Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008155.1 Hibiscus syriacus cultivar Beakdansim tig00110721_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: 962042
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:183726 original size:79 final size:79
Alignment explanation
Indices: 183594--183742 Score: 201
Period size: 79 Copynumber: 1.9 Consensus size: 79
183584 AACAAATGTG
* * * **
183594 AAAGAAAAATGCATATTGGTGCATTATAGGCATGAAATGATGCAATAGCTGAAATGTGTATGGGT
1 AAAGAAAAATGCATATGGGTGCATTATAGGCATGAAAGGATGCAAGAGCTGAAATGCATATGGGT
183659 ACATTGTCAGCATA
66 ACATTGTCAGCATA
* * *
183673 AAAGAATAATGCATATGGGTGCATTAGT-GGCATGAAAGGATGCCAGAGTTGAAATGCATATGGG
1 AAAGAAAAATGCATATGGGTGCATTA-TAGGCATGAAAGGATGCAAGAGCTGAAATGCATATGGG
*
183737 TGCATT
65 TACATT
183743 ATCAACAGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
79 59 0.98
80 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (79 bp):
AAAGAAAAATGCATATGGGTGCATTATAGGCATGAAAGGATGCAAGAGCTGAAATGCATATGGGT
ACATTGTCAGCATA
Found at i:183769 original size:45 final size:44
Alignment explanation
Indices: 183719--183933 Score: 218
Period size: 45 Copynumber: 4.8 Consensus size: 44
183709 AGGATGCCAG
183719 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATACTA
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATACTA
* *
183763 ACGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTA
1 A-GTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATACTA
* * * * * *
183808 GAGTTGAAATGTATGTAGGTACATTCTCAACA-AAAAAGTATATTA
1 -AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAA-TATACTA
* * * * * * *
183853 TGGTTGAGATGTATATGGGTACATCATCAACATAAAAGTATAC-A
1 -AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATACTA
*
183897 ATGATTGAAATGCATATGGGTGCATTATTAACAGAAA
1 A-G-TTGAAATGCATATGGGTGCATTATCAACAGAAA
183934 CGATGTTATA
Statistics
Matches: 139, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
44 7 0.05
45 127 0.91
46 5 0.04
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (44 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATACTA
Found at i:183838 original size:90 final size:90
Alignment explanation
Indices: 183680--183929 Score: 238
Period size: 90 Copynumber: 2.8 Consensus size: 90
183670 ATAAAAGAAT
** * * *
183680 AATGCATATGGGTGCATTAGT-GGCATG-AAAGGATGCCAGAGTTGAAATGCATATGGGTGCATT
1 AATGCATATGGGTGCATTA-TCAACA-GAAAAGTATGCCAGAGTTGAAATGCATATAGGTACATT
183743 ATCAACAGAAAAA-TATACTAACGTTGA
64 ATCAACA-AAAAAGTATACTAACGTTGA
* * * *
183770 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATGTAGGTACATTCT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCCAGAGTTGAAATGCATATAGGTACATTAT
* **
183835 CAACAAAAAAGTATATTATGGTTGA
66 CAACAAAAAAGTATACTAACGTTGA
* * * * * * * * *
183860 GATGTATATGGGTACATCATCAACATAAAAGTATACAATGA-TTGAAATGCATATGGGTGCATTA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCCA-GAGTTGAAATGCATATAGGTACATTA
*
183924 TTAACA
65 TCAACA
183930 GAAACGATGT
Statistics
Matches: 131, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
89 7 0.05
90 122 0.93
91 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (90 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCCAGAGTTGAAATGCATATAGGTACATTAT
CAACAAAAAAGTATACTAACGTTGA
Found at i:183955 original size:90 final size:87
Alignment explanation
Indices: 183717--183957 Score: 223
Period size: 90 Copynumber: 2.7 Consensus size: 87
183707 AAAGGATGCC
* * *
183717 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATACTAACGTTGAAATGCATATGGG
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAGATTTA-T-A-GTTGAAATGTATATGGG
* * * *
183782 TGCATTATCAACAGAAAAGTATGCT
63 TACATCATCAACAGAAAAGTATACA
* * * * * * * *
183807 AGAGTTGAAATGTATGTAGGTACATTCTCAACAAAAAAGTATATTATGGTTGAGATGTATATGGG
1 AGAGTTGAAATGCATATGGGTGCATTATCAAC-AGAAAG-AT-TTATAGTTGAAATGTATATGGG
*
183872 TACATCATCAACATAAAAGTATACA
63 TACATCATCAACAGAAAAGTATACA
* *
183897 ATGA-TTGAAATGCATATGGGTGCATTATTAACAGAAACGATGTTATAGTTTAAAATGTATA
1 A-GAGTTGAAATGCATATGGGTGCATTATCAACAGAAA-GAT-TTATAG-TTGAAATGTATA
183958 ATGATGTATT
Statistics
Matches: 118, Mismatches: 27, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
89 11 0.09
90 96 0.81
91 6 0.05
92 3 0.03
93 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (87 bp):
AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAGATTTATAGTTGAAATGTATATGGGTAC
ATCATCAACAGAAAAGTATACA
Found at i:185997 original size:36 final size:36
Alignment explanation
Indices: 185946--186084 Score: 208
Period size: 36 Copynumber: 3.9 Consensus size: 36
185936 ACGAAAGAAA
185946 GCATC-GCACTTCCGATTCAAATCGAACGGAAGGAG
1 GCATCGGCACTTCCGATTCAAATCGAACGGAAGGAG
* * *
185981 GCATCGGCACTTCCGATTCAAATTGAATGGAAGTAG
1 GCATCGGCACTTCCGATTCAAATCGAACGGAAGGAG
* *
186017 GCATCGGCACTTCCTATTCAAATCGAACGGAAGGAA
1 GCATCGGCACTTCCGATTCAAATCGAACGGAAGGAG
* *
186053 GCATCGACACTTCCGATTCTAATCGAACGGAA
1 GCATCGGCACTTCCGATTCAAATCGAACGGAA
186085 AGATGTATCG
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 5 0.05
36 87 0.95
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (36 bp):
GCATCGGCACTTCCGATTCAAATCGAACGGAAGGAG
Found at i:189541 original size:35 final size:37
Alignment explanation
Indices: 189502--189573 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
189492 TCATTAAACT
* * *
189502 TTTTTAT-ATTTTTAATTTTGTAAA-AAAGTATATAA
1 TTTTTATGAATTTAAATTTTGTAAAGAAAATATATAA
*
189537 TTTTTATGAATTTAAATTTTTTAAAGAAAATATATAA
1 TTTTTATGAATTTAAATTTTGTAAAGAAAATATATAA
189574 ATATTTTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 7 0.23
36 14 0.45
37 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (37 bp):
TTTTTATGAATTTAAATTTTGTAAAGAAAATATATAA
Found at i:190403 original size:18 final size:19
Alignment explanation
Indices: 190380--190424 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
190370 TTTATAGTAA
* *
190380 TTATATT-CTCTGGTAATC
1 TTATATTCCACTGATAATC
190398 TTATATTCCCACTGATAATC
1 TTATATT-CCACTGATAATC
190418 TTATATT
1 TTATATT
190425 TCGTGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (19 bp):
TTATATTCCACTGATAATC
Found at i:191331 original size:132 final size:133
Alignment explanation
Indices: 191146--191403 Score: 437
Period size: 132 Copynumber: 1.9 Consensus size: 133
191136 CTTCAACCCT
* * *
191146 TCATCGTGTAAATAGCCATCCATTTTTTTTCACCATCTAGTTCCCCGAATATTCCAGCCAGTCAT
1 TCATCATGTAAATAGCCATCCATTTTTCTTCACCATCTAGTTCCCCGAATATTCCACCCAGTCAT
* *
191211 CATTCATCTTCTTCTCCGTCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCACTTTACC
66 CATTCATCTTCCTCTCCATCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCACTTTACC
191276 CGC
131 CGC
* * *
191279 TCATCATGTGAATAGTCATCCA-TTTTCTTCACCATCTAGTTCCCCGAATATTCCTCCCAGTCAT
1 TCATCATGTAAATAGCCATCCATTTTTCTTCACCATCTAGTTCCCCGAATATTCCACCCAGTCAT
191343 CATTCATCTTCCTCTCCATCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCACTT
66 CATTCATCTTCCTCTCCATCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCACTT
191404 CATTACCATC
Statistics
Matches: 117, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
132 98 0.84
133 19 0.16
ACGTcount: A:0.21, C:0.38, G:0.07, T:0.34
Consensus pattern (133 bp):
TCATCATGTAAATAGCCATCCATTTTTCTTCACCATCTAGTTCCCCGAATATTCCACCCAGTCAT
CATTCATCTTCCTCTCCATCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCACTTTACC
CGC
Found at i:196406 original size:3 final size:3
Alignment explanation
Indices: 196398--196434 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
196388 TTAATCCTCG
196398 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
196435 TCATTATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:196507 original size:2 final size:2
Alignment explanation
Indices: 196500--196545 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
196490 CCTATTATTA
196500 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
196542 AT AT
1 AT AT
196546 TTATTTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196602 original size:28 final size:28
Alignment explanation
Indices: 196570--196625 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
196560 AATTATTTTT
* *
196570 TATTTAATCATTTTTTATATAGATATTA
1 TATTTAATCATTATATATATAGATATTA
* *
196598 TATTTCATCATTATATATATATATATTA
1 TATTTAATCATTATATATATAGATATTA
196626 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (28 bp):
TATTTAATCATTATATATATAGATATTA
Found at i:196616 original size:2 final size:2
Alignment explanation
Indices: 196609--196641 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
196599 ATTTCATCAT
196609 TA TA TA TA TA TA TA T- TA -A 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
196642 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:196630 original size:18 final size:18
Alignment explanation
Indices: 196609--196643 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
196599 ATTTCATCAT
196609 TATATATATATATATTAA
1 TATATATATATATATTAA
196627 TATATATATATATATTA
1 TATATATATATATATTA
