Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007365.1 Hibiscus syriacus cultivar Beakdansim tig00019758_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: 162358
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1558 original size:2 final size:2
Alignment explanation
Indices: 1551--1674 Score: 67
Period size: 2 Copynumber: 60.5 Consensus size: 2
1541 AACAACTACA
* * *
1551 AT AT AT AT AT AT A- AT AT AT AT AA ACT AT AT -T TT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
1592 AGT AT AT AT AT AT AT AC AA ACT AT AT AGT TT AT AT TT AT -T AT
1 A-T AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* * *
1634 -T AT ACT AT AT AA ACT AT AT AT AT AT GT AT AA ACT AT AT AT A
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT A
1675 ACATGTATAG
Statistics
Matches: 93, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
1 4 0.04
2 81 0.87
3 8 0.09
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1682 original size:20 final size:20
Alignment explanation
Indices: 1641--1695 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1631 TATTATACTA
*
1641 TATAAACTATATAT-ATATG
1 TATAAACTATATATAACATG
1660 TATAAACTATATATAACATG
1 TATAAACTATATATAACATG
*
1680 TATAGACTATACTATA
1 TATAAACTATA-TATA
1696 TAGTTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 14 0.44
20 14 0.44
21 4 0.12
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (20 bp):
TATAAACTATATATAACATG
Found at i:1749 original size:22 final size:22
Alignment explanation
Indices: 1723--1764 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1713 ATTAAACTAT
1723 ATATAAACTACATAGTTTATTA
1 ATATAAACTACATAGTTTATTA
* *
1745 ATATAAATTATATAGTTTAT
1 ATATAAACTACATAGTTTAT
1765 CTATAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATAAACTACATAGTTTATTA
Found at i:1786 original size:92 final size:93
Alignment explanation
Indices: 1690--1897 Score: 216
Period size: 92 Copynumber: 2.3 Consensus size: 93
1680 TATAGACTAT
* * *
1690 ACTATATAGTTTATATATGA-ACTATTAAACTAT-A-TATAAACTACATAGTTTATTA-ATATAA
1 ACTATATAGTTTATATATGATA-TATT-AACTATAATTATAAA-TA-ATA-TATACTATATACAA
* *
1751 ATTATATAGTTTA-T-CTATAAATTATATATAA
61 ATTATATAGTTTATTAATATAAATTATAAATAA
* * * ** *
1782 ACTATACAATTTATAT-TTATATATTATGTATAATTATAAATAATATATACTATGTACAAATTAT
1 ACTATATAGTTTATATATGATATATTAACTATAATTATAAATAATATATACTATATACAAATTAT
1846 ATAGTTTATTAATATAAATTATAAATAA
66 ATAGTTTATTAATATAAATTATAAATAA
1874 ACTATATAGTTTATATAT-ATATAT
1 ACTATATAGTTTATATATGATATAT
1898 AGTATATGGT
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
89 5 0.05
90 24 0.25
91 10 0.10
92 56 0.58
93 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (93 bp):
ACTATATAGTTTATATATGATATATTAACTATAATTATAAATAATATATACTATATACAAATTAT
ATAGTTTATTAATATAAATTATAAATAA
Found at i:1859 original size:33 final size:34
Alignment explanation
Indices: 1821--1903 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 34
1811 ATAATTATAA
** *
1821 ATAATATATACTATGTACAAATTATATAGTTTAT
1 ATAATATATACTATAAACAAACTATATAGTTTAT
* * *
1855 -TAATATAAATTATAAATAAACTATATAGTTTAT
1 ATAATATATACTATAAACAAACTATATAGTTTAT
*
1888 ATATATATATAGTATA
1 ATA-ATATATACTATA
1904 TGGTTTAGGG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 27 0.69
34 2 0.05
35 10 0.26
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (34 bp):
ATAATATATACTATAAACAAACTATATAGTTTAT
Found at i:2065 original size:22 final size:22
Alignment explanation
Indices: 2011--2091 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
2001 TACTATATGT
*
2011 AACTATATATACTATATAGT-T-
1 AACTATATAAACTATAT-GTATA
* *
2032 TAC-ATATGAACTATATGTATA
1 AACTATATAAACTATATGTATA
*
2053 AACTATATAAACTATATATATA
1 AACTATATAAACTATATGTATA
*
2075 AACTATGTAAACTATAT
1 AACTATATAAACTATAT
2092 AGTTTACATA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.04
20 12 0.24
21 4 0.08
22 32 0.64
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (22 bp):
AACTATATAAACTATATGTATA
Found at i:2092 original size:22 final size:22
Alignment explanation
Indices: 2040--2116 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
2030 TTTACATATG
* *
2040 AACTATATGTATAAACTATATA
1 AACTATATATATAAACTATGTA
2062 AACTATATATATAAACTATGTA
1 AACTATATATATAAACTATGTA
* *
2084 AACTATATAGTTTACA-TATG--
1 AACTATATA-TATAAACTATGTA
2104 AACTATATATATA
1 AACTATATATATA
2117 GTTTATTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.06
20 9 0.18
22 33 0.67
23 4 0.08
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (22 bp):
AACTATATATATAAACTATGTA
Found at i:2169 original size:24 final size:24
Alignment explanation
Indices: 2087--2191 Score: 115
Period size: 24 Copynumber: 4.2 Consensus size: 24
2077 CTATGTAAAC
*
2087 TATATAGTTTA-CATATGAACTATA
1 TATATAGTTTATTA-ATGAACTATA
2111 TATATAGTTTATTAATGAACTATA
1 TATATAGTTTATTAATGAACTATA
*
2135 TATATAGTTTATTAGTGAACTATA
1 TATATAGTTTATTAATGAACTATA
* *
2159 TAAACTA-TTTATATAATATATACTATA
1 TATA-TAGTTTAT-TAAT-GA-ACTATA
2186 TATATA
1 TATATA
2192 AACTATAGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
24 52 0.74
25 6 0.09
26 3 0.04
27 9 0.13
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.45
Consensus pattern (24 bp):
TATATAGTTTATTAATGAACTATA
Found at i:2198 original size:18 final size:18
Alignment explanation
Indices: 2156--2494 Score: 59
Period size: 18 Copynumber: 18.1 Consensus size: 18
2146 TTAGTGAACT
* *
2156 ATATAAACTATTTATATA
1 ATATATACTATATATATA
2174 ATATATACTATATATATA
1 ATATATACTATATATATA
* * *
2192 A-ACTATAGTTTATAT-TT
1 ATA-TATACTATATATATA
2209 ATATACTACATACTATAGTTGATA
1 ATATA-TAC-TA-TATA--T-ATA
*
2233 TTTATATACTATATAT-TA
1 -ATATATACTATATATATA
*
2251 TATATAAAC-A-ATATAT-
1 -ATATATACTATATATATA
* *
2267 -TATATAGTATA-ATTTA
