Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_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: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 17
Found at i:1890599 original size:24 final size:23
Alignment explanation
Indices: 1890542--1890590 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1890532 CATGTTTATA
*
1890542 AGAACCGAAAAACTTTGTTTACC
1 AGAATCGAAAAACTTTGTTTACC
* *
1890565 ATAATCGAAAAATTTTGTTTACC
1 AGAATCGAAAAACTTTGTTTACC
1890588 AGA
1 AGA
1890591 GCTGGAAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (23 bp):
AGAATCGAAAAACTTTGTTTACC
Found at i:1895168 original size:188 final size:188
Alignment explanation
Indices: 1894839--1895193 Score: 507
Period size: 188 Copynumber: 1.9 Consensus size: 188
1894829 AATAAAAAAT
* * * *
1894839 TTATGTCAAATTTATTTTGTCATAATATTTTTTCAAAATAAAAAATTTTGACAAAGTTATTTAAT
1 TTATGTCAAATATATTTCGTCACAATATTTTTTCAAAATAAAAAATTGTGACAAAGTTATTTAAT
* * * * *
1894904 CAAAATAATAATGTATAACAAATATTAATTGCTCATCATAAAAAATTGTGACAAGTAATATTCTT
66 CAAAATAATAATGTATAACAAATATTAATTGCTCATCATAAAAAATTATGAAAAATAAAATTATT
*
1894969 TCACGATAACAAATTGCAACAAAATGATTTAGTCACAATAACACGTTAAATTAAACAA
131 TCACAATAACAAATTGCAACAAAATGATTTAGTCACAATAACACGTTAAATTAAACAA
* * * *
1895027 TTATGTCAAATATATTTCGTCGCAATATTTTGTT-GAAATAAAAAATTGTGATAAATTTATTTAA
1 TTATGTCAAATATATTTCGTCACAATATTTT-TTCAAAATAAAAAATTGTGACAAAGTTATTTAA
* * *
1895091 TCAAAATAACT-ATTTATAACAAATATTAATTTCTCATTATAAAAAATTATGAAAAATAAAATTA
65 TCAAAATAA-TAATGTATAACAAATATTAATTGCTCATCATAAAAAATTATGAAAAATAAAATTA
* *
1895155 TTTCACAATAACAAATTGTAACAAAATTATTTAGTCACA
129 TTTCACAATAACAAATTGCAACAAAATGATTTAGTCACA
1895194 GTAAAAAAGT
Statistics
Matches: 146, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
188 143 0.98
189 3 0.02
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (188 bp):
TTATGTCAAATATATTTCGTCACAATATTTTTTCAAAATAAAAAATTGTGACAAAGTTATTTAAT
CAAAATAATAATGTATAACAAATATTAATTGCTCATCATAAAAAATTATGAAAAATAAAATTATT
TCACAATAACAAATTGCAACAAAATGATTTAGTCACAATAACACGTTAAATTAAACAA
Found at i:1895326 original size:21 final size:19
Alignment explanation
Indices: 1895300--1895342 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1895290 TTGATGTTAT
1895300 AATTTAACTTAATTGTGACAA
1 AATTT-ACTT-ATTGTGACAA
* *
1895321 AATTTACTTTTTGTGATAA
1 AATTTACTTATTGTGACAA
1895340 AAT
1 AAT
1895343 AATTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (19 bp):
AATTTACTTATTGTGACAA
Found at i:1898620 original size:198 final size:196
Alignment explanation
Indices: 1898278--1898708 Score: 625
Period size: 198 Copynumber: 2.2 Consensus size: 196
1898268 GAACATTACG
* * * * *
1898278 ATAACTAATTGTAACAAATTTATTTAGTTACAAT-AACGTAGTAAATTTAGTCAAGATAAAAATT
1 ATAACAAATTGTAACAAAATTATTTAGTCACAGTAAACGTA-TAAATTTAGTCAAGATAAAAAGT
* *
1898342 TATGTCAAATTTATTGTCACAATATTTTGTCAAAATAAAAAATTCTGATAAATTTATTTAATCAA
65 TATGTCAAATTTATTCTCACAATATTTTGTCAAAATAAAAAATTCTGACAAATTTATTTAATCAA
* *
1898407 AATAATAATTTATAACAAATATTAATTTCTCATCATAAAAAATTGTGACAAGTAATATTCTTTCA
130 AATAACAATTTATAACAAATATTAATTTCTCATCATAAAAAATTGTGACAAATAATATTCTTTCA
1898472 CA
195 CA
* *
1898474 ATAACAAATTGTAACAAAATGATTTAGTCACAGTAACACGT-TAAATTTAGTCAA-AGTAAACAG
1 ATAACAAATTGTAACAAAATTATTTAGTCACAGTAA-ACGTATAAATTTAGTCAAGA-TAAAAAG
* * * *
1898537 TTATGTCAAATTTATTTCTCCCCAATATTTTGTCAAAATTAAAAATTGTGACAATTTTATTTAAT
64 TTATGTCAAATTTA-TTCT-CACAATATTTTGTCAAAATAAAAAATTCTGACAAATTTATTTAAT
* * *
1898602 CAAAATAACAATTTATAACAAATATTAATTTCTCATTATAAAATATTGTGACAAATAGTATTCTT
127 CAAAATAACAATTTATAACAAATATTAATTTCTCATCATAAAAAATTGTGACAAATAATATTCTT
*
1898667 TTACA
192 TCACA
1898672 ATAACAAATTGTAACAAAATTATTTAGTCACAGTAAA
1 ATAACAAATTGTAACAAAATTATTTAGTCACAGTAAA
1898709 AAAAGTTATA
Statistics
Matches: 210, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
195 1 0.00
196 61 0.29
197 5 0.02
198 143 0.68
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (196 bp):
ATAACAAATTGTAACAAAATTATTTAGTCACAGTAAACGTATAAATTTAGTCAAGATAAAAAGTT
ATGTCAAATTTATTCTCACAATATTTTGTCAAAATAAAAAATTCTGACAAATTTATTTAATCAAA
ATAACAATTTATAACAAATATTAATTTCTCATCATAAAAAATTGTGACAAATAATATTCTTTCAC
A
Found at i:1905257 original size:2 final size:2
Alignment explanation
Indices: 1905252--1905281 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1905242 ACACACACAC
1905252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1905282 GCTTGTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1905412 original size:3 final size:3
Alignment explanation
Indices: 1905406--1905474 Score: 84
Period size: 3 Copynumber: 22.3 Consensus size: 3
1905396 TTCATTTAAA
** * *
1905406 ATT ATT ATT ATT ATT AAA ATT ATT ATT ATT AGT ATT ATT ATT ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1905454 ATT ATT ATAT ATT ATTT ATT A
1 ATT ATT AT-T ATT A-TT ATT A
1905475 AATATTACAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1906836 original size:18 final size:18
Alignment explanation
Indices: 1906813--1906873 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
1906803 TTGTTTAAAT
1906813 ATATTTTAATTTTATATA
1 ATATTTTAATTTTATATA
*
1906831 ATATTTTAATTAGTAT-TA
1 ATATTTTAATT-TTATATA
* *
1906849 TTATTTTATTTTTAATATA
1 ATATTTTAATTTT-ATATA
1906868 TATATT
1 -ATATT
1906874 ATTTGATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.03
18 24 0.71
19 5 0.15
20 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTTTAATTTTATATA
Found at i:1911531 original size:12 final size:12
Alignment explanation
Indices: 1911514--1911541 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1911504 ATTTATTTAA
1911514 AAAATTAATATT
1 AAAATTAATATT
1911526 AAAATTAATATT
1 AAAATTAATATT
1911538 AAAA
1 AAAA
1911542 AAATATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:1911544 original size:15 final size:14
Alignment explanation
Indices: 1911510--1911543 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
1911500 TAATATTTAT
1911510 TTAAAAAATTAATA
1 TTAAAAAATTAATA
1911524 TT--AAAATTAATA
1 TTAAAAAATTAATA
1911536 TTAAAAAA
1 TTAAAAAA
1911544 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.67
14 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAAAATTAATA
Found at i:1913063 original size:17 final size:19
Alignment explanation
Indices: 1913025--1913074 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
1913015 TTTTAATAAA
1913025 TTTTAACATAAAATATATAT
1 TTTTAA-ATAAAATATATAT
1913045 TTTTAAATAAAA-A-ATAT
1 TTTTAAATAAAATATATAT
*
1913062 TTTTAAATTAAAT
1 TTTTAAATAAAAT
1913075 TAATAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 15 0.54
18 1 0.04
19 6 0.21
20 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTAAATAAAATATATAT
Found at i:1913135 original size:25 final size:26
Alignment explanation
Indices: 1913050--1913139 Score: 91
Period size: 25 Copynumber: 3.5 Consensus size: 26
1913040 TATATTTTTA
*
1913050 AATAAAAAATATTTTTAAATTAA-ATT
1 AATATAAAATATTTTTAAATTAATA-T
*
1913076 AATAATAAAATATATTT-AA-TAAGT-T
1 AAT-ATAAAATATTTTTAAATTAA-TAT
1913101 AATATAAAAATATTTTTAAATTAATAT
1 AATAT-AAAATATTTTTAAATTAATAT
1913128 -ATATAAAATATT
1 AATATAAAATATT
1913140 ATAAATTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
24 2 0.04
25 25 0.46
26 12 0.22
27 15 0.28
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
AATATAAAATATTTTTAAATTAATAT
Found at i:1913144 original size:24 final size:24
Alignment explanation
Indices: 1913070--1913146 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
1913060 ATTTTTAAAT
1913070 TAAATTAATA-ATAAAATATATTTAA
1 TAAATTAATATATAAAA-ATATTT-A
* *
1913095 TAAGTT-A-ATATAAAAATATTTT
1 TAAATTAATATATAAAAATATTTA
1913117 TAAATTAATATATATAAAATA-TTA
1 TAAATTAATATATA-AAAATATTTA
1913141 TAAATT
1 TAAATT
1913147 TAAGTATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 5 0.11
23 8 0.18
24 20 0.45
25 11 0.25
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
TAAATTAATATATAAAAATATTTA
Found at i:1914671 original size:11 final size:11
Alignment explanation
Indices: 1914655--1914685 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1914645 TTGGTTAAAG
*
1914655 AGAGAGAGGCA
1 AGAGAGAGACA
1914666 AGAGAGAGACA
1 AGAGAGAGACA
1914677 AGAGAGAGA
1 AGAGAGAGA
1914686 AGGATTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.42, T:0.00
Consensus pattern (11 bp):
AGAGAGAGACA
Found at i:1925003 original size:19 final size:19
Alignment explanation
Indices: 1924979--1925032 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
1924969 TAAAAATTAT
1924979 AAATTTAATATTTTTTAAA
1 AAATTTAATATTTTTTAAA
*
1924998 AAATTTATTGA-TTTTT--A
1 AAATTTAAT-ATTTTTTAAA
1925015 AAA-TTAAT-TTTTTTAAA
1 AAATTTAATATTTTTTAAA
1925032 A
1 A
1925033 TATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 5 0.17
16 4 0.14
17 6 0.21
19 13 0.45
20 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AAATTTAATATTTTTTAAA
Found at i:1925538 original size:10 final size:11
Alignment explanation
Indices: 1925520--1925546 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1925510 AATATTAATT
1925520 TTAAAAAAATA
1 TTAAAAAAATA
1925531 TTAAAAAAATA
1 TTAAAAAAATA
1925542 TTAAA
1 TTAAA
