Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 9 of 206
Found at i:2684017 original size:23 final size:23
Alignment explanation
Indices: 2683988--2684084 Score: 167
Period size: 23 Copynumber: 4.2 Consensus size: 23
2683978 GCTATGTCGA
2683988 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
2684011 TTAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
2684034 TCAGGCACTTTATGTGTCGTATA
1 TCAGGCACTTTATGTGTCGTATT
*
2684057 CCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
2684080 TCAGG
1 TCAGG
2684085 TACCTCGTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:2684094 original size:16 final size:16
Alignment explanation
Indices: 2684073--2684108 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2684063 ACTTTATGTG
*
2684073 TCGTATTTCAGGTACC
1 TCGTATTTCAGGCACC
*
2684089 TCGTATTTTAGGCACC
1 TCGTATTTCAGGCACC
2684105 TCGT
1 TCGT
2684109 GTGTCGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (16 bp):
TCGTATTTCAGGCACC
Found at i:2684124 original size:21 final size:20
Alignment explanation
Indices: 2684098--2684137 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2684088 CTCGTATTTT
*
2684098 AGGCACCTCGTGTGTCGTATC
1 AGGCA-CTCATGTGTCGTATC
*
2684119 AGGCACTTATGTGTCGTAT
1 AGGCACTCATGTGTCGTAT
2684138 ACTGATCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.33
Consensus pattern (20 bp):
AGGCACTCATGTGTCGTATC
Found at i:2685021 original size:49 final size:47
Alignment explanation
Indices: 2684876--2685028 Score: 157
Period size: 47 Copynumber: 3.2 Consensus size: 47
2684866 TGGTTGGACC
* * *
2684876 ATGGCAAC-ATGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCT
1 ATGGCATCGATGTGATATGTGA-TTACGTGTAAGACCATAGCTGGGCT
* * *
2684923 ATGGCATCGGTGTAATATGTG-CTACTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCGATGTGATATGTGATTAC-GTGTAAGACCATAGCTGGGCT
* * * *
2684970 ATGGCATCAGTATGTGTTATGTGATTACGTGTAAGACCGTAGTTGGACT
1 ATGGCATC-G-ATGTGATATGTGATTACGTGTAAGACCATAGCTGGGCT
*
2685019 ATGACATCGA
1 ATGGCATCGA
2685029 GAAAACGAAG
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
46 2 0.02
47 36 0.41
48 12 0.14
49 34 0.39
50 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (47 bp):
ATGGCATCGATGTGATATGTGATTACGTGTAAGACCATAGCTGGGCT
Found at i:2685365 original size:29 final size:30
Alignment explanation
Indices: 2685272--2685379 Score: 121
Period size: 29 Copynumber: 3.7 Consensus size: 30
2685262 AAAAAAACTG
* *
2685272 CATTTTGACCCCT-AACTTTTTTGAAATTA
1 CATTTTGACCCCTAAAATTTCTTGAAATTA
** * *
2685301 CATTTCAACCCCTAAACTTTCTTAAAATTA
1 CATTTTGACCCCTAAAATTTCTTGAAATTA
*
2685331 CATTTTGA-CCCTAAAATTTCTTGAATTTA
1 CATTTTGACCCCTAAAATTTCTTGAAATTA
* *
2685360 CATTTTGGCCCCAAAAATTT
1 CATTTTGACCCCTAAAATTT
2685380 TACTGCGTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
29 36 0.55
30 30 0.45
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (30 bp):
CATTTTGACCCCTAAAATTTCTTGAAATTA
Found at i:2685912 original size:23 final size:24
Alignment explanation
Indices: 2685885--2685947 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 24
2685875 GCGGGGAAAA
2685885 AAGAAAGAAAGAAAAAGAA-GAAG
1 AAGAAAGAAAGAAAAAGAAGGAAG
* * **
2685908 GAGAAAGGAAGAGGAAGAAGGAAG
1 AAGAAAGAAAGAAAAAGAAGGAAG
**
2685932 AAGAGGGAAAGAAAAA
1 AAGAAAGAAAGAAAAA
2685948 AATTAATTAA
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (24 bp):
AAGAAAGAAAGAAAAAGAAGGAAG
Found at i:2685914 original size:27 final size:26
Alignment explanation
Indices: 2685884--2685945 Score: 63
Period size: 29 Copynumber: 2.3 Consensus size: 26
2685874 AGCGGGGAAA
2685884 AAAGAAAGAAAGAA-AAAGAAGAAGGAG
1 AAAGAAAGAAAGAAGAAAGAAG-AGG-G
* *
2685911 AAAGGAAGAGGAAGAAGGAAGAAGAGGG
1 AAA-GAA-AGAAAGAAGAAAGAAGAGGG
2685939 AAAGAAA
1 AAAGAAA
2685946 AAAATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.03
27 6 0.20
28 7 0.23
29 10 0.33
30 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (26 bp):
AAAGAAAGAAAGAAGAAAGAAGAGGG
Found at i:2686209 original size:18 final size:19
Alignment explanation
Indices: 2686186--2686229 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
2686176 GCAGGCCAAA
2686186 AAAAAAAGAA-AAAAAGAG
1 AAAAAAAGAAGAAAAAGAG
*
2686204 AGAAAAA-AAGAAAAAGAG
1 AAAAAAAGAAGAAAAAGAG
2686222 AAAAAAAG
1 AAAAAAAG
2686230 GGTTCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAGAAAAAGAG
Found at i:2686223 original size:16 final size:17
Alignment explanation
Indices: 2686197--2686229 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2686187 AAAAAAGAAA
2686197 AAAAGAGAGAAAAAAAG
1 AAAAGAGAGAAAAAAAG
2686214 AAAA-AGAGAAAAAAAG
1 AAAAGAGAGAAAAAAAG
2686230 GGTTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAGAGAAAAAAAG
Found at i:2686571 original size:18 final size:18
Alignment explanation
Indices: 2686550--2686649 Score: 64
Period size: 21 Copynumber: 5.3 Consensus size: 18
2686540 AAATATTAAA
*
2686550 AAAAAATTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
2686568 AAAAAAAATTCTCGTG-TTTC
1 ---AAAAATTTTCGTGTTTTC
* *
2686588 -GAAATTTTTGT-TTCTTC
1 AAAAATTTTCGTGTT-TTC
2686605 AAAAATTTTTCTCGTGTTTT-
1 AAAAA--TTT-TCGTGTTTTC
2686625 AAAAATTATTCGTGTTTTC
1 AAAAATT-TTCGTGTTTTC
2686644 AAAAAT
1 AAAAAT
2686650 AAGGCAATGA
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
16 9 0.14
17 3 0.05
18 14 0.22
19 7 0.11
20 12 0.19
21 16 0.25
22 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:2686571 original size:21 final size:21
Alignment explanation
Indices: 2686548--2686586 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2686538 GAAAATATTA
2686548 AAAAAAAATT-TCGTGTTTTC
1 AAAAAAAATTCTCGTGTTTTC
2686568 AAAAAAAATTCTCGTGTTT
1 AAAAAAAATTCTCGTGTTT
2686587 CGAAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAAAAAATTCTCGTGTTTTC
Found at i:2686630 original size:20 final size:20
Alignment explanation
Indices: 2686602--2686649 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
2686592 TTTTTGTTTC
*
2686602 TTCAAAAATTTTTCTCGTGTT
1 TTCAAAAATTTAT-TCGTGTT
2686623 TT-AAAAA-TTATTCGTGTT
1 TTCAAAAATTTATTCGTGTT
2686641 TTCAAAAAT
1 TTCAAAAAT
2686650 AAGGCAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 5 0.21
21 2 0.08
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (20 bp):
TTCAAAAATTTATTCGTGTT
Found at i:2686871 original size:17 final size:18
Alignment explanation
Indices: 2686827--2686888 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
2686817 GAATCCGTTA
* *
2686827 TTCAAAATTTTTCATGTT
1 TTCAAAAATTTTCGTGTT
*
2686845 TTCAAAAAATTTCTGTGTT
1 TTCAAAAATTTTC-GTGTT
2686864 TT-AAAAATTTTCGTGTT
1 TTCAAAAATTTTCGTGTT
2686881 TTCAAAAA
1 TTCAAAAA
2686889 AAATAATTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 7 0.18
18 25 0.66
19 6 0.16
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (18 bp):
TTCAAAAATTTTCGTGTT
Found at i:2695032 original size:5 final size:5
Alignment explanation
Indices: 2695022--2695051 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2695012 ATGAAGCAAC
2695022 ATAAA ATAAA ATAAA ATAAA ATGAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA AT-AAA ATAA
2695052 GAACCACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2695148 original size:3 final size:3
Alignment explanation
Indices: 2695140--2695194 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
2695130 AAACAAGCAA
* *
2695140 AAT AAT AAT AAT AAT TAT AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2695188 AAT AAT A
1 AAT AAT A
2695195 GAGACAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2696724 original size:13 final size:13
Alignment explanation
Indices: 2696685--2696737 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
2696675 AGTTTGGCAA
2696685 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
2696698 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
2696711 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
2696724 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
2696737 T
1 T
2696738 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 28 0.82
14 3 0.09
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:2696935 original size:21 final size:21
Alignment explanation
Indices: 2696911--2696953 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2696901 CTTGTTGCTA
2696911 ATATTTT-AATATATGAAATAT
1 ATATTTTAAATAT-TGAAATAT
*
2696932 ATATTTTAAATATTTAAATAT
1 ATATTTTAAATATTGAAATAT
2696953 A
1 A
2696954 ACCATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATTTTAAATATTGAAATAT
Found at i:2700092 original size:16 final size:17
Alignment explanation
Indices: 2700055--2700096 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2700045 CTAAGCTAGG
2700055 TACA-ATAT-ATATGTA
1 TACATATATAATATGTA
