Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 101 of 214
Found at i:29564358 original size:19 final size:19
Alignment explanation
Indices: 29564327--29564373 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
29564317 ATTTAATTAT
29564327 TATATTTAAATATT-TAAA
1 TATATTTAAATATTCTAAA
*
29564345 TATAGTTTATATATTCTAAA
1 TATA-TTTAAATATTCTAAA
*
29564365 TAAATTTAA
1 TATATTTAA
29564374 TAAATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 7 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TATATTTAAATATTCTAAA
Found at i:29564413 original size:30 final size:28
Alignment explanation
Indices: 29564374--29564439 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 28
29564364 ATAAATTTAA
29564374 TAAATAATTAATATTA-ATTACTTAGAAATAT
1 TAAA-AATTAATATTATA-TA-TTA-AAATAT
*
29564405 TTAAAATTAATATTATATATTAAAATAT
1 TAAAAATTAATATTATATATTAAAATAT
29564433 TAAAAAT
1 TAAAAAT
29564440 AAGTTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 12 0.38
29 3 0.09
30 13 0.41
31 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAAAATTAATATTATATATTAAAATAT
Found at i:29564438 original size:28 final size:30
Alignment explanation
Indices: 29564374--29564439 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 30
29564364 ATAAATTTAA
29564374 TAAATAATTAATATTAATTACTTAGAAATAT
1 TAAA-AATTAATATTAATTACTTAGAAATAT
*
29564405 TTAAAATTAATATT-ATATA-TTA-AAATAT
1 TAAAAATTAATATTAAT-TACTTAGAAATAT
29564433 TAAAAAT
1 TAAAAAT
29564440 AAGTTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 12 0.38
29 5 0.16
30 12 0.38
31 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (30 bp):
TAAAAATTAATATTAATTACTTAGAAATAT
Found at i:29572338 original size:13 final size:14
Alignment explanation
Indices: 29572308--29572341 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29572298 TCAAACCAAG
*
29572308 AATTAAGCACACAT
1 AATTAAGAACACAT
29572322 AATTAAGAACA-AT
1 AATTAAGAACACAT
29572335 AATTAAG
1 AATTAAG
29572342 TATTTATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.24
Consensus pattern (14 bp):
AATTAAGAACACAT
Found at i:29598569 original size:27 final size:27
Alignment explanation
Indices: 29598538--29598803 Score: 260
Period size: 27 Copynumber: 9.9 Consensus size: 27
29598528 AAGCCCAACT
29598538 TACCCCTAAAGGGTAAAATGACTGAAA
1 TACCCCTAAAGGGTAAAATGACTGAAA
** * *
29598565 TACCCCCGAAGGGTAAAATAACCGAAA
1 TACCCCTAAAGGGTAAAATGACTGAAA
* *
29598592 TACTCCTAAAGGGTAAAAT-AATCGAAA
1 TACCCCTAAAGGGTAAAATGACT-GAAA
* * *
29598619 TACCCCTAAATGGTAAAATGACCGAAG
1 TACCCCTAAAGGGTAAAATGACTGAAA
*
29598646 TACCTCC-AAAGGGTAAAATGACTGTAA
1 TACC-CCTAAAGGGTAAAATGACTGAAA
*
29598673 CA-CCCTCAAAGGGTAAAATGACTGAAA
1 TACCCCT-AAAGGGTAAAATGACTGAAA
* *
29598700 TA-CCCTCAAAGGATAGAATGA-TCGAAA
1 TACCCCT-AAAGGGTAAAATGACT-GAAA
* *
29598727 TA-CCCTCGAAGGGTAAAATGATTGAAA
1 TACCCCT-AAAGGGTAAAATGACTGAAA
*
29598754 TACCTCC-AAAGGGTAAAATGACTAAAA
1 TACC-CCTAAAGGGTAAAATGACTGAAA
*
29598781 TACCCC-ATAGGGTAAAATGACTG
1 TACCCCTAAAGGGTAAAATGACTG
29598804 TTATACCCAT
Statistics
Matches: 199, Mismatches: 31, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.01
26 20 0.10
27 170 0.85
28 5 0.03
29 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
TACCCCTAAAGGGTAAAATGACTGAAA
Found at i:29598637 original size:81 final size:81
Alignment explanation
Indices: 29598538--29598803 Score: 301
Period size: 81 Copynumber: 3.3 Consensus size: 81
29598528 AAGCCCAACT
* *
29598538 TACCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATAACCGAAATACTCCTAAAG
1 TACCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACTGAAATACTCCTAAAG
*
29598603 GGTAAAAT-AATCGAAA
66 GGTAAAATGACT-GAAA
* * * * * * *
29598619 TACCCCTAAATGGTAAAATGACCGAAGTACCTCCAAAGGGTAAAATGACTGTAACAC-CCTCAAA
1 TACCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACTGAAATACTCCT-AAA
29598683 GGGTAAAATGACTGAAA
65 GGGTAAAATGACTGAAA
* * * *
29598700 TA-CCCTCAAAGGATAGAATGA-TCGAAATACCCTCGAAGGGTAAAATGATTGAAATACCTCC-A
1 TACCCCT-AAAGGGTAAAATGACT-GAAATACCCCCGAAGGGTAAAATGACTGAAATA-CTCCTA
*
29598762 AAGGGTAAAATGACTAAAA
63 AAGGGTAAAATGACTGAAA
*
29598781 TACCCC-ATAGGGTAAAATGACTG
1 TACCCCTAAAGGGTAAAATGACTG
29598804 TTATACCCAT
Statistics
Matches: 152, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
80 19 0.12
81 125 0.82
82 6 0.04
83 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (81 bp):
TACCCCTAAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACTGAAATACTCCTAAAG
GGTAAAATGACTGAAA
Found at i:29599198 original size:28 final size:28
Alignment explanation
Indices: 29599138--29599201 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
29599128 GTTGCATTAT
* * *
29599138 CACACTATTATTATATTGGGCTAAGGCC
1 CACACTGTTATTATATCGAGCTAAGGCC
* *
29599166 CACACTGTTATTGTATCGAGCTAAGGCT
1 CACACTGTTATTATATCGAGCTAAGGCC
*
29599194 GACACTGT
1 CACACTGT
29599202 ACTGTTACTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (28 bp):
CACACTGTTATTATATCGAGCTAAGGCC
Found at i:29605749 original size:19 final size:19
Alignment explanation
Indices: 29605711--29605762 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
29605701 TTCTGTTGCT
* *
29605711 GTAAGTGTTTTTGGCTATCG
1 GTAAGTGTTTAT-ACTATCG
29605731 GTAAGTGTTTATACTATCG
1 GTAAGTGTTTATACTATCG
29605750 GTAAGTGTTTATA
1 GTAAGTGTTTATA
29605763 ATTCGCACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (19 bp):
GTAAGTGTTTATACTATCG
Found at i:29606220 original size:27 final size:27
Alignment explanation
Indices: 29606189--29606319 Score: 165
Period size: 27 Copynumber: 4.8 Consensus size: 27
29606179 AAGCCCAACT
*
29606189 TACCCTCGAAGGGTAAAATGACCGAAA
1 TACCCCCGAAGGGTAAAATGACCGAAA
*
29606216 TACCCCCGAAGGGTAAAATGACCAAAA
1 TACCCCCGAAGGGTAAAATGACCGAAA
*
29606243 TACCCCCGAAGGGTAAAATGACTGAAA
1 TACCCCCGAAGGGTAAAATGACCGAAA
* * *
29606270 TACCCCCCAAAGGGTAAAAAGATC-AGAA
1 TA-CCCCCGAAGGGTAAAATGACCGA-AA
**
29606298 TACCCCTAAAGGGTAAAATGAC
1 TACCCCCGAAGGGTAAAATGAC
29606320 TAAAATGCCC
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
27 70 0.77
28 21 0.23
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (27 bp):
TACCCCCGAAGGGTAAAATGACCGAAA
Found at i:29606302 original size:55 final size:55
Alignment explanation
Indices: 29606189--29606330 Score: 187
Period size: 55 Copynumber: 2.6 Consensus size: 55
29606179 AAGCCCAACT
* * * *
29606189 TACCCTCGAAGGGTAAAATGACCGAAATA-CCCCCGAAGGGTAAAATGACCAAAA
1 TACCCCCGAAGGGTAAAATGACTGAAATACCCCCCAAAGGGTAAAAAGACCAAAA
* *
29606243 TACCCCCGAAGGGTAAAATGACTGAAATACCCCCCAAAGGGTAAAAAGATCAGAA
1 TACCCCCGAAGGGTAAAATGACTGAAATACCCCCCAAAGGGTAAAAAGACCAAAA
** * *
29606298 TACCCCTAAAGGGTAAAATGACTAAAATGCCCC
1 TACCCCCGAAGGGTAAAATGACTGAAATACCCC
29606331 ATAGGTAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 27 0.35
55 50 0.65
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (55 bp):
TACCCCCGAAGGGTAAAATGACTGAAATACCCCCCAAAGGGTAAAAAGACCAAAA
Found at i:29608129 original size:49 final size:49
Alignment explanation
Indices: 29608050--29608582 Score: 820
Period size: 49 Copynumber: 11.1 Consensus size: 49
29608040 TATTTGAATA
29608050 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
29608097 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
29608146 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
29608193 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
29608242 AATGTGAAAGTTTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
**
29608291 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCTGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
29608340 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
29608389 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
29608436 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
29608485 AATGTGAACA-TG--TGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
29608532 AATGTGAACA-TG--TGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
29608579 AATG
1 AATG
29608583 AGAACACTTT
Statistics
Matches: 466, Mismatches: 13, Indels: 14
0.95 0.03 0.03
Matches are distributed among these distances:
47 186 0.40
49 279 0.60
50 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
Found at i:29608158 original size:96 final size:96
Alignment explanation
Indices: 29608050--29608582 Score: 817
Period size: 96 Copynumber: 5.5 Consensus size: 96
29608040 TATTTGAATA
29608050 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
29608115 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
*
29608146 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
29608211 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
* *
29608242 AATGTGAAAGTTTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAG--TGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
*
29608307 TATATGTGATAAGGCCTAATGGCTGATGTGATG
64 TATATGTGATAAGGCCTAATGGCCGATGTGATG
*
29608340 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
* *
29608403 TATATGTGATAAGGCCGAATGGCCAATGTGATG
64 TATATGTGATAAGGCCTAATGGCCGATGTGATG
*
29608436 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG--T
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA-AGTGTAT
* * * *
29608498 GTATGTGTGATAAGGCCGAATGGCCAATGTGATG
63 ATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