1 ATATATACTATATATATA
*
2283 CATATGA-ACTATATATAAAA
1 -ATAT-ATACTATATAT-ATA
*
2303 ATTATATAAACTATTTTATATA
1 A-TATAT--ACTA-TATATATA
* *
2325 TATATAAACTATATAGTTTA
1 -ATATATACTATATA-TATA
2345 CATATGA-ACTATATATATA
1 -ATAT-ATACTATATATATA
*
2364 GT-T-TA-T-TAGTGA-ACT-
1 ATATATACTATA-T-ATA-TA
* *
2379 ATATAAACTATTTATATA
1 ATATATACTATATATATA
*
2397 GTATATACTATATATATA
1 ATATATACTATATATATA
*
2415 A-ACTATAGTTTATATTATATA
1 ATA-TATA--CTATA-TATATA
* *
2436 CTACATACTATAT-TATA
1 ATATATACTATATATATA
* *
2453 TATATATATTATATA-AAA
1 -ATATATACTATATATATA
2471 ACTCTATATACTATATAGTATA
1 A---TATATACTATATA-TATA
2493 AT
1 AT
2495 TTACATATGA
Statistics
Matches: 230, Mismatches: 42, Indels: 97
0.62 0.11 0.26
Matches are distributed among these distances:
14 7 0.03
15 8 0.03
16 9 0.04
17 17 0.07
18 83 0.36
19 18 0.08
20 44 0.19
21 10 0.04
22 19 0.08
23 7 0.03
24 4 0.02
25 4 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (18 bp):
ATATATACTATATATATA
Found at i:2198 original size:20 final size:20
Alignment explanation
Indices: 2152--2493 Score: 94
Period size: 20 Copynumber: 17.1 Consensus size: 20
2142 TTTATTAGTG
*
2152 AACTATATAAACTATTTATAT-
1 AACTATAT--ACTATATATATA
2173 AA-TATATACTATATATATA
1 AACTATATACTATATATATA
* *
2192 AACTATAGT-TTATATTTATA
1 AACTATA-TACTATATATATA
* *
2212 TACTACATACTATAGT-TGAT-
1 AACTATATACTATA-TAT-ATA
**
2232 ATTTATATACTATATAT-TA
1 AACTATATACTATATATATA
* * *
2251 TA-TATAAACAATATAT-TA
1 AACTATATACTATATATATA
* * * * *
2269 TA-TAGTATAATTTACATATG
1 AACTA-TATACTATATATATA
*
2289 AACTATATA-TAAAAATTATATA
1 AACTATATACT--ATA-TATATA
*
2311 AACTATTTTA-TATATATATA
1 AACTA-TATACTATATATATA
* * * *
2331 AACTATATAGTTTACATATG
1 AACTATATACTATATATATA
*
2351 AACTATATA-TATAGTTTATTAGTG
1 AACTATATACTATA---TA-TA-TA
2375 AACTATATAAACTAT-T-TATA
1 AACTATAT--ACTATATATATA
* *
2395 TAGTATATACTATATATATA
1 AACTATATACTATATATATA
*
2415 AACTATAGT-TTATAT-TATA
1 AACTATA-TACTATATATATA
* *
2434 TACTACATACTATAT-TATA
1 AACTATATACTATATATATA
* *
2453 TA-TATATA-T-TATATAAA
1 AACTATATACTATATATATA
2470 AACTCTATATACTATATAGTATA
1 AA--CTATATACTATATA-TATA
2493 A
1 A
2494 TTTACATATG
Statistics
Matches: 240, Mismatches: 46, Indels: 68
0.68 0.13 0.19
Matches are distributed among these distances:
16 3 0.01
17 5 0.02
18 40 0.17
19 39 0.16
20 99 0.41
21 15 0.06
22 14 0.06
23 11 0.05
24 10 0.04
26 1 0.00
27 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (20 bp):
AACTATATACTATATATATA
Found at i:2205 original size:27 final size:27
Alignment explanation
Indices: 2175--2243 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
2165 ATTTATATAA
*
2175 TATATACTATATA-TATAAACTATAGTT
1 TATAT-CTATATACTACAAACTATAGTT
* *
2202 TATATTTATATACTACATACTATAGTT
1 TATATCTATATACTACAAACTATAGTT
* *
2229 GATATTTATATACTA
1 TATATCTATATACTA
2244 TATATTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 6 0.16
27 31 0.84
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (27 bp):
TATATCTATATACTACAAACTATAGTT
Found at i:2252 original size:27 final size:27
Alignment explanation
Indices: 2182--2252 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
2172 TAATATATAC
* *
2182 TATATA-TATAAACTATAGTTTATATT
1 TATATACTATATACTATAGTTGATATT
*
2208 TATATACTACATACTATAGTTGATATT
1 TATATACTATATACTATAGTTGATATT
*
2235 TATATACTATATATTATA
1 TATATACTATATACTATA
2253 TATAAACAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 6 0.15
27 33 0.85
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (27 bp):
TATATACTATATACTATAGTTGATATT
Found at i:2297 original size:32 final size:32
Alignment explanation
Indices: 2230--2298 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
2220 ACTATAGTTG
*
2230 ATAT-TTATATACTATATATTATATATAAACA
1 ATATATTATATACTATATATTACATATAAACA
* * *
2261 ATATATTATATAGTATA-ATTTACATATGAACT
1 ATATATTATATACTATATA-TTACATATAAACA
2293 ATATAT
1 ATATAT
2299 AAAAATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (32 bp):
ATATATTATATACTATATATTACATATAAACA
Found at i:2357 original size:223 final size:212
Alignment explanation
Indices: 2111--2539 Score: 648
Period size: 223 Copynumber: 2.0 Consensus size: 212
2101 ATGAACTATA
*
2111 TATATAGTTTATTAATGAACTATATATATAGTTTATTAGTGAACTATATAAACTATTTATATAAT
1 TATATAGTTTAATAATGAACTATATATATAGTTTATTAGTGAACTATATAAACTATTTATATAAT
2176 ATATACTATATATATAAACTATAGTTTATATTTATATACTACATACTATAGTTGATATTTATATA
66 ATATACTATATATATAAACTATAGTTTATA-TTATATACTACATACTATA-TT-ATA--TATATA
* *
2241 CTATATATTATATATAAA-CAATATATTATATAGTATAATTTACATATGAACTATATATAAAAAT
126 -TAT-TA-TATA-A-AAACCAATATACTATATAGTATAATTTACATATGAAC--TATAT-AAAAC
*
2305 TATATAAACTAT-TTTATATATATATAAAC
183 TATATAAACTATAGTTATATATATATAAAC
*
2334 TATATAGTTTACAT-ATGAACTATATATATAGTTTATTAGTGAACTATATAAACTATTTATATAG
1 TATATAGTTTA-ATAATGAACTATATATATAGTTTATTAGTGAACTATATAAACTATTTATATAA
2398 TATATACTATATATATAAACTATAGTTTATATTATATACTACATACTATATTATATATATATATT
65 TATATACTATATATATAAACTATAGTTTATATTATATACTACATACTATATTATATATATATATT
*
2463 ATATAAAAACTCTATATACTATATAGTATAATTTACATATGAACTATATAAAACTATATAAACTA
130 ATATAAAAAC-CAATATACTATATAGTATAATTTACATATGAACTATATAAAACTATATAAACTA
2528 TAGTTATATATA
194 TAGTTATATATA
2540 ACTATAATAT
Statistics
Matches: 196, Mismatches: 6, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
212 16 0.08
213 17 0.09
214 1 0.01
215 35 0.18
216 2 0.01
217 3 0.02
218 6 0.03
220 3 0.02
221 2 0.01
222 19 0.10
223 91 0.46
224 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (212 bp):
TATATAGTTTAATAATGAACTATATATATAGTTTATTAGTGAACTATATAAACTATTTATATAAT
ATATACTATATATATAAACTATAGTTTATATTATATACTACATACTATATTATATATATATATTA
TATAAAAACCAATATACTATATAGTATAATTTACATATGAACTATATAAAACTATATAAACTATA
GTTATATATATATAAAC
