Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008989.1 Hibiscus syriacus cultivar Beakdansim tig00112354_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: 534435
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:147152 original size:725 final size:725
Alignment explanation
Indices: 145760--147688 Score: 3509
Period size: 725 Copynumber: 2.7 Consensus size: 725
145750 CGCGTTCACC
** * *
145760 TTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
145825 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAA--GTCGA
*
145890 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTCG
129 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCG
*
145955 AGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
194 AGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
*
146020 GACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTCGATACTTATAATAA
259 GACACTTTATTGGCGCTATAAC-TCTTCTCTT-TTAAATTCCAAAAGTGTCGATACATATAATAA
* *
146084 ATTATCGACACTTTCAACATATCCGGTAGCGATTTACCTGTTTTGTCATTTTGAGACCGGTTTTG
322 ATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGGTTTTG
146149 TCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTG
387 TCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTG
*
146214 GCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTT
452 GCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAACAAATTATCGACACTT
* *
146279 TCAACATAACCGGTAGCGTTTTACATGTTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACC
517 TCAACATAACCGGTAGCGCTTTACATGTTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACA
*
146344 TGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTC
582 TGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTTTATTGGCGCTATAACTTC
146409 TTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGG
647 TTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGG
*
146474 TAGCGCTTTACTTG
712 TAGCGCTTTACCTG
146488 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
146553 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTAGATA
66 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTCGATA
*
146618 CTTATAATAAATTATTGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAG
131 CTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAG
146683 ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
196 ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
*
146748 CACTTTATTAGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACATATAATAAATTA
261 CACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACATATAATAAATTA
*
146813 TCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTCAT
326 TCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCAT
146878 ATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGC
391 ATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGC
* *
146943 TATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGATACTTATAACAAATTATCGACACTTTTAA
456 TATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAACAAATTATCGACACTTTCAA
* * *
147008 CATATCCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTT
521 CATAACCGGTAGCGCTTTACATGTTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACATGTT
*
147073 ATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTTTATTGGCGCTATAACTTTTTCT
586 ATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTTTATTGGCGCTATAACTTCTTCT
147138 CTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGC
651 CTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGC
147203 GCTTTACCTG
716 GCTTTACCTG
*
147213 TTTTGTCATTTCGAGACTGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
147278 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTCGATA
66 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTCGATA
* * *
147343 CTTATAATAAATTATCGACACTTTCAACATAACCGGTAGAGTTTTACCTGTTTTGTCATTTTGAG
131 CTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAG
147408 ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
196 ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
*
147473 CACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATTA
261 CACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACATATAATAAATTA
147538 TCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCAT
326 TCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCAT
* * *
147603 ATTTTTACCTGTTATATTGTTATGGATCGATAAATTTTTATAAAGTATCGACACTTTATTGACGA
391 ATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGC
*
147668 TAAAACTTCTTCTCTTTTAAA
456 TATAACTTCTTCTCTTTTAAA
147689 AAGGTAAAAT
Statistics
Matches: 1162, Mismatches: 38, Indels: 5
0.96 0.03 0.00
Matches are distributed among these distances:
724 2 0.00
725 890 0.77
726 152 0.13
728 118 0.10
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (725 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTCGATA
CTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAG
ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
CACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACATATAATAAATTA
TCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCAT
ATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGC
TATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAACAAATTATCGACACTTTCAA
CATAACCGGTAGCGCTTTACATGTTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACATGTT
ATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTTTATTGGCGCTATAACTTCTTCT
CTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGC
GCTTTACCTG
Found at i:148792 original size:2 final size:2
Alignment explanation
Indices: 148785--148847 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
148775 AGATTTTAAC
148785 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
148827 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
148848 TCATCTTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:149512 original size:36 final size:35
Alignment explanation
Indices: 149461--149581 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 35
149451 AAAACAAAGT
* * *
149461 TAAACGAACAAGTTCAGGAACATGTTCTTGAACATA
1 TAAACGAACATGTTCACGAACA-GTTCATGAACATA
* * **
149497 TAAACGAACACGTTCACGAACA-TTAAACAA-ATA
1 TAAACGAACATGTTCACGAACAGTTCATGAACATA
*
149530 GTAAACGAACATGTTCATGAACACGTTCATGAACATA
1 -TAAACGAACATGTTCACGAACA-GTTCATGAACATA
*
149567 TAAATGAACATGTTC
1 TAAACGAACATGTTC
149582 GTGAAAAATA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
33 3 0.04
34 24 0.35
36 39 0.57
37 3 0.04
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (35 bp):
TAAACGAACATGTTCACGAACAGTTCATGAACATA
Found at i:149573 original size:24 final size:24
Alignment explanation
Indices: 149478--149594 Score: 69
Period size: 24 Copynumber: 5.0 Consensus size: 24
149468 ACAAGTTCAG
* * *
149478 GAACATGTTCTTGAACATATAAAC
1 GAACACGTTCATGAACATATAAAT
* *
149502 GAACACGTTCACGAACAT-TAAAC
1 GAACACGTTCATGAACATATAAAT
* * ** * * **
149525 AAATA-GTAAACGAACATGTTCAT
1 GAACACGTTCATGAACATATAAAT
149548 GAACACGTTCATGAACATATAAAT
1 GAACACGTTCATGAACATATAAAT
* * *
149572 GAACATGTTCGTGAA-AAATAAAT
1 GAACACGTTCATGAACATATAAAT
149595 AAACGAACAC
Statistics
Matches: 70, Mismatches: 21, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
22 10 0.14
23 20 0.29
24 40 0.57
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (24 bp):
GAACACGTTCATGAACATATAAAT
Found at i:149586 original size:12 final size:12
Alignment explanation
Indices: 149536--149586 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
149526 AATAGTAAAC
149536 GAACATGTTCAT
1 GAACATGTTCAT
*
149548 GAACACGTTCAT
1 GAACATGTTCAT
* **
149560 GAACATATAAAT
1 GAACATGTTCAT
*
149572 GAACATGTTCGT
1 GAACATGTTCAT
149584 GAA
1 GAA
149587 AAATAAATAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (12 bp):
GAACATGTTCAT
Found at i:151540 original size:23 final size:23
Alignment explanation
Indices: 151514--151593 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
151504 GGTTCTAAGC
151514 GGTCATTCGGGACAATTCTATGT
1 GGTCATTCGGGACAATTCTATGT
* * *
151537 GGTCCTTCGAGACAAATTCTACGT
1 GGTCATTCGGGAC-AATTCTATGT
* *
151561 GGTCCTTCGGGACATTTCTATGT
1 GGTCATTCGGGACAATTCTATGT
151584 GG-CACTTCGG
1 GGTCA-TTCGG
151594 TGCATATTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 1 0.02
23 26 0.54
24 21 0.44
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (23 bp):
GGTCATTCGGGACAATTCTATGT
Found at i:151562 original size:24 final size:24
Alignment explanation
Indices: 151514--151574 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
151504 GGTTCTAAGC
* *
151514 GGTCATTCGGGAC-AATTCTATGT
1 GGTCCTTCGGGACAAATTCTACGT
*
151537 GGTCCTTCGAGACAAATTCTACGT
1 GGTCCTTCGGGACAAATTCTACGT
151561 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