1925547 TTCTAATTTT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:1926497 original size:2 final size:2
Alignment explanation
Indices: 1926490--1926605 Score: 104
Period size: 2 Copynumber: 62.0 Consensus size: 2
1926480 TCGGGCCAGG
* * * *
1926490 TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1926530 TA TA TA TA TA TA TA T- TA T- TT TA AA T- TA AA TT TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1926567 TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1926606 ATAATTATTT
Statistics
Matches: 91, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
1 8 0.09
2 83 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1926553 original size:46 final size:45
Alignment explanation
Indices: 1926490--1926590 Score: 168
Period size: 46 Copynumber: 2.2 Consensus size: 45
1926480 TCGGGCCAGG
1926490 TATATATATA-TATTTAAATTAAATATATAAATATTATATATATA
1 TATATATATATTATTTAAATTAAATATATAAATATTATATATATA
* *
1926534 TATATATATATTATTTTAAATTAAATTTATTAATATTATATATATA
1 TATATATATATTA-TTTAAATTAAATATATAAATATTATATATATA
1926580 TATATATATAT
1 TATATATATAT
1926591 ATATATATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
44 10 0.19
45 2 0.04
46 41 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (45 bp):
TATATATATATTATTTAAATTAAATATATAAATATTATATATATA
Found at i:1927081 original size:71 final size:68
Alignment explanation
Indices: 1926967--1927101 Score: 234
Period size: 71 Copynumber: 1.9 Consensus size: 68
1926957 ATAACTTGTA
1926967 ACTAGGTATCTAATTCTTTCGTATCATGAAGGTAGGGAATGATTGGATGGTGAAGGAGAATAATC
1 ACTAGGTATCTAATTCTTTCGTATCATGAAGGTAGGGAATGATTGGATGGTGAAGGAGAATAATC
1927032 GGT
66 GGT
*
1927035 ACTAGGTATCTAATTCTTTTGTATTCTTATGAAGGTAGGGAATGATTGGATGGTGAAGGAGAATA
1 ACTAGGTATCTAATTCTTTCGTA-TC--ATGAAGGTAGGGAATGATTGGATGGTGAAGGAGAATA
1927100 AT
63 AT
1927102 GAATTTCATA
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
68 22 0.35
69 2 0.03
71 39 0.62
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.33
Consensus pattern (68 bp):
ACTAGGTATCTAATTCTTTCGTATCATGAAGGTAGGGAATGATTGGATGGTGAAGGAGAATAATC
GGT
Found at i:1928216 original size:69 final size:69
Alignment explanation
Indices: 1928083--1928217 Score: 159
Period size: 70 Copynumber: 1.9 Consensus size: 69
1928073 AAACTTAAAT
* * *
1928083 ATATATTTTTAATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAGTTAAAAATAT
1 ATATATTTTAAAATTGAAATATACAAAAGTATATAATCATC-TTAATATTCAAAGTTAAAAATAT
1928148 AACAA
65 AACAA
* * *
1928153 ATATATTTTAAAATTGACATATTCAAAGAGTA-ATAATCATAC-TAATATTTAAA-TTAAATAAT
1 ATATATTTTAAAATTGAAATATACAAA-AGTATATAATCAT-CTTAATATTCAAAGTTAAA-AAT
1928215 ATA
63 ATA
1928218 TTTAATTTGC
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
68 5 0.09
69 16 0.29
70 30 0.54
71 5 0.09
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.39
Consensus pattern (69 bp):
ATATATTTTAAAATTGAAATATACAAAAGTATATAATCATCTTAATATTCAAAGTTAAAAATATA
ACAA
Found at i:1928398 original size:189 final size:187
Alignment explanation
Indices: 1928024--1928430 Score: 525
Period size: 189 Copynumber: 2.2 Consensus size: 187
1928014 AACATATAAC
* * * * *
1928024 AATATCTTTAATTTGAAATATTCAAAAGATAAAATCCTTTTACCATTCAAAACTTAAATATATAT
1 AATATATTTAATTTGCAATAGTCAAAAGGTAAAATCCTTTTACCATTCAAAACTTAAACATATAT
* * *
1928089 TTTTAATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAGTTAAAAATATAACAAA
66 TTTTAATTTCAAATATACAAAAGTATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAA
* * *
1928154 TATATTTTAAAATTGACATATTCAAAGAGTAATAATCATACTAATATTTAAATTAAA
131 TATATTTTAAAATTGACATATTAAAAGACTAATAATCATACTAATATTCAAATTAAA
* * * *
1928211 TAATATATTTAATTTGCAATAGT-AAAAGGTAAACTCTTTTTACTATTC-AAAGTTAAACATATA
1 -AATATATTTAATTTGCAATAGTCAAAAGGTAAAATCCTTTTACCATTCAAAACTTAAACATATA
*
1928274 TTAATTTAATTTCAAATATACAAAAGTATATAATTATCTTTTAATATTCAAAATTATAAAGATAA
65 TT--TTTAATTTCAAATATACAAAAGTATATAATTATC-TTTAATATTCAAAATTAAAAAGATAA
* * *
1928339 -AAATATTTTTTTAAAATTGACTTATTAAAAGACTAGGT-ATCATACTAATATTCAAATTAAA
127 CAAATA-TATTTTAAAATTGACATATTAAAAGACTA-ATAATCATACTAATATTCAAATTAAA
* *
1928400 AATTATCTTTTAATTTACAATAGTCAAAAGG
1 AA-TAT-ATTTAATTTGCAATAGTCAAAAGG
1928431 ACTATGAATT
Statistics
Matches: 190, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
186 15 0.08
187 21 0.11
188 59 0.31
189 73 0.38
190 16 0.08
191 6 0.03
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (187 bp):
AATATATTTAATTTGCAATAGTCAAAAGGTAAAATCCTTTTACCATTCAAAACTTAAACATATAT
TTTTAATTTCAAATATACAAAAGTATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAA
TATATTTTAAAATTGACATATTAAAAGACTAATAATCATACTAATATTCAAATTAAA
Found at i:1932384 original size:29 final size:29
Alignment explanation
Indices: 1932349--1932413 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1932339 AGCAAAGTAT
*
1932349 GTCGCCATGGAGTCAGGACGACCTTGTAG
1 GTCGCCATGCAGTCAGGACGACCTTGTAG
* * * *
1932378 GTCGCCATGCAGTCGGGGCGTCGTTGTAG
1 GTCGCCATGCAGTCAGGACGACCTTGTAG
1932407 GTCGCCA
1 GTCGCCA
1932414 GGTGAATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (29 bp):
GTCGCCATGCAGTCAGGACGACCTTGTAG
Found at i:1936531 original size:30 final size:30
Alignment explanation
Indices: 1936469--1936543 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
1936459 AAAAACTAAA
* * *
1936469 TTAAACAACACTAACTTAGCAAAATATTTT
1 TTAAACAACACTAAATTAACAAAATATATT
*
1936499 TTAAACAACACTAAATTAAACAAATTA-ATT
1 TTAAACAACACTAAATT-AACAAAATATATT
*
1936529 TTATACAA-ACTAAAT
1 TTAAACAACACTAAAT
1936544 GAACTAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.18
30 25 0.64
31 7 0.18
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (30 bp):
TTAAACAACACTAAATTAACAAAATATATT
Found at i:1937111 original size:26 final size:27
Alignment explanation
Indices: 1937082--1937132 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
1937072 TTTTACCCGA
1937082 TTCCTTCTTCTCCCTTTC-TTCTTCCT
1 TTCCTTCTTCTCCCTTTCTTTCTTCCT
1937108 TTCCTTCTTCTCCCTTTCTTTCTTC
1 TTCCTTCTTCTCCCTTTCTTTCTTC
1937133 ATAACCGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (27 bp):
TTCCTTCTTCTCCCTTTCTTTCTTCCT
Found at i:1937117 original size:15 final size:15
Alignment explanation
Indices: 1937082--1937132 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
1937072 TTTTACCCGA
1937082 TTCCTTCTTCTCCCT
1 TTCCTTCTTCTCCCT
1937097 TT-CTTC-T-T-CCT
1 TTCCTTCTTCTCCCT
1937108 TTCCTTCTTCTCCCT
1 TTCCTTCTTCTCCCT
*
1937123 TTCTTTCTTC
1 TTCCTTCTTC
1937133 ATAACCGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
11 5 0.16
12 5 0.16
13 2 0.06
14 5 0.16
15 14 0.45
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
TTCCTTCTTCTCCCT
Found at i:1937866 original size:45 final size:45
Alignment explanation
Indices: 1937802--1937892 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
1937792 TACGTGAGTT
1937802 TAGCCAATCAAAATAATTATAAATTTAATATAAATTTAAAATCAA
1 TAGCCAATCAAAATAATTATAAATTTAATATAAATTTAAAATCAA
1937847 TAGCCAATCAAAATAATTATAAATTTAATATAAATTTAAAATCAA
1 TAGCCAATCAAAATAATTATAAATTTAATATAAATTTAAAATCAA
1937892 T
1 T
1937893 CCATTAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (45 bp):
TAGCCAATCAAAATAATTATAAATTTAATATAAATTTAAAATCAA
Found at i:1946267 original size:21 final size:18
Alignment explanation
Indices: 1946209--1946281 Score: 89
Period size: 15 Copynumber: 4.0 Consensus size: 18
1946199 TAACAATTGG
1946209 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
1946227 TAACAA--G-TATCTTTT
1 TAACAATTGATATCTTTT
1946242 TAACAATTGATATTCTTTTGT
1 TAACAATTGATA-TC-TTT-T
1946263 TAACAATTGATATCATTTT
1 TAACAATTGATATC-TTTT
1946282 CATTAAACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
15 14 0.29
16 1 0.02
17 1 0.02
18 8 0.17
19 3 0.06
20 8 0.17
21 13 0.27
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:1946643 original size:20 final size:21
Alignment explanation
Indices: 1946596--1946643 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1946586 AAATTCCAGA
* *
1946596 ATGCTACAGGGGTATCGATAC
1 ATGCTACAGGGGTACCAATAC
1946617 ATGCTACAGGGGTACCAATAC
1 ATGCTACAGGGGTACCAATAC
1946638 -TGCTAC
1 ATGCTAC
1946644 TATTTATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
ATGCTACAGGGGTACCAATAC
Found at i:1947048 original size:34 final size:33
Alignment explanation
Indices: 1947004--1947073 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
1946994 TTTGTAAAGA
*
1947004 GGAAACGTTCTAGCTAAGCCCGTGTAAAAGCTAG
1 GGAAACGTTCTAGCTAAGCCCGTG-AAAAACTAG
* * * *
1947038 GGAAAGGTTCTAGTTTATCCCGTGAAAAACTAG
1 GGAAACGTTCTAGCTAAGCCCGTGAAAAACTAG
1947071 GGA
1 GGA
1947074 GTTGTAAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (33 bp):
GGAAACGTTCTAGCTAAGCCCGTGAAAAACTAG
Found at i:1947421 original size:23 final size:23
Alignment explanation
Indices: 1947359--1947447 Score: 96
Period size: 23 Copynumber: 4.0 Consensus size: 23
1947349 ACAACTCGTA
*
1947359 ATTTGCACCGAAGTACCACATA-
1 ATTTGCACCGAAGTGCCACATAG
*
1947381 A-TTGTC-TCGAA-TGACCACATAG
1 ATTTG-CACCGAAGTG-CCACATAG
*
1947403 GTTTGCACCGAAGTGCCACATAG
1 ATTTGCACCGAAGTGCCACATAG
*
1947426 ATTTGCACTGAAGTGCCACATA
1 ATTTGCACCGAAGTGCCACATA
1947448 TTTGTCCCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.25
