Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 24
Found at i:4197642 original size:22 final size:22
Alignment explanation
Indices: 4197614--4197707 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
4197604 AATTTGGAAA
*
4197614 ATCGCAACGAAAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
4197636 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
4197658 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
4197677 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
4197699 ATCGTAACG
1 ATCGCAACG
4197708 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 13 0.22
20 2 0.03
21 2 0.03
22 42 0.71
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:4197718 original size:41 final size:42
Alignment explanation
Indices: 4197636--4197725 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 42
4197626 ACTGTAGACT
*
4197636 ATCGCAACGACAACTGTAGACTATCGCAACGAATTTGG-AAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAAA
*
4197677 ATCGCAACGACAACTGTAGACTATCGTAACGCGAA-AT-GAAAA
1 ATCGCAACGACAACTGTAGACTATCGCAA--CGAATATGGAAAA
4197719 ATCGCAA
1 ATCGCAA
4197726 ACTGATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 29 0.66
42 11 0.25
43 4 0.09
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (42 bp):
ATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAAA
Found at i:4204047 original size:45 final size:45
Alignment explanation
Indices: 4203991--4204081 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
4203981 CAAGAAGTTA
* * *
4203991 AACAGGGTGAACGGGTGAAGAAATAAT-AGGCGGAACGAGTGATTG
1 AACAGGCTGAACAGGTGAAGAAATAATCA-GCGAAACGAGTGATTG
* *
4204036 AACAGGCTGAACAGGTGAAGGAATAATCAGCGAAACGAGTGGTTG
1 AACAGGCTGAACAGGTGAAGAAATAATCAGCGAAACGAGTGATTG
4204081 A
1 A
4204082 CCAAGTTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 39 0.98
46 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.35, T:0.15
Consensus pattern (45 bp):
AACAGGCTGAACAGGTGAAGAAATAATCAGCGAAACGAGTGATTG
Found at i:4204092 original size:45 final size:45
Alignment explanation
Indices: 4203998--4204092 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
4203988 TTAAACAGGG
* * *
4203998 TGAACGGGTGAAGAAATAATAGGCGGAACGAGTGATTGAACAGGC
1 TGAACAGGTGAAGAAATAATAGGCGAAACGAGTGATTGAACAAGC
* * * *
4204043 TGAACAGGTGAAGGAATAATCA-GCGAAACGAGTGGTTGACCAAGT
1 TGAACAGGTGAAGAAATAAT-AGGCGAAACGAGTGATTGAACAAGC
4204088 TGAAC
1 TGAAC
4204093 GATAGTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.33, T:0.17
Consensus pattern (45 bp):
TGAACAGGTGAAGAAATAATAGGCGAAACGAGTGATTGAACAAGC
Found at i:4208946 original size:36 final size:36
Alignment explanation
Indices: 4208899--4209007 Score: 193
Period size: 36 Copynumber: 3.0 Consensus size: 36
4208889 GAACAACAGA
*
4208899 AACATCAACACCACCAAGGATGGCTACGAAGGCAAC
1 AACATCGACACCACCAAGGATGGCTACGAAGGCAAC
4208935 AACATCGACACCACCAAGGATGGCTACGAAGGCAAC
1 AACATCGACACCACCAAGGATGGCTACGAAGGCAAC
4208971 AACATCGACACCACCAAGGATGGC-AGCGAAGGCAAC
1 AACATCGACACCACCAAGGATGGCTA-CGAAGGCAAC
4209007 A
1 A
4209008 TCATTAACAA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 1 0.01
36 70 0.99
ACGTcount: A:0.40, C:0.30, G:0.22, T:0.07
Consensus pattern (36 bp):
AACATCGACACCACCAAGGATGGCTACGAAGGCAAC
Found at i:4209074 original size:18 final size:18
Alignment explanation
Indices: 4209026--4209062 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4209016 AACAAAGCGG
* *
4209026 ACAACAACAACAACGACA
1 ACAATAACAACAACGAAA
4209044 ACAATAACAACAACGAAA
1 ACAATAACAACAACGAAA
4209062 A
1 A
4209063 TGAAAACAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.27, G:0.05, T:0.03
Consensus pattern (18 bp):
ACAATAACAACAACGAAA
Found at i:4209175 original size:24 final size:24
Alignment explanation
Indices: 4209148--4209193 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
4209138 GAATGAGGAC
*
4209148 AACACAAATGACAAGAACAATAGT
1 AACACAAATGACAACAACAATAGT
***
4209172 AACAGTGATGACAACAACAATA
1 AACACAAATGACAACAACAATA
4209194 ACTCTGCTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (24 bp):
AACACAAATGACAACAACAATAGT
Found at i:4209267 original size:39 final size:39
Alignment explanation
Indices: 4209214--4209336 Score: 219
Period size: 39 Copynumber: 3.2 Consensus size: 39
4209204 AGCACCAACT
* * *
4209214 CAGCCTTCTCCTTTGGAGCATAGGGATTCAGCTTACCAA
1 CAGCCTCCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
4209253 CAGCCTCCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
1 CAGCCTCCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
4209292 CAGCCTCCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
1 CAGCCTCCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
4209331 CAGCCT
1 CAGCCT
4209337 GCTCCCCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (39 bp):
CAGCCTCCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
Found at i:4216862 original size:20 final size:20
Alignment explanation
Indices: 4216818--4216873 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
4216808 TCGCGTTGCA
*
4216818 AAATTCTCGTTGCGAAAACG
1 AAATTCGCGTTGCGAAAACG
*
4216838 AAATTCGCGTTGCGAAATTCG
1 AAATTCGCGTTGCGAAA-ACG
*
4216859 -AATTCGAGTTGCGAA
1 AAATTCGCGTTGCGAA
4216874 TTTGAAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (20 bp):
AAATTCGCGTTGCGAAAACG
Found at i:4217004 original size:20 final size:20
Alignment explanation
Indices: 4216981--4217028 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
4216971 TTAATTTTGT
4216981 GTTGCGAATTCA-AAATTCAC
1 GTTGCGAATTCAGAAATT-AC
* *
4217001 GTTGCGAATTTAGAAATTGC
1 GTTGCGAATTCAGAAATTAC
4217021 GTTGCGAA
1 GTTGCGAA
4217029 ATTGGAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATTAC
Found at i:4217240 original size:18 final size:16
Alignment explanation
Indices: 4217219--4217261 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
4217209 GTAGAACTAG
4217219 ATATTTTGGATGTATTTT
1 ATATTTT-GAT-TATTTT
4217237 ATATTTAATGATTATTTT
1 ATATTT--TGATTATTTT
4217255 ATATTTT
1 ATATTTT
4217262 CAAAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
18 18 0.78
19 3 0.13
20 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (16 bp):
ATATTTTGATTATTTT
Found at i:4218498 original size:44 final size:43
Alignment explanation
Indices: 4218415--4218500 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 43
4218405 TTGAGTCTTG
* *
4218415 GTGGGCAGGATAATTTGAGAATGAGGATGGTTTCCGAAAGGACT
1 GTGGGCAGGATAATTTGAGAATAAGGACGGTTT-CGAAAGGACT
4218459 GTGGGCAGGATAATTTGATGAATAAGGACGGTGTT-GAAAGGA
1 GTGGGCAGGATAATTTGA-GAATAAGGACGGT-TTCGAAAGGA
4218501 TGCTGTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 25 0.66
45 11 0.29
46 2 0.05
ACGTcount: A:0.31, C:0.07, G:0.37, T:0.24
Consensus pattern (43 bp):
GTGGGCAGGATAATTTGAGAATAAGGACGGTTTCGAAAGGACT
Found at i:4218682 original size:18 final size:18
Alignment explanation
Indices: 4218659--4218716 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
4218649 GGTGGAGGAA
4218659 GAGGAAGTAGAGATGGGT
1 GAGGAAGTAGAGATGGGT
4218677 GAGGAAGTAGAGATGGGT
1 GAGGAAGTAGAGATGGGT
* *
4218695 GAGGAAGAAGAGATGGGA
1 GAGGAAGTAGAGATGGGT
4218713 GAGG
1 GAGG
4218717 GAGAAGAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.36, C:0.00, G:0.52, T:0.12
Consensus pattern (18 bp):
GAGGAAGTAGAGATGGGT
Found at i:4218721 original size:18 final size:18
Alignment explanation
Indices: 4218659--4218724 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
4218649 GGTGGAGGAA
*
4218659 GAGGAAGTAGAGATGGGT
1 GAGGAAGAAGAGATGGGT
*
4218677 GAGGAAGTAGAGATGGGT
1 GAGGAAGAAGAGATGGGT
*
4218695 GAGGAAGAAGAGATGGGA
1 GAGGAAGAAGAGATGGGT
*
4218713 GAGGGAGAAGAG
1 GAGGAAGAAGAG
4218725 GGAGTAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.38, C:0.00, G:0.52, T:0.11
Consensus pattern (18 bp):
GAGGAAGAAGAGATGGGT
Found at i:4218758 original size:18 final size:18
Alignment explanation
Indices: 4218735--4218783 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
4218725 GGAGTAAAAG
*
4218735 AAGAGGAACATGAGGAAC
1 AAGAGGAACATGAAGAAC
4218753 AAGAGGAGCAGCATGAAGAAC
1 AAGAGGA--A-CATGAAGAAC
*
4218774 AAGATGAACA
1 AAGAGGAACA
4218784 ACAGGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 9 0.35
19 1 0.04
20 1 0.04
21 15 0.58
ACGTcount: A:0.51, C:0.12, G:0.31, T:0.06
Consensus pattern (18 bp):
AAGAGGAACATGAAGAAC
Found at i:4235353 original size:24 final size:23
Alignment explanation
Indices: 4235321--4235376 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
4235311 CATTTAAATG
4235321 ATAAACGAACACAAATGAACAAA
1 ATAAACGAACACAAATGAACAAA
* *
4235344 CATAAACGAACATAAATGAACACA
1 -ATAAACGAACACAAATGAACAAA
4235368 ATAAACGAA
1 ATAAACGAA
4235377 TATTAACGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.11
Consensus pattern (23 bp):
ATAAACGAACACAAATGAACAAA
Found at i:4235391 original size:23 final size:23
Alignment explanation
Indices: 4235321--4235391 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
4235311 CATTTAAATG
* * *
4235321 ATAAACGAACACAAATGAACAAA
1 ATAAACGAACATAAACGAACACA
*
4235344 CATAAACGAACATAAATGAACACA
1 -ATAAACGAACATAAACGAACACA
* * *
4235368 ATAAACGAATATTAACGAATACA
1 ATAAACGAACATAAACGAACACA
4235391 A
1 A
4235392 ACGAATGAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 20 0.49
24 21 0.51
ACGTcount: A:0.61, C:0.17, G:0.08, T:0.14
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:4235606 original size:24 final size:24
Alignment explanation
Indices: 4235574--4235629 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
4235564 GATTAGGCTA
*
4235574 AACATAAATGAACACACATAAACG
1 AACATAAATGAACACAAATAAACG
*
4235598 AACATAAATGAACATAAATAAACG