151575 TTTCTATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 11 0.33
24 22 0.67
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTACGT
Found at i:158450 original size:54 final size:54
Alignment explanation
Indices: 158392--158504 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
158382 CCAGTATTGC
* *
158392 TAATAACTTTGCACCCGATACTGGTCACAGTCAGCAAGCAGTTCCTCCATCAAA
1 TAATAACTCTGCACCCGATACTGGTCACAGTCAGCAAGCAGTTACTCCATCAAA
* ** *
158446 TAATAACTCTGCCCCCGATACTGGTCACAGTCAGCAAGTTGTTACTCTATCAAA
1 TAATAACTCTGCACCCGATACTGGTCACAGTCAGCAAGCAGTTACTCCATCAAA
158500 TAATA
1 TAATA
158505 CAAGAGTACT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (54 bp):
TAATAACTCTGCACCCGATACTGGTCACAGTCAGCAAGCAGTTACTCCATCAAA
Found at i:163019 original size:30 final size:30
Alignment explanation
Indices: 162985--163051 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
162975 AAAACAGGTG
162985 GCATCATGATCTTAATATCCGTATGAAGCA
1 GCATCATGATCTTAATATCCGTATGAAGCA
163015 GCATCATGATCTTAATATCCGTATGAAGCA
1 GCATCATGATCTTAATATCCGTATGAAGCA
163045 GCATCAT
1 GCATCAT
163052 AATATATTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (30 bp):
GCATCATGATCTTAATATCCGTATGAAGCA
Found at i:170009 original size:130 final size:131
Alignment explanation
Indices: 169705--170052 Score: 382
Period size: 130 Copynumber: 2.7 Consensus size: 131
169695 AGAAGAATCA
* * * * * * * * * *
169705 ACATC-CATGCCTTAAAGCAGTCAATTCTTATTCCAATCGAAATAAAGAAATATTACAATTTCCT
1 ACATCTCATACCTTAAAGCAGTCATTTATTACTCTAATCAAAATGAAGAGATATTACTATTT-CA
** * ** * *
169769 TCC-AAAATTTGATATAAATATGAGAGAAAACGATAATATTTAATTATTTCCAATCAAGAATAAA
65 TCCTAAAATTAAATATTAATCCGAGAGAAAACGATAATATTCAATTATTTCCAACCAAGAATAAA
169833 TG
130 TG
* * *
169835 GCATCTCATGCCTTAAAGCAGTCATTTATTACTCTAATCGAAATGAAGAGATATTACTATTTCAT
1 ACATCTCATACCTTAAAGCAGTCATTTATTACTCTAATCAAAATGAAGAGATATTACTATTTCAT
* **
169900 CCTAAAATTAAATATTAATCCGAGAGAAAACGATAATA-TCAATTATTTTCAACCGGGAATAAAT
66 CCTAAAATTAAATATTAATCCGAGAGAAAACGATAATATTCAATTATTTCCAACCAAGAATAAAT
169964 G
131 G
* * * *
169965 ACCTCTCATACCTTAAAGCA-TATATTTATTACT-TCAATCAAAATGAATAGTTATTACTATTTC
1 ACATCTCATACCTTAAAGCAGT-CATTTATTACTCT-AATCAAAATGAAGAGATATTACTATTTC
*
170028 ATCCTAAAATTCAATATTAATCCGA
64 ATCCTAAAATTAAATATTAATCCGA
170053 ATGTTATTAT
Statistics
Matches: 187, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
129 2 0.01
130 106 0.57
131 79 0.42
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (131 bp):
ACATCTCATACCTTAAAGCAGTCATTTATTACTCTAATCAAAATGAAGAGATATTACTATTTCAT
CCTAAAATTAAATATTAATCCGAGAGAAAACGATAATATTCAATTATTTCCAACCAAGAATAAAT
G
Found at i:173635 original size:31 final size:30
Alignment explanation
Indices: 173553--173645 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 30
173543 AAAAAATTAA
* *
173553 ATAATTTAAGTACTTATTTTGACATAAAAT
1 ATAATTTTAGTACTTATTTTGACAAAAAAT
* *
173583 A-ATACTTTAGGTAAC-TGTTTTGACAAAAAAAT
1 ATA-ATTTTA-GT-ACTTATTTTGAC-AAAAAAT
*
173615 ATAATTTTAGTACTTATTTTGACTAAAAAT
1 ATAATTTTAGTACTTATTTTGACAAAAAAT
173645 A
1 A
173646 CTTTGGATAC
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
29 1 0.02
30 14 0.28
31 20 0.40
32 14 0.28
33 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.41
Consensus pattern (30 bp):
ATAATTTTAGTACTTATTTTGACAAAAAAT
Found at i:174390 original size:23 final size:22
Alignment explanation
Indices: 174341--174394 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
174331 TAAGCTACCA
174341 AAAGGCAGAGAAAACGTGCCAC
1 AAAGGCAGAGAAAACGTGCCAC
* * * *
174363 GAAGGTAGAGATAAACGTGTCAT
1 AAAGGCAGAGA-AAACGTGCCAC
174386 AAAGGCAGA
1 AAAGGCAGA
174395 TAACATGTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.44, C:0.15, G:0.30, T:0.11
Consensus pattern (22 bp):
AAAGGCAGAGAAAACGTGCCAC
Found at i:176483 original size:7 final size:7
Alignment explanation
Indices: 176471--176497 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
176461 AGAGGTAGGA
176471 GTTGGGC
1 GTTGGGC
176478 GTTGGGC
1 GTTGGGC
176485 GTTGGGC
1 GTTGGGC
176492 GTTGGG
1 GTTGGG
176498 ACTAATGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.59, T:0.30
Consensus pattern (7 bp):
GTTGGGC
Found at i:183467 original size:31 final size:31
Alignment explanation
Indices: 183431--183505 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
183421 GAGTATTGCT
183431 GAGCTCGACTCGACTCGAAAACCCTGAAAT-
1 GAGCTCGACTCGACTCGAAAACCCTGAAATA
* *
183461 GAAGCTCGACTTGACTCGAAAACTCTGAAATA
1 G-AGCTCGACTCGACTCGAAAACCCTGAAATA
*
183493 GAGCTCGATTCGA
1 GAGCTCGACTCGA
183506 AAACTCGAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.20
Consensus pattern (31 bp):
GAGCTCGACTCGACTCGAAAACCCTGAAATA
Found at i:207169 original size:67 final size:67
Alignment explanation
Indices: 207061--207195 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
207051 ATGTCTGATA
*
207061 TATGTATATATGTGTTTTCACTCAAGCTTTCATGTTGAATACGGTAATAACCTATATGCTTATAC
1 TATGTATATATGTGTTTTCACACAAGCTTTCATGTTGAATACGGTAATAACCTATATGCTTATAC
207126 TT
66 TT
* *
207128 TATGTATATATGTGTTTTCACACAAGCTTTCATGTTGAATACGGTCATAACCTATATGCTTATGC
1 TATGTATATATGTGTTTTCACACAAGCTTTCATGTTGAATACGGTAATAACCTATATGCTTATAC
207193 TT
66 TT
207195 T
1 T
207196 GTGCCCGAAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (67 bp):
TATGTATATATGTGTTTTCACACAAGCTTTCATGTTGAATACGGTAATAACCTATATGCTTATAC
TT
Found at i:214543 original size:28 final size:29
Alignment explanation
Indices: 214487--214543 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
214477 TTATGCACAA
* *
214487 TATCAATACACTTATATTATTAATTTAAT
1 TATCAATACACTTATAATATTAATCTAAT
214516 TATCAAT-CACTTA-AATATTAATACTAAT
1 TATCAATACACTTATAATATTAAT-CTAAT
214544 GATTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.32
28 10 0.40
29 7 0.28
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (29 bp):
TATCAATACACTTATAATATTAATCTAAT
Found at i:216309 original size:15 final size:14
Alignment explanation
Indices: 216285--216318 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
216275 AATTATATTT
*
216285 AAATAGTTCTTTTA
1 AAATAATTCTTTTA
216299 ACAATAATTCTTTTA
1 A-AATAATTCTTTTA
216314 AAATA
1 AAATA
216319 TAAAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (14 bp):
AAATAATTCTTTTA
Found at i:218666 original size:60 final size:60
Alignment explanation
Indices: 218588--218702 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
218578 CTGTTGTTGT
* *
218588 TGATTTTGTTTGTCTGCCTAGCTCTATCCTT-GCTGAGGAAGTAGCTCATAAAGCTGCTGA
1 TGATTTTGATTGTCTGCCTAACTCTA-CCTTGGCTGAGGAAGTAGCTCATAAAGCTGCTGA
* * * *
218648 TGATTTTGATTGTTTGCCTAATTCTACCTTGGTTGAGGAAGTTGCTCATAAAGCT
1 TGATTTTGATTGTCTGCCTAACTCTACCTTGGCTGAGGAAGTAGCTCATAAAGCT
218703 TTACTAGAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 4 0.08
60 44 0.92
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (60 bp):
TGATTTTGATTGTCTGCCTAACTCTACCTTGGCTGAGGAAGTAGCTCATAAAGCTGCTGA
Found at i:224304 original size:16 final size:17
Alignment explanation
Indices: 224285--224322 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
224275 TTTATTTTAT
*
224285 TGTATATGAGAAC-GTA
1 TGTATAGGAGAACTGTA
*
224301 TGTATAGGAGGACTGTA
1 TGTATAGGAGAACTGTA
224318 TGTAT
1 TGTAT
224323 GAGAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (17 bp):
TGTATAGGAGAACTGTA
Found at i:241856 original size:23 final size:23
Alignment explanation
Indices: 241830--241874 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
241820 CACCACAGCT
*
241830 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
241853 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
241875 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:242531 original size:19 final size:20
Alignment explanation
Indices: 242494--242531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
242484 TTTTTTTATA
*
242494 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
242514 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
242532 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:249320 original size:19 final size:20
Alignment explanation
Indices: 249283--249320 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
249273 TTTTTAAAAA
*
249283 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
249303 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
249321 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:250610 original size:13 final size:13
Alignment explanation
Indices: 250592--250618 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
250582 TTACAGAAGC
250592 GCATATGAAGACT
1 GCATATGAAGACT
250605 GCATATGAAGACT
1 GCATATGAAGACT
250618 G
1 G
250619 TTCAACTATG
