Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003074.1 Hibiscus syriacus cultivar Beakdansim tig00006408_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: 120092
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:55 original size:36 final size:36
Alignment explanation
Indices: 4--178 Score: 208
Period size: 36 Copynumber: 4.8 Consensus size: 36
1 AAA
4 AGTAGTGAAGCAAACCATCTTAAGCCTTCACCGAAG
1 AGTAGTGAAGCAAACCATCTTAAGCCTTCACCGAAG
* * * * *
40 AGTGGTGAAGTAAACCATCCTAAGGCTTCACCAAAG
1 AGTAGTGAAGCAAACCATCTTAAGCCTTCACCGAAG
* ** ** *
76 AATAGTGAAATAATTCATCTTAAGCCTTCACTGAAG
1 AGTAGTGAAGCAAACCATCTTAAGCCTTCACCGAAG
112 AGTAGTGAAGC-AACTCAATCTTAAGCCTTCACCGAAG
1 AGTAGTGAAGCAAAC-C-ATCTTAAGCCTTCACCGAAG
149 AGTAGTGAAGCAAATCCATCTGTAAGCCTT
1 AGTAGTGAAGCAAA-CCATCT-TAAGCCTT
179 TAGAGCAAGA
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
35 1 0.01
36 67 0.59
37 34 0.30
38 11 0.10
39 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (36 bp):
AGTAGTGAAGCAAACCATCTTAAGCCTTCACCGAAG
Found at i:607 original size:215 final size:213
Alignment explanation
Indices: 165--1089 Score: 989
Period size: 215 Copynumber: 4.2 Consensus size: 213
155 GAAGCAAATC
*
165 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACTTTCGGGTAGGA
1 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGA
*
230 TGTTTTCACATGAATTTGAGAAAATAAGAAAGTGATGTTTTAAGAAAATGAAATCTTTGAAAACT
66 TGTTTTCACATGAATTT--GAAAATGAGAAAGTGATG-TTTAAGAAAATGAAATCTTTGAAAACT
* * * ** *
295 AAGAAGGTGATTTCCAAAATTTCACGCTTAGTAAGTCTTTCAAGCCATAAATAAGTCTTTCGAGC
128 AAGAAGGCGATTTCCAAAATTTCACACTTA-TAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGC
* *
360 ATGATGCTTAAATCTTTCGGGT
192 ATGATGATTAAATCCTTCGGGT
* * *
382 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCATTTGGGCCATCCATCAGACCTTCGGGTAGGA
1 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGA
* * * *
447 TGTTTTCACATGAAGTTGAAAGATGAGAAAGT-ATTGTTTAAGAAAATGAAATCTTGGAGAAGTA
66 TGTTTTCACATGAATTTGAAA-ATGAGAAAGTGA-TGTTTAAGAAAATGAAATCTTTGAAAACTA
* * * * *
511 AAAAAGCGATTTCCAATATTTCACACTATATAAGTCCTTCGGGCCATCATTAAGTCTTTCGAGCG
129 AGAAGGCGATTTCCAAAATTTCACACT-TATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
*
576 TGATGTTTAAATCCTTCGGGT
193 TGATGATTAAATCCTTCGGGT
* * * * * *
597 TATTTGTAAGCCTTTTGAGTAAGATGATAAGTCCTTCGGTCCATCCAGAAGACCTTCGGGTAGGA
1 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGA
*
662 TGTTTTCACATGAATTTGAAAATGA-AAA-TGATGTTTAAGAAGATGAAA-CTTTTGAAAACTAA
66 TGTTTTCACATGAATTTGAAAATGAGAAAGTGATGTTTAAGAAAATGAAATC-TTTGAAAACTAA
* * * * *
724 GAAGGCGATTTCGAAAATTTCATTATTTTTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
130 GAAGGCGATTTCCAAAATTTCA-CACTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCAT
*
789 GATGATTGAATCCTTCGGGT
194 GATGATTAAATCCTTCGGGT
809 CATCTGTAAGCCTTTAGAGCAAGATGATTAAGTCCTTCGGGTCATCCATAAGACCTTCAGGCCAT
1 CATCTGTAAGCCTTTAGAGCAAGATGA-TAAGT-C--C---T--T-C----G-------GGCCAT
* * * *
874 CCATAAGACCTTCAGGTAGGATATTTTCACATAAATTTGAAGAATGAGAAAGTGATGTTTTTAGA
45 CCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAA-AATGAGAAAGTGATG-TTTAAGA
* * * ** * * * *
939 AAATGGAATTTTTGAAAAGTAAGAAAGG-TTTTTACATAGTAAATTTCCAAAATTTATAAGTCAT
108 AAATGAAATCTTTGAAAACTAAG-AAGGCGATTT-C-CA--AAATTT-C-ACACTTATAAGTCCT
*
1003 TCGGGCCATCAGTAAGTCTTTCGAGCATGATG-TTAAATCCTTCGGGT
166 TCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* *
1050 CATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTCGGG
1 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGG
1090 TAGGATGTTT
Statistics
Matches: 599, Mismatches: 70, Indels: 75
0.81 0.09 0.10
Matches are distributed among these distances:
211 1 0.00
212 120 0.20
213 11 0.02
214 5 0.01
215 176 0.29
216 14 0.02
217 77 0.13
219 1 0.00
220 2 0.00
221 1 0.00
222 1 0.00
226 1 0.00
227 1 0.00
231 1 0.00
232 1 0.00
233 42 0.07
234 6 0.01
235 3 0.01
236 5 0.01
237 28 0.05
238 5 0.01
239 2 0.00
240 5 0.01
241 45 0.08
242 44 0.07
243 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (213 bp):
CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGA
TGTTTTCACATGAATTTGAAAATGAGAAAGTGATGTTTAAGAAAATGAAATCTTTGAAAACTAAG
AAGGCGATTTCCAAAATTTCACACTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGA
TGATTAAATCCTTCGGGT
Found at i:818 original size:42 final size:42
Alignment explanation
Indices: 752--854 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
742 TTCATTATTT
* * * *
752 TTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA
1 TTAAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATGA
*
794 TTGAA-TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA
1 TT-AAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATGA
836 TTAAGTCCTTCGGGTCATC
1 TTAAGTCCTTCGGGTCATC
855 CATAAGACCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
41 2 0.04
42 50 0.93
43 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (42 bp):
TTAAGTCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATGA
Found at i:865 original size:20 final size:20
Alignment explanation
Indices: 837--889 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
827 GCAAGATGAT
* * *
837 TAAGTCCTTCGGGTCATCCA
1 TAAGACCTTCAGGCCATCCA
857 TAAGACCTTCAGGCCATCCA
1 TAAGACCTTCAGGCCATCCA
877 TAAGACCTTCAGG
1 TAAGACCTTCAGG
890 TAGGATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (20 bp):
TAAGACCTTCAGGCCATCCA
Found at i:1077 original size:241 final size:232
Alignment explanation
Indices: 623--1090 Score: 627
Period size: 233 Copynumber: 2.0 Consensus size: 232
613 GAGTAAGATG
* * * *
623 ATAAGTCCTTCGGTCCATCCAGAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAA
1 ATAAGACCTTCGGTCCATCCAGAAGACCTTCAGGTAGGATATTTTCACATAAATTTGAAAATGAA
* ** *
688 AATGATGTTTAAGAAGATGAAACTTTTGAAAACTAAGAAGGCGATTTCGAAAATTTCATTATTTT
66 AATGATGTTTAAGAAAATGAAACTTTTGAAAACTAAGAAGGCGATTTCGAAAATTTCAAAATTTA
* *
753 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTGAATCCTTCGGGTCATCTGTAA
131 TAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
818 GCCTTTAGAGCAAGATGATTAAGTCCTTCGGGTCATCC
196 GCCTTTAGAGCAAGATGA-TAAGTCCTTCGGGTCATCC
*
856 ATAAGACCTTCAGG-CCATCCATAAGACCTTCAGGTAGGATATTTTCACATAAATTTGAAGAATG
1 ATAAGACCTTC-GGTCCATCCAGAAGACCTTCAGGTAGGATATTTTCACATAAATTTGAA-AATG
* * * * ** *
920 AGAAAGTGATGTTTTTAGAAAATGGAATTTTTGAAAAGTAAGAAAGG-TTTTTACATAGTAAATT
64 A-AAA-TGATG-TTTAAGAAAATGAAACTTTTGAAAACTAAG-AAGGCGATTT-C---GAAAATT
984 TCCAAAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATG-TTAAATCCTTCGG
121 T-CAAAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* *
1048 GTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTCGGGT
185 GTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGT
1091 AGGATGTTTT
