Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 20
Found at i:634954 original size:172 final size:172
Alignment explanation
Indices: 634663--635020 Score: 558
Period size: 172 Copynumber: 2.1 Consensus size: 172
634653 CATCAAATAT
* *
634663 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
634728 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTATACTAAATTCAAGCATAGTATACCAACT
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATATAATACTAAATTCAAGCATAGTATACCAACT
* * *
634793 TTTTATAATTTACTCTAATTTCTTAAATTCCTCAAATTTTGC
131 TTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* *
634835 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
634899 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATA-TAATACTAAATTCAAGCATAGTATACCAA
* *
634963 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
129 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
635007 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
635021 AACTTTACAA
Statistics
Matches: 170, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
171 32 0.19
172 138 0.81
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (172 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATATAATACTAAATTCAAGCATAGTATACCAACT
TTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:635541 original size:22 final size:22
Alignment explanation
Indices: 635516--635578 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
635506 AGACGTGCAG
*
635516 CCTTGCAGGACCCGTGATTTCT
1 CCTTGCAGAACCCGTGATTTCT
* *
635538 CCTTGCAGAACCCGTGCTCTCT
1 CCTTGCAGAACCCGTGATTTCT
635560 CCTTGCAGAACCCGTGATT
1 CCTTGCAGAACCCGTGATT
635579 CTCACGTCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.16, C:0.35, G:0.21, T:0.29
Consensus pattern (22 bp):
CCTTGCAGAACCCGTGATTTCT
Found at i:636447 original size:28 final size:28
Alignment explanation
Indices: 636403--636474 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
636393 TGGATTTTCT
*
636403 TTTTATTTAATTCAA-TTTTCTGTT-TGG
1 TTTTAATTAATTCAATTTTTCT-TTATGG
*
636430 TTTTAATTAGATTTAATTTTTCTTTATGG
1 TTTTAATTA-ATTCAATTTTTCTTTATGG
636459 TTTTGAATT--TTCAATT
1 TTTT-AATTAATTCAATT
636475 ATTTATTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 14 0.37
28 7 0.18
29 13 0.34
30 4 0.11
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.62
Consensus pattern (28 bp):
TTTTAATTAATTCAATTTTTCTTTATGG
Found at i:637970 original size:14 final size:14
Alignment explanation
Indices: 637951--637992 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
637941 TGTTCGTTTG
637951 TGTTCATTCAT-TT
1 TGTTCATTCATGTT
*
637964 ATGTTCATTTATGTT
1 -TGTTCATTCATGTT
*
637979 TGTTCATTTATGTT
1 TGTTCATTCATGTT
637993 CGTTTATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 24 0.92
15 2 0.08
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.62
Consensus pattern (14 bp):
TGTTCATTCATGTT
Found at i:637978 original size:24 final size:24
Alignment explanation
Indices: 637939--638003 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
637929 CGTTCGATTA
*
637939 TATGTTCGTTTGTGTTCATTCATT
1 TATGTTCGTTTATGTTCATTCATT
* **
637963 TATGTTCATTTATGTTTGTTCATT
1 TATGTTCGTTTATGTTCATTCATT
637987 TATGTTCGTTTATGTTC
1 TATGTTCGTTTATGTTC
638004 GAACAGAGGG
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:0.14, C:0.11, G:0.15, T:0.60
Consensus pattern (24 bp):
TATGTTCGTTTATGTTCATTCATT
Found at i:638260 original size:14 final size:14
Alignment explanation
Indices: 638243--638279 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
638233 GTTTGATTAA
638243 GTTTGTTTTTTTGT
1 GTTTGTTTTTTTGT
638257 GTTTGTTTTTTTGT
1 GTTTGTTTTTTTGT
638271 GTTTGTTTT
1 GTTTGTTTT
638280 GTTCGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (14 bp):
GTTTGTTTTTTTGT
Found at i:638287 original size:23 final size:24
Alignment explanation
Indices: 638256--638357 Score: 104
Period size: 23 Copynumber: 4.4 Consensus size: 24
638246 TGTTTTTTTG
* * *
638256 TGTTTGTTTTTTTGTGTTTGTTT-
1 TGTTCGTTTTATTGTGTTCGTTTA
638279 TGTTCG-TTTATTGTGTTCGTTTA
1 TGTTCGTTTTATTGTGTTCGTTTA
* *
638302 TGTTC-ATTTATTATGTTCGTTTA
1 TGTTCGTTTTATTGTGTTCGTTTA
* *
638325 TATTCGTTCGT-TTGTGTTCGTTTA
1 TGTTCGTT-TTATTGTGTTCGTTTA
638349 TGTTCGTTT
1 TGTTCGTTT
638358 ATCATTTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
22 14 0.22
23 30 0.46
24 20 0.31
25 1 0.02
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.65
Consensus pattern (24 bp):
TGTTCGTTTTATTGTGTTCGTTTA
Found at i:638301 original size:13 final size:12
Alignment explanation
Indices: 638277--638359 Score: 70
Period size: 10 Copynumber: 7.1 Consensus size: 12
638267 TTGTGTTTGT
638277 TTTGTTCGTTTA
1 TTTGTTCGTTTA
638289 TTGTGTTCGTTTA
1 TT-TGTTCGTTTA
*
638302 --TGTTCATTTA
1 TTTGTTCGTTTA
638312 TTATGTTCGTTTA
1 TT-TGTTCGTTTA
638325 TATTCGTTCG-TT-
1 T-TT-GTTCGTTTA
*
638337 TGTGTTCGTTTA
1 TTTGTTCGTTTA
638349 --TGTTCGTTTA
1 TTTGTTCGTTTA
638359 T
1 T
638360 CATTTAAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
10 24 0.41
11 3 0.05
12 3 0.05
13 23 0.39
14 6 0.10
ACGTcount: A:0.11, C:0.10, G:0.18, T:0.61
Consensus pattern (12 bp):
TTTGTTCGTTTA
Found at i:638347 original size:24 final size:23
Alignment explanation
Indices: 638267--638359 Score: 118
Period size: 23 Copynumber: 4.0 Consensus size: 23
638257 GTTTGTTTTT
*
638267 TTGTGTTTGTTT-TGTTCGTTTA
1 TTGTGTTCGTTTATGTTCGTTTA
*
638289 TTGTGTTCGTTTATGTTCATTTA
1 TTGTGTTCGTTTATGTTCGTTTA
* *
638312 TTATGTTCGTTTATATTCGTTCGT-
1 TTGTGTTCGTTTATGTTCGTT--TA
638336 TTGTGTTCGTTTATGTTCGTTTA
1 TTGTGTTCGTTTATGTTCGTTTA
638359 T
1 T
638360 CATTTAAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.20
23 28 0.47
24 19 0.32
25 1 0.02
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.62
Consensus pattern (23 bp):
TTGTGTTCGTTTATGTTCGTTTA
Found at i:655430 original size:23 final size:23
Alignment explanation
Indices: 655390--655433 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
655380 AAATAATTAA
*
655390 AATAACTAAAAAATAATTGCATT
1 AATAACTAAAAAAAAATTGCATT
655413 AATAA-TAAAACAAAAATTGCA
1 AATAACTAAAA-AAAAATTGCA
655434 CGTGTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.61, C:0.09, G:0.05, T:0.25
Consensus pattern (23 bp):
AATAACTAAAAAAAAATTGCATT
Found at i:664208 original size:15 final size:14
Alignment explanation
Indices: 664182--664228 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
664172 TATGATAACA
664182 ATTTATTCAATATT
1 ATTTATTCAATATT
664196 ATTTATGTCAATATT
1 ATTTAT-TCAATATT
*
664211 A-TTATTAAAATATT
1 ATTTATT-CAATATT
664225 ATTT
1 ATTT
664229 CTACAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.03
14 17 0.59
15 11 0.38
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (14 bp):
ATTTATTCAATATT
Found at i:664435 original size:15 final size:16
Alignment explanation
Indices: 664404--664436 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
664394 TAATGATTAA
*
664404 ATAAAATTTATTTTAT
1 ATAAAAATTATTTTAT
664420 ATAAAAATTA-TTTAT
1 ATAAAAATTATTTTAT
664435 AT
1 AT
664437 TTTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAAAAATTATTTTAT
Found at i:664541 original size:17 final size:16
Alignment explanation
Indices: 664521--664552 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
664511 TTAAAAATAT
664521 TAATTAATATATTTTAA
1 TAATTAATAT-TTTTAA
664538 TAATTAATATTTTTA
1 TAATTAATATTTTTA
664553 TTAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTAATATTTTTAA
Found at i:672155 original size:15 final size:15
Alignment explanation
Indices: 672132--672164 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
672122 CTTGTTTTCA
672132 TTTGCCGCCCAAATG
1 TTTGCCGCCCAAATG
*
672147 TTTGTCGCCCAAATG
1 TTTGCCGCCCAAATG
672162 TTT
1 TTT
672165 CCCAACTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (15 bp):
TTTGCCGCCCAAATG
Found at i:679812 original size:16 final size:16
Alignment explanation
Indices: 679791--679826 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
679781 GTCCCAAAAT
679791 GTTACCTTTTTATAGA
1 GTTACCTTTTTATAGA
679807 GTTACCTTTTTATAGA
1 GTTACCTTTTTATAGA
679823 GTTA
1 GTTA
679827 TCAGGATCCT
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:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (16 bp):
GTTACCTTTTTATAGA
Found at i:681419 original size:82 final size:82
Alignment explanation
Indices: 681054--681421 Score: 452
Period size: 82 Copynumber: 4.4 Consensus size: 82
681044 TAGGCCAAAT
* * *
681054 AATAGTGGTGCATTATCATCTTCTGTAATTTTTCAGAGGTCATTCAATGCATAATTTAAACAATT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
**
681119 TTTCAGAAAAAAAAAAGTGA
66 TTTCAG---AAAACGAGTGA
* * *
681139 AATTGTGGTGCATCATCATCTTCTGTAACTTTTTCAGAGGTCATTCAATGCATAATTTAAACAAC
1 AATAGTGGTGCATTATCATCTTCTGCAAC-TTTTCAGAGGTCATTCAATGCATAATTTAAACAAC
*
681204 TTTTCAGAAAACGAATGA
65 TTTTCAGAAAACGAGTGA
* * * * *
681222 AATAGTGGCGCATTATCATTTTCTGCAACTTTTTAGATGTCATTTAATGCATAATTTAAACAACT
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
* *
681287 TTTCAGAAAACGGGTAA
66 TTTCAGAAAACGAGTGA
* * * *
681304 AATAGTAGTGCATTATCATCTTCTGCAACTTTTCAGATGTCATTCAATGCATAATTTAAATAACA
1 AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
* *
681369 TTTCAGACAATGAGTGA
66 TTTCAGAAAACGAGTGA
* *
681386 AATAGT-G-GCATCGTATCATCTTCAGAAACTTTTCAG
1 AATAGTGGTGCAT--TATCATCTTCTGCAACTTTTCAG
681422 TGATGTATCA
Statistics
Matches: 249, Mismatches: 31, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
80 4 0.02
81 1 0.00
82 145 0.58
83 32 0.13
85 26 0.10
86 41 0.16
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (82 bp):
AATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACT
TTTCAGAAAACGAGTGA
Found at i:687200 original size:12 final size:12
Alignment explanation
