Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 144 of 185
Found at i:44476705 original size:42 final size:43
Alignment explanation
Indices: 44476658--44476780 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 43
44476648 TAGAATTTCG
* *
44476658 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCGT-T
1 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCATCA
* * *
44476700 GTATATGATTTCGTGTAAGA-CACTGTCTGGGACAGTGGCATCA
1 ATATATGATTACGTGTAAGACCA-TGTCTGGGACATTGGCATCA
* * *
44476743 ATATTTGATTACATGTAAGACCATGTCTGGGACGTTGG
1 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGG
44476781 AATTGTACGA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.03
42 34 0.51
43 29 0.43
44 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCATCA
Found at i:44482044 original size:18 final size:18
Alignment explanation
Indices: 44482015--44482066 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
44482005 AGCAAGAAAC
44482015 TTGAGTTGAGCTCGCATCCT
1 TTGA-TTGAGCTCGCA-CCT
*
44482035 TTGA-TGAGCTCGCACTT
1 TTGATTGAGCTCGCACCT
44482052 TTGATTGAGCTCGCA
1 TTGATTGAGCTCGCA
44482067 AATATAGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 6 0.20
18 20 0.67
20 4 0.13
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (18 bp):
TTGATTGAGCTCGCACCT
Found at i:44488817 original size:39 final size:40
Alignment explanation
Indices: 44488702--44488825 Score: 124
Period size: 40 Copynumber: 3.1 Consensus size: 40
44488692 CGCTTGGACA
* * *
44488702 AAAAACGTCGGTAAAAATCGAGCATTAGCGGTGCTTTATG
1 AAAAACGCCGGTAAAAATCGAGCATTAGCGGTGTTTTTTG
* * ** * * * *
44488742 GAAATCGCCACTAAAGATCAAGCATTAGAGGCGTTTTTTG
1 AAAAACGCCGGTAAAAATCGAGCATTAGCGGTGTTTTTTG
* *
44488782 AAAAACGCCGGTAAAAAT-GGGCATTAGCGGTGTTTTTCG
1 AAAAACGCCGGTAAAAATCGAGCATTAGCGGTGTTTTTTG
44488821 AAAAA
1 AAAAA
44488826 ATGCTACAAA
Statistics
Matches: 63, Mismatches: 21, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
39 21 0.33
40 42 0.67
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (40 bp):
AAAAACGCCGGTAAAAATCGAGCATTAGCGGTGTTTTTTG
Found at i:44489313 original size:15 final size:14
Alignment explanation
Indices: 44489293--44489341 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
44489283 ACTATTTTAA
*
44489293 GGTTTAGGGAGTAT
1 GGTTTAGGGATTAT
44489307 GGGTTTAGGGATTAT
1 -GGTTTAGGGATTAT
*
44489322 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
44489336 GGTTTA
1 GGTTTA
44489342 AAGGTTGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:44489380 original size:15 final size:15
Alignment explanation
Indices: 44489352--44489393 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
44489342 AAGGTTGAGA
*
44489352 TTTAAGGTTTAGGGG
1 TTTAAGGGTTAGGGG
44489367 -TTAGAGGGTTAGGGG
1 TTTA-AGGGTTAGGGG
44489382 TTTAAGGGTTAG
1 TTTAAGGGTTAG
44489394 ACGTTATGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 18 0.75
16 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.36
Consensus pattern (15 bp):
TTTAAGGGTTAGGGG
Found at i:44489413 original size:21 final size:22
Alignment explanation
Indices: 44489374--44489414 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
44489364 GGGTTAGAGG
*
44489374 GTTAGGGGTTTAAGGGTTAGAC
1 GTTAGGGGTTTAAGAGTTAGAC
*
44489396 GTTATGGG-TTAAGAGTTAG
1 GTTAGGGGTTTAAGAGTTAG
44489415 GGATTTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.34
Consensus pattern (22 bp):
GTTAGGGGTTTAAGAGTTAGAC
Found at i:44489641 original size:15 final size:15
Alignment explanation
Indices: 44489603--44489637 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
44489593 CATATTTTAA
44489603 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
44489618 GGTTTAGGGATTAT-
1 GGTTTAGGGAGTATG
44489632 GGTTTA
1 GGTTTA
44489638 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:44489651 original size:14 final size:15
Alignment explanation
Indices: 44489632--44489688 Score: 73
Period size: 14 Copynumber: 3.9 Consensus size: 15
44489622 TAGGGATTAT
44489632 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
* *
44489646 GATTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
*
44489661 GGTTAAAGGGTTAGG
1 GGTTTAAGGGTTAGG
44489676 GGTTT-AGGGTTAG
1 GGTTTAAGGGTTAG
44489689 ACACATTAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
14 18 0.50
15 18 0.50
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:44489658 original size:21 final size:20
Alignment explanation
Indices: 44489624--44489664 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
44489614 TATGGGTTTA
*
44489624 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
44489644 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
44489665 AAAGGGTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:44489813 original size:284 final size:291
Alignment explanation
Indices: 44489401--44490115 Score: 920
Period size: 284 Copynumber: 2.5 Consensus size: 291
44489391 TAGACGTTAT
* * * ** *
44489401 GGGTTAAGAGTTAGGGATTTAGGGTTTAGGGATTCAGGGATCGAGTTAGGATTTTGGGCGTTTAG
1 GGGTTAACAATTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGATTTT-GG-GTTTAG
*
44489466 ATTAA--A--TTTTTAATATATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATA
64 ATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATA
* * *
44489527 AATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTATTTAAGATTTAAGGCCGGTTTAGAAGT
129 AATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCAGTTTAGAAGT
*
44489592 TCATATTTTAAGGTTTAGGGAG-T-A-T-GGG-T-TTAGGGATTATGGTTTAAGGGTTGGGATTT
194 TCATATTTTAAGATTTAGGGAGATGATTAGGGTTGTTAGGGATTATGGTTTAA-GGTTGGGATTT
44489651 AAGGTTTAGGGGTTAAAGGG-TTAGGGG-T-TTA-
258 AAGGTTTAGGGGTT-AAGGGTTTAGGGGTTATTAG
* * *
44489682 GGGTTAGACACATTAGGGGTTAAAAG-TTAGGGATTTAGGGGTCGGGTTAGGATTTTGGGTTTAG
1 GGGTTA-ACA-ATTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGATTTTGGGTTTAG
* *
44489746 ATTAATTATTTTTTTAATTTATATTTTTAATATGTTCTTATGTAATTGTAAAAGAGATAATAATA
64 ATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATA
*
44489811 AATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCAGTTTAGGAGT
129 AATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCAGTTTAGAAGT
*
44489876 TCATATTTTAATATTTAGGGAGTATGGATTTAGGGATTTGGATTAGGGATTATGGTTTAAGGTTG
194 TCATATTTTAAGATTTAGGGAG-AT-GA-TTAGGG--TT-G-TTAGGGATTATGGTTTAAGGTTG
*
44489941 GGATTTAAGGTTTAGGGGTTAGGGGTTTAGGGGTTAGACGTTAG
252 GGATTTAAGGTTTAGGGGTTAAGGGTTTAGGGGTT--A--TTAG
* * * * * * * * *
44489985 GGGTTAAGAGTTAGGGATTTAAGGTTTATGGATTCAGGGGCCGAGTTAAGATTTTGAGTTAAGAT
1 GGGTTAACAATTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGATTTTGGGTTTAGAT
44490050 TAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAA
66 TAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAA
44490115 T
131 T
44490116 CAAATATATT
Statistics
Matches: 373, Mismatches: 33, Indels: 35
0.85 0.07 0.08
Matches are distributed among these distances:
280 11 0.03
281 8 0.02
282 30 0.08
283 10 0.03
284 133 0.36
286 1 0.00
288 1 0.00
290 1 0.00
291 3 0.01
294 1 0.00
295 4 0.01
296 32 0.09
297 19 0.05
301 11 0.03
302 102 0.27
303 6 0.02
ACGTcount: A:0.29, C:0.03, G:0.27, T:0.42
Consensus pattern (291 bp):
GGGTTAACAATTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGATTTTGGGTTTAGAT
TAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAA
TTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCAGTTTAGAAGTTC
ATATTTTAAGATTTAGGGAGATGATTAGGGTTGTTAGGGATTATGGTTTAAGGTTGGGATTTAAG
GTTTAGGGGTTAAGGGTTTAGGGGTTATTAG
Found at i:44489923 original size:13 final size:14
Alignment explanation
Indices: 44489888--44489947 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 14
44489878 ATATTTTAAT
*
44489888 ATTTAGGGAGTATGG
1 ATTTAGGGA-TTTGG
44489903 ATTTAGGGATTTGG
1 ATTTAGGGATTTGG
44489917 A-TTAGGGATTATGG
1 ATTTAGGGATT-TGG
* *
44489931 -TTTAAGG-TTGGG
1 ATTTAGGGATTTGG
44489943 ATTTA
1 ATTTA
44489948 AGGTTTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 2 0.05
13 15 0.38
14 13 0.33
15 9 0.23
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (14 bp):
ATTTAGGGATTTGG
Found at i:44489962 original size:7 final size:7
Alignment explanation
Indices: 44489952--44490000 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
44489942 GATTTAAGGT
44489952 TTAGGGG
1 TTAGGGG
44489959 TTAGGGG
1 TTAGGGG
44489966 TTTAGGGG
1 -TTAGGGG
**
44489974 TTAGACG
1 TTAGGGG
44489981 TTAGGGG
1 TTAGGGG
* *
44489988 TTAAGAG
1 TTAGGGG
44489995 TTAGGG
1 TTAGGG
44490001 ATTTAAGGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.20, C:0.02, G:0.47, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:44489969 original size:15 final size:15
Alignment explanation
Indices: 44489948--44489990 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
44489938 TTGGGATTTA
44489948 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
44489963 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
44489978 ACG-TTAGGGGTTA
1 AGGTTTAGGGGTTA
44489991 AGAGTTAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.33
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:44490667 original size:175 final size:176
Alignment explanation
Indices: 44490475--44490825 Score: 659
Period size: 175 Copynumber: 2.0 Consensus size: 176
44490465 ATTATTTAAT
44490475 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
1 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
* *
