Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 170 of 356
Found at i:55124542 original size:53 final size:53
Alignment explanation
Indices: 55124484--55124591 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
55124474 TTGGTAATAG
55124484 TTGTAAATGAACATGGGTTATAAAACTTGAATGATTTATCAAAACGACTCTGT
1 TTGTAAATGAACATGGGTTATAAAACTTGAATGATTTATCAAAACGACTCTGT
55124537 TTGTAAATGAACATGGGTTATAAAACTTGAATGATTTATCAAAACGACTCTGT
1 TTGTAAATGAACATGGGTTATAAAACTTGAATGATTTATCAAAACGACTCTGT
55124590 TT
1 TT
55124592 TCAAAACCTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (53 bp):
TTGTAAATGAACATGGGTTATAAAACTTGAATGATTTATCAAAACGACTCTGT
Found at i:55127479 original size:5 final size:5
Alignment explanation
Indices: 55127469--55127500 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
55127459 GATGCCAACC
55127469 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
55127501 TTTATTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:55127776 original size:28 final size:28
Alignment explanation
Indices: 55127736--55127789 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
55127726 TAACATAGTC
55127736 CAAATTCGTACTAATAGACACTTATATT
1 CAAATTCGTACTAATAGACACTTATATT
55127764 CAAATTCGTACTAATAGACACTTATA
1 CAAATTCGTACTAATAGACACTTATA
55127790 CCTTTTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (28 bp):
CAAATTCGTACTAATAGACACTTATATT
Found at i:55131419 original size:15 final size:15
Alignment explanation
Indices: 55131399--55131433 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55131389 AAAGGCAAAT
*
55131399 GAAATCCTTTGTTTG
1 GAAATCCATTGTTTG
55131414 GAAATCCATTGTTTG
1 GAAATCCATTGTTTG
*
55131429 CAAAT
1 GAAAT
55131434 TTGACATCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (15 bp):
GAAATCCATTGTTTG
Found at i:55138035 original size:130 final size:130
Alignment explanation
Indices: 55137803--55138190 Score: 494
Period size: 130 Copynumber: 3.0 Consensus size: 130
55137793 CATGTGAAAT
* * *
55137803 AACTCACTGATTTACGATCACGATTGATATTATCAAGGCTCGTTGA-TTACGATCACAGCCTAAG
1 AACTCACTGATTTACGATCACGATTGATATTATTAAGGCTCGTTGATTTACAATCACAACCTAAG
* * * *
55137867 TTCAGTGATTTACGATCATAAACAATTTCTTTTGAGTTAGCTAATTTACGATCGCAACTCCAAAC
66 TTCATTGATTTACGATCATGAACAATTTCTTTTGAGTTAGTTGATTTACGATCGCAACTCCAAAC
* * * *
55137932 AACTCACTGATTTATGATCACGACTGATATTATTAAAGCGT-GTTGATTTACAATCACACCCTAA
1 AACTCACTGATTTACGATCACGATTGATATTATTAAGGC-TCGTTGATTTACAATCACAACCTAA
* *
55137996 GTTCATTAATTTACGATCATGAACAATTTCTTTTGAGTTAGTTGATTTACGATCACAACTCCAAA
65 GTTCATTGATTTACGATCATGAACAATTTCTTTTGAGTTAGTTGATTTACGATCGCAACTCCAAA
55138061 C
130 C
*** * * * * *
55138062 AACTTGTTAATTTACGATCATTG-TTGATATTATTAAGGCTCGTTGGTTTAGAGTCACAACCTAA
1 AACTCACTGATTTACGATCA-CGATTGATATTATTAAGGCTCGTTGATTTACAATCACAACCTAA
* * * * * *
55138126 GTTTATTGATTTATGATCATGAACAATTTCTTTTAAGTTTGTTGATTTATGATTGCAACTCCAAA
65 GTTCATTGATTTACGATCATGAACAATTTCTTTTGAGTTAGTTGATTTACGATCGCAACTCCAAA
55138191 TAGCTTGCTG
Statistics
Matches: 223, Mismatches: 32, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
129 41 0.18
130 181 0.81
131 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (130 bp):
AACTCACTGATTTACGATCACGATTGATATTATTAAGGCTCGTTGATTTACAATCACAACCTAAG
TTCATTGATTTACGATCATGAACAATTTCTTTTGAGTTAGTTGATTTACGATCGCAACTCCAAAC
Found at i:55138514 original size:130 final size:130
Alignment explanation
Indices: 55138292--55138624 Score: 402
Period size: 130 Copynumber: 2.6 Consensus size: 130
55138282 TGATTGCAAT
* * * *
55138292 TGATATTATTAAGACTCGCTGATTTATGATCACAGCCTAAGTTCATTGATTTACGATCATGAAAA
1 TGATATTATTAAGACTCGCTAATTTACGATCACAACCTAAGTTCATTGATTTACGATCATGAACA
* * * * ** *
55138357 ATTTCTTCTAAGTTAGCTGATTTATGAT-AGCAACTCCAAACAACTGGCTGACTTATGATTAC-G
66 ATTTCTTCCAAGTAAGCTAATTTATGATCA-CAACTCCAAACAAATGGCTGACTTACAATCACAG
55138420 AC
130 -C
*
55138422 TGATATTATTGAGACTCGCTAATTTACGATCACAACCTAAGTTCATTGATTTACGATCATGAACA
1 TGATATTATTAAGACTCGCTAATTTACGATCACAACCTAAGTTCATTGATTTACGATCATGAACA
* * * * * * *
55138487 ATTTCTTCCGAGTAAGTTAATTTATGATCACAACTTCAAACAAATTGTTGATTTACAATCACAGT
66 ATTTCTTCCAAGTAAGCTAATTTATGATCACAACTCCAAACAAATGGCTGACTTACAATCACAGC
* * * * *
55138552 TGTTATTATTAAGGCTCGCTAATTTACGATCACAA-TTAAGTTCATTGATTTACAATCATGGACA
1 TGATATTATTAAGACTCGCTAATTTACGATCACAACCTAAGTTCATTGATTTACGATCATGAACA
*
55138616 ATTTATTCC
66 ATTTCTTCC
55138625 CAAATTCAAA
Statistics
Matches: 175, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
129 34 0.19
130 139 0.79
131 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (130 bp):
TGATATTATTAAGACTCGCTAATTTACGATCACAACCTAAGTTCATTGATTTACGATCATGAACA
ATTTCTTCCAAGTAAGCTAATTTATGATCACAACTCCAAACAAATGGCTGACTTACAATCACAGC
Found at i:55142739 original size:6 final size:6
Alignment explanation
Indices: 55142728--55142757 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
55142718 TGCTAGTTTC
55142728 CATTTT CATTTT CATTTT CATTTT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
55142758 TGGAAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
CATTTT
Found at i:55145440 original size:25 final size:25
Alignment explanation
Indices: 55145412--55145481 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
55145402 TTTAAATAAT
55145412 TGGGGCAAAGCCCTTTTCCATAAAC
1 TGGGGCAAAGCCCTTTTCCATAAAC
**
55145437 TGGGGCAAAGCCCTTTTCGGTAAAC
1 TGGGGCAAAGCCCTTTTCCATAAAC
* * *
55145462 TAGGGTAAAGCCTTTTTCCA
1 TGGGGCAAAGCCCTTTTCCA
55145482 CATTTCCTCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (25 bp):
TGGGGCAAAGCCCTTTTCCATAAAC
Found at i:55145551 original size:21 final size:21
Alignment explanation
Indices: 55145527--55145596 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
55145517 TATAGTGAAT
* *
55145527 ATATCATAGCATATCATGTTC
1 ATATCATAACATATCATGTGC
*
55145548 ATATCATAATATATCATGTGC
1 ATATCATAACATATCATGTGC
55145569 ATATCATAACATATCATGTGC
1 ATATCATAACATATCATGTGC
55145590 ATATCAT
1 ATATCAT
55145597 GTCATATTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (21 bp):
ATATCATAACATATCATGTGC
Found at i:55145554 original size:5 final size:5
Alignment explanation
Indices: 55145527--55145603 Score: 57
Period size: 5 Copynumber: 14.8 Consensus size: 5
55145517 TATAGTGAAT
* * *
55145527 ATATC ATAGC ATATC ATGTTC ATATC ATAAT- ATATC ATGTGC ATATC
1 ATATC ATATC ATATC AT-ATC ATATC AT-ATC ATATC ATAT-C ATATC
* * *
55145574 ATAAC ATATC ATGTGC ATATC ATGTC ATAT
1 ATATC ATATC ATAT-C ATATC ATATC ATAT
55145604 TATGTATATC
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
4 2 0.04
5 39 0.71
6 14 0.25
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (5 bp):
ATATC
Found at i:55145582 original size:31 final size:31
Alignment explanation
Indices: 55145524--55145585 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
55145514 GCATATAGTG
**
55145524 AATATATCATAGCATATCATGTTCATATCAT
1 AATATATCATAGCATATCATGAACATATCAT
*
55145555 AATATATCATGTGCATATCAT-AACATATCAT
1 AATATATCAT-AGCATATCATGAACATATCAT
55145586 GTGCATATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (31 bp):
AATATATCATAGCATATCATGAACATATCAT
Found at i:55154129 original size:27 final size:27
Alignment explanation
Indices: 55154099--55154586 Score: 575
Period size: 27 Copynumber: 18.1 Consensus size: 27
55154089 ACACCCTAAA
* *
55154099 GGTAAAATGGTAATTTTATAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
** *
55154126 GGTAAAACGGTAATTTTGTAAATC-AA
1 GGTAAAATAGTAATTTTGTAAATCGAG
* *
55154152 TGTAAAATAGTAATTTTGTAAATCAAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
** * *
55154179 GGTAAAACGGTAA-TTTATCAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
*
55154205 GGTAAAATAATAATTTTGTAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* *
55154232 GGTAAAATGGTAATTCTGTAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* *
55154259 GGTAAAACAGTAATTTTATAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* * *
55154286 GGTAAAATAGTAATTCTATAAATCAAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* ** *
55154313 GGTAAAACAGTAATCCTGTCAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* * *
55154340 GGTAAAATGGTAATTCTATAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
*
55154367 GGTAAAACAGTAATTTTGTAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* *
55154394 GGTAAAATAGTAACTCTGTAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* *
55154421 GGTAAAATAGTAATTCTATAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* *
55154448 GGTAAAACAGTAATTTTGTAAATCAAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* *
55154475 GGTAAAATGGTAATTTTGTAAATTGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* *
55154502 GGTAAAACAGTAATTCTGTAAATCGAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* * *
55154529 GGTAAAATAGTAATTCTGTATATCAAG
1 GGTAAAATAGTAATTTTGTAAATCGAG
* * *
55154556 GGTAAAATGGTAATTCTGTAAATCGGG
1 GGTAAAATAGTAATTTTGTAAATCGAG
55154583 GGTA
1 GGTA
55154587 CTTTGGTAAT
Statistics
Matches: 393, Mismatches: 66, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 42 0.11
27 351 0.89
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (27 bp):
GGTAAAATAGTAATTTTGTAAATCGAG
Found at i:55154596 original size:81 final size:81
Alignment explanation
Indices: 55154099--55154613 Score: 656
Period size: 81 Copynumber: 6.4 Consensus size: 81
55154089 ACACCCTAAA
* * *
55154099 GGTAAAATGGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCAA-TGTAAAATAGT
1 GGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATAGT
* *
55154163 AATTTTGTAAATCAAG
66 AATTCTGTAAATCGAG
* * * * * *
55154179 GGTAAAACGGTAATT-TATCAATCGAGGGTAAAATAATAATTTTGTAAATCGAGGGTAAAATGGT
1 GGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATAGT
55154243 AATTCTGTAAATCGAG
66 AATTCTGTAAATCGAG
** * * * * *
55154259 GGTAAAACAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACAGT
1 GGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATAGT
* *
55154324 AATCCTGTCAATCGAG
66 AATTCTGTAAATCGAG
*
55154340 GGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAATAGT
1 GGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATAGT
*
55154405 AACTCTGTAAATCGAG
66 AATTCTGTAAATCGAG
* *
55154421 GGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATGGT
1 GGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATAGT
* *
55154486 AATTTTGTAAATTGAG
66 AATTCTGTAAATCGAG
** * * * * *
55154502 GGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTATATCAAGGGTAAAATGGT
1 GGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATAGT
*
55154567 AATTCTGTAAATCGGG
66 AATTCTGTAAATCGAG
*** * * *
55154583 GGTACTTTGGTAATTTTACAAGTCGAGGGTA
1 GGTAAAATGGTAATTCTATAAATCGAGGGTA
55154614 TTTTAGTAAT
Statistics
Matches: 379, Mismatches: 54, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
79 32 0.08
80 51 0.13
81 296 0.78
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (81 bp):
GGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATAGT
AATTCTGTAAATCGAG
Found at i:55154612 original size:27 final size:27
Alignment explanation
Indices: 55154582--55154705 Score: 112
Period size: 27 Copynumber: 4.6 Consensus size: 27
55154572 TGTAAATCGG
*
55154582 GGGTACTTTGGTAATTTTACAAGTC-GA
1 GGGTATTTTGGTAATTTTACAA-TCTGA
* *
55154609 GGGTATTTTAGTAATTTCACAAATCTGA
1 GGGTATTTTGGTAATTTTAC-AATCTGA
* * *
55154637 -GGTATTTTGGTAACTTTACAAACTAA
1 GGGTATTTTGGTAATTTTACAATCTGA
*
55154663 GGGTATGTTGGTAATTTTACAA-CT-A
1 GGGTATTTTGGTAATTTTACAATCTGA
**
55154688 GGGGTATTTCAGTAATTT
1 -GGGTATTTTGGTAATTT
55154706 GGTAAACTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
25 1 0.01
26 21 0.26
27 54 0.68
28 4 0.05
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAATCTGA
Found at i:55158210 original size:39 final size:39
Alignment explanation
Indices: 55158156--55158234 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
55158146 GTTTTCATGA
*
55158156 TAAAATGCTCAACTTGGAATGTTTGAAACTTTGATGTTC
1 TAAAATGCTCAACTTGGAATGTTTGAAACTTTGATATTC
55158195 TAAAATGCTCAACTTGGAATGTTTGAAACTTTGATATTC
1 TAAAATGCTCAACTTGGAATGTTTGAAACTTTGATATTC
55158234 T
1 T
55158235 TTCAGTTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (39 bp):
TAAAATGCTCAACTTGGAATGTTTGAAACTTTGATATTC
Found at i:55174743 original size:26 final size:25
Alignment explanation
Indices: 55174701--55174757 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
55174691 ACACACTGCA
* *
55174701 GCTCTTATGAGCATCCTG-TTATATG
1 GCTCTTACGAGCATCCTGATTA-AAG
*
55174726 GCTCTTCACGAGCTTCCTGATTAAAG
1 GCTCTT-ACGAGCATCCTGATTAAAG
55174752 GCTCTT
1 GCTCTT
55174758 TGTGAGCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 18 0.67
27 3 0.11
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (25 bp):
GCTCTTACGAGCATCCTGATTAAAG
Found at i:55174886 original size:24 final size:24
Alignment explanation
Indices: 55174834--55174920 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 24
55174824 TGGCTATCTG
* *
55174834 GAGCTTCCCGATTAATGGCTCTTCA-
1 GAGCTTCCCG-TTATTGGCTC-GCAT
*
55174859 GAGCTACCCGTTATTGGCTCGCAT
1 GAGCTTCCCGTTATTGGCTCGCAT
* **
55174883 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCGCAT
55174907 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
55174921 ATAGCCTGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
23 5 0.10
24 34 0.67
25 12 0.24
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGCAT
Found at i:55174900 original size:73 final size:73
Alignment explanation
Indices: 55174721--55174916 Score: 166
Period size: 73 Copynumber: 2.7 Consensus size: 73
55174711 GCATCCTGTT
* * * * * * *
55174721 ATATGGCTCTTCACGAGCTTCCTGATTAAAGGCTCTTTGTGAGCTTCCTGACTAATGGCTCTGAG
1 ATATGGCTC-GCATGAGCTTCCTGATT-ATGGCTATCTGTGAGCTTCCCGACTAATGGCTCTCAG
*
55174786 GAGCTTCCCA
64 GAGCTACCCA
* * * *
55174796 ATATGGCTCGCTTGAACTT-CTAGATACATGGCTATCTG-GAGCTTCCCGATTAATGGCTCTTCA
1 ATATGGCTCGCATGAGCTTCCT-GAT-TATGGCTATCTGTGAGCTTCCCGACTAATGGCTC-TCA
*
55174859 -GAGCTACCCG
63 GGAGCTACCCA
* * *
55174869 TTATTGGCTCGCATGAGCTTCCTGATTATGGCTCT-TATGAGCTTCCCG
1 ATA-TGGCTCGCATGAGCTTCCTGATTATGGCTATCTGTGAGCTTCCCG
55174917 TTATATAGCC
Statistics
Matches: 96, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
72 1 0.01
73 48 0.50
74 36 0.38
75 11 0.11
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (73 bp):
ATATGGCTCGCATGAGCTTCCTGATTATGGCTATCTGTGAGCTTCCCGACTAATGGCTCTCAGGA
GCTACCCA
Found at i:55174937 original size:49 final size:49
Alignment explanation
Indices: 55174835--55174938 Score: 115
Period size: 48 Copynumber: 2.1 Consensus size: 49
55174825 GGCTATCTGG
* *
55174835 AGCTTCCCGATTAATGGCTCTTCAGAGCTACCCGTTATTGGCTCGCATG
1 AGCTTCCCGATTAATGGCTCTTCAGAGCTACCCGTTATTGCCTCGCATA
* * *
55174884 AGCTTCCTGATT-ATGGCTCTT-ATGAGCTTCCCGTTATATAGCCT-GGATA
1 AGCTTCCCGATTAATGGCTCTTCA-GAGCTACCCGTTAT-T-GCCTCGCATA
55174933 AGCTTC
1 AGCTTC
55174939 TAGTTATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
47 1 0.02
48 22 0.47
49 21 0.45
50 3 0.06
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (49 bp):
AGCTTCCCGATTAATGGCTCTTCAGAGCTACCCGTTATTGCCTCGCATA
Found at i:55174938 original size:25 final size:25
Alignment explanation
Indices: 55174908--55174972 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
55174898 GGCTCTTATG
* **
55174908 AGCTTCCCGTTATATAGC-CTGGATA
1 AGCTTCCAGTTATATAGCTC-ACATA
*
55174933 AGCTTCTAGTTATATAGCTCACATA
1 AGCTTCCAGTTATATAGCTCACATA
*
55174958 AGCTTCCTGTTATAT
1 AGCTTCCAGTTATAT
55174973 GGCTTGAGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (25 bp):
AGCTTCCAGTTATATAGCTCACATA
Found at i:55180199 original size:9 final size:10
Alignment explanation
Indices: 55180174--55180198 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55180164 CTTAATTTAC
55180174 TTTTTTATTT
1 TTTTTTATTT
55180184 TTTTTTATTT
1 TTTTTTATTT
55180194 TTTTT
1 TTTTT
55180199 ACAATTACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:55192474 original size:39 final size:40
Alignment explanation
Indices: 55192373--55192636 Score: 310
Period size: 40 Copynumber: 6.7 Consensus size: 40
55192363 TTGAATGATG
* *
55192373 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
55192412 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
55192453 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
55192492 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* ** *
55192531 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGATTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
55192571 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
55192610 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
55192637 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 13, Indels: 16
0.88 0.06 0.07
Matches are distributed among these distances:
39 75 0.37
40 115 0.57
41 12 0.06
42 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:55200638 original size:40 final size:40
Alignment explanation
Indices: 55200400--55200624 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
55200390 TTGAATGATG
* * * *
55200400 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
55200440 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
55200480 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55200519 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
55200559 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
55200600 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55200625 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
39 35 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:55200646 original size:119 final size:119
Alignment explanation
Indices: 55200400--55200657 Score: 285
Period size: 119 Copynumber: 2.2 Consensus size: 119
55200390 TTGAATGATG
* *
55200400 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
55200465 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAA
* * * **
55200519 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
55200582 TTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAA
* *
55200639 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
55200658 TACGTGATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
118 4 0.03
119 82 0.69
120 32 0.27
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAA
Found at i:55214899 original size:28 final size:28
Alignment explanation
Indices: 55214834--55215015 Score: 312
Period size: 28 Copynumber: 6.5 Consensus size: 28
55214824 ATATTAAGTC
* *
55214834 CGCACACTCAGTGTTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
55214861 CGCACACTTAGTGCTATATAATCAACCT
1 CGCACACTTAGTGCTATATAATCAAACT
*
55214889 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
55214917 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
55214945 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
55214973 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
55215001 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55215016 GTACAATTTA
Statistics
Matches: 146, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
27 21 0.14
28 125 0.86
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55220361 original size:37 final size:37
Alignment explanation
Indices: 55220302--55220440 Score: 206
Period size: 37 Copynumber: 3.8 Consensus size: 37
55220292 AGCTCGGACG
* * *
55220302 AAATCTCTACACGAAGTTATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
* **
55220339 AAATCTCCACACGTAGTCATCGGGTCTTACTCGGGCA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
55220376 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
* *
55220413 TACTCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
55220441 TAGAGCTCGG
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 91 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
Found at i:55220388 original size:74 final size:74
Alignment explanation
Indices: 55220302--55220440 Score: 233
Period size: 74 Copynumber: 1.9 Consensus size: 74
55220292 AGCTCGGACG
* *
55220302 AAATCTCTACACGAAGTTATCGGGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTT
55220367 ACTCGGGCA
66 ACTCGGGCA
* * *