Statistics
Matches: 204, Mismatches: 20, Indels: 15
0.85 0.08 0.06
Matches are distributed among these distances:
233 51 0.25
234 7 0.03
235 3 0.01
236 5 0.02
237 28 0.14
238 5 0.02
240 14 0.07
241 46 0.23
242 45 0.22
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (232 bp):
ATAAGACCTTCGGTCCATCCAGAAGACCTTCAGGTAGGATATTTTCACATAAATTTGAAAATGAA
AATGATGTTTAAGAAAATGAAACTTTTGAAAACTAAGAAGGCGATTTCGAAAATTTCAAAATTTA
TAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
GCCTTTAGAGCAAGATGATAAGTCCTTCGGGTCATCC
Found at i:1090 original size:41 final size:41
Alignment explanation
Indices: 994--1090 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 41
984 TCCAAAATTT
* * *
994 ATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATG
* * * *
1035 TTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATG
1 ATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATG
1076 ATAAGTCCTTCGGGT
1 ATAAGTCCTTCGGGT
1091 AGGATGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
ATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATG
Found at i:1237 original size:41 final size:41
Alignment explanation
Indices: 1192--1286 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
1182 CTTTATAAGT
1192 CTTCGGGCCATCAAT-AA-TTTCGAGCATGATGATTAAGAATC
1 CTTCGGGCCATCAATAAATTTTCGAGCATGATGATT-A-AATC
* *
1233 CTTCGGGCCATCAGTAAATTTTTCGAGCATGATGCTTAAATC
1 CTTCGGGCCATCAATAAA-TTTTCGAGCATGATGATTAAATC
*
1275 CTTCGGGTCATC
1 CTTCGGGCCATC
1287 TGTAAGCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 14 0.29
42 17 0.35
43 1 0.02
44 16 0.33
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (41 bp):
CTTCGGGCCATCAATAAATTTTCGAGCATGATGATTAAATC
Found at i:1299 original size:232 final size:229
Alignment explanation
Indices: 1002--1434 Score: 608
Period size: 232 Copynumber: 1.9 Consensus size: 229
992 TTATAAGTCA
*
1002 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCTGTAAGTCTTTTG
1 TTCGGGCCATCAGTAAATCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCTGTAAGTCTTTTG
* * * *
1067 AGCAAGATGATAAGTCCTTCGGGTAGGATGTTTTGACA-TGAATTTGAAAAAT-GAAAGTGAT-G
66 AGCAAGATGATAAGACCTTC-GGTAGGAT-ATTTCA-AGTGAATTT-AAAAATAGAAAGTAATGG
* * * * *
1129 TTGTAAGAAAATGAGATATTTGAAAAGTAATAAGGTGATTT-CAGCATTTCGCACTTTATAAGT-
127 TT-TAAGAAAATGAAATATTTG--AAGTAAAAAGGTGATTTCCAACACTTCGCA-TATATAAGTC
1192 CTTCGGGCCATCAATAATTTCGAGCATGATGATTAAGAATCC
188 CTTCGGGCCATCAATAATTTCGAGCATGATGATTAAGAATCC
*
1234 TTCGGGCCATCAGTAAATTTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG-CTTTT
1 TTCGGGCCATCAGTAAATCTTTCGAGCATGATG-TTAAATCCTTCGGGTCATCTGTAAGTCTTTT
*
1298 GAGCAAGATGATAAGACCTTCGGTGGGATATTTCAAGTGAATTTAAAAATGAGAAAGTAATGGTT
65 GAGCAAGATGATAAGACCTTCGGTAGGATATTTCAAGTGAATTTAAAAAT-AGAAAGTAATGGTT
* *
1363 TAAGAAAATGAAATTTTTGAAGTAAAAAGGTGATTTCCAATACTTCGCATATATAAGTCCTTCGG
129 TAAGAAAATGAAATATTTGAAGTAAAAAGGTGATTTCCAACACTTCGCATATATAAGTCCTTCGG
1428 GCCATCA
194 GCCATCA
1435 GTAAGTCTTA
Statistics
Matches: 180, Mismatches: 14, Indels: 16
0.86 0.07 0.08
Matches are distributed among these distances:
229 31 0.17
230 33 0.18
231 32 0.18
232 59 0.33
233 25 0.14
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (229 bp):
TTCGGGCCATCAGTAAATCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCTGTAAGTCTTTTG
AGCAAGATGATAAGACCTTCGGTAGGATATTTCAAGTGAATTTAAAAATAGAAAGTAATGGTTTA
AGAAAATGAAATATTTGAAGTAAAAAGGTGATTTCCAACACTTCGCATATATAAGTCCTTCGGGC
CATCAATAATTTCGAGCATGATGATTAAGAATCC
Found at i:1302 original size:41 final size:44
Alignment explanation
Indices: 1192--1320 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 44
1182 CTTTATAAGT
*
1192 CTTCGGGCCATCAAT-AA--TTTCGAGCATGATGATTAAGAATC
1 CTTCGGGCCATCAGTAAACTTTTCGAGCATGATGATTAAGAATC
* *
1233 CTTCGGGCCATCAGTAAATTTTTCGAGCATGATGCTT-A-AATC
1 CTTCGGGCCATCAGTAAACTTTTCGAGCATGATGATTAAGAATC
* * * *
1275 CTTCGGGTCATCTGTAAGCTTTT-GAGCAAGATGA-TAAG-A-C
1 CTTCGGGCCATCAGTAAACTTTTCGAGCATGATGATTAAGAATC
1315 CTTCGG
1 CTTCGG
1321 TGGGATATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
40 8 0.11
41 25 0.33
42 25 0.33
43 1 0.01
44 16 0.21
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (44 bp):
CTTCGGGCCATCAGTAAACTTTTCGAGCATGATGATTAAGAATC
Found at i:1667 original size:20 final size:22
Alignment explanation
Indices: 1609--1669 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 22
1599 CAGTAAGTGC
1609 CATCAGTAAGTCTTTCGAGCAT
1 CATCAGTAAGTCTTTCGAGCAT
* * * *
1631 GATGAGGAAGTCCTTCG-G-AT
1 CATCAGTAAGTCTTTCGAGCAT
1651 CATCAGTAAGTCTTTCGAG
1 CATCAGTAAGTCTTTCGAG
1670 TACGATGATT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 15 0.50
21 2 0.07
22 13 0.43
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (22 bp):
CATCAGTAAGTCTTTCGAGCAT
Found at i:1687 original size:42 final size:42
Alignment explanation
Indices: 1609--1690 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1599 CAGTAAGTGC
* *
1609 CATCAGTAAGTCTTTCGAGCATGATGAGGAAGTCCTTCGGAT
1 CATCAGTAAGTCTTTCGAGCACGATGAGGAAATCCTTCGGAT
* **
1651 CATCAGTAAGTCTTTCGAGTACGATGATTAAATCCTTCGG
1 CATCAGTAAGTCTTTCGAGCACGATGAGGAAATCCTTCGG
1691 GTTATCCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCACGATGAGGAAATCCTTCGGAT
Found at i:5982 original size:21 final size:21
Alignment explanation
Indices: 5956--6010 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
5946 GGCAGAAATT
* *
5956 ATTGTAGCAGTGTATCGGTAC
1 ATTGTAGCACTGTATCAGTAC
5977 ATTGTAGCACTGTATCAGTAC
1 ATTGTAGCACTGTATCAGTAC
5998 ATTGTAGCACTGT
1 ATTGTAGCACTGT
6011 TCATTACTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
ATTGTAGCACTGTATCAGTAC
Found at i:6070 original size:19 final size:20
Alignment explanation
Indices: 6026--6076 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
6016 ACTGTTCACG
* * *
6026 ATACTATTTACACAGTATCG
1 ATACTATTCATACAGTATCA
6046 ATACTATTCATACAGTAT-A
1 ATACTATTCATACAGTATCA
6065 ATACTATTCATA
1 ATACTATTCATA
6077 AAAAACATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (20 bp):
ATACTATTCATACAGTATCA
Found at i:6530 original size:17 final size:17
Alignment explanation
Indices: 6508--6542 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6498 GAAGTTCTCA
6508 GTTGTCACAGAACATAT
1 GTTGTCACAGAACATAT
*
6525 GTTGTCATAGAACATAT
1 GTTGTCACAGAACATAT
6542 G
1 G
6543 GGGGAGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (17 bp):
GTTGTCACAGAACATAT
Found at i:11385 original size:28 final size:28
Alignment explanation
Indices: 11345--11401 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
11335 GTTTCTGAAA
**
11345 TCTCAGTTTGTGATATTTTATTTTCGTT
1 TCTCAGTTTGTGATATTGCATTTTCGTT
11373 TCTCAGTTTGTGATATTGCATTTTCGTT
1 TCTCAGTTTGTGATATTGCATTTTCGTT
11401 T
1 T
11402 ACTTTCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.58
