Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008129.1 Hibiscus syriacus cultivar Beakdansim tig00110684_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: 2577775
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1425493 original size:21 final size:21
Alignment explanation
Indices: 1425467--1425522 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1425457 TTCCGGAAAT
1425467 GTAATTCATTTTCCAGTTCCA
1 GTAATTCATTTTCCAGTTCCA
1425488 GTAATTCATTTTCCAGTTCCA
1 GTAATTCATTTTCCAGTTCCA
*
1425509 ATAATTCATTTTCC
1 GTAATTCATTTTCC
1425523 GAAAAACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (21 bp):
GTAATTCATTTTCCAGTTCCA
Found at i:1425931 original size:25 final size:25
Alignment explanation
Indices: 1425898--1425953 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 25
1425888 TTTAAACTGA
1425898 AAATTTAT-TTTTTGT-TATTTTTA-
1 AAATTTATATTTTT-TATATTTTTAT
1425921 AAATTTATATTTTTTATATTTTTAT
1 AAATTTATATTTTTTATATTTTTAT
1425946 AAATTTAT
1 AAATTTAT
1425954 CTTCTAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.30
24 13 0.43
25 8 0.27
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
AAATTTATATTTTTTATATTTTTAT
Found at i:1425963 original size:24 final size:24
Alignment explanation
Indices: 1425913--1425963 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1425903 TATTTTTTGT
* * *
1425913 TATTTTTAAAATTTATATTTTTTA
1 TATTTTTAAAATTTATACTTCTAA
1425937 TATTTTTATAAATTTAT-CTTCTAA
1 TATTTTTA-AAATTTATACTTCTAA
1425961 TAT
1 TAT
1425964 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTTAAAATTTATACTTCTAA
Found at i:1429996 original size:90 final size:90
Alignment explanation
Indices: 1429843--1430164 Score: 518
Period size: 90 Copynumber: 3.6 Consensus size: 90
1429833 AAGACTTACA
* * * * * * * * *
1429843 GATGGCCTGGAGGACTTACAAATCAAGAAACTCCCGAAGGTTTAGTTTCTAAAATCTCGTTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
1429908 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
* *
1429933 GATGGTCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGTCTCAGTTTCTTAGATCTCATTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
1429998 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
1430023 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
1430088 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
* * *
1430113 GATGACCCGAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTCAATTTCTTA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
1430165 ATTGTCACCA
Statistics
Matches: 216, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 216 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (90 bp):
GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
AACATCCTGCACTGAAGGTCTTATG
Found at i:1430226 original size:43 final size:43
Alignment explanation
Indices: 1430165--1430414 Score: 317
Period size: 43 Copynumber: 5.8 Consensus size: 43
1430155 CAATTTCTTA
* * *
1430165 ATTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAG
1 ATTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAG
*
1430208 ATTGTCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAG
1 ATTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAG
*
1430251 CA-TGTCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAG
1 -ATTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAG
* *
1430294 CA-TGTCATCAA-AGAACCCATACATATCACGATGGTCCTTCAAG
1 -ATTGTCATCAAGA-AACCCCTACATATCACGATGGTCCCTCAAG
* * * *
1430337 CTTGTTATCAAGGAACCCCTACATATCACGATGGTCCTTCAAG
1 ATTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAG
* * * *
1430380 CTTATCATCAAGAAGCCCCTACATATCATGATGGT
1 ATTGTCATCAAGAAACCCCTACATATCACGATGGT
1430415 TTCTCAATCT
Statistics
Matches: 187, Mismatches: 16, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
42 1 0.01
43 185 0.99
44 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (43 bp):
ATTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAG
Found at i:1430399 original size:129 final size:129
Alignment explanation
Indices: 1430167--1430421 Score: 377
Period size: 129 Copynumber: 2.0 Consensus size: 129
1430157 ATTTCTTAAT
* * *
1430167 TGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
1 TGTCACCAAAGAACCCATACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
*
1430232 ATCACGATGGTCTCTCAAGCATGTCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAGCA
66 ATCACGATGGTCTCTCAAGCATATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAGCA
* * * * *
1430296 TGTCATCAAAGAACCCATACATATCACGATGGTCCTTCAAGCTTGTTATCAAGGAACCCCTACAT
1 TGTCACCAAAGAACCCATACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
* * * *
1430361 ATCACGATGGTC-CTTCAAGCTTATCATCAAGAAGCCCCTACATATCATGATGGTTTCTCAA
66 ATCACGATGGTCTC-TCAAGCATATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAA
1430422 TCTATTGTGT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
128 1 0.01
129 111 0.99
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (129 bp):
TGTCACCAAAGAACCCATACATATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
ATCACGATGGTCTCTCAAGCATATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAGCA
Found at i:1430488 original size:39 final size:38
Alignment explanation
Indices: 1430424--1430785 Score: 268
Period size: 36 Copynumber: 9.7 Consensus size: 38
1430414 TTTCTCAATC
* *
1430424 TATTGTGTTTCGAGCGAAACTATCTCAAGCGAGATAAAA
1 TATT-TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
* *
1430463 TATTATGTTTCAAGTGAAACAATCTCAAGCGAGATAAAA
1 TATT-TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
* ** * * * *
1430502 TCTTCTGTTTCAAGTTAAATTGTCTCAAGGGAGA-CAAA
1 TATT-TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
** * *
1430540 -ATTTGTTTCAAGGGAAACCGTCTCAAGGGAGA-CAAA
1 TATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
** *
1430576 -ATTTGTTTCAAGGGAAACCGTCTCAAGGGAGAT-AAA
1 TATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
* *
1430612 TCTTTCTGTTTCAAGAGAAACTATCTCAAGCGAGATAAAA
1 T-ATT-TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
* * * *
1430652 TCTTCTGCTTT-GAGGGAAACTATCTCAAG-G-GA-GACA
1 TATT-TG-TTTCAAGGGAAACTATCTCAAGCGAGATAAAA
* *
1430688 -ATTTGTTTCAAGGGAAACCT-TCTCAAGGGAGA-CAAA
1 TATTTGTTTCAAGGGAAA-CTATCTCAAGCGAGATAAAA
** * *
1430724 -ATTTGTTTCAAGGGAAACCGTCTCAAGGGAGA-CAAA
1 TATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
*
1430760 -ATTTGTTTCAAGGGAAACTGTCTCAA
1 TATTTGTTTCAAGGGAAACTATCTCAA
1430786 AATTTGTATC
Statistics
Matches: 279, Mismatches: 33, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
33 3 0.01
34 16 0.06
35 6 0.02
36 128 0.46
37 4 0.01
38 6 0.02
39 109 0.39
40 7 0.03
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (38 bp):
TATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
Found at i:1430550 original size:21 final size:21
Alignment explanation
Indices: 1430521--1430590 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
1430511 TCAAGTTAAA
1430521 TTGTCTCAAGGGAGACAAAAT
1 TTGTCTCAAGGGAGACAAAAT
*
1430542 TTGTTTCAA-GG-G---AAA-
1 TTGTCTCAAGGGAGACAAAAT
**
1430557 CCGTCTCAAGGGAGACAAAAT
1 TTGTCTCAAGGGAGACAAAAT
*
1430578 TTGTTTCAAGGGA
1 TTGTCTCAAGGGA
1430591 AACCGTCTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
15 6 0.17
16 5 0.14
17 1 0.03
19 1 0.03
20 5 0.14
21 18 0.50
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (21 bp):
TTGTCTCAAGGGAGACAAAAT
Found at i:1430563 original size:36 final size:36
Alignment explanation
Indices: 1430468--1430785 Score: 336
Period size: 36 Copynumber: 8.6 Consensus size: 36
1430458 TAAAATATTA
* ** * *
1430468 TGTTTCAAGTGAAACAATCTCAAGCGAGATAAAATCTT
1 TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAA--TT
** **
1430506 CTGTTTCAAGTTAAATTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATT
1430543 TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATT
* *
1430579 TGTTTCAAGGGAAACCGTCTCAAGGGAGATAAATCTTT
1 TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAA--ATT
* ** * *
1430617 CTGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTT
1 -TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAA--TT
* **
1430656 CTGCTTT-GAGGGAAACTATCTCAAGGGAGAC--AATT
1 -TG-TTTCAAGGGAAACCGTCTCAAGGGAGACAAAATT
*
1430691 TGTTTCAAGGGAAACCTTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATT
1430727 TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATT
*
1430763 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGGGAAACCGTCTCAA
1430786 AATTTGTATC
Statistics
Matches: 244, Mismatches: 26, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
33 3 0.01
34 23 0.09
35 2 0.01
36 125 0.51
37 4 0.02
38 2 0.01
39 82 0.34
40 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAATT
Found at i:1430736 original size:21 final size:21
Alignment explanation
Indices: 1430710--1430774 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
1430700 GGAAACCTTC
1430710 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
** *
1430731 TCAA-GG-G---AAA-CCGTC
1 TCAAGGGAGACAAAATTTGTT
1430746 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
1430767 TCAAGGGA
1 TCAAGGGA
1430775 AACTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 6 0.19
16 5 0.16
17 1 0.03
19 1 0.03
20 5 0.16
21 14 0.44
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:1430753 original size:184 final size:189
Alignment explanation
Indices: 1430420--1430785 Score: 530
Period size: 184 Copynumber: 2.0 Consensus size: 189
1430410 ATGGTTTCTC
* * * *
1430420 AATCTATTGTGTTTCGAGCGAAACTATCTCAAGCGAGATAAAATATTATGTTTCAAGTGAAACAA
1 AATCTATTCTGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTATGTTTCAAGGGAAACAA
* ** *
1430485 TCTCAAGCGAGATAAAATCTTCTGTTTCAAGTTAAATTGTCTCAAGGGAGACAAAATTTGTTTCA
66 TCTCAAGCGAGAGAAAA-CTTCTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCA
1430550 AGGGAAACCGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGATA
130 AGGGAAACCGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGATA
* * * *
1430610 AATCT-TTCTGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTCTGCTTT-GAGGGAAACT