196644 TTTTTAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATATATATATATTAA
Found at i:196803 original size:19 final size:19
Alignment explanation
Indices: 196762--196833 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
196752 TTTATATATC
*
196762 TTTACTTTTTTTCATTTTA-
1 TTTA-TTTTTTTCCTTTTAT
*
196781 TTTATTTTTCTCCTTTTAT
1 TTTATTTTTTTCCTTTTAT
196800 TTTATTTGTTATT--TTTTAT
1 TTTATTT-TT-TTCCTTTTAT
196819 CTTTATTTTTTTCCT
1 -TTTATTTTTTTCCT
196834 GTTAACTCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 14 0.32
19 19 0.43
20 10 0.23
21 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTATTTTTTTCCTTTTAT
Found at i:196859 original size:4 final size:4
Alignment explanation
Indices: 196850--196874 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
196840 TCCTTTATGT
196850 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
196875 ATTTTCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:196992 original size:19 final size:20
Alignment explanation
Indices: 196968--197011 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
196958 CTTTACTTTG
*
196968 TTTTTATTTT-TAGTATCAT
1 TTTTTATTTTCTAATATCAT
*
196987 TTTTTATTTTCTAATTTCAT
1 TTTTTATTTTCTAATATCAT
197007 TTTTT
1 TTTTT
197012 TTACTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTATTTTCTAATATCAT
Found at i:197014 original size:22 final size:23
Alignment explanation
Indices: 196986--197043 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
196976 TTTAGTATCA
196986 TTTTTTATTTTC-TAATTTCATT
1 TTTTTTATTTTCTTAATTTCATT
* * *
197008 TTTTTTACTTTCTTTATTTTATT
1 TTTTTTATTTTCTTAATTTCATT
*
197031 TATTTTCATTTTC
1 T-TTTTTATTTTC
197044 CCCTATCTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 11 0.38
23 9 0.31
24 9 0.31
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTATTTTCTTAATTTCATT
Found at i:199732 original size:95 final size:95
Alignment explanation
Indices: 199618--199867 Score: 358
Period size: 95 Copynumber: 2.6 Consensus size: 95
199608 AAATCATAAT
* *
199618 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTA
1 ATTATA-ATATACATTAAAGATTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTA
*
199683 TGGATAATATTCAGCTAGCCTGATAAAGGTG
65 TGGATAATATTCAACTAGCCTGATAAAGGTG
* * *
199714 ATTATAATATACATTAAAGTTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACATTAAAGATTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTAT
*
199779 GGATATTATTCAACTAGCCTGATAAAGGTG
66 GGATAATATTCAACTAGCCTGATAAAGGTG
* * *
199809 ATTATAATAT-CTATATAATGATATTGAGCTGTCCCACTAGAGCAATTGGTTAAACGCCC
1 ATTATAATATAC-AT-TAA--AGATTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCC
199868 TGACTTTATA
Statistics
Matches: 139, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
94 1 0.01
95 95 0.68
96 9 0.06
98 34 0.24
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
ATTATAATATACATTAAAGATTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTAT
GGATAATATTCAACTAGCCTGATAAAGGTG
Found at i:201000 original size:151 final size:151
Alignment explanation
Indices: 200831--201201 Score: 571
Period size: 151 Copynumber: 2.4 Consensus size: 151
200821 AGCGTATGTT
*
200831 AACAAACAACTTTCCAGTTTCATTCAAAGTCAATTTCAAATTCACAGCGAAGGATATTGGACTCG
1 AACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAAATTCACAGCGAAGGATATTGGACTCG
* *
200896 AAACAACACAAGATTGGATTTCAACTTCACAACGAAGGATATCTAATTCAAATCTCAACTTCACA
66 AAACAACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACA
*
200961 GCGAAGGGGCGACTGTCTGTC
131 GCGAAGGGGCGACTGTCTGAC
* *
200982 AACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTTG
1 AACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAAATTCACAGCGAAGGATATTGGACTCG
* *
201047 AAACAACACAAGATTGGATTTCAACTTCACAACGAATGATATCCAATTCAAAGCTCCACTTCACA
66 AAACAACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACA
* *
201112 GTGAAGGGGTGACTGTCTGAC
131 GCGAAGGGGCGACTGTCTGAC
* * * * * * *
201133 GACAAAACAACTTTCCAAGTCTCTTTCAGAGTCAATTTTAATTTCACAACGAAGGATATTGAACT
1 AAC-AAACAACTTTCC-AGTTTCATTCAGAGTCAATTTCAAATTCACAGCGAAGGATATTGGACT
201198 CGAA
64 CGAA
201202 GCGGCACAAT
Statistics
Matches: 200, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
151 143 0.71
152 12 0.06
153 45 0.22
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (151 bp):
AACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAAATTCACAGCGAAGGATATTGGACTCG
AAACAACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACA
GCGAAGGGGCGACTGTCTGAC
Found at i:201419 original size:121 final size:120
Alignment explanation
Indices: 201283--201744 Score: 604
Period size: 121 Copynumber: 3.8 Consensus size: 120
201273 AAACAAATAC
* *
201283 TTGGATTTCAACTTCACGACGAAGGATATCAAATTCAAGGCTCAACTACACAACGAAGGGACCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCAT
* * * * *
201348 CCACGATTTCAACTTAACGACAAAGGATATCATGCCCACAACCAACCATCTCAAGA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAACAACAATC-CAACA
* * *
201404 TTGGATTTCAACTTCACGACGAAGGATATCTAATTCAAGGCTCAACTTCACGACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCAT
* *
201469 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAACAACAATGCAACCCA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAACAACAATCCAA--CA
* * ** *
201526 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTTAACTTCACAAC-AAATGAGTCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGA-CCA
* * * * * *
201590 TCTACGATTTCAACTTCACGACGAAGGATATCGTG-CCACAAGCAGCAATGCGACCA
65 TCCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAACAACAAT-CCAACA
* * * * * *
201646 TTGGATTTCAACTTCAAGATGAATGATATCCAATTCAAGGCTCAACTTCAAAACGTAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCAT
201711 CCACGATTTCAACTTCACGACAAAGGATATCGTG
66 CCACGATTTCAACTTCACGACAAAGGATATCGTG
201745 GCTAGAAGGG
Statistics
Matches: 300, Mismatches: 36, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
120 90 0.30
121 122 0.41
122 88 0.29
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (120 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCAT
CCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAACAACAATCCAACA
Found at i:201893 original size:84 final size:84
Alignment explanation
Indices: 201762--201991 Score: 337
Period size: 84 Copynumber: 2.8 Consensus size: 84
201752 GGGTTGTCTA
* *
201762 CCAACAAAAGACCTTCGAGTTCGATTACATTCATCTCAAATGCACATCATTTGCAGCATAGCTCA
1 CCAACAAAAGACCTTCGAGTTCGATTACACTCATCTCAAAAGCACATCATTTGCAGCATAGCTCA
201827 AGGCGAGAAGAGCTATCTG
66 AGGCGAGAAGAGCTATCTG
* *
201846 CCAACAAAAGACCTTCGAGTTCGATTACACTCATCTCAAAGGAACATCATTTGCAGCATAGCTCA
1 CCAACAAAAGACCTTCGAGTTCGATTACACTCATCTCAAAAGCACATCATTTGCAGCATAGCTCA
* * *
201911 AGGTGAGAAGGGTTATCTG
66 AGGCGAGAAGAGCTATCTG
* *
201930 CCAACAAAAGA-C--C---TTCGATTACACTCAGCTCAAAAGCACATCATTTGTAGCATAGCTCA
1 CCAACAAAAGACCTTCGAGTTCGATTACACTCATCTCAAAAGCACATCATTTGCAGCATAGCTCA
201989 AGG
66 AGG
201992 GATATCTTCC
Statistics
Matches: 136, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
78 45 0.33
81 1 0.01
83 1 0.01
84 89 0.65
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (84 bp):
CCAACAAAAGACCTTCGAGTTCGATTACACTCATCTCAAAAGCACATCATTTGCAGCATAGCTCA
AGGCGAGAAGAGCTATCTG
Found at i:207683 original size:33 final size:28
Alignment explanation
Indices: 207612--207670 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
207602 GTGAGTTTTG
207612 GTTATCTGAAGTTTCTTTTCTTGGTCAT
1 GTTATCTGAAGTTTCTTTTCTTGGTCAT
207640 GTTATCTGAAGTTTCTTTTCTTGGTCAT
1 GTTATCTGAAGTTTCTTTTCTTGGTCAT
207668 GTT
1 GTT
207671 GTCTCGGCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.54
Consensus pattern (28 bp):
GTTATCTGAAGTTTCTTTTCTTGGTCAT
Found at i:211195 original size:13 final size:14
Alignment explanation
Indices: 211166--211200 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
211156 CAATACTAAC
*
211166 ATATATAAGTATGA
1 ATATATATGTATGA
211180 ATATATATGT-TGA
1 ATATATATGTATGA
211193 ATATATAT
1 ATATATAT
211201 TTTGTACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (14 bp):
ATATATATGTATGA
Found at i:214353 original size:3 final size:3
Alignment explanation
Indices: 214338--214375 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
214328 TATTACTCTT
* *
214338 TTA TTA CTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
214376 TTGCTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:214423 original size:20 final size:21
Alignment explanation
Indices: 214395--214443 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
214385 TTTATATATC
*
214395 TTTACTTTTTTTTTCATTTTA-
1 TTTA-TTTTTTTCTCATTTTAT
*
214416 TTTATTTTTTTCTCCTTTTAT
1 TTTATTTTTTTCTCATTTTAT
214437 TTTATTT
1 TTTATTT
214444 GTTATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTTTTTCTCATTTTAT
Found at i:214451 original size:26 final size:25
Alignment explanation
Indices: 214405--214509 Score: 77
Period size: 26 Copynumber: 3.9 Consensus size: 25
214395 TTTACTTTTT
*
214405 TTTTCATTTTATTTATTTTTTTCTCC
1 TTTT-ATTTTATTTATTTTTTTATCC
* *
214431 TTTTATTTTATTTGTTATTTTTATTC