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:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:251072 original size:14 final size:14
Alignment explanation
Indices: 251053--251079 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
251043 AACTCATTTG
251053 ATCTGGATTAATCA
1 ATCTGGATTAATCA
251067 ATCTGGATTAATC
1 ATCTGGATTAATC
251080 GATCAATGAA
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:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
ATCTGGATTAATCA
Found at i:251894 original size:20 final size:20
Alignment explanation
Indices: 251856--251899 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
251846 CTTTAAACAT
251856 TAATTCTAAATCTCAAACTC
1 TAATTCTAAATCTCAAACTC
*
251876 TAATTCCTAAA-CTCTAACTC
1 TAATT-CTAAATCTCAAACTC
251896 TAAT
1 TAAT
251900 AAAAAAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATTCTAAATCTCAAACTC
Found at i:252039 original size:2 final size:2
Alignment explanation
Indices: 252032--252108 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
252022 ACCTTAACCC
252032 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
252074 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
252109 TCCAGAAAGC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:257173 original size:19 final size:19
Alignment explanation
Indices: 257149--257204 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
257139 TTTGATGCAA
257149 AAATTAATAAATAATATTT
1 AAATTAATAAATAATATTT
* * *
257168 AAATTAGTAACTAAT-TAT
1 AAATTAATAAATAATATTT
*
257186 AATTTATATAAATAA-ATTT
1 AAATTA-ATAAATAATATTT
257205 GCAAAAATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATTAATAAATAATATTT
Found at i:259235 original size:197 final size:199
Alignment explanation
Indices: 258900--259295 Score: 778
Period size: 197 Copynumber: 2.0 Consensus size: 199
258890 AAGGTAAATG
258900 ATCATTCCTAATCATACGGCAGTTAGAACTGATTGAAAGAAAGAATTTTTTAGTGGACATCAATG
1 ATCATTCCTAATCATACGGCAGTTAGAACTGATTGAAAGAAAGAATTTTTTAGTGGACATCAATG
258965 AATACAGTGTGACAGGCCAAAAAAAATGCAAACCTTTTGAGCCGGAGTAAATGGGGTCCATATAC
66 AATACAGTGTGACAGGCCAAAAAAAATGCAAACCTTTTGAGCCGGAGTAAATGGGGTCCATATAC
259030 ATTGGGTAAAGA-CAGAAGAGGATCCCATATTAATTATCACCCCTGGC-TTTGCAGAGCTTGCAT
131 ATTGGGTAAAGACCAGAAGAGGATCCCATATTAATTATCACCCCTGGCTTTTGCAGAGCTTGCAT
259093 CGTT
196 CGTT
259097 ATCATTCCTAATCATACGGCAGTTAGAACTGATTGAAAGAAAGAATTTTTTAGTGGACATCAATG
1 ATCATTCCTAATCATACGGCAGTTAGAACTGATTGAAAGAAAGAATTTTTTAGTGGACATCAATG
259162 AATACAGTGTGACAGGCCAAAAAAAATGCAAACCTTTTGAGCCGGAGTAAATGGGGTCCATATAC
66 AATACAGTGTGACAGGCCAAAAAAAATGCAAACCTTTTGAGCCGGAGTAAATGGGGTCCATATAC
259227 ATTGGGTAAAGACCAGAAGAGGATCCCATATTAATTATCACCCCTGGCTTTTGCAGAGCTTGCAT
131 ATTGGGTAAAGACCAGAAGAGGATCCCATATTAATTATCACCCCTGGCTTTTGCAGAGCTTGCAT
259292 CGTT
196 CGTT
259296 TTAATCTGTT
Statistics
Matches: 197, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
197 142 0.72
198 35 0.18
199 20 0.10
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (199 bp):
ATCATTCCTAATCATACGGCAGTTAGAACTGATTGAAAGAAAGAATTTTTTAGTGGACATCAATG
AATACAGTGTGACAGGCCAAAAAAAATGCAAACCTTTTGAGCCGGAGTAAATGGGGTCCATATAC
ATTGGGTAAAGACCAGAAGAGGATCCCATATTAATTATCACCCCTGGCTTTTGCAGAGCTTGCAT
CGTT
Found at i:263246 original size:9 final size:9
Alignment explanation
Indices: 263232--263344 Score: 73
Period size: 10 Copynumber: 11.8 Consensus size: 9
263222 GGCTGCTGGA
263232 AACCGGTTT
1 AACCGGTTT
263241 AACCGGTTTT
1 AACCGG-TTT
*
263251 CAACCTGTTCT
1 -AACCGGTT-T
*
263262 GACCGGTTT
1 AACCGGTTT
*
263271 GACCGGTTT
1 AACCGGTTT
*
263280 CAACCGGTTCG
1 -AACCGGTT-T
263291 AACCGGTTT
1 AACCGGTTT
* *
263300 GACCGGTCTG
1 AACCGGT-TT
*
263310 AACTGGTTT
1 AACCGGTTT
*
263319 AACCGGTCTG
1 AACCGGT-TT
*
263329 AACCGGGTT
1 AACCGGTTT
*
263338 GACCGGT
1 AACCGGT
263345 ATGACCCGAC
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
9 35 0.44
10 39 0.49
11 6 0.08
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:263287 original size:19 final size:19
Alignment explanation
Indices: 263248--263344 Score: 63
Period size: 19 Copynumber: 5.1 Consensus size: 19
263238 TTTAACCGGT
*
263248 TTTCAACCTGTTCTGACCGG
1 TTTCAACCGGTT-TGACCGG
* *
263268 TTT-GACCGGTTTCAACCGG
1 TTTCAACCGGTTT-GACCGG
263287 -TTCGAACCGGTTTGACCGG
1 TTTC-AACCGGTTTGACCGG
* * * *
263306 TCTGAACTGGTTTAACCGG
1 TTTCAACCGGTTTGACCGG
* * *
263325 TCTGAACCGGGTTGACCGG
1 TTTCAACCGGTTTGACCGG
263344 T
1 T
263345 ATGACCCGAC
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
18 3 0.05
19 46 0.75
20 12 0.20
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (19 bp):
TTTCAACCGGTTTGACCGG
Found at i:263295 original size:29 final size:30
Alignment explanation
Indices: 263232--263306 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
263222 GGCTGCTGGA
* *
263232 AACCGGTTTAACCGGTTTTCAACCTGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
263263 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
263291 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
263307 CTGAACTGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.02
29 27 0.66
30 13 0.32
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:263317 original size:29 final size:28
Alignment explanation
Indices: 263232--263334 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
263222 GGCTGCTGGA
* * *
263232 AACCGGTTTAACCGGTTTTCAACCTGTTCTG
1 AACCGGTTTGACCGG-TCTCAACC-GGT-TG
*
263263 -ACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTCTCAACCGGTT-G
* * *
263291 AACCGGTTTGACCGGTCTGAACTGGTTT
1 AACCGGTTTGACCGGTCTCAACCGGTTG
*
263319 AACCGGTCTGAACCGG
1 AACCGGTTTG-ACCGG
263335 GTTGACCGGT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
27 1 0.02
28 12 0.19
29 36 0.58
30 13 0.21
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (28 bp):
AACCGGTTTGACCGGTCTCAACCGGTTG
Found at i:263349 original size:9 final size:9
Alignment explanation
Indices: 263233--263350 Score: 74
Period size: 9 Copynumber: 12.3 Consensus size: 9
263223 GCTGCTGGAA
*
263233 ACCGGTTTA
1 ACCGGTTTG
*
263242 ACCGGTTTTCA
1 ACCGG-TTT-G
*
263253 ACCTGTTCTG
1 ACCGGTT-TG
263263 ACCGGTTTG
1 ACCGGTTTG
*
263272 ACCGGTTTCA
1 ACCGGTTT-G
*
263282 ACCGGTTCG
1 ACCGGTTTG
263291 AACCGGTTTG
1 -ACCGGTTTG
*
263301 ACCGGTCTG
1 ACCGGTTTG
* *
263310 AACTGGTTTA
1 -ACCGGTTTG
*
263320 ACCGGTCTG
1 ACCGGTTTG
*
263329 AACCGGGTTG
1 -ACCGGTTTG
*
263339 ACCGGTATG
1 ACCGGTTTG
263348 ACC
1 ACC
263351 CGACCCGACC
Statistics
Matches: 84, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
9 39 0.46
10 39 0.46
11 6 0.07
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:263373 original size:22 final size:22
Alignment explanation
Indices: 263347--263389 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
263337 TGACCGGTAT
263347 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
263369 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
263390 GGTGACCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:287080 original size:18 final size:18
Alignment explanation
Indices: 287059--287105 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
287049 GGTTGTGGAG
*
287059 TTGGTTTCGGTTTCGGCT
1 TTGGCTTCGGTTTCGGCT
287077 TTGGCTTCGGTTTCGGCT
1 TTGGCTTCGGTTTCGGCT
*
287095 TCGGCTTCGGT
1 TTGGCTTCGGT
287106 GTTGGAGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.21, G:0.34, T:0.45
Consensus pattern (18 bp):
TTGGCTTCGGTTTCGGCT
Found at i:287094 original size:12 final size:12
Alignment explanation
Indices: 287061--287104 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
287051 TTGTGGAGTT
*
287061 GGTTTCGGTTTC
1 GGTTTCGGCTTC
287073 GGCTTT-GGCTTC
1 GG-TTTCGGCTTC
287085 GGTTTCGGCTTC
1 GGTTTCGGCTTC
*
287097 GGCTTCGG
1 GGTTTCGG
287105 TGTTGGAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 3 0.11
12 22 0.79
13 3 0.11
ACGTcount: A:0.00, C:0.23, G:0.36, T:0.41
Consensus pattern (12 bp):
GGTTTCGGCTTC
Found at i:292572 original size:5 final size:5
Alignment explanation
Indices: 292559--292589 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
292549 TAGTACTGAA
*
292559 GTTCC GTTCT GTTCT GTTCT GTTCT GTTCT G
1 GTTCT GTTCT GTTCT GTTCT GTTCT GTTCT G
292590 CTTTTCAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.23, G:0.23, T:0.55
Consensus pattern (5 bp):
GTTCT
Found at i:296426 original size:6 final size:6
Alignment explanation
Indices: 296415--296448 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
296405 AAAAAGGGAC
296415 AGAGGG AGAGGG AGA-GG AGA-GG AGAGGG AGAGGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
296449 CCGCTAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:302711 original size:31 final size:30
Alignment explanation
