Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006868.1 Hibiscus syriacus cultivar Beakdansim tig00017479_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: 314544
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:180145 original size:2 final size:2
Alignment explanation
Indices: 180138--180171 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
180128 TATTAGAATC
180138 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
180172 CTAATAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:181374 original size:125 final size:124
Alignment explanation
Indices: 181154--181405 Score: 364
Period size: 125 Copynumber: 2.0 Consensus size: 124
181144 AACGTAGATA
* * * *
181154 AAATTTCAAAATAGACTATGTAAATAAAATATGTAACTAACCAAAGAGATTTAAATTTTAGATGT
1 AAATTTCAAAATAGACTATGTAAATAAAATATGTAACTAACCAAAAAGAATTAAATTTTAAATAT
* *
181219 AATTTTTTTATTTATTTTATATACTTGTATTTGATATTTATGTTTGTT-GTTTCTCCTAT
66 AATTTTTTTAATTATTTTATATACTTGTATTTGATATTTATGTTTGTTATTTTC-CCTAT
** * *
181278 AAATTTCAAGGTAGAC-ACTGTAAATAAAATATGTAATTAATCAAACAAGAATTAAATTTTAAAT
1 AAATTTCAAAATAGACTA-TGTAAATAAAATATGTAACTAACCAAA-AAGAATTAAATTTTAAAT
*
181342 ATAATTTTTTTAATTATTTTATATATTTGTATTTGATATTTATGTTTGTTATTTTCCCTAT
64 ATAATTTTTTTAATTATTTTATATACTTGTATTTGATATTTATGTTTGTTATTTTCCCTAT
181403 AAA
1 AAA
181406 ATGCAAAGAC
Statistics
Matches: 114, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
123 1 0.01
124 39 0.34
125 70 0.61
126 4 0.04
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (124 bp):
AAATTTCAAAATAGACTATGTAAATAAAATATGTAACTAACCAAAAAGAATTAAATTTTAAATAT
AATTTTTTTAATTATTTTATATACTTGTATTTGATATTTATGTTTGTTATTTTCCCTAT
Found at i:181471 original size:22 final size:22
Alignment explanation
Indices: 181441--181482 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
181431 TTACTTCTAA
181441 ATAAAAAAATAT-TAAACATTTG
1 ATAAAAAAATATCT-AACATTTG
*
181463 ATAATAAAATATCTAACATT
1 ATAAAAAAATATCTAACATT
181483 ATGGCAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAAAAAAATATCTAACATTTG
Found at i:184453 original size:13 final size:13
Alignment explanation
Indices: 184435--184459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
184425 GACCTACCTT
184435 TTGACTTTGACCG
1 TTGACTTTGACCG
184448 TTGACTTTGACC
1 TTGACTTTGACC
184460 AAAAAGTCAA
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGACTTTGACCG
Found at i:185769 original size:31 final size:31
Alignment explanation
Indices: 185734--185850 Score: 207
Period size: 31 Copynumber: 3.8 Consensus size: 31
185724 GAGTATTGTT
185734 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTGAAATG
185765 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTGAAATG
* *
185796 GAGCTCGACACGACTTGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTGAAATG
*
185827 GAGCTCAACTCGACTCGAAAACTC
1 GAGCTCGACTCGACTCGAAAACTC
185851 GCAAGCTTAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 81 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (31 bp):
GAGCTCGACTCGACTCGAAAACTCTGAAATG
Found at i:189158 original size:60 final size:60
Alignment explanation
Indices: 189063--189193 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
189053 TATGATACTT
* * **
189063 ATTTTAAATTGATCTTTAAACTTTTAAATATTTCAATTTCATCCGTAAACTATGGTTATC
1 ATTTTAAATTGATCTTTAAACTTTTAAACACTTCAATTTCATCCCCAAACTATGGTTATC
* *
189123 ATTTTAAATTAGTTC-TTAAACTTTTAAACACTTCAATTTCATCCCCAAACTATGATCT-TC
1 ATTTTAAATT-GATCTTTAAACTTTTAAACACTTCAATTTCATCCCCAAACTATGGT-TATC
*
189183 ATTCTAAATTG
1 ATTTTAAATTG
189194 GTCCCCAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 57 0.92
61 4 0.06
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (60 bp):
ATTTTAAATTGATCTTTAAACTTTTAAACACTTCAATTTCATCCCCAAACTATGGTTATC
Found at i:189204 original size:60 final size:59
Alignment explanation
Indices: 189080--189235 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 59
189070 ATTGATCTTT
* ** * * * **
189080 AAACTTTTAAATATTTCAATTTCATCCGTAAACTATGGTTATCATTTTAAATTAGTTCTT
1 AAACTTTTAAACA-TTCAATTTCATCCCCAAACTATGATTATCATTCTAAATTAGTCCCC
*
189140 AAACTTTTAAACACTTCAATTTCATCCCCAAACTATGATCT-TCATTCTAAATTGGTCCCC
1 AAACTTTTAAACA-TTCAATTTCATCCCCAAACTATGAT-TATCATTCTAAATTAGTCCCC
* *
189200 AAACTTTTTTATCATTCCAATTTCAT-CCCAAACTAT
1 AAAC-TTTTAAACATT-CAATTTCATCCCCAAACTAT
189236 ACGTGTATAC
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
60 64 0.79
61 17 0.21
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (59 bp):
AAACTTTTAAACATTCAATTTCATCCCCAAACTATGATTATCATTCTAAATTAGTCCCC
Found at i:189765 original size:2 final size:2
Alignment explanation
Indices: 189758--189784 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
189748 CTTCAGAAGT
189758 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
189785 GAATGTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:196836 original size:31 final size:26
Alignment explanation
Indices: 196773--196833 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
196763 ATTGCCGAGT
196773 TCGACTCGAAAACTTTAAATGTAGGC
1 TCGACTCGAAAACTTTAAATGTAGGC
196799 TCGACTCGAAAACTTTAAATGTAGGC
1 TCGACTCGAAAACTTTAAATGTAGGC
196825 TCGACTCGA
1 TCGACTCGA
196834 CTCCAAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (26 bp):
TCGACTCGAAAACTTTAAATGTAGGC
Found at i:196842 original size:31 final size:30
Alignment explanation
Indices: 196773--196843 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 30
196763 ATTGCCGAGT
196773 TCGACTCGAAAACTTTAAATGTAGGCTCGAC
1 TCGACTC-AAAACTTTAAATGTAGGCTCGAC
196804 TCG----AAAACTTTAAATGTAGGCTCGAC
1 TCGACTCAAAACTTTAAATGTAGGCTCGAC
196830 TCGACTCCAAAACT
1 TCGACT-CAAAACT
196844 CGCGAGCCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
26 26 0.74
31 9 0.26
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (30 bp):
TCGACTCAAAACTTTAAATGTAGGCTCGAC
Found at i:196954 original size:11 final size:11
Alignment explanation
Indices: 196940--197004 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
196930 AAAATTAAAG
196940 AGCTCGATTGA
1 AGCTCGATTGA
*
196951 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
196964 AGCTCGATTGA
1 AGCTCGATTGA
196975 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
196987 AGCTCGATTCA
1 AGCTCGATTGA
196998 AGCTCGA
1 AGCTCGA
197005 ACTCAATTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 4 0.09
11 21 0.48
12 7 0.16
13 10 0.23
14 2 0.05
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:196968 original size:24 final size:23
Alignment explanation
Indices: 196939--197008 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
196929 AAAAATTAAA
196939 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-ACTC
** *
196963 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGAACTC
*
196986 GAGCTCGATTCAAGCTCGAACTC
1 GAGCTCGATTGAAGCTCGAACTC
197009 AATTCAAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGAACTC
Found at i:197015 original size:17 final size:18
Alignment explanation
Indices: 196989--197030 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
196979 CGATTTTGAG
* *
196989 CTCG-ATTCAAGCTCGAA
1 CTCGAATTCAAACTCAAA
197006 CTC-AATTCAAACTCAAA
1 CTCGAATTCAAACTCAAA
197023 CTCGAATT
1 CTCGAATT
197031 TGAACCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.36, C:0.29, G:0.10, T:0.26
Consensus pattern (18 bp):
CTCGAATTCAAACTCAAA
Found at i:204380 original size:12 final size:12
