Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008247.1 Hibiscus syriacus cultivar Beakdansim tig00110897_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: 310145
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
File 2 of 2
Found at i:157698 original size:24 final size:24
Alignment explanation
Indices: 157688--157805 Score: 123
Period size: 24 Copynumber: 4.9 Consensus size: 24
157678 CATAATTCAC
*
157688 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAA
*
157712 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAAAATCCAA
* *
157736 GTCAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCATATCAAAATCCA-A
* * *
157761 -TC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAAAATCCAA
*
157784 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCATATCA-AAATC
157806 AAATCGAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
23 2 0.02
24 75 0.89
25 7 0.08
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCATATCAAAATCCAA
Found at i:157757 original size:48 final size:48
Alignment explanation
Indices: 157688--157802 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 48
157678 CATAATTCAC
* * * *
157688 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGATCAGA-TATCAGATCAGAATCCAA
* *
157736 GTCAAGTATCAGATCAGAATCCATATCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGATATCAGATCAGAATCCAA
157784 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
157803 ATCAAATCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGATATCAGATCAGAATCCAA
Found at i:157765 original size:12 final size:12
Alignment explanation
Indices: 157721--157783 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
157711 GGTCAAGTAT
157721 CATATCAGAATC
1 CATATCAGAATC
*
157733 CA-AGTCAAGTAT-
1 CATA-TC-AGAATC
*
157745 CAGATCAGAATC
1 CATATCAGAATC
157757 CATATCAGATAT-
1 CATATCAGA-ATC
*
157769 CAGATCAGAATC
1 CATATCAGAATC
157781 CAT
1 CAT
157784 GTCAAGTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (12 bp):
CATATCAGAATC
Found at i:157819 original size:48 final size:48
Alignment explanation
Indices: 157664--157819 Score: 138
Period size: 48 Copynumber: 3.2 Consensus size: 48
157654 AAACGGATAT
* * * * * * * *
157664 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAG
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * * *
157712 GTCA-AGTATCATATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAGA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* *
157760 ATCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAA
157808 ATC-GAAAATCAG
1 ATCAG-AAATCAG
157820 GTAAAATATT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
47 2 0.02
48 84 0.93
49 4 0.04
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:160356 original size:13 final size:13
Alignment explanation
Indices: 160338--160413 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
160328 CAACGGTTAA
160338 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
160351 CGGGTCAATGGGT
1 CGGGTCAACGGGT
160364 CGGGTCAACAGGTCGGGT
1 CGGGTC-A-A---CGGGT
*
160382 TGGGTCAACGGGT
1 CGGGTCAACGGGT
*
160395 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
160408 CAGGTC
1 CGGGTC
160414 GGGTCATGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 38 0.75
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 9 0.18
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:160381 original size:18 final size:18
Alignment explanation
Indices: 160360--160399 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
160350 TCGGGTCAAT
160360 GGGTCGGGTCAACAGGTC
1 GGGTCGGGTCAACAGGTC
* *
160378 GGGTTGGGTCAACGGGTC
1 GGGTCGGGTCAACAGGTC
160396 GGGT
1 GGGT
160400 AAACGGGTCA
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:0.12, C:0.17, G:0.50, T:0.20
Consensus pattern (18 bp):
GGGTCGGGTCAACAGGTC
Found at i:160387 original size:31 final size:31
Alignment explanation
Indices: 160346--160419 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
160336 AACGGGTCAA
* *
160346 CGGGTCGGGTCAATGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACGGGTCGGGTAAACAGGT
* *
160377 CGGGTTGGGTCAACGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTAAACAGGT
*
160408 CAGGTCGGGTCA
1 CGGGTCGGGTCA
160420 TGACCAGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.16, C:0.19, G:0.46, T:0.19
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTAAACAGGT
Found at i:160406 original size:26 final size:26
Alignment explanation
Indices: 160338--160413 Score: 71
Period size: 31 Copynumber: 2.7 Consensus size: 26
160328 CAACGGTTAA
