Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004171.1 Hibiscus syriacus cultivar Beakdansim tig00009126_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: 96570
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1217 original size:27 final size:27
Alignment explanation
Indices: 1170--1222 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1160 ATCAATTTTA
1170 TGAAAAATATAAATTTAAGAAGTAAAT
1 TGAAAAATATAAATTTAAGAAGTAAAT
1197 TGAACAAATATGAAA-TT-AGAAGTAAA
1 TGAA-AAATAT-AAATTTAAGAAGTAAA
1223 AATTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 8 0.33
29 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.26
Consensus pattern (27 bp):
TGAAAAATATAAATTTAAGAAGTAAAT
Found at i:1554 original size:2 final size:2
Alignment explanation
Indices: 1547--2161 Score: 133
Period size: 2 Copynumber: 308.5 Consensus size: 2
1537 AAATATTGAA
* *
1547 AT AT AT AT AA ACT AT AT AGT TT AT AT AT A- ACT AT AT AT A- AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* * * * * * *
1588 -T AT AT AT AT AA ACT AG AT AG AG AA ACT AT AT AGT TT AT AT TT
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT AT AT AT
* *
1630 AT AT -T AT -T AT AT ACT AT AT AT AA ACT AT AT AT AT -T AT GT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
1671 A- ACT AT AT ACT AT AT AA ACT AT AT AT AT AT GT AT AA ACT AT AT
1 AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT
* * * * *
1714 ACC AT GT AT A- ACT AT AG AGT TT AT AT AT GA- AT -T AT AT AT AA
1 A-T AT AT AT AT A-T AT AT A-T AT AT AT AT -AT AT AT AT AT AT AT
* * * * *
1755 AC A- AT AT AGT TT AT -T A- AT AT AA AT -T AT AT AGT TT AT AC AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
1795 AT AT AT AT AT AA AT -T AT AT AT A- AT A- AT TT A- AT AT AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* * * *
1834 CT -T AT AT TT AT AT AT -T AT GT AT A- AT -T AT AT ACT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
1873 AA AT -T AT AT AGT TT AT AT AGT -T AA AT AT AA AGT AT AT A- AGT
1 AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT A-T AT AT AT A-T
* * *
1914 AT AT AT AT -T AA ACT AT A- AT TT AT AT AT -T AT AT AT AT AA AGT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
1955 -T TT AGT AT AA ACT AT AC AT AT AT AT AT A- AGT AT A- AT AT AT
1 AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
1995 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AA AGT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * * * *
2035 AA AG ACT A- AA AT AT AT A- AGT AT AT A- AT AT AA AT AT CT AT AA
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * *
2076 ACT AT AT AT AA AT A- AA AGT AT AT AT ACT AT AA AGT AT A- AGT AT
1 A-T AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT A-T AT AT A-T AT
*
2119 AT AT AT A- ACT AT AA AGT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
2161 A
1 A
2162 AAAGTATAAT
Statistics
Matches: 441, Mismatches: 92, Indels: 160
0.64 0.13 0.23
Matches are distributed among these distances:
1 41 0.09
2 357 0.81
3 43 0.10
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1649 original size:9 final size:9
Alignment explanation
Indices: 1637--1697 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
1627 TTTATATTAT
1637 TATATACTA
1 TATATACTA
1646 TATATAAACTA
1 TATAT--ACTA
*
1657 TATATATTA
1 TATATACTA
*
1666 TGTATA--A
1 TATATACTA
1673 CTATATACTA
1 -TATATACTA
*
1683 TATAAACTA
1 TATATACTA
1692 TATATA
1 TATATA
1698 TATGTATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
7 1 0.02
8 5 0.12
9 26 0.62
10 1 0.02
11 9 0.21
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (9 bp):
TATATACTA
Found at i:1679 original size:17 final size:17
Alignment explanation
Indices: 1637--1729 Score: 89
Period size: 17 Copynumber: 5.2 Consensus size: 17
1627 TTTATATTAT
*
1637 TATATACTATATATAAAC
1 TATATACTATGTAT-AAC
*
1655 TATATATATTATGTATAAC
1 --TATATACTATGTATAAC
*
1674 TATATACTATATA-AAC
1 TATATACTATGTATAAC
*
1690 TATATATATATGTATAAAC
1 TATATA-CTATGTAT-AAC
*
1709 TATATACCATGTATAAC
1 TATATACTATGTATAAC
1726 TATA
1 TATA
1730 GAGTTTATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
16 9 0.15
17 23 0.37
18 6 0.10
19 12 0.19
20 12 0.19
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (17 bp):
TATATACTATGTATAAC
Found at i:1683 original size:37 final size:36
Alignment explanation
Indices: 1637--1729 Score: 129
Period size: 35 Copynumber: 2.6 Consensus size: 36
1627 TTTATATTAT
1637 TATATACTATATATAAACTATATATATTATGTAT-AAC
1 TATATAC-ATATATAAACTATATATA-TATGTATAAAC
1674 TATATAC-TATATAAACTATATATATATGTATAAAC
1 TATATACATATATAAACTATATATATATGTATAAAC
*
1709 TATATACCATGTAT-AACTATA
1 TATATA-CATATATAAACTATA
1730 GAGTTTATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
34 7 0.13
35 26 0.50
36 8 0.15
37 11 0.21
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (36 bp):
TATATACATATATAAACTATATATATATGTATAAAC
Found at i:1891 original size:18 final size:18
Alignment explanation
Indices: 1841--1882 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1831 CATCTTATAT
* *
1841 TTATATATTATGTAT-AA
1 TTATATACTATATATAAA
*
1858 TTATATACTATGTATAAA
1 TTATATACTATATATAAA
1876 TTATATA
1 TTATATA
1883 GTTTATATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (18 bp):
TTATATACTATATATAAA
Found at i:2119 original size:20 final size:19
Alignment explanation
Indices: 1897--2390 Score: 120
Period size: 22 Copynumber: 24.6 Consensus size: 19
1887 ATATAGTTAA
1897 ATATAAAGTATATAAGTATAT
1 ATATAAAG--TATAAGTATAT
* *
1918 ATATTAAACTATAATTTATAT
1 ATA-TAAAGTATAA-GTATAT
* *
1939 ATTATATA-TATAAAGT-TTT
1 A-TATAAAGTAT-AAGTATAT
*
1958 AGTATAAACTATACA-TATAT
1 A-TATAAAGTATA-AGTATAT
1978 ATAT-AAGTATAA-TATATT
1 ATATAAAGTATAAGTATA-T
*
1996 ATATATATA-TATATATATATAT
1 ATATA-A-AGTATA-A-GTATAT
* *
2018 ATATAAAGTATAATTATAA
1 ATATAAAGTATAAGTATAT
* *
2037 AGACTAAAATATATAAGTATAT
1 ATA-T-AAA-GTATAAGTATAT
*
2059 AATATAAA-TATCTATA-AACTAT
1 -ATATAAAGTA--TA-AGTA-TAT
*
2081 ATATAAA-TAAAAGTATATAT
1 ATATAAAGTATAAG--TATAT
2101 ACTATAAAGTATAAGTATAT
1 A-TATAAAGTATAAGTATAT
*
2121 ATAT-AACTATAAAGTATAT
1 ATATAAAGTAT-AAGTATAT
*
2140 A-ATATA-TATATA-TATAT
1 ATATAAAGTATA-AGTATAT
* *
2157 ATATAAAAGTATAATTATAA
1 ATAT-AAAGTATAAGTATAT
*
2177 AGACTAAAGTATATAAGTATA-
1 ATA-TAAAG--TATAAGTATAT
2198 ATATAAAGTATACA-TATAAAGT
1 ATATAAAGTATA-AGTAT--A-T
*
2220 ATATATAAGTTATAAGTATTAA
1 ATATA-AAG-TATAAGTA-TAT
* * *
2242 AGTATATATTATAAAGTATTAC
1 A-TATAAAGTAT-AAGTA-TAT
*
2264 ACTATATAA-TA-AAGTATTAA
1 A-TATA-AAGTATAAGTA-TAT
*
2284 ATATAAAGTATTAAAGTATACC
1 ATATAAAGTA-T-AAGTATA-T
2306 ATATAAAGTATTAAAGTATAT
1 ATATAAAGTA-T-AAGTATAT
*
2327 AAATAAA-TAT---TA-A-
1 ATATAAAGTATAAGTATAT
2340 ATATAAAGTATATA-TATAT
1 ATATAAAGTATA-AGTATAT
*
2359 AATATAAAGTATTAACTATAT
1 -ATATAAAGTA-TAAGTATAT
2380 A-ATATAAGTAT
1 ATATA-AAGTAT
2391 TAAAGTATAA
Statistics
Matches: 370, Mismatches: 38, Indels: 132
0.69 0.07 0.24
Matches are distributed among these distances:
13 6 0.02
14 4 0.01
15 2 0.01
17 14 0.04
18 35 0.09
19 50 0.14
20 82 0.22
21 67 0.18
22 87 0.24
23 16 0.04
24 6 0.02
25 1 0.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (19 bp):
ATATAAAGTATAAGTATAT
Found at i:2176 original size:62 final size:60
Alignment explanation
Indices: 1897--2176 Score: 160
Period size: 58 Copynumber: 4.7 Consensus size: 60
1887 ATATAGTTAA
*
1897 ATATAA-AGTATATA-AGTATATATATTAAACTATAATT-TATA-TAT-TATATATATAAAGT
1 ATATAATA-TATATATA-TATATATATAAAACTATAATTATA-AGTATATATATATATAAAGT
* * * * * * * *
1955 -TTTAGTATAAACTATACATATATATATAAGTATAA-TAT-ATTATATATATATATATA-T
1 ATATAATATATA-TATATATATATATAAAACTATAATTATAAGTATATATATATATAAAGT
* *
2012 ATAT-ATATATAAAGTATA-AT-TATAAAGACTAAAATATATAAGTATATA-ATATA-AATA-T
1 ATATAATATATATA-TATATATATATAAA-ACTATAAT-TATAAGTATATATATATATAA-AGT
* * * * *
2070 CTATAA-ACTATATATAAATAAAAGTATATATACTATAAAGTATAAGTATATATATAACTATAAA
1 ATATAATA-TATATATATAT-ATA-TATA-AAACTAT-AATTATAAGTATATATAT-A-TATAAA
2134 GT
59 GT
*
2136 ATATAATATATATATATATATATATAAAAGTATAATTATAA
1 ATATAATATATATATATATATATATAAAACTATAATTATAA
2177 AGACTAAAGT
Statistics
Matches: 164, Mismatches: 31, Indels: 50
0.67 0.13 0.20
Matches are distributed among these distances:
55 5 0.03
56 9 0.05
57 20 0.12
58 49 0.30
59 14 0.09
60 1 0.01
62 27 0.16
63 10 0.06
64 5 0.03
65 5 0.03
66 18 0.11
67 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (60 bp):
ATATAATATATATATATATATATATAAAACTATAATTATAAGTATATATATATATAAAGT
Found at i:2203 original size:11 final size:12
Alignment explanation
Indices: 1941--2400 Score: 117
Period size: 13 Copynumber: 37.4 Consensus size: 12
1931 ATTTATATAT
1941 TATATATATAAAG
1 TATA-ATATAAAG
* * *
1954 TTTTAGTATAAAC
1 -TATAATATAAAG
*
1967 TATACATATATA-
1 TATA-ATATAAAG
1979 TATAAGTAT-AA-
1 TATAA-TATAAAG
* *
1990 TATATTATATA-
1 TATAATATAAAG
*
2001 TATATATATATA-
1 TATA-ATATAAAG
2013 TATATATATAAAG
1 TATA-ATATAAAG
2026 TATAATTATAAAG
1 TATAA-TATAAAG
*
2039 ACTAAAATATATAAG
1 --TATAATATA-AAG
2054 TATATAATATAAA-
1 --TATAATATAAAG
* *
2067 TAT-CTATAAAC
1 TATAATATAAAG
2078 TAT-ATATAAA-
1 TATAATATAAAG
*
2088 TA-AA-AGTATA-
1 TATAATA-TAAAG
*
2098 TATACTATAAAG
1 TATAATATAAAG
*
2110 TATAAGTATATA-
1 TATAA-TATAAAG
2122 TATAACTATAAAG
1 TATAA-TATAAAG
*
2135 TAT-ATA-ATA-
1 TATAATATAAAG
*
2144 TAT-ATATATA-
1 TATAATATAAAG
2154 TAT-ATATAAAAG
1 TATAATAT-AAAG
2166 TATAATTATAAAG
1 TATAA-TATAAAG
2179 -ACTAAAGTATATAAG
1 TA-T-AA-TATA-AAG
2194 TATAATATAAAG
1 TATAATATAAAG
2206 TATACATATAAAG
1 TATA-ATATAAAG
2219 TAT-ATAT-AAG
1 TATAATATAAAG
2229 TTATAAGTATTAAAG
1 -TATAA-TA-TAAAG
2244 TATATATTATAAAG
1 TATA-A-TATAAAG
2258 TATTACACTATATAA-
1 TA-TA-A-TATA-AAG
2273 TA-AAGTATTAAA-
1 TATAA-TA-TAAAG
2285 TATAAAGTATTAAAG
1 TAT-AA-TA-TAAAG
2300 TATACCATATAAAG
1 TATA--ATATAAAG
2314 --T-AT-TAAAG
1 TATAATATAAAG
*
2322 TATATAAATAAA-
1 TATA-ATATAAAG
2334 TATTAAATATAAAG
1 TA-T-AATATAAAG
2348 TAT-ATAT--A-
1 TATAATATAAAG
2356 TATAATATAAAG
1 TATAATATAAAG
2368 TATTAACTATATAA-
1 TA-TAA-TATA-AAG
2382 TATAAGTATTAAAG
1 TATAA-TA-TAAAG
2396 TATAA
1 TATAA
2401 AGAGAATTAT
Statistics
Matches: 354, Mismatches: 34, Indels: 116
0.70 0.07 0.23
Matches are distributed among these distances:
8 8 0.02
9 14 0.04
10 33 0.09
11 43 0.12
12 69 0.19
13 78 0.22
14 64 0.18
15 41 0.12
16 4 0.01
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (12 bp):
TATAATATAAAG
Found at i:2233 original size:24 final size:24
Alignment explanation
Indices: 1943--2294 Score: 121
Period size: 25 Copynumber: 14.1 Consensus size: 24
1933 TTATATATTA
* * *
1943 TATATATAAAGTTTTAGTATAAAC
1 TATATATAAAGTATAAGTATAAAG
*
1967 TATACATATATA-TATAAGTATAATA-
1 TAT--ATATAAAGTATAAGTATAA-AG
* *
1992 TATTATATATA-TATATA-TATATA-
1 TA-TATATAAAGTATA-AGTATAAAG
*
2015 TATATATAAAGTATAATTATAAAG
1 TATATATAAAGTATAAGTATAAAG
* *
2039 ACTAAAATATATAAGTATATAATATAAA-
1 --T-ATATATA-AAGTATA-AGTATAAAG
* *
2067 TATCTATAAACTATATA-TAAATAAAAG
1 TATATATAAAGTATA-AGT--AT-AAAG
*
2094 TATATAT--ACTATAAAGTAT-AAG
1 TATATATAAAGTAT-AAGTATAAAG
*
2116 TATATATATAACTATAAAGTATATAA-
1 TATATATA-AAGTAT-AAGTATA-AAG
*
2142 TATATATATA-TATATA-TATAAAAG
1 TATATATAAAGTATA-AGTAT-AAAG
2166 TATAATTATAAAG-ACTAAAGTATATAAG
1 TAT-A-TATAAAGTA-T-AAGTATA-AAG
2194 TATAATATAAAGTATACA-TATAAAG
1 TAT-ATATAAAGTATA-AGTATAAAG
2219 TATATAT-AAGTTATAAGTATTAAAG
1 TATATATAAAG-TATAAGTA-TAAAG
* * *
2244 TATATAT-TA-TA-AAGTATTACAC
1 TATATATAAAGTATAAGTA-TAAAG
*
2266 TATATAATAAAGTATTAAATATAAAG
1 TATAT-ATAAAGTA-TAAGTATAAAG
2292 TAT
1 TAT
2295 TAAAGTATAC
Statistics
Matches: 263, Mismatches: 21, Indels: 86
0.71 0.06 0.23
Matches are distributed among these distances:
22 32 0.12
23 27 0.10
24 47 0.18
25 60 0.23
26 40 0.15
27 30 0.11
28 20 0.08
29 7 0.03
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (24 bp):
TATATATAAAGTATAAGTATAAAG
Found at i:2293 original size:56 final size:54
Alignment explanation
Indices: 2152--2402 Score: 221
Period size: 56 Copynumber: 4.5 Consensus size: 54
2142 TATATATATA
* * * *
2152 TATATATATAAAAGTA-TAATTATAAAG-ACTAAAGTATATA-AGTATAA-TATAAAG
1 TATATA-AT-AAAGTATTAAATATAAAGTATTAAAGTATATATA-TA-AAGTATTAAC
*
2206 TATACATATAAAGTATATATAAGT-TATAAGTATTAAAGTATATATTATAAAGTATTACAC
1 TATATA-ATAAAGTAT-TA-AA-TATA-AAGTATTAAAGTATATA-TATAAAGTATTA-AC
* *
2266 TATATAATAAAGTATTAAATATAAAGTATTAAAGTATACCATATAAAGTATTAAAG
1 TATATAATAAAGTATTAAATATAAAGTATTAAAGTATA-TATATAAAGTATT-AAC
*
2322 TATATAAATAAA-TATTAAATATAAAGTA-TATA-TATATAATATAAAGTATTAAC
1 TATAT-AATAAAGTATTAAATATAAAGTATTAAAGTATAT-ATATAAAGTATTAAC
2375 TATATAATATAAGTATTAAAGTATAAAG
1 TATATAATA-AAGTATTAAA-TATAAAG
2403 AGAATTATAT
Statistics
Matches: 168, Mismatches: 11, Indels: 35
0.79 0.05 0.16
Matches are distributed among these distances:
52 4 0.02
53 15 0.09
54 31 0.18
55 12 0.07
56 52 0.31
57 16 0.10
58 16 0.10
59 15 0.09
60 7 0.04
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (54 bp):
TATATAATAAAGTATTAAATATAAAGTATTAAAGTATATATATAAAGTATTAAC
Found at i:2349 original size:34 final size:34
Alignment explanation
Indices: 2128--2386 Score: 123
Period size: 34 Copynumber: 7.4 Consensus size: 34
2118 TATATATAAC
* *
2128 TATAAAGTATATAATATAT-ATATATA-TA-TATA
1 TATAAAGTATA-AATATATAATATAAAGTATTAAA
* * *
2160 TA-AAAGTATAATTATA-AAGACTAAAGTATATAAG
1 TATAAAGTATAAATATATAATA-TAAAGTAT-TAAA
*
2194 TAT-AA-TATAAAGTATA-CATATAAAGTATATATAA
1 TATAAAGTATAAA-TATATAATATAAAGTAT-TA-AA
*
2228 GT-TATAAGTATTAAAGTATATATTATAAAGTATTACACTATA
1 -TATA-AAGTA-TAAA-TATATAATATAAAGTATT--A--A-A
*
2270 TAATAAAGTATTAAATATA-AAGTATTAAAGTA-TACCA
1 T-ATAAAGTA-TAAATATATAA-TA-TAAAGTATTA-AA
2307 TATAAAGTATTAAAGTATATAA-ATAAA-TATTAAA
1 TATAAAGTA-TAAA-TATATAATATAAAGTATTAAA
* *
2341 TATAAAGTATATATATATAATATAAAGTATTAAC
1 TATAAAGTATAAATATATAATATAAAGTATTAAA
2375 TATATAA-TATAA
1 TATA-AAGTATAA
2387 GTATTAAAGT
Statistics
Matches: 181, Mismatches: 18, Indels: 54
0.72 0.07 0.21
Matches are distributed among these distances:
30 7 0.04
31 11 0.06
32 11 0.06
33 24 0.13
34 40 0.22
35 9 0.05
36 16 0.09
37 8 0.04
38 12 0.07
39 11 0.06
40 2 0.01
41 10 0.06
42 18 0.10
43 2 0.01
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.37
Consensus pattern (34 bp):
TATAAAGTATAAATATATAATATAAAGTATTAAA
Found at i:2398 original size:8 final size:7
Alignment explanation
Indices: 2082--2402 Score: 113
Period size: 7 Copynumber: 47.0 Consensus size: 7
2072 ATAAACTATA
2082 TATAAA-
1 TATAAAG
2088 TA-AAAG
1 TATAAAG
*
2094 TATATATAC
1 TATA-A-AG
2103 TATAAAG
1 TATAAAG
2110 TAT-AAG
1 TATAAAG
*
2116 TATATA-
1 TATAAAG
*
2122 TAT-AAC
1 TATAAAG
2128 TATAAAG
1 TATAAAG
2135 TATATAA-
1 TATA-AAG
*
2142 TATATA-
1 TATAAAG
*
2148 TATATA-
1 TATAAAG
*
2154 TATATA-
1 TATAAAG
2160 TA-AAAG
1 TATAAAG
*
2166 TAT-AAT
1 TATAAAG
2172 TATAAAG
1 TATAAAG
2179 -ACTAAAG
1 TA-TAAAG
2186 TATATAAG
1 TATA-AAG
2194 TAT-AA-
1 TATAAAG
2199 TATAAAG
1 TATAAAG
*
2206 TATACA-
1 TATAAAG
2212 TATAAAG
1 TATAAAG
2219 TATATATAAG
1 --TATA-AAG
2229 T-TATAAG
1 TATA-AAG
2236 TATTAAAG
1 TA-TAAAG
* *
2244 TATATAT
1 TATAAAG
2251 TATAAAG
1 TATAAAG
* *
2258 TATTACAC
1 TA-TAAAG
*
2266 TATATA-
1 TATAAAG
2272 -ATAAAG
1 TATAAAG
2278 TATTAAA-
1 TA-TAAAG
2285 TATAAAG
1 TATAAAG
2292 TATTAAAG
1 TA-TAAAG
*
2300 TATACCA-
1 TATA-AAG
2307 TATAAAG
1 TATAAAG
2314 TATTAAAG
1 TA-TAAAG
2322 TATATAA-
1 TATA-AAG
2329 -ATAAA-
1 TATAAAG
2334 TATTAAA-
1 TA-TAAAG
2341 TATAAAG
1 TATAAAG
*
2348 TATATA-
1 TATAAAG
2354 TATATAA-
1 TATA-AAG
2361 TATAAAG
1 TATAAAG
* *
2368 TATTAAC
1 TATAAAG
2375 TATATAA-
1 TATA-AAG
2382 TAT-AAG
1 TATAAAG
2388 TATTAAAG
1 TA-TAAAG
2396 TATAAAG
1 TATAAAG
2403 AGAATTATAT
Statistics
Matches: 248, Mismatches: 26, Indels: 81
0.70 0.07 0.23
Matches are distributed among these distances:
5 17 0.07
6 69 0.28
7 98 0.40
8 50 0.20
9 11 0.04
10 3 0.01
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (7 bp):
TATAAAG
Found at i:2399 original size:21 final size:21
Alignment explanation
Indices: 2233--2393 Score: 104
Period size: 20 Copynumber: 7.4 Consensus size: 21
2223 TATAAGTTAT
* *
2233 AAGTATTAAAGTATATATTATA
1 AAGTATT-AACTATATAATATA
2255 AAGTATTACACTATAT-A-ATA
1 AAGTATTA-ACTATATAATATA
*
2275 AAGTATTAAATATA-AAGTATTA
1 AAGTATTAACTATATAA-TA-TA
*
2297 AAGTA-T-ACCATATAAAGTATTA
1 AAGTATTAACTATAT-AA-TA-TA
*
2319 AAGTATATAAATAAATATTAAATATA
1 AAGTAT-TAACT--ATA-T-AATATA
2345 AAGTA-TATA-TATATAATATA
1 AAGTATTA-ACTATATAATATA
2365 AAGTATTAACTATATAATAT-
