Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007246.1 Hibiscus syriacus cultivar Beakdansim tig00019200_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: 322346
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 2
Found at i:160818 original size:7 final size:7
Alignment explanation
Indices: 160801--160888 Score: 58
Period size: 7 Copynumber: 12.4 Consensus size: 7
160791 AGACCCTGCA
160801 AAAAAAT
1 AAAAAAT
160808 -AAAAAT
1 AAAAAAT
160814 AAAAAAT
1 AAAAAAT
160821 --AAAAT
1 AAAAAAT
160826 AAGTAAAAT
1 AA--AAAAT
*
160835 AAATAAT
1 AAAAAAT
*
160842 AAATAAT
1 AAAAAAT
160849 AAATAAAT
1 AAA-AAAT
160857 AACAAAA-
1 AA-AAAAT
***
160864 GGTAAAT
1 AAAAAAT
160871 AAATAAAT
1 AAA-AAAT
160879 AAAAAAT
1 AAAAAAT
160886 AAA
1 AAA
160889 CTAAAAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
5 5 0.08
6 9 0.14
7 27 0.42
8 15 0.23
9 8 0.12
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (7 bp):
AAAAAAT
Found at i:160826 original size:18 final size:18
Alignment explanation
Indices: 160801--160895 Score: 59
Period size: 18 Copynumber: 4.9 Consensus size: 18
160791 AGACCCTGCA
160801 AAAAAATAAAAATAAAAAAT
1 AAAAAAT-AAAAT-AAAAAT
160821 AAAATAAGTAAAATAAATAAT
1 AAAA-AA-TAAAATAAA-AAT
* *
160842 AAATAAT-AAATAAATAAC
1 AAAAAATAAAATAAA-AAT
**
160860 AAAAGGT-AAATAAATAAAT
1 AAAAAATAAAAT-AA-AAAT
*
160879 AAAAAATAAACTAAAAA
1 AAAAAATAAAATAAAAA
160896 AAACATTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
18 21 0.35
19 12 0.20
20 13 0.22
21 13 0.22
22 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (18 bp):
AAAAAATAAAATAAAAAT
Found at i:160840 original size:4 final size:4
Alignment explanation
Indices: 160810--160893 Score: 70
Period size: 4 Copynumber: 20.8 Consensus size: 4
160800 AAAAAAATAA
*
160810 AAAT AAA- AAAT AAAAT AAGT AAAAT AAAT -AAT AAAT -AAT AAAT AAAT
1 AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
160857 AACA- AAAGGT AAAT AAAT AAAT AAA- AAAT AAACT AAA
1 AA-AT AAA--T AAAT AAAT AAAT AAAT AAAT AAA-T AAA
160894 AAAAACATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 21
0.74 0.02 0.23
Matches are distributed among these distances:
3 13 0.19
4 39 0.58
5 12 0.18
6 3 0.04
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:160898 original size:15 final size:15
Alignment explanation
Indices: 160801--160896 Score: 78
Period size: 15 Copynumber: 6.4 Consensus size: 15
160791 AGACCCTGCA
160801 AAAAAAT-AA-AAAT
1 AAAAAATAAATAAAT
*
160814 AAAAAATAAAATAAGT
1 AAAAAAT-AAATAAAT
160830 --AAAATAAAT-AAT
1 AAAAAATAAATAAAT
*
160842 AAATAATAAATAAAT
1 AAAAAATAAATAAAT
160857 AACAAAAGGTAAATAAAT
1 AA-AAAA--TAAATAAAT
160875 AAATAAA-AAATAAACT
1 AAA-AAATAAATAAA-T
160891 AAAAAA
1 AAAAAA
160897 AACATTTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
12 2 0.03
13 11 0.16
14 13 0.19
15 17 0.25
16 10 0.15
17 1 0.01
18 14 0.21
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:160967 original size:36 final size:35
Alignment explanation
Indices: 160908--161354 Score: 173
Period size: 36 Copynumber: 12.5 Consensus size: 35
160898 ACATTTTCCA
* *
160908 AAAATCTATATAATATA-TATTTTTAAAAATATTTT
1 AAAA-CTATATATTATATTTTTTTTAAAAATATTTT
* * *
160943 AAAATTATATATTATATGTTTTTTTAAAAACATTTC
1 AAAACTATATATTATAT-TTTTTTTAAAAATATTTT
* * *
160979 CAAA--AT-TA-TATA--GTTTTTAAAAATGTTTTTT
1 AAAACTATATATTATATTTTTTTTAAAAA--TATTTT
* ** * *
161010 AAAATTATATATTATA-AGTTTTT-GAAATGATTTA
1 AAAACTATATATTATATTTTTTTTAAAAAT-ATTTT
**
161044 AAAACTATATAATATATATATGTTCTTCAAAAAATATTTTT
1 AAAACTATAT-AT-TATAT-T-TT-TTTTAAAAATA-TTTT
** * * * * *
161085 TTAA--A-A-ACTATATATATTTTAAAAATGTTTA
1 AAAACTATATATTATATTTTTTTTAAAAATATTTT
* * * *
161116 AAAACTATATAATATATATTTTTAAAAAATGTTTT
1 AAAACTATATATTATATTTTTTTTAAAAATATTTT
* * * * *
161151 AAAAATTATATAGTATATTTATTTTCAAAATACTTTA
1 -AAAACTATATATTATATTTTTTTTAAAAATA-TTTT
* * * * * *
161188 AAAACTATATAATACATATATTTTCAAAAATATGTA
1 AAAACTATATATTATAT-TTTTTTTAAAAATATTTT
* * *
161224 AAAACTATATATTATATTTATTTTCAAAATACTTTA
1 AAAACTATATATTATATTTTTTTTAAAAATA-TTTT
* * * * *
161260 AAAACTATATAATATATAAATATTTTCAAACATGTTTT
1 AAAACTATAT-AT-TAT-ATTTTTTTTAAAAATATTTT
**
161298 CAAAACTATATATTATATATAGGTTTTAAAAATATTTT
1 -AAAACTATATATTATAT-T-TTTTTTAAAAATATTTT
161336 AAAACTATAATATATATAT
1 AAAACTAT-ATAT-TATAT
161355 ATATATCTAT
Statistics
Matches: 305, Mismatches: 73, Indels: 64
0.69 0.17 0.14
Matches are distributed among these distances:
29 10 0.03
31 11 0.04
32 12 0.04
33 7 0.02
34 27 0.09
35 49 0.16
36 99 0.32
37 27 0.09
38 25 0.08
39 26 0.09
40 3 0.01
41 9 0.03
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (35 bp):
AAAACTATATATTATATTTTTTTTAAAAATATTTT
Found at i:160990 original size:37 final size:37
Alignment explanation
Indices: 160894--160990 Score: 115
Period size: 36 Copynumber: 2.6 Consensus size: 37
160884 ATAAACTAAA
* *
160894 AAAAACATTTTCCAAAAATCTATATAATATATATTTTT
1 AAAAACA-TTTCCAAAATTATATATAATATATATTTTT
* * * * *
160932 AAAAATATTT-TAAAATTATATATTATATGTTTTTTT
1 AAAAACATTTCCAAAATTATATATAATATATATTTTT
160968 AAAAACATTTCCAAAATTATATA
1 AAAAACATTTCCAAAATTATATA
160991 GTTTTTAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
36 29 0.59
37 14 0.29
38 6 0.12
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (37 bp):
AAAAACATTTCCAAAATTATATATAATATATATTTTT
Found at i:161146 original size:108 final size:104
Alignment explanation
Indices: 160907--161198 Score: 259
Period size: 108 Copynumber: 2.8 Consensus size: 104
160897 AACATTTTCC
* * **
160907 AAAAATCTATATAATATATATTTTTAAAAAT-ATTTTAAAAT-TAT-ATAT-TATATGTTTTTTT
1 AAAAA-CTATATAATATATATTTTTAAAAATGATTTAAAAATATATAATATATATATGTTCTTCA
* *
160968 AAAAACATTTCCAAAATTATATAGTTTTTAAAAATGTTTTT
65 AAAAACATTTCAAAAACTATATAGTTTTTAAAAATG-TTTT
* * * *
161009 TAAAATTATATATTATA-AGTTTTT-GAAATGATTTAAAAACTATATAATATATATATGTTCTTC
1 AAAAACTATATAATATATA-TTTTTAAAAATGATTTAAAAA-TATATAATATATATATGTTCTTC
* *
161072 AAAAAATATTTTTTTAAAAACTATATA-TATTTTAAAAATG-TTT
64 AAAAAACA---TTTCAAAAACTATATAGT-TTTTAAAAATGTTTT
* * *
161115 AAAAACTATATAATATATATTTTTAAAAAATGTTTTAAAAAT-TAT-ATAGTATATTTATT-TTC
1 AAAAACTATATAATATATATTTTT-AAAAATGATTTAAAAATATATAATA-TATATATGTTCTTC
*
161177 AAAATAC-TTT-AAAAACTATATA
64 AAAAAACATTTCAAAAACTATATA
161199 ATACATATAT
Statistics
Matches: 155, Mismatches: 21, Indels: 30
0.75 0.10 0.15
Matches are distributed among these distances:
100 17 0.11
101 26 0.17
102 5 0.03