44490540 CAATATTTATTTTGAGAGTACTT-GGTTTTTTTATTTTGCAAACAATAAGTCAATTTATAAAAAA
66 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAAA
44490604 CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
131 CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
* *
44490650 TTGGATAATTCTAACTTAATAATTAATTATAGCCATTTTATCATTTGTTTTCTTATTAAAATATA
1 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
44490715 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAAA
66 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAAA
44490780 CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
131 CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
44490826 AAATGAAATA
Statistics
Matches: 171, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
175 86 0.50
176 85 0.50
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (176 bp):
TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
CAATATTTATTTTGAGAGTACTTGGGTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAAA
CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
Found at i:44493681 original size:23 final size:23
Alignment explanation
Indices: 44493654--44493701 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
44493644 CTCCAACTAT
44493654 CAAAACAGATCACTCCACCATCC
1 CAAAACAGATCACTCCACCATCC
44493677 CAAAACAGATCACTCCACCATCC
1 CAAAACAGATCACTCCACCATCC
44493700 CA
1 CA
44493702 CGTCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.44, G:0.04, T:0.12
Consensus pattern (23 bp):
CAAAACAGATCACTCCACCATCC
Found at i:44502750 original size:50 final size:51
Alignment explanation
Indices: 44502663--44502768 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 51
44502653 TGTATATATT
*
44502663 TTTAAAATATAAAAGAAATAATAAATTTTAAAATACA-TTTATCTAAAAAA
1 TTTAAAATATAAAAGAAATAATAAAATTTAAAATACACTTTATCTAAAAAA
* * * *
44502713 TTTAAAATATTACAA-AAATAA-AAAATTTAAATTTACATCTTTTTCTAAATAA
1 TTTAAAATA-TAAAAGAAATAATAAAATTTAAA-ATACA-CTTTATCTAAAAAA
44502765 TTTA
1 TTTA
44502769 CAAACAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
49 9 0.19
50 19 0.40
51 4 0.09
52 15 0.32
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (51 bp):
TTTAAAATATAAAAGAAATAATAAAATTTAAAATACACTTTATCTAAAAAA
Found at i:44503041 original size:16 final size:17
Alignment explanation
Indices: 44503015--44503046 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
44503005 AATCACAAAT
44503015 TTACTGAGTTTTTGAGG
1 TTACTGAGTTTTTGAGG
44503032 TTAC-GAGTTTTTGAG
1 TTACTGAGTTTTTGAG
44503047 TTTATCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (17 bp):
TTACTGAGTTTTTGAGG
Found at i:44503124 original size:16 final size:17
Alignment explanation
Indices: 44503100--44503133 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
44503090 ATTATATGTG
44503100 TTTAAATATAA-TTATA
1 TTTAAATATAATTTATA
*
44503116 TTTATATATAATTTATA
1 TTTAAATATAATTTATA
44503133 T
1 T
44503134 GTATTTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATATAATTTATA
Found at i:44511249 original size:12 final size:11
Alignment explanation
Indices: 44511232--44511288 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
44511222 AACAAATCAT
44511232 CTCTCATATTTC
1 CTCTCA-ATTTC
44511244 CTCTCAA-TTC
1 CTCTCAATTTC
44511254 CTCTCAATTTC
1 CTCTCAATTTC
*
44511265 CT-TCCAAAATT-
1 CTCT-C-AATTTC
44511276 CTCTCAATTTC
1 CTCTCAATTTC
44511287 CT
1 CT
44511289 TCCAAAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 15 0.39
11 12 0.32
12 11 0.29
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:44511279 original size:22 final size:22
Alignment explanation
Indices: 44511249--44511304 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
44511239 ATTTCCTCTC
44511249 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
44511272 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
44511294 AATTCTCTCAA
1 AATTCTCTCAA
44511305 ATCCATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:44511333 original size:51 final size:51
Alignment explanation
Indices: 44511276--44511379 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
44511266 TTCCAAAATT
*
44511276 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
44511327 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
44511378 CT
1 CT
44511380 TTTTTAAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:44512534 original size:7 final size:7
Alignment explanation
Indices: 44512524--44512548 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44512514 ATTCGATTGA
44512524 TATTTAG
1 TATTTAG
44512531 TATTTAG
1 TATTTAG
44512538 TATTTAG
1 TATTTAG
44512545 TATT
1 TATT
44512549 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:44513223 original size:18 final size:18
Alignment explanation
Indices: 44513197--44513233 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44513187 AGGTACGTTT
* *
44513197 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATATAC
44513215 CCTAACCCTTATATATAC
1 CCTAACCCTTATATATAC
44513233 C
1 C
44513234 ATTTTCCGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.35, G:0.05, T:0.32
Consensus pattern (18 bp):
CCTAACCCTTATATATAC
Found at i:44513478 original size:9 final size:9
Alignment explanation
Indices: 44513462--44513509 Score: 87
Period size: 9 Copynumber: 5.3 Consensus size: 9
44513452 GTCCTAAGTT
44513462 CGGAAGAAC
1 CGGAAGAAC
*
44513471 CAGAAGAAC
1 CGGAAGAAC
44513480 CGGAAGAAC
1 CGGAAGAAC
44513489 CGGAAGAAC
1 CGGAAGAAC
44513498 CGGAAGAAC
1 CGGAAGAAC
44513507 CGG
1 CGG
44513510 GTTTCATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.44, C:0.23, G:0.33, T:0.00
Consensus pattern (9 bp):
CGGAAGAAC
Found at i:44513790 original size:23 final size:23
Alignment explanation
Indices: 44513761--44514600 Score: 770
Period size: 23 Copynumber: 34.5 Consensus size: 23
44513751 TTTGATGTAA
*
44513761 TAAAAACCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
*** *
44513784 CCTAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
44513807 TAAAAACCCTAACGTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
44513830 TAAAAACTCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
44513853 TAAAAACCCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
*
44513877 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
*
44513903 TAAAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
44513926 TAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAA--C---CC-TAACCTAATTTAAT
44513955 TAAAAACCCTAAAACCTTAA-TTAA-
1 TAAAAACCCT--AACC-TAATTTAAT
*
44513979 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
*
44514005 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
44514028 TATAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
44514051 TAAAAACCCTAAACTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
44514074 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* * *
44514097 TAAAAATCATAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* * *
44514120 TAAAAATCCTAAACT--CTTAAT
1 TAAAAACCCTAACCTAATTTAAT
44514141 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
44514164 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
44514187 TAAAAACCCTAACCTTAACCAAATTTAAT
1 TAAAAACCCTAACC-T-----AATTTAAT
* * *
44514216 TAATAACTCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
44514239 TAAAAACCCTAAACC---CTTAAT
1 TAAAAACCCT-AACCTAATTTAAT
44514260 TAAAAACCCTAATCTTAACATAATTTAAT
1 TAAAAACCCTAA-C----C-TAATTTAAT
*
44514289 TAAAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
44514312 TAAAAACCCTAACATTAGCCTAATTTAAT
1 TAAAAACCCT---A--A-CCTAATTTAAT
44514341 TAAAAACCCTAACCTAACCTAATTTAAT
1 TAAAAA--C---CCTAACCTAATTTAAT
*
44514369 TAAAAACCCTAATCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
44514392 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
44514415 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
44514438 TAAAAACCCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
* *
44514462 AAACTCAAACCTTAACCTAATTTAAT
1 TAA---AAACCCTAACCTAATTTAAT
44514488 TAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAA--C---CC-TAACCTAATTTAAT
44514517 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
44514540 TAAAAACCCTAACCTAATTTAAAC
1 TAAAAACCCTAACCTAATTT-AAT
***
44514564 CCTAAACCCTAAACCCTAATTTAAT
1 TAAAAACCCT-AA-CCTAATTTAAT
44514589 TAAAAACCCTAA
1 TAAAAACCCTAA
44514601 TCTTAACATA
Statistics
Matches: 684, Mismatches: 61, Indels: 143
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.00
21 34 0.05
23 391 0.57
24 34 0.05
25 54 0.08
26 25 0.04
27 24 0.04
28 23 0.03
29 92 0.13
31 2 0.00
34 3 0.00
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.30
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:44513902 original size:29 final size:29
Alignment explanation
Indices: 44513869--44513966 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
44513859 CCCTAAACCC
44513869 TTAATTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTTAACCTAAT
44513898 TTAATTAAAAACCCTAACC-T-A---AA-
1 TTAATTAAAAACCCTAACCTTAACCTAAT
44513921 TTAATTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTTAACCTAAT
44513950 TTAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAA
44513967 AACCTTAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
23 19 0.30
24 3 0.05
25 1 0.02
27 1 0.02
28 3 0.05
29 36 0.57
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (29 bp):
TTAATTAAAAACCCTAACCTTAACCTAAT
