Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000001.1 Hibiscus syriacus cultivar Beakdansim tig00000002_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: 2159989
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1689456 original size:13 final size:13
Alignment explanation
Indices: 1689434--1689468 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1689424 GTAAAAGGGA
1689434 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
1689448 AAAATAAATAAAT
1 AAAATAAATAAAT
*
1689461 AAGATAAA
1 AAAATAAA
1689469 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1691297 original size:105 final size:105
Alignment explanation
Indices: 1690999--1692071 Score: 1543
Period size: 105 Copynumber: 10.3 Consensus size: 105
1690989 CATTGTTCCA
* * **
1690999 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTG-TTGTTGACAA
* * * * * *
1691063 CCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1691105 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
1691165 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
1691205 AGTCTAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
*
1691270 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1691310 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
*
1691370 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1691410 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAG
*
1691474 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1691515 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGTCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
*
1691575 AGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1691615 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAG
*
1691679 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1691720 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
1691785 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1691825 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAATTG-TTGTTGACAA
*
1691890 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
1691932 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTG-TTGTTGACAAG
* * * *
1691997 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1692038 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1692072 CGCGGATGGC
Statistics
Matches: 888, Mismatches: 57, Indels: 41
0.90 0.06 0.04
Matches are distributed among these distances:
100 257 0.29
101 10 0.01
102 13 0.01
103 10 0.01
104 11 0.01
105 367 0.41
106 100 0.11
107 98 0.11
109 22 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1691370 original size:205 final size:205
Alignment explanation
Indices: 1690999--1692071 Score: 1599
Period size: 205 Copynumber: 5.2 Consensus size: 205
1690989 CATTGTTCCA
* * ** *
1690999 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * ** *
1691063 CCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
1691128 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
129 GTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
1691193 TGCGTTGTCTGG
194 TGCGTTGTCTGG
* * * *
1691205 AGTCTAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
1691270 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
1691335 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
*
1691400 TGTTGTCTGG
196 CGTTGTCTGG
* *
1691410 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
1691475 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
1691540 TGAAATTGTCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTTGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1691605 CGTTGTCTGG
196 CGTTGTCTGG
* *
1691615 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1691680 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
1691745 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
1691810 ACTTGCGTTGTCTGG
191 ACTTGCGTTGTCTGG
* * * *
1691825 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
*
1691890 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * *
1691955 GTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
129 GTTGAAATTGGCTCTG-AA-TGA-AA--T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* *
1692020 TGAACTTGTGTTGTCTTG
188 TGAACTTGCGTTGTCTGG
* * *
1692038 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1692072 CGCGGATGGC
Statistics
Matches: 803, Mismatches: 48, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
205 481 0.60
206 45 0.06
207 2 0.00
209 5 0.01
210 96 0.12
211 6 0.01
212 90 0.11
213 53 0.07
214 4 0.00
216 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (205 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGG
Found at i:1691718 original size:310 final size:310
Alignment explanation
Indices: 1690999--1692071 Score: 1549
Period size: 310 Copynumber: 3.4 Consensus size: 310
1690989 CATTGTTCCA
* * **
1690999 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-A--TTGAAATTGTTTGTTGACAA
* * *
1691063 CCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
63 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
1691128 GTTGAAATTGAATCTGA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
128 GTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
1691188 GAACTTGCGTTGTCTGGAGTCTAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGA
193 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT--GAAT-GGA
* *
1691253 AGTTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
255 AATT-TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1691310 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-TGAAA-T-TTTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAAATTGTTTGTTGACAACCA
*
1691371 GCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
1691436 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
* *
1691501 CTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGTCTCTGAAT-GAAATTTT
196 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGGAAATTTT
* *
1691565 GTTGACAAGCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGG
261 GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1691615 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GAAA-TTGTTTGTTGACAAC
* **
1691679 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
64 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
1691744 TTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
1691809 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
194 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AA-T-GG-A
* *
1691874 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
255 AA-T-TTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1691932 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGA-AA-TTGTTTGTTGACAAC
* * * *
1691997 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTGCCACGATATCCTCCGTCGTG
64 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTG
*
1692062 GAGTTGAAAT
126 AAGTTGAAAT
1692072 CGCGGATGGC
Statistics
Matches: 696, Mismatches: 42, Indels: 38
0.90 0.05 0.05
Matches are distributed among these distances:
305 174 0.25
306 8 0.01
307 6 0.01
308 11 0.02
309 2 0.00
310 277 0.40
311 38 0.05
312 1 0.00
314 1 0.00
315 3 0.00
316 3 0.00
317 98 0.14
318 49 0.07
319 3 0.00
321 22 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (310 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAAATTGTTTGTTGACAACCA
GCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGGAAATTTT
GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1692795 original size:67 final size:65
Alignment explanation
Indices: 1692680--1693053 Score: 216
Period size: 65 Copynumber: 5.5 Consensus size: 65
1692670 ATCTGTTGTT
* * ** *
1692680 TCAAGGGAAACGAAATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACT
1 TCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGAGAAACT
1692745 GTC
63 GTC
* * *
1692748 TCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGAAACTGTC
1 TCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTGTC
** * * ** * * * *
1692813 TCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-ACTTAGTTCCAAA
1 TCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA-----T--A-A-ATTCAAAGATTTTGTTTCAAG
1692876 AGAAACTGTC
56 AGAAACTGTC
** * * * * * * *
1692886 TCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAACTGTC
1 TCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTGTC
* * * * *
1692951 TCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA-T-AGACGAAATTTGTTTCAAGA
1 TCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T-AA-ATTCA-AAG-ATTTTGTTTCAAGA
1693014 GAAACTGTC
57 GAAACTGTC
* *
1693023 TCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TCAAGGGAGACAAAATTTGTTTTAAGGGAAA
1693054 CTGTCTCAAG
Statistics
Matches: 235, Mismatches: 50, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
64 5 0.02
65 81 0.34
66 8 0.03
67 22 0.09
68 15 0.06
70 2 0.01
71 3 0.01
72 55 0.23
73 39 0.17
74 5 0.02
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (65 bp):
TCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTGTC
Found at i:1692844 original size:36 final size:35
Alignment explanation
Indices: 1692793--1693073 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
1692783 TTCAAAGGTT
* *
1692793 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1692829 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1692864 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
1692902 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
