Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 14 of 198
Found at i:4428263 original size:21 final size:21
Alignment explanation
Indices: 4428238--4428283 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4428228 TCTCTCAACC
*
4428238 AAAATTATTT-TAAAAAAATTT
1 AAAA-TATTTATAAAAAAATAT
*
4428259 AAAATATTTATAAAAATATAT
1 AAAATATTTATAAAAAAATAT
4428280 AAAA
1 AAAA
4428284 AAAAGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATATTTATAAAAAAATAT
Found at i:4440618 original size:26 final size:26
Alignment explanation
Indices: 4440580--4440667 Score: 140
Period size: 26 Copynumber: 3.3 Consensus size: 26
4440570 GTTTCTATTA
* *
4440580 AAAAGAGAGAATTTTCGTTTTCACACT
1 AAAA-AGAGAATTTTTGTTTTCACCCT
*
4440607 AAAAAGATAATTTTTGTTTTCACCCT
1 AAAAAGAGAATTTTTGTTTTCACCCT
4440633 AAAAAGAGAATTTTTGTTTTCACCCT
1 AAAAAGAGAATTTTTGTTTTCACCCT
4440659 AAAAAGAGA
1 AAAAAGAGA
4440668 GAAAACTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 53 0.93
27 4 0.07
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (26 bp):
AAAAAGAGAATTTTTGTTTTCACCCT
Found at i:4440678 original size:26 final size:26
Alignment explanation
Indices: 4440621--4440679 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
4440611 AGATAATTTT
****
4440621 TGTTTTCACCCTAAAAAGAGAATTTT
1 TGTTTTCACCCTAAAAAGAGAAAAAC
4440647 TGTTTTCACCCTAAAAAGAGAGAAAAC
1 TGTTTTCACCCTAAAAAGAGA-AAAAC
4440674 T-TTTTC
1 TGTTTTC
4440680 TAGTTCTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (26 bp):
TGTTTTCACCCTAAAAAGAGAAAAAC
Found at i:4448014 original size:28 final size:27
Alignment explanation
Indices: 4447965--4448022 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
4447955 TAATTAGTTT
* *
4447965 AATTTAATTTTTATTTAAATAATAATTA
1 AATTTAATTTTTATTGAAATAA-AAATA
*
4447993 AATTTAATTTTT-TATGATATAAAAATA
1 AATTTAATTTTTAT-TGAAATAAAAATA
4448020 AAT
1 AAT
4448023 ATTTTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
AATTTAATTTTTATTGAAATAAAAATA
Found at i:4448197 original size:16 final size:16
Alignment explanation
Indices: 4448164--4448193 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4448154 ACGTGTCTCC
4448164 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
4448180 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
4448194 TATTATGCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:4449407 original size:16 final size:18
Alignment explanation
Indices: 4449373--4449409 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
4449363 ATTAAATTTC
4449373 TTTATATATTCTTTATAA
1 TTTATATATTCTTTATAA
*
4449391 TTTATA-ATT-TTTTTAA
1 TTTATATATTCTTTATAA
4449407 TTT
1 TTT
4449410 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATATATTCTTTATAA
Found at i:4449456 original size:18 final size:21
Alignment explanation
Indices: 4449435--4449479 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
4449425 ATTTCAGAAT
4449435 TTTTATAAA-TATTTT-TAA-
1 TTTTATAAATTATTTTGTAAG
*
4449453 TTTTAAAAATTATTTTGTAAG
1 TTTTATAAATTATTTTGTAAG
4449474 TTTTAT
1 TTTTAT
4449480 TGAGAGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 3 0.14
21 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTATAAATTATTTTGTAAG
Found at i:4449621 original size:23 final size:23
Alignment explanation
Indices: 4449595--4449648 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
4449585 CTCAACTCGA
4449595 ACTCGAATTACTTATTTGTGTTG
1 ACTCGAATTACTTATTTGTGTTG
4449618 ACTCGAATTACTTATTTGTGTTG
1 ACTCGAATTACTTATTTGTGTTG
4449641 ACTCGAAT
1 ACTCGAAT
4449649 AACTCGATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (23 bp):
ACTCGAATTACTTATTTGTGTTG
Found at i:4456907 original size:126 final size:125
Alignment explanation
Indices: 4456698--4456924 Score: 316
Period size: 126 Copynumber: 1.8 Consensus size: 125
4456688 TTAAAAAAAA
* * *
4456698 TTAAAAGGATTCTTTGCTATTTAGGTTTAGCGAGAAAATCGAAACCCCGTAAGTTAGGGTACGAT
1 TTAAAAGGATACTTTGCTATTTAGGTTTAACGAGAAAATCGAAACCCCGTAAGTTAGGGTACAAT
4456763 CTCCCAAATCACTAAAATGC-AAAGCTATTGCCTTATTGAGATTCCTTTCATTTTTGAAATC
66 CTCCCAAATCACTAAAATGCGAAA--TATTGCCTTATTGAGATTCCTTTCATTTTTGAAATC
* *
4456824 TTAAAAGGATACTTTGTTATCTT-GGTTTAACGAGAAAATTGAAACCCCGTAAGTTAGGGTACAA
1 TTAAAAGGATACTTTGCTAT-TTAGGTTTAACGAGAAAATCGAAACCCCGTAAGTTAGGGTACAA
* * * *
4456888 TTTCTCAAATTTAC-GAAATGCGAAATATTGCCTTATT
65 TCTCCCAAA-TCACTAAAATGCGAAATATTGCCTTATT
4456925 TTAACAATTT
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
125 12 0.13
126 69 0.78
127 8 0.09
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (125 bp):
TTAAAAGGATACTTTGCTATTTAGGTTTAACGAGAAAATCGAAACCCCGTAAGTTAGGGTACAAT
CTCCCAAATCACTAAAATGCGAAATATTGCCTTATTGAGATTCCTTTCATTTTTGAAATC
Found at i:4458918 original size:34 final size:34
Alignment explanation
Indices: 4458875--4458944 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
4458865 AGACTTTTAA
4458875 GAAAGACAAATTTTGCCCAGTCTCACCGAGTCTT
1 GAAAGACAAATTTTGCCCAGTCTCACCGAGTCTT
4458909 GAAAGACAAATTTTGCCCAGTCTCACCGAGTCTT
1 GAAAGACAAATTTTGCCCAGTCTCACCGAGTCTT
4458943 GA
1 GA
4458945 CTTTCTGGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (34 bp):
GAAAGACAAATTTTGCCCAGTCTCACCGAGTCTT
Found at i:4459195 original size:44 final size:44
Alignment explanation
Indices: 4459059--4459335 Score: 241
Period size: 44 Copynumber: 6.4 Consensus size: 44
4459049 ATATTCTCTT
* ** * * * *
4459059 CTGCAACTTCAGGGTGACGAGATTTGTGGTTTTAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTGTGATTTTAATCTGCTTCA
* * *
4459103 CTGCAACGTCAGGGAGATAAGA-CTG-GA-TATGATCTGC-TCTA
1 CTGCAACTTCAGGGAGATAAGATCTGTGATTTTAATCTGCTTC-A
* *
4459144 CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTTCA
1 CTGCAACTTCAGGGAGATAAGATCTGTGATTTTAATCTGCTTCA
** **
4459188 CTGCAACTTCAGGGAGATAAGAT-TGGTTTTTTTCGTCTG-TTCCA
1 CTGCAACTTCAGGGAGATAAGATCT-GTGATTTTAATCTGCTT-CA
* ***
4459232 CTGCAACTTCAGGGAAATAAGA-CTG-GA-TGCGATCTGC-TCTA
1 CTGCAACTTCAGGGAGATAAGATCTGTGATTTTAATCTGCTTC-A
* * *
4459273 CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATTTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTGTGATTTTAATCTGCTTCA
4459317 CTGCAACTTCAGGGAGATA
1 CTGCAACTTCAGGGAGATA
4459336 GGATTGATTT
Statistics
Matches: 183, Mismatches: 36, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
40 2 0.01
41 55 0.30
42 7 0.04
43 10 0.05
44 106 0.58
45 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATCTGTGATTTTAATCTGCTTCA
Found at i:4459202 original size:85 final size:85
Alignment explanation
Indices: 4459054--4459209 Score: 213
Period size: 85 Copynumber: 1.8 Consensus size: 85
4459044 CTTCAATATT
* * * * * * * *
4459054 CTCTTCTGCAACTTCAGGGTGACGAGATTTGTGGTTTTAGTCTGCTCCACTGCAACGTCAGGGAG
1 CTCTACTGCAACTTCAGAGAGACAAGATCTGTGATTTTAATCCGCTCCACTGCAACGTCAGGGAG
4459119 ATAAGACTGGATATGATCTG
66 ATAAGACTGGATATGATCTG
* * *
4459139 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTTCACTGCAACTTCAGGGAG
1 CTCTACTGCAACTTCAGAGAGACAAGATCTGTGATTTTAATCCGCTCCACTGCAACGTCAGGGAG
4459204 ATAAGA
66 ATAAGA
4459210 TTGGTTTTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 60 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (85 bp):
CTCTACTGCAACTTCAGAGAGACAAGATCTGTGATTTTAATCCGCTCCACTGCAACGTCAGGGAG
ATAAGACTGGATATGATCTG
Found at i:4459255 original size:129 final size:129
Alignment explanation
Indices: 4459059--4459341 Score: 422
Period size: 129 Copynumber: 2.2 Consensus size: 129
4459049 ATATTCTCTT
* ** * *
4459059 CTGCAACTTCAGGGTGACGAGATTTGTGGTTTTAGTCTGCTCCACTGCAACGTCAGGGAGATAAG
1 CTGCAACTTCAGGGAGATAAGATTGGTGGTTTTAGTCTGCTCCACTGCAACGTCAGGGAAATAAG
* *
4459124 ACTGGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTTCA
66 ACTGGATACGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCA
** * * *
4459188 CTGCAACTTCAGGGAGATAAGATTGGTTTTTTTCGTCTGTTCCACTGCAACTTCAGGGAAATAAG
1 CTGCAACTTCAGGGAGATAAGATTGGTGGTTTTAGTCTGCTCCACTGCAACGTCAGGGAAATAAG
* **
4459253 ACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATTTGCTCCA
66 ACTGGATACGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCA
*
4459317 CTGCAACTTCAGGGAGATAGGATTG
1 CTGCAACTTCAGGGAGATAAGATTG
4459342 ATTTCTGTCG
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 138 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (129 bp):
CTGCAACTTCAGGGAGATAAGATTGGTGGTTTTAGTCTGCTCCACTGCAACGTCAGGGAAATAAG
ACTGGATACGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCA
Found at i:4460503 original size:27 final size:27
Alignment explanation
Indices: 4460485--4460556 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
4460475 TTCACCTTGG
**
4460485 CCTCTCCTTTTTCTTTTTTCGTTCTTA
1 CCTCTCCTTTTTCTTTTTTCGACCTTA
**
4460512 CCTCTCCTTTTTCTTTTTTCGTTCTTA
1 CCTCTCCTTTTTCTTTTTTCGACCTTA
*
4460539 -CT-TTCTTTTTCTTTTTTC
1 CCTCTCCTTTTTCTTTTTTC
4460557 TTTTCATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 15 0.34
26 2 0.05
27 27 0.61
ACGTcount: A:0.03, C:0.28, G:0.03, T:0.67
Consensus pattern (27 bp):
CCTCTCCTTTTTCTTTTTTCGACCTTA
Found at i:4463727 original size:19 final size:20
Alignment explanation
Indices: 4463703--4463749 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
4463693 TGTGAAACTC
*
4463703 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
4463722 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
4463742 -AATGCAAA
1 TAATGCAAA
4463750 AGAAAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:4476151 original size:3 final size:3
Alignment explanation
Indices: 4476143--4476224 Score: 141
Period size: 3 Copynumber: 28.0 Consensus size: 3
4476133 CATGTTTTAT