Indices: 687183--687207 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
687173 GTTTTTAAGA
687183 GAAGATAATGAG
1 GAAGATAATGAG
687195 GAAGATAATGAG
1 GAAGATAATGAG
687207 G
1 G
687208 GTGACAGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (12 bp):
GAAGATAATGAG
Found at i:688332 original size:20 final size:20
Alignment explanation
Indices: 688307--688354 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
688297 TGGGAAAATC
688307 GCAACGCGATACTGACTTTG
1 GCAACGCGATACTGACTTTG
688327 GCAACGCGATACTGACTTTG
1 GCAACGCGATACTGACTTTG
688347 GCAACGCG
1 GCAACGCG
688355 TTGCAATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (20 bp):
GCAACGCGATACTGACTTTG
Found at i:689708 original size:18 final size:18
Alignment explanation
Indices: 689687--689734 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
689677 TCCACTTCGG
689687 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
689705 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
689723 GAGCCATCACCT
1 GAGCCATCACCT
689735 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:690329 original size:19 final size:20
Alignment explanation
Indices: 690275--690330 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
690265 TAGTTTACTT
* *
690275 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
690295 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
690315 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
690331 AAATCACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:690356 original size:33 final size:33
Alignment explanation
Indices: 690314--690400 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
690304 GGAAATGGCT
690314 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
690347 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
* *
690380 ATCTCAACGCGAAATGAAAAT
1 ATCGCAATGCGAAATGAAAAT
690401 TGCAATGCGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.49, C:0.21, G:0.16, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGACAAA
Found at i:690368 original size:19 final size:19
Alignment explanation
Indices: 690314--690410 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
690304 GGAAATGGCT
690314 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
690333 ATCACAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
690347 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
690366 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
690380 ATCTCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
690399 ATTGCAATGCGA
1 ATCGCAATGCGA
690411 TTTGTGTTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 20
0.66 0.11 0.23
Matches are distributed among these distances:
14 18 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 28 0.48
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:690454 original size:33 final size:33
Alignment explanation
Indices: 690417--690497 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
690407 GCGATTTGTG
***
690417 TTTCGCGTTGCGATTTTGTCGTTACGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTACGATAGCCA
** *
690450 TTTCGTATTGCGATTTTGTCGTTGCGATAGCCA
1 TTTCGCGTTGCGATTTTGTCGTTACGATAGCCA
690483 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
690498 AGTCATTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 30 0.77
34 9 0.23
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.44
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTACGATAGCCA
Found at i:690492 original size:20 final size:20
Alignment explanation
Indices: 690469--690516 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
690459 GCGATTTTGT
690469 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATAGCCATTTCCG
* *
690489 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGCCATTTCCG
690509 CGTTGCGA
1 CGTTGCGA
690517 AAGTAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTCCG
Found at i:690527 original size:20 final size:20
Alignment explanation
Indices: 690487--690542 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
690477 TAGCCATTTC
* * *
690487 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
690507 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
690527 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
690543 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:692412 original size:14 final size:14
Alignment explanation
Indices: 692378--692416 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
692368 TTGATTGTTT
692378 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
692392 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
692406 TGTTGATTTGT
1 AATTGATTTGT
692417 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:694949 original size:12 final size:12
Alignment explanation
Indices: 694934--694958 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
694924 TTTTCGGGGA
694934 CTTTTTCTTCTT
1 CTTTTTCTTCTT
694946 CTTTTTCTTCTT
1 CTTTTTCTTCTT
694958 C
1 C
694959 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:695172 original size:24 final size:24
Alignment explanation
Indices: 695145--695191 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
695135 CAAAATCCGA
*
695145 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
695169 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
695192 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:695200 original size:24 final size:24
Alignment explanation
Indices: 695149--695200 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
695139 ATCCGAGTAT
* ** *
695149 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
695173 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
695197 TGAC
1 TGAC
695201 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:695954 original size:20 final size:20
Alignment explanation
Indices: 695933--696077 Score: 227
Period size: 20 Copynumber: 7.2 Consensus size: 20
695923 TGTATTATCT
* *
695933 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
695953 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
695973 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
695993 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
696013 CATTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
696033 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
* *
696053 CGTTGCGAAAGTCAGTATTG
1 CGTTGCGAAAGTCAGAATCG
696073 CGTTG
1 CGTTG
696078 ATATTTTGTA
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 119 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:696119 original size:20 final size:20
Alignment explanation
Indices: 695935--696142 Score: 175
Period size: 20 Copynumber: 10.3 Consensus size: 20
695925 TATTATCTCG
* * *
695935 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGTATCGCA
* * *
695955 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCAGTATCGCA
* * *
695975 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCAGTATCGCA
* *
695995 TTGCGAAAGTCAGAATCGCA
1 TTGCGATAGTCAGTATCGCA
* *
696015 TTGCGAAAGTCAGTATCGCG
1 TTGCGATAGTCAGTATCGCA
* *
696035 TTGCGAAAGTCAGTATCGCG
1 TTGCGATAGTCAGTATCGCA
* * *
696055 TTGCGAAAGTCAGTATTGCG
1 TTGCGATAGTCAGTATCGCA
** * * *
696075 TTGATATTTTGT-ATTATCGCG
1 TTGCGA--TAGTCAGTATCGCA
*
696096 TTGCGATAGTCAGTGTCGCA
1 TTGCGATAGTCAGTATCGCA
696116 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
696136 TTGCGAT
1 TTGCGAT
696143 TTTCCAAATT
Statistics
Matches: 166, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
19 3 0.02
20 150 0.90
21 11 0.07
22 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCA
Found at i:696142 original size:40 final size:40
Alignment explanation
Indices: 695928--696141 Score: 232
Period size: 40 Copynumber: 5.3 Consensus size: 40
695918 GATTCTGTAT
* * * *
695928 TATCTCGTTGCGATAGTCAGAATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAG
* *
695968 AATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAG
* *
696008 AATCGCATTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAG
* ** ** *
696048 TATCGCGTTGCGAAAGTCAGTATTGCGTTGATATTTTGT-AT
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGA--AAGTCAG
* * * *
696089 TATCGCGTTGCGATAGTCAGTGTCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAG
*
696129 TATCGCATTGCGA
1 TATCGCGTTGCGA
696142 TTTTCCAAAT
Statistics
Matches: 148, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
39 3 0.02
40 115 0.78
41 28 0.19
42 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (40 bp):
TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAG
Found at i:696163 original size:61 final size:60
Alignment explanation
Indices: 695969--696162 Score: 210
Period size: 61 Copynumber: 3.2 Consensus size: 60
695959 GAAAGTCAGA
* * *** *
695969 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTCAAT
* * ** * *
696029 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATTGCGTTGATATTTTGTATT
1 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT-CAAT
* * * *
696090 ATCGCGTTGCGATAGTCAGTGTCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAA-
1 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT-CAAT
696150 ATTCGCGTTGCGA
1 A-TCGCGTTGCGA
696163 TTTACTTATT
Statistics
Matches: 110, Mismatches: 22, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
60 48 0.44
61 62 0.56
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (60 bp):
ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTCAAT
Found at i:696224 original size:21 final size:22
Alignment explanation
Indices: 696172--696224 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
696162 ATTTACTTAT
696172 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
696193 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