Alignment explanation
Indices: 204363--204395 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
204353 ATTATACGGT
204363 ATGAACAGTATC
1 ATGAACAGTATC
204375 ATGAACAGTATC
1 ATGAACAGTATC
204387 ATGAACAGT
1 ATGAACAGT
204396 GAAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (12 bp):
ATGAACAGTATC
Found at i:205155 original size:30 final size:31
Alignment explanation
Indices: 205096--205188 Score: 136
Period size: 30 Copynumber: 3.0 Consensus size: 31
205086 CCCGAATGAC
* * *
205096 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
205127 CAGTCCATATGTCCCGAAGAA-ATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
205157 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
205188 C
1 C
205189 CCTCGACCCT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 28 0.49
31 28 0.49
32 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:210649 original size:31 final size:31
Alignment explanation
Indices: 210601--210725 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
210591 CCCGAAGGAC
* * *
210601 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
210632 CAGCCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
210663 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
210694 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
210725 C
1 C
210726 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:212850 original size:14 final size:13
Alignment explanation
Indices: 212827--212917 Score: 65
Period size: 14 Copynumber: 6.5 Consensus size: 13
212817 GTATATAACT
*
212827 TAAACCCTAAATCC
1 TAAA-CCTAAACCC
212841 TAAACTCTAAACCC
1 TAAAC-CTAAACCC
*
212855 TAACACATAAACCC
1 TAA-ACCTAAACCC
*
212869 TAAACCCTAAACTC
1 TAAA-CCTAAACCC
*
212883 TAAACCTTAAATCC
1 TAAACC-TAAACCC
* * *
212897 TATCACATAAACTC
1 TA-AACCTAAACCC
212911 TAAACCT
1 TAAACCT
212918 TAAATTGTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
13 7 0.12
14 49 0.82
15 4 0.07
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAACCTAAACCC
Found at i:212893 original size:28 final size:28
Alignment explanation
Indices: 212823--212965 Score: 98
Period size: 28 Copynumber: 5.1 Consensus size: 28
212813 TTATGTATAT
* *
212823 AACT-TAAACCCTAAATCCTAAACTCTA
1 AACTCTAAACCATAAATCCTAAACCCTA
* *
212850 AACCCT-AACACATAAACCCTAAACCCTA
1 AACTCTAAAC-CATAAATCCTAAACCCTA
* * *
212878 AACTCTAAACCTTAAATCCT-ATCACATA
1 AACTCTAAACCATAAATCCTAAAC-CCTA
* ** * *
212906 AACTCTAAACCTTAAATTGT-ATCACATA
1 AACTCTAAACCATAAATCCTAAAC-CCTA
*
212934 AACTCTGAACCATAAA-CCTTAAACCCTA
1 AACTCTAAACCATAAATCC-TAAACCCTA
212962 AACT
1 AACT
212966 TTATCACATA
Statistics
Matches: 93, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
27 8 0.09
28 80 0.86
29 5 0.05
ACGTcount: A:0.44, C:0.30, G:0.01, T:0.24
Consensus pattern (28 bp):
AACTCTAAACCATAAATCCTAAACCCTA
Found at i:213692 original size:14 final size:14
Alignment explanation
Indices: 213675--213715 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
213665 TTTATTCATC
213675 AATAATGTATTTTT
1 AATAATGTATTTTT
213689 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
213700 AATAATGTAATTTT
1 AATAATGTATTTTT
213714 AA
1 AA
213716 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:216202 original size:10 final size:9
Alignment explanation
Indices: 216177--216201 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
216167 AAATTTTTTT
216177 ATATTTTAA
1 ATATTTTAA
216186 ATATTTTAA
1 ATATTTTAA
216195 ATATTTT
1 ATATTTT
216202 TTGTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATATTTTAA
Found at i:230468 original size:60 final size:60
Alignment explanation
Indices: 230386--230502 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
230376 TAGTTAAGTG
* * *
230386 ATCATTTTGTATCTTTTAATAGTCAAGAGACTCAACAAAGCAACATCTTATAGTCGAAGA
1 ATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAGCAACATCCTATAGTCGAAGA
* *
230446 ATCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAGCATCATCCTATAGTCGA
1 ATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAGCAACATCCTATAGTCGA
230503 GGGACTATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (60 bp):
ATCATTTTATAACTTTTAATAGTCAAGAGACTCAACAAAGCAACATCCTATAGTCGAAGA
Found at i:234998 original size:21 final size:20
Alignment explanation
Indices: 234972--235028 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 20
234962 ATCAGTTTCC
* *
234972 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
234993 AAAATCGCAATGCGGCGAATATG
1 AAAATCGCAA--C-GCGAATATG
235016 AAAATCGCAACGC
1 AAAATCGCAACGC
235029 AAACACATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.35
23 13 0.42
24 5 0.16
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:235059 original size:20 final size:20
Alignment explanation
Indices: 235036--235188 Score: 177
Period size: 20 Copynumber: 7.7 Consensus size: 20
235026 CGCAAACACA
*
235036 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
235056 TAAATCGCAACGTG-ATCCG
1 TAAATCGCAACGCGTATCCG
**
235075 T-AATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
235094 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
235114 TATATCGCAACGCGTATCGG
1 TAAATCGCAACGCGTATCCG
* * *
235134 TAAATCGCAACG-ATAATACA
1 TAAATCGCAACGCGT-ATCCG
235154 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
235175 TAAATCGCAACGCG
1 TAAATCGCAACGCG
235189 ATATTTAAAG
Statistics
Matches: 109, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
18 11 0.10
19 11 0.10
20 71 0.65
21 15 0.14
22 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:235098 original size:58 final size:60
Alignment explanation
Indices: 235017--235188 Score: 208
Period size: 58 Copynumber: 2.9 Consensus size: 60
235007 GCGAATATGA
* *
235017 AAATCGCAACGCA-AACACATAAATCGCAATGCGTATCCGTAAATCGCAACGTG-ATCCGT
1 AAATCGCAACG-ATAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
235076 -AATCGCAACGCGT-ATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCGGT
1 AAATCGCAACG-ATAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
*
235135 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGATAATACAT-AAATCGCAATGCGTATCCGTAAATCGCAACGCG
235189 ATATTTAAAG
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
58 44 0.47
59 6 0.06
60 13 0.14
61 31 0.33
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGATAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:235611 original size:33 final size:33
Alignment explanation
Indices: 235572--235642 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
235562 TTCACTTAGA
235572 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
235605 TTTCATTTCGCGTTGCTATTCTCTCGTTGCTAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
235638 TTTCA
1 TTTCA
235643 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.24, G:0.15, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:235757 original size:20 final size:20
Alignment explanation
Indices: 235734--235797 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
235724 GCACGAGATA
235734 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
235754 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
235774 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
235795 AAT
1 AAT
235798 CGCAAAGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:235778 original size:41 final size:40
Alignment explanation
Indices: 235721--235797 Score: 136