1 AAGTATTAACTATATAATATA
2385 AAGTATTAA
1 AAGTATTAA
2394 AGTATAAAGA
Statistics
Matches: 116, Mismatches: 7, Indels: 34
0.74 0.04 0.22
Matches are distributed among these distances:
19 6 0.05
20 36 0.31
21 16 0.14
22 36 0.31
24 4 0.03
25 2 0.02
26 7 0.06
27 5 0.04
28 4 0.03
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (21 bp):
AAGTATTAACTATATAATATA
Found at i:3185 original size:16 final size:17
Alignment explanation
Indices: 3164--3196 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3154 AGTATTTAAC
3164 ATGCAATGC-ACATGAA
1 ATGCAATGCAACATGAA
*
3180 ATGCAATTCAACATGAA
1 ATGCAATGCAACATGAA
3197 TTAATATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.21
Consensus pattern (17 bp):
ATGCAATGCAACATGAA
Found at i:3219 original size:14 final size:14
Alignment explanation
Indices: 3200--3229 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3190 ACATGAATTA
*
3200 ATATGGAATGTCAC
1 ATATGGAATGCCAC
3214 ATATGGAATGCCAC
1 ATATGGAATGCCAC
3228 AT
1 AT
3230 GAATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (14 bp):
ATATGGAATGCCAC
Found at i:4582 original size:15 final size:16
Alignment explanation
Indices: 4562--4592 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4552 TTGCACTCTG
4562 GATGC-AAAAATTAAA
1 GATGCAAAAAATTAAA
4577 GATGCAAAAAATTAAA
1 GATGCAAAAAATTAAA
4593 CAAAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (16 bp):
GATGCAAAAAATTAAA
Found at i:10570 original size:26 final size:26
Alignment explanation
Indices: 10521--10571 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
10511 CTTACGCGAT
****
10521 ATAAATGATCAATATTTTTTTATTAA
1 ATAAATGATCAATATTAAAATATTAA
10547 ATAAATGATCAATATTAAAATATTA
1 ATAAATGATCAATATTAAAATATTA
10572 TTTTATTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (26 bp):
ATAAATGATCAATATTAAAATATTAA
Found at i:11387 original size:464 final size:465
Alignment explanation
Indices: 10521--11898 Score: 2085
Period size: 464 Copynumber: 3.0 Consensus size: 465
10511 CTTACGCGAT
10521 ATAAATGATCAATATTTTTTT-ATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
** * * * *
10585 TAAAAATATCTTATC-GCGCAT--G--T-C---AC-A-CACCGCAACATACCGAAATATACTGTT
66 TAAAAATATCTTATCAATGGATGAGTTTACAGTACAATCATC-CAACACACCGAAACATACTGTT
10639 AATTAAATATTAAAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTTTAC
130 AATTAAATATTAAAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTTTAC
10704 TACCTAAA-TTCTATTTTTTAACGTCATTAACGACAATGATGATGTTTCATGACATGTCAATTTT
195 TACCTAAACTT-TA-TTTTTAACG-CATTAACGACAATGATGATGTTTCATGACATGTCAATTTT
* * *
10768 TTTAATTTCCACATCATATTTTTATTTTTTCATCAGTATTTTAATTAATTTTATTCAACCAATTA
257 TTTAATTTCCACATCATCTTTTTATTTCTCCATCAGTATTTTAATTAATTTTATTCAACCAATTA
* * * * *
10833 AATGATGACATGTGTCAGCAAATATGGAGTTAAAATAAAAGAAAATATTTTTTTAGCATGAACCG
322 AATGATGACATGTGTCACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGAACCG
* * * *
10898 TACATAAATCTCTTACATGAAATGCAAGGCACTCAACCATTGAGTTAAGCTAATTATTTGTTAAT
387 TACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTAAT
10963 TTCATCATATTAAA
452 TTCATCATATTAAA
*
10977 ATAAATGATCAATATTTTTTTGATTAAATAAATGATTAATATTAAAATATTA-TTTATTAGTAAA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
* * *
11041 TAAAAATATCTTATCAATGGATGAGTTTACGGTGC-AT-GT-C-ACACACCGAAACATACTGTTA
66 TAAAAATATCTTATCAATGGATGAGTTTACAGTACAATCATCCAACACACCGAAACATACTGTTA
**
11102 ATTAAATATTAGTAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTTTACT
131 ATTAAATATTAAAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTTTACT
*
11167 ATCTAAACTTTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAATTTTTTT
196 ACCTAAACTTTATTTTTAACG-CATTAACGACAATGATGATGTTTCATGACATGTCAA---TTTT
* * *
11232 TTTAATTTTCACATCATCTTTTTATTTCTCCAACAATATTTTAATTAATTTTATTCAACCAATTA
257 TTTAATTTCCACATCATCTTTTTATTTCTCCATCAGTATTTTAATTAATTTTATTCAACCAATTA
*
11297 AATGATGACATGTG-CTACCAACTATGGGGATAAAATAAAATAAAATATTTTCTTAGCATGAACC
322 AATGATGACATGTGTC-ACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGAACC
*
11361 GTACATAAATCTCTTACATCAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTAA
386 GTACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTAA
11426 TTTCATCATATTAAA
451 TTTCATCATATTAAA
* *
11441 ATAAATTATGAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
*
11506 TAAAAATATCTTATTAATGGATGAGTTTACAGTACATATCATACACCGCAACACACCGAAACATA
66 TAAAAATATCTTATCAATGGATGAGTTTACAGTACA-ATCAT----C-CAACACACCGAAACATA
* *
11571 CTGTTAATTAAATATTAAAAAGATAAATTATACATTTAGTAATTATACTATCATTTTTATTTTGT
125 CTGTTAATTAAATATTAAAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGT
*
11636 TTTACTACCTAAACTTTA--TTT------TTAACGACAATGATGATGTTTCATGTCATGTCAATT
190 TTTACTACCTAAACTTTATTTTTAACGCATTAACGACAATGATGATGTTTCATGACATGTCAATT
*
11693 TTTTTAATTTCCACATCATCTTTTTATTTCTCCATTAGTA-TTTAATTAATTTTATTCAACCAAT
255 TTTTTAATTTCCACATCATCTTTTTATTTCTCCATCAGTATTTTAATTAATTTTATTCAACCAAT
11757 TAAATGATGACATGTGTCACCAACTAT-GGGATAAAATAAAAGAAAATATTTTCTTAGCATGAAC
320 TAAATGATGACATGTGTCACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGAAC
11821 CGTACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTA
385 CGTACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTA
11886 ATTTCATCATATT
450 ATTTCATCATATT
11899 TTTTATTTAA
Statistics
Matches: 845, Mismatches: 49, Indels: 51
0.89 0.05 0.05
Matches are distributed among these distances:
456 48 0.06
457 32 0.04
459 1 0.00
461 159 0.19
462 140 0.17
463 43 0.05
464 243 0.29
465 46 0.05
466 33 0.04
467 2 0.00
468 1 0.00
473 3 0.00
474 1 0.00
475 93 0.11
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (465 bp):
ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
TAAAAATATCTTATCAATGGATGAGTTTACAGTACAATCATCCAACACACCGAAACATACTGTTA
ATTAAATATTAAAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTTTACT
ACCTAAACTTTATTTTTAACGCATTAACGACAATGATGATGTTTCATGACATGTCAATTTTTTTA
ATTTCCACATCATCTTTTTATTTCTCCATCAGTATTTTAATTAATTTTATTCAACCAATTAAATG
ATGACATGTGTCACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGAACCGTACA
TAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTAATTTCA
TCATATTAAA
Found at i:12227 original size:22 final size:22
Alignment explanation
Indices: 12193--12242 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
12183 TTTAACATAT
* *
12193 TTATTT-TTAAAAATCATATTA
1 TTATTTATTAAAAATAATATCA
*
12214 TTATTTATTTAAAATAATATCA
1 TTATTTATTAAAAATAATATCA
*
12236 TTTTTTA
1 TTATTTA
12243 GATCATCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTTATTAAAAATAATATCA
Found at i:12553 original size:21 final size:23
Alignment explanation
Indices: 12508--12555 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
12498 TATATTAACT
* *
12508 TATTCTAAAAAGTATATTTATAA
1 TATTATAAAAAGTATATTTAAAA
12531 TATTATAAAAA-TAT-TTTAAAA
1 TATTATAAAAAGTATATTTAAAA
12552 TATT
1 TATT
12556 TATTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 3 0.13
23 10 0.43
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATAAAAAGTATATTTAAAA
Found at i:12565 original size:18 final size:20
Alignment explanation
Indices: 12542--12585 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
12532 ATTATAAAAA
12542 TATTTTAAAAT-AT-TTATT
1 TATTTTAAAATCATATTATT
12560 TATTTTTAAAATCATATTATT
1 TA-TTTTAAAATCATATTATT
12581 TATTT
1 TATTT
12586 ATTTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 9 0.39
20 5 0.22
21 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTAAAATCATATTATT
Found at i:12568 original size:19 final size:21
Alignment explanation
Indices: 12544--12604 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
12534 TATAAAAATA
12544 TTTTAAAAT-AT-TTATTTAT
1 TTTTAAAATCATATTATTTAT
12563 TTTTAAAATCATATTATTTATT
1 TTTTAAAATCATATTATTTA-T
* *
12585 TATTTGAAATAATATTATTT
1 T-TTTAAAATCATATTATTT
12605 TTAAATCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.25
20 2 0.06
21 7 0.19
22 2 0.06
23 16 0.44
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTAAAATCATATTATTTAT
Found at i:13304 original size:16 final size:16
Alignment explanation
Indices: 13283--13319 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
13273 TCAACCCTCG
13283 TAGAAGGAGCTTTCTA
1 TAGAAGGAGCTTTCTA
