Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001523.1 Hibiscus syriacus cultivar Beakdansim tig00002982_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: 1321709
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1168175 original size:16 final size:16
Alignment explanation
Indices: 1168150--1168188 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1168140 AATCCCCCTT
1168150 TTAC-ATTTATTACTA
1 TTACTATTTATTACTA
*
1168165 TTACTATTTATTATTA
1 TTACTATTTATTACTA
*
1168181 TTATTATT
1 TTACTATT
1168189 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (16 bp):
TTACTATTTATTACTA
Found at i:1168180 original size:3 final size:3
Alignment explanation
Indices: 1168156--1168201 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
1168146 CCTTTTACAT
* *
1168156 TTA TTA CTA TTA CTA TTTA TTA TTA TTA TTA TTA TT- TTA TT- TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1168200 TT
1 TT
1168202 TTAATATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1168180 original size:19 final size:19
Alignment explanation
Indices: 1168156--1168192 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1168146 CCTTTTACAT
1168156 TTATTACTATTACTATTTA
1 TTATTACTATTACTATTTA
* *
1168175 TTATTATTATTATTATTT
1 TTATTACTATTACTATTT
1168193 TATTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTACTATTACTATTTA
Found at i:1169126 original size:54 final size:54
Alignment explanation
Indices: 1169032--1169205 Score: 208
Period size: 54 Copynumber: 3.3 Consensus size: 54
1169022 AAGGAGCTTC
* * * *
1169032 AATGATTGA-GAA-ATCTGGGCAGAAGCCACTAGAAAGGATGAATATACTGTCA
1 AATGATTTACGAACATCTGGGCAGAAGCCACAAGAAAGGATGAATGTATTGTCA
* * * *
1169084 AATGCTTTACGAAGATCTGGGCAGAAGCCACAATAAAGGATGAATGTGTTGTCA
1 AATGATTTACGAACATCTGGGCAGAAGCCACAAGAAAGGATGAATGTATTGTCA
* * * *
1169138 AATGATTTATGAACATCTGGACATAAGCCACAAGAAAGGAGGAATGTATTGTCA
1 AATGATTTACGAACATCTGGGCAGAAGCCACAAGAAAGGATGAATGTATTGTCA
* *
1169192 AATGTTTTATGAAC
1 AATGATTTACGAAC
1169206 CAGTGATTAT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 7 0.07
53 3 0.03
54 94 0.90
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.25
Consensus pattern (54 bp):
AATGATTTACGAACATCTGGGCAGAAGCCACAAGAAAGGATGAATGTATTGTCA
Found at i:1170322 original size:20 final size:20
Alignment explanation
Indices: 1170297--1170367 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
1170287 TGTTTTCAAA
1170297 ACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAG
* * *
1170317 ACCTTC-AGTGCATGACGTTTTCAAA
1 ACCTTCGGGT-CAT--C--TGT-AAG
1170342 ACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAG
1170362 ACCTTC
1 ACCTTC
1170368 AGTGCATGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 2 0.05
20 17 0.45
21 2 0.05
22 1 0.03
23 1 0.03
24 2 0.05
25 11 0.29
26 2 0.05
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.31
Consensus pattern (20 bp):
ACCTTCGGGTCATCTGTAAG
Found at i:1170326 original size:45 final size:45
Alignment explanation
Indices: 1170262--1170962 Score: 1056
Period size: 45 Copynumber: 15.7 Consensus size: 45
1170252 CTATTTCCCA
**
1170262 CATCTGTAAGACCTTCAGTGCAAAATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1170307 CATCTGTAAGACCTTCAGTGCATGACGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1170352 CATCTGTAAGACCTTCAGTGCATGATGTTTTCGAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1170397 CATCTGCAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1170442 CATCTGTAAGACCTTTAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1170487 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1170532 CATCTGTAAGACCTTCATTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1170577 CATCTGTAAGACCTTCATTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1170622 CATCTGTAAGAGCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1170667 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1170712 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
1170757 CATCTGTAAGACCTTCAGTGCAGGATATTTTCAAAACCGCCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1170802 CATCTGTAAGACATTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
1170847 CATCTATAAGACTTTCAGTGCAAGATG--TT-AAAGTCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA-ACCTTCGGGT
** * * * *
1170890 CATCCATAAGACCTTCAGTGCAAGATG--TT-AAAGCCTTCAGGC
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1170932 CATCCT-TAAGACCTTCAGTGCAGGATATTTT
1 CAT-CTGTAAGACCTTCAGTGCATGATGTTTT
1170963 TAAAGGAGAT
Statistics
Matches: 607, Mismatches: 45, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
42 32 0.05
43 42 0.07
44 2 0.00
45 531 0.87
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1170682 original size:20 final size:20
Alignment explanation
Indices: 1170657--1170727 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
1170647 TGTTTTCAAA
1170657 ACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAG
* * *
1170677 ACCTTC-AGTGCATGATGTTTTCAAA
1 ACCTTCGGGT-CAT-CTG---T-AAG
1170702 ACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAG
1170722 ACCTTC
1 ACCTTC
1170728 AGTGCATGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 2 0.05
20 17 0.45
21 3 0.08
24 3 0.08
25 11 0.29
26 2 0.05
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (20 bp):
ACCTTCGGGTCATCTGTAAG
Found at i:1171201 original size:3 final size:3
Alignment explanation
Indices: 1171193--1171231 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1171183 TGTCACGACT
1171193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1171232 AATACATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1171973 original size:25 final size:25
Alignment explanation
Indices: 1171927--1171978 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1171917 GGCCACCGTG
* *
1171927 GGTGGTGATCGGCGCTGAAAACGGC
1 GGTGGTGATCGACGCAGAAAACGGC
1171952 GGTGGTGATCGACGCCAG-AAACGGC
1 GGTGGTGATCGACG-CAGAAAACGGC
1171977 GG
1 GG
1171979 CCGGCGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.21, C:0.21, G:0.44, T:0.13