* *
160338 CGGGTCAACGGGTCGGGTCAATGGGT
1 CGGGTAAACGGGTCGGGTCAACGGGT
*
160364 CGGGTCAACAGGTCGGGTTGGGTCAACGGGT
1 CGGGT-AA-A---CGGGTCGGGTCAACGGGT
*
160395 CGGGTAAACGGGTCAGGTC
1 CGGGTAAACGGGTCGGGTC
160414 GGGTCATGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 14 0.35
27 1 0.03
28 1 0.03
29 1 0.03
30 2 0.05
31 21 0.52
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (26 bp):
CGGGTAAACGGGTCGGGTCAACGGGT
Found at i:162526 original size:24 final size:24
Alignment explanation
Indices: 162516--162627 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
162506 CATAATTCAC
* * * *
162516 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTATCAGATCAGAATCCAT
* * *
162540 GTAAAGTATCAGGTCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
162564 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
162588 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
162612 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
162628 AAAATCAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.03
24 73 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:162647 original size:48 final size:48
Alignment explanation
Indices: 162547--162647 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 48
162537 TAGGTAAAGT
* * ** *
162547 ATCAGGTCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAAATCAGAA
*
162595 ATCAGATCAGAATCCATGTCAAGTATCAGATCAAAAAT-CAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATC-AAAATCCAAATCAG-AA
162643 ATCAG
1 ATCAG
162648 GTAAAATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 1 0.02
48 40 0.89
49 4 0.09
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAAATCAGAA
Found at i:165161 original size:13 final size:13
Alignment explanation
Indices: 165143--165173 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
165133 GCCGGTCAAG
*
165143 GGGTCAACGGGTC
1 GGGTCAACAGGTC
165156 GGGTCAACAGGTC
1 GGGTCAACAGGTC
165169 GGGTC
1 GGGTC
165174 GGGTAAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.23, G:0.45, T:0.16
Consensus pattern (13 bp):
GGGTCAACAGGTC
Found at i:165173 original size:18 final size:18
Alignment explanation
Indices: 165150--165197 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
165140 AAGGGGTCAA
165150 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
* *
165168 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACAGGT
165186 CGGGTCGGGTCA
1 CGGGTCGGGTCA
165198 TGACCGGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:171162 original size:33 final size:33
Alignment explanation
Indices: 171125--171203 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
171115 AGTTGGCAAG
171125 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
171158 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
171191 TTGGGAATTTCAT
1 TTGGAAATTTCAT
171204 ATTTGGTGGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.41
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
Found at i:171212 original size:30 final size:32
Alignment explanation
Indices: 171125--171219 Score: 122
Period size: 33 Copynumber: 3.0 Consensus size: 32
171115 AGTTGGCAAG
*
171125 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
*
171158 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
* *
171191 TTGGGAATTTCAT-AT-TTGGTGGCTAACTT
1 TTGGAAATTTCATCATGTTGGTGGCCAACTT
171220 GTACACATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
30 13 0.22
32 1 0.02
33 45 0.76
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (32 bp):
TTGGAAATTTCATCATGTTGGTGGCCAACTTA
Found at i:192678 original size:3 final size:3
Alignment explanation
Indices: 192670--192698 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
192660 AGAACAATGA
192670 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
192699 ATTGATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:192943 original size:12 final size:12
Alignment explanation
Indices: 192914--192947 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
192904 CTCCTACGAT
*
192914 ACAACAATCAATC
1 ACAACAAT-AAGC
192927 ACAACAATAAGC
1 ACAACAATAAGC
192939 ACAACAATA
1 ACAACAATA
192948 GTGATCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.59, C:0.26, G:0.03, T:0.12
Consensus pattern (12 bp):
ACAACAATAAGC
Found at i:193465 original size:20 final size:20
Alignment explanation
Indices: 193418--193475 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
193408 AAATAACTAA
193418 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
* * ***
193438 TAATTTCGCAACACGGTTTC
1 CAAATTCGCAACACGAACTC
* *
