Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008274.1 Hibiscus syriacus cultivar Beakdansim tig00110931_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: 1661830
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:502631 original size:31 final size:31
Alignment explanation
Indices: 502527--502636 Score: 89
Period size: 31 Copynumber: 3.4 Consensus size: 31
502517 TCAGTCAATG
* *
502527 CTGGTAATTCCTTGTATAGGTTCTA-CACCGA
1 CTGGTAATTCCTTTTATAGGTTC-AGCACTGA
** * *
502558 CTGGTAATTCCTATCTCTGGCAGGTTTAGTCTCTG-
1 CTGGTAATTCCT-T-T-T-ATAGGTTCAG-CACTGA
*
502593 CTAGTAATTCCTTTTATAGGTTCAGCACTGA
1 CTGGTAATTCCTTTTATAGGTTCAGCACTGA
502624 CTGGTAATTCCTT
1 CTGGTAATTCCTT
502637 ATGGACCTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
30 4 0.07
31 31 0.52
32 2 0.03
33 1 0.02
34 3 0.05
35 16 0.27
36 3 0.05
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (31 bp):
CTGGTAATTCCTTTTATAGGTTCAGCACTGA
Found at i:504219 original size:11 final size:11
Alignment explanation
Indices: 504203--504233 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
504193 TTAAATTCTC
504203 ATATTATTTAG
1 ATATTATTTAG
504214 ATATTATTTAG
1 ATATTATTTAG
504225 ATATT-TTTA
1 ATATTATTTA
504234 ATAATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (11 bp):
ATATTATTTAG
Found at i:505297 original size:60 final size:60
Alignment explanation
Indices: 505204--505396 Score: 198
Period size: 60 Copynumber: 3.2 Consensus size: 60
505194 AGTATATATG
* ** *
505204 CATAGTTTG-GGATGAAATTGGAATGATAAAAAAGTTTGGGGAACAATTTAGAATGAAGGT
1 CATAGTTTGAGGATGAAATTGAAATG-TTTAAAAGTTTGAGGAACAATTTAGAATGAAGGT
* * *
505264 CATAGTTTGAGGATGTAATTGAAATGTTTAAAAGTTTGAGG-ACTAAATTAGAATG-AGAAT
1 CATAGTTTGAGGATGAAATTGAAATGTTTAAAAGTTTGAGGAAC-AATTTAGAATGAAG-GT
* * * *
505324 CATAGTTTAAGGATGAAATTGAAATATTTAAAAGTTT-AGGAACCAATTT-GTAAGGAGGGT
1 CATAGTTTGAGGATGAAATTGAAATGTTTAAAAGTTTGAGGAA-CAATTTAG-AATGAAGGT
*
505384 CATACTTTGAGGA
1 CATAGTTTGAGGA
505397 CATGTGATGC
Statistics
Matches: 110, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
59 8 0.07
60 86 0.78
61 16 0.15
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (60 bp):
CATAGTTTGAGGATGAAATTGAAATGTTTAAAAGTTTGAGGAACAATTTAGAATGAAGGT
Found at i:506676 original size:2 final size:2
Alignment explanation
Indices: 506669--506752 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
506659 CACTGACCAA
506669 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
506711 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
506753 TACGGGCGGG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:508828 original size:26 final size:28
Alignment explanation
Indices: 508792--508844 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
508782 GGTGAACTTC
*
508792 TAAAATTTT-AAGATGAGA-TAAATTTA
1 TAAAATTTTAAAGATGAAATTAAATTTA
508818 TAAAATTTTAAAGATGAAATTAAATTT
1 TAAAATTTTAAAGATGAAATTAAATTT
508845 TTAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.38
27 8 0.33
28 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (28 bp):
TAAAATTTTAAAGATGAAATTAAATTTA
Found at i:512744 original size:15 final size:15
Alignment explanation
Indices: 512726--512761 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 15
512716 GGGTCTGAAC
512726 CTCTTCTTCATCTGA
1 CTCTTCTTCATCTGA
512741 --C-TCTTCATCTGA
1 CTCTTCTTCATCTGA
512753 CTCTTCTTC
1 CTCTTCTTC
512762 TACCATAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 6
0.75 0.00 0.25
Matches are distributed among these distances:
12 11 0.61
13 1 0.06
14 1 0.06
15 5 0.28
ACGTcount: A:0.11, C:0.36, G:0.06, T:0.47
Consensus pattern (15 bp):
CTCTTCTTCATCTGA
Found at i:512747 original size:12 final size:12
Alignment explanation
Indices: 512730--512758 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
512720 CTGAACCTCT
512730 TCTTCATCTGAC
1 TCTTCATCTGAC
512742 TCTTCATCTGAC
1 TCTTCATCTGAC
512754 TCTTC
1 TCTTC
512759 TTCTACCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.34, G:0.07, T:0.45
Consensus pattern (12 bp):
TCTTCATCTGAC
Found at i:514738 original size:165 final size:162
Alignment explanation
Indices: 514447--514775 Score: 631
Period size: 165 Copynumber: 2.0 Consensus size: 162
514437 TCACTGAGAG
514447 ACACATCAACCTTCCCATGAAGTAAGTAGTTTCAAGATACTCAAACTTATCAGGAAGTGATCCCA
1 ACACATCAACCTTCCCATGAAGTAAGTAGTTTCAAGATACTCAAACTTATCAGGAAGTGATCCCA
514512 TCACATCAGAGCCAGATCTCGTCTTCAAAGTCACGTCCATATTCATCAGATCAGTCACCAGCTGA
66 TCACATCAGAGCCAGATCTCGTCTTCAAAGTCACGTCCATATTCATCAGATCAGTCACCAGCTGA
514577 TTAAAGCTAGTAATGTGATCATTCATAGTGGT
131 TTAAAGCTAGTAATGTGATCATTCATAGTGGT
514609 ACACATCAACCTTCCCATGAAGTAGAGTAGTTTCAAGATACTCAAACTTATCAGGAAGTGATCCC
1 ACACATCAACCTTCCCATGAAGTA-AGTAGTTTCAAGATACTCAAACTTATCAGGAAGTGATCCC
514674 ATCAACATCAGAGCCAGATCTTCGTCTTCAAAGTCACGTCCATATTCATCAGATCAGTCACCAGC
65 ATC-ACATCAGAGCCAGATC-TCGTCTTCAAAGTCACGTCCATATTCATCAGATCAGTCACCAGC
514739 TGATTAAAGCTAGTAATGTGATCATTCATAGTGGT
128 TGATTAAAGCTAGTAATGTGATCATTCATAGTGGT
514774 AC
1 AC
514776 CTGGTACATA
Statistics
Matches: 164, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
162 24 0.15
163 43 0.26
164 16 0.10
165 81 0.49
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (162 bp):
ACACATCAACCTTCCCATGAAGTAAGTAGTTTCAAGATACTCAAACTTATCAGGAAGTGATCCCA
TCACATCAGAGCCAGATCTCGTCTTCAAAGTCACGTCCATATTCATCAGATCAGTCACCAGCTGA
TTAAAGCTAGTAATGTGATCATTCATAGTGGT
Found at i:515213 original size:55 final size:56
Alignment explanation
Indices: 515118--515229 Score: 217
Period size: 55 Copynumber: 2.0 Consensus size: 56
515108 ACAGTATTTC
515118 TTGCCAAAATTGAAGATGAAGAAGCGTCTGCCATTTCTGCTACAAATTCTATTTAA
1 TTGCCAAAATTGAAGATGAAGAAGCGTCTGCCATTTCTGCTACAAATTCTATTTAA
