Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 156 of 167
Found at i:51446093 original size:82 final size:82
Alignment explanation
Indices: 51445982--51446147 Score: 296
Period size: 82 Copynumber: 2.0 Consensus size: 82
51445972 TAAAATCTAC
* *
51445982 TTATATATGGAAACTTATCTTTTTGATTTGATTCCAATAAATCTGATTAAAATTTTAAATCAAAT
1 TTATATATGGAAACTTATCTTATTAATTTGATTCCAATAAATCTGATTAAAATTTTAAATCAAAT
51446047 TGAGTTAATGGTAGATT
66 TGAGTTAATGGTAGATT
*
51446064 TTATATATGGAAACTTATCTTATTAATTTGATTCCAATAAATCTGATTAAAATTTTATATCAAAT
1 TTATATATGGAAACTTATCTTATTAATTTGATTCCAATAAATCTGATTAAAATTTTAAATCAAAT
*
51446129 TGATTTAATGGTAGATT
66 TGAGTTAATGGTAGATT
51446146 TT
1 TT
51446148 GTGTATTTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (82 bp):
TTATATATGGAAACTTATCTTATTAATTTGATTCCAATAAATCTGATTAAAATTTTAAATCAAAT
TGAGTTAATGGTAGATT
Found at i:51451000 original size:18 final size:18
Alignment explanation
Indices: 51450977--51451012 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
51450967 TTAACTTAAT
51450977 TAAATCCTTAATTTCTAC
1 TAAATCCTTAATTTCTAC
51450995 TAAATCCTTAATTTCTAC
1 TAAATCCTTAATTTCTAC
51451013 CTCCTAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATCCTTAATTTCTAC
Found at i:51452992 original size:35 final size:35
Alignment explanation
Indices: 51452942--51453012 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
51452932 TTATCTTCAG
*
51452942 AGTTTGTTTCTTATAGATCATGTAATATTCCTTAC
1 AGTTTGTTTCGTATAGATCATGTAATATTCCTTAC
51452977 AGTTTGTTTCGTATAGATCATGTAATATTCCTTAC
1 AGTTTGTTTCGTATAGATCATGTAATATTCCTTAC
51453012 A
1 A
51453013 CTTATCTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (35 bp):
AGTTTGTTTCGTATAGATCATGTAATATTCCTTAC
Found at i:51460243 original size:54 final size:54
Alignment explanation
Indices: 51460161--51460459 Score: 580
Period size: 54 Copynumber: 5.5 Consensus size: 54
51460151 NNNNNNNTTG
51460161 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
51460215 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
51460269 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
51460323 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
51460377 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
* *
51460431 CAGTGGATTTAGCCTTGACTGGTAATCCC
1 CAGGGGATTTAGCCTGGACTGGTAATCCC
51460460 ACTGTAAGGA
Statistics
Matches: 243, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 243 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (54 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
Found at i:51460565 original size:38 final size:37
Alignment explanation
Indices: 51460503--51460575 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
51460493 CTGATATGAA
* * *
51460503 ATGTGTAAGACATAGTTGATAGATACCATGGCAACCG
1 ATGTGTAAAACATAGTTGAAAGATACCATAGCAACCG
*
51460540 ATGTGTAAAACCATGGTTGAAAGATACCATAGCAAC
1 ATGTGTAAAA-CATAGTTGAAAGATACCATAGCAAC
51460576 GTGACATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 9 0.29
38 22 0.71
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.23
Consensus pattern (37 bp):
ATGTGTAAAACATAGTTGAAAGATACCATAGCAACCG
Found at i:51460621 original size:46 final size:46
Alignment explanation
Indices: 51460549--51460665 Score: 164
Period size: 46 Copynumber: 2.5 Consensus size: 46
51460539 GATGTGTAAA
* *
51460549 ACCATGGTTGAAAGATACCATAGCAACGTGACATGAAAA-GAATAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAATAAG
*
51460595 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAG
* * *
51460641 ACCATAGTTGAAAGACACTATGGCA
1 ACCATGGTTGAAAGATACCATGGCA
51460666 TCACGTCAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 5 0.08
46 59 0.92
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (46 bp):
ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAG
Found at i:51460971 original size:23 final size:25
Alignment explanation
Indices: 51460926--51460972 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
51460916 AATAAATATA
*
51460926 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
51460951 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
51460973 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:51461668 original size:38 final size:38
Alignment explanation
Indices: 51461617--51461773 Score: 253
Period size: 38 Copynumber: 4.1 Consensus size: 38
51461607 ATATTTGATG
*
51461617 TATATCCGGGTTTTATCCCACAGGCTTCA-TGCTGGTAT
1 TATATCCGGGTTTTATCCCGCAGGCTT-AGTGCTGGTAT
* *
51461655 TATATCTGGGTTTTATCCCGCAGGCTTTGTGCTGGTAT
1 TATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
51461693 TATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
**
51461731 TATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
51461769 TATAT
1 TATAT
51461774 TCGAGCTTAA
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
38 111 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (38 bp):
TATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
Found at i:51461806 original size:40 final size:38
Alignment explanation
Indices: 51461617--51461794 Score: 187
Period size: 38 Copynumber: 4.6 Consensus size: 38
51461607 ATATTTGATG
* ** *
51461617 TATATCCGGGTTTTATCCCACAGGCTTCA-TGCTGGTAT
1 TATATCCGGCTTAAATCCCGCAGGCTT-AGTGCTGGTAT
* * ** *
51461655 TATATCTGGGTTTTATCCCGCAGGCTTTGTGCTGGTAT
1 TATATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTAT
* **
51461693 TATATCCGGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTAT
*
51461731 TATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTAT
* *
51461769 TATATTCGAGCTTAAAGTTCCGCAGG
1 TATATCCG-GCTTAAA-TCCCGCAGG
51461795 TTCTGTGCTG
Statistics
Matches: 127, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
38 113 0.89
39 6 0.05
40 8 0.06
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.36
Consensus pattern (38 bp):
TATATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTAT
Found at i:51465213 original size:12 final size:12
Alignment explanation
Indices: 51465198--51465224 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
51465188 ACTTGACACA
51465198 TTACCAAATTTT
1 TTACCAAATTTT
51465210 TTACCAAATTTT
1 TTACCAAATTTT
51465222 TTA
1 TTA
51465225 TATGTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (12 bp):
TTACCAAATTTT
Found at i:51467853 original size:87 final size:87
Alignment explanation
Indices: 51467732--51467901 Score: 286
Period size: 87 Copynumber: 2.0 Consensus size: 87
51467722 AATTGATAAT
* * * *
51467732 ATTATTAAAAGAGTTCTGTTAAATTGAATATATGATATCTTAATTTTCAGTTGTGTCCCTTCTTT
1 ATTATTAAAAGACTTCTATTAAACTGAATATATGATATCTTAATTTTCAGTTGTGTCCCTTCCTT
51467797 TTTCTATTTATTTCTATGGTCA
66 TTTCTATTTATTTCTATGGTCA
*
51467819 ATTATTAAAAGACTTCTATTAAACTGAATATATGATATTTTAATTTTCAGTTGTGTCCCTTCCTT
1 ATTATTAAAAGACTTCTATTAAACTGAATATATGATATCTTAATTTTCAGTTGTGTCCCTTCCTT
*
51467884 TTTCTATTTATTTTTATG
66 TTTCTATTTATTTCTATG
51467902 ATCGATGATC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (87 bp):
ATTATTAAAAGACTTCTATTAAACTGAATATATGATATCTTAATTTTCAGTTGTGTCCCTTCCTT
TTTCTATTTATTTCTATGGTCA
Found at i:51474439 original size:14 final size:14
Alignment explanation
Indices: 51474417--51474447 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
51474407 TAGTTTTTTC
*
51474417 TTTAGAAATTTCTA
1 TTTAAAAATTTCTA
51474431 TTTAAAAATTTCTA
1 TTTAAAAATTTCTA
51474445 TTT
1 TTT
51474448 GTACTGCTAA
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:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTAAAAATTTCTA
Found at i:51480432 original size:24 final size:25
Alignment explanation
Indices: 51480405--51480457 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
51480395 TATTTTTTAC
* *
51480405 ATATT-ATGTAATTTATATAAAACA
1 ATATTAATATAATATATATAAAACA
*
51480429 ATATTAAATATAATATATATAATACA
1 ATATT-AATATAATATATATAAAACA
51480455 ATA
1 ATA
51480458 ACGTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
26 19 0.79
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATTAATATAATATATATAAAACA
Found at i:51481163 original size:14 final size:14
Alignment explanation
Indices: 51481144--51481170 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51481134 TATTTAATAG
51481144 AATTTTTATTTTTA
1 AATTTTTATTTTTA
51481158 AATTTTTATTTTT
1 AATTTTTATTTTT
51481171 TACGATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
AATTTTTATTTTTA
Found at i:51481178 original size:16 final size:15
Alignment explanation
Indices: 51481144--51481188 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
51481134 TATTTAATAG
51481144 AATTTTTA-TTTTTA
1 AATTTTTATTTTTTA
51481158 AATTTTTATTTTTTA
1 AATTTTTATTTTTTA
* *
51481173 CGATTTTTATTATTTA
1 -AATTTTTATTTTTTA
51481189 TTTAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 8 0.30
15 6 0.22
16 13 0.48
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
AATTTTTATTTTTTA
Found at i:51483999 original size:53 final size:53
Alignment explanation
Indices: 51483941--51484091 Score: 207
Period size: 53 Copynumber: 2.9 Consensus size: 53
51483931 TTTATATAAT
* * **
51483941 ATATTTGAAAATAATAACATATTTATTACCCCCAATTACGACTGAATTCTTAA
1 ATATTTGAAAATAATAATATATTTATTACCCCCAATTACGACTCAATGATTAA
* *
51483994 ATATTT-AAATATAATAATGTATTTATTACCCCAAATTACGACTCAATGATTAA
1 ATATTTGAAA-ATAATAATATATTTATTACCCCCAATTACGACTCAATGATTAA
* *
51484047 ATATTTGAATATAATAATATATTTATTA-ACCCAATTACGACTCAA
1 ATATTTGAAAATAATAATATATTTATTACCCCCAATTACGACTCAA
51484092 GGATCACAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
52 18 0.21
53 66 0.77
54 2 0.02
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (53 bp):
ATATTTGAAAATAATAATATATTTATTACCCCCAATTACGACTCAATGATTAA
Found at i:51490476 original size:15 final size:15
Alignment explanation
Indices: 51490423--51490477 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
51490413 TCCACCACCG