103 3 0.02
104 4 0.03
105 27 0.17
106 33 0.21
107 3 0.02
108 37 0.24
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (104 bp):
AAAAACTATATAATATATATTTTTAAAAATGATTTAAAAATATATAATATATATATGTTCTTCAA
AAAACATTTCAAAAACTATATAGTTTTTAAAAATGTTTT
Found at i:161188 original size:72 final size:73
Alignment explanation
Indices: 160985--161358 Score: 331
Period size: 72 Copynumber: 5.1 Consensus size: 73
160975 TTTCCAAAAT
* * * *
160985 TATATAGTTTTTAAAAATGTTTTTTAAAATTATATATTATA-AGT-TTTT-GAAATGA-TTTAAA
1 TATATA-TTTTCAAAAATG-TTTTAAAAACTATATATTATATA-TATTTTAAAAAT-ACTTTAAA
161046 AACTATATAATA
62 AACTATATAATA
* *** * *
161058 TATATATGTTCTTCAAAAAATATTTTTTTAA--A-A-ACTATATATATTTTAAAAAT-GTTTAAA
1 TATATA--TT-TTC-AAAAATGTTTTAAAAACTATATATTATATATATTTTAAAAATACTTTAAA
161118 AACTATATAATA
62 AACTATATAATA
* * * * *
161130 TATAT-TTTTAAAAAATGTTTTAAAAATTATATAGTATATTTATTTTCAAAATACTTTAAAAACT
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTAAAAATACTTTAAAAACT
161194 ATATAATA
66 ATATAATA
* * * * *
161202 CATATATTTTCAAAAAT-ATGTAAAAACTATATATTATATTTATTTTCAAAATACTTTAAAAACT
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTAAAAATACTTTAAAAACT
161266 ATATAATA
66 ATATAATA
* * *
161274 TATAAATATTTTCAAACATGTTTTCAAAACTATATATTATATATAGGTTTTAAAAATA-TTTTAA
1 TAT--ATATTTTCAAAAATGTTTTAAAAACTATATATTATATATA--TTTTAAAAATACTTTAAA
161338 AACTATAATATATA
62 AACTAT-ATA-ATA
161352 TATATAT
1 TATATAT
161359 ATCTATATAT
Statistics
Matches: 252, Mismatches: 29, Indels: 37
0.79 0.09 0.12
Matches are distributed among these distances:
67 12 0.05
68 2 0.01
69 3 0.01
70 1 0.00
71 23 0.09
72 104 0.41
73 21 0.08
74 16 0.06
75 30 0.12
76 21 0.08
77 13 0.05
78 6 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (73 bp):
TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTAAAAATACTTTAAAAACT
ATATAATA
Found at i:163524 original size:53 final size:53
Alignment explanation
Indices: 163455--163976 Score: 819
Period size: 53 Copynumber: 9.8 Consensus size: 53
163445 TTAGAAACGA
* * *
163455 GTTCGCTCTCTTTTTCTTCAGGGAGTAGAACTCGCACAATCTTCTGCCTACGG
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
* * * * *
163508 GTTTGTTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATTTTTTTCTTACGG
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
163561 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
* * *
163614 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATTTTCTTCTTACAG
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
* * * *
163667 GTTCGCTCTCTCTTTTTTCAGGGAGTATAACTCGAACAATATTCTTCCTATGG
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
* * *
163720 GTTCCCTCTCTCTTTCTTTAGGGAGTAGAACTCGAACAATCTTCTTCCCACGG
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
* *
163773 GTTCTCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGA
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
*
163826 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCCACGG
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
* *
163879 GTTCGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTTCTACGG
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
* *
163932 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCAAAAAATCTTCT
1 GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCT
163977 GTTGCTTCAC
Statistics
Matches: 427, Mismatches: 42, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 427 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (53 bp):
GTTCGCTCTCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGG
Found at i:165334 original size:8 final size:8
Alignment explanation
Indices: 165314--165415 Score: 107
Period size: 8 Copynumber: 12.0 Consensus size: 8
165304 TTTTATTTGT
165314 CTTTTTT-
1 CTTTTTTC
165321 CTTTCTTTC
1 CTTT-TTTC
165330 CTTCTTTCTTC
1 C-T-TTT-TTC
165341 TCTTTTTTC
1 -CTTTTTTC
165350 CTTTTTTC
1 CTTTTTTC
*
165358 TTTTTTTC
1 CTTTTTTC
165366 CTTTTTTTC
1 C-TTTTTTC
*
165375 CTTTTTTT
1 CTTTTTTC
165383 CTTTTTTC
1 CTTTTTTC
*
165391 CTTTTTCC
1 CTTTTTTC
165399 CTTTTTTTC
1 C-TTTTTTC
165408 CTTTTTTC
1 CTTTTTTC
165416 ATCTTCAAGC
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
7 4 0.05
8 46 0.57
9 19 0.23
10 5 0.06
11 6 0.07
12 1 0.01
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (8 bp):
CTTTTTTC
Found at i:165355 original size:9 final size:9
Alignment explanation
Indices: 165315--165414 Score: 106
Period size: 9 Copynumber: 11.6 Consensus size: 9
165305 TTTATTTGTC
165315 TTTTTT-CT
1 TTTTTTCCT
*
165323 TTCTTTCCT
1 TTTTTTCCT
165332 TCTTTCTT-CT
1 T-TTT-TTCCT
165342 CTTTTTTCC-
1 -TTTTTTCCT
165351 TTTTTT-CT
1 TTTTTTCCT
165359 TTTTTTCCT
1 TTTTTTCCT
165368 TTTTTTCCT
1 TTTTTTCCT
165377 TTTTTT-C-
1 TTTTTTCCT
165384 TTTTTTCC-
1 TTTTTTCCT
*
165392 TTTTTCCCT
1 TTTTTTCCT
165401 TTTTTTCCT
1 TTTTTTCCT
165410 TTTTT
1 TTTTT
165415 CATCTTCAAG
Statistics
Matches: 79, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
7 7 0.09
8 26 0.33
9 35 0.44
10 8 0.10
11 3 0.04
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:165371 original size:25 final size:24
Alignment explanation
Indices: 165315--165415 Score: 96
Period size: 25 Copynumber: 4.0 Consensus size: 24
165305 TTTATTTGTC
*
165315 TTTTTTCTTTCTTTCCTTCTTTCTTCTC
1 TTTTTTCTTTTTTTCC-T-TTT-TTC-C
* *
165343 TTTTTTCCTTTTTTCTTTTTTTCC
1 TTTTTTCTTTTTTTCCTTTTTTCC
165367 TTTTTTTCCTTTTTTT-CTTTTTTCC
1 -TTTTTT-CTTTTTTTCCTTTTTTCC
*
165392 TTTTTCCCTTTTTTTCCTTTTTTC
1 TTTTT-TCTTTTTTTCCTTTTTTC
165416 ATCTTCAAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
24 14 0.22
25 25 0.40
26 10 0.16
27 1 0.02
28 13 0.21
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTTCTTTTTTTCCTTTTTTCC
Found at i:174237 original size:9 final size:9
Alignment explanation
Indices: 174225--174255 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
174215 GGCCTCCGTA
174225 GCCTCCGCC
1 GCCTCCGCC
174234 GCCTCCGCC
1 GCCTCCGCC
174243 GCCTCCGCC
1 GCCTCCGCC
174252 GCCT
1 GCCT
174256 AACGCTCCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.65, G:0.23, T:0.13
Consensus pattern (9 bp):
GCCTCCGCC
Found at i:174239 original size:18 final size:18
Alignment explanation
Indices: 174216--174255 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
174206 AGAACCCAAG
*
174216 GCCTCCGTAGCCTCCGCC
1 GCCTCCGCAGCCTCCGCC
*
174234 GCCTCCGCCGCCTCCGCC
1 GCCTCCGCAGCCTCCGCC
174252 GCCT
1 GCCT
174256 AACGCTCCGA
