Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007709.1 Hibiscus syriacus cultivar Beakdansim tig00109924_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: 657132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1608 original size:2 final size:2
Alignment explanation
Indices: 1603--1638 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1593 CAAACAAAAA
1603 AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1639 ATTTGAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18076 original size:7 final size:7
Alignment explanation
Indices: 18064--18091 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
18054 ATAATTGACC
18064 ATAAATT
1 ATAAATT
18071 ATAAATT
1 ATAAATT
18078 ATAAATT
1 ATAAATT
18085 ATAAATT
1 ATAAATT
18092 TGAATCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAAATT
Found at i:18512 original size:20 final size:20
Alignment explanation
Indices: 18487--18579 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
18477 TTTTCCCAAT
18487 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
18507 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
18527 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * ** *
18548 TCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
18569 TCGCAATGCGA
1 TCGCAATGCGA
18580 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:18529 original size:41 final size:41
Alignment explanation
Indices: 18484--18579 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
18474 CGATTTTCCC
18484 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
18525 AATTCGCAATGCGAATAAGTAAATCGTAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
18566 AAATCGCAATGCGA
1 AATTCGCAATGCGA
18580 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:18533 original size:21 final size:20
Alignment explanation
Indices: 18487--18579 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
18477 TTTTCCCAAT
*
18487 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
18507 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
18527 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* * **
18548 TCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
18569 TCGCAATGCGA
1 TCGCAATGCGA
18580 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:18593 original size:20 final size:20
Alignment explanation
Indices: 18568--18661 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
18558 AATTGGGAAA
*
18568 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
18588 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
18609 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
18629 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
18649 TTCGCAACGCGAT
1 ATCGCAACGCGAT
18662 TTACTTAGCA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:18610 original size:41 final size:41
Alignment explanation
Indices: 18565--18642 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
18555 GCGAATTGGG
* * *
18565 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
18606 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
18643 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:19243 original size:19 final size:19
Alignment explanation
Indices: 19219--19263 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
19209 GCAACGAGAT
*
19219 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
19238 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
19257 AATCGCA
1 AATCGCA
19264 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:19281 original size:19 final size:19
Alignment explanation
Indices: 19259--19410 Score: 170
Period size: 19 Copynumber: 8.1 Consensus size: 19
19249 GAAACCAAAA
*
19259 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
19278 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
19297 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
19316 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
19336 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
19350 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
19370 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
19389 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
19409 TC
1 TC
19411 AACCAAAAGA
Statistics
Matches: 115, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.09
16 2 0.02
17 3 0.03
19 51 0.44
20 49 0.43
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19337 original size:39 final size:38
Alignment explanation
Indices: 19259--19348 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
19249 GAAACCAAAA
* *
19259 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCATTGCGATTTTCATT
*
19297 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-ATTGCGATTTTCATT
19336 TCGCGTTGCGATT
1 TCGCGTTGCGATT
19349 CTCTCGTTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCATTGCGATTTTCATT
Found at i:19368 original size:33 final size:34
Alignment explanation
Indices: 19321--19385 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
19311 TAATTTCGCG
**
19321 GTTGCGATTTTCA-TTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTTCGCGTTGCGATTCTCTC
19354 GTTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTTTCGCGTTGCGATTCTC
19386 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (34 bp):
GTTGCGATAGTCATTTTCGCGTTGCGATTCTCTC
Found at i:19378 original size:20 final size:19
Alignment explanation
Indices: 19353--19410 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
19343 GCGATTCTCT
**
19353 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
* *
19373 CGTTGCGATTCTCATTATCT
1 CGTTGCGATTTTCATT-TCG
19393 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
19411 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:21470 original size:42 final size:42
Alignment explanation
Indices: 21410--21532 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
21400 GCCCGACTCG
* * *
21410 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
21452 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
21494 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
21533 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:21490 original size:21 final size:21
Alignment explanation
Indices: 21466--21532 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
21456 TCATTCCTCG
21466 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
21487 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
21508 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
21529 AGAG
1 AGAG
21533 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:22908 original size:14 final size:14
Alignment explanation
Indices: 22889--22924 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
22879 ATTGTTTAAT
22889 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
22903 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
22917 TGATTTGT
1 TGATTTGT
22925 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:23091 original size:19 final size:19
Alignment explanation
Indices: 23069--23186 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
23059 CGAAATTAAA
23069 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
23088 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
23103 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
23121 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
23136 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
23154 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
23173 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
23187 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:23115 original size:33 final size:33
Alignment explanation
Indices: 23073--23166 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
23063 ATTAAATTCG
23073 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
23106 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
23139 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
23167 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:26913 original size:14 final size:14
Alignment explanation
Indices: 26894--26930 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
26884 CGTCAATTAA
26894 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
26908 ACAAATCATCTTTT
1 ACAAATCAACATTT
26922 ACAAATCAA
1 ACAAATCAA
26931 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:28077 original size:14 final size:14
Alignment explanation
Indices: 28058--28094 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28048 CATCAATTAA
