Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007453.1 Hibiscus syriacus cultivar Beakdansim tig00020409_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: 90273
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:30 original size:12 final size:12
Alignment explanation
Indices: 13--46 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3 TATATATAAG
*
13 AATAATAACATA
1 AATAATAAAATA
25 AATAATAAAATA
1 AATAATAAAATA
37 AATGAATAAA
1 AAT-AATAAA
47 TATCCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:1227 original size:100 final size:101
Alignment explanation
Indices: 1037--2208 Score: 1634
Period size: 100 Copynumber: 11.3 Consensus size: 101
1027 CATTGTTCCA
* * ** *
1037 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA--TTGAAA-T-TTTGTTGACAAG
* * * * *
1102 CAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCG
61 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1143 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGAA-TGAAATTTTGTTGACAAGCAGCG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAATTTTGTTGACAAGCAGCG
1207 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1243 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATT--GAAATT-TTGTTGACAAGC
*
1308 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
62 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1348 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-TGAAATTTTGCTGACAAGCAGCG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAATTTTGTTGACAAGCAGCG
1412 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1448 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAGCG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAATTTTGTTGACAAGCAGCG
1512 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1548 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATT-GAAA-TT-TTGTTGACAAGC
*
1613 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
62 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
1653 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAACG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAATTTTGTTGACAAGCAGCG
*
1717 CTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1753 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATT-GAAA-TT-TTGTTGACAAGC
*
1818 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGC-ATGTCTGG
62 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1857 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATT--GAAATT-TTGTTGACAAGC
*
1922 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
62 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1962 AATCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATT--G-AAA-T-TTTGTTGACAA
*
2027 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
60 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
2069 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGA-AA--T-TTTGTTGACAAG
* * * *
2134 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
61 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2175 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
2209 CGCGGATGGC
Statistics
Matches: 983, Mismatches: 57, Indels: 49
0.90 0.05 0.04
Matches are distributed among these distances:
100 355 0.36
101 12 0.01
102 11 0.01
103 10 0.01
104 108 0.11
105 277 0.28
106 91 0.09
107 96 0.10
108 1 0.00
109 22 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (101 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAAATTTTGTTGACAAGCAGCG
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1357 original size:205 final size:207
Alignment explanation
Indices: 1037--2208 Score: 1690
Period size: 205 Copynumber: 5.7 Consensus size: 207
1027 CATTGTTCCA
* * **
1037 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG-ATTGGGAAATTG-TTGTTGACAAC
* * * * *
1102 CAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
**
1167 TTGAAATTGAATCTGAA-T-GAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
129 TTGAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
1229 CTTGCGTTGTCTGG
194 CTTGCGTTGTCTGG
* * *
1243 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGATTGGGAAATTGTTGTTGACAACC
*
1308 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1373 TGAAATTGGCTCTGAA-T-GAAA-TTTTGCTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
130 TGAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
1435 TTGCGTTGTCTGG
