Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 19
Found at i:2249403 original size:23 final size:24
Alignment explanation
Indices: 2249358--2249403 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
2249348 TTATCATGAT
* *
2249358 TCATTAATGGTGATTTTTTAATTTC
1 TCATTAAT-GTGAATTTTAAATTTC
2249383 TCATTAAT-TGAATTTTAAATT
1 TCATTAATGTGAATTTTAAATT
2249404 CAATTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (24 bp):
TCATTAATGTGAATTTTAAATTTC
Found at i:2251581 original size:60 final size:60
Alignment explanation
Indices: 2251506--2251620 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
2251496 TCTAGCAAAA
* * *
2251506 ACATGAAATTAAAGGATTAAAATAGTAAGAACT-AAAACTTAAAAGGCTATAACAATTAAG
1 ACATGAAATTAAAGGATTAAAATAGCAA-AAATAAAAACTTAAAAGGCTAAAACAATTAAG
*
2251566 ACAT-AAATTTAAAGGATTAAAATAGCAAAAATAAAAATTTAAAAGGCTAAAACAA
1 ACATGAAA-TTAAAGGATTAAAATAGCAAAAATAAAAACTTAAAAGGCTAAAACAA
2251621 AAAAAATAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 6 0.12
60 43 0.88
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23
Consensus pattern (60 bp):
ACATGAAATTAAAGGATTAAAATAGCAAAAATAAAAACTTAAAAGGCTAAAACAATTAAG
Found at i:2251634 original size:60 final size:60
Alignment explanation
Indices: 2251502--2251634 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
2251492 TAGATCTAGC
* * * *
2251502 AAAAACAT-GAAA-TTAAAGGATTAAAATAGTAAGAACTAAAACTTAAAAGGCTATAACA
1 AAAAAAATAGAAATTTAAAGGATTAAAATAGCAAGAAATAAAACTTAAAAGGCTAAAACA
** * * * *
2251560 ATTAAGACATAAATTTAAAGGATTAAAATAGCAA-AAATAAAAATTTAAAAGGCTAAAACA
1 AAAAAAATAGAAATTTAAAGGATTAAAATAGCAAGAAAT-AAAACTTAAAAGGCTAAAACA
2251620 AAAAAAATAGAAATT
1 AAAAAAATAGAAATT
2251635 CAAGGGACTA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
58 4 0.07
59 6 0.10
60 48 0.83
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.22
Consensus pattern (60 bp):
AAAAAAATAGAAATTTAAAGGATTAAAATAGCAAGAAATAAAACTTAAAAGGCTAAAACA
Found at i:2258874 original size:9 final size:9
Alignment explanation
Indices: 2258860--2258892 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2258850 TTTATCTCGA
2258860 TTTATTTAT
1 TTTATTTAT
2258869 TTTATTTAT
1 TTTATTTAT
2258878 TTT-TTTAT
1 TTTATTTAT
*
2258886 TTAATTT
1 TTTATTT
2258893 TTATCTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2258884 original size:17 final size:17
Alignment explanation
Indices: 2258859--2258892 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2258849 CTTTATCTCG
*
2258859 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
2258876 ATTTTTTTATTTAATTT
1 ATTTATTTATTTAATTT
2258893 TTATCTCATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:2258892 original size:13 final size:12
Alignment explanation
Indices: 2258859--2258894 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
2258849 CTTTATCTCG
2258859 ATTTATTTATTTT
1 ATTTATTT-TTTT
2258872 ATTTATTTTTTT
1 ATTTATTTTTTT
2258884 ATTTAATTTTT
1 ATTT-ATTTTT
2258895 ATCTCATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:2263013 original size:34 final size:34
Alignment explanation
Indices: 2262948--2263039 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
2262938 GAGTGTGCGC
* * * * *
2262948 AATAAGCACTACAGGTGCTATCATCATAAACAAA
1 AATATGCACTCCAAGTGCAATCATCAAAAACAAA
* *
2262982 AATATGCGCTCCAAGTGCAATCATCAAAAACATA
1 AATATGCACTCCAAGTGCAATCATCAAAAACAAA
*
2263016 AATATGCACTCCATGTGCAATCAT
1 AATATGCACTCCAAGTGCAATCAT
2263040 ATAAGGTACA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (34 bp):
AATATGCACTCCAAGTGCAATCATCAAAAACAAA
Found at i:2265247 original size:18 final size:18
Alignment explanation
Indices: 2265221--2265256 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2265211 AATCATCAAA
*
2265221 CATTTTTCAAAATTCTTT
1 CATTATTCAAAATTCTTT
2265239 CATTATTCAAAATTCTTT
1 CATTATTCAAAATTCTTT
2265257 TGATAAAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
CATTATTCAAAATTCTTT
Found at i:2265790 original size:37 final size:37
Alignment explanation
Indices: 2265742--2265882 Score: 147
Period size: 37 Copynumber: 3.8 Consensus size: 37
2265732 AACTGCACTC
*
2265742 TAGTCCTTCTTAGGATTATTTCTGTAGAAATTCATTT
1 TAGTCCTTCTTAGGATTATTTCTCTAGAAATTCATTT
** * * * *
2265779 TAGTTTTTCTTAAGATCATTTCTCTAGAAATTCGTTA
1 TAGTCCTTCTTAGGATTATTTCTCTAGAAATTCATTT
* * *
2265816 GAGTCCTTCTTAGGACTGTTTCTCTAGAAATTCATTT
1 TAGTCCTTCTTAGGATTATTTCTCTAGAAATTCATTT
* * * * *
2265853 TAGTCATTCTCATGATTGTTTCCCTAGAAA
1 TAGTCCTTCTTAGGATTATTTCTCTAGAAA
2265883 CCTCAACTTG
Statistics
Matches: 82, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 82 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (37 bp):
TAGTCCTTCTTAGGATTATTTCTCTAGAAATTCATTT
Found at i:2265880 original size:74 final size:74
Alignment explanation
Indices: 2265743--2265882 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 74
2265733 ACTGCACTCT
* * ** * *
2265743 AGTCCTTCTTAGGATTATTTCTGTAGAAATTCATTTTAGTTTTTCTTAAGATCATTTCTCTAGAA
1 AGTCCTTCTTAGGACTATTTCTCTAGAAATTCATTTTAGTCATTCTCAAGATCATTTCCCTAGAA
2265808 ATTCGTTAG
66 ATTCGTTAG
* * **
2265817 AGTCCTTCTTAGGACTGTTTCTCTAGAAATTCATTTTAGTCATTCTCATGATTGTTTCCCTAGAA
1 AGTCCTTCTTAGGACTATTTCTCTAGAAATTCATTTTAGTCATTCTCAAGATCATTTCCCTAGAA
2265882 A
66 A
2265883 CCTCAACTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 56 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (74 bp):
AGTCCTTCTTAGGACTATTTCTCTAGAAATTCATTTTAGTCATTCTCAAGATCATTTCCCTAGAA
ATTCGTTAG
Found at i:2265967 original size:45 final size:45
Alignment explanation
Indices: 2265889--2266250 Score: 325
Period size: 45 Copynumber: 8.0 Consensus size: 45
2265879 GAAACCTCAA
* *
2265889 CTTGACTTTCTCACAAAGATGAATCAA-CTTTTTAGTGTTGTCCTT
1 CTTGACTTTCTCACGAAGATGAGTCAATC-TTTTAGTGTTGTCCTT
* * *
2265934 CTTAACTTTCTCACGAAGATGAGTTAATCTTTTAGTGTTATCCTT
1 CTTGACTTTCTCACGAAGATGAGTCAATCTTTTAGTGTTGTCCTT
* * *
2265979 CTTGACTTTCTCGCGAAGTTGACTCAATCTTTTAGTGTTGTCCTT
1 CTTGACTTTCTCACGAAGATGAGTCAATCTTTTAGTGTTGTCCTT
* * *
2266024 CTTGTCTTTCTCACGAAGATGAGTCAATCTTTTAATGTTATCCTT
1 CTTGACTTTCTCACGAAGATGAGTCAATCTTTTAGTGTTGTCCTT
* * * * * * *
2266069 ATTGACTTTCTCACAAAGAGGAGTGAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCACGAAGATGAGTCAATCTTTTAGTGTTGTCCTT
** * ** *
2266114 CTTGACTTTCTCGTGAAGAAGAGTCCTTCTTTTAGTGTTTTCCTT
1 CTTGACTTTCTCACGAAGATGAGTCAATCTTTTAGTGTTGTCCTT
* ** * * * * * *
2266159 CTTGAATTTCTTGC-AACTAGGAGTCAACCTTTTATTGATGTCATT
1 CTTGACTTTCTCACGAA-GATGAGTCAATCTTTTAGTGTTGTCCTT
*** * * *
2266204 CTTGACTTTCTTGTGAAGA-GAAGTCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCACGAAGATG-AGTCAATCTTTTAGTGTTGTCCTT
2266249 CT
1 CT
2266251 CAATTTGACT
Statistics
Matches: 258, Mismatches: 55, Indels: 8
0.80 0.17 0.02
Matches are distributed among these distances:
44 3 0.01
45 252 0.98
46 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (45 bp):
CTTGACTTTCTCACGAAGATGAGTCAATCTTTTAGTGTTGTCCTT
Found at i:2266183 original size:135 final size:135
Alignment explanation
Indices: 2265889--2266250 Score: 366
Period size: 135 Copynumber: 2.7 Consensus size: 135
2265879 GAAACCTCAA
* * * * * * * *
2265889 CTTGACTTTCTCACAAAGATGAATCAACTTTTTAGTGTTGTCCTTCTTAACTTTCTCACGAAGAT
1 CTTGAATTTCTCACGAAGAGGAGTCAACCTTTTAATGTTGTCCTTCTTGACTTTCTCACGAAGAG
* * * * * **
2265954 GAGTTAATCTTTTAGTGTTATCCTTCTTGACTTTCTCGCGAAGTTGACTCAATCTTTTAGTGTTG
66 GAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAAGACTCAATCTTTTAGTGTTG
2266019 TCCTT
131 TCCTT
** * * * * *
2266024 CTTGTCTTTCTCACGAAGATGAGTCAATCTTTTAATGTTATCCTTATTGACTTTCTCACAAAGAG
1 CTTGAATTTCTCACGAAGAGGAGTCAACCTTTTAATGTTGTCCTTCTTGACTTTCTCACGAAGAG
* * * ** *
2266089 GAGTGAACCTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAAGAGTCCTTCTTTTAGTGTTT
66 GAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAAGACTCAATCTTTTAGTGTTG
2266154 TCCTT
131 TCCTT
** * * * * ***
2266159 CTTGAATTTCTTGC-AACTAGGAGTCAACCTTTTATTGATGTCATTCTTGACTTTCTTGTGAAGA
1 CTTGAATTTCTCACGAA-GAGGAGTCAACCTTTTAATGTTGTCCTTCTTGACTTTCTCACGAAGA
*
2266223 GAAGTCAACCTTTTAGTGATGTCATTCT
65 GGAGTCAACCTTTTAGTGATGTCATTCT
2266251 CAATTTGACT
Statistics
Matches: 185, Mismatches: 41, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
134 2 0.01
135 183 0.99
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (135 bp):
CTTGAATTTCTCACGAAGAGGAGTCAACCTTTTAATGTTGTCCTTCTTGACTTTCTCACGAAGAG
GAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAAGACTCAATCTTTTAGTGTTG
TCCTT
Found at i:2266281 original size:50 final size:45
Alignment explanation
Indices: 2265889--2266294 Score: 276
Period size: 45 Copynumber: 8.9 Consensus size: 45
2265879 GAAACCTCAA
* * * * * * *
2265889 CTTGACTTTCTCACAAAGATGAATCAACTTTTTAGTGTTGTCCTT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * * * * * *
2265934 CTTAACTTTCTCACGAAGATGAGTTAATCTTTTAGTGTTATCCTT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
** * * * *
2265979 CTTGACTTTCTCGCGAAGTTGACTCAATCTTTTAGTGTTGTCCTT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * * * * * *
2266024 CTTGTCTTTCTCACGAAGATGAGTCAATCTTTTAATGTTATCCTT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * *
2266069 ATTGACTTTCTCACAAAGAGGAGTGAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * *** * * *
2266114 CTTGACTTTCTCGTGAAGAAGAGTCCTTCTTTTAGTGTTTTCCTT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * *
2266159 CTTGAATTTCTTGC-AACTAGGAGTCAACCTTTTATTGATGTCATT
1 CTTGACTTTCTCGCGAA-GAGGAGTCAACCTTTTAGTGATGTCATT
* * *
2266204 CTTGACTTTCTTGTGAAGAGAAGTCAACCTTTTAGTGATGTCATTCT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCA-T-T
* * * *
2266251 CAATTTGACTTTCTCGCGGAGAGGATTCAA-CTTTTCGTTATGTC
1 C---TTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTC
2266295 CATCTTCTGC
Statistics
Matches: 289, Mismatches: 65, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
44 2 0.01
45 249 0.86
46 3 0.01
47 2 0.01
49 12 0.04
50 21 0.07
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (45 bp):
CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
Found at i:2269329 original size:31 final size:31
Alignment explanation
Indices: 2269293--2269352 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2269283 AACTTAAAAG
* *
2269293 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2269324 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
2269353 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2269861 original size:19 final size:15
Alignment explanation
Indices: 2269822--2269865 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
2269812 ATCAAAATAA
2269822 ATATAAAATTTTAAT
1 ATATAAAATTTTAAT
2269837 ATATAAAATAATTTATAT
1 ATATAAAAT--TTTA-AT
2269855 GATATAAAATT
1 -ATATAAAATT
2269866 AAATATCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.36