Found at i:2361 original size:24 final size:24
Alignment explanation
Indices: 2334--2414 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 24
2324 ATATATAAAC
2334 TATATAGTTTACATA-TGAACTATA
1 TATATAGTTTA-ATAGTGAACTATA
*
2358 TATATAGTTTATTAGTGAACTATA
1 TATATAGTTTAATAGTGAACTATA
* *
2382 TAAACTA-TTTATATAGTATATACTATA
1 TATA-TAGTTTA-ATAGT-GA-ACTATA
2409 TATATA
1 TATATA
2415 AACTATAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
23 2 0.04
24 27 0.57
25 6 0.13
26 3 0.06
27 9 0.19
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (24 bp):
TATATAGTTTAATAGTGAACTATA
Found at i:2403 original size:9 final size:8
Alignment explanation
Indices: 2391--2467 Score: 52
Period size: 9 Copynumber: 9.2 Consensus size: 8
2381 ATAAACTATT
2391 TATATAGTA
1 TATATA-TA
2400 TATACTATA
1 TATA-TATA
*
2409 TATATAAA
1 TATATATA
*
2417 CTATAGTTTA
1 -TATA-TATA
2427 TAT-TATA
1 TATATATA
*
2434 TACTACATA
1 TA-TATATA
2443 CTATAT-TA
1 -TATATATA
2451 TATATATA
1 TATATATA
2459 TAT-TATA
1 TATATATA
2466 TA
1 TA
2468 AAAACTCTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
7 16 0.29
8 11 0.20
9 22 0.40
10 6 0.11
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (8 bp):
TATATATA
Found at i:2487 original size:2 final size:2
Alignment explanation
Indices: 2168--2467 Score: 54
Period size: 2 Copynumber: 144.0 Consensus size: 2
2158 ATAAACTATT
* * *
2168 TA TA TA -A TA TA TA CTA TA TA TA TA AA CTA TA GTT TA TA TT TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA TA TA
* *
2210 TA TA CTA CA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA T- TA TA
1 TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA
* * * *
2253 TA TA AA CA -A TA TA T- TA TA TA GTA TA -A TT TA CA TA TGA -A CTA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA -TA
* * * * *
2294 TA TA TA AA AA T- TA TA TA AA CTA T- TT TA TA TA TA TA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * *
2336 TA TA GTT TA CA TA TGA -A CTA TA TA TA TA GTT TA T- TA GTGA -A
1 TA TA -TA TA TA TA T-A TA -TA TA TA TA TA -TA TA TA TA -T-A TA
* * *
2377 CTA TA TA AA CTA TT TA TA TA GTA TA TA CTA TA TA TA TA AA CTA TA
1 -TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA
* *
2422 GTT TA TA T- TA TA TA CTA CA TA CTA TA T- TA TA TA TA TA TA T-
1 -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
2462 TA TA TA
1 TA TA TA
2468 AAAACTCTAT
Statistics
Matches: 217, Mismatches: 39, Indels: 84
0.64 0.11 0.25
Matches are distributed among these distances:
1 15 0.07
2 166 0.76
3 35 0.16
4 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2487 original size:7 final size:6
Alignment explanation
Indices: 2168--2467 Score: 54
Period size: 7 Copynumber: 48.0 Consensus size: 6
2158 ATAAACTATT
* * * *
2168 TATATA -ATATA TACTATA TATATA AACTATA GTTTATA TTTATA TACTACA
1 TATATA TATATA TA-TATA TATATA TA-TATA -TATATA TATATA TA-TATA
* * *
2219 TACTATA GT-TGATA TTTATA TACTATA TAT-TA TATATA AACA-A TATAT-
1 TA-TATA -TAT-ATA TATATA TA-TATA TATATA TATATA TATATA TATATA
* * * * *
2267 TATATA GTATA-A TTTACA TATGA-A CTATATA TAAAAA T-TATA TAAACTA
1 TATATA -TATATA TATATA TAT-ATA -TATATA TATATA TATATA TATA-TA
* * * * *
2316 T-TTTA TATATA TATAAA CTATATA GTTTACA TATGA-A CTATATA TATAGTT
1 TATATA TATATA TATATA -TATATA -TATATA TAT-ATA -TATATA TATA-TA
* *
2367 TAT-TA GTGA-ACTA TATAAA CTATTTA TATAGTA TATACTA TATATA
1 TATATA -T-ATA-TA TATATA -TATATA TATA-TA TATA-TA TATATA
* * *
2413 TAAACTA TAGTTTA TAT-TA TATACTA CATACTA TAT-TA TATATA TATAT-
1 TATA-TA TA-TATA TATATA TATA-TA TATA-TA TATATA TATATA TATATA
2462 TATATA
1 TATATA
2468 AAAACTCTAT
Statistics
Matches: 217, Mismatches: 39, Indels: 76
0.65 0.12 0.23
Matches are distributed among these distances:
5 43 0.20
6 71 0.33
7 100 0.46
8 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:2578 original size:27 final size:27
Alignment explanation
Indices: 2542--2599 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
2532 TATATATAAC
*
2542 TATAATATAGTTGATATTTATATAGTA
1 TATAATATAGTTGATATTTATATACTA
*
2569 TATACTATAGTTGATATTTATATACTA
1 TATAATATAGTTGATATTTATATACTA
2596 TATA
1 TATA
2600 TAATTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (27 bp):
TATAATATAGTTGATATTTATATACTA
Found at i:2615 original size:14 final size:15
Alignment explanation
Indices: 2589--2633 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2579 TTGATATTTA
2589 TATACTATATATAAT
1 TATACTATATATAAT
2604 TATACT-TATATAATT
1 TATACTATATATAA-T
*
2619 TTTACTATATA-AAT
1 TATACTATATATAAT
2633 T
1 T
2634 CAAAGTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 9 0.33
15 14 0.52
16 4 0.15
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
TATACTATATATAAT
Found at i:3331 original size:23 final size:23
Alignment explanation
Indices: 3296--3361 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
3286 ATGCACATAA
3296 TTGTCCC-AAGGACCACATAGGT
1 TTGTCCCAAAGGACCACATAGGT
** **
3318 TTGTCCTGAAGGACCACATAATT
1 TTGTCCCAAAGGACCACATAGGT
*
3341 TTGTCCCAAATGACCACATAG
1 TTGTCCCAAAGGACCACATAG
3362 AACCCTCGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 6 0.17
23 30 0.83
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (23 bp):
TTGTCCCAAAGGACCACATAGGT
Found at i:3518 original size:34 final size:35
Alignment explanation
Indices: 3480--3556 Score: 129
Period size: 34 Copynumber: 2.2 Consensus size: 35
3470 ATGGGCATTT
3480 TCACATTGAGTATTTTCGTATACACA-TTCACATG
1 TCACATTGAGTATTTTCGTATACACAGTTCACATG
*
3514 TCACATTGAGTATTTTTGTATACACATGTTCACATG
1 TCACATTGAGTATTTTCGTATACACA-GTTCACATG
3550 TCACATT
1 TCACATT
3557 TTCATAATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 25 0.62
36 15 0.38