*
13299 TAGAAGGGGCTTTCTA
1 TAGAAGGAGCTTTCTA
13315 TAGAA
1 TAGAA
13320 TGTACCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (16 bp):
TAGAAGGAGCTTTCTA
Found at i:13720 original size:15 final size:15
Alignment explanation
Indices: 13702--13780 Score: 65
Period size: 15 Copynumber: 5.3 Consensus size: 15
13692 CATAAAATAT
*
13702 AATATCAGAAATTAA
1 AATACCAGAAATTAA
* *
13717 AATAACATTAAA-TACA
1 AATACCA-GAAATTA-A
13733 AA-ACCATG-AATTAA
1 AATACCA-GAAATTAA
* *
13747 AATACCAGAAAATAT
1 AATACCAGAAATTAA
13762 AATACCAGAAATTAA
1 AATACCAGAAATTAA
13777 AATA
1 AATA
13781 ATGTAAAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 6 0.12
15 39 0.76
16 6 0.12
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (15 bp):
AATACCAGAAATTAA
Found at i:13723 original size:30 final size:30
Alignment explanation
Indices: 13687--13825 Score: 120
Period size: 30 Copynumber: 4.6 Consensus size: 30
13677 ACCCTTATAC
*
13687 AATAACATAAAATATAATATCAGAAATTAA
1 AATAACATAAAATATAATACCAGAAATTAA
* * *
13717 AATAACATTAAATACAAAACCATG-AATTAA
1 AATAACATAAAATATAATACCA-GAAATTAA
* *
13747 AATACCAGAAAATATAATACCAGAAATTAA
1 AATAACATAAAATATAATACCAGAAATTAA
** * * *
13777 AATAATGTAAAATACAAAACTATG-AATTAA
1 AATAACATAAAATATAATACCA-GAAATTAA
* * *
13807 AATACCAGAAAATACAATA
1 AATAACATAAAATATAATA
13826 GTAGAAAATA
Statistics
Matches: 85, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
29 1 0.01
30 82 0.96
31 2 0.02
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (30 bp):
AATAACATAAAATATAATACCAGAAATTAA
Found at i:13765 original size:60 final size:60
Alignment explanation
Indices: 13695--13825 Score: 208
Period size: 60 Copynumber: 2.2 Consensus size: 60
13685 ACAATAACAT
* *
13695 AAAATATAATATCAGAAATTAAAATAACATTAAATACAAAACCATGAATTAAAATACCAG
1 AAAATATAATACCAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
** *
13755 AAAATATAATACCAGAAATTAAAATAATGTAAAATACAAAACTATGAATTAAAATACCAG
1 AAAATATAATACCAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
*
13815 AAAATACAATA
1 AAAATATAATA
13826 GTAGAAAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (60 bp):
AAAATATAATACCAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
Found at i:13832 original size:60 final size:59
Alignment explanation
Indices: 13695--13850 Score: 195
Period size: 60 Copynumber: 2.6 Consensus size: 59
13685 ACAATAACAT
*
13695 AAAATATAATATCAGAAATTAAAATAACATTAAATACAAAACCATGAATTAAAATACCAG
1 AAAATATAATAT-AGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
* ** *
13755 AAAATATAATACCAGAAATTAAAATAATGTAAAATACAAAACTATGAATTAAAATACCAG
1 AAAATATAATA-TAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
* * * * *
13815 AAAATACAATAGTAGAAAATACAATATCATATAATA
1 AAAATATAATA-TAGAAATTAAAATAACATAAAATA
13851 AAACTATATA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 81 1.00
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.24
Consensus pattern (59 bp):
AAAATATAATATAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
Found at i:23898 original size:3 final size:3
Alignment explanation
Indices: 23890--23935 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
23880 AAATATATAT
* *
23890 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTAA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
23936 ATTTACATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:24917 original size:18 final size:18
Alignment explanation
Indices: 24894--24928 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24884 GAGAATTCTA
24894 AACTCCCTCTGCCCTCTC
1 AACTCCCTCTGCCCTCTC
*
24912 AACTCCCTCTTCCCTCT
1 AACTCCCTCTGCCCTCT
24929 GTTTCTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.54, G:0.03, T:0.31
Consensus pattern (18 bp):
AACTCCCTCTGCCCTCTC
Found at i:27640 original size:6 final size:6
Alignment explanation
Indices: 27629--27663 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
27619 ACATTTTTTT
27629 CATTTG CATTTG CATCTTTG CATTTG CATTTG CAT
1 CATTTG CATTTG CA--TTTG CATTTG CATTTG CAT
27664 CTTTGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 21 0.78
8 6 0.22
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (6 bp):
CATTTG
Found at i:27654 original size:20 final size:20
Alignment explanation
Indices: 27629--27671 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
27619 ACATTTTTTT
27629 CATTTGCATTTGCATCTTTG
1 CATTTGCATTTGCATCTTTG
27649 CATTTGCATTTGCATCTTTG
1 CATTTGCATTTGCATCTTTG
27669 CAT
1 CAT
27672 AATTATAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (20 bp):
CATTTGCATTTGCATCTTTG
Found at i:27671 original size:14 final size:14
Alignment explanation
Indices: 27631--27657 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27621 ATTTTTTTCA
27631 TTTGCATTTGCATC
1 TTTGCATTTGCATC
27645 TTTGCATTTGCAT
1 TTTGCATTTGCAT
27658 TTGCATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.52
Consensus pattern (14 bp):
TTTGCATTTGCATC
Found at i:34774 original size:41 final size:42
Alignment explanation
Indices: 34683--34776 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
34673 TTGTTAGTCA
** * *
34683 TTCGGGTCATCTGTAAGTTTTTCGAGCATGATGCTTAAATCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGCTTAAAGCC
**
34725 TTTAGGTCATCTGTAAGCCTTTCGAGCAAGATG-TTAAAGCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGCTTAAAGCC
34766 TTCGGGTCATC
1 TTCGGGTCATC
34777 CATAGGACCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.36
42 28 0.64
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (42 bp):
TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGCTTAAAGCC
Found at i:37731 original size:105 final size:105
Alignment explanation
Indices: 37547--38070 Score: 581
Period size: 105 Copynumber: 4.9 Consensus size: 105
37537 AAAGATTATG
* *
37547 ATTCACCACAAAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTTGTCCT-
1 ATTCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTA
37611 AAAGTAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
66 AAAG-AGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * *
37652 ATTCACCAGAGAAGGAGGTGAACCAACATTTCCAGAACAGTTCATACTGAGAAGAACTCGTCCTA
1 ATTCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTA
* *
37717 AAAGAGAAAATTCATAATGAGAAGAACTTATTCCTTTCAA
66 AAAGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
*
37757 ATTCACCACAGAAGGAGGTGAACCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTCCTA
1 ATTCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTA
*
37822 AAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAA
66 AAAGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * * * * * **
37862 GTCCACCGCAGAAGGAGGTGGATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTTATCC
1 ATTCACCACAGAAGGAGGTGAACCAACA-TTTCCA-GAAGAGTTCATAATGAGAAGAACTCGTCC
* * * *
37927 -AATGAGGAAGAAGAAGTTTATAATTAGAAGAACTTGTTCAACCTTGGTTAA
64 TAA--AAG-AG-A-AAGTTCATAATGAGAAGAACTTGTT---CCTT--TCAA
* * * * * * * *
37978 ATTCCATCACAGAAGGATGTGGATCAATATTTTCAATGGAGAGTTCATAATGAGAAGAACTCAT-
1 ATT-CACCACAGAAGGAGGTGAACCAACA-TTTCCA-GAAGAGTTCATAATGAGAAGAACTCGTC
* * *
38042 -TCAATG-GAGAGTTCATAATGAGAAGAACT
63 CTAAAAGAGAAAGTTCATAATGAGAAGAACT
38071 CATCCAATGA
Statistics
Matches: 364, Mismatches: 40, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
105 214 0.59
106 10 0.03
107 27 0.07
108 2 0.01
109 2 0.01
110 19 0.05
111 24 0.07
112 1 0.00
114 6 0.02
116 5 0.01
117 54 0.15
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (105 bp):
ATTCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTA
AAAGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
Found at i:38050 original size:32 final size:32
Alignment explanation
Indices: 38009--38079 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
37999 GATCAATATT
38009 TTCAATGGAGAGTTCATAATGAGAAGAACTCA
1 TTCAATGGAGAGTTCATAATGAGAAGAACTCA
38041 TTCAATGGAGAGTTCATAATGAGAAGAACTCA
1 TTCAATGGAGAGTTCATAATGAGAAGAACTCA
*
38073 TCCAATG
1 TTCAATG
38080 ATAAAGGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (32 bp):
TTCAATGGAGAGTTCATAATGAGAAGAACTCA
Found at i:38073 original size:16 final size:16
Alignment explanation
Indices: 38022--38073 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
