Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008506.1 Hibiscus syriacus cultivar Beakdansim tig00111358_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: 1253200
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 1 of 6
Found at i:5496 original size:60 final size:60
Alignment explanation
Indices: 5371--5506 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 60
5361 ATAGTCATAT
* * * *
5371 GATCATTTTATAACTTTTAATAGTTGGGGATTCAACAAAACAATGCACTATAGTCTGATG
1 GATCATTTTGTAACTTTTAATAGTTGAGGACTCAACAAAACAATGCACTATAGTCTGAGG
* * *
5431 G-TCATTTTGTAATTTTTAATAGTTTGAGGACTCAACAAAGC-AT-CTCTTTATAGT-TGAGG
1 GATCATTTTGTAACTTTTAATAG-TTGAGGACTCAACAAAACAATGCAC--TATAGTCTGAGG
5490 GATCATTTGTGT-ACTTT
1 GATCATTT-TGTAACTTT
5507 ACCCCTTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
58 2 0.03
59 26 0.41
60 32 0.51
61 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTTGAGGACTCAACAAAACAATGCACTATAGTCTGAGG
Found at i:6282 original size:29 final size:32
Alignment explanation
Indices: 6250--6319 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 32
6240 AATTATATTT
* *
6250 TAATCATTATA-GTTATAAA-AGA-TATACAA
1 TAATCATTATATGTTATAAATAAATTATAAAA
6279 TAATCATTA-ATGTTATAAATAAATTATAAAA
1 TAATCATTATATGTTATAAATAAATTATAAAA
6310 TAATCATTAT
1 TAATCATTAT
6320 TACGTTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 17 0.49
30 2 0.06
31 15 0.43
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (32 bp):
TAATCATTATATGTTATAAATAAATTATAAAA
Found at i:9157 original size:41 final size:41
Alignment explanation
Indices: 9118--9204 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 41
9108 TTGTGGCAAG
9118 AAAAATA-TGC-AGAGTAA-ACAAATAAAAATTGCTAAGGCA
1 AAAAATACTGCAAGAGTAAGA-AAATAAAAATTGCTAAGGCA
* * *
9157 AAAATTACTTGCAAGAGTAAGAAAATAAAAGTTGCTAAGGCT
1 AAAAATAC-TGCAAGAGTAAGAAAATAAAAATTGCTAAGGCA
9199 AAAAAT
1 AAAAAT
9205 GTTCGAGTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 6 0.15
41 3 0.08
42 30 0.75
43 1 0.03
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (41 bp):
AAAAATACTGCAAGAGTAAGAAAATAAAAATTGCTAAGGCA
Found at i:15236 original size:130 final size:131
Alignment explanation
Indices: 14978--15307 Score: 366
Period size: 130 Copynumber: 2.5 Consensus size: 131
14968 CAATAATATA
* * *
14978 TAATTATTTTCAATCGAGAATAAATGACCTTTCATGTATTAAAACAATCATTTATTACTCCAGTT
1 TAATTATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAACAATCATTTATTACTCCAATT
* * * * * *
15043 G-AATAAAGATATATTACTATTTCATCTTAAAATTCAATATCGATTCAAGTGAAAATAATAACAT
66 GAAATAAAGAGATATTAATATTTCATCTAAAAATTCAATATCAATTCAAGAGAAAATAACAACAT
15107 C
131 C
* * * * * *
15108 TAATAATTTCCAATCAAGAATAAACGACCTTTCGTGCATTAAAACAATCATATATTACCCCAATT
1 TAATTATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAACAATCATTTATTACTCCAATT
* * * *
15173 GAAATAAAGAGATATTAAT-TTTCCGTCTAAAAAATT-GATATTAATTCGAA-AGAAAA-GACAA
66 GAAATAAAGAGATATTAATATTT-CATCT-AAAAATTCAATATCAATTC-AAGAGAAAATAACAA
15234 CATC
128 CATC
* * * * *
15238 AAATTATTTCCAATCGAGAATAAATGACCTCTT-ATGCCTTAAAGCAGTCATTTATTACTCCAAC
1 TAATTATTTCCAATCGAGAATAAATGACCT-TTCATGCATTAAAACAATCATTTATTACTCCAAT
15302 TGAAAT
65 TGAAAT
15308 GAAAAATAAT
Statistics
Matches: 165, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
130 123 0.75
131 34 0.21
132 8 0.05
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (131 bp):
TAATTATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAACAATCATTTATTACTCCAATT
GAAATAAAGAGATATTAATATTTCATCTAAAAATTCAATATCAATTCAAGAGAAAATAACAACAT
C
Found at i:15927 original size:17 final size:18
Alignment explanation
Indices: 15905--15938 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15895 AAGTGTTAAA
15905 ATGAAAATAAA-TAAAAC
1 ATGAAAATAAATTAAAAC
*
15922 ATGAAACTAAATTAAAA
1 ATGAAAATAAATTAAAA
15939 TAAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (18 bp):
ATGAAAATAAATTAAAAC
Found at i:17250 original size:3 final size:3
Alignment explanation
Indices: 17244--17288 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
17234 AAAAGAAAAA
* *
17244 AAT AAT ATT AATT ATT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17289 TAATGGGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:17594 original size:41 final size:42
Alignment explanation
Indices: 17540--17619 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
17530 AGGTCTTATG
* * * * *
17540 GATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGACTTACA
1 GATGACCCAAAGGACTTAAGCATCATGCTCAAAAGACTTACA
*
17581 GATGACCCAAAGGATTTAAGCATCATGCTCAAAAGACTT
1 GATGACCCAAAGGACTTAAGCATCATGCTCAAAAGACTT
17620 GTTAATGGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 14 0.44
42 18 0.56
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (42 bp):
GATGACCCAAAGGACTTAAGCATCATGCTCAAAAGACTTACA
Found at i:17948 original size:233 final size:233
Alignment explanation
Indices: 17506--18659 Score: 1570
Period size: 233 Copynumber: 5.0 Consensus size: 233
17496 GTAAAAGAGG
*
17506 GACATGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
1 GACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* ** * *
17571 AAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCAAAAGACTTGTTAATGGTCCGAAGG
66 AAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * * * * * *
17636 ACTTGTATAA-GTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTGCTTTTAAACAATATT-GA
131 ACTTATA-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAA-AATTTTCAA
17699 TTTTCAGATTTAAATGAGAAA-CTTTCCTCATATTTCGATA
194 TTTTCAGATTTAAATGAGAAACCTTT-CTCATATTTCGATA
* * * * *
17739 GATATCTGAAAACATCCTACCCAAAGTTCTTATGGATGGCCAGAAGGACTTATCATCTTGCTCGA
1 GACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* * * * *
17804 AAGGCTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGGCTCGAATG
66 AAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
*
17869 ACTTATAAATTTTGGAAATAGTTTACTAGGTAATAAACCTTTCTTACTTTTCAAAATTTTCAAAT
131 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAATTTTC-AAT
* *
17934 CTT-AG-TTATAAATGAGAAACCTTTCTCAAATTTCGATA
195 TTTCAGATT-TAAATGAGAAACCTTTCTCATATTTCGATA
** * * * *
17972 GACATGTGAAAACATCCTGCCTGAAGGTCTAATGGATGGCCCGAATGACTTATTATCTTGCTTGA
1 GACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* * * *
18037 AAGGA-TTACAGATGACCCAAAGGATTTAAACATCGTGCTTGAAAGACTTATTGATGGCCCGAAG
66 AA-GACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
*
18101 GACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
130 GACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAATTTTCAAT
* * *
18166 TTTCAGATTTAAATTAGAAACCTTTCTCATTTTTTGATA
195 TTTCAGATTTAAATGAGAAACCTTTCTCATATTTCGATA
* * *
18205 GACATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGACGGACTTATCATCTTGCTTGA
1 GACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* * * * *
18270 AATATTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAAACTTACTGATGGCCTGAA-G
66 AAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
**
18334 ACTTAT-AATTTTGTTAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAA-TTTCAATT
131 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAATTTTCAATT
* * *
18397 TTCAAATTTGAATGAGAAACCTTTCTCATTTTTCGATA
196 TTCAGATTTAAATGAGAAACCTTTCTCATATTTCGATA
* * * * * * * *
18435 GGCATGTAAAAACATCCCGCCCAAATGTCTTATAGATGGCTCAAAAGACTTATCATCTTGCTCGA
1 GACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* * **
18500 AAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCAAACA
66 AAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
18565 ACTTATAAATTTTGGAAATAGTTTACTAGGTAATAAACCTTTCTTACTTTTCAAAAATTTTGAAT
131 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC-AAAATTTTCAAT
*
18630 TTTCAGATTTGAATGAGAAACCTTTCTCAT
195 TTTCAGATTTAAATGAGAAACCTTTCTCAT
18660 TTCATTTTTT
Statistics
Matches: 812, Mismatches: 96, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
230 152 0.19
231 53 0.07
232 64 0.08
233 497 0.61
234 46 0.06
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (233 bp):
GACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
AAGACTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAATTTTCAATT
TTCAGATTTAAATGAGAAACCTTTCTCATATTTCGATA
Found at i:20519 original size:11 final size:11
Alignment explanation
Indices: 20505--20627 Score: 85
Period size: 11 Copynumber: 11.4 Consensus size: 11
20495 TCCTTTCTTC
20505 TTTCTTTATTT
1 TTTCTTTATTT
**
20516 TTTCCCT-TTT
1 TTTCTTTATTT
20526 TTTCTTTATTT
1 TTTCTTTATTT
20537 TTTCTTTATTT
1 TTTCTTTATTT
*
20548 TTT-TCTT-TTA
1 TTTCT-TTATTT
* *
20558 TCTCTTTTATCTC
1 TTTC-TTTAT-TT
20571 TTT-TTTATTT
1 TTTCTTTATTT
*
20581 TTTCTTTCTTT
1 TTTCTTTATTT
* * *
20592 TTTGTGTGTTT
1 TTTCTTTATTT
* *
20603 TTTCTATATCT
1 TTTCTTTATTT
20614 TTTC-TTATTT
1 TTTCTTTATTT
20624 TTTC
1 TTTC
20628 CTCTGCGTGT
Statistics
Matches: 86, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
10 25 0.29
11 56 0.65
12 2 0.02
13 3 0.03
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTCTTTATTT
Found at i:20542 original size:32 final size:35
Alignment explanation
Indices: 20503--20584 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 35
20493 TTTCCTTTCT
*
20503 TCTTTCTTTATTTTTTCCCTTTT-TTTC-TTTAT-
1 TCTTTCTTTATTTTTTCCCTTTTATCTCTTTTATC
* *
20535 TTTTTCTTTATTTTTT-TCTTTTATCTCTTTTATC
1 TCTTTCTTTATTTTTTCCCTTTTATCTCTTTTATC
20569 TCTTT-TTTATTTTTTC
1 TCTTTCTTTATTTTTTC
20585 TTTCTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
31 5 0.12
32 18 0.43
33 15 0.36
34 4 0.10
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (35 bp):
TCTTTCTTTATTTTTTCCCTTTTATCTCTTTTATC
Found at i:20592 original size:9 final size:8
Alignment explanation
Indices: 20502--20594 Score: 53
Period size: 9 Copynumber: 11.1 Consensus size: 8
20492 GTTTCCTTTC
*
20502 TTCTTTCT
1 TTCTTTTT
*
20510 TTATTTTT
1 TTCTTTTT
*
20518 TCCCTTTTT
1 T-TCTTTTT
*
20527 TTCTTTAT
1 TTCTTTTT
*
20535 TT-TTTCT
1 TTCTTTTT
*
20542 TTATTTTT
1 TTCTTTTT
20550 TTCTTTTAT
1 TTCTTTT-T
*
20559 CTCTTTTAT
1 TTCTTTT-T
*
20568 CTCTTTTT
1 TTCTTTTT
*
20576 TATTTTTTCT
1 T-TCTTTT-T
20586 TTCTTTTT
1 TTCTTTTT
20594 T
1 T
20595 GTGTGTTTTT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
7 6 0.09
8 27 0.40
9 32 0.48
10 2 0.03
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.78
Consensus pattern (8 bp):
TTCTTTTT
Found at i:20613 original size:44 final size:43
Alignment explanation
Indices: 20525--20627 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 43
20515 TTTTCCCTTT
*