*
51490423 GGATATCCTCCACAA
1 GGATATCCTCCTCAA
51490438 GGATA---TCCTCAA
1 GGATATCCTCCTCAA
*
51490450 GGTTATCCTCCTCAA
1 GGATATCCTCCTCAA
51490465 GGATATCCTCCTC
1 GGATATCCTCCTC
51490478 CTTACGCCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 10 0.29
15 24 0.71
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
GGATATCCTCCTCAA
Found at i:51497847 original size:15 final size:16
Alignment explanation
Indices: 51497805--51497848 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
51497795 ACCACAAGAG
*
51497805 GCTGCTAGAAGCAGAA
1 GCTGCAAGAAGCAGAA
*
51497821 GCTGCAA-TAGCAGAA
1 GCTGCAAGAAGCAGAA
51497836 GCTG-AAGAAGCAG
1 GCTGCAAGAAGCAG
51497849 CAAGAGAGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 2 0.08
15 16 0.67
16 6 0.25
ACGTcount: A:0.39, C:0.18, G:0.32, T:0.11
Consensus pattern (16 bp):
GCTGCAAGAAGCAGAA
Found at i:51497894 original size:21 final size:21
Alignment explanation
Indices: 51497870--51497909 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
51497860 GAGGTTGCTG
*
51497870 AAGCTGATGCAGAGGCAGCGC
1 AAGCTGATGCAGAAGCAGCGC
**
51497891 AAGCTTTTGCAGAAGCAGC
1 AAGCTGATGCAGAAGCAGC
51497910 AATGAAAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.33, T:0.15
Consensus pattern (21 bp):
AAGCTGATGCAGAAGCAGCGC
Found at i:51498227 original size:29 final size:29
Alignment explanation
Indices: 51498194--51498280 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
51498184 TGTTGACGAT
*
51498194 TTTTGCAGCAGGCACCCAGTCATCATCCC
1 TTTTGCAGCAGGCACCCAGTGATCATCCC
*
51498223 TTTTGCAGCAGGCACCCAGTGATCGTCCC
1 TTTTGCAGCAGGCACCCAGTGATCATCCC
*
51498252 TATTTGTAGCAGGCACCCAGTGATCATCC
1 T-TTTGCAGCAGGCACCCAGTGATCATCC
51498281 TTATTATTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 28 0.53
30 25 0.47
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (29 bp):
TTTTGCAGCAGGCACCCAGTGATCATCCC
Found at i:51498265 original size:30 final size:30
Alignment explanation
Indices: 51498195--51498285 Score: 139
Period size: 30 Copynumber: 3.1 Consensus size: 30
51498185 GTTGACGATT
*
51498195 TTTGCAGCAGGCACCCAGTCATCATCCCT-
1 TTTGCAGCAGGCACCCAGTGATCATCCCTA
*
51498224 TTTGCAGCAGGCACCCAGTGATCGTCCCTA
1 TTTGCAGCAGGCACCCAGTGATCATCCCTA
* *
51498254 TTTGTAGCAGGCACCCAGTGATCATCCTTA
1 TTTGCAGCAGGCACCCAGTGATCATCCCTA
51498284 TT
1 TT
51498286 ATTTGTAGCC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 27 0.48
30 29 0.52
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (30 bp):
TTTGCAGCAGGCACCCAGTGATCATCCCTA
Found at i:51502114 original size:57 final size:57
Alignment explanation
Indices: 51502026--51502140 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
51502016 AAAAATTATA
51502026 ATTTGTTGAGTAGAGTGATAAAAGAGTTCAATACTTTTAAGTAAAGTTTTAAGTTCG
1 ATTTGTTGAGTAGAGTGATAAAAGAGTTCAATACTTTTAAGTAAAGTTTTAAGTTCG
51502083 ATTTGTTGAGTAGAGTGATAAAAGAGTTCAATACTTTTAAGTAAAGTTTTAAGTTCG
1 ATTTGTTGAGTAGAGTGATAAAAGAGTTCAATACTTTTAAGTAAAGTTTTAAGTTCG
51502140 A
1 A
51502141 GTTTTGTGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (57 bp):
ATTTGTTGAGTAGAGTGATAAAAGAGTTCAATACTTTTAAGTAAAGTTTTAAGTTCG
Found at i:51502138 original size:27 final size:27
Alignment explanation
Indices: 51502050--51502138 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
51502040 GTGATAAAAG
51502050 AGTTCAATACTTTTAAGTAAAGTTTTA
1 AGTTCAATACTTTTAAGTAAAGTTTTA
* * * **
51502077 AGTTCGAT--TTGTTGAGTAGAGTGATAAAA
1 AGTTCAATACTT-TTAAGTAAAGT--T-TTA
51502106 GAGTTCAATACTTTTAAGTAAAGTTTTA
1 -AGTTCAATACTTTTAAGTAAAGTTTTA
51502134 AGTTC
1 AGTTC
51502139 GAGTTTTGTG
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
25 2 0.04
26 9 0.20
27 12 0.27
28 2 0.04
29 2 0.04
30 7 0.16
31 9 0.20
32 2 0.04
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (27 bp):
AGTTCAATACTTTTAAGTAAAGTTTTA
Found at i:51504261 original size:3 final size:3
Alignment explanation
Indices: 51504253--51504283 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
51504243 CACAACCTCA
51504253 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
51504284 GTAACAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:51508770 original size:70 final size:69
Alignment explanation
Indices: 51508623--51508776 Score: 175
Period size: 70 Copynumber: 2.2 Consensus size: 69
51508613 GTTGAACACT
* * * *
51508623 AGCAATAAGATGGACACAGGACATTGTTTATGTAGAGGTTATTTTTAAGAAATAAAGTTAATGCA
1 AGCAATAAGATGGACAAAGAACATTGTTTA-GCAGAGGTTATTTTTAAGAAATAAAATTAATGCA
*
51508688 AGCCC
65 AACCC
** * * *
51508693 AATAATAAGATGGACAAAGAACATTGTTTA-CAGAGGCTTCTTTTTAAGACAATAAAATTAGTTC
1 AGCAATAAGATGGACAAAGAACATTGTTTAGCAGAGG-TTATTTTTAAGA-AATAAAATTAATGC
*
51508757 AAATCC
64 AAACCC
51508763 AGCAATAAGATGGA
1 AGCAATAAGATGGA
51508777 GGTGGAAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
68 5 0.07
69 11 0.16
70 53 0.77
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (69 bp):
AGCAATAAGATGGACAAAGAACATTGTTTAGCAGAGGTTATTTTTAAGAAATAAAATTAATGCAA
ACCC
Found at i:51511945 original size:14 final size:14
Alignment explanation
Indices: 51511893--51511950 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
51511883 GCCTTAAACC
51511893 AAAATATTAAA-TTT
1 AAAAT-TTAAAGTTT
* **
51511907 AAAGTTTAGGGTTT
1 AAAATTTAAAGTTT
*
51511921 ATAATTT-AAGTTT
1 AAAATTTAAAGTTT
51511934 AAAATTTAAAGTTT
1 AAAATTTAAAGTTT
51511948 AAA
1 AAA
51511951 TTGAAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 13 0.38
14 21 0.62
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (14 bp):
AAAATTTAAAGTTT
Found at i:51511951 original size:13 final size:13
Alignment explanation
Indices: 51511894--51511952 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
51511884 CCTTAAACCA
51511894 AAATATTAAA-TTT
1 AAAT-TTAAAGTTT
**
51511907 AAAGTTTAGGGTTT
1 AAA-TTTAAAGTTT
51511921 ATAATTT-AAGTTT
1 A-AATTTAAAGTTT
51511934 AAAATTTAAAGTTT
1 -AAATTTAAAGTTT
51511948 AAATT
1 AAATT
51511953 GAAAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
13 20 0.54
14 15 0.41
15 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (13 bp):
AAATTTAAAGTTT
Found at i:51512260 original size:17 final size:20
Alignment explanation
Indices: 51512230--51512271 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
51512220 ATTCAACATA
51512230 TTTTAATAGTAAAAT-ATTT
1 TTTTAATAGTAAAATAATTT
51512249 TTTTAA-AG-AAAATAATTT
1 TTTTAATAGTAAAATAATTT
51512267 TTTTA
1 TTTTA
51512272 GCACTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 11 0.50
19 6 0.27
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTTAATAGTAAAATAATTT
Found at i:51519027 original size:18 final size:20
Alignment explanation
Indices: 51519004--51519049 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
51518994 GTATTATTGT
*
51519004 ATAAATTAT-CGAT-AATAC
1 ATAAATTATACCATCAATAC
51519022 ATAAATTATACCATCAATAC
1 ATAAATTATACCATCAATAC
51519042 ATTAAATT
1 A-TAAATT
51519050 TAACCCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
19 3 0.12
20 6 0.25
21 6 0.25
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAATTATACCATCAATAC
Found at i:51520713 original size:8 final size:8
Alignment explanation
Indices: 51520702--51520726 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
51520692 ATTTTATTGT
51520702 TTTATATA
1 TTTATATA
51520710 TTTATATA
1 TTTATATA
51520718 TTTATATA
1 TTTATATA
51520726 T
1 T
51520727 AAATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTATATA
Found at i:51521804 original size:16 final size:15
Alignment explanation
Indices: 51521772--51521800 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
51521762 TATCTGTCTT
51521772 TTTTTTAAATATTTA
1 TTTTTTAAATATTTA
51521787 TTTTTTAAATATTT
1 TTTTTTAAATATTT
51521801 TATTATAACC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTAAATATTTA
Found at i:51531929 original size:10 final size:11
Alignment explanation
Indices: 51531915--51531947 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
51531905 GGGAATGAAT
51531915 GAAAATAAAAA
1 GAAAATAAAAA
51531926 -AAAATAAAAA
1 GAAAATAAAAA
51531936 GAAAA-AAAAA
1 GAAAATAAAAA
51531946 GA
1 GA
51531948 TTGACTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (11 bp):
GAAAATAAAAA
Found at i:51532674 original size:13 final size:14
Alignment explanation
Indices: 51532658--51532693 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
51532648 CAATCTCATA
51532658 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
51532671 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
51532684 TCTC-ATTTCA
1 TCTCAATTTCA
51532694 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:51532683 original size:18 final size:19
Alignment explanation
Indices: 51532645--51532685 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
51532635 TGGTTCATGT
51532645 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
51532664 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
51532682 TTTC
1 TTTC
51532686 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:51532875 original size:39 final size:38
Alignment explanation
Indices: 51532808--51532942 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
51532798 ACCAATATGG
* * *
51532808 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
51532847 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
51532885 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
51532926 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
51532943 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:51533209 original size:18 final size:19
Alignment explanation
Indices: 51533183--51533221 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
51533173 TTTCAATTTA
*
51533183 ATTCAAATAATCAATATAT
1 ATTCAAATAATAAATATAT
*
51533202 ATTC-AATATTAAATATAT
1 ATTCAAATAATAAATATAT