1 AACATAAATGAACACAAATAAACG
4235622 AACATAAA
1 AACATAAA
4235630 CGAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.62, C:0.16, G:0.07, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACACAAATAAACG
Found at i:4235618 original size:14 final size:14
Alignment explanation
Indices: 4235577--4235629 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
4235567 TAGGCTAAAC
* * *
4235577 ATAAATGAACACAC
1 ATAAACGAACATAA
4235591 ATAAACGAACATAA
1 ATAAACGAACATAA
4235605 AT----GAACATAA
1 ATAAACGAACATAA
4235615 ATAAACGAACATAA
1 ATAAACGAACATAA
4235629 A
1 A
4235630 CGAATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 10 0.31
14 22 0.69
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:4239808 original size:22 final size:21
Alignment explanation
Indices: 4239766--4239805 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4239756 GAGTTTATTT
*
4239766 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4239787 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4239806 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4243506 original size:20 final size:20
Alignment explanation
Indices: 4243481--4243552 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
4243471 TTTTCCGACT
4243481 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* * ***
4243501 ATCGCAATACGAGTATGGCT
1 ATCGCAATGCGAATATGTAA
*
4243521 ATCGCAACGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
4243541 ATCGCAATGCGA
1 ATCGCAATGCGA
4243553 TTATTACTAT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:4243526 original size:40 final size:40
Alignment explanation
Indices: 4243477--4243572 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
4243467 GCGATTTTCC
*
4243477 GACTATCGCAATGCGAATATGTAAATCGCAATACGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATACGAGTAT
* * *
4243517 GGCTATCGCAACGCGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATACGAGTAT
*
4243557 TACTATCGCAACGCGA
1 GACTATCGCAACGCGA
4243573 TTCTGACTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCGCAATACGAGTAT
Found at i:4243564 original size:20 final size:20
Alignment explanation
Indices: 4243478--4243594 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
4243468 CGATTTTCCG
*
4243478 ACTATCGCAATGCGAATATGT
1 ACTATCGCAATGCGATTAT-T
* * * *
4243499 A-AATCGCAATACGAGTATG
1 ACTATCGCAATGCGATTATT
* * *
4243518 GCTATCGCAACGCGAATATGT
1 ACTATCGCAATGCGATTAT-T
*
4243539 A-AATCGCAATGCGATTATT
1 ACTATCGCAATGCGATTATT
* * *
4243558 ACTATCGCAACGCGATTCTG
1 ACTATCGCAATGCGATTATT
*
4243578 ACTGTCGCAATGCGATT
1 ACTATCGCAATGCGATT
4243595 TTCAAAGCGC
Statistics
Matches: 73, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
19 2 0.03
20 70 0.96
21 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ACTATCGCAATGCGATTATT
Found at i:4243811 original size:22 final size:22
Alignment explanation
Indices: 4243770--4243812 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4243760 GGTGACATCT
*
4243770 GTCCCCATCTACGACGAAATCA
1 GTCCCCATCTACGACAAAATCA
* *
4243792 GTCCCCATCTCCGGCAAAATC
1 GTCCCCATCTACGACAAAATC
4243813 CATCTATCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.40, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTACGACAAAATCA
Found at i:4244290 original size:20 final size:20
Alignment explanation
Indices: 4244195--4244288 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
4244185 GTGATTTTAG
*
4244195 TTTCGCGTTGTGATTGTCA-
1 TTTCGCGTTGCGATTGTCAT
* *
4244214 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTGTCAT
* *
4244234 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTGTCAT
* * *
4244254 TTTCGTGTTGTGATTTTCAT
1 TTTCGCGTTGCGATTGTCAT
*
4244274 TTTCGTGTTGCGATT
1 TTTCGCGTTGCGATT
4244289 TTAAGTTTCA
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 17 0.27
20 47 0.73
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGATTGTCAT
Found at i:4244297 original size:20 final size:20
Alignment explanation
Indices: 4244254--4244297 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4244244 CGATAGTCAT
* * *
4244254 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
4244274 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
4244294 TTTC
1 TTTC
4244298 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:4246230 original size:20 final size:20
Alignment explanation
Indices: 4246205--4246271 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
4246195 TAGTTTACTT
** *
4246205 TCGCAACGCGAAAATGATTA
1 TCGCAACGCGAATTTGACTA
*
4246225 TCGCAACGCGAATTTTACTA
1 TCGCAACGCGAATTTGACTA
4246245 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAATTTGACTA
4246265 TCGCAAC
1 TCGCAAC
4246272 AAAAGAATCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATTTGACTA
Found at i:4246340 original size:20 final size:20
Alignment explanation
Indices: 4246315--4246370 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
4246305 GTGATTCTCT
4246315 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
4246335 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
4246355 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
4246371 CATATTGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:4246963 original size:21 final size:21
Alignment explanation
Indices: 4246872--4246979 Score: 69
Period size: 21 Copynumber: 5.1 Consensus size: 21
4246862 GACTCACCTG
*
4246872 TCATCGTTCAAGAGGCCTC-C
1 TCATCGTTCAAGAGGCCACTC
* *
4246892 CCTATCGTTCAAGAGG-CATCTA
1 TC-ATCGTTCAAGAGGCCA-CTC
** * *
4246914 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCACTC
* * *
4246935 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCACTC
*
4246956 TCATCGTTGAAGAGGTCC-CTC
1 TCATCGTTCAAGAGG-CCACTC
4246977 TCA
1 TCA
4246980 ACATTCTAGA
Statistics
Matches: 63, Mismatches: 20, Indels: 9
0.68 0.22 0.10
Matches are distributed among these distances:
20 2 0.03
21 57 0.90
22 4 0.06
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCACTC
Found at i:4246976 original size:42 final size:43
Alignment explanation
Indices: 4246869--4246976 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 43
4246859 CCCGACTCAC
*
4246869 CTGTCATCGTTCAAGAGG--CCTCCCCTATCGTTCAAGAGGCAT
1 CTGTCATCGTTCAAGAGGTCCCT-CCCTACCGTTCAAGAGGCAT
* **
4246911 CTATCATCCCTCAAGA-GTCCCCTCCC-ACCGTTCAAGAGGCCA-
1 CTGTCATCGTTCAAGAGGT-CCCTCCCTACCGTTCAAGAGG-CAT
*
4246953 CTGTCATCGTTGAAGAGGTCCCTC
1 CTGTCATCGTTCAAGAGGTCCCTC
4246977 TCAACATTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
41 1 0.02
42 42 0.79
43 7 0.13
44 3 0.06
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.24
Consensus pattern (43 bp):
CTGTCATCGTTCAAGAGGTCCCTCCCTACCGTTCAAGAGGCAT
Found at i:4248865 original size:18 final size:17
Alignment explanation
Indices: 4248811--4248859 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
4248801 TTGGACTCCT
* *
4248811 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
4248829 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
4248847 AGTGCATTCGATG
1 AGTGCA-TCGATG
4248860 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:4248880 original size:64 final size:61
Alignment explanation
Indices: 4248811--4248990 Score: 195
Period size: 64 Copynumber: 2.8 Consensus size: 61
4248801 TTGGACTCCT
*
4248811 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-TAAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * * *
4248872 CCTGGTGCATCGATGCAT-GGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAAT
1 ---AGTGCATCGATGCATAAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAAT
4248936 CAG
59 CAG
4248939 AGTGCATCGATGCATGAAGAGTGCATCGATGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCAT-AAGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
4248991 CAATTTATTC
Statistics
Matches: 99, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 86 0.87
65 2 0.02
66 6 0.06
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (61 bp):
AGTGCATCGATGCATAAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:4248961 original size:19 final size:19
Alignment explanation
Indices: 4248937--4248973 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4248927 TAATTAAATC
4248937 AGAGTGCATCGATGCATGA
1 AGAGTGCATCGATGCATGA
4248956 AGAGTGCATCGATGCATG
1 AGAGTGCATCGATGCATG
4248974 GAATGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Found at i:4249025 original size:21 final size:21
Alignment explanation
Indices: 4249001--4249040 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4248991 CAATTTATTC
4249001 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
4249022 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
4249041 CTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:4249047 original size:21 final size:21
Alignment explanation
Indices: 4249001--4249047 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4248991 CAATTTATTC
*
4249001 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGCT
*
4249022 ATTGATGCATCGGTGCATGCT
1 ATTGATGCATCGATGCATGCT
*
4249043 TTTGA
1 ATTGA
4249048 AAAATTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGCT
Found at i:4251611 original size:24 final size:23
Alignment explanation
Indices: 4251540--4251619 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
4251530 CATGGTCTTG
*
4251540 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
4251563 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
4251584 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
4251608 TGCATCGATGCA
1 TGCATCGATGCA
4251620 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.23
