Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 137 of 193
Found at i:42952825 original size:6 final size:7
Alignment explanation
Indices: 42952781--42952830 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
42952771 ATTTAATCTT
42952781 TTAAAAA
1 TTAAAAA
42952788 TTATAAAGA
1 TTA-AAA-A
*
42952797 TATAAACTA
1 T-TAAA-AA
42952806 TTAAAAA
1 TTAAAAA
42952813 TTAAAAA
1 TTAAAAA
42952820 TTAAAAA
1 TTAAAAA
42952827 TTAA
1 TTAA
42952831 TTTTGTCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 22 0.59
8 7 0.19
9 6 0.16
10 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (7 bp):
TTAAAAA
Found at i:42966539 original size:13 final size:13
Alignment explanation
Indices: 42966521--42966550 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
42966511 CCTCAACAGA
42966521 AGCAAAGTATAGG
1 AGCAAAGTATAGG
42966534 AGCAAAGTATAGG
1 AGCAAAGTATAGG
42966547 AGCA
1 AGCA
42966551 CGGCAGTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.30, T:0.13
Consensus pattern (13 bp):
AGCAAAGTATAGG
Found at i:42973595 original size:22 final size:23
Alignment explanation
Indices: 42973570--42973612 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
42973560 AATTTGAAAT
*
42973570 TTAAAAATATAAA-ATTAAATTA
1 TTAAAAATAAAAAGATTAAATTA
42973592 TTAAAAATAAAAAGATTAAAT
1 TTAAAAATAAAAAGATTAAAT
42973613 ATCAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAAAATAAAAAGATTAAATTA
Found at i:42992241 original size:30 final size:31
Alignment explanation
Indices: 42992205--42992289 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 31
42992195 TTTTTTAAAT
*
42992205 CTCTTAAAAGTTGGTAAAAAAAAATTTG-GA
1 CTCTTAAAAGTTAGTAAAAAAAAATTTGAGA
* *
42992235 CTCTTAAAA---ACTAAAAAAAAATTTGAGG
1 CTCTTAAAAGTTAGTAAAAAAAAATTTGAGA
*
42992263 CCCTTAAAAGTTAGTAAAAAAAAATTT
1 CTCTTAAAAGTTAGTAAAAAAAAATTT
42992290 TGACCTATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 14 0.30
28 9 0.20
30 9 0.20
31 14 0.30
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (31 bp):
CTCTTAAAAGTTAGTAAAAAAAAATTTGAGA
Found at i:42992268 original size:28 final size:28
Alignment explanation
Indices: 42992219--42992341 Score: 105
Period size: 28 Copynumber: 4.3 Consensus size: 28
42992209 TAAAAGTTGG
* *
42992219 TAAAAAAAAA-TTTG-GACTCTTAAAAA
1 TAAAAAAAAATTTTGAGGCCCTTAAAAA
42992245 CTAAAAAAAAA-TTTGAGGCCCTTAAAAGTTA
1 -TAAAAAAAAATTTTGAGGCCCTTAAAA---A
42992276 GTAAAAAAAAATTTTGA---CCTATAAAAA
1 -TAAAAAAAAATTTTGAGGCCCT-TAAAAA
*
42992303 TTAAATAAAAAATTTTGGGGCCCTTAAAAA
1 -TAAA-AAAAAATTTTGAGGCCCTTAAAAA
42992333 TAAAAAAAA
1 TAAAAAAAA
42992342 CAAAAATTTA
Statistics
Matches: 81, Mismatches: 5, Indels: 19
0.77 0.05 0.18
Matches are distributed among these distances:
27 19 0.23
28 25 0.31
29 7 0.09
30 11 0.14
31 14 0.17
32 5 0.06
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (28 bp):
TAAAAAAAAATTTTGAGGCCCTTAAAAA
Found at i:42992271 original size:58 final size:60
Alignment explanation
Indices: 42992207--42992331 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 60
42992197 TTTTAAATCT
*
42992207 CTTAAAAGTTGGTAAAAAAAAATTTGGACTCT-TAAAAACTAAA-AAAAAA-TTTGAGGCC
1 CTTAAAAGTTAGTAAAAAAAAATTTGGAC-CTATAAAAACTAAATAAAAAATTTTGAGGCC
* * *
42992265 CTTAAAAGTTAGTAAAAAAAAATTTTGACCTATAAAAATTAAATAAAAAATTTTGGGGCC
1 CTTAAAAGTTAGTAAAAAAAAATTTGGACCTATAAAAACTAAATAAAAAATTTTGAGGCC
42992325 CTTAAAA
1 CTTAAAA
42992332 ATAAAAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
57 2 0.03
58 37 0.62
59 6 0.10
60 15 0.25
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (60 bp):
CTTAAAAGTTAGTAAAAAAAAATTTGGACCTATAAAAACTAAATAAAAAATTTTGAGGCC
Found at i:42992606 original size:41 final size:42
Alignment explanation
Indices: 42992560--42992686 Score: 109
Period size: 43 Copynumber: 3.0 Consensus size: 42
42992550 CAATTATTTA
*
42992560 ATTCAATGAATCAAAATATCATACATTAAAATAACACTTTTT
1 ATTCAATAAATCAAAATATCATACATTAAAATAACACTTTTT
* * * * * *
42992602 -TTCAAATTATAAACAACATTATCA-A-ATTCAAGT-TCAATTATTT
1 ATTC-AA-TA-AATCAA-AATATCATACATTAAAATAACACTT-TTT
42992645 AATTCAATAAATCAAAATATCATACATTAAAATAACACTTTT
1 -ATTCAATAAATCAAAATATCATACATTAAAATAACACTTTT
42992687 CTCAAATTAT
Statistics
Matches: 62, Mismatches: 13, Indels: 19
0.66 0.14 0.20
Matches are distributed among these distances:
41 9 0.15
42 12 0.19
43 20 0.32
44 12 0.19
45 9 0.15
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (42 bp):
ATTCAATAAATCAAAATATCATACATTAAAATAACACTTTTT
Found at i:42992638 original size:86 final size:85
Alignment explanation
Indices: 42992530--42992697 Score: 300
Period size: 86 Copynumber: 2.0 Consensus size: 85
42992520 CCACCAAAAG
*
42992530 AACATTATCAAATTCAAATTCAATTATTTAATTCAATGAATCAAAATATCATACATTAAAATAAC
1 AACATTATCAAATTCAAATTCAATTATTTAATTCAATAAATCAAAATATCATACATTAAAATAAC
*
42992595 ACTTTTTTTCAAATTATAAAC
66 AC-TTTTCTCAAATTATAAAC
*
42992616 AACATTATCAAATTCAAGTTCAATTATTTAATTCAATAAATCAAAATATCATACATTAAAATAAC
1 AACATTATCAAATTCAAATTCAATTATTTAATTCAATAAATCAAAATATCATACATTAAAATAAC
42992681 ACTTTTCTCAAATTATA
66 ACTTTTCTCAAATTATA
42992698 TATATATATA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
85 14 0.18
86 65 0.82
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.37
Consensus pattern (85 bp):
AACATTATCAAATTCAAATTCAATTATTTAATTCAATAAATCAAAATATCATACATTAAAATAAC
ACTTTTCTCAAATTATAAAC
Found at i:42998264 original size:21 final size:21
Alignment explanation
Indices: 42998216--42998267 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
42998206 GGAGTTTTTA
* *
42998216 GTATCGATAGAAGTATGACAT
1 GTATCGGTAGAAGTATCACAT
* * *
42998237 GTTTCGGTAGAAGTCTCACTT
1 GTATCGGTAGAAGTATCACAT
42998258 GTATCGGTAG
1 GTATCGGTAG
42998268 TACTGCTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTATCACAT
Found at i:43005305 original size:46 final size:46
Alignment explanation
Indices: 43005252--43005343 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
43005242 AAAATTAACC
43005252 GTCAATATTGCATATTATTTCAATTTGGTTGAAAATTAACCCTCAA
1 GTCAATATTGCATATTATTTCAATTTGGTTGAAAATTAACCCTCAA
43005298 GTCAATATTGCATATTATTTCAATTTGGTTGAAAATTAACCCTCAA
1 GTCAATATTGCATATTATTTCAATTTGGTTGAAAATTAACCCTCAA
43005344 CACTGATTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (46 bp):
GTCAATATTGCATATTATTTCAATTTGGTTGAAAATTAACCCTCAA
Found at i:43016436 original size:15 final size:15
Alignment explanation
Indices: 43016416--43016444 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43016406 TTTCACTATT
43016416 TATTTGAAAGGTATA
1 TATTTGAAAGGTATA
43016431 TATTTGAAAGGTAT
1 TATTTGAAAGGTAT
43016445 GATGTTAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
TATTTGAAAGGTATA
Found at i:43018567 original size:2 final size:2
Alignment explanation
Indices: 43018557--43018596 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
43018547 ACACACACAC
*
43018557 AT AT TT 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
43018597 TAAAATGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:43027358 original size:14 final size:14
Alignment explanation
Indices: 43027306--43027365 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 14
43027296 TATTTTTGTC
43027306 TTTTCTTTTC--TT
1 TTTTCTTTTCAATT
*
43027318 TTTT-TTCTCAA-T
1 TTTTCTTTTCAATT
43027330 TTTT-TTTTCAA-T
1 TTTTCTTTTCAATT
*
43027342 TTTTCTTTTCGACTT
1 TTTTCTTTTC-AATT
43027357 TTTTCTTTT
1 TTTTCTTTT
43027366 TTCTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 4 0.10
12 20 0.50
13 5 0.12
14 1 0.03
15 10 0.25
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTCAATT
Found at i:43028347 original size:12 final size:12
Alignment explanation
Indices: 43028332--43028376 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
43028322 TTTTTTGAAC
43028332 TTTTCAATTTTT
1 TTTTCAATTTTT
43028344 TTTTCAA---TT
1 TTTTCAATTTTT
43028353 TTTT-AATTTTT
1 TTTTCAATTTTT
43028364 TTTTCAAATTTTT
1 TTTTC-AATTTTT
43028377 AAAAACATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.07
9 6 0.21
11 6 0.21
12 7 0.25
13 7 0.25
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTCAATTTTT
Found at i:43028376 original size:20 final size:20
Alignment explanation
Indices: 43028317--43028378 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
43028307 AAATAAACTA
* * *
43028317 AATTTTTTTTTGAACTTTTC
1 AATTTTTTTTTCAAATTTTT
*
43028337 AATTTTTTTTTCAATTTTTT
1 AATTTTTTTTTCAAATTTTT
43028357 AATTTTTTTTTCAAATTTTT
1 AATTTTTTTTTCAAATTTTT
43028377 AA
1 AA
43028379 AAACATGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (20 bp):
AATTTTTTTTTCAAATTTTT
Found at i:43032203 original size:23 final size:23
Alignment explanation
Indices: 43032177--43032342 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
43032167 AGTGCTGGGC
43032177 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
43032200 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
43032219 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
43032239 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
43032262 ATCGGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
43032286 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
43032310 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
43032333 ATCAGAGAGC
1 AACAGAGAGC
43032343 GCGCTAGTGT
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 78 0.68
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:43032237 original size:39 final size:39
Alignment explanation
Indices: 43032183--43032257 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
43032173 GGGCAACAGA
*
43032183 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
43032222 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
43032258 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:43032296 original size:48 final size:46
Alignment explanation
Indices: 43032222--43032342 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
43032212 ACAAAGTACT
* * *
43032222 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
43032268 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
