Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001938.1 Hibiscus syriacus cultivar Beakdansim tig00003923_pilon, whole genome shotgun sequence
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: 75123
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2629 original size:23 final size:23
Alignment explanation
Indices: 2603--2655 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
2593 CAATGATTAA
*
2603 ATGTAAATTATATTCTTTAATTT
1 ATGTAAATTATATACTTTAATTT
*
2626 ATGTAAATTATATAGTTTAATTT
1 ATGTAAATTATATACTTTAATTT
2649 ATGTAAA
1 ATGTAAA
2656 GAAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (23 bp):
ATGTAAATTATATACTTTAATTT
Found at i:2930 original size:12 final size:11
Alignment explanation
Indices: 2904--2943 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2894 GATAATGATA
*
2904 ATTTAAATAAC
1 ATTTGAATAAC
*
2915 ATTTGATATAAA
1 ATTTGA-ATAAC
2927 ATTTGAATAAC
1 ATTTGAATAAC
2938 ATTTGA
1 ATTTGA
2944 GTTAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:3378 original size:20 final size:20
Alignment explanation
Indices: 3353--3394 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3343 GAAGCTTTTA
3353 CAGAAAATTGAAAACATTTG
1 CAGAAAATTGAAAACATTTG
*
3373 CAGAAAATTGAAAATATTTG
1 CAGAAAATTGAAAACATTTG
3393 CA
1 CA
3395 TAGCGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (20 bp):
CAGAAAATTGAAAACATTTG
Found at i:3996 original size:19 final size:19
Alignment explanation
Indices: 3980--4022 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
3970 TAGTGTATCA
3980 GTACATCCCAGGTGTATAG
1 GTACATCCCAGGTGTATAG
*
3999 GTACATCCCATGTGTATAG
1 GTACATCCCAGGTGTATAG
4018 GTACA
1 GTACA
4023 CTAATTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (19 bp):
GTACATCCCAGGTGTATAG
Found at i:4773 original size:24 final size:24
Alignment explanation
Indices: 4746--4796 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
4736 AAAATAATTC
4746 AAAACAAACAAATCC-AAACATCCA
1 AAAACAAACAAATCCAAAACAT-CA
*
4770 AAAACACACAAATCCAAAACATCA
1 AAAACAAACAAATCCAAAACATCA
4794 AAA
1 AAA
4797 TGTTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (24 bp):
AAAACAAACAAATCCAAAACATCA
Found at i:6769 original size:23 final size:21
Alignment explanation
Indices: 6721--6797 Score: 77
Period size: 23 Copynumber: 3.6 Consensus size: 21
6711 AACCCGTCAG
* * *
6721 GTGTATCGGTACAC-TCCAGA
1 GTGTATCGATACACATTCATA
6741 GTGTATCGATACACATTCA-A
1 GTGTATCGATACACATTCATA
*
6761 GGAATGTATCGGTACACATTCATA
1 -G--TGTATCGATACACATTCATA
6785 GTGTATCGATACA
1 GTGTATCGATACA
6798 TAGTGAGGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 14 0.29
21 15 0.31
23 18 0.38
24 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (21 bp):
GTGTATCGATACACATTCATA
Found at i:13091 original size:216 final size:217
Alignment explanation
Indices: 12712--13146 Score: 775
Period size: 216 Copynumber: 2.0 Consensus size: 217
12702 ATATAATAAG
12712 TAATTAATAAATAGAAGTTACCTGTAAATGGAAGAAACAAGACTGAATCTCAATTTCCAATGGTT
1 TAATTAATAAATAGAAGTTACCTGTAAATGGAAGAAACAAGACTGAATCTCAATTTCCAATGGTT
*
12777 TAACTTAACGTTAAATAACCTAAAAATTAAAATTAAAATTAAAATAATTAATAAACAATTTGAAA
66 TAACTTAACGTTAAACAACCT---AA-TAAAATTAAAATTAAAATAATTAATAAACAATTTGAAA
12842 TATTGAGATTAAAATTAAAAGTAAAACAATTCTACCATACCTTTACATAGCAGACTCATTACCCA
127 TATTGAGATTAAAATTAAAAGTAAAACAATTCTACCATACCTTTACATAGCAGACTCATTACCCA
*
12907 TAGTAAGGTAGTCTTCTTCTTTATTC
192 CAGTAAGGTAGTCTTCTTCTTTATTC
*
12933 TAATTAATAAATAGAAGTTACCTGTAAATGGAAGAAACAAGACTGAAATCTCAATTTCTAATGGT
1 TAATTAATAAATAGAAGTTACCTGTAAATGGAAGAAACAAGACTG-AATCTCAATTTCCAATGGT
12998 TTAACTTAACGTTAAACAACCT-A-AAAATTAAAATTAAAATAATTAATAAACAATTTGAAATAT
65 TTAACTTAACGTTAAACAACCTAATAAAATTAAAATTAAAATAATTAATAAACAATTTGAAATAT
*
13061 TGAGATTAAAATTAAAAGTAAAACAATTCTATCATACCTTTACATAGCAGACTCATTACCCACAG
130 TGAGATTAAAATTAAAAGTAAAACAATTCTACCATACCTTTACATAGCAGACTCATTACCCACAG
13126 TAAGGTAGTCTTCTTCTTTAT
195 TAAGGTAGTCTTCTTCTTTAT
13147 CCTCTGGCTC
Statistics
Matches: 209, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
216 124 0.59
218 1 0.00
221 45 0.22
222 39 0.19
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (217 bp):
TAATTAATAAATAGAAGTTACCTGTAAATGGAAGAAACAAGACTGAATCTCAATTTCCAATGGTT
TAACTTAACGTTAAACAACCTAATAAAATTAAAATTAAAATAATTAATAAACAATTTGAAATATT
GAGATTAAAATTAAAAGTAAAACAATTCTACCATACCTTTACATAGCAGACTCATTACCCACAGT
AAGGTAGTCTTCTTCTTTATTC
Found at i:14602 original size:6 final size:6
Alignment explanation
Indices: 14593--14655 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
14583 ATTCGAGTTC
* * * * * * * *
14593 GGGTTT GGGTTC AGGTGT GGGTTT GGGTTC GGGTGT GTGTTT GAGTTC
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT
14641 GGGTTT GGGTTT GGG
1 GGGTTT GGGTTT GGG
14656 GTTGAGGTTA
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.03, C:0.05, G:0.51, T:0.41
Consensus pattern (6 bp):
GGGTTT
Found at i:14614 original size:18 final size:18
Alignment explanation
Indices: 14593--14655 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
14583 ATTCGAGTTC
*
14593 GGGTTTGGGTTCAGGTGT
1 GGGTTTGGGTTCGGGTGT
14611 GGGTTTGGGTTCGGGTGT
1 GGGTTTGGGTTCGGGTGT
* * *
14629 GTGTTTGAGTTCGGGTTT
1 GGGTTTGGGTTCGGGTGT
14647 GGGTTTGGG
1 GGGTTTGGG
14656 GTTGAGGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.03, C:0.05, G:0.51, T:0.41
Consensus pattern (18 bp):
GGGTTTGGGTTCGGGTGT
Found at i:15421 original size:6 final size:6
Alignment explanation
Indices: 15410--15446 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
15400 ATAATTTGTA
*
15410 ATTAAT ATTAAT ATTAAT A-TAAA ATTAAT ATTAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT
15447 AAACTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTAAT
Found at i:15436 original size:17 final size:17
Alignment explanation
Indices: 15416--15449 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15406 TGTAATTAAT
15416 ATTAATATTAATATAAA
1 ATTAATATTAATATAAA
15433 ATTAATATTAATATAAA
1 ATTAATATTAATATAAA
15450 CTATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATATTAATATAAA
Found at i:15475 original size:21 final size:22
Alignment explanation
Indices: 15451--15505 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
15441 TAATATAAAC
*
15451 TATATTTTATAAATTATA-TAA
1 TATATTTTATAAACTATAGTAA
15472 TATATTTTATAAACTATAGTTAA
1 TATATTTTATAAACTATAG-TAA
*
15495 TATAATTTATA
1 TATATTTTATA
15506 TTAATATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 17 0.57
23 13 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTTTATAAACTATAGTAA
Found at i:16215 original size:34 final size:33
Alignment explanation
Indices: 16176--16246 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
16166 TTTTGTAAAG
* *
16176 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGT-AAAAAACTA
* *
16210 GGGAAAGGTTCTAGTTTATCCCGTAAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTAAAAAACTA
16243 GGGA
1 GGGA
16247 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGTAAAAAACTA
Found at i:17226 original size:3 final size:3
Alignment explanation
Indices: 17220--17329 Score: 145
Period size: 3 Copynumber: 36.0 Consensus size: 3
17210 GAAGGAAAGA
17220 AAG AAG AAGG AAG AGAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AA-G AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
17267 AAG AAG AAG AAG AAG AAG AA- AAG AAAG AAAG AAAG AAG -AG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG -AAG -AAG AAG AAG AAG AAG
*
17313 AAG AAG GAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG
17330 GTAGGCATTG
Statistics
Matches: 99, Mismatches: 2, Indels: 12
0.88 0.02 0.11
Matches are distributed among these distances:
2 6 0.06
3 76 0.77
4 17 0.17
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19227 original size:19 final size:18
Alignment explanation
Indices: 19203--19271 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
19193 AGGGTGTCAA
19203 AGTGCATCCATACACCTGC
1 AGTGCATCCATACA-CTGC
19222 AGTGCATCCA-AGCACT--
1 AGTGCATCCATA-CACTGC
*
19238 -GTGCATCCATGCATCTGC
1 AGTGCATCCATACA-CTGC
*
19256 AGTGCATCCATGCACT
1 AGTGCATCCATACACT
19272 ATGCATCGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
15 11 0.26
16 2 0.05
18 5 0.12
19 25 0.58
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (18 bp):
AGTGCATCCATACACTGC
Found at i:19243 original size:15 final size:15
Alignment explanation
Indices: 19223--19285 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 15
19213 TACACCTGCA
*
19223 GTGCATCCAAGCACT
1 GTGCATCCATGCACT
19238 GTGCATCCATGCATCT
1 GTGCATCCATGCA-CT
19254 GCAGTGCATCCATGCACT
1 ---GTGCATCCATGCACT
* *
19272 ATGCATCGATGCAC
1 GTGCATCCATGCAC
19286 CATGTAGTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
15 24 0.59
16 2 0.05
18 2 0.05
19 13 0.32
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (15 bp):
GTGCATCCATGCACT
Found at i:19247 original size:34 final size:34
Alignment explanation
Indices: 19204--19306 Score: 143
Period size: 34 Copynumber: 3.0 Consensus size: 34
19194 GGGTGTCAAA
* *
19204 GTGCATCCATACACCTGCAGTGCATCCAAGCACT
1 GTGCATCCATGCACCTGCAGTGCATCCATGCACT
*
19238 GTGCATCCATGCATCTGCAGTGCATCCATGCACT
1 GTGCATCCATGCACCTGCAGTGCATCCATGCACT
* * *
19272 ATGCATCGATGCACCATGTAGTGCATCCATGCACT
1 GTGCATCCATGCACC-TGCAGTGCATCCATGCACT
19307 CAAACACCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
34 43 0.70
35 18 0.30
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (34 bp):
GTGCATCCATGCACCTGCAGTGCATCCATGCACT
Found at i:22447 original size:19 final size:19
Alignment explanation
Indices: 22419--22525 Score: 123
Period size: 19 Copynumber: 5.8 Consensus size: 19
22409 AGGGTGTCAA
*
22419 AGTGCATCCATGCACCTGT
1 AGTGCATCCATGCACCTGC
*
22438 AGTGCGTCCATGCACCTGC
1 AGTGCATCCATGCACCTGC
*
22457 AGTGCATCCATGCATCTGC
1 AGTGCATCCATGCACCTGC
22476 AGTGCATCCATGCA-CT--
1 AGTGCATCCATGCACCTGC
* *
22492 A-TGCATCGATGCACCATGT
1 AGTGCATCCATGCACC-TGC
*
22511 AGTGCATCTATGCAC
1 AGTGCATCCATGCAC
22526 TCAAACACCG
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
15 11 0.14
16 2 0.03
17 1 0.01
18 2 0.03
19 49 0.64
20 12 0.16
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.25
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGC
Found at i:22957 original size:34 final size:33
Alignment explanation
Indices: 22918--22988 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
22908 TTTTGTAAAG
*
22918 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTG-AAAAACTA
* *
22952 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
22985 GGGA
1 GGGA
22989 GTTATAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
Found at i:23483 original size:20 final size:19
Alignment explanation
Indices: 23458--23496 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
23448 AGGCTAACTG
*
23458 CAAAATTAAATAAAACAAAA
1 CAAAATGAAA-AAAACAAAA
*
23478 CAAAATGAAAAAAAGAAAA
1 CAAAATGAAAAAAACAAAA
23497 AGGAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (19 bp):
CAAAATGAAAAAAACAAAA
Found at i:23517 original size:14 final size:14
Alignment explanation
Indices: 23500--23535 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
23490 AAGAAAAAGG
*
23500 AAAATAATAATAAT
1 AAAATAATAAAAAT
23514 AAAATAATAAAAAT
1 AAAATAATAAAAAT
23528 AAATATAA
1 AAA-ATAA
23536 CTACTAGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATAATAAAAAT
Found at i:23674 original size:122 final size:126
Alignment explanation
