Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 77 of 103
Found at i:28809374 original size:3 final size:3
Alignment explanation
Indices: 28809366--28809402 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28809356 CTTTCAGATG
28809366 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
28809403 ATCTTCTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:28814012 original size:4 final size:4
Alignment explanation
Indices: 28813986--28814030 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
28813976 GAATAAACTC
* * * *
28813986 TATA TAAA TAAA TAAA TAAA TATA TATA TATA TATA TATA TATA T
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA T
28814031 GCATGGAACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:28815164 original size:23 final size:22
Alignment explanation
Indices: 28815126--28815182 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
28815116 TGGTTGATAC
*
28815126 TTTTGTTTTTAA-TTTTATGTTA
1 TTTT-TTTTTAATTTTTATATTA
28815148 TTTATTTTTTAATTTTTATATTA
1 TTT-TTTTTTAATTTTTATATTA
*
28815171 TTTTTTATTAAT
1 TTTTTTTTTAAT
28815183 AATAAAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTTTTTAATTTTTATATTA
Found at i:28826620 original size:2 final size:2
Alignment explanation
Indices: 28826608--28826642 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
28826598 CCTTCCCTCC
* *
28826608 CT CT CT GT CT CT CT GT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
28826643 GTGTATGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.46, G:0.06, T:0.49
Consensus pattern (2 bp):
CT
Found at i:28828833 original size:5 final size:5
Alignment explanation
Indices: 28828825--28828854 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
28828815 GGCTTGGAGG
28828825 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
28828855 CCTTTCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:28829617 original size:17 final size:17
Alignment explanation
Indices: 28829592--28829625 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28829582 GCATGGTAGC
* *
28829592 GTTTTTTTTTTTTGTTT
1 GTTTGTTTTCTTTGTTT
28829609 GTTTGTTTTCTTTGTTT
1 GTTTGTTTTCTTTGTTT
28829626 CCTTTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (17 bp):
GTTTGTTTTCTTTGTTT
Found at i:28842463 original size:4 final size:4
Alignment explanation
Indices: 28842454--28842504 Score: 52
Period size: 4 Copynumber: 12.5 Consensus size: 4
28842444 TTTAAAACAT
*
28842454 ATAA ATAA ATGAA AT-A A-AA ATAA ATAA ATAA ATAA AAATA ATAA TATAA
1 ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA -ATAA
28842503 AT
1 AT
28842505 TGAGAAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 4 0.10
4 25 0.62
5 11 0.28
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:28842488 original size:18 final size:18
Alignment explanation
Indices: 28842454--28842504 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
28842444 TTTAAAACAT
28842454 ATAAATAAATGAAATAAAA
1 ATAAATAAAT-AAATAAAA
28842473 ATAAATAAATAAATAAAA
1 ATAAATAAATAAATAAAA
28842491 AT-AATAATATAAAT
1 ATAAATAA-ATAAAT
28842505 TGAGAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.16
18 16 0.52
19 10 0.32
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAAATAAATAAATAAAA
Found at i:28842503 original size:14 final size:14
Alignment explanation
Indices: 28842456--28842494 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
28842446 TAAAACATAT
28842456 AAATAAATGAAATAA
1 AAATAAAT-AAATAA
28842471 AAATAAATAAATAA
1 AAATAAATAAATAA
28842485 ATAA-AAATAA
1 A-AATAAATAA
28842495 TAATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:28844072 original size:2 final size:2
Alignment explanation
Indices: 28844065--28844092 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28844055 CTAAAACTCA
28844065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28844093 TCAAAGGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28866042 original size:40 final size:39
Alignment explanation
Indices: 28865980--28866057 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
28865970 TTATGAAAGA
* * *
28865980 CACCAATCGTGGCGAGTTGAAAACTCCATTAAGGTGAAT
1 CACCAATCGTGGCAAGTTGAAAACCCCACTAAGGTGAAT
*
28866019 CACCAATCTTGGCAAGGTTGAAAACCCCACTAAGGTGAA
1 CACCAATCGTGGCAA-GTTGAAAACCCCACTAAGGTGAA
28866058 AAATAGTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 13 0.38
40 21 0.62
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (39 bp):
CACCAATCGTGGCAAGTTGAAAACCCCACTAAGGTGAAT
Found at i:28867283 original size:617 final size:617
Alignment explanation
Indices: 28866103--28867336 Score: 2317
Period size: 617 Copynumber: 2.0 Consensus size: 617
28866093 AAGATACTAA
28866103 AACCTCTTACTTTTTAAAAGAGCCTAGAGAAATAAGCACTAATGCTTAAGAAAATATTATTTATT
1 AACCTCTTACTTTTTAAAAGAGCCTAGAGAAATAAGCACTAATGCTTAAGAAAATATTATTTATT
*
28866168 AACTCTCAACTCTGAATGTCTCATAACTAAGCCTAAGTGTCCTATTTATAGTATTATAGGCCCAA
66 AACTCTCAACTCTGAATGTCTCATAACTAAGCCTAAGTGTCCTATTTATAGTATTATAGGCACAA
* *
28866233 ATCCTAATAAAACTCTATTCCTAGTTATCTAATACAATTAGAATAATTAATAAAAGATTTAAATA
131 ATCCTAATAAAACTCTACTACTAGTTATCTAATACAATTAGAATAATTAATAAAAGATTTAAATA
28866298 AAATAGGTGTTCTATTCCTAAATAGAACATGACTATCCTAATTAAATACTAATTCTTAAAAGTAT
196 AAATAGGTGTTCTATTCCTAAATAGAACATGACTATCCTAATTAAATACTAATTCTTAAAAGTAT
28866363 TAAAATAAAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAAATCCTAAATCAACT
261 TAAAATAAAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAAATCCTAAATCAACT
*
28866428 AAATTAGCAAAAACTAAATACAATCCTAGACGCTTCTGCGTCATTCTCCTCGGGTCAGAAAAACT
326 AAATTAGCAAAAACTAAATACAATCCTAGACGCTCCTGCGTCATTCTCCTCGGGTCAGAAAAACT
28866493 CGGCTCTGACAAGTAGGCCTGGACATACTCCATGTTGATGTCTGGATCCATATATTATCATAGTC
391 CGGCTCTGACAAGTAGGCCTGGACATACTCCATGTTGATGTCTGGATCCATATATTATCATAGTC
28866558 CATACCAACCATTTGATCAATTCATCCATTGTTTTGAAGGTTGCTTTCCATTCATCTCCAAGTCG
456 CATACCAACCATTTGATCAATTCATCCATTGTTTTGAAGGTTGCTTTCCATTCATCTCCAAGTCG
* *
28866623 TATTCAAATTTGTTGATATCCTTTCTTCAAATCGATATTCAAAAACACTCTAAAGCCAATGAACA
521 TATTCAAATTTGTTGATATCCTTTCTTCAAATAGATATTCAAAAACACTATAAAGCCAATGAACA
28866688 TGTCATCCAATTGAGGGATAAGAAAATCATAC
586 TGTCATCCAATTGAGGGATAAGAAAATCATAC
*
28866720 NAACCTCTTACTTTTTAAAAGAGCCTAGAGAAATAAGCACTCATGCTTAAGAAAATATTATTTAT
1 -AACCTCTTACTTTTTAAAAGAGCCTAGAGAAATAAGCACTAATGCTTAAGAAAATATTATTTAT
28866785 TAACTCTCAACTCTGAATGTCTCATAACTAAGCCTAAGTGTCCTATTTATAGTATTATAGGCACA
65 TAACTCTCAACTCTGAATGTCTCATAACTAAGCCTAAGTGTCCTATTTATAGTATTATAGGCACA
* *
28866850 AATCCTAATAAAACTCTACTACTAGTTATCTAATACAATTAGAATAATTAATAAGATATTTAAAT
130 AATCCTAATAAAACTCTACTACTAGTTATCTAATACAATTAGAATAATTAATAAAAGATTTAAAT
**
28866915 AAAATAGGTGTTCTATTTTTAAATAGAACATGACTATCCTAATTAAATACTAATTCTTAAAAGTA
195 AAAATAGGTGTTCTATTCCTAAATAGAACATGACTATCCTAATTAAATACTAATTCTTAAAAGTA
28866980 TTAAAAT-AAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAAATCCTAAATCAAC
260 TTAAAATAAAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAAATCCTAAATCAAC
*
28867044 TAAATTAGCAAAAACTAAATACAATCTTAGACGCTCCTGCGTCATTCTCCTCGGGTCAGAAAAAC
325 TAAATTAGCAAAAACTAAATACAATCCTAGACGCTCCTGCGTCATTCTCCTCGGGTCAGAAAAAC
28867109 TCGGCTCTGACAAGTAGGCCTGGACATACTCCATGTTGATGTCTGGATCCATATATTATCATAGT
390 TCGGCTCTGACAAGTAGGCCTGGACATACTCCATGTTGATGTCTGGATCCATATATTATCATAGT
*
28867174 CCATACCAACCATTTGATTAATTCATCCATTGTTTTGAAGGTTGCTTTCCATTCATCTCCAAGTC
455 CCATACCAACCATTTGATCAATTCATCCATTGTTTTGAAGGTTGCTTTCCATTCATCTCCAAGTC
* *
28867239 GTATTCAAATTTGTTGATATCCTTTCTTCAAATAGATCTTCAAAAACACTATAGAGCCAATGAAC
520 GTATTCAAATTTGTTGATATCCTTTCTTCAAATAGATATTCAAAAACACTATAAAGCCAATGAAC
28867304 ATGTCATCCAATTGAGGGATAAGAAAATCATAC
585 ATGTCATCCAATTGAGGGATAAGAAAATCATAC
28867337 TTAACTGTAG
Statistics
Matches: 601, Mismatches: 15, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
617 343 0.57
618 258 0.43
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (617 bp):
AACCTCTTACTTTTTAAAAGAGCCTAGAGAAATAAGCACTAATGCTTAAGAAAATATTATTTATT
AACTCTCAACTCTGAATGTCTCATAACTAAGCCTAAGTGTCCTATTTATAGTATTATAGGCACAA
ATCCTAATAAAACTCTACTACTAGTTATCTAATACAATTAGAATAATTAATAAAAGATTTAAATA
AAATAGGTGTTCTATTCCTAAATAGAACATGACTATCCTAATTAAATACTAATTCTTAAAAGTAT
TAAAATAAAAATAAGAAAAGAATCCTAATCTAAATAAAATAAAAAAAATAAATCCTAAATCAACT
AAATTAGCAAAAACTAAATACAATCCTAGACGCTCCTGCGTCATTCTCCTCGGGTCAGAAAAACT
CGGCTCTGACAAGTAGGCCTGGACATACTCCATGTTGATGTCTGGATCCATATATTATCATAGTC
CATACCAACCATTTGATCAATTCATCCATTGTTTTGAAGGTTGCTTTCCATTCATCTCCAAGTCG
TATTCAAATTTGTTGATATCCTTTCTTCAAATAGATATTCAAAAACACTATAAAGCCAATGAACA
TGTCATCCAATTGAGGGATAAGAAAATCATAC
Found at i:28869265 original size:40 final size:40
Alignment explanation
Indices: 28869207--28869285 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
28869197 TTATGAAAGA
* *
28869207 CACCAATCATGGCGAGGTTGTAAACCCCACTAAGGTGAAT