55220376 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACATACTCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTT
55220441 TAGAGCTCGG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (74 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTT
ACTCGGGCA
Found at i:55220637 original size:47 final size:47
Alignment explanation
Indices: 55220559--55221062 Score: 814
Period size: 47 Copynumber: 10.6 Consensus size: 47
55220549 CCCTTCGGGA
* * * * *
55220559 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
* *
55220606 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55220653 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55220700 CTTATCACATATATATACACTTTCACATTCATCACA-CTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATC-GGCCATTAGGC
55220749 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55220796 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55220843 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55220890 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
55220937 CTTATCACATATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55220986 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55221033 CTTATCACATATATACACTTTCACCTTCAT
1 CTTATCACATATATACACTTTCACATTCAT
55221063 TCAAATATAC
Statistics
Matches: 428, Mismatches: 22, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
46 2 0.00
47 336 0.79
48 2 0.00
49 88 0.21
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55220885 original size:190 final size:188
Alignment explanation
Indices: 55220559--55221056 Score: 820
Period size: 190 Copynumber: 2.6 Consensus size: 188
55220549 CCCTTCGGGA
* * * * * *
55220559 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCA-GCCCTGTCACATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCA-TTAGGCCTTATCACATATATACA
*
55220623 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
65 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATCCATCACAT
*
55220688 CGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA-CTGGCCATTCGGC
130 CGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATC-GGCCATTAGGC
*
55220749 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
*
55220814 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATCCATCACATT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATCCATCACATC
55220879 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55220937 CTTATCACATATATATACACATTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
55221002 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
55221057 CTTCATTCAA
Statistics
Matches: 291, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
188 44 0.15
189 3 0.01
190 244 0.84
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATCCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55220980 original size:237 final size:237
Alignment explanation
Indices: 55220559--55221062 Score: 884
Period size: 237 Copynumber: 2.1 Consensus size: 237
55220549 CCCTTCGGGA
* * * * *
55220559 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCAGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTCAGCCCTATCACATATATACAC
*
55220624 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
55220689 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACACTGGCCATTCGGCCTTAT
131 GGCCATTAGGCCTTATCACATATATATACACATTCACATTCATCACACTGGCCATTCGGCCTTAT
55220754 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
196 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55220796 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCTTATCACATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTCA-GCCCTATCACATATATACA
*
55220860 CTTTCACATCCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
65 CTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
*
55220925 CGGCCATTAGGCCTTATCACATATATATACACATTCACATTCATCACATTGGCCATTCGGCCTTA
130 CGGCCATTAGGCCTTATCACATATATATACACATTCACATTCATCACACTGGCCATTCGGCCTTA
55220990 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
195 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55221033 CTTATCACATATATACACTTTCACCTTCAT
1 CTTATCACATATATACACTTTCACATTCAT
55221063 TCAAATATAC
Statistics
Matches: 254, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
236 2 0.01
237 252 0.99
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (237 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTCAGCCCTATCACATATATACAC
TTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATATACACATTCACATTCATCACACTGGCCATTCGGCCTTAT
CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55223403 original size:84 final size:84
Alignment explanation
Indices: 55223254--55223430 Score: 320
Period size: 84 Copynumber: 2.1 Consensus size: 84
55223244 TATTTTATTG
*
55223254 CCCATGCCCTTTATTTTATTAATCCTTAATAATGCACTACCCCAACATGTTTATGACATGTTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTAATAATGCACTACCCCAACATGTTTATGACATGTTTTT
55223319 AGCCATAACATCTTGTCCA
66 AGCCATAACATCTTGTCCA
*
55223338 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCTCAACATGTTTATGACATG-TTT
1 CCCATGCTCTTTATTTTATTAATCCTTA-ATAATGCACTACCCCAACATGTTTATGACATGTTTT
55223402 TAGCCATAACATCTTGTCCA
65 TAGCCATAACATCTTGTCCA
55223422 CCCATGCTC
1 CCCATGCTC
55223431 ATGGCCGGCC
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
84 59 0.66
85 31 0.34
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (84 bp):
CCCATGCTCTTTATTTTATTAATCCTTAATAATGCACTACCCCAACATGTTTATGACATGTTTTT
AGCCATAACATCTTGTCCA
Found at i:55229302 original size:46 final size:46
Alignment explanation
Indices: 55229252--55229424 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 46
55229242 TTGAGCATCC
*
55229252 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCT
1 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCT
* * * * * *
55229298 GAACTCGTTCAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTTGGCATT
1 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA--T-GC-CT
* * *
55229344 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 -GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCT
* *
55229391 GAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGG
55229425 GCGGGTTACA
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 3 0.03
46 56 0.55
47 25 0.25
48 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCT
Found at i:55229410 original size:93 final size:93
Alignment explanation
Indices: 55229246--55229417 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
55229236 GGATGGTTGA
* * * *
55229246 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTCAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTCAGT
55229311 TGAGTCCGAGTTCGTGAGATGTAACTTG
66 TGAGTCCGAGTTCGTGAGATGTAACTTG
* * * *
55229339 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTCAGT
55229404 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
55229418 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTCAGT
TGAGTCCGAGTTCGTGAGATGTAACTTG
Found at i:55237120 original size:40 final size:40
Alignment explanation
Indices: 55237015--55237158 Score: 177
Period size: 40 Copynumber: 3.6 Consensus size: 40
55237005 GCTACTCGTT
*
55237015 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
55237055 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
55237095 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
55237136 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
55237159 ACATCATTCG
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
39 3 0.03
40 75 0.82
41 13 0.14
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:55241775 original size:43 final size:44
Alignment explanation
Indices: 55241714--55241806 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
55241704 TCCTAATTGG
55241714 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
55241757 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
55241801 -AAAATA
1 GAAAATA
55241807 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:55241853 original size:19 final size:18
Alignment explanation
Indices: 55241829--55241868 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
55241819 GAATTAAAAC
55241829 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
*
55241848 TTATCTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
55241866 TTA
1 TTA
55241869 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:55243642 original size:8 final size:8
Alignment explanation
Indices: 55243629--55243657 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
55243619 GTTAGTTCTT
55243629 TTATTTTA
1 TTATTTTA
55243637 TTATTTTA
1 TTATTTTA
55243645 TTATTTTA
1 TTATTTTA
55243653 TTATT
1 TTATT
55243658 ATTAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTTTA
Found at i:55243667 original size:16 final size:16
Alignment explanation
Indices: 55243630--55243667 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55243620 TTAGTTCTTT
*
55243630 TATTTTATTATTTTAT
1 TATTTTATTATTTTAA
55243646 TATTTTATTATTATTAA
1 TATTTTATTATT-TTAA
55243663 T-TTTT
1 TATTTT
55243668 GTTGTGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTATTATTTTAA
Found at i:55247476 original size:40 final size:40
Alignment explanation
Indices: 55247421--55247657 Score: 384
Period size: 40 Copynumber: 5.9 Consensus size: 40
55247411 GCATGAGCAT
55247421 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
55247461 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
55247501 TTGATATATCCGGGCTAAAACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * * *
55247541 TTGATATATCTGGGCTAAGACCCGAAGGCAATTATGCAAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
55247581 TTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * * *
55247621 TTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
55247658 TTGCGGTTAT
Statistics
Matches: 181, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 181 1.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