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:0.03, C:0.60, G:0.23, T:0.15
Consensus pattern (18 bp):
GCCTCCGCAGCCTCCGCC
Found at i:178686 original size:64 final size:65
Alignment explanation
Indices: 178532--178687 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
178522 TACACTTGGG
* * * * * * *
178532 GTGCATCGGTACACTAATTACATTCAATGTTTCAAAAGAGCCAGGAGTGTATCGATGCATGGTTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAACCAAGAGTGGATCGATGCATGGTTT
*
178597 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAA-AATCAAGAGTGGATCGATGCATGG-T
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAA-AAGAACCAAGAGTGGATCGATGCATGGTT
178660 T
65 T
178661 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
178688 AATAGGGTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 29 0.35
65 51 0.62
66 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAACCAAGAGTGGATCGATGCATGGTTT
Found at i:179047 original size:13 final size:13
Alignment explanation
Indices: 179029--179062 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
179019 TAAGATTTTC
*
179029 TTTGAAAATCATT
1 TTTGAAAATCAAT
179042 TTTG-AAATCAAT
1 TTTGAAAATCAAT
179054 TTTGAAAAT
1 TTTGAAAAT
179063 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:181323 original size:44 final size:44
Alignment explanation
Indices: 181273--181364 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
181263 CACTGCAAAA
*
181273 TGTATCGATGCACATTCAAGGCATGCATCGATGCACTTTCATAG
1 TGTATCGATGCACATTCAAGGCATGCATCGATACACTTTCATAG
* * * * *
181317 TGTATCGGTGCATATTCAAGGGATGCATTGGTACACTTTCATAG
1 TGTATCGATGCACATTCAAGGCATGCATCGATACACTTTCATAG
181361 TGTA
1 TGTA
181365 CTAATGTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (44 bp):
TGTATCGATGCACATTCAAGGCATGCATCGATACACTTTCATAG
Found at i:187253 original size:64 final size:64
Alignment explanation
Indices: 187167--187291 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
187157 ATTACATTTA
* * * * *
187167 ATGTTTCAAAAGAGCCAGGAGTGTATCGGTGCATGGTCTGTGCAT-GGTACACAAAATGCATTCG
1 ATGTTTCAAAAGAACCAAGAGTGGATCGATGCATGGT-TGTGCATCGATACACAAAATGCATTCG
*
187231 ATGTTTCAATAA-AACCAAGAGTGGATCGATGTATGGTTGTGCATCGATACACAAAATGCAT
1 ATGTTTCAA-AAGAACCAAGAGTGGATCGATGCATGGTTGTGCATCGATACACAAAATGCAT
187292 CCGAAATAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 7 0.13
64 44 0.83
65 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (64 bp):
ATGTTTCAAAAGAACCAAGAGTGGATCGATGCATGGTTGTGCATCGATACACAAAATGCATTCG
Found at i:188805 original size:31 final size:31
Alignment explanation
Indices: 188767--188891 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
188757 CCCGAAGGAC
* * *
188767 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
188798 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
188829 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
188860 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
188891 C
1 C
188892 CCTCAACCCT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:189582 original size:64 final size:63
Alignment explanation
Indices: 189483--189643 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
189473 TAATGAAGGT
* * *
189483 ATGCATCGATGCACTACACCATGCATTGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
189546 GG
62 GC
*
189548 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
189612 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
189644 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:192864 original size:31 final size:31
Alignment explanation
Indices: 192826--193043 Score: 393
Period size: 31 Copynumber: 7.0 Consensus size: 31
192816 CCCGAAGGAC
* * *
192826 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
192857 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
192888 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
192919 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
192950 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
192981 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
193012 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
193043 C
1 C
193044 CCTAAACCCT
Statistics
Matches: 183, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 182 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:193788 original size:64 final size:63
Alignment explanation
Indices: 193635--193795 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 63
193625 TAATGAAGGT
* * * * *
193635 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCAATGCACTCCA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* * * *
193700 ATGTATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCAATGCACTCCATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGC
* * *
193764 ATGCATCAATGCACTGCATGTGCATTGATGCA
1 ATGCATCAATGCACTCCATATGCATCGATGCA
193796 CCTTAAACAA
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 55 0.68
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (63 bp):
ATGCATCAATGCACTCCATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:195876 original size:16 final size:15
Alignment explanation
Indices: 195839--195869 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
195829 AAAATGAATT
195839 ACATTTTTTTGGAAA
1 ACATTTTTTTGGAAA
*
195854 ACATTTTTTTTGAAA
1 ACATTTTTTTGGAAA
195869 A
1 A
195870 TTATTTTACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (15 bp):
ACATTTTTTTGGAAA
Found at i:196330 original size:22 final size:19
Alignment explanation
Indices: 196280--196327 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
196270 TTTTTACGAA
*
196280 ATTAATAAATAATATTAAT
1 ATTATTAAATAATATTAAT
*
196299 CTTATT-AATAATTATTATAT
1 ATTATTAAATAA-TATTA-AT
196319 ATTATTAAA
1 ATTATTAAA
196328 ATAAAAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.22
19 9 0.39
20 7 0.30
21 2 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTATTAAATAATATTAAT
Found at i:196802 original size:17 final size:17
Alignment explanation
Indices: 196777--196809 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
196767 ATAACATTTA
196777 TATTGATTTTTTTATAT
1 TATTGATTTTTTTATAT
*
196794 TATTTATTTTTTTATA
1 TATTGATTTTTTTATA
196810 ACGTTTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TATTGATTTTTTTATAT
Found at i:197638 original size:4 final size:4
Alignment explanation
Indices: 197625--197655 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
197615 TTAGAATTTG