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (35 bp):
TCACATTGAGTATTTTCGTATACACAGTTCACATG
Found at i:9303 original size:16 final size:16
Alignment explanation
Indices: 9282--9319 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
9272 CTCCCTGACG
9282 TGCATGTTCCTCACCC
1 TGCATGTTCCTCACCC
*
9298 TGCATGTTCCTCACCT
1 TGCATGTTCCTCACCC
9314 TGCATG
1 TGCATG
9320 CTCGGGGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.37, G:0.16, T:0.34
Consensus pattern (16 bp):
TGCATGTTCCTCACCC
Found at i:10191 original size:21 final size:22
Alignment explanation
Indices: 10167--10217 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
10157 ACCGAAGTGT
10167 CACATA-ATTGTCCAGAAGGAC
1 CACATAGATTGTCCAGAAGGAC
* * *
10188 CACATAGGTTTGTCCCGAAGGGC
1 CACATA-GATTGTCCAGAAGGAC
10211 CACATAG
1 CACATAG
10218 GTTTTGTCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 1 0.04
23 18 0.72
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (22 bp):
CACATAGATTGTCCAGAAGGAC
Found at i:10207 original size:23 final size:24
Alignment explanation
Indices: 10174--10241 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
10164 TGTCACATAA
*
10174 TTGTCCAGAAGGACCACATAGG-T
1 TTGTCCCGAAGGACCACATAGGTT
*
10197 TTGTCCCGAAGGGCCACATAGGTT
1 TTGTCCCGAAGGACCACATAGGTT
* *
10221 TTGTCCCAAAGGACAACATAG
1 TTGTCCCGAAGGACCACATAG
10242 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (24 bp):
TTGTCCCGAAGGACCACATAGGTT
Found at i:10232 original size:24 final size:23
Alignment explanation
Indices: 10174--10241 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
10164 TGTCACATAA
10174 TTGT-CCAGAAGGACCACATAGGT
1 TTGTCCCA-AAGGACCACATAGGT
* *
10197 TTGTCCCGAAGGGCCACATAGGTT
1 TTGTCCCAAAGGACCACATAGG-T
*
10221 TTGTCCCAAAGGACAACATAG
1 TTGTCCCAAAGGACCACATAG
10242 AACCCTCGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (23 bp):
TTGTCCCAAAGGACCACATAGGT
Found at i:12311 original size:16 final size:16
Alignment explanation
Indices: 12290--12322 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12280 AAAAAACAGT
*
12290 AAATAAATAGAAAATA
1 AAATAAAAAGAAAATA
12306 AAATAAAAAGAAAATA
1 AAATAAAAAGAAAATA
12322 A
1 A
12323 TCCTCACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:12845 original size:24 final size:24
Alignment explanation
Indices: 12800--12849 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12790 ATAAAGAACC
*
12800 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
12824 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
12848 AA
1 AA
12850 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:19770 original size:28 final size:28
Alignment explanation
Indices: 19727--19843 Score: 141
Period size: 29 Copynumber: 4.2 Consensus size: 28
19717 GACTATTACG
* **
19727 AAAATAACACATTTTTTGAAATAATTCCC
1 AAAATATCAC-TTTTTCAAAATAATTCCC
*
19756 AGAATATCACCTTTTTCAAAATAATTCCC
1 AAAATATCA-CTTTTTCAAAATAATTCCC
* *
19785 AAAATATCACTTTTTCGAAATAATTCCT
1 AAAATATCACTTTTTCAAAATAATTCCC
19813 AAAATATCA--TTTT-AAAATAATTCCC
1 AAAATATCACTTTTTCAAAATAATTCCC
19838 AAAATA
1 AAAATA
19844 ACATCGTCGG
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
25 16 0.21
26 4 0.05
28 26 0.33
29 31 0.40
30 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATATCACTTTTTCAAAATAATTCCC
Found at i:19819 original size:57 final size:54
Alignment explanation
Indices: 19727--19846 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 54
19717 GACTATTACG
* *
19727 AAAATAACACATTTTTTGAAATAATTCCCAGAATATCACCTTTTTCAAAATAATTCCC
1 AAAATAACACATTTTTCGAAATAATTCCCAAAATATCA---TTTT-AAAATAATTCCC
* *
19785 AAAATATCAC-TTTTTCGAAATAATTCCTAAAATATCATTTTAAAATAATTCCC
1 AAAATAACACATTTTTCGAAATAATTCCCAAAATATCATTTTAAAATAATTCCC
19838 AAAATAACA
1 AAAATAACA
19847 TCGTCGGGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
53 20 0.35
54 4 0.07
57 24 0.42
58 9 0.16
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (54 bp):
AAAATAACACATTTTTCGAAATAATTCCCAAAATATCATTTTAAAATAATTCCC
Found at i:26038 original size:18 final size:19
Alignment explanation
Indices: 26015--26249 Score: 58
Period size: 18 Copynumber: 12.8 Consensus size: 19
26005 ATAAACTATT
26015 TATATAGTATAT-TATACA
1 TATATAGTATATATATACA
*
26033 TATATAGTTTATATATAC-
1 TATATAGTATATATATACA
* * * *
26051 TACATAGTTTACAAATGAACTA
1 TATATAGTATATATAT--AC-A
** * *
26073 TATATAAAAACTCTATATATA
1 TATAT-AGTA-TATATATACA
*
26094 TATAAAGTATATGGTATATACA
1 TATATAGTATA---TATATACA
* **
26116 AACTATA-TAT-TATATAGT
1 TA-TATAGTATATATATACA
26134 TAT-TAGTATATATA-A-A
1 TATATAGTATATATATACA
**
26150 -ATATA-TAT-TATATAGT
1 TATATAGTATATATATACA
*
26166 TCAT-TAGTATATATAAAC-
1 T-ATATAGTATATATATACA
*
26184 TATATAGTATATATAAAC-
1 TATATAGTATATATATACA
* *
26202 TATACA-T-TATATAGTTC-
1 TATATAGTATATATA-TACA
*
26219 -AT-TAGTATATATAAAC-
1 TATATAGTATATATATACA
26235 TATATAGTATATATA
1 TATATAGTATATATA
26250 GTTTATATAT
Statistics
Matches: 159, Mismatches: 32, Indels: 52
0.65 0.13 0.21
Matches are distributed among these distances:
14 4 0.03
15 7 0.04
16 14 0.09
17 19 0.12
18 71 0.45
19 11 0.07
20 4 0.03
21 5 0.03
22 16 0.10
23 4 0.03
24 4 0.03
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (19 bp):
TATATAGTATATATATACA
Found at i:26177 original size:33 final size:32
Alignment explanation
Indices: 26085--26196 Score: 145
Period size: 33 Copynumber: 3.4 Consensus size: 32
26075 TATAAAAACT
* * *
26085 CTATATATATATAAAG-TATATGGTATATACAAA
1 CTATATAT-TATATAGTTAT-TAGTATATATAAA
26118 CTATATATTATATAGTTATTAGTATATATAAA
1 CTATATATTATATAGTTATTAGTATATATAAA
*
26150 ATATATATTATATAGTTCATTAGTATATATAAA
1 CTATATATTATATAGTT-ATTAGTATATATAAA
*
26183 CTATATAGTATATA
1 CTATATATTATATA
26197 TAAACTATAC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
