Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 141 of 335
Found at i:41368859 original size:80 final size:79
Alignment explanation
Indices: 41368741--41368942 Score: 284
Period size: 80 Copynumber: 2.5 Consensus size: 79
41368731 GAGATTTAAT
* * *
41368741 CGGATATAGCTACTCGCTC-AATGCCTTCGGGACATAGCCCGGATATAATAACT-AGCACCAATG
1 CGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCA-CACAAATG
41368804 CCTTCGGGACTTAGCC
64 CCTTCGGGACTTAGCC
*
41368820 CGGATATAGTAGCTCGCACAAATGCCTTCGGGACTTAGCCCGGATGTAATAACTCACACAAATGC
1 CGGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCACACAAATGC
41368885 CTTCGGGACTTAGCC
65 CTTCGGGACTTAGCC
* *
41368900 CGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
1 CGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
41368943 TTATCATCCG
Statistics
Matches: 112, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
78 2 0.02
79 16 0.14
80 92 0.82
81 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (79 bp):
CGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCACACAAATGCC
TTCGGGACTTAGCC
Found at i:41376174 original size:22 final size:22
Alignment explanation
Indices: 41376119--41376175 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
41376109 TTTTTGATTT
*
41376119 ATAACATT-TATATTGAAAATA
1 ATAATATTATATATTGAAAATA
41376140 ATAATATTA-ATATT-AAAA-A
1 ATAATATTATATATTGAAAATA
41376159 ATATATATATATATATT
1 ATA-ATAT-TATATATT
41376176 TTCCTCCCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 4 0.13
20 8 0.26
21 14 0.45
22 5 0.16
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATATTATATATTGAAAATA
Found at i:41381393 original size:12 final size:12
Alignment explanation
Indices: 41381376--41381416 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
41381366 ATTTATTTGG
41381376 TATTTTTATTAT
1 TATTTTTATTAT
*
41381388 TA-TTTTAATAT
1 TATTTTTATTAT
41381399 ATATTTTTATTAT
1 -TATTTTTATTAT
41381412 T-TTTT
1 TATTTT
41381417 ATGTAGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 12 0.48
12 5 0.20
13 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:41384326 original size:14 final size:14
Alignment explanation
Indices: 41384307--41384335 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41384297 TGGAACAAAC
41384307 TTTGTAATATAAAT
1 TTTGTAATATAAAT
41384321 TTTGTAATATAAAT
1 TTTGTAATATAAAT
41384335 T
1 T
41384336 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:41384354 original size:62 final size:62
Alignment explanation
Indices: 41384278--41384445 Score: 300
Period size: 62 Copynumber: 2.7 Consensus size: 62
41384268 TAACATTACA
*
41384278 ACATTACTACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
* * *
41384340 ACATTACAATATTAAAACTTGCAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
41384402 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
41384446 AGGTACATTC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 100 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (62 bp):
ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
Found at i:41388293 original size:16 final size:16
Alignment explanation
Indices: 41388272--41388302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41388262 ATAATGTTTT
41388272 TTATTTAAAAATAATC
1 TTATTTAAAAATAATC
*
41388288 TTATTTTAAAATAAT
1 TTATTTAAAAATAAT
41388303 ATATCAAATT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATTTAAAAATAATC
Found at i:41395786 original size:28 final size:28
Alignment explanation
Indices: 41395746--41395802 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
41395736 TTATGCGGAC
*
41395746 TTAAAACGAAAAGATATTGAATTTGAGA
1 TTAAAACGAAAAGATATTGAATTTCAGA
41395774 TTAAAACGAAAAGATATTGAATTTCAGA
1 TTAAAACGAAAAGATATTGAATTTCAGA
41395802 T
1 T
41395803 CGATGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (28 bp):
TTAAAACGAAAAGATATTGAATTTCAGA
Found at i:41397552 original size:43 final size:43
Alignment explanation
Indices: 41397505--41397607 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 43
41397495 CCTCGATTGA
* ** *
41397505 GATTTACGTATAAGACCATGTCTGGGACATCGGCATTG-TATCT
1 GATTTACGTATAAGACCATGTCAGGGACAGAGACATTGATAT-T
* * *
41397548 GATTT-TGTGTAAGACCCTGTCAGGGACAGAGACATTGATATT
1 GATTTACGTATAAGACCATGTCAGGGACAGAGACATTGATATT
* *
41397590 GAATTACATATAAGACCA
1 GATTTACGTATAAGACCA
41397608 CGTCGGCATT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
42 30 0.65
43 16 0.35
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (43 bp):
GATTTACGTATAAGACCATGTCAGGGACAGAGACATTGATATT
Found at i:41399668 original size:26 final size:26
Alignment explanation
Indices: 41399639--41399745 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
41399629 TGATACAAAT
41399639 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
41399665 TGATAATGGATTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41399691 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41399717 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
41399742 TGAT
1 TGAT
41399746 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 6 0.08
26 71 0.92
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41402536 original size:26 final size:26
Alignment explanation
Indices: 41402507--41402614 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
41402497 TGATACAAAT
41402507 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
41402533 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATATTCCA
41402559 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
41402585 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
41402611 TGAT
1 TGAT
41402615 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:41409382 original size:26 final size:26
Alignment explanation
Indices: 41409353--41409460 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
41409343 TGATACAAAT
41409353 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
41409379 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41409405 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41409431 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41409457 TGAT
1 TGAT
41409461 GGGCATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41411830 original size:3 final size:3
Alignment explanation
Indices: 41411822--41411851 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41411812 ACTAATAAAT
41411822 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41411852 CATCATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41419146 original size:15 final size:17
Alignment explanation
Indices: 41419122--41419157 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
41419112 GACCGTTTTT
41419122 AGGAGAGAGAATATGAA
1 AGGAGAGAGAATATGAA
41419139 AGGAGAGAGAATATGAA
1 AGGAGAGAGAATATGAA
41419156 AG
1 AG
41419158 CATAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.36, T:0.11
Consensus pattern (17 bp):
AGGAGAGAGAATATGAA
Found at i:41427325 original size:16 final size:16
Alignment explanation
Indices: 41427301--41427356 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
41427291 GGTTAGGGGG
41427301 AATGGAATAGAGCTGT
1 AATGGAATAGAGCTGT
* *
41427317 AATGTAATAGAGCTAT
1 AATGGAATAGAGCTGT
*
41427333 AATGGAATAGACCTGT
1 AATGGAATAGAGCTGT
41427349 AAT-GAATA
1 AATGGAATA
41427357 ATTCAGTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
15 5 0.14
16 30 0.86
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (16 bp):
AATGGAATAGAGCTGT
Found at i:41427386 original size:46 final size:44
Alignment explanation
Indices: 41427333--41427425 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
41427323 ATAGAGCTAT
41427333 AATGGAATAGACCTGTAATGAATAATTCAGT-TGTTTGGTTGAATGG
1 AATGGAATAGACCTGTAAT-AAT-ATTC-GTGTGTTTGGTTGAATGG
** * *
41427379 AATGGAATAGAGTTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGACCTGTAATAATATTCGTGTGTTTGGTTGAATGG
41427423 AAT
1 AAT
41427426 AGATGTTGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.52
45 2 0.05
46 17 0.40
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (44 bp):
AATGGAATAGACCTGTAATAATATTCGTGTGTTTGGTTGAATGG
Found at i:41437409 original size:148 final size:148
Alignment explanation
Indices: 41437238--41437507 Score: 432
Period size: 148 Copynumber: 1.8 Consensus size: 148
41437228 ACTATTTTGG
* * * * *
41437238 ATTTGTTTGTATTTAATTGTTTGGTTATTGTACATGACAGAAATGCATTTCTTTGTGTTAAATTA
1 ATTTATTTGTATTAAATTATTTGGTTATTGTACATAACAGAAATGCATTTCTTTGTATTAAATTA
* * *
41437303 TTTTTGTATTGGTTATTATCTGCCATTGCTTAGGTTGTATTAAAGTGTTTGGTTATTGTCTGCTA
66 TTCTTGTATTGGTTATTATCTGACATTGCTTAGGTTGTATTAAAATGTTTGGTTATTGTCTGCTA
41437368 TGTATATGACAGAAATGA
131 TGTATATGACAGAAATGA
* * *
41437386 ATTTATTTGTATTAAATTATTTGGTTATTGTACATAACAGAAATGGATTTGTTTGTATTAAATTG
1 ATTTATTTGTATTAAATTATTTGGTTATTGTACATAACAGAAATGCATTTCTTTGTATTAAATTA
*