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:4251632 original size:44 final size:42
Alignment explanation
Indices: 4251517--4251639 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 42
4251507 AAAACCCGAC
* *
4251517 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCATTGT-TAGTGCATCGATGCACATTCAAG
* * **
4251560 GCATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAG
*
4251605 GGATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATTGTT-AGTGCATCGATGCA
4251640 TTAAGCACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
43 17 0.27
44 28 0.44
45 19 0.30
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAG
Found at i:4255488 original size:20 final size:20
Alignment explanation
Indices: 4255446--4255488 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4255436 TTGCTTTCAT
* *
4255446 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
4255466 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
4255486 TTT
1 TTT
4255489 CTCAAAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:4257334 original size:18 final size:17
Alignment explanation
Indices: 4257280--4257328 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
4257270 TTGGACTCCT
* *
4257280 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
4257298 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
4257316 AGTGCATTCGATG
1 AGTGCA-TCGATG
4257329 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:4257349 original size:64 final size:61
Alignment explanation
Indices: 4257280--4257459 Score: 195
Period size: 64 Copynumber: 2.8 Consensus size: 61
4257270 TTGGACTCCT
*
4257280 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-TAAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * *
4257341 CATGGTGCATCGATGCAT-GGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAAT
1 -A--GTGCATCGATGCATAAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAAT
4257405 CAG
59 CAG
*
4257408 AGTGCATCGATGCATGAAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCAT-AAGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
4257460 CAATTTATTC
Statistics
Matches: 100, Mismatches: 8, Indels: 18
0.79 0.06 0.14
Matches are distributed among these distances:
62 3 0.03
63 1 0.01
64 85 0.85
65 2 0.02
66 7 0.07
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (61 bp):
AGTGCATCGATGCATAAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:4257430 original size:19 final size:19
Alignment explanation
Indices: 4257406--4257442 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4257396 TAATTAAATC
4257406 AGAGTGCATCGATGCATGA
1 AGAGTGCATCGATGCATGA
*
4257425 AGAGTGCATCGGTGCATG
1 AGAGTGCATCGATGCATG
4257443 GAATGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Found at i:4257494 original size:21 final size:21
Alignment explanation
Indices: 4257470--4257509 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4257460 CAATTTATTC
4257470 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
4257491 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
4257510 CTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:4257516 original size:21 final size:21
Alignment explanation
Indices: 4257470--4257516 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4257460 CAATTTATTC
*
4257470 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGCT
*
4257491 ATTGATGCATCGGTGCATGCT
1 ATTGATGCATCGATGCATGCT
*
4257512 TTTGA
1 ATTGA
4257517 AAAATTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGCT
Found at i:4266656 original size:18 final size:18
Alignment explanation
Indices: 4266633--4266667 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4266623 ACCGGTCAAC
*
4266633 GGTCAATGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
4266651 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
4266668 AACGGGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.20, G:0.49, T:0.20
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:4266660 original size:13 final size:13
Alignment explanation
Indices: 4266644--4266674 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
4266634 GTCAATGGGT
4266644 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
4266657 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
4266670 CGGGT
1 CGGGT
4266675 AAACGGGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:4267637 original size:30 final size:30
Alignment explanation
Indices: 4267603--4267668 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
4267593 ATAAGAGTTG
4267603 ATTTGTTTAATTCATG-AGTAAATAATTCTT
1 ATTTGTTTAATTCATGTA-TAAATAATTCTT
*
4267633 ATTTGTTTAATTGATGTATAAATAATTCTT
1 ATTTGTTTAATTCATGTATAAATAATTCTT
4267663 ATTTGT
1 ATTTGT
4267669 GCTTGTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (30 bp):
ATTTGTTTAATTCATGTATAAATAATTCTT
Found at i:4267850 original size:19 final size:20
Alignment explanation
Indices: 4267817--4267883 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 20
4267807 GCAATTTTCT
*
4267817 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAATCAAATTCC
*
4267837 CGTTG-GATAATCAAATTCG
1 CGTTGCGATAATCAAATTCC
* * * *
4267856 CATTGCGATAGTC-ATTTCG
1 CGTTGCGATAATCAAATTCC
4267875 CGTTGCGAT
1 CGTTGCGAT
4267884 TATCTCATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCC
Found at i:4267941 original size:74 final size:73
Alignment explanation
Indices: 4267779--4268186 Score: 471
Period size: 74 Copynumber: 5.5 Consensus size: 73
4267769 TCTACATCAT
* * * * * * *
4267779 ATTCGCGTTGCGATAGTCAATACACTTTGCAATTTTCTCGTTGCGATAGTCAAATTCCCGTTG-G
1 ATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCG
*
4267843 ATAATCAA
66 ATAGTCAA
* *
4267851 ATTCGCATTGCGATAGTCATTTCGCGTTGCGATTATCTCATTGCGATAGTCAAATTCGCGATT-C
1 ATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCG-TTGC
* *
4267915 TG-CAGGCTAA
65 -GATAGTC-AA
* *
4267925 ATTCGCGTTGCGATAGTCATATTCACGTTGCGATAGTCATTTTCGTGTTGCGATAGTCAAATTCG
1 ATTCGCGTTGCGATAGTCAT-TTCGCGTTGCGAT--T-A-TCTC--GTTGCGATAGTCAAATTCG
*
4267990 TGTTGCGATAGTCAA
59 CGTTGCGATAGTCAA
* *
4268005 ATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGC
1 ATTCGCGTTGCGATAGTCA-TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGC
4268070 GATAGTCAA
65 GATAGTCAA
* * * * *
4268079 ATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGTGATATTCAAATTCACGTTGC
1 ATTCGCGTTGCGATAGTCA-TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGC
*
4268144 GATAGTCAT
65 GATAGTCAA
4268153 ATTCGCGTTGCGATAGTCATATTCGCGTTGCGAT
1 ATTCGCGTTGCGATAGTCAT-TTCGCGTTGCGAT
4268187 AGTCAAATGA
Statistics
Matches: 292, Mismatches: 29, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
72 51 0.17
73 5 0.02
74 156 0.53
75 12 0.04
76 2 0.01
77 2 0.01
78 2 0.01
79 3 0.01
80 35 0.12
81 24 0.08
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (73 bp):
ATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCG
ATAGTCAA
Found at i:4267953 original size:20 final size:20
Alignment explanation
Indices: 4267925--4268191 Score: 288
Period size: 20 Copynumber: 13.9 Consensus size: 20
4267915 TGCAGGCTAA
4267925 ATTCGCGTTGCGATAGTCAT
1 ATTCGCGTTGCGATAGTCAT
*
4267945 ATTCACGTTGCGATAGTCAT
1 ATTCGCGTTGCGATAGTCAT
* * *
4267965 TTTCGTGTTGCGATAGTCAA
1 ATTCGCGTTGCGATAGTCAT
* *
4267985 ATTCGTGTTGCGATAGTCAA
1 ATTCGCGTTGCGATAGTCAT
4268005 ATTCGCGTTGCGATAGTCAT
1 ATTCGCGTTGCGATAGTCAT
* *
4268025 TTTCGCATTGCG--A-T--T
1 ATTCGCGTTGCGATAGTCAT
* *
4268040 A-TCCCGTTGCGATAGTCAA
1 ATTCGCGTTGCGATAGTCAT
*
4268059 ATTCGCGTTGCGATAGTCAA
1 ATTCGCGTTGCGATAGTCAT
4268079 ATTCGCGTTGCGATAGTCAT
1 ATTCGCGTTGCGATAGTCAT
* *
4268099 TTTCGCATTGCG--A-T--T
1 ATTCGCGTTGCGATAGTCAT
* * * *
4268114 A-TCCCGTTGTGATATTCAA
1 ATTCGCGTTGCGATAGTCAT
*
4268133 ATTCACGTTGCGATAGTCAT
1 ATTCGCGTTGCGATAGTCAT
4268153 ATTCGCGTTGCGATAGTCAT
1 ATTCGCGTTGCGATAGTCAT
4268173 ATTCGCGTTGCGATAGTCA
1 ATTCGCGTTGCGATAGTCA
4268192 AATGAATGTG
Statistics
Matches: 207, Mismatches: 28, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
14 15 0.07
15 2 0.01
16 2 0.01
17 4 0.02
18 2 0.01
19 2 0.01
20 180 0.87
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
ATTCGCGTTGCGATAGTCAT
Found at i:4268048 original size:94 final size:93
Alignment explanation
Indices: 4267945--4268194 Score: 308
Period size: 94 Copynumber: 2.7 Consensus size: 93
4267935 CGATAGTCAT
* * *
4267945 ATTCACGTTGCGATAGTCATTTTCGTGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCG
1 ATTCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
* * *
4268010 CGTTGCGA-TAGT-CATTTTCGCAT-TGCGA
66 CATTGCGATTA-TCCATTGT-G-ATATGCAA
* * * **
4268038 TTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTC
1 AT-TCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTC
* *
4268103 GCATTGCGATTATCCCGTTGTGATATTCAA
65 GCATTGCGATTAT-CCATTGTGATATGCAA
*
4268133 ATTCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAAT
1 ATTCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
4268195 GAATGTGTAA
Statistics
Matches: 133, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
93 1 0.01
94 121 0.91
95 7 0.05
96 4 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (93 bp):
ATTCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
CATTGCGATTATCCATTGTGATATGCAA
Found at i:4268053 original size:34 final size:34
Alignment explanation
Indices: 4268010--4268127 Score: 137
Period size: 34 Copynumber: 3.3 Consensus size: 34
4268000 GTCAAATTCG
4268010 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
** * *
4268044 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCGCATTGCGAT--T---A-TCC