Consensus pattern (25 bp):
GGTGGTGATCGACGCAGAAAACGGC
Found at i:1172563 original size:18 final size:17
Alignment explanation
Indices: 1172542--1172583 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1172532 TATTTTAGTC
1172542 ATTTTTTATT-TCCATTTT
1 ATTTTTTATTGTCC--TTT
1172560 ATTTTATTATTGTCCTTT
1 ATTTT-TTATTGTCCTTT
1172578 ATTTTT
1 ATTTTT
1172584 CAATACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 13 0.59
19 5 0.23
20 3 0.14
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTTTTATTGTCCTTT
Found at i:1178115 original size:20 final size:20
Alignment explanation
Indices: 1178092--1178139 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1178082 TGTAATAGTA
1178092 AATATGAAGTACAAATAAGT
1 AATATGAAGTACAAATAAGT
* *
1178112 AATATAAAGTATAAATAAGT
1 AATATGAAGTACAAATAAGT
1178132 AATATGAA
1 AATATGAA
1178140 AATGATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.27
Consensus pattern (20 bp):
AATATGAAGTACAAATAAGT
Found at i:1180493 original size:137 final size:137
Alignment explanation
Indices: 1180247--1181006 Score: 905
Period size: 137 Copynumber: 5.5 Consensus size: 137
1180237 CACTATTTAC
* * ** * * *
1180247 GTGAAAGCACTTCTTGTGGGATGCTCCTTTCAATTTTTTCCGA-ATATAGGTTATAATTTCCCTA
1 GTGAAAGCGCTTCTTGTGGGATGCGCCTTTCCTTTTTTTCAGAGA-ATATGTTATAATTGCCCTA
* * * * * * * *
1180311 TAACGTGTGATGTCCCACGACGGGACACTATTCACATCAACACCTATCATGTTCGATGGGACGTA
65 TTATGTGTGATGTCCCCCGATGGGGCACTATTCACATCAACACCTATCATGTTTGAGGGGACGCA
*
1180376 ACAATCTG
130 ACAATGTG
* * *
1180384 GTGAAAGCGCTTCTTATGAGATGCGCCTTTCCTTTTTTTCAGAGAATATGTTATAATTACCCTAT
1 GTGAAAGCGCTTCTTGTGGGATGCGCCTTTCCTTTTTTTCAGAGAATATGTTATAATTGCCCTAT
* * *
1180449 TATGTGTGATGTCCCTCGATGGGGTACTATTCACATCAACACCTATCATATTTGAGGGGACGCAA
66 TATGTGTGATGTCCCCCGATGGGGCACTATTCACATCAACACCTATCATGTTTGAGGGGACGCAA
*
1180514 AAATGTG
131 CAATGTG
* * * * *
1180521 GTGAAAGCACTTCTTGTGGGATGTGTCTTTCCTTTTTGTCAAAGAATATGTTATAATTGCCCTAT
1 GTGAAAGCGCTTCTTGTGGGATGCGCCTTTCCTTTTTTTCAGAGAATATGTTATAATTGCCCTAT
* * * * *
1180586 TATGTGTTATGTCCCCCCG-CGAGGCACTATTCACATCAACACCTATCATGTTTTAGGGGATGCA
66 TATGTGTGATGT-CCCCCGATGGGGCACTATTCACATCAACACCTATCATGTTTGAGGGGACGCA
*
1180650 ATAATGTG
130 ACAATGTG
* * * ** * * * *
1180658 GTAAAAGAGCTTCTTATGGGACACGCCTTTCCCTTTTGTCAGATAATATGTTATAATTGCCCAAT
1 GTGAAAGCGCTTCTTGTGGGATGCGCCTTTCCTTTTTTTCAGAGAATATGTTATAATTGCCCTAT
* * * *
1180723 TATGTGTGATATCCCCAGATGGGGCACTATTCCCATCAACACCTATCATGTTTTAGGGGACGCAA
66 TATGTGTGATGTCCCCCGATGGGGCACTATTCACATCAACACCTATCATGTTTGAGGGGACGCAA
*
1180788 CAATGAG
131 CAATGTG
* * * *
1180795 GTGAAAGCGCTTCTTGTAGGATGCACCTTTCATTTTTTTTTCAAAGAATATGTTATAATTGCCCT
1 GTGAAAGCGCTTCTTGTGGGATGCGCCTTTC--CTTTTTTTCAGAGAATATGTTATAATTGCCCT
* *
1180860 ATTATGTGTGATGTCCCCCGGT-GGGCACTATTCACGTCAACACCTATCATGTTTGAGGGGACGC
64 ATTATGTGTGATGTCCCCCGATGGGGCACTATTCACATCAACACCTATCATGTTTGAGGGGACGC
1180924 AACAATGTG
129 AACAATGTG
*** * * * * *
1180933 GTGAATTTGTTTCTTGTGGGACGCACCTTTCCTTTTTATCAGAGAATATGTTATAATTACCCTAT
1 GTGAAAGCGCTTCTTGTGGGATGCGCCTTTCCTTTTTTTCAGAGAATATGTTATAATTGCCCTAT
1180998 TATGTGTGA
66 TATGTGTGA
1181007 ATTTGGATTT
Statistics
Matches: 529, Mismatches: 89, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
136 44 0.08
137 362 0.68
138 78 0.15
139 45 0.09
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (137 bp):
GTGAAAGCGCTTCTTGTGGGATGCGCCTTTCCTTTTTTTCAGAGAATATGTTATAATTGCCCTAT
TATGTGTGATGTCCCCCGATGGGGCACTATTCACATCAACACCTATCATGTTTGAGGGGACGCAA
CAATGTG
Found at i:1181984 original size:21 final size:20
Alignment explanation
Indices: 1181960--1182019 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
1181950 AAACCCTGCG
*
1181960 GGCTAGACATGTAACCTTGTA
1 GGCTAGA-ATGTAACCCTGTA
* *
1181981 GGCTAGATATGTACCCCTGTG
1 GGCTAGA-ATGTAACCCTGTA
1182002 GGCTAGGAATGTAACCCT
1 GGCTA-GAATGTAACCCT
1182020 ACTGAGAGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (20 bp):
GGCTAGAATGTAACCCTGTA
Found at i:1182063 original size:42 final size:41
Alignment explanation
Indices: 1182015--1182102 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
1182005 TAGGAATGTA
* * *
1182015 ACCCTACTGAGAGGGCATATGAACTGGTAGGCTGGGCATAT
1 ACCCTACGGAGAGGACATATGAACTGGTAGGCTAGGCATAT
* *
1182056 ATCCCTACGGAGATGACATATGAACTGGTAGGCTAGGTATAT
1 A-CCCTACGGAGAGGACATATGAACTGGTAGGCTAGGCATAT
1182098 ACCCT
1 ACCCT
1182103 TGCATCGATG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 5 0.12
42 36 0.88
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (41 bp):
ACCCTACGGAGAGGACATATGAACTGGTAGGCTAGGCATAT
Found at i:1183957 original size:22 final size:22
Alignment explanation
Indices: 1183932--1183979 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1183922 ACATTATTTT
1183932 TATAAAAACTATTTATAA-AAAA
1 TATAAAAACTATTTA-AAGAAAA
*
1183954 TATAACAACTATTTAAAGAAAA
1 TATAAAAACTATTTAAAGAAAA
1183976 TATA
1 TATA
1183980 CTAATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (22 bp):
TATAAAAACTATTTAAAGAAAA
Found at i:1185100 original size:112 final size:114
Alignment explanation
Indices: 1184971--1185176 Score: 389
Period size: 112 Copynumber: 1.8 Consensus size: 114
1184961 TGGATTTACT
1184971 GTGAATGTCGGACATGATAAAATGAATAAGGAAATTTGATGCTTGAGATAGGTTATACCATAGAA
1 GTGAATGTCGGACATGATAAAATGAATAAGGAAATTTGATGCTTGAGATAGGTTATACCATAGAA
1185036 CTCGAGT-AAAATTATG-AATTATGATGATAACGTTAAAGATTATAAGA
66 CTCGAGTAAAAATTATGAAATTATGATGATAACGTTAAAGATTATAAGA
*
1185083 GTGAATGTTGGACATGATAAAATGAATAAGGAAATTTGATGCTTGAGATAGGTTATACCATAGAA
1 GTGAATGTCGGACATGATAAAATGAATAAGGAAATTTGATGCTTGAGATAGGTTATACCATAGAA
1185148 CTCGAGTAAAAATTATGAAATTATGATGA
66 CTCGAGTAAAAATTATGAAATTATGATGA
1185177 AACTTTTTTC
Statistics
Matches: 91, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
112 71 0.78
113 9 0.10
114 11 0.12
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.30
Consensus pattern (114 bp):
GTGAATGTCGGACATGATAAAATGAATAAGGAAATTTGATGCTTGAGATAGGTTATACCATAGAA
CTCGAGTAAAAATTATGAAATTATGATGATAACGTTAAAGATTATAAGA
