Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009632.1 Hibiscus syriacus cultivar Beakdansim tig00117028_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: 343994
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:207763 original size:25 final size:25
Alignment explanation
Indices: 207728--207803 Score: 125
Period size: 25 Copynumber: 3.0 Consensus size: 25
207718 AAGAATATAT
207728 ATATATATCCCGAAGGACCGCGTAGA
1 ATAT-TATCCCGAAGGACCGCGTAGA
*
207754 ATATTGTCCCGAAGGACCGCGTAGA
1 ATATTATCCCGAAGGACCGCGTAGA
*
207779 ATATTATCCCGAAGGGCCGCGTAGA
1 ATATTATCCCGAAGGACCGCGTAGA
207804 CCCTCTACTC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
25 43 0.91
26 4 0.09
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (25 bp):
ATATTATCCCGAAGGACCGCGTAGA
Found at i:212672 original size:23 final size:23
Alignment explanation
Indices: 212646--212690 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
212636 CACCACAGCT
*
212646 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
212669 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
212691 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:212833 original size:25 final size:25
Alignment explanation
Indices: 212805--212873 Score: 138
Period size: 25 Copynumber: 2.8 Consensus size: 25
212795 TATATATATA
212805 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
212830 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
212855 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
212874 CCCTCTACTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:214565 original size:21 final size:21
Alignment explanation
Indices: 214541--214585 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
214531 TTTTGTTCGT
* *
214541 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
214562 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
214583 TTG
1 TTG
214586 CCCAGAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:221037 original size:12 final size:13
Alignment explanation
Indices: 221020--221048 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
221010 CTTAATTGCA
221020 AAAATTAAAA-TT
1 AAAATTAAAATTT
221032 AAAATTAAAATTT
1 AAAATTAAAATTT
221045 AAAA
1 AAAA
221049 ATTCGATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:223173 original size:20 final size:19
Alignment explanation
Indices: 223135--223187 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
223125 ATTATTATTG
**
223135 TATTAAATTATTCTATTTT
1 TATTAAATTATAATATTTT
223154 TATTAAATATATAATATTTT
1 TATTAAAT-TATAATATTTT
*
223174 TAATAAAATTATAA
1 T-ATTAAATTATAA
223188 AAAATATAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.28
20 15 0.52
21 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAAATTATAATATTTT
Found at i:223224 original size:19 final size:18
Alignment explanation
Indices: 223205--223238 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
223195 AACGTTGATG
223205 ATGAT-TTAT-ATAAAAA
1 ATGATATTATAATAAAAA
223221 ATGATATTATAATAAAAA
1 ATGATATTATAATAAAAA
223239 TAAGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATGATATTATAATAAAAA
Found at i:228387 original size:22 final size:20
Alignment explanation
Indices: 228361--228400 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
228351 AATTTCGTCC
228361 TTATATTATACAATATATATAT
1 TTATATTATA-AAT-TATATAT
228383 TTATATTATAAATTATAT
1 TTATATTATAAATTATAT
228401 TTACATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATTATAAATTATATAT
Found at i:229595 original size:18 final size:18
Alignment explanation
Indices: 229548--229596 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
229538 TTATTTTTGT
* *
229548 TATTATTATTATTCTTTA
1 TATTATTACTATTATTTA
** *
229566 TATTATCCCTATTATTTC
1 TATTATTACTATTATTTA
229584 TATTATTACTATT
1 TATTATTACTATT
229597 TTTTTTGTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATTACTATTATTTA
Found at i:233593 original size:9 final size:9
Alignment explanation
Indices: 233568--233599 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
233558 AATGCCTCCA
233568 ATTGCATAC
1 ATTGCATAC
233577 A-T-CATAC
1 ATTGCATAC
233584 ATTGCATAC
1 ATTGCATAC
233593 ATTGCAT
1 ATTGCAT
233600 TTTATATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.29
8 2 0.10
9 13 0.62
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (9 bp):
ATTGCATAC
Found at i:241879 original size:105 final size:105
Alignment explanation
Indices: 241578--242212 Score: 1126
Period size: 105 Copynumber: 6.0 Consensus size: 105
241568 AGGTTTTACC
241578 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
241643 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
*
241683 CAGAGCCAATTTCAAACTTCACAACGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCAC
1 CAGAGCCAATTTC-AACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
241748 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTC
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
*
241789 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
241854 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
* * *
241894 CAGAGCCAACTTCAAACTTCACAACGAAAGATATTGGGCTCCAGACAACGTAAGTTCAACTTCAC
1 CAGAGCCAATTTC-AACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
241959 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