20525 TTTTCTTTATTTTTTCTTTATTTTTTTCTTTTATCTCTTTTATC
1 TTTT-TTTATTTTTTCTTTATTTTTTTCTTTTATCTCTTATATC
* * *
20569 TCTTTTTTATTTTTTCTTTCTTTTTTGTGTGTTT-TTTC-TATATC
1 T-TTTTTTATTTTTTCTTTATTTTTT-TCT-TTTATCTCTTATATC
*
20613 TTTTCTTATTTTTTC
1 TTTTTTTATTTTTTC
20628 CTCTGCGTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
43 13 0.25
44 27 0.53
45 8 0.16
46 3 0.06
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.77
Consensus pattern (43 bp):
TTTTTTTATTTTTTCTTTATTTTTTTCTTTTATCTCTTATATC
Found at i:20873 original size:2 final size:2
Alignment explanation
Indices: 20866--20901 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
20856 ATAACAAGGG
* *
20866 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20902 TTGAAGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:23987 original size:131 final size:130
Alignment explanation
Indices: 23819--24184 Score: 402
Period size: 131 Copynumber: 2.8 Consensus size: 130
23809 TAATTTTAAG
* *
23819 AGTGAAATTGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAATAG
1 AGTGAAAATGATAATATCTAAATATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAATAG
* * * * * *
23884 TCATTTATCACTCCAATTGAAATAAAGAGATATTACTATTTCATCTTAAAATTCAATATCGATTC
66 TCATTTATTACTCCAACTGAAATAAAGAGATATTACTATTCCACCTAAAAATT-AATATCAATTC
23949 A
130 A
* * * * * * *
23950 AGTGAAAATAATAACATCTAAAGATTTCCAATCGAGAATAAATGACATTTCGTGCATTAAAACAT
1 AGTGAAAATGATAATATCTAAATATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAATAG
* * * *
24015 TCATTTATTAC-CCAACTGAAATAAAGATATATTAATATTCCACCTAAAAATTGATATTAATTCA
66 TCATTTATTACTCCAACTGAAATAAAGAGATATTACTATTCCACCTAAAAATTAATATCAATTCA
* ** * *
24079 A-TAGAAAACGGCAATATC-AAATTATTTCCAATCGAGAATAAATGACCTCTT-AAGCCTT-AAA
1 AGT-GAAAATGATAATATCTAAA-TATTTCCAATCGAGAATAAATGACCT-TTCATGCATTAAAA
* *
24140 TATGTCATTTATTACTCCAACAGAAATGAAA-AGATAATACTATTC
63 TA-GTCATTTATTACTCCAACTGAAAT-AAAGAGATATTACTATTC
24185 TCAATGTCAA
Statistics
Matches: 194, Mismatches: 35, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
128 8 0.04
129 59 0.30
130 58 0.30
131 69 0.36
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (130 bp):
AGTGAAAATGATAATATCTAAATATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAATAG
TCATTTATTACTCCAACTGAAATAAAGAGATATTACTATTCCACCTAAAAATTAATATCAATTCA
Found at i:24139 original size:129 final size:131
Alignment explanation
Indices: 23831--24175 Score: 378
Period size: 129 Copynumber: 2.6 Consensus size: 131
23821 TGAAATTGAT
* * *
23831 AATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAATAGTCATTTATCACT
1 AATATCAAATTATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAATATTCATTTATTACT
* * * * * * * *
23896 CCAATTGAAATAAAGAGATATTACTATTTCATCTTAAAATTCAATATCGATTCAAGTGAAAATAA
66 CCAACTGAAATAAAGATATATTAATATTCCACCTAAAAATTCAATATCAATTCAAGTGAAAACAA
*
23961 T
131 C
* * * * *
23962 AACATCTAAA-GATTTCCAATCGAGAATAAATGACATTTCGTGCATTAAAACATTCATTTATTAC
1 AATATC-AAATTATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAATATTCATTTATTAC
* *
24026 -CCAACTGAAATAAAGATATATTAATATTCCACCTAAAAATT-GATATTAATTCAA-TAGAAAAC
65 TCCAACTGAAATAAAGATATATTAATATTCCACCTAAAAATTCAATATCAATTCAAGT-GAAAAC
**
24088 GGC
129 AAC
* *
24091 AATATCAAATTATTTCCAATCGAGAATAAATGACCTCTT-AAGCCTT-AAATATGTCATTTATTA
1 AATATCAAATTATTTCCAATCGAGAATAAATGACCT-TTCATGCATTAAAATAT-TCATTTATTA
*
24154 CTCCAACAGAAATGAAAAGATA
64 CTCCAACTGAAAT--AAAGATA
24176 ATACTATTCT
Statistics
Matches: 177, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
128 9 0.05
129 59 0.33
130 47 0.27
131 53 0.30
132 9 0.05
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (131 bp):
AATATCAAATTATTTCCAATCGAGAATAAATGACCTTTCATGCATTAAAATATTCATTTATTACT
CCAACTGAAATAAAGATATATTAATATTCCACCTAAAAATTCAATATCAATTCAAGTGAAAACAA
C
Found at i:26139 original size:3 final size:3
Alignment explanation
Indices: 26131--26168 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
26121 ATTAATTAAT
26131 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
26169 TCGAATAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:40121 original size:25 final size:26
Alignment explanation
Indices: 40055--40125 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
40045 TTGAGTGTTC
40055 ATAATATGAACTC-AAAAGTGCCTCGT
1 ATAAT-TGAACTCGAAAAGTGCCTCGT
* * * *
40081 ATAATTGTATTTGAAAA-TGCCTTGT
1 ATAATTGAACTCGAAAAGTGCCTCGT
*
40106 ATAATTGCACTCG-AAAGTGC
1 ATAATTGAACTCGAAAAGTGC
40126 TAAACAGGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 3 0.08
25 24 0.67
26 9 0.25
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (26 bp):
ATAATTGAACTCGAAAAGTGCCTCGT
Found at i:40353 original size:24 final size:24
Alignment explanation
Indices: 40323--40485 Score: 111
Period size: 24 Copynumber: 6.8 Consensus size: 24
40313 TGCATGAATA
*
40323 CACTAATATAGGAGTACAC-ATTG
1 CACTAATATAGGAGTACACAAATG
* * * *
40346 ATATTAATACAGGAGTGCACAAATG
1 -CACTAATATAGGAGTACACAAATG
*
40371 CACTAAT-TCAGGAGTACACGAATG
1 CACTAATAT-AGGAGTACACAAATG
*
40395 CACTAATATAGGAGTACAC-ATTGG
1 CACTAATATAGGAGTACACAAAT-G
* * **
40419 TATTAATACGGGAG-AGCACAAATG
1 CACTAATATAGGAGTA-CACAAATG
* *
40443 CACTAAT-TCAGGAGTGCACGAATG
1 CACTAATAT-AGGAGTACACAAATG
* *
40467 CATTAATATAGGAGCACAC
1 CACTAATATAGGAGTACAC
40486 TTTGGTACTA
Statistics
Matches: 105, Mismatches: 25, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
23 3 0.03
24 95 0.90
25 7 0.07
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (24 bp):
CACTAATATAGGAGTACACAAATG
Found at i:40405 original size:72 final size:72
Alignment explanation
Indices: 40278--40500 Score: 302
Period size: 72 Copynumber: 3.1 Consensus size: 72
40268 TAATGGTACA
* * ** * * *
40278 AATACATGAGTACACAAATTTACTAGAATCAGGAGTGCATGAATACACTAATATAGGAGTACACA
1 AATACAGGAGTGCACAAATGCACTA-ATTCAGGAGTGCACGAATGCACTAATATAGGAGTACACA
*
40343 TTGATATT
65 TTGGTATT
*
40351 AATACAGGAGTGCACAAATGCACTAATTCAGGAGTACACGAATGCACTAATATAGGAGTACACAT
1 AATACAGGAGTGCACAAATGCACTAATTCAGGAGTGCACGAATGCACTAATATAGGAGTACACAT
40416 TGGTATT
66 TGGTATT
* * * * *
40423 AATACGGGAGAGCACAAATGCACTAATTCAGGAGTGCACGAATGCATTAATATAGGAGCACACTT
1 AATACAGGAGTGCACAAATGCACTAATTCAGGAGTGCACGAATGCACTAATATAGGAGTACACAT
*
40488 TGGTACT
66 TGGTATT
40495 AATACA
1 AATACA
40501 AGATTGTTCA
Statistics
Matches: 133, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 112 0.84
73 21 0.16
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (72 bp):
AATACAGGAGTGCACAAATGCACTAATTCAGGAGTGCACGAATGCACTAATATAGGAGTACACAT
TGGTATT
Found at i:40474 original size:48 final size:47
Alignment explanation
Indices: 40278--40485 Score: 134
Period size: 48 Copynumber: 4.3 Consensus size: 47
40268 TAATGGTACA
* ** * * * *
40278 AATACATGAGTACACAAATTTACTAGAATCAGGAGTGCATGAATACACT
1 AATACAGGAGTACACAAATGCACTA-ATTCAGGAGTGCA-CAATGCATT
* * * * * *
40327 AATATAGGAGTACAC-ATTGATATTAATACAGGAGTGCACAAATGCACT
1 AATACAGGAGTACACAAATG-CACTAATTCAGGAGTGCAC-AATGCATT
* * * * *
40375 AATTCAGGAGTACACGAATGCACTAATAT-AGGAGTACACATTGGTATT
1 AATACAGGAGTACACAAATGCACTAAT-TCAGGAGTGCACAAT-GCATT
*
40423 AATACGGGAG-AGCACAAATGCACTAATTCAGGAGTGCACGAATGCATT
1 AATACAGGAGTA-CACAAATGCACTAATTCAGGAGTGCAC-AATGCATT
* *
40471 AATATAGGAGCACAC
1 AATACAGGAGTACAC
40486 TTTGGTACTA
Statistics
Matches: 123, Mismatches: 27, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
47 4 0.03
48 96 0.78
49 23 0.19
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.23
Consensus pattern (47 bp):
AATACAGGAGTACACAAATGCACTAATTCAGGAGTGCACAATGCATT
Found at i:46273 original size:26 final size:26
Alignment explanation
Indices: 46244--46296 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
46234 TAAGAAAATG
46244 TTGTGAACACTTAGAGGAAAGATTGA
1 TTGTGAACACTTAGAGGAAAGATTGA
*
46270 TTGTGAACCCTTAGAGGAAAGATTGA
1 TTGTGAACACTTAGAGGAAAGATTGA
46296 T
1 T
46297 CTTTGTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (26 bp):
TTGTGAACACTTAGAGGAAAGATTGA
Found at i:53880 original size:28 final size:28
Alignment explanation
Indices: 53839--53895 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
53829 AACAAAATCA
* * *
53839 TGCTTCACTAACCGGTTGCTTTGAATTT
1 TGCTCCACCAACCGGCTGCTTTGAATTT
53867 TGCTCCACCAACCGGCTGCTTTGAATTT
1 TGCTCCACCAACCGGCTGCTTTGAATTT
53895 T
1 T
53896 CAACAAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.39
Consensus pattern (28 bp):
TGCTCCACCAACCGGCTGCTTTGAATTT
Found at i:56145 original size:26 final size:26
Alignment explanation
Indices: 56096--56145 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
56086 ATCTTGAGAA
* *
56096 TAAAATCAAGTGATTTGTTTTTGGTG
1 TAAAATCAAGGGATTTGTTCTTGGTG
56122 TAAAATCAAGGGATCTTG-TCTTGG
1 TAAAATCAAGGGAT-TTGTTCTTGG
56146 ATGAAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (26 bp):
TAAAATCAAGGGATTTGTTCTTGGTG
Found at i:56714 original size:13 final size:13
Alignment explanation
Indices: 56696--56745 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
56686 AGATACAAAT
56696 ATGCAAATACCAA
1 ATGCAAATACCAA
56709 ATGCAAATA-C--
1 ATGCAAATACCAA
56719 --GCAAATACCAA
1 ATGCAAATACCAA
56730 ATGCAAATACGCAA
1 ATGCAAATAC-CAA
56744 AT
1 AT
56746 ACAAGATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
12 1 0.03
13 17 0.55
14 5 0.16
ACGTcount: A:0.52, C:0.22, G:0.10, T:0.16
Consensus pattern (13 bp):
ATGCAAATACCAA
Found at i:56715 original size:21 final size:21
Alignment explanation
Indices: 56691--56747 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
56681 TACAAAGATA
*
56691 CAAATATGCAAATACCAAATG
1 CAAATACGCAAATACCAAATG
56712 CAAATACGCAAATACCAAATG
1 CAAATACGCAAATACCAAATG
56733 CAAATACGCAAATAC
1 CAAATACGCAAATAC
56748 AAGATGTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.53, C:0.23, G:0.09, T:0.16
Consensus pattern (21 bp):
CAAATACGCAAATACCAAATG
Found at i:56747 original size:8 final size:8
Alignment explanation
Indices: 56691--56747 Score: 63
Period size: 8 Copynumber: 7.9 Consensus size: 8
56681 TACAAAGATA
*
56691 CAAATATG
1 CAAATACG
56699 CAAATAC-
1 CAAATACG
56706 CAAAT--G
1 CAAATACG
56712 CAAATACG
1 CAAATACG
56720 CAAATAC-
1 CAAATACG
56727 CAAAT--G
1 CAAATACG
56733 CAAATACG
1 CAAATACG
56741 CAAATAC
1 CAAATAC
56748 AAGATGTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
6 10 0.24
7 10 0.24
8 22 0.52
ACGTcount: A:0.53, C:0.23, G:0.09, T:0.16
Consensus pattern (8 bp):
CAAATACG
Found at i:59275 original size:26 final size:24
Alignment explanation
Indices: 59246--59297 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