Indices: 302637--302703 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
302627 TAATTTTTGA
*
302637 AAATTTAAAAATTTAGGTATTAAAATAAAT
1 AAATTTAATAATTTAGGTATTAAAATAAAT
*
302667 CAAATTTAATAATTTAGGTATT-AAATACAT
1 -AAATTTAATAATTTAGGTATTAAAATAAAT
302697 -AATTTAA
1 AAATTTAA
302704 CCTTAATTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 7 0.21
30 7 0.21
31 20 0.59
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATTTAATAATTTAGGTATTAAAATAAAT
Found at i:303814 original size:21 final size:22
Alignment explanation
Indices: 303771--303819 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
303761 CGTCGAATAC
*
303771 TTTAA-ATATGTAAATATATAA
1 TTTAATATATGTAAAAATATAA
303792 TTTAATATATGTAAAAATA-AA
1 TTTAATATATGTAAAAATATAA
303813 TTTAATA
1 TTTAATA
303820 ATTAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TTTAATATATGTAAAAATATAA
Found at i:304124 original size:2 final size:2
Alignment explanation
Indices: 304117--304144 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
304107 ATAGAACAAC
304117 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
304145 TACAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:308332 original size:44 final size:46
Alignment explanation
Indices: 308282--308372 Score: 141
Period size: 44 Copynumber: 2.0 Consensus size: 46
308272 CGGTCACAAT
* *
308282 CCGACCCGACCCGTTTACTCGACCCGTTGA-C-TCGACCCGTTGAC
1 CCGACCCGACCCGTTGACCCGACCCGTTGACCGTCGACCCGTTGAC
*
308326 CCGACCCGACCCGTTGACCCGACCCGTTGACCGTTGACCCGTTGAC
1 CCGACCCGACCCGTTGACCCGACCCGTTGACCGTCGACCCGTTGAC
308372 C
1 C
308373 GTTGACCGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 28 0.67
45 1 0.02
46 13 0.31
ACGTcount: A:0.15, C:0.44, G:0.22, T:0.19
Consensus pattern (46 bp):
CCGACCCGACCCGTTGACCCGACCCGTTGACCGTCGACCCGTTGAC
Found at i:308337 original size:18 final size:18
Alignment explanation
Indices: 308314--308351 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
308304 CCCGTTGACT
308314 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
308332 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
308350 CG
1 CG
308352 TTGACCGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.50, G:0.24, T:0.11
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:308344 original size:8 final size:8
Alignment explanation
Indices: 308333--308379 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
308323 GACCCGACCC
308333 GACCCGTT
1 GACCCGTT
308341 GACCC---
1 GACCCGTT
308346 GACCCGTT
1 GACCCGTT
308354 GA-CCGTT
1 GACCCGTT
308361 GACCCGTT
1 GACCCGTT
308369 GA-CCGTT
1 GACCCGTT
308376 GACC
1 GACC
308380 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:308344 original size:13 final size:13
Alignment explanation
Indices: 308284--308372 Score: 79
Period size: 13 Copynumber: 6.3 Consensus size: 13
308274 GTCACAATCC
308284 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
308297 TACTCGACCCGTT
1 GACCCGACCCGTT
*
308310 GACTCGACCCGTT
1 GACCCGACCCGTT
308323 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
308341 GACCCGACCCGTT
1 GACCCGACCCGTT
*
308354 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
308369 GACC
1 GACC
308373 GTTGACCGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
13 40 0.62
15 12 0.19
18 12 0.19
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:308361 original size:7 final size:7
Alignment explanation
Indices: 308349--308380 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
308339 TTGACCCGAC
308349 CCGTTGA
1 CCGTTGA
308356 CCGTTGA
1 CCGTTGA
308363 CCCGTTGA
1 -CCGTTGA
308371 CCGTTGA
1 CCGTTGA
308378 CCG
1 CCG
308381 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:308366 original size:15 final size:15
Alignment explanation
Indices: 308333--308379 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
308323 GACCCGACCC
*
308333 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
308346 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
308361 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
308376 GACC
1 GACC
308380 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:310994 original size:24 final size:24
Alignment explanation
Indices: 310910--311009 Score: 78
Period size: 24 Copynumber: 4.2 Consensus size: 24
310900 ATATTTTATC
* *
310910 TGATTTCTGATTTGAATTCTGTT-
1 TGATATCTGATCTGAATTCTGTTA
* * * *
310933 TAAACATCTGATCTGAAATCTGTTC
1 T-GATATCTGATCTGAATTCTGTTA
* *
310958 TGAT-TCCTAATCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTA
* *
310982 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTA
311006 TGAT
1 TGAT
311010 TTTTGATATC
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTA
Found at i:313193 original size:44 final size:46
Alignment explanation
Indices: 313143--313233 Score: 141
Period size: 44 Copynumber: 2.0 Consensus size: 46
313133 CGGTCACAAT
* *
313143 CCGACCCGACCCGTTTACTCGACCCGTTGA-C-TCGACCCGTTGAC
1 CCGACCCGACCCGTTGACCCGACCCGTTGACCGTCGACCCGTTGAC
*
313187 CCGACCCGACCCGTTGACCCGACCCGTTGACCGTTGACCCGTTGAC
1 CCGACCCGACCCGTTGACCCGACCCGTTGACCGTCGACCCGTTGAC
313233 C
1 C
313234 GTTGACCGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 28 0.67
45 1 0.02
46 13 0.31
ACGTcount: A:0.15, C:0.44, G:0.22, T:0.19
Consensus pattern (46 bp):
CCGACCCGACCCGTTGACCCGACCCGTTGACCGTCGACCCGTTGAC
Found at i:313198 original size:18 final size:18
Alignment explanation
Indices: 313175--313212 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
313165 CCCGTTGACT
313175 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
313193 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
313211 CG
1 CG
313213 TTGACCGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.50, G:0.24, T:0.11
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:313205 original size:8 final size:8
Alignment explanation
Indices: 313194--313240 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
313184 GACCCGACCC
313194 GACCCGTT
1 GACCCGTT
313202 GACCC---
1 GACCCGTT
313207 GACCCGTT
1 GACCCGTT
313215 GA-CCGTT
1 GACCCGTT
313222 GACCCGTT
1 GACCCGTT
313230 GA-CCGTT
1 GACCCGTT
313237 GACC
1 GACC
313241 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:313205 original size:13 final size:13
Alignment explanation
Indices: 313145--313233 Score: 79
Period size: 13 Copynumber: 6.3 Consensus size: 13
313135 GTCACAATCC
313145 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
313158 TACTCGACCCGTT
1 GACCCGACCCGTT
*
313171 GACTCGACCCGTT
1 GACCCGACCCGTT
313184 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
313202 GACCCGACCCGTT
1 GACCCGACCCGTT
*
313215 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
313230 GACC
1 GACC
313234 GTTGACCGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
13 40 0.62
15 12 0.19
18 12 0.19
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:313222 original size:7 final size:7
Alignment explanation
Indices: 313210--313241 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
313200 TTGACCCGAC
313210 CCGTTGA
1 CCGTTGA
313217 CCGTTGA
1 CCGTTGA
313224 CCCGTTGA
1 -CCGTTGA
313232 CCGTTGA
1 CCGTTGA
313239 CCG
1 CCG
313242 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:313227 original size:15 final size:15
Alignment explanation
Indices: 313194--313240 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
313184 GACCCGACCC
*
313194 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
313207 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
313222 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
313237 GACC
1 GACC
313241 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:315854 original size:24 final size:24
Alignment explanation
Indices: 315770--315869 Score: 78
Period size: 24 Copynumber: 4.2 Consensus size: 24
315760 ATATTTTATC
* *
315770 TGATTTCTGATTTGAATTCTGTT-
1 TGATATCTGATCTGAATTCTGTTA
* * * *
315793 TAAACATCTGATCTGAAATCTGTTC
1 T-GATATCTGATCTGAATTCTGTTA
* *
315818 TGAT-TCCTAATCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTA
* *
315842 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTA
315866 TGAT
1 TGAT
315870 TTTTGATATC
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTA
Found at i:320157 original size:21 final size:21
Alignment explanation
Indices: 320131--320187 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
320121 AAGGGGGTTA
320131 ACTGAAATCAATGGCTAAGGG
1 ACTGAAATCAATGGCTAAGGG
320152 ACTGAAATCAATGGCTAAGGG
1 ACTGAAATCAATGGCTAAGGG
*
320173 ACTAAAATCGAATGG
1 ACTGAAATC-AATGG
320188 ATCAATAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 29 0.85
22 5 0.15
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.19
Consensus pattern (21 bp):
ACTGAAATCAATGGCTAAGGG
