310073 ATATATATACATTTTCAC
1 ATATACATACACTTTCAC
60310091 GAATCTTGAT
Statistics
Matches: 297, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
48 45 0.15
49 252 0.85
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (49 bp):
ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:60310042 original size:195 final size:197
Alignment explanation
Indices: 60309711--60310077 Score: 576
Period size: 195 Copynumber: 1.9 Consensus size: 197
60309701 ATTCACATTA
* * * *
60309711 GCCATTCGGCTTTACCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 GCCATTAGGCCTTACCACATATACATATA-ACTTTCACATTCACCACATCGGCCATTAGGCCTTA
* *
60309776 TCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATATAC
65 TCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATACAC
*
60309841 TTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCACATTCATCACA
130 TTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCACATTCATCACA
60309906 TCG
195 TCG
*
60309909 GCCATTAGGCCTTATCACATATACATAT-ACTTTC-CATTCACCACATCGGCCATTAGGCCTTAT
1 GCCATTAGGCCTTACCACATATACATATAACTTTCACATTCACCACATCGGCCATTAGGCCTTAT
* * * * * *
60309972 CACATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCACATATATATACATT
66 CACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATACACT
*
60310037 TTCACATTCATCACATCGGCCATTAGGCCTCATCACATATA
131 TTCACATTCACCACATCGGCCATTAGGCCTCATCACATATA
60310078 TATACATTTT
Statistics
Matches: 154, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
195 124 0.81
196 6 0.04
198 24 0.16
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (197 bp):
GCCATTAGGCCTTACCACATATACATATAACTTTCACATTCACCACATCGGCCATTAGGCCTTAT
CACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATACACT
TTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCACATTCATCACAT
CG
Found at i:60314135 original size:40 final size:40
Alignment explanation
Indices: 60313899--60314122 Score: 378
Period size: 40 Copynumber: 5.6 Consensus size: 40
60313889 CCAGCATGAT
* * * *
60313899 TGCTCTTCGGGACCTAGCCCGGATGCATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
60313939 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
60313979 TGCTCCTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
60314019 TGCTCCTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
60314059 TGCTCGTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
60314099 TGCTCTTCGGAACTTAG-CCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATA
60314123 TAACCACAAG
Statistics
Matches: 177, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
39 7 0.04
40 170 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:60314165 original size:40 final size:40
Alignment explanation
Indices: 60314091--60314239 Score: 149
Period size: 40 Copynumber: 3.7 Consensus size: 40
60314081 ATACATCACT
* **
60314091 AGCACGAATGCTCTTCGGAACTTAG-CCGGATATAACCACA
1 AGCACAAATGC-CTTCGGGTCTTAGCCCGGATATAACCACA
* * * * *
60314131 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAACAACTC
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACCAC-A
** *
60314172 A-CACAAATGCCTTCGGGTCTTAGCCCGGATATATTCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACCACA
* *
60314211 AGCATAAATGCCTTCGGGACTTAGCCCGG
1 AGCACAAATGCCTTCGGGTCTTAGCCCGG
60314240 GTATCATTCA
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
39 11 0.12
40 77 0.87
41 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACCACA
Found at i:60314181 original size:120 final size:119
Alignment explanation
Indices: 60313916--60314236 Score: 337
Period size: 120 Copynumber: 2.7 Consensus size: 119
60313906 CGGGACCTAG
* * *
60313916 CCCGGATGCATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
1 CCCGGATACAACACTAGCACAAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
* * * * *
60313981 CTCCTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCCTCGGAACTTAG
66 CTCTTCGGAACTTAG-CCGGATAAACCACAAGCACGAATGCTCCTCGGAACTTAA
* * * *
60314036 TCCGGATACATCACTAGCACGAATGCTCGTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
1 CCCGGATACAACACTAGCACAAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
* **
60314101 CTCTTCGGAACTTAGCCGGATATAACCACAAGCAC-AATTGC-CTTCGGGTCTTAA