29608532 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATG
29608583 AGAACACTTT
Statistics
Matches: 416, Mismatches: 15, Indels: 14
0.93 0.03 0.03
Matches are distributed among these distances:
94 37 0.09
96 238 0.57
97 2 0.00
98 139 0.33
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (96 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:29608527 original size:38 final size:39
Alignment explanation
Indices: 29608485--29608576 Score: 105
Period size: 47 Copynumber: 2.2 Consensus size: 39
29608475 CAATGTGATG
29608485 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGA
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCC------A
29608530 TGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCC-
1 --AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
29608570 AATGTGA
1 AATGTGA
29608577 TGAATGAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
38 7 0.16
47 38 0.84
ACGTcount: A:0.30, C:0.11, G:0.32, T:0.27
Consensus pattern (39 bp):
AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
Found at i:29610311 original size:38 final size:38
Alignment explanation
Indices: 29610247--29610321 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
29610237 AATCCGAGTT
*
29610247 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
29610285 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
29610322 ATTAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:29610437 original size:40 final size:40
Alignment explanation
Indices: 29610375--29610735 Score: 562
Period size: 40 Copynumber: 9.1 Consensus size: 40
29610365 AGGTCTCGAC
29610375 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
29610414 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
29610454 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * *
29610494 GATGTATCCGGGTTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
29610534 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
29610574 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
29610614 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * ** * *
29610654 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * *
29610694 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
29610734 GA
1 GA
29610736 CGTGTATTCG
Statistics
Matches: 297, Mismatches: 24, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
39 4 0.01
40 293 0.99
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:29612074 original size:41 final size:41
Alignment explanation
Indices: 29612029--29612159 Score: 101
Period size: 41 Copynumber: 3.1 Consensus size: 41
29612019 AAAACATGTC
29612029 ATAAACATGTTGGGGTAGTGCATTATGTAAGGATTAATAAA
1 ATAAACATGTTGGGGTAGTGCATTATGTAAGGATTAATAAA
* ** * * *
29612070 ATAAAGA-GTAT-GGGT-G-GACAAGATGTTATGG-CTAAAAACA
1 ATAAACATGT-TGGGGTAGTG-CATTATG-TAAGGATTAATAA-A
29612110 TGTCATAAACATGTTGGGGTAGTGCATTATGTAAGGATTAATAAA
1 ----ATAAACATGTTGGGGTAGTGCATTATGTAAGGATTAATAAA
29612155 ATAAA
1 ATAAA
29612160 GGGCATGGGC
Statistics
Matches: 65, Mismatches: 12, Indels: 26
0.63 0.12 0.25
Matches are distributed among these distances:
38 1 0.02
39 11 0.17
40 11 0.17
41 12 0.18
44 7 0.11
45 11 0.17
46 11 0.17
47 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.29
Consensus pattern (41 bp):
ATAAACATGTTGGGGTAGTGCATTATGTAAGGATTAATAAA
Found at i:29612168 original size:85 final size:85
Alignment explanation
Indices: 29611990--29612168 Score: 340
Period size: 85 Copynumber: 2.1 Consensus size: 85
29611980 GGCCGGCCAT
29611990 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
29612055 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
29612075 GAGTATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
29612140 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
29612160 GGGCATGGG
1 GAGCATGGG
29612169 CAATAAAATA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.27
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:29613543 original size:96 final size:96
Alignment explanation
Indices: 29613435--29614014 Score: 929
Period size: 96 Copynumber: 6.0 Consensus size: 96
29613425 TATTTGAATA
29613435 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
29613500 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
* *
29613531 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
*
29613594 TATGTGATAAGGCCTAATAGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
*
29613625 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
29613690 TATATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATATGTGATAAGGCCTAATGGCCGATGTGATG
*
29613723 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
29613788 TATATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATATGTGATAAGGCCTAATGGCCGATGTGATG
*
29613821 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
*
29613886 TATGTGATAAGGCCGAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
* * * *
29613917 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG--TG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA-AGTGTATA
* * * *
29613978 TATGTGTGATAAGGCCGAAAGGCCAATGTGATG
64 TATATGTGATAAGGCCTAATGGCCGATGTGATG
29614011 AATG
1 AATG
29614015 AGAACACTTT
Statistics
Matches: 464, Mismatches: 14, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
94 81 0.17
96 237 0.51
97 2 0.00
98 144 0.31
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (96 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:29613947 original size:39 final size:39
Alignment explanation
Indices: 29613904--29613995 Score: 112
Period size: 47 Copynumber: 2.2 Consensus size: 39
29613894 AAGGCCGAAT
29613904 GGCCGATGTGATGAATGTGAACATGTGTATGTGTGATAA
1 GGCCGATGTGATGAATGTGAACATGTGTATGTGTGATAA
29613943 GGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAA
1 GGCC-----G---ATGTGATGAATGTGAACATGTGTATGTGTGATAA
29613990 GGCCGA
1 GGCCGA
29613996 AAGGCCAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
39 5 0.11
42 1 0.02
44 1 0.02
47 38 0.84
ACGTcount: A:0.28, C:0.11, G:0.34, T:0.27
Consensus pattern (39 bp):
GGCCGATGTGATGAATGTGAACATGTGTATGTGTGATAA
Found at i:29614020 original size:47 final size:48
Alignment explanation
Indices: 29613435--29614014 Score: 897
Period size: 49 Copynumber: 12.1 Consensus size: 48
29613425 TATTTGAATA
*
29613435 AATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
29613482 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
29613531 AATGTGAAAGTG-TATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
29613578 AATGTGAAAGTG-TATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
29613625 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATG
29613674 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATG
29613723 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATG
29613772 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
29613821 AATGTGAAAGTG-TATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
29613868 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * *
29613917 AATGTGAACA-TG-TGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
29613964 AATGTGAACA-TG-TGTATGTGTGATAAGGCCGAAAGGCCAATGTGATG
1 AATGTGAA-AGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
29614011 AATG
1 AATG
29614015 AGAACACTTT
Statistics
Matches: 516, Mismatches: 10, Indels: 14
0.96 0.02 0.03
Matches are distributed among these distances:
47 232 0.45
49 283 0.55
50 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (48 bp):
AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:29615272 original size:26 final size:25
Alignment explanation
Indices: 29615234--29615287 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
29615224 GTTGCCACAT
29615234 ATACTGTTCTGGCAGCTTCGCTGCG
1 ATACTGTTCTGGCAGCTTCGCTGCG
* *
29615259 ATACTTTTACTGGCAGCTTTGCTGCG
1 ATACTGTT-CTGGCAGCTTCGCTGCG
29615285 ATA
1 ATA
29615288 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (25 bp):
ATACTGTTCTGGCAGCTTCGCTGCG
Found at i:29621174 original size:27 final size:27
Alignment explanation
Indices: 29621117--29621187 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
29621107 CTATACATGT
29621117 ATGCTCACACGAGCTGT-AAAATCAGA
1 ATGCTCACACGAGCTGTGAAAATCAGA
* *
29621143 ATGCTCACACGAGTTGTGAAAAT-AGGC
1 ATGCTCACACGAGCTGTGAAAATCA-GA
*
29621170 CTGCTCACACGAGCTGTG
1 ATGCTCACACGAGCTGTG
29621188 GGTCGAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 17 0.44
27 22 0.56
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (27 bp):
ATGCTCACACGAGCTGTGAAAATCAGA
Found at i:29625051 original size:22 final size:22
Alignment explanation
Indices: 29625024--29625066 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29625014 AGTGATATAA
29625024 GGTGGTGCCAAGGTGGTGATAC
1 GGTGGTGCCAAGGTGGTGATAC
** *
29625046 GGTGGTGTTAGGGTGGTGATA
1 GGTGGTGCCAAGGTGGTGATA
29625067 TGTTGGTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.07, G:0.49, T:0.28
Consensus pattern (22 bp):
GGTGGTGCCAAGGTGGTGATAC
Found at i:29639601 original size:12 final size:12
Alignment explanation
Indices: 29639559--29639602 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
29639549 TTAGTGAGTA
* *
29639559 ACACGGCCTAGC
1 ACACGGGCTGGC
*
