Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 147 of 210
Found at i:44737258 original size:25 final size:25
Alignment explanation
Indices: 44737230--44737363 Score: 72
Period size: 25 Copynumber: 5.3 Consensus size: 25
44737220 TAAGGAATCC
44737230 CAAATAATTTGTCACATAGGCCTTT
1 CAAATAATTTGTCACATAGGCCTTT
* ** *
44737255 CAAATAACTCCTCACA-AGGACTTT
1 CAAATAATTTGTCACATAGGCCTTT
* * * **
44737279 CTTAATAATATGCCATGTAGGCCTTT
1 C-AAATAATTTGTCACATAGGCCTTT
* * * * * *
44737305 CAGATAACTCGCCACAAAGGCTTTT
1 CAAATAATTTGTCACATAGGCCTTT
* * * *
44737330 CAGATAATATGTCACATGGGCTTTT
1 CAAATAATTTGTCACATAGGCCTTT
44737355 CTAAATAAT
1 C-AAATAAT
44737364 ATGCCATATA
Statistics
Matches: 77, Mismatches: 29, Indels: 5
0.69 0.26 0.05
Matches are distributed among these distances:
24 8 0.10
25 55 0.71
26 14 0.18
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (25 bp):
CAAATAATTTGTCACATAGGCCTTT
Found at i:44737337 original size:50 final size:50
Alignment explanation
Indices: 44737246--44737340 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
44737236 ATTTGTCACA
*
44737246 TAGGCCTTTCAAATAACTCCTCACAAGGACTTTCTTAATAATATGCCATG
1 TAGGCCTTTCAAATAACTCCTCACAAGGACTTTCTCAATAATATGCCATG
*
44737296 TAGGCCTTTCAGATAACTCGC-CACAAAGG-CTTT-TCAGATAATATG
1 TAGGCCTTTCAAATAACTC-CTCAC-AAGGACTTTCTCA-ATAATATG
44737341 TCACATGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
49 2 0.05
50 33 0.82
51 5 0.12
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (50 bp):
TAGGCCTTTCAAATAACTCCTCACAAGGACTTTCTCAATAATATGCCATG
Found at i:44737367 original size:76 final size:76
Alignment explanation
Indices: 44737276--44737422 Score: 197
Period size: 76 Copynumber: 1.9 Consensus size: 76
44737266 TCACAAGGAC
* * * *
44737276 TTTCTTAATAATATGCCATGTAGGCCTTTCAGATAACTCGCCACAAAGGCTTT-TCAGATAATAT
1 TTTCTAAATAATATGCCATATAAGCCTTTCAAATAACTCGCCACAAAGGCTTTCT-AGATAATAT
*
44737340 GTCACATGGGCT
65 GCCACATGGGCT
* * * *
44737352 TTTCTAAATAATATGCCATATAAGTCTTTTAAATAACTTGCCACAAATGCTTTCTAGATAATATG
1 TTTCTAAATAATATGCCATATAAGCCTTTCAAATAACTCGCCACAAAGGCTTTCTAGATAATATG
44737417 CCACAT
66 CCACAT
44737423 AGGATTTTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 60 0.98
77 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (76 bp):
TTTCTAAATAATATGCCATATAAGCCTTTCAAATAACTCGCCACAAAGGCTTTCTAGATAATATG
CCACATGGGCT
Found at i:44737406 original size:50 final size:50
Alignment explanation
Indices: 44737352--44737472 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 50
44737342 CACATGGGCT
* * *
44737352 TTTCTAAATAATATGCCATATAAG-TCTTTTAAATAACTTGCCACAAATGC
1 TTTCTAAATAATATGCCACATAAGAT-TTTTAAATAACTCGCCACAAAGGC
* * * * *
44737402 TTTCTAGATAATATGCCACATAGGATTTTTAGATAACTCGTCATAAAGGC
1 TTTCTAAATAATATGCCACATAAGATTTTTAAATAACTCGCCACAAAGGC
*
44737452 TTTCCAAATAATATGCCACAT
1 TTTCTAAATAATATGCCACAT
44737473 TGGCTCTATT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (50 bp):
TTTCTAAATAATATGCCACATAAGATTTTTAAATAACTCGCCACAAAGGC
Found at i:44737412 original size:25 final size:26
Alignment explanation
Indices: 44737384--44737439 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
44737374 AGTCTTTTAA
* *
44737384 ATAACT-TGCCACAAATGCTTTCTAG
1 ATAACTATGCCACAAAGGATTTCTAG
* *
44737409 ATAA-TATGCCACATAGGATTTTTAG
1 ATAACTATGCCACAAAGGATTTCTAG
44737434 ATAACT
1 ATAACT
44737440 CGTCATAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 23 0.92
26 1 0.04
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (26 bp):
ATAACTATGCCACAAAGGATTTCTAG
Found at i:44743542 original size:43 final size:43
Alignment explanation
Indices: 44743484--44743636 Score: 161
Period size: 43 Copynumber: 3.6 Consensus size: 43
44743474 TAAATTTAGT
*
44743484 GATACGG-GGAATCAGCACATAGCAAACCCTTTCACAGTCAAA
1 GATACGGTGGAATCAGCACATAGCAAACCCTTTCACAATCAAA
* * * * * **
44743526 GATAGGGTGGAATCAGCACTTAGCAACCACCTTT-ATATTCAGT
1 GATACGGTGGAATCAGCACATAGCAAAC-CCTTTCACAATCAAA
*
44743569 GATACGG-GAAATCAGCACATAGC-AACCACTTTCACAATCAAA
1 GATACGGTGGAATCAGCACATAGCAAACC-CTTTCACAATCAAA
* *
44743611 TATACGGTGGAATCAGCACTTAGCAA
1 GATACGGTGGAATCAGCACATAGCAA
44743637 CCACCTTTAG
Statistics
Matches: 87, Mismatches: 18, Indels: 10
0.76 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 6 0.07
42 31 0.36
43 43 0.49
44 6 0.07
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (43 bp):
GATACGGTGGAATCAGCACATAGCAAACCCTTTCACAATCAAA
Found at i:44743592 original size:42 final size:43
Alignment explanation
Indices: 44743446--44743680 Score: 214
Period size: 42 Copynumber: 5.6 Consensus size: 43
44743436 ATCCATTACT
* * * *
44743446 CGGTGGATTCAGCACTTAGCAACCACC-TTAAATTTAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACATTCAATGATA
* * * *
44743488 CGG-GGAATCAGCACATAGCAAAC-CCTTTCACAGTCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-ACATTCAATGATA
* * *
44743530 GGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACATTCAATGATA
* * *
44743573 CGG-GAAATCAGCACATAGCAACCA-CTTTCACAATCAAAT-ATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-ACATTC-AATGATA
* * * *
44743615 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATT
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACATTCAATGATA
* *
44743658 TGG-GGAATTAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
44743681 CCTCGGGGAA
Statistics
Matches: 157, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.01
41 23 0.15
42 64 0.41
43 59 0.38
44 9 0.06
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTACATTCAATGATA
Found at i:44743601 original size:85 final size:85
Alignment explanation
Indices: 44743446--44743645 Score: 314
Period size: 85 Copynumber: 2.4 Consensus size: 85
44743436 ATCCATTACT
* * *
44743446 CGGTGGATTCAGCACTTAGCAACCACC-TTAAATTTAGTGATACGGGGAATCAGCACATAGCAAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGAAATCAGCACATAGCAAA
*
44743510 CCCTTTCACAGTCAAAGATA
66 CCCTTTCACAATCAAAGATA
* *
44743530 GGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGAAATCAGCACATAGC-AA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGAAATCAGCACATAGCAAA
*
44743594 CCACTTTCACAATCAAATATA
66 CC-CTTTCACAATCAAAGATA
44743615 CGGTGGAATCAGCACTTAGCAACCACCTTTA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA
44743646 GAATCAATAA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
84 29 0.27
85 77 0.73
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGAAATCAGCACATAGCAAA
CCCTTTCACAATCAAAGATA
Found at i:44743671 original size:85 final size:83
Alignment explanation
Indices: 44743446--44743681 Score: 303
Period size: 85 Copynumber: 2.8 Consensus size: 83
44743436 ATCCATTACT
* *
44743446 CGGTGGATTCAGCACTTAGCAACCACC-TTAAATTTAGTGATACGGGGAATCAGCACATAGCAAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAA-TCAGTGATACGGGGAATCAGCACATAGC-AA
*
44743510 CCCTTTCACAGTCAAAGATA
64 CCCTTTCACAATCAAAGATA
* * *
44743530 GGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGAAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-AATCAGTGATACGGGGAATCAGCACATAGCAAC
*
44743595 CACTTTCACAATCAAATATA
65 C-CTTTCACAATCAAAGATA
* * ** * *
44743615 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTGGGGAATTAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-AATCAGTGATACGGGGAATCAGCACATAGCAAC
44743680 CC
65 CC
44743682 CTCGGGGAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
84 30 0.23
85 101 0.77
86 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (83 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATCAGTGATACGGGGAATCAGCACATAGCAACC
CTTTCACAATCAAAGATA
Found at i:44743688 original size:26 final size:26
Alignment explanation
Indices: 44743659--44743709 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
44743649 TCAATAATTT
44743659 GGGGAAT-TAGCACTTAGCAACCCCTC
1 GGGGAATCT-GCACTTAGCAACCCCTC
*
44743685 GGGGAATCTGCACTTAGCGACCCCT
1 GGGGAATCTGCACTTAGCAACCCCT
44743710 TTTTATCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (26 bp):
GGGGAATCTGCACTTAGCAACCCCTC
Found at i:44749324 original size:25 final size:26
Alignment explanation
Indices: 44749296--44749346 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
44749286 TGTAAGTTAC
44749296 AAAAAAATATCTCTAGA-AATTTTCT
1 AAAAAAATATCTCTAGAGAATTTTCT
* * *
44749321 AAAATAATCTCTTTAGAGAATTTTCT
1 AAAAAAATATCTCTAGAGAATTTTCT
44749347 CTATACAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (26 bp):
AAAAAAATATCTCTAGAGAATTTTCT
Found at i:44749468 original size:11 final size:11
Alignment explanation
Indices: 44749452--44749496 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
44749442 CTTAATAACT
44749452 TTAATATTAAA
1 TTAATATTAAA
44749463 TTAATA-TAATA
1 TTAATATTAA-A
* *
44749474 TTTATATTAAT
1 TTAATATTAAA
44749485 TTAATATTAAA
1 TTAATATTAAA
44749496 T
1 T
44749497 CTCATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 3 0.11
11 22 0.79
12 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:44749484 original size:17 final size:17
Alignment explanation
Indices: 44749453--44749496 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
44749443 TTAATAACTT
44749453 TAATA-TTAAATTAATA
1 TAATATTTAAATTAATA
* *
44749469 TAATATTTATATTAATT
1 TAATATTTAAATTAATA
44749486 TAATA-TTAAAT
1 TAATATTTAAAT
44749497 CTCATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTTAAATTAATA
Found at i:44749703 original size:23 final size:23
Alignment explanation
Indices: 44749669--44749720 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
44749659 CAACCAATGT