193458 CAAATTCGTAACTCGAAC
1 CAAATTCGCAACACGAAC
193476 ATAAATATTT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:195331 original size:24 final size:24
Alignment explanation
Indices: 195321--195437 Score: 132
Period size: 24 Copynumber: 4.9 Consensus size: 24
195311 CATAATTCAC
* *
195321 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAA
*
195345 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
*
195369 GTCAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCAGATCAAAATCCA-A
* *
195394 -TC-AG-ATACAGATCAGAATCCAT
1 GTCAAGTAT-CAGATCAAAATCCAA
195416 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
195438 AAATCGAAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.02
23 18 0.22
24 55 0.67
25 7 0.09
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:195420 original size:47 final size:48
Alignment explanation
Indices: 195321--195434 Score: 160
Period size: 47 Copynumber: 2.4 Consensus size: 48
195311 CATAATTCAC
* * *
195321 GTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGATCAAGTATCAGATCAGAATCCAA
* *
195369 GTCAAGTATCAGATCAGAATCCATATC-AG-ATACAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAAGTAT-CAGATCAGAATCCAA
195416 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
195435 ATCAAATCGA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
46 2 0.03
47 35 0.58
48 23 0.38
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAAGTATCAGATCAGAATCCAA
Found at i:197955 original size:13 final size:13
Alignment explanation
Indices: 197937--198012 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
197927 CAACGGTTAA
197937 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
197950 CGGGTCAATGGGT
1 CGGGTCAACGGGT
*
197963 CAGGTCAACAGGTCGGGT
1 CGGGTC-A-A---CGGGT
197981 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
197994 CAGGTAAACGGGT
1 CGGGTCAACGGGT
198007 CGGGTC
1 CGGGTC
198013 GGGTCATGAC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
13 37 0.74
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 9 0.18
ACGTcount: A:0.18, C:0.21, G:0.43, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:197980 original size:18 final size:18
Alignment explanation
Indices: 197959--197994 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
197949 TCGGGTCAAT
197959 GGGTCAGGTCAACAGGTC
1 GGGTCAGGTCAACAGGTC
* *
197977 GGGTCGGGTCAACGGGTC
1 GGGTCAGGTCAACAGGTC
197995 AGGTAAACGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.17
Consensus pattern (18 bp):
GGGTCAGGTCAACAGGTC
Found at i:197981 original size:31 final size:31
Alignment explanation
Indices: 197945--198018 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
197935 AACGGGTCAA
* *
197945 CGGGTCGGGTCAATGGGTCAGGTCAACAGGT
1 CGGGTCGGGTCAACGGGTCAGGTAAACAGGT
*
197976 CGGGTCGGGTCAACGGGTCAGGTAAACGGGT
1 CGGGTCGGGTCAACGGGTCAGGTAAACAGGT
198007 CGGGTCGGGTCA
1 CGGGTCGGGTCA
198019 TGACCGGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.18, C:0.20, G:0.45, T:0.18
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCAGGTAAACAGGT
Found at i:200097 original size:24 final size:24
Alignment explanation
Indices: 200087--200201 Score: 178
Period size: 24 Copynumber: 4.8 Consensus size: 24
200077 CATAATTCAC
* * *
200087 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
200111 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
200135 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
200159 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
200183 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
200202 ATCAAATCGA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:200218 original size:48 final size:48
Alignment explanation
Indices: 200063--200218 Score: 138
Period size: 48 Copynumber: 3.2 Consensus size: 48
200053 AAACGGATAT
* * * * * * * *
200063 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAG
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
200111 GTCA-AGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAGA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
200159 GTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAA
200207 ATC-GAAAATCAG
1 ATCAG-AAATCAG
200219 GTAAAATATT
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.02
48 85 0.93
49 4 0.04
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:200218 original size:72 final size:71
Alignment explanation
Indices: 200067--200218 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 71
200057 GGATATATCA
* * * *
200067 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
