Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 127 of 135
Found at i:41493015 original size:29 final size:30
Alignment explanation
Indices: 41492912--41493128 Score: 146
Period size: 29 Copynumber: 7.5 Consensus size: 30
41492902 AAACTTTTCC
* * *
41492912 AAAATTA-CATTTTAACCCTGATTTCACCA
1 AAAATTACCATTTTAACCCCGATTTCATCT
* * *
41492941 AAAATTACTATTTT-ACCCTCGA-ATC-TTT
1 AAAATTACCATTTTAACCC-CGATTTCATCT
* * *
41492969 TAAA-TCCCATTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTAACCCCGATTTCATCT
* ** *
41492998 AAAATTACCATTTTACCCCCGA-AGCTTCT
1 AAAATTACCATTTTAACCCCGATTTCATCT
*** * *
41493027 AAAATTATGTTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTAACCCCGATTTCATCT
* ** * *
41493057 AAAATTACCATTTT-ACCCCTAAATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCATCT
41493086 AAAATT-CCATTTTTAACCCCGATTTCATC-
1 AAAATTACCA-TTTTAACCCCGATTTCATCT
41493115 AAAATTACCATTTT
1 AAAATTACCATTTT
41493129 GCCCTCGGGT
Statistics
Matches: 135, Mismatches: 43, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
27 10 0.07
28 12 0.09
29 66 0.49
30 47 0.35
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCATCT
Found at i:41493061 original size:59 final size:58
Alignment explanation
Indices: 41492912--41493128 Score: 260
Period size: 59 Copynumber: 3.8 Consensus size: 58
41492902 AAACTTTTCC
* * * *
41492912 AAAATTACA-TTTTAACCCTGATTTCACCAAAAATTACTATTTTACCCTCGAATCTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTT
* * * *
41492969 TAAATCCCA-TTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTT-T
*** * **
41493027 AAAATTATGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATC-TTT
*
41493086 AAAATTCCATTTTTAACCCCGATTTCATC-AAAATTACCATTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
41493129 GCCCTCGGGT
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
57 48 0.36
58 19 0.14
59 66 0.49
60 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.37
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTT
Found at i:41497509 original size:3 final size:3
Alignment explanation
Indices: 41497501--41497551 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
41497491 GGAGTGTAAA
41497501 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41497549 AAT
1 AAT
41497552 TAAGAAGTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41497951 original size:13 final size:11
Alignment explanation
Indices: 41497924--41497966 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
41497914 AGTTAAATAT
41497924 TATTTTATTAA
1 TATTTTATTAA
41497935 TATTTTACTTAA
1 TATTTTA-TTAA
*
41497947 -ATATTTATTAT
1 TAT-TTTATTAA
41497958 TATTTTATT
1 TATTTTATT
41497967 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:41500408 original size:17 final size:18
Alignment explanation
Indices: 41500381--41500414 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41500371 ACAACTTTTC
*
41500381 AAAGTAAAAACTAAAAAT
1 AAAGTAAAAACCAAAAAT
41500399 AAAG-AAAAACCAAAAA
1 AAAGTAAAAACCAAAAA
41500415 AAGAGAGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (18 bp):
AAAGTAAAAACCAAAAAT
Found at i:41503070 original size:17 final size:17
Alignment explanation
Indices: 41503043--41503138 Score: 111
Period size: 17 Copynumber: 5.5 Consensus size: 17
41503033 AACTTTTAAT
*
41503043 TTTTAAAATTTTAATTTA
1 TTTT-AAATTTAAATTTA
41503061 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
41503078 TTTTTAAATTTAAATTCA
1 -TTTTAAATTTAAATTTA
* *
41503096 TTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
41503113 CTTTAAATTCAAATTTA
1 TTTTAAATTTAAATTTA
*
41503130 TTCTAAATT
1 TTTTAAATT
41503139 AAAAAAAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
17 46 0.70
18 20 0.30
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:41503091 original size:6 final size:6
Alignment explanation
Indices: 41503048--41503129 Score: 53
Period size: 6 Copynumber: 14.2 Consensus size: 6
41503038 TTAATTTTTA
* * **
41503048 AAATTT TAATTT -ATTTT AAATTT AAATTT ATTTTT AAATTT AAA-TT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * * * *
41503094 CATTTT GAGTTT AAATTT -ACTTT AAATTC AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A
41503130 TTCTAAATTA
Statistics
Matches: 56, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
5 11 0.20
6 45 0.80
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (6 bp):
AAATTT
Found at i:41503947 original size:16 final size:16
Alignment explanation
Indices: 41503918--41503960 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41503908 TAATAATGTT
*
41503918 TAATAATACTACTGTTAC
1 TAATAATA--ACTGTAAC
*
41503936 TAATAATAACTGTAAT
1 TAATAATAACTGTAAC
41503952 TAATAATAA
1 TAATAATAA
41503961 TAATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
18 8 0.35
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (16 bp):
TAATAATAACTGTAAC
Found at i:41503970 original size:19 final size:19
Alignment explanation
Indices: 41503948--41503992 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
41503938 ATAATAACTG
*
41503948 TAATTAATAATAATAATAA
1 TAATAAATAATAATAATAA
* *
41503967 TAATAAATATTGATAATAA
1 TAATAAATAATAATAATAA
*
41503986 TGATAAA
1 TAATAAA
41503993 AAAAGAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
TAATAAATAATAATAATAA
Found at i:41505189 original size:58 final size:59
Alignment explanation
Indices: 41505090--41505487 Score: 368
Period size: 59 Copynumber: 6.8 Consensus size: 59
41505080 TAAACTATCC
* * * *
41505090 AAAAAATATATTTTTACCC-CTAAACTTTCCAAAATTTCATTTTTGACCCTTATTTTTCT
1 AAAAATTATATTTTTACCCTC-GAACTTTCAAAAATTCCATTTTTGACCCTTATTTTTCT
* * * *
41505149 TAAAATTATATTTTTTCCCTCGAACTTT-TAAAATTCCATTTTTGA-CCTCATTTTTTCT
1 AAAAATTATATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCCTTA-TTTTTCT
* * * * * * *
41505207 AAAAATTATATTTTTACCCCCAAACTTTCCAAAATTCAATTTTTAACCATTACTTTTCCT
1 AAAAATTATATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCCTTA-TTTTTCT
* * *
41505267 --AAATTATATTTTTACCC-CAGAACTTTCTAAAATCCCATTTTT-AACCTTGATTTTTCT
1 AAAAATTATATTTTTACCCTC-GAACTTTCAAAAATTCCATTTTTGACCCTT-ATTTTTCT
* * * *
41505324 AAAAATTATATTTTTACCCTTGAA-TTTCCAAAAATTCTATTTTTGA-CCTCGATTTTTCC
1 AAAAATTATATTTTTACCCTCGAACTTT-CAAAAATTCCATTTTTGACCCT-TATTTTTCT
** * * *
41505383 AAAAATTACCTTTTTACCCCCAAACTTTCAAAAATTCCATTTTTGACCCTAATTTTTCT
1 AAAAATTATATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCCTTATTTTTCT
* * *
41505442 AAAAATTACCA-TTTTACCCTTGAACTTAT-AAAAACTCCATTTTTGA
1 AAAAATTA-TATTTTTACCCTCGAACTT-TCAAAAATTCCATTTTTGA
41505488 TCTCAAACCT
Statistics
Matches: 279, Mismatches: 44, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
57 15 0.05
58 86 0.31
59 159 0.57
60 19 0.07
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (59 bp):
AAAAATTATATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTGACCCTTATTTTTCT
Found at i:41505233 original size:117 final size:116
Alignment explanation
Indices: 41505090--41505449 Score: 424
Period size: 117 Copynumber: 3.1 Consensus size: 116
41505080 TAAACTATCC
* *
41505090 AAAAAATATATTTTTACCCCTAAACTTTCCAAAATTTC-ATTTTTGACCCTTATTTTTCTTAAAA
1 AAAAATTATATTTTTACCCCTAAACTTTCCAAAA-TTCAATTTTTGACCCTTATTTTTCCTAAAA
*
41505154 TTATATTTTTTCCCTCGAACTTT-TAAAATTCCATTTTTGACCTCATTTTTTCT
65 TTATATTTTTACCC-CGAACTTTCTAAAATTCCATTTTTGACCTCA-TTTTTCT
* * * *
41505207 AAAAATTATATTTTTACCCCCAAACTTTCCAAAATTCAATTTTTAACCATTACTTTTCCT-AAAT
1 AAAAATTATATTTTTACCCCTAAACTTTCCAAAATTCAATTTTTGACCCTTATTTTTCCTAAAAT
* * *
41505271 TATATTTTTACCCCAGAACTTTCTAAAATCCCATTTTTAACCTTGATTTTTCT
66 TATATTTTTACCCC-GAACTTTCTAAAATTCCATTTTTGACC-TCATTTTTCT
* * * * *
41505324 AAAAATTATATTTTTACCCTTGAA-TTTCCAAAAATTCTATTTTTGA-CCTCGATTTTTCCAAAA
1 AAAAATTATATTTTTACCCCTAAACTTTCC-AAAATTCAATTTTTGACCCT-TATTTTTCCTAAA
** * * *
41505387 ATTACCTTTTTACCCCCAAACTTTCAAAAATTCCATTTTTGACCCTAATTTTTCT
64 ATTATATTTTTA-CCCCGAACTTTCTAAAATTCCATTTTTGA-CCTCATTTTTCT
41505442 AAAAATTA
1 AAAAATTA
41505450 CCATTTTACC
Statistics
Matches: 208, Mismatches: 26, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
115 1 0.00
116 33 0.16
117 116 0.56
118 52 0.25
119 6 0.03
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45
Consensus pattern (116 bp):
AAAAATTATATTTTTACCCCTAAACTTTCCAAAATTCAATTTTTGACCCTTATTTTTCCTAAAAT
TATATTTTTACCCCGAACTTTCTAAAATTCCATTTTTGACCTCATTTTTCT
Found at i:41505337 original size:30 final size:30
Alignment explanation
Indices: 41505303--41505390 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 30
41505293 CTAAAATCCC
*
41505303 ATTTTTAACCTTGATTTTTCTAAAAATTAT
1 ATTTTTAACCTTGATTTTTCCAAAAATTAT
* * *
41505333 ATTTTTACCCTTGA-ATTTCCAAAAATTCT
1 ATTTTTAACCTTGATTTTTCCAAAAATTAT
* *
41505362 ATTTTTGACCTCGATTTTTCCAAAAATTA
1 ATTTTTAACCTTGATTTTTCCAAAAATTA
41505391 CCTTTTTACC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.48
Consensus pattern (30 bp):
ATTTTTAACCTTGATTTTTCCAAAAATTAT
Found at i:41505397 original size:30 final size:29
Alignment explanation
Indices: 41505304--41505400 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 29
41505294 TAAAATCCCA
* * **
41505304 TTTTTAACCTTGATTTTTCTAAAAATTATA
1 TTTTT-ACCTCGATTTTTCCAAAAATTACC
* * *
41505334 TTTTTACCCTTGA-ATTTCCAAAAATT-CTA
1 TTTTTA-CCTCGATTTTTCCAAAAATTAC-C
41505363 TTTTTGACCTCGATTTTTCCAAAAATTACC
1 TTTTT-ACCTCGATTTTTCCAAAAATTACC
41505393 TTTTTACC
1 TTTTTACC
41505401 CCCAAACTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
29 26 0.46
30 29 0.52
31 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.48
Consensus pattern (29 bp):
TTTTTACCTCGATTTTTCCAAAAATTACC
Found at i:41505440 original size:29 final size:28
Alignment explanation
Indices: 41505099--41505461 Score: 110
Period size: 29 Copynumber: 12.4 Consensus size: 28
41505089 CAAAAAATAT
** * *
41505099 ATTTTTACCCCTAAACTTTCCAAAATTTC
1 ATTTTTA-CCCTAATTTTTCAAAAATTCC
* * **
41505128 ATTTTTGACCCTTATTTTTCTTAAAATTAT
1 ATTTTT-ACCCTAATTTTTC-AAAAATTCC
* *
41505158 ATTTTTTCCCTCGAACTTTT--AAAATTCC
1 ATTTTTACCCT--AATTTTTCAAAAATTCC
* **
41505186 ATTTTTGA-CCTCATTTTTTCTAAAAATTAT
1 ATTTTT-ACCCT-AATTTTTC-AAAAATTCC
* ** * *
41505216 ATTTTTACCCCCAAACTTTCCAAAATTCA
1 ATTTTTA-CCCTAATTTTTCAAAAATTCC
* * * ** **
41505245 ATTTTTAACCATTACTTTTCCTAAATTAT
1 ATTTTT-ACCCTAATTTTTCAAAAATTCC
* ** * *
41505274 ATTTTTACCCCAGAACTTTCTAAAATCCC
1 ATTTTTACCCTA-ATTTTTCAAAAATTCC
* * **
41505303 ATTTTTAACCTTGATTTTTCTAAAAATTAT
1 ATTTTT-ACCCTAATTTTTC-AAAAATTCC
* *
41505333 ATTTTTACCCTTGAA-TTTCCAAAAATTCT
1 ATTTTTACCC-T-AATTTTTCAAAAATTCC
*
41505362 ATTTTTGA-CCTCGATTTTTCCAAAAATTACC
1 ATTTTT-ACCCT-AATTTTT-CAAAAATT-CC
* **
41505393 -TTTTTACCCCCAAACTTTCAAAAATTCC
1 ATTTTTA-CCCTAATTTTTCAAAAATTCC
41505421 ATTTTTGACCCTAATTTTTCTAAAAATTACC
1 ATTTTT-ACCCTAATTTTTC-AAAAATT-CC
41505452 A-TTTTACCCT
1 ATTTTTACCCT