Indices: 23540--23788 Score: 461
Period size: 126 Copynumber: 2.0 Consensus size: 126
23530 ATATAACTAC
23540 TAGGTATAAAAAAATAATAAATATGAGAGAAATGAAATACT-AAAAAAC-AAAAAAACAAATCTA
1 TAGGTATAAAAAAATAATAAATATGAGAGAAATGAAATACTAAAAAAACAAAAAAAACAAATCTA
23603 ACCTACTAATCACTTCACC-AAGTAAGGGAGAAAATTTGGTTAAGAGAGGACAAAAAAGGG
66 ACCTACTAATCACTTCACCAAAGTAAGGGAGAAAATTTGGTTAAGAGAGGACAAAAAAGGG
23663 TAGGTAT-AAAAAATAATAAATATGAGAGAAATGAAATACTAAAAAAACAAAAAAAACAAATCTA
1 TAGGTATAAAAAAATAATAAATATGAGAGAAATGAAATACTAAAAAAACAAAAAAAACAAATCTA
23727 ACCTACTAATCACTTCACCGAAAGTAAGGGAGAAAATTTGGTTAAGAGAGGACAAAAAAGGG
66 ACCTACTAATCACTTCACC-AAAGTAAGGGAGAAAATTTGGTTAAGAGAGGACAAAAAAGGG
23789 AGCCCTATAT
Statistics
Matches: 122, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
122 33 0.27
123 14 0.11
124 34 0.28
126 41 0.34
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.18
Consensus pattern (126 bp):
TAGGTATAAAAAAATAATAAATATGAGAGAAATGAAATACTAAAAAAACAAAAAAAACAAATCTA
ACCTACTAATCACTTCACCAAAGTAAGGGAGAAAATTTGGTTAAGAGAGGACAAAAAAGGG
Found at i:23858 original size:4 final size:4
Alignment explanation
Indices: 23849--23881 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
23839 CTAAAACATA
23849 AAAT AAAT AAAT AAACT -AAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT A
23882 TATATTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 1 0.04
4 25 0.93
5 1 0.04
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:23920 original size:19 final size:19
Alignment explanation
Indices: 23896--23947 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
23886 TTAAAGAATG
23896 ATATAAAAT-ATATACATAT
1 ATATAAAATAATATA-ATAT
*
23915 ATATAAGATAATATAATAT
1 ATATAAAATAATATAATAT
*
23934 -TAAATAAATAATAT
1 ATATA-AAATAATAT
23948 GAAAGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATATAAAATAATATAATAT
Found at i:25165 original size:38 final size:38
Alignment explanation
Indices: 25114--25186 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
25104 GAAATGATTG
25114 GTTTATGATTGGTTTGTTAATCTGGACTAAATCACGAC
1 GTTTATGATTGGTTTGTTAATCTGGACTAAATCACGAC
25152 GTTTATGATTGGTTTGTTAATCTGGACTAAATCAC
1 GTTTATGATTGGTTTGTTAATCTGGACTAAATCAC
25187 TAAATGACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (38 bp):
GTTTATGATTGGTTTGTTAATCTGGACTAAATCACGAC
Found at i:26277 original size:124 final size:124
Alignment explanation
Indices: 26008--26581 Score: 857
Period size: 124 Copynumber: 4.6 Consensus size: 124
25998 CTTTATCGTA
* * *
26008 AAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGCTTTGAATTGGATATCCTTCATTAT
1 AAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGT
* * *
26073 GAAGTTAAAATCC-A-ATGGAGATGGATGTTGCTTGTGGGCATGATATCCTTCGTCA-TG
66 GAAGTTGAAATCCAATATAGAGATGGATGCTGCTTGTGGGCATGATATCCTTCGT-AGTG
* *
26130 AAGTTAAAATCGTGGATGGCTCATTCGTTGTGAAGTTGATCTTTGAATTGGATATCCTTCGTTGT
1 AAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGT
*
26195 GAAGTTGAAATCCAATATAGAGATGGATGCTGCTTGTGGGCATAATATCCTTCGTAGTG
66 GAAGTTGAAATCCAATATAGAGATGGATGCTGCTTGTGGGCATGATATCCTTCGTAGTG
* * * *
26254 AAGTTGAAATCATGGATAGCTCATTCGTTGTGAAGTTAAGCTTTGAATTGGATATCCTTCATTGT
1 AAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGT
* * * * * * *
26319 GAAGTTAAAATCCAATCTAGAGATAGATGATGCTTGTGGGCACGATATCCTTTGTCGTG
66 GAAGTTGAAATCCAATATAGAGATGGATGCTGCTTGTGGGCATGATATCCTTCGTAGTG
*
26378 AAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTTAATTGGATATCCTTCGTTGT
1 AAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGT
* * * * *
26443 GAAGTTGAAATCCAATCTAGAGATGGGTACTGCTTGTGGGCATGATATCCTTTGTCGTG
66 GAAGTTGAAATCCAATATAGAGATGGATGCTGCTTGTGGGCATGATATCCTTCGTAGTG
* * *
26502 AAGTTGAAATCGTGGATGGCTCATTCGTTATGAAATTGAGCTTTGAATTGGACATCCTTCGTTGT
1 AAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGT
26567 GAAGTTGAAATCCAA
66 GAAGTTGAAATCCAA
26582 GGGTTGTTTC
Statistics
Matches: 411, Mismatches: 38, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
122 72 0.18
123 2 0.00
124 337 0.82
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.35
Consensus pattern (124 bp):
AAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGT
GAAGTTGAAATCCAATATAGAGATGGATGCTGCTTGTGGGCATGATATCCTTCGTAGTG
Found at i:26740 original size:64 final size:62
Alignment explanation
Indices: 26665--26888 Score: 296
Period size: 64 Copynumber: 3.6 Consensus size: 62
26655 GCATTGTTTC
*
26665 GAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAA-TT-TTTGTT
*
26729 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAA-----GTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAATTTTTGTT
* ** *
26786 GAGTCCAATATACTTATCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAATTTATTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAA-TT-TTTGTT
* * *
26850 GAGTTCAATATCTTTCGCTGTGAAGTTGCAATTGACTCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
26889 AAAAGCTGCA
Statistics
Matches: 140, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
57 52 0.37
64 88 0.63
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (62 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAATTTTTGTT
Found at i:26814 original size:57 final size:57
Alignment explanation
Indices: 26726--26839 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
26716 AAAGTTGTTT
* *
26726 GTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAA
1 GTTGAGTCCAATATACTTCATTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAA
*
26783 GTTGAGTCCAATATACTT-ATCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAA
1 GTTGAGTCCAATATACTTCAT-TGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAA
26840 TTTATTTGTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