32 33 0.46
33 38 0.54
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (32 bp):
CTATATATTATATAGTTATTAGTATATATAAA
Found at i:26211 original size:51 final size:51
Alignment explanation
Indices: 26137--26291 Score: 247
Period size: 51 Copynumber: 3.0 Consensus size: 51
26127 ATATAGTTAT
26137 TAGTATATATAAAATATATATTATATAGTTCATTAGTATATATAAACTATA
1 TAGTATATATAAAATATATATTATATAGTTCATTAGTATATATAAACTATA
* *
26188 TAGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATA
1 TAGTATATATAAAATATATATTATATAGTTCATTAGTATATATAAACTATA
*** * *
26239 TAGTATATATAGTTTATATATTATATAGTTCATTAATATATATAACCTATA
1 TAGTATATATAAAATATATATTATATAGTTCATTAGTATATATAAACTATA
26290 TA
1 TA
26292 TTAATTTATT
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 96 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.44
Consensus pattern (51 bp):
TAGTATATATAAAATATATATTATATAGTTCATTAGTATATATAAACTATA
Found at i:26225 original size:33 final size:35
Alignment explanation
Indices: 26188--26252 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
26178 ATAAACTATA
26188 TAGTATATATAAACTATACA-T-TATATAGTTCAT
1 TAGTATATATAAACTATACAGTATATATAGTTCAT
*
26221 TAGTATATATAAACTATATAGTATATATAGTT
1 TAGTATATATAAACTATACAGTATATATAGTT
26253 TATATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 19 0.66
34 1 0.03
35 9 0.31
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (35 bp):
TAGTATATATAAACTATACAGTATATATAGTTCAT
Found at i:26256 original size:18 final size:18
Alignment explanation
Indices: 26086--26265 Score: 98
Period size: 18 Copynumber: 10.6 Consensus size: 18
26076 ATAAAAACTC
* *
26086 TATA-TATATATAAAGTA
1 TATAGTATATATAGATTA
* * * *
26103 TATGGTATATACAAACTA
1 TATAGTATATATAGATTA
26121 TATA-T-TATATAG-TTA
1 TATAGTATATATAGATTA
* *
26136 T-TAGTATATATAAAATA
1 TATAGTATATATAGATTA
26153 TATA-T-TATATAG-TTCA
1 TATAGTATATATAGATT-A
* *
26169 T-TAGTATATATAAACTA
1 TATAGTATATATAGATTA
* *
26186 TATAGTATATATAAACTA
1 TATAGTATATATAGATTA
*
26204 TACA-T-TATATAG-TTCA
1 TATAGTATATATAGATT-A
* *
26220 T-TAGTATATATAAACTA
1 TATAGTATATATAGATTA
*
26237 TATAGTATATATAGTTTA
1 TATAGTATATATAGATTA
*
26255 TATATTATATA
1 TATAGTATATA
26266 GTTCATTAAT
Statistics
Matches: 125, Mismatches: 23, Indels: 29
0.71 0.13 0.16
Matches are distributed among these distances:
14 2 0.02
15 9 0.07
16 29 0.23
17 25 0.20
18 60 0.48
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (18 bp):
TATAGTATATATAGATTA
Found at i:26425 original size:61 final size:61
Alignment explanation
Indices: 26351--26483 Score: 185
Period size: 61 Copynumber: 2.2 Consensus size: 61
26341 TATAATGATC
* **
26351 AAATTGAACAAATTTTAAATAAGAAGCTTAAATTAATAAATTGTAACAATAAATTTGGACA
1 AAATTGAACAAATTTTAAATAAGAAACTTAAATTAATAAATTACAACAATAAATTTGGACA
* * * * * *
26412 AAATTGAAGAAATTTTAAATATGAAACTTAAATTAATATATTACATCATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATAAGAAACTTAAATTAATAAATTACAACAATAAATTTGGACA
26473 AAATTGAACAA
1 AAATTGAACAA
26484 CTTTAAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATAAGAAACTTAAATTAATAAATTACAACAATAAATTTGGACA
Found at i:27377 original size:31 final size:31
Alignment explanation
Indices: 27333--27459 Score: 182
Period size: 31 Copynumber: 4.1 Consensus size: 31
27323 GCTCGTATAA
* * *
27333 TAATCTGTTCATATGTCCCGAAGAACATAAG
1 TAATCAGTCCATATGTCCCGAAGAACATAGG
* *
27364 CAATTAGTCCATATGTCCCGAAGAACATAGG
1 TAATCAGTCCATATGTCCCGAAGAACATAGG
** *
27395 TAATCAGTTAATATGTCCTGAAGAACATAGG
1 TAATCAGTCCATATGTCCCGAAGAACATAGG
27426 TAATCAGTCCATATGTCCCGAAGAACATAGG
1 TAATCAGTCCATATGTCCCGAAGAACATAGG
27457 TAA
1 TAA
27460 CCCTCGACTC
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 83 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (31 bp):
TAATCAGTCCATATGTCCCGAAGAACATAGG
Found at i:30834 original size:31 final size:31
Alignment explanation
Indices: 30790--30916 Score: 182
Period size: 31 Copynumber: 4.1 Consensus size: 31
30780 GCTCGTATAA
* * * *
30790 TAATCTGTTCATATGTCCCAAAGAACATAAG
1 TAATCAGTCCATATGTCCCGAAGAACATAGG
*
30821 TAATTAGTCCATATGTCCCGAAGAACATAGG
1 TAATCAGTCCATATGTCCCGAAGAACATAGG
** *
30852 TAATCAGTTAATATGTCCTGAAGAACATAGG
1 TAATCAGTCCATATGTCCCGAAGAACATAGG
30883 TAATCAGTCCATATGTCCCGAAGAACATAGG
1 TAATCAGTCCATATGTCCCGAAGAACATAGG
30914 TAA
1 TAA
30917 CCCTCGACTC
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 84 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (31 bp):
TAATCAGTCCATATGTCCCGAAGAACATAGG
Found at i:32786 original size:103 final size:102
Alignment explanation
Indices: 32580--32893 Score: 350
Period size: 103 Copynumber: 3.1 Consensus size: 102
32570 TTTATAACTT
* * * *
32580 TTCATCCGTGTTCATCCCAAAAACCTCATTTGATATTTACAAACACCAAAACCGAAACCATTTCG
1 TTCATCCGTATTCATCCCAAAAACCTCATTTGATATTCACAAACACCAAAACCCAAACCATTTCA
* * * *
32645 TGTTTTTTTCGATCAAACTCCCATAATTTCAACCTTTG
66 T-ATTTTTTCGATCAAACTCCCAAAAATTCATCCTTTG
* *
32683 TTCATCCGTATTCATCCCAAAAACTCTCATTTGATCTTCAGAAACACCAAAACCCAAACCATTTC
1 TTCATCCGTATTCATCCCAAAAAC-CTCATTTGATATTCACAAACACCAAAACCCAAACCATTTC
* **
32748 ATATTTTTTCGATCAAACACCCAAAAATTCATTTTTTG
65 ATATTTTTTCGATCAAACTCCCAAAAATTCATCCTTTG
* * * *
32786 TTCATTCC--AGTTCTTCCC-CAAACCATTATTTGATATTCACAAACACCAAAACCTAAACCCA-
1 TTCA-TCCGTA-TTCATCCCAAAAACC-TCATTTGATATTCACAAACACCAAAACCCAAA-CCAT
* * *
32847 TTCCTATTTTTTTGATCAAACTCCCAAAAGTTCATCCATTT-
62 TTCATATTTTTTCGATCAAACTCCCAAAAATTCATCC-TTTG
32888 TTCATC
1 TTCATC
32894 TGTGTTCTTC
Statistics
Matches: 180, Mismatches: 25, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
101 3 0.02
102 68 0.38
103 69 0.38
104 40 0.22
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (102 bp):
TTCATCCGTATTCATCCCAAAAACCTCATTTGATATTCACAAACACCAAAACCCAAACCATTTCA
