Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007930.1 Hibiscus syriacus cultivar Beakdansim tig00110338_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: 2280901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:175393 original size:84 final size:83
Alignment explanation
Indices: 175221--175755 Score: 676
Period size: 84 Copynumber: 6.4 Consensus size: 83
175211 GGGTATCTGG
* * * * *
175221 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
*
175286 AGAAGGGCTATCTGTCAA
66 AGAAGGGTTATCTGTCAA
* * *
175304 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGG
1 -CAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTACAGCATAACTCAAGG
*
175369 TTAGAAGGGTTATCTGTCAA
64 CTAGAAGGGTTATCTGTCAA
* *
175389 CAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
175454 AGAAGGGTTATCTGTCAA
66 AGAAGGGTTATCTGTCAA
* * * * * * *
175472 AAAACACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
* ** *
175537 ATAAGGGTTATCTACCGA
66 AGAAGGGTTATCTGTCAA
* * * * * *
175555 CAAAAGTCCTTCGAGTTTGATTACACTCAGCTCAAAGGCATATCAATTGCAGCATAACTCAAAGC
1 C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
*
175620 TAGAAGGATTATCTGTCAA
65 TAGAAGGGTTATCTGTCAA
* * *
175639 CAAAGACC-TCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAATG
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACTCAAGG
* *
175703 CGAGAAGGGTTATCTGTCAT
64 CTAGAAGGGTTATCTGTCAA
* * *
175723 CAAAGACCTTCGAGTTTGATTTCATTCAGCTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
175756 GGGGCATATC
Statistics
Matches: 390, Mismatches: 56, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
82 33 0.08
83 124 0.32
84 168 0.43
85 65 0.17
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (83 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
AGAAGGGTTATCTGTCAA
Found at i:175592 original size:167 final size:165
Alignment explanation
Indices: 175205--175755 Score: 694
Period size: 167 Copynumber: 3.3 Consensus size: 165
175195 TTCTAACTCA
* *
175205 AAGAAGGGGTATCTG--GCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
1 AAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
* * * * *
175268 GCAGCATAGCTTAAGTCAAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATTACACTCA
66 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCA
* * * *
175333 GCTTCGAGGGCACATCATTTACAACATAACTCAAGGT
130 GC-TCAAAGGCACATCATTTACAACATAGCTCAAGGC
* *
175370 TAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATT
1 AAGAAGGGTTATCTGTC-ACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
** * * *
175435 TATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAACACCTTCGAGTTCGATTTCACTCA
65 TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCA
*
175500 GCTCAAAGGCACATCATTTGCAACATAGCTCAAGGC
130 GCTCAAAGGCACATCATTTACAACATAGCTCAAGGC
* ** * * * *
175536 AATAAGGGTTATCTACCGACAAAAGTCCTTCGAGTTTGATTACACTCAGCTCAAAGGCATATCAA
1 AAGAAGGGTTATCTGTC-AC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAT
* * *
175601 TTGCAGCATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACC-TCGAGTTTGATTACACTC
64 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTC
* *
175665 AGCTCAAAGGCACATCAAATTTACAGCATAGCTCAATGC
129 AGCTCAAAGGCACATC--ATTTACAACATAGCTCAAGGC
* * * *
175704 GAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTTTGATTTCATTCAGCTCA
1 AAGAAGGGTTATCTGTCA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
175756 GGGGCATATC
Statistics
Matches: 332, Mismatches: 47, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
165 13 0.04
166 76 0.23
167 136 0.41
168 107 0.32
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (165 bp):
AAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
CTCAAAGGCACATCATTTACAACATAGCTCAAGGC
Found at i:175711 original size:251 final size:251
Alignment explanation
Indices: 175226--175755 Score: 740
Period size: 251 Copynumber: 2.1 Consensus size: 251
175216 TCTGGCAAAG
* * * *
175226 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
1 ACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
** * * * *
175291 GGCTATCTGTCAACCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACA
66 GGCTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCAAAGGCACATCAATTACA
* * *
175356 ACATAACTCAAGGTTAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
131 ACATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
* *
175421 AAAGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAAC
196 AAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAAAAAC
*
175477 ACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAATAAG
1 ACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
* * * * * *
175542 GGTTATCTACCGACAAAAGTCCTTCGAGTTTGATTACACTCAGC-TCAAAGGCATATCAATTGCA
66 GGCTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCAAAGGCACATCAATTACA
* * *
175606 GCATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACC-TCGAGTTTGATTACACTCAGCTC
131 ACATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
* * ** *
175670 AAAGGCACATCAAATTTACAGCATAGCTCAATGCGAGAAGGGTTATCTGTCATCAAAG
196 AAAGGCACATC--ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAAAAAC
* *
175728 ACCTTCGAGTTTGATTTCATTCAGCTCA
1 ACCTTCGAGTTCGATTTCACTCAGCTCA
175756 GGGGCATATC
Statistics
Matches: 245, Mismatches: 32, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
249 32 0.13
250 52 0.21
251 161 0.66
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (251 bp):
ACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
GGCTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCAAAGGCACATCAATTACA
ACATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAAAAAC
Found at i:177032 original size:30 final size:30
Alignment explanation
Indices: 176998--177060 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
176988 GTCTTTCTAG
*
176998 TTTCTATTAATACTATTTTAATCCTTTAAT
1 TTTCTATTAATACTATTTTAATACTTTAAT
** * *
177028 TTTCTATTTGTGCTATTTTAGTACTTTAAT
1 TTTCTATTAATACTATTTTAATACTTTAAT
177058 TTT
1 TTT
177061 TTTCCTTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTCTATTAATACTATTTTAATACTTTAAT
Found at i:177215 original size:18 final size:17
Alignment explanation
Indices: 177184--177218 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
177174 ATTTTCTTTC
177184 ATTTCTTTTATTTATTT
1 ATTTCTTTTATTTATTT
*
177201 ATTTACTTTTTTTTATTT
1 ATTT-CTTTTATTTATTT
177219 CGATCTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTCTTTTATTTATTT
Found at i:181552 original size:20 final size:20
Alignment explanation
Indices: 181515--181552 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
181505 TTTATATAAT
*
181515 TTAATTTTATAATTAATATG
1 TTAATTTTATAATGAATATG
181535 TTAATTGTTA-AATGAATA
1 TTAATT-TTATAATGAATA
181553 ATATTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (20 bp):
TTAATTTTATAATGAATATG
Found at i:182839 original size:38 final size:38
Alignment explanation
Indices: 182778--182869 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 38
182768 ATTTTTTTAT
*
182778 TAATATTTTTAATTAAAT-TTAAAATATTA-AGAAGAATA
1 TAATATTTTTAATTAAATATAAAAATATTATA-AA-AATA
*
182816 TAATATTTTTAATTAATAATAAAAAAATATTATAAAAATA
1 TAATATTTTTAATT-A-AATATAAAAATATTATAAAAATA
*
182856 TAATATTTTAAATT
1 TAATATTTTTAATT
182870 TTTACCGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 14 0.30
39 1 0.02
40 20 0.43
41 11 0.23
42 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (38 bp):
TAATATTTTTAATTAAATATAAAAATATTATAAAAATA
Found at i:188029 original size:28 final size:28
Alignment explanation
Indices: 187998--188053 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
187988 CCAAAGAGCT
*
187998 ATAATCACCAAATTCAAATAGTTTGCCA
1 ATAATCACCAAATTCAAATAATTTGCCA
188026 ATAATCACCAAATTCAAATAATTTGCCA
1 ATAATCACCAAATTCAAATAATTTGCCA
188054 TTCTTATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (28 bp):
ATAATCACCAAATTCAAATAATTTGCCA
Found at i:194172 original size:27 final size:27
Alignment explanation
Indices: 194141--194208 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
194131 TCTATTTACA
194141 AAATCATATCTCTATAGGAATGATAAC
1 AAATCATATCTCTATAGGAATGATAAC
*
194168 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGATAAC
194195 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
194209 ATTCCTACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 9 0.22
27 31 0.77
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGATAAC
Found at i:197803 original size:16 final size:16
Alignment explanation
Indices: 197782--197813 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
197772 TTATTTACTA
197782 TGTTATTTTCCAATAC
1 TGTTATTTTCCAATAC
197798 TGTTATTTTCCAATAC
1 TGTTATTTTCCAATAC
197814 AAATATCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTTATTTTCCAATAC
Found at i:204297 original size:101 final size:101
Alignment explanation
Indices: 204167--204368 Score: 395
Period size: 101 Copynumber: 2.0 Consensus size: 101
204157 ACTAGCATCG
204167 GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGAGAAA
1 GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGAGAAA
204232 AGACCAATTTTAATCTATATAATGAATCAATCATAA
66 AGACCAATTTTAATCTATATAATGAATCAATCATAA
*
204268 GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGGGAAA
1 GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGAGAAA
204333 AGACCAATTTTAATCTATATAATGAATCAATCATAA
66 AGACCAATTTTAATCTATATAATGAATCAATCATAA
204369 CCAAATTATT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (101 bp):
GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGAGAAA
AGACCAATTTTAATCTATATAATGAATCAATCATAA
Found at i:208092 original size:20 final size:20
Alignment explanation
Indices: 208069--208111 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
208059 ATGTTAGACT
208069 TTTTTTTCTCCATCTTTTAC
1 TTTTTTTCTCCATCTTTTAC
208089 TTTTTTTCTCCATCTTTTAC
1 TTTTTTTCTCCATCTTTTAC
208109 TTT
1 TTT
208112 GCATGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTTTCTCCATCTTTTAC
Found at i:210032 original size:36 final size:37
Alignment explanation
Indices: 209958--210033 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
209948 TCTAATCTAA
209958 CATTGATTTTCAGTAAATTTTAACTTAAAAATGTTAT
1 CATTGATTTTCAGTAAATTTTAACTTAAAAATGTTAT
**
209995 CATTGATTTTTGGTAAATTTTAACTT-AAAATGTTAT
1 CATTGATTTTCAGTAAATTTTAACTTAAAAATGTTAT
210031 CAT
1 CAT
210034 GTATAATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
36 13 0.35
37 24 0.65
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (37 bp):
CATTGATTTTCAGTAAATTTTAACTTAAAAATGTTAT
