Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002570.1 Hibiscus syriacus cultivar Beakdansim tig00005213_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: 126710
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:118 original size:18 final size:18
Alignment explanation
Indices: 95--141 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
85 ATTTATGAGA
95 GAATTGAAAT-ATGTGAAG
1 GAATTGAAATCA-GTGAAG
*
113 GAATTGGAATCAGTGAAG
1 GAATTGAAATCAGTGAAG
*
131 GAATTGGAATC
1 GAATTGAAATC
142 TGTCAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.30, T:0.26
Consensus pattern (18 bp):
GAATTGAAATCAGTGAAG
Found at i:152 original size:16 final size:17
Alignment explanation
Indices: 111--174 Score: 94
Period size: 16 Copynumber: 3.8 Consensus size: 17
101 AAATATGTGA
* *
111 AGGAATTGGAATCAGTGA
1 AGGAATTGGAATCTGT-C
129 AGGAATTGGAATCTGTC
1 AGGAATTGGAATCTGTC
146 A-GAATTGGAATCTGTC
1 AGGAATTGGAATCTGTC
162 AGGAATTGGAATC
1 AGGAATTGGAATC
175 CAATTCTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
16 16 0.37
17 12 0.28
18 15 0.35
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.27
Consensus pattern (17 bp):
AGGAATTGGAATCTGTC
Found at i:1052 original size:231 final size:227
Alignment explanation
Indices: 547--1073 Score: 631
Period size: 231 Copynumber: 2.3 Consensus size: 227
537 ACTATTTTTT
* *
547 CAATATATGAATTAGAAACTCGACCCGACACGACCAAAATAATAAAAAATATTTTTATTCAATAA
1 CAATATATGAATTAGAAACCCGACCCG--AC--CCGAAATAA-AAAAAATATTTTTATTCAATAA
* *
612 AAACATTGACTTAATTGAAAAAAAATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATA
61 AAACAGTGACTTAATTGAAAAAAAATATATAGAGGGGTATTATTGTAATCATTCCTAAATATATA
* * *
677 AGGTAAAATTATATATTTTGTTCGGGTCGGTCTGGTTTTTTTCACCCTAAACCCGAACCCGACCC
126 AAGTAAAATTATATATATTGTT--GG-CGGTCTGGTATTTTTCACCCTAAACCCGAACCCGACCC
* *
742 GACCCGAATATCACACTTAAAAAACTCAACTCGACCCGAA
188 GACCCAAATATCACACTTAAAAAACTCAACCCGACCCGAA
* **
782 CAA-A-ATAAAGTT--TCACCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAA
1 CAATATATGAA-TTAGAAACCCGACCCGACCCGAAAT-A-AAAAAAA-TATTTTTATTCAATAAA
*
843 AACAGTGACTTAATTGAAAAATATATATATATATATATAGGGGTATTATTGTAATCATTCCTAAA
62 AACAGTGACTTAATTG--AAA-A-A-A-A-ATATATAGAGGGGTATTATTGTAATCATTCCTAAA
*
908 TATATAAAGTAAAATTATATATATT-TT-G-GGTCTGGTATTTTTCACCCTAAACCCGAACTCGA
120 TATATAAAGTAAAATTATATATATTGTTGGCGGTCTGGTATTTTTCACCCTAAACCCGAACCCGA
* * *
970 CCCTACCCAAATATCACACTTAAAAAAC-CGACCCGA-CCGACC
185 CCCGACCCAAATATCACACTTAAAAAACTCAACCCGACCCGA-A
1012 CGAATATATGAATTAGAAACCCGACCCGACCCGAAATAAAAAAAAAATATTTTTATTCAATA
1 C-AATATATGAATTAGAAACCCGACCCGACCCGAAAT--AAAAAAAATATTTTTATTCAATA
1074 TATGAATAAG
Statistics
Matches: 254, Mismatches: 20, Indels: 38
0.81 0.06 0.12
Matches are distributed among these distances:
228 6 0.02
229 11 0.04
230 42 0.17
231 60 0.24
232 15 0.06
233 25 0.10
234 30 0.12
235 6 0.02
236 3 0.01
237 56 0.22
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (227 bp):
CAATATATGAATTAGAAACCCGACCCGACCCGAAATAAAAAAAATATTTTTATTCAATAAAAACA
GTGACTTAATTGAAAAAAAATATATAGAGGGGTATTATTGTAATCATTCCTAAATATATAAAGTA
AAATTATATATATTGTTGGCGGTCTGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCAAA
TATCACACTTAAAAAACTCAACCCGACCCGAA
Found at i:7952 original size:31 final size:32
Alignment explanation
Indices: 7907--7991 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 32
7897 ATTTACGCAG
*
7907 GATGGT-GAAGAGATTATAAGGAGAAAGAGAA
1 GATGGTGGAAGAGATTAGAAGGAGAAAGAGAA
* * *
7938 GATGGTGGAA-AGATTAGAATGAGGAAGATAA
1 GATGGTGGAAGAGATTAGAAGGAGAAAGAGAA
* * *
7969 GATGATGGAGAGAGTTTTGAAGG
1 GATGGTGGA-AGAGATTAGAAGG
7992 TGAGGGTGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
31 31 0.72
32 4 0.09
33 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (32 bp):
GATGGTGGAAGAGATTAGAAGGAGAAAGAGAA
Found at i:13298 original size:18 final size:19
Alignment explanation
Indices: 13264--13304 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
13254 TATTTCAAAG
*
13264 ATATGAAATATGGTTTG-A
1 ATATGAAATATGATTTGTA