4268084 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
*
4268118 CGTTGTGATA
1 CGTTGCGATA
4268128 TTCAAATTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
34 37 0.54
35 1 0.01
36 1 0.01
38 1 0.01
39 1 0.01
40 28 0.41
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:4268122 original size:54 final size:54
Alignment explanation
Indices: 4268064--4268166 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
4268054 GTCAAATTCG
* *
4268064 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATATTCGCATTGCGATTATCC
* * *
4268118 CGTTGTGATATTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATATTCGCATTGCGAT
4268167 AGTCATATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATATTCGCATTGCGATTATCC
Found at i:4270063 original size:24 final size:24
Alignment explanation
Indices: 4270029--4270082 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4270019 CTGAAACATC
4270029 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
4270053 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4270077 ATCAAA
1 ATCAAA
4270083 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4270926 original size:20 final size:20
Alignment explanation
Indices: 4270899--4270966 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
4270889 TGAAATTCAA
*
4270899 CATTGCGACAGTCAGAATTG
1 CATTGCGACAGTCAGAATCG
* *
4270919 CGTTGCGATAGTCAGAATCG
1 CATTGCGACAGTCAGAATCG
* * *
4270939 CATTGCGATAGTAATAATCG
1 CATTGCGACAGTCAGAATCG
4270959 CATTGCGA
1 CATTGCGA
4270967 TTTACATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (20 bp):
CATTGCGACAGTCAGAATCG
Found at i:4270965 original size:40 final size:40
Alignment explanation
Indices: 4270921--4271030 Score: 114
Period size: 40 Copynumber: 2.8 Consensus size: 40
4270911 CAGAATTGCG
4270921 TTGCGATAGT-CAGAATCGCATTGCGATAGTAATAATCGCA
1 TTGCGAT-GTACAGAATCGCATTGCGATAGTAATAATCGCA
* * * * ** *
4270961 TTGCGATTTACATATTCGCGTTGCGATAGCCATACTCGCA
1 TTGCGATGTACAGAATCGCATTGCGATAGTAATAATCGCA
* * *
4271001 TTGCGATTTACATATTCGCATTGCGATAGT
1 TTGCGATGTACAGAATCGCATTGCGATAGT
4271031 CGGAAAATCG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
39 1 0.02
40 59 0.98
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (40 bp):
TTGCGATGTACAGAATCGCATTGCGATAGTAATAATCGCA
Found at i:4270967 original size:20 final size:20
Alignment explanation
Indices: 4270921--4271030 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 20
4270911 CAGAATTGCG
* *
4270921 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTAATAATCGCA
4270941 TTGCGATAGTAATAATCGCA
1 TTGCGATAGTAATAATCGCA
* * *
4270961 TTGCGAT-TTACATATTCGCG
1 TTGCGATAGTA-ATAATCGCA
** *
4270981 TTGCGATAGCCATACTCGCA
1 TTGCGATAGTAATAATCGCA
* *
4271001 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGTA-ATAATCGCA
4271021 TTGCGATAGT
1 TTGCGATAGT
4271031 CGGAAAATCG
Statistics
Matches: 71, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.03
20 68 0.96
21 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTAATAATCGCA
Found at i:4278352 original size:33 final size:32
Alignment explanation
Indices: 4278307--4278385 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 32
4278297 GTGTTGGCCG
*
4278307 TAGGTCGTCATGCCTTCCGGGCGACCTTGTTCA
1 TAGGTCGCCATGCCTT-CGGGCGACCTTGTTCA
**
4278340 TAGGTCGCCATGCCCTTCGGGCGACCTTGTTTG
1 TAGGTCGCCATG-CCTTCGGGCGACCTTGTTCA
4278373 TAGGTCGCCATGC
1 TAGGTCGCCATGC
4278386 ACTCCCAGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.02
33 37 0.88
34 4 0.10
ACGTcount: A:0.11, C:0.30, G:0.29, T:0.29
Consensus pattern (32 bp):
TAGGTCGCCATGCCTTCGGGCGACCTTGTTCA
Found at i:4280719 original size:5 final size:5
Alignment explanation
Indices: 4280709--4280737 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4280699 TTCGGCGAGA
4280709 GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
4280738 AGAAGAAGAA
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:4284846 original size:49 final size:49
Alignment explanation
Indices: 4284745--4284906 Score: 294
Period size: 49 Copynumber: 3.3 Consensus size: 49
4284735 AATAATTATT
4284745 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGA-TT--
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
4284791 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
4284840 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
4284889 TAGTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
4284907 TATTAGTAAT
Statistics
Matches: 112, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
46 44 0.39
47 2 0.02
49 58 0.52
50 8 0.07
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:4284872 original size:21 final size:21
Alignment explanation
Indices: 4284848--4284927 Score: 51
Period size: 21 Copynumber: 4.0 Consensus size: 21
4284838 GATAGTAATG
4284848 ATTAGTAATAATGAAATTATT
1 ATTAGTAATAATGAAATTATT
* * *
4284869 ATTAATATTTAATG--ATT-TG
1 ATTAGTA-ATAATGAAATTATT
* ** * *
4284888 A-TAGTAATGATTTAGTAATT
1 ATTAGTAATAATGAAATTATT
4284908 ATTAGTAATAATGAAATTAT
1 ATTAGTAATAATGAAATTAT
4284928 AATAATGATT
Statistics
Matches: 39, Mismatches: 15, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
17 3 0.08
18 4 0.10
19 3 0.08
20 5 0.13
21 19 0.49
22 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTAGTAATAATGAAATTATT
Found at i:4285291 original size:14 final size:14
Alignment explanation
Indices: 4285272--4285414 Score: 69
Period size: 14 Copynumber: 9.6 Consensus size: 14
4285262 TATGATTTAG
4285272 TAATGATTTGATAA
1 TAATGATTTGATAA
*
4285286 TAATGATTTAATAA
1 TAATGATTTGATAA
* *
4285300 TAAT--TTTAATATT
1 TAATGATTTGATA-A
*
4285313 TAATGATTTGATGATTTTG
1 TAATGATTTGAT-A----A
*
4285332 TAATGATTTCATAA
1 TAATGATTTGATAA
*
4285346 TAATCA-TT-ATAA
1 TAATGATTTGATAA
*
4285358 TAATGATTTAATAA
1 TAATGATTTGATAA
* *
4285372 TAACGATAATAATGATTTAG
1 TAATGAT--T--TGA--TAA
4285392 TAATGATTTGATAA
1 TAATGATTTGATAA
4285406 TAATGATTT
1 TAATGATTT
4285415 ATTATTAATA
Statistics
Matches: 101, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
12 16 0.16
13 8 0.08
14 43 0.43
15 5 0.05
16 5 0.05
18 4 0.04
19 12 0.12
20 8 0.08
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:4285297 original size:11 final size:11
Alignment explanation
Indices: 4285263--4285487 Score: 64
Period size: 11 Copynumber: 18.6 Consensus size: 11
4285253 TAATAATTAT
*
4285263 ATGATTTAGTA
1 ATGATTTAATA
4285274 ATGATTTGATAATA
1 ATGA-TT--TAATA
4285288 ATGATTTAATA
1 ATGATTTAATA
*
4285299 ATAATTT--TA
1 ATGATTTAATA
4285308 AT-ATTTAATGA
1 ATGATTTAAT-A
**
4285319 TTTGATGATTTTGTA
1 ----ATGATTTAATA
4285334 ATGATTTCATAATA
1 ATGA-TT--TAATA
*
4285348 ATCATTATAATA
1 ATGATT-TAATA
4285360 ATGATTTAATA
1 ATGATTTAATA
* **
4285371 ATAACGATAATA
1 ATGA-TTTAATA
*
4285383 ATGATTTAGTA
1 ATGATTTAATA
4285394 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
4285408 ATGATTTATTA
1 ATGATTTAATA
* *
4285419 TTAATATT--TA
1 ATGAT-TTAATA
4285429 ATGATTTGATACTA
1 ATGATTT-A-A-TA
* *
4285443 ATTATTTACTA
1 ATGATTTAATA
4285454 ATGATTACTAATA
1 ATGATT--TAATA
4285467 ATGAAATTATAATA
1 ATG--ATT-TAATA
4285481 ATGATTT
1 ATGATTT
4285488 GATACTAATA
Statistics
Matches: 160, Mismatches: 26, Indels: 56
0.66 0.11 0.23
Matches are distributed among these distances:
8 4 0.03
9 6 0.04
10 6 0.04
11 51 0.32
12 30 0.19
13 14 0.09
14 38 0.24
15 6 0.04
16 5 0.03
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:4285329 original size:60 final size:58
Alignment explanation
Indices: 4285263--4285438 Score: 209
Period size: 60 Copynumber: 3.0 Consensus size: 58
4285253 TAATAATTAT
4285263 ATGATTTAGTAATGATTTGATAATAATGATTTAATAATAATTTTAATATTTAATGATTTG
1 ATGATTTAGTAATGATTTGATAATAATGATTTAATAAT-A-TTTAATATTTAATGATTTG
* * * * * * *
4285323 ATGATTTTGTAATGATTTCATAATAATCATTATAATAATGATTTAATA-ATAACGATAATA
1 ATGATTTAGTAATGATTTGATAATAATGATT-TAATAAT-ATTTAATATTTAATGAT-TTG
4285383 ATGATTTAGTAATGATTTGATAATAATGATTT-AT--TA-TTAATATTTAATGATTTG
1 ATGATTTAGTAATGATTTGATAATAATGATTTAATAATATTTAATATTTAATGATTTG
4285437 AT
1 AT
4285439 ACTAATTATT
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
54 9 0.09
55 7 0.07
56 1 0.01
58 2 0.02
59 7 0.07
60 64 0.65
61 8 0.08
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.47
Consensus pattern (58 bp):
ATGATTTAGTAATGATTTGATAATAATGATTTAATAATATTTAATATTTAATGATTTG
Found at i:4285358 original size:23 final size:26
Alignment explanation
Indices: 4285332--4285395 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
4285322 GATGATTTTG
* *
4285332 TAATGATTTCATAATAATC-ATTATAA
1 TAATGATTTAATAATAA-CGATTAAAA
4285358 TAATGATTTAATAATAACGA-T--AA
1 TAATGATTTAATAATAACGATTAAAA
*
4285381 TAATGATTTAGTAAT
1 TAATGATTTAATAAT
4285396 GATTTGATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 16 0.46
25 2 0.06
26 17 0.49
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (26 bp):
TAATGATTTAATAATAACGATTAAAA
Found at i:4285399 original size:34 final size:35
Alignment explanation
Indices: 4285342--4285408 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
4285332 TAATGATTTC
4285342 ATAATAATCATTATAATAATGATTTAATAATAACG
1 ATAATAATCATTATAATAATGATTTAATAATAACG
* * *
4285377 ATAATAATGATT-TAGTAATGATTTGATAATAA
1 ATAATAATCATTATAATAATGATTTAATAATAA
4285409 TGATTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (35 bp):
ATAATAATCATTATAATAATGATTTAATAATAACG
Found at i:4285444 original size:21 final size:22
Alignment explanation
Indices: 4285406--4285450 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
4285396 GATTTGATAA
*
4285406 TAATGATTTATTATTAA-TATT
1 TAATGATTTATTACTAATTATT
4285427 TAATGATTTGA-TACTAATTATT
1 TAATGATTT-ATTACTAATTATT