59236 CCTTAACAAC
59246 AAGAACACAAATGAAACATAAAAAAA
1 AAGAACAC-AATGAAACA-AAAAAAA
* * *
59272 AAGAATACATTTAAACAAAAAAAA
1 AAGAACACAATGAAACAAAAAAAA
59296 AA
1 AA
59298 TCCTCTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.39
25 7 0.30
26 7 0.30
ACGTcount: A:0.73, C:0.10, G:0.06, T:0.12
Consensus pattern (24 bp):
AAGAACACAATGAAACAAAAAAAA
Found at i:59374 original size:24 final size:24
Alignment explanation
Indices: 59346--59393 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
59336 TAGGTATCTC
59346 TTTCACTCTCTTTTTTTC-TCCCCT
1 TTTCACTCT-TTTTTTTCTTCCCCT
59370 TTTCACTCTTTTTTTTCTTCCCCT
1 TTTCACTCTTTTTTTTCTTCCCCT
59394 CAAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTCACTCTTTTTTTTCTTCCCCT
Found at i:64324 original size:65 final size:65
Alignment explanation
Indices: 64200--64324 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 65
64190 GCACCAATAT
* * *
64200 AGATCACTCATATGACTCATGTACCTTTATTGTACATGAGGTGGAGTGATAACTGAATACTACAC
1 AGATCACTCATATGACTCATGTACCTTGATGGTACATGAGGTGGAGTGATAACTAAATACTACAC
* * * *
64265 AGATCATTCATATGACTCATGTACCTTGGTGGTGCATGAGGTGGAGTGATAATTAAATAC
1 AGATCACTCATATGACTCATGTACCTTGATGGTACATGAGGTGGAGTGATAACTAAATAC
64325 AAACGAGACT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (65 bp):
AGATCACTCATATGACTCATGTACCTTGATGGTACATGAGGTGGAGTGATAACTAAATACTACAC
Found at i:64577 original size:17 final size:17
Alignment explanation
Indices: 64557--64603 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
64547 TAGATGCAAA
*
64557 ACAATAAAAGATACAGT
1 ACAATAAAAGAAACAGT
* *
64574 ACAATAAGAGAAATAGT
1 ACAATAAAAGAAACAGT
*
64591 GCAATAAAAGAAA
1 ACAATAAAAGAAA
64604 GGATATAGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.09, G:0.15, T:0.15
Consensus pattern (17 bp):
ACAATAAAAGAAACAGT
Found at i:75786 original size:20 final size:21
Alignment explanation
Indices: 75761--75806 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
75751 TCTTGCAACT
* *
75761 ATCGAATTATTTGA-AAAAGG
1 ATCGAACTATTTCACAAAAGG
75781 ATCGAACTATTTCACAAAAGG
1 ATCGAACTATTTCACAAAAGG
75802 ATCGA
1 ATCGA
75807 TCCCTTGTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGAACTATTTCACAAAAGG
Found at i:79246 original size:23 final size:23
Alignment explanation
Indices: 79216--79296 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
79206 TGAACGGATG
*
79216 TAAACGAACATAAATGAGCACAA
1 TAAACGAACATAAATGAACACAA
*
79239 TAAACGAACGTAAATGAACACAA
1 TAAACGAACATAAATGAACACAA
* * * *
79262 -ACGAACAAACGTAAAAGAAGACAA
1 TA--AACGAACATAAATGAACACAA
*
79286 TAAATGAACAT
1 TAAACGAACAT
79297 CAACGAACGT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 1 0.02
23 27 0.57
24 18 0.38
25 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (23 bp):
TAAACGAACATAAATGAACACAA
Found at i:79523 original size:20 final size:20
Alignment explanation
Indices: 79500--79537 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
79490 ATAAATGTAC
79500 ACACATAAAAGAACATAAAT
1 ACACATAAAAGAACATAAAT
79520 ACACATAAAAGAACATAA
1 ACACATAAAAGAACATAA
79538 TCGAACGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.16, G:0.05, T:0.13
Consensus pattern (20 bp):
ACACATAAAAGAACATAAAT
Found at i:83645 original size:130 final size:130
Alignment explanation
Indices: 83313--83679 Score: 495
Period size: 131 Copynumber: 2.8 Consensus size: 130
83303 ATAATTCTAA
* * * *
83313 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAACCTCTCATGTCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
* * * * *
83378 ATTATTTATTACTCCAATAGAAATGAAGAGATGTCAGTAATTCGTCTTAAAATTCAATATTGATT
66 ATCATTTATTACTCCAATAGAAATGAAGAGATATCACT-ATTCGTCTTAAAAATCAATATTAATT
83443 C
130 C
* * * * * **
83444 AAGTGAAAAAGATAATATCTAATGATTTTCAATCGATAATAAATGACCTCTTGTGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
* *
83509 GTCATTTATTACTCCAATTGAAATGAAGAGATATCACTATTCTGTCTTAAAAATCAATATTAATT
66 ATCATTTATTACTCCAATAGAAATGAAGAGATATCACTATTC-GTCTTAAAAATCAATATTAATT
83574 C
130 C
*
83575 GAGAGAAAACG-TAATATCTAATTATTTCCAATCGATAATGAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
** *
83639 ATCATTTATTACTCCAACCGAAATGAA-ATGATATTACTATT
66 ATCATTTATTACTCCAATAGAAATGAAGA-GATATCACTATT
83680 TTCAATATTG
Statistics
Matches: 204, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
129 1 0.00
130 87 0.43
131 116 0.57
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (130 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
ATCATTTATTACTCCAATAGAAATGAAGAGATATCACTATTCGTCTTAAAAATCAATATTAATTC
Found at i:85698 original size:3 final size:3
Alignment explanation
Indices: 85690--85719 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
85680 GGCTGCAATA
85690 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
85720 GTCAGGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:87639 original size:108 final size:108
Alignment explanation
Indices: 87439--87694 Score: 286
Period size: 108 Copynumber: 2.4 Consensus size: 108
87429 AAAATTTAAA
* * * * * *
87439 AGTCACTACATATGACCAAAGTGTAAAAACACGATAAACTTATAGGGGCTAAACAATAAATAGAC
1 AGTCCCTACAGATGACCAAAATGTAAAAACACGCTAAACTTAGAGGGACTAAACAATAAATAGAC
* * *
87504 CAAAAATTATATAACATGCAAATAAAAGGGAAAA-AATAG-TTT
66 CAAAAATTACATAACA-GCAAAGAAAAGGGAAAATAACAGATTT
* * * * *
87546 CAGT-CCTCACAGATGACCAAAATGCAAAAACACGCTAAAGTTAGAGGGACTAAATAGTGAATAG
1 -AGTCCCT-ACAGATGACCAAAATGTAAAAACACGCTAAACTTAGAGGGACTAAACAATAAATAG
87610 ACCAAAAATTACATAACA-CATAAGGAAAAGGGAAAATAACAGATTT
64 ACCAAAAATTACATAACAGCA-AA-GAAAAGGGAAAATAACAGATTT
* * *
87656 GGTCCCTACAGGTGACCAAAATGTAAAAGCACGCTAAAC
1 AGTCCCTACAGATGACCAAAATGTAAAAACACGCTAAAC
87695 CTAAGGGGTC
Statistics
Matches: 123, Mismatches: 19, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
106 2 0.02
107 4 0.03
108 77 0.63
109 34 0.28
110 6 0.05
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (108 bp):
AGTCCCTACAGATGACCAAAATGTAAAAACACGCTAAACTTAGAGGGACTAAACAATAAATAGAC
CAAAAATTACATAACAGCAAAGAAAAGGGAAAATAACAGATTT
Found at i:88683 original size:24 final size:24
Alignment explanation
Indices: 88656--88708 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
88646 TCGGGTCTCG
88656 GTTTTATTTTGTAAAGGGGCCCGA
1 GTTTTATTTTGTAAAGGGGCCCGA
* * *
88680 GTTTCATTTTGTAAGGGGGGCCGA
1 GTTTTATTTTGTAAAGGGGCCCGA
*
88704 TTTTT
1 GTTTT
88709 TCTTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.30, T:0.42
Consensus pattern (24 bp):
GTTTTATTTTGTAAAGGGGCCCGA
Found at i:89329 original size:25 final size:24
Alignment explanation
Indices: 89273--89331 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
89263 TAAATATTTA
89273 TTTTGATAAAAATAATTGAAGGATT
1 TTTTGA-AAAAATAATTGAAGGATT
** * *
89298 TAATGAAAAAATATTTGAGGGAATT
1 TTTTGAAAAAATAATTGAAGG-ATT
89323 TTTTGAAAA
1 TTTTGAAAA
89332 CTTTAACCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (24 bp):
TTTTGAAAAAATAATTGAAGGATT
Found at i:92271 original size:3 final size:3
Alignment explanation
Indices: 92265--92362 Score: 166
Period size: 3 Copynumber: 33.7 Consensus size: 3
92255 TATGATGATG
92265 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
92312 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
92358 ATA AT
1 ATA AT
92363 TTGTCGATTG
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
2 5 0.06
3 85 0.94
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:92939 original size:59 final size:60
Alignment explanation
Indices: 92772--92939 Score: 169
Period size: 60 Copynumber: 2.8 Consensus size: 60
92762 GTTTCCAAAC
* * * * * * *
92772 TATAACTTTTATTTTAAATTGGTCCTTAAAATTTTGAATATTCCTATTTCTTCCTTAAAT
1 TATAACTCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTTCAATTTCATCCCTAAAT
* ** ** *
92832 TATAACTCTCATTCTAAATTAATCCTTAAACTTTTGACCATTTTAATTTCATCCCT-AAT
1 TATAACTCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTTCAATTTCATCCCTAAAT
* * *
92891 CTATATC-CTCTTTTTAAATTGGTCCTCAAACTTTTGAATATTTCAATTT
1 -TATAACTCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTTCAATTT
92940 TCCCCAAATT
Statistics
Matches: 85, Mismatches: 22, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
59 37 0.44
60 48 0.56
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.48
Consensus pattern (60 bp):
TATAACTCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTTCAATTTCATCCCTAAAT
Found at i:93174 original size:54 final size:56
Alignment explanation
Indices: 93076--93236 Score: 163
Period size: 60 Copynumber: 2.8 Consensus size: 56
93066 ATATGCATGG
* *
93076 TTTA-GGATGAAATTGGAATGTTCAAAAAGTTTAGGGACTAATTTAAA-G-TT-AT-A
1 TTTAGGGATGAAATT-GAATATTC-AAAAGTTTAGAGACTAATTTAAATGATTCATCA
*
93129 GTTTGGGGATGAAATTGAAATATTCAAAAGTTT-GAAGACTAATTTAAAATGATATTCATCA
1 -TTTAGGGATGAAATTG-AATATTCAAAAGTTTAG-AGACTAATTT-AAATG--ATTCATCA
*
93190 TTTAGGGATGAAATTTGAATATTTAAAAGTTTAGAGACTAATTTAAA
1 TTTAGGGATGAAA-TTGAATATTCAAAAGTTTAGAGACTAATTTAAA
93237 ATGAGTATTA
Statistics
Matches: 90, Mismatches: 5, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
53 1 0.01
54 21 0.23
55 19 0.21
56 1 0.01
59 5 0.06
60 38 0.42
61 5 0.06
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (56 bp):
TTTAGGGATGAAATTGAATATTCAAAAGTTTAGAGACTAATTTAAATGATTCATCA
Found at i:95336 original size:41 final size:40
Alignment explanation
Indices: 95291--95461 Score: 109
Period size: 41 Copynumber: 4.2 Consensus size: 40
95281 ATTTCTACAG
* *
95291 GTAAAAACTGAGATTAAAAATTAGGGACTTCAATTATAAAA
1 GTAAAAAATGAGATTAAAAATTAAGGACTTCAATTAT-AAA
** * * ** *
95332 GTAAAAGGTGACATTGAAAAAATTAAGG-CATCGGTTATAAG
1 GTAAAAAATGAGATT--AAAAATTAAGGACTTCAATTATAAA
* * * *
95373 GTAAAAATTGAGATTGAAAATT-AGGAGTCTCATTTATAAA
1 GTAAAAAATGAGATTAAAAATTAAGGACT-TCAATTATAAA
* *
95413 -TAAAAAAT-AGGATCACAAAATTAAGGAC-TCACTTATAAAA
1 GTAAAAAATGA-GATTA-AAAATTAAGGACTTCAATTAT-AAA
95453 GTAAAAAAT
1 GTAAAAAAT
95462 TAAAATTAGA
Statistics
Matches: 99, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
38 4 0.04
39 23 0.23
40 17 0.17
41 38 0.38
42 7 0.07
43 10 0.10
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (40 bp):
GTAAAAAATGAGATTAAAAATTAAGGACTTCAATTATAAA
Found at i:101627 original size:9 final size:9
Alignment explanation
Indices: 101613--101638 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
101603 GAACTCTAAA
101613 TGAAGAAAG
1 TGAAGAAAG
101622 TGAAGAAAG
1 TGAAGAAAG
101631 TGAAGAAA
1 TGAAGAAA
101639 ACAAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.12
Consensus pattern (9 bp):
TGAAGAAAG
Found at i:101822 original size:12 final size:12