22 3 0.05
23 35 0.64
24 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (23 bp):
ATTTGCACCGAAGTGCCACATAG
Found at i:1948378 original size:20 final size:22
Alignment explanation
Indices: 1948349--1948405 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
1948339 ATTCTTTTGG
*
1948349 GTATCAATACTACCCTT-ACA-
1 GTATCGATACTACCCTTAACAT
*
1948369 GTATCGATAC--CTCTTCAACAT
1 GTATCGATACTACCCTT-AACAT
1948390 GTATCGATACTACCCT
1 GTATCGATACTACCCT
1948406 CAAATTTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 4 0.14
20 12 0.41
21 10 0.34
23 3 0.10
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (22 bp):
GTATCGATACTACCCTTAACAT
Found at i:1950446 original size:20 final size:20
Alignment explanation
Indices: 1950395--1950447 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1950385 TACTCAATCA
1950395 AGTATCGATACTTATACTTG
1 AGTATCGATACTTATACTTG
* *
1950415 -GATATTGATACTTATCCTTG
1 AG-TATCGATACTTATACTTG
*
1950435 AGTATCGTTACTT
1 AGTATCGATACTT
1950448 TCTTAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
AGTATCGATACTTATACTTG
Found at i:1952318 original size:16 final size:16
Alignment explanation
Indices: 1952297--1952336 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1952287 TTTAGTGACT
1952297 AAATTGTAGCTTTCGA
1 AAATTGTAGCTTTCGA
* *
1952313 AAATTGCAGCTTTTGA
1 AAATTGTAGCTTTCGA
1952329 AAATTGTA
1 AAATTGTA
1952337 AGGGCAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (16 bp):
AAATTGTAGCTTTCGA
Found at i:1967702 original size:7 final size:7
Alignment explanation
Indices: 1967690--1967723 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
1967680 AAAAAGAGGG
1967690 AGAGAGT
1 AGAGAGT
1967697 AGAGAGT
1 AGAGAGT
1967704 AGAGAGT
1 AGAGAGT
1967711 AGAGAGT
1 AGAGAGT
1967718 AGAGAG
1 AGAGAG
1967724 AAATAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (7 bp):
AGAGAGT
Found at i:1974802 original size:25 final size:25
Alignment explanation
Indices: 1974774--1974851 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
1974764 AAAAATTTGG
*
1974774 GAAAGAAAAAATATAGAAAAAAAGA
1 GAAAGAAAAAATAGAGAAAAAAAGA
*
1974799 GAAAGAAAAAAT-GAGAAAAAATGA
1 GAAAGAAAAAATAGAGAAAAAAAGA
*
1974823 GAAA-AAAGGAAA-AGAGAGAAAAAGA
1 GAAAGAAA--AAATAGAGAAAAAAAGA
1974848 GAAA
1 GAAA
1974852 TGAAGAAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
23 3 0.07
24 14 0.30
25 29 0.63
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (25 bp):
GAAAGAAAAAATAGAGAAAAAAAGA
Found at i:1974817 original size:35 final size:35
Alignment explanation
Indices: 1974777--1974851 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
1974767 AATTTGGGAA
* *
1974777 AGAAAAAATATAGAAAAAAAGAGAAAGA-A-AAAATG
1 AGAAAAAAT-GAGAAAAAAAGA-AAAGAGAGAAAAAG
*
1974812 AGAAAAAATGAGAAAAAAGGAAAAGAGAGAAAAAG
1 AGAAAAAATGAGAAAAAAAGAAAAGAGAGAAAAAG
1974847 AGAAA
1 AGAAA
1974852 TGAAGAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 5 0.14
34 11 0.31
35 19 0.54
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.05
Consensus pattern (35 bp):
AGAAAAAATGAGAAAAAAAGAAAAGAGAGAAAAAG
Found at i:1974846 original size:10 final size:9
Alignment explanation
Indices: 1974802--1974851 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 9
1974792 AAAAAGAGAA
1974802 AGAAAAAATG
1 AGAAAAAA-G
1974812 AGAAAAAATG
1 AGAAAAAA-G
1974822 AGAAAAAAG
1 AGAAAAAAG
*
1974831 -GAAAAGAG
1 AGAAAAAAG
1974839 AG-AAAAAG
1 AGAAAAAAG
1974847 AGAAA
1 AGAAA
1974852 TGAAGAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 14 0.39
9 4 0.11
10 18 0.50
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:1974862 original size:20 final size:20
Alignment explanation
Indices: 1974834--1974872 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1974824 AAAAAAGGAA
*
1974834 AAGAGAGAA-AAAGAGAAATG
1 AAGAAAGAATAAAGA-AAATG
1974854 AAGAAAGAATAAAGAAAAT
1 AAGAAAGAATAAAGAAAAT
1974873 CGATCAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (20 bp):
AAGAAAGAATAAAGAAAATG
Found at i:1976916 original size:33 final size:33
Alignment explanation
Indices: 1976833--1977800 Score: 1314
Period size: 33 Copynumber: 29.2 Consensus size: 33
1976823 GTAGATCATA
*
1976833 ATCGACATTCAAATCCATCACAGAAGGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1976866 ATCGACATTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
1976900 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
1976933 ATCAACGTTAAAATCTATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1976966 ATCGACATTTAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1976999 ATCGACATTCAAATCTATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1977032 ATCGACATTTAAATCCATCACAGAAAGAGGTAG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1977065 ATCGACGTTCAAATCCATCACAGAAACAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1977098 ATCGACATTTCAAATCCATCACAGAAGGAGGTGA
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * *
1977132 ATCGACATTTTAAATCCATCATAGAAGGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* *
1977166 ATCGACATTCAAATCCATCACAAAAAGAGGTGT
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1977199 ATCGACATTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* *
1977233 ATCGACATTGAAATCCATCACAGAAAGAGGTAG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * *
1977266 ATCGACGTTGAAATCCATCATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1977299 ATTGACATTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1977332 ATCGATATTCAAATCCATCACAGAAATAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1977365 ATCGACGTTCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
1977398 ATCGACGTTCAAATCCATCATA-AAAAATGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * * *
1977430 AGCGACATTTTAAACCCATCATAGAATGAGGTGG
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
1977464 ATCGACATTCAAATCCATCACAGAAAGA-GTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
1977496 ATCGACATTCAAATCCATCACAGAAAGA-GTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1977528 ATCGACAATCAAATCCATCACAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * *
1977561 ATCCACGTTCAAATCCATCACAGAAAGATGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*
1977594 ATCGACATTCAAATCCATCACAGAAAGAAGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
*** *
1977627 ATCGACATTTTGATCCATCACAGAAAGAGGTGA
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1977660 ATCAACATTCAAATCCATCATAGAAAGAGGTGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* *
1977693 ATCGACATTTCAAATCCATCACAGAAAGAGGCGA
1 ATCGACA-TTCAAATCCATCACAGAAAGAGGTGG
* * * * *
1977727 ATTGGCATTCAAATTCATCAAAGAAAGAGATGG
1 ATCGACATTCAAATCCATCACAGAAAGAGGTGG
* * * *
1977760 ATCGACA-TCTTAATCTATCACAGAAGGAGTTGG
1 ATCGACATTC-AAATCCATCACAGAAAGAGGTGG
*
1977793 ATCAACAT
1 ATCGACAT
1977801 CAACTTTTTG
Statistics
Matches: 825, Mismatches: 101, Indels: 17
0.87 0.11 0.02
Matches are distributed among these distances:
32 78 0.09
33 582 0.71
34 165 0.20
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (33 bp):
ATCGACATTCAAATCCATCACAGAAAGAGGTGG
Found at i:1977841 original size:44 final size:44
Alignment explanation
Indices: 1977773--1977872 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 44
1977763 GACATCTTAA
* * * * * *
1977773 TCTATCACAGAAGGAGTTGGATCAACATCAACTTTTTGCTCGAT
1 TCTATCACAGAAAGAGATAGATCAACATCAACGTCTCGCTCGAT
* * *
1977817 TCTATCACAGAAAGAGATATATCAACATCGACGTCTCGTTCGAT
1 TCTATCACAGAAAGAGATAGATCAACATCAACGTCTCGCTCGAT
*
1977861 TCCATCACAGAA
1 TCTATCACAGAA
1977873 GGAGTTGGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (44 bp):
TCTATCACAGAAAGAGATAGATCAACATCAACGTCTCGCTCGAT
Found at i:1979214 original size:19 final size:17
Alignment explanation
Indices: 1979177--1979234 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
1979167 CATATTTTAT
*
1979177 TTTTTTATTTTTTGGTTA
1 TTTTTTATTTTTT-ATTA
1979195 TTTTTTAATATTTTTATTA
1 TTTTTT-AT-TTTTTATTA
* *
1979214 TTTGTTATTTTTAATTA
1 TTTTTTATTTTTTATTA
1979231 TTTT
1 TTTT
1979235 AATTTAGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.32
18 8 0.24
19 10 0.29
20 5 0.15
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTTATTTTTTATTA
Found at i:1979217 original size:27 final size:26
Alignment explanation
Indices: 1979171--1979234 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
1979161 TATGTACATA
*
1979171 TTTT-ATT-TTTTTATTTTTTGGTTATT
1 TTTTAATTATTTTTATTATTT-GTTA-T
1979197 TTTTAA-TATTTTTATTATTTGTTAT
1 TTTTAATTATTTTTATTATTTGTTAT
1979222 TTTTAATTATTTT
1 TTTTAATTATTTT
1979235 AATTTAGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 7 0.21
26 15 0.44
27 12 0.35
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTAATTATTTTTATTATTTGTTAT
Found at i:1979239 original size:16 final size:16
Alignment explanation
Indices: 1979197--1979239 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1979187 TTTGGTTATT
*
1979197 TTTTAATATTTTTATTA
1 TTTTAAT-TTTTAATTA
*
1979214 TTTGTTATTTTTAATTA
1 TTT-TAATTTTTAATTA
1979231 TTTTAATTT
1 TTTTAATTT
1979240 AGTTCATCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTAATTTTTAATTA
Found at i:1987319 original size:30 final size:30
Alignment explanation
Indices: 1987283--1987344 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1987273 TAAATGGGAG
1987283 AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
1 AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
1987313 AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
1 AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
1987343 AA
1 AA
1987345 TTTGATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (30 bp):
AAGTGTTAAAGTAAGGGGGAGTAATTTCAA
Found at i:1987371 original size:32 final size:32
Alignment explanation
Indices: 1987330--1987391 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1987320 AAAGTAAGGG
*
1987330 GGAGTAATTTCAAAATTTGATTTCAAAATCGA
1 GGAGTAATTTCAAAACTTGATTTCAAAATCGA
1987362 GGAGTAATTTCAAAACTTGATTTCAAAATC
1 GGAGTAATTTCAAAACTTGATTTCAAAATC
1987392 TTAAATTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (32 bp):
GGAGTAATTTCAAAACTTGATTTCAAAATCGA
Found at i:1988755 original size:35 final size:35
Alignment explanation
Indices: 1988716--1988787 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1988706 TAAAAAAACC
* *
1988716 CTATTTTATACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCATAATCCAACT
1988751 CTATTTTAGACTAGTATTTGAGTCATAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCATAATCCAACT
1988786 CT
1 CT
1988788 TCTTTGTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCATAATCCAACT
Found at i:1989465 original size:106 final size:106
Alignment explanation
Indices: 1989273--1989489 Score: 265
Period size: 106 Copynumber: 2.0 Consensus size: 106
1989263 TGCGTTGCTC
* * * *
1989273 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTTTTGATA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*** * *
1989338 GTTAGTCGCCCCTTAGCTGTGAAATTGAGCTTGTGTTGTCT
66 ACCAGCCGCCCCTTAGCTGTGAAATTGAACTTGTGTTGTCT
* * *
1989379 CGAGTCTAATATCCTTCG-CTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTGTTGAC
1 CGAGTCCAATATCCTCCGTC-GTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGAC
* * * *
1989443 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGCCCCTTAGCTGTGAAATTGAACTTGTGTTGTCT
*
1989485 TGAGT
1 CGAGT
1989490 GTTGAGCCTG
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
105 1 0.01
106 92 0.99
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (106 bp):
CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTAGCTGTGAAATTGAACTTGTGTTGTCT
Found at i:1989724 original size:280 final size:281
Alignment explanation
Indices: 1989209--1989770 Score: 820
Period size: 280 Copynumber: 2.0 Consensus size: 281
1989199 TCTTCGTGAA
* *
1989209 GTTGAGCCTGGGAATTGGATATCCTTCGTCGTGAAATTGAAATCCAATGTAAGTTGCGTTGCTCC
1 GTTGAGCCTGGGAATTGGATATCCTTCGTCGTGAAATTGAAATCCAATGTAAGCTGCATTGCTCC
* * * * * *
1989274 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTTTTGATAG
66 GACTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAG
** ** * * * *
1989339 TTAGTCGCCCCTTAGCTGTGAAATTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAA
131 CCACCCGCCCCTTAGCCGTGAAATTGAGCTTGTGCTGTCTCGAGTCCAATATCCCTCGCTGTGAA
* * ** *
1989404 GTTGAAATTGACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
196 GTTGAAATTGACTCTGAAACTGGGAAATTGTTCATTGACAACCAGCCGTCCATTCGTTGTGAAGT
*
1989469 TGAACTTGTGTTGTCTTGAGT
261 TGAACTTGTGTTGTCTCGAGT
* * * *
1989490 GTTGAGCCTGGTAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-GTAAGCTGTATTGCTCT
1 GTTGAGCCTGGGAATTGGATATCCTTCGTCGTGAAATTGAAATCCAATGTAAGCTGCATTGCTCC
*
1989554 GACTCCAATATCTTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAG
66 GACTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAG
* * * *
1989619 CCACCCGCCTCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCCTCGCTGTGAA
131 CCACCCGCCCCTTAGCCGTGAAATTGAGCTTGTGCTGTCTCGAGTCCAATATCCCTCGCTGTGAA
* *
1989684 GTTGAAATTGGCTTTGAAACTGGGAAATTGTTCATTGACAACCAGCCGTCCATTCGTTGTGAAGT
196 GTTGAAATTGACTCTGAAACTGGGAAATTGTTCATTGACAACCAGCCGTCCATTCGTTGTGAAGT
1989749 TGAACTTGTGTTGTCTCGAGT
261 TGAACTTGTGTTGTCTCGAGT
1989770 G
1 G
1989771 GCACGATATC
Statistics
Matches: 248, Mismatches: 33, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
280 203 0.82
281 45 0.18
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (281 bp):
GTTGAGCCTGGGAATTGGATATCCTTCGTCGTGAAATTGAAATCCAATGTAAGCTGCATTGCTCC
GACTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAG
CCACCCGCCCCTTAGCCGTGAAATTGAGCTTGTGCTGTCTCGAGTCCAATATCCCTCGCTGTGAA
GTTGAAATTGACTCTGAAACTGGGAAATTGTTCATTGACAACCAGCCGTCCATTCGTTGTGAAGT
TGAACTTGTGTTGTCTCGAGT
Found at i:1989746 original size:106 final size:106
Alignment explanation
Indices: 1989573--1989769 Score: 252
Period size: 106 Copynumber: 1.9 Consensus size: 106
1989563 ATCTTCCGTC
* ** * *
1989573 GTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAGCCACCCGCCTCTTCGCCGT
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTCATTAACAACCACCCGCCTATTCGCCGT
* *
1989638 GAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCCTCGCT
66 GAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCCTCGCT
* * * * **
1989679 GTGAAGTTGAAATTGGCTTTGAAACTGGGAAATTGTTCATTGACAACCAGCCGTCC-ATTCGTTG
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTCATTAACAACCACCCG-CCTATTCGCCG
*
1989743 TGAAGTTGAACTTGTGTTGTCTCGAGT
65 TGAAGTTGAACTTGTGCTGTCTCGAGT
1989770 GGCACGATAT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
106 74 0.97
107 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (106 bp):
GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTCATTAACAACCACCCGCCTATTCGCCGT
GAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCCTCGCT
Found at i:1993278 original size:26 final size:26
Alignment explanation
Indices: 1993242--1993319 Score: 147
Period size: 26 Copynumber: 3.0 Consensus size: 26
1993232 TCTGGATAGC
1993242 CTTAACTTTGTCGGGATCAACCTCAA
1 CTTAACTTTGTCGGGATCAACCTCAA
1993268 CTTAACTTTGTCGGGATCAACCTCAA
1 CTTAACTTTGTCGGGATCAACCTCAA
*
1993294 CTTAACTTTGTAGGGATCAACCTCAA
1 CTTAACTTTGTCGGGATCAACCTCAA
1993320 TATTTTTTCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (26 bp):
CTTAACTTTGTCGGGATCAACCTCAA
Found at i:1998315 original size:13 final size:13
Alignment explanation
Indices: 1998298--1998331 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1998288 ATCTAATAAT
1998298 AAAAAATAATGAG
1 AAAAAATAATGAG
*
1998311 GAAAAATAATGAG
1 AAAAAATAATGAG
1998324 AAAAAATA
1 AAAAAATA
1998332 CAAAGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAAATAATGAG
Found at i:1998564 original size:23 final size:24
Alignment explanation
Indices: 1998535--1998584 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1998525 ATAATAATAG
*
1998535 TAATAATAAGTATTAAAATAAAAAAA
1 TAATAAT-AGTAAT-AAATAAAAAAA
1998561 TAATAATAGTAATAAATAAAAAAA
1 TAATAATAGTAATAAATAAAAAAA
1998585 AGAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 5 0.22
26 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
TAATAATAGTAATAAATAAAAAAA
Found at i:1998580 original size:29 final size:31
Alignment explanation
Indices: 1998519--1998592 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
1998509 TAAACAAGGT
*
1998519 ATAAAAATAATAATAGTAATAATAAGTATTAAA
1 ATAAAAA-AATAATAATAATAATAAG-ATTAAA
*
1998552 ATAAAAAAATAATAATAGTAATAA-A-TAAA
1 ATAAAAAAATAATAATAATAATAAGATTAAA
1998581 A-AAAAGAAATAA
1 ATAAAA-AAATAA
1998593 AAGAAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 4 0.11
29 11 0.29
30 1 0.03
32 15 0.39
33 7 0.18
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (31 bp):
ATAAAAAAATAATAATAATAATAAGATTAAA
Found at i:1998583 original size:26 final size:26
Alignment explanation
Indices: 1998535--1998585 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1998525 ATAATAATAG
* *
1998535 TAATAATAAGTATTAAAATAAAAAAA
1 TAATAATAAGTAATAAAAAAAAAAAA
*
1998561 TAATAAT-AGTAATAAATAAAAAAAA
1 TAATAATAAGTAATAAAAAAAAAAAA
1998586 GAAATAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
TAATAATAAGTAATAAAAAAAAAAAA
Found at i:1998634 original size:2 final size:2
Alignment explanation
Indices: 1998627--1998671 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1998617 TTAAAGTAAA
1998627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1998669 AT A
1 AT A
1998672 AATAAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1998712 original size:22 final size:22
Alignment explanation
Indices: 1998671--1998720 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
1998661 ATATATATAT
1998671 AAATAAAAAATAAAGTATAAAT-G
1 AAATAAAAAATAAAG-AT-AATGG
1998694 AAATAAAAAATAATA-ATAATGG
1 AAATAAAAAATAA-AGATAATGG
1998716 AAATA
1 AAATA
1998721 TAAGTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 13 0.52
24 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (22 bp):
AAATAAAAAATAAAGATAATGG
Found at i:1999234 original size:35 final size:36
Alignment explanation
Indices: 1999195--1999271 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 36
1999185 AAAAAAACCC
*
1999195 TATTTTAGACTAATATTTGAGTCCTAATCTAACT-T
1 TATTTTAGACTAATATTTGAGTCCTAATCAAACTCT