Found at i:211845 original size:24 final size:24
Alignment explanation
Indices: 211813--211861 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
211803 AGTTCCAATC
211813 ACCTCTACCACGTTTCTTTTGTTG
1 ACCTCTACCACGTTTCTTTTGTTG
**
211837 ACCTCTACCATTTTTCTTTTGTTG
1 ACCTCTACCACGTTTCTTTTGTTG
211861 A
1 A
211862 AAAGCTTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.10, T:0.49
Consensus pattern (24 bp):
ACCTCTACCACGTTTCTTTTGTTG
Found at i:215078 original size:25 final size:25
Alignment explanation
Indices: 215045--215103 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
215035 GTATTTTATG
* *
215045 TTATTAGGG-CGAACTTTTAAAATT
1 TTATGAGGGACGAACTTATAAAATT
*
215069 TTATGGAGGGATGAACTTATAAAATT
1 TTAT-GAGGGACGAACTTATAAAATT
215095 TTATGAGGG
1 TTATGAGGG
215104 GTGAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 17 0.57
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (25 bp):
TTATGAGGGACGAACTTATAAAATT
Found at i:215108 original size:25 final size:26
Alignment explanation
Indices: 215055--215108 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
215045 TTATTAGGGC
*
215055 GAACTTTTAAAATTTTATGGAGGGAT
1 GAACTTATAAAATTTTATGGAGGGAT
*
215081 GAACTTATAAAATTTTAT-GAGGGGT
1 GAACTTATAAAATTTTATGGAGGGAT
215106 GAA
1 GAA
215109 AAAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (26 bp):
GAACTTATAAAATTTTATGGAGGGAT
Found at i:220450 original size:11 final size:10
Alignment explanation
Indices: 220432--220456 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
220422 ATAAAAATAA
220432 TATTTTTTTT
1 TATTTTTTTT
220442 TATTTTTTTT
1 TATTTTTTTT
220452 TATTT
1 TATTT
220457 CGGATCAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:221047 original size:12 final size:12
Alignment explanation
Indices: 221030--221055 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
221020 AAAACTGTTC
221030 TTTAGCGGCGTT
1 TTTAGCGGCGTT
221042 TTTAGCGGCGTT
1 TTTAGCGGCGTT
221054 TT
1 TT
221056 AAGAGTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:221301 original size:82 final size:82
Alignment explanation
Indices: 221182--221523 Score: 357
Period size: 82 Copynumber: 4.2 Consensus size: 82
221172 CGTGTTTTCG
* * ** * * *
221182 ACAAACGCCGCAATAG-GTCCATCTATAGTGGTATTTTTCAATAAACGCCACAACAGATTAGTAT
1 ACAAACGCCGCAATAGAGTTCACCTATAGTGGCGTTTTTCAATAAACGCCGCAACAGATTAGAAC
* *
221246 TTTAGCGGAGTTTTAAT
66 TTTAGCGGCGTTTTTAT
** * * * *
221263 ACAAACGCCGCAATAG-GTGAACTCTATAGTGGCGTTTTTTAATAAATGTCGCAACAAATTAGAA
1 ACAAACGCCGCAATAGAGTTCAC-CTATAGTGGCGTTTTTCAATAAACGCCGCAACAGATTAGAA
*
221327 CTTTAGCGGTGTTTTTAT
65 CTTTAGCGGCGTTTTTAT
* * * * *
221345 AAAAATGCCGTAATAGAGTTCACCTATTGTGGCGTTTTTTAAATAAACGCCGCAACAGATTAGAA
1 ACAAACGCCGCAATAGAGTTCACCTATAGTGGCG-TTTTTCAATAAACGCCGCAACAGATTAGAA
221410 CTTTAGCGGCGTTTTTAT
65 CTTTAGCGGCGTTTTTAT
* * * * ** * *
221428 ACAAATGTCGCAATAGTGTTTACCTATAGTGATGTTTTTCAATAAACGCCGCAAGATATTA-ATA
1 ACAAACGCCGCAATAGAGTTCACCTATAGTGGCGTTTTTCAATAAACGCCGCAACAGATTAGA-A
*
221492 TTTTAGCGGCGTTTTTAT
65 CTTTAGCGGCGTTTTTAT
*
221510 ACAAACGCCACAAT
1 ACAAACGCCGCAAT
221524 TTATCAATAA
Statistics
Matches: 217, Mismatches: 40, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
81 20 0.09
82 124 0.57
83 73 0.34
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (82 bp):
ACAAACGCCGCAATAGAGTTCACCTATAGTGGCGTTTTTCAATAAACGCCGCAACAGATTAGAAC
TTTAGCGGCGTTTTTAT
Found at i:221440 original size:41 final size:41
Alignment explanation
Indices: 221232--221440 Score: 131
Period size: 41 Copynumber: 5.1 Consensus size: 41
221222 ATAAACGCCA
* * * * *
221232 CAACAGATTAGTATTTTAGCGGAGTTTTAATACAAACGCCG
1 CAACAGATTAGAACTTTAGCGGCGTTTTTATACAAATGCCG
* * * * *
221273 CAATAG-GT-GAACTCTATAGTGGCGTTTTT-TAATAAATGTCG
1 CAACAGATTAGAACT-T-TAGCGGCGTTTTTAT-ACAAATGCCG
* * *
221314 CAACAAATTAGAACTTTAGCGGTGTTTTTATAAAAATGCCG
1 CAACAGATTAGAACTTTAGCGGCGTTTTTATACAAATGCCG
* * * * * * * *
221355 TAATAGAGTT-CACCTATT-GTGGCGTTTTTTAAATAAACGCCG
1 CAACAGA-TTAGAACT-TTAGCGGCG-TTTTTATACAAATGCCG
*
221397 CAACAGATTAGAACTTTAGCGGCGTTTTTATACAAATGTCG
1 CAACAGATTAGAACTTTAGCGGCGTTTTTATACAAATGCCG
221438 CAA
1 CAA
221441 TAGTGTTTAC
Statistics
Matches: 121, Mismatches: 36, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
39 3 0.02
40 3 0.02
41 76 0.63
42 34 0.28
43 5 0.04
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (41 bp):
CAACAGATTAGAACTTTAGCGGCGTTTTTATACAAATGCCG
Found at i:230578 original size:85 final size:84
Alignment explanation
Indices: 230353--231141 Score: 800
Period size: 84 Copynumber: 9.5 Consensus size: 84
230343 AAACTTTTTG
*
230353 CAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCA
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGACTACGCTCA
* *
230417 GCTCCAAGGAACATCATTTG
65 GCTCCAAGGCACATCATTTA
* * * * * * * *
230437 CATCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-GAAGACCCTT-GAGTTTGATTACGCTCA
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAAGA-CCTTCGAGTTCGACTACGCTCA
* * *
230497 ACTTCGAGGGCACATCATTTA
65 GC-TCCAAGGCACATCATTTA
* *
230518 CAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
** * *
230583 CTTTGAGGGAACATCATTTA
66 C-TCCAAGGCACATCATTTA
*
230603 CAGCATAACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
** *
230668 CTCCAAGGCGTATCATTTG
66 CTCCAAGGCACATCATTTA
* * * *
230687 CAACATAACTTAAGTCGAGAATGGTTATCT-TCCAACC-AAAGACCTTCGAGTTCGACTACGCTC
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGT-C-ACCAAAAGACCTTCGAGTTCGACTACGCTC
230750 AGCTCCAAGGCACATCATTTA
64 AGCTCCAAGGCACATCATTTA
** * * * * * * *
230771 CAGCATAGTTTAAGTCGAGAAGGGCTATCTG---CC-GAAGACCCTCGAGTTCGATTACGCTCAA
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
*
230832 CTTCAAGGACACATCATTTA
66 CTCCAAGG-CACATCATTTA
* * * * *
230852 CAACATAACTCAAGGCTAAAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTCGACTACGCTCAT
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
*
230917 CTCAAAGGCACATCATTTA
66 CTCCAAGGCACATCATTTA
** * * *
230936 CAGCATATGTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGGAGTTCGACTACGCCCA
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAAGACC-TTCGAGTTCGACTACGCTCA
*
231001 GCTCCAAGGCACATCATTTG
65 GCTCCAAGGCACATCATTTA
* * * * ** * *
231021 CAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAAG-CCCCCGAGTTCGATTACACTCAG
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
* *
231082 CTCTGAGGGCACATCATTTA
66 CTC-CAAGGCACATCATTTA
* * * * *
231102 CAGTATAACTCAAGGCTAAAAGAGTTATCTGTCAACAAAA
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAA
231142 ACATTTGAGA
Statistics
Matches: 583, Mismatches: 102, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
80 73 0.13
81 114 0.20
82 7 0.01
83 1 0.00
84 194 0.33
85 194 0.33
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (84 bp):
CAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
CTCCAAGGCACATCATTTA
Found at i:230736 original size:84 final size:82
Alignment explanation
Indices: 230353--231140 Score: 744
Period size: 85 Copynumber: 9.5 Consensus size: 82
230343 AAACTTTTTG
*
230353 CAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGTCTAGAAGGGTTATCT-TC-ACCAAAGACCTTCGAGTTCGACTACGCTCAG
* *
230418 CTCCAAGGAACATCATTTG
64 CTCCAAGGCACATCATTTA
* * * * * * * * * *
230437 CATCATAGCTTAAGTCGAGAAGGGCTATC-T-GCCGAAGACCCTT-GAGTTTGATTACGCTCAAC
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTTCACCAAAGA-CCTTCGAGTTCGACTACGCTCAGC
* *
230499 TTCGAGGGCACATCATTTA
65 -TCCAAGGCACATCATTTA
*
230518 CAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGTCTAGAAGGGTTATCT-TCACC-AAAGACCTTCGAGTTCGACTACGCTCAG
** * *
230583 CTTTGAGGGAACATCATTTA
64 C-TCCAAGGCACATCATTTA
*
230603 CAGCATAACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGTCTAGAAGGGTTATCT-TCACC-AAAGACCTTCGAGTTCGACTACGCTCAG
** *
230668 CTCCAAGGCGTATCATTTG
64 CTCCAAGGCACATCATTTA
* * * *
230687 CAACATAACTTAAGTCGAGAATGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTT-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAG
230752 CTCCAAGGCACATCATTTA
64 CTCCAAGGCACATCATTTA
** * * * * * * * *
230771 CAGCATAGTTTAAGTCGAGAAGGGCTATC-T-GCCGAAGACCCTCGAGTTCGATTACGCTCAACT
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
*
230834 TCAAGGACACATCATTTA
66 CCAAGG-CACATCATTTA
* * * * *
230852 CAACATAACTCAAGGCTAAAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTCGACTACGCTCAT
1 CAGCATAACTCAAGTCTAGAAGGGTTATCT-TCAC-CAAAGACCTTCGAGTTCGACTACGCTCAG
*
230917 CTCAAAGGCACATCATTTA
64 CTCCAAGGCACATCATTTA
** * * *
230936 CAGCATATGTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGGAGTTCGACTACGCCCA
1 CAGCATAACTCAAGTCTAGAAGGGTTATCT-TCACC-AAAGACC-TTCGAGTTCGACTACGCTCA
*
231001 GCTCCAAGGCACATCATTTG
63 GCTCCAAGGCACATCATTTA
* * * * * * ** * *
231021 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGC-CAAAAG-CCCCCGAGTTCGATTACACTCAGCT
1 CAGCATAACTCAAGTCTAGAAGGGTTATCTTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
* *
231084 CTGAGGGCACATCATTTA
66 C-CAAGGCACATCATTTA
* * * * *
231102 CAGTATAACTCAAGGCTAAAAGAGTTATCTGTCAACAAA
1 CAGCATAACTCAAGTCTAGAAGGGTTATCT-TCACCAAA
231141 AACATTTGAG
Statistics
Matches: 575, Mismatches: 110, Indels: 39
0.79 0.15 0.05
Matches are distributed among these distances:
80 73 0.13
81 110 0.19
82 5 0.01
83 8 0.01
84 186 0.32
85 193 0.34
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (82 bp):
CAGCATAACTCAAGTCTAGAAGGGTTATCTTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCACATCATTTA
Found at i:230895 original size:165 final size:164
Alignment explanation
Indices: 230356--231104 Score: 738
Period size: 165 Copynumber: 4.5 Consensus size: 164
230346 CTTTTTGCAG
* * *
230356 CATAACTCAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * *
230421 CAAGGAACATCATTTGCATCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCTTGAGTTT
66 CAAGGAACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCTCGAGTTC
* *
230486 GATTACGCTCAACTTCGAGGGCACATCATTTACAG
131 GATTACGCTCAACTTC-AAGGCACATCATTTACAA
* *
230521 CATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTT
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-T
** * * * * * * * *
230586 TGAGGGAACATCATTTACAGCATAACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTCG
65 CCAAGGAACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-GAAGACCCTCG
* * * ** *
230651 AGTTCGACTACGCTCAGCTCCAAGGCGTATCATTTGCAA
126 AGTTCGATTACGCTCAACTTCAAGGCACATCATTTACAA
* * * * *
230690 CATAACTTAAGTCGAGAATGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTGT-CAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT
* *
230754 CCAAGGCACATCATTTACAGCATAGTTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCTCGAGTT
65 CCAAGGAACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCTCGAGTT
230819 CGATTACGCTCAACTTCAAGGACACATCATTTACAA
130 CGATTACGCTCAACTTCAAGG-CACATCATTTACAA
* *
230855 CATAACTCAAGGCTAAAAGGGTTATCTGTC-ACTAAAAGACCTTCGAGTTCGACTACGCTCATCT
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAAGACCTTCGAGTTCGACTACGCTCAGCT
* * * * * * * *
230919 CAAAGGCACATCATTTACAGCATATG-TCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTT
65 CCAAGGAACATCATTTACAGCATA-GCTTAAGTCGAGAAGGGCTATCTG---CC-GAAGACC-CT
* * * * * * *
230983 GGAGTTCGACTACGCCCAGCTCCAAGGCACATCATTTGCAG
124 CGAGTTCGATTACGCTCAACTTCAAGGCACATCATTTACAA
* * * * * ** * *
231024 CATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAAG-CCCCCGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
231085 TGAGGGCACATCATTTACAG
66 -CAAGGAACATCATTTACAG
231105 TATAACTCAA
Statistics
Matches: 483, Mismatches: 85, Indels: 31
0.81 0.14 0.05
Matches are distributed among these distances:
164 33 0.07
165 185 0.38
166 63 0.13
167 1 0.00
168 43 0.09
169 110 0.23
170 48 0.10
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
CAAGGAACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCTCGAGTTC
GATTACGCTCAACTTCAAGGCACATCATTTACAA
Found at i:230990 original size:334 final size:334
Alignment explanation
Indices: 230349--231104 Score: 1126
Period size: 334 Copynumber: 2.3 Consensus size: 334
230339 TAAAAAACTT
* *
230349 TTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGC
1 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGC
* * *
230414 TCAGCTCCAAGGAACATCATTTGCATCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCT
66 TCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCT
* * * * * *
230479 TGAGTTTGATTACGCTCAACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
131 CGAGTTCGATTACGCTCAACTTCAAGGACACATCATTTACAACATAACTCAAGGCTAAAAGGGTT
** *
230544 ATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTTTGAGGGAACATCATTTACAGCAT
196 ATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAAGGAACATCATTTACAGCAT
*
230609 AACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
261 AACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCCCAGCTCCAA
**
230674 GGCGTATCA
326 GGCACATCA
* * *
230683 TTTGCAACATAACTTAAGTCGAGAATGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGC
1 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGC
*
230748 TCAGCTCCAAGGCACATCATTTACAGCATAGTTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCT
66 TCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCT
230813 CGAGTTCGATTACGCTCAACTTCAAGGACACATCATTTACAACATAACTCAAGGCTAAAAGGGTT
131 CGAGTTCGATTACGCTCAACTTCAAGGACACATCATTTACAACATAACTCAAGGCTAAAAGGGTT
* * * *
230878 ATCTGTCACTAAAAGACCTTCGAGTTCGACTACGCTCATC-TCAAAGGCACATCATTTACAGCAT
196 ATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAAGGAACATCATTTACAGCAT
** * *
230942 ATGTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGGAGTTCGACTACGCCCAGCTCCA
261 AACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACC-TTCGAGTTCGACTACGCCCAGCTCCA
231007 AGGCACATCA
325 AGGCACATCA
* * ** * *
231017 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A--AAAG-CCCCCGAGTTCGATTACAC
1 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGC
* *
231078 TCAGCTCTGAGGGCACATCATTTACAG
66 TCAGCTC-CAAGGCACATCATTTACAG
231105 TATAACTCAA
Statistics
Matches: 380, Mismatches: 40, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
330 22 0.06
331 21 0.06
333 56 0.15
334 281 0.74
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (334 bp):
TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCCT
CGAGTTCGATTACGCTCAACTTCAAGGACACATCATTTACAACATAACTCAAGGCTAAAAGGGTT
ATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAAGGAACATCATTTACAGCAT
AACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCCCAGCTCCAA
GGCACATCA
Found at i:231101 original size:250 final size:245
Alignment explanation
Indices: 230353--231141 Score: 924
Period size: 250 Copynumber: 3.2 Consensus size: 245
230343 AAACTTTTTG
* * * *
230353 CAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCTAAAAGGGTTATCTGTC-ACAAAAGACCTTCGAGTTCGACTACGCTCAG
* * * *
230418 CTCCAAGGAACATCATTTGCATCATAGCTTAAGTCGAGAAGGGCTATCTG---CCGAAGACCCTT
65 CTCCAAGGCACATCATTTGCAACATAG-TTAAGTCGAGAAGGGTTATCTGTCACCAAAGA-CCTT
* * * * * * * * * *
230480 GAGTTTGATTACGCTCAACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
128 GAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTA
* * * *
230545 TCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTTTGAGGGAACATCATTTA
192 TC--T-GCCAAAAGACCCTCGAGTTCGATTACGCTCAGC-TTGAGGGCACATCATTTA
* *
230603 CAGCATAACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCTAAAAGGGTTATCTGTCA-CAAAAGACCTTCGAGTTCGACTACGCTCAG
** * *
230668 CTCCAAGGCGTATCATTTGCAACATAACTTAAGTCGAGAATGGTTATCT-TCCAACCAAAGACCT
65 CTCCAAGGCACATCATTTGCAACAT-AGTTAAGTCGAGAAGGGTTATCTGT-C-ACCAAAGACCT
*
230732 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGTTTAAGTCGAGAAGGGCT
127 T-GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCT
* * * *
230797 ATCTGCC-GAAGACCCTCGAGTTCGATTACGCTCAACTTCAAGGACACATCATTTA
191 ATCTGCCAAAAGACCCTCGAGTTCGATTACGCTCAGCTT-GAGGGCACATCATTTA
* *
230852 CAACATAACTCAAGGCTAAAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTCGACTACGCTCAT
1 CAGCATAACTCAAGGCTAAAAGGGTTATCTGTCAC-AAAAGACCTTCGAGTTCGACTACGCTCAG
* * * * * *
230917 CTCAAAGGCACATCATTTACAGCATATGTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTT
65 CTCCAAGGCACATCATTTGCAACATA-GTTAAGTCGAGAAGGGTTATCTGTCACC-AAAGACC-T
* *
230982 TGGAGTTCGACTACGCCCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
127 T-GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCT
* *
231047 ATCTGCCAAAAG-CCCCCGAGTTCGATTACACTCAGCTCTGAGGGCACATCATTTA
191 ATCTGCCAAAAGACCCTCGAGTTCGATTACGCTCAGCT-TGAGGGCACATCATTTA
* *
231102 CAGTATAACTCAAGGCTAAAAGAGTTATCTGTCAACAAAA
1 CAGCATAACTCAAGGCTAAAAGGGTTATCTGTC-ACAAAA
231142 ACATTTGAGA
Statistics
Matches: 465, Mismatches: 57, Indels: 34
0.84 0.10 0.06
Matches are distributed among these distances:
248 7 0.02
249 143 0.31
250 242 0.52
251 8 0.02
253 43 0.09
254 22 0.05
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (245 bp):
CAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACAAAAGACCTTCGAGTTCGACTACGCTCAGC
TCCAAGGCACATCATTTGCAACATAGTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTGAG
TTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG
CCAAAAGACCCTCGAGTTCGATTACGCTCAGCTTGAGGGCACATCATTTA
Found at i:231184 original size:21 final size:21
Alignment explanation
Indices: 231159--231220 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
231149 AGATTGTTTC
231159 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCT
*
231180 CTTGAGAC-AA--TT-TCTCT
1 CTTGAAACAAATTTTGTCTCT
231197 -TT-AAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCT
231216 CTTGA
1 CTTGA
231221 GACAGTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 3 0.09
16 4 0.12
17 5 0.15
18 4 0.12
19 5 0.15
20 4 0.12
21 8 0.24
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (21 bp):
CTTGAAACAAATTTTGTCTCT
Found at i:231204 original size:36 final size:36
Alignment explanation
Indices: 231154--231456 Score: 428
Period size: 36 Copynumber: 8.4 Consensus size: 36
231144 ATTTGAGATT
231154 GTTT-CCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
231189 ATTTCTCTTTAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * * *
231225 GTTTCCCTTAAAACAAATTTCGTATCCCATGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
231261 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
231297 GTTTCCCTTTAAACATATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
231333 GTTTCCCTTGAAACATATTTTGTCTCTGTTTAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
231369 TTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
231405 GTTTCCCTTGAAACAAATTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
231442 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
231457 CCAATCTTTG
Statistics
Matches: 234, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
35 3 0.01
36 200 0.85
37 31 0.13
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:233646 original size:3 final size:3
Alignment explanation
Indices: 233638--233675 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
233628 CGTTTCTGTG
233638 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
233676 CAAAGAGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:237519 original size:19 final size:20
Alignment explanation
Indices: 237485--237526 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
237475 TTAATAGATT
* *
237485 ATTTATGAAATCATTAATAA
1 ATTTATGAAATAATTAACAA
237505 ATTTAT-AAATAATTAACAA
1 ATTTATGAAATAATTAACAA
237524 ATT
1 ATT
237527 AGTCAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTATGAAATAATTAACAA
Found at i:241436 original size:21 final size:21
Alignment explanation
Indices: 241394--241446 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
241384 ATTCTGACTA
241394 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* ** *
241415 TCGCGTTGCGATTTTTCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
241436 TCGCAATGCGA
1 TCGCATTGCGA
241447 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:241461 original size:20 final size:20
Alignment explanation
Indices: 241436--241550 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
241426 TTTTTCTAAT
241436 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
241456 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
241477 TAGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
241497 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
241518 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
241538 TCTCAATGCGAAT
1 TCGCAATGCGAAT
241551 CTGACTATCG
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 44 0.58
21 32 0.42
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:241483 original size:41 final size:41
Alignment explanation
Indices: 241438--241550 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 41
241428 TTTCTAATTC
* *
241438 GCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATA
1 GCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAATA
* *
241479 GCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATC
1 GCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAATA
*