17 5 0.20
18 2 0.08
19 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATATAAAATTTTAAT
Found at i:2269891 original size:28 final size:28
Alignment explanation
Indices: 2269860--2270027 Score: 198
Period size: 24 Copynumber: 6.4 Consensus size: 28
2269850 TATATGATAT
2269860 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATATCTATAATATAATATTAA
*
2269889 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
2269913 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATATCTATAATATAATATTAA
* *
2269941 AACATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
*
2269965 AAATTTAATATCTATAATATAATATTAA
1 AAAATTAATATCTATAATATAATATTAA
*
2269993 AAAATTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
2270017 AAAATTAATAT
1 AAAATTAATAT
2270028 TAAAATTAAA
Statistics
Matches: 122, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
24 43 0.35
25 11 0.09
26 20 0.16
27 9 0.07
28 33 0.27
29 6 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAATTAATATCTATAATATAATATTAA
Found at i:2269928 original size:52 final size:52
Alignment explanation
Indices: 2269860--2270027 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
2269850 TATATGATAT
2269860 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
*
2269913 AAAATTAATATCTATAATATAATATTAAAACATTAATATTTAATTTATTTAA
1 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
*
2269965 AAATTTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
2270017 AAAATTAATAT
1 AAAATTAATAT
2270028 TAAAATTAAA
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 105 0.95
53 6 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (52 bp):
AAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
Found at i:2273473 original size:24 final size:24
Alignment explanation
Indices: 2273431--2273486 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2273421 TCACGATAGT
* * *
2273431 AGAGAAAATATGTGCCACAATAAC
1 AGAGAAAACATATGCCACAAGAAC
* *
2273455 AGAGAAAACATATGTCACAAGAGC
1 AGAGAAAACATATGCCACAAGAAC
2273479 AGAGAAAA
1 AGAGAAAA
2273487 GCGTGTCACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.20, T:0.12
Consensus pattern (24 bp):
AGAGAAAACATATGCCACAAGAAC
Found at i:2275536 original size:15 final size:15
Alignment explanation
Indices: 2275516--2275544 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2275506 CAGAGATGTG
2275516 GGATCGGCGGCTGAT
1 GGATCGGCGGCTGAT
2275531 GGATCGGCGGCTGA
1 GGATCGGCGGCTGA
2275545 GATCAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (15 bp):
GGATCGGCGGCTGAT
Found at i:2277716 original size:22 final size:21
Alignment explanation
Indices: 2277661--2277717 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2277651 CGCGATTCTG
*
2277661 ACTATCACATTGCGATTTTCA
1 ACTATCGCATTGCGATTTTCA
* *
2277682 AAT-TCGCGTTGCGATTTTCCA
1 ACTATCGCATTGCGATTTT-CA
*
2277703 ACTATCGCAATGCGA
1 ACTATCGCATTGCGA
2277718 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 13 0.46
21 6 0.21
22 9 0.32
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (21 bp):
ACTATCGCATTGCGATTTTCA
Found at i:2277731 original size:20 final size:20
Alignment explanation
Indices: 2277706--2277797 Score: 141
Period size: 20 Copynumber: 4.6 Consensus size: 20
2277696 TTTTCCAACT
2277706 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
2277726 ATCGCAATGCAAATATGTAA
1 ATCGCAATGCGAATATGTAA
2277746 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
2277766 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
2277786 ATCGCAATGCGA
1 ATCGCAATGCGA
2277798 TTCTGACTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 1 0.01
20 66 0.99
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:2277798 original size:20 final size:20
Alignment explanation
Indices: 2277703--2277852 Score: 117
Period size: 20 Copynumber: 7.5 Consensus size: 20
2277693 CGATTTTCCA
*
2277703 ACTATCGCAATGCGAATATG
1 ACTATCGCAATGCGATTATG
* * *
2277723 TA-AATCGCAATGCAAATATG
1 -ACTATCGCAATGCGATTATG
* *
2277743 TA-AATCGCAATGCGAATATG
1 -ACTATCGCAATGCGATTATG
*
2277763 TA-AATCGCAATGCGATTATG
1 -ACTATCGCAATGCGATTATG
*
2277783 ACTATCGCAATGCGATTCTG
1 ACTATCGCAATGCGATTATG
* *
2277803 ACTATCGCAACGCGATTCTG
1 ACTATCGCAATGCGATTATG
* * * *
2277823 GCTGTCGCAACGCGATTCTG
1 ACTATCGCAATGCGATTATG
*
2277843 ACTGTCGCAA
1 ACTATCGCAA
2277853 CACTGAATTT
Statistics
Matches: 118, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
19 1 0.01
20 116 0.98
21 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (20 bp):
ACTATCGCAATGCGATTATG
Found at i:2277853 original size:20 final size:20
Alignment explanation
Indices: 2277766--2277853 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
2277756 GAATATGTAA
* *
2277766 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
2277786 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2277806 ATCGCAACGCGATTCTGGCT
1 ATCGCAACGCGATTCTGACT
*
2277826 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2277846 GTCGCAAC
1 ATCGCAAC
2277854 ACTGAATTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2278725 original size:24 final size:24
Alignment explanation
Indices: 2278667--2278713 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2278657 AGTCGGTATT
*
2278667 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
2278691 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
2278714 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:2281010 original size:18 final size:18
Alignment explanation
Indices: 2280987--2281021 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2280977 AGAAAAAGGC
*
2280987 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
2281005 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2281022 CAACCGGCTT
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:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2281333 original size:140 final size:138
Alignment explanation
Indices: 2281081--2281348 Score: 491
Period size: 140 Copynumber: 1.9 Consensus size: 138
2281071 AAATGTTGTA
*
2281081 TTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
2281146 TGATCTGTTCAGTTGCTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGCTATCACTTATTACACATTCATTTGAATATCGCAA--CGAATTTGACTAT
2281211 TATGTGTATT
129 TATGTGTATT
2281221 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
2281286 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGAATTTGACTAT
66 TGATATGTTCAGTTGCTATCACTTATTACACATTCATTTGAATATCGCAACGAATTTGACTAT
2281349 CGCAACGCGA
Statistics
Matches: 125, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
138 13 0.10
140 112 0.90
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (138 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGCTATCACTTATTACACATTCATTTGAATATCGCAACGAATTTGACTATTA
TGTGTATT
Found at i:2281361 original size:20 final size:20
Alignment explanation
Indices: 2281321--2281686 Score: 284
Period size: 20 Copynumber: 19.6 Consensus size: 20
2281311 TTACACATTC
*
2281321 ATTTGAATATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
2281339 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2281359 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
2281378 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2281393 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
2281413 ATATGACTATCGTAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
2281432 A----A-AATCGCAACCCGA
1 ATTTGACTATCGCAACGCGA
* * *
2281447 ATTTGTCTATCGCAACACAA
1 ATTTGACTATCGCAACGCGA
2281467 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2281487 ATTTGATTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
2281507 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
2281527 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2281541 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2281561 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2281581 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
2281601 ATTTGATTATCGCAAAGGGT
1 ATTTGACTATCGCAACGCGA
* *
2281621 ATTTGACTGTCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
2281641 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
2281655 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2281675 A-TTGACTTTCGC
1 ATTTGACTATCGC
2281687 GTTTTGATTT
Statistics
Matches: 277, Mismatches: 43, Indels: 55
0.74 0.11 0.15
Matches are distributed among these distances:
14 38 0.14
15 6 0.02
16 2 0.01
18 16 0.06
19 15 0.05
20 199 0.72
21 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2281414 original size:54 final size:53
Alignment explanation
Indices: 2281329--2281484 Score: 224
Period size: 54 Copynumber: 2.9 Consensus size: 53
2281319 TCATTTGAAT
* * *
2281329 ATCGCAA-CGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
* *
2281381 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGTAACGCAAAA
1 ATCGCAAC-CGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
* *
2281435 ATCGCAACCCGAATTTGTCTATCGCAACACAAATTTGACTATCGCAACGC
1 ATCGCAA-CCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGC
2281485 GAATTTGATT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
52 7 0.08
54 84 0.91
55 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (53 bp):
ATCGCAACCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
Found at i:2281439 original size:34 final size:34
Alignment explanation
Indices: 2281401--2281467 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
2281391 GAATTTGACT
* *
2281401 ATCGCAACACGAATATGACTATCGTAACGCAAAA
1 ATCGCAACACGAATATGACTATCGCAACACAAAA
* * *
2281435 ATCGCAACCCGAATTTGTCTATCGCAACACAAA
1 ATCGCAACACGAATATGACTATCGCAACACAAA
2281468 TTTGACTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.19
Consensus pattern (34 bp):
ATCGCAACACGAATATGACTATCGCAACACAAAA
Found at i:2281502 original size:94 final size:93
Alignment explanation
Indices: 2281381--2281615 Score: 319
Period size: 94 Copynumber: 2.5 Consensus size: 93
2281371 CAACTCAAAA
* *
2281381 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGTAACGCA-AAAATCGCAACCC
1 ATCGCAACGCGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAACG-AGAAAATCGCAACCC
*
2281445 GAATTTGTCTATCGCAACACAAATTTGACT
64 GAATTTGACTATCGCAACACAAATTTGACT
* * * *
2281475 ATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACCG-AATTTGACTATCGCAACGAGAAAATCGCAACCCG
* * *
2281540 AATTTGACTATCGCAACGCGAATTTGAGT
65 AATTTGACTATCGCAACACAAATTTGACT
* *
2281569 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAA
1 ATCGCAACGCGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAA
2281616 AGGGTATTTG
Statistics
Matches: 124, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
93 2 0.02