Found at i:55260045 original size:46 final size:46
Alignment explanation
Indices: 55259995--55260161 Score: 160
Period size: 46 Copynumber: 3.6 Consensus size: 46
55259985 GAGCATCGAA
* *
55259995 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAG
* * * * * * *
55260041 CTCGTTGAGTTGAGTTCGGGTTC-GTGA--GATGTAACTAGGCATCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCCGAG
* * * *
55260088 CCCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAG
55260134 CTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTA
55260162 GGGGCGGGTT
Statistics
Matches: 93, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 51 0.55
47 25 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAG
Found at i:55269009 original size:43 final size:42
Alignment explanation
Indices: 55268962--55269123 Score: 148
Period size: 43 Copynumber: 3.8 Consensus size: 42
55268952 ATCGAGATGT
* *
55268962 GATTATATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTA-TGA
** *
55269005 GATTACATGTAAGACCATGTCTGAAACATTGGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-T-ATGA
* * * * * * *
55269048 GCTTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATGA
* * *
55269090 GATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAT
55269124 TGTACGAGCT
Statistics
Matches: 95, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 8 0.08
42 22 0.23
43 62 0.65
44 2 0.02
45 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATGA
Found at i:55275006 original size:33 final size:33
Alignment explanation
Indices: 55274968--55275038 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
55274958 TATTAGTAAT
* *
55274968 TATTATTTACTTAT-AATAT-AAGTAAATATATTA
1 TATTA-TTA-TTATAAATATAAAATAAATAAATTA
55275001 TATTATTATTATAAATATAAAATAAATAAATTA
1 TATTATTATTATAAATATAAAATAAATAAATTA
*
55275034 AATTA
1 TATTA
55275039 ATACAATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 4 0.12
32 8 0.24
33 21 0.64
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (33 bp):
TATTATTATTATAAATATAAAATAAATAAATTA
Found at i:55275136 original size:4 final size:4
Alignment explanation
Indices: 55275127--55275154 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
55275117 AGCATTTAAG
55275127 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
55275155 TATTATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:55275163 original size:5 final size:5
Alignment explanation
Indices: 55275153--55275184 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
55275143 AATAAATAAA
55275153 TATAT TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TA
55275185 GTTTAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:55275305 original size:16 final size:17
Alignment explanation
Indices: 55275269--55275305 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
55275259 GGGGAAGGAA
55275269 AGAAAGAAATAAAAAGG
1 AGAAAGAAATAAAAAGG
*
55275286 -GAAAGAAA-AAGAAGG
1 AGAAAGAAATAAAAAGG
55275301 AGAAA
1 AGAAA
55275306 TTAGGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (17 bp):
AGAAAGAAATAAAAAGG
Found at i:55276875 original size:15 final size:15
Alignment explanation
Indices: 55276855--55276883 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55276845 ATGCCTCACA
55276855 CAACGTGTTATCAAT
1 CAACGTGTTATCAAT
55276870 CAACGTGTTATCAA
1 CAACGTGTTATCAA
55276884 GCAATAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (15 bp):
CAACGTGTTATCAAT
Found at i:55277699 original size:40 final size:40
Alignment explanation
Indices: 55277654--55277734 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
55277644 AGGCTAAATG
55277654 GACAATTGAACCATGGAAAATTAGTTAGTGGGTTTGATGA
1 GACAATTGAACCATGGAAAATTAGTTAGTGGGTTTGATGA
55277694 GACAATTGAACCATGGAAAATTAGTTAGTGGGTTTGATGA
1 GACAATTGAACCATGGAAAATTAGTTAGTGGGTTTGATGA
55277734 G
1 G
55277735 GTTATGTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (40 bp):
GACAATTGAACCATGGAAAATTAGTTAGTGGGTTTGATGA
Found at i:55292910 original size:27 final size:27
Alignment explanation
Indices: 55292878--55293111 Score: 141
Period size: 27 Copynumber: 8.7 Consensus size: 27
55292868 TTAGTTTACC
* **
55292878 AAATTACTAAAATGTCCTCAATTTATA
1 AAATTACCAAAATACCCTCAATTTATA
* *
55292905 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCAATTTATA
* **** * *
55292932 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCAATTTATA
* * * *** *
55292959 TAATTACTAAAATACACTTGGTTTACA
1 AAATTACCAAAATACCCTCAATTTATA
* *
55292986 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTC-AATTTATA
** * *
55293013 AAATTACCAAAATACCACT-GGTTTGTG
1 AAATTACCAAAATACC-CTCAATTTATA
** *
55293040 AAATTACTGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCAATTTATA
* *
55293067 AAATTATCAAAATACCC-CTGATTTATA
1 AAATTACCAAAATACCCTC-AATTTATA
*
55293094 AAATTACAAAAATACCCT
1 AAATTACCAAAATACCCT
55293112 TGACTTTCAA
Statistics
Matches: 160, Mismatches: 41, Indels: 11
0.75 0.19 0.05
Matches are distributed among these distances:
26 3 0.02
27 156 0.98
28 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCAATTTATA
Found at i:55293170 original size:27 final size:27
Alignment explanation
Indices: 55292960--55293220 Score: 179
Period size: 27 Copynumber: 9.6 Consensus size: 27
55292950 CGATTTACAT
* *
55292960 AATTACTAAAATACACTTGGTTTACAA
1 AATTACTAAAATACCCTTGGTTTATAA
* * * *
55292987 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACTAAAATACCCTTGGTTTATAA
* * *
55293014 AATTACCAAAATACCAC-TGGTTTGTGA
1 AATTACTAAAATACC-CTTGGTTTATAA
* *** *
55293041 AATTACTGAAATACCCTCAATTTGTAA
1 AATTACTAAAATACCCTTGGTTTATAA
* *
55293068 AATTA-TCAAAATACCCCTGATTTATAA
1 AATTACT-AAAATACCCTTGGTTTATAA
* * *
55293095 AATTACAAAAATACCCTTGACTTTCAAAA
1 AATTACTAAAATACCCTTG-GTTT-ATAA
* *
55293124 AATTA-TAGAAATACCATTGGTTTACAA
1 AATTACTA-AAATACCCTTGGTTTATAA
* *
55293151 AATTACTAAAATACCCTTGGTTTGTAG
1 AATTACTAAAATACCCTTGGTTTATAA
* * * ** *
55293178 ATTTACCAAAACACCCTT-GTAGAATGA
1 AATTACTAAAATACCCTTGGT-TTATAA
55293205 AATTACTAAAATACCC
1 AATTACTAAAATACCC
55293221 CTAATAGGTA
Statistics
Matches: 183, Mismatches: 42, Indels: 18
0.75 0.17 0.07
Matches are distributed among these distances:
26 4 0.02
27 151 0.83
28 10 0.05
29 18 0.10
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACTAAAATACCCTTGGTTTATAA
Found at i:55293276 original size:27 final size:26
Alignment explanation
Indices: 55293214--55293291 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
55293204 AAATTACTAA
*
55293214 AATACCCCTAATAGGTAAAAAGACCGT
1 AATACCCCT-ATAGGTAAAATGACCGT
* *
55293241 AA-AGTCCCTATAGGGTAAAGTGACCGT
1 AATA-CCCCTATA-GGTAAAATGACCGT
*
55293268 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTATA-GGTAAAATGAC
55293292 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 4 0.10
27 36 0.88
28 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (26 bp):
AATACCCCTATAGGTAAAATGACCGT
Found at i:55294136 original size:25 final size:25
Alignment explanation
Indices: 55294098--55294167 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
55294088 AAGAAGTGCC
* *
55294098 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
55294123 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
55294148 AAAAGGGCTTTTCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
55294168 ATTACAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:55294416 original size:30 final size:31
Alignment explanation
Indices: 55294382--55294464 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
55294372 CGCTTACAGT
55294382 AAAGGCTTCGG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
55294412 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
55294443 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
55294465 TCGAGACTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 16 0.32
31 34 0.68
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:55301134 original size:43 final size:43
Alignment explanation
Indices: 55301068--55301226 Score: 193
Period size: 43 Copynumber: 3.7 Consensus size: 43
55301058 AGCTCATATA
*
55301068 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
*
55301111 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCAAATATCG
*
55301153 ATGCCAACGTCCCAGACGTGGTCTTATACGTAA--AACATAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAA-AT-A-TCG
* *
55301197 ATGCCAATGTCCCAGATGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
55301227 ATAACACACA
Statistics
Matches: 101, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
40 2 0.02
41 3 0.03
42 30 0.30
43 37 0.37
44 29 0.29
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
Found at i:55322175 original size:28 final size:28
Alignment explanation
Indices: 55322112--55322209 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
55322102 ATATTAAGTC
*
55322112 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
55322139 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
55322167 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
55322195 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55322210 GTACAATTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.32
28 46 0.68
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55330172 original size:28 final size:28
Alignment explanation
Indices: 55330109--55330231 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
55330099 ATATTAAGTC
*
55330109 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
55330136 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
55330164 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
55330192 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
55330221 CGCACACTTAG
1 CGCACACTTAG
55330232 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.25
28 49 0.56
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55338056 original size:29 final size:29
Alignment explanation
Indices: 55338024--55338181 Score: 178
Period size: 29 Copynumber: 5.4 Consensus size: 29
55338014 GGCTAATGAT
*
55338024 TATGAAAAAGGATGGTGACGACCATCGAA