*
696214 TTGCATTGCGA
1 TCGCATTGCGA
696225 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:696540 original size:20 final size:20
Alignment explanation
Indices: 696515--696554 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
696505 TTTATATCTA
*
696515 AGTGA-TAAATGTACAAAAAT
1 AGTGATTAAATATA-AAAAAT
696535 AGTGATTAAATATAAAAAAT
1 AGTGATTAAATATAAAAAAT
696555 TTAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (20 bp):
AGTGATTAAATATAAAAAAT
Found at i:696553 original size:21 final size:20
Alignment explanation
Indices: 696515--696553 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
696505 TTTATATCTA
* *
696515 AGTGATAAATGTACAAAAAT
1 AGTGATAAATATAAAAAAAT
696535 AGTGATTAAATATAAAAAA
1 AGTGA-TAAATATAAAAAA
696554 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
AGTGATAAATATAAAAAAAT
Found at i:702610 original size:183 final size:183
Alignment explanation
Indices: 702410--703041 Score: 858
Period size: 183 Copynumber: 3.5 Consensus size: 183
702400 ATGTATGCAT
* * ** * * *
702410 AACAATATATCAGGTAAAAATATGAGAAAACCGGGCTCAATATGACAAAATCGGTAAAACGCTAC
1 AACAATATAACAGGTAAAAATATGAAAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTAC
* * * *
702475 CAGATATGTTGAAAGTATTGA-AATGATTGAAATAAGTATAGACACTTTTGGAATTTTAAAA-AA
66 CAGATATGTTGAAAGTATCGATTA-CATTGAAATAAGTATCGACACTTTTGGAA-TTTAAAAGAA
* *
702538 AAGTAGTACTAGCGCCTAAAAAGTATCAATAATTTATAAAAATGTATCGATACAC
129 AAGTAGTACTAGAGCCTAAAAAGTATCGATAATTTATAAAAATGTATCGATACAC
* * *
702593 AACAATATAACAGGTAAAAATATGATAAAACCGGTTTCATTATGACAAAACCAGTAAAGTGCTAC
1 AACAATATAACAGGTAAAAATATGAAAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTAC
* * *
702658 CGGATATGTTGAAAGTATCGATTACATTTAAATAAGTATCGACACTTTTGGAATTTAAAATAAAA
66 CAGATATGTTGAAAGTATCGATTACATTGAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAA
*
702723 GTAGTACTAGAGCCTAAAAAGTATCGATAATTTATAAAAATGTATCAATACAC
131 GTAGTACTAGAGCCTAAAAAGTATCGATAATTTATAAAAATGTATCGATACAC
* *
702776 AACAATATAACATGT-AAAATATGATAAAAATCGGTTTCATTATTG-CAAAACCGGTAAAGCGCT
1 AACAATATAACAGGTAAAAATATGA-AAAAACCGGTTTCATTA-TGACAAAACCGGTAAAGCGCT
* * *
702839 ACCGGATATGTTGAAAGTACCGATTCCATTGAAATAAGTATCGACACTTTTGGAATTTAAAAGAA
64 ACCAGATATGTTGAAAGTATCGATTACATTGAAATAAGTATCGACACTTTTGGAATTTAAAAGAA
** * * * * * *
702904 AAACAGTAATAGTGTCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCAC
129 AAGTAGTACTAGAGCCTAAAAAGTATCGATAATTTATAAAAATGTATCGATACAC
* * * *
702959 AATAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGATAAAGCGCTAC
1 AACAATATAACAGGTAAAAATATGAAAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTAC
*
703024 CAGATATGTTGAATGTAT
66 CAGATATGTTGAAAGTAT
703042 GGATACTTTA
Statistics
Matches: 398, Mismatches: 45, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
182 18 0.05
183 368 0.92
184 12 0.03
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (183 bp):
AACAATATAACAGGTAAAAATATGAAAAAACCGGTTTCATTATGACAAAACCGGTAAAGCGCTAC
CAGATATGTTGAAAGTATCGATTACATTGAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAA
GTAGTACTAGAGCCTAAAAAGTATCGATAATTTATAAAAATGTATCGATACAC
Found at i:708422 original size:39 final size:39
Alignment explanation
Indices: 708363--709112 Score: 1108
Period size: 39 Copynumber: 19.3 Consensus size: 39
708353 AATTTCTTAT
708363 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
*
708402 AAAATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
708441 AAAATCTTCTGTTTTGAGGGAAACTATCTCTAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
*
708480 AAAATCTTCTGTTTCGAGGGAAACTATCTTAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
*
708519 AAAATCTTCTGTTTTGAGGGAAACTATCTCAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
708558 AAAATCTTCTGTTTCTA-GGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
*
708596 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
708635 AAAATCTTTTGTTTCGAGGGAAACTATCTCAAGC-ACGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGA-GAC
708674 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
708713 AAAATCTTATGTTTCGAGGGAAACTATCTCTAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* * *
708752 AAAATCTTCTATTTTGAGGGAAACTATCTCAAACGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* * *
708791 AAAATCTTTTGTTTCGAGGGATACTATCTCAAGTGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
708830 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* * *
708869 AAAATCTTATGTTTCTAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
708908 AAAATCTTCTGTTTCGAGGGAAACTATCTAAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* *
708947 AAAATCTTCTATTTCGAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
*
708986 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
** * * ** * * *
709025 AAAAAATTTTGTTTCAAATGAAAATATCTCAAGTGAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
* * * * * *
709064 AAAATTTTATGTTTCAAGTGAAACTATCTCAAGCAAGAT
1 AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
709103 AAAATCTTCT
1 AAAATCTTCT
709113 TTTTAAAAAA
Statistics
Matches: 650, Mismatches: 58, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
38 37 0.06
39 612 0.94
40 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (39 bp):
AAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGAC
Found at i:715297 original size:20 final size:19
Alignment explanation
Indices: 715270--715309 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
715260 GAACCTAGAG
715270 CCTCTAAAATGACCCTAAA
1 CCTCTAAAATGACCCTAAA
*
715289 CCTCTTAAAATTACCCTAAA
1 CCTC-TAAAATGACCCTAAA
715309 C
1 C
715310 TGCTCGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.25
Consensus pattern (19 bp):
CCTCTAAAATGACCCTAAA
Found at i:717093 original size:199 final size:200
Alignment explanation
Indices: 716602--717426 Score: 1312
Period size: 200 Copynumber: 4.1 Consensus size: 200
716592 CAAACATGTA
* * *
716602 TCAACACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCAATCATTATAAAGTAATAGGT
1 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * * ** * *
716667 AAATTTACAATGTAACCGGTAAAACTATATCGGCCTTATGATAGAATAGGTCAACATAATATATC
66 AAATTTACAATGTAACCGGTAAAAATATACCAGTTTTATGACAGAATAGGTCAACATAATGTATC
* **
716732 GATACTTTTTAAATTTGTGTCGATACTTTTGGTCTAGAATGAATGCCCAACGAGGTGCACGTATA
131 GATACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATA
716797 AAGTG
196 AAGTG
*
716802 TCAATACGTTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
1 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
716867 AAATTTACAATGTAACCGGTAAAAATATACCAGTTTTATGACAGAATAGGTCAACATAATGTATC
66 AAATTTACAATGTAACCGGTAAAAATATACCAGTTTTATGACAGAATAGGTCAACATAATGTATC
* * * *
716932 AATACATTTTACATTTGTGTCGATACTTTTGGTCCAGAATAAATGCCCAACGAGGT-CACACATA
131 GATACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATA
716996 AAGTG
196 AAGTG
* *
717001 TCGATACATTTATTGTAAGTATCAATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
1 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * * *
717066 AAATTTACAATGTAACTGGTCAAAATATACCAGTTTTATAACAGAATAGGTCAACATAATGTATT
66 AAATTTACAATGTAACCGGTAAAAATATACCAGTTTTATGACAGAATAGGTCAACATAATGTATC
* * *
717131 GATACTTTTTACATTTGTGTTGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATA
131 GATACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATA
717196 AAGTG
196 AAGTG
*
717201 TCAATATATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
1 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
717266 AAATTTACAATGTAACCGGTAAAAATATACC-GATTTTATGACAGAATAGGTCAACATAATGTAT
66 AAATTTACAATGTAACCGGTAAAAATATACCAG-TTTTATGACAGAATAGGTCAACATAATGTAT
* * * * *
717330 CGATACTTTTTAAATTTATGTCGATACATTTGGTCCAAAATGAATCCCCAACTAGGTGCACACAT
130 CGATACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACAT
717395 AAAGTG
195 AAAGTG
* *
717401 TCGATACATTTATTGTAATTATCGAT
1 TCAATACATTTATTGTAAGTATCGAT
717427 GCATAATGAT
Statistics
Matches: 575, Mismatches: 48, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
199 187 0.33
200 388 0.67
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (200 bp):
TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
AAATTTACAATGTAACCGGTAAAAATATACCAGTTTTATGACAGAATAGGTCAACATAATGTATC
GATACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACACATA
AAGTG
Found at i:717354 original size:399 final size:400
Alignment explanation
Indices: 716607--717423 Score: 1343
Period size: 399 Copynumber: 2.0 Consensus size: 400
716597 ATGTATCAAC
* *
716607 ACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCAATCATTATAAAGTAATAGGTAAATT
1 ACATTTATTGTAAGTATCAATCCCAAAAACATCGAAACCAATAATTATAAAGTAATAGGTAAATT
* * * *
716672 TACAATGTAACCGGTAAAACTATATCGGCCTTATGATAGAATAGGTCAACATAATATATCGATAC
66 TACAATGTAACCGGTAAAACTATACCAGCCTTATAACAGAATAGGTCAACATAATATATCGATAC
* *
716737 TTTTTAAATTTGTGTCGATACTTTTGGTCTAGAATGAATGCCCAACGAGGTGCACGTATAAAGTG
131 TTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTG
*
716802 TCAATACGTTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
196 TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
716867 AAATTTACAATGTAACCGGTAAAAATATACCAGTTTTATGACAGAATAGGTCAACATAATGTATC
261 AAATTTACAATGTAACCGGTAAAAATATACCAGTTTTATGACAGAATAGGTCAACATAATGTATC
* * * * *
716932 AATACATTTTACATTTGTGTCGATACTTTTGGTCCAGAATAAATGCCCAACGAGGT-CACACATA
326 AATACATTTTAAATTTATGTCGATACATTTGGTCCAAAATAAATCCCCAACGAGGTGCACACATA
716996 AAGTGTCGAT
391 AAGTGTCGAT
*
717006 ACATTTATTGTAAGTATCAATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATT
1 ACATTTATTGTAAGTATCAATCCCAAAAACATCGAAACCAATAATTATAAAGTAATAGGTAAATT
* ** * *
717071 TACAATGTAACTGGTCAAAA-TATACCAGTTTTATAACAGAATAGGTCAACATAATGTATTGATA
66 TACAATGTAACCGGT-AAAACTATACCAGCCTTATAACAGAATAGGTCAACATAATATATCGATA
* *
717135 CTTTTTACATTTGTGTTGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGT
130 CTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGT
*
717200 GTCAATATATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGG
195 GTCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGG
717265 TAAATTTACAATGTAACCGGTAAAAATATACC-GATTTTATGACAGAATAGGTCAACATAATGTA
260 TAAATTTACAATGTAACCGGTAAAAATATACCAG-TTTTATGACAGAATAGGTCAACATAATGTA
* * * *
717329 TCGATACTTTTTAAATTTATGTCGATACATTTGGTCCAAAATGAATCCCCAACTAGGTGCACACA
324 TCAATACATTTTAAATTTATGTCGATACATTTGGTCCAAAATAAATCCCCAACGAGGTGCACACA
717394 TAAAGTGTCGAT
389 TAAAGTGTCGAT
*
717406 ACATTTATTGTAATTATC
1 ACATTTATTGTAAGTATC
717424 GATGCATAAT
Statistics
Matches: 387, Mismatches: 28, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
398 1 0.00
399 347 0.90
400 39 0.10
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (400 bp):
ACATTTATTGTAAGTATCAATCCCAAAAACATCGAAACCAATAATTATAAAGTAATAGGTAAATT
TACAATGTAACCGGTAAAACTATACCAGCCTTATAACAGAATAGGTCAACATAATATATCGATAC
TTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTG
TCAATACATTTATTGTAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
AAATTTACAATGTAACCGGTAAAAATATACCAGTTTTATGACAGAATAGGTCAACATAATGTATC
AATACATTTTAAATTTATGTCGATACATTTGGTCCAAAATAAATCCCCAACGAGGTGCACACATA
AAGTGTCGAT
Found at i:718798 original size:17 final size:16
Alignment explanation
Indices: 718771--718808 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
718761 AATTTACAAT
718771 TAATTTAAATAATATC
1 TAATTTAAATAATATC
718787 TAATTGTAAATAATATC
1 TAATT-TAAATAATATC
718804 TAATT
1 TAATT
718809 AATTTGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (16 bp):
TAATTTAAATAATATC
Found at i:718948 original size:9 final size:9
Alignment explanation
Indices: 718934--718958 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
718924 ATATTTAAAG
718934 GTTAATTCA
1 GTTAATTCA
718943 GTTAATTCA
1 GTTAATTCA
718952 GTTAATT
1 GTTAATT
718959 AACCGATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (9 bp):
GTTAATTCA
Found at i:719636 original size:2 final size:2
Alignment explanation
Indices: 719629--719666 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
719619 AAATGTATCG
719629 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
719667 TCCATACTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:720485 original size:164 final size:157
Alignment explanation
Indices: 720136--720546 Score: 518
Period size: 164 Copynumber: 2.6 Consensus size: 157
720126 ATCAACTTTG
* * * * * **
720136 ATAATACGCAACCTATTACGTTACATAAGTGCTACCTAATATGTTATTATGCTTGATAATGTTTC
1 ATAA-ACGCTACCTATTACGTTATATAAGCGCTA-CTAATATGTTATTGTGCTTGATAATATTAA
* *
720201 CAGTAATTAACCGGTTATGTTATCATTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAA
64 CAGTAATTAACCGGTTATGTTATCATTAGTAACATTTTAGACGTTTACCTAATATGTTGTAATAA
720266 CAAATTAAGTAATTAACCTATTTTATTAT
129 CAAATTAAGTAATTAACCTATTTTATTAT
* * * *
720295 ATAAGCGCTGCCTATTACGTTATATAAGCGCTACTTAAAATGCTATTGTGCTTGATAATATTAAC
1 ATAAACGCTACCTATTACGTTATATAAGCGCTAC-TAATATGTTATTGTGCTTGATAATATTAAC
* *
720360 GGTAATTAACCGGTTATGTTATCCTTAGTAACATTTTAGACGTTTACC-AATATGTTGGGGATTG
65 AGTAATTAACCGGTTATGTTATCATTAGTAACATTTTAGACGTTTACCTAATA---T---G-TTG
*
720424 TAATAACAAATTTAGTAATTAACCTATTTTATTAT
123 TAATAACAAATTAAGTAATTAACCTATTTTATTAT
* * ** * *
720459 ATAAATGTTACCTATTACGTTATATAAGCATTAACTAATATGTTATTGTGTTTAATAATATTAAC
1 ATAAACGCTACCTATTACGTTATATAAGCGCT-ACTAATATGTTATTGTGCTTGATAATATTAAC
720524 AGTAATTAACCGGTTATGTTATC
65 AGTAATTAACCGGTTATGTTATC
720547 GTCTATATTT
Statistics
Matches: 216, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
157 5 0.02
158 92 0.43
159 4 0.02
160 1 0.00
163 1 0.00
164 111 0.51
165 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (157 bp):
ATAAACGCTACCTATTACGTTATATAAGCGCTACTAATATGTTATTGTGCTTGATAATATTAACA
GTAATTAACCGGTTATGTTATCATTAGTAACATTTTAGACGTTTACCTAATATGTTGTAATAACA
AATTAAGTAATTAACCTATTTTATTAT
Found at i:722925 original size:21 final size:21
Alignment explanation
Indices: 722901--722940 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
722891 TTCCTGCACC
*
722901 ACTTATTTA-ATATCCTTTTAT
1 ACTTATCTATATA-CCTTTTAT
722922 ACTTATCTATATACCTTTT
1 ACTTATCTATATACCTTTT
722941 CCTTGGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATCTATATACCTTTTAT
Found at i:723253 original size:12 final size:13
Alignment explanation
Indices: 723231--723260 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
723221 TCCAAAGCAA
723231 TTCTCTCATCTTC
1 TTCTCTCATCTTC
723244 TTCT-TCATCTTC
1 TTCTCTCATCTTC
723256 TTCTC
1 TTCTC
723261 CCAACGTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.57
Consensus pattern (13 bp):
TTCTCTCATCTTC
Found at i:724374 original size:22 final size:18
Alignment explanation
Indices: 724330--724402 Score: 101
Period size: 18 Copynumber: 3.8 Consensus size: 18
724320 AGGGTTATGA
724330 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGATAT
724348 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGG--ATAT
*
724368 ACAGTGGTCCTTCGTGATAT
1 --AGTGGTCCTTCGGGATAT
724388 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
724403 CAAATATTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
18 28 0.57
20 8 0.16
22 13 0.27
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGGATAT
Found at i:725013 original size:22 final size:22
Alignment explanation
Indices: 724985--725027 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
724975 GTAGCAGTAC
724985 TGTAGCAGGGGAATCGATTCCA
1 TGTAGCAGGGGAATCGATTCCA
*
725007 TGTAGCAGGGGAATCGGTTCC
1 TGTAGCAGGGGAATCGATTCC
725028 CTATTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (22 bp):
TGTAGCAGGGGAATCGATTCCA
Found at i:725627 original size:18 final size:18
Alignment explanation
Indices: 725600--725652 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
725590 ACTGTATATT
725600 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
725618 TGTCCAGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
725636 TGTCCCGAAGGACCACT
1 TGTCCCGAATGACCACT
725653 CCTTAAGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:728782 original size:29 final size:29
Alignment explanation
Indices: 728749--728914 Score: 191
Period size: 29 Copynumber: 5.9 Consensus size: 29
728739 ACCCGACCTG
* *
728749 GTGACATTCTGTG-AATTTTTGTGAAAAAT
1 GTGACATTCTGGGAAATATTT-TGAAAAAT
728778 GTGACATTCTGGGAAATATTTTG-AAAA-
1 GTGACATTCTGGGAAATATTTTGAAAAAT
*
728805 -TGACATTCTAGGAAATATTTTGAAAAAT
1 GTGACATTCTGGGAAATATTTTGAAAAAT
* *
728833 GTGACATTCTGGGAAATATTTTGAAAGAG
1 GTGACATTCTGGGAAATATTTTGAAAAAT
* * *
728862 GTGACATTCTGGGAATTATTTAGAAAGAAA
1 GTGACATTCTGGGAAATATTTTGAAA-AAT
*
728892 GTGACATT-TTGGAAAT-TTTTGAA
1 GTGACATTCTGGGAAATATTTTGAA
728915 TGTGGACTAT
Statistics
Matches: 119, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
26 21 0.18
27 4 0.03
28 10 0.08
29 69 0.58
30 15 0.13
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (29 bp):
GTGACATTCTGGGAAATATTTTGAAAAAT
Found at i:728834 original size:55 final size:57
Alignment explanation
Indices: 728749--728914 Score: 200
Period size: 55 Copynumber: 2.9 Consensus size: 57
728739 ACCCGACCTG
*
728749 GTGACATTCT-GTG-AATTTTTGTGAAAAATGTGACATTCTGGGAAATATTTTGAAA-A
1 GTGACATTCTAG-GAAATATTT-TGAAAAATGTGACATTCTGGGAAATATTTTGAAAGA
728805 -TGACATTCTAGGAAATATTTTGAAAAATGTGACATTCTGGGAAATATTTTGAAAGA
1 GTGACATTCTAGGAAATATTTTGAAAAATGTGACATTCTGGGAAATATTTTGAAAGA
* * * * *
728861 GGTGACATTCTGGGAATTATTTAGAAAGAAAGTGACATT-TTGGAAAT-TTTTGAA
1 -GTGACATTCTAGGAAATATTTTGAAA-AATGTGACATTCTGGGAAATATTTTGAA
728915 TGTGGACTAT
Statistics
Matches: 98, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
55 44 0.45
56 8 0.08
57 7 0.07
58 29 0.30
59 10 0.10
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (57 bp):
GTGACATTCTAGGAAATATTTTGAAAAATGTGACATTCTGGGAAATATTTTGAAAGA
Found at i:736232 original size:19 final size:19
Alignment explanation
Indices: 736208--736291 Score: 114
Period size: 19 Copynumber: 4.4 Consensus size: 19
736198 CGGTCCAAAT
* *
736208 CGGTCTGAACCGGTTTAAC
1 CGGTCTGAACCGGGTTGAC
*
736227 CGGTCTGAACCGGTTTGAC
1 CGGTCTGAACCGGGTTGAC
*
736246 CGGTCCGAACCGGGTTGAC
1 CGGTCTGAACCGGGTTGAC
* *
736265 CGGTCCGAACCGGGCTGAC
1 CGGTCTGAACCGGGTTGAC
736284 CGGTCTGA
1 CGGTCTGA
736292 CCTGACCCGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 60 1.00
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (19 bp):
CGGTCTGAACCGGGTTGAC
Found at i:736311 original size:13 final size:12
Alignment explanation
Indices: 736289--736332 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
736279 CTGACCGGTC
*
736289 TGACCTGACCCG
1 TGACCCGACCCG
736301 TTGACCCGACCCG
1 -TGACCCGACCCG
736314 TGACCCGA-CC-
1 TGACCCGACCCG
736324 TGACCCGAC
1 TGACCCGAC
736333 TCGGTGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 8 0.28
11 2 0.07
12 8 0.28
13 11 0.38
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (12 bp):
TGACCCGACCCG
Found at i:736389 original size:29 final size:29
Alignment explanation
Indices: 736357--736487 Score: 142
Period size: 29 Copynumber: 4.5 Consensus size: 29
736347 TGAATTTTTG
736357 TGAAAAATGTGACATACTAGGAAATATTT
1 TGAAAAATGTGACATACTAGGAAATATTT
* * *
736386 TGAAAAAGGTGATATTA-TGGGAAATATTT
1 TGAAAAATGTGACA-TACTAGGAAATATTT
*
736415 TG-AAAATAGTGACATTCTAGGAAATATTT
1 TGAAAAAT-GTGACATACTAGGAAATATTT
* *
736444 TGAAAAATGTGAAATTCT-GCGAAATATTT
1 TGAAAAATGTGACATACTAG-GAAATATTT
* *
736473 TGAAAGAGGTGACAT
1 TGAAAAATGTGACAT
736488 TTTGAAAATT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
28 6 0.07
29 73 0.85
30 7 0.08
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (29 bp):
TGAAAAATGTGACATACTAGGAAATATTT
Found at i:736488 original size:58 final size:58