* * *
44749669 CAGCCACTGGAACATCGCTGTTG
1 CAGCCACCGGAACACCACTGTTG
44749692 CAGCCACCGGAACACCACTGTTG
1 CAGCCACCGGAACACCACTGTTG
44749715 CAGCCA
1 CAGCCA
44749721 TCGACACTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.37, G:0.23, T:0.15
Consensus pattern (23 bp):
CAGCCACCGGAACACCACTGTTG
Found at i:44766340 original size:32 final size:32
Alignment explanation
Indices: 44766279--44766475 Score: 153
Period size: 32 Copynumber: 6.2 Consensus size: 32
44766269 AATTTGATTG
* * *
44766279 GCACAAAGCCATCAG-AAGCAGTGATATGATCA
1 GCACACAGCCATCAGTAA-CGGTAATATGATCA
* * *
44766311 ACACGCAGCCATCAGTAACGGTAACATGATCA
1 GCACACAGCCATCAGTAACGGTAATATGATCA
* * * * *
44766343 GCATAAAGCCATCAGTAACAGTGATATGATCG
1 GCACACAGCCATCAGTAACGGTAATATGATCA
* * * **
44766375 GCACACAACCATCAGTAATGGTGATATGATTG
1 GCACACAGCCATCAGTAACGGTAATATGATCA
* *
44766407 GCACACAGCCATCGGTAACGGTAATATGATCG
1 GCACACAGCCATCAGTAACGGTAATATGATCA
* * * * * * *
44766439 GCAAAAATCCATCAGTAGCAGTACTATGATCG
1 GCACACAGCCATCAGTAACGGTAATATGATCA
44766471 GCACA
1 GCACA
44766476 TCCCTCTACA
Statistics
Matches: 131, Mismatches: 33, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
32 129 0.98
33 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (32 bp):
GCACACAGCCATCAGTAACGGTAATATGATCA
Found at i:44766438 original size:64 final size:64
Alignment explanation
Indices: 44766273--44766455 Score: 199
Period size: 64 Copynumber: 2.9 Consensus size: 64
44766263 TTGAGTAATT
** * *
44766273 TGATTGGCACAAAGCCATCAG-AAGCAGTGATATGATCAACACGCAGCCATCAGTAACGGTAACA
1 TGATTGGCACAAAGCCATCAGTAA-CAGTGATATGATCGGCACACAACCATCAGTAACGGTAACA
** * * * *
44766337 TGATCAGCATAAAGCCATCAGTAACAGTGATATGATCGGCACACAACCATCAGTAATGGTGATA
1 TGATTGGCACAAAGCCATCAGTAACAGTGATATGATCGGCACACAACCATCAGTAACGGTAACA
* * * * *
44766401 TGATTGGCACACAGCCATCGGTAACGGTAATATGATCGGCA-AAAATCCATCAGTA
1 TGATTGGCACAAAGCCATCAGTAACAGTGATATGATCGGCACACAA-CCATCAGTA
44766456 GCAGTACTAT
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
63 3 0.03
64 94 0.95
65 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (64 bp):
TGATTGGCACAAAGCCATCAGTAACAGTGATATGATCGGCACACAACCATCAGTAACGGTAACA
Found at i:44768035 original size:53 final size:52
Alignment explanation
Indices: 44767967--44768194 Score: 196
Period size: 53 Copynumber: 4.3 Consensus size: 52
44767957 TATCCTTTGG
* *
44767967 GGGTATTTCGGTAATTTTACCTATCGTGGGTATTTTGATAATTTTA-CCATCAA
1 GGGTATTTTGATAATTTTACCTATCG-GGGTATTTTGATAA-TTTACCCATCAA
** * * *
44768020 GGGTATTTCAATAATTTTACACT-TCGACGGTATTTCGATAATTTTACCTAT-AGA
1 GGGTATTTTGATAATTTTAC-CTATCG-GGGTATTTTGATAA-TTTACCCATCA-A
* * * * *
44768074 GGGTATTTTGGTAATTTTACCCATTAGGGGTA-TTTCAGTAATTTACCCATCGA
1 GGGTATTTTGATAATTTTACCTA-TCGGGGTATTTTGA-TAATTTACCCATCAA
* * * * *
44768127 GGGTATTTTAATAA-TTTACCAATCGAGGTATTTTGGTAATTTACCCATCGA
1 GGGTATTTTGATAATTTTACCTATCGGGGTATTTTGATAATTTACCCATCAA
44768178 GGGTATTTTGATAATTT
1 GGGTATTTTGATAATTT
44768195 AGGCCCATTA
Statistics
Matches: 142, Mismatches: 24, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
51 34 0.24
52 12 0.08
53 64 0.45
54 30 0.21
55 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (52 bp):
GGGTATTTTGATAATTTTACCTATCGGGGTATTTTGATAATTTACCCATCAA
Found at i:44768078 original size:80 final size:80
Alignment explanation
Indices: 44767926--44768194 Score: 298
Period size: 80 Copynumber: 3.4 Consensus size: 80
44767916 TATAATAGTC
* * * *
44767926 ATTTTACCCTAT-ACGGGTATTTCAATAATTTTATCCTTTGGGGGTATTTCGGTAATTTTACCTA
1 ATTTTACCC-ATCAAGGGTATTTCAATAATTTTA-CCTTCGAGGGTATTTCGATAATTTTACCTA
* *
44767990 TCGTGGGTATTTTGATA
64 TCGAGGGTATTTTGGTA
*
44768007 ATTTTA-CCATCAAGGGTATTTCAATAATTTTACACTTCGACGGTATTTCGATAATTTTACCTAT
1 ATTTTACCCATCAAGGGTATTTCAATAATTTTAC-CTTCGAGGGTATTTCGATAATTTTACCTAT
*
44768071 AGAGGGTATTTTGGTA
65 CGAGGGTATTTTGGTA
* * * * ** *
44768087 ATTTTACCCATTAGGGGTATTTCAGTAA-TTTACCCATCGAGGGTATTTTAATAA-TTTACCAAT
1 ATTTTACCCATCAAGGGTATTTCAATAATTTTA-CCTTCGAGGGTATTTCGATAATTTTACCTAT
44768150 CGA-GGTATTTTGGTA
65 CGAGGGTATTTTGGTA
* **
44768165 A-TTTACCCATCGAGGGTATTTTGATAATTT
1 ATTTTACCCATCAAGGGTATTTCAATAATTT
44768195 AGGCCCATTA
Statistics
Matches: 160, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
77 20 0.12
78 15 0.09
79 13 0.08
80 87 0.54
81 25 0.16
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (80 bp):
ATTTTACCCATCAAGGGTATTTCAATAATTTTACCTTCGAGGGTATTTCGATAATTTTACCTATC
GAGGGTATTTTGGTA
Found at i:44768195 original size:26 final size:27
Alignment explanation
Indices: 44767940--44768194 Score: 218
Period size: 27 Copynumber: 9.6 Consensus size: 27
44767930 TACCCTATAC
** * * * *
44767940 GGGTATTTCAATAATTTTATCCTTTGG
1 GGGTATTTTGATAATTTTACCCATCGA
* * * *
44767967 GGGTATTTCGGTAATTTTACCTATCGT
1 GGGTATTTTGATAATTTTACCCATCGA
*
44767994 GGGTATTTTGATAATTTTA-CCATCAA
1 GGGTATTTTGATAATTTTACCCATCGA
** * *
44768020 GGGTATTTCAATAATTTTACACTTCGA
1 GGGTATTTTGATAATTTTACCCATCGA
* * * *
44768047 CGGTATTTCGATAATTTTACCTATAGA
1 GGGTATTTTGATAATTTTACCCATCGA
* *
44768074 GGGTATTTTGGTAATTTTACCCAT-TA
1 GGGTATTTTGATAATTTTACCCATCGA
*
44768100 GGGGTA-TTTCAGTAA-TTTACCCATCGA
1 -GGGTATTTTGA-TAATTTTACCCATCGA
* *
44768127 GGGTATTTTAATAA-TTTACCAATCGA
1 GGGTATTTTGATAATTTTACCCATCGA
*
44768153 -GGTATTTTGGTAA-TTTACCCATCGA
1 GGGTATTTTGATAATTTTACCCATCGA
44768178 GGGTATTTTGATAATTT
1 GGGTATTTTGATAATTT
44768195 AGGCCCATTA
Statistics
Matches: 184, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
25 22 0.12
26 65 0.35
27 97 0.53
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGATAATTTTACCCATCGA
Found at i:44768999 original size:21 final size:21
Alignment explanation
Indices: 44768973--44769014 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
44768963 GGATTTCGAA
*
44768973 AAACACTTTAATGTGACATGC
1 AAACACTTCAATGTGACATGC
44768994 AAACACTTCAATGTGACATGC
1 AAACACTTCAATGTGACATGC
44769015 CAGATTCGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.26
Consensus pattern (21 bp):
AAACACTTCAATGTGACATGC
Found at i:44772975 original size:28 final size:28
Alignment explanation
Indices: 44772924--44772977 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
44772914 CAGTAACAGT
*
44772924 ATAGTGTGGGCCATAGCCTAATACAGAA
1 ATAGTGTGGGCCATAGCCCAATACAGAA
*
44772952 ATAGTGTGGGCC-TAAGCCCGATACAG
1 ATAGTGTGGGCCAT-AGCCCAATACAG
44772978 TATCAGTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (28 bp):
ATAGTGTGGGCCATAGCCCAATACAGAA
Found at i:44773204 original size:31 final size:32
Alignment explanation
Indices: 44773169--44773235 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
44773159 GAAAGGTTAC
*
44773169 AAGCCATAACTA-CAGTAATATGATTGGCACA
1 AAGCCATAACTAGCAGTAATATGATCGGCACA
* * *
44773200 AAGCCATCAGTAGCGGTAATATGATCGGCACA
1 AAGCCATAACTAGCAGTAATATGATCGGCACA
44773232 AAGC
1 AAGC
44773236 TATCAGTAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (32 bp):
AAGCCATAACTAGCAGTAATATGATCGGCACA
Found at i:44773221 original size:32 final size:32
Alignment explanation
Indices: 44773183--44773245 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
44773173 CATAACTACA
*
44773183 GTAATATGATTGGCACAAAGCCATCAGTAGCG
1 GTAATATGATCGGCACAAAGCCATCAGTAGCG
*
44773215 GTAATATGATCGGCACAAAGCTATCAGTAGC
1 GTAATATGATCGGCACAAAGCCATCAGTAGC
44773246 ATCGTAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (32 bp):
GTAATATGATCGGCACAAAGCCATCAGTAGCG
Found at i:44773285 original size:27 final size:27
Alignment explanation
Indices: 44773261--44773324 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
44773251 AGCAAAGCTG
*
44773261 CCAGTAATAGT-ATATGTGGCCAAGCCA
1 CCAGTAACAGTGAT-TGTGGCCAAGCCA
44773288 CCAGTAACAGTGATTGTGG-CAGAGCCA
1 CCAGTAACAGTGATTGTGGCCA-AGCCA
*
44773315 CTAGT-ACAGT
1 CCAGTAACAGT
44773325 ACTTCCTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 7 0.21
27 24 0.73
28 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCCAAGCCA
Found at i:44773416 original size:24 final size:23
Alignment explanation
Indices: 44773389--44773447 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
44773379 CCATGCTCAG
*
44773389 AATCAGTCATTCAAATTACAGACA
1 AATCAGTCATTCAAA-CACAGACA
*
44773413 AATCAGTCATACCAAACACAGACA
1 AATCAGTCAT-TCAAACACAGACA
44773437 AATCAGTCATT
1 AATCAGTCATT
44773448 TGACCTCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.22
Consensus pattern (23 bp):
AATCAGTCATTCAAACACAGACA
Found at i:44773524 original size:27 final size:27
Alignment explanation
Indices: 44773487--44773634 Score: 181
Period size: 27 Copynumber: 5.5 Consensus size: 27
44773477 ACACCAGGGC
*
44773487 ATTACAGTTATTTTACCTTACAGGGGT
1 ATTACGGTTATTTTACCTTACAGGGGT
* **
44773514 ATTACTGTTATTTTAACC-TACAGGGAC
1 ATTACGGTTATTTT-ACCTTACAGGGGT
* *
44773541 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTTATTTTACCTTACAGGGGT
*
44773568 ATTACGGTTATTTTACCTTACAGGGGC
1 ATTACGGTTATTTTACCTTACAGGGGT
* * *
44773595 ATTACGGTCATTTTACCATATAGGGGT
1 ATTACGGTTATTTTACCTTACAGGGGT
*
44773622 ATTACGGTCATTT
1 ATTACGGTTATTT
44773635 CACCCTAAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
26 3 0.03
27 99 0.94
28 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (27 bp):
ATTACGGTTATTTTACCTTACAGGGGT
Found at i:44773545 original size:54 final size:53
Alignment explanation
Indices: 44773481--44773634 Score: 211
Period size: 54 Copynumber: 2.9 Consensus size: 53
44773471 ATTTACACAC
* * * *
44773481 CAGGGCATTACAGTTATTTTACCTTACAGGGGTATTACTGTTATTTTAACC-TA
1 CAGGGCATTACGGTCATTTTACCATACAGGGGTATTACGGTTATTTT-ACCTTA