28058 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
28072 ACAAATCATCTTTT
1 ACAAATCAACATTT
28086 ACAAATCAA
1 ACAAATCAA
28095 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:28314 original size:586 final size:588
Alignment explanation
Indices: 26782--28929 Score: 4074
Period size: 586 Copynumber: 3.7 Consensus size: 588
26772 ACTATCGCAA
*
26782 TGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
1 TGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
*
26847 CAAATCAACTATTACATTTCAACACAAATTATGTACACGTCAATTAAACAAATCAACATTTACAA
66 CAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAA
26912 ATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTA
131 ATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCAATTA
26977 TTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTA
195 TTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTA
27042 ACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
260 ACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
27107 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
325 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
27172 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
390 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
27237 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
455 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
27302 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
520 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
27367 TCGT
585 TCGT
*
27371 TGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
1 TGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
27436 CAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAA
66 CAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAA
*
27501 ATCA---ATT--AAA-CAA-T---C-A--AAAAATAATAATAATTCTTATTTCTTCATCAATTAT
131 ATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAATTAT
27553 TGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAA
196 TGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAA
*
27618 CCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAA
261 CCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAAA
27683 TTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAAC
326 TTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAAC
27748 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
391 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
27813 AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
456 AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
*
27878 ATGCGAAAATGGTTATCGCAACGAAAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTCT
521 ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTCT
27943 CGT
586 CGT
27946 TGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
1 TGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
28011 CAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAA
66 CAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAA
28076 ATCATCTTTTACAAATCAATTAAACAATC-AAAA-AATAATAATTCTTATTTCTTCATCAATTAT
131 ATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAATTAT
28139 TGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAA
196 TGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAA
*
28204 CCTGCAGAAACCAAACATTTTCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAAA
261 CCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAAA
28269 TTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAAC
326 TTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAAC
28334 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
391 TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
*
28399 AGTTTAAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
456 AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
28464 ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTCT
521 ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTCT
28529 CGT
586 CGT
28532 TGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
1 TGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
28597 CAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAA
66 CAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAA
28662 ATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTA
131 ATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCAATTA
* *
28727 TTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACTCAGTTCACTTAAGGATTA
195 TTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTA
28792 ACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
260 ACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
28857 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
325 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
28922 CTTACATT
390 CTTGCATT
28930 TGACTTACCA
Statistics
Matches: 1529, Mismatches: 14, Indels: 32
0.97 0.01 0.02
Matches are distributed among these distances:
575 560 0.37
578 3 0.00
579 1 0.00
580 3 0.00
581 3 0.00
582 2 0.00
583 3 0.00
584 3 0.00
585 1 0.00
586 581 0.38
587 4 0.00
588 4 0.00
589 361 0.24
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (588 bp):
TGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAA
CAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAA
ATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAATTAT
TGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAA
CCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAAA
TTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAAC
TTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTG
AGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCA
ATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTCT
CGT
Found at i:28663 original size:14 final size:14
Alignment explanation
Indices: 28644--28680 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28634 CATCAATTAA
28644 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
28658 ACAAATCATCTTTT
1 ACAAATCAACATTT
28672 ACAAATCAA
1 ACAAATCAA
28681 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:29296 original size:14 final size:14
Alignment explanation
Indices: 29277--29334 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
29267 TTTCATTTCG
29277 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
29291 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
29307 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
29323 CGTTGCGATTTT
1 CGTTGCGATTTT
29335 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:29305 original size:32 final size:33
Alignment explanation
Indices: 29262--29350 Score: 162
Period size: 32 Copynumber: 2.7 Consensus size: 33
29252 CTCCATCCCG
29262 GCGATTTTCATTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTTTGTCGTT
29295 GCGA-TTTCATTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTTTGTCGTT
*
29327 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
29351 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 32 0.59
33 22 0.41
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTTTGTCGTT
Found at i:29369 original size:20 final size:19
Alignment explanation
Indices: 29335--29389 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
29325 TTGCGATTTT
*
29335 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
29354 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
29374 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
29390 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:29888 original size:18 final size:18
Alignment explanation
Indices: 29862--29906 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
29852 GTCGATCAGA
*
29862 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
29880 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
29898 TGATGGCTC
1 TGATGGCTC
29907 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:31246 original size:20 final size:20
Alignment explanation
Indices: 31221--31258 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31211 AATAGTTTCT
31221 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
31241 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
31259 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:31546 original size:22 final size:22
Alignment explanation
Indices: 31521--31564 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31511 GATTTAGATA
*
31521 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
31543 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