195 TTGCGTTGTCTGG
* * *
1448 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAACCA
1509 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
1574 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGA-ATTGGAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
1639 CTTGCATTGTCTGG
194 CTTGCGTTGTCTGG
** * *
1653 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAACCA
* *
1714 ACGCTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
1779 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGA-ATTGGAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
1844 CTTGC-ATGTCTGG
194 CTTGCGTTGTCTGG
*
1857 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAATTGTTGTTGACAACC
* * *
1922 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAATCCAATATCCTTCGATGTGAAGT
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
1987 TGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 TGAAATTGGCTCTG-AATT-GG-AAAGT-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
2052 GAACTTGCGTTGTCTGG
191 GAACTTGCGTTGTCTGG
* * *
2069 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAATTG-TTGTTGACAAC
* * * * * *
2134 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTG
*
2199 GAGTTGAAAT
126 AAGTTGAAAT
2209 CGCGGATGGC
Statistics
Matches: 892, Mismatches: 54, Indels: 30
0.91 0.06 0.03
Matches are distributed among these distances:
200 90 0.10
201 6 0.01
202 1 0.00
203 7 0.01
204 45 0.05
205 421 0.47
206 47 0.05
207 2 0.00
208 5 0.01
209 88 0.10
210 3 0.00
211 45 0.05
212 59 0.07
213 49 0.05
214 3 0.00
216 21 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (207 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGG
Found at i:1601 original size:305 final size:310
Alignment explanation
Indices: 1037--2208 Score: 1772
Period size: 305 Copynumber: 3.8 Consensus size: 310
1027 CATTGTTCCA
* * *
1037 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA-C-TGAAATTGTTTGTTGACAAC
* * * * *
1102 CAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
63 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
**
1167 TTGAAATTGAATCTGAA-TGAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
128 TTGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
1230 TTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTT
193 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
1295 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
258 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
1348 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-T-TTTGCTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTGTTGACAACCAG
*
1410 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1475 AAATTGGCTCTGAA-TGAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 AAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
*
1538 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTT
196 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTT
*
1603 GTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
261 GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
** * *
1653 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-T-TTTGTTGACAAGCAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTGTTGACAACCAG
*
1715 CGCTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1780 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGA-ATT-GAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
1845 TTGC-ATGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
193 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
* * *
1909 GTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
258 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* * * *
1962 AATCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AACT--G-AAATTGTTTGTTGACAA
2027 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
62 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
2092 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
127 GTTGAAATTGGCTCTG-AATTGA-AAG-T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* * * * *
2157 TGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
188 TGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
2209 CGCGGATGGC
Statistics
Matches: 797, Mismatches: 44, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
305 378 0.47
306 2 0.00
307 5 0.01
308 4 0.01
309 146 0.18
310 48 0.06
311 37 0.05
313 1 0.00
314 3 0.00