2700070 TACATATATAATATGT-
1 TACATATATAATATGTA
*
2700086 TATATATATAA
1 TACATATATAA
2700097 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 14 0.58
17 6 0.25
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (17 bp):
TACATATATAATATGTA
Found at i:2701044 original size:22 final size:20
Alignment explanation
Indices: 2701006--2701045 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2700996 AAAATAAATA
*
2701006 TTTATATTTTTATATTTAAC
1 TTTAAATTTTTATATTTAAC
2701026 TTTAAATTATTTATTATTTA
1 TTTAAATT-TTTA-TATTTA
2701046 TTCTTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAAATTTTTATATTTAAC
Found at i:2702394 original size:15 final size:14
Alignment explanation
Indices: 2702365--2702427 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 14
2702355 GTTTAGTCAC
* *
2702365 TAGGGTTTTTTGGTT
1 TAGGG-TTTTAGGGT
2702380 TAGGGTTTTAGGGTT
1 TAGGGTTTTAGGG-T
*
2702395 TAAGG--TTAGGGT
1 TAGGGTTTTAGGGT
2702407 TAGGG--TTAGGGT
1 TAGGGTTTTAGGGT
2702419 TAGGGTTTT
1 TAGGGTTTT
2702428 GTTAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 17 0.41
13 6 0.15
14 8 0.20
15 10 0.24
ACGTcount: A:0.14, C:0.00, G:0.40, T:0.46
Consensus pattern (14 bp):
TAGGGTTTTAGGGT
Found at i:2702409 original size:6 final size:6
Alignment explanation
Indices: 2702387--2702425 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
2702377 GTTTAGGGTT
*
2702387 TTAGGG TTTAAGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG -TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
2702426 TTGTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:2702519 original size:34 final size:36
Alignment explanation
Indices: 2702480--2702600 Score: 100
Period size: 34 Copynumber: 3.6 Consensus size: 36
2702470 ATAAATCAAG
2702480 GTTTAGAGTTTTTTTAAA-AAATT-ATTAAATTAGA
1 GTTTAGAGTTTTTTTAAATAAATTAATTAAATTAGA
* * *
2702514 TTTTAGAG--GTTTTAAATAAATTAATTAAATTAGG
1 GTTTAGAGTTTTTTTAAATAAATTAATTAAATTAGA
* *
2702548 GCTTAGAG--TTTTTAAGA-AAATTAACTAAATTATG-
1 GTTTAGAGTTTTTTTAA-ATAAATTAATTAAATTA-GA
*
2702582 GTTT--AGTTTTTTAAAATAA
1 GTTTAGAGTTTTTTTAAATAA
2702601 TTTTGTCTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
32 9 0.13
33 6 0.08
34 54 0.76
35 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (36 bp):
GTTTAGAGTTTTTTTAAATAAATTAATTAAATTAGA
Found at i:2703742 original size:20 final size:22
Alignment explanation
Indices: 2703717--2703762 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 22
2703707 ATAATTCAAT
2703717 AATTCAACTA-GATC-AACTCA
1 AATTCAACTATGATCAAACTCA
*
2703737 AATTCAAGTATGATCTAAACTCA
1 AATTCAACTATGATC-AAACTCA
2703760 AAT
1 AAT
2703763 GATTCAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 4 0.18
23 9 0.41
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28
Consensus pattern (22 bp):
AATTCAACTATGATCAAACTCA
Found at i:2706792 original size:21 final size:21
Alignment explanation
Indices: 2706763--2706817 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
2706753 ATTTTCGAGG
2706763 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
2706784 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
2706805 ATATACAATCTTA
1 ATATACAATCTTA
2706818 AAAGATATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:2711358 original size:28 final size:30
Alignment explanation
Indices: 2711318--2711375 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
2711308 AGACCCTAAG
2711318 AGTCAATTTC-T-GTAGAAGGTCCTTTAAT
1 AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
2711346 AGTCAATTTCTGTAGTAGAAGGTCCTTTAA
1 AGTCAATTTC-GTAGTAGAAGGTCCTTTAA
2711376 CTTCTCCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (30 bp):
AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
Found at i:2716664 original size:34 final size:32
Alignment explanation
Indices: 2716614--2716708 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 32
2716604 TTTAGAGTTT
*
2716614 TTTTAAAAAAATAATTAAATTAGGTTTTAGGGG
1 TTTT-AAAAAATAATTAAATTAGGTTTTAGAGG
** *
2716647 TTTTAAATAAATGAATTAAATTAGGGATTAGAGT
1 TTTTAAA-AAAT-AATTAAATTAGGTTTTAGAGG
*
2716681 TTTTAAAAAATTAACTAAATTATGGTTT
1 TTTTAAAAAA-TAATTAAATTA-GGTTT
2716709 AGTTTTTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
32 3 0.06
33 20 0.39
34 28 0.55
ACGTcount: A:0.43, C:0.01, G:0.15, T:0.41
Consensus pattern (32 bp):
TTTTAAAAAATAATTAAATTAGGTTTTAGAGG
Found at i:2716717 original size:33 final size:32
Alignment explanation
Indices: 2716613--2716725 Score: 109
Period size: 33 Copynumber: 3.4 Consensus size: 32
2716603 GTTTAGAGTT
* *
2716613 TTTTTAAAAAAATAATTAAATTAGGTTTTAGGG
1 TTTTTAAAAAATTAATTAAATTAGG-TTTAGTG
* * * *
2716646 GTTTTAAATAAATGAATTAAATTAGGGATTAGAG
1 TTTTTAAA-AAATTAATTAAATTA-GGTTTAGTG
* *
2716680 TTTTTAAAAAATTAACTAAATTATGGTTTAGTT
1 TTTTTAAAAAATTAATTAAATTA-GGTTTAGTG
*
2716713 TTTTTAAATAATT
1 TTTTTAAAAAATT
2716726 TTGTCTTTAG
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
33 38 0.58
34 25 0.38
35 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (32 bp):
TTTTTAAAAAATTAATTAAATTAGGTTTAGTG
Found at i:2717901 original size:16 final size:16
Alignment explanation
Indices: 2717877--2717914 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2717867 ATCTAAACTC
* *
2717877 AAATGATTCAAACTTG
1 AAATAATTCAAACTTA
2717893 AAATAATTCAAACTTA
1 AAATAATTCAAACTTA
2717909 AAATAA
1 AAATAA
2717915 GTCGAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (16 bp):
AAATAATTCAAACTTA
Found at i:2721291 original size:15 final size:13
Alignment explanation
Indices: 2721268--2721301 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
2721258 TTTTTATAAT
2721268 TTAATTTTAAAAA
1 TTAATTTTAAAAA
2721281 TATAATATTTAAAAA
1 T-TAAT-TTTAAAAA
2721296 TTAATT
1 TTAATT
2721302 AAATATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.11
14 8 0.42
15 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTAATTTTAAAAA
Found at i:2723211 original size:17 final size:17
Alignment explanation
Indices: 2723178--2723211 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2723168 AATGGAATTT
*
2723178 TAAATTTTGAGATATAA
1 TAAATTTTGAGAGATAA
*
2723195 TAAATTTTGTGAGATAA
1 TAAATTTTGAGAGATAA
2723212 GGTTAGAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
TAAATTTTGAGAGATAA
Found at i:2723935 original size:17 final size:16
Alignment explanation
Indices: 2723899--2723928 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2723889 CCAAAAATTT
2723899 ATTTTAAAAATAAAAA
1 ATTTTAAAAATAAAAA
2723915 ATTTTAAAAA-AAAA
1 ATTTTAAAAATAAAA
2723929 GTAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTTTAAAAATAAAAA
Found at i:2730439 original size:18 final size:18
Alignment explanation
Indices: 2730416--2730453 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2730406 ATCGTGTTTG
2730416 ATTTTT-ATTTCTAAATTT
1 ATTTTTGATTT-TAAATTT
*
2730434 ATTTTTGATTTTAGATTT
1 ATTTTTGATTTTAAATTT
2730452 AT
1 AT
2730454 CCTTAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
ATTTTTGATTTTAAATTT
Found at i:2735128 original size:23 final size:25
Alignment explanation
Indices: 2735085--2735146 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
2735075 TTAACAATAC
2735085 TGAAGTTTATTTTTATATTTTGT-TT
1 TGAA-TTTATTTTTATATTTTGTATT
* * *
2735110 TG-ATTTATTTTTGTCTTTTTTATT
1 TGAATTTATTTTTATATTTTGTATT
*
2735134 TGAATTTTTTTTT
1 TGAATTTATTTTT
2735147 TCATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 15 0.48
24 5 0.16
25 11 0.35
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.73
Consensus pattern (25 bp):
TGAATTTATTTTTATATTTTGTATT
Found at i:2735153 original size:24 final size:23
Alignment explanation
Indices: 2735090--2735158 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
2735080 AATACTGAAG
* *
2735090 TTTATTTTTAT-ATTTTGTTTTGA
1 TTTATTTTTGTCATTTT-ATTTGA
*
2735113 TTTATTTTTGTCTTTTTTATTTGAA
1 TTTATTTTTGTC-ATTTTATTTG-A
*
2735138 TTT-TTTTTTTCATTTTATTTG
1 TTTATTTTTGTCATTTTATTTG
2735159 TACCATTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 19 0.50
24 11 0.29
25 8 0.21
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.75
Consensus pattern (23 bp):
TTTATTTTTGTCATTTTATTTGA
Found at i:2737026 original size:30 final size:30
Alignment explanation
Indices: 2736971--2737028 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2736961 TAATATCAAC
** *
2736971 AATAAATTAAAAATTGGTATGAACAATAAT
1 AATAAATTAAAAATTAATATCAACAATAAT
*
2737001 AATAAATTAAAGATTAATATCAACAATA
1 AATAAATTAAAAATTAATATCAACAATA
2737029 TTTTATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAAATTAAAAATTAATATCAACAATAAT
Found at i:2739997 original size:18 final size:18
Alignment explanation
Indices: 2739976--2740017 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2739966 GAAAATGAAC