4285449 TA
1 TA
4285451 CTAATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (22 bp):
TAATGATTTATTACTAATTATT
Found at i:4286074 original size:14 final size:14
Alignment explanation
Indices: 4286050--4286083 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4286040 GATTGTAATG
4286050 ATTAGTAATCATGAA
1 ATTA-TAATCATGAA
4286065 ATTATAATCATGAA
1 ATTATAATCATGAA
4286079 ATTAT
1 ATTAT
4286084 GTTGAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (14 bp):
ATTATAATCATGAA
Found at i:4292233 original size:22 final size:21
Alignment explanation
Indices: 4292207--4292260 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
4292197 TTAGTGCAGA
*
4292207 GGGAATCGATACCCCCTTGA-AG
1 GGGAATCGATACCCCC--CACAG
* *
4292229 GGGAACCGATTCCCCCCACAG
1 GGGAATCGATACCCCCCACAG
4292250 GGGAATCGATA
1 GGGAATCGATA
4292261 TTCCCCTGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 11 0.42
22 14 0.54
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.15
Consensus pattern (21 bp):
GGGAATCGATACCCCCCACAG
Found at i:4298284 original size:22 final size:22
Alignment explanation
Indices: 4298254--4298355 Score: 111
Period size: 22 Copynumber: 4.6 Consensus size: 22
4298244 TAGTACAGGA
*
4298254 GGAATCGATACCCCC-TTGAAGG
1 GGAATCGATTCCCCCTTTGAA-G
* *
4298276 GGAACCGATTCCCCCTTTGAAT
1 GGAATCGATTCCCCCTTTGAAG
4298298 GGAATCGATTCCCCCTTTGAATG
1 GGAATCGATTCCCCCTTTGAA-G
*
4298321 GGAACCGATTCCCTCCTTT--AG
1 GGAATCGATTCCC-CCTTTGAAG
*
4298342 GGAATCGATACCCC
1 GGAATCGATTCCCC
4298356 ACACGGGTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.01
21 12 0.17
22 34 0.49
23 17 0.25
24 5 0.07
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.25
Consensus pattern (22 bp):
GGAATCGATTCCCCCTTTGAAG
Found at i:4298346 original size:44 final size:43
Alignment explanation
Indices: 4298254--4298355 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 43
4298244 TAGTACAGGA
*
4298254 GGAATCGATACCCCCTTGAAGGGGAACCGATTCCCCCTTTGAAT
1 GGAATCGATACCCCCTTGAAGGGGAACCGATTCCCCCTTT-AAG
* *
4298298 GGAATCGATTCCCCCTTTGAATGGGAACCGATTCCCTCCTTT-AG
1 GGAATCGATACCCCC-TTGAAGGGGAACCGATTCCC-CCTTTAAG
4298342 GGAATCGATACCCC
1 GGAATCGATACCCC
4298356 ACACGGGTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
44 28 0.54
45 19 0.37
46 5 0.10
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.25
Consensus pattern (43 bp):
GGAATCGATACCCCCTTGAAGGGGAACCGATTCCCCCTTTAAG
Found at i:4302627 original size:18 final size:18
Alignment explanation
Indices: 4302606--4302664 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
4302596 AGAACAACAC
4302606 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACGAGCA
4302624 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACGAGCA
* *
4302642 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACGAGCA
4302660 GAGGA
1 GAGGA
4302665 TCAAATGCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.46, C:0.22, G:0.32, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACGAGCA
Found at i:4303158 original size:2 final size:2
Alignment explanation
Indices: 4303151--4303197 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
4303141 GCAGCTTAAG
*
4303151 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4303192 AT AT AT
1 AT AT AT
4303198 CAATTGGCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4304405 original size:14 final size:14
Alignment explanation
Indices: 4304386--4304412 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4304376 CAAATTATAA
4304386 TAATGATTTAATAC
1 TAATGATTTAATAC
4304400 TAATGATTTAATA
1 TAATGATTTAATA
4304413 ATTTTTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
TAATGATTTAATAC
Found at i:4304545 original size:14 final size:14
Alignment explanation
Indices: 4304526--4304583 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
4304516 CAATTAACCA
4304526 TAATAATGATTTAG
1 TAATAATGATTTAG
*
4304540 TAATAATCA-TTA-
1 TAATAATGATTTAG
4304552 TAATAATGATTT-G
1 TAATAATGATTTAG
*
4304565 ATAATAATGATTTAA
1 -TAATAATGATTTAG
4304580 TAAT
1 TAAT
4304584 CAAGTTGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 8 0.22
13 5 0.14
14 24 0.65
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (14 bp):
TAATAATGATTTAG
Found at i:4304554 original size:26 final size:26
Alignment explanation
Indices: 4304525--4304613 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
4304515 TCAATTAACC
4304525 ATAATAATGATTT-AGTAATAATCATT
1 ATAATAATGATTTGA-TAATAATCATT
*
4304551 ATAATAATGATTTGATAATAATGATT
1 ATAATAATGATTTGATAATAATCATT
* * *
4304577 -TAATAATCAAGTTGAT-A-AATTATT
1 ATAATAAT-GATTTGATAATAATCATT
*
4304601 ATTATAATGATTT
1 ATAATAATGATTT
4304614 ATTATTAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
24 9 0.17
25 14 0.26
26 29 0.55
27 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (26 bp):
ATAATAATGATTTGATAATAATCATT
Found at i:4304615 original size:13 final size:13
Alignment explanation
Indices: 4304599--4304683 Score: 50
Period size: 14 Copynumber: 6.2 Consensus size: 13
4304589 TGATAAATTA
4304599 TTATTA-TAATGAT
1 TTATTATTAAT-AT
4304612 TTATTATTAATAT
1 TTATTATTAATAT
*
4304625 TTAATGATTTAAT-T
1 TT-ATTA-TTAATAT
* *
4304639 ATGATTTAGTAAT-T
1 -TTA-TTATTAATAT
*
4304653 ATTATTAATAATGAT
1 -TTATTATTAAT-AT
4304668 TTATTATTAATAT
1 TTATTATTAATAT
4304681 TTA
1 TTA
4304684 ATGATTTGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
13 22 0.38
14 27 0.47
15 9 0.16
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (13 bp):
TTATTATTAATAT
Found at i:4304625 original size:22 final size:22
Alignment explanation
Indices: 4304595--4304640 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4304585 AAGTTGATAA
*
4304595 ATTATTATTATAATGATTT-ATT
1 ATTAATATT-TAATGATTTAATT
4304617 ATTAATATTTAATGATTTAATT
1 ATTAATATTTAATGATTTAATT
4304639 AT
1 AT
4304641 GATTTAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTAATATTTAATGATTTAATT
Found at i:4304671 original size:56 final size:59
Alignment explanation
Indices: 4304594--4304720 Score: 199
Period size: 56 Copynumber: 2.2 Consensus size: 59
4304584 CAAGTTGATA
*
4304594 AATTATTATT-ATAATGATTTATTATTAATATTTAATGATTT-A-ATT-ATGATTTAGT
1 AATTATTATTAATAATGATTTATTATTAATATTTAATGATTTGATATTAATGATTAAGT
4304649 AATTATTATTAATAATGATTTATTATTAATATTTAATGATTTGATATTAATGATTAAGT
1 AATTATTATTAATAATGATTTATTATTAATATTTAATGATTTGATATTAATGATTAAGT
* *
4304708 AATGATTAGTAAT
1 AATTATTATTAAT
4304721 GATTAGTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
55 10 0.15
56 31 0.48
57 1 0.02
58 3 0.05
59 20 0.31
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (59 bp):
AATTATTATTAATAATGATTTATTATTAATATTTAATGATTTGATATTAATGATTAAGT
Found at i:4304683 original size:69 final size:69
Alignment explanation
Indices: 4304599--4304763 Score: 169
Period size: 69 Copynumber: 2.4 Consensus size: 69
4304589 TGATAAATTA
* * * *
4304599 TTATTATAATGATTT-ATTA-TTAATATTTAATGATTTAA-TTATGATTTAGTAATTATTATTAA
1 TTATTATAATGATTTAATGATTTAATA-TTAATGA-TTAAGTAATGA-TTAGTAATGATTAGTAA
4304661 TAATGAT
63 TAATGAT
*
4304668 TTATTATTAAT-ATTTAATGATTTGATATTAATGATTAAGTAATGATTAGTAATGATTAGTAATA
1 TTATTA-TAATGATTTAATGATTTAATATTAATGATTAAGTAATGATTAGTAATGATTAGTAATA
*
4304732 ATGAAA
65 ATG-AT
* * *
4304738 TTGTAATAATGATTTAATCA-TTAATA
1 TTATTATAATGATTTAATGATTTAATA
4304764 ATGATTTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
69 43 0.54
70 32 0.40
71 5 0.06
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (69 bp):
TTATTATAATGATTTAATGATTTAATATTAATGATTAAGTAATGATTAGTAATGATTAGTAATAA
TGAT
Found at i:4304720 original size:10 final size:10
Alignment explanation
Indices: 4304696--4304730 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
4304686 GATTTGATAT
4304696 TAATGATTAAG
1 TAATGATT-AG
4304707 TAATGATTAG
1 TAATGATTAG
4304717 TAATGATTAG
1 TAATGATTAG
4304727 TAAT
1 TAAT
4304731 AATGAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (10 bp):
TAATGATTAG
Found at i:4305032 original size:14 final size:13
Alignment explanation
Indices: 4305013--4305142 Score: 101
Period size: 14 Copynumber: 10.1 Consensus size: 13
4305003 TATGATTTAG
4305013 TAATGATTTGATAA
1 TAATGATTT-ATAA
4305027 TAATGATTT-TAA
1 TAATGATTTATAA
* * * * *
4305039 TATTTA-ATGTAC
1 TAATGATTTATAA
*
4305051 TAATGA-TT-TAG
1 TAATGATTTATAA
4305062 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
4305076 TAATCA-TTATAA
1 TAATGATTTATAA
4305088 TAATGATTTAGTAA
1 TAATGATTTA-TAA
*
4305102 TAATCA-TTATAA
1 TAATGATTTATAA
4305114 TAATGATTTGATAA
1 TAATGATTT-ATAA
4305128 TAATGATTTAGTAA
1 TAATGATTTA-TAA
4305142 T
1 T
4305143 TATTATTAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 18
0.75 0.10 0.14
Matches are distributed among these distances:
11 9 0.10
12 33 0.35
13 11 0.12
14 41 0.44
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:4305057 original size:49 final size:49
Alignment explanation
Indices: 4305004--4305161 Score: 178
Period size: 49 Copynumber: 3.2 Consensus size: 49
4304994 TAATAATTAT
*
4305004 ATGATTTAGTAATGATTTGATAATAATGATTT-TAAT-ATTTAATGTACTA
1 ATGATTTAGTAATGATTTGATAATAATGATTTATAATGATTT-A-GTAATA
*
4305053 ATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATA
1 ATGATTTAGTAATGATTTGATAATAATGATT-T-ATAATGATTTAGTAATA
* * * *
4305104 ATCATTATAATAATGATTTGATAATAATGATTTAGTAATTA-TTATTAATA
1 ATGATT-TAGTAATGATTTGATAATAATGATTTA-TAATGATTTAGTAATA
*
4305154 ATTATTTA
1 ATGATTTA
4305162 TTATGAATAT
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
49 32 0.34
50 15 0.16
51 16 0.17
52 28 0.29
53 4 0.04
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (49 bp):