Found at i:321265 original size:60 final size:58
Alignment explanation
Indices: 321146--321277 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 58
321136 TCATTATACG
*
321146 TCCTCAAACTATGATTCTCATTCTAAATTGCTTCCTAAACTTTTAAATGGTTTAATTTCA
1 TCCTCAAACTATGATTATCATTCTAAATTGC-TCCTAAACTTTTAAAT-GTTTAATTTCA
* * * *
321206 TCCTTAAATTATGATTATCATTTTAAATTAG-TCCTCAAACTTTTGAACAT-TTTAGTTTCA
1 TCCTCAAACTATGATTATCATTCTAAATT-GCTCCT-AAACTTTT-AA-ATGTTTAATTTCA
*
321266 TCCCCAAACTAT
1 TCCTCAAACTAT
321278 ACCCTCCTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
59 4 0.07
60 51 0.85
61 3 0.05
62 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (58 bp):
TCCTCAAACTATGATTATCATTCTAAATTGCTCCTAAACTTTTAAATGTTTAATTTCA
Found at i:321341 original size:76 final size:76
Alignment explanation
Indices: 321206--321353 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 76
321196 TTTAATTTCA
* * *
321206 TCCTTAAATTATGATTATCATTTTAAATTAGTCCTCAAACTTTTGAACATTTTAGTTTCATCCCC
1 TCCTAAAACTATGATTATCATTTTAAATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCC
321271 AAACTATACCC
66 AAACTATACCC
** *
321282 TCCTAAAACTATGATTATTGTTTTAAATTGGTCC-CTAAACTTTT-AA-ATGGTTTAATTTCATC
1 TCCTAAAACTATGATTATCATTTTAAATTAGTCCTC-AAACTTTTGAACAT--TTTAATTTCATC
**
321344 CTTAAACTAT
63 CCCAAACTAT
321354 GATTATCATT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
74 2 0.03
75 3 0.05
76 56 0.92
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.43
Consensus pattern (76 bp):
TCCTAAAACTATGATTATCATTTTAAATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCC
AAACTATACCC
Found at i:321395 original size:136 final size:136
Alignment explanation
Indices: 321146--321418 Score: 456
Period size: 136 Copynumber: 2.0 Consensus size: 136
321136 TCATTATACG
* * *
321146 TCCTCAAACTATGATTCTCATTCTAAATTGCTTCCTAAACTTTTAAATGGTTTAATTTCATCCTT
1 TCCTAAAACTATGATTATCATTCTAAATTGCTCCCTAAACTTTTAAATGGTTTAATTTCATCCTT
* * *
321211 AAATTATGATTATCATTTTAAATTAGTCCTCAAACTTTTGAACATTTTAGTTTCATCCCCAAACT
66 AAACTATGATTATCATTTTAAATTAGTCATCAAACTTTTGAACATTTTAGTTTAATCCCCAAACT
321276 ATACCC
131 ATACCC
** * *
321282 TCCTAAAACTATGATTATTGTTTTAAATTGGTCCCTAAACTTTTAAATGGTTTAATTTCATCCTT
1 TCCTAAAACTATGATTATCATTCTAAATTGCTCCCTAAACTTTTAAATGGTTTAATTTCATCCTT
321347 AAACTATGATTATCATTTTAAATTAGTCATCAAACTTTTGAACATTTTAGTTTAATCCCCAAACT
66 AAACTATGATTATCATTTTAAATTAGTCATCAAACTTTTGAACATTTTAGTTTAATCCCCAAACT
321412 ATACCC
131 ATACCC
321418 T
1 T
321419 TCATTCTAAA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
136 127 1.00
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (136 bp):
TCCTAAAACTATGATTATCATTCTAAATTGCTCCCTAAACTTTTAAATGGTTTAATTTCATCCTT
AAACTATGATTATCATTTTAAATTAGTCATCAAACTTTTGAACATTTTAGTTTAATCCCCAAACT
ATACCC
Found at i:321411 original size:60 final size:59
Alignment explanation
Indices: 321287--321413 Score: 132
Period size: 60 Copynumber: 2.1 Consensus size: 59
321277 TACCCTCCTA
** * * **
321287 AAACTATGATTATTGTTTTAAATTGGTCCCTAAACTTTTAAATGGTTTAATTTCATCCTT
1 AAACTATGATTATCATTTTAAATTAGTCCCTAAACTTTTAAAT-GTTTAATTTAATCCCC
* *
321347 AAACTATGATTATCATTTTAAATTAGT-CATCAAACTTTTGAACAT-TTTAGTTTAATCCCC
1 AAACTATGATTATCATTTTAAATTAGTCCCT-AAACTTTT-AA-ATGTTTAATTTAATCCCC
321407 AAACTAT
1 AAACTAT
321414 ACCCTTCATT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
59 2 0.04
60 50 0.89
61 2 0.04
62 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (59 bp):
AAACTATGATTATCATTTTAAATTAGTCCCTAAACTTTTAAATGTTTAATTTAATCCCC
Found at i:321641 original size:32 final size:32
Alignment explanation
Indices: 321605--321670 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
321595 TTTGATTCGG
*
321605 CCCCTC-ATTTTCTATGGTTAATTATACTTTGC
1 CCCCTCAATTTT-TATGATTAATTATACTTTGC
*
321637 CCCCTCAATTTTTATGATTACTTATACTTTGC
1 CCCCTCAATTTTTATGATTAATTATACTTTGC
321669 CC
1 CC
321671 TCCCTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.20, C:0.27, G:0.08, T:0.45
Consensus pattern (32 bp):
CCCCTCAATTTTTATGATTAATTATACTTTGC
Found at i:321897 original size:60 final size:61
Alignment explanation
Indices: 321824--321982 Score: 178
Period size: 60 Copynumber: 2.6 Consensus size: 61
321814 ATGAAATTGG
* * * * **
321824 AAAGTTTAGGGACTAATTTAGAATAAGGGTCATAGTTTAAGGATGAAATTGGAAT-TTTTA
1 AAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTTAAGGATGAAATTAGAATATTAAA
* * * * * *
321884 AAAGTTTAAGGACTAATTTATAATGAGTA-TTACAGTTTGAGGATGAAATTATAATATTAAA
1 AAAGTTTAGGGACTAATTTAAAATGAG-AGTCATAGTTTAAGGATGAAATTAGAATATTAAA
*
321945 AAAATTTAGGGACTAATTTAAAATGAGAGTCATAGTTT
1 AAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTT
321983 GGAGAAATTT
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
60 46 0.57
61 34 0.43
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (61 bp):
AAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTTAAGGATGAAATTAGAATATTAAA
Found at i:336138 original size:21 final size:23
Alignment explanation
Indices: 336112--336154 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
336102 TTAATTATCA
336112 TAATTT-A-TACATGGACTAATG
1 TAATTTAACTACATGGACTAATG
336133 TAATTTAACTTACATGGACTAA
1 TAATTTAAC-TACATGGACTAA
336155 ATGTGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
24 12 0.63
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (23 bp):
TAATTTAACTACATGGACTAATG
Found at i:336204 original size:24 final size:24
Alignment explanation
Indices: 336177--336236 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
336167 AAAGTTAATC
336177 ATTTAACTTACATGGACTAATGTA
1 ATTTAACTTACATGGACTAATGTA
336201 ATTTAACTTACATGGACTAATGTA
1 ATTTAACTTACATGGACTAATGTA
336225 ATTTAACTTACA
1 ATTTAACTTACA
336237 AATATATAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (24 bp):
ATTTAACTTACATGGACTAATGTA
Found at i:347967 original size:7 final size:7
Alignment explanation
Indices: 347955--347980 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
347945 TTAATAATTT
347955 TTTTATA
1 TTTTATA
347962 TTTTATA
1 TTTTATA
347969 TTTTATA
1 TTTTATA
347976 TTTTA
1 TTTTA
347981 AATTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTATA
Found at i:351238 original size:18 final size:18
Alignment explanation
Indices: 351204--351250 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
351194 TGGCTTCATT
*
351204 TGCAGGGACACAACAGAAG
1 TGCAGGG-CATAACAGAAG
351223 TGCAGGGCATAACAGAAG
1 TGCAGGGCATAACAGAAG
351241 TGCAGGGCAT
1 TGCAGGGCAT
351251 GCGACAAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.36, C:0.19, G:0.34, T:0.11
Consensus pattern (18 bp):
TGCAGGGCATAACAGAAG
Found at i:356645 original size:22 final size:22
Alignment explanation
Indices: 356620--356663 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
356610 ATAGTTAATT
356620 TTTA-AAAAAATAATAATTATAA
1 TTTATAAAAAATAA-AATTATAA
**
356642 TTTATAATTAATAAAATTATAA
1 TTTATAAAAAATAAAATTATAA
356664 ATGACTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTATAAAAAATAAAATTATAA
Found at i:358481 original size:10 final size:10
Alignment explanation
Indices: 358449--358481 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
358439 ATTTTCTTAC
358449 AAAA-AAAAA
1 AAAACAAAAA
*
358458 AAAACAAAAC
1 AAAACAAAAA
358468 AAAACAAAAA
1 AAAACAAAAA
358478 AAAA
1 AAAA
358482 ACTGTAGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:368270 original size:454 final size:459
Alignment explanation
Indices: 367410--368330 Score: 1602
Period size: 454 Copynumber: 2.0 Consensus size: 459
367400 ACTAATATGT
367410 TTTTAAGGCAAAATTTGTGGAATAATGTCTTGAAAAAAAAATTTGCTCAAATGATGCAGTCGAAG
1 TTTTAAGGCAAAATTTGTGGAATAATGTCTTGAAAAAAAAATTTGCTCAAATGATGCAGTCGAAG
*
367475 GATTATTTGCCCAACTGGAGCGAATACTACAGTTTTTCATAGGTCGCCATGGCGACCAACCATGT
66 GAGTATTTGCCCAACTGGAGCGAATACTACAGTTTTTCATAGG-CG-C-T-GCG----ACCATGT
* * *
367540 CTTCCAAATGATCTATGTTGGTCGCCATGTGCTCCGAACAACGATTACCTAAATTTCCCTAAGTA
123 CTTCCAAATGACCTATGTTGGTCGCCATGTGCTCCAAACAACAATTACCTAAATTTCCCTAAGTA
367605 ACAAATATTACCTACATCGGTAATTAGGTTTTTTAACTACGCTGAAATGGAGGTCGCCATGTATG
188 ACAAATATTACCTACATCGGTAATTAGGTTTTTTAACTACGCTGAAATGGAGGTCGCCATGTATG
367670 CCGGGCGACCTTATAGGTCGCCATGTGATCCCGGCGACCAAACTGACCACAGCTCGCAGGGACGG
253 CCGGGCGACCTTATAGGTCGCCATGTGATCCCGGCGACCAAACTGACCACAGCTCGCAGGGACGG
* *
367735 CATGGCGAGCTCCTTGGTCGCCAGGAGCGCCTGACGACATATGTTCGAACTGTAGATTTCACCAT
318 CATGGCGACCTCCTTAGTCGCCAGGAGCGCCTGACGACATATGTTCGAACTGTAGATTTCACCAT
*
367800 ATCTCAACAAATAATTTCAGTTAGACCTTATTTCAACAAATAATTTTTTTTCAAAACTCTGTAGC
383 ATCTCAACAAATAATTTCAGTTAGACCTTATTTCAACAAATAATTTTTTTTCAAAACTCTGCAGC
367865 AGCAAATCAGCC
448 AGCAAATCAGCC
*
367877 TTTTAAGGCAAAATTTGTGGAATAATGTCTTGAAAAAAAAATTTGCTCAGATGATGCAGTCGAAG
1 TTTTAAGGCAAAATTTGTGGAATAATGTCTTGAAAAAAAAATTTGCTCAAATGATGCAGTCGAAG