Period size: 41 Copynumber: 1.9 Consensus size: 40
235711 TTGCAGAAGA
*
235721 GTCGCACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
235761 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGC-ACGAGAGAAATGAAAATCGCAACGAGAGAAT
235798 CGCAAAGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 5 0.14
41 30 0.86
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (40 bp):
GTCGCACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:235794 original size:21 final size:21
Alignment explanation
Indices: 235722--235796 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
235712 TGCAGAAGAG
*
235722 TCGC-ACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
235742 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
235762 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
235783 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
235797 TCGCAAAGCG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
20 21 0.46
21 25 0.54
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:235800 original size:14 final size:14
Alignment explanation
Indices: 235781--235836 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
235771 GAGAAATGAA
235781 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
235795 AATCGCAAAGCGATATG
1 AATCGC-AA-CGAGA-G
235812 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
*
235827 AATTGCAACG
1 AATCGCAACG
235837 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 15 0.43
15 3 0.09
16 8 0.23
17 3 0.09
18 6 0.17
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:235870 original size:19 final size:19
Alignment explanation
Indices: 235848--235945 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
235838 GAAACCAAAA
*
235848 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
235867 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
235881 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
235900 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
235914 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
235933 TCGCGTTGCGATT
1 TCGCGTTGCGATT
235946 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:235889 original size:14 final size:14
Alignment explanation
Indices: 235870--235959 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
235860 TTTCATTTCG
235870 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
235884 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
235903 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
235917 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
235936 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
235950 CGTTGCGATT
1 CGTTGCGATT
235960 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:235895 original size:33 final size:33
Alignment explanation
Indices: 235853--235967 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
235843 CAAAATCGCA
235853 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
235886 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
235919 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
235952 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
235968 AACCAAAGAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:237238 original size:19 final size:19
Alignment explanation
Indices: 237214--237349 Score: 139
Period size: 19 Copynumber: 7.6 Consensus size: 19
237204 CTTCCTCCAA
237214 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
237233 TTCGCGTTGCGA--TTC-T
1 TTCGCGTTGCGATTTTCAT
237249 TT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
237266 TTCGCGTTGTGA--TTC-T
1 TTCGCGTTGCGATTTTCAT
*
237282 GT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
237299 TTCGCGTTGCGATTTTGGT
1 TTCGCGTTGCGATTTTCAT
*
237318 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTCA-T
*
237338 TTCGTGTTGCGA
1 TTCGCGTTGCGA
237350 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 15 0.15
16 11 0.11
17 11 0.11
19 48 0.49
20 12 0.12
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:237256 original size:14 final size:14
Alignment explanation
Indices: 237237--237293 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
237227 TTTCATTTCG
237237 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
237251 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
* *
237268 CGCGTTGTGATTCTGT
1 --CGTTGCGATTCTTT
237284 CGTTGCGATT
1 CGTTGCGATT
237294 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:237260 original size:33 final size:33
Alignment explanation
Indices: 237218--237312 Score: 172
Period size: 33 Copynumber: 2.9 Consensus size: 33
237208 CTCCAATTCG
*
237218 CGTTGCGATTTTCATTTCGCGTTGCGATTCTTT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTGT
*
237251 CGTTGCGATTTTCATTTCGCGTTGTGATTCTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTGT
237284 CGTTGCGATTTTCATTTCGCGTTGCGATT
1 CGTTGCGATTTTCATTTCGCGTTGCGATT
237313 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTGT
Found at i:239286 original size:14 final size:14
Alignment explanation
Indices: 239267--239302 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
239257 ATTGTTTAAT
239267 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
239281 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
239295 TGATTTGT
1 TGATTTGT
239303 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:239424 original size:19 final size:19
Alignment explanation
Indices: 239408--239522 Score: 163
Period size: 19 Copynumber: 6.4 Consensus size: 19
239398 AAAAATGACT
239408 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
239427 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
239446 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
239465 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
239479 ATCGCAATGCG-AATG-AA
1 ATCGCAATGCGAAATGAAA
239496 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
239516 ATCGCAA
1 ATCGCAA
239523 CGAGAGAACC
Statistics
Matches: 87, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 14 0.16
18 2 0.02
19 49 0.56
20 9 0.10
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:239513 original size:51 final size:52
Alignment explanation
Indices: 239426--239540 Score: 198
Period size: 51 Copynumber: 2.2 Consensus size: 52
239416 GCGAAATGAA
239426 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
239478 AATCGCAATGCG-AATG-AAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
*
239529 AACCGCAATGCG
1 AATCGCAATGCG
239541 TTTATAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
50 12 0.20
51 37 0.61
52 12 0.20
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:239584 original size:33 final size:34
Alignment explanation
Indices: 239547--239700 Score: 149
Period size: 33 Copynumber: 4.5 Consensus size: 34
239537 TGCGTTTATA
239547 ATTTCGCATTGCGATTCTCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGATTGCGATTTTC
*
239580 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG-ATTGCGATT-T-TC
* * *
239620 GTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCG-ATTGCGATTTTC
*
239652 ATTTCGCATTGCGATTCTATCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGATTGCGATTTTC
239685 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
239701 TTCATTTCGC
Statistics
Matches: 100, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
32 9 0.09