315 3 0.00
316 94 0.12
317 41 0.05
318 10 0.01
319 3 0.00
321 22 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (310 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTT
GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:2902 original size:68 final size:63
Alignment explanation
Indices: 2812--2967 Score: 188
Period size: 68 Copynumber: 2.4 Consensus size: 63
2802 AAGATATCTG
* * **
2812 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTA-AGGGAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TG-TTTAGA-GGAAATAAATTCAAAGA
2876 TTT
63 --T
* *
2879 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTAGAGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTAGAGGAAATAAATTCAAAGAT
*
2943 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
2968 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
63 22 0.28
64 2 0.03
66 19 0.24
67 4 0.05
68 32 0.41
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (63 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTAGAGGAAATAAATTCAAAGAT
Found at i:2965 original size:63 final size:64
Alignment explanation
Indices: 2812--3194 Score: 197
Period size: 63 Copynumber: 5.8 Consensus size: 64
2802 AAGATATCTG
* * * **
2812 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TG-TTTAAGGGAAATAAATTCAAAGA-
2877 TT
63 TT
*
2879 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTT-AGAGGAAATAAATTCAAAGA-
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAG-GGAAATAAATTCAAAGAT
2942 T
64 T
* ** *
2943 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTT-AAGGGAAA-----T--A-A-A
** *
3007 GACAAA-ACT
55 TTCAAAGATT
* * * * **** * * * * *
3016 TAGTTCCAAAAGAAACTGTCTCAAGGGAAATGGTATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-AAGGGAAATAAATTCAAAGATT
* * * * * * ** *
3081 TTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAACTCAT-TTCAAGGGAAAT-GTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT-TTGTTTAAGGGAAATAAATTCAAAGATT
*
3143 TATGTTTCAAGAG-AACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTT-AAGGGAAA
3195 CTGTCTCAAG
Statistics
Matches: 234, Mismatches: 60, Indels: 47
0.69 0.18 0.14
Matches are distributed among these distances:
62 22 0.09
63 50 0.21
64 29 0.12
65 32 0.14
66 20 0.09
67 3 0.01
68 32 0.14
69 1 0.00
71 1 0.00
72 3 0.01
73 41 0.18
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (64 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAGGGAAATAAATTCAAAGATT
Found at i:2994 original size:36 final size:36
Alignment explanation
Indices: 2943--3248 Score: 139
Period size: 36 Copynumber: 8.9 Consensus size: 36
2933 ATTCAAAGAT
* *
2943 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAAC
2979 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* * * * **** *
3015 TTAGTTCCAAAAGAAACTGTCTCAAGGGAAATGGTAT
1 TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* * **
3052 TTGTTTCAA-AGAAAACATAT-TC-----A-A-ATATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAAC
* *
3081 TTGTTTCAAGGGAAATTGTCTCAAGAGAGAC-AAAC
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
** * * * ***
3116 TCATTTCAAGGGAAA-TGTTTC-A-A-TG--TTTA-
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* * *
3145 -TGTTTCAAGAG-AACTGTCTCAAGGGAGAAAAAATT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-C
* **
3180 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
*
3216 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
3249 TGATGAGCAC
Statistics
Matches: 204, Mismatches: 42, Indels: 48
0.69 0.14 0.16
Matches are distributed among these distances:
27 2 0.01
28 15 0.07
29 16 0.08
30 3 0.01
31 3 0.01
32 1 0.00
33 2 0.01
34 6 0.03
35 21 0.10
36 87 0.43
37 48 0.24
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
Found at i:4131 original size:22 final size:22
Alignment explanation
Indices: 4106--4156 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4096 TTGTGTTTGG
4106 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
4128 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
4150 TCAAAGG
1 TCAAAGG
4157 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:4788 original size:20 final size:21
Alignment explanation
Indices: 4762--4810 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
4752 CTTTTTGTTC
*
4762 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
4783 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
4803 CCTTTTTT