43032316 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
43032343 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:43034718 original size:182 final size:182
Alignment explanation
Indices: 43034409--43034792 Score: 687
Period size: 182 Copynumber: 2.1 Consensus size: 182
43034399 TGATCCGTAG
43034409 AAATCCCTAAATTATGCTAATAGCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAAT
1 AAATCCCTAAATTATGCTAATAGCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAAT
43034474 TGAAATTTCTTTCTAATTAAAACCCCTATTATCGCATTAATTCGATCTATGGATTCCCCTATTAA
66 TGAAATTTCTTTCTAATTAAAACCCCTATTATCGCATTAATTCGATCTATGGATTCCCCTATTAA
43034539 ATTTGACTCTAATCCGATAGATTTATGTTGTCCTATTTCTAGAATTGCATGC
131 ATTTGACTCTAATCCGATAGATTTATGTTGTCCTATTTCTAGAATTGCATGC
43034591 AAATCCCTAAATTATGCTAATAGCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAAT
1 AAATCCCTAAATTATGCTAATAGCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAAT
* * *
43034656 TGAAATTTCTTTCTAATTAAAACCCCTATTGTCGCATTAATTTGATCTATGGATTTCCCTATTAA
66 TGAAATTTCTTTCTAATTAAAACCCCTATTATCGCATTAATTCGATCTATGGATTCCCCTATTAA
* * *
43034721 ATTTGACTCTAATCCGGTAGATTTATGTTGTCTTATTTCTAGGATTGCATGC
131 ATTTGACTCTAATCCGATAGATTTATGTTGTCCTATTTCTAGAATTGCATGC
* *
43034773 AACTCCACTCAATTATGCTA
1 AAATCC-CTAAATTATGCTA
43034793 GATCTACTCT
Statistics
Matches: 193, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
182 181 0.94
183 12 0.06
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (182 bp):
AAATCCCTAAATTATGCTAATAGCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAAT
TGAAATTTCTTTCTAATTAAAACCCCTATTATCGCATTAATTCGATCTATGGATTCCCCTATTAA
ATTTGACTCTAATCCGATAGATTTATGTTGTCCTATTTCTAGAATTGCATGC
Found at i:43036581 original size:7 final size:7
Alignment explanation
Indices: 43036534--43036567 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
43036524 ATATCAACAA
43036534 ATATATT
1 ATATATT
*
43036541 -TAAATT
1 ATATATT
43036547 ATATATT
1 ATATATT
43036554 ATATATT
1 ATATATT
43036561 ATATATT
1 ATATATT
43036568 TATTATATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATATATT
Found at i:43036589 original size:18 final size:18
Alignment explanation
Indices: 43036547--43036589 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
43036537 TATTTAAATT
*
43036547 ATATATTATATATTATAT
1 ATATATTATATATTATAA
* *
43036565 ATTTATTATATCTTATAA
1 ATATATTATATATTATAA
43036583 ATATATT
1 ATATATT
43036590 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATATTATATATTATAA
Found at i:43036604 original size:20 final size:21
Alignment explanation
Indices: 43036581--43036621 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
43036571 TATATCTTAT
*
43036581 AAATATATTTAAA-ATAAATA
1 AAATATATATAAATATAAATA
43036601 AAATATATATAAATATAAATA
1 AAATATATATAAATATAAATA
43036622 TAAAAACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATATATATAAATATAAATA
Found at i:43037313 original size:3 final size:3
Alignment explanation
Indices: 43037305--43037346 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
43037295 TAGATAGACA
43037305 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
43037347 CTACATTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43038186 original size:2 final size:2
Alignment explanation
Indices: 43038179--43038225 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
43038169 TAGCTCATAA
* *
43038179 AC AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC GC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
43038221 AC AC A
1 AC AC A
43038226 TATATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.49, G:0.04, T:0.00
Consensus pattern (2 bp):
AC
Found at i:43042360 original size:25 final size:25
Alignment explanation
Indices: 43042302--43042362 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
43042292 CAGAACTGTG
*
43042302 TGTGCTCTCTG--ATTAGCACTATG
1 TGTGCTCTCTGTTATTAGCACTATC
43042325 TGTGCTCTCTGTTATTAGCACT-TCC
1 TGTGCTCTCTGTTATTAGCACTAT-C
43042350 TGTGCTCTCTGTT
1 TGTGCTCTCTGTT
43042363 TAGTACTTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.32
24 1 0.03
25 22 0.65
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (25 bp):
TGTGCTCTCTGTTATTAGCACTATC
Found at i:43042371 original size:23 final size:23
Alignment explanation
Indices: 43042302--43042371 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
43042292 CAGAACTGTG
* *
43042302 TGTGCTCTCTGATTAGCACTAT-G
1 TGTGCTCTCTGTTTAGCACT-TCC
43042325 TGTGCTCTCTGTTATTAGCACTTCC
1 TGTGCTCTCTG-T-TTAGCACTTCC
*
43042350 TGTGCTCTCTGTTTAGTACTTC
1 TGTGCTCTCTGTTTAGCACTTC
43042372 GATACTCTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 20 0.49
24 2 0.05
25 19 0.46
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (23 bp):
TGTGCTCTCTGTTTAGCACTTCC
Found at i:43048729 original size:54 final size:54
Alignment explanation
Indices: 43048665--43049110 Score: 516
Period size: 54 Copynumber: 8.3 Consensus size: 54
43048655 AAATGCTGCA
* * * *
43048665 CAGAGCAACACCAACAACAATGAAAATGCGGGTCAGGATGAGAACAATGCCACT
1 CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
* * * * * * *
43048719 CAAAGTAACACTGACAACAATGAAAATGTGGGTCAGAAAGAGAACAATGCCGCT
1 CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
* * * *
43048773 CAGAGCAACACTGAGAACAATGAAAATGTGGGTCAGAATGAGAACAATGCCGCT
1 CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
* * *
43048827 CAGAGCAACACTGAGAACAATGAAAATGCAGGTCAGAACGAGAACAATGCAACT
1 CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
* * *
43048881 CAGAGCAACACCGAGAACAATGAGAATGGGGGTCAGAACGAGAAAAATGCCACT
1 CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
* * * * * *
43048935 CCA-AGTAACACCGACAACAATGAGAATGCGGGTCAGACCAAGAACAATGCCGCT
1 -CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
* * * * *
43048989 CTGAGTAACACCGAGAATAATGAGAATGCGGGTCAGAACGAGAACAATGCCGCT
1 CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
** * * * * * *
43049043 CCTAGTAACACCAAAAACAATGAGAATGCAGGTCAGAACGAGAACAATGCGACT
1 CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
43049097 CAGAGCAACACCGA
1 CAGAGCAACACCGA
43049111 CGAAAACAAC
Statistics
Matches: 343, Mismatches: 47, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 340 0.99
55 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (54 bp):
CAGAGCAACACCGAGAACAATGAAAATGCGGGTCAGAACGAGAACAATGCCACT
Found at i:43048788 original size:27 final size:27
Alignment explanation
Indices: 43048758--43048848 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 27
43048748 GGGTCAGAAA
43048758 GAGAACAATGCCGCTCAGAGCAACACT
1 GAGAACAATGCCGCTCAGAGCAACACT
**** ** *
43048785 GAGAACAATGAAAATGTGGGTCAGA-A-T
1 GAGAACAATGCCGCTCAGAG-CA-ACACT
43048812 GAGAACAATGCCGCTCAGAGCAACACT
1 GAGAACAATGCCGCTCAGAGCAACACT
43048839 GAGAACAATG
1 GAGAACAATG
43048849 AAAATGCAGG
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
25 1 0.02
26 3 0.07
27 38 0.83
28 3 0.07
29 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.13
Consensus pattern (27 bp):
GAGAACAATGCCGCTCAGAGCAACACT
Found at i:43048869 original size:27 final size:27
Alignment explanation
Indices: 43048839--43048929 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
43048829 GAGCAACACT
43048839 GAGAACAATGAAAATGCAGGTCAGAAC
1 GAGAACAATGAAAATGCAGGTCAGAAC
* *
43048866 GAGAACAATGCAACT-CAGAG-CA-ACACC
1 GAGAACAATGAAAATGCAG-GTCAGA-A-C
* **
43048893 GAGAACAATGAGAATGGGGGTCAGAAC
1 GAGAACAATGAAAATGCAGGTCAGAAC
*
43048920 GAGAAAAATG
1 GAGAACAATG
43048930 CCACTCCAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 38 0.76
28 4 0.08
29 1 0.02
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.10
Consensus pattern (27 bp):
GAGAACAATGAAAATGCAGGTCAGAAC
Found at i:43049164 original size:66 final size:66
Alignment explanation
Indices: 43049049--43049194 Score: 213
Period size: 66 Copynumber: 2.2 Consensus size: 66
43049039 CGCTCCTAGT
* * *
43049049 AACACCAAAAACAATGAGAATGCAGGTCAGAACGAGAACAATGCGACTCAGAGCAACACCGACGA
1 AACAACAACAACAATGAAAATGCAGGTCAGAACGAGAACAATGCGACTCAGAGCAACACCGAC-A
43049114 A-
65 AC
* * *
43049115 AACAACAACAACAATGAAAATGCAGGTCAGAATGAGAACAATGTGACTCAGAGCAACACTGACAA
1 AACAACAACAACAATGAAAATGCAGGTCAGAACGAGAACAATGCGACTCAGAGCAACACCGACAA
43049180 C
66 C
*
43049181 AGCAACAACAACAA
1 AACAACAACAACAA
43049195 CAACAACAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
65 2 0.03
66 70 0.97
ACGTcount: A:0.49, C:0.23, G:0.18, T:0.09
Consensus pattern (66 bp):
AACAACAACAACAATGAAAATGCAGGTCAGAACGAGAACAATGCGACTCAGAGCAACACCGACAA
C
Found at i:43049276 original size:51 final size:51
Alignment explanation
Indices: 43049196--43049294 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
43049186 CAACAACAAC
*
43049196 AACAACAACGAAAATGCAAGTCAAAATGAGAACAATGCCGCTCAGAGCAGT
1 AACAACAACGAAAATGCAAGTCAAAATGAGAACAATGCAGCTCAGAGCAGT
** *
43049247 AACAACAACGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGC
1 AACAACAACGAAAATGCAAGTCAAAATGAGAACAATGCAGCTCAGAGC
43049295 TTCACCGACA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (51 bp):
AACAACAACGAAAATGCAAGTCAAAATGAGAACAATGCAGCTCAGAGCAGT
Found at i:43049317 original size:63 final size:63
Alignment explanation
Indices: 43049250--43049373 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 63
43049240 GAGCAGTAAC
* * * **
43049250 AACAACGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACCAAT
1 AACAACGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCAACACCGACACCACCAAT
* ** *
43049313 AACAATGAAAATGCAAGTCAGAACGAAAACAATGTTTCTCAGAGCAACACTGACACCACCA
1 AACAACGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCAACACCGACACCACCA
43049374 CCAATGAGAG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.15
Consensus pattern (63 bp):
AACAACGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCAACACCGACACCACCAAT
Found at i:43059364 original size:6 final size:6
Alignment explanation
Indices: 43059355--43059383 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
43059345 TTGGGCTGTC
43059355 GTTGCT GTTGCT GTTGCT GTTGCT GTTGC