4476143 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
4476191 ATA ATA ATA ATA ATA A-C ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4476225 GTTTTACTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 3 0.04
3 72 0.96
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4483790 original size:2 final size:2
Alignment explanation
Indices: 4483773--4483840 Score: 109
Period size: 2 Copynumber: 33.5 Consensus size: 2
4483763 CCTAATATGA
* *
4483773 AT AT AT GT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4483815 AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT -AT AT A
4483841 CGTCAGGGGC
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 59 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4486375 original size:24 final size:23
Alignment explanation
Indices: 4486349--4486409 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
4486339 TATATTACAA
*
4486349 TTTATAAATATTTAATAATAAATAT
1 TTTAT-AATATATAAT-ATAAATAT
*
4486374 TTTATAGTATATAATATAAATAT
1 TTTATAATATATAATATAAATAT
*
4486397 TTTA-ATTATATAA
1 TTTATAATATATAA
4486410 ATATGAGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.24
23 12 0.36
24 8 0.24
25 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTATAATATATAATATAAATAT
Found at i:4486421 original size:23 final size:23
Alignment explanation
Indices: 4486361--4486409 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
4486351 TATAAATATT
4486361 TAATAATAAATATTTTATAGTATA
1 TAAT-ATAAATATTTTATAGTATA
*
4486385 TAATATAAATATTTTA-ATTATA
1 TAATATAAATATTTTATAGTATA
4486407 TAA
1 TAA
4486410 ATATGAGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.33
23 12 0.50
24 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATATAAATATTTTATAGTATA
Found at i:4486688 original size:20 final size:21
Alignment explanation
Indices: 4486640--4486689 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
4486630 ACTAAAAACC
*
4486640 TTGATTCAACTGGTTCAATTG
1 TTGATTCAACTGGTTCAATCG
* *
4486661 TCGGTTCAA-TGGTTCAATCG
1 TTGATTCAACTGGTTCAATCG
4486681 TTGATTCAA
1 TTGATTCAA
4486690 ACGGTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (21 bp):
TTGATTCAACTGGTTCAATCG
Found at i:4491545 original size:22 final size:22
Alignment explanation
Indices: 4491517--4491558 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
4491507 TTTATTGTTC
4491517 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
4491539 AAACATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
4491559 CTCCCACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:4494235 original size:2 final size:2
Alignment explanation
Indices: 4494223--4494263 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
4494213 CATCTCCTTA
4494223 AT AT CAT 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
4494264 TCAGCTCTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4496285 original size:28 final size:26
Alignment explanation
Indices: 4496225--4496295 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
4496215 AACCCGTGGG
4496225 TTCTTTCTTCTCTTTCTCTTTTCCTTT
1 TTCTTTCTT-TCTTTCTCTTTTCCTTT
* * *
4496252 TTCTTTCTTTCTATTTTGTTTTGCTTT
1 TTCTTTCTTTCT-TTCTCTTTTCCTTT
*
4496279 TGTCTTTCTTTATTTCT
1 T-TCTTTCTTTCTTTCT
4496296 TTTATTACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.08
27 24 0.65
28 10 0.27
ACGTcount: A:0.03, C:0.21, G:0.04, T:0.72
Consensus pattern (26 bp):
TTCTTTCTTTCTTTCTCTTTTCCTTT
Found at i:4500402 original size:16 final size:16
Alignment explanation
Indices: 4500381--4500414 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4500371 CCAATATCCA
* *
4500381 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
4500397 ATTATCACATTTACAC
1 ATTATCACATTTACAC
4500413 AT
1 AT
4500415 ATATATTCAT
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:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:4506146 original size:8 final size:8
Alignment explanation
Indices: 4506104--4506146 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
4506094 ATAGTAAAAA
*
4506104 TATAATTT
1 TATATTTT
4506112 TATTATTTT
1 TA-TATTTT
*
4506121 AATATTTT
1 TATATTTT
*
4506129 TATATCTT
1 TATATTTT
4506137 TATATTTT
1 TATATTTT
4506145 TA
1 TA
4506147 AAAGATTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
8 23 0.79
9 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
TATATTTT
Found at i:4507519 original size:2 final size:2
Alignment explanation
Indices: 4507512--4507543 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4507502 CAATTAGCTA
4507512 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
4507544 GTCAGACGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4517922 original size:27 final size:26
Alignment explanation
Indices: 4517862--4517923 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
4517852 CTCTTCCCTA
4517862 ATTTTCAAATGTTGAGAAAACTAAAT
1 ATTTTCAAATGTTGAGAAAACTAAAT
** *
4517888 ATCCTCAAATGTTGAGAAAGATTAAAT
1 ATTTTCAAATGTTGAGAAA-ACTAAAT
*
4517915 GTTTTCAAA
1 ATTTTCAAA
4517924 GATACAAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 17 0.59
27 12 0.41
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (26 bp):
ATTTTCAAATGTTGAGAAAACTAAAT
Found at i:4521332 original size:33 final size:34
Alignment explanation
Indices: 4521281--4521355 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
4521271 AGATTTAAAC
4521281 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
* *
4521315 AAATTAATT-CTAACACTTATTTGAGCTGACCTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
4521348 AATTTAAT
1 AAATTAAT
4521356 AAACTAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:4523153 original size:18 final size:18
Alignment explanation
Indices: 4523130--4523168 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4523120 CTCTTTTTGC
*
4523130 TCTTTTTC-ATTCTGTTTT
1 TCTTTTTCGATT-TCTTTT
4523148 TCTTTTTCGATTTCTTTT
1 TCTTTTTCGATTTCTTTT
4523166 TCT
1 TCT
4523169 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.72
Consensus pattern (18 bp):
TCTTTTTCGATTTCTTTT
Found at i:4525154 original size:24 final size:25
Alignment explanation
Indices: 4525115--4525161 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
4525105 CTACTTCTAA
4525115 AGAAAACTCAAGAGAGAATTCTTGG
1 AGAAAACTCAAGAGAGAATTCTTGG
4525140 AGAAAACTCAA-AGAGAATTCTT
1 AGAAAACTCAAGAGAGAATTCTT
4525162 CACTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (25 bp):
AGAAAACTCAAGAGAGAATTCTTGG
Found at i:4528280 original size:35 final size:35
Alignment explanation
Indices: 4528234--4528304 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
4528224 AACGTATATA
4528234 AAATACTTCATGTATTAAAAAATAAAATCCCCATC
1 AAATACTTCATGTATTAAAAAATAAAATCCCCATC
4528269 AAATACTTCATGTATTAAAAAATAAAATCCCCATC
1 AAATACTTCATGTATTAAAAAATAAAATCCCCATC
4528304 A
1 A
4528305 TTTGCGTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (35 bp):
AAATACTTCATGTATTAAAAAATAAAATCCCCATC
Found at i:4532529 original size:29 final size:30
Alignment explanation
Indices: 4532466--4532529 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
4532456 TAAATTAAGA
**
4532466 GTTATTTTTTAAATTTAATGTATTTATTTT
1 GTTATTTTTTAAATTTAATGTATTTATTGG
* *
4532496 ATTATTTTTTACA-TTAAT-TATCTTATTGG
1 GTTATTTTTTAAATTTAATGTAT-TTATTGG
4532525 GTTAT
1 GTTAT
4532530 CTAAGTAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.11
29 14 0.50
30 11 0.39
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (30 bp):
GTTATTTTTTAAATTTAATGTATTTATTGG
Found at i:4542664 original size:21 final size:19
Alignment explanation
Indices: 4542639--4542678 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
4542629 CGGCCCCATT
4542639 TTTAATAAACACAAAAAAATA
1 TTTAA-AAA-ACAAAAAAATA
*
4542660 TTTAAAAAATAAAAAAATA
1 TTTAAAAAACAAAAAAATA
4542679 AAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
TTTAAAAAACAAAAAAATA
Found at i:4546685 original size:46 final size:46
Alignment explanation
Indices: 4546612--4546796 Score: 246
Period size: 46 Copynumber: 4.0 Consensus size: 46
4546602 ACAAGGCTAT
* *
4546612 AACTCAGTATGGTTTTCTTCACGGAAATACCATATCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
4546658 AACTCAGTATGGTTTTTTTTACCGAAATACCATACCTATTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
*** *
4546704 AACTCAGTATGGTTTTCTTCATTAAAATACCATACCTACTTTTTAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
4546750 AACTCAGTATGGTTTTC-TCAACTGGAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTC-ACCGAAATACCATACCTACTTTTCAC
4546796 A
1 A
4546797 CTTTGCCATG
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
45 2 0.02
46 119 0.98
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:4548043 original size:17 final size:17
Alignment explanation
Indices: 4548021--4548053 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4548011 AAATTCTTTT
4548021 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
4548038 TAAATCACAAAATTCA
1 TAAATCACAAAATTCA
4548054 CTAATTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:4548548 original size:37 final size:37
Alignment explanation
Indices: 4548489--4548591 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 37
4548479 CAGCGCTATA
*
4548489 TAAATTTGACACCCAGTG-CTCATCATTTAAACCGAAG
1 TAAA-TTGGCACCCAGTGCCTCATCATTTAAACCGAAG
* *
4548526 TAAATTGGTATCCAGTGCCTCATCATTTAAACCGAAG
1 TAAATTGGCACCCAGTGCCTCATCATTTAAACCGAAG
4548563 TAAATTGGCACCCAGTGCCTCATCGATTT
1 TAAATTGGCACCCAGTGCCTCATC-ATTT
4548592 GAAGTCGAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
