Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 79 of 135
Found at i:31080472 original size:158 final size:158
Alignment explanation
Indices: 31080179--31080497 Score: 476
Period size: 158 Copynumber: 2.0 Consensus size: 158
31080169 TAATTACTTT
* * ** *
31080179 TTTATTAAGTAAAGCTAAAAATCAGTATAAGATAATTTTAATGTAATTCCATAAGAGCCTCGATA
1 TTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTAATGTAATTCCATAAGAGCCTCAATA
* * * * *
31080244 TAACCCAATGCCTTTAAATATGGAGAGTGATTCTACTTGATCCTCAAGTAACCATTTTTCAAGTT
66 TAACCCAATGCCTTTAAACATGGAAAATGACTCTACTTGATCATCAAGTAACCATTTTTCAAGTT
*
31080309 GTCAACCTTAACTCAACTGGTATTCATG
131 GTCAACCTTAACTCAACTGATATTCATG
* *
31080337 TTTATAAAGTAAAACTAAAAATCAACATAGGATAATTTTGATGTAATTCCATAAGAGCCTCAATA
1 TTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTAATGTAATTCCATAAGAGCCTCAATA
* *
31080402 TAATCCAATGCCTTTAAACATGGAAAATGACTCTACTTGATTATCAAGTAACCATTTTTCAAGTT
66 TAACCCAATGCCTTTAAACATGGAAAATGACTCTACTTGATCATCAAGTAACCATTTTTCAAGTT
* * *
31080467 TTCAACCTTAACTCAATTGATCTTCATG
131 GTCAACCTTAACTCAACTGATATTCATG
31080495 TTT
1 TTT
31080498 TGCGTTCTAA
Statistics
Matches: 143, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
158 143 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (158 bp):
TTTATAAAGTAAAACTAAAAATCAACATAAGATAATTTTAATGTAATTCCATAAGAGCCTCAATA
TAACCCAATGCCTTTAAACATGGAAAATGACTCTACTTGATCATCAAGTAACCATTTTTCAAGTT
GTCAACCTTAACTCAACTGATATTCATG
Found at i:31081660 original size:24 final size:25
Alignment explanation
Indices: 31081632--31081681 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
31081622 TGAATTACAC
*
31081632 TTTA-TGGATTGCAGTAGAATGGTT
1 TTTATTGGAATGCAGTAGAATGGTT
31081656 TTTATTTTGGAATGCAGTAGAATGGT
1 TTTA--TTGGAATGCAGTAGAATGGT
31081682 GAAGATGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
27 18 0.82
ACGTcount: A:0.26, C:0.04, G:0.28, T:0.42
Consensus pattern (25 bp):
TTTATTGGAATGCAGTAGAATGGTT
Found at i:31083621 original size:58 final size:58
Alignment explanation
Indices: 31083548--31083666 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
31083538 CTTTCTTTTT
* *
31083548 AGTCGAAAGAGAGAAAGATTCGTCTTTACATAGTGACTAGTCATCTTGTTCCTAAGCC
1 AGTCGAAAGAAAGAAAGATTCGTCTTTACATAGTGACTAGCCATCTTGTTCCTAAGCC
*
31083606 AGTCGAAAGAAAGAAAGATTCGTCTTTACATAGTGGCTAGCCATCTTGTTCCTAAGCC
1 AGTCGAAAGAAAGAAAGATTCGTCTTTACATAGTGACTAGCCATCTTGTTCCTAAGCC
31083664 AGT
1 AGT
31083667 AGCATATTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (58 bp):
AGTCGAAAGAAAGAAAGATTCGTCTTTACATAGTGACTAGCCATCTTGTTCCTAAGCC
Found at i:31083816 original size:13 final size:13
Alignment explanation
Indices: 31083798--31083822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31083788 ATTATTAATA
31083798 TTATTTTGTGTGT
1 TTATTTTGTGTGT
31083811 TTATTTTGTGTG
1 TTATTTTGTGTG
31083823 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:31085220 original size:41 final size:41
Alignment explanation
Indices: 31085175--31085336 Score: 209
Period size: 41 Copynumber: 4.0 Consensus size: 41
31085165 AAATTATTCA
*
31085175 GACTATACGTCTAGGAGGCTAAGTGCCGGTGAATTAAATCG
1 GACTATACGTCTAGGAGGCTAAGTGCCGGTGAATTGAATCG
* * *
31085216 GACTATACGTCTAGTAGGATAAATGCCGGTGAATTGAATCG
1 GACTATACGTCTAGGAGGCTAAGTGCCGGTGAATTGAATCG
* *
31085257 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATACGTCTAGGAGGCTAAGTGCCGGTGAATTGAATC-G
* * * * *
31085299 G-CTACAAGCCTAGGAGGCTAAGTGCCAGTGAACTGAAT
1 GACTATACGTCTAGGAGGCTAAGTGCCGGTGAATTGAAT
31085337 TAAACTATAA
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
41 105 0.98
42 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
GACTATACGTCTAGGAGGCTAAGTGCCGGTGAATTGAATCG
Found at i:31086088 original size:41 final size:41
Alignment explanation
Indices: 31086031--31086135 Score: 140
Period size: 41 Copynumber: 2.6 Consensus size: 41
31086021 GACTATACGT
**
31086031 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTACAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAAACTACAAGC
* *
31086072 CTAGCAGGCTAAGTGCCGGTGAACTGAATTAAACTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAAACTACAAGC
* *
31086113 CTATCAGG-TGAAGTGCCAGTGAA
1 CTAGCAGGCT-AAGTGCCGGTGAA
31086136 TCTGTTTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.02
41 56 0.98
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAAACTACAAGC
Found at i:31089790 original size:20 final size:19
Alignment explanation
Indices: 31089751--31089790 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
31089741 AAATAGTGAG
* *
31089751 AATTTATTTTCTAAGTATA
1 AATTTATTTTCCAAGAATA
31089770 AATTCTATTTTCCAAGAATA
1 AATT-TATTTTCCAAGAATA
31089790 A
1 A
31089791 CGATTCTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTTATTTTCCAAGAATA
Found at i:31098344 original size:37 final size:37
Alignment explanation
Indices: 31098302--31098376 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
31098292 AACCAGGGAT
31098302 AGGGAAGGGAACGACCAAAAGATGAAAGAGCAAATGA
1 AGGGAAGGGAACGACCAAAAGATGAAAGAGCAAATGA
31098339 AGGGAAGGGAACGACCAAAAGATGAAAGAGCAAATGA
1 AGGGAAGGGAACGACCAAAAGATGAAAGAGCAAATGA
31098376 A
1 A
31098377 CATGAAAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.52, C:0.11, G:0.32, T:0.05
Consensus pattern (37 bp):
AGGGAAGGGAACGACCAAAAGATGAAAGAGCAAATGA
Found at i:31101953 original size:367 final size:367
Alignment explanation
Indices: 31101280--31102015 Score: 1456
Period size: 367 Copynumber: 2.0 Consensus size: 367
31101270 AATTAAAATC
31101280 TTTTTACAGTATAACTAATTCCATGTTGAAGCATATAAATTTGAAACCATATCTATTTGAAAACT
1 TTTTTACAGTATAACTAATTCCATGTTGAAGCATATAAATTTGAAACCATATCTATTTGAAAACT
31101345 TTTTCAAAGTAAAATAATAATAATAATATACTTTAGTATAATAAACTTGAATCATCAAATAACTT
66 TTTTCAAAGTAAAATAATAATAATAATATACTTTAGTATAATAAACTTGAATCATCAAATAACTT
31101410 ATTTAGGTCTTAAAATTATTATTTTAGAACATTTATTAATTTTTAACTTTCTTTATATTTATTCT
131 ATTTAGGTCTTAAAATTATTATTTTAGAACATTTATTAATTTTTAACTTTCTTTATATTTATTCT
31101475 TTAGAATTTTTTTAAAAATTATTATATTTTTTTAAATATAATTTTTAGAATTTTTATAAATATTT
196 TTAGAATTTTTTTAAAAATTATTATATTTTTTTAAATATAATTTTTAGAATTTTTATAAATATTT
31101540 GTGCATTTTGATTTTTTTTTAAATTTGTTGAGAAAGAGACCAATTTACTGATTTTCAAAATTGTT
261 GTGCATTTTGATTTTTTTTTAAATTTGTTGAGAAAGAGACCAATTTACTGATTTTCAAAATTGTT
31101605 ACGGACCAAAAGGGTATTTACACCAATCTGTTATTCAAATTA
326 ACGGACCAAAAGGGTATTTACACCAATCTGTTATTCAAATTA
31101647 TTTTTACAGTATAACTAATTCCATGTTGAAGCATATAAATTTGAAACCATATCTATTTGAAAACT
1 TTTTTACAGTATAACTAATTCCATGTTGAAGCATATAAATTTGAAACCATATCTATTTGAAAACT
31101712 TTTTCAAAGTAAAATAATAATAATAATATACTTTAGTATAATAAACTTGAATCATCAAATAACTT
66 TTTTCAAAGTAAAATAATAATAATAATATACTTTAGTATAATAAACTTGAATCATCAAATAACTT
31101777 ATTTAGGTCTTAAAATTATTATTTTAGAACATTTATTAATTTTTAACTTTCTTTATATTTATTCT
131 ATTTAGGTCTTAAAATTATTATTTTAGAACATTTATTAATTTTTAACTTTCTTTATATTTATTCT
31101842 TTAGAATTTTTTTAAAAATTATTATATTTTTTTAAATATAATTTTTAGAATTTTTATAAATATTT
196 TTAGAATTTTTTTAAAAATTATTATATTTTTTTAAATATAATTTTTAGAATTTTTATAAATATTT
31101907 -TGCATTTTTGATTTTTTTTTAAATTTGTTGAGAAAGAGACCAATTTACTGATTTTCAAAATTGT
261 GTGCA-TTTTGATTTTTTTTTAAATTTGTTGAGAAAGAGACCAATTTACTGATTTTCAAAATTGT
31101971 TACGGACCAAAAGGGTATTTACACCAATCTGTTATTCAAATTA
325 TACGGACCAAAAGGGTATTTACACCAATCTGTTATTCAAATTA
31102014 TT
1 TT
31102016 CGAGTTATTT
Statistics
Matches: 368, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
366 4 0.01
367 364 0.99
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (367 bp):
TTTTTACAGTATAACTAATTCCATGTTGAAGCATATAAATTTGAAACCATATCTATTTGAAAACT
TTTTCAAAGTAAAATAATAATAATAATATACTTTAGTATAATAAACTTGAATCATCAAATAACTT
ATTTAGGTCTTAAAATTATTATTTTAGAACATTTATTAATTTTTAACTTTCTTTATATTTATTCT
TTAGAATTTTTTTAAAAATTATTATATTTTTTTAAATATAATTTTTAGAATTTTTATAAATATTT
GTGCATTTTGATTTTTTTTTAAATTTGTTGAGAAAGAGACCAATTTACTGATTTTCAAAATTGTT
ACGGACCAAAAGGGTATTTACACCAATCTGTTATTCAAATTA
Found at i:31105552 original size:34 final size:31
Alignment explanation
Indices: 31105521--31105589 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 31
31105511 GTGATGAGAA
* *
31105521 TTGAGTATGGTATGAAATGATGTATTTATGAG
1 TTGAGTAT-ATATGAAATGATGTATTCATGAG
31105553 TTGA--ATATATGAAATGATGTATTCATGAG
1 TTGAGTATATATGAAATGATGTATTCATGAG
31105582 TTGAGTAT
1 TTGAGTAT
31105590 TGAATGGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 25 0.76
30 2 0.06
31 2 0.06
32 4 0.12
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (31 bp):
TTGAGTATATATGAAATGATGTATTCATGAG
Found at i:31105564 original size:29 final size:29
Alignment explanation
Indices: 31105531--31105593 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
31105521 TTGAGTATGG
*
31105531 TATGAAATGATGTATTTATGAGTTGAATA
1 TATGAAATGATGTATTCATGAGTTGAATA
*
31105560 TATGAAATGATGTATTCATGAGTTGAGTA
1 TATGAAATGATGTATTCATGAGTTGAATA
31105589 T-TGAA
1 TATGAA
31105594 TGGTTAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.40
Consensus pattern (29 bp):
TATGAAATGATGTATTCATGAGTTGAATA
Found at i:31112928 original size:18 final size:18
Alignment explanation
Indices: 31112905--31112941 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31112895 AATCTTTCTT
31112905 TCTTTCTTCC-TCTGTTTC
1 TCTTTC-TCCTTCTGTTTC
31112923 TCTTTCTCCTTCTGTTTC
1 TCTTTCTCCTTCTGTTTC
31112941 T
1 T
31112942 GTTACTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.00, C:0.32, G:0.05, T:0.62
Consensus pattern (18 bp):
TCTTTCTCCTTCTGTTTC
Found at i:31120025 original size:29 final size:29
Alignment explanation
Indices: 31119983--31120039 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
31119973 AGCCCCGTGA
* *
31119983 CAAGTGGTATCCGAGCTGTTGGTTCGAAC
1 CAAGTGATATCCGAGCTATTGGTTCGAAC
* *
31120012 CAAGTGATGTCCGAGTTATTGGTTCGAA
1 CAAGTGATATCCGAGCTATTGGTTCGAA
31120040 GGCACCGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (29 bp):
CAAGTGATATCCGAGCTATTGGTTCGAAC
Found at i:31120836 original size:25 final size:25
Alignment explanation
Indices: 31120807--31120947 Score: 99
Period size: 25 Copynumber: 5.7 Consensus size: 25
31120797 GAAACTCTTT
31120807 CGAGCCATGA-AACGGGAAGCTTATG
1 CGAGCCAT-ATAACGGGAAGCTTATG
* *
31120832 TGAGCCATATAACGGGAAGCTTTTG
1 CGAGCCATATAACGGGAAGCTTATG
** * *
31120857 CGAGCCA-ATTATTGGGAAGCTCATA
1 CGAGCCATA-TAACGGGAAGCTTATG
* *
31120882 CGAGCCATA-AACGGGAAGCTCAAG
1 CGAGCCATATAACGGGAAGCTTATG
* * * * *
31120906 AGAGCCAAATATCAGGAAGCTCATG
1 CGAGCCATATAACGGGAAGCTTATG
* * *
31120931 AGAGCCATGTAATGGGA
1 CGAGCCATATAACGGGA
31120948 TGCTCATAAG
Statistics
Matches: 90, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
24 20 0.22
