Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 63 of 204
Found at i:20118693 original size:45 final size:46
Alignment explanation
Indices: 20118642--20118750 Score: 193
Period size: 46 Copynumber: 2.4 Consensus size: 46
20118632 ATCACTGTCC
*
20118642 TGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTACCACT
1 TGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCACT
*
20118687 TGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCACT
1 TGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCACT
20118733 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
20118751 CACTTATCAC
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 19 0.31
46 42 0.69
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (46 bp):
TGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCACT
Found at i:20118727 original size:46 final size:45
Alignment explanation
Indices: 20118642--20118860 Score: 191
Period size: 37 Copynumber: 5.2 Consensus size: 45
20118632 ATCACTGTCC
*
20118642 TGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTACCACT
1 TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTACCACT
*
20118687 TGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCACT
1 TGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTACCACT
****
20118733 TGATCAGATAA--GT-G-T-AG---CCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTACCACT
****
20118770 TGATCAGATAA--GT-G-T-A---ACCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTACCACT
* **
20118807 TGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCACT
1 TGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTACCACT
20118853 TGATCAGA
1 TGATCAGA
20118861 AGTACTCAAA
Statistics
Matches: 156, Mismatches: 7, Indels: 21
0.85 0.04 0.11
Matches are distributed among these distances:
37 64 0.41
39 2 0.01
40 3 0.02
41 1 0.01
42 1 0.01
43 2 0.01
44 2 0.01
45 19 0.12
46 62 0.40
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (45 bp):
TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTACCACT
Found at i:20131671 original size:20 final size:21
Alignment explanation
Indices: 20131646--20131685 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20131636 TACCTTTTGT
20131646 GGTATCACAATATCC-CCTTA
1 GGTATCACAATATCCACCTTA
* *
20131666 GGTATCGCGATATCCACCTT
1 GGTATCACAATATCCACCTT
20131686 CTAAGAAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (21 bp):
GGTATCACAATATCCACCTTA
Found at i:20132441 original size:42 final size:42
Alignment explanation
Indices: 20132364--20132444 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
20132354 CAAAAAAATC
*
20132364 AAAAATCCCAAAAATATTTTCCATCTTTGTCTTTAATTTTTA
1 AAAAATCCCAAAAATATTTTCCATCATTGTCTTTAATTTTTA
* * *
20132406 AAAAAT-CCAAAAATATTTTTCTTCATTGTTTTTTAATTT
1 AAAAATCCCAAAAATATTTTCCATCATTG-TCTTTAATTT
20132445 GTGTTATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 19 0.56
42 15 0.44
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (42 bp):
AAAAATCCCAAAAATATTTTCCATCATTGTCTTTAATTTTTA
Found at i:20141070 original size:26 final size:26
Alignment explanation
Indices: 20141035--20141094 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
20141025 ATTTCTCTTG
*
20141035 AAATTTTACCGGGGGTAAAATCATCA
1 AAATTTTACCGAGGGTAAAATCATCA
* *
20141061 AATTTTTACCGAGGGTAAAATTATCA
1 AAATTTTACCGAGGGTAAAATCATCA
20141087 AAATTTTA
1 AAATTTTA
20141095 TTGAGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (26 bp):
AAATTTTACCGAGGGTAAAATCATCA
Found at i:20149412 original size:1 final size:1
Alignment explanation
Indices: 20149406--20149457 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
20149396 CAAAGGAGTA
* * * * *
20149406 TTTTTTTTTATTTTTTTATTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20149458 GTTGAAAAGA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.04, C:0.00, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:20149429 original size:15 final size:14
Alignment explanation
Indices: 20149406--20149457 Score: 70
Period size: 15 Copynumber: 3.7 Consensus size: 14
20149396 CAAAGGAGTA
*
20149406 TTTTTTTTTATT-T
1 TTTTTTTTTTTTGT
*
20149419 TTTTATTTTTTTGT
1 TTTTTTTTTTTTGT
20149433 TTTGTTTTTTTTTGT
1 TTT-TTTTTTTTTGT
20149448 TTTTTTTTTT
1 TTTTTTTTTT
20149458 GTTGAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.29
14 11 0.32
15 13 0.38
ACGTcount: A:0.04, C:0.00, G:0.06, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTTTGT
Found at i:20149441 original size:22 final size:22
Alignment explanation
Indices: 20149406--20149460 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
20149396 CAAAGGAGTA
* *
20149406 TTTTT-TTTTATTTTTTTAT-T
1 TTTTTGTTTTGTTTTTTTTTGT
20149426 TTTTTGTTTTGTTTTTTTTTGT
1 TTTTTGTTTTGTTTTTTTTTGT
*
20149448 TTTTTTTTTTGTT
1 TTTTTGTTTTGTT
20149461 GAAAAGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 5 0.17
21 12 0.40
22 13 0.43
ACGTcount: A:0.04, C:0.00, G:0.07, T:0.89
Consensus pattern (22 bp):
TTTTTGTTTTGTTTTTTTTTGT
Found at i:20149906 original size:7 final size:6
Alignment explanation
Indices: 20149890--20149946 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
20149880 TGTTTCCTGC
* *
20149890 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
*
20149940 AATAAT A
1 AAAAAT A
20149947 GGAAAATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
5 5 0.11
6 28 0.62
7 7 0.16
8 5 0.11
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:20152324 original size:31 final size:29
Alignment explanation
Indices: 20152256--20152327 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
20152246 CTCAAGTTAT
* *
20152256 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTATGTTTCAAATGTAAC
* **
20152285 GTTTTAGTCACTTATGTTATCATGTTGTAAC
1 ATTTTAGTCACTTATGTT-TCA-AATGTAAC
20152316 ATTTTAGTCACT
1 ATTTTAGTCACT
20152328 GAGCCGTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.49
30 2 0.06
31 16 0.46
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTTCAAATGTAAC
Found at i:20154991 original size:44 final size:44
Alignment explanation
Indices: 20154933--20155021 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
20154923 ATGGCCAAAT
20154933 CTTAAATAGGTGGCACTTTGGAATAAACACAGGTTTTGTTCTTA
1 CTTAAATAGGTGGCACTTTGGAATAAACACAGGTTTTGTTCTTA
*
20154977 CTTAAATAGGTGGCACTTTGGAATGAACACAGGTTTTGTTCTTA
1 CTTAAATAGGTGGCACTTTGGAATAAACACAGGTTTTGTTCTTA
20155021 C
1 C
20155022 ATATGCATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (44 bp):
CTTAAATAGGTGGCACTTTGGAATAAACACAGGTTTTGTTCTTA
Found at i:20166143 original size:11 final size:11
Alignment explanation
Indices: 20166122--20166172 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
20166112 ATAAATCCTT
20166122 TCTCTAATTTCC
1 TCTC-AATTTCC
20166134 TCTCAATTTCC
1 TCTCAATTTCC
* *
20166145 ACTCAATTTGC
1 TCTCAATTTCC
20166156 TCTCAATTTCC
1 TCTCAATTTCC
20166167 TCTCAA
1 TCTCAA
20166173 ATCCCTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
11 31 0.89
12 4 0.11
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:20167346 original size:21 final size:22
Alignment explanation
Indices: 20167322--20167378 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
20167312 TAGTCGATTG
20167322 GTATTTA-GTATT-TAGGATTAT
1 GTATTTATGTATTAT-GGATTAT
*
20167343 GTA-TTATGTATTATGTATTAT
1 GTATTTATGTATTATGGATTAT
20167364 GTA-TTATGTATTATG
1 GTATTTATGTATTATG
20167379 TATATAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 3 0.09
21 29 0.88
22 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (22 bp):
GTATTTATGTATTATGGATTAT
Found at i:20167348 original size:7 final size:7
Alignment explanation
Indices: 20167338--20167381 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
20167328 AGTATTTAGG
20167338 ATTATGT
1 ATTATGT
20167345 ATTATGT
1 ATTATGT
20167352 ATTATGT
1 ATTATGT
20167359 ATTATGT
1 ATTATGT
20167366 ATTATGT
1 ATTATGT
20167373 ATTATGT
1 ATTATGT
20167380 AT
1 AT
20167382 ATAACTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (7 bp):
ATTATGT
Found at i:20168059 original size:18 final size:18
Alignment explanation
Indices: 20168023--20168065 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
20168013 TGCCAGGTGC
* *
20168023 GTATCCTAGTCCTTTTAT
1 GTATCCTAATCCTTATAT
*
20168041 GTATCCTAATTCTTATAT
1 GTATCCTAATCCTTATAT
*
20168059 GTTTCCT
1 GTATCCT
20168066 TTTTCTAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (18 bp):
GTATCCTAATCCTTATAT
Found at i:20168833 original size:30 final size:27
Alignment explanation
Indices: 20168770--20168834 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
20168760 TTCTTGATTT
*
20168770 ATATTATAAAAATATTATTTAATTAAA
1 ATATTATAAAAATATTATTAAATTAAA
* *
20168797 ATATTATAAATTATATTAATTAAAGTTAAG
1 ATATTATAAA-AATATT-ATTAAA-TTAAA
20168827 ATATTATA
1 ATATTATA
20168835 TTATTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 5 0.16
29 5 0.16
30 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (27 bp):
ATATTATAAAAATATTATTAAATTAAA
Found at i:20169191 original size:6 final size:6
Alignment explanation
Indices: 20169180--20169217 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
20169170 AGAAAGAAAG
*
20169180 AAAGAA AAAGAA AAAGAA AAAGAAA AAAGAG AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAG-AA AAAGAA AAAGAA A
20169218 GGGAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:20169206 original size:13 final size:13
Alignment explanation
Indices: 20169172--20169217 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
20169162 AACAGGGGAG
20169172 AAAGAAAGAAAGAA
1 AAAGAAA-AAAGAA
20169186 AAAG-AAAAAGAA
1 AAAGAAAAAAGAA
*
20169198 AAAGAAAAAAGAG
1 AAAGAAAAAAGAA
