Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 163 of 208
Found at i:52777471 original size:19 final size:19
Alignment explanation
Indices: 52777447--52777496 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
52777437 TTGTTATTTC
52777447 TATTATTATTA-AATTAGTT
1 TATTATTATTATAATTA-TT
*
52777466 TATTATTATTATTATTATT
1 TATTATTATTATAATTATT
*
52777485 TATTATCATTAT
1 TATTATTATTAT
52777497 TAGTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTATTATTATAATTATT
Found at i:52777487 original size:16 final size:16
Alignment explanation
Indices: 52777468--52777498 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52777458 AATTAGTTTA
*
52777468 TTATTATTATTATTAT
1 TTATTATCATTATTAT
52777484 TTATTATCATTATTA
1 TTATTATCATTATTA
52777499 GTTTTATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATCATTATTAT
Found at i:52778181 original size:12 final size:12
Alignment explanation
Indices: 52778160--52778191 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
52778150 TTTTATAGCC
*
52778160 TTATTCATTTCT
1 TTATTTATTTCT
52778172 TTATTTATTTCT
1 TTATTTATTTCT
52778184 TTATTTAT
1 TTATTTAT
52778192 ATTTTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTATTTCT
Found at i:52796189 original size:79 final size:79
Alignment explanation
Indices: 52796058--52796215 Score: 289
Period size: 79 Copynumber: 2.0 Consensus size: 79
52796048 ATTAAGATTG
*
52796058 CTCTTTTCGATATGGCTCCTTTGAAGGTTCCGGGTAGTGATGATTTTCATGCTCTCTTTTTCTAA
1 CTCTTTTCGATATGGCTCCTTTGAAGGTTCCAGGTAGTGATGATTTTCATGCTCTCTTTTTCTAA
52796123 AATCAGTGGGTAGT
66 AATCAGTGGGTAGT
* *
52796137 CTCTTTTCGATATGGCTCCTTTGAAGGTTCTAGGTAGTGATGATTTTCATGCTCTTTTTTTCTAA
1 CTCTTTTCGATATGGCTCCTTTGAAGGTTCCAGGTAGTGATGATTTTCATGCTCTCTTTTTCTAA
52796202 AATCAGTGGGTAGT
66 AATCAGTGGGTAGT
52796216 TGTTGGAAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.43
Consensus pattern (79 bp):
CTCTTTTCGATATGGCTCCTTTGAAGGTTCCAGGTAGTGATGATTTTCATGCTCTCTTTTTCTAA
AATCAGTGGGTAGT
Found at i:52798786 original size:16 final size:16
Alignment explanation
Indices: 52798761--52798799 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
52798751 TTAGTTCGCT
*
52798761 GTAATAGAATAGAGGC
1 GTAATAGAATAGAAGC
*
52798777 GTAATGGAATAGAAGC
1 GTAATAGAATAGAAGC
52798793 GTAATAG
1 GTAATAG
52798800 TAATTCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.31, T:0.21
Consensus pattern (16 bp):
GTAATAGAATAGAAGC
Found at i:52799097 original size:40 final size:40
Alignment explanation
Indices: 52799053--52799137 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 40
52799043 ATTTAATAAA
* ** *
52799053 AATATATAATTTAATAAAATTCTTA-ATATTAGATATTCTT
1 AATATATAAATTAATAAAATAATAATATATTAGATATT-TT
*
52799093 AATAT-TAAATTACTAAAATAATAATATATTAGATATTTT
1 AATATATAAATTAATAAAATAATAATATATTAGATATTTT
52799132 -ATATAT
1 AATATAT
52799138 TTTTCTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
38 4 0.11
39 17 0.45
40 17 0.45
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (40 bp):
AATATATAAATTAATAAAATAATAATATATTAGATATTTT
Found at i:52800901 original size:4 final size:4
Alignment explanation
Indices: 52800892--52800941 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
52800882 CATGATGTTC
*
52800892 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
52800940 AT
1 AT
52800942 TTGGTTTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:52802766 original size:191 final size:191
Alignment explanation
Indices: 52802436--52802819 Score: 723
Period size: 191 Copynumber: 2.0 Consensus size: 191
52802426 ATGAGGGCAG
*
52802436 AATATGGAATAGAAAATAAGAAACGGTAAGGAATCCCTAATCGACGCTCAGTGTGGGGAATGCCT
1 AATATGGAACAGAAAATAAGAAACGGTAAGGAATCCCTAATCGACGCTCAGTGTGGGGAATGCCT
52802501 ATTACAGCCAATGGGCGTAATAGGGACGGAATGGATTCGGGACGTAATGCTATTACGGGCAACCA
66 ATTACAGCCAATGGGCGTAATAGGGACGGAATGGATTCGGGACGTAATGCTATTACGGGCAACCA
* *
52802566 AACGCCCGTTTGGTGGTGGGCCCGCAGAATAGGGGGAATGCATTCCTATTTCTCCTAACCA
131 AACGCCCGTTTGGTGGTGGGCCCACAGAATAGGGGGAATGCATTCCTATTTCTCCCAACCA
52802627 AATATGGAACAGAAAATAAGAAACGGTAAGGAATCCCTAATCGACGCTCAGTGTGGGGAATGCCT
1 AATATGGAACAGAAAATAAGAAACGGTAAGGAATCCCTAATCGACGCTCAGTGTGGGGAATGCCT
52802692 ATTACAGCCAATGGGCGTAATAGGGACGGAATGGATTCGGGACGTAATGCTATTACGGGCAACCA
66 ATTACAGCCAATGGGCGTAATAGGGACGGAATGGATTCGGGACGTAATGCTATTACGGGCAACCA
* *
52802757 AATGCCCGTTTGGTGGTGGGCCTACAGAATAGGGGGAATGCATTCCTATTTCTCCCAACCA
131 AACGCCCGTTTGGTGGTGGGCCCACAGAATAGGGGGAATGCATTCCTATTTCTCCCAACCA
52802818 AA
1 AA
52802820 CATAGTGTAA
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
191 188 1.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (191 bp):
AATATGGAACAGAAAATAAGAAACGGTAAGGAATCCCTAATCGACGCTCAGTGTGGGGAATGCCT
ATTACAGCCAATGGGCGTAATAGGGACGGAATGGATTCGGGACGTAATGCTATTACGGGCAACCA
AACGCCCGTTTGGTGGTGGGCCCACAGAATAGGGGGAATGCATTCCTATTTCTCCCAACCA
Found at i:52806703 original size:3 final size:3
Alignment explanation
Indices: 52806695--52806762 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
52806685 CTAGCGTTGC
52806695 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
52806743 ATT ATC GTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
52806763 ACTTATTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:52806840 original size:14 final size:13
Alignment explanation
Indices: 52806821--52806856 Score: 63
Period size: 14 Copynumber: 2.7 Consensus size: 13
52806811 ATATCATAAG
52806821 TTTTATATTATTA
1 TTTTATATTATTA
52806834 TTGTTATATTATTA
1 TT-TTATATTATTA
52806848 TTTTATATT
1 TTTTATATT
52806857 TACTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTATATTATTA
Found at i:52806866 original size:14 final size:14
Alignment explanation
Indices: 52806821--52806865 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
52806811 ATATCATAAG
52806821 TTTTATA-TTATTA
1 TTTTATATTTATTA
52806834 TTGTTATA-TTATTA
1 TT-TTATATTTATTA
52806848 TTTTATATTTACTTA
1 TTTTATATTTA-TTA
52806863 TTT
1 TTT
52806866 AAATTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.24
14 16 0.55
15 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTTATATTTATTA
Found at i:52806926 original size:22 final size:24
Alignment explanation
Indices: 52806901--52806951 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
52806891 ATTATTACTA
* *
52806901 TTATAGC-TATT-TATTTATATCT
1 TTATAGCTTATTATATATATACCT
*
52806923 TTATATCTTATTATATATATACCT
1 TTATAGCTTATTATATATATACCT
52806947 TTATA
1 TTATA
52806952 AACGTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.25
23 4 0.17
24 14 0.58
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATAGCTTATTATATATATACCT
Found at i:52807878 original size:108 final size:108
Alignment explanation
Indices: 52807594--52808013 Score: 533
Period size: 108 Copynumber: 3.8 Consensus size: 108
52807584 AAAAATAATA
* * * * * *
52807594 AAGGCAATGTTTTGCTTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AAGGCAATATTTTGCGTTTGGAAATTCGAG-AAACGTGCCCTAAGGTACTGGGTTTC-A-ATTTC
*
52807659 TCGTTCGACCAAATAGGCTAAATATCCTTTT-AAAAACTTTTCAAAAAT
63 TCGTTCGACCAAAT-GACTAAATATCCTTTTCAAAAA-TTTTC-AAAAT
* * *
52807707 AAGGCAATGTTTTGCGTTTAGAAATTCGAGGAACACGTGCCCTAAGGTACTGGGTTTCGATTTCT
1 AAGGCAATATTTTGCGTTTGGAAATTCGA-GAA-ACGTGCCCTAAGGTACTGGGTTTCAATTTCT
* * *
52807772 CATTCCACCAAATGACTTAATATCCTTTTCAAAAATTTTCAAAAT
64 CGTTCGACCAAATGACTAAATATCCTTTTCAAAAATTTTCAAAAT
*
52807817 AAGGCAATATTTTGAGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTGGGTTTCAATTTCTCG
1 AAGGCAATATTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTGGGTTTCAATTTCTCG
52807882 TTCGACCAAAT-AGCTAAATATCCTTTTCAAAAATTTTCAAAAT
66 TTCGACCAAATGA-CTAAATATCCTTTTCAAAAATTTTCAAAAT
* * * * *
52807925 AAGGCAATATTTTGCGTTTGGAAATTCGAGGAGCGTGCTCTAAGGTACTGGGTTTCGATTTCACG
1 AAGGCAATATTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTGGGTTTCAATTTCTCG
*
52807990 TT-TAGCCAAATTG-CTAAATATCCT
66 TTCGA-CCAAA-TGACTAAATATCCT
52808014 CTTGAATTTT
Statistics
Matches: 275, Mismatches: 25, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
107 2 0.01
108 147 0.53
109 4 0.01
110 31 0.11
111 19 0.07
112 21 0.08
113 29 0.11
114 22 0.08
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (108 bp):
AAGGCAATATTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTGGGTTTCAATTTCTCG
TTCGACCAAATGACTAAATATCCTTTTCAAAAATTTTCAAAAT
Found at i:52811518 original size:29 final size:26
Alignment explanation
Indices: 52811454--52811519 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 26
52811444 TCGATTAAAC
*
52811454 AATTT-TTAAACAATTTTTTAATTTA
1 AATTTATTAAACAATTTTTTAATTCA
52811479 AAGTATCTATTAAACAATTTTTTAAACATTCA
1 AA-T-T-TATTAAACAATTTTTT--A-ATTCA
52811511 AATTTATTA
1 AATTTATTA
52811520 GTTTAAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
25 2 0.06
26 1 0.03
27 1 0.03
28 1 0.03
29 19 0.58
30 1 0.03
31 2 0.06
32 6 0.18
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (26 bp):
AATTTATTAAACAATTTTTTAATTCA
Found at i:52811612 original size:12 final size:12
Alignment explanation
Indices: 52811574--52811612 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
52811564 AAAAACCAAA
52811574 TTTTAAAATTAT
1 TTTTAAAATTAT
* *
52811586 TTTTATAGTTAAT
1 TTTTAAAATT-AT
52811599 TTTTAAAATTAT
1 TTTTAAAATTAT
52811611 TT
1 TT
52811613 AACATTAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:52811731 original size:14 final size:14
Alignment explanation
Indices: 52811706--52811749 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
52811696 ATAACTTAAG
52811706 TAATTAAAATATAA
1 TAATTAAAATATAA
* *
52811720 TATTTTAAATATAAA
1 TAATTAAAATAT-AA
52811735 TAATTAAAATATAA
1 TAATTAAAATATAA
52811749 T
1 T
52811750 CTAAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATTAAAATATAA
Found at i:52811736 original size:15 final size:15
Alignment explanation
Indices: 52811706--52811748 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
52811696 ATAACTTAAG
52811706 TAATTAAAATAT-AA
1 TAATTAAAATATAAA
* *
52811720 TATTTTAAATATAAA
1 TAATTAAAATATAAA
52811735 TAATTAAAATATAA
1 TAATTAAAATATAA
52811749 TCTAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTAAAATATAAA
Found at i:52813101 original size:30 final size:28
Alignment explanation
Indices: 52813043--52813110 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 28
52813033 GTAATATATT
52813043 TATTTAATTACTTTTTATTTAAGTAAATAGA
1 TATTT-ATTACTTTTTATTTAAGTAAAT--A
52813074 TATTTATTA-TTTATTA-TTAAGTAAAATA
1 TATTTATTACTTT-TTATTTAAGT-AAATA
52813102 TATTTATTA
1 TATTTATTA
52813111 ATTAAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
28 10 0.29
29 9 0.26
30 11 0.31
31 5 0.14
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (28 bp):
TATTTATTACTTTTTATTTAAGTAAATA
Found at i:52814543 original size:28 final size:30
Alignment explanation
Indices: 52814506--52814573 Score: 95
Period size: 28 Copynumber: 2.3 Consensus size: 30
52814496 ATTATTTAAT
* *
52814506 TAATAAATATCT-TTTACTT-AATAATAAA
1 TAATAAATATCTATTTACTTAAACAAAAAA
52814534 TAATAAATATCTATTTACTTAAACAAAAAA
1 TAATAAATATCTATTTACTTAAACAAAAAA
52814564 TAATTAAATA
1 TAA-TAAATA
52814574 AATATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 12 0.34
29 7 0.20
30 10 0.29
31 6 0.17
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.38
Consensus pattern (30 bp):
TAATAAATATCTATTTACTTAAACAAAAAA
Found at i:52814612 original size:15 final size:16
Alignment explanation
Indices: 52814589--52814621 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
52814579 ATTATAATTG
52814589 TACAAATATA-ATTTT
1 TACAAATATATATTTT
*
52814604 TACACATATATATTTT
1 TACAAATATATATTTT
52814620 TA
1 TA
52814622 TTACCATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TACAAATATATATTTT
Found at i:52815018 original size:16 final size:16
Alignment explanation
Indices: 52814992--52815030 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
52814982 AGTCTTCACT
52814992 TTTTCGATGCCCGTAAA
1 TTTT-GATGCCCGTAAA
52815009 TTTTGATGCCCGTAAA
1 TTTTGATGCCCGTAAA
52815025 TTTTGA
1 TTTTGA
52815031 GTCACTCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (16 bp):
TTTTGATGCCCGTAAA
Found at i:52816299 original size:22 final size:22
Alignment explanation
Indices: 52816274--52816365 Score: 105
Period size: 22 Copynumber: 4.2 Consensus size: 22
52816264 AAATTCAATA
* *
52816274 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
52816296 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
*
52816318 TCAATTCCCTTC-AAAATTTTC
1 TCAATTCCCTTCAAAAATTCTC
* *
52816339 ATCAATTTCCTTCCAAAATTCTC
1 -TCAATTCCCTTCAAAAATTCTC
52816362 TCAA
1 TCAA
52816366 ACTCTCAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
21 7 0.11
22 46 0.75
23 8 0.13
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:52816381 original size:52 final size:50
Alignment explanation
Indices: 52816315--52816416 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 50
52816305 TTCAAAATTT
** * *
52816315 CTCTCAATTCCCTTCAAAATTTTCATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCAAAATCCTC-TCAATTTCCTTCAAAAAATCTC-CAAA
*
52816367 CTCTCAAATT-CCTTCCAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
52816417 TCCATATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
50 4 0.09
51 20 0.45
52 16 0.36
53 4 0.09
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (50 bp):
CTCTCAATTCCCTTCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:52816657 original size:24 final size:23
Alignment explanation
Indices: 52816602--52816657 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
52816592 TAAATTTTAA
*
52816602 ATTTTTTTAAGATATTTTTATTT
1 ATTTTTTTAAGATATTTTTATAT
52816625 ATGTATTTTT-AGATATTTATTAATAT
1 AT-T-TTTTTAAGATATTT-TT-ATAT
52816651 ATTTTTT
1 ATTTTTT
52816658 GTTATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
ATTTTTTTAAGATATTTTTATAT
Found at i:52818827 original size:28 final size:28
Alignment explanation
Indices: 52818796--52819150 Score: 400
Period size: 28 Copynumber: 13.1 Consensus size: 28
52818786 CTAACCCTAC
52818796 TTAATTAAAAACCCTAACCTAACTTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
52818824 TTAATTAAAAACCCTAACCTAA-TT-A-
1 TTAATTAAAAACCCTAACCTAACTTAAT
**
52818849 --AATTAAAAACCCTAACCTTATTTTAAT
1 TTAATTAAAAACCCTAACC-TAACTTAAT
* * *
52818876 TAAATTAAAAACCCTAACCTAACCTACT
1 TTAATTAAAAACCCTAACCTAACTTAAT
* *
52818904 TAAATTAAAAACCCTAACCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
52818932 TTAATTAAAAACCCTAACCTAA-TT-A-
1 TTAATTAAAAACCCTAACCTAACTTAAT
**
52818957 --AATTAAAAACCCTAACCTTATTTTAAT
1 TTAATTAAAAACCCTAACC-TAACTTAAT
* * *
52818984 TAAATTAAAAACCCTAACCTAACCTACT
1 TTAATTAAAAACCCTAACCTAACTTAAT
* **
52819012 TAAATTAAAAACCCTAACCTAACCCAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
52819040 TTAATTAAAAACCCTAACCTAATTTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
* *
52819068 TAAATTAAAAACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCTAA-CCTAACTTAAT
52819097 TTAATTAAAAACCCTAA-C---C-TAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
52819120 TTAATTAAAAACCCTAACCT-ACTTAAA
1 TTAATTAAAAACCCTAACCTAACTTAAT
52819147 TTAA
1 TTAA
52819151 AAACCCTAAT
Statistics
Matches: 286, Mismatches: 24, Indels: 35
0.83 0.07 0.10
Matches are distributed among these distances:
23 55 0.19
24 6 0.02
25 4 0.01
26 5 0.02
27 11 0.04
28 146 0.51
29 59 0.21
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (28 bp):
TTAATTAAAAACCCTAACCTAACTTAAT
Found at i:52818913 original size:108 final size:107
Alignment explanation
Indices: 52818785--52819140 Score: 549
Period size: 108 Copynumber: 3.3 Consensus size: 107
52818775 GATTAAAATC
*
52818785 CCTAACCCTACTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTAATTAA
1 CCTAA-CCTACTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAATTAA
52818850 ATTAAAAACCCTAACCTTATTTTAATTAAATTAAAAACCCTAA
65 ATTAAAAACCCTAACCTTATTTTAATTAAATTAAAAACCCTAA
52818893 CCTAACCTACTTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAATTAA
1 CCTAACCTACTT-AATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAATTAA
52818958 ATTAAAAACCCTAACCTTATTTTAATTAAATTAAAAACCCTAA
65 ATTAAAAACCCTAACCTTATTTTAATTAAATTAAAAACCCTAA
*
52819001 CCTAACCTACTTAAATTAAAAACCCTAACCTAACCCAATTTAATTAAAAACCCTAACCTAATTTA
1 CCTAACCTACTT-AATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACC-----TA
* *** *
52819066 ATTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA
60 ATTAAATTAAAAACCCTAACCTTATTTTAATTAAATTAAAAACCCTAA
52819114 CCTAA--T--TTAATTAAAAACCCTAACCTA
1 CCTAACCTACTTAATTAAAAACCCTAACCTA
52819141 CTTAAATTAA
Statistics
Matches: 235, Mismatches: 7, Indels: 12
0.93 0.03 0.05
Matches are distributed among these distances:
107 7 0.03
108 175 0.74
109 2 0.01
111 1 0.00
113 50 0.21
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (107 bp):
CCTAACCTACTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAA
TTAAAAACCCTAACCTTATTTTAATTAAATTAAAAACCCTAA
Found at i:52819135 original size:18 final size:18
Alignment explanation
Indices: 52819091--52819166 Score: 53
Period size: 23 Copynumber: 3.7 Consensus size: 18
52819081 CTAACCCTAA
52819091 CCTAATTTAATTAAAAACCC
1 CCTAATTTAATTAAAAA--C
52819111 TAACCTAATTTAATTAAAAAC
1 ---CCTAATTTAATTAAAAAC
52819132 CCTAACCTACTTAAATTAAAAAC
1 CCTAA--T--TT-AATTAAAAAC
*
52819155 CCTAATTAAATT
1 CCTAATTTAATT
52819167 GTAGTTTTAC
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
18 9 0.19
19 1 0.02
20 1 0.02
21 2 0.04
22 2 0.04
23 32 0.68
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (18 bp):
CCTAATTTAATTAAAAAC
Found at i:52820271 original size:85 final size:84
Alignment explanation
Indices: 52820123--52820308 Score: 327
Period size: 85 Copynumber: 2.2 Consensus size: 84
52820113 CAAACTTGCT
*
52820123 ACTGTAGCGAAATCGCGTCCACGAAGGCGCGATTTGACATTATTTGCTCAGAAACGTCAAAAAAA
1 ACTGTAGCGAAATCGCGTCCACGAAGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
52820188 AATTATTTCCTACATGACCA
66 AA-TATTTCCTACATGACCA
* * *
52820208 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGATACTATTTGCTCAGAAACGTCGAAAAAA
1 ACTGTAGCGAAATCGCGTCCACGAAGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
52820273 AATATTTCCTACATGACCA
66 AATATTTCCTACATGACCA
52820292 ACTGTAGCGAAATCGCG
1 ACTGTAGCGAAATCGCG
52820309 CGATTTCACA
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 34 0.35
85 63 0.65
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (84 bp):
ACTGTAGCGAAATCGCGTCCACGAAGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
AATATTTCCTACATGACCA
Found at i:52821187 original size:28 final size:28
Alignment explanation
Indices: 52821162--52821216 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
52821152 AAAAAATTAT
*
52821162 CATTTTAAAAATAAATTGGGATAATTTC
1 CATTTCAAAAATAAATTGGGATAATTTC
*
52821190 CATTTCAAAAATAAATTTGGATAATTT
1 CATTTCAAAAATAAATTGGGATAATTT
52821217 GTTTGATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (28 bp):
CATTTCAAAAATAAATTGGGATAATTTC
Found at i:52825470 original size:18 final size:18
Alignment explanation
Indices: 52825449--52825501 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
52825439 GAATTATAAA
52825449 GTATAAAAATATATATAT
1 GTATAAAAATATATATAT
* *
52825467 GTATATAAGAATATGTATGT
1 GTATA-AA-AATATATATAT
*
52825487 ATATAAAAACTATAT
1 GTATAAAAA-TATAT
52825502 GAAAATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 7 0.25
19 8 0.29
20 13 0.46
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (18 bp):
GTATAAAAATATATATAT