* *
2739976 TTTTAAATTTTTTTTATT
1 TTTTAAAGTTTTTATATT
2739994 TTTTAAAGTTTTTATATT
1 TTTTAAAGTTTTTATATT
2740012 TTTTAA
1 TTTTAA
2740018 GAATTAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTAAAGTTTTTATATT
Found at i:2749162 original size:51 final size:52
Alignment explanation
Indices: 2749073--2749171 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 52
2749063 GATAAAAGTT
2749073 CAAATTAATTACTTTTAGTTTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
1 CAAATTAATTACTTTTAG-TTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
** *
2749126 CAAATTAATTGTTTTTAG-TTTAGAAATAAAATTGTAAGTATTGAAA
1 CAAATTAATTACTTTTAGTTTTAGAAATAAAATTGTAAATATTGAAA
2749172 CTTTTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 27 0.63
53 16 0.37
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.40
Consensus pattern (52 bp):
CAAATTAATTACTTTTAGTTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
Found at i:2765785 original size:29 final size:30
Alignment explanation
Indices: 2765753--2765811 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
2765743 TTAAGTTTAC
2765753 AATGTATTATTTTAT-TTAT-ATAT-TTTTTT
1 AATG-ATT-TTTTATCTTATAATATGTTTTTT
2765782 AATGATTTTTTATCTTATAATATGTTTTTT
1 AATGATTTTTTATCTTATAATATGTTTTTT
2765812 TCTAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 6 0.22
28 7 0.26
29 8 0.30
30 6 0.22
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (30 bp):
AATGATTTTTTATCTTATAATATGTTTTTT
Found at i:2765881 original size:17 final size:18
Alignment explanation
Indices: 2765861--2765894 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2765851 TATATGAATA
*
2765861 TATTTTTTATA-ACATAC
1 TATTTTATATATACATAC
2765878 TATTTTATATATACATA
1 TATTTTATATATACATA
2765895 TATAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTATATATACATAC
Found at i:2766121 original size:3 final size:3
Alignment explanation
Indices: 2766113--2766185 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
2766103 ATATATTGAT
2766113 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2766161 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2766186 CTTGGTGAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2768512 original size:51 final size:51
Alignment explanation
Indices: 2768379--2768574 Score: 229
Period size: 51 Copynumber: 3.9 Consensus size: 51
2768369 AGTGAAAGTG
* * * *
2768379 ATGGTCACGTGTGTAGTACTATGTGCAGGGTACTACGTGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
*
2768428 ATGGGTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* * * * * *
2768479 TTCGATCACGTGTGTAGTACTATGTGCAAGCTACT-TCGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTAT-GTGTACCGGATAGTA
*
2768531 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
2768575 AACATCATTG
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 2 0.02
50 41 0.33
51 77 0.63
52 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
Found at i:2768566 original size:102 final size:101
Alignment explanation
Indices: 2768383--2768567 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 101
2768373 AAAGTGATGG
* *
2768383 TCACGTGTGTAGTACTATGTGCAGGGTACTACGTGTACCGGAATGATGGGTCACATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAATGATGGGTCACATGTGTAGTAC
2768448 TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* *
2768484 TCACGTGTGTAGTACTATGTGCAAGCTACTTCGTGTATCGG-ATGGTAAT-GGTCACATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAAT-G--ATGGGTCACATGTGTAG
2768547 TACTATGTGCAGGCTACTATG
63 TACTATGTGCAGGCTACTATG
2768568 TGAACCGAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
100 2 0.03
101 38 0.49
102 35 0.45
103 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAATGATGGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:2775766 original size:15 final size:15
Alignment explanation
Indices: 2775746--2775776 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2775736 AGTAGTAAAA
2775746 TCTGAAACATTGATG
1 TCTGAAACATTGATG
2775761 TCTGAAACATTGATG
1 TCTGAAACATTGATG
2775776 T
1 T
2775777 AGTAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (15 bp):
TCTGAAACATTGATG
Found at i:2777766 original size:103 final size:103
Alignment explanation
Indices: 2777588--2777956 Score: 528
Period size: 103 Copynumber: 3.6 Consensus size: 103
2777578 TAACCGTTAT
* * * * * *
2777588 CGGTGGATTCCGCACTTAGCAACCACCAAT-GAATCGAGGAATCAGCACACAGCAACCCCTTGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATAG-GTAGGGGAATCAGCACACAGCAACCCCTCGGG
* * *
2777652 GGAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATG
65 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * **
2777690 CGGTGGAATCAGCACTTAGCAACCACCAA-ATGAGTCGGGGAGTCAGCACTTAGCAACCCCTCGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATA-G-GTAGGGGAATCAGCACACAGCAACCCCTCGG
2777754 GGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
64 GGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* **
2777794 CGGTGGGATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCTCGGGG
2777859 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* *
2777897 TGGTGGGATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCT
2777957 TTATATGCAA
Statistics
Matches: 246, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
102 27 0.11
103 177 0.72
104 41 0.17
105 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:2777843 original size:33 final size:33
Alignment explanation
Indices: 2777801--2777953 Score: 111
Period size: 33 Copynumber: 4.5 Consensus size: 33
2777791 ATACGGTGGG
2777801 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
1 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
*
2777834 ATCAGCACTTAGCAACC-CC--T-CG--GGGGA
1 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
* ** *
2777861 ATCAGCACTTAGCAACCCCCTTTCACATTTAAAATATGGTGGG
1 ATCAGCACTTAGCAA-CCAC---CA-A--T-AGGTA-GG-GGA
2777904 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
1 ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
**
2777937 ATCAGCACACAGCAACC
1 ATCAGCACTTAGCAACC
2777954 CCTTTATATG
Statistics
Matches: 94, Mismatches: 10, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
27 20 0.21
28 2 0.02
29 2 0.02
30 1 0.01
32 3 0.03
33 34 0.36
34 2 0.02
35 3 0.03
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
42 5 0.05
43 17 0.18
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATAGGTAGGGGA
Found at i:2785899 original size:45 final size:45
Alignment explanation
Indices: 2785830--2785916 Score: 158
Period size: 45 Copynumber: 1.9 Consensus size: 45
2785820 GTGTATAACT
2785830 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
1 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
2785875 TATCTCATCTATTGAAT-CTGATAAGTATGATTTATCTTCCTT
1 TATCTCATCTATTGAATCCT-ATAAGTATGATTTATCTTCCTT
2785917 AATAAGGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.47
Consensus pattern (45 bp):
TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
Found at i:2786495 original size:28 final size:31
Alignment explanation
Indices: 2786446--2786502 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
2786436 CGCATAAGTG
2786446 TATATATATTATAAATATTTAAAG-TTAATA
1 TATATATATTATAAATATTTAAAGCTTAATA
2786476 TATATATATTAT-AATA-TTAAAGCTTAA
1 TATATATATTATAAATATTTAAAGCTTAA
2786503 AAGTTAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 6 0.23
29 8 0.31
30 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (31 bp):
TATATATATTATAAATATTTAAAGCTTAATA
Found at i:2786593 original size:25 final size:25
Alignment explanation
Indices: 2786559--2786624 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
2786549 AAACAAATGG
* * *
2786559 AAAATGAAGGAGAGAAAGAAACGAA
1 AAAAAGAAGGAAAGAAAGAAAAGAA
*
2786584 ACAAAGAAGGAAAGAAAGAAAAGAA
1 AAAAAGAAGGAAAGAAAGAAAAGAA
*
2786609 AAAAAGAAAGAAAGAA
1 AAAAAGAAGGAAAGAA
2786625 GGAGAATAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.71, C:0.03, G:0.24, T:0.02
Consensus pattern (25 bp):
AAAAAGAAGGAAAGAAAGAAAAGAA
Found at i:2786602 original size:4 final size:4
Alignment explanation
Indices: 2786571--2786624 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
2786561 AATGAAGGAG
* * *
2786571 AGAA AGAA ACGAA ACAA AGAA GGAA AGAA AGAAA AGAA AAAA AGAA AGAA
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA
2786621 AGAA
1 AGAA
2786625 GGAGAATAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2786617 original size:21 final size:21
Alignment explanation
Indices: 2786571--2786624 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2786561 AATGAAGGAG
*
2786571 AGAAAGAAACG-AAACAAAGAA
1 AGAAAGAAA-GAAAACAAAAAA
* *
2786592 GGAAAGAAAGAAAAGAAAAAA
1 AGAAAGAAAGAAAACAAAAAA