20169211 AAAGAAA
1 AAAGAAA
20169218 GGGAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 10 0.33
13 16 0.53
14 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:20169223 original size:19 final size:19
Alignment explanation
Indices: 20169169--20169224 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
20169159 AGAAACAGGG
*
20169169 GAGAAAGAAAGAAAGAAAAA
1 GAGAAAGAAAGAGA-AAAAA
* *
20169189 GAAAAAGAAAAAGAAAAAA
1 GAGAAAGAAAGAGAAAAAA
*
20169208 GAGAAAGAAAGGGAAAA
1 GAGAAAGAAAGAGAAAA
20169225 TTAGGGTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (19 bp):
GAGAAAGAAAGAGAAAAAA
Found at i:20169862 original size:3 final size:3
Alignment explanation
Indices: 20169854--20169906 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
20169844 ATTAGGTAAG
20169854 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20169902 TAT TA
1 TAT TA
20169907 AGATGAGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20170937 original size:20 final size:20
Alignment explanation
Indices: 20170912--20170951 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20170902 CGGTAAAATG
*
20170912 ATTTCTGGAAAATGTTTTAC
1 ATTTCTGGAAAATGATTTAC
*
20170932 ATTTCTGTAAAATGATTTAC
1 ATTTCTGGAAAATGATTTAC
20170952 TGGAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTTCTGGAAAATGATTTAC
Found at i:20170947 original size:34 final size:35
Alignment explanation
Indices: 20170899--20170964 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
20170889 AGTAAAATGC
*
20170899 TTTCGGTAAAATGATTT-CTGGAAAATGTTTTACA
1 TTTCGGTAAAATGATTTACTGGAAAATATTTTACA
*
20170933 TTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTCGGTAAAATGATTTACTGGAAAATATTTT
20170965 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (35 bp):
TTTCGGTAAAATGATTTACTGGAAAATATTTTACA
Found at i:20182198 original size:10 final size:11
Alignment explanation
Indices: 20182171--20182196 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20182161 TAAAAATAAA
20182171 AAAAATATTTT
1 AAAAATATTTT
20182182 AAAAATATTTT
1 AAAAATATTTT
20182193 AAAA
1 AAAA
20182197 TAAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:20182199 original size:30 final size:32
Alignment explanation
Indices: 20182146--20182210 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 32
20182136 CAGCCCATTT
*
20182146 TTTTAAAATTTATTTTAAAAATAAAAAAAATA
1 TTTTAAAATATATTTTAAAAATAAAAAAAATA
*
20182178 TTTTAAAA-ATATTTT-AAAATAAAAAATATA
1 TTTTAAAATATATTTTAAAAATAAAAAAAATA
20182208 TTT
1 TTT
20182211 ATTATATTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 17 0.55
31 6 0.19
32 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
TTTTAAAATATATTTTAAAAATAAAAAAAATA
Found at i:20183281 original size:23 final size:23
Alignment explanation
Indices: 20183251--20183297 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
20183241 AGGGCAGAGA
20183251 AACAAAGAACCAGCAAAGGGCAG
1 AACAAAGAACCAGCAAAGGGCAG
*
20183274 AACAAAGAACCAGCAGAGGGCAG
1 AACAAAGAACCAGCAAAGGGCAG
20183297 A
1 A
20183298 GATGAGGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.21, G:0.28, T:0.00
Consensus pattern (23 bp):
AACAAAGAACCAGCAAAGGGCAG
Found at i:20183586 original size:27 final size:27
Alignment explanation
Indices: 20183556--20183610 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
20183546 CTAAGACGGG
20183556 AATCCCCTAAGCCCCTATTCATTTATT
1 AATCCCCTAAGCCCCTATTCATTTATT
* *
20183583 AATCCCCTAAGCCCCTGTTTATTTATT
1 AATCCCCTAAGCCCCTATTCATTTATT
20183610 A
1 A
20183611 TATGTGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.31, G:0.05, T:0.38
Consensus pattern (27 bp):
AATCCCCTAAGCCCCTATTCATTTATT
Found at i:20186006 original size:21 final size:22
Alignment explanation
Indices: 20185980--20186034 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
20185970 AAATAAGGTG
20185980 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
20186001 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
*
20186022 GCAGTGAGATTAG
1 GCGGTGAGATTAG
20186035 AAACAGCGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:20190286 original size:6 final size:6
Alignment explanation
Indices: 20190275--20190312 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
20190265 TTTGCAACCC
*
20190275 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
20190313 GAAGAAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:20190298 original size:18 final size:18
Alignment explanation
Indices: 20190275--20190310 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20190265 TTTGCAACCC
20190275 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
20190293 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
20190311 GAGAAGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGG
Found at i:20190319 original size:18 final size:18
Alignment explanation
Indices: 20190280--20190321 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20190270 AACCCAAGGG
**
20190280 GAAGGGGAAAGGGAAGGG
1 GAAGGGGAAAGGGAAGAA
*
20190298 GAAGGGGAAAGGGGAGAA
1 GAAGGGGAAAGGGAAGAA
20190316 GAAGGG
1 GAAGGG
20190322 TAACCAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
GAAGGGGAAAGGGAAGAA
Found at i:20192068 original size:51 final size:51
Alignment explanation
Indices: 20191998--20192117 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
20191988 ATATTTCCTC
* * *
20191998 TCAA-TTCCTCTCAAATTCCTTCCAAAATTCTCTCAAATCTATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
20192048 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
* * *
20192099 TAAATTTCTTATCAATTTC
1 TCAATTTCCTCTCAATTTC
20192118 TTGTTTTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 4 0.06
51 59 0.94
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
Found at i:20193263 original size:7 final size:7
Alignment explanation
Indices: 20193253--20193277 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20193243 ATTCGATTGA
20193253 TATTTAG
1 TATTTAG
20193260 TATTTAG
1 TATTTAG
20193267 TATTTAG
1 TATTTAG
20193274 TATT
1 TATT
20193278 ATCTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:20193956 original size:18 final size:18
Alignment explanation
Indices: 20193930--20193964 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20193920 AGGTACGTTT
*
20193930 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
20193948 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
20193965 TCCTTTTCCG
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:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:20194565 original size:29 final size:29
Alignment explanation
Indices: 20194522--20194945 Score: 131
Period size: 21 Copynumber: 16.3 Consensus size: 29
20194512 CTCTAAACCC
20194522 TTAATTAAAAACCCTAACCCTAGCCTAAT
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
*
20194551 TTAATTAAAAGCCCTAA----A-CC--A-
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
*
20194572 TTAAATAAAAACCCTAACCCTAGCCTAAT
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
*
20194601 TTAATTAAAAGCCCTAA----A-CC---T
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
* *
20194622 TTAAATAAAAACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
* * *
20194651 TCAGTTAAAAACCTTAA----A-CC---T
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
* ***
20194672 TTAATTAAAAACTCTAA-CCTAATTTAAT
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
* * *
20194700 TCATTTAAAAACCCTAA----A-CC---C
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
* *
20194721 TTAATTAAAAACCATAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
20194750 TTAATTAAAAACCCTAAACCCTAACCCTAGCCTAAT
1 TTAATT---AA----AAACCCTAACCCTAGCCTAAT
*
20194786 TTAATTAAAAGCCCTAAACCCT----T-A-
1 TTAATTAAAAACCCT-AACCCTAGCCTAAT
* *
20194810 --AA-TAAAAACCCTAAACCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
20194836 TTAATTAAAAACCCTAAACCCT----T-A-
1 TTAATTAAAAACCCT-AACCCTAGCCTAAT
*
20194860 --AA-TAAAAACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
* *
20194886 TCAATTAAAAACCTTAAACCCT----T-A-
1 TTAATTAAAAACCCT-AACCCTAGCCTAAT
20194910 --AA-TAAAAACCCTAACCCTAGCCTAAT
1 TTAATTAAAAACCCTAACCCTAGCCTAAT
20194936 TTAATTAAAA
1 TTAATTAAAA
20194946 GCTCTGAACC
Statistics
Matches: 292, Mismatches: 35, Indels: 136
0.63 0.08 0.29
Matches are distributed among these distances:
20 17 0.06
21 87 0.30
22 7 0.02
24 10 0.03
25 13 0.04
26 9 0.03
28 22 0.08
29 81 0.28
30 17 0.06
32 2 0.01
33 2 0.01
36 25 0.09
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (29 bp):
TTAATTAAAAACCCTAACCCTAGCCTAAT
Found at i:20194568 original size:50 final size:50
Alignment explanation
Indices: 20194476--20195001 Score: 591
Period size: 50 Copynumber: 10.9 Consensus size: 50
20194466 TATGACATTT
* * * *
20194476 AATAAAAACCCT-AGCCTAACCTAATTCATTTAAAAACTCTAAACCCTTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
* * * *
20194525 ATTAAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCATTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
* * *
20194575 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCTTTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
* * * *
20194625 AATAAAAACCCTAACCCTAACCTAATTCAGTTAAAAACCTTAAACCTTTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
* * ** * *
20194675 ATTAAAAACTCTAA-CCTAATTTAATTCATTTAAAAACCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
* *
20194724 ATTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCTAAACCC---
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
* ** *
20194771 --T---AACCCT-AGCCTAATTTAA-TT----AAAAGCCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
*
20194810 AATAAAAACCCTAAACCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
* *
20194860 AATAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCTTAAACCCTTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
* * * *
20194910 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCTCTGAACCCTTA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
** * *
20194960 AATAAAAACCCTAA-CCTAATTTAATTCATTTAAAAACCCTAA
1 AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA
20195002 CCTTAACGTA
Statistics
Matches: 407, Mismatches: 54, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
36 14 0.03
40 2 0.00
41 10 0.02
42 5 0.01
44 6 0.01
45 10 0.02
46 2 0.00
49 73 0.18
50 285 0.70
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (50 bp):
AATAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
Found at i:20194781 original size:235 final size:235
Alignment explanation
Indices: 20194530--20195001 Score: 721
Period size: 235 Copynumber: 2.0 Consensus size: 235
20194520 CCTTAATTAA
* *
20194530 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCATTAAATAAAAACCCTAACCCTAG
1 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCATTAAATAAAAACCCTAAACCTAA
* * *
20194595 CCTAATTTAATTAAAAGCCCTAAACCTTTAAATAAAAACCCTAACCCTAACCTAATTCAGTTAAA
66 CCTAATTTAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
* * * ** *
20194660 AACCTTAAACCTTTAATTAAAAACTCTAA-CCTAATTTAATTCATTTAAAAACCCTAAACCCTTA
131 AACCTTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCCTAAACCCTTA
* *
20194724 ATTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCT
196 AATAAAAACCATAA-CCTAACCTAATTCAATTAAAAACCCT
*
20194765 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAAACCTAA
1 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCATTAAATAAAAACCCTAAACCTAA
20194830 CCTAATTTAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
66 CCTAATTTAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
* * * * *
20194895 AACCTTAAACCCTTAAATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCTCTGAACCCTTA
131 AACCTTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCCTAAACCCTTA
* ** *
20194960 AATAAAAACCCTAACCTAATTTAATTCATTTAAAAACCCT
196 AATAAAAACCATAACCTAACCTAATTCAATTAAAAACCCT
20195000 AA
1 AA
20195002 CCTTAACGTA
Statistics
Matches: 213, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
235 174 0.82
236 39 0.18
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (235 bp):
AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCATTAAATAAAAACCCTAAACCTAA
CCTAATTTAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
AACCTTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCCTAAACCCTTA
AATAAAAACCATAACCTAACCTAATTCAATTAAAAACCCT
Found at i:20194790 original size:185 final size:186
Alignment explanation
Indices: 20194580--20194945 Score: 590
Period size: 185 Copynumber: 2.0 Consensus size: 186
20194570 CATTAAATAA
* *
20194580 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCTTTAAATAAAAACCCTAACCCTAA
1 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAAACCTAA
* * * * * ** *
20194645 CCTAATTCAGTTAAAAACCTTAAACCTTTAATTAAAAACTCTAA-CCTAATTTAATTCATTTAAA
66 CCTAATTCAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
*
20194709 AACCCTAAACCCTTAATTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCT
131 AACCCTAAACCCTTAAATAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCT
20194765 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAAACCTAA
1 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAAACCTAA
*
20194830 CCTAATTTAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
66 CCTAATTCAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
* * *
20194895 AACCTTAAACCCTTAAATAAAAACCCTAACCCTAGCCTAATTTAATTAAAA
131 AACCCTAAACCCTTAAATAAAAACCATAACCCTAACCTAATTTAATTAAAA
20194946 GCTCTGAACC
Statistics
Matches: 165, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
185 101 0.61
186 64 0.39
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (186 bp):
AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAAACCTAA
CCTAATTCAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
AACCCTAAACCCTTAAATAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCT
Found at i:20194806 original size:36 final size:36
Alignment explanation
Indices: 20194729--20194807 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
20194719 CCTTAATTAA
*
20194729 AAACCATAACCCTAACCTAATTTAATTAAAAACCCT
1 AAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
* *
20194765 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCT
1 AAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
20194801 AAACCCT
1 AAACCCT
20194808 TAAATAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.43, C:0.30, G:0.03, T:0.24
Consensus pattern (36 bp):
AAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
Found at i:20194868 original size:136 final size:139
Alignment explanation
Indices: 20194629--20195001 Score: 466
Period size: 136 Copynumber: 2.6 Consensus size: 139
20194619 CCTTTAAATA
* * * * * * * *
20194629 AAAACCCTAACCCTAACCTAATTCAGTTAAAAACCTTAAACCTTTAATTAAAAACTCTAACCTAA
1 AAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAACCTAA
* *
20194694 TTTAATTCATTTAAAAACCCTAAACCCTTAATTAAAAACCATAACCCTAACCTAATTTAATT-AA
66 TTTAATTCATTTAAAAACCCTAAACCCTTAAATAAAAACCATAACCCTAACCTAATTCAATTAAA
20194758 -AAACCC-T
131 CAAACCCAT
20194765 -AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAAACCTA
1 AAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCT-AACCTA
** * * *
20194829 ACCTAATTTAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAA
65 ATTTAATTCATTTAAAAACCCTAAACCCTTAAATAAAAACCATAACCCTAACCTAATTCAATT--
20194894 AAACCTTAAACCCTTAAAT
128 AAA-C--AAACCC----AT
* *
20194913 AAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCTCTGAACCCTTAAATAAAAACCCTAACCTA
1 -AAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAACCTA
20194978 ATTTAATTCATTTAAAAACCCTAA
65 ATTTAATTCATTTAAAAACCCTAA
20195002 CCTTAACGTA
Statistics
Matches: 201, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
135 49 0.24
136 62 0.31
139 2 0.01
143 6 0.03
148 1 0.00
149 26 0.13
150 55 0.27
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.27
Consensus pattern (139 bp):
AAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAACCTAA
TTTAATTCATTTAAAAACCCTAAACCCTTAAATAAAAACCATAACCCTAACCTAATTCAATTAAA
CAAACCCAT
Found at i:20194994 original size:285 final size:284
Alignment explanation
Indices: 20194481--20195001 Score: 801
Period size: 285 Copynumber: 1.8 Consensus size: 284
20194471 CATTTAATAA
* * * * * *
20194481 AAACCCTAGCCTAACCTAATTCATTTAAAAACTCTAAACCCTTAATTAAAAACCCTAACCCTAGC
1 AAACCCTACCCTAACCTAATTCAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAAACCTAAC
* * *
20194546 CTAATTTAATTAAAAGCCCTAAACCATTAAATAAAAACCCTAACCCTAGCCTAATTTAATTAAAA
66 CTAATTTAATTAAAAACCCTAAACCATTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAAA
* * * *
20194611 GCCCTAAACCTTTAAATAAAAACCCTAACCCTAACCTAATTCAGTTAAAAACCTTAAACCTTTAA
131 ACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCTTAAACCCTTAA
* *
20194676 TTAAAAACTCTAACCTAATTTAATTCATTTAAAAACCCTAAACCCTTAATTAAAAACCATAACCC
196 ATAAAAACCCTAACCTAATTTAATTCATTTAAAAACCCTAAACCCTTAATTAAAAACCATAACCC
20194741 TAACCTAATTTAATTAAAAACCCT
261 TAACCTAATTTAATTAAAAACCCT
* * *
20194765 AAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAAACCTAA
1 AAACCCT-ACCCTAACCTAATTCAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAAACCTAA
*
20194830 CCTAATTTAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
65 CCTAATTTAATTAAAAACCCTAAACCATTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAA
* * * * *
20194895 AACCTTAAACCCTTAAATAAAAACCCTAACCCTAGCCTAATTTAATT-AAAAGCTCTGAACCCTT
130 AACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCT-TAAACCCTT
20194959 AAATAAAAACCCTAACCTAATTTAATTCATTTAAAAACCCTAA
194 AAATAAAAACCCTAACCTAATTTAATTCATTTAAAAACCCTAA
20195002 CCTTAACGTA
Statistics
Matches: 211, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
284 13 0.06
285 198 0.94
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.26
Consensus pattern (284 bp):
AAACCCTACCCTAACCTAATTCAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAAACCTAAC
CTAATTTAATTAAAAACCCTAAACCATTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAAA
ACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCTTAAACCCTTAA
ATAAAAACCCTAACCTAATTTAATTCATTTAAAAACCCTAAACCCTTAATTAAAAACCATAACCC
TAACCTAATTTAATTAAAAACCCT
Found at i:20195156 original size:116 final size:116
Alignment explanation
Indices: 20195010--20195227 Score: 418
Period size: 116 Copynumber: 1.9 Consensus size: 116
20195000 AACCTTAACG
*
20195010 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
20195075 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
*
20195126 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
20195191 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
20195228 CAATTTATCA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 100 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
Found at i:20195244 original size:17 final size:18
Alignment explanation
Indices: 20195203--20195244 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
20195193 TTTACTAACC
* *
20195203 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
20195221 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
20195238 ATTAATA
1 ATTAATA
20195245 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:20196360 original size:126 final size:123
Alignment explanation
Indices: 20196061--20196411 Score: 463
Period size: 126 Copynumber: 2.8 Consensus size: 123