31565 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:31777 original size:20 final size:20
Alignment explanation
Indices: 31752--31845 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
31742 GATTATGTAT
31752 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
31772 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
31792 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
31813 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
31833 TATCGCATTGCGA
1 TATCGCGTTGCGA
31846 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:31846 original size:20 final size:20
Alignment explanation
Indices: 31732--31846 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
31722 CGCTTTGAAA
*
31732 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
31753 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
31773 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
31793 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
31814 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
31834 ATCGCATTGCGAT
1 ATCGCATTGCGAT
31847 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:31865 original size:41 final size:41
Alignment explanation
Indices: 31774--31908 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
31764 AAAGTCAGTA
* * * ** *
31774 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
31814 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
31856 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
31897 TCGCGTTGCGAT
1 TCGCGTTGCGAT
31909 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:31879 original size:20 final size:20
Alignment explanation
Indices: 31835--31927 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
31825 ATAGTCAGTA
* **
31835 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
31856 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
31876 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
31897 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
31917 TCGCATTGCGA
1 TCGCATTGCGA
31928 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:31909 original size:41 final size:41
Alignment explanation
Indices: 31835--31930 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
31825 ATAGTCAGTA
*
31835 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
31876 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
31917 TCGCATTGCGAATT
1 TCGCATTGCGAATT
31931 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:33307 original size:7 final size:7
Alignment explanation
Indices: 33295--33322 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
33285 ATAATTGACC
33295 ATAAATT
1 ATAAATT
33302 ATAAATT
1 ATAAATT
33309 ATAAATT
1 ATAAATT
33316 ATAAATT
1 ATAAATT
33323 TGAATCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAAATT
Found at i:34337 original size:20 final size:20
Alignment explanation
Indices: 34294--34334 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
34284 GTGATTCTTT
*
34294 AATTAATAAATTTAAATATA
1 AATTAATAAATTTAAAAATA
34314 AATTAA-AAATTTAAAAATA
1 AATTAATAAATTTAAAAATA
34333 AA
1 AA
34335 ATTTCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTAATAAATTTAAAAATA
Found at i:36741 original size:33 final size:33
Alignment explanation
Indices: 36700--36768 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
36690 ATTCTAAAAT
36700 AAAAAATTCATTATAAACTATCAAATC-GAGTCA
1 AAAAAATTCATTATAAACTATCAAATCGGA-TCA
*
36733 AAAAAATTCATTGTAAACTATCAAATCGGATCA
1 AAAAAATTCATTATAAACTATCAAATCGGATCA
36766 AAA
1 AAA
36769 CCCATCATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.26
Consensus pattern (33 bp):
AAAAAATTCATTATAAACTATCAAATCGGATCA
Found at i:50147 original size:27 final size:26
Alignment explanation
Indices: 50101--50151 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
50091 AAATTAAGTT
50101 TTATTTCTCTTATTTCTTTAGATTTAA
1 TTATTTCTCTTATTTCTTTA-ATTTAA
50128 TTATTT-T-TTATGTTCTTTTAATTT
1 TTATTTCTCTTAT-TTC-TTTAATTT
50152 CGAAACTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 4 0.18
26 8 0.36
27 10 0.45
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.69
Consensus pattern (26 bp):
TTATTTCTCTTATTTCTTTAATTTAA
Found at i:52513 original size:22 final size:23
Alignment explanation
Indices: 52481--52536 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
52471 AATAAATAAT
*
52481 CTTACAATTAATGTAAT-AAAATTA
1 CTTA-AATTAATGTAATGAAAA-AA
52505 -TTAAATTAA-GTAATGAAAAAA
1 CTTAAATTAATGTAATGAAAAAA
52526 CTTAAATTAAT
1 CTTAAATTAAT
52537 AATATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 6 0.21
22 19 0.68
23 3 0.11
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (23 bp):
CTTAAATTAATGTAATGAAAAAA
Found at i:56907 original size:23 final size:22
Alignment explanation
Indices: 56881--56923 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
56871 GTAGGTGAAA
56881 TTTAATTCTAACCATTGATATAC
1 TTTAATTCTAACCATT-ATATAC
* *
56904 TTTATTTTTAACCATTATAT
1 TTTAATTCTAACCATTATAT
56924 TAATAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTAATTCTAACCATTATATAC
Found at i:60215 original size:12 final size:12
Alignment explanation
Indices: 60198--60222 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60188 GTAAAGATGA
60198 AGGGCTTATTTG
1 AGGGCTTATTTG
60210 AGGGCTTATTTG
1 AGGGCTTATTTG
60222 A
1 A
60223 ATATAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.32, T:0.40
Consensus pattern (12 bp):
AGGGCTTATTTG
Found at i:63076 original size:27 final size:28
Alignment explanation
Indices: 63041--63105 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
63031 AGAAAATATC
* *
63041 ATATATAAAAAGC-AATATATATATGTA
1 ATATATAAAAACCAAAGATATATATGTA
**
63068 ATATATAAAGCCCTAAAGATATATATGTA
1 ATATATAAAAACC-AAAGATATATATGTA
63097 ATATATAAA
1 ATATATAAA
63106 GCCCTAAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 10 0.31
29 22 0.69
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (28 bp):
ATATATAAAAACCAAAGATATATATGTA
Found at i:63093 original size:31 final size:29
Alignment explanation
Indices: 63057--63114 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
63047 AAAAAGCAAT
63057 ATATATATGTAATATATAAAGCCCTAAAG
1 ATATATATGTAATATATAAAGCCCTAAAG
63086 ATATATATGTAATATATAAAGCCCTAAAG
1 ATATATATGTAATATATAAAGCCCTAAAG
63115 CTTATACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (29 bp):
ATATATATGTAATATATAAAGCCCTAAAG
Found at i:63740 original size:2 final size:2
Alignment explanation
Indices: 63733--63760 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
63723 GAATTCAAGT
63733 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63761 AAGAGAGGTA
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):
TA
Found at i:63880 original size:5 final size:5
Alignment explanation
Indices: 63870--63898 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
63860 GACTAACCTT
63870 GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
63899 AAAAAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:70546 original size:11 final size:11
Alignment explanation
Indices: 70528--70565 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
70518 TATACGTAAA
70528 AATATTAGATT
1 AATATTAGATT
*
70539 AGTATTAGATT
1 AATATTAGATT
70550 AATATT--ATT
1 AATATTAGATT
70559 AATATTA
1 AATATTA
70566 TTAATGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (11 bp):
AATATTAGATT
Found at i:74401 original size:43 final size:42
Alignment explanation
Indices: 74354--74712 Score: 241
Period size: 43 Copynumber: 8.3 Consensus size: 42
74344 GAGCTTAAAC
*
74354 TATAAAAGTAAAAAGT-ATGATTGAAAAAATTAGGGACC-CTAAT
1 TATAAAGGTAAAAAGTGA-GATTGAAAAAATTAGGG-CCTC-AAT
* *
74397 TATAAAGGTAAAAAGTGATATT-AGAAAAA-TATGGGCATCAAT
1 TATAAAGGTAAAAAGTGAGATTGA-AAAAATTA-GGGCCTCAAT
* * *
74439 TTTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGTCTAAAT
1 TATAAAGGTAAAAAGTGAGATTG-AAAAAATTAGGGCCTCAAT
* * *
74482 TAT-ATGAGTAAAAAATGGGATTGAAAAAATTAGGGACCTCAAT
1 TATAAAG-GTAAAAAGTGAGATTGAAAAAATTAGGG-CCTCAAT
* * *
74525 TATAAAGGTAAAAAGTGAGATTG-AAAAAGTAGGAG-TTTAAT
1 TATAAAGGTAAAAAGTGAGATTGAAAAAATTAGG-GCCTCAAT
* * * * * ***
74566 TTTAAAGGTACAAGGTGGGATTGAAAAACTTAGGATATCAAT
1 TATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGCCTCAAT
* * * * * *
74608 AATAAATGTAAAAAAAAATGGGATTGAAAAAAAATTAAGGACCTCCAT
1 TATAAAGGT---AAAAAGTGAGATTG--AAAAAATT-AGGGCCTCAAT
*
74656 TATAAAGATAAAAAGT-AGGATT-ACAAAAATTAGGGACCTCAAT
1 TATAAAGGTAAAAAGTGA-GATTGA-AAAAATTAGGG-CCTCAAT
*