Consensus pattern (28 bp):
TCTCAGTTTGTGATATTGCATTTTCGTT
Found at i:11621 original size:32 final size:32
Alignment explanation
Indices: 11578--11671 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 32
11568 AATAAACCCT
* * ***
11578 AAAATAATTAAATAATTAAAACATTACAATTG
1 AAAAAAATTAAATAATAAAAACATTACAAAAC
11610 AAAAAAATTAAATAATAAAAACATTA-AAAAC
1 AAAAAAATTAAATAATAAAAACATTACAAAAC
* *
11641 AAAGAAAATTAAATAAAAAAAACAGTACAAA
1 AAA-AAAATTAAATAATAAAAACATTACAAA
11672 CTAAATAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 5 0.09
32 45 0.85
33 3 0.06
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.21
Consensus pattern (32 bp):
AAAAAAATTAAATAATAAAAACATTACAAAAC
Found at i:11651 original size:16 final size:16
Alignment explanation
Indices: 11610--11662 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
11600 ATTACAATTG
*
11610 AAAAAAATTAAATAAT
1 AAAAAAATTAAATAAC
*
11626 AAAAACATTAAA-AAC
1 AAAAAAATTAAATAAC
11641 AAAGAAAATTAAATAA-
1 AAA-AAAATTAAATAAC
11657 AAAAAA
1 AAAAAA
11663 CAGTACAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 8 0.25
16 22 0.69
17 2 0.06
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAAAATTAAATAAC
Found at i:11695 original size:23 final size:23
Alignment explanation
Indices: 11634--11695 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
11624 ATAAAAACAT
*
11634 TAAAAACAA-AGAAAATTAAATAA
1 TAAAAACAATA-AAAACTAAATAA
* * *
11657 AAAAAACAGTACAAACTAAATAA
1 TAAAAACAATAAAAACTAAATAA
11680 TAAAAACAATAAAAAC
1 TAAAAACAATAAAAAC
11696 AATTAAATAC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.73, C:0.10, G:0.03, T:0.15
Consensus pattern (23 bp):
TAAAAACAATAAAAACTAAATAA
Found at i:11702 original size:26 final size:26
Alignment explanation
Indices: 11647--11704 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 26
11637 AAACAAAGAA
* *
11647 AATTAAATAAAAAAAACAGTACAAAC
1 AATTAAATAAAAAAAACAATAAAAAC
*
11673 ---TAAATAATAAAAACAATAAAAAC
1 AATTAAATAAAAAAAACAATAAAAAC
11696 AATTAAATA
1 AATTAAATA
11705 CAAACATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
23 20 0.77
26 6 0.23
ACGTcount: A:0.71, C:0.09, G:0.02, T:0.19
Consensus pattern (26 bp):
AATTAAATAAAAAAAACAATAAAAAC
Found at i:11715 original size:13 final size:13
Alignment explanation
Indices: 11687--11728 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
11677 TAATAAAAAC
*
11687 AATAAAAACAATTA
1 AATACAAAC-ATTA
11701 AATACAAACATTA
1 AATACAAACATTA
*
11714 AATACAAACGTTA
1 AATACAAACATTA
11727 AA
1 AA
11729 AATTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21
Consensus pattern (13 bp):
AATACAAACATTA
Found at i:13554 original size:16 final size:17
Alignment explanation
Indices: 13533--13566 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13523 GAAATAATAT
13533 CCCCAATTAC-TGGAAA
1 CCCCAATTACATGGAAA
*
13549 CCCCAATTGCATGGAAA
1 CCCCAATTACATGGAAA
13566 C
1 C
13567 ATCCTCTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.32, G:0.15, T:0.18
Consensus pattern (17 bp):
CCCCAATTACATGGAAA
Found at i:13923 original size:152 final size:152
Alignment explanation
Indices: 13647--13954 Score: 616
Period size: 152 Copynumber: 2.0 Consensus size: 152
13637 CTAGTGCAGA
13647 AATAAGGTTGGACTCGAGATTACAATGTCTTTTATATTTCACTATGTAACCAAATACAACCTCGA
1 AATAAGGTTGGACTCGAGATTACAATGTCTTTTATATTTCACTATGTAACCAAATACAACCTCGA
13712 TTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGTTACGAATAAAAACTTCTAATATA
66 TTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGTTACGAATAAAAACTTCTAATATA
13777 CGATCATTCCCCTAATTAAATT
131 CGATCATTCCCCTAATTAAATT
13799 AATAAGGTTGGACTCGAGATTACAATGTCTTTTATATTTCACTATGTAACCAAATACAACCTCGA
1 AATAAGGTTGGACTCGAGATTACAATGTCTTTTATATTTCACTATGTAACCAAATACAACCTCGA
13864 TTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGTTACGAATAAAAACTTCTAATATA
66 TTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGTTACGAATAAAAACTTCTAATATA
13929 CGATCATTCCCCTAATTAAATT
131 CGATCATTCCCCTAATTAAATT
13951 AATA
1 AATA
13955 GTATACAAAT
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 156 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (152 bp):
AATAAGGTTGGACTCGAGATTACAATGTCTTTTATATTTCACTATGTAACCAAATACAACCTCGA
TTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGTTACGAATAAAAACTTCTAATATA
CGATCATTCCCCTAATTAAATT
Found at i:14020 original size:152 final size:150
Alignment explanation
Indices: 13689--13985 Score: 390
Period size: 152 Copynumber: 2.0 Consensus size: 150
13679 TATATTTCAC
* * *
13689 TATGTAACCAAATACAACCTCGATTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGT
1 TATGTAACAAAATACAACATCAATTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGT
*
13754 TACGAATAAAAACTTCTAATATACGATCATTCCCCTAATTAAATTAATAAGGTTGGACTCGAGAT
66 TACGAATAAAAACTTCTAATATACGATCATTCCCCTAATTAAATTAATAAGGTT-GAC-CGAAAT
* * *** ** *
13819 TACAATGTCTTTTATATTTCAC
129 TAAAATATAAATTATATACCAA
* * *
13841 TATGTAACCAAATACAACCTCGATTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGT
1 TATGTAACAAAATACAACATCAATTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGT
13906 TACGAATAAAAACTTCTAATATACGATCATTCCCCTAATTAAATTAAT-A-GTAT-A-C-AAATT
66 TACGAATAAAAACTTCTAATATACGATCATTCCCCTAATTAAATTAATAAGGT-TGACCGAAATT
13966 AAAATATAAATTA-ATACCAA
130 AAAATATAAATTATATACCAA
13986 AAATATAAAT
Statistics
Matches: 135, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
145 4 0.03
146 12 0.09
147 1 0.01
149 1 0.01
150 2 0.01
151 2 0.01
152 113 0.84
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (150 bp):
TATGTAACAAAATACAACATCAATTAAATATGACCAGATATGATGCAATATGTATAACTTAGAGT
TACGAATAAAAACTTCTAATATACGATCATTCCCCTAATTAAATTAATAAGGTTGACCGAAATTA
AAATATAAATTATATACCAA
Found at i:14167 original size:16 final size:15
Alignment explanation
Indices: 14144--14173 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
14134 TAGTACAATA
14144 AAATAATATAATATT
1 AAATAATATAATATT
14159 AAATAAATATAATAT
1 AAAT-AATATAATAT
14174 AATAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAATATAATATT
Found at i:14183 original size:21 final size:20
Alignment explanation
Indices: 14140--14183 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
14130 GAATTAGTAC
**
14140 AATAAAATAATATAATATTA
1 AATAAAATAATATAATAAAA
14160 AATAAATATAATATAATAAAA
1 AATAAA-ATAATATAATAAAA
14181 AAT
1 AAT
14184 TATCTTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAAATAATATAATAAAA
Found at i:19600 original size:2 final size:2
Alignment explanation
Indices: 19593--19670 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
19583 CACCTATTTA
19593 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
19635 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