1 CACCAATCATGGCAAGGTTGAAAACCCCACTAAGGTGAAT
* *
28869247 CACCAATCTTGGTAAGGTTGAAAACCCCACTAAGGTGAA
1 CACCAATCATGGCAAGGTTGAAAACCCCACTAAGGTGAA
28869286 AAATAGTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (40 bp):
CACCAATCATGGCAAGGTTGAAAACCCCACTAAGGTGAAT
Found at i:28871099 original size:2 final size:2
Alignment explanation
Indices: 28871092--28871145 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
28871082 CAAATTAAAT
28871092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28871134 TA TA TA TA TA TA
1 TA TA TA TA TA TA
28871146 ACTAAACATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28872258 original size:9 final size:9
Alignment explanation
Indices: 28872246--28872278 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
28872236 TTATTTAATT
28872246 GTGTTAAAC
1 GTGTTAAAC
*
28872255 GTGTTAACC
1 GTGTTAAAC
28872264 GTGTTAAAC
1 GTGTTAAAC
28872273 GTGTTA
1 GTGTTA
28872279 TTAATCGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (9 bp):
GTGTTAAAC
Found at i:28881080 original size:14 final size:14
Alignment explanation
Indices: 28881049--28881081 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28881039 TAATTAGTTA
28881049 AAAAAATCATAAAC
1 AAAAAATCATAAAC
*
28881063 -AAAAGTCATAAAC
1 AAAAAATCATAAAC
28881076 AAAAAA
1 AAAAAA
28881082 ATAAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 2
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.73, C:0.12, G:0.03, T:0.12
Consensus pattern (14 bp):
AAAAAATCATAAAC
Found at i:28881352 original size:8 final size:8
Alignment explanation
Indices: 28881339--28881375 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
28881329 ATCAAACTCA
28881339 AAAAAAAT
1 AAAAAAAT
28881347 AAAAAAAT
1 AAAAAAAT
28881355 -AAAAAAT
1 AAAAAAAT
*
28881362 AAACAAA-
1 AAAAAAAT
28881369 AAAAAAA
1 AAAAAAA
28881376 GAGAGTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.08
Consensus pattern (8 bp):
AAAAAAAT
Found at i:28881360 original size:15 final size:15
Alignment explanation
Indices: 28881338--28881375 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
28881328 GATCAAACTC
28881338 AAAAAAAATAAA-AA
1 AAAAAAAATAAACAA
28881352 AATAAAAAATAAACAA
1 AA-AAAAAATAAACAA
28881368 AAAAAAAA
1 AAAAAAAA
28881376 GAGAGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 16 0.73
16 4 0.18
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.08
Consensus pattern (15 bp):
AAAAAAAATAAACAA
Found at i:28882385 original size:3 final size:3
Alignment explanation
Indices: 28882365--28882403 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
28882355 TATAAAAACA
*
28882365 AAT AAT AAA AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28882404 TTCCATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:28882609 original size:7 final size:7
Alignment explanation
Indices: 28882597--28882652 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
28882587 TCATTTAAAA
28882597 AAATAAT
1 AAATAAT
28882604 AAATAAT
1 AAATAAT
28882611 AAATAAT
1 AAATAAT
28882618 AAATAA-
1 AAATAAT
28882624 ATAATAAT
1 A-AATAAT
**
28882632 TGATAA-
1 AAATAAT
*
28882638 AGATAA-
1 AAATAAT
28882644 AAATAAT
1 AAATAAT
28882651 AA
1 AA
28882653 TGATAATTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
6 11 0.26
7 31 0.74
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:28882637 original size:25 final size:22
Alignment explanation
Indices: 28882594--28882658 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 22
28882584 AAATCATTTA
*
28882594 AAAAAATAATAAATAATAAATAAT
1 AAAAAATAAT-AATGATAAA-AAT
*
28882618 AAATAAATAATAATTGATAAAGAT
1 AAA-AAATAATAA-TGATAAAAAT
28882642 -AAAAATAATAATGATAA
1 AAAAAATAATAATGATAA
28882659 TTCAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 6 0.16
22 9 0.24
23 2 0.05
24 7 0.19
25 13 0.35
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAAATAATAATGATAAAAAT
Found at i:28886067 original size:19 final size:18
Alignment explanation
Indices: 28886043--28886094 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
28886033 TCAAAATCCA
28886043 AAAAAATAAAAAATAAAA-
1 AAAAAA-AAAAAATAAAAG
* *
28886061 TAAAAAACAAAATAAAAAG
1 AAAAAAAAAAAAT-AAAAG
*
28886080 AAAAAAAAGAAATAA
1 AAAAAAAAAAAATAA
28886095 TACATGAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 6 0.22
18 11 0.41
19 10 0.37
ACGTcount: A:0.85, C:0.02, G:0.04, T:0.10
Consensus pattern (18 bp):
AAAAAAAAAAAATAAAAG
Found at i:28886084 original size:12 final size:12
Alignment explanation
Indices: 28886045--28886078 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
28886035 AAAATCCAAA
*
28886045 AAAATAAAAAAT
1 AAAATAAAAAAC
28886057 AAAATAAAAAAC
1 AAAATAAAAAAC
28886069 AAAATAAAAA
1 AAAATAAAAA
28886079 GAAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAATAAAAAAC
Found at i:28886774 original size:2 final size:2
Alignment explanation
Indices: 28886767--28886852 Score: 85
Period size: 2 Copynumber: 45.0 Consensus size: 2
28886757 ATTGACAAGT
* *
28886767 TA TA TA TA TA TA TA TA AA TA CTA TA T- TA -A TA T- TA T- TA GA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
28886806 TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA CTA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
28886847 TA TA TA
1 TA TA TA
28886853 GTTTTGAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
1 6 0.09
2 60 0.86
3 4 0.06
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28888439 original size:2 final size:2
Alignment explanation
Indices: 28888432--28888481 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
28888422 AATGGGATTG
28888432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28888474 AT AT AT AT
1 AT AT AT AT
28888482 CCAATGCCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28888788 original size:54 final size:54
Alignment explanation
Indices: 28888725--28888831 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
28888715 ACTTAGATTC
28888725 TTAGAATGCTTATGGTTAAGAGTGAATAAAATCAAATTAAATCAATTATTCATA
1 TTAGAATGCTTATGGTTAAGAGTGAATAAAATCAAATTAAATCAATTATTCATA
28888779 TTAGAATGCTTATGGTTAAGAGTGAATAAAATCAAATTAAATCAATTATTCAT
1 TTAGAATGCTTATGGTTAAGAGTGAATAAAATCAAATTAAATCAATTATTCAT
28888832 CTAAATTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (54 bp):
TTAGAATGCTTATGGTTAAGAGTGAATAAAATCAAATTAAATCAATTATTCATA
Found at i:28913471 original size:17 final size:17
Alignment explanation
Indices: 28913442--28913474 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28913432 GATAGTGAGT
28913442 TACTATCAAGAATGTTA
1 TACTATCAAGAATGTTA
28913459 TACT-TCAAGGAATGTT
1 TACTATCAA-GAATGTT
28913475 CAAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (17 bp):
TACTATCAAGAATGTTA
Found at i:28928637 original size:280 final size:278
Alignment explanation
Indices: 28927843--28928651 Score: 960
Period size: 279 Copynumber: 2.9 Consensus size: 278
28927833 TCTATAGAAT
* * * * *
28927843 ACGACAAATTCATTTATAAGGAAACACGTGTAAATTAATGAATTCGTAAAATTTATGAATGATCA
1 ACGACAAATTCAATTATAACGAAACACGTGTAAGTTAATAAACTCGTAAAATTTATGAA-GATCA
* * * * * * *
28927908 TAAATATATTGATAAAATTGAAAGTGAAAATATAG-AGTCAGAATTACATATTGATTCGTATCTC
65 TAAATATATTGATAAATTTAAAAGTGAAAAGAAAGAATTAAG-ATTACGTATTGATTCGTATCTC
* * *
28927972 ATTAATGATTTATAACAAATTCAAAGAAAATTAATAGTTTACGACAAATTCAAAAATGATTGAAG
129 ATCAATGATTTACAACAAATTCAAAGAAAATTAATAATTTACGACAAATTCAAAAATGATTGAAG
* * * * * * * * * *
28928037 TATAAAAGATACGACGAGCAACCAATAATCATGTAAAAGCATACAAGTAGATGACCATATACAAA
194 TATAAAAGATATGACGATCTACTAATAATCACGTAAAAGCATATACGTAGATGATCACACACAAA
*
28928102 TCAATGATTTTTTACATAAC
259 TCAATGATTTTTTACAAAAC
* * * * *
28928122 GCGACAAATTCAATTATAACGAAACATGCGTAAGTTGATAAACTCGACAAAATTTAT-AATTGAT
1 ACGACAAATTCAATTATAACGAAACACGTGTAAGTTAATAAACTCG-TAAAATTTATGAA--GAT
* * *
28928186 CATAAATATATTG-TAAATTTAAAAGTAAAAAGAAAGAATTAAGATAACGTATTGATTCGAATCT
63 CATAAATATATTGATAAATTTAAAAGTGAAAAGAAAGAATTAAGATTACGTATTGATTCGTATCT
* * *
28928250 CATCAATGATTTACGACAAATTTAAAGAAAATTAATGATTTACGACAAATTCAAAAATGATTGAA
128 CATCAATGATTTACAACAAATTCAAAGAAAATTAATAATTTACGACAAATTCAAAAATGATTGAA
** * **
28928315 GTATAAAAGATATGACGAT-TAACTAATAATTGCATAAAAGCATATACGTAGATGATTGCACACA
193 GTATAAAAGATATGACGATCT-ACTAATAATCACGTAAAAGCATATACGTAGATGATCACACACA
*
28928379 AATCAATGATTTTTTAGAAAAC
257 AATCAATGATTTTTTACAAAAC
* * * *
28928401 ACGACAAATTCAATTATAATGAAACACATGTAAGTTTATAAACTCGTTAGAATTTATGACAGATC
1 ACGACAAATTCAATTATAACGAAACACGTGTAAGTTAATAAACTCG-TAAAATTTATGA-AGATC
* *
28928466 ATAAATATATTGATAAATTTAAAAGTGAAAAGGAAGAATTAAGATTACGTATTGATTTGTATCTC
64 ATAAATATATTGATAAATTTAAAAGTGAAAAGAAAGAATTAAGATTACGTATTGATTCGTATCTC
* * * * * * *
28928531 ATCAATAATTTACAACAAATACAAATAAAACTAATAATTTACAACAAATTTAAAGATGATTGAAG
129 ATCAATGATTTACAACAAATTCAAAGAAAATTAATAATTTACGACAAATTCAAAAATGATTGAAG