20196051 CCCAAACATG
* * * * *
20196061 CTACTATAGCAAAATCGCGTCCACGATGGAGCGATTTCACAAATTCTTCCCAAATAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGAT-GAGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
20196126 TATAAGCGATTTTATATTATTTGCTCAGAAATGTC-AAAAAAAATATTTCTTACATGAC
65 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTACATGAC
* * *
20196184 CTACTGTAGCAAAAGCGCG-CTGACGATGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAAGCGCGTC-CACGATG-AGCAATTTCACAAATTCTTCTCAAATAGCATCCTG
* * * *
20196248 CTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAATAATTATTTCTTTCGTGAC
64 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-AA-TATTTCTTACATGAC
* *
20196310 CTACTGTAGCAAAAGCACGTCCACGAGTGAGCAATTTCACAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGA-TGAGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
* **
20196375 TAGAAGTGATTTTATATTATTTTATCAGAAACGTCAA
65 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAA
20196412 CTCGAAATTA
Statistics
Matches: 197, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
122 2 0.01
123 84 0.43
124 6 0.03
125 2 0.01
126 100 0.51
127 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGTCCACGATGAGCAATTTCACAAATTCTTCTCAAATAGCATCCTGCT
AGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTACATGAC
Found at i:20196745 original size:39 final size:38
Alignment explanation
Indices: 20196696--20196769 Score: 130
Period size: 39 Copynumber: 1.9 Consensus size: 38
20196686 AAACATTATC
20196696 ATAAATATAATAAATATTTTATTATATTAAAATATACAA
1 ATAAATATAATAAATATTTTATTATATT-AAATATACAA
*
20196735 ATAAATATAATAAATATTTTATTGTATTAAATATA
1 ATAAATATAATAAATATTTTATTATATTAAATATA
20196770 ATTTTTTAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 7 0.21
39 27 0.79
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (38 bp):
ATAAATATAATAAATATTTTATTATATTAAATATACAA
Found at i:20196891 original size:51 final size:51
Alignment explanation
Indices: 20196835--20196941 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
20196825 TAGGTTTTGG
* *
20196835 ATAATGGGTTTAATTATTATTGGGTTAGTGATTTAATATAAATATAAATGT
1 ATAATGGGTTTAATTATTATTGAGTTAGTGATTTAATATAAATATAAATAT
20196886 ATAATGGGTTTAATTATTATTGAGTTAGTGATTTAATATAAATATAAATAT
1 ATAATGGGTTTAATTATTATTGAGTTAGTGATTTAATATAAATATAAATAT
20196937 ATAAT
1 ATAAT
20196942 TATTATTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (51 bp):
ATAATGGGTTTAATTATTATTGAGTTAGTGATTTAATATAAATATAAATAT
Found at i:20201522 original size:18 final size:19
Alignment explanation
Indices: 20201499--20201627 Score: 90
Period size: 18 Copynumber: 6.8 Consensus size: 19
20201489 TTAAGAATTT
20201499 TTTATTAAATTATATA-TA
1 TTTATTAAATTATATATTA
20201517 TTTATTAAATTATATATTA
1 TTTATTAAATTATATATTA
20201536 TTT-TTATAGTATTATATATTA
1 TTTATTA-A--ATTATATATTA
* *
20201557 TAATTTTTTAATTA-ATA-TA
1 T--TTATTAAATTATATATTA
* * * * *
20201576 ATAATTATATTA-AGAAT-
1 TTTATTAAATTATATATTA
*
20201593 TTTATTAAACTATATATTA
1 TTTATTAAATTATATATTA
20201612 TTTTATTAAATTATAT
1 -TTTATTAAATTATAT
20201628 TTAATAATAA
Statistics
Matches: 86, Mismatches: 14, Indels: 20
0.72 0.12 0.17
Matches are distributed among these distances:
17 17 0.20
18 23 0.27
19 8 0.09
20 17 0.20
21 16 0.19
23 3 0.03
24 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTATTAAATTATATATTA
Found at i:20201570 original size:21 final size:20
Alignment explanation
Indices: 20201494--20201581 Score: 58
Period size: 21 Copynumber: 4.2 Consensus size: 20
20201484 TATATTTAAG
20201494 AATTTTTT-ATTAA-ATTAT
1 AATTTTTTAATTAATATTAT
20201512 ATATATTTATTAAATTATATATTAT
1 A-AT-TTT-TT-AATTA-ATATTAT
*
20201537 --TTTTATAGTATTATATATTAT
1 AATTTTTTA--ATTA-ATATTAT
*
20201558 AATTTTTTAATTAATATAAT
1 AATTTTTTAATTAATATTAT
20201578 AATT
1 AATT
20201582 ATATTAAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
18 1 0.02
19 3 0.05
20 14 0.25
21 21 0.38
22 1 0.02
23 10 0.18
24 1 0.02
25 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
AATTTTTTAATTAATATTAT
Found at i:20201633 original size:55 final size:54
Alignment explanation
Indices: 20201548--20201693 Score: 134
Period size: 58 Copynumber: 2.6 Consensus size: 54
20201538 TTTATAGTAT
* * * *
20201548 TATATATTATAATTT-TTTAATTA-ATATAATAATTATATTAAGAATTTTATTAAAC
1 TATATATTAT--TTTATTAAATTATATTTAATAATTATATTAA-AATATGATTAAAC
* * *
20201603 TATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGGTTAAAT
1 TATATATTATTTTATTAAATTATA-TT--TAATAATTATATTAAAATATGATTAAAC
* *
20201660 TATTTATTATTTTTATTAAATTATTTTTAATAAT
1 TATATATTA-TTTTATTAAATTATATTTAATAAT
20201694 AATTTTATTA
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
53 3 0.04
54 7 0.09
55 18 0.24
56 1 0.01
57 19 0.25
58 28 0.37
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (54 bp):
TATATATTATTTTATTAAATTATATTTAATAATTATATTAAAATATGATTAAAC
Found at i:20201674 original size:58 final size:57
Alignment explanation
Indices: 20201573--20201707 Score: 180
Period size: 58 Copynumber: 2.3 Consensus size: 57
20201563 TTTAATTAAT
* *
20201573 ATAATAATTATATTAAGAATTTTATTAAACTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AATATGATTAAACTATATATTATTTTATTAAATTATATTTA
* * * * *
20201631 ATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAAATATGATTAAACTATATATTA-TTTTATTAAATTATATTTA
*
20201689 ATAATAATTTTATTAAAAT
1 ATAATAATTATATTAAAAT
20201708 TTAATAACAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
57 17 0.25
58 50 0.75
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGATTAAACTATATATTATTTTATTAAATTATATTTA
Found at i:20201684 original size:14 final size:14
Alignment explanation
Indices: 20201665--20201705 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
20201655 TAAATTATTT
20201665 ATTATTTTTATTAA
1 ATTATTTTTATTAA
*
20201679 ATTATTTTTAAT-A
1 ATTATTTTTATTAA
*
20201692 A-TAATTTTATTAA
1 ATTATTTTTATTAA
20201705 A
1 A
20201706 ATTTAATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTTTTATTAA
Found at i:20201895 original size:16 final size:15
Alignment explanation
Indices: 20201874--20201928 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
20201864 TGAATTACTG
20201874 ATTACAGCTCTATTCA
1 ATTACAGC-CTATTCA
*
20201890 ATTACAACCCTATTCA
1 ATTAC-AGCCTATTCA
*
20201906 ATTACAGCCTTATTCC
1 ATTACAGCC-TATTCA
20201922 ATTACAG
1 ATTACAG
20201929 TGAACCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.09
16 29 0.85
17 2 0.06
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (15 bp):
ATTACAGCCTATTCA
Found at i:20203192 original size:3 final size:3
Alignment explanation
Indices: 20203184--20203264 Score: 153
Period size: 3 Copynumber: 27.0 Consensus size: 3
20203174 TATCTAGTAT
20203184 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
20203232 GAT GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
20203265 ACCTGAGAAC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:20204297 original size:27 final size:24
Alignment explanation
Indices: 20204267--20204337 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 24
20204257 TAATAAATTT
*
20204267 AAAAATATAAAAAAAAATATTTTTA
1 AAAAATATAAAAATAAATA-TTTTA
*
20204292 ACAAAA-ATAATAATATATAAAATTTTA
1 A-AAAATATAA-AA-ATA-AATATTTTA
20204319 AAAAATATAAAAATAAATA
1 AAAAATATAAAAATAAATA
20204338 ATATTTAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
24 3 0.08
25 8 0.21
26 12 0.32
27 12 0.32
28 3 0.08
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAAATATAAAAATAAATATTTTA
Found at i:20204579 original size:30 final size:29
Alignment explanation
Indices: 20204533--20204601 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
20204523 ATATTTTAAA
20204533 AATATATAATAATAAATTTAAAAT-TTATATT
1 AATAT-TAATAATAAA--TAAAATATTATATT
*
20204564 AATATTAATATTAAATAAAATAATTATATT
1 AATATTAATAATAAATAAAAT-ATTATATT
20204594 AATATTAA
1 AATATTAA
20204602 AAAAACTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 6 0.17
30 24 0.69
31 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AATATTAATAATAAATAAAATATTATATT
Found at i:20204789 original size:29 final size:28
Alignment explanation
Indices: 20204742--20204891 Score: 81
Period size: 29 Copynumber: 5.5 Consensus size: 28
20204732 TAAAATTTAA
*
20204742 ATTTATTATTATACTTTTTGAAAATATTT
1 ATTTATTTTTATA-TTTTTGAAAATATTT
* *
20204771 ATTTATTTTTATATATTTT-TAAAT-TTC
1 ATTTATTTTTATAT-TTTTGAAAATATTT
* *
20204798 ATATATTATTAT-TTGTTGTGAACAATA-TT
1 ATTTATTTTTATATT-TT-TGAA-AATATTT
*
20204827 -TTTATTTTTATATAATTTT--TAA-ATTT
1 ATTTATTTTTATAT--TTTTGAAAATATTT
20204853 A-TTA---TTATATTTTTAGAAAATATTT
1 ATTTATTTTTATATTTTT-GAAAATATTT
*
20204878 ATCTATTTTTATAT
1 ATTTATTTTTATAT
20204892 GTATTTTTTG
Statistics
Matches: 90, Mismatches: 12, Indels: 38
0.64 0.09 0.27
Matches are distributed among these distances:
21 4 0.04
23 6 0.07
24 2 0.02
25 7 0.08
26 12 0.13
27 13 0.14
28 15 0.17
29 28 0.31
30 2 0.02
31 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
ATTTATTTTTATATTTTTGAAAATATTT
Found at i:20204847 original size:56 final size:49
Alignment explanation
Indices: 20204737--20204891 Score: 193
Period size: 56 Copynumber: 2.9 Consensus size: 49
20204727 TAATATAAAA
*
20204737 TTTAAATTTATTATTATACTTTTTGAAAATATTTATTTATTTTTATATATT
1 TTTAAATTTATTATTATATTTTTTGAAAATA-TT-TTTATTTTTATATATT
20204788 TTTAAATTTCATATATTATTATTTGTTGTGAACAATATTTTTATTTTTATATAATT
1 TTTAAATTT-AT-TATTA-TATTT-TT-TGAA-AATATTTTTATTTTTATAT-ATT
*
20204844 TTTAAATTTATTATTATATTTTTAGAAAATATTTATCTATTTTTATAT
1 TTTAAATTTATTATTATATTTTTTGAAAATATTT-T-TATTTTTATAT
20204892 GTATTTTTTG
Statistics
Matches: 93, Mismatches: 2, Indels: 17
0.83 0.02 0.15
Matches are distributed among these distances:
50 7 0.08
51 13 0.14
52 15 0.16
53 10 0.11
54 9 0.10
55 17 0.18
56 18 0.19
57 4 0.04
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (49 bp):
TTTAAATTTATTATTATATTTTTTGAAAATATTTTTATTTTTATATATT
Found at i:20206078 original size:53 final size:54
Alignment explanation
Indices: 20206011--20206116 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 54
20206001 TATTTTTCAA
*
20206011 TTTGTAAGACACAATGTTGTCGGTATTGAACAAAATTGTTTAA-TTATTTTTTG
1 TTTGTAAGACACAATATTGTCGGTATTGAACAAAATTGTTTAACTTATTTTTTG
* * * * *
20206064 TTTGTAATATACAATATTTTCGGTTTTGAACAAAATTGTTTAACTTTTTTTTT
1 TTTGTAAGACACAATATTGTCGGTATTGAACAAAATTGTTTAACTTATTTTTT
20206117 TTAGTATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 38 0.83
54 8 0.17
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (54 bp):
TTTGTAAGACACAATATTGTCGGTATTGAACAAAATTGTTTAACTTATTTTTTG
Found at i:20207946 original size:22 final size:22
Alignment explanation
Indices: 20207921--20207962 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20207911 TTAATATAAT
* * *
20207921 AAAATTTATATTTTAATTTCTA
1 AAAAGTTATAATTAAATTTCTA
20207943 AAAAGTTATAATTAAATTTC
1 AAAAGTTATAATTAAATTTC
20207963 GCAACAAGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAAGTTATAATTAAATTTCTA
Found at i:20217177 original size:21 final size:19
Alignment explanation
Indices: 20217153--20217191 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
20217143 TAGACTATCG
*
20217153 AGAAAATATAAGTTACAACAA
1 AGAAAACAT-AGTTA-AACAA
20217174 AGAAAACATAGTTAAACA
1 AGAAAACATAGTTAAACA
20217192 GAGATTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (19 bp):
AGAAAACATAGTTAAACAA
Found at i:20225535 original size:23 final size:23
Alignment explanation
Indices: 20225509--20225552 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20225499 TCTATGTAAA
*
20225509 CCAACGAATATTTAACATGTGGT
1 CCAACAAATATTTAACATGTGGT
* *
20225532 CCAATAAATATTTAAGATGTG
1 CCAACAAATATTTAACATGTG
20225553 ATGCCATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (23 bp):
CCAACAAATATTTAACATGTGGT
Found at i:20226058 original size:19 final size:17
Alignment explanation
Indices: 20226031--20226084 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
20226021 ATTGATTTTG
20226031 ATTTTTATAATTTTTAAT
1 ATTTTTAT-ATTTTTAAT
20226049 ATTTTATATATATTTTAAT
1 ATTTT-TATAT-TTTTAAT
*
20226068 -TTTTTAGATTTTTAAT
1 ATTTTTATATTTTTAAT
20226084 A
1 A
20226085 AATTTTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 7 0.22
17 4 0.12
18 11 0.34
19 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTATATTTTTAAT
Found at i:20226089 original size:26 final size:27
Alignment explanation
Indices: 20226041--20226091 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
20226031 ATTTTTATAA
*
20226041 TTTTTAATATTTTATATATATTTTAAT
1 TTTTTAATATTTTATATAAATTTTAAT
20226068 TTTTTAGAT-TTTTA-ATAAATTTTA
1 TTTTTA-ATATTTTATATAAATTTTA
20226092 GATAGTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 11 0.50
28 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTTAATATTTTATATAAATTTTAAT
Found at i:20235595 original size:21 final size:22
Alignment explanation
Indices: 20235569--20235623 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
20235559 ACAGCGGTGG
*
20235569 AGGTGAGATTAGTTACTGTA-A
1 AGGTGAGATTAGATACTGTAGA
* *
20235590 AGGTGAGATTGGATACTGTAGT
1 AGGTGAGATTAGATACTGTAGA
20235612 A-GTGAGATTAGA
1 AGGTGAGATTAGA
20235624 AACAATGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.31
Consensus pattern (22 bp):
AGGTGAGATTAGATACTGTAGA
Found at i:20240632 original size:16 final size:17
Alignment explanation
Indices: 20240606--20240642 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
20240596 GTTTTTTCCG
20240606 GGAGAAGTGGGAAAGAA
1 GGAGAAGTGGGAAAGAA
*
20240623 GGAG-AGTGGGAAAGCA
1 GGAGAAGTGGGAAAGAA
20240639 GGAG
1 GGAG
20240643 TTGAAGAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.41, C:0.03, G:0.51, T:0.05
Consensus pattern (17 bp):
GGAGAAGTGGGAAAGAA
Found at i:20246491 original size:13 final size:13
Alignment explanation
Indices: 20246470--20246518 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
20246460 CAAACAAGGG
20246470 ACATAAGAAATTA
1 ACATAAGAAATTA
*
20246483 ACATCAG-AATATA
1 ACATAAGAAAT-TA
*
20246496 AAATAAGAAATTA
1 ACATAAGAAATTA
20246509 ACATAA-AAAT
1 ACATAAGAAAT
20246519 AAAAACAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 7 0.23
13 20 0.67
14 3 0.10
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.22
Consensus pattern (13 bp):
ACATAAGAAATTA
Found at i:20246519 original size:26 final size:25
Alignment explanation
Indices: 20246472--20246523 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
20246462 AACAAGGGAC
* *
20246472 ATAAGAAATTAACATCAGAATATAAA
1 ATAAGAAATTAACATAAAAATA-AAA
20246498 ATAAGAAATTAACATAAAAATAAAA
1 ATAAGAAATTAACATAAAAATAAAA
20246523 A
1 A
20246524 CAAATCACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (25 bp):
ATAAGAAATTAACATAAAAATAAAA
Found at i:20253604 original size:24 final size:26
Alignment explanation
Indices: 20253516--20253604 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 26
20253506 TTACCGGTTT
* * **
20253516 CAGCTCTTATGAGCTTATCGATACT-
1 CAGCTCGTATGAGCTTATCCATTTTA
* * *
20253541 CAACTCGTATGAGCTTATCGATTTTT
1 CAGCTCGTATGAGCTTATCCATTTTA
* *
20253567 CAGCTCGGAGGAGCTTA-CCA-TTTA
1 CAGCTCGTATGAGCTTATCCATTTTA
20253591 CAGCTCGTATGAGC
1 CAGCTCGTATGAGC
20253605 ATACATGTAC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
24 15 0.29
25 23 0.44
26 14 0.27
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (26 bp):
CAGCTCGTATGAGCTTATCCATTTTA
Found at i:20272170 original size:2 final size:2
Alignment explanation
Indices: 20272163--20272207 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
20272153 ATTCATCTAC
20272163 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
20272205 TA T
1 TA T
20272208 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20272540 original size:2 final size:2
Alignment explanation
Indices: 20272533--20272577 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
20272523 AGACTACTAC
20272533 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
20272575 TA T
1 TA T
20272578 TCATTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20274321 original size:3 final size:3
Alignment explanation
Indices: 20274313--20274346 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
20274303 ACCTACTTCT
20274313 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20274347 CATTTTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20276074 original size:46 final size:45
Alignment explanation
Indices: 20275968--20276091 Score: 198
Period size: 46 Copynumber: 2.8 Consensus size: 45
20275958 CATATGACCT
* *
20275968 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
20276011 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
20276057 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
20276092 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 3 0.04
45 21 0.28
46 42 0.57
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (45 bp):
CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:20276095 original size:37 final size:37
Alignment explanation
Indices: 20276053--20276228 Score: 264
Period size: 37 Copynumber: 4.8 Consensus size: 37
20276043 AGCTGAAGCT
* **
20276053 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
20276090 GCCACTTATCACTTTATTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
20276127 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
20276164 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTAT-
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* **
20276200 AGCACTTATCACTTTGTCACTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
20276229 AGTACTCAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 26 0.20
37 104 0.80
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:20283539 original size:33 final size:33
Alignment explanation
Indices: 20283502--20283570 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
20283492 CATATTATGA
20283502 GATATATGAATTTTTGTGAGACAATGTTAGATT
1 GATATATGAATTTTTGTGAGACAATGTTAGATT
20283535 GATATATGAATTTTTGTGAGACAATGTTAGATT
1 GATATATGAATTTTTGTGAGACAATGTTAGATT
20283568 GAT
1 GAT
20283571 TTCGGGTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (33 bp):
GATATATGAATTTTTGTGAGACAATGTTAGATT
Found at i:20285576 original size:23 final size:23
Alignment explanation
Indices: 20285549--20285593 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
20285539 GGCTTTGCCG
20285549 ATCAGGCACTTTATGTGTCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
20285572 ATCAGGCACTTTATGTGTCGTA
1 ATCAGGCACTTTATGTGTCGTA
20285594 TCAGACACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAC
Found at i:20291436 original size:98 final size:98
Alignment explanation
Indices: 20291267--20291461 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
20291257 ACACAATAAA
*
20291267 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
20291332 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
* *
20291365 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
20291430 CCTTTAGAATCTCAAACTCGAAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGAAATATTTCCTT
20291462 CATGATTTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
Found at i:20292415 original size:19 final size:19
Alignment explanation
Indices: 20292390--20292538 Score: 199
Period size: 19 Copynumber: 7.8 Consensus size: 19
20292380 AAAGGGTATC
*
20292390 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