29639571 ACACGGTCTGGC
1 ACACGGGCTGGC
29639583 ACACGGGCTGGC
1 ACACGGGCTGGC
29639595 ACACGGGC
1 ACACGGGC
29639603 GTTTGACACG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.20, C:0.36, G:0.34, T:0.09
Consensus pattern (12 bp):
ACACGGGCTGGC
Found at i:29641916 original size:12 final size:12
Alignment explanation
Indices: 29641899--29641924 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29641889 CATTCCGAAG
29641899 TATATATATACA
1 TATATATATACA
29641911 TATATATATACA
1 TATATATATACA
29641923 TA
1 TA
29641925 AGTATGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:29642457 original size:28 final size:27
Alignment explanation
Indices: 29642400--29642551 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
29642390 TTAATTGTGC
*
29642400 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
29642427 AGCACTAAGCGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
29642455 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
29642482 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
29642510 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
29642537 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29642552 GACTTAATAT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 65 0.56
28 52 0.44
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:29642461 original size:55 final size:55
Alignment explanation
Indices: 29642400--29642551 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
29642390 TTAATTGTGC
* *
29642400 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGCGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
29642455 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
29642510 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
29642552 GACTTAATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:29650657 original size:28 final size:27
Alignment explanation
Indices: 29650600--29650751 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
29650590 TAAATTGTGC
*
29650600 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
29650627 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
29650655 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
29650682 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
29650710 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
29650737 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29650752 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:29650665 original size:55 final size:55
Alignment explanation
Indices: 29650600--29650751 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
29650590 TAAATTGTGC
*
29650600 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
29650655 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
29650710 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
29650752 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:29653313 original size:16 final size:16
Alignment explanation
Indices: 29653292--29653323 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29653282 TAGGTCACTA
*
29653292 ACAGAGTCTTTGAAGC
1 ACAGAGTCTTTAAAGC
29653308 ACAGAGTCTTTAAAGC
1 ACAGAGTCTTTAAAGC
29653324 TGCACATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (16 bp):
ACAGAGTCTTTAAAGC
Found at i:29667591 original size:39 final size:40
Alignment explanation
Indices: 29667387--29667650 Score: 254
Period size: 40 Copynumber: 6.7 Consensus size: 40
29667377 TTGAATGCTG
* * * *
29667387 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
**
29667427 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
29667466 TTCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGATAC-AAA
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
29667506 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * * **
29667547 ACCGGGTTAAGTCCCGAA-GCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
29667586 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
29667625 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
29667651 AACGAGGAGC
Statistics
Matches: 193, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
39 67 0.35
40 112 0.58
41 13 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:29667668 original size:79 final size:79
Alignment explanation
Indices: 29667507--29667683 Score: 196
Period size: 78 Copynumber: 2.3 Consensus size: 79
29667497 AGATACAAAT
* * *
29667507 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAAACCGGGTTAAGTCCCGAAGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGCATTCG
** ** *
29667572 TGCGAGTTGTTAAA
66 AACGAGGAGCTAAA
* * * * *
29667586 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAA-GCATTC
*
29667650 GAACGAGGAGCTATA
65 GAACGAGGAGCTAAA
*
29667665 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
29667684 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
78 46 0.57
79 35 0.43
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGCATTCG
AACGAGGAGCTAAA
Found at i:29683854 original size:77 final size:77
Alignment explanation
Indices: 29683771--29683925 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
29683761 ATAACTTTGT
29683771 AATCAGATGCGGAAAGAATGTTATTTTTTTTCTAATTTCCTGCACATTCAATCATATTTCGATAT
1 AATCAGATGCGGAAAGAATGTTATTTTTTTTCTAATTTCCTGCACATTCAATCATATTTCGATAT
29683836 ATCCATGTACCA
66 ATCCATGTACCA
29683848 AATCAGATGCGGAAAGAATGTTATTTTTTTTCTAATTTCCTGCACATTCAATCATATTTCGATAT
1 AATCAGATGCGGAAAGAATGTTATTTTTTTTCTAATTTCCTGCACATTCAATCATATTTCGATAT
29683913 ATCCATGTACCA
66 ATCCATGTACCA
29683925 A
1 A
29683926 TGCATACTTG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (77 bp):
AATCAGATGCGGAAAGAATGTTATTTTTTTTCTAATTTCCTGCACATTCAATCATATTTCGATAT
ATCCATGTACCA
Found at i:29686516 original size:17 final size:17
Alignment explanation
Indices: 29686491--29686540 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
29686481 TGTAAATAAT
29686491 AACTACTAGAAATCATA
1 AACTACTAGAAATCATA
*
29686508 AATTACTAGAAATC--A
1 AACTACTAGAAATCATA
29686523 AACTACTAGAAATCATA
1 AACTACTAGAAATCATA
29686540 A
1 A
29686541 TTAGCTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 14 0.48
17 15 0.52
ACGTcount: A:0.54, C:0.16, G:0.06, T:0.24
Consensus pattern (17 bp):
AACTACTAGAAATCATA
Found at i:29686531 original size:15 final size:15
Alignment explanation
Indices: 29686491--29686537 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
29686481 TGTAAATAAT
29686491 AACTACTAGAAATCATA
1 AACTACTAGAAATC--A
*
29686508 AATTACTAGAAATCA
1 AACTACTAGAAATCA
29686523 AACTACTAGAAATCA
1 AACTACTAGAAATCA
29686538 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.54
17 13 0.46
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.23
Consensus pattern (15 bp):
AACTACTAGAAATCA
Found at i:29688299 original size:28 final size:28
Alignment explanation
Indices: 29688267--29688322 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
29688257 TTTTGACTAG
29688267 TAGGAGTAATATTACAGGTGAAAAAATT
1 TAGGAGTAATATTACAGGTGAAAAAATT
* *
29688295 TAGGAGTAATATTAGAGGTGCAAAAATT
1 TAGGAGTAATATTACAGGTGAAAAAATT
29688323 AGTTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.29
Consensus pattern (28 bp):
TAGGAGTAATATTACAGGTGAAAAAATT
Found at i:29691631 original size:21 final size:22
Alignment explanation
Indices: 29691605--29691645 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
29691595 CAAGTCTATC
*
29691605 AAATAAACATA-AACTTCAAAG
1 AAATAAACATACAAATTCAAAG
*
29691626 AAATAAGCATACAAATTCAA
1 AAATAAACATACAAATTCAA
29691646 CCATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.61, C:0.15, G:0.05, T:0.20
Consensus pattern (22 bp):
AAATAAACATACAAATTCAAAG
Found at i:29692315 original size:42 final size:41
Alignment explanation
Indices: 29692222--29692323 Score: 150
Period size: 42 Copynumber: 2.5 Consensus size: 41
29692212 TGAAATGGCC
* *
29692222 CTGCTCACACGAGCTGTGGGTCGGCATGTAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
*
29692263 CTACTCACACGAGCTGTGGGTCAGAATGTAAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGT-AGCTACACGATG
* *
29692305 CTGCTTACACGAGTTGTGG
1 CTGCTCACACGAGCTGTGG
29692324 AGAATTCACA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
41 26 0.48
42 28 0.52
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.24
Consensus pattern (41 bp):
CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
Found at i:29701897 original size:17 final size:17
Alignment explanation
Indices: 29701875--29701909 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29701865 CATAGATATT
29701875 AACTAACACAAAAATAA
1 AACTAACACAAAAATAA
**
29701892 AACTAATGCAAAAATAA
1 AACTAACACAAAAATAA
29701909 A
1 A
29701910 TACATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.14, G:0.03, T:0.14
Consensus pattern (17 bp):
AACTAACACAAAAATAA
Found at i:29710434 original size:75 final size:77
Alignment explanation
Indices: 29710311--29710521 Score: 336
Period size: 75 Copynumber: 2.8 Consensus size: 77
29710301 TGAGTCCCCC
* * * *
29710311 AAGGGGTTGCTAAGTGTTGTTTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA-T
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
29710375 TTTAAATGTG-A
66 TTTAAATGTGAA
*
29710386 AAGGGGTTACTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
*