197625 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
197656 GACTATCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:197949 original size:19 final size:19
Alignment explanation
Indices: 197925--197963 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
197915 TATTATTCAC
197925 TGTTACTTTCGATTTATAA
1 TGTTACTTTCGATTTATAA
197944 TGTTACTTTCGATTTATAA
1 TGTTACTTTCGATTTATAA
197963 T
1 T
197964 CCACGGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (19 bp):
TGTTACTTTCGATTTATAA
Found at i:198145 original size:12 final size:12
Alignment explanation
Indices: 198128--198168 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
198118 AACCACGGGC
198128 AAAAGAAGCGAA
1 AAAAGAAGCGAA
**
198140 AAAAGAAAAGAA
1 AAAAGAAGCGAA
*
198152 AGAAGAAGCGAA
1 AAAAGAAGCGAA
198164 AAAAG
1 AAAAG
198169 CCGTAAGAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAGAAGCGAA
Found at i:198331 original size:3 final size:3
Alignment explanation
Indices: 198325--198351 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
198315 ATGTTTTAAA
198325 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
198352 GAACTGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:199593 original size:180 final size:181
Alignment explanation
Indices: 199259--199620 Score: 701
Period size: 180 Copynumber: 2.0 Consensus size: 181
199249 GGTACATAGT
199259 TGTCATCTTCCTTCGCCTCAAGGAATAAAAGTCCACAAGGATTTCAAAGCAAAAGCAGCAGCAGG
1 TGTCATCTTCCTTCGCCTCAAGGAATAAAAGTCCACAAGGATTTCAAAGCAAAAGCAGCAGCAGG
199324 GGCAAAGAGAGCAAAAACCCAAACGCTTGTGGAATTTCATACGCTGCGCAACAGAGCTGGAAGAT
66 GGCAAAGAGAGCAAAAACCCAAACGCTTGTGGAATTTCATACGCTGCGCAACAGAGCTGGAAGAT
199389 GCAGGAATCAAATTCGAGAAGACGGAGAATCAGAGGAAAGGGATAGACTAC
131 GCAGGAATCAAATTCGAGAAGACGGAGAATCAGAGGAAAGGGATAGACTAC
199440 TGTCATCTTCCTTCGCCTCAAGGAATAAAAGTCCACAAGGATTTCAAAGCAAAAGCAGCAGCAGG
1 TGTCATCTTCCTTCGCCTCAAGGAATAAAAGTCCACAAGGATTTCAAAGCAAAAGCAGCAGCAGG
199505 GGC-AAGAGAAGC-AAAACCCAAACGCTTGTGGAATTTCATACGCTGCGCAACAGAGCTGGAAGA
66 GGCAAAGAG-AGCAAAAACCCAAACGCTTGTGGAATTTCATACGCTGCGCAACAGAGCTGGAAGA
199568 TGCAGGAATCAAATTCGAGAAGACGGAGAATCAGAGGAAAGGGATAGACTAC
130 TGCAGGAATCAAATTCGAGAAGACGGAGAATCAGAGGAAAGGGATAGACTAC
199620 T
1 T
199621 CTTTCGATAT
Statistics
Matches: 180, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
180 109 0.61
181 71 0.39
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.16
Consensus pattern (181 bp):
TGTCATCTTCCTTCGCCTCAAGGAATAAAAGTCCACAAGGATTTCAAAGCAAAAGCAGCAGCAGG
GGCAAAGAGAGCAAAAACCCAAACGCTTGTGGAATTTCATACGCTGCGCAACAGAGCTGGAAGAT
GCAGGAATCAAATTCGAGAAGACGGAGAATCAGAGGAAAGGGATAGACTAC
Found at i:203688 original size:39 final size:39
Alignment explanation
Indices: 203595--203689 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
203585 GACCATATTG
* **
203595 CTTACCGCAGGCTCCTCGGCTTTGTGCTCGGGGTAAGTC
1 CTTACCGCAGGCTCCTCGGCTTTATGCTCAAGGTAAGTC
* *
203634 CTTTCCGTAGGCTCCTCGGCTTTATGCTCAAGGTAAGTC
1 CTTACCGCAGGCTCCTCGGCTTTATGCTCAAGGTAAGTC
* *
203673 CTTACTGCAGTCTCCTC
1 CTTACCGCAGGCTCCTC
203690 TACTTTGTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.13, C:0.32, G:0.24, T:0.32
Consensus pattern (39 bp):
CTTACCGCAGGCTCCTCGGCTTTATGCTCAAGGTAAGTC
Found at i:203716 original size:39 final size:39
Alignment explanation
Indices: 203653--203796 Score: 119
Period size: 39 Copynumber: 3.7 Consensus size: 39
203643 GGCTCCTCGG
* * * *
203653 CTTTATGCTCAAGGTAAGTCCTTACTGCAGTCTCCTCTA
1 CTTTGTGCACAAGATAAGACCTTACTGCAGTCTCCTCTA
* * * * *
203692 CTTTGTGCACATGATAAGATCTTACTGCA-TGCTCATTTG
1 CTTTGTGCACAAGATAAGACCTTACTGCAGT-CTCCTCTA
** * * *
203731 CTTTGTGCACAAGATAAGACCTTACCACGGACTCCTCAA
1 CTTTGTGCACAAGATAAGACCTTACTGCAGTCTCCTCTA
* * *
203770 CTTTGTGCACAGGGTAAGCCCTTACTG
1 CTTTGTGCACAAGATAAGACCTTACTG
203797 AGTGTACATG
Statistics
Matches: 79, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
38 1 0.01
39 78 0.99
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (39 bp):
CTTTGTGCACAAGATAAGACCTTACTGCAGTCTCCTCTA
Found at i:204165 original size:2 final size:2
Alignment explanation
Indices: 204158--204195 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
204148 TGATTTTCTG
204158 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
204196 GTTTATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206854 original size:62 final size:62
Alignment explanation
Indices: 206786--206909 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
206776 AATAAAAATA
206786 AATAAAATTTCCTTAAATAATGAATCTATACTTAAATTGATTAAGAAAAATATTTATTTTCT
1 AATAAAATTTCCTTAAATAATGAATCTATACTTAAATTGATTAAGAAAAATATTTATTTTCT
206848 AATAAAATTTCCTTAAATAATGAATCTATACTTAAATTGATTAAGAAAAATATTTATTTTCT
1 AATAAAATTTCCTTAAATAATGAATCTATACTTAAATTGATTAAGAAAAATATTTATTTTCT
206910 TTTTGCAGCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (62 bp):
AATAAAATTTCCTTAAATAATGAATCTATACTTAAATTGATTAAGAAAAATATTTATTTTCT
Found at i:209490 original size:14 final size:14
Alignment explanation
Indices: 209471--209507 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
209461 ACAACAACAA
209471 CAAAAAGAAAAATC
1 CAAAAAGAAAAATC
209485 CAAAAAGAAAAATC
1 CAAAAAGAAAAATC
209499 CAAAAAGAA
1 CAAAAAGAA
209508 GTGCAAGTGA
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:0.73, C:0.14, G:0.08, T:0.05
Consensus pattern (14 bp):
CAAAAAGAAAAATC
Found at i:214368 original size:2 final size:2
Alignment explanation
Indices: 214361--214452 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
214351 TCGGGCCGGG
* * * *
214361 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
214401 TT TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- 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
214439 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
214453 ATTATTTTTA
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
1 6 0.09
2 61 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:214485 original size:12 final size:13
Alignment explanation
Indices: 214469--214513 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
214459 TTTAATATTT
*
214469 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
*
214481 ATCGGGGCGGATA
1 ATCGGGGCGGGTA
214494 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
214507 ATCGGGG
1 ATCGGGG
214514 AGGGGATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.16, C:0.16, G:0.51, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:218783 original size:39 final size:40