1 AATCTATTCTGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTATG-TTTCAAGGGAAACA
*
1430673 ATCTCAAG-G-GAGACAA-TT-TGTTTCAAGGGAAACCT-TCTCAAGGGAGACAAAATTTGTTTC
65 ATCTCAAGCGAGAGAAAACTTCTGTTTCAAGGGAAA-CTGTCTCAAGGGAGACAAAATTTGTTTC
*
1430733 AAGGGAAACCGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAA
129 AAGGGAAACCGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAA
1430786 AATTTGTATC
Statistics
Matches: 160, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
184 89 0.56
185 3 0.02
187 5 0.03
188 1 0.01
189 54 0.34
190 8 0.05
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (189 bp):
AATCTATTCTGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTATGTTTCAAGGGAAACAA
TCTCAAGCGAGAGAAAACTTCTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
GGGAAACCGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGGGAGATA
Found at i:1430845 original size:34 final size:34
Alignment explanation
Indices: 1430804--1430924 Score: 152
Period size: 34 Copynumber: 3.6 Consensus size: 34
1430794 TCTCAGAGAA
* *
1430804 AAATTGTCTCAAGCGAGACGGAATTTGTTTTAAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
*
1430838 AAATTGTCTCAAGCGAGACGAAATTTATTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* * * *
1430872 AAAGTGTATCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* * *
1430906 AAATTATCTTAAGTGAGAC
1 AAATTGTCTCAAGCGAGAC
1430925 AAAAAAAATT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (34 bp):
AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
Found at i:1431171 original size:32 final size:32
Alignment explanation
Indices: 1431059--1431172 Score: 156
Period size: 32 Copynumber: 3.5 Consensus size: 32
1431049 TTCGATATTA
* *
1431059 AATCTCCAAAGATGACCCAACATTTTAATGTTG
1 AATCTCCAAAGATGCCCCAACA-TTTGATGTTG
* *
1431092 AATCTCCAAATATACCCCAACATTTGATGTTG
1 AATCTCCAAAGATGCCCCAACATTTGATGTTG
*
1431124 AATCTCCAAAGATGCCCCAATATTTGATGTTG
1 AATCTCCAAAGATGCCCCAACATTTGATGTTG
* *
1431156 AATCTTCAAAAATGCCC
1 AATCTCCAAAGATGCCC
1431173 TCTATTGTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
32 53 0.74
33 19 0.26
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (32 bp):
AATCTCCAAAGATGCCCCAACATTTGATGTTG
Found at i:1432203 original size:12 final size:12
Alignment explanation
Indices: 1432186--1432281 Score: 54
Period size: 12 Copynumber: 7.6 Consensus size: 12
1432176 TTCTCGTCCC
1432186 TTTTTCTTTACT
1 TTTTTCTTTACT
*
1432198 TTTTTCTTTTCTTTT
1 TTTTTCTTTAC---T
1432213 TTTTTCTTTA-T
1 TTTTTCTTTACT
1432224 TTTTTCTTTA-T
1 TTTTTCTTTACT
* *
1432235 TATCCTTGCTTTAAT
1 T-T--TTTCTTTACT
*
1432250 TATTTTATTCT-CT
1 T-TTTTCTT-TACT
*
1432263 TTTTTCTTTTCT
1 TTTTTCTTTACT
1432275 TTTTTCT
1 TTTTTCT
1432282 CTGTTTCTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
11 14 0.21
12 26 0.38
13 6 0.09
14 8 0.12
15 14 0.21
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTACT
Found at i:1432226 original size:11 final size:11
Alignment explanation
Indices: 1432204--1432235 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1432194 TACTTTTTTC
1432204 TTTTCTTT-TT
1 TTTTCTTTATT
1432214 TTTTCTTTATT
1 TTTTCTTTATT
1432225 TTTTCTTTATT
1 TTTTCTTTATT
1432236 ATCCTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTATT
Found at i:1432278 original size:23 final size:22
Alignment explanation
Indices: 1432252--1432310 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
1432242 GCTTTAATTA
1432252 TTTTATTCTCTTTTTTC-TTTTC
1 TTTT-TTCTCTTTTTTCTTTTTC
*
1432274 TTTTTTCTC-TGTTTCTTTTTC
1 TTTTTTCTCTTTTTTCTTTTTC
*
1432295 TTTTTTTTCTCTTTTT
1 TTTTTTCTCT-TTTTT
1432311 GTTCTGATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 5 0.16
21 18 0.58
22 4 0.13
23 4 0.13
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTTCTCTTTTTTCTTTTTC
Found at i:1432281 original size:21 final size:21
Alignment explanation
Indices: 1432196--1432310 Score: 67
Period size: 21 Copynumber: 5.3 Consensus size: 21
1432186 TTTTTCTTTA
*
1432196 CTTTTTTCTTTTCTTTTTTTTT
1 CTTTTTTCTTTTC-TTTTTTCT
*
1432218 CTTTATT-TTTTCTTTATTATC-
1 CTTTTTTCTTTTCTTT-TT-TCT
** * *
1432239 CTTGCTTTAATTAT-TTTATTCT
1 CTT--TTTTCTTTTCTTTTTTCT
1432261 CTTTTTTCTTTTCTTTTTTCT
1 CTTTTTTCTTTTCTTTTTTCT
* *
1432282 C-TGTTTCTTTTTCTTTTTTTT
1 CTTTTTTC-TTTTCTTTTTTCT
1432303 CTCTTTTT
1 CT-TTTTT
1432311 GTTCTGATTG
Statistics
Matches: 70, Mismatches: 13, Indels: 19
0.69 0.13 0.19
Matches are distributed among these distances:
20 14 0.20
21 33 0.47
22 11 0.16
23 9 0.13
24 3 0.04
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.77
Consensus pattern (21 bp):
CTTTTTTCTTTTCTTTTTTCT
Found at i:1433517 original size:13 final size:13
Alignment explanation
Indices: 1433499--1433527 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1433489 TGTAGCATGT
1433499 AAATGCAAATGCA
1 AAATGCAAATGCA
1433512 AAATGCAAATGCA
1 AAATGCAAATGCA
1433525 AAA
1 AAA
1433528 GGTGTCATTC
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:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (13 bp):
AAATGCAAATGCA
Found at i:1440826 original size:23 final size:23
Alignment explanation
Indices: 1440800--1440844 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1440790 TAATTTTATC
*
1440800 TTTATGACATATTTTTATTTGTA
1 TTTATGACATACTTTTATTTGTA
* *
1440823 TTTATGATATGCTTTTATTTGT
1 TTTATGACATACTTTTATTTGT
1440845 CTTTCGGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.62
Consensus pattern (23 bp):
TTTATGACATACTTTTATTTGTA
Found at i:1447424 original size:112 final size:112
Alignment explanation
Indices: 1447227--1447448 Score: 435
Period size: 112 Copynumber: 2.0 Consensus size: 112
1447217 CTTTACATTT
1447227 CTCGGCGTGCCTTTTCGGCTTCCCGGCCTTCTTGTTTTCGTGCTTTGTTTGGCTTGTATATTGTG
1 CTCGGCGTGCCTTTTCGGCTTCCCGGCCTTCTTGTTTTCGTGCTTTGTTTGGCTTGTATATTGTG
*
1447292 GTGTACTGTGTTTTTGTGGTTCCCCCGATGTTGTGTTTTTTGTTCTA
66 GTGTACTGTGTTTTTGTGGTTCCCCCGATGTTGTGTTTTTGGTTCTA
1447339 CTCGGCGTGCCTTTTCGGCTTCCCGGCCTTCTTGTTTTCGTGCTTTGTTTGGCTTGTATATTGTG
1 CTCGGCGTGCCTTTTCGGCTTCCCGGCCTTCTTGTTTTCGTGCTTTGTTTGGCTTGTATATTGTG
1447404 GTGTACTGTGTTTTTGTGGTTCCCCCGATGTTGTGTTTTTGGTTC
66 GTGTACTGTGTTTTTGTGGTTCCCCCGATGTTGTGTTTTTGGTTC
1447449 GATCCTTTTG
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.04, C:0.21, G:0.27, T:0.49
Consensus pattern (112 bp):
CTCGGCGTGCCTTTTCGGCTTCCCGGCCTTCTTGTTTTCGTGCTTTGTTTGGCTTGTATATTGTG
GTGTACTGTGTTTTTGTGGTTCCCCCGATGTTGTGTTTTTGGTTCTA
Found at i:1447963 original size:21 final size:18
Alignment explanation
Indices: 1447921--1447978 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
1447911 GAGGGAAAAA
*
1447921 AAAAGAAAATAAATAAAT
1 AAAACAAAATAAATAAAT
*
1447939 AAAACCAAATAAAT-AAT
1 AAAACAAAATAAATAAAT
*
1447956 AATA-AAAATAAAATAAAAT
1 AAAACAAAAT-AAAT-AAAT
1447975 AAAA
1 AAAA
1447979 AACAAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 10 0.31
18 12 0.38
19 6 0.19
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAACAAAATAAATAAAT
Found at i:1447970 original size:5 final size:5
Alignment explanation
Indices: 1447916--1447978 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
1447906 GAAAAGAGGG
* * * *
1447916 AAAAA AAAAG AAAAT -AAAT -AAAT AAAAC CAAAT -AAAT AATAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT -AAAAT
1447965 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
1447979 AACAAAACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 12 0.24
5 29 0.59
6 6 0.12
7 2 0.04
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:1447990 original size:26 final size:26
Alignment explanation
Indices: 1447935--1447991 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1447925 GAAAATAAAT
* * *
1447935 AAATAAAACCAAATAAATAATAATAA
1 AAATAAAACAAAATAAAAAACAATAA
*
1447961 AAATAAAATAAAATAAAAAACAA-AA
1 AAATAAAACAAAATAAAAAACAATAA
1447986 CAAATA
1 -AAATA
1447992 TATATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (26 bp):
AAATAAAACAAAATAAAAAACAATAA
Found at i:1448119 original size:37 final size:37
Alignment explanation
Indices: 1448040--1448140 Score: 127
Period size: 35 Copynumber: 2.8 Consensus size: 37
1448030 ACATTTCCAA
* *
1448040 AAAATGTTTTTCAAAAACTATATATTATATACTTTTTT
1 AAAATATTTTTTAAAAACTATATA-TATATACTTTTTT
1448078 AAAATATTTTTTAAAAA-TAATATATATATA-TTTTTT
1 AAAATATTTTTTAAAAACT-ATATATATATACTTTTTT
* *
1448114 CAAA-ATGTTTTAAAAACTATATATATA
1 AAAATATTTTTTAAAAACTATATATATA
1448141 ATTCAAAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
35 20 0.35
36 10 0.18
37 7 0.12
38 20 0.35
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (37 bp):
AAAATATTTTTTAAAAACTATATATATATACTTTTTT
Found at i:1448134 original size:29 final size:28
Alignment explanation
Indices: 1448101--1448225 Score: 80
Period size: 29 Copynumber: 4.3 Consensus size: 28
1448091 AAAATAATAT
1448101 ATATATATTTTTTCAAAATGTTTTAAAA
1 ATATATATTTTTTCAAAATGTTTTAAAA
**
1448129 ACTATATATATAATTCAAAA-GTTTTAAAA
1 A-TATATAT-TTTTTCAAAATGTTTTAAAA
* * * *
1448158 TATATTAAAATGTTTTAAAAACTATATGTT----
1 -ATA-T-ATATTTTTTCAAAA-TGT-T-TTAAAA
1448188 ATATATATTTTTTCAAAATGTTTTAAAA
1 ATATATATTTTTTCAAAATGTTTTAAAA
1448216 ACTATATATT
1 A-TATATATT
1448226 ATATATATGT
Statistics
Matches: 71, Mismatches: 12, Indels: 27
0.65 0.11 0.25
Matches are distributed among these distances:
24 2 0.03
25 1 0.01
26 2 0.03
27 11 0.15
28 3 0.04
29 29 0.41
30 16 0.23
31 3 0.04
32 1 0.01
33 1 0.01
34 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (28 bp):
ATATATATTTTTTCAAAATGTTTTAAAA
Found at i:1448215 original size:38 final size:38
Alignment explanation
Indices: 1448164--1448308 Score: 179
Period size: 38 Copynumber: 3.8 Consensus size: 38
1448154 AAAATATATT
* *
1448164 AAAATGTTTTAAAAACTATATGTTATATATATTTTTTC
1 AAAATGTTTTAAAAACTATATATTATATATATGTTTTC
*
1448202 AAAATGTTTTAAAAACTATATATTATATATATGTTTCC
1 AAAATGTTTTAAAAACTATATATTATATATATGTTTTC
* *
1448240 AGAATGTTTTAGAAA-T-TATA-TAGTATATATGTTTTC
1 AAAATGTTTTAAAAACTATATATTA-TATATATGTTTTC
* *