41505462 TGAACTTATA
Statistics
Matches: 242, Mismatches: 66, Indels: 52
0.67 0.18 0.14
Matches are distributed among these distances:
27 5 0.02
28 22 0.09
29 121 0.50
30 80 0.33
31 14 0.06
ACGTcount: A:0.30, C:0.22, G:0.02, T:0.45
Consensus pattern (28 bp):
ATTTTTACCCTAATTTTTCAAAAATTCC
Found at i:41505530 original size:29 final size:29
Alignment explanation
Indices: 41505498--41505571 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
41505488 TCTCAAACCT
* *
41505498 TCCAAAAATTACCATTTTACCCCTGAATG
1 TCCAAAAATTACCATTTTACCCCCGAATA
* * *
41505527 TCC-AAAATTACTATTTTGCCCCCGAGTA
1 TCCAAAAATTACCATTTTACCCCCGAATA
*
41505555 TCCAAAAATCA-CATTTT
1 TCCAAAAATTACCATTTT
41505572 TCAACTCCGA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 28 0.76
29 9 0.24
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAATA
Found at i:41505543 original size:59 final size:58
Alignment explanation
Indices: 41505101--41505543 Score: 251
Period size: 59 Copynumber: 7.6 Consensus size: 58
41505091 AAAAATATAT
* * * ** *
41505101 TTTTACCCCTAAACTTTCCAAAATT-TCATTTTTGACCCTTATTTTTCTTAAAATTA-TA
1 TTTTACCCCTGAACTTTCCAAAATTCT-ATTTTTGACTC-AATTTTTCCAAAAATTACCA
** * * * * *
41505159 TTTTTTCCCTCGAACTTT-TAAAATTCCATTTTTGACCTCATTTTTTCTAAAAATTA-TA
1 TTTTACCCCT-GAACTTTCCAAAATTCTATTTTTGA-CTCAATTTTTCCAAAAATTACCA
** * * * * *
41505217 TTTTTACCCCCAAACTTTCCAAAATTCAATTTTTAAC-CATTACTTTTCC-TAAATTA-TA
1 -TTTTACCCCTGAACTTTCCAAAATTCTATTTTTGACTCA--ATTTTTCCAAAAATTACCA
* * * * * ** * *
41505275 TTTTTACCCCAGAACTTTCTAAAATCCCATTTTTAACCTTGATTTTTCTAAAAATTA-TA
1 -TTTTACCCCTGAACTTTCCAAAATTCTATTTTTGA-CTCAATTTTTCCAAAAATTACCA
* * *
41505334 TTTTTACCCTTGAA-TTTCCAAAAATTCTATTTTTGACCTCGATTTTTCCAAAAATTACCT
1 -TTTTACCCCTGAACTTTCC-AAAATTCTATTTTTGA-CTCAATTTTTCCAAAAATTACCA
** * * * *
41505394 TTTTACCCCCAAACTTTCAAAAATTCCATTTTTGACCCTAATTTTTCTAAAAATTACCA
1 TTTTACCCCTGAACTTTCCAAAATTCTATTTTTGACTC-AATTTTTCCAAAAATTACCA
* * * * ***
41505453 TTTTACCCTTGAACTTAT-AAAAACTCCATTTTTGATCTCAAACCTTCCAAAAATTACCA
1 TTTTACCCCTGAACTT-TCCAAAATTCTATTTTTGA-CTCAATTTTTCCAAAAATTACCA
*
41505512 TTTTACCCCTGAA-TGTCCAAAATTACTATTTT
1 TTTTACCCCTGAACTTTCCAAAATT-CTATTTT
41505544 GCCCCCGAGT
Statistics
Matches: 304, Mismatches: 63, Indels: 35
0.76 0.16 0.09
Matches are distributed among these distances:
57 3 0.01
58 102 0.34
59 192 0.63
60 7 0.02
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (58 bp):
TTTTACCCCTGAACTTTCCAAAATTCTATTTTTGACTCAATTTTTCCAAAAATTACCA
Found at i:41505543 original size:118 final size:118
Alignment explanation
Indices: 41505276--41505520 Score: 287
Period size: 118 Copynumber: 2.1 Consensus size: 118
41505266 TAAATTATAT
* * * * * * *
41505276 TTTTA-CCCCAGAACTTTCTAAAATCCCATTTTTAACCTTGATTTTTCTAAAAATTATATTTTTA
1 TTTTACCCCCA-AACTGTCAAAAATTCCATTTTTGACCCTAATTTTTCTAAAAATTACATTTTTA
* * * * * *** *
41505340 CCCTTGAATTTCCAAAAATTCTATTTTTGACCTCGATTTTTCCAAAAATTACCT
65 CCCTTGAACTTACAAAAACTCCATTTTTGACCTCAAACCTTCCAAAAATTACCA
*
41505394 TTTTACCCCCAAACTTTCAAAAATTCCATTTTTGACCCTAATTTTTCTAAAAATTACCA-TTTTA
1 TTTTACCCCCAAACTGTCAAAAATTCCATTTTTGACCCTAATTTTTCTAAAAATTA-CATTTTTA
* *
41505458 CCCTTGAACTTATAAAAACTCCATTTTTGATCTCAAACCTTCCAAAAATTACCA
65 CCCTTGAACTTACAAAAACTCCATTTTTGACCTCAAACCTTCCAAAAATTACCA
41505512 TTTTACCCC
1 TTTTACCCC
41505521 TGAATGTCCA
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
118 102 0.94
119 6 0.06
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (118 bp):
TTTTACCCCCAAACTGTCAAAAATTCCATTTTTGACCCTAATTTTTCTAAAAATTACATTTTTAC
CCTTGAACTTACAAAAACTCCATTTTTGACCTCAAACCTTCCAAAAATTACCA
Found at i:41517957 original size:201 final size:200
Alignment explanation
Indices: 41517611--41518250 Score: 888
Period size: 201 Copynumber: 3.2 Consensus size: 200
41517601 GCGATTATCC
* * * * *
41517611 ACAAGTGAGGCAGTCATATTCCTGATGAGATACAAAGAAGTATACCAACTCAAGGCTCAAAGTGA
1 ACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATGTGA
* * *
41517676 GCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCGGGTTGAAGCAATAAAATGGTC
66 GCAAATC-TTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* * *
41517741 AGCTTCCTAATGAGATATTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
130 AGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGA
41517806 ATTGAA
195 ATTGAA
** *
41517812 ACAAGTGA-GACGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTTGAGGCTCAATGCG
1 ACAAGTGATG-CGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATGTG
*
41517876 AGCAAATCTTGAAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
65 AGCAAATCTTG-AACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* * * *
41517941 TAGCTTTCTGATGAGATATTGAAAAGTGGACGAAATTCGTCTTTCTGATGAGATACAAAGAAGCG
129 TAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCG
41518006 AATTGAA
194 AATTGAA
* * * * * * *
41518013 ACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTC--A---AGGCTCAA
* *
41518078 TGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAA
61 TGTGAGCAAATCTT-GAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
*
41518143 TGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCG-CTTTCCTGATGAGATACAAAG
125 TGGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTC-TTCCTGATGAGATACAAAG
* *
41518207 AAACGGATTGAA
189 AAGCGAATTGAA
*
41518219 ACAAGTGATGCGGTCATCTTCTTGATGAGATA
1 ACAAGTGATGCGGTCATCTTCCTGATGAGATA
41518251 TTGAGAAGAA
Statistics
Matches: 389, Mismatches: 40, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
200 4 0.01
201 220 0.57
202 1 0.00
205 1 0.00
206 162 0.42
207 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (200 bp):
ACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATGTGA
GCAAATCTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
GCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGAA
TTGAA
Found at i:41518163 original size:206 final size:204
Alignment explanation
Indices: 41517665--41518272 Score: 841
Period size: 206 Copynumber: 3.0 Consensus size: 204
41517655 CCAACTCAAG
* * *
41517665 GCTCAAAGTGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCGGGTTGAAGCA
1 GCTCAATGTGAGCAAATC-TTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * *
41517730 ATAAAATGGTCAGCTTCCTAATGAGATATTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATA
65 ATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATA
* * * *
41517795 CAGAGAAGCGAATTGAAACAAGTGA-GACGGTCATCTTCCTGATGAGATACAGAGAAGTATACC-
130 CAAAGAAGCGAATTGAAACAAGTGATG-CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
*** *
41517858 AA-C--TTGAG
194 AATCAACCCAC
* *
41517866 GCTCAATGCGAGCAAATCTTGAAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
1 GCTCAATGTGAGCAAATCTTG-AACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * *
41517931 ATAAAATGGTTAGCTTTCTGATGAGATATTGAAAAGTGGACGAAATTCGTCTTTCTGATGAGATA
65 ATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATA
*
41517996 CAAAGAAGCGAATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
130 CAAAGAAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
41518061 ATCAAACCCAC
195 ATC-AACCCAC
* * *
41518072 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTA
1 GCTCAATGTGAGCAAATCTT-GAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
*
41518137 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCG-CTTTCCTGATGAGAT
65 ATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTT-CTGATGAGAT
* * * * *
41518201 ACAAAGAAACGGATTGAAACAAGTGATGCGGTCATCTTCTTGATGAGATATTGAGAAGAAGGCCA
129 ACAAAGAAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
*
41518266 AGTCAAC
194 AATCAAC
41518273 GACACCAAAC
Statistics
Matches: 361, Mismatches: 37, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
200 3 0.01
201 170 0.47
202 3 0.01
203 1 0.00
205 7 0.02
206 176 0.49
207 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (204 bp):
GCTCAATGTGAGCAAATCTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
TAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATAC
AAAGAAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAACCCAC
Found at i:41518604 original size:17 final size:17
Alignment explanation
Indices: 41518577--41518672 Score: 111
Period size: 17 Copynumber: 5.5 Consensus size: 17
41518567 AACTTTTAAT
*
41518577 TTTTAAAATTTTAATTTA
1 TTTT-AAATTTAAATTTA
*
41518595 TTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
*
41518612 TTTTTAAATTTAAATTAA
1 -TTTTAAATTTAAATTTA
* *
41518630 TTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
41518647 CTTTAAATTCAAATTTA
1 TTTTAAATTTAAATTTA
41518664 TTTTAAATT
1 TTTTAAATT
41518673 AAAAAAAATT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
17 47 0.71
18 19 0.29
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:41518633 original size:35 final size:35
Alignment explanation
Indices: 41518575--41518672 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
41518565 CCAACTTTTA
* *
41518575 ATTTTTAAAATTTTAATTTATTTTAAATTTGAATTT
1 ATTTTT-AAATTTAAATTTATTTTAAATTTAAATTT
* * *
41518611 ATTTTTAAATTTAAATTAATTTTGAGTTTAAATTT
1 ATTTTTAAATTTAAATTTATTTTAAATTTAAATTT
* *
41518646 A-CTTTAAATTCAAATTTATTTTAAATT
1 ATTTTTAAATTTAAATTTATTTTAAATT
41518673 AAAAAAAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 21 0.40
35 25 0.48
36 6 0.12
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (35 bp):
ATTTTTAAATTTAAATTTATTTTAAATTTAAATTT
Found at i:41518646 original size:6 final size:6
Alignment explanation
Indices: 41518582--41518672 Score: 55
Period size: 6 Copynumber: 15.8 Consensus size: 6
41518572 TTAATTTTTA
* * * **
41518582 AAATTT TAATTT -ATTTT AAATTT GAATTT ATTTTT AAATTT AAA-TT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * * * *
41518628 AATTTT GAGTTT AAATTT -ACTTT AAATTC AAATTT -ATTTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
41518673 AAAAAAAATT
Statistics
Matches: 61, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
5 16 0.26
6 45 0.74
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (6 bp):
AAATTT
Found at i:41520674 original size:85 final size:86
Alignment explanation
Indices: 41520512--41520894 Score: 459
Period size: 85 Copynumber: 4.5 Consensus size: 86
41520502 TTAGTAGCGC
* * * * * * *
41520512 TTGTAGGAAAAGCGCCGCTAAAAATCATGATT-TATAGTGGCGTTTGTGGGAAAAGCGTCGCTAA
1 TTGTGGGAAAAACGTCGCTAAAGACCATG-TTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAA
* *
41520576 AGATCATGTTCTATAGCGACGT
65 AGACCATGTTCTATAGCGGCGT
* * * *
41520598 TTATGGGAAAAAC-TCTGCTAAAGACCATGTTCTATAGTGGCGTTTG-GAGAAAAGCGCTGCTAA
1 TTGTGGGAAAAACGTC-GCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAA
*
41520661 AGACCATGTTCTATAGCTGCGT
65 AGACCATGTTCTATAGCGGCGT
* * * *
41520683 TTGTGGGAAAAACGTCACTAAAGACCATGTTTTATAGCGGCGTTTATGGGGAAAGCGCCGCTAAA
1 TTGTGGGAAAAACGTCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
*
41520748 GACCATGTTCTATAGTGGCGT
66 GACCATGTTCTATAGCGGCGT
* * *
41520769 TTGTGGGAAAAGCGTCGCTAAAGACCATGTTATATAGCGACGTTTGTGGGAAAA-CGCCGCTAAA
1 TTGTGGGAAAAACGTCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
* *
41520833 GACCATGTTCTACAGCGGCAT
66 GACCATGTTCTATAGCGGCGT
** * * *
41520854 TTGTGGGAAAAGTGCCGCTGAAGATCATGTTCTATAGCGGC
1 TTGTGGGAAAAACGTCGCTAAAGACCATGTTCTATAGCGGC
41520895 ATTTTTCCAT
Statistics
Matches: 256, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
85 137 0.54
86 119 0.46
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (86 bp):
TTGTGGGAAAAACGTCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
GACCATGTTCTATAGCGGCGT
Found at i:41520746 original size:128 final size:128
Alignment explanation
Indices: 41520518--41520890 Score: 477
Period size: 128 Copynumber: 2.9 Consensus size: 128
41520508 GCGCTTGTAG
* * * * *
41520518 GAAAAGCGCCGCTAAAAATCATGATTTATAG-TGGCGTTTGTGGGAAAAGCGTCGCTAAAGATCA
1 GAAAAGCGCTGCTAAAGACCATG-TTTATAGCT-GCGTTTGTGGGAAAAACGTCGCTAAAGACCA
* * * *
41520582 TGTTCTATAGCGACGTTTATGGGAAAAACTCTGCTAAAGACCATGTTCTATAGTGGCGTTTG-GA
64 TGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGTGGCGTTTGTGA
*
41520646 GAAAAGCGCTGCTAAAGACCATGTTCTATAGCTGCGTTTGTGGGAAAAACGTCACTAAAGACCAT
1 GAAAAGCGCTGCTAAAGACCATGTT-TATAGCTGCGTTTGTGGGAAAAACGTCGCTAAAGACCAT
* * *
41520711 GTTTTATAGCGGCGTTTATGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGTGGCGTTTGTGG
65 GTTCTATAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGTGGCGTTTGTGA
*
41520775 GAAAAGCG-TCGCTAAAGACCATGTTATATAGC-GACGTTTGTGGG-AAAACGCCGCTAAAGACC
1 GAAAAGCGCT-GCTAAAGACCATGTT-TATAGCTG-CGTTTGTGGGAAAAACGTCGCTAAAGACC
* * * * * *
41520837 ATGTTCTACAGCGGCATTTGTGGGAAAAGTGCCGCTGAAGATCATGTTCTATAG
63 ATGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGACCATGTTCTATAG
41520891 CGGCATTTTT
Statistics
Matches: 216, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
127 2 0.01
128 173 0.80
129 41 0.19
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (128 bp):
GAAAAGCGCTGCTAAAGACCATGTTTATAGCTGCGTTTGTGGGAAAAACGTCGCTAAAGACCATG
TTCTATAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGTGGCGTTTGTGA
Found at i:41520892 original size:171 final size:170
Alignment explanation
Indices: 41520512--41520894 Score: 482
Period size: 171 Copynumber: 2.2 Consensus size: 170
41520502 TTAGTAGCGC
* * * * *
41520512 TTGTAGGAAAAGCGCCGCTAAAAATCATGATTTATAGTGGCGTTTGTGGGAAAAGCGTCGCTAAA
1 TTGTGGGAAAAGCGCCGCTAAAGATCATG-TTTATAGCGGCGTTTATGGGAAAAGCGCCGCTAAA
* * * *
41520577 GATCATGTTCTATAGCGACGTTTATGGGAAAAACTCTGCTAAAGACCATGTTCTATAGTGGCGTT
65 GACCATGTTCTATAGCGACGTTTATGGGAAAAACTCTGCTAAAGACCATGTTATATAGCGACGTT
* * * *
41520642 TGGAGAAAAGCGCTGCTAAAGACCATGTTCTATAGCTGCGT
130 TGGAGAAAAGCGCCGCTAAAGACCATGTTCTACAGCGGCAT
* * * * *
41520683 TTGTGGGAAAAACGTCACTAAAGACCATGTTTTATAGCGGCGTTTATGGGGAAAGCGCCGCTAAA
1 TTGTGGGAAAAGCGCCGCTAAAGATCATG-TTTATAGCGGCGTTTATGGGAAAAGCGCCGCTAAA
* * * *
41520748 GACCATGTTCTATAGTGGCGTTTGTGGGAAAAGCGTC-GCTAAAGACCATGTTATATAGCGACGT
65 GACCATGTTCTATAGCGACGTTTATGGGAAAAAC-TCTGCTAAAGACCATGTTATATAGCGACGT
*
41520812 TTGTGGGAAAA-CGCCGCTAAAGACCATGTTCTACAGCGGCAT
129 TTG-GAGAAAAGCGCCGCTAAAGACCATGTTCTACAGCGGCAT
* *
41520854 TTGTGGGAAAAGTGCCGCTGAAGATCATGTTCTATAGCGGC
1 TTGTGGGAAAAGCGCCGCTAAAGATCATGTT-TATAGCGGC
41520895 ATTTTTCCAT
Statistics
Matches: 179, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
170 2 0.01
171 169 0.94
172 8 0.04
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (170 bp):
TTGTGGGAAAAGCGCCGCTAAAGATCATGTTTATAGCGGCGTTTATGGGAAAAGCGCCGCTAAAG
ACCATGTTCTATAGCGACGTTTATGGGAAAAACTCTGCTAAAGACCATGTTATATAGCGACGTTT
GGAGAAAAGCGCCGCTAAAGACCATGTTCTACAGCGGCAT
Found at i:41520898 original size:43 final size:43
Alignment explanation
Indices: 41520512--41520894 Score: 466
Period size: 43 Copynumber: 9.0 Consensus size: 43
41520502 TTAGTAGCGC
* * * *
41520512 TTGTAGGAAAAGCGCCGCTAAAAATCATGATT-TATAGTGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGACCATG-TTCTATAGCGGCGT
* * *
41520555 TTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTATAGCGACGT
1 TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGT
* * * * *
41520598 TTATGGGAAAAACTCTGCTAAAGACCATGTTCTATAGTGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGT
* * *
41520641 TTG-GAGAAAAGCGCTGCTAAAGACCATGTTCTATAGCTGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGT
* * * *
41520683 TTGTGGGAAAAACGTCACTAAAGACCATGTTTTATAGCGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGT
* * *
41520726 TTATGGGGAAAGCGCCGCTAAAGACCATGTTCTATAGTGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGT
* * *
41520769 TTGTGGGAAAAGCGTCGCTAAAGACCATGTTATATAGCGACGT
1 TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGT
* *
41520812 TTGTGGGAAAA-CGCCGCTAAAGACCATGTTCTACAGCGGCAT
1 TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGT
* * *
41520854 TTGTGGGAAAAGTGCCGCTGAAGATCATGTTCTATAGCGGC
1 TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
41520895 ATTTTTCCAT
Statistics
Matches: 289, Mismatches: 48, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
42 76 0.26
43 213 0.74
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (43 bp):
TTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGT
Found at i:41521755 original size:18 final size:18
Alignment explanation
Indices: 41521732--41521766 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41521722 TAATTTATCA
*
41521732 AATATTATATAAATATAT
1 AATATTATAAAAATATAT
*
41521750 AATATTTTAAAAATATA
1 AATATTATAAAAATATA
41521767 AAAATTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATTATAAAAATATAT
Found at i:41527070 original size:13 final size:13
Alignment explanation
Indices: 41527052--41527081 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41527042 TTTAAACCAA
*
41527052 ACTTCTCAAAAGT
1 ACTTCTCAAAAGC
41527065 ACTTCTCAAAAGC
1 ACTTCTCAAAAGC
41527078 ACTT
1 ACTT
41527082 TTTCACAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTCTCAAAAGC
Found at i:41530796 original size:29 final size:32
Alignment explanation
Indices: 41530731--41530797 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 32
41530721 TCAAATTTAT
41530731 ATATGAATTTTGATCTAATGTGCAATTTGATAC
1 ATATGAATTTTGATCT-ATGTGCAATTTGATAC
41530764 --ATGAATTTTGAT-T-TGGTGCAA-TT-ATAC
1 ATATGAATTTTGATCTAT-GTGCAATTTGATAC
41530791 ATATGAA
1 ATATGAA
41530798 ACTTGAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
27 4 0.13
28 3 0.10
29 11 0.35
30 1 0.03
31 12 0.39
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.42
Consensus pattern (32 bp):
ATATGAATTTTGATCTATGTGCAATTTGATAC
Found at i:41531027 original size:30 final size:30
Alignment explanation
Indices: 41530982--41531062 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
41530972 AAATTGAATC
*
41530982 AAATCAAACTATCATGTATAAAATTGCACA-A
1 AAATCAAAGT-TCATGTATAAAA-TGCACATA
* *
41531013 AAATCAAAGTTCATGTATGATAATGCACATT
1 AAATCAAAGTTCATGTAT-AAAATGCACATA
*
41531044 ACATCAAAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
41531063 GTTTTGATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 15 0.34
31 29 0.66
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.30
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATGCACATA
Found at i:41537882 original size:29 final size:28
Alignment explanation
Indices: 41537852--41537914 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
41537842 CTAATTAAAA
*
41537852 TTTTCAGAATTTTTGAGGAGTTTAATGAAT
1 TTTTCAAAATTTTT-AGGA-TTTAATGAAT
* *
41537882 TTTTTAAAATTTTTAGGATTTAATTAAAT
1 TTTTCAAAATTTTTAGGATTTAA-TGAAT
41537911 TTTT
1 TTTT
41537915 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 5 0.17
29 12 0.41
30 12 0.41
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.54
Consensus pattern (28 bp):
TTTTCAAAATTTTTAGGATTTAATGAAT
Found at i:41539872 original size:59 final size:59
Alignment explanation
Indices: 41539784--41540275 Score: 720
Period size: 59 Copynumber: 8.4 Consensus size: 59
41539774 GGATACCCCG
* * * * * *
41539784 GGGGGCAAAATGGTAA-TTTTGGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
41539842 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAACGGAA-TTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * * *
41539899 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAACGTAATTTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
41539958 GGGGGTAAAATGGTAATTTTCGGAGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
41540017 GAGGATAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
41540076 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAACGAAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
41540135 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * *
41540194 GGGGGTAAAATGGTAATTTTCGGTGAAATTGGGGTCAAAAAATGGAATTTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGT-TAAAAATGGAATTTTAGAAGATTC
41540254 GGGGGTAAAATGGTAATTTTTG
1 GGGGGTAAAATGGTAATTTTTG
41540276 AGAGTTTTGG
Statistics
Matches: 392, Mismatches: 38, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
57 43 0.11
58 30 0.08
59 277 0.71
60 42 0.11
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
Found at i:41540295 original size:30 final size:30
Alignment explanation
Indices: 41540232--41540336 Score: 108
Period size: 30 Copynumber: 3.5 Consensus size: 30
41540222 TTGGGGTCAA
* * * *
41540232 AAAATGGAATTTT--AAAAGATTCGGGGGT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
* *
41540260 AAAATGGTAATTTTTG-AGAGTTTTGGGGTT
1 AAAAT-GTAATTTTGGAAAAGTTTTGGGGTT
41540290 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
*
41540320 AAAATATAATTTCTGGA
1 AAAATGTAATTT-TGGA
41540337 TTGTTTGGGG
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 5 0.08
29 16 0.25
30 39 0.61
31 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTGGGGTT
Found at i:41540738 original size:161 final size:163
Alignment explanation
Indices: 41540425--41540742 Score: 484
Period size: 161 Copynumber: 2.0 Consensus size: 163
41540415 ACCTATTTGA
*
41540425 AAACCTTGAAAAATCTCAGGGCCAATTTTGTAATTAAACAATAGTTGATTTAAGGATTAAATTAA
1 AAACCTTGAAAAATCTCAGGGCCAATTTCGTAATTAAACAATAGTTGATTTAAGGATTAAATTAA
* *
41540490 GACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCTAAAAAGATGACACGTGGCAACCTC
66 GACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAACCTC
*
41540555 TGGTGCAGACAAACAGTCAAAGGACTAGTTTAT
131 TGGTACAGACAAACAGTCAAAGGACTAGTTTAT
*
41540588 AAACCTTGAAAAAT-T-ATTGGGCCAATTTCGTAATTAAA-ACTAAGTTGATTT-AGGATTAAAT
1 AAACCTTGAAAAATCTCA--GGGCCAATTTCGTAATTAAACAAT-AGTTGATTTAAGGATTAAAT
* * *
41540649 TAAGACAAATTAGAAATAAAAAGGACTAAATGCA-AAATAATCCCAAAACATGACACGTGGCAAT