25 69 0.77
26 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.18
Consensus pattern (25 bp):
CGAGCCATATAACGGGAAGCTTATG
Found at i:31120913 original size:49 final size:50
Alignment explanation
Indices: 31120821--31120953 Score: 135
Period size: 49 Copynumber: 2.7 Consensus size: 50
31120811 CCATGAAACG
* * *** * * **
31120821 GGAAGCTTATGTGAGCCATATAACGGGAAGCTTTTGCGAGCCAATTATTG
1 GGAAGCTCATGAGAGCCATATAACGGGAAGCTCAAGAGAGCCAAATATCA
31120871 GGAAGCTCAT-ACGAGCCATA-AACGGGAAGCTCAAGAGAGCCAAATATCA
1 GGAAGCTCATGA-GAGCCATATAACGGGAAGCTCAAGAGAGCCAAATATCA
* * *
31120920 GGAAGCTCATGAGAGCCATGTAATGGGATGCTCA
1 GGAAGCTCATGAGAGCCATATAACGGGAAGCTCA
31120954 TAAGAGTTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
49 39 0.57
50 29 0.43
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (50 bp):
GGAAGCTCATGAGAGCCATATAACGGGAAGCTCAAGAGAGCCAAATATCA
Found at i:31120936 original size:74 final size:75
Alignment explanation
Indices: 31120807--31120955 Score: 176
Period size: 74 Copynumber: 2.0 Consensus size: 75
31120797 GAAACTCTTT
* * * * * ** * *
31120807 CGAGCCATGAAACGGGAAGCTTATGTGAGCCATATAACGGGAAGCTTTTGCGAGCCAAT-TATTG
1 CGAGCCATGAAACGGGAAGCTCAAGAGAGCCAAATAACAGGAAGCTCATGAGAGCC-ATGTAATG
31120871 GGAAGCTCATA
65 GGAAGCTCATA
*
31120882 CGAGCCAT-AAACGGGAAGCTCAAGAGAGCCAAATATCAGGAAGCTCATGAGAGCCATGTAATGG
1 CGAGCCATGAAACGGGAAGCTCAAGAGAGCCAAATAACAGGAAGCTCATGAGAGCCATGTAATGG
*
31120946 GATGCTCATA
66 GAAGCTCATA
31120956 AGAGTTAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
73 2 0.03
74 52 0.84
75 8 0.13
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (75 bp):
CGAGCCATGAAACGGGAAGCTCAAGAGAGCCAAATAACAGGAAGCTCATGAGAGCCATGTAATGG
GAAGCTCATA
Found at i:31130704 original size:14 final size:15
Alignment explanation
Indices: 31130687--31130715 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31130677 ATAATTTATT
31130687 AATTTA-TTTTAATA
1 AATTTATTTTTAATA
31130701 AATTTATTTTTAATA
1 AATTTATTTTTAATA
31130716 TAAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTATTTTTAATA
Found at i:31132203 original size:46 final size:46
Alignment explanation
Indices: 31132151--31132245 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
31132141 ACAAAGATAG
*
31132151 AAACCAAAATATTATCTCCTAAACTTTAGCATATAATCTCCTAATT
1 AAACCAAAATACTATCTCCTAAACTTTAGCATATAATCTCCTAATT
*
31132197 AAACCAAAATACTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATACTATCTCCTAAACTTTAGCATATAATCTCCTAATT
31132243 AAA
1 AAA
31132246 AGAAAATAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33
Consensus pattern (46 bp):
AAACCAAAATACTATCTCCTAAACTTTAGCATATAATCTCCTAATT
Found at i:31149235 original size:29 final size:29
Alignment explanation
Indices: 31149182--31149241 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
31149172 TGCTATAAGT
31149182 TTTTATACTCTTTATTTATCTGAATTTTAG
1 TTTTATACTCTTTATTTATCTGAA-TTTAG
*
31149212 TTTTATACT-TTTATTT-TTTAGAATTTAG
1 TTTTATACTCTTTATTTATCT-GAATTTAG
31149240 TT
1 TT
31149242 CCTCTACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.32
29 10 0.36
30 9 0.32
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (29 bp):
TTTTATACTCTTTATTTATCTGAATTTAG
Found at i:31152672 original size:13 final size:14
Alignment explanation
Indices: 31152654--31152683 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31152644 AGATCGTCTG
31152654 TATTATT-TTTTTA
1 TATTATTATTTTTA
31152667 TATTATTATTTTTA
1 TATTATTATTTTTA
31152681 TAT
1 TAT
31152684 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTATTATTTTTA
Found at i:31152675 original size:16 final size:16
Alignment explanation
Indices: 31152654--31152684 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31152644 AGATCGTCTG
*
31152654 TATTATTTTTTTATAT
1 TATTATTTTTATATAT
31152670 TATTATTTTTATATA
1 TATTATTTTTATATA
31152685 AAAATAAATT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTTTATATAT
Found at i:31154429 original size:33 final size:34
Alignment explanation
Indices: 31154362--31154429 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
31154352 AGTTAGATTT
* *
31154362 AAATATTTTTAACTTATATTAATAATAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
* *
31154396 AAATATATTTAAATTAT-TTTATATTAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
31154429 A
1 A
31154430 TTAAACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
AAATATATTTAAATTATATTAATAATAAATAATA
Found at i:31154456 original size:22 final size:23
Alignment explanation
Indices: 31154426--31154469 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
31154416 ATATTAAATA
*
31154426 ATAATTAAACTTATATATTTATG
1 ATAATTAAACTTATAAATTTATG
*
31154449 ATAA-TAAATTTATAAATTTAT
1 ATAATTAAACTTATAAATTTAT
31154470 TAGATTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATAATTAAACTTATAAATTTATG
Found at i:31160626 original size:22 final size:22
Alignment explanation
Indices: 31160611--31160653 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
31160601 AAAATATAAT
31160611 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTAC-AC
31160634 TGTAATATCCCGAAAATTAC
1 TGTAATATCCCGAAAATTAC
31160654 TACAGTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (22 bp):
TGTAATATCCCGAAAATTACAC
Found at i:31160626 original size:23 final size:23
Alignment explanation
Indices: 31160611--31160661 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
31160601 AAAATATAAT
*
31160611 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAAATACTAC
*
31160634 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAAATACTAC
*
31160657 AGTAA
1 TGTAA
31160662 GAAAGTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATATCCCGAAAAATACTAC
Found at i:31165937 original size:27 final size:27
Alignment explanation
Indices: 31165891--31165971 Score: 89
Period size: 25 Copynumber: 3.1 Consensus size: 27
31165881 TTCGGGAATG
*
31165891 CTCATATGAGCACATA-AACGGGAAGCT
1 CTCATCTGAGC-CATATAACGGGAAGCT
31165918 CTC-TCTCGAGCCATATAACGGGAA-C-
1 CTCATCT-GAGCCATATAACGGGAAGCT
* *
31165943 CTCATGTGAGCCATGTAACGGGAAGCT
1 CTCATCTGAGCCATATAACGGGAAGCT
31165970 CT
1 CT
31165972 AGAGAACTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
25 19 0.41
26 10 0.22
27 17 0.37
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (27 bp):
CTCATCTGAGCCATATAACGGGAAGCT
Found at i:31167826 original size:17 final size:18
Alignment explanation
Indices: 31167804--31167838 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31167794 TTATGGTCCT
*
31167804 AAAATTCCAA-AAACATA
1 AAAATTACAAGAAACATA
31167821 AAAATTACAAGAAACATA
1 AAAATTACAAGAAACATA
31167839 CTAAAATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.14, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAATTACAAGAAACATA
Found at i:31169634 original size:3 final size:3
Alignment explanation
Indices: 31169626--31169663 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
31169616 AGCCAACTAG
31169626 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
31169664 GATTCTCAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:31195153 original size:18 final size:18
Alignment explanation
Indices: 31195086--31195160 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
31195076 ATTTTTTTAA
*
31195086 TTATAACATATATTTAATT
1 TTATAATATATATTT-ATT
* *
31195105 TTAT-ATATATCTTTGTT
1 TTATAATATATATTTATT
* *
31195122 TTA-AATTTTTTATTTATT
1 TTATAA-TATATATTTATT
*
31195140 TTATAATATATATTTAGT
1 TTATAATATATATTTATT
31195158 TTA
1 TTA
31195161 ATTTTGCCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
17 6 0.14
18 31 0.72
19 6 0.14
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
TTATAATATATATTTATT
Found at i:31195161 original size:36 final size:35
Alignment explanation
Indices: 31195096--31195165 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
31195086 TTATAACATA
*
31195096 TATTTAATTTTATATATATCTTTGTTTTAAATTTTT
1 TATTTAATTTTATATATATATTTGTTTT-AATTTTT
31195132 TATTT-ATTTTATAATATATATTTAG-TTTAATTTT
1 TATTTAATTTTAT-ATATATATTT-GTTTTAATTTT
31195166 GCCAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 13 0.42
36 17 0.55
37 1 0.03
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (35 bp):
TATTTAATTTTATATATATATTTGTTTTAATTTTT
Found at i:31200192 original size:21 final size:21
Alignment explanation
Indices: 31200151--31200221 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
31200141 CACATTAAGA
**
31200151 ATATAAAAAATGGA-AATAAAT
1 ATATAAAAAATCTAGAA-AAAT
*
31200172 ATATAAAAAATTTAGAAAAAT
1 ATATAAAAAATCTAGAAAAAT
* * *
31200193 GTATAAATAATCTAGAAAAAAA
1 ATATAAAAAATCTAG-AAAAAT
31200215 ATATAAA
1 ATATAAA
31200222 TTATAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 28 0.68
22 13 0.32
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.25
Consensus pattern (21 bp):
ATATAAAAAATCTAGAAAAAT
Found at i:31206610 original size:11 final size:11
Alignment explanation
Indices: 31206591--31206631 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
31206581 AACACCGAAT
*
31206591 TTTTTGGGTAA
1 TTTTCGGGTAA
31206602 TTTTCGGGTAA
1 TTTTCGGGTAA
31206613 --TTCGGGTAA
1 TTTTCGGGTAA
31206622 TTTTCGGGTA
1 TTTTCGGGTA
31206632 TTCGGTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.17, C:0.07, G:0.29, T:0.46
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:31206618 original size:9 final size:9
Alignment explanation
Indices: 31206604--31206695 Score: 98
Period size: 9 Copynumber: 10.2 Consensus size: 9
31206594 TTGGGTAATT
31206604 TTCGGGTAA
1 TTCGGGTAA
31206613 TTCGGGTAA
1 TTCGGGTAA
31206622 TTTTCGGGT-A
1 --TTCGGGTAA
*
31206632 TTCGGTTAA
1 TTCGGGTAA
* *
31206641 TTTGGTTAA
1 TTCGGGTAA
*
31206650 TTCGGTTAA
1 TTCGGGTAA
*
31206659 TTCGGTTAA
1 TTCGGGTAA
31206668 -TCGGGTAA
1 TTCGGGTAA
*
31206676 TTCTGGTAA
1 TTCGGGTAA
31206685 TTCGGGTAA
1 TTCGGGTAA
31206694 TT
1 TT
31206696 TTTAACCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
8 13 0.18
9 52 0.71
10 1 0.01
11 7 0.10
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:31216191 original size:28 final size:28
Alignment explanation
Indices: 31216160--31216226 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
31216150 TTTTTTAAAA
31216160 TTAAAATATTT-AATACA-TTTTATACTTT
1 TTAAAATATTTAAAT-CATTTTTATA-TTT
31216188 TTAAACA-ATTTAAATCATTTTTATATTT
1 TTAAA-ATATTTAAATCATTTTTATATTT
*
31216216 TAAAAATATTT
1 TTAAAATATTT
31216227 TTTGTACTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 1 0.03
28 22 0.65
29 11 0.32