*
1999230 TATTTTAGACTAATATTTGAGTTCTAATCAAACTCT
1 TATTTTAGACTAATATTTGAGTCCTAATCAAACTCT
1999266 T-TTTTA
1 TATTTTA
1999272 TTGATTACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 37 0.95
36 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (36 bp):
TATTTTAGACTAATATTTGAGTCCTAATCAAACTCT
Found at i:2003517 original size:2 final size:2
Alignment explanation
Indices: 2003510--2003570 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
2003500 AAAATCTCTA
*
2003510 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2003552 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2003571 GTTTTTAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2011251 original size:18 final size:17
Alignment explanation
Indices: 2011206--2011240 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2011196 TATTTCATTG
*
2011206 TAAA-ATTTAAAAAAAT
1 TAAATATTTTAAAAAAT
2011222 TAAATATTTTAAAAAAT
1 TAAATATTTTAAAAAAT
2011239 TA
1 TA
2011241 CACTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAATATTTTAAAAAAT
Found at i:2011286 original size:30 final size:30
Alignment explanation
Indices: 2011220--2011294 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
2011210 ATTTAAAAAA
* * * *
2011220 ATTAAATATTTTAAAAAATTACACTTTTTT
1 ATTAAATATTTCAAAAAATAACAATATTTT
2011250 AATTAAATATTTCAAAAAATAACAGATATTTT
1 -ATTAAATATTTCAAAAAATAACA-ATATTTT
*
2011282 -TTAAAAATTTCAA
1 ATTAAATATTTCAA
2011295 CTTTTATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 12 0.32
31 21 0.55
32 5 0.13
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (30 bp):
ATTAAATATTTCAAAAAATAACAATATTTT
Found at i:2011352 original size:16 final size:17
Alignment explanation
Indices: 2011326--2011374 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
2011316 ATGAATGATA
2011326 ATTTGTTAATTAAATCTT
1 ATTT-TTAATTAAATCTT
**
2011344 A-TTTTAATTAAAAGTT
1 ATTTTTAATTAAATCTT
2011360 ATTTTTTAATTAAAT
1 A-TTTTTAATTAAAT
2011375 ATTTTTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 2 0.08
18 12 0.46
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTTTAATTAAATCTT
Found at i:2011407 original size:17 final size:17
Alignment explanation
Indices: 2011385--2011417 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2011375 ATTTTTCATT
2011385 TTTGTTTACATATTTTA
1 TTTGTTTACATATTTTA
2011402 TTTGTTTACATATTTT
1 TTTGTTTACATATTTT
2011418 CAAAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTGTTTACATATTTTA
Found at i:2015236 original size:13 final size:13
Alignment explanation
Indices: 2015172--2015239 Score: 73
Period size: 13 Copynumber: 5.2 Consensus size: 13
2015162 GTCATAAATC
*
2015172 TATGACGCGCATT
1 TATGACGCACATT
**
2015185 TATGATACACATT
1 TATGACGCACATT
*
2015198 TATGACGCGCATT
1 TATGACGCACATT
**
2015211 TATGATACACATT
1 TATGACGCACATT
*
2015224 TATGACGCTCATT
1 TATGACGCACATT
2015237 TAT
1 TAT
2015240 AACTCGCATT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:2015249 original size:26 final size:26
Alignment explanation
Indices: 2015172--2015239 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
2015162 GTCATAAATC
2015172 TATGACGCGCATTTATGATACACATT
1 TATGACGCGCATTTATGATACACATT
2015198 TATGACGCGCATTTATGATACACATT
1 TATGACGCGCATTTATGATACACATT
*
2015224 TATGACGCTCATTTAT
1 TATGACGCGCATTTAT
2015240 AACTCGCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (26 bp):
TATGACGCGCATTTATGATACACATT
Found at i:2021366 original size:32 final size:31
Alignment explanation
Indices: 2021328--2021410 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
2021318 TTTTTTAAAT
*
2021328 TTTCAAAAAACAACATATTTTTTAAATACA-AA
1 TTTCAAAAAA-AACATATTCTTT-AATACAGAA
*
2021360 TTTCAAAAATTAAA-ATATTCTTTAATTCAGAA
1 TTTCAAAAA--AAACATATTCTTTAATACAGAA
2021392 TTTCAAAAAAATACATATT
1 TTTCAAAAAAA-ACATATT
2021411 AAAAAATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
30 2 0.05
31 6 0.14
32 33 0.75
33 2 0.05
34 1 0.02
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (31 bp):
TTTCAAAAAAAACATATTCTTTAATACAGAA
Found at i:2021439 original size:23 final size:24
Alignment explanation
Indices: 2021409--2021467 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
2021399 AAAATACATA
2021409 TTAAAAAATT-TCAATGTAAA-ATT
1 TTAAAAAATTAT-AATGTAAATATT
* *
2021432 TTAAAAAATATATATTTTAAATATT
1 TTAAAAAAT-TATAATGTAAATATT
2021457 TTAAAAAATTA
1 TTAAAAAATTA
2021468 CACTTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 9 0.29
24 9 0.29
25 13 0.42
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TTAAAAAATTATAATGTAAATATT
Found at i:2021474 original size:25 final size:24
Alignment explanation
Indices: 2021425--2021474 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
2021415 AATTTCAATG
*
2021425 TAAAATTTTAAAAAATATATATTT
1 TAAAATTTTAAAAAATATACATTT
2021449 TAAATATTTTAAAAAAT-TACACTTT
1 TAAA-ATTTTAAAAAATATACA-TTT
2021474 T
1 T
2021475 TTAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAATTTTAAAAAATATACATTT
Found at i:2021635 original size:17 final size:17
Alignment explanation
Indices: 2021613--2021645 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2021603 ATTTTTCATT
2021613 TTTGTTTACATATTTTA
1 TTTGTTTACATATTTTA
2021630 TTTGTTTACATATTTT
1 TTTGTTTACATATTTT
2021646 CAAAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTGTTTACATATTTTA
Found at i:2030779 original size:55 final size:55
Alignment explanation
Indices: 2030695--2030846 Score: 270
Period size: 55 Copynumber: 2.8 Consensus size: 55
2030685 GGGTAACACG
* * *
2030695 ATAAA-CTATAGTCGGGACGAATTCCCTACATTGTATCTTGGCGAACACAAGATT
1 ATAAAGCTGTAGTTGGGATGAATTCCCTACATTGTATCTTGGCGAACACAAGATT
2030749 ATAAAGCTGTAGTTGGGATGAATTCCCTACATTGTATCTTGGCGAACACAAGATT
1 ATAAAGCTGTAGTTGGGATGAATTCCCTACATTGTATCTTGGCGAACACAAGATT
2030804 ATAAAGCTGTAGTTGGGATGAATTCCCTACATTGTATCTTGGC
1 ATAAAGCTGTAGTTGGGATGAATTCCCTACATTGTATCTTGGC
2030847 TTATAGAGAA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
54 5 0.05
55 89 0.95
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (55 bp):
ATAAAGCTGTAGTTGGGATGAATTCCCTACATTGTATCTTGGCGAACACAAGATT
Found at i:2035812 original size:30 final size:30
Alignment explanation
Indices: 2035776--2035842 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
2035766 ACAGAACCGG
* *
2035776 CGGTTCACATCGATTTT-GTCGGTTCCCAGC
1 CGGTTCACACCGATTTTACT-GGTTCCCAGC
2035806 CGGTTCACACCGATTTTACTGGTTCCCAGC
1 CGGTTCACACCGATTTTACTGGTTCCCAGC
*
2035836 CGATTCA
1 CGGTTCA
2035843 TTGCAAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.31
Consensus pattern (30 bp):
CGGTTCACACCGATTTTACTGGTTCCCAGC
Found at i:2036995 original size:6 final size:6
Alignment explanation
Indices: 2036984--2037010 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2036974 ATACTTAAAA
2036984 ATAATT ATAATT ATAATT ATAATT ATA
1 ATAATT ATAATT ATAATT ATAATT ATA
2037011 TCATCTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:2040599 original size:29 final size:29
Alignment explanation
Indices: 2040533--2040601 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
2040523 ACGTTTGGTA
2040533 ACTGAACTTTAGTTTTTCTTATTTCACTC
1 ACTGAACTTTAGTTTTTCTTATTTCACTC
* * * *
2040562 AGTGTACTTTCA-TTTTTTTTAATTT-ACTT
1 ACTGAACTTT-AGTTTTTCTT-ATTTCACTC
2040591 ACTGAACTTTA
1 ACTGAACTTTA
2040602 TAGATTGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.03
29 26 0.81
30 5 0.16
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (29 bp):
ACTGAACTTTAGTTTTTCTTATTTCACTC
Found at i:2046340 original size:27 final size:27
Alignment explanation
Indices: 2046309--2046376 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
2046299 TCTATTTACA
2046309 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
2046336 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
2046363 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
2046377 ATTCCTACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:2050723 original size:13 final size:13
Alignment explanation
Indices: 2050705--2050769 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 13
2050695 CGACCCGTTT
*
2050705 ACCCGTTTACCCG
1 ACCCGTTGACCCG
2050718 ACCCGTTGACCCGACCCG
1 ACCCGTTGA--C---CCG
2050736 ACCCGTTGACCCG
1 ACCCGTTGACCCG
2050749 ACCC---GACCCG
1 ACCCGTTGACCCG
2050759 ACCCGTTGACC
1 ACCCGTTGACC
2050770 GTTGACCGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
10 10 0.23
13 19 0.44
15 1 0.02
16 1 0.02
18 12 0.28
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:2050733 original size:5 final size:5
Alignment explanation
Indices: 2050725--2050763 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
2050715 CCGACCCGTT
2050725 GACCC GACCC GACCC GTTGACCC GACCC GACCC GACCC G
1 GACCC GACCC GACCC ---GACCC GACCC GACCC GACCC G
2050764 TTGACCGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 26 0.84
8 5 0.16
ACGTcount: A:0.18, C:0.54, G:0.23, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:2050751 original size:23 final size:23
Alignment explanation
Indices: 2050725--2050769 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2050715 CCGACCCGTT
2050725 GACCCGACCCGACCCGTTGACCC
