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 134 of 193
Found at i:42214219 original size:3 final size:3
Alignment explanation
Indices: 42214211--42214244 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
42214201 GTTAAAAATT
* *
42214211 TAA TAA TAA TAA TAA TAA TAA TAT TCA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
42214245 TTTTTTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:42214434 original size:30 final size:31
Alignment explanation
Indices: 42214367--42214447 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
42214357 ATATTAAAAC
* *
42214367 TATACATGAATTATGATTTGATGTGCAATTG
1 TATACATAAATTATGATTTAATGTGCAATTG
*
42214398 TATACATAAATTATGATTTAATGTG-AATTT
1 TATACATAAATTATGATTTAATGTGCAATTG
*
42214428 TATACATGAAATTTTGATTT
1 TATACAT-AAATTATGATTT
42214448 GTTCCAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 11 0.24
31 34 0.76
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46
Consensus pattern (31 bp):
TATACATAAATTATGATTTAATGTGCAATTG
Found at i:42214607 original size:31 final size:31
Alignment explanation
Indices: 42214572--42214659 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 31
42214562 TTCTTTAAAT
*
42214572 GTATATGATTAAATCAAAATTAAAGTTTCAA
1 GTATATAATTAAATCAAAATTAAAGTTTCAA
* * * * * *
42214603 GTATACATTTGAACCACAATTAAAGTTTCAC
1 GTATATAATTAAATCAAAATTAAAGTTTCAA
* *
42214634 GTGTATAATTACATC-AAATTAAAGTT
1 GTATATAATTAAATCAAAATTAAAGTT
42214660 CATATATACA
Statistics
Matches: 43, Mismatches: 14, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
30 10 0.23
31 33 0.77
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.35
Consensus pattern (31 bp):
GTATATAATTAAATCAAAATTAAAGTTTCAA
Found at i:42220759 original size:4 final size:4
Alignment explanation
Indices: 42220752--42220778 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42220742 ATAGGATAGA
42220752 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
42220779 AATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:42221228 original size:32 final size:32
Alignment explanation
Indices: 42221180--42221241 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
42221170 TTGATTTAGG
*
42221180 TGGGTAAATTGGGTTTGTGTA-TTTTGGGTCA
1 TGGGTAAATTGGGTTTGGGTAGTTTTGGGTCA
*
42221211 TGGGTAATTTAGGGTTTGGGTAGTTTTGGGT
1 TGGGTAAATT-GGGTTTGGGTAGTTTTGGGT
42221242 TTTGAGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 9 0.33
32 10 0.37
33 8 0.30
ACGTcount: A:0.15, C:0.02, G:0.39, T:0.45
Consensus pattern (32 bp):
TGGGTAAATTGGGTTTGGGTAGTTTTGGGTCA
Found at i:42221232 original size:16 final size:16
Alignment explanation
Indices: 42221188--42221243 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
42221178 GGTGGGTAAA
*
42221188 TTGGGTTTGTGT-ATT
1 TTGGGTTTGGGTAATT
*
42221203 TTGGGTCATGGGTAATT
1 TTGGGT-TTGGGTAATT
* *
42221220 TAGGGTTTGGGTAGTT
1 TTGGGTTTGGGTAATT
42221236 TTGGGTTT
1 TTGGGTTT
42221244 TGAGTAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.18
16 19 0.58
17 8 0.24
ACGTcount: A:0.11, C:0.02, G:0.38, T:0.50
Consensus pattern (16 bp):
TTGGGTTTGGGTAATT
Found at i:42221251 original size:33 final size:32
Alignment explanation
Indices: 42221190--42221251 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
42221180 TGGGTAAATT
* *
42221190 GGGTTTGTGTATTTTGGGTCATGGGTAATTTA
1 GGGTTTGGGTATTTTGGGTCATGAGTAATTTA
**
42221222 GGGTTTGGGTAGTTTTGGGTTTTGAGTAAT
1 GGGTTTGGGTA-TTTTGGGTCATGAGTAAT
42221252 ATGTTAATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 10 0.40
33 15 0.60
ACGTcount: A:0.15, C:0.02, G:0.37, T:0.47
Consensus pattern (32 bp):
GGGTTTGGGTATTTTGGGTCATGAGTAATTTA
Found at i:42222659 original size:21 final size:21
Alignment explanation
Indices: 42222630--42222669 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42222620 TATTTACCGA
* *
42222630 TTTCTATTGAGAGAAATTAGT
1 TTTCAATTGAAAGAAATTAGT
*
42222651 TTTCAATTGAAAGTAATTA
1 TTTCAATTGAAAGAAATTA
42222670 CTATGTTTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (21 bp):
TTTCAATTGAAAGAAATTAGT
Found at i:42225560 original size:31 final size:31
Alignment explanation
Indices: 42225525--42225587 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
42225515 TACTCTAATA
* *
42225525 ACTTAAATAAAAGCTTTCAAATAGTTCAATG
1 ACTTAAATAAAAACTTTCAAATAATTCAATG
*
42225556 ACTTAACTAAAAACTTTCAAATAATTCAATG
1 ACTTAAATAAAAACTTTCAAATAATTCAATG
42225587 A
1 A
42225588 TCATTTTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTCAATG
Found at i:42225969 original size:20 final size:20
Alignment explanation
Indices: 42225931--42225969 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42225921 AATATTGTTG
* **
42225931 AAAACACTTACATTTTAAAA
1 AAAAAACTTACATGATAAAA
42225951 AAAAAACTTACATGATAAA
1 AAAAAACTTACATGATAAA
42225970 TCTTAAAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAAAACTTACATGATAAAA
Found at i:42231767 original size:22 final size:22
Alignment explanation
Indices: 42231741--42231784 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
42231731 CCAATCCATC
42231741 CCTTAATTCCAAAGTAATCTTT
1 CCTTAATTCCAAAGTAATCTTT
42231763 CCTTAATTCCAAAGTAATCTTT
1 CCTTAATTCCAAAGTAATCTTT
42231785 AACAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (22 bp):
CCTTAATTCCAAAGTAATCTTT
Found at i:42248149 original size:16 final size:16
Alignment explanation
Indices: 42248126--42248197 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
42248116 CGTTTGGTTC
42248126 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
42248142 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
** *
42248158 ATTGTAATGGAATATA
1 GCTGTAATGGAATAGA
42248174 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
42248190 GCTGTAAT
1 GCTGTAAT
42248198 CAGTAATTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.04, G:0.29, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:42248272 original size:44 final size:46
Alignment explanation
Indices: 42248179--42248272 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
42248169 ATATAGCTGT
* * *
42248179 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGATTGG
1 AATGGAATAGAACTGTAATCAATAATTCAATTGTTTGGTTGAATGG
*
42248225 AATGGAATAGAACTGTAAT-AAT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATCAATAATTCAAT-TGTTTGGTTGAATGG
42248269 AATG
1 AATG
42248273 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 2 0.05
46 18 0.42
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAACTGTAATCAATAATTCAATTGTTTGGTTGAATGG
Found at i:42248436 original size:58 final size:56
Alignment explanation
Indices: 42248367--42248512 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
42248357 AATTTTAATG
*
42248367 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
42248425 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
42248483 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
42248513 TATAATATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.04
58 43 0.55
59 15 0.19
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:42254157 original size:15 final size:15
Alignment explanation
Indices: 42254119--42254178 Score: 79
Period size: 15 Copynumber: 4.1 Consensus size: 15
42254109 ACCTCAGAGA
*
42254119 ATTCACTAGCAGA-T
1 ATTCAATAGCAGATT
*
42254133 -TTCTATAGCAGATT
1 ATTCAATAGCAGATT
42254147 ATTCAATAGCAGATT
1 ATTCAATAGCAGATT
*
42254162 ATTCAAGAGCAGATT