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAAAATATTTAAATCATTTTTATATTT
Found at i:31216252 original size:97 final size:97
Alignment explanation
Indices: 31216139--31216333 Score: 363
Period size: 97 Copynumber: 2.0 Consensus size: 97
31216129 TGCCATTAGC
*
31216139 AATTAATTAATTTTTTTAAAATTAAAATATTTAATACATTTTATACTTTTTAAACAATTTAAATC
1 AATTAATTAATGTTTTTAAAATTAAAATATTTAATACATTTTATACTTTTTAAACAATTTAAATC
*
31216204 ATTTTTATATTTTAAAAATATTTTTTGTACTT
66 ATTTTTATATTTTAAAAATAATTTTTGTACTT
*
31216236 AATTAATTAATGTTTTTAAAATTAAAATATTTAATATATTTTATACTTTTTAAACAATTTAAATC
1 AATTAATTAATGTTTTTAAAATTAAAATATTTAATACATTTTATACTTTTTAAACAATTTAAATC
31216301 ATTTTTATATTTTAAAAATAATTTTTGTACTT
66 ATTTTTATATTTTAAAAATAATTTTTGTACTT
31216333 A
1 A
31216334 TTTTTATATT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (97 bp):
AATTAATTAATGTTTTTAAAATTAAAATATTTAATACATTTTATACTTTTTAAACAATTTAAATC
ATTTTTATATTTTAAAAATAATTTTTGTACTT
Found at i:31216288 original size:28 final size:28
Alignment explanation
Indices: 31216257--31216320 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
31216247 GTTTTTAAAA
31216257 TTAAAATATTT-AAT-ATATTTTATACTTT
1 TTAAAATATTTAAATCAT-TTTTATA-TTT
31216285 TTAAACA-ATTTAAATCATTTTTATATTT
1 TTAAA-ATATTTAAATCATTTTTATATTT
*
31216313 TAAAAATA
1 TTAAAATA
31216321 ATTTTTGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
27 1 0.03
28 17 0.55
29 11 0.35
30 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAAAATATTTAAATCATTTTTATATTT
Found at i:31216323 original size:29 final size:28
Alignment explanation
Indices: 31216257--31216324 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
31216247 GTTTTTAAAA
31216257 TTAAAAT-ATTTAATATATTTTATACTT
1 TTAAAATAATTTAATATATTTTATACTT
* *
31216284 TTTAAACAATTTAA-ATCATTTTTATA-TT
1 TTAAAATAATTTAATAT-A-TTTTATACTT
31216312 TTAAAAATAATTT
1 TT-AAAATAATTT
31216325 TTGTACTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 7 0.21
28 11 0.33
29 15 0.45
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
TTAAAATAATTTAATATATTTTATACTT
Found at i:31216367 original size:33 final size:31
Alignment explanation
Indices: 31216301--31216367 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
31216291 AATTTAAATC
*
31216301 ATTTTTATATTTTAAAAATAATTTTTGTACTT
1 ATTTTTATATTTTAAAAATAATTATTG-ACTT
31216333 ATTTTTATATTTTAAAAAATTAATTAATTG-CTT
1 ATTTTTATATTTT-AAAAA-TAATT-ATTGACTT
31216366 AT
1 AT
31216368 ATGACATCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 13 0.42
33 10 0.32
34 5 0.16
35 3 0.10
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
ATTTTTATATTTTAAAAATAATTATTGACTT
Found at i:31217359 original size:18 final size:18
Alignment explanation
Indices: 31217326--31217374 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
31217316 ATTCACCTAA
*
31217326 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
31217345 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
31217363 ACCCAACCCAAC
1 ACCCAACCCAAC
31217375 ACAATCATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.41, C:0.45, G:0.02, T:0.12
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:31217492 original size:9 final size:9
Alignment explanation
Indices: 31217478--31217535 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
31217468 GTAGTGATTC
*
31217478 AATTCGGTT
1 AATTCGGGT
31217487 AATTCGGGT
1 AATTCGGGT
31217496 AATTCGGGT
1 AATTCGGGT
* *
31217505 AATTTGGTT
1 AATTCGGGT
31217514 AATTCGGGT
1 AATTCGGGT
*
31217523 AATTCGGTT
1 AATTCGGGT
31217532 AATT
1 AATT
31217536 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:31217501 original size:18 final size:18
Alignment explanation
Indices: 31217478--31217535 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
31217468 GTAGTGATTC
* *
31217478 AATTCGGTTAATTCGGGT
1 AATTCGGGTAATTCGGTT
*
31217496 AATTCGGGTAATTTGGTT
1 AATTCGGGTAATTCGGTT
31217514 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
31217532 AATT
1 AATT
31217536 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:31217513 original size:27 final size:27
Alignment explanation
Indices: 31217478--31217536 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
31217468 GTAGTGATTC
*
31217478 AATTCGGTTAATTCGGGTAATTCGGGT
1 AATTTGGTTAATTCGGGTAATTCGGGT
*
31217505 AATTTGGTTAATTCGGGTAATTCGGTT
1 AATTTGGTTAATTCGGGTAATTCGGGT
31217532 AATTT
1 AATTT
31217537 TTAACCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.08, G:0.25, T:0.42
Consensus pattern (27 bp):
AATTTGGTTAATTCGGGTAATTCGGGT
Found at i:31220743 original size:73 final size:74
Alignment explanation
Indices: 31220647--31220797 Score: 288
Period size: 73 Copynumber: 2.1 Consensus size: 74
31220637 TGGACACTGC
31220647 TTTT-CACTTGTGTAATACACTTTAATTAATTTATATAAATAATAAAAATAAACTATTGTGATCA
1 TTTTACACTTGTGTAATACACTTTAATTAATTTATATAAATAATAAAAATAAACTATTGTGATCA
31220711 ATATTATTA
66 ATATTATTA
31220720 TTTTACACTTGTGT-ATACACTTTAATTAATTTATATAAATAATAAAAATAAACTATTGTGATCA
1 TTTTACACTTGTGTAATACACTTTAATTAATTTATATAAATAATAAAAATAAACTATTGTGATCA
31220784 ATATTATTA
66 ATATTATTA
31220793 TTTTA
1 TTTTA
31220798 TTAATAAAAC
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
73 68 0.88
74 9 0.12
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (74 bp):
TTTTACACTTGTGTAATACACTTTAATTAATTTATATAAATAATAAAAATAAACTATTGTGATCA
ATATTATTA
Found at i:31221724 original size:3 final size:3
Alignment explanation
Indices: 31221716--31221743 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31221706 GTGGAGAAAT
31221716 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
31221744 GCACCTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:31222451 original size:14 final size:14
Alignment explanation
Indices: 31222432--31222463 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31222422 CTCCTTCATA
*
31222432 TCAAGATGAATGTC
1 TCAAGATGAATATC
31222446 TCAAGATGAATATC
1 TCAAGATGAATATC
31222460 TCAA
1 TCAA
31222464 TTGATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (14 bp):
TCAAGATGAATATC
Found at i:31222947 original size:2 final size:2
Alignment explanation
Indices: 31222940--31222965 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31222930 TGTTCACGTT
31222940 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
31222966 AAGCCTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31228193 original size:6 final size:6
Alignment explanation
Indices: 31228182--31228208 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31228172 AAGTAGTAGT
31228182 CTCAGG CTCAGG CTCAGG CTCAGG CTC
1 CTCAGG CTCAGG CTCAGG CTCAGG CTC
31228209 TATAGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.30, T:0.19
Consensus pattern (6 bp):
CTCAGG
Found at i:31233885 original size:17 final size:16
Alignment explanation
Indices: 31233858--31233891 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
31233848 CATACATTTT
31233858 AAAAATAATAAACATA
1 AAAAATAATAAACATA
*
31233874 AAAAATATATAAATATA
1 AAAAATA-ATAAACATA
31233891 A
1 A
31233892 TATATTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATAATAAACATA
Found at i:31234236 original size:21 final size:21
Alignment explanation
Indices: 31234195--31234236 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31234185 TATATATAGG
*
31234195 TATAATAATATTAATATCTAA
1 TATAATAATAATAATATCTAA
31234216 TATAATAATAAATAATA-CTAA
1 TATAATAAT-AATAATATCTAA
31234237 CAATAAGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAATAATAATAATATCTAA
Found at i:31237318 original size:19 final size:19
Alignment explanation
Indices: 31237294--31237331 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31237284 GATTTCTAGA
31237294 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
31237313 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
31237332 TGTTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:31237433 original size:18 final size:18
Alignment explanation
Indices: 31237407--31237449 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
31237397 AAAAGTTGTT
*
31237407 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
31237425 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
31237443 TTTATAT
1 TTTATAT
31237450 TTTGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:31242664 original size:19 final size:19
Alignment explanation
Indices: 31242640--31242677 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31242630 GATTTCTAGA
31242640 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
31242659 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
31242678 TGTTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:31244826 original size:8 final size:8
Alignment explanation
Indices: 31244813--31244838 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31244803 TGTTACAGGC
31244813 AACAAAGA
1 AACAAAGA
31244821 AACAAAGA
1 AACAAAGA
31244829 AACAAAGA
1 AACAAAGA
31244837 AA
1 AA
31244839 GGCAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.12, T:0.00
Consensus pattern (8 bp):
AACAAAGA
Found at i:31249189 original size:17 final size:17
Alignment explanation
Indices: 31249167--31249206 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
31249157 ACATTTTAAA
*
31249167 TAAAAACTTAGAAATTT
1 TAAAAAATTAGAAATTT
* *
31249184 TAAAAAATTATAATTTT
1 TAAAAAATTAGAAATTT
31249201 TAAAAA
1 TAAAAA
31249207 GTTAAACTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAAAAATTAGAAATTT
Found at i:31249352 original size:16 final size:17
Alignment explanation
Indices: 31249316--31249353 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31249306 CAGTTTAATT
31249316 TTTTAAAAATTATAAGC
1 TTTTAAAAATTATAAGC
* *
31249333 TTTTAAAATTTCTAAG-
1 TTTTAAAAATTATAAGC
31249349 TTTTA
1 TTTTA
31249354 TTTAAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTTAAAAATTATAAGC
Found at i:31253301 original size:132 final size:131
Alignment explanation
Indices: 31253128--31253531 Score: 498
Period size: 132 Copynumber: 3.1 Consensus size: 131
31253118 CGTCAGTCTA
* * * * * *
31253128 CTCCACTAATGCTTAAGGAGATAAGATCTGTAAAT-TTCAATCAATTCCACTGTTGCCCAGGGAG
1 CTCCACTACTACTTAGGGAGACAAGATCTG-AAATCTTCAATCTATTCCACTGCTGCCCAGGGAG
*
31253192 ATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCGCCATCCTT-AA
65 ATAGAATTACTGGCTTCAATGTACTCCACTGTAACC--AGGGAGGTAAAATCTGCCATCCTTCAA
31253256 TCTG
128 TCTG
*
31253260 CTCCACTACTACTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGACCAGGGAGA
1 CTCCACTACTACTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAGA
*
31253325 TAGAATTAC-GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT-CTTCGAT
66 TAGAATTACTGGCTTCAATGTACTCCACTGTAA-C-CAGGGAGGTAAAATCTGCCATCCTTCAAT
31253388 CTG
129 CTG
* * * * * *
31253391 CTTCACTGTCTA-TGCAGGAAGGCAAGATCTAAAATCTTCAATTCTATTCCACTGCTGCCCAGGG
1 CTCCACT-ACTACT-TAGGGAGACAAGATCTGAAATCTTCAA-TCTATTCCACTGCTGCCCAGGG
*
31253455 A-AGTAGAATTACTGGCTTTAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTGCCAT-CTT
63 AGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCA-G-GGAGGTAAAATCTGCCATCCTT
*
31253518 CGATCTG
125 CAATCTG
*
31253525 CTTCACT
1 CTCCACT
31253532 GTCTATGCAG
Statistics
Matches: 244, Mismatches: 17, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
130 3 0.01
131 58 0.24
132 92 0.38
133 34 0.14
134 57 0.23
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (131 bp):
CTCCACTACTACTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAGA
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCAGGGAGGTAAAATCTGCCATCCTTCAATCT
G
Found at i:31253562 original size:134 final size:133
Alignment explanation
Indices: 31253150--31253555 Score: 569
Period size: 134 Copynumber: 3.1 Consensus size: 133
31253140 TTAAGGAGAT
* *
31253150 AAGATCTGTAAAT-TTCAATCAATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGT
1 AAGATCTG-AAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGT
* * * * *
31253214 ACTCCACTGTAACCTTA-G-GGAGGTAAAATCCGCCATCCTT-AATCTGCTCCACT-ACTACT-T
65 ACTCCACTGTAACC--ACGAGGAGGTAAAATCTGCCAT-CTTCGATCTGCTTCACTGTCTA-TGC
* *
31253274 AGGGAGAC
126 AGGAAGGC
*
31253282 AAGATCTGAAATCTTCAATCTATTCCACTGCTGACCAGGGAGATAGAATTAC-GGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
31253346 CTCCACTGTAACCAC-AGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCACTGTCTATGCAGGA
66 CTCCACTGTAACCACGA-GGAGGTAAAATCTGCCATCTTCGATCTGCTTCACTGTCTATGCAGGA
31253410 AGGC
130 AGGC
* *
31253414 AAGATCTAAAATCTTCAATTCTATTCCACTGCTGCCCAGGGA-AGTAGAATTACTGGCTTTAATG
1 AAGATCTGAAATCTTCAA-TCTATTCCACTGCTGCCCAGGGAGA-TAGAATTACTGGCTTCAATG
31253478 TACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCACTGTCTATGCAGG
64 TACTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCACTGTCTATGCAGG
31253543 AAGGC
129 AAGGC
31253548 AAGATCTG
1 AAGATCTG
31253556 CTATCTTTAA
Statistics
Matches: 249, Mismatches: 14, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
129 1 0.00
130 3 0.01
131 58 0.23
132 71 0.29
133 31 0.12
134 84 0.34
135 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (133 bp):
AAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
CTCCACTGTAACCACGAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCACTGTCTATGCAGGAA
GGC
Found at i:31253606 original size:88 final size:88
Alignment explanation
Indices: 31253514--31253735 Score: 356
Period size: 88 Copynumber: 2.5 Consensus size: 88
31253504 AAATCTGCCA
* * *
31253514 TCTTCGATCTGCTTCACTGTCTA-TGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTG
1 TCTTCGATTTGCTTCATTGTC-AGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTG
31253578 CCACCGAAGGAGGCAAGGTTAGTG
65 CCACCGAAGGAGGCAAGGTTAGTG
*
31253602 TCTTCGATTTGCTTCATTGTCAGTACAGGAAGGCAAAATCTGCTATCTTTAACCTGCTCCGCTGC
1 TCTTCGATTTGCTTCATTGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGC
*
31253667 CACCGAGGGAGGCAAGGTTAGTG
66 CACCGAAGGAGGCAAGGTTAGTG
* * *
31253690 TCTTCGATTTGCTTCGTTGTCAGTACAAGAAGGCAAGATCTACTAT
1 TCTTCGATTTGCTTCATTGTCAGTACAGGAAGGCAAGATCTGCTAT
31253736 ATTCAGTCTG
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
87 1 0.01
88 123 0.99
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (88 bp):
TCTTCGATTTGCTTCATTGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGC
CACCGAAGGAGGCAAGGTTAGTG
Found at i:31255059 original size:16 final size:16
Alignment explanation
Indices: 31255033--31255071 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
31255023 GCCTCTCCAC
*
31255033 TTTT-ATTTTTCCA-T
1 TTTTCATTTTTTCACT
31255047 TTTTCATTTTTTCACT
1 TTTTCATTTTTTCACT
31255063 TTTTCATTT
1 TTTTCATTT
31255072 CTCATCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 8 0.36
16 10 0.45
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTCATTTTTTCACT
Found at i:31259631 original size:3 final size:3
Alignment explanation
Indices: 31259623--31259655 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
31259613 TGAATAATGG
31259623 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31259656 GACAAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31259769 original size:65 final size:65
Alignment explanation
Indices: 31259692--31259999 Score: 332
Period size: 65 Copynumber: 4.5 Consensus size: 65
31259682 AATGAAAAGA
31259692 AAATATAAATAATATCAAATTTAAATATTTAAAAGGTGAAAGAATAACAAATAAATAGATAAAAC
1 AAATATAAATAATATCAAATTTAAATATTTAAAAGGTGAAAGAATAACAAATAAATAGATAAAAC
* * * *
31259757 AAATATAAATAATATTAAATTTAAATGTTTAAAA-GTAAAAGAAAAACAAATAAATAGATAAAAC
1 AAATATAAATAATATCAAATTTAAATATTTAAAAGGTGAAAGAATAACAAATAAATAGATAAAAC
* * * * *
31259821 AAATATTAGTAATATCAAAATTAAAATATTTAAAAAGT-AAAAAATAACAAATAAATAAATAGAT
1 AAATATAAATAATATC-AAATTTAAATATTTAAAAGGTGAAAGAATAAC----AAATAAATAGAT
31259885 AAAAC
61 AAAAC
* * * *
31259890 AAATATAAATAATATCAAATTTTAAGTATTAAAAAGAGCAAAAGAATAACGAATAAATAAATAAA
1 AAATATAAATAATATCAAA-TTTAAATATTTAAAAG-G----TG-A-AA-GAAT-AACAAATAAA
31259955 TAGATAAAAC
56 TAGATAAAAC
* *
31259965 AAATATAGATAGTATCAAATTTAAATATTTAAAAG
1 AAATATAAATAATATCAAATTTAAATATTTAAAAG
31260000 TAATTAATTG
Statistics
Matches: 202, Mismatches: 24, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
64 41 0.20
65 56 0.28
66 2 0.01
68 3 0.01
69 43 0.21
70 1 0.00
74 14 0.07
75 34 0.17
76 1 0.00
77 2 0.01
78 3 0.01
79 2 0.01
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (65 bp):
AAATATAAATAATATCAAATTTAAATATTTAAAAGGTGAAAGAATAACAAATAAATAGATAAAAC
Found at i:31259964 original size:75 final size:69
Alignment explanation
Indices: 31259692--31259999 Score: 332
Period size: 69 Copynumber: 4.5 Consensus size: 69
31259682 AATGAAAAGA
* *
31259692 AAATATAAATAATATCAAATTTAAATATTTAAAAG-GTGAAAGAATAAC----AAATAAATAGAT
1 AAATATAAATAATATCAAATTTAAATATTTAAAAGAG-CAAAAAATAACAAATAAATAAATAGAT
31259752 AAAAC
65 AAAAC
* * * * *
31259757 AAATATAAATAATATTAAATTTAAATGTTT-AAA-AG--TAAAAGAA-AAACAAATAAATAGATA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAGAGCAAAAAATAACAAATAAATAAATAGATA
31259817 AAAC
66 AAAC
* * * *
31259821 AAATATTAGTAATATCAAAATTAAAATATTTAAAA-AGTAAAAAATAACAAATAAATAAATAGAT
1 AAATATAAATAATATC-AAATTTAAATATTTAAAAGAGCAAAAAATAACAAATAAATAAATAGAT
31259885 AAAAC
65 AAAAC
* *
31259890 AAATATAAATAATATCAAATTTTAAGTATTAAAAAGAGCAAAAGAATAACGAATAAATAAATAAA
1 AAATATAAATAATATCAAA-TTTAAATATTTAAAAGAGCAAAA-AATAAC----AAATAAATAAA
31259955 TAGATAAAAC
60 TAGATAAAAC
* *
31259965 AAATATAGATAGTATCAAATTTAAATATTTAAAAG
1 AAATATAAATAATATCAAATTTAAATATTTAAAAG
31260000 TAATTAATTG
Statistics
Matches: 203, Mismatches: 23, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
61 5 0.02
64 34 0.17
65 40 0.20
66 5 0.02
68 9 0.04
69 46 0.23
70 6 0.03
71 6 0.03
74 14 0.07
75 38 0.19
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (69 bp):
AAATATAAATAATATCAAATTTAAATATTTAAAAGAGCAAAAAATAACAAATAAATAAATAGATA
AAAC
Found at i:31263177 original size:22 final size:19
Alignment explanation
Indices: 31263140--31263180 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
31263130 ATGACTTTTA
31263140 AATAATTTTTTTATTAAGT
1 AATAATTTTTTTATTAAGT
* *
31263159 AATAA-TATTTTATTAATT
1 AATAATTTTTTTATTAAGT
31263177 AATA
1 AATA
31263181 TTATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AATAATTTTTTTATTAAGT
Found at i:31281657 original size:88 final size:88
Alignment explanation
Indices: 31281549--31281926 Score: 234
Period size: 88 Copynumber: 4.3 Consensus size: 88
31281539 GGCTTCAGTA
** * *
31281549 TACTCCACTGTAACCTCAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACTACTGTCTAGGG
1 TACTCCACTGT-TGCTCAGGGAGATAAAATCTGTCATCTTCAATCTACTCCACTACTGTCTAGGG
*
31281614 AGATAAAATTTGTAATCTTCAATC
65 AGATAAAATCTGTAATCTTCAATC
* * * * * *
31281638 TATTCCACTGTTGCACAGGGAGATAGAATTACTG---GCTTCAATGTACTCCACTGTAAC-CTC-
1 TACTCCACTGTTGCTCAGGGAGATA-AAAT-CTGTCATCTTCAATCTACTCCAC--T-ACTGTCT
* * ** **
31281698 AGGGAGGTAAAATCCGCCATCTTTGATC
61 AGGGAGATAAAATCTGTAATCTTCAATC
* ** * * * * ** * *
31281726 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGA
1 TACTCCACTGTTGCTCAGGGAGATAAAATCTGTCATCTTCAATCTACTCCACTACTGTCTAGGGA
* *
31281791 GATAGAATTACTG--A-CTTCAATG
66 GATA-AAAT-CTGTAATCTTCAATC
* * * * ** *
31281813 TACTCCACTGTATCCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTG-CTTAGG
1 TACTCCACTGT-TGCTCAGGGAGATAAAATCTGTCATCTTCAATCTACTCCACTACTGTC-TAGG
*
31281877 GAGATAAGATCTGTAATCTTCAATC
64 GAGATAAAATCTGTAATCTTCAATC
* * *
31281902 TATTCCACTGTTGCCCTGGGAGATA
1 TACTCCACTGTTGCTCAGGGAGATA
31281927 GAATTACTGG
Statistics
Matches: 209, Mismatches: 63, Indels: 35
0.68 0.21 0.11
Matches are distributed among these distances:
86 6 0.03
87 34 0.16
88 112 0.54
89 50 0.24
90 7 0.03
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (88 bp):
TACTCCACTGTTGCTCAGGGAGATAAAATCTGTCATCTTCAATCTACTCCACTACTGTCTAGGGA
GATAAAATCTGTAATCTTCAATC
Found at i:31281719 original size:132 final size:132
Alignment explanation
Indices: 31281524--31282034 Score: 873
Period size: 132 Copynumber: 3.9 Consensus size: 132
31281514 GTAACTTCAA
* * * *
31281524 GGAGATAAGAA-TACTGGCTTCAGTATACTCCACTGTAACCTCAGGGAGGTAAAATCTGTCATCT
1 GGAGAT-AGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
* * * *
31281588 TCGATCTACTCCACTACTG-TCTAGGGAGATAAAATTTGTAATCTTCAATCTATTCCACTGTTGC
65 TTGATCTGCTCCACTACTGCT-TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGC
*
31281652 ACAG
129 CCAG
31281656 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
31281721 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCC
31281786 AG
131 AG
* *
31281788 GGAGATAGAATTACTGACTTCAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCGCCATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
31281853 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCC
*
31281918 TG
131 AG
*
31281920 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
31281985 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCT
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCT
31282035 GTTTCGCTGT
Statistics
Matches: 362, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
131 4 0.01