* *
367942 GAGTATTTGCCCAACTGGGGCGAATGCTACAGTTTTTCATA-G-G-T-CG-CCATGTCTTCCAAA
66 GAGTATTTGCCCAACTGGAGCGAATACTACAGTTTTTCATAGGCGCTGCGACCATGTCTTCCAAA
368002 TGACCTATGTTGGTCGCCATGTGCTCCAAACAACAATTACCTAAATTTCCCTAAGTAACAAATAT
131 TGACCTATGTTGGTCGCCATGTGCTCCAAACAACAATTACCTAAATTTCCCTAAGTAACAAATAT
*
368067 TACCTACATCGGTAATTAGGTTTTTTAACTACGCTGAAATGGAGGTCGCCATGTATGTCGGGCGA
196 TACCTACATCGGTAATTAGGTTTTTTAACTACGCTGAAATGGAGGTCGCCATGTATGCCGGGCGA
368132 CC-TATAAGGTCGCCATGTGATCCCGGCGACCAAACTGACCACAGCTCGCAGGGACGGCATGGCG
261 CCTTAT-AGGTCGCCATGTGATCCCGGCGACCAAACTGACCACAGCTCGCAGGGACGGCATGGCG
*
368196 ACCTCCTTAGTCGCCAGGAGCGCCTGACGACATATGTTCGAACTGTAGATTTCACCATATCTCAG
325 ACCTCCTTAGTCGCCAGGAGCGCCTGACGACATATGTTCGAACTGTAGATTTCACCATATCTCAA
*
368261 CAAATAATTTCAGTTGGACCTTATTTCAACAAATAATTTTTTTTCAAAACTCTGCAGCAGCAAAT
390 CAAATAATTTCAGTTAGACCTTATTTCAACAAATAATTTTTTTTCAAAACTCTGCAGCAGCAAAT
368326 CAGCC
455 CAGCC
368331 ATGTTTTTAA
Statistics
Matches: 440, Mismatches: 13, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
453 3 0.01
454 330 0.75
459 2 0.00
461 1 0.00
464 1 0.00
466 1 0.00
467 102 0.23
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (459 bp):
TTTTAAGGCAAAATTTGTGGAATAATGTCTTGAAAAAAAAATTTGCTCAAATGATGCAGTCGAAG
GAGTATTTGCCCAACTGGAGCGAATACTACAGTTTTTCATAGGCGCTGCGACCATGTCTTCCAAA
TGACCTATGTTGGTCGCCATGTGCTCCAAACAACAATTACCTAAATTTCCCTAAGTAACAAATAT
TACCTACATCGGTAATTAGGTTTTTTAACTACGCTGAAATGGAGGTCGCCATGTATGCCGGGCGA
CCTTATAGGTCGCCATGTGATCCCGGCGACCAAACTGACCACAGCTCGCAGGGACGGCATGGCGA
CCTCCTTAGTCGCCAGGAGCGCCTGACGACATATGTTCGAACTGTAGATTTCACCATATCTCAAC
AAATAATTTCAGTTAGACCTTATTTCAACAAATAATTTTTTTTCAAAACTCTGCAGCAGCAAATC
AGCC
Found at i:369392 original size:20 final size:20
Alignment explanation
Indices: 369369--369465 Score: 142
Period size: 20 Copynumber: 4.8 Consensus size: 20
369359 ACAAGTTCCA
*
369369 AAATCGCAACGCGAATAGAT
1 AAATCGCAACGCGAATAGGT
369389 AAATCGCAACGCGAATAGGT
1 AAATCGCAACGCGAATAGGT
*
369409 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATAGGT
**
369429 AAATCGCAACGATAAT-GTGT
1 AAATCGCAACGCGAATAG-GT
369449 AAATCGCAACGCGAATA
1 AAATCGCAACGCGAATA
369466 TGAAAACCGC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGAATAGGT
Found at i:369396 original size:40 final size:40
Alignment explanation
Indices: 369352--369438 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
369342 AACTCCAATT
*
369352 TCGCAACAC-AAGTTCCAAAATCGCAACGCGAATA-GATAAA
1 TCGCAACACGAA-TACCAAAATCGCAACGCGAATATG-TAAA
* ***
369392 TCGCAACGCGAATAGGTAAATCGCAACGCGAATATGTAAA
1 TCGCAACACGAATACCAAAATCGCAACGCGAATATGTAAA
369432 TCGCAAC
1 TCGCAAC
369439 GATAATGTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 37 0.93
41 3 0.08
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.16
Consensus pattern (40 bp):
TCGCAACACGAATACCAAAATCGCAACGCGAATATGTAAA
Found at i:369484 original size:20 final size:20
Alignment explanation
Indices: 369459--369502 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
369449 AAATCGCAAC
*
369459 GCGAATATGAAAACCGCGTT
1 GCGAATATGAAAACCGCATT
* *
369479 GCGAATTTGAAAATCGCATT
1 GCGAATATGAAAACCGCATT
369499 GCGA
1 GCGA
369503 TAGTACTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (20 bp):
GCGAATATGAAAACCGCATT
Found at i:369493 original size:40 final size:40
Alignment explanation
Indices: 369368--369496 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 40
369358 CACAAGTTCC
*
369368 AAAATCGCAACGCGAATA-GATAAATCGCAACGCGAATAGG
1 AAAATCGCAACGCGAATATGA-AAATCGCAACGCGAATATG
* * ** *
369408 TAAATCGCAACGCGAATATGTAAATCGCAACGATAATGTG
1 AAAATCGCAACGCGAATATGAAAATCGCAACGCGAATATG
* * *** *
369448 TAAATCGCAACGCGAATATGAAAACCGCGTTGCGAATTTG
1 AAAATCGCAACGCGAATATGAAAATCGCAACGCGAATATG
369488 AAAATCGCA
1 AAAATCGCA
369497 TTGCGATAGT
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 72 0.99
41 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (40 bp):
AAAATCGCAACGCGAATATGAAAATCGCAACGCGAATATG
Found at i:369555 original size:20 final size:20
Alignment explanation
Indices: 369495--369547 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
369485 TTGAAAATCG
*
369495 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTAATGTTTA
*
369515 CATTGCGAGAGTAATGTTTA
1 CATTGCGATAGTAATGTTTA
369535 CATTGCGATAGTA
1 CATTGCGATAGTA
369548 TTGCTTACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (20 bp):
CATTGCGATAGTAATGTTTA
Found at i:369599 original size:57 final size:57
Alignment explanation
Indices: 369534--369656 Score: 183
Period size: 57 Copynumber: 2.2 Consensus size: 57
369524 AGTAATGTTT
* *
369534 ACATTGCGATAGTATTGCTTACTTATAACAGTAATTAGCGTTGCGAATTTGAAAATC
1 ACATTGCGATAGTACTGCTTACCTATAACAGTAATTAGCGTTGCGAATTTGAAAATC
* * * *
369591 ACGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
1 ACATTGCGATAGTACTGCTTACCTATAACAGTAATTAGCGTTGCGAATTTGAAAATC
*
369648 GCATTGCGA
1 ACATTGCGA
369657 ATTTGAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (57 bp):
ACATTGCGATAGTACTGCTTACCTATAACAGTAATTAGCGTTGCGAATTTGAAAATC
Found at i:369656 original size:20 final size:20
Alignment explanation
Indices: 369631--369676 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
369621 GTAATTAGCG
369631 TTGCGAATTTGAAAATCGCA
1 TTGCGAATTTGAAAATCGCA
369651 TTGCGAATTTGAAAATCGCA
1 TTGCGAATTTGAAAATCGCA
369671 TTGCGA
1 TTGCGA
369677 TAGTATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGCA
Found at i:369664 original size:77 final size:77
Alignment explanation
Indices: 369574--369733 Score: 250
Period size: 77 Copynumber: 2.1 Consensus size: 77
369564 GTAATTAGCG
*
369574 TTGCGAATTTGAAAATCACGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGC-GTTGCGAA
1 TTGCGAATTTGAAAATCACATTGCGATAGTACTGTTTACCTATATCGGTAATTA-CTGTTGCGAA
*
369638 TTTGAAAATCGCA
65 TTTGAAAATCACA
* * *
369651 TTGCGAATTTGAAAATCGCATTGCGATAGTATTGTTTACCTATATCGGTAATTACTGTTGTGAAT
1 TTGCGAATTTGAAAATCACATTGCGATAGTACTGTTTACCTATATCGGTAATTACTGTTGCGAAT
*
369716 TTGAAAATCACG
66 TTGAAAATCACA
369728 TTGCGA
1 TTGCGA
369734 TTTCCTAAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
76 1 0.01
77 75 0.99
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (77 bp):
TTGCGAATTTGAAAATCACATTGCGATAGTACTGTTTACCTATATCGGTAATTACTGTTGCGAAT
TTGAAAATCACA
Found at i:369763 original size:20 final size:20
Alignment explanation
Indices: 369740--369780 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
369730 GCGATTTCCT
*
369740 AAACTGAGTTGCGAATTTGG
1 AAACTGAGTTGCGAAATTGG
*
369760 AAACTGTGTTGCGAAATTGG
1 AAACTGAGTTGCGAAATTGG
369780 A
1 A
369781 GTTCGCGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
AAACTGAGTTGCGAAATTGG
Found at i:372753 original size:17 final size:15
Alignment explanation
Indices: 372731--372765 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
372721 AATTTATTTT
372731 TTAAAATTTTATATAAA
1 TTAAAATTTT-TA-AAA
372748 TTAAAATTTTTAAAA
1 TTAAAATTTTTAAAA
372763 TTA
1 TTA
372766 TCAGGTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 2 0.11
17 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAAAATTTTTAAAA
Found at i:378203 original size:29 final size:29
Alignment explanation
Indices: 378161--378231 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
378151 ATAAAAAAAA
378161 TGATTACTTGTGTTAT-CATTTTATTAAGTTT
1 TGATTA-TT-TGTTATAC-TTTTATTAAGTTT
378192 TGATTATTTGTTATACTTTTATTAAGTTT
1 TGATTATTTGTTATACTTTTATTAAGTTT
* *
378221 TAATTACTTGT
1 TGATTATTTGT
378232 GTTGTGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 28 0.76
30 3 0.08
31 6 0.16
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.59
Consensus pattern (29 bp):
TGATTATTTGTTATACTTTTATTAAGTTT
Found at i:384357 original size:38 final size:39
Alignment explanation
Indices: 384294--384381 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 39
384284 GAAAATGTGG
*
384294 AGATACTTACTGGGGGAAAAATAAATGTAGGCAATATGA
1 AGATACTTACTGGGGAAAAAATAAATGTAGGCAATATGA
384333 AGATACTTAC-GGGGAAAAAATAAATGTAGGCAATATGA
1 AGATACTTACTGGGGAAAAAATAAATGTAGGCAATATGA
384371 AGATACTTACT
1 AGATACTTACT
384382 AGAAAAGGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 37 0.79
39 10 0.21
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (39 bp):
AGATACTTACTGGGGAAAAAATAAATGTAGGCAATATGA
Found at i:406054 original size:25 final size:26
Alignment explanation
Indices: 406026--406082 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
406016 TTAACTTAAA
*
406026 ATTTTCATATTAACTT-ATTAAATAT
1 ATTTTCATATTAACTTAATTAAAAAT
**
406051 ATTTTTTTATTAACTTGAATTAAAAAT
1 ATTTTCATATTAACTT-AATTAAAAAT
406078 ATTTT
1 ATTTT
406083 AGTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 14 0.52
27 13 0.48