1448276 AAAAGGCTTTCAAAAAACTATATATTATATATA
1 AAAATG-TTT-TAAAAACTATATATTATATATA
1448309 CTTTAAAAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
35 2 0.02
36 20 0.22
37 4 0.04
38 52 0.57
39 1 0.01
40 10 0.11
41 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (38 bp):
AAAATGTTTTAAAAACTATATATTATATATATGTTTTC
Found at i:1451223 original size:123 final size:125
Alignment explanation
Indices: 1451004--1451253 Score: 486
Period size: 123 Copynumber: 2.0 Consensus size: 125
1450994 GGATTACTAC
1451004 CTTTTAAGTACATATTGCAATGCTTACGGTGGCAGAATTTGGTGATAGAGTTGAAGGGGAGACAA
1 CTTTTAAGTACATATTGCAATGCTTACGGTGGCAGAATTTGGTGATAGAGTTGAAGGGGAGACAA
1451069 CTTAAAACTTTTTTTAAAAAATAAAGGTTTAAATTAAAAAATTT-AA-TTTTTTGAAGAG
66 CTTAAAACTTTTTTTAAAAAATAAAGGTTTAAATTAAAAAATTTAAATTTTTTTGAAGAG
1451127 CTTTTAAGTACATATTGCAATGCTTACGGTGGCAGAATTTGGTGATAGAGTTGAAGGGGAGACAA
1 CTTTTAAGTACATATTGCAATGCTTACGGTGGCAGAATTTGGTGATAGAGTTGAAGGGGAGACAA
1451192 CTTAAAACTTTTTTTAAAAAATAAAGGTTTAAATTAAAAAATTTAAATTTTTTTGAAGAG
66 CTTAAAACTTTTTTTAAAAAATAAAGGTTTAAATTAAAAAATTTAAATTTTTTTGAAGAG
1451252 CT
1 CT
1451254 CAATTTATGT
Statistics
Matches: 125, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
123 109 0.87
124 2 0.02
125 14 0.11
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (125 bp):
CTTTTAAGTACATATTGCAATGCTTACGGTGGCAGAATTTGGTGATAGAGTTGAAGGGGAGACAA
CTTAAAACTTTTTTTAAAAAATAAAGGTTTAAATTAAAAAATTTAAATTTTTTTGAAGAG
Found at i:1451394 original size:15 final size:15
Alignment explanation
Indices: 1451374--1451404 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1451364 GAACTTCTAA
1451374 TATTTTTTAAGAAAT
1 TATTTTTTAAGAAAT
1451389 TATTTTTTAAGAAAT
1 TATTTTTTAAGAAAT
1451404 T
1 T
1451405 TTAAGGATTT
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:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TATTTTTTAAGAAAT
Found at i:1453770 original size:15 final size:16
Alignment explanation
Indices: 1453739--1453771 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1453729 GGGATTTAGA
*
1453739 AATAATGAAATTAAAT
1 AATAATGAAAATAAAT
1453755 AATAAT-AAAATAAAT
1 AATAATGAAAATAAAT
1453770 AA
1 AA
1453772 AAAATGACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AATAATGAAAATAAAT
Found at i:1456210 original size:25 final size:25
Alignment explanation
Indices: 1456181--1456230 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1456171 AATATAAAGG
*
1456181 AAAATAAATAACAAGAAATAAAAAT
1 AAAATAAACAACAAGAAATAAAAAT
**
1456206 AAAATAAACAACAATTAATAAAAAT
1 AAAATAAACAACAAGAAATAAAAAT
1456231 GGATTGCCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAATAAACAACAAGAAATAAAAAT
Found at i:1457285 original size:21 final size:19
Alignment explanation
Indices: 1457261--1457318 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
1457251 ATGTTTAATG
1457261 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
1457280 ACAAAAGGATATCAATTGTT-
1 A-AAAA-GATACCAATTGTTA
*
1457300 AAAAAGATACTAATTGTTA
1 AAAAAGATACCAATTGTTA
1457319 CCAATTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 5 0.15
21 12 0.36
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:1457308 original size:18 final size:17
Alignment explanation
Indices: 1457261--1457318 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 17
1457251 ATGTTTAATG
1457261 AAAAAGATACCAATTGTT
1 AAAAAGATA-CAATTGTT
1457279 AACAAAAGGATATCAATTGTT
1 -A-AAAA-GATA-CAATTGTT
1457300 AAAAAGATACTAATTGTT
1 AAAAAGATAC-AATTGTT
1457318 A
1 A
1457319 CCAATTGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 1 0.03
18 12 0.34
19 5 0.14
20 5 0.14
21 12 0.34
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (17 bp):
AAAAAGATACAATTGTT
Found at i:1459726 original size:18 final size:20
Alignment explanation
Indices: 1459685--1459727 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1459675 TCTTCGAGGA
1459685 TCTTCTCAAGGATGTTAAGC
1 TCTTCTCAAGGATGTTAAGC
*
1459705 -CTTCT-AAGGA-GTTAGGC
1 TCTTCTCAAGGATGTTAAGC
1459722 TCTTCT
1 TCTTCT
1459728 GCCAATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 10 0.48
19 5 0.24
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TCTTCTCAAGGATGTTAAGC
Found at i:1460008 original size:33 final size:34
Alignment explanation
Indices: 1459971--1460041 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1459961 CCTTTACAGC
*
1459971 TCCCTAG-TTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* * *
1460004 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
1460038 TCCC
1 TCCC
1460042 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:1463348 original size:13 final size:12
Alignment explanation
Indices: 1463329--1463365 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
1463319 TAGAGATTTG
1463329 GAAATAAATAAA
1 GAAATAAATAAA
1463341 GTAAATAAATAAA
1 G-AAATAAATAAA
1463354 -AAATAAA-AAA
1 GAAATAAATAAA
1463364 GA
1 GA
1463366 TTATGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.13
11 8 0.35
12 1 0.04
13 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
GAAATAAATAAA
Found at i:1468268 original size:24 final size:24
Alignment explanation
Indices: 1468224--1468269 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1468214 CGTGCACTCA
* *
1468224 TGTATTAGTACCTTTGGGTACTAT
1 TGTATTAGTACATTTAGGTACTAT
*
1468248 TGTATTAGTACATTTATGTACT
1 TGTATTAGTACATTTAGGTACT
1468270 CTGGGCAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (24 bp):
TGTATTAGTACATTTAGGTACTAT
Found at i:1469787 original size:21 final size:21
Alignment explanation
Indices: 1469761--1469808 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1469751 TTAGGCTAGA
1469761 AGTATCGATACTCATTCATCG
1 AGTATCGATACTCATTCATCG
1469782 AGTATCGATACTCATTCATCG
1 AGTATCGATACTCATTCATCG
1469803 AGTATC
1 AGTATC
1469809 AATAGTGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (21 bp):
AGTATCGATACTCATTCATCG
Found at i:1470056 original size:21 final size:21
Alignment explanation
Indices: 1470030--1470085 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1470020 CCCTAGCTTG
1470030 GGAGTATCGATACTCAATCTA
1 GGAGTATCGATACTCAATCTA
*
1470051 GGAGTATTGATACTCAATCTA
1 GGAGTATCGATACTCAATCTA
1470072 GGAGTATCGATACT
1 GGAGTATCGATACT
1470086 ACCCTTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (21 bp):
GGAGTATCGATACTCAATCTA
Found at i:1481598 original size:36 final size:37
Alignment explanation
Indices: 1481530--1481599 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1481520 GGAATTCAAG
1481530 GGGTACCGATACCTTGAAGAATAGTATCGATACCCAT
1 GGGTACCGATACCTTGAAGAATAGTATCGATACCCAT
* *
1481567 GGGTACCGATTCCTT-AAGGAA-GGTATCGATACC
1 GGGTACCGATACCTTGAA-GAATAGTATCGATACC
1481600 ATCTTAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 13 0.43
37 17 0.57
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (37 bp):
GGGTACCGATACCTTGAAGAATAGTATCGATACCCAT
Found at i:1482314 original size:22 final size:23
Alignment explanation
Indices: 1482285--1482336 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1482275 GAGTCAAGGG
*
1482285 TTTCATAGGTCCTTCAGGACATA
1 TTTCATAGGTCCTTCAGGACAAA
* *
1482308 -TTCATAGTTCCTTTAGGACAAA
1 TTTCATAGGTCCTTCAGGACAAA
1482330 TTTCATA
1 TTTCATA
1482337 TGCCACTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (23 bp):
TTTCATAGGTCCTTCAGGACAAA
Found at i:1488276 original size:37 final size:36
Alignment explanation
Indices: 1488225--1488296 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
1488215 AAGGAATTCA
*
1488225 AGGGGTACCGATACCTTGAA-GAATAGTATCGATACCC
1 AGGGGTACCAATACCTT-AATGAA-AGTATCGATACCC
* *
1488262 AGGGGTATCAATACCTTAATGAAGGTATCGATACC
1 AGGGGTACCAATACCTTAATGAAAGTATCGATACC
1488297 ATCTTGAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (36 bp):
AGGGGTACCAATACCTTAATGAAAGTATCGATACCC
Found at i:1489013 original size:22 final size:23
Alignment explanation
Indices: 1488984--1489035 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1488974 GAGTCGAGGG
* *
1488984 TTTCATAGGTCATTCGTGACATA
1 TTTCATAGGTCATTCGGGACAAA
*
1489007 -TTCATAGGTCCTTCGGGACAAA
1 TTTCATAGGTCATTCGGGACAAA
1489029 TTTCATA
1 TTTCATA
1489036 TGCCAATCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (23 bp):
TTTCATAGGTCATTCGGGACAAA
Found at i:1491870 original size:18 final size:17
Alignment explanation
Indices: 1491843--1491877 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1491833 TATGTTATAG
*
1491843 AAGTTTTGCTTTTTTGT
1 AAGTTTTGCTTGTTTGT
1491860 AAGTGTTTGCTTGTTTGT
1 AAGT-TTTGCTTGTTTGT
1491878 TTATTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.11, C:0.06, G:0.23, T:0.60
Consensus pattern (17 bp):
AAGTTTTGCTTGTTTGT
Found at i:1499219 original size:18 final size:18
Alignment explanation
Indices: 1499186--1499220 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1499176 CAACTCAAAA
1499186 AAATTTAAAATCAAAATC
1 AAATTTAAAATCAAAATC
1499204 AAATTATAAAAT-AAAAT
1 AAATT-TAAAATCAAAAT
1499221 TCATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATTTAAAATCAAAATC
Found at i:1500002 original size:18 final size:18
Alignment explanation
Indices: 1499979--1500027 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1499969 TTCTGGTGCA
1499979 GTTTTGATTATCGTTTCC
1 GTTTTGATTATCGTTTCC
*
1499997 GTTTTGATTATTGTTTCC
1 GTTTTGATTATCGTTTCC
*
1500015 GTTTTGATCATCG
1 GTTTTGATTATCG
1500028 GTCACTCCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.55
Consensus pattern (18 bp):
GTTTTGATTATCGTTTCC
Found at i:1503069 original size:31 final size:31
Alignment explanation
Indices: 1503030--1503116 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
1503020 ACGTGTGAAT
* * *
1503030 TTTG-ATTTGGTTGAATTTTACACAT-GAAA
1 TTTGAATTTGATTCAATTGTACACATGGAAA
*
1503059 GTTTGAATTTGATTCAATTGTACCCATGGAAA
1 -TTTGAATTTGATTCAATTGTACACATGGAAA
* *
1503091 TTTGATTTTGATTCAGTTGTACACAT
1 TTTGAATTTGATTCAATTGTACACAT
1503117 TTAAAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.08
31 40 0.83
32 4 0.08
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (31 bp):
TTTGAATTTGATTCAATTGTACACATGGAAA