TATTTTTTCGATCAAACTCCCAAAAATTCATCCTTTG
Found at i:32911 original size:102 final size:102
Alignment explanation
Indices: 32580--32905 Score: 363
Period size: 102 Copynumber: 3.2 Consensus size: 102
32570 TTTATAACTT
* * *
32580 TTCATCCGTGTTCATCCCAAAAACCTCATTTGATATTTACAAACACCAAAACCGAAACCATTTCG
1 TTCATCCGTGTTCATCCCAAAAACCTCATTTGATATTCACAAACACCAAAACCCAAACCATTTCA
* * * *
32645 TGTTTTTTTCGATCAAACTCCCATAATTTCAACCTTTG
66 TATTTTTTT-GATCAAACTCCCAAAAATTCATCCTTTG
* * *
32683 TTCATCCGTATTCATCCCAAAAACTCTCATTTGATCTTCAGAAACACCAAAACCCAAACCATTTC
1 TTCATCCGTGTTCATCCCAAAAAC-CTCATTTGATATTCACAAACACCAAAACCCAAACCATTTC
* * **
32748 ATATTTTTTCGATCAAACACCCAAAAATTCATTTTTTG
65 ATATTTTTTTGATCAAACTCCCAAAAATTCATCCTTTG
* * * * *
32786 TTCATTCC-AGTTCTTCCC-CAAACCATTATTTGATATTCACAAACACCAAAACCTAAACCCA-T
1 TTCA-TCCGTGTTCATCCCAAAAACC-TCATTTGATATTCACAAACACCAAAACCCAAA-CCATT
* *
32848 TCCTATTTTTTTGATCAAACTCCCAAAAGTTCATCCATTT-
63 TCATATTTTTTTGATCAAACTCCCAAAAATTCATCC-TTTG
* *
32888 TTCATCTGTGTTCTTCCC
1 TTCATCCGTGTTCATCCC
32906 CAAACCCTTA
Statistics
Matches: 187, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
101 3 0.02
102 76 0.41
103 62 0.33
104 46 0.25
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (102 bp):
TTCATCCGTGTTCATCCCAAAAACCTCATTTGATATTCACAAACACCAAAACCCAAACCATTTCA
TATTTTTTTGATCAAACTCCCAAAAATTCATCCTTTG
Found at i:33104 original size:6 final size:6
Alignment explanation
Indices: 33093--33173 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
33083 ACCCCTAACT
* * * *
33093 CAAACC CAAACC CTAA-C CAGAACC TAAACC TAAACC CAAACC TAATA-C
1 CAAACC CAAACC CAAACC CA-AACC CAAACC CAAACC CAAACC CAA-ACC
* **
33141 CAAACC CGAACC CAAACC TGAACC CAAACC CAA
1 CAAACC CAAACC CAAACC CAAACC CAAACC CAA
33174 TCTCGAACCC
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
5 3 0.05
6 53 0.90
7 3 0.05
ACGTcount: A:0.47, C:0.42, G:0.04, T:0.07
Consensus pattern (6 bp):
CAAACC
Found at i:33108 original size:18 final size:18
Alignment explanation
Indices: 33085--33122 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
33075 CTTCTCTAAC
33085 CCCTAACTCA-AACCCAAA
1 CCCTAAC-CAGAACCCAAA
*
33103 CCCTAACCAGAACCTAAA
1 CCCTAACCAGAACCCAAA
33121 CC
1 CC
33123 TAAACCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.42, C:0.45, G:0.03, T:0.11
Consensus pattern (18 bp):
CCCTAACCAGAACCCAAA
Found at i:33145 original size:24 final size:24
Alignment explanation
Indices: 33093--33173 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
33083 ACCCCTAACT
*
33093 CAAACCCAAACCCTAACC-AGAAC
1 CAAACCCAAACCCAAACCTAGAAC
*
33116 CTAAACCTAAACCCAAACCTA-ATAC
1 C-AAACCCAAACCCAAACCTAGA-AC
*
33141 CAAACCCGAACCCAAACCT-GAACC
1 CAAACCCAAACCCAAACCTAGAA-C
33165 CAAACCCAA
1 CAAACCCAA
33174 TCTCGAACCC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.04
24 42 0.88
25 4 0.08
ACGTcount: A:0.47, C:0.42, G:0.04, T:0.07
Consensus pattern (24 bp):
CAAACCCAAACCCAAACCTAGAAC
Found at i:33181 original size:18 final size:17
Alignment explanation
Indices: 33125--33183 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
33115 CCTAAACCTA
* *
33125 AACCCAAACCTAATACCA
1 AACCCAAACCCAAT-CCG
* *
33143 AACCCGAACCCAAACCTG
1 AACCCAAACCCAATCC-G
33161 AACCCAAACCCAATCTCG
1 AACCCAAACCCAATC-CG
33179 AACCC
1 AACCC
33184 GAACATGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 2 0.06
18 30 0.91
19 1 0.03
ACGTcount: A:0.42, C:0.44, G:0.05, T:0.08
Consensus pattern (17 bp):
AACCCAAACCCAATCCG
Found at i:33236 original size:18 final size:18
Alignment explanation
Indices: 33213--33267 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
33203 AACTAGAACC
*
33213 CTAAATCTGAACCCAAAT
1 CTAAATCCGAACCCAAAT
*
33231 CTAAATCCGAACCCAAAC
1 CTAAATCCGAACCCAAAT
* * *
33249 CCAAATCCAAACCCGAAT
1 CTAAATCCGAACCCAAAT
33267 C
1 C
33268 CAAACTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.44, C:0.36, G:0.05, T:0.15
Consensus pattern (18 bp):
CTAAATCCGAACCCAAAT
Found at i:33254 original size:24 final size:24
Alignment explanation
Indices: 33222--33272 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
33212 CCTAAATCTG
* *
33222 AACCCAAATCTAAATCCGAACCCA
1 AACCCAAATCCAAACCCGAACCCA
*
33246 AACCCAAATCCAAACCCGAATCCA
1 AACCCAAATCCAAACCCGAACCCA
33270 AAC
1 AAC
33273 TATTTGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.39, G:0.04, T:0.10
Consensus pattern (24 bp):
AACCCAAATCCAAACCCGAACCCA
Found at i:33260 original size:12 final size:12
Alignment explanation
Indices: 33222--33272 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
33212 CCTAAATCTG
*
33222 AACCCAAATCTA
1 AACCCAAATCCA
* * *
33234 AATCCGAACCCA
1 AACCCAAATCCA
33246 AACCCAAATCCA
1 AACCCAAATCCA
*
33258 AACCCGAATCCA
1 AACCCAAATCCA
33270 AAC
1 AAC
33273 TATTTGAAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.47, C:0.39, G:0.04, T:0.10
Consensus pattern (12 bp):
AACCCAAATCCA
Found at i:36015 original size:23 final size:23
Alignment explanation
Indices: 35989--36043 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
35979 CTTAATGTAG
*
35989 GATGCTTGTTGAATTGATGCAAT
1 GATGCTTGTTGAATTGATACAAT
*
36012 GATGCTTGTTGAATTGATACAGT
1 GATGCTTGTTGAATTGATACAAT
36035 GATGCTTGT
1 GATGCTTGT
36044 CAGTTGCTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (23 bp):
GATGCTTGTTGAATTGATACAAT
Found at i:41587 original size:20 final size:20
Alignment explanation
Indices: 41559--41628 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
41549 CTGGGTTTAG
*
41559 GTATTGATACTGGAAGAACA
1 GTATCGATACTGGAAGAACA
41579 GTATCGATACTGGAAGAACA
1 GTATCGATACTGGAAGAACA
41599 GTATCGATACTGGAAGAACA
1 GTATCGATACTGGAAGAACA
41619 GTATCGATAC
1 GTATCGATAC