56 1 0.02
57 52 0.98
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (57 bp):
GTTGAGTCCAATATACTTCATTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAA
Found at i:26825 original size:121 final size:121
Alignment explanation
Indices: 26665--26888 Score: 349
Period size: 121 Copynumber: 1.9 Consensus size: 121
26655 GCATTGTTTC
* * *
26665 GAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTTGTTTGTTG
1 GAGTCCAATATACTTAGCTGTAAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTTATTTGTTG
*
26730 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTT
66 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTT
* * * *
26786 GAGTCCAATATACTTATCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAATTTATTTGTTG
1 GAGTCCAATATACTTAGCTGTAAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTTATTTGTTG
* * *
26851 AGTTCAATATCTTTCGCTGTGAAGTTGCAATTGACTCT
66 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
26889 AAAAGCTGCA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
121 92 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (121 bp):
GAGTCCAATATACTTAGCTGTAAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTTATTTGTTG
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTT
Found at i:31126 original size:20 final size:20
Alignment explanation
Indices: 31112--31161 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 20
31102 GTAAAAAAGT
31112 GATAAAATAAATAAAATAAA
1 GATAAAATAAATAAAATAAA
31132 GATAAAAT--A-AAAATAAA
1 GATAAAATAAATAAAATAAA
*
31149 -ACAAAATAAATAA
1 GATAAAATAAATAA
31162 CATGGTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 6 0.23
17 8 0.31
18 2 0.08
19 2 0.08
20 8 0.31
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (20 bp):
GATAAAATAAATAAAATAAA
Found at i:31128 original size:5 final size:5
Alignment explanation
Indices: 31113--31231 Score: 59
Period size: 5 Copynumber: 23.0 Consensus size: 5
31103 TAAAAAAGTG
*
31113 ATAAA AT-AA ATAAA ATAAA GATAAA ATAAAA ATAAA ACAAA AT-AA ATAACA
1 ATAAA ATAAA ATAAA ATAAA -ATAAA AT-AAA ATAAA ATAAA ATAAA ATAA-A
* * * * *
31164 TGGTAAC AT-AA ATAAA ACTAAA ACAAA ATGAA ATGAAA A-AATA AAAAA
1 --ATAAA ATAAA ATAAA A-TAAA ATAAA ATAAA AT-AAA ATAA-A ATAAA
*
31212 ATAATA ATGAA A-AAA ATAAA
1 ATAA-A ATAAA ATAAA ATAAA
31232 TATATATATA
Statistics
Matches: 87, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
4 16 0.18
5 43 0.49
6 25 0.29
8 3 0.03
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (5 bp):
ATAAA
Found at i:31136 original size:11 final size:10
Alignment explanation
Indices: 31113--31231 Score: 59
Period size: 11 Copynumber: 11.5 Consensus size: 10
31103 TAAAAAAGTG
31113 ATAAAAT-AA
1 ATAAAATAAA
31122 ATAAAATAAA
1 ATAAAATAAA
31132 GATAAAATAAAA
1 -ATAAAAT-AAA
*
31144 ATAAAACAAA
1 ATAAAATAAA
31154 AT-AAATAACA
1 ATAAAATAA-A
* *
31164 TGGTAACAT-AA
1 --ATAAAATAAA
31175 ATAAAACTAAA
1 ATAAAA-TAAA
* *
31186 ACAAAATGAA
1 ATAAAATAAA
31196 ATGAAAA-AATA
1 AT-AAAATAA-A
*
31207 AAAAAATAATA
1 ATAAAATAA-A
*
31218 ATGAAA-AAA
1 ATAAAATAAA
31227 ATAAA
1 ATAAA
31232 TATATATATA
Statistics
Matches: 84, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
9 21 0.25
10 20 0.24
11 35 0.42
12 5 0.06
13 3 0.04
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (10 bp):
ATAAAATAAA
Found at i:31139 original size:16 final size:15
Alignment explanation
Indices: 31120--31158 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
31110 GTGATAAAAT
*
31120 AAATAAAATAAAGATA
1 AAATAAAATAAA-ACA
31136 AAATAAAAATAAAACA
1 AAAT-AAAATAAAACA
31152 AAATAAA
1 AAATAAA
31159 TAACATGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 10 0.48
17 8 0.38
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (15 bp):
AAATAAAATAAAACA
Found at i:31495 original size:19 final size:19
Alignment explanation
Indices: 31471--31522 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
31461 TTAAAGAATG
31471 ATATAAAAT-ATATACATAT
1 ATATAAAATAATATA-ATAT
*
31490 ATATAAGATAATATAATAT
1 ATATAAAATAATATAATAT
*
31509 -TAAATAAATAATAT
1 ATATA-AAATAATAT
31523 GAAAGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATATAAAATAATATAATAT
Found at i:32670 original size:36 final size:36
Alignment explanation
Indices: 32630--32720 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
32620 ATATGTTAAT
* * *
32630 ATTAATATAAACTATAGTTTATAAACTATCCGCTAC
1 ATTAATATAAATTATAGTTTATAAACTATACACTAC
* * * *
32666 ATTAATACAAATTATAATTTATAAACTATATACTAT
1 ATTAATATAAATTATAGTTTATAAACTATACACTAC
32702 ATTAATATAAATTATAGTT
1 ATTAATATAAATTATAGTT
32721 AAGATAATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (36 bp):
ATTAATATAAATTATAGTTTATAAACTATACACTAC
Found at i:32717 original size:15 final size:15
Alignment explanation
Indices: 32699--32749 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
32689 AACTATATAC
32699 TATATTAATATAAAT
1 TATATTAATATAAAT
*
32714 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
32729 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
32745 TATAT
1 TATAT
32750 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:32772 original size:20 final size:21
Alignment explanation
Indices: 32731--32772 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
32721 AAGATAATTA
32731 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
32753 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
32773 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:32836 original size:14 final size:14
Alignment explanation
Indices: 32817--32861 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
32807 AGTGCAGTAA
*
32817 TATAAACTATTGTT
1 TATAAACTATAGTT
32831 TATAAACTATAGTT
1 TATAAACTATAGTT
* *