Alignment explanation
Indices: 736360--736477 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 58
736350 ATTTTTGTGA
* * *
736360 AAAAT-GTGACATACTAGGAAATATTTTGAAAAAGGTGATATTATGGGAAATATTTTG
1 AAAATAGTGACATTCTAGGAAATATTTTGAAAAAGGTGAAATTATGCGAAATATTTTG
* *
736417 AAAATAGTGACATTCTAGGAAATATTTTGAAAAATGTGAAATTCTGCGAAATATTTTG
1 AAAATAGTGACATTCTAGGAAATATTTTGAAAAAGGTGAAATTATGCGAAATATTTTG
736475 AAA
1 AAA
736478 GAGGTGACAT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 5 0.09
58 50 0.91
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (58 bp):
AAAATAGTGACATTCTAGGAAATATTTTGAAAAAGGTGAAATTATGCGAAATATTTTG
Found at i:738264 original size:19 final size:20
Alignment explanation
Indices: 738225--738264 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
738215 GTTAGTTAGC
**
738225 AAAAATAATATTTTTTTATA
1 AAAAATAATATTTTTAGATA
738245 AAAAATAATA-TTTTAGATA
1 AAAAATAATATTTTTAGATA
738264 A
1 A
738265 TATTTTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAAATAATATTTTTAGATA
Found at i:738306 original size:12 final size:12
Alignment explanation
Indices: 738289--738313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
738279 TATTAAAAAA
738289 TAATAATATTTT
1 TAATAATATTTT
738301 TAATAATATTTT
1 TAATAATATTTT
738313 T
1 T
738314 TAAGCGTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATAATATTTT
Found at i:740173 original size:14 final size:14
Alignment explanation
Indices: 740137--740173 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
740127 GAATATAAAC
*
740137 GAACACAAACGAAG
1 GAACATAAACGAAG
*
740151 GAACGTAAACGAAG
1 GAACATAAACGAAG
740165 GAACATAAA
1 GAACATAAA
740174 ATTAATTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.16, G:0.22, T:0.05
Consensus pattern (14 bp):
GAACATAAACGAAG
Found at i:746054 original size:63 final size:63
Alignment explanation
Indices: 745979--746099 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
745969 TCAATGAAAT
745979 AAACATCAAATGT-AATGAGTGCATCGATGCATAGGG-AGTGCATCGATACACCCATTAAAATGG
1 AAACATCAAATGTAAAT-AGTGCATCGATGCAT-GGGTAGTGCATCGATACACCCATTAAAATGG
* * * * *
746042 AAACATCGAATGTAAATTGTGTATCGATGCATGGGTAGTGCATCGATGCACCTATTAA
1 AAACATCAAATGTAAATAGTGCATCGATGCATGGGTAGTGCATCGATACACCCATTAA
746100 GGGATGCATC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 3 0.06
63 45 0.88
64 3 0.06
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (63 bp):
AAACATCAAATGTAAATAGTGCATCGATGCATGGGTAGTGCATCGATACACCCATTAAAATGG
Found at i:747131 original size:8 final size:8
Alignment explanation
Indices: 747106--747146 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
747096 TTACATGTTT
747106 TATATGATG
1 TATATG-TG
747115 ATATATGTG
1 -TATATGTG
*
747124 TATGTGTG
1 TATATGTG
747132 TATATGTG
1 TATATGTG
747140 TATATGT
1 TATATGT
747147 TACAGGAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 21 0.72
9 2 0.07
10 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (8 bp):
TATATGTG
Found at i:747218 original size:24 final size:24
Alignment explanation
Indices: 747182--747227 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
747172 TTATGACATT
747182 TGTTATGTGATATACATGAATATA
1 TGTTATGTGATATACATGAATATA
*
747206 TGTTAATGT-ATATATATGAATA
1 TGTT-ATGTGATATACATGAATA
747228 AATATCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.43
Consensus pattern (24 bp):
TGTTATGTGATATACATGAATATA
Found at i:747237 original size:24 final size:25
Alignment explanation
Indices: 747186--747237 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
747176 GACATTTGTT
* * *
747186 ATGTGATATACATGAATATATGTTA
1 ATGTGATATACATGAATAAATATCA
*
747211 ATGT-ATATATATGAATAAATATCA
1 ATGTGATATACATGAATAAATATCA
747235 ATG
1 ATG
747238 ACTCATATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (25 bp):
ATGTGATATACATGAATAAATATCA
Found at i:754660 original size:46 final size:46
Alignment explanation
Indices: 754586--754678 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
754576 AATATACCGC
* * *
754586 TATATATTTTCATTTGTGGCATCATTTCATGCCAATTATGCACTGT
1 TATACATTTTCATTTATGACATCATTTCATGCCAATTATGCACTGT
*
754632 TATACATTTTCATTTATGACATCCTTTCATGCCAATTATGCACTGT
1 TATACATTTTCATTTATGACATCATTTCATGCCAATTATGCACTGT
754678 T
1 T
754679 CTTCATCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (46 bp):
TATACATTTTCATTTATGACATCATTTCATGCCAATTATGCACTGT
Found at i:755444 original size:54 final size:54
Alignment explanation
Indices: 754965--755459 Score: 554
Period size: 54 Copynumber: 9.2 Consensus size: 54
754955 TATTAAGATA
* * * * * * *
754965 CACACGTAGTGCCTATACGGTCGTTCATCAACCTATAATGAATTCCGT-ATGTTG
1 CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGA-ATTG
* * * * * **
755019 CACACATAGTGTCTG-TACGGTTGTTCATCAACATATAATGAATTTCGTGGGTTG
1 CACACTTAGTG-CCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTG
* * * * * *
755073 CACACATAGTGCATG-TATGGTTTTTCATCAACATATGATGAATTCCATGAATTG
1 CACACTTAGTGC-CGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTG
* * *
755127 CACACATAGTACCGAAATGGTTGTTCATCAACATATGATGAATTCCGTGAA---
1 CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTG
* * *
755178 AACACATAGTGCCGAAATGGTTGTTCATCAACATATGATGAATTCCGT-AAGTTG
1 CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAA-TTG
* * *
755232 CACACTTAGTGCCAAAACGGTTGTTCATAAACATATGATGAATTCTGTGAATTG
1 CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTG
* * * * *
755286 CACACTTAGTGTCAAAACGGTTGTTCATCAACATATGATAAATTTCGTGAGTTG
1 CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTG
* * *
755340 CACACTTAGTGCCGAAAAGGTTGTTCATTAGCATATGATGAATTCCGTGAATTG
1 CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTG
*
755394 CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAATTG
1 CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTG
*
755448 TACACTTAGTGC
1 CACACTTAGTGC
755460 TTATTTGGTA
Statistics
Matches: 386, Mismatches: 46, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.01
51 46 0.12
53 2 0.01
54 333 0.86
55 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (54 bp):
CACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAATTG
Found at i:758887 original size:18 final size:19
Alignment explanation
Indices: 758828--758889 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 19
758818 GTTCTTAAGT
758828 TAATAATTTATTTATTTTT-
1 TAAT-ATTTATTTATTTTTA
*
758847 TAAT-TTTATCTTTAATTTCTA
1 TAATATTTA--TTT-ATTTTTA
758868 TAATATTT-TTTATTTTTA
1 TAATATTTATTTATTTTTA
758886 TAAT
1 TAAT
758890 TTAGTTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
17 4 0.11
18 10 0.28
19 10 0.28
20 5 0.14
21 4 0.11
22 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATATTTATTTATTTTTA
Found at i:773736 original size:22 final size:22
Alignment explanation
Indices: 773691--773736 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
773681 ACTTGTTATT
* *
773691 ATATATATAATTTTTATCATGA
1 ATATATATAATATTTATCACGA
*
773713 ATATATATAATATTTATTACGA
1 ATATATATAATATTTATCACGA
773735 AT
1 AT
773737 GTTACTTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
ATATATATAATATTTATCACGA
Found at i:773996 original size:61 final size:61
Alignment explanation
Indices: 773912--774039 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
773902 CAGGACCCTA
* *
773912 AGTGCAGGTGGTGGACACAACCTTATGTGTCATATCTGGATTAGCACTAGAGTGTAAACCT
1 AGTGCAGGTGGTGGACACAACCTTATGTGTCATATCGGGATTAGCACTAGAGCGTAAACCT
* * * * *
773973 AGTGTAGGTGGTGGGCACGACCTTATGTGTCATATCGGGATTAGCACTAGAGCGTAAGCTT
1 AGTGCAGGTGGTGGACACAACCTTATGTGTCATATCGGGATTAGCACTAGAGCGTAAACCT
774034 AGTGCA
1 AGTGCA
774040 AGTTTAGCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (61 bp):
AGTGCAGGTGGTGGACACAACCTTATGTGTCATATCGGGATTAGCACTAGAGCGTAAACCT
Found at i:774275 original size:39 final size:39
Alignment explanation
Indices: 774220--774322 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 39
774210 TTTGAAAATA
* * *
774220 TTTTTGAAAAAAATATAATATATAGTTTGTAGAATA-CGAT
1 TTTTTG-AAAAAATATAATATATACTTTGTAAAATATC-AG
* * *
774260 TTTTTGAAAACATATAATTTATACTTTTTAAAATATCAG
1 TTTTTGAAAAAATATAATATATACTTTGTAAAATATCAG
*
774299 TTTTTGAAAATATATATATATATA
1 TTTTTGAAAAAATATA-ATATATA
774323 TATATATATA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 40 0.75
40 13 0.25
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (39 bp):
TTTTTGAAAAAATATAATATATACTTTGTAAAATATCAG
Found at i:774315 original size:2 final size:2
Alignment explanation
Indices: 774308--774344 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
774298 GTTTTTGAAA
774308 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
774345 GTTTTGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:774403 original size:34 final size:34
Alignment explanation
Indices: 774332--774511 Score: 175
Period size: 35 Copynumber: 5.1 Consensus size: 34
774322 ATATATATAT
**
774332 ATATATATATATAGTTTTGAAAACAATTTTTGAAAA
1 ATATAT-TATATAGTTTTGAAAATGATTTTTG-AAA
*
774368 ATATATTATGTAGTTTTGAAAATGATTTTTGAAA
1 ATATATTATATAGTTTTGAAAATGATTTTTGAAA
* *
774402 ATATATTATATAGTTTTGAAAAATAATTTGTGGATATA
1 ATATATTATATAGTTTTG-AAAATGATTT-TTGA-A-A
*
774440 TATATATATATTATAGTTTCGAAAATGA-TTTTGAAA
1 -ATATAT-TA-TATAGTTTTGAAAATGATTTTTGAAA
* * *
774476 ATATATAATATAGTTTTTAAAA-GTTGTTTTGAAA
1 ATATATTATATAGTTTTGAAAATGAT-TTTTGAAA
774510 AT
1 AT
774512 GTACAATTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
32 1 0.01
33 12 0.10
34 31 0.25
35 37 0.30
36 10 0.08
37 2 0.02
38 4 0.03
39 8 0.07
40 8 0.07
41 9 0.07
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (34 bp):
ATATATTATATAGTTTTGAAAATGATTTTTGAAA
Found at i:774441 original size:129 final size:134
Alignment explanation
Indices: 774186--774454 Score: 308
Period size: 129 Copynumber: 2.0 Consensus size: 134