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTTCATATTAACTTAATTAAAAAT
Found at i:406057 original size:27 final size:26
Alignment explanation
Indices: 406033--406082 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
406023 AAAATTTTCA
*
406033 TATTAACTT-ATTAAATATATTTTTT
1 TATTAACTTAATTAAAAATATTTTTT
406058 TATTAACTTGAATTAAAAATATTTT
1 TATTAACTT-AATTAAAAATATTTT
406083 AGTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
27 13 0.59
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (26 bp):
TATTAACTTAATTAAAAATATTTTTT
Found at i:414137 original size:22 final size:21
Alignment explanation
Indices: 414048--414180 Score: 64
Period size: 22 Copynumber: 6.5 Consensus size: 21
414038 AATTTGGAAA
*
414048 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG-CAACTGTAAACT
*
414070 ATCGCAACGCGAAATG-AAA--
1 ATCGCAACGC-AACTGTAAACT
* * * * *
414089 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCAACTGTAAACT
414110 A--GCAACGACAACTGTAAACT
1 ATCGCAACG-CAACTGTAAACT
* *
414130 ATCGCAACGCGAAATG-AAA-A
1 ATCGCAACGC-AACTGTAAACT
* * * *
414150 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCAACTGTAAACT
414171 ATCGCAACGC
1 ATCGCAACGC
414181 GAATTGGAAA
Statistics
Matches: 82, Mismatches: 19, Indels: 21
0.67 0.16 0.17
Matches are distributed among these distances:
18 2 0.02
19 18 0.22
20 21 0.26
21 18 0.22
22 23 0.28
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCAACTGTAAACT
Found at i:414144 original size:60 final size:61
Alignment explanation
Indices: 414051--414171 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 61
414041 TTGGAAAATC
* *
414051 GCAACGACAACTGTAGACTATCGCAACGCGAAATG-AAAATCGCAATGCGATTTTCAACTA
1 GCAACGACAACTGTAAACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTA
414111 GCAACGACAACTGTAAACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTA
1 GCAACGACAACTGTAAACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTA
414172 TCGCAACGCG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 34 0.59
61 24 0.41
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (61 bp):
GCAACGACAACTGTAAACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTA
Found at i:414155 original size:20 final size:20
Alignment explanation
Indices: 414130--414198 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
414120 ACTGTAAACT
*
414130 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAATTGAAAA
* * **
414150 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-ATTGAAAA
*
414171 ATCGCAACGCGAATTGGAAA
1 ATCGCAACGCGAATTGAAAA
414191 ATCGCAAC
1 ATCGCAAC
414199 ACGATTTTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAATTGAAAA
Found at i:414171 original size:41 final size:41
Alignment explanation
Indices: 414126--414227 Score: 177
Period size: 41 Copynumber: 2.5 Consensus size: 41
414116 GACAACTGTA
*
414126 AACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTC
1 AACTATCGCAACGCGAAATGAAAAATCGCAACACGATTTTC
* *
414167 AACTATCGCAACGCGAATTGGAAAATCGCAACACGATTTTC
1 AACTATCGCAACGCGAAATGAAAAATCGCAACACGATTTTC
414208 AACTATCGCAACGCGAAATG
1 AACTATCGCAACGCGAAATG
414228 CAACGCGAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (41 bp):
AACTATCGCAACGCGAAATGAAAAATCGCAACACGATTTTC
Found at i:414195 original size:61 final size:59
Alignment explanation
Indices: 414051--414198 Score: 183
Period size: 60 Copynumber: 2.4 Consensus size: 59
414041 TTGGAAAATC
* * *
414051 GCAACGACAACTGTAGACTATCGCAACGCGAAATGAAAATCGCAATGCGATTTTCAACTA
1 GCAACGACAACTGGAAAC-ATCGCAACGCGAAATGAAAATCGCAACGCGATTTTCAACTA
*
414111 GCAACGACAACTGTAAACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTA
1 GCAACGACAACTGGAAAC-ATCGCAACGCGAAATG-AAAATCGCAACGCGATTTTCAACTA
*
414172 TCGCAACG-CGAATTGGAAA-ATCGCAAC
1 --GCAACGAC-AACTGGAAACATCGCAAC
414199 ACGATTTTCA
Statistics
Matches: 80, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
60 34 0.43
61 32 0.40
62 1 0.01
63 13 0.16
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (59 bp):
GCAACGACAACTGGAAACATCGCAACGCGAAATGAAAATCGCAACGCGATTTTCAACTA
Found at i:414513 original size:5 final size:5
Alignment explanation
Indices: 414490--414530 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
414480 CATATAATTA
414490 TTTA- TTTA- TTTATT TTTAT TTTAT TTTAT TTTAT TATTAT T
1 TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT T-TTAT T
414531 GTTAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.24
5 17 0.50
6 9 0.26
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:414972 original size:14 final size:15
Alignment explanation
Indices: 414937--414965 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
414927 GCTCAGCAAA
414937 CAAA-CCCCAAAATC
1 CAAATCCCCAAAATC
414951 CAAATCCCCAAAATC
1 CAAATCCCCAAAATC
414966 AGTTCCCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.10
Consensus pattern (15 bp):
CAAATCCCCAAAATC
Found at i:415354 original size:38 final size:38
Alignment explanation
Indices: 415303--415376 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
415293 AAGGGAGAAA
415303 GGCTTTGGTTATAAAGGTTATGCTTTCCATCGTGTCCT
1 GGCTTTGGTTATAAAGGTTATGCTTTCCATCGTGTCCT
*
415341 GGCTTTGGTTATAAAGGTTCTGCTTTCCATCGTGTC
1 GGCTTTGGTTATAAAGGTTATGCTTTCCATCGTGTC
415377 ATTAAAGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (38 bp):
GGCTTTGGTTATAAAGGTTATGCTTTCCATCGTGTCCT
Found at i:415650 original size:19 final size:19
Alignment explanation
Indices: 415628--415668 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
415618 ATTTGTTTAA
*
415628 TTTAATTTTATTATTATTT
1 TTTAATTTTATTAATATTT
*
415647 TTTAATTTTTTTAATATTT
1 TTTAATTTTATTAATATTT
415666 TTT
1 TTT
415669 TATTATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTAATTTTATTAATATTT
Found at i:415658 original size:9 final size:10
Alignment explanation
Indices: 415628--415668 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
415618 ATTTGTTTAA
415628 TTTAAT-TTT
1 TTTAATATTT
* *
415637 ATTATTATTT
1 TTTAATATTT
415647 TTTAAT-TTT
1 TTTAATATTT
415656 TTTAATATTT
1 TTTAATATTT
415666 TTT
1 TTT
415669 TATTATTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTAATATTT
Found at i:415676 original size:11 final size:11
Alignment explanation
Indices: 415633--415676 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
415623 TTTAATTTAA
415633 TTTTATTATTAT
1 TTTTATTATT-T
*
415645 TTTT-TAATTT
1 TTTTATTATTT
*
415655 TTTTAATATTT
1 TTTTATTATTT
415666 TTTTATTATTT
1 TTTTATTATTT
415677 CTTATTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 5 0.19
11 18 0.67
12 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTATTT
Found at i:415681 original size:10 final size:10
Alignment explanation
Indices: 415632--415682 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
415622 GTTTAATTTA
415632 ATTTTATTATT
1 ATTTT-TTATT
*
415643 ATTTTTTAAT
1 ATTTTTTATT
*
415653 -TTTTTTAAT
1 ATTTTTTATT
415662 ATTTTTTTATT
1 A-TTTTTTATT
*
415673 ATTTCTTATT
1 ATTTTTTATT
415683 CAATACTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 9 0.26
10 12 0.34
11 14 0.40
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:420517 original size:2 final size:2
Alignment explanation
Indices: 420510--420536 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
420500 CTAATTGGTA
420510 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
420537 ATTAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:424544 original size:21 final size:21
Alignment explanation
Indices: 424520--424572 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
424510 ATTCTCTTTC
424520 CTTTGGTTTTATAAAAGTT-TT
1 CTTT-GTTTTATAAAAGTTATT
* *
424541 CTTT-TCTTTTTCAAAGTTATT
1 CTTTGT-TTTATAAAAGTTATT
424562 CTTTGTTTTAT
1 CTTTGTTTTAT
424573 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.04
20 10 0.38
21 14 0.54
22 1 0.04
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
CTTTGTTTTATAAAAGTTATT
Found at i:434329 original size:12 final size:12
Alignment explanation
Indices: 434309--434347 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
434299 TATCTCTATC
*
434309 AATTCAAAAAAT
1 AATTTAAAAAAT
434321 AATTTAAAAAAAT
1 AATTT-AAAAAAT
434334 AATTTAAAAAAT
1 AATTTAAAAAAT
434346 AA
1 AA
434348 AAACTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (12 bp):
AATTTAAAAAAT
Found at i:434330 original size:13 final size:13
Alignment explanation
Indices: 434314--434344 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
434304 CTATCAATTC
434314 AAAAAATAATTTA
1 AAAAAATAATTTA
434327 AAAAAATAATTTA
1 AAAAAATAATTTA
434340 AAAAA
1 AAAAA
434345 TAAAAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAATAATTTA
Found at i:452881 original size:18 final size:17