515174 TTGCCAAAATTGAAGATGAAGAAGCGTC-GCCATTTCTGCTACAAATTCTATTTAA
1 TTGCCAAAATTGAAGATGAAGAAGCGTCTGCCATTTCTGCTACAAATTCTATTTAA
515229 T
1 T
515230 AGCTGCCAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 28 0.50
56 28 0.50
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (56 bp):
TTGCCAAAATTGAAGATGAAGAAGCGTCTGCCATTTCTGCTACAAATTCTATTTAA
Found at i:516744 original size:29 final size:29
Alignment explanation
Indices: 516711--516775 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
516701 ATGGTTCTTC
* *
516711 TTTAAAAGAAAATT-TAATTGCGACTTATT
1 TTTAAAACAAAATTCTAATTACGACTT-TT
**
516740 TTTAAAACAATTTTCTAATTACGACTTTT
1 TTTAAAACAAAATTCTAATTACGACTTTT
516769 TTTAAAA
1 TTTAAAA
516776 TGATTTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (29 bp):
TTTAAAACAAAATTCTAATTACGACTTTT
Found at i:516930 original size:57 final size:57
Alignment explanation
Indices: 516858--516973 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
516848 AAAGATACAT
*
516858 TTTTAAAGATCAAATTCTATCTAAAATCAAAGTATGATCTTTTTTATTGAACATTGA
1 TTTTAAAGATCAAATTCTATCTAAAATCAAAGTATGATCATTTTTATTGAACATTGA
*
516915 TTTTAAAGATTAAATTCTATCTAAAATCAAAGTATGATCATTTTTATTGAACATTGA
1 TTTTAAAGATCAAATTCTATCTAAAATCAAAGTATGATCATTTTTATTGAACATTGA
516972 TT
1 TT
516974 AATTTTATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (57 bp):
TTTTAAAGATCAAATTCTATCTAAAATCAAAGTATGATCATTTTTATTGAACATTGA
Found at i:542231 original size:21 final size:19
Alignment explanation
Indices: 542205--542249 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
542195 ACTAATGGTG
542205 ACGACGGTATTGGCGATAACA
1 ACGACGG-A-TGGCGATAACA
542226 ACGAC-GATGGCGATAACA
1 ACGACGGATGGCGATAACA
*
542244 ATGACG
1 ACGACG
542250 ATAGAACGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.68
19 1 0.05
20 1 0.05
21 5 0.23
ACGTcount: A:0.36, C:0.20, G:0.29, T:0.16
Consensus pattern (19 bp):
ACGACGGATGGCGATAACA
Found at i:542238 original size:18 final size:18
Alignment explanation
Indices: 542215--542251 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
542205 ACGACGGTAT
542215 TGGCGATAACAACGACGA
1 TGGCGATAACAACGACGA
*
542233 TGGCGATAACAATGACGA
1 TGGCGATAACAACGACGA
542251 T
1 T
542252 AGAACGGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (18 bp):
TGGCGATAACAACGACGA
Found at i:545480 original size:45 final size:45
Alignment explanation
Indices: 545429--545518 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
545419 CGTTAGTGAT
*
545429 TTGCTGCTAAGCAAAGCTACTGAAACATCATTCTAAAATGGGATA
1 TTGCTGCTAAGCAAAGCTACTCAAACATCATTCTAAAATGGGATA
* * ** *
545474 TTGCTGCTGATCATGGCTACTCAAACATCATTCTCAAATGGGATA
1 TTGCTGCTAAGCAAAGCTACTCAAACATCATTCTAAAATGGGATA
545519 ATATGCTAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (45 bp):
TTGCTGCTAAGCAAAGCTACTCAAACATCATTCTAAAATGGGATA
Found at i:546927 original size:207 final size:207
Alignment explanation
Indices: 545875--547306 Score: 2514
Period size: 207 Copynumber: 7.0 Consensus size: 207
545865 CCTTTTTGTT
545875 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
545940 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
66 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
546005 TACA-TTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
131 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
546069 GAGAGTGTCTAC
196 GAGAGTGTCTAC
546081 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
*
546146 GATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
66 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
*
546211 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGATACGCAATGCACA
131 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
*
546276 GGGAGTGTCTAC
196 GAGAGTGTCTAC
546288 TCGCCTTTTTTCTTTATA-T-TATGAAAAAGGTAA-AGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
546350 GATATGGATTTCGGAC-C-GGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGAT-CATAA
66 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
*
546412 T--ATTTTTTCTCCTCCTTTCAGACAAAACAACGAACATGGGGCATGCATATGGATACGCAATGC
131 TACATTTTTT-T--TCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGC
546475 ACAGAGAGTGTCTAC
193 ACAGAGAGTGTCTAC
*
546490 TCGCCTTTTTTCTTTATATTATATGAAAAATGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
*
546555 GATATGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCAT-A
66 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
546619 -ACA--TTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
131 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
546681 GAGAGTGTCTAC
196 GAGAGTGTCTAC
546693 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
*
546758 GATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
66 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
*
546823 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGATACGCAATGCACA
131 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
*
546888 GGGAGTGTCTAC
196 GAGAGTGTCTAC
546900 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
546965 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
66 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
*
547030 TACATTTTTTCTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
131 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
547095 GAGAGTGTCTAC
196 GAGAGTGTCTAC
*
547107 TCGCCTTTTTTCTTTATA-T-TATGAAAAA--T-GTA--A-TAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
* * *
547164 GATATGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGCTGGGTGATACATAA
66 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
* *
547229 TATATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCCTGCATATGGATACGC-ATGCACA
131 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
* *
547293 AATAGTGTCT-C
196 GAGAGTGTCTAC
547304 TCG
1 TCG
547307 AGAGTGTTTC
Statistics
Matches: 1182, Mismatches: 28, Indels: 41
0.94 0.02 0.03
Matches are distributed among these distances:
197 4 0.00
198 15 0.01
199 147 0.12
200 2 0.00
201 6 0.01
202 123 0.10
203 193 0.16
204 58 0.05
205 72 0.06
206 140 0.12
207 418 0.35
208 4 0.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (207 bp):
TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
GAGAGTGTCTAC
Found at i:546928 original size:410 final size:411
Alignment explanation
Indices: 545875--547306 Score: 2504
Period size: 410 Copynumber: 3.5 Consensus size: 411
545865 CCTTTTTGTT
545875 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATA-T-TATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
545940 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
64 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
546005 TACA-TTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
129 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
546069 GAGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGC
194 GAGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGC
*
546134 ATAGATGGGTGGGATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTG
259 ATAGATGGGTGGGATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTG
*
546199 GGTGATCCATAATACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGAT
324 GGTGATCCATAATACA-TTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGAT
*
546264 ACGCAATGCACAGGGAGTGTCTAC
388 ACGCAATGCACAGAGAGTGTCTAC
546288 TCGCCTTTTTTCTTTATATTATGAAAAAGGTAA-AGGATTAGATAAATGGCATAGATGGGTGGGA
1 TCGCCTTTTTTCTTTATATTATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGGGA
546352 TATGGATTTCGGAC-C-GGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGAT-CATAAT-
66 TATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAATA
*
546413 -ATTTTTTCTCCTCCTTTCAGACAAAACAACGAACATGGGGCATGCATATGGATACGCAATGCAC
131 CATTTTTT-T--TCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCAC
*
546477 AGAGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAATGTAATAGGATTAGATAAATGG
193 AGAGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGG
*
546542 CATAGATGGGTGGGATATGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGTT
258 CATAGATGGGTGGGATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTT
546607 GGGTGATCCAT-A-ACA-TTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGAT
323 GGGTGATCCATAATACATTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGAT
546669 ACGCAATGCACAGAGAGTGTCTAC
388 ACGCAATGCACAGAGAGTGTCTAC
546693 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATA-T-TATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
*
546758 GATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
64 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
*
546823 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGATACGCAATGCACA
129 TACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACA
*
546888 GGGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGC
194 GAGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGC
546953 ATAGATGGGTGGGATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTG
259 ATAGATGGGTGGGATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTG
547018 GGTGATCCATAATACATTTTTTCTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGAT
324 GGTGATCCATAATACATTTTTT-TCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGAT
547083 ACGCAATGCACAGAGAGTGTCTAC
388 ACGCAATGCACAGAGAGTGTCTAC
*
547107 TCGCCTTTTTTCTTTATATTATGAAAAA--T-GTA--A-TAGATAAATGGCATAGATGGGTGGGA
1 TCGCCTTTTTTCTTTATATTATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGGGA
* * *
547166 TATGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGCTGGGTGATACATAATA
66 TATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAATA
* * *
547231 TATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCCTGCATATGGATACGC-ATGCACAAA
131 CATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACAGA
*
547295 TAGTGTCT-CTCG
196 GAGTGTCTACTCG
547307 AGAGTGTTTC
Statistics
Matches: 980, Mismatches: 23, Indels: 41
0.94 0.02 0.04
Matches are distributed among these distances:
404 4 0.00
405 102 0.10
406 145 0.15
407 25 0.03
408 85 0.09
409 194 0.20
410 275 0.28
411 21 0.02
412 14 0.01
413 31 0.03
414 84 0.09
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (411 bp):
TCGCCTTTTTTCTTTATATTATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGGGA
TATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAATA
CATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACAGA
GAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCAT
AGATGGGTGGGATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGG
TGATCCATAATACATTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACG
CAATGCACAGAGAGTGTCTAC
Found at i:547292 original size:612 final size:611
Alignment explanation
Indices: 545875--547306 Score: 2553
Period size: 612 Copynumber: 2.3 Consensus size: 611
545865 CCTTTTTGTT
*
545875 TCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAA--T-GTA-GATTAGATAAATGGCATAGATGGGTGG
*
545940 GATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
62 GATATGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
546005 TACATTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACAG
127 TACATTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACAG
546070 AGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCA
192 AGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCA
546135 TAGATGGGTGGGATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGG
257 TAGATGGGTGGGATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGG
546200 GTGATCCATAATACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGATA
322 GTGATCCATAATACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGATA
546265 CGCAATGCACAGGGAGTGTCTACTCGCCTTTTTTCTTTATATTATGAAAAAGGTAAAGGATTAGA
387 CGCAATGCACAGGGAGTGTCTACTCGCCTTTTTTCTTTATATTATGAAAAAGGTAAAGGATTAGA
546330 TAAATGGCATAGATGGGTGGGATATGGATTTCGGACCGGGGTGAGAGAATTGAGAATGTCAGACC
452 TAAATGGCATAGATGGGTGGGATATGGATTTCGGACCGGGGTGAGAGAATTGAGAATGTCAGACC
*
546395 GTGTTGGGTGATCATAATATTTTTTCTCCTCCTTTCAGACAAAACAACGAACATGGGGCATGCAT
517 GTGTTGGGTGATCATAATAATTTTTCTCCTCCTTTCAGACAAAACAACGAACATGGGGCATGCAT
546460 ATGGATACGCAATGCACAGAGAGTGTCTAC
582 ATGGATACGCAATGCACAGAGAGTGTCTAC
546490 TCGCCTTTTTTCTTTATATTATATGAAAAATGTAATAGGATTAGATAAATGGCATAGATGGGTGG
1 TCGCCTTTTTTCTTTATATTATATGAAAAATG---TA-GATTAGATAAATGGCATAGATGGGTGG
546555 GATATGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCAT-A
62 GATATGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAA
546619 -ACA-TTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACAG
127 TACATTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACAG
546682 AGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCA
192 AGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCA
546747 TAGATGGGTGGGATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGG
257 TAGATGGGTGGGATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGG
546812 GTGATCCATAATACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGATA
322 GTGATCCATAATACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGATA
546877 CGCAATGCACAGGGAGTGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATT
387 CGCAATGCACAGGGAGTGTCTACTCGCCTTTTTTCTTTATA-T-TATGAAAAAGGTAA-AGGATT
546942 AGATAAATGGCATAGATGGGTGGGATATGGATTTCGGACACGGGGGTGAGAGAATTGAGAATGTC
449 AGATAAATGGCATAGATGGGTGGGATATGGATTTCGGAC-C-GGGGTGAGAGAATTGAGAATGTC
*
547007 AGACCGTGTTGGGTGATCCATAATACATTTTT-T-CTCCTTTCAGACAAAACAACGAACATGTGG
512 AGACCGTGTTGGGTGAT-CATAATA-ATTTTTCTCCTCCTTTCAGACAAAACAACGAACATGGGG
547070 CATGCATATGGATACGCAATGCACAGAGAGTGTCTAC
575 CATGCATATGGATACGCAATGCACAGAGAGTGTCTAC
547107 TCGCCTTTTTTCTTTATA-T-TATGAAAAATGTA-A-TAGATAAATGGCATAGATGGGTGGGATA
1 TCGCCTTTTTTCTTTATATTATATGAAAAATGTAGATTAGATAAATGGCATAGATGGGTGGGATA
* * *
547168 TGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGCTGGGTGATACATAATATA
66 TGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAATACA
* * *
547233 TTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCCTGCATATGGATACGC-ATGCACAAATA
131 -TTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACAGAGA
547297 GTGTCT-CTCG
195 GTGTCTACTCG
547307 AGAGTGTTTC
Statistics
Matches: 793, Mismatches: 10, Indels: 32
0.95 0.01 0.04
Matches are distributed among these distances:
609 85 0.11
610 2 0.00
611 6 0.01
612 313 0.39
613 55 0.07
614 15 0.02
615 178 0.22
616 2 0.00
617 124 0.16
618 8 0.01
619 5 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (611 bp):
TCGCCTTTTTTCTTTATATTATATGAAAAATGTAGATTAGATAAATGGCATAGATGGGTGGGATA
TGGATTTCGGACACGGGGGTTAGAGAATTGAGAATGTCAGACCGTGTTGGGTGATCCATAATACA
TTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCATGCATATGGATACGCAATGCACAGAGAG
TGTCTACTCGCCTTTTTTCTTTATATTATATGAAAAAGGTAATAGGATTAGATAAATGGCATAGA
TGGGTGGGATATGAATTTCGGACACGGGGGTGAGAGAATTGAGAATGTCAGACCGTGTTGGGTGA
TCCATAATACATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGACATGCATATGGATACGCA
ATGCACAGGGAGTGTCTACTCGCCTTTTTTCTTTATATTATGAAAAAGGTAAAGGATTAGATAAA
TGGCATAGATGGGTGGGATATGGATTTCGGACCGGGGTGAGAGAATTGAGAATGTCAGACCGTGT
TGGGTGATCATAATAATTTTTCTCCTCCTTTCAGACAAAACAACGAACATGGGGCATGCATATGG
ATACGCAATGCACAGAGAGTGTCTAC
Found at i:547353 original size:106 final size:108
Alignment explanation
Indices: 547221--547437 Score: 386
Period size: 106 Copynumber: 2.0 Consensus size: 108
547211 GTGCTGGGTG
547221 ATACATAATATATTTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCCTGCATATGGATACGC
1 ATACATAATATA-TTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCCTGCATATGGATACGC
547286 -ATGCACAAATAGTGTCT-CTCGAGAGTGTTTCATTTTAGCTGAT
65 AATGCACAAATAGTGTCTACTCGAGAGT-TTTCATTTTAGCTGAT
547329 ATACATAATATA-TTTTTTCCTTTCAGACAAAACAACGAACATGTGGCCTGCATATGGATACGCA
1 ATACATAATATATTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCCTGCATATGGATACGCA
*
547393 ATGCACAAATAGTGTCTACTCGAGTGTTTTCATTTTAGCTGAT
66 ATGCACAAATAGTGTCTACTCGAGAGTTTTCATTTTAGCTGAT
547436 AT
1 AT
547438 CTATCCTTTT
Statistics
Matches: 106, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
106 51 0.48
107 35 0.33
108 20 0.19
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (108 bp):
ATACATAATATATTTTTTTCCTTTCAGACAAAACAACGAACATGTGGCCTGCATATGGATACGCA
ATGCACAAATAGTGTCTACTCGAGAGTTTTCATTTTAGCTGAT
Found at i:547562 original size:71 final size:71
Alignment explanation
Indices: 547446--547591 Score: 292
Period size: 71 Copynumber: 2.1 Consensus size: 71
547436 ATCTATCCTT
547446 TTTGGTTCAGAATCATACACAGGGTTTTGTTGGTCTTTAAATGGAGTCTAGAATTGGTCATTGGA
1 TTTGGTTCAGAATCATACACAGGGTTTTGTTGGTCTTTAAATGGAGTCTAGAATTGGTCATTGGA
547511 GAAAGC
66 GAAAGC
547517 TTTGGTTCAGAATCATACACAGGGTTTTGTTGGTCTTTAAATGGAGTCTAGAATTGGTCATTGGA
1 TTTGGTTCAGAATCATACACAGGGTTTTGTTGGTCTTTAAATGGAGTCTAGAATTGGTCATTGGA
547582 GAAAGC
66 GAAAGC
547588 TTTG
1 TTTG
547592 AAGCTTTTTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.36
Consensus pattern (71 bp):
TTTGGTTCAGAATCATACACAGGGTTTTGTTGGTCTTTAAATGGAGTCTAGAATTGGTCATTGGA
GAAAGC
Found at i:563312 original size:18 final size:18
Alignment explanation