13282 ATATGAAATTAT-ATTTGTA
1 ATATGAAA-TATGATTTGTA
13301 ATAT
1 ATAT
13305 TTTAATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (19 bp):
ATATGAAATATGATTTGTA
Found at i:14217 original size:2 final size:2
Alignment explanation
Indices: 14210--14253 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
14200 GATATGCATA
14210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14252 AT
1 AT
14254 TTTATGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20517 original size:18 final size:18
Alignment explanation
Indices: 20494--20533 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20484 AAAGGCGATG
*
20494 GCGGCATCATATATGACT
1 GCGGCATCATAAATGACT
*
20512 GCGGCATCATAAATGGCT
1 GCGGCATCATAAATGACT
20530 GCGG
1 GCGG
20534 TGGCTGCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (18 bp):
GCGGCATCATAAATGACT
Found at i:40046 original size:13 final size:13
Alignment explanation
Indices: 40030--40055 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40020 ATAATTATTT
40030 TTAAGATAACTCA
1 TTAAGATAACTCA
40043 TTAAGATAACTCA
1 TTAAGATAACTCA
40056 ATACTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTAAGATAACTCA
Found at i:40120 original size:32 final size:30
Alignment explanation
Indices: 40083--40147 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
40073 AATATAAAAT
*
40083 ATTTTATTAATATTTT-AATATATTAACCATAA
1 ATTTTATTAAT-TTTTAAATA-ATTAA-AATAA
*
40115 ATTTTATTTATTTTTAAATAATTAAAATAA
1 ATTTTATTAATTTTTAAATAATTAAAATAA
40145 ATT
1 ATT
40148 ATTAAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 7 0.23
31 9 0.30
32 14 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTTATTAATTTTTAAATAATTAAAATAA
Found at i:40145 original size:30 final size:32
Alignment explanation
Indices: 40083--40147 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
40073 AATATAAAAT
*
40083 ATTTTATTAATATTTTAATATATTAACCATAA
1 ATTTTATTAATATTTTAATATATTAACAATAA
*
40115 ATTTTATTTAT-TTTTAA-ATAATTAA-AATAA
1 ATTTTATTAATATTTTAATAT-ATTAACAATAA
40145 ATT
1 ATT
40148 ATTAAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 9 0.30
31 11 0.37
32 10 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTTTATTAATATTTTAATATATTAACAATAA
Found at i:40198 original size:39 final size:38
Alignment explanation
Indices: 40122--40199 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
40112 TAAATTTTAT
*
40122 TTATTTTTAAATAATTAAAATAAATTATTAAGTAATAAA
1 TTATTTTTAAAGAATTAAAATAAATTATTAAG-AATAAA
* *
40161 TTATTTTTAAAGATATTAATATTAAATTGTTAA-AATAAA
1 TTATTTTTAAAGA-ATTAA-AATAAATTATTAAGAATAAA
40200 ATATAAATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 18 0.53
40 5 0.15
41 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (38 bp):
TTATTTTTAAAGAATTAAAATAAATTATTAAGAATAAA
Found at i:40362 original size:20 final size:19
Alignment explanation
Indices: 40334--40375 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40324 AATTTTTTAC
*
40334 TGTAGATATTGTTTAGTATT
1 TGTAGATATT-TATAGTATT
*
40354 TGTATATATTTATAGTATT
1 TGTAGATATTTATAGTATT
40373 TGT
1 TGT
40376 GTTAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (19 bp):
TGTAGATATTTATAGTATT
Found at i:41015 original size:29 final size:29
Alignment explanation
Indices: 40969--41033 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
40959 CCATATGTCA
* * *
40969 CCATGCACGCCCGGCGTCTTTATAGGTCG
1 CCATGCAAGCCCGACGTCCTTATAGGTCG
40998 CCATGCAAGCCCGACGTCCTTATAGGTCG
1 CCATGCAAGCCCGACGTCCTTATAGGTCG
41027 CCATGCA
1 CCATGCA
41034 CGCCGGTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.18, C:0.35, G:0.25, T:0.22
Consensus pattern (29 bp):
CCATGCAAGCCCGACGTCCTTATAGGTCG
Found at i:41269 original size:29 final size:29
Alignment explanation
Indices: 41223--41299 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
41213 AGCAAAAACC
41223 GGCGTGCATGGCGACCTATAAGGACAACG
1 GGCGTGCATGGCGACCTATAAGGACAACG
* ** *
41252 GGCTTGCATGGCGACCTATAAGGACGCCT
1 GGCGTGCATGGCGACCTATAAGGACAACG
41281 GGCGTGCATGGCGACCTAT
1 GGCGTGCATGGCGACCTAT