66 CTCTTCGGAACTTAGCCGGATA-AACCACAAGCACGAA-TGCTCCTCGGAACTTAA
* * ** * * **
60314155 CCCGGGTATAACAACTCA-CACAAATGC-CTTCGGGTCTTAGCCCGGATATATTCACTAGCATAA
1 CCCGGATACAAC-ACT-AGCACAAATGCTCTTCGGAACTTAGTCCGGATACA-TCACTAGCACGA
*
60314218 ATGC-CTTCGGGACTTAGCC
63 ATGCTCTTCGGAACTTAGCC
60314237 CGGGTATCAT
Statistics
Matches: 172, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
119 58 0.34
120 113 0.66
121 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (119 bp):
CCCGGATACAACACTAGCACAAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATG
CTCTTCGGAACTTAGCCGGATAAACCACAAGCACGAATGCTCCTCGGAACTTAA
Found at i:60316151 original size:37 final size:36
Alignment explanation
Indices: 60316101--60316187 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
60316091 TACGAAGTCT
60316101 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
60316137 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
60316174 TCACCCGGAACATA
1 T-ACCCGG-ACATA
60316188 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:60316325 original size:49 final size:49
Alignment explanation
Indices: 60316256--60316615 Score: 569
Period size: 49 Copynumber: 7.4 Consensus size: 49
60316246 TTTACCACAT
*
60316256 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
60316305 ATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
60316354 ATATACATATACTTTCACATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
60316403 ATATACATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
60316452 ATATACATATACTTTC-CATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * * *
60316500 ATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * *
60316549 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
60316598 ATATATATACATTTTCAC
1 ATATACATACACTTTCAC
60316616 GAATCTTGAT
Statistics
Matches: 297, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
48 45 0.15
49 252 0.85
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (49 bp):
ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:60316567 original size:195 final size:197
Alignment explanation
Indices: 60316236--60316602 Score: 576
Period size: 195 Copynumber: 1.9 Consensus size: 197
60316226 ATTCACATTA
* * * *
60316236 GCCATTCGGCTTTACCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 GCCATTAGGCCTTACCACATATACATATA-ACTTTCACATTCACCACATCGGCCATTAGGCCTTA
* *
60316301 TCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATATAC
65 TCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATACAC
*
60316366 TTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCACATTCATCACA
130 TTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCACATTCATCACA
60316431 TCG
195 TCG
*
60316434 GCCATTAGGCCTTATCACATATACATAT-ACTTTC-CATTCACCACATCGGCCATTAGGCCTTAT
1 GCCATTAGGCCTTACCACATATACATATAACTTTCACATTCACCACATCGGCCATTAGGCCTTAT
* * * * * *
60316497 CACATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCACATATATATACATT
66 CACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATACACT
*
60316562 TTCACATTCATCACATCGGCCATTAGGCCTCATCACATATA
131 TTCACATTCACCACATCGGCCATTAGGCCTCATCACATATA
60316603 TATACATTTT
Statistics
Matches: 154, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
195 124 0.81
196 6 0.04
198 24 0.16
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (197 bp):
GCCATTAGGCCTTACCACATATACATATAACTTTCACATTCACCACATCGGCCATTAGGCCTTAT
CACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATACACT
TTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCACATTCATCACAT
CG
Found at i:60326602 original size:28 final size:24
Alignment explanation
Indices: 60326549--60326596 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
60326539 TCACAGTAAC
60326549 CATGGAATTGTTTGATTGATTACT
1 CATGGAATTGTTTGATTGATTACT
60326573 CATGGAATTGTTTGATTGATTACT
1 CATGGAATTGTTTGATTGATTACT
60326597 TTCTCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.46
Consensus pattern (24 bp):
CATGGAATTGTTTGATTGATTACT
Found at i:60350085 original size:2 final size:2
Alignment explanation
Indices: 60350078--60350102 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60350068 TTAACCAATA
60350078 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