*
44773534 CAGGGACATTACGGTCATTTTACCCTACAGGGGTATTACGGTTATTTTACCTTA
1 CAGGG-CATTACGGTCATTTTACCATACAGGGGTATTACGGTTATTTTACCTTA
* *
44773588 CAGGGGCATTACGGTCATTTTACCATATAGGGGTATTACGGTCATTT
1 CA-GGGCATTACGGTCATTTTACCATACAGGGGTATTACGGTTATTT
44773635 CACCCTAAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
53 8 0.09
54 80 0.88
55 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (53 bp):
CAGGGCATTACGGTCATTTTACCATACAGGGGTATTACGGTTATTTTACCTTA
Found at i:44773608 original size:81 final size:81
Alignment explanation
Indices: 44773487--44773641 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 81
44773477 ACACCAGGGC
* * *
44773487 ATTACAGTTATTTTACCTTACAGGGGTATTACTGTTATTTTAACC-TACAGGGACATTACGGTCA
1 ATTACAGTTATTTTACCTTACAGGGGCATTACGGTCATTTT-ACCATACAGGGACATTACGGTCA
*
44773551 TTTTACCCTACAGGGGT
65 TTTCACCCTACAGGGGT
* * **
44773568 ATTACGGTTATTTTACCTTACAGGGGCATTACGGTCATTTTACCATATAGGGGTATTACGGTCAT
1 ATTACAGTTATTTTACCTTACAGGGGCATTACGGTCATTTTACCATACAGGGACATTACGGTCAT
44773633 TTCACCCTA
66 TTCACCCTA
44773642 AAACCACGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
80 3 0.05
81 62 0.95
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (81 bp):
ATTACAGTTATTTTACCTTACAGGGGCATTACGGTCATTTTACCATACAGGGACATTACGGTCAT
TTCACCCTACAGGGGT
Found at i:44774265 original size:32 final size:32
Alignment explanation
Indices: 44774158--44774267 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 32
44774148 TAATGTGATT
44774158 GGCACAAAGCCATCAGTAGCAGTGATATGACC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* * * * * * *
44774190 GGCACACAA-CTATTAGTAACGGTAACATGATC
1 GGCACA-AAGCCATCAGTAGCAGTGATATGACC
*
44774222 GGCATAAAGCCATCAGTAGCAGTGATATGACC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
*
44774254 GGCACACAGCCATC
1 GGCACAAAGCCATC
44774268 GATAACGATA
Statistics
Matches: 59, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
31 2 0.03
32 55 0.93
33 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (32 bp):
GGCACAAAGCCATCAGTAGCAGTGATATGACC
Found at i:44774315 original size:32 final size:31
Alignment explanation
Indices: 44774153--44774323 Score: 103
Period size: 32 Copynumber: 5.4 Consensus size: 31
44774143 TTCAGTAATG
*
44774153 TGATTGGCACAAAGCCATCAGTAGCAGTGATA
1 TGATTGGCACAAAGCCATCGGTAGCAGT-ATA
** * ** * * *
44774185 TGACCGGCACACAA-CTATTAGTAACGGTAACA
1 TGATTGGCACA-AAGCCATCGGTAGCAGT-ATA
* * *
44774217 TGATCGGCATAAAGCCATCAGTAGCAGTGATA
1 TGATTGGCACAAAGCCATCGGTAGCAGT-ATA
** * * *
44774249 TGACCGGCACACAGCCATCGATAAC-GATAATA
1 TGATTGGCACAAAGCCATCGGTAGCAG-T-ATA
*
44774281 TGATTAGCACAAAGCCATCGGTAGCAGTATTA
1 TGATTGGCACAAAGCCATCGGTAGCAGTA-TA
44774313 TGATTGGCACA
1 TGATTGGCACA
44774324 TCCCTCTACA
Statistics
Matches: 104, Mismatches: 30, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
31 4 0.04
32 97 0.93
33 3 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (31 bp):
TGATTGGCACAAAGCCATCGGTAGCAGTATA
Found at i:44774323 original size:64 final size:64
Alignment explanation
Indices: 44774148--44774308 Score: 216
Period size: 64 Copynumber: 2.5 Consensus size: 64
44774138 ATAAGTTCAG
* * * *
44774148 TAATGTGATTGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAACTATTAGTAACGG
1 TAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAACCATGAGTAACGA
* * * *
44774212 TAACATGATCGGCATAAAGCCATCAGTAGCAGTGATATGACCGGCACACAGCCATCGA-TAACGA
1 TAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAACCAT-GAGTAACGA
* *
44774276 TAATATGATTAGCACAAAGCCATCGGTAGCAGT
1 TAATATGATTGGCACAAAGCCATCAGTAGCAGT
44774309 ATTATGATTG
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 82 0.99
65 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (64 bp):
TAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAACCATGAGTAACGA
Found at i:44775058 original size:21 final size:21
Alignment explanation
Indices: 44775033--44775072 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
44775023 TTATTTGGAC
*
44775033 TTTTAACCAACACTTATAATG
1 TTTTAACCAACACATATAATG
44775054 TTTTAACCAACACATATAA
1 TTTTAACCAACACATATAA
44775073 CTTATCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (21 bp):
TTTTAACCAACACATATAATG
Found at i:44785451 original size:63 final size:63
Alignment explanation
Indices: 44785375--44785515 Score: 210
Period size: 63 Copynumber: 2.2 Consensus size: 63
44785365 CAAGTCCATA
* * * *
44785375 TGTCTCACTCGTGTGACTCTAACATGAACTCAGTGAGTTACACGGCTTGAACATATGCCTGTG
1 TGTCTCACTCGTGTGACTCTAACATGAACTCAGTGAGTTACACGGCCTGAACACACGCCCGTG
* ** *
44785438 TGTCTCACCCGTGTGACTCTAGTATGAACTCAGTGAGTTACACGGCCTGGACACACGCCCGTG
1 TGTCTCACTCGTGTGACTCTAACATGAACTCAGTGAGTTACACGGCCTGAACACACGCCCGTG
44785501 TGTCTCACTCGTGTG
1 TGTCTCACTCGTGTG
44785516 GACCCTACAT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (63 bp):
TGTCTCACTCGTGTGACTCTAACATGAACTCAGTGAGTTACACGGCCTGAACACACGCCCGTG
Found at i:44786156 original size:39 final size:39
Alignment explanation
Indices: 44786113--44786192 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
44786103 AATTGAGAAG
44786113 AAGAAAAATAAAAGAAAAACAAAGAAAAGGAGACAAGAC
1 AAGAAAAATAAAAGAAAAACAAAGAAAAGGAGACAAGAC
44786152 AAGAAAAATAAAAGAAAAACAAAGAAAAGGAGACAAGAC
1 AAGAAAAATAAAAGAAAAACAAAGAAAAGGAGACAAGAC
44786191 AA
1 AA
44786193 AGTTACTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.72, C:0.07, G:0.17, T:0.03
Consensus pattern (39 bp):
AAGAAAAATAAAAGAAAAACAAAGAAAAGGAGACAAGAC
Found at i:44796164 original size:30 final size:30
Alignment explanation
Indices: 44796128--44796188 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
44796118 GAAATTCTGT
44796128 ACTACCATTTATAACTCATCAGAATTTTGG
1 ACTACCATTTATAACTCATCAGAATTTTGG
44796158 ACTACCATTTATAACTCATCAGAATTTTGG
1 ACTACCATTTATAACTCATCAGAATTTTGG
44796188 A
1 A
44796189 AAACTCAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (30 bp):
ACTACCATTTATAACTCATCAGAATTTTGG
Found at i:44797841 original size:21 final size:21
Alignment explanation
Indices: 44797815--44797867 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
44797805 GTTGTTAAGA
44797815 AAGAAGTTGCTGCTGCAAG-AG
1 AAGAAGTTGCTGCTG-AAGAAG
* *
44797836 AGGAAGTTGTTGCTGAAGAAG
1 AAGAAGTTGCTGCTGAAGAAG
44797857 AAGAAGTTGCT
1 AAGAAGTTGCT
44797868 AAAAATGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.23
Consensus pattern (21 bp):
AAGAAGTTGCTGCTGAAGAAG
Found at i:44803307 original size:37 final size:36
Alignment explanation
Indices: 44803248--44803322 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
44803238 TCAATTTCAC
* *
44803248 AATTCTATTGTTCTTAAATATCACAGATTCAACTGAT
1 AATTCTATGGTTCTTAAATATCACAAATTCAA-TGAT
* * *
44803285 AATTTTATGGTTCTTCAGTATCACAAATTCAATGAT
1 AATTCTATGGTTCTTAAATATCACAAATTCAATGAT
44803321 AA
1 AA
44803323 GTAAGGAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (36 bp):
AATTCTATGGTTCTTAAATATCACAAATTCAATGAT
Found at i:44809178 original size:11 final size:11
Alignment explanation
Indices: 44809162--44809191 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
44809152 ATCCAACGTA
*
44809162 ATTTATATGAT
1 ATTTATATAAT
44809173 ATTTATATAAT
1 ATTTATATAAT
44809184 ATTTATAT
1 ATTTATAT
44809192 TAGAAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTATATAAT
Found at i:44817682 original size:11 final size:11
Alignment explanation
Indices: 44817666--44817690 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44817656 TGCAATTCAG
44817666 TTTTTTTGTTT
1 TTTTTTTGTTT
44817677 TTTTTTTGTTT
1 TTTTTTTGTTT
44817688 TTT
1 TTT
44817691 GATAATTTTT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:44818245 original size:2 final size:2
Alignment explanation
Indices: 44818238--44818262 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44818228 ATCTAGACCA
44818238 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
44818263 GCCTTCATTT
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:44819861 original size:2 final size:2
Alignment explanation
Indices: 44819854--44819897 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
44819844 TCAAATTAGG
44819854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44819896 AT
1 AT
44819898 CTTGTCTGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44828264 original size:16 final size:16
Alignment explanation
Indices: 44828245--44828275 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44828235 ATATTAATGT
*
44828245 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
44828261 TATTTAATATTAAAA
1 TATTTAATATTAAAA
44828276 TAATACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:44830118 original size:28 final size:27
Alignment explanation
Indices: 44830087--44830161 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
44830077 TTATTAATAT
*
44830087 AAATAATAAATAATTTAATCATATTTTA
1 AAATAATAAATAATTTAAT-ATAATTTA
* *
44830115 AAATAAT-AATTATTAAATATAATTTA
1 AAATAATAAATAATTTAATATAATTTA
* *
44830141 ATAAAAATATATAATTTAATA
1 A-AATAATAAATAATTTAATA
44830162 ATGTAATAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 8 0.21
27 14 0.37
28 16 0.42
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
AAATAATAAATAATTTAATATAATTTA
Found at i:44830139 original size:27 final size:28
Alignment explanation
Indices: 44830087--44830156 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
44830077 TTATTAATAT
*
44830087 AAATAATAAATAATTTAATCATATTTTA
1 AAATAATAAATAATTAAATCATATTTTA
* *
44830115 AAATAAT-AATTATTAAAT-ATAATTTA
1 AAATAATAAATAATTAAATCATATTTTA