38012 AATGGAGAGT
38022 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
**
38038 TCATTCAATG-G-AGAGT
1 TCA-T-AATGAGAAGAAC
38054 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
38070 TCAT
1 TCAT
38074 CCAATGATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.14
15 2 0.07
16 16 0.57
17 2 0.07
18 4 0.14
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.25
Consensus pattern (16 bp):
TCATAATGAGAAGAAC
Found at i:38169 original size:144 final size:146
Alignment explanation
Indices: 37892--38192 Score: 401
Period size: 144 Copynumber: 2.1 Consensus size: 146
37882 GATCAACATT
* * * * *
37892 TTCAATGAAGAGTTCATAATGAGAAGAACTTATCCAATGAGGAAGAAGAAGTTTATAATTAGAAG
1 TTCAATGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGAAAGAAGAAATTCATAATGAGAAG
* * * *
37957 AACTTGTTCAACCTTGGTTAAATTCCATCACAGAAGGATGTGGATCAATATTTTCAATGGAGAGT
66 AACTTGTT--ACCTT-GTCAAATCCCATCACAGAAGGAGGTGGATCAATATTTTCAAAGGAGAGT
38022 TCATAATGAGAAGAACTCA
128 TCATAATGAGAAGAACTCA
* * *
38041 TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGATAAAGGAGAAAATTCATAATGAGAA
1 TTCAATGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGAAAGAAG-AAATTCATAATGAGAA
* *
38106 GAACTTGTT-CCTT-TCAAGTCCCA-CACAGAAGGAGGTGGATTAATATTTTCAAAGGAGAGTTC
65 GAACTTGTTACCTTGTCAAATCCCATCACAGAAGGAGGTGGATCAATATTTTCAAAGGAGAGTTC
*
38168 ATAATGAGAATAACTCA
130 ATAATGAGAAGAACTCA
*
38185 TCCAATGA
1 TTCAATGA
38193 GGAAGAAGAA
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
144 58 0.43
145 7 0.05
147 4 0.03
149 43 0.32
150 22 0.16
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (146 bp):
TTCAATGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGAAAGAAGAAATTCATAATGAGAAG
AACTTGTTACCTTGTCAAATCCCATCACAGAAGGAGGTGGATCAATATTTTCAAAGGAGAGTTCA
TAATGAGAAGAACTCA
Found at i:38280 original size:117 final size:117
Alignment explanation
Indices: 38041--38584 Score: 796
Period size: 117 Copynumber: 4.7 Consensus size: 117
38031 GAAGAACTCA
** * *
38041 TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGATAAAGGAGAAAATTCATAATGAGAA
1 TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAG-AAGTTCATAATGAGAA
* *
38106 GAACTTGTTC--C--T--TTCAAGTCCCA-CACAGAAGGAGGTGGATTAATATT
65 GAACTTGTTCAACATTGGTTCAA-TTCCATCACAGAAGGAGGTGGATCAATATT
* *
38153 TTCAAAGGAGAGTTCATAATGAGAATAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAG
1 TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAG
*
38218 AACTTGTTCAACATTGGTTTAATTCCATCACAGAAGGAGGTGGATCAATATT
66 AACTTGTTCAACATTGGTTCAATTCCATCACAGAAGGAGGTGGATCAATATT
* *
38270 TTCAATGGAGAGTTCATAATAAGAAGAACTCATCCAATGAGGATGAAGAAGTTCATAATGAGAAG
1 TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAG
* * *
38335 AACTTGTTCAACTTTGGTTCGATTCCATCACAGAAGGAGGTGGATCAACATT
66 AACTTGTTCAACATTGGTTCAATTCCATCACAGAAGGAGGTGGATCAATATT
38387 TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAG
1 TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAG
* * ** * * *
38452 AACTTATTCAACCTTGGTTTGATTCCCTCACAGAATGAGGTGAATCAATATT
66 AACTTGTTCAACATTGGTTCAATTCCATCACAGAAGGAGGTGGATCAATATT
* * *
38504 TTTAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGAAAGAAGAAGTTCATAATGAGAAG
1 TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAG
*
38569 AACTTGTTTAACATTG
66 AACTTGTTCAACATTG
38585 CATCAGCATT
Statistics
Matches: 393, Mismatches: 32, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
111 25 0.06
112 43 0.11
113 1 0.00
115 1 0.00
116 4 0.01
117 319 0.81
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (117 bp):
TTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAG
AACTTGTTCAACATTGGTTCAATTCCATCACAGAAGGAGGTGGATCAATATT
Found at i:38297 original size:261 final size:256
Alignment explanation
Indices: 37793--38308 Score: 818
Period size: 261 Copynumber: 2.0 Consensus size: 256
37783 CATTTCCTGA
* *
37793 AGAGTTCATAATGAGAAGAACTCGTCCTAAAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTT
1 AGAGTTCATAATGAGAAGAACTCATCCTAAAAGAGAAAATTCATAATAAGAAGAACTTGTTCCTT
* * *
37858 TCAAGTCCACCGCAGAAGGAGGTGGATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTT
66 TCAAGTCCACCACAGAAGGAGGTGGATCAACATTTTCAAAGAAGAGTTCATAATGAGAAGAACTC
* * *
37923 ATCCAATGAGGAAGAAGAAGTTTATAATTAGAAGAACTTGTTCAACCTTGGTTAAATTCCATCAC
131 ATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTAAATTCCATCAC
* * *
37988 AGAAGGATGTGGATCAATATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATTCAATGG
196 AGAAGGAGGTGGATCAATATTTTCAATGGAGAGTTCATAATAAGAAGAACTCATCCAATGG
*
38049 AGAGTTCATAATGAGAAGAACTCATCCAATGATAAAGGAGAAAATTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCC--T-A-AAA-GAGAAAATTCATAATAAGAAGAACTTGT
* * *
38114 TCCTTTCAAGTCC-CACACAGAAGGAGGTGGATTAATATTTTCAAAGGAGAGTTCATAATGAGAA
61 TCCTTTCAAGTCCAC-CACAGAAGGAGGTGGATCAACATTTTCAAAGAAGAGTTCATAATGAGAA
* *
38178 TAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTTAATTC
125 GAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTAAATTC
38243 CATCACAGAAGGAGGTGGATCAATATTTTCAATGGAGAGTTCATAATAAGAAGAACTCATCCAAT
190 CATCACAGAAGGAGGTGGATCAATATTTTCAATGGAGAGTTCATAATAAGAAGAACTCATCCAAT
38308 G
255 G
38309 AGGATGAAGA
Statistics
Matches: 237, Mismatches: 17, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
256 26 0.11
258 1 0.00
259 1 0.00
260 4 0.02
261 205 0.86
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (256 bp):
AGAGTTCATAATGAGAAGAACTCATCCTAAAAGAGAAAATTCATAATAAGAAGAACTTGTTCCTT
TCAAGTCCACCACAGAAGGAGGTGGATCAACATTTTCAAAGAAGAGTTCATAATGAGAAGAACTC
ATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTAAATTCCATCAC
AGAAGGAGGTGGATCAATATTTTCAATGGAGAGTTCATAATAAGAAGAACTCATCCAATGG
Found at i:38403 original size:378 final size:361
Alignment explanation
Indices: 37690--38425 Score: 990
Period size: 378 Copynumber: 2.0 Consensus size: 361
37680 TTTCCAGAAC
* *
37690 AGTTCATACTGAGAAGAACTCGTCCTAAAAGAGAAAATTCATAATGAGAAGAACTTATTCCTTTC
1 AGTTCATAATGAGAAGAACTCATCCTAAAAGAGAAAATTCATAATGAGAAGAACTTATTCCTTTC
* ** *
37755 AAATTCACCACAGAAGGAGGTGAACCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTCC
66 AAATCCACCACAGAAGGAGGTGAACCAACATTTCAAGAAGAGTTCATAATGAGAAGAACTCATCC
*
37820 TAAAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAAGTCCACCGCAGAAGGAGGTGGAT
131 TAAAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAGGAGGTGGAT
* * *
37885 CAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTTATCCAATGAGGAAGAAGAAGTTTATAA
196 CAACATTTTCAATGAAGAGTTCATAATAAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAA
* * *
37950 TTAGAAGAACTTGTTCAACCTTGGTTAAATTCCATCACAGAAGGATGTGGATCAATATTTTCAAT
261 TGAGAAGAACTTGTTCAACCTTGGTTAAATTCCATCACAGAAGGAGGTGGATCAACATTTTCAAT
*
38015 GGAGAGTTCATAATGAGAAGAACTCATTCAATGGAG
326 GGAGAGTTCATAATGAGAAGAACTCATCCAATGGAG
*
38051 AGTTCATAATGAGAAGAACTCATCCAATGATAAAGGAGAAAATTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCC--T-A-AAA-GAGAAAATTCATAATGAGAAGAACTTATTC
* * ** * * *
38116 CTTTCAAGTCC-CACACAGAAGGAGGTGGATTAATATTTTCAAAGGAGAGTTCATAATGAGAATA
61 CTTTCAAATCCAC-CACAGAAGGAGGTGAACCAACA-TTTC-AAGAAGAGTTCATAATGAGAAGA
* * * *
38180 ACTCATCC-AATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTGGTTTAATTCC
123 ACTCATCCTAA--AAG-AG-A-AAGTTCATAATAAGAAGAACTTGTTC--C--T--TTCAAGTCC
* * *
38244 ATCACAGAAGGAGGTGGATCAATATTTTCAATGGAGAGTTCATAATAAGAAGAACTCATCCAATG
177 ACCACAGAAGGAGGTGGATCAACATTTTCAATGAAGAGTTCATAATAAGAAGAACTCATCCAATG
* * **
38309 AGGATGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTGGTTCGATTCCATCACAGAAGGAG
242 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTAAATTCCATCACAGAAGGAG
38374 GTGGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATG
307 GTGGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAATG
38426 AGGAAGAAGA
Statistics
Matches: 323, Mismatches: 33, Indels: 21
0.86 0.09 0.06
Matches are distributed among these distances:
361 23 0.07
363 1 0.00
364 1 0.00
365 4 0.01
366 56 0.17
367 6 0.02
368 26 0.08
369 2 0.01
370 2 0.01
371 1 0.00
372 25 0.08
374 1 0.00
376 1 0.00
378 174 0.54
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (361 bp):
AGTTCATAATGAGAAGAACTCATCCTAAAAGAGAAAATTCATAATGAGAAGAACTTATTCCTTTC
AAATCCACCACAGAAGGAGGTGAACCAACATTTCAAGAAGAGTTCATAATGAGAAGAACTCATCC
TAAAAGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAGGAGGTGGAT
CAACATTTTCAATGAAGAGTTCATAATAAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTGGTTAAATTCCATCACAGAAGGAGGTGGATCAACATTTTCAAT
GGAGAGTTCATAATGAGAAGAACTCATCCAATGGAG
Found at i:38461 original size:20 final size:20
Alignment explanation
Indices: 38399--38461 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
38389 CAATGGAGAG
*
38399 TTCATAATGAGAAGAACTCA
1 TTCATAATGAGAAGAACTAA
* *
38419 -TC-CAATGAGGAAGAA-GAA
1 TTCATAATGA-GAAGAACTAA
*
38437 GTTCATAATGAGAAGAACTTA
1 -TTCATAATGAGAAGAACTAA
38458 TTCA
1 TTCA
38462 ACCTTGGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 12 0.38
21 6 0.19
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTAA
Found at i:38804 original size:3 final size:3
Alignment explanation
Indices: 38792--38838 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
38782 GGCTTAAATA
* * *
38792 TAT T-T TAT TAT TAT TAT TAT CAT TAT TAT TACT AAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
38837 TA
1 TA
38839 ATTTACATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:42474 original size:11 final size:11
Alignment explanation
Indices: 42458--42482 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42448 AGATAAAAAA
42458 TAAAATAAATG
1 TAAAATAAATG
42469 TAAAATAAATG
1 TAAAATAAATG
42480 TAA
1 TAA
42483 CTCACCCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (11 bp):
TAAAATAAATG
Found at i:44704 original size:18 final size:18
Alignment explanation
Indices: 44683--44718 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44673 TGAGATTCGA
44683 TTTAAATTTAAAATTTAT
1 TTTAAATTTAAAATTTAT
*
44701 TTTAAATTTTAAATTTAT
1 TTTAAATTTAAAATTTAT
44719 ACCTAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATTTAAAATTTAT
Found at i:46228 original size:2 final size:2
Alignment explanation
Indices: 46221--46251 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46211 AATCAAGATA
46221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46252 CAATTGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46370 original size:2 final size:2
Alignment explanation
Indices: 46363--46390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46353 TTAATATTAA
46363 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
46391 TTTGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47109 original size:45 final size:45
Alignment explanation
Indices: 47048--47160 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
47038 GAGCGGTAGA
*
47048 AAAAATAACATTTTAGGTAGCGCCCAAAATTAACA-TTTCTGATAG
1 AAAAATAATATTTTAGGTAGCGCCCAAAATTAACATTTTC-GATAG
* * * * *
47093 AAAAATAATATTTTAGGTAGAGCTCAATATTAATATTTTCGGTAG
1 AAAAATAATATTTTAGGTAGCGCCCAAAATTAACATTTTCGATAG
*
47138 AAAAATACT-TTATTAGGTAGCGC
1 AAAAATAATATT-TTAGGTAGCGC
47161 TTTACAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 2 0.03
45 52 0.90
46 4 0.07
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33
Consensus pattern (45 bp):
AAAAATAATATTTTAGGTAGCGCCCAAAATTAACATTTTCGATAG
Found at i:47495 original size:45 final size:45
Alignment explanation
Indices: 47386--47471 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
47376 TGGTAAAACG
* *
47386 CTACCTAAAACATTATTTTTCTATCAGAAATATTAATATTGAACA
1 CTACTTAAAATATTATTTTTCTATCAGAAATATTAATATTGAACA
*
47431 CTACTTAAAATATTATTTTTCTA-CTGAAAATATTAATATTG
1 CTACTTAAAATATTATTTTTCTATCAG-AAATATTAATATTG
47472 GATGCTATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.42
Consensus pattern (45 bp):
CTACTTAAAATATTATTTTTCTATCAGAAATATTAATATTGAACA
Found at i:47638 original size:61 final size:60
Alignment explanation
Indices: 47539--47686 Score: 235
Period size: 61 Copynumber: 2.5 Consensus size: 60
47529 TATAGAAAAA
*
47539 TAAT-ATTTTGTTGAGGCAGGTTGGATATTGTGTCTTCTCTGTTACTGTTCTTTTTTCCTG
1 TAATGATTTTGTTGAGGCAGGTTGGATATTGTGTCTTCTCTGTTACTGTTC-TTTTCCCTG
* *
47599 TAATGATTTTGTTGAGGCAGGTTGGATATTGTGTCTTCTCTGTTATTTTTCTTTTCCCTG
1 TAATGATTTTGTTGAGGCAGGTTGGATATTGTGTCTTCTCTGTTACTGTTCTTTTCCCTG
* *
47659 TAATGATTTAGTTGAGGCAGGTTAGATA
1 TAATGATTTTGTTGAGGCAGGTTGGATA
47687 CTGTCTTCGT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 38 0.46
61 44 0.54
ACGTcount: A:0.17, C:0.11, G:0.23, T:0.49
Consensus pattern (60 bp):
TAATGATTTTGTTGAGGCAGGTTGGATATTGTGTCTTCTCTGTTACTGTTCTTTTCCCTG
Found at i:51852 original size:18 final size:19
Alignment explanation
Indices: 51813--51853 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
51803 AGAGGTTGGA
**
51813 TTTTTAGAGTCTTAGATTT
1 TTTTTAGAGTCTTAGAAAT
51832 TTTTTAGA-TCTTAGAAAT
1 TTTTTAGAGTCTTAGAAAT
51850 TTTT
1 TTTT
51854 GGGGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (19 bp):
TTTTTAGAGTCTTAGAAAT
Found at i:51852 original size:19 final size:19
Alignment explanation
Indices: 51813--51853 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
51803 AGAGGTTGGA
*
51813 TTTTTAGAGTCTTAGATTT
1 TTTTTAGAGTCTTAGAATT
51832 TTTTTAGA-TCTTAGAAATT
1 TTTTTAGAGTCTTAG-AATT
51851 TTT
1 TTT
51854 GGGGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (19 bp):
TTTTTAGAGTCTTAGAATT
Found at i:58483 original size:23 final size:24
Alignment explanation
Indices: 58429--58484 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
58419 AAAATAATTT
58429 TGTCTTTGTAGCACGTTTTTCCTC
1 TGTCTTTGTAGCACGTTTTTCCTC
58453 TG-CGTTTG-AGACACGTTTTT-CTC
1 TGTC-TTTGTAG-CACGTTTTTCCTC
58476 TGTCTTTGT
1 TGTCTTTGT
58485 GGTACGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.09, C:0.21, G:0.20, T:0.50
Consensus pattern (24 bp):
TGTCTTTGTAGCACGTTTTTCCTC
Found at i:59295 original size:21 final size:22
Alignment explanation
Indices: 59246--59295 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
59236 ATATAGATTT
59246 AAGGAGTATAGATACTCAAACG
1 AAGGAGTATAGATACTCAAACG
* *
59268 AA-TAGTATGGATACTCAAAC-
1 AAGGAGTATAGATACTCAAACG
59288 AAGGAGTA
1 AAGGAGTA
59296 CATGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (22 bp):
AAGGAGTATAGATACTCAAACG
Found at i:59860 original size:29 final size:30
Alignment explanation
Indices: 59828--59887 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
59818 GTCGAAGATG
*
59828 TTAGGAA-AAAAAAACAAATAAGT-AATGAA
1 TTAGGAAGAAAAAAA-AAATAAATAAATGAA
*
59857 TTAGGAAGAATAAAAAAATAAATAAATGAA
1 TTAGGAAGAAAAAAAAAATAAATAAATGAA
59887 T
1 T
59888 ATAAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.65, C:0.02, G:0.13, T:0.20
Consensus pattern (30 bp):
TTAGGAAGAAAAAAAAAATAAATAAATGAA
Found at i:60130 original size:14 final size:14
Alignment explanation
Indices: 60098--60127 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
60088 TATGGGAAAG
60098 AAATAACAATAATA
1 AAATAACAATAATA
60112 AAATAA-AATAATA
1 AAATAACAATAATA
60125 AAA
1 AAA
60128 ATAGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAACAATAATA
Found at i:60135 original size:13 final size:14
Alignment explanation
Indices: 60098--60130 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
60088 TATGGGAAAG
60098 AAATAACAATAAT-A
1 AAATAA-AATAATAA
60112 AAATAAAATAATAA
1 AAATAAAATAATAA
60126 AAATA
1 AAATA
60131 GATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAATAA
Found at i:60908 original size:28 final size:25
Alignment explanation
Indices: 60876--60926 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 25
60866 TGTTGGCTTG
*
60876 TGTTTTTCGTGTTTGGTTATGATGATTC
1 TGTTTTT-GTG-TGGGTT-TGATGATTC
60904 TGTTTTTGTGTGGGTTTGATGAT
1 TGTTTTTGTGTGGGTTTGATGAT
60927 ATGGGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 5 0.23
27 3 0.14
28 7 0.32
ACGTcount: A:0.10, C:0.04, G:0.29, T:0.57
Consensus pattern (25 bp):
TGTTTTTGTGTGGGTTTGATGATTC
Found at i:61457 original size:4 final size:4
Alignment explanation
Indices: 61448--61510 Score: 53
Period size: 4 Copynumber: 16.8 Consensus size: 4
61438 ATAGACCTAA
* * * * *
61448 AAAT AAAT AAAT AAAT AAAT AAAC GAGT AAAT -AAT -AAT AAA- CAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
61493 AAAT AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
61511 ATACTATATA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
3 11 0.23
4 36 0.77