Indices: 563289--563358 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
563279 ACCGGTCACA
563289 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
563307 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
563325 ACCC-A----ACCCATTG
1 ACCCGACCCGACCCGTTG
563338 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
563356 ACC
1 ACC
563359 GTTGACTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 10 0.23
14 1 0.02
17 1 0.02
18 31 0.72
ACGTcount: A:0.20, C:0.50, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:563339 original size:31 final size:31
Alignment explanation
Indices: 563294--563354 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
563284 TCACAACCCG
* *
563294 ACCCGACCCGTTGACCCGACCCGACCCGTTT
1 ACCCAACCCATTGACCCGACCCGACCCGTTT
563325 ACCCAACCCATTGACCCGACCCGACCCGTT
1 ACCCAACCCATTGACCCGACCCGACCCGTT
563355 GACCGTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.49, G:0.16, T:0.15
Consensus pattern (31 bp):
ACCCAACCCATTGACCCGACCCGACCCGTTT
Found at i:564589 original size:18 final size:18
Alignment explanation
Indices: 564563--564598 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
564553 TCGAAAGGAC
*
564563 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
564581 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
564599 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:565754 original size:24 final size:24
Alignment explanation
Indices: 565727--565817 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
565717 TCAAATTTGA
* *
565727 ATTCTGTTATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
565751 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACATGG
* * * *
565774 ATTCTAATCTGATACATGATATGG
1 ATTCTGATATGATACTTGACATGG
565798 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
565818 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 21 0.38
24 35 0.62
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:573228 original size:13 final size:14
Alignment explanation
Indices: 573212--573245 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
573202 CATATGAAAA
*
573212 TTTATAATT-TATT
1 TTTAAAATTATATT
573225 TTTAAAATTATATT
1 TTTAAAATTATATT
573239 TTTAAAA
1 TTTAAAA
573246 AATTGCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAAAATTATATT
Found at i:577557 original size:32 final size:31
Alignment explanation
Indices: 577507--577610 Score: 84
Period size: 32 Copynumber: 3.3 Consensus size: 31
577497 AATTTTCTAA
* *
577507 ATTATAAAATAGTAATTAAAAT-TATTAAAATT
1 ATTATAAAACAATAATT-AAATCTA-TAAAATT
* *
577539 ATTATAAAACAATTATTAAATCTATCAAATT
1 ATTATAAAACAATAATTAAATCTATAAAATT
* ** * *
577570 ATTATAAAATAATCGTTAAATTTTATCAAATT
1 ATTATAAAACAATAATTAAA-TCTATAAAATT
*
577602 AATATAAAA
1 ATTATAAAA
577611 AGAAAATTAG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
31 27 0.44
32 34 0.56
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (31 bp):
ATTATAAAACAATAATTAAATCTATAAAATT
Found at i:577572 original size:31 final size:32
Alignment explanation
Indices: 577534--577610 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
577524 AAAATTATTA
*
577534 AAATTATTATAAAACAATTATTAAA-TCTATC
1 AAATTATTATAAAACAATCATTAAATTCTATC
* * *
577565 AAATTATTATAAAATAATCGTTAAATTTTATC
1 AAATTATTATAAAACAATCATTAAATTCTATC
*
577597 AAATTAATATAAAA
1 AAATTATTATAAAA
577611 AGAAAATTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 22 0.55
32 18 0.45
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.39
Consensus pattern (32 bp):
AAATTATTATAAAACAATCATTAAATTCTATC
Found at i:579829 original size:2 final size:2
Alignment explanation
Indices: 579822--579851 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
579812 TCCTCTCAAT
*
579822 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
579852 ATTTATCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:579986 original size:14 final size:14
Alignment explanation
Indices: 579969--580015 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
579959 TTTCTGACTA
579969 AAAATTATAATAAT
1 AAAATTATAATAAT
* *
579983 AAAATTCTATTAA-
1 AAAATTATAATAAT
579996 AAAA-TATAATAAT
1 AAAATTATAATAAT
580009 AAAATTA
1 AAAATTA
580016 GTTTTGAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 6 0.22
13 8 0.30
14 13 0.48
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATTATAATAAT
Found at i:580003 original size:26 final size:27
Alignment explanation
Indices: 579946--580014 Score: 104
Period size: 26 Copynumber: 2.6 Consensus size: 27
579936 TTTATTTAAG
*
579946 TATAATAATAAAATTTCTGACTAAAAAT
1 TATAATAATAAAA-TTCTGACTAAAAAA
*
579974 TATAATAATAAAATTCT-ATTAAAAAA
1 TATAATAATAAAATTCTGACTAAAAAA
580000 TATAATAATAAAATT
1 TATAATAATAAAATT
580015 AGTTTTGAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 22 0.56
27 4 0.10
28 13 0.33
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (27 bp):
TATAATAATAAAATTCTGACTAAAAAA
Found at i:580499 original size:22 final size:21
Alignment explanation
Indices: 580473--580516 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
580463 TTTGTTTTAG
* *
580473 TTATTATAATATTAATATATTT
1 TTATTATAAAAATAA-ATATTT
*
580495 TTATTCTAAAAATAAATATTT
1 TTATTATAAAAATAAATATTT
580516 T
1 T
580517 ACTCTGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATTATAAAAATAAATATTT
Found at i:581842 original size:23 final size:23
Alignment explanation
Indices: 581816--581860 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
581806 CACCACAGCT
*
581816 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
581839 CGTAGAATTGCACCGCAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
581861 ATATAATGAT