1692931 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1692966 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1693003 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1693038 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1693074 CTCTTCTAGT
Statistics
Matches: 204, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 134 0.66
37 33 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1692989 original size:138 final size:137
Alignment explanation
Indices: 1692741--1693047 Score: 418
Period size: 138 Copynumber: 2.2 Consensus size: 137
1692731 TTTCAAGAGT
* ** * * *
1692741 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
1692806 AACTGTCTCAAGATAGACGAAAATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
66 AACTGTCTCAAGAGAGACGAAAATTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTT
1692871 CCAAAAGA
130 CCAAAAGA
** * *
1692879 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * *
1692944 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTT
66 AACTGTCTCAAGAGAGACGAAAA-TTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTT
* *
1693008 TCAAGAGA
130 CCAAAAGA
*
1693016 AACTGTCTCAAGAGAGACAAAATTTGTTTCAA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAA
1693048 GGGAAACTGT
Statistics
Matches: 147, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
137 44 0.30
138 103 0.70
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACGAAAATTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:1693095 original size:35 final size:36
Alignment explanation
Indices: 1692935--1693107 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
1692925 AATATTTTGT
* * **
1692935 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
1692971 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
1693007 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
1693043 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
1693077 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
1693108 TCTTGTTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 92 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:1693999 original size:22 final size:22
Alignment explanation
Indices: 1693974--1694024 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1693964 TTGTGTTTGG
1693974 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1693996 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1694018 TCAAAGG
1 TCAAAGG
1694025 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1694670 original size:20 final size:22
Alignment explanation
Indices: 1694647--1694696 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1694637 TTTTTAATTT
1694647 TTGTTCTTT-CTTTTTTG-TTC
1 TTGTTCTTTCCTTTTTTGCTTC
*
1694667 TTGTTTTTTCCTTTTTTGCTTC
1 TTGTTCTTTCCTTTTTTGCTTC
1694689 TT-TTCTTT
1 TTGTTCTTT
1694697 TTTCTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 13 0.50
22 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (22 bp):
TTGTTCTTTCCTTTTTTGCTTC
Found at i:1694707 original size:22 final size:22
Alignment explanation
Indices: 1694653--1694705 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
1694643 ATTTTTGTTC
1694653 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
1694674 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
1694697 TTTCTTTTT
1 TTTCTTTTT
1694706 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:1697696 original size:9 final size:9
Alignment explanation
Indices: 1697682--1697715 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1697672 TAAAAGGGAA
1697682 AAATAAAAT
1 AAATAAAAT
1697691 AAATAAAAT
1 AAATAAAAT
1697700 AAAT-AAAT
1 AAATAAAAT
1697708 AAGATAAA
1 AA-ATAAA
1697716 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1697703 original size:13 final size:13
Alignment explanation
Indices: 1697681--1697715 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1697671 GTAAAAGGGA
1697681 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
1697695 AAAATAAATAAAT
1 AAAATAAATAAAT
*
1697708 AAGATAAA
1 AAAATAAA
1697716 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1698188 original size:2 final size:2
Alignment explanation
Indices: 1698181--1698215 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1698171 TATTAAAGAA
*
1698181 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1698216 ATAATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1698234 original size:18 final size:17
Alignment explanation
Indices: 1698213--1698255 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1698203 ATATATACAT
1698213 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
1698231 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
1698248 ATAA-AATA
1 ATAATAATA
1698256 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:1698252 original size:14 final size:13
Alignment explanation
Indices: 1698215--1698253 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1698205 ATATACATAT
1698215 AATAATAATAACATA
1 AATAATAA-AA-ATA
1698230 AATAATAAAAATA
1 AATAATAAAAATA
1698243 AATGAATAAAA
1 AAT-AATAAAA
1698254 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:1699495 original size:40 final size:39
Alignment explanation
Indices: 1699440--1699536 Score: 126
Period size: 40 Copynumber: 2.4 Consensus size: 39
1699430 AACACCTTAA
*
1699440 AAAATAAACAAACGAACACGAATCGAACT-TGAATA-ATTT
1 AAAATAAACAAACGAACACGAATC-AAATATGAATACA-TT
*
1699479 CAAAATAAACAAACGAACATGAATCAAATATGAATACCATT
1 -AAAATAAACAAACGAACACGAATCAAATATGAATA-CATT
1699520 AAAATAAACAAACGAAC
1 AAAATAAACAAACGAAC
1699537 TCAACCATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
39 3 0.06
40 46 0.88
41 2 0.04
42 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.08, T:0.18
Consensus pattern (39 bp):
AAAATAAACAAACGAACACGAATCAAATATGAATACATT
Found at i:1701964 original size:17 final size:17
Alignment explanation
Indices: 1701942--1701999 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
1701932 AACGGTCAAC
1701942 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
1701959 GGTCAACGGTCGGGTCA
1 GGTCAACGGTCGGGTCG
*
1701976 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1701993 GGTCAAC
1 GGTCAAC
1702000 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1701969 original size:7 final size:7
Alignment explanation
Indices: 1701909--1701952 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
1701899 GTCAAAGAAA
1701909 GTCAACG
1 GTCAACG
1701916 GTC-ACG
1 GTCAACG
1701922 GTCAACG
1 GTCAACG
1701929 GTCAACG
1 GTCAACG
1701936 GTCAACG
1 GTCAACG
1701943 GTCAACG
1 GTCAACG
1701950 GTC
1 GTC
1701953 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1709221 original size:17 final size:17
Alignment explanation
Indices: 1709199--1709239 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1709189 CACGGTCAAC
*
1709199 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
1709216 GGTCAATAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1709233 GGTCAAC
1 GGTCAAC
1709240 CCGGTTCAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.22, G:0.41, T:0.20
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1709257 original size:19 final size:20
Alignment explanation
Indices: 1709233--1709303 Score: 101
Period size: 19 Copynumber: 3.6 Consensus size: 20
1709223 AGTCGGGTCG
*
1709233 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
1709252 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
1709271 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
1709291 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1709304 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 30 0.64
20 16 0.34
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:1709270 original size:10 final size:10
Alignment explanation
Indices: 1709235--1709303 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
1709225 TCGGGTCGGG
*
1709235 TCAACCCGGT
1 TCAAACCGGT
*
1709245 TCAGACCGG-
1 TCAAACCGGT
1709254 TCAAACCGGT
1 TCAAACCGGT
*
1709264 TCGAACCGG-
1 TCAAACCGGT
1709273 TCAAACCGGT
1 TCAAACCGGT
*
1709283 TCAAAACTGG-
1 TC-AAACCGGT
1709293 TCAAACCGGT
1 TCAAACCGGT
1709303 T
1 T
1709304 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1716639 original size:30 final size:30
Alignment explanation
Indices: 1716596--1716655 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1716586 CCCGTGCAGG
*
1716596 TGATTAAATAGTTAAAAACTTCTAATTAGA
1 TGATTAAACAGTTAAAAACTTCTAATTAGA
*
1716626 TGATTACACAGTTAAAAACTTCTAATTAGA
1 TGATTAAACAGTTAAAAACTTCTAATTAGA
1716656 CAAATTATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (30 bp):
TGATTAAACAGTTAAAAACTTCTAATTAGA
Found at i:1718906 original size:71 final size:69
Alignment explanation
Indices: 1718801--1718938 Score: 161
Period size: 70 Copynumber: 2.0 Consensus size: 69
1718791 AAATATAGTG
* *
1718801 GTTTTATAATAAACGCCACTATAGATAGACTTATTGCTACGTTTTTAAAAAAAACGTCACTATTA
1 GTTTTATAATAAACGCCACTATAGATAGACTTATTGC-ACGTTTGTAAAAAAAACGCCACTATTA
1718866 TTGAT
65 TTGAT
* * * * * * *
1718871 GTTTTATTAATAAAACGTCATTATA-ATGGATTTATTGCGCGTTTGTCAAGAAAACGCCACTATT
1 GTTTTA-TAAT-AAACGCCACTATAGATAGACTTATTGCACGTTTGTAAAAAAAACGCCACTATT
1718935 ATTG
64 ATTG
1718939 CCTCGAAATC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
70 31 0.54
71 15 0.26
72 11 0.19
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (69 bp):
GTTTTATAATAAACGCCACTATAGATAGACTTATTGCACGTTTGTAAAAAAAACGCCACTATTAT
TGAT
Found at i:1735409 original size:146 final size:148
Alignment explanation
Indices: 1735148--1735444 Score: 555
Period size: 146 Copynumber: 2.0 Consensus size: 148
1735138 TTGTGCAACG