29710451 TTTGAATGTGAA
66 TTTAAATGTGAA
* *
29710463 AAGGGGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAATCCAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCAC
29710522 TGATAACGGA
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
75 58 0.46
76 10 0.08
77 57 0.46
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (77 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
TTTAAATGTGAA
Found at i:29710437 original size:33 final size:33
Alignment explanation
Indices: 29710390--29710515 Score: 101
Period size: 33 Copynumber: 3.5 Consensus size: 33
29710380 ATGTGAAAGG
*
29710390 GGTTACTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
29710423 GGTTGCTAAGTGCTGATTCCACC-ATATTTTTGAATGTGAAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-A----T-CAT-TG----GT
*
29710467 GGTTGCTAAGTGCTAATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
29710500 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
29710516 ATCCACTGAT
Statistics
Matches: 73, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
33 36 0.49
34 3 0.04
37 2 0.03
38 3 0.04
39 3 0.04
40 2 0.03
43 3 0.04
44 21 0.29
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:29726270 original size:71 final size:69
Alignment explanation
Indices: 29726185--29726330 Score: 220
Period size: 71 Copynumber: 2.1 Consensus size: 69
29726175 TATTATCTTC
*
29726185 AAGTAAGTTTTTTTATTTAAAAAAATTTATGAGCCAGATAATGAAAATAGAGACCCCAAATACGG
1 AAGTAAGTTTTTTTATTTAAAAAAATTTATGAGCCAGATAATCAAAATAGAGACCCCAAATACGG
29726250 AAGA
66 AAGA
* * * * *
29726254 AAGTAAGTTTTTTTTTATTTAAAAAACTTTGTGAGCCAGATAATCAAAATAGAGATCCTAAATAT
1 AAGTAAG--TTTTTTTATTTAAAAAAATTTATGAGCCAGATAATCAAAATAGAGACCCCAAATAC
29726319 GGAAGA
64 GGAAGA
29726325 AAGTAA
1 AAGTAA
29726331 ATCAACACAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
69 7 0.10
71 62 0.90
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (69 bp):
AAGTAAGTTTTTTTATTTAAAAAAATTTATGAGCCAGATAATCAAAATAGAGACCCCAAATACGG
AAGA
Found at i:29730171 original size:20 final size:20
Alignment explanation
Indices: 29730129--29730171 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29730119 CTAACCAAAG
** *
29730129 ATATACTATAAATATTAATA
1 ATATACTATAAATAGAAAAA
29730149 ATATACTATAAATAGAAAAA
1 ATATACTATAAATAGAAAAA
29730169 ATA
1 ATA
29730172 AATGCAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATACTATAAATAGAAAAA
Found at i:29760359 original size:16 final size:16
Alignment explanation
Indices: 29760338--29760370 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29760328 TCTAATGAGG
29760338 TTTTTTT-TTTCTAAA
1 TTTTTTTATTTCTAAA
*
29760353 TTTTTTTATTTCTCAA
1 TTTTTTTATTTCTAAA
29760369 TT
1 TT
29760371 AGGTGCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTATTTCTAAA
Found at i:29775069 original size:26 final size:27
Alignment explanation
Indices: 29775040--29775090 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
29775030 GACCGTAATG
29775040 CCCCTAGAGGGTAAATGACT-ATTTTT
1 CCCCTAGAGGGTAAATGACTGATTTTT
*
29775066 CCCCTCGAGGGTAAATGACTGATTT
1 CCCCTAGAGGGTAAATGACTGATTT
29775091 GTGCTATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (27 bp):
CCCCTAGAGGGTAAATGACTGATTTTT
Found at i:29780874 original size:17 final size:17
Alignment explanation
Indices: 29780852--29780886 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29780842 CATAGATATT
29780852 AACTAACACAAAAATAA
1 AACTAACACAAAAATAA
**
29780869 AACTAATGCAAAAATAA
1 AACTAACACAAAAATAA
29780886 A
1 A
29780887 TACATAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.14, G:0.03, T:0.14
Consensus pattern (17 bp):
AACTAACACAAAAATAA
Found at i:29783254 original size:16 final size:16
Alignment explanation
Indices: 29783233--29783300 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
29783223 TTTGGTTCGC
29783233 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29783249 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
29783265 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
29783281 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29783297 TGTA
1 TGTA
29783301 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:29783556 original size:16 final size:16
Alignment explanation
Indices: 29783516--29783570 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
29783506 TTAATCATAT
*
29783516 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
29783532 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
29783547 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
29783565 -TAAAAT
1 TTAAAAT
29783571 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:29783563 original size:18 final size:17
Alignment explanation
Indices: 29783536--29783570 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29783526 TTTTTATTAA
*
29783536 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29783554 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29783571 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29783683 original size:18 final size:17
Alignment explanation
Indices: 29783656--29783690 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29783646 TTACTATTAA
*
29783656 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29783674 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29783691 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29783736 original size:61 final size:60
Alignment explanation
Indices: 29783551--29783741 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
29783541 TTTTAATTAA
* *
29783551 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATTAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATAAATTTTCT-AAATCAT
* * * * * *
29783612 AATATATGATACT-GTAAAA-T-ATAA-ATTAACATAATTAC-TAT-TAAATATATT-TTAATTA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATT-CTTATATAAAT-T-TTCTAAATCA
*
29783670 A
60 T
*
29783671 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCT-AAATCAT
29783732 AATATATAAT
1 AATATATAAT
29783742 ACTATGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 30 0.31
60 18 0.18
61 39 0.40
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAATCAT
Found at i:29783819 original size:120 final size:120
Alignment explanation
Indices: 29783514--29783797 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
29783504 ATTTAATCAT
*
29783514 ATTTAAACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAAT-
* * * *
29783579 ATT-AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
64 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
* *
29783635 AATTAACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
* *
29783700 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
29783755 ATTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
29783798 TTTTCAATTA
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 133 0.89
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:29787309 original size:14 final size:14
Alignment explanation
Indices: 29787290--29787317 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29787280 CAAGACCGTC
29787290 ATGGCCACCAATCT
1 ATGGCCACCAATCT
29787304 ATGGCCACCAATCT
1 ATGGCCACCAATCT
29787318 CTTCATCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (14 bp):
ATGGCCACCAATCT
Found at i:29794519 original size:77 final size:75
Alignment explanation
Indices: 29794279--29794558 Score: 347
Period size: 69 Copynumber: 3.8 Consensus size: 75
29794269 TGATTCCCCC
* **
29794279 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTTAGTGCTGATTCCACCATATT
1 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACTGTATT
29794344 TTAAATGTGA
66 TTAAATGTGA
* * * * *
29794354 AGGGGGTTGCTAAGTGCTGATTCCCC----CA-AGG-GGTTGCTAAGTGCTGATCCCACTGTATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACTGTATT
29794413 TTAAATGTGA
66 TTAAATGTGA
* *
29794423 AAGGGGTTGTTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACTGTATT
1 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACTGTA-T
*
29794488 TTTGAATGTGAA
65 TTTAAATGTG-A
* * * * * *
29794500 AAAGGGTTGCTAAGTGTTGATTCCCTGAATCATTGGTTGTTGCTACGTGCTGAATCCAC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCAC
29794559 CGAAAACGAA
Statistics
Matches: 173, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
69 56 0.32
70 2 0.01
71 2 0.01
73 2 0.01
74 2 0.01
75 48 0.28
76 9 0.05
77 52 0.30
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.35
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACTGTATT
TTAAATGTGA
Found at i:29800789 original size:27 final size:27
Alignment explanation
Indices: 29800758--29800935 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29800748 TAAATTGTAC
29800758 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29800785 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29800811 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29800839 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29800867 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29800894 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29800921 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29800936 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29800872 original size:82 final size:81