1 GTTGCT GTTGCT GTTGCT GTTGCT GTTGC
43059384 AGCCATTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.34, T:0.48
Consensus pattern (6 bp):
GTTGCT
Found at i:43060760 original size:63 final size:63
Alignment explanation
Indices: 43060653--43060779 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
43060643 AATATAAATA
* * *
43060653 ATACATTTTTGGTTGATTGAATCTTAGCTCGATTGACATAGACATTGTTGTTGATGCAGGAGG
1 ATACATGTTTAGTTGATTGAATCTTAGCTCAATTGACATAGACATTGTTGTTGATGCAGGAGG
* * *
43060716 ATACATGTTTAGTTGATTGAGTCTTAGCTCAATTGGCATGGACATTGTTGTTGATGCAGGAGG
1 ATACATGTTTAGTTGATTGAATCTTAGCTCAATTGACATAGACATTGTTGTTGATGCAGGAGG
43060779 A
1 A
43060780 CGTGTGTTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (63 bp):
ATACATGTTTAGTTGATTGAATCTTAGCTCAATTGACATAGACATTGTTGTTGATGCAGGAGG
Found at i:43064561 original size:16 final size:18
Alignment explanation
Indices: 43064540--43064572 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
43064530 ATCAAAGATT
43064540 TATTTT-ATTTT-TTATA
1 TATTTTAATTTTATTATA
43064556 TATTTTAATTTTATTAT
1 TATTTTAATTTTATTAT
43064573 GCACTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTTTAATTTTATTATA
Found at i:43071147 original size:22 final size:20
Alignment explanation
Indices: 43071121--43071175 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
43071111 AATAGTAAAA
43071121 ATATATTTTTAATTGATATTTT
1 ATATATTTTTAATT-A-ATTTT
43071143 ATATAATTTTATAATTAATTTT
1 ATAT-ATTTT-TAATTAATTTT
*
43071165 AAAT-TTTTTAA
1 ATATATTTTTAA
43071176 AAATATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.10
20 4 0.13
22 12 0.40
23 6 0.20
24 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATATTTTTAATTAATTTT
Found at i:43076334 original size:183 final size:186
Alignment explanation
Indices: 43076024--43076372 Score: 596
Period size: 183 Copynumber: 1.9 Consensus size: 186
43076014 AAATTTTTTA
43076024 CAACCTGCATTGCGATATCCAATCCCTCCTTGTCTTTCTTCACTGTTAAGAATGGAATTAAAGTC
1 CAACCTGCATTGCGATATCCAATCCCTCCTTGTCTTTCTTCACTGTTAAGAATGGAATTAAAGTC
* *
43076089 TCCAGCTAAACATCATGGACTATCAACATCCCTCGCAATCACCCCCAAATTATCCCATAATAAA-
66 TCCAGCTAAACACCATGGACTATCAACAGCCCTCGCAATCACCCCCAAATTATCCCATAATAAAC
43076153 TCT-CT-CCGATGAGGGCTAGCATACACAGCAGGTTAAGAATGGAATTAAATCTCT
131 TCTACTCCCGATGAGGGCTAGCATACACAGCAGGTTAAGAATGGAATTAAATCTCT
* * *
43076207 CAACCTGCATTTCGATATCCAGTCCCTCCTTGTCTTTCTTCACTGTTAAGAATGGAATTGAAGTC
1 CAACCTGCATTGCGATATCCAATCCCTCCTTGTCTTTCTTCACTGTTAAGAATGGAATTAAAGTC
*
43076272 TCCAGCTAAACACCATGGACTATCAACAGCCCTCGCAATCACCCCCAAATTATCCTATAATAAAT
66 TCCAGCTAAACACCATGGACTATCAACAGCCCTCGCAATCACCCCCAAATTATCCCATAATAAA-
43076337 CTCTCAACTCCCGATGAGGGCTAGCATACACAGCAG
130 CTCT--ACTCCCGATGAGGGCTAGCATACACAGCAG
43076373 TGTACAAAAG
Statistics
Matches: 154, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
183 123 0.80
185 3 0.02
188 2 0.01
189 26 0.17
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (186 bp):
CAACCTGCATTGCGATATCCAATCCCTCCTTGTCTTTCTTCACTGTTAAGAATGGAATTAAAGTC
TCCAGCTAAACACCATGGACTATCAACAGCCCTCGCAATCACCCCCAAATTATCCCATAATAAAC
TCTACTCCCGATGAGGGCTAGCATACACAGCAGGTTAAGAATGGAATTAAATCTCT
Found at i:43077269 original size:6 final size:6
Alignment explanation
Indices: 43077258--43077292 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
43077248 AATACCCACT
43077258 CCTTTG CCTTTG CCTTTG CCTTTG CCTTTG CCTTT
1 CCTTTG CCTTTG CCTTTG CCTTTG CCTTTG CCTTT
43077293 AATTCCGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.14, T:0.51
Consensus pattern (6 bp):
CCTTTG
Found at i:43081079 original size:13 final size:13
Alignment explanation
Indices: 43081061--43081090 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
43081051 ACCAAAGTTT
43081061 GTAAGAATAAGGG
1 GTAAGAATAAGGG
43081074 GTAAGAATAAGGG
1 GTAAGAATAAGGG
43081087 GTAA
1 GTAA
43081091 CTCTCCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.17
Consensus pattern (13 bp):
GTAAGAATAAGGG
Found at i:43083771 original size:28 final size:27
Alignment explanation
Indices: 43083727--43083779 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
43083717 ATTTTTATTA
*
43083727 AATATAAGAATCACATTGGACAAAAAAT
1 AATATAAGAATCACATTAGA-AAAAAAT
*
43083755 AATATAA-ATATCGCATTAGAAAAAA
1 AATATAAGA-ATCACATTAGAAAAAA
43083780 GTATCAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (27 bp):
AATATAAGAATCACATTAGAAAAAAAT
Found at i:43087230 original size:24 final size:23
Alignment explanation
Indices: 43087179--43087243 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
43087169 TTATTGTTCA
43087179 CGAACATGTTCAAGTAAC-TTAAT
1 CGAACATGTTCAAG-AACATTAAT
*
43087202 CGAACATGTTCATGAACATTTAAT
1 CGAACATGTTCAAGAACA-TTAAT
* *
43087226 TGAACATGTTCACGAACA
1 CGAACATGTTCAAGAACA
43087244 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.08
23 13 0.35
24 21 0.57
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (23 bp):
CGAACATGTTCAAGAACATTAAT
Found at i:43092453 original size:6 final size:6
Alignment explanation
Indices: 43092446--43092480 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
43092436 GGTTACAAAC
*
43092446 TAAAAC TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
43092481 CAAAGCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:43100912 original size:16 final size:16
Alignment explanation
Indices: 43100893--43100926 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43100883 ACTTAACTTT
43100893 TAAAAAAATTAAAATA
1 TAAAAAAATTAAAATA
**
43100909 TAAAAATTTTAAAATA
1 TAAAAAAATTAAAATA
43100925 TA
1 TA
43100927 TTTTTTTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAAAATTAAAATA
Found at i:43106182 original size:23 final size:22
Alignment explanation
Indices: 43106143--43106187 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
43106133 AAAAAATTAT
* *
43106143 TAAATATTAAAATAATATAATA
1 TAAATATTAAAAAAATAAAATA
43106165 TAAATATTTAAAAAAATAAAATA
1 TAAATA-TTAAAAAAATAAAATA
43106188 ATATGGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATATTAAAAAAATAAAATA
Found at i:43112415 original size:6 final size:6
Alignment explanation
Indices: 43112404--43112430 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43112394 AAGACAATAG
43112404 AAAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA
43112431 CTCATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:43114265 original size:15 final size:15
Alignment explanation
Indices: 43114235--43114276 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
43114225 ATAATTTGTA
*
43114235 ATAATTAATTTTAATG
1 ATAATT-ATTTGAATG
43114251 ATAATTATTTGAATG
1 ATAATTATTTGAATG
*
43114266 ATTATTATTTG
1 ATAATTATTTG
43114277 TATGCGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (15 bp):
ATAATTATTTGAATG
Found at i:43124761 original size:7 final size:7
Alignment explanation
Indices: 43124749--43124829 Score: 53
Period size: 7 Copynumber: 12.1 Consensus size: 7
43124739 TTTTTTTTAT
43124749 CTTAAAC
1 CTTAAAC
43124756 CTTAAAC
1 CTTAAAC
*
43124763 CCTAAAC
1 CTTAAAC
*
43124770 CTTAAAT
1 CTTAAAC
* *
43124777 CTAAAAT
1 CTTAAAC
43124784 CTTAAAC
1 CTTAAAC
* *
43124791 ATTGAAC
1 CTTAAAC
** *
43124798 CCAAAAT
1 CTTAAAC
43124805 C-TAAAC
1 CTTAAAC
43124811 C-TAAAC
1 CTTAAAC
43124817 C-TAAAC
1 CTTAAAC
43124823 C-TAAAC
1 CTTAAAC
43124829 C
1 C
43124830 CAAACCCGTA
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
6 22 0.37
7 37 0.63
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.23
Consensus pattern (7 bp):
CTTAAAC
Found at i:43124789 original size:21 final size:20
Alignment explanation
Indices: 43124749--43124821 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
43124739 TTTTTTTTAT
**
43124749 CTTAAACCTTAAACCCTAAAC
1 CTTAAACC-TAAAATCTAAAC
*
43124770 CTTAAATCTAAAATCTTAAAC
1 CTTAAACCTAAAATC-TAAAC
* * *
43124791 ATTGAACCCAAAATCTAAAC
1 CTTAAACCTAAAATCTAAAC
43124811 C-TAAACCTAAA
1 CTTAAACCTAAA
43124822 CCTAAACCCA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 8 0.20
20 10 0.24
21 23 0.56
ACGTcount: A:0.48, C:0.26, G:0.01, T:0.25
Consensus pattern (20 bp):
CTTAAACCTAAAATCTAAAC
Found at i:43124816 original size:6 final size:6
Alignment explanation
Indices: 43124805--43124835 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
43124795 AACCCAAAAT
*
43124805 CTAAAC CTAAAC CTAAAC CTAAAC CCAAAC C
1 CTAAAC CTAAAC CTAAAC CTAAAC CTAAAC C
43124836 CGTAACCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.48, C:0.39, G:0.00, T:0.13
Consensus pattern (6 bp):
CTAAAC
Found at i:43124946 original size:14 final size:14
Alignment explanation
Indices: 43124894--43124979 Score: 56
Period size: 13 Copynumber: 6.2 Consensus size: 14
43124884 TTTTGAAGCC
43124894 AAACCTTAAACCCT
1 AAACCTTAAACCCT
*
43124908 AAA-CATATAA-CCT
1 AAACCTTA-AACCCT
*
43124921 CAAATACTTAAACCCT
1 -AAA-CCTTAAACCCT
43124937 AAACCTTAAACCC-
1 AAACCTTAAACCCT
*
43124950 AAA-ATTCAAACCC-
1 AAACCTT-AAACCCT
* *
43124963 GAACCTTAAATCCT
1 AAACCTTAAACCCT
43124977 AAA
1 AAA
43124980 TCTCGAACCC
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
12 2 0.04
13 22 0.39
14 21 0.38
15 5 0.09
16 6 0.11
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:43124971 original size:26 final size:27
Alignment explanation
Indices: 43124930--43124996 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
43124920 TCAAATACTT
43124930 AAACCCTAAACCTTAAACCCAAAAT-TC
1 AAACCC-AAACCTTAAACCCAAAATCTC
* * *
43124957 AAACCCGAACCTTAAATCCTAAATCTC
1 AAACCCAAACCTTAAACCCAAAATCTC
*
43124984 GAACCCAAACCTT
1 AAACCCAAACCTT
43124997 GAACTTCAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 15 0.44
27 19 0.56
ACGTcount: A:0.43, C:0.34, G:0.03, T:0.19
Consensus pattern (27 bp):
AAACCCAAACCTTAAACCCAAAATCTC
Found at i:43126767 original size:17 final size:17
Alignment explanation
Indices: 43126742--43126776 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43126732 CGTCATACAT
43126742 AATTATGATTTTGCGTG
1 AATTATGATTTTGCGTG
* *
43126759 AATTCTGATTTTGTGTG
1 AATTATGATTTTGCGTG
43126776 A
1 A
43126777 GTTTTATGCA