41437451 TTCTTGTATTGGTTATTGTCTGACATTGCTTAGGTTGTATTAAAATGTTTGGTTATT
66 TTCTTGTATTGGTTATTATCTGACATTGCTTAGGTTGTATTAAAATGTTTGGTTATT
41437508 ATCTACCACT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
148 110 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (148 bp):
ATTTATTTGTATTAAATTATTTGGTTATTGTACATAACAGAAATGCATTTCTTTGTATTAAATTA
TTCTTGTATTGGTTATTATCTGACATTGCTTAGGTTGTATTAAAATGTTTGGTTATTGTCTGCTA
TGTATATGACAGAAATGA
Found at i:41442166 original size:40 final size:40
Alignment explanation
Indices: 41442111--41442245 Score: 252
Period size: 40 Copynumber: 3.4 Consensus size: 40
41442101 TATGTGCATA
41442111 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
41442151 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
41442191 GCATTCGTGCGAGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
41442231 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
41442246 GTTACATCCG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 92 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:41442269 original size:80 final size:80
Alignment explanation
Indices: 41442111--41442269 Score: 228
Period size: 80 Copynumber: 2.0 Consensus size: 80
41442101 TATGTGCATA
* *
41442111 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
1 GCATTCGTGCGAGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTACAACCG
* ** *
41442176 GGTTAAGTCCCGAAG
66 AGCCAAATCCCGAAG
* * *
41442191 GCATTCGTGCGAGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTACATCCG
1 GCATTCGTGCGAGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTACAACCG
*
41442256 AGCCAAATTCCGAA
66 AGCCAAATCCCGAA
41442270 AGTATTTATG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (80 bp):
GCATTCGTGCGAGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTACAACCG
AGCCAAATCCCGAAG
Found at i:41443883 original size:48 final size:48
Alignment explanation
Indices: 41443752--41443874 Score: 210
Period size: 48 Copynumber: 2.6 Consensus size: 48
41443742 GTGTCAATGT
* *
41443752 CATGTCCCAGATAGGTCTTACACTAGCTTGTATATCTCGAGGCTGATG
1 CATGTCCCAGATATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
*
41443800 CATGTCCCAGATATATCTTACACTAGCTTGTATATCTCGAGGCCGATG
1 CATGTCCCAGATATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
*
41443848 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGATATGTCTTACACTAGC
41443875 ACACATATCA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (48 bp):
CATGTCCCAGATATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
Found at i:41449029 original size:19 final size:19
Alignment explanation
Indices: 41449005--41449043 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41448995 TGTAGGCAAA
41449005 TTTGGCAATAGTTTGCCTT
1 TTTGGCAATAGTTTGCCTT
*
41449024 TTTGGCAATATTTTGCCTT
1 TTTGGCAATAGTTTGCCTT
41449043 T
1 T
41449044 CTTTTTGTAA
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:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (19 bp):
TTTGGCAATAGTTTGCCTT
Found at i:41449453 original size:47 final size:47
Alignment explanation
Indices: 41449381--41449478 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
41449371 ATACTCTCTT
* *
41449381 AATACCAACAATCACATAAGTTGG-TTTTCTATTTCAACAACAACAAC
1 AATACCAACAATCACATAAGCTGGTTTTTC-ATTTAAACAACAACAAC
* * **
41449428 AATACCAGCTATCACATAAGCTGGTTTTTCATTTAAACAACAGGAAC
1 AATACCAACAATCACATAAGCTGGTTTTTCATTTAAACAACAACAAC
41449475 AATA
1 AATA
41449479 TTACAAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
47 39 0.89
48 5 0.11
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (47 bp):
AATACCAACAATCACATAAGCTGGTTTTTCATTTAAACAACAACAAC
Found at i:41451874 original size:20 final size:20
Alignment explanation
Indices: 41451849--41451909 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
41451839 AGAACATACG
41451849 TTTATTATTAATTAGTTTCA
1 TTTATTATTAATTAGTTTCA
41451869 TTTATTATTGTACA-TA-TTTCA
1 TTTATTA-T-TA-ATTAGTTTCA
41451890 TTTATTATTAATTAGTTTCA
1 TTTATTATTAATTAGTTTCA
41451910 GAACATACGT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 13 0.36
21 13 0.36
22 4 0.11
23 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTATTATTAATTAGTTTCA
Found at i:41452204 original size:2 final size:2
Alignment explanation
Indices: 41452197--41452227 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41452187 ATAATAAATT
41452197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41452228 CTAAACCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41457036 original size:8 final size:9
Alignment explanation
Indices: 41457015--41457046 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
41457005 AAATTCGAAT
41457015 TTTTTTCGA
1 TTTTTTCGA
41457024 TTTTTTCGA
1 TTTTTTCGA
41457033 TTTTTTCGA
1 TTTTTTCGA
41457042 GTTTT
1 -TTTT
41457047 GCTCACTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTTTCGA
Found at i:41458245 original size:135 final size:135
Alignment explanation
Indices: 41458097--41458477 Score: 432
Period size: 140 Copynumber: 2.8 Consensus size: 135
41458087 TCTTATTTAA
41458097 ATTTGTATTTTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTTAATTTTTTTAACTTATTA
1 ATTTGTA--TTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTTAATTTTTTTAACTTATTA
* * * * * *
41458162 GTTCTTTAGTTAGATGGTTAGATAGTTGTAATTACATTATTGAGTCTCGAATTTGACTCCTCTCT
64 GTTCTTTTGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGTCTCGAATTCGACTCCTCTAT
*
41458227 TACTTTT
129 TACTTAT
* **
41458234 ATTTGTATTTTTTATTTTATGTTGCTTCAAGCGTTTTAAATTTTTAATTGATGTTTTTTAACATT
1 ATTTGTATTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTT-A---AT-TTTTTTAAC-TT
* * * *
41458299 -TTAATTCTTTTGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGTCTCGAGTTCGATTTCT
60 ATTAGTTCTTTTGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGTCTCGAATTCGACTCCT
41458363 CTATTACTTAT
125 CTATTACTTAT
* * * * *
41458374 ATTTGTA-TTTTT-TTTCATGTTGCTTCAATTTTTTTTAA---TTAATATTTTTAACATATTAGC
1 ATTTGTATTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTTAATTTTTTTAACTTATTAGT
* * * *
41458434 TCATTTTGTTAGATGGTTAGATAATTACGATTACATCATTGAGT
66 TC-TTTTGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGT
41458478 ATGAGGTTTA
Statistics
Matches: 209, Mismatches: 27, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
129 1 0.00
130 13 0.06
131 39 0.19
134 1 0.00
135 37 0.18
136 1 0.00
137 7 0.03
138 21 0.10
139 7 0.03
140 80 0.38
141 2 0.01
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (135 bp):
ATTTGTATTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTTAATTTTTTTAACTTATTAGT
TCTTTTGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGTCTCGAATTCGACTCCTCTATTA
CTTAT
Found at i:41458599 original size:15 final size:16
Alignment explanation
Indices: 41458570--41458603 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41458560 TTTATGATAT
*
41458570 TTTTTAATTATTTTTA
1 TTTTTAACTATTTTTA
41458586 TTTTTAACTA-TTTTA
1 TTTTTAACTATTTTTA
41458601 TTT
1 TTT
41458604 ATAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAACTATTTTTA
Found at i:41466283 original size:44 final size:44
Alignment explanation
Indices: 41466218--41466303 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
41466208 TTGATATCTC
* *
41466218 AAAGTCCATGGTTGTACCATGGCGA-TTAAGGAAGAATTGACGAA
1 AAAGTCCATGGTTATAACATGGC-ATTTAAGGAAGAATTGACGAA
*
41466262 AAAGTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGACG
1 AAAGTCCATGGTT-ATAACATGGCATTTAAGGAAGAATTGACG
41466304 GTTAAGGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCATTTAAGGAAGAATTGACGAA
Found at i:41466623 original size:55 final size:54
Alignment explanation
Indices: 41466494--41466690 Score: 236
Period size: 54 Copynumber: 3.6 Consensus size: 54
41466484 TTGGTAAGAT
* * *
41466494 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * * * *
41466548 AAGGAAATCATATAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGAA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGG-C
* * **
41466604 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGGGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
41466656 AAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCA
41466691 ATGGTAAGTT
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
52 4 0.03
53 32 0.26
54 41 0.34
55 40 0.33
56 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:41475943 original size:29 final size:29
Alignment explanation
Indices: 41475909--41475966 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
41475899 CCACTGGTAG
*
41475909 GTCGAATCTCTCAAGAGCTATACTGCACA
1 GTCGAATCTCTCAAAAGCTATACTGCACA
41475938 GTCGAATCTCTCAAAAGCTATACTGCACA
1 GTCGAATCTCTCAAAAGCTATACTGCACA
41475967 TTTCATGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (29 bp):
GTCGAATCTCTCAAAAGCTATACTGCACA
Found at i:41477945 original size:16 final size:17