* * * * * *
28928596 CACAAATGATATGATGATCTATTAATAATCACGTAAAAGCATATACATAGATGATC
194 TATAAAAGATATGACGATCTACTAATAATCACGTAAAAGCATATACGTAGATGATC
28928652 TATCATTGAT
Statistics
Matches: 445, Mismatches: 77, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
279 266 0.60
280 177 0.40
281 2 0.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (278 bp):
ACGACAAATTCAATTATAACGAAACACGTGTAAGTTAATAAACTCGTAAAATTTATGAAGATCAT
AAATATATTGATAAATTTAAAAGTGAAAAGAAAGAATTAAGATTACGTATTGATTCGTATCTCAT
CAATGATTTACAACAAATTCAAAGAAAATTAATAATTTACGACAAATTCAAAAATGATTGAAGTA
TAAAAGATATGACGATCTACTAATAATCACGTAAAAGCATATACGTAGATGATCACACACAAATC
AATGATTTTTTACAAAAC
Found at i:28945017 original size:25 final size:26
Alignment explanation
Indices: 28944989--28945050 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
28944979 AATAAACGTG
28944989 ATTATAGGA-ATTAGAAATCACCATA
1 ATTATAGGAGATTAGAAATCACCATA
* * * *
28945014 ATTATA-AAGATTGGGAATCATCATA
1 ATTATAGGAGATTAGAAATCACCATA
28945039 ATTATAGG-GATT
1 ATTATAGGAGATT
28945051 TTATTTTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (26 bp):
ATTATAGGAGATTAGAAATCACCATA
Found at i:28945083 original size:22 final size:23
Alignment explanation
Indices: 28945043--28945088 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
28945033 ATCATAATTA
28945043 TAGGGATTTTATTTTCTTTATTC
1 TAGGGATTTTATTTTCTTTATTC
28945066 TAGGGATTTTA-TTTCTTTATTC
1 TAGGGATTTTATTTTCTTTATTC
28945088 T
1 T
28945089 TTTCCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61
Consensus pattern (23 bp):
TAGGGATTTTATTTTCTTTATTC
Found at i:28946718 original size:2 final size:2
Alignment explanation
Indices: 28946680--28946704 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28946670 ATAAATACGT
28946680 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
28946705 TTCAAAGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:28953544 original size:58 final size:57
Alignment explanation
Indices: 28953454--28953570 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 57
28953444 GAATTGAATA
* *
28953454 TTGAATTATGTTACATATACAGTCGTTGGATTTGATGATTTTTTGAGGTACATTATGC
1 TTGAATTATGTTACATATACAGTCATTGGATTTGAT-ATTTTTTGAGATACATTATGC
*
28953512 TTGAATTATGTTACATATATAGTCATTGGATTTGATATTTTTTGAGATACATTATGC
1 TTGAATTATGTTACATATACAGTCATTGGATTTGATATTTTTTGAGATACATTATGC
28953569 TT
1 TT
28953571 TTCCCATGTC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 22 0.39
58 34 0.61
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (57 bp):
TTGAATTATGTTACATATACAGTCATTGGATTTGATATTTTTTGAGATACATTATGC
Found at i:28955565 original size:2 final size:2
Alignment explanation
Indices: 28955558--28955604 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
28955548 TGTAATTTTA
28955558 AT AT 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 AT AT AT
28955599 AT AT AT
1 AT AT AT
28955605 GTGCTTTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28957149 original size:2 final size:2
Alignment explanation
Indices: 28957142--28957179 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
28957132 AAACCAAGAA
*
28957142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28957180 GTAATCATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:28959790 original size:29 final size:29
Alignment explanation
Indices: 28959740--28959811 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
28959730 ATTAAAATGA
* *
28959740 AACAA-AATA-TTTTTGAATATGGCGTGT
1 AACAATAATATTTTTTCAACATGGCGTGT
28959767 AACAATAATATTTTTTCAACATGGCGTGT
1 AACAATAATATTTTTTCAACATGGCGTGT
28959796 AACAATAATATTTTTT
1 AACAATAATATTTTTT
28959812 TTTTCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 5 0.12
28 4 0.10
29 32 0.78
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
AACAATAATATTTTTTCAACATGGCGTGT
Found at i:28959827 original size:33 final size:29
Alignment explanation
Indices: 28959740--28959833 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
28959730 ATTAAAATGA
* * *
28959740 AACAA-AATA-TTTTTGAATATGGCGTGT
1 AACAATAATATTTTTTCAAAATAGCGTGT
* *
28959767 AACAATAATATTTTTTCAACATGGCGTGT
1 AACAATAATATTTTTTCAAAATAGCGTGT
28959796 AACAATAATATTTTTTTTTTCAAAATAGCGTGT
1 AACAATAATA----TTTTTTCAAAATAGCGTGT
28959829 AACAA
1 AACAA
28959834 CCTAACCATG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.09
28 4 0.07
29 26 0.46
33 22 0.39
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (29 bp):
AACAATAATATTTTTTCAAAATAGCGTGT
Found at i:28959875 original size:45 final size:45
Alignment explanation
Indices: 28959824--28959935 Score: 163
Period size: 45 Copynumber: 2.5 Consensus size: 45
28959814 TTCAAAATAG
*
28959824 CGTGTAACAACCTAACCATGACGTGTCACATGTTTTTGTAGATGGA
1 CGTGTAACAACCTAACCATGACGTGTCACATATTTTTGTAGAT-GA
** * *
28959870 -GTGTAACAACCTAACCATGGTGTGTCATATATTTTTGTATATGA
1 CGTGTAACAACCTAACCATGACGTGTCACATATTTTTGTAGATGA
28959914 CGTGTAACAACCTAACCATGAC
1 CGTGTAACAACCTAACCATGAC
28959936 ATGTAACAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
44 2 0.03
45 56 0.97
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (45 bp):
CGTGTAACAACCTAACCATGACGTGTCACATATTTTTGTAGATGA
Found at i:28959934 original size:21 final size:21
Alignment explanation
Indices: 28959910--28959960 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
28959900 ATTTTTGTAT
28959910 ATGACGTGTAACAACCTAACC
1 ATGACGTGTAACAACCTAACC
*
28959931 ATGACATGTAACAACCTAACC
1 ATGACGTGTAACAACCTAACC
28959952 ATGACGTGT
1 ATGACGTGT
28959961 CACATGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (21 bp):
ATGACGTGTAACAACCTAACC
Found at i:28959987 original size:24 final size:24
Alignment explanation
Indices: 28959955--28960025 Score: 133
Period size: 24 Copynumber: 3.0 Consensus size: 24
28959945 CCTAACCATG
28959955 ACGTGTCACATGTTTTTGTACATA
1 ACGTGTCACATGTTTTTGTACATA
28959979 ACGTGTCACATGTTTTTGTACATA
1 ACGTGTCACATGTTTTTGTACATA
*
28960003 ACGTGTAACATGTTTTTGTACAT
1 ACGTGTCACATGTTTTTGTACAT
28960026 TGTGTGTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (24 bp):
ACGTGTCACATGTTTTTGTACATA
Found at i:28960032 original size:24 final size:24
Alignment explanation
Indices: 28959955--28960060 Score: 131
Period size: 24 Copynumber: 4.4 Consensus size: 24
28959945 CCTAACCATG
*
28959955 ACGTGTCACATGTTTTTGTACATA
1 ACGTGTAACATGTTTTTGTACATA
*
28959979 ACGTGTCACATGTTTTTGTACATA
1 ACGTGTAACATGTTTTTGTACATA
*
28960003 ACGTGTAACATGTTTTTGTACATT
1 ACGTGTAACATGTTTTTGTACATA
** * * *
28960027 GTGTGTAATATATTTTTGTACATG
1 ACGTGTAACATGTTTTTGTACATA
*
28960051 ACGTATAACA
1 ACGTGTAACA
28960061 ACCTAACATG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.42
Consensus pattern (24 bp):
ACGTGTAACATGTTTTTGTACATA
Found at i:28960117 original size:21 final size:21
Alignment explanation
Indices: 28960091--28960146 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
28960081 TGTTTTTGTA
*
28960091 CATGACATTTAACAACTTAAC
1 CATGACATGTAACAACTTAAC
* *
28960112 CATGACATGTAATAACTTAAT
1 CATGACATGTAACAACTTAAC
*
28960133 CATGACGTGTAACA
1 CATGACATGTAACA
28960147 TGTTTTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (21 bp):
CATGACATGTAACAACTTAAC
Found at i:28960161 original size:24 final size:24
Alignment explanation
Indices: 28960133--28960183 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
28960123 ATAACTTAAT
* *
28960133 CATGACGTGTAACATGTTTTTATA
1 CATGACATGTAACATATTTTTATA
28960157 CATGACATGTAACATATTTTTATA
1 CATGACATGTAACATATTTTTATA
28960181 CAT
1 CAT
28960184 AACGCGTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (24 bp):
CATGACATGTAACATATTTTTATA
Found at i:28960185 original size:182 final size:183
Alignment explanation
Indices: 28959856--28960187 Score: 452
Period size: 182 Copynumber: 1.8 Consensus size: 183
28959846 GTGTCACATG
* * ** * * * *
28959856 TTTTTGTAGATGGAGTGTAACAACCTAACCATGGTGTGTCATATATTTTTGTATATGACGTGTAA
1 TTTTTGTACATGGAGTATAACAACCTAACCATGACGTATCACATATTTTTGTACATGACATGTAA
* * * *
28959921 CAACCTAACCATGACATGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATAACGTGTC
66 CAACCTAACCATGACATGTAACAACCTAACCATGACGTGTAACATGTTTTTATACATAACATGTA
* *
28959986 ACATGTTTTTGTACATAACGTGTAACATGTTTTTGTACATTGTGTGTAATATA
131 ACATATTTTTATACATAACGTGTAACATGTTTTTGTACATTGTGTGTAATATA
* *
28960039 TTTTTGTACAT-GACGTATAACAACCTAA-CATGACGTATCACATGTTTTTGTACATGACATTTA
1 TTTTTGTACATGGA-GTATAACAACCTAACCATGACGTATCACATATTTTTGTACATGACATGTA
* * * * *
28960102 ACAACTTAACCATGACATGTAATAACTTAATCATGACGTGTAACATGTTTTTATACATGACATGT
65 ACAACCTAACCATGACATGTAACAACCTAACCATGACGTGTAACATGTTTTTATACATAACATGT
28960167 AACATATTTTTATACATAACG
130 AACATATTTTTATACATAACG
28960188 CGTGACATCA
Statistics
Matches: 127, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
182 104 0.82
183 23 0.18