* ** *
20292409 TCAAAGATTATACATCATA
1 TCTAAGATTGCATATCATA
20292428 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* ** *
20292447 TCAAAGATTATACATCATA
1 TCTAAGATTGCATATCATA
20292466 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
20292485 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
20292504 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
20292523 TATAAGATTGCATATC
1 TCTAAGATTGCATATC
20292539 CTCAAAAATT
Statistics
Matches: 112, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 112 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:20293724 original size:23 final size:23
Alignment explanation
Indices: 20293696--20293740 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
20293686 CCTTCTGGCA
20293696 TAGTACTTCT-ATACTTCTGTTAT
1 TAGTACTT-TGATACTTCTGTTAT
*
20293719 TAGTACTTTGGTACTTCTGTTA
1 TAGTACTTTGATACTTCTGTTA
20293741 CTAGCACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (23 bp):
TAGTACTTTGATACTTCTGTTAT
Found at i:20293752 original size:23 final size:23
Alignment explanation
Indices: 20293707--20293753 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20293697 AGTACTTCTA
* * *
20293707 TACTTCTGTTATTAGTACTTTGG
1 TACTTCTGTTACTAGCACATTGG
20293730 TACTTCTGTTACTAGCACATTGG
1 TACTTCTGTTACTAGCACATTGG
20293753 T
1 T
20293754 GCTTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (23 bp):
TACTTCTGTTACTAGCACATTGG
Found at i:20299272 original size:38 final size:38
Alignment explanation
Indices: 20299221--20299296 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
20299211 AGCTAGTGAT
20299221 TGACTACCATCCGGGAAAGGCCAATGTTGTTGCTAATG
1 TGACTACCATCCGGGAAAGGCCAATGTTGTTGCTAATG
*
20299259 TGACTACCATCCGGGAAAGGCCAATGTTGTTGGTAATG
1 TGACTACCATCCGGGAAAGGCCAATGTTGTTGCTAATG
20299297 CTTTAAGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (38 bp):
TGACTACCATCCGGGAAAGGCCAATGTTGTTGCTAATG
Found at i:20303760 original size:43 final size:43
Alignment explanation
Indices: 20303647--20303760 Score: 183
Period size: 43 Copynumber: 2.7 Consensus size: 43
20303637 GATGTGATTT
* * *
20303647 CGTGTAAGACCATATCTGGGACATTGGAATCGAAGTGAGATAA
1 CGTGTAAGACCATGTCTGGAACATTGGCATCGAAGTGAGATAA
* *
20303690 CGTGTAAGACCATGTTTGGTACATTGGCATCGAAGTGAGATAA
1 CGTGTAAGACCATGTCTGGAACATTGGCATCGAAGTGAGATAA
20303733 CGTGTAAGACCATGTCTGGAACATTGGC
1 CGTGTAAGACCATGTCTGGAACATTGGC
20303761 TTCGTATATG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGAACATTGGCATCGAAGTGAGATAA
Found at i:20307982 original size:34 final size:35
Alignment explanation
Indices: 20307944--20308017 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
20307934 ATCATTTATT
* *
20307944 TATACTTATCAAT-TACATGTGCCGAATGC-ACATA
1 TATACTTAT-AATCCACATATGCCGAATGCAACATA
20307978 TATACTTATAATCCACATATGCCGAATGCATACATA
1 TATACTTATAATCCACATATGCCGAATGCA-ACATA
20308014 TATA
1 TATA
20308018 TATCCAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 3 0.09
34 23 0.66
36 9 0.26
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (35 bp):
TATACTTATAATCCACATATGCCGAATGCAACATA
Found at i:20308262 original size:41 final size:41
Alignment explanation
Indices: 20308184--20308383 Score: 206
Period size: 41 Copynumber: 4.8 Consensus size: 41
20308174 TTAATTTAAA
* * * *
20308184 CAGATTCACCGGCACTTAGCCTGTTAGGATTAAAGCCTGATT
1 CAGA-TCATCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
20308226 TAGATCATCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCATCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
20308267 CAGATCA-CTGGCACTTAGCCTGCTAGGCTTATAACCTGGTT
1 CAGATCATC-GGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * * * *
20308308 TAGATCACCGGCACTTAGCCTGCTAGGTTTTAAAACCTGATT
1 CAGATCATCGGCACTTAGCCTGCTAGG-CTTATAGCCTGATT
** * *
20308350 CAG-TACATCGGCTTTTAGCTTGCTAGACTTATAG
1 CAGAT-CATCGGCACTTAGCCTGCTAGGCTTATAG
20308384 TCCGAAATGT
Statistics
Matches: 133, Mismatches: 21, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
40 1 0.01
41 98 0.74
42 34 0.26
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (41 bp):
CAGATCATCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:20308331 original size:82 final size:84
Alignment explanation
Indices: 20308184--20308352 Score: 236
Period size: 82 Copynumber: 2.0 Consensus size: 84
20308174 TTAATTTAAA
* *
20308184 CAGATTCACCGGCACTTAGCCTGTTAGGATTAAAGCCTGATTTAGATCATCGGCACTTAGCCTGC
1 CAGATTCACCGGCACTTAGCCTGCTAGGATTAAAGCCTGATTTAGATCACCGGCACTTAGCCTGC
* *
20308249 TAGG-CTTATAGCCTGATT
66 TAGGTCTTAAAACCTGATT
* * *
20308267 CAGA-TCACTGGCACTTAGCCTGCTAGGCTTATAA-CCTGGTTTAGATCACCGGCACTTAGCCTG
1 CAGATTCACCGGCACTTAGCCTGCTAGGATTA-AAGCCTGATTTAGATCACCGGCACTTAGCCTG
*
20308330 CTAGGTTTTAAAACCTGATT
65 CTAGGTCTTAAAACCTGATT
20308350 CAG
1 CAG
20308353 TACATCGGCT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
82 56 0.74
83 20 0.26
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (84 bp):
CAGATTCACCGGCACTTAGCCTGCTAGGATTAAAGCCTGATTTAGATCACCGGCACTTAGCCTGC
TAGGTCTTAAAACCTGATT
Found at i:20308856 original size:78 final size:78
Alignment explanation
Indices: 20308701--20308910 Score: 202
Period size: 78 Copynumber: 2.8 Consensus size: 78
20308691 AATTTATAAC
* * **
20308701 ATACTATGTACAT-T-TA-ACATTCGAATCTCAC-ATATACCTATATAATTTCATAC-CCCATTT
1 ATAC-ATGTACATATATACACATTCGAATCTAACAATATACATATATAATTTCATACTTACATTT
20308761 CAATACAAAAACTT
65 CAATACAAAAACTT
*
20308775 ATACATGTACATATATACACATTCGAATCTAACATATATACATATATAATTTTATACTTACA-TT
1 ATACATGTACATATATACACATTCGAATCTAACA-ATATACATATATAATTTCATACTTACATTT
**
20308839 CGAA-ACAAGTACTT
65 C-AATACAAAAACTT
* * * * ** * *
20308853 ATACTTGTATACACATACATTTTCGAATTTAAC-ATATACATATATAGTTTCATACTTA
1 ATACATGTACATATATACACATTCGAATCTAACAATATACATATATAATTTCATACTTA
20308911 TACTCAATAT
Statistics
Matches: 113, Mismatches: 16, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
73 8 0.07
74 5 0.04
75 2 0.02
76 37 0.33
78 57 0.50
79 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (78 bp):
ATACATGTACATATATACACATTCGAATCTAACAATATACATATATAATTTCATACTTACATTTC
AATACAAAAACTT
Found at i:20309314 original size:74 final size:75
Alignment explanation
Indices: 20309063--20309431 Score: 514
Period size: 74 Copynumber: 4.8 Consensus size: 75
20309053 TCTTGTAAAC
* * *
20309063 ATATATAACATTCA-AC-ATTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGA
1 ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGA
20309125 ACTTTATATACAT
66 AC-TTATAT--AT
* *
20309138 ATAAATATAACATACATACTTGTAACTAAATTCAAGAATTTATTCATGTATATACATATATATAT
1 AT--ATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATAC--ATATATAT
20309203 CCGAACTTTATATAT
62 CCGAAC-TTATATAT
* *
20309218 ATAAATATAACATGCATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCC
1 AT--ATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCC
20309283 GAACTT-TATAT
64 GAACTTATATAT
* *
20309294 ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATGTATATACATATATAACCGA
1 ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGA
20309359 ACTT-TATAT
66 ACTTATATAT
*
20309368 ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATGTATATACATATATTATCC
1 ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
20309432 ACTATTAGTT
Statistics
Matches: 274, Mismatches: 12, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
74 126 0.46
75 6 0.02
76 7 0.03
77 13 0.05
78 16 0.06
79 13 0.05
80 73 0.27
82 20 0.07
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (75 bp):
ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGA
ACTTATATAT
Found at i:20309423 original size:148 final size:156
Alignment explanation
Indices: 20309063--20309431 Score: 535
Period size: 154 Copynumber: 2.4 Consensus size: 156
20309053 TCTTGTAAAC
* * *
20309063 ATATATAACATTCA-AC-ATTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGA
1 ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGA
* *
20309125 ACTTTATATACATATAAATATAACATACATACTTGTAACTAAATTCAAGAATTTATTCATGTATA
66 ACTTTATATA-ATAT-AATATAACATACATACTTGTAACTAAATTCAAGAACTTATACATGTATA
20309190 TACATATATATATCCGAACTTTATATAT
129 TACATATATATATCCGAACTTTATATAT
* *
20309218 ATAAATATAACATGCATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCC
1 AT--ATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCC
*
20309283 GAAC-TT-TAT-ATAT-ATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATGTATA
64 GAACTTTATATAATATAATATAACATACATACTTGTAACTAAATTCAAGAACTTATACATGTATA
20309344 TACATATATA-A-CCGAAC-TT-TATAT
129 TACATATATATATCCGAACTTTATATAT
*
20309368 ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATGTATATACATATATTATCC
1 ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
20309432 ACTATTAGTT
Statistics
Matches: 198, Mismatches: 10, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
148 53 0.27
149 5 0.03
150 7 0.04
151 2 0.01
152 6 0.03
153 1 0.01
154 55 0.28
155 2 0.01
156 4 0.02
157 11 0.06
158 5 0.03
159 16 0.08
160 31 0.16
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (156 bp):
ATATATAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGA
ACTTTATATAATATAATATAACATACATACTTGTAACTAAATTCAAGAACTTATACATGTATATA
CATATATATATCCGAACTTTATATAT
Found at i:20314760 original size:38 final size:38
Alignment explanation
Indices: 20314695--20314768 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
20314685 ATAACTCCAT
*
20314695 AATCCCATATTTTCCTTCTAAAGTCACTCCAACACTTC
1 AATCCCATATTTTCCTTCTAAAATCACTCCAACACTTC
* *
20314733 AATCCCATATTTTTC-TCTTAAAATCACTCTAACACT
1 AATCCCATATTTTCCTTC-TAAAATCACTCCAACACT
20314769 CCCCCACCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 2 0.06
38 30 0.94