94 121 0.98
95 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (93 bp):
ATCGCAACGCGAATTTGACTATCGCAACCGAATTTGACTATCGCAACGAGAAAATCGCAACCCGA
ATTTGACTATCGCAACACAAATTTGACT
Found at i:2281533 original size:74 final size:74
Alignment explanation
Indices: 2281321--2281597 Score: 242
Period size: 74 Copynumber: 3.8 Consensus size: 74
2281311 TTACACATTC
* * * *
2281321 ATTTGAATATCGCAA--CGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCA-AAAAT
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGACTATCGCAAC-GAGAAAAT
* *
2281383 CGCAACGCGA
65 CGCAACACAA
* * * * * * * * * *** ***
2281393 ATTTGACTATCGCAACACGAATATGACTATCGTAACGCAAAAATCG-C-AACCCGAATTTGTCTA
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACGC-GAATTTGACTATCGC-AACGAGAAAA
2281456 TCGCAACACAA
64 TCGCAACACAA
* *
2281467 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACG-GCTATTTGACTATCGCAACGAGAAAAT
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACGCG-AATTTGACTATCGCAACGAGAAAAT
* *
2281531 CGCAACGCGA
65 CGCAACACAA
*
2281541 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGAGTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGACTATCGCAACG
2281598 CGAATTTGAT
Statistics
Matches: 158, Mismatches: 38, Indels: 16
0.75 0.18 0.08
Matches are distributed among these distances:
72 14 0.09
73 6 0.04
74 130 0.82
75 8 0.05
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATC
GCAACACAA
Found at i:2281562 original size:114 final size:114
Alignment explanation
Indices: 2281435--2281686 Score: 380
Period size: 114 Copynumber: 2.2 Consensus size: 114
2281425 TAACGCAAAA
* *
2281435 ATCGCAACCCGAATTTGTCTATCGCAACACAAATTTGACTATCGCAACGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACACAAATTTGACTATCGCAACGCGAATTTGATTATCGC
* * *
2281500 AACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACT
66 AAAGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACT
* * * *
2281549 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACACAAATTTGACTATCGCAACGCGAATTTGATTATCGC
* * *
2281614 AAAGGGTATTTGACTGTCGCAACGAGAAAATCGCAAAGCGTATTAGACT
66 AAAGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACT
*
2281663 ATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGC
2281687 GTTTTGATTT
Statistics
Matches: 124, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
113 9 0.07
114 115 0.93
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (114 bp):
ATCGCAACGCGAATTTGACTATCGCAACACAAATTTGACTATCGCAACGCGAATTTGATTATCGC
AAAGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACT
Found at i:2281705 original size:20 final size:20
Alignment explanation
Indices: 2281680--2281718 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2281670 CGCGAATTGA
* *
2281680 CTTTCGCGTTTTGATTTTGT
1 CTTTCGCATTGTGATTTTGT
2281700 CTTTCGCATTGTGATTTTG
1 CTTTCGCATTGTGATTTTG
2281719 AGTTTAGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.15, G:0.21, T:0.56
Consensus pattern (20 bp):
CTTTCGCATTGTGATTTTGT
Found at i:2281889 original size:14 final size:15
Alignment explanation
Indices: 2281857--2281893 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2281847 AATATTAAAC
*
2281857 AAATCAACTTTTACT
1 AAATCAATTTTTACT
2281872 -AATCAATTTTTA-T
1 AAATCAATTTTTACT
2281885 AAATCAATT
1 AAATCAATT
2281894 AAACAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 19 0.95
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATCAATTTTTACT
Found at i:2283332 original size:21 final size:21
Alignment explanation
Indices: 2283303--2283368 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2283293 GAATGTTGGG
* *
2283303 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
2283324 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
*
2283345 AGGGGACTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
2283366 AGG
1 AGG
2283369 TGAGTCGGGC
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.20
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:2283877 original size:18 final size:19
Alignment explanation
Indices: 2283854--2283919 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
2283844 GAAACTTAAA
2283854 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
2283872 ATCGCAACTCGAAAATGACT
1 ATCGCAACACG-AAATGACT
*
2283892 ATCGCAACGCGAAAGTGACT
1 ATCGCAACACGAAA-TGACT
*
2283912 ATAGCAAC
1 ATCGCAAC
2283920 GAGAGAATCG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 10 0.24
19 3 0.07
20 29 0.69
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:2283890 original size:20 final size:20
Alignment explanation
Indices: 2283865--2283920 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2283855 TCGCAACACG
*
2283865 AATGACTATCGCAACTCGAA
1 AATGACTATCGCAACGCGAA
2283885 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
* *
2283905 AGTGACTATAGCAACG
1 AATGACTATCGCAACG
2283921 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:2283988 original size:20 final size:20
Alignment explanation
Indices: 2283963--2284050 Score: 158
Period size: 20 Copynumber: 4.4 Consensus size: 20
2283953 GCGATTCTTT
**
2283963 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2283983 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2284003 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2284023 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2284043 CGTTGCGA
1 CGTTGCGA
2284051 AAGTAAACTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2283989 original size:34 final size:37
Alignment explanation
Indices: 2283945--2284050 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 37
2283935 CGATTTTCAT
*
2283945 TTCGCATTGCGAT-TC-TTT-CGTTGCGATAGTCAAA
1 TTCGCGTTGCGATATCATTTCCGTTGCGATAGTCAAA
**
2283979 TTCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATA-TCA-TTTC-CGTTGCGATAGTCAAA
2284019 TTCGCGTTGCGATAGTCATTTTCGCGTTGCGA
1 TTCGCGTTGCGATA-TCA-TTTC-CGTTGCGA
2284051 AAGTAAACTA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
34 12 0.19
36 2 0.03
38 3 0.05
40 46 0.73
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.39
Consensus pattern (37 bp):
TTCGCGTTGCGATATCATTTCCGTTGCGATAGTCAAA
Found at i:2284216 original size:18 final size:18
Alignment explanation
Indices: 2284193--2284242 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
2284183 TTTACTAAGC
2284193 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
2284211 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
2284229 AATCTAAGTAAAAT
1 AATCTAAGTGAAAT
2284243 TACGAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:2285985 original size:20 final size:20
Alignment explanation
Indices: 2285962--2286029 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
2285952 TCTGAAACTT
2285962 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
2285982 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
2286002 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
2286021 AAAATCGCA
1 AAAATCGCA
2286030 TTGCGATTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 12 0.28
20 31 0.72
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:2286663 original size:20 final size:20
Alignment explanation
Indices: 2286633--2286807 Score: 181
Period size: 20 Copynumber: 8.7 Consensus size: 20
2286623 GCGTTTTGAA
*
2286633 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
2286653 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
2286673 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* * *
2286693 AATCTCGTTGTGATAGTTAG
1 AATCGCGTTGCGATAGTCAG
*
2286713 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* * *
2286733 AATCGCATTGCGAT-TTACAT
1 AATCGCGTTGCGATAGT-CAG
* * *
2286753 ATTCGCATTGCGATAGTCGAAA
1 AATCGCGTTGCGATAGTC--AG
**
2286775 AATCGCAATGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
2286795 AATCGCGTTGCGA
1 AATCGCGTTGCGA
2286808 ATCTGGAAAC
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 110 0.85
21 1 0.01
22 17 0.13
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:2287657 original size:12 final size:12
Alignment explanation
Indices: 2287602--2287663 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
2287592 ACTATAATAT
2287602 ATATTTTCAAAA
1 ATATTTTCAAAA
*
2287614 ATCGTTTTCAAAA
1 AT-ATTTTCAAAA
* * *
2287627 CTATATATT-ATAT
1 --ATATTTTCAAAA
2287640 ATATTTTCAAAA
1 ATATTTTCAAAA
2287652 ATATTTTCAAAA
1 ATATTTTCAAAA
2287664 CTATATATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
11 6 0.16
12 16 0.42
13 11 0.29
14 3 0.08
15 2 0.05
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:2287668 original size:37 final size:35
Alignment explanation
Indices: 2287535--2287689 Score: 210
Period size: 34 Copynumber: 4.4 Consensus size: 35
2287525 TTCGGATAAG
2287535 ATATTTT-AAAAATCGTTTTCAAAACTATATA-AT
1 ATATTTTCAAAAATCGTTTTCAAAACTATATATAT
*
2287568 ATATTTTCAAAAATGGTTTTCAAAACTATA-ATAT
1 ATATTTTCAAAAATCGTTTTCAAAACTATATATAT
2287602 ATATTTTCAAAAATCGTTTTCAAAACTATATATTATAT
1 ATATTTTCAAAAATCGTTTTCAAAAC--TATA-TATAT
*
2287640 ATATTTTCAAAAAT-ATTTTCAAAACTATATATTATAT
1 ATATTTTCAAAAATCGTTTTCAAAAC--TATA-TATAT
2287677 ATATTTTCAAAAA
1 ATATTTTCAAAAA
2287690 AAGATTTTTT
Statistics
Matches: 113, Mismatches: 3, Indels: 8
0.91 0.02 0.06
Matches are distributed among these distances:
33 8 0.07
34 48 0.42
36 4 0.04
37 35 0.31
38 18 0.16
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (35 bp):
ATATTTTCAAAAATCGTTTTCAAAACTATATATAT
Found at i:2292619 original size:14 final size:15
Alignment explanation
Indices: 2292593--2292632 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2292583 ATAAAAAAAT
2292593 AATAT-TTAC-AT-A
1 AATATATTACTATAA
2292605 AATATATTACTATAA
1 AATATATTACTATAA
*
2292620 AATATAATACTAT
1 AATATATTACTAT
2292633 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 5 0.21
13 4 0.17
14 2 0.08
15 13 0.54
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATATTACTATAA
Found at i:2294414 original size:18 final size:18
Alignment explanation
Indices: 2294393--2294430 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2294383 CCTTACACAC
2294393 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
*
2294411 TTTGCCACGACAACACCA
1 TTTGCCACAACAACACCA
2294429 TT
1 TT
2294431 CATACTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.08, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:2300866 original size:18 final size:18
Alignment explanation
Indices: 2300845--2300882 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2300835 CCTTACACAC
2300845 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
2300863 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
2300881 TT
1 TT
2300883 CATACTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:2303979 original size:21 final size:22