1 TATGAAAAGGGATGGTGACGACCATCGAA
* *
55338053 TATGAAAATGGATGGTGACAACCATCGAA
1 TATGAAAAGGGATGGTGACGACCATCGAA
* * * *
55338082 TATGAAAAGGGATAGCT-TCAACTATC-AA
1 TATGAAAAGGGAT-GGTGACGACCATCGAA
* *
55338110 TTATGAAAAAGGATAGTGACGACCATC-AA
1 -TATGAAAAGGGATGGTGACGACCATCGAA
*
55338139 TTATGAAAAGGGATGATGACGACCATCGAA
1 -TATGAAAAGGGATGGTGACGACCATCGAA
55338169 TATGAAAAGGGAT
1 TATGAAAAGGGAT
55338182 AGCCTTGGCT
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.03
29 103 0.94
30 4 0.04
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCGAA
Found at i:55338200 original size:87 final size:87
Alignment explanation
Indices: 55337996--55338205 Score: 289
Period size: 87 Copynumber: 2.4 Consensus size: 87
55337986 TCATCAACTA
* * * *
55337996 ATGAAAAGAGACAGCTTCGGCTAATGATTATGAAAAAGGATGGTGACGACCATCGAATATGAAAA
1 ATGAAAAGGGATAGCTTCGGCTATTGATTATGAAAAAGGATAGTGACGACCATCGAATATGAAAA
* *
55338061 TGGATGGTGACAACCATCGAAT
66 GGGATGATGACAACCATCGAAT
** **
55338083 ATGAAAAGGGATAGCTTCAACTATCAATTATGAAAAAGGATAGTGACGACCATC-AATTATGAAA
1 ATGAAAAGGGATAGCTTCGGCTATTGATTATGAAAAAGGATAGTGACGACCATCGAA-TATGAAA
*
55338147 AGGGATGATGACGACCATCGAAT
65 AGGGATGATGACAACCATCGAAT
55338170 ATGAAAAGGGATAGCCTT-GGCTATTGATTATGAAAA
1 ATGAAAAGGGATAG-CTTCGGCTATTGATTATGAAAA
55338206 GCTATTGCTC
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
86 2 0.02
87 101 0.95
88 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTCGGCTATTGATTATGAAAAAGGATAGTGACGACCATCGAATATGAAAA
GGGATGATGACAACCATCGAAT
Found at i:55343282 original size:27 final size:27
Alignment explanation
Indices: 55342782--55343300 Score: 659
Period size: 27 Copynumber: 19.3 Consensus size: 27
55342772 CGATTTGTAA
* *
55342782 AATTACCGAAAAACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * * *
55342809 AATTACTAAAATACCTCTGTAAGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55342836 AATTACCGAAATACCCCTGTAGTGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* **
55342863 AATTACTGAAATACCCCTGTAATGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55342890 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
55342917 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
55342944 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
55342971 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
55342998 AATTACTGAAATACCTCTATATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55343025 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
55343052 AATTATCGAAATATCCTTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
55343079 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55343106 AATTACCGAAATACCCCTGTAGGCTA-
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55343132 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55343159 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55343186 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
55343213 AATTACAGAAATACTCTTGTAGGGTAGG
1 AATTACCGAAATACCCCTGTAGGGTA-G
*
55343241 AA-TACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
55343267 AATTACCGAGAA-A-CCCTCGTGGGGTAA
1 AATTACCGA-AATACCCCT-GTAGGGTAG
55343294 AATTACC
1 AATTACC
55343301 ATTTTACCCC
Statistics
Matches: 434, Mismatches: 53, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
26 31 0.07
27 398 0.92
28 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:55343744 original size:6 final size:6
Alignment explanation
Indices: 55343713--55343806 Score: 77
Period size: 6 Copynumber: 15.3 Consensus size: 6
55343703 TTGCATTCAC
* * *
55343713 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
55343762 -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG ATTCT- AGTTCTG AT
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
55343807 AATGTTTCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 5 0.07
6 56 0.80
7 7 0.10
8 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:55343745 original size:19 final size:19
Alignment explanation
Indices: 55343723--55343780 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
55343713 ATTCTGATTT
55343723 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
55343742 TGATTCTG--A--T--T-T
1 TGATTCTGTTACCTGATAC
55343754 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
55343773 TGATTCTG
1 TGATTCTG
55343781 ATTCTAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 16 0.53
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:55343748 original size:31 final size:31
Alignment explanation
Indices: 55343713--55343792 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
55343703 TTGCATTCAC
55343713 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
55343744 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* *
55343775 ATTCTGATTCTAATTCTG
1 ATTCTGATTTTGATTCTG
55343793 ATTCTAGTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:55347605 original size:27 final size:27
Alignment explanation
Indices: 55347565--55347676 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
55347555 AGGAAGCGTC
* *
55347565 CTGGTGGCTATGCCACAATTACCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
55347592 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
55347619 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
55347647 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
55347673 CTGG
1 CTGG
55347677 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:55347671 original size:54 final size:54
Alignment explanation
Indices: 55347565--55347676 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
55347555 AGGAAGCGTC
* *
55347565 CTGGTGGCTATGCCACAATTACCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTACCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
55347619 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTACCTG-ATCTGGTGACTCTGCCACATATATCTGTT
55347673 CTGG
1 CTGG
55347677 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTACCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:55348701 original size:26 final size:26
Alignment explanation
Indices: 55348672--55348769 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
55348662 TTAGTTTACC
**
55348672 AAATTACTGAAATACCCCCAGTTGTA
1 AAATTACCCAAATACCCCCAGTTGTA
*
55348698 AAATTA-CCAAAGTACCCCCAGTTTATA
1 AAATTACCCAAA-TACCCCCAG-TTGTA
* * *
55348725 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACCCAAATA-CCCCCAGTTGTA
*
55348752 AAATTACCGAAATACCCC
1 AAATTACCCAAATACCCC
55348770 TATAAGGTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
25 3 0.05
26 18 0.31
27 29 0.49
28 9 0.15
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.27
Consensus pattern (26 bp):
AAATTACCCAAATACCCCCAGTTGTA
Found at i:55349172 original size:27 final size:27
Alignment explanation
Indices: 55348753--55349190 Score: 528
Period size: 27 Copynumber: 16.3 Consensus size: 27
55348743 CGATTTGTAA
* *
55348753 AATTACCGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * * *
55348780 AATTACTAAAATACCCATGTAAGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
**
55348807 AATTACC-AGAATACCCCTGTAGTATAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
* *
55348834 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55348861 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55348888 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55348915 AATTACCGAAATACCCCTGTATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
55348942 AATTACCGAAATAGCCCTGTATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55348969 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55348996 AATTACCGAAATACCCCTGTATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
55349023 AATTATCGAAATAGCCCTGTACGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
55349050 AATTATCGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
55349077 AATTACTGAAATACCCCTGTCA-GGTAG
1 AATTACCGAAATACCCCTGT-AGGGTAG
*
55349104 AATTACCGAAATACCCTTGTAGGGTAGG
1 AATTACCGAAATACCCCTGTAGGGTA-G
* *
55349132 AA-TA-CTAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
55349157 AATTACCGAGAA-A-CCCTCGTGGGGTAA
1 AATTACCGA-AATACCCCT-GTAGGGTAG
55349184 AATTACC
1 AATTACC
55349191 ATTTTACCCC
Statistics
Matches: 358, Mismatches: 44, Indels: 18
0.85 0.10 0.04
Matches are distributed among these distances:
25 3 0.01
26 25 0.07
27 323 0.90
28 7 0.02
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:55349479 original size:27 final size:26
Alignment explanation
Indices: 55349435--55349486 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
55349425 CTCGCTGCAA
*
55349435 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
55349462 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
55349487 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:55349640 original size:31 final size:31
Alignment explanation
Indices: 55349605--55349706 Score: 150
Period size: 31 Copynumber: 3.3 Consensus size: 31
55349595 TTGCATTCAC
*
55349605 ATTCTGATTTTGATTTTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
55349636 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * *
55349667 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
55349698 ATTCCGATT
1 ATTCTGATT
55349707 CTAGTTCTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:55349661 original size:25 final size:24
Alignment explanation
Indices: 55349608--55349680 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
55349598 CATTCACATT
*
55349608 CTGATTTTGATTTTG-TTACCTGATA
1 CTGATTCTGATTTTGATT--CTGATA
*
55349633 CTGATTCTGATTTTGATTCTGTTA
1 CTGATTCTGATTTTGATTCTGATA
* *
55349657 CCTGATACTGATTCTGATTCTGAT
1 -CTGATTCTGATTTTGATTCTGAT
55349681 TCTGTCACCT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 5 0.12
25 34 0.83
26 2 0.05
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.49
Consensus pattern (24 bp):
CTGATTCTGATTTTGATTCTGATA
Found at i:55349701 original size:6 final size:6
Alignment explanation
Indices: 55349605--55349684 Score: 65
Period size: 6 Copynumber: 13.0 Consensus size: 6