1735148 ATGTGGCCTCGTACAGTTTGGTGAGATGATCCCATATCTCCTTAGCTGTCTTTTTCTCCTCGATG
1 ATGTGGCCTCGTACAGTTTGGTGAGATGATCCCA-ATCTCCTTAGCTGTCTTTTTCTCCTCGATG
1735213 CTTGACATACTTCATCTGCTATGCTAGATGAAAGTTTGCCATAGCATTTCCGTCCATTTCGATCC
65 CTTGACATACTTCATCTGCTATGCTAGATGAAAGTTTGCCATAGCATTTCCGTCCATTTCGATCC
1735278 ATTTGCTGTCATCTGCAAA
130 ATTTGCTGTCATCTGCAAA
1735297 ATGTGGCCTTCGTACAG-TTGGTGAGATGATCCC-ATCTCCTTAGCTGTCTTTTTCTCCTCGATG
1 ATGTGGCC-TCGTACAGTTTGGTGAGATGATCCCAATCTCCTTAGCTGTCTTTTTCTCCTCGATG
1735360 CTTGACATA-TTCATCTGCTATGCTAGATGAAAGTTTGCCATAGCATTTCCGTCCATTTCGATCC
65 CTTGACATACTTCATCTGCTATGCTAGATGAAAGTTTGCCATAGCATTTCCGTCCATTTCGATCC
1735424 ATTTGCTGTCATCTGCAAA
130 ATTTGCTGTCATCTGCAAA
1735443 AT
1 AT
1735445 CCATAGCATT
Statistics
Matches: 147, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
146 76 0.52
147 39 0.27
149 24 0.16
150 8 0.05
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (148 bp):
ATGTGGCCTCGTACAGTTTGGTGAGATGATCCCAATCTCCTTAGCTGTCTTTTTCTCCTCGATGC
TTGACATACTTCATCTGCTATGCTAGATGAAAGTTTGCCATAGCATTTCCGTCCATTTCGATCCA
TTTGCTGTCATCTGCAAA
Found at i:1735468 original size:48 final size:48
Alignment explanation
Indices: 1735397--1735496 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
1735387 TGAAAGTTTG
1735397 CCATAGCATTTCCGTCCATTTCGATCCATTTGCTGTCATCTGCAAAAT
1 CCATAGCATTTCCGTCCATTTCGATCCATTTGCTGTCATCTGCAAAAT
1735445 CCATAGCATTTCCGTCCATTTCGATCCATTTGCTGTCATCTGCAAAAT
1 CCATAGCATTTCCGTCCATTTCGATCCATTTGCTGTCATCTGCAAAAT
1735493 CCAT
1 CCAT
1735497 CGGCCTTTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (48 bp):
CCATAGCATTTCCGTCCATTTCGATCCATTTGCTGTCATCTGCAAAAT
Found at i:1736684 original size:24 final size:24
Alignment explanation
Indices: 1736657--1736707 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1736647 AAGTTTAGCC
1736657 ATTA-AAATATAAAATAATCATTAA
1 ATTATAAATATAAAATAAT-ATTAA
* * *
1736681 ATTATTATTATTAAATAATATTAA
1 ATTATAAATATAAAATAATATTAA
1736705 ATT
1 ATT
1736708 TTATTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTATAAATATAAAATAATATTAA
Found at i:1736718 original size:25 final size:25
Alignment explanation
Indices: 1736668--1736713 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1736658 TTAAAATATA
1736668 AAATAATCATTAAATTATTATTATT
1 AAATAATCATTAAATTATTATTATT
1736693 AAATAAT-ATTAAATT-TTATTA
1 AAATAATCATTAAATTATTATTA
1736714 AATTATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATAATCATTAAATTATTATTATT
Found at i:1737550 original size:14 final size:14
Alignment explanation
Indices: 1737533--1737573 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
1737523 GCTCGAATGG
1737533 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
1737547 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
*
1737561 CCTCTGTCGGATG
1 CCTCGGTCGGATG
1737574 GCTTCGGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.07, C:0.34, G:0.34, T:0.24
Consensus pattern (14 bp):
CCTCGGTCGGATGC
Found at i:1744206 original size:29 final size:29
Alignment explanation
Indices: 1744174--1744235 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
1744164 GAAATGAAAT
1744174 ATTACCTTACACATTACTGGGAATGTTAC
1 ATTACCTTACACATTACTGGGAATGTTAC
*
1744203 ATTACCTTACACATTATTGGGAATGTTAC
1 ATTACCTTACACATTACTGGGAATGTTAC
1744232 ATTA
1 ATTA
1744236 TTGTGTTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (29 bp):
ATTACCTTACACATTACTGGGAATGTTAC
Found at i:1744423 original size:28 final size:28
Alignment explanation
Indices: 1744392--1744449 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1744382 TTCATAGAAA
*
1744392 ATATATTATTGTATT-ATTTTCAATTTAT
1 ATATATT-TTGTATTAATTTTAAATTTAT
*
1744420 ATATATTTTTTATTAAATTTTAAATTTAT
1 ATATATTTTGTATT-AATTTTAAATTTAT
1744449 A
1 A
1744450 AAATTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 7 0.27
29 13 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATATATTTTGTATTAATTTTAAATTTAT
Found at i:1746363 original size:2 final size:2
Alignment explanation
Indices: 1746356--1746380 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1746346 ACTTTATCTG
1746356 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1746381 GGCTAAATTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1748036 original size:30 final size:30
Alignment explanation
Indices: 1747968--1748042 Score: 125
Period size: 29 Copynumber: 2.5 Consensus size: 30
1747958 GACGTCCTGG
1747968 GGTAGGTCGCCATGCACGCCCAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAGCGACCTA
**
1747998 -CCAGGTCGCCATGCACGCCCAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAGCGACCTA
1748027 GGTAGGTCGCCATGCA
1 GGTAGGTCGCCATGCA
1748043 ATCTCCAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.20, C:0.37, G:0.29, T:0.13
Consensus pattern (30 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCTA
Found at i:1750360 original size:2 final size:2
Alignment explanation
Indices: 1750353--1750395 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1750343 TCTTGTTTGC
1750353 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1750395 T
1 T
1750396 TGACAGTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1755294 original size:19 final size:19
Alignment explanation
Indices: 1755254--1755295 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1755244 AGTAACAACC
* *
1755254 ATTAAAAATATTATTAAAT
1 ATTAAAAATAATATAAAAT
1755273 ATTAAAAA-AATATAAAATT
1 ATTAAAAATAATATAAAA-T
1755292 ATTA
1 ATTA
1755296 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTAAAAATAATATAAAAT
Found at i:1755560 original size:21 final size:19
Alignment explanation
Indices: 1755527--1755575 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
1755517 AACTATTGTA
1755527 GCAGGGGTTTAGAAACCAG
1 GCAGGGGTTTAGAAACCAG
*
1755546 GCAGGGTGATTTAGATACCAG
1 GCAGGG-G-TTTAGAAACCAG
*
1755567 ACAGGGGTT
1 GCAGGGGTT
1755576 GTAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 8 0.31
20 2 0.08
21 16 0.62
ACGTcount: A:0.29, C:0.14, G:0.37, T:0.20
Consensus pattern (19 bp):
GCAGGGGTTTAGAAACCAG
Found at i:1757990 original size:197 final size:197
Alignment explanation
Indices: 1757454--1758043 Score: 1141
Period size: 197 Copynumber: 3.0 Consensus size: 197
1757444 TAACTATACT
1757454 TTTTCTTTTTCTTTTTTTCGAATGGTAAAAAGATAAACAATGGAACTATCTTAGCTAAACATTGT
1 TTTTCTTTTTCTTTTTTTCGAATGGTAAAAAGATAAACAATGGAACTATCTTAGCTAAACATTGT
1757519 CATGCATGACACAACTTGACTCATCTTCATGCAGCAACAAAACAACTTCCGCAGGAGGCGTCCGG
66 CATGCATGACACAACTTGACTCATCTTCATGCAGCAACAAAACAACTTCCGCAGGAGGCGTCCGG
1757584 AGAGCTTCAACACCGAACGGTAAATTCCGCGTCAACTTAGGCATATACCTTCCGCAACCTCATTA
131 AGAGCTTCAACACCGAACGGTAAATTCCGCGTCAACTTAGGCATATACCTTCCGCAACCTCATTA
1757649 CA
196 CA
1757651 TTTTCTTTTTCTTTTTTTCG-A--GTAAAAAGATAAACAATGGAACTATCTTAGCTAAACATTGT
1 TTTTCTTTTTCTTTTTTTCGAATGGTAAAAAGATAAACAATGGAACTATCTTAGCTAAACATTGT
1757713 CATGCATGACACAACTTGACTCATCTTCATGCAGCAACAAAACAACTTCCGCAGGAGGCGTCCGG
66 CATGCATGACACAACTTGACTCATCTTCATGCAGCAACAAAACAACTTCCGCAGGAGGCGTCCGG
*
1757778 AGAGCTTCAACACCGAACGATAAATTCCGCGTCAACTTAGGCATATACCTTCCGCAACCTCATTA
131 AGAGCTTCAACACCGAACGGTAAATTCCGCGTCAACTTAGGCATATACCTTCCGCAACCTCATTA
1757843 CA
196 CA
1757845 TTTTCTTTTTCTTTTTTTCGAATGGTAAAAAGATAAACAATGGAACTATCTTAGCTAAACATTGT
1 TTTTCTTTTTCTTTTTTTCGAATGGTAAAAAGATAAACAATGGAACTATCTTAGCTAAACATTGT
*
1757910 CATGCACGACACAACTTGACTCATCTTCATGCAGCAACAAAACAACTTCCGCAGGAGGCGTCCGG
66 CATGCATGACACAACTTGACTCATCTTCATGCAGCAACAAAACAACTTCCGCAGGAGGCGTCCGG
1757975 AGAGCTTCAACACCGAACGGTAAATTCCGCGTCAACTTAGGCATATACCTTCCGCAACCTCATTA
131 AGAGCTTCAACACCGAACGGTAAATTCCGCGTCAACTTAGGCATATACCTTCCGCAACCTCATTA
1758040 CA
196 CA
1758042 TT
1 TT
1758044 CTTGAGGAAC
Statistics
Matches: 387, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
194 192 0.50
195 1 0.00
196 1 0.00
197 193 0.50
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (197 bp):
TTTTCTTTTTCTTTTTTTCGAATGGTAAAAAGATAAACAATGGAACTATCTTAGCTAAACATTGT
CATGCATGACACAACTTGACTCATCTTCATGCAGCAACAAAACAACTTCCGCAGGAGGCGTCCGG
AGAGCTTCAACACCGAACGGTAAATTCCGCGTCAACTTAGGCATATACCTTCCGCAACCTCATTA
CA
Found at i:1759215 original size:2 final size:2
Alignment explanation
Indices: 1759208--1759256 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1759198 AATTTATTCT
1759208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1759250 TA TA TA T
1 TA TA TA T
1759257 GGGATATGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1761190 original size:26 final size:25
Alignment explanation
Indices: 1761161--1761214 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1761151 ATATGAATTC
1761161 ATTTTAAAAAATGACATTAATATT-TT
1 ATTTTAAAAAAT-A-ATTAATATTGTT
*
1761187 ATTTTTAAATAATAATTAATATTGTT
1 A-TTTTAAAAAATAATTAATATTGTT
1761213 AT
1 AT
1761215 AATGATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 10 0.40
26 5 0.20
27 10 0.40
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (25 bp):
ATTTTAAAAAATAATTAATATTGTT
Found at i:1761207 original size:25 final size:28
Alignment explanation
Indices: 1761162--1761214 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1761152 TATGAATTCA
1761162 TTTTAAAAAATGACATTAATATT-TTAT
1 TTTTAAAAAATGACATTAATATTGTTAT
*
1761189 TTTTAAATAAT-A-ATTAATATTGTTAT
1 TTTTAAAAAATGACATTAATATTGTTAT
1761215 AATGATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 5 0.21
27 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTTAAAAAATGACATTAATATTGTTAT
Found at i:1777760 original size:36 final size:38
Alignment explanation
Indices: 1777710--1777781 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 38
1777700 AACACACCGG