36 10 0.17
37 45 0.76
38 4 0.07
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (37 bp):
TAAATTGGCACCCAGTGCCTCATCATTTAAACCGAAG
Found at i:4548838 original size:148 final size:148
Alignment explanation
Indices: 4548570--4548869 Score: 478
Period size: 148 Copynumber: 2.0 Consensus size: 148
4548560 AAGTAAATTG
* * * *
4548570 GCACCCAGTGCCTCATCGATTTGAAGTCGAAGAAATCTCTGAACTCTTCCAATCCTATGGCATGC
1 GCACCCAGTGCCTCATCGACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCCTATGACATGC
*
4548635 CATCCATATCCGACTCAGCCTGATACAGTTAATAGAGTTTAATTTCACTTTCCAAATACAACCAA
66 CATCCATATCCGACTCAGCCTAATACAGTTAATAGAGTTTAATTTCACTTTCCAAATACAACCAA
4548700 TATTCAATTACCATATTT
131 TATTCAATTACCATATTT
* * *
4548718 GCACCTAGTGCCTCATTGACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCTTATGACATGC
1 GCACCCAGTGCCTCATCGACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCCTATGACATGC
*
4548783 CA-CCTATATCCGACTCAG-CTCAATACAGTTAATAGGGTTTAATTTCACTTTCCAAATACAACC
66 CATCC-ATATCCGACTCAGCCT-AATACAGTTAATAGAGTTTAATTTCACTTTCCAAATACAACC
*
4548846 AATATTCAATTATCATATTT
129 AATATTCAATTACCATATTT
4548866 GCAC
1 GCAC
4548870 ATATATATTC
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
147 4 0.03
148 136 0.97
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.30
Consensus pattern (148 bp):
GCACCCAGTGCCTCATCGACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCCTATGACATGC
CATCCATATCCGACTCAGCCTAATACAGTTAATAGAGTTTAATTTCACTTTCCAAATACAACCAA
TATTCAATTACCATATTT
Found at i:4548915 original size:2 final size:2
Alignment explanation
Indices: 4548910--4548955 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4548900 TATATTCATA
4548910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4548952 AT AT
1 AT AT
4548956 CAATTCAATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4549240 original size:19 final size:20
Alignment explanation
Indices: 4549203--4549243 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
4549193 TACAACACAA
*
4549203 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
4549223 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
4549242 TT
1 TT
4549244 GTCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:4549672 original size:14 final size:14
Alignment explanation
Indices: 4549653--4549682 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4549643 TGCGTCTTTC
*
4549653 TTTCTTTTTTTCTT
1 TTTCTTTCTTTCTT
4549667 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
4549681 TT
1 TT
4549683 CTGTTTTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTCTTTCTTTCTT
Found at i:4551962 original size:22 final size:23
Alignment explanation
Indices: 4551932--4551980 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
4551922 AGACATATCC
* * *
4551932 ACATCGAACCTTAATTTCTCGAG
1 ACATCGAACCCTAATGTCCCGAG
4551955 ACAT-GAACCCTAATGTCCCGAG
1 ACATCGAACCCTAATGTCCCGAG
4551977 ACAT
1 ACAT
4551981 ATCCATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (23 bp):
ACATCGAACCCTAATGTCCCGAG
Found at i:4557689 original size:30 final size:31
Alignment explanation
Indices: 4557636--4557700 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
4557626 AATGAGAATA
*** *
4557636 TTTTTAAAAAAAATGGTACTTAAAACATATT
1 TTTTTAAAAAAAAACATACTTAAAAAATATT
4557667 TTTTTAAAAAAAAACATA-TTAAAAAATATT
1 TTTTTAAAAAAAAACATACTTAAAAAATATT
4557697 TTTT
1 TTTT
4557701 AATTAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
TTTTTAAAAAAAAACATACTTAAAAAATATT
Found at i:4561015 original size:2 final size:2
Alignment explanation
Indices: 4561010--4561036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4561000 TATTACAATA
4561010 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4561037 ATTGGCTCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4563275 original size:31 final size:33
Alignment explanation
Indices: 4563221--4563281 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
4563211 TACATTGATT
*
4563221 TTATTTAATATTAAATTTTTTATTTTGATTCAA
1 TTATTTAATATGAAATTTTTTATTTTGATTCAA
4563254 TTATTT-ATATGAAA-TTTTTATTTTGATT
1 TTATTTAATATGAAATTTTTTATTTTGATT
4563282 TTGAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 14 0.52
32 7 0.26
33 6 0.22
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (33 bp):
TTATTTAATATGAAATTTTTTATTTTGATTCAA
Found at i:4564104 original size:12 final size:12
Alignment explanation
Indices: 4564087--4564133 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
4564077 ACTTTGTAGG
*
4564087 TTTTTTATTTAA
1 TTTTTTAATTAA
*
4564099 TTTTTTAGAATAA
1 TTTTTTA-ATTAA
4564112 TTTGTTTAATT-A
1 TTT-TTTAATTAA
4564124 TTTTTTAATT
1 TTTTTTAATT
4564134 TAAATGACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 7 0.23
12 11 0.37
13 8 0.27
14 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (12 bp):
TTTTTTAATTAA
Found at i:4566140 original size:34 final size:35
Alignment explanation
Indices: 4566097--4566180 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
4566087 GCAAAAGAGT
**
4566097 TTGCGCCCAGCGCTAGTTGGATAAACCGACA-AA-
1 TTGCGCCCAGCGCTAGTCAGATAAACCGACAGAAG
* * *
4566130 TGTGTGCCCAGCACTAGTCAGATAAACTGACAGAAG
1 T-TGCGCCCAGCGCTAGTCAGATAAACCGACAGAAG
4566166 TTGCGCCCAGCGCTA
1 TTGCGCCCAGCGCTA
4566181 ATCGAATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
33 1 0.02
34 25 0.61
35 14 0.34
36 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (35 bp):
TTGCGCCCAGCGCTAGTCAGATAAACCGACAGAAG
Found at i:4566371 original size:40 final size:40
Alignment explanation
Indices: 4566257--4566376 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 40
4566247 CAGCGCTCCG
*
4566257 ACGATATAAATAGTGAGCCTAGCTCTAGTTGGATAAACCA
1 ACGATATAAATAGTGAGCCCAGCTCTAGTTGGATAAACCA
* * * *
4566297 AC-A-AT--AT-TTGCGCCCAGCGCTAGTCGGATAAACCA
1 ACGATATAAATAGTGAGCCCAGCTCTAGTTGGATAAACCA
* *
4566332 ACGATATAAATAGTGAGCCCAACTCTAGTTGGATGAACCA
1 ACGATATAAATAGTGAGCCCAGCTCTAGTTGGATAAACCA
4566372 ACGAT
1 ACGAT
4566377 GATTGCACCT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
35 25 0.39
36 3 0.05
37 2 0.03
38 2 0.03
39 3 0.05
40 29 0.45
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (40 bp):
ACGATATAAATAGTGAGCCCAGCTCTAGTTGGATAAACCA
Found at i:4566391 original size:75 final size:75
Alignment explanation
Indices: 4566257--4566400 Score: 218
Period size: 75 Copynumber: 1.9 Consensus size: 75
4566247 CAGCGCTCCG
* * *
4566257 ACGATATAAATAGTGAGCCTAGCTCTAGTTGGATAAACCAACAATATTTGCGCCCAGCGCTAGTC
1 ACGATATAAATAGTGAGCCCAACTCTAGTTGGATAAACCAACAATATTTGCACCCAGCGCTAGTC
4566322 GGATAAACCA
66 GGATAAACCA
* * *
4566332 ACGATATAAATAGTGAGCCCAACTCTAGTTGGATGAACCAACGATGA-TTGCACCTAGCGCTAGT
1 ACGATATAAATAGTGAGCCCAACTCTAGTTGGATAAACCAACAAT-ATTTGCACCCAGCGCTAGT
4566396 CGGAT
65 CGGAT
4566401 GAACTGACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
75 61 0.98
76 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (75 bp):
ACGATATAAATAGTGAGCCCAACTCTAGTTGGATAAACCAACAATATTTGCACCCAGCGCTAGTC
GGATAAACCA
Found at i:4566498 original size:37 final size:37
Alignment explanation
Indices: 4566455--4566527 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
4566445 ATTTCATAAT
4566455 CTCAATATCACATTCACTTCAATTATCTATTAATCAA
1 CTCAATATCACATTCACTTCAATTATCTATTAATCAA
*
4566492 CTCAATATCATATTCACTTCAATTATCTATTAATCA
1 CTCAATATCACATTCACTTCAATTATCTATTAATCA
4566528 TTCATTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (37 bp):
CTCAATATCACATTCACTTCAATTATCTATTAATCAA
Found at i:4566522 original size:17 final size:17
Alignment explanation
Indices: 4566466--4566522 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
4566456 TCAATATCAC
4566466 ATTCACTTCAATTATCT
1 ATTCACTTCAATTATCT
4566483 ATTAATCAAC-TCAA-TATCAT
1 A-T--TC-ACTTCAATTATC-T
4566503 ATTCACTTCAATTATCT
1 ATTCACTTCAATTATCT
4566520 ATT
1 ATT
4566523 AATCATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
16 2 0.06
17 11 0.33
18 5 0.15
19 5 0.15
20 8 0.24
21 2 0.06
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTCACTTCAATTATCT
Found at i:4573314 original size:90 final size:90
Alignment explanation
Indices: 4573095--4573331 Score: 271
Period size: 91 Copynumber: 2.6 Consensus size: 90
4573085 GTTTTTTTCA
* * * * * *
4573095 GGGAAAATTATAATAATCACTACTTAATCCATTTCATTGTTGGGGCACTTGGGCTTTAGTATCGT
1 GGGATAATTATAATAATCACTATTTATTTCATTTCATT-TTGGGGCACTTGGGCTTCAGTATAGT
* **
4573160 ATTGCAATAATTTTTTTTAATTTTTT
65 ACTGCAATAATTTTTTAAAATTTTTT
* * * * *
4573186 GGGATAAATATAATAATCACTATTCATTTTATTTCATTTTCGGGGCACTTGGGCTTCAGTTTATT
1 GGGATAATTATAATAATCACTATTTATTTCATTTCATTTT-GGGGCACTTGGGCTTCAGTATAGT
4573251 ACTGCAAT-ATTTTTTAAAATTTTTT
65 ACTGCAATAATTTTTTAAAATTTTTT
* * *
4573276 GGGATAATTATAATAATCA-TGATTTATTTCATGTCATTTTTGGGCCACTTAGGCTT
1 GGGATAATTATAATAATCACT-ATTTATTTCATTTCA-TTTTGGGGCACTTGGGCTT
4573332 GATTTTGGGG
Statistics
Matches: 123, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
89 1 0.01
90 60 0.49
91 62 0.50
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (90 bp):
GGGATAATTATAATAATCACTATTTATTTCATTTCATTTTGGGGCACTTGGGCTTCAGTATAGTA
CTGCAATAATTTTTTAAAATTTTTT
Found at i:4573621 original size:18 final size:18
Alignment explanation
Indices: 4573598--4573650 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
4573588 CTCAAGTCCA
4573598 ATTCTCTTTATTCTCTCC
1 ATTCTCTTTATTCTCTCC
4573616 ATTCTCTTTATTCTCT-C
1 ATTCTCTTTATTCTCTCC
**
4573633 ATTTCTCTCAATTCTCTC
1 A-TTCTCTTTATTCTCTC
4573651 AAGATTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 2 0.06
18 29 0.94