Alignment explanation
Indices: 29800759--29800914 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29800749 AAATTGTACA
* *
29800759 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29800823 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29800840 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29800905 TGCGAGTTGA
65 TGCGAATTGA
29800915 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29800926 original size:82 final size:81
Alignment explanation
Indices: 29800755--29800935 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
29800745 GATTAAATTG
* *
29800755 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29800820 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29800836 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29800900 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29800918 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29800936 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29802332 original size:23 final size:23
Alignment explanation
Indices: 29802306--29802351 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29802296 ACTGGTGAAT
29802306 TCAGTGTTCTCGTCTTAACAATA
1 TCAGTGTTCTCGTCTTAACAATA
29802329 TCAGTGTTCTCGTCTTAACAATA
1 TCAGTGTTCTCGTCTTAACAATA
29802352 GTTAAACGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (23 bp):
TCAGTGTTCTCGTCTTAACAATA
Found at i:29813561 original size:69 final size:69
Alignment explanation
Indices: 29813476--29813619 Score: 216
Period size: 69 Copynumber: 2.1 Consensus size: 69
29813466 TATTATCTTC
* * * *
29813476 AAGTAAGTTTTTTTATTTAAAAAAATTTATGAGCCAGATAATCGAAATAGAGACCCCAAATACGG
1 AAGTAAGTTTTTTTATTTAAAAAAATTTATAAGCCAGATAATCAAAATAAAGACCCCAAATACAG
29813541 AAGA
66 AAGA
* * * *
29813545 AAGTAATTTTTTTTATTTAAAAAACTTTGTAAGCCAGATAATCAAAATAAAGACCCTAAATACAG
1 AAGTAAGTTTTTTTATTTAAAAAAATTTATAAGCCAGATAATCAAAATAAAGACCCCAAATACAG
29813610 AAGA
66 AAGA
29813614 AAGTAA
1 AAGTAA
29813620 ATCAACACAC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.28
Consensus pattern (69 bp):
AAGTAAGTTTTTTTATTTAAAAAAATTTATAAGCCAGATAATCAAAATAAAGACCCCAAATACAG
AAGA
Found at i:29817433 original size:20 final size:20
Alignment explanation
Indices: 29817391--29817433 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29817381 CTAACCAAAG
** *
29817391 ATATACTATAAATATTAATA
1 ATATACTATAAATAGAAAAA
29817411 ATATACTATAAATAGAAAAA
1 ATATACTATAAATAGAAAAA
29817431 ATA
1 ATA
29817434 AATGCAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATACTATAAATAGAAAAA
Found at i:29834225 original size:16 final size:16
Alignment explanation
Indices: 29834204--29834235 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29834194 GTTTTCTTGC
*
29834204 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
29834220 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
29834236 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:29834521 original size:51 final size:51
Alignment explanation
Indices: 29834463--29834649 Score: 186
Period size: 51 Copynumber: 3.7 Consensus size: 51
29834453 TCGGTTCACA
*
29834463 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATACACG
* * * * * * *
29834514 TAGTAGCCTACACATAATACTACACACGTGATCGA--AGCTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGATACACG
* * * *
29834565 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGA-ACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATC-CGATACACG
*
29834615 TAGTAGCCTGCACATAGTACTACACACATGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
29834650 AACTTTCACT
Statistics
Matches: 109, Mismatches: 21, Indels: 14
0.76 0.15 0.10
Matches are distributed among these distances:
49 2 0.02
50 36 0.33
51 68 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATACACG
Found at i:29837089 original size:20 final size:20
Alignment explanation
Indices: 29837064--29837102 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29837054 TACTTTCTTC
29837064 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
29837084 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
29837103 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:29837442 original size:50 final size:50
Alignment explanation
Indices: 29837302--29837494 Score: 151
Period size: 50 Copynumber: 3.9 Consensus size: 50
29837292 TAATAACATG
* * * ** *
29837302 CCAAAGCCATGTCCCAGACATGTTCTTACATGGGATGTTTC-T-T-GTACTA
1 CCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCG-A-TA
* * * * * ** *
29837351 CAAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATC-AGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGA-TA
* * *
29837401 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGATA
1 CCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGATA
* * *
29837451 CCAACGCCATGTCCTAGACATGGTCTTATGTGGGACCTCTCATA
1 CCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATA
29837495 ACCTCAATAA
Statistics
Matches: 112, Mismatches: 28, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
49 32 0.29
50 78 0.70
51 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGATA
Found at i:29840531 original size:9 final size:9
Alignment explanation
Indices: 29840517--29840544 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29840507 TGCAACTGAG
29840517 CTTTCAATT
1 CTTTCAATT
29840526 CTTTCAATT
1 CTTTCAATT
29840535 CTTTCAATT
1 CTTTCAATT
29840544 C
1 C
29840545 CAATGGGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (9 bp):
CTTTCAATT
Found at i:29858167 original size:27 final size:27
Alignment explanation
Indices: 29858137--29858192 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
29858127 CATGTTTAAA
29858137 ATTTGGCATGCTTTAGACATCCATAGC
1 ATTTGGCATGCTTTAGACATCCATAGC
*
29858164 ATTTGGCATGCTTTAGACATCCATGGC
1 ATTTGGCATGCTTTAGACATCCATAGC
29858191 AT
1 AT
29858193 CTCATACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
ATTTGGCATGCTTTAGACATCCATAGC
Found at i:29874208 original size:5 final size:5
Alignment explanation
Indices: 29874198--29874244 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
29874188 AGAAGAGGGA
29874198 AAAAG AAAAG AAAAG AAAAG AAAA- AGAAAG AAAA- AGAAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG A-AAAG AAAAG AAA
29874245 GGAGGAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 6 0.16
5 30 0.81
6 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:29874220 original size:21 final size:20
Alignment explanation
Indices: 29874196--29874240 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
29874186 TGAGAAGAGG
29874196 GAAAAAGAAA-AGAAAAGAAAA
1 GAAAAAGAAAGA-AAAAG-AAA
29874217 GAAAAAGAAAGAAAAAGAAA
1 GAAAAAGAAAGAAAAAGAAA
29874237 GAAA
1 GAAA
29874241 GAAAGGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 15 0.65
22 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
GAAAAAGAAAGAAAAAGAAA
Found at i:29877757 original size:27 final size:27
Alignment explanation
Indices: 29877727--29877904 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29877717 ATATTGAGTC
* * * *
29877727 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29877754 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29877781 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29877809 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29877836 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29877863 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29877890 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29877905 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29877866 original size:82 final size:81
Alignment explanation
Indices: 29877748--29877903 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29877738 TGCTATATAA
* *
29877748 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29877813 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29877830 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29877894 CACTTAGTGC
65 CACTTAGTGC
29877904 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29885814 original size:27 final size:27
Alignment explanation
Indices: 29885784--29885961 Score: 212
Period size: 27 Copynumber: 6.6 Consensus size: 27
29885774 ATATTGAGTC
* * * *
29885784 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29885811 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29885838 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29885866 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * **
29885893 CGCACACTTAGTGCTTCATATTCATTT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
29885920 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29885947 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29885962 GTACAATTTA
Statistics
Matches: 129, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29885923 original size:82 final size:81
Alignment explanation
Indices: 29885805--29885960 Score: 240
Period size: 82 Copynumber: 1.9 Consensus size: 81
29885795 TGCTATATAA
* *
29885805 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29885870 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * * **
29885887 TCAATTCGCACACTTAGTGCTTCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
29885952 ACTTAGTGC
66 ACTTAGTGC