* *
44830141 ATAAAAATATATAATT
1 A-AATAATAAATAATT
44830157 TAATAATGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 8 0.24
27 14 0.41
28 12 0.35
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
AAATAATAAATAATTAAATCATATTTTA
Found at i:44831232 original size:22 final size:21
Alignment explanation
Indices: 44831200--44831255 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
44831190 TTTTTTATTT
*
44831200 TTTATTATATTGTTAATACTG
1 TTTATTATATTATTAATACTG
*
44831221 TTTATTTATATTATTATTAC--
1 TTTA-TTATATTATTAATACTG
44831241 TTTATTATTATTATT
1 TTTATTA-TATTATT
44831256 TTATTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.10
20 11 0.35
21 4 0.13
22 13 0.42
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTATTATATTATTAATACTG
Found at i:44831237 original size:3 final size:3
Alignment explanation
Indices: 44831229--44831292 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
44831219 TGTTTATTTA
*
44831229 TAT TAT TAT TAC T-T TAT TAT TAT TAT T-T TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
44831274 TAT CTAT TAT AAT TAT TAT
1 TAT -TAT TAT TAT TAT TAT
44831293 GCTTATTTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:44831251 original size:17 final size:16
Alignment explanation
Indices: 44831222--44831290 Score: 81
Period size: 14 Copynumber: 4.3 Consensus size: 16
44831212 TTAATACTGT
44831222 TTATTTA-TATTATTA
1 TTATTTATTATTATTA
44831237 TTACTTTATTATTATTA
1 TTA-TTTATTATTATTA
44831254 -T-TTTATTATTATTA
1 TTATTTATTATTATTA
*
44831268 TTATATTATCTATTATAA
1 TTAT-TTAT-TATTATTA
44831286 TTATT
1 TTATT
44831291 ATGCTTATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 13 0.28
15 4 0.09
16 6 0.13
17 13 0.28
18 11 0.23
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTATTATTATTA
Found at i:44838890 original size:23 final size:23
Alignment explanation
Indices: 44838838--44838891 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
44838828 CTTTTTCGAG
* *
44838838 TAATTATTCTTTTATTCTTTTTC
1 TAATCATTCTTTTATTCTATTTC
44838861 TACATCATTCTTTTATTC-ATTTC
1 TA-ATCATTCTTTTATTCTATTTC
44838884 ATAATCAT
1 -TAATCAT
44838892 ATTTTGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATCATTCTTTTATTCTATTTC
Found at i:44843754 original size:89 final size:89
Alignment explanation
Indices: 44843623--44843958 Score: 271
Period size: 89 Copynumber: 3.8 Consensus size: 89
44843613 TCCCTGAGCA
** * * * *
44843623 GCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTTACAGTGAAGCAGATCGAAGA
1 GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
*
44843688 C-CTTAACCTTGCCTCCCCGAGTTT
66 CAC-CAACCTTGCCTCCCCGAGTTT
*
44843712 GCAGTAGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
1 GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
* ** *
44843777 CACCAGCCTTGCCTCCTTGGGTTT
66 CACCAACCTTGCCTCCCCGAGTTT
* ** * * * *** * **
44843801 ACAGTGGAACAGACTGTAGATAGCAGATCTTGTCTTCCTGTATTGGTAACGAAGTAGATCGAAGA
1 GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
* * * ** *
44843866 TACCAGCCTTGTCTCCCTAAG-TA
66 CACCAACCTTGCCTCCCCGAGTTT
* ** * * * * *** * *
44843889 GTAGTGGAGTAGGTTAAAAATAGCAGATTTTGCCTTCTTGTACTGGTAGTGAAGCAGATCGAAGA
1 GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
44843954 CACCA
66 CACCA
44843959 GTCTTATCGC
Statistics
Matches: 198, Mismatches: 48, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
88 54 0.27
89 143 0.72
90 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (89 bp):
GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
CACCAACCTTGCCTCCCCGAGTTT
Found at i:44845784 original size:22 final size:21
Alignment explanation
Indices: 44845733--44845784 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
44845723 TTTTTAGTTT
*
44845733 TTTATTATATTGTTAATACTG
1 TTTATTATATTATTAATACTG
* *
44845754 TTTATTTATATTATTATTGCTG
1 TTTA-TTATATTATTAATACTG
44845776 TATTATTAT
1 T-TTATTAT
44845785 TAGTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 19 0.73
23 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.62
Consensus pattern (21 bp):
TTTATTATATTATTAATACTG
Found at i:44845817 original size:21 final size:23
Alignment explanation
Indices: 44845791--44845834 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
44845781 TTATTAGTTT
44845791 ATTATTATA-TTATATAT-TATA
1 ATTATTATACTTATATATATATA
*
44845812 ATTATTATACTTATTTATATATA
1 ATTATTATACTTATATATATATA
44845835 CGTATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTATTATACTTATATATATATA
Found at i:44847830 original size:16 final size:16
Alignment explanation
Indices: 44847809--44847850 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
44847799 AATAATTTGA
*
44847809 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
44847825 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
44847841 TAATTTTAAT
1 TAATTTTAAT
44847851 TTTATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:44847834 original size:22 final size:22
Alignment explanation
Indices: 44847824--44847884 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
44847814 TTACTAACAA
* *
44847824 TTAATTTTAATAACAATTAATT
1 TTAATTTTAATAAAAAATAATT
*
44847846 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
44847868 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
44847885 CGGGCCGGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:44848643 original size:19 final size:19
Alignment explanation
Indices: 44848619--44848655 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44848609 ATAATAATAC
44848619 AAATAATAATATAATTAAT
1 AAATAATAATATAATTAAT
*
44848638 AAATAATAATATTATTAA
1 AAATAATAATATAATTAA
44848656 ATTAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATAATATAATTAAT
Found at i:44850979 original size:12 final size:13
Alignment explanation
Indices: 44850959--44850991 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
44850949 TAAATAATTC
*
44850959 TATTCATATTTTA
1 TATTTATATTTTA
44850972 T-TTTATATTTTA
1 TATTTATATTTTA
44850984 TATTTATA
1 TATTTATA
44850992 ATTAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTATATTTTA
Found at i:44851763 original size:16 final size:16
Alignment explanation
Indices: 44851738--44851773 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
44851728 ATATCTCAAT
44851738 TATATGTATATAAAAA
1 TATATGTATATAAAAA
*
44851754 TATATTTATATAAAAA
1 TATATGTATATAAAAA
44851770 TATA
1 TATA
44851774 AATGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TATATGTATATAAAAA
Found at i:44851862 original size:15 final size:14
Alignment explanation
Indices: 44851829--44851867 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
44851819 ATATTTTTTA
*
44851829 AAAAATAAAATGAT
1 AAAAATAAAATAAT
44851843 AAAAATAAATATAAT
1 AAAAATAAA-ATAAT
*
44851858 TAAAATAAAA
1 AAAAATAAAA
44851868 ATTTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:44852410 original size:26 final size:24
Alignment explanation
Indices: 44852381--44852432 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
44852371 AAAAAGTAAA
*
44852381 AATTAAAAAGTTTTCCATTTTTTTTT
1 AATTAAAAAG-TTT-AATTTTTTTTT
**
44852407 AATTTGAAAGTTTAATTTTTTTTT
1 AATTAAAAAGTTTAATTTTTTTTT
44852431 AA
1 AA
44852433 AAATCATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
25 3 0.13
26 8 0.35
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (24 bp):
AATTAAAAAGTTTAATTTTTTTTT
Found at i:44853343 original size:24 final size:24
Alignment explanation
Indices: 44853297--44853343 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
44853287 GGGACAGAGA
*
44853297 AAAAAGAAAAAGAAAACTAGATAG
1 AAAAAGAAAAAGAAAAATAGATAG
*
44853321 AAAAAGAAAGAGATAAAAT-GATA
1 AAAAAGAAAAAGA-AAAATAGATA
44853344 TTAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAAATAGATAG
Found at i:44855654 original size:3 final size:3
Alignment explanation
Indices: 44855646--44855703 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
44855636 TTTTACACTC
*
44855646 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
44855694 TAT TAG TAT T
1 TAT TAT TAT T
44855704 TTAACATGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:44855782 original size:17 final size:18
Alignment explanation
Indices: 44855750--44855852 Score: 85
Period size: 17 Copynumber: 5.9 Consensus size: 18
44855740 CATATCGTGT
44855750 TTATA-ATTTATATATTA
1 TTATATATTTATATATTA
* *
44855767 TTATTTATTTAT-TATTT
1 TTATATATTTATATATTA
*
44855784 TTATATATTTACA-ATT-
1 TTATATATTTATATATTA
*
44855800 TCTATATATATATATA-TA
1 T-TATATATTTATATATTA
*
44855818 -TATATATATATATA-TA
1 TTATATATTTATATATTA
44855834 TATATATATATTATATATT
1 T-TATATAT-TTATATATT
44855853 CTTTCCTCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
16 17 0.24
17 32 0.46
18 14 0.20
19 6 0.09
20 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATATTTATATATTA
Found at i:44855794 original size:8 final size:8
Alignment explanation
Indices: 44855749--44855852 Score: 75
Period size: 8 Copynumber: 14.2 Consensus size: 8
44855739 ACATATCGTG
44855749 TTTATA-A
1 TTTATATA
44855756 TTTATATA
1 TTTATATA
44855764 -TTAT-TA
1 TTTATATA
*
44855770 TTTATTTA
1 TTTATATA
44855778 -TTAT-T-
1 TTTATATA
44855783 TTTATATA
1 TTTATATA
*
44855791 TTTACA-A
1 TTTATATA
*
44855798 TTTCTATA
1 TTTATATA
44855806 --TATATA
1 TTTATATA
*
44855812 TATATATA
1 TTTATATA
*
44855820 TATATATA
1 TTTATATA
*
44855828 TATATATA
1 TTTATATA
*
44855836 TATATATA
1 TTTATATA
44855844 -TTATATA
1 TTTATATA
44855851 TT
1 TT
44855853 CTTTCCTCTA
Statistics
Matches: 82, Mismatches: 5, Indels: 19