2786613 AGAAAGAAAGAA
1 AGAAAGAAAGAA
2786625 GGAGAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAAGAAAGAAAACAAAAAA
Found at i:2787543 original size:41 final size:40
Alignment explanation
Indices: 2787498--2787608 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 40
2787488 CGACTTCGAG
2787498 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
* * *
2787538 TTCGATGAGGCACTGGGTGCCAA--T-TTACTTCGGTTTAA
1 -TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
* *
2787576 CCGATAAGACACTGGGTGTCAATTTATTACTTC
1 TCGATGAGACACTGGGTGTCAATTTATTACTTC
2787609 AAATTATCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
37 18 0.30
38 13 0.22
39 2 0.03
40 7 0.12
41 20 0.33
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
Found at i:2787599 original size:37 final size:38
Alignment explanation
Indices: 2787499--2787601 Score: 127
Period size: 37 Copynumber: 2.7 Consensus size: 38
2787489 GACTTCGAGT
*
2787499 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAA--T-TTACTTCGGATTAATC
* * *
2787540 CGATGAGGCACTGGGTGCCAATTTACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTTACTTCGGATTAATC
*
2787577 CGATAAGACACTGGGTGTCAATTTA
1 CGATGAGACACTGGGTGTCAATTTA
2787602 TTACTTCAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 22 0.40
38 13 0.24
39 1 0.02
41 19 0.35
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAATTTACTTCGGATTAATC
Found at i:2797392 original size:2 final size:2
Alignment explanation
Indices: 2797385--2797431 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2797375 TTTAGTTTGT
2797385 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
2797427 TA TA T
1 TA TA T
2797432 TAATAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2798314 original size:27 final size:27
Alignment explanation
Indices: 2798275--2798352 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
2798265 TAGTATTGAC
*
2798275 GCCTATCTCAGAGGTGCCAATGGTGGT
1 GCCTATCTGAGAGGTGCCAATGGTGGT
* *
2798302 GCCTATCTGAGAGGTGCCATTAGTGGT
1 GCCTATCTGAGAGGTGCCAATGGTGGT
* *
2798329 GCC-ATGTTGAGAGGCGCCAATGGT
1 GCCTAT-CTGAGAGGTGCCAATGGT
2798353 ATTATTTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.05
27 41 0.95
ACGTcount: A:0.19, C:0.21, G:0.35, T:0.26
Consensus pattern (27 bp):
GCCTATCTGAGAGGTGCCAATGGTGGT
Found at i:2798437 original size:15 final size:16
Alignment explanation
Indices: 2798417--2798453 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2798407 ACAAAATCAA
2798417 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
2798432 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
2798448 ATAAAA
1 ATAAAA
2798454 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:2798734 original size:27 final size:27
Alignment explanation
Indices: 2798677--2799010 Score: 494
Period size: 27 Copynumber: 12.8 Consensus size: 27
2798667 ATTATAAAAT
2798677 AATTACAATATTCATAC--AA--ACAA
1 AATTACAATATTCATACAAAATTACAA
*
2798700 TATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
*
2798727 AATTACAATATTCATATAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
2798754 AATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
* *
2798781 AATTACAATATTCATATAAAATTACGA
1 AATTACAATATTCATACAAAATTACAA
2798808 AATTACAATATTCATAC--AA--ACAA
1 AATTACAATATTCATACAAAATTACAA
*
2798831 TATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
2798858 AATTACAATATTCATAC--AA--ACAA
1 AATTACAATATTCATACAAAATTACAA
*
2798881 TATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
*
2798908 AATTACAATATTCATATAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
* *
2798935 TATTACAATATTCATACAAAATTATAA
1 AATTACAATATTCATACAAAATTACAA
2798962 AATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
*
2798989 AATTACAATATTCTTACAAAAT
1 AATTACAATATTCATACAAAAT
2799011 ACTAATCCAA
Statistics
Matches: 280, Mismatches: 19, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
23 55 0.20
25 10 0.04
27 215 0.77
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (27 bp):
AATTACAATATTCATACAAAATTACAA
Found at i:2798973 original size:181 final size:181
Alignment explanation
Indices: 2798677--2799008 Score: 619
Period size: 181 Copynumber: 1.8 Consensus size: 181
2798667 ATTATAAAAT
2798677 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
* *
2798742 ATAAAATTACAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATATAAAATTACG
66 ATAAAATTACAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAATTACA
2798807 AAATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAA
131 AAATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAA
2798858 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
* *
2798923 ATAAAATTACAATATTACAATATTCATACAAAATTATAAAATTACAATATTCATACAAAATTACA
66 ATAAAATTACAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAATTACA
*
2798988 AAATTACAATATTCTTACAAA
131 AAATTACAATATTCATACAAA
2799009 ATACTAATCC
Statistics
Matches: 146, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
181 146 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (181 bp):
AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
ATAAAATTACAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAATTACA
AAATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAA
Found at i:2799008 original size:19 final size:19
Alignment explanation
Indices: 2798677--2798958 Score: 122
Period size: 19 Copynumber: 15.3 Consensus size: 19
2798667 ATTATAAAAT
2798677 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
2798699 ATATTACAATATTCATACAA
1 A-ATTACAATATTCATACAA
*
2798719 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
* **
2798735 TATT-C-ATATAAAATTACAA
1 AATTACAATAT-TCA-TACAA
2798754 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
*
2798773 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
* ** *
2798789 TATT-C-ATATAAAATTACGA
1 AATTACAATAT-TCA-TACAA
2798808 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
2798830 ATATTACAATATTCATACAA
1 A-ATTACAATATTCATACAA
*
2798850 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
* *
2798866 TATT-C-ATA--CAAACAA
1 AATTACAATATTCATACAA
*
2798881 TATTACAATATTCATACAA
1 AATTACAATATTCATACAA
*
2798900 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
* **
2798916 TATT-C-ATATAAAATTACAA
1 AATTACAATAT-TCA-TACAA
*
2798935 TATTACAATATTCATACAA
1 AATTACAATATTCATACAA
2798954 AATTA
1 AATTA
2798959 TAAAATTACA
Statistics
Matches: 199, Mismatches: 28, Indels: 69
0.67 0.09 0.23
Matches are distributed among these distances:
14 4 0.02
15 16 0.08
16 33 0.17
17 3 0.02
18 8 0.04
19 76 0.38
20 10 0.05
21 14 0.07
22 3 0.02
23 32 0.16
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:2799062 original size:61 final size:61
Alignment explanation
Indices: 2798989--2799334 Score: 431
Period size: 61 Copynumber: 5.4 Consensus size: 61
2798979 AAAATTACAA
* *
2798989 AATTACAATATTCTTACAAAATACTAATCCAAAACTATAAATAAAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
* *
2799050 AATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
* * * *
2799111 AATTACACTATTCATTCAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACGA
1 AATTACAATATTCATACAAAA-TAC--TA---AT-CAAAA-ACT-AT-AAATAA-A-AAAT---T
2799176 AATTAATTATAAAAT
51 AA-T--T-ATAAAAT
*
2799191 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
*
2799252 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATATAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
2799313 AATTACAATATTCATACAAAAT
1 AATTACAATATTCATACAAAAT
2799335 TATAATATTC
Statistics
Matches: 250, Mismatches: 16, Indels: 38
0.82 0.05 0.12
Matches are distributed among these distances:
61 165 0.66
62 4 0.02
64 3 0.01
65 2 0.01
67 2 0.01
68 9 0.04
69 4 0.02
70 5 0.02
71 6 0.02
72 4 0.02
73 9 0.04
74 2 0.01
76 2 0.01
77 3 0.01
79 4 0.02
80 26 0.10
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (61 bp):
AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
Found at i:2799111 original size:80 final size:80
Alignment explanation
Indices: 2799027--2799212 Score: 234
Period size: 80 Copynumber: 2.3 Consensus size: 80
2799017 CCAAAACTAT
* *
2799027 AAATAA-AAAATTAATT-ATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAA
1 AAATAATAAAACT-ATTCATAAAA-AATTACAATATTCATACAAAATACTAATCAAAAAATACAA
2799090 ATACAAAATTAATTATA
64 ATACAAAATTAATTATA
* * ** *
2799107 AAATAATTACACTATTCATTCAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAAT
1 AAATAATAAAACTATTCATAAAAAATTACAATATTCATACAAAATACTAATCAAAAAATACAAAT
*
2799172 ACGAAATTAATTATA
66 ACAAAATTAATTATA
* *
2799187 AAATAATTACAA-TATTCATACAAAAT
1 AAATAA-TAAAACTATTCATAAAAAAT
2799213 ACTAATCAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 82 0.90
81 9 0.10