Alignment explanation
Indices: 101805--101829 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
101795 GACTACCTTT
101805 TATCATTATATC
1 TATCATTATATC
101817 TATCATTATATC
1 TATCATTATATC
101829 T
1 T
101830 TTCTATTTCC
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TATCATTATATC
Found at i:105765 original size:54 final size:54
Alignment explanation
Indices: 105670--106050 Score: 407
Period size: 54 Copynumber: 7.1 Consensus size: 54
105660 CGAATGACAC
* * * **
105670 GCTCTATTTCTCCATAACAAAGG-ACGCAAGAGCTCGCTCAGTCTTGGAAATTT
1 GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGGAAATTT
* * * *
105723 GCTTTACT-CTACCATGAA-AAAAGAACGCTAGAGCGTACTCAGTC-TAGAGAATTT
1 GCTCTACTCCT-CCAT-AACAAAGGAACGCTAGAGCTTACTCAGTCTTGGA-AATTT
* * * *
105777 GCTCTACTCCTCCATAACAAAGGAATGCTAGAACTTACTCATTCTTGAAAATTT
1 GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGGAAATTT
* * * *
105831 TCTCTACTCCTCGC--AACAAATGAACACTAGAGCTTACTTAGTCTTGGAAATTT
1 GCTCTACTCCTC-CATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGGAAATTT
* * * *
105884 GCTCTACTCCTCCATAACAAAGGAACGTTAGAGTTTAGTCATTCTTGGAAATTT
1 GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGGAAATTT
* * * * *
105938 TCTCTACTCCTCCATAACAAAGGAATGCTGGAGCTTATTCAGTCTTGAAAATTT
1 GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGGAAATTT
* *
105992 GCTCTACTCCTCCATAA-AATAGGAACGCTAGAGCTTAATCAGTCTTGGATATTT
1 GCTCTACTCCTCCATAACAA-AGGAACGCTAGAGCTTACTCAGTCTTGGAAATTT
*
106046 ACTCT
1 GCTCT
106051 TCTGATTTGA
Statistics
Matches: 270, Mismatches: 47, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
52 3 0.01
53 64 0.24
54 198 0.73
55 5 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (54 bp):
GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGGAAATTT
Found at i:105986 original size:161 final size:161
Alignment explanation
Indices: 105707--106050 Score: 428
Period size: 161 Copynumber: 2.1 Consensus size: 161
105697 AAGAGCTCGC
*
105707 TCAGTCTTGGAAATTTGCTTTACTCTACCATGAAAAAAGAACGCTAGAGCGTACTCAGTCTAGAG
1 TCAGTCTTGGAAATTTGCTCTACTCTACCATGAAAAAAGAACGCTAGAGCGTACTCAGTCTAGAG
* *
105772 AATTTGCTCTACTCCTCCATAACAAAGGAATGCTAGAACTTACTCATTCTTGAAAATTTTCTCTA
66 AATTTGCTCTACTCCTCCATAACAAAGGAATGCTAGAACTTACTCAGTCTTGAAAATTTGCTCTA
*
105837 CTCCTCGCA-ACAAAT-GAACACTAGAGCTTAC
131 CTCCTC-CATA-AAATAGAACACTAGAGCTTAA
* * * ** * * *
105868 TTAGTCTTGGAAATTTGCTCTACTCCT-CCAT-AACAAAGGAACGTTAGAGTTTAGTCATTCTTG
1 TCAGTCTTGGAAATTTGCTCTACT-CTACCATGAA-AAAAGAACGCTAGAGCGTACTCAGTCTAG
* * * *
105931 -GAAATTTTCTCTACTCCTCCATAACAAAGGAATGCTGGAGCTTATTCAGTCTTGAAAATTTGCT
64 AG-AATTTGCTCTACTCCTCCATAACAAAGGAATGCTAGAACTTACTCAGTCTTGAAAATTTGCT
*
105995 CTACTCCTCCATAAAATAGGAACGCTAGAGCTTAA
128 CTACTCCTCCATAAAATA-GAACACTAGAGCTTAA
* *
106030 TCAGTCTTGGATATTTACTCT
1 TCAGTCTTGGAAATTTGCTCT
106051 TCTGATTTGA
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
160 9 0.06
161 114 0.73
162 34 0.22
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (161 bp):
TCAGTCTTGGAAATTTGCTCTACTCTACCATGAAAAAAGAACGCTAGAGCGTACTCAGTCTAGAG
AATTTGCTCTACTCCTCCATAACAAAGGAATGCTAGAACTTACTCAGTCTTGAAAATTTGCTCTA
CTCCTCCATAAAATAGAACACTAGAGCTTAA
Found at i:106016 original size:108 final size:108
Alignment explanation
Indices: 105670--106050 Score: 407
Period size: 107 Copynumber: 3.5 Consensus size: 108
105660 CGAATGACAC
* * * *** * * *
105670 GCTCTATTTCTCCATAACAAAGG-ACGCAAGAGCTCGCTCAGTCTTGGAAATTTGCTTTACT-CT
1 GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTAATCATTCTTGGAAATTTTCTCTACTCCT
* * * *
105733 ACCATGAA-AAAAGAACGCTAGAGCGTACTCAGTCTAGAGAATTT
66 -CCAT-AACAAAAGAACGCTAGAGCTTATTCAGTCTTGAAAATTT
* * * *
105777 GCTCTACTCCTCCATAACAAAGGAATGCTAGAACTTACTCATTCTTGAAAATTTTCTCTACTCCT
1 GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTAATCATTCTTGGAAATTTTCTCTACTCCT
* * *
105842 CGC--AACAAATGAACACTAGAGCTTACTT-AGTCTTGGAAATTT
66 C-CATAACAAAAGAACGCTAGAGCTTA-TTCAGTCTTGAAAATTT
* * *
105884 GCTCTACTCCTCCATAACAAAGGAACGTTAGAGTTTAGTCATTCTTGGAAATTTTCTCTACTCCT
1 GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTAATCATTCTTGGAAATTTTCTCTACTCCT
* * *
105949 CCATAACAAAGGAATGCTGGAGCTTATTCAGTCTTGAAAATTT
66 CCATAACAAAAGAACGCTAGAGCTTATTCAGTCTTGAAAATTT
* * *
105992 GCTCTACTCCTCCATAA-AATAGGAACGCTAGAGCTTAATCAGTCTTGGATATTTACTCT
1 GCTCTACTCCTCCATAACAA-AGGAACGCTAGAGCTTAATCATTCTTGGAAATTTTCTCT
106051 TCTGATTTGA
Statistics
Matches: 230, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
106 3 0.01
107 112 0.49
108 112 0.49
109 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (108 bp):
GCTCTACTCCTCCATAACAAAGGAACGCTAGAGCTTAATCATTCTTGGAAATTTTCTCTACTCCT
CCATAACAAAAGAACGCTAGAGCTTATTCAGTCTTGAAAATTT
Found at i:106662 original size:39 final size:38
Alignment explanation
Indices: 106610--107171 Score: 503
Period size: 39 Copynumber: 14.4 Consensus size: 38
106600 AGTGCAACTA
*
106610 GTCTCAAGTGAGACAAAATTAATGTTTCAAGGGAAACAT
1 GTCTCAAGGGAGACAAAATT-ATGTTTCAAGGGAAACAT
* * *
106649 GTCACAAGGGAGACAAAA-TATGTTTTCAAGGGAAATAG
1 GTCTCAAGGGAGACAAAATTATG-TTTCAAGGGAAACAT
* * *
106687 GTCCCAAGAGAGACAAAAATCTATGTTTCAAGGAAAACAT
1 GTCTCAAGGGAGAC-AAAAT-TATGTTTCAAGGGAAACAT
* * *
106727 GTCTTAAGGGAGACAAAATCTATGTTCCAAGGGAAACAA
1 GTCTCAAGGGAGACAAAAT-TATGTTTCAAGGGAAACAT
*
106766 GTCTCAAGGGAGACAAAATCTATGTTTCAAGGGAAACAA
1 GTCTCAAGGGAGACAAAAT-TATGTTTCAAGGGAAACAT
* *
106805 GTCTCAA-GGAGGACAAAAATCATTGTTTCAAGGGAAACAA
1 GTCTCAAGGGA-GAC-AAAATTA-TGTTTCAAGGGAAACAT
* * * * *
106845 GCCTTAAGAGAGACAAAA-TCTGTAATTC-AGGGCAAACAA
1 GTCTCAAGGGAGACAAAATTATGT--TTCAAGGG-AAACAT
* *
106884 GTCCCAAGAGAGACAAACATATATGTTTCAAGGGAAACAT
1 GTCTCAAGGGAGACAAA-AT-TATGTTTCAAGGGAAACAT
* * * * *
106924 TTCTCAAGGGAGACCAAATATGTGTTTCAATGGAAACGT
1 GTCTCAAGGGAGACAAAAT-TATGTTTCAAGGGAAACAT
* *
106963 GTCTC--GGGTAG-CAAAATATATATTTCAA-GAAAACAT
1 GTCTCAAGGG-AGACAAAAT-TATGTTTCAAGGGAAACAT
* * *
106999 GTCTCAAGAGAGACAAAAATCCATGTTTCAAGGAAAACAT
1 GTCTCAAGGGAGAC-AAAAT-TATGTTTCAAGGGAAACAT
* *
107039 ATCTCAAGGGAGACAAAATCTATGTTTCAA-GGAAACAG
1 GTCTCAAGGGAGACAAAAT-TATGTTTCAAGGGAAACAT
*
107077 GTCTCAATGGAGACAAAATATATGTTTCAAGGGAAACAT
1 GTCTCAAGGGAGACAAAAT-TATGTTTCAAGGGAAACAT
* * * *
107116 GTATCAAGGGAGAGAAAAATCTTTGTTTCAAGGGAAACAA
1 GTCTCAAGGGAGA-CAAAAT-TATGTTTCAAGGGAAACAT
* *
107156 GCCTCAAAGGAGACAA
1 GTCTCAAGGGAGACAA
107172 TAAACTTTTC
Statistics
Matches: 436, Mismatches: 64, Indels: 46
0.80 0.12 0.08
Matches are distributed among these distances:
36 11 0.03
37 25 0.06
38 71 0.16
39 188 0.43
40 127 0.29
41 10 0.02
42 4 0.01
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (38 bp):
GTCTCAAGGGAGACAAAATTATGTTTCAAGGGAAACAT
Found at i:106758 original size:23 final size:22
Alignment explanation
Indices: 106732--106804 Score: 59
Period size: 23 Copynumber: 3.5 Consensus size: 22
106722 AACATGTCTT
*
106732 AAGGGAGACAAAATCTATGTTCC
1 AAGGGAAACAAAATCTATGTT-C
*
106755 AAGGGAAAC-AAGTC-----TC
1 AAGGGAAACAAAATCTATGTTC
*
106771 AAGGGAGACAAAATCTATGTTTC
1 AAGGGAAACAAAATCTATG-TTC
106794 AAGGGAAACAA
1 AAGGGAAACAA
106805 GTCTCAAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
16 9 0.24
17 5 0.13
22 4 0.11
23 20 0.53
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (22 bp):
AAGGGAAACAAAATCTATGTTC
Found at i:106824 original size:79 final size:79
Alignment explanation
Indices: 106595--107171 Score: 554
Period size: 79 Copynumber: 7.4 Consensus size: 79
106585 ATGGGAGATT
* * * * *
106595 TTTCAAGTGCAACTAGTCTCAAGTGAGACAAAAT-TAATGTTTCAAGGGAAACATGTCACAAGGG
1 TTTCAAGGGAAACAAGTCTCAAGGGAGACAAAATCT-ATGTTTCAAGGGAAACATGTCTCAAGGG
106659 AGAC-AAAA--TATG
65 AGACAAAAATCTATG
* * * * * *
106671 TTTTCAAGGGAAATAGGTCCCAAGAGAGACAAAAATCTATGTTTCAAGGAAAACATGTCTTAAGG
1 -TTTCAAGGGAAACAAGTCTCAAGGGAGAC-AAAATCTATGTTTCAAGGGAAACATGTCTCAAGG
106736 GAGAC-AAAATCTATG
64 GAGACAAAAATCTATG
* *
106751 TTCCAAGGGAAACAAGTCTCAAGGGAGACAAAATCTATGTTTCAAGGGAAACAAGTCTCAA-GGA
1 TTTCAAGGGAAACAAGTCTCAAGGGAGACAAAATCTATGTTTCAAGGGAAACATGTCTCAAGGGA
106815 GGACAAAAATC-ATTG
66 -GACAAAAATCTA-TG
* * * * ** * * *
106830 TTTCAAGGGAAACAAGCCTTAAGAGAGACAAAATCTGTAATTC-AGGGCAAACAAGTCCCAAGAG
1 TTTCAAGGGAAACAAGTCTCAAGGGAGACAAAATCTATGTTTCAAGGG-AAACATGTCTCAAGGG
* *
106894 AGACAAACATATATG
65 AGACAAAAATCTATG
** * * * * *
106909 TTTCAAGGGAAACATTTCTCAAGGGAGACCAAATATGTGTTTCAATGGAAACGTGTCTC--GGGT
1 TTTCAAGGGAAACAAGTCTCAAGGGAGACAAAATCTATGTTTCAAGGGAAACATGTCTCAAGGG-
* *
106972 AG-C-AAAATATATA
65 AGACAAAAATCTATG
* * * * * *
106985 TTTCAA-GAAAACATGTCTCAAGAGAGACAAAAATCCATGTTTCAAGGAAAACATATCTCAAGGG
1 TTTCAAGGGAAACAAGTCTCAAGGGAGAC-AAAATCTATGTTTCAAGGGAAACATGTCTCAAGGG
107049 AGAC-AAAATCTATG
65 AGACAAAAATCTATG
* * * *
107063 TTTCAA-GGAAACAGGTCTCAATGGAGACAAAATATATGTTTCAAGGGAAACATGTATCAAGGGA
1 TTTCAAGGGAAACAAGTCTCAAGGGAGACAAAATCTATGTTTCAAGGGAAACATGTCTCAAGGGA
* *
107127 GAGAAAAATCTTTG
66 GACAAAAATCTATG
* *
107141 TTTCAAGGGAAACAAGCCTCAAAGGAGACAA
1 TTTCAAGGGAAACAAGTCTCAAGGGAGACAA
107172 TAAACTTTTC
Statistics
Matches: 410, Mismatches: 72, Indels: 34
0.79 0.14 0.07
Matches are distributed among these distances:
75 19 0.05
76 36 0.09
77 63 0.15
78 128 0.31
79 154 0.38
80 10 0.02
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (79 bp):
TTTCAAGGGAAACAAGTCTCAAGGGAGACAAAATCTATGTTTCAAGGGAAACATGTCTCAAGGGA
GACAAAAATCTATG
Found at i:116013 original size:24 final size:24
Alignment explanation
Indices: 115986--116034 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
115976 TATGCATTGT
115986 TATACATAAGCTATGTGATACATG
1 TATACATAAGCTATGTGATACATG
116010 TATACATAAGCTATGTGATACATG
1 TATACATAAGCTATGTGATACATG
116034 T
1 T
116035 TATTCTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (24 bp):
TATACATAAGCTATGTGATACATG
Found at i:116283 original size:21 final size:22
Alignment explanation
Indices: 116258--116394 Score: 136
Period size: 21 Copynumber: 6.3 Consensus size: 22
116248 GAGTCAAGGG
*
116258 TTCTATGCGGTCCTTTGGGACA
1 TTCTATGTGGTCCTTTGGGACA
**
116280 -TCTATGTGGTCCTAAGGGACAA
1 TTCTATGTGGTCCTTTGGGAC-A
* * **
116302 TTCTACGTGGTTCTTCAGGACA
1 TTCTATGTGGTCCTTTGGGACA
* *
116324 TTTCTATGCGGTCCTTCGGGACA
1 -TTCTATGTGGTCCTTTGGGACA
*
116347 -TCTATGTGCTCCTTTGGGACA
1 TTCTATGTGGTCCTTTGGGACA
*
116368 -TCTATGTGGTCCTTTGGGGCA
1 TTCTATGTGGTCCTTTGGGACA
116389 TTCTAT
1 TTCTAT
116395 ATGGCACTTC
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
21 54 0.57
22 7 0.07
23 33 0.35
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (22 bp):
TTCTATGTGGTCCTTTGGGACA