41300 GGTGGTTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.18
Consensus pattern (29 bp):
GGCGTGCATGGCGACCTATAAGGACAACG
Found at i:44847 original size:14 final size:14
Alignment explanation
Indices: 44830--44877 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
44820 TTCGAAATTT
*
44830 AATTATGGAAAATA
1 AATTATGGAAAATG
*
44844 AATTACTGGAAATTG
1 AATTA-TGGAAAATG
*
44859 AATTAAGGAAAATG
1 AATTATGGAAAATG
44873 AATTA
1 AATTA
44878 CATTTTTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.52, C:0.02, G:0.17, T:0.29
Consensus pattern (14 bp):
AATTATGGAAAATG
Found at i:44868 original size:29 final size:29
Alignment explanation
Indices: 44823--44878 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
44813 TGATTTTTTC
* *
44823 GAAATTTAATTATGGAAAATAAATTACTG
1 GAAATTGAATTAAGGAAAATAAATTACTG
*
44852 GAAATTGAATTAAGGAAAATGAATTAC
1 GAAATTGAATTAAGGAAAATAAATTAC
44879 ATTTTTGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.16, T:0.30
Consensus pattern (29 bp):
GAAATTGAATTAAGGAAAATAAATTACTG
Found at i:45111 original size:26 final size:25
Alignment explanation
Indices: 45055--45111 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
45045 ATAAAAAATG
45055 ATTTTTAATAAAATGTATATTTAAA
1 ATTTTTAATAAAATGTATATTTAAA
* *
45080 A-ATTTAA-AATATGTGATAATTTAAA
1 ATTTTTAATAAAATGT-AT-ATTTAAA
45105 ATTTTTA
1 ATTTTTA
45112 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 6 0.23
24 7 0.27
25 9 0.35
26 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (25 bp):
ATTTTTAATAAAATGTATATTTAAA
Found at i:45116 original size:13 final size:13
Alignment explanation
Indices: 45098--45124 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
45088 ATATGTGATA
45098 ATTTAAAATTTTT
1 ATTTAAAATTTTT
45111 ATTTAAAATTTTT
1 ATTTAAAATTTTT
45124 A
1 A
45125 AAGAATAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTAAAATTTTT
Found at i:46476 original size:17 final size:17
Alignment explanation
Indices: 46454--46489 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
46444 TGCATTCAGA
46454 TTTGTTCGTATATTTAT
1 TTTGTTCGTATATTTAT
*
46471 TTTGTTCGTATCTTTAT
1 TTTGTTCGTATATTTAT
46488 TT
1 TT
46490 AAAATTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.08, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTGTTCGTATATTTAT
Found at i:46810 original size:5 final size:5
Alignment explanation
Indices: 46800--46843 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
46790 GTGATAAATT
46800 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
46844 GTTTTAGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAC
Found at i:46887 original size:22 final size:23
Alignment explanation
Indices: 46856--46903 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
46846 TTTAGACTAT
*
46856 ATGCTTTTAAAAT-TCATATTTC
1 ATGCTATTAAAATATCATATTTC
46878 ATGCTATTAAAATAATCATATTTC
1 ATGCTATTAAAAT-ATCATATTTC
46902 AT
1 AT
46904 AACCGATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.52
24 11 0.48
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (23 bp):
ATGCTATTAAAATATCATATTTC
Found at i:48682 original size:33 final size:32
Alignment explanation
Indices: 48600--48690 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 32
48590 TTAAAAACCA
* * *
48600 ATTTAAAATAATTATTAAATTTTTATCGAACT
1 ATTTAAAATAATCATTAAATTTTTATCAAAAT
* * *
48632 ATTTAAAAATGACCATTACATTTTTATCAAAAT
1 ATTT-AAAATAATCATTAAATTTTTATCAAAAT
*
48665 ATTATAAAATAATCATTAAACTTTTA
1 ATT-TAAAATAATCATTAAATTTTTA
48691 CACTTATTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
32 4 0.09
33 42 0.89
34 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (32 bp):
ATTTAAAATAATCATTAAATTTTTATCAAAAT
Found at i:53772 original size:42 final size:41
Alignment explanation
Indices: 53698--53796 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 41
53688 TCTTATGGAG
* * *
53698 GACCCGAAGGATTTATCATCTTGCTCTAAAGGCTTACAGAT
1 GACCCGGAGGATTTATCATCATGCTCGAAAGGCTTACAGAT
* *
53739 GACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGAT
1 GACCCGGAGGATTT-ATCATCATGCTCGAAAGGCTTACAGAT
* *
53781 GGCCCGGAGGACTTAT
1 GACCCGGAGGATTTAT
53797 AAATTGGGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 15 0.30
42 35 0.70
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (41 bp):
GACCCGGAGGATTTATCATCATGCTCGAAAGGCTTACAGAT
Found at i:54001 original size:42 final size:41
Alignment explanation
Indices: 53909--54009 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
53899 AGGTCTTATG
* * * *
53909 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGGAGGACTTAGCATCATGCTCTAAAGACTTACA
* * *
53950 GATGACCCGGAGGATTTAAGCATCATGCT-TGAAAGACTTACT
1 GATGGCCCGGAGGACTT-AGCATCATGCTCT-AAAGACTTACA
53992 GATGGCCCGGAGGACTTA
1 GATGGCCCGGAGGACTTA
54010 TAAATTGGGA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (41 bp):
GATGGCCCGGAGGACTTAGCATCATGCTCTAAAGACTTACA
Found at i:54039 original size:214 final size:214
Alignment explanation
Indices: 53669--54853 Score: 2113
Period size: 214 Copynumber: 5.5 Consensus size: 214
53659 ATCCTGGTGA
* * *
53669 AAAACATCCTGCCCGAATGTCTTATGGA-GGACCCGAAGGATTTATCATCTTGCTCTAAAGGCTT
1 AAAACATCCTACCCGAAGGTCTTATGGATGG-CCCGAAGGACTTATCATCTTGCTCTAAAGGCTT
* * *
53733 ACAGATGACCCGGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATA
65 ACAGATGACCCGGAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATA
* *
53798 AATTGGGAAATTTTGAAACTTGCATTCTTTGTTTTCAAAAAATCCATCTTCTTAAAACATCATTT
130 AATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTT
53863 TTCTTTTTCAAATTCATTTG
195 TTCTTTTTCAAATTCATTTG
53883 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
*
53948 CAGATGACCCGGAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
54013 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
*
54078 TATTTTTCAAATTCATTTG
196 TCTTTTTCAAATTCATTTG
* *
54097 AAAACATCCTACCCGTAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
*
54162 CAGATGACCCGGAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
54227 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
54292 TCTTTTTCAAATTCATTTG
196 TCTTTTTCAAATTCATTTG
* *
54311 AAAACATCCTACCCGTAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * * *
54376 CAGATGACCCAGAGGATTTAATCATCATGCTCGGAAGGCTTACTGATGGCCCGGAGGACTTATAA
66 CAGATGACCCGGAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
* *
54441 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAATATCATTTC
131 ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
*
54506 TCTTTTTCAAATTCATTTA
196 TCTTTTTCAAATTCATTTG
54525 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* *
54590 CAGATGACCCGGAGGATTTAATCATCATGC-TCAGAAGACTTACTGATGGCCAGGAGGACTTATA
66 CAGATGACCCGGAGGATTTAATCATCATGCTTGA-AAGACTTACTGATGGCCCGGAGGACTTATA
54654 AATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTT
130 AATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTT
*
54719 TTCTTTTTCAAATTCATTTA
195 TTCTTTTTCAAATTCATTTG
54739 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
54804 CAGATGACCCGGAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGC
66 CAGATGACCCGGAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGC
54854 TTTACTTCAT
Statistics
Matches: 936, Mismatches: 32, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
214 932 1.00
215 4 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (214 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
CAGATGACCCGGAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCGGAGGACTTATAA
ATTGGGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAAATCCATCTTCTTAAAACATCATTTT
TCTTTTTCAAATTCATTTG
Found at i:54407 original size:42 final size:40
Alignment explanation
Indices: 54337--54438 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 40
54327 AGGTCTTATG
* *
54337 GATGACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGACCCG-AGGACTTATCATCATGCTCGAAAGGCTTACA
* * *
54378 GATGACCCAGAGGATTTAATCATCATGCTCGGAAGGCTTACT
1 GATGACCC-GAGGACTT-ATCATCATGCTCGAAAGGCTTACA
*
54420 GATGGCCCGGAGGACTTAT
1 GATGACCC-GAGGACTTAT