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:0.31, G:0.24, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:582098 original size:149 final size:149
Alignment explanation
Indices: 581839--582142 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
581829 CGAAGTGCCC
* *
581839 CGTAGAATTGCACCGCAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGCAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
581904 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
581969 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
*
581988 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGCAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
582053 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
582118 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
582137 CGTAGA
1 CGTAGA
582143 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGCAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:582876 original size:2 final size:2
Alignment explanation
Indices: 582869--582894 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
582859 ATTTCATTTC
582869 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
582895 CCTCAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:583151 original size:18 final size:18
Alignment explanation
Indices: 583130--583164 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
583120 TCCCATCTAG
583130 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
583148 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
583165 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:583773 original size:21 final size:21
Alignment explanation
Indices: 583743--583787 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
583733 ATTTTGTCGT
583743 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
583764 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
583785 TTG
1 TTG
583788 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:586931 original size:23 final size:23
Alignment explanation
Indices: 586905--586949 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
586895 CACCACAGCT
* *
586905 CGTATAAATGCACTGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
586928 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
586950 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:587198 original size:149 final size:149
Alignment explanation
Indices: 586928--587231 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
586918 TGAAGTGCCC
* *
586928 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
586993 CATATGCATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
587058 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
587077 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
587142 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
587207 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
587226 CGTAGA
1 CGTAGA
587232 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:588244 original size:18 final size:18
Alignment explanation
Indices: 588223--588257 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
588213 TCCCATCTAG
588223 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
588241 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
588258 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:588866 original size:21 final size:21
Alignment explanation
Indices: 588836--588880 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
588826 ATTTTGTCGT
* *
588836 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
588857 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
588878 TTG
1 TTG
588881 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:591808 original size:19 final size:20
Alignment explanation
Indices: 591784--591832 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
591774 CTATTCAATA
591784 AAATTAATATAAAT-TAATT
1 AAATTAATATAAATATAATT
*
591803 AAATTATTAT-AATATAATT
1 AAATTAATATAAATATAATT
*
591822 AAAATAATATA
1 AAATTAATATA
591833 GAAAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTAATATAAATATAATT
Found at i:599730 original size:14 final size:16
Alignment explanation
Indices: 599669--599734 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
599659 AATCATAATT
*
599669 ATTTTA-AATAATTAA
1 ATTTTATAATAAGTAA
*
599684 ATTTTATAAAAAGTATA
1 ATTTTATAATAAGTA-A
599701 TATTTTTATCAATAA-TAA
1 -A-TTTTAT-AATAAGTAA
599719 ATTTTA-AATAA-TAA
1 ATTTTATAATAAGTAA
599733 AT
1 AT
599735 AAAGAACAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
14 10 0.23
15 6 0.14
16 11 0.26
17 2 0.05
18 2 0.05
19 8 0.19
20 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
ATTTTATAATAAGTAA
Found at i:604753 original size:31 final size:32
Alignment explanation
Indices: 604693--604777 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 32
604683 ATTTAATTTG
*
604693 AATTTCTAAAAATTTTGAAGGAGTCAAATTGA
1 AATTTTTAAAAATTTTGAAGGAGTCAAATTGA
*
604725 AATTTTTTAAAAA-TTT-AAGG-GTCAAAATTTA
1 AA-TTTTTAAAAATTTTGAAGGAGTC-AAATTGA
*
604756 AATTTTT-AAAATTTTGGAGGAG
1 AATTTTTAAAAATTTTGAAGGAG
604778 CCATGACCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 4 0.09
30 11 0.24
31 15 0.33
32 6 0.13
33 9 0.20
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (32 bp):
AATTTTTAAAAATTTTGAAGGAGTCAAATTGA
Found at i:606935 original size:14 final size:14
Alignment explanation
Indices: 606918--606947 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
606908 TCTCTCTCAA
606918 TCTGCCTGTCTCTG
1 TCTGCCTGTCTCTG
606932 TCTGCCTGTCTCTG
1 TCTGCCTGTCTCTG
606946 TC
1 TC
606948 CCTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.37, G:0.20, T:0.43
Consensus pattern (14 bp):