63 TAAGACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAAC
* *
41540713 CTCTGGTATAGTCAAACAGTCAAAGGACTA
128 CTCTGGTACAGACAAACAGTCAAAGGACTA
41540743 AATTAAAAGA
Statistics
Matches: 142, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
161 54 0.38
162 46 0.32
163 42 0.30
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (163 bp):
AAACCTTGAAAAATCTCAGGGCCAATTTCGTAATTAAACAATAGTTGATTTAAGGATTAAATTAA
GACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAACCTC
TGGTACAGACAAACAGTCAAAGGACTAGTTTAT
Found at i:41541533 original size:10 final size:10
Alignment explanation
Indices: 41541517--41541563 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
41541507 CTTAAAAGAT
41541517 TTATTAATTA
1 TTATTAATTA
*
41541527 ATATTAATTA
1 TTATTAATTA
41541537 TTATTAATTA
1 TTATTAATTA
41541547 TTATT-ATTA
1 TTATTAATTA
*
41541556 TCATTAAT
1 TTATTAAT
41541564 GTCATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
TTATTAATTA
Found at i:41542027 original size:20 final size:20
Alignment explanation
Indices: 41542002--41542040 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41541992 AGCTGGTGGG
* *
41542002 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCCGGTGGCCAGCAGA
41542022 TGGAGCCGGTGGCCAGCAG
1 TGGAGCCGGTGGCCAGCAG
41542041 CAGTAGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.46, T:0.15
Consensus pattern (20 bp):
TGGAGCCGGTGGCCAGCAGA
Found at i:41542103 original size:12 final size:12
Alignment explanation
Indices: 41542086--41542110 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41542076 TGGACTATTG
41542086 TAATTGGGCCCT
1 TAATTGGGCCCT
41542098 TAATTGGGCCCT
1 TAATTGGGCCCT
41542110 T
1 T
41542111 GTAAATGGGC
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:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (12 bp):
TAATTGGGCCCT
Found at i:41542112 original size:26 final size:28
Alignment explanation
Indices: 41542083--41542135 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
41542073 ATTTGGACTA
*
41542083 TTGTAATTGGGCC-CT-TAATTGGGCCC
1 TTGTAAATGGGCCACTATAATTGGGCCC
*
41542109 TTGTAAATGGGCCATTATAATTGGGCC
1 TTGTAAATGGGCCACTATAATTGGGCC
41542136 GTGGGCCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 1 0.04
28 10 0.43
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (28 bp):
TTGTAAATGGGCCACTATAATTGGGCCC
Found at i:41542121 original size:14 final size:14
Alignment explanation
Indices: 41542083--41542135 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
41542073 ATTTGGACTA
41542083 TTGTAATTGGGCCC
1 TTGTAATTGGGCCC
41542097 -T-TAATTGGGCCC
1 TTGTAATTGGGCCC
* *
41542109 TTGTAAATGGGCCA
1 TTGTAATTGGGCCC
*
41542123 TTATAATTGGGCC
1 TTGTAATTGGGCC
41542136 GTGGGCCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 11 0.33
13 2 0.06
14 20 0.61
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (14 bp):
TTGTAATTGGGCCC
Found at i:41542193 original size:6 final size:6
Alignment explanation
Indices: 41542159--41542254 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
41542149 ATTTGGACTT
* ** *
41542159 TTTAAA TTTAATA TTTTAAT TTTTTA TTTAAA TTTAAA TTCAAA -TTAAA
1 TTTAAA TTTAA-A -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
41542208 TTTAGATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA --TAAA TTTAAA
1 TTTA-A-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41542255 ATCAATTTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
4 4 0.06
5 8 0.11
6 46 0.65
7 3 0.04
8 10 0.14
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:41542218 original size:25 final size:23
Alignment explanation
Indices: 41542187--41542245 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
41542177 ATTTTTTATT
* *
41542187 TAAATTTAAATTCAAATTAAATT
1 TAAATTTAAATTCAAAATAAATC
*
41542210 TAGATATTTAAATTTAAAATAAATC
1 TA-A-ATTTAAATTCAAAATAAATC
41542235 TAAATTTAAAT
1 TAAATTTAAAT
41542246 AAATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 10 0.32
24 2 0.06
25 19 0.61
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTCAAAATAAATC
Found at i:41542221 original size:31 final size:31
Alignment explanation
Indices: 41542183--41542256 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
41542173 TTTAATTTTT
*
41542183 TATTTAAATTTAAATTCAAAT-TAAATTTAGA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAGA
41542214 TATTTAAATTTAAAATAAATCTAAATTTA-A
1 TATTTAAATTTAAAATAAATCTAAATTTAGA
41542244 -A--TAAATTTAAAAT
1 TATTTAAATTTAAAAT
41542257 CAATTTAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
27 12 0.29
29 1 0.02
30 5 0.12
31 23 0.56
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAGA
Found at i:41542256 original size:17 final size:17
Alignment explanation
Indices: 41542184--41542254 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
41542174 TTAATTTTTT
*
41542184 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAAAT-AA
*
41542202 A-TTAAATTT-AGAT--
1 ATTTAAATTTAAAATAA
41542215 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
41542232 ATCTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
41542248 ATTTAAA
1 ATTTAAA
41542255 ATCAATTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.18
15 3 0.07
16 14 0.32
17 17 0.39
18 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:41542698 original size:68 final size:68
Alignment explanation
Indices: 41542587--41543231 Score: 1110
Period size: 68 Copynumber: 9.5 Consensus size: 68
41542577 TGATCTTGCT
* * * *
41542587 CGTGTTATCCACTCTACTTCAATTTCAAAGGGATGACCTTGCTCTTATTTCAATTTCGGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
41542652 AGA
66 AGA
**
41542655 TATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
**
41542720 ATT
66 AGA
41542723 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
41542788 AGA
66 AGA
*
41542791 CGTGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
41542856 AGA
66 AGA
*
41542859 CGTGTCATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
41542924 AGA
66 AGA
*
41542927 CATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
41542992 AAA
66 AGA
*
41542995 CGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
41543060 AAA
66 AGA
* *
41543063 CGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
41543128 AAA
66 AGA
* *
41543131 CGTGTTATTCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
41543196 AGA
66 AGA
*
41543199 CATGTTATCCACTCTACTTCAATTTCAAGGGGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGA
41543232 CGATGTTGAG
Statistics
Matches: 550, Mismatches: 27, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 550 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (68 bp):
CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
AGA
Found at i:41543938 original size:14 final size:13
Alignment explanation
Indices: 41543919--41543956 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
41543909 GACCTCTCCG
41543919 TTTTTATTTTTATT
1 TTTTTATTTTTA-T
*
41543933 TTTTTATTATTAT
1 TTTTTATTTTTAT
41543946 TTTTTATTTTT
1 TTTTTATTTTT
41543957 TTTATGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:41543953 original size:13 final size:14
Alignment explanation
Indices: 41543919--41543950 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
41543909 GACCTCTCCG
*
41543919 TTTTTATTTTTATT
1 TTTTTATTATTATT
41543933 TTTTTATTATTATT
1 TTTTTATTATTATT
41543947 TTTT
1 TTTT
41543951 ATTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTATTATT
Found at i:41555300 original size:59 final size:59
Alignment explanation
Indices: 41555212--41555759 Score: 762
Period size: 59 Copynumber: 9.3 Consensus size: 59
41555202 GGATACCCCG
* * * * * *
41555212 GGGGGCAAAATGGTAATTTT-GGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
41555270 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAA-TTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * * * * * *
41555327 GAGGGTAAAATGATAATTTTTGGTAAAATCGGGGTCAAAAACGTAATTTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * *
41555386 GGGGGTAAAATGGTAATTTTCGATGAAATCGAGGTTAAAAATGGAATTTTGGAAGTTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
41555445 GGGGATAAAATGGTAATTTTCAGAGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
41555504 GGGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTCAAAAATGAAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
*
41555563 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
41555621 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGATTT
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
41555680 GGGGATAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAGATGGAATTTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAA-ATGGAATTTTAGAAGATTC
41555740 GGGGGTAAAATGGTAATTTT
1 GGGGGTAAAATGGTAATTTT
41555760 TGAGAGTTTT
Statistics
Matches: 431, Mismatches: 54, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
57 40 0.09
58 89 0.21
59 266 0.62
60 36 0.08
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
Found at i:41555395 original size:29 final size:29
Alignment explanation
Indices: 41555263--41555759 Score: 217
Period size: 30 Copynumber: 16.9 Consensus size: 29
41555253 GGAATCTTAA
* *
41555263 AAGATTCGGGGGTAAAATGGTAATTTTTG
1 AAGATTCGGGGGTAAAAAGGTAATTTTAG
** * * * *
41555292 GTGAAATCGAGGTTAAAATGG-AA-TTTAG
1 AAG-ATTCGGGGGTAAAAAGGTAATTTTAG
* * * * *
41555320 AAGCTTCGAGGGTAAAATGATAATTTTTGG
1 AAGATTCGGGGGTAAAAAGGTAA-TTTTAG
* * *
41555350 TAA-AATC-GGGGTCAAAAACGTAATTTTAA
1 -AAGATTCGGGGGT-AAAAAGGTAATTTTAG
* *
41555379 AAGATTCGGGGGTAAAATGGTAATTTTCG
1 AAGATTCGGGGGTAAAAAGGTAATTTTAG
* * * * *
41555408 ATGAAATCGAGGTTAAAAATGG-AATTTTGG
1 AAG-ATTCGGGGGTAAAAA-GGTAATTTTAG
* * *
41555438 AAGTTTCGGGGATAAAATGGTAATTTTCAG
1 AAGATTCGGGGGTAAAAAGGTAATTTT-AG
* *
41555468 -AGAAATCGGGGTTAAAAATGG-AATTTTAG
1 AAG-ATTCGGGGGTAAAAA-GGTAATTTTAG
* *
41555497 AAGATTCGGGGGTAAAATGGTAATTTTCG
1 AAGATTCGGGGGTAAAAAGGTAATTTTAG
** * * * *
41555526 GTGAAATC-GAGGTCAAAAATGAAATTTTAG
1 AAG-ATTCGGGGGT-AAAAAGGTAATTTTAG
* *
41555556 AAGATTCGGGGGTAAAATGGTAATTTTTG
1 AAGATTCGGGGGTAAAAAGGTAATTTTAG
** * * *
41555585 GTGAAATCGGGGTTAAAATGG-AATTTTAG
1 AAG-ATTCGGGGGTAAAAAGGTAATTTTAG
* *
41555614 AAGATTCGGGGGTAAAATGGTAATTTTCG
1 AAGATTCGGGGGTAAAAAGGTAATTTTAG
** * * *
41555643 GTGAAATCAGGGTTAAAAATGG-AATTTTAG
1 AAG-ATTCGGGGGTAAAAA-GGTAATTTTAG
* * * *
41555673 AAGATTTGGGGATAAAATGGTAATTTTCG
1 AAGATTCGGGGGTAAAAAGGTAATTTTAG
** * *
41555702 GTGAAATC-GGGGTCAAAAGATGG-AATTTTAA
1 AAG-ATTCGGGGGT-AAAA-A-GGTAATTTTAG
*
41555733 AAGATTCGGGGGTAAAATGGTAATTTT
1 AAGATTCGGGGGTAAAAAGGTAATTTT
41555760 TGAGAGTTTT
Statistics
Matches: 338, Mismatches: 100, Indels: 60
0.68 0.20 0.12
Matches are distributed among these distances:
27 13 0.04
28 32 0.09
29 132 0.39
30 139 0.41
31 20 0.06
32 2 0.01