60350103 AACATGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:60353290 original size:28 final size:28
Alignment explanation
Indices: 60353250--60353326 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
60353240 CCCCTATTTT
60353250 TTTTTCAGATTTTATAGTTTTACACATG
1 TTTTTCAGATTTTATAGTTTTACACATG
* * * *
60353278 TTTTTCAGATTTTACAGTTTTGCTCTTG
1 TTTTTCAGATTTTATAGTTTTACACATG
* *
60353306 TTTCTCAAATTTTATAGTTTT
1 TTTTTCAGATTTTATAGTTTT
60353327 TTTTTCTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.57
Consensus pattern (28 bp):
TTTTTCAGATTTTATAGTTTTACACATG
Found at i:60353364 original size:28 final size:27
Alignment explanation
Indices: 60353286--60353383 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 27
60353276 TGTTTTTCAG
* *
60353286 ATTTTACAGTTTTGCTCTTGTTTCTCAA
1 ATTTTACAGTTTTCCTC-TATTTCTCAA
* **
60353314 ATTTTATAGTTTTTTTTTCTATTTCTCAA
1 ATTTTACAG--TTTTCCTCTATTTCTCAA
* *
60353343 ATTTTACAGTTTTACCTCTATTTTTAAA
1 ATTTTACAGTTTT-CCTCTATTTCTCAA
60353371 ATTTTACAGTTTT
1 ATTTTACAGTTTT
60353384 GACCCATATT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
27 4 0.07
28 31 0.53
29 17 0.29
30 6 0.10
ACGTcount: A:0.22, C:0.13, G:0.06, T:0.58
Consensus pattern (27 bp):
ATTTTACAGTTTTCCTCTATTTCTCAA
Found at i:60354000 original size:84 final size:86
Alignment explanation
Indices: 60353882--60354039 Score: 225
Period size: 84 Copynumber: 1.9 Consensus size: 86
60353872 CAAACAAGTG
*
60353882 GTGGCTTATCCACCAAACCCAGTGGTAGTTTGTTTAATCTATG-AA-TATATTGTGCACTCACAA
1 GTGGCTTATCCACCAAACCCAGTGGTAGTTTGTTTAAT-T-TGCAACCATATTGTGCACTCACAA
*
60353945 TAAGTGGCAGTAACTGTAAATAT
64 CAAGTGGCAGTAACTGTAAATAT
* * *
60353968 GTGGCTTGTCCA-GAAACCCAGT-GTAGTTTGTTTAATTTGCAACCATGTTGTGCACTCACAACA
1 GTGGCTTATCCACCAAACCCAGTGGTAGTTTGTTTAATTTGCAACCATATTGTGCACTCACAACA
60354031 AGTGGCAGT
66 AGTGGCAGT
60354040 TTAACTACAA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
82 2 0.03
83 3 0.05
84 40 0.62
85 9 0.14
86 11 0.17
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (86 bp):
GTGGCTTATCCACCAAACCCAGTGGTAGTTTGTTTAATTTGCAACCATATTGTGCACTCACAACA
AGTGGCAGTAACTGTAAATAT
Found at i:60355262 original size:116 final size:116
Alignment explanation
Indices: 60355058--60355292 Score: 461
Period size: 116 Copynumber: 2.0 Consensus size: 116
60355048 TACGCATTTC
*
60355058 TGAATGGACATGAGTTGGTGACAATATGTGTACGGATAAAATGGGAATGTTTTTATTTATAAGTG
1 TGAATGGACATGAGTTGATGACAATATGTGTACGGATAAAATGGGAATGTTTTTATTTATAAGTG
60355123 GCATGAGTTTTGTTAAAAATGCCCGTTTGGACGTAGTAAACAATTAGGATA
66 GCATGAGTTTTGTTAAAAATGCCCGTTTGGACGTAGTAAACAATTAGGATA
60355174 TGAATGGACATGAGTTGATGACAATATGTGTACGGATAAAATGGGAATGTTTTTATTTATAAGTG
1 TGAATGGACATGAGTTGATGACAATATGTGTACGGATAAAATGGGAATGTTTTTATTTATAAGTG
60355239 GCATGAGTTTTGTTAAAAATGCCCGTTTGGACGTAGTAAACAATTAGGATA
66 GCATGAGTTTTGTTAAAAATGCCCGTTTGGACGTAGTAAACAATTAGGATA
60355290 TGA
1 TGA
60355293 TTGACATACC
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.34
Consensus pattern (116 bp):
TGAATGGACATGAGTTGATGACAATATGTGTACGGATAAAATGGGAATGTTTTTATTTATAAGTG
GCATGAGTTTTGTTAAAAATGCCCGTTTGGACGTAGTAAACAATTAGGATA
Found at i:60355358 original size:20 final size:20
Alignment explanation
Indices: 60355333--60355370 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
60355323 TTGTATGGGG
60355333 TTGCACTTCGGTGCCTCTTT
1 TTGCACTTCGGTGCCTCTTT
*
60355353 TTGCACTTTGGTGCCTCT
1 TTGCACTTCGGTGCCTCT
60355371 GATTGCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.29, G:0.21, T:0.45
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTTT
Found at i:60355376 original size:20 final size:20
Alignment explanation
Indices: 60355333--60355391 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
60355323 TTGTATGGGG
* **
60355333 TTGCACTTCGGTGCCTCTTT
1 TTGCACTTTGGTGCCTCTGA
60355353 TTGCACTTTGGTGCCTCTGA
1 TTGCACTTTGGTGCCTCTGA
*
60355373 TTGCACATTT-TTGCCTCTG
1 TTGCAC-TTTGGTGCCTCTG
60355392 TCTGTACTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.08, C:0.27, G:0.20, T:0.44
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTGA
Found at i:60357117 original size:28 final size:28
Alignment explanation
Indices: 60357052--60357152 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
60357042 ATAGTGAATC
*