55349595 TTGCATTCAC
* * * *
55349605 ATTCTG ATTTTG ATTTTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
*
55349654 -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
55349685 TCACCTAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 4 0.07
6 49 0.82
7 5 0.08
8 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:55353193 original size:53 final size:53
Alignment explanation
Indices: 55353124--55353226 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
55353114 TATATCAGGA
*
55353124 TTACCCATTCGAGCTAAATCCTTTCTATAATGAGGTCAATAGGAATACTCATC
1 TTACCCATTCGAGCTAAATCCTTTCTATAATAAGGTCAATAGGAATACTCATC
*
55353177 TTACCCATTCGGGCTAAATCCTTTCTATAATAAGGTCAATAGGAATACTC
1 TTACCCATTCGAGCTAAATCCTTTCTATAATAAGGTCAATAGGAATACTC
55353227 GTCCGAGCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (53 bp):
TTACCCATTCGAGCTAAATCCTTTCTATAATAAGGTCAATAGGAATACTCATC
Found at i:55356476 original size:23 final size:23
Alignment explanation
Indices: 55356446--55356491 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
55356436 GTCAATATAT
*
55356446 GTATGTGATATA-TATTTAAATGA
1 GTATGTGAT-TACTATGTAAATGA
55356469 GTATGTGATTACTATGTAAATGA
1 GTATGTGATTACTATGTAAATGA
55356492 ATCAATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (23 bp):
GTATGTGATTACTATGTAAATGA
Found at i:55370400 original size:46 final size:44
Alignment explanation
Indices: 55370350--55370516 Score: 131
Period size: 46 Copynumber: 3.6 Consensus size: 44
55370340 TTCATAGCCG
*
55370350 ATGCATGTCCCAGACATGTCTTACACTGGCTTACATTTTGAGGCCA
1 ATGCATGTCCCAGACATGTCTTACACTGGCTT-CATATT-AGGCCA
* * * * *
55370396 ATGCATG-CCCTAGACATGTCTTACATTAGCGC-TCGTCTCAATGCCA
1 ATGCATGTCCC-AGACATGTCTTACACT-G-GCTTCATAT-TAGGCCA
* * **
55370442 ATACCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCTG
1 AT-GCATGTCCCAGACAT-GTCTTACACTGGCT-TCATATTA-GGCCA
*
55370490 ATACATGTCCCAGACATGTCTTACACT
1 ATGCATGTCCCAGACATGTCTTACACT
55370517 AGCTCACATA
Statistics
Matches: 96, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
45 3 0.03
46 44 0.46
47 28 0.29
48 21 0.22
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (44 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTTCATATTAGGCCA
Found at i:55372990 original size:17 final size:17
Alignment explanation
Indices: 55372968--55373000 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
55372958 GTCCTTAATC
55372968 TCTTTGGGATAATATTA
1 TCTTTGGGATAATATTA
55372985 TCTTTGGGATAATATT
1 TCTTTGGGATAATATT
55373001 CATTCTCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (17 bp):
TCTTTGGGATAATATTA
Found at i:55373972 original size:19 final size:19
Alignment explanation
Indices: 55373936--55373974 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
55373926 GTTTCATCAT
* *
55373936 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
55373955 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
55373974 A
1 A
55373975 AAATAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:55374480 original size:55 final size:56
Alignment explanation
Indices: 55374415--55374519 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 56
55374405 TGCATTGCTG
* *
55374415 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGTGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCAGTGCCA
* * * *
55374471 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACATATAATTTGTGGCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCA
55374520 TAGCCACTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
55 20 0.48
56 22 0.52
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCAGTGCCA
Found at i:55374492 original size:27 final size:27
Alignment explanation
Indices: 55374440--55374519 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
55374430 GTGACAGAGT
*
55374440 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGGGC
*
55374469 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGGGC
*
55374496 CACCAGAACATATAATTTGTGGCA
1 CACCAGAACAGAT-ATTTGTGGCA
55374520 TAGCCACTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
27 23 0.50
28 16 0.35
29 7 0.15
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.23
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGGGC
Found at i:55374682 original size:28 final size:29
Alignment explanation
Indices: 55374635--55374697 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
55374625 AAATTAACCC
*
55374635 TAGGGGTATAAAGGTCA-TTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTTGCATACA
*
55374663 TAGGGGTATAATGGTAATTTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTTGCATACA
55374692 TCAGGG
1 T-AGGG
55374698 TATTCTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 15 0.48
29 12 0.39
30 4 0.13
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (29 bp):
TAGGGGTATAAAGGTAATTTTTGCATACA
Found at i:55377609 original size:40 final size:40
Alignment explanation
Indices: 55377526--55377746 Score: 232
Period size: 40 Copynumber: 5.5 Consensus size: 40
55377516 ACCCAAGTAT
** * *
55377526 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
55377564 CTTCGGGTCTTAGCCCGGATATGGTCGCTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
55377604 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
55377644 CTTCGGGTTTTGGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
55377684 CTTCGGATCTTAGTCCGGATATAATCACTTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCAC-TAGCACAAATGC
* *
55377725 CTTCGAGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
55377747 CATTCGAATA
Statistics
Matches: 151, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 14 0.09
40 97 0.64
41 28 0.19
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:55380474 original size:19 final size:19
Alignment explanation
Indices: 55380450--55380488 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
55380440 TTATTGAGTT
55380450 AGTACCCGCATACTCTAAA
1 AGTACCCGCATACTCTAAA
* *
55380469 AGTACCTGTATACTCTAAA
1 AGTACCCGCATACTCTAAA
55380488 A
1 A
55380489 TGAATCGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (19 bp):
AGTACCCGCATACTCTAAA
Found at i:55381160 original size:118 final size:118
Alignment explanation
Indices: 55380950--55381189 Score: 435
Period size: 118 Copynumber: 2.0 Consensus size: 118
55380940 TACAATAAAA
*
55380950 ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACGCCCTGTGTCTTAGGT
1 ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACACCCTGTGTCTTAGGT
*
55381015 CGTGTGATCCAAATTAAGCCCTAAAAACAACCCATTTCAAGACCTATGCATGC
66 CGTGTGATCCAAATTAAGCCCCAAAAACAACCCATTTCAAGACCTATGCATGC
55381068 ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACACCCTGTGTCTTAGGT
1 ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACACCCTGTGTCTTAGGT
* * *
55381133 CGTGTGATCCAAATTAAGCCCCCAAAACAAGCCATTTCAAGACCTATGCATGT
66 CGTGTGATCCAAATTAAGCCCCAAAAACAACCCATTTCAAGACCTATGCATGC
55381186 ATAG
1 ATAG
55381190 CAAGATACAT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (118 bp):
ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACACCCTGTGTCTTAGGT
CGTGTGATCCAAATTAAGCCCCAAAAACAACCCATTTCAAGACCTATGCATGC
Found at i:55382539 original size:40 final size:41
Alignment explanation
Indices: 55382446--55382546 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
55382436 AATATACACC
* *
55382446 GGCACCAATCCTGATTATATACACCGGCACAAAGCCTACTA
1 GGCACAAAGCCTGATTATATACACCGGCACAAAGCCTACTA
* ** *
55382487 GGCATAAAGCCTGATTATATACATTGGCACAAAG-CTGCTA
1 GGCACAAAGCCTGATTATATACACCGGCACAAAGCCTACTA
*
55382527 GGCACAAAGCCTGATAATAT
1 GGCACAAAGCCTGATTATAT
55382547 CTCCAATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 23 0.44
41 29 0.56
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.22
Consensus pattern (41 bp):
GGCACAAAGCCTGATTATATACACCGGCACAAAGCCTACTA
Found at i:55385439 original size:27 final size:27
Alignment explanation
Indices: 55385395--55385655 Score: 83
Period size: 27 Copynumber: 9.7 Consensus size: 27
55385385 TATTGAAATG
* *
55385395 CCCTCGACTTGTAAAATTACCAAAGTA
1 CCCTCGATTTATAAAATTACCAAAGTA
* * ***
55385422 CCCTCGATTTATAGAATTATCATTTTA
1 CCCTCGATTTATAAAATTACCAAAGTA
* ***
55385449 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCAAAGTA
* ****
55385476 CCCTC-AGTTTACAAAATTA-CTGTTTCA
1 CCCTCGA-TTTATAAAATTACCAAAGT-A
* *
55385503 CCCTCGA-TTATGAAATTACTGAAA-TA
1 CCCTCGATTTATAAAATTAC-CAAAGTA
** * *
55385529 CCC-CTG-TAGGATAGAATTACCAAAATA
1 CCCTC-GAT-TTATAAAATTACCAAAGTA
* * *
55385556 CCC-CTAGTTTGTAAAATTACCAAAATA
1 CCCTCGA-TTTATAAAATTACCAAAGTA
* * *
55385583 CCACTC-ATTTGTGAAATTACTGAAA-TA
1 CC-CTCGATTTATAAAATTAC-CAAAGTA
* * *
55385610 CCCTCAATTTGTAAAATTACCAAAATA
1 CCCTCGATTTATAAAATTACCAAAGTA
*
55385637 CCC-CTGATTTACAAAATTA
1 CCCTC-GATTTATAAAATTA
55385656 TTGAAATACC
Statistics
Matches: 182, Mismatches: 35, Indels: 34
0.73 0.14 0.14
Matches are distributed among these distances:
25 1 0.01
26 29 0.16
27 144 0.79
28 7 0.04
29 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCAAAGTA
Found at i:55385582 original size:54 final size:53
Alignment explanation
Indices: 55385515--55385642 Score: 125
Period size: 54 Copynumber: 2.4 Consensus size: 53
55385505 CTCGATTATG
** *
55385515 AAATTACTGAAATACCCCTGTAGGAT-AGAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCCTGTAGG-TGA-AATTACCAAAATACCCTC-AATTTGTA
* * ** **
55385569 AAATTACCAAAATACCACTCATTTGTGAAATTACTGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCCT-GTAGGTGAAATTACCAAAATACCCTCAATTTGTA
55385623 AAATTACCAAAATACCCCTG
1 AAATTACCAAAATACCCCTG
55385643 ATTTACAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
54 56 0.93
55 4 0.07
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (53 bp):
AAATTACCAAAATACCCCTGTAGGTGAAATTACCAAAATACCCTCAATTTGTA
Found at i:55385675 original size:54 final size:54
Alignment explanation
Indices: 55385551--55385693 Score: 153
Period size: 54 Copynumber: 2.6 Consensus size: 54
55385541 AGAATTACCA
* ***
55385551 AAATACCC-CTAGTTTGTAAAATTACCAAAATACCACTCATTTGTGAAATTACTG