Alignment explanation
Indices: 452858--452920 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 17
452848 TTCATCCCGT
452858 AGGACCACTATGTCTCGA
1 AGGACCACTATGTC-CGA
*
452876 AGGACCACTGTATATGTCCCA
1 AGGACCAC----TATGTCCGA
452897 TAGGACCACTATGTCCCGA
1 -AGGACCACTATGT-CCGA
452916 AGGAC
1 AGGAC
452921 TACTCCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
18 18 0.49
19 3 0.08
21 2 0.05
22 14 0.38
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (17 bp):
AGGACCACTATGTCCGA
Found at i:454509 original size:64 final size:62
Alignment explanation
Indices: 454404--454560 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
454394 TAATGAAGGT
* * * **
454404 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATT-TTA-AAAG
* *
454468 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATGTTTCTATTTTAAAAG
*
454531 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
454561 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.05
64 68 0.85
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:464136 original size:33 final size:34
Alignment explanation
Indices: 464089--464154 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
464079 CTCATGTTCA
464089 AAGTTTGACCACCAACCAAGATGAAATTTCCAAT
1 AAGTTTGACCACCAACCAAGATGAAATTTCCAAT
464123 AAGTTTG-CCACCAACCAAGATGAAATTTCCAA
1 AAGTTTGACCACCAACCAAGATGAAATTTCCAA
464155 CGTGTTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (34 bp):
AAGTTTGACCACCAACCAAGATGAAATTTCCAAT
Found at i:464284 original size:2 final size:2
Alignment explanation
Indices: 464277--464320 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
464267 AAATAAATAA
464277 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
464319 AT
1 AT
464321 TCTGAACATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:464954 original size:31 final size:31
Alignment explanation
Indices: 464897--464955 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
464887 CAATTTAGTC
* * *
464897 ATATTTTTAAATAAATTTTAACATAAAACAT
1 ATATTTTTAAATAAATATAAAAATAAAACAT
464928 ATATTTTTAAATGAAA-ATAAAAATAAAA
1 ATATTTTTAAAT-AAATATAAAAATAAAA
464956 TGCTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (31 bp):
ATATTTTTAAATAAATATAAAAATAAAACAT
Found at i:466115 original size:29 final size:30
Alignment explanation
Indices: 466059--466115 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
466049 GTAAGTTTAG
* *
466059 TTTTTATTTCATTTTAGTGTTTGCCGTTAA
1 TTTTTATTTCATTTTAGTGATTCCCGTTAA
466089 TTTTTATTTCATTTTAGT-ATTCCCGTT
1 TTTTTATTTCATTTTAGTGATTCCCGTT
466116 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.16, C:0.12, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTTTATTTCATTTTAGTGATTCCCGTTAA
Found at i:480910 original size:17 final size:17
Alignment explanation
Indices: 480888--480934 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
480878 TATAGAGCCT
480888 TTGAATCATTCAGGCCA
1 TTGAATCATTCAGGCCA
480905 TTGAATCATTCAGGCCA
1 TTGAATCATTCAGGCCA
480922 TTGAATCATTCAG
1 TTGAATCATTCAG
480935 TGCTTAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (17 bp):
TTGAATCATTCAGGCCA
Found at i:481677 original size:17 final size:17
Alignment explanation
Indices: 481655--481689 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
481645 TTTCGGTTTG
481655 AAAAAAACAGGTTTTTA
1 AAAAAAACAGGTTTTTA
*
481672 AAAAAAACCGGTTTTTA
1 AAAAAAACAGGTTTTTA
481689 A
1 A
481690 TCCGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (17 bp):
AAAAAAACAGGTTTTTA
Found at i:481741 original size:20 final size:20
Alignment explanation
Indices: 481716--481760 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
481706 GTCATCCAAT
* *
481716 TTTTTAAACCTCAGACCGGA
1 TTTTTAAACCCCAAACCGGA
481736 TTTTTAAACCCCAAACCGGA
1 TTTTTAAACCCCAAACCGGA
481756 TTTTT
1 TTTTT
481761 TTTCCGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAAACCGGA
Found at i:494264 original size:21 final size:21
Alignment explanation
Indices: 494238--494282 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
494228 GATTTCTGGG
* *
494238 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
494259 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
494280 CAA
1 CAA
494283 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:495123 original size:31 final size:31
Alignment explanation
Indices: 495085--495209 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
495075 AGGGTCGAGG
495085 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
495116 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
495147 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
495178 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
495209 G
1 G
495210 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:498394 original size:21 final size:21
Alignment explanation
Indices: 498368--498412 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
498358 GATTTCTGGG
* *
498368 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
498389 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
498410 CAA
1 CAA
498413 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:499250 original size:31 final size:31
Alignment explanation
Indices: 499212--499336 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
499202 AGGGTCGAGG
499212 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
499243 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
499274 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
499305 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
499336 G
1 G
499337 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:511073 original size:15 final size:15
Alignment explanation
Indices: 511053--511082 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
511043 AATTAAAATC
511053 AAATTGAACTTAATA
1 AAATTGAACTTAATA
*
511068 AAATTGAATTTAATA
1 AAATTGAACTTAATA
511083 TTATGAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (15 bp):
AAATTGAACTTAATA
Found at i:512134 original size:2 final size:2
Alignment explanation
Indices: 512127--512157 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
512117 AGTGTACAAT
512127 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 T
512158 GTATGTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:513358 original size:16 final size:16
Alignment explanation
Indices: 513337--513369 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
513327 TACTATTCAT
*
513337 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
513353 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
513369 G
1 G
513370 GTCGACGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:529579 original size:24 final size:23
Alignment explanation
Indices: 529533--529592 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
529523 GAAATAAAAA
* *
529533 ATAAAAAAATTAAATTAAGTTAAT
1 ATAAAAATATTTAA-TAAGTTAAT
*
529557 AGTAAATATATTTAATAAGTTAAT
1 A-TAAAAATATTTAATAAGTTAAT
529581 ATAAAAATATTT
1 ATAAAAATATTT
529593 TAATTTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 10 0.32
24 11 0.35
25 10 0.32
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (23 bp):
ATAAAAATATTTAATAAGTTAAT
Found at i:529596 original size:24 final size:24
Alignment explanation
Indices: 529534--529592 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
529524 AAATAAAAAA
* *
529534 TAAAAAAATTAAATTAAGTTAATAG
1 TAAAAATATTTAA-TAAGTTAATAG
*
529559 TAAATATATTTAATAAGTTAATA-
1 TAAAAATATTTAATAAGTTAATAG
529582 TAAAAATATTT
1 TAAAAATATTT
529593 TAATTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 10 0.33
24 10 0.33
25 10 0.33
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (24 bp):
TAAAAATATTTAATAAGTTAATAG
Found at i:529718 original size:2 final size:2
Alignment explanation
Indices: 529711--529756 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
529701 AATTTAAAAG
529711 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
529753 TA TA
1 TA TA
529757 AAGTTAAAAA
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):
TA
Found at i:529910 original size:38 final size:38
Alignment explanation
Indices: 529868--529950 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 38
529858 AAAAATTAAC
529868 TTAGAAAGTTAAT-GTG-AAATAATTAAGAAATTAAGAAT
1 TTAGAAAGTT-ATGGTGCAAA-AATTAAGAAATTAAGAAT
* * * *
529906 TTAGAATGTTATGGTGTCAAAATTTAAGAAATTAGGATT
1 TTAGAAAGTTATGGTG-CAAAAATTAAGAAATTAAGAAT
529945 TTAGAA
1 TTAGAA
529951 TGCTAGAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
37 2 0.05
38 12 0.32
39 21 0.55
40 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.18, T:0.35
Consensus pattern (38 bp):
TTAGAAAGTTATGGTGCAAAAATTAAGAAATTAAGAAT
Done.