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:0.23, C:0.06, G:0.23, T:0.49
Consensus pattern (17 bp):
AATTATGATTTTGCGTG
Found at i:43127933 original size:34 final size:34
Alignment explanation
Indices: 43127853--43127941 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
43127843 TATAAATCAC
43127853 ATTAATAAATAATT--TAAAAA-TATAAAATAAAA
1 ATTAATAAA-AATTCATAAAAATTATAAAATAAAA
* * *
43127885 ATGAATCAATATTCATAAAGAATTATAAAA-AAAA
1 ATTAATAAAAATTCATAAA-AATTATAAAATAAAA
43127919 ATTAATAAAAATTCA-AAAAATTA
1 ATTAATAAAAATTCATAAAAATTA
43127942 GCATGTGGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
31 3 0.06
32 12 0.26
33 7 0.15
34 18 0.38
35 7 0.15
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.29
Consensus pattern (34 bp):
ATTAATAAAAATTCATAAAAATTATAAAATAAAA
Found at i:43132247 original size:16 final size:16
Alignment explanation
Indices: 43132226--43132256 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43132216 TAAACTCAAA
*
43132226 TTTTAATTTTTAATTT
1 TTTTAAATTTTAATTT
43132242 TTTTAAATTTTAATT
1 TTTTAAATTTTAATT
43132257 CATTTTGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAAATTTTAATTT
Found at i:43132319 original size:17 final size:17
Alignment explanation
Indices: 43132292--43132346 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
43132282 GTTTAAACTT
43132292 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
*
43132309 TTAAGTTTAAAGTT-AA
1 TTAAGTTTAAATTTAAA
*
43132325 TCTGAA-TTTAATTTTAAA
1 T-T-AAGTTTAAATTTAAA
43132343 TTAA
1 TTAA
43132347 TTAAAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 5 0.16
17 22 0.69
18 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:43133090 original size:26 final size:26
Alignment explanation
Indices: 43133048--43133108 Score: 52
Period size: 27 Copynumber: 2.3 Consensus size: 26
43133038 AATAAATATA
*
43133048 ATATTAATTAATAAATAATAAATCATA
1 ATATTAAATAATAAATAATAAAT-ATA
* * *
43133075 GTATTAAATGAT-AATAATAATTATTA
1 ATATTAAATAATAAATAATAAATA-TA
43133101 ATAATTAA
1 AT-ATTAA
43133109 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
25 1 0.04
26 12 0.44
27 14 0.52
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (26 bp):
ATATTAAATAATAAATAATAAATATA
Found at i:43133099 original size:20 final size:19
Alignment explanation
Indices: 43133040--43133101 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
43133030 AATTTTCTAA
* *
43133040 TAAATATAATATTAATTAA
1 TAAATATAATAATAATTAT
* *
43133059 TAAATAATAAATCAT-AGTAT
1 TAAAT-AT-AATAATAATTAT
43133079 TAAATGATAATAATAATTAT
1 TAAAT-ATAATAATAATTAT
43133099 TAA
1 TAA
43133102 TAATTAATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 10 0.30
20 19 0.58
21 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (19 bp):
TAAATATAATAATAATTAT
Found at i:43134345 original size:59 final size:58
Alignment explanation
Indices: 43134269--43134525 Score: 252
Period size: 58 Copynumber: 4.4 Consensus size: 58
43134259 AATTGCATTT
* * ** ** *
43134269 TTTTACCCCGGACT-TCCAAAAATTTCATTTTTGACATTGAAACTTCAAAAATTACCA
1 TTTTACCCCCGAATGTCCAAAAATTTCATTTTAAACCCTGAAACTTTAAAAATTACCA
** * * * * *
43134326 TTTTACCCCTAAACTTTCC-AAAATTCTAATTTT-AGCCCTAAAACTTTTAAAATTACCA
1 TTTTACCCCCGAA-TGTCCAAAAATT-TCATTTTAAACCCTGAAACTTTAAAAATTACCA
* * *
43134384 TTTTACCCCCGAATGTCCAAAAACTCCATTTTAAACCCCGAAACTTTTAAAAATTACCA
1 TTTTACCCCCGAATGTCCAAAAATTTCATTTTAAACCCTGAAAC-TTTAAAAATTACCA
* * *
43134443 TTTTACCCCCGAATGTCCAAAAA-CTCTATTTTTAACCCTGAAACTTTTAAAATTACCA
1 TTTTACCCCCGAATGTCCAAAAATTTC-ATTTTAAACCCTGAAACTTTAAAAATTACCA
* *
43134501 TTTTACCCCCGGATGTCCAGAAATT
1 TTTTACCCCCGAATGTCCAAAAATT
43134526 CTATTTTTGA
Statistics
Matches: 163, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
57 19 0.12
58 84 0.52
59 60 0.37
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.34
Consensus pattern (58 bp):
TTTTACCCCCGAATGTCCAAAAATTTCATTTTAAACCCTGAAACTTTAAAAATTACCA
Found at i:43134348 original size:29 final size:29
Alignment explanation
Indices: 43134308--43134509 Score: 116
Period size: 29 Copynumber: 7.0 Consensus size: 29
43134298 TTTGACATTG
*
43134308 AAAC-TTCAAAAATTACCATTTTACCCCT
1 AAACTTTCCAAAATTACCATTTTACCCCT
* *
43134336 AAACTTTCCAAAATT-CTAATTTTAGCCCT
1 AAACTTTCCAAAATTAC-CATTTTACCCCT
* *
43134365 AAAACTTT-TAAAATTACCATTTTACCCCC
1 -AAACTTTCCAAAATTACCATTTTACCCCT
* * * *
43134394 GAA-TGTCCAAAAACT-CCATTTTAAACCCCG
1 AAACTTTCC-AAAATTACCATTTT--ACCCCT
** *
43134424 AAACTTTTAAAAATTACCATTTTACCCCC
1 AAACTTTCCAAAATTACCATTTTACCCCT
* * *
43134453 GAA-TGTCCAAAA--ACTCTATTTTTAACCCT
1 AAACTTTCCAAAATTAC-C-A-TTTTACCCCT
*
43134482 GAAACTTT-TAAAATTACCATTTTACCCC
1 -AAACTTTCCAAAATTACCATTTTACCCC
43134510 CGGATGTCCA
Statistics
Matches: 129, Mismatches: 28, Indels: 33
0.68 0.15 0.17
Matches are distributed among these distances:
26 2 0.02
27 3 0.02
28 21 0.16
29 62 0.48
30 27 0.21
31 12 0.09
32 2 0.02
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTTCCAAAATTACCATTTTACCCCT
Found at i:43134552 original size:58 final size:57
Alignment explanation
Indices: 43134307--43134533 Score: 276
Period size: 58 Copynumber: 3.9 Consensus size: 57
43134297 TTTTGACATT
** ** * * * *
43134307 GAAACTTCAAAAATTACCATTTTACCCCTAAACTTTCC-AAAATTCTAATTTTAGCCC
1 GAAACTTTTAAAATTACCATTTTACCCCCGAA-TGTCCAAAAACTCTATTTTTAACCC
* * *
43134364 TAAAACTTTTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTAAACCCC
1 -GAAACTTTTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCTATTTTTAA-CCC
43134423 GAAACTTTTAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCTATTTTTAACCC
1 GAAACTTTT-AAAATTACCATTTTACCCCCGAATGTCCAAAAACTCTATTTTTAACCC
* * *
43134481 TGAAACTTTTAAAATTACCATTTTACCCCCGGATGTCCAGAAATTCTATTTTT
1 -GAAACTTTTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCTATTTTT
43134534 GATCCCGATC
Statistics
Matches: 148, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
57 4 0.03
58 89 0.60
59 55 0.37
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (57 bp):
GAAACTTTTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCTATTTTTAACCC
Found at i:43134552 original size:117 final size:117
Alignment explanation
Indices: 43134307--43134519 Score: 322
Period size: 117 Copynumber: 1.8 Consensus size: 117
43134297 TTTTGACATT
* * * * *
43134307 GAAAC-TTCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTAATTTTAGCCCTAAAACT
1 GAAACTTTTAAAAATTACCATTTTACCCCCAAACTGTCCAAAACTCTAATTTTAACCCTAAAACT
43134371 TTTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTAAACCCC
66 TTTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTAAACCCC
* * *
43134423 GAAACTTTTAAAAATTACCATTTTACCCCCGAA-TGTCCAAAAACTCTATTTTTAACCCTGAAAC
1 GAAACTTTTAAAAATTACCATTTTACCCCCAAACTGTCC-AAAACTCTAATTTTAACCCTAAAAC
*
43134487 TTTTAAAATTACCATTTTACCCCCGGATGTCCA
65 TTTTAAAATTACCATTTTACCCCCGAATGTCCA
43134520 GAAATTCTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
116 9 0.10
117 77 0.90
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (117 bp):
GAAACTTTTAAAAATTACCATTTTACCCCCAAACTGTCCAAAACTCTAATTTTAACCCTAAAACT
TTTAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTAAACCCC
Found at i:43140170 original size:10 final size:11
Alignment explanation
Indices: 43140133--43140174 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
43140123 GAACAAAGGA
43140133 AAAAGAAGAAAG
1 AAAA-AAGAAAG
43140145 AAAAAAGAAAG
1 AAAAAAGAAAG
*
43140156 -CAAAAGAAAAG
1 AAAAAAG-AAAG
43140167 AAAAAAGA
1 AAAAAAGA
43140175 GGAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 5 0.19
11 12 0.46
12 9 0.35
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:43140189 original size:22 final size:23
Alignment explanation
Indices: 43140128--43140193 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
43140118 TCAATGAACA
43140128 AAGGAAAAAGAAGAAAGAAAAAAG
1 AAGGAAAAAGAAG-AAGAAAAAAG
* *
43140152 AAAGCAAAAGAA-AAGAAAAAAG
1 AAGGAAAAAGAAGAAGAAAAAAG
*
43140174 -AGGAAAAATAAGAAGAAAAA
1 AAGGAAAAAGAAGAAGAAAAA
43140194 TAAAAATAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 8 0.22
22 18 0.50
24 10 0.28
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (23 bp):
AAGGAAAAAGAAGAAGAAAAAAG
Found at i:43141908 original size:39 final size:39
Alignment explanation
Indices: 43141864--43142011 Score: 151
Period size: 39 Copynumber: 3.8 Consensus size: 39
43141854 AAATGAAGAT
43141864 TTTGATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCA
1 TTTGATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCA
* * * * *
43141903 TTTGATCTTTTACCTCGAGCTTGGGGTAGATCATCATCAACCA
1 TTTGATCTCTTACCCCGAGCTTGGGGCAGAT--TGA--AGCCA
* * *
43141946 ----ATCTCTTACCTCGAGCCTGGGGCAGATTGCAGCCA
1 TTTGATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCA
*
43141981 TTTGATCTTTTACCCCGAGCTTGGGGCAGAT
1 TTTGATCTCTTACCCCGAGCTTGGGGCAGAT
43142012 CGTCATCAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
35 4 0.05
37 1 0.01
39 76 0.87
41 2 0.02
43 4 0.05
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (39 bp):
TTTGATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCA
Found at i:43141961 original size:78 final size:78
Alignment explanation
Indices: 43141868--43142115 Score: 322
Period size: 78 Copynumber: 3.2 Consensus size: 78
43141858 GAAGATTTTG
* * *
43141868 ATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCATTTGATCTTTTACCTCGAGCTTGGGGTAGA
1 ATCTCTTACCTCGAGCCTGGGGCAGATTGAAGCCATTTGATCTTTTACCTCGAGCTTGGGGCAGA
43141933 TCATCATCAACCA
66 TCATCATCAACCA
* *
43141946 ATCTCTTACCTCGAGCCTGGGGCAGATTGCAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCTCGAGCCTGGGGCAGATTGAAGCCATTTGATCTTTTACCTCGAGCTTGGGGCAGA
* *
43142011 TCGTCATCAATCA
66 TCATCATCAACCA
* * ** * *
43142024 ATCTTTTACC-CTGAGCCTGGGGCAGATT-ACAACCATCCGACCTTTTA-CTCCGAGCTTGGAGC
1 ATCTCTTACCTC-GAGCCTGGGGCAGATTGA-AGCCATTTGATCTTTTACCT-CGAGCTTGGGGC
43142086 AGATCATCATCAACCA
63 AGATCATCATCAACCA
*
43142102 ATCTCCTACCTCGA
1 ATCTCTTACCTCGA
43142116 TCATGGGGTG
Statistics
Matches: 147, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