Found at i:52825479 original size:20 final size:18
Alignment explanation
Indices: 52825449--52825501 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
52825439 GAATTATAAA
52825449 GTATA-AAAATATATATAT
1 GTATATAAAA-ATATATAT
* *
52825467 GTATATAAGAATATGTAT
1 GTATATAAAAATATATAT
52825485 GTATATAAAAACTATAT
1 GTATATAAAAA-TATAT
52825502 GAAAATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (18 bp):
GTATATAAAAATATATAT
Found at i:52828600 original size:14 final size:14
Alignment explanation
Indices: 52828581--52828620 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52828571 TTGTTTGGCA
52828581 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
52828595 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
52828609 GGAAAATGTTTT
1 GTAAAATGTTTT
52828621 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:52828629 original size:20 final size:20
Alignment explanation
Indices: 52828604--52828643 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52828594 CGTAAAATGA
*
52828604 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
52828624 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
52828644 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:52828633 original size:34 final size:35
Alignment explanation
Indices: 52828589--52828655 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
52828579 CAGTAAAATG
*
52828589 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
52828623 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
52828656 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:52828659 original size:14 final size:15
Alignment explanation
Indices: 52828583--52828659 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
52828573 GTTTGGCAGT
* *
52828583 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
52828597 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
52828611 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
52828631 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
52828646 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
52828660 TGTTTGGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:52828714 original size:32 final size:31
Alignment explanation
Indices: 52828636--52828720 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
52828626 TCTGTAAAAT
* *
52828636 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGGCA
* * *
52828669 AATCTGTGTAAAATATTTTCTGCTGTTTGGCA
1 GATTTCTG-AAAATATTTTCTGCTGTTTGGCA
52828701 GATTTCCTGAAAATATTTTC
1 GATTT-CTGAAAATATTTTC
52828721 CGGAAAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
31 1 0.02
32 36 0.86
33 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGGCA
Found at i:52828772 original size:14 final size:14
Alignment explanation
Indices: 52828753--52828780 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52828743 ATTTTACATA
52828753 TATTAATATATATT
1 TATTAATATATATT
52828767 TATTAATATATATT
1 TATTAATATATATT
52828781 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:52829087 original size:71 final size:72
Alignment explanation
Indices: 52828971--52829113 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 72
52828961 ATAATAATAT
* *
52828971 TATCCAAATACATAATTAATGGTACACCAGATAGTAACAACATTGT-CTAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
52829035 CCACATA
66 CCACATA
*
52829042 TATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTGTCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
52829107 CCACATA
66 CCACATA
52829114 AATATATCAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 44 0.65
72 24 0.35
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (72 bp):
TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATATTACA
CCACATA
Found at i:52830102 original size:35 final size:36
Alignment explanation
Indices: 52830056--52830124 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
52830046 ATTCAACCAT
52830056 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
*
52830091 TTCAATATCCAACAAGCTTAAAACGTAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
52830125 TCTAACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:52834167 original size:28 final size:27
Alignment explanation
Indices: 52834135--52834202 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
52834125 AAGCTTTGAG
52834135 GAATGGAAAATGTCTGCTGCTTAGA-AGA
1 GAATGGAAAATGTCT-CTGCTTAGAGA-A
52834163 GAATGGAAAATG--TCTGCTTAGAGAA
1 GAATGGAAAATGTCTCTGCTTAGAGAA
52834188 GAATGGAAAATGTCT
1 GAATGGAAAATGTCT
52834203 TACCAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
25 22 0.59
26 2 0.05
27 1 0.03
28 12 0.32
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.25
Consensus pattern (27 bp):
GAATGGAAAATGTCTCTGCTTAGAGAA
Found at i:52834700 original size:19 final size:19
Alignment explanation
Indices: 52834657--52834701 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
52834647 AGTTTTATTT
52834657 AATA-AAATAAATTTGTAA
1 AATATAAATAAATTTGTAA
*
52834675 CAT-TAAAT-AATTTGTTAA
1 AATATAAATAAATTTG-TAA
52834693 AATATAAAT
1 AATATAAAT
52834702 TATATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 6 0.27
18 11 0.50
19 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
AATATAAATAAATTTGTAA
Found at i:52835883 original size:125 final size:124
Alignment explanation
Indices: 52835739--52836019 Score: 370
Period size: 125 Copynumber: 2.3 Consensus size: 124
52835729 TTTTTTCGAG
* ** ** * *
52835739 TTGACGTTTCTG-GTTAAATAGTGGGAAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
* *
52835803 GAAATAGTGGCCTCGTGGACGCGATTTCGCTACAG-TGGTCATGT-GAGAAATAATTTTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAG-GAAATAA-TTTTTT
* * * *
52835863 TTGACGTTTTCTGAGGAAATAGTATAAAATTGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
*
52835928 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTT
*
52835988 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTGTAAAATCGC
52836020 GCCCTCGTGG
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
124 28 0.21
125 90 0.66
126 17 0.12
127 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTG
AAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTT
Found at i:52836070 original size:84 final size:85
Alignment explanation
Indices: 52835929--52836132 Score: 401
Period size: 85 Copynumber: 2.4 Consensus size: 85
52835919 AGAAATTGTG
52835929 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAA-TTTTTTTTGAC
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGAC
52835993 GTTTCTGAGCAAATAGTGTC
66 GTTTCTGAGCAAATAGTGTC
52836013 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGAC
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGAC
52836078 GTTTCTGAGCAAATAGTGTC
66 GTTTCTGAGCAAATAGTGTC
52836098 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
52836133 AGTAAGTTTG
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 53 0.45
85 66 0.55
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (85 bp):
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGAC
GTTTCTGAGCAAATAGTGTC
Found at i:52837111 original size:18 final size:18
Alignment explanation
Indices: 52837088--52837140 Score: 52
Period size: 23 Copynumber: 2.7 Consensus size: 18
52837078 GTAAAACTAC
52837088 AATTTAATTAGGGTTTTT
1 AATTTAATTAGGGTTTTT
52837106 AATTTAAGTAGGTTAGGGTTTTT
1 AATTT-A--A--TTAGGGTTTTT
*
52837129 AATTAAATTAGG
1 AATTTAATTAGG
52837141 TTAGGGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
18 10 0.34
19 1 0.03
20 1 0.03
21 1 0.03
22 1 0.03
23 15 0.52
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (18 bp):
AATTTAATTAGGGTTTTT
Found at i:52837125 original size:23 final size:23
Alignment explanation
Indices: 52837095--52837168 Score: 130
Period size: 23 Copynumber: 3.2 Consensus size: 23
52837085 TACAATTTAA
* *
52837095 TTAGGGTTTTTAATTTAAGTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52837118 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52837141 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
52837164 TTAGG
1 TTAGG
52837169 TTAGGGTTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.47
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAGG
Found at i:52837145 original size:28 final size:28
Alignment explanation
Indices: 52837104--52837361 Score: 267
Period size: 28 Copynumber: 9.1 Consensus size: 28
52837094 ATTAGGGTTT
*
52837104 TTAATTTAAG-TAGGTTAGGGTTTTTAA
1 TTAAATTAAGTTAGGTTAGGGTTTTTAA
52837131 TT--A--AA-TTAGGTTAGGGTTTTTAA
1 TTAAATTAAGTTAGGTTAGGGTTTTTAA
52837154 TTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTAAATTA----A-GTTA-GGTTAGGGTTTTTAA
* *
52837188 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTAAATTAAGTTAGGTTAGGGTTTTTAA
*
52837216 TTAAATTACGTTAGGTTAGGGTTTTTAA
1 TTAAATTAAGTTAGGTTAGGGTTTTTAA
* * *
52837244 TTTAAGTAGGTTAGGTTAGGGTTTTTAA
1 TTAAATTAAGTTAGGTTAGGGTTTTTAA
* * * *
52837272 TTTAATTAAAATAAGGTTAGAGTTTTTAA
1 TTAAATT-AAGTTAGGTTAGGGTTTTTAA
* * *
52837301 TTTAATTAAAATAAGGTTAGGGTTTTTAA
1 TTAAATT-AAGTTAGGTTAGGGTTTTTAA
*
52837330 TTAAATTAGGTTAGGTTAGGGTTTTTAA
1 TTAAATTAAGTTAGGTTAGGGTTTTTAA
52837358 TTAA
1 TTAA
52837362 GTAGGGTTAG
Statistics
Matches: 199, Mismatches: 19, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
23 21 0.11
25 1 0.01
27 3 0.02
28 93 0.47
29 54 0.27
30 1 0.01
31 1 0.01
33 3 0.02
34 22 0.11
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (28 bp):
TTAAATTAAGTTAGGTTAGGGTTTTTAA
Found at i:52837214 original size:62 final size:60
Alignment explanation
Indices: 52837126--52837359 Score: 274
Period size: 57 Copynumber: 4.0 Consensus size: 60
52837116 GGTTAGGGTT
52837126 TTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTA--TTAGGTTAGGGTTAGGGTTTTTAA
*