241520 GCAATGCGAATACGTAAATCTCAATGCGAAT
1 GCAATGCGAATACGTAAATCGCAATGCGAAT
241551 CTGACTATCG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (41 bp):
GCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAATA
Found at i:242130 original size:20 final size:20
Alignment explanation
Indices: 242080--242118 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
242070 TTCTAAACTT
*
242080 AAAATCGCAACATGAAAATA
1 AAAATCGCAACACGAAAATA
242100 AAAATCGCAACACGAAAAT
1 AAAATCGCAACACGAAAAT
242119 GACTATCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATA
Found at i:242217 original size:33 final size:33
Alignment explanation
Indices: 242180--242243 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
242170 TTCATTTCTA
242180 TCTCGTTGTGATTTTAATTTCGCGTTGCGATTC
1 TCTCGTTGTGATTTTAATTTCGCGTTGCGATTC
242213 TCTCGTTGTGATTTTAATTTCGCGTTGCGAT
1 TCTCGTTGTGATTTTAATTTCGCGTTGCGAT
242244 AGTCATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (33 bp):
TCTCGTTGTGATTTTAATTTCGCGTTGCGATTC
Found at i:242269 original size:20 final size:19
Alignment explanation
Indices: 242222--242292 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
242212 CTCTCGTTGT
*
242222 GATTTTAATTT-CGCGTTGC
1 GATTTTCATTTCCGC-TTGC
**
242241 GATAGTCATTTCCGCATTGC
1 GATTTTCATTTCCGC-TTGC
242261 GATTTTCATTCTCTCG-TTGC
1 GATTTTCATT-TC-CGCTTGC
242281 GATTTTCATTTC
1 GATTTTCATTTC
242293 AACCAAAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 10 0.23
20 29 0.67
21 2 0.05
22 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
GATTTTCATTTCCGCTTGC
Found at i:243334 original size:20 final size:20
Alignment explanation
Indices: 243319--243422 Score: 165
Period size: 20 Copynumber: 5.2 Consensus size: 20
243309 AGAATCTCGT
*
243319 TGCGATTACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
243339 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
243359 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
* *
243379 TGCGATTACCTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
243399 TGCGAATACGT-AATCGCAT
1 TGCGAATACGTAAATCGCAA
243418 TGCGA
1 TGCGA
243423 TTTATGTAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
19 12 0.15
20 66 0.85
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
TGCGAATACGTAAATCGCAA
Found at i:243363 original size:40 final size:41
Alignment explanation
Indices: 243319--243505 Score: 186
Period size: 40 Copynumber: 4.6 Consensus size: 41
243309 AGAATCTCGT
*
243319 TGCGATTACGTAAATCGCAATGCGA-ATACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGATTTACGTAAATCGCAA
* *
243359 TGCGAATACGTAAATCGCAATGCGA-TTACCTAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGATTTACGTAAATCGCAA
* * * *
243399 TGCGAATACGT-AATCGCATTGCGATTTATGT-AATCGCAT
1 TGCGATTACGTAAATCGCAATGCGATTTACGTAAATCGCAA
* * * *
243438 TGCGATTTACGT-ATTCGCATTGCGATTTAGGAAAATCGCAA
1 TGCGA-TTACGTAAATCGCAATGCGATTTACGTAAATCGCAA
* ** *
243479 CGCGAATTTGGGAAATCGCAATGCGAT
1 TGCG-ATTACGTAAATCGCAATGCGAT
243506 AGTCAGAATC
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 24 0.19
40 74 0.60
41 13 0.10
42 13 0.10
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (41 bp):
TGCGATTACGTAAATCGCAATGCGATTTACGTAAATCGCAA
Found at i:243386 original size:60 final size:60
Alignment explanation
Indices: 243319--243505 Score: 191
Period size: 60 Copynumber: 3.1 Consensus size: 60
243309 AGAATCTCGT
243319 TGCGATTACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAA
* * * * *
243379 TGCGATTACCTAAATCGCAATGCGAATACGT-AATCGCATTGCGATTTATGT-AATCGCAT
1 TGCGATTACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGA-ATACGTAAATCGCAA
* * * * * * ** *
243438 TGCGATTTACGT-ATTCGCATTGCGATTTAGGAAAATCGCAACGCGAATTTGGGAAATCGCAA
1 TGCGA-TTACGTAAATCGCAATGCGA-ATACGTAAATCGCAATGCGAA-TACGTAAATCGCAA
243500 TGCGAT
1 TGCGAT
243506 AGTCAGAATC
Statistics
Matches: 103, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
59 35 0.34
60 42 0.41
61 14 0.14
62 12 0.12
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (60 bp):
TGCGATTACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:243433 original size:20 final size:20
Alignment explanation
Indices: 243318--243466 Score: 137
Period size: 20 Copynumber: 7.5 Consensus size: 20
243308 CAGAATCTCG
243318 TTGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
243338 ATGCGA-ATACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
243358 ATGCGA-ATACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
243378 ATGCGA-TTACCTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
243398 ATGCGA-ATACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
243417 TTGCGATTTATGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
243437 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
243457 TTGCGATTTA
1 TTGCGATTTA
243467 GGAAAATCGC
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
19 12 0.10
20 105 0.90
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:243492 original size:22 final size:21
Alignment explanation
Indices: 243462--243504 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
243452 TCGCATTGCG
243462 ATTTAGGAAAATCGCAACGCGA
1 ATTTAGG-AAATCGCAACGCGA
* *
243484 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
243505 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:260787 original size:16 final size:16
Alignment explanation
Indices: 260768--260808 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
260758 GTTTATAAAA
260768 TAACTGGTTCGGTTTC
1 TAACTGGTTCGGTTTC
260784 TAACTGGTTCGGTTTC
1 TAACTGGTTCGGTTTC
*
260800 TAACCGGTT
1 TAACTGGTT
260809 TGGAGGGCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (16 bp):
TAACTGGTTCGGTTTC
Found at i:260863 original size:15 final size:15
Alignment explanation
Indices: 260845--260900 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
260835 TAACCGGTTT
260845 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
260860 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
260877 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
260892 CGATTTTAA
1 CGGTTTTAA
260901 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:260873 original size:17 final size:17
Alignment explanation
Indices: 260848--260898 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
260838 CCGGTTTCGG
260848 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
260865 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
260880 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
260897 TT
1 TT
260899 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:261317 original size:13 final size:13
Alignment explanation
Indices: 261296--261350 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
261286 AAGTTCGATA
*
261296 AATTCAAATACTT
1 AATTGAAATACTT
261309 AATTGAAATACTT
1 AATTGAAATACTT
* *
261322 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
261336 AATTGAAATACTT
1 AATTGAAATACTT
261349 AA
1 AA
261351 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:261432 original size:32 final size:33
Alignment explanation
Indices: 261336--261434 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
261326 AACTCAACAT
* * *
261336 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
261369 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
261402 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
261434 A
1 A
261435 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:261453 original size:21 final size:21
Alignment explanation
Indices: 261429--261468 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
261419 ACTTCAAGTT
261429 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
261450 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
261469 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:269957 original size:15 final size:15
Alignment explanation
Indices: 269937--269971 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
269927 CGGACATTGA
269937 AATATTATGTAAAAT
1 AATATTATGTAAAAT
269952 AATATTATGTAAAAT
1 AATATTATGTAAAAT
*
269967 TATAT
1 AATAT
269972 ATTTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (15 bp):
AATATTATGTAAAAT
Found at i:272665 original size:18 final size:16
Alignment explanation
Indices: 272643--272693 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 16
272633 TAAACAAATC
272643 AAATAAATTAAATATTA
1 AAATAAATTAAA-ATTA
272660 ACAAT-AATTAAAATTA
1 A-AATAAATTAAAATTA
272676 AAATAAAATTTAAAATTA
1 AAAT-AAA-TTAAAATTA
272694 TTACCGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.10
16 5 0.17
17 10 0.33
18 12 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAAATTAAAATTA
Found at i:272670 original size:17 final size:15
Alignment explanation
Indices: 272643--272681 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 15
272633 TAAACAAATC
272643 AAATAAATTAAATATTA
1 AAAT-AATTAAA-ATTA
272660 ACAATAATTAAAATTA
1 A-AATAATTAAAATTA
272676 AAATAA
1 AAATAA
272682 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 8 0.38
18 3 0.14
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATTAAAATTA
Found at i:274581 original size:21 final size:21
Alignment explanation
Indices: 274557--274623 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
274547 AATATGTAAA
* *
274557 TCGCATTTCGATTTTCCAAAT
1 TCGCATTGCGATATTCCAAAT
*
274578 TCGCGTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
** *
274599 TCGCAACGCGATAGT-CAAAT
1 TCGCATTGCGATATTCCAAAT
274619 TCGCA
1 TCGCA
274624 ACACGAAAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 10 0.26
21 29 0.74
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATATTCCAAAT
Found at i:274619 original size:20 final size:20
Alignment explanation
Indices: 274493--274638 Score: 75
Period size: 20 Copynumber: 7.2 Consensus size: 20
274483 AAATGACCAA
*
274493 CAAATTCGCAACGCGAT-CT
1 CAAATTCGCAACGCGATAGT
* **
274512 CAAATTCGCAAC-CCAGTTTT
1 CAAATTCGCAACGCGA-TAGT
*
274532 CAATTTCGCAACGCGAATATGT
1 CAAATTCGCAACGCG-ATA-GT
*** **
274554 -AAA-TCGCATTTCGATTTT
1 CAAATTCGCAACGCGATAGT
*** *
274572 CCAAATTCGCGTTGCGATATT
1 -CAAATTCGCAACGCGATAGT
274593 CCAAATTCGCAACGCGATAGT
1 -CAAATTCGCAACGCGATAGT
* *
274614 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACGCGATAGT
274634 CAAAT
1 CAAAT
274639 GTTTTTACGC
Statistics
Matches: 98, Mismatches: 21, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
18 3 0.03
19 15 0.15
20 45 0.46
21 33 0.34
22 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:277317 original size:18 final size:20
Alignment explanation