33 46 0.46
34 13 0.13
35 6 0.06
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTCTCGATTGCGATTTTC
Found at i:239593 original size:19 final size:19
Alignment explanation
Indices: 239569--239785 Score: 240
Period size: 19 Copynumber: 12.4 Consensus size: 19
239559 GATTCTCTCG
239569 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
239588 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
239607 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
239621 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
239641 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
239660 TTGCGA--TTC-TATCG--
1 TTGCGATTTTCATTTCGCA
239674 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
239693 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
239712 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
239726 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
239745 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
239759 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
239778 TTGCGATT
1 TTGCGATT
239786 GTAATTTCCG
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 21 0.12
18 2 0.01
19 79 0.47
20 15 0.09
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:239679 original size:105 final size:104
Alignment explanation
Indices: 239547--239757 Score: 404
Period size: 105 Copynumber: 2.0 Consensus size: 104
239537 TGCGTTTATA
*
239547 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
239612 ATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
66 ATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
239652 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
239717 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
239756 AT
1 AT
239758 GTTGGGATTT
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 17 0.16
105 88 0.84
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (104 bp):
ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:239730 original size:33 final size:33
Alignment explanation
Indices: 239588--239785 Score: 197
Period size: 33 Copynumber: 5.8 Consensus size: 33
239578 TCATTTCGCA
239588 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
239621 TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTT-CGCATTGCGA--TTC-TCTCG
* * * * *
239658 CATTGCGATTCTATCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
239693 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
239726 TTGCGATTTTCATTTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
* *
239759 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
239786 GTAATTTCCG
Statistics
Matches: 137, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.07
32 5 0.04
33 81 0.59
34 11 0.08
35 2 0.01
36 3 0.02
37 6 0.04
39 10 0.07
40 6 0.04
41 4 0.03
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:239793 original size:52 final size:52
Alignment explanation
Indices: 239547--239757 Score: 404
Period size: 52 Copynumber: 4.0 Consensus size: 52
239537 TGCGTTTATA
239547 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
239599 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
*
239652 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
239704 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
239756 AT
1 AT
239758 GTTGGGATTT
Statistics
Matches: 156, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
52 105 0.67
53 51 0.33
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:241528 original size:122 final size:123
Alignment explanation
Indices: 241303--241547 Score: 483
Period size: 122 Copynumber: 2.0 Consensus size: 123
241293 TGGCTCTCCA
241303 AGCTTGAGAATATGATATACTAATCTTGAAACGAGCATTCATGTCAGTCATAATTTCATGTCCCC
1 AGCTTGAGAATATGATATACTAATCTTGAAACGAGCATTCATGTCAGTCATAATTTCATGTCCCC
241368 GATATACCCTGCCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTT
66 GATATACCCTGCCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTT
241426 AGCTTGAGAATATGATATACTAATCTTGAAACGAGCATTCATGTCAGTCAT-ATTTCATGTCCCC
1 AGCTTGAGAATATGATATACTAATCTTGAAACGAGCATTCATGTCAGTCATAATTTCATGTCCCC
241490 GATATACCCTGCCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTT
66 GATATACCCTGCCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTT
241548 GTTTGCCTGT
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 71 0.58
123 51 0.42
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (123 bp):
AGCTTGAGAATATGATATACTAATCTTGAAACGAGCATTCATGTCAGTCATAATTTCATGTCCCC
GATATACCCTGCCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTT
Found at i:242777 original size:20 final size:20
Alignment explanation
Indices: 242749--242958 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
242739 AAATTTCAGT
* * *
242749 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
242769 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
242789 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
242809 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
242829 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
242849 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
** *
242869 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
242889 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
242909 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
242929 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
242949 GTTGCGATTT
1 GTTGCGATTT
242959 TGGAAAATCG
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:242975 original size:21 final size:20
Alignment explanation
Indices: 242925--243022 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
242915 ATTTATGTGT
* * * *
242925 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
242945 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
242966 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
242986 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
243007 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
243023 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:243017 original size:41 final size:41
Alignment explanation
Indices: 242925--243022 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
242915 ATTTATGTGT
* * *
242925 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
242966 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
243007 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
243023 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 42 0.91
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:245435 original size:2 final size:2
Alignment explanation
Indices: 245428--245470 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
245418 GATCCTCCAG
245428 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
245470 A
1 A
245471 AAAATCAAGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:246936 original size:35 final size:29
Alignment explanation
Indices: 246857--246919 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
246847 CTTTAGTTCG
246857 ATTTTGTAAATTCAATTTCATACATAGAT
1 ATTTTGTAAATTCAATTTCATACATAGAT
*
246886 ATTTTGTAAATTCAATTTCATACATATAT
1 ATTTTGTAAATTCAATTTCATACATAGAT
246915 ATTTT
1 ATTTT
246920 TTTTTTGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (29 bp):
ATTTTGTAAATTCAATTTCATACATAGAT
Found at i:250485 original size:31 final size:31
Alignment explanation