51533220 AT
1 AT
51533222 ATCTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATAAATATAT
Found at i:51534538 original size:5 final size:5
Alignment explanation
Indices: 51534528--51534584 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
51534518 TTACTTATTT
* *
51534528 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
51534576 ATAT- ATATA
1 ATATA ATATA
51534585 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:51534544 original size:12 final size:12
Alignment explanation
Indices: 51534527--51534582 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
51534517 TTTACTTATT
51534527 TATATAATATAA
1 TATATAATATAA
51534539 TATATAATATAATA
1 TATATAATAT-A-A
51534553 TACTATAATATAA
1 TA-TATAATATAA
*
51534566 TA-ATAATTTAA
1 TATATAATATAA
51534577 TATATA
1 TATATA
51534583 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:51534597 original size:26 final size:26
Alignment explanation
Indices: 51534529--51534584 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
51534519 TACTTATTTA
*
51534529 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
51534556 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
51534581 TATA
1 TATA
51534585 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:51535234 original size:65 final size:64
Alignment explanation
Indices: 51535153--51535344 Score: 307
Period size: 62 Copynumber: 3.0 Consensus size: 64
51535143 TCCCTTTTGC
* * *
51535153 TTTTATAATTAGACGTTGGCGTTCTCCTTTTCCAAAGGCTTTCTTCCCTTTCCTTCTCCAGCAAG
1 TTTTTTAATTACACGTTGGCGCTCTCCTTTTCCAAAGGCTTTCTTCCC-TTCCTTCTCCAGCAAG
* *
51535218 TTTTTTAATTACACGTTGGCGCTCTCCTTTTCCAAAGGCTTTCGTCCC-T-CTCCTCCAGCAAG
1 TTTTTTAATTACACGTTGGCGCTCTCCTTTTCCAAAGGCTTTCTTCCCTTCCTTCTCCAGCAAG
51535280 TTTTTTAATTACACGTTGGCGCTCTCCTTTTCCAAAGGCTTTCTTCCCTCTCCTTCTCCAGCAAG
1 TTTTTTAATTACACGTTGGCGCTCTCCTTTTCCAAAGGCTTTCTTCCCT-TCCTTCTCCAGCAAG
51535345 CATGGAAGAG
Statistics
Matches: 117, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
62 59 0.50
63 1 0.01
64 1 0.01
65 56 0.48
ACGTcount: A:0.16, C:0.31, G:0.14, T:0.40
Consensus pattern (64 bp):
TTTTTTAATTACACGTTGGCGCTCTCCTTTTCCAAAGGCTTTCTTCCCTTCCTTCTCCAGCAAG
Found at i:51541948 original size:12 final size:12
Alignment explanation
Indices: 51541931--51541973 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
51541921 TAAAATTATG
51541931 TTATATTAATAA
1 TTATATTAATAA
51541943 TTATATTAATAA
1 TTATATTAATAA
*
51541955 TT-TA-TAAGAA
1 TTATATTAATAA
*
51541965 TTAGATTAA
1 TTATATTAA
51541974 ATAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 17 0.63
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (12 bp):
TTATATTAATAA
Found at i:51545965 original size:23 final size:23
Alignment explanation
Indices: 51545939--51546006 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 23
51545929 CCCAAATAAG
51545939 ATTAAGTACCAACATGAAAACAA
1 ATTAAGTACCAACATGAAAACAA
* * * *
51545962 ATT-ATTACC-CCA--AATA-AG
1 ATTAAGTACCAACATGAAAACAA
51545980 ATTAAGTACCAACATGAAAACAA
1 ATTAAGTACCAACATGAAAACAA
51546003 ATTA
1 ATTA
51546007 TTAGGTGCCA
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 4 0.12
19 8 0.25
20 2 0.06
21 2 0.06
22 8 0.25
23 8 0.25
ACGTcount: A:0.53, C:0.18, G:0.07, T:0.22
Consensus pattern (23 bp):
ATTAAGTACCAACATGAAAACAA
Found at i:51545972 original size:41 final size:41
Alignment explanation
Indices: 51545927--51546009 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
51545917 ATCAAGTTAG
51545927 ACCCCAAATAAGATTAAGTACCAACATGAAAACAAATTATT
1 ACCCCAAATAAGATTAAGTACCAACATGAAAACAAATTATT
51545968 ACCCCAAATAAGATTAAGTACCAACATGAAAACAAATTATT
1 ACCCCAAATAAGATTAAGTACCAACATGAAAACAAATTATT
51546009 A
1 A
51546010 GGTGCCAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (41 bp):
ACCCCAAATAAGATTAAGTACCAACATGAAAACAAATTATT
Found at i:51554781 original size:42 final size:42
Alignment explanation
Indices: 51554702--51554784 Score: 105
Period size: 45 Copynumber: 1.9 Consensus size: 42
51554692 CTAATTAATT
*
51554702 TATTTTTTTCAAATCATTATAATAGAATATTTTTTTCAAATATA
1 TATTTTTTCCAAATCATTATAATAGAATA--TTTTTCAAATATA
* *
51554746 TATTTTTTCCGAACTCATTATGATAGAATA-TTTTCAAAT
1 TATTTTTTCC-AAATCATTATAATAGAATATTTTTCAAAT
51554785 CAAATAAAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 9 0.26
44 9 0.26
45 17 0.49
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (42 bp):
TATTTTTTCCAAATCATTATAATAGAATATTTTTCAAATATA
Found at i:51556853 original size:61 final size:61
Alignment explanation
Indices: 51556782--51556906 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
51556772 GTTTTAGTCA
51556782 AAATTTAAATTAAAAATAATAATTAGACTATTCTTTAATGTTTAATGGTCAAATTTAACTC
1 AAATTTAAATTAAAAATAATAATTAGACTATTCTTTAATGTTTAATGGTCAAATTTAACTC
51556843 AAATTTAAATTAAAAATAATAATTAGACTATTCTTTAATGTTTAATGGTCAAATTTAACTC
1 AAATTTAAATTAAAAATAATAATTAGACTATTCTTTAATGTTTAATGGTCAAATTTAACTC
51556904 AAA
1 AAA
51556907 AGAATAATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (61 bp):
AAATTTAAATTAAAAATAATAATTAGACTATTCTTTAATGTTTAATGGTCAAATTTAACTC
Found at i:51556880 original size:30 final size:30
Alignment explanation
Indices: 51556785--51556880 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
51556775 TTAGTCAAAA
51556785 TTTAAATTAAAAATAATAATTAGACTATTC
1 TTTAAATTAAAAATAATAATTAGACTATTC
* *** * **
51556815 TTTAATGTTTAATGGTCAA-ATTTA-ACTCA-AA
1 TTTAA--ATTAAAAAT-AATAATTAGACT-ATTC
51556846 TTTAAATTAAAAATAATAATTAGACTATTC
1 TTTAAATTAAAAATAATAATTAGACTATTC
51556876 TTTAA
1 TTTAA
51556881 TGTTTAATGG
Statistics
Matches: 45, Mismatches: 14, Indels: 14
0.62 0.19 0.19
Matches are distributed among these distances:
28 2 0.04
29 10 0.22
30 13 0.29
31 8 0.18
32 10 0.22
33 2 0.04
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTAAATTAAAAATAATAATTAGACTATTC
Found at i:51558062 original size:11 final size:11
Alignment explanation
Indices: 51558046--51558070 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
51558036 TCGAATATTC
51558046 ATGTCCAAAAT
1 ATGTCCAAAAT
51558057 ATGTCCAAAAT
1 ATGTCCAAAAT
51558068 ATG
1 ATG
51558071 CATAAATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (11 bp):
ATGTCCAAAAT
Found at i:51578110 original size:3 final size:3
Alignment explanation
Indices: 51578102--51578126 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
51578092 ACCCAGTTTA
51578102 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
51578127 CGTTTTGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:51584272 original size:21 final size:21
Alignment explanation
Indices: 51584242--51584320 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 21
51584232 ATAATGATAC
*
51584242 TTTTAGAATTCAATTAAAATA
1 TTTTAAAATTCAATTAAAATA
* *
51584263 TTTTAAAATTTGCTATAATAATGATAA
1 TTTTAAAA-TT-C-A-ATTAA-AAT-A
*
51584290 TTTTAGAATTCAATTAAAATA
1 TTTTAAAATTCAATTAAAATA
51584311 TTTTAAAATT
1 TTTTAAAATT
51584321 TGAAGAGCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 17 0.38
22 4 0.09
23 5 0.11
24 2 0.04
25 5 0.11
26 4 0.09
27 8 0.18
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTTAAAATTCAATTAAAATA
Found at i:51584295 original size:48 final size:48
Alignment explanation
Indices: 51584224--51584322 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
51584214 AATGACTTGA
*
51584224 TTGCTATAATAATGATACTTTTAGAATTCAATTAAAATATTTTAAAAT
1 TTGCTATAATAATGATAATTTTAGAATTCAATTAAAATATTTTAAAAT
51584272 TTGCTATAATAATGATAATTTTAGAATTCAATTAAAATATTTTAAAAT
1 TTGCTATAATAATGATAATTTTAGAATTCAATTAAAATATTTTAAAAT
51584320 TTG
1 TTG
51584323 AAGAGCAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (48 bp):
TTGCTATAATAATGATAATTTTAGAATTCAATTAAAATATTTTAAAAT
Found at i:51590194 original size:14 final size:14
Alignment explanation
Indices: 51590175--51590221 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
51590165 TTTTCAATTT
51590175 TTAAAATATAAAGA
1 TTAAAATATAAAGA
* *
51590189 TTAAAAATTTCAA-A
1 TT-AAAATATAAAGA
*
51590203 TTAAAATATAAAGG
1 TTAAAATATAAAGA
51590217 TTAAA
1 TTAAA
51590222 TTCACAATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 8 0.31
14 10 0.38
15 8 0.31
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (14 bp):
TTAAAATATAAAGA
Found at i:51590542 original size:19 final size:19
Alignment explanation
Indices: 51590504--51590540 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
51590494 TTTTATTGAC
51590504 ATAATATTTAAAATTTTTT
1 ATAATATTTAAAATTTTTT
*
51590523 ATAAT-TTTATAATTTTTT
1 ATAATATTTAAAATTTTTT
51590541 TACTATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATAATATTTAAAATTTTTT
Found at i:51591834 original size:31 final size:32
Alignment explanation
Indices: 51591799--51591859 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
51591789 AAACTTTTAG
51591799 ATAGTTAAATGACTAAAATG-AAATTTTTTGA
1 ATAGTTAAATGACTAAAATGTAAATTTTTTGA
* * *
51591830 ATAGTTTAATGATTAAATTGTAAATTTTTT
1 ATAGTTAAATGACTAAAATGTAAATTTTTT
51591860 AATTAAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (32 bp):
ATAGTTAAATGACTAAAATGTAAATTTTTTGA
Found at i:51594468 original size:19 final size:20
Alignment explanation
Indices: 51594432--51594478 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
51594422 TCCAACAAAA
* *
51594432 AAAAATTCAGAATAATTT-T
1 AAAAATTTAAAATAATTTAT
51594451 CAAAAATTTAAAAT-ATTTAT
1 -AAAAATTTAAAATAATTTAT
51594471 AAAAATTT
1 AAAAATTT
51594479 CATAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATTTAAAATAATTTAT
Found at i:51594665 original size:16 final size:16
Alignment explanation
Indices: 51594644--51594674 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51594634 TTTGAAAGAA
51594644 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
51594660 TTTCAAATTTATATG
1 TTTCAAATATATATG
51594675 CTCTAATATG