Alignment explanation
Indices: 2303927--2303979 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
2303917 ACGTATAATT
*
2303927 ATAAATTAGTTTAAAATTTAAAG
1 ATAAATTA-TTTAAAATTAAAAG
*
2303950 ATAAATTATTTAAAA-TAAAAT
1 ATAAATTATTTAAAATTAAAAG
*
2303971 ATTAATTAT
1 ATAAATTAT
2303980 ATTATTTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 12 0.44
22 7 0.26
23 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
ATAAATTATTTAAAATTAAAAG
Found at i:2304311 original size:40 final size:41
Alignment explanation
Indices: 2304240--2304318 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 41
2304230 GGGAACTTCG
2304240 TTTATGTTTGTTTATTTATTAAACGAACGAACATGAACAAGAT
1 TTTATGTTTGTTTA--TATTAAACGAACGAACATGAACAAGAT
*
2304283 TTTATGTTTGTTTA-ATTAAATGAACGAACATGAACA
1 TTTATGTTTGTTTATATTAAACGAACGAACATGAACA
2304319 GAATGTTCGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 21 0.60
43 14 0.40
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (41 bp):
TTTATGTTTGTTTATATTAAACGAACGAACATGAACAAGAT
Found at i:2307624 original size:29 final size:30
Alignment explanation
Indices: 2307584--2307654 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
2307574 AATGTAATAT
*
2307584 ATTTTACGTAAAACAGTTTT-AGGTAATTC
1 ATTTTACATAAAACAGTTTTCAGGTAATTC
* *
2307613 ATTTTATATAAAACAGTTTTCATGTAATTC
1 ATTTTACATAAAACAGTTTTCAGGTAATTC
2307643 ATTTTACATAAA
1 ATTTTACATAAA
2307655 TTATTTTCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (30 bp):
ATTTTACATAAAACAGTTTTCAGGTAATTC
Found at i:2307642 original size:30 final size:29
Alignment explanation
Indices: 2307575--2307654 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
2307565 TTTCCAGAAA
*
2307575 ATGTAATAT-ATTTTACGTAAAACAGTTTT
1 ATGTAAT-TCATTTTACATAAAACAGTTTT
* *
2307604 AGGTAATTCATTTTATATAAAACAGTTTT
1 ATGTAATTCATTTTACATAAAACAGTTTT
2307633 CATGTAATTCATTTTACATAAA
1 -ATGTAATTCATTTTACATAAA
2307655 TTATTTTCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 1 0.02
29 24 0.55
30 19 0.43
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (29 bp):
ATGTAATTCATTTTACATAAAACAGTTTT
Found at i:2308216 original size:16 final size:17
Alignment explanation
Indices: 2308185--2308218 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
2308175 CAATAATTTT
2308185 AAATACTTAATTTAAAAA
1 AAATACTT-ATTTAAAAA
2308203 AAATACTT-TTTAAAAA
1 AAATACTTATTTAAAAA
2308219 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATACTTATTTAAAAA
Found at i:2308760 original size:17 final size:18
Alignment explanation
Indices: 2308734--2308769 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2308724 TTACGTTAAG
2308734 ATTTT-TTTTTTAAAAAT
1 ATTTTATTTTTTAAAAAT
2308751 ATTTTATTTTTTAAAAAT
1 ATTTTATTTTTTAAAAAT
2308769 A
1 A
2308770 AAAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATTTTTTAAAAAT
Found at i:2309070 original size:13 final size:13
Alignment explanation
Indices: 2309054--2309078 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2309044 TATCATTTTT
2309054 ATTTATTAAAAAA
1 ATTTATTAAAAAA
2309067 ATTTATTAAAAA
1 ATTTATTAAAAA
2309079 TTGAAATTTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTATTAAAAAA
Found at i:2309183 original size:3 final size:3
Alignment explanation
Indices: 2309177--2309224 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
2309167 TCGTCCTGAA
* *
2309177 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAA TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2309224 T
1 T
2309225 TTTTACAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2309201 original size:20 final size:20
Alignment explanation
Indices: 2309176--2309224 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
2309166 TTCGTCCTGA
*
2309176 ATATTATTATTATTATTATT
1 ATATTATTATTATTATTAAT
2309196 ATATTATTATTATTATTAAT
1 ATATTATTATTATTATTAAT
2309216 ATAATTATT
1 AT-ATTATT
2309225 TTTTACAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTATTATTATTATTAAT
Found at i:2309850 original size:33 final size:33
Alignment explanation
Indices: 2309804--2309867 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
2309794 CTCGTCTAAG
2309804 TCGTTTGGATGCAATAT-ATAGAGTTAAAGGACT
1 TCGTTTGGATGCAAT-TGATAGAGTTAAAGGACT
*
2309837 TCGTTTGGGTGCAATTGATAGAGTTAAAGGA
1 TCGTTTGGATGCAATTGATAGAGTTAAAGGA
2309868 ATGGGATTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (33 bp):
TCGTTTGGATGCAATTGATAGAGTTAAAGGACT
Found at i:2313880 original size:27 final size:27
Alignment explanation
Indices: 2313849--2313939 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 27
2313839 ATTTTGTTAT
*
2313849 AATTATATAATATGTCGTAAATTTTAA
1 AATTATAGAATATGTCGTAAATTTTAA
* *
2313876 AATTATAGAATAT-TCTATAATTATTTTGTTAT
1 AATTATAGAATATGTC-GTAA--A--TT-TTAA
*
2313908 AATTATAGAATATGTCGTAACTTTTAA
1 AATTATAGAATATGTCGTAAATTTTAA
2313935 AATTA
1 AATTA
2313940 AAATAAATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
26 2 0.04
27 23 0.45
28 2 0.04
29 1 0.02
31 2 0.04
32 19 0.37
33 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (27 bp):
AATTATAGAATATGTCGTAAATTTTAA
Found at i:2313912 original size:32 final size:32
Alignment explanation
Indices: 2313837--2313923 Score: 96
Period size: 27 Copynumber: 2.9 Consensus size: 32
2313827 GTTATAAATT
* *
2313837 TTATTTTGTTATAATTATATAATATGTCGTAA
1 TTATTTTGTTATAATTATAGAATATGTCATAA
*
2313869 --A--TT-TTAAAATTATAGAATAT-TCTATAA
1 TTATTTTGTTATAATTATAGAATATGTC-ATAA
2313896 TTATTTTGTTATAATTATAGAATATGTC
1 TTATTTTGTTATAATTATAGAATATGTC
2313924 GTAACTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
26 2 0.05
27 18 0.41
28 2 0.05
29 1 0.02
30 1 0.02
31 2 0.05
32 16 0.36
33 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (32 bp):
TTATTTTGTTATAATTATAGAATATGTCATAA
Found at i:2323261 original size:50 final size:50
Alignment explanation
Indices: 2323186--2323285 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2323176 TGGAATGGTC
2323186 GTACAAGTTGTCATTGTAAGTGTCTTTGCTCCAAAAAAGTTGACAGAATA
1 GTACAAGTTGTCATTGTAAGTGTCTTTGCTCCAAAAAAGTTGACAGAATA
2323236 GTACAAGTTGTCATTGTAAGTGTCTTTGCTCCAAAAAAGTTGACAGAATA
1 GTACAAGTTGTCATTGTAAGTGTCTTTGCTCCAAAAAAGTTGACAGAATA
2323286 AGTAGATTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (50 bp):
GTACAAGTTGTCATTGTAAGTGTCTTTGCTCCAAAAAAGTTGACAGAATA
Found at i:2331960 original size:17 final size:18
Alignment explanation
Indices: 2331938--2331972 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2331928 TTTTACCGGA
2331938 TTAAAAACCGG-TTTTTT
1 TTAAAAACCGGATTTTTT
*
2331955 TTAAAAATCGGATTTTTT
1 TTAAAAACCGGATTTTTT
2331973 CAAACCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAAAAACCGGATTTTTT
Found at i:2335035 original size:82 final size:83
Alignment explanation
Indices: 2334935--2335236 Score: 322
Period size: 83 Copynumber: 3.7 Consensus size: 83
2334925 AAATGGTAAA
* * * * * * *
2334935 TTTAGCGGCGTATGTATACAAATGTCGCAGTAGGGTTCATATATAGTGGCATTTGTT-CAAAAAA
1 TTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTAATATATAGTGACATTTGTTACAACAAA
2334999 CACCGCAACAGATAGTAC
66 CACCGCAACAGATAGTAC
* * * * * *
2335017 TTTAGCGGTGTTTTTATACAAATGCCGTAATAGGGTTCATATATAGTGGC-GTCGTTACAACAAA
1 TTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTAATATATAGTGACATTTGTTACAACAAA
*
2335081 CACCGCAACAAATAAGTAC
66 CACCGCAACAGAT-AGTAC
* * * * *
2335100 TTTAGCGGCATTTTTATACAAATGCCGTAATAGGGTTAATCTATAGTGACATTT-TTCCAACAAG
1 TTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTAATATATAGTGACATTTGTTACAACAAA
* * *
2335164 CGCCACAATAGAGTAGTAC
66 CACCGCAACAGA-TAGTAC
* * ** *
2335183 TTTAGCAGTGTTTTTATAGGAATGCCACAATAGGGTTAATATATAGTGACATTT
1 TTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTAATATATAGTGACATTT
2335237 TTTCAATAAA
Statistics
Matches: 185, Mismatches: 31, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
81 4 0.02
82 62 0.34
83 117 0.63
84 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (83 bp):
TTTAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTAATATATAGTGACATTTGTTACAACAAA
CACCGCAACAGATAGTAC
Found at i:2335129 original size:83 final size:82
Alignment explanation
Indices: 2334935--2335147 Score: 284
Period size: 82 Copynumber: 2.6 Consensus size: 82
2334925 AAATGGTAAA
* * * * * * *
2334935 TTTAGCGGCGTATGTATACAAATGTCGCAGTAGGGTTCATATATAGTGGCATTTGTTCAAAAAAC
1 TTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCATATATAGTGGCAGTCGTTCAAAAAAC
*
2335000 ACCGCAACAGATAGTAC
66 ACCGCAACAAATAGTAC
* *
2335017 TTTAGCGGTGTTTTTATACAAATGCCGTAATAGGGTTCATATATAGTGGC-GTCGTTACAACAAA
1 TTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCATATATAGTGGCAGTCGTT-CAAAAAA
2335081 CACCGCAACAAATAAGTAC
65 CACCGCAACAAAT-AGTAC
* * *
2335100 TTTAGCGGCATTTTTATACAAATGCCGTAATAGGGTTAATCTATAGTG
1 TTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCATATATAGTG
2335148 ACATTTTTCC
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
81 4 0.03
82 62 0.54
83 49 0.43
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (82 bp):
TTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCATATATAGTGGCAGTCGTTCAAAAAAC
ACCGCAACAAATAGTAC
Found at i:2335470 original size:41 final size:41
Alignment explanation
Indices: 2335364--2335454 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
2335354 CTTTTTGATA
* * * * *
2335364 AAACGCCGCAAAATACTCTTACTTTAGTGGTATTTGTATAC
1 AAACGCCGCGAAAGACACATACTTTAGTGGTATTTGTAAAC
* * *
2335405 AAACGCTGCGAAAGACACATACTTTCGTGGTGTTTGTAAAC
1 AAACGCCGCGAAAGACACATACTTTAGTGGTATTTGTAAAC
2335446 AAACGCCGC
1 AAACGCCGC
2335455 TATAGACTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (41 bp):
AAACGCCGCGAAAGACACATACTTTAGTGGTATTTGTAAAC
Found at i:2339647 original size:19 final size:21
Alignment explanation
Indices: 2339620--2339662 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
2339610 CTCTCGGCTT
*
2339620 ATGAGAAAA-TTAT-CTAAGC
1 ATGACAAAAGTTATACTAAGC
*
2339639 ATGACAAAAGTTATACTTAGC
1 ATGACAAAAGTTATACTAAGC
2339660 ATG
1 ATG
2339663 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (21 bp):
ATGACAAAAGTTATACTAAGC
Found at i:2339972 original size:27 final size:26
Alignment explanation
Indices: 2339933--2339983 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
2339923 GAAGGAGCAT
* *
2339933 TGACTAGATCTTCTAGAAAATTACCGC
1 TGACTAGACCTTCTA-AAAACTACCGC
*
2339960 TGACTGGACCTTCTAAAAACTACC
1 TGACTAGACCTTCTAAAAACTACC
2339984 ACGTCATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (26 bp):
TGACTAGACCTTCTAAAAACTACCGC
Found at i:2346380 original size:21 final size:21
Alignment explanation
Indices: 2346351--2346393 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2346341 TTATCATTGC
*
2346351 AAGAATTCATGGCCTCTACAA