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (183 bp):
TTTTTGTACATGGAGTATAACAACCTAACCATGACGTATCACATATTTTTGTACATGACATGTAA
CAACCTAACCATGACATGTAACAACCTAACCATGACGTGTAACATGTTTTTATACATAACATGTA
ACATATTTTTATACATAACGTGTAACATGTTTTTGTACATTGTGTGTAATATA
Found at i:28960195 original size:24 final size:24
Alignment explanation
Indices: 28960141--28960195 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
28960131 ATCATGACGT
* * *
28960141 GTAACATGTTTTTATACATGACAT
1 GTAACATATTTTTATACATAACAC
*
28960165 GTAACATATTTTTATACATAACGC
1 GTAACATATTTTTATACATAACAC
*
28960189 GTGACAT
1 GTAACAT
28960196 CATGACGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (24 bp):
GTAACATATTTTTATACATAACAC
Found at i:28969991 original size:20 final size:19
Alignment explanation
Indices: 28969946--28969984 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28969936 TTTGACTTAC
* *
28969946 AATAAAAAATTAAAAATTT
1 AATAAAAAATAAAAAAATT
28969965 AATAAAAAATAAAAAAATT
1 AATAAAAAATAAAAAAATT
28969984 A
1 A
28969985 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAATAAAAAAATT
Found at i:28974346 original size:18 final size:17
Alignment explanation
Indices: 28974307--28974352 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 17
28974297 CTAAATTAAA
28974307 AAATATTTAAAAAATAT
1 AAATATTTAAAAAATAT
28974324 AAATATTTAAATAAATAAT
1 AAATATTTAAA-AAAT-AT
28974343 AATATATTTA
1 AA-ATATTTA
28974353 TTGGTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 4 0.15
20 7 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATTTAAAAAATAT
Found at i:28977690 original size:28 final size:29
Alignment explanation
Indices: 28977649--28977708 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
28977639 GTCTATGGGC
*
28977649 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCAGTTTTAGGGGGCAAAAATGT
* * *
28977677 AATTTTTGATTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAGTTTTA-GGGGGCAAAAATGT
28977707 AA
1 AA
28977709 ATATCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
AATTTTTCAGTTTTAGGGGGCAAAAATGT
Found at i:28980328 original size:20 final size:20
Alignment explanation
Indices: 28980292--28980329 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28980282 TAGTTTAGAT
* *
28980292 TTTTTGTAAGTACTTTGTAA
1 TTTTTGTAAATAATTTGTAA
28980312 TTTTTGTAAATAATTTGT
1 TTTTTGTAAATAATTTGT
28980330 TCAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTTTGTAAATAATTTGTAA
Found at i:28982612 original size:2 final size:2
Alignment explanation
Indices: 28982607--28982637 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28982597 ATATATAGGT
28982607 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28982638 CGGAGTACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28984243 original size:2 final size:2
Alignment explanation
Indices: 28984236--28984265 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28984226 CACATATTTA
*
28984236 TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28984266 CCCTTTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:28987972 original size:23 final size:21
Alignment explanation
Indices: 28987946--28987987 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
28987936 GTCATTCTCT
28987946 TTCTTCTTC-TCTAAATATTC
1 TTCTTCTTCTTCTAAATATTC
28987966 TTCTTCTTCTTCTAAATATTC
1 TTCTTCTTCTTCTAAATATTC
28987987 T
1 T
28987988 AACAATCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (21 bp):
TTCTTCTTCTTCTAAATATTC
Found at i:28992877 original size:20 final size:21
Alignment explanation
Indices: 28992852--28992890 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28992842 ATTCTCTTTC
28992852 TTCTTC-TCTAAATATTCTTA
1 TTCTTCTTCTAAATATTCTTA
*
28992872 TTCTTCTTCTAAATTTTCT
1 TTCTTCTTCTAAATATTCT
28992891 AGCACCACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (21 bp):
TTCTTCTTCTAAATATTCTTA
Found at i:28995450 original size:35 final size:33
Alignment explanation
Indices: 28995365--28995451 Score: 79
Period size: 35 Copynumber: 2.5 Consensus size: 33
28995355 TAAAAATTAT
* *
28995365 AAATTATTAATATTTTAAATAAATTATTATAAAT
1 AAATTATTAA-ATTTTAAATAAATAATTATAAAA
*
28995399 TAA-TACTTAAACTTTTAAATTTAAA-AATTATAAAA
1 AAATTA-TTAAA-TTTTAAA--TAAATAATTATAAAA
28995434 AAATTATTAACATTTTAA
1 AAATTATTAA-ATTTTAA
28995452 TAATAAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
33 3 0.07
34 13 0.30
35 20 0.47
36 7 0.16
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (33 bp):
AAATTATTAAATTTTAAATAAATAATTATAAAA
Found at i:28995459 original size:22 final size:22
Alignment explanation
Indices: 28995434--28995559 Score: 84
Period size: 22 Copynumber: 5.8 Consensus size: 22
28995424 AATTATAAAA
*
28995434 AAATTATTAACATTTTAATAAT
1 AAATTATTAATATTTTAATAAT
*
28995456 AAATTATTAATA-TTTAGATTAT
1 AAATTATTAATATTTTA-ATAAT
* * * * *
28995478 TAATTATTAAAAAAGTATTATTATT
1 AAATTATT--AATA-TTTTAATAAT
*
28995503 AAATTACT-A-A---TAATAAT
1 AAATTATTAATATTTTAATAAT
*
28995520 AAATTTATTAATATTTTAATCAT
1 AAA-TTATTAATATTTTAATAAT
28995543 AAATTATTAATATTTTA
1 AAATTATTAATATTTTA
28995560 GGTAAATTAT
Statistics
Matches: 79, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
17 8 0.10
18 4 0.05
19 1 0.01
20 1 0.01
21 5 0.06
22 37 0.47
23 9 0.11
24 3 0.04
25 8 0.10
26 3 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
AAATTATTAATATTTTAATAAT
Found at i:28995572 original size:50 final size:50
Alignment explanation
Indices: 28995518--28995623 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
28995508 ACTAATAATA
* * * *
28995518 ATAAATTTATTAATATTTTAATCATAAATTATTAATATTTT-AGGTAAATT
1 ATAAAATTATTAATATTTTAATCATAAATTAATAAAATTTTAAAG-AAATT
* *
28995568 ATAAAATTATTAATATTTTAGTTATAAATTAATAAAATTTTAAAGAAATT
1 ATAAAATTATTAATATTTTAATCATAAATTAATAAAATTTTAAAGAAATT
28995618 ATAAAA
1 ATAAAA
28995624 AAATCAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
50 47 0.96
51 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (50 bp):
ATAAAATTATTAATATTTTAATCATAAATTAATAAAATTTTAAAGAAATT
Found at i:28995574 original size:28 final size:30
Alignment explanation
Indices: 28995543--28995610 Score: 97
Period size: 28 Copynumber: 2.3 Consensus size: 30
28995533 TTTTAATCAT
*
28995543 AAATTATTAATATTTTAG-GTAAATT-ATA
1 AAATTATTAATATTTTAGTATAAATTAATA
28995571 AAATTATTAATATTTTAGTTATAAATTAATA
1 AAATTATTAATATTTTAG-TATAAATTAATA
28995602 AAATT-TTAA
1 AAATTATTAA
28995611 AGAAATTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 18 0.50
30 10 0.28
31 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (30 bp):
AAATTATTAATATTTTAGTATAAATTAATA
Found at i:28995607 original size:22 final size:23
Alignment explanation
Indices: 28995566--28995609 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28995556 TTTAGGTAAA
* *
28995566 TTATAAAATTATTAATATTTTAG
1 TTATAAAATTAATAAAATTTTAG
28995589 TTAT-AAATTAATAAAATTTTA
1 TTATAAAATTAATAAAATTTTA
28995610 AAGAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATAAAATTAATAAAATTTTAG
Found at i:28995633 original size:50 final size:50
Alignment explanation
Indices: 28995529--28995634 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
28995519 TAAATTTATT
* * * ** *
28995529 AATATTTTAATCATAAATTATTAATATTTTAGGTAAATTATAAAATTATT
1 AATATTTTAATCATAAATTAATAAAATTTTAAGTAAATTATAAAAAAATC
* *
28995579 AATATTTTAGTTATAAATTAATAAAATTTTAAAG-AAATTATAAAAAAATC
1 AATATTTTAATCATAAATTAATAAAATTTT-AAGTAAATTATAAAAAAATC
28995629 AATATT
1 AATATT
28995635 GCAAATTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 45 0.96
51 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (50 bp):
AATATTTTAATCATAAATTAATAAAATTTTAAGTAAATTATAAAAAAATC
Found at i:28995825 original size:17 final size:18
Alignment explanation
Indices: 28995792--28995826 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28995782 TATTTTTAAT
*
28995792 ATATTTTCAAGAAAATTA
1 ATATTTTCAAAAAAATTA
28995810 ATATTTT-AAAAAAATTA
1 ATATTTTCAAAAAAATTA
28995827 TAAATTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
ATATTTTCAAAAAAATTA
Found at i:28998205 original size:2 final size:2
Alignment explanation
Indices: 28998192--28998221 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28998182 AGACGAATTA
*
28998192 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28998222 CATTCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28999652 original size:2 final size:2
Alignment explanation
Indices: 28999645--28999677 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28999635 AAGAAATTAT
28999645 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28999678 AAGACTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29002172 original size:2 final size:2
Alignment explanation
Indices: 29002165--29002193 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29002155 CCTGGTCCTG