1 CCTTTTTT
4811 GCTTCTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:4818 original size:11 final size:10
Alignment explanation
Indices: 4781--4831 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
4771 TTTTTGTTCT
4781 TTCTTTTTTG
1 TTCTTTTTTG
4791 TTCTTGTTTT-
1 TTCTT-TTTTG
4801 TTCCTTTTTTG
1 TT-CTTTTTTG
*
4812 CTTCTTTTTTTT
1 -TTC-TTTTTTG
4824 TTCTTTTT
1 TTCTTTTT
4832 GCCCTTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 16 0.46
11 11 0.31
12 8 0.23
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:4833 original size:21 final size:22
Alignment explanation
Indices: 4771--4831 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
4761 CCCTTTTTTA
4771 TTTTTGTTCTTTCTTTTTTG-TTC
1 TTTTT-TT-TTTCTTTTTTGCTTC
* *
4794 TTGTTTTTTCCTTTTTTGCTTC
1 TTTTTTTTTTCTTTTTTGCTTC
4816 TTTTTTTTTTCTTTTT
1 TTTTTTTTTTCTTTTT
4832 GCCCTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.30
22 19 0.58
23 4 0.12
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTTTTTTTTCTTTTTTGCTTC
Found at i:7063 original size:9 final size:9
Alignment explanation
Indices: 7049--7082 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
7039 TAAAAGGGAA
7049 AAATAAAAT
1 AAATAAAAT
7058 AAATAAAAT
1 AAATAAAAT
7067 AAAT-AAAT
1 AAATAAAAT
7075 AAGATAAA
1 AA-ATAAA
7083 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:7070 original size:13 final size:13
Alignment explanation
Indices: 7048--7082 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
7038 GTAAAAGGGA
7048 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
7062 AAAATAAATAAAT
1 AAAATAAATAAAT
*
7075 AAGATAAA
1 AAAATAAA
7083 GGAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:7140 original size:2 final size:2
Alignment explanation
Indices: 7133--7161 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7123 GAAAAAGGAA
7133 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 A
7162 CATCAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7563 original size:2 final size:2
Alignment explanation
Indices: 7556--7598 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
7546 TATTAAAGAA
7556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7598 A
1 A
7599 ATAATAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7611 original size:18 final size:18
Alignment explanation
Indices: 7568--7626 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
7558 ATATATATAT
7568 ATATATATATATATATATATA
1 ATATATATA-ATA-ATA-ATA
7589 TATATATATAATAATAATA
1 -ATATATATAATAATAATA
* *
7608 ATATAAATAATAAAAATA
1 ATATATATAATAATAATA
7626 A
1 A
7627 ATGAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 17 0.49
19 3 0.09
20 3 0.09
21 3 0.09
22 9 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATATATAATAATAATA
Found at i:8725 original size:23 final size:21
Alignment explanation
Indices: 8690--8733 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
8680 ATAATTATTT
8690 AAAAAATTAAATAAAAATATAA
1 AAAAAATTAAATAAAAA-ATAA
*
8712 AAAAATATTTAATAAAAAATAA
1 AAAAA-ATTAAATAAAAAATAA
8734 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAAATTAAATAAAAAATAA
Found at i:9780 original size:43 final size:43
Alignment explanation
Indices: 9724--10034 Score: 263
Period size: 43 Copynumber: 7.3 Consensus size: 43
9714 GGTAACAAAA
** **
9724 AAACGCCGCAATAGGTAAAGATATACAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAAC
* * * * * *
9767 AAACGCCGTAATAGGTGTTGATATTTAGCGACATTTTTCCCAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAAC
* * * *
9810 AAATGCTGCAATAGGTTTTGAGATTTAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAAC
* *
9853 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTCC-AC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCG-TTTGTCCAAC
* * * *
9896 AAACGGCGCAATAGGTCTTGAGATTTAGCGGCGTTT-T-GACAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCA-AC
* * ** *
9938 AAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCTC-AC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTC-CAAC
* * * * * **
9981 AAACGCCGCAAAAGATCTTG-TATATAGCGGCGTTTTTTAGAAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCG-TTTGTCCAAC
10024 AAACGCCGCAA
1 AAACGCCGCAA
10035 AATGTCATAT
Statistics
Matches: 220, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
41 1 0.00
42 46 0.21
43 167 0.76
44 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAAC
Found at i:9848 original size:86 final size:86