Found at i:116340 original size:23 final size:23
Alignment explanation
Indices: 116258--116347 Score: 69
Period size: 23 Copynumber: 4.0 Consensus size: 23
116248 GAGTCAAGGG
**
116258 TTCTATGCGGTCCTTTGGGACA-
1 TTCTATGCGGTCCTTCAGGACAT
* * *
116280 -TCTATGTGGTCC-TAAGGGACAA
1 TTCTATGCGGTCCTTCA-GGACAT
* * *
116302 TTCTACGTGGTTCTTCAGGACAT
1 TTCTATGCGGTCCTTCAGGACAT
*
116325 TTCTATGCGGTCCTTCGGGACAT
1 TTCTATGCGGTCCTTCAGGACAT
116348 CTATGTGCTC
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.02
21 16 0.30
23 34 0.64
24 2 0.04
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCAGGACAT
Found at i:116711 original size:2 final size:2
Alignment explanation
Indices: 116704--116738 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
116694 GATATGAGGT
116704 TA TA TA 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 TA TA TA T
116739 TAAGTGGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:123839 original size:30 final size:30
Alignment explanation
Indices: 123765--123892 Score: 91
Period size: 30 Copynumber: 4.2 Consensus size: 30
123755 AACGATCAAT
* * *
123765 GGATCTTGTAGTTTTGAGCAAAAGATAAAG
1 GGATCTCGTAATTTTGAGCGAAAGATAAAG
* *
123795 GGGTCTTC-TTATTTTGAGCGAAAGATAAAG
1 GGATC-TCGTAATTTTGAGCGAAAGATAAAG
* * * *
123825 GGATCTCGTAATTTTCAAGTGAATGATCAAG
1 GGATCTCGTAATTTT-GAGCGAAAGATAAAG
* * *
123856 AGATCAT-GTAATTTTG-GTTGAAAGATGAAG
1 GGATC-TCGTAATTTTGAG-CGAAAGATAAAG
123886 GGATCTC
1 GGATCTC
123893 ATTTTGGCTT
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
29 4 0.05
30 47 0.62
31 24 0.32
32 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (30 bp):
GGATCTCGTAATTTTGAGCGAAAGATAAAG
Found at i:132231 original size:24 final size:24
Alignment explanation
Indices: 132204--132249 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
132194 GTTTTATTAA
132204 TATTTTCATTTTA-AAAATATATTT
1 TATTTT-ATTTTATAAAATATATTT
*
132228 TATTTTATTTTATTAAATATAT
1 TATTTTATTTTATAAAATATAT
132250 AGTTAAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTTATTTTATAAAATATATTT
Found at i:139513 original size:22 final size:22
Alignment explanation
Indices: 139488--139546 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
139478 AATATGAGTA
139488 CCAAGATTAGGGTTTTCACTAC
1 CCAAGATTAGGGTTTTCACTAC
*
139510 CCAATATTAGGGTTTTCACTAC
1 CCAAGATTAGGGTTTTCACTAC
*
139532 CCAAGATTCGGGTTT
1 CCAAGATTAGGGTTT
139547 GTTGATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (22 bp):
CCAAGATTAGGGTTTTCACTAC
Found at i:143917 original size:17 final size:17
Alignment explanation
Indices: 143888--143931 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
143878 TTAAGAACTA
*
143888 TGAATATATGATAAATG-
1 TGAATAAATGAT-AATGT
*
143905 TGATTAAATGATAATGT
1 TGAATAAATGATAATGT
143922 TGAATAAATG
1 TGAATAAATG
143932 TTATGTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (17 bp):
TGAATAAATGATAATGT
Found at i:144027 original size:16 final size:16
Alignment explanation
Indices: 143995--144040 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
143985 ATGGATAATG
*
143995 CTACATG-AAACTGTT
1 CTACATGAAAAATGTT
144010 CTACATGAAAAATGTT
1 CTACATGAAAAATGTT
*
144026 CTACCT-AAAAATGTT
1 CTACATGAAAAATGTT
144041 ATATGTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (16 bp):
CTACATGAAAAATGTT
Found at i:144426 original size:19 final size:19
Alignment explanation
Indices: 144402--144438 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
144392 ACGTTGGGCT
*
144402 AATTAAATAAATGGATATA
1 AATTAAACAAATGGATATA
*
144421 AATTAAACAAATTGATAT
1 AATTAAACAAATGGATAT
144439 GGATTGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTAAACAAATGGATATA
Found at i:151545 original size:15 final size:14
Alignment explanation
Indices: 151500--151550 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
151490 ATGAAAGTTT
151500 TTTATATGAATATG
1 TTTATATGAATATG
* *
151514 TTTATGT-AA-AGG
1 TTTATATGAATATG
151526 CTTTATATGAATATG
1 -TTTATATGAATATG
151541 ATTTATATGA
1 -TTTATATGA
151551 GTAAATTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
12 2 0.07
13 8 0.28
14 8 0.28
15 11 0.38
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (14 bp):
TTTATATGAATATG
Found at i:151733 original size:15 final size:16
Alignment explanation
Indices: 151720--151754 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
151710 TATGTGAAAC
151720 TGTTCTACGTGAAAAA
1 TGTTCTACGTGAAAAA
*
151736 TGTTCTACCT-AAAAA
1 TGTTCTACGTGAAAAA
151751 TGTT
1 TGTT
151755 ATATGTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (16 bp):
TGTTCTACGTGAAAAA
Found at i:152002 original size:24 final size:24
Alignment explanation
Indices: 151970--152015 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
151960 ATAAAAATCG
*
151970 ACGTGGCACTTCGGTGCAAATTCT
1 ACGTGGCACTTAGGTGCAAATTCT
151994 ACGTGGCACTTAGGTGCAAATT
1 ACGTGGCACTTAGGTGCAAATT
152016 ATATGAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (24 bp):
ACGTGGCACTTAGGTGCAAATTCT
Found at i:152120 original size:19 final size:19
Alignment explanation
Indices: 152096--152132 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
152086 ATGTTGAGCT
*
152096 AATTAAATAAATGGATATA
1 AATTAAACAAATGGATATA
*
152115 AATTAAACAAATTGATAT
1 AATTAAACAAATGGATAT
152133 GGATTGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTAAACAAATGGATATA
Found at i:161942 original size:41 final size:41
Alignment explanation
Indices: 161890--162091 Score: 228
Period size: 41 Copynumber: 4.9 Consensus size: 41
161880 ATTTTTTCCT
* *
161890 CAAACGCCGCAATAGTGATAATCAATAGTTGCATTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGA
* *
161931 CAAACGTCGCAATAGTGTTACTCAATAGTGGCATTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGA
* * * * * * *
161972 CAAAACACTGTAATAGAGTTAATCACTACTGGCGTTTTTAGA
1 C-AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGA
* * *
162014 CAAACGCTGTAATATTGTTAATCAATAGTGGCATTTTTTA-A
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCA-TTTTTAGA
* *
162055 CAAACGCCACAATAGT-ATAATCAATAGTGGCATTTTT
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTT
162092 TTGTATAAAC
Statistics
Matches: 135, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
39 5 0.04
40 15 0.11
41 77 0.57
42 38 0.28
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
CAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGA
Found at i:161987 original size:83 final size:82
Alignment explanation
Indices: 161847--162091 Score: 221
Period size: 83 Copynumber: 3.0 Consensus size: 82
161837 CGTTTATACC
* * * ** * *
161847 ACAAACGCTACAATAG-ATTACA-CATATAGCGGCATTTTTTCCTCAAACGCCGCAATAGTGATA
1 ACAAACGCTGCAATAGTGTTA-ATCA-ATAGTGGCATTTTTT-AACAAACACCACAATAGTGATA
*
161910 ATCAATAGTTGCATTTTTAG
63 ATCAATAGTGGCATTTTTAG
* *** * *
161930 ACAAACG-TCGCAATAGTGTTACTCAATAGTGGCA-TTTTTAGACAAAACACTGTAATAGAGTTA
1 ACAAACGCT-GCAATAGTGTTAATCAATAGTGGCATTTTTTA-AC-AAACACCACAATAGTGATA
* * *
161993 ATCACTACTGGCGTTTTTAG
63 ATCAATAGTGGCATTTTTAG
* * *
162013 ACAAACGCTGTAATATTGTTAATCAATAGTGGCATTTTTTAACAAACGCCACAATAGT-ATAATC
1 ACAAACGCTGCAATAGTGTTAATCAATAGTGGCATTTTTTAACAAACACCACAATAGTGATAATC
162077 AATAGTGGCATTTTT
66 AATAGTGGCATTTTT
162092 TTGTATAAAC
Statistics
Matches: 128, Mismatches: 27, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
81 17 0.13
82 17 0.13
83 82 0.64
84 12 0.09
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (82 bp):
ACAAACGCTGCAATAGTGTTAATCAATAGTGGCATTTTTTAACAAACACCACAATAGTGATAATC
AATAGTGGCATTTTTAG
Found at i:162102 original size:83 final size:81
Alignment explanation
Indices: 161872--162091 Score: 230
Period size: 83 Copynumber: 2.7 Consensus size: 81
161862 GATTACACAT
* ** *
161872 ATAGCGGCATTTTTTCCTCAAACGCCGCAATAGTGATAATCAATAGTTGCATTTTTAGACAAACG
1 ATAGTGGCATTTTTT-AACAAACGCCGCAATAGT-ATAATCAATAGTGGCATTTTTAGACAAACG
*
161937 TCGCAATAGTGTTACTCA
64 TCGCAATAGTGTTAATCA
* * * * * *
161955 ATAGTGGCA-TTTTTAGACAAAACACTGTAATAG-AGTTAATCACTACTGGCGTTTTTAGACAAA
1 ATAGTGGCATTTTTTA-AC-AAACGCCGCAATAGTA--TAATCAATAGTGGCATTTTTAGACAAA
* *
162018 CG-CTGTAATATTGTTAATCA
62 CGTC-GCAATAGTGTTAATCA
*
162038 ATAGTGGCATTTTTTAACAAACGCCACAATAGTATAATCAATAGTGGCATTTTT
1 ATAGTGGCATTTTTTAACAAACGCCGCAATAGTATAATCAATAGTGGCATTTTT
162092 TTGTATAAAC
Statistics
Matches: 110, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
81 18 0.16
82 17 0.15
83 69 0.63
84 6 0.05
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (81 bp):
ATAGTGGCATTTTTTAACAAACGCCGCAATAGTATAATCAATAGTGGCATTTTTAGACAAACGTC
GCAATAGTGTTAATCA
Found at i:163391 original size:43 final size:43
Alignment explanation
Indices: 163335--163434 Score: 164
Period size: 43 Copynumber: 2.3 Consensus size: 43
163325 CGTTTTTTTA
163335 CAAACGCCGCAATAGGTACAATATTTAGTGGCGTTTTTCACAC
1 CAAACGCCGCAATAGGTACAATATTTAGTGGCGTTTTTCACAC
* * **
163378 CAAATGCCGCAATAGGTATAATATTTAGTGGCGTTTTTTGCAC
1 CAAACGCCGCAATAGGTACAATATTTAGTGGCGTTTTTCACAC
163421 CAAACGCCGCAATA
1 CAAACGCCGCAATA
163435 TTTGGGGATA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (43 bp):
CAAACGCCGCAATAGGTACAATATTTAGTGGCGTTTTTCACAC
Found at i:171315 original size:21 final size:21
Alignment explanation
Indices: 171263--171315 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
171253 CGGAAAATAA
*
171263 AGCAAGGGAAGCAGAGAGAGC
1 AGCAACGGAAGCAGAGAGAGC
* **
171284 AGCAACAGAAGCAGCTAGAGC
1 AGCAACGGAAGCAGAGAGAGC
*
171305 AGCAGCGGAAG
1 AGCAACGGAAG
171316 TAGACAAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.38, T:0.02
Consensus pattern (21 bp):
AGCAACGGAAGCAGAGAGAGC
Found at i:171783 original size:54 final size:54
Alignment explanation
Indices: 171693--171798 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
171683 GTTAAAAAAT
171693 GCCGCAATATACCATACATTTAGCGGCATTTGTATACTAGAAACGCCGCTAAAC
1 GCCGCAATATACCATACATTTAGCGGCATTTGTATACTAGAAACGCCGCTAAAC
* * *
171747 GCCGCAATATACCATACATTTAGCGGCGTTTTTATACTATAAACGCCGCTAA
1 GCCGCAATATACCATACATTTAGCGGCATTTGTATACTAGAAACGCCGCTAA
171799 TTCTCAACTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (54 bp):
GCCGCAATATACCATACATTTAGCGGCATTTGTATACTAGAAACGCCGCTAAAC
Found at i:175883 original size:20 final size:20
Alignment explanation
Indices: 175858--175924 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
175848 TCTTATTGAT
175858 GAAAGTGTACGCAAATGGAA
1 GAAAGTGTACGCAAATGGAA
* ** * *
175878 GAAAGTCT-CGGGTCTTATTGAT
1 GAAAGTGTAC--G-CAAATGGAA
175900 GAAAGTGTACGCAAATGGAA
1 GAAAGTGTACGCAAATGGAA
175920 GAAAG
1 GAAAG