60357052 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
60357081 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
60357109 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
60357139 CGCACACTTAGTGC
1 CGCACACTTAGTGC
60357153 CATACCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:60357201 original size:29 final size:29
Alignment explanation
Indices: 60357169--60357241 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
60357159 CTTCGAGCTC
*
60357169 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
60357198 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
60357227 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
60357242 ATCTCTCACC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:60364982 original size:29 final size:30
Alignment explanation
Indices: 60364912--60364985 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
60364902 ATAGTGAATC
60364912 CGCACACTTAGTGCTATATGATATTCAACT
1 CGCACACTTAGTGCTATATGATATTCAACT
60364942 CGCACACTTAGTGCTATAT-A-A-TCAAAGCT
1 CGCACACTTAGTGCTATATGATATTC-AA-CT
60364971 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
60364986 GTTACAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
27 2 0.05
28 3 0.07
29 18 0.43
30 19 0.45
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATGATATTCAACT
Found at i:60365065 original size:29 final size:29
Alignment explanation
Indices: 60365033--60365105 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
60365023 CTTCGAGCTC
*
60365033 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
60365062 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
60365091 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
60365106 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:60366003 original size:27 final size:26
Alignment explanation
Indices: 60365959--60366010 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
60365949 CTCGCTGCAA
*
60365959 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
60365986 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
60366011 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:60366075 original size:33 final size:32
Alignment explanation
Indices: 60366026--60366089 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
60366016 CTCGCTGCAA
* *
60366026 TCTGGTGGCTTCGCCACATATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
60366059 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
60366090 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:60366103 original size:27 final size:26
Alignment explanation
Indices: 60366051--60366110 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
60366041 ACATATATAT
*
60366051 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
60366077 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
60366104 ATATCTG
1 ATATCTG
60366111 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:60372731 original size:27 final size:27
Alignment explanation
Indices: 60372693--60372819 Score: 105
Period size: 27 Copynumber: 4.7 Consensus size: 27
60372683 TAAGTTGTAG
*
60372693 AATTACTAAAATACCCTTGGTTTATAA
1 AATTACTAAAATACCCTTGATTTATAA
* * *
60372720 AATTACCAAAATACCTCTAG-TTTGTAA
1 AATTACTAAAATACC-CTTGATTTATAA
* * * * *
60372747 AATTAATGAAATACCCTCGACTTGTAA
1 AATTACTAAAATACCCTTGATTTATAA
* * * *
60372774 AATTACCAAAGTACCCTCGATTTACAA
1 AATTACTAAAATACCCTTGATTTATAA
60372801 AATTA-TAGAAATACCCTTG
1 AATTACTA-AAATACCCTTG
60372820 TAAGGTAGAA
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
26 4 0.05
27 72 0.91
28 3 0.04
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACTAAAATACCCTTGATTTATAA
Found at i:60373559 original size:27 final size:26
Alignment explanation
Indices: 60373515--60373566 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
60373505 CTCGCTACAA
*
60373515 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
60373542 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
60373567 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:60373620 original size:31 final size:32
Alignment explanation
Indices: 60373582--60373642 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
60373572 CTCGCTGCAA
* *