Indices: 277280--277317 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
277270 CCTATCATCA
277280 TTCAAGAGGCACCTCCTATCG
1 TTCAAGAGG-ACCTCCTATCG
277301 TTCAAGAGG-CC-CCTATC
1 TTCAAGAGGACCTCCTATC
277318 ATCATCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
21 9 0.53
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (20 bp):
TTCAAGAGGACCTCCTATCG
Found at i:277317 original size:42 final size:42
Alignment explanation
Indices: 277270--277362 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
277260 GCCCGATACA
* * *
277270 CCTATCATCATTC-AAGAGGCACCTCCTATCGTTCAAGAGGCC
1 CCTATCATCA-TCGAAGAAGCACCTCCCACCGTTCAAGAGGCC
* *
277312 CCTATCATCATCGAATAAGCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCATCGAAGAAGCACCTCCCACCGTTCAAGAGGCC
* *
277354 ACTGTCATC
1 CCTATCATC
277363 GTTTAAGTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.23
Consensus pattern (42 bp):
CCTATCATCATCGAAGAAGCACCTCCCACCGTTCAAGAGGCC
Found at i:278814 original size:14 final size:14
Alignment explanation
Indices: 278795--278834 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
278785 TTTTGATTAA
278795 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
278809 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
278823 TTGATTTGTAAA
1 TTGATTTGTAAA
278835 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:278827 original size:61 final size:66
Alignment explanation
Indices: 278744--278884 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
278734 TTTTACATTG
278744 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
278804 A
66 A
* ** * * *
278805 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTG
278869 TA
65 TA
278871 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
278885 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
61 26 0.38
62 4 0.06
63 1 0.01
64 6 0.09
66 31 0.46
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (66 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
A
Found at i:279020 original size:34 final size:34
Alignment explanation
Indices: 278982--279053 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
278972 ATAGTCAAAT
278982 TCGCAACG-TGATTTT-CGGTTTGCGAATTTGACTA
1 TCGCAACGTTGATTTTGC-G-TTGCGAATTTGACTA
* *
279016 TCGCAACGTTTATTTTGCGTTGCGAATTTGACTT
1 TCGCAACGTTGATTTTGCGTTGCGAATTTGACTA
279050 TCGC
1 TCGC
279054 GTTGATCGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 26 0.76
35 7 0.21
36 1 0.03
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.40
Consensus pattern (34 bp):
TCGCAACGTTGATTTTGCGTTGCGAATTTGACTA
Found at i:279364 original size:18 final size:18
Alignment explanation
Indices: 279341--279394 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
279331 AAGCCGGTTG
* *
279341 TGATTGGGATTTTGATTT
1 TGATTGCGACTTTGATTT
279359 TGATTGCGACTTTGATTT
1 TGATTGCGACTTTGATTT
279377 TGATTGCGACTTTGATTT
1 TGATTGCGACTTTGATTT
279395 CCTTTTGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.52
Consensus pattern (18 bp):
TGATTGCGACTTTGATTT
Found at i:281722 original size:24 final size:24
Alignment explanation
Indices: 281655--281714 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
281645 CCATCACATC
281655 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
281679 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
281703 ATCAAATTTCGA
1 ATCAAAATTCGA
281715 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:281855 original size:12 final size:12
Alignment explanation
Indices: 281834--281867 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
281824 GGTTGTGGGT
*
281834 TTTGAGATTGTG
1 TTTGATATTGTG
281846 TTTGATATTGTG
1 TTTGATATTGTG
*
281858 TTTGGTATTG
1 TTTGATATTG
281868 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:282698 original size:21 final size:21
Alignment explanation
Indices: 282674--282717 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
282664 TTCGCGTTGT
*
282674 GAATTTGGAATATCGCAACGC
1 GAATTTGGAAAATCGCAACGC
*
282695 GAATTTGGAAAATCGCAATGC
1 GAATTTGGAAAATCGCAACGC
282716 GA
1 GA
282718 TTTACATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (21 bp):
GAATTTGGAAAATCGCAACGC
Found at i:282774 original size:20 final size:20
Alignment explanation
Indices: 282725--282778 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
282715 CGATTTACAT
282725 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
282745 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
282765 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
282779 TTTGAGATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:287064 original size:35 final size:35
Alignment explanation
Indices: 287018--287093 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
287008 AAAAATATCC
* * *
287018 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
287053 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
287088 TCAATT
1 TCAATT
287094 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:287632 original size:130 final size:130
Alignment explanation
Indices: 287491--287738 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
287481 TATTTATATA
* **
287491 ATCAATTTGGTCATAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
287556 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
* *
287621 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGGTCTGACATGTG
1 ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
287686 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
287739 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:287769 original size:130 final size:129
Alignment explanation
Indices: 287500--287769 Score: 301
Period size: 130 Copynumber: 2.1 Consensus size: 129
287490 AATCAATTTG
* ** *
287500 GTCATAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACAT
1 GTCA-AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACAT
* *** * * ****
287565 GATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTG
65 GATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAA
* *
287630 GTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGGTCTGACATGTGTTAACACAT
1 GT-CAAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACAT
* * * *
287695 GATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAA
65 GATCATGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAA
287759 GAA
127 GAA
287762 GT-AAAATT
1 GTCAAAATT
287770 TGGGTCTTGG
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
130 101 0.88
131 1 0.01
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (129 bp):
GTCAAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATG
ATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAA
Found at i:288097 original size:28 final size:27
Alignment explanation
Indices: 288066--288128 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
288056 AGTTGATACA
*
288066 ATATTTTAAAATAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
288094 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
288122 ATATTTT
1 ATATTTT
288129 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:288229 original size:16 final size:17
Alignment explanation
Indices: 288204--288242 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
288194 TTTAATTTCT
288204 TATT-AAAAAATA-AAA
1 TATTCAAAAAATATAAA
288219 TATTCAAAAAATATAAA
1 TATTCAAAAAATATAAA
288236 TGATTCA
1 T-ATTCA
288243 TACATTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 4 0.19
18 5 0.24
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (17 bp):
TATTCAAAAAATATAAA
Found at i:289961 original size:17 final size:17
Alignment explanation
Indices: 289939--289971 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
289929 TCTAAAATTT
289939 TAAAAA-CATATAAAAAA
1 TAAAAATCAT-TAAAAAA
289956 TAAAAATCATTAAAAA
1 TAAAAATCATTAAAAA
289972 TATTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAATCATTAAAAAA
Found at i:301937 original size:31 final size:31
Alignment explanation
Indices: 301883--301953 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
301873 ACCTGACCCG
*
301883 AACCCAACTTGACCTTTTGAGATAAAATCCT-
1 AACCCAACTTGACCTTTTAAGATAAAAT-CTA
*
301914 AACCCAA-TTCGACTTTTTAAGATAAAATCTA
1 AACCCAACTT-GACCTTTTAAGATAAAATCTA
301945 AACCCAACT
1 AACCCAACT
301954 CAACCCGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 4 0.11
31 30 0.86
32 1 0.03
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.28
Consensus pattern (31 bp):
AACCCAACTTGACCTTTTAAGATAAAATCTA
Found at i:303329 original size:15 final size:15
Alignment explanation
Indices: 303311--303355 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
303301 GTTAATCAAC
*
303311 TTTGTCATAATATGA
1 TTTGTCATAGTATGA
*
303326 TTTGTCATAGTACGA
1 TTTGTCATAGTATGA
303341 TTTGTCATAGTATGA
1 TTTGTCATAGTATGA
303356 GTGATAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (15 bp):
TTTGTCATAGTATGA
Found at i:305078 original size:25 final size:25
Alignment explanation
Indices: 305047--305197 Score: 131
Period size: 25 Copynumber: 5.3 Consensus size: 25
305037 AGTTAGTATA
305047 TTAGTATGAACAATAAAATAAAATG
1 TTAGTATGAACAATAAAATAAAATG
*
305072 TTAGTATGAACAATAAAATAAAAATA
1 TTAGTATGAACAATAAAAT-AAAATG
305098 TTAGTATGTTAGTACGAATGATAAAATAAAATGTTAGTATG
1 TTAGTATG--A--AC--A--ATAAAATAAAA--------TG
305139 TTAGTATGAACAATAAAATAAAATG
1 TTAGTATGAACAATAAAATAAAATG
305164 TTAGTATGAACAATAAAAATAAAATG
1 TTAGTATGAACAAT-AAAATAAAATG
305190 TTAGTATG
1 TTAGTATG
305198 TTATTAGTTA
Statistics
Matches: 106, Mismatches: 2, Indels: 35
0.74 0.01 0.24
Matches are distributed among these distances:
25 35 0.33
26 32 0.30
28 1 0.01
30 2 0.02
32 1 0.01
33 15 0.14
34 7 0.07
35 1 0.01
37 2 0.02
39 1 0.01
41 9 0.08
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.31
Consensus pattern (25 bp):
TTAGTATGAACAATAAAATAAAATG
Found at i:305124 original size:59 final size:57
Alignment explanation
Indices: 305014--305197 Score: 174
Period size: 59 Copynumber: 3.2 Consensus size: 57
305004 ATGTTAGTAA
* * * *
305014 GTTAGTATAAATAATAAAATAAAAGTTAGTATATTAGTATGAACAATAAAATAAAAT
1 GTTAGTATGAACAATAAAATAAAAATTAGTATATTAGTACGAACAATAAAATAAAAT
* **
305071 GTTAGTATGAACAATAAAATAAAAATATTAGTATGTTAGTACGAATGATAAAATAAAAT
1 GTTAGTATGAACAATAAAAT-AAAA-ATTAGTATATTAGTACGAACAATAAAATAAAAT
* ** ** * *
305130 GTTAGTATGTTAGTATGAACAAT-AAAA-TAAAATGTTAGTATGAACAATAAAAATAAAAT
1 GTTAGTATG-AACAAT-AA-AATAAAAATTAGTATATTAGTACGAACAAT-AAAATAAAAT
305189 GTTAGTATG
1 GTTAGTATG
305198 TTATTAGTTA
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
57 18 0.17
58 20 0.19
59 57 0.54
60 6 0.06
61 2 0.02
62 3 0.03