19671 GGCATTCTAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20507 original size:18 final size:18
Alignment explanation
Indices: 20484--20518 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20474 CAAAATTATT
20484 TAAATAAATTCAAATAAA
1 TAAATAAATTCAAATAAA
*
20502 TAAATAAATTCTAATAA
1 TAAATAAATTCAAATAA
20519 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATAAATTCAAATAAA
Found at i:20720 original size:9 final size:8
Alignment explanation
Indices: 20692--20739 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
20682 GTTTACAATT
*
20692 AAATAATC
1 AAATAATA
20700 AAATAA-A
1 AAATAATA
20707 AAATATATA
1 AAATA-ATA
20716 AAATAATA
1 AAATAATA
20724 ATAATAATA
1 A-AATAATA
20733 AAATAAT
1 AAATAAT
20740 TAATTACTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
7 5 0.14
8 17 0.47
9 14 0.39
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (8 bp):
AAATAATA
Found at i:20771 original size:16 final size:16
Alignment explanation
Indices: 20747--20777 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20737 AATTAATTAC
20747 TTAAAGAATAAAAAAT
1 TTAAAGAATAAAAAAT
*
20763 TTAATGAATAAAAAA
1 TTAAAGAATAAAAAA
20778 ATAAATTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
TTAAAGAATAAAAAAT
Found at i:21046 original size:35 final size:35
Alignment explanation
Indices: 20998--21064 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
20988 TCATTCCTCT
**
20998 TAAAGCGTGTTTCATCGAACACGCCTCCTTCTTCC
1 TAAAGCGCATTTCATCGAACACGCCTCCTTCTTCC
**
21033 TAAAGCGCATTTCATCGAACGTGCCTCCTTCT
1 TAAAGCGCATTTCATCGAACACGCCTCCTTCT
21065 CTCAGGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (35 bp):
TAAAGCGCATTTCATCGAACACGCCTCCTTCTTCC
Found at i:21370 original size:2 final size:2
Alignment explanation
Indices: 21363--21394 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21353 AGATTCAACA
21363 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
21395 GAATAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24780 original size:18 final size:18
Alignment explanation
Indices: 24743--24786 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
24733 GGTCCACCAT
24743 TTCTTCTTCTTCTTCTGC
1 TTCTTCTTCTTCTTCTGC
*
24761 TTTTTCTTCTTCTT-TCGC
1 TTCTTCTTCTTCTTCT-GC
24779 TTCTTCTT
1 TTCTTCTT
24787 TCTTTAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.00, C:0.30, G:0.05, T:0.66
Consensus pattern (18 bp):
TTCTTCTTCTTCTTCTGC
Found at i:27207 original size:17 final size:17
Alignment explanation
Indices: 27185--27238 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
27175 AATGTTAATA
27185 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
27202 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
27219 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
27236 TTT
1 TTT
27239 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:28799 original size:21 final size:21
Alignment explanation
Indices: 28769--28816 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
28759 GCAGGGGTAC
* *
28769 ATGCCCAGCCCCCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
28790 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
28811 ATGCCA
1 ATGCCA
28817 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:28846 original size:21 final size:21
Alignment explanation
Indices: 28820--28913 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
28810 TATGCCATCT
28820 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
28841 CCGCAGGGTTACATTTCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
28862 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
28883 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
28904 CCGCAGGGTT
1 CCGCAGGGTT
28914 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:29387 original size:34 final size:33
Alignment explanation
Indices: 29281--29387 Score: 108
Period size: 34 Copynumber: 3.2 Consensus size: 33
29271 ATAAATGTTT
*
29281 TTAAAATACAAATTATATTATTTA-AAATTTAAAA
1 TTAAAATAAAAATTATATTA-TTAGAAATTT-AAA
* * *
29315 TAAAAATAAAAATAATATTATTAGAAAATTAAA
1 TTAAAATAAAAATTATATTATTAGAAATTTAAA
* * *
29348 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTAGAAATTTAA-A
29383 TTAAA
1 TTAAA
29388 TTTCAACTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
33 6 0.10
34 53 0.88
35 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTAGAAATTTAAA
Found at i:29968 original size:128 final size:128
Alignment explanation
Indices: 29740--30040 Score: 575
Period size: 128 Copynumber: 2.4 Consensus size: 128
29730 TTACCTGATT
*
29740 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTC
29805 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
*
29868 TACTGATATATTTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTC
29933 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
*
29996 TACTGATATATCTAGTGTCCCCGATGGACATGAGTGACATAATAG
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAG
30041 GAAGGCATTC
Statistics
Matches: 169, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 169 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
Found at i:32818 original size:159 final size:159
Alignment explanation
Indices: 32529--32848 Score: 615
Period size: 159 Copynumber: 2.0 Consensus size: 159
32519 CTTGGTAGAA
32529 AAATATTATTTAATTAAAAAAATCATAGAACTTTAAATAATTAAATATAATAATTTAATTACTTA
1 AAATATTATTTAATTAAAAAAATCATAGAACTTTAAATAATTAAATATAATAATTTAATTACTTA
32594 ATTTTGACTAAAAAATAATTTGGATACTTAAAACAAAAGGAATACATAATCTGAATATCTATTTT
66 ATTTTGACTAAAAAATAATTTGGATACTTAAAACAAAAGGAATACATAATCTGAATATCTATTTT
32659 TACTTAAAGCCTAAAAAATATTAACTTTT
131 TACTTAAAGCCTAAAAAATATTAACTTTT
*
32688 AAATATTATTTAATT-AAAAAATCATAGAACTTTAAATAATTAAATATGATAATTTAATTACTTA
1 AAATATTATTTAATTAAAAAAATCATAGAACTTTAAATAATTAAATATAATAATTTAATTACTTA
32752 ATTTTGACTTAAAAAATAATTTGGATACTTAAAACAAAAGGAATACATAATCTGAATATCTATTT
66 ATTTTGAC-TAAAAAATAATTTGGATACTTAAAACAAAAGGAATACATAATCTGAATATCTATTT
32817 TTACTTAAAGCCTAAAAAATATTAACTTTT
130 TTACTTAAAGCCTAAAAAATATTAACTTTT
32847 AA
1 AA
32849 CTTTTAATTA
Statistics
Matches: 159, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
158 56 0.35
159 103 0.65
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (159 bp):
AAATATTATTTAATTAAAAAAATCATAGAACTTTAAATAATTAAATATAATAATTTAATTACTTA
ATTTTGACTAAAAAATAATTTGGATACTTAAAACAAAAGGAATACATAATCTGAATATCTATTTT
TACTTAAAGCCTAAAAAATATTAACTTTT
Found at i:33360 original size:21 final size:21
Alignment explanation
Indices: 33335--33400 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
33325 CTTTCGTCAC
33335 TCTCAGTCTACATGGTAACAT
1 TCTCAGTCTACATGGTAACAT
* * *
33356 TCTCA--CATGATATCGT--CAC
1 TCTCAGTC-T-ACATGGTAACAT
33375 TCTCAGTCTACATGGTAACAT
1 TCTCAGTCTACATGGTAACAT