1 TTTTATTTTATTTATT-TTTTTATCC
*
214457 -TTTATCTTTATTTTTTTCCTTTTAACTCC
1 TTTTAT-TTTATTTATTT--TTTT-A-TCC
* *
214486 TTTATGTTTTATTTATTTATTTAT
1 TTT-TATTTTATTTATTTTTTTAT
214510 TTGTATTTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
25 17 0.27
26 21 0.33
27 5 0.08
28 4 0.06
29 2 0.03
30 12 0.19
31 2 0.03
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTTATTTTATTTATTTTTTTATCC
Found at i:214656 original size:24 final size:24
Alignment explanation
Indices: 214621--214673 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
214611 TTTTAGTATC
214621 ATTTTTTATTTC-TTATTTCATTT
1 ATTTTTTATTTCTTTATTTCATTT
* *
214644 GTTTTTTACTTTCTTTATTTTATTT
1 ATTTTTTA-TTTCTTTATTTCATTT
214669 ATTTT
1 ATTTT
214674 CATTTTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
24 4 0.16
25 14 0.56
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (24 bp):
ATTTTTTATTTCTTTATTTCATTT
Found at i:219912 original size:2 final size:2
Alignment explanation
Indices: 219905--219944 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
219895 AGGTGCTGTT
*
219905 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
219945 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:222672 original size:2 final size:2
Alignment explanation
Indices: 222665--222722 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
222655 TCAATCACAA
222665 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
222707 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
222723 TACCGCTTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:225141 original size:64 final size:64
Alignment explanation
Indices: 225005--225165 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
224995 AATTGTTCAG
* * * *
225005 TGTGTATCGATGCACAGGAAGTGCATCGATGTA-CCCATTAAAATGGAAACATCGAATACAATT
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGACAATT
* * * ***
225068 AGTGTATCGATGCATAAGAAGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATT
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGACAATT
*
225132 TGTGTATCGATGCAT-GGTTAGTGCATCGATGCAC
1 TGTGTATCGATGCATAGG-AAGTGCATCGATGCAC
225166 ATATTAAAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
63 30 0.36
64 53 0.64
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (64 bp):
TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGACAATT
Found at i:225198 original size:20 final size:20
Alignment explanation
Indices: 225173--225210 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
225163 CACATATTAA
225173 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
225193 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
225211 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:226391 original size:17 final size:18
Alignment explanation
Indices: 226362--226398 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
226352 CATTTAGGTG
226362 ATGAAATGATGAAT-TAT
1 ATGAAATGATGAATATAT
226379 ATGAACATG-TGAATATAT
1 ATGAA-ATGATGAATATAT
226397 AT
1 AT
226399 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.35
Consensus pattern (18 bp):
ATGAAATGATGAATATAT
Found at i:227014 original size:10 final size:10
Alignment explanation
Indices: 226999--227023 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
226989 TGTGCTATGA
226999 ATGATATTAT
1 ATGATATTAT
227009 ATGATATTAT
1 ATGATATTAT
227019 ATGAT
1 ATGAT
227024 GATATGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (10 bp):
ATGATATTAT
Found at i:230380 original size:45 final size:45
Alignment explanation
Indices: 230281--230384 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
230271 AATTGTTCAG
* *
230281 TGTGTATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 TGTGTATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATT
* * * **
230326 AGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATT
1 TGTGTATCGATGCA-CCCATTAAAAATGAAAACATCGAAGGCAATT
230371 TGTGTATCGATGCA
1 TGTGTATCGATGCA
230385 TGGGTAGTGC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 44 0.90
46 5 0.10
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (45 bp):
TGTGTATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATT
Found at i:236310 original size:17 final size:18
Alignment explanation
Indices: 236288--236323 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
236278 CAAGATTAAT
236288 ACAATTAAAATAC-ATTA
1 ACAATTAAAATACAATTA
236305 ACAATTAAAATACAATTA
1 ACAATTAAAATACAATTA
236323 A
1 A
236324 AATGTCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (18 bp):
ACAATTAAAATACAATTA
Found at i:236799 original size:23 final size:23
Alignment explanation
Indices: 236781--236827 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
236771 TTTATGGCAT
*
236781 ATTTTCATATGCTTATATGATAC
1 ATTTTCATATGCTTATATGACAC
*
236804 ATTTTCATATGCTTTTATGACAC
1 ATTTTCATATGCTTATATGACAC
236827 A
1 A
236828 CTATTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.47
Consensus pattern (23 bp):
ATTTTCATATGCTTATATGACAC
Found at i:237063 original size:18 final size:18
Alignment explanation
Indices: 237040--237098 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
237030 TTGGTCTTTA
237040 GTAGTTTGATCTATTGTT
1 GTAGTTTGATCTATTGTT
*
237058 GTAGTTTGGA---ATT-TA
1 GTAGTTT-GATCTATTGTT
* *
237073 GTACTTTGATCTACTGTT
1 GTAGTTTGATCTATTGTT
237091 GTAGTTTG
1 GTAGTTTG
237099 TTTTACTGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 3 0.10
17 2 0.06
18 15 0.48
19 2 0.06
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.51
Consensus pattern (18 bp):
GTAGTTTGATCTATTGTT
Found at i:237081 original size:33 final size:33
Alignment explanation
Indices: 237036--237098 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
237026 GTTGTTGGTC
* *
237036 TTTAGTAGTTTGATCTATTGTTGTAGTTTGGAA
1 TTTAGTACTTTGATCTACTGTTGTAGTTTGGAA
237069 TTTAGTACTTTGATCTACTGTTGTAGTTTG
1 TTTAGTACTTTGATCTACTGTTGTAGTTTG
237099 TTTTACTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.19, C:0.06, G:0.22, T:0.52
Consensus pattern (33 bp):
TTTAGTACTTTGATCTACTGTTGTAGTTTGGAA
Found at i:240326 original size:64 final size:63
Alignment explanation
Indices: 240237--240387 Score: 180
Period size: 64 Copynumber: 2.3 Consensus size: 63
240227 ATGCACATTC
* *
240237 ATAAGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCA-TCGATGCAT
1 ATAA-TGCATCGATGCA-TCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACT-GATGCAC
240300 A
63 A
* * *
240301 GATAATGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCATTTTATGCACTGATGCACA
1 -ATAATGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACTGATGCACA
*
240365 AGTAGTGCATCGATGCATACCTT
1 A-TAATGCATCGATGCAT-CCTT
240388 CATTGAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
63 4 0.05
64 63 0.83
65 9 0.12
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (63 bp):
ATAATGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACTGATGCACA
Found at i:244460 original size:19 final size:19
Alignment explanation
Indices: 244436--244487 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
244426 AATGTCTTTG
244436 ATGCATCGATGCATAGATA
1 ATGCATCGATGCATAGATA
244455 ATGCATCGATGCATAGATA
1 ATGCATCGATGCATAGATA
*
244474 ATGTATCGATGCAT
1 ATGCATCGATGCAT
244488 CCTTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCATAGATA
Found at i:244495 original size:83 final size:83
Alignment explanation
Indices: 244395--244552 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 83
244385 TCATAAGTGC
* * *
244395 ATCGATGCATTCCTTTAAAAGAAGAACATCGAATGTC-TTTGATGCATCGATGCA-TAGATAATG
1 ATCGATGCATTCCTTTAAAAGAAGAACACCGAATG-CATTTGATGCACCGATGCACAAG-TAATG
244458 CATCGATGCATAGATAATGT
64 CATCGATGCATAGATAATGT
* * * *
244478 ATCGATGCA-TCCTTTTAAAATAATAACACCGAATGCATTTTATGCACCGATGCACAAGTAGTGC
1 ATCGATGCATTCC-TTTAAAAGAAGAACACCGAATGCATTTGATGCACCGATGCACAAGTAATGC
244542 ATCGATGCATA
65 ATCGATGCATA
244553 CCTTCATTGA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
82 4 0.06
83 59 0.91
84 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (83 bp):
ATCGATGCATTCCTTTAAAAGAAGAACACCGAATGCATTTGATGCACCGATGCACAAGTAATGCA
TCGATGCATAGATAATGT
Found at i:248541 original size:64 final size:63
Alignment explanation
Indices: 248452--248602 Score: 178
Period size: 64 Copynumber: 2.3 Consensus size: 63
248442 ATGCACATTC
* * *
248452 ATAAGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATA
1 ATAA-TGCATCGATGCA-TCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACA
* * * *
248516 GATAATGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCATTTTATGCACCGATTCACA
1 -ATAATGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACA
*
248580 AGTAGTGCATCGATGCATACCTT
1 A-TAATGCATCGATGCAT-CCTT
248603 CATTGAAAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 4 0.05
64 63 0.84
65 8 0.11
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (63 bp):
ATAATGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACA
Found at i:250348 original size:35 final size:35
Alignment explanation