1 ATTCAATAGCAGATT
42254177 AT
1 AT
42254179 GCAGTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
13 10 0.25
14 1 0.03
15 29 0.73
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (15 bp):
ATTCAATAGCAGATT
Found at i:42257983 original size:16 final size:16
Alignment explanation
Indices: 42257959--42257991 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42257949 CATTTGGTTC
42257959 ACTGAAATGGAATAAA
1 ACTGAAATGGAATAAA
*
42257975 ACTGCAATGGAATAAA
1 ACTGAAATGGAATAAA
42257991 A
1 A
42257992 TTGTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (16 bp):
ACTGAAATGGAATAAA
Found at i:42258300 original size:12 final size:13
Alignment explanation
Indices: 42258274--42258306 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42258264 TTAAATTATA
42258274 TTAAAATACTATT
1 TTAAAATACTATT
42258287 TTAAAATA-TATT
1 TTAAAATACTATT
*
42258299 TTTAAATA
1 TTAAAATA
42258307 AATATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAAATACTATT
Found at i:42264368 original size:17 final size:16
Alignment explanation
Indices: 42264334--42264376 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
42264324 TGAAATTATT
42264334 TTAAAAATAAAAATTA
1 TTAAAAATAAAAATTA
42264350 TTAAAAAGTATAAAA-TA
1 TTAAAAA-TA-AAAATTA
42264367 TTAAATAATA
1 TTAAA-AATA
42264377 TATATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.29
17 11 0.46
18 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
TTAAAAATAAAAATTA
Found at i:42264378 original size:17 final size:17
Alignment explanation
Indices: 42264308--42264378 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 17
42264298 ATTAATATTT
42264308 TAAAATTA--AAAAAGTA
1 TAAAATTATTAAAAA-TA
*
42264324 TGAAATTATTTTAAAAATA
1 TAAAATTA--TTAAAAATA
42264343 -AAAATTATTAAAAAGTA
1 TAAAATTATTAAAAA-TA
42264360 TAAAA-TATTAAATAATA
1 TAAAATTATTAAA-AATA
42264377 TA
1 TA
42264379 TATTTAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
16 14 0.30
17 13 0.28
18 12 0.26
19 2 0.04
20 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (17 bp):
TAAAATTATTAAAAATA
Found at i:42267438 original size:18 final size:16
Alignment explanation
Indices: 42267403--42267452 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 16
42267393 TTTAGTTGTA
*
42267403 ATTTATTTAAAAATTTT
1 ATTTAATTAAAAA-TTT
*
42267420 AATTAATT--AAATTT
1 ATTTAATTAAAAATTT
42267434 ATTTAATTAAAAATTT
1 ATTTAATTAAAAATTT
42267450 ATT
1 ATT
42267453 CTCATCCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 9 0.32
17 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAATTAAAAATTT
Found at i:42271573 original size:12 final size:12
Alignment explanation
Indices: 42271556--42271580 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42271546 TGATATGACA
42271556 TTATTGAATTAG
1 TTATTGAATTAG
42271568 TTATTGAATTAG
1 TTATTGAATTAG
42271580 T
1 T
42271581 AAAATATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATTGAATTAG
Found at i:42275922 original size:20 final size:20
Alignment explanation
Indices: 42275888--42275929 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42275878 AAAGCAATTA
**
42275888 AAAAAAGAATTCAAAACAAG
1 AAAAAAGAACCCAAAACAAG
*
42275908 AAAAAAGAACCCAAAACCAG
1 AAAAAAGAACCCAAAACAAG
42275928 AA
1 AA
42275930 GAAGAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.69, C:0.17, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAAAAGAACCCAAAACAAG
Found at i:42276400 original size:6 final size:6
Alignment explanation
Indices: 42276389--42276419 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42276379 CGAAGCGTTA
42276389 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
42276420 ATGACGCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:42277033 original size:23 final size:24
Alignment explanation
Indices: 42276957--42277033 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 24
42276947 TACTATAAAA
*
42276957 TAAATAT-TAAATTTTATTAAGTT
1 TAAATATATAAATTTTATTAAATT
** * *
42276980 GTTTATATATAAATTTTTAATAAATG
1 -TAAATATATAAA-TTTTATTAAATT
*
42277006 AAAATATATAAA-TTTATTAAATT
1 TAAATATATAAATTTTATTAAATT
42277029 TAAAT
1 TAAAT
42277034 TAATACAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
23 13 0.32
24 5 0.12
25 13 0.32
26 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TAAATATATAAATTTTATTAAATT
Found at i:42280057 original size:25 final size:24
Alignment explanation
Indices: 42280017--42280064 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
42280007 GTCAATTTTT
42280017 TAATAAAATAATTAATATAAATTG
1 TAATAAAATAATTAATATAAATTG
*
42280041 TAATGAAATTAATTAATATAAATT
1 TAAT-AAAATAATTAATATAAATT
42280065 ATAAAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TAATAAAATAATTAATATAAATTG
Found at i:42288032 original size:31 final size:31
Alignment explanation
Indices: 42287995--42288067 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
42287985 CCCCAAAAAA
* * * *
42287995 TTAAGTATCAACTTAAGAAAAAGTGTCAAAT
1 TTAAGTACCAAATTAAGAAAAAATATCAAAT
42288026 TTAAGTACCAAATTAAGAAAAAATATCAAAT
1 TTAAGTACCAAATTAAGAAAAAATATCAAAT
* *
42288057 TCAATTACCAA
1 TTAAGTACCAA
42288068 TTTGTTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (31 bp):
TTAAGTACCAAATTAAGAAAAAATATCAAAT
Found at i:42288515 original size:23 final size:22
Alignment explanation
Indices: 42288480--42288522 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
42288470 TTTCAATCCT
*
42288480 TTAAAAATGATAAAACTATAAA
1 TTAAAAATAATAAAACTATAAA
*
42288502 TTAATAAATAATAAAATTATA
1 TTAA-AAATAATAAAACTATA
42288523 TTTTGACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAAATAATAAAACTATAAA
Found at i:42298239 original size:21 final size:21
Alignment explanation
Indices: 42298202--42298250 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
42298192 TATAAAATTA
*
42298202 ATTTTTCTAAAAATATTTT-T
1 ATTTTTCGAAAAATATTTTCT
*
42298222 ATTTTTCGAAATATTATTTTCCT
1 ATTTTTCGAAA-AATATTTT-CT
42298245 ATTTTT
1 ATTTTT
42298251 AAATGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.42
21 7 0.29
23 7 0.29
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTCGAAAAATATTTTCT
Found at i:42305002 original size:27 final size:27
Alignment explanation
Indices: 42304971--42305032 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
42304961 GTATTTTTGG
42304971 GTGGTGCCTGTCTGGTAGGCGGCACCA
1 GTGGTGCCTGTCTGGTAGGCGGCACCA
42304998 GTGGTGCCTGTCTGGTAGGCGGCACCA
1 GTGGTGCCTGTCTGGTAGGCGGCACCA
42305025 GTGGTGCC
1 GTGGTGCC
42305033 AACCTACCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.10, C:0.26, G:0.42, T:0.23
Consensus pattern (27 bp):
GTGGTGCCTGTCTGGTAGGCGGCACCA
Found at i:42305044 original size:27 final size:27
Alignment explanation
Indices: 42304987--42305050 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
42304977 CCTGTCTGGT
*** ***
42304987 AGGCGGCACCAGTGGTGCCTGTCTGGT
1 AGGCGGCACCAGTGGTGCCAACCTACC
42305014 AGGCGGCACCAGTGGTGCCAACCTACC
1 AGGCGGCACCAGTGGTGCCAACCTACC
42305041 AGGCGGCACC
1 AGGCGGCACC
42305051 TGATTCACTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.33, G:0.36, T:0.14
Consensus pattern (27 bp):
AGGCGGCACCAGTGGTGCCAACCTACC
Found at i:42306051 original size:17 final size:17
Alignment explanation
Indices: 42306018--42306050 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
42306008 AATTCAATTG
42306018 ATATATTTAAATATTTT
1 ATATATTTAAATATTTT
42306035 ATATA-TTAAATATTTT