33396 TCTCA
1 TCTCA
33401 CATGGTATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
19 13 0.39
20 2 0.06
21 18 0.55
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (21 bp):
TCTCAGTCTACATGGTAACAT
Found at i:33383 original size:40 final size:40
Alignment explanation
Indices: 33328--33409 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
33318 CCATTATCTT
33328 TCGTCACTCTCAGTCTACATGGTAACATTCTCACATGATA
1 TCGTCACTCTCAGTCTACATGGTAACATTCTCACATGATA
*
33368 TCGTCACTCTCAGTCTACATGGTAACATTCTCACATGGTA
1 TCGTCACTCTCAGTCTACATGGTAACATTCTCACATGATA
33408 TC
1 TC
33410 ATTCACTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (40 bp):
TCGTCACTCTCAGTCTACATGGTAACATTCTCACATGATA
Found at i:35015 original size:36 final size:36
Alignment explanation
Indices: 34966--35338 Score: 432
Period size: 36 Copynumber: 10.5 Consensus size: 36
34956 AGAAATACAA
* * * *
34966 GAACGAAAAGAAGCATCGGCACTTCTGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* * *
35002 GAACGGAATGAAGCATCGGCACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
*
35038 GAACGGAAGGAGGCATCGACACTTCCGA-T----TC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* * *
35069 GAACAGAATGAGGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* * *
35105 AAATGGAAGAAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* * * *
35141 GAACGGAATGAGGCACCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* *
35177 AAACGGAAGGAGGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* * *
35213 AAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* * *
35249 AAACGGAAGGAAACATCGACACTTCCGATTTAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* * *
35285 GAATGGAAGGAAGCATCGACTCTTCTGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* *
35321 GAACGGAAAGAAGTATCG
1 GAACGGAAGGAAGCATCG
35339 CACCTTCGTT
Statistics
Matches: 289, Mismatches: 43, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
31 28 0.10
32 1 0.00
35 1 0.00
36 259 0.90
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
Found at i:37735 original size:22 final size:23
Alignment explanation
Indices: 37670--37735 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
37660 AGGAAAATAA
*
37670 CCTGCTATGAAAACAGAGAAAAG
1 CCTGCTATGAAAGCAGAGAAAAG
* *
37693 CCTACTATGAAAGTAGAGAAAAG
1 CCTGCTATGAAAGCAGAGAAAAG
*
37716 CGTGCTATG-AAGCAGAGAAA
1 CCTGCTATGAAAGCAGAGAAA
37736 TTTATGTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 10 0.27
23 27 0.73
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.15
Consensus pattern (23 bp):
CCTGCTATGAAAGCAGAGAAAAG
Found at i:42567 original size:29 final size:29
Alignment explanation
Indices: 42525--42585 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
42515 CATCTCATCG
42525 CCGAAAATGCTAAATTCGCCGCTCCACCA
1 CCGAAAATGCTAAATTCGCCGCTCCACCA
42554 CCGAAAATGCTAAATTCGCCGCTCCACCA
1 CCGAAAATGCTAAATTCGCCGCTCCACCA
42583 CCG
1 CCG
42586 GTCGAAGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.39, G:0.15, T:0.16
Consensus pattern (29 bp):
CCGAAAATGCTAAATTCGCCGCTCCACCA
Found at i:46447 original size:11 final size:11
Alignment explanation
Indices: 46431--46461 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
46421 ATTGCTTAAA
46431 CATTCTAGACT
1 CATTCTAGACT
*
46442 CATTCTAGATT
1 CATTCTAGACT
46453 CATTCTAGA
1 CATTCTAGA
46462 ACGTTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (11 bp):
CATTCTAGACT
Found at i:50938 original size:11 final size:11
Alignment explanation
Indices: 50922--50952 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
50912 ATTGCTTAAA
50922 CATTCTAGACT
1 CATTCTAGACT
*
50933 CATTCTAGATT
1 CATTCTAGACT
50944 CATTCTAGA
1 CATTCTAGA
50953 ACGTTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (11 bp):
CATTCTAGACT
Found at i:51924 original size:3 final size:3
Alignment explanation
Indices: 51913--51942 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
51903 CTTCTTCTGC
*
51913 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51943 TCCCCCCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:54166 original size:6 final size:6
Alignment explanation
Indices: 54155--54186 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
54145 GAAAAGGTAG
*
54155 GATGAA GATGAA GATGAA GACGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GA
54187 GATAGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.34, T:0.12
Consensus pattern (6 bp):
GATGAA
Found at i:62676 original size:31 final size:31
Alignment explanation
Indices: 62613--62676 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
62603 TGACATATGC
* * * **
62613 CATGTGTTTAAAATAATGACATGACACGTGA
1 CATGTGTTCAAAATAATGACATAAAAAATGA
*
62644 CATGTGTTCAAAATGATGACATAAAAAATGA
1 CATGTGTTCAAAATAATGACATAAAAAATGA
62675 CA
1 CA
62677 CATATCTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (31 bp):
CATGTGTTCAAAATAATGACATAAAAAATGA
Found at i:63503 original size:16 final size:16
Alignment explanation
Indices: 63479--63517 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
63469 TAGCATGTTT
*
63479 AAAAAAATT-AAAATA
1 AAAAAAATTGAAAAGA
63494 AAACAAAATTGAAAAGA
1 AAA-AAAATTGAAAAGA
63511 AAAAAAA
1 AAAAAAA
63518 GAAAGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 10 0.48
17 8 0.38
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (16 bp):
AAAAAAATTGAAAAGA
Found at i:65194 original size:10 final size:10
Alignment explanation
Indices: 65179--65245 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 10
65169 CATTTAAATG
65179 ATAAACGAAC
1 ATAAACGAAC
65189 ATAAACGAACAC
1 ATAAACG-A-AC
*
65201 AAATGAACGAAC
1 --ATAAACGAAC
65213 ATAAACGAAC
1 ATAAACGAAC
*
65223 ATAATAAATGAAC
1 ---ATAAACGAAC
65236 ATAAACGAAC
1 ATAAACGAAC
65246 TACACAAACA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 25 0.54
11 1 0.02
12 4 0.09
13 10 0.22
14 6 0.13
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:65211 original size:24 final size:23
Alignment explanation
Indices: 65179--65245 Score: 98
Period size: 24 Copynumber: 2.9 Consensus size: 23
65169 CATTTAAATG
65179 ATAAACGAACATAAACGAACACAA
1 ATAAACGAACATAAACGAACA-AA
* *
65203 ATGAACGAACATAAACGAACATA
1 ATAAACGAACATAAACGAACAAA
*
65226 ATAAATGAACATAAACGAAC
1 ATAAACGAACATAAACGAAC
65246 TACACAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACAAA
Found at i:65616 original size:3 final size:3
Alignment explanation
Indices: 65608--65642 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
65598 TTATTCTGAT
65608 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65643 AATAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:65656 original size:23 final size:22
Alignment explanation
Indices: 65606--65656 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