Found at i:1186296 original size:31 final size:31
Alignment explanation
Indices: 1186256--1186321 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1186246 TTGAGAAAAC
* *
1186256 TTCAGAAAACATATCGTTCAGACAATTACAA
1 TTCAAAAAACATATCGTTCAGACAATCACAA
* * *
1186287 TTCAAAAAACATATTGTTTAGACAATCACAG
1 TTCAAAAAACATATCGTTCAGACAATCACAA
1186318 TTCA
1 TTCA
1186322 TGAAATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (31 bp):
TTCAAAAAACATATCGTTCAGACAATCACAA
Found at i:1186369 original size:29 final size:31
Alignment explanation
Indices: 1186256--1186380 Score: 83
Period size: 31 Copynumber: 4.1 Consensus size: 31
1186246 TTGAGAAAAC
* ** * * *
1186256 TTCAGAAAACATATCGTTCAGACAATTACAA
1 TTCAGGAAACATATTATTAAGACAATCACAG
** * *
1186287 TTCAAAAAACATATTGTTTAGACAATCACAG
1 TTCAGGAAACATATTATTAAGACAATCACAG
* * * *
1186318 TTCATGAAATATATTAGTAAGACAGTC-C-G
1 TTCAGGAAACATATTATTAAGACAATCACAG
* *
1186347 TTCAGGAAACATATTATTCAGACATCTCACAG
1 TTCAGGAAACATATTATTAAGACA-ATCACAG
1186379 TT
1 TT
1186381 ATTTCAGAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
29 21 0.28
30 3 0.04
31 47 0.64
32 3 0.04
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.30
Consensus pattern (31 bp):
TTCAGGAAACATATTATTAAGACAATCACAG
Found at i:1186399 original size:35 final size:35
Alignment explanation
Indices: 1186353--1186466 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 35
1186343 TCCGTTCAGG
* * * *
1186353 AAACATATTATTCAGACATCTCACAGTTATTTCAG
1 AAACATGTTATTCAGACATCTCACAGATAATTCAA
* *
1186388 AAACATGTTATTCGGACATCTCATAGATAATTCAA
1 AAACATGTTATTCAGACATCTCACAGATAATTCAA
* ** * *
1186423 AAATATGTGGTTCAGACATCTCAGAGGTAATTCAA
1 AAACATGTTATTCAGACATCTCACAGATAATTCAA
1186458 AAACATGTT
1 AAACATGTT
1186467 TGATAACCAA
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.32
Consensus pattern (35 bp):
AAACATGTTATTCAGACATCTCACAGATAATTCAA
Found at i:1196413 original size:21 final size:20
Alignment explanation
Indices: 1196367--1196416 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1196357 CTCTTGTTAG
* *
1196367 GTATCGATACTACTGGCATG
1 GTATCGATACTACTGGAATA
*
1196387 GTATCGATACTACTTGAATAA
1 GTATCGATACTACTGGAAT-A
1196408 GTATCGATA
1 GTATCGATA
1196417 TTGTTCATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (20 bp):
GTATCGATACTACTGGAATA
Found at i:1197374 original size:13 final size:13
Alignment explanation
Indices: 1197356--1197412 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1197346 ATCATAAATC
*
1197356 TATGACGCGCATT
1 TATGACGCACATT
*
1197369 TATGACACACATT
1 TATGACGCACATT
*
1197382 TATGA--CAAATT
1 TATGACGCACATT
**
1197393 TATGACGTGCATT
1 TATGACGCACATT
1197406 TATGACG
1 TATGACG
1197413 TTCATTGAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 10 0.28
13 26 0.72
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:1197480 original size:84 final size:83
Alignment explanation
Indices: 1197388--1197631 Score: 269
Period size: 85 Copynumber: 2.9 Consensus size: 83
1197378 CATTTATGAC
*
1197388 AAATTTATGACGTGCATTTATGACGTT-CATTGAGCGTCATTGAAGCCCCGTCATAAATAAAGAT
1 AAATTTATGAC-TGCATATATGAC-TTACATTGAGCGTCATTGAAGCCCCGTCATAAATAAAGAT
*
1197452 GTCACACATTTGTGTGTCAT
64 GACACACATTTGTGTGTCAT
* * * ** **
1197472 AAATTTATGACTCACATGTATGACTTACATTGAACGTCATTGAAGCCCCAGTCATAAATCTACTT
1 AAATTTATGACT-GCATATATGACTTACATTGAGCGTCATTGAAGCCCC-GTCATAAATAAAGAT
*
1197537 GACATACATTTGTGTGTCAT
64 GACACACATTTGTGTGTCAT
* * *
1197557 AAATTTATGACACGCATATATGACTTACATT-ACGTGTCATTGAAGCACACGTCATTAAA-AAAG
1 AAATTTATGAC-TGCATATATGACTTACATTGA-GCGTCATTGAAGC-CCCGTCA-TAAATAAAG
*
1197620 ACGACACACATT
62 ATGACACACATT
1197632 CATGTGTCGT
Statistics
Matches: 132, Mismatches: 21, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
83 3 0.02
84 42 0.32
85 81 0.61
86 6 0.05
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (83 bp):
AAATTTATGACTGCATATATGACTTACATTGAGCGTCATTGAAGCCCCGTCATAAATAAAGATGA
CACACATTTGTGTGTCAT
Found at i:1197666 original size:2 final size:2
Alignment explanation
Indices: 1197659--1197717 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1197649 TTTCGTAAAT
1197659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1197701 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1197718 GTAGATTGAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1204457 original size:21 final size:22
Alignment explanation
Indices: 1204433--1204473 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1204423 GCTATTTTAG
1204433 GGGAGGAGGAGGA-GGAGAGGT
1 GGGAGGAGGAGGAGGGAGAGGT
* *
1204454 GGGATGAGGTGGAGGGAGAG
1 GGGAGGAGGAGGAGGGAGAG
1204474 ACGGTGGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.66, T:0.07
Consensus pattern (22 bp):
GGGAGGAGGAGGAGGGAGAGGT
Found at i:1226634 original size:20 final size:18
Alignment explanation
Indices: 1226601--1226637 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1226591 CTATTAAAAT
1226601 TTATAAAATTATTTTATA
1 TTATAAAATTATTTTATA
1226619 TTATAAGAAGTTATTTTAT
1 TTATAA-AA-TTATTTTAT
1226638 TAAGTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTATAAAATTATTTTATA
Found at i:1226719 original size:21 final size:20
Alignment explanation
Indices: 1226681--1226720 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1226671 ACACCCAACT
**
1226681 ATTTTTTATGTTCTAAATTC
1 ATTTTTTATGTTAAAAATTC
1226701 ATTTATTTATGTTAAAAATT
1 ATTT-TTTATGTTAAAAATT
1226721 TGATGACAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTTTATGTTAAAAATTC
Found at i:1226868 original size:20 final size:20
Alignment explanation
Indices: 1226830--1226868 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1226820 GGGGTGTAAA
* *
1226830 TTGACACCCTTTTAGAAAAG
1 TTGACACCCTTTGAAAAAAG
1226850 TTGACACCCTTTGAAAAAA
1 TTGACACCCTTTGAAAAAA
1226869 ATATTAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGACACCCTTTGAAAAAAG
Found at i:1233751 original size:14 final size:14
Alignment explanation
Indices: 1233732--1233768 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1233722 AATCGGACAG