1777710 AATATATAGGATACAGGA-CCCACAAA-ACAGCAAAAGA
1 AATATATAGGATACAGGACCCCA-AAATACAGCAAAAGA
1777747 AATATAT-GGATACAGGACCCCAAAATACAGCAAAA
1 AATATATAGGATACAGGACCCCAAAATACAGCAAAA
1777782 TTGTACCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 13 0.39
37 20 0.61
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.12
Consensus pattern (38 bp):
AATATATAGGATACAGGACCCCAAAATACAGCAAAAGA
Found at i:1777771 original size:35 final size:39
Alignment explanation
Indices: 1777710--1777781 Score: 116
Period size: 36 Copynumber: 1.9 Consensus size: 39
1777700 AACACACCGG
1777710 AATATATAGGATACAGGACCCAC-AAA-ACAGCAAAAGA
1 AATATATAGGATACAGGACCCACAAAATACAGCAAAAGA
1777747 AATATAT-GGATACAGGACCC-CAAAATACAGCAAAA
1 AATATATAGGATACAGGACCCACAAAATACAGCAAAA
1777782 TTGTACCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 1 0.03
36 16 0.48
37 16 0.48
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.12
Consensus pattern (39 bp):
AATATATAGGATACAGGACCCACAAAATACAGCAAAAGA
Found at i:1785794 original size:80 final size:80
Alignment explanation
Indices: 1785648--1785808 Score: 265
Period size: 80 Copynumber: 2.0 Consensus size: 80
1785638 TAAACCTATA
*
1785648 AAATTAGCAAATTTTCTTTTGTAATGATATTACAATATTAATTCGAGTTAATATTGGTTATCTCT
1 AAATTAGCAAATTTTCTTTTGTAATGATATTACAATATTAATTCGAGTTAATATTGGTTATATCT
1785713 ACTATCTTGGTCAGAG
66 ACTATCTT-GTCAGAG
1785729 AAATTAGCAAATTTTC-TTTGTAATGATATTACAATATTAAGTTCCGAGTTAATATTGG-TA-AT
1 AAATTAGCAAATTTTCTTTTGTAATGATATTACAATATTAA-TT-CGAGTTAATATTGGTTATAT
1785791 CTACTATCTTGTCAGAG
64 CTACTATCTTGTCAGAG
1785808 A
1 A
1785809 GTAGAGACAC
Statistics
Matches: 77, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
79 8 0.10
80 35 0.45
81 20 0.26
82 14 0.18
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.42
Consensus pattern (80 bp):
AAATTAGCAAATTTTCTTTTGTAATGATATTACAATATTAATTCGAGTTAATATTGGTTATATCT
ACTATCTTGTCAGAG
Found at i:1797604 original size:2 final size:2
Alignment explanation
Indices: 1797597--1797645 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1797587 TTCGTTCTAA
1797597 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
1797639 AT AT AT A
1 AT AT AT A
1797646 ACTTTTTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1800829 original size:14 final size:13
Alignment explanation
Indices: 1800811--1800835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1800801 TAACTCGATT
1800811 TTTTTTTTCATTA
1 TTTTTTTTCATTA
1800824 TTTTTTTTCATT
1 TTTTTTTTCATT
1800836 TTTAAATAAA
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTCATTA
Found at i:1800932 original size:29 final size:29
Alignment explanation
Indices: 1800875--1800932 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1800865 CAAATCATCG
* *
1800875 ATTTTCAATTTATTTAATTGATTTTGTTT
1 ATTTTCAATTTATTCAATTGATTTGGTTT
* * *
1800904 ATTTTTAATTTATTCATTTGGTTTGGTTT
1 ATTTTCAATTTATTCAATTGATTTGGTTT
1800933 GATTGTGATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (29 bp):
ATTTTCAATTTATTCAATTGATTTGGTTT
Found at i:1803476 original size:16 final size:16
Alignment explanation
Indices: 1803428--1803477 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
1803418 AATTAAATTT
1803428 GGGTTGCTTTCGGTTC
1 GGGTTGCTTTCGGTTC
* * *
1803444 AGGTTGATTTTGGTTC
1 GGGTTGCTTTCGGTTC
1803460 GGGTTGCTTTCGGTTC
1 GGGTTGCTTTCGGTTC
1803476 GG
1 GG
1803478 ATTGGATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.04, C:0.14, G:0.38, T:0.44
Consensus pattern (16 bp):
GGGTTGCTTTCGGTTC
Found at i:1815970 original size:30 final size:30
Alignment explanation
Indices: 1815934--1816001 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
1815924 TTTGGAGTCA
*
1815934 TCATCTTCCCAGTCGTTGACGGCCTCATCT
1 TCATCTTCCCAGTCGTGGACGGCCTCATCT
* *
1815964 TTATCTTCCCAGTCGTGGTCGGCCTCATCT
1 TCATCTTCCCAGTCGTGGACGGCCTCATCT
1815994 TCATCTTC
1 TCATCTTC
1816002 GTCGTCAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.12, C:0.35, G:0.16, T:0.37
Consensus pattern (30 bp):
TCATCTTCCCAGTCGTGGACGGCCTCATCT
Found at i:1816017 original size:27 final size:28
Alignment explanation
Indices: 1815987--1816045 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
1815977 CGTGGTCGGC
* *
1815987 CTCATCT-TCATCTTCGTCGTCAACAAA
1 CTCATCTATCATCTTCATAGTCAACAAA
*
1816014 CTCA-CTATCATCTTCATAGTCATCAAA
1 CTCATCTATCATCTTCATAGTCAACAAA
1816041 CTCAT
1 CTCAT
1816046 TTTTGTAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.34
Consensus pattern (28 bp):
CTCATCTATCATCTTCATAGTCAACAAA
Found at i:1835861 original size:32 final size:32
Alignment explanation
Indices: 1835820--1835884 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1835810 AGTGTCGGTT
1835820 TGAGTTTGATTTCCCATTATTCTCATTATCCA
1 TGAGTTTGATTTCCCATTATTCTCATTATCCA
1835852 TGAGTTTGATTTCCCATTATTCTCATTATCCA
1 TGAGTTTGATTTCCCATTATTCTCATTATCCA
1835884 T
1 T
1835885 TTTAAAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.48
Consensus pattern (32 bp):
TGAGTTTGATTTCCCATTATTCTCATTATCCA
Found at i:1835884 original size:16 final size:16
Alignment explanation
Indices: 1835833--1835885 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1835823 GTTTGATTTC
1835833 CCATTATTCTCATTAT
1 CCATTATTCTCATTAT
* *
1835849 CCATGAGTT-TGATT-T
1 CCATTA-TTCTCATTAT
1835864 CCCATTATTCTCATTAT
1 -CCATTATTCTCATTAT
1835881 CCATT
1 CCATT
1835886 TTAAAACTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.23, C:0.25, G:0.06, T:0.47
Consensus pattern (16 bp):
CCATTATTCTCATTAT
Found at i:1839992 original size:15 final size:15
Alignment explanation
Indices: 1839972--1840002 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1839962 GTATGAGCAA
1839972 CTACTTCGTTCGCTT
1 CTACTTCGTTCGCTT
1839987 CTACTTCGTTCGCTT
1 CTACTTCGTTCGCTT
1840002 C
1 C
1840003 CACCGTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.35, G:0.13, T:0.45
Consensus pattern (15 bp):
CTACTTCGTTCGCTT
Found at i:1840456 original size:22 final size:21
Alignment explanation
Indices: 1840430--1840489 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
1840420 TTAAGTCTCA
1840430 ATATTAATTAAATTTAATAAAT
1 ATATTAATTAAATTTAA-AAAT
*
1840452 TTATTAAATT-AATATTAAAAAT
1 ATATT-AATTAAAT-TTAAAAAT
1840474 ATATTAA-TATAATTTA
1 ATATTAATTA-AATTTA
1840490 GTGGCTATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.03
21 5 0.16
22 18 0.56
23 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTAATTAAATTTAAAAAT
Found at i:1856505 original size:12 final size:12
Alignment explanation
Indices: 1856488--1856512 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1856478 AATGCGTCTC
1856488 TCATATTTTTTT
1 TCATATTTTTTT
1856500 TCATATTTTTTT
1 TCATATTTTTTT
1856512 T
1 T
1856513 TAAATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATATTTTTTT
Found at i:1861401 original size:27 final size:27
Alignment explanation
Indices: 1861363--1861425 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
1861353 ATAATGGTTT
*
1861363 TGAATCATTCAGAATATACTTTTGTGC
1 TGAATCATTCAGAATATACTTCTGTGC
* *
1861390 TGAATCATTCAGAATGTACTTCTGTGT
1 TGAATCATTCAGAATATACTTCTGTGC
*
1861417 TAAATCATT
1 TGAATCATT
1861426 TAACACTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (27 bp):
TGAATCATTCAGAATATACTTCTGTGC
Found at i:1870717 original size:2 final size:2
Alignment explanation
Indices: 1870710--1870767 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1870700 TTCGTTGTGA
1870710 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
1870752 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1870768 GCAAAGAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1872718 original size:27 final size:27
Alignment explanation
Indices: 1872699--1872821 Score: 223
Period size: 27 Copynumber: 4.6 Consensus size: 27
1872689 GTATACGTTC
*
1872699 ATTTTTATTT-TAA-ATTAGTATAATT
1 ATTTATATTTATAATATTAGTATAATT
1872724 ATTTATATTTATAATATTAGTATAATT
1 ATTTATATTTATAATATTAGTATAATT
1872751 ATTTATATTTATAATATTAGTATAATT
1 ATTTATATTTATAATATTAGTATAATT
1872778 ATTTATATTTATAATATTAGTATAATT
1 ATTTATATTTATAATATTAGTATAATT
1872805 ATTTATATTTATAATAT
1 ATTTATATTTATAATAT
1872822 GTAATTATAA
Statistics
Matches: 95, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
25 9 0.09
26 3 0.03
27 83 0.87
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (27 bp):
ATTTATATTTATAATATTAGTATAATT
Found at i:1875514 original size:31 final size:31
Alignment explanation
Indices: 1875467--1875613 Score: 168
Period size: 31 Copynumber: 4.7 Consensus size: 31
1875457 ACTACAGAGT
* * *
1875467 TGGTCATTAATATTATCTATTGGTTACAAAA
1 TGGTCACTAATGTTATCGATTGGTTACAAAA
*
1875498 TGGTCACTACTGTTATCGATTGGTTACAAAA
1 TGGTCACTAATGTTATCGATTGGTTACAAAA
* *
1875529 TGGTCACTAATATTATCGATTGGTTACAAAC
1 TGGTCACTAATGTTATCGATTGGTTACAAAA
* * *
1875560 TGGTCACTCAAAGTTATCGATTGGTTGCAAAC
1 TGGTCACT-AATGTTATCGATTGGTTACAAAA
* * *
1875592 TGGGCACTCAACGTTATAGATT
1 TGGTCACT-AATGTTATCGATT
1875614 CGTTTTCCCT
Statistics
Matches: 102, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 63 0.62
32 39 0.38
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (31 bp):
TGGTCACTAATGTTATCGATTGGTTACAAAA
Found at i:1875564 original size:62 final size:63
Alignment explanation
Indices: 1875467--1875599 Score: 187
Period size: 62 Copynumber: 2.1 Consensus size: 63
1875457 ACTACAGAGT
* * **
1875467 TGGTCATTAATATTATCTATTGGTTACAAAATGGTCACT-ACTGTTATCGATTGGTTACAAAA
1 TGGTCACTAATATTATCGATTGGTTACAAAATGGTCACTCAAAGTTATCGATTGGTTACAAAA
* * *
1875529 TGGTCACTAATATTATCGATTGGTTACAAACTGGTCACTCAAAGTTATCGATTGGTTGCAAAC