Indices: 250292--250366 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
250282 TTCATGTTCA
*
250292 AAATTCGAAAACACTTCAATTACATTCTAAACCTC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCTC
* * * * * *
250327 AAATTCCAAAATACTTTAATTATATTTTGAACCTT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCTC
250362 AAATT
1 AAATT
250367 AAAGTATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.36
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCTC
Found at i:252519 original size:18 final size:18
Alignment explanation
Indices: 252506--252597 Score: 92
Period size: 18 Copynumber: 5.4 Consensus size: 18
252496 AAGGGGTACA
252506 GATTCCCCTGGGGGTATC
1 GATTCCCCTGGGGGTATC
*
252524 GATTCCCC---GGG-AAC
1 GATTCCCCTGGGGGTATC
252538 AGATTCCCCTGGGGGTATC
1 -GATTCCCCTGGGGGTATC
*
252557 GATTCCCC---GGG-AAC
1 GATTCCCCTGGGGGTATC
252571 AGATTCCCCTGGGGGTATC
1 -GATTCCCCTGGGGGTATC
252590 GATTCCCC
1 GATTCCCC
252598 CCTAAATAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 4 0.07
15 22 0.37
18 30 0.50
19 4 0.07
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (18 bp):
GATTCCCCTGGGGGTATC
Found at i:252544 original size:15 final size:15
Alignment explanation
Indices: 252524--252579 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
252514 TGGGGGTATC
252524 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
252539 GATTCCCCTGGGGGTATC-
1 GATTCCCC---GGG-AACA
252557 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
252572 GATTCCCC
1 GATTCCCC
252580 TGGGGGTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 2 0.06
15 19 0.56
18 11 0.32
19 2 0.06
ACGTcount: A:0.20, C:0.34, G:0.27, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:252545 original size:33 final size:33
Alignment explanation
Indices: 252503--252597 Score: 190
Period size: 33 Copynumber: 2.9 Consensus size: 33
252493 TCCAAGGGGT
252503 ACAGATTCCCCTGGGGGTATCGATTCCCCGGGA
1 ACAGATTCCCCTGGGGGTATCGATTCCCCGGGA
252536 ACAGATTCCCCTGGGGGTATCGATTCCCCGGGA
1 ACAGATTCCCCTGGGGGTATCGATTCCCCGGGA
252569 ACAGATTCCCCTGGGGGTATCGATTCCCC
1 ACAGATTCCCCTGGGGGTATCGATTCCCC
252598 CCTAAATAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (33 bp):
ACAGATTCCCCTGGGGGTATCGATTCCCCGGGA
Found at i:253449 original size:31 final size:31
Alignment explanation
Indices: 253411--253582 Score: 308
Period size: 31 Copynumber: 5.5 Consensus size: 31
253401 AGGGTCGAGG
253411 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
253442 GTTTACCTATGTTATTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
253473 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
253504 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
253535 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
253566 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
253583 AGAATCTATG
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 135 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:254042 original size:12 final size:12
Alignment explanation
Indices: 254025--254056 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
254015 GTTTAAAATA
254025 GAAGAATTAAGT
1 GAAGAATTAAGT
254037 GAAGAATTAAGT
1 GAAGAATTAAGT
254049 GAAGAATT
1 GAAGAATT
254057 GATGATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (12 bp):
GAAGAATTAAGT
Found at i:255058 original size:31 final size:31
Alignment explanation
Indices: 255020--255237 Score: 375
Period size: 31 Copynumber: 7.0 Consensus size: 31
255010 AGGGTCGAGG
255020 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
255051 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
255082 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
255113 GTTTATCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
255144 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
255175 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
255206 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
255237 G
1 G
255238 GTCCTTCGGG
Statistics
Matches: 179, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 178 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:255743 original size:21 final size:21
Alignment explanation
Indices: 255718--255760 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
255708 AAAGAATATA
255718 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
255739 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
255760 T
1 T
255761 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:258960 original size:18 final size:18
Alignment explanation
Indices: 258937--258971 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
258927 TTCCATCCGG
*
258937 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
258955 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
258972 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:260274 original size:7 final size:7
Alignment explanation
Indices: 260261--260294 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
260251 TGGTCAACTC
260261 CGGTCAA
1 CGGTCAA
*
260268 TGGTCAA
1 CGGTCAA
260275 CGGGTCAA
1 C-GGTCAA
260283 CGGTCAA
1 CGGTCAA
260290 CGGTC
1 CGGTC
260295 GGGTCAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.24, C:0.26, G:0.32, T:0.18
Consensus pattern (7 bp):
CGGTCAA
Found at i:260282 original size:15 final size:15
Alignment explanation
Indices: 260262--260292 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
260252 GGTCAACTCC
*
260262 GGTCAATGGTCAACG
1 GGTCAACGGTCAACG
260277 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
260292 G
1 G
260293 TCGGGTCAAC
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:0.26, C:0.23, G:0.35, T:0.16
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:260314 original size:18 final size:18
Alignment explanation
Indices: 260291--260365 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
260281 AACGGTCAAC
260291 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
260309 GGTCGGGTCAA----T-G
1 GGTCGGGTCAACGGGTCG
* *
260322 GGTCAGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCG
260340 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
260358 GGTCGGGT
1 GGTCGGGT
260366 TGTGACCGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:260325 original size:13 final size:13
Alignment explanation
Indices: 260269--260312 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
260259 TCCGGTCAAT
*
260269 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
260284 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
260296 GGTCAACGGGTCG
1 GGTCAACGGGTCG
260309 GGTC
1 GGTC
260313 GGGTCAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 4 0.15
15 7 0.26
ACGTcount: A:0.18, C:0.25, G:0.41, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:260336 original size:31 final size:31
Alignment explanation
Indices: 260284--260356 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
260274 ACGGGTCAAC
* *
260284 GGTCAAC-GGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
*
260314 GGTCAATGGGTCAGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
260345 GGTCAACGGGTC
1 GGTCAACGGGTC
260357 GGGTCGGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
Found at i:264165 original size:18 final size:18
Alignment explanation
Indices: 264142--264176 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
264132 TTCCATCCGG
*
264142 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
264160 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
264177 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:265518 original size:18 final size:18
Alignment explanation
Indices: 265495--265569 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
265485 AACGGTCAAC
265495 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
265513 GGTCGGGTCAA----T-G
1 GGTCGGGTCAACGGGTCG
* *
265526 GGTCAGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCG
265544 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
265562 GGTCGGGT
1 GGTCGGGT
265570 TGTGACCGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:265529 original size:13 final size:13
Alignment explanation
Indices: 265473--265516 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
265463 TCCGGTCCAT
*
265473 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
265488 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
265500 GGTCAACGGGTCG
1 GGTCAACGGGTCG
265513 GGTC
1 GGTC
265517 GGGTCAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 4 0.15
15 7 0.26
ACGTcount: A:0.18, C:0.25, G:0.41, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:265540 original size:31 final size:31
Alignment explanation
Indices: 265488--265560 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
265478 ACGGGTCAAC
* *
265488 GGTCAAC-GGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
*
265518 GGTCAATGGGTCAGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
265549 GGTCAACGGGTC
1 GGTCAACGGGTC
265561 GGGTCGGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