ATGATTTAGTAATGATTTGATAATAATGATTTATAATGATTTAGTAATA
Found at i:4305091 original size:26 final size:26
Alignment explanation
Indices: 4305013--4305131 Score: 129
Period size: 26 Copynumber: 4.7 Consensus size: 26
4305003 TATGATTTAG
* *
4305013 TAATGATTTGATAATAATGATTTTAA
1 TAATGATTTGATAATAATCATTATAA
* * * * * *
4305039 TATTTA-ATG-TACTAATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
4305062 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
4305088 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
4305114 TAATGATTTGATAATAAT
1 TAATGATTTGATAATAAT
4305132 GATTTAGTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
23 6 0.08
24 12 0.16
25 12 0.16
26 46 0.60
27 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:4305164 original size:14 final size:12
Alignment explanation
Indices: 4305004--4305232 Score: 96
Period size: 14 Copynumber: 18.5 Consensus size: 12
4304994 TAATAATTAT
*
4305004 ATGATT-TAGTA
1 ATGATTATAATA
4305015 ATGATTTGATAATA
1 ATGA-TT-ATAATA
*
4305029 ATGATTTTAATA
1 ATGATTATAATA
* * * * *
4305041 TTTAATGTACTA
1 ATGATTATAATA
*
4305053 ATGATT-TAGTA
1 ATGATTATAATA
4305064 ATGATTTGATAATA
1 ATGA-TT-ATAATA
*
4305078 ATCATTATAATA
1 ATGATTATAATA
4305090 ATGATTTAGTAATA
1 ATGA-TTA-TAATA
*
4305104 ATCATTATAATA
1 ATGATTATAATA
4305116 ATGATTTGATAATA
1 ATGA-TT-ATAATA
*
4305130 ATGATT-TAGTA
1 ATGATTATAATA
*
4305141 ATTATTATTAATA
1 ATGATTA-TAATA
* *
4305154 ATTATTTATTATGA
1 ATGA-TTATAAT-A
*
4305168 AT-ATT-TAATT
1 ATGATTATAATA
*
4305178 AT--TTGATACTA
1 ATGATT-ATAATA
* *
4305189 AAGATT-TACTA
1 ATGATTATAATA
*
4305200 ATGATTACTAGTA
1 ATGATTA-TAATA
4305213 ATGAAATTATAATA
1 ATG--ATTATAATA
4305227 ATGATT
1 ATGATT
4305233 TGATACTAAA
Statistics
Matches: 168, Mismatches: 28, Indels: 43
0.70 0.12 0.18
Matches are distributed among these distances:
9 2 0.01
10 2 0.01
11 38 0.23
12 41 0.24
13 35 0.21
14 46 0.27
15 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (12 bp):
ATGATTATAATA
Found at i:4305164 original size:17 final size:17
Alignment explanation
Indices: 4305139--4305180 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4305129 AATGATTTAG
*
4305139 TAATTATTATTAATAAT
1 TAATTATTATGAATAAT
* *
4305156 TATTTATTATGAATATT
1 TAATTATTATGAATAAT
4305173 TAATTATT
1 TAATTATT
4305181 TGATACTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATGAATAAT
Found at i:4306420 original size:14 final size:14
Alignment explanation
Indices: 4306401--4306434 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4306391 TTTTAATCAA
4306401 AATAAATATTTTAT
1 AATAAATATTTTAT
4306415 AATAAATATTTTAT
1 AATAAATATTTTAT
*
4306429 ATTAAA
1 AATAAA
4306435 ATAGATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAAATATTTTAT
Found at i:4307776 original size:4 final size:4
Alignment explanation
Indices: 4307767--4307795 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
4307757 AACTATTCCC
4307767 ACTA ACTA ACTA ACTA ACTA ACTA ACTA A
1 ACTA ACTA ACTA ACTA ACTA ACTA ACTA A
4307796 TAATTTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACTA
Found at i:4308250 original size:29 final size:27
Alignment explanation
Indices: 4308154--4308257 Score: 91
Period size: 29 Copynumber: 3.7 Consensus size: 27
4308144 TAGGATGTTG
*
4308154 GGAGTGCATGGCGACCTACAAGGCCGCCC
1 GGAGGGCATGGCGACCTACAAGG-C-CCC
* * * *
4308183 GAATGGCATGGCAACCTATAAGGCCACC
1 GGAGGGCATGGCGACCTACAAGGCC-CC
* * *
4308211 GGATGGTATGGTGACCTACAAGGTCTCCC
1 GGAGGGCATGGCGACCTACAAGG-C-CCC
4308240 GGAGGGCATGGCGACCTA
1 GGAGGGCATGGCGACCTA
4308258 TGTGTTGGGG
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
27 1 0.02
28 21 0.36
29 36 0.61
30 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.15
Consensus pattern (27 bp):
GGAGGGCATGGCGACCTACAAGGCCCC
Found at i:4309918 original size:231 final size:232
Alignment explanation
Indices: 4309515--4309976 Score: 917
Period size: 231 Copynumber: 2.0 Consensus size: 232
4309505 TGCAGTATCA
4309515 AAAGACTTTACCACTTCCATCCATGGCTTGTCTATGATCAAGACGGAATTTCTTGCGATGTGTCC
1 AAAGACTTTACCACTTCCATCCATGGCTTGTCTATGATCAAGACGGAATTTCTTGCGATGTGTCC
4309580 CATAAATAAAACGGGGTCCCGAAAACCAATTATATCCAAATTATTTGTTCAACCGGTCTGTTTAG
66 CATAAATAAAACGGGGTCCCGAAAACCAATTATATCCAAATTATTTGTTCAACCGGTCTGTTTAG
4309645 ACTCTTTTTGACGACCATCACTCAACAAACGTTTCCATTTCGTTTTTGTGAGAGAACCTTGAAGA
131 ACTCTTTTTGACGACCATCACTCAACAAACGTTTCCATTTCGTTTTTGTGAGAGAACCTTGAAGA
4309710 TTCAACAAGGCTTCATGAACCAA-TCACTTTCATTGC
196 TTCAACAAGGCTTCATGAACCAATTCACTTTCATTGC
4309746 AAAGACTTTACCACTTCCATCCATGGCTTGTCTATGATCAAGACGGAATTTCTTGCGATGTGTCC
1 AAAGACTTTACCACTTCCATCCATGGCTTGTCTATGATCAAGACGGAATTTCTTGCGATGTGTCC
4309811 CATAAATAAAACGGGGTCCCGAAAACCAATTATATCCAAATTATTTGTTCAACCGGTCTGTTTAG
66 CATAAATAAAACGGGGTCCCGAAAACCAATTATATCCAAATTATTTGTTCAACCGGTCTGTTTAG
4309876 ACTCTTTTTGACGACCATCACTCAACAAACGTTTCCATTTCGTTTTTGTGAGAGAACCTTGAAGA
131 ACTCTTTTTGACGACCATCACTCAACAAACGTTTCCATTTCGTTTTTGTGAGAGAACCTTGAAGA
4309941 TTCAACAAGGCTTCATGAACCAATTCACTTTCATTG
196 TTCAACAAGGCTTCATGAACCAATTCACTTTCATTG
4309977 TCTTCATCTA
Statistics
Matches: 230, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
231 218 0.95
232 12 0.05
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (232 bp):
AAAGACTTTACCACTTCCATCCATGGCTTGTCTATGATCAAGACGGAATTTCTTGCGATGTGTCC
CATAAATAAAACGGGGTCCCGAAAACCAATTATATCCAAATTATTTGTTCAACCGGTCTGTTTAG
ACTCTTTTTGACGACCATCACTCAACAAACGTTTCCATTTCGTTTTTGTGAGAGAACCTTGAAGA
TTCAACAAGGCTTCATGAACCAATTCACTTTCATTGC
Found at i:4342681 original size:7 final size:7
Alignment explanation
Indices: 4342664--4342796 Score: 53
Period size: 7 Copynumber: 18.4 Consensus size: 7
4342654 AGAAATAAAT
4342664 AAAAGAGA
1 AAAAGA-A
4342672 AAAAGAA
1 AAAAGAA
4342679 AAAATGAGA
1 AAAA-GA-A
4342688 AAAA-AGA
1 AAAAGA-A
4342695 AAAAGAA
1 AAAAGAA
**
4342702 AATGGGAA
1 AA-AAGAA
*
4342710 AAACG--
1 AAAAGAA
4342715 AAAAGAA
1 AAAAGAA
4342722 AAAA-AA
1 AAAAGAA
*
4342728 AAATGAA
1 AAAAGAA
4342735 AAGGAAGAA
1 AA--AAGAA
4342744 AAAATG--
1 AAAA-GAA
*
4342750 AAATGAA
1 AAAAGAA
*
4342757 AGAGAGAA
1 A-AAAGAA
*
4342765 AAATGAA
1 AAAAGAA
*
4342772 AAATGAAA
1 AAAAG-AA
4342780 AAAAGAA
1 AAAAGAA
*
4342787 AAATGAA
1 AAAAGAA
4342794 AAA
1 AAA
4342797 TGGAGAGAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
5 5 0.05
6 8 0.08
7 47 0.48
8 26 0.27
9 11 0.11
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:4342689 original size:16 final size:16
Alignment explanation
Indices: 4342664--4342698 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
4342654 AGAAATAAAT
4342664 AAAAGAG-AAAAAGAA
1 AAAAGAGAAAAAAGAA
4342679 AAAATGAGAAAAAAGAA
1 AAAA-GAGAAAAAAGAA
4342696 AAA
1 AAA
4342699 GAAAATGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 3 0.17
17 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGAGAAAAAAGAA
Found at i:4342703 original size:22 final size:22
Alignment explanation
Indices: 4342664--4342808 Score: 86
Period size: 23 Copynumber: 6.3 Consensus size: 22
4342654 AGAAATAAAT
*
4342664 AAAAGAGAAAAAGAAAAAATGAG
1 AAAAAAGAAAAAG-AAAAATGAG
*
4342687 AAAAAAGAAAAAG-AAAATGGG
1 AAAAAAGAAAAAGAAAAATGAG
*
4342708 AAAAACG-AAAAGAAAAA--A-
1 AAAAAAGAAAAAGAAAAATGAG
*
4342726 AAAAATGAAAAGGAAGAAAAAATGAAATG
1 AAAAAAG-AAA--AAG-AAAAATG--A-G
*
4342755 AAAGAGAGAAAAATGAAAAATGA-
1 AAA-AAAGAAAAA-GAAAAATGAG
4342778 AAAAAAGAAAAATGAAAAATGGAG
1 AAAAAAGAAAAA-GAAAAAT-GAG
4342802 AGAAAAA
1 A-AAAAA
4342809 AGGAGGTCAA
Statistics
Matches: 97, Mismatches: 8, Indels: 32
0.71 0.06 0.23
Matches are distributed among these distances:
18 6 0.06
20 7 0.07
21 17 0.18
22 19 0.20
23 22 0.23
24 1 0.01
25 6 0.06
27 10 0.10
28 1 0.01
29 6 0.06
30 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (22 bp):
AAAAAAGAAAAAGAAAAATGAG
Found at i:4342718 original size:20 final size:21
Alignment explanation
Indices: 4342664--4342723 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
4342654 AGAAATAAAT
4342664 AAAAGAGAAAAAGAAAAAATGAGA
1 AAAA-AGAAAAAG-A-AAATGAGA
*
4342688 AAAAAGAAAAAGAAAATGGGA
1 AAAAAGAAAAAGAAAATGAGA
*
4342709 AAAACG-AAAAGAAAA
1 AAAAAGAAAAAGAAAA
4342724 AAAAAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.26
21 12 0.35
22 1 0.03
23 8 0.24
24 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAATGAGA
Found at i:4342759 original size:17 final size:17
Alignment explanation
Indices: 4342673--4342773 Score: 61
Period size: 17 Copynumber: 5.9 Consensus size: 17
4342663 TAAAAGAGAA
4342673 AAAGAAAAAATGAGAAA-
1 AAAGAAAAAATGA-AAAG
4342690 AAAG-AAAAA-GAAAATG
1 AAAGAAAAAATGAAAA-G
* *
4342706 ---GGAAAAACGAAAAG
1 AAAGAAAAAATGAAAAG
*
4342720 AAAAAAAAAAATGAAAAG
1 -AAAGAAAAAATGAAAAG
* *
4342738 GAAGAAAAAATGAAATG
1 AAAGAAAAAATGAAAAG
4342755 AAAGAGAGAAAAATGAAAA
1 -AA-AGA-AAAAATGAAAA
4342774 ATGAAAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
13 1 0.02
14 9 0.14
15 7 0.11
16 5 0.08
17 18 0.28
18 12 0.18
19 3 0.05
20 10 0.15
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (17 bp):
AAAGAAAAAATGAAAAG
Found at i:4342781 original size:15 final size:15
Alignment explanation
Indices: 4342750--4342796 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
4342740 AGAAAAAATG
*
4342750 AAATGAAAGA-GAGAA
1 AAATGAAAAATGA-AA
4342765 AAATGAAAAATGAAA
1 AAATGAAAAATGAAA
*
4342780 AAAAGAAAAATGAAA
1 AAATGAAAAATGAAA
4342795 AA
1 AA
4342797 TGGAGAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 27 0.93
16 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
AAATGAAAAATGAAA
Found at i:4342797 original size:7 final size:7
Alignment explanation
Indices: 4342762--4342798 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