Alignment explanation
Indices: 9750--10034 Score: 344
Period size: 86 Copynumber: 3.3 Consensus size: 86
9740 AAAGATATAC
* * *
9750 AGCGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGATATTTAGCGACATTTTTCCCACAAA-T
1 AGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCACAAACG
*
9814 GCTGCAATAGGTTTTGAGATTT
66 GC-GCAATAGGTCTTGAGATTT
* *
9836 AGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTCCACAAACG
1 AGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCACAAACG
9901 GCGCAATAGGTCTTGAGATTT
66 GCGCAATAGGTCTTGAGATTT
* * * * *
9922 AGCGGCGTTT-T-GACACAAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCTCACAAAC
1 AGCGGCGTTTGTCCA-ACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCACAAAC
* * * * *
9985 GCCGCAAAAGATCTTG-TATAT
65 GGCGCAATAGGTCTTGAGATTT
* **
10006 AGCGGCGTTTTTTAGAACAAACGCCGCAA
1 AGCGGCG-TTTGTCCAACAAACGCCGCAA
10035 AATGTCATAT
Statistics
Matches: 176, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
84 11 0.06
85 60 0.34
86 101 0.57
87 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (86 bp):
AGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCACAAACG
GCGCAATAGGTCTTGAGATTT
Found at i:10026 original size:128 final size:129
Alignment explanation
Indices: 9743--10034 Score: 338
Period size: 128 Copynumber: 2.3 Consensus size: 129
9733 AATAGGTAAA
* * * * * * * *
9743 GATATACAGCGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGATATTTAGCGACATTTTTCCC
1 GATATATAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGACAGTTTTCAC
* * * * * * *
9808 ACAAATGCTGCAATAGGTTTTGAGATTTAGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTT
66 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTGTCCAACAAACGCCGCAAAAGATCTT
* * * * *
9872 GATATTTAGCGGCGTTTTTTCCACAAACGGCGCAATAGGTCTTGAGATTTAGCGGC-GTTTTGAC
1 GATATATAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGACAGTTTTCAC
* *
9936 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCTC-ACAAACGCCGCAAAAGATCTT
66 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTGTC-CAACAAACGCCGCAAAAGATCTT
*
10000 G-TATATAGCGGCGTTTTTTAGAACAAACGCCGCAA
1 GATATATAGCGGCGTTTTTT-CAACAAACGCCGCAA
10035 AATGTCATAT
Statistics
Matches: 135, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
127 17 0.13
128 71 0.53
129 47 0.35
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (129 bp):
GATATATAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGACAGTTTTCAC
ACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTGTCCAACAAACGCCGCAAAAGATCTT
Found at i:10071 original size:43 final size:43
Alignment explanation
Indices: 9981--10075 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
9971 TTTTTCTCAC
* * * *
9981 AAACGCCGCAAAAGATCTTGTATATAGCGGCGTTTTTTAGAAC
1 AAACGCCGCAAAAGATCATATATATAGCGGCGTTTTTAAGAAA
* *
10024 AAACGCCGCAAAATG-TCATATCTATATCGGCG-TTTTAAGATAA
1 AAACGCCGCAAAA-GATCATATATATAGCGGCGTTTTTAAGA-AA
10067 AAACGCCGC
1 AAACGCCGC
10076 TAATTACCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 7 0.16
43 36 0.82
44 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGATCATATATATAGCGGCGTTTTTAAGAAA
Found at i:11028 original size:75 final size:76
Alignment explanation
Indices: 10935--11087 Score: 290
Period size: 75 Copynumber: 2.0 Consensus size: 76
10925 GTTTAGTTTC
10935 GAAAGAAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTA
1 GAAAGAAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTA
11000 CAGACATTGTA
66 CAGACATTGTA
11011 GAAA-AAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTA
1 GAAAGAAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTA
*
11075 CGGACATTGTA
66 CAGACATTGTA
11086 GA
1 GA
11088 CAGATACATA
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 72 0.95
76 4 0.05
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (76 bp):
GAAAGAAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTA
CAGACATTGTA
Found at i:22384 original size:79 final size:80
Alignment explanation
Indices: 22238--22395 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 80
22228 ATTGACATAT
* *
22238 GTTCGGATTTTCATTTGAATACTTTTATTTATTATTTTTTCCACCATTAACATTATTATAAGAAA
1 GTTCAGATTTTCATTTGAATACTTTTATTTATTACTTTTTCCACCATTAACATTATTATAAGAAA
22303 AATAAGTTTTAGGAA
66 AATAAGTTTTAGGAA
22318 GTTCAGATTTTCATTTGAATACTTTTATTTATT-CTTTTTCCACCATTAACATTATTATAAGAAA
1 GTTCAGATTTTCATTTGAATACTTTTATTTATTACTTTTTCCACCATTAACATTATTATAAGAAA