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (29 bp):
AAGATTCGGGGGTAAAAAGGTAATTTTAG
Found at i:41555781 original size:30 final size:30
Alignment explanation
Indices: 41555731--41555822 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 30
41555721 ATGGAATTTT
* * * *
41555731 AAAAGATTCGGGGGTAAAATGGTAATTTTTG
1 AAAAGTTTTGGGGTTAAAAT-GTAATTTTGG
*
41555762 -AGAGTTTTGGGGTTAAAATGTAATTTTGG
1 AAAAGTTTTGGGGTTAAAATGTAATTTTGG
*
41555791 AAAAGTTTTGGGGTTAAAATATAATTTCTGG
1 AAAAGTTTTGGGGTTAAAATGTAATTT-TGG
41555822 A
1 A
41555823 TTGTTTGGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 9 0.17
30 39 0.75
31 4 0.08
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (30 bp):
AAAAGTTTTGGGGTTAAAATGTAATTTTGG
Found at i:41556219 original size:161 final size:163
Alignment explanation
Indices: 41555911--41556228 Score: 484
Period size: 161 Copynumber: 2.0 Consensus size: 163
41555901 ACCCATTTGA
*
41555911 AAACCTTGAAAAATCTCAGGGCCAATTTTGTAATTAAACAATAGTTGATTTAAGGATTAAATTAA
1 AAACCTTGAAAAATCTCAGGGCCAATTTCGTAATTAAACAATAGTTGATTTAAGGATTAAATTAA
* *
41555976 GACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCTAAAAAGATGACACGTGGCAACCTC
66 GACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAACCTC
*
41556041 TGGTGCAGTCAAACAGTCAAAGGACTAGTTTAT
131 TGGTACAGTCAAACAGTCAAAGGACTAGTTTAT
* *
41556074 AAACCTTGAAAAAT-T-ATTGGGCTAATTTCGTAATTAAA-ACTAAGTTGATTT-AGGATTAAAT
1 AAACCTTGAAAAATCTCA--GGGCCAATTTCGTAATTAAACAAT-AGTTGATTTAAGGATTAAAT
* * *
41556135 TAAGACAAATTAGAAATAAAAAGGACTAAATGCA-AAATAATCCCAAAACATGACACGTGGCAAT
63 TAAGACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAAC
*
41556199 CTCTGGTATAGTCAAACAGTCAAAGGACTA
128 CTCTGGTACAGTCAAACAGTCAAAGGACTA
41556229 AATTAAAAGA
Statistics
Matches: 142, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
161 55 0.39
162 46 0.32
163 41 0.29
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (163 bp):
AAACCTTGAAAAATCTCAGGGCCAATTTCGTAATTAAACAATAGTTGATTTAAGGATTAAATTAA
GACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAACCTC
TGGTACAGTCAAACAGTCAAAGGACTAGTTTAT
Found at i:41557020 original size:10 final size:10
Alignment explanation
Indices: 41557004--41557050 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
41556994 CTTAAAAGAT
41557004 TTATTAATTA
1 TTATTAATTA
*
41557014 ATATTAATTA
1 TTATTAATTA
41557024 TTATTAATTA
1 TTATTAATTA
41557034 TTATT-ATTA
1 TTATTAATTA
*
41557043 TCATTAAT
1 TTATTAAT
41557051 GTCATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
TTATTAATTA
Found at i:41557513 original size:20 final size:20
Alignment explanation
Indices: 41557488--41557526 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41557478 AGTTGGTGGG
* *
41557488 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCCGGTGGCCAGCAGA
41557508 TGGAGCCGGTGGCCAGCAG
1 TGGAGCCGGTGGCCAGCAG
41557527 CAGTAGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.46, T:0.15
Consensus pattern (20 bp):
TGGAGCCGGTGGCCAGCAGA
Found at i:41557589 original size:12 final size:12
Alignment explanation
Indices: 41557572--41557596 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41557562 TGGACTATTG
41557572 TAATTGGGCCCT
1 TAATTGGGCCCT
41557584 TAATTGGGCCCT
1 TAATTGGGCCCT
41557596 T
1 T
41557597 GTAAATGGGC
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:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (12 bp):
TAATTGGGCCCT
Found at i:41557607 original size:14 final size:14
Alignment explanation
Indices: 41557569--41557621 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
41557559 ATTTGGACTA
41557569 TTGTAATTGGGCCC
1 TTGTAATTGGGCCC
41557583 -T-TAATTGGGCCC
1 TTGTAATTGGGCCC
* *
41557595 TTGTAAATGGGCCA
1 TTGTAATTGGGCCC
41557609 TTGTAATTGGGCC
1 TTGTAATTGGGCC
41557622 GTGGGCCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.32
13 2 0.06
14 21 0.62
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (14 bp):
TTGTAATTGGGCCC
Found at i:41557679 original size:6 final size:6
Alignment explanation
Indices: 41557645--41557740 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
41557635 ATTTGGACTT
* ** *
41557645 TTTAAA TTTAATA TTTTAAT TTTTTA TTTAAA TTTAAA TTCAAA -TTAAA
1 TTTAAA TTTAA-A -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
41557694 TTTAGATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA --TAAA TTTAAA
1 TTTA-A-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41557741 ATCAATTTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
4 4 0.06
5 8 0.11
6 46 0.65
7 3 0.04
8 10 0.14
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:41557704 original size:25 final size:23
Alignment explanation
Indices: 41557673--41557731 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
41557663 ATTTTTTATT
* *
41557673 TAAATTTAAATTCAAATTAAATT
1 TAAATTTAAATTCAAAATAAATC
*
41557696 TAGATATTTAAATTTAAAATAAATC
1 TA-A-ATTTAAATTCAAAATAAATC
41557721 TAAATTTAAAT
1 TAAATTTAAAT
41557732 AAATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 10 0.32
24 2 0.06
25 19 0.61
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTCAAAATAAATC
Found at i:41557707 original size:31 final size:31
Alignment explanation
Indices: 41557669--41557742 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
41557659 TTTAATTTTT
*
41557669 TATTTAAATTTAAATTCAAAT-TAAATTTAGA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAGA
41557700 TATTTAAATTTAAAATAAATCTAAATTTA-A
1 TATTTAAATTTAAAATAAATCTAAATTTAGA
41557730 -A--TAAATTTAAAAT
1 TATTTAAATTTAAAAT
41557743 CAATTTAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
27 12 0.29
29 1 0.02
30 5 0.12
31 23 0.56
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAGA
Found at i:41557742 original size:17 final size:17
Alignment explanation
Indices: 41557670--41557740 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
41557660 TTAATTTTTT
*
41557670 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAAAT-AA
*
41557688 A-TTAAATTT-AGAT--
1 ATTTAAATTTAAAATAA
41557701 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
41557718 ATCTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
41557734 ATTTAAA
1 ATTTAAA
41557741 ATCAATTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.18
15 3 0.07
16 14 0.32
17 17 0.39
18 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:41560927 original size:25 final size:25
Alignment explanation
Indices: 41560893--41560942 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
41560883 GTCTAAGAAA
41560893 CATGTAATTGATGGGGTAAATTATG
1 CATGTAATTGATGGGGTAAATTATG
41560918 CATGTAATTGATGGGGTAAATTATG
1 CATGTAATTGATGGGGTAAATTATG
41560943 TTAATCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (25 bp):
CATGTAATTGATGGGGTAAATTATG
Found at i:41561937 original size:33 final size:33
Alignment explanation
Indices: 41561895--41561962 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
41561885 ACATTGGGAA
*
41561895 AGGAATGGAAATTGCTACTATAAGTGAAAGGCG
1 AGGAATGGAAATTGCTACTATAAATGAAAGGCG
41561928 AGGAATGGAAATTGCTACTATAAATGAAAGGCG
1 AGGAATGGAAATTGCTACTATAAATGAAAGGCG
41561961 AG
1 AG
41561963 ATCACGACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.41, C:0.09, G:0.29, T:0.21
Consensus pattern (33 bp):
AGGAATGGAAATTGCTACTATAAATGAAAGGCG
Found at i:41563776 original size:15 final size:16
Alignment explanation
Indices: 41563750--41563786 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
41563740 AAACGTAGAT
*
41563750 TATAAATAATTAATAA
1 TATAATTAATTAATAA
41563766 T-TAATTAATTAATAA
1 TATAATTAATTAATAA
41563781 TATAAT
1 TATAAT
41563787 GTTTCAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATTAATTAATAA
Found at i:41579992 original size:29 final size:28
Alignment explanation
Indices: 41579950--41580084 Score: 84
Period size: 29 Copynumber: 4.7 Consensus size: 28
41579940 AAATTAGGTC
* * *
41579950 AAAATGGGAGTTTTTGAAAGTTCAGGGGT
1 AAAATGGTAATTTTGGAAAGTTC-GGGGT
*
41579979 AAAATGGTAATTTTGGTAAA-ATCGGGGT
1 AAAATGGTAATTTTGG-AAAGTTCGGGGT
* *
41580007 CGAAAATAG-AAATTTGGAAAGTTCGAGGGT
1 --AAAATGGTAATTTTGGAAAGTTCG-GGGT
41580037 -AAATGGTAATTTTTGGTGAAA--TCGAGGGT
1 AAAATGGTAA-TTTT-G-GAAAGTTCG-GGGT
41580066 AAAAATGG-AATTTTGGAAA
1 -AAAATGGTAATTTTGGAAA
41580085 ACTTGAGGGT
Statistics
Matches: 86, Mismatches: 9, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
27 9 0.10
28 11 0.13
29 40 0.47
30 16 0.19
31 10 0.12
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.30
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAAGTTCGGGGT
Found at i:41580027 original size:58 final size:58
Alignment explanation
Indices: 41579965--41580110 Score: 158
Period size: 58 Copynumber: 2.5 Consensus size: 58
41579955 GGGAGTTTTT
*
41579965 GAAAGTTC-AGGGGTAAAATGGTAA-TTTTGGTAAAATCG-GGGTCGAAAATAGAAATTTG
1 GAAAGTTCGA-GGGT-AAATGGTAATTTTTGGTAAAATCGAGGGT-AAAAATAGAAATTTG
* * *
41580023 GAAAGTTCGAGGGTAAATGGTAATTTTTGGTGAAATCGAGGGTAAAAATGGAATTTTG
1 GAAAGTTCGAGGGTAAATGGTAATTTTTGGTAAAATCGAGGGTAAAAATAGAAATTTG
*
41580081 GAAAACTT-GAGGGTAAAAAT-GTAATTTTTG
1 G-AAAGTTCGAGGGT--AAATGGTAATTTTTG
41580111 AAAAGTTTTA
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 9 0.12
58 44 0.57
59 20 0.26
60 4 0.05
ACGTcount: A:0.37, C:0.04, G:0.29, T:0.30
Consensus pattern (58 bp):
GAAAGTTCGAGGGTAAATGGTAATTTTTGGTAAAATCGAGGGTAAAAATAGAAATTTG
Found at i:41580136 original size:30 final size:30
Alignment explanation
Indices: 41580096--41580384 Score: 236
Period size: 30 Copynumber: 9.7 Consensus size: 30
41580086 CTTGAGGGTA
*
41580096 AAAATGTAATTTTTGAAAAGTTTTAAGGTT
1 AAAATATAATTTTTGAAAAGTTTTAAGGTT
* * * *
41580126 AAAACATAATTTTAG-AAAGTTTTAGGGTC
1 AAAATATAATTTTTGAAAAGTTTTAAGGTT
* * * *
41580155 AAAATGTAATTTTGGAAAAGTTTTAGGGTC
1 AAAATATAATTTTTGAAAAGTTTTAAGGTT
** * ***
41580185 AAAATATAATTTTCAAAAAATTTCGGGGTT
1 AAAATATAATTTTTGAAAAGTTTTAAGGTT
41580215 AAAATATAA-TTTTGAAATAG-TTTAAGGGTT
1 AAAATATAATTTTTGAAA-AGTTTTAA-GGTT
* * *
41580245 AAAA-AGTAATTTATAAAAAGTTTT-AGGGT
1 AAAATA-TAATTTTTGAAAAGTTTTAAGGTT
* **
41580274 -CAATATAATTTTCAAAAAGTTTTAAGGTT
1 AAAATATAATTTTTGAAAAGTTTTAAGGTT
*
41580303 AAAATATAA-TTTTGAAAAAG-TTTAGGGGTT
1 AAAATATAATTTTTG-AAAAGTTTTA-AGGTT
* *
41580333 AAAATGTAATTTTGGAAAAG-TTTAAGGGTT
1 AAAATATAATTTTTGAAAAGTTTTAA-GGTT
*
41580363 AAAATATAATTTTTGAACAGTT
1 AAAATATAATTTTTGAAAAGTT
41580385 CAAGGACTTT
Statistics
Matches: 207, Mismatches: 38, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
28 18 0.09
29 48 0.23
30 127 0.61
31 14 0.07
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (30 bp):
AAAATATAATTTTTGAAAAGTTTTAAGGTT
Found at i:41580159 original size:88 final size:88
Alignment explanation
Indices: 41580061--41580375 Score: 352
Period size: 88 Copynumber: 3.5 Consensus size: 88