54439 AAATTGGGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (40 bp):
GATGACCCGAGGACTTATCATCATGCTCGAAAGGCTTACA
Found at i:54632 original size:42 final size:41
Alignment explanation
Indices: 54551--54652 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
54541 AGGTCTTATG
* * *
54551 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGGAGGACTTATCATCATGCTCTAAAGACTTACA
* * *
54592 GATGACCCGGAGGATTTAATCATCATGCTC-AGAAGACTTACT
1 GATGGCCCGGAGGACTT-ATCATCATGCTCTA-AAGACTTACA
*
54634 GATGGCCAGGAGGACTTAT
1 GATGGCCCGGAGGACTTAT
54653 AAATTGGGAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
41 17 0.34
42 33 0.66
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (41 bp):
GATGGCCCGGAGGACTTATCATCATGCTCTAAAGACTTACA
Found at i:54846 original size:42 final size:41
Alignment explanation
Indices: 54765--54851 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 41
54755 AGGTCTTATG
* * *
54765 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGACCCGAAGGACTTATCATCATGCTCTAAAGACTTACA
* * *
54806 GATGACCCGGAGGATTTAATCATCATGCT-TGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTCT-AAAGACTTACA
54848 GATG
1 GATG
54852 GCTTTACTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 15 0.39
42 23 0.61
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCTAAAGACTTACA
Found at i:57029 original size:5 final size:5
Alignment explanation
Indices: 57019--57063 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
57009 ATTTTCAATT
57019 TTTTC TTTTC TTTTC TTTCTTC TTTTC TTTTCC TTTTC TCTTTC T
1 TTTTC TTTTC TTTTC -TT-TTC TTTTC TTTT-C TTTTC T-TTTC T
57064 ACATTTCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 19 0.53
6 14 0.39
7 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:57041 original size:12 final size:11
Alignment explanation
Indices: 57019--57063 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
57009 ATTTTCAATT
57019 TTTTC-TTTTC
1 TTTTCTTTTTC
57029 TTTTCTTTCTTC
1 TTTTCTTT-TTC
*
57041 TTTTCTTTTCC
1 TTTTCTTTTTC
*
57052 TTTTCTCTTTC
1 TTTTCTTTTTC
57063 T
1 T
57064 ACATTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 5 0.17
11 14 0.47
12 11 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:57043 original size:17 final size:16
Alignment explanation
Indices: 57019--57063 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
57009 ATTTTCAATT
*
57019 TTTTCTTTTCTTTTCT
1 TTTTCTTTTCTTTTCC
57035 TTCTTCTTTTCTTTTCC
1 TT-TTCTTTTCTTTTCC
57052 TTTTCTCTTTCT
1 TTTTCT-TTTCT
57064 ACATTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTCTTTTCC
Found at i:57063 original size:22 final size:22
Alignment explanation
Indices: 57019--57063 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
57009 ATTTTCAATT
*
57019 TTTTCTTTTCTTTTCTTTCTTC
1 TTTTCTTTTCTTTTCTCTCTTC
57041 TTTTCTTTTCCTTTTCTCT-TTC
1 TTTTCTTTT-CTTTTCTCTCTTC
57063 T
1 T
57064 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTCTTTTCTCTCTTC
Found at i:57070 original size:25 final size:23
Alignment explanation
Indices: 57020--57083 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
57010 TTTTCAATTT
* *
57020 TTTCTTTTCTTT-TCTTTCTTCT
1 TTTCTTTTCTTTCTCTTTCTACA
57042 TTTCTTTTCCTTTTCTCTTTCTACA
1 TTTCTTTT-C-TTTCTCTTTCTACA
*
57067 TTTCTCTTCTTTCTCTT
1 TTTCTTTTCTTTCTCTT
57084 CATAATGACA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.22
23 9 0.25
24 4 0.11
25 15 0.42
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTCTTTTCTTTCTCTTTCTACA
Found at i:59679 original size:21 final size:21
Alignment explanation
Indices: 59635--59771 Score: 161
Period size: 21 Copynumber: 6.6 Consensus size: 21
59625 CATGCGAAGT
*
59635 GGTCTTCTCGTCTTTACG-AA
1 GGTCTTCTCGTCTTTATGAAA
59655 GGTCTTCTCGTCTTTATGAAA
1 GGTCTTCTCGTCTTTATGAAA
59676 GGTCTTCTCGTCTTTATGAAA
1 GGTCTTCTCGTCTTTATGAAA
* * *
59697 GGTCTTCTCGTATTGATGAAT
1 GGTCTTCTCGTCTTTATGAAA
* * *
59718 GGCCTTCTCGTCTTGATGAAT
1 GGTCTTCTCGTCTTTATGAAA
* *
59739 GGCCTTCTCGT-TTTGATGAAT
1 GGTCTTCTCGTCTTT-ATGAAA
*
59760 GGCCTTCTCGTC