52837188 TTTAATTAAATTAGGTTAGGGTTTTTAATT-AA--ATTACGTTA-GGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTATTAGGTTAGGGTTAGGGTTTTTAA
* ** * ** * *
52837244 TTTAAGTAGGTTAGGTTAGGGTTTTTAATTTAATTA--A-AATAAGGTTAGAGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTATTAGGTTAGGGTTAGGGTTTTTAA
*
52837301 TTTAATTAAAATAAGGTTAGGGTTTTTAATT-AA--ATTAGGTTA-GGTTAGGGTTTTTAA
1 TTTAATT-AAATTAGGTTAGGGTTTTTAATTAAATTATTAGGTTAGGGTTAGGGTTTTTAA
52837358 TT
1 TT
52837360 AAGTAGGGTT
Statistics
Matches: 150, Mismatches: 14, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
55 1 0.01
56 44 0.29
57 49 0.33
58 22 0.15
59 2 0.01
61 2 0.01
62 30 0.20
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.47
Consensus pattern (60 bp):
TTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTATTAGGTTAGGGTTAGGGTTTTTAA
Found at i:52837299 original size:24 final size:26
Alignment explanation
Indices: 52837271--52837343 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 26
52837261 AGGGTTTTTA
52837271 ATTTAATTAAAATAAGGTTAGAGTTTTT
1 ATTTAATTAAAATAAGGTTAGAG--TTT
*
52837299 AATTTAATTAAAATAAGGTTAG-GGTT
1 -ATTTAATTAAAATAAGGTTAGAGTTT
*
52837325 -TTTAATT-AAATTAGGTTAG
1 ATTTAATTAAAATAAGGTTAG
52837344 GTTAGGGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.26
24 7 0.17
26 2 0.05
28 1 0.02
29 21 0.50
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (26 bp):
ATTTAATTAAAATAAGGTTAGAGTTT
Found at i:52839690 original size:29 final size:30
Alignment explanation
Indices: 52839652--52839708 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
52839642 TGAAAATATT
*
52839652 AAAAATTTTAAAATTAT-TTAAAAAAATAA
1 AAAAAATTTAAAATTATCTTAAAAAAATAA
*
52839681 AAAAAATTTAAAATTTTCTTAAAAAAAT
1 AAAAAATTTAAAATTATCTTAAAAAAAT
52839709 GAAATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAAAATTTAAAATTATCTTAAAAAAATAA
Found at i:52839780 original size:22 final size:22
Alignment explanation
Indices: 52839750--52839791 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52839740 ATTTGGAGAT
*
52839750 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
52839772 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
52839792 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:52839818 original size:22 final size:23
Alignment explanation
Indices: 52839793--52839884 Score: 95
Period size: 22 Copynumber: 4.2 Consensus size: 23
52839783 ATTTGAGAGT
52839793 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
52839815 TTGATG-GAAATTTT-GAAGGGAA
1 TTGA-GAGAAATTTTGGAAGGAAA
* *
52839837 TTAAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
52839859 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
52839881 TTGA
1 TTGA
52839885 TATTGAATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
21 10 0.17
22 37 0.64
23 11 0.19
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:52840792 original size:2 final size:2
Alignment explanation
Indices: 52840785--52840813 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52840775 ATCAGTTCTT
52840785 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
52840814 TTTCTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:52852505 original size:26 final size:26
Alignment explanation
Indices: 52852451--52852511 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
52852441 GCCTAGCGAG
* *
52852451 CTTGAGTTTAAATGGGTCAGAGGACC
1 CTTGAGTTTAAATGGGTCAGAGAAAC
*
52852477 CTTGAGTTTAAGTGGGTC-GAAGAAAC
1 CTTGAGTTTAAATGGGTCAG-AGAAAC
*
52852503 CTTAAGTTT
1 CTTGAGTTT
52852512 GATTTGGTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.03
26 29 0.97
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (26 bp):
CTTGAGTTTAAATGGGTCAGAGAAAC
Found at i:52855752 original size:25 final size:24
Alignment explanation
Indices: 52855724--52855779 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
52855714 TTTTTATGTA
52855724 ATCTATATCTATATTTATAATTCAT
1 ATCTATATCTATATTTAT-ATTCAT
* * *
52855749 ATCTATGTTTATATTTATATTTAT
1 ATCTATATCTATATTTATATTCAT
52855773 A-CTATAT
1 ATCTATAT
52855780 ATTAAGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.19
24 6 0.22
25 16 0.59
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (24 bp):
ATCTATATCTATATTTATATTCAT
Found at i:52858347 original size:34 final size:34
Alignment explanation
Indices: 52858304--52858406 Score: 197
Period size: 34 Copynumber: 3.0 Consensus size: 34
52858294 TCAACAAGAT
*
52858304 CTCATATTTGGAAAAATCGACTCAAAACCTAGTA
1 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
52858338 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
1 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
52858372 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
1 CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
52858406 C
1 C
52858407 ATGTCATATA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (34 bp):
CTCATATTTGGCAAAATCGACTCAAAACCTAGTA
Found at i:52860451 original size:23 final size:22
Alignment explanation
Indices: 52860408--52860451 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
52860398 TTCTAAGTCG
52860408 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
52860431 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
52860452 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:52860558 original size:45 final size:45
Alignment explanation
Indices: 52860496--52860589 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
52860486 AACAGATACT
* * *
52860496 CGGTGGATTCAGAACATAGCAACCACGTTATTAATCAATAATGTC
1 CGGTGGAATCAGAACATAGCAACCACCTTACTAATCAATAATGTC
* * *
52860541 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGAACATAGCAACCACCTTACTAATCAATAATGTC
52860586 CGGT
1 CGGT
52860590 TCACATAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGAACATAGCAACCACCTTACTAATCAATAATGTC
Found at i:52860658 original size:51 final size:50
Alignment explanation
Indices: 52860586--52860781 Score: 223
Period size: 51 Copynumber: 3.9 Consensus size: 50
52860576 CAATGATGTT
* * *
52860586 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * * * *
52860637 TGATACACGTAGTAGCTTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
** * * * *
52860688 CGGTATGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
52860738 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
52860782 CACTTTCACT
Statistics
Matches: 116, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 72 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:52860771 original size:101 final size:101
Alignment explanation
Indices: 52860593--52860777 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 101
52860583 GTTCGGTTCA
* * *
52860593 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCTTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
52860658 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* *
52860695 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
52860759 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
52860778 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 34 0.44
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:52865901 original size:16 final size:16
Alignment explanation
Indices: 52865880--52865928 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
52865870 TTCGCTGTAT
52865880 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
52865896 TGGAATAGAGGCGAAA
1 TGGAATAGAGGCGTAA
52865912 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
52865928 T
1 T
52865929 AGTAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.37, T:0.18
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:52866003 original size:44 final size:45
Alignment explanation
Indices: 52865910--52866004 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 45
52865900 ATAGAGGCGA
*
52865910 AATGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGT
1 AATGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGG
* *
52865955 AATGGAATAGAGGCGTAATAGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGTAAATCAAT-TGTTTGGTTGAATGG
52865999 AATGGA
1 AATGGA
52866005 GGTGTAATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.50
45 22 0.48
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (45 bp):
AATGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGG
Found at i:52866181 original size:18 final size:17
Alignment explanation
Indices: 52866160--52866194 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52866150 TTATTATTAA
*
52866160 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52866178 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52866195 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52866351 original size:10 final size:12
Alignment explanation
Indices: 52866318--52866369 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
52866308 TATAATACTA
52866318 TAAAATATAATT
1 TAAAATATAATT
52866330 TAAAATATAATT
1 TAAAATATAATT
*
52866342 TAAAATAATTATT
1 TAAAAT-ATAATT
*
52866355 ATTAAATATAATT
1 -TAAAATATAATT
52866368 TA
1 TA
52866370 TAATCTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 19 0.56
13 10 0.29
14 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:52866388 original size:145 final size:144
Alignment explanation
Indices: 52866083--52866373 Score: 380
Period size: 145 Copynumber: 2.0 Consensus size: 144
52866073 GATTATTGTT
* *
52866083 ATTGTTATTAAATTTTAATAAGATTATTAATATCATTAATAAATAATTTAATCATATTTTAACAT
1 ATTGTTATT-AATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAACAT
** * *
52866148 AATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTG
65 AATTATTATTAAATATATAATAATTAAAATATATAATTTAATAAAAATCTTAATAATCAATATTA
*
52866213 TTATATGAATTTATT
130 TTATATGAATTTATA
*