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.32
Consensus pattern (57 bp):
GTTAGTATGAACAATAAAATAAAAATTAGTATATTAGTACGAACAATAAAATAAAAT
Found at i:305142 original size:67 final size:59
Alignment explanation
Indices: 305069--305200 Score: 183
Period size: 59 Copynumber: 2.1 Consensus size: 59
305059 ATAAAATAAA
305069 ATGTTAGTATGAACAATAAAATAAAAATATTAGTATGTTAGTACGAATGATAAAATAAAATGTTA
1 ATGTTAGTATGAACAATAAAAT-AAAATATTAGTATG--A--AC-AAT-A-AAAATAAAATGTTA
305134 GT
58 GT
*
305136 ATGTTAGTATGAACAATAAAATAAAATGTTAGTATGAACAATAAAAATAAAATGTTAGT
1 ATGTTAGTATGAACAATAAAATAAAATATTAGTATGAACAATAAAAATAAAATGTTAGT
305195 ATGTTA
1 ATGTTA
305201 TTAGTTAAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
59 22 0.34
60 1 0.02
61 3 0.05
62 2 0.03
64 1 0.02
66 13 0.20
67 22 0.34
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (59 bp):
ATGTTAGTATGAACAATAAAATAAAATATTAGTATGAACAATAAAAATAAAATGTTAGT
Found at i:305159 original size:92 final size:91
Alignment explanation
Indices: 304988--305200 Score: 324
Period size: 92 Copynumber: 2.3 Consensus size: 91
304978 CGGGTTAGCT
* *
304988 TGAACAA-ATAAAT-AAAATGTTAGTAAGTTAGTATAAATAATAAAATAAAAGTTAGTATATTAG
1 TGAACAATA-AAATAAAAATGTTAGTATGTTAGTACAAATAATAAAATAAAAGTTAGTATATTAG
305051 TATGAACAATAAAATAAAATGTTAGTA
65 TATGAACAATAAAATAAAATGTTAGTA
* * * *
305078 TGAACAATAAAATAAAAATATTAGTATGTTAGTACGAATGATAAAATAAAATGTTAGTATGTTAG
1 TGAACAATAAAATAAAAATGTTAGTATGTTAGTACAAATAATAAAATAAAA-GTTAGTATATTAG
305143 TATGAACAATAAAATAAAATGTTAGTA
65 TATGAACAATAAAATAAAATGTTAGTA
305170 TGAACAATAAAA-ATAAAATGTTAGTATGTTA
1 TGAACAATAAAATA-AAAATGTTAGTATGTTA
305201 TTAGTTAAAT
Statistics
Matches: 112, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
90 11 0.10
91 34 0.30
92 67 0.60
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.31
Consensus pattern (91 bp):
TGAACAATAAAATAAAAATGTTAGTATGTTAGTACAAATAATAAAATAAAAGTTAGTATATTAGT
ATGAACAATAAAATAAAATGTTAGTA
Found at i:305171 original size:33 final size:33
Alignment explanation
Indices: 304988--305171 Score: 208
Period size: 33 Copynumber: 5.8 Consensus size: 33
304978 CGGGTTAGCT
*
304988 TGAACAA-ATAAATAAAATGTTAGTAAGTTAGTA
1 TGAACAATA-AAATAAAATGTTAGTATGTTAGTA
* * *
305021 TAAATAATAAAATAAAA-GTTAGTATATTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
305053 TGAACAATAAAAT--AA----A--ATGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
*
305078 TGAACAATAAAATAAAAATATTAGTATGTTAGTA
1 TGAACAATAAAAT-AAAATGTTAGTATGTTAGTA
* **
305112 CGAATGATAAAATAAAATGTTAGTATGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
305145 TGAACAATAAAATAAAATGTTAGTATG
1 TGAACAATAAAATAAAATGTTAGTATG
305172 AACAATAAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
25 21 0.17
27 1 0.01
28 2 0.02
30 2 0.02
32 25 0.20
33 56 0.44
34 20 0.16
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.32
Consensus pattern (33 bp):
TGAACAATAAAATAAAATGTTAGTATGTTAGTA
Found at i:305215 original size:59 final size:59
Alignment explanation
Indices: 305047--305215 Score: 168
Period size: 59 Copynumber: 2.8 Consensus size: 59
305037 AGTTAGTATA
* * *
305047 TTAGTATGAACAATAAAATAAAATGTTAGTATG--AACAATAAAATAAAAATATTAGTATG
1 TTAGTATGAACAATAAAATAAAATGTTAGTATGTTAA-TATAAAATTAAAATA-TAGAATG
* ** *
305106 TTAGTACGAATGATAAAATAAAATGTTAGTATGTTAGTATGAACAA-TAAAATA-A-AATG
1 TTAGTATGAACAATAAAATAAAATGTTAGTATGTTAATAT-AA-AATTAAAATATAGAATG
* *
305164 TTAGTATGAACAATAAAAATAAAATGTTAGTATGTTATTAGTTAAATTAAAA
1 TTAGTATGAACAAT-AAAATAAAATGTTAGTATGTTAATA-TAAAATTAAAA
305216 GAAACAAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
58 16 0.18
59 61 0.67
60 3 0.03
61 9 0.10
62 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (59 bp):
TTAGTATGAACAATAAAATAAAATGTTAGTATGTTAATATAAAATTAAAATATAGAATG
Found at i:307033 original size:134 final size:133
Alignment explanation
Indices: 306725--307035 Score: 462
Period size: 134 Copynumber: 2.3 Consensus size: 133
306715 AGATTGAGAA
*
306725 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCAAGGCAGACTTGTTCCACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCA-GGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * *
306790 CAGGGAAGATCATATCTTAAAAATGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAAATAT
65 CAAGGAAGATCAAATCTTAAAAATGAGGGATTTGTTCCGCTTCTTCTTAAGGGAAAATCAAATAT
306855 GGGG
130 GGGG
* * *
306859 ACATTGATTCATTCCACTGTTCTTCAGGAAAGATTGAATCGAGGCAGACTTGTTCTACTGTTCCT
1 ACGTTGATTCATTCCACTGTTCTTCAGG-AAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * * *
306924 CAAGGAAGATCAAATCTTGAAAGA-GAGGGATTTGTTCTGCTTCTTCTTAAGGGAATATCATATA
65 CAAGGAAGATCAAATCTT-AAAAATGAGGGATTTGTTCCGCTTCTTCTTAAGGGAAAATCAAATA
306988 TGGGG
129 TGGGG
* *
306993 ACGTTGATTCATTCCACTATTCCTCATGGAAGATTGAATCGAG
1 ACGTTGATTCATTCCACTGTTCTTCA-GGAAGATTGAATCGAG
307036 TTCGATTCAC
Statistics
Matches: 160, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
133 2 0.01
134 152 0.95
135 6 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (133 bp):
ACGTTGATTCATTCCACTGTTCTTCAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTC
AAGGAAGATCAAATCTTAAAAATGAGGGATTTGTTCCGCTTCTTCTTAAGGGAAAATCAAATATG
GGG
Found at i:307758 original size:233 final size:231
Alignment explanation
Indices: 307345--308038 Score: 856
Period size: 233 Copynumber: 3.0 Consensus size: 231
307335 TTTGGAAAAT
* * *
307345 CATGCGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGAAA
1 CATGCGAAAACATCCTGCCCAAAGGTCTTATGGAT-GCCCGAA-GACTTATTATCTTGCTCGAAA
* ** *
307410 GGCTTATAGATGACCCGAATGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCC-AAAGGA
64 GACTTATAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAA-GA
** *
307474 CTTACCAATCCTAGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTT
128 CTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTT
307539 TCAGATTTAAATGAGAAAATTTTCTCATTTTTCAAGAGA
193 TCAGATTTAAATGAGAAAATTTTCTCATTTTTCAAGAGA
* * *
307578 CATGCAAAAACATCCTGCCCAAAGGTCTTGTGGATGACCCGAATGACTTATTATCTTGCTTGAAA
1 CATGCGAAAACATCCTGCCCAAAGGTCTTATGGATG-CCCGAA-GACTTATTATCTTGCTCGAAA
*** * * * *
307643 GACTTATAGATGACTTAAAGGATTTAAGCATCATGATCAAAAGACTTACTGATAACCCGAAAGAC
64 GACTTATAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAAGAC
* * * *
307708 TTACCAATTTTGGAAACAATTTACTAAGTAAGAAACTTTTCTTACTTTTCAAAAATTTTAATTTT
129 TTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTT
* **
307773 CAGATTTAAATGAGAAATTTTTCTCATTTTTTGAGAGA
194 CAGATTTAAATGAGAAAATTTTCTCATTTTTCAAGAGA
* * * * *
307811 CATGTGAAAACATCCTACCTGAAA-GTCTTATGGATCGCCCGACAAACTTA-TCTCTTGCTCGAA
1 CATGCGAAAACATCCTGCC-CAAAGGTCTTATGGAT-GCCCGA-AGACTTATTATCTTGCTCGAA
* * * * * *
307874 AGACTTACATATAACCCGAATGATTTAAGCATCATGCTCGAGAGACTTACTGATAGCTCGAAGGA
63 AGACTTATAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAAGA
* * *
307939 CTTACCAAATTTGGGAATAGTTTACTAGGTAATAAACTTTTCTTACTTTTCAAAAATTTC-ATTT
128 CTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTT
* * *
308003 TCTGAATACACTAAATGAGAAACTTTTCTCATTTTT
193 TCAG-AT---TTAAATGAGAAAATTTTCTCATTTTT
308039 TAAATTTATA
Statistics
Matches: 393, Mismatches: 59, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
231 7 0.02
232 119 0.30
233 235 0.60
234 8 0.02
235 24 0.06
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (231 bp):
CATGCGAAAACATCCTGCCCAAAGGTCTTATGGATGCCCGAAGACTTATTATCTTGCTCGAAAGA
CTTATAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAAGACTT
ACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCA
GATTTAAATGAGAAAATTTTCTCATTTTTCAAGAGA
Found at i:309664 original size:18 final size:19
Alignment explanation
Indices: 309618--309666 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
309608 TTGGACTCTC
*
309618 AGTGCATCGGTGCACTAAA
1 AGTGCATCGATGCACTAAA
309637 AGTGCATCGATGCA-TAAA
1 AGTGCATCGATGCACTAAA
309655 A-TGCATTCGATG
1 AGTGCA-TCGATG
309667 TTTTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 13 0.46
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAA
Found at i:309767 original size:45 final size:46
Alignment explanation
Indices: 309678--309769 Score: 159
Period size: 45 Copynumber: 2.0 Consensus size: 46
309668 TTTGATAAAG
* *
309678 ACTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGC
1 ACTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGC
309724 ACTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGC
1 ACTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGC
309769 A
1 A
309770 TTCGATGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 22 0.50
46 22 0.50
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
ACTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGC
Found at i:310378 original size:13 final size:13
Alignment explanation
Indices: 310360--310384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
310350 AGCCATTAGT
310360 TTCATAATCAATA
1 TTCATAATCAATA
310373 TTCATAATCAAT
1 TTCATAATCAAT
310385 GTGACATGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:313997 original size:32 final size:31
Alignment explanation
Indices: 313961--314037 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
313951 CGGGGCCGTG
*
313961 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
313993 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
314024 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
314038 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:314020 original size:63 final size:62
Alignment explanation
Indices: 313905--314037 Score: 153
Period size: 63 Copynumber: 2.1 Consensus size: 62
313895 AAAACGTTAC
* * ** *
313905 CCTAAGGAAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTA
1 CCTAA-GAAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTA
* *
313968 CCTAAGAACACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTA
1 CCTAAGAA-ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTA
314031 CCTAAGA
1 CCTAAGA
314038 GTCACATTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 4 0.07
63 53 0.88
64 3 0.05
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.17
Consensus pattern (62 bp):
CCTAAGAAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTA
Found at i:314938 original size:22 final size:22
Alignment explanation
Indices: 314912--314954 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
314902 GAAAGTCAAC
314912 GGTCAACGGTCAGGTCGGGTCG
1 GGTCAACGGTCAGGTCGGGTCG
*
314934 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCAGGTCGGGTC
314955 AGACCGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCAGGTCGGGTCG
Found at i:314989 original size:20 final size:21
Alignment explanation