32845 TACATA-TATAGTT
1 TATAAACTATAGTT
32858 TATA
1 TATA
32862 TAACATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TATAAACTATAGTT
Found at i:32875 original size:20 final size:21
Alignment explanation
Indices: 32848--32974 Score: 116
Period size: 20 Copynumber: 5.9 Consensus size: 21
32838 TATAGTTTAC
32848 ATATATAGTTTATATA-ACAT
1 ATATATAGTTTATATATACAT
* *
32868 ATAAATAGATTGTATATATAAAT
1 ATATATAG-TT-TATATATACAT
* *
32891 ATACTATAGGTTATATATATAT
1 ATA-TATAGTTTATATATACAT
32913 ATATATAGTTTATATATAC-T
1 ATATATAGTTTATATATACAT
*
32933 AT-TCATAGTTTATACATACAT
1 ATAT-ATAGTTTATATATACAT
*
32954 GTACTATAAGTTATATATATA
1 ATA-TAT-AGTT-TATATATA
32975 GTTTACATGT
Statistics
Matches: 87, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.01
20 24 0.28
21 18 0.21
22 21 0.24
23 12 0.14
24 11 0.13
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATATAGTTTATATATACAT
Found at i:32888 original size:24 final size:24
Alignment explanation
Indices: 32858--32917 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
32848 ATATATAGTT
*
32858 TATATAACATATA-AATAGATTGTA
1 TATATAA-ATATACAATAGATTATA
* *
32882 TATATAAATATACTATAGGTTATA
1 TATATAAATATACAATAGATTATA
*
32906 TATATATATATA
1 TATATAAATATA
32918 TAGTTTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (24 bp):
TATATAAATATACAATAGATTATA
Found at i:32919 original size:65 final size:63
Alignment explanation
Indices: 32848--32974 Score: 166
Period size: 63 Copynumber: 2.0 Consensus size: 63
32838 TATAGTTTAC
* *
32848 ATATATAGTTTATATA-ACATATAAATAGATTGTATATATAAATATACTATAGGTTATATATATA
1 ATATATAGTTTATATATAC-TATAAATAG-TT-TATACATAAATATACTATAAGTTATATATATA
32912 T
63 T
** * *
32913 ATATATAGTTTATATATACTATTCATAGTTTATACATACATGTACTATAAGTTATATATATA
1 ATATATAGTTTATATATACTATAAATAGTTTATACATAAATATACTATAAGTTATATATATA
32975 GTTTACATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 28 0.51
64 2 0.04
65 23 0.42
66 2 0.04
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (63 bp):
ATATATAGTTTATATATACTATAAATAGTTTATACATAAATATACTATAAGTTATATATATAT
Found at i:34273 original size:48 final size:49
Alignment explanation
Indices: 34217--34311 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
34207 TTTCAACAGG
** * *
34217 ATTTCTATAAACTATATACTTTA-TTACTTTATATAGTTTATGCATAGT
1 ATTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATACATAGT
*
34265 ATTTCTATAAACTATATAAGTAATTTAGTTTATATAGTTTATACATA
1 ATTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATACATA
34312 TATGTACTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 20 0.49
49 21 0.51
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.48
Consensus pattern (49 bp):
ATTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATACATAGT
Found at i:34322 original size:49 final size:48
Alignment explanation
Indices: 34221--34323 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 48
34211 AACAGGATTT
** * * *
34221 CTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAGTATTT
1 CTATAAACTATATAAGTAATTACTTTATATAGTTTATACATAGTATTA
*
34269 CTATAAACTATATAAGTAATTTAGTTTATATAGTTTATACATA-TATGTA
1 CTATAAACTATATAAGTAA-TTACTTTATATAGTTTATACATAGTAT-TA
34318 CTATAA
1 CTATAA
34324 GTTACATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 19 0.40
49 28 0.60
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (48 bp):
CTATAAACTATATAAGTAATTACTTTATATAGTTTATACATAGTATTA
Found at i:34340 original size:35 final size:36
Alignment explanation
Indices: 34295--34372 Score: 86
Period size: 37 Copynumber: 2.2 Consensus size: 36
34285 TAATTTAGTT
* * *
34295 TATATAGTTT-ATACATATATGTACTATAAGTTACA
1 TATATTGTTTAATACATACATATACTATAAGTTACA
** *
34330 TATATTGTTTACATGTATACATATACTATAGGTTACA
1 TATATTGTTTA-ATACATACATATACTATAAGTTACA
34367 TATATT
1 TATATT
34373 AACTATTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 9 0.26
37 26 0.74
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (36 bp):
TATATTGTTTAATACATACATATACTATAAGTTACA
Found at i:34470 original size:7 final size:7
Alignment explanation
Indices: 34460--34512 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
34450 AGTGTATAAA
34460 GTTTAGG
1 GTTTAGG
34467 GTTTAGG
1 GTTTAGG
34474 GTTTAGG
1 GTTTAGG
* **
34481 TTTTAAT
1 GTTTAGG
*
34488 GTTTATG
1 GTTTAGG
* *
34495 ATTTAAG
1 GTTTAGG
34502 GTTTAGG
1 GTTTAGG
34509 GTTT
1 GTTT
34513 CTATAAACGG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (7 bp):
GTTTAGG
Found at i:34479 original size:14 final size:14
Alignment explanation
Indices: 34460--34512 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
34450 AGTGTATAAA
*
34460 GTTTAGGGTTTAGG
1 GTTTAGGGTTTAAG
* *
34474 GTTTAGGTTTTAAT
1 GTTTAGGGTTTAAG
* *
34488 GTTTATGATTTAAG
1 GTTTAGGGTTTAAG
34502 GTTTAGGGTTT
1 GTTTAGGGTTT
34513 CTATAAACGG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:34720 original size:13 final size:13
Alignment explanation
Indices: 34673--34805 Score: 69
Period size: 13 Copynumber: 10.2 Consensus size: 13
34663 ATATACTTTT
34673 TATAGTTTATACATA
1 TATAGTTTAT--ATA
**
34688 TATAACTTATATA
1 TATAGTTTATATA
* *
34701 CACAGTTTATATA
1 TATAGTTTATATA
*
34714 TATAGTTCATATAAA
1 TATAGTT--TATATA
* * *
34729 CATAATTTACATA
1 TATAGTTTATATA
*
34742 TATAGCTTATA-A
1 TATAGTTTATATA
34754 TA-A--TTATATA
1 TATAGTTTATATA
* * *
34764 GTTTA-TAATATAAA
1 -TATAGT-TTATATA
34778 TATAGTTTATATA
1 TATAGTTTATATA
34791 TATAGTTTATATA
1 TATAGTTTATATA
34804 TA
1 TA
34806 AACTTATATT
Statistics
Matches: 87, Mismatches: 23, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 2 0.02
12 4 0.05
13 51 0.59
14 6 0.07
15 18 0.21
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:34752 original size:26 final size:26
Alignment explanation