74699 TATAAAGATAAAAA
1 TATAAAGGTAAAAA
74713 ATTAAAATTA
Statistics
Matches: 248, Mismatches: 46, Indels: 44
0.73 0.14 0.13
Matches are distributed among these distances:
41 23 0.09
42 72 0.29
43 105 0.42
44 6 0.02
45 21 0.08
47 7 0.03
48 14 0.06
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (42 bp):
TATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGCCTCAAT
Found at i:74623 original size:128 final size:129
Alignment explanation
Indices: 74372--74712 Score: 349
Period size: 128 Copynumber: 2.6 Consensus size: 129
74362 TAAAAAGTAT
*
74372 GATTGAAAAAATTAGGGACC-CTAATTATAAAGGTAAAAAGTGATATTAGAAAAATATGGGCATC
1 GATTGAAAAAATTAGGGACCTC-AATTATAAAGGTAAAAAGTGAGATTAGAAAAATATGGGCATC
* * * * *
74436 AATTTTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGTCTAAATTATATG-AGTAAAAAATGG
65 AATTTTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGATATAAAATAAATGAAGAAAAAAATGG
*
74500 GATTGAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGAGATT-GAAAAAGTA-GGAG-TT
1 GATTGAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGAGATTAGAAAAA-TATGG-GCAT
* * * * *
74562 TAATTTTAAAGGTACAAGGTGGGATTG-AAAAACTTAGGATATCAATAATAAATGTAA-AAAAAA
64 CAATTTTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGATAT-AA-AATAAATG-AAGAAAAAA
74625 ATGG
126 ATGG
* * * *
74629 GATTGAAAAAAAATTAAGGACCTCCATTATAAAGATAAAAAGT-AGGATTACAAAAAT-TAGGGA
1 GATTG--AAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGA-GATTAGAAAAATAT-GGG-
* * *
74692 CCTCAATTATAAAGATAAAAA
61 CATCAATTTTAAAGGTAAAAA
74713 ATTAAAATTA
Statistics
Matches: 176, Mismatches: 22, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
126 12 0.07
127 34 0.19
128 53 0.30
129 15 0.09
130 2 0.01
131 39 0.22
132 7 0.04
133 14 0.08
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (129 bp):
GATTGAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTGAGATTAGAAAAATATGGGCATCA
ATTTTAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGATATAAAATAAATGAAGAAAAAAATGG
Found at i:83344 original size:3 final size:3
Alignment explanation
Indices: 83336--83360 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
83326 TTAATACTAA
83336 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
83361 CTATGTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:84053 original size:18 final size:18
Alignment explanation
Indices: 84030--84075 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
84020 GGTGGAGATA
* *
84030 GGTGGGTAGGAGGCGGAC
1 GGTGGGTAAGAGGCAGAC
84048 GGTGGGTAAGAGGCAGAC
1 GGTGGGTAAGAGGCAGAC
*
84066 GGTGGATAAG
1 GGTGGGTAAG
84076 CCGTCGGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.54, T:0.13
Consensus pattern (18 bp):
GGTGGGTAAGAGGCAGAC
Found at i:84441 original size:11 final size:11
Alignment explanation
Indices: 84423--84460 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
84413 TATACGTAAA
84423 AATATTAGATT
1 AATATTAGATT
*
84434 AGTATTAGATT
1 AATATTAGATT
84445 AATATT--ATT
1 AATATTAGATT
84454 AATATTA
1 AATATTA
84461 TTAATGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (11 bp):
AATATTAGATT
Found at i:88276 original size:43 final size:44
Alignment explanation
Indices: 88229--88585 Score: 209
Period size: 43 Copynumber: 8.3 Consensus size: 44
88219 GAGCTTAAAC
*
88229 TATAAAAGTAAAAAGTATGATTGAAAAAATTAGGGACTCT-AAT
1 TATAAAAGTAAAAAGTAGGATTGAAAAAATTAGGGACTCTCAAT
* * *
88272 TATAAAGGTAAAAAGT--GATATTAGAAAAA-TATGGG-C-ATCAAT
1 TATAAAAGTAAAAAGTAGGAT-TGA-AAAAATTA-GGGACTCTCAAT
* * *
88314 TTTAAATGTAAAAAGT-GAGATTGAAAAAAATTAGGG-C-CTAAAT
1 TATAAAAGTAAAAAGTAG-GATTG-AAAAAATTAGGGACTCTCAAT
** * *
88357 TATATGAGTAAAAAATGGGATTGAAAAAATTAGGGA-TCTCAAT
1 TATAAAAGTAAAAAGTAGGATTGAAAAAATTAGGGACTCTCAAT
* * * *
88400 TATAAAGGTAAAAAGT-GAGATTG--AAAAGTA-GGAGT-TTAAT
1 TATAAAAGTAAAAAGTAG-GATTGAAAAAATTAGGGACTCTCAAT
* * * * *
88440 TATAAAGGTACAAGGTGGGATTGAAAAAATTA-GGA-TATCAAT
1 TATAAAAGTAAAAAGTAGGATTGAAAAAATTAGGGACTCTCAAT
* * * * * *
88482 AATAAATGTAAAAAAAATGGGATTGAAAAAAAATTAAGGAC-CTCCAT
1 TATAAAAGT--AAAAAGTAGGATTG--AAAAAATTAGGGACTCTCAAT
88529 TAT-AAAGATAAAAAGTAGGATT-ACAAAAATTAGGGAC-CTCAAT
1 TATAAAAG-TAAAAAGTAGGATTGA-AAAAATTAGGGACTCTCAAT
88572 TAT-AAAGATAAAAA
1 TATAAAAG-TAAAAA
88586 ATTAAAATTA
Statistics
Matches: 252, Mismatches: 37, Indels: 50
0.74 0.11 0.15
Matches are distributed among these distances:
40 26 0.10
41 13 0.05
42 56 0.22
43 106 0.42
44 18 0.07
45 11 0.04
46 12 0.05
47 10 0.04
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (44 bp):
TATAAAAGTAAAAAGTAGGATTGAAAAAATTAGGGACTCTCAAT
Found at i:88498 original size:128 final size:126
Alignment explanation
Indices: 88247--88585 Score: 330
Period size: 128 Copynumber: 2.6 Consensus size: 126
88237 TAAAAAGTAT
*
88247 GATTGAAAAAATTAGGGACTCTAATTATAAAGGTAAAAAGTGATATTAGAAAAATATGGGCATCA
1 GATTGAAAAAATTAGGGACTC-AATTATAAAGGTAAAAAGTGAGATTAGAAAAATATGGGCATCA
* * * * * * *
88312 ATTTTAAATGTAAAAAGTGAGATTGAAAAAAATTAGGGCCTAAATTATATGAGTAAAAAATGG
65 ATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGACATAAAATAAATGA-AAAAAAATGG
* * *
88375 GATTGAAAAAATTAGGGATCTCAATTATAAAGGTAAAAAGTGAGATT-GAAAAGTA-GGAG-TTT
1 GATTGAAAAAATTAGGGA-CTCAATTATAAAGGTAAAAAGTGAGATTAGAAAAATATGG-GCATC
* * * *
88437 AATTATAAAGGTACAAGGTGGGATTG-AAAAAATTAGGATATCAATAATAAATGTAAAAAAAATG
64 AATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGACAT-AA-AATAAATG-AAAAAAAATG
88501 G
126 G
* * * *
88502 GATTGAAAAAAAATTAAGGACCTCCATTATAAAGATAAAAAGT-AGGATTACAAAAAT-TAGGGA
1 GATTG--AAAAAATTAGGGA-CTCAATTATAAAGGTAAAAAGTGA-GATTAGAAAAATAT-GGG-
* *
88565 CCTCAATTATAAAGATAAAAA
60 CATCAATTATAAAGGTAAAAA
88586 ATTAAAATTA
Statistics
Matches: 172, Mismatches: 26, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
125 12 0.07
126 26 0.15
127 28 0.16
128 44 0.26
129 39 0.23
130 6 0.03
131 2 0.01
132 15 0.09
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (126 bp):
GATTGAAAAAATTAGGGACTCAATTATAAAGGTAAAAAGTGAGATTAGAAAAATATGGGCATCAA
TTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGACATAAAATAAATGAAAAAAAATGG
Found at i:92986 original size:22 final size:21
Alignment explanation
Indices: 92955--93003 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
92945 TGGACTTAAA
* *
92955 TTAATGGTGTCTACATTGTGCT
1 TTAATCGTGTCTA-ATTATGCT
*
92977 TTAATCGTGTGTAATTATGCT
1 TTAATCGTGTCTAATTATGCT
*
92998 CTAATC
1 TTAATC
93004 ATGCTTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (21 bp):
TTAATCGTGTCTAATTATGCT
Found at i:94585 original size:22 final size:22
Alignment explanation
Indices: 94543--94586 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
94533 GAGTTTAATA
**
94543 TTAAGTAACTCGTTTCGGCTCG
1 TTAAGTAACTCGAGTCGGCTCG
94565 TTAAG-AACTCGAGTCGAGCTCG
1 TTAAGTAACTCGAGTCG-GCTCG
94587 AGTCCGAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
TTAAGTAACTCGAGTCGGCTCG
Found at i:100194 original size:30 final size:30
Alignment explanation
Indices: 100130--100194 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
100120 TTTAATAGCT
100130 TTTAAAGTTTTATTTAAAAAAAATAAATTC
1 TTTAAAGTTTTATTTAAAAAAAATAAATTC
* * *
100160 -TTAAAGTTTT-TATTAAAAATAATTATTTC
1 TTTAAAGTTTTAT-TTAAAAAAAATAAATTC
100189 TTTAAA
1 TTTAAA
100195 TTCGATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 24 0.80
30 5 0.17
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTAAAGTTTTATTTAAAAAAAATAAATTC
Found at i:100434 original size:16 final size:16
Alignment explanation
Indices: 100382--100438 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
100372 GATCCAAACA
*
100382 TAAAAAATAATATGAT
1 TAAAAAATAATATAAT
* *
100398 TAAATAA-AAT-TAAA
1 TAAAAAATAATATAAT
*
100412 AATAAAAATAATATAAT
1 TA-AAAAATAATATAAT
100429 TAAAAAATAA
1 TAAAAAATAA
100439 AAAGTAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 3 0.10
15 7 0.23
16 17 0.55
17 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAAAAATAATATAAT
Found at i:100454 original size:23 final size:22
Alignment explanation
Indices: 100400--100441 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
100390 AATATGATTA
*
100400 AATAAAATT-AAAAATAAAAAT
1 AATATAATTAAAAAATAAAAAT
100421 AATATAATTAAAAAATAAAAA
1 AATATAATTAAAAAATAAAAA
100442 GTAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AATATAATTAAAAAATAAAAAT
Found at i:100840 original size:17 final size:19
Alignment explanation
Indices: 100811--100846 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
100801 ATATATTATT
100811 TAAAAAATAAATT-AATTA
1 TAAAAAATAAATTGAATTA
100829 TAAAAAAT-AATTGAATTA