29002165 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
29002194 CTTGCCATTT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29004033 original size:13 final size:14
Alignment explanation
Indices: 29004005--29004033 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29003995 GCCATCATTA
29004005 TTTTATAAAGTATC
1 TTTTATAAAGTATC
29004019 TTTTATAAA-TATC
1 TTTTATAAAGTATC
29004032 TT
1 TT
29004034 CATGGCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTTATAAAGTATC
Found at i:29004368 original size:6 final size:6
Alignment explanation
Indices: 29004353--29004392 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
29004343 CACATAGCTA
*
29004353 CCTT-C CCTTCC CCTTCC CCTTCC CCTTCC CCTCCC CCTTC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTC
29004393 TCCTCCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTTCC
Found at i:29004397 original size:12 final size:12
Alignment explanation
Indices: 29004353--29004398 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
29004343 CACATAGCTA
*
29004353 CCTT-CCCTTCC
1 CCTTCCCCTCCC
*
29004364 CCTTCCCCTTCC
1 CCTTCCCCTCCC
29004376 CCTTCCCCTCCC
1 CCTTCCCCTCCC
*
29004388 CCTTCTCCTCC
1 CCTTCCCCTCC
29004399 TTTTCCTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (12 bp):
CCTTCCCCTCCC
Found at i:29006270 original size:2 final size:2
Alignment explanation
Indices: 29006257--29006287 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29006247 ACATATGCAC
*
29006257 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29006288 AGATTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29009193 original size:2 final size:2
Alignment explanation
Indices: 29009186--29009239 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
29009176 GTACTCCACC
29009186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29009228 AT AT AT AT AT AT
1 AT AT AT AT AT AT
29009240 GCACCAATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29020915 original size:17 final size:17
Alignment explanation
Indices: 29020887--29020926 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
29020877 TCTTTAAACA
29020887 AAACTT-TTTTTAAGAG
1 AAACTTATTTTTAAGAG
29020903 AAACTTATTTTTAAGAG
1 AAACTTATTTTTAAGAG
*
29020920 AATCTTA
1 AAACTTA
29020927 AAATCTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (17 bp):
AAACTTATTTTTAAGAG
Found at i:29021591 original size:49 final size:49
Alignment explanation
Indices: 29021518--29021611 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
29021508 AAAGGGCTAT
* **
29021518 TTATAATAGCTAACTAAACTTAAACCTACTTGGTGTGCAAGTAAAATAA
1 TTATAATAGCTAACTAAACCTAAACCTACTTAATGTGCAAGTAAAATAA
*
29021567 TTATAATAGCTAACTAAACCTAAACTTACTTAATGTGCAAGTAAA
1 TTATAATAGCTAACTAAACCTAAACCTACTTAATGTGCAAGTAAA
29021612 GAAAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (49 bp):
TTATAATAGCTAACTAAACCTAAACCTACTTAATGTGCAAGTAAAATAA
Found at i:29023542 original size:27 final size:27
Alignment explanation
Indices: 29023511--29023563 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
29023501 TTCATAGGAT
*
29023511 TCATCAAATATGGGATTTGAGATTACC
1 TCATCAAATATAGGATTTGAGATTACC
* *
29023538 TCATCAGATATAGGATTTGGGATTAC
1 TCATCAAATATAGGATTTGAGATTAC
29023564 TTGAGGGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (27 bp):
TCATCAAATATAGGATTTGAGATTACC
Found at i:29027372 original size:15 final size:16
Alignment explanation
Indices: 29027352--29027383 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29027342 GGTCTTTTTC
29027352 TTTTCATTTTC-CTCT
1 TTTTCATTTTCTCTCT
29027367 TTTTCATTTTCTCTCT
1 TTTTCATTTTCTCTCT
29027383 T
1 T
29027384 ATTGATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTCATTTTCTCTCT
Found at i:29031994 original size:14 final size:16
Alignment explanation
Indices: 29031975--29032008 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29031965 AATATAATAG
29031975 TATATAA-T-ATTACT
1 TATATAATTAATTACT
29031989 TATATAATTAATTACT
1 TATATAATTAATTACT
29032005 TATA
1 TATA
29032009 ACACTAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 1 0.06
16 10 0.56
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATAATTAATTACT
Found at i:29041466 original size:13 final size:14
Alignment explanation
Indices: 29041443--29041473 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
29041433 GAAACTTAAT
29041443 TTTCTTTTATTTTC
1 TTTCTTTTATTTTC
29041457 TTTC-TTTATTTTC
1 TTTCTTTTATTTTC
29041470 TTTC
1 TTTC
29041474 CATTGCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTTATTTTC
Found at i:29050253 original size:38 final size:37
Alignment explanation
Indices: 29050210--29050284 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 37
29050200 CACATGCCGG
29050210 TGATGATGGCGGTGTGGGAGATGGATGATGATAGTGC
1 TGATGATGGCGGTGTGGGAGATGGATGATGATAGTGC
*
29050247 NTGATGATGGTGGTGTGGGAGATGGATGATGATAGTGC
1 -TGATGATGGCGGTGTGGGAGATGGATGATGATAGTGC
29050285 CCGTGTGCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.04, G:0.45, T:0.28
Consensus pattern (37 bp):
TGATGATGGCGGTGTGGGAGATGGATGATGATAGTGC
Found at i:29050381 original size:40 final size:38
Alignment explanation
Indices: 29050288--29050393 Score: 149
Period size: 38 Copynumber: 2.7 Consensus size: 38
29050278 ATAGTGCCCG
* *
29050288 TGTGCACGATGTGGGGGGATGTACACGATGACACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGACACGGAT
* * *
29050326 TGTGCACGATGTGGGGGGATGCACATGATGGACTCGGCT
1 TGTGCACGATGTGGGGGGATGTACATGAT-GACACGGAT
29050365 ATGTGCACGATGTGGGGGGATGTACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
29050394 GCCGGGTGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 27 0.45
39 6 0.10
40 27 0.45
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGACACGGAT
Found at i:29059123 original size:3 final size:3
Alignment explanation
Indices: 29059115--29059151 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
29059105 GAGACGACAT
*
29059115 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29059152 TATTATTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:29061141 original size:29 final size:31
Alignment explanation
Indices: 29061102--29061162 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
29061092 CGTCATAATA
*
29061102 ATTATTACATCA-CTT-TTAAATATTACATT
1 ATTATTACATCATCTTATTAAATATCACATT
*
29061131 ATTATTACATCATCTTATTCAATATCACATT
1 ATTATTACATCATCTTATTAAATATCACATT
29061162 A
1 A
29061163 ACAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.43
30 3 0.11
31 13 0.46
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (31 bp):
ATTATTACATCATCTTATTAAATATCACATT
Found at i:29063190 original size:2 final size:2
Alignment explanation
Indices: 29063185--29063235 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
29063175 ACACACACAA
29063185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29063227 AT AC AT AT A
1 AT AT AT AT A
29063236 CATCATTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29066843 original size:7 final size:7
Alignment explanation
Indices: 29066827--29066856 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
29066817 TTTCCCCTAT
29066827 TTCTCCC
1 TTCTCCC
*
29066834 TTCTCTC
1 TTCTCCC
29066841 TTCTCCC
1 TTCTCCC
29066848 TTCTCCC
1 TTCTCCC
29066855 TT
1 TT
29066857 ATCCTCTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (7 bp):
TTCTCCC
Found at i:29067472 original size:25 final size:25
Alignment explanation
Indices: 29067439--29067505 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
29067429 AGGAAGGGGG
29067439 AGATCTTGGGTGAGAGAGCAAAAAA
1 AGATCTTGGGTGAGAGAGCAAAAAA
*
29067464 AGATCTTGGGTGAGAGAGCAAAAAG
1 AGATCTTGGGTGAGAGAGCAAAAAA
29067489 AGATCTTGGGTGAGAGA
1 AGATCTTGGGTGAGAGA
29067506 AAGGGGAGGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.39, C:0.07, G:0.36, T:0.18
Consensus pattern (25 bp):
AGATCTTGGGTGAGAGAGCAAAAAA
Found at i:29142093 original size:24 final size:24
Alignment explanation
Indices: 29142058--29142128 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
29142048 AGAAGAGAAT
*
29142058 AAAGAAACATAAGCCACAAAAACC
1 AAAGCAACATAAGCCACAAAAACC
* *
29142082 AAAGGAATATAAGCCACAAAAACC
1 AAAGCAACATAAGCCACAAAAACC
29142106 AAAGCAACATAAGCCACAAAAAC
1 AAAGCAACATAAGCCACAAAAAC
29142129 TAGAGGCATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.61, C:0.24, G:0.10, T:0.06
Consensus pattern (24 bp):
AAAGCAACATAAGCCACAAAAACC
Found at i:29150551 original size:2 final size:2
Alignment explanation
Indices: 29150544--29150577 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
29150534 GACAAAGGAA
29150544 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29150578 TTTTGAACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:29152641 original size:31 final size:31