1 GGTCTTCTCGTC
59772 CTTGGTACGA
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.18
21 88 0.82
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (21 bp):
GGTCTTCTCGTCTTTATGAAA
Found at i:59716 original size:42 final size:42
Alignment explanation
Indices: 59638--59771 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 42
59628 GCGAAGTGGT
* * * * *
59638 CTTCTCGTCTTTACG-AAGGTCTTCTCGTCTTTATGAAAGGT
1 CTTCTCGTCTTTATGAAAGGTCTTCTCGTATTGATGAATGGC
59679 CTTCTCGTCTTTATGAAAGGTCTTCTCGTATTGATGAATGGC
1 CTTCTCGTCTTTATGAAAGGTCTTCTCGTATTGATGAATGGC
* * * *
59721 CTTCTCGTCTTGATGAATGGCCTTCTCGTTTTGATGAATGGC
1 CTTCTCGTCTTTATGAAAGGTCTTCTCGTATTGATGAATGGC
59763 CTTCTCGTC
1 CTTCTCGTC
59772 CTTGGTACGA
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 14 0.17
42 69 0.83
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (42 bp):
CTTCTCGTCTTTATGAAAGGTCTTCTCGTATTGATGAATGGC
Found at i:65791 original size:29 final size:29
Alignment explanation
Indices: 65749--65807 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
65739 CACACTAATC
*
65749 AACAATGGCCTTTAGAGTACAAATTAAGG
1 AACAATGACCTTTAGAGTACAAATTAAGG
65778 AACAATGACCTTTAGAGTACAAATTAAGG
1 AACAATGACCTTTAGAGTACAAATTAAGG
65807 A
1 A
65808 CCTCAGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.24
Consensus pattern (29 bp):
AACAATGACCTTTAGAGTACAAATTAAGG
Found at i:67799 original size:79 final size:79
Alignment explanation
Indices: 67667--67967 Score: 368
Period size: 79 Copynumber: 3.8 Consensus size: 79
67657 TAATTATAAC
* * * * * ** * *
67667 ATTCTTTTATGTTGAAAATGCACCCATATGCATTTCAACTTTGTCATCATTTCATGCCAATAATG
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
67732 CACCCATATGCATT
66 CACCCATATGCATT
* * *
67746 ATTCTTTTATGCCGATAATGTACCCATATACATTTCAGCTAAGGCACCCTTTCATGTCAATAATG
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
67811 CACCCATATGCATT
66 CACCCATATGCATT
* * * *** * ** *
67825 ATTCTTTTATGTTGAAAATGCACCCATATGTGTTTCAACTTTGGCATCCTTTCATGCCAATAATA
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
67890 CACCCATATGCATT
66 CACCCATATGCATT
* * * *
67904 ATTCTTTTACGTCGATAATGTACTCATATACATTTCAGATAAGGCATCCTTCCATGCCAATAAT
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAAT
67968 ATACACACAT
Statistics
Matches: 184, Mismatches: 38, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
79 184 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (79 bp):
ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
CACCCATATGCATT
Found at i:67965 original size:158 final size:158
Alignment explanation
Indices: 67667--67967 Score: 494
Period size: 158 Copynumber: 1.9 Consensus size: 158
67657 TAATTATAAC
* *
67667 ATTCTTTTATGTTGAAAATGCACCCATATGCATTTCAACTTTGTCATCATTTCATGCCAATAATG
1 ATTCTTTTATGTTGAAAATGCACCCATATGCATTTCAACTTTGGCATCATTTCATGCCAATAATA
* *
67732 CACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATACATTTCAGCTAAGGCACCCTT
66 CACCCATATGCATTATTCTTTTACGCCGATAATGTACCCATATACATTTCAGATAAGGCACCCTT
* *
67797 TCATGTCAATAATGCACCCATATGCATT
131 CCATGCCAATAATGCACCCATATGCATT
** *
67825 ATTCTTTTATGTTGAAAATGCACCCATATGTGTTTCAACTTTGGCATCCTTTCATGCCAATAATA
1 ATTCTTTTATGTTGAAAATGCACCCATATGCATTTCAACTTTGGCATCATTTCATGCCAATAATA
* * *
67890 CACCCATATGCATTATTCTTTTACGTCGATAATGTACTCATATACATTTCAGATAAGGCATCCTT
66 CACCCATATGCATTATTCTTTTACGCCGATAATGTACCCATATACATTTCAGATAAGGCACCCTT
67955 CCATGCCAATAAT
131 CCATGCCAATAAT
67968 ATACACACAT
Statistics
Matches: 131, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
158 131 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (158 bp):
ATTCTTTTATGTTGAAAATGCACCCATATGCATTTCAACTTTGGCATCATTTCATGCCAATAATA
CACCCATATGCATTATTCTTTTACGCCGATAATGTACCCATATACATTTCAGATAAGGCACCCTT
CCATGCCAATAATGCACCCATATGCATT
Found at i:75396 original size:3 final size:3
Alignment explanation
Indices: 75388--75413 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
75378 TCTACGTATA
75388 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