1 AAATACCCTC-AGTTTGTAAAATTACCAAAATACCCCTCATTTACAAAATTACTG
* * *
55385605 AAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTATTG
1 AAATACCCTCAGTTTGTAAAATTACCAAAATACCCCTCATTTACAAAATTACTG
* ** * * *
55385659 AAATACCTTTGGTTTGTAGATTTACCAAAACACCC
1 AAATACCCTCAGTTTGTAAAATTACCAAAATACCC
55385694 TTGTAAGATG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 73 0.99
55 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
AAATACCCTCAGTTTGTAAAATTACCAAAATACCCCTCATTTACAAAATTACTG
Found at i:55386609 original size:25 final size:25
Alignment explanation
Indices: 55386571--55386640 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
55386561 AGGAAGTGCT
* *
55386571 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
55386596 AAAAGGGTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
55386621 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
55386641 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:55386653 original size:24 final size:24
Alignment explanation
Indices: 55386570--55386653 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 24
55386560 GAGGAAGTGC
* *
55386570 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
* *
55386595 GAAAAGGGTTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
55386619 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
55386643 TAAAAGAGGCT
1 TAAAAG-GGCT
55386654 AGGCCTCCAG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
23 5 0.10
24 8 0.16
25 37 0.74
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:55386893 original size:30 final size:30
Alignment explanation
Indices: 55386859--55386941 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 30
55386849 CGCTTACAGT
55386859 AAAGGCTTCGGCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCAGTGATATGATTTATGA
* *
55386889 AAAGGATTAGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGG-CCAGTGATATGATTTATGA
*
55386920 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTC-GGCCAGTGATATG
55386942 TCGAGATTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 14 0.30
31 31 0.67
32 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
AAAGGCTTCGGCCAGTGATATGATTTATGA
Found at i:55392681 original size:28 final size:28
Alignment explanation
Indices: 55392626--55392689 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
55392616 CTCAATTTCT
* * **
55392626 AGACCACCGCTGAGCTACCGTTGTCGTC
1 AGACAACCGCTGAGCTACCATTACCGTC
*
55392654 -GAACAACCGCTGAGCTACTATTACCGTC
1 AG-ACAACCGCTGAGCTACCATTACCGTC
55392682 AGACAACC
1 AGACAACC
55392690 ACTGCCAGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.03
28 27 0.93
29 1 0.03
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.19
Consensus pattern (28 bp):
AGACAACCGCTGAGCTACCATTACCGTC
Found at i:55415690 original size:6 final size:6
Alignment explanation
Indices: 55415675--55415752 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
55415665 AATTTGTTAC
* * *
55415675 CTGATA CTGATT CTGATT CTGATT CTG-TCAC CTGATT CTAAATT -TGATT
1 CTGATT CTGATT CTGATT CTGATT CTGAT--T CTGATT CT-GATT CTGATT
* *
55415724 CTGATT CTCATT TTGATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGATT CTGA-TT CTGAT
55415753 AATGTTTCCT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
5 5 0.09
6 43 0.77
7 7 0.12
8 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:55429474 original size:40 final size:40
Alignment explanation
Indices: 55429292--55429514 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
55429282 TCCTCGTTCA
* * * * *
55429292 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
55429331 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
55429371 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
55429411 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
55429451 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
55429491 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55429515 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:55429523 original size:41 final size:41
Alignment explanation
Indices: 55429446--55429523 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
55429436 TTAGTATCTC
* * *
55429446 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
55429487 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
55429524 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:55436749 original size:40 final size:40
Alignment explanation
Indices: 55436567--55436789 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
55436557 TCCTCGTTCA
* * * * *
55436567 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
55436606 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
55436646 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
55436686 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
55436726 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
55436766 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55436790 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:55436798 original size:41 final size:41
Alignment explanation
Indices: 55436721--55436798 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
55436711 TTAGTATCTC
* * *
55436721 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
55436762 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
55436799 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:55438653 original size:23 final size:23
Alignment explanation
Indices: 55438618--55438677 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
55438608 TGTCCCTAAG
* *
55438618 CACACGGGTGTGTGCTTTGCCTC
1 CACACGGGCGTGTGCTTTCCCTC
*
55438641 CACAAGGGCGTGTGCTTTCCCTC
1 CACACGGGCGTGTGCTTTCCCTC
*
55438664 CACACGGGCATGTG
1 CACACGGGCGTGTG
55438678 AGGCATAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (23 bp):
CACACGGGCGTGTGCTTTCCCTC
Found at i:55441263 original size:13 final size:13
Alignment explanation
Indices: 55441241--55441317 Score: 91
Period size: 13 Copynumber: 5.9 Consensus size: 13
55441231 AGTTCTTCAT
*
55441241 TGCTTCTGAAAAG
1 TGCTTTTGAAAAG
55441254 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
55441267 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
55441280 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
55441293 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
*
55441306 TGCTTTGGAAAA
1 TGCTTTTGAAAA
55441318 ATTTAAGTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:55441299 original size:39 final size:39
Alignment explanation
Indices: 55441241--55441317 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
55441231 AGTTCTTCAT
*
55441241 TGCTTCTGAAAAGTGCTTTTGAAAAGTGCTGTGGAAAAG
1 TGCTTCTGAAAAGTACTTTTGAAAAGTGCTGTGGAAAAG
* * * *
55441280 TGCTTTTGAGAAGTACTTTTGAGAAGTGCTTTGGAAAA
1 TGCTTCTGAAAAGTACTTTTGAAAAGTGCTGTGGAAAA
55441318 ATTTAAGTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.34
Consensus pattern (39 bp):
TGCTTCTGAAAAGTACTTTTGAAAAGTGCTGTGGAAAAG
Found at i:55442431 original size:30 final size:30
Alignment explanation
Indices: 55442397--55442458 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
55442387 ACTTATTTTC
55442397 TTGTT-AATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAAATTTT-TTATTATTTTAAAGGCAT
*
55442427 TTGTTAAATTTTTTATTATTTTAGAGGCAT
1 TTGTTAAATTTTTTATTATTTTAAAGGCAT
55442457 TT
1 TT
55442459 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (30 bp):
TTGTTAAATTTTTTATTATTTTAAAGGCAT
Found at i:55443631 original size:20 final size:20
Alignment explanation
Indices: 55443582--55443636 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
55443572 GATAAAAATA
*
55443582 AAAAGGAAAAAAAA-GACAG
1 AAAAGTAAAAAAAATGACAG
* *
55443601 AAAATTCAAAAAAATCGA-AG
1 AAAAGTAAAAAAAAT-GACAG
55443621 AAAAGTAAAAATAAAT
1 AAAAGTAAAAA-AAAT
55443637 AAATAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 11 0.39
20 11 0.39
21 6 0.21
ACGTcount: A:0.71, C:0.05, G:0.13, T:0.11
Consensus pattern (20 bp):
AAAAGTAAAAAAAATGACAG
Found at i:55444572 original size:15 final size:15
Alignment explanation
Indices: 55444542--55444589 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
55444532 TGAAAAATGA
55444542 ATTTTTAAATAATTTTT
1 ATTTTT-AA-AATTTTT
55444559 ATTTTTAAAATTTTT
1 ATTTTTAAAATTTTT
* **
55444574 GTTTTTTGAATTTTT
1 ATTTTTAAAATTTTT
55444589 A
1 A
55444590 AGATTAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 19 0.70
16 2 0.07
17 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
ATTTTTAAAATTTTT
Found at i:55446658 original size:50 final size:51
Alignment explanation
Indices: 55446579--55446680 Score: 179
Period size: 50 Copynumber: 2.0 Consensus size: 51
55446569 ACACCTTGCT
* *
55446579 AACCTACACAAGTTAGAAGGTAGAAGCACCACCAAAAATAACACTTTCTTC
1 AACCTACAAAAGTTAGAAGGTAGAAGCACCACCAAAAACAACACTTTCTTC
55446630 AACC-ACAAAAGTTAGAAGGTAGAAGCACCACCAAAAACAACACTTTCTTC
1 AACCTACAAAAGTTAGAAGGTAGAAGCACCACCAAAAACAACACTTTCTTC
55446680 A
1 A
55446681 CCCAATTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 45 0.92
51 4 0.08
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (51 bp):
AACCTACAAAAGTTAGAAGGTAGAAGCACCACCAAAAACAACACTTTCTTC
Found at i:55449427 original size:30 final size:30
Alignment explanation
Indices: 55449391--55449448 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
55449381 ATACGAGAAA
*
55449391 AGACACGGGCGTGTGTCTTAGCCATGTGCG
1 AGACACGGGCGTGTGGCTTAGCCATGTGCG
55449421 AGACACGGGCGTGTGGCTTAGCCATGTG
1 AGACACGGGCGTGTGGCTTAGCCATGTG
55449449 TCCCCTGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.22, G:0.38, T:0.22
Consensus pattern (30 bp):
AGACACGGGCGTGTGGCTTAGCCATGTGCG
Found at i:55463547 original size:40 final size:40
Alignment explanation
Indices: 55463503--55463578 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
55463493 TCGATTCAAA
* *
55463503 ATAGCTTTGGCTATAATTA-GCACTAAGTGTGAGAAATGGT
1 ATAGCTTCGGCTAT-ATGAGGCACTAAGTGTGAGAAATGGT
* *
55463543 ATAGCTTCGGCTGTATGAGGCACTAAGTGTGCGAAA
1 ATAGCTTCGGCTATATGAGGCACTAAGTGTGAGAAA