242000 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* *
242065 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
* * *
242105 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
242170 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
242210 CAG
1 CAG
242213 CTCCACAACG
Statistics
Matches: 507, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
105 304 0.60
106 203 0.40
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
Found at i:241944 original size:211 final size:211
Alignment explanation
Indices: 241577--242208 Score: 1167
Period size: 211 Copynumber: 3.0 Consensus size: 211
241567 CAGGTTTTAC
241577 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
241642 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
241707 CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
241772 CAAACATTTCCCAATT
196 CAAACATTTCCCAATT
*
241788 CCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
241853 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAACTTCAAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
*
241918 CGAAAGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
241983 CAAACATTTCTCAATT
196 CAAACATTTCCCAATT
*
241999 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* *
242064 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGGAGCCAATTTC-AACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
* * *
242128 CGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
242193 CAAACATTTCCCAATT
196 CAAACATTTCCCAATT
242209 TCAGCTCCAC
Statistics
Matches: 407, Mismatches: 14, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
210 86 0.21
211 321 0.79
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (211 bp):
CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
CGAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAAACATTTCCCAATT
Found at i:242161 original size:316 final size:316
Alignment explanation
Indices: 241578--242212 Score: 1166
Period size: 316 Copynumber: 2.0 Consensus size: 316
241568 AGGTTTTACC
* *
241578 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAACTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
241643 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAAC
*
241708 GAAGGATATTGGGCTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
131 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
*
241773 AAACATTTCCCAATTCCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
196 AAACATTTCCAAATTCCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
241838 TAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
261 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
*
241894 CAGAGCCAACTTCAAACTTCACAACGAAAGATATTGGGCTCCAGACAACGTAAGTTCAACTTCAC
1 CAGAGCCAACTTC-AACTTCACAACGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
241959 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTC-AACTTCACAA
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAA
242023 CGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
130 CGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
242088 CAAACATTTCTCAAATT-CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAA
195 CAAACATTTC-CAAATTCCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
242152 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
259 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
242210 CAG
1 CAG
242213 CTCCACAACG
Statistics
Matches: 309, Mismatches: 8, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
316 201 0.65
317 108 0.35
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (316 bp):
CAGAGCCAACTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAAACTTCACAAC
GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
AAACATTTCCAAATTCCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
Found at i:242308 original size:20 final size:20
Alignment explanation
Indices: 242270--242311 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
242260 CCAGAACTCT
*
242270 GAGTTCGATTTCAGCTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
242290 GAGTTTGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
242310 GA
1 GA
242312 CGAAGGATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:242555 original size:22 final size:20
Alignment explanation
Indices: 242529--242568 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
242519 AATTTCGTCC
242529 TTATATTATACAATATATATAT
1 TTATATTATA-AAT-TATATAT
242551 TTATATTATAAATTATAT
1 TTATATTATAAATTATAT
242569 TTACATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATTATAAATTATATAT
Found at i:244140 original size:17 final size:19
Alignment explanation
Indices: 244115--244165 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
244105 CTTTTTGCTA
244115 TTATACTATT-TATT-TAT
1 TTATACTATTATATTATAT
*
244132 TTATGCTATTATATTATAT
1 TTATACTATTATATTATAT
* *
244151 TTTTATTATTATATT
1 TTATACTATTATATT
244166 CGTATAAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 15 0.54
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATACTATTATATTATAT
Found at i:244142 original size:25 final size:25
Alignment explanation
Indices: 244100--244157 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
244090 TATTTCTCCC
*
244100 TTTTACTTTTTGCTATTATACTAT-T
1 TTTTA-TTTATGCTATTATACTATAT