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:51598524 original size:3 final size:3
Alignment explanation
Indices: 51598516--51598540 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
51598506 AAGGCGGAAA
51598516 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
51598541 GCCGCCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:51606045 original size:46 final size:46
Alignment explanation
Indices: 51605884--51606037 Score: 240
Period size: 46 Copynumber: 3.4 Consensus size: 46
51605874 TGTCTTCGAC
** * * * *
51605884 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA--TATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
51605928 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
51605974 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
51606020 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
51606038 TTTCTGTCCT
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
44 33 0.32
46 69 0.68
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (46 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
Found at i:51609192 original size:19 final size:15
Alignment explanation
Indices: 51609154--51609184 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
51609144 ATAATATTTC
51609154 TATTAATTTATTTAA
1 TATTAATTTATTTAA
51609169 TATTAATTTATTTAA
1 TATTAATTTATTTAA
51609184 T
1 T
51609185 TTGAATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTAATTTATTTAA
Found at i:51610811 original size:8 final size:8
Alignment explanation
Indices: 51610798--51610833 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
51610788 GATTTATGAA
51610798 CATTTTCC
1 CATTTTCC
51610806 CATTTTCC
1 CATTTTCC
51610814 CATTTTCC
1 CATTTTCC
*
51610822 CATTTTCT
1 CATTTTCC
51610830 CATT
1 CATT
51610834 CATGTGGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.00, T:0.53
Consensus pattern (8 bp):
CATTTTCC
Found at i:51619277 original size:6 final size:6
Alignment explanation
Indices: 51619266--51619292 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
51619256 AGAAATTGAT
51619266 GCTCAA GCTCAA GCTCAA GCTCAA GCT
1 GCTCAA GCTCAA GCTCAA GCTCAA GCT
51619293 TGTCACTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.19
Consensus pattern (6 bp):
GCTCAA
Found at i:51623603 original size:30 final size:28
Alignment explanation
Indices: 51623535--51623603 Score: 68
Period size: 32 Copynumber: 2.3 Consensus size: 28
51623525 AGAATTTCTA
* *
51623535 TAAATTTTGAGGGTTAAGTTAAAATTTT
1 TAAATTTTGAGGGTTAAGTAAAAAATTT
51623563 TAAAAGTTTTGAAAGGGTTAA-TGAAAAAATTT
1 T-AAA-TTTTG--AGGGTTAAGT-AAAAAATTT
51623595 TAAATTTTG
1 TAAATTTTG
51623604 TTTCTTGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
28 1 0.03
29 3 0.09
30 10 0.29
31 4 0.12
32 16 0.47
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.42
Consensus pattern (28 bp):
TAAATTTTGAGGGTTAAGTAAAAAATTT
Found at i:51624447 original size:30 final size:30
Alignment explanation
Indices: 51624413--51624500 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
51624403 CTTAAAAAAA
*
51624413 TTTGAAAGCTCTAACTAAAATTTTTAAACT
1 TTTGAAAGCTCTAATTAAAATTTTTAAACT
* * *
51624443 TTTGAAAG-TTTAATTAGAAATTTTAAAAGT
1 TTTGAAAGCTCTAATTA-AAATTTTTAAACT
* *
51624473 TTTGAAGGAC-CTAATTAAAATATTTAAA
1 TTTGAAAG-CTCTAATTAAAATTTTTAAA
51624501 AAATTTGGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 6 0.13
30 35 0.74
31 6 0.13
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (30 bp):
TTTGAAAGCTCTAATTAAAATTTTTAAACT
Found at i:51642315 original size:203 final size:211
Alignment explanation
Indices: 51641942--51642511 Score: 753
Period size: 203 Copynumber: 2.7 Consensus size: 211
51641932 TATCAAATGT
* * * *
51641942 GACAGTAAGACTTCAGAACCATACGTTCTGTGGGTTTTAAGGAATAAACAATTTAAGCCAGCATC
1 GACAATAAGACTTCAGAACCATACGTTCTGTGGTTTTTAACGAATAAACAATTTAAGCCAACATC
* * * * *
51642007 TTAATTTCATTTAGAGAACACATGAAATGCCAATAACCAACAAGATCATCACCTTGCAAGGACAA
66 TTAATTCCATTTAGAGAACACATGAAATGCCAATAAACAACAAGATCATCACATTGC-A-TACGA
*
51642072 TCAATAAGCACACTTAACAATATGCAGCCACTCCATGGACCATACTAATCAAACG-CCTTTAACA
129 TCAATAAGCACACTTAACAATACGCAGCCACTCCATGGACCATACTAATCAAA-GTCCTTTAACA
51642136 CCATA-AC-AAGACC-A-A
193 CCATAGACTAAGACCAATA
* * * * * * * **
51642151 -ACAATAAGACTTCAAAACTATATGTACTGTAGTTTTTAATGAATAAACTACGTAAGCCAACATC
1 GACAATAAGACTTCAGAACCATACGTTCTGTGGTTTTTAACGAATAAACAATTTAAGCCAACATC
* * * * *
51642215 -TAAATCCATTTAGAGAACATATAAAATGCCAATAATCAACAGGATCATCACATTGCATA-GA-C
66 TTAATTCCATTTAGAGAACACATGAAATGCCAATAAACAACAAGATCATCACATTGCATACGATC
*
51642277 AATAAGCACACTTAATAATACGCAGCCACTCCATGGACCATACTAATCAAAGTCCTTTAACACCA
131 AATAAGCACACTTAACAATACGCAGCCACTCCATGGACCATACTAATCAAAGTCCTTTAACACCA
* *
51642342 TAGCCTATGACCAAATA
196 TAGACTAAGACC-AATA
*
51642359 TGACAATAAGACTTCAGAACCATACATTCTGTGGTTTTTAACGAATAAACAATTTAAGCCAACAT
1 -GACAATAAGACTTCAGAACCATACGTTCTGTGGTTTTTAACGAATAAACAATTTAAGCCAACAT
*
51642424 CTTAATTCCATTTAGAGAACACATGAAATGCCAATAAACAACAAGATCATCACATTGCAATGACT
65 CTTAATTCCATTTAGAGAACACATGAAATGCCAATAAACAACAAGATCATCACATTGC-AT-ACG
51642489 ATCAATAAGCACACTTAACAATA
128 ATCAATAAGCACACTTAACAATA
51642512 AAGAAAATAC
Statistics
Matches: 306, Mismatches: 42, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
202 1 0.00
203 64 0.21
204 2 0.01
205 6 0.02
206 1 0.00
207 50 0.16
208 53 0.17
210 54 0.18
211 51 0.17
212 2 0.01
213 1 0.00
214 1 0.00
215 20 0.07
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (211 bp):
GACAATAAGACTTCAGAACCATACGTTCTGTGGTTTTTAACGAATAAACAATTTAAGCCAACATC
TTAATTCCATTTAGAGAACACATGAAATGCCAATAAACAACAAGATCATCACATTGCATACGATC
AATAAGCACACTTAACAATACGCAGCCACTCCATGGACCATACTAATCAAAGTCCTTTAACACCA
TAGACTAAGACCAATA
Found at i:51644055 original size:12 final size:12
Alignment explanation
Indices: 51644038--51644068 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
51644028 ACTAATCCAC
51644038 CGAATTGATTGT
1 CGAATTGATTGT
51644050 CGAATTGATTGT
1 CGAATTGATTGT
51644062 CGAATTG
1 CGAATTG
51644069 TCAATTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.39
Consensus pattern (12 bp):
CGAATTGATTGT
Found at i:51644157 original size:31 final size:31
Alignment explanation
Indices: 51644122--51644186 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
51644112 AATAGCCCAA
*
51644122 TGACTTAAATAAAAACTTTTGTATAGTTTAG
1 TGACTTAAATAAAAACTTTTGAATAGTTTAG
*
51644153 TGACTTAAATAAAAACTTTTGAATGGTTTAG
1 TGACTTAAATAAAAACTTTTGAATAGTTTAG
51644184 TGA
1 TGA
51644187 TCAAATTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAGTTTAG
Found at i:51649209 original size:42 final size:38
Alignment explanation
Indices: 51649163--51649251 Score: 117
Period size: 37 Copynumber: 2.3 Consensus size: 38
51649153 TAAAAATTAT
51649163 TTATATTAAAAAAACACTATCATAAATATAATAAATATTTTA
1 TTATATTAAAAAAACAC-AT-A-AAA-ATAATAAATATTTTA
*
51649205 TTATATT-AAAAAACACATAAAAATATTAAATATTTTA
1 TTATATTAAAAAAACACATAAAAATAATAAATATTTTA
*
51649242 TTGTATTAAA
1 TTATATTAAA
51649252 TATAATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
37 20 0.45
38 5 0.11
39 1 0.02
40 2 0.05
41 9 0.20
42 7 0.16
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (38 bp):
TTATATTAAAAAAACACATAAAAATAATAAATATTTTA
Found at i:51652247 original size:46 final size:46
Alignment explanation
Indices: 51652137--51652495 Score: 425
Period size: 46 Copynumber: 7.6 Consensus size: 46
51652127 TTTGACATGA
* * * *
51652137 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTC-T--T-ATTC-TTTTCATGTCACGT
*
51652187 TGCCATGGTATCTTTCAATCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
* * *
51652233 TGCCATGGTGTCTTTCAACTATGGTCTTTCTCATTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTC--T-T-ATTC-TTTTCATGTCACGT
*
51652283 TGCCATGATATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
*
51652329 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
** * * *
51652375 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
** * * * *
51652421 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
51652467 TGCCATGGTATCTTTCAACCATGGTCTTA
1 TGCCATGGTATCTTTCAACCATGGTCTTA
51652496 CACATTTCAT
Statistics
Matches: 281, Mismatches: 21, Indels: 18
0.88 0.07 0.06
Matches are distributed among these distances:
45 10 0.04
46 204 0.73
47 2 0.01
48 2 0.01
49 2 0.01
50 56 0.20
51 5 0.02
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
Found at i:51652253 original size:96 final size:96
Alignment explanation
Indices: 51652137--51652495 Score: 468
Period size: 92 Copynumber: 3.8 Consensus size: 96
51652127 TTTGACATGA
* * *
51652137 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTCATTTTC-TGTCATGTTGCCATGGTATCTT
1 TGCCATGGTATCTTTCAACCATGGTCTTA-TCATTCATTTTCATGTCATGTTGCCATGGTATCTT
*
51652201 TCAATCATGGTCTTATTCTTTTCATGTCACGT
65 TCAACCATGGTCTTATTCTTTTCATGTCACGT
* * * *
51652233 TGCCATGGTGTCTTTCAACTATGGTCTTTCTCATTCATTTTC-TGTCATGTTGCCATGATATCTT
1 TGCCATGGTATCTTTCAACCATGGTC-TTATCATTCATTTTCATGTCATGTTGCCATGGTATCTT
51652297 TCAACCATGGTCTTATTCTTTTCATGTCACGT
65 TCAACCATGGTCTTATTCTTTTCATGTCACGT
*
51652329 TGCCATGGTATCTTTCAACCATGGTC-T-T-ATTCA-TTTCATGTCACGTTGCCATGGTATCTTT
1 TGCCATGGTATCTTTCAACCATGGTCTTATCATTCATTTTCATGTCATGTTGCCATGGTATCTTT
** * * *
51652390 CAACCATGGTCTTACACATTTCATATCAGGT
66 CAACCATGGTCTTATTCTTTTCATGTCACGT
* * * *
51652421 TGCCATGGTATCTTTCAACCATGGTCTTA-CA--C-GTTTCATATCAGGCTGCCATGGTATCTTT
1 TGCCATGGTATCTTTCAACCATGGTCTTATCATTCATTTTCATGTCATGTTGCCATGGTATCTTT
51652482 CAACCATGGTCTTA
66 CAACCATGGTCTTA
51652496 CACATTTCAT
Statistics
Matches: 241, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
91 4 0.02
92 118 0.49
93 2 0.01
94 2 0.01
96 113 0.47
97 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (96 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATCATTCATTTTCATGTCATGTTGCCATGGTATCTTT