55463579 ATCATTCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.10
40 28 0.90
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (40 bp):
ATAGCTTCGGCTATATGAGGCACTAAGTGTGAGAAATGGT
Found at i:55475328 original size:14 final size:14
Alignment explanation
Indices: 55475311--55475383 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
55475301 AGAGTTTTAC
55475311 ATTGATTCTTTTGG
1 ATTGATTCTTTTGG
55475325 ATTGATTCTTTTGG
1 ATTGATTCTTTTGG
*** *
55475339 ACCTTCGA--CCAATGTC
1 A--TT-GATTCTTTTG-G
55475355 ATTGATTCTTTTGG
1 ATTGATTCTTTTGG
55475369 ATTGATTCTTTTGG
1 ATTGATTCTTTTGG
55475383 A
1 A
55475384 CCTTCGACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
13 2 0.04
14 32 0.71
15 6 0.13
16 3 0.07
17 2 0.04
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (14 bp):
ATTGATTCTTTTGG
Found at i:55475373 original size:44 final size:44
Alignment explanation
Indices: 55475310--55475397 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
55475300 AAGAGTTTTA
55475310 CATTGATTCTTTTGGATTGATTCTTTTGGACCTTCGACCAATGT
1 CATTGATTCTTTTGGATTGATTCTTTTGGACCTTCGACCAATGT
55475354 CATTGATTCTTTTGGATTGATTCTTTTGGACCTTCGACCAATGT
1 CATTGATTCTTTTGGATTGATTCTTTTGGACCTTCGACCAATGT
55475398 AGAGAAGCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (44 bp):
CATTGATTCTTTTGGATTGATTCTTTTGGACCTTCGACCAATGT
Found at i:55478440 original size:13 final size:13
Alignment explanation
Indices: 55478422--55478450 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55478412 TTTAGTTTAA
55478422 TTAGTTAATTAGT
1 TTAGTTAATTAGT
55478435 TTAGTTAATTAGT
1 TTAGTTAATTAGT
55478448 TTA
1 TTA
55478451 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:55483890 original size:6 final size:6
Alignment explanation
Indices: 55483879--55483918 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
55483869 TCCTCCTATC
55483879 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
55483919 ATTATTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:55486374 original size:60 final size:60
Alignment explanation
Indices: 55486296--55486432 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
55486286 CAGTGTTAAC
* *
55486296 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAG--TCGAGA-TATAT
* *
55486357 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
*
55486417 TGGGCCTTGCCCATAT
1 TGGGCCTAGCCCATAT
55486433 TAACATAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 53 0.78
61 13 0.19
62 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
Found at i:55486396 original size:28 final size:27
Alignment explanation
Indices: 55486295--55486396 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
55486285 TCAGTGTTAA
* *
55486295 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
55486323 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
55486355 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
55486383 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
55486397 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:55488754 original size:15 final size:15
Alignment explanation
Indices: 55488734--55488762 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55488724 TTTCCCTATC
55488734 TAATAATAATAATTA
1 TAATAATAATAATTA
55488749 TAATAATAATAATT
1 TAATAATAATAATT
55488763 TTAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:55488771 original size:15 final size:15
Alignment explanation
Indices: 55488738--55488771 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
55488728 CCTATCTAAT
*
55488738 AATAATAATTATAAT
1 AATAATAATTATAAA
*
55488753 AATAATAATTTTAAA
1 AATAATAATTATAAA
55488768 AATA
1 AATA
55488772 TATCTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATAATTATAAA
Found at i:55488894 original size:19 final size:18
Alignment explanation
Indices: 55488857--55488900 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
55488847 ATACATGCAG
55488857 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
55488874 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
55488893 TACTAATT
1 TAATAATT
55488901 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:55490339 original size:13 final size:13
Alignment explanation
Indices: 55490321--55490349 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55490311 TTTAGTTTAA
55490321 TTAGTTAATTAGT
1 TTAGTTAATTAGT
55490334 TTAGTTAATTAGT
1 TTAGTTAATTAGT
55490347 TTA
1 TTA
55490350 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:55491054 original size:47 final size:45
Alignment explanation
Indices: 55491003--55491123 Score: 122
Period size: 47 Copynumber: 2.6 Consensus size: 45
55490993 GAGGCCAATG
*
55491003 CATGTCTCAGACATGTCTTACACTAGCTCTCGTCTCAA-T-GCCGATTC
1 CATGTCTCAGACATGTCTTACACTAGCTCTC--AT-AAGTGGCCGA-TC
* *
55491050 CATGT-TCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATG
1 CATGTCT-CAGACAT-GTCTTACACTAGCTCTCATAA-GTGGCCGATC
*
55491097 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCTCAGACATGTCTTACACTAGC
55491124 ACACAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
45 2 0.03
46 14 0.22
47 26 0.41
48 21 0.33
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (45 bp):
CATGTCTCAGACATGTCTTACACTAGCTCTCATAAGTGGCCGATC
Found at i:55491070 original size:94 final size:94
Alignment explanation
Indices: 55490909--55491123 Score: 235
Period size: 94 Copynumber: 2.3 Consensus size: 94
55490899 ATGCCGATGC
* * *
55490909 CATGTCCCAGACATGGTCTTACACTAGGTCATC--CATGAA-GTCGATGCCATGTCCTAGACATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTC-TCGTC-TCAATGCCGATGCCATGTCCTAGACATG
* * *
55490971 GTCTTACAGTAG-TTTACAT-CTCGAGGCCAATG
63 GTCTTACACTAGCTCT-CATAAT-GAGGCCAATG
* *
55491003 CATGTCTCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATTCCATGTTCC-AGACATGGT
1 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATG-TCCTAGACATGGT
* * *
55491067 CTTACACTGGCTCTCATAATGTGGCCGATG
65 CTTACACTAGCTCTCATAATGAGGCCAATG
55491097 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
55491124 ACACAAATAA
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
92 2 0.02
93 17 0.17
94 78 0.76
95 6 0.06
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTCCTAGACATGGTC
TTACACTAGCTCTCATAATGAGGCCAATG
Found at i:55493715 original size:47 final size:47
Alignment explanation
Indices: 55493644--55494048 Score: 684
Period size: 47 Copynumber: 8.6 Consensus size: 47
55493634 CCCTTCGGGA
* * * * * *
55493644 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
55493691 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55493738 CTTAGCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55493785 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55493832 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55493879 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55493926 CTTATCACATACATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACAT--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
55493975 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55494022 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
55494049 TATTCAAATA
Statistics
Matches: 342, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 296 0.87
49 46 0.13
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55499949 original size:27 final size:27
Alignment explanation
Indices: 55499917--55499971 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
55499907 CGTTGCAAAA
55499917 GTCCTCCCTATCAG-GAATGATCACTGG
1 GTCCTCCCTA-CAGAGAATGATCACTGG
*
55499944 GTCCTCCCTACCGAGAATGATCACTGG
1 GTCCTCCCTACAGAGAATGATCACTGG
55499971 G
1 G
55499972 CCCATAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.24
Consensus pattern (27 bp):
GTCCTCCCTACAGAGAATGATCACTGG
Found at i:55502144 original size:22 final size:23
Alignment explanation
Indices: 55502114--55502157 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
55502104 ATTAATAAAC
*
55502114 ACAATTTTTCTTTT-AAAATTTA
1 ACAACTTTTCTTTTGAAAATTTA
*
55502136 ACAACTTTTTTTTTGAAAATTT
1 ACAACTTTTCTTTTGAAAATTT
55502158 TAACTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (23 bp):
ACAACTTTTCTTTTGAAAATTTA
Found at i:55502161 original size:24 final size:22
Alignment explanation
Indices: 55502114--55502157 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
55502104 ATTAATAAAC
55502114 ACAATTTTTCTTTTAAAATTTA
1 ACAATTTTTCTTTTAAAATTTA
55502136 ACAACTTTTT-TTTTGAAAATTT
1 ACAA-TTTTTCTTTT-AAAATTT
55502158 TAACTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (22 bp):
ACAATTTTTCTTTTAAAATTTA
Found at i:55508884 original size:27 final size:27
Alignment explanation
Indices: 55508836--55508995 Score: 159
Period size: 27 Copynumber: 5.9 Consensus size: 27
55508826 GCGAGGCTGC
* *
55508836 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
55508863 CAGATATTATGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
55508889 CAGAAATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
55508916 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
55508943 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
55508970 TAGATAAATTGTGGCATAGCCACCAG
1 CAGAT--ATTGTGGCAGAGCCACCAG
55508996 GACGCTTCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
26 9 0.08
27 82 0.73
28 19 0.17
29 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:55508936 original size:54 final size:54
Alignment explanation
Indices: 55508854--55508995 Score: 214
Period size: 54 Copynumber: 2.6 Consensus size: 54
55508844 GTGACGAAGT
* *
55508854 CACCAGATACAGAT-ATTATGGCAGAGCCACCAGAACAGAAATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGAAATATGTGGCAGAGC
* *
55508908 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGAAATATGTGGCAGAGC
*
55508962 CACCAGATTAGATAAATTGTGGCATAGCCACCAG
1 CACCAGATCAGAT-AATTGTGGCATAGCCACCAG
55508996 GACGCTTCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
53 5 0.06
54 56 0.69
55 20 0.25
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGAAATATGTGGCAGAGC
Done.