Found at i:44514557 original size:125 final size:124
Alignment explanation
Indices: 44513884--44514612 Score: 633
Period size: 125 Copynumber: 5.9 Consensus size: 124
44513874 TAAAAACCCT
* * **
44513884 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAAATTAATTAAAAACCCTAACCTTAACCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC-TAATTTAA
**** * *
44513949 TTTAATTAAAAACCCTAA---AACCTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
65 --TAAACCCAAACCTTAACCTAA-TTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
* * *
44514009 AACCCTAGCCTAATTTAATTATAAACCCTAACCTAATTTAATTAAAAACCCTAAACTAATTTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
* * * *
44514074 TAA---AAACCCTAACCTAATTTAATTAAAAA---T---CATAGCCTAATTTAATTAAA
66 AAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
* * *
44514124 AATCCTAAACT--CTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA-
* * * *
44514187 TAAAAACCCTAACCTTAACCAAATTTAATTAATAA--CT---C-TAGCCTAATTTAATTAAA
65 T--AAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
*
44514243 AACCCTAAACC---CTTAATTAAAAACCCTAATCTTAACATAATTTAATTAAAAACCCTAACCTA
1 AACCCT-AACCTAATTTAATTAAAAACCCTAA-C----C-TAATTTAATTAAAAACCCTAACCTA
* * * *
44514305 AATTAATTAAAAACCCTAACATTAGCCTAATTTAATTAAAAACCCTAACC-TAACCTAATTTAAT
59 ATTTAA-T--AAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
44514369 TAAA
121 TAAA
* *
44514373 AACCCTAATCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA-
* * * * *
44514438 TAAA---AACCCTAAACC---CTTAATTAAAAACTCAAACCTTAACCTAATTTAATTAAA
65 TAAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
44514492 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
1 AA--C---CC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
* * *
44514557 -TT--TAAACCCTAAACCCTAAACCCTAATTTAATTAAAAACCCTAATCTTAACATAAT
60 TTTAATAAACCC-AAA-CCTTAA-CCTAATTTAATTAAAAACCCTAACCTTAACCTAAT
44514613 GTTAGATTTG
Statistics
Matches: 512, Mismatches: 51, Indels: 77
0.80 0.08 0.12
Matches are distributed among these distances:
113 48 0.09
114 1 0.00
115 26 0.05
116 2 0.00
118 18 0.04
119 92 0.18
120 6 0.01
121 22 0.04
122 4 0.01
124 14 0.03
125 167 0.33
126 37 0.07
127 5 0.01
129 3 0.01
130 49 0.10
131 1 0.00
132 17 0.03
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (124 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
AAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
Found at i:44514741 original size:116 final size:116
Alignment explanation
Indices: 44514606--44514826 Score: 381
Period size: 116 Copynumber: 1.9 Consensus size: 116
44514596 CCTAATCTTA
* *
44514606 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAA-TAATAATTTTACATAATTT
1 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAA-AAATTAATAATTGTACATAATTT
*
44514670 GATAATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTC
65 GATAATTTTACTAACCATTAATACAATTTTTTGACGTAATAATTTTACATTC
*
44514722 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTATATAATTTG
1 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTACATAATTTG
*
44514787 ATAATTTTCCTAACCATTAATACAATTTTTTGACGTAATA
66 ATAATTTTACTAACCATTAATACAATTTTTTGACGTAATA
44514827 CAATTTATCA
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
115 3 0.03
116 96 0.97
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (116 bp):
ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTACATAATTTG
ATAATTTTACTAACCATTAATACAATTTTTTGACGTAATAATTTTACATTC
Found at i:44518153 original size:126 final size:125
Alignment explanation
Indices: 44517858--44518235 Score: 537
Period size: 126 Copynumber: 3.0 Consensus size: 125
44517848 CCCAAACATG
* * *
44517858 CTACTGTAGCAAAAGCGCGTCCACGAGGGCCCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
* * * *
44517923 TAGAAGCAATTTTATATTATTTGCTTAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
* * *
44517982 CTACTGTAGCAAAAGA-GCG-CTGACGAGGCCGCGATTTCACAAATTCTTATCAAATAACATCCT
1 CTACTGTAGCAAAA-ACGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCT
44518045 GCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCATGAC
64 GCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTCCATGAC
* *
44518108 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
** **** *
44518173 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
44518233 CTA
1 CTA
44518236 AAAACCTTTA
Statistics
Matches: 226, Mismatches: 22, Indels: 11
0.87 0.08 0.04
Matches are distributed among these distances:
123 1 0.00
124 88 0.39
125 27 0.12
126 109 0.48
127 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
Found at i:44533729 original size:21 final size:22
Alignment explanation
Indices: 44533700--44533746 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
44533690 CAGAAGGAGT
*
44533700 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
*
44533722 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
44533743 GAGT
1 GAGT
44533747 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:44536583 original size:25 final size:26
Alignment explanation
Indices: 44536546--44536595 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
44536536 GTTGTAAATT
44536546 GGAAAAATATCTTCAG-AAATTTTCC
1 GGAAAAATATCTTCAGAAAATTTTCC
* * *
44536571 GGAACAATCTCTTTAGAAAATTTTC
1 GGAAAAATATCTTCAGAAAATTTTC
44536596 TCTCTATAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (26 bp):
GGAAAAATATCTTCAGAAAATTTTCC
Found at i:44538566 original size:22 final size:22
Alignment explanation
Indices: 44538541--44538587 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
44538531 TTCCATTTCA
44538541 CCTATTACCTTATTAACACACC
1 CCTATTACCTTATTAACACACC
44538563 CCTATTACCTTATTAACACACC
1 CCTATTACCTTATTAACACACC
44538585 CCT
1 CCT
44538588 TCTTTAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (22 bp):
CCTATTACCTTATTAACACACC
Found at i:44539421 original size:21 final size:21
Alignment explanation
Indices: 44539375--44539428 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
44539365 ATGTCAATTA
*
44539375 TATTTTTATTTATGAAAAGTG
1 TATTTTTATTTATAAAAAGTG
* *
44539396 AATTTTTTTTTATAAAAGAGT-
1 TATTTTTATTTATAAAA-AGTG
*
44539417 TATTTTGATTTA
1 TATTTTTATTTA
44539429 ACAATCAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (21 bp):
TATTTTTATTTATAAAAAGTG
Found at i:44541231 original size:29 final size:30
Alignment explanation
Indices: 44541188--44541246 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
44541178 GTTTTTACAC
*
44541188 TTTCACAATCATTTTATTTCCTCTTAATCG
1 TTTCACAATCATTTTATTACCTCTTAATCG
* * *
44541218 TTTCACCA-CATTTTCTTACTTCTTAATCG
1 TTTCACAATCATTTTATTACCTCTTAATCG
44541247 GCTCCCTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTCACAATCATTTTATTACCTCTTAATCG
Found at i:44548715 original size:19 final size:19
Alignment explanation
Indices: 44548688--44548726 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
44548678 TGATTTATTT
*
44548688 TAAGCTTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
44548707 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
44548726 T
1 T
44548727 GACTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:44551139 original size:27 final size:27
Alignment explanation
Indices: 44551088--44551145 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
44551078 GTAATTAATC
** * *
44551088 AAGAGTTATATCTTTTGGTTATTGATA
1 AAGAGTTATATCACTTGATTATTGACA
*
44551115 AAGAGTTATATCACTTGATTTTTGACA
1 AAGAGTTATATCACTTGATTATTGACA
44551142 AAGA
1 AAGA
44551146 ACTATAACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (27 bp):
AAGAGTTATATCACTTGATTATTGACA
Found at i:44553500 original size:11 final size:11
Alignment explanation
Indices: 44553477--44553523 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
44553467 AACAAATCCT
44553477 CTCTCATATTTC
1 CTCTCA-ATTTC
44553489 CTCTCAATTTC
1 CTCTCAATTTC
* *
44553500 CTTTCAATTTT
1 CTCTCAATTTC
44553511 CTCTCAATTTC
1 CTCTCAATTTC
44553522 CT
1 CT
44553524 TCCAAAATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:44553534 original size:22 final size:22
Alignment explanation
Indices: 44553489--44553535 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
44553479 CTCATATTTC
* **
44553489 CTCTCAATTTCCTTTCAATTTT
1 CTCTCAATTTCCTTCCAAAATT
44553511 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
44553533 CTC
1 CTC
44553536 ATAAATCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.47
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:44553558 original size:51 final size:51
Alignment explanation
Indices: 44553501--44553626 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 51
44553491 CTCAATTTCC
* * *
44553501 TTTCAATTTTCTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAA
1 TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTC-TCAAACCCATATTTAA
* *
44553552 TTTCAATTTCCTCTCAAATTCATTCCAAAAATCTCTCAAACCCATATTTAA
1 TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAA
*
44553603 TTTCAATTTGCTCTCAATTTCCTT
1 TTTCAATTTCCTCTCAATTTCCTT
44553627 TTTTTAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.30, C:0.25, G:0.01, T:0.44
Consensus pattern (51 bp):
TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAA
Found at i:44555897 original size:25 final size:25
Alignment explanation
Indices: 44555864--44555977 Score: 98
Period size: 25 Copynumber: 4.7 Consensus size: 25
44555854 TTTAAATTTA
*
44555864 TTATTTGATGTATTAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