Indices: 34682--34753 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
34672 TTATAGTTTA
* * *
34682 TACATATATAACTTATATACACAGTT
1 TACATATATAGCTTATAAACACAATT
* * *
34708 TATATATATAGTTCATATAAACATAATT
1 TACATATATAG--CTTATAAACACAATT
34736 TACATATATAGCTTATAA
1 TACATATATAGCTTATAA
34754 TAATTATATA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 15 0.42
28 21 0.58
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (26 bp):
TACATATATAGCTTATAAACACAATT
Found at i:34780 original size:18 final size:19
Alignment explanation
Indices: 34741--34794 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 19
34731 TAATTTACAT
* *
34741 ATATAGCTTATAATA-ATT
1 ATATAGTTTATAATATATA
34759 ATATAGTTTATAATATA-A
1 ATATAGTTTATAATATATA
34777 ATATAGTTTAT-ATATATA
1 ATATAGTTTATAATATATA
34795 GTTTATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 5 0.16
18 26 0.81
19 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (19 bp):
ATATAGTTTATAATATATA
Found at i:34939 original size:2 final size:2
Alignment explanation
Indices: 34925--35093 Score: 51
Period size: 2 Copynumber: 89.0 Consensus size: 2
34915 GTAAATTATT
*
34925 TA TA TA -A TA -A TA TA TA TG TA CT- TA -A TA TA CTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * * * *
34965 TA AA CTA TA TA CA TA AA TC T- TA TA TA T- TA TA TA TT TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
35006 TA TA AA T- TA CA TA GTT TA T- TA -A TA AA T- TA CA TA TA AA CTA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
35046 TA TA TA T- TA TA TA TT TG TC TT TA TA TA T- TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35085 TA TA T- TA TA
1 TA TA TA TA TA
35094 ATTTTTTTAA
Statistics
Matches: 120, Mismatches: 28, Indels: 38
0.65 0.15 0.20
Matches are distributed among these distances:
1 14 0.12
2 100 0.83
3 6 0.05
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:34971 original size:15 final size:15
Alignment explanation
Indices: 34953--35052 Score: 55
Period size: 15 Copynumber: 6.7 Consensus size: 15
34943 TACTTAATAT
34953 ACTATATATATATAA
1 ACTATATATATATAA
*
34968 ACTATATACATA-AA
1 ACTATATATATATAA
* *
34982 TCT-TATATATTATAT
1 ACTATATATA-TATAA
*
34997 A-TTTATATATATAA
1 ACTATATATATATAA
* * * *
35011 ATTACATAGTTTATTA
1 ACTATATA-TATATAA
* *
35027 A-TAAATTACATATAA
1 ACTATA-TATATATAA
35042 ACTATATATAT
1 ACTATATATAT
35053 TATATATTTG
Statistics
Matches: 62, Mismatches: 16, Indels: 14
0.67 0.17 0.15
Matches are distributed among these distances:
13 5 0.08
14 12 0.19
15 34 0.55
16 11 0.18
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (15 bp):
ACTATATATATATAA
Found at i:35644 original size:33 final size:33
Alignment explanation
Indices: 35607--35673 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
35597 TGACCTGAAC
35607 TCAATCCGTATCCGGTAAACATCCAACCTAAAT
1 TCAATCCGTATCCGGTAAACATCCAACCTAAAT
* *
35640 TCAATCCGTATCCGGTAAACATCCGACCTGAAT
1 TCAATCCGTATCCGGTAAACATCCAACCTAAAT
35673 T
1 T
35674 TTATCTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (33 bp):
TCAATCCGTATCCGGTAAACATCCAACCTAAAT
Found at i:37992 original size:37 final size:36
Alignment explanation
Indices: 37958--38026 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
37948 TACAAATTGT
37958 AAAATATTTATATA-TTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAGTTTT-TTTAAAAAATTAAATTC
* *
37994 ATAATATTTATATAGTTTTTTTACAAAATTAAA
1 AAAATATTTATATAGTTTTTTTAAAAAATTAAA
38027 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (36 bp):
AAAATATTTATATAGTTTTTTTAAAAAATTAAATTC
Found at i:42468 original size:32 final size:32
Alignment explanation
Indices: 42427--42573 Score: 150
Period size: 32 Copynumber: 4.6 Consensus size: 32
42417 ACAGAGTCAA
* * *
42427 TATTGCATTCAGATAATGCACAATAGAATCAT
1 TATTACATTCAGATAATGCACAGTAGAATCAG
*
42459 TATTACATTCAGATAATGCATAGTAGAATCAG
1 TATTACATTCAGATAATGCACAGTAGAATCAG
* * * * * *
42491 TATTGCATCCAGATAATGCATAGCAGAGTTAG
1 TATTACATTCAGATAATGCACAGTAGAATCAG
* * * *
42523 AATGACATTCAGATAATGCACAGTATAACCAG
1 TATTACATTCAGATAATGCACAGTAGAATCAG
* *
42555 TATCACATTTAGATAATGC
1 TATTACATTCAGATAATGC
42574 GTAGCAGATA
Statistics
Matches: 93, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 93 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TATTACATTCAGATAATGCACAGTAGAATCAG
Found at i:42942 original size:18 final size:19
Alignment explanation
Indices: 42919--42961 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
42909 TTTAAGTAGT
*
42919 AATAAAAACGATTAAA-TA
1 AATAAAAACAATTAAAGTA
*
42937 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
42956 AA-AAAA
1 AATAAAA
42962 TAAGATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.19
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:47523 original size:12 final size:12
Alignment explanation
Indices: 47498--47567 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
47488 ACGGAGATAT
* *
47498 CAGAAATCAAAA
1 CAGAATTCAGAA
47510 CAGAATTCAGAA
1 CAGAATTCAGAA
47522 CAGATATT-AGAA
1 CAGA-ATTCAGAA
* * *
47534 CAGAATCCATAT
1 CAGAATTCAGAA
*
47546 CAGAAATCAGAA
1 CAGAATTCAGAA
47558 CAGAATTCAG
1 CAGAATTCAG
47568 GTCATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.89
13 3 0.07
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:47525 original size:24 final size:24
Alignment explanation
Indices: 47498--47567 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
47488 ACGGAGATAT
*
47498 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * * *
47522 CAGATATTAGAACAGAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
47546 CAGAAATCAGAACAGAATTCAG
1 CAGAAATCAGAACAGAATTCAG
47568 GTCATGTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:47602 original size:24 final size:24