0.77 0.05 0.18
Matches are distributed among these distances:
6 12 0.15
7 30 0.37
8 40 0.49
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:44855807 original size:2 final size:2
Alignment explanation
Indices: 44855802--44855851 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
44855792 TTACAATTTC
44855802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44855844 T- TA TA TA T
1 TA TA TA TA T
44855852 TCTTTCCTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44860654 original size:6 final size:6
Alignment explanation
Indices: 44860645--44860673 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
44860635 CAACAAAACA
44860645 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
44860674 GAAACAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:44861198 original size:14 final size:15
Alignment explanation
Indices: 44861179--44861224 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
44861169 TAAATGAATG
44861179 AAATGAAAAAT-GAA
1 AAATGAAAAATAGAA
*
44861193 AAATG-AAAATAAAA
1 AAATGAAAAATAGAA
* *
44861207 AAATAAAAAATGGAA
1 AAATGAAAAATAGAA
44861222 AAA
1 AAA
44861225 GTAAAATGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 5 0.19
14 11 0.42
15 10 0.38
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (15 bp):
AAATGAAAAATAGAA
Found at i:44862451 original size:27 final size:27
Alignment explanation
Indices: 44862421--44862499 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
44862411 GCATAATTAG
44862421 GTTCATAAAATGGATTATACAGGTCAT
1 GTTCATAAAATGGATTATACAGGTCAT
* * *
44862448 GTTCCT----TAGA-TA-ACAGATCA-
1 GTTCATAAAATGGATTATACAGGTCAT
44862468 GTTTCATAAAATGGATTATACAGGTCAT
1 G-TTCATAAAATGGATTATACAGGTCAT
44862496 GTTC
1 GTTC
44862500 CCTAGAGAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 1 0.03
21 11 0.29
22 2 0.05
23 3 0.08
25 3 0.08
26 2 0.05
27 15 0.39
28 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (27 bp):
GTTCATAAAATGGATTATACAGGTCAT
Found at i:44862478 original size:48 final size:48
Alignment explanation
Indices: 44862422--44862517 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
44862412 CATAATTAGG
* *
44862422 TTCATAAAATGGATTATACAGGTCATGTTCCTTAGATAACAGATCAGT
1 TTCATAAAATGGATTATACAGGTCATGTTCCCTAGAGAACAGATCAGT
44862470 TTCATAAAATGGATTATACAGGTCATGTTCCCTAGAGAACAGATCAGT
1 TTCATAAAATGGATTATACAGGTCATGTTCCCTAGAGAACAGATCAGT
44862518 GAAGATAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (48 bp):
TTCATAAAATGGATTATACAGGTCATGTTCCCTAGAGAACAGATCAGT
Found at i:44862668 original size:89 final size:88
Alignment explanation
Indices: 44862517--44863288 Score: 898
Period size: 89 Copynumber: 8.7 Consensus size: 88
44862507 AACAGATCAG
* *
44862517 TGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
44862582 CCCTGGTTTTGCAACGGAGCAGAC
66 CCCTGG-TTTGCAGCGGAGCAGAC
* * * *
44862606 TGAAGATAGCAGATTTTACCTTCCTGTACTGACAGCAAAGCAGATCGAAGACACTAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* ** *
44862671 CCTTGGGTTTGCATTGGAGTAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
* * * * * * * *
44862695 TGAAGATGGTAAATCTTGCCTTCCTATATTGATAGCGAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* *
44862760 ACCTAGGTTTGCAGCGGAACAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
*
44862784 TGAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
44862849 CCCTGGTTTTGTAGCGGAGCAGAC
66 CCCTGG-TTTGCAGCGGAGCAGAC
* *
44862873 TGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * * ** *
44862938 CCTTCAGTTTACAGTAGAGTAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
* * *
44862962 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAATATACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* *
44863027 CTCTGGGTTTGCAGTGGAGCAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
* * *
44863051 TGAAGATAGCAGATCTTGCCTTCCTATACTGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
44863116 CCCTAGGTTTGCAACGGAGCAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
** * * * * **
44863140 TGAAGATAGCAGATCTTGCCTTATTGTACTGACAACGAAGCAGATAGAAGACATCAGCCTTATCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* **** ** * **
44863205 CCTTGAACAGCAGTAGAGTAGGT
66 CCCTGGTTTGCAGCGGAGCAGAC
* * * * *
44863228 TGAAAATAGCAGATCTTGCCTTCCTGTACT-AGCAGAGAAGCAGATTGAGGATACCAGTCTT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACACCAGTCTT
44863289 ATCGCCTTAA
Statistics
Matches: 578, Mismatches: 101, Indels: 9
0.84 0.15 0.01
Matches are distributed among these distances:
87 1 0.00
88 60 0.10
89 514 0.89
90 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
CCCTGGTTTGCAGCGGAGCAGAC
Found at i:44863001 original size:267 final size:264
Alignment explanation
Indices: 44862517--44863272 Score: 1023
Period size: 267 Copynumber: 2.8 Consensus size: 264
44862507 AACAGATCAG
* *
44862517 TGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * *
44862582 CCCTGGTTTTGCAACGGAGCAGACTGAAGATAGCAGATTTTACCTTCCTGTACTGACAGCAAAGC
66 CCCTGGTTTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
* * * * * *
44862647 AGATCGAAGACACTAGTCTTGCCTCCTTGGGTTTGCATTGGAGTAGACTGAAGATGGTAAATCTT
131 AGATCGAAGACAC-AGTCTTGCCTCCTT--GTTTACAGTAGAGTAGACTGAAGATAGCAGATCTT
* * *
44862712 GCCTTCCTATATTGATAGCGAAGCAGATCAAAGACACCAGCCTTGCCTAC-CTAGGTTTGCAGCG
193 GCCTTCCTGTACTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCT-CTCTAGGTTTGCAGCG
44862776 GAACAGAC
257 GAACAGAC
*
44862784 TGAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * *
44862849 CCCTGGTTTTGTAGCGGAGCAGACTGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGC
66 CCCTGGTTTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
44862914 AGATCGAAGACACAAGTCTTGCCTCCTTCAGTTTACAGTAGAGTAGACTGAAGATAGCAGATCTT
131 AGATCGAAGACAC-AGTCTTGCCTCCTT--GTTTACAGTAGAGTAGACTGAAGATAGCAGATCTT
* * * * *
44862979 GCCTTCCTGTACTGACAGCGAAGCAGATCGAATATACCAGCCTTGCCTCTCTGGGTTTGCAGTGG
193 GCCTTCCTGTACTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCTCTAGGTTTGCAGCGG
*
44863044 AGCAGAC
258 AACAGAC
* * *
44863051 TGAAGATAGCAGATCTTGCCTTCCTATACTGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
** *
44863116 CCCTAGG-TTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTATTGTACTGACAACGAAG
66 CCCT-GGTTTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAG
* * ** *** ** *
44863180 CAGATAGAAGACATCAGCCTTATCTCCTTGAACAGCAGTAGAGTAGGTTGAAAATAGCAGATCTT
130 CAGATCGAAGACA-CAGTCTTGCCTCCTTGTTTA-CAGTAGAGTAGACTGAAGATAGCAGATCTT
*
44863245 GCCTTCCTGTACT-AGCAGAGAAGCAGAT
193 GCCTTCCTGTACTGA-CAGCGAAGCAGAT
44863273 TGAGGATACC
Statistics
Matches: 436, Mismatches: 48, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
265 3 0.01
266 53 0.12
267 377 0.86
268 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (264 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
CCCTGGTTTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
AGATCGAAGACACAGTCTTGCCTCCTTGTTTACAGTAGAGTAGACTGAAGATAGCAGATCTTGCC
TTCCTGTACTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCTCTAGGTTTGCAGCGGAAC
AGAC
Found at i:44863582 original size:50 final size:51
Alignment explanation
Indices: 44863528--44863690 Score: 161
Period size: 50 Copynumber: 3.3 Consensus size: 51
44863518 ATTACAGTTA
44863528 AACAGATTGAAGCCACAACGA-CGAATCTTACTTCCCTGGCAGTGTAGTGG
1 AACAGATTGAAGCCACAACGAGCGAATCTTACTTCCCTGGCAGTGTAGTGG
* * * * ** ** * * **
44863578 AACAGATTGAAGCTAC-GCCAGTGAATCTTGTTTCCCCAGCATTGTAATTT
1 AACAGATTGAAGCCACAACGAGCGAATCTTACTTCCCTGGCAGTGTAGTGG
* * *
44863628 AATAGATTGAAGCCATAAC-AGCGAATCTTACTTCCCTGGCGGTGTAGTGG
1 AACAGATTGAAGCCACAACGAGCGAATCTTACTTCCCTGGCAGTGTAGTGG
*
44863678 AACAGATTAAAGC
1 AACAGATTGAAGC
44863691 TACGACGACA
Statistics
Matches: 83, Mismatches: 28, Indels: 4
0.72 0.24 0.03
Matches are distributed among these distances:
49 2 0.02
50 80 0.96
51 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (51 bp):
AACAGATTGAAGCCACAACGAGCGAATCTTACTTCCCTGGCAGTGTAGTGG
Found at i:44863635 original size:100 final size:100
Alignment explanation
Indices: 44863473--44863735 Score: 316
Period size: 100 Copynumber: 2.6 Consensus size: 100
44863463 TTGGCATTAC
* * *
44863473 AGTGGAATAGATTGAAGCTACGACGGAAAATCTTATTTCCCCGACATTACAGTTAAACAGATTGA
1 AGTGGAACAGATTGAAGCTACGACAGAAAATCTTATTTCCCCGACATTACAATTAAACAGATTGA
44863538 AGCCACAAC-GACGAATCTTACTTCCCTGGCAGTGT
66 AGCCACAACAG-CGAATCTTACTTCCCTGGCAGTGT
* ** * ** * *
44863573 AGTGGAACAGATTGAAGCTACGCCAGTGAATCTTGTTTCCCC-AGCATTGTAATTTAATAGATTG
1 AGTGGAACAGATTGAAGCTACGACAGAAAATCTTATTTCCCCGA-CATTACAATTAAACAGATTG
* *
44863637 AAGCCATAACAGCGAATCTTACTTCCCTGGCGGTGT
65 AAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGT
* * * * *
44863673 AGTGGAACAGATTAAAGCTACGAC-GACAAATCTTGTTTCCCCGACATTGCAGTTAAATAGATT
1 AGTGGAACAGATTGAAGCTACGACAGA-AAATCTTATTTCCCCGACATTACAATTAAACAGATT
44863736 TAAGATGACA
Statistics
Matches: 139, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
99 2 0.01
100 135 0.97
101 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (100 bp):
AGTGGAACAGATTGAAGCTACGACAGAAAATCTTATTTCCCCGACATTACAATTAAACAGATTGA
AGCCACAACAGCGAATCTTACTTCCCTGGCAGTGT
Found at i:44863801 original size:44 final size:44
Alignment explanation
Indices: 44863748--44864122 Score: 200
Period size: 44 Copynumber: 8.6 Consensus size: 44
44863738 AGATGACAAG
44863748 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
* * * ** * * *
44863792 TCCTATCTCCCTGAAGTTACAGTCGAGTGGATTAAAGTTGC-A-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAG--CCAATAA