65596 TTTTATTCTG
*
65606 ATTTATTATTATTATTATTATT
1 ATTTATTATTATTATAATTATT
65628 ATTTTATTATTATTAAATAATT-TT
1 A-TTTATTATTATT--ATAATTATT
65652 ATTTA
1 ATTTA
65657 CAGGCCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 16 0.64
24 3 0.12
25 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTATTATTATTATAATTATT
Found at i:66891 original size:21 final size:21
Alignment explanation
Indices: 66867--66939 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 21
66857 CATTTTAATC
66867 TTATTATTTAATTTTATTTAA
1 TTATTATTTAATTTTATTTAA
*
66888 TTATTATTT-ATTTTCATTT-T
1 TTATTATTTAATTTT-ATTTAA
*
66908 TTATGT-TTAAATTATTACTTTAA
1 TTAT-TATTTAATT-TTA-TTTAA
66931 TTATTATTT
1 TTATTATTT
66940 TATCATTATG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 11 0.27
21 18 0.44
22 6 0.15
23 6 0.15
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (21 bp):
TTATTATTTAATTTTATTTAA
Found at i:66901 original size:39 final size:42
Alignment explanation
Indices: 66858--66939 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 42
66848 AATATTTTAC
66858 ATTTTAATCTTATTA-TTT-AATT-TTA-TTTAATTATTATTT
1 ATTTTAAT-TTATTAGTTTAAATTATTACTTTAATTATTATTT
* *
66897 ATTTTCATTTTTTATGTTTAAATTATTACTTTAATTATTATTT
1 ATTTTAATTTATTA-GTTTAAATTATTACTTTAATTATTATTT
66940 TATCATTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
38 5 0.14
39 7 0.19
40 3 0.08
41 4 0.11
42 3 0.08
43 14 0.39
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (42 bp):
ATTTTAATTTATTAGTTTAAATTATTACTTTAATTATTATTT
Found at i:66968 original size:2 final size:2
Alignment explanation
Indices: 66955--66998 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
66945 TTATGTAGCC
*
66955 AT AT AA 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
66997 AT
1 AT
66999 TAAATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67877 original size:15 final size:16
Alignment explanation
Indices: 67859--67888 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
67849 CTTTCAAATT
67859 TTTTTATACT-TATAG
1 TTTTTATACTATATAG
67874 TTTTTATACTATATA
1 TTTTTATACTATATA
67889 CATTCTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTTATACTATATAG
Found at i:68450 original size:46 final size:46
Alignment explanation
Indices: 68384--68471 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
68374 TGATTTCATT
* *
68384 TTTTTTCAAACAAAGCATGGAACTAGAAATCATGCA-GTTAGGTTAA
1 TTTTTCCAAACAAAGCATGGAACTAGAAAGCATG-ATGTTAGGTTAA
*
68430 TTTTTCCAAACAAAGTATGGAACTAGAAAGCATGATGTTAGG
1 TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGATGTTAGG
68472 ATTTATACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (46 bp):
TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGATGTTAGGTTAA
Found at i:69254 original size:43 final size:44
Alignment explanation
Indices: 69186--69269 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
69176 GGCTTTAGAG
* *
69186 AAGTTAGGAAGGAAAGTTATTCCCTATATGT-AAAGTTTTGCTA
1 AAGTTAGGAAGGAAAGTTATCCCCTACATGTAAAAGTTTTGCTA
** *
69229 AAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTG
1 AAGTTAGGAAGGAAAGTTATCCCCTACATGTAAAAGTTTTG
69270 TTTGATGCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 26 0.74
44 9 0.26
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (44 bp):
AAGTTAGGAAGGAAAGTTATCCCCTACATGTAAAAGTTTTGCTA
Found at i:69370 original size:8 final size:7
Alignment explanation
Indices: 69346--69402 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 7
69336 TTTTCATACA
69346 TGCA-TT
1 TGCATTT
69352 TGCATTT
1 TGCATTT
69359 TGCATCTT
1 TGCAT-TT
69367 TGCATTT
1 TGCATTT
*
69374 T-TATTT
1 TGCATTT
*
69380 T-TA-TT
1 TGCATTT
69385 TGCA-TT
1 TGCATTT
69391 TGCATTT
1 TGCATTT
69398 TGCAT
1 TGCAT
69403 ATTTTTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
5 3 0.07
6 18 0.40
7 17 0.38
8 7 0.16
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (7 bp):
TGCATTT
Found at i:69428 original size:31 final size:31
Alignment explanation
Indices: 69349--69435 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
69339 TCATACATGC
* *
69349 ATTTGCATTTTGCATCTTTGCATTTTTATTTTT
1 ATTTGCA-TTTACAT-TTTGCATTTTTATTTAT
*
69382 ATTTGCATTTGCATTTTGCATATTTT-TTTAT
1 ATTTGCATTTACATTTTGCAT-TTTTATTTAT
* *
69413 GTTTGTATTTACATTTT-CATTTT
1 ATTTGCATTTACATTTTGCATTTT
69436 CTGCATTTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.06
30 3 0.06
31 25 0.51
32 11 0.22
33 7 0.14
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.63
Consensus pattern (31 bp):
ATTTGCATTTACATTTTGCATTTTTATTTAT
Found at i:76450 original size:12 final size:12
Alignment explanation
Indices: 76425--76506 Score: 67
Period size: 12 Copynumber: 6.8 Consensus size: 12
76415 ACGGAGATAT
* *
76425 CAGAAATCAAAA
1 CAGAATTCAGAA
76437 CAGAATTCAGAA
1 CAGAATTCAGAA
*
76449 CAG-ATATCAAAA
1 CAGAAT-TCAGAA
*
76461 TAGAATTCAGAA
1 CAGAATTCAGAA
* *
76473 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
76485 CATAAATCAGAA
1 CAGAATTCAGAA
*
76497 CATAATTCAG
1 CAGAATTCAG
76507 GTCATGTATC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
11 2 0.04
12 51 0.93
13 2 0.04
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:76452 original size:24 final size:24
Alignment explanation
Indices: 76425--76477 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
76415 ACGGAGATAT
76425 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* *
76449 CAGATATCAAAATAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
76473 CAGAA
1 CAGAA
76478 TCCAGATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.15, G:0.13, T:0.15
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCAGAA
Found at i:85229 original size:20 final size:21
Alignment explanation
Indices: 85206--85249 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
85196 TATCGATATT
*
85206 GAGGG-TTCGGTATCGAGACC
1 GAGGGCTTCGGTATCAAGACC
* *
85226 GAGGGCTTTGTTATCAAGACC
1 GAGGGCTTCGGTATCAAGACC
85247 GAG
1 GAG
85250 ATTCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (21 bp):
GAGGGCTTCGGTATCAAGACC
Found at i:86628 original size:3 final size:3
Alignment explanation
Indices: 86620--86716 Score: 78
Period size: 3 Copynumber: 33.0 Consensus size: 3
86610 CCATTTGCTT
* *
86620 TTA TTA TTA TTA -TA TTA TTA -TA TTA TTA TT- TTA TT- TATA CTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* * *
86662 TTA TTA TTA TT- TTA TTTA TTA GTTT TTA TTA TTA ATA ATA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
86708 TTA CTA TTA
1 TTA TTA TTA
86717 CAGGCCCAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
2 9 0.12
3 62 0.82
4 5 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:86637 original size:8 final size:8
Alignment explanation