1 GACCCGACCCGACCCGTTGACCC
2050748 GACCCGACCCGACCCGTTGACC
1 GACCCGACCCGACCCGTTGACC
2050770 GTTGACCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (23 bp):
GACCCGACCCGACCCGTTGACCC
Found at i:2050769 original size:18 final size:18
Alignment explanation
Indices: 2050713--2050758 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
2050703 TTACCCGTTT
2050713 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
2050731 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
2050749 ACCCGACCCG
1 ACCCGACCCG
2050759 ACCCGTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.52, G:0.22, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:2050838 original size:29 final size:29
Alignment explanation
Indices: 2050777--2050853 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
2050767 ACCGTTGACC
*** *
2050777 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
2050806 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
2050835 GGTGCTATTTTGGTAATTA
1 GGTGCTATTCTGGGAATTA
2050854 TTTTTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:2057979 original size:13 final size:13
Alignment explanation
Indices: 2057938--2057968 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2057928 CGACCCGTTT
*
2057938 ACCCGTTTACCCG
1 ACCCGTTGACCCG
2057951 ACCCGTTGACCCG
1 ACCCGTTGACCCG
2057964 ACCCG
1 ACCCG
2057969 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:2058048 original size:29 final size:29
Alignment explanation
Indices: 2057987--2058062 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
2057977 ACCGTTGACC
** *
2057987 GGTGCTATTCTGGGAATTAATTCGATTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
2058016 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
2058045 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
2058063 TTTTTTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:2062345 original size:13 final size:13
Alignment explanation
Indices: 2062321--2062350 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2062311 GACAAAGAGA
2062321 AATTTCAAAGATT
1 AATTTCAAAGATT
2062334 AATTTCAAAGATT
1 AATTTCAAAGATT
2062347 AATT
1 AATT
2062351 GGGAAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (13 bp):
AATTTCAAAGATT
Found at i:2069459 original size:7 final size:7
Alignment explanation
Indices: 2069447--2069517 Score: 58
Period size: 7 Copynumber: 10.3 Consensus size: 7
2069437 TTGCATTTAT
2069447 ATTTTGC
1 ATTTTGC
2069454 ATTTTGC
1 ATTTTGC
**
2069461 A-TTCCC
1 ATTTTGC
2069467 ATTTTGC
1 ATTTTGC
2069474 ATTTTGC
1 ATTTTGC
*
2069481 ATTATGC
1 ATTTTGC
**
2069488 A-TTCCC
1 ATTTTGC
2069494 ATTTTTGC
1 A-TTTTGC
2069502 ATCTTTGC
1 AT-TTTGC
2069510 A-TTTGC
1 ATTTTGC
2069516 AT
1 AT
2069518 GAACATCTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
6 13 0.27
7 26 0.53
8 10 0.20
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.51
Consensus pattern (7 bp):
ATTTTGC
Found at i:2069462 original size:20 final size:20
Alignment explanation
Indices: 2069437--2069483 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2069427 AATTCCTTTA
* *
2069437 TTGCATTTATATTTTGCATT
1 TTGCATTCACATTTTGCATT
*
2069457 TTGCATTCCCATTTTGCATT
1 TTGCATTCACATTTTGCATT
2069477 TTGCATT
1 TTGCATT
2069484 ATGCATTCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTGCATTCACATTTTGCATT
Found at i:2069516 original size:28 final size:28
Alignment explanation
Indices: 2069449--2069540 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 28
2069439 GCATTTATAT
2069449 TTTGCATTTTGCATTCCCA-TTTTGCAT-
1 TTTGCA-TTTGCATTCCCATTTTTGCATC
2069476 TTTGCATTATGCATTCCCATTTTTGCATC
1 TTTGCATT-TGCATTCCCATTTTTGCATC
*** *
2069505 TTTGCATTTGCATGAACATCTTTGCATC
1 TTTGCATTTGCATTCCCATTTTTGCATC
2069533 TTTGCATT
1 TTTGCATT
2069541 AGAACCTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
26 2 0.03
27 16 0.28
28 32 0.55
29 8 0.14
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (28 bp):
TTTGCATTTGCATTCCCATTTTTGCATC
Found at i:2070915 original size:9 final size:8
Alignment explanation
Indices: 2070893--2070980 Score: 68
Period size: 10 Copynumber: 9.5 Consensus size: 8
2070883 AACACACACA
2070893 AAAATAAAG
1 AAAA-AAAG
2070902 AAAAAAATAG
1 -AAAAAA-AG
2070912 AAAACATAAAG
1 AAAA-A-A-AG
2070923 AAAAAAAG
1 AAAAAAAG
2070931 AAAAAAAG
1 AAAAAAAG
2070939 AAAAAATAG
1 AAAAAA-AG
2070948 AGAAAAAAG
1 A-AAAAAAG
2070957 AAGAAAGAAG
1 AA-AAA-AAG
2070967 AAGAAAGAAG
1 AA-AAA-AAG
2070977 AAAA
1 AAAA
2070981 TAGACAGATC
Statistics
Matches: 70, Mismatches: 1, Indels: 15
0.81 0.01 0.17
Matches are distributed among these distances:
8 17 0.24
9 18 0.26
10 28 0.40
11 7 0.10
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2070936 original size:21 final size:20
Alignment explanation
Indices: 2070892--2070955 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 20
2070882 AAACACACAC
*
2070892 AAAAATAAAGAAAAAAATAGA
1 AAAAATAAAGAAAAAAAGA-A
*
2070913 AAACATAAAGAAAAAAAGAA
1 AAAAATAAAGAAAAAAAGAA
* * *
2070933 AAAAAGAAA-AAATAGAGAA
1 AAAAATAAAGAAAAAAAGAA
2070952 AAAA
1 AAAA
2070956 GAAGAAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
19 12 0.32
20 8 0.22
21 17 0.46
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (20 bp):
AAAAATAAAGAAAAAAAGAA
Found at i:2070953 original size:17 final size:17
Alignment explanation
Indices: 2070919--2070984 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
2070909 TAGAAAACAT
*
2070919 AAAGAAAAAA-AGAAAA
1 AAAGAAAAAATAGAGAA
2070935 AAAGAAAAAATAGAGAAA
1 AAAGAAAAAATAGAG-AA
* *
2070953 AAAGAAGAAAGA-AGAA
1 AAAGAAAAAATAGAGAA
2070969 GAAAGAAGAAAATAGA
1 -AAAGAA-AAAATAGA
2070985 CAGATCCAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
16 12 0.30
17 11 0.28
18 16 0.40
19 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (17 bp):
AAAGAAAAAATAGAGAA
Found at i:2070960 original size:29 final size:28
Alignment explanation
Indices: 2070898--2070972 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 28
2070888 ACACAAAAAT
* *
2070898 AAAGAA-AAAAATAGAAAACATAAAGAA
1 AAAGAAGAAAAAAAGAAAAAATAAAGAA
*
2070925 AAA-AAGAAAAAAAGAAAAAATAGAGAAA
1 AAAGAAGAAAAAAAGAAAAAATAAAG-AA
2070953 AAAGAAGAAAGAAGAAGAAA
1 AAAGAAGAAA-AA-AAGAAA
2070973 GAAGAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 19 0.47
28 5 0.12
29 6 0.15
30 2 0.05
31 6 0.15
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (28 bp):
AAAGAAGAAAAAAAGAAAAAATAAAGAA
Found at i:2072645 original size:3 final size:3
Alignment explanation
Indices: 2072639--2072688 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
2072629 ATTTTTTTTC
2072639 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2072686 TTA
1 TTA
2072689 AATAAATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2073433 original size:13 final size:13
Alignment explanation
Indices: 2073415--2073456 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
2073405 ACCACCGTTA
2073415 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
2073428 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
*
2073441 CGGTGGCTGGCGG
1 CGGTGGCCGGCGG
2073454 CGG
1 CGG
2073457 AGTACGGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.00, C:0.29, G:0.62, T:0.10
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:2074051 original size:19 final size:19
Alignment explanation
Indices: 2074013--2074048 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2074003 CAATTTAGTC
2074013 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
2074032 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
2074049 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:2074826 original size:24 final size:23
Alignment explanation
Indices: 2074786--2074843 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
2074776 TTAATTTATA
*
2074786 ATTTTTTTATATATATACATATT
1 ATTTTTATATATATATACATATT
* *
2074809 ATTTTTATAGTATTTATATATATT
1 ATTTTTATA-TATATATACATATT
2074833 ATTATTTATAT
1 ATT-TTTATAT
2074844 TACAAGTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.27
24 16 0.53
25 6 0.20
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTTATATATATATACATATT
Found at i:2079107 original size:2 final size:2
Alignment explanation
Indices: 2079100--2079125 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2079090 TCATCCTTTA
2079100 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2079126 CCTTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2079442 original size:18 final size:17
Alignment explanation
Indices: 2079419--2079469 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
2079409 CTTATCCAGC
2079419 AAAGAAAGAAGAAAAAAA
1 AAAGAAA-AAGAAAAAAA
2079437 AAAGAAAAAAGAAAAAAA
1 AAAG-AAAAAGAAAAAAA
2079455 AAAGAAAAAGAAAAA
1 AAAGAAAAAGAAAAA
2079470 TTGAATCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.34
18 18 0.56
19 3 0.09
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAA
Found at i:2079443 original size:11 final size:11
Alignment explanation
Indices: 2079423--2079469 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
2079413 TCCAGCAAAG
*
2079423 AAAGAAGAAAA
1 AAAGAAAAAAA
*