Indices: 314964--315021 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
314954 CAGACCGGTC
*
314964 AAACCGGTTCGAACCGGTTG-
1 AAACCGGTTCAAACCGGTTGA
*
314984 AAACC-GATCAAACCGGTTGA
1 AAACCGGTTCAAACCGGTTGA
315004 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCAAACCGGTT
315022 TCCAGCAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 12 0.36
20 19 0.58
21 2 0.06
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCAAACCGGTTGA
Found at i:314994 original size:29 final size:28
Alignment explanation
Indices: 314957--315018 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 28
314947 GTCGGGTCAG
*
314957 ACCGGTCAAACCGGTTCG-AACCGGTTGAA
1 ACCGATCAAACCGGTT-GAAACCGGTT-AA
314986 ACCGATCAAACCGGTTGAAAACCGGTTAA
1 ACCGATCAAACCGGTTG-AAACCGGTTAA
315015 ACCG
1 ACCG
315019 GTTTCCAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 1 0.03
29 21 0.70
30 8 0.27
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.16
Consensus pattern (28 bp):
ACCGATCAAACCGGTTGAAACCGGTTAA
Found at i:315009 original size:11 final size:9
Alignment explanation
Indices: 314957--315021 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
314947 GTCGGGTCAG
*
314957 ACCGGTCAA
1 ACCGGTTAA
*
314966 ACCGGTTCGA
1 ACCGGTT-AA
314976 ACCGGTTGAA
1 ACCGGTT-AA
* *
314986 ACCGATCAA
1 ACCGGTTAA
314995 ACCGGTTGAAA
1 ACCGGTT--AA
315006 ACCGGTTAA
1 ACCGGTTAA
315015 ACCGGTT
1 ACCGGTT
315022 TCCAGCAGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 22 0.49
10 14 0.31
11 9 0.20
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:315021 original size:9 final size:10
Alignment explanation
Indices: 314964--315021 Score: 59
Period size: 9 Copynumber: 5.9 Consensus size: 10
314954 CAGACCGGTC
314964 AAACCGGTTCG
1 AAACCGGTT-G
314975 -AACCGGTTG
1 AAACCGGTTG
* *
314984 AAACC-GATC
1 AAACCGGTTG
314993 AAACCGGTTG
1 AAACCGGTTG
315003 AAAACCGGTT-
1 -AAACCGGTTG
315013 AAACCGGTT
1 AAACCGGTT
315022 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 17 0.43
10 14 0.35
11 9 0.22
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:321336 original size:63 final size:63
Alignment explanation
Indices: 321220--321343 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
321210 CCCTAAGGGA
* * ** * *
321220 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTATCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
321283 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
321344 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 47 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:322243 original size:5 final size:5
Alignment explanation
Indices: 322233--322285 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
322223 AACGATCAAC
* *
322233 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
322282 GGTC
1 GGTC
322286 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:322250 original size:17 final size:17
Alignment explanation
Indices: 322228--322286 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 17
322218 CGGTCAACGA
322228 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
322245 TCAACGGTCGGGTCGGGTCGGG
1 TCAA----C-GGTCGGGTCGGG
322267 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
322284 TCA
1 TCA
322287 GACCGGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 19 0.51
18 1 0.03
21 1 0.03
22 16 0.43
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.19
Consensus pattern (17 bp):
TCAACGGTCGGGTCGGG
Found at i:322261 original size:22 final size:22
Alignment explanation
Indices: 322233--322285 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
322223 AACGATCAAC
322233 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
322255 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
322277 GGTCGGGTC
1 GGTCGGGTC
322286 AGACCGGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:322306 original size:19 final size:18
Alignment explanation
Indices: 322282--322359 Score: 111
Period size: 19 Copynumber: 4.2 Consensus size: 18
322272 GGTCGGGTCG
322282 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
322300 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
*
322319 GGTTCAGACCGATCAAACC
1 GG-TCAGACCGGTCAAACC
*
322338 GGTCAGAACCGGTTAAACC
1 GGTCAG-ACCGGTCAAACC
322357 GGT
1 GGT
322360 TTCCAGCAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
18 6 0.11
19 48 0.89
ACGTcount: A:0.28, C:0.31, G:0.27, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:322360 original size:9 final size:9
Alignment explanation
Indices: 322282--322359 Score: 84
Period size: 9 Copynumber: 8.3 Consensus size: 9
322272 GGTCGGGTCG
*
322282 GGTCAGACC
1 GGTCAAACC
322291 GGTCAAACC
1 GGTCAAACC
*
322300 GGCTCAGACC
1 GG-TCAAACC
322310 GGTCAAACC
1 GGTCAAACC
*
322319 GGTTCAGACC
1 GG-TCAAACC
*
322329 GATCAAACC
1 GGTCAAACC
322338 GGTCAGAACC
1 GGTCA-AACC
*
322348 GGTTAAACC
1 GGTCAAACC
322357 GGT
1 GGT
322360 TTCCAGCAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
9 35 0.60
10 23 0.40
ACGTcount: A:0.28, C:0.31, G:0.27, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:327918 original size:18 final size:19
Alignment explanation
Indices: 327879--327921 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
327869 ACACCTTCAA
*
327879 ATGATTCTGAACGTTGGGG
1 ATGATTCTAAACGTTGGGG
327898 ATGATTCTAAACGTT-GGG
1 ATGATTCTAAACGTTGGGG
327916 ATGATT
1 ATGATT
327922 AGTGGAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.35
Consensus pattern (19 bp):
ATGATTCTAAACGTTGGGG
Found at i:328095 original size:18 final size:19
Alignment explanation
Indices: 328049--328095 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
328039 GGACTCTCAG
*
328049 TGCATCGATGCACTAAGAG
1 TGCATCGATGCACTAAGAA
328068 TGCATCGATGCA-TAA-AA
1 TGCATCGATGCACTAAGAA
328085 TGCATTCGATG
1 TGCA-TCGATG
328096 TTTTGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 12 0.46
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAA
Found at i:328180 original size:64 final size:63
Alignment explanation
Indices: 328067--328209 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 63
328057 TGCACTAAGA
328067 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTAAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAA-CCTAAGTGCATCGATGCATGGTAT
* * *
328131 GTGCATCGATGTATAAAATGCATTTGATG-TTTGAAAAA-TTAATTGGTGCATCGATGCATGG-A
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAACCTAA---GTGCATCGATGCATGGTA
328193 TT
63 -T
*
328195 GGTGCATCGGTGCAT
1 -GTGCATCGATGCAT
328210 CATTTTGGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
61 3 0.04
63 10 0.14
64 44 0.64
65 12 0.17
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAACCTAAGTGCATCGATGCATGGTAT
Found at i:328197 original size:20 final size:20
Alignment explanation
Indices: 328172--328209 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
328162 TGAAAAATTA
328172 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
328192 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
328210 CATTTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:332434 original size:20 final size:20
Alignment explanation
Indices: 332405--332447 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
332395 ATTCCACCAC
* *
332405 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCATAA
*
332425 ATGCATCTATATGATCATAA
1 ATGCAACTATATGATCATAA
332445 ATG
1 ATG
332448 GGCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCATAA
Found at i:335901 original size:30 final size:30
Alignment explanation
Indices: 335867--335930 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
335857 ACCTATCTAG
*
335867 AGGTCATAAAGATCCTCGGTAACTATCCAT
1 AGGTCATAAAGATCCTCGGCAACTATCCAT
* *
335897 AGGTCATAAAGATCCTTGGCAACTGTCCAT
1 AGGTCATAAAGATCCTCGGCAACTATCCAT
335927 AGGT
1 AGGT
335931 TCCAAAGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (30 bp):
AGGTCATAAAGATCCTCGGCAACTATCCAT
Found at i:335938 original size:30 final size:30
Alignment explanation
Indices: 335874--335964 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
335864 TAGAGGTCAT
* * * *
335874 AAAGATCCTCGGTAACTATCCATAGG-TCAT
1 AAAGATCCTAGGAAACTGTCCATAGGTTC-C
* *
335904 AAAGATCCTTGGCAACTGTCCATAGGTTCC
1 AAAGATCCTAGGAAACTGTCCATAGGTTCC
* *
335934 AAAGAACCTAGGTAAACTGTCCATATGTTCC
1 AAAGATCCTAGG-AAACTGTCCATAGGTTCC
335965 TTAGAACATA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 33 0.65
31 18 0.35
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (30 bp):
AAAGATCCTAGGAAACTGTCCATAGGTTCC
Found at i:335955 original size:31 final size:31
Alignment explanation
Indices: 335917--336041 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
335907 GATCCTTGGC
*
335917 AACTGTCCATAGGTTCCAAAGAACCTAGGTA
1 AACTGTCCATAGGTTCCAAAGAACATAGGTA
* **
335948 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTTCCAAAGAACATAGGTA
*** * *
335979 TGTTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATAGGT-TCCAAAGAACATAGGTA
* **
336010 ATTA-TGTCCATATGTTCCGTAGAACATAGGTA
1 A--ACTGTCCATAGGTTCCAAAGAACATAGGTA
336042 TACCCTCGAC
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
31 51 0.68
32 24 0.32
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATAGGTTCCAAAGAACATAGGTA
Found at i:340757 original size:30 final size:30
Alignment explanation
Indices: 340721--340792 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
340711 CCCGAAGGAC
* *
340721 CTATCCAGAGTTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
*
340751 CTATCCAGAGGTCATAAAGATCCTTGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
*
340781 CTATCCATAGGT
1 CTATCCAGAGGT
340793 TCCGAAGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:340899 original size:32 final size:32
Alignment explanation
Indices: 340786--340903 Score: 95
Period size: 31 Copynumber: 3.8 Consensus size: 32
340776 GGCAACTATC
* * * *
340786 CATAGGTTCCGAAGAACCTAGGTAA-ACTG-T
1 CATATGTTCCGTAGAACATAGGTAATTCTGTT
* *
340816 CTATATGTTCCTTAGAACATAGGT-ATAT-TGTC
1 C-ATATGTTCCGTAGAACATAGGTAAT-TCTGTT
*
340848 CATATG-TCTCG-AAAGACATAGGTAATTCTGTT
1 CATATGTTC-CGTAGA-ACATAGGTAATTCTGTT
340880 CATATGTTCCGTAGAACATAGGTA
1 CATATGTTCCGTAGAACATAGGTA
340904 TACCCTCGAC
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
30 6 0.09
31 35 0.51
32 23 0.34
33 4 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (32 bp):
CATATGTTCCGTAGAACATAGGTAATTCTGTT
Found at i:344567 original size:19 final size:19
Alignment explanation
Indices: 344543--344581 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
344533 TCGAATGCAT