Indices: 86624--86708 Score: 58
Period size: 8 Copynumber: 11.1 Consensus size: 8
86614 TTGCTTTTAT
86624 TATTATTA
1 TATTATTA
86632 TATTATTA
1 TATTATTA
86640 TATTATTA
1 TATTATTA
*
86648 TTTTATT-
1 TATTATTA
86655 TA-TACTGT-
1 TATTA-T-TA
86663 TATTATTA
1 TATTATTA
*
86671 TTTTATT-
1 TATTATTA
86678 TATTAGTT-
1 TATTA-TTA
86686 T-TTATTA
1 TATTATTA
* *
86693 T-TAATAA
1 TATTATTA
86700 TATTATTA
1 TATTATTA
86708 T
1 T
86709 TACTATTACA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
6 4 0.06
7 16 0.26
8 40 0.65
9 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTATTA
Found at i:87407 original size:32 final size:32
Alignment explanation
Indices: 87366--87432 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
87356 AGGCGGTGGT
87366 CGGCGGCGGAGTTAACGGCGGATGACGGTTGC
1 CGGCGGCGGAGTTAACGGCGGATGACGGTTGC
*
87398 CGGCGGCGGAGTTAACTGCGGATGACGGTTGC
1 CGGCGGCGGAGTTAACGGCGGATGACGGTTGC
87430 CGG
1 CGG
87433 TCGGTGACCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.16
Consensus pattern (32 bp):
CGGCGGCGGAGTTAACGGCGGATGACGGTTGC
Found at i:88137 original size:29 final size:30
Alignment explanation
Indices: 88068--88138 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
88058 TTTTAACCAC
* *
88068 TATTTAGTTATAT-TTTAATTTTATATGTT
1 TATTTAGTCATATATTTAATTTTATATGAT
88097 TATTT--TCAATATATTTAATTATTAT-T-AT
1 TATTTAGTC-ATATATTTAATT-TTATATGAT
88125 TATTTAGTCATATA
1 TATTTAGTCATATA
88139 AATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
27 1 0.03
28 10 0.29
29 18 0.51
30 6 0.17
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (30 bp):
TATTTAGTCATATATTTAATTTTATATGAT
Found at i:90814 original size:54 final size:54
Alignment explanation
Indices: 90751--91131 Score: 494
Period size: 54 Copynumber: 7.1 Consensus size: 54
90741 TCATTGACCA
90751 AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAG
1 AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAG
* * *
90805 AACATCTGGGCAAAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGCTTTACG
1 AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAG
* * * ** * *
90859 GACATCTGTGCAGAAGTTACAGGAAAGGATGAATGTGTTGTCGAATGTTTTAAG
1 AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAG
* * * * *
90913 AACATCTGAGCATAAGCCAAAAGAAATGATGAATGTGTTGTCAAATGTTTTATG
1 AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAG
* * *
90967 AACATCTGGGCAAAAGCCACAAGTAAA-GATGAATGTGTTGTCAATTGCTTTACG
1 AACATCTGGGCAAAAGCCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTAAG
* * * * *
91021 AACATCTGTGCAGAAGTCACAGGAAAGGATGAATGTGTTGTCGAATGTTTTAAG
1 AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAG
* * * * *
91075 AACATCTGAGCAGAAGACACAAGAAATGATGAATGTGTTGTCAAGTGTTTTAAG
1 AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAG
91129 AAC
1 AAC
91132 CAGTAATTAT
Statistics
Matches: 282, Mismatches: 43, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
53 3 0.01
54 276 0.98
55 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (54 bp):
AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAG
Found at i:91018 original size:162 final size:162
Alignment explanation
Indices: 90751--91131 Score: 654
Period size: 162 Copynumber: 2.4 Consensus size: 162
90741 TCATTGACCA
* *
90751 AACATCTGGGCAAAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAAGAACATCTGGGC
1 AACATCTGAGCAAAAGCCACAAGAAATGATGAATGTGTTGTCAAATGTTTTAAGAACATCTGGGC
* *
90816 AAAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGCTTTACGGACATCTGTGCAGAAGTTACAG
66 AAAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGCTTTACGAACATCTGTGCAGAAGTCACAG
90881 GAAAGGATGAATGTGTTGTCGAATGTTTTAAG
131 GAAAGGATGAATGTGTTGTCGAATGTTTTAAG
* * *
90913 AACATCTGAGCATAAGCCAAAAGAAATGATGAATGTGTTGTCAAATGTTTTATGAACATCTGGGC
1 AACATCTGAGCAAAAGCCACAAGAAATGATGAATGTGTTGTCAAATGTTTTAAGAACATCTGGGC
* *
90978 AAAAGCCACAAGTAAAGATGAATGTGTTGTCAATTGCTTTACGAACATCTGTGCAGAAGTCACAG
66 AAAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGCTTTACGAACATCTGTGCAGAAGTCACAG
91043 GAAAGGATGAATGTGTTGTCGAATGTTTTAAG
131 GAAAGGATGAATGTGTTGTCGAATGTTTTAAG
* * *
91075 AACATCTGAGCAGAAGACACAAGAAATGATGAATGTGTTGTCAAGTGTTTTAAGAAC
1 AACATCTGAGCAAAAGCCACAAGAAATGATGAATGTGTTGTCAAATGTTTTAAGAAC
91132 CAGTAATTAT
Statistics
Matches: 205, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 205 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (162 bp):
AACATCTGAGCAAAAGCCACAAGAAATGATGAATGTGTTGTCAAATGTTTTAAGAACATCTGGGC
AAAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGCTTTACGAACATCTGTGCAGAAGTCACAG
GAAAGGATGAATGTGTTGTCGAATGTTTTAAG
Found at i:91524 original size:22 final size:22
Alignment explanation
Indices: 91498--91566 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
91488 AAAATAATAT
91498 ATTCTCTTTTCAAAGATGATAG
1 ATTCTCTTTTCAAAGATGATAG
* *
91520 ATTCTCTCTTCAAAGATGATAC
1 ATTCTCTTTTCAAAGATGATAG
* *
91542 ATTCTCTTTTCAAAGAAGAAAG
1 ATTCTCTTTTCAAAGATGATAG
91564 ATT
1 ATT
91567 TATTGGATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
ATTCTCTTTTCAAAGATGATAG
Found at i:92124 original size:112 final size:113
Alignment explanation
Indices: 91935--92502 Score: 541
Period size: 122 Copynumber: 4.8 Consensus size: 113
91925 TACACTCAAT
* * * *
91935 GGATCAACATTTCTAGAAGAGTTCATAATAAGAAGAACTCATTTGAAGAAGGAAGAAAAAGTTCA
1 GGATCAACATTTCCAGAGGAGTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCA
* * * **
92000 TAATGAGAAGAACTTGTTCAACCTTTCGCTCAAATTCATCAC-TCGAT-
65 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTTATCACATAAATA
* *
92047 GGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGGAGAAGAAGTTCA
1 GGATCAACATTTCCAGAG-GAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCA
*
92112 TAATGAGAAGAACTTGTTCAA-CTCTTTGCTCGATTTTATCACAGAAGAAGATAAATCA
65 TAATGAGAAGAACTTGTTCAACCT-TTTGCTCGAATTTATCAC--------ATAAAT-A
* * * *
92170 GCATCAACATTTCCAGAGGTGTTCATAATGAA-AAGAACTTATCTGAAGAAGGAGAAGAGGTTCA
1 GGATCAACATTTCCAGAGGAGTTCATAAT-AAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCA
*
92234 TAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTTATCACAGAAGGAGATAAATCA
65 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTTATCAC--------ATAAAT-A
* * * *
92292 GTATCAACATTTCCAGAGGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAATAAGTTCAT
1 GGATCAACATTTCCAGAGGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCAT
*** *
92357 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACGCTATCACAGAAAGAGATA
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTTATCAC--ATA-A-ATA
* * * * * *
92409 GATCAACATCAACATTTCCAAAAGAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAA
1 G-----GATCAACATTTCCAGAGGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAG
*