41580051 GGTGAAATCG
* * * * * **
41580061 AGGGTAAAAATGGAATTTTGGAAAA-CTTGAGGGTAAAAATGTAATTTTTGAAAAGTTTTAAGGT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGT-AAAATATAATTTTCAAAAAGTTTTAAGGT
*
41580125 TAAAACATAATTTTAGAAAGTTTT
65 TAAAATATAATTTTAGAAAGTTTT
* * ***
41580149 AGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTCAAAAAATTTCGGGGT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGT-AAAATATAATTTTCAAAAAGTTTTAAGGT
*
41580214 TAAAATATAATTTT-GAAATAGTTTA
65 TAAAATATAATTTTAG-AA-AGTTTT
* * *
41580239 AGGGTTAAAAAGTAATTTAT-AAAAAGTTTTAGGGT-CAATATAATTTTCAAAAAGTTTTAAGGT
1 AGGGTTAAAATGTAATTT-TGGAAAAGTTTTAGGGTAAAATATAATTTTCAAAAAGTTTTAAGGT
*
41580302 TAAAATATAATTTTGAAAAAG-TTT
65 TAAAATATAATTTT-AGAAAGTTTT
*
41580326 AGGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTT
1 A-GGGTTAAAATGTAATTTTGGAAAAGTTTTAGGG-TAAAATATAATTTT
41580376 TGAACAGTTC
Statistics
Matches: 189, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
87 4 0.02
88 91 0.48
89 47 0.25
90 46 0.24
91 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (88 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTAAAATATAATTTTCAAAAAGTTTTAAGGTT
AAAATATAATTTTAGAAAGTTTT
Found at i:41580230 original size:118 final size:115
Alignment explanation
Indices: 41580091--41580384 Score: 374
Period size: 118 Copynumber: 2.5 Consensus size: 115
41580081 GAAAACTTGA
*
41580091 GGGTAAAAATGTAATTTTTGAAAAGTTTTAA-GGTTAAAACATAATTTTAGAAAGTTTTAGGGTC
1 GGGTTAAAATGTAA-TTTTGAAAAG-TTTAAGGGTTAAAA-ATAATTTTAGAAAGTTTTAGGGTC
* ** * *
41580155 AAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTCAAAAAATTTCG
63 --AATATAATTTTCAAAAAGTTTTAAGGTCAAAATATAATTTTCAAAAAATTTAG
* *
41580210 GGGTTAAAATATAATTTTGAAATAGTTTAAGGGTTAAAAAGTAATTTATAAAAAGTTTTAGGGTC
1 GGGTTAAAATGTAATTTTGAAA-AGTTTAAGGGTTAAAAA-TAATTT-TAGAAAGTTTTAGGGTC
* * *
41580275 AATATAATTTTCAAAAAGTTTTAAGGTTAAAATATAATTTTGAAAAAGTTTAG
63 AATATAATTTTCAAAAAGTTTTAAGGTCAAAATATAATTTTCAAAAAATTTAG
*
41580328 GGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTTGAACAGTT
1 GGGTTAAAATGTAATTTT-GAAAAGTTTAAGGGTTAAAA-ATAATTTTAGAA-AGTT
41580385 CAAGGACTTT
Statistics
Matches: 154, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
117 3 0.02
118 102 0.66
119 33 0.21
120 16 0.10
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.38
Consensus pattern (115 bp):
GGGTTAAAATGTAATTTTGAAAAGTTTAAGGGTTAAAAATAATTTTAGAAAGTTTTAGGGTCAAT
ATAATTTTCAAAAAGTTTTAAGGTCAAAATATAATTTTCAAAAAATTTAG
Found at i:41581575 original size:16 final size:16
Alignment explanation
Indices: 41581556--41581589 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41581546 TATTTATAAT
*
41581556 TATTAATTATTATTAA
1 TATTAATTACTATTAA
41581572 TATTAATTACTATTAA
1 TATTAATTACTATTAA
41581588 TA
1 TA
41581590 CCAATACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTAATTACTATTAA
Found at i:41582318 original size:17 final size:17
Alignment explanation
Indices: 41582296--41582367 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
41582286 CATTTATTTA
*
41582296 TAAATTTATAA-TAATTT
1 TAAATTTA-AATTAAATT
41582313 TAAATTTAAATTAAATT
1 TAAATTTAAATTAAATT
*
41582330 CAAATTTAAATTAAATT
1 TAAATTTAAATTAAATT
* *
41582347 TAATTTTAAAATAAATT
1 TAAATTTAAATTAAATT
41582364 TAAA
1 TAAA
41582368 ATGGCTTGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
16 2 0.04
17 46 0.96
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTAAATT
Found at i:41582322 original size:6 final size:6
Alignment explanation
Indices: 41582311--41582367 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
41582301 TTATAATAAT
* *
41582311 TTTAAA TTTAAA -TTAAA TTCAAA TTTAAA -TTAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
41582357 -ATAAA TTTAAA
1 TTTAAA TTTAAA
41582368 ATGGCTTGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 14 0.33
6 28 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:41582326 original size:11 final size:12
Alignment explanation
Indices: 41582311--41582367 Score: 66
Period size: 11 Copynumber: 5.0 Consensus size: 12
41582301 TTATAATAAT
41582311 TTTAAATTTAAA
1 TTTAAATTTAAA
*
41582323 -TTAAATTCAAA
1 TTTAAATTTAAA
41582334 TTTAAA-TTAAA
1 TTTAAATTTAAA
*
41582345 TTTAATTTTAAA
1 TTTAAATTTAAA
*
41582357 -ATAAATTTAAA
1 TTTAAATTTAAA
41582368 ATGGCTTGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
11 28 0.74
12 10 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:41583723 original size:17 final size:17
Alignment explanation
Indices: 41583700--41583752 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
41583690 ATTGAACCCA
41583700 ATTTTAAGTTTAAATTT
1 ATTTTAAGTTTAAATTT
*
41583717 TTTTTAAGTTTAAATTT
1 ATTTTAAGTTTAAATTT
*
41583734 ATTTTAAATTTAAAATTT
1 ATTTTAAGTTT-AAATTT
41583752 A
1 A
41583753 AATTTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
ATTTTAAGTTTAAATTT
Found at i:41583728 original size:6 final size:6
Alignment explanation
Indices: 41583719--41583760 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
41583709 TTAAATTTTT
* *
41583719 TTTAAG TTTAAA TTT-AT TTTAAA TTTAAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
41583761 AAAAATGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
5 4 0.13
6 21 0.68
7 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:41583758 original size:13 final size:13
Alignment explanation
Indices: 41583736--41583761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41583726 TTAAATTTAT
41583736 TTTAAATTTAAAA
1 TTTAAATTTAAAA
41583749 TTTAAATTTAAAA
1 TTTAAATTTAAAA
41583762 AAAATGTCCA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAATTTAAAA
Found at i:41583807 original size:21 final size:20
Alignment explanation
Indices: 41583767--41583807 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
41583757 TAAAAAAAAT
**
41583767 GTCCAAATACAAATTTTAAA
1 GTCCAAATACAAATACTAAA
41583787 GTCCAAATTACAAATACTAAA
1 GTCCAAA-TACAAATACTAAA
41583808 ACCCATACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.27
Consensus pattern (20 bp):
GTCCAAATACAAATACTAAA
Found at i:41584573 original size:13 final size:14
Alignment explanation
Indices: 41584550--41584590 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
41584540 ATGTATCAAT
41584550 AACA-AATAAAAAA
1 AACATAATAAAAAA
* *
41584563 AAGAT-ATAAAAAC
1 AACATAATAAAAAA
41584576 AACATAATAAAAAA
1 AACATAATAAAAAA
41584590 A
1 A
41584591 CAAACAGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.12
Consensus pattern (14 bp):
AACATAATAAAAAA
Found at i:41584606 original size:32 final size:31
Alignment explanation
Indices: 41584548--41584608 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
41584538 GAATGTATCA
41584548 ATAACAAATAAAAAAAAGATATAAAAACAAC
1 ATAACAAATAAAAAAAAGATATAAAAACAAC
* *
41584579 ATAATAAA-AAAACAAACAGATTTAAAAACA
1 ATAACAAATAAAA-AAA-AGATATAAAAACA
41584609 CGAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 10 0.38
32 12 0.46
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (31 bp):
ATAACAAATAAAAAAAAGATATAAAAACAAC
Found at i:41585384 original size:30 final size:30
Alignment explanation
Indices: 41585344--41585495 Score: 159
Period size: 30 Copynumber: 5.1 Consensus size: 30
41585334 CTCAGAAGGT
41585344 CCCTCGAACTTCTCAAAAATCACATTTTGA
1 CCCTCGAACTTCTCAAAAATCACATTTTGA
* * *
41585374 CCCACGAACTT-TCTAAAAATCGCA-TTTCA
1 CCCTCGAACTTCTC-AAAAATCACATTTTGA
* * *
41585403 GCCCTCAAAATTCTCAAAAATCACATTTTGG
1 -CCCTCGAACTTCTCAAAAATCACATTTTGA
* *
41585434 CCCTCAAACTTCTCAAAAATCACATTTTAA
1 CCCTCGAACTTCTCAAAAATCACATTTTGA
* *
41585464 CCC-CTGAACTT-TCCAAAATTACATTTTGA
1 CCCTC-GAACTTCTCAAAAATCACATTTTGA
41585493 CCC
1 CCC
41585496 CAAATATAAC
Statistics
Matches: 101, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
29 25 0.25
30 71 0.70
31 5 0.05
ACGTcount: A:0.34, C:0.30, G:0.06, T:0.30
Consensus pattern (30 bp):
CCCTCGAACTTCTCAAAAATCACATTTTGA
Found at i:41586984 original size:27 final size:27
Alignment explanation
Indices: 41586954--41587035 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
41586944 GGCTTGAGGA
*
41586954 GTTATTCTGATTTTGGCTCAAAAGAGT
1 GTTATTCTGATTTTGGCTCAAAAGAGC
* *
41586981 GTTATTCTGATTCTGGTTCAAAAGAGC
1 GTTATTCTGATTTTGGCTCAAAAGAGC
* *
41587008 GTTATTCTGATTCTGGGCTCATAAGAGC
1 GTTATTCTGATT-TTGGCTCAAAAGAGC
41587036 TAACCATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 36 0.77
28 11 0.23
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
GTTATTCTGATTTTGGCTCAAAAGAGC
Found at i:41587056 original size:24 final size:24
Alignment explanation
Indices: 41587021--41587101 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 24
41587011 ATTCTGATTC
* *
41587021 TGGGCTCATAAGAGCTAACCATTT
1 TGGGCTCGTAAGAGCTAACCATTA
* * *
41587045 TGGGCTTGTAAGAGCTAACTATTC
1 TGGGCTCGTAAGAGCTAACCATTA
* * *
41587069 TAGGCTCGTAGGAACTAACCATTA
1 TGGGCTCGTAAGAGCTAACCATTA
41587093 TGGGCTCGT
1 TGGGCTCGT
41587102 GTGGGCTAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (24 bp):
TGGGCTCGTAAGAGCTAACCATTA
Found at i:41589924 original size:16 final size:16
Alignment explanation
Indices: 41589900--41589930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41589890 AATGATGATT
41589900 ACCAACAACAACCATC
1 ACCAACAACAACCATC
*
41589916 ACCAGCAACAACCAT
1 ACCAACAACAACCAT
41589931 ATAATTGGAA
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:0.42, G:0.03, T:0.06
Consensus pattern (16 bp):
ACCAACAACAACCATC
Found at i:41604367 original size:11 final size:13
Alignment explanation
Indices: 41604341--41604365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41604331 TATTAACCTA
41604341 AATAAAAAATTAT
1 AATAAAAAATTAT
41604354 AATAAAAAATTA
1 AATAAAAAATTA
41604366 ATGTGAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAAAATTAT
Found at i:41613109 original size:5 final size:5
Alignment explanation
Indices: 41613099--41613137 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
41613089 ACACAACTAA
*
41613099 TAATT TAATT TAATT TAATT TAATT TAA-T TGATT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT
41613138 ATTATCGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 28 0.90
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:41616083 original size:22 final size:22
Alignment explanation
Indices: 41616057--41616109 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
41616047 GTGAAATGGC
* *
41616057 AACAAAGCAGTGAGAAAACAAA
1 AACAAAACAATGAGAAAACAAA
* *
41616079 AACAAAACAATGAGTAAACAAT
1 AACAAAACAATGAGAAAACAAA
*
41616101 AGCAAAACA
1 AACAAAACA
41616110 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.64, C:0.15, G:0.13, T:0.08
Consensus pattern (22 bp):
AACAAAACAATGAGAAAACAAA
Found at i:41619786 original size:29 final size:28
Alignment explanation
Indices: 41619736--41619928 Score: 163