29885961 TGTACAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
81 15 0.22
82 52 0.78
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29892427 original size:14 final size:15
Alignment explanation
Indices: 29892408--29892436 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29892398 GAGAAGAAGG
29892408 AAAAAG-AAAAGAAA
1 AAAAAGAAAAAGAAA
29892422 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
29892437 GAAGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Found at i:29892430 original size:20 final size:20
Alignment explanation
Indices: 29892407--29892446 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29892397 GGAGAAGAAG
29892407 GAAAAAGAAAAGAA-AAAAAA
1 GAAAAAG-AAAGAAGAAAAAA
29892427 GAAAAAGAAAGAAGAAAAAA
1 GAAAAAGAAAGAAGAAAAAA
29892447 TTTAAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
GAAAAAGAAAGAAGAAAAAA
Found at i:29892437 original size:10 final size:10
Alignment explanation
Indices: 29892401--29892439 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
29892391 AATTAGGGAG
*
29892401 AAGAAGGAAA
1 AAGAAAGAAA
29892411 AAGAAAAGAAA
1 AAG-AAAGAAA
29892422 AA-AAAGAAA
1 AAGAAAGAAA
29892431 AAGAAAGAA
1 AAGAAAGAA
29892440 GAAAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 9 0.35
10 9 0.35
11 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:29903852 original size:9 final size:9
Alignment explanation
Indices: 29903838--29903874 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29903828 TTAAATCATG
29903838 ATTATGTTA
1 ATTATGTTA
29903847 ATTATGTTA
1 ATTATGTTA
29903856 ATTATGTTA
1 ATTATGTTA
*
29903865 ATTAAGTTA
1 ATTATGTTA
29903874 A
1 A
29903875 ATTAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (9 bp):
ATTATGTTA
Found at i:29906982 original size:72 final size:72
Alignment explanation
Indices: 29906865--29907030 Score: 307
Period size: 72 Copynumber: 2.3 Consensus size: 72
29906855 GATACCTAGG
29906865 TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
1 TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
29906930 AACCAAT
66 AACCAAT
*
29906937 TTAAGTATTGATACAGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
1 TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
29907002 AACCAAT
66 AACCAAT
*
29907009 TTAAGTATTAATACCGT-TTTAG
1 TTAAGTATTGATACCGTATTTAG
29907031 AATTTTTCAA
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 5 0.05
72 86 0.95
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (72 bp):
TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
AACCAAT
Found at i:29911136 original size:10 final size:10
Alignment explanation
Indices: 29911121--29911149 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
29911111 ATTGTGTGTT
29911121 TGAATAGAAA
1 TGAATAGAAA
29911131 TGAATAG-AA
1 TGAATAGAAA
29911140 TGAATAGAAA
1 TGAATAGAAA
29911150 ATGAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:29914837 original size:28 final size:28
Alignment explanation
Indices: 29914784--29914864 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
29914774 TCTAAGGGCA
*
29914784 TTCGATCATTTTA-CCTTACAG-GGGTAC
1 TTCGGTCATTTTACCCTT-CAGAGGGTAC
*
29914811 TTCGGTCATTTTACCCTTCAGAGGGTAT
1 TTCGGTCATTTTACCCTTCAGAGGGTAC
* *
29914839 TTTGGTCAATTTACCCTTCA-AGGGTA
1 TTCGGTCATTTTACCCTTCAGAGGGTA
29914865 TTTCAGTCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.44
28 27 0.56
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (28 bp):
TTCGGTCATTTTACCCTTCAGAGGGTAC
Found at i:29938390 original size:15 final size:15
Alignment explanation
Indices: 29938370--29938404 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29938360 GCTGAATATA
*
29938370 ATAATTATAATAATT
1 ATAATTACAATAATT
*
29938385 ATAATTACCATAATT
1 ATAATTACAATAATT
29938400 ATAAT
1 ATAAT
29938405 ATTGTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATTACAATAATT
Found at i:29961532 original size:18 final size:19
Alignment explanation
Indices: 29961509--29961544 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29961499 TCCCTTAATG
29961509 ATTAGATTCTCAA-AATCC
1 ATTAGATTCTCAATAATCC
*
29961527 ATTAGATTGTCAATAATC
1 ATTAGATTCTCAATAATC
29961545 GTAGCAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (19 bp):
ATTAGATTCTCAATAATCC
Found at i:29976277 original size:40 final size:39
Alignment explanation
Indices: 29976210--29976339 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
29976200 GGACTAAGAT
* *
29976210 CCGAAGGCCTTTGTGCGAGA-TACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGA-ATTACTAAATCCGGGTTATGTC
**
29976250 CCGAAGGCATTCGTGCGAATTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGAATTACTAAATCCGGGTTATGTC
* * *
29976290 CCGAAGGCATTGTGTGAGTTACTAAATCCGGGCTATGTC
1 CCGAAGGCATTGTGCGAATTACTAAATCCGGGTTATGTC
29976329 CCGAAGGCATT
1 CCGAAGGCATT
29976340 TGAACGAGGA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 38 0.48
40 41 0.52
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAATTACTAAATCCGGGTTATGTC
Found at i:29984145 original size:40 final size:39
Alignment explanation
Indices: 29984078--29984207 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
29984068 GGACTAAGAT
* *
29984078 CCGAAGGCCTTTGTGCGAGA-TACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGA-ATTACTAAATCCGGGTTATGTC
**
29984118 CCGAAGGCATTCGTGCGAATTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGAATTACTAAATCCGGGTTATGTC
* * *
29984158 CCGAAGGCATTGTGTGAGTTACTAAATCCGGGCTATGTC
1 CCGAAGGCATTGTGCGAATTACTAAATCCGGGTTATGTC
29984197 CCGAAGGCATT
1 CCGAAGGCATT
29984208 TGAACGAGGA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 38 0.48
40 41 0.52
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAATTACTAAATCCGGGTTATGTC
Found at i:29984227 original size:79 final size:79
Alignment explanation
Indices: 29984078--29984242 Score: 179
Period size: 79 Copynumber: 2.1 Consensus size: 79
29984068 GGACTAAGAT
* * ** ** *
29984078 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTGTTA
1 CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
**
29984143 AATCCGGGTTATGTC
66 AATCC-GGTTAAATC
* * * * *
29984158 CCGAAGG-CATTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
*
29984222 TATCCGGTTAAATC
66 AATCCGGTTAAATC
29984236 CCGAAGG
1 CCGAAGG
29984243 TACGTGATTT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
78 14 0.20
79 49 0.70
80 7 0.10
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAAGAGCTA
AATCCGGTTAAATC
Found at i:29992079 original size:14 final size:15
Alignment explanation
Indices: 29992060--29992092 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
29992050 TATAATAAGA
29992060 AAAGAAAT-AAAAAT
1 AAAGAAATCAAAAAT
29992074 AAAGAAATCGAAAAAT
1 AAAGAAATC-AAAAAT
29992090 AAA
1 AAA
29992093 TTAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
16 9 0.53
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAGAAATCAAAAAT
Found at i:30002273 original size:21 final size:20
Alignment explanation
Indices: 30002247--30002312 Score: 89
Period size: 20 Copynumber: 3.2 Consensus size: 20
30002237 TACGGGATTT
30002247 ACACTTCGGGTGTCCCTGTTC
1 ACACTTC-GGTGTCCCTGTTC
* *
30002268 ACACTTCGGTGCCCCTATAT-
1 ACACTTCGGTGTCCCTGT-TC
30002288 ACACTTCGGTGTCCCTGTTC
1 ACACTTCGGTGTCCCTGTTC
30002308 ACACT
1 ACACT
30002313 ATGGTGCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.77
21 8 0.21
ACGTcount: A:0.15, C:0.35, G:0.18, T:0.32
Consensus pattern (20 bp):
ACACTTCGGTGTCCCTGTTC
Found at i:30002283 original size:20 final size:20
Alignment explanation
Indices: 30002247--30002321 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
30002237 TACGGGATTT
*
30002247 ACACTTCGGGTGTCCCTGTTC
1 ACACTTC-GGTGCCCCTGTTC
*
30002268 ACACTTCGGTGCCCCTATAT-
1 ACACTTCGGTGCCCCTGT-TC
*
30002288 ACACTTCGGTGTCCCTGTTC
1 ACACTTCGGTGCCCCTGTTC
30002308 ACACTAT-GGTGCCC
1 ACACT-TCGGTGCCC
30002322 TTATTTGCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.02
20 36 0.78
21 9 0.20
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.31
Consensus pattern (20 bp):
ACACTTCGGTGCCCCTGTTC
Found at i:30003991 original size:111 final size:111
Alignment explanation
Indices: 30003797--30004014 Score: 337
Period size: 111 Copynumber: 2.0 Consensus size: 111
30003787 CGACCTAGCG
* *
30003797 CACGGGCGTGTGGTTTGGCCATGTGACCAAACTCAGAGAGTTACACGGGTGACGACACGGGTAAG
1 CACGGGCGTGTGGTTTGGCCATGTGACCAAACTCAGAGAGTTACACGGGTAACGACACGGATAAG
* *
30003862 GACAGAAGCTAGGACATGAACGTGTGTCCTTATTTCGATTGTGGCA
66 GACACAAGCTAGGACATGAACGTGTGTCCTTACTTCGATTGTGGCA
* * * *
30003908 CACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAGAGTTACACGGGTAAGGACTCGGATGAG
1 CACGGGCGTGTGGTTTGGCCATGTGACCAAACTCAGAGAGTTACACGGGTAACGACACGGATAAG
* * *
30003973 GACACAAGTTGGGACATGAATGTGTGTCCTTACTTCGATTGT
66 GACACAAGCTAGGACATGAACGTGTGTCCTTACTTCGATTGT
30004015 TACACGGCCT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 96 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (111 bp):
CACGGGCGTGTGGTTTGGCCATGTGACCAAACTCAGAGAGTTACACGGGTAACGACACGGATAAG
GACACAAGCTAGGACATGAACGTGTGTCCTTACTTCGATTGTGGCA
Found at i:30005976 original size:26 final size:25
Alignment explanation
Indices: 30005916--30005990 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
30005906 TGAGGTCAGG