Alignment explanation
Indices: 47530--47604 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
47520 AACAGATATT
* *
47530 AGAACAGAATCCATA-TCAGAAATC
1 AGAACAGAATTCA-AGTCATAAATC
* **
47554 AGAACAGAATTCAGGTCATGTATC
1 AGAACAGAATTCAAGTCATAAATC
*
47578 AGAACATAATTCAAGTCGA-AAATC
1 AGAACAGAATTCAAGTC-ATAAATC
47602 AGA
1 AGA
47605 TAAAATAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 39 0.98
25 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (24 bp):
AGAACAGAATTCAAGTCATAAATC
Found at i:48753 original size:18 final size:18
Alignment explanation
Indices: 48732--48767 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
48722 CTGTCATCCG
*
48732 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
48750 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
48768 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:49821 original size:29 final size:28
Alignment explanation
Indices: 49788--49885 Score: 106
Period size: 29 Copynumber: 3.4 Consensus size: 28
49778 AATTTTACAG
*
49788 AAATATCACCAAAATCGAATTAATTCCCA
1 AAATAGCACCAAAA-CGAATTAATTCCCA
**
49817 AAATAGCACCAAAACCGAATTAATTCCTT
1 AAATAGCACCAAAA-CGAATTAATTCCCA
* * *
49846 GAATAGCACCAAAACTGAATTATTTTCCA
1 AAATAGCACCAAAAC-GAATTAATTCCCA
*
49875 AAATATCACCA
1 AAATAGCACCA
49886 GTTTCGAATT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 1 0.02
29 56 0.98
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.24
Consensus pattern (28 bp):
AAATAGCACCAAAACGAATTAATTCCCA
Found at i:52513 original size:18 final size:19
Alignment explanation
Indices: 52490--52533 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
52480 TTTAAGTAGT
*
52490 AATAAAAACGATTAAA-TA
1 AATAAAAACAATTAAAGTA
*
52508 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
52527 AA-AAAAA
1 AATAAAAA
52534 TAAGAGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:55532 original size:20 final size:22
Alignment explanation
Indices: 55507--55556 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
55497 GGAGATTAAG
*
55507 TTGAAAATTTTAAC-AAATTA-
1 TTGAAAATTGTAACAAAATTAT
55527 TTGAAAATTGTAACATAAATTAT
1 TTGAAAATTGTAACA-AAATTAT
55550 TTGAAAA
1 TTGAAAA
55557 ATCAAAGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.50
22 6 0.23
23 7 0.27
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (22 bp):
TTGAAAATTGTAACAAAATTAT
Found at i:56380 original size:103 final size:103
Alignment explanation
Indices: 56249--56458 Score: 287
Period size: 103 Copynumber: 2.0 Consensus size: 103
56239 TTTTAAAAAG
* * * * *
56249 TTTTCTATTTTTAATATGACAAGTATGTAGAATATGACCATGATAATGACAATGTGAGCATTTT-
1 TTTTCTATTTTAAATAGGACAAGAATGTAGAATATGACCATGATAATGACAATGTAAACATTTTA
* *
56313 TCATTATTAAACTAAATGCATTATTTTTACAAATGATT
66 CCATTATTAAACTAAATGAATTATTTTTACAAATGATT
* *
56351 TTTTACTATTTTAAATAGGACAAGAATGTAGACTATGACCATGATAATGACGATGTAAACATTTT
1 TTTT-CTATTTTAAATAGGACAAGAATGTAGAATATGACCATGATAATGACAATGTAAACATTTT
* * * *
56416 ACCATTATTGAATTAGATGAATTATTTTTAGAAATGATT
65 ACCATTATTAAACTAAATGAATTATTTTTACAAATGATT
56455 TTTT
1 TTTT
56459 TCTTTTGTTA
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 4 0.04
103 53 0.57
104 36 0.39
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (103 bp):
TTTTCTATTTTAAATAGGACAAGAATGTAGAATATGACCATGATAATGACAATGTAAACATTTTA
CCATTATTAAACTAAATGAATTATTTTTACAAATGATT
Found at i:57974 original size:21 final size:20
Alignment explanation
Indices: 57948--58002 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
57938 CTTCTACGAG
57948 GGGATCAATCCTTTGGTCGAA
1 GGGATCAATCCTTT-GTCGAA
* **
57969 GGGATCAATACTTT-TTTAA
1 GGGATCAATCCTTTGTCGAA
57988 GGGATCAATCCTTTG
1 GGGATCAATCCTTTG
58003 AGCCAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (20 bp):
GGGATCAATCCTTTGTCGAA
Found at i:62164 original size:26 final size:25
Alignment explanation
Indices: 62127--62192 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
62117 AGAAATTGGG
*
62127 TTTTTTTATAAATAA-AATATTTTTC
1 TTTTTTAATAAA-AATAATATTTTTC
62152 TTTTTTAATTAAAAATAATATTTTT-
1 TTTTTTAA-TAAAAATAATATTTTTC
* *
62177 ATTATTAA-AAAAATAA
1 TTTTTTAATAAAAATAA
62193 ACTATAGTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 8 0.22
25 15 0.42
26 13 0.36
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTTTTAATAAAAATAATATTTTTC
Found at i:63250 original size:14 final size:13
Alignment explanation
Indices: 63231--63302 Score: 75
Period size: 14 Copynumber: 5.8 Consensus size: 13
63221 TTGTTCGAAT
63231 ATAAATGAACGTAC
1 ATAAATGAACG-AC
63245 ATAAATG-A--AC
1 ATAAATGAACGAC
63255 ATAAATGAACGAAC
1 ATAAATGAACG-AC
63269 ATAAATG-A--AC
1 ATAAATGAACGAC
63279 ATAAATGAACGAAC
1 ATAAATGAACG-AC
63293 ATAAATGAAC
1 ATAAATGAAC
63303 ATATAATCGA
Statistics
Matches: 50, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
10 18 0.36
11 2 0.04
13 2 0.04
14 28 0.56
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.18
Consensus pattern (13 bp):
ATAAATGAACGAC
Found at i:63263 original size:24 final size:24
Alignment explanation
Indices: 63231--63315 Score: 143
Period size: 24 Copynumber: 3.5 Consensus size: 24
63221 TTGTTCGAAT
*
63231 ATAAATGAACGTACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
63255 ATAAATGAACGAACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
63279 ATAAATGAACGAACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
63303 ATATAATCGAACG
1 ATA-AAT-GAACG
63316 TTCACGAACG
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
24 50 0.86
25 3 0.05
26 5 0.09
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (24 bp):
ATAAATGAACGAACATAAATGAAC
Found at i:63314 original size:12 final size:11
Alignment explanation