** **
44863836 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AAGATAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAAGCCAATAA
* * * * * ****
44863880 GTCTTATCCCCCTAAAGTTACAGTGGGGTAGACTG-AAGATGGTGAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAAGCCAAT-AA
* * * * *
44863926 TTTTATCTCCCTAAAGTTACAGTGGAGTAGATTAAAGCCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
* * * ** *
44863970 TCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATC-A-GA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
* * * * *
44864012 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG-CATCC---AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAAGCCAATAA
* *
44864053 TCTTA-CTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAG-AAACTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGA-AAGCCAA-TAA
* * *
44864096 TCCTATTTCCCTGAAGTTACAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
44864123 TGGATCGAAG
Statistics
Matches: 255, Mismatches: 60, Indels: 32
0.73 0.17 0.09
Matches are distributed among these distances:
40 24 0.09
41 5 0.02
42 31 0.12
43 6 0.02
44 117 0.46
45 69 0.27
46 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
Found at i:44864636 original size:10 final size:10
Alignment explanation
Indices: 44864616--44864646 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
44864606 AAGATATAAG
44864616 ATTATTTATTT
1 ATTA-TTATTT
44864627 ATTATTATTT
1 ATTATTATTT
44864637 ATTATTATTT
1 ATTATTATTT
44864647 TTTGGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTATTATTT
Found at i:44865444 original size:3 final size:3
Alignment explanation
Indices: 44865436--44865499 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
44865426 TTTTACACTC
44865436 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
44865484 TAT AAT TAT TAG TAT T
1 TAT TAT TAT TAT TAT T
44865500 TTAACCATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:44865624 original size:2 final size:2
Alignment explanation
Indices: 44865617--44865652 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
44865607 AACATACCTC
44865617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44865653 TCTTTCCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:44868725 original size:42 final size:42
Alignment explanation
Indices: 44868665--44868754 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
44868655 TGTCTCAGCC
** *
44868665 CGTGTCCTTGCCCATGTAACTCA-CTGACTTGAGACACACGGT
1 CGTGTCCCAGCCCATGTAACT-ATCTAACTTGAGACACACGGT
* * **
44868707 CGTGTCCCAGCCCGTGTAACTATCTAACTTGGGTTACACGGT
1 CGTGTCCCAGCCCATGTAACTATCTAACTTGAGACACACGGT
44868749 CGTGTC
1 CGTGTC
44868755 ACAAACCGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (42 bp):
CGTGTCCCAGCCCATGTAACTATCTAACTTGAGACACACGGT
Found at i:44869396 original size:21 final size:21
Alignment explanation
Indices: 44869367--44869408 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
44869357 ACTATAATTT
44869367 AAAATGTAC-CTGAGTATAAC
1 AAAATGTACGCTGAGTATAAC
44869387 AAAATTGTACGCTGAGTATAAC
1 AAAA-TGTACGCTGAGTATAAC
44869409 TCAGAGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 11 0.55
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (21 bp):
AAAATGTACGCTGAGTATAAC
Found at i:44872569 original size:17 final size:17
Alignment explanation
Indices: 44872521--44872584 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 17
44872511 GTTCAAGTAC
44872521 ATTTTGTTTTCTTCATGTTT
1 ATTTTGTTTT-TT-A-GTTT
*
44872541 ATTTTTTATTTTTAGTTT
1 ATTTTGT-TTTTTAGTTT
44872559 ATTTTGTTTTTT-GTTTT
1 ATTTTGTTTTTTAG-TTT
*
44872576 GTTTTGTTT
1 ATTTTGTTT
44872585 GCTTGAGGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 16 0.41
18 10 0.26
19 1 0.03
20 8 0.21
21 3 0.08
ACGTcount: A:0.09, C:0.03, G:0.11, T:0.77
Consensus pattern (17 bp):
ATTTTGTTTTTTAGTTT
Found at i:44872570 original size:18 final size:19
Alignment explanation
Indices: 44872521--44872570 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
44872511 GTTCAAGTAC
44872521 ATTTTGTTTTCTTCATGTTT
1 ATTTTGTTTT-TTCATGTTT
*
44872541 ATTTT-TTATTTTTA-GTTT
1 ATTTTGTT-TTTTCATGTTT
44872559 ATTTTGTTTTTT
1 ATTTTGTTTTTT
44872571 GTTTTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 13 0.48
19 7 0.26
20 7 0.26
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.76
Consensus pattern (19 bp):
ATTTTGTTTTTTCATGTTT
Found at i:44874900 original size:20 final size:21
Alignment explanation
Indices: 44874868--44874906 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
44874858 TTTTAAAATT
44874868 TAAAATTATTAAA-AAAATCA
1 TAAAATTATTAAACAAAATCA
44874888 TAAATATTA-TAAACAAAAT
1 TAAA-ATTATTAAACAAAAT
44874907 TTATAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATTATTAAACAAAATCA
Found at i:44881128 original size:11 final size:11
Alignment explanation
Indices: 44881112--44881142 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
44881102 TTTTAATAAG
44881112 GTATCGATATA
1 GTATCGATATA
44881123 GTATCGATATA
1 GTATCGATATA
44881134 GTATCGATA
1 GTATCGATA
44881143 CCTAACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (11 bp):
GTATCGATATA
Found at i:44884981 original size:3 final size:3
Alignment explanation
Indices: 44884973--44885042 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
44884963 TGCTCTACAT
44884973 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
44885021 TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
44885043 CATCTCAATA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:44886603 original size:2 final size:2
Alignment explanation
Indices: 44886598--44886642 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
44886588 AAAAAAATAA
44886598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44886640 AT A
1 AT A
44886643 AAGTTGTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44890059 original size:19 final size:19
Alignment explanation
Indices: 44890035--44890071 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44890025 ATAATAATAC
44890035 AAATAATAATATAATTAAT
1 AAATAATAATATAATTAAT
*
44890054 AAATAATAATATTATTAA
1 AAATAATAATATAATTAA
44890072 ATTAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATAATATAATTAAT
Found at i:44891493 original size:21 final size:21
Alignment explanation
Indices: 44891459--44891498 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44891449 GGACTGAATC
* *
44891459 GAAAACATATAAAAGTTTTGA
1 GAAAACATAGAAAAATTTTGA
*
44891480 GAAAACTTAGAAAAATTTT
1 GAAAACATAGAAAAATTTT
44891499 CCAATAAGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (21 bp):
GAAAACATAGAAAAATTTTGA
Found at i:44892590 original size:26 final size:24
Alignment explanation
Indices: 44892557--44892625 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
44892547 AGCCATGATC
*
44892557 GGTAAGCTCATTTCGAGCTGAAGAAA
1 GGTAAGCTCATATCGAGCTG-A-AAA
*
44892583 GGTAAGCTC-TATCGAGCTGAAAT
1 GGTAAGCTCATATCGAGCTGAAAA
*
44892606 GGTAAGCTCATA-AGAGCTGA
1 GGTAAGCTCATATCGAGCTGA
44892626 TATTCGGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.46
24 3 0.08
25 9 0.23
26 9 0.23
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (24 bp):
GGTAAGCTCATATCGAGCTGAAAA
Found at i:44892622 original size:23 final size:24
Alignment explanation
Indices: 44892557--44892642 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
44892547 AGCCATGATC
* * *
44892557 GGTAAGCTCATTTCGAGCTGAAGAAA
1 GGTAAGCTCATATAGAGCTG-A-AAT
*
44892583 GGTAAGCTC-TATCGAGCTGAAAT
1 GGTAAGCTCATATAGAGCTGAAAT
*
44892606 GGTAAGCTCATA-AGAGCTGATATT
1 GGTAAGCTCATATAGAGCTGA-AAT
44892630 CGGTAAGCTCATA
1 -GGTAAGCTCATA
44892643 CGAGTTGTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.34
24 5 0.09
25 21 0.40
26 9 0.17
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (24 bp):
GGTAAGCTCATATAGAGCTGAAAT
Found at i:44896274 original size:34 final size:34
Alignment explanation
Indices: 44896218--44896309 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
44896208 TGATCTGATT
* * * *
44896218 TAATATGACATTTTAATCTGATATATGTTTTTGG
1 TAATATGACATTCTGATATGATATATGATTTTGG
* *
44896252 -AATTATGATATTCTGATGTGATATATGATTTTGG
1 TAA-TATGACATTCTGATATGATATATGATTTTGG
44896286 TAATATGACATTCTGATATGATAT
1 TAATATGACATTCTGATATGATAT
44896310 TTGTATAAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
33 2 0.04
34 45 0.92
35 2 0.04
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (34 bp):
TAATATGACATTCTGATATGATATATGATTTTGG
Found at i:44897256 original size:18 final size:17
Alignment explanation
Indices: 44897233--44897266 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
44897223 ATGTTTCTAG
*
44897233 AATAAATATTATTTATTT
1 AATAAAT-TTAATTATTT
44897251 AATAAATTTAATTATT
1 AATAAATTTAATTATT
44897267 ACAATTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATAAATTTAATTATTT
Found at i:44901766 original size:39 final size:38
Alignment explanation
Indices: 44901704--44901834 Score: 163
Period size: 39 Copynumber: 3.4 Consensus size: 38
44901694 GACACAAAGT
* * *
44901704 TGCGATCAGGGGTACTGAAGTACAACAGGGGCATGTAAG
1 TGCGATCAGGGGTAC-CAAGTACAATAGGGGCACGTAAG
*
44901743 TGCGATCAGTGGTACCAACGTACAATAGGGGCACGTAAG
1 TGCGATCAGGGGTACCAA-GTACAATAGGGGCACGTAAG
* **
44901782 TGCAATTTGGGGTACCGAAGTACAATAGGGGCACGTAAG
1 TGCGATCAGGGGTACC-AAGTACAATAGGGGCACGTAAG
*
44901821 TGCTATCAGGGGTA
1 TGCGATCAGGGGTA
44901835 TGATTATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.03