*
244125 TATTTATTTATGCTATTATATTATAT
1 T-TTTATTTATGCTATTATACTATAT
244151 TTTTATT
1 TTTTATT
244158 ATTATATTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (25 bp):
TTTTATTTATGCTATTATACTATAT
Found at i:247876 original size:23 final size:21
Alignment explanation
Indices: 247850--247916 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 21
247840 ATCATTTTAA
247850 TCAAAATATTAATTATTAAATAT
1 TCAAAATA-TAATTATT-AATAT
*
247873 TCAAAATATATTTATTAATATT
1 TCAAAATATAATTATTAATA-T
247895 TCTAATAATATAA-TATT-ATAT
1 TC-AA-AATATAATTATTAATAT
247916 T
1 T
247917 TTTAATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 6 0.15
22 13 0.33
23 14 0.36
24 6 0.15
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TCAAAATATAATTATTAATAT
Found at i:247905 original size:22 final size:22
Alignment explanation
Indices: 247885--247931 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
247875 AAAATATATT
247885 TATTAATATTTCTAATAATATAA
1 TATT-ATATTTCTAATAATATAA
* *
247908 TATTATATTTTTAATATTATAA
1 TATTATATTTCTAATAATATAA
247930 TA
1 TA
247932 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTTCTAATAATATAA
Found at i:247945 original size:32 final size:32
Alignment explanation
Indices: 247879--247958 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
247869 ATATTCAAAA
* *
247879 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
247911 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
247943 TATATTATAATAATAT
1 TATATT-TATTAATAT
247959 AACATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:247950 original size:23 final size:23
Alignment explanation
Indices: 247921--247971 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
247911 TATATTTTTA
247921 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
*
247944 ATATTATAATAATATAACATATT
1 ATATTATAATAAAATAACATATT
247967 ATATT
1 ATATT
247972 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:248092 original size:27 final size:26
Alignment explanation
Indices: 248034--248094 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
248024 ATTTCATAGA
*
248034 AATAATATTATTAAATTATTAATAAT
1 AATAATATTATTAAATTAATAATAAT
*
248060 GAATAATATTATTTAAATTTAATATTAAT
1 -AATAATATTA-TTAAA-TTAATAATAAT
248089 -ATAATA
1 AATAATA
248095 ATCTAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 16 0.53
28 5 0.17
29 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AATAATATTATTAAATTAATAATAAT
Found at i:250385 original size:15 final size:16
Alignment explanation
Indices: 250353--250395 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
250343 ACAAAAACAA
*
250353 ATATAAAGAAATATAC
1 ATATAAATAAATATAC
250369 ATATAAATAAA-ATAC
1 ATATAAATAAATATAC
250384 ATA-AAATAAATA
1 ATATAAATAAATA
250396 AGATAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 10 0.40
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (16 bp):
ATATAAATAAATATAC
Found at i:250394 original size:18 final size:18
Alignment explanation
Indices: 250371--250410 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
250361 AAATATACAT
250371 ATAAATAAAATACATAA-A
1 ATAAATAAAATA-ATAACA
*
250389 ATAAATAAGATAATAACA
1 ATAAATAAAATAATAACA
250407 ATAA
1 ATAA
250411 TAATGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAAATAAAATAATAACA
Found at i:250454 original size:14 final size:13
Alignment explanation
Indices: 250437--250515 Score: 54
Period size: 13 Copynumber: 5.7 Consensus size: 13
250427 AAAAAAAAGG
*
250437 ATAAAATGAAATTT
1 ATAAAAT-AAATAT
250451 ATAAAATAAATAT
1 ATAAAATAAATAT
*
250464 ATAACATATAATAAT
1 ATAAAATA-AAT-AT
*
250479 AGTAATAAAAATATAT
1 A-TAA-AATAA-ATAT
250495 ATAAAAT-AATA-
1 ATAAAATAAATAT
250506 ATAATAATAA
1 ATAA-AATAA
250516 GGTAAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
11 4 0.08
12 6 0.11
13 14 0.26
14 12 0.23
15 6 0.11
16 7 0.13
17 4 0.08
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (13 bp):
ATAAAATAAATAT
Found at i:250479 original size:3 final size:3
Alignment explanation
Indices: 250471--250536 Score: 57
Period size: 3 Copynumber: 22.0 Consensus size: 3
250461 TATATAACAT
* *
250471 ATA ATA ATA GTA ATA AAA AT- ATA TATA A-A ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
*
250515 AGGTA A-A ATA ATA ATA AAA ATA
1 A--TA ATA ATA ATA ATA ATA ATA
250537 TAGTGAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 6 0.12
3 39 0.76
4 3 0.06
5 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:250503 original size:29 final size:32
Alignment explanation
Indices: 250451--250515 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 32
250441 AATGAAATTT
*
250451 ATAAAATAAATATATAACATATAATAATAGTA
1 ATAAAATAAATATATAACATATAATAATAATA
*
250483 ATAAAA-ATATATATAA-A-ATAATAATAATA
1 ATAAAATAAATATATAACATATAATAATAATA
250512 ATAA
1 ATAA
250516 GGTAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 15 0.48
30 1 0.03
31 9 0.29
32 6 0.19
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (32 bp):
ATAAAATAAATATATAACATATAATAATAATA
Found at i:250507 original size:32 final size:32
Alignment explanation
Indices: 250451--250607 Score: 92
Period size: 34 Copynumber: 4.8 Consensus size: 32
250441 AATGAAATTT
*
250451 ATAAAATAAATATATAACATATAATAATAGTA
1 ATAAAATAAATATATAAAATATAATAATAGTA
* *
250483 ATAAAA-ATATATATAAAATAATAATAATAATA