**
44555889 TTATTTGATGTAATACGCATAGAAAGT
1 TTATTTGATGTAATA-AAATAG-AAGT
** *
44555916 TT-TTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
44555934 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
44555960 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
44555978 ACCCTAATCT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 5 0.07
21 4 0.06
23 2 0.03
24 3 0.04
25 35 0.51
26 10 0.14
27 6 0.09
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:44556019 original size:29 final size:29
Alignment explanation
Indices: 44555977--44556852 Score: 1189
Period size: 29 Copynumber: 29.4 Consensus size: 29
44555967 ATGTAATAAA
44555977 AACCCTAATC-TAACCTAATTAAAAACCCT
1 AACCCTAA-CATAACCTAATTAAAAACCCT
*
44556006 AACCCTAACATAACCTAATTAAAGACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* * *****
44556035 AACCCTAACCCTAACCTTAACCTAACCTAATTAAA
1 AACCCTAA-CATAACC-TAA-TTAA---AAACCCT
* *
44556070 AACCATAACCCTAACAAACCTAATTAAAAACCCT
1 AACCCTAA--C--A-TAACCTAATTAAAAACCCT
*
44556104 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
44556133 AACCCTAACCTAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556162 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* * *
44556191 AGCCCTAACCTAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556220 AACCCTAACATAACTTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556249 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556278 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
44556307 AACCCTAACATAACCTAATTAAAAA-CCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556335 AAACCTTAACATAACCTAATTAAAAACCCT
1 -AACCCTAACATAACCTAATTAAAAACCCT
* *
44556365 AACCCTAACCTAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556394 AACCCATAACATAACCTAATTAAAAACCCA
1 AACCC-TAACATAACCTAATTAAAAACCCT
*
44556424 AACCCTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
44556453 AACCCTAACATAACTTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556482 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
44556511 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
44556540 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
44556569 AACCCTAACTTAACCTAACCTAATTAAAAACCCT
1 AACCCTAAC---A--TAACCTAATTAAAAACCCT
*
44556603 AACCCTAACTTAACCTAACCTAATTAAAAACCTT
1 AACCCTAAC---A--TAACCTAATTAAAAACCCT
44556637 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556666 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556695 AACCCTAACATAACCTAATTAAAAACCTT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556724 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
44556753 AACCTTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556782 AACCCTAACATAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556811 ACCCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
44556840 AGCCCTAACATAA
1 AACCCTAACATAA
44556853 TAATTTTACA
Statistics
Matches: 770, Mismatches: 58, Indels: 38
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.01
29 630 0.82
30 37 0.05
31 4 0.01
32 5 0.01
34 70 0.09
35 8 0.01
36 2 0.00
37 3 0.00
38 3 0.00
39 4 0.01
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (29 bp):
AACCCTAACATAACCTAATTAAAAACCCT
Found at i:44556046 original size:41 final size:41
Alignment explanation
Indices: 44556000--44556084 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
44555990 CCTAATTAAA
* *
44556000 AACCCTAACCCTAACATAACCTAATTAAAGACCCTAACCCT
1 AACCCTAACCCTAACATAACCTAATTAAAAACCATAACCCT
* *
44556041 AACCCTAACCTTAACCTAACCTAATTAAAAACCATAACCCT
1 AACCCTAACCCTAACATAACCTAATTAAAAACCATAACCCT
44556082 AAC
1 AAC
44556085 AAACCTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.44, C:0.35, G:0.01, T:0.20
Consensus pattern (41 bp):
AACCCTAACCCTAACATAACCTAATTAAAAACCATAACCCT
Found at i:44556060 original size:11 final size:12
Alignment explanation
Indices: 44556030--44556062 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
44556020 CTAATTAAAG
*
44556030 ACCCTAACCCTA
1 ACCCTAACCTTA
44556042 ACCCTAACCTTA
1 ACCCTAACCTTA
44556054 A-CCTAACCT
1 ACCCTAACCT
44556063 AATTAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.21
Consensus pattern (12 bp):
ACCCTAACCTTA
Found at i:44556910 original size:55 final size:55
Alignment explanation
Indices: 44556850--44557006 Score: 296
Period size: 55 Copynumber: 2.9 Consensus size: 55
44556840 AGCCCTAACA
44556850 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
*
44556905 TAATAATTTTACATAGTTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
*
44556960 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAATACAATT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATT
44557007 ATCAATTAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 99 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (55 bp):
TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
Found at i:44557401 original size:15 final size:16
Alignment explanation
Indices: 44557376--44557410 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
44557366 TAACATGAGC
44557376 GCATGGATAACGAAGT
1 GCATGGATAACGAAGT
44557392 GCAT-GATAACGAAGT
1 GCATGGATAACGAAGT
44557407 GCAT
1 GCAT
44557411 CAAACTTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (16 bp):
GCATGGATAACGAAGT
Found at i:44560349 original size:124 final size:124
Alignment explanation
Indices: 44560047--44560398 Score: 548
Period size: 124 Copynumber: 2.8 Consensus size: 124
44560037 CCCAAACTTG
*
44560047 CTACTGTAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGG
1 CTACTGTAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
44560112 TAGAAGCGATTTTATACT-TTTGCTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATC---AAAAAAAAATATTTCTTACATGAC
*
44560173 CTACTATAGCAAAAT-ATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAATCA-CGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTG
* * *
44560237 GTAGAAGTGATTTTATACTATTTGCTCAGAAACTTCAAAAAAAATTATTTCTTACATGAC
65 GTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAATATTTCTTACATGAC
* * *
44560297 CTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
44560362 TAGATGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACATCAA
44560399 CTCGAAATAA
Statistics
Matches: 210, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
124 115 0.55
125 2 0.01
126 78 0.37
127 15 0.07
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAATATTTCTTACATGAC
Found at i:44570624 original size:42 final size:42
Alignment explanation
Indices: 44570578--44570708 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
44570568 GCCTGAAGGC
* * *
44570578 TGAACAGAAGCTCATGAGAGCTAAACGGAAACCTATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
** * *
44570620 TGAACAGAAGCTTGTAAGAGCTGAACGAAAACCCATAAGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
* * * * * *
44570662 TTAACTGAAGCTCAAAAGAGTTGAATGGAAACCCATTAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
44570704 TGAAC
1 TGAAC
44570709 GAAAACTCAT
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
Found at i:44570644 original size:21 final size:21
Alignment explanation
Indices: 44570563--44570645 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
44570553 ACATCATTTT
*
44570563 CAGAAGCCT-GAAG-GCTGAA
1 CAGAAGCCTATAAGAGCTGAA
* *
44570582 CAGAAG-CTCATGAGAGCTAAA
1 CAGAAGCCT-ATAAGAGCTGAA
* * * *
44570603 CGGAAACCTATAAGGGTTGAA
1 CAGAAGCCTATAAGAGCTGAA
* *
44570624 CAGAAGCTTGTAAGAGCTGAA
1 CAGAAGCCTATAAGAGCTGAA
44570645 C
1 C
44570646 GAAAACCCAT
Statistics
Matches: 45, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
18 2 0.04
19 6 0.13
20 2 0.04
21 33 0.73
22 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.16
Consensus pattern (21 bp):
CAGAAGCCTATAAGAGCTGAA
Found at i:44574703 original size:13 final size:13
Alignment explanation
Indices: 44574685--44574710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44574675 TGATTTATAT
44574685 GTGTGAAAATTTC
1 GTGTGAAAATTTC
44574698 GTGTGAAAATTTC
1 GTGTGAAAATTTC
44574711 ATCGTTTGTG
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:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:44582857 original size:42 final size:43
Alignment explanation
Indices: 44582740--44582909 Score: 143
Period size: 43 Copynumber: 3.9 Consensus size: 43
44582730 CAGGATTCTA
* *
44582740 ATATGAGTTATCGTGTAAGACCACGTCTGGGAC-GTTGGCGTCGAT
1 ATATGA-TT-TCGTGTAAGACCATGTCTGGGACAG-TGGCATCGAT
* *
44582785 TTGA-GATTTACGTGTAAGATCATGTCTGGGACA-TCGGCATCG-T
1 AT-ATGATTT-CGTGTAAGACCATGTCTGGGACAGT-GGCATCGAT
* * *
44582828 ATATGATTTCGTGTAAGACCCTGTTTGGGACAGTGGCATTGAT
1 ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
* * * *
44582871 ATTTGATTACATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 ATATGATTTCGTGTAAGACCATGTCTGGGACAG-TGGCAT
44582910 TGTAAGAGCT
Statistics
Matches: 102, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 28 0.27
43 42 0.41
44 28 0.27
45 3 0.03
46 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
Found at i:44586118 original size:7 final size:7
Alignment explanation
Indices: 44586103--44586133 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
44586093 TCGAGCTTGA
*
44586103 AAAAGAG
1 AAAATAG
44586110 AAAATAG
1 AAAATAG
44586117 AAAATAG
1 AAAATAG
44586124 AAAATAG
1 AAAATAG
44586131 AAA
1 AAA
44586134 TAAAGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (7 bp):