ACGTcount: A:0.13, C:0.32, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTCTCTTTATTCTCTCC
Found at i:4573638 original size:9 final size:9
Alignment explanation
Indices: 4573596--4573652 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
4573586 CACTCAAGTC
4573596 CAATTCTCT
1 CAATTCTCT
**
4573605 TTATTCTCT
1 CAATTCTCT
*
4573614 CCATTCTCT
1 CAATTCTCT
**
4573623 TTATTCTCT
1 CAATTCTCT
*
4573632 CATTTCTCT
1 CAATTCTCT
4573641 CAATTCTCT
1 CAATTCTCT
4573650 CAA
1 CAA
4573653 GATTAGTTCC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.51
Consensus pattern (9 bp):
CAATTCTCT
Found at i:4576118 original size:88 final size:87
Alignment explanation
Indices: 4575955--4576195 Score: 227
Period size: 88 Copynumber: 2.7 Consensus size: 87
4575945 GTGCAACAAT
*
4575955 AATTTTTATTTTTAA-TTTTCTAGGATAAATATAATAATCACTATTTATTTTATTTCATTTTCAA
1 AATTTTT-TTTTTAATTTTTC-AGGAT-AATATAATAATCACAATTTA-TTTATTTCATTTTCAA
** ** *
4576019 GGCACTTGGGCTTGTGTCTGGTGCTG
62 GGCACCAGGGCTTGAATCTGGTACTG
***
4576045 -ATTTTTTTTTTAATTTTTCAGGATATATATAATAATCACAATTTATTTCATTTCATTTTTGGGG
1 AATTTTTTTTTTAATTTTTCAGGATA-ATATAATAATCACAATTTATTT-ATTTCATTTTCAAGG
* *
4576109 TACCAGGGCTTGAATCTTGTACTG
64 CACCAGGGCTTGAATCTGGTACTG
** * *
4576133 CAACTTTTTTTTAAAATTTTTCGGGATAATTATAATAACCA-ATATTTATTTATTTTCATTTTC
1 -AA-TTTTTTTTTTAATTTTTCAGGATAA-TATAATAATCACA-ATTTATTTA-TTTCATTTTC
4576196 GGAGGACTTC
Statistics
Matches: 126, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
87 4 0.03
88 59 0.47
89 11 0.09
90 4 0.03
91 48 0.38
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.50
Consensus pattern (87 bp):
AATTTTTTTTTTAATTTTTCAGGATAATATAATAATCACAATTTATTTATTTCATTTTCAAGGCA
CCAGGGCTTGAATCTGGTACTG
Found at i:4576276 original size:5 final size:5
Alignment explanation
Indices: 4576268--4576295 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4576258 ATAATCACTA
4576268 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4576296 TTGAGGTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:4576463 original size:90 final size:90
Alignment explanation
Indices: 4576278--4576650 Score: 372
Period size: 90 Copynumber: 4.2 Consensus size: 90
4576268 TTTATTTTAT
* * * * * * * *
4576278 TTTATTTTATTTTATTTTTTGAGGTACTTGGACTTGAGTTTGGTGTTGC-A-ATTTTTTT-AGTT
1 TTTATTTCATTTCATTTTCTG-GGAACTTGGGCTTGAGTATGGTGCTGCAATATTTTTTTAATTT
** *
4576340 TTACGAGATAATTATAATAATCACTG
65 TTTTGAGATAATTATAATAATCACTA
* *
4576366 TTTATTTCATTTCATTTTC-GAGGGACTTGGGCTTGAGTATGGTACTGCAATATTTTTTTAATTT
1 TTTATTTCATTTCATTTTCTG-GGAACTTGGGCTTGAGTATGGTGCTGCAATATTTTTTTAATTT
** *
4576430 TTTTGAGATGGTTATAATAATAACTA
65 TTTTGAGATAATTATAATAATCACTA
* * * *
4576456 TTTATTTCATTTCATTTTCTGGGCACTTGGACTTGAGTATGATGCTGTAA-ATTTTTTT-ATTTT
1 TTTATTTCATTTCATTTTCTGGGAACTTGGGCTTGAGTATGGTGCTGCAATATTTTTTTAATTTT
* *
4576519 TTTGAGACAATTATAAT-A-CATTA
66 TTTGAGATAATTATAATAATCACTA
* * *
4576542 TTTATTTCATTTCA-TTTCTGGGAAACTTGGGCTTGAGTTTGGGGCTGCAATGAATATTTTTAA-
1 TTTATTTCATTTCATTTTCTGGG-AACTTGGGCTTGAGTATGGTGCTGCAAT--ATTTTTTTAAT
*
4576605 TTTTTTGGGATAATTATAATAATCACTA
63 TTTTTTGAGATAATTATAATAATCACTA
*
4576633 TTT-TTTTAGTTTCATTTT
1 TTTATTTCA-TTTCATTTT
4576651 TGGTGTTTGA
Statistics
Matches: 236, Mismatches: 36, Indels: 22
0.80 0.12 0.07
Matches are distributed among these distances:
85 8 0.03
86 38 0.16
87 25 0.11
88 36 0.15
89 41 0.17
90 72 0.31
91 13 0.06
92 3 0.01
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (90 bp):
TTTATTTCATTTCATTTTCTGGGAACTTGGGCTTGAGTATGGTGCTGCAATATTTTTTTAATTTT
TTTGAGATAATTATAATAATCACTA
Found at i:4576575 original size:176 final size:178
Alignment explanation
Indices: 4575721--4576650 Score: 455
Period size: 177 Copynumber: 5.2 Consensus size: 178
4575711 CAATATAAAT
* *
4575721 ATAATAA-TATTTATTTTATTTCATTTTC-GAGGCACTTGGGCTTGAGTATGGTGCT-ACAATTT
1 ATAATAACTATTTATTTTATTTCATTTTCTGAGGCACTTGGACTTGAGTATGATGCTGA-AATTT
* * * * * * * *
4575783 TTTAAAATTTTATGAGATAATTATAATAAT---TA-CTA-TTCATTTCA-TTTCCAGGGTACTTA
65 TTT-TAGTTTTACGAGACAATTATAATAATCACTATTTATTTCATTTCATTTTCGA-GGAACTTG
* * * * * *
4575842 GGCTTGAGTCTGTTG-TTGCAATAA-ATTTTTTTATTTTTCGGGATAATTATA
128 GGCTTGAGTATG-GGACTGCAATAATA-TTTTTAATTTTTTGAGATAATTATA
* * * * * * * *
4575893 ATAATCATTATTTGTTTCATTTCATTTTCTTAGGTACTTGGACTTGAGTCT-AGTGC-AACAATA
1 ATAATAACTATTTATTTTATTTCATTTTCTGAGGCACTTGGACTTGAGTATGA-TGCTGA-AAT-
* * * * * * *
4575956 ATTTTTATTTTTAATTTTCTAGGATAAATATAATAATCACTATTTATTTTATTTCATTTTCAAGG
63 TTTTTTAGTTTT-A----CGA-GACAATTATAATAATCACTATTTATTTCATTTCATTTTCGAGG
* * * ** * *
4576021 CACTTGGGCTTGTGTCTGGTG-CTG--ATTTTTTTTTTAA-TTTTTCAGGAT-ATATATA
122 AACTTGGGCTTGAGTATGG-GACTGCAATAATATTTTTAATTTTTTGA-GATAAT-TATA
* * * * * ** * * * * *
4576076 ATAATCACAATTTATTTCATTTCATTTT-TGGGGTACCAGGGCTTGAATCTTG-TACTGCAACTT
1 ATAATAACTATTTATTTTATTTCATTTTCTGAGGCACTTGGACTTGAGT-ATGATGCTG-AA-AT
* * * * * *
4576139 TTTTTTAAAATTTTTCGGGATAATTATAATAACCAATATTTATTT-ATTTTCATTTTCGGAGG-A
63 TTTTTT--AGTTTTACGAGACAATTATAATAATCACTATTTATTTCA-TTTCATTTTC-GAGGAA
* * * * *** *
4576202 CTTCGGTTTGAGTCTGGCTG-CTACAATAAT-TCTTTTAATTTTCCAATATAAATATAATA
124 CTTGGGCTTGAGTATGG--GACTGCAATAATAT-TTTTAATTTTTTGAGAT-AAT-T-ATA
** * * * * * *
4576261 ATCACTATTTATTTTATTTTATTTTATTTTATTTTTTGAGGTACTTGGACTTGAGTTTGGTGTTG
1 AT-A--A--TA-ACTA-TTTATTTTATTTCATTTTCTGAGGCACTTGGACTTGAGTATGATGCTG
* * * *
4576326 CAATTTTTTTAGTTTTACGAGATAATTATAATAATCACTGTTTATTTCATTTCATTTTCGAGGGA
59 AAATTTTTTTAGTTTTACGAGACAATTATAATAATCACTATTTATTTCATTTCATTTTCGAGGAA
* * **
4576391 CTTGGGCTTGAGTATGGTACTGCAAT-ATTTTTTTAATTTTTTTGAGATGGTTATA
124 CTTGGGCTTGAGTATGGGACTGCAATAATATTTTTAA-TTTTTTGAGATAATTATA
*
4576446 ATAATAACTATTTATTTCATTTCATTTTCTG-GGCACTTGGACTTGAGTATGATGCTGTAAATTT
1 ATAATAACTATTTATTTTATTTCATTTTCTGAGGCACTTGGACTTGAGTATGATGCTG-AAATTT
* ** *
4576510 TTTTATTTTTTTGAGACAATTATAAT-A-CATTATTTATTTCATTTCA-TTTCTG-GGAAACTTG
65 TTTTAGTTTTACGAGACAATTATAATAATCACTATTTATTTCATTTCATTTTC-GAGG-AACTTG
* * *
4576571 GGCTTGAGTTTGGGGCTGCAATGAATATTTTTAATTTTTTGGGATAATTATA
128 GGCTTGAGTATGGGACTGCAAT-AATATTTTTAATTTTTTGAGATAATTATA
*
4576623 ATAATCACTATTT-TTTTAGTTTCATTTT
1 ATAATAACTATTTATTTTA-TTTCATTTT
4576651 TGGTGTTTGA
Statistics
Matches: 581, Mismatches: 119, Indels: 111
0.72 0.15 0.14
Matches are distributed among these distances:
172 6 0.01
173 19 0.03
174 30 0.05
175 11 0.02
176 46 0.08
177 59 0.10
178 55 0.09
179 52 0.09
180 24 0.04
181 1 0.00
182 34 0.06
183 53 0.09
184 9 0.02
185 43 0.07
186 7 0.01
187 9 0.02
188 19 0.03
189 56 0.10
190 2 0.00
191 8 0.01
192 20 0.03
193 18 0.03
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (178 bp):
ATAATAACTATTTATTTTATTTCATTTTCTGAGGCACTTGGACTTGAGTATGATGCTGAAATTTT
TTTAGTTTTACGAGACAATTATAATAATCACTATTTATTTCATTTCATTTTCGAGGAACTTGGGC
TTGAGTATGGGACTGCAATAATATTTTTAATTTTTTGAGATAATTATA
Found at i:4588226 original size:2 final size:2
Alignment explanation
Indices: 4588219--4588243 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4588209 TTGTGGTTGT
4588219 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 T
4588244 CAGCATTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4590623 original size:44 final size:44
Alignment explanation
Indices: 4590560--4590647 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
4590550 CAAATTATAC
4590560 AATGTATAAACATTGAGGTTAATTTTTTTAGAATCGGTACTAAA
1 AATGTATAAACATTGAGGTTAATTTTTTTAGAATCGGTACTAAA
4590604 AATGTATAAACATTGAGGTTAATTTTTTTAGAATCGGTACTAAA
1 AATGTATAAACATTGAGGTTAATTTTTTTAGAATCGGTACTAAA
4590648 TTGACATCGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (44 bp):
AATGTATAAACATTGAGGTTAATTTTTTTAGAATCGGTACTAAA
Found at i:4590885 original size:10 final size:10
Alignment explanation
Indices: 4590853--4590903 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
4590843 TGTATAATGA
4590853 TTTATTTTCC
1 TTTATTTTCC
* *
4590863 TTAACTTTCC
1 TTTATTTTCC
*
4590873 TTTATTTTAC
1 TTTATTTTCC
*
4590883 TTTCTTTTCC
1 TTTATTTTCC
4590893 TTTATTCTTCC
1 TTTATT-TTCC
4590904 CCTTTACTAC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
10 28 0.88
11 4 0.12
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTATTTTCC
Found at i:4591597 original size:7 final size:7
Alignment explanation
Indices: 4591585--4591609 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4591575 AATTAACATT
4591585 AAAATGA
1 AAAATGA
4591592 AAAATGA
1 AAAATGA
4591599 AAAATGA
1 AAAATGA
4591606 AAAA
1 AAAA
4591610 CAACCCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAATGA
Found at i:4598179 original size:22 final size:22
Alignment explanation
Indices: 4598154--4598203 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
4598144 CATACATTTT
*
4598154 ATTTAGTCTTT-TTTACTTTCG
1 ATTTAGTCTTTCTATACTTTCG
*
4598175 AATTTAGTCTTTCTATACTTTTG
1 -ATTTAGTCTTTCTATACTTTCG
4598198 ATTTAG
1 ATTTAG
4598204 CAATTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (22 bp):
ATTTAGTCTTTCTATACTTTCG
Found at i:4601531 original size:31 final size:30
Alignment explanation
Indices: 4601479--4601536 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
4601469 ATAAAAAAGG
**
4601479 TATAAAATTATTAAATGTTAAAATAATATAA
1 TATAAAATTATTAAAAATTAAAA-AATATAA
4601510 TATAAATATT-TTAAAAATTAAAAAATA
1 TATAAA-ATTATTAAAAATTAAAAAATA
4601537 ATATGGGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.17
31 17 0.71
32 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
TATAAAATTATTAAAAATTAAAAAATATAA
Found at i:4603318 original size:15 final size:15
Alignment explanation
Indices: 4603298--4603350 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