75414 AAACAGTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:90933 original size:120 final size:120
Alignment explanation
Indices: 90708--91658 Score: 1083
Period size: 120 Copynumber: 8.0 Consensus size: 120
90698 ATTCAAGTGA
* *
90708 TCCCAGAAAACTACCTCCTGAACTTGTTCAGCAGAAGTT-TGGTTGGTATCTTCTAAGTGCATTG
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTAT-GTTGGTATCTTCTAAGTGCATTG
* * * * *
90772 AACTCTTATTCTCTTGAGTAAGACTTGTGTCTTCTTTAACTTCCATTTTGTCACTT
65 AACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
* * * *
90828 TCCTAGAAAACTACCTCCTGAACTGCTCCAGCAGCAGTTATGTTGGTATCTTCTGAGTGCATTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
* *
90893 ACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCATCAACTTCAATTTTGTCACTT
66 ACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
* * * * * * *
90948 TCCAAGGAAACTACCTCTTGAACTGTTTCAGCAGCCGTTATGTTGGTATCTTCTAAGTGAAATGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
* * * * * *
91013 ACACCGATCCTCTT----TATA--TGTGTCCTCTTTAACTTCCATTTTGTTACTT
66 ACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
* ** * * * *
91062 TCCCTGAAAACTGTCTCCTGAACTGGTTCAG-AGGCAGTTATGTCGGTATGTTCTAATTGCAGTG
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCA-GCAGTTATGTTGGTATCTTCTAAGTGCATTG
* * * *
91126 AACTCTGATCCTCTTGAACAAGACCTGTGTCCTCTTTATCTTCAATTTTATCACTT
65 AACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
* * * * *
91182 TCCCAGATAACTACCTCCTGAACTGGTTCAGCAGCAGTTACGTTAGTATCTTCCAAATGCATTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
* * * *
91247 ACTTTGATCCTCTTGAGCAAGACTCGTATCCTCATGT-ACTTCAATTTTGTCACTT
66 ACTCTGATCCTCTTGAGCAAGACTTGTGTCCTC-TTTAACTTCAATTTTGTCACTT
* * * *
91302 TCCCAGAAAACTACCTCCTGAACTGGTTCAGAAGAAGTTATGTTGGTATTTTCTGAGTGCATTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
* * * * * **
91367 ACCCTGATCCCCTTGAGCAAAACCTGTGTCTTCTTTAACTTCCGTTTTGTCACTT
66 ACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
** * * * * * ** * *
91422 TCCCAGGTAACTACATACTGAACTGGTACAACAGCAGTTACGTTGGTATCTTCTGTGTGAACTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
** ** *
91487 ACTCTGATCCTCTTGAGCAAGACCCGTGTCCTCTTTAACTTCCGTTTCGTCACTT
66 ACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
* * * *
91542 TCCCAGATAACTACATCCTGAACTGGTTCAGCAGCAGTTATGTCGGTATCATCTAAGTGCATTGA
1 TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
** * *
91607 ACTCTGAAACTGTTGAGCAAGACTTGTGTCCTCTTGAACTTCAATTTTGTCA
66 ACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCA
91659 AGTCTGCAGT
Statistics
Matches: 691, Mismatches: 129, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
113 1 0.00
114 89 0.13
116 2 0.00
118 2 0.00
119 2 0.00
120 591 0.86
121 4 0.01
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (120 bp):
TCCCAGAAAACTACCTCCTGAACTGGTTCAGCAGCAGTTATGTTGGTATCTTCTAAGTGCATTGA
ACTCTGATCCTCTTGAGCAAGACTTGTGTCCTCTTTAACTTCAATTTTGTCACTT
Found at i:99223 original size:18 final size:18
Alignment explanation
Indices: 99200--99238 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
99190 ATGTAGTCAC
99200 CCAACTATTACTTTCATT
1 CCAACTATTACTTTCATT
99218 CCAACTATTACTTTCATT
1 CCAACTATTACTTTCATT
99236 CCA
1 CCA
99239 TTCTAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (18 bp):
CCAACTATTACTTTCATT
Found at i:108642 original size:31 final size:30
Alignment explanation
Indices: 108607--108681 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
108597 AAACAAAACG
108607 CTCTCACCCCGTAAAA-ATTCACACAACAATC
1 CTCTCA-CCCGTAAAACA-TCACACAACAATC
* *
108638 CTCTCAACCG-AAAACATCACACAATAATC
1 CTCTCACCCGTAAAACATCACACAACAATC
108667 CTCTCAACCCGTAAA
1 CTCTC-ACCCGTAAA
108682 TATCACCCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 21 0.55
30 8 0.21
31 9 0.24
ACGTcount: A:0.40, C:0.37, G:0.04, T:0.19
Consensus pattern (30 bp):
CTCTCACCCGTAAAACATCACACAACAATC
Found at i:112529 original size:3 final size:3
Alignment explanation
Indices: 112523--112548 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
112513 ATCACCATCA