Found at i:267390 original size:22 final size:21
Alignment explanation
Indices: 267326--267389 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
267316 TGCATTCATA
*
267326 AAAGGAATTTGTGAGTTTTTTT
1 AAAGGAAATTGTGA-TTTTTTT
267348 AAAGGAAATTGTGATTTTTTT
1 AAAGGAAATTGTGATTTTTTT
*
267369 AAAGTAAATTGTGATTTTTTT
1 AAAGGAAATTGTGATTTTTTT
267390 TTAATTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 27 0.68
22 13 0.32
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (21 bp):
AAAGGAAATTGTGATTTTTTT
Found at i:267829 original size:76 final size:76
Alignment explanation
Indices: 267704--267850 Score: 242
Period size: 76 Copynumber: 1.9 Consensus size: 76
267694 ATACATTTCA
* *
267704 TTTTTTTATAACGAACTACGTGTTTTTTTCTCGGTCAAAAATTAGAACGTGCATGTTT-TTCCCC
1 TTTTTTTATAACGAACTACGTGCTTTTTTCTCGGTCAAAAATTAGAACGTACATGTTTCTT-CCC
267768 CTCTTTTTATTT
65 CTCTTTTTATTT
* *
267780 TTTTTTTATAACGAACTACGTGCTTTTTTCTCGGTGAAAAATTAGAACGTACATGTTTCTTTCCC
1 TTTTTTTATAACGAACTACGTGCTTTTTTCTCGGTCAAAAATTAGAACGTACATGTTTCTTCCCC
267845 TCTTTT
66 TCTTTT
267851 CTTTTGCTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
76 64 0.97
77 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (76 bp):
TTTTTTTATAACGAACTACGTGCTTTTTTCTCGGTCAAAAATTAGAACGTACATGTTTCTTCCCC
TCTTTTTATTT
Found at i:282241 original size:30 final size:30
Alignment explanation
Indices: 282205--282274 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
282195 GTTATATGAG
* * *
282205 CTATGTGATAAATGTATGGAAATCACATGT
1 CTATGTGATAAAGGTATGAAAATAACATGT
* *
282235 CTATGTGACAAAGGTATGAAAATAATATGT
1 CTATGTGATAAAGGTATGAAAATAACATGT
*
282265 CTATGAGATA
1 CTATGTGATA
282275 CACTATGTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGAAAATAACATGT
Found at i:282985 original size:23 final size:23
Alignment explanation
Indices: 282967--283027 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
282957 CTCATATAAA
*
282967 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
282990 TGCACCGTAGTGCCGCATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
283013 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
283028 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:283161 original size:18 final size:18
Alignment explanation
Indices: 283138--283191 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
283128 GAATACATAT
283138 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
283156 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
*
283174 ATATCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
283192 TACAATCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:283618 original size:21 final size:21
Alignment explanation
Indices: 283594--283637 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
283584 TTTTTATTCG
*
283594 CTTGAAGGGGTATCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
*
283615 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
283636 CT
1 CT
283638 AGCCCAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:287395 original size:23 final size:23
Alignment explanation
Indices: 287369--287429 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
287359 CTCATATAAA
*
287369 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
287392 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
287415 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
287430 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:287561 original size:20 final size:18
Alignment explanation
Indices: 287543--287579 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
287533 TACATATATG
287543 TCCCGAAGGACCACAATA
1 TCCCGAAGGACCACAATA
287561 TCCCGAAGGACCAC-ATA
1 TCCCGAAGGACCACAATA
287578 TC
1 TC
287580 ATTCCTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.35, C:0.35, G:0.16, T:0.14
Consensus pattern (18 bp):
TCCCGAAGGACCACAATA
Found at i:287653 original size:62 final size:63
Alignment explanation
Indices: 287466--287782 Score: 167
Period size: 62 Copynumber: 5.2 Consensus size: 63
287456 ATCATTCCTT
* * *
287466 AAGAAT-CATATACATATACTAGGGATCAAGTATGCGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATCCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCA
* * * * * * *
287528 AAGAATACATAT--ATGTCCCGAAGGACCACA--A--TATC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATAT-CCTAGGGATCA-AGTATGTGTCTCAC-AA-GACTTCACACAT-GTT
*
287583 CCTT
61 CC-A
* *
287587 AAGAAT-CATATACATATGCTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATCCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCA
* * * * * *
287649 AAGAATACATAT--ATGTCCCGAAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATAT-CCTAGGGATCA-AGTATGTGTCTCAC-AA-GACTTCACACAT-GTT
*
287704 CCTT
61 CC-A
* *
287708 AAGAAT-CATATACATATGCTAGGGATCAAGTATGTGTCTCACTAGACTTCACACATGTTCCA
1 AAGAATACATATACATATCCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCA
287770 AAGAATACATATA
1 AAGAATACATATA
287783 TGTCCCGAAG
Statistics
Matches: 181, Mismatches: 39, Indels: 69
0.63 0.13 0.24
Matches are distributed among these distances:
57 14 0.08
58 24 0.13
59 38 0.21
60 8 0.04
61 8 0.04
62 45 0.25
63 30 0.17
64 14 0.08
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (63 bp):
AAGAATACATATACATATCCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCA
Found at i:287659 original size:121 final size:121
Alignment explanation
Indices: 287445--287799 Score: 674
Period size: 121 Copynumber: 2.9 Consensus size: 121
287435 TAATGTCCAT
* *
287445 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
287510 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATATCCCG
287566 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
*
287631 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATATCCCG
*
287687 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
287752 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACA
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACA
287800 TAGACCCTCG
Statistics
Matches: 230, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 230 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (121 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATATCCCG
Found at i:287684 original size:18 final size:18
Alignment explanation
Indices: 287661--287696 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
287651 GAATACATAT
287661 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
287679 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
287697 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:289055 original size:21 final size:21
Alignment explanation
Indices: 289031--289074 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
289021 TTTTTATTCG
*
289031 CTTGAAGGGGTATCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
*
289052 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
289073 CT
1 CT
289075 AGCCCAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:290032 original size:23 final size:25
Alignment explanation
Indices: 290006--290053 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
289996 CAATCTTATA
290006 TGGCACTACGGTGC-AA-TTCTACG
1 TGGCACTACGGTGCAAATTTCTACG
*
290029 TGGCACTTCGGTGCAAATTTCTACG
1 TGGCACTACGGTGCAAATTTCTACG
290054 CGATCCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.59
24 2 0.09
25 7 0.32
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (25 bp):
TGGCACTACGGTGCAAATTTCTACG
Found at i:290740 original size:12 final size:12
Alignment explanation
Indices: 290706--290765 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
290696 TTTTAGCATT
*
290706 TGGTACTGTAGCA
1 TGGTACTGT-TCA
* *
290719 GGGTATTGTTCA
1 TGGTACTGTTCA
290731 TGGTACTGTTCA
1 TGGTACTGTTCA
290743 T--TACTGTTCA
1 TGGTACTGTTCA
*
290753 CGGTACTGTTCA
1 TGGTACTGTTCA
290765 T
1 T
290766 ACCGTATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
10 9 0.24
12 22 0.58
13 7 0.18
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (12 bp):
TGGTACTGTTCA
Found at i:293964 original size:22 final size:22
Alignment explanation
Indices: 293916--293966 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
293906 AACCCTTCTT
*
293916 TCCTTTTATCATTTTTTTCCTG
1 TCCTTTTATCATTTTTTTCATG
293938 TCCTTTTATCATTTTTTTCAT-
1 TCCTTTTATCATTTTTTTCATG
293959 TCCCTTTT
1 T-CCTTTT
293967 TGTATTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.65
Consensus pattern (22 bp):
TCCTTTTATCATTTTTTTCATG
Found at i:294897 original size:16 final size:16
Alignment explanation
Indices: 294876--294911 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
294866 GATTATCGCC
294876 TAATCAAACGGAAGAA
1 TAATCAAACGGAAGAA
294892 TAATCAAACGGAAGAA
1 TAATCAAACGGAAGAA
294908 TAAT
1 TAAT
294912 GCTTTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (16 bp):
TAATCAAACGGAAGAA
Found at i:295492 original size:2 final size:2
Alignment explanation
Indices: 295485--295563 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