Found at i:1503455 original size:29 final size:29
Alignment explanation
Indices: 1503386--1503448 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1503376 GCTGCCAATT
*
1503386 TTTTTTGTATTTATAATTAGGGCCCTCAA
1 TTTTTTATATTTATAATTAGGGCCCTCAA
*
1503415 TTTTTTATATTTATAATTGGGGCTCCT-AA
1 TTTTTTATATTTATAATTAGGGC-CCTCAA
1503444 TTTTT
1 TTTTT
1503449 ATAATTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (29 bp):
TTTTTTATATTTATAATTAGGGCCCTCAA
Found at i:1503631 original size:118 final size:119
Alignment explanation
Indices: 1503414--1503657 Score: 348
Period size: 118 Copynumber: 2.1 Consensus size: 119
1503404 AGGGCCCTCA
* * * * * *
1503414 ATTTTTTATATTTATAATTGGGGCTCCTAATTTTTATAATTTCATAAAGTTTTTAGTTTTTGAAC
1 ATTTTTTATATTTATAATTAGGCCCCCTAATTTTTATAAATTCATAAAATGTTTAGTTTTTGAAC
* * *
1503479 CTCTTTTTCTATTTCTCTTATTAATTCATCCAATTTTGGATT-AA-ATTTAACC
66 CTCATTTTCCATTTCTCTTATTAATTCATCCAATTTTGAATTAAATATTTAACC
*
1503531 ATTTTTTATATTTATAATTAGGCCCCCTAATTTTTATAAATTCATAAAAATGTTTAGTTTTTGAC
1 ATTTTTTATATTTATAATTAGGCCCCCTAATTTTTATAAATTCAT-AAAATGTTTAGTTTTTGAA
* *
1503596 CCTCATTTTCCATTTCTCTTATTTATTCATTCAATTTTGAATTAAATATTTAACC
65 CCTCATTTTCCATTTCTCTTATTAATTCATCCAATTTTGAATTAAATATTTAACC
*
1503651 ATGTTTT
1 ATTTTTT
1503658 CTCTTTTTTC
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
117 41 0.37
118 54 0.49
119 2 0.02
120 14 0.13
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (119 bp):
ATTTTTTATATTTATAATTAGGCCCCCTAATTTTTATAAATTCATAAAATGTTTAGTTTTTGAAC
CTCATTTTCCATTTCTCTTATTAATTCATCCAATTTTGAATTAAATATTTAACC
Found at i:1507234 original size:37 final size:37
Alignment explanation
Indices: 1507184--1507254 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
1507174 AACTATAATT
* *
1507184 TTGAATTTTATAAATGAATATTATCTATATATATATA
1 TTGAAATTTATAAATGAATAATATCTATATATATATA
*
1507221 TTGAAATTTATAAATGAATAATATGTATATATAT
1 TTGAAATTTATAAATGAATAATATCTATATATAT
1507255 GATAATGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (37 bp):
TTGAAATTTATAAATGAATAATATCTATATATATATA
Found at i:1520617 original size:44 final size:43
Alignment explanation
Indices: 1520503--1520625 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 43
1520493 AAAACCCGAC
*
1520503 GGATGCATCGATGCA-TG-GAAGTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCACTGTCAAGTGT--ATCGATGCACATTCAAG
* * * * *
1520546 GCATGCATTGGTGCACCT-TCATGGTGTATCAATGCACATTCAATG
1 GGATGCATCGATGCA-CTGTCA-AGTGTATCGATGCACATTCAA-G
*
1520591 GGATGCATCGATGCACTGTTAAGTGTATCGATGCA
1 GGATGCATCGATGCACTGTCAAGTGTATCGATGCA
1520626 TGAAGCACAA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
43 12 0.19
44 29 0.47
45 17 0.27
46 4 0.06
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (43 bp):
GGATGCATCGATGCACTGTCAAGTGTATCGATGCACATTCAAG
Found at i:1526262 original size:64 final size:65
Alignment explanation
Indices: 1526194--1526336 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 65
1526184 TGCACTAAGA
1526194 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-GCC-TGAGTGCATCGATGCATGG-C
1 GTGCATCGATGCATAAAATGCATTCGATG-TTCAAAATATGCCATG-GTGCATCGATGCATGGAC
1526256 TG
64 TG
* * * ** * * *
1526258 GTGCATCGATGCATCAAATGTATTTGATGTTCAATTTATTCCATGGTGTATCGATGCATGGATTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAAAATATGCCATGGTGCATCGATGCATGGACTG
*
1526323 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
1526337 CACTTTGAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
63 7 0.10
64 43 0.64
65 17 0.25
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTCAAAATATGCCATGGTGCATCGATGCATGGACTG
Found at i:1528166 original size:21 final size:20
Alignment explanation
Indices: 1528142--1528181 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1528132 GTTTTTTCAC
*
1528142 TTTTATTTTCTTGTTTTTACTT
1 TTTTACTTT-TTGTTTTTAC-T
1528164 TTTTACTTTTTGTTTTTA
1 TTTTACTTTTTGTTTTTA
1528182 AAATGCTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTACTTTTTGTTTTTACT
Found at i:1535068 original size:53 final size:53
Alignment explanation
Indices: 1534992--1535154 Score: 206
Period size: 50 Copynumber: 3.1 Consensus size: 53
1534982 ATTGCACCTA
* * * *
1534992 AGTGCCGAACTGGTAATTAACAAACTCATTATGAATTCCATGGTTGCACACAT
1 AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTACACACAT
* * *
1535045 AGTGTCAAAATGGTAATTCACAAACTC---ATGAATTCCATGGTTTCACAAAT
1 AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTACACACAT
* * *
1535095 AGTGCCGAAGTGGTAATTCACAAACTCATTATAAATTCCATGGATTACACACAT
1 AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTCCATGG-TTACACACAT
1535149 AGTGCC
1 AGTGCC
1535155 GATAATATAT
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
50 45 0.48
53 35 0.37
54 14 0.15
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (53 bp):
AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTACACACAT
Found at i:1538545 original size:2 final size:2
Alignment explanation
Indices: 1538534--1538638 Score: 203
Period size: 2 Copynumber: 53.0 Consensus size: 2
1538524 CTTCAAACTC
1538534 AT AT -T 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
1538575 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
1538617 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1538639 TTATGAACAT
Statistics
Matches: 102, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 101 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1542570 original size:20 final size:21
Alignment explanation
Indices: 1542541--1542586 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1542531 CTCTTCAAGA
*
1542541 AGTATCGATACTC-GAG-GTCC
1 AGTATAGATACTCAGAGTGT-C
1542561 AGTATAGATACTCAGAGTGTC
1 AGTATAGATACTCAGAGTGTC
1542582 AGTAT
1 AGTAT
1542587 CTATATTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 9 0.39
22 2 0.09
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (21 bp):
AGTATAGATACTCAGAGTGTC
Found at i:1542650 original size:18 final size:20
Alignment explanation
Indices: 1542627--1542695 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1542617 GCTGATTTTG
1542627 GTATCGATACTCAT-G-AGA
1 GTATCGATACTCATGGTAGA
*
1542645 GTATCGATACCCATGGTAGA
1 GTATCGATACTCATGGTAGA
* ** *
1542665 TTATCGATACTCCCGATAGA
1 GTATCGATACTCATGGTAGA
1542685 GGTATCGATAC
1 -GTATCGATAC
1542696 AAGGTAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 13 0.32
19 1 0.02
20 18 0.44
21 9 0.22
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (20 bp):
GTATCGATACTCATGGTAGA
Found at i:1542671 original size:20 final size:18
Alignment explanation
Indices: 1542627--1542674 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1542617 GCTGATTTTG
*
1542627 GTATCGATACTCATGAGA
1 GTATCGATACCCATGAGA
1542645 GTATCGATACCCATGGTAGA
1 GTATCGATACCCAT-G-AGA
*
1542665 TTATCGATAC
1 GTATCGATAC
1542675 TCCCGATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 1 0.04
20 12 0.46
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (18 bp):
GTATCGATACCCATGAGA
Found at i:1548103 original size:21 final size:20
Alignment explanation
Indices: 1548060--1548103 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1548050 CTTCAAGAAT
*
1548060 TATCGATACTTGGGGTCTAG
1 TATCGATACTTAGGGTCTAG
1548080 TATCGATACTCATAGGGT-TAG
1 TATCGATACT--TAGGGTCTAG
1548101 TAT
1 TAT
1548104 TGAAACTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 6 0.29
22 5 0.24
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (20 bp):
TATCGATACTTAGGGTCTAG
Found at i:1549224 original size:19 final size:19
Alignment explanation
Indices: 1549186--1549221 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1549176 TAAATTATGA
*
1549186 TAAATAGTTTTAATATAAT
1 TAAATAGTTTTAAAATAAT
1549205 TAAAT-GTTTTAAAATAA
1 TAAATAGTTTTAAAATAA
1549222 ATTTTTGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
TAAATAGTTTTAAAATAAT
Found at i:1568007 original size:23 final size:23
Alignment explanation
Indices: 1567979--1568027 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1567969 TGGTGGTTGA
*
1567979 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
1568002 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
1568025 TTT
1 TTT
1568028 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:1578177 original size:22 final size:22
Alignment explanation
Indices: 1578149--1578196 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1578139 GTGGTGGTTG
*
1578149 ATTTAATGG-ATGTTTAGACTTT
1 ATTTAATGGTATATTTA-ACTTT
*
1578171 ATTTAATGGTATATTTAAGTTT
1 ATTTAATGGTATATTTAACTTT
1578193 ATTT
1 ATTT
1578197 TGGTTCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (22 bp):
ATTTAATGGTATATTTAACTTT
Found at i:1589131 original size:20 final size:21
Alignment explanation
Indices: 1589084--1589132 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1589074 TGAAAAATTA
1589084 CTCAATATCGATAACCCTACC
1 CTCAATATCGATAACCCTACC
*** *
1589105 AGGAATATCGAT-ACCCTCCC
1 CTCAATATCGATAACCCTACC
1589125 CTCAATAT
1 CTCAATAT
1589133 TAATACTCAC
Statistics
Matches: 21, Mismatches: 7, Indels: 1
0.72 0.24 0.03
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.33, C:0.35, G:0.08, T:0.24
Consensus pattern (21 bp):
CTCAATATCGATAACCCTACC
Found at i:1589239 original size:20 final size:21
Alignment explanation
Indices: 1589209--1589265 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
1589199 TACTCCTCCT
*
1589209 ATGATTATTGATACTCAATCA
1 ATGAGTATTGATACTCAATCA
* * *
1589230 AT-AGTATTGATAATCATTGA
1 ATGAGTATTGATACTCAATCA
1589250 ATGAGTATTGATACTC
1 ATGAGTATTGATACTC
1589266 CTAGCCCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (21 bp):
ATGAGTATTGATACTCAATCA
Found at i:1591118 original size:39 final size:39
Alignment explanation
Indices: 1591070--1591192 Score: 183
Period size: 39 Copynumber: 3.2 Consensus size: 39
1591060 TAGAGAAAAT
1591070 GAGCCTGTAGTAAGGACTTACCCTGAGCACAAAGTCGAG
1 GAGCCTGTAGTAAGGACTTACCCTGAGCACAAAGTCGAG
* * *
1591109 GAGCATGTAGTAAGGAATTACCCTGAGCACAAAGCCGAG
1 GAGCCTGTAGTAAGGACTTACCCTGAGCACAAAGTCGAG
* * * *
1591148 GAACCTGAAGTAAGGACTTGCCCTGAGCACAAAATCGAG