1 ATAAAATAAATATATAAAAT-ATAATAATAGTA
* **
250515 AGGTAAAAT-AATA-ATAAAAATATAGTGAA-AAAA
1 A--TAAAATAAATATAT-AAAATATAAT-AATAGTA
* **
250548 ATAAAAATAAAAGATAGTATGATATAATAATAGTA
1 AT-AAAAT-AAATATA-TAAAATATAATAATAGTA
* *
250583 AAAAAATGAAA-ATAGAAAA-ATAATA
1 ATAAAAT-AAATATATAAAATATAATA
250608 GAAAAACTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
31 18 0.19
32 25 0.26
33 13 0.14
34 28 0.29
35 11 0.11
36 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (32 bp):
ATAAAATAAATATATAAAATATAATAATAGTA
Found at i:250820 original size:2 final size:2
Alignment explanation
Indices: 250813--250851 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
250803 GAAAATAATA
* *
250813 AT AT AT AT AT AT AT AT AT AT AT AT TT AA AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250852 TTGAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:254030 original size:8 final size:7
Alignment explanation
Indices: 254012--254060 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
254002 CCCACTTTAT
254012 TTTTTTC
1 TTTTTTC
*
254019 TTTTCTC
1 TTTTTTC
254026 TTTTTTC
1 TTTTTTC
*
254033 CTTTTTC
1 TTTTTTC
254040 TTTTGTTC
1 TTTT-TTC
254048 TTTTGTTC
1 TTTT-TTC
254056 TTTTT
1 TTTTT
254061 ATTTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
7 22 0.59
8 15 0.41
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:254065 original size:22 final size:22
Alignment explanation
Indices: 254024--254065 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
254014 TTTTCTTTTC
*
254024 TCTTTTTTCCTTTTTCTTTTGT
1 TCTTTTTTCCTTTTTATTTTGT
254046 TCTTTTGTT-CTTTTTATTTT
1 TCTTTT-TTCCTTTTTATTTT
254066 TTTTTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (22 bp):
TCTTTTTTCCTTTTTATTTTGT
Found at i:264537 original size:30 final size:32
Alignment explanation
Indices: 264491--264550 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 32
264481 AAATTTACAA
264491 AATAATAAATATATATAACAT-ATAATAATAGT
1 AATAATAAATATATATAA-ATAATAATAATAGT
264523 AATAA-AAA-ATATATAAATAATAATAATA
1 AATAATAAATATATATAAATAATAATAATA
264551 ATAAAGGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 2 0.07
30 17 0.63
31 3 0.11
32 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (32 bp):
AATAATAAATATATATAAATAATAATAATAGT
Found at i:264619 original size:23 final size:24
Alignment explanation
Indices: 264537--264605 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
264527 AAAAATATAT
*
264537 AAATAATAATAATAATAAAG-GCAAA
1 AAATAATAATAA-AATATAGTG-AAA
264562 AGAATAATAA-AAAATATAGTGAAA
1 A-AATAATAATAAAATATAGTGAAA
*
264586 AAATAAAAATAAAATATAGT
1 AAATAATAATAAAATATAGT
264606 ATGATATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.18
24 20 0.51
25 4 0.10
26 8 0.21
ACGTcount: A:0.68, C:0.01, G:0.09, T:0.22
Consensus pattern (24 bp):
AAATAATAATAAAATATAGTGAAA
Found at i:267483 original size:5 final size:5
Alignment explanation
Indices: 267473--267503 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
267463 AGATAATAAT
*
267473 ATTTA ATTTA ATTTA ATTTA ATTTA AATTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA A
267504 CAGGAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTTA
Found at i:268673 original size:2 final size:2
Alignment explanation
Indices: 268666--268690 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
268656 ATAGCCCATC
268666 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
268691 GTTCGGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:271084 original size:23 final size:23
Alignment explanation
Indices: 271054--271109 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
271044 GACATATGGT
271054 TGATTCCCTTCCATCAAATGTGC
1 TGATTCCCTTCCATCAAATGTGC
*
271077 TGATTCCCTTCTATCAAATGTGC
1 TGATTCCCTTCCATCAAATGTGC
*
271100 TCATTACCCT
1 TGATT-CCCT
271110 CACCTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.38
Consensus pattern (23 bp):
TGATTCCCTTCCATCAAATGTGC
Found at i:275994 original size:3 final size:3
Alignment explanation
Indices: 275986--276029 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
275976 TCCAGAGAAC
* * *
275986 TCT TCT TCT TCT TCT TCT TCT TTT TCT TTT TCT TAT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
276030 CAGTCGTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:285589 original size:30 final size:30
Alignment explanation
Indices: 285553--285618 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
285543 AGTGAACCGA
* *
285553 CGGTTCAAACCGGTTTTGCCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTCCCAGTTTTCAGC
** *
285583 CGGTTCACCCCGGTTTTCCCAGTTTTCAGG
1 CGGTTCAAACCGGTTTTCCCAGTTTTCAGC
285613 CGGTTC
1 CGGTTC
285619 TTCTGGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.11, C:0.30, G:0.26, T:0.33
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTCCCAGTTTTCAGC
Found at i:287029 original size:24 final size:27
Alignment explanation
Indices: 286979--287029 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
286969 TTTAAAAAAA
* *
286979 ATTATATAAAAAATACTTAAACTTATT
1 ATTATATAAAAAATACTCAAACATATT
287006 ATTAT-TAAAAAA-ACTCAAA-ATATT
1 ATTATATAAAAAATACTCAAACATATT
287030 TTTAAAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 6 0.27
26 7 0.32
27 5 0.23
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTATATAAAAAATACTCAAACATATT
Found at i:287056 original size:19 final size:19
Alignment explanation
Indices: 287014--287056 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
287004 TTATTATTAA
* * *
287014 AAAAACTCAAAATATTTTT
1 AAAATCTCAAAAAATTCTT
287033 AAAATCTCAAAAAATTCTT
1 AAAATCTCAAAAAATTCTT
287052 AAAAT
1 AAAAT
287057 ATATAATCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATCTCAAAAAATTCTT
Found at i:289464 original size:17 final size:17
Alignment explanation
Indices: 289430--289462 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
289420 TTAATTATAA
289430 ATTATATAATTATATTT
1 ATTATATAATTATATTT
*
289447 ATTATTTAA-TATATTT
1 ATTATATAATTATATTT
289463 TACCTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATAATTATATTT
Found at i:289669 original size:18 final size:18
Alignment explanation
Indices: 289646--289682 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
289636 CCGGTTCTTC
289646 CGACCGGTCGAACCGATT
1 CGACCGGTCGAACCGATT
* *
289664 CGACCGGTTGAATCGATT
1 CGACCGGTCGAACCGATT
289682 C
1 C
289683 AATCGGTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.22
Consensus pattern (18 bp):
CGACCGGTCGAACCGATT
Found at i:297968 original size:16 final size:16
Alignment explanation
Indices: 297947--297985 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
297937 AATTAATGAT
297947 TATTATTAATTAAAAA
1 TATTATTAATTAAAAA
297963 TATTA-TAA-TAAAAA
1 TATTATTAATTAAAAA
297977 TATT-TTAAT
1 TATTATTAAT
297986 ACTTTTATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 13 0.62
15 3 0.14
16 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTATTAATTAAAAA
Found at i:306800 original size:13 final size:13
Alignment explanation
Indices: 306782--306809 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
306772 TTTTTAAGTG
306782 TTTAAATATAAAT
1 TTTAAATATAAAT
306795 TTTAAATATAAAT
1 TTTAAATATAAAT
306808 TT
1 TT
306810 ACGAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAATATAAAT
Found at i:307349 original size:12 final size:13
Alignment explanation
Indices: 307332--307360 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
307322 CTTAATTACA
307332 AAAATTAAAA-TT
1 AAAATTAAAATTT
307344 AAAATTAAAATTT
1 AAAATTAAAATTT
307357 AAAA
1 AAAA
307361 ATTCGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:309701 original size:46 final size:44
Alignment explanation
Indices: 309649--309748 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
309639 TTTCGCTGTA
* * *
309649 AAGTTGAAATCCAATGTTGTTTGTGAG-CACGATATCCTTCGTCGTG
1 AAGTTGAAAT-CAATGATGTTT-CGAGTC-CAATATCCTTCGTCGTG
**
309695 AAGTTGAAATCGTTGATGTTTCGAGTCCAATATCCTTCGTCGTG
1 AAGTTGAAATCAATGATGTTTCGAGTCCAATATCCTTCGTCGTG
309739 AAGTTGAAAT
1 AAGTTGAAAT
309749 TGGCTCTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 29 0.60
45 9 0.19
46 10 0.21
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (44 bp):
AAGTTGAAATCAATGATGTTTCGAGTCCAATATCCTTCGTCGTG
Found at i:309734 original size:170 final size:169
Alignment explanation
Indices: 309354--309833 Score: 906
Period size: 170 Copynumber: 2.8 Consensus size: 169
309344 TTGTTTGTGA
*
309354 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
*
309419 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTCGCTGTAAAGTT
66 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTCGCTGTAAAGTT
309484 GAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
131 GAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
309523 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
*
309588 ATGAAACTGGGAAGCCCCTTCGTTGTGGAGTTGAGCTTTGAATTGGATATCTTTCGCTGTAAAGT
66 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATC-TTCGCTGTAAAGT
309653 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
130 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
*
309693 TGAAGTTGAAATCGTTGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
309758 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
66 ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATAT-CTTCGCTGTAAAGT
309823 TGAAATCCAAT
130 TGAAATCCAAT
309834 CTTCAGTAAA
Statistics
Matches: 304, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
169 113 0.37
170 190 0.62
171 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (169 bp):
TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
ATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCTTCGCTGTAAAGTT
GAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
Found at i:310717 original size:9 final size:10
Alignment explanation
Indices: 310702--310728 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
310692 AACATTTTTC
310702 TCTTTTTTGT
1 TCTTTTTTGT
310712 TCTTTTTTGT
1 TCTTTTTTGT
310722 TCTTTTT
1 TCTTTTT
310729 CTTTTTCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (10 bp):
TCTTTTTTGT
Found at i:317478 original size:39 final size:39
Alignment explanation
Indices: 317424--317503 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
317414 TTAACAGTAG
* *
317424 ATGCAGCTTTCCCTTTTGTAGAGGATGAGTCAC-CGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTC-CTCGGGTA
*
317463 ATGCAACTTTCCCTTTAGTAGCGGATGAGTCCTCGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
317502 AT
1 AT
317504 ACTCCGGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (39 bp):
ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
Found at i:320950 original size:12 final size:13
Alignment explanation
Indices: 320933--320961 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
320923 CTTAATTACA
320933 AAAATTAAAA-TT
1 AAAATTAAAATTT
320945 AAAATTAAAATTT
1 AAAATTAAAATTT
320958 AAAA
1 AAAA
320962 ATTTGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:326171 original size:3 final size:3
Alignment explanation
Indices: 326163--326188 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
326153 GAAAAATGCA
326163 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
326189 CACAACCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:326505 original size:44 final size:44
Alignment explanation
Indices: 326455--326540 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
326445 GTTGTGGAAA
* * * *
326455 AAATGATTGTCTTGTGTAGAGTCTCGTCGGAATTACATTTTGGT
1 AAATGATTGGCTCGTATAGAGTCTCATCGGAATTACATTTTGGT
* *
326499 AAATGATTGGCTCGTATAGGGTCTCATCGGAATTACTTTTTG
1 AAATGATTGGCTCGTATAGAGTCTCATCGGAATTACATTTTG
326541 ATTTAATGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (44 bp):
AAATGATTGGCTCGTATAGAGTCTCATCGGAATTACATTTTGGT
Found at i:327093 original size:15 final size:15
Alignment explanation
Indices: 327081--327110 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
327071 TTTGAAAATT
327081 TTATTTTTAAAAAAAA
1 TTATTTTT-AAAAAAA
327097 TTATTTTTAAAAAA
1 TTATTTTTAAAAAA
327111 CCCTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATTTTTAAAAAAA
Found at i:327379 original size:20 final size:19
Alignment explanation
Indices: 327328--327380 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
327318 TTTGGTTCAC
*
327328 GGAATGTAGATTACCAATG
1 GGAATGTAGATTACCAATA
*
327347 GGAATGTAGATTACCAGTA
1 GGAATGTAGATTACCAATA
327366 GGAATGTAAGATTAC
1 GGAATGT-AGATTAC
327381 TAGGGAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.26
Consensus pattern (19 bp):
GGAATGTAGATTACCAATA
Found at i:329912 original size:6 final size:6
Alignment explanation
Indices: 329901--329926 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
329891 ATGACAATGC
329901 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
329927 TTTATTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:332258 original size:95 final size:94
Alignment explanation
Indices: 332129--332384 Score: 327
Period size: 95 Copynumber: 2.7 Consensus size: 94
332119 TATAATATTA
* * *
332129 TATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACACCCCAACTTTATGGA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGA
* *
332194 TAAGAGTCAGCTAGCCTGATAAAGGTGAT
66 TAAGAGTCAGCTAGCATGATAAAGGTAAT
* * * *
332223 TATACTATACAATAAAGCTTGAGTTGCCCCCCTAAAGCAATTGGTTAAACGCCCTGGCTTTATGG
1 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
** * *
332288 ATATTATTCAGCTAGCATGATAAATGTAAT
65 ATAAGAGTCAGCTAGCATGATAAAGGTAAT
* *
332318 TATATTTATACAATAATA--TTGAGTAGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
1 TATA--TATACAATAA-AGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTAT
332381 GGAT
63 GGAT
332385 TTAGCTAGCC
Statistics
Matches: 139, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
94 4 0.03
95 124 0.89
96 10 0.07
97 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGA
TAAGAGTCAGCTAGCATGATAAAGGTAAT
Found at i:333688 original size:84 final size:84
Alignment explanation
Indices: 333497--334005 Score: 452
Period size: 84 Copynumber: 6.2 Consensus size: 84
333487 TAAACAAACT
* * * * *
333497 ATTTGCAGCATAGCTTAAGTCAAGAAGGGATAT-C-T-ACC-AAAGACCCTCGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
* *
333558 CTCAGCTTTGAGGGCACATC
66 CTCAGCTCT-AAGGCACATC
* * *
333578 ATTTACAGCATAACTCAAGGT-TAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAA-GTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTAC
* *
333642 GCTCAGCTCTAAGACATATC
65 GCTCAGCTCTAAGGCACATC
** * ** *
333662 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCCAATAAAAGACCTTCGAGTTCGACTATG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
* *
333727 CTCAACTCCAAGGCACATC
66 CTCAGCTCTAAGGCACATC
** * * * *
333746 ATTTGCAGCATAGTTTAAGTCGAGAAGGGCTAT--AT-GCC-AAAGACCCTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
* * *
333807 CTTAGCTTCGAGGGCACATC
66 CTCAGC-TCTAAGGCACATC
* * * * * *
333827 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
*
333892 CTCAGCTCTAAGGCATATC
66 CTCAGCTCTAAGGCACATC
* * * * * * * * *
333911 A-TTGTAGTATAGCTTAAGTCGAGAAGGGCTAT-C-T-GCC-AAAGGCTTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
* *
333971 CTCAGCTCCGAGGGCACATC
66 CTCAGCT-CTAAGGCACATC
*
333991 ATTTACAGCATAACT
1 ATTTGCAGCATAACT
334006 CAAGGCTAGA
Statistics
Matches: 340, Mismatches: 75, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
79 26 0.08
80 37 0.11
81 71 0.21
82 3 0.01
83 26 0.08
84 121 0.36
85 56 0.16
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCCGTCACCAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCTAAGGCACATC
Found at i:333950 original size:164 final size:165
Alignment explanation
Indices: 333620--334017 Score: 530
Period size: 164 Copynumber: 2.4 Consensus size: 165
333610 TCCGTCACCA
* * * * * * * *
333620 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGACATATCATTTGCAGCATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