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (80 bp):
AAATAATAAAACTATTCATAAAAAATTACAATATTCATACAAAATACTAATCAAAAAATACAAAT
ACAAAATTAATTATA
Found at i:2799135 original size:19 final size:19
Alignment explanation
Indices: 2799111--2799151 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2799101 ATTATAAAAT
* *
2799111 AATTACACTATTCATTCAA
1 AATTACAATATTCATACAA
2799130 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
2799149 AAT
1 AAT
2799152 ACTAATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:2799169 original size:141 final size:141
Alignment explanation
Indices: 2798984--2799441 Score: 529
Period size: 141 Copynumber: 3.2 Consensus size: 141
2798974 CATACAAAAT
* * *
2798984 TACAAAATTACAATATTCTTACAAAATACTAATCCAAAACTATAAATAAAAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATAAAAAATTAATTATAAAA
2799049 TAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAAT
66 TAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAAT
*
2799114 TACACTATTCA
131 TACAATATTCA
* **
2799125 TTCAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACGAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATAAAAAATTAATTATAAAA
*
2799190 TAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAAT
66 TAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAAT
2799255 TACAATATTCA
131 TACAATATTCA
* * *
2799266 TACAAAA-TAC--TAATCA-A-AAACTA-TAAAT-ATAAAAT-TAATTATAAAATAATTACAATA
1 TACAAAATTACAATATTCATACAAAATACT-AATCAAAAAATATAA--ATAAAA-AATT---A-A
* * * * ** * *
2799323 TTCATACAA-AATTATAATATTCATATAAAATTACAAAATTACAATATTCATACAAAATTATAAT
58 TT-ATAAAATAATTACAATATTCATACAAAA-TAC-TAA-T-CAA-AAAC-TAC-AAA-TACAAA
2799387 ATTAATTATAAAATAATTACAATATTCA
114 ATTAATTATAAAATAATTACAATATTCA
2799415 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
2799442 TACCCATTGG
Statistics
Matches: 270, Mismatches: 25, Indels: 31
0.83 0.08 0.10
Matches are distributed among these distances:
134 3 0.01
135 7 0.03
136 12 0.04
137 5 0.02
138 5 0.02
140 4 0.01
141 161 0.60
142 8 0.03
143 2 0.01
144 1 0.00
145 3 0.01
146 2 0.01
147 2 0.01
148 3 0.01
149 39 0.14
150 3 0.01
152 5 0.02
153 1 0.00
154 4 0.01
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (141 bp):
TACAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATAAAAAATTAATTATAAAA
TAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAAT
TACAATATTCA
Found at i:2799219 original size:202 final size:210
Alignment explanation
Indices: 2798903--2799422 Score: 680
Period size: 202 Copynumber: 2.5 Consensus size: 210
2798893 CATACAAAAT
* * ** * *
2798903 TACAAAATTACAATATTCATATAAAATTACAATATTACAATATTCATACAAAATTATAAAATTAC
1 TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATAAATACAAAATTAGAATATT--
* *
2798968 AATATTCATACAAAATTACAAAATTACAATATTCTTACAAAATACTAATCCAAAACTATAAATAA
64 -A-ATT-AT--AAAA-T----AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAA
2799033 AAAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAA
119 AAAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAA
*
2799098 TTAATTATAAAATAATTACACTATTCA
184 TTAATTATAAAATAATTACAATATTCA
* * *
2799125 TTCAAAATTACAATATTCATACAAAA-TAC-TAA-T-CAA-A-AAATA-TAAA-TACGAA-ATTA
1 TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATAAATACAAAATTA-GAATATTA
*
2799181 ATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTA
65 ATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTA
* *
2799246 TAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATATAAAATTAATTATAAA
130 TAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAA
2799311 ATAATTACAATATTCA
195 ATAATTACAATATTCA
* * ** *
2799327 TACAAAATTATAATATTCATATAAAATTACAAAATTACAATATTCATACAAAATTATAATATTAA
1 TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATAAATACAAAATTAGAATATTAA
2799392 TTATAAAATAATTACAATATTCATACAAAAT
66 TTATAAAATAATTACAATATTCATACAAAAT
2799423 TACAATATTC
Statistics
Matches: 266, Mismatches: 22, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
202 153 0.58
203 3 0.01
204 2 0.01
205 1 0.00
206 4 0.02
207 5 0.02
208 3 0.01
209 7 0.03
210 41 0.15
211 1 0.00
214 5 0.02
215 5 0.02
216 3 0.01
217 1 0.00
218 3 0.01
219 1 0.00
220 1 0.00
221 3 0.01
222 24 0.09
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.32
Consensus pattern (210 bp):
TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATAAATACAAAATTAGAATATTAA
TTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTAT
AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAA
TAATTACAATATTCA
Found at i:2799252 original size:80 final size:79
Alignment explanation
Indices: 2799050--2799220 Score: 247
Period size: 80 Copynumber: 2.2 Consensus size: 79
2799040 ATTATAAAAT
* * *
2799050 AATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAATT
1 AATTAC-ATAATCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAATAATT
* *
2799115 ACACTATTCATTCAA
65 ACAATATTCATACAA
* *
2799130 AATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACGAAATTAATTATAAAATAATT
1 AATTAC-ATAATCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAATAATT
2799195 ACAATATTCATACAA
65 ACAATATTCATACAA
2799210 AA-TAC-TAATCA
1 AATTACATAATCA
2799221 AAAACTATAA
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
77 5 0.06
79 3 0.04
80 77 0.91
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (79 bp):
AATTACATAATCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAATAATTA
CAATATTCATACAA
Found at i:2799269 original size:34 final size:34
Alignment explanation
Indices: 2799231--2799336 Score: 118
Period size: 34 Copynumber: 3.3 Consensus size: 34
2799221 AAAACTATAA
2799231 ATACAAAATTAATTATAAAATAATTACAATATTC
1 ATACAAAATTAATTATAAAATAATTACAATATTC
* * * * *
2799265 ATACAAAA-TACTAATCAAA-AACTATAA-A-T-
1 ATACAAAATTAATTATAAAATAATTACAATATTC
2799294 AT--AAAATTAATTATAAAATAATTACAATATTC
1 ATACAAAATTAATTATAAAATAATTACAATATTC
2799326 ATACAAAATTA
1 ATACAAAATTA
2799337 TAATATTCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
27 4 0.07
28 8 0.15
29 8 0.15
30 2 0.04
31 2 0.04
32 8 0.15
33 8 0.15
34 15 0.27
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (34 bp):
ATACAAAATTAATTATAAAATAATTACAATATTC
Found at i:2799341 original size:19 final size:19
Alignment explanation
Indices: 2799313--2799444 Score: 120
Period size: 19 Copynumber: 6.3 Consensus size: 19
2799303 ATTATAAAAT
2799313 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
*
2799332 AATTATAATATTCATATAAAATTACAA
1 AATTACAATATTC-------A-TACAA
2799359 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
2799378 AATTATAATATTAATTATAAAA
1 AATTACAATA-T--TCATACAA
2799400 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
2799420 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
2799439 AATTAC
1 AATTAC
2799445 CCATTGGCGC
Statistics
Matches: 93, Mismatches: 8, Indels: 24
0.74 0.06 0.19
Matches are distributed among these distances:
19 51 0.55
20 8 0.09
22 7 0.08
23 9 0.10
26 1 0.01
27 17 0.18
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:2799373 original size:46 final size:44
Alignment explanation
Indices: 2799313--2799444 Score: 189
Period size: 46 Copynumber: 3.0 Consensus size: 44
2799303 ATTATAAAAT
2799313 AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
1 AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
*
2799357 AAAATTACAATATTCATACAAAATTATAATATTAATTATAAAA-T--
1 --AATTACAATATTCATACAAAATTATAATATTCA-TATAAAATTAC
* *
2799401 AATTACAATATTCATACAAAATTACAATATTCATACAAAATTAC
1 AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
2799445 CCATTGGCGC
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
41 6 0.08
42 32 0.41
46 33 0.42
47 7 0.09
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (44 bp):
AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
Found at i:2799390 original size:27 final size:27
Alignment explanation
Indices: 2799327--2799382 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2799317 ACAATATTCA
* *
2799327 TACAAAATTATAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
2799354 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
2799381 TA
1 TA
2799383 TAATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:2799418 original size:42 final size:42
Alignment explanation
Indices: 2799293--2799431 Score: 199
Period size: 42 Copynumber: 3.2 Consensus size: 42
2799283 AAACTATAAA
*
2799293 TATAAAATTAATTATAAAATAATTACAATATTCATACAAAAT
1 TATAATATTAATTATAAAATAATTACAATATTCATACAAAAT
*
2799335 TATAATATTCA-TATAAAATTACAAAATTACAATATTCATACAAAAT
1 TATAATATTAATTATAAAA-T----AATTACAATATTCATACAAAAT
2799381 TATAATATTAATTATAAAATAATTACAATATTCATACAAAAT
1 TATAATATTAATTATAAAATAATTACAATATTCATACAAAAT
*
2799423 TACAATATT
1 TATAATATT