22382 AATAAGTTTTAGGA
66 AATAAGTTTTAGGA
22396 TAAACTATAC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
79 44 0.58
80 32 0.42
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (80 bp):
GTTCAGATTTTCATTTGAATACTTTTATTTATTACTTTTTCCACCATTAACATTATTATAAGAAA
AATAAGTTTTAGGAA
Found at i:23035 original size:20 final size:21
Alignment explanation
Indices: 23001--23045 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
22991 TACTAAAAAT
*
23001 GATAAAAATATTAATATTTTA
1 GATAAAAATAATAATATTTTA
23022 GATAAAAA-AATAATATTTTA
1 GATAAAAATAATAATATTTTA
23042 GATA
1 GATA
23046 TTTTTTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
GATAAAAATAATAATATTTTA
Found at i:32485 original size:6 final size:6
Alignment explanation
Indices: 32474--32516 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
32464 CTATATTGTA
32474 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT T
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT T
32517 GCTCTGGGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTCCT
Found at i:32867 original size:21 final size:20
Alignment explanation
Indices: 32829--32867 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
32819 GAAGGAAAAG
* *
32829 ATGAAATGAGGTAGAAGACA
1 ATGAAATGAGGAAAAAGACA
32849 ATGAAGATGAGGAAAAAGA
1 ATGAA-ATGAGGAAAAAGA
32868 AAAGAGTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.31, T:0.13
Consensus pattern (20 bp):
ATGAAATGAGGAAAAAGACA
Found at i:51827 original size:31 final size:31
Alignment explanation
Indices: 51792--51850 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
51782 CAATGACTAT
* *
51792 ATCTTAATTAAAATGAAATAAAAGTGATCAC
1 ATCTTAATTAAAACGAAACAAAAGTGATCAC
*
51823 ATCTTAATTAAAACGAAACGAAAGTGAT
1 ATCTTAATTAAAACGAAACAAAAGTGAT
51851 TACGAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (31 bp):
ATCTTAATTAAAACGAAACAAAAGTGATCAC
Found at i:53210 original size:58 final size:58
Alignment explanation
Indices: 53100--53209 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 58
53090 CTTATATAAC
* **
53100 AAATAAGTAGCTAAAATATACAAGTTTTTCATTTAAGTACTTAAAGTATTTTTGGTCA
1 AAATAAGTACCTAAAATATACAAGTTTTTCATCCAAGTACTTAAAGTATTTTTGGTCA
* **
53158 AAATAAGTACCTAAAGTATTTAA-TTTTTCATCCAAGTACTTAAAGTATTTTT
1 AAATAAGTACCTAAAATATACAAGTTTTTCATCCAAGTACTTAAAGTATTTTT
53210 TAATTAATGT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 27 0.59
58 19 0.41
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (58 bp):
AAATAAGTACCTAAAATATACAAGTTTTTCATCCAAGTACTTAAAGTATTTTTGGTCA
Found at i:56721 original size:31 final size:31
Alignment explanation
Indices: 56638--56721 Score: 75
Period size: 35 Copynumber: 2.6 Consensus size: 31
56628 TTGTATAATA
56638 TTAC-AAATTGTAAAATATTTATATATTTTCT
1 TTACAAAATT-TAAAATATTTATATATTTTCT
*
56669 TTA-AAAATTAAATTCATAATATTTATATAATTTT-T
1 TTACAAAA-T---TT-AAAATATTTATAT-ATTTTCT
56704 TTACAAAATTTAAAATAT
1 TTACAAAATTTAAAATAT
56722 AAAAAAGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
31 12 0.28
32 3 0.07
34 1 0.02
35 18 0.42
36 9 0.21
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (31 bp):
TTACAAAATTTAAAATATTTATATATTTTCT
Found at i:60914 original size:20 final size:20
Alignment explanation
Indices: 60891--60931 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
60881 GTATTTGTCG
60891 ATGGTAGAGAAGAAGCTACA
1 ATGGTAGAGAAGAAGCTACA
*
60911 ATGGTAGAGTAGAAGCTACA
1 ATGGTAGAGAAGAAGCTACA
60931 A
1 A
60932 CCATTGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.17
Consensus pattern (20 bp):
ATGGTAGAGAAGAAGCTACA
Found at i:60992 original size:20 final size:20
Alignment explanation
Indices: 60967--61007 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
60957 TTATTTGTCG
60967 ATGGTAGA-TAAGAAGCTACA
1 ATGGTAGAGT-AGAAGCTACA
60987 ATGGTAGAGTAGAAGCTACA
1 ATGGTAGAGTAGAAGCTACA
61007 A
1 A
61008 CCATTGTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.20
Consensus pattern (20 bp):
ATGGTAGAGTAGAAGCTACA
Found at i:61008 original size:76 final size:76
Alignment explanation
Indices: 60882--61034 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
60872 AAGTAGCATG
60882 TATTTGTCGATGGTAGAGAAGAAGCTACAATGGTAGAGTAGAAGCTACAACCATTGTAACTTTGA
1 TATTTGTCGATGGTAGAGAAGAAGCTACAATGGTAGAGTAGAAGCTACAACCATTGTAACTTTGA
60947 ATTCTGTCTCT
66 ATTCTGTCTCT
*
60958 TATTTGTCGATGGTAGATAAGAAGCTACAATGGTAGAGTAGAAGCTACAACCATTGTAACTTTGA
1 TATTTGTCGATGGTAGAGAAGAAGCTACAATGGTAGAGTAGAAGCTACAACCATTGTAACTTTGA