1 TAAAAAATAAATTGAATTA
100847 ATATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAAAAATAAATTGAATTA
Found at i:122131 original size:22 final size:22
Alignment explanation
Indices: 122104--122181 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
122094 CAGTCTGAAT
* *
122104 GCTGAACGGTTCAACATTCAAC
1 GCTGAATGGTTCAGCATTCAAC
* *
122126 GTTGAATAGTTCAGCATTCAAC
1 GCTGAATGGTTCAGCATTCAAC
122148 GCTGAATGGTTCAGCATTCAAC
1 GCTGAATGGTTCAGCATTCAAC
*
122170 GCTGAATAGTTC
1 GCTGAATGGTTC
122182 CATTCAGAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (22 bp):
GCTGAATGGTTCAGCATTCAAC
Found at i:122840 original size:26 final size:26
Alignment explanation
Indices: 122806--122858 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
122796 ATTAATGATA
* *
122806 AAAATAAATAAATATAGATAGCAAAT
1 AAAAGAAATAAATACAGATAGCAAAT
122832 AAAAGAAATAAATACAGATAGCAAAT
1 AAAAGAAATAAATACAGATAGCAAAT
122858 A
1 A
122859 GGAGTAGACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (26 bp):
AAAAGAAATAAATACAGATAGCAAAT
Found at i:123378 original size:23 final size:23
Alignment explanation
Indices: 123352--123397 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
123342 AATGAGAGAT
*
123352 ATATATAA-TAAAATCTTATAAAA
1 ATATATAATTAAAAT-ATATAAAA
*
123375 ATATTTAATTAAAATATATAAAA
1 ATATATAATTAAAATATATAAAA
123398 TAATTACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATATAATTAAAATATATAAAA
Found at i:128256 original size:179 final size:180
Alignment explanation
Indices: 127955--128313 Score: 711
Period size: 179 Copynumber: 2.0 Consensus size: 180
127945 ACATACTCCT
127955 ATAAAATTTACAAATTCCAATACACAAAGAAAGGCACTACAAAAAAAAACCCATACAAATGTGTT
1 ATAAAATTTACAAATTCCAATACACAAAGAAAGGCACTACAAAAAAAAACCCATACAAATGTGTT
128020 ACCACCACCAGAAACAATGCTTTATATTTATATATATTGTGAAATTAATGATATACTTACCTGGC
66 ACCACCACCAGAAACAATGCTTTATATTTATATATATTGTGAAATTAATGATATACTTACCTGGC
128085 TGTTCTGCAACTGAATACACACATCATCTATGTTACCCTCGTGTTAATCA
131 TGTTCTGCAACTGAATACACACATCATCTATGTTACCCTCGTGTTAATCA
128135 ATAAAATTTACAAATTCCAATACACAAAGAAAGGCACTAC-AAAAAAAACCCATACAAATGTGTT
1 ATAAAATTTACAAATTCCAATACACAAAGAAAGGCACTACAAAAAAAAACCCATACAAATGTGTT
128199 ACCACCACCAGAAACAATGCTTTATATTTATATATATTGTGAAATTAATGATATACTTACCTGGC
66 ACCACCACCAGAAACAATGCTTTATATTTATATATATTGTGAAATTAATGATATACTTACCTGGC
128264 TGTTCTGCAACTGAATACACACATCATCTATGTTACCCTCGTGTTAATCA
131 TGTTCTGCAACTGAATACACACATCATCTATGTTACCCTCGTGTTAATCA
128314 CTCCACAGAG
Statistics
Matches: 179, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
179 139 0.78
180 40 0.22
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (180 bp):
ATAAAATTTACAAATTCCAATACACAAAGAAAGGCACTACAAAAAAAAACCCATACAAATGTGTT
ACCACCACCAGAAACAATGCTTTATATTTATATATATTGTGAAATTAATGATATACTTACCTGGC
TGTTCTGCAACTGAATACACACATCATCTATGTTACCCTCGTGTTAATCA
Found at i:134160 original size:21 final size:21
Alignment explanation
Indices: 134050--134159 Score: 175
Period size: 21 Copynumber: 5.2 Consensus size: 21
134040 CACCAGTCGT
134050 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
134071 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
*
134092 TGCGATTTTGGATTATCGCAA
1 TGCGATTTTGGACTATCGCAA
134113 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
** * *
134134 TGCGAACTTCGATTATCGCAA
1 TGCGATTTTGGACTATCGCAA
134155 TGCGA
1 TGCGA
134160 ATATGTAAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
TGCGATTTTGGACTATCGCAA
Found at i:134199 original size:21 final size:20
Alignment explanation
Indices: 134169--134246 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 20
134159 AATATGTAAA
*
134169 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAA-T
*
134190 TCGCATTGCGATAGTCGACT
1 TCGCATTGCGATAGTCGAAT
*
134210 ATCGCATTGCGAT-TTAC-ATAT
1 -TCGCATTGCGATAGT-CGA-AT
134231 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
134247 AAAAATCGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 16 0.33
21 32 0.67
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCGAAT
Found at i:134257 original size:21 final size:21
Alignment explanation
Indices: 134166--134259 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 21
134156 GCGAATATGT
* *
134166 AAATCGCAATGCGATAGTCGA
1 AAATCGCATTGCGATAGTCAA
** *
134187 AGTTCGCATTGCGATAGTCGA
1 AAATCGCATTGCGATAGTCAA
** *
134208 CTATCGCATTGCGAT--TTACA
1 AAATCGCATTGCGATAGTCA-A
* *
134228 TATTCGCATTGCGATAGTCAA
1 AAATCGCATTGCGATAGTCAA
134249 AAATCGCATTG
1 AAATCGCATTG
134260 TGAATCTGGA
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.02
20 13 0.23
21 40 0.71
22 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (21 bp):
AAATCGCATTGCGATAGTCAA
Found at i:143495 original size:20 final size:21
Alignment explanation
Indices: 143462--143500 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
143452 AAATTTTAAA
143462 TTTTTATATCTTTTAGATTTT
1 TTTTTATATCTTTTAGATTTT
*
143483 TTTTTATAT-TTTTTGATT
1 TTTTTATATCTTTTAGATT
143501 GATAATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTATATCTTTTAGATTTT
Found at i:146486 original size:60 final size:59
Alignment explanation
Indices: 146390--146544 Score: 165
Period size: 59 Copynumber: 2.6 Consensus size: 59
146380 CATACATACT
* * * *
146390 CAAACTATGATATTCTTTCTAAATTAGTCCCTAAACTTCTAAATATTTTATTTTTATCCC
1 CAAACTATGATATTCATTCTAAATTAGTCCCTAAACTT-TAAACATTTTAGTTTCATCCC
* *
146450 TAAACTATGACTATT-ATTCTAAATTTA-T-CCTCAAACTTTTAACATTTTAGTTTCATCCC
1 CAAACTATGA-TATTCATTCTAAA-TTAGTCCCT-AAACTTTAAACATTTTAGTTTCATCCC
* *
146509 CAAACTAT-ATTTGTCATTCTAAATTGGTCCCTAAAC
1 CAAACTATGATAT-TCATTCTAAATTAGTCCCTAAAC
146545 GTTTCCAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 15
0.77 0.09 0.15
Matches are distributed among these distances:
57 2 0.03
58 4 0.05
59 40 0.51
60 26 0.33
61 7 0.09
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.43
Consensus pattern (59 bp):
CAAACTATGATATTCATTCTAAATTAGTCCCTAAACTTTAAACATTTTAGTTTCATCCC
Found at i:147263 original size:28 final size:27
Alignment explanation
Indices: 147198--147256 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
147188 TTGATATATG
147198 AAAAATATTATAATGTTTTTCATTTAA
1 AAAAATATTATAATGTTTTTCATTTAA
*
147225 AAAAATATTATGATGTTTTTCATTTAA
1 AAAAATATTATAATGTTTTTCATTTAA
147252 AAAAA
1 AAAAA
147257 ATGTTATTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (27 bp):
AAAAATATTATAATGTTTTTCATTTAA
Found at i:147484 original size:14 final size:14
Alignment explanation
Indices: 147467--147501 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
147457 TAAGATAAAT
147467 ATAATCAATAAAAA
1 ATAATCAATAAAAA
*
147481 ATAATTAATAAAAA
1 ATAATCAATAAAAA
*
147495 AAAATCA
1 ATAATCA
147502 GAGTGAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAATCAATAAAAA
Found at i:157053 original size:21 final size:21
Alignment explanation
Indices: 157024--157072 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
157014 CCCGCCACAC
* *
157024 CCACAATAGCGCCTGCGACGG
1 CCACAATAGCACCCGCGACGG
*
157045 CCGCAATAGCACCCGCGACGG
1 CCACAATAGCACCCGCGACGG
157066 CCACAAT
1 CCACAAT
157073 CACGGTAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.41, G:0.24, T:0.08
Consensus pattern (21 bp):
CCACAATAGCACCCGCGACGG
Found at i:159027 original size:54 final size:54
Alignment explanation
Indices: 158955--159072 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 54
158945 AAGAAATGCG
* * *
158955 ATACCTCTGGAGACAGTTTATACATACTTTAACGAACCTGATATAAATTATTTT
1 ATACCTCCGGAGACAGTTTATACATACTTCAACGAACATGATATAAATTATTTT
* * *
159009 ATTCCTCCGGAGACAGTTTATACATGCTTCAACGAATATGATATAAATTATTTT
1 ATACCTCCGGAGACAGTTTATACATACTTCAACGAACATGATATAAATTATTTT
159063 ATACCTCCGG
1 ATACCTCCGG
159073 GTTAACACCT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (54 bp):
ATACCTCCGGAGACAGTTTATACATACTTCAACGAACATGATATAAATTATTTT
Found at i:160936 original size:13 final size:13
Alignment explanation
Indices: 160918--160942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
160908 ACCTGATTCT
160918 AAATTATTTTAAA
1 AAATTATTTTAAA
160931 AAATTATTTTAA
1 AAATTATTTTAA
160943 TTAGATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTATTTTAAA
Found at i:161390 original size:18 final size:18
Alignment explanation
Indices: 161367--161412 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
161357 TTTCCCTCGG
161367 CGAGGAAGAAGACACGGT
1 CGAGGAAGAAGACACGGT
161385 CGAGGAAGAAGACACGGT
1 CGAGGAAGAAGACACGGT
161403 CGAGGAAGAA
1 CGAGGAAGAA
161413 AAGAATTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.15, G:0.39, T:0.04