52866228 ATTGTTATTAAATTTTAATCAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAACAT
1 ATTGTTATT-AATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAACAT
*
52866293 AATTATTATTAAATATATAAT-ACTATAAA-ATATAATTTAA-AATATAAT-TTAA-AAT-AATT
65 AATTATTATTAAATATATAATAATTA-AAATATATAATTTAATAA-A-AATCTTAATAATCAA-T
52866352 ATTATTAAATAT-AATTTATA
126 ATTATT--ATATGAATTTATA
52866372 AT
1 AT
52866374 CTACTTTATT
Statistics
Matches: 131, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
142 2 0.02
143 11 0.08
144 28 0.21
145 90 0.69
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (144 bp):
ATTGTTATTAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTTAACATA
ATTATTATTAAATATATAATAATTAAAATATATAATTTAATAAAAATCTTAATAATCAATATTAT
TATATGAATTTATA
Found at i:52869110 original size:21 final size:20
Alignment explanation
Indices: 52869086--52869124 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
52869076 GTTAAAAATA
52869086 ATTATCATTTTCATCATTTGG
1 ATTATCATTTTCAT-ATTTGG
52869107 ATTATCATTTTCATATTT
1 ATTATCATTTTCATATTT
52869125 TAATCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTATCATTTTCATATTTGG
Found at i:52870887 original size:21 final size:22
Alignment explanation
Indices: 52870858--52870909 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
52870848 CTCCACTATT
* *
52870858 TTTTCATTTTTTGTTT-GATTTG
1 TTTT-ATTTTTTATTTGGATTTC
*
52870880 TTTTATTTTTTATTTGGTTTTC
1 TTTTATTTTTTATTTGGATTTC
52870902 TTTTATTT
1 TTTTATTT
52870910 CATTGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.10, C:0.04, G:0.10, T:0.77
Consensus pattern (22 bp):
TTTTATTTTTTATTTGGATTTC
Found at i:52871641 original size:3 final size:3
Alignment explanation
Indices: 52871633--52871692 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
52871623 CCTGTCATTG
*** *
52871633 TTA TTA TTA TTA TTA TTA AGC TAA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
52871680 TTA TCA TTA TTA T
1 TTA TTA TTA TTA T
52871693 GTATATTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:52871810 original size:12 final size:12
Alignment explanation
Indices: 52871793--52871826 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
52871783 TTATTTTATA
52871793 ATCTATATACAT
1 ATCTATATACAT
52871805 ATCTATAT--AT
1 ATCTATATACAT
52871815 ATCTATATACAT
1 ATCTATATACAT
52871827 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (12 bp):
ATCTATATACAT
Found at i:52871918 original size:16 final size:17
Alignment explanation
Indices: 52871899--52871930 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52871889 TACTTACATT
52871899 TTTATATAC-TATATAA
1 TTTATATACATATATAA
52871915 TTTATATACATATATA
1 TTTATATACATATATA
52871931 CATACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTATATACATATATAA
Found at i:52871941 original size:24 final size:24
Alignment explanation
Indices: 52871901--52871946 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
52871891 CTTACATTTT
*
52871901 TATATACTATATAATTTATATACA
1 TATATACTACATAATTTATATACA
*
52871925 TATATACATACAT-ATTTTTATA
1 TATATAC-TACATAATTTATATA
52871947 GTATGTGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATACTACATAATTTATATACA
Found at i:52889123 original size:18 final size:18
Alignment explanation
Indices: 52889096--52889142 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
52889086 AGATAGGGAC
52889096 AGAGAAAAGGAAAAGGAA
1 AGAGAAAAGGAAAAGGAA
* **
52889114 AGAGACAAGGCGAAGGAA
1 AGAGAAAAGGAAAAGGAA
*
52889132 AGGGAAAAGGA
1 AGAGAAAAGGA
52889143 GAGAGACAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.38, T:0.00
Consensus pattern (18 bp):
AGAGAAAAGGAAAAGGAA
Found at i:52891080 original size:76 final size:76
Alignment explanation
Indices: 52890992--52891145 Score: 254
Period size: 76 Copynumber: 2.0 Consensus size: 76
52890982 TTTTTTTGGG
* * *
52890992 TGTGTAATTTACCTATTAGCAGGTTTAATATTTTCCTTTAATATGGATTATGTTAATTAAGGTTC
1 TGTGTAATTTACCTACTAGCAGATTTAATATTTACCTTTAATATGGATTATGTTAATTAAGGTTC
52891057 AATGAAGAGCC
66 AATGAAGAGCC
* *
52891068 TGTGTAATTTACCTACTAGCAGATTTAGTATTTACCTTTAATATGGATTATGTTAATTTAGGTTC
1 TGTGTAATTTACCTACTAGCAGATTTAATATTTACCTTTAATATGGATTATGTTAATTAAGGTTC
*
52891133 AATGAAGATCC
66 AATGAAGAGCC
52891144 TG
1 TG
52891146 GTTCTGAGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (76 bp):
TGTGTAATTTACCTACTAGCAGATTTAATATTTACCTTTAATATGGATTATGTTAATTAAGGTTC
AATGAAGAGCC
Found at i:52897916 original size:18 final size:18
Alignment explanation
Indices: 52897893--52897928 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
52897883 TATTAGAATT
52897893 TTGTATCAAAAA-ATTATA
1 TTGTAT-AAAAATATTATA
52897911 TTGTATAAAAATATTATA
1 TTGTATAAAAATATTATA
52897929 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (18 bp):
TTGTATAAAAATATTATA
Found at i:52902732 original size:139 final size:139
Alignment explanation
Indices: 52902482--52902898 Score: 736
Period size: 139 Copynumber: 3.0 Consensus size: 139
52902472 TATTTTCAAA
*
52902482 CCATGACATCCTCTATTCTCAATATTTTGATCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
1 CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
* *
52902547 CAGTTCCCACAATGACTAAGACAATTATTTAGAATAGGTAACATGAAAACGGACTCCCACTTCAG
66 CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
52902612 ATGTGTAAT
131 ATGTGTAAT
52902621 CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
1 CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
52902686 CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
66 CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
52902751 ATGTGTAAT
131 ATGTGTAAT
52902760 CCATGACAT-C-C---TCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
1 CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
* * *
52902820 CAGTTCCAACAACAACTAAGACAATTATTTAGAATAGGTTACATGAAAATGGACTCCCACTTCAG
66 CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
*
52902885 ATGAGTAAT
131 ATGTGTAAT
52902894 CCATG
1 CCATG
52902899 GAAATTCATC
Statistics
Matches: 271, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
134 124 0.46
137 1 0.00
138 1 0.00
139 145 0.54
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (139 bp):
CCATGACATCCTCTATTCTCAATATTTTGCTCCACTTTTTAACTTGTAACGTTTCAGCAACTTAA
CAGTTCCCACAATAACTAAGACAATTATTTAGAATAGGTAACATGAAAATGGACTCCCACTTCAG
ATGTGTAAT
Found at i:52909618 original size:23 final size:23
Alignment explanation
Indices: 52909573--52909650 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
52909563 AAGAATCTTT
* * * *
52909573 ACTGTTCATTATAGAGAATCTTC
1 ACTGTTTATTACAGGGAAACTTC
52909596 ACTGTTTATTACA-GGAAACCTTC
1 ACTGTTTATTACAGGGAAA-CTTC
* * **
52909619 ATTGTTCATTGTAGGGAAACTTC
1 ACTGTTTATTACAGGGAAACTTC
52909642 ACTGTTTAT
1 ACTGTTTAT
52909651 CCGTAATTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 3 0.07
23 35 0.81
24 5 0.12
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (23 bp):
ACTGTTTATTACAGGGAAACTTC
Found at i:52912491 original size:45 final size:44
Alignment explanation
Indices: 52912346--52912559 Score: 221
Period size: 44 Copynumber: 4.8 Consensus size: 44
52912336 CATGATTCAG
* * * * *
52912346 ATGAGTAAGACCATAGTTGAAAGATGCTATGGAATCAGGATAAA
1 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATAAA
* * * * * * *
52912390 ACGAGTAAGACCATGGCTGAAAAATGCTATGACATCAAGATAAA
1 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATAAA
*
52912434 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATGGAA
1 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGAT-AAA
* * * * *
52912479 GTGAGTAAGACCATGGCTGAAAGACATTATGACATCATGGTAAA
1 ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATAAA
* * *
52912523 TAGGACTAAGACCATAGTTGAAAGACGTTATGGCATC
1 -ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATC
52912560 TTTTGATAGT
Statistics
Matches: 140, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
44 73 0.52
45 67 0.48
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (44 bp):
ATGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATAAA
Found at i:52915028 original size:7 final size:7
Alignment explanation
Indices: 52915009--52915069 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
52914999 GAACCTCAAA
52915009 CCTAAAC
1 CCTAAAC
52915016 CC-AAAC
1 CCTAAAC
52915022 CCTAAAC
1 CCTAAAC
*
52915029 CTTAAAC
1 CCTAAAC
*
52915036 CATAAAAC
1 CCT-AAAC
*
52915044 CC-ACAC
1 CCTAAAC
*
52915050 CTTAAAC
1 CCTAAAC
*
52915057 CTTAAAC
1 CCTAAAC
52915064 CCTAAA
1 CCTAAA
52915070 TTTAAACTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 10 0.23
7 29 0.66
8 5 0.11
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:52915041 original size:14 final size:14
Alignment explanation
Indices: 52915000--52915069 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
52914990 CTTTACTCTG
52915000 AACCTCAAA-CCTA
1 AACCTCAAACCCTA
52915013 AACC-CAAACCCTA
1 AACCTCAAACCCTA
* *
52915026 AACCTTAAACCATAA
1 AACCTCAAACCCT-A
* *
52915041 AACC-CACACCTTA
1 AACCTCAAACCCTA
*
52915054 AACCTTAAACCCTA
1 AACCTCAAACCCTA
52915068 AA
1 AA
52915070 TTTAAACTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
12 4 0.09
13 17 0.38
14 19 0.42
15 5 0.11
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (14 bp):
AACCTCAAACCCTA
Found at i:52915053 original size:21 final size:22
Alignment explanation
Indices: 52915018--52915069 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
52915008 ACCTAAACCC
52915018 AAACCCTAAACCTTAAACCATA
1 AAACCCTAAACCTTAAACCATA
* *
52915040 AAACCC-ACACCTTAAACC-TT
1 AAACCCTAAACCTTAAACCATA
52915060 AAACCCTAAA
1 AAACCCTAAA
52915070 TTTAAACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 13 0.50
22 6 0.23
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (22 bp):
AAACCCTAAACCTTAAACCATA