77 2 0.01
78 144 0.98
79 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (78 bp):
ATCTCTTACCTCGAGCCTGGGGCAGATTGAAGCCATTTGATCTTTTACCTCGAGCTTGGGGCAGA
TCATCATCAACCA
Found at i:43142028 original size:39 final size:39
Alignment explanation
Indices: 43141907--43142105 Score: 161
Period size: 39 Copynumber: 5.1 Consensus size: 39
43141897 AAGCCATTTG
* * *
43141907 ATCTTTTACCTCGAGCTTGGGGTAGATCATCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
* * * * * **
43141946 ATCTCTTACCTCGAGCCTGGGGCAGAT--TGCAGCCATTTG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCAT-CA-TCAATCA
*
43141985 ATCTTTTACCCCGAGCTTGGGGCAGATCGTCATCAATCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
* * * * * *
43142024 ATCTTTTACCCTGAGCCTGGGGCAGATTA-CAACCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAAT-CA
* * * *
43142063 ACCTTTTACTCCGAGCTTGGAGCAGATCATCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
43142102 ATCT
1 ATCT
43142106 CCTACCTCGA
Statistics
Matches: 121, Mismatches: 33, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
37 1 0.01
38 7 0.06
39 106 0.88
40 6 0.05
41 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
Found at i:43142504 original size:201 final size:201
Alignment explanation
Indices: 43142154--43142977 Score: 1319
Period size: 201 Copynumber: 4.1 Consensus size: 201
43142144 ACAAGTGAGC
* * *
43142154 CGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTTAGGGCTCAATGAGAGCAAATCTTC
1 CGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCAATGAGAGCAAATCTTC
* * *
43142219 GAATCCTAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAATGGTTAGCTTCCTGA
66 GAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
* *
43142284 TGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAA
131 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAA
43142349 ACGGGA
196 ACGGGA
*
43142355 CGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCAATGATAGCAAATCTTC
1 CGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCAATGAGAGCAAATCTTC
*
43142420 GAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGTTTCCTGA
66 GAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
* * * *
43142485 TAAGATACTTAGAAGTGGACCAAATTCGTCTTCTTAATGAGATACAGAGAAGCGGATTGAAACAA
131 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAA
43142550 ACGGGA
196 ACGGGA
* * *
43142556 CGATTATCTTCTTGATGAGATACAGAGAAGTATACCAACTCAGGGCTTAATGAGAGCAAATCTTC
1 CGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCAATGAGAGCAAATCTTC
43142621 GAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
66 GAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
43142686 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAA
131 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAA
*
43142751 ATGGGA
196 ACGGGA
* * * * *
43142757 CGATTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGTGAGCAAATTTTT
1 CGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCAATGAGAGCAAATCTTC
* * * *
43142822 GAACCCCAACTTTCTGATGAGATACTGAGAAGCAGG-CTGAAGTAATAAAATGGTTAGCTTCCTG
66 GAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTC-GAAGCAATAAAATGGTTAGCTTCCTG
* * * *
43142886 ATGAGATACTGAGAAGTAGATCAAATTCGTCTTCCTGATGAGATACAGAGAAACAGATTGAAACA
130 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACA
*
43142951 AACGATG-
195 AACG-GGA
*
43142958 CGGTCATCTTCCTGATGAGA
1 CGGTTATCTTCCTGATGAGA
43142978 CACGCTCGAT
Statistics
Matches: 582, Mismatches: 39, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
200 1 0.00
201 580 1.00
202 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.24
Consensus pattern (201 bp):
CGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCAATGAGAGCAAATCTTC
GAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAA
ACGGGA
Found at i:43143141 original size:180 final size:180
Alignment explanation
Indices: 43142801--43143153 Score: 462
Period size: 180 Copynumber: 2.0 Consensus size: 180
43142791 CCAACTCAGG
* * * *
43142801 GCTCGATGTGAGCAAATTTTTGAACCCCAACTTTCTGATGAGATACTGAGAAGCAGGCTGAAGTA
1 GCTCGATATGAGCAAATCTTCGAACCCCAACTTTCTAATGAGATACTGAGAAGCAGGCTGAAGTA
* * * * *
43142866 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTAGATCAAATTCGTCTTCCTGATGAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCGTCTTCCTCATGAAACA
** *
43142931 CAGAGAAACAGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGACAC
131 CAGAGAAACAGATCAAAACAAACAATGCGGTCATCTTCCTGATGAGACAC
* *
43142981 GCTCGATATGAGCAAATCTTCGAATCCC-AGTTTCCTAATGAGATACTGAGAAGCAGG-TCGAAG
1 GCTCGATATGAGCAAATCTTCGAACCCCAACTTT-CTAATGAGATACTGAGAAGCAGGCT-GAAG
43143044 TAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAG-AGAACCAAA-TCTGTCTTCCTCATGA
64 TAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTAG-ACCAAATTC-GTCTTCCTCATGA
*** * **
43143107 AACACAGAGAAGTGGATCAAAATAAGTAATGCGGTCATCTTCCTGAT
127 AACACAGAGAAACAGATCAAAACAAACAATGCGGTCATCTTCCTGAT
43143154 TAGATACTGA
Statistics
Matches: 149, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
179 9 0.06
180 140 0.94
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (180 bp):
GCTCGATATGAGCAAATCTTCGAACCCCAACTTTCTAATGAGATACTGAGAAGCAGGCTGAAGTA
ATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCGTCTTCCTCATGAAACA
CAGAGAAACAGATCAAAACAAACAATGCGGTCATCTTCCTGATGAGACAC
Found at i:43143608 original size:11 final size:11
Alignment explanation
Indices: 43143589--43143637 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
43143579 ACTTTTAAGT
43143589 TTAAATTTAAA
1 TTAAATTTAAA
*
43143600 TTAAGTTTAAA
1 TTAAATTTAAA
*
43143611 GTT-AATTTGAAT
1 -TTAAATTT-AAA
43143623 TTAAATTTAAA
1 TTAAATTTAAA
43143634 TTAA
1 TTAA
43143638 TTAAAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:43143610 original size:17 final size:17
Alignment explanation
Indices: 43143583--43143637 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
43143573 GTTTAAACTT
43143583 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
* *
43143600 TTAAGTTTAAAGTTAAT
1 TTAAGTTTAAATTTAAA
43143617 TTGAA-TTTAAATTTAAA
1 TT-AAGTTTAAATTTAAA
43143634 TTAA
1 TTAA
43143638 TTAAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 2 0.06
17 29 0.88
18 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:43143623 original size:6 final size:6
Alignment explanation
Indices: 43143568--43143635 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
43143558 TTGAATTTAG
* * * *
43143568 TTTAAG TTTAAA CTTTTAAG TTTAAA TTTAAA -TTAAG TTTAAA GTT-AA
1 TTTAAA TTTAAA --TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
43143616 TTTGAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
43143636 AATTAAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
5 8 0.16
6 37 0.74
8 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:43143637 original size:22 final size:22
Alignment explanation
Indices: 43143592--43143639 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
43143582 TTTAAGTTTA
*
43143592 AATTTAAATTAAGTTTAAAGTT
1 AATTTAAATTAAATTTAAAGTT
*
43143614 AATTTGAATTTAAATTTAAA-TT
1 AATTT-AAATTAAATTTAAAGTT
43143636 AATT
1 AATT
43143640 AAAAAAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (22 bp):
AATTTAAATTAAATTTAAAGTT
Found at i:43144375 original size:27 final size:26
Alignment explanation
Indices: 43144329--43144387 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 26
43144319 CAAAGTTTTC
43144329 TAATAAATATAATATTATTTAATAAA
1 TAATAAATATAATATTATTTAATAAA
*
43144355 TAATAAATCATAGTATTATTTAATAAA
1 TAATAAAT-ATAATATTATTTAATAAA
43144382 TAATAA
1 TAATAA
43144388 GTCAAGAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATAAATATAATATTATTTAATAAA
Found at i:43145575 original size:30 final size:30
Alignment explanation
Indices: 43145510--43145701 Score: 153
Period size: 29 Copynumber: 6.5 Consensus size: 30
43145500 CTAAACTGTC
* * * *
43145510 TAAAAATTACATTTTTTACCC-CAAACTTC
1 TAAAAATTCCATTTTTGACCCTAAAACTTT
*
43145539 TAAAAATTCCATTTTTGATCCTAAAACTTT
1 TAAAAATTCCATTTTTGACCCTAAAACTTT
* * ** *
43145569 TGAAAATTACATTTTT-ACCCTCGAACTTC
1 TAAAAATTCCATTTTTGACCCTAAAACTTT
* *
43145598 TAGAAATTCCATTTTTAACCCTAAAAC-TT
1 TAAAAATTCCATTTTTGACCCTAAAACTTT
* *
43145627 CAAAAATTACCA-TTTTGCCCCT-AAACTTT
1 TAAAAATT-CCATTTTTGACCCTAAAACTTT
* * *
43145656 TCAAAATTCCAATTTTAACACC-AAAACTTT
1 TAAAAATTCCATTTTTGAC-CCTAAAACTTT
*
43145686 CAAAAATTACCATTTT
1 TAAAAATT-CCATTTT
43145702 ACTCCCGGAT
Statistics
Matches: 127, Mismatches: 28, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
28 7 0.06
29 68 0.54
30 46 0.36
31 6 0.05
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
TAAAAATTCCATTTTTGACCCTAAAACTTT
Found at i:43145596 original size:59 final size:58
Alignment explanation
Indices: 43145502--43145788 Score: 205
Period size: 59 Copynumber: 4.9 Consensus size: 58
43145492 GGAGGTCCCT
* * *
43145502 AAACTGTCTAAAAATTACATTTTTTACCC-CAAACTTCTAAAAATTCCATTTTTGATCCTA
1 AAACT-TC-AAAAATTACA-TTTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCCCA
** * * *
43145562 AAACTTTTGAAAATTACATTTTTACCCTCGAACTTCTAGAAATTCCATTTTTAACCCTA
1 AAAC-TTCAAAAATTACATTTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCCCA
** * * * * * *
43145621 AAACTTCAAAAATTACCATTTTGCCCCT-AAACTTTTCAAAATTCCAATTTTAACACCA
1 AAACTTCAAAAATTA-CATTTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCCCA
* * * *
43145679 AAACTTTCAAAAATTACCA-TTTTACTCC-CGGA-TGTCCAAAAACTCCATTTTTGACCCCG
1 AAAC-TTCAAAAATTA-CATTTTTAC-CCTCGAACT-TCTAAAAATTCCATTTTTGACCCCA
*
43145738 AAACTTTC-AAAATTAC-TATTTTA-CCTCCGAA-TGTCCAAAAATTCCATTTTT
1 AAAC-TTCAAAAATTACAT-TTTTACCCT-CGAACT-TCTAAAAATTCCATTTTT
43145789 TATCTCGATT
Statistics
Matches: 185, Mismatches: 31, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
56 2 0.01
57 1 0.01
58 84 0.45
59 92 0.50
60 5 0.03
61 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (58 bp):
AAACTTCAAAAATTACATTTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCCCA
Found at i:43145718 original size:29 final size:27
Alignment explanation