4603288 TGACTAATTT
*
4603298 AAAATAAAAATTTTA
1 AAAATAAAAATTATA
*
4603313 AAAATAAATATTATA
1 AAAATAAAAATTATA
4603328 AAAA-AATAGATATTATA
1 AAAATAA-A-A-ATTATA
4603345 AAAATA
1 AAAATA
4603351 TTGATTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.06
15 18 0.58
17 10 0.32
18 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
AAAATAAAAATTATA
Found at i:4603334 original size:17 final size:17
Alignment explanation
Indices: 4603312--4603348 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
4603302 TAAAAATTTT
4603312 AAAAATAAATATTATAA
1 AAAAATAAATATTATAA
*
4603329 AAAAATAGATATTATAA
1 AAAAATAAATATTATAA
4603346 AAA
1 AAA
4603349 TATTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAATATTATAA
Found at i:4605766 original size:31 final size:31
Alignment explanation
Indices: 4605728--4605828 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 31
4605718 TTAATAGAAC
4605728 ATTTGGTACCTCAACTTGACACGTTTTCTTA
1 ATTTGGTACCTCAACTTGACACGTTTTCTTA
* * ** * *
4605759 ATTTGGTACCTAAAGTT----TTTTTTGTCCA
1 ATTTGGTACCTCAACTTGACACGTTTTCT-TA
*
4605787 ATTTGGGACCTCAACTTGACACGTTTTCTTA
1 ATTTGGTACCTCAACTTGACACGTTTTCTTA
4605818 ATTTGGTACCT
1 ATTTGGTACCT
4605829 AAAGCTTAAT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
27 5 0.10
28 15 0.29
31 26 0.51
32 5 0.10
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTCAACTTGACACGTTTTCTTA
Found at i:4606390 original size:60 final size:60
Alignment explanation
Indices: 4606229--4606392 Score: 170
Period size: 60 Copynumber: 2.7 Consensus size: 60
4606219 TAAAAAATTT
* * *
4606229 AAGTACCAAATT-GTACCTAAAAAAAACTTAGGTACCAAATTAGGAAAAAAATACCAAGTTC
1 AAGTACCAAATTGGGA-C-AAAAAAAATTTAGGTACCAAATTAAGAAAAAAATACCAAGTTC
* * ** * **
4606290 AAGTACCAAATTGGGACCAAAAAAGTTTAGGTAAATAAATTAAG-AAAAAGTGTCAAGTTC
1 AAGTACCAAATTGGGACAAAAAAAATTTAGGT-ACCAAATTAAGAAAAAAATACCAAGTTC
* *
4606350 AAGTATCAAATTGGGACAAAAAAAATATTAAGTACCAAATTAA
1 AAGTACCAAATTGGGACAAAAAAAAT-TTAGGTACCAAATTAA
4606393 AAATATTATA
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
60 56 0.67
61 26 0.31
62 2 0.02
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.23
Consensus pattern (60 bp):
AAGTACCAAATTGGGACAAAAAAAATTTAGGTACCAAATTAAGAAAAAAATACCAAGTTC
Found at i:4615918 original size:164 final size:164
Alignment explanation
Indices: 4615642--4615968 Score: 489
Period size: 164 Copynumber: 2.0 Consensus size: 164
4615632 AAATCAAGAA
* * *
4615642 CAAAACTAGGTGCGGAAATGTACTTGAATTCATCGATTTCTTGAAATTTATGGATTTTGAGGTTT
1 CAAAACTAGATGCGGAAACGTACTTGAATTCATCGATTTCTTGAAATTTATGGATCTTGAGGTTT
* * *
4615707 TAATCTTCCAAATTAGCACACAAGTAATCTAGAGAAGATGACTCTCTCTTTTCTAAAGATGGGAT
66 TAATCTTCCAAATTAACACACAAGTAATCTAGAAAAGATGACTCTCTCTTTTCTAAAGATGAGAT
* *
4615772 ATTAGAAAAGTTATCTTGTGTGTAATTTGGGGAC
131 ATTAGAAAAGTTACCTTGTGTGTAATTTAGGGAC
* *
4615806 CAAAACTAGATGCGGAAGCGTA-TCTGAATTCATCGATTTCTTGAAATTTATGGATCTTGGGGTT
1 CAAAACTAGATGCGGAAACGTACT-TGAATTCATCGATTTCTTGAAATTTATGGATCTTGAGGTT
* * *
4615870 TTGATCTTCCAAATTAACACTA-AAGTAATCTAGAAAAGGT-AGCTCTCTCTTTTTTAAAGATGA
65 TTAATCTTCCAAATTAACAC-ACAAGTAATCTAGAAAAGATGA-CTCTCTCTTTTCTAAAGATGA
4615933 GATATTAGAAAAGTTACCTTGTGTGTAATTTAGGGA
128 GATATTAGAAAAGTTACCTTGTGTGTAATTTAGGGA
4615969 ACATAACCTT
Statistics
Matches: 147, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
163 2 0.01
164 144 0.98
165 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (164 bp):
CAAAACTAGATGCGGAAACGTACTTGAATTCATCGATTTCTTGAAATTTATGGATCTTGAGGTTT
TAATCTTCCAAATTAACACACAAGTAATCTAGAAAAGATGACTCTCTCTTTTCTAAAGATGAGAT
ATTAGAAAAGTTACCTTGTGTGTAATTTAGGGAC
Found at i:4621868 original size:14 final size:14
Alignment explanation
Indices: 4621851--4621883 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4621841 TTTATATCAA
4621851 ATTAAAGTATAAAT
1 ATTAAAGTATAAAT
*
4621865 ATTAAATTATAAAT
1 ATTAAAGTATAAAT
4621879 -TTAAA
1 ATTAAA
4621884 CAGAATAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
ATTAAAGTATAAAT
Found at i:4622713 original size:20 final size:20
Alignment explanation
Indices: 4622690--4622731 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4622680 AGGTGAATTG
*
4622690 TTTTT-TTATTTATTTTTGA
1 TTTTTCTTATTTATTTTTCA
4622709 TTTTTCTTATTTATTTTTCA
1 TTTTTCTTATTTATTTTTCA
4622729 TTT
1 TTT
4622732 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTCTTATTTATTTTTCA
Found at i:4623296 original size:3 final size:3
Alignment explanation
Indices: 4623290--4623334 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
4623280 TTTTAACTGT
4623290 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4623335 AACATACATG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4623416 original size:2 final size:2
Alignment explanation
Indices: 4623404--4623491 Score: 62
Period size: 2 Copynumber: 46.0 Consensus size: 2
4623394 ATGGTTTTTA
* *
4623404 AT AT A- AT AT AT AT AT AT AT AT AT AT AC AT AT AT TT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
4623446 -T CAC AT A- AT GT -T TT CT -T AT AT A- AT AT AT AT AT AT AT AT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4623484 AT AT AT AT
1 AT AT AT AT
4623492 GCATGTTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
1 6 0.09
2 62 0.89
3 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4625121 original size:16 final size:16
Alignment explanation
Indices: 4625100--4625130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4625090 TATTTTGTTT
4625100 TGATTGCATGACATCA
1 TGATTGCATGACATCA
*
4625116 TGATTGCATTACATC
1 TGATTGCATGACATC
4625131 TGTATCTTAG
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:0.19, G:0.16, T:0.35
Consensus pattern (16 bp):
TGATTGCATGACATCA
Found at i:4625527 original size:13 final size:13
Alignment explanation
Indices: 4625509--4625534 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4625499 GAAGAGATTT
4625509 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
4625522 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
4625535 AAAATTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:4625605 original size:19 final size:20
Alignment explanation
Indices: 4625568--4625607 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4625558 TCTTTTCGCA
* *
4625568 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
4625588 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
4625607 T
1 T
4625608 AAACACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:4627494 original size:19 final size:19
Alignment explanation
Indices: 4627470--4627509 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4627460 GCAAATGTTC
4627470 TTTCATTCTTTACGATTTT
1 TTTCATTCTTTACGATTTT
**
4627489 TTTCATTCTTTTGGATTTT
1 TTTCATTCTTTACGATTTT
4627508 TT
1 TT
4627510 CTGCCAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.68
Consensus pattern (19 bp):
TTTCATTCTTTACGATTTT
Found at i:4628491 original size:7 final size:7
Alignment explanation
Indices: 4628466--4628507 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
4628456 AGTGATGTGA
4628466 AAAAATG
1 AAAAATG
4628473 AAAAGATG
1 AAAA-ATG
4628481 -AAAATG
1 AAAAATG
4628487 AAAAATG
1 AAAAATG
4628494 AAAAA-G
1 AAAAATG
4628500 TAAAAATG
1 -AAAAATG
4628508 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:4628505 original size:21 final size:21
Alignment explanation
Indices: 4628466--4628507 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4628456 AGTGATGTGA
*
4628466 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
4628487 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
4628508 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:4630406 original size:44 final size:43
Alignment explanation
Indices: 4629951--4630412 Score: 227
Period size: 44 Copynumber: 10.5 Consensus size: 43
4629941 CCATTAATTC
* * *
4629951 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGCAGTGGAATAGATTGAAG-CTACAGATCT
* * * * *
4629995 TATCTCCCTAGACAGTAGTGGAGTAGATCGAATG-TGACAGATTT
1 TATCTCCCTAGGCAGCAGTGGAATAGATTGAA-GCT-ACAGATCT
* * * *
4630039 TACCTCCCTGAGGTTA-CAGTGGAGTACATTGAAGC--CAGTAAT-T
1 TATCTCCCT-AGG-CAGCAGTGGAATAGATTGAAGCTACAG--ATCT
*
4630082 CTATCTCCCTAGGCAGCAGTGGAATATATTGAAGACTACAGATCT
1 -TATCTCCCTAGGCAGCAGTGGAATAGATTGAAG-CTACAGATCT
* * * * * * * * *
4630127 TATCTCCCTAAGTAGTAGTGGAACAGA-TCAAGGATGGCGGATTT
1 TATCTCCCTAGGCAGCAGTGGAATAGATTGAA-GCT-ACAGATCT
* * * *
4630171 TACCTCCCTAAGGTTA-CAGTGGAGTACATTGAAGC--CAGTAAT-T
1 TATCTCCCT-AGG-CAGCAGTGGAATAGATTGAAGCTACAG--ATCT
* *
4630214 CTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTATAGATCT
1 -TATCTCCCTAGGCAGCAGTGGAATAGATTGAAG-CTACAGATCT
* * * * *
4630259 TATCTCCCT-GGACAGTAGTGGAGTAGATCGAATG-TGGCAGATTT
1 TATCTCCCTAGG-CAGCAGTGGAATAGATTGAA-GCT-ACAGATCT
* * * *
4630303 TACCTCCCTGAGGTTA-CAGTGGAGTATATTGAAGC--CAGTAAT-T
1 TATCTCCCT-AGG-CAGCAGTGGAATAGATTGAAGCTACAG--ATCT
*
4630346 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGACTACAGATCT
1 -TATCTCCCTAGGCAGCAGTGGAATAGATTGAAG-CTACAGATCT
*
4630391 TATCTCCCTAAGCAGCAGTGGA
1 TATCTCCCTAGGCAGCAGTGGA
4630413 GCAGATCAAA
Statistics
Matches: 317, Mismatches: 61, Indels: 80
0.69 0.13 0.17
Matches are distributed among these distances:
42 11 0.03
43 67 0.21
44 176 0.56
45 46 0.15
46 17 0.05
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (43 bp):
TATCTCCCTAGGCAGCAGTGGAATAGATTGAAGCTACAGATCT
Found at i:4630523 original size:132 final size:132
Alignment explanation
Indices: 4629769--4630512 Score: 1102
Period size: 132 Copynumber: 5.6 Consensus size: 132