774176 GCTTATTTAG
*
774186 TATATATATTAATATAATATAGTTTTTGAAAATATTTTTGAAAAAAATATAATATATAGTTTGTA
1 TATATATATTAATATAATATAGTTTTTGAAAAAATTTTTG-AAAAAATATAATATATAGTTTGTA
* * * *
774251 GAATACGATTTTTTGAAAACATATAATTTATACTTTTTAAAATATCAGTTTTTGAAAATATATAT
65 GAAAACGATTTTTTGAAAACATATAATTTATACTTTTGAAAATATCAATTTGTGAAAATATATAT
774316 ATATA
130 ATATA
* *
774321 TATATATATATATATATATATATAG-TTTTGAAAACAATTTTTG-AAAAATATATTATGTAGTTT
1 TATATATAT-TA-ATATA-ATATAGTTTTTGAAAA-AATTTTTGAAAAAATATAATATATAGTTT
* * * *
774384 -T-GAAAATGA-TTTTTG-AAA-ATAT-ATTATATAGTTTTGAAAA-AT-AATTTGTGGATATAT
62 GTAGAAAACGATTTTTTGAAAACATATAATT-TATACTTTTGAAAATATCAATTTGTGAAAATAT
774441 ATATATATA
126 ATATATATA
774450 T-TATA
1 TATATA
774455 GTTTCGAAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
128 4 0.03
129 21 0.18
130 5 0.04
131 16 0.14
132 3 0.03
133 6 0.05
134 6 0.05
135 10 0.08
136 20 0.17
137 14 0.12
138 13 0.11
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (134 bp):
TATATATATTAATATAATATAGTTTTTGAAAAAATTTTTGAAAAAATATAATATATAGTTTGTAG
AAAACGATTTTTTGAAAACATATAATTTATACTTTTGAAAATATCAATTTGTGAAAATATATATA
TATA
Found at i:774557 original size:17 final size:17
Alignment explanation
Indices: 774517--774579 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
774507 AAAATGTACA
* *
774517 ATTTTTTTATA-TAGTT
1 ATTTATTTATATTATTT
*
774533 AGTTATTTATATTATTT
1 ATTTATTTATATTATTT
*
774550 ATTTATTTCA-CTTATTT
1 ATTTATTT-ATATTATTT
774567 ATTTTATTT-TATT
1 A-TTTATTTATATT
774580 TTTTTCGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
16 9 0.24
17 20 0.54
18 8 0.22
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTATTTATATTATTT
Found at i:775737 original size:9 final size:10
Alignment explanation
Indices: 775721--775751 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
775711 TTTAATATTT
775721 TTATTTTTCA
1 TTATTTTTCA
775731 TTA-TTTTCA
1 TTATTTTTCA
775740 TTATTTTTCA
1 TTATTTTTCA
775750 TT
1 TT
775752 TTATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (10 bp):
TTATTTTTCA
Found at i:775767 original size:25 final size:26
Alignment explanation
Indices: 775706--775770 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
775696 CAATATATTT
*
775706 TTTTATT-TAATATTTTTATTTTTCA
1 TTTTATTCTATTATTTTTATTTTTCA
775731 TTATT-TTC-ATTATTTTTCA-TTTT-A
1 TT-TTATTCTATTATTTTT-ATTTTTCA
775755 TTTTATTCTATTATTT
1 TTTTATTCTATTATTT
775771 AACATTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
23 2 0.06
24 6 0.18
25 23 0.68
26 3 0.09
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTATTCTATTATTTTTATTTTTCA
Found at i:779314 original size:3 final size:3
Alignment explanation
Indices: 779306--779346 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
779296 ATTAGGGTTA
*
779306 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAT AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
779347 AACCCTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:785360 original size:3 final size:3
Alignment explanation
Indices: 785345--785379 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
785335 TTCATTTAAA
785345 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
785380 AAAAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:786984 original size:119 final size:117
Alignment explanation
Indices: 786768--786984 Score: 249
Period size: 119 Copynumber: 1.8 Consensus size: 117
786758 TATTTATTTA
* * * * * *
786768 ATTTTTAATATCAAAGAAAAGGGCAGTCTTAATATAACTGGATGTCCTATTCTGGTATTTTAAAA
1 ATTTTTAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTTAAAA
*
786833 TTAAATATTATAAAAAAATTATAATTTATTTTTATTTAAATTATTATATTAAT
66 ATAAATATTATAAAAAAATTAT-ATTTATTTTTATTTAAATTATTATATTAAT
* * * *
786886 ATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATATTTCTAA
1 ATTT-TTAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTT-TAA
* * *
786951 CTAAATAAATATTTTATATAAATTAT-TTT-TTTTT
64 --AAATAAATATTATAAAAAAATTATATTTATTTTT
786985 CATAATTATA
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
118 4 0.05
119 51 0.63
120 6 0.07
122 20 0.25
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (117 bp):
ATTTTTAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTTAAAA
ATAAATATTATAAAAAAATTATATTTATTTTTATTTAAATTATTATATTAAT
Found at i:790842 original size:15 final size:15
Alignment explanation
Indices: 790822--790853 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
790812 ATCAATACCT
790822 TTTTGCATACATACA
1 TTTTGCATACATACA
*
790837 TTTTGCATACATTCA
1 TTTTGCATACATACA
790852 TT
1 TT
790854 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:798175 original size:1 final size:1
Alignment explanation
Indices: 798169--798299 Score: 91
Period size: 1 Copynumber: 131.0 Consensus size: 1
798159 ATGCTTTAAG
* * * * * * * *
798169 AAAAAAAAACAAAAAACAAAAAAACAAAAAAAGAAAAAAGAAGAAAAAAAGAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * * *
798234 AAGAAAAAAGAAGAAAAAAGAAAAAAAGAAAGAAAAAAAGAGAAAAGAAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
798299 A
1 A
798300 GGGGGTCAAG
Statistics
Matches: 92, Mismatches: 38, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 92 1.00
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:798189 original size:17 final size:16
Alignment explanation
Indices: 798166--798299 Score: 135
Period size: 17 Copynumber: 7.9 Consensus size: 16
798156 ATTATGCTTT
798166 AAGAAAAAAAAACAAAA
1 AAGAAAAAAAAA-AAAA
* *
798183 AACAAAAAAACAAAAA
1 AAGAAAAAAAAAAAAA
798199 AAGAAAAAAGAAGAAAAA
1 AAGAAAAAA-AA-AAAAA
798217 AAGAAAAAAGAAAAAAA
1 AAGAAAAAA-AAAAAAA
*
798234 AAGAAAAAAGAAGAAAA
1 AAGAAAAAA-AAAAAAA
798251 AAGAAAAAAAGAAAGAAA
1 AAGAAAAAAA-AAA-AAA
* *
798269 AA-AAGAGAAAAGAAAA
1 AAGAA-AAAAAAAAAAA
798285 AAGAAAAAGAAAAAA
1 AAGAAAAA-AAAAAA
798300 GGGGGTCAAG
Statistics
Matches: 100, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
16 20 0.20
17 54 0.54
18 26 0.26
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAAAA
Found at i:798299 original size:8 final size:8
Alignment explanation
Indices: 798166--798292 Score: 114
Period size: 8 Copynumber: 15.0 Consensus size: 8
798156 ATTATGCTTT
798166 AAGAAAAA
1 AAGAAAAA
*
798174 AAAACAAAA
1 AAGA-AAAA
*
798183 AACAAAAA
1 AAGAAAAA
*
798191 AACAAAAA
1 AAGAAAAA
798199 AAGAAAAAA
1 AAG-AAAAA
798208 GAAGAAAAA
1 -AAGAAAAA
798217 AAG-AAAA
1 AAGAAAAA
798224 AAGAAAAA
1 AAGAAAAA
*
798232 AAAAGAAAA
1 AAGA-AAAA
798241 AAGAAGAAAA
1 AAG-A-AAAA
798251 AAGAAAAA
1 AAGAAAAA
798259 AAGAAAGAA
1 AAGAAA-AA
*
798268 AAAAAGAGAA
1 AAGAA-A-AA
798278 AAG-AAAA
1 AAGAAAAA
798285 AAGAAAAA
1 AAGAAAAA
798293 GAAAAAAGGG
Statistics
Matches: 103, Mismatches: 7, Indels: 18
0.80 0.05 0.14
Matches are distributed among these distances:
7 12 0.12
8 42 0.41
9 31 0.30
10 18 0.17
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:798300 original size:7 final size:7
Alignment explanation
Indices: 798166--798300 Score: 105
Period size: 7 Copynumber: 20.4 Consensus size: 7
798156 ATTATGCTTT
798166 AAGAAAA
1 AAGAAAA
798173 AA-AAACA
1 AAGAAA-A
798180 AA-AAACA
1 AAGAAA-A
798187 AA-AAAA
1 AAGAAAA
*
798193 CA-AAAA
1 AAGAAAA
798199 AAGAAAA
1 AAGAAAA
798206 AAG--AA
1 AAGAAAA
*
798211 GA-AAAA
1 AAGAAAA
798217 AAGAAAA
1 AAGAAAA
798224 AAGAAAA
1 AAGAAAA
798231 AA-AAAGA
1 AAGAAA-A
*
798238 AA-AAAG
1 AAGAAAA
798244 AAGAAAA
1 AAGAAAA
798251 AAG-AAA
1 AAGAAAA
*
798257 AA-AAGA
1 AAGAAAA
798263 AAGAAAAA
1 AAG-AAAA
*
798271 AAGAGAA
1 AAGAAAA
798278 AAGAAAA
1 AAGAAAA
798285 AAG-AAA
1 AAGAAAA
798291 AAGAAAA
1 AAGAAAA
798298 AAG
1 AAG
798301 GGGGTCAAGA
Statistics
Matches: 107, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
5 3 0.03
6 33 0.31
7 65 0.61
8 6 0.06
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:798300 original size:27 final size:25
Alignment explanation
Indices: 798169--798299 Score: 124
Period size: 25 Copynumber: 5.2 Consensus size: 25
798159 ATGCTTTAAG
* *
798169 AAAAAAAAA-CAAAAA-ACAAAAAA
1 AAAAAAAAAGAAAAAAGAAAAAAAA
* *
798192 ACAAAAAAAGAAAAAAGAAGAAAAA
1 AAAAAAAAAGAAAAAAGAAAAAAAA
*
798217 AAGAAAAAAGAAAAAA-AAAGAAAAA
1 AAAAAAAAAGAAAAAAGAAA-AAAAA
798242 AGAAGAAAAAAGAAAAAAAGAAAGAAAAA
1 A-AA-AAAAAAG-AAAAAAGAAA-AAAAA
* * *
798271 AAGAGAAAAGAAAAAAGAAAAAGAA
1 AAAAAAAAAGAAAAAAGAAAAAAAA
798296 AAAA
1 AAAA
798300 GGGGGTCAAG
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
23 8 0.09
24 7 0.08
25 33 0.37
26 11 0.12
27 13 0.15
28 7 0.08
29 10 0.11
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAAGAAAAAAAA
Found at i:799870 original size:91 final size:90
Alignment explanation
Indices: 799698--799879 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 90
799688 AGAAATAAGA
* * * *
799698 AGACCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCACAA
* *
799763 AAACCCATCATTGAATTTGAAAGATG
66 AAACCAATCATTGAA-TTAAAAGATG
799789 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCAC-A
1 AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCACAA
*
799853 GAACCAATCATTGGAATTAAAAGATG
66 AAACCAATCATT-GAATTAAAAGATG
799879 A
1 A
799880 ACTGCATGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 21 0.25
91 62 0.75
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (90 bp):
AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCACAA
AAACCAATCATTGAATTAAAAGATG
Found at i:800962 original size:115 final size:113
Alignment explanation
Indices: 800576--801255 Score: 795
Period size: 115 Copynumber: 5.9 Consensus size: 113
800566 GATTAAAATC
** ****
800576 CATCATTCAATGGATCAACATTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAG--
1 CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
* * *
800639 -GAAGAAGTTCATAATGAGAAGAACTTGCTCAACTTTTTGCTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