Consensus pattern (18 bp):
CGAGGAAGAAGACACGGT
Found at i:164612 original size:13 final size:13
Alignment explanation
Indices: 164585--164652 Score: 54
Period size: 13 Copynumber: 5.3 Consensus size: 13
164575 ACCGTGATTT
* *
164585 TTAAAATTTAAAA
1 TTAAAATATATAA
164598 TTAAAATATATAA
1 TTAAAATATATAA
164611 TTCAAAA-ATATAA
1 TT-AAAATATATAA
164624 TCTAAAA-AT-TAA
1 T-TAAAATATATAA
*
164636 -TAAAATAGTAAAA
1 TTAAAATA-TATAA
164649 TTAA
1 TTAA
164653 TTAAAATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 5 0.11
11 1 0.02
12 4 0.09
13 28 0.61
14 8 0.17
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (13 bp):
TTAAAATATATAA
Found at i:165023 original size:30 final size:31
Alignment explanation
Indices: 164954--165020 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
164944 TGTAATACAA
* *
164954 TCCCCCAACATTTAGTCTATTTTCATTATGG
1 TCCCCCAACATTTAGTCTATTTGCAATATGG
* *
164985 TCCCCCAACTTTTAGTCTGTTTGCAATATGG
1 TCCCCCAACATTTAGTCTATTTGCAATATGG
165016 TCCCC
1 TCCCC
165021 AACGTAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCTATTTGCAATATGG
Found at i:165114 original size:29 final size:29
Alignment explanation
Indices: 165055--165114 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
165045 GCAAATGGAC
* * * *
165055 TAAAAGTTGGGGGATTCTATTGCAAGTTT
1 TAAAAGTTGGGGGATCCTAATGAAAGCTT
165084 TAAAAGTTGGGGGA-CCTAAATGAAAGCTT
1 TAAAAGTTGGGGGATCCT-AATGAAAGCTT
165113 TA
1 TA
165115 GAAAAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.32
Consensus pattern (29 bp):
TAAAAGTTGGGGGATCCTAATGAAAGCTT
Found at i:166121 original size:34 final size:36
Alignment explanation
Indices: 166080--166173 Score: 129
Period size: 34 Copynumber: 2.7 Consensus size: 36
166070 CACAATCATC
*
166080 AATTACATTTTAAACCCCAAATTCC-AAAATAC-TT
1 AATTACATTCTAAACCCCAAATTCCAAAAATACTTT
* *
166114 CATTACATTCTAAACCTCAAATTCCAAAAATACTTT
1 AATTACATTCTAAACCCCAAATTCCAAAAATACTTT
* *
166150 AATTACATGCTCAACCCCAAATTC
1 AATTACATTCTAAACCCCAAATTC
166174 ATAATTCATT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 22 0.43
35 7 0.14
36 22 0.43
ACGTcount: A:0.41, C:0.27, G:0.01, T:0.31
Consensus pattern (36 bp):
AATTACATTCTAAACCCCAAATTCCAAAAATACTTT
Found at i:167008 original size:35 final size:35
Alignment explanation
Indices: 166969--167048 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
166959 GGGGTTGGGT
166969 ATGTAATTGAAGTATTTTGGAATTTGA-GGTTTAGA
1 ATGTAATTGAAGTATTTTGG-ATTTGAGGGTTTAGA
*
167004 ATGTAATTGAAGTATTTTGGATTTTAGGGTTTAGA
1 ATGTAATTGAAGTATTTTGGATTTGAGGGTTTAGA
*
167039 GTGTAATTGA
1 ATGTAATTGA
167049 TGACTGTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 5 0.12
35 37 0.88
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGGATTTGAGGGTTTAGA
Found at i:183811 original size:27 final size:27
Alignment explanation
Indices: 183781--183832 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
183771 ACATAAATTG
* *
183781 ATTTTACATAATATTTGTAT-TATTTTA
1 ATTTTAAATAA-ATTTATATCTATTTTA
183808 ATTTTAAATAAATTTATATCTATTT
1 ATTTTAAATAAATTTATATCTATTT
183833 GTAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTAAATAAATTTATATCTATTTTA
Found at i:188921 original size:14 final size:13
Alignment explanation
Indices: 188902--188935 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
188892 TCTATATTAG
188902 TTATAATTCTTATA
1 TTATAATTCTTA-A
*
188916 TTATAAATCTTAA
1 TTATAATTCTTAA
188929 TTATAAT
1 TTATAAT
188936 CATTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATAATTCTTAA
Found at i:189056 original size:23 final size:23
Alignment explanation
Indices: 189038--189087 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
189028 TTTTTATATA
189038 ATAA-TTAA-TTAATAATTTAAAT
1 ATAATTTAATTTAA-AATTTAAAT
189060 ATAATTTAATTTAAAATTTTAAAAT
1 ATAATTTAATTTAAAA-TTT-AAAT
189085 ATA
1 ATA
189088 TATAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 6 0.25
24 7 0.29
25 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAATTTAATTTAAAATTTAAAT
Found at i:189575 original size:12 final size:12
Alignment explanation
Indices: 189560--189602 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
189550 TACTTATATA
*
189560 TATATATGTATG
1 TATATACGTATG
*
189572 TATAAACGTATG
1 TATATACGTATG
* *
189584 TATATACTTATA
1 TATATACGTATG
189596 TATATAC
1 TATATAC
189603 ATGTGTGTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (12 bp):
TATATACGTATG
Found at i:189720 original size:12 final size:12
Alignment explanation
Indices: 189703--189860 Score: 70
Period size: 12 Copynumber: 13.4 Consensus size: 12
189693 CATTATACAC
*
189703 ATATACTAATGT
1 ATATACTAATAT
*
189715 ATATACTTATAT
1 ATATACTAATAT
*
189727 ATATAC--ATAC
1 ATATACTAATAT
* **
189737 ACATA-TGTTAT
1 ATATACTAATAT
189748 ATATACT-A-AT
1 ATATACTAATAT
*
189758 ATATACTTATAT
1 ATATACTAATAT
*
189770 AT-TA-TAAACAT
1 ATATACT-AATAT
*
189781 ACTTATATTATATAT
1 A--TATACTA-ATAT
189796 ATATA-TATATAT
1 ATATACTA-ATAT
189808 ATATA-TATATAT
1 ATATACTA-ATAT
189820 ATATA-TATATAT
1 ATATACTA-ATAT
189832 ATATA-TATATAT
1 ATATACTA-ATAT
189844 ATATA-TATATAT
1 ATATACTA-ATAT
189856 ATATA
1 ATATA
189861 TATAAGTATA
Statistics
Matches: 124, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
10 17 0.14
11 13 0.10
12 81 0.65
13 5 0.04
14 3 0.02
15 5 0.04
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (12 bp):
ATATACTAATAT
Found at i:189727 original size:2 final size:2
Alignment explanation
Indices: 189722--190016 Score: 164
Period size: 2 Copynumber: 152.0 Consensus size: 2
189712 TGTATATACT
* * * *
189722 TA TA TA TA TA CA TA CA CA TA TG T- TA TA TA TA CTA -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
* *
189763 CT- TA TA TA T- TA TA AA CA TA CT- TA TA T- TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
189803 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
189845 TA TA TA TA TA TA TA TA TA TA -A GTA TA -A TG TA TA CT- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
* * * * * *
189885 TA TA TA CT- TA TA TA -A GTT TA TA TT TA TA T- TG TA TG CA TA AA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
189926 TA TA -A TG TA CA T- TA TGA TA TA TA TA CA TG CA TCA TA T- TA TCA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA T-A TA TA TA T-A
*
189968 TA -A CA T- TCA TCA TA TA TA T- TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
190008 TA TA T- TA TA
1 TA TA TA TA TA
190017 ATTGTTTCAA
Statistics
Matches: 229, Mismatches: 32, Indels: 64
0.70 0.10 0.20
Matches are distributed among these distances:
1 21 0.09
2 191 0.83
3 17 0.07
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:189735 original size:43 final size:43
Alignment explanation
Indices: 189687--189771 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
189677 TGTGTGTGTG
*
189687 TACATACA-TTAT-ACACATATACTAATGTATATACTTATATATA
1 TACATACACATATGACACATATACTAA--TATATACTTATATATA
** *
189730 TACATACACATATGTTATATATACTAATATATACTTATATAT
1 TACATACACATATGACACATATACTAATATATACTTATATAT
189772 TATAAACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 23 0.64
44 3 0.08
45 10 0.28
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.41
Consensus pattern (43 bp):
TACATACACATATGACACATATACTAATATATACTTATATATA
Found at i:190933 original size:21 final size:21
Alignment explanation
Indices: 190909--190953 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
190899 GTTTGTTAAT
*
190909 GATGTGGCCCGATTTAAACGA
1 GATGTGACCCGATTTAAACGA
190930 GATGTGACCCGATTTAAACGA
1 GATGTGACCCGATTTAAACGA
190951 GAT
1 GAT
190954 CCGCCTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (21 bp):
GATGTGACCCGATTTAAACGA
Found at i:195136 original size:12 final size:12
Alignment explanation
Indices: 195119--195163 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
195109 AGGGGATGAT
195119 GATGATGAAGAA
1 GATGATGAAGAA
*
195131 GATGATGATGAA
1 GATGATGAAGAA
195143 GA--A-GAAGAA
1 GATGATGAAGAA
*
195152 GATGAAGAAGAA
1 GATGATGAAGAA
195164 AAATAAGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 1 0.04
12 19 0.68
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (12 bp):
GATGATGAAGAA
Found at i:195136 original size:15 final size:15
Alignment explanation
Indices: 195116--195162 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
195106 ACAAGGGGAT
195116 GATGATGATGAAGAA
1 GATGATGATGAAGAA
195131 GATGATGATGAAGAA
1 GATGATGATGAAGAA
* *
195146 GAAGAAGATGAAGAA
1 GATGATGATGAAGAA
195161 GA
1 GA