Indices: 250448--250521 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
250438 TAATGGACTT
*
250448 TTAGGCCCCTGATTTTGAC-TTGCATATGCAA
1 TTAGGCCCCTGACTTTGACTTTG-ATATGCAA
** *
250479 TTAGGCCATTGACTTTGGCTTTGATATGCAA
1 TTAGGCCCCTGACTTTGACTTTGATATGCAA
**
250510 TTTTGCCCCTGA
1 TTAGGCCCCTGA
250522 ACGTTTCTGG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (31 bp):
TTAGGCCCCTGACTTTGACTTTGATATGCAA
Found at i:250704 original size:24 final size:24
Alignment explanation
Indices: 250659--250713 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
250649 TAAATTTTAT
*
250659 ATTTAAAATTTTAACTTGATAATA
1 ATTTAAAATTTTAACTTGATAAGA
* *
250683 ATTTAAATATTTT-TCTTTATAAGA
1 ATTTAAA-ATTTTAACTTGATAAGA
*
250707 AATTAAA
1 ATTTAAA
250714 GGCAGAAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
ATTTAAAATTTTAACTTGATAAGA
Found at i:258158 original size:24 final size:25
Alignment explanation
Indices: 258130--258191 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
258120 AGGGGCAATA
*
258130 TTTTCAAAACTTTTGATTAA-ACAT
1 TTTTCAAAACTTTTGACTAATACAT
*
258154 TTTTCAAAACTCTT--CTAATACAT
1 TTTTCAAAACTTTTGACTAATACAT
258177 TTTT-AAAACTTTTGA
1 TTTTCAAAACTTTTGA
258192 AAATAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 11 0.34
23 8 0.25
24 13 0.41
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (25 bp):
TTTTCAAAACTTTTGACTAATACAT
Found at i:258196 original size:23 final size:23
Alignment explanation
Indices: 258129--258196 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
258119 AAGGGGCAAT
*
258129 ATTTTCAAAACTTTTGATTAA-AC
1 ATTTTTAAAACTTTTGA-TAATAC
* *
258152 ATTTTTCAAAACTCTT-CTAATAC
1 ATTTTT-AAAACTTTTGATAATAC
*
258175 ATTTTTAAAACTTTTGAAAATA
1 ATTTTTAAAACTTTTGATAATA
258197 AAAGAAGAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 11 0.31
23 17 0.47
24 8 0.22
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (23 bp):
ATTTTTAAAACTTTTGATAATAC
Found at i:258411 original size:32 final size:32
Alignment explanation
Indices: 258337--258411 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
258327 GCATCTTTAA
* *
258337 AGATTCAACAGTAAATGTTGGGGCACATTTGG
1 AGATTCAACATTAAATATTGGGGCACATTTGG
* * * *
258369 AGATTTAACATTGAATATTGTGGCATATTTGG
1 AGATTCAACATTAAATATTGGGGCACATTTGG
*
258401 GGATTCAACAT
1 AGATTCAACAT
258412 CCTGATGCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (32 bp):
AGATTCAACATTAAATATTGGGGCACATTTGG
Found at i:259044 original size:43 final size:43
Alignment explanation
Indices: 258996--259116 Score: 206
Period size: 43 Copynumber: 2.8 Consensus size: 43
258986 CGAAGGGGTC
258996 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACAT
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACAT
*
259039 ATCCACGATTTCAACTCCACGACGGAGGATATTGTACCAACAT
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACAT
* **
259082 ATCCACGATTTCAACTCCACAATAGAGGATATCGT
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGT
259117 GCCCATACAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACAT
Found at i:259129 original size:43 final size:43
Alignment explanation
Indices: 258995--259138 Score: 198
Period size: 43 Copynumber: 3.3 Consensus size: 43
258985 ACGAAGGGGT
258995 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* *
259038 TATCCACGATTTCAACTCCACGACGGAGGATATTGTACCAACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * ** * * *
259081 TATCCACGATTTCAACTCCACAATAGAGGATATCGTGCCCATA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
*
259124 CATCCACGGTTTCAA
1 CATCCACGATTTCAA
259139 TTTCACAGCG
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 90 1.00
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:259475 original size:43 final size:43
Alignment explanation
Indices: 259373--259464 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
259363 ATGAAGGAGC
* *
259373 CATCCACAATTTCAACTCCACGACGGAGGATATCGTACCAACG
1 CATCCACAATTTCAACTCCACGAAGGAGGATATCGTACCAACA
* * *
259416 GATCCACAATTTCAACTCCACGAAGGAGGATATCGTGCCCACA
1 CATCCACAATTTCAACTCCACGAAGGAGGATATCGTACCAACA
259459 CATCCA
1 CATCCA
259465 TGGTTTCAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.33, G:0.16, T:0.18
Consensus pattern (43 bp):
CATCCACAATTTCAACTCCACGAAGGAGGATATCGTACCAACA
Found at i:259699 original size:34 final size:30
Alignment explanation
Indices: 259656--259745 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 30
259646 TAACTTGGAT
259656 TTCAACTTCACGACGAAGGATATCCAATTCAAGG
1 TTCAACTTCACGACGAAGGATATCC-A--CAA-G
* * * *
259690 TTCAACTTCATGACGAATGGGTCATCCACGAT
1 TTCAACTTCACGACGAA-GGAT-ATCCACAAG
259722 TTCAACTTCACGACGAAGGATATC
1 TTCAACTTCACGACGAAGGATATC
259746 GTGTCCACCA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
30 3 0.06
31 3 0.06
32 16 0.33
33 2 0.04
34 16 0.33
35 4 0.08
36 4 0.08
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (30 bp):
TTCAACTTCACGACGAAGGATATCCACAAG
Found at i:259806 original size:121 final size:122
Alignment explanation
Indices: 259634--259869 Score: 339
Period size: 121 Copynumber: 1.9 Consensus size: 122
259624 TTGGCCTCGA
*
259634 AACAATGCAACCTAACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGTTCAACTTC
1 AACAATGCAACC--ACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
** *
259699 ATGACGAATGGGTCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGC
64 ACAACGAAGGGGTCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGC
* * * * *
259758 AACAATGCAACC-CTTGGATTTCAATTTCATGACGAATGATATCCAATTCGATGCTCAACTTCAC
1 AACAATGCAACCACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCAC
* * *
259822 AATGAAGGGGTCATTCACGATTTCAACTTCACGATGAAGGATATCGTG
66 AACGAAGGGGTCATCCACGATTTCAACTTCACGACGAAGGATATCGTG
259870 GTCATTTGCA
Statistics
Matches: 100, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
121 88 0.88
124 12 0.12
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (122 bp):
AACAATGCAACCACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCAC
AACGAAGGGGTCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGC
Found at i:260012 original size:84 final size:84
Alignment explanation
Indices: 259871--260439 Score: 913
Period size: 84 Copynumber: 6.8 Consensus size: 84
259861 GATATCGTGG
* * * * * * * * *
259871 TCATTTGCAGCTTAGCTCAAGGCAAGAAGGGCTATCTGCTAACAAAAGTCCTTCGAGTTCTATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* * *
259936 CACTCAACTCAAAGGCACA
66 CGCTCAGCTCCAAGGCACA
*
259955 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
*
260020 CGCTCAGCTCCAAGACACA
66 CGCTCAGCTCCAAGGCACA
* *
260039 TCATTTCCAGCATAACTCAAGGCTAGAAGGGTTATCTTACCAACCAAAGACCTTCGAGTTCGACT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATC-TGCCAACCAAAGACCTTCGAGTTCGACT
* *
260104 ATGCTCAGCTTCAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
* *
260124 TCACTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
260189 CGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* *
260208 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
260273 CGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
*
260292 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
260357 CGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
*
260376 TCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
260440 CAGCATAACT
Statistics
Matches: 451, Mismatches: 33, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
84 375 0.83