39 75 0.95
40 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.34, T:0.20
Consensus pattern (38 bp):
TGCGATCAGGGGTACCAAGTACAATAGGGGCACGTAAG
Found at i:44901821 original size:19 final size:19
Alignment explanation
Indices: 44901762--44901821 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
44901752 TGGTACCAAC
44901762 GTACAATAGGGGCACGTAA
1 GTACAATAGGGGCACGTAA
* * *
44901781 GTGCAATTTGGGGTACCG-AA
1 GTACAA-TAGGGGCA-CGTAA
44901801 GTACAATAGGGGCACGTAA
1 GTACAATAGGGGCACGTAA
44901820 GT
1 GT
44901822 GCTATCAGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 2 0.06
19 15 0.47
20 13 0.41
21 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.33, T:0.20
Consensus pattern (19 bp):
GTACAATAGGGGCACGTAA
Found at i:44903426 original size:10 final size:10
Alignment explanation
Indices: 44903411--44903439 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
44903401 GGTTGGCGGA
44903411 GGAGTTCCAT
1 GGAGTTCCAT
44903421 GGAGTTCCAT
1 GGAGTTCCAT
44903431 GGAGTTCCA
1 GGAGTTCCA
44903440 ATGACATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (10 bp):
GGAGTTCCAT
Found at i:44903913 original size:26 final size:26
Alignment explanation
Indices: 44903884--44903961 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 26
44903874 CTTAATTTTT
44903884 TAAATTATCTATGCATTTTTAGGAAA
1 TAAATTATCTATGCATTTTTAGGAAA
** *
44903910 TAAATTAGGTAT-TATTTTT------
1 TAAATTATCTATGCATTTTTAGGAAA
44903929 TAAATTATCTATGCATTTTTAGGAAA
1 TAAATTATCTATGCATTTTTAGGAAA
44903955 TAAATTA
1 TAAATTA
44903962 GGTATTGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 10 0.26
20 6 0.15
25 6 0.15
26 17 0.44
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (26 bp):
TAAATTATCTATGCATTTTTAGGAAA
Found at i:44903942 original size:45 final size:45
Alignment explanation
Indices: 44903878--44903967 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
44903868 TCATGCCTTA
44903878 ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
1 ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
44903923 ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
1 ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
44903968 GGTTTGTTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (45 bp):
ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
Found at i:44905609 original size:18 final size:17
Alignment explanation
Indices: 44905571--44905617 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
44905561 ATATTTGGAT
44905571 TATAAAATATGAAAAAC
1 TATAAAATATGAAAAAC
*
44905588 TATATAAATATTATAAAA-
1 TATA-AAATATGA-AAAAC
44905606 TATAAATATATG
1 TATAAA-ATATG
44905618 TACGTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 15 0.60
19 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
TATAAAATATGAAAAAC
Found at i:44905763 original size:3 final size:3
Alignment explanation
Indices: 44905755--44905803 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
44905745 TATGTATTGA
*
44905755 AAT AAT AAT AAT AAC AAT AAT AAT AATT AAT -AT AAT AA- AATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA-T AAT
44905800 AAT A
1 AAT A
44905804 TAAAAGGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 5 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44907217 original size:44 final size:42
Alignment explanation
Indices: 44907168--44907573 Score: 292
Period size: 44 Copynumber: 9.5 Consensus size: 42
44907158 ATCTGCTCTT
* *
44907168 CTGCAACTTCAGGGAGATAGGATTATTTTCTTCAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTA-TTTCTT-AATCCGCTCCA
* *
44907212 CTGCAACTTTAGAGAGATAAGATCTGA-TT-TTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGAT-T-ATTTCTTAATCCGCTCCA
* * *
44907254 TTGCAACTTCAGGGAGATAGGAGTATTTTCTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTA-TTTC-TTAATCCGCTCCA
* * * * *
44907298 TTGCAACTTCAGGGAGATAGGAGTATTTTCTTCAATCTGTTCCA
1 CTGCAACTTCAGGGAGATAAGATTA-TTTCTT-AATCCGCTCCA
** * * **
44907342 CTGCAACTTCAGGGAGATAAGA--ATGGACATGATCCGCTCTT
1 CTGCAACTTCAGGGAGATAAGATTAT-TTCTTAATCCGCTCCA
* *
44907383 CTGCAACTTCAGAGAGATAAGATCTGA-TT-TTAATCCGCTCAA
1 CTGCAACTTCAGGGAGATAAGAT-T-ATTTCTTAATCCGCTCCA
* * * * * **
44907425 CTGCAACTTCAGGGAGATAAGACTAGATGC--GATCTGCTCTT
1 CTGCAACTTCAGGGAGATAAGATTA-TTTCTTAATCCGCTCCA
* * *
44907466 CTGTAACTTCAGAGAGATAAGATCTGA-TT-TTAATCCACTCCA
1 CTGCAACTTCAGGGAGATAAGAT-T-ATTTCTTAATCCGCTCCA
* * *
44907508 CTGCAACTTCAGGGAGATAGGATTATTTTCTACAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTA-TTTCT-TAATCCGCTCCA
*
44907552 TTGCAACTTCAGGGAGATAAGA
1 CTGCAACTTCAGGGAGATAAGA
44907574 CTGAAGTTTC
Statistics
Matches: 287, Mismatches: 52, Indels: 46
0.75 0.14 0.12
Matches are distributed among these distances:
40 3 0.01
41 59 0.21
42 93 0.32
43 6 0.02
44 123 0.43
45 2 0.01
46 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (42 bp):
CTGCAACTTCAGGGAGATAAGATTATTTCTTAATCCGCTCCA
Found at i:44907220 original size:85 final size:86
Alignment explanation
Indices: 44907117--44907577 Score: 285
Period size: 86 Copynumber: 5.4 Consensus size: 86
44907107 TATCATTTTG
* ** * * *
44907117 ATCTGCTTCACTATAACTTTAGGGAGATAAGA-CTGGA-CGCGATCTGCT-CTTCTGCAACTTCA
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGATCT-GATCGCAATCCGCTCCAT-TGCAACTTCA
*
44907179 GGGAGATAGGATTATTTTCTTCA
64 GGGAGATAGGAGTATTTTCTTCA
* ***
44907202 ATCTGCTCCACTGCAACTTTAGAGAGATAAGATCTGATTTTAATCCGCTCCATTGCAACTTCAGG
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGATCGCAATCCGCTCCATTGCAACTTCAGG
*
44907267 GAGATAGGAGTATTTTCTTTA
66 GAGATAGGAGTATTTTCTTCA
* * * * * ** * * * *
44907288 ATCCGCTCCATTGCAACTTCAGGGAGATAGGAGTATTTTCTTCAATCTGTTCCACTGCAACTTCA
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGA-TCTGATC-GCAATCCGCTCCATTGCAACTTCA
* *** * *
44907353 GGGAGATA--AGAATGGACAT-G
64 GGGAGATAGGAGTATTTTCTTCA
* ** * * *** * *
44907373 ATCCGCTCTTCTGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCAACTGCAACTTCAGG
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGATCGCAATCCGCTCCATTGCAACTTCAGG
* *** * *
44907438 GAGATA--AG-ACTAGATGCG
66 GAGATAGGAGTATTTTCTTCA
** * * * *** * *
44907456 ATCTGCTCTTCTGTAACTTCAGAGAGATAAGATCTGATTTTAATCCACTCCACTGCAACTTCAGG
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGATCGCAATCCGCTCCATTGCAACTTCAGG
* *
44907521 GAGATAGGATTATTTTCTACA
66 GAGATAGGAGTATTTTCTTCA
* *
44907542 ATCTGCTCCATTGCAACTTCAGGGAGATAAGA-CTGA
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGA
44907578 AGTTTCACCG
Statistics
Matches: 300, Mismatches: 67, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
82 1 0.00
83 98 0.33
84 3 0.01
85 62 0.21
86 103 0.34
87 5 0.02
88 28 0.09
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (86 bp):
ATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGATCGCAATCCGCTCCATTGCAACTTCAGG
GAGATAGGAGTATTTTCTTCA
Found at i:44907400 original size:41 final size:41
Alignment explanation
Indices: 44907342--44907487 Score: 141
Period size: 41 Copynumber: 3.5 Consensus size: 41
44907332 ATCTGTTCCA
* * *
44907342 CTGCAACTTCAGGGAGATAAGAATGGACATGATCCGCTCTT
1 CTGCAACTTCAGAGAGATAAGAATAGATATGATCCGCTCTT
* * * **
44907383 CTGCAACTTCAGAGAGATAAG-ATCTGATTTTAATCCGCTCAA
1 CTGCAACTTCAGAGAGATAAGAAT-AGA-TATGATCCGCTCTT
* * ** *
44907425 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTT
1 CTGCAACTTCAGAGAGATAAGAATAGATATGATCCGCTCTT
*
44907466 CTGTAACTTCAGAGAGATAAGA
1 CTGCAACTTCAGAGAGATAAGA
44907488 TCTGATTTTA
Statistics
Matches: 84, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
40 2 0.02
41 50 0.60
42 31 0.37
43 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (41 bp):
CTGCAACTTCAGAGAGATAAGAATAGATATGATCCGCTCTT
Found at i:44907441 original size:83 final size:83
Alignment explanation
Indices: 44907212--44907526 Score: 337
Period size: 83 Copynumber: 3.7 Consensus size: 83
44907202 ATCTGCTCCA
* *
44907212 CTGCAACTTTAGAGAGATAAGATCTGATTTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGAG
1 CTGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATA--AG
* *** * * *
44907277 TATTTTCTTTAATCCGCTCCAT
64 AATAGAC-ATGATCCGCT-CTT
* * * * * *
44907299 -TGCAACTTCAGGGAGATAGGAGTAT-TTTCTTCAATCTGTTCCACTGCAACTTCAGGGAGATAA
1 CTGCAACTTCAGAGAGATAAGA-TCTGATT-TT-AATCCGCTCCACTGCAACTTCAGGGAGATAA
*
44907362 GAATGGACATGATCCGCTCTT
63 GAATAGACATGATCCGCTCTT
* *
44907383 CTGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCAACTGCAACTTCAGGGAGATAAGAC
1 CTGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGAA
*** *
44907448 TAGATGCGATCTGCTCTT
66 TAGACATGATCCGCTCTT
* *
44907466 CTGTAACTTCAGAGAGATAAGATCTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATA
1 CTGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
44907527 GGATTATTTT
Statistics
Matches: 192, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
83 101 0.53
84 6 0.03
85 29 0.15
86 25 0.13
87 4 0.02
88 27 0.14
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (83 bp):
CTGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGAA
TAGACATGATCCGCTCTT
Found at i:44919852 original size:18 final size:17
Alignment explanation
Indices: 44919814--44919860 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
44919804 ATATTTGGAT
44919814 TATAAAATATGAAAAAC
1 TATAAAATATGAAAAAC
*
44919831 TATATAAATATTATAAAA-
1 TATA-AAATATGA-AAAAC
44919849 TATAAATATATG
1 TATAAA-ATATG
44919861 TACGTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 15 0.60
19 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