Alignment explanation
Indices: 29152599--29152670 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
29152589 ATAATGAAAT
29152599 CGACTCATATGTTTAGGACAACGTCTCAAAC
1 CGACTCATATGTTTAGGACAACGTCTCAAAC
* *
29152630 CGATTCATATGTTTAGGACAGCGTCTCAAAC
1 CGACTCATATGTTTAGGACAACGTCTCAAAC
29152661 CGACTCATAT
1 CGACTCATAT
29152671 CCTTTAAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (31 bp):
CGACTCATATGTTTAGGACAACGTCTCAAAC
Found at i:29158505 original size:27 final size:27
Alignment explanation
Indices: 29158444--29158768 Score: 154
Period size: 27 Copynumber: 11.9 Consensus size: 27
29158434 TTTTCATAGT
* *
29158444 GTATAACAATTAAATTTTTCAACATGTC
1 GTATAACAACTAAA-TTTTCAACATGAC
*
29158472 GTGTAACAACTAAATTTTCAACATGAC
1 GTATAACAACTAAATTTTCAACATGAC
* * *
29158499 GCATAACAACTACATTTTTCAACATAAC
1 GTATAACAACTA-AATTTTCAACATGAC
* * * *
29158527 ATGTAACAA-TAAATTTTTAACATAAC
1 GTATAACAACTAAATTTTCAACATGAC
* * * * * *
29158553 GTGTAATAACTACATTTTTCAAAATAAT
1 GTATAACAACTA-AATTTTCAACATGAC
* * *
29158581 ATGTAACAACTAAATTTT-AACATGGC
1 GTATAACAACTAAATTTTCAACATGAC
* * * * * *
29158607 ATGTAATAACTATATTTTTAACATGAT
1 GTATAACAACTAAATTTTCAACATGAC
* * *
29158634 GTTTAACAACTAAATTTTGAACATCAC
1 GTATAACAACTAAATTTTCAACATGAC
* * * * * *
29158661 GCATAATAACTGCATTTTTGAATAT-AGC
1 GTATAACAACT-AAATTTTCAACATGA-C
* * * *
29158689 ATGTAACAACTAAATTTTTAACAAGAC
1 GTATAACAACTAAATTTTCAACATGAC
* * * *
29158716 ATATAATAACTAAATTTTAGAACATGGC
1 GTATAACAACTAAATTTT-CAACATGAC
* * *
29158744 ATGTAAC-ACTACATTTTTCAACATG
1 GTATAACAACTA-AATTTTCAACATG
29158769 GCATTAACAA
Statistics
Matches: 228, Mismatches: 60, Indels: 19
0.74 0.20 0.06
Matches are distributed among these distances:
26 40 0.18
27 101 0.44
28 87 0.38
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (27 bp):
GTATAACAACTAAATTTTCAACATGAC
Found at i:29158506 original size:55 final size:55
Alignment explanation
Indices: 29158457--29158768 Score: 266
Period size: 55 Copynumber: 5.7 Consensus size: 55
29158447 TAACAATTAA
* *
29158457 ATTTTTCAACATGTCGTGTAACAACTAAATTTTCAACATGACGCATAACAACTAC
1 ATTTTTCAACATGTCATGTAACAACTAAATTTTCAACATGACGCATAATAACTAC
** * * **
29158512 ATTTTTCAACATAACATGTAACAA-TAAATTTTTAACATAACGTGTAATAACTAC
1 ATTTTTCAACATGTCATGTAACAACTAAATTTTCAACATGACGCATAATAACTAC
* * *
29158566 ATTTTTCAAAATAAT-ATGTAACAACTAAATTTT-AACATG--GCATGTAATAACTAT
1 ATTTTTCAACAT-GTCATGTAACAACTAAATTTTCAACATGACGCA--TAATAACTAC
* * *
29158620 ATTTTT-AACATG--ATGTTTAACAACTAAATTTTGAACATCACGCATAATAACTGC
1 ATTTTTCAACATGTCATG--TAACAACTAAATTTTCAACATGACGCATAATAACTAC
* * * * ** *
29158674 ATTTTTGAATATAG-CATGTAACAACTAAATTTTTAACAAGACATATAATAACTAA
1 ATTTTTCAACAT-GTCATGTAACAACTAAATTTTCAACATGACGCATAATAACTAC
** * *
29158729 ATTTTAGAACATGGCATGTAAC-ACTACATTTTTCAACATG
1 ATTTTTCAACATGTCATGTAACAACTA-AATTTTCAACATG
29158769 GCATTAACAA
Statistics
Matches: 211, Mismatches: 32, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
51 3 0.01
52 1 0.00
53 19 0.09
54 89 0.42
55 92 0.44
56 4 0.02
57 3 0.01
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (55 bp):
ATTTTTCAACATGTCATGTAACAACTAAATTTTCAACATGACGCATAATAACTAC
Found at i:29158564 original size:54 final size:55
Alignment explanation
Indices: 29158457--29158767 Score: 272
Period size: 54 Copynumber: 5.7 Consensus size: 55
29158447 TAACAATTAA
** * * * * *
29158457 ATTTTTCAACATGTCGTGTAACAACTAAATTTTCAACATGACGCATAACAACTAC
1 ATTTTTCAACATAACATGTAACAACTAAATTTTTAACATAACGTATAATAACTAC
*
29158512 ATTTTTCAACATAACATGTAACAA-TAAATTTTTAACATAACGTGTAATAACTAC
1 ATTTTTCAACATAACATGTAACAACTAAATTTTTAACATAACGTATAATAACTAC
* * ** * * *
29158566 ATTTTTCAAAATAATATGTAACAACTAAA-TTTTAACATGGCATGTAATAACTAT
1 ATTTTTCAACATAACATGTAACAACTAAATTTTTAACATAACGTATAATAACTAC
* ** * * * * *
29158620 ATTTTT-AACATGATGTTTAACAACTAAATTTTGAACATCACGCATAATAACTGC
1 ATTTTTCAACATAACATGTAACAACTAAATTTTTAACATAACGTATAATAACTAC
* * * * *
29158674 ATTTTTGAATATAGCATGTAACAACTAAATTTTTAACA-AGACATATAATAACTAA
1 ATTTTTCAACATAACATGTAACAACTAAATTTTTAACATA-ACGTATAATAACTAC
** ** *
29158729 ATTTTAGAACATGGCATGTAAC-ACTACATTTTTCAACAT
1 ATTTTTCAACATAACATGTAACAACTAAATTTTT-AACAT
29158768 GGCATTAACA
Statistics
Matches: 208, Mismatches: 42, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
53 18 0.09
54 107 0.51
55 83 0.40
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (55 bp):
ATTTTTCAACATAACATGTAACAACTAAATTTTTAACATAACGTATAATAACTAC
Found at i:29158786 original size:24 final size:26
Alignment explanation
Indices: 29158736--29158786 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
29158726 TAAATTTTAG
29158736 AACATGGCATGTAACACTACATTTTTC
1 AACATGGCATGTAACAC-ACATTTTTC
29158763 AACATGGCAT-TAACA-ACATTTTTC
1 AACATGGCATGTAACACACATTTTTC
29158787 CACAATAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
26 5 0.21
27 10 0.42
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (26 bp):
AACATGGCATGTAACACACATTTTTC
Found at i:29162494 original size:30 final size:31
Alignment explanation
Indices: 29162442--29162499 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
29162432 TTTATTGTGT
*
29162442 TGAATCAAGTCTTTATAGTTTTATTTTGGAC
1 TGAATCAAGTATTTATAGTTTTATTTTGGAC
*
29162473 TGAAT-AAGTATTTATATTTTTATTTTG
1 TGAATCAAGTATTTATAGTTTTATTTTG
29162500 AGTCAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (31 bp):
TGAATCAAGTATTTATAGTTTTATTTTGGAC
Found at i:29162592 original size:13 final size:13
Alignment explanation
Indices: 29162574--29162598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29162564 TATGACACTC
29162574 ACATGACATGCTG
1 ACATGACATGCTG
29162587 ACATGACATGCT
1 ACATGACATGCT
29162599 ATCATTTTAG
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
ACATGACATGCTG
Found at i:29163958 original size:3 final size:3
Alignment explanation
Indices: 29163950--29163974 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29163940 CCCTTCCGCT
29163950 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
29163975 TCTCACCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:29181685 original size:26 final size:26
Alignment explanation
Indices: 29181636--29181687 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
29181626 TGCAATTTTT
* *
29181636 TGTTGTTTTTGTAAGTCAAGCATCTC
1 TGTTGTTTTTGTAAATAAAGCATCTC
*
29181662 TGTTGTTTTTGTAAATAAATCATCTC
1 TGTTGTTTTTGTAAATAAAGCATCTC
29181688 ACCCCTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.48
Consensus pattern (26 bp):
TGTTGTTTTTGTAAATAAAGCATCTC
Found at i:29184993 original size:21 final size:23
Alignment explanation
Indices: 29184967--29185035 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
29184957 TTCTAATTTT
29184967 TAATAAAATATTAATATTAAATTA
1 TAATAAAATATTAATATTAAA-TA
29184991 TAAATAAAATATTAATATT---TA
1 T-AATAAAATATTAATATTAAATA
29185012 TACATAAAATATTAATATTTAAAT
1 TA-ATAAAATATTAATA-TTAAAT
29185036 TCATCAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.03
21 17 0.44
22 2 0.05
24 1 0.03
25 18 0.46
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAATATTAATATTAAATA
Found at i:29184996 original size:25 final size:25
Alignment explanation
Indices: 29184968--29185036 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 25
29184958 TCTAATTTTT
29184968 AATAAAATATTAATATTAAATTATA
1 AATAAAATATTAATATTAAATTATA
29184993 AATAAAATATTAATA-T---TTATA
1 AATAAAATATTAATATTAAATTATA
*
29185014 CATAAAATATTAATATTTAAATT
1 AATAAAATATTAATA-TTAAATT
29185037 CATCAATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 19 0.50
23 1 0.03
24 1 0.03
25 15 0.39
26 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAAAATATTAATATTAAATTATA
Found at i:29186607 original size:20 final size:20
Alignment explanation
Indices: 29186582--29186621 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29186572 ATTAGATTAT
* *
29186582 AAATAAAATTAATATTTAAA
1 AAATAAAATAAAAATTTAAA
29186602 AAATAAAATAAAAATTTAAA
1 AAATAAAATAAAAATTTAAA
29186622 TAATCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATAAAATAAAAATTTAAA
Found at i:29188111 original size:62 final size:62
Alignment explanation
Indices: 29187977--29188119 Score: 148
Period size: 62 Copynumber: 2.3 Consensus size: 62
29187967 CCCCCGTTTC
*
29187977 CAATAATTTTTAAA-TTTTATAATTTATATATATTTTTAAAAAATTTTATAATTTTATCCTTT
1 CAATAA-TTTTAAATTTTTATAATTTATATATATTTTTAAAAAATTTTATAATTTCATCCTTT
* * * * * * *
29188039 CAATATTTTTAAATTTTTATAATTTGTCTTTACTTTTT-AGAAATTTTATAATTTCGTTCTTAT
1 CAATAATTTTAAATTTTTATAATTTATATATA-TTTTTAAAAAATTTTATAATTTCATCCTT-T
*
29188102 TAA-AATTTTAAAATTTTT
1 CAATAATTTT-AAATTTTT
29188120 CTAACATCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
61 7 0.10
62 44 0.66
63 16 0.24
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (62 bp):