112523 TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TC
112549 AGGAGCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:114610 original size:29 final size:31
Alignment explanation
Indices: 114578--114635 Score: 102
Period size: 29 Copynumber: 1.9 Consensus size: 31
114568 AAAAATTAAA
114578 TAAATAAAATACTAA-AAAA-ATTAAATAAT
1 TAAATAAAATACTAACAAAATATTAAATAAT
114607 TAAATAAAATACTAACAAAATATTAAATA
1 TAAATAAAATACTAACAAAATATTAAATA
114636 GAATAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 15 0.56
30 4 0.15
31 8 0.30
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (31 bp):
TAAATAAAATACTAACAAAATATTAAATAAT
Found at i:117683 original size:32 final size:33
Alignment explanation
Indices: 117643--117710 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
117633 ATATACTTCA
* *
117643 CACAACTACC-CTTCTGACAAGAA-TTTATTTCT
1 CACAACTACCTC-TATGACAAGAATTTTAGTTCT
117675 CACAACTACCTCTATGACAAGAATTTTAGTTCT
1 CACAACTACCTCTATGACAAGAATTTTAGTTCT
117708 CAC
1 CAC
117711 GGGTATGTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.32
Consensus pattern (33 bp):
CACAACTACCTCTATGACAAGAATTTTAGTTCT
Found at i:118504 original size:43 final size:41
Alignment explanation
Indices: 118451--118532 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
118441 GTAGCTGATG
* * *
118451 ATATTCTAAATAAATACCGATATATTTATAAGTACTCTATAAA
1 ATATTATAAATAAATA-CGAAATA-TTACAAGTACTCTATAAA
* *
118494 ATATTATAAATGAATACTAAATATTACAAGTACTCTATA
1 ATATTATAAATAAATACGAAATATTACAAGTACTCTATA
118533 TTATTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 15 0.44
42 5 0.15
43 14 0.41
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (41 bp):
ATATTATAAATAAATACGAAATATTACAAGTACTCTATAAA
Found at i:119169 original size:25 final size:23
Alignment explanation
Indices: 119139--119195 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
119129 TATAATACTC
119139 TTAATATAAGACAATTTAGAACATA
1 TTAATATAA-A-AATTTAGAACATA
* *
119164 TTAATATTTAAAATTTTAGAATATA
1 TTAATA--TAAAAATTTAGAACATA
119189 TTAATAT
1 TTAATAT
119196 TTAAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 1 0.04
25 23 0.82
26 1 0.04
27 3 0.11
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (23 bp):
TTAATATAAAAATTTAGAACATA
Found at i:119196 original size:25 final size:25
Alignment explanation
Indices: 119153--119200 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
119143 TATAAGACAA
119153 TTTAGAACATATTAATATTTAAAAT
1 TTTAGAACATATTAATATTTAAAAT
*
119178 TTTAGAATATATTAATATTTAAA
1 TTTAGAACATATTAATATTTAAA
119201 TTAATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TTTAGAACATATTAATATTTAAAAT
Found at i:119205 original size:12 final size:13
Alignment explanation
Indices: 119186--119216 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
119176 ATTTTAGAAT
119186 ATATTAATATTTA
1 ATATTAATATTTA
119199 A-ATTAATATTTA
1 ATATTAATATTTA
119211 ATATTA
1 ATATTA
119217 TTAATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTAATATTTA
Found at i:119221 original size:16 final size:16
Alignment explanation
Indices: 119162--119250 Score: 56
Period size: 16 Copynumber: 5.1 Consensus size: 16
119152 ATTTAGAACA
*
119162 TATTAATATTTAAAAT
1 TATTAATATTTAATAT
119178 T-TTAGAATATATTAATATT
1 TATT--AATAT-TTAATA-T
119197 TAAATTAATATTTAATAT
1 T--ATTAATATTTAATAT
*
119215 TATTAAT-TATTATTAT
1 TATTAATAT-TTAATAT
119231 TATTATATTATTTAGATAT
1 TATTA-A-TATTTA-ATAT
119250 T
1 T
119251 TCTATTTATA
Statistics
Matches: 58, Mismatches: 3, Indels: 21
0.71 0.04 0.26
Matches are distributed among these distances:
15 3 0.05
16 18 0.31
17 6 0.10
18 11 0.19
19 13 0.22
20 5 0.09
22 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATTAATATTTAATAT
Found at i:124007 original size:2 final size:2
Alignment explanation
Indices: 124000--124033 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
123990 GATAAAACCA
124000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124034 TAAATATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.