60373582 TCTGGTGGCTTCGCCAC-ATATATATATCTTT
1 TCTGGTGGCCTAGCCACAATATATATATCTTT
*
60373613 TCTGGTGGCCTAGCCACAATATCTATATCT
1 TCTGGTGGCCTAGCCACAATATATATATCT
60373643 GGTGACTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTTT
Found at i:60376321 original size:13 final size:13
Alignment explanation
Indices: 60376303--60376327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60376293 GCTCGACAGG
60376303 GACACGCCCGTGT
1 GACACGCCCGTGT
60376316 GACACGCCCGTG
1 GACACGCCCGTG
60376328 AGCGATTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.32, T:0.12
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:60377227 original size:10 final size:9
Alignment explanation
Indices: 60377212--60377246 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
60377202 AGTTGTTATC
*
60377212 AAAAAAAGG
1 AAAAAAAGA
60377221 AAAAAAAGA
1 AAAAAAAGA
60377230 AAAGAAAAGA
1 AAA-AAAAGA
60377240 AAAAAAA
1 AAAAAAA
60377247 CACTAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:60377665 original size:19 final size:19
Alignment explanation
Indices: 60377643--60377683 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
60377633 CCGAACTTTC
*
60377643 AAATTTTTAT-ATTTTTAGA
1 AAATTTTAATAATTTTTA-A
60377662 AAATTTTAATAATTTTTAA
1 AAATTTTAATAATTTTTAA
60377681 AAA
1 AAA
60377684 GTATTGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AAATTTTAATAATTTTTAA
Found at i:60380063 original size:9 final size:9
Alignment explanation
Indices: 60380035--60380102 Score: 66
Period size: 9 Copynumber: 7.6 Consensus size: 9
60380025 TTTATACAAA
60380035 TAATTCGGT
1 TAATTCGGT
* *
60380044 TAATCCAGT
1 TAATTCGGT
60380053 TAATTCGGT
1 TAATTCGGT
* *
60380062 TAATTTGAT
1 TAATTCGGT
*
60380071 TAATTCGGG
1 TAATTCGGT
60380080 TAATTCAGG-
1 TAATTC-GGT
*
60380089 TAATTTGGT
1 TAATTCGGT
60380098 TAATT
1 TAATT
60380103 TTATACTTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
8 2 0.04
9 43 0.91
10 2 0.04
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:60380075 original size:36 final size:36
Alignment explanation
Indices: 60380035--60380103 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
60380025 TTTATACAAA
* *
60380035 TAATTCGGTTAATCCAGTTAATTCGGTTAATTTGAT
1 TAATTCGGGTAATCCAGGTAATTCGGTTAATTTGAT
* *
60380071 TAATTCGGGTAATTCAGGTAATTTGGTTAATTT
1 TAATTCGGGTAATCCAGGTAATTCGGTTAATTT
60380104 TATACTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45
Consensus pattern (36 bp):
TAATTCGGGTAATCCAGGTAATTCGGTTAATTTGAT
Found at i:60380102 original size:18 final size:18
Alignment explanation
Indices: 60380035--60380102 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
60380025 TTTATACAAA
*
60380035 TAATTCGGTTAATCCAGT
1 TAATTCGGTTAATTCAGT
*
60380053 TAATTCGGTTAATT-TGAT
1 TAATTCGGTTAATTCAG-T
* *
60380071 TAATTCGGGTAATTCAGG
1 TAATTCGGTTAATTCAGT
*
60380089 TAATTTGGTTAATT
1 TAATTCGGTTAATT
60380103 TTATACTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
17 1 0.02
18 39 0.95
19 1 0.02
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (18 bp):
TAATTCGGTTAATTCAGT
Found at i:60380102 original size:27 final size:27
Alignment explanation
Indices: 60380035--60380102 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
60380025 TTTATACAAA
* * *
60380035 TAATTCGGTTAATCCAGTTAATTCGGT
1 TAATTTGGTTAATTCAGGTAATTCGGT
* *
60380062 TAATTTGATTAATTCGGGTAATTCAGG-
1 TAATTTGGTTAATTCAGGTAATTC-GGT
60380089 TAATTTGGTTAATT
1 TAATTTGGTTAATT
60380103 TTATACTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (27 bp):
TAATTTGGTTAATTCAGGTAATTCGGT
Found at i:60380217 original size:28 final size:28
Alignment explanation
Indices: 60380176--60380252 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
60380166 GAATTAATCG
*
60380176 AAAAAATTCAGTTTGGTTAATTTTCTT-A
1 AAAAAATTCGGTTTGGTTAATTTT-TTGA
60380204 AAAAAATTCGGTTTGGTTAATTTTTTGA
1 AAAAAATTCGGTTTGGTTAATTTTTTGA
* *
60380232 AAAAATTTCGGTTCGGTTAAT
1 AAAAAATTCGGTTTGGTTAAT
60380253 CGTTAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 2 0.04
28 43 0.96
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (28 bp):
AAAAAATTCGGTTTGGTTAATTTTTTGA
Found at i:60380261 original size:27 final size:27
Alignment explanation