2799432 CATACAAAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
41 7 0.08
42 40 0.46
46 33 0.38
47 7 0.08
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.37
Consensus pattern (42 bp):
TATAATATTAATTATAAAATAATTACAATATTCATACAAAAT
Found at i:2803569 original size:20 final size:20
Alignment explanation
Indices: 2803546--2803583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2803536 TCTTAAGATT
*
2803546 TTAAACATATTTTTACACTG
1 TTAAACATATTTTAACACTG
*
2803566 TTAAATATATTTTAACAC
1 TTAAACATATTTTAACAC
2803584 CATTTTTATT
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:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (20 bp):
TTAAACATATTTTAACACTG
Found at i:2807395 original size:27 final size:23
Alignment explanation
Indices: 2807344--2807391 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2807334 TTTTTCAAAG
2807344 AATTTTTTAAATAAATAAGAAAT
1 AATTTTTTAAATAAATAAGAAAT
2807367 AATTTTTTAAATAAATAAGAAAT
1 AATTTTTTAAATAAATAAGAAAT
2807390 AA
1 AA
2807392 ATAAACTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AATTTTTTAAATAAATAAGAAAT
Found at i:2810783 original size:31 final size:31
Alignment explanation
Indices: 2810748--2810813 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
2810738 TTACAATTAG
*
2810748 GTCATTGAA-ATATTCAAAAATTTTTATTTAA
1 GTCATT-AAGATATTCAAAAAATTTTATTTAA
* *
2810779 GTCATTAAGCTATTCAAAAAATTTTATTTGA
1 GTCATTAAGATATTCAAAAAATTTTATTTAA
2810810 GTCA
1 GTCA
2810814 CTGGATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (31 bp):
GTCATTAAGATATTCAAAAAATTTTATTTAA
Found at i:2814872 original size:24 final size:24
Alignment explanation
Indices: 2814844--2814894 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2814834 CTCCCTTCAA
*
2814844 TCGTAGACGTAGCCCTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
* *
2814868 TCGTAGGCGGAGCCGTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
2814892 TCG
1 TCG
2814895 CAGGCCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (24 bp):
TCGTAGACGGAGCCCTTCTCCAAT
Found at i:2814899 original size:24 final size:24
Alignment explanation
Indices: 2814854--2814899 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2814844 TCGTAGACGT
*
2814854 AGCCCTTCTCCAATTCGTAGGCGG
1 AGCCCTTCTCCAATTCGCAGGCGG
*
2814878 AGCCGTTCTCCAATTCGCAGGC
1 AGCCCTTCTCCAATTCGCAGGC
2814900 CTCTTCGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.35, G:0.24, T:0.24
Consensus pattern (24 bp):
AGCCCTTCTCCAATTCGCAGGCGG
Found at i:2817223 original size:18 final size:18
Alignment explanation
Indices: 2817200--2817240 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2817190 ATATTACAAA
*
2817200 ATTTTGATGAT-AAACATG
1 ATTTTGATCATGAAA-ATG
2817218 ATTTTGATCATGAAAATG
1 ATTTTGATCATGAAAATG
2817236 ATTTT
1 ATTTT
2817241 CCAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
ATTTTGATCATGAAAATG
Found at i:2829660 original size:20 final size:20
Alignment explanation
Indices: 2829637--2829677 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2829627 AGGGTTCAAG
*
2829637 GTTTGGGCTTC-AGAGTTTGA
1 GTTTGGGATTCGAG-GTTTGA
2829657 GTTTGGGATTCGAGGTTTGA
1 GTTTGGGATTCGAGGTTTGA
2829677 G
1 G
2829678 GTTTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.15, C:0.07, G:0.39, T:0.39
Consensus pattern (20 bp):
GTTTGGGATTCGAGGTTTGA
Found at i:2829674 original size:34 final size:33
Alignment explanation
Indices: 2829612--2829675 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
2829602 TGGTACAAGA
*
2829612 TTCAGATTTGGGTTTAGGGTTCAAGGTTTGGGC
1 TTCAGATTTGAGTTTAGGGTTCAAGGTTTGGGC
*
2829645 TTCAGAGTTTGAGTTT-GGGATTCGAGGTTTG
1 TTCAGA-TTTGAGTTTAGGG-TTCAAGGTTTG
2829676 AGGTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.41
Consensus pattern (33 bp):
TTCAGATTTGAGTTTAGGGTTCAAGGTTTGGGC
Found at i:2835172 original size:18 final size:18
Alignment explanation
Indices: 2835141--2835175 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2835131 TTAGTAATTA
2835141 TTTTAAGATAAAAATATC
1 TTTTAAGATAAAAATATC
* *
2835159 TTTTATGATTAAAATAT
1 TTTTAAGATAAAAATAT
2835176 GTTAAGGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTTAAGATAAAAATATC
Found at i:2839838 original size:3 final size:3
Alignment explanation
Indices: 2839830--2839859 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2839820 TTTCTCTCTC
2839830 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2839860 TTTCTCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2840626 original size:106 final size:106
Alignment explanation
Indices: 2840510--2840713 Score: 408
Period size: 106 Copynumber: 1.9 Consensus size: 106
2840500 TAAAAAAAAA
2840510 TTAACCTTGTTATCCATTGATCTTTAAATATTTAATAAGAAAAAGTAAGGAGACTAAATTTCTGA
1 TTAACCTTGTTATCCATTGATCTTTAAATATTTAATAAGAAAAAGTAAGGAGACTAAATTTCTGA
2840575 AATAAAAAAGTAGGACTAAATTATAAATGGAAATGAAAATT
66 AATAAAAAAGTAGGACTAAATTATAAATGGAAATGAAAATT
2840616 TTAACCTTGTTATCCATTGATCTTTAAATATTTAATAAGAAAAAGTAAGGAGACTAAATTTCTGA
1 TTAACCTTGTTATCCATTGATCTTTAAATATTTAATAAGAAAAAGTAAGGAGACTAAATTTCTGA
2840681 AATAAAAAAGTAGGACTAAATTATAAATGGAAA
66 AATAAAAAAGTAGGACTAAATTATAAATGGAAA
2840714 GAATACAGGG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (106 bp):
TTAACCTTGTTATCCATTGATCTTTAAATATTTAATAAGAAAAAGTAAGGAGACTAAATTTCTGA
AATAAAAAAGTAGGACTAAATTATAAATGGAAATGAAAATT
Found at i:2851668 original size:7 final size:7
Alignment explanation
Indices: 2851656--2851686 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2851646 AATATCATTT
2851656 AAAAATA
1 AAAAATA
2851663 AAAAATA
1 AAAAATA
2851670 AAAAATA
1 AAAAATA
2851677 AAAAATA
1 AAAAATA
2851684 AAA
1 AAA
2851687 TTTTACTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:2870321 original size:17 final size:17
Alignment explanation
Indices: 2870294--2870346 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
2870284 CAAATTCATA
*
2870294 TATAAACTTTGATTTAG
1 TATAAATTTTGATTTAG
2870311 TATATAA-TTTGA--TA-
1 TATA-AATTTTGATTTAG
2870325 TATAAATTTTGATTTAG
1 TATAAATTTTGATTTAG
2870342 TATAA
1 TATAA
2870347 TATACATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 9 0.29
15 2 0.06
16 2 0.06
17 14 0.45
18 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (17 bp):
TATAAATTTTGATTTAG
Found at i:2870345 original size:19 final size:18
Alignment explanation
Indices: 2870292--2870345 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 18
2870282 TTCAAATTCA
2870292 TATATAAACTTTGATTTAG
1 TATATAAA-TTTGATTTAG
2870311 TATAT-AATTTGA--TA-
1 TATATAAATTTGATTTAG
*
2870325 TATA-AATTTTGATTTAG
1 TATATAAATTTGATTTAG
2870342 TATA
1 TATA
2870346 ATATACATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 10 0.33
15 2 0.07
16 2 0.07
17 9 0.30
18 2 0.07
19 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (18 bp):
TATATAAATTTGATTTAG
Found at i:2870651 original size:12 final size:12
Alignment explanation
Indices: 2870634--2870658 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2870624 CATAAGACGT
2870634 TATAATATAATA
1 TATAATATAATA
2870646 TATAATATAATA
1 TATAATATAATA
2870658 T
1 T
2870659 CAGATATTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAATATAATA
Found at i:2871596 original size:19 final size:19
Alignment explanation
Indices: 2871556--2871596 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2871546 TTAGTATATG
**
2871556 TATATATATGTTTGTGGTT
1 TATATATATGTTTGTGAAT
2871575 TATATATATGTTTGTGAAT
1 TATATATATGTTTGTGAAT
2871594 TAT
1 TAT
2871597 GAGAGGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (19 bp):
TATATATATGTTTGTGAAT
Found at i:2873262 original size:28 final size:27
Alignment explanation
Indices: 2873225--2873314 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 27
2873215 TTTTATATAA
2873225 TAATTTTTTTTGCAATATTATAATTTTT
1 TAATTTTTTTTGCAAT-TTATAATTTTT
* *
2873253 TAATTTTTTTT--AATTTTTAATAATTT
1 TAATTTTTTTTGCAATTTATAAT-TTTT
*
2873279 T-ATTCTTTTTGCAATTT-TATATTATTT
1 TAATTTTTTTTGCAATTTATA-ATT-TTT
*
2873306 TAATATTTT
1 TAATTTTTT
2873315 AATAATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
25 14 0.28
26 9 0.18
27 11 0.22
28 16 0.32
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (27 bp):
TAATTTTTTTTGCAATTTATAATTTTT
Found at i:2873314 original size:27 final size:27
Alignment explanation
Indices: 2873230--2873314 Score: 86
Period size: 26 Copynumber: 3.2 Consensus size: 27
2873220 TATAATAATT
*
2873230 TTTTTTGCAATATTATAATT-TTTTAA
1 TTTTTTGCAATTTTATAATTATTTTAA
** * *
2873256 TTTTTTTTAATTTT-TAATAATTTTAT
1 TTTTTTGCAATTTTATAATTATTTTAA
2873282 TCTTTTTGCAATTTTAT-ATTATTTTAA
1 T-TTTTTGCAATTTTATAATTATTTTAA
*
2873309 TATTTT
1 TTTTTT
2873315 AATAATTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
25 4 0.09
26 21 0.46