Alignment explanation
Indices: 41477914--41477946 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41477904 TCCATAAGTA
41477914 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
41477931 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
41477947 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:41478294 original size:46 final size:47
Alignment explanation
Indices: 41478232--41478551 Score: 377
Period size: 46 Copynumber: 7.0 Consensus size: 47
41478222 TTTGACATGA
* * * * *
41478232 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGT
* * * * *
41478278 TGCCATGGTATTTTTCAACCATGGTCTTATTCA-TTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGT
* * *** *
41478324 TGCCATGGTATCTTTCAACCATTGTCTTATTCA-TTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGT
* *
41478370 TGTCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGT
* *
41478416 TACCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGT
41478462 TGCCATGGTATCTTTCAACCATGGTCTTA--CATATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCAT-TTTCATATCAGGT
* *
41478508 TGTCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAG
41478552 AGAGCACACT
Statistics
Matches: 244, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
44 2 0.01
45 4 0.02
46 236 0.97
48 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCAGGT
Found at i:41478389 original size:92 final size:92
Alignment explanation
Indices: 41478232--41478544 Score: 430
Period size: 92 Copynumber: 3.4 Consensus size: 92
41478222 TTTGACATGA
* * * * *
41478232 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATTTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
* * *
41478297 CATGGTCTTATTCATTTCATGTCACGC
66 CATGGTCTTATTCATTTCATATCAGGT
* * * *
41478324 TGCCATGGTATCTTTCAACCATTGTCTTATTCATTTCCCGTCATGTTGTCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
41478389 CATGGTCTTATTCATTTCATATCAGGT
66 CATGGTCTTATTCATTTCATATCAGGT
* * * * *
41478416 TACCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
*
41478481 CATGGTCTTACAT-ATTTCATATCAGGT
66 CATGGTCTTA-TTCATTTCATATCAGGT
* *
41478508 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTC
41478545 ATATCAGAGA
Statistics
Matches: 196, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
92 195 0.99
93 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTATTCATTTCATATCAGGT
Found at i:41478490 original size:138 final size:138
Alignment explanation
Indices: 41478242--41478551 Score: 426
Period size: 138 Copynumber: 2.2 Consensus size: 138
41478232 TGCCATAGTG
* * * * *
41478242 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATTTTTCAACCATGGTCTT
1 TCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTACCATGGTATCTTTCAACCATGGTCTT
** * * * * * *
41478306 ATTCATTTCATGTCACGCTGCCATGGTATCTTTCAACCATTGTCTTA-TTCATTTCCCGTCATGT
65 ACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACAT-ATTTCACATCAGGT
41478370 TGTCATGGTA
129 TGTCATGGTA
*
41478380 TCTTTCAACCATGGTCTTATTCATTTCATATCAGGTTACCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTACCATGGTATCTTTCAACCATGGTCTTA
* * *
41478445 CACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAGGTTG
66 CACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACATATTTCACATCAGGTTG
41478510 TCATGGTA
131 TCATGGTA
*
41478518 TCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TCTTTCAACCATGGTCTTACTCATTTCATATCAG
41478552 AGAGCACACT
Statistics
Matches: 151, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
137 4 0.03
138 146 0.97
139 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (138 bp):
TCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTACCATGGTATCTTTCAACCATGGTCTTA
CACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACATATTTCACATCAGGTTG
TCATGGTA
Found at i:41493477 original size:38 final size:39
Alignment explanation
Indices: 41493386--41493477 Score: 123
Period size: 40 Copynumber: 2.4 Consensus size: 39
41493376 CGGTACCATT
* *
41493386 TGGTGTGTAGGGTTGGATGAGTTGATTATATCCCCATACT
1 TGGTGTGTAGGGTTGGATGAGTCGATTATATCCCCA-ACA
* *
41493426 TGGTGTGTAGGGTTGGATGGGTCGATTCTATCCCC-ACA
1 TGGTGTGTAGGGTTGGATGAGTCGATTATATCCCCAACA
*
41493464 TGGTGTGTTGGGTT
1 TGGTGTGTAGGGTT
41493478 TGACGGAGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 15 0.32
40 32 0.68
ACGTcount: A:0.15, C:0.13, G:0.35, T:0.37
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGATGAGTCGATTATATCCCCAACA
Found at i:41494429 original size:13 final size:13
Alignment explanation
Indices: 41494411--41494436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41494401 GCAGGGGAGA
41494411 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
41494424 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
41494437 GGGGAAAAGA
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:41497253 original size:49 final size:49
Alignment explanation
Indices: 41497197--41497295 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
41497187 GAAGAATGAC
41497197 TTACGGGTAAGATTACATCGTCATCAGAAGCTCATAAAGCTAGTCCTCT
1 TTACGGGTAAGATTACATCGTCATCAGAAGCTCATAAAGCTAGTCCTCT
41497246 TTACGGGTAAGATTACATCGTCATCAGAAGCTCATAAAGCTAGTCCTCT
1 TTACGGGTAAGATTACATCGTCATCAGAAGCTCATAAAGCTAGTCCTCT
41497295 T
1 T
41497296 GAACATGCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (49 bp):
TTACGGGTAAGATTACATCGTCATCAGAAGCTCATAAAGCTAGTCCTCT
Found at i:41497334 original size:21 final size:21
Alignment explanation
Indices: 41497308--41497399 Score: 175
Period size: 21 Copynumber: 4.4 Consensus size: 21
41497298 ACATGCCAAT
*
41497308 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCGTAAGAGCTGAAC
41497329 AGAAGCTCGTAAGAGCTGAAC
1 AGAAGCTCGTAAGAGCTGAAC
41497350 AGAAGCTCGTAAGAGCTGAAC
1 AGAAGCTCGTAAGAGCTGAAC
41497371 AGAAGCTCGTAAGAGCTGAAC
1 AGAAGCTCGTAAGAGCTGAAC
41497392 AGAAGCTC
1 AGAAGCTC
41497400 AAAATAGTTG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (21 bp):
AGAAGCTCGTAAGAGCTGAAC
Found at i:41500222 original size:26 final size:29
Alignment explanation
Indices: 41500193--41500250 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 29
41500183 TTAATAAAGC
* *
41500193 ATATTA-ATAATTTATTATAT-TAT-TAT
1 ATATTAGATAATTAAATATATATATATAT
41500219 ATA-TAGATAATTAAATATATATATATAT
1 ATATTAGATAATTAAATATATATATATAT
41500247 ATAT
1 ATAT
41500251 ATATGTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.08
26 15 0.58
27 3 0.12
28 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
ATATTAGATAATTAAATATATATATATAT
Found at i:41501575 original size:3 final size:3
Alignment explanation
Indices: 41501567--41501610 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
41501557 TATATTGTTC
* *
41501567 TTA TTA TTA CTA TTA TTA TT- TTA CCTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
41501611 TATATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:41501594 original size:15 final size:15
Alignment explanation
Indices: 41501567--41501624 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
41501557 TATATTGTTC
41501567 TTATTATTACTATTA
1 TTATTATTACTATTA
41501582 TTATT-TTACCTATTA
1 TTATTATTA-CTATTA
*
41501597 TTATTATTATTATTTA
1 TTATTATTACTA-TTA
41501613 TATATT-TTACTA
1 T-TATTATTACTA
41501625 CAAATTGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 3 0.08
15 18 0.49
16 12 0.32
17 4 0.11
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATTACTATTA
Found at i:41503346 original size:22 final size:22
Alignment explanation
Indices: 41503318--41503361 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41503308 TCAAGTATTA
41503318 ACCAAATCAACCGTTTGAACAT
1 ACCAAATCAACCGTTTGAACAT
41503340 ACCAAATCAACCGTTTGAACAT
1 ACCAAATCAACCGTTTGAACAT
41503362 TCCTACTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.09, T:0.23
Consensus pattern (22 bp):
ACCAAATCAACCGTTTGAACAT
Found at i:41511990 original size:8 final size:8
Alignment explanation
Indices: 41511977--41512014 Score: 53
Period size: 7 Copynumber: 5.0 Consensus size: 8
41511967 CAATAAATAA
41511977 AAAATATT
1 AAAATATT
41511985 AAAATATT
1 AAAATATT
41511993 -AAATATT
1 AAAATATT
*
41512000 AAAATA-A
1 AAAATATT
41512007 AAAATATT
1 AAAATATT
41512015 TTATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:41512011 original size:15 final size:15
Alignment explanation
Indices: 41511971--41512014 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
41511961 AATTTTCAAT
41511971 AAATAAAAAATATTA
1 AAATAAAAAATATTA
**
41511986 AAATATTAAATATTA
1 AAATAAAAAATATTA
41512001 AAATAAAAAATATT
1 AAATAAAAAATATT
41512015 TTATAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAAAAATATTA
Found at i:41512022 original size:12 final size:12
Alignment explanation
Indices: 41512004--41512038 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
41511994 AATATTAAAA
*