344543 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
344562 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
344581 T
1 T
344582 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:344598 original size:65 final size:64
Alignment explanation
Indices: 344480--344688 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 64
344470 TATTCAAATG
* *
344480 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
344541 ATTC
61 ATTT
*
344545 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATTGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
344610 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
344674 CATGCATCGATGCAC
1 CATGCACCGATGCAC
344689 ACTTGGTGCA
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 7 0.06
64 51 0.41
65 64 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:344706 original size:64 final size:65
Alignment explanation
Indices: 344529--344691 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
344519 GAATTAATTG
* * * *
344529 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* * ** **
344594 AACATTGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
344657 A
65 A
344658 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
344692 TGGTGCACCG
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 35 0.42
65 48 0.58
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:346782 original size:20 final size:21
Alignment explanation
Indices: 346749--346788 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
346739 TTTTAACGTA
346749 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
346769 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
346789 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Found at i:346796 original size:22 final size:20
Alignment explanation
Indices: 346748--346792 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
346738 ATTTTAACGT
346748 AATTGATATTCATTTTAAAC
1 AATTGATATTCATTTTAAAC
*
346768 CATTGATA-TCAATTTTCAAAC
1 AATTGATATTC-ATTTT-AAAC
346789 AATT
1 AATT
346793 TGATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTGATATTCATTTTAAAC
Found at i:351727 original size:64 final size:65
Alignment explanation
Indices: 351625--351751 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 65
351615 CGAATGCATT
* *
351625 CCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAG
1 CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAG
** *
351690 CCATGCATCGATGCAC-CAGGCTATTTTTC-AAACATCGAATGCATTTCATGCATTGATGCACA
1 CCATGCATCGATGCACTCAGAATA-TTTTCAAAACATCGAATGCATTTCATGCATCGATGCACA
351752 CTTGGTGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
64 35 0.62
65 21 0.38
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (65 bp):
CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAG
Found at i:353747 original size:20 final size:20
Alignment explanation
Indices: 353718--353760 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
353708 ATTCCACCAC
*
353718 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
353738 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
353758 ATG
1 ATG
353761 GGCTTTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:354633 original size:57 final size:57
Alignment explanation
Indices: 354567--354957 Score: 685
Period size: 57 Copynumber: 6.8 Consensus size: 57
354557 TAAAATACCT
* *
354567 ATACGGAAATTCATAAACTAATTATGAATTTCTTAACTTTTTGCACACAAATTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
354624 ATACTGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
354681 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
354738 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
354795 ATACGGAAATTTATAAACTTATTATGAATTTCTTAACTTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAAC-TTTTTGCACACAAAGTGCCC
*
354853 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGGCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
354910 ATACAGAAATTCATAAACTAATTATGAATTTCTTAACATTTTT-CACAC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAAC-TTTTTGCACAC
354958 TCAGTGACAT
Statistics
Matches: 321, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
57 260 0.81
58 61 0.19
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (57 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:354927 original size:172 final size:171
Alignment explanation
Indices: 354537--354957 Score: 704
Period size: 172 Copynumber: 2.5 Consensus size: 171
354527 AAATTCATAT
* * * * *
354537 AATTTCTT-AGTTTTTACACATAAAATACCTATACGGAAATTCATAAACTAATTATGAATTTCTT
1 AATTTCTTAACTTTTTGCACACAAAGTGCCTATACGGAAATTCATAAACTAATTATGAATTTCTT
* *
354601 AACTTTTTGCACACAAATTGCCCATACTGAAATTCATAAACTTATTATGAATTTCTTAACTTTTT
66 AACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTT
354666 GCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATG
131 GCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATG
*
354707 AATTTCTTAACTTTTTGCACACAAAGTGCCTATACGGAAATTCATAAACTTATTATGAATTTCTT
1 AATTTCTTAACTTTTTGCACACAAAGTGCCTATACGGAAATTCATAAACTAATTATGAATTTCTT
*
354772 AACTTTTTGCACACAAAGTGCCCATACGGAAATTTATAAACTTATTATGAATTTCTTAACTTTTT
66 AACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC-TTTT
354837 TGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATG
130 TGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATG
*
354879 AATTTCTTAACTTTTTGCACACAAAGTGGCC-ATACAGAAATTCATAAACTAATTATGAATTTCT
1 AATTTCTTAACTTTTTGCACACAAAGT-GCCTATACGGAAATTCATAAACTAATTATGAATTTCT
354943 TAACATTTTT-CACAC
65 TAAC-TTTTTGCACAC
354958 TCAGTGACAT
Statistics
Matches: 236, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
170 8 0.03
171 107 0.45
172 113 0.48
173 8 0.03
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (171 bp):
AATTTCTTAACTTTTTGCACACAAAGTGCCTATACGGAAATTCATAAACTAATTATGAATTTCTT
AACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTT
GCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATG
Found at i:356244 original size:76 final size:75
Alignment explanation
Indices: 356163--356310 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
356153 TAAACTCAAA
356163 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
356227 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * *
356239 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
356304 TTAATTA
66 TTAATTA
356311 GGATTTAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 24 0.36
76 43 0.64
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:356402 original size:65 final size:65
Alignment explanation
Indices: 356275--356410 Score: 188
Period size: 65 Copynumber: 2.1 Consensus size: 65
356265 CTTTATCTTT
* *
356275 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAAAATATTATATTATTTTTTTAG
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAAAATATTATACTATGTTTTTAG
* * *
356340 GTATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTAAGATGTTTTAGCT-TGTTTTT
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTAAAATATTATA-CTATGTTTTT
356403 AG
64 AG
356405 G-ATTTT
1 GTATTTT
356411 GAAGGCTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
64 10 0.16
65 53 0.83
66 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.55
Consensus pattern (65 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAAAATATTATACTATGTTTTTAG
Found at i:357492 original size:8 final size:8
Alignment explanation
Indices: 357479--357518 Score: 53
Period size: 8 Copynumber: 4.6 Consensus size: 8
357469 ATATTTTTGG
357479 TTTTATTT
1 TTTTATTT
357487 TTTTATTTT
1 TTTTA-TTT
357496 CGTTTTATTT
1 --TTTTATTT
357506 TTTTATTT
1 TTTTATTT
357514 TTTTA
1 TTTTA
357519 GTGAACTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 18 0.62
9 3 0.10
10 3 0.10
11 5 0.17
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (8 bp):
TTTTATTT
Found at i:357495 original size:20 final size:20
Alignment explanation
Indices: 357470--357515 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
357460 CATTTCGTTA
*
357470 TATTTTTGGTTTTATTTTTT
1 TATTTTTCGTTTTATTTTTT
357490 TA-TTTTCGTTTTATTTTTT
1 TATTTTTCGTTTTATTTTTT
357509 TATTTTT
1 TATTTTT
357516 TTAGTGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (20 bp):
TATTTTTCGTTTTATTTTTT
Found at i:359450 original size:76 final size:75
Alignment explanation
Indices: 359359--359523 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
359349 TTAAACTCAA
* *
359359 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTATATTTTAGTTTAAATAGG-TTTTAGT
359423 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
359435 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTATATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTATATTTTAGTTTAAATAGGTTTTAGTAT
*
359500 TTTAATTAGG
66 TTTAATTAAG
*
359510 ATTTAGAATATTAT
1 ATTTAGGATATTAT
359524 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 37 0.47
76 42 0.53
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTATATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:359598 original size:64 final size:66
Alignment explanation
Indices: 359473--359607 Score: 181
Period size: 64 Copynumber: 2.1 Consensus size: 66
359463 TTTATCTTTA
* *
359473 TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTAT-TTTTTTAG
1 TATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAGGATTTAGAATATTATACTATGTTTTTTAG
359537 G
66 G
* *
359538 TATTTTAGTTTAAATA-GTTTAAGTATTTTAATTAGGATTTA-AGATGTTTTAGCT-TGTTTTTT
1 TATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAGGATTTAGA-ATATTATA-CTATGTTTTTT
359600 AGG
64 AGG
359603 -ATTTT
1 TATTTT
359608 GAAGGCTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
63 1 0.02
64 36 0.57
65 26 0.41
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.56
Consensus pattern (66 bp):
TATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAGGATTTAGAATATTATACTATGTTTTTTAG
G
Found at i:360195 original size:21 final size:22
Alignment explanation
Indices: 360170--360210 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
360160 CTTTAATTTG
360170 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
360191 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
360211 TATTTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:364228 original size:12 final size:12
Alignment explanation
Indices: 364201--364231 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
364191 GAAAAAGAAC
364201 TTTTTGCTATAA
1 TTTTTGCTATAA
364213 -TTTTGCTATAA
1 TTTTTGCTATAA
364224 TTTTTGCT
1 TTTTTGCT
364232 TTAGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.61
Consensus pattern (12 bp):
TTTTTGCTATAA
Done.