132 357 0.99
133 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCC
AG
Found at i:31281923 original size:44 final size:44
Alignment explanation
Indices: 31281549--31282034 Score: 202
Period size: 44 Copynumber: 11.0 Consensus size: 44
31281539 GGCTTCAGTA
** * * * *
31281549 TACTCCACTGTAACCTCAGGGAGGTAAAATCTGTCATCTTCGATC
1 TACTCCACTGTTGCC-CAGGGAGATAAGATCTGTAATCTTCAATC
** * * * *
31281594 TACTCCACTACTGTCTAGGGAGATAAAATTTGTAATCTTCAATC
1 TACTCCACTGTTGCCCAGGGAGATAAGATCTGTAATCTTCAATC
* * * * *
31281638 TATTCCACTGTTGCACAGGGAGAT-AGA-AT-TACTGGCTTCAATG
1 TACTCCACTGTTGCCCAGGGAGATAAGATCTGTAAT--CTTCAATC
** * * * ** **
31281681 TACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATC
1 TACTCCACTGTTGCC-CAGGGAGATAAGATCTGTAATCTTCAATC
* ** **
31281726 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
1 TACTCCACTGTTGCCCAGGGAGATAAGATCTGTAATCTTCAATC
* *
31281770 TATTCCACTGTTGCCCAGGGAGAT-AGAATTACTG--A-CTTCAATG
1 TACTCCACTGTTGCCCAGGGAGATAAG-A-T-CTGTAATCTTCAATC
* * * ** **
31281813 TACTCCACTGTAT-CCTCAGGGAGGTAAAATCCGCCATCTTTGATC
1 TACTCCACTGT-TGCC-CAGGGAGATAAGATCTGTAATCTTCAATC
* ** **
31281858 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
1 TACTCCACTGTTGCCCAGGGAGATAAGATCTGTAATCTTCAATC
* * * * *
31281902 TATTCCACTGTTGCCCTGGGAGAT-AGA-AT-TACTGGCTTCAATG
1 TACTCCACTGTTGCCCAGGGAGATAAGATCTGTAAT--CTTCAATC
** * * **** **
31281945 TACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATC
1 TACTCCACTGTTGCC-CAGGGAGATAAGATCTGTAATCTTCAATC
* ** **
31281990 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
1 TACTCCACTGTTGCCCAGGGAGATAAGATCTGTAATCTTCAATC
31282034 T
1 T
31282035 GTTTCGCTGT
Statistics
Matches: 306, Mismatches: 113, Indels: 45
0.66 0.24 0.10
Matches are distributed among these distances:
41 6 0.02
42 4 0.01
43 64 0.21
44 169 0.55
45 58 0.19
46 3 0.01
47 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
TACTCCACTGTTGCCCAGGGAGATAAGATCTGTAATCTTCAATC
Found at i:31282186 original size:88 final size:88
Alignment explanation
Indices: 31282065--31282258 Score: 309
Period size: 88 Copynumber: 2.2 Consensus size: 88
31282055 AGGCAAGATT
* * * *
31282065 CTGAGGGAGGCAAGAC-TTTATTTTCGATCTGCTTCGCTGTCGATGCAGGAAGTCAAGATTTGCT
1 CTGAGGGAGGCAAGGCTTTTATTTTCGATCTGCTTCGCAGTCGATACAGGAAGGCAAGATTTGCT
* *
31282129 ATCTTTAACTTACTCTACTGCAA
66 ATCTTTAACTTACTCCACTACAA
*
31282152 CTGACGGAGGCAAGGCTTTTATTTTCGATCTGCTTCGCAGTCGATACAGGAAGGCAAGATTTGCT
1 CTGAGGGAGGCAAGGCTTTTATTTTCGATCTGCTTCGCAGTCGATACAGGAAGGCAAGATTTGCT
*
31282217 ATCTTTAACTTGCTCCACTACAA
66 ATCTTTAACTTACTCCACTACAA
31282240 CTGAGGGAGGCAAGGCTTT
1 CTGAGGGAGGCAAGGCTTT
31282259 ATAATTTCAC
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 14 0.14
88 83 0.86
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (88 bp):
CTGAGGGAGGCAAGGCTTTTATTTTCGATCTGCTTCGCAGTCGATACAGGAAGGCAAGATTTGCT
ATCTTTAACTTACTCCACTACAA
Found at i:31284502 original size:19 final size:19
Alignment explanation
Indices: 31284478--31284517 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
31284468 GGTTTGGCAG
31284478 AAAAAATCCAAAAGAATGA
1 AAAAAATCCAAAAGAATGA
**
31284497 AAAAAATCGTAAAGAATGA
1 AAAAAATCCAAAAGAATGA
31284516 AA
1 AA
31284518 TAACATTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAAATCCAAAAGAATGA
Found at i:31286461 original size:13 final size:13
Alignment explanation
Indices: 31286443--31286468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31286433 TGTTCAATTT
31286443 TTTACTAGAAAAC
1 TTTACTAGAAAAC
31286456 TTTACTAGAAAAC
1 TTTACTAGAAAAC
31286469 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:31289765 original size:130 final size:132
Alignment explanation
Indices: 31289571--31289848 Score: 463
Period size: 131 Copynumber: 2.1 Consensus size: 132
31289561 GCGAAATGTT
* *
31289571 ACCTTATAACGAAACTTCTTTTATTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTAGGCCTA
1 ACCTTATAACAAAATTTCTTTTATTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTAGGCCTA
* * *
31289636 AC-AAAAAAATTTGAAACCCCGTAAGTTAGGGTTCGATTTTCTCGAATGGCCAAAATGCAAAGCA
66 ACAAAAAAAAATTGAAACCCCGTAAGTTAGGGTTCGATTTTCTCAAATGGCCAAAACGCAAAGCA
31289700 TG
131 TG
*
31289702 GCCTTATAACAAAATTTCTTTT-TTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTT-GAGCCT
1 ACCTTATAACAAAATTTCTTTTATTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTAG-GCCT
*
31289765 AACAAAAAAAAATTGAAACCCCGTAAGTTAGGGTTCGATTTTGTCAAATGGCCAAAACGCAAAGC
65 AACAAAAAAAAATTGAAACCCCGTAAGTTAGGGTTCGATTTTCTCAAATGGCCAAAACGCAAAGC
31289830 ATG
130 ATG
31289833 ACCTTATAACAAAATT
1 ACCTTATAACAAAATT
31289849 CTTACTTTGC
Statistics
Matches: 137, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
129 1 0.01
130 42 0.31
131 94 0.69
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (132 bp):
ACCTTATAACAAAATTTCTTTTATTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTAGGCCTA
ACAAAAAAAAATTGAAACCCCGTAAGTTAGGGTTCGATTTTCTCAAATGGCCAAAACGCAAAGCA
TG
Found at i:31294145 original size:70 final size:71
Alignment explanation
Indices: 31294049--31294200 Score: 279
Period size: 70 Copynumber: 2.1 Consensus size: 71
31294039 AAACATTAAA
31294049 ATTACTTTATAATTATTTTTTATTTTTAAAATTAAATATATTACTCACCAACCTTTATCATGCAT
1 ATTACTTTATAATTATTTTTTATTTTTAAAATTAAATATATTACTCACCAACCTTTATCATGCAT
31294114 CTTTCC
66 CTTTCC
31294120 ATTACTTTAT-ATTATTTTTTATTTTTAAAATTAAATATATTACTCACCAACCTTTATCATGCAT
1 ATTACTTTATAATTATTTTTTATTTTTAAAATTAAATATATTACTCACCAACCTTTATCATGCAT
31294184 CTTTCC
66 CTTTCC
*
31294190 CTTAACTTTAT
1 ATT-ACTTTAT
31294201 CAAGCATCTT
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
70 62 0.78
71 17 0.22
ACGTcount: A:0.32, C:0.17, G:0.01, T:0.50
Consensus pattern (71 bp):
ATTACTTTATAATTATTTTTTATTTTTAAAATTAAATATATTACTCACCAACCTTTATCATGCAT
CTTTCC
Found at i:31294207 original size:24 final size:24
Alignment explanation
Indices: 31294171--31294216 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
31294161 ACTCACCAAC
*
31294171 CTTTATCATGCATCTTTCCCTTAA
1 CTTTATCAAGCATCTTTCCCTTAA
31294195 CTTTATCAAGCATCTTTCCCTT
1 CTTTATCAAGCATCTTTCCCTT
31294217 TATCATGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.04, T:0.46
Consensus pattern (24 bp):
CTTTATCAAGCATCTTTCCCTTAA
Found at i:31296375 original size:15 final size:15
Alignment explanation
Indices: 31296339--31296375 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
31296329 TTTTCGAATT
31296339 TTAGTTTTGTTTTTA
1 TTAGTTTTGTTTTTA
*
31296354 ATA-TTTTGTTTTTA
1 TTAGTTTTGTTTTTA
31296368 TTAGTTTT
1 TTAGTTTT
31296376 AAGACATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (15 bp):
TTAGTTTTGTTTTTA
Found at i:31298521 original size:20 final size:20
Alignment explanation
Indices: 31298488--31298537 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
31298478 GCAACTACAA
* *
31298488 TAATAATGAGAATACCAAAT
1 TAATAATAATAATACCAAAT
* *
31298508 TAATAATAATAATATCAATT
1 TAATAATAATAATACCAAAT
*
31298528 TTATAATAAT
1 TAATAATAAT
31298538 GGTACTAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAATAATAATACCAAAT
Found at i:31299737 original size:15 final size:16
Alignment explanation
Indices: 31299717--31299751 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
31299707 GGAAATTAAT
31299717 TATTAAAAA-TAAAAA
1 TATTAAAAATTAAAAA
*
31299732 TATTAAAAATTATAAA
1 TATTAAAAATTAAAAA
31299748 TATT
1 TATT
31299752 GATTCGGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TATTAAAAATTAAAAA
Found at i:31305355 original size:79 final size:80
Alignment explanation
Indices: 31305263--31305420 Score: 219
Period size: 79 Copynumber: 2.0 Consensus size: 80
31305253 GCAAAATTAA
* * * ** * *
31305263 ATAAATTCGCAATCAACACTAAATTTATTTTTTAAAATCATGAAAAATTCTAACCTAATAGTATT
1 ATAAATTCACAATCAACACGAAATTTATTCTACAAAATCATGAAAAATTCAAACATAATAGTATT
31305328 AGCAA-TTAACTTTT
66 AGCAATTTAACTTTT
* *
31305342 ATAAATTCACAATCAATACGAAATTTATTCTACAAAATCATGAAAAATTCAAACATAGTAGTATT
1 ATAAATTCACAATCAACACGAAATTTATTCTACAAAATCATGAAAAATTCAAACATAATAGTATT
*
31305407 AGTAATTTAACTTT
66 AGCAATTTAACTTT
31305421 CATCAAATCA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 60 0.88
80 8 0.12
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (80 bp):
ATAAATTCACAATCAACACGAAATTTATTCTACAAAATCATGAAAAATTCAAACATAATAGTATT
AGCAATTTAACTTTT
Found at i:31306696 original size:43 final size:43
Alignment explanation
Indices: 31306548--31306803 Score: 208
Period size: 43 Copynumber: 6.0 Consensus size: 43
31306538 GGAAAAATGT
* * ** * *
31306548 CGCTATAGAACATGACCTTCAGCAGCGAC-TTCCCCATAAACAC
1 CGCTAAAGAACATGACCTTTAGTGGC-ACTTTCCCCACAAACGC
* * *** * ** ***
31306591 CGCTATAGAATATGACCTTTAACAGCGCTTTCCTGACAAATAT
1 CGCTAAAGAACATGACCTTTAGTGGCACTTTCCCCACAAACGC
* * ** *
31306634 CGCTAAATAATATGACCTTTAACGGCACTTTCCCCACAAACGT
1 CGCTAAAGAACATGACCTTTAGTGGCACTTTCCCCACAAACGC
* * * * *
31306677 CGTTAAAGAACATGGCCTTTAGTGACACTATCCCTACAAACGC
1 CGCTAAAGAACATGACCTTTAGTGGCACTTTCCCCACAAACGC
* *
31306720 CGCTGAAGAACATGACCTTTAGTGGCATTTTCCCCACAAACGC
1 CGCTAAAGAACATGACCTTTAGTGGCACTTTCCCCACAAACGC
* * *
31306763 CACTAAAGAACATGTCCTTTAGTGGCACTTTTCCCACAAAC
1 CGCTAAAGAACATGACCTTTAGTGGCACTTTCCCCACAAAC
31306804 ACCATTAACT
Statistics
Matches: 173, Mismatches: 39, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
42 1 0.01
43 172 0.99
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (43 bp):
CGCTAAAGAACATGACCTTTAGTGGCACTTTCCCCACAAACGC
Found at i:31307710 original size:82 final size:83
Alignment explanation
Indices: 31307594--31307745 Score: 225
Period size: 82 Copynumber: 1.8 Consensus size: 83
31307584 GTGGAGATTT
* * * * * *
31307594 TAGTGGCGTTTTTGGTCAATCGCCGCTAGTGTTAAGGTA-TTAGCAGCGTTTTTGTCTTAGCGCC
1 TAGTGGCGTTTTTGGTCAAACGCCACTAATGTTAAGGTATTTAGCAGCGTTTCTATCATAGCGCC
31307658 GCTATAGGTTGGGGGTAA
66 GCTATAGGTTGGGGGTAA
* *
31307676 TAGTGGCGTTTTTGGTGAAACGCCACTAATGTTAAGGTATTTAGCGGCGTTTCTATCATAGCGCC
1 TAGTGGCGTTTTTGGTCAAACGCCACTAATGTTAAGGTATTTAGCAGCGTTTCTATCATAGCGCC
31307741 GCTAT
66 GCTAT
31307746 TGTTGTGAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
82 35 0.57
83 26 0.43
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (83 bp):
TAGTGGCGTTTTTGGTCAAACGCCACTAATGTTAAGGTATTTAGCAGCGTTTCTATCATAGCGCC
GCTATAGGTTGGGGGTAA
Found at i:31307765 original size:82 final size:82
Alignment explanation
Indices: 31307590--31307770 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 82
31307580 AATGGTGGAG
* * * * * *
31307590 ATTTTAGTGGCGTTTTTGGTCAATCGCCGCTAGTGTTAAGGTATTAGCAGCGTTTTTGTCTTAGC