61023 ATTCTGTCTCT
66 ATTCTGTCTCT
61034 T
1 T
61035 GTTAGGCTTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (76 bp):
TATTTGTCGATGGTAGAGAAGAAGCTACAATGGTAGAGTAGAAGCTACAACCATTGTAACTTTGA
ATTCTGTCTCT
Found at i:63512 original size:21 final size:23
Alignment explanation
Indices: 63469--63528 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
63459 AACAATTCTC
*
63469 TTCATGAAAAGATTAA-ATCC-T
1 TTCATGAAAAGGTTAAGATCCTT
*
63490 TTCATGAAAAGGTTAAGCT-CTT
1 TTCATGAAAAGGTTAAGATCCTT
* *
63512 TTCATCAAAAGGATAAG
1 TTCATGAAAAGGTTAAG
63529 TTATTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (23 bp):
TTCATGAAAAGGTTAAGATCCTT
Found at i:63563 original size:21 final size:21
Alignment explanation
Indices: 63476--63564 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 21
63466 CTCTTCATGA
* *
63476 AAAGATTAAATCCTTTCAT-G
1 AAAGATTAAGTCTTTTCATAG
*
63496 AAAAGGTTAAGCTCTTTTCATCA-
1 -AAAGATTAAG-TCTTTTCAT-AG
* *
63519 AAAGGA-TAAGT-TATTTAATTG
1 AAA-GATTAAGTCT-TTTCATAG
63540 AAAGATTAAGTCTTTTCATAG
1 AAAGATTAAGTCTTTTCATAG
63561 AAAG
1 AAAG
63565 GTCTTAACCT
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
20 3 0.06
21 32 0.62
22 16 0.31
23 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AAAGATTAAGTCTTTTCATAG
Found at i:67104 original size:22 final size:21
Alignment explanation
Indices: 67052--67128 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
67042 AACAATTCTC
* * *
67052 TTCATGAAAAGATTAAATCCT
1 TTCATCAAAAGGTTAAGTCCT
*
67073 TTCATGAAAAGGTTAAG-CACTT
1 TTCATCAAAAGGTTAAGTC-C-T
*
67095 TTCATCAAAAGGATAAGTCCT
1 TTCATCAAAAGGTTAAGTCCT
*
67116 TTCATCGAAAGGT
1 TTCATCAAAAGGT
67129 CTTAACATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 28 0.60
22 17 0.36
23 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (21 bp):
TTCATCAAAAGGTTAAGTCCT
Found at i:71536 original size:678 final size:678
Alignment explanation
Indices: 70239--72275 Score: 3491
Period size: 678 Copynumber: 3.0 Consensus size: 678
70229 CATATGCAAT
*
70239 ATTGACTGGTATCTGGTCTCACAAAGCCATCAGACACTAGCAACTGCGAATATCACGTCTAGCTA
1 ATTGACTAGTATCTGGTCTCACAAAGCCATCAGACACTAGCAACTGCGAATATCACGTCTAGCTA
*
70304 ACCCATCCCTCGCGAGTGTTAGGCCTCGAACCTAAATTAGATGTTGAAGTGCCTCGCGCACTTAC
66 ACCCATCCCTCGCGAGTGTTAGGCCTCGAACCTAAATTAGCTGTTGAAGTGCCTCGCGCACTTAC
70369 TATGGTGTATCCGAGTAAGGACATCACACCTGCCAACCTACCCTTCGCGAGTGTTAAGTCCTCGA
131 TATGGTGTATCCGAGTAAGGACATCACACCTGCCAACCTACCCTTCGCGAGTGTTAAGTCCTCGA
*
70434 CACTTAGTCAGTCGTAAAAGTGTCTCGCGTACTTGCTTCAGGTGTTATCGAATATCCTGTACCAC
196 CACTTAGTCAGTCGTAAAAGTGTCTCGCGTACTTGCTTCAGGTGTTATCGAATATCCTATACCAC
*
70499 TAGACGATCATTACCACTTGAACTAAACGGATGCGACTATAATACATACCTAAGGCCAATAGACT
261 TAGACGATCATTACCACTTGAACTAAACGGATGCGACTATAATACATACCTAAGGCCAAGAGACT
*
70564 ATACAACACTGACATCGCTAACTGACTCCTCGTGAGTGTTCGATCCTCATGCCCTCACTAACTTT
326 ATACAACACTGACATCGCTAACTGACTCCTCGTGAGTGTTCGAGCCTCATGCCCTCACTAACTTT
*
70629 TGAAGTGCCTCGTGCACTGACAATGCCCCACTAGGACAACTAAAGTAACCTTGGTATACCCTAGT
391 TGAAGTGCCTCGTGCACTGACAATGCCCCACTAGGACAACTAAGGTAACCTTGGTATACCCTAGT
70694 ATAATTAGACTTGAAAAAGTGAGGTCATCCTCTCTCTAAATGCTATCTTATTCGTTCTCTATCTA
456 ATAATTAGACTTGAAAAAGTGAGGTCATCCTCTCTCTAAATGCTATCTTATTCGTTCTCTATCTA
* *
70759 GAACGTTACGCGAAGGATTAATGGTCTAATAATGTTGTTATTTACTACGCTACTGCGCTCTGGTC
521 GAACGTTACGCGAAGGATTAATGGTCTAATAATGTTGTTATTTACTACGCTACTGCACTATGGTC
*
70824 GCTCGTTACTAACATATAATTTACTTATTCACTGGCTATAACGAAGTCTCTATGCGATCTCGAGG
586 GCTCGTTACTAACATATAATTTACTTATTCACTGGCTATAGCGAAGTCTCTATGCGATCTCGAGG
70889 TTTTACGACGATTCTGAGGTTGTTGTTC
651 TTTTACGACGATTCTGAGGTTGTTGTTC
*
70917 ATTGACTAGTATCTGGTCTCACAAAGCCATCAGACACTAGCAACTGCGAATATCACGTCTAGGTA
1 ATTGACTAGTATCTGGTCTCACAAAGCCATCAGACACTAGCAACTGCGAATATCACGTCTAGCTA
** * * *
70982 ACCCATCCCTCATGAGTGTTAGGCCTCGAACCTAAATTAGCCGTTGAAGTGCCTTGTGCACTTAC
66 ACCCATCCCTCGCGAGTGTTAGGCCTCGAACCTAAATTAGCTGTTGAAGTGCCTCGCGCACTTAC
*
71047 TATAGTGTATCCGAGTAAGGACATCACACCTGCCAACCTACCCTTCGCGAGTGTTAAGTCCTCGA
131 TATGGTGTATCCGAGTAAGGACATCACACCTGCCAACCTACCCTTCGCGAGTGTTAAGTCCTCGA
71112 CACTTAGTCAGTCGTAAAAGTGTCTCGCGTACTTGCTTCAGGTGTTATCGAATATCCTATACCAC
196 CACTTAGTCAGTCGTAAAAGTGTCTCGCGTACTTGCTTCAGGTGTTATCGAATATCCTATACCAC
71177 TAGACGATCATTACCACTTGAACTAAACGGATGCGACTATAATACATACCTAAGGCCAAGAGACT
261 TAGACGATCATTACCACTTGAACTAAACGGATGCGACTATAATACATACCTAAGGCCAAGAGACT
*
71242 ATACAACACTGACATCGCTAACTGACTCCTCGTGAGTGTTCGAGCCTCATGCCCTCACTGACTTT