175925 ATATTGTTAT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 1 0.03
20 17 0.52
21 2 0.06
22 12 0.36
23 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.30, T:0.21
Consensus pattern (20 bp):
GAAAGTGTACGCAAATGGAA
Found at i:175899 original size:42 final size:42
Alignment explanation
Indices: 175840--175924 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
175830 TTTGATTAGC
175840 GTCTCGGGTCTTATTGATGAAAGTGTACGCAAATGGAAGAAA
1 GTCTCGGGTCTTATTGATGAAAGTGTACGCAAATGGAAGAAA
175882 GTCTCGGGTCTTATTGATGAAAGTGTACGCAAATGGAAGAAA
1 GTCTCGGGTCTTATTGATGAAAGTGTACGCAAATGGAAGAAA
175924 G
1 G
175925 ATATTGTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (42 bp):
GTCTCGGGTCTTATTGATGAAAGTGTACGCAAATGGAAGAAA
Found at i:177213 original size:2 final size:2
Alignment explanation
Indices: 177201--177379 Score: 130
Period size: 2 Copynumber: 92.0 Consensus size: 2
177191 TTGAAACAAT
* * *
177201 TA TA AA TA TA TA TA TA TA TA TA TA TA T- TA TA GTT TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
177243 T- TA TA T- TA TA TA TA TA AA TA TA T- TA TA AA CTA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* *
177284 TA TA -A CTA TA TA TT TA TA TA TA TA TA T- TA TA GTT TA TA T- TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
177325 TA T- TA T- TA TA TA TA TA TA TA -A CTA TG TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
*
177364 CTA TA TA -A CA TA TA TA
1 -TA TA TA TA TA TA TA TA
177380 AATTATAGAA
Statistics
Matches: 141, Mismatches: 17, Indels: 38
0.72 0.09 0.19
Matches are distributed among these distances:
1 12 0.09
2 121 0.86
3 8 0.06
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:177269 original size:31 final size:29
Alignment explanation
Indices: 177211--177378 Score: 75
Period size: 31 Copynumber: 5.7 Consensus size: 29
177201 TATAAATATA
*
177211 TATATATATATATATATTATAGTTTATATTTAT
1 TATATATATATATA-AATATA--TTATA-TTAT
* * * * *
177244 TATA-TTATATATATAAATA-TATTATAAAC
1 TATATATATATATAAATATATTA-TAT-TAT
*
177273 TATATAGTATATATAACTATA-TAT-TTA-
1 TATATA-TATATATAAATATATTATATTAT
**
177300 TATATATATATTATAGTTTATATTATATTAT
1 TATATATATA-TATA-AATATATTATATTAT
* *
177331 TATATATATATATAACTAT-GTATA-TA-
1 TATATATATATATAAATATATTATATTAT
177357 TATATA-ACTATATAACATATAT
1 TATATATA-TATATAA-ATATAT
177379 AAATTATAGA
Statistics
Matches: 105, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
25 1 0.01
26 17 0.16
27 15 0.14
28 12 0.11
29 14 0.13
30 8 0.08
31 26 0.25
32 8 0.08
33 4 0.04
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (29 bp):
TATATATATATATAAATATATTATATTAT
Found at i:177322 original size:57 final size:58
Alignment explanation
Indices: 177201--177362 Score: 169
Period size: 57 Copynumber: 2.9 Consensus size: 58
177191 TTGAAACAAT
* *
177201 TATAAATATA-TATAT-A-TATATATATAT-TATAGTTTATATTTAT-TATATTATATA
1 TATAAATATATTATATAACTATATATATATATA-ACTATATATTTATATATATTATATA
177255 TATAAATATATTATA-AACTATATAGTATATATAACTATATATTTATATATA-TATAT-
1 TATAAATATATTATATAACTATATA-TATATATAACTATATATTTATATATATTATATA
** * * * *
177311 TATAGTTTATATTATATTATTATATATATATATAACTATGTATATATATATA
1 TATA-AATATATTATATAACTATATATATATATAACTATATATTTATATATA
177363 ACTATATAAC
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 54 0.59
58 13 0.14
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (58 bp):
TATAAATATATTATATAACTATATATATATATAACTATATATTTATATATATTATATA
Found at i:177515 original size:2 final size:2
Alignment explanation
Indices: 177504--177650 Score: 51
Period size: 2 Copynumber: 74.0 Consensus size: 2
177494 TATACACGGT
* * * *
177504 TA TA TT TA TA TA TG TA TA -A T- TA TA AA TA TA TA TA CTA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * * *
177545 CA AA T- TA TA TA GTT TA TA TA GTT TA AA TA TA AA GTA TA TA -A
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
*
177586 GTA TA TA TA TA TA TA TA TA -A CTA TA TA CA TA TA TA -A TA -A TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
177627 TA AA GTA TA -A GTA T- TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA
177651 GTACAATTAC
Statistics
Matches: 105, Mismatches: 23, Indels: 34
0.65 0.14 0.21
Matches are distributed among these distances:
1 9 0.09
2 87 0.83
3 9 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:177600 original size:16 final size:15
Alignment explanation
Indices: 177590--177650 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 15
177580 ATATAAGTAT
177590 ATATATATATATATA
1 ATATATATATATATA
*
177605 ACTATATACATATATA
1 A-TATATATATATATA
*
177621 ATA-ATATAAAGTATA
1 ATATATATATA-TATA
177636 AGTAT-TATATATATA
1 A-TATATATATATATA
177651 GTACAATTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 5 0.13
15 12 0.32
16 21 0.55
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:177602 original size:20 final size:20
Alignment explanation
Indices: 177504--177628 Score: 69
Period size: 20 Copynumber: 6.2 Consensus size: 20
177494 TATACACGGT
* *
177504 TATATTTATATATGTATAA-
1 TATATATATATATATATAAG
* *
177523 T-TATAAATATATATACTATG
1 TATATATATATATATA-TAAG
* * *
177543 TACAAATTATATAGTTTATATAG
1 TATATA-TATATA-TATATA-AG
* * *
177566 TTTAAATATAAAGTATATAAG
1 TATATATATATA-TATATAAG
*
177587 TATATATATATATATATAAC
1 TATATATATATATATATAAG
*
177607 TATATACATATATA-ATAA-
1 TATATATATATATATATAAG
177625 TATA
1 TATA
177629 AAGTATAAGT
Statistics
Matches: 82, Mismatches: 18, Indels: 13
0.73 0.16 0.12
Matches are distributed among these distances:
18 15 0.18
19 7 0.09
20 21 0.26
21 13 0.16
22 18 0.22
23 8 0.10
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATATATATATATATAAG
Found at i:177960 original size:29 final size:27
Alignment explanation
Indices: 177927--178073 Score: 125
Period size: 29 Copynumber: 5.0 Consensus size: 27
177917 ATAGTACAAT
177927 TATAAAGACTAAAGTATATAAGCATATAA
1 TATAAAGA-TAAAGTATATAA-CATATAA
* *
177956 TATAAAGTATATAA-TATAAAATATATAA
1 TATAAAG-ATA-AAGTATATAACATATAA
* *
177984 TAATTAAATATAAAGTATATAAAATATAA
1 T-A-TAAAGATAAAGTATATAACATATAA
*
178013 CTATAAAGACTAAAGTATATAAGTATATAA
1 -TATAAAGA-TAAAGTATATAA-CATATAA
178043 TATAAAGTATATAAAGTATATATACATATAA
1 TATAAAG---ATAAAGTATATA-ACATATAA
178074 AGTATAAGTG
Statistics
Matches: 98, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
28 14 0.14
29 51 0.52
30 14 0.14
31 17 0.17
32 2 0.02
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (27 bp):
TATAAAGATAAAGTATATAACATATAA
Found at i:177969 original size:14 final size:14
Alignment explanation
Indices: 177950--178056 Score: 89
Period size: 14 Copynumber: 7.4 Consensus size: 14
177940 GTATATAAGC
177950 ATATAATATAAAGT
1 ATATAATATAAAGT
*
177964 ATATAATATAAAAT
1 ATATAATATAAAGT
177978 ATATAATAATTAAA-T
1 ATATAAT-A-TAAAGT
*
177993 ATA-AAGTATATAA-A
1 ATATAA-TATA-AAGT
178007 ATATAACTATAAAG-
1 ATATAA-TATAAAGT
178021 ACTA-AAGTATATAAGT
1 A-TATAA-TATA-AAGT
178037 ATATAATATAAAGT
1 ATATAATATAAAGT
178051 ATATAA
1 ATATAA
178057 AGTATATATA
Statistics
Matches: 79, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
13 2 0.03
14 47 0.59
15 23 0.29
16 7 0.09
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.34
Consensus pattern (14 bp):
ATATAATATAAAGT
Found at i:177973 original size:7 final size:7
Alignment explanation
Indices: 177950--178056 Score: 64
Period size: 7 Copynumber: 14.9 Consensus size: 7
177940 GTATATAAGC
177950 ATATAAT
1 ATATAAT
177957 ATA-AAGT
1 ATATAA-T
177964 ATATAAT
1 ATATAAT
*
177971 ATAAAAT
1 ATATAAT
177978 ATATAAT
1 ATATAAT
177985 A-ATTAA-
1 ATA-TAAT
177991 ATATAAAGT
1 ATAT-AA-T
*
178000 ATATAAA
1 ATATAAT
178007 ATATAACT
1 ATATAA-T
*
178015 ATA-AAG
1 ATATAAT
178021 ACTA-AAGT
1 A-TATAA-T
178029 ATATAAGT
1 ATATAA-T
178037 ATATAAT
1 ATATAAT
178044 ATA-AAGT
1 ATATAA-T
178051 ATATAA
1 ATATAA
178057 AGTATATATA
Statistics
Matches: 81, Mismatches: 6, Indels: 25
0.72 0.05 0.22
Matches are distributed among these distances:
6 8 0.10
7 49 0.60
8 20 0.25
9 4 0.05
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.34
Consensus pattern (7 bp):
ATATAAT
Found at i:178032 original size:22 final size:21
Alignment explanation
Indices: 177927--178056 Score: 79
Period size: 22 Copynumber: 6.0 Consensus size: 21
177917 ATAGTACAAT
177927 TATAAAGACTAAAGTATATAAGC
1 TATAAAGA-TAAAGTATATAA-C
*
177950 -ATATAATATAAAGTATATAA-
1 TATA-AAGATAAAGTATATAAC
* *
177970 TATAAA-ATATA-TAATAATTAAA
1 TATAAAGATAAAGT-AT-A-TAAC
* **
177992 TATAAAGTATATAAAATATAAC
1 TATAAAG-ATAAAGTATATAAC
*
178014 TATAAAGACTAAAGTATATAAG
1 TATAAAGA-TAAAGTATATAAC
*
178036 TATATAATATAAAGTATATAA
1 TATA-AAGATAAAGTATATAA
178057 AGTATATATA
Statistics
Matches: 87, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
18 1 0.01
19 6 0.07
20 3 0.03
21 7 0.08
22 56 0.64
23 7 0.08
24 7 0.08
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (21 bp):
TATAAAGATAAAGTATATAAC
Found at i:178056 original size:9 final size:9
Alignment explanation
Indices: 178023--178079 Score: 54
Period size: 9 Copynumber: 7.0 Consensus size: 9
178013 CTATAAAGAC
178023 TAAAGTATA
1 TAAAGTATA
178032 T-AAGTATA
1 TAAAGTATA
178040 T--A--ATA
1 TAAAGTATA
178045 TAAAGTATA
1 TAAAGTATA
178054 TAAAGTATA
1 TAAAGTATA
* *
178063 TATA-CATA
1 TAAAGTATA
178071 TAAAGTATA
1 TAAAGTATA
178080 AGTGTATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
5 4 0.10
7 2 0.05
8 14 0.36
9 19 0.49
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (9 bp):
TAAAGTATA
Found at i:178082 original size:23 final size:24
Alignment explanation
Indices: 177955--178079 Score: 60
Period size: 22 Copynumber: 5.5 Consensus size: 24
177945 TAAGCATATA
177955 ATATAAAG--TATATAATATAAA-
1 ATATAAAGTATATATAATATAAAG
177976 ATATATAA-TA-AT-TAAATATAAAG
1 ATATA-AAGTATATAT-AATATAAAG
*
177999 TATATAAA--ATATA-ACTATAAAG
1 -ATATAAAGTATATATAATATAAAG
* * *
178021 A-CTAAAGTATATA-AGTATATA-
1 ATATAAAGTATATATAATATAAAG
*
178042 ATATAAAGTATATA-AAGTATATATAC
1 ATATAAAGTATATATAA-TATA-A-AG
178068 ATATAAAGTATA
1 ATATAAAGTATA
178080 AGTGTATATA
Statistics
Matches: 82, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
20 4 0.05
21 8 0.10
22 44 0.54
23 8 0.10
24 5 0.06
25 1 0.01
26 12 0.15
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (24 bp):
ATATAAAGTATATATAATATAAAG
Found at i:178086 original size:25 final size:25
Alignment explanation
Indices: 177955--178098 Score: 94
Period size: 25 Copynumber: 5.9 Consensus size: 25
177945 TAAGCATATA
*
177955 ATATAAAG--TATATAATATAAAAT
1 ATATAAAGTATATATAATATAAAGT