195163 AAAATAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.34, T:0.15
Consensus pattern (15 bp):
GATGATGATGAAGAA
Found at i:195136 original size:18 final size:18
Alignment explanation
Indices: 195113--195163 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
195103 GAAACAAGGG
*
195113 GATGATGATGATGAAGAA
1 GATGATGATGAAGAAGAA
195131 GATGATGATGAAGAAGAA
1 GATGATGATGAAGAAGAA
* *
195149 GAAGATGAAGAAGAA
1 GATGATGATGAAGAA
195164 AAATAAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.33, T:0.16
Consensus pattern (18 bp):
GATGATGATGAAGAAGAA
Found at i:195171 original size:12 final size:15
Alignment explanation
Indices: 195122--195175 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
195112 GGATGATGAT
* *
195122 GATGAAGAAGATGAT
1 GATGAAGAAGAAGAA
195137 GATGAAGAAGAAGAA
1 GATGAAGAAGAAGAA
195152 GATGAAGAAGAA-AA
1 GATGAAGAAGAAGAA
195166 -AT-AAGAAGAA
1 GATGAAGAAGAA
195176 TTAGAAGCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
12 8 0.22
13 2 0.05
14 2 0.05
15 25 0.68
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (15 bp):
GATGAAGAAGAAGAA
Found at i:202486 original size:3 final size:3
Alignment explanation
Indices: 202478--202519 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
202468 GAAAATTGCA
202478 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
202520 GAAATAAGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:204979 original size:15 final size:16
Alignment explanation
Indices: 204961--204999 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
204951 TATTATTTTG
204961 ATTAAAAAT-CAAAAT
1 ATTAAAAATACAAAAT
*
204976 ATTAAGAATACAAAAT
1 ATTAAAAATACAAAAT
*
204992 ACTAAAAA
1 ATTAAAAA
205000 CCACCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (16 bp):
ATTAAAAATACAAAAT
Found at i:207227 original size:19 final size:20
Alignment explanation
Indices: 207205--207242 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
207195 TTATGTTTAA
*
207205 AATTTAAAT-TTAGATAAAT
1 AATTCAAATATTAGATAAAT
*
207224 AATTCAATTATTAGATAAA
1 AATTCAAATATTAGATAAA
207243 CTGAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (20 bp):
AATTCAAATATTAGATAAAT
Found at i:211036 original size:18 final size:21
Alignment explanation
Indices: 210994--211042 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 21
210984 TTTTTTTTAC
*
210994 TTTCAATTTTATATATAGATT
1 TTTCTATTTTATATATAGATT
211015 TTTCTATTTTA-ATA-AG-TT
1 TTTCTATTTTATATATAGATT
211033 TTTCTATTTT
1 TTTCTATTTT
211043 TGTGATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.44
19 2 0.07
20 3 0.11
21 10 0.37
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTCTATTTTATATATAGATT
Found at i:211989 original size:5 final size:5
Alignment explanation
Indices: 211979--212003 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
211969 CCACAATTAT
211979 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
212004 TTAAAAATAT
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):
ATTTA
Found at i:218915 original size:84 final size:84
Alignment explanation
Indices: 218796--219143 Score: 373
Period size: 84 Copynumber: 4.1 Consensus size: 84
218786 TGAACTTCAG
* * * *
218796 TATCCGATTTGTCTTTCGAGAGCCTCGGTGGTTGAAATGCACTATCTGATTTGCTCACTAGGAGC
1 TATCTGATTTGTCCTTCGAGAGCCTCGGTGATTGAAATGCACTATCTGATTTGTTCACTAGGAGC
* * *
218861 CTGGGGGATTGACCTCCCC
66 CAGGGGAATTGAACTCCCC
* * * *
218880 TGTCTGGTTTGTCCTTCGAGATCCTCGGTGATTGAACA-GCACT-TCCTGATCTGTTCACTAGGA
1 TATCTGATTTGTCCTTCGAGAGCCTCGGTGATTGAA-ATGCACTAT-CTGATTTGTTCACTAGGA
* *
218943 GCCCGGGGAATTGAACTCCGC
64 GCCAGGGGAATTGAACTCCCC
* * * ** *
218964 TATCTGATTCGTCCTTCGAGATCCTCGGTGATTGAACTGCACTATCCAACTTGTTCACT-GGAAG
1 TATCTGATTTGTCCTTCGAGAGCCTCGGTGATTGAAATGCACTATCTGATTTGTTCACTAGG-AG
* *
219028 CCAGGCGTATTGAACTCCCC
65 CCAGGGGAATTGAACTCCCC
* * * * *
219048 TATCTGATTTGTCCTTCAAGAGCCTCGGTGATTGAACTGCACTATCCGACTTGTTCACT-GCAAG
1 TATCTGATTTGTCCTTCGAGAGCCTCGGTGATTGAAATGCACTATCTGATTTGTTCACTAG-GAG
219112 CCAGGTGG-ATTGAACTCCCC
65 CCAGG-GGAATTGAACTCCCC
*
219132 CATCTGATTTGT
1 TATCTGATTTGT
219144 TCTTACGAAC
Statistics
Matches: 226, Mismatches: 31, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
83 3 0.01
84 220 0.97
85 3 0.01
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (84 bp):
TATCTGATTTGTCCTTCGAGAGCCTCGGTGATTGAAATGCACTATCTGATTTGTTCACTAGGAGC
CAGGGGAATTGAACTCCCC
Found at i:219009 original size:42 final size:42
Alignment explanation
Indices: 218781--219093 Score: 187
Period size: 42 Copynumber: 7.5 Consensus size: 42
218771 GGAAGCCTAG
* * * *
218781 GGTG-TTGAACTTCAGTATCCGATTTGTCTTTCGAGAGCCTC
1 GGTGATTGAACTGCACTATCTGATTTGTCCTTCGAGAGCCTC
* * * *
218822 GGTGGTTGAAATGCACTATCTGATTTGCTCAC-TAG-GAGCCTG
1 GGTGATTGAACTGCACTATCTGATTTG-TC-CTTCGAGAGCCTC
* * * * * * *
218864 GGGGATTGACCTCCCCTGTCTGGTTTGTCCTTCGAGATCCTC
1 GGTGATTGAACTGCACTATCTGATTTGTCCTTCGAGAGCCTC
* * *
218906 GGTGATTGAACAGCACT-TCCTGATCTGTTCAC-TAG-GAGCC-C
1 GGTGATTGAACTGCACTAT-CTGATTTG-TC-CTTCGAGAGCCTC
* * * * *
218947 GGGGAATTGAACTCCGCTATCTGATTCGTCCTTCGAGATCCTC
1 GGTG-ATTGAACTGCACTATCTGATTTGTCCTTCGAGAGCCTC
** * * *
218990 GGTGATTGAACTGCACTATCCAACTTGTTCAC-TGGA-AGCC-A
1 GGTGATTGAACTGCACTATCTGATTTG-TC-CTTCGAGAGCCTC
* * * *
219031 GGCGTATTGAACTCCCCTATCTGATTTGTCCTTCAAGAGCCTC
1 GGTG-ATTGAACTGCACTATCTGATTTGTCCTTCGAGAGCCTC
219074 GGTGATTGAACTGCACTATC
1 GGTGATTGAACTGCACTATC
219094 CGACTTGTTC
Statistics
Matches: 196, Mismatches: 57, Indels: 37
0.68 0.20 0.13
Matches are distributed among these distances:
40 3 0.02
41 24 0.12
42 146 0.74
43 21 0.11
44 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (42 bp):
GGTGATTGAACTGCACTATCTGATTTGTCCTTCGAGAGCCTC
Found at i:219123 original size:42 final size:42
Alignment explanation
Indices: 218993--219127 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 42
218983 GATCCTCGGT
* * *
218993 GATTGAACTGCACTATCCAACTTGTTCACTGGAAGCCAGGCG
1 GATTGAACTGCACTATCCGACTTGTTCACTGCAAGCCAGGTG
* * * * * * *
219035 TATTGAACTCCCCTATCTGATTTG-TC-CTTCAAGAGCCTCGGT-
1 GATTGAACTGCACTATCCGACTTGTTCACTGC-A-AGCC-AGGTG
219077 GATTGAACTGCACTATCCGACTTGTTCACTGCAAGCCAGGTG
1 GATTGAACTGCACTATCCGACTTGTTCACTGCAAGCCAGGTG
219119 GATTGAACT
1 GATTGAACT
219128 CCCCCATCTG
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.03
41 6 0.09
42 54 0.77
43 5 0.07
44 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (42 bp):
GATTGAACTGCACTATCCGACTTGTTCACTGCAAGCCAGGTG
Found at i:219144 original size:42 final size:42
Alignment explanation
Indices: 219014--219145 Score: 126
Period size: 42 Copynumber: 3.1 Consensus size: 42
219004 ACTATCCAAC
* * *
219014 TTGTTCACTGGAAGCCAGGCGTATTGAACTCCCCTATCTGAT
1 TTGTTCACTGCAAGCCAGGTGGATTGAACTCCCCTATCTGAT
* * * * * *
219056 TTG-TC-CTTCAAGAGCCTCGGT-GATTGAACTGCACTATCCGAC
1 TTGTTCACTGC-A-AGCC-AGGTGGATTGAACTCCCCTATCTGAT
*
219098 TTGTTCACTGCAAGCCAGGTGGATTGAACTCCCCCATCTGAT
1 TTGTTCACTGCAAGCCAGGTGGATTGAACTCCCCTATCTGAT
219140 TTGTTC
1 TTGTTC
219146 TTACGAACAA
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.03
41 6 0.09
42 52 0.76
43 5 0.07
44 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.31
Consensus pattern (42 bp):
TTGTTCACTGCAAGCCAGGTGGATTGAACTCCCCTATCTGAT
Found at i:222535 original size:14 final size:14
Alignment explanation
Indices: 222516--222547 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
222506 ATGTTAGGTG
*
222516 GAGAAAGAAAGAGA
1 GAGAAAGAAAGAAA
222530 GAGAAAGAAAGAAA
1 GAGAAAGAAAGAAA
222544 GAGA
1 GAGA
222548 GATTTCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
GAGAAAGAAAGAAA
Found at i:224561 original size:27 final size:29
Alignment explanation
Indices: 224493--224561 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
224483 ATTTAGACCG
* *
224493 TCATTAAACTTTTATAATATTTTTATTTTAA
1 TCATTAAA--TTTATAATATTTATATTATAA
224524 TCA-TAATATTTA-AA-ATTTATATTATAA
1 TCATTAA-ATTTATAATATTTATATTATAA
224551 TCATTAAATTT
1 TCATTAAATTT
224562 TCAATACACT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 18 0.53
28 5 0.15
29 4 0.12
30 3 0.09
31 4 0.12
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (29 bp):
TCATTAAATTTATAATATTTATATTATAA
Found at i:225827 original size:25 final size:25
Alignment explanation
Indices: 225797--225931 Score: 270
Period size: 25 Copynumber: 5.4 Consensus size: 25
225787 ATGCATTACT
225797 GTAGCAATCAAGTCATTGATCACTG
1 GTAGCAATCAAGTCATTGATCACTG
225822 GTAGCAATCAAGTCATTGATCACTG
1 GTAGCAATCAAGTCATTGATCACTG
225847 GTAGCAATCAAGTCATTGATCACTG
1 GTAGCAATCAAGTCATTGATCACTG