1 GAGCCTGTAGTAAGGACTTACCCTGAGCACAAAGTCGAG
1591187 GAGCCT
1 GAGCCT
1591193 ACGGAAAACG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (39 bp):
GAGCCTGTAGTAAGGACTTACCCTGAGCACAAAGTCGAG
Found at i:1591250 original size:44 final size:44
Alignment explanation
Indices: 1591196--1591346 Score: 196
Period size: 44 Copynumber: 3.4 Consensus size: 44
1591186 GGAGCCTACG
* * * * *
1591196 GAAAACGGTAAGGTCTTACCCATACATATAGCAGAGGAGCCTGT
1 GAAAATGGTAAGGTCTTACCCTTGCACATAGTAGAGGAGCCTGT
* * *
1591240 GAAAATGGTAAGGTCTTATCCTTGCACATAGTACAGGAGCCTTT
1 GAAAATGGTAAGGTCTTACCCTTGCACATAGTAGAGGAGCCTGT
* *
1591284 AAAAATGGCAAGGTCTTACCCTTGCACATAGTAGAGGAGCCTGT
1 GAAAATGGTAAGGTCTTACCCTTGCACATAGTAGAGGAGCCTGT
1591328 -AGAAATGGTAAGGTCTTAC
1 GA-AAATGGTAAGGTCTTAC
1591347 AAGTCATAGA
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 1 0.01
44 91 0.99
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (44 bp):
GAAAATGGTAAGGTCTTACCCTTGCACATAGTAGAGGAGCCTGT
Found at i:1593082 original size:94 final size:95
Alignment explanation
Indices: 1592957--1593179 Score: 270
Period size: 94 Copynumber: 2.4 Consensus size: 95
1592947 GTACTGATGA
* * * * *
1592957 AGTAGTATCGATACCGTGGTAAGGGTATCGATACCAGGTA-ACATCGAACCTAATTTTGGTATCG
1 AGTAGTATTGATACCATGGTAAGGATATCGATACCAAG-ACACATCCAACCTAATTTTGGTATCG
* * * *
1593021 ATACTTG-AGGGGGTATCGGTACCAGAGTAT
65 ATACTGGAAGGGGGTATCGATACCAGAATAG
* * *
1593051 AGTAGTATTGATACCATGGTGAGGATATCGATACCAAGACATATCCAAGCTAATTTTGGTATCGA
1 AGTAGTATTGATACCATGGTAAGGATATCGATACCAAGACACATCCAACCTAATTTTGGTATCGA
*
1593116 TACTGGAAGGGGGTATCGATACCATAATAG
66 TACTGGAAGGGGGTATCGATACCAGAATAG
* * * *
1593146 GGTAGTATTGATACCATGGGAAGGGTATCAATAC
1 AGTAGTATTGATACCATGGTAAGGATATCGATAC
1593180 TAAAGGGCCA
Statistics
Matches: 109, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
93 1 0.01
94 60 0.55
95 48 0.44
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (95 bp):
AGTAGTATTGATACCATGGTAAGGATATCGATACCAAGACACATCCAACCTAATTTTGGTATCGA
TACTGGAAGGGGGTATCGATACCAGAATAG
Found at i:1593578 original size:59 final size:59
Alignment explanation
Indices: 1593505--1594328 Score: 1218
Period size: 59 Copynumber: 14.0 Consensus size: 59
1593495 TTACCAAAAT
* * *
1593505 GGCACTTCGTGTGCTAACATGAGAATGAATTCATACTAAGTGTATAAATTTTCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* * *
1593564 CGCACTTCGTGTGCTAATATGAGAAGGAATTCATACTAAGTGTGTGAATTTCCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
** * * * *
1593623 GGCACTTTATGTGCTAACATGATAAGGAATTCATACTAAGTGTCTAAATTTCCATATAA
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
*
1593682 GGCACTTAGTGTGCTAACATGAGAAGGAATTCATACTATA-TGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTA-AGTGTATGAATTTCCATATAG
* * * *
1593741 GGCACTTTGTGTGCTAGCATAAGAAGGAATTTATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* * *
1593800 GGCACTTCGTGTGCTAACATAAGAAGGAATTCATACTAAGTGTATCAATTTTCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* * * *
1593859 GGCACTTCGTCTACTAACATGATAAGGAATTCATACTAAGTGTATGAATCTCCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* *
1593918 GGCACTTAGTGTACTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* * *
1593977 GGCACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTACATATAT
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* *
1594036 GGTACTTCGTGTGCTAACATGAGAAGGAATTTATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* *
1594095 GACACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* *
1594154 GGCACTTTGTGTGCTAATATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* * ** * * * *
1594213 GGAACTTAGCATGTTAACATGAGATGGAATTCATACTAAGTGTACGAATTTCCATGTAG
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
* * *
1594272 GGCACTTCGTGTGGTAACATGAGAAGGAATTCATATTATGTGTATGAATTTCCATAT
1 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1594329 GGGAAATAAA
Statistics
Matches: 689, Mismatches: 74, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
58 1 0.00
59 687 1.00
60 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (59 bp):
GGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
Found at i:1594634 original size:22 final size:23
Alignment explanation
Indices: 1594609--1594651 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1594599 TGTTCGTCTA
*
1594609 TTTAAGTTAA-TATATGTTTTCT
1 TTTAAGTTAATTAAATGTTTTCT
1594631 TTTAAGTTAATTAAATGTTTT
1 TTTAAGTTAATTAAATGTTTT
1594652 ATAAAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTAAGTTAATTAAATGTTTTCT
Found at i:1595513 original size:17 final size:17
Alignment explanation
Indices: 1595491--1595527 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1595481 CAAGGTGATC
1595491 GAGTAGTGCACGAGTAT
1 GAGTAGTGCACGAGTAT
*
1595508 GAGTAGTGCATGAGTAT
1 GAGTAGTGCACGAGTAT
1595525 GAG
1 GAG
1595528 ACTGAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.08, G:0.38, T:0.24
Consensus pattern (17 bp):
GAGTAGTGCACGAGTAT
Found at i:1600508 original size:94 final size:94
Alignment explanation
Indices: 1600385--1600605 Score: 275
Period size: 94 Copynumber: 2.4 Consensus size: 94
1600375 TATTGATGAG
* * * *
1600385 GTAGTATCGATACCAAGATAAGGGTATCGATACCAGGTA-ACATCGAACCTAATTTTAGTATCGA
1 GTAGTATCGATACCATGGTAAGAGTATCGATACCAAG-ACACATCGAACCTAATTTTAGTATCGA
* * *
1600449 TACCAGAGGGGGTATCGATACCATAATATA
65 TACCAGAAGGGGTATCAATACCATAATAGA
* * * *
1600479 GTAGTATCGATACCATGGTGAGATTATCGATACCAAGACACATCGAAGCTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGAGTATCGATACCAAGACACATCGAACCTAATTTTAGTATCGAT
* * * *
1600544 GCCGGAAGGGGTATTAATACCATAATAGG
66 ACCAGAAGGGGTATCAATACCATAATAGA
1600573 GTAGTATCGATACCATGGTAA-AGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGA-GTATCGATAC
1600606 TGAAGGGCTA
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
93 2 0.02
94 106 0.98
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (94 bp):
GTAGTATCGATACCATGGTAAGAGTATCGATACCAAGACACATCGAACCTAATTTTAGTATCGAT
ACCAGAAGGGGTATCAATACCATAATAGA
Found at i:1601005 original size:59 final size:59
Alignment explanation
Indices: 1600941--1601173 Score: 314
Period size: 59 Copynumber: 4.0 Consensus size: 59
1600931 CGGCACTTTG
1600941 TGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTAC-ATATAGGACACTTCA
1 TGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTT-CTATATAGGACACTTCA
* * * *
1601000 TGTGCTAACATGAG-AGGAATTCATACTAAGTGTATGAATTTC-ATATAAGCCACTCCG
1 TGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCTATATAGGACACTTCA
* * * * *
1601057 TGTGCTTACATGATAAGGAATT-AGTACTAAATGTATGAATTTCTTTATAGGGCACTT-A
1 TGTGCTAACATGAGAAGGAATTCA-TACTAAGTGTATGAATTTCTATATAGGACACTTCA
*
1601115 GTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCTATATATGACACTTC
1 -TGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCTATATAGGACACTTC
1601174 GAGTATGAAT
Statistics
Matches: 150, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
57 25 0.17
58 52 0.35
59 72 0.48
60 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (59 bp):
TGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCTATATAGGACACTTCA
Found at i:1601238 original size:87 final size:87
Alignment explanation
Indices: 1601089--1601261 Score: 256
Period size: 87 Copynumber: 2.0 Consensus size: 87
1601079 AGTACTAAAT
** * * * *
1601089 GTATGAATTTCTTTATAGGGCACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGA
1 GTATGAATTTCCATATAGGGAACATAGTGTGCTAACATAAGAAGGAATTCATACTAAATGTATGA
* *
1601154 ATTTCTATATATGACACTTCGA
66 ATTTCCATATAGGACACTTCGA
*
1601176 GTATGAATTTCCATATAGGGAACATAGTGTGCTAACTTAAGAAGGAATTCATACTAAATGTATGA
1 GTATGAATTTCCATATAGGGAACATAGTGTGCTAACATAAGAAGGAATTCATACTAAATGTATGA
*
1601241 ATTTCCATATAGGGCACTTCG
66 ATTTCCATATAGGACACTTCG
1601262 TGTGCCAACA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (87 bp):
GTATGAATTTCCATATAGGGAACATAGTGTGCTAACATAAGAAGGAATTCATACTAAATGTATGA
ATTTCCATATAGGACACTTCGA
Found at i:1601248 original size:59 final size:59
Alignment explanation
Indices: 1601176--1601432 Score: 320
Period size: 59 Copynumber: 4.4 Consensus size: 59
1601166 GACACTTCGA
* * * *
1601176 GTATGAATTTCCATATAGGGAACATAGTGTGCTAACTTAAGAAGGAATTCATACTAAAT
1 GTATGAATTTCCATATAGGGAACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGT
* * * *
1601235 GTATGAATTTCCATATAGGGCACTTCGTGTGCCAACATGAGAAGGAATGCATACTAAGT
1 GTATGAATTTCCATATAGGGAACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGT
* * * *
1601294 GTATGAATTTCCATATAGGGCACTTAGTGTACTAACATGAGAAGAAATCCATACTAAGT
1 GTATGAATTTCCATATAGGGAACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGT
* * * * * *
1601353 ATACGAATTTCCATATA-GGACACTTCGTGTGCTAACATGAGAATGAATTCATATTAATT
1 GTATGAATTTCCATATAGGGA-ACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGT
*
1601412 GTATGAATTTCCACAT-GGGAA
1 GTATGAATTTCCATATAGGGAA
1601433 ATAAATTGTG
Statistics
Matches: 170, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
58 3 0.02
59 167 0.98
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (59 bp):
GTATGAATTTCCATATAGGGAACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGT
Found at i:1601323 original size:205 final size:203
Alignment explanation
Indices: 1600973--1601379 Score: 550
Period size: 205 Copynumber: 2.0 Consensus size: 203
1600963 CATACTAAGT
* * *
1600973 GTATGAATTTACATATAGGACACTTCATGTGCTAACATGAGAGGAATTCATACTAAGTGTATGAA
1 GTATGAATTTACATATAGGACACATCATGTGCTAACATAAGAGGAATTCATACTAAATGTATGAA
** * * **
1601038 TTTCATATAAGCCACTCCGTGTGCTTACATGATAAGGAATTAGTACTAAATGTATGAATTTCTTT
66 TTTCATATAAGCCACTCCGTGTGCCAACATGAGAAGGAATCAGTACTAAATGTATGAATTTCCAT
* * * * * * *
1601103 ATAGGGCACTTAGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCTATATATGA
131 ATAGGGCACTTAGTGTACTAACATGAGAAGAAATCCATACTAAGTATACGAATTTCCATATAGGA
1601168 CACTTCGA
196 CACTTCGA
* *
1601176 GTATGAATTTCCATATAGGGA-ACAT-AGTGTGCTAACTTAAGAAGGAATTCATACTAAATGTAT
1 GTATGAATTTACATATA-GGACACATCA-TGTGCTAACATAAG-AGGAATTCATACTAAATGTAT
* * * *
1601239 GAATTTCCATATAGGGCACTTCGTGTGCCAACATGAGAAGGAATGCA-TACTAAGTGTATGAATT