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:61555 original size:30 final size:29
Alignment explanation
Indices: 61521--61583 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
61511 ATACTATATA
* *
61521 ATATATATTTAAAAAAAATGTTTTAAAACT
1 ATATATATTTAAAAAAAAT-TTTCAAAACC
* *
61551 ATATATATTTCAAAAATATTTTCAAAACC
1 ATATATATTTAAAAAAAATTTTCAAAACC
61580 ATAT
1 ATAT
61584 GTTAACGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (29 bp):
ATATATATTTAAAAAAAATTTTCAAAACC
Found at i:61675 original size:35 final size:37
Alignment explanation
Indices: 61629--61881 Score: 223
Period size: 38 Copynumber: 6.8 Consensus size: 37
61619 AAAAAATTTC
61629 AACTATATATTATATAA-ATTTCAAAATGATTTT-AA
1 AACTATATATTATATAAGATTTCAAAATGATTTTAAA
* * *
61664 AACTATTTATTATATAAGTTTTCAAAATGGTTTTAAA
1 AACTATATATTATATAAGATTTCAAAATGATTTTAAA
* * * *
61701 AACTATATAATATATATGGTTTCAAAAAT-ATCTTCAAA
1 AACTATATATTATATAAGATTTC-AAAATGAT-TTTAAA
* * * *
61739 AACTATATAATATATATGTTTTCAAAAAAATG-TTTTCAA
1 AACTATATATTATATAAGATTTC---AAAATGATTTTAAA
* *
61778 AACTATA-A-TATATATGTTTTCAAAAATG-TTTTCAAA
1 AACTATATATTATATAAGATTTC-AAAATGATTTT-AAA
* *
61814 AACTATATATATATATAAGTTTTCAAAATGATATTAAA
1 AACTATATAT-TATATAAGATTTCAAAATGATTTTAAA
*
61852 AACTATATATTATATACGTAGTTTCAAAAT
1 AACTATATATTATATAAG-A-TTTCAAAAT
61882 ATGTATATAT
Statistics
Matches: 187, Mismatches: 17, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
35 27 0.14
36 23 0.12
37 43 0.23
38 52 0.28
39 35 0.19
40 7 0.04
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.41
Consensus pattern (37 bp):
AACTATATATTATATAAGATTTCAAAATGATTTTAAA
Found at i:61762 original size:75 final size:75
Alignment explanation
Indices: 61662--61867 Score: 265
Period size: 75 Copynumber: 2.7 Consensus size: 75
61652 AAATGATTTT
* *
61662 AAAACTATTTATTATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATATGGTTTCAAA
1 AAAACTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATATGGTTTCAAA
61727 AATATCTTCA
66 AATATCTTCA
* * *
61737 AAAACTATATAATATATATGTTTTCAAAAAAAT-GTTTTCAAAAC--TATAATATATATGTTTTC
1 AAAACTATATAATATATAAGTTTTC---AAAATGGTTTTAAAAACTATATAATATATATGGTTTC
* *
61799 AAAAATGTTTTCA
63 AAAAATATCTTCA
* * *
61812 AAAACTATATATATATATAAGTTTTCAAAATGATATTAAAAACTATATATTATATA
1 AAAACTATATA-ATATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATA
61868 CGTAGTTTCA
Statistics
Matches: 112, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
73 5 0.04
74 8 0.07
75 61 0.54
76 23 0.21
77 10 0.09
78 5 0.04
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (75 bp):
AAAACTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATATGGTTTCAAA
AATATCTTCA
Found at i:61808 original size:12 final size:12
Alignment explanation
Indices: 61791--61815 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61781 TATAATATAT
61791 ATGTTTTCAAAA
1 ATGTTTTCAAAA
61803 ATGTTTTCAAAA
1 ATGTTTTCAAAA
61815 A
1 A
61816 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:62874 original size:164 final size:164
Alignment explanation
Indices: 62479--63637 Score: 1826
Period size: 164 Copynumber: 7.0 Consensus size: 164
62469 CCTTTTTGCA
* *
62479 TTGAGCTATGCTGTAAATCTGGTT-TG-CCTCTGAA-CTGAGTGTAATCGAACTCGAA-GGTCTT
1 TTGAGTTATGCTGTAAA--T-GTTATGCCCT-TGAAGCTGAGTGTAATCGAACT-TAAGGGTC-T
* * * * * * * * *
62540 TTGGTGACAGATAACCCTTTTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCG
60 TT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTAGGAGCTGAGCG
* * ** * *
62605 TAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGAC
121 TAGTCGAACTCAAAGGTCTTT-GCTAACAGATAACCCTTCTAGCC
* * * * * * *
62650 TTAAGTTGTGCTGCAAATGATATGTCCTCGAAGCTGAGTGTAATCGAACTCGAA-GGTCTTTGGC
1 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTCTTTGGC
*
62714 AGATAGCCCTTCTCGACTTAAGCTATTATGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAAC
65 AGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAAC
62779 TCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
130 TCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
*
62814 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTAAGTGTAATCGAACTTAAGGGTCTTTGGCA
1 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
*
62879 GATAGCCCTTTTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
66 GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
*
62944 CAAAGGTCTTTGCTAGCAGATAACCCTTCTAGCC
131 CAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
62978 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
1 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
63043 GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
66 GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
63108 CAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
131 CAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
*
63142 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGTTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
1 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
*
63207 GATAGCCCTTCTCGACTTAAGCTATTCTACAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
66 GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
*
63272 CAAAGGTCTTTGCTAGCAGATAACCCTTCTAGCC
131 CAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
63306 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
1 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
63371 GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
66 GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
63436 CAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
131 CAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
63470 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
1 TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
*
63535 GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
66 GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
* * * * * *
63600 CGAAGGTC-TTGGTGACAGGTAGCCCTTCTGGCC
131 CAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
63633 TTGAG
1 TTGAG
63638 CTAAGCTGCA
Statistics
Matches: 935, Mismatches: 49, Indels: 16
0.94 0.05 0.02
Matches are distributed among these distances:
163 27 0.03
164 787 0.84
165 33 0.04
166 34 0.04
167 1 0.00
168 3 0.00
169 9 0.01
170 28 0.03
171 13 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
TTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCA
GATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACT
CAAAGGTCTTTGCTAACAGATAACCCTTCTAGCC
Found at i:66990 original size:19 final size:19
Alignment explanation
Indices: 66966--67011 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
66956 AGTTAATGTG
66966 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
66985 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
67004 AATGCAAA
1 AATGCAAA
67012 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:68735 original size:30 final size:30
Alignment explanation
Indices: 68699--68759 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
68689 GTCGAAGATG
*
68699 TTAGGAAAAAAAAAACAAATAAGT-AATGAA
1 TTAGGAAAAAAAAAA-AAATAAATAAATGAA
* *
68729 TTAGGAAGAATAAAAAAATAAATAAATGAA
1 TTAGGAAAAAAAAAAAAATAAATAAATGAA
68759 T
1 T
68760 ATAAATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.66, C:0.02, G:0.13, T:0.20
Consensus pattern (30 bp):
TTAGGAAAAAAAAAAAAATAAATAAATGAA
Found at i:68998 original size:22 final size:22
Alignment explanation
Indices: 68973--69015 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
68963 ATGGGAAAGA
*
68973 AATAACAATA-ATAAAATAAAAT
1 AATAAAAATAGATAAAA-AAAAT
68995 AATAAAAATAGATAAAAAAAA
1 AATAAAAATAGATAAAAAAAA
69016 GGTTAAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AATAAAAATAGATAAAAAAAAT
Found at i:69004 original size:14 final size:14
Alignment explanation
Indices: 68972--69001 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
68962 TATGGGAAAG
68972 AAATAACAATAATA
1 AAATAACAATAATA
68986 AAATAA-AATAATA
1 AAATAACAATAATA
68999 AAA
1 AAA
69002 ATAGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAACAATAATA
Found at i:69009 original size:13 final size:14
Alignment explanation
Indices: 68972--69004 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