41512004 TAAAAAATATTT
1 TAAAAAATAATT
*
41512016 TATAAAATAATT
1 TAAAAAATAATT
41512028 TAAAAAATAAT
1 TAAAAAATAAT
41512039 ATGGGCGGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAAAAATAATT
Found at i:41516488 original size:37 final size:37
Alignment explanation
Indices: 41516435--41516537 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
41516425 CGAATAGTCC
* *
41516435 CCACACGTAGTTATCGGGTCTTACCTGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
41516472 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
41516509 CCACACGTAGTCATTGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
41516538 ATATATTTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:41516736 original size:48 final size:48
Alignment explanation
Indices: 41516678--41518303 Score: 2892
Period size: 48 Copynumber: 33.9 Consensus size: 48
41516668 ATATACACAC
* *
41516678 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41516726 ATCTCATACATATTTCACACTAGCCATTTGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41516774 ATCTCATTCATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41516822 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41516870 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41516918 ATCTCATTCATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41516966 ATCTCATTCATATTTCACATTAGCCATTCGGTTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517014 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517062 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41517110 ATCTCATACATATTTCACACTAGCCATTTGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517158 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41517206 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517254 ATCTCATTCATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517302 ATCTCATTCATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517350 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41517398 ATCTCATACATATTTCACACTAGCCATTTGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41517446 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517494 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517542 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517590 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517638 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517686 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517734 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517782 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41517830 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517878 ATCTCATTCATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41517926 ATCTCATTCATATTTCACATTAGCCATTCGGTTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41517974 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41518022 ATCTCATACATATTTCACACTAGCCATTTGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41518070 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41518118 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41518166 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41518214 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41518262 ATCTCATACATATTTCACAGTAGCCATTCGGCTTTACCACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACAT
41518304 TAGCCATTCG
Statistics
Matches: 1522, Mismatches: 56, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 1522 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:41518307 original size:22 final size:22
Alignment explanation
Indices: 41518277--41518324 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
41518267 ATACATATTT
41518277 CACAGTAGCCATTCGGCTTTAC
1 CACAGTAGCCATTCGGCTTTAC
*
41518299 CACATTAGCCATTCGGCTTTAC
1 CACAGTAGCCATTCGGCTTTAC
41518321 CACA
1 CACA
41518325 CACATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (22 bp):
CACAGTAGCCATTCGGCTTTAC
Found at i:41519424 original size:2 final size:2
Alignment explanation
Indices: 41519419--41519444 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41519409 ATATTCACAC
41519419 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41519445 TATGCCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41522542 original size:23 final size:22
Alignment explanation
Indices: 41522516--41522571 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
41522506 TTTTTAGAGA
* * *
41522516 ATTAAAATTAAATTGTAATTTGT
1 ATTAAAATTAAAATATAATTT-C
* *
41522539 ATTATAATAAAAATATAATTTC
1 ATTAAAATTAAAATATAATTTC
41522561 ATTAAAATTAA
1 ATTAAAATTAA
41522572 GTTTTTATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (22 bp):
ATTAAAATTAAAATATAATTTC
Found at i:41523551 original size:18 final size:19
Alignment explanation
Indices: 41523507--41523569 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 19
41523497 AAAAATATAT
* *
41523507 TAAAAATTCTACAAAGTAAA
1 TAAAAATTATA-AAAGTTAA
41523527 TAAAAATTATAAAAGTTAA
1 TAAAAATTATAAAAGTTAA
* *
41523546 -AAAAATAATATAA-TTAA
1 TAAAAATTATAAAAGTTAA
41523563 TAAAAAT
1 TAAAAAT
41523570 GATAGAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 4 0.11
18 17 0.45
19 7 0.18
20 10 0.26
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
TAAAAATTATAAAAGTTAA
Found at i:41523962 original size:29 final size:27
Alignment explanation
Indices: 41523900--41523959 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
41523890 TTATTTTATA
* *
41523900 ATTTATTTTTAAATTTTTATAGTTTTT
1 ATTTGTTTTTAAATTTTTATAATTTTT
41523927 ATTTGTTTTTAGAATTTTTAATATATTTTT
1 ATTTGTTTTTA-AATTTTT-ATA-ATTTTT
41523957 ATT
1 ATT
41523960 GTTAATACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.36
28 7 0.25
29 3 0.11
30 8 0.29
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (27 bp):
ATTTGTTTTTAAATTTTTATAATTTTT
Found at i:41526412 original size:13 final size:13
Alignment explanation
Indices: 41526394--41526420 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41526384 GTAATGAGAG
41526394 TATAAATGTTTTT
1 TATAAATGTTTTT
41526407 TATAAATGTTTTT
1 TATAAATGTTTTT
41526420 T
1 T
41526421 CTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TATAAATGTTTTT
Found at i:41532624 original size:2 final size:2
Alignment explanation
Indices: 41532617--41532649 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41532607 TTAAAAGGAA
41532617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41532650 AACATGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41532827 original size:13 final size:15
Alignment explanation
Indices: 41532802--41532833 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41532792 AAACAATTTA
41532802 AAAATATAC-AAAAG
1 AAAATATACAAAAAG
41532816 AAAATA-ACAAAAAG
1 AAAATATACAAAAAG
41532830 AAAA
1 AAAA
41532834 AAAGCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAATATACAAAAAG
Found at i:41539422 original size:131 final size:131
Alignment explanation
Indices: 41539277--41539578 Score: 331
Period size: 132 Copynumber: 2.3 Consensus size: 131
41539267 TTGTCTGCTT
* * * * *
41539277 AAAACAATCAAATATCCCTTCAAAATTGCACTCATATCTT-TTAAAAATCCTTT-AAAATAGAGG
1 AAAACAATCGAATATCCCTTCAGAATTTCACTCATAT-TTATTAAAAA-CCTTTCAAAACAAAGG
* * * *
41539340 CAATACTCGGGGTTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCATTTG
64 CAATACTCGAGGTTTGACAATTCGAGAATCATGCCCTATCGTGCTGGGTTGTAATCTCTCATTTG
41539405 TTC
129 TTC
** * *
41539408 AAAACAATCGAATATTCCCTT-AGGTTTTTTACTCATGTTTATTAAAAACCTTTCAAAACAAAGG
1 AAAACAATCGAATA-TCCCTTCA-GAATTTCACTCATATTTATTAAAAACCTTTCAAAACAAAGG
** ** * * * * *
41539472 TTATGTTTGATGTTTGGCAATTCGAGAATCGTGCCCTATCGTGCTGGGTTGTAATCTCTCTTTTG
64 CAATACTCGAGGTTTGACAATTCGAGAATCATGCCCTATCGTGCTGGGTTGTAATCTCTCATTTG
41539537 TTC
129 TTC
* *
41539540 AAAACAATCGAATATCTCTTCGGAATTTCACTCATATTT
1 AAAACAATCGAATATCCCTTCAGAATTTCACTCATATTT
41539579 TCTAAGGTGA
Statistics
Matches: 138, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
131 39 0.28
132 99 0.72
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (131 bp):
AAAACAATCGAATATCCCTTCAGAATTTCACTCATATTTATTAAAAACCTTTCAAAACAAAGGCA
ATACTCGAGGTTTGACAATTCGAGAATCATGCCCTATCGTGCTGGGTTGTAATCTCTCATTTGTT
C
Found at i:41546456 original size:2 final size:2
Alignment explanation
Indices: 41546449--41546481 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
41546439 ATACTTTTAC
*
41546449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41546482 AGATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:41546757 original size:7 final size:7
Alignment explanation
Indices: 41546745--41546769 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41546735 TTATATGACA
41546745 AAGCATT
1 AAGCATT
41546752 AAGCATT
1 AAGCATT
41546759 AAGCATT
1 AAGCATT
41546766 AAGC
1 AAGC
41546770 TCATATATAC
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (7 bp):