41629 CATAAGGTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (20 bp):
GTATCGATACTGGAAGAACA
Found at i:42292 original size:23 final size:23
Alignment explanation
Indices: 42265--42351 Score: 156
Period size: 23 Copynumber: 3.8 Consensus size: 23
42255 CAGCTCATAT
42265 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
42288 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
42311 AAATGCACCGAAATGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
42334 AAATGCACAGAAGTGCCA
1 AAATGCACCGAAGTGCCA
42352 TATACAATGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.38, C:0.25, G:0.24, T:0.13
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:42338 original size:13 final size:13
Alignment explanation
Indices: 42278--42339 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
42268 TGCACCGAAG
42278 TGCCACGTAGAAA
1 TGCCACGTAGAAA
* *
42291 TG-CAC--CGAAG
1 TGCCACGTAGAAA
42301 TGCCACGTAGAAA
1 TGCCACGTAGAAA
*
42314 TG-CAC--CGAAA
1 TGCCACGTAGAAA
42324 TGCCACGTAGAAA
1 TGCCACGTAGAAA
42337 TGC
1 TGC
42340 ACAGAAGTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
10 11 0.30
11 6 0.16
12 6 0.16
13 14 0.38
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (13 bp):
TGCCACGTAGAAA
Found at i:42603 original size:3 final size:3
Alignment explanation
Indices: 42589--42626 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
42579 AGAGATATTC
*
42589 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
42627 ATGTACGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:43756 original size:29 final size:29
Alignment explanation
Indices: 43717--43790 Score: 130
Period size: 29 Copynumber: 2.5 Consensus size: 29
43707 TATGTGATAT
*
43717 GAGAACATGACATGAGGTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
43747 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
43776 GAGAAATGACATGAG
1 GAGAAATGACATGAG
43791 TATATGAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 38 0.88
30 5 0.12
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:44807 original size:21 final size:21
Alignment explanation
Indices: 44769--44820 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
44759 CATATACATA
*
44769 TTCCAAATGACCAAATATGTG
1 TTCCAAATGACCAAATATATG
**
44790 -TCTCAAATGACCGCATATATG
1 TTC-CAAATGACCAAATATATG
44811 TTCCAAATGA
1 TTCCAAATGA
44821 TTACATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (21 bp):
TTCCAAATGACCAAATATATG
Found at i:48162 original size:2 final size:2
Alignment explanation
Indices: 48150--48200 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
48140 ATGAAAGTCT
48150 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48191 TA TA TA TA TA
1 TA TA TA TA TA
48201 AAAAAACAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64631 original size:15 final size:15
Alignment explanation
Indices: 64613--64645 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
64603 ATCAACATAT
64613 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
64628 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
64643 ATA
1 ATA
64646 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:65071 original size:37 final size:37
Alignment explanation
Indices: 64998--65072 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
64988 TTTAGAAAAT
*
64998 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
65035 ATTTATATAATTTT-TTTGACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
65072 A
1 A
65073 AGTTTAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:70146 original size:2 final size:2
Alignment explanation
Indices: 70090--70134 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
70080 ATAAATTAGC
70090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70132 TA T
1 TA T
70135 GTGTGTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77131 original size:4 final size:4
Alignment explanation
Indices: 77122--77148 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
77112 CCCATTCGAA
77122 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
77149 AATGTTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:77942 original size:21 final size:21
Alignment explanation
Indices: 77900--77942 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
77890 TTTCTGGGCT
* *
77900 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
77921 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
77942 A
1 A
77943 ACGAACCAGA
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:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:78015 original size:23 final size:22
Alignment explanation
Indices: 77971--78015 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
77961 AATGTCATGG
*
77971 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
77993 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
78016 AAGTTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:79270 original size:23 final size:23
Alignment explanation
Indices: 79242--79310 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
79232 CATTATTATA
*
79242 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
79265 CT-GCACTCCGGTGCAATTCTACG
1 -TGGCACTACGGTGCAATTCTACG
* *
79288 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
79311 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:81537 original size:29 final size:29
Alignment explanation
Indices: 81480--81538 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
81470 ATAAAACAGA
*
81480 ATAAAAAATAAAGATAAAAATAATATATT
1 ATAAAAAATAAAGATAAAAATAAAATATT
*
81509 ATAAAACATAAA-ATAAAAATAAAAGTATT
1 ATAAAAAATAAAGATAAAAATAAAA-TATT
81538 A
1 A
81539 GTATCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.25
Consensus pattern (29 bp):