4342752 ATGAAAGAGA
4342762 GAAAAAT
1 GAAAAAT
4342769 GAAAAAT
1 GAAAAAT
*
4342776 GAAAAAAA
1 G-AAAAAT
4342784 GAAAAAT
1 GAAAAAT
4342791 GAAAAAT
1 GAAAAAT
4342798 G
1 G
4342799 GAGAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (7 bp):
GAAAAAT
Found at i:4343905 original size:51 final size:51
Alignment explanation
Indices: 4343840--4344094 Score: 330
Period size: 51 Copynumber: 4.9 Consensus size: 51
4343830 AAATTCGTTT
4343840 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
4343891 GTTGAAGATGGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
4343942 GTTGAAGATTGAGTCATATACTCTCTGAAGGAATAGGGAGCGGACACGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * **
4343993 ATTGAAGATCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * * * *
4344045 ATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 GTTGAAGATTG----AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
4344095 CATTTTATGA
Statistics
Matches: 181, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
51 139 0.77
52 12 0.07
56 30 0.17
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:4344132 original size:55 final size:55
Alignment explanation
Indices: 4343850--4344146 Score: 216
Period size: 51 Copynumber: 5.6 Consensus size: 55
4343840 GTTGAAGATT
* * * * *
4343850 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA-AGTTCGTTGAAGA-TG---
1 GAGTCTTATACTCTCTGAA-GAATAGAGAGCAGACACATTTCATTGAAGATTGTTC
* * * * *
4343901 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA-AGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAA-GAATAGAGAGCAGACACATTTCATTGAAGATTGTTC
* * * *
4343952 GAGTCATATACTCTCTGAAGGAATAGGGAGCGGACACGTTT-ATTGAAGA----TC
1 GAGTCTTATACTCTCTGAA-GAATAGAGAGCAGACACATTTCATTGAAGATTGTTC
* * *
4344003 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATTGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAA-GAATAGAGAGCAGACACATTTCATTGAAGATTGTTC
* *
4344059 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAA-GAATAGAGAGCAGACACATTTCATTGAAGATTGTTC
*
4344114 GAGTCTTATACT-TCCTGAAGAAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAG-AATAGAGAGCAG
4344147 GCTCGTCATT
Statistics
Matches: 218, Mismatches: 15, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
50 1 0.00
51 128 0.59
52 10 0.05
54 2 0.01
55 39 0.18
56 37 0.17
57 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGAATAGAGAGCAGACACATTTCATTGAAGATTGTTC
Found at i:4344161 original size:55 final size:54
Alignment explanation
Indices: 4344009--4344177 Score: 153
Period size: 55 Copynumber: 3.1 Consensus size: 54
4343999 GATCGAGTTC
* * * * *
4344009 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATTGAAGATTGTTCAAGTCT
1 TATACTCTCTGAATGAATAGAGAGCAGACACATAT--TTGAAGATTGTTCAAGTCT
* *
4344065 TATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTCGAGTCT
1 TATACTCTCTGAATGAATAGAGAGCAGACACATATT-TGAAGATTGTTCAAGTCT
* * * * * *
4344120 TATACT-TCCTGAA-GAAATAGGGAGCAGGCTCGTCATTTGAAGATTTTTCAAGTTT
1 TATACTCT-CTGAATG-AATAGAGAGCAGACACAT-ATTTGAAGATTGTTCAAGTCT
4344175 TAT
1 TAT
4344178 TTATCCTGAC
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
54 3 0.03
55 60 0.62
56 33 0.34
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (54 bp):
TATACTCTCTGAATGAATAGAGAGCAGACACATATTTGAAGATTGTTCAAGTCT
Found at i:4347122 original size:62 final size:63
Alignment explanation
Indices: 4346989--4347145 Score: 178
Period size: 62 Copynumber: 2.5 Consensus size: 63
4346979 GAATAAATTG
* * * *
4346989 AACATCGAATGCATTATATGCATCGATGCACATACCATGCATCGATGCTCAGGTTTTTTATGAA
1 AACATCGAATGCATT-TATGCATCGATGCACAGACCATGCATCGATACTCAGGCTATTTATGAA
* *
4347053 AACATCGAAAGCATTTGATGCA-CGATGCATAGA-CATGCATCGATACACTCAGGCTATTT-TG-
1 AACATCGAATGCATTT-ATGCATCGATGCACAGACCATGCATCGAT--ACTCAGGCTATTTATGA
4347114 A
63 A
*
4347115 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
4347146 TCTTAGTGCA
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
62 29 0.37
63 21 0.27
64 29 0.37
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACAGACCATGCATCGATACTCAGGCTATTTATGAA
Found at i:4347145 original size:17 final size:19
Alignment explanation
Indices: 4347117--4347164 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
4347107 TATTTTGAAA
4347117 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
4347135 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
4347154 CA-CGATGCACT
1 CATCGATGCACT
4347165 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:4347501 original size:52 final size:52
Alignment explanation
Indices: 4347441--4347551 Score: 197
Period size: 53 Copynumber: 2.1 Consensus size: 52
4347431 CACTACTTGT
4347441 ACTCATTGTATTTA-TCTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAA
1 ACTCATTGTATTTATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAA
4347492 ACTCAATTGTATTTATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAA
1 ACTC-ATTGTATTTATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAA
*
4347545 ACACATT
1 ACTCATT
4347552 TGCCTTGTGA
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
51 4 0.07
52 13 0.23
53 40 0.70
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (52 bp):
ACTCATTGTATTTATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAA
Found at i:4355767 original size:65 final size:63
Alignment explanation
Indices: 4355698--4355857 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 63
4355688 GAATAAATTG
* * *
4355698 AACATTGAATGCATTATATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATT-TATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
4355761 AA
63 -A
*
4355763 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATGCACTTAGGCTATTTTGA
1 AACATCGAATGCATTT-ATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
*
4355827 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
4355858 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
64 30 0.35
65 52 0.60
66 4 0.05
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
Found at i:4355857 original size:17 final size:19
Alignment explanation
Indices: 4355829--4355877 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4355819 TATTTTGAAA
4355829 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
4355847 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
4355866 CACCGATGCACT
1 CATCGATGCACT
4355878 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:4357872 original size:31 final size:31
Alignment explanation
Indices: 4357836--4357894 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
4357826 AGTTGTATGG
*
4357836 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
4357867 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
4357895 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Found at i:4358573 original size:12 final size:13
Alignment explanation
Indices: 4358551--4358580 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
4358541 TCCAAAGCAA
4358551 TTCTCTCATCTTC
1 TTCTCTCATCTTC
4358564 TTCT-TCATCTTC
1 TTCTCTCATCTTC
4358576 TTCTC
1 TTCTC
4358581 CCAAACGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.57
Consensus pattern (13 bp):
TTCTCTCATCTTC
Found at i:4365770 original size:23 final size:23
Alignment explanation
Indices: 4365744--4365791 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
4365734 ATAAAGTACA
*
4365744 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
4365767 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
4365790 AT
1 AT
4365792 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:4366248 original size:23 final size:23
Alignment explanation
Indices: 4366222--4366280 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
4366212 AACCACTACC
4366222 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
4366245 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
4366268 TATTACATCATAT
1 TATTACATTATAT
4366281 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:4366345 original size:21 final size:22
Alignment explanation
Indices: 4366296--4366345 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
4366286 CCTATTATTG
4366296 AAAGTG-TCCATACTTTTTATA
1 AAAGTGATCCATACTTTTTATA
* * *
4366317 AAAATGATCGATACTTTTT-TT
1 AAAGTGATCCATACTTTTTATA
4366338 AAAGTGAT
1 AAAGTGAT
4366346 GTAATTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (22 bp):
AAAGTGATCCATACTTTTTATA
Found at i:4366674 original size:23 final size:23
Alignment explanation
Indices: 4366648--4366706 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
4366638 AACCACTACC
4366648 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
4366671 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
4366694 TATTACATCATAT
1 TATTACATTATAT
4366707 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:4366749 original size:21 final size:22
Alignment explanation
Indices: 4366724--4366768 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4366714 TATTATATTG
4366724 AAAATG-TCCATACTT-TTTATA
1 AAAATGATCCATACTTCTTT-TA
*
4366745 AAAATGATCGATACTTCTTTTA
1 AAAATGATCCATACTTCTTTTA
4366767 AA
1 AA
4366769 GTTATGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 12 0.57
23 3 0.14
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (22 bp):
AAAATGATCCATACTTCTTTTA
Found at i:4367128 original size:23 final size:23
Alignment explanation
Indices: 4367062--4367134 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
4367052 ATACTTTACA
* *
4367062 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
4367085 ATATAAACGATACATATTACATT
1 ATATAAACGCTACCTATTACATT
* * *
4367108 ATATAAGCGCTACCTAGTACATC