1 TGGTCACTAATATTATCGATTGGTTACAAAATGGTCACTCAAAGTTATCGATTGGTTACAAAA
*
1875592 TGGGCACT
1 TGGTCACT
1875600 CAACGTTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
62 36 0.58
63 26 0.42
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (63 bp):
TGGTCACTAATATTATCGATTGGTTACAAAATGGTCACTCAAAGTTATCGATTGGTTACAAAA
Found at i:1876259 original size:77 final size:78
Alignment explanation
Indices: 1876156--1876453 Score: 306
Period size: 77 Copynumber: 4.0 Consensus size: 78
1876146 TTAACAATAT
1876156 TTTTTAATGATTTTTTTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTGGATTATTTGT
1 TTTTTAATGATTTTTTTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTGGATTATTTGT
1876221 TTTTTTTAGAAGA
66 TTTTTTTAGAAGA
1876234 TTTTTAATGA-TTTTTTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTGGATTA-TTG-
1 TTTTTAATGATTTTTTTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTGGATTATTTGT
*
1876296 -TTTTTTAGAGGA
66 TTTTTTTAGAAGA
** * * * ***** * * * *
1876308 -GATGAAAGAGTGAAGAGATAAATATTTTATTAAACA-TTT-T----------TTTTGGATTATT
1 TTTTTAATGATTTTTTTG-TCAGT-TATTA-TAAATATTTTATTAAACATTTTTTTTGGATTATT
1876360 TGTTTTTTTTAGAAGA
63 TGTTTTTTTTAGAAGA
1876376 TTTTTAATGATTTTTTTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTTGGATTATTTG
1 TTTTTAATGATTTTTTTGTCAGTTATTATAAATATTTTATTAAACA-TTTTTTTTGGATTATTTG
1876441 TTTTTTTTAGAAG
65 TTTTTTTTAGAAG
1876454 GAGATGAAGA
Statistics
Matches: 170, Mismatches: 29, Indels: 41
0.71 0.12 0.17
Matches are distributed among these distances:
65 10 0.06
66 8 0.05
67 7 0.04
68 15 0.09
69 7 0.04
73 5 0.03
74 13 0.08
75 4 0.02
76 10 0.06
77 54 0.32
78 10 0.06
79 27 0.16
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (78 bp):
TTTTTAATGATTTTTTTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTGGATTATTTGT
TTTTTTTAGAAGA
Found at i:1876426 original size:142 final size:144
Alignment explanation
Indices: 1876183--1876471 Score: 521
Period size: 142 Copynumber: 2.0 Consensus size: 144
1876173 GTCAGTTATT
1876183 ATAAATATTTTATTAAACATTTTTTTTGGATTATTTGTTTTTTTTAGAAGATTTTTAATGATTTT
1 ATAAATATTTTATTAAACATTTTTTTTGGATTATTTGTTTTTTTTAGAAGATTTTTAATGATTTT
1876248 TTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTGGATTA-TTG-TTTTTTAG-AGGAGA
66 TTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTGGATTATTTGTTTTTTTAGAAGGAGA
1876310 TGAAAGAGTGAAGAG
131 TG-AAGAGTGAAGAG
1876325 ATAAATATTTTATTAAACATTTTTTTTGGATTATTTGTTTTTTTTAGAAGATTTTTAATGATTTT
1 ATAAATATTTTATTAAACATTTTTTTTGGATTATTTGTTTTTTTTAGAAGATTTTTAATGA-TTT
1876390 TTTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTTGGATTATTTGTTTTTTTTAGAAGG
65 TTTGTCAGTTATTATAAATATTTTATTAAACA-TTTTTTTTGGATTATTTG-TTTTTTTAGAAGG
1876455 AGATGAAGAGTGAAGAG
128 AGATGAAGAGTGAAGAG
1876472 GCTGTTAGCG
Statistics
Matches: 141, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
142 61 0.43
143 35 0.25
144 14 0.10
145 3 0.02
147 20 0.14
148 8 0.06
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (144 bp):
ATAAATATTTTATTAAACATTTTTTTTGGATTATTTGTTTTTTTTAGAAGATTTTTAATGATTTT
TTGTCAGTTATTATAAATATTTTATTAAACATTTTTTTTGGATTATTTGTTTTTTTAGAAGGAGA
TGAAGAGTGAAGAG
Found at i:1877901 original size:85 final size:85
Alignment explanation
Indices: 1877758--1877929 Score: 344
Period size: 85 Copynumber: 2.0 Consensus size: 85
1877748 ATCATTACTT
1877758 TGCCTTTGGATTTGTCACTCCCATCCGATGATATAACAATCTGACAACCCTAGAGGAAAAAGAAA
1 TGCCTTTGGATTTGTCACTCCCATCCGATGATATAACAATCTGACAACCCTAGAGGAAAAAGAAA
1877823 GTTCTAGTTTTTAAGAAAAA
66 GTTCTAGTTTTTAAGAAAAA
1877843 TGCCTTTGGATTTGTCACTCCCATCCGATGATATAACAATCTGACAACCCTAGAGGAAAAAGAAA
1 TGCCTTTGGATTTGTCACTCCCATCCGATGATATAACAATCTGACAACCCTAGAGGAAAAAGAAA
1877908 GTTCTAGTTTTTAAGAAAAA
66 GTTCTAGTTTTTAAGAAAAA
1877928 TG
1 TG
1877930 TAAAATGTAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (85 bp):
TGCCTTTGGATTTGTCACTCCCATCCGATGATATAACAATCTGACAACCCTAGAGGAAAAAGAAA
GTTCTAGTTTTTAAGAAAAA
Found at i:1879512 original size:18 final size:18
Alignment explanation
Indices: 1879489--1879529 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1879479 AAATCTATAT
1879489 CAACCTCTCTCAGGAAAG
1 CAACCTCTCTCAGGAAAG
*
1879507 CAACCTCTCTTAGGAAAG
1 CAACCTCTCTCAGGAAAG
1879525 CAACC
1 CAACC
1879530 AGAGGGCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.17
Consensus pattern (18 bp):
CAACCTCTCTCAGGAAAG
Found at i:1884801 original size:6 final size:6
Alignment explanation
Indices: 1884790--1884837 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
1884780 CGAAGACACG
1884790 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
1884838 CACGACCACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAC
Found at i:1884845 original size:6 final size:6
Alignment explanation
Indices: 1884836--1884926 Score: 98
Period size: 6 Copynumber: 15.5 Consensus size: 6
1884826 TATTACTATT
* *
1884836 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCCCG ACCCCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * * *
1884884 ACCCCGG ACC-CG ACCCCG ACCCCG ACCCCG ACC-CG ACC-CG ACC
1 ACCAC-G ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1884927 CGAGACGAGA
Statistics
Matches: 82, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
5 14 0.17
6 64 0.78
7 4 0.05
ACGTcount: A:0.24, C:0.58, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1884851 original size:12 final size:12
Alignment explanation
Indices: 1884840--1884926 Score: 108
Period size: 12 Copynumber: 7.4 Consensus size: 12
1884830 ACTATTACCA
*
1884840 CGACCACGACCA
1 CGACCACGACCC
*
1884852 CGACCACGACCA
1 CGACCACGACCC
1884864 CGACCACGACCC
1 CGACCACGACCC
*
1884876 CGACCCCGACCC
1 CGACCACGACCC
1884888 CGGACC-CGACCC
1 C-GACCACGACCC
*
1884900 CGACCCCGACCC
1 CGACCACGACCC
1884912 CGACC-CGA-CC
1 CGACCACGACCC
1884922 CGACC
1 CGACC
1884927 CGAGACGAGA
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
10 7 0.10
11 7 0.10
12 53 0.75
13 4 0.06
ACGTcount: A:0.23, C:0.59, G:0.18, T:0.00
Consensus pattern (12 bp):
CGACCACGACCC
Found at i:1884935 original size:5 final size:5
Alignment explanation
Indices: 1884927--1884962 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
1884917 CGACCCGACC
1884927 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1884963 GCGGCGGCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.36, C:0.22, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:1885465 original size:6 final size:6
Alignment explanation
Indices: 1885454--1885528 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
1885444 TCTCGTCTCG
1885454 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1885502 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1885529 AATACGTGTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1885645 original size:21 final size:21
Alignment explanation
Indices: 1885621--1885677 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1885611 TGCGATTTTG
1885621 GACTATCGCAATGCGGACTTC
1 GACTATCGCAATGCGGACTTC
1885642 GACTATCGCAATGCGGACTTC
1 GACTATCGCAATGCGGACTTC
1885663 GACTATCGCAATGCG
1 GACTATCGCAATGCG
1885678 AATATGTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (21 bp):
GACTATCGCAATGCGGACTTC
Found at i:1885708 original size:20 final size:19
Alignment explanation
Indices: 1885667--1885724 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1885657 GACTTCGACT
1885667 ATCGCAATGCGAATATGT-AA
1 ATCGCAATGCG-ATA-GTCAA
1885687 ATCGCAATGCGATAGTCCAA
1 ATCGCAATGCGATAGT-CAA
*
1885707 ATTCGCATTGCGATAGTC
1 A-TCGCAATGCGATAGTC
1885725 GATTATCGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 15 0.44
21 14 0.41
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (19 bp):
ATCGCAATGCGATAGTCAA
Found at i:1885718 original size:21 final size:21
Alignment explanation
Indices: 1885688--1885781 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
1885678 AATATGTAAA
*
1885688 TCGCAATGCGATAGTCCAAAT
1 TCGCATTGCGATAGTCCAAAT
* *
1885709 TCGCATTGCGATAGT-CGATT
1 TCGCATTGCGATAGTCCAAAT
* ** *
1885729 ATCGCATTGCGAT-TTATATAT
1 -TCGCATTGCGATAGTCCAAAT
* *
1885750 TGGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAT
1885771 TCGCATTGCGA
1 TCGCATTGCGA
1885782 ATCTGGAAAC
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
20 15 0.27
21 40 0.73
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:1885732 original size:62 final size:62
Alignment explanation
Indices: 1885661--1885781 Score: 154
Period size: 62 Copynumber: 2.0 Consensus size: 62
1885651 AATGCGGACT
*
1885661 TCGACTATCGCAATGCGA-ATATGTAAATCGCAATGCGATAGTCCAAATTCGCATTGCGATAG
1 TCGACTATCGCAATGCGATATATAT-AATCGCAATGCGATAGTCCAAATTCGCATTGCGATAG
* * * * * * *
1885723 TCGATTATCGCATTGCGATTTATATATTGGCATTGCGATAGTCCAAGTTCGCATTGCGA
1 TCGACTATCGCAATGCGATATATATAATCGCAATGCGATAGTCCAAATTCGCATTGCGA
1885782 ATCTGGAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
62 46 0.92
63 4 0.08
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (62 bp):
TCGACTATCGCAATGCGATATATATAATCGCAATGCGATAGTCCAAATTCGCATTGCGATAG
Found at i:1893233 original size:47 final size:47
Alignment explanation
Indices: 1893164--1893260 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
1893154 AAACATTTGT
1893164 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1893211 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1893258 AAA
1 AAA
1893261 CACCAAGTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.23
Consensus pattern (47 bp):
AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
Found at i:1893294 original size:20 final size:21
Alignment explanation