63 GAATTT-CATATAAGCCACTCCGTGTGCCAACATGAGAAGGAAT-CAGTACTAAATGTATGAATT
1601303 TCCATATAGGGCACTTAGTGTACTAACATGAGAAGAAATCCATACTAAGTATACGAATTTCCATA
126 TCCATATAGGGCACTTAGTGTACTAACATGAGAAGAAATCCATACTAAGTATACGAATTTCCATA
1601368 TAGGACACTTCG
191 TAGGACACTTCG
1601380 TGTGCTAACA
Statistics
Matches: 177, Mismatches: 22, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
202 1 0.01
203 31 0.18
204 29 0.16
205 115 0.65
206 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (203 bp):
GTATGAATTTACATATAGGACACATCATGTGCTAACATAAGAGGAATTCATACTAAATGTATGAA
TTTCATATAAGCCACTCCGTGTGCCAACATGAGAAGGAATCAGTACTAAATGTATGAATTTCCAT
ATAGGGCACTTAGTGTACTAACATGAGAAGAAATCCATACTAAGTATACGAATTTCCATATAGGA
CACTTCGA
Found at i:1601384 original size:118 final size:118
Alignment explanation
Indices: 1601176--1601432 Score: 354
Period size: 118 Copynumber: 2.2 Consensus size: 118
1601166 GACACTTCGA
* * * * * *
1601176 GTATGAATTTCCATATAGGGAACATAGTGTGCTAACTTAAGAAGGAATTCATACTAAATGTATGA
1 GTATGAATTTCCATATAGGGAACATAGTGTACTAACATAAGAAGAAATCCATACTAAATATACGA
*
1601241 ATTTCCATATAGGGCACTTCGTGTGCCAACATGAGAAGGAATGCATACTAAGT
66 ATTTCCATATAGGACACTTCGTGTGCCAACATGAGAAGGAATGCATACTAAGT
* * * *
1601294 GTATGAATTTCCATATAGGGCACTTAGTGTACTAACATGAGAAGAAATCCATACTAAGTATACGA
1 GTATGAATTTCCATATAGGGAACATAGTGTACTAACATAAGAAGAAATCCATACTAAATATACGA
* * * * *
1601359 ATTTCCATATAGGACACTTCGTGTGCTAACATGAGAATGAATTCATATTAATT
66 ATTTCCATATAGGACACTTCGTGTGCCAACATGAGAAGGAATGCATACTAAGT
*
1601412 GTATGAATTTCCACAT-GGGAA
1 GTATGAATTTCCATATAGGGAA
1601433 ATAAATTGTG
Statistics
Matches: 121, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
117 4 0.03
118 117 0.97
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (118 bp):
GTATGAATTTCCATATAGGGAACATAGTGTACTAACATAAGAAGAAATCCATACTAAATATACGA
ATTTCCATATAGGACACTTCGTGTGCCAACATGAGAAGGAATGCATACTAAGT
Found at i:1612354 original size:2 final size:2
Alignment explanation
Indices: 1612349--1612374 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1612339 GTTTTTTACC
1612349 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
1612375 TTACACACAC
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:1612421 original size:2 final size:2
Alignment explanation
Indices: 1612414--1612462 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1612404 TATTATAGTT
* *
1612414 AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AT AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1612456 AC AC AC A
1 AC AC AC A
1612463 TATCAATAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.45, G:0.00, T:0.04
Consensus pattern (2 bp):
AC
Found at i:1612434 original size:16 final size:16
Alignment explanation
Indices: 1612413--1612460 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
1612403 CTATTATAGT
1612413 TACACACACACACACA
1 TACACACACACACACA
1612429 TACACACACACACACA
1 TACACACACACACACA
1612445 TACACACACACACACA
1 TACACACACACACACA
1612461 CATATCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (16 bp):
TACACACACACACACA
Found at i:1616551 original size:90 final size:90
Alignment explanation
Indices: 1616442--1616797 Score: 300
Period size: 90 Copynumber: 4.0 Consensus size: 90
1616432 AAATTCAAAG
*
1616442 TTGAATTTGCTTCCACTACTCTTCCGTTGAGTTTGATACTTTGCTAAAAAAACCCGTTCCACTAC
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTAAAAAAACCCGTTCCACTAC
*
1616507 TCTTTTGTGGAGTTCAGATTTATGA
66 TCTTTCGTGGAGTTCAGATTTATGA
* * ** *
1616532 TTGAATTTTCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATTCTGTTCCACTAC
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTAAAAAAACCCGTTCCACTAC
** * * *
1616597 TCTTTCGTGGA-AACTGAATTTTTGTCT
66 TCTTTCGTGGAGTTCAG-ATTTATG--A
* * * * * * * ***
1616624 TTG-TTCTTGCCTTTGATTCATTACTCTTTCATGAAGTTTGATACTTTGCTGAAAAAATTTGTTC
1 TTGAAT-TTG-C--T--TCCACTACTCTTCCGTGGAGTTTGATACTTTGCTAAAAAAACCCGTTC
1616688 CACTACTCTTTCGTGGAGTTCAGATTT-T--
60 CACTACTCTTTCGTGGAGTTCAGATTTATGA
* * * * * *
1616716 CT---TTTACTT-CACTACTCTTCCATGAAGATTTCATACTTTGCT-AAAAAATCCGTTCCACTA
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAG-TTTGATACTTTGCTAAAAAAACCCGTTCCACTA
1616776 CTCTTTCGTGGAGTTCAGATTT
65 CTCTTTCGTGGAGTTCAGATTT
1616798 TGTTCTTGCT
Statistics
Matches: 224, Mismatches: 31, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
83 54 0.24
84 14 0.06
86 1 0.00
88 1 0.00
89 4 0.02
90 76 0.34
91 1 0.00
92 6 0.03
93 1 0.00
95 1 0.00
96 1 0.00
97 62 0.28
98 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (90 bp):
TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTAAAAAAACCCGTTCCACTAC
TCTTTCGTGGAGTTCAGATTTATGA
Found at i:1616598 original size:46 final size:46
Alignment explanation
Indices: 1616452--1616607 Score: 147
Period size: 46 Copynumber: 3.4 Consensus size: 46
1616442 TTGAATTTGC
* * ** *
1616452 TTCCACTACTCTTCCGTTGAGTTTGATACTTTGCTAAAAAAACCCG
1 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATTCTG
** * * * ** * *
1616498 TTCCACTACTCTTTTGTGGAG-TTCAGA-TTT-ATGATTGAATTTTC
1 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGA-AAAATTCTG
1616542 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATTCTG
1 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATTCTG
*
1616588 TTCCACTACTCTTTCGTGGA
1 TTCCACTACTCTTCCGTGGA
1616608 AACTGAATTT
Statistics
Matches: 82, Mismatches: 24, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
43 2 0.02
44 24 0.29
45 8 0.10
46 45 0.55
47 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.40
Consensus pattern (46 bp):
TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATTCTG
Found at i:1616784 original size:83 final size:83
Alignment explanation
Indices: 1616640--1616798 Score: 257
Period size: 83 Copynumber: 1.9 Consensus size: 83
1616630 TTGCCTTTGA
* * * **
1616640 TTCATTACTCTTTCATGAAGTTTGATACTTTGCTGAAAAAATTTGTTCCACTACTCTTTCGTGGA
1 TTCACTACTCTTCCATGAAGTTTCATACTTTGCTGAAAAAATCCGTTCCACTACTCTTTCGTGGA
1616705 GTTCAGATTTTCTTTTAC
66 GTTCAGATTTTCTTTTAC
1616723 TTCACTACTCTTCCATGAAGATTTCATACTTTGCT-AAAAAATCCGTTCCACTACTCTTTCGTGG
1 TTCACTACTCTTCCATGAAG-TTTCATACTTTGCTGAAAAAATCCGTTCCACTACTCTTTCGTGG
1616787 AGTTCAGATTTT
65 AGTTCAGATTTT
1616799 GTTCTTGCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
83 57 0.81
84 13 0.19
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.43
Consensus pattern (83 bp):
TTCACTACTCTTCCATGAAGTTTCATACTTTGCTGAAAAAATCCGTTCCACTACTCTTTCGTGGA
GTTCAGATTTTCTTTTAC
Found at i:1616841 original size:180 final size:184
Alignment explanation
Indices: 1616447--1616845 Score: 449
Period size: 180 Copynumber: 2.2 Consensus size: 184
1616437 CAAAGTTGAA
1616447 TTTGCTTCCACTACTCTTCCGTTG-AGTTTGATACTTTGCTAAAAAAACCCGTTCCACTACTCTT
1 TTTGCTT-CACTACTCTTCCG-TGAAGTTTGATACTTTGCTAAAAAAACCCGTTCCACTACTCTT
* * * * * *
1616511 TTGTGGAGTTCAGATTTATGATTGAATTTTCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGC
64 TCGTGGAGTTCAGATTTAT-ACT--ATTTACTTCCACTACTCTTCCATGAAGTTTCATACTTTGC
* * *
1616576 TGAAAAATTCTGTTCCACTACTCTTTCGTGGAAACTGAATTTTTGTCTTTGTTCTTGCC
126 TGAAAAAATCCGTTCCACTACTCTTTCGTGGAAACAGAATTTTTGTCTTTGTTCTTGCC
* * * * * ***
1616635 TTTGATTCATTACTCTTTCATGAAGTTTGATACTTTGCTGAAAAAATTTGTTCCACTACTCTTTC
1 TTTGCTTCACTACTCTTCCGTGAAGTTTGATACTTTGCTAAAAAAACCCGTTCCACTACTCTTTC
1616700 GTGGAGTTCAGATTT-T-CT-TTTACTT-CACTACTCTTCCATGAAGATTTCATACTTTGCT-AA
66 GTGGAGTTCAGATTTATACTATTTACTTCCACTACTCTTCCATGAAG-TTTCATACTTTGCTGAA
** *
1616760 AAAATCCGTTCCACTACTCTTTCGTGGAGTTCAG-A-TTTTGT-TCTTGCTAT-TTGCG
130 AAAATCCGTTCCACTACTCTTTCGTGGA-AACAGAATTTTTGTCT-TTG-T-TCTTGCC
*
1616815 TTTGCTTTACTACTCTTCCGTGAAGTTTGAT
1 TTTGCTTCACTACTCTTCCGTGAAGTTTGAT
1616846 TTGACTTGAA
Statistics
Matches: 180, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
178 1 0.01
179 9 0.05
180 76 0.42
181 22 0.12
184 1 0.01
186 3 0.02
187 62 0.34
188 6 0.03
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (184 bp):
TTTGCTTCACTACTCTTCCGTGAAGTTTGATACTTTGCTAAAAAAACCCGTTCCACTACTCTTTC
GTGGAGTTCAGATTTATACTATTTACTTCCACTACTCTTCCATGAAGTTTCATACTTTGCTGAAA
AAATCCGTTCCACTACTCTTTCGTGGAAACAGAATTTTTGTCTTTGTTCTTGCC
Found at i:1620044 original size:233 final size:232
Alignment explanation
Indices: 1619638--1620101 Score: 829
Period size: 233 Copynumber: 2.0 Consensus size: 232
1619628 GTATAATTAG
1619638 ACCAGGATCTTTGTCTATATTTACCCCTATTTCTTGATCATTTATTGGGTAGCTTCTTTGGATGA
1 ACCAGGATCTTTGTCTATATTTACCCCTATTTCTTGATCATTTATTGGGTAGCTTCTTTGGATGA
* *
1619703 GCTTTAAGGTTCACAAATCTTAGCTTTCCCCTGAGCTATCTCTTGGTCAAATCCCATCATACTTC
66 GCTTTAAGGTTCACAAATCTCAGCTTTCCCCTGAGCTATCTCTTAGTCAAATCCCATCATACTTC
*
1619768 CTAATTGGCAATTGGGCTTAGTTTGAATTTTAGAACCAATATCTTTAGTGGCAATAGTTGTATCA
131 CTAATTGGCAATTGGGCTTAGTTTGAATTTCAGAACCAATATCTTTAGTGGCAATAGTTGTATCA
1619833 TGGTTCTGGATGTTTCTTGCAACTATACTTGAAGTAT
196 TGGTTCTGGATGTTTCTTGCAACTATACTTGAAGTAT
1619870 ACCAGGATCTTTGTCTATATTTACCCCTCATTTCTTGATCATTTATTGGGTAGCTTCTTTGGATG
1 ACCAGGATCTTTGTCTATATTTACCCCT-ATTTCTTGATCATTTATTGGGTAGCTTCTTTGGATG
* * * *
1619935 AGCTTTTAGGTTCACAAATCTCATCTTTCCCCTGAGCTATCTCTTAGTCAAATTCCATCATATTT
65 AGCTTTAAGGTTCACAAATCTCAGCTTTCCCCTGAGCTATCTCTTAGTCAAATCCCATCATACTT
* *
1620000 CCTAATTGGTAATTGGGCTTAGTTTGAATTTCAGAACCAATATCTTTAGTGGTAATAGTTGTATC
130 CCTAATTGGCAATTGGGCTTAGTTTGAATTTCAGAACCAATATCTTTAGTGGCAATAGTTGTATC
*
1620065 ATGGTTCTGGATGTTTCTTGCAACTATATTTGAAGTA
195 ATGGTTCTGGATGTTTCTTGCAACTATACTTGAAGTA
1620102 GCATTCTCTT
Statistics
Matches: 221, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
232 28 0.13
233 193 0.87
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (232 bp):
ACCAGGATCTTTGTCTATATTTACCCCTATTTCTTGATCATTTATTGGGTAGCTTCTTTGGATGA
GCTTTAAGGTTCACAAATCTCAGCTTTCCCCTGAGCTATCTCTTAGTCAAATCCCATCATACTTC
CTAATTGGCAATTGGGCTTAGTTTGAATTTCAGAACCAATATCTTTAGTGGCAATAGTTGTATCA
TGGTTCTGGATGTTTCTTGCAACTATACTTGAAGTAT
Found at i:1620457 original size:17 final size:16
Alignment explanation
Indices: 1620430--1620466 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1620420 AATTTACAAT
*
1620430 TAATTTAAATAATATC
1 TAATTTAAATAATATA