1 ATATAAACGCTACCTATTACATT
4367131 ATAT
1 ATAT
4367135 TTTTACCTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:4367515 original size:21 final size:20
Alignment explanation
Indices: 4367485--4367561 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 20
4367475 GATAGATACT
*
4367485 TTACAATATAACCACTACCTA
1 TTACATTATAA-CACTACCTA
*
4367506 TTACATTATATAAACGATACCTA
1 TTACATTATA-ACAC--TACCTA
*
4367529 TTACATTATATAAGCGCTACCTA
1 TTACA-T-TATAA-CACTACCTA
4367552 TTACATTATA
1 TTACATTATA
4367562 TTTTTACCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 22 0.48
24 2 0.04
25 5 0.11
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (20 bp):
TTACATTATAACACTACCTA
Found at i:4367526 original size:23 final size:23
Alignment explanation
Indices: 4367500--4367562 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
4367490 ATATAACCAC
4367500 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
4367523 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
4367546 TACCTATTACATTATAT
1 TACCTATTACATTATAT
4367563 TTTTACCTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:4367901 original size:430 final size:430
Alignment explanation
Indices: 4365858--4368182 Score: 4319
Period size: 428 Copynumber: 5.4 Consensus size: 430
4365848 TATTACATTA
4365858 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
4365923 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
*
4365988 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
* *
4366053 ATAATAATATATATCGTAATGTAAAAAATAAATCATTAGACGCCTATAATTATTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
4366118 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
4366183 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATAT
326 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATAT
4366248 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
* *
4366288 TA-T-TATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTGATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
*
4366351 TTATGTTTCAAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
4366416 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
*
4366481 ATAATAATATATATCGTAACGT-AAAAA-AAATCATTAGACGTCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
* *
4366544 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAACGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
4366609 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATAT
326 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATAT
4366674 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
4366714 TATTATATTGAAAATGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
*
4366779 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTGATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
4366844 ATTTGCAC-AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
130 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
4366908 AATAAT-A-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
4366971 CTTAAAACTCACTCAAAGGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
260 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
4367036 TTTATAAAAAGGATAAATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATA
325 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATA
*
4367101 TTACATTATATAAGCGCTACCTAGTACATCATATTTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
4367142 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
4367207 TTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTAC-ATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
4367270 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
*
4367335 ATAATAATATATATCGTAACATAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
4367400 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
* *
4367465 TTATAAAAATGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
326 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATAT
*
4367530 TACATTATATAAGCGCTACCTATTACATTATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
4367570 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
4367635 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
4367700 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
* *
4367765 ATAATAATATATATCGTAATGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATT
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
* *
4367830 TTAAAACTCACTCAAAGGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGTACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
* *
4367895 TTATAAAATGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
326 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATAT
4367960 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
4368000 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
*
4368065 TTATGTTTCAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
*
4368129 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAA
4368183 ATTAAATTTA
Statistics
Matches: 1845, Mismatches: 40, Indels: 21
0.97 0.02 0.01
Matches are distributed among these distances:
425 26 0.01
426 312 0.17
427 13 0.01
428 907 0.49
429 197 0.11
430 390 0.21
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATAT
TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:4367956 original size:23 final size:23
Alignment explanation
Indices: 4367930--4367992 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
4367920 ATATAACCAC
4367930 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
4367953 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
4367976 TACCTATTACATCATAT
1 TACCTATTACATTATAT
4367993 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:4368466 original size:39 final size:39
Alignment explanation
Indices: 4368412--4368498 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
4368402 TCAAGTTGTA
*
4368412 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
4368451 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
4368490 GATTTTGAT
1 GATTTTGAT
4368499 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:4368792 original size:18 final size:18
Alignment explanation
Indices: 4368769--4368805 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4368759 CGAAATATAT
4368769 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
4368787 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
4368805 A
1 A
4368806 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:4369737 original size:198 final size:198
Alignment explanation
Indices: 4369401--4370374 Score: 1799
Period size: 198 Copynumber: 4.9 Consensus size: 198
4369391 ACTATTTAAC
*
4369401 CAAAAATATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
1 CAAAAATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
*
4369466 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGTTTTT
66 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTT
*
4369531 GGGATCGACACTTTTTATATATGGATCGACATTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
131 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
*
4369596 GAC
196 GAA
*
4369599 CAAAAATATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
1 CAAAAATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
*
4369664 ATATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTT
66 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTT
4369729 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
131 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
*
4369794 GAG
196 GAA
4369797 CAAAAATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
1 CAAAAATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
4369862 GTATACTTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTT
66 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTT
4369926 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
131 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
4369991 GAA
196 GAA
4369994 CAAAAATATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC
1 CAAAAATATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC
*
4370059 GGTATACTTGTACCGGTTAGATTGAAAAAATACATATTACATTATACTTTTGGGTTCGATGTTTT
65 GGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTT
*
4370124 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CCAGTTTTCCATTCATTCT
130 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCT
4370188 GGAA
195 GGAA
* *
4370192 CAAAAATATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTTATAAAACT
1 CAAAAATATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC
*
4370257 GGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTT
65 GGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTT
4370322 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
129 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
4370375 GGCCATATTG
Statistics
Matches: 758, Mismatches: 14, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
197 144 0.19
198 457 0.60
199 152 0.20
200 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (198 bp):
CAAAAATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTT
GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
GAA
Found at i:4370525 original size:19 final size:19
Alignment explanation
Indices: 4370493--4370540 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
4370483 TTATATTCAC
4370493 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
4370511 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
4370530 ATACAAAATTA
1 ATACAAAATTA
4370541 ACCATACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Done.