1 ATATATTTAAATATTTT
42306051 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTTAAATATTTT
Found at i:42306069 original size:12 final size:13
Alignment explanation
Indices: 42306042--42306069 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42306032 TTTATATATT
42306042 AAATATTTTTTAA
1 AAATATTTTTTAA
42306055 AAATATTTTTTAA
1 AAATATTTTTTAA
42306068 AA
1 AA
42306070 CAAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:42307935 original size:6 final size:6
Alignment explanation
Indices: 42307924--42307954 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42307914 TTTCAGCCGG
42307924 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC C
1 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC C
42307955 GCAGTCGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGAGC
Found at i:42308398 original size:6 final size:6
Alignment explanation
Indices: 42308387--42308439 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
42308377 GGCCATTAAA
* *
42308387 TATGTT TATGTT TATGTT TATGTT TATATT TATGTT CT-TATT TATGTT
1 TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT
42308435 TATGT
1 TATGT
42308440 ATGCAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 1 0.02
6 39 0.95
7 1 0.02
ACGTcount: A:0.19, C:0.02, G:0.13, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:42308568 original size:26 final size:26
Alignment explanation
Indices: 42308512--42308588 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 26
42308502 TGCTAAACCT
* *
42308512 AATTAAATTAATTCAAACATAAAAAT
1 AATTAAATAAATTCAAACATAAAAAG
* ** *
42308538 TATTAAATAAATTCAAATTTAAATAG
1 AATTAAATAAATTCAAACATAAAAAG
* *
42308564 AATTAATTCCAAATTCAATCATAAA
1 AATTAAAT--AAATTCAAACATAAA
42308589 TTTAATTAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
26 26 0.68
28 12 0.32
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (26 bp):
AATTAAATAAATTCAAACATAAAAAG
Found at i:42311764 original size:20 final size:23
Alignment explanation
Indices: 42311741--42311781 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
42311731 ATTTAATTTA
42311741 ATTTTTT-TA-AATT-TTATAAT
1 ATTTTTTCTACAATTCTTATAAT
42311761 ATTTTTTCTACAATTCTTATA
1 ATTTTTTCTACAATTCTTATA
42311782 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 4 0.22
23 5 0.28
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTTCTACAATTCTTATAAT
Found at i:42311920 original size:27 final size:27
Alignment explanation
Indices: 42311890--42311957 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
42311880 AAAATACGAG
42311890 TTGGTGCCACCTGATAAAAAGGCACCA
1 TTGGTGCCACCTGATAAAAAGGCACCA
42311917 TTGGTGCCACCTGATAAAAAGGCACCA
1 TTGGTGCCACCTGATAAAAAGGCACCA
*
42311944 TTGGTGCCGCCTGA
1 TTGGTGCCACCTGA
42311958 CAGGTAGGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (27 bp):
TTGGTGCCACCTGATAAAAAGGCACCA
Found at i:42311966 original size:27 final size:27
Alignment explanation
Indices: 42311909--42311997 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
42311899 CCTGATAAAA
* * ***
42311909 AGGCACCATTGGTGCCACCTGATAAAA
1 AGGCACCATTGGTGCCGCCTGACAGGT
42311936 AGGCACCATTGGTGCCGCCTGACAGGT
1 AGGCACCATTGGTGCCGCCTGACAGGT
* *
42311963 AGGCACCACTGGTGCCGCCTGTCAGGT
1 AGGCACCATTGGTGCCGCCTGACAGGT
42311990 AGGCACCA
1 AGGCACCA
42311998 CCCATTTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.17
Consensus pattern (27 bp):
AGGCACCATTGGTGCCGCCTGACAGGT
Found at i:42313571 original size:59 final size:59
Alignment explanation
Indices: 42313495--42313631 Score: 172
Period size: 58 Copynumber: 2.3 Consensus size: 59
42313485 TTTTTTTATC
* *
42313495 TGGTACCTAAACTTTTTTTTACTTAATTTGGCAATTGAACTTGACACTTTTTCT-TAATT
1 TGGTACCTAAAGTTTTTTTTACTCAATTTGGCAATTGAACTTGACA-TTTTTCTCTAATT
* * * * *
42313554 TGGTATCTAAAG-TTTTTTGACTCAATTTGGTACTTGAACTTGACATTTTTTTCTAATT
1 TGGTACCTAAAGTTTTTTTTACTCAATTTGGCAATTGAACTTGACATTTTTCTCTAATT
42313612 TGGTACCT-AAGCTTTTTTTT
1 TGGTACCTAAAG-TTTTTTTT
42313632 TTAAATTCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
57 9 0.14
58 41 0.62
59 16 0.24
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.50
Consensus pattern (59 bp):
TGGTACCTAAAGTTTTTTTTACTCAATTTGGCAATTGAACTTGACATTTTTCTCTAATT
Found at i:42315420 original size:6 final size:6
Alignment explanation
Indices: 42315403--42315441 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
42315393 AAATAACCTT
42315403 AAATCAA AAATCA AAATCA AAATCA AAATCA AAATCA AA
1 AAATC-A AAATCA AAATCA AAATCA AAATCA AAATCA AA
42315442 TAAACCCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATCA
Found at i:42315453 original size:47 final size:47
Alignment explanation
Indices: 42315382--42315493 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
42315372 ATTAAAATCC
* *
42315382 AATCAAAATTGAAAT-AACCTTAAATCAAAAATCAAAATCAAAATCAA
1 AATCAAAA-TCAAATAAACCCTAAATCAAAAATCAAAATCAAAATCAA
* * * *
42315429 AATCAAAATCAAATAAACCCTAAATTAAAAATCATAATCAATATCGA
1 AATCAAAATCAAATAAACCCTAAATCAAAAATCAAAATCAAAATCAA
* * *
42315476 CATCAAATTCGAATAAAC
1 AATCAAAATCAAATAAAC
42315494 ACAAAAAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 5 0.09
47 50 0.91
ACGTcount: A:0.58, C:0.17, G:0.03, T:0.22
Consensus pattern (47 bp):
AATCAAAATCAAATAAACCCTAAATCAAAAATCAAAATCAAAATCAA
Found at i:42317171 original size:24 final size:24
Alignment explanation
Indices: 42317141--42317191 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
42317131 ACAAATAATA
*
42317141 TTAGCTCTCAC-AAGCTCAGAATGG
1 TTAGCTCTCACAAACCT-AGAATGG
*
42317165 TTAGCTCTTACAAACCTAGAATGG
1 TTAGCTCTCACAAACCTAGAATGG
42317189 TTA
1 TTA
42317192 ACCAGTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (24 bp):
TTAGCTCTCACAAACCTAGAATGG
Found at i:42320203 original size:12 final size:14
Alignment explanation
Indices: 42320174--42320202 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42320164 CTTAGTGTTA
42320174 TTTAAATATAATTT
1 TTTAAATATAATTT
42320188 TTTAAATAT-ATTT
1 TTTAAATATAATTT
42320201 TT
1 TT
42320203 ATTTTGTTGG
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTAAATATAATTT
Found at i:42320517 original size:19 final size:20
Alignment explanation
Indices: 42320481--42320520 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42320471 TTAAATAGAC
* *
42320481 TTTTAAAAGATCAGAAAAAT
1 TTTTAAAAGATAAAAAAAAT
42320501 TTTTAAAA-ATAAAAAAAAT
1 TTTTAAAAGATAAAAAAAAT
42320520 T
1 T
42320521 AGTTTAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (20 bp):
TTTTAAAAGATAAAAAAAAT
Found at i:42323091 original size:16 final size:16
Alignment explanation
Indices: 42323070--42323101 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42323060 CCACGTTCAT
42323070 TATCTTCTCCATTTAC
1 TATCTTCTCCATTTAC
42323086 TATCTTCTCCATTTAC
1 TATCTTCTCCATTTAC
42323102 AAAGCCCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (16 bp):
TATCTTCTCCATTTAC
Found at i:42323597 original size:24 final size:24
Alignment explanation
Indices: 42323536--42323598 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
42323526 TAGAGTAATA
* * *
42323536 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
42323560 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
42323584 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
42323599 AATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:42325583 original size:24 final size:24
Alignment explanation