AAAATAG
Found at i:44587582 original size:24 final size:24
Alignment explanation
Indices: 44587549--44587595 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
44587539 AAGGGGTAAC
* *
44587549 AAGAAGATGAAATGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
*
44587573 AAGAATATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTGAAAGGTT
44587596 GAACATCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTA
Found at i:44590724 original size:41 final size:41
Alignment explanation
Indices: 44590558--44590713 Score: 276
Period size: 41 Copynumber: 3.8 Consensus size: 41
44590548 TTTATCGTTA
* *
44590558 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
44590599 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCTG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
44590640 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
44590681 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
44590714 AAGAGCCGGT
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 110 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:44590986 original size:33 final size:31
Alignment explanation
Indices: 44590928--44590990 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
44590918 ATAGATATGT
44590928 ATATATATATATGTTGCATTCGCATAGGTGG
1 ATATATATATATGTTGCATTCGCATAGGTGG
* *
44590959 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTC-GCATAGGTG
44590991 AAAATAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 12 0.43
32 7 0.25
33 9 0.32
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.40
Consensus pattern (31 bp):
ATATATATATATGTTGCATTCGCATAGGTGG
Found at i:44598257 original size:41 final size:41
Alignment explanation
Indices: 44598200--44598305 Score: 194
Period size: 41 Copynumber: 2.6 Consensus size: 41
44598190 TTTATCGTTA
* *
44598200 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
44598241 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
44598282 GTGACACATTTCAGACTATAAGTC
1 GTGACACATTTCAGACTATAAGTC
44598306 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:44615965 original size:43 final size:42
Alignment explanation
Indices: 44615807--44615963 Score: 133
Period size: 43 Copynumber: 3.7 Consensus size: 42
44615797 TATGAGTTAT
* *
44615807 CGTGTAAGACCACGTCTGGGACGTTGGCGTCGAT-TTGAGATTTA
1 CGTGTAA-ACCACGTCTGGGACGTTGGCATCGATATT-TGA-TTA
* * * * * *
44615851 CGTGTAAATCATGTCTGGGACATCGGCATCG-TATATGATTT
1 CGTGTAAACCACGTCTGGGACGTTGGCATCGATATTTGATTA
* *
44615892 CGTGTAAACC-CTGTTTGGGACAG-TGGCATTGATATTTGATTA
1 CGTGTAAACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTA
*
44615934 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAA-ACCACGTCTGGGACGTTGGCAT
44615964 TGTAAGAGCT
Statistics
Matches: 88, Mismatches: 18, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
41 25 0.28
42 18 0.20
43 37 0.42
44 8 0.09
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (42 bp):
CGTGTAAACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:44619110 original size:13 final size:13
Alignment explanation
Indices: 44619092--44619139 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
44619082 GGTCAGCTGA
44619092 AAAAAGAAAATAG
1 AAAAAGAAAATAG
44619105 AAAAAGAAAATAG
1 AAAAAGAAAATAG
* * *
44619118 AAATA-AAGATAA
1 AAAAAGAAAATAG
44619130 AAAAAGAAAA
1 AAAAAGAAAA
44619140 GAAAATCTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
AAAAAGAAAATAG
Found at i:44619139 original size:7 final size:7
Alignment explanation
Indices: 44619090--44619144 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
44619080 ATGGTCAGCT
44619090 GAAAAAA
1 GAAAAAA
*
44619097 GAAAATA
1 GAAAAAA
44619104 G-AAAAA
1 GAAAAAA
*
44619110 GAAAATA
1 GAAAAAA
44619117 GAAATAAA
1 GAAA-AAA
44619125 GATAAAAA
1 GA-AAAAA
44619133 -AAGAAAA
1 GAA-AAAA
44619140 GAAAA
1 GAAAA
44619145 TCTCATGTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
6 6 0.15
7 22 0.56
8 9 0.23
9 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (7 bp):
GAAAAAA
Found at i:44620542 original size:24 final size:24
Alignment explanation
Indices: 44620514--44620560 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
44620504 AAAGGGTAAC
* *
44620514 AAGAAGATGAAATGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
*
44620538 AAGAATATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTGAAAGGTT
44620561 GAACATCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTA
Found at i:44623667 original size:41 final size:41
Alignment explanation
Indices: 44623501--44623656 Score: 285
Period size: 41 Copynumber: 3.8 Consensus size: 41
44623491 TTTATCGTTA
* *
44623501 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
44623542 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
44623583 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
44623624 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
44623657 AAGAGCCGGT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:44623927 original size:33 final size:32
Alignment explanation
Indices: 44623869--44623931 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
44623859 GATAGATATG
*
44623869 TATATATATATGTTGCATTCTGCATAGGTGGA
1 TATATATATATGTTGCATTCGGCATAGGTGGA
* *
44623901 TATATTTATGTGTATGCATTCGGCATAGGTG
1 TATATATATATGT-TGCATTCGGCATAGGTG
44623932 AAAATAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (32 bp):
TATATATATATGTTGCATTCGGCATAGGTGGA
Found at i:44630125 original size:93 final size:93
Alignment explanation
Indices: 44629966--44630156 Score: 382
Period size: 93 Copynumber: 2.1 Consensus size: 93
44629956 CATTCGGCCA
44629966 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
1 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
44630031 CGTTGCTTTGAATACTTCAAAACCCATG
66 CGTTGCTTTGAATACTTCAAAACCCATG
44630059 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
1 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
44630124 CGTTGCTTTGAATACTTCAAAACCCATG
66 CGTTGCTTTGAATACTTCAAAACCCATG
44630152 TCTTA
1 TCTTA
44630157 ATTTTGTGAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.47
Consensus pattern (93 bp):
TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
CGTTGCTTTGAATACTTCAAAACCCATG
Found at i:44631397 original size:41 final size:41
Alignment explanation
Indices: 44631231--44631386 Score: 285
Period size: 41 Copynumber: 3.8 Consensus size: 41
44631221 TTTATCGTTA
* *
44631231 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
44631272 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
44631313 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
44631354 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
44631387 AAGAGCCGGT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:44631660 original size:33 final size:32
Alignment explanation
Indices: 44631601--44631664 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
44631591 ATAGATATGT
*
44631601 ATATATATATATGTTGCATTCTGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
44631633 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
44631665 AAAATAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:44640541 original size:7 final size:7
Alignment explanation
Indices: 44640529--44640564 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
44640519 TGGTTGTAAA
*
44640529 TGGACTT
1 TGGACAT
*
44640536 TGGACTT
1 TGGACAT
44640543 TGGACAT
1 TGGACAT
44640550 TGGACAT
1 TGGACAT
44640557 TGGACAT
1 TGGACAT
44640564 T
1 T
44640565 TATTTTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (7 bp):
TGGACAT
Found at i:44642114 original size:24 final size:24
Alignment explanation
Indices: 44642069--44642132 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
44642059 GAGTTACAAG
* *
44642069 AAGATGAAAGGTTAAAGGTTAAAA
1 AAGATGAAAGGTGAAAGCTTAAAA
* **
44642093 AAGATGAAAGGTGGAAGCTTAAGG
1 AAGATGAAAGGTGAAAGCTTAAAA
*
44642117 GAGATGAAAGGTGAAA
1 AAGATGAAAGGTGAAA
44642133 AGTTGATCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (24 bp):
AAGATGAAAGGTGAAAGCTTAAAA
Found at i:44642323 original size:29 final size:29
Alignment explanation
Indices: 44642257--44642323 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
44642247 TTATCAAAAC
44642257 TACACATGAACTTTGATTCAATATGCAATT
1 TACACATGAACTTTGATT-AATATGCAATT
* * *
44642287 TGATACATGAAGTTTGATT-TTATGCAATT
1 T-ACACATGAACTTTGATTAATATGCAATT
44642316 ATACACAT
1 -TACACAT
44642324 TAAACTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
29 14 0.45
30 2 0.06
31 15 0.48
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (29 bp):
TACACATGAACTTTGATTAATATGCAATT
Found at i:44646453 original size:51 final size:51
Alignment explanation
Indices: 44646377--44646479 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
44646367 TGAATTGCAT
*
44646377 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAGAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
*
44646428 CGAGTGTAGGCTTGAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
44646479 C
1 C
44646480 TTACTTTTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (51 bp):
CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
Found at i:44649520 original size:112 final size:114
Alignment explanation
Indices: 44649379--44649585 Score: 276
Period size: 112 Copynumber: 1.8 Consensus size: 114
44649369 TTGTTTTTCA