ACGTcount: A:0.31, C:0.31, G:0.01, T:0.36
Consensus pattern (38 bp):
AATCCCATATTTTCCTTCTAAAATCACTCCAACACTTC
Found at i:20316249 original size:22 final size:22
Alignment explanation
Indices: 20316169--20316236 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
20316159 GTCCCAAAAA
* **
20316169 AGAGCTTAGTACGTGAAACATG
1 AGAGCTTAGTACGTTAGCCATG
20316191 AGAGCTTAGTACGTTAGCCATG
1 AGAGCTTAGTACGTTAGCCATG
20316213 AGAGCTTAGTACGTTAGCCATG
1 AGAGCTTAGTACGTTAGCCATG
20316235 AG
1 AG
20316237 GGTTTAGTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (22 bp):
AGAGCTTAGTACGTTAGCCATG
Found at i:20316355 original size:19 final size:20
Alignment explanation
Indices: 20316331--20316371 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
20316321 ATCAAGAAAA
20316331 TTATATAACATT-AAAAATT
1 TTATATAACATTCAAAAATT
* *
20316350 TTATATAATATTCTAAAATT
1 TTATATAACATTCAAAAATT
20316370 TT
1 TT
20316372 CAGTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATAACATTCAAAAATT
Found at i:20316392 original size:24 final size:20
Alignment explanation
Indices: 20316331--20316384 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
20316321 ATCAAGAAAA
* *
20316331 TTATATAACATT-AAAAATT
1 TTATATAAAATTCTAAAATT
*
20316350 TTATATAATATTCTAAAATT
1 TTATATAAAATTCTAAAATT
20316370 TTCAGTATAAAATTC
1 TT-A-TATAAAATTC
20316385 CATAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 11 0.38
20 8 0.28
21 1 0.03
22 9 0.31
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (20 bp):
TTATATAAAATTCTAAAATT
Found at i:20316464 original size:17 final size:18
Alignment explanation
Indices: 20316442--20316480 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20316432 AAAACTGAAA
* *
20316442 AAAAAAT-TTAAAGGTTT
1 AAAAAATATAAAAGATTT
20316459 AAAAAATATAAAAGATTT
1 AAAAAATATAAAAGATTT
20316477 AAAA
1 AAAA
20316481 CTCAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
AAAAAATATAAAAGATTT
Found at i:20320735 original size:17 final size:18
Alignment explanation
Indices: 20320697--20320736 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20320687 AAAGTTGTTT
**
20320697 ATATTATTTTTAAATTTT
1 ATATTATTTTTAAATTAA
20320715 ATATTATTTTT-AATTAA
1 ATATTATTTTTAAATTAA
20320732 ATATT
1 ATATT
20320737 TCTAGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTATTTTTAAATTAA
Found at i:20330489 original size:31 final size:32
Alignment explanation
Indices: 20330453--20330513 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
20330443 CTTAGATAAT
20330453 TTTAAAGAG-TTTTATTAGGATTCAATTACCC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACCC
20330484 TTTAAAGAGTTTTTATTAGGATTCAATTAC
1 TTTAAAGAGTTTTTATTAGGATTCAATTAC
20330514 TCTTGTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACCC
Found at i:20332074 original size:34 final size:35
Alignment explanation
Indices: 20332009--20332074 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
20331999 GGCCTCATGA
* *
20332009 TACATCAATATTCAGTTACGAAAAACCTCATCATT
1 TACATCAATATTCAGCTACGAAAAACATCATCATT
*
20332044 TACA-CAATATTCAGCTAC-AAAATTCATCATC
1 TACATCAATATTCAGCTACGAAAA-ACATCATC
20332075 TTAGGACAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.15
34 19 0.70
35 4 0.15
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (35 bp):
TACATCAATATTCAGCTACGAAAAACATCATCATT
Found at i:20337968 original size:25 final size:25
Alignment explanation
Indices: 20337940--20337987 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
20337930 ATATTGTTTT
20337940 ATTTTAATATTTAAT-AATTTTTTAC
1 ATTTT-ATATTTAATAAATTTTTTAC
* *
20337965 ATTTTTTATTTATTAAATTTTTT
1 ATTTTATATTTAATAAATTTTTT
20337988 TATATAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
ATTTTATATTTAATAAATTTTTTAC
Found at i:20338328 original size:45 final size:45
Alignment explanation
Indices: 20338264--20338356 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
20338254 GCGGATGGCC
*
20338264 CGACTCATGAACATGTCTAACCACGTATAAGAATCCTGCATTTCA
1 CGACTCATGAACAGGTCTAACCACGTATAAGAATCCTGCATTTCA
20338309 CGACTCATGAACAGGTCTAACCACGTATAAGAATCCTGCATTTCA
1 CGACTCATGAACAGGTCTAACCACGTATAAGAATCCTGCATTTCA
20338354 CGA
1 CGA
20338357 ATCTTGCATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (45 bp):
CGACTCATGAACAGGTCTAACCACGTATAAGAATCCTGCATTTCA
Found at i:20338364 original size:16 final size:16
Alignment explanation
Indices: 20338339--20338370 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20338329 CCACGTATAA
20338339 GAATCCTGCATTTCAC
1 GAATCCTGCATTTCAC
*
20338355 GAATCTTGCATTTCAC
1 GAATCCTGCATTTCAC
20338371 AAGTGTCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.34
Consensus pattern (16 bp):
GAATCCTGCATTTCAC
Found at i:20338616 original size:23 final size:23
Alignment explanation
Indices: 20338590--20338634 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
20338580 AGAAAGAATT
*
20338590 AAGTTTCAATTAAAAATAATAAG
1 AAGTTTCAATTAAAAAGAATAAG
*
20338613 AAGTTTCAATTGAAAAGAATAA
1 AAGTTTCAATTAAAAAGAATAA
20338635 AGTTTTCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (23 bp):
AAGTTTCAATTAAAAAGAATAAG
Found at i:20338639 original size:21 final size:21
Alignment explanation
Indices: 20338582--20338639 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
20338572 GAAATTATAG
*
20338582 AAAGAATTAAGTTTCAATTAA
1 AAAGAATAAAGTTTCAATTAA
* *
20338603 AAATAATAAGAAGTTTCAATTGA
1 AAAGAAT-A-AAGTTTCAATTAA
20338626 AAAGAATAAAGTTT
1 AAAGAATAAAGTTT
20338640 TCGAAGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 12 0.39
22 1 0.03
23 18 0.58
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.31
Consensus pattern (21 bp):
AAAGAATAAAGTTTCAATTAA
Found at i:20341405 original size:23 final size:23
Alignment explanation
Indices: 20341375--20341437 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
20341365 TCCGCATAAT
* *
20341375 GTCCACAGCTCGCCTTCTCCCGC
1 GTCCACAGCTCGCCATCTCCCAC
20341398 GTCCACAGCTCGCCATCTCCCAC
1 GTCCACAGCTCGCCATCTCCCAC
**
20341421 GTCCACAATTCGCCATC
1 GTCCACAGCTCGCCATC
20341438 CCCCTATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.16, C:0.49, G:0.14, T:0.21
Consensus pattern (23 bp):
GTCCACAGCTCGCCATCTCCCAC
Found at i:20341414 original size:56 final size:56
Alignment explanation
Indices: 20341286--20341414 Score: 179
Period size: 56 Copynumber: 2.3 Consensus size: 56
20341276 TCCCTCTGCT
* *
20341286 GTCCACAGCTCACCATTCCCTAGTCCGCCTAATGTCCACAGCTCGCCTTCTCCCAC
1 GTCCACAGCTCACCATCCCCTAGTCCGCATAATGTCCACAGCTCGCCTTCTCCCAC
* * * *
20341342 ATCCATAACTCACCATCCTCCT-GTCCGCATAATGTCCACAGCTCGCCTTCTCCCGC
1 GTCCACAGCTCACCATCC-CCTAGTCCGCATAATGTCCACAGCTCGCCTTCTCCCAC
*
20341398 GTCCACAGCTCGCCATC
1 GTCCACAGCTCACCATC
20341415 TCCCACGTCC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
56 59 0.95
57 3 0.05
ACGTcount: A:0.19, C:0.46, G:0.12, T:0.23
Consensus pattern (56 bp):
GTCCACAGCTCACCATCCCCTAGTCCGCATAATGTCCACAGCTCGCCTTCTCCCAC
Found at i:20341469 original size:33 final size:33
Alignment explanation
Indices: 20341432--20341500 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
20341422 TCCACAATTC
* *
20341432 GCCATCCCCCTATTCACTTGATGTCCACAGCTT
1 GCCATCCCCCTATCCACCTGATGTCCACAGCTT
* *
20341465 GCCATCCCCCTGTCCGCCTGATGTCCACAGCTT
1 GCCATCCCCCTATCCACCTGATGTCCACAGCTT
20341498 GCC
1 GCC
20341501 TTCTCTTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.14, C:0.43, G:0.16, T:0.26
Consensus pattern (33 bp):
GCCATCCCCCTATCCACCTGATGTCCACAGCTT
Found at i:20351819 original size:42 final size:42
Alignment explanation
Indices: 20351773--20351862 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
20351763 AACCTTAATA
*
20351773 GGTTTCAATTCAGCTCTTT-TGAGCTT-CAGTTTAACCCCTATG
1 GGTTTCAATTCAGCT-TTTATGAGCTTCCA-TTCAACCCCTATG
** *
20351815 GGTTTCTGTTCAGCTTTTATGAGCTTCCATTCAACCCTTATG
1 GGTTTCAATTCAGCTTTTATGAGCTTCCATTCAACCCCTATG
20351857 GGTTTC
1 GGTTTC
20351863 CGTTTAGCAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 3 0.07
42 37 0.88
43 2 0.05
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (42 bp):
GGTTTCAATTCAGCTTTTATGAGCTTCCATTCAACCCCTATG
Found at i:20354252 original size:61 final size:61
Alignment explanation
Indices: 20354128--20354400 Score: 287
Period size: 61 Copynumber: 4.5 Consensus size: 61
20354118 TTGTCATAAG
* * * * *
20354128 GGCTTACCTTTCTAGAGTTTTGCCACAAAGGC-ATCCCTTACATCCAGTACTCGCCACAGA
1 GGCTTTCCTGTCTAGAGTTATGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAA
* * * * * *
20354188 GGCTTTCCTGTCTAGAGTTGTGTCACAATGGCTGTCCTTTACATCCAATACTCGTCACAAA
1 GGCTTTCCTGTCTAGAGTTATGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAA
* * * * *
20354249 GGCTTTCTTGTCTAGAGATATGCCACAAAGGTTATCCTTTACATCTAGTACTCGCCTCAAA
1 GGCTTTCCTGTCTAGAGTTATGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAA
* * * * * * * * *
20354310 GTCTATCCTATCTCGAGTTATGCCACAAAGGTTGTCATTTACATCCACTTCTCGCCACAAA
1 GGCTTTCCTGTCTAGAGTTATGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAA
* * *
20354371 GGCTTTCTTGTCCAAAGTTATGCCACAAAG
1 GGCTTTCCTGTCTAGAGTTATGCCACAAAG
20354401 ACGTCCTTTA
Statistics
Matches: 172, Mismatches: 40, Indels: 1
0.81 0.19 0.00
Matches are distributed among these distances:
60 27 0.16
61 145 0.84
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (61 bp):
GGCTTTCCTGTCTAGAGTTATGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAA
Found at i:20354351 original size:122 final size:121
Alignment explanation
Indices: 20354138--20354400 Score: 328
Period size: 122 Copynumber: 2.2 Consensus size: 121
20354128 GGCTTACCTT
* * * *
20354138 TCTAGAGTTTTGCCACAAAGGCATCCCTTACATCCAGTACTCGCCACAGAGGCTTTCCTGTCTAG