Indices: 42325522--42325584 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
42325512 TAGAGTAATA
* *
42325522 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
42325546 AGAGTTTAATTGAAACAAATGAAC
1 AGAGTTTAACTGAAACAAATAAAC
42325570 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
42325585 AATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:42338237 original size:16 final size:16
Alignment explanation
Indices: 42338192--42338230 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
42338182 TAAATTACAG
* *
42338192 ATTACAGTTCTATTTC
1 ATTATAGTTATATTTC
42338208 ATTATAGTTATATTTC
1 ATTATAGTTATATTTC
42338224 ATTATAG
1 ATTATAG
42338231 CTTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (16 bp):
ATTATAGTTATATTTC
Found at i:42339362 original size:13 final size:13
Alignment explanation
Indices: 42339339--42339375 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
42339329 TGCATGGAGA
*
42339339 TTTCTAAAGCACT
1 TTTCAAAAGCACT
*
42339352 TTTTAAAAGCACT
1 TTTCAAAAGCACT
42339365 TTTCAAAAGCA
1 TTTCAAAAGCA
42339376 ATGTTAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (13 bp):
TTTCAAAAGCACT
Found at i:42339525 original size:30 final size:30
Alignment explanation
Indices: 42339484--42339545 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
42339474 CAACAAGTCT
*
42339484 ATTTTTTTGGACCATTTTATAACTAATTTA
1 ATTTTTATGGACCATTTTATAACTAATTTA
42339514 ATTTTTATGGACCATTTTATAACTAATTTA
1 ATTTTTATGGACCATTTTATAACTAATTTA
42339544 AT
1 AT
42339546 AGAATACGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (30 bp):
ATTTTTATGGACCATTTTATAACTAATTTA
Found at i:42340646 original size:73 final size:72
Alignment explanation
Indices: 42340501--42340648 Score: 226
Period size: 73 Copynumber: 2.0 Consensus size: 72
42340491 GAAGGAAAAG
* * *
42340501 AAAGGTTTGAAAGGAAACTAGTTTATTTTTTTTCCTTTTTTTGGTAGAAGGAAAATAGGATGGAA
1 AAAGGATTGAAAGGAAACTAGTTTAGTTTTTTTCCTTTTTTTGGTAGAAGGAAAATAGGAGGGAA
**
42340566 GGGAGGA
66 GAAAGGA
42340573 AAAGGATTGAAAGGAAACTAGTTT-GTTTTTTTCCATTTTTTTTGGTAGAAGGAAAATAGGAGGG
1 AAAGGATTGAAAGGAAACTAGTTTAGTTTTTTTCC--TTTTTTTGGTAGAAGGAAAATAGGAGGG
42340637 AAGAAAGGA
64 AAGAAAGGA
42340646 AAA
1 AAA
42340649 TGGGTTTAGA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
71 9 0.13
72 23 0.33
73 37 0.54
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.32
Consensus pattern (72 bp):
AAAGGATTGAAAGGAAACTAGTTTAGTTTTTTTCCTTTTTTTGGTAGAAGGAAAATAGGAGGGAA
GAAAGGA
Found at i:42341610 original size:6 final size:6
Alignment explanation
Indices: 42341601--42341626 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42341591 CAAAGATAGG
42341601 GATAAA GATAAA GATAAA GATAAA GA
1 GATAAA GATAAA GATAAA GATAAA GA
42341627 AGTTGAGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.15
Consensus pattern (6 bp):
GATAAA
Found at i:42341705 original size:12 final size:12
Alignment explanation
Indices: 42341688--42341744 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
42341678 AAACGAAAAG
42341688 GAAAAGGAACGT
1 GAAAAGGAACGT
* *
42341700 GAAAAGGAAAGG
1 GAAAAGGAACGT
* *
42341712 GAGAAGGAACGC
1 GAAAAGGAACGT
*
42341724 GAGAAGGAACGT
1 GAAAAGGAACGT
42341736 GAAAAGGAA
1 GAAAAGGAA
42341745 AGGGAGAAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.51, C:0.07, G:0.39, T:0.04
Consensus pattern (12 bp):
GAAAAGGAACGT
Found at i:42341742 original size:24 final size:24
Alignment explanation
Indices: 42341682--42341754 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
42341672 AGAAAGAAAC
* * *
42341682 GAAAAGGAAAAGGAACGTGAAAAG
1 GAAAGGGAAAAGGAACGCGAGAAG
*
42341706 GAAAGGGAGAAGGAACGCGAGAAG
1 GAAAGGGAAAAGGAACGCGAGAAG
* * * *
42341730 GAACGTGAAAAGGAAAGGGAGAAG
1 GAAAGGGAAAAGGAACGCGAGAAG
42341754 G
1 G
42341755 CTGGAAGCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.51, C:0.05, G:0.41, T:0.03
Consensus pattern (24 bp):
GAAAGGGAAAAGGAACGCGAGAAG
Found at i:42341754 original size:12 final size:12
Alignment explanation
Indices: 42341703--42341754 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
42341693 GGAACGTGAA
42341703 AAGGAAAGGGAG
1 AAGGAAAGGGAG
* *
42341715 AAGGAACGCGAG
1 AAGGAAAGGGAG
* * *
42341727 AAGGAACGTGAA
1 AAGGAAAGGGAG
42341739 AAGGAAAGGGAG
1 AAGGAAAGGGAG
42341751 AAGG
1 AAGG
42341755 CTGGAAGCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.44, T:0.02
Consensus pattern (12 bp):
AAGGAAAGGGAG
Found at i:42351682 original size:4 final size:4
Alignment explanation
Indices: 42351675--42351709 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
42351665 CATGCATGCT
*
42351675 TGTA TGTA TGTA TGTA TGTG TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
42351710 TTTGCAGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:42352670 original size:18 final size:19
Alignment explanation
Indices: 42352638--42352679 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
42352628 ATTTAACCCT
*
42352638 TTTTTTTTCACATAATACA
1 TTTTTTTTCACATAACACA
*
42352657 TTTTTTTTC-TATAACACA
1 TTTTTTTTCACATAACACA
42352675 TTTTT
1 TTTTT
42352680 ACATTTGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTTTCACATAACACA
Found at i:42354727 original size:22 final size:24
Alignment explanation
Indices: 42354669--42354731 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
42354659 TAACGTTTTA
*
42354669 AAAATTATAAAAATATATGTTATT
1 AAAATAATAAAAATATATGTTATT
*
42354693 AAAATAATGAAAATATAT-TT-TT
1 AAAATAATAAAAATATATGTTATT
** *
42354715 ACTATCATAAAAATATA
1 AAAATAATAAAAATATA
42354732 CCATCTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 2 0.06
24 16 0.48
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
AAAATAATAAAAATATATGTTATT
Found at i:42356706 original size:20 final size:20
Alignment explanation
Indices: 42356681--42356721 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42356671 TAAATACGTA
* * *
42356681 CACATATTTTCAATTTGTTT
1 CACATATCTTAAATATGTTT
42356701 CACATATCTTAAATATGTTT
1 CACATATCTTAAATATGTTT
42356721 C
1 C
42356722 GGTTATGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (20 bp):
CACATATCTTAAATATGTTT
Found at i:42359372 original size:3 final size:3
Alignment explanation
Indices: 42359364--42359395 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42359354 ATAGTTCTAA
42359364 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42359396 CATTTTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:42363826 original size:24 final size:24
Alignment explanation
Indices: 42363794--42363841 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
42363784 AATAATCTTC
*
42363794 TAATTAAACTCTGTTTATTTGTTT
1 TAATTAAACTCTATTTATTTGTTT
*
42363818 TAATTAAACTTTATTTATTTGTTT
1 TAATTAAACTCTATTTATTTGTTT
42363842 CAGTCAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60
Consensus pattern (24 bp):
TAATTAAACTCTATTTATTTGTTT
Found at i:42363850 original size:24 final size:25
Alignment explanation
Indices: 42363799--42363857 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
42363789 TCTTCTAATT
* * *
42363799 AAACTC-TGTTTATTTGTTTTAATT
1 AAACTCTTATTTATTTGTTTCAATC
*
42363823 AAACT-TTATTTATTTGTTTCAGTC
1 AAACTCTTATTTATTTGTTTCAATC
42363847 AAACTCTTATT
1 AAACTCTTATT
42363858 AGTTTAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (25 bp):
AAACTCTTATTTATTTGTTTCAATC
Found at i:42366939 original size:12 final size:12