* * * * * * * ** * *
800686 CATCACTCGGTAGAACAACAGTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
800751 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTTGTTTGAATT
* *
800800 CATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 CATCATTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
800864 AGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGTTTGAATT
62 AGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
800915 CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
800980 GAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
63 GAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
801031 CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAG-A
1 CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
* * * **
801092 AGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
* * * *
801139 CTATCACAGAAGCAGATAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
1 C-AT--------CA-TTTGA-T-GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
* * * *
801204 TCTGAAGGAGAAAGAAGACGTTCATAATGAGAAGAACTTATTCAACCTTTTG
54 TCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
801256 AATGACTCTA
Statistics
Matches: 508, Mismatches: 36, Indels: 38
0.87 0.06 0.07
Matches are distributed among these distances:
108 5 0.01
109 41 0.08
110 59 0.12
113 38 0.07
114 53 0.10
115 111 0.22
116 64 0.13
117 50 0.10
118 3 0.01
119 1 0.00
120 43 0.08
123 3 0.01
124 37 0.07
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
Found at i:801291 original size:124 final size:122
Alignment explanation
Indices: 801044--801343 Score: 376
Period size: 124 Copynumber: 2.5 Consensus size: 122
801034 CATTTGATGG
*
801044 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-A-AGAAGAAGAAGTTCACAA
1 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCACAA
* * * * * * * *
801107 TGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGC
66 TGAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAGAAAATAGATCAAC
* *
801164 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGACGTTCAT
1 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-GAG-AAGAAGAAGTTCAC
* * *
801229 AATGAGAAGAACTTATTCAACCTTTTGAATGACTCTATCACCGAAGAAAATAGGTCAAC
64 AATGAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAGAAAATAGATCAAC
* * *
801288 ATCATCC---CCAGGGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 ATCAACCTTTCCA-GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGA-AGAAGAA
801344 TTTATTCAAC
Statistics
Matches: 156, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
120 44 0.28
121 12 0.08
122 32 0.21
123 2 0.01
124 66 0.42
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (122 bp):
ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCACAA
TGAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAGAAAATAGATCAAC
Found at i:801493 original size:3 final size:3
Alignment explanation
Indices: 801478--801512 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
801468 TTCATTTAAA
801478 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
801513 AATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:801531 original size:14 final size:14
Alignment explanation
Indices: 801512--801538 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
801502 TATTATTATT
801512 AAATAATAATAATA
1 AAATAATAATAATA
801526 AAATAATAATAAT
1 AAATAATAATAAT
801539 TACAGGCCCA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:804128 original size:16 final size:16
Alignment explanation
Indices: 804107--804138 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
804097 AAAGTGTCGC
804107 AATCGCCTTTCGGATA
1 AATCGCCTTTCGGATA
804123 AATCGCCTTTCGGATA
1 AATCGCCTTTCGGATA
804139 GATTCAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
AATCGCCTTTCGGATA
Found at i:804453 original size:22 final size:23
Alignment explanation
Indices: 804428--804478 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
804418 TAAAAAATTA
*
804428 AAAAGATA-TTAAATTG-CAAAAT
1 AAAAGATACTT-AATTGACAAAAG
804450 AAAA-ATACTTAATTGAACAAAAG
1 AAAAGATACTTAATTG-ACAAAAG
804473 AAAAGA
1 AAAAGA
804479 AAAATGCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 9 0.38
24 1 0.04
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.22
Consensus pattern (23 bp):
AAAAGATACTTAATTGACAAAAG
Found at i:804568 original size:22 final size:22
Alignment explanation
Indices: 804538--804583 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
804528 ACATGCCGAG
*
804538 AAATAAAAATTAACAGAATGAA
1 AAATAAAAATAAACAGAATGAA
* *
804560 AAATGAAAATAAATAGAATGAA
1 AAATAAAAATAAACAGAATGAA
804582 AA
1 AA
804584 CAAATCACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (22 bp):
AAATAAAAATAAACAGAATGAA
Found at i:804879 original size:103 final size:105
Alignment explanation
Indices: 804772--804960 Score: 267
Period size: 106 Copynumber: 1.8 Consensus size: 105
804762 AAAGAATATG
* * *
804772 TAAAA-AAAATGAAAACATGAATTAAATG-AAAAAGA-ACTAAATTAAAAAAAGAAATAAAATGA
1 TAAAATAAAATG-AAACATGAATTAAATGAAAAAAAAGACCAAATTAAAAAAAGAAAAAAAATGA
*
804834 ATGACGGATTTGAAAGAAAAAAATATAATTAAAATTAAATT
65 ATGACGAATTTGAAAGAAAAAAATATAATTAAAATTAAATT
** *
804875 TAAAATCCAATGTAACATGAATTAAATGAAAAAAAATGACCAAATTAAAAAAAGAAAAAAAATGA
1 TAAAATAAAATGAAACATGAATTAAATGAAAAAAAA-GACCAAATTAAAAAAAGAAAAAAAATGA
*
804940 ATGGCGAATTTGAAAGAAAAA
65 ATGACGAATTTGAAAGAAAAA
804961 CGAAATTAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
103 20 0.27
104 10 0.14
106 44 0.59
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.21
Consensus pattern (105 bp):
TAAAATAAAATGAAACATGAATTAAATGAAAAAAAAGACCAAATTAAAAAAAGAAAAAAAATGAA
TGACGAATTTGAAAGAAAAAAATATAATTAAAATTAAATT
Found at i:805938 original size:3 final size:3
Alignment explanation
Indices: 805930--805973 Score: 63
Period size: 3 Copynumber: 14.3 Consensus size: 3
805920 AAAACGTTAA
805930 AAT AAT AAT AAT -AT AAAT ATAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT -AAT A-AT AAT AAT AAT AAT AAT AAT AAT A
805974 TAACACATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 31 0.82
4 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:805958 original size:25 final size:25
Alignment explanation
Indices: 805930--805996 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
805920 AAAACGTTAA
*
805930 AATAATAATAATATAAATATATAAT
1 AATAATAATAATATAAATATATAAC
*
805955 AATAATAATAATA-ATA-ATATAAC
1 AATAATAATAATATAAATATATAAC
*
805978 ACATTAT-ATAATATAAATA
1 A-ATAATAATAATATAAATA
805997 ACATATTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 13 0.37
24 8 0.23
25 14 0.40
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (25 bp):
AATAATAATAATATAAATATATAAC
Found at i:805999 original size:21 final size:23
Alignment explanation
Indices: 805962--806010 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
805952 AATAATAATA
805962 ATAATAATAATATAACACATTAT
1 ATAATAATAATATAACACATTAT
*
805985 ATAAT-ATAA-ATAACATATTAT
1 ATAATAATAATATAACACATTAT
806006 ATAAT
1 ATAAT
806011 GAGGTTGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.64
22 4 0.16
23 5 0.20
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAATAATAATATAACACATTAT
Found at i:809050 original size:18 final size:18
Alignment explanation
Indices: 808991--809059 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
808981 ACTATTTGTC
*
808991 CCGAAGGACCATTATG-T
1 CCGAAGGACCACTATGTT
*
809008 CCTGAAGGACCACTGATTATT
1 CC-GAAGGACCACT-A-TGTT
*
809029 CCGAAGAACCACTATGTT
1 CCGAAGGACCACTATGTT
809047 CCGAAGGACCACT
1 CCGAAGGACCACT
809060 GATAATCCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.05
18 25 0.58
19 2 0.05
20 11 0.26
21 3 0.07
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (18 bp):
CCGAAGGACCACTATGTT
Found at i:811427 original size:2 final size:2
Alignment explanation
Indices: 811420--811453 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
811410 TTCGAAATCA
811420 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
811454 TTCGAAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:817243 original size:129 final size:130
Alignment explanation
Indices: 817097--817330 Score: 289
Period size: 129 Copynumber: 1.8 Consensus size: 130
817087 ACCGTTGGAC
* * *
817097 CCTTAGTGCATTAGTGCAATAGG-A-GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-
1 CCTTAGTGCATCAGTGC-AT-GGTATATGCATCGATGCATCAAATGCATTCGATG-TTCAAAATA
817159 AGCCA-GAGTGCATCGATGCATGG-CTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATA
63 AGCCATG-GTGCATCGATGCATGGACTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATA
817222 AAAT
127 AAAT
* * * ** **
817226 CCTTAGTGCATCGGTGCATGGTATATGCATCGATGCATGAAATGCATTTGATGTTCAATTTAATT
1 CCTTAGTGCATCAGTGCATGGTATATGCATCGATGCATCAAATGCATTCGATGTTCAAAATAAGC
* *
817291 CATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
66 CATGGTGCATCGATGCATGGACTGGTGCATCGATGCATCA
817331 CTCTGAAAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
127 2 0.02
128 9 0.10
129 59 0.67
130 18 0.20
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (130 bp):
CCTTAGTGCATCAGTGCATGGTATATGCATCGATGCATCAAATGCATTCGATGTTCAAAATAAGC
CATGGTGCATCGATGCATGGACTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAT
Found at i:817320 original size:65 final size:64
Alignment explanation
Indices: 817121--817330 Score: 228
Period size: 65 Copynumber: 3.2 Consensus size: 64
817111 TGCAATAGGA
* * * *
817121 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCATAGTGCATCGATGCATGGTTG
* *
817185 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGGT-T
817250 -
64 G
* * * ** * *
817250 ATGCATCGATGCATGAAATGCATTTGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-TT