Indices: 63243--63314 Score: 60
Period size: 10 Copynumber: 6.2 Consensus size: 11
63233 AAATGAACGT
63243 ACATAAAT-GA
1 ACATAAATCGA
63253 ACATAAATGAACGA
1 ACATAAAT---CGA
63267 ACATAAAT-GA
1 ACATAAATCGA
63277 ACATAAATGAACGA
1 ACATAAAT---CGA
63291 ACATAAAT-GA
1 ACATAAATCGA
63301 ACATATAATCGA
1 ACATA-AATCGA
63313 AC
1 AC
63315 GTTCACGAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
10 25 0.48
11 3 0.06
12 4 0.08
14 20 0.38
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.18
Consensus pattern (11 bp):
ACATAAATCGA
Found at i:63843 original size:21 final size:19
Alignment explanation
Indices: 63801--63843 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
63791 TCATTAGAAA
**
63801 TAAAAAATATTTTTTTGGT
1 TAAAAAATATTTTTTTAAT
63820 TAAAAAATATTTATTTTCAAT
1 TAAAAAATATTT-TTTT-AAT
63841 TAA
1 TAA
63844 TGCTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (19 bp):
TAAAAAATATTTTTTTAAT
Found at i:69852 original size:5 final size:5
Alignment explanation
Indices: 69842--69866 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
69832 TGTATGAGTT
69842 TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA
69867 ACATAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:73426 original size:27 final size:28
Alignment explanation
Indices: 73396--73480 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 28
73386 ATAATATATG
73396 ATAAC-TTCGTTTTTATTTAATTAAGAT
1 ATAACTTTCGTTTTTATTTAATTAAGAT
*
73423 ATAATCAGTTTCATTTTTATTTAATTAAGAT
1 ATAA-C--TTTCGTTTTTATTTAATTAAGAT
*
73454 ATAATTACTTTCGTTTTTAATTAATTA
1 AT-A--ACTTTCGTTTTTATTTAATTA
73481 TGAAGTGATC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
27 4 0.08
28 1 0.02
31 40 0.83
32 1 0.02
33 1 0.02
34 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.53
Consensus pattern (28 bp):
ATAACTTTCGTTTTTATTTAATTAAGAT
Found at i:73440 original size:31 final size:31
Alignment explanation
Indices: 73405--73480 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
73395 GATAACTTCG
*
73405 TTTTTATTTAATTAAGATATAATCAGTTTCA
1 TTTTTATTTAATTAAGATATAATCACTTTCA
* *
73436 TTTTTATTTAATTAAGATATAATTACTTTCG
1 TTTTTATTTAATTAAGATATAATCACTTTCA
*
73467 TTTTTAATTAATTA
1 TTTTTATTTAATTA
73481 TGAAGTGATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (31 bp):
TTTTTATTTAATTAAGATATAATCACTTTCA
Found at i:73629 original size:30 final size:28
Alignment explanation
Indices: 73592--73668 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 28
73582 TAGTAACTTA
*
73592 AAATAAAATCTATTTTAAAAGTTAAAATA-
1 AAATAAAATAT-TTTTAAAA-TTAAAATAT
73621 AGAATAAAATATGTTTCT-AAATTAAAATAT
1 A-AATAAAATAT-TTT-TAAAATTAAAATAT
73651 AAATAAAATATTTTTAAA
1 AAATAAAATATTTTTAAA
73669 TGAAGTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
27 1 0.02
28 5 0.12
29 19 0.45
30 16 0.38
31 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (28 bp):
AAATAAAATATTTTTAAAATTAAAATAT
Found at i:73632 original size:54 final size:54
Alignment explanation
Indices: 73539--73740 Score: 162
Period size: 54 Copynumber: 3.7 Consensus size: 54
73529 TTAAGATAAG
* ** *
73539 AATAAAATATA-TTTAATAATTTAAAATAATAATGTAATATATTTAGTAACTTAA
1 AATAAAATATATTTTAA-AAGTTAAAATAATAATAAAATATATTTAATAACTTAA
* * * * *
73593 AATAAAATCTATTTTAAAAGTTAAAATAAGAATAAAATATGTTT-CTAAATTAA
1 AATAAAATATATTTTAAAAGTTAAAATAATAATAAAATATATTTAATAACTTAA
* * ** *
73646 AATATAAATAAAATATTTTTAAA-TGAAGTTAATAATAAAATATATTTAATAACTTAG
1 AATA-AAAT---ATATTTTAAAAGTTAAAATAATAATAAAATATATTTAATAACTTAA
* * * *
73703 TATAAAAGATATTTTTAAAGTTAATAT-AT-ATAAAATAT
1 AATAAAATATATTTTAAAAGTTAAAATAATAATAAAATAT
73741 TATGAATTTA
Statistics
Matches: 118, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
52 9 0.08
53 24 0.20
54 40 0.34
55 5 0.04
56 22 0.19
57 18 0.15
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (54 bp):
AATAAAATATATTTTAAAAGTTAAAATAATAATAAAATATATTTAATAACTTAA
Found at i:73649 original size:29 final size:26
Alignment explanation
Indices: 73590--73694 Score: 93
Period size: 27 Copynumber: 3.7 Consensus size: 26
73580 TTTAGTAACT
*
73590 TAAAATAAAATCTATTTTAAAAGTTAAAA
1 TAAAATAAAA--TATTTTTAAA-TTAAAA
73619 TAAGAATAAAATATGTTTCTAAATTAAAA
1 TAA-AATAAAATAT-TTT-TAAATTAAAA
* **
73648 TATAAATAAAATATTTTTAAATGAAGT
1 TA-AAATAAAATATTTTTAAATTAAAA
*
73675 TAATAATAAAATATATTTAA
1 TAA-AATAAAATATTTTTAA
73695 TAACTTAGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.02
27 24 0.36
28 6 0.09
29 24 0.36
30 11 0.17
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (26 bp):
TAAAATAAAATATTTTTAAATTAAAA
Found at i:73707 original size:27 final size:26
Alignment explanation
Indices: 73652--73720 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
73642 TTAAAATATA
*
73652 AATAAAATATTTTTAAATGAAGTTAAT
1 AATAAAATATTTTT-AATGAACTTAAT
*
73679 AATAAAATATATTTAAT-AACTTAGTAT
1 AATAAAATATTTTTAATGAACTTA--AT
*
73706 AA-AAGATATTTTTAA
1 AATAAAATATTTTTAA
73721 AGTTAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 5 0.14
26 14 0.39
27 17 0.47
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (26 bp):
AATAAAATATTTTTAATGAACTTAAT
Found at i:73730 original size:24 final size:24
Alignment explanation
Indices: 73653--73730 Score: 59
Period size: 24 Copynumber: 3.1 Consensus size: 24
73643 TAAAATATAA
* *
73653 ATAAAATATTTTTAAATGAAGTTAAT
1 ATAAAAGATATTT-AAT-AAGTTAAT
* * *
73679 AATAAAATATATTTAATAACTTAGT
1 -ATAAAAGATATTTAATAAGTTAAT
*
73704 ATAAAAGATATTT-TTAAAGTTAAT
1 ATAAAAGATATTTAAT-AAGTTAAT
73728 ATA
1 ATA
73731 TATAAAATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 1 0.02
24 21 0.49
25 6 0.14
26 3 0.07
27 12 0.28
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (24 bp):
ATAAAAGATATTTAATAAGTTAAT
Done.