1620446 TAATTATAAATAATATA
1 TAATT-TAAATAATATA
1620463 TAAT
1 TAAT
1620467 AAATTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTAAATAATATA
Found at i:1620544 original size:11 final size:11
Alignment explanation
Indices: 1620528--1620552 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1620518 AATATTGATT
1620528 TGGGTTTTAAA
1 TGGGTTTTAAA
1620539 TGGGTTTTAAA
1 TGGGTTTTAAA
1620550 TGG
1 TGG
1620553 ATTGGGCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGGTTTTAAA
Found at i:1623829 original size:23 final size:20
Alignment explanation
Indices: 1623803--1623858 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 20
1623793 ATTTGTACAT
1623803 ATAAAAAAACAAAAGTTAGTAAA
1 ATAAAAAAACAAAA-TTA--AAA
*
1623826 ATAATAAAA-AAAATTAAAA
1 ATAAAAAAACAAAATTAAAA
*
1623845 AAAAATAAAACAAA
1 ATAAA-AAAACAAA
1623859 TTTATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.21
20 4 0.14
21 6 0.21
22 4 0.14
23 8 0.29
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.16
Consensus pattern (20 bp):
ATAAAAAAACAAAATTAAAA
Found at i:1623846 original size:20 final size:20
Alignment explanation
Indices: 1623823--1623860 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1623813 AAAAGTTAGT
*
1623823 AAAATAATAAAAAAAATTAA
1 AAAAAAATAAAAAAAATTAA
*
1623843 AAAAAAATAAAACAAATT
1 AAAAAAATAAAAAAAATT
1623861 TATTATTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAAATAAAAAAAATTAA
Found at i:1625704 original size:20 final size:19
Alignment explanation
Indices: 1625658--1625704 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1625648 AATTATCAAT
*
1625658 TGGGCCTCCAAACTTGAAA
1 TGGGCCTTCAAACTTGAAA
**
1625677 TGATCCTTCAAACTTGTAAA
1 TGGGCCTTCAAACTTG-AAA
1625697 TGGGCCTT
1 TGGGCCTT
1625705 TGGGCTGTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (19 bp):
TGGGCCTTCAAACTTGAAA
Found at i:1626516 original size:22 final size:23
Alignment explanation
Indices: 1626485--1626532 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1626475 AGGAACGTGC
*
1626485 CACAAGAGCAGAGAAAA-AGTGT
1 CACAAAAGCAGAGAAAAGAGTGT
*
1626507 CACAAAAGCAGAGAAAAGCGTGT
1 CACAAAAGCAGAGAAAAGAGTGT
1626530 CAC
1 CAC
1626533 GAGAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.48, C:0.19, G:0.25, T:0.08
Consensus pattern (23 bp):
CACAAAAGCAGAGAAAAGAGTGT
Found at i:1626805 original size:20 final size:21
Alignment explanation
Indices: 1626764--1626806 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1626754 TAAGTACACT
*
1626764 AAAAATAATATCATTAGTTTA
1 AAAAATAATATCATTAGCTTA
1626785 AAAAATAAT-TCATGT-GCTTA
1 AAAAATAATATCAT-TAGCTTA
1626805 AA
1 AA
1626807 TATATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAAATAATATCATTAGCTTA
Found at i:1628553 original size:2 final size:2
Alignment explanation
Indices: 1628546--1628589 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1628536 AAACTATTCA
1628546 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
1628588 AT
1 AT
1628590 TCTCCAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1649957 original size:152 final size:152
Alignment explanation
Indices: 1649675--1649976 Score: 491
Period size: 152 Copynumber: 2.0 Consensus size: 152
1649665 TAGTATAGTC
* *
1649675 ATACATTAGGATATATAGTCTACTGCATTAACTGAACTTGAGAATTCCTCCAATCCCTGTGGAGA
1 ATACATTAGGATATATAGTCTACTGCATTAACTGAACTTCAGAATTCCTCCAATCCCTGTGAAGA
* *
1649740 TAATACTCACTCATTACTATATTACTTGTTCGATTGTGTAAACTTGCACATCTTTTTCAGTCCAA
66 TAATACTCACTAACTACTATATTACTTGTTCGATTGTGTAAACTTGCACATCTTTTTCAGTCCAA
1649805 TTTATAGTACACTCATACACTT
131 TTTATAGTACACTCATACACTT
* *
1649827 ATACATTAGGATATATAGTCTACTGCATTAGCTTAACTTCAGAATTCCTCCAATCCCTGTGAAGA
1 ATACATTAGGATATATAGTCTACTGCATTAACTGAACTTCAGAATTCCTCCAATCCCTGTGAAGA
* *
1649892 TGATACTCACTAACTACTATATTACTTGTTCTATTGTGTAAACTTGCACATCTTTTGT-A-TGCC
66 TAATACTCACTAACTACTATATTACTTGTTCGATTGTGTAAACTTGCACATCTTTT-TCAGT-CC
*
1649955 AATTTGTAGTACACTCATACAC
129 AATTTATAGTACACTCATACAC
1649977 GTAACAAGTT
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
151 1 0.01
152 137 0.99
153 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (152 bp):
ATACATTAGGATATATAGTCTACTGCATTAACTGAACTTCAGAATTCCTCCAATCCCTGTGAAGA
TAATACTCACTAACTACTATATTACTTGTTCGATTGTGTAAACTTGCACATCTTTTTCAGTCCAA
TTTATAGTACACTCATACACTT
Found at i:1657968 original size:14 final size:15
Alignment explanation
Indices: 1657949--1657978 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1657939 CATCTTACCA
1657949 TCACAT-TTCCATTT
1 TCACATATTCCATTT
1657963 TCACATATTCCATTT
1 TCACATATTCCATTT
1657978 T
1 T
1657979 ACCACAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (15 bp):
TCACATATTCCATTT
Found at i:1665689 original size:95 final size:95
Alignment explanation
Indices: 1665514--1665696 Score: 226
Period size: 95 Copynumber: 1.9 Consensus size: 95
1665504 CTATAGCAAG
* * *** *
1665514 GGGTATCGATACCTAGAAACATCGAATCTAATTTTGGTATCGATATCGGTAGGGGGTATCAGTAC
1 GGGTATCGATACCTAGAAACATCGAACCTAATTTTGGTATCGATACCCAAAGGGAGTATCAGTAC
*
1665579 CATAGTAGGATAGTATCGATACCGTGGTAA
66 CATAGTAAGATAGTATCGATACCGTGGTAA
* * *
1665609 GGGTATCGATACCTGGCAACATCGAACCTATTTTTGGTATCGATACCCAAAGGGAGTATC-GATA
1 GGGTATCGATACCTAGAAACATCGAACCTAATTTTGGTATCGATACCCAAAGGGAGTATCAG-TA
* *
1665673 CCATATTATAGA-AGTATCGGTACC
65 CCATAGTA-AGATAGTATCGATACC
1665697 AAGGTAGTAG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
94 1 0.01
95 71 0.96
96 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (95 bp):
GGGTATCGATACCTAGAAACATCGAACCTAATTTTGGTATCGATACCCAAAGGGAGTATCAGTAC
CATAGTAAGATAGTATCGATACCGTGGTAA
Found at i:1666061 original size:195 final size:195
Alignment explanation
Indices: 1665729--1666125 Score: 731
Period size: 195 Copynumber: 2.0 Consensus size: 195
1665719 ATAGATAAAA
* *
1665729 ATATTAAAAATAGGCTGATATGTTCTTTTTAGTATTGTTTAAGTACAATGGTTTGAAAATATTTT
1 ATATTAAAAATAGGCTGATATATTCTTTTGAGTATTGTTTAAGTACAATGGTTTGAAAATATTTT
1665794 AACATTGAGTATGGTATATGACTTTATGGATTGCTTAAGTAGATTAAAACCAAGCTCCTGAAACA
66 AACATTGAGTATGGTATATGACTTTATGGATTGCTTAAGTAGATTAAAACCAAGCTCCTGAAACA
*
1665859 AGCAAAACTAAGGGTAAAGACAAAGTACCAGAGTAATCAACCCTACCTTTTGGACTCATAGAAGG
131 AGCAAAACTAAGGGCAAAGACAAAGTACCAGAGTAATCAACCCTACCTTTTGGACTCATAGAAGG
1665924 ATATTAAAAATAGGCTGATATATTCTTTTGAGTATTGTTTAAGTACAATGGTTTGAAAATATTTT
1 ATATTAAAAATAGGCTGATATATTCTTTTGAGTATTGTTTAAGTACAATGGTTTGAAAATATTTT
* * *
1665989 AACATTGAGTATGGTATATGTCTTTATGGATTGCTTAAGTATATTAGAACCAAGCTCCTGAAACA
66 AACATTGAGTATGGTATATGACTTTATGGATTGCTTAAGTAGATTAAAACCAAGCTCCTGAAACA
*
1666054 AGCAAAACTAAGGGCAAAGACAAAGTACCAGAGTAATCAGCCCTACCTTTTGGACTCATAGAAGG
131 AGCAAAACTAAGGGCAAAGACAAAGTACCAGAGTAATCAACCCTACCTTTTGGACTCATAGAAGG
1666119 ATATTAA
1 ATATTAA
1666126 GGTGAGTGCA
Statistics
Matches: 195, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
195 195 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (195 bp):
ATATTAAAAATAGGCTGATATATTCTTTTGAGTATTGTTTAAGTACAATGGTTTGAAAATATTTT
AACATTGAGTATGGTATATGACTTTATGGATTGCTTAAGTAGATTAAAACCAAGCTCCTGAAACA
AGCAAAACTAAGGGCAAAGACAAAGTACCAGAGTAATCAACCCTACCTTTTGGACTCATAGAAGG
Found at i:1666285 original size:55 final size:55
Alignment explanation
Indices: 1666214--1666372 Score: 212
Period size: 55 Copynumber: 2.9 Consensus size: 55
1666204 CTATGAGTAC
*
1666214 TACAGGCACTTTGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCACCG
1 TACAAGCACTTTGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCACCG
* **
1666269 TACATGCACTTTGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCG
1 TACAAGCACTTTGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCACCG
* * * ** * *
1666324 TACAAACACTATGTGTCCA-ACCCACAGAATACATCATGGGTTGATGAAT
1 TACAAGCACTTTGTGTGCATATTCACAGAATTCATCATGAGTTGATGAAT
1666373 TCTTGTATAT
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
54 24 0.26
55 67 0.74
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (55 bp):
TACAAGCACTTTGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCACCG
Found at i:1668304 original size:22 final size:22
Alignment explanation
Indices: 1668277--1668321 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1668267 ATCAATAGTT
* *
1668277 TATATATGTTGTTTATCACGAA
1 TATATATGATGCTTATCACGAA
*
1668299 TATATATGATGCTTATCATGAA
1 TATATATGATGCTTATCACGAA
1668321 T
1 T
1668322 GTTATTTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (22 bp):
TATATATGATGCTTATCACGAA
Found at i:1673375 original size:21 final size:19
Alignment explanation
Indices: 1673347--1673387 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1673337 CATTACAGGA
1673347 ATTTATGGCCTCGACGAAAG
1 ATTTATGGCCTCGAC-AAAG
*
1673367 ATTTCATGGCCTCTACAAAG
1 ATTT-ATGGCCTCGACAAAG
1673387 A
1 A
1673388 CTTTGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (19 bp):
ATTTATGGCCTCGACAAAG
Found at i:1680311 original size:45 final size:45
Alignment explanation
Indices: 1680211--1680314 Score: 129
Period size: 47 Copynumber: 2.3 Consensus size: 45
1680201 TTTATTGGTT
* *
1680211 AATAAATGGCAAGTATATTGATAAAAAAAGCTTACGAGCTTATGG
1 AATAAATGGTAAATATATTGATAAAAAAAGCTTACGAGCTTATGG
* * *
1680256 AATTTAAATGGTAAATATTTTGCTAAAATAAGCTTACGAGCTTATTGG
1 AA--TAAATGGTAAATATATTGATAAAAAAAGCTTACGAGCTTA-TGG
1680304 -ATAAATGGTAA
1 AATAAATGGTAA
1680315 GAGATTTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
45 12 0.24
47 36 0.71
48 3 0.06
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (45 bp):
AATAAATGGTAAATATATTGATAAAAAAAGCTTACGAGCTTATGG
Found at i:1688379 original size:21 final size:21
Alignment explanation
Indices: 1688353--1688392 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1688343 CCCCCTTTGA
*
1688353 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1688374 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1688393 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1688435 original size:8 final size:8
Alignment explanation
Indices: 1688422--1688446 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1688412 GGCAAGAACA
1688422 CCCAAAAC
1 CCCAAAAC
1688430 CCCAAAAC