1 AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATC
*
200132 CAAGTC
66 CAAATC
* * * *
200138 AAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAA
1 AA-AATCAGATCAGAATCCACGTCAAG-TATCAGATCAAAATCCAGGTCAAGTATCAGATCAG-A
200202 AT-CAAATC
63 ATCCAAATC
200210 GAAAATCAG
1 -AAAATCAG
200219 GTAAAATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
71 4 0.06
72 58 0.87
73 5 0.07
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATC
CAAATC
Found at i:202717 original size:18 final size:17
Alignment explanation
Indices: 202683--202732 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 17
202673 TGGTCACGCC
202683 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
202700 GGTCAACAGGTTGGGTCG
1 GGTCAAC-GGTCGGGTCG
*
202718 GGTCAAGGGTCGGGT
1 GGTCAACGGTCGGGT
202733 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.14, C:0.18, G:0.48, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:202728 original size:30 final size:30
Alignment explanation
Indices: 202694--202752 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
202684 GTCAACGGTC
* *
202694 GGGTCGGGTCAACAGGTTGGGTCGGGTCAA
1 GGGTCGGGTAAACAGGTCGGGTCGGGTCAA
*
202724 GGGTCGGGTAAACGGGTCGGGTCGGGTCA
1 GGGTCGGGTAAACAGGTCGGGTCGGGTCA
202753 TGACCGGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.49, T:0.19
Consensus pattern (30 bp):
GGGTCGGGTAAACAGGTCGGGTCGGGTCAA
Found at i:202729 original size:12 final size:13
Alignment explanation
Indices: 202712--202746 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
202702 TCAACAGGTT
202712 GGGTCGGGTCAA-
1 GGGTCGGGTCAAC
*
202724 GGGTCGGGTAAAC
1 GGGTCGGGTCAAC
202737 GGGTCGGGTC
1 GGGTCGGGTC
202747 GGGTCATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.14, C:0.17, G:0.51, T:0.17
Consensus pattern (13 bp):
GGGTCGGGTCAAC
Found at i:203979 original size:38 final size:32
Alignment explanation
Indices: 203896--203957 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
203886 TAAGTTGGCA
203896 ATTGGAAATTTCATCTTGGTTGGTGGCCAACT
1 ATTGGAAATTTCATCTTGGTTGGTGGCCAACT
203928 ATTGGAAATTTCATCTTGGTTGGTGGCCAA
1 ATTGGAAATTTCATCTTGGTTGGTGGCCAA
203958 ACTTTGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.37
Consensus pattern (32 bp):
ATTGGAAATTTCATCTTGGTTGGTGGCCAACT
Found at i:208057 original size:33 final size:33
Alignment explanation
Indices: 208009--208086 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
207999 AGTTGGCAAG
208009 TTGGAAA-TTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
208041 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
208074 TTGGGAATTTCAT
1 TTGGAAATTTCAT
208087 ATTTGGTGGC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 7 0.16
33 37 0.84
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
Found at i:208095 original size:30 final size:32
Alignment explanation
Indices: 208009--208102 Score: 113
Period size: 33 Copynumber: 3.0 Consensus size: 32
207999 AGTTGGCAAG
*
208009 TTGGAAA-TTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
*
208041 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
* *
208074 TTGGGAATTTCAT-AT-TTGGTGGCTAACTT
1 TTGGAAATTTCATCATGTTGGTGGCCAACTT
208103 GTACACATCG
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 13 0.22
32 8 0.14
33 37 0.64
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (32 bp):
TTGGAAATTTCATCATGTTGGTGGCCAACTTA
Found at i:217740 original size:34 final size:34
Alignment explanation
Indices: 217702--217817 Score: 207
Period size: 34 Copynumber: 3.4 Consensus size: 34
217692 CTTTTTTGTT
217702 CTCTCT-TCGTCTGTTTCTCTGTTGTTCTCCATTG
1 CTCTCTGT-GTCTGTTTCTCTGTTGTTCTCCATTG
217736 CTCTCTGTGTCTGTTTCTCTGTTGTTCTCCATTG
1 CTCTCTGTGTCTGTTTCTCTGTTGTTCTCCATTG
*
217770 CTCTCTGTGTCTGTTTCTCTGTTGTTCTCCGTTG
1 CTCTCTGTGTCTGTTTCTCTGTTGTTCTCCATTG
217804 CTCTCTGTGTCTGT
1 CTCTCTGTGTCTGT
217818 CTTTCTTACA
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
34 79 0.99
35 1 0.01
ACGTcount: A:0.02, C:0.28, G:0.18, T:0.53
Consensus pattern (34 bp):
CTCTCTGTGTCTGTTTCTCTGTTGTTCTCCATTG
Found at i:218304 original size:3 final size:3
Alignment explanation
Indices: 218296--218346 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
218286 TATATATATT
* * *
218296 TAA TAA TAAA TAA TAA TAA TAA TAA TATA TTA TAT TAA TAA TAA TTA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
218343 TAA T
1 TAA T
218347 TATTATTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:218307 original size:22 final size:20
Alignment explanation
Indices: 218281--218344 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 20