85 76 0.17
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (84 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:260471 original size:57 final size:57
Alignment explanation
Indices: 260383--260496 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
260373 ACATCATTTG
260383 CAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 CAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
260440 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATCAAAGACCTTCGAGTTCGACT
1 CAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
260497 ACGCTCAGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (57 bp):
CAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
Found at i:260553 original size:141 final size:141
Alignment explanation
Indices: 260299--260580 Score: 514
Period size: 141 Copynumber: 2.0 Consensus size: 141
260289 ACATCATTTG
260299 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
260364 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACCAAAGACCTT
66 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACAAAAGACCTT
260429 CGA-GTTCGACT
131 C-ATGTTCGACT
260440 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATC-AAAGACCTTCGAGTTCGACTACGCTCA
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTCA
*
260504 GCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
65 GCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACAAAAGACCT
260569 TCATGTTCGACT
130 TCATGTTCGACT
260581 ACGCTCAGCT
Statistics
Matches: 137, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
140 1 0.01
141 135 0.99
142 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (141 bp):
CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACAAAAGACCTT
CATGTTCGACT
Found at i:260581 original size:84 final size:83
Alignment explanation
Indices: 260440--260854 Score: 517
Period size: 83 Copynumber: 5.0 Consensus size: 83
260430 GAGTTCGACT
* *
260440 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATCAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACACTCAG
*
260505 CTCCAAGGCACATCATTTG
65 CTCAAAGGCACATCATTTG
* *
260524 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTC-ATGTTCGACTACGCTCA
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGA-GTTCGACTACACTCA
* *
260588 GCTCCAAGACACATCATTTG
64 GCTCAAAGGCACATCATTTG
* * * * *
260608 CAGCATAACTTAAGGCGAGAAGGGTTATCTACCACCAAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGC
260673 TCAAAGGCACATCATTTG
66 TCAAAGGCACATCATTTG
* * * * *
260691 CAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCACC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGC
* *
260756 TCAAAGGCATATCAAATTTA
66 TCAAAGGCACATC--ATTTG
* * * ** * * *
260776 CAGCATAGCTCAAGGCGAGAAGGGTTATTTGTCATGAAAGACCTTCGAGTTCGATTTCATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGC
* *
260841 TCATAGGCATATCA
66 TCAAAGGCACATCA
260855 ACCGCATGGT
Statistics
Matches: 298, Mismatches: 28, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
83 112 0.38
84 112 0.38
85 74 0.25
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (83 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGC
TCAAAGGCACATCATTTG
Found at i:260606 original size:225 final size:224
Alignment explanation
Indices: 260215--260661 Score: 799
Period size: 225 Copynumber: 2.0 Consensus size: 224
260205 ACATCATTTG
*
260215 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAG
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
260280 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
66 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
* *
260345 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTA
131 CGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTCAAGGCGAGAAAGGTTA
*
260410 TCTGCCAACCAAAGACCTTCGAGTTCGACT
196 TCTACC-ACCAAAGACCTTCGAGTTCGACT
260440 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATC-AAAGACCTTCGAGTTCGACTACGCTCA
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTCA
260504 GCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
65 GCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
* *
260569 TC-ATGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGGCGAGAAGGGT
130 TCGA-GTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTCAAGGCGAGAAAGGT
260633 TATCTACCACCAAAGACCTTCGAGTTCGA
194 TATCTACCACCAAAGACCTTCGAGTTCGA
260662 TTACATTCAG
Statistics
Matches: 214, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
224 22 0.10
225 191 0.89
226 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (224 bp):
CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
CGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTCAAGGCGAGAAAGGTTA
TCTACCACCAAAGACCTTCGAGTTCGACT
Found at i:260841 original size:168 final size:167
Alignment explanation
Indices: 260440--260854 Score: 555
Period size: 168 Copynumber: 2.5 Consensus size: 167
260430 GAGTTCGACT
* * **
260440 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATCAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGCC-ATCAAAGACCTTCGAGTTCGATTACATTCAG
* *
260505 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
65 CTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTT
* * * *
260570 CATGTTCGACTACGCTCAGCTCCAAGACACATCATTTG
130 CATGTTCGACTACACTCACCTCAAAGACACATCATTTA
* * *
260608 CAGCATAACTTAAGGCGAGAAGGGTTATCTACCACCAAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCATCAAAGACCTTCGAGTTCGATTACATTCAGC
* *
260673 TCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAAC-AAAGACCTTC
66 TCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTC
* * *
260737 GA-GTTCGATTACACTCACCTCAAAGGCATATCAAATTTA
131 -ATGTTCGACTACACTCACCTCAAAGACACATC--ATTTA
* * * * *
260776 CAGCATAGCTCAAGGCGAGAAGGGTTATTTGTCATGAAAGACCTTCGAGTTCGATTTCATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCATCAAAGACCTTCGAGTTCGATTACATTCAGC
* *
260841 TCATAGGCATATCA
66 TCAAAGGCACATCA
260855 ACCGCATGGT
Statistics
Matches: 216, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
166 34 0.16
167 79 0.37
168 103 0.48
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (167 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGCCATCAAAGACCTTCGAGTTCGATTACATTCAGC
TCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTC
ATGTTCGACTACACTCACCTCAAAGACACATCATTTA
Found at i:267120 original size:24 final size:24
Alignment explanation
Indices: 267082--267195 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
267072 ATTTGAATTA
*
267082 TGATCTGA-ACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
267105 TGATATGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
*
267129 TGATATGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTC
* * * *
267153 TGATTTGATACTTGACCTAGATTT
1 TGATATGATACTTGACATGGATTC
267177 TGATATGATACTTGACATG
1 TGATATGATACTTGACATG
267196 AATTATGTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
23 8 0.10
24 70 0.89
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.39
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:267130 original size:12 final size:12
Alignment explanation
Indices: 267093--267155 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
267083 GATCTGAACT
267093 TGACATGGATTC
1 TGACATGGATTC
*
267105 TGATAT-GATATC
1 TGACATGGAT-TC
267117 TGACATGGATTC
1 TGACATGGATTC
* *
267129 TGATAT-GATAC
1 TGACATGGATTC
*