Indices: 1893253--1893294 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1893243 CAACTTAATA
1893253 AGCAAAAACACCAAGTAGCAT
1 AGCAAAAACACCAAGTAGCAT
1893274 AGCAAAAACACCAAGTA-CAT
1 AGCAAAAACACCAAGTAGCAT
1893294 A
1 A
1893295 CACTACAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.10
Consensus pattern (21 bp):
AGCAAAAACACCAAGTAGCAT
Found at i:1895954 original size:6 final size:6
Alignment explanation
Indices: 1895943--1895981 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1895933 TATGCTTCCA
1895943 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1895982 CTGCATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:1899652 original size:19 final size:19
Alignment explanation
Indices: 1899630--1899667 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1899620 TTATATATTT
1899630 AGGAATAATTGTTATAATA
1 AGGAATAATTGTTATAATA
1899649 AGGAATAATTGTTATAATA
1 AGGAATAATTGTTATAATA
1899668 TTCTCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (19 bp):
AGGAATAATTGTTATAATA
Found at i:1899722 original size:2 final size:2
Alignment explanation
Indices: 1899715--1899746 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1899705 AATAAAAATA
1899715 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
1899747 TATTTGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1905009 original size:24 final size:26
Alignment explanation
Indices: 1904955--1905019 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 26
1904945 TTAAAAAAGA
* * * *
1904955 AAAATAAAATAAAATAAAGAAAGTAT
1 AAAATATATTAAAAGAAAGAAAATAT
* *
1904981 TAAAT-T-TTAAAAGAAATAAAATAT
1 AAAATATATTAAAAGAAAGAAAATAT
1905005 AAAATATATTAAAAG
1 AAAATATATTAAAAG
1905020 GAGGGAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 18 0.60
25 1 0.03
26 11 0.37
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (26 bp):
AAAATATATTAAAAGAAAGAAAATAT
Found at i:1906186 original size:9 final size:9
Alignment explanation
Indices: 1906144--1906194 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
1906134 GACCTGTAAA
*
1906144 AAATGATAT
1 AAATAATAT
1906153 AAATATATAAT
1 AAATA-AT-AT
*
1906164 AAATAAATAA
1 AAAT-AATAT
1906174 AAATAATAT
1 AAATAATAT
1906183 AAATAATAT
1 AAATAATAT
1906192 AAA
1 AAA
1906195 ACAATGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 20 0.56
10 7 0.19
11 8 0.22
12 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (9 bp):
AAATAATAT
Found at i:1906377 original size:23 final size:23
Alignment explanation
Indices: 1906351--1906396 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1906341 TTTTCCAACT
* *
1906351 CATATATTATACGTTTTCAAAAA
1 CATATACTATACATTTTCAAAAA
*
1906374 CATATACTATATATTTTCAAAAA
1 CATATACTATACATTTTCAAAAA
1906397 ACTACATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (23 bp):
CATATACTATACATTTTCAAAAA
Found at i:1908636 original size:18 final size:18
Alignment explanation
Indices: 1908613--1908660 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1908603 AAATTGTCCT
* *
1908613 TATTATATATTTGTATAA
1 TATTATATATTTGAAAAA
*
1908631 TATTATA-AGTTGAAAAA
1 TATTATATATTTGAAAAA
1908648 TATTTATATATTT
1 TA-TTATATATTT
1908661 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TATTATATATTTGAAAAA
Found at i:1923347 original size:30 final size:29
Alignment explanation
Indices: 1923287--1923505 Score: 194
Period size: 29 Copynumber: 7.6 Consensus size: 29
1923277 CACATTCAAA
* * **
1923287 AATTCCTAAAATGTTACAATTTTCAAAAT
1 AATTCCTAGAATGTCACCTTTTTCAAAAT
* * *
1923316 AATTCATAGAATGTTACCTTTCTTTAAAAT
1 AATTCCTAGAATGTCACCTTT-TTCAAAAT
*
1923346 AATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCTAGAATGTCACCTTTTTCAAAAT
** *
1923375 AATTCCTAGAATGTCATTTTTTTCACAA-
1 AATTCCTAGAATGTCACCTTTTTCAAAAT
** *
1923403 AATTCCCCGAATGTCACTTTTTTCCAAAAT
1 AATTCCTAGAATGTCACCTTTTT-CAAAAT
* *
1923433 AATTACC-AAAATGTCACATTTTT-AAAAT
1 AATT-CCTAGAATGTCACCTTTTTCAAAAT
* * *
1923461 AATT-CTCATAATATCACCTTTTTTAAAAT
1 AATTCCT-AGAATGTCACCTTTTTCAAAAT
*
1923490 AATTCCCAGAATGTCA
1 AATTCCTAGAATGTCA
1923506 ATGGGTCGGG
Statistics
Matches: 156, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
28 42 0.27
29 68 0.44
30 43 0.28
31 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.38
Consensus pattern (29 bp):
AATTCCTAGAATGTCACCTTTTTCAAAAT
Found at i:1923528 original size:17 final size:17
Alignment explanation
Indices: 1923502--1923534 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1923492 TTCCCAGAAT
*
1923502 GTCAATGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
1923519 GTCAACGGGTCGGGTC
1 GTCAACGGGTCGGGTC
1923535 AGACCGGTCA
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:0.12, C:0.21, G:0.45, T:0.21
Consensus pattern (17 bp):
GTCAACGGGTCGGGTCG
Found at i:1924876 original size:18 final size:18
Alignment explanation
Indices: 1924853--1924909 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
1924843 CTAATTCATG
1924853 ACATATTCCAATTCCTTC
1 ACATATTCCAATTCCTTC
*
1924871 ACATATTCCAATTTCTTC
1 ACATATTCCAATTCCTTC
* * *
1924889 ACAGATTCAAATTCGTTC
1 ACATATTCCAATTCCTTC
1924907 ACA
1 ACA
1924910 GTTTTTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (18 bp):
ACATATTCCAATTCCTTC
Found at i:1940373 original size:60 final size:60
Alignment explanation
Indices: 1940275--1940451 Score: 201
Period size: 60 Copynumber: 3.0 Consensus size: 60
1940265 GCATCATGTG
* * **
1940275 TCCCTAAACTATAACTCTCATTTTAAACTGGTCCTTAAACTTTTGAATATTCCAATTTCA
1 TCCCTAAACTATGACTCTCATTCTAAACCAGTCCTTAAACTTTTGAATATTCCAATTTCA
* * * * *
1940335 TCCCCAAACTATGATTCTCATTCTAAACCAGTCCTTAAACTTTTTAACATTCTAATTTCA
1 TCCCTAAACTATGACTCTCATTCTAAACCAGTCCTTAAACTTTTGAATATTCCAATTTCA
* * * * ** * *
1940395 TCCCTAAACTATGACACTCTTTCTAAATCAATCCCCAAACTTTTGGATCTTCCAATT
1 TCCCTAAACTATGACTCTCATTCTAAACCAGTCCTTAAACTTTTGAATATTCCAATT
1940452 GAATTCCCAA
Statistics
Matches: 95, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.38
Consensus pattern (60 bp):
TCCCTAAACTATGACTCTCATTCTAAACCAGTCCTTAAACTTTTGAATATTCCAATTTCA
Found at i:1940702 original size:31 final size:31
Alignment explanation
Indices: 1940607--1940702 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
1940597 GTGATTAAAA
* * *
1940607 AGTTTGAAGACCAATTTAGAATGA-AGTCCAT
1 AGTTTGAGGACTAATTTAGAATGATA-TTCAT
* * * * *
1940638 AGTTTGGGGATTAAATT-GAA--ATGTTCAGA
1 AGTTTGAGGACTAATTTAGAATGATATTCA-T
1940667 AGTTTGAGGACTAATTTAGAATGATATTCAT
1 AGTTTGAGGACTAATTTAGAATGATATTCAT
1940698 AGTTT
1 AGTTT
1940703 AGGGATGAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
28 4 0.09
29 14 0.30
30 6 0.13
31 17 0.36
32 6 0.13
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.35
Consensus pattern (31 bp):
AGTTTGAGGACTAATTTAGAATGATATTCAT
Found at i:1946366 original size:20 final size:20
Alignment explanation
Indices: 1946341--1946383 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1946331 GATTTCTGGG
*
1946341 CAAGGGAATCGATACCCATT
1 CAAGGGAACCGATACCCATT
*
1946361 CAAGGGAACCGATACCCTTT
1 CAAGGGAACCGATACCCATT
1946381 CAA
1 CAA
1946384 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (20 bp):
CAAGGGAACCGATACCCATT
Found at i:1947149 original size:31 final size:31
Alignment explanation
Indices: 1947111--1947265 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
1947101 AAGGGTCGAG
1947111 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1947142 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* **
1947173 GTTTACCTATGTTCTTCGGAACATACAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1947204 GTTTACCTATGTCCTTCGGGACATA-GGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1947234 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1947265 G
1 G
1947266 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 23 0.21
31 89 0.79
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1950009 original size:20 final size:20
Alignment explanation
Indices: 1949984--1950024 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1949974 TTTCTGGGCA
* *
1949984 AGGGGAATCGGTACCCATTC
1 AGGGGAACCGATACCCATTC
*
1950004 AGGGGAACCGATACCCCTTC
1 AGGGGAACCGATACCCATTC
1950024 A
1 A
1950025 AACGACAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (20 bp):
AGGGGAACCGATACCCATTC
Found at i:1950792 original size:30 final size:31
Alignment explanation
Indices: 1950741--1950924 Score: 277
Period size: 31 Copynumber: 6.0 Consensus size: 31
1950731 AAGGGCGAGG
1950741 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1950772 GTTTACCTATGTTC-TCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1950802 GTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1950832 G-TTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1950862 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1950893 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1950924 G
1 G
1950925 GTCCTTGGGA
Statistics
Matches: 140, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
29 15 0.11
30 56 0.40
31 68 0.49
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1951027 original size:25 final size:25
Alignment explanation
Indices: 1950999--1951048 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1950989 ATACCTTAGT
1950999 TCTCACTAGTGTACATGGGCTAATA
1 TCTCACTAGTGTACATGGGCTAATA
1951024 TCTCACTAGTGTACATGGGCTAATA
1 TCTCACTAGTGTACATGGGCTAATA
1951049 AAGTGATTAA
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:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (25 bp):
TCTCACTAGTGTACATGGGCTAATA
Found at i:1953028 original size:63 final size:65
Alignment explanation
Indices: 1952912--1953058 Score: 176