27 20 0.43
28 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTTTGCAATTTTATAATTATTTTAA
Found at i:2873375 original size:27 final size:27
Alignment explanation
Indices: 2873344--2873396 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2873334 TTAGTAATTT
* *
2873344 TTTTTATAATTTTTGAAAATTCTAATAA
1 TTTTCATAA-TTTTAAAAATTCTAATAA
*
2873372 TTTTCATTATTTTAAAAATTCTAAT
1 TTTTCATAATTTTAAAAATTCTAAT
2873397 TTTTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTTCATAATTTTAAAAATTCTAATAA
Found at i:2874326 original size:17 final size:19
Alignment explanation
Indices: 2874306--2874347 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2874296 AAATTCTGAA
2874306 AATTTT-AAAA-TATTTTG
1 AATTTTAAAAATTATTTTG
2874323 AATTTTAAAAATTATTTTG
1 AATTTTAAAAATTATTTTG
2874342 AATTTT
1 AATTTT
2874348 TTTTGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.26
18 4 0.17
19 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:2887630 original size:55 final size:54
Alignment explanation
Indices: 2887568--2887671 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
2887558 AAAAAATTTA
* * *
2887568 ACAATTTATTTATTTTTTTATTATTTGCAGTGTCGAACCATGCTTTGCTTAAATC
1 ACAATTTAATCATTTTTTT-TTATTTACAGTGTCGAACCATGCTTTGCTTAAATC
*
2887623 ACAATTTAATCCTTTTTTTTTATTTACAGTGTCGAACCATGCTTTGCTT
1 ACAATTTAATCATTTTTTTTTATTTACAGTGTCGAACCATGCTTTGCTT
2887672 TTGATTAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 29 0.64
55 16 0.36
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (54 bp):
ACAATTTAATCATTTTTTTTTATTTACAGTGTCGAACCATGCTTTGCTTAAATC
Found at i:2888694 original size:31 final size:31
Alignment explanation
Indices: 2888650--2888716 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2888640 TTAATATAAT
* *
2888650 ATTTGGTAATTGAATTTGACAATTTTTCTTA
1 ATTTGATAATTGAACTTGACAATTTTTCTTA
* *
2888681 ATTTGATATTTGAACTTGACTATTTTTCTTA
1 ATTTGATAATTGAACTTGACAATTTTTCTTA
2888712 ATTTG
1 ATTTG
2888717 GTACTTGTCA
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:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (31 bp):
ATTTGATAATTGAACTTGACAATTTTTCTTA
Found at i:2889328 original size:4 final size:4
Alignment explanation
Indices: 2889319--2889344 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2889309 TTGGTCATAT
2889319 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
2889345 ATGCAAACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:2889901 original size:18 final size:18
Alignment explanation
Indices: 2889878--2889920 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2889868 GAATATGTTT
2889878 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
2889896 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
2889914 TTAATTA
1 TTAATTA
2889921 CACTTTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:2908714 original size:21 final size:21
Alignment explanation
Indices: 2908675--2908714 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2908665 ACAAAAACTC
*
2908675 GAAATTCCAATTCTATCTTCT
1 GAAATTCCAATTATATCTTCT
* *
2908696 GAAATTTCAATTATTTCTT
1 GAAATTCCAATTATATCTT
2908715 ACTTGAAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.47
Consensus pattern (21 bp):
GAAATTCCAATTATATCTTCT
Found at i:2917680 original size:13 final size:13
Alignment explanation
Indices: 2917664--2917689 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2917654 TTATAACTTG
2917664 AATTTAATATTTA
1 AATTTAATATTTA
2917677 AATTTAATATTTA
1 AATTTAATATTTA
2917690 TTTTTCAATT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTAATATTTA
Found at i:2927713 original size:17 final size:17
Alignment explanation
Indices: 2927688--2927722 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2927678 TCACTGGCAA
2927688 ATTAAATTTTAACAACT
1 ATTAAATTTTAACAACT
* *
2927705 ATTAGATTTTAGCAACT
1 ATTAAATTTTAACAACT
2927722 A
1 A
2927723 AGAGTACGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTAAATTTTAACAACT
Found at i:2928692 original size:51 final size:51
Alignment explanation
Indices: 2928636--2928732 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
2928626 GTTGTTGCTT
* **
2928636 TGGTTAAGATACTTAGTAGTTTGTTTTAATTTTTGAAGATTTTATGGCTAG
1 TGGTTAAGATACTTAGTAATTTGTTTTAATCATTGAAGATTTTATGGCTAG
* * *
2928687 TGGTTAAGTTACTTATTAATTTGTTTTAGTCATTGAAGATTTTATG
1 TGGTTAAGATACTTAGTAATTTGTTTTAATCATTGAAGATTTTATG
2928733 TCTCAATACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.51
Consensus pattern (51 bp):
TGGTTAAGATACTTAGTAATTTGTTTTAATCATTGAAGATTTTATGGCTAG
Found at i:2929363 original size:13 final size:13
Alignment explanation
Indices: 2929345--2929369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2929335 AATATTGCCT
2929345 TTATTATTATTTG
1 TTATTATTATTTG
2929358 TTATTATTATTT
1 TTATTATTATTT
2929370 TTTAGAAAAA
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTATTATTTG
Found at i:2930198 original size:18 final size:16
Alignment explanation
Indices: 2930175--2930210 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
2930165 ATAGGGTTTT
2930175 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
2930193 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
2930209 TA
1 TA
2930211 TATTATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:2930295 original size:39 final size:38
Alignment explanation
Indices: 2930251--2930326 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 38
2930241 CATCACAAAG
* * *
2930251 TTAAAATAATAATGTATGATAATAATAAAATAAAATAAT
1 TTAAAATAATAATGCATAATAA-AATAAAAAAAAATAAT
* *
2930290 TTAAAATAATAGTGCATAATAAAGTAAAAAAAAATAA
1 TTAAAATAATAATGCATAATAAAATAAAAAAAAATAA
2930327 GTAACTGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 13 0.41
39 19 0.59
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (38 bp):
TTAAAATAATAATGCATAATAAAATAAAAAAAAATAAT
Found at i:2930371 original size:3 final size:3
Alignment explanation
Indices: 2930363--2930406 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2930353 CAATAATGTC
2930363 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2930407 ATTAATATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2930418 original size:11 final size:11
Alignment explanation
Indices: 2930363--2930430 Score: 55
Period size: 12 Copynumber: 5.8 Consensus size: 11
2930353 CAATAATGTC
*
2930363 AATAATAATAAT
1 AATAATAA-ACT
*
2930375 AATAATAATAAT
1 AATAATAA-ACT
*
2930387 AATAATAATAAT
1 AATAATAA-ACT
*
2930399 AATAATAAATT
1 AATAATAAACT
*
2930410 AATATTAAACT
1 AATAATAAACT
2930421 AATTAATAAA
1 AA-TAATAAA
2930431 ACAATGGGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
11 13 0.25
12 38 0.75
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAATAAACT
Found at i:2931386 original size:11 final size:11
Alignment explanation
Indices: 2931357--2931472 Score: 58
Period size: 12 Copynumber: 11.3 Consensus size: 11
2931347 AAATTAAAAC
*
2931357 AAAA-ATTTAA
1 AAAATATTTTA
2931367 AAAAGTATTTTA
1 AAAA-TATTTTA
2931379 AAAATATTTT-
1 AAAATATTTTA
2931389 -AAA-A-TTTA
1 AAAATATTTTA
*
2931397 AAAA-A-TTAA
1 AAAATATTTTA
2931406 AAAAGTATTTTA
1 AAAA-TATTTTA
*
2931418 AAAAAATTTT-
1 AAAATATTTTA
2931428 -AAA-A--TTA
1 AAAATATTTTA
* *
2931435 AAAAAATTTAAA
1 AAAATATTT-TA
2931447 AAAAGTATTTTA
1 AAAA-TATTTTA
*
2931459 AAAGTATTTTA
1 AAAATATTTTA
2931470 AAA
1 AAA
2931473 TTAAAAAAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 27
0.71 0.07 0.23
Matches are distributed among these distances:
6 2 0.02
7 3 0.04
8 5 0.06
9 18 0.21
10 4 0.05
11 23 0.27
12 25 0.30
13 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:2931434 original size:30 final size:28
Alignment explanation
Indices: 2931389--2931461 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 28
2931379 AAAATATTTT
* *
2931389 AAAATTTAAAAAATTAAAAAAGTATTTTAAA
1 AAAATTT-TAAAATTAAAAAA--ATTTAAAA
2931420 AAAATTTTAAAATTAAAAAAATTTAAAA
1 AAAATTTTAAAATTAAAAAAATTTAAAA
2931448 AAAGTATTTTAAAA
1 AAA--ATTTTAAAA
2931462 GTATTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
28 10 0.26
30 21 0.55
31 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTTTAAAATTAAAAAAATTTAAAA
Found at i:2931448 original size:17 final size:17
Alignment explanation
Indices: 2931415--2931448 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2931405 AAAAAGTATT
*
2931415 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTAAAAA
2931432 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
2931449 AAGTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:2931449 original size:41 final size:40
Alignment explanation
Indices: 2931339--2931482 Score: 209
Period size: 39 Copynumber: 3.5 Consensus size: 40
2931329 ACCAAAAATT
2931339 TATTTTAAAAATTAAAACAAAAATTTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTTAAAAAAGTATTTTAAAAA
*
2931383 TATTTTAAAATTTAAAAAA-TTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAA
* *
2931422 AATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAATTT-AAAAAAGTATTTTAAAAA
2931463 TATTTTAAAATTAAAAAAAT
1 TATTTTAAAATTAAAAAAAT
2931483 AAAAATATTT
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
39 37 0.40
40 7 0.08
41 37 0.40
43 6 0.06
44 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAA
Found at i:2952171 original size:2 final size:2
Alignment explanation
Indices: 2952164--2952206 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
2952154 AATTCAACCA
2952164 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2952207 GATCAAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2953377 original size:4 final size:4
Alignment explanation
Indices: 2953339--2953408 Score: 95
Period size: 4 Copynumber: 17.0 Consensus size: 4
2953329 ATAGAAGGAG
* * *
2953339 AGAA AGAA ACGAA ACAG AGAA GGAA AGAA AGGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA
2953389 AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA
2953409 GGAGAAAAGT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
4 50 0.86
5 8 0.14
ACGTcount: A:0.70, C:0.03, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2953778 original size:120 final size:121
Alignment explanation
Indices: 2953547--2953782 Score: 429
Period size: 120 Copynumber: 1.9 Consensus size: 121
2953537 ATTATTAAGT
2953547 TTTTAAGTGATGTTTATGTTGAATAATTTTAGTATTAGGGATTAAATTGATAGATTTTTAAGTTA
1 TTTTAAGTGATGTTTATGTTGAATAATTTTAGTATTAGGGATTAAATTGATAGA---TTAAGTTA
2953612 AAAGTGAAAAAGAATTGAATTGTAGAATAAATTGTAAATTTTGAGTAATAAATTGTAAA
63 AAAGTGAAAAAGAATTGAATTGTAGAATAAATTGTAAATTTTGAGTAATAAATTGTAAA
*
2953671 TTTTAAGTGCTGTTTATGTTGAATAATTTTAGTATTAGGGATTAAATTGATAGA-TAAGTTAAAA
1 TTTTAAGTGATGTTTATGTTGAATAATTTTAGTATTAGGGATTAAATTGATAGATTAAGTTAAAA
2953735 GTGAAAAAGAATTGAATTGTAGAATAAATTGTAAATTTTGAGTAATAA
66 GTGAAAAAGAATTGAATTGTAGAATAAATTGTAAATTTTGAGTAATAA
2953783 GGACTAAATT
Statistics
Matches: 111, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
120 58 0.52
124 53 0.48
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.40
Consensus pattern (121 bp):
TTTTAAGTGATGTTTATGTTGAATAATTTTAGTATTAGGGATTAAATTGATAGATTAAGTTAAAA
GTGAAAAAGAATTGAATTGTAGAATAAATTGTAAATTTTGAGTAATAAATTGTAAA
Found at i:2954218 original size:24 final size:24
Alignment explanation
Indices: 2954191--2954237 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2954181 ATTGAAATGG
2954191 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
2954215 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
2954238 GGTTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:2954532 original size:40 final size:38
Alignment explanation
Indices: 2954441--2954539 Score: 119
Period size: 40 Copynumber: 2.6 Consensus size: 38
2954431 TGGATTAATT
**
2954441 TGATGAGGCACTGGGTGCC-AATTTACTTCAGTTTAAC
1 TGATGAGGCACTGGGTGCCAAATTTACTTCAAATTAAC
* * * *
2954478 CGATGAGACACTGGGTGCCAAATTATTATTTCAAATTATC
1 TGATGAGGCACTGGGTGCCAAA-T-TTACTTCAAATTAAC
2954518 TGATGAGGCACTGGGTGCCAAA
1 TGATGAGGCACTGGGTGCCAAA
2954540 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 17 0.33
38 2 0.04
39 1 0.02
40 31 0.61
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (38 bp):
TGATGAGGCACTGGGTGCCAAATTTACTTCAAATTAAC
Found at i:2957385 original size:27 final size:27
Alignment explanation
Indices: 2957322--2957394 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
2957312 CTATACGTAT
* *
2957322 ATATATTATAAAATATGGAAGATATAAC
1 ATATACTATAAAATAT-AAAGATATAAC
2957350 A-ATACTATAAAATATAAATG-TATATAC
1 ATATACTATAAAATATAAA-GATATA-AC
*
2957377 ATATA-TATAAACTATAAA
1 ATATACTATAAAATATAAA
2957395 AATGAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 6 0.15
27 29 0.74
28 4 0.10
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (27 bp):
ATATACTATAAAATATAAAGATATAAC
Found at i:2957642 original size:3 final size:3
Alignment explanation
Indices: 2957527--2957628 Score: 143
Period size: 3 Copynumber: 33.7 Consensus size: 3
2957517 GTATAACAAG
* * **
2957527 AAT AAT AAAT AAT -AT AAT AAT AAT GATT ACT AAT GGT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
2957573 AAT AAT 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 AAT AAT
2957621 AAT AAT AA
1 AAT AAT AA
2957629 AATGTCAAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
2 2 0.02
3 82 0.92
4 5 0.06
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2961588 original size:3 final size:3
Alignment explanation
Indices: 2961573--2961607 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2961563 ATGAATTTCA
* *
2961573 TAT TAT TAC TAT TAT TAT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2961608 GTTTTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2961588 original size:12 final size:12
Alignment explanation
Indices: 2961573--2961604 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2961563 ATGAATTTCA
2961573 TATTATTACTAT
1 TATTATTACTAT
2961585 TATTATTACTAT
1 TATTATTACTAT
2961597 TATTATTA
1 TATTATTA
2961605 TTAGTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTACTAT
Found at i:2961983 original size:5 final size:5
Alignment explanation
Indices: 2961960--2962030 Score: 60
Period size: 5 Copynumber: 14.4 Consensus size: 5
2961950 TCTATTTTCC
* *
2961960 TTTAT TGTTAT TATTAT TTTA- TTTCT TTTAT TTTAT TTTAT TTTAC TTTAT
1 TTTAT T-TTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
*
2962011 GTTCA- TTTA- TTTA- TTTAT TT
1 -TTTAT TTTAT TTTAT TTTAT TT
2962031 ATATGTCCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
4 14 0.25
5 28 0.51
6 13 0.24
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:2961988 original size:9 final size:9
Alignment explanation
Indices: 2961945--2962074 Score: 60
Period size: 10 Copynumber: 14.3 Consensus size: 9
2961935 ATTTTATGAT
*
2961945 TTTTATCTA
1 TTTTATTTA
*
2961954 TTTTCCTTTA
1 TTTT-ATTTA
2961964 TTGTTA-TTA
1 TT-TTATTTA
*
2961973 TTAT-TTTA
1 TTTTATTTA
2961981 TTTCT-TTTA
1 TTT-TATTTA
2961990 TTTTATTTTA
1 TTTTA-TTTA
2962000 TTTTACTTTA
1 TTTTA-TTTA
*
2962010 TGTTCATTTA
1 T-TTTATTTA
2962020 -TTTATTTA
1 TTTTATTTA
*
2962028 TTTATATGTCCA
1 TTT-TAT-T-TA
2962040 TTTT-TTTA
1 TTTTATTTA
*
2962048 -TGT-TTTA
1 TTTTATTTA
*
2962055 GTTTATTTA
1 TTTTATTTA
2962064 -TTTATTTA
1 TTTTATTTA
2962072 TTT
1 TTT
2962075 GTTGTTGTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
7 6 0.06
8 25 0.26
9 26 0.27
10 27 0.28
11 7 0.07
12 4 0.04
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (9 bp):
TTTTATTTA
Found at i:2962024 original size:4 final size:4
Alignment explanation
Indices: 2961986--2962074 Score: 54
Period size: 4 Copynumber: 20.8 Consensus size: 4
2961976 TTTTATTTCT
* *
2961986 TTTA TTTTA TTTTA TTTTA CTTTA TGTTCA TTTA TTTA TTTA TTTA TATG
1 TTTA -TTTA -TTTA -TTTA -TTTA T-TT-A TTTA TTTA TTTA TTTA TTTA
** * *
2962036 TCCA TTTT TTTA TGT- TTTA GTTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTT
2962075 GTTGTTGTAT
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
3 2 0.03
4 38 0.56
5 26 0.38
6 2 0.03
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:2962381 original size:108 final size:107
Alignment explanation
Indices: 2962211--2962404 Score: 264
Period size: 109 Copynumber: 1.8 Consensus size: 107
2962201 AAAGAAAATT
* * *
2962211 TTTCTAAATGAGGCAATATTTAGCTTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTGGGTGT
1 TTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTGGGTGT
2962276 CGATTTTTCTCGTTCAACCAAATAGTTAAATATCTTTTCAAAAA
66 CGA--TTTCTCGTTCAACCAAATAGTTAAATATCTTTTCAAAAA
* * * * * * *
2962320 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTGCCCTAAGGTGCTGGGTTT
1 TTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTGGGTGT
*
2962384 CGATTTCTCGTTTAACCAAAT
66 CGATTTCTCGTTCAACCAAAT
2962405 TGCCAAATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
106 17 0.23
108 24 0.32
109 33 0.45
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (107 bp):
TTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTGGGTGT
CGATTTCTCGTTCAACCAAATAGTTAAATATCTTTTCAAAAA
Found at i:2969820 original size:26 final size:23
Alignment explanation
Indices: 2969784--2969838 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
2969774 TTTATATAAC
*
2969784 TAAATTTAAAATAAAAAATAAAGTAA
1 TAAAATTAAAA-AAAAAATAAA--AA
*
2969810 TAAAATTAAAAAAAAACTAAAAA
1 TAAAATTAAAAAAAAAATAAAAA
2969833 TAAAAT
1 TAAAAT
2969839 GAAATTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 8 0.30
25 9 0.33
26 10 0.37
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (23 bp):
TAAAATTAAAAAAAAAATAAAAA
Done.