CAATAATTTTAAATTTTTATAATTTATATATATTTTTAAAAAATTTTATAATTTCATCCTTT
Found at i:29188484 original size:15 final size:15
Alignment explanation
Indices: 29188464--29188498 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29188454 TTTATTTATT
*
29188464 TATTTTAATTTTTAA
1 TATTTTAAATTTTAA
29188479 TATTTTAAATTTTAA
1 TATTTTAAATTTTAA
29188494 -ATTTT
1 TATTTT
29188499 TTCTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTAAATTTTAA
Found at i:29188911 original size:18 final size:18
Alignment explanation
Indices: 29188879--29188913 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29188869 TTATTTAAAA
29188879 ATTAAGATTATTGTGATT
1 ATTAAGATTATTGTGATT
29188897 ATTAA-ATTATATGTGAT
1 ATTAAGATTAT-TGTGAT
29188914 CATACTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (18 bp):
ATTAAGATTATTGTGATT
Found at i:29191161 original size:15 final size:16
Alignment explanation
Indices: 29191141--29191179 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
29191131 TATATATATA
29191141 TTATAATG-AATAATT
1 TTATAATGTAATAATT
*
29191156 TTATAA-GTTATAATT
1 TTATAATGTAATAATT
29191171 TTATAATGT
1 TTATAATGT
29191180 TAACACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.86
16 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
TTATAATGTAATAATT
Found at i:29191939 original size:17 final size:17
Alignment explanation
Indices: 29191917--29191956 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
29191907 AATAGAAAGT
* * *
29191917 AAATATATTTATATTTA
1 AAATATATATATACTAA
29191934 AAATATATATATACTAA
1 AAATATATATATACTAA
29191951 AAATAT
1 AAATAT
29191957 TAGTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATATATATACTAA
Found at i:29192154 original size:2 final size:2
Alignment explanation
Indices: 29192147--29192184 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
29192137 CTCCTTTTAA
29192147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29192185 AGTTATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29192614 original size:21 final size:20
Alignment explanation
Indices: 29192584--29192622 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
29192574 GTTAAATTAC
*
29192584 TACCCAAACCTAATTATAAGA
1 TACCCAAACC-AAGTATAAGA
*
29192605 TACCCTAACCAAGTATAA
1 TACCCAAACCAAGTATAA
29192623 CCGGGTCGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.26, G:0.05, T:0.23
Consensus pattern (20 bp):
TACCCAAACCAAGTATAAGA
Found at i:29192886 original size:22 final size:22
Alignment explanation
Indices: 29192845--29192890 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
29192835 CATTTGCTTA
29192845 TTCTATAGCTTAAAATCTTTGAG
1 TTCTATAGCTTAAAATCTTT-AG
29192868 TTCTATA-CTT-AAATGCTTTAG
1 TTCTATAGCTTAAAAT-CTTTAG
29192889 TT
1 TT
29192891 TTTCTTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (22 bp):
TTCTATAGCTTAAAATCTTTAG
Found at i:29193074 original size:15 final size:15
Alignment explanation
Indices: 29193054--29193084 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29193044 CTAACAAATT
29193054 TCATAAGTCCTTTCA
1 TCATAAGTCCTTTCA
*
29193069 TCATAATTCCTTTCA
1 TCATAAGTCCTTTCA
29193084 T
1 T
29193085 TAGACACTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (15 bp):
TCATAAGTCCTTTCA
Found at i:29195321 original size:55 final size:54
Alignment explanation
Indices: 29195229--29195405 Score: 176
Period size: 55 Copynumber: 3.2 Consensus size: 54
29195219 TGAAGAGTTA
** **
29195229 TTTTAGCGTGTCACGGCTGTTAATGGCGTGTTATGGGTTAACTAGTTATTTAGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACT-GTTATTTAGGT
* * * * *
29195284 TGTTAGCATGTCACGGCTGTTCCTGGGGTGTGGTGGGTTAACTG-AATTTATGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTGTTATTTA--GGT
* * * * * *
29195339 TTTTGGCGTGTCATGGTTGTTCCTGGTGTGTCGTGGGTTAACTGGTTTTTTGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACT-GTTATTTAGGT
29195394 TTTTAGCGTGTC
1 TTTTAGCGTGTC
29195406 TTGGATGTTG
Statistics
Matches: 99, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
53 5 0.05
54 1 0.01
55 89 0.90
56 1 0.01
57 3 0.03
ACGTcount: A:0.12, C:0.12, G:0.33, T:0.42
Consensus pattern (54 bp):
TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTGTTATTTAGGT
Found at i:29195460 original size:20 final size:21
Alignment explanation
Indices: 29195435--29195503 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
29195425 GTCAGTAATT
29195435 ACAGTGAT-TGGCGTGTCACG
1 ACAGTGATATGGCGTGTCACG
*
29195455 ACAGTGATGCATGGCGTGTCACA
1 ACAGTGAT--ATGGCGTGTCACG
* *
29195478 ATACTGATGCATGGCGTGTCACG
1 ACAGTGAT--ATGGCGTGTCACG
29195501 ACA
1 ACA
29195504 TTTGACTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 8 0.20
23 33 0.80
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (21 bp):
ACAGTGATATGGCGTGTCACG
Found at i:29195473 original size:23 final size:23
Alignment explanation
Indices: 29195443--29195503 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
29195433 TTACAGTGAT
*
29195443 TGGCGTGTCACGACAGTGATGCA
1 TGGCGTGTCACGACACTGATGCA
* *
29195466 TGGCGTGTCACAATACTGATGCA
1 TGGCGTGTCACGACACTGATGCA
29195489 TGGCGTGTCACGACA
1 TGGCGTGTCACGACA
29195504 TTTGACTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (23 bp):
TGGCGTGTCACGACACTGATGCA
Found at i:29195519 original size:31 final size:31
Alignment explanation
Indices: 29195484--29195565 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
29195474 CACAATACTG
*
29195484 ATGCATGGCGTGTCACGACATTTGAC-TTGAT
1 ATGCATGGCGTGTCACAACATTTGACATT-AT
* *
29195515 ATGCATGGCGTGTTACAACATTTTACATTAT
1 ATGCATGGCGTGTCACAACATTTGACATTAT
* *
29195546 TTGCATGGCGTGTAACAACA
1 ATGCATGGCGTGTCACAACA
29195566 CGACTGACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
31 43 0.96
32 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (31 bp):
ATGCATGGCGTGTCACAACATTTGACATTAT
Found at i:29199134 original size:31 final size:31
Alignment explanation
Indices: 29199039--29199346 Score: 260
Period size: 31 Copynumber: 10.0 Consensus size: 31
29199029 AATAAGGAAT
* * *
29199039 AAATA-TGAGACACACCATGCATAACAAGTT
1 AAATATTGTGACACGCCATGCATAACAAGTA
* * * * * * *
29199069 AAATGTTGTCACACGTCGTGCACATCAAATA
1 AAATATTGTGACACGCCATGCATAACAAGTA
* * * *
29199100 AAATATTGTAACACGCCATTCGTAACAAGAA
1 AAATATTGTGACACGCCATGCATAACAAGTA
**
29199131 AAATGA-AATGACACGCCATGCATAACAAGTA
1 AAAT-ATTGTGACACGCCATGCATAACAAGTA
*
29199162 AAATGTTGTGACACGCCATGCATAACAAGTA
1 AAATATTGTGACACGCCATGCATAACAAGTA
** * * *
29199193 AAAGGTTGTGACACGCCAAGGATAACAAGCA
1 AAATATTGTGACACGCCATGCATAACAAGTA
* *
29199224 AAATGTTCTGACACGCCATGCATAACAAGTA
1 AAATATTGTGACACGCCATGCATAACAAGTA
** * * * *
29199255 AAAGGTTGTGACACACCAAGGATAACAAGCA
1 AAATATTGTGACACGCCATGCATAACAAGTA
* * *
29199286 AAATGTTCTGACACGCCATGCATAACAATTA
1 AAATATTGTGACACGCCATGCATAACAAGTA
* * * *
29199317 AATTGTTCTGACCCGCCATGCATAACAAGT
1 AAATATTGTGACACGCCATGCATAACAAGT
29199347 TCTGGTGTGT
Statistics
Matches: 221, Mismatches: 54, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
30 4 0.02
31 216 0.98
32 1 0.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (31 bp):
AAATATTGTGACACGCCATGCATAACAAGTA
Found at i:29199207 original size:93 final size:93
Alignment explanation
Indices: 29199047--29199346 Score: 323
Period size: 93 Copynumber: 3.2 Consensus size: 93
29199037 ATAAATATGA
* * * * * * * * * *
29199047 GACACACCATGCATAACAAGTTAAATGTTGTCACACGTCGTGCACATCAAATAAAATATTGTAAC
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGAC
* ***
29199112 ACGCCATTCGTAACAAGAAAAATGAAAT
66 ACGCCATACGTAACAAGAAAAATGTTCT
*
29199140 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGTAAAAGGTTGTGAC
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGAC
* *
29199205 ACGCCA-AGGATAACAAGCAAAATGTTCT
66 ACGCCATACG-TAACAAGAAAAATGTTCT
* * * * * *
29199233 GACACGCCATGCATAACAAGTAAAAGGTTGTGACACACCAAGGATAACAAGCAAAATGTTCTGAC
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGAC
* * ** *
29199298 ACGCCATGCATAACAATTAAATTGTTCT
66 ACGCCATACGTAACAAGAAAAATGTTCT
*
29199326 GACCCGCCATGCATAACAAGT
1 GACACGCCATGCATAACAAGT
29199347 TCTGGTGTGT
Statistics
Matches: 174, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
92 1 0.01
93 173 0.99
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (93 bp):
GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGAC
ACGCCATACGTAACAAGAAAAATGTTCT
Found at i:29199345 original size:62 final size:62
Alignment explanation
Indices: 29199139--29199345 Score: 306
Period size: 62 Copynumber: 3.3 Consensus size: 62
29199129 AAAAATGAAA
* * *
29199139 TGACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGTAAAAGGTTG
1 TGACACGCCAAGCATAACAAGCAAAATGTTCTGACACGCCATGCATAACAAGTAAAAGGTTG
*
29199201 TGACACGCCAAGGATAACAAGCAAAATGTTCTGACACGCCATGCATAACAAGTAAAAGGTTG
1 TGACACGCCAAGCATAACAAGCAAAATGTTCTGACACGCCATGCATAACAAGTAAAAGGTTG