** * *
44649379 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGATGCGAAGAAAGATGACAACCAAGCACCCCA
1 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAAAGATGACAACCAAACACCCCA
*
44649444 -CCCTGGTTACTCAGCCCAACATACTCCTAATTTATTATATTTATATATG
66 TCCC-GGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
* * * *
44649493 TTTTT-TTT-CTTAAGAATATATTGAACCTTTTGACATAAAGAGAGATGACAGCCAAACACCCCA
1 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAAAGATGACAACCAAACACCCCA
* * *
44649556 TCCCGGTTACTTAGCCTAACACATTCCTAA
66 TCCCGGTTACTCAGCCCAACACACTCCTAA
44649586 AAAATTTTTG
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
112 69 0.86
113 6 0.08
114 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (114 bp):
TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAAAGATGACAACCAAACACCCCA
TCCCGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
Found at i:44650742 original size:4 final size:4
Alignment explanation
Indices: 44650726--44650768 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
44650716 TATCCAAACA
44650726 AAAT AAAGT -AAT AAAT -AAT AAAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAA-T AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAA
44650769 AATAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 4 0.11
4 27 0.77
5 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:44650743 original size:12 final size:11
Alignment explanation
Indices: 44650735--44650790 Score: 64
Period size: 10 Copynumber: 5.2 Consensus size: 11
44650725 AAAATAAAGT
44650735 AATAAATAATAA
1 AATAAATAAT-A
44650747 AATAAATAAATA
1 AATAAAT-AATA
44650759 AATAAATAA-A
1 AATAAATAATA
44650769 AATAAA-AATA
1 AATAAATAATA
*
44650779 AAGAAA-AATA
1 AATAAATAATA
44650789 AA
1 AA
44650791 AACTGGGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
9 2 0.05
10 19 0.46
11 2 0.05
12 15 0.37
13 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (11 bp):
AATAAATAATA
Found at i:44650756 original size:16 final size:17
Alignment explanation
Indices: 44650735--44650790 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 17
44650725 AAAATAAAGT
*
44650735 AATAAATAATAAA-ATA
1 AATAAATAATAAAGAAA
*
44650751 AATAAATAAATAAATAAA
1 AATAAAT-AATAAAGAAA
44650769 AATAAA-AATAAAGAAA
1 AATAAATAATAAAGAAA
44650785 AATAAA
1 AATAAA
44650791 AACTGGGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 22 0.61
17 6 0.17
18 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AATAAATAATAAAGAAA
Found at i:44650777 original size:20 final size:18
Alignment explanation
Indices: 44650725--44650790 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 18
44650715 ATATCCAAAC
44650725 AAAATAAAGTAATAAATAAT
1 AAAATAAA--AATAAATAAT
44650745 AAAAT--AAATAAATAA-
1 AAAATAAAAATAAATAAT
44650760 ATAAATAAAAATAAA-AAT
1 A-AAATAAAAATAAATAAT
*
44650778 -AAAGAAAAATAAA
1 AAAATAAAAATAAA
44650791 AACTGGGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
15 1 0.02
16 25 0.61
17 2 0.05
18 8 0.20
20 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAATAAAAATAAATAAT
Found at i:44654440 original size:14 final size:14
Alignment explanation
Indices: 44654423--44654467 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
44654413 TGACAGAATA
44654423 ATGACATGAGAAAG
1 ATGACATGAGAAAG
44654437 ATGACATGAGAATA-
1 ATGACATGAGAA-AG
44654451 ATGACATGAGAAAG
1 ATGACATGAGAAAG
44654465 ATG
1 ATG
44654468 TGCAAATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (14 bp):
ATGACATGAGAAAG
Found at i:44654871 original size:27 final size:28
Alignment explanation
Indices: 44654816--44654886 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
44654806 CAATATTTTA
* * *
44654816 TAATTTAA-TCAAT-TATTTAATTGATT
1 TAATTTAACCCAATATATTTAATTAAAT
44654842 TAATTTAACCCAATATATTTAA-TAAAT
1 TAATTTAACCCAATATATTTAATTAAAT
44654869 TAATTTAACCCAATATAT
1 TAATTTAACCCAATATAT
44654887 AATTTAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 8 0.20
27 25 0.62
28 7 0.17
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (28 bp):
TAATTTAACCCAATATATTTAATTAAAT
Found at i:44659529 original size:23 final size:23
Alignment explanation
Indices: 44659486--44659530 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
44659476 TATTTGTTTT
* *
44659486 ATATTTAAATATTATTTTTAATA
1 ATATTTAAATATTAATATTAATA
44659509 ATATTTAAATATTAATATTAAT
1 ATATTTAAATATTAATATTAAT
44659531 TTATACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTAAATATTAATATTAATA
Found at i:44664499 original size:3 final size:3
Alignment explanation
Indices: 44664491--44664516 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44664481 AATGGAGAGA
44664491 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
44664517 AATATATATG
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:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:44665539 original size:25 final size:25
Alignment explanation
Indices: 44665505--44665552 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
44665495 CATAAACGCA
44665505 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAGCGTCCTGATATAG
*
44665530 GCTCTTTATGAGCTTCCTGATAT
1 GCTCTTTATGAGCGTCCTGATAT
44665553 GACTCACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (25 bp):
GCTCTTTATGAGCGTCCTGATATAG
Found at i:44676332 original size:30 final size:30
Alignment explanation
Indices: 44676293--44676350 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
44676283 TTTTATAAAT
44676293 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
44676323 AATTTATATTTCATATATTAAAATATTT
1 AATTAATATTTCATATATTAAAATATTT
44676351 TTTTATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 19 0.76
31 4 0.16
32 2 0.08
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:44685292 original size:27 final size:28
Alignment explanation
Indices: 44685244--44685311 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
44685234 AAAAATATTA
* **
44685244 AAAAATATTTTTTAATTTTTTTTACTTTT
1 AAAAATA-ATTTTAATGATTTTTACTTTT
* *
44685273 -GAAATAATTTTAATGATTTTTATTTTT
1 AAAAATAATTTTAATGATTTTTACTTTT
44685300 AAAAATAATTTT
1 AAAAATAATTTT
44685312 TATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (28 bp):
AAAAATAATTTTAATGATTTTTACTTTT
Found at i:44685292 original size:28 final size:27
Alignment explanation
Indices: 44685274--44685324 Score: 61
Period size: 25 Copynumber: 1.9 Consensus size: 27
44685264 TTTACTTTTG
*
44685274 AAATAATTTTAATGATTTTTATTTTTAA
1 AAATAATTTTAAT-ATTTTTACTTTTAA
*
44685302 AAATAATTTT--TATTTTTATTTTT
1 AAATAATTTTAATATTTTTACTTTT
44685325 TATTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.52
26 1 0.04
28 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
AAATAATTTTAATATTTTTACTTTTAA
Found at i:44685322 original size:12 final size:12
Alignment explanation
Indices: 44685305--44685344 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
44685295 TTTTTAAAAA
44685305 TAATTTTTATTTT
1 TAATTTTTA-TTT
*
44685318 TATTTTTTATTT
1 TAATTTTTATTT
*
44685330 TAATTTTAATTT
1 TAATTTTTATTT
44685342 TAA
1 TAA
44685345 AAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TAATTTTTATTT
Found at i:44685325 original size:27 final size:28
Alignment explanation
Indices: 44685244--44685325 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 28
44685234 AAAAATATTA
*
44685244 AAAAATATTTTTTAATTTTT-TTTACTTTT
1 AAAAATAATTTTTAATTTTTATTT--TTTT
* *
44685273 -GAAATAA-TTTTAATGATTTT-TATTTTT
1 AAAAATAATTTTTAAT--TTTTATTTTTTT
44685300 AAAAATAATTTTT-ATTTTTATTTTTT
1 AAAAATAATTTTTAATTTTTATTTTTT
44685326 ATTTTAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.09
27 16 0.37
28 13 0.30
29 10 0.23
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (28 bp):
AAAAATAATTTTTAATTTTTATTTTTTT
Found at i:44686147 original size:52 final size:53
Alignment explanation
Indices: 44686069--44686178 Score: 186
Period size: 52 Copynumber: 2.1 Consensus size: 53
44686059 AATGCTTGAA
* *
44686069 ATTTGTCGTCCGAAGGTTGAGTGCTAGTAATTAATTTGTTTTCAAACTT-ATC
1 ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
*
44686121 ATTTGTCCTCCTAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
1 ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
44686174 ATTTG
1 ATTTG
44686179 CTTGCTCGAC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 46 0.85
53 8 0.15
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (53 bp):
ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
Found at i:44698277 original size:87 final size:87
Alignment explanation
Indices: 44698131--44698305 Score: 314
Period size: 87 Copynumber: 2.0 Consensus size: 87
44698121 AATTTAGTAT
44698131 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
1 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
* *
44698196 GTTAATTATTAACTTAAAAATC
66 GTCAATAATTAACTTAAAAATC
44698218 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
1 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
* *
44698283 GTCACTAATTAACTTAAACATC
66 GTCAATAATTAACTTAAAAATC
44698305 T
1 T
44698306 TAACCACTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (87 bp):
TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
GTCAATAATTAACTTAAAAATC
Found at i:44698473 original size:14 final size:15
Alignment explanation
Indices: 44698445--44698474 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44698435 ACAAGAGTTG
44698445 AAATAAAATAATAAA
1 AAATAAAATAATAAA
44698460 AAATAAAA-AATAAA
1 AAATAAAATAATAAA
44698474 A
1 A