Alignment explanation
Indices: 218706--218789 Score: 145
Period size: 39 Copynumber: 2.1 Consensus size: 40
218696 TGCCCTTGAT
218706 AAAG-ATATGCAGATGGAACTCTTAACTGAAATTTTCATTG
1 AAAGAATATGCAGATGGAACTC-TAACTGAAATTTTCATTG
218746 AAAGAATATGCAGATGGAACTC-AACTGAAATTTTCATTG
1 AAAGAATATGCAGATGGAACTCTAACTGAAATTTTCATTG
218785 AAAGA
1 AAAGA
218790 GGTCGGATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 22 0.51
40 4 0.09
41 17 0.40
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.29
Consensus pattern (40 bp):
AAAGAATATGCAGATGGAACTCTAACTGAAATTTTCATTG
Found at i:219513 original size:27 final size:28
Alignment explanation
Indices: 219456--219513 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
219446 AGAGGTGCAT
219456 AAAAAATCCGAATATCCGATTTTGGGTAA
1 AAAAAATCCGAATATCCGATTTTGGG-AA
*
219485 AAAATATCCGAA-A-CCGGATTTT-GGAA
1 AAAAAATCCGAATATCC-GATTTTGGGAA
219511 AAA
1 AAA
219514 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 7 0.26
29 11 0.41
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGGGAA
Found at i:219612 original size:24 final size:25
Alignment explanation
Indices: 219585--219646 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
219575 AAATTGAACG
*
219585 ACCGGTTTTTTTA-CCGGATTAAAA
1 ACCGGTTTTTTTATCCGGATAAAAA
*
219609 ACCGATTTTTTTATCCGGATAAAAA
1 ACCGGTTTTTTTATCCGGATAAAAA
219634 ACCGGTTTTTTTA
1 ACCGGTTTTTTTA
219647 AAAACTGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 12 0.35
25 22 0.65
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (25 bp):
ACCGGTTTTTTTATCCGGATAAAAA
Found at i:219700 original size:40 final size:41
Alignment explanation
Indices: 219603--219700 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 41
219593 TTTTACCGGA
*
219603 TTAAAAACCGATTTTTTTATCCGGATAAAAAACCGGTTTTT
1 TTAAAAACCGGTTTTTTTATCCGGATAAAAAACCGGTTTTT
* * *
219644 TTAAAAACTGG-ATTTTTATCC-GA-AAAAATCCGGTTTTTT
1 TTAAAAACCGGTTTTTTTATCCGGATAAAAAACCGG-TTTTT
*
219683 TTTAAAACCGGTTTTTTT
1 TTAAAAACCGGTTTTTTT
219701 CAAACCGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 9 0.19
39 16 0.33
40 14 0.29
41 9 0.19
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (41 bp):
TTAAAAACCGGTTTTTTTATCCGGATAAAAAACCGGTTTTT
Found at i:226696 original size:15 final size:15
Alignment explanation
Indices: 226678--226708 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
226668 AAATTCTAAA
226678 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
226693 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
226708 T
1 T
226709 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:237922 original size:23 final size:23
Alignment explanation
Indices: 237879--237922 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
237869 TAATTGAATT
*
237879 TTAAAATATTAATGGGTTTAAGG
1 TTAAAATATTAATAGGTTTAAGG
*
237902 TTAAAAT-TTATTAGGTCTTAA
1 TTAAAATATTAATAGGT-TTAA
237923 TATTTCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (23 bp):
TTAAAATATTAATAGGTTTAAGG
Found at i:239000 original size:2 final size:2
Alignment explanation
Indices: 238993--239021 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
238983 CAAATCTTTT
238993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
239022 TTGATGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:240817 original size:2 final size:2
Alignment explanation
Indices: 240810--240843 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
240800 ACAAATGATA
240810 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
240844 TTGATAATCA
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
Found at i:243622 original size:20 final size:20
Alignment explanation
Indices: 243599--243636 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
243589 AACCGCTAAA
* *
243599 GAACCGATAGAACCGGTTGG
1 GAACCGACAAAACCGGTTGG
243619 GAACCGACAAAACCGGTT
1 GAACCGACAAAACCGGTT
243637 CACACGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.29, T:0.13
Consensus pattern (20 bp):
GAACCGACAAAACCGGTTGG
Found at i:251206 original size:16 final size:17
Alignment explanation
Indices: 251180--251211 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
251170 TTCATTCAAT
251180 TTTTCCATGACATTTAC
1 TTTTCCATGACATTTAC
251197 TTTT-CATGACATTTA
1 TTTTCCATGACATTTA
251212 GATAGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTTCCATGACATTTAC
Found at i:254017 original size:27 final size:27
Alignment explanation
Indices: 253986--254040 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
253976 TCATGAAGGC
253986 AAAATTAATCAGGGAAATGAAATTGTT
1 AAAATTAATCAGGGAAATGAAATTGTT
* *
254013 AAAATTACTCGGGGAAATGAAATTGTT
1 AAAATTAATCAGGGAAATGAAATTGTT
254040 A
1 A
254041 CCTTCGTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.29
Consensus pattern (27 bp):
AAAATTAATCAGGGAAATGAAATTGTT
Found at i:255269 original size:29 final size:28
Alignment explanation
Indices: 255228--255283 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
255218 AAGAGATAAA
*
255228 ATTTTATTTCAAGTGAAACAATCTCAAT
1 ATTTTATTTCAAGGGAAACAATCTCAAT
*
255256 ATTTGTATTTCAAGGGAAATAATCTCAA
1 ATTT-TATTTCAAGGGAAACAATCTCAA
255284 GCGAGACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (28 bp):
ATTTTATTTCAAGGGAAACAATCTCAAT
Found at i:255327 original size:66 final size:66
Alignment explanation
Indices: 255168--255489 Score: 268
Period size: 66 Copynumber: 4.9 Consensus size: 66
255158 AGATGATTTT
* * * * * **
255168 TTTCGAGTAAAACAATTTCAAAGTTTGTATTTCAAGGGAAATTATCTCAGAAGAGATAAAATTTT
1 TTTCAAGTGAAACGATTTCAAAGTTTGTATTTCAAGGGAAACTATCTCAGACGAGATAAAAAATT
*
255233 A
66 C
* * *
255234 TTTCAAGTGAAACAATCTCAATA-TTTGTATTTCAAGGGAAA-TAATCTCA-AGCGAGACAACAA
1 TTTCAAGTGAAACGATTTCAA-AGTTTGTATTTCAAGGGAAACT-ATCTCAGA-CGAGATAA-AA
255296 AATTC
62 AATTC
* * * **
255301 TTTCAAGTGAAA-GTTTTCAAAGTTTGTAATACAAGATAAACTATCTCAGACGAGAT--AAAA-T
1 TTTCAAGTGAAACGATTTCAAAGTTTGTATTTCAAGGGAAACTATCTCAGACGAGATAAAAAATT
255362 -
66 C
* * * * *
255362 TTTCGAGTGAAATGATTTCAAATTTTATGTTTCAAGGGAAACTATCTCA-AGCGAGATAAAAATA
1 TTTCAAGTGAAACGATTTCAAAGTTTGTATTTCAAGGGAAACTATCTCAGA-CGAGATAAAAA-A
255426 TTTC
64 -TTC
* * * * * *
255430 TTTCGAGTAAAAC-TTTTCAAAGTTTGTATTTCAAGCGAAACTATTTCAGGCGAGATAAAA
1 TTTCAAGTGAAACGATTTCAAAGTTTGTATTTCAAGGGAAACTATCTCAGACGAGATAAAA
255490 TTTTTGTTTC
Statistics
Matches: 206, Mismatches: 34, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
61 12 0.06
62 35 0.17
63 4 0.02