295475 ACTTTATTAA
295485 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
295527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
295564 AGATATTTGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:297920 original size:16 final size:17
Alignment explanation
Indices: 297876--297925 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
297866 TATATTTTTG
297876 TTATAGTTTAAATTATA
1 TTATAGTTTAAATTATA
* *
297893 TT-T-TTTTGAATT-TA
1 TTATAGTTTAAATTATA
297907 TTATAGTTTAAATTGATA
1 TTATAGTTTAAATT-ATA
297925 T
1 T
297926 GATTCATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 8 0.32
17 2 0.08
18 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
TTATAGTTTAAATTATA
Found at i:305191 original size:19 final size:19
Alignment explanation
Indices: 305167--305207 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
305157 GAGGATTCTG
305167 ATGACCCAGAGATCATAGT
1 ATGACCCAGAGATCATAGT
305186 ATGACCCAGAGATCATAGT
1 ATGACCCAGAGATCATAGT
305205 ATG
1 ATG
305208 TACACTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (19 bp):
ATGACCCAGAGATCATAGT
Found at i:307720 original size:64 final size:63
Alignment explanation
Indices: 307648--307790 Score: 157
Period size: 64 Copynumber: 2.2 Consensus size: 63
307638 TTGGACCCTT
* *
307648 AGTGCATCGGTGCA-CTAAGAGTGCATCGATGCATCAAGTGCATTTGATG-TTTCA-AAATAGCC
1 AGTGCATCGGTGCAGCT--G-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
*
307710 AG
62 AC
* * *
307712 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGGTGCA--GCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAC
307777 AGTGCATCGGTGCA
1 AGTGCATCGGTGCA
307791 TGGTAATTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
64 40 0.60
65 22 0.33
66 3 0.04
67 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (63 bp):
AGTGCATCGGTGCAGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAC
Found at i:307804 original size:65 final size:65
Alignment explanation
Indices: 307667--307827 Score: 175
Period size: 65 Copynumber: 2.5 Consensus size: 65
307657 GTGCACTAAG
* * *
307667 AGTGCATCGATGCATCAAGTGCATTTGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * *
307731 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGC
307794 T
65 T
* * * **
307795 AATTTCATCGATGCATGAAATATATTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
307828 CAATTTAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 28 0.35
65 50 0.62
66 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:307869 original size:65 final size:64
Alignment explanation
Indices: 307668--307877 Score: 166
Period size: 65 Copynumber: 3.2 Consensus size: 64
307658 TGCACTAAGA
* * * * *
307668 GTGCATCGATGCATCAAGTGCATTTGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGG-C
1 GTGCATCGATGCATCAAATACATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGAT
307730 TG
63 TG
* *
307732 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAA
1 GTGCATCGATGCATCAAATACATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGG--A
307797 TT-
62 TTG
* * **
307799 -T-CATCGATGCATGAAATATATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATACATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGGAT
307860 TG
63 TG
*
307862 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
307878 CTCTGAAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
62 6 0.05
63 3 0.03
64 48 0.40
65 56 0.47
66 5 0.04
67 1 0.01
68 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATACATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGATTG
Found at i:309999 original size:13 final size:13
Alignment explanation
Indices: 309971--310009 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
309961 TGGGCAATGT
*
309971 TTTGAAAA-ACTA
1 TTTGAAAATAATA
309983 TTTGAAAATAATA
1 TTTGAAAATAATA
*
309996 TTTGTAAATAATA
1 TTTGAAAATAATA
310009 T
1 T
310010 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:316412 original size:18 final size:17
Alignment explanation
Indices: 316358--316406 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
316348 TTGGACCCTT
* *
316358 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
316376 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
316394 AGTGCATTCGATG
1 AGTGCA-TCGATG
316407 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:316495 original size:57 final size:56
Alignment explanation
Indices: 316387--316495 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 56
316377 AGTGCATCGA
* *
316387 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
* * *
316443 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGG
316496 TAAGTGCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 19 0.41
57 24 0.52
58 3 0.07
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
Found at i:316511 original size:56 final size:55
Alignment explanation
Indices: 316387--316512 Score: 139
Period size: 57 Copynumber: 2.2 Consensus size: 55
316377 AGTGCATCGA
* *
316387 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAA-TGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTAG
* * *
316443 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TAAG
1 TGCATC-AATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-AG
*
316500 TGCATCGATGCAT
1 TGCATCAATGCAT
316513 GAAATGCATT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
56 24 0.40
57 33 0.55
58 3 0.05
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (55 bp):
TGCATCAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTAG
Found at i:318520 original size:29 final size:30
Alignment explanation
Indices: 318469--318558 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 30
318459 AAATTTTTGC
***
318469 TAGTGGCTAAAATATACGTTTTG-AAAGTT
1 TAGTGGCTAAAATATAAACTTTGAAAAGTT
*
318498 TAGTGGCTAAAGTATAAACTTTGTAAAAGTT
1 TAGTGGCTAAAATATAAACTTTG-AAAAGTT
* *
318529 TAG-GAGC-AAAAAATATAATTTTGAAAAGTT
1 TAGTG-GCTAAAATATA-AACTTTGAAAAGTT
318559 ATATATTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 19 0.38
30 14 0.28
31 17 0.34
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (30 bp):
TAGTGGCTAAAATATAAACTTTGAAAAGTT
Found at i:321311 original size:22 final size:20
Alignment explanation
Indices: 321279--321330 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
321269 CCGTAAGGGG
* *
321279 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTA-AG-A
*
321301 GTATCGATACCATGGTAAGA
1 GTATCGATACCATAGTAAGA
321321 GTATCGATAC
1 GTATCGATAC
321331 TAGGCAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 11 0.41
21 1 0.04
22 15 0.56
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (20 bp):
GTATCGATACCATAGTAAGA
Found at i:321419 original size:95 final size:95
Alignment explanation
Indices: 321226--321399 Score: 224
Period size: 95 Copynumber: 1.8 Consensus size: 95
321216 CAAAGAGGGG
* * * ** *
321226 GTATCGATACCAAGCAACATCGAATCAAAAACCTGTGTCGATACCGTAAGGGGGTATCGGTACCA
1 GTATCGATACTAAGCAACATCGAACCAAAAACCTGTATCGATACCAAAAGGGGGTATCGATACCA
* *
321291 TAGTATGGTAGTATCGATACCATGGTAAGA
66 TAGTATAGAAGTATCGATACCATGGTAAGA
* * * *
321321 GTATCGATACTAGGCAACATCGAACCTAAAA-TTAGTATCGATACCAAAAGGGGGTATTGATACC
1 GTATCGATACTAAGCAACATCGAACCAAAAACCT-GTATCGATACCAAAAGGGGGTATCGATACC
321385 ATAGTATAGAAGTAT
65 ATAGTATAGAAGTAT
321400 TGGTACTAGA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
94 1 0.02
95 65 0.98
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (95 bp):
GTATCGATACTAAGCAACATCGAACCAAAAACCTGTATCGATACCAAAAGGGGGTATCGATACCA
TAGTATAGAAGTATCGATACCATGGTAAGA
Found at i:321431 original size:22 final size:21
Alignment explanation
Indices: 321374--321432 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
321364 CCAAAAGGGG
321374 GTATTGATACCATAGTA-TAGAA
1 GTATTGATA-CATAG-AGTAGAA
* *
321396 GTATTGGTAC-TAGAGTAGTA
1 GTATTGATACATAGAGTAGAA
321416 GTATTGATACTATAGAG
1 GTATTGATAC-ATAGAG
321433 CCAGAAACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 16 0.52
21 1 0.03
22 13 0.42
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
GTATTGATACATAGAGTAGAA
Found at i:321820 original size:58 final size:56
Alignment explanation
Indices: 321775--321916 Score: 148
Period size: 56 Copynumber: 2.6 Consensus size: 56
321765 ATTGTAAGAT
**
321775 ATTCATACTAAGTGTAT-AGATTTGTGTATGGGCACTTTGTGTGCAAAAATAAGGAA
1 ATTCATACTAAGTGTATGA-ATTTCCGTATGGGCACTTTGTGTGCAAAAATAAGGAA
* *** * *
321831 ATTCATGCTAAGTGTATGAATTTCCGTATGGGCACTAAATGTGC-GAACTAA-GAA
1 ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAATAAGGAA
* *
321885 ATTCTTACCAAGTGTATGAATGTT-CGTATGGG
1 ATTCATACTAAGTGTATGAAT-TTCCGTATGGG
321917 AAAATATATG
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
54 29 0.40
55 7 0.10
56 36 0.49
57 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (56 bp):
ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAATAAGGAA
Found at i:324656 original size:17 final size:17
Alignment explanation
Indices: 324634--324677 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