Alignment explanation
Indices: 42366922--42366946 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42366912 AATCCTCCCA
42366922 CTTCACCACCAC
1 CTTCACCACCAC
42366934 CTTCACCACCAC
1 CTTCACCACCAC
42366946 C
1 C
42366947 ACCAGCACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CTTCACCACCAC
Found at i:42375669 original size:2 final size:2
Alignment explanation
Indices: 42375658--42375696 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
42375648 TAACTCCGGA
* *
42375658 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AC AC 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
42375697 CATAAAGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:42393319 original size:17 final size:17
Alignment explanation
Indices: 42393299--42393348 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
42393289 TTATTTTATA
42393299 TAATATATTTGTTTAAT
1 TAATATATTTGTTTAAT
42393316 TAATATTAATTT-TTT-AT
1 TAATA-T-ATTTGTTTAAT
*
42393333 AAATATATTTGTTTAA
1 TAATATATTTGTTTAA
42393349 GTTACTTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 12 0.43
18 4 0.14
19 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
TAATATATTTGTTTAAT
Found at i:42407054 original size:15 final size:17
Alignment explanation
Indices: 42407023--42407062 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
42407013 GATAGAGTGA
42407023 AATA-AAAATTGGAAAG
1 AATAGAAAATTGGAAAG
42407039 -ATAGAAAATT-GAAAG
1 AATAGAAAATTGGAAAG
42407054 AATAGAAAA
1 AATAGAAAA
42407063 AATAAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (17 bp):
AATAGAAAATTGGAAAG
Found at i:42410517 original size:37 final size:37
Alignment explanation
Indices: 42410476--42410549 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
42410466 ACTTTTGAAA
42410476 AGTTCAGTAACTATTTTGTAACTTTTTAAAATTAAAT
1 AGTTCAGTAACTATTTTGTAACTTTTTAAAATTAAAT
*
42410513 AGTTCAGTGACTATTTTGTAACTTTTTAAAATTAAAT
1 AGTTCAGTAACTATTTTGTAACTTTTTAAAATTAAAT
42410550 GATGAAAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.46
Consensus pattern (37 bp):
AGTTCAGTAACTATTTTGTAACTTTTTAAAATTAAAT
Found at i:42413251 original size:20 final size:21
Alignment explanation
Indices: 42413220--42413258 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42413210 TATTGTTTTC
*
42413220 ATTAATAATTATTTAATTAAT
1 ATTAATAATTATATAATTAAT
42413241 ATTAA-AATTATATAATTA
1 ATTAATAATTATATAATTA
42413259 TAAAATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATAATTATATAATTAAT
Found at i:42413498 original size:6 final size:6
Alignment explanation
Indices: 42413488--42413540 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
42413478 CTCATTCTCA
* * *
42413488 CTTTTT -TTTTT CTTTTT CCCTTTTC CTTTTT CTTTTG GTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT --CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
42413537 CTTT
1 CTTT
42413541 CTTTGATAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 5 0.13
6 28 0.74
8 5 0.13
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (6 bp):
CTTTTT
Found at i:42420577 original size:17 final size:17
Alignment explanation
Indices: 42420555--42420593 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42420545 AGGTGGAGAA
* * *
42420555 CTTGTTCGTTGAGAGTT
1 CTTGTTCATAGAGAATT
42420572 CTTGTTCATAGAGAATT
1 CTTGTTCATAGAGAATT
42420589 CTTGT
1 CTTGT
42420594 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:42420679 original size:23 final size:22
Alignment explanation
Indices: 42420635--42420683 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
42420625 GAATTCTTGT
* *
42420635 TAAAATAAAATACAGTGGTAAAA
1 TAAAATAAAATAAAGTGCT-AAA
42420658 TAAAATAAAAGTAAAGT-CTAAA
1 TAAAATAAAA-TAAAGTGCTAAA
42420680 TAAA
1 TAAA
42420684 CTAGACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.22
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGCTAAA
Found at i:42425108 original size:18 final size:18
Alignment explanation
Indices: 42425087--42425128 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42425077 CAAAAATTCC
**
42425087 AAAATTTATGTTTTTTAA
1 AAAATTTATAATTTTTAA
*
42425105 AAAAATTATAATTTTTAA
1 AAAATTTATAATTTTTAA
42425123 AAAATT
1 AAAATT
42425129 AAAGAATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAAATTTATAATTTTTAA
Found at i:42437619 original size:26 final size:25
Alignment explanation
Indices: 42437586--42437634 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
42437576 TATTTTTTTC
*
42437586 TATTTTTAATAGTTTATTCAATTTA
1 TATTTTTAATAATTTATTCAATTTA
*
42437611 TATTCTTTAATAATTTATTTAATT
1 TATT-TTTAATAATTTATTCAATT
42437635 AAACTAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (25 bp):
TATTTTTAATAATTTATTCAATTTA
Found at i:42453773 original size:17 final size:17
Alignment explanation
Indices: 42453751--42453791 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
42453741 AGAGTTAAAA
42453751 AATAATTTTATCAT-TTT
1 AATAATTTTAT-ATGTTT
42453768 AATAA-TTTATATGTTT
1 AATAATTTTATATGTTT
42453784 -ATAATTTT
1 AATAATTTT
42453792 TAAAGGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
AATAATTTTATATGTTT
Found at i:42460966 original size:49 final size:49
Alignment explanation
Indices: 42460913--42461007 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
42460903 AAACAATTCT
42460913 AATGATTAAAAAGTGATTCCATTTTAGTCTAGAAAATTATGAACATCTA
1 AATGATTAAAAAGTGATTCCATTTTAGTCTAGAAAATTATGAACATCTA
*
42460962 AATGATTAAAATGTGATTCCATTTTAGTCTAGAAAATTATGAACAT
1 AATGATTAAAAAGTGATTCCATTTTAGTCTAGAAAATTATGAACAT
42461008 TTTACATGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (49 bp):
AATGATTAAAAAGTGATTCCATTTTAGTCTAGAAAATTATGAACATCTA
Found at i:42470819 original size:24 final size:24
Alignment explanation
Indices: 42470768--42470819 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42470758 TTTATAAGTC
* *
42470768 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
42470792 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
42470816 AAAT
1 AAAT
42470820 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:42472882 original size:23 final size:24
Alignment explanation
Indices: 42472840--42472900 Score: 97
Period size: 23 Copynumber: 2.6 Consensus size: 24
42472830 CTTTTGAGAG
42472840 AAAAAGAGGTGTAATTTTTAAAAA
1 AAAAAGAGGTGTAATTTTTAAAAA
42472864 AAAAAGAGGTGTAA-TTTTAAAAA
1 AAAAAGAGGTGTAATTTTTAAAAA
* *
42472887 AAAAACAGATGTAA
1 AAAAAGAGGTGTAA
42472901 AAATGATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.57, C:0.02, G:0.16, T:0.25
Consensus pattern (24 bp):
AAAAAGAGGTGTAATTTTTAAAAA
Found at i:42473310 original size:29 final size:27
Alignment explanation
Indices: 42473278--42473390 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 27
42473268 AAAAATTCAA
*
42473278 ATTTGACCCATAAATTTTCTACAAATTAC
1 ATTTGACCC-TAAATTTTCTA-AAATTGC
*
42473307 ATTTTAGCTCCTAAATTTTCTAAAAATTGC
1 ATTTGA-C-CCTAAATTTTCT-AAAATTGC
*
42473337 ATTTGACCCTTAAACTTTCTAAAATTGC
1 ATTTGACCC-TAAATTTTCTAAAATTGC
* *
42473365 ATTTTAACCCCAAACTTTTC-AAAATT
1 A-TTTGACCCTAAA-TTTTCTAAAATT
42473391 TTGATTTTGA
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
28 20 0.28
29 26 0.37
30 22 0.31
31 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.40
Consensus pattern (27 bp):
ATTTGACCCTAAATTTTCTAAAATTGC
Found at i:42473322 original size:30 final size:28
Alignment explanation
Indices: 42473278--42473370 Score: 98