Found at i:52915055 original size:28 final size:27
Alignment explanation
Indices: 52915000--52915069 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
52914990 CTTTACTCTG
*
52915000 AACCTCAAACCT-AAACCCAAACCCTA
1 AACCTTAAACCTAAAACCCAAACCCTA
* *
52915026 AACCTTAAACCATAAAACCCACACCTTA
1 AACCTTAAACC-TAAAACCCAAACCCTA
52915054 AACCTTAAACCCTAAA
1 AACCTTAAA-CCTAAA
52915070 TTTAAACTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 1 0.03
28 25 0.66
29 2 0.05
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (27 bp):
AACCTTAAACCTAAAACCCAAACCCTA
Found at i:52915093 original size:26 final size:27
Alignment explanation
Indices: 52915053--52915104 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
52915043 CCCACACCTT
*
52915053 AAACCTTAAACCCTAAA-TTTAAACTC
1 AAACCATAAACCCTAAACTTTAAACTC
* *
52915079 AAACCATAAATCCTAAACTTTGAACT
1 AAACCATAAACCCTAAACTTTAAACT
52915105 TTGAACCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (27 bp):
AAACCATAAACCCTAAACTTTAAACTC
Found at i:52915164 original size:13 final size:13
Alignment explanation
Indices: 52915146--52915201 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
52915136 GCCTTGAACC
52915146 TGAGGTTCGAGTT
1 TGAGGTTCGAGTT
*
52915159 TGAGGTTCAGGGTT
1 TGAGGTTC-GAGTT
** *
52915173 CAAGGTTTGAGTT
1 TGAGGTTCGAGTT
52915186 T-ATGGTTCGAGTT
1 TGA-GGTTCGAGTT
52915199 TGA
1 TGA
52915202 TGTTTAAGGT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
12 1 0.03
13 22 0.67
14 10 0.30
ACGTcount: A:0.18, C:0.07, G:0.36, T:0.39
Consensus pattern (13 bp):
TGAGGTTCGAGTT
Found at i:52915192 original size:20 final size:20
Alignment explanation
Indices: 52915148--52915214 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
52915138 CTTGAACCTG
* * *
52915148 AGGTTCGAGTTTGAGGTTCA
1 AGGTTCAAGTTTGATGTTTA
*
52915168 GGGTTCAAGGTTTGA-GTTTA
1 AGGTTCAA-GTTTGATGTTTA
* *
52915188 TGGTTCGAGTTTGATGTTTA
1 AGGTTCAAGTTTGATGTTTA
52915208 AGGTTCA
1 AGGTTCA
52915215 CGATTTTGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.16
20 26 0.68
21 6 0.16
ACGTcount: A:0.19, C:0.07, G:0.33, T:0.40
Consensus pattern (20 bp):
AGGTTCAAGTTTGATGTTTA
Found at i:52915239 original size:7 final size:7
Alignment explanation
Indices: 52915229--52915261 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
52915219 TTTGGATTTA
52915229 GGTTTGG
1 GGTTTGG
52915236 GGTTTGG
1 GGTTTGG
*
52915243 GGTTTGA
1 GGTTTGG
52915250 GGTTTGG
1 GGTTTGG
52915257 GGTTT
1 GGTTT
52915262 AAGGTTTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.03, C:0.00, G:0.52, T:0.45
Consensus pattern (7 bp):
GGTTTGG
Found at i:52915248 original size:14 final size:14
Alignment explanation
Indices: 52915229--52915268 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
52915219 TTTGGATTTA
*
52915229 GGTTTGGGGTTTGG
1 GGTTTGAGGTTTGG
52915243 GGTTTGAGGTTTGG
1 GGTTTGAGGTTTGG
*
52915257 GGTTTAAGGTTT
1 GGTTTGAGGTTT
52915269 AGGATTCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.45
Consensus pattern (14 bp):
GGTTTGAGGTTTGG
Found at i:52915267 original size:21 final size:21
Alignment explanation
Indices: 52915228--52915268 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52915218 TTTTGGATTT
**
52915228 AGGTTTGGGGTTTGGGGTTTG
1 AGGTTTGGGGTTTAAGGTTTG
52915249 AGGTTTGGGGTTTAAGGTTT
1 AGGTTTGGGGTTTAAGGTTT
52915269 AGGATTCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.46, T:0.44
Consensus pattern (21 bp):
AGGTTTGGGGTTTAAGGTTTG
Found at i:52928650 original size:18 final size:18
Alignment explanation
Indices: 52928627--52928661 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52928617 TCATTCTTTC
52928627 ACTCACAATACTTTTAAT
1 ACTCACAATACTTTTAAT
* *
52928645 ACTCACCATGCTTTTAA
1 ACTCACAATACTTTTAA
52928662 CTCTCACATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (18 bp):
ACTCACAATACTTTTAAT
Found at i:52931057 original size:10 final size:10
Alignment explanation
Indices: 52931042--52931071 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
52931032 TAGGCAAAAG
52931042 AAAAAAGAAA
1 AAAAAAGAAA
52931052 AAAAAAGAAA
1 AAAAAAGAAA
52931062 AAAAAAGAAA
1 AAAAAAGAAA
52931072 GAAAGGGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:52933720 original size:18 final size:18
Alignment explanation
Indices: 52933679--52933713 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52933669 TCATTCTTTC
52933679 ACTCACAATGCTTTTAAT
1 ACTCACAATGCTTTTAAT
*
52933697 ACTCACCATGCTTTTAA
1 ACTCACAATGCTTTTAA
52933714 CTCTCACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (18 bp):
ACTCACAATGCTTTTAAT
Found at i:52935497 original size:24 final size:24
Alignment explanation
Indices: 52935465--52935524 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
52935455 AAAAATATAG
* *
52935465 AGTTATCCACATGACAGTAAAATA
1 AGTTGTCCACATGACAATAAAATA
* *
52935489 AGTTGTCCACATGTCAATTAAATA
1 AGTTGTCCACATGACAATAAAATA
**
52935513 ACATGTCCACAT
1 AGTTGTCCACAT
52935525 CAACTGGGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (24 bp):
AGTTGTCCACATGACAATAAAATA
Found at i:52941123 original size:22 final size:20
Alignment explanation
Indices: 52941083--52941123 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
52941073 TGTATTTAAA
*
52941083 TAATTTATAAAAAATAATTT
1 TAATTTAGAAAAAATAATTT
52941103 TAATTATAGAAAATAATAATT
1 TAATT-TAGAAAA-AATAATT
52941124 ATTTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAATTTAGAAAAAATAATTT
Found at i:52942360 original size:35 final size:34
Alignment explanation
Indices: 52942283--52942369 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 34
52942273 CTTTAAACGT
* *
52942283 GTCTATCCCAACCTTTTAAAGGTTGCCTTATACG
1 GTCTATCCCAACCTTTTAAACGTTGCCTTAGACG
* * *
52942317 GATATATCCCAACCTTTTAAACGTTGTCTTAGATG
1 G-TCTATCCCAACCTTTTAAACGTTGCCTTAGACG
*
52942352 AGTCTATCCTAACCTTTT
1 -GTCTATCCCAACCTTTT
52942370 TAAAGTCACC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.02
35 42 0.95
36 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (34 bp):
GTCTATCCCAACCTTTTAAACGTTGCCTTAGACG
Found at i:52942932 original size:18 final size:18
Alignment explanation
Indices: 52942909--52942943 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
52942899 TAAAATATTA
52942909 TTTTAATATTT-TTATACG
1 TTTTAAT-TTTATTATACG
52942927 TTTTAATTTTATTATAC
1 TTTTAATTTTATTATAC
52942944 ACACTCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTAATTTTATTATACG
Found at i:52948762 original size:27 final size:27
Alignment explanation
Indices: 52948731--52948786 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
52948721 GACATACGGA
*
52948731 CATGTAACACGACTGTGTGACCCTACT
1 CATGTAACACGACTATGTGACCCTACT
52948758 CATGTAACACGACTATGTGACCCTACT
1 CATGTAACACGACTATGTGACCCTACT
52948785 CA
1 CA
52948787 GAGAGTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (27 bp):
CATGTAACACGACTATGTGACCCTACT
Found at i:52951022 original size:98 final size:98
Alignment explanation
Indices: 52950853--52951047 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
52950843 ATACAATAAA
*
52950853 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATC
52950918 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* * * *
52950951 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATTACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATC
*
52951016 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
52951048 CATGATTTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:52953184 original size:45 final size:43
Alignment explanation
Indices: 52953082--52953513 Score: 260
Period size: 45 Copynumber: 9.8 Consensus size: 43
52953072 TAGGCTTTAA
* * * * *
52953082 TCTGTTCCTACTGCAACTTTAGAGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCC-ACTGCAACTTCAGGGAGATAAGACTTG-CTTCTT-AG
* *
52953128 CCTGC-CTCACTGCAACTTCA-GGAGGATACGACTTGCTTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC-TT-CTTAG
* * * * *
52953173 TCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCTTAG
* * * * *
52953214 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGAGGTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTCTTAG
** * * *
52953257 TCCACTCCAATGCAACTTCAGGGAGATAGGATTATCGGCTT-TTA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTTCTTAG
* *
52953301 TCTGCTCCACTGCAACTTCA-GG-GATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTCTT-AG
* *
52953344 CCTGC-CTCACTGCAACTTCA-GGAGGATACGACTTGCTTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC-TT-CTTAG
* *
52953389 TCTGGTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT---TGC-TTC-TTAG
* *
52953437 TCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTAACTTAG
1 TCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCT-TCTTAG
* *
52953481 TCTGCTCCATTGTAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
52953514 AGTTGCGATT
Statistics
Matches: 304, Mismatches: 51, Indels: 64
0.73 0.12 0.15
Matches are distributed among these distances:
39 1 0.00
40 23 0.08
41 11 0.04
42 15 0.05
43 27 0.09
44 72 0.24
45 98 0.32
46 18 0.06
47 4 0.01
48 35 0.12
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCTTAG
Found at i:52953416 original size:216 final size:219
Alignment explanation
Indices: 52952913--52953432 Score: 866
Period size: 219 Copynumber: 2.4 Consensus size: 219
52952903 GATTTGCCAT
* * *
52952913 CCTCATTGCAACTTCAGGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCATCTTCAGGGA
1 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGA
*
52952978 GATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGATGTTTTAATCCAC
66 GATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGAGGTTTTAATCCAC
* * * * * *
52953043 TCCACTATAATTTCAGGGAGATAGGATTGTAGGCTTTAATCTGTTCCTACTGCAACTTTAGAGAG