218271 ATGTAATTTG
218281 TAATATATATATATTTAATAA
1 TAATATATATATA-TTAATAA
218302 TAA-ATA-ATA-A-TAATAA
1 TAATATATATATATTAATAA
218318 TAATATAT-TATATTAATAA
1 TAATATATATATATTAATAA
218337 TAAT-TATA
1 TAATATATA
218345 ATTATTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 9 0.24
17 5 0.13
18 5 0.13
19 13 0.34
20 3 0.08
21 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATATATATATTAATAA
Found at i:218316 original size:31 final size:31
Alignment explanation
Indices: 218281--218346 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
218271 ATGTAATTTG
218281 TAAT-ATATATATATT-TAATAATAAATAATAA
1 TAATAATA-ATATATTATAATAAT-AATAATAA
* *
218312 TAATAATAATATATTATATTAATAATAATTA
1 TAATAATAATATATTATAATAATAATAATAA
218343 TAAT
1 TAAT
218347 TATTATTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TAATAATAATATATTATAATAATAATAATAA
Found at i:218348 original size:16 final size:16
Alignment explanation
Indices: 218299--218348 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
218289 ATATATTTAA
*
218299 TAATAAATAATAATAA-
1 TAAT-AATAATTATAAT
218315 TAATAATATATTAT-AT
1 TAATAATA-ATTATAAT
218331 TAATAATAATTATAAT
1 TAATAATAATTATAAT
218347 TA
1 TA
218349 TTATTATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATAATTATAAT
Found at i:218353 original size:22 final size:22
Alignment explanation
Indices: 218309--218354 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
218299 TAATAAATAA
218309 TAATAATAATAATATATTATAT
1 TAATAATAATAATATATTATAT
*
218331 TAATAATAATTATA-ATTATTAT
1 TAATAATAATAATATATTA-TAT
218353 TA
1 TA
218355 TGAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATATATTATAT
Found at i:239053 original size:12 final size:12
Alignment explanation
Indices: 239024--239057 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
239014 CTCCTACGAT
*
239024 ACAACAATCAATC
1 ACAACAAT-AAGC
239037 ACAACAATAAGC
1 ACAACAATAAGC
239049 ACAACAATA
1 ACAACAATA
239058 GTGATCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.59, C:0.26, G:0.03, T:0.12
Consensus pattern (12 bp):
ACAACAATAAGC
Found at i:239576 original size:20 final size:20
Alignment explanation
Indices: 239529--239586 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
239519 AAAATAACAA
239529 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
* * ***
239549 TAATTTCGCAACACGGTTTC
1 CAAATTCGCAACACGAACTC
* *
239569 CAAATTCGTAACTCGAAC
1 CAAATTCGCAACACGAAC
239587 ATAAATATTT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:241465 original size:24 final size:24
Alignment explanation
Indices: 241455--241572 Score: 141
Period size: 24 Copynumber: 4.9 Consensus size: 24
241445 CATAATTCAC
* *
241455 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAA
*
241479 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
*
241503 GTCAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCAGATCAAAATCCA-A
* *
241528 -TC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
241551 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
241573 AAATCGAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
23 2 0.02
24 75 0.89
25 7 0.08
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:241524 original size:48 final size:48
Alignment explanation
Indices: 241455--241569 Score: 169
Period size: 48 Copynumber: 2.4 Consensus size: 48
241445 CATAATTCAC
* * *
241455 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGATCAGA-TATCAGATCAGAATCCAA
* *
241503 GTCAAGTATCAGATCAGAATCCATATCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGATATCAGATCAGAATCCAA
241551 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
241570 ATCAAATCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 60 0.98
49 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGATATCAGATCAGAATCCAA
Found at i:241586 original size:48 final size:48
Alignment explanation
Indices: 241431--241586 Score: 147
Period size: 48 Copynumber: 3.2 Consensus size: 48
241421 AAACGGATAT
* * * * * * * *
241431 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAG
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
241479 GTCA-AGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAGA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* *
241527 ATCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAA
241575 ATC-GAAAATCAG
1 ATCAG-AAATCAG
241587 GTAAAATATT
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.02
48 85 0.93
49 4 0.04
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:244093 original size:8 final size:8