267140 TTGACTTGGATTC
1 -TGACATGGATTC
267153 TGA
1 TGA
267156 TTTGATACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:269770 original size:28 final size:28
Alignment explanation
Indices: 269686--269770 Score: 120
Period size: 28 Copynumber: 3.1 Consensus size: 28
269676 CTATTTAATA
*
269686 TTATATAATATATAAAATTTTGAAAACA-
1 TTATATAATATAT-AATTTTTGAAAACAT
* *
269714 -TATACAATATATAATTTTTGAAAATAT
1 TTATATAATATATAATTTTTGAAAACAT
269741 TTATATAATATATAATTTTTGAAAACAT
1 TTATATAATATATAATTTTTGAAAACAT
269769 TT
1 TT
269771 TGAAAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 12 0.24
27 11 0.22
28 27 0.54
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (28 bp):
TTATATAATATATAATTTTTGAAAACAT
Found at i:269773 original size:39 final size:39
Alignment explanation
Indices: 269729--269869 Score: 201
Period size: 39 Copynumber: 3.6 Consensus size: 39
269719 AATATATAAT
*
269729 TTTTGAAAATATTTATATAATATATAATTTTTGAAAACA
1 TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
* * * *
269768 TTTTGAAAATAAATATATAATATATAGTTTTTAAAAATA
1 TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
* * *
269807 TTTTAAAAAAATATATATAACATATAATTTTTGAAAACA
1 TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
*
269846 TTTTGAAAATATATATATTATATA
1 TTTTGAAAATATATATATAATATA
269870 GTTTTTAAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (39 bp):
TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
Found at i:269835 original size:78 final size:77
Alignment explanation
Indices: 269742--269886 Score: 247
Period size: 78 Copynumber: 1.9 Consensus size: 77
269732 TGAAAATATT
*
269742 TATATAATATATAATTTTTGAAAACATTTTGAAAATAAATATATAATATATAGTTTTT-AAAAAT
1 TATATAACATATAATTTTTGAAAACATTTTGAAAAT--ATATATAATATATAGTTTTTAAAAAAT
269806 ATTTTAAAAAAATA
64 ATTTTAAAAAAATA
*
269820 TATATAACATATAATTTTTGAAAACATTTTGAAAATATATATATTATATAGTTTTTAAAAAATAT
1 TATATAACATATAATTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAAATAT
269885 TT
66 TT
269887 ATATATTATA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
76 19 0.30
77 10 0.16
78 35 0.55
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (77 bp):
TATATAACATATAATTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAAATAT
TTTAAAAAAATA
Found at i:269884 original size:25 final size:24
Alignment explanation
Indices: 269846--269892 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
269836 TTTGAAAACA
*
269846 TTTTGAAAATATATATATTATATAG
1 TTTTGAAAAAATATATA-TATATAG
* *
269871 TTTTTAAAAAATATTTATATAT
1 TTTTGAAAAAATATATATATAT
269893 TATATATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTTGAAAAAATATATATATATAG
Found at i:271201 original size:21 final size:19
Alignment explanation
Indices: 271168--271212 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
271158 TTGATCCAAC
*
271168 ATTTTTATTTATTTATTTT
1 ATTTTTATTTATTCATTTT
271187 ATTTTTATTTTTATTCATTTT
1 ATTTTTA--TTTATTCATTTT
271208 ATTTT
1 ATTTT
271213 CTTTGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
21 16 0.70
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTTATTTATTCATTTT
Found at i:274524 original size:20 final size:20
Alignment explanation
Indices: 274495--274566 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
274485 ACCTGACTCG
*
274495 AAATAATATATTTATTGAAA
1 AAATATTATATTTATTGAAA
*
274515 AAATATTATATTTATTCAATA
1 AAATATTATATTTATTGAA-A
274536 AAA-A-TAGTGATTTAATTG-AA
1 AAATATTA-T-ATTT-ATTGAAA
274556 AAATATTATAT
1 AAATATTATAT
274567 AGAGGGTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 11 0.26
22 5 0.12
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (20 bp):
AAATATTATATTTATTGAAA
Found at i:277114 original size:2 final size:2
Alignment explanation
Indices: 277107--277132 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
277097 ACTTGATTAC
277107 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
277133 TATTAATAAC
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:277459 original size:53 final size:53
Alignment explanation
Indices: 277336--277448 Score: 199
Period size: 53 Copynumber: 2.1 Consensus size: 53
277326 AGACTTGATA
* *
277336 AATCTTCGGAAAACGGGTTTGTTCTCTATCGTTTCAAGGAGCAGAACTCGAAC
1 AATCTTCAGAAAACGGGTTTGCTCTCTATCGTTTCAAGGAGCAGAACTCGAAC
*
277389 AATCTTCAGAAAACGGGTTTGCTCTCTATCGTTTCAAGGAGTAGAACTCGAAC
1 AATCTTCAGAAAACGGGTTTGCTCTCTATCGTTTCAAGGAGCAGAACTCGAAC
277442 AATCTTC
1 AATCTTC
277449 TGCCTACGGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (53 bp):
AATCTTCAGAAAACGGGTTTGCTCTCTATCGTTTCAAGGAGCAGAACTCGAAC
Found at i:277884 original size:21 final size:21
Alignment explanation
Indices: 277832--277888 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
277822 TTTTACACTT
277832 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
* *
277853 AGGAAATCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
277874 AGGGTACCGATTCCC
1 AGGGAACCGATTCCC
277889 CCACGCTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:278105 original size:13 final size:13
Alignment explanation
Indices: 278084--278138 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
278074 AAGTTCGATA
*
278084 AATTCAAATACTT
1 AATTGAAATACTT
278097 AATTGAAATACTT
1 AATTGAAATACTT
* *
278110 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
278124 AATTGAAATACTT
1 AATTGAAATACTT
278137 AA
1 AA
278139 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:278220 original size:32 final size:33
Alignment explanation
Indices: 278124--278222 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
278114 AACTCAACAT
* * *
278124 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
278157 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
278190 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
278222 A
1 A
278223 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:278241 original size:21 final size:21
Alignment explanation
Indices: 278217--278256 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
278207 ACTTCAAGTT
278217 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
278238 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
278257 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:280566 original size:12 final size:12
Alignment explanation
Indices: 280549--280594 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
280539 TTCGGATAAA
280549 AACCGGTTTTTT
1 AACCGGTTTTTT
280561 AACCGGTTTTTTT
1 AACCGG-TTTTTT
280574 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
280588 ATCCGGT
1 AACCGGT
280595 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:280579 original size:15 final size:14
Alignment explanation
Indices: 280548--280587 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
280538 TTTCGGATAA
280548 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
280561 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
280574 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
280588 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:280826 original size:53 final size:53
Alignment explanation
Indices: 280746--281591 Score: 1282
Period size: 53 Copynumber: 16.0 Consensus size: 53
280736 TGCACCCCTA
*
280746 CCTACGGGTTCGCTCTCTGTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* * *
280799 CCTACGGGTTCGCTATCTCTTTTTTCAGGGAGTAGAACTCGAACAATCATCTG
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