TATAAAATATGAAAAAC
Found at i:44920021 original size:15 final size:15
Alignment explanation
Indices: 44920001--44920039 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
44919991 ATATGTATTG
44920001 AAATAATAATAATAA
1 AAATAATAATAATAA
* *
44920016 AAATAATAGTAATTA
1 AAATAATAATAATAA
*
44920031 ATATAATAA
1 AAATAATAA
44920040 AATTAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATAATAATAATAA
Found at i:44920022 original size:12 final size:12
Alignment explanation
Indices: 44920005--44920055 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
44919995 GTATTGAAAT
44920005 AATAATAATAAA
1 AATAATAATAAA
* *
44920017 AATAATAGTAATT
1 AATAATAATAA-A
44920030 AAT-ATAATAAA
1 AATAATAATAAA
*
44920041 ATTAATAATATAA
1 AATAATAATA-AA
44920054 AA
1 AA
44920056 GGAACTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
11 2 0.07
12 22 0.73
13 6 0.20
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:44925155 original size:2 final size:2
Alignment explanation
Indices: 44925148--44925185 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
44925138 AAAACCATTC
* *
44925148 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44925186 CAAAAGTACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44935827 original size:46 final size:46
Alignment explanation
Indices: 44935760--44935852 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
44935750 ATAGTCTAAA
44935760 TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
1 TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
44935806 TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
1 TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
44935852 T
1 T
44935853 CGTTGCATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (46 bp):
TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
Found at i:44937518 original size:3 final size:3
Alignment explanation
Indices: 44937510--44937544 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
44937500 ACCTAAGGCA
44937510 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
44937545 ATGGCATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:44939562 original size:3 final size:3
Alignment explanation
Indices: 44939554--44939656 Score: 197
Period size: 3 Copynumber: 34.3 Consensus size: 3
44939544 AGCTTAGATG
44939554 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
44939602 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44939650 ATA ATA A
1 ATA ATA A
44939657 ACACTTCTTA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:44940713 original size:23 final size:23
Alignment explanation
Indices: 44940678--44940732 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
44940668 ATAATTTTTT
*
44940678 TATAAATA-AAAATATAAAAATAA
1 TATAAATATTAAAT-TAAAAATAA
* *
44940701 T-TAGATATTAAATTAAAATTAA
1 TATAAATATTAAATTAAAAATAA
44940723 TATAAATATT
1 TATAAATATT
44940733 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TATAAATATTAAATTAAAAATAA
Found at i:44940771 original size:109 final size:107
Alignment explanation
Indices: 44940646--44940854 Score: 332
Period size: 109 Copynumber: 1.9 Consensus size: 107
44940636 GTAAACATTA
44940646 AAAAATGTTAAAATGACTAAATATAATTTTTTTATAAATA-AAAATATA-AAAATAATTAGATAT
1 AAAAATGTTAAAATGACT-AA-ATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGATAT
44940709 TAAATTAAAATTAATATAAATATTTTAAAAAATAATATGTATAACT
64 TAAATTAAAATTAATAT--ATATTTTAAAAAATAATATGTATAACT
* * *
44940755 AAAAATTTTAAGATGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAGTTAGATATTA
1 AAAAATGTTAAAATGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGATATTA
*
44940820 AATTAAAATTAATATATATTTTTAAAAATAATATG
66 AATTAAAATTAATATATATTTTAAAAAATAATATG
44940855 GGTAGACTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
107 37 0.39
108 10 0.11
109 47 0.50
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (107 bp):
AAAAATGTTAAAATGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGATATTA
AATTAAAATTAATATATATTTTAAAAAATAATATGTATAACT
Found at i:44941548 original size:30 final size:30
Alignment explanation
Indices: 44941507--44941563 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
44941497 TTATAACTTG
*
44941507 TTGTTAATATTTTAATATATAAAATATAAA
1 TTGTAAATATTTTAATATATAAAATATAAA
44941537 TTGTAAATATTTTAATATATAAAATAT
1 TTGTAAATATTTTAATATATAAAATAT
44941564 TTTAAGCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (30 bp):
TTGTAAATATTTTAATATATAAAATATAAA
Found at i:44941563 original size:17 final size:17
Alignment explanation
Indices: 44941512--44941568 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
44941502 ACTTGTTGTT
44941512 AATATTTTAATATATAA
1 AATATTTTAATATATAA
* *
44941529 AATA--TAAAT-TGT-A
1 AATATTTTAATATATAA
44941542 AATATTTTAATATATAA
1 AATATTTTAATATATAA
44941559 AATATTTTAA
1 AATATTTTAA
44941569 GCAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.16
14 2 0.06
15 8 0.25
16 2 0.06
17 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATATTTTAATATATAA
Found at i:44941844 original size:12 final size:12
Alignment explanation
Indices: 44941819--44941852 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
44941809 TTTTCAGCTC
44941819 CTTTTCAGAAGTG
1 CTTTTCA-AAGTG
44941832 CTTTTCAAAGTG
1 CTTTTCAAAGTG
44941844 CTTTTCAAA
1 CTTTTCAAA
44941853 AGTACTTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (12 bp):
CTTTTCAAAGTG
Found at i:44941866 original size:25 final size:25
Alignment explanation
Indices: 44941819--44941866 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
44941809 TTTTCAGCTC
* * *
44941819 CTTTTCAGAAGTGCTTTTCAAAGTG
1 CTTTTCAAAAGTACTTCTCAAAGTG
*
44941844 CTTTTCAAAAGTACTTCTGAAAG
1 CTTTTCAAAAGTACTTCTCAAAG
44941867 CTAAAAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (25 bp):
CTTTTCAAAAGTACTTCTCAAAGTG
Found at i:44941905 original size:14 final size:14
Alignment explanation
Indices: 44941886--44941925 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
44941876 TCAGCCAAAA
44941886 GCAGCTTGTTCTTC
1 GCAGCTTGTTCTTC
44941900 GCAGCTTGTTCTTC
1 GCAGCTTGTTCTTC
*
44941914 ACAGCTT-TTCTT
1 GCAGCTTGTTCTT
44941926 TCAAAAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.10, C:0.28, G:0.17, T:0.45
Consensus pattern (14 bp):
GCAGCTTGTTCTTC
Found at i:44945958 original size:14 final size:13
Alignment explanation
Indices: 44945923--44945986 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
44945913 CATTTTTCCT
*
44945923 TCCTAAATTCTCAA
1 TCCTCAATT-TCAA
44945937 CTCC-CAATCTTCAA
1 -TCCTCAAT-TTCAA
44945951 TCCTCAATTTCCAA
1 TCCTCAATTT-CAA
*
44945965 T-TTCCAATTTCAA
1 TCCT-CAATTTCAA
44945978 TCCTCAATT
1 TCCTCAATT
44945987 ATTTTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
13 15 0.37
14 22 0.54
15 4 0.10
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.38
Consensus pattern (13 bp):
TCCTCAATTTCAA
Found at i:44946874 original size:18 final size:18
Alignment explanation
Indices: 44946851--44946885 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44946841 CCTTCGTCCT
* *
44946851 CTAAGGGGAAGCAGAAAG
1 CTAAGGGAAAGAAGAAAG
44946869 CTAAGGGAAAGAAGAAA
1 CTAAGGGAAAGAAGAAA
44946886 CCGACTAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:44954566 original size:69 final size:68
Alignment explanation
Indices: 44954433--44954567 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
44954423 TTTAATAGAT
*
44954433 TTAATATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATT
1 TTAATATTAAATTAAATTTAATACTTATCTTAATAGTATTATATTAATTTAATATTAAAGTGATT
44954498 ATC
66 ATC
* *
44954501 TTAATATTAAATTAAATTTAATATTTATCTTCATAAGTATTATATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTAAATTTAATACTTATCTTAAT-AGTATTATATTAATTTAATATTAAAGTGAT
44954566 TA
65 TA
44954568 AGTTTAATCA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 32 0.51
69 31 0.49
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (68 bp):
TTAATATTAAATTAAATTTAATACTTATCTTAATAGTATTATATTAATTTAATATTAAAGTGATT
ATC
Found at i:44954570 original size:32 final size:32
Alignment explanation
Indices: 44954467--44954570 Score: 84
Period size: 32 Copynumber: 3.1 Consensus size: 32
44954457 TTATCTTAAT
*
44954467 AGTATTTTATTAATTTAATATTAAAGTGATTA
1 AGTATTATATTAATTTAATATTAAAGTGATTA
* * *** *
44954499 TCTTAATATTAAATTAAATTTAATATTTATCTTCA-TA
1 ----AGTATTATATT-AATTTAATA-TTAAAGTGATTA
44954536 AGTATTATATTAATTTAATATTAAAGTGATTA
1 AGTATTATATTAATTTAATATTAAAGTGATTA
44954568 AGT
1 AGT
44954571 TTAATCATAG
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
31 5 0.10
32 14 0.27
33 9 0.17
36 8 0.15
37 11 0.21
38 5 0.10
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (32 bp):
AGTATTATATTAATTTAATATTAAAGTGATTA
Found at i:44960675 original size:2 final size:2
Alignment explanation
Indices: 44960668--44960697 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44960658 NNNNNNNCAA
44960668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44960698 TGTTTTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44965739 original size:28 final size:28
Alignment explanation
Indices: 44965708--44965777 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
44965698 TTCCCGGGAC
* *
44965708 ATTTTTCAAAACCCATCTCGTCAAAATT
1 ATTTTTCAAAACCCATATCATCAAAATT
*
44965736 ATTTTTCAGAACCCATATCATCAAAATT
1 ATTTTTCAAAACCCATATCATCAAAATT
*
44965764 ATTTTTAAAAACCC
1 ATTTTTCAAAACCC
44965778 CTAAACCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (28 bp):
ATTTTTCAAAACCCATATCATCAAAATT
Done.