Period size: 64 Copynumber: 2.3 Consensus size: 65
1952902 CTATTCAATA
* * *
1952912 GGTACCGATACCCTCTCAAACGAGAAAATTTCAGAATGTCATAGGGGTACCGATACCC-CAG-AT
1 GGTACCGATACCCCCTTAAACGAGAAAATTACAGAATGTCATAGGGGTACCGATACCCTCAGTAT
* ** *
1952975 GGGTACCGATACCCCCTTGAACGA-AAAATTACAGAATGTTGT-GAGGGTGCCGATACCCTCAGT
1 -GGTACCGATACCCCCTTAAACGAGAAAATTACAGAATGTCATAG-GGGTACCGATACCCTCAGT
1953038 AT
64 AT
*
1953040 GGTATCGATACCCCCTTAA
1 GGTACCGATACCCCCTTAA
1953059 GGAGAAATGA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
62 1 0.01
63 28 0.39
64 40 0.56
65 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (65 bp):
GGTACCGATACCCCCTTAAACGAGAAAATTACAGAATGTCATAGGGGTACCGATACCCTCAGTAT
Found at i:1953906 original size:23 final size:23
Alignment explanation
Indices: 1953871--1953932 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
1953861 GACATCTTAT
*
1953871 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
*
1953894 GTGGCACTTCGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
1953917 ATGGCACTTCGGTGCA
1 ATGGCACTTCGGTGCA
1953933 TTTATACGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:1956707 original size:18 final size:18
Alignment explanation
Indices: 1956668--1956708 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1956658 CCCAATCGGT
*
1956668 CAGAAGCAACAATAGATT
1 CAGAAGCAACAATAGATC
* *
1956686 CAGAGGCAACAATAGGTC
1 CAGAAGCAACAATAGATC
1956704 CAGAA
1 CAGAA
1956709 ATAACAATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (18 bp):
CAGAAGCAACAATAGATC
Found at i:1959054 original size:30 final size:30
Alignment explanation
Indices: 1959019--1959078 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1959009 AAGCATAATA
* *
1959019 AAATGTTTATACTCTAATATTTGGTTAAAT
1 AAATGTTTATACCCTAACATTTGGTTAAAT
1959049 AAATGTTTATACCCTAACATTTGGTTAAAT
1 AAATGTTTATACCCTAACATTTGGTTAAAT
1959079 TACAAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (30 bp):
AAATGTTTATACCCTAACATTTGGTTAAAT
Found at i:1962767 original size:20 final size:20
Alignment explanation
Indices: 1962450--1962778 Score: 436
Period size: 20 Copynumber: 16.2 Consensus size: 20
1962440 CGCCGAAATA
*
1962450 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
1962470 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
1962490 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
1962510 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
1962532 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
1962552 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
1962574 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1962594 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1962614 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1962634 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1962654 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1962674 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1962694 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1962714 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
1962734 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
1962754 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1962774 AAAAT
1 AAAAT
1962779 GAGTAAATTT
Statistics
Matches: 281, Mismatches: 13, Indels: 30
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 241 0.86
21 3 0.01
22 29 0.10
23 2 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:1962882 original size:6 final size:6
Alignment explanation
Indices: 1962871--1962999 Score: 258
Period size: 6 Copynumber: 21.5 Consensus size: 6
1962861 GACACGTATT
1962871 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1962919 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1962967 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1963000 CGAGACGAGA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 123 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1963503 original size:6 final size:6
Alignment explanation
Indices: 1963492--1963626 Score: 270
Period size: 6 Copynumber: 22.5 Consensus size: 6
1963482 TCTCGTCTCG
1963492 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1963540 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1963588 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1963627 AATACGTGTC
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 129 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1963777 original size:40 final size:40
Alignment explanation
Indices: 1963722--1964089 Score: 426
Period size: 40 Copynumber: 9.1 Consensus size: 40
1963712 GAATTTACTC
1963722 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
1963762 ATTTTCTGAATCGCGTTGCGATTTTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
1963802 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
1963842 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
1963882 ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * *
1963924 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
**** *
1963966 ATTTTCTTTTG-A-C-CGTTGCGATT-TTCTTTTCAACGTTGCG
1 ATTTTC---TGAATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
* * **
1964006 ATTTTCTAAATCACGTTGCGATT-TTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* * *
1964046 ATTTTCTAAATCGCGTTGCGATT-TT-TATTTCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
1964085 ATTTT
1 ATTTT
1964090 GTTGGTCATT
Statistics
Matches: 292, Mismatches: 25, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
37 1 0.00
38 2 0.01
39 18 0.06
40 199 0.68
41 5 0.02
42 64 0.22
43 1 0.00
44 1 0.00
45 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (40 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:1964033 original size:20 final size:20
Alignment explanation
Indices: 1963722--1964089 Score: 346
Period size: 20 Copynumber: 18.2 Consensus size: 20
1963712 GAATTTACTC
1963722 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
1963742 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
1963762 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
1963782 ATTTT-TGGAATCGCGTTGCG
1 ATTTTCT-GAATCGCGTTGCG
*
1963802 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
1963822 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
1963842 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
1963862 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
1963882 ATTTTCTGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
1963902 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
1963924 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
1963944 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
1963966 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
1963986 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
* *
1964006 ATTTTCTAAATCACGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
1964026 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
1964046 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
1964066 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
1964085 ATTTT
1 ATTTT
1964090 GTTGGTCATT
Statistics
Matches: 296, Mismatches: 27, Indels: 51
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.00
18 2 0.01
19 23 0.08
20 223 0.75
21 19 0.06
22 27 0.09
25 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:1969526 original size:9 final size:9
Alignment explanation
Indices: 1969512--1969541 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1969502 TTTTTCAATG
1969512 AAAAATATA
1 AAAAATATA
1969521 AAAAATATA
1 AAAAATATA
*
1969530 TAAAATATA
1 AAAAATATA
1969539 AAA
1 AAA
1969542 GGATAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAATATA
Found at i:1969871 original size:14 final size:14
Alignment explanation
Indices: 1969852--1969878 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1969842 AAAGAGATGG
1969852 AAAAAGGAAAAAGA
1 AAAAAGGAAAAAGA
1969866 AAAAAGGAAAAAG
1 AAAAAGGAAAAAG
1969879 TGAAGATGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAAGGAAAAAGA
Found at i:1992966 original size:86 final size:89
Alignment explanation
Indices: 1992792--1992969 Score: 218
Period size: 89 Copynumber: 2.0 Consensus size: 89
1992782 AAAGGAACCA
* * *
1992792 AAGAAGTTTGAGCAAACTATACTGACTGTAACAATTACCCTATCAATTAACAAACTATAGAAAAA
1 AAGAAGTTTGAGCAAACTATA-TAACTGAAACAATTACCCTATCAATTAACAAAC-ACAGAAAAA
* *
1992857 AAATTATTGCTAACATTGCCAACTTG
64 AAATTATTCCCAACATTGCCAACTTG
* * * * * *
1992883 AAGAAGTTTGAGCAACCTAT-TAATTGAAACTATTACCCTATCAATTAACAAGC-CAG-AGAACA
1 AAGAAGTTTGAGCAAACTATATAACTGAAACAATTACCCTATCAATTAACAAACACAGAAAAAAA
1992945 ATTATTCCCAACATTGCCAACTTG
66 ATTATTCCCAACATTGCCAACTTG
1992969 A
1 A
1992970 CCATAAACAA
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
86 27 0.36
87 2 0.03
89 28 0.37
91 19 0.25
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (89 bp):
AAGAAGTTTGAGCAAACTATATAACTGAAACAATTACCCTATCAATTAACAAACACAGAAAAAAA
ATTATTCCCAACATTGCCAACTTG
Found at i:1997471 original size:16 final size:17
Alignment explanation
Indices: 1997450--1997482 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1997440 TTATTATTAT
1997450 TTATTT-ATAAAGATAA
1 TTATTTGATAAAGATAA
*
1997466 TTATTTGATAAATATAA
1 TTATTTGATAAAGATAA
1997483 AATTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TTATTTGATAAAGATAA
Found at i:1997591 original size:15 final size:15
Alignment explanation
Indices: 1997542--1997591 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1997532 GATAAATAAG
1997542 ATTATATAAAT-ATGA
1 ATTATATAAATCAT-A
*
1997557 ATTCATAT-AATCTTA