92474 TTCATAATGAGAAGAATTTGTTCAACCTT
61 TTCATAATGAGAAGAACTTGTTCAACCTT
92503 GCCTTAATTC
Statistics
Matches: 396, Mismatches: 37, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
111 2 0.01
112 62 0.16
113 31 0.08
116 4 0.01
117 3 0.01
118 2 0.01
121 4 0.01
122 268 0.68
123 20 0.05
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (113 bp):
GGATCAACATTTCCAGAGGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTTATCACATAAATA
Found at i:92198 original size:122 final size:122
Alignment explanation
Indices: 92049--92499 Score: 638
Period size: 122 Copynumber: 3.7 Consensus size: 122
92039 CACTCGATGG
* *
92049 ATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGGAGAAGAAGTTCATA
1 ATCAACATTTCCAGAG-GAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATA
*
92114 ATGAGAAGAACTTGTTCAACTCTTTGCTCGATTTTATCACAGAAGAAGATAAATCAGC
65 ATGAGAAGAACTTGTTCAACTCTTTGCTCGAATTTATCACAGAAGAAGATAAATCAGC
* * *
92172 ATCAACATTTCCAGAGGTGTTCATAATGAA-AAGAACTTATCTGAAGAAGGAGAAGAGGTTCATA
1 ATCAACATTTCCAGAGGAGTTCATAAT-AAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATA
* * *
92236 ATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTTATCACAGAAGGAGATAAATCAGT
65 ATGAGAAGAACTTGTTCAACTCTTTGCTCGAATTTATCACAGAAGAAGATAAATCAGC
* * *
92294 ATCAACATTTCCAGAGGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAATAAGTTCATAA
1 ATCAACATTTCCAGAGGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
*** * *
92359 TGAGAAGAACTTGTTCAAC-CTTTTGCTCGACGCTATCACAGAA-AGAGATAGATCAAC
66 TGAGAAGAACTTGTTCAACTC-TTTGCTCGAATTTATCACAGAAGA-AGATAAATCAGC
* * * * *
92416 ATCAACATTTCCAAAAGAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCATAA
1 ATCAACATTTCCAGAGGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
*
92481 TGAGAAGAATTTGTTCAAC
66 TGAGAAGAACTTGTTCAAC
92500 CTTGCCTTAA
Statistics
Matches: 298, Mismatches: 26, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
121 1 0.00
122 279 0.94
123 18 0.06
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
ATCAACATTTCCAGAGGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACTCTTTGCTCGAATTTATCACAGAAGAAGATAAATCAGC
Found at i:92358 original size:244 final size:245
Alignment explanation
Indices: 91937--92499 Score: 708
Period size: 244 Copynumber: 2.3 Consensus size: 245
91927 CACTCAATGG
* * *
91937 ATCAACATTTCTAGAAGAGTTCATAAT-AAGAAGAACTCATTTGAAGAAGGAAGAA-AAAGTTCA
1 ATCAACATTTCCAAAAGAGTTCATAATGAA-AAGAACTCATCTGAAGAAGG-AGAAGAAA-TTCA
* * * * ** *
92000 TAATGAGAAGAACTTGTTCAACCTTTCGCTCAAATTCATCAC---------TCGAT--GGATCAA
63 TAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTTATCACAGAAGGAGATAAATCAGTATCAA
*
92054 CATTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGGAGAAGAAGTTCATAATGAG
128 CATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAG
*** *
92119 AAGAACTTGTTCAA-CTCTTTGCTCGATTTTATCACAG-AAGAAGATAAATCAGC
193 AAGAACTTGTTCAACCT-TTTGCTCGACGCTATCACAGAAAG-AGATAAATCAAC
* * * * **
92172 ATCAACATTTCCAGAGGTGTTCATAATGAAAAGAACTTATCTGAAGAAGGAGAAGAGGTTCATAA
1 ATCAACATTTCCAAAAGAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAGAAGAAATTCATAA
92237 TGAGAAGAACTTGTTCAACTTTTTGCTCGAATTTATCACAGAAGGAGATAAATCAGTATCAACAT
66 TGAGAAGAACTTGTTCAACTTTTTGCTCGAATTTATCACAGAAGGAGATAAATCAGTATCAACAT
** * *
92302 TTCCAGAG-GTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAATAAGTTCATAATGAGAAG
131 TTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAG
*
92366 AACTTGTTCAACCTTTTGCTCGACGCTATCACAGAAAGAGATAGATCAAC
196 AACTTGTTCAACCTTTTGCTCGACGCTATCACAGAAAGAGATAAATCAAC
* *
92416 ATCAACATTTCCAAAAGAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCATAA
1 ATCAACATTTCCAAAAGAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAGAAGAAATTCATAA
*
92481 TGAGAAGAATTTGTTCAAC
66 TGAGAAGAACTTGTTCAAC
92500 CTTGCCTTAA
Statistics
Matches: 280, Mismatches: 33, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
234 46 0.16
235 43 0.15
236 2 0.01
243 3 0.01
244 164 0.59
245 22 0.08
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (245 bp):
ATCAACATTTCCAAAAGAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAGAAGAAATTCATAA
TGAGAAGAACTTGTTCAACTTTTTGCTCGAATTTATCACAGAAGGAGATAAATCAGTATCAACAT
TTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAG
AACTTGTTCAACCTTTTGCTCGACGCTATCACAGAAAGAGATAAATCAAC
Found at i:94150 original size:28 final size:29
Alignment explanation
Indices: 94118--94172 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
94108 AAATAATATT
**
94118 TATTTATTTATTT-ATTTTATAAAAATCC
1 TATTTATAAATTTAATTTTATAAAAATCC
*
94146 TATTTATAAATTTAATTTTATATAAAT
1 TATTTATAAATTTAATTTTATAAAAAT
94173 TACTTTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (29 bp):
TATTTATAAATTTAATTTTATAAAAATCC
Found at i:94476 original size:148 final size:148
Alignment explanation
Indices: 94197--94477 Score: 388
Period size: 148 Copynumber: 1.9 Consensus size: 148
94187 TAATCATATT
* * * *
94197 TTAATATTTATTTATTTTTTAATATTAAGAAATTTGCTGTCTTAAAGCACCTAGAAGTCATTTTC
1 TTAATATTTATTTATTTTTTAATATGAAGAAATATACTGTCTTAAAGCACCTAGAAGTCATTTTA
* * * * * * *
94262 TAATATTCTTAAATAAATAAATATCCTATTTTTATAAATTATATATATTAATTTATTTTAATTAT
66 TAACATTCTTAAATAAATAAATATCCTATTTATAAAAATAAGATATATTAATATATATTAATTAT
94327 TTTTAGAGAAATGTTTTA
131 TTTTAGAGAAATGTTTTA
*
94345 TTAATATTTATTTATTTTTTAATATGAAGAAATATACTGTCTTAAAGCACCTAGAAGTCCTTTTA
1 TTAATATTTATTTATTTTTTAATATGAAGAAATATACTGTCTTAAAGCACCTAGAAGTCATTTTA
* *
94410 TAACATT-TCTAAGTAAATAAATATCTTATTTATAAAAATAAAGATATA-T-ATATATATTAATA
66 TAACATTCT-TAAATAAATAAATATCCTATTTATAAAAAT-AAGATATATTAATATATATTAAT-
94472 TATTTT
128 TATTTT
94478 CTTAAAATTA
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
147 11 0.09
148 99 0.85
149 6 0.05
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (148 bp):
TTAATATTTATTTATTTTTTAATATGAAGAAATATACTGTCTTAAAGCACCTAGAAGTCATTTTA
TAACATTCTTAAATAAATAAATATCCTATTTATAAAAATAAGATATATTAATATATATTAATTAT
TTTTAGAGAAATGTTTTA
Found at i:94807 original size:16 final size:17
Alignment explanation
Indices: 94774--94813 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
94764 CTCCCGAAAC
94774 ATTTTTTAATCAAAATT
1 ATTTTTTAATCAAAATT
* *
94791 ATTTTTT-ATCCACATT
1 ATTTTTTAATCAAAATT
94807 ATTTTTT
1 ATTTTTT
94814 CTTGCCAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTTAATCAAAATT
Found at i:98871 original size:20 final size:20
Alignment explanation
Indices: 98856--98902 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
98846 CCTTTGCCGG
*
98856 TTACTTTCATTTTTTGCAGA
1 TTACTTTCATTATTTGCAGA
*
98876 TTACTTTCATTATTTGTAGA
1 TTACTTTCATTATTTGCAGA
98896 TTACTTT
1 TTACTTT
98903 TATAAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.57
Consensus pattern (20 bp):
TTACTTTCATTATTTGCAGA
Done.