1 TCTAGAGTTATGCCACAAAGGCATCCCTTACATCCAGTACTCGCCACAAAGGCTATCCTATCTAG
* * * * *
20354203 AGTTGTGTCACAATGGCTGTCCTTTACATCCAATACTCGTCACAAAGGCTTTCTTG
66 AGTTATGCCACAAAGGCTGTCATTTACATCCAATACTCGCCACAAAGGCTTTCTTG
* * * * * * *
20354259 TCTAGAGATATGCCACAAAGGTTATCCTTTACATCTAGTACTCGCCTCAAAGTCTATCCTATCTC
1 TCTAGAGTTATGCCACAAAGG-CATCCCTTACATCCAGTACTCGCCACAAAGGCTATCCTATCTA
* * *
20354324 GAGTTATGCCACAAAGGTTGTCATTTACATCCACTTCTCGCCACAAAGGCTTTCTTG
65 GAGTTATGCCACAAAGGCTGTCATTTACATCCAATACTCGCCACAAAGGCTTTCTTG
* *
20354381 TCCAAAGTTATGCCACAAAG
1 TCTAGAGTTATGCCACAAAG
20354401 ACGTCCTTTA
Statistics
Matches: 119, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
121 19 0.16
122 100 0.84
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (121 bp):
TCTAGAGTTATGCCACAAAGGCATCCCTTACATCCAGTACTCGCCACAAAGGCTATCCTATCTAG
AGTTATGCCACAAAGGCTGTCATTTACATCCAATACTCGCCACAAAGGCTTTCTTG
Found at i:20354599 original size:53 final size:53
Alignment explanation
Indices: 20354525--20354625 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 53
20354515 TTGTTATTTT
*
20354525 CCATATGATGTCATAACCCACCAGTTACTG-TCTTACACAATATAGTCTTATTC
1 CCATATGATGCCATAACCCACCAGTTAC-GATCTTACACAATATAGTCTTATTC
* *
20354578 CCATATGATGCCATAACCCACCAGTTACGATCTTACACTATATGGTCT
1 CCATATGATGCCATAACCCACCAGTTACGATCTTACACAATATAGTCT
20354626 GTAACACCCC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.02
53 43 0.98
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.32
Consensus pattern (53 bp):
CCATATGATGCCATAACCCACCAGTTACGATCTTACACAATATAGTCTTATTC
Found at i:20356052 original size:50 final size:50
Alignment explanation
Indices: 20355937--20356185 Score: 300
Period size: 50 Copynumber: 4.8 Consensus size: 50
20355927 GATAATAACA
* * ** *
20355937 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
20355988 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
20356038 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
20356088 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
20356143 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
20356186 TTACCCAAAT
Statistics
Matches: 171, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
50 93 0.54
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:20356124 original size:100 final size:104
Alignment explanation
Indices: 20355936--20356185 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 104
20355926 TGATAATAAC
**
20355936 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGGTGCCCATGCCATG
* *
20356001 TCCCAGACATGGTCTTACGGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* * *
20356038 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCCATGCCATGT
*
20356102 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* *
20356143 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
20356186 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
100 49 0.37
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:20363714 original size:50 final size:50
Alignment explanation
Indices: 20363599--20363837 Score: 280
Period size: 50 Copynumber: 4.6 Consensus size: 50
20363589 GATAATAACA
* * ** *
20363599 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
20363650 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * ** *
20363700 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTGTCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
20363750 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
20363805 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
20363838 TGAGATCTCT
Statistics
Matches: 160, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
50 91 0.57
51 33 0.21
53 3 0.02
54 1 0.01
55 1 0.01
56 31 0.19
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:20363786 original size:100 final size:104
Alignment explanation
Indices: 20363598--20363848 Score: 330
Period size: 100 Copynumber: 2.4 Consensus size: 104
20363588 TGATAATAAC
** * *
20363598 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTTATATCGATGCCCATGCCATG
* *
20363663 TCCCAGACATGGTCTTACGGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* * *
20363700 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTGTCTCGATGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATATCGATGCCCATGCCATGT
*
20363764 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* * *
20363805 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGATCTCTT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
20363849 TACCCAAATG
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
100 47 0.36
101 36 0.28
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATATCGATGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:20363963 original size:13 final size:13
Alignment explanation
Indices: 20363942--20363973 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20363932 GCTTGGATCA
*
20363942 TCATCAAATAAAT
1 TCATAAAATAAAT
20363955 TCATAAAATAAAT
1 TCATAAAATAAAT
20363968 TCATAA
1 TCATAA
20363974 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:20364220 original size:30 final size:30
Alignment explanation
Indices: 20364185--20364242 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
20364175 CCTCGACTCT
*
20364185 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
20364215 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
20364243 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:20371424 original size:25 final size:25
Alignment explanation
Indices: 20371382--20371450 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
20371372 TATTTGAATT
* * *
20371382 TTTTTATAATTATAAATATATAAATA
1 TTTTTATTATT-TTAATAAATAAATA
**
20371408 TTTTTATTATTTTAATAAATTTATA
1 TTTTTATTATTTTAATAAATAAATA
*
20371433 TATTTATTATTTT-ATAAA
1 TTTTTATTATTTTAATAAA
20371451 AAGTAATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 5 0.14
25 22 0.59
26 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTTATTATTTTAATAAATAAATA
Found at i:20373989 original size:20 final size:20
Alignment explanation
Indices: 20373914--20373989 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
20373904 ATTCTTTTTG
*
20373914 TTGTTTGAATCAATTGTTTA
1 TTGTTTGAATCAATTCTTTA
*
20373934 TTGTTTGAATCAATTCATTA
1 TTGTTTGAATCAATTCTTTA
* * ** *
20373954 TTGCTTAAATTGATTCTTTG
1 TTGTTTGAATCAATTCTTTA
20373974 TTGTTT-AACTCAATTC
1 TTGTTTGAA-TCAATTC
20373990 AAAAGCCAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 2 0.05
20 42 0.95
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.53
Consensus pattern (20 bp):
TTGTTTGAATCAATTCTTTA
Found at i:20374082 original size:22 final size:21
Alignment explanation
Indices: 20374057--20374122 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
20374047 AAAAGTATTG
20374057 TTGTTTCTTTTGAATCGATTAT
1 TTGTTTC-TTTGAATCGATTAT
* *
20374079 TTGTTATC-TTAAATCGATTCT
1 TTGTT-TCTTTGAATCGATTAT
* *
20374100 TTGCTTATTTGAATCGATTAT
1 TTGTTTCTTTGAATCGATTAT
20374121 TT
1 TT
20374123 TTTTGATTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 28 0.78
22 5 0.14
23 2 0.06
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.56
Consensus pattern (21 bp):
TTGTTTCTTTGAATCGATTAT
Found at i:20374094 original size:21 final size:21
Alignment explanation
Indices: 20374069--20374122 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
20374059 GTTTCTTTTG
20374069 AATCGATTATTTG-TTATCTTA
1 AATCGATTATTTGCTTAT-TTA
* *
20374090 AATCGATTCTTTGCTTATTTG
1 AATCGATTATTTGCTTATTTA
20374111 AATCGATTATTT
1 AATCGATTATTT
20374123 TTTTGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (21 bp):
AATCGATTATTTGCTTATTTA
Found at i:20374132 original size:21 final size:22
Alignment explanation
Indices: 20374108--20374161 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
20374098 CTTTGCTTAT
20374108 TTGAATCGATTATTTTT-TTGA
1 TTGAATCGATTATTTTTGTTGA
** * * *
20374129 TTGACCCAATTCTTTTTGTTGT
1 TTGAATCGATTATTTTTGTTGA
20374151 TTGAATCGATT
1 TTGAATCGATT
20374162 CATTATTGCT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.54
Consensus pattern (22 bp):
TTGAATCGATTATTTTTGTTGA
Found at i:20374179 original size:20 final size:20
Alignment explanation
Indices: 20374154--20374203 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
20374144 TTGTTGTTTG
20374154 AATCGATTCATTATTGCTTA
1 AATCGATTCATTATTGCTTA
* * *
20374174 AATCGATTCTTTGTTGTTTA
1 AATCGATTCATTATTGCTTA
*
20374194 ACTCGATTCA
1 AATCGATTCA
20374204 AACGCTAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (20 bp):
AATCGATTCATTATTGCTTA
Found at i:20374951 original size:24 final size:24
Alignment explanation
Indices: 20374911--20374964 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
20374901 TATATATAAT
* * *
20374911 AATA-AATTATATTTAAATAATTA
1 AATATAATGATATATAAAAAATTA
20374934 AATATAATGATATATAAAAAATTA
1 AATATAATGATATATAAAAAATTA
*
20374958 TATATAA
1 AATATAA
20374965 AAAATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AATATAATGATATATAAAAAATTA
Found at i:20374960 original size:55 final size:54
Alignment explanation
Indices: 20374894--20375009 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 54
20374884 AAAATATTTC
*
20374894 AAAAACTTATATAT-AATAATAAATTATATTTAA-ATAATTAAATATAATGATATAT
1 AAAAAATTATATATAAATAATAAATTATATTTAATA-AATT--ATATAATGATATAT
*
20374949 AAAAAATTATATATAAAAAATTATAAATTATATTTAATAAATTATATAATGATATAT
1 AAAAAATTATATAT---AAATAATAAATTATATTTAATAAATTATATAATGATATAT
20375006 AAAA
1 AAAA
20375010 TATATTAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
55 13 0.24
57 18 0.33
59 22 0.41
60 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (54 bp):
AAAAAATTATATATAAATAATAAATTATATTTAATAAATTATATAATGATATAT
Done.