Period size: 30 Copynumber: 3.2 Consensus size: 28
42473268 AAAAATTCAA
* * *
42473278 ATTTGACCCATAAATTTTCTACAAATTAC
1 ATTTTACCCTTAAATTTTCTA-AAATTGC
42473307 ATTTTAGCTCC-TAAATTTTCTAAAAATTGC
1 ATTTTA-C-CCTTAAATTTTCT-AAAATTGC
* *
42473337 ATTTGACCCTTAAACTTTCTAAAATTGC
1 ATTTTACCCTTAAATTTTCTAAAATTGC
42473365 ATTTTA
1 ATTTTA
42473371 ACCCCAAACT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
28 15 0.27
29 15 0.27
30 22 0.40
31 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.42
Consensus pattern (28 bp):
ATTTTACCCTTAAATTTTCTAAAATTGC
Found at i:42473379 original size:28 final size:29
Alignment explanation
Indices: 42473283--42473390 Score: 96
Period size: 28 Copynumber: 3.7 Consensus size: 29
42473273 TTCAAATTTG
* * *
42473283 ACCCATAAATTTTCTACAAATTACATTTTA
1 ACCC-TAAACTTTCTAAAAATTGCATTTTA
* * *
42473313 GCTCCTAAATTTTCTAAAAATTGCA-TTTG
1 AC-CCTAAACTTTCTAAAAATTGCATTTTA
42473342 ACCCTTAAACTTTCT-AAAATTGCATTTTA
1 ACCC-TAAACTTTCTAAAAATTGCATTTTA
* *
42473371 ACCCCAAACTTT-TCAAAATT
1 ACCCTAAACTTTCTAAAAATT
42473391 TTGATTTTGA
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
27 1 0.02
28 24 0.36
29 20 0.30
30 19 0.29
31 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (29 bp):
ACCCTAAACTTTCTAAAAATTGCATTTTA
Found at i:42473384 original size:58 final size:58
Alignment explanation
Indices: 42473278--42473405 Score: 145
Period size: 58 Copynumber: 2.2 Consensus size: 58
42473268 AAAAATTCAA
* * * *
42473278 ATTTGACCCATAAATTTTCTACAAATTACATTTTAGCTCCTAAATTTTCTAAAA-ATTG
1 ATTTGACCCTTAAACTTTCTACAAATTACATTTTAACTCCCAAATTTTC-AAAATATTG
* *
42473336 CATTTGACCCTTAAACTTTCTA-AAATTGCATTTTAAC-CCCAAACTTTTCAAAATTTTG
1 -ATTTGACCCTTAAACTTTCTACAAATTACATTTTAACTCCCAAA-TTTTCAAAATATTG
42473394 ATTTTGACCCTT
1 A-TTTGACCCTT
42473406 TTCCTTATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
57 10 0.17
58 31 0.52
59 19 0.32
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.41
Consensus pattern (58 bp):
ATTTGACCCTTAAACTTTCTACAAATTACATTTTAACTCCCAAATTTTCAAAATATTG
Found at i:42475148 original size:24 final size:24
Alignment explanation
Indices: 42475120--42475167 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
42475110 AAATTCGTAA
*
42475120 GTAAAATAAATTATGCTAATAAAT
1 GTAAAATAAATTATACTAATAAAT
*
42475144 GTAAAATATATTATACTAATAAAT
1 GTAAAATAAATTATACTAATAAAT
42475168 ACTATATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
GTAAAATAAATTATACTAATAAAT
Found at i:42475501 original size:3 final size:3
Alignment explanation
Indices: 42475493--42475517 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42475483 AATTTCTCTT
42475493 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
42475518 GTCTCTGCCT
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):
CAC
Found at i:42475678 original size:14 final size:14
Alignment explanation
Indices: 42475659--42475694 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
42475649 AAGCTGAGGA
42475659 AAGAGCTTTTGTTG
1 AAGAGCTTTTGTTG
42475673 AAGAGCTTTTGTTG
1 AAGAGCTTTTGTTG
42475687 AAGGAGCT
1 AA-GAGCT
42475695 GAAAGGAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.25, C:0.08, G:0.31, T:0.36
Consensus pattern (14 bp):
AAGAGCTTTTGTTG
Found at i:42481044 original size:13 final size:13
Alignment explanation
Indices: 42481026--42481098 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
42481016 AAGATTTTGC
42481026 ATTATAATAATGT
1 ATTATAATAATGT
** *
42481039 ATTATAAATTTTTAT
1 ATTAT-AA-TAATGT
42481054 ATTAT-ATAAT-T
1 ATTATAATAATGT
* **
42481065 TTTATAGATTTTGT
1 ATTATA-ATAATGT
42481079 ATTATAATAATGT
1 ATTATAATAATGT
42481092 ATTATAA
1 ATTATAA
42481099 ATTTTTATAG
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
11 5 0.11
12 2 0.05
13 21 0.48
14 8 0.18
15 8 0.18
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (13 bp):
ATTATAATAATGT
Found at i:42481058 original size:15 final size:16
Alignment explanation
Indices: 42481038--42481070 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42481028 TATAATAATG
42481038 TATTATA-AATTTTTA
1 TATTATATAATTTTTA
42481053 TATTATATAATTTTTA
1 TATTATATAATTTTTA
42481069 TA
1 TA
42481071 GATTTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATATAATTTTTA
Found at i:42487261 original size:25 final size:27
Alignment explanation
Indices: 42487205--42487265 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 27
42487195 ATTTATTTAC
* *
42487205 TAATTATATTATATAATTTTAATAGAAA
1 TAATTA-ATTATATAATATTAATAAAAA
42487233 TAATTAATTA-ATAATATT-ATAAAAA
1 TAATTAATTATATAATATTAATAAAAA
42487258 TAATTAAT
1 TAATTAAT
42487266 CAAATTACGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 14 0.45
26 7 0.23
27 4 0.13
28 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TAATTAATTATATAATATTAATAAAAA
Found at i:42490004 original size:20 final size:20
Alignment explanation
Indices: 42489981--42490019 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42489971 ATTTTTTATG
*
42489981 ATATGCTATCATTTAATTTT
1 ATATGCTATCAATTAATTTT
42490001 ATATGCTATCAATTAATTT
1 ATATGCTATCAATTAATTT
42490020 ATTGATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (20 bp):
ATATGCTATCAATTAATTTT
Found at i:42494643 original size:2 final size:2
Alignment explanation
Indices: 42494636--42494668 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42494626 TTTCATCAAT
42494636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42494669 GTTTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42498037 original size:23 final size:24
Alignment explanation
Indices: 42498011--42498058 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
42498001 AATTTTCACT
42498011 AATACAAAGATA-GTAC-AATTACA
1 AATA-AAAGATATGTACAAATTACA
*
42498034 AATATAAGATATGTACAAATTACA
1 AATAAAAGATATGTACAAATTACA
42498058 A
1 A
42498059 GTATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 8 0.36
24 8 0.36
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.25
Consensus pattern (24 bp):
AATAAAAGATATGTACAAATTACA
Found at i:42498063 original size:24 final size:22
Alignment explanation
Indices: 42498017--42498064 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
42498007 CACTAATACA
42498017 AAGATAGTACAATTACAAATAT
1 AAGATAGTACAATTACAAATAT
*
42498039 AAGATATGTACAAATTACAAGTAT
1 AAGATA-GTAC-AATTACAAATAT
42498063 AA
1 AA
42498065 ATAAATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.26
23 4 0.17
24 13 0.57
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (22 bp):
AAGATAGTACAATTACAAATAT
Found at i:42498810 original size:16 final size:16
Alignment explanation
Indices: 42498789--42498820 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42498779 AGTAATACCG
42498789 GTAGCATATTATTGCC
1 GTAGCATATTATTGCC
42498805 GTAGCATATTATTGCC
1 GTAGCATATTATTGCC
42498821 ATATCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
GTAGCATATTATTGCC
Found at i:42498828 original size:16 final size:16
Alignment explanation
Indices: 42498790--42498829 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
42498780 GTAATACCGG
*
42498790 TAGCATATTATTGCCG
1 TAGCATATTATTGCCA
42498806 TAGCATATTATTGCCA
1 TAGCATATTATTGCCA
*
42498822 TATCATAT
1 TAGCATAT
42498830 ATCAGTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (16 bp):
TAGCATATTATTGCCA
Found at i:42502306 original size:29 final size:29
Alignment explanation
Indices: 42502271--42502330 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