177978 ATAT-AA-TA-AT-TAAATATAAAGT
1 ATATAAAGTATATAT-AATATAAAGT
* *
178000 ATATAAAATATAACTATAAAGACTAAAG-
1 ATATAAAGTAT-A-TAT-AATA-TAAAGT
178028 -TATATAAG--TATATAATATAAAGT
1 ATATA-AAGTATATATAATATAAAGT
178051 ATATAAAGTATATATACATATAAAGT
1 ATATAAAGTATATATA-ATATAAAGT
**
178077 ATA-AGTGTATATATATATATAA
1 ATATAAAGTATATATA-ATATAA
178099 TAAACTATAT
Statistics
Matches: 98, Mismatches: 7, Indels: 30
0.73 0.05 0.22
Matches are distributed among these distances:
21 1 0.01
22 22 0.22
23 12 0.12
24 9 0.09
25 23 0.23
26 14 0.14
27 5 0.05
28 7 0.07
29 5 0.05
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (25 bp):
ATATAAAGTATATATAATATAAAGT
Found at i:178087 original size:23 final size:24
Alignment explanation
Indices: 178035--178095 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
178025 AAGTATATAA
178035 GTATATAATATAAAGTATATAAAGT
1 GTATATAATATAAAG-ATATAAAGT
*
178060 ATATATACATATAAAG-TAT-AAGT
1 GTATATA-ATATAAAGATATAAAGT
178083 GTATATATATATA
1 GTATATA-ATATA
178096 TAATAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 15 0.47
24 3 0.09
25 6 0.19
26 8 0.25
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.38
Consensus pattern (24 bp):
GTATATAATATAAAGATATAAAGT
Found at i:178088 original size:17 final size:17
Alignment explanation
Indices: 178023--178089 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
178013 CTATAAAGAC
*
178023 TAAAGTATATAAGTATA
1 TAAAGTATATATGTATA
*
178040 T-AA-TATA-AAGTATA
1 TAAAGTATATATGTATA
**
178054 TAAAGTATATATACATA
1 TAAAGTATATATGTATA
178071 TAAAGTATA-AGTGTATA
1 TAAAGTATATA-TGTATA
178088 TA
1 TA
178090 TATATATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 8 0.20
15 6 0.15
16 7 0.17
17 20 0.49
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.36
Consensus pattern (17 bp):
TAAAGTATATATGTATA
Found at i:178089 original size:27 final size:29
Alignment explanation
Indices: 178059--178122 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
178049 GTATATAAAG
*
178059 TATATATACAT-ATAAAGTATA-AGTGTA
1 TATATATACATAATAAACTATATAGTGTA
* *
178086 TATATATATATAATAAACTATATAGTTTA
1 TATATATACATAATAAACTATATAGTGTA
*
178115 TATTTATA
1 TATATATA
178123 TTATTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 10 0.32
28 9 0.29
29 12 0.39
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (29 bp):
TATATATACATAATAAACTATATAGTGTA
Found at i:178091 original size:19 final size:17
Alignment explanation
Indices: 177950--178079 Score: 63
Period size: 15 Copynumber: 8.1 Consensus size: 17
177940 GTATATAAGC
177950 ATATA-ATATAAAGTAT
1 ATATATATATAAAGTAT
177966 ATA-ATATA-AAA-TAT
1 ATATATATATAAAGTAT
177980 ATA-ATA-ATTAAA-TAT
1 ATATATATA-TAAAGTAT
*
177995 A-A-AGTATATAAAATAT
1 ATATA-TATATAAAGTAT
* *
178011 AACTATAAAGACTAAAGTAT
1 -A-TATATATA-TAAAGTAT
178031 ATA-AGTATAT-AA-TAT
1 ATATA-TATATAAAGTAT
178046 A-A-AGTATATAAAGTAT
1 ATATA-TATATAAAGTAT
*
178062 ATATACATATAAAGTAT
1 ATATATATATAAAGTAT
178079 A
1 A
178080 AGTGTATATA
Statistics
Matches: 92, Mismatches: 6, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
13 1 0.01
14 19 0.21
15 23 0.25
16 16 0.17
17 16 0.17
18 5 0.05
19 4 0.04
20 8 0.09
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (17 bp):
ATATATATATAAAGTAT
Found at i:178156 original size:22 final size:22
Alignment explanation
Indices: 178124--178183 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
178114 ATATTTATAT
*
178124 TATTATATATAAACTATACATA
1 TATTATGTATAAACTATACATA
*
178146 TATTATGTATAAAC--TAGATA
1 TATTATGTATAAACTATACATA
**
178166 TACCATGTATAAACTATA
1 TATTATGTATAAACTATA
178184 TAGTTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.53
22 15 0.47
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (22 bp):
TATTATGTATAAACTATACATA
Found at i:178224 original size:11 final size:11
Alignment explanation
Indices: 178210--178391 Score: 70
Period size: 11 Copynumber: 16.4 Consensus size: 11
178200 TATTGAACTC
*
178210 TATATAAACTA
1 TATATAAATTA
**
178221 TATAGTTTATTA
1 TATA-TAAATTA
178233 -ATATAAA-T-
1 TATATAAATTA
*
178241 TATATAATTTA
1 TATATAAATTA
178252 TATATAAATTA
1 TATATAAATTA
*
178263 TATATGAATTA
1 TATATAAATTA
*
178274 TATTTAAA-TA
1 TATATAAATTA
* **
178284 TATACAGCTTCTA
1 TATATA-AAT-TA
* *
178297 TTTATATATTA
1 TATATAAATTA
*
178308 TGTAT-AATTA
1 TATATAAATTA
* *
178318 TAAATTATATATA
1 TATA-TAAAT-TA
*
178331 TGTATAAATTA
1 TATATAAATTA
**
178342 TATAGTTTATTA
1 TATA-TAAATTA
*
178354 -ATATAAACTA
1 TATATAAATTA
* *
178364 TAAATTATATATA
1 TATA-TAAAT-TA
178377 TATATAAATTA
1 TATATAAATTA
178388 TATA
1 TATA
178392 GTTTATATAG
Statistics
Matches: 120, Mismatches: 37, Indels: 28
0.65 0.20 0.15
Matches are distributed among these distances:
9 7 0.06
10 19 0.16
11 56 0.47
12 23 0.19
13 15 0.12
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
TATATAAATTA
Found at i:178238 original size:22 final size:20
Alignment explanation
Indices: 178210--178400 Score: 90
Period size: 22 Copynumber: 9.2 Consensus size: 20
178200 TATTGAACTC
* *
178210 TATATAAACTATATAGTTTA
1 TATATAAATTATATAATTTA
178230 TTAATATAAATTATATAATTTA
1 -T-ATATAAATTATATAATTTA
*
178252 TATATAAATTATATATGAATTA
1 TATATAAATTATATA--ATTTA
*
178274 TATTTAAA-TATATACAGCTTCTA
1 TATATAAATTATATA-A--TT-TA
* * * *
178297 TTTATATATTATGT-A-TAA
1 TATATAAATTATATAATTTA
178315 T-TATAAATTATAT-A--TA
1 TATATAAATTATATAATTTA
* *
178331 TGTATAAATTATATAGTTTA
1 TATATAAATTATATAATTTA
* *
178351 TTAATATAAACTATAAATTATATATA
1 -T-ATATAAA-T-TATA-TA-ATTTA
*
178377 TATATAAATTATATAGTTTA
1 TATATAAATTATATAATTTA
178397 TATA
1 TATA
178401 GTTTAAATAA
Statistics
Matches: 131, Mismatches: 22, Indels: 35
0.70 0.12 0.19
Matches are distributed among these distances:
16 2 0.02
17 23 0.18
18 2 0.02
19 1 0.01
20 24 0.18
21 11 0.08
22 39 0.30
23 9 0.07
24 14 0.11
25 3 0.02
26 3 0.02
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (20 bp):
TATATAAATTATATAATTTA
Found at i:178318 original size:17 final size:17
Alignment explanation
Indices: 178298--178391 Score: 69
Period size: 17 Copynumber: 5.8 Consensus size: 17
178288 CAGCTTCTAT
* *
178298 TTATATATTATGTATAA
1 TTATAAATTATATATAA
178315 TTATAAATTATATAT-A
1 TTATAAATTATATATAA
*
178331 TGTATAAA-T-TATATAG
1 T-TATAAATTATATATAA
178347 TT-T--ATTA-ATATAAA
1 TTATAAATTATATAT-AA
*
178361 CTATAAATTATATAT-A
1 TTATAAATTATATATAA
178377 TATATAAATTATATA
1 T-TATAAATTATATA
178392 GTTTATATAG
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
12 1 0.02
13 5 0.08
14 3 0.05
15 7 0.11
16 5 0.08
17 36 0.59
18 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (17 bp):
TTATAAATTATATATAA
Found at i:178327 original size:24 final size:24
Alignment explanation
Indices: 178298--178446 Score: 114
Period size: 24 Copynumber: 6.2 Consensus size: 24
178288 CAGCTTCTAT
*
178298 TTATATAT-TATGTATAATTATAAA
1 TTATATATATATATA-AATTATAAA
* *
178322 TTATATATATGTATAAATTATATAG
1 TTATATATATATATAAATTATA-AA
*
178347 TT-TAT-TA-ATATAAACTATAAA
1 TTATATATATATATAAATTATAAA
*
178368 TTATATATATATATAAATTATATAG
1 TTATATATATATATAAATTATA-AA
* *
178393 TT-TATATAGT-T-TAAATAAAAGAA
1 TTATATATA-TATATAAATTATA-AA
* *
178416 TATATGTATATATATAAACTATAAA
1 T-TATATATATATATAAATTATAAA
178441 TTATAT
1 TTATAT
178447 TGTATGTATG
Statistics
Matches: 97, Mismatches: 17, Indels: 22
0.71 0.12 0.16
Matches are distributed among these distances:
21 3 0.03
22 13 0.13
23 13 0.13
24 42 0.43
25 20 0.21
26 6 0.06
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (24 bp):
TTATATATATATATAAATTATAAA
Found at i:189587 original size:7 final size:7
Alignment explanation
Indices: 189575--189610 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
189565 ATTAATTGAA
189575 AATATTT
1 AATATTT
189582 AATATTT
1 AATATTT
189589 AATATTT
1 AATATTT
*
189596 AATATGT
1 AATATTT
*
189603 ATTATTT
1 AATATTT
189610 A
1 A
189611 TAAATTTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (7 bp):
AATATTT
Found at i:189641 original size:24 final size:24
Alignment explanation
Indices: 189613--189660 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
189603 ATTATTTATA
189613 AATTTCAGTTAATT-TGATTAATGG
1 AATTT-AGTTAATTATGATTAATGG
* *
189637 AATTTTGTTCATTATGATTAATGG
1 AATTTAGTTAATTATGATTAATGG
189661 TTAAAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (24 bp):
AATTTAGTTAATTATGATTAATGG
Found at i:193587 original size:40 final size:40
Alignment explanation
Indices: 193502--193600 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
193492 CGAATTTGAC
* * * *
193502 AAATTCGCAACACGAATTTCTTTTTTGCAAATCGATTTTT
1 AAATTCGCAAAACGAGTTTCGTTTTCGCAAATCGATTTTT
*
193542 AAATTCGCAAAACGAGTTTCGTTTTCGCAACTCG-TTTTT
1 AAATTCGCAAAACGAGTTTCGTTTTCGCAAATCGATTTTT
* *
193581 CTAATTCGCAAAGCGAGTTT
1 -AAATTCGCAAAACGAGTTT
193601 TAATTTCGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 5 0.10
40 46 0.90
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (40 bp):
AAATTCGCAAAACGAGTTTCGTTTTCGCAAATCGATTTTT
Found at i:193804 original size:22 final size:22
Alignment explanation
Indices: 193779--193833 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
193769 TCTCTCACTC
*
193779 TCTCCGGCGACATCCGTCTCCA
1 TCTCCGGCGACATCCGTCCCCA
*
193801 TCTCCGGTGACATCCGTCCCCA
1 TCTCCGGCGACATCCGTCCCCA
193823 TCTCCGGCGAC
1 TCTCCGGCGAC
193834 CCCCCCTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.13, C:0.45, G:0.20, T:0.22
Consensus pattern (22 bp):
TCTCCGGCGACATCCGTCCCCA
Found at i:194193 original size:20 final size:20
Alignment explanation
Indices: 194164--194264 Score: 99
Period size: 20 Copynumber: 5.3 Consensus size: 20
194154 CAAGGAACTT
*
194164 AAATTTGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
194184 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
194204 ATAA-TCGCAACACG---A--
1 A-AATTCGCAACACGAAAATG
* *
194219 AAA-TCGTAACTCGAAAATG
1 AAATTCGCAACACGAAAATG
* *
194238 AAAATCGCAACTCGAAAATG
1 AAATTCGCAACACGAAAATG
194258 AAATTCG
1 AAATTCG
194265 AGTTGCGAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
17 2 0.03
19 3 0.04
20 51 0.74
21 2 0.03
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:195765 original size:42 final size:40
Alignment explanation
Indices: 195719--195842 Score: 135
Period size: 42 Copynumber: 3.0 Consensus size: 40
195709 CCCCACTTTT
*
195719 TCATCAAGTTGATTCTCTACTTCGACACCGAGATCCATCACC
1 TCATC-AGTTGATTCTC-ACTTCGACACCGAGATCTATCACC
* *
195761 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCTAACACC
1 TCATC-AGTTGATTCT-CACTTCGACACCGAGATCTATCACC