1 ATT-ATATAAATCATA
1997572 GATTATATAAATCATA
1 -ATTATATAAATCATA
1997588 ATTA
1 ATTA
1997592 AGTGTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (15 bp):
ATTATATAAATCATA
Found at i:1998636 original size:20 final size:20
Alignment explanation
Indices: 1998579--1998643 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
1998569 TATCGCAACA
1998579 CGAATATGTAAATCGCAATG
1 CGAATATGTAAATCGCAATG
***
1998599 CG-ATAGTCGGCTATCGCAATG
1 CGAATA-T-GTAAATCGCAATG
1998620 CGAATATGTAAATCGCAATG
1 CGAATATGTAAATCGCAATG
1998640 CGAA
1 CGAA
1998644 CTTCGACTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 3 0.08
20 17 0.47
21 13 0.36
22 3 0.08
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (20 bp):
CGAATATGTAAATCGCAATG
Found at i:1998657 original size:21 final size:20
Alignment explanation
Indices: 1998550--1998663 Score: 65
Period size: 21 Copynumber: 5.5 Consensus size: 20
1998540 GTTTCCAAAT
*
1998550 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAA-TTCGACTA
** *
1998571 TCGCAACACGAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
* *
1998591 TCGCAATGCGATAGTCGGCTA
1 TCGCAATGCGA-ATTCGACTA
*
1998612 TCGCAATGCGAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
1998632 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAA-TTCGACTA
*
1998653 TCGCATTGCGA
1 TCGCAATGCGA
1998664 TTTACATATT
Statistics
Matches: 71, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
20 30 0.42
21 41 0.58
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATTCGACTA
Found at i:1998663 original size:41 final size:41
Alignment explanation
Indices: 1998550--1998663 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 41
1998540 GTTTCCAAAT
* **
1998550 TCGCAACGCGAACTTCGACTATCGCAACACGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAA
* *
1998591 TCGCAATGCGATA-GTCGGCTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGA-ACTTCGACTATCGCAATGCGAATATGTAAA
*
1998632 TCGCAATGCGAACTTCGACTATCGCATTGCGA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGA
1998664 TTTACATATT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.02
41 61 0.97
42 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAA
Found at i:1998738 original size:21 final size:21
Alignment explanation
Indices: 1998673--1998740 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
1998663 ATTTACATAT
**
1998673 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAA
* * **
1998694 TCGCATTACGATAGTCGACTA
1 TCGCATTGCGATAGTCCAAAA
1998715 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
1998736 TCGCA
1 TCGCA
1998741 ACGACTGGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAA
Found at i:1999052 original size:21 final size:21
Alignment explanation
Indices: 1999026--1999171 Score: 170
Period size: 21 Copynumber: 6.8 Consensus size: 21
1999016 ATTTTGGACT
*
1999026 ATCGCAACGAACTTAGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1999047 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
1999068 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1999089 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
1999112 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1999133 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1999154 ATCGCACGCGAACTTGGA
1 ATCGCA-ACGAACTTGGA
1999172 CTATCGCAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.08
21 61 0.56
22 9 0.08
23 30 0.28
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1999102 original size:65 final size:64
Alignment explanation
Indices: 1999026--1999168 Score: 195
Period size: 65 Copynumber: 2.2 Consensus size: 64
1999016 ATTTTGGACT
*
1999026 ATCGCAA--CGAACTTAGAATAAATCGCAACGCGAACTTCGACT-ATCGCAACGAATTTGGAATA
1 ATCGCAACGCGAACTTAGAATAAATCGCAA--CGAACTTCGAATAATCGCAACGAATTTGGAATA
1999088 A
64 A
* * *
1999089 ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTAGAATAAATCGCAACGAACTTCGAAT-AATCGCAACGAATTTGGAATAA
1999154 ATCGC-ACGCGAACTT
1 ATCGCAACGCGAACTT
1999169 GGACTATCGC
Statistics
Matches: 72, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
63 16 0.22
64 10 0.14
65 46 0.64
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (64 bp):
ATCGCAACGCGAACTTAGAATAAATCGCAACGAACTTCGAATAATCGCAACGAATTTGGAATAA
Found at i:2007143 original size:62 final size:61
Alignment explanation
Indices: 2007047--2007163 Score: 225
Period size: 62 Copynumber: 1.9 Consensus size: 61
2007037 GAGAGGGAGC
2007047 GGGGGCGGCGATCGGAACGTCAGGCAGCGGGAGGCGTAGGTTAATCTGGCGTCGCTCACGA
1 GGGGGCGGCGATCGGAACGTCAGGCAGCGGGAGGCGTAGGTTAATCTGGCGTCGCTCACGA
2007108 GGGGGCGGCGATCGGAAACGTCAGGCAGCGGGAGGCGTAGGTTAATCTGGCGTCGC
1 GGGGGCGGCGATCGG-AACGTCAGGCAGCGGGAGGCGTAGGTTAATCTGGCGTCGC
2007164 ACGAACTACT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 15 0.27
62 40 0.73
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.15
Consensus pattern (61 bp):
GGGGGCGGCGATCGGAACGTCAGGCAGCGGGAGGCGTAGGTTAATCTGGCGTCGCTCACGA
Found at i:2008840 original size:21 final size:21
Alignment explanation
Indices: 2008789--2008829 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2008779 AAAAAATATA
2008789 AAATAATTATTTAAA-TTTATC
1 AAATAATTA-TTAAATTTTATC
2008810 AAATAATTATTAAATTTTAT
1 AAATAATTATTAAATTTTAT
2008830 TAGAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAATTATTAAATTTTATC
Found at i:2010961 original size:21 final size:21
Alignment explanation
Indices: 2010929--2010972 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2010919 AATAATCAAT
*
2010929 ATTTTTTAAAATTATTATGAA
1 ATTTTTTAAAATTATTATAAA
2010950 ATTTTATT-AAATTATTATAAA
1 ATTTT-TTAAAATTATTATAAA
2010971 AT
1 AT
2010973 ATTTCAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTTTAAAATTATTATAAA
Found at i:2010967 original size:11 final size:11
Alignment explanation
Indices: 2010935--2010972 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2010925 CAATATTTTT
2010935 TAAAATTATTA
1 TAAAATTATTA
*
2010946 TGAAATT-TTA
1 TAAAATTATTA
*
2010956 TTAAATTATTA
1 TAAAATTATTA
2010967 TAAAAT
1 TAAAAT
2010973 ATTTCAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TAAAATTATTA
Found at i:2026326 original size:25 final size:23
Alignment explanation
Indices: 2026298--2026343 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2026288 ATATAATGTT
2026298 GTAATAAATTCAAAAAAATATTACA
1 GTAAT-AATT-AAAAAAATATTACA
* *
2026323 GTAATTATTAAAAAAGTATTA
1 GTAATAATTAAAAAAATATTA
2026344 GAATAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (23 bp):
GTAATAATTAAAAAAATATTACA
Found at i:2027869 original size:58 final size:59
Alignment explanation
Indices: 2027769--2027941 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 59
2027759 TGATAGTTTA
* *
2027769 GGATGAAATTGGAATGTTCAAAAAGCTTGGAGACCAATTTAGAATGA-AGGTC-TAAT-TAG
1 GGATGAAATTGAAATGTTC-AAAAG-TTTGAGACCAATTTAGAATGATA-GTCATAATCTAG
* *
2027828 GGATGAAATTGAAATGTTCAAAAGTTTGATGACTAATTTAGAATGATAGTCATAGTCTAG
1 GGATGAAATTGAAATGTTCAAAAGTTTGA-GACCAATTTAGAATGATAGTCATAATCTAG
* * * * * * *
2027888 GGATGAAACTGAAATATTTAAAAGTTTAAGAACCAATTTAAAATAAGAGTCATA
1 GGATGAAATTGAAATGTTCAAAAGTTTGAG-ACCAATTTAGAATGATAGTCATA
2027942 CTTTGAGGAC
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
57 4 0.04
58 23 0.24
59 23 0.24
60 47 0.48
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (59 bp):
GGATGAAATTGAAATGTTCAAAAGTTTGAGACCAATTTAGAATGATAGTCATAATCTAG
Found at i:2028157 original size:59 final size:59
Alignment explanation
Indices: 2028027--2028198 Score: 147
Period size: 59 Copynumber: 2.9 Consensus size: 59
2028017 AACTATAATC
* * * * * * *
2028027 CTCACTTTGAATTAGTCCTTAAACTTTTAAATATTTTAATTTCATCCTCAATTTATGCCT
1 CTCATTTTAAATTAGTCCTTAAAC-TTTGAACATTCTAATTCCATCCTCAAATTATGCCT
2028087 CTCATTTTAAATTAGTCCTTAAACTTTGAACATTCTAATTCCATCCAT-AAATTATGACC-
1 CTCATTTTAAATTAGTCCTTAAACTTTGAACATTCTAATTCCATCC-TCAAATTATG-CCT
* * * * *
2028146 CTC-TTTATAAATTGGT-CTCCAAACTTTGAATC-TTCCAATTTCATCCCCAAATT
1 CTCATTT-TAAATTAGTCCT-TAAACTTTGAA-CATTCTAATTCCATCCTCAAATT
2028199 TATCCAAATA
Statistics
Matches: 94, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
58 5 0.05
59 63 0.67
60 26 0.28
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (59 bp):
CTCATTTTAAATTAGTCCTTAAACTTTGAACATTCTAATTCCATCCTCAAATTATGCCT
Found at i:2028435 original size:60 final size:59
Alignment explanation
Indices: 2028330--2028470 Score: 151
Period size: 60 Copynumber: 2.3 Consensus size: 59
2028320 GGAATGTTAA
* * * *
2028330 AAAAGTTTAGAGACTAATTTAGAATGAATGCCATAGTTTGAGGATGAAGTTGAAATATTC
1 AAAAGTTTAG-GACTAATTTAGAATGAATGCCAAAATTTGAGGATGAAATTGAAACATTC
* * *
2028390 AAAAGTTTGAGGACTAATTTAGAATG-ATAGTCAAAATTT-AGGGATGAAATTGAGACATTT
1 AAAAGTTT-AGGACTAATTTAGAATGAAT-GCCAAAATTTGA-GGATGAAATTGAAACATTC
*
2028450 AAAAGTTTAAGGACCAATTTA
1 AAAAGTTT-AGGACTAATTTA
2028471 AAGTGAGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.04
60 64 0.93
61 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (59 bp):
AAAAGTTTAGGACTAATTTAGAATGAATGCCAAAATTTGAGGATGAAATTGAAACATTC
Found at i:2040175 original size:52 final size:52
Alignment explanation
Indices: 2040100--2040204 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
2040090 AGTTACATTT
2040100 CATCGGCTATAACGGGGACTGGTTGAAAAACCGATGTTGGAAACAAATCTTA
1 CATCGGCTATAACGGGGACTGGTTGAAAAACCGATGTTGGAAACAAATCTTA
2040152 CATCGGCTATAACGGGGACTGGTTGAAAAACCGATGTTGGAAACAAATCTTA
1 CATCGGCTATAACGGGGACTGGTTGAAAAACCGATGTTGGAAACAAATCTTA
2040204 C
1 C
2040205 CAAGGTTACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (52 bp):
CATCGGCTATAACGGGGACTGGTTGAAAAACCGATGTTGGAAACAAATCTTA
Done.