64 3 0.01
65 4 0.02
66 78 0.38
67 59 0.29
68 11 0.05
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (66 bp):
TTTCAAGTGAAACGATTTCAAAGTTTGTATTTCAAGGGAAACTATCTCAGACGAGATAAAAAATT
C
Found at i:255484 original size:129 final size:129
Alignment explanation
Indices: 255163--255493 Score: 375
Period size: 129 Copynumber: 2.5 Consensus size: 129
255153 AAGTGAGATG
* * * * *
255163 ATTTTTTTCGAGTAAAACAATTTCAAAGTTTGTATTTCAAGGGAAATTATCTCAGAAGAGATAAA
1 ATTTCTTTCGAGTAAAAC-TTTTCAAAGTTTGTATTTCAAGAGAAACTATCTCAGACGAGATAAA
255228 ATTTTATTTCAAGTGAAACAATCTCAATATTTGTATTTCAAGGGAAATAATCTCAAGCGAGACAA
65 A---T-TTTCAAGTGAAACAATCTCAATATTTGTATTTCAAGGGAAATAATCTCAAGCGAGACAA
255293 CAAA
126 CAAA
* * * * * *
255297 A-TTCTTTCAAGTGAAAGTTTTCAAAGTTTGTAATACAAGATAAACTATCTCAGACGAGATAAAA
1 ATTTCTTTCGAGTAAAACTTTTCAAAGTTTGTATTTCAAGAGAAACTATCTCAGACGAGATAAAA
* ** * *
255361 TTTTCGAGTGAAATGATTTCAA-ATTT-TATGTTTCAAGGGAAACT-ATCTCAAGCGAGATAA-A
66 TTTTCAAGTGAAACAATCTCAATATTTGTA--TTTCAAGGGAAA-TAATCTCAAGCGAGACAACA
255422 AA
128 AA
* * *
255424 TATTTCTTTCGAGTAAAACTTTTCAAAGTTTGTATTTCAAGCGAAACTATTTCAGGCGAGATAAA
1 -ATTTCTTTCGAGTAAAACTTTTCAAAGTTTGTATTTCAAGAGAAACTATCTCAGACGAGATAAA
255489 ATTTT
65 ATTTT
255494 TGTTTCGACA
Statistics
Matches: 167, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
126 2 0.01
127 7 0.04
128 45 0.27
129 60 0.36
132 40 0.24
133 12 0.07
134 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (129 bp):
ATTTCTTTCGAGTAAAACTTTTCAAAGTTTGTATTTCAAGAGAAACTATCTCAGACGAGATAAAA
TTTTCAAGTGAAACAATCTCAATATTTGTATTTCAAGGGAAATAATCTCAAGCGAGACAACAAA
Found at i:255602 original size:36 final size:36
Alignment explanation
Indices: 255560--256045 Score: 196
Period size: 36 Copynumber: 13.9 Consensus size: 36
255550 TCTTAAAATT
* *
255560 TGTGTTTCAAGGAAAACAATCTCAAGTGAGATAAAA
1 TGTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAA
* * *
255596 TGTGTTTTAAGAAAAAAAAAATCTCAAGTTAGATGAAA
1 TGTGTTTTAAG--AAAAACAATCTCAAGTGAGATAAAA
* **
255634 T-TCGTTTTAAGAAAAACAATCTCAAGCGAGACGAAA
1 TGT-GTTTTAAGAAAAACAATCTCAAGTGAGATAAAA
* * * *
255670 TTTATTTTTAA-AAAAACAATCTCAAGCGAGACAAAA
1 TGT-GTTTTAAGAAAAACAATCTCAAGTGAGATAAAA
* * * * *
255706 TTTATTTTAAGAAAAATAATCTCAATTGAGATAATA
1 TGTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAA
* * ** ** * * *
255742 TTTCTTTTAAGTGAAATGATTTTAA---AG-T---T
1 TGTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAA
* * * ** * * *
255771 TGTGTTTCAA-AGGATATTATCTCATGCGAGATAAAC
1 TGTGTTTTAAGA-AAAACAATCTCAAGTGAGATAAAA
* * *
255807 TTTGTTTTTAAG-AAAAGAATCTCAAGTGAGATGAAA
1 TGTG-TTTTAAGAAAAACAATCTCAAGTGAGATAAAA
* * *
255843 TTTGTTTTAAG-AAAAGAATCTCAAGTGAGATGAAA
1 TGTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAA
* * * *
255878 TTTGTTTTAAGAAAAAACAATATCAAGTAAGAT--GA
1 TGTGTTTTAAG-AAAAACAATCTCAAGTGAGATAAAA
* * *
255913 TTTTTTTTAAGAAAAA-ATAT-T--AGTGAG-TCGAAA
1 TGTGTTTTAAGAAAAACA-ATCTCAAGTGAGAT-AAAA
* * * *
255946 TTTATTTTAAGAAAAACAATTTCAAGTGAG--ACAA
1 TGTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAA
**
255980 T-T-TTTTAAAGAAAAACAATCTC-AGTGAGACGAAA
1 TGTGTTTT-AAGAAAAACAATCTCAAGTGAGATAAAA
* * *
256014 T-TGTTTTAA-AAAGATAATTTCAAGTGAGATAA
1 TGTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
256046 GATTTTGTTT
Statistics
Matches: 357, Mismatches: 63, Indels: 62
0.74 0.13 0.13
Matches are distributed among these distances:
29 15 0.04
30 1 0.00
31 5 0.01
32 13 0.04
33 47 0.13
34 26 0.07
35 63 0.18
36 127 0.36
37 30 0.08
38 30 0.08
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (36 bp):
TGTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAA
Found at i:255858 original size:35 final size:35
Alignment explanation
Indices: 255789--256056 Score: 211
Period size: 35 Copynumber: 7.7 Consensus size: 35
255779 AAAGGATATT
* * *
255789 ATCTCATGCGAGAT-AAACTTTGTTTTTAAGAAAAGA
1 ATCTCAAGTGAGATGAAA-TTTG-TTTTAAGAAAACA
*
255825 ATCTCAAGTGAGATGAAATTTGTTTTAAGAAAAGA
1 ATCTCAAGTGAGATGAAATTTGTTTTAAGAAAACA
255860 ATCTCAAGTGAGATGAAATTTGTTTTAAGAAAAAACA
1 ATCTCAAGTGAGATGAAATTTGTTTTAAG--AAAACA
* * *
255897 ATATCAAGTAAGATG--ATTTTTTTTAAGAAAA-A
1 ATCTCAAGTGAGATGAAATTTGTTTTAAGAAAACA
* * *
255929 ATAT-TAGTGAG-TCGAAATTTATTTTAAGAAAAACA
1 ATCTCAAGTGAGAT-GAAATTTGTTTTAAG-AAAACA
* * *
255964 ATTTCAAGTGAGA--CAATTT-TTTAAAGAAAAACA
1 ATCTCAAGTGAGATGAAATTTGTTTTAAG-AAAACA
* *
255997 ATCTC-AGTGAGACGAAA-TTGTTTTAA-AAAGATA
1 ATCTCAAGTGAGATGAAATTTGTTTTAAGAAA-ACA
*
256030 ATTTCAAGTGAGAT-AAGATTTTGTTTT
1 ATCTCAAGTGAGATGAA-A-TTTGTTTT
256057 GAGTGAAAAC
Statistics
Matches: 195, Mismatches: 19, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
30 1 0.01
31 6 0.03
32 15 0.08
33 42 0.22
34 24 0.12
35 57 0.29
36 29 0.15
37 21 0.11
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (35 bp):
ATCTCAAGTGAGATGAAATTTGTTTTAAGAAAACA
Found at i:256051 original size:68 final size:67
Alignment explanation
Indices: 255807--256051 Score: 237
Period size: 66 Copynumber: 3.6 Consensus size: 67
255797 CGAGATAAAC
* * * *
255807 TTTGTTTTTAAGAAAAGAATCTCAAGTGAGATGAAATTTGTTTTAAGAAAAGAATCTCAAGTGAG
1 TTTG-TTTTAAAAAAACAATTTCAAGTGAGAT-AAATTT-TTTTAAGAAAAAAATCTC-AGTGAG
*
255872 ATGAAA
62 ACGAAA
* * * * *
255878 TTTGTTTTAAGAAAAAACAATATCAAGTAAGATGATTTTTTTTAAGAAAAAATAT-T-AGTGAGT
1 TTTGTTTT-A-AAAAAACAATTTCAAGTGAGATAAATTTTTTTAAGAAAAAA-ATCTCAGTGAGA
255941 CGAAA
63 CGAAA
* * *
255946 TTTATTTTAAGAAAAACAATTTCAAGTGAGA-CAATTTTTTAAAGAAAAACAATCTCAGTGAGAC
1 TTTGTTTTAA-AAAAACAATTTCAAGTGAGATAAATTTTTTTAAGAAAAA-AATCTCAGTGAGAC
256010 GAAA
64 GAAA
* *
256014 -TTGTTTTAAAAAGATAATTTCAAGTGAGATAAGATTTT
1 TTTGTTTTAAAAAAACAATTTCAAGTGAGATAA-ATTTT
256052 GTTTTGAGTG
Statistics
Matches: 145, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
66 36 0.25
67 30 0.21
68 33 0.23
70 17 0.12
71 11 0.08
72 18 0.12
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (67 bp):
TTTGTTTTAAAAAAACAATTTCAAGTGAGATAAATTTTTTTAAGAAAAAAATCTCAGTGAGACGA
AA
Found at i:262854 original size:19 final size:20
Alignment explanation
Indices: 262832--262871 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
262822 TGTTTTGAAA
262832 TTTTGGC-TTTTTTGTTTTT
1 TTTTGGCTTTTTTTGTTTTT
*
262851 TTTTGTCTTTTTTTGTTTTT
1 TTTTGGCTTTTTTTGTTTTT
262871 T
1 T
262872 GTTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.82
Consensus pattern (20 bp):
TTTTGGCTTTTTTTGTTTTT
Found at i:262861 original size:11 final size:10
Alignment explanation