ATAAAAAATAAAGATAAAAATAAAATATT
Found at i:81951 original size:30 final size:30
Alignment explanation
Indices: 81917--81986 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
81907 TGGTGATTCA
81917 AAGGACCAAAATGATATTAACAATGACTTG
1 AAGGACCAAAATGATATTAACAATGACTTG
81947 AAGGACCAAAATGATATTAACAATGACTTG
1 AAGGACCAAAATGATATTAACAATGACTTG
81977 AAGGACCAAA
1 AAGGACCAAA
81987 CAACAATACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (30 bp):
AAGGACCAAAATGATATTAACAATGACTTG
Found at i:83026 original size:26 final size:26
Alignment explanation
Indices: 82990--83042 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
82980 ACCGAGAAGA
*
82990 TAGAATATGAGTGATCTATTTTGAGT
1 TAGAATATGAGTGACCTATTTTGAGT
83016 TAGAATATGAGTGACCTATTTTGAGT
1 TAGAATATGAGTGACCTATTTTGAGT
83042 T
1 T
83043 GATGTCCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.42
Consensus pattern (26 bp):
TAGAATATGAGTGACCTATTTTGAGT
Found at i:83609 original size:3 final size:3
Alignment explanation
Indices: 83595--83648 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
83585 AAAATACTGT
* * *
83595 TAA TAA -AA TAA TAA TAA TAA TAA TAA CAA TAT TAA TAA GTAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
83640 TAA TTAA TA
1 TAA -TAA TA
83649 TGCAAAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:96871 original size:17 final size:16
Alignment explanation
Indices: 96845--96878 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
96835 AGTATTAAAT
*
96845 AATTTTATTTAGTATTA
1 AATTTAATTTAGT-TTA
96862 AATTTAATTTAGTTTA
1 AATTTAATTTAGTTTA
96878 A
1 A
96879 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
AATTTAATTTAGTTTA
Found at i:128888 original size:16 final size:16
Alignment explanation
Indices: 128870--128901 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
128860 TTTTGTGGGC
128870 TTTAGTACTTGTTCTCT
1 TTTA-TACTTGTTCTCT
128887 TTTATACTTGTTCTC
1 TTTATACTTGTTCTC
128902 ATGAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.12, C:0.19, G:0.09, T:0.59
Consensus pattern (16 bp):
TTTATACTTGTTCTCT
Found at i:137492 original size:2 final size:2
Alignment explanation
Indices: 137485--137512 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
137475 CATGCCCGCG
137485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
137513 GAACTCATTA
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):
TA
Found at i:141877 original size:11 final size:11
Alignment explanation
Indices: 141861--141893 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
141851 AACTCAATTT
*
141861 TATTTTATTAC
1 TATTTTATTAA
141872 TATTTTATTAA
1 TATTTTATTAA
141883 TATTTTATTAA
1 TATTTTATTAA
141894 ATTCTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:142123 original size:97 final size:97
Alignment explanation
Indices: 141957--142151 Score: 354
Period size: 97 Copynumber: 2.0 Consensus size: 97
141947 ATTACAGACC
*
141957 CATAAACCCAAATCTCCTACGGTGTTGTCGGCTTTGGTTTCATCTTGATTGGATTCTAGAAATTC
1 CATAAACCCAAATCTCCTACGGTGTTGTCGGCGTTGGTTTCATCTTGATTGGATTCTAGAAATTC
*
142022 GTCAACCCCTTAAACCCAAACCAAATCTCTTT
66 GTCAACCCCTTAAACCCAAACCAAATCACTTT
* *
142054 CATAATCCCAAATCTCCTACGGTGTTGTCGGCGTTGGTTTCATCTTGATTGTATTCTAGAAATTC
1 CATAAACCCAAATCTCCTACGGTGTTGTCGGCGTTGGTTTCATCTTGATTGGATTCTAGAAATTC
142119 GTCAACCCCTTAAACCCAAACCAAATCACTTT
66 GTCAACCCCTTAAACCCAAACCAAATCACTTT
142151 C
1 C
142152 CCCCTGATTT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (97 bp):
CATAAACCCAAATCTCCTACGGTGTTGTCGGCGTTGGTTTCATCTTGATTGGATTCTAGAAATTC
GTCAACCCCTTAAACCCAAACCAAATCACTTT
Found at i:147622 original size:28 final size:28
Alignment explanation
Indices: 147542--147622 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
147532 AAATTTTATA
* *
147542 AGTAACTTCAAGACTTCAAATATC-TTAG
1 AGTAACTTCAATACTTCAAAT-TCATTAC
* * *
147570 AGTAACTTCAATAATACATATTTCATT-C
1 AGTAACTTCAATACTTCA-AATTCATTAC
147598 AGTAACTTCAATACTTCAAAGTTCA
1 AGTAACTTCAATACTTCAAA-TTCA
147623 AAACAAATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 1 0.02
28 37 0.88
29 4 0.10
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.35
Consensus pattern (28 bp):
AGTAACTTCAATACTTCAAATTCATTAC
Found at i:148733 original size:19 final size:19
Alignment explanation
Indices: 148709--148748 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
148699 TTTGAGATAT
148709 ATGTACATTGCCCATCACC
1 ATGTACATTGCCCATCACC
148728 ATGTACATTGCCCATCACC
1 ATGTACATTGCCCATCACC
148747 AT
1 AT
148749 TGCGTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.35, G:0.10, T:0.28
Consensus pattern (19 bp):
ATGTACATTGCCCATCACC
Found at i:153726 original size:41 final size:42
Alignment explanation
Indices: 153631--153711 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
153621 ACATCAACAA
* *
153631 AGTTGATTTAAGTAATAAATAGTTTGATACAATTTAGATAAG
1 AGTTGGTTTAAGTAATAAACAGTTTGATACAATTTAGATAAG
153673 AGTTGGTTTAAGTAATAAACAGTTTGATA-AATTTAGATA
1 AGTTGGTTTAAGTAATAAACAGTTTGATACAATTTAGATA
153712 TATATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 10 0.27
42 27 0.73
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.38
Consensus pattern (42 bp):
AGTTGGTTTAAGTAATAAACAGTTTGATACAATTTAGATAAG
Found at i:157851 original size:24 final size:24
Alignment explanation
Indices: 157799--157852 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
157789 CATTTATAGT
*
157799 TAAATTAAATATTTATATGTAACA
1 TAAAATAAATATTTATATGTAACA
*
157823 AAAAATAAATACTTATATAT-TAA-A
1 TAAAATAAATA-TT-TATATGTAACA
157847 TAAAAT
1 TAAAAT
157853 TAGTATGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 15 0.60
25 5 0.20
26 5 0.20
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (24 bp):
TAAAATAAATATTTATATGTAACA
Done.