1233732 CAGATTCTGCAAAA
1 CAGATTCTGCAAAA
1233746 CAGATTCTGCAAAA
1 CAGATTCTGCAAAA
1233760 CAGATTCTG
1 CAGATTCTG
1233769 TTGGTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (14 bp):
CAGATTCTGCAAAA
Found at i:1236886 original size:16 final size:16
Alignment explanation
Indices: 1236865--1236896 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1236855 ATTGATGAAA
1236865 AAGTGAAATCATCAAT
1 AAGTGAAATCATCAAT
*
1236881 AAGTGATATCATCAAT
1 AAGTGAAATCATCAAT
1236897 GGTTGCGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
AAGTGAAATCATCAAT
Found at i:1244217 original size:16 final size:16
Alignment explanation
Indices: 1244196--1244227 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1244186 ATTGATGAAA
1244196 AAGTGAAATCATCAAT
1 AAGTGAAATCATCAAT
*
1244212 AAGTGATATCATCAAT
1 AAGTGAAATCATCAAT
1244228 GGTTGCGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
AAGTGAAATCATCAAT
Found at i:1246413 original size:21 final size:21
Alignment explanation
Indices: 1246389--1246436 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1246379 TGTAGTTGCA
1246389 AGATTTCCCAGCTCTAGCTTC
1 AGATTTCCCAGCTCTAGCTTC
1246410 AGATTTCCCAGCTCTAGCTTC
1 AGATTTCCCAGCTCTAGCTTC
1246431 AGATTT
1 AGATTT
1246437 TATAAATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (21 bp):
AGATTTCCCAGCTCTAGCTTC
Found at i:1248438 original size:22 final size:23
Alignment explanation
Indices: 1248384--1248447 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
1248374 TATAGTTTTC
*
1248384 ATTAAATAATACATATATTACAT
1 ATTATATAATACATATATTACAT
*
1248407 ATAAGTATATAATACATA-ATTGCAT
1 AT---TATATAATACATATATTACAT
*
1248432 ATTATATAATCCATAT
1 ATTATATAATACATAT
1248448 TAAATAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
22 12 0.35
23 2 0.06
25 8 0.24
26 12 0.35
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (23 bp):
ATTATATAATACATATATTACAT
Found at i:1248460 original size:30 final size:30
Alignment explanation
Indices: 1248422--1248515 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 30
1248412 TATATAATAC
1248422 ATAA-TTGCATATTATATAATCCATATTAA
1 ATAATTTGCATATTATATAATCCATATTAA
* * * *
1248451 ATAGTTTGCATATTTTATAGTTCATATTAA
1 ATAATTTGCATATTATATAATCCATATTAA
* *
1248481 ATAATTAGCATATTATATAATCTATATTAA
1 ATAATTTGCATATTATATAATCCATATTAA
*
1248511 GTAAT
1 ATAAT
1248516 AGTCCATATT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
29 3 0.06
30 50 0.94
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.45
Consensus pattern (30 bp):
ATAATTTGCATATTATATAATCCATATTAA
Found at i:1248464 original size:16 final size:16
Alignment explanation
Indices: 1248443--1248495 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1248433 TTATATAATC
1248443 CATATTAAATAGTTTG
1 CATATTAAATAGTTTG
**
1248459 CATATTTTATAG-TT-
1 CATATTAAATAGTTTG
* *
1248473 CATATTAAATAATTAG
1 CATATTAAATAGTTTG
1248489 CATATTA
1 CATATTA
1248496 TATAATCTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 9 0.31
15 3 0.10
16 17 0.59
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (16 bp):
CATATTAAATAGTTTG
Found at i:1248500 original size:16 final size:15
Alignment explanation
Indices: 1248422--1248501 Score: 74
Period size: 14 Copynumber: 5.3 Consensus size: 15
1248412 TATATAATAC
1248422 ATAATTGCATATTAT
1 ATAATTGCATATTAT
* *
1248437 ATAA-TCCATATTAA
1 ATAATTGCATATTAT
* *
1248451 ATAGTTTGCATATTTT
1 ATA-ATTGCATATTAT
* *
1248467 ATAGTT-CATATTAA
1 ATAATTGCATATTAT
1248481 ATAATTAGCATATTAT
1 ATAATT-GCATATTAT
1248497 ATAAT
1 ATAAT
1248502 CTATATTAAG
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
14 22 0.44
15 6 0.12
16 22 0.44
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATTGCATATTAT
Found at i:1250426 original size:11 final size:12
Alignment explanation
Indices: 1250406--1250437 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1250396 TATCAAAGAT
1250406 AAACATAAAATA
1 AAACATAAAATA
1250418 AAACA-AAAATA
1 AAACATAAAATA
1250429 AAA-ATAAAA
1 AAACATAAAA
1250438 CGAGATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 13 0.68
12 5 0.26
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAACATAAAATA
Found at i:1251238 original size:34 final size:32
Alignment explanation
Indices: 1251177--1251282 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
1251167 AGTTAGTAAT
* * *
1251177 AACAA-AAAACAAAAGTTAGTATGTTAGTAT-G
1 AACAATAAAATAAAAGTTAGAATCTTAGT-TCG
1251208 AACAAATAAAATAAAAAGTTAGAATCTTAGTTCG
1 AAC-AATAAAAT-AAAAGTTAGAATCTTAGTTCG
* * **
1251242 AACGATAAAATAAATGTTAGAAAGTTAGTTCG
1 AACAATAAAATAAAAGTTAGAATCTTAGTTCG
1251274 AACAATAAA
1 AACAATAAA
1251283 GGTTAAAAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
31 3 0.05
32 28 0.44
33 12 0.19
34 20 0.32
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (32 bp):
AACAATAAAATAAAAGTTAGAATCTTAGTTCG
Found at i:1251307 original size:27 final size:26
Alignment explanation
Indices: 1251247--1251309 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
1251237 GTTCGAACGA
* *
1251247 TAAAATAAATGTTAGAAAGTTAGTTC
1 TAAAATAAAGGTTAGAAAGTTAGTAC
*
1251273 GAACAATAAAGGTTA-AAAGGTTAGTGAC
1 TAA-AATAAAGGTTAGAAA-GTTAGT-AC
1251301 TAAAATAAA
1 TAAAATAAA
1251310 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 5 0.17
27 22 0.73
28 3 0.10
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (26 bp):
TAAAATAAAGGTTAGAAAGTTAGTAC
Found at i:1252679 original size:3 final size:3
Alignment explanation
Indices: 1252671--1252773 Score: 147
Period size: 3 Copynumber: 35.0 Consensus size: 3
1252661 CCCACAAATG
* * * *
1252671 TAA TAA TAA TTA TAG TAT TAG T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1252718 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1252765 TAA TAA TAA
1 TAA TAA TAA
1252774 GACCCGGCCA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 3 0.03
3 87 0.97
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1253236 original size:61 final size:61
Alignment explanation
Indices: 1253053--1253485 Score: 222