Period size: 30 Copynumber: 6.5 Consensus size: 28
41619726 AAAAGTCCCT
* **
41619736 AAACTGTCCAAAAAGTATATTTTTACACCG
1 AAACT-TCCAAAAATTCCATTTTTAC-CCG
*
41619766 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTA-CCCG
* *
41619795 AAACTTCCAAAAATTCCAACTTTGACTCCG
1 AAACTTCCAAAAATTCC-ATTTTTAC-CCG
* *
41619825 AAACTTTCAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATTCCATTTTT-ACC-CG
* *
41619855 AAACTTTCAAAAATTACCA-TTTTACCCCC
1 AAACTTCCAAAAATT-CCATTTTTA-CCCG
* *
41619884 AAAATGTCCAAAAACTCCATTTTTGACCCG
1 AAACT-TCCAAAAATTCCATTTTT-ACCCG
*
41619914 AAACTTTCAAAAATT
1 AAACTTCCAAAAATT
41619929 ACCAAATTAC
Statistics
Matches: 133, Mismatches: 20, Indels: 21
0.76 0.11 0.12
Matches are distributed among these distances:
29 57 0.43
30 72 0.54
31 4 0.03
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTTACCCG
Found at i:41619942 original size:59 final size:59
Alignment explanation
Indices: 41619771--41619966 Score: 209
Period size: 59 Copynumber: 3.3 Consensus size: 59
41619761 CACCGAAACT
* * * * *
41619771 TCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATT-CCAACTTTGACTCCGAAACT-
1 TCCAAAAATTCCATTTTTGA-CCCGAAACTTTCAAAAATTACCAA-TTT-ACCCCCAAAATG
* * *
41619830 TTCAAAAATTCCATTTTTGACCTTGAAACTTTCAAAAATTACCATTTTACCCCCAAAATG
1 TCCAAAAATTCCATTTTTGACC-CGAAACTTTCAAAAATTACCAATTTACCCCCAAAATG
* * ** *
41619890 TCCAAAAACTCCATTTTTGACCCGAAACTTTCAAAAATTACCAAATTACCCCCCGAGTG
1 TCCAAAAATTCCATTTTTGACCCGAAACTTTCAAAAATTACCAATTTACCCCCAAAATG
*
41619949 TCCAAAAATTCGATTTTT
1 TCCAAAAATTCCATTTTT
41619967 AATTCTGATT
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
59 74 0.64
60 38 0.33
61 3 0.03
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.31
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCGAAACTTTCAAAAATTACCAATTTACCCCCAAAATG
Found at i:41622081 original size:15 final size:14
Alignment explanation
Indices: 41622056--41622102 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
41622046 TTAAAAAATA
41622056 TTTATATTATATTAT
1 TTTATA-TATATTAT
*
41622071 TTTAGTATATAATAT
1 TTTA-TATATATTAT
41622086 TTT-TATATATT-T
1 TTTATATATATTAT
41622098 TTTAT
1 TTTAT
41622103 TTATTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 4 0.14
13 8 0.29
15 14 0.50
16 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTATATATATTAT
Found at i:41623187 original size:21 final size:21
Alignment explanation
Indices: 41623161--41623217 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
41623151 TTGCAACTTC
*
41623161 TATCGATACAAGTATCCTAAA
1 TATCGATACAAGCATCCTAAA
*
41623182 TATCGATACAAGCATCCTAAC
1 TATCGATACAAGCATCCTAAA
41623203 TATCGATACAAGCAT
1 TATCGATACAAGCAT
41623218 ACACAAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (21 bp):
TATCGATACAAGCATCCTAAA
Found at i:41623233 original size:24 final size:21
Alignment explanation
Indices: 41623164--41623235 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
41623154 CAACTTCTAT
* *
41623164 CGATACAAGTATCCTAAA-TAT
1 CGATACAAGCATCC-AAACTAC
* *
41623185 CGATACAAGCATCCTAACTAT
1 CGATACAAGCATCCAAACTAC
41623206 CGATACAAGCATACACAAAACTAC
1 CGATACAAGCAT-C-C-AAACTAC
41623230 CGATAC
1 CGATAC
41623236 CTATTATGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 2 0.05
21 28 0.65
22 1 0.02
23 1 0.02
24 11 0.26
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (21 bp):
CGATACAAGCATCCAAACTAC
Found at i:41623917 original size:52 final size:51
Alignment explanation
Indices: 41623855--41624102 Score: 289
Period size: 52 Copynumber: 4.8 Consensus size: 51
41623845 TCAGAATTTG
* * * *
41623855 TAAAGGATTCATATACTCACGATCACACGTAGTCATCGAATTTCAAAATCCA
1 TAAAGGATTCATATACTCATGATGACACGTAGTCATCGAA-CTCATAATCCA
** * * *
41623907 TAAATTATTCATATACTCATGATGACACGTAATCATCGGACCTCATAATCCG
1 TAAAGGATTCATATACTCATGATGACACGTAGTCATC-GAACTCATAATCCA
* * * *
41623959 TAAAGGATTCATATAATCATGGTGACACGTAGTCATCGAAACTCACAATCCG
1 TAAAGGATTCATATACTCATGATGACACGTAGTCATCG-AACTCATAATCCA
*
41624011 TAAAGGATTCATATACTCATGATGACACGTAGTCATCAGAACTCATAATTCA
1 TAAAGGATTCATATACTCATGATGACACGTAGTCATC-GAACTCATAATCCA
* * * * *
41624063 TAAAGAATTCATATACTCATGAAGACGCATAGTTATCGAA
1 TAAAGGATTCATATACTCATGATGACACGTAGTCATCGAA
41624103 TCTTTTACAT
Statistics
Matches: 167, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
51 4 0.02
52 160 0.96
53 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (51 bp):
TAAAGGATTCATATACTCATGATGACACGTAGTCATCGAACTCATAATCCA
Found at i:41624009 original size:104 final size:104
Alignment explanation
Indices: 41623818--41624084 Score: 327
Period size: 104 Copynumber: 2.6 Consensus size: 104
41623808 GCATTTAATT
* * * * * * * *
41623818 CTCACGATGACACATAATAATCGAACGTCAGAATTTGTAAAGGATTCATATACTCACGATCACAC
1 CTCATGATGACACGTAATCATCGGACCTCATAATTCGTAAAGGATTCATATACTCATGATCACAC
** **
41623883 GTAGTCATCGAATTTCAAAATCCATAAATTATTCATATA
66 GTAGTCATCGAAACTCAAAATCCATAAAGGATTCATATA
* * * *
41623922 CTCATGATGACACGTAATCATCGGACCTCATAATCCGTAAAGGATTCATATAATCATGGTGACAC
1 CTCATGATGACACGTAATCATCGGACCTCATAATTCGTAAAGGATTCATATACTCATGATCACAC
* *
41623987 GTAGTCATCGAAACTCACAATCCGTAAAGGATTCATATA
66 GTAGTCATCGAAACTCAAAATCCATAAAGGATTCATATA
* * * * *
41624026 CTCATGATGACACGTAGTCATCAGAACTCATAATTCATAAAGAATTCATATACTCATGA
1 CTCATGATGACACGTAATCATCGGACCTCATAATTCGTAAAGGATTCATATACTCATGA
41624085 AGACGCATAG
Statistics
Matches: 137, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
104 137 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (104 bp):
CTCATGATGACACGTAATCATCGGACCTCATAATTCGTAAAGGATTCATATACTCATGATCACAC
GTAGTCATCGAAACTCAAAATCCATAAAGGATTCATATA
Found at i:41630608 original size:19 final size:19
Alignment explanation
Indices: 41630558--41630611 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
41630548 TTTAAATAAG
*
41630558 TCTAATTTTTTTATTTAAA
1 TCTAATATTTTTATTTAAA
41630577 T-T--TA--TTT-TTTAAA
1 TCTAATATTTTTATTTAAA
41630590 TCTAATATTTTTATTTAAA
1 TCTAATATTTTTATTTAAA
41630609 TCT
1 TCT
41630612 TTTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 12
0.68 0.02 0.29
Matches are distributed among these distances:
13 7 0.25
14 4 0.14
16 3 0.11
18 4 0.14
19 10 0.36
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
TCTAATATTTTTATTTAAA
Found at i:41636385 original size:18 final size:19
Alignment explanation
Indices: 41636362--41636403 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
41636352 CAAAAATTTC
**
41636362 AAAATTTAT-ATTTTTTAA
1 AAAATTTATAATAATTTAA
41636380 AAAA-TTATAATAATTTAA
1 AAAATTTATAATAATTTAA
41636398 AAAATT
1 AAAATT
41636404 CTAACGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 15 0.75
19 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATTTATAATAATTTAA
Found at i:41638377 original size:24 final size:24
Alignment explanation
Indices: 41638349--41638398 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
41638339 ATCCAATCCT
41638349 TGTAGCCATTAATTACAATATATA
1 TGTAGCCATTAATTACAATATATA
41638373 TGTAGCCATTAATTACAATATATA
1 TGTAGCCATTAATTACAATATATA
41638397 TG
1 TG
41638399 ATTTGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (24 bp):
TGTAGCCATTAATTACAATATATA
Found at i:41641132 original size:23 final size:24
Alignment explanation
Indices: 41641106--41641150 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41641096 ACTTAGACCC
41641106 TTAAATT-TTTTTAAAAAATTTCA
1 TTAAATTATTTTTAAAAAATTTCA
**
41641129 TTAAATTATTTTTTTAAAATTT
1 TTAAATTATTTTTAAAAAATTT
41641151 TAATTAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAAATTATTTTTAAAAAATTTCA
Found at i:41641147 original size:25 final size:26
Alignment explanation
Indices: 41641110--41641158 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
41641100 AGACCCTTAA
*
41641110 ATTTTTTTAAAAAATTTCATTAAATT
1 ATTTTTTTAAAAAATTTAATTAAATT
*
41641136 ATTTTTTT-AAAATTTTAATTAAA
1 ATTTTTTTAAAAAATTTAATTAAA
41641159 CCTAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTTTTAAAAAATTTAATTAAATT
Found at i:41642095 original size:29 final size:30
Alignment explanation
Indices: 41642040--41642100 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
41642030 TCTAGTGTTA
** *
41642040 TTTGACTTTAGTTTTTTTTATTTTTGAAGT
1 TTTGACTTTAGAATTTTATATTTTTGAAGT
41642070 TTTGACTTTAGAATTTTAT-TTTTTGAAGT
1 TTTGACTTTAGAATTTTATATTTTTGAAGT
41642099 TT
1 TT
41642101 ATTTAACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.20, C:0.03, G:0.13, T:0.64
Consensus pattern (30 bp):
TTTGACTTTAGAATTTTATATTTTTGAAGT
Found at i:41647674 original size:16 final size:17
Alignment explanation
Indices: 41647629--41647675 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
41647619 AAATAACTTA
41647629 AACTC-AAT-CTAAAAT
1 AACTCAAATCCTAAAAT
*
41647644 AACTTAAATCC-AAAAT
1 AACTCAAATCCTAAAAT
41647660 AACTCAAA-CCTAAAAT
1 AACTCAAATCCTAAAAT
41647676 TAACCGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.22
16 20 0.74
17 1 0.04
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.23
Consensus pattern (17 bp):
AACTCAAATCCTAAAAT
Found at i:41651136 original size:8 final size:8
Alignment explanation
Indices: 41651125--41651166 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
41651115 TTACTCATTT
41651125 TAAAATTA
1 TAAAATTA
*
41651133 TAAAAATA
1 TAAAATTA
41651141 TAAAA-TA
1 TAAAATTA
*
41651148 TTAAAATAA
1 -TAAAATTA
41651157 TAAAATTA
1 TAAAATTA
41651165 TA
1 TA
41651167 TTTTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 2 0.07
8 26 0.90
9 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAATTA
Found at i:41651144 original size:16 final size:17
Alignment explanation
Indices: 41651125--41651166 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
41651115 TTACTCATTT
41651125 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATAA
*
41651141 TAAAA-TATTAAAATAA
1 TAAAATTATAAAAATAA
41651157 TAAAATTATA
1 TAAAATTATA
41651167 TTTTTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:41652741 original size:31 final size:31
Alignment explanation
Indices: 41652684--41652743 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
41652674 CTCCATAACT
*
41652684 TAAATAAAAACTTTCAACTAACTCAGTGATG
1 TAAATAAAAACTTTCAAATAACTCAGTGATG
* * *
41652715 TAAATGAAAACTTTCAAATGATTCAGTGA
1 TAAATAAAAACTTTCAAATAACTCAGTGA
41652744 CTATTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (31 bp):
TAAATAAAAACTTTCAAATAACTCAGTGATG
Found at i:41653977 original size:21 final size:20
Alignment explanation
Indices: 41653928--41653984 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
41653918 AACTTGAATA
*
41653928 ATTTCACTCGATTC-AATTC
1 ATTTCACTCGACTCGAATTC
* *
41653947 AATTCAACTCAACTCGAATTTC
1 ATTTC-ACTCGACTCGAA-TTC
41653969 ATTTCACTCGACTCGA
1 ATTTCACTCGACTCGA
41653985 TTTGAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.13
20 7 0.23
21 12 0.40