* *
333684 AGAAGGGTTATATGCCAATAAAAGACCTTCGAGTTCGACTATGCTCAACTCCAAGGCACATCATT
66 AGAAGGGTTATATGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATT
*
333749 TGCAGCATAGTTTAAGTCGAGAAGGGCTATATGCC
131 TGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCC
* * *
333784 AAAGACCCTCGAGTTCGACTACGCTTAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
* * * * * *
333849 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATCA-T
66 AGAAGGGTTATATGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATT
* * *
333913 TGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
131 TGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCC
* * * * *
333948 AAAGGCTTTCGAGTTCGATTACACTCAGCTCCGAGGGCACATCATTTACAGCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
334013 AGAAG
66 AGAAG
334018 AATTATCTAT
Statistics
Matches: 202, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
164 121 0.60
165 81 0.40
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (165 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
AGAAGGGTTATATGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATT
TGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCC
Found at i:334088 original size:36 final size:36
Alignment explanation
Indices: 334048--334310 Score: 240
Period size: 36 Copynumber: 7.4 Consensus size: 36
334038 CTTTGAGATT
* *
334048 GTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
334084 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
334120 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATTTA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA--CA
* * * *
334150 -TTTCCCTTAAAACAAAATTTAT-TTTCCCTTAAGACA
1 GTTTCCCTTGAAAC-AAATTT-TGTCTCTCTTGAGACA
** *
334186 GTTTCTTTTGAAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
* *
334223 GTTTCTCTTGAAACAAATTTTGCCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
334259 TTTTCCCTTGAGACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
334296 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
334311 CCAATCTTTG
Statistics
Matches: 183, Mismatches: 30, Indels: 27
0.76 0.12 0.11
Matches are distributed among these distances:
28 1 0.01
29 16 0.09
30 6 0.03
36 87 0.48
37 72 0.39
38 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:334234 original size:37 final size:36
Alignment explanation
Indices: 334181--334310 Score: 188
Period size: 37 Copynumber: 3.6 Consensus size: 36
334171 TTTTCCCTTA
*
334181 AGACAGTTTCTTTTGAAACTAAGTTTTGTCTCTCTTG
1 AGACAGTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTG
* *
334218 AGACAGTTTCTCTTGAAACAAATTTTGCCTCTCTTG
1 AGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTG
* * *
334254 AGACATTTTCCCTTGAGACAAAGTTTTGTCTCTCTTG
1 AGACAGTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTG
334291 AGACAGTTTCTCTTGAAACA
1 AGACAGTTTCTCTTGAAACA
334311 CCAATCTTTG
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
36 32 0.40
37 49 0.60
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
AGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTG
Found at i:334428 original size:37 final size:36
Alignment explanation
Indices: 334363--334493 Score: 199
Period size: 37 Copynumber: 3.6 Consensus size: 36
334353 CTCTAAGACA
334363 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
* *
334399 GTTTATCTTGAAACACCAAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACA-CAAAAAAAAACCTTTGAAAAT
334436 GTTTCTCTTGAAACACAAAAAAAAACCCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAA-CCTTTGAAAAT
* *
334473 ATTTCTCTTTGAAACCCAAAA
1 GTTTCTC-TTGAAACACAAAA
334494 GACCTTCGAG
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
36 24 0.28
37 50 0.58
38 12 0.14
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (36 bp):
GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
Found at i:338527 original size:19 final size:19
Alignment explanation
Indices: 338503--338553 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
338493 ACCAACAAAA
338503 TCGCAATGCGATCGCTAAT
1 TCGCAATGCGATCGCTAAT
338522 TCGCAATGCGATCGCTAAT
1 TCGCAATGCGATCGCTAAT
*
338541 TCGCAACGCGATC
1 TCGCAATGCGATC
338554 TCCATTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGATCGCTAAT
Found at i:338669 original size:20 final size:20
Alignment explanation
Indices: 338644--338736 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
338634 TTTTCCCAAT
338644 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
338664 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
*
338684 TTCGCAATACGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
338705 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
338726 TCGCAATGCGA
1 TCGCAATGCGA
338737 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:338686 original size:41 final size:41
Alignment explanation
Indices: 338641--338736 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
338631 CGATTTTCCC
338641 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
338682 AATTCGCAATACGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
338723 AAATCGCAATGCGA
1 AATTCGCAATGCGA
338737 TACTGACTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:338690 original size:21 final size:20
Alignment explanation