131 TCCAATACAACTTCAGGGAGATAGGATTATAGGCTTTAATCTGCTCCTACTGCAACTTCAGAGAG
52953108 ATAAGATTTGCCATCTTCAGCCTG
196 ATAAGATTTGCCATCTTCAGCCTG
*
52953132 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGTAACTTCAGGGA
1 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGA
* *
52953197 GATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCAC
66 GATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGAGGTTTTAATCCAC
* * *
52953262 TCCAATGCAACTTCAGGGAGATAGGATTATCGGCTTTTATCTGCTCC-ACTGCAACTTCAG-G-G
131 TCCAATACAACTTCAGGGAGATAGGATTATAGGCTTTAATCTGCTCCTACTGCAACTTCAGAGAG
52953324 ATAAGATTTGCCATCTTCAGCCTG
196 ATAAGATTTGCCATCTTCAGCCTG
*
52953348 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGGTCCACTGCAACTTCAGGGA
1 CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGA
52953413 GATAAGACTAGATGCGATCT
66 GATAAGACTAGATGCGATCT
52953433 TTAGTCTGCC
Statistics
Matches: 283, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
216 108 0.38
217 1 0.00
218 12 0.04
219 162 0.57
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (219 bp):
CCTCACTGCAACTTCAGGAGGATACGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGA
GATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAGATAAGATCTGAGGTTTTAATCCAC
TCCAATACAACTTCAGGGAGATAGGATTATAGGCTTTAATCTGCTCCTACTGCAACTTCAGAGAG
ATAAGATTTGCCATCTTCAGCCTG
Found at i:52953460 original size:93 final size:92
Alignment explanation
Indices: 52953301--52953522 Score: 301
Period size: 92 Copynumber: 2.5 Consensus size: 92
52953291 TCGGCTTTTA
* *
52953301 TCTGCTCCACTGCAACTTCA-GG-GATAAGA-T--TTGCCATCTTCAGCCTGCCTCACTGCAACT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTTGCGATCTTCAGCCTGCCCCACTGCAACT
* **
52953361 TCAGGAGGATACGACTTGCTTTGCTTAG
66 TCAGGAGGATAAGACTTGC-TAACTTAG
* * * *
52953389 TCTGGTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTTTAGTCTGCCCCACTGCAACT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTTGCGATCTTCAGCCTGCCCCACTGCAACT
52953454 TCAGGAGGATAAGACTTGCTAACTTAG
66 TCAGGAGGATAAGACTTGCTAACTTAG
* *
52953481 TCTGCTCCATTGTAACTTCAGGGAGATAAGACTAGTTGCGAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTTGCGAT
52953523 TTGTTATCTT
Statistics
Matches: 116, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
88 19 0.16
89 2 0.02
90 7 0.06
91 1 0.01
92 44 0.38
93 43 0.37
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (92 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTTGCGATCTTCAGCCTGCCCCACTGCAACT
TCAGGAGGATAAGACTTGCTAACTTAG
Found at i:52955175 original size:98 final size:98
Alignment explanation
Indices: 52955005--52955199 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
52954995 ATACAATAAA
*
52955005 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
* *
52955070 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCATTAGAATCCCAAACTAGGAATATTTCCTTT
* * *
52955103 ACTTTAAAAGAACATCCACTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
52955168 CCATTAGAATCTCAAACTAGGAATATTTCCTT
66 CCATTAGAATCCCAAACTAGGAATATTTCCTT
52955200 CATGATTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCATTAGAATCCCAAACTAGGAATATTTCCTTT
Found at i:52967345 original size:17 final size:17
Alignment explanation
Indices: 52967323--52967358 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
52967313 TTAGTTTGTA
52967323 GACCAAAATTATAAAAT
1 GACCAAAATTATAAAAT
52967340 GACCAAAATTATAAAAT
1 GACCAAAATTATAAAAT
52967357 GA
1 GA
52967359 AAACTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.22
Consensus pattern (17 bp):
GACCAAAATTATAAAAT
Found at i:52971820 original size:109 final size:110
Alignment explanation
Indices: 52971440--52971838 Score: 580
Period size: 110 Copynumber: 3.6 Consensus size: 110
52971430 AAAAATATTT
*
52971440 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAC---AAAA-AATTTTTTTTTATTTTT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAAGAAATTTTTTTTA-TTTT
52971501 TTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAATAAAAAAAAAA
65 TTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAT-AAAAAAAAA
* * * *****
52971548 TTTTGGGTGCTGGTCTGTCAATGGCCGGCACCCAGTACACAGTACACGAAA-AAAAGTTATTTTT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAAGAAATTTTTTTTATTTTT
52971612 TTCGTGTCAGAATCAGAT-AAAAAATACGAAAAAAATAAAAAAAAAA
66 TTCGTGTCAGAATCAGATAAAAAAATACG-AAAAAAT-AAAAAAAAA
* *
52971658 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACACGAAAATTTTTTTTATTTT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAAG-AAATTTTTTTTATTTT
52971723 TTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAT-AAAAAAAA
65 TTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAATAAAAAAAAA
52971768 -TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAGAAAGAAATTTTTTTTTATTT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTA-AAAGAAA-TTTTTTTTATTT
52971832 TTTTCGT
64 TTTTCGT
52971839 ATTTTTTATC
Statistics
Matches: 264, Mismatches: 17, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
108 39 0.15
109 56 0.21
110 116 0.44
111 8 0.03
112 35 0.13
113 10 0.04
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (110 bp):
TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAAGAAATTTTTTTTATTTTT
TTCGTGTCAGAATCAGATAAAAAAATACGAAAAAATAAAAAAAAA
Found at i:52971954 original size:113 final size:114
Alignment explanation
Indices: 52971816--52972517 Score: 1005
Period size: 113 Copynumber: 6.2 Consensus size: 114
52971806 CAGTAGAAAG
* * *
52971816 AAATTTTTTTTTATTTTTTTCGTA-TTTTTTATCTGATTTTAACACGAAAAAAAATAAAAAAATT
1 AAATTTTTTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAT-AAAAATTT
* *
52971880 TTTT-TATGTACTGTGTACTGGGTGTCGGCCATTGACAGGCCAGCACCCA
65 TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
**
52971929 AAATTTTTTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATTAAATTTTT
1 AAATTTTTTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAA-TAAAAATTT
* * *
52971994 TTTTCTTTGTACTGTGTACTAGGTGTCGGCCATTAACAGGCCAGCACCCA
65 TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
* *
52972044 ACA-TTTTTTTTATTTTTTTCGTA-TTTTTTATTTGATTCTGACACGAAAAAAAATAAAAAAATT
1 AAATTTTTTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAT--AAAAA-T
*
52972107 TTATTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCA
63 TT-TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
* * * *
52972160 AAAATTTTTTTAATTTTTTTCGTA-TTTTTTCTCTGATTCTGACACGAAAAAAAATTAAAATTTT
1 AAATTTTTTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATAAAAATTTT
* **
52972224 TTTCTTTCTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACAAA
66 TTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
52972273 AAATTTTTTATTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAT---AAT
1 AAA--TTTT-TTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATAAAAAT
*
52972335 TTTTTT-TGTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
63 TTTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
*
52972386 AAA--TTTTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATAAAATTTTT
1 AAATTTTTTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATAAAAATTTT
* *
52972449 TTTC-GTGTACTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
66 TTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
*
52972497 AAATTTTTTTTTTGTTTTTTT
1 AAA-TTTTTTTTTATTTTTTT
52972518 TCTTTTTCGT
Statistics
Matches: 535, Mismatches: 35, Indels: 37
0.88 0.06 0.06
Matches are distributed among these distances:
108 49 0.09
109 2 0.00
111 54 0.10
112 1 0.00
113 146 0.27
114 86 0.16
115 55 0.10
116 64 0.12
117 78 0.15
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (114 bp):
AAATTTTTTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATAAAAATTTT
TTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
Found at i:52986339 original size:119 final size:120
Alignment explanation
Indices: 52986127--52986443 Score: 582
Period size: 119 Copynumber: 2.6 Consensus size: 120
52986117 GAATTTTTGT
52986127 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
*
52986192 TAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTA
66 TAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTAGTAAATTTA
* *
52986247 TATAAGAATATTGATTACTAAGAA-TTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
52986311 TAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTAGTAAATTTA
66 TAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTAGTAAATTTA
* *
52986366 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAACATTTTTTTAATAA
1 TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
52986431 TAATTATGTTAAA
66 TAATTATGTTAAA
52986444 ATATGATTAA
Statistics
Matches: 190, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
119 116 0.61
120 74 0.39
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
TATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAA
TAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTAGTAAATTTA
Found at i:52986574 original size:18 final size:17
Alignment explanation
Indices: 52986546--52986580 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52986536 ATTATTAAGA
*
52986546 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52986563 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52986581 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52986584 original size:157 final size:157
Alignment explanation
Indices: 52986379--52986686 Score: 553
Period size: 157 Copynumber: 2.0 Consensus size: 157
52986369 AAGAATATTG
* * *
52986379 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAACATTTTTTTAATAATAATTATGTTAAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
* *
52986444 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
52986509 ATAATTTACCAAAACAAATTTCTGGTA