22 7 0.23
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (20 bp):
ATTTCACTCGACTCGAATTC
Found at i:41663199 original size:25 final size:25
Alignment explanation
Indices: 41663137--41663199 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
41663127 ATAGAAATTC
* * *
41663137 AATTATTATTATAAATTAGTGTTGT
1 AATTATTATTGTAAATTAGTATTAT
* * *
41663162 AATTAATAGTGTAAATTATTATTAT
1 AATTATTATTGTAAATTAGTATTAT
*
41663187 TATTATTATTGTA
1 AATTATTATTGTA
41663200 GCTAGCAAAG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (25 bp):
AATTATTATTGTAAATTAGTATTAT
Found at i:41664321 original size:35 final size:35
Alignment explanation
Indices: 41664282--41664352 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
41664272 GAAATTGCAG
41664282 GGAAGGTTAGATGGTTATAAAGGGGGTTATATCGC
1 GGAAGGTTAGATGGTTATAAAGGGGGTTATATCGC
*
41664317 GGAAGGTTAGATGGTTATAAATGGGGTTATATCGC
1 GGAAGGTTAGATGGTTATAAAGGGGGTTATATCGC
41664352 G
1 G
41664353 TTCGGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.06, G:0.37, T:0.30
Consensus pattern (35 bp):
GGAAGGTTAGATGGTTATAAAGGGGGTTATATCGC
Found at i:41665067 original size:31 final size:31
Alignment explanation
Indices: 41665000--41665067 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
41664990 TGATGATTGA
* * * *
41665000 ACTATTTGAAAGTTTTTATTTAAGTCATTAT
1 ACTATTCGAAAGTTTTTATTTAAATCACTAG
41665031 ACTATTCGAAAGTTTTTATTTAAATCACTAG
1 ACTATTCGAAAGTTTTTATTTAAATCACTAG
*
41665062 GCTATT
1 ACTATT
41665068 AAGTTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (31 bp):
ACTATTCGAAAGTTTTTATTTAAATCACTAG
Found at i:41665704 original size:29 final size:31
Alignment explanation
Indices: 41665639--41665705 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
41665629 TACAACATGC
*
41665639 TTTAAGTTTTTATATTTTCTGTATTTTTGAAA
1 TTTAA-TTTTTATATTTTCTGTATTTTTAAAA
41665671 TTTAATTTTTATA-TTT-T-TATTTTTAAAAA
1 TTTAATTTTTATATTTTCTGTATTTTT-AAAA
41665700 TTTAAT
1 TTTAAT
41665706 CCTCTATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 7 0.21
29 10 0.30
30 3 0.09
31 8 0.24
32 5 0.15
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (31 bp):
TTTAATTTTTATATTTTCTGTATTTTTAAAA
Found at i:41665977 original size:14 final size:15
Alignment explanation
Indices: 41665952--41665994 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
41665942 TTTGATAAGT
41665952 TAAAAAATTAAGTGC
1 TAAAAAATTAAGTGC
*
41665967 TAAAAAA-TAAGTGT
1 TAAAAAATTAAGTGC
41665981 TAGAAAAATTAAGT
1 TA-AAAAATTAAGT
41665995 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 12 0.48
16 5 0.20
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (15 bp):
TAAAAAATTAAGTGC
Found at i:41667259 original size:18 final size:18
Alignment explanation
Indices: 41667220--41667261 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
41667210 ATTTAACAGA
41667220 ATTTTATAATATTTAAAT
1 ATTTTATAATATTTAAAT
*
41667238 -TTTTATAA-ATTATTAAT
1 ATTTTATAATATT-TAAAT
41667255 ATTTTAT
1 ATTTTAT
41667262 TTAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 12 0.57
18 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTATAATATTTAAAT
Found at i:41667802 original size:22 final size:24
Alignment explanation
Indices: 41667756--41667802 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
41667746 AAAATACTTA
41667756 TAATTTTGATTATTTTAGCATATTT
1 TAATTTTGA-TATTTTAGCATATTT
41667781 TAATTTTGA-ATTTTA-CATATTT
1 TAATTTTGATATTTTAGCATATTT
41667803 GAATATCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
25 9 0.41
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TAATTTTGATATTTTAGCATATTT
Found at i:41668811 original size:53 final size:53
Alignment explanation
Indices: 41668731--41668833 Score: 206
Period size: 53 Copynumber: 1.9 Consensus size: 53
41668721 CATGTGGTTC
41668731 ATTGAAAATTCATCTTTTAGAACATTCCAACCTTTTTTTTTCCAATGATATGA
1 ATTGAAAATTCATCTTTTAGAACATTCCAACCTTTTTTTTTCCAATGATATGA
41668784 ATTGAAAATTCATCTTTTAGAACATTCCAACCTTTTTTTTTCCAATGATA
1 ATTGAAAATTCATCTTTTAGAACATTCCAACCTTTTTTTTTCCAATGATA
41668834 CGAAGAGACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (53 bp):
ATTGAAAATTCATCTTTTAGAACATTCCAACCTTTTTTTTTCCAATGATATGA
Found at i:41678570 original size:25 final size:26
Alignment explanation
Indices: 41678528--41678580 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
41678518 CAATTTCTGG
* * *
41678528 CCGTTGGTTTCTGACCATTTGCTTGA
1 CCGTTGGGTTCTGACCATTGGATTGA
41678554 CCGTTGGGTT-TGACCATTGGATTGA
1 CCGTTGGGTTCTGACCATTGGATTGA
41678579 CC
1 CC
41678581 TTGTAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (26 bp):
CCGTTGGGTTCTGACCATTGGATTGA
Found at i:41679396 original size:2 final size:2
Alignment explanation
Indices: 41679389--41679425 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41679379 GATTGTTCAA
41679389 AT AT 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 AT AT A
41679426 CCCAATCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41679594 original size:5 final size:6
Alignment explanation
Indices: 41679559--41679591 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
41679549 ATTTTTATAG
41679559 ATTTTA ATTTTA ATTTTA ATTTTA A-TTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTT
41679592 AATCTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:41681166 original size:48 final size:48
Alignment explanation
Indices: 41681095--41681199 Score: 192
Period size: 48 Copynumber: 2.2 Consensus size: 48
41681085 TGACTAACAA
* *
41681095 TACTGACGTGGTAATTTTTTTTCACTTAGACAAGTCCATGTATGTAAT
1 TACTGACGTGGTAATTTTTTTTCACTTAGACAAGTCCACGTATGCAAT
41681143 TACTGACGTGGTAATTTTTTTTCACTTAGACAAGTCCACGTATGCAAT
1 TACTGACGTGGTAATTTTTTTTCACTTAGACAAGTCCACGTATGCAAT
41681191 TACTGACGT
1 TACTGACGT
41681200 AGCACTATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (48 bp):
TACTGACGTGGTAATTTTTTTTCACTTAGACAAGTCCACGTATGCAAT
Found at i:41681259 original size:20 final size:18
Alignment explanation
Indices: 41681231--41681278 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
41681221 ACACTTCAAT
*
41681231 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
41681251 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
41681271 AAATTATT
1 AAATTATT
41681279 AAAATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 13 0.52
21 2 0.08
22 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:41681282 original size:29 final size:29
Alignment explanation
Indices: 41681240--41681296 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
41681230 TAAATAATTT
*
41681240 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTAATTTTTAAAATA
41681269 TAAAATTATTAAAATTAATTTTTAAAAT
1 TAAAATTATTAAAATTAATTTTTAAAAT
41681297 TAATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAAATTATTAAAATTAATTTTTAAAATA
Found at i:41681308 original size:12 final size:13
Alignment explanation
Indices: 41681243--41681347 Score: 83
Period size: 13 Copynumber: 7.9 Consensus size: 13
41681233 ATAATTTTAA
*
41681243 AATTATTAAAATT
1 AATTTTTAAAATT
*
41681256 ATTTTTTAAAATAT
1 AATTTTTAAAAT-T
*
41681270 AAAATTATTAAAATT
1 --AATTTTTAAAATT
41681285 AATTTTTAAAATT
1 AATTTTTAAAATT
41681298 AATTTTT-AAA-T
1 AATTTTTAAAATT
41681309 AA-TTTTAATAATTT
1 AATTTTTAA-AA-TT
* *
41681323 TATATTTTAAAAAT
1 AAT-TTTTAAAATT
41681337 AA-TTTTAAAAT
1 AATTTTTAAAAT
41681348 CATTTGCTGA
Statistics
Matches: 74, Mismatches: 9, Indels: 19
0.73 0.09 0.19
Matches are distributed among these distances:
10 4 0.05
11 4 0.05
12 13 0.18
13 29 0.39
14 5 0.07
15 3 0.04
16 16 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTTTAAAATT
Found at i:41681704 original size:25 final size:25
Alignment explanation
Indices: 41681666--41681715 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
41681656 ATTAAGTGAT
*
41681666 ACATCAGATCTTATGTGGAATAATG
1 ACATCAGATCTTATGTGAAATAATG
* *
41681691 ACATCATATTTTATGTGAAATAATG
1 ACATCAGATCTTATGTGAAATAATG
41681716 TAAAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (25 bp):
ACATCAGATCTTATGTGAAATAATG
Found at i:41694713 original size:148 final size:142
Alignment explanation
Indices: 41694469--41694940 Score: 618
Period size: 148 Copynumber: 3.3 Consensus size: 142
41694459 AGTCCTTTAA
*
41694469 GTGATCACCATTTATCCATGCCTTAACATTTTAAACCAAA-ATAGACTAGAAAAATAAACAGTAT
1 GTGATCACCATTTAGCCATGCCTTAACATTTTAAACCAAATATAGACTAGAAAAATAAACAG-AT
41694533 ACACTATAAGTTACAGTCATCATGCCTCCACTCATCGACCCGAATATGAAACCTAAAGATTGTAA
65 A-A-TATAAGTTACA-TCATCATGCCTCCACTCATCGACCCGAATATGAAACCTAAAGATTGTAA
41694598 CTTATTAACCCTTCAT
127 CTTATTAACCCTTCAT
*
41694614 GTGATCACCATTTAGCCATACACCTTAACATTTTAAACCAAATATAGACTAGAAAAATAAACAGC
1 GTGATCACCATTTAGCCAT--GCCTTAACATTTTAAACCAAATATAGACTAGAAAAATAAACAG-
*
41694679 ATATATTATAAGTTACATTCATCATGCCTCCACTCATCCACCCGAATATGAAACCTAAAGATTGT
63 ATA-A-TATAAGTTACA-TCATCATGCCTCCACTCATCGACCCGAATATGAAACCTAAAGATTGT
41694744 AACTTATTAACCCTTCAT
125 AACTTATTAACCCTTCAT
*
41694762 GTGATCACCATTTAGCCATGCGCCTTAACATTTTAAATCAAATATAGACTAGAAAAAT--A-A-A
1 GTGATCACCATTTAGCCAT--GCCTTAACATTTTAAACCAAATATAGACTAGAAAAATAAACAGA
* * * * * * ** * *
41694823 -AAGATAAGTTACAT--GCATGCCTCCACTCATTGACCCAAACATTAAATGTAAATAATGTAACT
64 TAATATAAGTTACATCATCATGCCTCCACTCATCGACCCGAATATGAAACCTAAAGATTGTAACT
* **
41694885 TTTTAGTCCTTCAT
129 TATTAACCCTTCAT
*
41694899 GTGATCACCATTTATCCATGCCTTAACATTTTAAACCAAATA
1 GTGATCACCATTTAGCCATGCCTTAACATTTTAAACCAAATA
41694941 CATGGAAATA
Statistics
Matches: 298, Mismatches: 26, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
135 22 0.07
137 67 0.22
139 1 0.00
140 10 0.03
141 1 0.00
142 1 0.00
143 1 0.00
145 19 0.06
146 1 0.00
147 20 0.07
148 155 0.52
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (142 bp):
GTGATCACCATTTAGCCATGCCTTAACATTTTAAACCAAATATAGACTAGAAAAATAAACAGATA
ATATAAGTTACATCATCATGCCTCCACTCATCGACCCGAATATGAAACCTAAAGATTGTAACTTA
TTAACCCTTCAT
Found at i:41702121 original size:17 final size:16
Alignment explanation
Indices: 41702098--41702138 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41702088 ATAGTAAAAA
41702098 TATAATTTTAT-TATT
1 TATAATTTTATATATT
41702113 T-TAATAATTTATATATT
1 TATAAT--TTTATATATT
41702130 TATAATTTT
1 TATAATTTT
41702139 TAAAAGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.18
15 1 0.05
16 8 0.36
17 5 0.23
18 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:41704812 original size:29 final size:29
Alignment explanation
Indices: 41704769--41704824 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
41704759 ATAAAGACTT
* * *
41704769 GATCAAATTAGTCCCTCTACTTTTAAATG
1 GATCAAATTAATCCCTATACTATTAAATG
*
41704798 GATCAATTTAATCCCTATACTATTAAA
1 GATCAAATTAATCCCTATACTATTAAA
41704825 AAATTCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (29 bp):
GATCAAATTAATCCCTATACTATTAAATG
Done.