1 CCCAAAAC
1688438 CCCAAAAC
1 CCCAAAAC
1688446 C
1 C
1688447 TATTCTGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCAAAAC
Found at i:1699289 original size:37 final size:37
Alignment explanation
Indices: 1699248--1699319 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
1699238 AAGTTTGAGG
*
1699248 TTGCTTTTATCACATTGATTTTTCATATAAACTTTTA
1 TTGCTTTTATCAAATTGATTTTTCATATAAACTTTTA
* * *
1699285 TTGCTTTTATGAAATTGATTTTTCATCTCAACTTT
1 TTGCTTTTATCAAATTGATTTTTCATATAAACTTT
1699320 ACTTTTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (37 bp):
TTGCTTTTATCAAATTGATTTTTCATATAAACTTTTA
Found at i:1699466 original size:37 final size:37
Alignment explanation
Indices: 1699418--1699493 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
1699408 TCAAACACTT
*
1699418 CTACGTTAACAACTTCTTTAGTCCCTGCAGATCAACC
1 CTACATTAACAACTTCTTTAGTCCCTGCAGATCAACC
*
1699455 CTACATTAACAACTTCTTTAGTCCCTGCATATCAACC
1 CTACATTAACAACTTCTTTAGTCCCTGCAGATCAACC
1699492 CT
1 CT
1699494 TACTCTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.33, G:0.08, T:0.32
Consensus pattern (37 bp):
CTACATTAACAACTTCTTTAGTCCCTGCAGATCAACC
Found at i:1702636 original size:13 final size:14
Alignment explanation
Indices: 1702610--1702638 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1702600 ATTCTTGGTG
1702610 TTACTCAGTACTCC
1 TTACTCAGTACTCC
1702624 TTACTCA-TACTCC
1 TTACTCAGTACTCC
1702637 TT
1 TT
1702639 CTTCTTACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.34, G:0.03, T:0.41
Consensus pattern (14 bp):
TTACTCAGTACTCC
Found at i:1710143 original size:13 final size:13
Alignment explanation
Indices: 1710125--1710151 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1710115 GACCATTTTC
1710125 AAGGTCAATGGCA
1 AAGGTCAATGGCA
1710138 AAGGTCAATGGCA
1 AAGGTCAATGGCA
1710151 A
1 A
1710152 GCGAATGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.30, T:0.15
Consensus pattern (13 bp):
AAGGTCAATGGCA
Found at i:1710321 original size:18 final size:19
Alignment explanation
Indices: 1710294--1710331 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1710284 AACATGTGCA
1710294 ATTTTATTTTATTT-TGTT
1 ATTTTATTTTATTTATGTT
* *
1710312 ATTTTCTTTTCTTTATGTT
1 ATTTTATTTTATTTATGTT
1710331 A
1 A
1710332 ATGTTTCAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
ATTTTATTTTATTTATGTT
Found at i:1717186 original size:20 final size:20
Alignment explanation
Indices: 1717148--1717188 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1717138 TTGATATAAG
* *
1717148 TTTTACTTTTCATTTTTTAT
1 TTTTACTTTTCAATATTTAT
1717168 TTTTACTTTTCAATATTTAT
1 TTTTACTTTTCAATATTTAT
1717188 T
1 T
1717189 ATATTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTACTTTTCAATATTTAT
Found at i:1719043 original size:10 final size:10
Alignment explanation
Indices: 1719028--1719057 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1719018 TAATCGGATT
1719028 GAAATTTTGA
1 GAAATTTTGA
1719038 GAAATTTTGA
1 GAAATTTTGA
1719048 GAAATTTTGA
1 GAAATTTTGA
1719058 AGGATGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (10 bp):
GAAATTTTGA
Found at i:1724268 original size:19 final size:18
Alignment explanation
Indices: 1724227--1724273 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1724217 ATTTTATGCA
*
1724227 AATTTTTTTATTTATTTT
1 AATTTCTTTATTTATTTT
*
1724245 TATTTCATTTA-TTATATTT
1 AATTTC-TTTATTTAT-TTT
1724264 AATTTCTTTA
1 AATTTCTTTA
1724274 AATTGATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
AATTTCTTTATTTATTTT
Found at i:1727655 original size:138 final size:137
Alignment explanation
Indices: 1727476--1727728 Score: 328
Period size: 138 Copynumber: 1.8 Consensus size: 137
1727466 CGAAGTGCCA
* * * *
1727476 AAATGGAAATTCACAAACTTATTATGAATTCCATGGATGCACACATAGT-GTCGAAAGTAAACAT
1 AAATGGAAATTCACAAACTCATTATGAATACCATAGATGCACACATAGTACT-GAAAGTAAACAT
* * * * *
1727540 ATTATTAATACGAAAATGTACCGTTATGCATTAAACAAAATCAATCGATAACTTTTATACATAAT
65 AGTACTAATACGAAAATGCACCGATATGCATTAAA-AAAATCAATCAATAACTTTTATACATAAT
1727605 TGTATATCG
129 TGTATATCG
* * ** *
1727614 AAATGGTAATTCACAAACTCATTATGAATACCATAGTTGCACATTTAGTACTGAAAGTACACATA
1 AAATGGAAATTCACAAACTCATTATGAATACCATAGATGCACACATAGTACTGAAAGTAAACATA
* * *
1727679 GTACTGATACGAAAATGCACTGATATGCATTAAAAAAATCGATCAATAAC
66 GTACTAATACGAAAATGCACCGATATGCATTAAAAAAATCAATCAATAAC
1727729 CATTTCATAC
Statistics
Matches: 97, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
137 14 0.14
138 82 0.85
139 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (137 bp):
AAATGGAAATTCACAAACTCATTATGAATACCATAGATGCACACATAGTACTGAAAGTAAACATA
GTACTAATACGAAAATGCACCGATATGCATTAAAAAAATCAATCAATAACTTTTATACATAATTG
TATATCG
Found at i:1730862 original size:18 final size:18
Alignment explanation
Indices: 1730823--1730860 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1730813 TTATTTTTAC
*
1730823 TTTAATTGCTTTTACTTA
1 TTTAATCGCTTTTACTTA
1730841 TTTAATCGCTTTTA-TTA
1 TTTAATCGCTTTTACTTA
1730858 TTT
1 TTT
1730861 TATTATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTAATCGCTTTTACTTA
Found at i:1737063 original size:17 final size:16
Alignment explanation
Indices: 1737023--1737064 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1737013 AAACCTGTTC
* *
1737023 GAAAGAAAGAGAGAGA
1 GAAAGAAAAAGAGACA
1737039 GAAA-AAAAAGAGACA
1 GAAAGAAAAAGAGACA
1737054 TGAAAGAAAAA
1 -GAAAGAAAAA
1737065 ATGGAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 8 0.36
17 5 0.23
ACGTcount: A:0.69, C:0.02, G:0.26, T:0.02
Consensus pattern (16 bp):
GAAAGAAAAAGAGACA
Found at i:1738262 original size:24 final size:24
Alignment explanation
Indices: 1738217--1738266 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1738207 ATAAAGAACC
*
1738217 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1738241 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
1738265 AA
1 AA
1738267 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1740620 original size:15 final size:15
Alignment explanation
Indices: 1740587--1740629 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1740577 AAAATAATAT
* *
1740587 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
1740602 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
1740616 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
1740630 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:1743800 original size:24 final size:24
Alignment explanation
Indices: 1743755--1743804 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1743745 ATAAAGAACC
*
1743755 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1743779 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
1743803 AA
1 AA
1743805 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1745930 original size:18 final size:18
Alignment explanation
Indices: 1745888--1745926 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1745878 ATTATTTTTA
*
1745888 ATTTAATTGCTTTTACTT
1 ATTTAATCGCTTTTACTT
1745906 ATTTAATCGCTTTTA-TT
1 ATTTAATCGCTTTTACTT
1745923 ATTT
1 ATTT
1745927 TAATATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (18 bp):
ATTTAATCGCTTTTACTT
Found at i:1751939 original size:21 final size:19
Alignment explanation
Indices: 1751913--1751954 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
1751903 TACTCCACAA
1751913 CAGTATCGATACTACTTGCAT
1 CAGTATCGATACTA-TT-CAT
1751934 CAGTATCGATACTATTCAT
1 CAGTATCGATACTATTCAT
1751953 CA
1 CA
1751955 TTTTCATCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 14 0.67
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (19 bp):
CAGTATCGATACTATTCAT
Found at i:1752917 original size:28 final size:29
Alignment explanation
Indices: 1752875--1752988 Score: 144
Period size: 29 Copynumber: 4.0 Consensus size: 29
1752865 AAAAATAATA
* * *
1752875 TTTTGATATATTACAATAAA-GACCAAAAC
1 TTTTTATAAATTACAAAAAATG-CCAAAAC
1752904 -TTTTATAAATTACAAACAAATGCC-AAAC
1 TTTTTATAAATTACAAA-AAATGCCAAAAC
1752932 TTTTTATAAATTACAAAAAATGCCAAAAC
1 TTTTTATAAATTACAAAAAATGCCAAAAC
* *
1752961 TTTTTATAAATTACAACAAATGCAAAAA
1 TTTTTATAAATTACAAAAAATGCCAAAA
1752989 AAAATTAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
28 24 0.32
29 51 0.67
30 1 0.01
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (29 bp):
TTTTTATAAATTACAAAAAATGCCAAAAC
Found at i:1753005 original size:87 final size:85
Alignment explanation
Indices: 1752910--1753075 Score: 201
Period size: 87 Copynumber: 1.9 Consensus size: 85
1752900 AAACTTTTAT
1752910 AAATTACAAACAAATGCCAAACT-TTTTATAAATTACAAAAAATGCCAAAACTTTTTATAAATTA
1 AAATTAC-AACAAATGCC-AACTCTTTTATAAATTACAAAAAATGCCAAAACTTTTTATAAATTA
1752974 CAA-CAAATGCAAAAAAAAATTAA
64 CAATCAAA-G-AAAAAAAAATTAA
* * * * * ***
1752997 AAATTACAACTAATTCCAATTGCTTTTATAAATTACAACAAATTCCAATTGTTTTTATAAATTAC
1 AAATTACAACAAATGCCAACT-CTTTTATAAATTACAAAAAATGCCAAAACTTTTTATAAATTAC
1753062 AATCAAAGAAAAAA
65 AATCAAAGAAAAAA
1753076 CTTCTAATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
85 3 0.04
86 14 0.21
87 47 0.69
88 4 0.06
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (85 bp):
AAATTACAACAAATGCCAACTCTTTTATAAATTACAAAAAATGCCAAAACTTTTTATAAATTACA
ATCAAAGAAAAAAAAATTAA
Found at i:1753029 original size:29 final size:29
Alignment explanation
Indices: 1752903--1753068 Score: 122
Period size: 29 Copynumber: 5.7 Consensus size: 29
1752893 AAGACCAAAA
* *
1752903 CTTTTATAAATTACAAACAAATGCCAA--A
1 CTTTTATAAATTAC-AACAAATTCCAATTG
* * **
1752931 CTTTTTATAAATTACAAAAAATGCCAA-AA
1 C-TTTTATAAATTACAACAAATTCCAATTG
* * ***
1752960 CTTTTTATAAATTACAACAAATGCAAAAAA
1 C-TTTTATAAATTACAACAAATTCCAATTG
*** * *
1752990 AAATTAAAAATTACAACTAATTCCAATTG
1 CTTTTATAAATTACAACAAATTCCAATTG
1753019 CTTTTATAAATTACAACAAATTCCAATTG
1 CTTTTATAAATTACAACAAATTCCAATTG
*
1753048 TTTTTATAAATTACAATCAAA
1 CTTTTATAAATTACAA-CAAA
1753069 GAAAAAACTT
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.10
29 97 0.84
30 6 0.05
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33
Consensus pattern (29 bp):
CTTTTATAAATTACAACAAATTCCAATTG
Done.