4629759 GGTAGATAGT
*
4629769 GGATTTTACCTTCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGCA
1 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCA
* * *
4629833 ACAGTGGAATAGATGGAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAAAT
65 ACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
*
4629898 GGT
130 GGC
* *
4629901 GGATTTTACCTCCCTGAGGTTACAGTAGAGTACATTGAAGCCATTAATTCTATCTCCCTGGGCAA
1 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAA
* *
4629966 CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCT-AGACAGTAGTGGAGTAGATCGAATG-
66 CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATC-AAAGA
*
4630029 TGAC
129 TGGC
* * *
4630033 AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAG
1 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAA
* * * * *
4630098 CAGTGGAATATATTGAAGACTACAGATCTTATCTCCCTAAGTAGTAGTGGAACAGATCAAGGATG
66 CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
4630163 GC
131 GC
* * *
4630165 GGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAG
1 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAA
* * * *
4630230 CAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCT-GGACAGTAGTGGAGTAGATCGAATG-
66 CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATC-AAAGA
4630293 TGGC
129 TGGC
* * *
4630297 AGATTTTACCTCCCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
1 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAA
* *
4630362 CAGTGGAATAGATTGAAGACTACAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGATG
66 CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
4630427 GC
131 GC
* * *
4630429 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTTCTTGGGCAA
1 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAA
*
4630494 CAGTGGAATAGATCGAAGA
66 CAGTGGAATAGATTGAAGA
4630513 AAGCAGATCT
Statistics
Matches: 554, Mismatches: 49, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
131 9 0.02
132 536 0.97
133 9 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAA
CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
GC
Found at i:4630523 original size:264 final size:264
Alignment explanation
Indices: 4629770--4630512 Score: 1245
Period size: 264 Copynumber: 2.8 Consensus size: 264
4629760 GTAGATAGTG
* *
4629770 GATTTTACCTTCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGCAA
1 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAG
* * *
4629834 CAGTGGAATAGATGGAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAAATG
65 CAGTGGAATAGATTGAAGACTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGATG
* * *
4629899 GTGGATTTTACCTCCCTGAGGTTACAGTAGAGTACATTGAAGCCATTAATTCTATCTCCCTGGGC
130 GCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGC
4629964 AACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGACAGTAGTGGAGTAGATCGAATG
195 AACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGACAGTAGTGGAGTAGATCGAATG
4630029 TGACA
260 TGACA
*
4630034 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAGC
1 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
* * *
4630099 AGTGGAATATATTGAAGACTACAGATCTTATCTCCCTAAGTAGTAGTGGAACAGATCAAGGATGG
66 AGTGGAATAGATTGAAGACTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGATGG
* *
4630164 CGGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCA
131 CGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
* * *
4630229 GCAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCTGGACAGTAGTGGAGTAGATCGAATGT
196 ACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGACAGTAGTGGAGTAGATCGAATGT
*
4630294 GGCA
261 GACA
*
4630298 GATTTTACCTCCCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
1 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
* *
4630363 AGTGGAATAGATTGAAGACTACAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGATGG
66 AGTGGAATAGATTGAAGACTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGATGG
* * *
4630428 CGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTTCTTGGGCA
131 CGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
*
4630493 ACAGTGGAATAGATCGAAGA
196 ACAGTGGAATAGATTGAAGA
4630513 AAGCAGATCT
Statistics
Matches: 446, Mismatches: 32, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
264 445 1.00
265 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (264 bp):
GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
AGTGGAATAGATTGAAGACTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGATGG
CGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
ACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGACAGTAGTGGAGTAGATCGAATGT
GACA
Found at i:4631657 original size:12 final size:12
Alignment explanation
Indices: 4631635--4631664 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
4631625 ATTTTCGAAG
4631635 CAAACAAAAAAAA
1 CAAA-AAAAAAAA
4631648 CAAAAAAAAAAA
1 CAAAAAAAAAAA
4631660 CAAAA
1 CAAAA
4631665 GATTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:4636977 original size:42 final size:41
Alignment explanation
Indices: 4636840--4637001 Score: 164
Period size: 42 Copynumber: 3.9 Consensus size: 41
4636830 AGCTCGTACA
* * * * *
4636840 ATGCCAACGTCTCAGACGTGGTCTTACATGTAATCACATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAA-CACA-ATCG
* * * * *
4636883 ATGCCACTGTCCCAAACAGGGTCTTATACGAAACA-AATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAACACAAT-CG
4636924 ATGCCAATGTCCCAGACATGGTCTTACACGTAACACAAGTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAACACAA-TCG
* *
4636966 ATGCCAATGTCCTAGACGTGGTCTTACACGATAACA
1 ATGCCAATGTCCCAGACATGGTCTTACACG-TAACA
4637002 TATACCGAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
40 2 0.02
41 32 0.33
42 34 0.35
43 30 0.31
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAACACAATCG
Found at i:4661106 original size:15 final size:17
Alignment explanation
Indices: 4661076--4661108 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
4661066 TGACAAAAGA
4661076 AAAATAAGACAAAAACC
1 AAAATAAGACAAAAACC
4661093 AAAA-AAGA-AAAAACC
1 AAAATAAGACAAAAACC
4661108 A
1 A
4661109 CGTGTTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.76, C:0.15, G:0.06, T:0.03
Consensus pattern (17 bp):
AAAATAAGACAAAAACC
Found at i:4661249 original size:17 final size:17
Alignment explanation
Indices: 4661224--4661258 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4661214 ACATATTTGG
4661224 TATAAATTTTAAAATGA
1 TATAAATTTTAAAATGA
* *
4661241 TATATATTTTAAAGTGA
1 TATAAATTTTAAAATGA
4661258 T
1 T
4661259 GCATAATTTT
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:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (17 bp):
TATAAATTTTAAAATGA
Found at i:4661269 original size:18 final size:16
Alignment explanation
Indices: 4661228--4661270 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
4661218 ATTTGGTATA
4661228 AATTTTAAAATGATAT
1 AATTTTAAAATGATAT
*
4661244 ATATTTTAAAGTGATGCAT
1 A-ATTTTAAAATGAT--AT
4661263 AATTTTAA
1 AATTTTAA
4661271 TTTAATCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 12 0.52
18 7 0.30
19 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (16 bp):
AATTTTAAAATGATAT
Found at i:4667146 original size:55 final size:55
Alignment explanation
Indices: 4667052--4667176 Score: 178
Period size: 55 Copynumber: 2.3 Consensus size: 55
4667042 TAGACGTGCT
*
4667052 ACATAACAATCGATTTAAACATATAAACAATCTACTCAAAAGAAGCAACATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGACTCAAAAGAAGCAACATTCCA
* * * * * *
4667107 ACATAACAATTGATTTAAACGTATAAATAATCGATTCAAAAGAAGCAGCATTTCA
1 ACATAACAATCGATTTAAACATATAAACAATCGACTCAAAAGAAGCAACATTCCA
*
4667162 ACATAAAAATCGATT
1 ACATAACAATCGATT
4667177 CAAAAGAAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.25
Consensus pattern (55 bp):
ACATAACAATCGATTTAAACATATAAACAATCGACTCAAAAGAAGCAACATTCCA
Found at i:4667454 original size:35 final size:35
Alignment explanation
Indices: 4667408--4667477 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
4667398 CTTGGCCCTC
*
4667408 TCAACGCTCCTCCTACTACTGCCTTTTCTCTGCTT
1 TCAACACTCCTCCTACTACTGCCTTTTCTCTGCTT
*
4667443 TCAACACTCCTCCTACTATTGCCTTTTCTCTGCTT
1 TCAACACTCCTCCTACTACTGCCTTTTCTCTGCTT
4667478 GTTGATATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.13, C:0.39, G:0.07, T:0.41
Consensus pattern (35 bp):
TCAACACTCCTCCTACTACTGCCTTTTCTCTGCTT
Found at i:4670745 original size:41 final size:41
Alignment explanation
Indices: 4670662--4670763 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
4670652 TGATTTAGTA
4670662 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAGATATTT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAGATATTT
*
4670703 CACCGGCATTAAGCCTGCTAGACATATAGTCTGA-AGTGTTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAGA-TATTT
* * *
4670744 CACTGGCAATAAGCTTGCTA
1 CACCGGCATTAAGCCTGCTA
4670764 AGCACTATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
40 3 0.05
41 52 0.95
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAGATATTT
Found at i:4672448 original size:13 final size:13
Alignment explanation
Indices: 4672430--4672455 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4672420 CAATCAAATG
4672430 CACACAAAATAAT
1 CACACAAAATAAT
4672443 CACACAAAATAAT
1 CACACAAAATAAT
4672456 ATTAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
CACACAAAATAAT
Found at i:4675015 original size:26 final size:25
Alignment explanation
Indices: 4674996--4675072 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 25
4674986 ATATCACATG