1 ATTTTAGTGGCGTTTTTGGTCAAACGCCACTAATGTTAAGGTATTAGCAGCGTTTCTATCATAGC
*
31307655 GCCGCTATAGGTTGGGG
66 GCCGCTATAGGTTGGGA
* ** * *
31307672 GTAATAGTGGCGTTTTTGGTGAAACGCCACTAATGTTAAGGTATTTAGCGGCGTTTCTATCATAG
1 ATTTTAGTGGCGTTTTTGGTCAAACGCCACTAATGTTAAGGTA-TTAGCAGCGTTTCTATCATAG
* *
31307737 CGCCGCTAT-TGTTGTGA
65 CGCCGCTATAGGTTGGGA
*
31307754 ATTTTACTGGCGTTTTT
1 ATTTTAGTGGCGTTTTT
31307771 ATGTATGCGC
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
82 54 0.68
83 26 0.32
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.39
Consensus pattern (82 bp):
ATTTTAGTGGCGTTTTTGGTCAAACGCCACTAATGTTAAGGTATTAGCAGCGTTTCTATCATAGC
GCCGCTATAGGTTGGGA
Found at i:31308753 original size:21 final size:21
Alignment explanation
Indices: 31308714--31308753 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31308704 TTTTGGATTT
* *
31308714 GGGGTTGGTGGTTTGGGGTCG
1 GGGGTTGGTGATTTAGGGTCG
*
31308735 GGGGTTTGTGATTTAGGGT
1 GGGGTTGGTGATTTAGGGT
31308754 TTAAGGTTTT
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:0.05, C:0.03, G:0.55, T:0.38
Consensus pattern (21 bp):
GGGGTTGGTGATTTAGGGTCG
Found at i:31308761 original size:21 final size:21
Alignment explanation
Indices: 31308736--31308826 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 21
31308726 TTGGGGTCGG
31308736 GGGTTTGTGATTTAGGGTTTA
1 GGGTTTGTGATTTAGGGTTTA
* ** * *
31308757 AGGTTT-TGGGGTTCGGGATTTG
1 GGGTTTGT-GATTTAGGG-TTTA
* * ***
31308779 GGGTTGGTGGTTTAGGGTCGG
1 GGGTTTGTGATTTAGGGTTTA
31308800 GGGTTTGTGATTTAGGGTTTA
1 GGGTTTGTGATTTAGGGTTTA
31308821 GGGTTT
1 GGGTTT
31308827 TGGGATTTGG
Statistics
Matches: 51, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
20 1 0.02
21 35 0.69
22 14 0.27
23 1 0.02
ACGTcount: A:0.10, C:0.02, G:0.45, T:0.43
Consensus pattern (21 bp):
GGGTTTGTGATTTAGGGTTTA
Found at i:31308787 original size:64 final size:64
Alignment explanation
Indices: 31308708--31308840 Score: 230
Period size: 64 Copynumber: 2.1 Consensus size: 64
31308698 TAGGGATTTT
* *
31308708 GGATTTGGGGTTGGTGGTTTGGGGTCGGGGGTTTGTGATTTAGGGTTTAAGGTTTTGGGGTTCG
1 GGATTTGGGGTTGGTGGTTTAGGGTCGGGGGTTTGTGATTTAGGGTTTAAGGTTTTGGGATTCG
* *
31308772 GGATTTGGGGTTGGTGGTTTAGGGTCGGGGGTTTGTGATTTAGGGTTTAGGGTTTTGGGATTTG
1 GGATTTGGGGTTGGTGGTTTAGGGTCGGGGGTTTGTGATTTAGGGTTTAAGGTTTTGGGATTCG
31308836 GGATT
1 GGATT
31308841 AAGGTTTAGG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.09, C:0.02, G:0.47, T:0.41
Consensus pattern (64 bp):
GGATTTGGGGTTGGTGGTTTAGGGTCGGGGGTTTGTGATTTAGGGTTTAAGGTTTTGGGATTCG
Found at i:31318281 original size:43 final size:42
Alignment explanation
Indices: 31318226--31318382 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 42
31318216 CAAGGTCTTT
* **
31318226 TAGCGGCGTTTGTGACCAAAGCGCCGCTAAAGGTCAACATATA
1 TAGCGGCGTTTGTAAATAAAGCGCCGCTAAAGGTCAA-ATATA
* * *
31318269 TAGCGGCGTTTGTAAATAAAGCGCCGCTATAGG-CTAATGTA
1 TAGCGGCGTTTGTAAATAAAGCGCCGCTAAAGGTCAAATATA
* * * *
31318310 TTTGCGGCGTTTGT-ACTGAAAGCGCCGCTAAAGGTCAAGGTATC
1 -TAGCGGCGTTTGTAAAT-AAAGCGCCGCTAAAGGTCAA-ATATA
*
31318354 TAGTGGCGTTTGTAAATAAAGCGCCGCTA
1 TAGCGGCGTTTGTAAATAAAGCGCCGCTA
31318383 TAGGCTAATG
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
41 6 0.06
42 29 0.31
43 54 0.58
44 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTGTAAATAAAGCGCCGCTAAAGGTCAAATATA
Found at i:31318324 original size:42 final size:43
Alignment explanation
Indices: 31318271--31318426 Score: 169
Period size: 42 Copynumber: 3.7 Consensus size: 43
31318261 AACATATATA
31318271 GCGGCGTTTGTAAAT-AAAGCGCCGCTATAGGCTAATGTATTT
1 GCGGCGTTTGTAAATGAAAGCGCCGCTATAGGCTAATGTATTT
* * * *
31318313 GCGGCGTTTGT-ACTGAAAGCGCCGCTAAAGG-TCAAGGTATCTA
1 GCGGCGTTTGTAAATGAAAGCGCCGCTATAGGCT-AATGTAT-TT
* *
31318356 GTGGCGTTTGTAAAT-AAAGCGCCGCTATAGGCTAATGTTTTTTT
1 GCGGCGTTTGTAAATGAAAGCGCCGCTATAGGCTAATG--TATTT
* *
31318400 GCGGCGTTT-TTAGTGAAAGCGCCGCTA
1 GCGGCGTTTGTAAATGAAAGCGCCGCTA
31318427 AAGGTCAAGC
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
41 3 0.03
42 32 0.34
43 32 0.34
44 24 0.26
45 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTGTAAATGAAAGCGCCGCTATAGGCTAATGTATTT
Found at i:31318463 original size:43 final size:42
Alignment explanation
Indices: 31318243--31318472 Score: 173
Period size: 43 Copynumber: 5.4 Consensus size: 42
31318233 GTTTGTGACC
* **
31318243 AAAGCGCCGCTAAAGGTCAA-CATATATAGCGGCGTTTGTAAAT
1 AAAGCGCCGCTAAAGGTCAAGC-TATTTAGCGGCGTTT-TAGTT
* * *
31318286 AAAGCGCCGCTATAGG-CTAATG-TATTT-GCGGCGTTTGTACTG
1 AAAGCGCCGCTAAAGGTC-AA-GCTATTTAGCGGCGTTT-TAGTT
* * * **
31318328 AAAGCGCCGCTAAAGGTCAAGGTATCTAGTGGCGTTTGTAAAT
1 AAAGCGCCGCTAAAGGTCAAGCTATTTAGCGGCGTTT-TAGTT
* * * * *
31318371 AAAGCGCCGCTATAGG-CTAATGTTTTTTTGCGGCGTTTTTAGTG
1 AAAGCGCCGCTAAAGGTC-AA-GCTATTTAGCGGCG-TTTTAGTT
*
31318415 AAAGCGCCGCTAAAGGTCAAGCTCTTTAGCGGCGTTTTAGGTT
1 AAAGCGCCGCTAAAGGTCAAGCTATTTAGCGGCGTTTTA-GTT
*
31318458 TAAGCGCCGCTAAAG
1 AAAGCGCCGCTAAAG
31318473 ATAATAACCT
Statistics
Matches: 150, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.01
42 40 0.27
43 77 0.51
44 28 0.19
45 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGGTCAAGCTATTTAGCGGCGTTTTAGTT
Found at i:31318469 original size:87 final size:85
Alignment explanation
Indices: 31318228--31318451 Score: 317
Period size: 85 Copynumber: 2.6 Consensus size: 85
31318218 AGGTCTTTTA
*
31318228 GCGGCGTTTGTGAC-CAAAGCGCCGCTAAAGGTCAA-CATATATAGCGGCGTTTGTAAATAAAGC
1 GCGGCGTTTGT-ACTGAAAGCGCCGCTAAAGGTCAAGC-TATATAGCGGCGTTTGTAAATAAAGC
31318291 GCCGCTATAGGCTAATGTATTT
64 GCCGCTATAGGCTAATGTATTT
* * *
31318313 GCGGCGTTTGTACTGAAAGCGCCGCTAAAGGTCAAGGTATCTAGTGGCGTTTGTAAATAAAGCGC
1 GCGGCGTTTGTACTGAAAGCGCCGCTAAAGGTCAAGCTATATAGCGGCGTTTGTAAATAAAGCGC
*
31318378 CGCTATAGGCTAATGTTTTTTT
66 CGCTATAGGCTAATG--TATTT
* * * *
31318400 GCGGCGTTTTTAGTGAAAGCGCCGCTAAAGGTCAAGCTCTTTAGCGGCGTTT
1 GCGGCGTTTGTACTGAAAGCGCCGCTAAAGGTCAAGCTATATAGCGGCGTTT
31318452 TAGGTTTAAG
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
84 2 0.02
85 72 0.58
87 50 0.40
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (85 bp):
GCGGCGTTTGTACTGAAAGCGCCGCTAAAGGTCAAGCTATATAGCGGCGTTTGTAAATAAAGCGC
CGCTATAGGCTAATGTATTT
Found at i:31321109 original size:29 final size:29
Alignment explanation
Indices: 31321077--31321134 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
31321067 GATTTGTTAA
*
31321077 AACGTAGAATTTTAT-TTGTAAAATTTATT
1 AACGAAGAATTTTATATT-TAAAATTTATT
*
31321106 AACGAATAATTTTATATTTAAAATTTATT
1 AACGAAGAATTTTATATTTAAAATTTATT
31321135 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (29 bp):
AACGAAGAATTTTATATTTAAAATTTATT
Found at i:31321302 original size:29 final size:29
Alignment explanation
Indices: 31321270--31321327 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
31321260 GATTTGTTAA
*
31321270 AACGTAGAATTTTAT-TTGTAAAATTTATT
1 AACGAAGAATTTTATATT-TAAAATTTATT
*
31321299 AACGAATAATTTTATATTTAAAATTTATT
1 AACGAAGAATTTTATATTTAAAATTTATT
31321328 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (29 bp):
AACGAAGAATTTTATATTTAAAATTTATT
Found at i:31321322 original size:193 final size:193
Alignment explanation
Indices: 31320993--31321380 Score: 751
Period size: 193 Copynumber: 2.0 Consensus size: 193
31320983 ATAAATGATC
31320993 TTATTGTGGATTCTTTTATAATTACGATGTTTACCGTATGAGATGTGAGAAGATAATTTTCTTTC
1 TTATTGTGGATTCTTTTATAATTACGATGTTTACCGTATGAGATGTGAGAAGATAATTTTCTTTC
31321058 TTTATTTTGGATTTGTTAAAACGTAGAATTTTATTTGTAAAATTTATTAACGAATAATTTTATAT
66 TTTATTTTGGATTTGTTAAAACGTAGAATTTTATTTGTAAAATTTATTAACGAATAATTTTATAT
*
31321123 TTAAAATTTA-TTTAATTTTTTAAATAATGATATATTAAAATACACTATATTCATAGTACAAAA
131 TTAAAATTTATTTTAATTTTTT-AATAATGATATATTAAAATACACTATATTAATAGTACAAAA
31321186 TTATTGTGGATTCTTTTATAATTACGATGTTTACCGTATGAGATGTGAGAAGATAATTTTCTTTC
1 TTATTGTGGATTCTTTTATAATTACGATGTTTACCGTATGAGATGTGAGAAGATAATTTTCTTTC
31321251 TTTATTTTGGATTTGTTAAAACGTAGAATTTTATTTGTAAAATTTATTAACGAATAATTTTATAT
66 TTTATTTTGGATTTGTTAAAACGTAGAATTTTATTTGTAAAATTTATTAACGAATAATTTTATAT
31321316 TTAAAATTTATTTTAATTTTTTAATAATGATATATTAAAATACACTATATTAATAGTACAAAA
131 TTAAAATTTATTTTAATTTTTTAATAATGATATATTAAAATACACTATATTAATAGTACAAAA
31321379 TT
1 TT
31321381 TAATAGAAAA
Statistics
Matches: 193, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
193 182 0.94
194 11 0.06
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (193 bp):
TTATTGTGGATTCTTTTATAATTACGATGTTTACCGTATGAGATGTGAGAAGATAATTTTCTTTC
TTTATTTTGGATTTGTTAAAACGTAGAATTTTATTTGTAAAATTTATTAACGAATAATTTTATAT
TTAAAATTTATTTTAATTTTTTAATAATGATATATTAAAATACACTATATTAATAGTACAAAA
Found at i:31322353 original size:3 final size:3
Alignment explanation
Indices: 31322345--31322445 Score: 193
Period size: 3 Copynumber: 33.7 Consensus size: 3
31322335 CCAGAAGCTG
31322345 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
31322393 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CAT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31322441 CTT CT
1 CTT CT
31322446 ACGTTATCAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:31330940 original size:19 final size:19
Alignment explanation
Indices: 31330901--31330940 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
31330891 GACCCATATT
*
31330901 AAATATATATTTGATTAAA
1 AAATATATATTTAATTAAA
31330920 AAATATATATTTAATATAAA
1 AAATATATATTTAAT-TAAA
31330940 A
1 A
31330941 TTCGGGCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
AAATATATATTTAATTAAA
Found at i:31332014 original size:117 final size:118
Alignment explanation
Indices: 31331796--31332031 Score: 456
Period size: 117 Copynumber: 2.0 Consensus size: 118
31331786 AGAGAACAGA
31331796 GTATTAAAGTAGTAGGAATTCAAAGAAGAAATATCGAGTCATGTTCAAATAACAATGATACTTAA
1 GTATTAAAGTA-TAGGAATTCAAAGAAGAAATATCGAGTCATGTTCAAATAACAATGATACTTAA
31331861 AAAAGATAAATGGCGGGTTTTTTACAAAAATAATATAAAAAAATAAAAAATTAC
65 AAAAGATAAATGGCGGGTTTTTTACAAAAATAATATAAAAAAATAAAAAATTAC
31331915 GTATTAAAGT-TAGGAATTCAAAGAAGAAATATCGAGTCATGTTCAAATAACAATGATACTTAAA
1 GTATTAAAGTATAGGAATTCAAAGAAGAAATATCGAGTCATGTTCAAATAACAATGATACTTAAA
31331979 AAAGATAAATGGCGGGTTTTTTACAAAAATAATATAAAAAAATAAAAAATTAC
66 AAAGATAAATGGCGGGTTTTTTACAAAAATAATATAAAAAAATAAAAAATTAC
31332032 CAAAATGTTA
Statistics
Matches: 117, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
117 107 0.91
119 10 0.09
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (118 bp):
GTATTAAAGTATAGGAATTCAAAGAAGAAATATCGAGTCATGTTCAAATAACAATGATACTTAAA
AAAGATAAATGGCGGGTTTTTTACAAAAATAATATAAAAAAATAAAAAATTAC