Alignment explanation
Indices: 244060--244122 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
244050 TCAAAGTTTT
244060 GGTCAACAG
1 GGTCAAC-G
244069 TGGTCAACG
1 -GGTCAACG
*
244078 CCGGTCAACA
1 --GGTCAACG
244088 GGTCAAC-
1 GGTCAACG
*
244095 GGTTAACG
1 GGTCAACG
*
244103 GGTTAACG
1 GGTCAACG
244111 GGTCAACG
1 GGTCAACG
244119 GGTC
1 GGTC
244123 GGGTCAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 6 0.13
8 26 0.55
9 1 0.02
10 14 0.30
ACGTcount: A:0.25, C:0.24, G:0.33, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:244127 original size:13 final size:13
Alignment explanation
Indices: 244109--244210 Score: 105
Period size: 13 Copynumber: 7.5 Consensus size: 13
244099 AACGGGTTAA
244109 CGGGTCAACGGGT
1 CGGGTCAACGGGT
***
244122 CGGGTCAATTTGT
1 CGGGTCAACGGGT
*
244135 CGGGTCAACAGGT
1 CGGGTCAACGGGT
*
244148 CGGGTCAATGGGT
1 CGGGTCAACGGGT
244161 CGGGTCAACAGGTCGGGT
1 CGGGTC-A-A---CGGGT
244179 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
244192 CGGGTAAACGGGT
1 CGGGTCAACGGGT
244205 CGGGTC
1 CGGGTC
244211 GGGTCATGAC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
13 59 0.81
14 1 0.01
15 1 0.01
16 1 0.01
17 1 0.01
18 10 0.14
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.20
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:244152 original size:31 final size:31
Alignment explanation
Indices: 244117--244216 Score: 120
Period size: 31 Copynumber: 3.4 Consensus size: 31
244107 AACGGGTCAA
**
244117 CGGGTCGGGTCAATTTGTCGGGTCAACA---
1 CGGGTCGGGTCAATGGGTCGGGTCAACAGGT
244145 --GGTCGGGTCAATGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAATGGGTCGGGTCAACAGGT
* * *
244174 CGGGTCGGGTCAACGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAATGGGTCGGGTCAACAGGT
244205 CGGGTCGGGTCA
1 CGGGTCGGGTCA
244217 TGACCGGTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 24 0.39
31 38 0.61
ACGTcount: A:0.16, C:0.20, G:0.44, T:0.20
Consensus pattern (31 bp):
CGGGTCGGGTCAATGGGTCGGGTCAACAGGT
Found at i:244155 original size:39 final size:43
Alignment explanation
Indices: 244109--244210 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 43
244099 AACGGGTTAA
**
244109 CGGGTCAACGGGTCGGGTC-A-A-T-TTGTCGGGTCAACAGGT
1 CGGGTCAACGGGTCGGGTCAACAGTCGGGTCGGGTCAACAGGT
* *
244148 CGGGTCAATGGGTCGGGTCAACAGGTCGGGTCGGGTCAACGGGT
1 CGGGTCAACGGGTCGGGTCAACA-GTCGGGTCGGGTCAACAGGT
*
244192 CGGGTAAACGGGTCGGGTC
1 CGGGTCAACGGGTCGGGTC
244211 GGGTCATGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
39 18 0.35
40 1 0.02
41 1 0.02
43 1 0.02
44 31 0.60
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.20
Consensus pattern (43 bp):
CGGGTCAACGGGTCGGGTCAACAGTCGGGTCGGGTCAACAGGT
Found at i:244178 original size:18 final size:18
Alignment explanation
Indices: 244157--244196 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
244147 TCGGGTCAAT
244157 GGGTCGGGTCAACAGGTC
1 GGGTCGGGTCAACAGGTC
*
244175 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACAGGTC
244193 GGGT
1 GGGT
244197 AAACGGGTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.20, G:0.50, T:0.17
Consensus pattern (18 bp):
GGGTCGGGTCAACAGGTC
Found at i:246323 original size:24 final size:24
Alignment explanation
Indices: 246313--246430 Score: 139
Period size: 24 Copynumber: 4.9 Consensus size: 24
246303 CATAATTCAC
* *
246313 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAA
*
246337 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
* *
246361 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAA
* * *
246385 GTC-AGATATCCGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
246409 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
246431 AAATCGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 2 0.02
24 76 0.90
25 6 0.07
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:246382 original size:48 final size:48
Alignment explanation
Indices: 246313--246427 Score: 169
Period size: 48 Copynumber: 2.4 Consensus size: 48
246303 CATAATTCAC
* *
246313 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGGTCAGA-TATCAGATCAGAATCCAA
* * *
246361 GTCAAGTATCAGATCAGAATCCATGTCAGATATCCGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCAA
246409 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
246428 ATCAAATCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 60 0.98
49 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCAA
Found at i:248952 original size:13 final size:13
Alignment explanation
Indices: 248934--248994 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
248924 GGTCAACGCC