44698475 GGTGAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAATAATAAA
Found at i:44698474 original size:6 final size:7
Alignment explanation
Indices: 44698445--44698474 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
44698435 ACAAGAGTTG
44698445 AAATAAA
1 AAATAAA
44698452 ATAATAAA
1 A-AATAAA
44698460 AAATAAA
1 AAATAAA
44698467 AAATAAA
1 AAATAAA
44698474 A
1 A
44698475 GGTGAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:44709694 original size:14 final size:14
Alignment explanation
Indices: 44709675--44709701 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44709665 CATAAATGAT
44709675 AAAATTTTCACACG
1 AAAATTTTCACACG
44709689 AAAATTTTCACAC
1 AAAATTTTCACAC
44709702 ATATCACATA
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:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (14 bp):
AAAATTTTCACACG
Found at i:44713550 original size:9 final size:9
Alignment explanation
Indices: 44713536--44713570 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
44713526 ATTATTTTAG
44713536 AAAATTTTT
1 AAAATTTTT
*
44713545 AAAA-TTTA
1 AAAATTTTT
44713553 AAAATTTTT
1 AAAATTTTT
44713562 AAAATTTTT
1 AAAATTTTT
44713571 TTGAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AAAATTTTT
Found at i:44713558 original size:17 final size:18
Alignment explanation
Indices: 44713531--44713568 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
44713521 AAATTATTAT
44713531 TTTAGAAAATTTTTAAAA
1 TTTAGAAAATTTTTAAAA
44713549 TTTA-AAAATTTTTAAAA
1 TTTAGAAAATTTTTAAAA
44713566 TTT
1 TTT
44713569 TTTTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTAGAAAATTTTTAAAA
Found at i:44713595 original size:28 final size:29
Alignment explanation
Indices: 44713539--44713602 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
44713529 ATTTTAGAAA
* *
44713539 ATTTTTAAAATTTAAAAATTTTTAAAATT
1 ATTTTTGAAATTAAAAAATTTTTAAAATT
*
44713568 -TTTTTGAAATTAAAAAATTATTT-TAATT
1 ATTTTTGAAATTAAAAAATT-TTTAAAATT
44713596 ATTTTTG
1 ATTTTTG
44713603 TATTTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTTGAAATTAAAAAATTTTTAAAATT
Found at i:44716960 original size:25 final size:25
Alignment explanation
Indices: 44716931--44716978 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
44716921 ATTTATTACT
44716931 TACAAATTTCTTTACACATCCAGTG
1 TACAAATTTCTTTACACATCCAGTG
44716956 TACAAATTTCTTTACACATCCAG
1 TACAAATTTCTTTACACATCCAG
44716979 CATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.35
Consensus pattern (25 bp):
TACAAATTTCTTTACACATCCAGTG
Found at i:44717003 original size:42 final size:44
Alignment explanation
Indices: 44716956--44717050 Score: 140
Period size: 42 Copynumber: 2.2 Consensus size: 44
44716946 ACATCCAGTG
* *
44716956 TACAAATTTCTTTACACATCCAGCAT-A-TATAAATTTATTACT
1 TACAAATTTCTCTACACATCCAGCATAAGTAAAAATTTATTACT
**
44716998 TACAAATTTCTCTACACATCCAGTGTAAGTAAAAATTTATTACT
1 TACAAATTTCTCTACACATCCAGCATAAGTAAAAATTTATTACT
44717042 TACAAATTT
1 TACAAATTT
44717051 ATTACTTACA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 23 0.49
43 1 0.02
44 23 0.49
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (44 bp):
TACAAATTTCTCTACACATCCAGCATAAGTAAAAATTTATTACT
Found at i:44717050 original size:15 final size:15
Alignment explanation
Indices: 44717030--44717065 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
44717020 GTGTAAGTAA
44717030 AAATTTATTACTTAC
1 AAATTTATTACTTAC
44717045 AAATTTATTACTTAC
1 AAATTTATTACTTAC
44717060 AAATTT
1 AAATTT
44717066 CTTTACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTATTACTTAC
Found at i:44717296 original size:16 final size:16
Alignment explanation
Indices: 44717254--44717309 Score: 96
Period size: 16 Copynumber: 3.5 Consensus size: 16
44717244 TTTTACTAAT
44717254 ATTATAA-TTTTCATC
1 ATTATAATTTTTCATC
44717269 ATTATAATTTTTTCATC
1 ATTATAA-TTTTTCATC
44717286 ATTATAATTTTTCATC
1 ATTATAATTTTTCATC
44717302 ATTATAAT
1 ATTATAAT
44717310 ATCAAGGCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.18
16 17 0.44
17 15 0.38
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATAATTTTTCATC
Found at i:44720122 original size:22 final size:22
Alignment explanation
Indices: 44720065--44720130 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
44720055 GTCAATTATG
44720065 TGTTAATTCAAGACTTATGTAA
1 TGTTAATTCAAGACTTATGTAA
** *
44720087 TGTT--TTTTA-A-TTATGTAG
1 TGTTAATTCAAGACTTATGTAA
44720105 TGTTAATTCAAGACTTATGTAA
1 TGTTAATTCAAGACTTATGTAA
44720127 TGTT
1 TGTT
44720131 TTCAATTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 11 0.32
19 1 0.03
20 6 0.18
21 1 0.03
22 15 0.44
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (22 bp):
TGTTAATTCAAGACTTATGTAA
Found at i:44720198 original size:20 final size:18
Alignment explanation
Indices: 44720171--44720225 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
44720161 TAATAGTTTT
44720171 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
* * *
44720189 AGATTTATGTAATGCTTT-T
1 A-A-TTATGTAGTGATTTAA
44720208 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
44720226 TTCGAGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
17 12 0.43
18 2 0.07
19 2 0.07
20 12 0.43
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (18 bp):
AATTATGTAGTGATTTAA
Found at i:44720215 original size:17 final size:16
Alignment explanation
Indices: 44720156--44720227 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 16
44720146 ACTCAAAGAC
44720156 TTATGTAATAGTTTTAA
1 TTATGTAAT-GTTTTAA
* *
44720173 TTATGTAGTGATTTAAAGA
1 TTATGTAATG-TTT-TA-A
44720192 TTTATGTAATGCTTTTAA
1 -TTATGTAATG-TTTTAA
* *
44720210 TTATGTAGTGATTTAA
1 TTATGTAATGTTTTAA
44720226 TT
1 TT
44720228 CGAGTAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
16 8 0.18
17 20 0.45
18 2 0.05
19 2 0.05
20 12 0.27
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.51
Consensus pattern (16 bp):
TTATGTAATGTTTTAA
Found at i:44720219 original size:37 final size:36
Alignment explanation
Indices: 44720074--44720225 Score: 196
Period size: 37 Copynumber: 4.0 Consensus size: 36
44720064 GTGTTAATTC
* *
44720074 AAGACTTATGTAATGTTTTTTAATTATGTAGTGTTAATTC
1 AAGACTTATGTAATG--TTTTAATTATGTAGTG--ATTTA
* *
44720114 AAGACTTATGTAATGTTTTCAATTATGTAGTGACTCA
1 AAGACTTATGTAATGTTTT-AATTATGTAGTGATTTA
44720151 AAGACTTATGTAATAGTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAAT-GTTTTAATTATGTAGTGATTTA
*
44720188 AAGATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATG-TTTTAATTATGTAGTGATTTA
44720225 A
1 A
44720226 TTCGAGTAAT
Statistics
Matches: 103, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
36 1 0.01
37 66 0.64
38 9 0.09
39 12 0.12
40 15 0.15
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (36 bp):
AAGACTTATGTAATGTTTTAATTATGTAGTGATTTA
Found at i:44720243 original size:9 final size:9
Alignment explanation
Indices: 44720231--44720313 Score: 85
Period size: 9 Copynumber: 8.8 Consensus size: 9
44720221 TTTAATTCGA
44720231 GTAATTTGG
1 GTAATTTGG
44720240 GTAATTTTCGG
1 GTAA-TTT-GG
*
44720251 GTAATTCGG
1 GTAATTTGG
44720260 GTAATTTGG
1 GTAATTTGG
44720269 GTAATTTTCGG
1 GTAA-TTT-GG
* *
44720280 ATAATTCGG
1 GTAATTTGG
*
44720289 GTAATTCGG
1 GTAATTTGG
*
44720298 GTAATTCGG
1 GTAATTTGG
44720307 GTAATTT
1 GTAATTT
44720314 TTAACCAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
9 43 0.67
10 10 0.16
11 11 0.17
ACGTcount: A:0.23, C:0.07, G:0.29, T:0.41
Consensus pattern (9 bp):
GTAATTTGG
Found at i:44720265 original size:29 final size:29
Alignment explanation
Indices: 44720223--44720312 Score: 139
Period size: 29 Copynumber: 3.2 Consensus size: 29
44720213 TGTAGTGATT
*
44720223 TAATTCGAGTAATTTGGGTAATTTTCGGG
1 TAATTCGGGTAATTTGGGTAATTTTCGGG
*
44720252 TAATTCGGGTAATTTGGGTAATTTTCGGA
1 TAATTCGGGTAATTTGGGTAATTTTCGGG
*
44720281 TAATTCGGGTAATTCGGGTAA--TTCGGG
1 TAATTCGGGTAATTTGGGTAATTTTCGGG
44720308 TAATT
1 TAATT
44720313 TTTAACCAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
27 10 0.18
29 47 0.82
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (29 bp):
TAATTCGGGTAATTTGGGTAATTTTCGGG
Found at i:44720273 original size:38 final size:37
Alignment explanation
Indices: 44720223--44720313 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 37
44720213 TGTAGTGATT
* *
44720223 TAATTCGAGTAATTT-GGGTAATTTTCGGGTAATTCGGG
1 TAATTCGGGTAATTTCGGATAA--TTCGGGTAATTCGGG
*
44720261 TAATTTGGGTAATTTTCGGATAATTCGGGTAATTCGGG
1 TAATTCGGGTAA-TTTCGGATAATTCGGGTAATTCGGG
44720299 TAATTCGGGTAATTT
1 TAATTCGGGTAATTT
44720314 TTAACCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 3 0.06
38 36 0.77
39 3 0.06
40 5 0.11
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (37 bp):
TAATTCGGGTAATTTCGGATAATTCGGGTAATTCGGG
Found at i:44720422 original size:28 final size:30
Alignment explanation
Indices: 44720341--44720422 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
44720331 ACACATATTT
44720341 TTCGGTTAATTCGGTTAACCAAAAAAATTTCGG
1 TTCGGTTAA-TCGGTTAA--AAAAAAATTTCGG
*** **
44720374 TTCGGTTAATTATTTTTAAAAAAA-TTCGG
1 TTCGGTTAATCGGTTAAAAAAAAATTTCGG
44720403 TTCGGTTAA-CGGTTAAAAAA
1 TTCGGTTAATCGGTTAAAAAA
44720423 TTTGGGAGGT
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
28 6 0.15
29 14 0.36
30 7 0.18
32 3 0.08
33 9 0.23
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (30 bp):
TTCGGTTAATCGGTTAAAAAAAAATTTCGG
Found at i:44721952 original size:16 final size:16