131 ATAATTTACCAAAACAAATTTCTGGTA
*
52986536 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
52986601 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
*
52986666 ATCATTTACCAAAACAAATTT
131 ATAATTTACCAAAACAAATTT
52986687 ATGCTAAGGG
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 144 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
ATAATTTACCAAAACAAATTTCTGGTA
Found at i:52986837 original size:16 final size:16
Alignment explanation
Indices: 52986816--52986883 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
52986806 GATTTGCTAT
52986816 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52986832 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
52986848 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
*
52986864 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
52986880 TACA
1 TACA
52986884 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:52987273 original size:19 final size:19
Alignment explanation
Indices: 52987220--52987280 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 19
52987210 TGTATACTAA
52987220 TTTTTATAATTACTTATAAACTT
1 TTTTTATAATT--TT-TAAA-TT
*
52987243 TTATTT-TTATTTTTAAATT
1 TT-TTTATAATTTTTAAATT
52987262 TTTTTATAATTTTTAAATT
1 TTTTTATAATTTTTAAATT
52987281 ATTCATTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 3 0.09
19 16 0.47
20 4 0.12
21 2 0.06
23 6 0.18
24 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTATAATTTTTAAATT
Found at i:52991057 original size:43 final size:43
Alignment explanation
Indices: 52990997--52991087 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
52990987 CAATGAGTTC
* * *
52990997 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCT-TTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATAT-TATTT
*
52991039 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATTATTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATTATTT
52991082 ATTACC
1 ATTACC
52991088 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATTATTT
Found at i:52992056 original size:16 final size:19
Alignment explanation
Indices: 52992008--52992067 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
52991998 TATTTAGTCA
52992008 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
52992028 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
52992046 TAATAAATTATTTAATAT-T
1 TAATAAATTA-TTAATATAT
52992065 TAA
1 TAA
52992068 ATTTTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.09
17 4 0.11
18 8 0.23
19 5 0.14
20 6 0.17
21 4 0.11
22 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:52992510 original size:43 final size:43
Alignment explanation
Indices: 52992450--52992540 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
52992440 CTTTGAGTTC
* * *
52992450 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
52992492 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
52992535 ATTACC
1 ATTACC
52992541 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:52992999 original size:43 final size:43
Alignment explanation
Indices: 52992944--52993117 Score: 246
Period size: 43 Copynumber: 4.1 Consensus size: 43
52992934 GTTTGTTCTA
* *
52992944 TAGCGACGTTTGTGACAAAAGCGCCGCTAAAAGTCATGGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
* *
52992987 TAGCGGCGTTTGTGATAAAAGCGTCGCTAAAGGTCA---TCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
* * *
52993027 TTGCGGCGTTTATGATAAAAGCACCGCTAAAAGTCATGGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
* *
52993070 TAGCGGCGTTTGTGATAAAAGCGCCACTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
52993113 TAGCG
1 TAGCG
52993118 ACCTTTTTTC
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
40 35 0.31
43 79 0.69
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGGTCTT
Found at i:52993047 original size:83 final size:83
Alignment explanation
Indices: 52992950--52993106 Score: 269
Period size: 83 Copynumber: 1.9 Consensus size: 83
52992940 TCTATAGCGA
* * * *
52992950 CGTTTGTGACAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGTCGCT
1 CGTTTATGACAAAAGCACCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCACT
52993015 AAAGGTCATCTTTTGCGG
66 AAAGGTCATCTTTTGCGG
*
52993033 CGTTTATGATAAAAGCACCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCACT
1 CGTTTATGACAAAAGCACCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCACT
52993098 AAAGGTCAT
66 AAAGGTCAT
52993107 GGTCTTTAGC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (83 bp):
CGTTTATGACAAAAGCACCGCTAAAAGTCATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCACT
AAAGGTCATCTTTTGCGG
Found at i:52993637 original size:43 final size:43
Alignment explanation
Indices: 52993527--52993742 Score: 258
Period size: 43 Copynumber: 5.1 Consensus size: 43
52993517 GCTTGTTATA
* * *
52993527 TAGCGGCGTTTGTGACAAAAGCGCCGCTAAAAGTCATGTTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTCTT
* * ** * * *
52993570 TAG-TGTGTTTGTGACCAATGCGTCGCTAAATGTCATGGTTTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTCTT
* * *
52993612 TAGTGGCGTTTGTGATAAAAGCGTCG--AAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTCTT
* * * *
52993653 TAACGGTGTTTATGATAAAAGCGCTGCTAAATGTCATGGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTCTT
52993696 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTCTT
1 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTCTT
52993739 TAGC
1 TAGC
52993743 TATGTTTTTT
Statistics
Matches: 144, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
41 33 0.23
42 34 0.24
43 77 0.53
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
TAGCGGCGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTCTT
Found at i:52996023 original size:13 final size:13
Alignment explanation
Indices: 52996005--52996030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52995995 AAAGTGCGAG
52996005 CCTGTTGAAGACA
1 CCTGTTGAAGACA
52996018 CCTGTTGAAGACA
1 CCTGTTGAAGACA
52996031 ATATGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGTTGAAGACA
Found at i:52998913 original size:161 final size:162
Alignment explanation
Indices: 52998559--52998951 Score: 540
Period size: 161 Copynumber: 2.4 Consensus size: 162
52998549 CAATCCCCCA
*
52998559 ATACCTCAAATTATTGCAGTTT-TCAACTTTTACTTCCCTTAAACTTTGGAGGCTTATGTTTGAC
1 ATACCTCAAATTATTGCAGTTTCT-AACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGAC
* * *
52998623 ACTTCCGAACCTTGGATTATTTCTTCTAATTGGGAGCAATCACTTATCTGCAGAGTTTGCAACCT
65 ACTTCCGAACCTTGGATTATTTCTTCTAATTGGGAGCAATCACATATCTGCAAAGCTTGCAACCT
* *
52998688 CCTAAGGCTATTAGCAATAGACATTGGGAAGAG
130 CCCAAGGCTATTAGAAATAGACATTGGGAAGAG
* * *
52998721 ATACATCAAATTATTGCCGTTTCTGACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGACA
1 ATACCTCAAATTATTGCAGTTTCTAACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGACA
** * * * * * *
52998786 CTTTTGAGCCTTGGATT-GTTCTT-TCAATTGGGAGCAGTCTCATATCTTCAAAGCTTGCAATCT
66 CTTCCGAACCTTGGATTATTTCTTCT-AATTGGGAGCAATCACATATCTGCAAAGCTTGCAACCT
* *
52998849 CCCAAGGCTATTAGAAATAGCCATTGGGAAGGG
130 CCCAAGGCTATTAGAAATAGACATTGGGAAGAG
* * * *
52998882 ATACCTCAAATTATTGTAGTTTCTAACTTCTACTTCCCTTACACTTTGGAGGTTTATGTCTGACA
1 ATACCTCAAATTATTGCAGTTTCTAACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGACA
52998947 CTTCC
66 CTTCC
52998952 AATTGGGAGC
Statistics
Matches: 201, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
160 1 0.00
161 126 0.63
162 73 0.36
163 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (162 bp):
ATACCTCAAATTATTGCAGTTTCTAACTTCTACTTCCCTTAAACTTTGGAGGCTTATGTTTGACA
CTTCCGAACCTTGGATTATTTCTTCTAATTGGGAGCAATCACATATCTGCAAAGCTTGCAACCTC
CCAAGGCTATTAGAAATAGACATTGGGAAGAG
Found at i:53006448 original size:31 final size:30
Alignment explanation
Indices: 53006384--53006479 Score: 156
Period size: 30 Copynumber: 3.2 Consensus size: 30
53006374 ACACATTATT
* *
53006384 ATATATGCATTACATTAGTAAACAAAAATA
1 ATATATGCAATACATTAGTAAACAAAAAGA
53006414 ATATATGCAATACATTAGTAAACAAAAAAGA
1 ATATATGCAATACATTAGTAAAC-AAAAAGA
*
53006445 ATATATGCACTACATTAGTAAACAAAAAGA
1 ATATATGCAATACATTAGTAAACAAAAAGA
53006475 ATATA
1 ATATA
53006480 CCTATCGACT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 34 0.55
31 28 0.45
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (30 bp):
ATATATGCAATACATTAGTAAACAAAAAGA
Found at i:53013564 original size:14 final size:14
Alignment explanation
Indices: 53013545--53013575 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53013535 GGAATTATTT
*
53013545 TAATCTAAATTTAC
1 TAATCTAAATTAAC
53013559 TAATCTAAATTAAC
1 TAATCTAAATTAAC
53013573 TAA
1 TAA
53013576 GAATTGTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:53023334 original size:3 final size:3
Alignment explanation
Indices: 53023326--53023357 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53023316 TTGGATTGGT
53023326 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53023358 TTTAATGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:53031823 original size:12 final size:13
Alignment explanation
Indices: 53031806--53031834 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
53031796 TTAAACTAAG
53031806 TAAATAAAT-AAA
1 TAAATAAATAAAA
53031818 TAAATAAATAAAA
1 TAAATAAATAAAA
53031831 TAAA
1 TAAA
53031835 AATAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:53033216 original size:23 final size:22
Alignment explanation
Indices: 53033164--53033216 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53033154 TCCACGTCTT
*
53033164 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53033186 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53033209 TTTCTTTT
1 TTTCTTTT
53033217 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Done.