Indices: 43145686--43145787 Score: 82
Period size: 29 Copynumber: 3.6 Consensus size: 27
43145676 CCAAAACTTT
*
43145686 CAAAAATTACCATTTTACTCCCGGATGTC
1 CAAAAATT-CCATTTTAC-CCCGAATGTC
* *
43145715 CAAAAACTCCATTTTTGACCCCGAAACT-TT
1 CAAAAATTCCA-TTTT-ACCCCG-AA-TGTC
*
43145745 C-AAAATTACTATTTTACCTCCGAATGTC
1 CAAAAATT-CCATTTTACC-CCGAATGTC
43145773 CAAAAATTCCATTTT
1 CAAAAATTCCATTTT
43145788 TTATCTCGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
27 1 0.02
28 16 0.28
29 33 0.57
30 7 0.12
31 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (27 bp):
CAAAAATTCCATTTTACCCCGAATGTC
Found at i:43145719 original size:58 final size:57
Alignment explanation
Indices: 43145523--43145788 Score: 220
Period size: 58 Copynumber: 4.6 Consensus size: 57
43145513 AAATTACATT
* * * * **
43145523 TTTTACCCCAAACT-TCTAAAAATTCCATTTTTGATCCTAAAACTTTTGAAAATTA-CA
1 TTTTACCCCGAA-TGTCCAAAAATTCCATTTTT-AACCCAAAACTTTCAAAAATTACCA
* *
43145580 TTTTTACCCTCGAACT-TCTAGAAATTCCATTTTTAACCCTAAAAC-TTCAAAAATTACCA
1 -TTTTACCC-CGAA-TGTCCAAAAATTCCATTTTTAACCC-AAAACTTTCAAAAATTACCA
* * * * *
43145639 TTTTGCCCCTAAACTTTTC-AAAATTCCAATTTTAACACCAAAACTTTCAAAAATTACCA
1 TTTTACCCC-GAA-TGTCCAAAAATTCCATTTTTAAC-CCAAAACTTTCAAAAATTACCA
* * * * *
43145698 TTTTACTCCCGGATGTCCAAAAACTCCATTTTTGACCCCGAAACTTTC-AAAATTACTA
1 TTTTAC-CCCGAATGTCCAAAAATTCCATTTTT-AACCCAAAACTTTCAAAAATTACCA
43145756 TTTTACCTCCGAATGTCCAAAAATTCCATTTTT
1 TTTTACC-CCGAATGTCCAAAAATTCCATTTTT
43145789 TATCTCGATT
Statistics
Matches: 173, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
57 2 0.01
58 92 0.53
59 74 0.43
60 5 0.03
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.36
Consensus pattern (57 bp):
TTTTACCCCGAATGTCCAAAAATTCCATTTTTAACCCAAAACTTTCAAAAATTACCA
Found at i:43145864 original size:28 final size:28
Alignment explanation
Indices: 43145805--43145864 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
43145795 GATTTTTCTA
* * *
43145805 AAAATTACCATTTTGCCCTCGAGAGTCT
1 AAAATTACCATTTTACCCCCGAGAGTCC
43145833 AAAATTACCATTTTACCCCCGAGTA-TCC
1 AAAATTACCATTTTACCCCCGAG-AGTCC
43145861 AAAA
1 AAAA
43145865 AGTCTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAGAGTCC
Found at i:43152432 original size:21 final size:22
Alignment explanation
Indices: 43152408--43152449 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43152398 GCAAATTCTC
*
43152408 ATTAATCCT-TTCAAAATTTTA
1 ATTAAACCTCTTCAAAATTTTA
*
43152429 ATTAAACCTCTTGAAAATTTT
1 ATTAAACCTCTTCAAAATTTT
43152450 CAAAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAAACCTCTTCAAAATTTTA
Found at i:43159303 original size:3 final size:3
Alignment explanation
Indices: 43159295--43159320 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43159285 TTAATGAATT
43159295 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
43159321 TAAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:43164451 original size:97 final size:97
Alignment explanation
Indices: 43164284--43164479 Score: 365
Period size: 97 Copynumber: 2.0 Consensus size: 97
43164274 AAAAAGAATG
*
43164284 AAGGATGCAAATACTATGGTTAATTCATCAAAAGAAATTTGTTAACTTACCCAGAAAGAACCCTA
1 AAGGATACAAATACTATGGTTAATTCATCAAAAGAAATTTGTTAACTTACCCAGAAAGAACCCTA
*
43164349 TAAAACATCAGGTAACAAGACTTTTTAAAACA
66 CAAAACATCAGGTAACAAGACTTTTTAAAACA
*
43164381 AAGGATACAAATACTATGGTTAATTCATTAAAAGAAATTTGTTAACTTACCCAGAAAGAACCCTA
1 AAGGATACAAATACTATGGTTAATTCATCAAAAGAAATTTGTTAACTTACCCAGAAAGAACCCTA
43164446 CAAAACATCAGGTAACAAGACTTTTTAAAACA
66 CAAAACATCAGGTAACAAGACTTTTTAAAACA
43164478 AA
1 AA
43164480 AACCATGCAT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (97 bp):
AAGGATACAAATACTATGGTTAATTCATCAAAAGAAATTTGTTAACTTACCCAGAAAGAACCCTA
CAAAACATCAGGTAACAAGACTTTTTAAAACA
Found at i:43165269 original size:39 final size:39
Alignment explanation
Indices: 43165226--43165309 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
43165216 GAACACTTAA
*
43165226 ACTTACCCCATGATACTTCTTGAAGTTATATAATTAACG
1 ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
*
43165265 ACTTACCCCATGATGCTTCTTGAAGTTATATAAATAACG
1 ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
43165304 ACTTAC
1 ACTTAC
43165310 TCCTCCTCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (39 bp):
ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
Found at i:43173945 original size:36 final size:36
Alignment explanation
Indices: 43173869--43173949 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
43173859 GGCCAGCAGG
* * *
43173869 CCGGCCAGACCCTGCACCATTGCTTGCGCTAACAGG
1 CCGGCCAGACCCAGCACCATTGCTAGCGCTAACAGA
*
43173905 CCGGCCAGACCCAGCACCATTGCTAGCAGC-ACCAGA
1 CCGGCCAGACCCAGCACCATTGCTAGC-GCTAACAGA
43173941 CCGGCCAGA
1 CCGGCCAGA
43173950 ACCAAAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 38 0.95
37 2 0.05
ACGTcount: A:0.23, C:0.41, G:0.25, T:0.11
Consensus pattern (36 bp):
CCGGCCAGACCCAGCACCATTGCTAGCGCTAACAGA
Found at i:43174034 original size:36 final size:36
Alignment explanation
Indices: 43173965--43174142 Score: 189
Period size: 36 Copynumber: 4.9 Consensus size: 36
43173955 AACCACTGTT
* * *
43173965 AGGCCGACCTGG-CCCAGTACCATTGTTTACACCACC
1 AGGCCGACCAGGCCCCA-TACCATTGCTAACACCACC
* * * **
43174001 AGGTCGACTAGG-CCCAGTACCATTGCTAGCACCATT
1 AGGCCGACCAGGCCCCA-TACCATTGCTAACACCACC
* *
43174037 AGGCCGACCGGGCCCCATACCATTGCTAGCACCACC
1 AGGCCGACCAGGCCCCATACCATTGCTAACACCACC
* * *
43174073 AGGCCGGCCAGGTCCCAAACCATTGCTAACACCACC
1 AGGCCGACCAGGCCCCATACCATTGCTAACACCACC
* *
43174109 AGGCCGCCCTGGCCCCATACCATTGCTAACACCA
1 AGGCCGACCAGGCCCCATACCATTGCTAACACCA
43174143 TGCTGTTTTC
Statistics
Matches: 119, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
36 115 0.97
37 4 0.03
ACGTcount: A:0.24, C:0.40, G:0.20, T:0.16
Consensus pattern (36 bp):
AGGCCGACCAGGCCCCATACCATTGCTAACACCACC
Found at i:43178411 original size:19 final size:18
Alignment explanation
Indices: 43178387--43178431 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
43178377 CTGAAAATGA
43178387 TTTTTGGAAAATGAATTAT
1 TTTTTGGAAAATGAA-TAT
* *
43178406 TTTTTGAAAAAATTAATAT
1 TTTTTG-GAAAATGAATAT
43178425 TTTTTGG
1 TTTTTGG
43178432 TGGTTGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (18 bp):
TTTTTGGAAAATGAATAT
Found at i:43178598 original size:21 final size:21
Alignment explanation
Indices: 43178558--43178598 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43178548 TTATTTAATT
*
43178558 AATTTTATTTTATATCTATTA
1 AATTTTATTTTACATCTATTA
43178579 AATTTATATTTTACAT-TATT
1 AATTT-TATTTTACATCTATT
43178599 TTTACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
AATTTTATTTTACATCTATTA
Found at i:43186297 original size:167 final size:167
Alignment explanation
Indices: 43186011--43186347 Score: 622
Period size: 167 Copynumber: 2.0 Consensus size: 167
43186001 CCATTTTCGT
*
43186011 TTTCATGTGATTCTTGGGAACCAAACAAGAGCTAATAAACTTTTCGGCATATCTGGGAAATTTCA
1 TTTCATGTGATTCTTGGGAACCAAACAAGAGCTAAAAAACTTTTCGGCATATCTGGGAAATTTCA
* * *
43186076 CGTGGACCCCACATCAGATCAACCCGAATCATCCATCATGTTCACTGGTTTTCAATCTTCCACCG
66 CGTGGACACCACATCAAATCAACCCGAATCATCCATCATGTTCACTGATTTTCAATCTTCCACCG
43186141 TCTGATCATATTCCGGAATAGGTCCACTTCATAGGAA
131 TCTGATCATATTCCGGAATAGGTCCACTTCATAGGAA
43186178 TTTCATGTGATTCTTGGGAACCAAACAAGAGCTAAAAAACTTTTCGGCATATCTGGGAAATTTCA
1 TTTCATGTGATTCTTGGGAACCAAACAAGAGCTAAAAAACTTTTCGGCATATCTGGGAAATTTCA
43186243 CGTGGACACCACATCAAATCAACCCGAATCATCCATCATGTTC-CTTGATTTTCAATCTTCCACC
66 CGTGGACACCACATCAAATCAACCCGAATCATCCATCATGTTCAC-TGATTTTCAATCTTCCACC
43186307 GTCTGATCATATTCCGGAATAGGTCCACTTCATAGGAA
130 GTCTGATCATATTCCGGAATAGGTCCACTTCATAGGAA
43186345 TTT
1 TTT
43186348 TGTTTTTTAT
Statistics
Matches: 165, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
166 1 0.01
167 164 0.99
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (167 bp):
TTTCATGTGATTCTTGGGAACCAAACAAGAGCTAAAAAACTTTTCGGCATATCTGGGAAATTTCA
CGTGGACACCACATCAAATCAACCCGAATCATCCATCATGTTCACTGATTTTCAATCTTCCACCG
TCTGATCATATTCCGGAATAGGTCCACTTCATAGGAA
Found at i:43188654 original size:16 final size:17
Alignment explanation
Indices: 43188625--43188673 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 17
43188615 TTTTTATTGT
*
43188625 ATAAAAAAATAATAATA
1 ATAAAATAATAATAATA
43188642 ATAAAATTAAATATTATAATA
1 ATAAAA-T-AATA--ATAATA
43188663 ATAAAATAATA
1 ATAAAATAATA
43188674 TGAGATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 6 0.22
19 8 0.30
20 1 0.04
21 12 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAAATAATAATAATA
Found at i:43188681 original size:21 final size:21
Alignment explanation
Indices: 43188636--43188676 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
43188626 TAAAAAAATA
*
43188636 ATAATAATAAAATTAAATATT
1 ATAATAATAAAATTAAATATG
43188657 ATAATAATAAAA-T-AATATG
1 ATAATAATAAAATTAAATATG
43188676 A
1 A
43188677 GATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATAATAATAAAATTAAATATG
Found at i:43190106 original size:20 final size:22
Alignment explanation
Indices: 43190058--43190113 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 22
43190048 ATACTATGTT
43190058 AATAATTAATTGATTTTACACTCAA
1 AATAATTAATTGATTTT--A-TCAA
43190083 AATAATTAATTGATTTT-T-AA
1 AATAATTAATTGATTTTATCAA
*
43190103 AATATTTAATT
1 AATAATTAATT
43190114 TTACATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
25 17 0.57
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (22 bp):
AATAATTAATTGATTTTATCAA
Found at i:43192219 original size:3 final size:3
Alignment explanation
Indices: 43192211--43192239 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
43192201 GTGATCAATT
43192211 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43192240 TGATAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:43193845 original size:67 final size:70
Alignment explanation
Indices: 43193724--43193883 Score: 222
Period size: 67 Copynumber: 2.3 Consensus size: 70
43193714 ACTCAATTTT
***
43193724 ATTTTTTTTATT-TTTATTTATTTATTTATTTTTATTTTTATGAACATAAATAAATATAAAATAA