*
4674996 CATGCTC-ACATAACAGATATTAAA
1 CATGCTCAACATAACAGATATCAAA
*
4675020 CATGCTCATACATAACAGATATTAAA
1 CATGCTCA-ACATAACAGATATCAAA
4675046 CATGCTCATACATAACAG--ATCAAA
1 CATGCTCA-ACATAACAGATATCAAA
4675070 CAT
1 CAT
4675073 ATAACATCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
24 15 0.30
26 35 0.70
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (25 bp):
CATGCTCAACATAACAGATATCAAA
Found at i:4679722 original size:29 final size:29
Alignment explanation
Indices: 4679680--4679741 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
4679670 CCCGTAAGTT
4679680 AGGACACAATGTCTTGAATTTCCAATACG
1 AGGACACAATGTCTTGAATTTCCAATACG
4679709 AGGACACAATGTCTTGAATTTCCAATACG
1 AGGACACAATGTCTTGAATTTCCAATACG
4679738 AGGA
1 AGGA
4679742 TAAACACCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (29 bp):
AGGACACAATGTCTTGAATTTCCAATACG
Found at i:4680244 original size:3 final size:3
Alignment explanation
Indices: 4680236--4680305 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
4680226 ATTAAAAGTG
4680236 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4680284 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
4680306 CGATGATTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4681198 original size:21 final size:21
Alignment explanation
Indices: 4681172--4681214 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4681162 ATATTTCAAA
4681172 ATGAAA-AAAAGAAAAAAAATG
1 ATGAAATAAAA-AAAAAAAATG
*
4681193 ATGAAATAAAAAAATAAAATG
1 ATGAAATAAAAAAAAAAAATG
4681214 A
1 A
4681215 GAGAACCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (21 bp):
ATGAAATAAAAAAAAAAAATG
Found at i:4682093 original size:143 final size:143
Alignment explanation
Indices: 4681860--4682483 Score: 872
Period size: 143 Copynumber: 4.4 Consensus size: 143
4681850 AATAAGATTG
* * * *
4681860 GTGGCTTTAATCTGCTCTATTGTAA-TCTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAA
1 GTGGCTTCAATCTGCTCCACTGCAACT-TCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAA
* * *
4681924 TCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGTTGTCTTTAGTCTACTCCGCTGCAACTTCT
65 TCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTACTCCGCTGCAACTTCA
*
4681989 GGGATATAAGGCTA
130 GGGAGATAAGGCTA
* * * * * *
4682003 GTGGCTTCAATTTGCTCCACTGCAACTTTATGAAGAAAAAATTCGCCATAATTTGTTGCTTTAAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAAT
* * *
4682068 CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCGCTGCAACTTCAG
66 CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTACTCCGCTGCAACTTCAG
* *
4682133 GGGGATAAGGCTG
131 GGAGATAAGGCTA
* * *
4682146 GTGGCTTTAATCTGTTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAAT
* ** ** * * *
4682211 ATGTTCCGTTGCAACGTTAAGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCGCTGCAACTTTAG
66 CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTACTCCGCTGCAACTTCAG
*
4682276 GGAGATAAGGCTG
131 GGAGATAAGGCTA
* * * *
4682289 GTGGCTTTAATCTGCTCCATTGCAACTTCAGGAAGATAAGATTCACCATAATTTGTGGCTTTAAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAAT
* * *
4682354 CTATTCCGCTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTACTCTGCTGCAACTTCAG
66 CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTACTCCGCTGCAACTTCAG
4682419 GGAGATAAGGCTA
131 GGAGATAAGGCTA
* *
4682432 GTGGCTTCAATCTGCTCCACTGTAACTTCAGGAAGATAAGATTTGCCATAAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAAT
4682484 GACTTCAATC
Statistics
Matches: 422, Mismatches: 58, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
143 421 1.00
144 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (143 bp):
GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAAT
CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTACTCCGCTGCAACTTCAG
GGAGATAAGGCTA
Found at i:4682184 original size:44 final size:44
Alignment explanation
Indices: 4682112--4682471 Score: 139
Period size: 44 Copynumber: 7.7 Consensus size: 44
4682102 CTATCTTCAG
**
4682112 TCTGCTCCGCTGCAACTTCAGGGGGATAAGGCTGGTGGCTTTAA
1 TCTGCTCCGCTGCAACTTCAGGAAGATAAGGCTGGTGGCTTTAA
* * * *
4682156 TCTGTTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAA
1 TCTGCTCCGCTGCAACTTCAGGAAGATAAG----G-C-----TGGTGGCTTTAA
* * * * ** * * * *
4682210 TATGTTCCGTTGCAACGTTAAGGAA-ATAAGATTCGTTGTCTTCAG
1 TCTGCTCCGCTGCAAC-TTCAGGAAGATAAGGCT-GGTGGCTTTAA
* *
4682255 TCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTTAA
1 TCTGCTCCGCTGCAACTTCAGGAAGATAAGGCTGGTGGCTTTAA
** * *
4682299 TCTGCTCCATTGCAACTTCAGGAAGATAAGATTCACCATAATTTGTGGCTTTAA
1 TCTGCTCCGCTGCAACTTCAGGAAGATAAG-----GC-----TGGTGGCTTTAA
** ** ** * * * *
4682353 TCTATTCCGCTGCAACGCCAGGGAA-ATAAGATTCGTTGTCTTCAG
1 TCTGCTCCGCTGCAACTTCA-GGAAGATAAGGCT-GGTGGCTTTAA
* * * * *
4682398 TCTACTCTGCTGCAACTTCAGGGAGATAAGGCTAGTGGCTTCAA
1 TCTGCTCCGCTGCAACTTCAGGAAGATAAGGCTGGTGGCTTTAA
* *
4682442 TCTGCTCCACTGTAACTTCAGGAAGATAAG
1 TCTGCTCCGCTGCAACTTCAGGAAGATAAG
4682472 ATTTGCCATA
Statistics
Matches: 226, Mismatches: 64, Indels: 52
0.66 0.19 0.15
Matches are distributed among these distances:
44 102 0.45
45 52 0.23
48 1 0.00
49 2 0.01
54 58 0.26
55 11 0.05
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (44 bp):
TCTGCTCCGCTGCAACTTCAGGAAGATAAGGCTGGTGGCTTTAA
Found at i:4687943 original size:9 final size:9
Alignment explanation
Indices: 4687929--4687973 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
4687919 AGTGATAATG
4687929 ATAAAAATA
1 ATAAAAATA
4687938 ATAAAAAT-
1 ATAAAAATA
4687946 -TAAAAA-A
1 ATAAAAATA
4687953 A-AAAAATA
1 ATAAAAATA
*
4687961 ATAATAATA
1 ATAAAAATA
4687970 ATAA
1 ATAA
4687974 CAACAACAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
7 11 0.35
8 2 0.06
9 18 0.58
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
ATAAAAATA
Found at i:4690889 original size:469 final size:467
Alignment explanation
Indices: 4690009--4690917 Score: 1333
Period size: 469 Copynumber: 1.9 Consensus size: 467
4689999 CGAATCTACC
* * * *
4690009 TTAAGATCACTAATTCGAGTTTCAAACAAAGGAAAAAAATTTGGAGAAAACTCTCTTCTATACTC
1 TTAAGATCACTAATTCGAGTTTCAAACAAAGCAAAAAAATCTAGAGAAAACTCGCTTCTATACTC
*
4690074 CTTTAAAAAATTGTGAAAATGAGGGTGTCCACACCCCTGATAGTTTGAAAATAAAAAAGAAAAAA
66 CTTTAAAAAATTGTGAAAATGAGGGTGTCCACACCCCTGACAGTTTGAAAATAAAAAAGAAAAAA
* * *
4690139 TTGAAATCCACCATCATTAGATAAAAAAAATGAAGAAATATACTTTTACCATTAAAATCATGCAG
131 TTAAAATCCACCATCATCAGATAAAAAAAATGAAGAAATATACTTTTACCATTAAAATCATGCAA
** * *
4690204 CCTTTGCATCCACTAGAAATTCATCCTCTGAGCCCTCAACATCGACAACATTCCCCATCATCGCC
196 CCTCCGAATCCACTAAAAATTCATCCTCTGAGCCCTCAACATCGACAACATTCCCCATCATCGCC
* * *
4690269 ATATCTTCCTCAACCTCACAATTCAACCCTTGTATAATATCTTCTATTTCCCCCACCATTGACAC
261 ATATCTTCCCCAACCTCACAATTCAACCCTTGTATAATATCTTCTATTGCCCCCACCACTGACAC
* *
4690334 TGAACGTTGCTCACTTTCTAACATGTTCATCAGCTATTGGCCCATGTTATCACCCATCCCACTTC
326 TGAACGCTGCTCACTTTCCAACATGTTCATCAGCTATTGGCCCATGTTATCACCCATCCCACTTC
* * *
4690399 TTGCCTCATCATCTGGCCTTTGCCCAAAATTT-TCTCCCATTTTATTTTGCGAATCTGAAACTCG
391 TTGCCTCATCATCTAGCCTTTGCCCAAAATTTCCCT-CCATTTTAGTTTGCGAATCTGAAACTCG
4690463 GGAGCATTGGCCA
455 GGAGCATTGGCCA
4690476 TTAAGATCACTAATTCGAGTTTCAAACAAAGCAAAAAAATCTAGAGAAAACTCGCTTCTATACTC
1 TTAAGATCACTAATTCGAGTTTCAAACAAAGCAAAAAAATCTAGAGAAAACTCGCTTCTATACTC
* *
4690541 CTTTAAAAAATTGTGAAAAT-AGGGGTGTCCACACCCCTGACAGTTTGAAAATATAAAATAAAAA
66 CTTTAAAAAATTGTGAAAATGA-GGGTGTCCACACCCCTGACAGTTTGAAAATAAAAAAGAAAAA
* *** * * *
4690605 A-TAAAATCCACCATTATCAGATAAATTTTTTATTGAAGAAATCTACTTTTACCATTGAAATCAT
130 ATTAAAATCCACCATCATCAGATAAA---AAAAATGAAGAAATATACTTTTACCATTAAAATCAT
*
4690669 GCAACCTCCGAATCCACTAAAAATTCATCCTCTGAGCCCTCAACATCGACAACATTCCCCGTCAT
192 GCAACCTCCGAATCCACTAAAAATTCATCCTCTGAGCCCTCAACATCGACAACATTCCCCATCAT
** *
4690734 CGCCATATCTTCCCCAACCTCATGATTCAGCCCTTGTATAATATCTTCTATTGCCCCCACCACTG
257 CGCCATATCTTCCCCAACCTCACAATTCAACCCTTGTATAATATCTTCTATTGCCCCCACCACTG
* * ** * * *
4690799 ACACTGAAGGCTGCTCACTTTCCGACA-GTTTTGTCAGTTCTTGGCCCATGTTATCACCCATTCC
322 ACACTGAACGCTGCTCACTTTCCAACATG-TTCATCAGCTATTGGCCCATGTTATCACCCATCCC
** *
4690863 GTTTCCTT-CCTCATCATCTAGCCTTTGCCTAAAATTTCCCTCCATTTTAGTTTGC
386 ACTT-CTTGCCTCATCATCTAGCCTTTGCCCAAAATTTCCCTCCATTTTAGTTTGC
4690918 AAATTTAAAA
Statistics
Matches: 392, Mismatches: 43, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
466 22 0.06
467 121 0.31
468 1 0.00
469 243 0.62
470 5 0.01
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.30
Consensus pattern (467 bp):
TTAAGATCACTAATTCGAGTTTCAAACAAAGCAAAAAAATCTAGAGAAAACTCGCTTCTATACTC
CTTTAAAAAATTGTGAAAATGAGGGTGTCCACACCCCTGACAGTTTGAAAATAAAAAAGAAAAAA
TTAAAATCCACCATCATCAGATAAAAAAAATGAAGAAATATACTTTTACCATTAAAATCATGCAA
CCTCCGAATCCACTAAAAATTCATCCTCTGAGCCCTCAACATCGACAACATTCCCCATCATCGCC
ATATCTTCCCCAACCTCACAATTCAACCCTTGTATAATATCTTCTATTGCCCCCACCACTGACAC
TGAACGCTGCTCACTTTCCAACATGTTCATCAGCTATTGGCCCATGTTATCACCCATCCCACTTC
TTGCCTCATCATCTAGCCTTTGCCCAAAATTTCCCTCCATTTTAGTTTGCGAATCTGAAACTCGG
GAGCATTGGCCA
Found at i:4692532 original size:11 final size:12
Alignment explanation
Indices: 4692511--4692545 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
4692501 TAATAAATTT
4692511 TTTATGAATTTTG
1 TTTAT-AATTTTG
4692524 TTTAT-ATTTTG
1 TTTATAATTTTG
4692535 TTTATAATTTT
1 TTTATAATTTT
4692546 TAATAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
12 5 0.24
13 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (12 bp):
TTTATAATTTTG
Found at i:4697856 original size:17 final size:17
Alignment explanation
Indices: 4697834--4697871 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