817314 G
64 G
*
817315 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
817331 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
63 3 0.02
64 51 0.42
65 64 0.52
66 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTTG
Found at i:817859 original size:2 final size:2
Alignment explanation
Indices: 817852--817896 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
817842 CATGAATTAG
817852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
817895 AT
1 AT
817897 GATTTAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:821773 original size:4 final size:4
Alignment explanation
Indices: 821758--821800 Score: 77
Period size: 4 Copynumber: 10.5 Consensus size: 4
821748 CATGTAACAA
821758 ATAC ACTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC A-TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
821801 GTCATTATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 34 0.89
5 4 0.11
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:822189 original size:18 final size:18
Alignment explanation
Indices: 822166--822238 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
822156 ACTGAATATT
822166 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
822184 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
822203 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
822222 TGCCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
822239 GATAATCCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:822213 original size:38 final size:38
Alignment explanation
Indices: 822165--822241 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
822155 CACTGAATAT
* *
822165 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGCCCCGAAGGACCACTGA
*
822203 TTGTTCCGAAGAACCACTATGCCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGCCCCGAAGGACCACTGA
822241 T
1 T
822242 AATCCATCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.19
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGCCCCGAAGGACCACTGA
Found at i:823202 original size:2 final size:2
Alignment explanation
Indices: 823190--823243 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
823180 CATGAATTAG
* * *
823190 AT AT AT TT AT AT AT AT AT GT AT AC 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
823232 AT AT AT AT AT AT
1 AT AT AT AT AT AT
823244 TCATATGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:834547 original size:22 final size:22
Alignment explanation
Indices: 834517--834562 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
834507 ACATGCCGAG
* *
834517 AAATAAAAATTAACAGAATGAA
1 AAATAAAAATAAACAGAACGAA
* *
834539 AAATGAAAATAAATAGAACGAA
1 AAATAAAAATAAACAGAACGAA
834561 AA
1 AA
834563 CAAATCATAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (22 bp):
AAATAAAAATAAACAGAACGAA
Found at i:835919 original size:3 final size:3
Alignment explanation
Indices: 835911--835959 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
835901 AAATCGTTAA
* * *
835911 AAT AAT AAT ACT -AT AAT TAT -AT AAT AAT AAT AAT AAT GAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
835956 AAT A
1 AAT A
835960 CATTATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 5 0.13
3 33 0.87
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:835967 original size:12 final size:11
Alignment explanation
Indices: 835911--835971 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
835901 AAATCGTTAA
835911 AATAATAATACT
1 AATAATAATA-T
*
835923 -ATAATTATAT
1 AATAATAATAT
835933 AATAATAATAAT
1 AATAATAAT-AT
*
835945 AATGATAATAT
1 AATAATAATAT
*
835956 AATACATTATAT
1 AATA-ATAATAT
835968 AATA
1 AATA
835972 TAAATAACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
10 1 0.02
11 20 0.49
12 20 0.49
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
AATAATAATAT
Found at i:835969 original size:23 final size:22
Alignment explanation
Indices: 835929--835993 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 22
835919 TACTATAATT
*
835929 ATATAATAATAATAATAATGATA
1 ATATAATAATTAT-ATAATGATA
835952 ATATAATACATTATATAAT-ATA
1 ATATAATA-ATTATATAATGATA
*
835974 A-ATAACATATTATATAATGA
1 ATATAATA-ATTATATAATGA
835994 GGTCGGATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 15 0.41
22 5 0.14
23 13 0.35
24 4 0.11
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (22 bp):
ATATAATAATTATATAATGATA
Found at i:836827 original size:20 final size:19
Alignment explanation
Indices: 836794--836842 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
836784 TTCCAAAATA
* *
836794 ATCAAATTTCACATTCTAGC
1 ATCAAA-TTCACATTATAAC
836814 ATCAAATTCAACATTATAAC
1 ATCAAATTC-ACATTATAAC
*
836834 ATTAAATTC
1 ATCAAATTC
836843 CAGCATAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (19 bp):
ATCAAATTCACATTATAAC
Found at i:838600 original size:21 final size:21
Alignment explanation
Indices: 838576--838619 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
838566 CAACACACCT
838576 CTATTCGTATTCGCTCATTCA
1 CTATTCGTATTCGCTCATTCA
*
838597 CTATTCGTGTTCGCTCATTCA
1 CTATTCGTATTCGCTCATTCA
838618 CT
1 CT
838620 GAATGAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (21 bp):
CTATTCGTATTCGCTCATTCA
Found at i:839625 original size:41 final size:41
Alignment explanation
Indices: 839579--839657 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
839569 CTATTTTTTA
* *
839579 TTAATTATTTTATATATTACAATTAATTTGATGAAAATAAT
1 TTAATTATTTGATATAATACAATTAATTTGATGAAAATAAT
**
839620 TTAATTATTTGATATAATGTAATTAATTTGATGAAAAT
1 TTAATTATTTGATATAATACAATTAATTTGATGAAAAT
839658 TGATTTAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (41 bp):
TTAATTATTTGATATAATACAATTAATTTGATGAAAATAAT
Found at i:839631 original size:22 final size:23
Alignment explanation
Indices: 839599--839657 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 23
839589 TATATATTAC
*
839599 AATTAATTTGATGAAAATAATTT
1 AATTAATTTGATGAAAATAATGT
839622 AATT-ATTTGAT----ATAATGT
1 AATTAATTTGATGAAAATAATGT
839640 AATTAATTTGATGAAAAT
1 AATTAATTTGATGAAAAT
839658 TGATTTAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
18 10 0.33
19 7 0.23
22 7 0.23
23 6 0.20
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (23 bp):
AATTAATTTGATGAAAATAATGT
Found at i:840173 original size:41 final size:40
Alignment explanation
Indices: 840100--840177 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
840090 AATGAATTAC
* *
840100 ATCAATTACAACTATTAAATACTTAAAAATATATTTTTTAA
1 ATCAATTACAACTATCAAATAC-AAAAAATATATTTTTTAA
840141 ATCAATTACAACTATCAAATA-AAAATACATATATTTT
1 ATCAATTACAACTATCAAATACAAAA-A-ATATATTTT
840178 AAAATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 3 0.09
40 1 0.03
41 29 0.88
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (40 bp):
ATCAATTACAACTATCAAATACAAAAAATATATTTTTTAA
Found at i:848246 original size:28 final size:28
Alignment explanation
Indices: 848206--848263 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
848196 ACACATACAT
848206 TCATCTGGTCAGACTTGAAAATTAAAAG
1 TCATCTGGTCAGACTTGAAAATTAAAAG
848234 TCATCTGGTCAGACTTGAAAATTAAAAG
1 TCATCTGGTCAGACTTGAAAATTAAAAG
848262 TC
1 TC
848264 TGACCTGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (28 bp):
TCATCTGGTCAGACTTGAAAATTAAAAG
Found at i:848273 original size:25 final size:26
Alignment explanation
Indices: 848215--848274 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
848205 TTCATCTGGT
**
848215 CAGACTTGAAAATTAAAAGTCATCTGGT
1 CAGACTTGAAAATTAAAAG--ATCTGAC
848243 CAGACTTGAAAATTAAAAG-TCTGAC
1 CAGACTTGAAAATTAAAAGATCTGAC
*
848268 CTGACTT
1 CAGACTT
848275 TTTTTGGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 10 0.34
28 19 0.66
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (26 bp):
CAGACTTGAAAATTAAAAGATCTGAC
Found at i:851471 original size:18 final size:18
Alignment explanation
Indices: 851448--851487 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
851438 AATTCGGTTT
851448 AAAATAAGTT-AATTAATC
1 AAAATAA-TTGAATTAATC
851466 AAAATAATTGAATTAATC
1 AAAATAATTGAATTAATC
851484 AAAA
1 AAAA
851488 ATTTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATAATTGAATTAATC
Found at i:851695 original size:17 final size:18
Alignment explanation
Indices: 851667--851703 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
851657 TAACGGTTAA
851667 AATAACAATTTTTAATTT
1 AATAACAATTTTTAATTT
851685 AATAA-AATTTTTAATTT
1 AATAACAATTTTTAATTT
851702 AA
1 AA
851704 GTTCAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAACAATTTTTAATTT
Found at i:852192 original size:33 final size:34
Alignment explanation
Indices: 852126--852193 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
852116 GTTGGAAAAT
* *
852126 ATTTATATTTTTTTAAAAAAATTAAATTCATAAA
1 ATTTATAATTTTTTAAAAAAATTAAAATCATAAA
*
852160 ATTTATAATTTTTT-ACAAAATTAAAAAT-ATAAA
1 ATTTATAATTTTTTAAAAAAATT-AAAATCATAAA
852193 A
1 A
852194 AAAATTAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (34 bp):
ATTTATAATTTTTTAAAAAAATTAAAATCATAAA
Found at i:853329 original size:21 final size:20
Alignment explanation
Indices: 853243--853400 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
853233 AAATGACCAA
**
853243 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
853262 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
853282 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
853302 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
853323 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
853344 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
853364 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
853385 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
853401 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Done.