CAACCATGGTCTTATTCTTTTCATGTCACGT
Found at i:51654581 original size:21 final size:22
Alignment explanation
Indices: 51654557--51654606 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
51654547 AAATCCGAAT
51654557 TTTTCCCTTT-TTCCTTCTTTC
1 TTTTCCCTTTCTTCCTTCTTTC
*
51654578 TTTT--TTTTCCTTCCTTCTTTC
1 TTTTCCCTTT-CTTCCTTCTTTC
*
51654599 TTTCCCCT
1 TTTTCCCT
51654607 GCTCTCTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 6
0.71 0.10 0.19
Matches are distributed among these distances:
19 3 0.14
21 18 0.82
23 1 0.05
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTCCCTTTCTTCCTTCTTTC
Found at i:51654586 original size:17 final size:17
Alignment explanation
Indices: 51654564--51654597 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51654554 AATTTTTCCC
*
51654564 TTTTTCCTTCTTTCTTT
1 TTTTTCCTTCCTTCTTT
51654581 TTTTTCCTTCCTTCTTT
1 TTTTTCCTTCCTTCTTT
51654598 CTTTCCCCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCCTTCCTTCTTT
Found at i:51654650 original size:15 final size:16
Alignment explanation
Indices: 51654629--51654666 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
51654619 CGTTTCATCC
51654629 TTTCTTTCTTTTTCTA
1 TTTCTTTCTTTTTCTA
*
51654645 -TTCTTTTTTTTTCTA
1 TTTCTTTCTTTTTCTA
51654660 TTTCTTT
1 TTTCTTT
51654667 TACTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTCTTTTTCTA
Found at i:51658500 original size:20 final size:20
Alignment explanation
Indices: 51658475--51658517 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
51658465 GATGTAGAGA
* *
51658475 GAAATGCGCCAGATCCTGCT
1 GAAATGCACCAGATCCTGAT
*
51658495 GAAATGCACCAGCTCCTGAT
1 GAAATGCACCAGATCCTGAT
51658515 GAA
1 GAA
51658518 GGGGCTATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (20 bp):
GAAATGCACCAGATCCTGAT
Found at i:51665707 original size:42 final size:42
Alignment explanation
Indices: 51665649--51665743 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
51665639 TTCATAGTAG
51665649 TTAAT-AAATTTAATAGCTCTTATTTGAGTCAAGATTAAAAT
1 TTAATAAAATTTAATAGCTCTTATTTGAGTCAAGATTAAAAT
* *
51665690 TTAATAAAATTTAATAGCTCTTGTTTGAGTCAAGATTGAAAT
1 TTAATAAAATTTAATAGCTCTTATTTGAGTCAAGATTAAAAT
51665732 TT-A-AAAATTTAA
1 TTAATAAAATTTAA
51665744 AAAATATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
40 9 0.18
41 6 0.12
42 36 0.71
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (42 bp):
TTAATAAAATTTAATAGCTCTTATTTGAGTCAAGATTAAAAT
Found at i:51667234 original size:28 final size:28
Alignment explanation
Indices: 51667201--51667259 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
51667191 ATTTAGATTT
* *
51667201 TAAAATTAAAAA-A-AATGATTAAATTAC
1 TAAAAATAAAAATATAACGATTAAATT-C
51667228 TAAAAATAAAAATATAACGATTAAATTC
1 TAAAAATAAAAATATAACGATTAAATTC
51667256 TAAA
1 TAAA
51667260 TTAGGTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.39
28 6 0.21
29 11 0.39
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAAAATAAAAATATAACGATTAAATTC
Found at i:51674641 original size:215 final size:217
Alignment explanation
Indices: 51674043--51675089 Score: 1543
Period size: 215 Copynumber: 4.9 Consensus size: 217
51674033 ATGTGAGCCT
* *
51674043 TGAGATAAAACCCGAAGTAGAATTAAGACACATCAATATATATATCCATTTGTATATCTCAATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTC---A-
* ** *
51674108 ATATATATATAACATACGCATGTCTAGTTAGAATATTTAGACAAGTTGTCGGCCACCTTATCTGT
62 ATATATATAT-ACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGT
* *
51674173 AAAATGTGATCATTTTGGCAAATATTCCATATTTAAGAACTTTCCTGGAAAATTTTCTGAAACTA
126 AAAATGTGATCATTTTAGCAAATATTCCAT-CTTAAGAACTTTCCTGGAAAATTTTCTGAAACTA
*
51674238 TGACCCATCAAGGCTCTTGGCAGAATCG
190 TGACCCATCAAGGCTCTTAGCAGAATCG
* *
51674266 TAAGATAAAACCTGAAGCAGAATTGAGACACATCAATATATATATATCCATTTGTATATCTCAAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATC-A-ATATATATATCCATTTGTATATCTCAAT
* * * * *
51674331 AGATATACACATACGCATGTGTGGTTAGAATATTTGGACAAGTTGTCCTCTACCTTATCTGTAAA
64 ATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAA
51674396 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGAC
129 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGAC
*
51674461 CCATCAAGGCTCTTAGCAGAATGG
194 CCATCAAGGCTCTTAGCAGAATCG
* *
51674485 TGAGATAAAACCCGAAGCAGAATTGAGACACTTC-A-ATATATATCCAATTGTATATCTCAATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTCAATAT
* *
51674548 ATATATACATACGCATGTCTAGTTAGACTATTTGGACAAGTTGTCATCTATCTTATCTGTAAAAT
66 ATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAAT
*
51674613 GTGATTATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCC
131 GTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCC
* *
51674678 ATCAAGACTCTTAGCAGAGTCG
196 ATCAAGGCTCTTAGCAGAATCG
* *
51674700 TGAGATAGAACCCGAAGCAGAACTGAGACACATCAATATATATATCCATTTG----------T-T
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTCAATAT
*
51674754 ATATATACATACGCATGTCTAGTTAGAATATTTGGTCAAGTTGTCATCTACCTTATCTGTAAAAT
66 ATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAAT
* * *
51674819 GTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAATTTTTCTGAAACTATGACTC
131 GTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCC
* *
51674884 ATCAAGGCTCTTAGCTGAGTCG
196 ATCAAGGCTCTTAGCAGAATCG
* * * *
51674906 TGAGGTAAAACCCAAAGCAGAATTGAGCCACACCAATATATATATCCATTTGTATATCTCAATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTCAATAT
*
51674971 ATATATACACATACGCGTGTCTAGTTAGAAT-TTTGGACAAG-T-T-ATCTACCTTATCTGTAAA
66 ATATAT--ACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAA
*
51675032 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTTCTGAAA
129 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAA
51675090 AACTTTTTTT
Statistics
Matches: 754, Mismatches: 53, Indels: 42
0.89 0.06 0.05
Matches are distributed among these distances:
206 190 0.25
207 1 0.00
215 274 0.36
216 4 0.01
217 22 0.03
218 9 0.01
219 112 0.15
220 77 0.10
221 8 0.01
222 1 0.00
223 30 0.04
224 1 0.00
225 25 0.03
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (217 bp):
TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTCAATAT
ATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAAT
GTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCC
ATCAAGGCTCTTAGCAGAATCG
Found at i:51674781 original size:421 final size:431
Alignment explanation
Indices: 51674043--51675089 Score: 1564
Period size: 421 Copynumber: 2.4 Consensus size: 431
51674033 ATGTGAGCCT
* *
51674043 TGAGATAAAACCCGAAGTAGAATTAAGACACATCAATATATATATCCATTTGTATATCTCAATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTC---A-
* ** *
51674108 ATATATATATAACATACGCATGTCTAGTTAGAATATTTAGACAAGTTGTCGGCCACCTTATCTGT
62 ATATATATATAACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGT
* *
51674173 AAAATGTGATCATTTTGGCAAATATTCCATATTTAAGAACTTTCCTGGAAAATTTTCTGAAACTA
127 AAAATGTGATCATTTTAGCAAATATTCCAT-CTTAAGAACTTTCCTGGAAAATTTTCTGAAACTA
* * * *
51674238 TGACCCATCAAGGCTCTTGGCAGAATCGTAAGATAAAACCTGAAGCAGAATTGAGACACATCAAT
191 TGACCCATCAAGACTCTTAGCAGAATCGTAAGATAAAACCCGAAGCAGAACTGAGACACATCAAT
* *
51674303 ATATATATATCCATTTGTATATCTCAATAGATATACACATACGCATGTGTGGTTAGAATATTTGG
256 ATATATATATCCATTTG---ATCT-AATA-ATATA-ACATACGCATGTCTAGTTAGAATATTTGG
*
51674368 ACAAGTTGTCCTCTACCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACT
315 ACAAGTTGTCATCTACCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACT
* *
51674433 TTCCTGGAAAATTTTCTGAAACTATGACCCATCAAGGCTCTTAGCAGAATGG
380 TTACTGGAAAATTTTCTGAAACTATGACCCATCAAGGCTCTTAGCAGAATCG
* *
51674485 TGAGATAAAACCCGAAGCAGAATTGAGACACTTC-A-ATATATATCCAATTGTATATCTCAATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTCAATAT
* *
51674548 ATATAT-ACATACGCATGTCTAGTTAGACTATTTGGACAAGTTGTCATCTATCTTATCTGTAAAA
66 ATATATAACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAA
*
51674612 TGTGATTATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACC
131 TGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACC
* * *
51674677 CATCAAGACTCTTAGCAGAGTCGTGAGATAGAACCCGAAGCAGAACTGAGACACATC-A-ATATA
196 CATCAAGACTCTTAGCAGAATCGTAAGATAAAACCCGAAGCAGAACTGAGACACATCAATATATA
*
51674740 TATATCCATTTG-T-T-AT-ATAT-ACATACGCATGTCTAGTTAGAATATTTGGTCAAGTTGTCA
261 TATATCCATTTGATCTAATAATATAACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCA
*
51674800 TCTACCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAAT
326 TCTACCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAAA
* * *
51674865 TTTTCTGAAACTATGACTCATCAAGGCTCTTAGCTGAGTCG
391 TTTTCTGAAACTATGACCCATCAAGGCTCTTAGCAGAATCG
* * * *
51674906 TGAGGTAAAACCCAAAGCAGAATTGAGCCACACCAATATATATATCCATTTGTATATCTCAATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTCAATAT
*
51674971 ATATATACACATACGCGTGTCTAGTTAGAAT-TTTGGACAAG-T-T-ATCTACCTTATCTGTAAA
66 ATATATA-ACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAA
*
51675032 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTTCTGAAA
130 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAA
51675090 AACTTTTTTT
Statistics
Matches: 560, Mismatches: 41, Indels: 29
0.89 0.07 0.05
Matches are distributed among these distances:
421 238 0.43
422 2 0.00
423 38 0.07
424 10 0.02
425 23 0.04
427 1 0.00
428 1 0.00
432 17 0.03
433 1 0.00
434 88 0.16
435 76 0.14
436 10 0.02
437 1 0.00
440 22 0.04
441 1 0.00
442 31 0.06
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (431 bp):
TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTCAATAT
ATATATAACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAA
TGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACC
CATCAAGACTCTTAGCAGAATCGTAAGATAAAACCCGAAGCAGAACTGAGACACATCAATATATA
TATATCCATTTGATCTAATAATATAACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCA
TCTACCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAAA
TTTTCTGAAACTATGACCCATCAAGGCTCTTAGCAGAATCG
Found at i:51674875 original size:206 final size:208
Alignment explanation
Indices: 51674544--51675089 Score: 807
Period size: 206 Copynumber: 2.6 Consensus size: 208
51674534 GTATATCTCA
* *
51674544 ATATATATATACATACGCATGTCTAGTTAGACTATTTGGACAAGTTGTCATCTATCTTATCTGTA
1 ATATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTA
* *
51674609 AAATGTGATTATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATG
66 AAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTTCTGAAACTATG
* * *
51674674 ACCCATCAAGACTCTTAGCAGAGTCGTGAGATAGAACCCGAAGCAGAACTGAGACACATCAATAT
131 ACCCATCAAGACTCTTAGCAGAGTCGTGAGATAAAACCCAAAGCAGAACTGAGACACACCAATAT
51674739 ATATATCCATTTG
196 ATATATCCATTTG
*
51674752 -T-TATATATACATACGCATGTCTAGTTAGAATATTTGGTCAAGTTGTCATCTACCTTATCTGTA
1 ATATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTA
*
51674815 AAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTACTGGAAATTTTTCTGAAACTATG
66 AAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTTCTGAAACTATG
* * * * * *
51674880 ACTCATCAAGGCTCTTAGCTGAGTCGTGAGGTAAAACCCAAAGCAGAATTGAGCCACACCAATAT
131 ACCCATCAAGACTCTTAGCAGAGTCGTGAGATAAAACCCAAAGCAGAACTGAGACACACCAATAT
51674945 ATATATCCATTTG
196 ATATATCCATTTG
*
51674958 TATATCTCAATATATATATACACATACGCGTGTCTAGTTAGAAT-TTTGGACAAG-T-T-ATCTA
1 ---------ATATATATAT--ACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTA
51675019 CCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTT
55 CCTTATCTGTAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTT
51675084 CTGAAA
120 CTGAAA
51675090 AACTTTTTTT
Statistics
Matches: 307, Mismatches: 18, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
206 190 0.62
207 1 0.00
215 75 0.24
216 2 0.01
217 8 0.03
218 9 0.03
219 22 0.07
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (208 bp):
ATATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTA
AAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTTCTGAAACTATG
ACCCATCAAGACTCTTAGCAGAGTCGTGAGATAAAACCCAAAGCAGAACTGAGACACACCAATAT
ATATATCCATTTG
Found at i:51677384 original size:3 final size:3
Alignment explanation
Indices: 51677376--51677410 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
51677366 TGATTTCTTT
51677376 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
51677411 TTTAGTTCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:51679525 original size:24 final size:23
Alignment explanation
Indices: 51679496--51679547 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 23
51679486 GTAACAAGTC
51679496 CATCTTCTTAGCTTTCACTAGAG
1 CATCTTCTTAGCTTTCACTAGAG
51679519 TCATCTTCTTAGCTTTCACTAGAG
1 -CATCTTCTTAGCTTTCACTAGAG
51679543 CATCT
1 CATCT
51679548 GTGGTGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (23 bp):
CATCTTCTTAGCTTTCACTAGAG
Found at i:51689050 original size:16 final size:16
Alignment explanation
Indices: 51689029--51689061 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
51689019 TGTTTGTGTG
51689029 TACATGAAATATATGT
1 TACATGAAATATATGT
51689045 TACATGAAATATATGT
1 TACATGAAATATATGT
51689061 T
1 T
51689062 TGTATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (16 bp):
TACATGAAATATATGT
Found at i:51691784 original size:28 final size:28
Alignment explanation
Indices: 51691729--51691782 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
51691719 CTGACACAAT
51691729 CTGTTAAAAAAAATTGAATCTGAAAAAA
1 CTGTTAAAAAAAATTGAATCTGAAAAAA
*
51691757 CTGTT-AAAAAAA-TGAATTTGAAAAAA
1 CTGTTAAAAAAAATTGAATCTGAAAAAA
51691783 AAAATATCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.52
27 7 0.28
28 5 0.20
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (28 bp):
CTGTTAAAAAAAATTGAATCTGAAAAAA
Found at i:51691987 original size:15 final size:16
Alignment explanation
Indices: 51691962--51691993 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
51691952 AGAGGGAGGG
51691962 AGAACAGAAGAAAAAA
1 AGAACAGAAGAAAAAA
51691978 AGAA-AGAAGAAAAAA
1 AGAACAGAAGAAAAAA
51691993 A
1 A
51691994 TTCAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAACAGAAGAAAAAA
Found at i:51692193 original size:126 final size:123
Alignment explanation
Indices: 51691971--51692215 Score: 445
Period size: 126 Copynumber: 2.0 Consensus size: 123
51691961 GAGAACAGAA
51691971 GAAAAAAAGAAAGAAGAAAAAAATTCAGTAAAAAAAAGATTACAGAAGAGAAGAGAGGGAGAAAG
1 GAAAAAAAGAAAGAAGAAAAAAATTCAGTAAAAAAAAGATTACAGAAGAGAAGAGAGGGAGAAAG
*
51692036 AAGGAGAAGAAGAAATTAAAGGTATTTTTTTGTTATTTTTAAATACAACAGATTTTCT
66 AAGGAGAAGAAAAAATTAAAGGTATTTTTTTGTTATTTTTAAATACAACAGATTTTCT
51692094 GAAAAAAAGAAAGAAGGAAAAAAATTTCAGTAAAAAAAAAGATTACAGAAGAGAAGAGAGGGAGA
1 GAAAAAAAGAAAGAA-GAAAAAAA-TTCAGT-AAAAAAAAGATTACAGAAGAGAAGAGAGGGAGA
*
51692159 AAGAAGGAGAAGAAAAAATTAAAGGTATTTTTTTGTTATTTTTAAATATAACAGATT
63 AAGAAGGAGAAGAAAAAATTAAAGGTATTTTTTTGTTATTTTTAAATACAACAGATT
51692216 ATAATAAGAA
Statistics
Matches: 117, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
123 15 0.13
124 8 0.07
125 6 0.05
126 88 0.75
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.22
Consensus pattern (123 bp):
GAAAAAAAGAAAGAAGAAAAAAATTCAGTAAAAAAAAGATTACAGAAGAGAAGAGAGGGAGAAAG
AAGGAGAAGAAAAAATTAAAGGTATTTTTTTGTTATTTTTAAATACAACAGATTTTCT
Found at i:51695821 original size:72 final size:72
Alignment explanation
Indices: 51695732--51695876 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
51695722 ATCCGCCCCC
* * * *
51695732 TGACGAGCCCGGGAAATAGTTATT-GTCCAATAAATCTGGATGATAAGAAGTATCGGCCGAATGT
1 TGACGAGCCCGGGAAATAGTCATTACT-CAAGAAATCTGGATGATAAGAAGTATCAGCCGAATGT
*
51695796 GAATGCGA
65 GAATACGA
* ** *
51695804 TGACGAGCCCGGTAAATAGTCATTACTCTGGAAATCTGGATGATAAGAAGTATTAGCCGAATGTG
1 TGACGAGCCCGGGAAATAGTCATTACTCAAGAAATCTGGATGATAAGAAGTATCAGCCGAATGTG
51695869 AATACGA
66 AATACGA
51695876 T
1 T
51695877 TGCTCAGATT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 62 0.98
73 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (72 bp):
TGACGAGCCCGGGAAATAGTCATTACTCAAGAAATCTGGATGATAAGAAGTATCAGCCGAATGTG
AATACGA
Found at i:51697945 original size:200 final size:200
Alignment explanation
Indices: 51697602--51698063 Score: 870
Period size: 200 Copynumber: 2.3 Consensus size: 200
51697592 ATTAGTACAT
*
51697602 AAATTAAATTGAAATATTAAATAAGAAATAAAACAATATGCTATTTGGAAAATAACTATTATTGT
1 AAATTAAATTGAAATATTAAATAAGAAATAAAACAATATGTTATTTGGAAAATAACTATTATTGT
* *
51697667 AATGACATACATGTTTTATTAGGTATAAGTATTTAAATTTTTGTTTTTGTAATGTGAAATATGTG
66 AATGACATACATGTTTTATTAGGTATAAGTATTTAAATTTTTGTTTTTGTAACGTGAAACATGTG
* *
51697732 TAAATATATATATAATCATATTAGTGAATCTGCTAATACATACTTTACCCGGGTAAAGTGTTCAT
131 TAAATATATATATAATCATATTAGTGAATCTGCTAATACATACTTTACCCGGGTAAAGTATGCAT
51697797 TATTA
196 TATTA
51697802 AAATTAAATTGAAATATTAAATAAGAAATAAAACAATATGTTATTTGGAAAATAACTATTATTGT
1 AAATTAAATTGAAATATTAAATAAGAAATAAAACAATATGTTATTTGGAAAATAACTATTATTGT
51697867 AATGACATACATGTTTTATTAGGTATAAGTATTTAAATTTTTGTTTTTGTAACGTGAAACATGTG
66 AATGACATACATGTTTTATTAGGTATAAGTATTTAAATTTTTGTTTTTGTAACGTGAAACATGTG
51697932 TAAATATATATATAATCATATTAGTGAATCTGCTAATACATACTTTACCCGGGTAAAGTATGCAT
131 TAAATATATATATAATCATATTAGTGAATCTGCTAATACATACTTTACCCGGGTAAAGTATGCAT
51697997 TATTA
196 TATTA
*
51698002 AAATTAAATTGAAATATTAAATAAGAAATAAAACAATATGTTATTTGAAAAATAACTATTAT
1 AAATTAAATTGAAATATTAAATAAGAAATAAAACAATATGTTATTTGGAAAATAACTATTAT
51698064 GTTTTATTAG
Statistics
Matches: 256, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 256 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.39
Consensus pattern (200 bp):
AAATTAAATTGAAATATTAAATAAGAAATAAAACAATATGTTATTTGGAAAATAACTATTATTGT
AATGACATACATGTTTTATTAGGTATAAGTATTTAAATTTTTGTTTTTGTAACGTGAAACATGTG
TAAATATATATATAATCATATTAGTGAATCTGCTAATACATACTTTACCCGGGTAAAGTATGCAT
TATTA
Found at i:51698625 original size:22 final size:21
Alignment explanation
Indices: 51698573--51698626 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
51698563 TTTGTCCTTT
51698573 TATTATTTGTATTTTTAAAATA
1 TATTATTT-TATTTTTAAAATA
*
51698595 T-TCGGATTTTATTTTTTAAAATA
1 TAT--TATTTTA-TTTTTAAAATA
51698618 TATTATTTT
1 TATTATTTT
51698627 CGTATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
21 1 0.04
22 8 0.31
23 16 0.62
24 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (21 bp):
TATTATTTTATTTTTAAAATA
Found at i:51698727 original size:135 final size:133
Alignment explanation
Indices: 51698312--51699051 Score: 1166
Period size: 135 Copynumber: 5.5 Consensus size: 133
51698302 ATTGAATAGG
** * *
51698312 TGTATTTCTAAAATATTATGAATTTATTTTTTAAAATATACTATTTTAGTATTTTATTTTTTTAT
1 TGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA-TTTTTTAT
51698377 CTTATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTAT
65 CTTATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTAT
51698442 TATT
130 TATT
*
51698446 TGTATTTCTAAAATATTCGAATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
1 TGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
* * *
51698511 TTATTTTAGTACATAAATGTATAACTTTAGTATTTTTTTATATAACCTTAATTTTGTCCTTTTAT
66 TTATTTTAGTACATAAATGTATAACTTTAGT-GTTTTTTATATAACCCTAATTTTGTCCCTTTAT
51698576 TATT
130 TATT
* *
51698580 TGTATTTTTAAAATATTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATC
1 TGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
51698645 TAATATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTA
66 T--TATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTA
51698710 TTATT
129 TTATT
51698715 TGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTTA
1 TGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA--TTTTTTA
*
51698780 TCTTATTTTAGTACATAAATGTATAACTTTAGTTTTTTTTATATAACCCTAATTTTGTCCCTTTA
64 TCTTATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTA
51698845 TTATT
129 TTATT
** *
51698850 TGTATTTCTAAAATATTTAGATTTTATTTTTTAAAATATACTATTTTCGTATTTCA-TTTTTATC
1 TGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
* * *
51698914 GTATTTTAGTACATAAATGTATTACTTTAGTGTTTTTTTAAATAACCCTAATTTTGTCCC--T-T
66 TTATTTTAGTACATAAATGTATAACTTTAGTG-TTTTTTATATAACCCTAATTTTGTCCCTTTAT
*
51698976 TGTT
130 TATT
* * * * * *
51698980 TATATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA-TTCTTATA
1 TGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
51699044 TTATTTTA
66 TTATTTTA
51699052 TACTATTTTT
Statistics
Matches: 567, Mismatches: 33, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
130 68 0.12
131 1 0.00
132 37 0.07
133 66 0.12
134 148 0.26
135 207 0.37
136 30 0.05
137 10 0.02
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (133 bp):
TGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
TTATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTATT
ATT
Found at i:51698818 original size:269 final size:268
Alignment explanation
Indices: 51698312--51699037 Score: 1185
Period size: 269 Copynumber: 2.7 Consensus size: 268
51698302 ATTGAATAGG
* * *
51698312 TGTATTTCTAAAATATTATGAATTTATTTTTTAAAATATACTATTTTAGTATTTTATTTTTTTAT
1 TGTATTTCTAAAATATTAAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA-TTTTTTAT
51698377 CTTATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTAT
65 CTTATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTAT
*
51698442 TATTTGTATTTCTAAAATATTCGAATTTTATTTTTTAAAATATACTATTTTCGTATTTTA--TTT
130 TATTTGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTT
*
51698505 TTTATCTTATTTTAGTACATAAATGTATAACTTTAGTATTTTTTTATATAACCTTAATTTTGTCC
195 TTTATCTTATTTTAGTACATAAATGTATAACTTTAGT-TTTTTTTATATAACCCTAATTTTGTCC
*
51698570 TTTTATTATT
259 CTTTATTATT
* ** *
51698580 TGTATTTTTAAAATATTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATC
1 TGTATTTCTAAAATATTAAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
51698645 TAATATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTA
66 T--TATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTA
51698710 TTATTTGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
129 TTATTTGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTT
51698775 TTTTATCTTATTTTAGTACATAAATGTATAACTTTAGTTTTTTTTATATAACCCTAATTTTGTCC
194 TTTTATCTTATTTTAGTACATAAATGTATAACTTTAGTTTTTTTTATATAACCCTAATTTTGTCC
51698840 CTTTATTATT
259 CTTTATTATT
* *
51698850 TGTATTTCTAAAATATTTAGATTTTATTTTTTAAAATATACTATTTTCGTATTTCA-TTTTTATC
1 TGTATTTCTAAAATATTAAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
* * *
51698914 GTATTTTAGTACATAAATGTATTACTTTAGTGTTTTTTTAAATAACCCTAATTTTGTCCC--T-T
66 TTATTTTAGTACATAAATGTATAACTTTAGTG-TTTTTTATATAACCCTAATTTTGTCCCTTTAT
* * * * *
51698976 TGTTTATATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATT
130 TATTTGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATT
51699038 CTTATATTAT
Statistics
Matches: 431, Mismatches: 22, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
265 58 0.13
266 1 0.00
267 40 0.09
268 76 0.18
269 130 0.30
270 86 0.20
271 40 0.09
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (268 bp):
TGTATTTCTAAAATATTAAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATC
TTATTTTAGTACATAAATGTATAACTTTAGTGTTTTTTATATAACCCTAATTTTGTCCCTTTATT
ATTTGTATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTT
TTATCTTATTTTAGTACATAAATGTATAACTTTAGTTTTTTTTATATAACCCTAATTTTGTCCCT
TTATTATT
Found at i:51699093 original size:16 final size:16
Alignment explanation
Indices: 51699069--51699120 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
51699059 TTTCTTATTT
*
51699069 TATTGTATTTTTTTCA
1 TATTATATTTTTTTCA
*
51699085 TATTCTA-TTTTTTCA
1 TATTATATTTTTTTCA
**
51699100 TTAAGATATTTTTTTCA
1 -TATTATATTTTTTTCA
51699117 TATT
1 TATT
51699121 TTCTTTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 8 0.29
16 12 0.43
17 8 0.29
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.65
Consensus pattern (16 bp):
TATTATATTTTTTTCA
Found at i:51699454 original size:10 final size:11
Alignment explanation
Indices: 51699429--51699457 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
51699419 ATAAAATTAA
51699429 AAATTAAATCT
1 AAATTAAATCT
51699440 AAATTAAAT-T
1 AAATTAAATCT
51699450 AAATTAAA
1 AAATTAAA
51699458 ATCAACAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATTAAATCT
Found at i:51699547 original size:20 final size:19
Alignment explanation
Indices: 51699522--51699566 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
51699512 TCCTTCCCTC
51699522 TTTTCTCCTTCTCTTTTTCT
1 TTTTCTCCTTCT-TTTTTCT
** *
51699542 TTTTCTTTTTCTTTTTTTT
1 TTTTCTCCTTCTTTTTTCT
51699561 TTTTCT
1 TTTTCT
51699567 TCCCTTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTCCTTCTTTTTTCT
Found at i:51699563 original size:19 final size:20
Alignment explanation
Indices: 51699530--51699567 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
51699520 TCTTTTCTCC
51699530 TTCTCTTTTTCTTTTTCTTT
1 TTCTCTTTTTCTTTTTCTTT
*
51699550 TTCT-TTTTTTTTTTTCTT
1 TTCTCTTTTTCTTTTTCTT
51699568 CCCTTCCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTCTCTTTTTCTTTTTCTTT
Found at i:51699564 original size:6 final size:6
Alignment explanation
Indices: 51699533--51699562 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
51699523 TTTCTCCTTC
51699533 TCTTTT TCTTTT TCTTTT TCTTTT T-TTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
51699563 TTCTTCCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TCTTTT
Found at i:51699835 original size:11 final size:11
Alignment explanation
Indices: 51699821--51699859 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
51699811 TTTATACTAA
51699821 TTTTTTACTTG
1 TTTTTTACTTG
*
51699832 TTTTATACTCT-
1 TTTTTTACT-TG
51699843 TTTTTTACTTG
1 TTTTTTACTTG
51699854 TTTTTT
1 TTTTTT
51699860 TAACAGATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.74
Consensus pattern (11 bp):
TTTTTTACTTG
Found at i:51699836 original size:22 final size:22
Alignment explanation
Indices: 51699811--51699857 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
51699801 TTGTTTCAAC
51699811 TTTATACTAATTTTTTACTTGT
1 TTTATACTAATTTTTTACTTGT
**
51699833 TTTATACTCTTTTTTTACTTGT
1 TTTATACTAATTTTTTACTTGT
51699855 TTT
1 TTT
51699858 TTTAACAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTATACTAATTTTTTACTTGT
Found at i:51701339 original size:9 final size:9
Alignment explanation
Indices: 51701325--51701350 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
51701315 TCACCCAAAT
51701325 ATATATATA
1 ATATATATA
51701334 ATATATATA
1 ATATATATA
51701343 ATATATAT
1 ATATATAT
51701351 TCATTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATATATATA
Found at i:51701515 original size:17 final size:17
Alignment explanation
Indices: 51701493--51701530 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
51701483 TTTTCAAAAG
**
51701493 TAATTTTTATTTTTTTA
1 TAATTTTTATAATTTTA
51701510 TAATTTTTATAATTTTA
1 TAATTTTTATAATTTTA
51701527 TAAT
1 TAAT
51701531 ATCTGAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TAATTTTTATAATTTTA
Found at i:51701516 original size:9 final size:9
Alignment explanation
Indices: 51701493--51701530 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
51701483 TTTTCAAAAG
51701493 TAATTTTTA
1 TAATTTTTA
*
51701502 T-TTTTTTA
1 TAATTTTTA
51701510 TAATTTTTA
1 TAATTTTTA
51701519 TAA-TTTTA
1 TAATTTTTA
51701527 TAAT
1 TAAT
51701531 ATCTGAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 15 0.60
9 10 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TAATTTTTA
Found at i:51701783 original size:60 final size:59
Alignment explanation
Indices: 51701661--51701785 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 59
51701651 AACTTGGTAA
* ** * *
51701661 TTTTTCTTAATTTGATACTTAAACTTTTTTCGGTCCAATTTGATACTCAAATTTGACAC
1 TTTTTCTTAAGTTGATACTTAAACTTTTTGAGGTCCAATTTGATACTCAAACTCGACAC
* ** *
51701720 TTTTTCTTTAAGTTGGTACTTAAACTTTTTGAGGTCCAATTT-AGTACTTGAACTCGACTC
1 TTTTTC-TTAAGTTGATACTTAAACTTTTTGAGGTCCAATTTGA-TACTCAAACTCGACAC
51701780 TTTTTC
1 TTTTTC
51701786 CTAATTTGGT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
59 7 0.13
60 48 0.87
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (59 bp):
TTTTTCTTAAGTTGATACTTAAACTTTTTGAGGTCCAATTTGATACTCAAACTCGACAC
Found at i:51702067 original size:60 final size:57
Alignment explanation
Indices: 51701942--51702106 Score: 233
Period size: 59 Copynumber: 2.8 Consensus size: 57
51701932 ATTGAATCTA
*
51701942 AAAAAAAAGTTTAGGTACCAAATTAGGAAAACATGCCAAGTTCAGGTACTAACTTGGGT
1 AAAAAAAA-TTTAGGTACCAAATTAGGAAAA-ATGTCAAGTTCAGGTACTAACTTGGGT
* * *
51702001 CCAAAAAAAATTTAAGTACCAAATTAGGAAAAATATCAAGTTCAGGTACTAATTTGGGT
1 --AAAAAAAATTTAGGTACCAAATTAGGAAAAATGTCAAGTTCAGGTACTAACTTGGGT
*
51702060 AAAAAAAA-TTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTAGGTAC
1 AAAAAAAATTTAGGTACCAAATTAGGAAAAA-TGTCAAGTTCAGGTAC
51702107 CAAATATTAT
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
56 21 0.22
57 22 0.23
59 24 0.25
60 21 0.22
61 8 0.08
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (57 bp):
AAAAAAAATTTAGGTACCAAATTAGGAAAAATGTCAAGTTCAGGTACTAACTTGGGT
Found at i:51703234 original size:3 final size:3
Alignment explanation
Indices: 51703226--51703251 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
51703216 ATCACATGTT
51703226 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
51703252 TGGATGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:51703330 original size:73 final size:73
Alignment explanation
Indices: 51703252--51704240 Score: 1969
Period size: 73 Copynumber: 13.5 Consensus size: 73
51703242 TATTATTATT
*