Indices: 60380176--60380261 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
60380166 GAATTAATCG
* *
60380176 AAAAAATTCAGTTTGGTTAATTTTC-TTA
1 AAAAAATTCGGTTCGGTTAA--TTCGTTA
* **
60380204 AAAAAATTCGGTTTGGTTAATTTTTTGA
1 AAAAAATTCGGTTCGGTTAATTCGTT-A
*
60380232 AAAAATTTCGGTTCGGTTAA-TCGTTA
1 AAAAAATTCGGTTCGGTTAATTCGTTA
60380258 AAAA
1 AAAA
60380262 TTTTGAAGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
26 7 0.14
27 5 0.10
28 38 0.76
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (27 bp):
AAAAAATTCGGTTCGGTTAATTCGTTA
Found at i:60381721 original size:70 final size:67
Alignment explanation
Indices: 60381635--60381763 Score: 168
Period size: 70 Copynumber: 1.9 Consensus size: 67
60381625 AATAAGAAAA
** * ** *
60381635 GGCAAAACTATGTCGTTTTGGGAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATTAAGT
1 GGCAAAACTACATCGTTTTGAGAAATGTTTACC-CAT-T-AAGTTAAAAGGCAAAACCATTAAGT
60381700 TAAAT
63 TAAAT
*
60381705 GGCAAAACTACATCGTTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
1 GGCAAAACTACATCGTTTTGAGAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
60381764 TATTTTTTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 21 0.40
68 1 0.02
69 1 0.02
70 29 0.56
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (67 bp):
GGCAAAACTACATCGTTTTGAGAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTAAGTTAA
AT
Found at i:60381880 original size:25 final size:25
Alignment explanation
Indices: 60381852--60381902 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
60381842 GAAAAATAGG
*
60381852 ATTTTTTAACTCAACTCGACTCAAA
1 ATTTTTTAACTCAACTCGACTAAAA
* *
60381877 ATTTTTTGACTCAATTCGACTAAAA
1 ATTTTTTAACTCAACTCGACTAAAA
60381902 A
1 A
60381903 AATTCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (25 bp):
ATTTTTTAACTCAACTCGACTAAAA
Found at i:60385920 original size:37 final size:37
Alignment explanation
Indices: 60385870--60385940 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
60385860 GGCCAAAAAT
60385870 AGGCCATTTACAAGGCTAACTTGCCACCCATTAATTG
1 AGGCCATTTACAAGGCTAACTTGCCACCCATTAATTG
60385907 AGGCCATTTACAAGGCTAACTTGCCACCCATTAA
1 AGGCCATTTACAAGGCTAACTTGCCACCCATTAA
60385941 GGGTTCTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (37 bp):
AGGCCATTTACAAGGCTAACTTGCCACCCATTAATTG
Found at i:60386032 original size:21 final size:23
Alignment explanation
Indices: 60385991--60386032 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
60385981 TCAAATTCCA
60385991 ACCATTTCATAACCAAAACATAT
1 ACCATTTCATAACCAAAACATAT
*
60386014 ACCATTT-AT-ACCAATACAT
1 ACCATTTCATAACCAAAACAT
60386033 TATCAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (23 bp):
ACCATTTCATAACCAAAACATAT
Found at i:60386892 original size:43 final size:42
Alignment explanation
Indices: 60386810--60386935 Score: 137
Period size: 43 Copynumber: 3.0 Consensus size: 42
60386800 AGAAAGCTCG
* ***
60386810 TACAATGCCAACGTCCTAGACGAGGTCTTACATGTAATCAAA
1 TACAATGCCAACGTCCTAGACAAGGTCTTACACAAAATCAAA
*
60386852 TATCAATGCC-ACTGTCCTAGACAAGGTCATACACAAAATCAAA
1 TA-CAATGCCAAC-GTCCTAGACAAGGTCTTACACAAAATCAAA
* * **
60386895 TACGATGCCAACGTCCCAGACATTGTCTTACACATAAATCA
1 TACAATGCCAACGTCCTAGACAAGGTCTTACACA-AAATCA
60386936 TAAGTTGATT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
42 28 0.40
43 42 0.60
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.23
Consensus pattern (42 bp):
TACAATGCCAACGTCCTAGACAAGGTCTTACACAAAATCAAA
Found at i:60391985 original size:39 final size:40
Alignment explanation
Indices: 60391846--60392139 Score: 422
Period size: 39 Copynumber: 7.5 Consensus size: 40
60391836 CAGATGATAA
* * **
60391846 CGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGGCTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
60391886 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
60391926 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
60391966 CGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
60392005 CGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
** *
60392044 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTATTATAT-
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
60392083 CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
60392123 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