2079434 AAA-AAAGAAA
1 AAAGAAAAAAA
2079444 AAAGAAAAAAA
1 AAAGAAAAAAA
2079455 AAAGAAAAAGAA
1 AAAGAAAAA-AA
2079467 AAA
1 AAA
2079470 TTGAATCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 8 0.26
11 18 0.58
12 5 0.16
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:2079469 original size:7 final size:7
Alignment explanation
Indices: 2079423--2079469 Score: 50
Period size: 6 Copynumber: 7.3 Consensus size: 7
2079413 TCCAGCAAAG
2079423 AAAGAAGA
1 AAAGAA-A
2079431 AAA-AAA
1 AAAGAAA
2079437 AAAGAAA
1 AAAGAAA
2079444 AAAG--A
1 AAAGAAA
2079449 AAA-AAA
1 AAAGAAA
2079455 AAAG-AA
1 AAAGAAA
2079461 AAAGAAA
1 AAAGAAA
2079468 AA
1 AA
2079470 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
5 4 0.12
6 14 0.41
7 13 0.38
8 3 0.09
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:2081838 original size:83 final size:83
Alignment explanation
Indices: 2081699--2082129 Score: 747
Period size: 83 Copynumber: 5.2 Consensus size: 83
2081689 AATGGAACAA
*
2081699 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
2081764 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
*
2081782 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
2081847 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
*
2081865 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
2081930 AATCATTGAATTTGGAAG
66 AATCATTGAATTTAGAAG
* *
2081948 ATTAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
2082013 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
* * * *
2082031 ATGAATTTGTTCATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
*
2082095 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTAGAAG
2082114 ATGAATTTGCTCATAG
1 ATGAATTTGCTCATAG
2082130 TAGAAATAAG
Statistics
Matches: 332, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 4 0.01
83 328 0.99
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (83 bp):
ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTAGAAG
Found at i:2083480 original size:22 final size:22
Alignment explanation
Indices: 2083449--2083503 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2083439 ATCTACACTC
* *
2083449 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTACCTT
* *
2083471 TTTAAAGATGACAGATTATCTT
1 TTCAAAGATGACAGATTACCTT
2083493 TTCAAAGATGA
1 TTCAAAGATGA
2083504 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTACCTT
Found at i:2084173 original size:91 final size:91
Alignment explanation
Indices: 2084065--2084269 Score: 360
Period size: 91 Copynumber: 2.3 Consensus size: 91
2084055 CCTTTCTAGA
2084065 GAAAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACCTTTTTG-AATGACTCTATCACA
1 GAAAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAA-CTTTTTGAAATGACTCTATCACA
*
2084129 -GAAAGGAGGTCATCATCATCCCCAGCG
65 GGAAA-GAGGTCAACATCATCCCCAGCG
2084156 GAAAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACTTTTTGAAATGACTCTATCACAG
1 GAAAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACTTTTTGAAATGACTCTATCACAG
*
2084221 GAAATAGGTCAACATCATCCCCAGCG
66 GAAAGAGGTCAACATCATCCCCAGCG
2084247 GAAAGTTCATAATGAGAAGAACT
1 GAAAGTTCATAATGAGAAGAACT
2084270 ATTCTGAAGA
Statistics
Matches: 110, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
90 7 0.06
91 99 0.90
92 4 0.04
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (91 bp):
GAAAGTTCATAATGAGAAGAACTCATCAAGAGCTTATTCAACTTTTTGAAATGACTCTATCACAG
GAAAGAGGTCAACATCATCCCCAGCG
Found at i:2084642 original size:76 final size:76
Alignment explanation
Indices: 2084513--2085280 Score: 1288
Period size: 76 Copynumber: 10.1 Consensus size: 76
2084503 ACTATTTCCC
* *
2084513 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2084578 AAGCCTTCGGG
66 AAGCCTTCGGG
2084589 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2084654 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
2084665 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCTTTAGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
2084730 AATCCTTCGGG
66 AAGCCTTCGGG
*
2084741 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2084806 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
2084817 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCTTTAGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
2084882 AATCCTTCGGG
66 AAGCCTTCGGG
*
2084893 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2084958 AAGCCTTCGGG
66 AAGCCTTCGGG
*
2084969 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTC
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
2085034 AAAGCCTTCGGG
65 AAAGCCTTCGGG
*
2085046 TCATCTGCAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
2085111 AAAACCTTCGGG
65 AAAGCCTTCGGG
* *
2085123 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTTGATGTTTTC
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-CTTTTTGATGTTTTC
*
2085188 AAAAACC-TCAGGG
65 -AAAGCCTTC-GGG
* * *
2085201 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
2085266 AA-CCCTCAGGG
66 AAGCCTTC-GGG
2085277 TCAT
1 TCAT
2085281 TCATAAGACC
Statistics
Matches: 657, Mismatches: 30, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
75 2 0.00
76 424 0.65
77 176 0.27
78 55 0.08
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGG
Found at i:2085441 original size:3 final size:3
Alignment explanation
Indices: 2085429--2085468 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2085419 CTAATTTTTC
2085429 TTA TTA -TA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2085469 AATTAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2085448 original size:14 final size:14
Alignment explanation
Indices: 2085429--2085473 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
2085419 CTAATTTTTC
2085429 TTATTA-TATTATTA
1 TTATTATTATTA-TA
2085443 TTATTATTATTATA
1 TTATTATTATTATA
*
2085457 TTATTATTATTAAA
1 TTATTATTATTATA
2085471 TTA
1 TTA
2085474 AATAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:2085451 original size:17 final size:17
Alignment explanation
Indices: 2085429--2085473 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
2085419 CTAATTTTTC
2085429 TTATTATATTATTATTA
1 TTATTATATTATTATTA
2085446 TTATTAT-TATATTATTA
1 TTATTATAT-TATTATTA
*
2085463 TTATTAAATTA
1 TTATTATATTA
2085474 AATAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 23 0.92
18 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATATTATTATTA
Found at i:2085454 original size:20 final size:20
Alignment explanation
Indices: 2085429--2085468 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2085419 CTAATTTTTC
2085429 TTATTATATTATTATTATTA
1 TTATTATATTATTATTATTA
2085449 TTATTATATTATTATTATTA
1 TTATTATATTATTATTATTA
2085469 AATTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATATTATTATTATTA
Found at i:2086209 original size:13 final size:13
Alignment explanation
Indices: 2086191--2086219 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2086181 ACCACCGTTA
2086191 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
2086204 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
2086217 CGG
1 CGG
2086220 GGGGGCTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:2086814 original size:18 final size:17
Alignment explanation
Indices: 2086779--2086810 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2086769 CAATTTAGTC
2086779 ATTTATTTATATGTTTA
1 ATTTATTTATATGTTTA
2086796 ATTTATTT-TATGTTT
1 ATTTATTTATATGTTT
2086811 TTAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
ATTTATTTATATGTTTA
Found at i:2087069 original size:40 final size:39
Alignment explanation
Indices: 2087010--2087089 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 39
2087000 AACCCCTTTT
2087010 ATTATTAAAAGAACAAATTTTTGGTTATAAAACGCAGATC
1 ATTATTAAAAGAACAAATTTTTGGTTATAAAA-GCAGATC
2087050 ATTATTAAAAAGAAC-AATTTTTGGTTATAAAAGCAGATC
1 ATTATT-AAAAGAACAAATTTTTGGTTATAAAAGCAGATC
2087089 A
1 A
2087090 GTTCATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 8 0.21
40 23 0.59
41 8 0.21
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (39 bp):
ATTATTAAAAGAACAAATTTTTGGTTATAAAAGCAGATC
Found at i:2087409 original size:14 final size:14
Alignment explanation
Indices: 2087390--2087421 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2087380 TAAGTGCATT
2087390 TATACATACATACA
1 TATACATACATACA
2087404 TATACATACATACA
1 TATACATACATACA
2087418 TATA
1 TATA
2087422 TAATTCTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (14 bp):
TATACATACATACA
Found at i:2087663 original size:55 final size:53
Alignment explanation
Indices: 2087597--2087897 Score: 246
Period size: 55 Copynumber: 5.5 Consensus size: 53
2087587 TGTTTTTTTG
* *
2087597 GAAATTAAGTCTGATTTTCAGAAGTTTCTTAACAATTTTCAAATGAGCTTTTAAA
1 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-AATTTTCAAATGA-CTTTTAAA
* * *
2087652 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGACCTTTCAAA
1 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-AATTTTCAAATGA-CTTTTAAA
** ** *
2087707 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAAA
1 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGAAATTTTCAAATGACTTTTAAA