1 AAGAATTCATGGCCTCCACAA
* *
2346372 AAGATTTCATGGCTTCCACAA
1 AAGAATTCATGGCCTCCACAA
2346393 A
1 A
2346394 GACCTTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (21 bp):
AAGAATTCATGGCCTCCACAA
Found at i:2368798 original size:32 final size:32
Alignment explanation
Indices: 2368757--2368826 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
2368747 ATGTGTAGAA
2368757 TATCTTTGGTAGATTGCAATACTATTTGCTCT
1 TATCTTTGGTAGATTGCAATACTATTTGCTCT
2368789 TATCTTTGGTAGATTGCAATACTATTTGCTCT
1 TATCTTTGGTAGATTGCAATACTATTTGCTCT
2368821 TA-CTTT
1 TATCTTT
2368827 TCCCCTGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 34 0.89
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (32 bp):
TATCTTTGGTAGATTGCAATACTATTTGCTCT
Found at i:2372620 original size:11 final size:11
Alignment explanation
Indices: 2372606--2372632 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2372596 TACAAATAAT
2372606 ATAATTACTAA
1 ATAATTACTAA
2372617 ATAATTACTAA
1 ATAATTACTAA
2372628 ATAAT
1 ATAAT
2372633 ATTTAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATTACTAA
Found at i:2372954 original size:27 final size:24
Alignment explanation
Indices: 2372916--2372979 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 24
2372906 ATATATATAT
*
2372916 ATATATGAAATAGTGAATGAAATAAAA
1 ATATATAAAATA-TGAA-GAAA-AAAA
2372943 ATATATAAAATATGAAG-AAAAAA
1 ATATATAAAATATGAAGAAAAAAA
2372966 A-AT-TAAAATATGAA
1 ATATATAAAATATGAA
2372980 AAACCAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 11 0.31
22 2 0.06
23 5 0.14
24 2 0.06
25 1 0.03
26 4 0.11
27 11 0.31
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (24 bp):
ATATATAAAATATGAAGAAAAAAA
Found at i:2372957 original size:22 final size:20
Alignment explanation
Indices: 2372932--2372982 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 20
2372922 GAAATAGTGA
*
2372932 ATGAAATAAAAATATATAAAAT
1 ATGAAA-AAAAAAAT-TAAAAT
2372954 ATGAAGAAAAAAAATTAAAAT
1 ATGAA-AAAAAAAATTAAAAT
2372975 ATGAAAAA
1 ATGAAAAA
2372983 CCAGATTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 11 0.41
22 12 0.44
23 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (20 bp):
ATGAAAAAAAAAATTAAAAT
Found at i:2375027 original size:21 final size:22
Alignment explanation
Indices: 2375003--2375044 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2374993 GCTCTAGTTC
2375003 TTAAAAA-AGAATATATCATCT
1 TTAAAAACAGAATATATCATCT
*
2375024 TTAAAAACAGAATTTATCATC
1 TTAAAAACAGAATATATCATC
2375045 CTTGTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (22 bp):
TTAAAAACAGAATATATCATCT
Found at i:2387078 original size:31 final size:31
Alignment explanation
Indices: 2387043--2387105 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2387033 AGATCAAATT
* *
2387043 AAATTGATAGCTTTACCTTTCTCTTTAGCCG
1 AAATTGACAACTTTACCTTTCTCTTTAGCCG
**
2387074 AAATTGACAACTTTGTCTTTCTCTTTAGCCG
1 AAATTGACAACTTTACCTTTCTCTTTAGCCG
2387105 A
1 A
2387106 CTTGGCTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (31 bp):
AAATTGACAACTTTACCTTTCTCTTTAGCCG
Found at i:2392095 original size:5 final size:5
Alignment explanation
Indices: 2392047--2392076 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2392037 TTTCATTCAA
2392047 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
2392077 GAGATACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:2399341 original size:40 final size:40
Alignment explanation
Indices: 2399297--2399663 Score: 136
Period size: 40 Copynumber: 9.2 Consensus size: 40
2399287 ACCCCGTACG
*
2399297 ATACATCACCTTGCTTATCA-TTGGGTTTGTATCCCATACA
1 ATACATCACCTTGCTTAT-AGTTGGGTGTGTATCCCATACA
* * * * * *
2399337 ATACATTACCACTT--TTATATTTAGATGTGTA-CCACGTACG
1 ATACATCA-C-CTTGCTTATAGTTGGGTGTGTATCC-CATACA
* *
2399377 ATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCATACA
1 ATACATCACCTTGCTTATAGTTGGGTGTGTATCCCATACA
* * * * * **
2399417 ATACATCA-C-T-CTTCATATTTAGATGTTTA-CCCTGTATG
1 ATACATCACCTTGCTT-ATAGTTGGGTGTGTATCCC-ATACA
* * * * *
2399455 ATACATCATCTTGCTTGTAATTAGGTGTGTATCCCGTACA
1 ATACATCACCTTGCTTATAGTTGGGTGTGTATCCCATACA
* * *** *
2399495 ATACATCACCACCTT-CTTAT--TTAGATGTGTA-CTTTGTACG
1 ATACAT---CACCTTGCTTATAGTTGGGTGTGTATC-CCATACA
* * * *
2399535 ATACATCACCTTGCTTGTAG-AGGGGGTTGTATCCCGTACA
1 ATACATCACCTTGCTTATAGTTGGGTG-TGTATCCCATACA
* * * * * * *
2399575 ATACATCACCACTT--TCATATTTAGATGTATA-CCCCTACG
1 ATACATCA-C-CTTGCTTATAGTTGGGTGTGTATCCCATACA
* * *
2399614 ATACATCATCTTGTTTGTAGTTGGGTGTGTATCCCATACA
1 ATACATCACCTTGCTTATAGTTGGGTGTGTATCCCATACA
2399654 ATACATCACC
1 ATACATCACC
2399664 ACTTTCATAT
Statistics
Matches: 237, Mismatches: 62, Indels: 56
0.67 0.17 0.16
Matches are distributed among these distances:
37 15 0.06
38 28 0.12
39 33 0.14
40 133 0.56
41 13 0.05
42 10 0.04
43 5 0.02
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (40 bp):
ATACATCACCTTGCTTATAGTTGGGTGTGTATCCCATACA
Found at i:2399408 original size:80 final size:79
Alignment explanation
Indices: 2399275--2399676 Score: 506
Period size: 80 Copynumber: 5.1 Consensus size: 79
2399265 TTTGTTACTC
* * * * *
2399275 ATTTAGGTGTGCACCCCGTACGATACATCACCTTGCTTATCA-TTGGGTTTGTATCCCATACAAT
1 ATTTAGATGTGTA-CCCGTACGATACATCATCTTGCTTGT-AGTTGGGTGTGTATCCCATACAAT
* *
2399339 ACATTACCACTTTTAT
64 ACATCACCACTTTCAT
2399355 ATTTAGATGTGTACCACGTACGATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCATACAATA
1 ATTTAGATGTGTACC-CGTACGATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCATACAATA
*
2399420 CATCA-CTC-TTCAT
65 CATCACCACTTTCAT
* * * * *
2399433 ATTTAGATGTTTACCCTGTATGATACATCATCTTGCTTGTAATTAGGTGTGTATCCCGTACAATA
1 ATTTAGATGTGTACCC-GTACGATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCATACAATA
* *
2399498 CATCACCACCTTCTT
65 CATCACCACTTTCAT
** * * * *
2399513 ATTTAGATGTGTACTTTGTACGATACATCACCTTGCTTGTAG-AGGGGGTTGTATCCCGTACAAT
1 ATTTAGATGTGTAC-CCGTACGATACATCATCTTGCTTGTAGTTGGGTG-TGTATCCCATACAAT
2399577 ACATCACCACTTTCAT
64 ACATCACCACTTTCAT
* * *
2399593 ATTTAGATGTATACCCCTACGATACATCATCTTGTTTGTAGTTGGGTGTGTATCCCATACAATAC
1 ATTTAGATGTGTACCCGTACGATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCATACAATAC
2399658 ATCACCACTTTCAT
66 ATCACCACTTTCAT
2399672 ATTTA
1 ATTTA
2399677 AAATTCTAGA
Statistics
Matches: 279, Mismatches: 35, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.00
78 67 0.24
79 67 0.24
80 144 0.52
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (79 bp):
ATTTAGATGTGTACCCGTACGATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCATACAATAC
ATCACCACTTTCAT
Found at i:2399566 original size:158 final size:159
Alignment explanation
Indices: 2399289--2399676 Score: 514
Period size: 158 Copynumber: 2.4 Consensus size: 159
2399279 AGGTGTGCAC
* * * * * *
2399289 CCCGTACGATACATCACCTTGCTTATCATTGGGTTTGTATCCCATACAATACATTACCA-CTTTT
1 CCCGTACGATACATCATCTTGCTTGTAATTGGGTGTGTATCCCATACAATACATCACCACCTTCT
* **
2399353 ATATTTAGATGTGTACCACGTACGATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCATACAA
66 -TATTTAGATGTGTACCACGTACGATACATCACCTTGCTTGTAGGGGGGTGTGTATCCCATACAA
* *
2399418 TACATCA-CTC-TTCATATTTAGATGTTTA
130 TACATCACCACTTTCATATTTAGATGTATA
* * *
2399446 CCCTGTATGATACATCATCTTGCTTGTAATTAGGTGTGTATCCCGTACAATACATCACCACCTTC
1 CCC-GTACGATACATCATCTTGCTTGTAATTGGGTGTGTATCCCATACAATACATCACCACCTTC
*** *
2399511 TTATTTAGATGTGTACTTTGTACGATACATCACCTTGCTTGTAGAGGGGGT-TGTATCCCGTACA
65 TTATTTAGATGTGTACCACGTACGATACATCACCTTGCTTGTAG-GGGGGTGTGTATCCCATACA
2399575 ATACATCACCACTTTCATATTTAGATGTATA
129 ATACATCACCACTTTCATATTTAGATGTATA
* * * * *
2399606 CCCCTACGATACATCATCTTGTTTGTAGTTGGGTGTGTATCCCATACAATACATCACCACTTTCA
1 CCCGTACGATACATCATCTTGCTTGTAATTGGGTGTGTATCCCATACAATACATCACCACCTTCT
2399671 TATTTA
66 TATTTA
2399677 AAATTCTAGA
Statistics
Matches: 200, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
157 3 0.01
158 107 0.54
159 70 0.35
160 20 0.10
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (159 bp):
CCCGTACGATACATCATCTTGCTTGTAATTGGGTGTGTATCCCATACAATACATCACCACCTTCT
TATTTAGATGTGTACCACGTACGATACATCACCTTGCTTGTAGGGGGGTGTGTATCCCATACAAT
ACATCACCACTTTCATATTTAGATGTATA
Found at i:2400697 original size:12 final size:12
Alignment explanation
Indices: 2400667--2400706 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2400657 TTCAAAGAAA
2400667 TTAAAA-TTATT
1 TTAAAATTTATT
2400678 TT--AATTTATT
1 TTAAAATTTATT
2400688 TTAAAATTTATT
1 TTAAAATTTATT
2400700 TTAAAAT
1 TTAAAAT
2400707 ATGGATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.08
10 7 0.27
11 2 0.08
12 15 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:2400718 original size:22 final size:22
Alignment explanation
Indices: 2400693--2401097 Score: 581
Period size: 22 Copynumber: 18.6 Consensus size: 22
2400683 TTATTTTAAA
2400693 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2400715 ATTTATTTTTAAAATATGGATTG
1 ATTTA-TTTTAAAATATGGATTG
*
2400738 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
2400760 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2400782 ATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTG
*
2400804 ATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTG
**
2400826 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
2400847 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
2400870 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2400892 CTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
2400914 ----A-TTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
2400931 ATTCATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2400953 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
2400975 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
2400997 ATTTATTTTAAAATATGGGA-AA
1 ATTTATTTTAAAATAT-GGATTG
2401019 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
2401041 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
2401063 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2401085 ATTTATTTTAAAA
1 ATTTATTTTAAAA
2401098 AATTTATTAT
Statistics
Matches: 343, Mismatches: 30, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
17 13 0.04
18 1 0.00
21 5 0.01
22 298 0.87
23 26 0.08
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:2400920 original size:17 final size:17
Alignment explanation
Indices: 2400898--2400957 Score: 66
Period size: 17 Copynumber: 3.2 Consensus size: 17
2400888 ATTGCTTTAT
2400898 TTTAAAATATGGATTGA
1 TTTAAAATATGGATTGA
*
2400915 TTTAAAATATGGAAAAATTCA
1 TTTAAAATATGG----ATTGA
2400936 TTTTAAAATATGGATTGA
1 -TTTAAAATATGGATTGA
2400954 TTTA
1 TTTA
2400958 TTTTAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 16 0.44
18 4 0.11
21 4 0.11
22 12 0.33
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (17 bp):