60392140 TACTTGGTTT
Statistics
Matches: 238, Mismatches: 12, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
38 2 0.01
39 125 0.53
40 110 0.46
41 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:60392060 original size:118 final size:118
Alignment explanation
Indices: 60391846--60392139 Score: 425
Period size: 118 Copynumber: 2.5 Consensus size: 118
60391836 CAGATGATAA
* * **
60391846 CGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGGCTA-ATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGG-TAAGTCCCGAAGGCATTTG
**
60391910 TGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
64 TGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
60391965 CCGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTAAGTCCCGAAGGCATTTGT
1 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTAAGTCCCGAAGGCATTTGT
*
60392029 GCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTATTATAT
65 GCGAGTTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
* * *
60392083 CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTAAGTCCCGAAGG
60392140 TACTTGGTTT
Statistics
Matches: 160, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
117 8 0.05
118 114 0.71
119 33 0.21
120 5 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (118 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTAAGTCCCGAAGGCATTTGTG
CGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
Found at i:60400061 original size:39 final size:40
Alignment explanation
Indices: 60399987--60400240 Score: 369
Period size: 40 Copynumber: 6.5 Consensus size: 40
60399977 CGGATGATAA
* *
60399987 CGGGCTAAGT-CCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
60400026 CGGGCTAAGTCCCGAAGGCATTTGTGC-AGTTACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
60400065 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
60400104 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
**
60400144 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
60400184 CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
60400224 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
60400241 TACTTGGTTT
Statistics
Matches: 203, Mismatches: 7, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
38 16 0.08
39 67 0.33
40 120 0.59
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:60404846 original size:48 final size:48
Alignment explanation
Indices: 60404787--60405338 Score: 701
Period size: 48 Copynumber: 11.8 Consensus size: 48
60404777 CACATTTGGT
* *
60404787 CATTCGGCTTTACCACATATACATATCTCATATATATTTCACAGTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
60404835 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
* * * * * ** * *
60404883 ACATAT--AC-ATATCTC--ATACATATTTC--ACAT-TAGC-CATTCGG
1 -CAT-TCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
* ** * *
60404924 CTTTACCAC-ATA-TACATACCT-CATA---CAT--AT--TTCACATTAGC
1 CATT-CGGCTTTACCACATA--TACATATCTCATACATATTTCACATTAGC
*
60404965 CACTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
* *
60405013 CATTCGGCTTTACCACATATACATATCTCATATATATTTCACAGTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
*
60405061 CATTCGGCTTTACCACATATACATACCTCATACATATTTCACATTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
* *
60405109 CACTCGGCTTTACCACATATACATATCTCATACATATTTCACAGTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
60405157 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
* *
60405205 CATTCGGCTTTACCACATATACATATCTCATATATATTTCACAGTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
*
60405253 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACGTTAGC
1 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
60405301 CATTCGGCTTTACCACATATACATATCTCATACATATT
1 CATTCGGCTTTACCACATATACATATCTCATACATATT
60405339 AATCTTGTAC
Statistics
Matches: 442, Mismatches: 40, Indels: 44
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.00
40 6 0.01
41 22 0.05
42 12 0.03
43 5 0.01
44 7 0.02
45 11 0.02
46 2 0.00
47 4 0.01
48 368 0.83
49 3 0.01
50 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.35
Consensus pattern (48 bp):
CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGC
Done.