248934 GGTCAACGGGTCG
1 GGTCAACGGGTCG
248947 GGTCAACAGGTCGGGTCG
1 GGTC-A-A---CGGGTCG
248965 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
248978 GGTAAACGGGTCG
1 GGTCAACGGGTCG
248991 GGTC
1 GGTC
248995 GGGTCATGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 26 0.63
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.27
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:248961 original size:18 final size:18
Alignment explanation
Indices: 248940--248980 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
248930 CGCCGGTCAA
248940 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
248958 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
248976 CGGGT
1 CGGGT
248981 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:248971 original size:31 final size:31
Alignment explanation
Indices: 248934--249000 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
248924 GGTCAACGCC
*
248934 GGTCAACGGGTCGGGTCAACAGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACAGGTCGGGTCG
*
248965 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACAGGTCGGGTCG
248996 GGTCA
1 GGTCA
249001 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACAGGTCGGGTCG
Found at i:271928 original size:12 final size:12
Alignment explanation
Indices: 271899--271932 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
271889 CTCCTACGAT
*
271899 ACAACAATCAATC
1 ACAACAAT-AAGC
271912 ACAACAATAAGC
1 ACAACAATAAGC
271924 ACAACAATA
1 ACAACAATA
271933 GTGATCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.59, C:0.26, G:0.03, T:0.12
Consensus pattern (12 bp):
ACAACAATAAGC
Found at i:272451 original size:20 final size:20
Alignment explanation
Indices: 272404--272461 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
272394 AAATAACTAA
272404 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
* * ***
272424 TAATTTCGCAACACGGTTTC
1 CAAATTCGCAACACGAACTC
* *
272444 CAAATTCGTAACTCGAAC
1 CAAATTCGCAACACGAAC
272462 ATAAATATTT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:274348 original size:24 final size:24
Alignment explanation
Indices: 274321--274454 Score: 94
Period size: 24 Copynumber: 5.5 Consensus size: 24
274311 TATATCAAAA
* * *
274321 ATCAAATCATAATTCACGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
274345 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
274369 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
274393 ATTAGAT-AAGAATCCATA-TC-AGAT
1 ATCAAATCAA-AATCCA-AGTCAAG-T
* * *
274417 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
*
274441 ATCAGATCAGAAAT
1 ATCAAATCA-AAAT
274455 TAAATCGAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.03
24 80 0.89
25 7 0.08
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAATCAAAATCCAAGTCAAGT
Found at i:274407 original size:48 final size:48
Alignment explanation
Indices: 274338--274452 Score: 144
Period size: 48 Copynumber: 2.4 Consensus size: 48
274328 CATAATTCAC
* *
274338 GTCAAGTATCATATCAA-AATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGAT-AAGAATCCAGATCAGA-TATCAGATCAGAATCCAA
* * *
274386 GTCAAGTATTAGATAAGAATCCATATCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATAAGAATCCAGATCAGATATCAGATCAGAATCCAA
*
274434 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATAAGAA
274453 ATTAAATCGA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 2 0.03
48 55 0.95
49 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATAAGAATCCAGATCAGATATCAGATCAGAATCCAA
Found at i:276970 original size:13 final size:13
Alignment explanation
Indices: 276952--277025 Score: 76
Period size: 13 Copynumber: 5.3 Consensus size: 13
276942 CAACGGTTAA
276952 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
276965 CGGGTCAATGGGT
1 CGGGTCAACGGGT
276978 CGGGTCAACAGGTCAGGT
1 CGGGTCAAC--G---GGT
*
276996 CAGGTCAACGGGT
1 CGGGTCAACGGGT
*
277009 CGGGTAAACGGGT
1 CGGGTCAACGGGT
277022 CGGG
1 CGGG
277026 CCGGGTCATG
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
13 38 0.75
15 1 0.02
16 1 0.02
18 11 0.22
ACGTcount: A:0.19, C:0.20, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:276996 original size:18 final size:18
Alignment explanation
Indices: 276975--277009 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
276965 CGGGTCAATG
*
276975 GGTCGGGTCAACAGGTCA
1 GGTCAGGTCAACAGGTCA
*
276993 GGTCAGGTCAACGGGTC
1 GGTCAGGTCAACAGGTC
277010 GGGTAAACGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.40, T:0.17
Consensus pattern (18 bp):
GGTCAGGTCAACAGGTCA
Found at i:277033 original size:31 final size:31