326 ATACAACACTGACATCGCTAACTGACTCCTCGTGAGTGTTCGAGCCTCATGCCCTCACTAACTTT
* *
71307 TGAAGTGCCTCTTGCACTGACAATGCCCCATTAGGACAACTAAGGTAACCTTGGTATACCCTAGT
391 TGAAGTGCCTCGTGCACTGACAATGCCCCACTAGGACAACTAAGGTAACCTTGGTATACCCTAGT
71372 ATAATTAGACTTGAAAAAGTGAGGTCATCCTCTCTCTAAATGCTATCTTATTCGTTCTCTATCTA
456 ATAATTAGACTTGAAAAAGTGAGGTCATCCTCTCTCTAAATGCTATCTTATTCGTTCTCTATCTA
*
71437 GAACGTTACTCGAAGGATTAATGGTCTAATAATGTTGTTATTTACTACGCTACTGCACTATGGTC
521 GAACGTTACGCGAAGGATTAATGGTCTAATAATGTTGTTATTTACTACGCTACTGCACTATGGTC
*
71502 GCTCGTTACTAACATATAATTTACTTATTCACTGGCTATAGTGAAGTCTCTATGCGATCTCGAGG
586 GCTCGTTACTAACATATAATTTACTTATTCACTGGCTATAGCGAAGTCTCTATGCGATCTCGAGG
71567 TTTTACGACGATTCTGAGGTTGTTGTTC
651 TTTTACGACGATTCTGAGGTTGTTGTTC
*
71595 ATTGACTAGTATCTGGTCTCACAAAGCCATCAGACACTAGCAACTGCGAATATCACGTCTAACTA
1 ATTGACTAGTATCTGGTCTCACAAAGCCATCAGACACTAGCAACTGCGAATATCACGTCTAGCTA
* ** *
71660 ACCCATCCCTGGCGAGTGTTAGGCCTCGCGCCTAAATTAGCTGTTGAAGTGCCACGCGCACTTAC
66 ACCCATCCCTCGCGAGTGTTAGGCCTCGAACCTAAATTAGCTGTTGAAGTGCCTCGCGCACTTAC
* * *
71725 TATGGTGTATCCGGGTAAGGACATCACACCTGCCAACCTACCCTTCGCGAGTGTTAAGTTCTTGA
131 TATGGTGTATCCGAGTAAGGACATCACACCTGCCAACCTACCCTTCGCGAGTGTTAAGTCCTCGA
* * * *
71790 CACTTAGTCAGTCGCAAAAGTGCCTCGCGTACTTACTTCAGGTGTTATCGGATATCCTATACCAC
196 CACTTAGTCAGTCGTAAAAGTGTCTCGCGTACTTGCTTCAGGTGTTATCGAATATCCTATACCAC
* * * *
71855 TAGACGATCATTACCACTTGAATTAGACTGATGCGACTATAATACATACCTAAGGCCAAGAGGCT
261 TAGACGATCATTACCACTTGAACTAAACGGATGCGACTATAATACATACCTAAGGCCAAGAGACT
* * *
71920 ATACAACACTGACATCGCTAACTGACTCCTCGTGAATGTTCGAGTCTCACGCCCTCACTAACTTT
326 ATACAACACTGACATCGCTAACTGACTCCTCGTGAGTGTTCGAGCCTCATGCCCTCACTAACTTT
* * * *
71985 TGAAGTACCTCGTGCACTAACAATGCCCCACTAGGATAACTAAGGTAACCTGGGTATACCCTAGT
391 TGAAGTGCCTCGTGCACTGACAATGCCCCACTAGGACAACTAAGGTAACCTTGGTATACCCTAGT
* * * * * * * *
72050 ATAATTAGACTCGCATAAGTGAGGTCATACTCTCTCTAAGTGTTATCTCATCCGTTCTCTATCTA
456 ATAATTAGACTTGAAAAAGTGAGGTCATCCTCTCTCTAAATGCTATCTTATTCGTTCTCTATCTA
* * * *
72115 GAACGTTACGCGAAGGCTTAATGGTCTAATACTGTTGTTATTTACTACGCTGCTCCAC-ACTGGT
521 GAACGTTACGCGAAGGATTAATGGTCTAATAATGTTGTTATTTACTACGCTACTGCACTA-TGGT
* * * * *
72179 CGCTCGTTACTAACGTATAATTTACTTATTCTCTAGCTCTAGCAAAGTCTCTATGCGATCTCGAG
585 CGCTCGTTACTAACATATAATTTACTTATTCACTGGCTATAGCGAAGTCTCTATGCGATCTCGAG
* *
72244 GTTTTACGACGATTCTTAAGTTGTTGTTC
650 GTTTTACGACGATTCTGAGGTTGTTGTTC
72273 ATT
1 ATT
72276 TACTTACTAT
Statistics
Matches: 1283, Mismatches: 75, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
677 1 0.00
678 1282 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (678 bp):
ATTGACTAGTATCTGGTCTCACAAAGCCATCAGACACTAGCAACTGCGAATATCACGTCTAGCTA
ACCCATCCCTCGCGAGTGTTAGGCCTCGAACCTAAATTAGCTGTTGAAGTGCCTCGCGCACTTAC
TATGGTGTATCCGAGTAAGGACATCACACCTGCCAACCTACCCTTCGCGAGTGTTAAGTCCTCGA
CACTTAGTCAGTCGTAAAAGTGTCTCGCGTACTTGCTTCAGGTGTTATCGAATATCCTATACCAC
TAGACGATCATTACCACTTGAACTAAACGGATGCGACTATAATACATACCTAAGGCCAAGAGACT
ATACAACACTGACATCGCTAACTGACTCCTCGTGAGTGTTCGAGCCTCATGCCCTCACTAACTTT
TGAAGTGCCTCGTGCACTGACAATGCCCCACTAGGACAACTAAGGTAACCTTGGTATACCCTAGT
ATAATTAGACTTGAAAAAGTGAGGTCATCCTCTCTCTAAATGCTATCTTATTCGTTCTCTATCTA
GAACGTTACGCGAAGGATTAATGGTCTAATAATGTTGTTATTTACTACGCTACTGCACTATGGTC
GCTCGTTACTAACATATAATTTACTTATTCACTGGCTATAGCGAAGTCTCTATGCGATCTCGAGG
TTTTACGACGATTCTGAGGTTGTTGTTC
Found at i:80412 original size:3 final size:3
Alignment explanation
Indices: 80397--80451 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
80387 TCTTTATTCA
* * * *
80397 TTC TTC TTT TTC TTC TTC -TC ATTC TGC TTC TCC TTC TTA TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC
80442 TTC TTC TTC T
1 TTC TTC TTC T
80452 CATCCACCTC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.04, C:0.31, G:0.02, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:82811 original size:66 final size:66
Alignment explanation
Indices: 82705--82837 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
82695 AGCCACAAGC
82705 AACATGTAAATGATATAAATGTCCATCCACCACTTATCATATGCATTCCAAGTTGTGATTCATAA
1 AACATGTAAATGATATAAATGTCCATCCACCACTTATCATATGCATTCCAAGTTGTGATTCATAA
82770 T
66 T
82771 AACATGTAAATGATATAAATGTCCATCCACCACTTATCATATGCATTCCAAGTTGTGATTCATAA
1 AACATGTAAATGATATAAATGTCCATCCACCACTTATCATATGCATTCCAAGTTGTGATTCATAA
82836 T
66 T
82837 A
1 A
82838 CCTTTTTATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (66 bp):
AACATGTAAATGATATAAATGTCCATCCACCACTTATCATATGCATTCCAAGTTGTGATTCATAA
T
Done.