AAGCATT
Found at i:41547427 original size:3 final size:3
Alignment explanation
Indices: 41547419--41547459 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
41547409 CATAAACCTT
*
41547419 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41547460 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41552435 original size:22 final size:22
Alignment explanation
Indices: 41552407--41552455 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
41552397 ACAACTCAGA
*
41552407 GCTCGCATCAAATTACAACAGG
1 GCTCGCATCAAAATACAACAGG
* *
41552429 GCTCGCATGAAAATATAACAGG
1 GCTCGCATCAAAATACAACAGG
41552451 GCTCG
1 GCTCG
41552456 TATGCACACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (22 bp):
GCTCGCATCAAAATACAACAGG
Found at i:41552775 original size:14 final size:15
Alignment explanation
Indices: 41552756--41552788 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
41552746 AACTGCAACC
41552756 CTTTTCTTACGCT-A
1 CTTTTCTTACGCTAA
41552770 CTTTTCTTACGCTAA
1 CTTTTCTTACGCTAA
41552785 CTTT
1 CTTT
41552789 GATAGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.15, C:0.27, G:0.06, T:0.52
Consensus pattern (15 bp):
CTTTTCTTACGCTAA
Found at i:41558270 original size:2 final size:2
Alignment explanation
Indices: 41558263--41558295 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41558253 TTAAAGAGAA
41558263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41558296 AAAGATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41558369 original size:13 final size:13
Alignment explanation
Indices: 41558351--41558382 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41558341 TTGTTAAACT
41558351 AGAAACCTTTTAC
1 AGAAACCTTTTAC
41558364 AGAAACCTTTTAC
1 AGAAACCTTTTAC
41558377 AGAAAC
1 AGAAAC
41558383 AAAATAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (13 bp):
AGAAACCTTTTAC
Found at i:41560293 original size:16 final size:17
Alignment explanation
Indices: 41560261--41560295 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41560251 TAATACAAGA
*
41560261 AATAATATATGAAAAGT
1 AATAATATATAAAAAGT
41560278 AATAATATA-AAAAAGT
1 AATAATATATAAAAAGT
41560294 AA
1 AA
41560296 AACAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
AATAATATATAAAAAGT
Found at i:41562451 original size:206 final size:206
Alignment explanation
Indices: 41562073--41563041 Score: 1418
Period size: 206 Copynumber: 4.7 Consensus size: 206
41562063 AAATCTGCTT
* * *
41562073 CTTCGATTTGTT-TCCGGACAATGCAGAGATGCCAAATCATCTTAGATTTGCTTCAGCATAAGCA
1 CTTCGATTTGTTCT-CTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCA
* *
41562137 CGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCTTTGTAAGCATAAGGATACCAAACCATCT
65 CGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCT
* * * ** * *
41562202 TGGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATTTGCTATGTGTCTGCCCTCCGTCAAATAT
130 TGGATCTGCTTCAGTATAAACATATGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
41562267 GGAGACGCCAAA
195 GGAGACGCCAAA
* * *
41562279 CTTCGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAT
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
*
41562344 GCGAAAACCAAATCAGCTATGTCTTAGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
* *
41562409 GGATCTGCTTCAGTATAAACATATGAAGGCCAGATCTGCTATGTGTCTGCTCTCTGTCGAATATG
131 GGATCTGCTTCAGTATAAACATATGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
*
41562474 GAGACGCCAAG
196 GAGACGCCAAA
* * * *
41562485 CTTTGATTTGTTATCTGACAATACAGATATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
*
41562550 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAATGATACCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
* * * * ** * * * * *
41562615 GGATCTGCTTTAGTCTAATCATCTGAAGGTTAAATCTACTATGTGTCTGCCTTCTGTCGAATATA
131 GGATCTGCTTCAGTATAAACATATGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
41562680 GAGACGCCAAA
196 GAGACGCCAAA
* * * **
41562691 CTTCAATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGTTTCATTGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * * * *
41562756 GTGAAAGCCAAATCAGCTATGTCTTCGATTTTGTTCCTTGTAAACACAAGGATGCCAAATCATCT
66 GCGAAAACCAAATCAGCTATGTCTTCGA-TTTGCTCCTTGTAAGCACAAGGATACCAAACCATCT
* *
41562821 TGGATCTGCTTCAGTATAAACATATGAAGGCCAGATCTGCTATGTGTCTGCTCTCCGTTGAATAT
130 TGGATCTGCTTCAGTATAAACATATGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
41562886 GGAGACGCCAAA
195 GGAGACGCCAAA
* *
41562898 CTTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * *
41562963 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
41563028 GGATCTTGCTTCAG
131 GGATC-TGCTTCAG
41563042 CCAGATCTGC
Statistics
Matches: 688, Mismatches: 72, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
206 494 0.72
207 194 0.28
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
GGATCTGCTTCAGTATAAACATATGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
GAGACGCCAAA
Found at i:41563939 original size:22 final size:22
Alignment explanation
Indices: 41563913--41563956 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41563903 TTCACCATGG
41563913 CCTCTCCATTT-TTCTCTTTTTT
1 CCTCTCC-TTTCTTCTCTTTTTT
* *
41563935 CCTCTTCTTTCTTTTCTTTTTT
1 CCTCTCCTTTCTTCTCTTTTTT
41563957 TTTTCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (22 bp):
CCTCTCCTTTCTTCTCTTTTTT
Found at i:41575044 original size:20 final size:21
Alignment explanation
Indices: 41575005--41575058 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
41574995 TGTTATAAAA
*
41575005 ATAATATATATATTAAATAAG
1 ATAATATATATAATAAATAAG
* *
41575026 ATAAT-TATATAATATATAAT
1 ATAATATATATAATAAATAAG
*
41575046 ATAAAAGTATATA
1 ATAATA-TATATA
41575059 GGTTTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 16 0.59
21 5 0.19
22 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
ATAATATATATAATAAATAAG
Found at i:41576835 original size:8 final size:8
Alignment explanation
Indices: 41576822--41576848 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41576812 GGCTATTACA
41576822 ACATATAT
1 ACATATAT
41576830 ACATATAT
1 ACATATAT
41576838 ACATATAT
1 ACATATAT
41576846 ACA
1 ACA
41576849 ATAATGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (8 bp):
ACATATAT
Found at i:41578219 original size:28 final size:28
Alignment explanation
Indices: 41578179--41578236 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
41578169 GCTTGTAACA
41578179 GTTTCCTTCATTGGATTTTTGACACATT
1 GTTTCCTTCATTGGATTTTTGACACATT
**
41578207 GTTTCCTTCATTGGATTTTTGTTACATT
1 GTTTCCTTCATTGGATTTTTGACACATT
41578235 GT
1 GT
41578237 CCATTAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (28 bp):
GTTTCCTTCATTGGATTTTTGACACATT
Found at i:41587324 original size:40 final size:41
Alignment explanation
Indices: 41587279--41587445 Score: 164
Period size: 40 Copynumber: 4.2 Consensus size: 41
41587269 CGGAATATAA
*
41587279 CCGGATATAATCAAGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
41587319 CCGGATAGAAT-AACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41587359 CCGGATGT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41587399 CCGGATATAAT-TTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
41587438 CCGGATAT
1 CCGGATAT
41587446 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
39 17 0.16
40 87 0.83
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (41 bp):
CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41588293 original size:17 final size:19
Alignment explanation
Indices: 41588270--41588315 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
41588260 AAGAAGCATG
41588270 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
41588288 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
41588306 AATCATGCTC
1 AATCATGCTC
41588316 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:41595331 original size:40 final size:40
Alignment explanation
Indices: 41595286--41595452 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
41595276 CGGAATATAA
41595286 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41595326 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
41595366 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41595406 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41595445 CCGGATAT
1 CCGGATAT
41595453 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41596294 original size:17 final size:19
Alignment explanation
Indices: 41596271--41596316 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
41596261 AAGAAGCATG
41596271 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
41596289 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
41596307 AATCATGCTC
1 AATCATGCTC
41596317 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:41596802 original size:8 final size:8
Alignment explanation