68962 TATGGGAAAG
68972 AAATAACAATAAT-A
1 AAATAA-AATAATAA
68986 AAATAAAATAATAA
1 AAATAAAATAATAA
69000 AAATA
1 AAATA
69005 GATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAATAA
Found at i:70327 original size:4 final size:4
Alignment explanation
Indices: 70318--70380 Score: 53
Period size: 4 Copynumber: 16.8 Consensus size: 4
70308 ATAGACCTAA
* * * * *
70318 AAAT AAAT AAAT AAAT AAAT AAAC GAGT AAAT -AAT -AAT AAA- CAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
70363 AAAT AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
70381 ATACTATATA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
3 11 0.23
4 36 0.77
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:70425 original size:30 final size:29
Alignment explanation
Indices: 70391--70453 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
70381 ATACTATATA
* *
70391 ATATATATTTAAAAAAAATGTTTTAAAACT
1 ATATATATTTAAAAAAAAT-TTTCAAAACC
* *
70421 ATATATATTTCAAAAATATTTTCAAAACC
1 ATATATATTTAAAAAAAATTTTCAAAACC
70450 ATAT
1 ATAT
70454 GTTAACGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (29 bp):
ATATATATTTAAAAAAAATTTTCAAAACC
Found at i:70545 original size:35 final size:37
Alignment explanation
Indices: 70499--70749 Score: 221
Period size: 37 Copynumber: 6.8 Consensus size: 37
70489 AAAAAATTTC
70499 AACTATATATTATATAA-ATTTCAAAATGATTTT-AA
1 AACTATATATTATATAAGATTTCAAAATGATTTTAAA
* * *
70534 AACTATTTATTATATAAGTTTTCAAAATGGTTTTAAA
1 AACTATATATTATATAAGATTTCAAAATGATTTTAAA
* * * *
70571 AACTATATAATATATATGGTTTCAAAAAT-ATCTTCAAA
1 AACTATATATTATATAAGATTTC-AAAATGAT-TTTAAA
* * * *
70609 AACTATATAATATATATGTTTTCAAAAAAATG-TTTTCAA
1 AACTATATATTATATAAGATTTC---AAAATGATTTTAAA
* *
70648 AACTATA-A-TATATATGTTTTCAAAAATG-TTTTCAAA
1 AACTATATATTATATAAGATTTC-AAAATGATTTT-AAA
* *
70684 AACTATATA-TATATAAGTTTTCAAAATGATATTAAA
1 AACTATATATTATATAAGATTTCAAAATGATTTTAAA
*
70720 AACTATATATTATATACGTAGTTTCAAAAT
1 AACTATATATTATATAAG-A-TTTCAAAAT
70750 ATGTATATAT
Statistics
Matches: 186, Mismatches: 17, Indels: 22
0.83 0.08 0.10
Matches are distributed among these distances:
35 27 0.15
36 41 0.22
37 58 0.31
38 33 0.18
39 20 0.11
40 7 0.04
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.41
Consensus pattern (37 bp):
AACTATATATTATATAAGATTTCAAAATGATTTTAAA
Found at i:70632 original size:75 final size:75
Alignment explanation
Indices: 70532--70735 Score: 263
Period size: 75 Copynumber: 2.7 Consensus size: 75
70522 AAATGATTTT
* *
70532 AAAACTATTTATTATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATATGGTTTCAAA
1 AAAACTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATATGGTTTCAAA
70597 AATATCTTCA
66 AATATCTTCA
* * *
70607 AAAACTATATAATATATATGTTTTCAAAAAAAT-GTTTTCAAAAC--TATAATATATATGTTTTC
1 AAAACTATATAATATATAAGTTTTC---AAAATGGTTTTAAAAACTATATAATATATATGGTTTC
* *
70669 AAAAATGTTTTCA
63 AAAAATATCTTCA
* * *
70682 AAAACTATAT-ATATATAAGTTTTCAAAATGATATTAAAAACTATATATTATATA
1 AAAACTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATA
70736 CGTAGTTTCA
Statistics
Matches: 111, Mismatches: 12, Indels: 13
0.82 0.09 0.10
Matches are distributed among these distances:
71 5 0.05
72 8 0.07
74 23 0.21
75 60 0.54
77 10 0.09
78 5 0.05
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (75 bp):
AAAACTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATATGGTTTCAAA
AATATCTTCA
Found at i:70678 original size:12 final size:12
Alignment explanation
Indices: 70661--70685 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70651 TATAATATAT
70661 ATGTTTTCAAAA
1 ATGTTTTCAAAA
70673 ATGTTTTCAAAA
1 ATGTTTTCAAAA
70685 A
1 A
70686 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:78995 original size:21 final size:21
Alignment explanation
Indices: 78971--79013 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
78961 AAATCTATTC
* * *
78971 GATCTTCCCCCAATTTCTTCT
1 GATCCTCCCACAAATTCTTCT
78992 GATCCTCCCACAAATTCTTCT
1 GATCCTCCCACAAATTCTTCT
79013 G
1 G
79014 TTACAACCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.37, G:0.07, T:0.37
Consensus pattern (21 bp):
GATCCTCCCACAAATTCTTCT
Found at i:79572 original size:37 final size:36
Alignment explanation
Indices: 79505--79623 Score: 175
Period size: 37 Copynumber: 3.2 Consensus size: 36
79495 CAAAATCATC
**
79505 ATTTCCAAAACTAGTGGAAAAACCTAATTTGAGCAT
1 ATTTCCAATGCTAGTGGAAAAACCTAATTTGAGCAT
79541 ATTTCCAATGCTAGTGGAAAAAACCTAATTTGAGCAT
1 ATTTCCAATGCTAGTGG-AAAAACCTAATTTGAGCAT
* *
79578 TTTTCCAATGCTAGTGGAAATACCTAATTTGAGCATT
1 ATTTCCAATGCTAGTGGAAAAACCTAATTTGAGCA-T
*
79615 TTTTCCAAT
1 ATTTCCAAT
79624 ATTCAAGTGA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
36 32 0.42
37 45 0.58
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (36 bp):
ATTTCCAATGCTAGTGGAAAAACCTAATTTGAGCAT
Found at i:80215 original size:31 final size:31
Alignment explanation
Indices: 80180--80242 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
80170 AATTCGGTGA
80180 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTAGGAACTCCC
80211 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTAGGAACTCCC
80242 A
1 A
80243 AACTCTTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (31 bp):
ATTCAATATGTCCTTCTCACTAGGAACTCCC
Found at i:84969 original size:36 final size:36
Alignment explanation
Indices: 84919--85031 Score: 163
Period size: 36 Copynumber: 3.1 Consensus size: 36
84909 CAAAATCATC
*
84919 ATTTCCAATACTAGTGGAAAAACCTAATTTGAGCAT
1 ATTTCCAATGCTAGTGGAAAAACCTAATTTGAGCAT
84955 ATTTCCAATGCTAGTGGAAAAACCTAATTTGAGCAT
1 ATTTCCAATGCTAGTGGAAAAACCTAATTTGAGCAT
* * * * *
84991 TTTTCCAACGCTAGTAGAAACACCTAATTTAAGCAT
1 ATTTCCAATGCTAGTGGAAAAACCTAATTTGAGCAT
*
85027 TTTTC
1 ATTTC
85032 TAATATTCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (36 bp):
ATTTCCAATGCTAGTGGAAAAACCTAATTTGAGCAT
Found at i:86978 original size:22 final size:22
Alignment explanation
Indices: 86950--87025 Score: 134
Period size: 22 Copynumber: 3.5 Consensus size: 22
86940 ACACATGTAT
86950 TAATTTATTAGTAAATTAAAGG
1 TAATTTATTAGTAAATTAAAGG
*
86972 TAATTTATTAGTAAATTAAACG
1 TAATTTATTAGTAAATTAAAGG
86994 TAATTTATTAGTAAATTAAAGG
1 TAATTTATTAGTAAATTAAAGG
*
87016 AAATTTATTA
1 TAATTTATTA
87026 TTATATTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.42
Consensus pattern (22 bp):
TAATTTATTAGTAAATTAAAGG
Found at i:88064 original size:20 final size:20
Alignment explanation
Indices: 88023--88076 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
88013 GAGATAAATT
88023 AAATAAAATAAAT-TTATCAA
1 AAATAAAA-AAATATTATCAA
* * *
88043 AACTAATAAAATATTATTAA
1 AAATAAAAAAATATTATCAA
88063 AAATAAAAAAATAT
1 AAATAAAAAAATAT
88077 CAAACATATG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATAAAAAAATATTATCAA
Found at i:94421 original size:29 final size:29
Alignment explanation
Indices: 94389--94475 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
94379 CATTTCCCTC
* *
94389 TTATTTACCTTTTAGGCACCCTTCCATCT
1 TTATTTACCTGTCAGGCACCCTTCCATCT
*
94418 TTATTTCCCTGTCAGGCACCCTTCCATCT
1 TTATTTACCTGTCAGGCACCCTTCCATCT
* * *
94447 TTATTTTCCTGTCAGTCACCCTTCTATCT
1 TTATTTACCTGTCAGGCACCCTTCCATCT
94476 ATTTCTCGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.15, C:0.33, G:0.08, T:0.44
Consensus pattern (29 bp):
TTATTTACCTGTCAGGCACCCTTCCATCT
Found at i:94921 original size:18 final size:18
Alignment explanation
Indices: 94886--94919 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
94876 TTTTGTTAGT
94886 ATTTTATTTAATTATTTA
1 ATTTTATTTAATTATTTA
*
94904 ATTTTTTTTAA-TATTT
1 ATTTTATTTAATTATTT
94920 TACTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTATTTAATTATTTA
Found at i:94921 original size:30 final size:31
Alignment explanation
Indices: 94858--94929 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
94848 CTTTAAGGTA
* *
94858 TATTTATTATATTTAATATTTTGTTAGTATTT
1 TATTTAAT-TATTTAATATTTTGTTAATATTT
*
94890 TATTTAATTATTTAAT-TTTTTTTAATATTT
1 TATTTAATTATTTAATATTTTGTTAATATTT
*
94920 TACTTAATTA
1 TATTTAATTA
94930 ATTTTTCTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 21 0.58
31 8 0.22
32 7 0.19
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (31 bp):
TATTTAATTATTTAATATTTTGTTAATATTT
Done.