Period size: 61 Copynumber: 7.1 Consensus size: 61
1253043 AATTGTTTAC
* *
1253053 TGAAGATGACGTTGTTCATTCTTGTT-AAGAAGTCGGGTCAATCTGGAGATAATTTGGTGT
1 TGAAGATGACGTTGTTCATTCTTGTTGAAGAAATCAGGTCAATCTGGAGATAATTTGGTGT
* * ** * * * * * ** **
1253113 TGAAGACGACTTTACTCATCCATGTTGAAGAGAT-ATGGCCACT-TTCAGATAATATTTTTGT
1 TGAAGATGACGTTGTTCATTCTTGTTGAAGAAATCA-GGTCAATCTGGAGATAAT-TTGGTGT
* * *
1253174 TGAAGATGACGTTGTTCCTTTTTGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGTGT
1 TGAAGATGACGTTGTTCATTCTTGTTGAAGAAATCAGGTCAATCTGGAGATAATTTGGTGT
* * * * * * ** * * *
1253235 TGAAGATGAC-TCTGCTGATCCGTGTTGAAGAAATCTGGTCACT-TTTATATAAATTGTTTGT
1 TGAAGATGACGT-TGTTCATTCTTGTTGAAGAAATCAGGTCAATCTGGAGATAATTTG-GTGT
* * * * * * **
1253296 TGAAGATGGCATTATTCCTTCTCGTTGAGGAAATCAGGTCAATC-GGAGATAATACGGTGT
1 TGAAGATGACGTTGTTCATTCTTGTTGAAGAAATCAGGTCAATCTGGAGATAATTTGGTGT
* * ** * * ** * ** *
1253356 TGAAGAAT-AC-TCTGCTCATTCGTGTTGAAGAGTTCTA-GCCACT-TTCAGGTAAATTTTTTGC
1 TGAAG-ATGACGT-TGTTCATTCTTGTTGAAGAAATC-AGGTCAATCTGGAGAT-AATTTGGTGT
* * * * *
1253417 TGAAAATGACGCTGTTCCTTCTTGTT-AAGGAAGTCTGGTCAATCTGGAGATAATTTGGTGT
1 TGAAGATGACGTTGTTCATTCTTGTTGAA-GAAATCAGGTCAATCTGGAGATAATTTGGTGT
1253478 TGAAGATG
1 TGAAGATG
1253486 TTCTTGTTGA
Statistics
Matches: 255, Mismatches: 99, Indels: 37
0.65 0.25 0.09
Matches are distributed among these distances:
59 1 0.00
60 73 0.29
61 167 0.65
62 14 0.05
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (61 bp):
TGAAGATGACGTTGTTCATTCTTGTTGAAGAAATCAGGTCAATCTGGAGATAATTTGGTGT
Found at i:1253265 original size:122 final size:121
Alignment explanation
Indices: 1253006--1253485 Score: 552
Period size: 121 Copynumber: 4.0 Consensus size: 121
1252996 AACGACACTA
* * * * * * *
1253006 CTCATCCGTGATGAAGAGTTCTGGCCGCTTTCAAATTAATTGTTTACTGAAGATGACGTTGTTCA
1 CTCATCCGTGTTGAAGAGATCTGGCCACTTTCAGATAAATT-TTTGCTGAAGATGACGTTGTTCC
* * * * * *
1253071 TTCTTGTT-AAGAAGTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTTTA
65 TTCTTGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTG
* * *
1253127 CTCATCCATGTTGAAGAGATATGGCCACTTTCAGATAATATTTTTGTTGAAGATGACGTTGTTCC
1 CTCATCCGTGTTGAAGAGATCTGGCCACTTTCAGATAA-ATTTTTGCTGAAGATGACGTTGTTCC
*
1253192 TTTTTGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTG
65 TTCTTGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTG
* * * * * * * * *
1253249 CTGATCCGTGTTGAAGAAATCTGGTCACTTTTATATAAATTGTTTGTTGAAGATGGCATTATTCC
1 CTCATCCGTGTTGAAGAGATCTGGCCACTTTCAGATAAATT-TTTGCTGAAGATGACGTTGTTCC
* **
1253314 TTCTCGTTGAGGAAATCAGGTCAATC-GGAGATAATACGGTGTTGAAGAAT-ACTCTG
65 TTCTTGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGTGTTGAAG-ATGACTCTG
* * * * * *
1253370 CTCATTCGTGTTGAAGAGTTCTAGCCACTTTCAGGTAAATTTTTTGCTGAAAATGACGCTGTTCC
1 CTCATCCGTGTTGAAGAGATCTGGCCACTTTCAGATAAA-TTTTTGCTGAAGATGACGTTGTTCC
* * *
1253435 TTCTTGTTAAGGAAGTCTGGTCAATCTGGAGATAATTTGGTGTTGAAGATG
65 TTCTTGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGATG
1253486 TTCTTGTTGA
Statistics
Matches: 300, Mismatches: 52, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
121 157 0.52
122 143 0.48
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (121 bp):
CTCATCCGTGTTGAAGAGATCTGGCCACTTTCAGATAAATTTTTGCTGAAGATGACGTTGTTCCT
TCTTGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGATGACTCTG
Found at i:1253748 original size:139 final size:136
Alignment explanation
Indices: 1253493--1253956 Score: 461
Period size: 139 Copynumber: 3.3 Consensus size: 136
1253483 ATGTTCTTGT
* * * ** *
1253493 TGAGGAAGTCTGATTGTCTAAGGATGACACTACTCTTACGCGTTGAGGAGATCTGGTCGGTGGAT
1 TGAGGAAGTCTGATTGCCTGAGGATGACACTGCTCTTACGCGTTGA-GAGATCT-GTTTGTGGAC
* * * * * *
1253558 GACATTGTTACTACGTGATGAGGA-TATCTAGTCATATTTAGGGATATTTTGGAGACAATATGAT
64 GACATTGTTCCTACGTGATGAGGAGT-TCAACT-ATCTTTAGGGATAATTTGGAGACAAAATGAT
1253622 TCCTACGTGA
127 TCCTACGTGA
*
1253632 TGAGGAAGTCTGATTGCCTGAGGATGACACTGCTCTTACGCGTTGAGAAGATTTGATTTGTGGAC
1 TGAGGAAGTCTGATTGCCTGAGGATGACACTGCTCTTACGCGTTGAG-AGATCTG-TTTGTGGAC
* * * *
1253697 GACATTATTCCTACATGATGAGGACGTTCAACTGTCTTTAGGGATAATTTGGAGACAAAACGATT
64 GACATTGTTCCTACGTGATGAGGA-GTTCAACTATCTTTAGGGATAATTTGGAGACAAAATGATT
**
1253762 CAAACGTGA
128 CCTACGTGA
* * * * * *
1253771 TGAGGAACTCTAATTGCCT-AGGGATGACACTGTTCCTACGCATTGATGAGATCCGTTTGGTGGA
1 TGAGGAAGTCTGATTGCCTGA-GGATGACACTGCTCTTACGCGTTGA-GAGATCTGTTT-GTGGA
* * * *
1253835 CGACATTGTTCCTACGTGATGAGGA-TGTCTAGCCATCTTTAGGGATAATTTAGAGACAACAT-A
63 CGACATTGTTCCTACGTGATGAGGAGT-TC-AACTATCTTTAGGGATAATTTGGAGACAAAATGA
*
1253898 GTTCCTATGTGA
126 -TTCCTACGTGA
* * * *
1253910 TGAGGAAGTCTGATTACCTGAGAATGACGCTGCT-TCTACACGTTGAG
1 TGAGGAAGTCTGATTGCCTGAGGATGACACTGCTCT-TACGCGTTGAG
1253957 GAGAGCTAGT
Statistics
Matches: 267, Mismatches: 46, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
137 1 0.00
138 10 0.04
139 249 0.93
140 6 0.02
141 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (136 bp):
TGAGGAAGTCTGATTGCCTGAGGATGACACTGCTCTTACGCGTTGAGAGATCTGTTTGTGGACGA
CATTGTTCCTACGTGATGAGGAGTTCAACTATCTTTAGGGATAATTTGGAGACAAAATGATTCCT
ACGTGA
Found at i:1254247 original size:67 final size:67
Alignment explanation
Indices: 1254170--1254349 Score: 263
Period size: 68 Copynumber: 2.7 Consensus size: 67
1254160 AAGGGAAAAT
* * *
1254170 TGTCTAAAGTGGGACAAAACTTTGTTTCAAGAGAAACGATCTCAAAGGTTTATGTTTCAAGAGAA
1 TGTCTCAAGTGAGACAAAACTTTGTTTTAAGAGAAACGATCTCAAAGGTTTATGTTTCAAGAGAA
1254235 AC
66 AC
* *
1254237 TGTCTCAAGTGAGACAAAACTTTTTTTTTAAGAGAAACGATCTCAAAGGTTTATGTTTCAATAGA
1 TGTCTCAAGTGAGACAAAAC-TTTGTTTTAAGAGAAACGATCTCAAAGGTTTATGTTTCAAGAGA
*
1254302 AAT
65 AAC
* *
1254305 TGTCTCAAGTGAGACAAAA-TTTGTTTTTAGAGAAAACAATCTCAA
1 TGTCTCAAGTGAGACAAAACTTTGTTTTAAGAG-AAACGATCTCAA
1254350 GTGAGATCAA
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
66 11 0.11
67 29 0.28
68 62 0.61
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (67 bp):
TGTCTCAAGTGAGACAAAACTTTGTTTTAAGAGAAACGATCTCAAAGGTTTATGTTTCAAGAGAA
AC
Found at i:1254376 original size:36 final size:37
Alignment explanation