Indices: 338644--338736 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
338634 TTTTCCCAAT
*
338644 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
338664 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
* *
338684 TTCGCAATACGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
338705 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
338726 TCGCAATGCGA
1 TCGCAATGCGA
338737 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:338749 original size:41 final size:41
Alignment explanation
Indices: 338663--338797 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 41
338653 GAATAAGTAA
* * * *
338663 ATCGCAACGCGAATTGGGAAATTCGCAATACGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
338704 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
338745 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
338786 TTCGCAACGCGA
1 ATCGCAACGCGA
338798 TACTGACTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 72 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:338750 original size:20 final size:20
Alignment explanation
Indices: 338725--338819 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
338715 AATTGGGAAA
*
338725 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
338745 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
338766 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
338786 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
338806 TTCGCAACGCGATA
1 ATCGCAACGCGATA
338820 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:339034 original size:22 final size:22
Alignment explanation
Indices: 339006--339049 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
338996 CACTCTCTCA
339006 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
339028 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
339050 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:339335 original size:20 final size:20
Alignment explanation
Indices: 339310--339347 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
339300 CGATTCTCTC
339310 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
339330 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
339348 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:340679 original size:18 final size:18
Alignment explanation
Indices: 340653--340697 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
340643 TCCACTTCGG
*
340653 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
340671 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
340689 GAGCCATCA
1 GAGCCATCA
340698 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:341126 original size:14 final size:13
Alignment explanation
Indices: 341106--341151 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
341096 TGCGAAATGA
341106 AAATCGCAACGAG
1 AAATCGCAACGAG
*
341119 AGAATCGCAA--TG
1 A-AATCGCAACGAG
341131 AAATCGCAACGAG
1 AAATCGCAACGAG
341144 -AATCGCAA
1 AAATCGCAA
341152 TGCGAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
11 8 0.29
12 10 0.36
13 2 0.07
14 8 0.29
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (13 bp):
AAATCGCAACGAG
Found at i:341137 original size:11 final size:12
Alignment explanation
Indices: 341118--341153 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
341108 ATCGCAACGA
341118 GAGAATCGCAAT
1 GAGAATCGCAAT
*
341130 GA-AATCGCAAC
1 GAGAATCGCAAT
341141 GAGAATCGCAAT
1 GAGAATCGCAAT
341153 G
1 G
341154 CGAAATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (12 bp):
GAGAATCGCAAT
Found at i:341148 original size:23 final size:25
Alignment explanation
Indices: 341101--341153 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
341091 CGCAATGCGA
341101 AATGAAAATCGCAACGAGAGAATCGC
1 AATGAAAATCGCAAC-AGAGAATCGC
341127 AATG-AAATCGCAAC-GAGAATCGC
1 AATGAAAATCGCAACAGAGAATCGC
341150 AATG
1 AATG
341154 CGAAATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 13 0.48
25 10 0.37
26 4 0.15
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (25 bp):
AATGAAAATCGCAACAGAGAATCGC
Found at i:341317 original size:14 final size:14
Alignment explanation
Indices: 341298--341334 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
341288 CATCAATTAA
341298 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
341312 ACAAATCACCTTTT
1 ACAAATCAACTTTT
341326 ACAAATCAA
1 ACAAATCAA
341335 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:342745 original size:21 final size:21
Alignment explanation
Indices: 342679--342745 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
342669 TGTGAATCGG
*
342679 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
342699 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
342721 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
342742 CTCT
1 CTCT
342746 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:342783 original size:40 final size:40
Alignment explanation
Indices: 342718--342795 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
342708 CGATGACAGT
* * *
342718 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGAGG
* * *
342758 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
342796 TAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.22, C:0.18, G:0.40, T:0.21
Consensus pattern (40 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGAGG
Done.