*
30005916 CGAGCTGGTGTTTGTAGTAGGACTGG
1 CGAGCTGGTGTTTGTAGTAGG-CTGA
* * *
30005942 TGAGTTGGTATTTGTAGTAGGCTTGA
1 CGAGCTGGTGTTTGTAGTAGGC-TGA
*
30005968 CGAGCTGGTGTTCGTCAGTAGGC
1 CGAGCTGGTGTTTGT-AGTAGGC
30005991 CAGACAAGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 1 0.03
26 31 0.79
27 7 0.18
ACGTcount: A:0.16, C:0.12, G:0.39, T:0.33
Consensus pattern (25 bp):
CGAGCTGGTGTTTGTAGTAGGCTGA
Found at i:30012625 original size:40 final size:40
Alignment explanation
Indices: 30012588--30012807 Score: 243
Period size: 39 Copynumber: 5.5 Consensus size: 40
30012578 GCTACTCGTT
* * *
30012588 CAAACGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
30012628 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
30012668 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
30012707 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
30012746 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
30012787 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
30012808 TGGACATCAT
Statistics
Matches: 156, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
38 2 0.01
39 71 0.46
40 71 0.46
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:30012688 original size:79 final size:78
Alignment explanation
Indices: 30012605--30012804 Score: 224
Period size: 79 Copynumber: 2.5 Consensus size: 78
30012595 CTTTGGGACA
* *
30012605 TAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA
1 TAGCCCGG-TATAGTAACTCGCACAA-TGCCTTCGGGACTTAACCCGGAATTAGTAACTCACACA
30012670 AATGCCTTCGG-GCT
64 AATGCCTTCGGAGCT
* * * *
30012684 TAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACACA
1 TAGCCCGGTA-TAGTAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCACACA
*
30012748 AATGCCTTCGGATCT
64 AATGCCTTCGGAGCT
* * * * *
30012763 TAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
1 TAGCCCGG-TATAGTAAC-TCGCACAATGCCTTCGGGACTTA
30012805 GCCTGGACAT
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
78 35 0.35
79 54 0.53
80 12 0.12
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (78 bp):
TAGCCCGGTATAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCACACAAA
TGCCTTCGGAGCT
Found at i:30021231 original size:15 final size:15
Alignment explanation
Indices: 30021213--30021263 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
30021203 ATGGCCGTGT
30021213 GTCACACACGGCTAA
1 GTCACACACGGCTAA
* * **
30021228 GTCACACGC-CCGTGT
1 GTCACACACGGC-TAA
30021243 GTCACACACGGCTAA
1 GTCACACACGGCTAA
30021258 GTCACA
1 GTCACA
30021264 TGCCTGTGTG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.16
Consensus pattern (15 bp):
GTCACACACGGCTAA
Found at i:30021243 original size:30 final size:30
Alignment explanation
Indices: 30021207--30021276 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
30021197 TGTCGCATGG
30021207 CCGTGTGTCACACACGGCTAAGTCACACGC
1 CCGTGTGTCACACACGGCTAAGTCACACGC
*
30021237 CCGTGTGTCACACACGGCTAAGTCACATGC
1 CCGTGTGTCACACACGGCTAAGTCACACGC
*
30021267 CTGTGTGTCA
1 CCGTGTGTCA
30021277 GGCCGTATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.21
Consensus pattern (30 bp):
CCGTGTGTCACACACGGCTAAGTCACACGC
Found at i:30025669 original size:27 final size:27
Alignment explanation
Indices: 30025636--30025910 Score: 195
Period size: 27 Copynumber: 10.2 Consensus size: 27
30025626 CCCAATATTT
* * *
30025636 GTAAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGATCGAAATACCCCTATAGG
* **
30025663 GTAAAATGATCGAAATACCCTCGA-ACA
1 GTAAAATGATCGAAATACCC-CTATAGG
* *
30025690 GTAAAATGATTGAAATACCCCCGA-AGG
1 GTAAAATGATCGAAATA-CCCCTATAGG
*
30025717 GTAAAATGATCGAAATA-CCCTCAAAGG
1 GTAAAATGATCGAAATACCCCT-ATAGG
* * *
30025744 GTAAAATGACCAAAATA-CCCTCAAAGG
1 GTAAAATGATCGAAATACCCCT-ATAGG
*
30025771 GTAAAATGATCGAAAAATCCCC-ATAGG
1 GTAAAATGATCGAAATA-CCCCTATAGG
* * * * * *
30025798 GCAAAATGGTCGTAATGCCCCTGTAGA
1 GTAAAATGATCGAAATACCCCTATAGG
* * *
30025825 GTAAAATGATTGTAATACCCTTATAGG
1 GTAAAATGATCGAAATACCCCTATAGG
* *
30025852 GTTAAATGA-CTGAAATACCCCTATAAG
1 GTAAAATGATC-GAAATACCCCTATAGG
* * *
30025879 GTAAAAT-ATCCGTAATGCCCCTAGAGG
1 GTAAAATGAT-CGAAATACCCCTATAGG
30025906 GTAAA
1 GTAAA
30025911 TGACTATTTT
Statistics
Matches: 197, Mismatches: 41, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
25 3 0.02
26 6 0.03
27 180 0.91
28 5 0.03
29 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (27 bp):
GTAAAATGATCGAAATACCCCTATAGG
Found at i:30025873 original size:54 final size:54
Alignment explanation
Indices: 30025636--30025885 Score: 220
Period size: 54 Copynumber: 4.6 Consensus size: 54
30025626 CCCAATATTT
* * **
30025636 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATCGAAATACCCTCGA-ACA
1 GTAAAATGACTGAAATACCCCTGTAGGGTAAAATGATCGAAATACCCTC-ATAGG
* * * *
30025690 GTAAAATGATTGAAATACCCCCGAAGGGTAAAATGATCGAAATACCCTCAAAGG
1 GTAAAATGACTGAAATACCCCTGTAGGGTAAAATGATCGAAATACCCTCATAGG
** ** *
30025744 GTAAAATGACCAAAATA-CCCTCAAAGGGTAAAATGATCGAAAAATCCC-CATAGG
1 GTAAAATGACTGAAATACCCCT-GTAGGGTAAAATGATCGAAATA-CCCTCATAGG
* * * * * * * *
30025798 GCAAAATG-GTCGTAATGCCCCTGTAGAGTAAAATGATTGTAATACCCTTATAGG
1 GTAAAATGACT-GAAATACCCCTGTAGGGTAAAATGATCGAAATACCCTCATAGG
* * *
30025852 GTTAAATGACTGAAATACCCCTATAAGGTAAAAT
1 GTAAAATGACTGAAATACCCCTGTAGGGTAAAAT
30025886 ATCCGTAATG
Statistics
Matches: 154, Mismatches: 35, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
53 7 0.05
54 139 0.90
55 8 0.05
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (54 bp):
GTAAAATGACTGAAATACCCCTGTAGGGTAAAATGATCGAAATACCCTCATAGG
Found at i:30026004 original size:24 final size:24
Alignment explanation
Indices: 30025933--30026029 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
30025923 CCCTCGAGTG
* *
30025933 TAAATGATTGATTTGTCTGTGATG
1 TAAATGACTGATTTGTCTGTGATT
** *
30025957 TAAATGAGGGATTTATCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*
30025981 TAAATGACTAATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*** * *
30026005 GGTATAACTGATTTGTCTATGATT
1 TAAATGACTGATTTGTCTGTGATT
30026029 T
1 T
30026030 GTATTACTGA
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:30026033 original size:24 final size:24
Alignment explanation
Indices: 30025991--30026041 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
30025981 TAAATGACTA
*
30025991 ATTTGTCTGTGATTGGTATAACTG
1 ATTTGTCTATGATTGGTATAACTG
* *
30026015 ATTTGTCTATGATTTGTATTACTG
1 ATTTGTCTATGATTGGTATAACTG
30026039 ATT
1 ATT
30026042 CTGAGCATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.51
Consensus pattern (24 bp):
ATTTGTCTATGATTGGTATAACTG
Found at i:30026254 original size:32 final size:32
Alignment explanation
Indices: 30026213--30026382 Score: 195
Period size: 32 Copynumber: 5.4 Consensus size: 32
30026203 GCTGCGATAC
**
30026213 TACTGATGGCTTTGTGTTGATCATATTA-TCGT
1 TACTGATGGCTTTGTGCCGATCATATTACT-GT
30026245 TACTGATGGCTTTGTGCCGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
30026277 TACTAATGGCTTTGTGCCGATCATATTACCG-
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * * * *
30026308 CACTGATAG-TTGTGTGCCGGTCATATCACTGC
1 TACTGATGGCTT-TGTGCCGATCATATTACTGT
*
30026340 TACTGATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
30026371 TACTTATGGCTT
1 TACTGATGGCTT
30026383 GTAGCCATTC
Statistics
Matches: 118, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.02
31 33 0.28
32 80 0.68
33 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:30026349 original size:63 final size:64
Alignment explanation
Indices: 30026212--30026368 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 64
30026202 TGCTGCGATA
** * * * *
30026212 CTACTGATGGCTTTGTGTTGATCATATTATCGTTACTGATGGCTTTGTGCCGATCATATTACTG
1 CTACTGATGGCTTTGTGCCGATCATATTACCGTCACTGATAGCTTTGTGCCGATCATATCACTG
* * *
30026276 TTACTAATGGCTTTGTGCCGATCATATTACCG-CACTGATAG-TTGTGTGCCGGTCATATCACTG
1 CTACTGATGGCTTTGTGCCGATCATATTACCGTCACTGATAGCTT-TGTGCCGATCATATCACTG
*
30026339 CTACTGATGGCTTTGTGCCAATCATATTAC
1 CTACTGATGGCTTTGTGCCGATCATATTAC
30026369 TGTACTTATG
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
62 2 0.03
63 51 0.64
64 27 0.34
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (64 bp):
CTACTGATGGCTTTGTGCCGATCATATTACCGTCACTGATAGCTTTGTGCCGATCATATCACTG
Found at i:30026730 original size:32 final size:33
Alignment explanation
Indices: 30026670--30026731 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
30026660 GATACTGTAA
* *
30026670 TGGGCTAAGGCCCACACTACACTTTTACTGTTT
1 TGGGCTAAAGCCCACACTACACTGTTACTGTTT
*
30026703 TGGGCTAAAG-CCACACTATACTGTTACTG
1 TGGGCTAAAGCCCACACTACACTGTTACTG
30026732 GATAGGGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (33 bp):
TGGGCTAAAGCCCACACTACACTGTTACTGTTT
Found at i:30026740 original size:32 final size:33
Alignment explanation
Indices: 30026671--30026740 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 33
30026661 ATACTGTAAT
* * ** *
30026671 GGGCTAAGGCCCACACTACACTTTTACTGTTTT
1 GGGCTAAAGCCCACACTACACTGTTACTGGATA
*
30026704 GGGCTAAAG-CCACACTATACTGTTACTGGATA
1 GGGCTAAAGCCCACACTACACTGTTACTGGATA
30026736 GGGCT
1 GGGCT
30026741 CAGGCCCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (33 bp):
GGGCTAAAGCCCACACTACACTGTTACTGGATA
Found at i:30031694 original size:28 final size:28