225872 GTAGCAATCAAGTCATTGATCACTG
1 GTAGCAATCAAGTCATTGATCACTG
225897 GTAGCAATCAAGTCATTGATCACTG
1 GTAGCAATCAAGTCATTGATCACTG
225922 GTAGCAATCA
1 GTAGCAATCA
225932 TGAATGGTCT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 110 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (25 bp):
GTAGCAATCAAGTCATTGATCACTG
Found at i:228921 original size:23 final size:23
Alignment explanation
Indices: 228891--228952 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
228881 ATATGTTTAT
228891 CAACATGTTCATTTAGTTTCCAC
1 CAACATGTTCATTTAGTTTCCAC
*
228914 CAACATGTTCATTTAGTTTTCAC
1 CAACATGTTCATTTAGTTTCCAC
*
228937 CAACATGTTCGTTTAG
1 CAACATGTTCATTTAG
228953 CGCTGAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (23 bp):
CAACATGTTCATTTAGTTTCCAC
Found at i:231450 original size:17 final size:18
Alignment explanation
Indices: 231425--231458 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
231415 AGTTGTTTGT
*
231425 TTTTGAAAT-TAATTAAG
1 TTTTAAAATATAATTAAG
231442 TTTTAAAATATAATTAA
1 TTTTAAAATATAATTAA
231459 ATTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTTAAAATATAATTAAG
Found at i:242841 original size:80 final size:79
Alignment explanation
Indices: 242708--242867 Score: 257
Period size: 80 Copynumber: 2.0 Consensus size: 79
242698 TACATGGTGT
*
242708 TGATGTTTTAGGCTTATAAACTCGTGTAGTAATTCTAGAATGAACTCTGCTTCGTAGACTTCTAT
1 TGATGTTTTAGGCTTATAAACTCGTGTAGTAATTCTAGAATGAACTCTACTTCGTAGAC-TCTAT
*
242773 CAATAAAATTATATA
65 CAATAAAACTATATA
* * **
242788 TGATGTTTTAGTCTTATAAACTCGTGTAGTAATTTTAGAATGTGCTCTACTTCGTAGACTCTATC
1 TGATGTTTTAGGCTTATAAACTCGTGTAGTAATTCTAGAATGAACTCTACTTCGTAGACTCTATC
242853 AATAAAACTATATA
66 AATAAAACTATATA
242867 T
1 T
242868 TATTTACATT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
79 20 0.27
80 54 0.73
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (79 bp):
TGATGTTTTAGGCTTATAAACTCGTGTAGTAATTCTAGAATGAACTCTACTTCGTAGACTCTATC
AATAAAACTATATA
Found at i:253282 original size:15 final size:15
Alignment explanation
Indices: 253262--253293 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
253252 TTCCTCCATT
253262 TCCCTCACTTTCCTC
1 TCCCTCACTTTCCTC
*
253277 TCCCTCTCTTTCCTC
1 TCCCTCACTTTCCTC
253292 TC
1 TC
253294 TTCTTCAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44
Consensus pattern (15 bp):
TCCCTCACTTTCCTC
Found at i:255999 original size:37 final size:38
Alignment explanation
Indices: 255929--256001 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
255919 AACACGAACC
* *
255929 CGACCTGAATATCACACTTAAAAAAACTCGACCCGACT
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
255967 CGACCCGAATATCACACTT-AAAAAACCCGACCCGA
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGA
256002 ACAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.40, C:0.34, G:0.11, T:0.15
Consensus pattern (38 bp):
CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
Found at i:260757 original size:38 final size:39
Alignment explanation
Indices: 260714--260795 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 39
260704 TCATTAAACC
* *
260714 TTTTTAT-ATTTTCAATTTTGTAAATAAAAAT-TATAAAT-
1 TTTTTATGAATTTAAATTTT-TAAA-AAAAATATATAAATA
*
260752 TTTTTATGAATTTAAATTTTTAAAGAAAATATATAAATA
1 TTTTTATGAATTTAAATTTTTAAAAAAAATATATAAATA
260791 TTTTT
1 TTTTT
260796 CAACTTGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 5 0.13
38 18 0.47
39 15 0.39
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (39 bp):
TTTTTATGAATTTAAATTTTTAAAAAAAATATATAAATA
Found at i:262690 original size:16 final size:17
Alignment explanation
Indices: 262659--262690 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
262649 ATTTACGGGC
262659 TAAAATATATAATTTTT
1 TAAAATATATAATTTTT
262676 TAAAAT-TAT-ATTTTT
1 TAAAATATATAATTTTT
262691 GGTCACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAATATATAATTTTT
Found at i:267294 original size:22 final size:22
Alignment explanation
Indices: 267266--267308 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
267256 AAATTTTACA
*
267266 AATGACTAATGTGTAATAGTTG
1 AATGACTAATATGTAATAGTTG
267288 AATGACTAATATGTAATAGTT
1 AATGACTAATATGTAATAGTT
267309 CGATAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (22 bp):
AATGACTAATATGTAATAGTTG
Found at i:289536 original size:16 final size:16
Alignment explanation
Indices: 289515--289556 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
289505 AGATAATATC
289515 TAAAAGTATTATTACT
1 TAAAAGTATTATTACT
289531 TAAAAGTATTATTACT
1 TAAAAGTATTATTACT
289547 TAAAAGTATT
1 TAAAAGTATT
289557 TTTAACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (16 bp):
TAAAAGTATTATTACT
Found at i:290075 original size:21 final size:21
Alignment explanation
Indices: 290037--290077 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
290027 TGATAGTTTA
* *
290037 TGATGGTACATAATATTGATG
1 TGATGGTACACAAAATTGATG
*
290058 TGATGGTTCACAAAATTGAT
1 TGATGGTACACAAAATTGAT
290078 ATGAAAGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (21 bp):
TGATGGTACACAAAATTGATG
Found at i:290846 original size:6 final size:7
Alignment explanation
Indices: 290820--290845 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
290810 AATTTTAAAT
290820 ATTTTTA
1 ATTTTTA
290827 ATTTTTA
1 ATTTTTA
290834 ATTTTTA
1 ATTTTTA
290841 ATTTT
1 ATTTT
290846 ATTGAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTA
Found at i:295216 original size:39 final size:39
Alignment explanation
Indices: 295161--295244 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
295151 GAAATGTAGT
295161 CCTCAGAAGAAATTAGACTTATTTATACTATGTTATGCA
1 CCTCAGAAGAAATTAGACTTATTTATACTATGTTATGCA
* * *
295200 CCTCAGAAGAACTTAGACTTATTTATATTATGTTATGTA
1 CCTCAGAAGAAATTAGACTTATTTATACTATGTTATGCA
295239 CCTCAG
1 CCTCAG
295245 CTACTAGTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (39 bp):
CCTCAGAAGAAATTAGACTTATTTATACTATGTTATGCA
Found at i:297460 original size:18 final size:15
Alignment explanation
Indices: 297431--297487 Score: 105
Period size: 15 Copynumber: 3.8 Consensus size: 15
297421 CCTACCCCTG
*
297431 CCTCTTCCACCACCA
1 CCTCTCCCACCACCA
297446 CCTCTCCCACCACCA
1 CCTCTCCCACCACCA
297461 CCTCTCCCACCACCA
1 CCTCTCCCACCACCA
297476 CCTCTCCCACCA
1 CCTCTCCCACCA
297488 TAAGATATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.19, C:0.65, G:0.00, T:0.16
Consensus pattern (15 bp):
CCTCTCCCACCACCA
Found at i:302396 original size:13 final size:13
Alignment explanation
Indices: 302380--302405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
302370 TCTGTGAATA
302380 TCTACTAATATTC
1 TCTACTAATATTC
302393 TCTACTAATATTC
1 TCTACTAATATTC
302406 AACAAGAGGG
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:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
TCTACTAATATTC
Found at i:302519 original size:23 final size:23
Alignment explanation
Indices: 302479--302522 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
302469 GGAAAAAAAG
*
302479 ACATACTATGAAAGTAGACAATA
1 ACATACTATAAAAGTAGACAATA
* *
302502 ACATATTATAAAATTAGACAA
1 ACATACTATAAAAGTAGACAA
302523 ATCATACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (23 bp):
ACATACTATAAAAGTAGACAATA
Found at i:313315 original size:20 final size:20
Alignment explanation
Indices: 313290--313327 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
313280 CTCTAGGACA
313290 CCTATTCAGTATCAATGACG
1 CCTATTCAGTATCAATGACG
313310 CCTATTCAGTATCAATGA
1 CCTATTCAGTATCAATGA
313328 AGCGACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (20 bp):
CCTATTCAGTATCAATGACG
Found at i:319070 original size:5 final size:5
Alignment explanation
Indices: 319060--319091 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
319050 TTAACCCATT
319060 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
319092 GCATGTGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:319345 original size:8 final size:8
Alignment explanation
Indices: 319332--319361 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
319322 ATTATAGTAA
319332 AATTTATT
1 AATTTATT
319340 AATTTATT
1 AATTTATT
*
319348 AATTAATT
1 AATTTATT
319356 AATTTA
1 AATTTA
319362 AATCACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
AATTTATT
Found at i:321160 original size:2 final size:2
Alignment explanation
Indices: 321153--321184 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
321143 TAAATTGTGC
321153 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
321185 TTTACGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.