Indices: 41596789--41596819 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
41596779 TCCATGCTCA
41596789 TTTTTTTC
1 TTTTTTTC
41596797 TTTTTTTC
1 TTTTTTTC
41596805 TTTTTTT-
1 TTTTTTTC
41596812 TTTTTTTC
1 TTTTTTTC
41596820 CATTTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:41596810 original size:15 final size:15
Alignment explanation
Indices: 41596790--41596819 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41596780 CCATGCTCAT
41596790 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
*
41596805 TTTTTTTTTTTTTTC
1 TTTTTTCTTTTTTTC
41596820 CATTTCTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:41598466 original size:12 final size:12
Alignment explanation
Indices: 41598449--41598473 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41598439 TCAATTTCTA
41598449 TATATATATATT
1 TATATATATATT
41598461 TATATATATATT
1 TATATATATATT
41598473 T
1 T
41598474 TAAATGTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATATATT
Found at i:41600505 original size:25 final size:25
Alignment explanation
Indices: 41600468--41600518 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
41600458 TCAAACATGC
41600468 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTT-ACCCTAGGGGT
* *
41600494 ATTTCGGT-AATTTATCCTAGGGGT
1 ATTTAGGTCAATTTACCCTAGGGGT
41600518 A
1 A
41600519 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 11 0.48
25 5 0.22
26 7 0.30
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (25 bp):
ATTTAGGTCAATTTACCCTAGGGGT
Found at i:41602055 original size:26 final size:26
Alignment explanation
Indices: 41601999--41602079 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
41601989 TGAAATTCCC
41601999 ATCATGGAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATT
41602024 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41602050 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41602076 ATCA
1 ATCA
41602080 ATTTGTACCA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 20 0.36
26 35 0.64
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:41607531 original size:25 final size:26
Alignment explanation
Indices: 41607494--41607545 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
41607484 TCAAACATGC
41607494 ATTTAGGTCAA-TTTAACCCTAGGGGT
1 ATTTAGGTCAATTTTAA-CCTAGGGGT
* *
41607520 ATTTCGGT-AATTTTTACCTAGGGGT
1 ATTTAGGTCAATTTTAACCTAGGGGT
41607545 A
1 A
41607546 AACAGTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTTAACCTAGGGGT
Found at i:41609041 original size:26 final size:26
Alignment explanation
Indices: 41609010--41609091 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
41609000 TGAAATTTCC
41609010 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41609036 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41609062 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41609088 ATCA
1 ATCA
41609092 ATTTGTACCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:41612969 original size:21 final size:22
Alignment explanation
Indices: 41612910--41612973 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
41612900 CAGAAGCAGT
* *
41612910 ATACGACACATAAAGTGCTTGA
1 ATACGACACATATAGTGCCTGA
** *
41612932 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
41612952 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
41612974 TCGGCAAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:41613934 original size:7 final size:7
Alignment explanation
Indices: 41613922--41613980 Score: 118
Period size: 7 Copynumber: 8.4 Consensus size: 7
41613912 TTACTTTACT
41613922 ATATATA
1 ATATATA
41613929 ATATATA
1 ATATATA
41613936 ATATATA
1 ATATATA
41613943 ATATATA
1 ATATATA
41613950 ATATATA
1 ATATATA
41613957 ATATATA
1 ATATATA
41613964 ATATATA
1 ATATATA
41613971 ATATATA
1 ATATATA
41613978 ATA
1 ATA
41613981 AAACATAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:41614434 original size:22 final size:23
Alignment explanation
Indices: 41614406--41614455 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
41614396 TTATTTAATA
41614406 ATAATAAT-TTTA-ATATAAAAT
1 ATAATAATATTTATATATAAAAT
*
41614427 CATAATAATATTTATATATAATAT
1 -ATAATAATATTTATATATAAAAT
41614451 ATAAT
1 ATAAT
41614456 CGAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 9 0.36
24 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAATAATATTTATATATAAAAT
Found at i:41614631 original size:20 final size:19
Alignment explanation
Indices: 41614585--41614631 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
41614575 AGTCCTTTTT
*
41614585 CCTAATTTCTCCTAATTAAG
1 CCTAA-TTCACCTAATTAAG
41614605 -CTAAATTCACCTAATTAAAG
1 CCT-AATTCACCTAATT-AAG
41614625 CCTAATT
1 CCTAATT
41614632 AAATATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (19 bp):
CCTAATTCACCTAATTAAG
Found at i:41615826 original size:4 final size:4
Alignment explanation
Indices: 41615817--41615852 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
41615807 CTATTTTAAT
41615817 TTTA TTTA TTTA TTTA -TTA -TTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
41615853 ATTATTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:41615839 original size:18 final size:18
Alignment explanation
Indices: 41615818--41615863 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
41615808 TATTTTAATT
41615818 TTATTTATTTATTTATTA
1 TTATTTATTTATTTATTA
41615836 TTATTTATTTATTTATTA
1 TTATTTATTTATTTATTA
*
41615854 TTATTCATTT
1 TTATTTATTT
41615864 TCTGATCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTATTTATTTATTA
Found at i:41615858 original size:14 final size:15
Alignment explanation
Indices: 41615817--41615855 Score: 62
Period size: 14 Copynumber: 2.6 Consensus size: 15
41615807 CTATTTTAAT
41615817 TTTATTTATTTATTTA
1 TTTA-TTATTTATTTA
41615833 -TTATTATTTATTTA
1 TTTATTATTTATTTA
41615847 TTTATTATT
1 TTTATTATT
41615856 ATTCATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:41616017 original size:3 final size:3
Alignment explanation
Indices: 41615992--41616101 Score: 184
Period size: 3 Copynumber: 36.7 Consensus size: 3
41615982 CTCTAGCTCT
* * * *
41615992 TTA TCA TTA TCA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41616040 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41616088 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
41616102 CTATACATGT
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:41619067 original size:14 final size:14
Alignment explanation
Indices: 41619048--41619100 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
41619038 TACTATATAT
41619048 ATAATATAATAATA
1 ATAATATAATAATA
* *
41619062 ATAATATAGTATCTA
1 ATAATATAATA-ATA
41619077 AT-ATATAATAATA
1 ATAATATAATAATA
*
41619090 A-AACATAATAA
1 ATAATATAATAA
41619101 ATATCTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.34
14 17 0.53
15 4 0.12
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (14 bp):
ATAATATAATAATA
Found at i:41619106 original size:31 final size:33
Alignment explanation
Indices: 41619044--41619106 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
41619034 ACTTTACTAT
*
41619044 ATATATAATATAATAATAATAATATAGTATCTA
1 ATATATAATATAATAATAATAATATAATATCTA
*
41619077 ATATATAATAATAA-AA-CATAATA-AATATCT
1 ATATATAAT-ATAATAATAATAATATAATATCT
41619107 TTATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.22
32 6 0.22
33 11 0.41
34 4 0.15
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (33 bp):
ATATATAATATAATAATAATAATATAATATCTA
Found at i:41633814 original size:65 final size:66
Alignment explanation
Indices: 41633704--41633859 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 66
41633694 TGTATATATG
** * * *
41633704 TAAGACCATAGTTGGGTTATGGCATATTGATGATAAGACTGTAGCT-GACTATAGCATTCTAATG
1 TAAGACCATAGCGGGGCTATGGCATACTGATGATAAGACTATAGCTGGACTATAGCATTCTAATG
41633768 A
66 A
* * * * *
41633769 TAAGACCATAGCGGGGCTATGTCATACTGATGATAAGAAC-ATAGCTGGGCTCTGGCATTCTGAT
1 TAAGACCATAGCGGGGCTATGGCATACTGATGATAAG-ACTATAGCTGGACTATAGCATTCTAAT
41633833 GA
65 GA
* * * *
41633835 TAAGGCCATAACCGGGTTATGGCAT
1 TAAGACCATAGCGGGGCTATGGCAT
41633860 TATGAACGTA
Statistics
Matches: 74, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
65 37 0.50
66 37 0.50
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (66 bp):
TAAGACCATAGCGGGGCTATGGCATACTGATGATAAGACTATAGCTGGACTATAGCATTCTAATG
A
Found at i:41633858 original size:33 final size:33
Alignment explanation
Indices: 41633704--41633860 Score: 129
Period size: 33 Copynumber: 4.8 Consensus size: 33
41633694 TGTATATATG
** *
41633704 TAAGACCATAGTTGGGTTATGGCATAT-TGATGA
1 TAAGACCATAGCCGGGCTATGGCAT-TCTGATGA
** * * * *
41633737 TAAGACTGTAG-CTGACTATAGCATTCTAATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTGATGA
* * *
41633769 TAAGACCATAGCGGGGCTATGTCATACTGATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTGATGA
* * *
41633802 TAAGAACATAGCTGGGCTCTGGCATTCTGATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTGATGA
* * *
41633835 TAAGGCCATAACCGGGTTATGGCATT
1 TAAGACCATAGCCGGGCTATGGCATT
41633861 ATGAACGTAA
Statistics
Matches: 94, Mismatches: 28, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
31 1 0.01
32 22 0.23
33 71 0.76
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (33 bp):
TAAGACCATAGCCGGGCTATGGCATTCTGATGA
Found at i:41636540 original size:2 final size:2
Alignment explanation
Indices: 41636533--41636572 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
41636523 ATGATTTGTG
41636533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41636573 GTAAGTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41652738 original size:5 final size:5
Alignment explanation
Indices: 41652728--41652758 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
41652718 AAAGCAAAAG
41652728 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA G
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA G
41652759 GGACGAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:41653175 original size:18 final size:17
Alignment explanation
Indices: 41653157--41653189 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41653147 TATGATGATT
41653157 TTTTA-ATATAAAAATA
1 TTTTATATATAAAAATA
*
41653173 TTTTATATATTAAAATA
1 TTTTATATATAAAAATA
41653190 ATAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTATATATAAAAATA
Found at i:41653393 original size:14 final size:14
Alignment explanation
Indices: 41653370--41653403 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41653360 AACTTATGAT
41653370 AAATTATTATAAAA
1 AAATTATTATAAAA
* *
41653384 AAATTTTTATATAA
1 AAATTATTATAAAA
41653398 AAATTA
1 AAATTA
41653404 AATTAAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTATTATAAAA
Found at i:41654648 original size:2 final size:2
Alignment explanation
Indices: 41654641--41654678 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41654631 TGAAAAAGCC
41654641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41654679 CAAGCTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41656855 original size:21 final size:21
Alignment explanation
Indices: 41656831--41656875 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41656821 CCAATCAATT
* * *
41656831 AACCTATTCAAAATATGATAA
1 AACCTACTAAAAACATGATAA
*
41656852 AACCTACTAAAAACATGCTAA
1 AACCTACTAAAAACATGATAA
41656873 AAC
1 AAC
41656876 AATCATCTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.22
Consensus pattern (21 bp):
AACCTACTAAAAACATGATAA
Found at i:41658829 original size:13 final size:14
Alignment explanation
Indices: 41658806--41658834 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41658796 ATGTCTACTC
41658806 TTCTCTTCTTTCTT
1 TTCTCTTCTTTCTT
41658820 TTCT-TTCTTTCTT
1 TTCTCTTCTTTCTT
41658833 TT
1 TT
41658835 ATTTTGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTCTTCTTTCTT
Found at i:41668173 original size:19 final size:21
Alignment explanation
Indices: 41668132--41668179 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
41668122 TTAAAATTTT
41668132 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
41668153 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
41668172 AACTAAAA
1 AACTAAAA
41668180 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:41671919 original size:8 final size:8
Alignment explanation
Indices: 41671906--41671976 Score: 62
Period size: 8 Copynumber: 9.4 Consensus size: 8
41671896 TATTGATTAA
41671906 TTTTAAAT
1 TTTTAAAT
*
41671914 TTTTAAGT
1 TTTTAAAT
* *
41671922 TTTTTAGT
1 TTTTAAAT
41671930 TTTTAAA-
1 TTTTAAAT
41671937 -TTTAAAT
1 TTTTAAAT
*
41671944 TTTT-TAT
1 TTTTAAAT
41671951 TTTTAAA-
1 TTTTAAAT
41671958 TTTT-AAT
1 TTTTAAAT
41671965 TTTTAATAT
1 TTTTAA-AT
41671974 TTT
1 TTT
41671977 AATTTTAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 8 0.16
7 14 0.27
8 24 0.47
9 5 0.10
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (8 bp):
TTTTAAAT
Found at i:41671989 original size:7 final size:7
Alignment explanation
Indices: 41671902--41671989 Score: 88
Period size: 7 Copynumber: 12.3 Consensus size: 7
41671892 CCACTATTGA
41671902 TTAATTT
1 TTAATTT
*
41671909 TAAATTT
1 TTAATTT
41671916 TTAAGTTTT
1 TTAA--TTT
*
41671925 TTAGTTT
1 TTAATTT
*
41671932 TTAAATT
1 TTAATTT
*
41671939 TAAATTT
1 TTAATTT
*
41671946 TTTATTT
1 TTAATTT
*
41671953 TTAAATT
1 TTAATTT
41671960 TTAATTT
1 TTAATTT
41671967 TTAATATT
1 TTAAT-TT
41671975 TTAA-TT
1 TTAATTT
41671981 TTAATTT
1 TTAATTT
41671988 TT
1 TT
41671990 GAGTTTATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
6 6 0.09
7 47 0.72
8 6 0.09
9 6 0.09
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (7 bp):
TTAATTT
Found at i:41672913 original size:41 final size:41
Alignment explanation
Indices: 41672847--41672994 Score: 197
Period size: 41 Copynumber: 3.6 Consensus size: 41
41672837 AGGGTTATAT
* *
41672847 GACTTTTAGCGGCGTTGTACTAAAAGCGCCACTATTGCTCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* * * *
41672888 GACTTTTAGTGGTGTTTTAGCAAAAGCGCCGCTATTGCTCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* **
41672929 GACTTTTAGCGGCGTTTTACCAAAAACGCCACTATTGCTTT
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* *
41672970 GACTTTTAGCAGCGTTTTAACAAAA
1 GACTTTTAGCGGCGTTTTACCAAAA
41672995 AACACCGCTA
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
Found at i:41672987 original size:82 final size:83
Alignment explanation
Indices: 41672847--41673028 Score: 224
Period size: 82 Copynumber: 2.2 Consensus size: 83
41672837 AGGGTTATAT
* * * ** * *
41672847 GACTTTTAGCGGCGTTGTACTAAAAGCGCCACTATTGCTCCGACTTTTAGTGGTGTTTTAGC-AA
1 GACTTTTAGCGGCGTTTTACCAAAAACGCCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
* *
41672911 AAGCGCCGCTATTGCTCC
66 AAACACCGCTATTGCTCC
**
41672929 GACTTTTAGCGGCGTTTTACCAAAAACGCCACTATTGCTTTGACTTTTAGCAGCGTTTTAACAAA
1 GACTTTTAGCGGCGTTTTACCAAAAACGCCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
*
41672994 AAACACCGCTATTGCTCT
66 AAACACCGCTATTGCTCC
* *
41673012 G-TTTTTAGCGGCATTTT
1 GACTTTTAGCGGCGTTTT
41673029 TAGTAGAACA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
82 67 0.79
83 18 0.21
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (83 bp):
GACTTTTAGCGGCGTTTTACCAAAAACGCCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
AAACACCGCTATTGCTCC
Found at i:41673009 original size:42 final size:40
Alignment explanation
Indices: 41672847--41673028 Score: 186
Period size: 41 Copynumber: 4.5 Consensus size: 40
41672837 AGGGTTATAT
* *
41672847 GACTTTTAGCGGCGTTGTACTAAAAGCGCCACTATTGCTCC
1 GACTTTTAGCGGCGTTTTAC-AAAAACGCCACTATTGCTCC
* * * *
41672888 GACTTTTAGTGGTGTTTTAGCAAAAGCGCCGCTATTGCTCC
1 GACTTTTAGCGGCGTTTTA-CAAAAACGCCACTATTGCTCC
**
41672929 GACTTTTAGCGGCGTTTTACCAAAAACGCCACTATTGCTTT
1 GACTTTTAGCGGCGTTTTA-CAAAAACGCCACTATTGCTCC
* * * *
41672970 GACTTTTAGCAGCGTTTTAACAAAAAACACCGCTATTGCTCT
1 GACTTTTAGCGGCGTTTT-AC-AAAAACGCCACTATTGCTCC
* *
41673012 G-TTTTTAGCGGCATTTT
1 GACTTTTAGCGGCGTTTT
41673029 TAGTAGAACA
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
41 100 0.83
42 20 0.17
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (40 bp):
GACTTTTAGCGGCGTTTTACAAAAACGCCACTATTGCTCC
Found at i:41673030 original size:42 final size:41
Alignment explanation
Indices: 41672846--41673052 Score: 177
Period size: 41 Copynumber: 5.0 Consensus size: 41
41672836 TAGGGTTATA
* * * * *
41672846 TGACTTTTAGCGGCGTTGTACTAAAAGCGCCACTATTGCTC
1 TGACTTTTAGCGGCGTTTTACAAAAAACACCGCTATTGCTC
* * * * *
41672887 CGACTTTTAGTGGTGTTTTAGC-AAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTA-CAAAAAACACCGCTATTGCTC
* * * * *
41672928 CGACTTTTAGCGGCGTTTTACCAAAAACGCCACTATTGCTT
1 TGACTTTTAGCGGCGTTTTACAAAAAACACCGCTATTGCTC
*
41672969 TGACTTTTAGCAGCGTTTTAACAAAAAACACCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTT-ACAAAAAACACCGCTATTGCTC
* * ** *
41673011 TG-TTTTTAGCGGCATTTTTA-GTAGAACACCGCTATTGCTC
1 TGACTTTTAGCGGC-GTTTTACAAAAAACACCGCTATTGCTC
41673051 TG
1 TG
41673053 TGTTTTACAA
Statistics
Matches: 140, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
40 20 0.14
41 95 0.68
42 25 0.18
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (41 bp):
TGACTTTTAGCGGCGTTTTACAAAAAACACCGCTATTGCTC
Found at i:41680374 original size:3 final size:3
Alignment explanation
Indices: 41680366--41680390 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41680356 ATTTTCAATT
41680366 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
41680391 AAACAATAAG
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:41683425 original size:46 final size:45
Alignment explanation
Indices: 41683307--41683507 Score: 108
Period size: 46 Copynumber: 4.4 Consensus size: 45