* * * ** *
29199263 TGACACACCAAGGATAACAAGCAAAATGTTCTGACACGCCATGCATAACAATTAAATTGTTC
1 TGACACGCCAAGCATAACAAGCAAAATGTTCTGACACGCCATGCATAACAAGTAAAAGGTTG
* *
29199325 TGACCCGCCATGCATAACAAG
1 TGACACGCCAAGCATAACAAG
29199346 TTCTGGTGTG
Statistics
Matches: 132, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 132 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (62 bp):
TGACACGCCAAGCATAACAAGCAAAATGTTCTGACACGCCATGCATAACAAGTAAAAGGTTG
Found at i:29199909 original size:23 final size:22
Alignment explanation
Indices: 29199860--29199915 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
29199850 TATTGGTATC
* *
29199860 AAATTAATTATGTATAGGCAAA
1 AAATTAATTGTGTATAGGAAAA
29199882 AAATTAATTGTGTATAGGTAAAA
1 AAATTAATTGTGTATAGG-AAAA
29199905 AAATTAATTGT
1 AAATTAATTGT
29199916 ACAAAGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (22 bp):
AAATTAATTGTGTATAGGAAAA
Found at i:29199974 original size:14 final size:14
Alignment explanation
Indices: 29199955--29200015 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
29199945 TATATCTGTT
*
29199955 TACAATGAATTGTA
1 TACAATAAATTGTA
*
29199969 TACAATAAAAAGTGTA
1 TACAAT--AAATTGTA
*
29199985 TACAAAAAATGTGTA
1 TACAATAAAT-TGTA
* *
29200000 TAAAATGAATTGTA
1 TACAATAAATTGTA
29200014 TA
1 TA
29200016 AAAAAATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
14 15 0.41
15 11 0.30
16 11 0.30
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (14 bp):
TACAATAAATTGTA
Found at i:29199986 original size:16 final size:15
Alignment explanation
Indices: 29199965--29200001 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
29199955 TACAATGAAT
29199965 TGTATACAATAAAAAG
1 TGTATACAA-AAAAAG
*
29199981 TGTATACAAAAAATG
1 TGTATACAAAAAAAG
29199996 TGTATA
1 TGTATA
29200002 AAATGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (15 bp):
TGTATACAAAAAAAG
Found at i:29200023 original size:13 final size:13
Alignment explanation
Indices: 29199975--29200023 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
29199965 TGTATACAAT
*
29199975 AAAAAGTGTATACA
1 AAAAATTGTATA-A
29199989 AAAAATGTGTATAA
1 AAAAAT-TGTATAA
*
29200003 AATGAATTGTATAA
1 AA-AAATTGTATAA
29200017 AAAAATT
1 AAAAATT
29200024 TATGTGTACC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (13 bp):
AAAAATTGTATAA
Found at i:29201554 original size:31 final size:31
Alignment explanation
Indices: 29201518--29201588 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
29201508 TATAAAATAC
*
29201518 CAAGTAAAATGTTGTCACACGCCATACAAAA
1 CAAGTAAAATGTCGTCACACGCCATACAAAA
* * * * *
29201549 CAAGTAAAGTGTCGTGACATGCCATGCATAA
1 CAAGTAAAATGTCGTCACACGCCATACAAAA
29201580 CAAGATAAA
1 CAAG-TAAA
29201589 CTTGGTGACA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (31 bp):
CAAGTAAAATGTCGTCACACGCCATACAAAA
Found at i:29201597 original size:31 final size:31
Alignment explanation
Indices: 29201534--29201727 Score: 173
Period size: 31 Copynumber: 6.3 Consensus size: 31
29201524 AAATGTTGTC
* * * *
29201534 ACACGCCATACAAAACAAG-TAAAGTGTCGTG
1 ACACGCCATGCATAACAAGATAAACT-TGGTG
*
29201565 ACATGCCATGCATAACAAGATAAACTTGGTG
1 ACACGCCATGCATAACAAGATAAACTTGGTG
* * * * *
29201596 ACACGCCAAGGATAATGAGGA-AAA-TGTTGTG
1 ACACGCCATGCATAA-CAAGATAAACT-TGGTG
29201627 ACACGCCATGCATAACAAGATAAACTTGGTG
1 ACACGCCATGCATAACAAGATAAACTTGGTG
* * * *
29201658 ACACGCCAAGGATAACCAGGA-AAA-TGTTGTG
1 ACACGCCATGCATAA-CAAGATAAACT-TGGTG
*
29201689 ACACGCCATGCATAAGAAGATAAACTTGGTG
1 ACACGCCATGCATAACAAGATAAACTTGGTG
29201720 ACACGCCA
1 ACACGCCA
29201728 AGGAAAATAA
Statistics
Matches: 129, Mismatches: 25, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
30 8 0.06
31 107 0.83
32 14 0.11
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (31 bp):
ACACGCCATGCATAACAAGATAAACTTGGTG
Found at i:29201636 original size:62 final size:61
Alignment explanation
Indices: 29201562--29201786 Score: 326
Period size: 62 Copynumber: 3.6 Consensus size: 61
29201552 GTAAAGTGTC
*
29201562 GTGACATGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGATAATGAGGAAAATGTT
1 GTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGATAAT-AGGAAAATGTT
*
29201624 GTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGATAACCAGGAAAATGTT
1 GTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGATAA-TAGGAAAATGTT
* * * *
29201686 GTGACACGCCATGCATAAGAAGATAAACTTGGTGACACGCCAAGGAAAATAAGCAAATGTT
1 GTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGATAATAGGAAAATGTT
* * *
29201747 CTGACACGCCATGCATATCAAAATCAAACGTT-GTGACACG
1 GTGACACGCCATGCATAACAAGAT-AAAC-TTGGTGACACG
29201787 TCATAAATAA
Statistics
Matches: 149, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
61 29 0.19
62 118 0.79
63 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (61 bp):
GTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGATAATAGGAAAATGTT
Found at i:29201797 original size:124 final size:124
Alignment explanation
Indices: 29201562--29201818 Score: 335
Period size: 124 Copynumber: 2.1 Consensus size: 124
29201552 GTAAAGTGTC
* * * *
29201562 GTGACATGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGATAATGAGGAAAATGTTGTG
1 GTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGAAAATGAAGAAAATGTTCTG
* *
29201627 ACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGATAACCAGGA-A-AATGTT
66 ACACGCCATGCATAACAAAATAAACTTGGTGACACGCCAAGAATAA-CA-GATATAATGTT
* *
29201686 GTGACACGCCATGCATAAGAAGATAAACTTGGTGACACGCCAAGGAAAAT-AAGCAAATGTTCTG
1 GTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGAAAATGAAGAAAATGTTCTG
* * *
29201750 ACACGCCATGCATATCAAAATCAAACGTT-GTGACACGTCATA-AATAACATATATAATGTT
66 ACACGCCATGCATAACAAAAT-AAAC-TTGGTGACACGCCA-AGAATAACAGATATAATGTT
29201810 GTGACACGC
1 GTGACACGC
29201819 TAAAAATGAC
Statistics
Matches: 117, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
122 1 0.01
123 33 0.28
124 80 0.68
125 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (124 bp):
GTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGAAAATGAAGAAAATGTTCTG
ACACGCCATGCATAACAAAATAAACTTGGTGACACGCCAAGAATAACAGATATAATGTT
Found at i:29202420 original size:156 final size:156
Alignment explanation
Indices: 29202153--29202439 Score: 439
Period size: 156 Copynumber: 1.8 Consensus size: 156
29202143 AACTACAATA
29202153 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACAGTTACAACTTT
1 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACAGTTACAACTTT
* * * **
29202218 AATATCCTCACTGGCGACTCGTTAGCAGTCTGCGATGGAGCCGGACCGATTGGTGCTTCAGGACC
66 AATATCCTCACCGCCGACTCGTTAGCAGTCTACGATGGAGCCGGACCGATCAGTGCTTCAGGACC
29202283 TATTGTCGATTTCGCCTACTGTAATT
131 TATTGTCGATTTCGCCTACTGTAATT
* * * *
29202309 ACATATTTAACTGTGTTATTCAATAATCATGTTTGGAATTGTTGAACATTAACCGTTACAACTTT
1 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACAGTTACAACTTT
* * * * * *
29202374 AATATCCTTACCGCCGACTCGTTAGCTGTCTACGGTTGAGCTGGACCGATCAGTGCTTGAGGACC
66 AATATCCTCACCGCCGACTCGTTAGCAGTCTACGATGGAGCCGGACCGATCAGTGCTTCAGGACC
29202439 T
131 T
29202440 GTCGTCGCTT
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
156 116 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (156 bp):
ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACAGTTACAACTTT
AATATCCTCACCGCCGACTCGTTAGCAGTCTACGATGGAGCCGGACCGATCAGTGCTTCAGGACC
TATTGTCGATTTCGCCTACTGTAATT
Found at i:29202468 original size:156 final size:156
Alignment explanation
Indices: 29202153--29202482 Score: 428
Period size: 156 Copynumber: 2.1 Consensus size: 156
29202143 AACTACAATA
*
29202153 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACAGTTACAACTTT
1 ACATATTTAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACAGTTACAACTTT
* * * **
29202218 AATATCCTCACTGGCGACTCGTTAGCAGTCTGCGATGGAGCCGGACCGATTGGTGCTTCAGGACC
66 AATATCCTCACCGCCGACTCGTTAGCAGTCTACGATGGAGCCGGACCGATCAGTGCTTCAGGACC
* ** * *
29202283 TATTGTCGATTTCGCCTACTGTAATT
131 TATCGTCGATTTCGCAAACTGCAAGT
* * *
29202309 ACATATTTAACTGTGTTATTCAATAATCATGTTTGGAATTGTTGAACATTAACCGTTACAACTTT
1 ACATATTTAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACAGTTACAACTTT
* * * * * *
29202374 AATATCCTTACCGCCGACTCGTTAGCTGTCTACGGTTGAGCTGGACCGATCAGTGCTTGAGGACC
66 AATATCCTCACCGCCGACTCGTTAGCAGTCTACGATGGAGCCGGACCGATCAGTGCTTCAGGACC
* * *
29202439 TGTCGTCGCTTTCGTAAACTGCAAGT
131 TATCGTCGATTTCGCAAACTGCAAGT
*
29202465 ACATAAATT-ACTGTGTTA
1 ACAT-ATTTAACTGTGTTA
29202483 CTCGATAAAT
Statistics
Matches: 149, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
156 146 0.98
157 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (156 bp):
ACATATTTAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACAGTTACAACTTT
AATATCCTCACCGCCGACTCGTTAGCAGTCTACGATGGAGCCGGACCGATCAGTGCTTCAGGACC
TATCGTCGATTTCGCAAACTGCAAGT
Done.