280852 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* *
280905 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTTGAACAATCTTCTT
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* * * * * * *
280958 CCTATGGGTTTGCTCTCTCTTTCTTAATGGAGTAGAAATCGAACAATATTCTT
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* * * *
281011 CTTACGGGTTCACTATCTCTTTCTTCAAGGAGTAGAACTCGAACAATCTTCTG
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* * *
281064 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCAAACAATTTTCTT
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* *
281117 CCTACGAGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTTGAACAATCTTCTG
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
** *
281170 CCTACGGGTTCTTTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTT
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* * * *
281223 CCTACGGGTTCACTCACTCTTTCTTTAGGGAGTAGAACTCGAACAATCTTCTC
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* * * *
281276 CCTACGGGTTCGGTCTCTCTTTTTTCAGGGAGTAGAACTCAAACAATCTTCTT
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* *
281329 CCTACGGGTTCGCTCT-TTTTTTTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* *
281381 CCTACTGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAATAATCTTCTG
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* ** *
281434 CTTACGGGTTCGCTCTCTCTTTCTTCAAAGAGTAGAACTCGAACAATCTTCTT
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
281487 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAG-ACTCGAACAATCTTCTG
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
* *
281539 CCTATGGGTTCGCTCTCTCTTTCTTCAGGAAGTAGGAACTCGAACAATCTTCT
1 CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTA-GAACTCGAACAATCTTCT
281592 TTTGCTTCAT
Statistics
Matches: 715, Mismatches: 75, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
52 96 0.13
53 603 0.84
54 16 0.02
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (53 bp):
CCTACGGGTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTG
Found at i:281274 original size:28 final size:28
Alignment explanation
Indices: 281190--281274 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
281180 CTTTCTCTCT
*
281190 TTCTTCAGGGAGTAGAACTCGAACAATC
1 TTCTTTAGGGAGTAGAACTCGAACAATC
* **
281218 TTCTTCCTACGG-GT-TCACTC--AC--TC
1 TTCTT--TAGGGAGTAGAACTCGAACAATC
281242 TTTCTTTAGGGAGTAGAACTCGAACAATC
1 -TTCTTTAGGGAGTAGAACTCGAACAATC
281271 TTCT
1 TTCT
281275 CCCTACGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 18
0.62 0.11 0.27
Matches are distributed among these distances:
23 4 0.10
24 4 0.10
25 9 0.22
26 2 0.05
27 2 0.05
28 13 0.32
29 4 0.10
30 3 0.07
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (28 bp):
TTCTTTAGGGAGTAGAACTCGAACAATC
Found at i:281667 original size:37 final size:37
Alignment explanation
Indices: 281592--281673 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
281582 ACAATCTTCT
* *
281592 TTTGCTTCATTACTTCCTTGTGAAGGCTTCTAGATGA
1 TTTGCTTCACTACTTCCTTGTGAAGGCTTCAAGATGA
* *
281629 TTTGCTTCACTAC-TCTTTAGTGAAGGCTT-AAGTTTGA
1 TTTGCTTCACTACTTCCTT-GTGAAGGCTTCAAG-ATGA
281666 TTTGCTTC
1 TTTGCTTC
281674 GAAGGTTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 6 0.15
37 33 0.85
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (37 bp):
TTTGCTTCACTACTTCCTTGTGAAGGCTTCAAGATGA
Found at i:282862 original size:21 final size:21
Alignment explanation
Indices: 282836--282888 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
282826 TTTATTTGAC
282836 TTTTTTTCTTTATTTTTTCTT
1 TTTTTTTCTTTATTTTTTCTT
282857 TTTTTTTCTTTATTTTTTCTT
1 TTTTTTTCTTTATTTTTTCTT
*
282878 TTTTTCTCTTT
1 TTTTTTTCTTT
282889 TTTCATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTTTTCTTTATTTTTTCTT
Found at i:282900 original size:11 final size:10
Alignment explanation
Indices: 282836--282891 Score: 85
Period size: 10 Copynumber: 5.4 Consensus size: 10
282826 TTTATTTGAC
282836 TTTTTTTCTT
1 TTTTTTTCTT
282846 TATTTTTTCTT
1 T-TTTTTTCTT
282857 TTTTTTTCTT
1 TTTTTTTCTT
282867 TATTTTTTCTT
1 T-TTTTTTCTT
*
282878 TTTTTCTCTT
1 TTTTTTTCTT
282888 TTTT
1 TTTT
282892 CATTTTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
10 23 0.53
11 20 0.47
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:282900 original size:18 final size:17
Alignment explanation
Indices: 282837--282905 Score: 72
Period size: 18 Copynumber: 4.1 Consensus size: 17
282827 TTATTTGACT
*
282837 TTTTTTCTTTATTTTTTC
1 TTTTTTCTTT-TTTTATC
*
282855 TTTTTT-TTTCTTTA--
1 TTTTTTCTTTTTTTATC
*
282869 TTTTTTCTTTTTTTCTC
1 TTTTTTCTTTTTTTATC
282886 TTTTTTCATTTTTTTATC
1 TTTTTTC-TTTTTTTATC
282904 TT
1 TT
282906 CAAGCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.14
15 6 0.14
16 3 0.07
17 10 0.24
18 17 0.40
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTTTTTTATC
Found at i:282900 original size:21 final size:19
Alignment explanation
Indices: 282835--282891 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
282825 TTTTATTTGA
282835 CTTTTTTTCTTTATTTTTTCT
1 CTTTTTTTCTTT-TTTTTT-T
* *
282856 TTTTTTTTCTTTATTTTTT
1 CTTTTTTTCTTTTTTTTTT
*
282875 CTTTTTTTCTCTTTTTT
1 CTTTTTTTCTTTTTTTT
282892 CATTTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 15 0.48
20 5 0.16
21 11 0.35
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (19 bp):
CTTTTTTTCTTTTTTTTTT
Found at i:294250 original size:2 final size:2
Alignment explanation
Indices: 294243--294292 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
294233 TAGTTACTTG
294243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- 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
294283 AT AT AT AT AT
1 AT AT AT AT AT
294293 TAATAACTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:298000 original size:2 final size:2
Alignment explanation
Indices: 297995--298045 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
297985 ACATTCAAGT
297995 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
298037 TA TA TA TA T
1 TA TA TA TA T
298046 GCCATTCAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:300344 original size:20 final size:21
Alignment explanation
Indices: 300316--300354 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
300306 TTATGACGGA
*
300316 TTTTAAC-TTAAAATGTTATT
1 TTTTAACTTTAAAAAGTTATT
*
300336 TTTTTACTTTAAAAAGTTA
1 TTTTAACTTTAAAAAGTTA
300355 CACAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (21 bp):
TTTTAACTTTAAAAAGTTATT
Found at i:308701 original size:19 final size:20
Alignment explanation
Indices: 308658--308705 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
308648 TCTAAATCCT
*
308658 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
308678 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
308697 TTTTCAAAA
1 TTTTCAAAA
308706 AAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:311065 original size:27 final size:27
Alignment explanation
Indices: 311035--311094 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
311025 GTTTTATTAT
* *
311035 AATATTATATAATATTAAAAAATAA-AA
1 AATATTAT-GAATATGAAAAAATAATAA
* *
311062 AATATGATGCATATGAAAAAATAATAA
1 AATATTATGAATATGAAAAAATAATAA
311089 AATATT
1 AATATT
311095 CATGTCATCG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (27 bp):
AATATTATGAATATGAAAAAATAATAA
Done.