Alignment explanation
Indices: 30031654--30031710 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
30031644 GAACTTTGAG
30031654 TATGTGAACCTCAAATCTAAGTGGACAA
1 TATGTGAACCTCAAATCTAAGTGGACAA
30031682 TATGTGAACCTCAAATCTAAGTGGACAA
1 TATGTGAACCTCAAATCTAAGTGGACAA
30031710 T
1 T
30031711 CCCTTAGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (28 bp):
TATGTGAACCTCAAATCTAAGTGGACAA
Found at i:30047863 original size:20 final size:20
Alignment explanation
Indices: 30047811--30047863 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
30047801 ACATTTGTGC
*
30047811 CTCTATTTGCACTTTGGTGT
1 CTCTATTTGCACTTTGATGT
* *
30047831 CTCTACTTACACTTTGATGT
1 CTCTATTTGCACTTTGATGT
*
30047851 CTCTGTTTGCACT
1 CTCTATTTGCACT
30047864 ACAGTGCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.25, G:0.15, T:0.47
Consensus pattern (20 bp):
CTCTATTTGCACTTTGATGT
Found at i:30064882 original size:5 final size:5
Alignment explanation
Indices: 30064868--30064918 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
30064858 TAAATATACA
*
30064868 ATAT- ATATG ATATG ATATG ATATG ATATG ATATG ATATG -TA-C ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
30064915 ATAT
1 ATAT
30064919 ATGTATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 8 0.19
5 34 0.81
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:30067044 original size:18 final size:18
Alignment explanation
Indices: 30067009--30067046 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30066999 GAAATATTTA
*
30067009 TTTTGATATTTTTAATAT
1 TTTTGATATTTATAATAT
30067027 TTTTGATATATTAT-ATAT
1 TTTTGATAT-TTATAATAT
30067045 TT
1 TT
30067047 AAAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTGATATTTATAATAT
Found at i:30073877 original size:2 final size:2
Alignment explanation
Indices: 30073870--30073898 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30073860 AGTCATATGC
30073870 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 A
30073899 AACATATCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30082533 original size:30 final size:28
Alignment explanation
Indices: 30082475--30082552 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 28
30082465 AAAAGGGTAC
* * *
30082475 AAAA-TATATACATGTACATATATAAAA
1 AAAATTATATACATATATATAGATAAAA
30082502 AAAATTATATACATATATATAGATTATAAA
1 AAAATTATATACATATATATAGA-TA-AAA
*
30082532 AAAGATAAT-TACATATATATA
1 AAA-ATTATATACATATATATA
30082553 TAAACAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
27 4 0.09
28 15 0.35
29 2 0.05
30 18 0.42
31 4 0.09
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAATTATATACATATATATAGATAAAA
Found at i:30082687 original size:38 final size:40
Alignment explanation
Indices: 30082598--30082693 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 40
30082588 ATTAATTTAG
* * *
30082598 AAATATATATATATA-A-ATTTATGAAGAATAATATAAGA
1 AAATATATATATATACATATTTATCAAAAAAAATATAAGA
* *
30082636 AAACATATGTATATACATATTTATCAAAAAAAATAT-A-A
1 AAATATATATATATACATATTTATCAAAAAAAATATAAGA
* *
30082674 AAGTATATATATATGCATAT
1 AAATATATATATATACATAT
30082694 AAAAGTTAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
38 30 0.64
39 2 0.04
40 15 0.32
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (40 bp):
AAATATATATATATACATATTTATCAAAAAAAATATAAGA
Found at i:30082740 original size:17 final size:18
Alignment explanation
Indices: 30082710--30082745 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
30082700 TAGGAAATAA
*
30082710 AAAATTGTATATGTATAT
1 AAAATTGTAAATGTATAT
30082728 AAAA-TGTAAATGTATAT
1 AAAATTGTAAATGTATAT
30082745 A
1 A
30082746 TATGTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (18 bp):
AAAATTGTAAATGTATAT
Found at i:30082788 original size:61 final size:61
Alignment explanation
Indices: 30082679--30082795 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
30082669 TATAAAAGTA
* * *
30082679 TATATATATGCATATAAAAGTTAGGAAATAAAAAATTGTATATGTATATAAAATGTAAATG
1 TATATATATGCATATAAAAGTTAGCAAATAAAAAATTGAATATATATATAAAATGTAAATG
* * *
30082740 TATATATATGTATATAAAAGTTATGCAAATAGAACAA-T-AATATATATATAATATGT
1 TATATATATGCATATAAAAGTTA-GCAAATA-AAAAATTGAATATATATATAAAATGT
30082796 GCATGTGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
61 37 0.77
62 7 0.15
63 4 0.08
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (61 bp):
TATATATATGCATATAAAAGTTAGCAAATAAAAAATTGAATATATATATAAAATGTAAATG
Found at i:30082882 original size:3 final size:3
Alignment explanation
Indices: 30082874--30082909 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
30082864 GTATATATAG
* *
30082874 TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30082910 CTTAATAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:30082952 original size:7 final size:7
Alignment explanation
Indices: 30082933--30082962 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
30082923 AAATCAAATT
30082933 TAATAAA
1 TAATAAA
30082940 -AATAAA
1 TAATAAA
30082946 TAATAAA
1 TAATAAA
30082953 TAATAAA
1 TAATAAA
30082960 TAA
1 TAA
30082963 AAAAAGACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAATAAA
Found at i:30083263 original size:23 final size:22
Alignment explanation
Indices: 30083220--30083277 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
30083210 AAAGGGTATC
* *
30083220 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
30083241 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
30083264 TTCATATCATATCT
1 TACAAATCATATCT
30083278 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:30083280 original size:19 final size:19
Alignment explanation
Indices: 30083248--30083303 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
30083238 GATTACAAAA
30083248 TCATATC-T-TCTAAGATT
1 TCATATCATATCTAAGATT
30083265 TCATATCATATCTAAGATT
1 TCATATCATATCTAAGATT
*
30083284 GCATATATCATATCTAAGAT
1 TC--ATATCATATCTAAGAT
30083304 CATATCTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.21
18 1 0.03
19 10 0.29
21 16 0.47
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (19 bp):
TCATATCATATCTAAGATT
Found at i:30083323 original size:14 final size:12
Alignment explanation
Indices: 30083290--30083315 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30083280 GATTGCATAT
30083290 ATCATATCTAAG
1 ATCATATCTAAG
30083302 ATCATATCTAAG
1 ATCATATCTAAG
30083314 AT
1 AT
30083316 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:30086065 original size:33 final size:32
Alignment explanation
Indices: 30086018--30086115 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
30086008 TACGCGGTTC
* * *
30086018 TGTGAAATGGTAACAAATATCAGCCTTTCATTT
1 TGTGAAATGATAACAAATATCA-ACTTTAATTT
30086051 TGTGAAATGATAACAAAT-TACAACTTTAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTAATTT
* *
30086083 TGTAAAATGATAACAAATATCAACTTCAATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
30086115 T
1 T
30086116 TTTTAAATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
32 38 0.66
33 20 0.34
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTAATTT
Found at i:30090991 original size:17 final size:18
Alignment explanation
Indices: 30090930--30090991 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
30090920 AAACTAAATC
30090930 AAAATCTAA-TAAAACCT
1 AAAATCTAATTAAAACCT
** *
30090947 AATAAGAT-TTTAAAACCT
1 AA-AATCTAATTAAAACCT
*
30090965 AAAATTTAATTAAAACCT
1 AAAATCTAATTAAAACCT
30090983 -AAATCTAAT
1 AAAATCTAAT
30090992 AATACTTAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
17 13 0.37
18 22 0.63
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATCTAATTAAAACCT
Found at i:30091505 original size:17 final size:17
Alignment explanation
Indices: 30091485--30091531 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
30091475 GAATTCGCCA
* *
30091485 TTTGGCGAACTCTAGGT
1 TTTGGCAAACTCTAGGG
30091502 TTTGGCAAACTCTAGGG
1 TTTGGCAAACTCTAGGG
*
30091519 ATTGGCAAACTCT
1 TTTGGCAAACTCT
30091532 TCTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (17 bp):
TTTGGCAAACTCTAGGG
Found at i:30096467 original size:72 final size:72
Alignment explanation
Indices: 30096312--30096467 Score: 168
Period size: 72 Copynumber: 2.2 Consensus size: 72
30096302 AAGGTTGAGG
* * * *
30096312 GTGTCGTGACATACCCATAAAGATGGCTGCAGTGGAGTATACTAGTTGCTACGTCACGACATAGG
1 GTGTCGTGACATACCCATAAAGATGGCTGCAGAGGAGCATACTAGTTGCTACGTCACGACACAAG
30096377 CGTTGGT
66 CGTTGGT
* * ** * * * * * *
30096384 GTTTCATGACATACCTTTGAAGATGGCTGTAGAGGAGCATATTGGTTGCTATGTCATGACACAAG
1 GTGTCGTGACATACCCATAAAGATGGCTGCAGAGGAGCATACTAGTTGCTACGTCACGACACAAG
*
30096449 TGTTGGT
66 CGTTGGT
*
30096456 GTGTCGCGACAT
1 GTGTCGTGACAT
30096468 CGACTCTATG
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (72 bp):
GTGTCGTGACATACCCATAAAGATGGCTGCAGAGGAGCATACTAGTTGCTACGTCACGACACAAG
CGTTGGT
Found at i:30103334 original size:22 final size:22
Alignment explanation
Indices: 30103302--30103345 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30103292 TATATAAAAA
30103302 GAGCTTAAATACAAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
* *
30103324 GAGCTTGAATACTAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
30103346 AATTGAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (22 bp):
GAGCTTAAATACAAATGAGTTT
Done.