1 ATTTTTTTTATTATTTATTTATTTATTTATTTTTATGAATATGAACATAAATAAATATAAAATAA
*
43193788 TATTT
66 TATTA
*
43193793 ATTTTATTTTATTATTTATTTATTTA-TTA-TTTTATGAATAT-AA-ATAAATAAATGTAAAATA
1 ATTTT-TTTTATTATTTATTTATTTATTTATTTTTATGAATATGAACATAAATAAATATAAAATA
43193854 ATATTA
65 ATATTA
43193860 ATTTTGTTTTATTATTTATTTATT
1 ATTTT-TTTTATTATTTATTTATT
43193884 ATCATAAATA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
67 45 0.54
68 2 0.02
69 14 0.17
70 10 0.12
71 12 0.14
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.60
Consensus pattern (70 bp):
ATTTTTTTTATTATTTATTTATTTATTTATTTTTATGAATATGAACATAAATAAATATAAAATAA
TATTA
Found at i:43193884 original size:63 final size:62
Alignment explanation
Indices: 43193740--43193885 Score: 183
Period size: 63 Copynumber: 2.3 Consensus size: 62
43193730 TTTATTTTTA
* *
43193740 TTTATTTATTTATTT-TTATTTTTATGAACATAAATAAATATAAAATAATATTTATTTTATTT
1 TTTATTTATTTATTTATTA-TTTTATGAACATAAATAAATATAAAATAATATTTAATTTATGT
*
43193802 TATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATA-TTAATTT-T
1 T-TTATTTATTTATTTATTATTTTATGAACATAAATAAAT--A--TAAAATAATATTTAATTTAT
43193865 GT
61 GT
43193867 TTTA-TTATTTATTTATTAT
1 TTTATTTATTTATTTATTAT
43193886 CATAAATAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
62 1 0.01
63 48 0.64
64 6 0.08
65 4 0.05
66 6 0.08
67 10 0.13
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.58
Consensus pattern (62 bp):
TTTATTTATTTATTTATTATTTTATGAACATAAATAAATATAAAATAATATTTAATTTATGT
Found at i:43193899 original size:63 final size:67
Alignment explanation
Indices: 43193769--43193902 Score: 186
Period size: 67 Copynumber: 2.1 Consensus size: 67
43193759 TTTTATGAAC
* * **
43193769 ATAAATAAATATAAAATAATATTTATTTTATTTTATTATTTATTTATTTATTATTTTATGAATAT
1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTTATCATTAAATGAATAT
43193834 AA
66 AA
* *
43193836 ATAAATAAATGTAAAATAATATTAATTTTGTTTTATTATTTATTTA-TTATCA-TAAAT-AA-AT
1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTTATCATTAAATGAATAT
43193897 AA
66 AA
43193899 ATAA
1 ATAA
43193903 CAAATCAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
63 8 0.13
64 2 0.03
65 3 0.05
66 5 0.08
67 43 0.70
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (67 bp):
ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTTATCATTAAATGAATAT
AA
Found at i:43198870 original size:8 final size:8
Alignment explanation
Indices: 43198858--43198908 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
43198848 ACAAAAAATT
43198858 AAAAAGAGG
1 AAAAAGA-G
43198867 AAAAAAGAG
1 -AAAAAGAG
43198876 AAAAAGAG
1 AAAAAGAG
43198884 AAAAAGA-
1 AAAAAGAG
*
43198891 AGAAA-AG
1 AAAAAGAG
43198898 AAAAAGA-
1 AAAAAGAG
43198905 AAAA
1 AAAA
43198909 GGGGAGGTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 1 0.03
7 12 0.32
8 16 0.43
9 1 0.03
10 7 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:43198887 original size:26 final size:26
Alignment explanation
Indices: 43198841--43198896 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
43198831 GAAATTTAAA
* *
43198841 AAAAAAGACAAAAAATTAAAAAGAGG
1 AAAAAAGACAAAAAATGAAAAAGAAG
*
43198867 AAAAAAGAGAAAAAGA-GAAAAAGAAG
1 AAAAAAGACAAAAA-ATGAAAAAGAAG
43198893 AAAA
1 AAAA
43198897 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (26 bp):
AAAAAAGACAAAAAATGAAAAAGAAG
Found at i:43198899 original size:14 final size:15
Alignment explanation
Indices: 43198858--43198908 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
43198848 ACAAAAAATT
43198858 AAAAAGAGGAAAAAAGA
1 AAAAAGA-G-AAAAAGA
43198875 GAAAAAGAGAAAAAGA
1 -AAAAAGAGAAAAAGA
*
43198891 AGAAA-AGAAAAAGA
1 AAAAAGAGAAAAAGA
43198905 AAAA
1 AAAA
43198909 GGGGAGGTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.39
15 4 0.13
16 7 0.23
17 1 0.03
18 7 0.23
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAAAGA
Found at i:43199894 original size:50 final size:50
Alignment explanation
Indices: 43199831--43199946 Score: 180
Period size: 50 Copynumber: 2.3 Consensus size: 50
43199821 ATCTTTTAAC
* *
43199831 CCTAAAG-TGGTGGAGGTGCAGATTGAAACTGTAACGGTAAATCTCATACA
1 CCTAAAGCT-GTGGAGGTGCAGATTGAAACCGTAACGGCAAATCTCATACA
*
43199881 CCTAAAGCTGTGGAGGTGCAGATTGAAACCGTAATGGCAAATCTCATACA
1 CCTAAAGCTGTGGAGGTGCAGATTGAAACCGTAACGGCAAATCTCATACA
*
43199931 CCTAAAGCTGTAGAGG
1 CCTAAAGCTGTGGAGG
43199947 GGCAAAATGA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 60 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (50 bp):
CCTAAAGCTGTGGAGGTGCAGATTGAAACCGTAACGGCAAATCTCATACA
Found at i:43199966 original size:50 final size:50
Alignment explanation
Indices: 43199869--43199995 Score: 157
Period size: 50 Copynumber: 2.5 Consensus size: 50
43199859 CTGTAACGGT
* * * * *
43199869 AAATCTCATACACCTAAAGCTGTGGAGGTGCAGATTGAAACCGTAATGGC
1 AAATCTCATACACCTAAAGCTGTAGAGGGGCAAAATGAAACCATAATGGC
* *
43199919 AAATCTCATACACCTAAAGCTGTAGAGGGGCAAAATGAAGCTATAATGGC
1 AAATCTCATACACCTAAAGCTGTAGAGGGGCAAAATGAAACCATAATGGC
**
43199969 AAATCTCAGT-CATTTAAAGCTGTAGAG
1 AAATCTCA-TACACCTAAAGCTGTAGAG
43199996 AAGAAGATTG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
50 66 0.99
51 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (50 bp):
AAATCTCATACACCTAAAGCTGTAGAGGGGCAAAATGAAACCATAATGGC
Found at i:43200347 original size:80 final size:80
Alignment explanation
Indices: 43200081--43200333 Score: 382
Period size: 80 Copynumber: 3.2 Consensus size: 80
43200071 TTACCCTAAC
* * *
43200081 CCGATCTTTTAACCCGATCATGAGGTAAATTG-AAAAATCCAATCTTTTACCCTAACTAGAGGGC
1 CCGATCTTTTACCCCGATCATGGGGCAAATTGAAAAAATCCAATCTTTTACCCTAACTAGAGGGC
43200145 AAGATTGAAGACCAT
66 AAGATTGAAGACCAT
* * *
43200160 TCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAGAGGGC
1 CCGATCTTTTACCCCGATCATGGGGCAAATTGAAAAAATCCAATCTTTTACCCTAACTAGAGGGC
43200225 AAGATTGAAGACCAT
66 AAGATTGAAGACCAT
* * * * *
43200240 CCGATATTTTACCCCGATCATGGGGCAAATTGAAAAAATCTAATTTTTTAACCTAACTAGAGGGT
1 CCGATCTTTTACCCCGATCATGGGGCAAATTGAAAAAATCCAATCTTTTACCCTAACTAGAGGGC
*
43200305 AAGATTGAAGACCAC
66 AAGATTGAAGACCAT
*
43200320 CCAATCTTTTACCC
1 CCGATCTTTTACCC
43200334 TAACTAGAGG
Statistics
Matches: 156, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
79 27 0.17
80 129 0.83
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (80 bp):
CCGATCTTTTACCCCGATCATGGGGCAAATTGAAAAAATCCAATCTTTTACCCTAACTAGAGGGC
AAGATTGAAGACCAT
Found at i:43200406 original size:80 final size:80
Alignment explanation
Indices: 43200322--43201455 Score: 1788
Period size: 80 Copynumber: 14.2 Consensus size: 80
43200312 AAGACCACCC
*
43200322 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGAGGC
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
43200387 AGATTGAAGAAATCT
66 AGATTGAAGAAATCT
* * *
43200402 AATCTTTTACCCTAACAAGAGGGCAAGATTAAAGATCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
43200467 AGATTGAAGAAATTT
66 AGATTGAAGAAATCT
* *
43200482 AATCTTTTACCCTAACTAGAGGGTAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGT
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
43200547 AAATTGAAGAAATCT
66 AGATTGAAGAAATCT
*
43200562 AATCTTTTAACCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
43200627 AGATTGAAGAAATCC
66 AGATTGAAGAAATCT
* *
43200642 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGAGGC
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
43200707 AGATTGAAGAAATCT
66 AGATTGAAGAAATCT
* *
43200722 AATCTTTTACCCTAACCAGAGGGCAAGATTAAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
43200787 AGATTGAAGAAATTT
66 AGATTGAAGAAATCT
* * * *
43200802 AATCTTTTACTCTAACTAGAGGGTAAGATTGAAGACCATCCGATCTTTTACCCGGATCATGGGGT
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
43200867 AGATTGAAGAAATCT
66 AGATTGAAGAAATCT
* * *
43200882 AATCTTTTACCTTAACGAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCGGATCATGGGGC
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
43200947 AGAGTGAAGAAATCT
66 AGATTGAAGAAATCT
** * *
43200962 AATCTTTTACTTTAACGAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCTATCATGGGGG
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCAT-GGGG
43201027 CAGATTGAAGAAATCT
65 CAGATTGAAGAAATCT
43201043 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGG
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCAT-GGGG
* *
43201108 CAAATTAAAGAAAT-T
65 CAGATTGAAGAAATCT
* * * **
43201123 CAATCTTTTACTCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTATCCTAATCATGGGG
1 -AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGG
* *
43201188 CAGATTAAAGAAATCC
65 CAGATTGAAGAAATCT
* * *
43201204 AATCTTTTACCCTAATTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATTGGGT
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
43201269 AGATTGAAGAAATCT
66 AGATTGAAGAAATCT
*
43201284 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGAGGC
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
43201349 AGATTGAAGAAATCT
66 AGATTGAAGAAATCT
* * * * * *
43201364 AATCTTTTACCCTAACCAAAGGGC-AGATTGAAGACCATCAGATCTCTTACCTCGACCATGGGGC
1 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
43201428 AAATTGAA-ACAATCT
66 AGATTGAAGA-AATCT
43201443 AATCTTTTACCCT
1 AATCTTTTACCCT
43201456 TAAAGTTATA
Statistics
Matches: 974, Mismatches: 76, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
78 1 0.00
79 60 0.06
80 766 0.79
81 147 0.15
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (80 bp):
AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
AGATTGAAGAAATCT
Found at i:43202061 original size:8 final size:8
Alignment explanation
Indices: 43202048--43202079 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
43202038 AATATTTATT
43202048 TTATTTTA
1 TTATTTTA
43202056 TTATTTTA
1 TTATTTTA
43202064 TTA-TTTA
1 TTATTTTA
43202071 TTATTTTA
1 TTATTTTA
43202079 T
1 T
43202080 GAATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Found at i:43202072 original size:15 final size:14
Alignment explanation
Indices: 43202043--43202079 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
43202033 AAAATAATAT