4697824 CCAGGTGTTC
*
4697834 ATTTTCTTGAAAGAATA
1 ATTTTCTTCAAAGAATA
4697851 ATTTTCTTCAAAGAATA
1 ATTTTCTTCAAAGAATA
4697868 ATTT
1 ATTT
4697872 GGGTTCGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (17 bp):
ATTTTCTTCAAAGAATA
Found at i:4698994 original size:15 final size:15
Alignment explanation
Indices: 4698970--4698999 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4698960 ACACATTATA
*
4698970 TTCTATATATATAGT
1 TTCTAAATATATAGT
4698985 TTCTAAATATATAGT
1 TTCTAAATATATAGT
4699000 ATGCTAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (15 bp):
TTCTAAATATATAGT
Found at i:4699550 original size:21 final size:21
Alignment explanation
Indices: 4699521--4699575 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
4699511 AATTCTAAAA
*
4699521 TTTAA-AATTTTTATAGCTTT
1 TTTAATAATTTTTATAGATTT
* *
4699541 TTT-ATGAATTTTTTTATATTT
1 TTTAAT-AATTTTTATAGATTT
4699562 TTTAATAATTTTTA
1 TTTAATAATTTTTA
4699576 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 22 0.79
22 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAATAATTTTTATAGATTT
Found at i:4699561 original size:10 final size:11
Alignment explanation
Indices: 4699528--4699574 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
4699518 AAATTTAAAA
**
4699528 TTTTTATAGCT
1 TTTTTATAATT
4699539 TTTTTATGAATT
1 TTTTTAT-AATT
4699551 TTTTTAT-ATT
1 TTTTTATAATT
*
4699561 TTTTAATAATT
1 TTTTTATAATT
4699572 TTT
1 TTT
4699575 AAAATTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 9 0.29
11 13 0.42
12 9 0.29
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:4716302 original size:19 final size:21
Alignment explanation
Indices: 4716258--4716302 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
4716248 TTGTGTTATC
* *
4716258 GAAATCATTGTATATGAATAT
1 GAAATAATTGTATATAAATAT
4716279 G-AATAATTG-ATATAAAT-T
1 GAAATAATTGTATATAAATAT
4716297 GAAATA
1 GAAATA
4716303 TTTAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 2 0.10
19 11 0.52
20 7 0.33
21 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (21 bp):
GAAATAATTGTATATAAATAT
Found at i:4719880 original size:20 final size:19
Alignment explanation
Indices: 4719852--4719890 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4719842 TAACTAAAAT
*
4719852 GTAAACTTACTAATAGTTTA
1 GTAAACTTA-AAATAGTTTA
*
4719872 GTAACCTTAAAATAGTTTA
1 GTAAACTTAAAATAGTTTA
4719891 CCCTAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (19 bp):
GTAAACTTAAAATAGTTTA
Found at i:4724210 original size:16 final size:16
Alignment explanation
Indices: 4724172--4724212 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
4724162 AATTTTACAA
*
4724172 ATTATAAAATAGTTAT
1 ATTATAAAATAATTAT
**
4724188 AAAATAAAATAATTAT
1 ATTATAAAATAATTAT
4724204 ATTATAAAA
1 ATTATAAAA
4724213 AATATTTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTATAAAATAATTAT
Found at i:4732360 original size:6 final size:6
Alignment explanation
Indices: 4732349--4732375 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4732339 TGTTTCTTCA
4732349 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT
4732376 TTATTCGTTC
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:4738473 original size:2 final size:2
Alignment explanation
Indices: 4738466--4738497 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4738456 TTGGATACAA
4738466 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
4738498 TATGCTCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4739034 original size:41 final size:41
Alignment explanation
Indices: 4738972--4739322 Score: 495
Period size: 41 Copynumber: 8.6 Consensus size: 41
4738962 GGTTTTAAAA
* * * *
4738972 CCTAGCAGGCTAAGTGTCGGTGATCTAAATCAAGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
4739013 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAAGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
4739054 CGTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
4739095 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* * *
4739136 CCTAGCAGGCTAAGTGCCGGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
4739177 TCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* * * *
4739218 CCTAGCAGGCTAAGTGCCAGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
4739259 CCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* * *
4739300 CCTAACAAGCTAAGTGCCAGTGA
1 CCTAGCAGGCTAAGTGCCGGTGA
4739323 ATTTGTTTAT
Statistics
Matches: 274, Mismatches: 36, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 274 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
Found at i:4739613 original size:2 final size:2
Alignment explanation
Indices: 4739606--4739633 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4739596 TATTTGAATA
4739606 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
4739634 GCATTCGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4745154 original size:2 final size:2
Alignment explanation
Indices: 4745147--4745173 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4745137 AAAGAATAAA
4745147 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4745174 ATTCACAGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4747682 original size:20 final size:20
Alignment explanation
Indices: 4747668--4747705 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4747658 ATAAAAGTTA
4747668 TTAAATTTTAATAAAAATAT
1 TTAAATTTTAATAAAAATAT
*
4747688 TTAAATTTTATTAAAAAT
1 TTAAATTTTAATAAAAAT
4747706 TAGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAATTTTAATAAAAATAT
Found at i:4747750 original size:20 final size:22
Alignment explanation
Indices: 4747727--4747774 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4747717 TATAAAAATC
*
4747727 ATAAAAAAT-GTAATT-TTTTT
1 ATAAAAAATAGAAATTATTTTT
*
4747747 ATAAAATATAGAAATTATTTTT
1 ATAAAAAATAGAAATTATTTTT
4747769 ATAAAA
1 ATAAAA
4747775 TTTTATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 5 0.21
22 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
ATAAAAAATAGAAATTATTTTT
Found at i:4748256 original size:10 final size:10
Alignment explanation
Indices: 4748243--4748299 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
4748233 TGTATTTTAT
4748243 TTTTTTACAA
1 TTTTTTACAA
4748253 TTTTTATA-AA
1 TTTTT-TACAA
*
4748263 -ATTTTACAA
1 TTTTTTACAA
*
4748272 TTTTTTATAA
1 TTTTTTACAA
*
4748282 TTTTTGTACGA
1 TTTTT-TACAA
4748293 TTTTTTA
1 TTTTTTA
4748300 TTTTTACTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
8 2 0.05
9 5 0.13
10 21 0.55
11 10 0.26
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTTTACAA
Found at i:4748267 original size:19 final size:18
Alignment explanation
Indices: 4748245--4748285 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
4748235 TATTTTATTT
4748245 TTTTACAATTTTTATAAAA
1 TTTTACAATTTTT-TAAAA
*
4748264 TTTTACAATTTTTTATAA
1 TTTTACAATTTTTTAAAA
4748282 TTTT
1 TTTT
4748286 TGTACGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTACAATTTTTTAAAA
Found at i:4748286 original size:19 final size:21
Alignment explanation
Indices: 4748243--4748300 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
4748233 TGTATTTTAT
4748243 TTTTTTACAA-TTTTTATAAA
1 TTTTTTACAATTTTTTATAAA
*
4748263 -ATTTTACAATTTTTTAT-AA
1 TTTTTTACAATTTTTTATAAA
*
4748282 TTTTTGTACGATTTTTTAT
1 TTTTT-TACAATTTTTTAT
4748301 TTTTACTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 10 0.31
20 10 0.31
21 12 0.38
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTTTACAATTTTTTATAAA
Found at i:4748295 original size:21 final size:20
Alignment explanation
Indices: 4748245--4748300 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
4748235 TATTTTATTT
4748245 TTTTACAA-TTTTTATAAAA
1 TTTTACAATTTTTTATAAAA
**
4748264 TTTTACAATTTTTTATAATT
1 TTTTACAATTTTTTATAAAA
*
4748284 TTTGTACGATTTTTTAT
1 TTT-TACAATTTTTTAT
4748301 TTTTACTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 8 0.25
20 12 0.38
21 12 0.38
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTACAATTTTTTATAAAA
Found at i:4748315 original size:15 final size:16
Alignment explanation
Indices: 4748295--4748333 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
4748285 TTGTACGATT
*
4748295 TTTTATTT-TTACTAA
1 TTTTATTTATTAATAA
4748310 TTTTATTTAATTAATAA
1 TTTTATTT-ATTAATAA
4748327 TTTTATT
1 TTTTATT
4748334 GATTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
17 13 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATTTATTAATAA
Found at i:4755861 original size:2 final size:2
Alignment explanation
Indices: 4755854--4755902 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
4755844 ATTTTGTAGC
* *
4755854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT TT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4755895 AT CT AT AT
1 AT AT AT AT
4755903 TTTTGTAGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4757587 original size:44 final size:44
Alignment explanation
Indices: 4757537--4757640 Score: 190
Period size: 44 Copynumber: 2.3 Consensus size: 44
4757527 TCTTTAATAC
4757537 AATGGATATTTGATTGATTTTTTAGTAGGACGATAATCAGGGTA
1 AATGGATATTTGATTGATTTTTTAGTAGGACGATAATCAGGGTA
*
4757581 AATGGATATTTGATTGATTTTTTAGTAGGACGATAATCAGGGTG
1 AATGGATATTTGATTGATTTTTTAGTAGGACGATAATCAGGGTA
4757625 AATGGATATTGTGATT
1 AATGGATATT-TGATT
4757641 CAAGCTATGC
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
44 53 0.91
45 5 0.09
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.39
Consensus pattern (44 bp):
AATGGATATTTGATTGATTTTTTAGTAGGACGATAATCAGGGTA
Done.