Indices: 1254307--1254420 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
1254297 ATAGAAATTG
**
1254307 TCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAACAA
1 TCTCAAGTGAGACAAAATTTGTTTCAAGAGAAAACAA
* ***
1254344 TCTCAAGTGAGATC-AATTTTGTTTCAAG-GAAAATTG
1 TCTCAAGTGAGA-CAAAATTTGTTTCAAGAGAAAACAA
* * * *
1254380 CCTCAAATGAGACGAAACTTTGTTTCAGGAG-AAACAA
1 TCTCAAGTGAGAC-AAAATTTGTTTCAAGAGAAAACAA
1254417 TCTC
1 TCTC
1254421 TAAGGTGACA
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
35 1 0.02
36 15 0.25
37 41 0.69
38 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (37 bp):
TCTCAAGTGAGACAAAATTTGTTTCAAGAGAAAACAA
Found at i:1259556 original size:9 final size:8
Alignment explanation
Indices: 1259537--1259601 Score: 51
Period size: 8 Copynumber: 8.1 Consensus size: 8
1259527 AAAGATAAAC
1259537 ATAAAAAA
1 ATAAAAAA
1259545 ATAAAAATA
1 ATAAAAA-A
*
1259554 ATAAAACA
1 ATAAAAAA
***
1259562 AGGTAAAA
1 ATAAAAAA
*
1259570 ATAATAAA
1 ATAAAAAA
*
1259578 ATTAAAAA
1 ATAAAAAA
*
1259586 TTAAAAAA
1 ATAAAAAA
1259594 A-AAAAAA
1 ATAAAAAA
1259601 A
1 A
1259602 CTATCGAATA
Statistics
Matches: 42, Mismatches: 14, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
7 7 0.17
8 28 0.67
9 7 0.17
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (8 bp):
ATAAAAAA
Found at i:1260155 original size:15 final size:14
Alignment explanation
Indices: 1260133--1260164 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1260123 TTTAAAGTGA
1260133 AAATAAATAAAATT
1 AAATAAATAAAATT
1260147 AAATAAAATAAAATT
1 AAAT-AAATAAAATT
1260162 AAA
1 AAA
1260165 AATAATTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATAAATAAAATT
Found at i:1260397 original size:33 final size:32
Alignment explanation
Indices: 1260328--1260429 Score: 98
Period size: 32 Copynumber: 3.2 Consensus size: 32
1260318 GGGTTGGTAA
* * * *
1260328 GTTAGTAAGAACAA-AACACAAAAGTTAGTAT
1 GTTAGTATGAACAATAAAAAAAAAGTTAGAAT
*
1260359 ATTAGTATGAACAAATAAAAAAAAAGTTAGAAT
1 GTTAGTATGAAC-AATAAAAAAAAAGTTAGAAT
* * * * *
1260392 GTTAGTTTGATCAATAAAATAAATGTTAGAAA
1 GTTAGTATGAACAATAAAAAAAAAGTTAGAAT
1260424 GTTAGT
1 GTTAGT
1260430 TCAAATAATA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
31 10 0.17
32 25 0.43
33 23 0.40
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (32 bp):
GTTAGTATGAACAATAAAAAAAAAGTTAGAAT
Found at i:1260473 original size:32 final size:32
Alignment explanation
Indices: 1260370--1260461 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 32
1260360 TTAGTATGAA
*
1260370 CAAATAA-AAAA-AAA-GTTAGAATGTTAGTT
1 CAAATAATAAAATAAATGTTAGAAAGTTAGTT
**
1260399 -TGATCAATAAAATAAATGTTAGAAAGTTAGTT
1 CAAAT-AATAAAATAAATGTTAGAAAGTTAGTT
* *
1260431 CAAATAATAAAGTAAATGTTAGAAGGTTAGT
1 CAAATAATAAAATAAATGTTAGAAAGTTAGT
1260462 GAGTAAAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 4 0.08
31 3 0.06
32 38 0.75
33 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.30
Consensus pattern (32 bp):
CAAATAATAAAATAAATGTTAGAAAGTTAGTT
Found at i:1261399 original size:65 final size:64
Alignment explanation
Indices: 1261250--1261408 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 64
1261240 TGGACTAAGA
* * * *
1261250 GTGCATCGATGTATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGAGTATCGATGCATGGCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGAGCATCGATGCATGGAT
* * *
1261313 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGATA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGAGCATCGATGCATG-GA
1261377 T
64 T
* *
1261378 GTGCATCGATGCATGAAATGCATTCAATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
1261409 CAATTTATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 27 0.32
64 24 0.29
65 33 0.39
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGAGCATCGATGCATGGAT
Found at i:1264159 original size:23 final size:22
Alignment explanation
Indices: 1264132--1264210 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
1264122 GCATGGCCTT
1264132 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
1264154 CGTGCATTGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1264176 GTGTATCGATGCACATTCAAACGG
1 GTGCATCGATGCACATTC-AA-GG
1264200 GTGCATCGATG
1 GTGCATCGATG
1264211 AACTGTTAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 14 0.33
22 2 0.05
23 16 0.37
24 11 0.26
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1264194 original size:21 final size:22
Alignment explanation
Indices: 1264132--1264194 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
1264122 GCATGGCCTT
1264132 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTC-AGGC
* * * *
1264155 GTGCATTGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGC
*
1264176 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
1264195 AACGGGTGCA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 15 0.47
22 2 0.06
23 15 0.47
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGC
Found at i:1270066 original size:65 final size:67
Alignment explanation
Indices: 1269919--1270077 Score: 186
Period size: 65 Copynumber: 2.4 Consensus size: 67
1269909 GCACTAAGAT
* * * * *
1269919 TGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCTTGAGTGTATCGGTGCATGGCTGG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCTGA
1269983 TA
66 TA
* *
1269985 --CATCAATGCATTAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGG-T-
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCATGGCTG
1270045 ATA
65 ATA
* *
1270048 TGCATCGATGAATGAAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
1270078 CAATTTATTC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 2 0.03
64 25 0.32
65 49 0.62
66 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (67 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCTGA
TA
Found at i:1276517 original size:23 final size:23
Alignment explanation
Indices: 1276475--1276536 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1276465 ATAGGGCAGA
* *
1276475 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