* * * * * ** *
2087760 GAAGCTAAGCCTAATTTTTACGGA-TTTCTTGATGTTTTCAAATGAATTTTCAAA
1 GAAACTAAGTCTGATTTTCA-GAAGTTTCTTGAAATTTTCAAATGACTTTT-AAA
* * * ** * *
2087814 TAAATTAAG-CTTGATTTTTAGGGGTTTTCTTGATATTTTCAAATGAATTTTTAAA
1 GAAACTAAGTC-TGATTTTCAGAAG-TTTCTTGAAATTTTCAAATG-ACTTTTAAA
* * * *
2087869 GAAACTAAGCCTAATTTTTAGGAGTTTCT
1 GAAACTAAGTCTGATTTTCAGAAGTTTCT
2087898 CGATGATAAC
Statistics
Matches: 209, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
53 51 0.24
54 34 0.16
55 118 0.56
56 6 0.03
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (53 bp):
GAAACTAAGTCTGATTTTCAGAAGTTTCTTGAAATTTTCAAATGACTTTTAAA
Found at i:2088031 original size:42 final size:41
Alignment explanation
Indices: 2087969--2088064 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
2087959 ATGAATAAGT
* *
2087969 CTTTCGGGCCAT-TAGTAAGTCTTTCGAGCATGATGCTTAAATC
1 CTTT-GGGCCATCTA-TAAGTCTTTCGAGCAAGATG-ATAAATC
* *
2088012 CTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTC
1 CTTTGGGCCATCTATAAGTCTTTCGAGCAAGATGATAAATC
2088053 CTTTGGGCCATC
1 CTTTGGGCCATC
2088065 CATATGACCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 16 0.34
42 25 0.53
43 6 0.13
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (41 bp):
CTTTGGGCCATCTATAAGTCTTTCGAGCAAGATGATAAATC
Found at i:2088419 original size:275 final size:274
Alignment explanation
Indices: 2087925--2088467 Score: 831
Period size: 275 Copynumber: 2.0 Consensus size: 274
2087915 TGAAAGATTT
* *
2087925 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTTCGGGCCATTAGTAAGTC
1 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTTCGGGACATCAGTAAGTC
2087990 TTTCGAGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCT
66 TTTCGAGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCT
* * ** * *
2088055 TTGGGCCATCCATATGACCTTTGGGCAGGATGTTTTCAAATGAGTTTTTAGAAATTAAGCCTGAT
131 TTGGACCATCCATAAGACCTACGAGCAGGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGAT
* * * * * *
2088120 TTTCAGGGGTTTCTTGATGATTATCTCTAAAGAGTTTTTAAAAGGAAGTTAAGTCTATTTTTTAA
196 TTTCAGGGGTTTCTTGAAGATTATCTCCAAAGAATTTTT-AAAGGAAGCTAAGCCTAATTTTTAA
2088185 GGGTTCCTTAACAGC
260 GGGTTCCTTAACAGC
* *
2088200 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTTCTTT-GTGACATCAGTAAGT
1 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAG-TCTTTCGGGACATCAGTAAGT
* ** *
2088264 CTTTTGAGTGTGATGCTTAAAT-CTTTCGGGTCATCTATAAGTCTTTCGAGCAAGATTATAAGT-
65 CTTTCGAGCATGATGCTTAAATCCTTT-GGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTC
2088327 CTTTCGGACCATCCATAAGACCTACGAGCAGGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCT
129 CTTT-GGACCATCCATAAGACCTACGAGCAGGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCT
*
2088392 GATTTTCAGGTGTTTCTTGAAGATTATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTT
193 GATTTTCAGGGGTTTCTTGAAGATTATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTT
*
2088457 AGGGGTTCCTT
258 AAGGGTTCCTT
2088468 GATGACAACT
Statistics
Matches: 243, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
274 38 0.16
275 200 0.82
276 5 0.02
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (274 bp):
TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTTCGGGACATCAGTAAGTC
TTTCGAGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCT
TTGGACCATCCATAAGACCTACGAGCAGGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGAT
TTTCAGGGGTTTCTTGAAGATTATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTTAAG
GGTTCCTTAACAGC
Found at i:2089029 original size:17 final size:17
Alignment explanation
Indices: 2089007--2089040 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2088997 TCAAATGGAG
2089007 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
2089024 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
2089041 GCTTGTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
AGTTCATAATGAGAAGA
Found at i:2089265 original size:138 final size:138
Alignment explanation
Indices: 2089017--2089505 Score: 714
Period size: 139 Copynumber: 3.5 Consensus size: 138
2089007 AGTTCATAAT
* * *
2089017 GAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGAA-TTTAGCTCGATTCATCGAATATGGAGTTG
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTAGCTCGATTCATCGCATATGGAGTTG
*
2089081 AATCAGCAACACCTCACTCAAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGACTCAT
65 AATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGACTCAT
2089146 CCGATGAAG
130 CCGATGAAG
* * * *
2089155 GAGAAGAAGTTCATAATGAGAAGAGCTTATTCGACCTTAGCTCGATTCATTGCATATGGAGTTGA
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
* * *
2089220 ATCAGCAACGCCTCACTCGAGGGATCAACATTTCTAATGGAGAGTTCATAATGAGAATAACTCAT
66 ATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAA-GACTCAT
2089285 CCGATGAAG
130 CCGATGAAG
* *
2089294 GAGAAGACA-TTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCGTCACATATGGAGTTG
1 GAGAAGA-AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTG
*
2089358 AATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCA
65 AATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAG-ACTCA
**
2089423 TTTGAT-AAGG
129 TCCGATGAA-G
* * * *
2089433 GAGACGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCGCATAAGGAGTTG
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCGCATATGGAGTTG
*
2089498 GATCAGCA
65 AATCAGCA
2089506 TCATCGTTTC
Statistics
Matches: 316, Mismatches: 28, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
137 1 0.00
138 115 0.36
139 178 0.56
140 22 0.07
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (138 bp):
GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
ATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGACTCATC
CGATGAAG
Found at i:2096089 original size:17 final size:17
Alignment explanation
Indices: 2096067--2096099 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2096057 TACTGGGTGG
*
2096067 CCAGTATCGATACCTAC
1 CCAGTACCGATACCTAC
2096084 CCAGTACCGATACCTA
1 CCAGTACCGATACCTA
2096100 GTGCACAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.21
Consensus pattern (17 bp):
CCAGTACCGATACCTAC
Found at i:2099852 original size:24 final size:24
Alignment explanation
Indices: 2099811--2099865 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2099801 GTCGGGCAGA
** *
2099811 GCTGGCTATGATTTAGCCTGTGTT
1 GCTGGCTATGATCCAGCCTGGGTT
*
2099835 GCTGGTTATGATCCAGCCTGGGTT
1 GCTGGCTATGATCCAGCCTGGGTT
*
2099859 GTTGGCT
1 GCTGGCT
2099866 GAGTACCAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.11, C:0.18, G:0.33, T:0.38
Consensus pattern (24 bp):
GCTGGCTATGATCCAGCCTGGGTT
Found at i:2115373 original size:34 final size:34
Alignment explanation
Indices: 2115333--2115403 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
2115323 TCCATATCCA
*
2115333 TTTTTGTTAGTTCCTATGTTCATTTGAACATCAT
1 TTTTTGTTAGTTCCTACGTTCATTTGAACATCAT
2115367 TTTTTGTTAGTTCCTACGTTCATTTGAACATCAT
1 TTTTTGTTAGTTCCTACGTTCATTTGAACATCAT
2115401 TTT
1 TTT
2115404 AAGTTGCCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (34 bp):
TTTTTGTTAGTTCCTACGTTCATTTGAACATCAT
Found at i:2119202 original size:26 final size:26
Alignment explanation
Indices: 2119172--2119228 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
2119162 CTGGAACATG
2119172 TCTCACATTACCAAGTGTTCGAACAA
1 TCTCACATTACCAAGTGTTCGAACAA
2119198 TCTCACATTACCAAGTGTTCGAACAA
1 TCTCACATTACCAAGTGTTCGAACAA
2119224 TCTCA
1 TCTCA
2119229 TCGAACATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (26 bp):
TCTCACATTACCAAGTGTTCGAACAA
Found at i:2123412 original size:19 final size:19
Alignment explanation
Indices: 2123384--2123424 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2123374 TATATTACCA
*
2123384 TTAATGAAATTATAAGATT
1 TTAATAAAATTATAAGATT
*
2123403 TTAATAAAATTATGAGATT
1 TTAATAAAATTATAAGATT
2123422 TTA
1 TTA
2123425 GAGTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (19 bp):
TTAATAAAATTATAAGATT
Found at i:2123554 original size:14 final size:14
Alignment explanation
Indices: 2123515--2123547 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2123505 ATAAATATTA
2123515 ATTATGATTCTTAT
1 ATTATGATTCTTAT
2123529 ATTATGATTCTTAT
1 ATTATGATTCTTAT
*
2123543 GTTAT
1 ATTAT
2123548 AGATCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:2124352 original size:16 final size:18
Alignment explanation
Indices: 2124308--2124354 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2124298 ATTGTTTAAA
*
2124308 TTATATTATTT-ATTAATT
1 TTATA-TATTTAAATAATT
2124326 TTATATATTTAAATAATT
1 TTATATATTTAAATAATT
2124344 TT-T-TATTTAAA
1 TTATATATTTAAA
2124355 GTATGTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATATTTAAATAATT
Found at i:2124478 original size:19 final size:20
Alignment explanation
Indices: 2124436--2124483 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2124426 TGACACGTGT
*
2124436 ATAATGTAT-GTATAACTTA
1 ATAATGTATAGCATAACTTA
*
2124455 TTAATGTATAGCATAA-TTA
1 ATAATGTATAGCATAACTTA
*
2124474 ATAATATATA
1 ATAATGTATA
2124484 ATGTATATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (20 bp):
ATAATGTATAGCATAACTTA
Done.