51703252 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703317 ATTTTAAG
66 ATTTTAAG
51703325 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703390 ATTTTAAG
66 ATTTTAAG
51703398 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703463 ATTTTAAG
66 ATTTTAAG
51703471 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703536 ATTTTAAG
66 ATTTTAAG
51703544 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703609 ATTTTAAG
66 ATTTTAAG
51703617 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703682 ATTTTAAG
66 ATTTTAAG
51703690 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703755 ATTTTAAG
66 ATTTTAAG
51703763 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703828 ATTTTAAG
66 ATTTTAAG
51703836 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703901 ATTTTAAG
66 ATTTTAAG
51703909 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51703974 ATTTTAAG
66 ATTTTAAG
51703982 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51704047 ATTTTAAG
66 ATTTTAAG
51704055 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51704120 ATTTTAAG
66 ATTTTAAG
51704128 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
51704193 ATTTTAAG
66 ATTTTAAG
51704201 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
51704241 GTCAAGTTGT
Statistics
Matches: 915, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 915 1.00
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:51718016 original size:6 final size:6
Alignment explanation
Indices: 51718001--51718043 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
51717991 AAGCAGTGGG
* *
51718001 ATTCCA ATTCCT ATTCCT ATTCCT ATTCCT ATTCCC ATTCCT A
1 ATTCCT ATTCCT ATTCCT ATTCCT ATTCCT ATTCCT ATTCCT A
51718044 ACCAAGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTCCT
Found at i:51727151 original size:26 final size:26
Alignment explanation
Indices: 51727122--51727202 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 26
51727112 TCCCTTTGAA
* * *
51727122 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
51727148 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
* * *
51727176 CCATTCTTAATATTTCGTACACTAAGT
1 TCATTC--AATATCTCGCACACTAAGT
51727203 ACCATATTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 5 0.11
27 2 0.04
28 38 0.84
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:51727167 original size:28 final size:28
Alignment explanation
Indices: 51727136--51727207 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
51727126 TCGATATTTT
*
51727136 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* *
51727164 GCACACTAAGTGCCATTCTTAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* *
51727192 GTACACTAAGTACCAT
1 GCACACTAAGTGCCAT
51727208 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:51735156 original size:24 final size:25
Alignment explanation
Indices: 51735105--51735173 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 25
51735095 ACATATATTC
51735105 TCAATTCAATTACAATTTTT-CACACTT
1 TCAATTCAA-T-C-ATTTTTCCACACTT
51735132 TCAATTCAATCATTTTTCCAC-CTT
1 TCAATTCAATCATTTTTCCACACTT
*
51735156 TCAA-TCAATAATTATTTC
1 TCAATTCAATCATT-TTTC
51735174 ACAACTTCAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 8 0.21
24 17 0.44
25 4 0.10
26 1 0.03
27 9 0.23
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (25 bp):
TCAATTCAATCATTTTTCCACACTT
Found at i:51735182 original size:24 final size:25
Alignment explanation
Indices: 51735118--51735180 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
51735108 ATTCAATTAC
51735118 AATTTTTCAC-ACTTTCAATTCAAT
1 AATTTTTCACAACTTTCAATTCAAT
* *
51735142 CATTTTTC-CACCTTTCAA-TCAAT
1 AATTTTTCACAACTTTCAATTCAAT
51735165 AATTATTTCACAACTT
1 AATT-TTTCACAACTT
51735181 CACACATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 9 0.28
24 18 0.56
25 5 0.16
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTTTTCACAACTTTCAATTCAAT
Found at i:51735323 original size:3 final size:3
Alignment explanation
Indices: 51735315--51735367 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
51735305 TAATTCCCAC
* * * *
51735315 TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAC TAA TAC TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
51735363 TAA TA
1 TAA TA
51735368 CTTACCTCAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:51735368 original size:18 final size:18
Alignment explanation
Indices: 51735313--51735369 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
51735303 TTTAATTCCC
*
51735313 ACTAATAATAATAATAAT
1 ACTAATACTAATAATAAT
*
51735331 AATAATACTAATAATAAT
1 ACTAATACTAATAATAAT
*
51735349 ACTAATACTAATATTAAT
1 ACTAATACTAATAATAAT
51735367 ACT
1 ACT
51735370 TACCTCACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
ACTAATACTAATAATAAT
Found at i:51735369 original size:12 final size:12
Alignment explanation
Indices: 51735313--51735367 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
51735303 TTTAATTCCC
51735313 ACTAATAATAAT
1 ACTAATAATAAT
*
51735325 AATAATAATAAT
1 ACTAATAATAAT
51735337 ACTAATAATAAT
1 ACTAATAATAAT
*
51735349 ACTAATACTAAT
1 ACTAATAATAAT
*
51735361 ATTAATA
1 ACTAATA
51735368 CTTACCTCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (12 bp):
ACTAATAATAAT
Found at i:51736045 original size:11 final size:11
Alignment explanation
Indices: 51736031--51736056 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
51736021 TTTTTTCTTC
51736031 TTTCTCCCCTG
1 TTTCTCCCCTG
51736042 TTTCTCCCCTG
1 TTTCTCCCCTG
51736053 TTTC
1 TTTC
51736057 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:51740522 original size:22 final size:22
Alignment explanation
Indices: 51740493--51740560 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
51740483 TGCACAAACG
51740493 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
51740515 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
51740537 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
51740560 A
1 A
51740561 TAATAGNNNN
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:51746371 original size:5 final size:5
Alignment explanation
Indices: 51746361--51746389 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
51746351 TCTTTGTGTT
51746361 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
51746390 TCACAGTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:51747153 original size:15 final size:15
Alignment explanation
Indices: 51747133--51747164 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
51747123 GCATAAAGTT
51747133 TTTTTCCTTTTCTTC
1 TTTTTCCTTTTCTTC
*
51747148 TTTTTCTTTTTCTTC
1 TTTTTCCTTTTCTTC
51747163 TT
1 TT
51747165 CTTCTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCCTTTTCTTC
Found at i:51747169 original size:15 final size:15
Alignment explanation
Indices: 51747140--51747171 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
51747130 GTTTTTTTCC
*
51747140 TTTTCTTCTTTTTCT
1 TTTTCTTCTTCTTCT
51747155 TTTTCTTCTTCTTCT
1 TTTTCTTCTTCTTCT
51747170 TT
1 TT
51747172 CTCTCGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTTCTTCTTCT
Found at i:51756796 original size:2 final size:2
Alignment explanation
Indices: 51756789--51756928 Score: 280
Period size: 2 Copynumber: 70.0 Consensus size: 2
51756779 TGAAGCTTTG
51756789 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
51756831 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
51756873 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
51756915 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
51756929 TGACCAAAGA
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 138 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:51757289 original size:29 final size:28
Alignment explanation
Indices: 51757240--51757294 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
51757230 TACTATTAGA
*
51757240 TATATTTATAATATATGTTACTAAATTAT
1 TATATTTATAATATATATTAC-AAATTAT
*
51757269 TATATTTA-ATTATAATATTACAAATT
1 TATATTTATAATAT-ATATTACAAATT
51757295 TCAAGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (28 bp):
TATATTTATAATATATATTACAAATTAT
Found at i:51762507 original size:21 final size:22
Alignment explanation
Indices: 51762481--51762525 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
51762471 CTTTTGTTTG
51762481 ATAAATT-A-AATGCAAAACTAA
1 ATAAATTCACAAT-CAAAACTAA
51762502 ATAAATTCACAATCAAAACTAA
1 ATAAATTCACAATCAAAACTAA
51762524 AT
1 AT
51762526 TTATTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 12 0.55
23 3 0.14
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAAATTCACAATCAAAACTAA
Found at i:51768710 original size:40 final size:37
Alignment explanation
Indices: 51768623--51768710 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 37
51768613 TTAAATACAT
*
51768623 ATATTTTTAT-ATTTATAATTTCTTTTATATTTTAAG
1 ATATTTTTATAATTTATAATTTCTTTTAAATTTTAAG
* *
51768659 AAATTTATATAATTTTATATATTTTCTTTTAAAATTTTAA-
1 ATATTTTTATAA-TTTATA-A-TTTCTTTT-AAATTTTAAG
51768699 ATATTTTTATAA
1 ATATTTTTATAA
51768711 AAAATTAGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
36 8 0.19
37 1 0.02
38 6 0.14
39 1 0.02
40 18 0.43
41 8 0.19
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (37 bp):
ATATTTTTATAATTTATAATTTCTTTTAAATTTTAAG
Found at i:51769149 original size:30 final size:31
Alignment explanation
Indices: 51769104--51769161 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
51769094 GTTTGACGAA
51769104 AAGTGACCAAAATAGAAACGATCTAAAACGT
1 AAGTGACCAAAATAGAAACGATCTAAAACGT
*
51769135 AAGTGACC-AAATAGAAATGATCTAAAA
1 AAGTGACCAAAATAGAAACGATCTAAAA
51769162 TATTAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.53, C:0.14, G:0.16, T:0.17
Consensus pattern (31 bp):
AAGTGACCAAAATAGAAACGATCTAAAACGT
Done.