42502261 TTTCACCTAA
*
42502271 TGTGCAA-TATTATACATGAAATTTTATTT
1 TGTGCAACT-TTATACATGAAATTTTAATT
*
42502300 TGTGCAACTTTATACATTAAATTTTAATT
1 TGTGCAACTTTATACATGAAATTTTAATT
42502329 TG
1 TG
42502331 ATTCAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (29 bp):
TGTGCAACTTTATACATGAAATTTTAATT
Found at i:42502462 original size:31 final size:31
Alignment explanation
Indices: 42502427--42502509 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
42502417 ATTTCTTTAA
42502427 ATGTATATAATTGAATCAAAACTAAAGTTTT-
1 ATGTATATAATTGAATCAAAA-TAAAGTTTTC
* * * *
42502458 ATGTATACATTTGAATCACAATCAAGTTTTC
1 ATGTATATAATTGAATCAAAATAAAGTTTTC
* *
42502489 ATGTGTATAATTGCA-CAAAAT
1 ATGTATATAATTGAATCAAAAT
42502510 CAAAATTCAT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
30 13 0.31
31 29 0.69
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (31 bp):
ATGTATATAATTGAATCAAAATAAAGTTTTC
Found at i:42507359 original size:18 final size:19
Alignment explanation
Indices: 42507338--42507376 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
42507328 AAATCGATTG
42507338 AATTAAAAAATT-TAAAAT
1 AATTAAAAAATTATAAAAT
**
42507356 AATTTGAAAATTATAAAAT
1 AATTAAAAAATTATAAAAT
42507375 AA
1 AA
42507377 GAAAATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATTAAAAAATTATAAAAT
Found at i:42511254 original size:6 final size:6
Alignment explanation
Indices: 42511245--42511278 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
42511235 TAAAAAGGAA
42511245 AACATG AACATG AACATG AACATG AACATG AACA
1 AACATG AACATG AACATG AACATG AACATG AACA
42511279 AGAAGATGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.15
Consensus pattern (6 bp):
AACATG
Found at i:42517551 original size:21 final size:21
Alignment explanation
Indices: 42517527--42517566 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42517517 TAAAGCGACG
*
42517527 TGGTTTTGCCTTTTAATTTAA
1 TGGTTTTGACTTTTAATTTAA
42517548 TGGTTTTGACTTTTAATTT
1 TGGTTTTGACTTTTAATTT
42517567 TGAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.15, T:0.60
Consensus pattern (21 bp):
TGGTTTTGACTTTTAATTTAA
Found at i:42518378 original size:26 final size:24
Alignment explanation
Indices: 42518312--42518369 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
42518302 TCAATTATAG
* *
42518312 TTTTTA-AAAAAGTAATGGATTTT
1 TTTTTAGAATAAGTAATGGAGTTT
*
42518335 TTTTTATAATAAGTAATGGAGTTT
1 TTTTTAGAATAAGTAATGGAGTTT
42518359 TTTTTAGAATA
1 TTTTTAGAATA
42518370 GTTACAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (24 bp):
TTTTTAGAATAAGTAATGGAGTTT
Found at i:42524728 original size:28 final size:28
Alignment explanation
Indices: 42524690--42524744 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
42524680 AAATGAGCAT
*
42524690 CATGACCTTTGGGTCAATAAGGAGTAAG
1 CATGACCTTTGGGTCAACAAGGAGTAAG
*
42524718 CATGACCTTTGGGTCAACAGGGAGTAA
1 CATGACCTTTGGGTCAACAAGGAGTAA
42524745 ATTGGATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAAGGAGTAAG
Found at i:42525489 original size:21 final size:21
Alignment explanation
Indices: 42525436--42525490 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
42525426 GAAGTTTTTA
*
42525436 GTACTGGTAGAAGCATGATTT
1 GTACCGGTAGAAGCATGATTT
*
42525457 GTACCGGCAGAAGCATGATTT
1 GTACCGGTAGAAGCATGATTT
**
42525478 GTTTCGGTAGAAG
1 GTACCGGTAGAAG
42525491 GTTCACTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (21 bp):
GTACCGGTAGAAGCATGATTT
Found at i:42533201 original size:32 final size:32
Alignment explanation
Indices: 42533142--42533210 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
42533132 TAAAATCATT
*
42533142 TTTTTAATTTTAAAAAGTTTATCTTTTTATAA
1 TTTTTAATTTTAAAAAGTTGATCTTTTTATAA
* *
42533174 TTTTTATTTTTAAAAA-TATGAT-TTTTT-TAT
1 TTTTTAATTTTAAAAAGT-TGATCTTTTTATAA
42533204 TTTTTAA
1 TTTTTAA
42533211 AATTTTATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 8 0.25
31 6 0.19
32 18 0.56
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (32 bp):
TTTTTAATTTTAAAAAGTTGATCTTTTTATAA
Found at i:42533207 original size:24 final size:24
Alignment explanation
Indices: 42533174--42533229 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
42533164 CTTTTTATAA
*
42533174 TTTTTATTTTTAAAAATATGAT-T
1 TTTTTATTTTTTAAAATATGATGT
* *
42533197 TTTTTATTTTTTAAAATTTTATGT
1 TTTTTATTTTTTAAAATATGATGT
42533221 TTTTTATTT
1 TTTTTATTT
42533230 AAAATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTATTTTTTAAAATATGATGT
Found at i:42533938 original size:22 final size:23
Alignment explanation
Indices: 42533889--42533944 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
42533879 CATAAAATTT
* *
42533889 TAAAAATTATAATTTTTTAAAAA
1 TAAAAATCATAATTTTTCAAAAA
*
42533912 TAAAAATCA-AATTTTTCAATAA
1 TAAAAATCATAATTTTTCAAAAA
*
42533934 -AAAAATTATAA
1 TAAAAATCATAA
42533945 AATTGAACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 7 0.25
22 13 0.46
23 8 0.29
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAAATCATAATTTTTCAAAAA
Found at i:42534321 original size:19 final size:18
Alignment explanation
Indices: 42534288--42534328 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
42534278 TATTTATATA
*
42534288 ATTTTGTAGTTAATACAT
1 ATTTTGTAATTAATACAT
42534306 ATTTTCGTAATTAATACAT
1 ATTTT-GTAATTAATACAT
42534325 -TTTT
1 ATTTT
42534329 ATTTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (18 bp):
ATTTTGTAATTAATACAT
Found at i:42534760 original size:16 final size:16
Alignment explanation
Indices: 42534739--42534769 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42534729 TATTAGTGTT
42534739 TTTTTTAATGGTATAG
1 TTTTTTAATGGTATAG
*
42534755 TTTTTTATTGGTATA
1 TTTTTTAATGGTATA
42534770 ATAACAAATT
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:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (16 bp):
TTTTTTAATGGTATAG
Found at i:42534878 original size:51 final size:51
Alignment explanation
Indices: 42534772--42534883 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
42534762 TTGGTATAAT
* * * * * *
42534772 AACAAATTTAGGCCTTAAAATTTACAAATTCTGTTATTTTGATCTTAATTT
1 AACAAATTTAGCCCGTAAAATTTACAAATTCTGTTAATTTGATCATAAGTA
* * * * *
42534823 AACAAATTTAGCCCGTAACATTTACATATTCTTTTAATTTGGTCATAGGTA
1 AACAAATTTAGCCCGTAAAATTTACAAATTCTGTTAATTTGATCATAAGTA
42534874 AACAAATTTA
1 AACAAATTTA
42534884 ACTTACATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (51 bp):
AACAAATTTAGCCCGTAAAATTTACAAATTCTGTTAATTTGATCATAAGTA
Found at i:42537530 original size:8 final size:8
Alignment explanation
Indices: 42537517--42537542 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
42537507 AATGAAAATG
42537517 AATAAACA
1 AATAAACA
42537525 AATAAACA
1 AATAAACA
42537533 AATAAACA
1 AATAAACA
42537541 AA
1 AA
42537543 CTAGAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAACA
Found at i:42538918 original size:13 final size:13
Alignment explanation
Indices: 42538900--42538930 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42538890 TATCATATGC
*
42538900 ATATTATAATTTT
1 ATATTATAATATT
42538913 ATATTATAATATT
1 ATATTATAATATT
42538926 ATATT
1 ATATT
42538931 TGAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATTATAATATT
Found at i:42550272 original size:31 final size:32
Alignment explanation
Indices: 42550218--42550277 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
42550208 TAGGCCTTTT