Alignment explanation
Indices: 44721921--44721957 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
44721911 ATGTGAATAA
44721921 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
44721937 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
44721953 TATTA
1 TATTA
44721958 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:44721966 original size:18 final size:18
Alignment explanation
Indices: 44721943--44722028 Score: 56
Period size: 18 Copynumber: 4.7 Consensus size: 18
44721933 TTATTATTTT
44721943 TAAAATTTATTATTAAAA
1 TAAAATTTATTATTAAAA
*
44721961 TAAAATTTAAATATT-AAA
1 TAAAATTT-ATTATTAAAA
44721979 T--AATTTATTA--AAAA
1 TAAAATTTATTATTAAAA
* *
44721993 TAATAAATTATATTAATTATAT
1 T-A-AAATT-TATT-ATTAAAA
44722015 TAATAATTTATTAT
1 TAA-AATTTATTAT
44722029 ATGACTAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
14 4 0.08
15 3 0.06
16 5 0.09
18 16 0.30
19 11 0.21
20 6 0.11
21 5 0.09
22 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAATTTATTATTAAAA
Found at i:44722108 original size:9 final size:9
Alignment explanation
Indices: 44722094--44722118 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
44722084 ATTTTATATT
44722094 AATATTTGA
1 AATATTTGA
44722103 AATATTTGA
1 AATATTTGA
44722112 AATATTT
1 AATATTT
44722119 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (9 bp):
AATATTTGA
Found at i:44722965 original size:98 final size:98
Alignment explanation
Indices: 44722778--44722974 Score: 313
Period size: 98 Copynumber: 2.0 Consensus size: 98
44722768 GTACAATAAA
*
44722778 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * * **
44722843 CCTTTAGAATCTCAAATTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
* *
44722876 ACTTTAAAAGAACATCCACTTATTCAAGATTTAAGAAATCATACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
44722941 CCTTTAAAATCCCAAACTCAGAATATTTTCTTT
66 CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
44722974 A
1 A
44722975 TTATTTTTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
Found at i:44724625 original size:17 final size:17
Alignment explanation
Indices: 44724603--44724644 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
44724593 CAAATCTGCT
* * *
44724603 TTTGGGCTTCTGTTTGG
1 TTTGGGCCTCAGTTGGG
44724620 TTTGGGCCTCAGTTGGG
1 TTTGGGCCTCAGTTGGG
44724637 TTTGGGCC
1 TTTGGGCC
44724645 ACATCGGGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.17, G:0.38, T:0.43
Consensus pattern (17 bp):
TTTGGGCCTCAGTTGGG
Found at i:44741782 original size:98 final size:98
Alignment explanation
Indices: 44741608--44741804 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
44741598 GTACAATAAA
*
44741608 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
44741673 CCTTTAGAATCCCAAATTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
*
44741706 ACTTTAAAAGAACATCCACTTATCTAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
44741771 CCTTTAAAATCCCAAACTCGGAATATTTTCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
44741804 A
1 A
44741805 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.30
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:44749248 original size:14 final size:16
Alignment explanation
Indices: 44749222--44749255 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
44749212 ATTGTTTGGA
44749222 TATTGTATAATTTT-T
1 TATTGTATAATTTTGT
44749237 TATTGT-TAATTTTGT
1 TATTGTATAATTTTGT
44749252 TATT
1 TATT
44749256 ATTTTAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (16 bp):
TATTGTATAATTTTGT
Found at i:44752610 original size:20 final size:21
Alignment explanation
Indices: 44752584--44752629 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
44752574 AGCCGGGATC
44752584 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
*
44752605 -CTAACTAATACTAATTTAAT
1 ACTAACTAATACTAATCTAAT
44752625 ACTAA
1 ACTAA
44752630 TAGAATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:44752626 original size:11 final size:11
Alignment explanation
Indices: 44752584--44752630 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
44752574 AGCCGGGATC
44752584 ACTAA-CTAAT
1 ACTAATCTAAT
44752594 ACTAATCTAAT
1 ACTAATCTAAT
44752605 -CTAA-CTAAT
1 ACTAATCTAAT
*
44752614 ACTAATTTAAT
1 ACTAATCTAAT
44752625 ACTAAT
1 ACTAAT
44752631 AGAATAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
9 5 0.15
10 13 0.39
11 15 0.45
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:44752645 original size:22 final size:22
Alignment explanation
Indices: 44752620--44752663 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44752610 TAATACTAAT
44752620 TTAATACTAATA-GAATAGAATA
1 TTAAT-CTAATACGAATAGAATA
*
44752642 TTAATCTAATACTAATAGAATA
1 TTAATCTAATACGAATAGAATA
44752664 GAAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (22 bp):
TTAATCTAATACGAATAGAATA
Found at i:44752646 original size:27 final size:27
Alignment explanation
Indices: 44752611--44752666 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
44752601 TAATCTAACT
*
44752611 AATACTAATTTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
*
44752638 AATATTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
44752665 AA
1 AA
44752667 AAAATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (27 bp):
AATACTAATCTAATACTAATAGAATAG
Found at i:44752651 original size:5 final size:6
Alignment explanation
Indices: 44752588--44752658 Score: 50
Period size: 6 Copynumber: 13.2 Consensus size: 6
44752578 GGGATCACTA
*
44752588 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -TTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
* * *
44752631 A-GAAT A-GAAT ATTAAT -CTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT A
44752659 GAATAGAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
4 3 0.06
5 25 0.46
6 26 0.48
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (6 bp):
ACTAAT
Found at i:44752692 original size:18 final size:18
Alignment explanation
Indices: 44752649--44752699 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
44752639 ATATTAATCT
*
44752649 AATACTAATAGAATAG-A
1 AATACTAATATAATAGAA
44752666 AA-A--AATATAATAGAA
1 AATACTAATATAATAGAA
44752681 AATACTAATATAATAGAA
1 AATACTAATATAATAGAA
44752699 A
1 A
44752700 GAAAAGAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 9 0.31
15 3 0.10
16 2 0.07
17 2 0.07
18 13 0.45
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.24
Consensus pattern (18 bp):
AATACTAATATAATAGAA
Found at i:44756103 original size:40 final size:40
Alignment explanation
Indices: 44756048--44756364 Score: 544
Period size: 40 Copynumber: 7.9 Consensus size: 40
44756038 GCATGAGCAT
44756048 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
44756088 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
44756128 TTGATAAATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
44756168 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
44756208 TTGATATATCCGGGCTAAAACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * *
44756248 TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
44756288 TTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * * *
44756328 TTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
44756365 TTGCGGTTAT
Statistics
Matches: 261, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 261 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (40 bp):
TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
Found at i:44763217 original size:63 final size:63
Alignment explanation
Indices: 44763118--44763243 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
44763108 TATGGGATAC
44763118 CTACAAAGGGAAAATCAAAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
1 CTACAAAGGGAAAATCAAAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
* *
44763181 CTACAAAGGGAAATTCAGAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
1 CTACAAAGGGAAAATCAAAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
44763244 TAGAGATCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.20
Consensus pattern (63 bp):
CTACAAAGGGAAAATCAAAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
Found at i:44764143 original size:26 final size:26
Alignment explanation
Indices: 44764106--44764167 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
44764096 CATTTGAAAG
44764106 TCCTAG-TTTTCGACGACTGTCTCTT
1 TCCTAGATTTTCGACGACTGTCTCTT
*
44764131 TCCTAGATTTTCGACGATTGTCTCTT
1 TCCTAGATTTTCGACGACTGTCTCTT
44764157 TCCTAGATTTT
1 TCCTAGATTTT
44764168 TCTTATTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 6 0.17
26 29 0.83
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (26 bp):
TCCTAGATTTTCGACGACTGTCTCTT
Found at i:44765800 original size:41 final size:41
Alignment explanation
Indices: 44765737--44765922 Score: 309
Period size: 41 Copynumber: 4.5 Consensus size: 41
44765727 TTTAACATAT
* * * *
44765737 TCACCAGCACTTAGCCTACTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
44765778 TCATCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
44765819 TCACCGGCACTCAGCCTGCTAGGTTTATAACCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
44765860 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
44765901 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
44765923 ACTTAAAGTC
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 135 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Done.