43202043 TTATTTTA-TTTTA
1 TTATTTTATTTTTA
43202056 TTATTTTATTATTTA
1 TTATTTTATT-TTTA
43202071 TTATTTTAT
1 TTATTTTAT
43202080 GAATATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 1 0.05
15 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTTATTTTTA
Found at i:43202079 original size:63 final size:65
Alignment explanation
Indices: 43201987--43202140 Score: 176
Period size: 63 Copynumber: 2.4 Consensus size: 65
43201977 TTCTTATTAT
*
43201987 TTTTATT-TATTTATTTATTT-TTATTTTTATGAACATAAATAAAT-A-TAAAATAATATTTATT
1 TTTTATTAT-TTTA-TTATTTATTA-TTTTATGAACATAAATAAATAAGTAAAATAATATTAATT
43202048 TTA
63 TTA
* *
43202051 TTTTATTATTTTATTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATCATATTAATTT
1 TTTTATTATTTTATTATTTATTATTTTATGAACATAAATAAAT-AA-GTAAAATAATATTAATTT
*
43202116 TG
64 TA
43202118 TTTTATTA-TTTATT-TATTATTAT
1 TTTTATTATTTTATTAT-TTATTAT
43202141 AAATAAATAA
Statistics
Matches: 79, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
63 25 0.32
64 14 0.18
65 3 0.04
66 13 0.16
67 24 0.30
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (65 bp):
TTTTATTATTTTATTATTTATTATTTTATGAACATAAATAAATAAGTAAAATAATATTAATTTTA
Found at i:43202097 original size:67 final size:69
Alignment explanation
Indices: 43201980--43202140 Score: 186
Period size: 67 Copynumber: 2.3 Consensus size: 69
43201970 TCCATTTTTC
*** *
43201980 TTATTATTTTTATTTATTTATTTATTTTTATTTTTATGAACATAAATAAATATAAAATAATATTT
1 TTATTA-TTTTA-TTATTTA-TTA-TTTTATGAATATGAACATAAATAAATATAAAATAATATTA
43202045 ATTTTATT
62 ATTTTATT
* *
43202053 TTATTATTTTATTATTTATTATTTTATGAATAT-AA-ATAAATAAATGTAAAATCATATTAATTT
1 TTATTATTTTATTATTTATTATTTTATGAATATGAACATAAATAAATATAAAATAATATTAATTT
*
43202116 TGTT
66 TATT
43202120 TTATTA-TTTATT-TATTATTAT
1 TTATTATTTTATTAT-TTATTAT
43202141 AAATAAATAA
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
65 1 0.01
66 13 0.16
67 34 0.43
68 2 0.03
69 9 0.11
70 3 0.04
71 7 0.09
72 5 0.06
73 6 0.08
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59
Consensus pattern (69 bp):
TTATTATTTTATTATTTATTATTTTATGAATATGAACATAAATAAATATAAAATAATATTAATTT
TATT
Found at i:43203408 original size:30 final size:31
Alignment explanation
Indices: 43203374--43203434 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
43203364 TTAAGAACCG
*
43203374 GTGACTTAAATAAAACTTTT-GAATACTTTA
1 GTGACTTAAATAAAAATTTTCGAATACTTTA
*
43203404 GTGACTTAAATAAAAATTTTCGAATAGTTTA
1 GTGACTTAAATAAAAATTTTCGAATACTTTA
43203435 ATGGTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.39
Consensus pattern (31 bp):
GTGACTTAAATAAAAATTTTCGAATACTTTA
Found at i:43207026 original size:31 final size:31
Alignment explanation
Indices: 43206941--43207036 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
43206931 ATTTAGTATC
*
43206941 TGAACTTGACACTTTTTCTTAATTTGGTACT
1 TGAACTTGACACTTTTTCCTAATTTGGTACT
* * *
43206972 TAAACTT-----TTTTTGACTCATTTGGTACT
1 TGAACTTGACACTTTTT-CCTAATTTGGTACT
43206999 TGAACTTGACACTTTTTCCTAATTTGGTA-T
1 TGAACTTGACACTTTTTCCTAATTTGGTACT
43207029 CTGAACTT
1 -TGAACTT
43207037 TTTTTGGATC
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
26 5 0.10
27 17 0.33
30 1 0.02
31 23 0.45
32 5 0.10
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (31 bp):
TGAACTTGACACTTTTTCCTAATTTGGTACT
Found at i:43207036 original size:58 final size:60
Alignment explanation
Indices: 43206940--43207082 Score: 179
Period size: 58 Copynumber: 2.4 Consensus size: 60
43206930 TATTTAGTAT
* *
43206940 CTGAACTTGACACTTTTTCTTAATTTGGTACTTAAACTTTTTTT-GA-CTC-ATTTGGTAC
1 CTGAACTTGACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGATC-CAATTTGATAC
* *
43206998 TTGAACTTGACACTTTTTCCTAATTTGGTA-TCTGAACTTTTTTTGGATCCAATTTGATAC
1 CTGAACTTGACACTTTTTCCTAATTTGGTACT-TAAACTTTTTTTGGATCCAATTTGATAC
*
43207058 CTGAATTTGACA-TTTTTCCCTAATT
1 CTGAACTTGACACTTTTT-CCTAATT
43207083 GGACACCTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
57 1 0.01
58 39 0.53
59 8 0.11
60 26 0.35
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (60 bp):
CTGAACTTGACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGATCCAATTTGATAC
Found at i:43216740 original size:18 final size:18
Alignment explanation
Indices: 43216717--43216751 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43216707 AAGGTTTGAT
43216717 CTCTTTTATGTTATAAGA
1 CTCTTTTATGTTATAAGA
43216735 CTCTTTTATGTTATAAG
1 CTCTTTTATGTTATAAG
43216752 TTTCGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (18 bp):
CTCTTTTATGTTATAAGA
Found at i:43220826 original size:15 final size:15
Alignment explanation
Indices: 43220785--43220833 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
43220775 TGCAAGTTTA
43220785 AATATGAATCTATTTAG
1 AATATGAAT-TATTT-G
*
43220802 AATAT-TATTATTTG
1 AATATGAATTATTTG
*
43220816 AATATGAATTAATTG
1 AATATGAATTATTTG
43220831 AAT
1 AAT
43220834 TATTTGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 6 0.21
15 15 0.54
16 2 0.07
17 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (15 bp):
AATATGAATTATTTG
Found at i:43231116 original size:20 final size:20
Alignment explanation
Indices: 43231067--43231119 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
43231057 TTGAATCAAA
*
43231067 TTTATAATTTTAATATATTT
1 TTTATAATTTTAAAATATTT
*
43231087 TTT-TATTTTTAAAATATTT
1 TTTATAATTTTAAAATATTT
*
43231106 TTTATACTTTTAAA
1 TTTATAATTTTAAA
43231120 TAATTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATAATTTTAAAATATTT
Found at i:43231125 original size:20 final size:21
Alignment explanation
Indices: 43231067--43231125 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
43231057 TTGAATCAAA
43231067 TTTATAATTTT-AATATATTT
1 TTTATAATTTTAAATATATTT
*
43231087 TTT-TATTTTTAAA-ATATTT
1 TTTATAATTTTAAATATATTT
*
43231106 TTTATACTTTTAAATA-ATTT
1 TTTATAATTTTAAATATATTT
43231126 ATTTGATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 15 0.44
20 18 0.53
21 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATAATTTTAAATATATTT
Found at i:43231486 original size:28 final size:30
Alignment explanation
Indices: 43231451--43231519 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
43231441 TTACTTTTTT
* *
43231451 ATCACTCAATTA-TGAT-TTTTTTAATTTG
1 ATCACTCAATTATTAATATTTTTAAATTTG
*
43231479 ATCACTCAACTATTAATATTTTTAAATTTG
1 ATCACTCAATTATTAATATTTTTAAATTTG
*
43231509 -TCACCCAATTA
1 ATCACTCAATTA
43231520 ATCGAGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 11 0.32
29 12 0.35
30 11 0.32
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.46
Consensus pattern (30 bp):
ATCACTCAATTATTAATATTTTTAAATTTG
Found at i:43236384 original size:27 final size:27
Alignment explanation
Indices: 43236346--43236400 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
43236336 TTCAAGTGTT
43236346 TTTTTCCATTAAAGTAAAACAACAATA
1 TTTTTCCATTAAAGTAAAACAACAATA
43236373 TTTTTCCATTAAAGTAAAACAACAATA
1 TTTTTCCATTAAAGTAAAACAACAATA
43236400 T
1 T
43236401 GCTTTCAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.35
Consensus pattern (27 bp):
TTTTTCCATTAAAGTAAAACAACAATA
Found at i:43240062 original size:18 final size:16
Alignment explanation
Indices: 43240011--43240053 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
43240001 GTTTATAATG
* *
43240011 TTTTATATAATGCTAT
1 TTTTATATATTGCAAT
43240027 TTTTATATATTGCAAT
1 TTTTATATATTGCAAT
43240043 TTTTATATATT
1 TTTTATATATT
43240054 ATGTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTATATATTGCAAT
Found at i:43245661 original size:15 final size:15
Alignment explanation
Indices: 43245636--43245675 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
43245626 AACAAGTGAT
43245636 CCTTCAGTTGAGCCAC
1 CCTT-AGTTGAGCCAC
*
43245652 CCTTAGTTGAGTCAC
1 CCTTAGTTGAGCCAC
43245667 CCTTAGTTG
1 CCTTAGTTG
43245676 CGTCTCCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (15 bp):
CCTTAGTTGAGCCAC
Found at i:43251947 original size:16 final size:16
Alignment explanation
Indices: 43251903--43251954 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
43251893 CAATAAGCAG
43251903 AACAAAAAAGAAAAATA
1 AACAAAAAA-AAAAATA
* *
43251920 AACCAAACAAAAAATA
1 AACAAAAAAAAAAATA
*
43251936 AGCAAAAAAAAAAA-A
1 AACAAAAAAAAAAATA
43251951 AACA
1 AACA
43251955 CGTAACGTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 4 0.14
16 18 0.62
17 7 0.24
ACGTcount: A:0.81, C:0.12, G:0.04, T:0.04
Consensus pattern (16 bp):
AACAAAAAAAAAAATA
Found at i:43263880 original size:15 final size:15
Alignment explanation
Indices: 43263860--43263919 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 15
43263850 ATTTCAATAC
*
43263860 TACTTAAATTTTCAT
1 TACTTAAATTTTCAA
*
43263875 TACTTAATTTTTCAA
1 TACTTAAATTTTCAA
*
43263890 TACTT-ACTTTTCAA
1 TACTTAAATTTTCAA
** *
43263904 CCCTTAATTTTTCAA
1 TACTTAAATTTTCAA
43263919 T
1 T
43263920 TTATCAAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
14 11 0.30
15 26 0.70
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (15 bp):
TACTTAAATTTTCAA
Found at i:43263898 original size:19 final size:19
Alignment explanation
Indices: 43263851--43263898 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 19
43263841 TAATATCTAA
43263851 TTTCAATAC-TACTTAAAT
1 TTTCAATACTTACTTAAAT
*
43263869 TTTC---A-TTACTTAATT
1 TTTCAATACTTACTTAAAT
43263884 TTTCAATACTTACTT
1 TTTCAATACTTACTT
43263899 TTCAACCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
15 13 0.54
18 5 0.21
19 6 0.25
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTCAATACTTACTTAAAT
Found at i:43264596 original size:14 final size:14
Alignment explanation
Indices: 43264542--43264593 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
43264532 AAAAATAAAA
*
43264542 AAAATTAAATTATACT
1 AAAATAAAATT-TA-T
*
43264558 AAATTAAAATTTAT
1 AAAATAAAATTTAT
*
43264572 AAACTAAAATTTA-
1 AAAATAAAATTTAT
43264585 AAAATAAAA
1 AAAATAAAA
43264594 ATTCAACTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 8 0.25
14 13 0.41
15 2 0.06
16 9 0.28
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAAAATTTAT
Done.