Indices: 262839--262880 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
262829 AAATTTTGGC
262839 TTTTTTGTTT
1 TTTTTTGTTT
*
262849 TTTTTTGTCT
1 TTTTTTGTTT
262859 TTTTTTGTTT
1 TTTTTTGTTT
*
262869 TTTGTT-TTT
1 TTTTTTGTTT
262878 TTT
1 TTT
262881 AAAAAAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 6 0.21
10 23 0.79
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:262872 original size:17 final size:16
Alignment explanation
Indices: 262839--262880 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
262829 AAATTTTGGC
*
262839 TTTTTTGTTTTTTTTTG
1 TTTTTT-TTGTTTTTTG
262856 TCTTTTTTTGTTTTTTG
1 T-TTTTTTTGTTTTTTG
262873 TTTTTTTT
1 TTTTTTTT
262881 AAAAAAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (16 bp):
TTTTTTTTGTTTTTTG
Found at i:269688 original size:2 final size:2
Alignment explanation
Indices: 269681--269723 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
269671 ACATTTTAAA
269681 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
269723 A
1 A
269724 CTATTCAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:270016 original size:17 final size:17
Alignment explanation
Indices: 269994--270031 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
269984 CTATGTTGGT
*
269994 TTTTC-TTTAATTTTCAA
1 TTTTCTTTTAAATTTC-A
270011 TTTTCTTTTAAATTTCA
1 TTTTCTTTTAAATTTCA
270028 TTTT
1 TTTT
270032 TATTGTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTCTTTTAAATTTCA
Found at i:270032 original size:18 final size:17
Alignment explanation
Indices: 269993--270032 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
269983 TCTATGTTGG
*
269993 TTTTTCTTTAATTTTCA
1 TTTTTCTTTAAATTTCA
*
270010 ATTTTCTTTTAAATTTCA
1 TTTTTC-TTTAAATTTCA
270028 TTTTT
1 TTTTT
270033 ATTGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTCTTTAAATTTCA
Found at i:274380 original size:21 final size:21
Alignment explanation
Indices: 274354--274394 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
274344 ATATCATTCA
274354 AAACAAAAT-AAACATCCAAAC
1 AAAC-AAATCAAACATCCAAAC
*
274375 AAACAATTCAAACATCCAAA
1 AAACAAATCAAACATCCAAA
274395 TTTCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.63, C:0.24, G:0.00, T:0.12
Consensus pattern (21 bp):
AAACAAATCAAACATCCAAAC
Found at i:286833 original size:21 final size:20
Alignment explanation
Indices: 286787--286825 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
286777 CTCATTAAAG
286787 AAGTATAGATACTCAAGGTC
1 AAGTATAGATACTCAAGGTC
* *
286807 TAGTATCGATACTCCAAGG
1 AAGTATAGATACT-CAAGG
286826 GTAAGTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AAGTATAGATACTCAAGGTC
Found at i:288030 original size:49 final size:49
Alignment explanation
Indices: 287830--288050 Score: 180
Period size: 49 Copynumber: 4.6 Consensus size: 49
287820 ACAGGAGGAG
* * * * * *
287830 TGAATCATCAAGGTTTTCCAAATTTGATTTCCATGAAGGGGTGATGGAA
1 TGAATCATCAAGGTTTTTCAGATTTGATCTCCACGAAGAGATGATGGAA
* * * * * *
287879 TGAATCATCAAAG-TTTTCATATTTAATCTCTACGAAGAGATGGTGGGA
1 TGAATCATCAAGGTTTTTCAGATTTGATCTCCACGAAGAGATGATGGAA
** ** * * * *
287927 CAAATCGCCAAAAG--TTTCAGATTTGATCTCCACGAAGTGATGGTAGG-G
1 TGAATCATC-AAGGTTTTTCAGATTTGATCTCCACGAAGAGATGAT-GGAA
* * *
287975 TAAATCATCAAGGTTTTTCAGATTTGATTTCCATGAAGAGATGATGGAA
1 TGAATCATCAAGGTTTTTCAGATTTGATCTCCACGAAGAGATGATGGAA
*
288024 TGAATCATCAAGGTTTTCCAGATTTGA
1 TGAATCATCAAGGTTTTTCAGATTTGA
288051 GAGCGAAGAG
Statistics
Matches: 136, Mismatches: 31, Indels: 10
0.77 0.18 0.06
Matches are distributed among these distances:
47 3 0.02
48 64 0.47
49 69 0.51
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (49 bp):
TGAATCATCAAGGTTTTTCAGATTTGATCTCCACGAAGAGATGATGGAA
Found at i:288142 original size:48 final size:48
Alignment explanation
Indices: 287937--288147 Score: 112
Period size: 49 Copynumber: 4.4 Consensus size: 48
287927 CAAATCGCCA
* ** * *
287937 AAAGTTTC-AGATTTGATCTCCACGAAGTGATGGTAGG-GTAAATCATC
1 AAAGTTTCTAGATTTGATCTCCATGAAGAAATAGT-GGAGCAAATCATC
* * * * ***
287984 AAGGTTTTTCAGATTTGATTTCCATGAAGAGAT-GATGGAATGAATCATC
1 AAAGTTTCT-AGATTTGATCTCCATGAAGAAATAG-TGGAGCAAATCATC
* * *** * * * *
288033 AAGGTTTTCCAGATTTGA-GAGC--GAAGAGATAGTGGGGCAAATTATT
1 AAAG-TTTCTAGATTTGATCTCCATGAAGAAATAGTGGAGCAAATCATC
* *
288079 AAAGTTTCTAGATTTGGTCTCCATGAAGAAATAGTGGAGCTAATCATC
1 AAAGTTTCTAGATTTGATCTCCATGAAGAAATAGTGGAGCAAATCATC
*
288127 AAAGTTT-TCATATTTGATCTC
1 AAAGTTTCT-AGATTTGATCTC
288148 TACGAAGATA
Statistics
Matches: 123, Mismatches: 31, Indels: 19
0.71 0.18 0.11
Matches are distributed among these distances:
45 11 0.09
46 20 0.16
47 8 0.07
48 40 0.33
49 41 0.33
50 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (48 bp):
AAAGTTTCTAGATTTGATCTCCATGAAGAAATAGTGGAGCAAATCATC
Found at i:288155 original size:48 final size:47
Alignment explanation
Indices: 287881--288164 Score: 170
Period size: 48 Copynumber: 6.0 Consensus size: 47
287871 TGATGGAATG
* * * * *
287881 AATCATCAAAGTTTTCATATTTAATCTCTACGAAGAGATGGTGGGACA
1 AATCATCAAAGTTTTCAGATTTGATCTCCACGAAGAGATAGTGGG-CT
** * *
287929 AATCGCCAAAAG-TTTCAGATTTGATCTCCACGAAGTGATGGTAGGG-T
1 AATCATC-AAAGTTTTCAGATTTGATCTCCACGAAGAGATAGT-GGGCT
* * * **
287976 AAATCATCAAGGTTTTTCAGATTTGATTTCCATGAAGAGAT-GATGGAAT
1 -AATCATCAAAG-TTTTCAGATTTGATCTCCACGAAGAGATAG-TGGGCT
* * *
288025 GAATCATCAAGGTTTTCCAGATTTGA----GAGCGAAGAGATAGTGGGGCA
1 -AATCATCAAAGTTTT-CAGATTTGATCTCCA-CGAAGAGATAGT-GGGCT
* * * * *
288072 AATTATTAAAG-TTTCTAGATTTGGTCTCCATGAAGAAATAGTGGAGCT
1 AATCATCAAAGTTTTC-AGATTTGATCTCCACGAAGAGATAGTGG-GCT
* * * *
288120 AATCATCAAAGTTTTCATATTTGATCTCTACGAAGATATGGTGGG
1 AATCATCAAAGTTTTCAGATTTGATCTCCACGAAGAGATAGTGGG
288165 GAAAACGCCA
Statistics
Matches: 182, Mismatches: 36, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
44 1 0.01
45 11 0.06
46 17 0.09
47 9 0.05
48 86 0.47
49 58 0.32
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (47 bp):
AATCATCAAAGTTTTCAGATTTGATCTCCACGAAGAGATAGTGGGCT
Found at i:289565 original size:17 final size:17
Alignment explanation
Indices: 289543--289580 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
289533 TATGTTGGTT
*
289543 TTTTC-TTTAATTTTCCA
1 TTTTCTTTTAAATTT-CA
289560 TTTTCTTTTAAATTTCA
1 TTTTCTTTTAAATTTCA
289577 TTTT
1 TTTT
289581 TATTATTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTCTTTTAAATTTCA
Found at i:289609 original size:21 final size:19
Alignment explanation