TTTAAAATATGGATTGA
Found at i:2403456 original size:100 final size:101
Alignment explanation
Indices: 2403250--2403542 Score: 507
Period size: 100 Copynumber: 2.9 Consensus size: 101
2403240 TTTAAAGTTG
*
2403250 AACTCGAATTAAGTTCATTCGAATTAAATATTAACTAAATTTTAAACTAGTCAAACTTGAATAAC
1 AACTCGAATTAAGTTCATTCGAATTAAGTATTAACTAAATTTTAAACTAGTCAAACTTGAATAAC
2403315 TTATCATCCATCTCAACTCATTTACAACCTTTATAT
66 TTATCATCCATCTCAACTCATTTACAACCTTTATAT
*
2403351 AACTCGAATTAAGTTCATTCGAATCAAGTATTAACTAAATTTTAAACTAGTC-AACTTGAATAAC
1 AACTCGAATTAAGTTCATTCGAATTAAGTATTAACTAAATTTTAAACTAGTCAAACTTGAATAAC
* * *
2403415 TTATCAGCGATCTCAACTCATTTACAACCTTTATGT
66 TTATCATCCATCTCAACTCATTTACAACCTTTATAT
*
2403451 AACTCGAATTAAGTTCATTCAAATTAAGTATTAACTAAATTTTAAACTAGTCAAACTTGAATAAC
1 AACTCGAATTAAGTTCATTCGAATTAAGTATTAACTAAATTTTAAACTAGTCAAACTTGAATAAC
* *
2403516 CTATCATCTATCTCAACTCATTTACAA
66 TTATCATCCATCTCAACTCATTTACAA
2403543 AGCATCTTAG
Statistics
Matches: 181, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
100 95 0.52
101 86 0.48
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (101 bp):
AACTCGAATTAAGTTCATTCGAATTAAGTATTAACTAAATTTTAAACTAGTCAAACTTGAATAAC
TTATCATCCATCTCAACTCATTTACAACCTTTATAT
Found at i:2403576 original size:8 final size:8
Alignment explanation
Indices: 2403551--2403589 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
2403541 AAAGCATCTT
*
2403551 AGAGAGAG
1 AGAGAGGG
*
2403559 AGAGGGGGG
1 AGA-GAGGG
2403568 AGAGAGGG
1 AGAGAGGG
2403576 AGAGAGGG
1 AGAGAGGG
2403584 AGAGAG
1 AGAGAG
2403590 AGAGTAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:2404060 original size:101 final size:101
Alignment explanation
Indices: 2403885--2404088 Score: 327
Period size: 101 Copynumber: 2.0 Consensus size: 101
2403875 TTTGAAGTTG
* **
2403885 AACTCGAATTAAGTTCATTCGAATTAAATATTATCTAAATTTTAAACTCGTCAAACTTGAATAAC
1 AACTCGAATTAAGTTCATTCGAATTAAATATTAACTAAATTTTAAACTAATCAAACTTGAATAAC
* * *
2403950 TTATCATCTATTTCAACTCATTTACAACCTTTATAT
66 CTATCATCTATCTCAACTCATTTACAACCTTCATAT
* * *
2403986 AACTCGAATTAAGTTCATTTGAATTAAGTGTTAACTAAATTTTAAACTAATCAAACTTGAATAAC
1 AACTCGAATTAAGTTCATTCGAATTAAATATTAACTAAATTTTAAACTAATCAAACTTGAATAAC
2404051 CTATCATCTATCTCAACTCATTTACAACCTTCATAT
66 CTATCATCTATCTCAACTCATTTACAACCTTCATAT
2404087 AA
1 AA
2404089 TGTGAACACT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (101 bp):
AACTCGAATTAAGTTCATTCGAATTAAATATTAACTAAATTTTAAACTAATCAAACTTGAATAAC
CTATCATCTATCTCAACTCATTTACAACCTTCATAT
Found at i:2413951 original size:2 final size:2
Alignment explanation
Indices: 2413944--2413968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2413934 TATCAGAAGC
2413944 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2413969 GGCTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2416229 original size:98 final size:94
Alignment explanation
Indices: 2416065--2416257 Score: 325
Period size: 98 Copynumber: 2.0 Consensus size: 94
2416055 CAGAAAACCT
2416065 TATAATCATACTTCATAAAAGATAAGATGGCTGGAATTCGCCATTCAAATCCAATAAACTGAAGG
1 TATAATCATACTTCATAAAAGATAAGATGGCTGGAATTCGCCATTCAAATCCAATAAACTGAAGG
2416130 ACCAC-ATGAAGCTCAAAACAATCACTTG
66 ACCACAATGAAGCTCAAAACAATCACTTG
2416158 TATAATCATACTTCATAAAAGAGATAAGATATGGCTGGAATTTCGCCATTCAAATCCAATAAACT
1 TATAATCATACTTCAT-AAA-AGATAAG--ATGGCTGGAA-TTCGCCATTCAAATCCAATAAACT
2416223 GAAGGACCACAGATGAAGCTCAAAACAATCACTTG
61 GAAGGACCACA-ATGAAGCTCAAAACAATCACTTG
2416258 ACCACTTCTA
Statistics
Matches: 93, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
93 16 0.17
94 3 0.03
95 7 0.08
97 10 0.11
98 34 0.37
100 23 0.25
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (94 bp):
TATAATCATACTTCATAAAAGATAAGATGGCTGGAATTCGCCATTCAAATCCAATAAACTGAAGG
ACCACAATGAAGCTCAAAACAATCACTTG
Found at i:2418594 original size:25 final size:25
Alignment explanation
Indices: 2418565--2418614 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2418555 GTCTTTCTTT
2418565 GCAGGTTGGGTGATGGCTTTATAGC
1 GCAGGTTGGGTGATGGCTTTATAGC
2418590 GCAGGTTGGGTGATGGCTTTATAGC
1 GCAGGTTGGGTGATGGCTTTATAGC
2418615 CATCACCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.32
Consensus pattern (25 bp):
GCAGGTTGGGTGATGGCTTTATAGC
Found at i:2418968 original size:3 final size:3
Alignment explanation
Indices: 2418960--2419024 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
2418950 TTTAAATATT
* * * *
2418960 TAA TAA TAA T-A TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2419007 TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2419025 ATAAATCAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2418975 original size:18 final size:17
Alignment explanation
Indices: 2418960--2419028 Score: 86
Period size: 18 Copynumber: 4.0 Consensus size: 17
2418950 TTTAAATATT
2418960 TAATAATAATATAATAA
1 TAATAATAATATAATAA
*
2418977 TAATAATATTTATAATAA
1 TAATAATA-ATATAATAA
* *
2418995 TAATAATTATTATAGTAA
1 TAATAA-TAATATAATAA
2419013 TAATAATAATA-AATAA
1 TAATAATAATATAATAA
2419029 ATCAAAATGG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
16 4 0.09
17 12 0.26
18 28 0.61
19 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:2419499 original size:121 final size:120
Alignment explanation
Indices: 2419257--2420153 Score: 937
Period size: 121 Copynumber: 7.6 Consensus size: 120
2419247 GAGTCATTCC
* * *
2419257 AAAGGTTGAATAAG--CTTCTTATTTTGAACTTCTTCTT--TTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * ** *
2419318 ATGAAC-TTCTCTGGAAAGGTTGATGCTAATCTATCTGCTTCTGTGATAGAACTATGCA
66 ATGAACATTCTCTGGAAAAGTTGATGC-CATCTATCTACTTC--TGATAGGTCGA-GCA
* * *
2419376 AAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
2419440 ATGAACTTTCTCTGGAAAAGTTGGTGCCGATCTATCTCCTTCTGATAGCGTCGAGCA
66 ATGAACATTCTCTGGAAAAGTTGATGCC-ATCTATCTACTTCTGATAG-GTCGAGCA
* *
2419497 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * **** *
2419562 ATGAACACT-TCTGGCAAA-TTGAT-CCATC-A---AGAGATGA-A-TTCGAGCA
66 ATGAACATTCTCTGGAAAAGTTGATGCCATCTATCTACTTCTGATAGGTCGAGCA
2419608 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
2419672 ATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCA
66 ATGAACATTCTCTGGAAAAGTTGATGCC-ATCTATCTACTTC--TGATAG-GTCGAGCA
* *
2419731 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * **** *
2419796 ATGAACACT-TCTGGCAAATGTTTAT-CCATC-A---AGAGATGA-A-TTCGAGCA
66 ATGAACATTCTCTGG-AAAAGTTGATGCCATCTATCTACTTCTGATAGGTCGAGCA
* *
2419844 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
2419909 ATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCA
66 ATGAACATTCTCTGGAAAAGTTGATGCC-ATCTATCTACTTC--TGATAG-GTCGAGCA
* * *
2419968 AAAGATTAAACAAG---TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * **** *
2420030 ATGAACACT-TCTGGCAAAGTTTAT-CCATC-A---AGAGATGA-A-TTCGAGCA
66 ATGAACATTCTCTGGAAAAGTTGATGCCATCTATCTACTTCTGATAGGTCGAGCA
*
2420077 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
2420142 ATGAACACTTCT
66 ATGAACA-TTCT
2420154 GGCAAATGTT
Statistics
Matches: 655, Mismatches: 83, Indels: 85
0.80 0.10 0.10
Matches are distributed among these distances:
109 18 0.03
110 66 0.10
111 19 0.03
112 62 0.09
113 87 0.13
114 14 0.02
115 5 0.01
116 4 0.01
117 2 0.00
118 6 0.01
119 17 0.03
120 20 0.03
121 133 0.20
122 63 0.10
123 47 0.07
124 92 0.14
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (120 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACATTCTCTGGAAAAGTTGATGCCATCTATCTACTTCTGATAGGTCGAGCA
Found at i:2419750 original size:124 final size:119
Alignment explanation
Indices: 2419591--2420171 Score: 657
Period size: 113 Copynumber: 4.9 Consensus size: 119
2419581 TGATCCATCA
*
2419591 AGAGATGAATTCGAGCAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 AGAGATGAAGTCGAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
**
2419655 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTC
66 GATGAGTTCTTCTCATTATGAACACT-TCTGGAAAAGTTGAT-CC-ATCTA--TCCTTC
* * * *
2419714 TGTGAT-AGCGTCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
1 AGAGATGA-AGTCGAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
2419778 AGATGAGTTCTTCTCATTATGAACACTTCTGGCAAA--TG-T---T-TATCCATC
65 AGATGAGTTCTTCTCATTATGAACACTTCTGGAAAAGTTGATCCATCTATCCTTC
* *
2419826 AAGAGATGAATTCGAGCAAAA-AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTT
1 -AGAGATGAAGTCGAGCAAAAGA-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
**
2419890 CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTC
64 CAGATGAGTTCTTCTCATTATGAACACT-TCTGGAAAAGTTGAT-CC-ATCTA--TCCTTC
* * * * *
2419951 TGTGAT-AGCGTCGAGCAAAAGATTAAACAAG---TTCTCATTATGAATTTCTTCTTCCTTCTTC
1 AGAGATGA-AGTCGAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
2420012 AGATGAGTTCTTCTCATTATGAACACTTCTGGCAAAGTTTATCCATC-A------
65 AGATGAGTTCTTCTCATTATGAACACTTCTGGAAAAGTTGATCCATCTATCCTTC
*
2420060 AGAGATGAATTCGAGCAAAA-AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
1 AGAGATGAAGTCGAGCAAAAGA-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
2420124 AGATGAGTTCTTCTCATTATGAACACTTCTGGCAAATGTTTATCCATC
65 AGATGAGTTCTTCTCATTATGAACACTTCTGG-AAAAGTTGATCCATC
2420172 AAGAGATGAA
Statistics
Matches: 395, Mismatches: 38, Indels: 60
0.80 0.08 0.12
Matches are distributed among these distances:
108 1 0.00
109 22 0.06
110 1 0.00
112 67 0.17
113 92 0.23
114 11 0.03
115 1 0.00
116 2 0.01
117 2 0.01
118 3 0.01
119 2 0.01
120 14 0.04
121 55 0.14
122 2 0.01
123 26 0.07
124 88 0.22
125 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (119 bp):
AGAGATGAAGTCGAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGAGTTCTTCTCATTATGAACACTTCTGGAAAAGTTGATCCATCTATCCTTC
Found at i:2419942 original size:237 final size:236
Alignment explanation
Indices: 2419373--2420147 Score: 1413
Period size: 234 Copynumber: 3.3 Consensus size: 236
2419363 ATAGAACTAT
* * * *
2419373 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
2419437 ATTATGAACTTTCTCTGGAAAAGTTGGTGCCGATCTATCTCCTTC--TGATAGCGTCGAGCAAAA
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAA
2419500 GATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
131 GATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
*
2419565 AACACTTCTGGCAAA-TTGATCCATCAAGAGATGAATTCGA
196 AACACTTCTGGCAAAGTTTATCCATCAAGAGATGAATTCGA
2419605 GC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2419669 ATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAA
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAA
2419734 GATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
131 GATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
2419799 AACACTTCTGGCAAATGTTTATCCATCAAGAGATGAATTCGA
196 AACACTTCTGGCAAA-GTTTATCCATCAAGAGATGAATTCGA
*