41683297 GCCACGTCCT
* *
41683307 AGACATGGTCTTACACTG-ACACATCTCGTAGCCGATGCATATCCC
1 AGACAT-GTCTTACACTGCACTCGTCTCGTAGCCGATGCATATCCC
* * * *
41683352 AGACATGTCTTACATTGGCTTA-T-GTCTCG-AGGCTGATGCATTTTCC
1 AGACATGTCTTACACT-GC--ACTCGTCTCGTA-GCCGATGCATATCCC
* * *
41683398 AGACATGTCTTACACTAGCACTCGTCTC-AATGCCGATGGCATGTCCT
1 AGACATGTCTTACACT-GCACTCGTCTCGTA-GCCGAT-GCATATCCC
* * ** * * * *
41683445 AGACATGGCCTTACACTAGCTCTTATAAT-GTGGCCAATGCATGTCCC
1 AGACAT-GTCTTACACT-GCACTCGT-CTCGTAGCCGATGCATATCCC
41683492 AGACATGTCTTACACT
1 AGACATGTCTTACACT
41683508 AGCCCACAAT
Statistics
Matches: 121, Mismatches: 23, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
44 10 0.08
45 9 0.07
46 54 0.45
47 26 0.21
48 21 0.17
49 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (45 bp):
AGACATGTCTTACACTGCACTCGTCTCGTAGCCGATGCATATCCC
Found at i:41686520 original size:28 final size:27
Alignment explanation
Indices: 41686454--41686523 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
41686444 ATAGTGAGTC
*
41686454 CGCACACTTAGTGCTATATAATCAGCT
1 CGCACACTTAGTGCTATATAATCAACT
* * *
41686481 CGCACACATAGTGCTATATGATCAAATT
1 CGCACACTTAGTGCTATATAATC-AACT
41686509 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41686524 GTACAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:41692023 original size:16 final size:16
Alignment explanation
Indices: 41691968--41692024 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
41691958 TGTCATGTTG
*
41691968 CCATGGTATCTTTCAA
1 CCATGGTATTTTTCAA
* * * *
41691984 CCATGGTCTTGTGCATTG
1 CCATGGTATTTTTCA--A
41692002 CCATGGTATTTTTCAA
1 CCATGGTATTTTTCAA
41692018 CCATGGT
1 CCATGGT
41692025 CTTATTCATT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
CCATGGTATTTTTCAA
Found at i:41692212 original size:46 final size:46
Alignment explanation
Indices: 41691999--41692221 Score: 342
Period size: 46 Copynumber: 4.9 Consensus size: 46
41691989 GTCTTGTGCA
*
41691999 TTGCCATGGTATTTTTCAACCATGGTCTTATTCA-TTC-TCGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT-GTCATG
* *
41692044 TTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
*
41692090 TTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
** *
41692136 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
**
41692182 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
41692222 TTCAGAAAGC
Statistics
Matches: 168, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
45 32 0.19
46 135 0.80
47 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
Found at i:41695293 original size:20 final size:20
Alignment explanation
Indices: 41695268--41695310 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
41695258 GGTTCTAGAA
*
41695268 GTTGCGTTCTGTCTGTTCTT
1 GTTGCGTTCTGTCGGTTCTT
41695288 GTTGCGTTCTGTCGGTTCTT
1 GTTGCGTTCTGTCGGTTCTT
41695308 GTT
1 GTT
41695311 CTATTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.28, T:0.53
Consensus pattern (20 bp):
GTTGCGTTCTGTCGGTTCTT
Found at i:41697183 original size:11 final size:11
Alignment explanation
Indices: 41697167--41697191 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41697157 TGATCTTTGA
41697167 CTTCCGGTGAT
1 CTTCCGGTGAT
41697178 CTTCCGGTGAT
1 CTTCCGGTGAT
41697189 CTT
1 CTT
41697192 TGAGCTAGTT
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:0.08, C:0.28, G:0.24, T:0.40
Consensus pattern (11 bp):
CTTCCGGTGAT
Found at i:41697677 original size:46 final size:46
Alignment explanation
Indices: 41697525--41697789 Score: 242
Period size: 46 Copynumber: 5.7 Consensus size: 46
41697515 GGGTAAGTTA
* *
41697525 CCGATGCCATGTGCCAGACATGGTATTACACTGGCTATCATCATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTA-CATC-TCGA-G
*
41697574 CCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACATCTCGTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTACATCTCG-AG
* * *
41697620 CTGATG-CATGTCCCAGACAT-GACTTACACTGGCTTACGTCTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TACATCTCGA-G
* * * *
41697666 CCGATG-CATGTCCCAGACAT-GTCTTGCACTAGC-ACTCCTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTA--CATCTCGA-G
* * *
41697712 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-ACAT-CTCG-AG
41697760 CCGATG-CATGTCCCAGACAT-GTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
41697790 AGCCCACAAT
Statistics
Matches: 182, Mismatches: 22, Indels: 27
0.79 0.10 0.12
Matches are distributed among these distances:
44 12 0.07
45 15 0.08
46 68 0.37
47 33 0.18
48 20 0.11
49 34 0.19
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (46 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTACATCTCGAG
Found at i:41697764 original size:94 final size:92
Alignment explanation
Indices: 41697526--41697797 Score: 306
Period size: 94 Copynumber: 2.9 Consensus size: 92
41697516 GGTAAGTTAC
* *
41697526 CGATGCCATGTGCCAGACATGGTATTACACTGGCTATCATCATCGAGGCCGATGCCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCAT-ATCGAGGCCGATG-CATGTCCCAG
*
41697591 ACATGGTCTTACACT-G-ACACATCTCGTAG
63 ACAT-GTCTTACACTAGCACACATCTCATAG
* * *
41697620 CTGATG-CATGTCCCAGACAT-GACTTACACTGGCTTACGTCTCGAGGCCGATGCATGTCCCAGA
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATATCGAGGCCGATGCATGTCCCAGA
* * *
41697683 CATGTCTTGCACTAGCACTCCTCTCA-ATG
64 CATGTCTTACACTAGCACACATCTCATA-G
41697712 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GCA-GCCGATGCATGTCCCA
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCAT-ATCG-AGGCCGATGCATGTCCCA
*
41697775 GACATGTCTTACACTAGCCCACA
62 GACATGTCTTACACTAGCACACA
41697798 ATAACCCATA
Statistics
Matches: 151, Mismatches: 16, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
90 9 0.06
91 16 0.11
92 25 0.17
93 29 0.19
94 65 0.43
95 7 0.05
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.25
Consensus pattern (92 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATATCGAGGCCGATGCATGTCCCAGACA
TGTCTTACACTAGCACACATCTCATAG
Found at i:41700148 original size:10 final size:9
Alignment explanation
Indices: 41700133--41700209 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 9
41700123 GAGAACTACC
41700133 AAAATAAAA
1 AAAATAAAA
41700142 TAAAATAAAA
1 -AAAATAAAA
*
41700152 ACAAATAAAC
1 A-AAATAAAA
41700162 AAAATAATAA
1 AAAATAA-AA
*
41700172 AAGAT-AAA
1 AAAATAAAA
*
41700180 GAAAT-AAA
1 AAAATAAAA
*
41700188 TAAAT-AAA
1 AAAATAAAA
*
41700196 TAAATAAAGA
1 AAAATAAA-A
41700206 AAAA
1 AAAA
41700210 GAAATGACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 20 0.36
9 10 0.18
10 26 0.46
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.16
Consensus pattern (9 bp):
AAAATAAAA
Found at i:41700170 original size:27 final size:26
Alignment explanation
Indices: 41700140--41700203 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
41700130 ACCAAAATAA
41700140 AATAAAATAAAAACAAATAAACAAAAT
1 AATAAAATAAAAACAAATAAA-AAAAT
* * * *
41700167 AATAAAAGATAAAGAAATAAATAAAT
1 AATAAAATAAAAACAAATAAAAAAAT
41700193 AA-ATAAATAAA
1 AATA-AAATAAA
41700204 GAAAAAGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.03
26 11 0.37
27 18 0.60
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (26 bp):
AATAAAATAAAAACAAATAAAAAAAT
Found at i:41700190 original size:4 final size:4
Alignment explanation
Indices: 41700154--41700203 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
41700144 AAATAAAAAC
* * *
41700154 AAAT AAAC AAA- ATAAT AAA- AGAT AAAG AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
41700201 AAA
1 AAA
41700204 GAAAAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
3 3 0.08
4 34 0.89
5 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:41700190 original size:12 final size:12
Alignment explanation
Indices: 41700175--41700207 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
41700165 ATAATAAAAG
41700175 ATAAAGAAATAA
1 ATAAAGAAATAA
*
41700187 ATAAATAAATAA
1 ATAAAGAAATAA
41700199 ATAAAGAAA
1 ATAAAGAAA
41700208 AAGAAATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (12 bp):
ATAAAGAAATAA
Found at i:41702003 original size:13 final size:14
Alignment explanation
Indices: 41701985--41702020 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
41701975 ATCCCATCCC
41701985 AAAACAGATACAG-
1 AAAACAGATACAGT
41701998 AAAACAGATACAGT
1 AAAACAGATACAGT
41702012 AATAACAGA
1 AA-AACAGA
41702021 CTAAACATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 2 0.10
15 6 0.29
ACGTcount: A:0.61, C:0.14, G:0.14, T:0.11
Consensus pattern (14 bp):
AAAACAGATACAGT
Found at i:41705761 original size:2 final size:2
Alignment explanation
Indices: 41705756--41705788 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41705746 CATATGTGTG
41705756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41705789 CACAATAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.