Indices: 289577--289619 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
289567 TTAAATTTCA
*
289577 TTTTTATTATTTCCTTATTT
1 TTTTTATTATTTACTT-TTT
*
289597 TTTTTCTTAATTTACTTTTT
1 TTTTTATT-ATTTACTTTTT
289617 TTT
1 TTT
289620 ATGATGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTATTATTTACTTTTT
Found at i:290373 original size:14 final size:14
Alignment explanation
Indices: 290354--290380 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
290344 GAGGAGTCAA
290354 ATTAATTATTATTC
1 ATTAATTATTATTC
290368 ATTAATTATTATT
1 ATTAATTATTATT
290381 TTTTTAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTAATTATTATTC
Found at i:290710 original size:10 final size:10
Alignment explanation
Indices: 290688--290743 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
290678 TCATATATTT
290688 AAAATCAATA
1 AAAATCAATA
*
290698 AAAATACAAAA
1 AAAAT-CAATA
*
290709 AAAATGAATTA
1 AAAATCAA-TA
*
290720 AAAATGAATA
1 AAAATCAATA
*
290730 AAATTCAATA
1 AAAATCAATA
290740 AAAA
1 AAAA
290744 ATGTAAAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
10 20 0.53
11 18 0.47
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (10 bp):
AAAATCAATA
Found at i:290712 original size:21 final size:20
Alignment explanation
Indices: 290688--290743 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
290678 TCATATATTT
290688 AAAATCAATAAAAATACAAAA
1 AAAATCAATAAAAAT-CAAAA
* * *
290709 AAAATGAATTAAAAATGAATA
1 AAAATCAA-TAAAAATCAAAA
*
290730 AAATTCAATAAAAA
1 AAAATCAATAAAAA
290744 ATGTAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 16 0.55
22 7 0.24
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATCAATAAAAATCAAAA
Found at i:297882 original size:29 final size:30
Alignment explanation
Indices: 297840--297903 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
297830 ACAAGCCTTA
* * *
297840 GAAAAATTGGGGATCATTTCGTAAGTTTT-
1 GAAAAATTGGGGATAAATTCGTAAATTTTG
* *
297869 GAAAAGTTTGGGATAAATTCGTAAATTTTG
1 GAAAAATTGGGGATAAATTCGTAAATTTTG
297899 GAAAA
1 GAAAA
297904 TTGATGAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (30 bp):
GAAAAATTGGGGATAAATTCGTAAATTTTG
Found at i:299376 original size:47 final size:45
Alignment explanation
Indices: 299279--299403 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
299269 GCAAGTATGC
* * *
299279 AAATAAGCTTACAAGCTTAT-GAAT-GATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
* *
299322 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
*
299369 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
299404 AGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 19 0.26
44 3 0.04
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:299799 original size:12 final size:12
Alignment explanation
Indices: 299782--299806 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
299772 TATTTTCGGA
299782 AGTTACTGTAGC
1 AGTTACTGTAGC
299794 AGTTACTGTAGC
1 AGTTACTGTAGC
299806 A
1 A
299807 TGAACAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
AGTTACTGTAGC
Found at i:309653 original size:3 final size:3
Alignment explanation
Indices: 309645--309675 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
309635 GAACAATTTT
309645 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
309676 CACTTTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:310986 original size:14 final size:14
Alignment explanation
Indices: 310967--311025 Score: 91
Period size: 14 Copynumber: 4.2 Consensus size: 14
310957 TCGGTAATAT
310967 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
310981 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
310995 TTTCGTTTATGTTC
1 GTTCGTTTATGTTC
* *
311009 GTTCATTTATATTC
1 GTTCGTTTATGTTC
311023 GTT
1 GTT
311026 TATGTGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.10, C:0.14, G:0.17, T:0.59
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:311009 original size:38 final size:38
Alignment explanation
Indices: 310964--311045 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
310954 CGTTCGGTAA
* * * *
310964 TATGTTCGTTTATGTT-CGTTCGTTTATGTTCTTTCGTT
1 TATGTTCGTTCAT-TTACATTCGTTTATGTGCATTCGTT
*
311002 TATGTTCGTTCATTTATATTCGTTTATGTGCATTCGTT
1 TATGTTCGTTCATTTACATTCGTTTATGTGCATTCGTT
311040 TATGTT
1 TATGTT
311046 TAGCCCAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
37 2 0.05
38 36 0.95
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (38 bp):
TATGTTCGTTCATTTACATTCGTTTATGTGCATTCGTT
Found at i:311036 original size:14 final size:14
Alignment explanation
Indices: 310968--311045 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
310958 CGGTAATATG
*
310968 TTCGTTTATGTTCG
1 TTCGTTTATGTTCA
*
310982 TTCGTTTATGTTCT
1 TTCGTTTATGTTCA
*
310996 TTCGTTTATGTTCG
1 TTCGTTTATGTTCA
*
311010 TTCATTTA---T-A
1 TTCGTTTATGTTCA
*
311020 TTCGTTTATGTGCA
1 TTCGTTTATGTTCA
311034 TTCGTTTATGTT
1 TTCGTTTATGTT
311046 TAGCCCAATC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
10 7 0.13
11 1 0.02
14 45 0.85
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.59
Consensus pattern (14 bp):
TTCGTTTATGTTCA
Found at i:311041 original size:24 final size:24
Alignment explanation
Indices: 310996--311042 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
310986 TTTATGTTCT
* *
310996 TTCGTTTATGTTCGTTCATTTATA
1 TTCGTTTATGTGCATTCATTTATA
*
311020 TTCGTTTATGTGCATTCGTTTAT
1 TTCGTTTATGTGCATTCATTTAT
311043 GTTTAGCCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (24 bp):
TTCGTTTATGTGCATTCATTTATA
Found at i:315838 original size:43 final size:43
Alignment explanation
Indices: 315790--315871 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
315780 TTCAAATATG
* * *
315790 TTTTTATTATATTAGTTTGATGTATTCG-GAGATTGTTATCTTA
1 TTTTTAATACATTAGTTTGATGTATTAGTGA-ATTGTTATCTTA
* *
315833 TTTTTAATACGTTAGTTTGGTGTATTAGTGAATTGTTAT
1 TTTTTAATACATTAGTTTGATGTATTAGTGAATTGTTAT
315872 TTTAGGGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 31 0.94
44 2 0.06
ACGTcount: A:0.23, C:0.04, G:0.18, T:0.55
Consensus pattern (43 bp):
TTTTTAATACATTAGTTTGATGTATTAGTGAATTGTTATCTTA
Found at i:318264 original size:3 final size:3
Alignment explanation
Indices: 318256--318314 Score: 91
Period size: 3 Copynumber: 19.3 Consensus size: 3
318246 TACACAAAAT
*
318256 ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
*
318302 CTA ATA ATA ATA A
1 ATA ATA ATA ATA A
318315 ACAATTGTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Done.