Found at i:31332064 original size:28 final size:28
Alignment explanation
Indices: 31332028--31332098 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
31332018 AAATAAAAAA
*
31332028 TTACCAAAATGT-TATACATTTTTTTTAT
1 TTACCAAAATATATATA-ATTTTTTTTAT
31332056 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
31332084 TTACCAAAATATATA
1 TTACCAAAATATATA
31332099 AAAAAAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 37 0.90
29 4 0.10
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:31332110 original size:19 final size:18
Alignment explanation
Indices: 31332086--31332123 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31332076 TTTTTTATTT
*
31332086 ACCAAAATATATAAAAAAA
1 ACCAAAA-AAATAAAAAAA
31332105 ACCAAAAAAATAAAAAAA
1 ACCAAAAAAATAAAAAAA
31332123 A
1 A
31332124 AATCTGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCAAAAAAATAAAAAAA
Found at i:31332195 original size:27 final size:27
Alignment explanation
Indices: 31332165--31332232 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
31332155 AAGGGAACAC
31332165 TGTTGGCGGCACCAAACAAGGAAACCT
1 TGTTGGCGGCACCAAACAAGGAAACCT
**
31332192 TGTTGGCGGCACCAAACAAGGATTCCT
1 TGTTGGCGGCACCAAACAAGGAAACCT
31332219 TGTTGGCGGCACCA
1 TGTTGGCGGCACCA
31332233 CCTTAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (27 bp):
TGTTGGCGGCACCAAACAAGGAAACCT
Found at i:31332302 original size:18 final size:17
Alignment explanation
Indices: 31332279--31332356 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 17
31332269 GAAGGAGAGG
31332279 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
31332297 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
31332314 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
31332330 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
31332348 GGAAAGAAA
1 GG-AAGAAA
31332357 AGGAAANNNN
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
15 9 0.18
16 4 0.08
17 4 0.08
18 20 0.39
19 14 0.27
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:31332312 original size:10 final size:10
Alignment explanation
Indices: 31332281--31332352 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
31332271 AGGAGAGGGG
*
31332281 AAGAAGAAGA
1 AAGAAAAAGA
31332291 AAGAAAGGAAGA
1 AAGAAA--AAGA
31332303 AAGAAAAAGA
1 AAGAAAAAGA
* *
31332313 AGGAAAAGGA
1 AAGAAAAAGA
31332323 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
31332337 AAGAAAAAGA
1 AAGAAAAAGA
*
31332347 AGGAAA
1 AAGAAA
31332353 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:31332312 original size:22 final size:23
Alignment explanation
Indices: 31332281--31332362 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
31332271 AGGAGAGGGG
*
31332281 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
31332303 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
31332325 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
*
31332351 AAGAAAAGGAAA
1 AAGAAAAAGAAA
31332363 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 12 0.26
23 10 0.22
24 20 0.43
25 3 0.07
26 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:31332318 original size:14 final size:13
Alignment explanation
Indices: 31332284--31332357 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 13
31332274 AGAGGGGAAG
31332284 AAGAAGAAAG-AA
1 AAGAAGAAAGAAA
*
31332296 AGGAAGAAAGAAA
1 AAGAAGAAAGAAA
31332309 AAGAAGGAAAAGGAAA
1 AAGAA-G-AAA-GAAA
31332325 GGAGAGGAAAGAAAGAAA
1 --A-A-G-AAGAAAGAAA
31332343 AAGAAGGAAAGAAA
1 AAGAA-GAAAGAAA
31332357 A
1 A
31332358 GGAAANNNNN
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 11 0.22
15 4 0.08
16 5 0.10
18 5 0.10
19 4 0.08
20 2 0.04
21 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAA
Found at i:31332359 original size:10 final size:10
Alignment explanation
Indices: 31332301--31332362 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
31332291 AAGAAAGGAA
*
31332301 GAAAGAAAAA
1 GAAAGAAAAG
*
31332311 GAAGGAAAAG
1 GAAAGAAAAG
* *
31332321 GAAAGGAGAG
1 GAAAGAAAAG
31332331 GAAAG-AAA-
1 GAAAGAAAAG
31332339 GAAA-AAGAAG
1 GAAAGAA-AAG
31332349 GAAAGAAAAG
1 GAAAGAAAAG
31332359 GAAA
1 GAAA
31332363 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 5 0.12
9 4 0.10
10 31 0.74
11 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:31335102 original size:27 final size:27
Alignment explanation
Indices: 31335029--31335106 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
31335019 NNNNNNNNNN
** *
31335029 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTCTT
31335056 TGGTGCCGCCAACAGGGTTCCCTTCTT
1 TGGTGCCGCCAACAGGGTTCCCTTCTT
*
31335083 TGGTGCCGCCAACAGTGTTCCCTT
1 TGGTGCCGCCAACAGGGTTCCCTT
31335107 GACCCAGGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTCTT
Found at i:31335181 original size:22 final size:22
Alignment explanation
Indices: 31335156--31335200 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
31335146 GTTTTTTTTG
31335156 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
31335178 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
31335200 A
1 A
31335201 ATGTATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
ATATATTTTGGTAAATAAAAAA
Found at i:31335745 original size:28 final size:28
Alignment explanation
Indices: 31335692--31335745 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
31335682 CATCCCTGTG
* *
31335692 TATGCTATTATTAATTTTAATCTTATTT
1 TATGCTATTATTAATTCTAATATTATTT
*
31335720 TATGCTATT-TTAATTACTATTATTAT
1 TATGCTATTATTAATT-CTAATATTAT
31335746 ACTTATAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (28 bp):
TATGCTATTATTAATTCTAATATTATTT
Found at i:31336205 original size:115 final size:117
Alignment explanation
Indices: 31335995--31336226 Score: 328
Period size: 115 Copynumber: 2.0 Consensus size: 117
31335985 TTGATATCAT
** *
31335995 CATAAAATGCAAATTAGTTTAAAATTTTAAATATTTTTACTTTGATATTAAAATCATAGGCTTTC
1 CATAAAATGCAAATTAGTTTAAAATTTTAAATATTTTTACTTCAATATTAAAATCAAAGGCTTTC
* *
31336060 ATGAGTAAAAATTACAGGTCTTGAGCTTATTTAACTA-AAAAA-A-CATAAG
66 ATGAGTAAAAATTACAAGTCTTGAGATTATTTAACTACAAAAATAGCATAAG
* *
31336109 CATAAAATGTAAATTAGTTTAAAGTTTTAAAATATTTTTACTTCAATATTAAAATCAAAGGCTTT
1 CATAAAATGCAAATTAGTTTAAAATTTT-AAATATTTTTACTTCAATATTAAAATCAAAGGCTTT
* * *
31336174 CATGATTAAAAATTATAAGT-TGTGGGATTATTTAACTACAAAAATAGCATAAG
65 CATGAGTAAAAATTACAAGTCT-TGAGATTATTTAACTACAAAAATAGCATAAG
31336227 GACTAGTTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
114 27 0.26
115 64 0.62
116 5 0.05
117 1 0.01
118 6 0.06
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (117 bp):
CATAAAATGCAAATTAGTTTAAAATTTTAAATATTTTTACTTCAATATTAAAATCAAAGGCTTTC
ATGAGTAAAAATTACAAGTCTTGAGATTATTTAACTACAAAAATAGCATAAG
Found at i:31337407 original size:102 final size:103
Alignment explanation
Indices: 31337280--31337492 Score: 392
Period size: 102 Copynumber: 2.1 Consensus size: 103
31337270 GCACGGGGAT
31337280 ATTTATTCCTTTGGTCCTCCCCCTTTTATGCCCGATTTAATTTAGCCTTTTTTAAATATTTTAAT
1 ATTTATTCC-TTGGTCCTCCCCCTTTTATGCCCGATTTAATTTAGCCTTTTTTAAATATTTTAAT
31337345 TTTGACCCCAAAATTCTGTTTAATTTTGGTTTAGTCCCC
65 TTTGACCCCAAAATTCTGTTTAATTTTGGTTTAGTCCCC
31337384 ATTTATTCC-TGGTCCTCCCCCTTTTATGCCCGATTTAATTTAGCCTTTTTTAAATATTTTAATT
1 ATTTATTCCTTGGTCCTCCCCCTTTTATGCCCGATTTAATTTAGCCTTTTTTAAATATTTTAATT
**
31337448 TTGACCCCAAAATTCTGTTTAATTTTTTTTTAGTCCCC
66 TTGACCCCAAAATTCTGTTTAATTTTGGTTTAGTCCCC
31337486 ATTTATT
1 ATTTATT
31337493 ATTATTATTA
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 98 0.92
104 9 0.08
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.49
Consensus pattern (103 bp):
ATTTATTCCTTGGTCCTCCCCCTTTTATGCCCGATTTAATTTAGCCTTTTTTAAATATTTTAATT
TTGACCCCAAAATTCTGTTTAATTTTGGTTTAGTCCCC
Found at i:31337494 original size:3 final size:3
Alignment explanation
Indices: 31337488--31337522 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
31337478 TAGTCCCCAT
*
31337488 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31337523 CCTATAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31337527 original size:12 final size:12
Alignment explanation
Indices: 31337489--31337527 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
31337479 AGTCCCCATT
*
31337489 TATTATTATTAT
1 TATTATTATTAC
31337501 TATTATTATTAC
1 TATTATTATTAC
*
31337513 TATTATTATTCC
1 TATTATTATTAC
31337525 TAT
1 TAT
31337528 AGTCATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:31342925 original size:169 final size:170
Alignment explanation
Indices: 31342629--31342967 Score: 563
Period size: 169 Copynumber: 2.0 Consensus size: 170
31342619 TCTTCCGGGC
* *
31342629 CAATGCCACTCTTTTCAGTTTATCACGATTTTTTCATTGAAGTTGAAATTCTTTCTCTTCGAGTT
1 CAATGCCACTCTTTCCAGTTTATCACGATTTTTTCATTGAAGTTGAAATTCATTCTCTTCGAGTT
* * *
31342694 TTGACTGAGCTGAAGTAGGATAAAGATCCAATCCCGACACGATTAGTTGAACTTAATTGAAGAAA
66 TTGACTGAGCTGAAGTAGGATAAAGATCCAATCCCGACACGACTAGTTAAACCTAATTGAAGAAA
* *
31342759 AAGGCTAGAAACTATTCATCAGGGTCAGATGTACCAAGAA
131 AAGGCTAGAAACTATTCATCAAGGTCAGATATACCAAGAA
31342799 CAATGCCACTCTTTCCAGTTTATCACG-TTTTTTCATTGAAGTTGAAATTCATTCTCTTCGAGTT
1 CAATGCCACTCTTTCCAGTTTATCACGATTTTTTCATTGAAGTTGAAATTCATTCTCTTCGAGTT
* * * * *
31342863 TTGGCTGAGCTGAAGTAGGATGAAGATCCAATTCCGATACGACTAGTTAAACCTAGTTGAAGAAA
66 TTGACTGAGCTGAAGTAGGATAAAGATCCAATCCCGACACGACTAGTTAAACCTAATTGAAGAAA
31342928 AAGGCTAGAAACTATTCATCAAGGTCAGATATACCAAGAA
131 AAGGCTAGAAACTATTCATCAAGGTCAGATATACCAAGAA
31342968 ATGACTGATG
Statistics
Matches: 157, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
169 131 0.83
170 26 0.17
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (170 bp):
CAATGCCACTCTTTCCAGTTTATCACGATTTTTTCATTGAAGTTGAAATTCATTCTCTTCGAGTT
TTGACTGAGCTGAAGTAGGATAAAGATCCAATCCCGACACGACTAGTTAAACCTAATTGAAGAAA
AAGGCTAGAAACTATTCATCAAGGTCAGATATACCAAGAA
Found at i:31344601 original size:44 final size:44
Alignment explanation
Indices: 31344539--31344758 Score: 246
Period size: 45 Copynumber: 5.0 Consensus size: 44
31344529 AGCAGGTTGA
31344539 AAAG-AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * *** *
31344582 AAAGATACCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
*
31344627 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * *** * *
31344671 AAAGAGAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT-
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
* * *
31344715 AGAAGAAAATAGATCTTGTCTTCATGTACTAGTGTGAAGTAGAT
1 A-AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGAT
31344759 TAGATATAGC
Statistics
Matches: 143, Mismatches: 30, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
43 4 0.03
44 69 0.48
45 70 0.49
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (44 bp):
AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
Found at i:31344694 original size:89 final size:89
Alignment explanation
Indices: 31344543--31345048 Score: 460
Period size: 89 Copynumber: 5.7 Consensus size: 89
31344533 GGTTGAAAAG
*
31344543 AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCAT
1 AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCAT
*
31344608 ACTGGTGGTGAAGTAGATCGAAGA
66 ACTGGTGGCGAAGTAGATCGAAGA
*
31344632 AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAGAGCAGATCTTGTCTTCCCAT
1 AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCAT
*
31344697 ACTGGTGGCGAAGTAGATAGAAGA
66 ACTGGTGGCGAAGTAGATCGAAGA
* * * * * * *
31344721 AAATAGATCTTGTCTTCATGTACTAGTGTGAAGTAGATTAGATATAGCAGATCTTGCCTT-CC-T
1 AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCAT
****
31344784 ACATAAACAGCGAAGTAGATCGAAGA
66 AC-T-GGTGGCGAAGTAGATCGAAGA
*** * * ** ** * * ** ** * *
31344810 TGGCTGAT-TT-TACCTCATCGTGGTTACAGTGGAGTACATTGAAGCCAGTA-AT-TCTATC-TC
1 AAACAGATCTTGT-CTTCAT-GTACTGGC-GTGAAGTAGATCAAAGATAGCAGATCT-TGTCTTC
* * * *
31344870 CC-TGGGCAGCAGT-G-GAA-TAGATTGTAGA
62 CCAT--ACTG--GTGGCGAAGTAGATCGAAGA
***
31344898 TTTCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA-CTAGATCTTGTCTTCCCA
1 AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGC-AGATCTTGTCTTCCCA
*
31344962 TACTGGTGGCAAAGTAGATCGAAGA
65 TACTGGTGGCGAAGTAGATCGAAGA
*
31344987 AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGCCTTCC
1 AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCC
31345049 TGCATAGACA
Statistics
Matches: 325, Mismatches: 70, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
86 2 0.01
87 19 0.06
88 39 0.12
89 246 0.76
90 18 0.06
91 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (89 bp):
AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCAT
ACTGGTGGCGAAGTAGATCGAAGA
Found at i:31344773 original size:44 final size:44
Alignment explanation
Indices: 31344544--31344781 Score: 228
Period size: 44 Copynumber: 5.4 Consensus size: 44
31344534 GTTGAAAAGA
* *
31344544 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
1 AACAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAGAGAT
* *** *
31344588 ACCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGAA
1 AACAGATCTTGTCTTCATGTACTGGT-GTGAAGTAGATCAG-AGAT
* * *
31344633 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAG
1 AACAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAGAGAT
* *** * *
31344677 AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT-AGAAGAA
1 AACAGATCTTGTCTTCATGTACTGGT-GTGAAGTAGATCAG-AGAT
* * * *
31344722 AATAGATCTTGTCTTCATGTACTAGTGTGAAGTAGATTAGATAT
1 AACAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAGAGAT
* *
31344766 AGCAGATCTTGCCTTC
1 AACAGATCTTGTCTTC
31344782 CTACATAAAC
Statistics
Matches: 154, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
44 83 0.54
45 71 0.46
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (44 bp):
AACAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAGAGAT
Found at i:31344952 original size:44 final size:43
Alignment explanation
Indices: 31344901--31345047 Score: 179
Period size: 44 Copynumber: 3.3 Consensus size: 43
31344891 TTGTAGATTT
31344901 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
*** * * *
31344944 CTAGATCTTGTCTTCCCATACTGGTG-GCAAAGTAGATCGAAGAAAA
1 C-AGATCTTGTCTTCATGTACTGGCGTG--AAGTAGATCAAAG-ATA
31344990 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
*
31345033 GCAGATCTTGCCTTC
1 -CAGATCTTGTCTTC
31345048 CTGCATAGAC
Statistics
Matches: 85, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
43 4 0.05
44 45 0.53
45 32 0.38
46 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
Found at i:31345109 original size:266 final size:266
Alignment explanation
Indices: 31344634--31345174 Score: 863
Period size: 266 Copynumber: 2.0 Consensus size: 266
31344624 ATCGAAGAAA
31344634 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAGAGCAGATCTTGTCTTCCCATAC
1 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAGAGCAGATCTTGTCTTCCCATAC
* * * * * *
31344699 TGGTGGCGAAGTAGATAGAAGAAAATAGATCTTGTCTTCATGTACTAGTGTGAAGTAGATTAGAT
66 TGGTGGCAAAGTAGATAGAAGAAAACAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAG
* * *
31344764 ATAGCAGATCTTGCCTTCCTACATAAACAGCGAAGTAGATCGAAGATGGCTGATTTTACCTCATC
131 ATAGCAGATCTTGCCTTCCTACATAAACAGCGAAGCAGATCGAAGATGCCTAATTTTACCTCATC
* *
31344829 GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGC-AGCAGTGGAATAGATT
196 GAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCGA-CAGTGGAATAGAGT
*
31344893 GTAGATT
260 GAAGATT
* *
31344900 TCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA-CTAGATCTTGTCTTCCCATA
1 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAGAGC-AGATCTTGTCTTCCCATA
* *
31344964 CTGGTGGCAAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAA
65 CTGGTGGCAAAGTAGATAGAAGAAAACAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAA
* * *
31345029 GATAGCAGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGATGCCTAATTTTACCTC-C
130 GATAGCAGATCTTGCCTTCCTACATAAACAGCGAAGCAGATCGAAGATGCCTAATTTTACCTCAT
31345093 CTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCGACAGTGGAATAGAG
195 C-GAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCGACAGTGGAATAGAG
31345158 TGAAGATT
259 TGAAGATT
31345166 ACAGATCTT
1 ACAGATCTT
31345175 ATCTCCCTAA
Statistics
Matches: 252, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
265 2 0.01
266 249 0.99
267 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (266 bp):
ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAGAGCAGATCTTGTCTTCCCATAC
TGGTGGCAAAGTAGATAGAAGAAAACAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAG
ATAGCAGATCTTGCCTTCCTACATAAACAGCGAAGCAGATCGAAGATGCCTAATTTTACCTCATC
GAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCGACAGTGGAATAGAGTG
AAGATT
Found at i:31345348 original size:44 final size:44
Alignment explanation
Indices: 31345299--31345400 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 44
31345289 TTGAAGATGA
* * * *
31345299 CAGATCTTGTTTTCATGTATTGGCGTGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAATAGATCAAAGAAAG
* *
31345343 TAGATCTTGTCTTCATGTATTGGCATGAAATAGATCAAAGAGAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAATAGATCAAAGAAAG
*
31345387 CAGATCTTATCTTC
1 CAGATCTTGTCTTC
31345401 CCATACTGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (44 bp):
CAGATCTTGTCTTCATGTATTGGCATGAAATAGATCAAAGAAAG
Found at i:31346933 original size:12 final size:12
Alignment explanation
Indices: 31346900--31346933 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31346890 TAGTCCCCAT
*
31346900 TTATTATTATTA
1 TTATTACTATTA
31346912 TTATTACTATTA
1 TTATTACTATTA
*
31346924 TTATTCCTAT
1 TTATTACTAT
31346934 AGTCATTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTACTATTA
Found at i:31348421 original size:5 final size:5
Alignment explanation
Indices: 31348411--31348437 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
31348401 TTTATAACAT
31348411 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
31348438 TATATGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:31349313 original size:31 final size:31
Alignment explanation
Indices: 31349277--31349339 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
31349267 TGTCATTCAC
* *
31349277 CATCTATGACGAGTGTTTGTTATTATTTTCT
1 CATCTATGACGAGTCTTTATTATTATTTTCT
31349308 CATCTATGACGAGTCTTTATTATTATTTTCT
1 CATCTATGACGAGTCTTTATTATTATTTTCT
31349339 C
1 C
31349340 CCTAAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.51
Consensus pattern (31 bp):
CATCTATGACGAGTCTTTATTATTATTTTCT
Found at i:31349755 original size:25 final size:25
Alignment explanation
Indices: 31349727--31349782 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
31349717 AATTAAAATT
*
31349727 AAAATTAAATAGTAAAATTTAATAA
1 AAAATTAAATAGCAAAATTTAATAA
* * * *
31349752 AAAATCAAGTGGCAAAATTTAATAT
1 AAAATTAAATAGCAAAATTTAATAA
31349777 AAAATT
1 AAAATT
31349783 GAAGTGGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (25 bp):
AAAATTAAATAGCAAAATTTAATAA
Found at i:31352433 original size:167 final size:172
Alignment explanation
Indices: 31352157--31352492 Score: 610
Period size: 167 Copynumber: 2.0 Consensus size: 172
31352147 TGTTGCAAGT
*
31352157 CAGGTATTGTATTTAAGCATGTAAAAATTTAGTCCCTTAACAGGAGATTCATATTCTATGACCTC
1 CAGGTATTGTATTGAAGCATGTAAAAATTTAGTCCCTTAACAGGAGATTCATATTCTATGACCTC
*
31352222 CATAAATCTGTAAGAGCTAAAAGAAGCAAAGTAACCAATTCGAGCCTAATAAATAGCACTTTAAA
66 CATAAATCTGTAAGAGCTAAAAGAAGCAAAGTAACAAATTCGAGCCTAATAAATAGCACTTTAAA
31352287 T-AA-AT-A-TA-GGCTTATATTTACTATTAGTCCAATAAGG
131 TAAATATAAGTATGGCTTATATTTACTATTAGTCCAATAAGG
31352324 CAGGTATTGTATTGAAGCATGTAAAAATTTAGTCCCTTAACAGGAGATTCATATTCTATGACCTC
1 CAGGTATTGTATTGAAGCATGTAAAAATTTAGTCCCTTAACAGGAGATTCATATTCTATGACCTC
31352389 CATAAATCTGTAAGAGCTAAAAGAAGCAAAGTAACAAATTCGAGCCTAATAAATAGCACTTTAAA
66 CATAAATCTGTAAGAGCTAAAAGAAGCAAAGTAACAAATTCGAGCCTAATAAATAGCACTTTAAA
31352454 TAAATATAATGTATGGCTTATATTTACTATTAGTCCAAT
131 TAAATATAA-GTATGGCTTATATTTACTATTAGTCCAAT
31352493 TTCAAAGCTA
Statistics
Matches: 161, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
167 129 0.80
168 2 0.01
169 2 0.01
170 1 0.01
172 2 0.01
173 25 0.16
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (172 bp):
CAGGTATTGTATTGAAGCATGTAAAAATTTAGTCCCTTAACAGGAGATTCATATTCTATGACCTC
CATAAATCTGTAAGAGCTAAAAGAAGCAAAGTAACAAATTCGAGCCTAATAAATAGCACTTTAAA
TAAATATAAGTATGGCTTATATTTACTATTAGTCCAATAAGG
Found at i:31368438 original size:57 final size:59
Alignment explanation
Indices: 31368323--31368469 Score: 201
Period size: 57 Copynumber: 2.5 Consensus size: 59
31368313 ATTGACGATA
31368323 AAAAAGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAAGATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
*
31368385 AAAAAGATCTAGTCCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* * *
31368441 AAAATGGATTTAGCCCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
31368470 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
56 5 0.06
57 45 0.58
58 1 0.01
59 1 0.01
61 1 0.01
62 25 0.32
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Done.