*
42550218 TCAAAATTTTCAAAAAATCCAATTAAACCGTC
1 TCAAAAGTTTCAAAAAATCCAATTAAACCGTC
* *
42550250 TCAAAAGTTT-AAAAATTTCAATTAAACC
1 TCAAAAGTTTCAAAAAATCCAATTAAACC
42550278 CCTCAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30
Consensus pattern (32 bp):
TCAAAAGTTTCAAAAAATCCAATTAAACCGTC
Found at i:42550283 original size:30 final size:30
Alignment explanation
Indices: 42550218--42550316 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 30
42550208 TAGGCCTTTT
* * *
42550218 TCAAAATTTTCAAAAAATCCAATTAAACCGTC
1 TCAAAATTTT-AAAAATTTCAATTAAACC-CC
*
42550250 TCAAAAGTTTAAAAATTTCAATTAAACCCC
1 TCAAAATTTTAAAAATTTCAATTAAACCCC
** * * *
42550280 TCAATTTTTTGAAACTCTC-ATTAAACCCC
1 TCAAAATTTTAAAAATTTCAATTAAACCCC
42550309 TCAAAATT
1 TCAAAATT
42550317 GACCATTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
29 16 0.29
30 14 0.25
31 16 0.29
32 9 0.16
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.32
Consensus pattern (30 bp):
TCAAAATTTTAAAAATTTCAATTAAACCCC
Found at i:42550647 original size:29 final size:30
Alignment explanation
Indices: 42550590--42550660 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
42550580 TAGTACCTTG
42550590 AAAATTTTGAAAAAATTAATTAAATCCCCT
1 AAAATTTTGAAAAAATTAATTAAATCCCCT
*
42550620 AAAATTTT-AAAAATTTCAATTAAA-CCCCT
1 AAAATTTTGAAAAAATT-AATTAAATCCCCT
* *
42550649 CAATTTTTGAAA
1 AAAATTTTGAAA
42550661 CTCTCATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTTTGAAAAAATTAATTAAATCCCCT
Found at i:42552518 original size:2 final size:2
Alignment explanation
Indices: 42552511--42552537 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42552501 ATTTGGTTTT
42552511 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
42552538 TTGGGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:42561576 original size:17 final size:18
Alignment explanation
Indices: 42561545--42561580 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42561535 TTAATTCGTT
42561545 TCGAAATTAAGTAATTAA
1 TCGAAATTAAGTAATTAA
*
42561563 TCGAATTTAA-TAATTAA
1 TCGAAATTAAGTAATTAA
42561580 T
1 T
42561581 AATACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (18 bp):
TCGAAATTAAGTAATTAA
Found at i:42564993 original size:101 final size:100
Alignment explanation
Indices: 42564756--42564985 Score: 327
Period size: 101 Copynumber: 2.3 Consensus size: 100
42564746 TTAGGAGGCA
* *
42564756 GCAACAACATCAATGCCAACTAAACTAACACTCAATCGGCAACCTTAATTAATTCTAAAATGGAT
1 GCAACAACATCAATGCCAACTAAACTAGCACTCAATCAGCAACCTTAATTAATTCTAAAATGGAT
*
42564821 GGAACTAAGAACTTTCTAATACAATCACAAACATT
66 GGAACTAAGAACTTTCTAATACAATCACAAACACT
* * *
42564856 GCAACACCACCAATGCCTACTAAACTAGCACTCAATCAGCAACCTTAATTAATTCTAAAAATGGA
1 GCAACAACATCAATGCCAACTAAACTAGCACTCAATCAGCAACCTTAATTAATTCT-AAAATGGA
* * ***
42564921 TGGGACTAAGGACTTTCTAATA-AGATCACAGGGACT
65 TGGAACTAAGAACTTTCTAATACA-ATCACAAACACT
*
42564957 GCAACAACATCAATGCCAAATAAACTAGC
1 GCAACAACATCAATGCCAACTAAACTAGC
42564986 TTTCAATCGG
Statistics
Matches: 113, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
100 52 0.46
101 61 0.54
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (100 bp):
GCAACAACATCAATGCCAACTAAACTAGCACTCAATCAGCAACCTTAATTAATTCTAAAATGGAT
GGAACTAAGAACTTTCTAATACAATCACAAACACT
Found at i:42570042 original size:58 final size:59
Alignment explanation
Indices: 42569881--42570078 Score: 199
Period size: 58 Copynumber: 3.3 Consensus size: 59
42569871 CATGCATATT
* * * ** * *
42569881 AGATAAAAAATTCAATTTTTGGGTGTTGTTCATGCAATGGTCGACACCTCC---TTTCTC
1 AGATAAAAAATCCATTTTTTTGGTGTTGGCCATGCAATGGCCGACACC-CCTTTTTTATC
* *
42569938 AGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTGTC
1 AGAT-AAAAAA--TC-CATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTATC
**
42570001 AGATAAAAAATCCATTTTTTT-GTGTTGGCCATCGC-ATGGCCGACACTTCTTTTTTATC
1 AGATAAAAAATCCATTTTTTTGGTGTTGGCCAT-GCAATGGCCGACACCCCTTTTTTATC
*
42570059 AGATAAAAAATCCAATTTTT
1 AGATAAAAAATCCATTTTTT
42570079 GGGCATGGTC
Statistics
Matches: 120, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
57 4 0.03
58 56 0.47
59 10 0.08
60 5 0.04
61 30 0.25
62 6 0.05
63 9 0.08
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (59 bp):
AGATAAAAAATCCATTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTATC
Found at i:42570201 original size:59 final size:59
Alignment explanation
Indices: 42570129--42570369 Score: 247
Period size: 59 Copynumber: 4.1 Consensus size: 59
42570119 AAATTTTTTT
* * * * * *
42570129 GGTGTTGGCCATGCAATGGTCGACACCTAAAGATTGGATTTTTTATCTGATAAAAAAGG
1 GGTGTCGGCCATGCAATGGCCAACACATAAAAATTGGATTTTTTATCTGACAAAAAAGG
* * * *
42570188 GGTGTTGGTCATGCAATGGCC-A-ACATAAAAAGTTGCATTTTTTATCTAACAAAAAAGG
1 GGTGTCGGCCATGCAATGGCCAACACATAAAAA-TTGGATTTTTTATCTGACAAAAAAGG
* * * * **
42570246 GGTGTCAGTCATTG-TATGGCCAACAC-TCAAAAATTGGATTTTTAATCTGATGAAAAAGG
1 GGTGTCGGCCA-TGCAATGGCCAACACAT-AAAAATTGGATTTTTTATCTGACAAAAAAGG
* * * *
42570305 GATGTCGGCCATGCAATGACCAACACAAAAAAATTGTATTTTTTATCTGACAAAAAAGG
1 GGTGTCGGCCATGCAATGGCCAACACATAAAAATTGGATTTTTTATCTGACAAAAAAGG
42570364 GGTGTC
1 GGTGTC
42570370 AACCATTGCA
Statistics
Matches: 149, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
57 7 0.05
58 41 0.28
59 94 0.63
60 7 0.05
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (59 bp):
GGTGTCGGCCATGCAATGGCCAACACATAAAAATTGGATTTTTTATCTGACAAAAAAGG
Found at i:42571367 original size:38 final size:38
Alignment explanation
Indices: 42571314--42571387 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
42571304 AAACTCCCTA
42571314 GTTGGTTACCCAATTTTTAGGGCACTTTCATTTTGGAT
1 GTTGGTTACCCAATTTTTAGGGCACTTTCATTTTGGAT
* * *
42571352 GTTGGTTATCTAATTTTTAGGGCGCTTTCATTTTGG
1 GTTGGTTACCCAATTTTTAGGGCACTTTCATTTTGG
42571388 TCATCCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.47
Consensus pattern (38 bp):
GTTGGTTACCCAATTTTTAGGGCACTTTCATTTTGGAT
Found at i:42573111 original size:42 final size:42
Alignment explanation
Indices: 42573050--42573144 Score: 147
Period size: 42 Copynumber: 2.2 Consensus size: 42
42573040 ATAAAATAAG
* *
42573050 TTATTATTATTTATTATTGTCTTTGTCCAAATTGATATTG-TTT
1 TTATTTTTA-TTATTATTGTCTTTATCC-AATTGATATTGTTTT
42573093 TTATTTTTATTATTATTGTCTTTATCCAATTGATATTGTTTT
1 TTATTTTTATTATTATTGTCTTTATCCAATTGATATTGTTTT
42573135 TTATTTTTAT
1 TTATTTTTAT
42573145 AATATCCTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
41 11 0.22
42 30 0.61
43 8 0.16
ACGTcount: A:0.22, C:0.06, G:0.07, T:0.64
Consensus pattern (42 bp):
TTATTTTTATTATTATTGTCTTTATCCAATTGATATTGTTTT
Found at i:42579118 original size:98 final size:98
Alignment explanation
Indices: 42578949--42579146 Score: 351
Period size: 98 Copynumber: 2.0 Consensus size: 98
42578939 TTTTTGATAT
* *
42578949 TTTTCGCCTTGAGTCATGTTATTTATGTTCTTAATTATATTATTTATACTTATATTTTATTTATC
1 TTTTCGCCTTGAATCATGCTATTTATGTTCTTAATTATATTATTTATACTTATATTTTATTTATC
42579014 ATTCATTTAAGAAATGATCGGAGAAAATGGAGC
66 ATTCATTTAAGAAATGATCGGAGAAAATGGAGC
*
42579047 TTTTCGCCTTGAATTATGCTATTTATGTTCTTAATTATATTATTTATACTTATATTTTATTTATC
1 TTTTCGCCTTGAATCATGCTATTTATGTTCTTAATTATATTATTTATACTTATATTTTATTTATC
* *
42579112 ATTCATTTAGGAAATGATTGGAGAAAATGGAGC
66 ATTCATTTAAGAAATGATCGGAGAAAATGGAGC
42579145 TT
1 TT
42579147 AAAATTTATT
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (98 bp):
TTTTCGCCTTGAATCATGCTATTTATGTTCTTAATTATATTATTTATACTTATATTTTATTTATC
ATTCATTTAAGAAATGATCGGAGAAAATGGAGC
Done.