* * *
195803 TC-T-AGCTGACTCTACACCTCGACACCGAGATCTATCACC
1 TCATCAGTTGATTCT-CACTTCGACACCGAGATCTATCACC
195842 T
1 T
195843 ATTCCATCAC
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
39 31 0.44
41 1 0.01
42 38 0.54
43 1 0.01
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (40 bp):
TCATCAGTTGATTCTCACTTCGACACCGAGATCTATCACC
Found at i:195968 original size:21 final size:21
Alignment explanation
Indices: 195942--196132 Score: 172
Period size: 21 Copynumber: 9.1 Consensus size: 21
195932 ACCTCCACGG
*
195942 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
195963 GATGAGTTCGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*
195984 GATGAGGTCGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
**
196005 GAAT-A-CAATGGTGCTTTACGT
1 G-ATGAGGTA-GGTGCTTTACGT
*
196026 GGTGAGGTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* **
196047 AATG-GCAATGGTGCTTTACGT
1 GATGAGGTA-GGTGCTTTACGT
* *
196068 GATGAGGTAGGTGTTTTACAT
1 GATGAGGTAGGTGCTTTACGT
* * * *
196089 GGTGAGGTAGCTTCTTTACAT
1 GATGAGGTAGGTGCTTTACGT
* *
196110 GATAAGGTAGGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
196131 GA
1 GA
196133 GATTATTTCA
Statistics
Matches: 137, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.02
21 129 0.94
22 5 0.04
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:196413 original size:21 final size:21
Alignment explanation
Indices: 196390--196461 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
196380 ACTCCCATTG
* *
196390 TTCAGGATTCACCTCTCATCG
1 TTCAGGATCCACCTCTCATCA
* *
196411 TTCAAGATCCACCTCCCATCA
1 TTCAGGATCCACCTCTCATCA
196432 TTCAGGATCCACCTCTCATCA
1 TTCAGGATCCACCTCTCATCA
*
196453 TTCATGATC
1 TTCAGGATC
196462 TACCCCACAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.24, C:0.36, G:0.10, T:0.31
Consensus pattern (21 bp):
TTCAGGATCCACCTCTCATCA
Found at i:196427 original size:42 final size:42
Alignment explanation
Indices: 196381--196461 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
196371 CAGGGTCTAA
** * *
196381 CTCCCATTGTTCAGGATTCACCTCTCATCGTTCAAGATCCAC
1 CTCCCATCATTCAGGATCCACCTCTCATCATTCAAGATCCAC
*
196423 CTCCCATCATTCAGGATCCACCTCTCATCATTCATGATC
1 CTCCCATCATTCAGGATCCACCTCTCATCATTCAAGATC
196462 TACCCCACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.22, C:0.37, G:0.10, T:0.31
Consensus pattern (42 bp):
CTCCCATCATTCAGGATCCACCTCTCATCATTCAAGATCCAC
Found at i:196472 original size:21 final size:21
Alignment explanation
Indices: 196406--196482 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
196396 ATTCACCTCT
*
196406 CATCGTTCAAGATCCACCTCC-
1 CATCATTCAAGATCCACC-CCA
* * *
196427 CATCATTCAGGATCCACCTCT
1 CATCATTCAAGATCCACCCCA
* *
196448 CATCATTCATGATCTACCCCA
1 CATCATTCAAGATCCACCCCA
*
196469 CATCGTTCAAGATC
1 CATCATTCAAGATC
196483 AACATTTCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
20 1 0.02
21 45 0.98
ACGTcount: A:0.26, C:0.38, G:0.09, T:0.27
Consensus pattern (21 bp):
CATCATTCAAGATCCACCCCA
Found at i:197392 original size:10 final size:9
Alignment explanation
Indices: 197377--197427 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
197367 GCTGCTGGAA
197377 ACCGGTTCTG
1 ACCGGTT-TG
197387 ACCGGTTTG
1 ACCGGTTTG
*
197396 ACCGGTTTCA
1 ACCGGTTT-G
*
197406 ACCGGTTCG
1 ACCGGTTTG
197415 AACCGGTTTG
1 -ACCGGTTTG
197425 ACC
1 ACC
197428 CGACCCGACC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 13 0.37
10 22 0.63
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:197434 original size:5 final size:5
Alignment explanation
Indices: 197424--197464 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
197414 GAACCGGTTT
*
197424 GACCC GACCC GACCC GACCC GACCGTT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACC
197465 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:197456 original size:17 final size:17
Alignment explanation
Indices: 197434--197471 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
197424 GACCCGACCC
197434 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
197451 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
197468 GACC
1 GACC
197472 GTTGACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:201017 original size:20 final size:20
Alignment explanation
Indices: 200985--201037 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
200975 ACTCGATATT
*
200985 CAAAA-TCGCAACTCAAAAA
1 CAAAATTCGTAACTCAAAAA
*** *
201004 TTGAATTCGTAACTCGAAAA
1 CAAAATTCGTAACTCAAAAA
201024 CAAAATTCGTAACT
1 CAAAATTCGTAACT
201038 AGGAATTGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (20 bp):
CAAAATTCGTAACTCAAAAA
Found at i:201132 original size:20 final size:20
Alignment explanation
Indices: 201043--201137 Score: 50
Period size: 20 Copynumber: 4.7 Consensus size: 20
201033 TAACTAGGAA
* * *
201043 TTGAGTTACGAATTCGATTT
1 TTGAGTTGCAAATTCAATTT
* *
201063 TTGAGTTGCGAAATTGAA-TA
1 TTGAGTTGC-AAATTCAATTT
* **
201083 TCGAGTTGCGATTTTC-ATGTT
1 TTGAGTTGC-AAATTCAAT-TT
* *
201104 TCGAATTGCAAATTCAATTT
1 TTGAGTTGCAAATTCAATTT
*
201124 TTGAGTTGCGAATT
1 TTGAGTTGCAAATT
201138 TGAGCTGCGA
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
19 1 0.02
20 38 0.69
21 16 0.29
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGAGTTGCAAATTCAATTT
Found at i:203686 original size:3 final size:3
Alignment explanation
Indices: 203680--203745 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
203670 TCTTCGGGGA
** ***
203680 CTT CTT CTT CTT CTT CTT CTT CTT -TT CTT CGG GGA CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
203727 CTT ATT CTT TTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT C
203746 AGGGTTATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.03, C:0.29, G:0.06, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:203701 original size:35 final size:35
Alignment explanation
Indices: 203655--203745 Score: 155
Period size: 35 Copynumber: 2.6 Consensus size: 35
203645 ACGTGGCTCT
203655 TTCTTCTTCTTCTTTTCTTCGGGGACTTCTTCTTC
1 TTCTTCTTCTTCTTTTCTTCGGGGACTTCTTCTTC
203690 TTCTTCTTCTTCTTTTCTTCGGGGACTTCTTCTTC
1 TTCTTCTTCTTCTTTTCTTCGGGGACTTCTTCTTC
* *
203725 TTCTTATTCTTTTTCTTCTTC
1 TTCTTCTTCTTCTT-TTCTTC
203746 AGGGTTATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
35 47 0.89
36 6 0.11
ACGTcount: A:0.03, C:0.27, G:0.09, T:0.60
Consensus pattern (35 bp):
TTCTTCTTCTTCTTTTCTTCGGGGACTTCTTCTTC
Found at i:204150 original size:12 final size:12
Alignment explanation
Indices: 204129--204162 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
204119 AGTTGTGGAT
*
204129 TTTGAGATTGTG
1 TTTGATATTGTG
204141 TTTGATATTGTG
1 TTTGATATTGTG
*
204153 TTTGGTATTG
1 TTTGATATTG
204163 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:204779 original size:16 final size:15
Alignment explanation
Indices: 204757--204795 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
204747 GAAATCATTG
204757 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
204773 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
204788 AAAAATTA
1 AAAAATTA
204796 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:204960 original size:20 final size:21
Alignment explanation
Indices: 204935--204983 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
204925 AAACATTTGT
* *
204935 GTTGCGAAATT-AAAATTCGC
1 GTTGCGAAATTCAAAAATCGA
204955 GTTGCG-AATTCAAAAATCGA
1 GTTGCGAAATTCAAAAATCGA
204975 GTTGCGAAA
1 GTTGCGAAA
204984 ACGGAATTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 19 0.76
21 2 0.08
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (21 bp):
GTTGCGAAATTCAAAAATCGA
Found at i:205084 original size:40 final size:40
Alignment explanation
Indices: 204995--205084 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 40
204985 CGGAATTCGT
**
204995 GTTGTGAAAATGAAACTCGCGTTACGAATTAGAAAATCTT
1 GTTGTGAAAATGAAACTCGCGTTACGAATTAGAAAATCGA
* *
205035 GTTGCGAAAATGAAACTC-C-TACTGCGAATTTA-AAAATCGA
1 GTTGTGAAAATGAAACTCGCGT--TACGAA-TTAGAAAATCGA
205075 GTTGTGAAAA
1 GTTGTGAAAA
205085 AAAATTCGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
38 1 0.02
39 1 0.02
40 37 0.88
41 3 0.07
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (40 bp):
GTTGTGAAAATGAAACTCGCGTTACGAATTAGAAAATCGA
Found at i:205093 original size:19 final size:19
Alignment explanation
Indices: 205066--205120 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
205056 CTGCGAATTT
**
205066 AAAAA-TCGAGTTGTGAAA
1 AAAAATTCGAGTTGCAAAA
205084 AAAAATTCGAGTTGCAAAA
1 AAAAATTCGAGTTGCAAAA
205103 AAAAATTCGAGTTGCAAA
1 AAAAATTCGAGTTGCAAA
205121 TTTGACTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
18 5 0.15
19 29 0.85
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (19 bp):
AAAAATTCGAGTTGCAAAA
Found at i:205179 original size:20 final size:20
Alignment explanation
Indices: 205133--205204 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
205123 TGACTTCTGT
**
205133 GTTGCGAATTCCAAATTCTTT
1 GTTGCGAATTCCAAATTC-GA
205154 GTTGCGAATTCCAAATTCGA
1 GTTGCGAATTCCAAATTCGA
205174 GTTGCGAATTCCAAATTCGA
1 GTTGCGAATTCCAAATTCGA
*
205194 GTTACGAATTC
1 GTTGCGAATTC
205205 GGAAATTGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTCCAAATTCGA
Found at i:207139 original size:2 final size:2
Alignment explanation
Indices: 207134--207177 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
207124 CGTGTGTGTG
207134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
207176 TA
1 TA
207178 AACCCATCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:217459 original size:17 final size:17
Alignment explanation
Indices: 217437--217472 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
217427 AATTGTCATC
217437 AATGAACCTGTAACTGA
1 AATGAACCTGTAACTGA
217454 AATGAACCTGTAACTGA
1 AATGAACCTGTAACTGA
217471 AA
1 AA
217473 GTGGAGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (17 bp):
AATGAACCTGTAACTGA
Found at i:223314 original size:35 final size:37
Alignment explanation
Indices: 223275--223352 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
223265 TAGTGGAAAC
*
223275 AAGCAATGC-AA-TCAAGCCTTCACAAGA-GAGTAGTG
1 AAGCAATGCAAATTC-AGCCTTCACAAAAGGAGTAGTG
223310 AAGCAATGCAAATTCAGCCTTCACAAAAGGAGTAGTG
1 AAGCAATGCAAATTCAGCCTTCACAAAAGGAGTAGTG
223347 AAGCAA
1 AAGCAA
223353 GATCAGATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 9 0.23
36 14 0.36
37 16 0.41
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (37 bp):
AAGCAATGCAAATTCAGCCTTCACAAAAGGAGTAGTG
Done.