Alignment explanation
Indices: 276960--277033 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
276950 AACGGGTCAA
* *
276960 CGGGTCGGGTCAATGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACGGGTCGGGTAAACAGGT
* * *
276991 CAGGTCAGGTCAACGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTAAACAGGT
*
277022 CGGGCCGGGTCA
1 CGGGTCGGGTCA
277034 TGACCGGTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.16
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTAAACAGGT
Found at i:279142 original size:24 final size:24
Alignment explanation
Indices: 279132--279245 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
279122 CATAATTCAC
* * *
279132 GTCAAGTATCATATCAAAAT-CAG
1 GTCAAGTATCAGATCAGAATCCAT
*
279155 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
279179 GTCAATTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
279203 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
279227 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
279246 ATCAAATCGA
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
23 19 0.23
24 61 0.74
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:279262 original size:48 final size:47
Alignment explanation
Indices: 279112--279262 Score: 144
Period size: 48 Copynumber: 3.2 Consensus size: 47
279102 GGATATATCA
* * * * * *
279112 AAAATCAAATCATAATTCACGTCAAGTATCATATCA-AAATCAGGTC
1 AAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAAATCAAGTC
* * *
279158 AAGTATCAGATCAGAATCCAAGTCAATTATCAGATCAG-AATCCATGTC
1 AA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAAAT-CAAGTC
* * *
279206 AGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAATCAAATC
1 A-AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAAATCAAGTC
279254 GAAAATCAG
1 -AAAATCAG
279263 GTAAAATATT
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
46 2 0.02
47 30 0.35
48 49 0.57
49 5 0.06
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (47 bp):
AAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAAATCAAGTC
Found at i:281782 original size:16 final size:17
Alignment explanation
Indices: 281750--281788 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
281740 TGGTCAACAT
281750 TGGTCAACGCCGGTCAAC
1 TGGTCAACG-CGGTCAAC
281768 TGGTCAACG-GGTCAAC
1 TGGTCAACGCGGTCAAC
*
281784 AGGTC
1 TGGTC
281789 GGGTCGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
18 9 0.45
ACGTcount: A:0.23, C:0.28, G:0.31, T:0.18
Consensus pattern (17 bp):
TGGTCAACGCGGTCAAC
Found at i:281798 original size:18 final size:18
Alignment explanation
Indices: 281775--281817 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
281765 AACTGGTCAA
281775 CGGGTCAACAGGTCGGGT
1 CGGGTCAACAGGTCGGGT
*
281793 CGGGTCAACGGGTCGGGT
1 CGGGTCAACAGGTCGGGT
281811 CGGGTCA
1 CGGGTCA
281818 TGACCGGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.23, G:0.47, T:0.16
Consensus pattern (18 bp):
CGGGTCAACAGGTCGGGT
Found at i:287743 original size:33 final size:33
Alignment explanation
Indices: 287706--287784 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
287696 AGTTGGCAAG
287706 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
287739 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
287772 TTGGGAATTTCAT
1 TTGGAAATTTCAT
287785 ATTTGGTGGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.41
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
Found at i:287793 original size:30 final size:32
Alignment explanation
Indices: 287706--287800 Score: 122
Period size: 33 Copynumber: 3.0 Consensus size: 32
287696 AGTTGGCAAG
*
287706 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
*
287739 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
* *
287772 TTGGGAATTTCAT-AT-TTGGTGGCTAACTT
1 TTGGAAATTTCATCATGTTGGTGGCCAACTT
287801 GTACACATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
30 13 0.22
32 1 0.02
33 45 0.76
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (32 bp):
TTGGAAATTTCATCATGTTGGTGGCCAACTTA
Found at i:301163 original size:17 final size:18
Alignment explanation
Indices: 301141--301198 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
301131 TCTCCATCAC
301141 AAAAAAAATGTT-GAAAA
1 AAAAAAAATGTTCGAAAA
301158 AAAAAATAGCA-GTTCG-AAA
1 AAAAAA-A--ATGTTCGAAAA
*
301177 AAAAAAACTGTTCGAAAA
1 AAAAAAAATGTTCGAAAA
301195 AAAA
1 AAAA
301199 GACATGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
17 11 0.32
18 9 0.26
19 12 0.35
20 2 0.06
ACGTcount: A:0.66, C:0.07, G:0.12, T:0.16
Consensus pattern (18 bp):
AAAAAAAATGTTCGAAAA
Done.