2419841 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2419906 ATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAA
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAA
*
2419971 GATTAAACAAG---TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
131 GATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
2420033 AACACTTCTGGCAAAGTTTATCCATCAAGAGATGAATTCGA
196 AACACTTCTGGCAAAGTTTATCCATCAAGAGATGAATTCGA
2420074 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2420139 ATTATGAAC
66 ATTATGAAC
2420148 ACTTCTGGCA
Statistics
Matches: 528, Mismatches: 9, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
231 38 0.07
232 65 0.12
233 99 0.19
234 163 0.31
236 26 0.05
237 137 0.26
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (236 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAA
GATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
AACACTTCTGGCAAAGTTTATCCATCAAGAGATGAATTCGA
Found at i:2420146 original size:346 final size:338
Alignment explanation
Indices: 2419490--2420183 Score: 895
Period size: 346 Copynumber: 2.0 Consensus size: 338
2419480 TCTGATAGCG
2419490 TCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
2419555 TCTCATTATGAACACTTCTGGCAAATTGATCCATCAAGAGATGAATTCGAGCAAAAGTTGAACAA
66 TCTCATTATGAACACTTCTGGAAAATTGATCCATCAAGAGATGAAGTCGAGCAAAAGTTAAACAA
**
2419620 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
131 G-T-TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCT
* * *
2419685 GGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAGATTAAACAAGTTCTT
194 GGAAAAGTTGATGCCGATCTA-------CAGAGATAGAGTCGAGCAAAAGATTAAACAAGTTCTT
2419750 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAAAT
252 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAAAT
2419815 GTTTATCCATCAAGAGATGAAT
317 GTTTATCCATCAAGAGATGAAT
* *
2419837 TCGAGCAAAA-AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTC
1 TCGAGCAAAAGA-TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
** * * *
2419901 TTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGAT-AGCGTCGA
65 TTCTCATTATGAACACT-TCTGGAAAA-TTGAT-CC-ATC-A--------AGAGATGA-AGTCGA
*
2419965 GCAAAAGATTAAACAAG-TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
116 GCAAAAG-TTAAACAAGTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
2420029 TATGAACACT-TCTGGCAAAGTTTAT-CC-ATC-A-AGAGAT-GAATTCGAGCAAAA-AGTTGAA
180 TATGAACACTCTCTGGAAAAGTTGATGCCGATCTACAGAGATAG-AGTCGAGCAAAAGA-TTAAA
2420087 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTT
243 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTT
2420152 CTGGCAAATGTTTATCCATCAAGAGATGAAT
308 CTGGCAAATGTTTATCCATCAAGAGATGAAT
2420183 T
1 T
2420184 TAAATCTTTG
Statistics
Matches: 309, Mismatches: 20, Indels: 37
0.84 0.05 0.10
Matches are distributed among these distances:
345 2 0.01
346 116 0.38
347 75 0.24
348 8 0.03
349 5 0.02
350 2 0.01
351 3 0.01
352 1 0.00
354 1 0.00
355 3 0.01
356 2 0.01
357 13 0.04
358 54 0.17
359 1 0.00
360 15 0.05
361 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (338 bp):
TCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACACTTCTGGAAAATTGATCCATCAAGAGATGAAGTCGAGCAAAAGTTAAACAA
GTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGG
AAAAGTTGATGCCGATCTACAGAGATAGAGTCGAGCAAAAGATTAAACAAGTTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAAATGTTTATCCA
TCAAGAGATGAAT
Found at i:2420644 original size:95 final size:95
Alignment explanation
Indices: 2420481--2420680 Score: 373
Period size: 95 Copynumber: 2.1 Consensus size: 95
2420471 TGCAACATGT
2420481 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
1 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
* *
2420546 GTTCTTTTAATACTGAGAAATCTTGATTTC
66 GTTCTTTTAATACCGAGAAATCTTGAATTC
*
2420576 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCATAGATATCGATA
1 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
2420641 GTTCTTTTAATACCGAGAAATCTTGAATTC
66 GTTCTTTTAATACCGAGAAATCTTGAATTC
2420671 TGATTCTGAT
1 TGATTCTGAT
2420681 GAGGAGAATA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 102 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (95 bp):
TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
GTTCTTTTAATACCGAGAAATCTTGAATTC
Found at i:2421230 original size:83 final size:82
Alignment explanation
Indices: 2421021--2421303 Score: 388
Period size: 83 Copynumber: 3.3 Consensus size: 82
2421011 CAATCAGAAG
* *
2421021 CAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAATTCAATAAATGGTTCTGTG
1 CAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTC----AAT-GAT-TGT-
2421086 GTTCATACCAAACCAGATCAGATAACT
59 -TT--TACCAAACCAGATCAGATAACT
2421113 CAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTACC
1 CAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATGATTG-TTTTACC
2421178 AAACCAGATCAGATAACT
65 AAACCAGATCAGATAACT
* * * *
2421196 CAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCAAAATT-AATGACTGGTTCTAAC
1 CAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATGA-TTGTTTTACC
*
2421260 AAACCAAATCAGATAACT
65 AAACCAGATCAGATAACT
2421278 CAAAGAACACTTCCAGAAGATGCTAT
1 CAAAGAACACTTCCAGAAGATGCTAT
2421304 TGGGTCTTCT
Statistics
Matches: 182, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
82 53 0.29
83 71 0.39
85 2 0.01
86 2 0.01
87 3 0.02
88 3 0.02
92 48 0.26
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (82 bp):
CAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATGATTGTTTTACCA
AACCAGATCAGATAACT
Found at i:2422366 original size:16 final size:17
Alignment explanation
Indices: 2422313--2422367 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
2422303 TTCATAGAAG
*
2422313 AATAAATTGAATTTTCGAA
1 AATAAATTGAATCTT--AA
2422332 AATAAATTGAATCTT-A
1 AATAAATTGAATCTTAA
2422348 AATAAATTGAA-CTTAA
1 AATAAATTGAATCTTAA
2422364 AATA
1 AATA
2422368 GATAGAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 3 0.09
16 17 0.50
19 14 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (17 bp):
AATAAATTGAATCTTAA
Found at i:2422690 original size:1 final size:1
Alignment explanation
Indices: 2422684--2422725 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
2422674 ATCTTGACCC
* * *
2422684 TTTTTTTTTCTTTTTTCTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2422726 CTTCTCTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:2422699 original size:7 final size:7
Alignment explanation
Indices: 2422687--2422730 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
2422677 TTGACCCTTT
2422687 TTTTTTC
1 TTTTTTC
2422694 TTTTTTC
1 TTTTTTC
*
2422701 TTTTTTT
1 TTTTTTC
*
2422708 TTTTTTT
1 TTTTTTC
2422715 TTTTTTC
1 TTTTTTC
2422722 TTTTCTTC
1 TTTT-TTC
2422730 T
1 T
2422731 CTTCAAGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
7 30 0.88
8 4 0.12
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:2422710 original size:21 final size:21
Alignment explanation
Indices: 2422684--2422725 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2422674 ATCTTGACCC
2422684 TTTTTTTTTCTTTTTTCTTTT
1 TTTTTTTTTCTTTTTTCTTTT
*
2422705 TTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTCTTTTTTCTTTT
2422726 CTTCTCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (21 bp):
TTTTTTTTTCTTTTTTCTTTT
Found at i:2429998 original size:15 final size:15
Alignment explanation
Indices: 2429975--2430006 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2429965 TGAAATGAAT
2429975 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2429990 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2430005 AA
1 AA
2430007 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2434345 original size:44 final size:44
Alignment explanation
Indices: 2434297--2434385 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
2434287 TATGTTATTT
2434297 ACCCTAAATATATTATTTTAATATAAAGGACTAAAATAAATAAA
1 ACCCTAAATATATTATTTTAATATAAAGGACTAAAATAAATAAA
2434341 ACCCTAAATATATTATTTTAATATAAAGGACTAAAATAAATAAA
1 ACCCTAAATATATTATTTTAATATAAAGGACTAAAATAAATAAA
2434385 A
1 A
2434386 TTAAAATTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.31
Consensus pattern (44 bp):
ACCCTAAATATATTATTTTAATATAAAGGACTAAAATAAATAAA
Found at i:2435390 original size:3 final size:3
Alignment explanation
Indices: 2435382--2435441 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
2435372 TTAATATATT
* * * *
2435382 TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TTA TTA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2435430 TAA TAA TAA TAA
1 TAA TAA TAA TAA
2435442 ATAAATCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2435391 original size:15 final size:15
Alignment explanation
Indices: 2435373--2435434 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
2435363 TATATATATT
2435373 TAATATATTTAATAA
1 TAATATATTTAATAA
2435388 TAATA-A--TAATAA
1 TAATATATTTAATAA
*
2435400 TAAT-TATAATAATAA
1 TAATATAT-TTAATAA
*
2435415 TAAT-TATTATAGTAA
1 TAATATATT-TAATAA
2435430 TAATA
1 TAATA
2435435 ATAATAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
12 11 0.28
14 1 0.03
15 27 0.69
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
TAATATATTTAATAA
Found at i:2437179 original size:229 final size:224
Alignment explanation
Indices: 2436740--2437186 Score: 770
Period size: 229 Copynumber: 2.0 Consensus size: 224
2436730 GTAAATTATC
* *
2436740 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA-CTTTAGT
*
2436805 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
65 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATTTT
2436870 GTGTAAATTAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAA
130 GTGTAAATTAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAA
2436935 ACATAAATTACATAACTTTCAAAAAAGTATA
195 ACATAAATTACATAACTTT-AAAAAAGTATA
*
2436966 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTAAATTA-TTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATT--ATTACTTTA
*
2437030 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
63 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-AAAT
*
2437095 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
127 TTTGTGTAAATT-AATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
2437160 TGAAACATAAATTACATAACTTTAAAA
191 TGAAACATAAATTACATAACTTTAAAA
2437187 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 6, Indels: 8
0.94 0.03 0.04
Matches are distributed among these distances:
226 36 0.17
227 77 0.37
228 19 0.09
229 78 0.37
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (224 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTACTTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATTTTG
TGTAAATTAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAA
CATAAATTACATAACTTTAAAAAAGTATA
Found at i:2438109 original size:24 final size:24
Alignment explanation
Indices: 2438082--2438131 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2438072 TATATCAAAA
*
2438082 ATCAAAACATAATCCAGATCAAGT
1 ATCAAAACAAAATCCAGATCAAGT
* * *
2438106 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGATCAAGT
2438130 AT
1 AT
2438132 TCGATCAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGATCAAGT
Found at i:2438211 original size:24 final size:24
Alignment explanation
Indices: 2438092--2438216 Score: 139
Period size: 24 Copynumber: 5.2 Consensus size: 24
2438082 ATCAAAACAT
* *
2438092 AATCCA-GATCAAGTATCATATCAA
1 AATCCATG-TCAAGTATCAGATCAG
*
2438116 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCATGTCAAGTA-TCAGATCAG
*
2438140 AATCCAAGTCAAGTATCAGATCAG
1 AATCCATGTCAAGTATCAGATCAG
* *
2438164 AATCAATGT-AAGATATCATATCAG
1 AATCCATGTCAAG-TATCAGATCAG
2438188 AATCCATGTCAAGTATCAGATCAG
1 AATCCATGTCAAGTATCAGATCAG
2438212 TAATC
1 -AATC
2438217 AAATCAAAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
23 5 0.06
24 72 0.83
25 10 0.11
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (24 bp):
AATCCATGTCAAGTATCAGATCAG
Found at i:2443213 original size:13 final size:12
Alignment explanation
Indices: 2443181--2443210 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2443171 TATCACGTAT
*
2443181 TATTGAAAATAC
1 TATTGGAAATAC
2443193 TATTGGAAATAC
1 TATTGGAAATAC
2443205 TATTGG
1 TATTGG
2443211 GAATGGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (12 bp):
TATTGGAAATAC
Found at i:2449026 original size:10 final size:10
Alignment explanation
Indices: 2449011--2449044 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2449001 CGTCTCGGCT
2449011 CGGCACGACA
1 CGGCACGACA
*
2449021 CGGCACGGCA
1 CGGCACGACA
*
2449031 CGGCACGACT
1 CGGCACGACA
2449041 CGGC
1 CGGC
2449045 TCGGCTCGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.41, G:0.35, T:0.03
Consensus pattern (10 bp):
CGGCACGACA
Found at i:2453304 original size:19 final size:20
Alignment explanation
Indices: 2453260--2453304 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2453250 ATATTTGTTT
*
2453260 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
2453280 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
2453299 AATAAA
1 AATAAA
2453305 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:2453359 original size:25 final size:27
Alignment explanation
Indices: 2453305--2453356 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2453295 TCAAAATAAA
* *
2453305 ATATTAAAAGAGTATATTAATATTGTT
1 ATATTAAAAGAGTATATTAAAAATGTT
2453332 ATATTAAAAGA-TA-ATTATAAAATGT
1 ATATTAAAAGAGTATATTA-AAAATGT
2453357 ATAAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 7 0.32
27 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (27 bp):
ATATTAAAAGAGTATATTAAAAATGTT
Found at i:2466794 original size:31 final size:31
Alignment explanation
Indices: 2466709--2466795 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
2466699 TATGATAATA
* * *
2466709 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAATAATTTTATAATCTTTTA-ATAAATT
*
2466740 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAATAATTTTATAATCTTTTAATAAATT
* *
2466771 TAATAAGT-ATTTTTTAATTTTTTAA
1 TAATAA-TAATTTTATAATCTTTTAA
2466796 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 42 0.89
32 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (31 bp):
TAATAATAATTTTATAATCTTTTAATAAATT
Found at i:2469270 original size:31 final size:31
Alignment explanation
Indices: 2469211--2469277 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2469201 TCTAATATAA
** *
2469211 TCCCCCAACATTTAGTTTGTTTGTAATATGG
1 TCCCCCAACATTTAGTTCATTTGCAATATGG
*
2469242 TCCCTCAACATTTAGTTCATTTGCAATATGG
1 TCCCCCAACATTTAGTTCATTTGCAATATGG
2469273 TCCCC
1 TCCCC
2469278 GACGTAACTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39
Consensus pattern (31 bp):
TCCCCCAACATTTAGTTCATTTGCAATATGG
Found at i:2469894 original size:15 final size:15
Alignment explanation
Indices: 2469876--2469907 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2469866 TTAATTTTAA
2469876 CAGTGCTGACTGATT
1 CAGTGCTGACTGATT
2469891 CAGTGCTGACTGATT
1 CAGTGCTGACTGATT
2469906 CA
1 CA
2469908 TCAAAACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (15 bp):
CAGTGCTGACTGATT
Found at i:2470031 original size:16 final size:16
Alignment explanation
Indices: 2470010--2470054 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
2470000 ACATAACATC
2470010 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
* *
2470026 TGAATCATTTAACATT
1 TGAATCATTCAGCATT
2470042 TGAATCATTCAGC
1 TGAATCATTCAGC
2470055 GCTTAATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:2471850 original size:31 final size:31
Alignment explanation
Indices: 2471810--2471876 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
2471800 TATAATATAA
*
2471810 TCCCCCAACATTTAGTCCATTTACAATATGG
1 TCCCTCAACATTTAGTCCATTTACAATATGG
* *
2471841 TCCCTCAACATTTAGTCTATTTGCAATATGG
1 TCCCTCAACATTTAGTCCATTTACAATATGG
2471872 TCCCT
1 TCCCT
2471877 GACATAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.36
Consensus pattern (31 bp):
TCCCTCAACATTTAGTCCATTTACAATATGG
Found at i:2477500 original size:20 final size:20
Alignment explanation
Indices: 2477471--2477509 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2477461 TATGGGTTCA
2477471 AATATCGATACTGGATGAAC
1 AATATCGATACTGGATGAAC
*
2477491 AATATTGATACTGGATGAA
1 AATATCGATACTGGATGAA
2477510 TTGGGATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (20 bp):
AATATCGATACTGGATGAAC
Found at i:2477668 original size:25 final size:25
Alignment explanation
Indices: 2477589--2477668 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
2477579 ATATGGTATA
* *
2477589 GATACCAACACTGGAAAAGGTTATT
1 GATACCAACACTGGAAAAGGGTACT
* * * *
2477614 GATACCGGA-ATTGAAAAAGGGTACC
1 GATACC-AACACTGGAAAAGGGTACT
* *
2477639 AATACCAACAGTGGAAAAGGGTACT
1 GATACCAACACTGGAAAAGGGTACT
2477664 GATAC
1 GATAC
2477669 TGGATAATAC
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (25 bp):
GATACCAACACTGGAAAAGGGTACT
Found at i:2480287 original size:28 final size:25
Alignment explanation
Indices: 2480223--2480288 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 25
2480213 TGGTGCAAGT
*
2480223 TATATAGGCACTTTCGAGTGCATTT
1 TATATAGGCACTTTCGAGTGCATTA
2480248 TACTGATAAGGCACTTTCGAGTGCAATTGA
1 TA-T-AT-AGGCACTTTCGAGTGC-ATT-A
2480278 TATATGAGGCA
1 TATAT-AGGCA
2480289 TCTAGAGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 2 0.06
26 1 0.03
27 2 0.06
28 23 0.68
29 4 0.12
30 2 0.06
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (25 bp):
TATATAGGCACTTTCGAGTGCATTA
Found at i:2480966 original size:244 final size:244
Alignment explanation
Indices: 2480293--2481272 Score: 1890
Period size: 244 Copynumber: 4.0 Consensus size: 244
2480283 GAGGCATCTA
* *
2480293 GAGTGTATATTGCGCACACTCATCTAATTCACGTACCTTGTATTCTCATCTAATGTACATTGGGC
1 GAGTGTATATTGCGCACACTCATCTGATTCACGTAGCTTGTATTCTCATCTAATGTACATTGGGC
2480358 TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
66 TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
2480423 TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCATTGTATGCCTTTTATGTGAT
131 TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCATTGTATGCCTTTTATGTGAT
2480488 AAAGTGTCTATATAGGTTGTATGAATCGAAAGAAATCTAATGTTTTTTCT
196 AAAGTGTCTATATAGGTTGTATGAATCGAAAGAAATCTAATG-TTTTTCT
2480538 GAGTGTATATTGCGCACACTCATCTGATTCACGTAGCTTGTATTCTCATCTAATGTACATTGGGC
1 GAGTGTATATTGCGCACACTCATCTGATTCACGTAGCTTGTATTCTCATCTAATGTACATTGGGC
2480603 TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
66 TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
2480668 TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCA-TGTATGCCTTTTATGTGAT
131 TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCATTGTATGCCTTTTATGTGAT
* *
2480732 AAAGTGTCTATATATGTTGTATGAATCAAAAGAAATCTAATGTTTTTCT
196 AAAGTGTCTATATAGGTTGTATGAATCGAAAGAAATCTAATGTTTTTCT
2480781 GAGTGTATATTGCGCACACTCATCTGATTCACGTAGCTTGTATTCTCATCTAATGTACATTGGGC
1 GAGTGTATATTGCGCACACTCATCTGATTCACGTAGCTTGTATTCTCATCTAATGTACATTGGGC
2480846 TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
66 TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
2480911 TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCATTGTATGCCTTTTATGTGAT
131 TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCATTGTATGCCTTTTATGTGAT
2480976 AAAGTGTCTATATAGGTTGTATGAATCGAAAGAAATCTAATGTTTTTCT
196 AAAGTGTCTATATAGGTTGTATGAATCGAAAGAAATCTAATGTTTTTCT
2481025 GAGTGTATATTGCGCACACTCATCTGATTCACGTAGCTTGTATTCTCATCTAATGTACATTGGGC
1 GAGTGTATATTGCGCACACTCATCTGATTCACGTAGCTTGTATTCTCATCTAATGTACATTGGGC
2481090 TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
66 TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
2481155 TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCATTGTATGCCTTTTATGTGAT
131 TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCATTGTATGCCTTTTATGTGAT
* *
2481220 AAAGTGTCTATATATGTTGTTTGAATCGAAAGAAATCTAATGTTTTTCT
196 AAAGTGTCTATATAGGTTGTATGAATCGAAAGAAATCTAATGTTTTTCT
2481269 GAGT
1 GAGT
2481273 ATTCTGAGTT
Statistics
Matches: 726, Mismatches: 8, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
243 182 0.25
244 371 0.51
245 173 0.24
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.37
Consensus pattern (244 bp):
GAGTGTATATTGCGCACACTCATCTGATTCACGTAGCTTGTATTCTCATCTAATGTACATTGGGC
TATACTTATATGAAATTGAAAAGTGTAGGTTATATGATATGAATATGTAAACATCAAACGTTATT
TGATTAAACGATAGTAAAGAATTCGCCAAGTGCTATGATTTGGCATTGTATGCCTTTTATGTGAT
AAAGTGTCTATATAGGTTGTATGAATCGAAAGAAATCTAATGTTTTTCT
Found at i:2486975 original size:23 final size:25
Alignment explanation
Indices: 2486949--2487002 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 25
2486939 AAATCCAGCA
2486949 AAGAAATTCAAAGCACTC-AAAA-G
1 AAGAAATTCAAAGCACTCAAAAAGG
*
2486972 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAATTCAAAGCACTCAAAAAGG
2486997 AAGAAA
1 AAGAAA
2487003 ATAAAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 17 0.61
24 4 0.14
25 7 0.25
ACGTcount: A:0.59, C:0.13, G:0.17, T:0.11
Consensus pattern (25 bp):
AAGAAATTCAAAGCACTCAAAAAGG
Found at i:2495950 original size:21 final size:21
Alignment explanation
Indices: 2495909--2495952 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2495899 TCACATTTCG
*
2495909 TTTTATCTATTATTGTATTTA
1 TTTTATCTATTATTATATTTA
*
2495930 TTTTATGTATTTATTAT-TTTA
1 TTTTATCTA-TTATTATATTTA
2495951 TT
1 TT
2495953 AATTCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTATCTATTATTATATTTA
Done.