1276497 GGGAACTGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAG
1276520 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
1276537 AGGGGAATCG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.23
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:1280155 original size:3 final size:3
Alignment explanation
Indices: 1280140--1280239 Score: 146
Period size: 3 Copynumber: 33.0 Consensus size: 3
1280130 CCTGTAAATG
* *
1280140 TAA TAA AAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1280188 TAA CAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TTAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
1280234 TAA TAA
1 TAA TAA
1280240 GACCCGAGCA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1286360 original size:16 final size:17
Alignment explanation
Indices: 1286329--1286361 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1286319 AATAGAAAAC
*
1286329 CTACCCAGACATGATTT
1 CTACCCAGAAATGATTT
1286346 CTACCCA-AAATGATTT
1 CTACCCAGAAATGATTT
1286362 ATTTTTACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.30
Consensus pattern (17 bp):
CTACCCAGAAATGATTT
Found at i:1289646 original size:144 final size:143
Alignment explanation
Indices: 1289503--1290072 Score: 502
Period size: 144 Copynumber: 3.9 Consensus size: 143
1289493 AAGTGATCGG
* * * *
1289503 TTAAAAACGGTTAATAATGTAAACGGTAAAAAAATTTAGGCACTAACTATTATATTAAACTACGT
1 TTAAAAATGGTTAATAATGTAAACGGTAAAAAAA-ATAGG-ACTAACTATTACATTAAAATAC-T
* * * *
1289568 ACCGATTTTTTTTAACGTTACTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTAAATT
63 ACCGGTTTTTTTGAAGGTTACTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATT
*
1289633 AAAATAGCTATCGGTTTGT
128 AAAATAGCTATCAG---GT
* * * * *
1289652 TTAAAGATTGTTAATAATGCAAACGATAAAATAAAATA-GACGATACTTATTACATTAAAATATC
1 TTAAAAATGGTTAATAATGTAAACGGTAAAA-AAAATAGGACTA-AC-TATTACATTAAAATA-C
* ** *
1289716 TATCGGTTTGTTTTGAAGGTTGTTAATAATGTAAACTGTAAAAAAAAAATAGGCGCTACCTATTA
62 TACCGGTTT-TTTTGAAGGTTACTAATAATGTAAACGGT--AAAAAAAATAGGCGCTACCTATTA
* *
1289781 TATTAAAATACCTA-CAGGT
124 CATTAAAATAGCTATCAGGT
** * *
1289800 TT-----TTTTTAAGGTAATGTAAATGGTAAAAAAAAATAGGATCTATCTATTACATTAAAATAC
1 TTAAAAATGGTTAA--TAATGTAAACGGT-AAAAAAAATAGGA-CTAACTATTACATTAAAATA-
* * * *
1289860 CTACCGGTTTTTTTGAAGGTTATTAATAATGTAAACAGTAAAAAAAATAGGTGTTACCTATTACA
61 CTACCGGTTTTTTTGAAGGTTACTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACA
*
1289925 TTAAAATATG-TA-CCGGT
126 TTAAAATA-GCTATCAGGT
*** * *
1289942 TTTTTAA-GGTTCTTAATAATGTGAACGG--AAAAAAATAGG-CGATACCTATTACATTAAAATA
1 TTAAAAATGG---TTAATAATGTAAACGGTAAAAAAAATAGGAC--TAACTATTACATTAAAATA
*
1290003 CTTACCGGTTTTTTT-AAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTAC
61 C-TACCGGTTTTTTTGAAGGTTACTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTAC
1290067 ATTAAA
125 ATTAAA
1290073 CTACATACCG
Statistics
Matches: 353, Mismatches: 44, Indels: 54
0.78 0.10 0.12
Matches are distributed among these distances:
142 40 0.11
143 57 0.16
144 69 0.20
145 40 0.11
146 7 0.02
147 15 0.04
148 7 0.02
149 52 0.15
150 28 0.08
151 2 0.01
152 36 0.10
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (143 bp):
TTAAAAATGGTTAATAATGTAAACGGTAAAAAAAATAGGACTAACTATTACATTAAAATACTACC
GGTTTTTTTGAAGGTTACTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAA
ATAGCTATCAGGT
Found at i:1289667 original size:74 final size:73
Alignment explanation
Indices: 1289512--1290083 Score: 574
Period size: 74 Copynumber: 7.8 Consensus size: 73
1289502 GTTAAAAACG
* * * * * *
1289512 GTTAATAATGTAAACGGTAAAAAAATTTAGGCACTAACTATTATATTAAACTACGTACCGATTTT
1 GTTAATAATGTAAACGGTAAAAAAA-ATAGGCGCTACCTATTACATTAAAATAC-TACCGGTTTT
* *
1289577 TTTTAACGTT
64 TTTAAAGGTT
** * * *
1289587 ACTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTAAATTAAAATAGCTATCGGTTTGT
1 GTTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATA-CTACCGGTTTTT
*
1289652 TTAAAGATT
65 TTAAAGGTT
* * * * * *
1289661 GTTAATAATGCAAACGATAAAATAAAATAGACGATACTTATTACATTAAAATATCTATCGGTTTG
1 GTTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATA-CTACCGGTTT-
*
1289726 TTTTGAAGGTT
63 TTTTAAAGGTT
* * *
1289737 GTTAATAATGTAAACTGTAAAAAAAAAATAGGCGCTACCTATTATATTAAAATACCTACAGGTTT
1 GTTAATAATGTAAACGGT--AAAAAAAATAGGCGCTACCTATTACATTAAAATA-CTACCGGTTT
*
1289802 TTTTTAA-G--
63 TTTTAAAGGTT
* ** *
1289810 G----TAATGTAAATGGTAAAAAAAAATAGGATCTATCTATTACATTAAAATACCTACCGGTTTT
1 GTTAATAATGTAAACGGT-AAAAAAAATAGGCGCTACCTATTACATTAAAATA-CTACCGGTTTT
*
1289871 TTTGAAGGTT
64 TTTAAAGGTT
* * * * *
1289881 ATTAATAATGTAAACAGTAAAAAAAATAGGTGTTACCTATTACATTAAAATATGTACCGG-TTTT
1 GTTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATA-CTACCGGTTTTT
1289945 TT-AAGGTT
65 TTAAAGGTT
* * *
1289953 CTTAATAATGTGAACGG--AAAAAAATAGGCGATACCTATTACATTAAAATACTTACCGGTTTTT
1 GTTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATAC-TACCGGTTTTT
1290016 TT-AAGGTT
65 TTAAAGGTT
* *
1290024 GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAACTACATACCGG
1 GTTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATAC-TACCGG
1290084 ATATGTTGAA
Statistics
Matches: 416, Mismatches: 65, Indels: 34
0.81 0.13 0.07
Matches are distributed among these distances:
68 47 0.11
69 12 0.03
70 37 0.09
71 26 0.06
72 20 0.05
73 45 0.11
74 90 0.22
75 72 0.17
76 29 0.07
77 34 0.08
78 4 0.01
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (73 bp):
GTTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACTACCGGTTTTTT
TAAAGGTT
Found at i:1289854 original size:68 final size:69
Alignment explanation
Indices: 1289742--1290072 Score: 230
Period size: 68 Copynumber: 4.7 Consensus size: 69
1289732 AGGTTGTTAA
* * *
1289742 TAATGTAAACTGTAAAAAAAAAATAGGCGCTACCTATTATATTAAAATACCTACAGGTTTTTTTT
1 TAATGTAAACTGTAAAAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACAGGTTTTTTTG
1289807 AAGG
66 AAGG
* * *
1289811 TAATGTAAA-TGGT-AAAAAAAAATAGGATCTATCTATTACATTAAAATACCTACCGGTTTTTTT
1 TAATGTAAACT-GTAAAAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACAGGTTTTTTT
1289874 GAAGG
65 GAAGG
* * * * ** *
1289879 TTAT-TAATAATGTAAACAGTAAAAAAAATAGGTGTTACCTATTACATTAAAATATGTACCGG-T
1 TAATGTAA-ACTGT--A-A--AAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACAGGTT
1289942 TTTTT-AAGG
60 TTTTTGAAGG
** * * * * * *
1289951 TTCT-TAATAATGTGAACGGAAAAAAATAGGCGATACCTATTACATTAAAATACTTACCGGTTTT
1 TAATGTAA-ACTGT-AA--AAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACAGGTTTT
1290015 TTT-AAGG
62 TTTGAAGG
* *
1290022 T--TGCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAA
1 TAATG-TAA-ACTGT-AA----AAAAAAAATAGGAGCTACCTATTACATTAAA
1290073 CTACATACCG
Statistics
Matches: 221, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
67 3 0.01
68 56 0.25
69 13 0.06
70 38 0.17
71 23 0.10
72 17 0.08
73 35 0.16
74 36 0.16
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (69 bp):
TAATGTAAACTGTAAAAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACAGGTTTTTTTG
AAGG
Found at i:1289999 original size:70 final size:70
Alignment explanation
Indices: 1289843--1290072 Score: 302
Period size: 70 Copynumber: 3.2 Consensus size: 70
1289833 TAGGATCTAT
* * *
1289843 CTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTATTAATAATGTAAACAGTAAAAAAAAT
1 CTATTACATTAAAATA-TTACCGGTTTTTTT-AAGGTTCTTAATAATGTAAAC-G-GAAAAAAAT
* *
1289908 AGGTGTTAC
62 AGGCGATAC
*
1289917 CTATTACATTAAAATATGTACCGG-TTTTTTAAGGTTCTTAATAATGTGAACGGAAAAAAATAGG
1 CTATTACATTAAAATAT-TACCGGTTTTTTTAAGGTTCTTAATAATGTAAACGGAAAAAAATAGG
1289981 CGATAC
65 CGATAC
1289987 CTATTACATTAAAATACTTACCGGTTTTTTTAAGGTTGC-TAATAATGTAAACGGTAAAAAAAAT
1 CTATTACATTAAAATA-TTACCGGTTTTTTTAAGGTT-CTTAATAATGTAAACGG--AAAAAAAT
*
1290051 AGGCGCTAC
62 AGGCGATAC
1290060 CTATTACATTAAA
1 CTATTACATTAAA
1290073 CTACATACCG
Statistics
Matches: 142, Mismatches: 8, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
70 37 0.26
71 28 0.20
72 20 0.14
73 35 0.25
74 22 0.15
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (70 bp):
CTATTACATTAAAATATTACCGGTTTTTTTAAGGTTCTTAATAATGTAAACGGAAAAAAATAGGC
GATAC
Found at i:1290414 original size:111 final size:112
Alignment explanation
Indices: 1290163--1290401 Score: 417
Period size: 111 Copynumber: 2.1 Consensus size: 112
1290153 TAGTGTCTAT
*
1290163 AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAA
** * *
1290228 ACCAGTTTTTTTATAACAAAACTGGTAAAGAGCTACCGGATATGTTG
66 ACCAGTTTCATTATAACAAAACCGGTAAAGAGCTACCAGATATGTTG
1290275 AAAGTATCGATACTTTATAAAAATGTATCGATACACAACAATATAACAGGTAAAAA-ATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAA
*
1290339 ACCAGTTTCATTATAACAAGACCGGTAAAGAGCTACCAGATATGTTG
66 ACCAGTTTCATTATAACAAAACCGGTAAAGAGCTACCAGATATGTTG
1290386 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
1290402 TTGTACATGT
Statistics
Matches: 121, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
111 66 0.55
112 55 0.45
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (112 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACACAACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATAACAAAACCGGTAAAGAGCTACCAGATATGTTG
Found at i:1299300 original size:21 final size:23
Alignment explanation
Indices: 1299238--1299301 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
1299228 GCATGGCCTT
1299238 GTTCATCGATGCACATTCAAGGC
1 GTTCATCGATGCACATTCAAGGC
* * * * *
1299261 GTTCATTGGTGCACCTTCATGGT
1 GTTCATCGATGCACATTCAAGGC
1299284 G-T-ATCGATGCACATTCAA
1 GTTCATCGATGCACATTCAA
1299302 ACGGGTGCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 12 0.38
22 1 0.03
23 19 0.59
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (23 bp):
GTTCATCGATGCACATTCAAGGC
Found at i:1305247 original size:65 final size:67
Alignment explanation
Indices: 1305100--1305258 Score: 186
Period size: 65 Copynumber: 2.4 Consensus size: 67
1305090 GCACTAAGAT
* * * * *
1305100 TGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCTTGAGTGTATCGGTGCATGGCTGG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCTGA
1305164 TA
66 TA
* *
1305166 --CATCAATGCATTAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGG-T-
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCATGGCTG
1305226 ATA
65 ATA
* *
1305229 TGCATCGATGAATGAAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
1305259 CAATTTATTC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 2 0.03
64 25 0.32
65 49 0.62
66 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (67 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCTGA
TA
Found at i:1311690 original size:23 final size:23
Alignment explanation
Indices: 1311648--1311709 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1311638 ATAGGGCAGA
* *
1311648 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
1311670 GGGAACTGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAG
1311693 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
1311710 AGGGGAATCG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.23
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:1315337 original size:3 final size:3
Alignment explanation
Indices: 1315322--1315421 Score: 146
Period size: 3 Copynumber: 33.0 Consensus size: 3
1315312 CCTGTAAATG
* *
1315322 TAA TAA AAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1315370 TAA TAA TAA CAA TAA TAA TAA TAA TAA CAA TAA TAA TTAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
1315416 TAA TAA
1 TAA TAA
1315422 GACCCGAGCA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1320847 original size:19 final size:18
Alignment explanation
Indices: 1320809--1320861 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1320799 AAGATTTGAA
1320809 AAAAAAATGAGAATATATATT
1 AAAAAAATGA-AA-ATATA-T
**
1320830 GTAAAAATGAAAATATAT
1 AAAAAAATGAAAATATAT
1320848 AAAAAAATGAAAAT
1 AAAAAAATGAAAAT
1320862 GCAAATGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 13 0.46
19 5 0.18
20 2 0.07
21 8 0.29
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (18 bp):
AAAAAAATGAAAATATAT
Done.