324624 TTGGTATAAT
*
324634 ACTCTTCTTTGAAAATA
1 ACTCTTATTTGAAAATA
324651 ACTCTTATTTGAAAATA
1 ACTCTTATTTGAAAATA
324668 ACTCTTATTT
1 ACTCTTATTT
324678 TTTATTAACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (17 bp):
ACTCTTATTTGAAAATA
Found at i:331874 original size:95 final size:96
Alignment explanation
Indices: 331699--331888 Score: 251
Period size: 95 Copynumber: 2.0 Consensus size: 96
331689 ATACCTATGA
* *
331699 GGTAGTATCGATACCATGATAAGGGGTATCGATACACAGCAACATCGAATCCAATTTTGGTATCG
1 GGTAGTATCGAGACCATGATAAGGGGTATCAATACACAGCAACATCGAATCCAATTTTGGTATCG
* * *
331764 ATACTAGTATGGGGTACCGGTACCATAGTAG
66 ATACCAGTATAGGGTACCGATACCATAGTAG
* * *
331795 GGTAGTATCGAGACCATGGTAA-GGGTATCAATAC-TAGACAACATCGAA-CCTATTTTTGGTAT
1 GGTAGTATCGAGACCATGATAAGGGGTATCAATACACAG-CAACATCGAATCC-AATTTTGGTAT
* *
331857 CGATACCGGTATAGGGTATCGATACCATAGTA
64 CGATACCAGTATAGGGTACCGATACCATAGTA
331889 TAGAAGTATT
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
94 4 0.05
95 58 0.71
96 20 0.24
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (96 bp):
GGTAGTATCGAGACCATGATAAGGGGTATCAATACACAGCAACATCGAATCCAATTTTGGTATCG
ATACCAGTATAGGGTACCGATACCATAGTAG
Found at i:332336 original size:59 final size:58
Alignment explanation
Indices: 332245--332411 Score: 266
Period size: 59 Copynumber: 2.9 Consensus size: 58
332235 TTACTAAATA
*
332245 GCACTTTGTGTGC-AAAGTGTTAAGAAATTCATACTAAGTGTATGAATTT-TAGTATAGG
1 GCACTTTGTGTGCTAAA-TGATAAGAAATTCATACTAAGTGTATGAATTTCTA-TATAGG
*
332303 GCACTTTGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCTATATTGG
1 GCACTTTGTGTGCTAA-ATGATAAGAAATTCATACTAAGTGTATGAATTTCTATATAGG
*
332362 GCACCTTGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTC
1 GCACTTTGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTC
332412 CTTATGGGAA
Statistics
Matches: 103, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
58 47 0.46
59 53 0.51
60 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (58 bp):
GCACTTTGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTATATAGG
Found at i:333196 original size:68 final size:68
Alignment explanation
Indices: 332786--333178 Score: 552
Period size: 68 Copynumber: 5.8 Consensus size: 68
332776 AAAAGATCAA
* * *
332786 GAGGCCTAACTGTGCATATGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAACTGCC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
332851 TTT
66 TTT
* * * * * * * *
332854 TAGGCCTAATTGTACATATCACATAAATGTGTCATTTATGTCAGTTAGATGAAATACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
332919 TTT
66 TTT
* * *
332922 GAGGCCTAACTTTGCATATGACAGAAAGCTGTCATTTATACCAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
332987 TTT
66 TTT
* * * * *
332990 GAGTCCTAACTATGCTTATGACAGAAAGGTGTCATTTATGTCAGTTAGATGAAAGACTAAGTTTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
333055 TTT
66 TTT
* * * *
333058 GAGGTCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGACTAAATGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
333123 TTT
66 TTT
* * *
333126 GAGGCCTAACTGTGTATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAA
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
333179 TGGTTAAGTA
Statistics
Matches: 285, Mismatches: 40, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 285 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
TTT
Found at i:333265 original size:81 final size:81
Alignment explanation
Indices: 333154--333363 Score: 287
Period size: 81 Copynumber: 2.6 Consensus size: 81
333144 TGACATAAAG
* *
333154 GTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAACTG
1 GTGTCAATTATGTCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAACTG
*
333219 TGCAATTGGAAAAAAT
66 TGAAATTGGAAAAAAT
* * *
333235 GTGTCAATTATGTCAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAATAATAATGGCCTAACTG
1 GTGTCAATTATGTCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAACTG
* *
333300 TGAAATTGGTAGAAAT
66 TGAAATTGGAAAAAAT
* ** * *
333316 ATACCAATTATGTCAGTTAGATAAACAGTT-AGATACCGTTGAGTAAAA
1 GTGTCAATTATGTCAGTTAGATGAACGGTTAAG-TACCGTTGAGTAAAA
333364 AATGAAAGGT
Statistics
Matches: 114, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
80 2 0.02
81 112 0.98
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.30
Consensus pattern (81 bp):
GTGTCAATTATGTCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAACTG
TGAAATTGGAAAAAAT
Found at i:335936 original size:37 final size:37
Alignment explanation
Indices: 335847--335950 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
335837 CTTTTCGTCC
* * *
335847 TACTAGGATTCAAACTCCTAAAAATAAGACAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* *
335884 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
335921 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
335951 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:336390 original size:19 final size:18
Alignment explanation
Indices: 336366--336403 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
336356 TATATGTATA
336366 TATTTAATTATATT-TAATT
1 TATTT-ATT-TATTATAATT
336385 TATTTATTTATTATAATT
1 TATTTATTTATTATAATT
336403 T
1 T
336404 TTTTTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATTTATTATAATT
Found at i:336403 original size:10 final size:9
Alignment explanation
Indices: 336366--336403 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
336356 TATATGTATA
336366 TATTTAATT
1 TATTTAATT
336375 ATATTTAATT
1 -TATTTAATT
336385 TATTT-ATT
1 TATTTAATT
336393 TATTATAATT
1 TATT-TAATT
336403 T
1 T
336404 TTTTTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 6 0.23
10 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:336648 original size:61 final size:59
Alignment explanation
Indices: 336516--336651 Score: 143
Period size: 61 Copynumber: 2.2 Consensus size: 59
336506 TTTTCTAACG
336516 TTATATATATTATATATATATTCTTACTTCATTTATTTTATTTCTATGATTACTATTTTT
1 TTAT-TATATTATATATATATTCTTACTTCATTTATTTTATTTCTATGATTACTATTTTT
* ** *
336576 TTAGTTAATATTATATGTATATT-TATTTTTCATTTA-TTTATTAT-TATTATTACTATTTAGTA
1 TTA-TT-ATATTATATATATATTCT-TACTTCATTTATTTTATT-TCTATGATTACTATTT--T-
336638 T
59 T
336639 TTATTATATTATA
1 TTATTATATTATA
336652 CATACATTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
60 24 0.37
61 34 0.52
62 3 0.05
63 4 0.06
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (59 bp):
TTATTATATTATATATATATTCTTACTTCATTTATTTTATTTCTATGATTACTATTTTT
Found at i:336660 original size:20 final size:19
Alignment explanation
Indices: 336637--336685 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
336627 ACTATTTAGT
336637 ATTTATTATATTATACATAC
1 ATTTATTAT-TTATACATAC
* *
336657 ATTT-TTATTTATATATAT
1 ATTTATTATTTATACATAC
*
336675 ATATATTATTT
1 ATTTATTATTT
336686 TATTTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 11 0.44
19 10 0.40
20 4 0.16
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTATTATTTATACATAC
Found at i:336696 original size:15 final size:17
Alignment explanation
Indices: 336678--336722 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
336668 TATATATATA
336678 TATTATTTTA-TTT-AT
1 TATTATTTTATTTTCAT
336693 TATTA-TTTATTTTCAT
1 TATTATTTTATTTTCAT
*
336709 TA-TATTTTAGTTTC
1 TATTATTTTATTTTC
336723 TTTGCTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (17 bp):
TATTATTTTATTTTCAT
Found at i:340724 original size:24 final size:24
Alignment explanation
Indices: 340691--340755 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
340681 CAAAAAGGGC
* *
340691 AAAAACAAAAAAAAAAAAGAAGCA
1 AAAAACAAAAAAAAAAAAAAAACA
*
340715 AAAAAGAAAAAAAAAAAAAAAACA
1 AAAAACAAAAAAAAAAAAAAAACA
* *
340739 AAAATCAAAAAGAAAAA
1 AAAAACAAAAAAAAAAA
340756 GGGACAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.02
Consensus pattern (24 bp):
AAAAACAAAAAAAAAAAAAAAACA
Found at i:340731 original size:30 final size:30
Alignment explanation
Indices: 340691--340755 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
340681 CAAAAAGGGC
* *
340691 AAAAACAAAAAAAAAA-AAGAAGCAAAAAAG
1 AAAAAAAAAAAAAAAACAAAAAGC-AAAAAG
*
340721 AAAAAAAAAAAAAAAACAAAAATCAAAAAG
1 AAAAAAAAAAAAAAAACAAAAAGCAAAAAG
340751 AAAAA
1 AAAAA
340756 GGGACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.02
Consensus pattern (30 bp):
AAAAAAAAAAAAAAAACAAAAAGCAAAAAG
Found at i:340755 original size:1 final size:1
Alignment explanation
Indices: 340691--340742 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
340681 CAAAAAGGGC
* * ** * *
340691 AAAAACAAAAAAAAAAAAGAAGCAAAAAAGAAAAAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
340743 TCAAAAAGAA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:341839 original size:18 final size:18
Alignment explanation
Indices: 341804--341839 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
341794 TCAACACCAA
**
341804 ATATTGGGGCATTTTTTG
1 ATATTGGGGCATCATTTG
341822 ATATTGGGGCATCATTTG
1 ATATTGGGGCATCATTTG
341840 GGGATTCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.28, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCATTTG
Found at i:343628 original size:106 final size:106
Alignment explanation
Indices: 342352--343627 Score: 1969
Period size: 106 Copynumber: 12.0 Consensus size: 106
342342 ATATCGTGCC
* * * * * * * *
342352 ACTCGAGACAACAG-AAGTTCAACTTCACAACAAAGGGACGGTTGGTTATCAACAAATAATTTCC
1 ACTCCAGACAAC-GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* *
342416 CAAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
342458 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
342523 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
342564 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
342629 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
342670 ACTCAAGACAACGTAAGTTCAACTTCATGACGAAGGGACCGCTGGTTCTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
342735 AATTTCAGAGCCAATTTCAACTTCACTACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
342776 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
342841 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
342882 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
342947 AATTTCAAAGCCAATTTCAACATCACAACGAAGAATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
342988 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCGACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
343053 AATTTCGGAGGCAATTTCAACTTCATAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
343094 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
343159 AATTTTGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
343200 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
343265 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTCG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
343306 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
343371 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
343412 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* **
343477 AATTTCGGAGCCAATTTCAACTTCACAATAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
343518 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
343583 GATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
343624 ACTC
1 ACTC
343628 GGAACAATGC
Statistics
Matches: 1077, Mismatches: 92, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
106 1077 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:343856 original size:28 final size:28
Alignment explanation
Indices: 343824--343880 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
343814 TTATCTGTCA
343824 ACAAAGACCTTCGAGTTCGATTACGCTC
1 ACAAAGACCTTCGAGTTCGATTACGCTC
343852 ACAAAGACCTTCGAGTTCGATTACGCTC
1 ACAAAGACCTTCGAGTTCGATTACGCTC
343880 A
1 A
343881 GCTCCAAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (28 bp):
ACAAAGACCTTCGAGTTCGATTACGCTC
Found at i:344495 original size:37 final size:37
Alignment explanation
Indices: 344405--344509 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
344395 CCTTTTCGTC
* *
344405 CTACTAGGAATCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
344442 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * * *
344479 CTACTATTATTTAAACTCTTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
344510 CCACAAGCAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:344938 original size:21 final size:21
Alignment explanation
Indices: 344892--344938 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
344882 TAATTTAACC
344892 TTATTTTATATGTATATGTAT
1 TTATTTTATATGTATATGTAT
* * *
344913 ATATTTTATTAT-TTTATTTAT
1 TTATTTTA-TATGTATATGTAT
344934 TTATT
1 TTATT
344939 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
TTATTTTATATGTATATGTAT
Found at i:345241 original size:21 final size:23
Alignment explanation
Indices: 345201--345242 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
345191 TTATATTATA
345201 TATATATATATATATATATTTTT
1 TATATATATATATATATATTTTT
*
345224 TATATAT-TATTTAT-TATTT
1 TATATATATATATATATATTT
345243 CATTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATATATATATATATATTTTT
Found at i:345249 original size:8 final size:7
Alignment explanation
Indices: 345126--345250 Score: 57
Period size: 7 Copynumber: 17.7 Consensus size: 7
345116 AAATTATGTA
345126 TATTTAT
1 TATTTAT
345133 T-TTTCAT
1 TATTT-AT
345140 TATTTAT
1 TATTTAT
345147 TA-TTAT
1 TATTTAT
*
345153 TA-TTAC
1 TATTTAT
345159 TATTTAGT
1 TATTTA-T
345167 T-TTTAT
1 TATTTAT
345173 TA--TAT
1 TATTTAT
**
345178 TATACAT
1 TATTTAT
*
345185 ACATTT-T
1 -TATTTAT
345192 TATATTAT
1 TAT-TTAT
*
345200 ATATATAT
1 -TATTTAT
*
345208 ATATATAT
1 -TATTTAT
*
345216 ATATTTTT
1 -TATTTAT
*
345224 TATATAT
1 TATTTAT
345231 TATTTAT
1 TATTTAT
345238 TATTTCAT
1 TATTT-AT
345246 TATTT
1 TATTT
345251 TTTAGTTTCT
Statistics
Matches: 93, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
5 5 0.05
6 18 0.19
7 36 0.39
8 31 0.33
9 3 0.03
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (7 bp):
TATTTAT
Found at i:350492 original size:25 final size:25
Alignment explanation
Indices: 350445--350493 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
350435 AATTTATTTT
*
350445 TTATTTTTTAAAAAATCTTAAAATTA
1 TTATTTTTGAAAAAATC-TAAAATTA
350471 TTATTTTTAGAAAAAATC-AAAAT
1 TTATTTTT-GAAAAAATCTAAAAT
350494 CCTTTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 8 0.38
27 8 0.38
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
TTATTTTTGAAAAAATCTAAAATTA
Found at i:353824 original size:13 final size:13
Alignment explanation
Indices: 353806--353832 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
353796 AATATATGTT
353806 TTGTCTATCATGA
1 TTGTCTATCATGA
353819 TTGTCTATCATGA
1 TTGTCTATCATGA
353832 T
1 T
353833 GCTAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTCTATCATGA
Found at i:354187 original size:123 final size:123
Alignment explanation
Indices: 353968--354215 Score: 469
Period size: 123 Copynumber: 2.0 Consensus size: 123
353958 AAATTCCAAA
353968 TCTTTCAATTTCAAAGCACCAACTAGGGATGACAAATGGGCGGGTCGGGTACGGATACCCCCTTC
1 TCTTTCAATTTCAAAGCACCAACTAGGGATGACAAATGGGCGGGTCGGGTACGGATACCCCCTTC
*
354033 CCTATCCTCATACTCACATAATATTTTCAAATTCATCACCCATGATGGGTAAAATTTC
66 CCTATCCTCATACTCACATAATATTTTCAAATTCACCACCCATGATGGGTAAAATTTC
* *
354091 TCTTTCAATTTCAAAGCACCAACTAGGGATGACAAATGGGCGGGTCGGGTGCGGATGCCCCCTTC
1 TCTTTCAATTTCAAAGCACCAACTAGGGATGACAAATGGGCGGGTCGGGTACGGATACCCCCTTC
354156 CCTATCCTCATACTCACATAATATTTTCAAATTCACCACCCATGATGGGTAAAATTTC
66 CCTATCCTCATACTCACATAATATTTTCAAATTCACCACCCATGATGGGTAAAATTTC
354214 TC
1 TC
354216 AAATCCACAC
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (123 bp):
TCTTTCAATTTCAAAGCACCAACTAGGGATGACAAATGGGCGGGTCGGGTACGGATACCCCCTTC
CCTATCCTCATACTCACATAATATTTTCAAATTCACCACCCATGATGGGTAAAATTTC
Found at i:356198 original size:20 final size:20
Alignment explanation
Indices: 356156--356199 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
356146 TATTTGGATT
* * * *
356156 TTTTTTAAAATTTTGAGATA
1 TTTTGTAAAATATTGAAAAA
356176 TTTTGTAAAATATTGAAAAA
1 TTTTGTAAAATATTGAAAAA
356196 TTTT
1 TTTT
356200 AATTTTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (20 bp):
TTTTGTAAAATATTGAAAAA
Found at i:356213 original size:14 final size:14
Alignment explanation
Indices: 356194--356220 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
356184 AATATTGAAA
356194 AATTTTAATTTTTT
1 AATTTTAATTTTTT
356208 AATTTTAATTTTT
1 AATTTTAATTTTT
356221 AAAATTTAAA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATTTTAATTTTTT
Found at i:357978 original size:40 final size:38
Alignment explanation
Indices: 357888--357979 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 38
357878 ATTAATTAAA
* *
357888 AATTTTATATAAAATTTTTTTATAATTATATATTATTT
1 AATTTTATATAAAATTTTTTTATAATTATAAAATATTT
* * * *
357926 AAATTAATTATAAACTGTTTTTTTTAATTATAAAATATTT
1 AATTTTA-TATAAAAT-TTTTTTATAATTATAAAATATTT
357966 AATTTTTATATAAA
1 AA-TTTTATATAAA
357980 TTAAAAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
38 5 0.12
39 7 0.16
40 28 0.65
41 3 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (38 bp):
AATTTTATATAAAATTTTTTTATAATTATAAAATATTT
Found at i:358589 original size:20 final size:20
Alignment explanation
Indices: 358550--358589 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
358540 ATGATACGAC
*
358550 ACTTACATGACAGTTCACAA
1 ACTTACATGACAATTCACAA
* *
358570 ACTTACATGATAATTTACAA
1 ACTTACATGACAATTCACAA
358590 TATTAATGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (20 bp):
ACTTACATGACAATTCACAA
Found at i:358714 original size:17 final size:17
Alignment explanation
Indices: 358692--358740 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
358682 TGACTTGTTT
*
358692 AATTAAAAAAATATTTA
1 AATTAAAAAAATATTAA
358709 AATT--AAAAATA-TAA
1 AATTAAAAAAATATTAA
358723 AATATAAAAAAATATTAA
1 AAT-TAAAAAAATATTAA
358741 GATATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
17 11 0.41
18 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAAAAAATATTAA
Done.