TCTGCCTGTCTCTG
Found at i:618867 original size:14 final size:15
Alignment explanation
Indices: 618833--618873 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
618823 ATCCTATAGT
* *
618833 TTTTAATACTATCAC
1 TTTTAATTCTTTCAC
618848 TTTTAATTCTTTCA-
1 TTTTAATTCTTTCAC
618862 TTTTAATTCTTT
1 TTTTAATTCTTT
618874 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAATTCTTTCAC
Found at i:619179 original size:18 final size:18
Alignment explanation
Indices: 619153--619189 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
619143 ATTAATTTAT
619153 TTTAATTATTTTTTAATA
1 TTTAATTATTTTTTAATA
*
619171 TTTATTTATTTTTTAATA
1 TTTAATTATTTTTTAATA
619189 T
1 T
619190 CGAAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTAATTATTTTTTAATA
Found at i:621283 original size:27 final size:26
Alignment explanation
Indices: 621231--621284 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
621221 TTTGCATTTG
*
621231 TACATTTTTACGTTTGTATTTACATT
1 TACATTTTTACCTTTGTATTTACATT
621257 TACA-TTTTACCTTTGCATATTTACATT
1 TACATTTTTACCTTTG--TATTTACATT
621284 T
1 T
621285 GGCATCTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 10 0.40
26 4 0.16
27 11 0.44
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.56
Consensus pattern (26 bp):
TACATTTTTACCTTTGTATTTACATT
Found at i:621289 original size:15 final size:14
Alignment explanation
Indices: 621247--621299 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 14
621237 TTTACGTTTG
*
621247 TATTTACATTTACA
1 TATTTACATTTGCA
*
621261 T-TTTACCTTTGCA
1 TATTTACATTTGCA
621274 TATTTACATTTGGCA
1 TATTTACATTT-GCA
* *
621289 TCTTTGCATTT
1 TATTTACATTT
621300 TTTATGTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.34
14 9 0.28
15 12 0.38
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.53
Consensus pattern (14 bp):
TATTTACATTTGCA
Found at i:623502 original size:2 final size:2
Alignment explanation
Indices: 623495--623538 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
623485 TCCTTTAATA
623495 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
623537 AT
1 AT
623539 CCTTTGTTGT
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:626509 original size:21 final size:21
Alignment explanation
Indices: 626483--626527 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
626473 GATTTCTGGG
* *
626483 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
626504 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
626525 CAA
1 CAA
626528 ACGAACAAGA
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:627241 original size:74 final size:74
Alignment explanation
Indices: 627083--627250 Score: 214
Period size: 74 Copynumber: 2.3 Consensus size: 74
627073 AACAAGAAGC
* * *
627083 AAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGAAATGTTGAAATATTCTGAATAT
1 AAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACAT
627148 TTATCAGCA
66 TTATCAGCA
* * ** *
627157 AAATGCTGGGGCATGCTGAAAACCCATTTCAATCAG-ATCAGAACTGTTGATGCATTTTGAACAC
1 AAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACA-
*
627221 TTGTATTAGC-
65 TT-TATCAGCA
*
627231 CAATGTTGGGGCATGCTGAA
1 AAATGTTGGGGCATGCTGAA
627251 GGCCCCAACA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
73 21 0.26
74 54 0.67
75 6 0.07
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (74 bp):
AAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACAT
TTATCAGCA
Found at i:628548 original size:21 final size:22
Alignment explanation
Indices: 628516--628592 Score: 88
Period size: 21 Copynumber: 3.6 Consensus size: 22
628506 ACATCTACAT
628516 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
628538 TCTTC-AAGATGATAGATTC-C
1 TCTTCAAAGATGATAGATTCTC
* * *
628558 TTTTTAAAGATG-TCATATTCTC
1 TCTTCAAAGATGAT-AGATTCTC
*
628580 TTTTCAAAGATGA
1 TCTTCAAAGATGA
628593 AAGCTTTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.11
21 25 0.53
22 17 0.36
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:629191 original size:114 final size:113
Alignment explanation
Indices: 628991--629443 Score: 698
Period size: 114 Copynumber: 4.0 Consensus size: 113
628981 TAGGAAAAAG
* * *
628991 TCAAATTCATCACTCGATGGATCAGCATTGCCAGGTAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTCGATGGATCAACATT-CCAGGTAGAAGTTCATAATGAGAAGAACTCATCTG
*
629056 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
629105 TCAAATCCATCACTCGATGGATCAACATTACCAGGTAGAAAGTTCATAATGAGAAGAACTCATCT
1 TCAAATCCATCACTCGATGGATCAACATT-CCAGGTAG-AAGTTCATAATGAGAAGAACTCATCT
*
629170 GAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
629219 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTG-AGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTCGATGGATCAAC-ATTCCAGGTAGAAGTTCATAATGAGAAGAACTCATCTG
629283 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
629332 TTC-AATTCATCACTCGATGGATCAACATTGCAGGTAGAAGGTCATAATGAGAAGAACTCATTTG
1 -TCAAATCCATCACTCGATGGATCAACATTCCAGGTAGAAGTTCATAATGAGAAGAACTCATCTG
*
629396 AAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
629444 ATGACTCTAT
Statistics
Matches: 312, Mismatches: 22, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
112 80 0.26
113 91 0.29
114 109 0.35
115 32 0.10
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCACTCGATGGATCAACATTCCAGGTAGAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:631345 original size:18 final size:18
Alignment explanation
Indices: 631319--631355 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
631309 ATTAATTTAT
631319 TTTAATTATTTTTTAATA
1 TTTAATTATTTTTTAATA
*
631337 TTTATTTATTTTTTAATA
1 TTTAATTATTTTTTAATA
631355 T
1 T
631356 CGAAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTAATTATTTTTTAATA
Found at i:637155 original size:20 final size:19
Alignment explanation
Indices: 637130--637188 Score: 68
Period size: 17 Copynumber: 3.2 Consensus size: 19
637120 CCGTTAGACA
637130 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTA-CCCCT
*
637150 GGGGGGAATCTGTACCCCT
1 GGGGGGAATCGGTACCCCT
* *
637169 --GGGCAATCTGTACCCCT
1 GGGGGGAATCGGTACCCCT
637186 GGG
1 GGG
637189 CAATCTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 16 0.46
19 6 0.17
20 13 0.37
ACGTcount: A:0.15, C:0.29, G:0.37, T:0.19
Consensus pattern (19 bp):
GGGGGGAATCGGTACCCCT
Found at i:637178 original size:17 final size:17
Alignment explanation
Indices: 637156--637195 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
637146 CCCTGGGGGG
637156 AATCTGTACCCCTGGGC
1 AATCTGTACCCCTGGGC
637173 AATCTGTACCCCTGGGC
1 AATCTGTACCCCTGGGC
637190 AATCTG
1 AATCTG
637196 ATTTTTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.25
Consensus pattern (17 bp):
AATCTGTACCCCTGGGC
Found at i:643428 original size:18 final size:18
Alignment explanation
Indices: 643402--643436 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
643392 TCGAAAGGAC
*
643402 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
643420 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
643437 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:648658 original size:18 final size:18
Alignment explanation
Indices: 648632--648666 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
648622 TCGAAAGGAC
*
648632 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
648650 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
648667 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:657935 original size:2 final size:2
Alignment explanation
Indices: 657928--657952 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
657918 ACTTAATTAA
657928 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 A
657953 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:658482 original size:23 final size:23
Alignment explanation
Indices: 658456--658506 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
658446 GTCAAATTTT
658456 AATTCCCTCCAACAAGGGAATTG
1 AATTCCCTCCAACAAGGGAATTG
658479 AATTCCCTCCAACAAGGGAATTG
1 AATTCCCTCCAACAAGGGAATTG
658502 AATTC
1 AATTC
658507 TATCATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (23 bp):
AATTCCCTCCAACAAGGGAATTG
Found at i:672362 original size:165 final size:168
Alignment explanation
Indices: 672063--672381 Score: 495
Period size: 165 Copynumber: 1.9 Consensus size: 168
672053 AGTACTGAAT
* ** *
672063 GTGCAATTAAACAAAGATGAAAATTGGCTTAAAAAAGAATCACAATTCGCATGCTCCACTCTACT
1 GTGCAATTAAAAAAAGACAAAAATTGGCTTAAAAAAGAATCACAATTCACATGCTCCACTCTACT
672128 CAACCCAAACTCCATAGTTCCAGACATAAAGGAAAAAAGACACATAAATGCATTTGAAATCCTTT
66 CAACCCAAACTCCATAGTTCCAGACATAAAGGAAAAAAGACACATAAATGCATTTGAAATCCTTT
*
672193 AGCAAAATGAGGTTTTTATTTAACAATGAATAGATCAC
131 AGCAAAATGAGGGTTTTATTTAACAATGAATAGATCAC
* * *
672231 GTGCAATTAAAAAAAGACAAAAATTGGCTTGAAAAAAGAATCACATTTCACAT-CTCTAGTCTAC
1 GTGCAATTAAAAAAAGACAAAAATTGGCTT-AAAAAAGAATCACAATTCACATGCTCCACTCTAC
*
672295 T-AACCCAAACTCCATAGTTCCAGACAT-AAGG-AAAAAGACACTTAAATG-AGTTTGAAATCCT
65 TCAACCCAAACTCCATAGTTCCAGACATAAAGGAAAAAAGACACATAAATGCA-TTTGAAATCCT
*
672356 TTAGCAACATGAGGGTTTTATTTAAC
129 TTAGCAAAATGAGGGTTTTATTTAAC
672382 TACGAATTAA
Statistics
Matches: 139, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
164 1 0.01
165 51 0.37
166 4 0.03
167 26 0.19
168 37 0.27
169 20 0.14
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (168 bp):
GTGCAATTAAAAAAAGACAAAAATTGGCTTAAAAAAGAATCACAATTCACATGCTCCACTCTACT
CAACCCAAACTCCATAGTTCCAGACATAAAGGAAAAAAGACACATAAATGCATTTGAAATCCTTT
AGCAAAATGAGGGTTTTATTTAACAATGAATAGATCAC
Found at i:684266 original size:49 final size:49
Alignment explanation
Indices: 684209--684307 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
684199 GTTTCAGGGG
684209 AAATATACCAATGTTGGCAAGCAATACACCGACAACCATTAGATGAACT
1 AAATATACCAATGTTGGCAAGCAATACACCGACAACCATTAGATGAACT
684258 AAATATACCAATGTTGGCAAGCAATACACCGACAACCATTAGATGAACT
1 AAATATACCAATGTTGGCAAGCAATACACCGACAACCATTAGATGAACT
684307 A
1 A
684308 TCTTGCTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.20
Consensus pattern (49 bp):
AAATATACCAATGTTGGCAAGCAATACACCGACAACCATTAGATGAACT
Found at i:692104 original size:8 final size:8
Alignment explanation
Indices: 692105--692137 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
692095 ATAAAATTAT
692105 ATTTTTAAA
1 ATTT-TAAA
692114 ATTTTAAA
1 ATTTTAAA
692122 ATTTTAAA
1 ATTTTAAA
692130 ATTTTAAA
1 ATTTTAAA
692138 TACATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 20 0.83
9 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTTAAA
Found at i:692112 original size:25 final size:24
Alignment explanation
Indices: 692056--692115 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
692046 CCATTTTAAT
*
692056 TTATTTAAAAAAACTATAAATTTA
1 TTATTTAAAATAACTATAAATTTA
* *
692080 TTAATTAAAATAATTATAAAATTATA
1 TTATTTAAAATAACTAT-AAATT-TA
692106 TT-TTTAAAAT
1 TTATTTAAAAT
692116 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 14 0.47
25 12 0.40
26 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATTTAAAATAACTATAAATTTA
Found at i:693680 original size:6 final size:6
Alignment explanation
Indices: 693669--693696 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
693659 CAGAGGAGAA
693669 TGGGAC TGGGAC TGGGAC TGGGAC TGGG
1 TGGGAC TGGGAC TGGGAC TGGGAC TGGG
693697 TGGTTGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.54, T:0.18
Consensus pattern (6 bp):
TGGGAC
Found at i:704507 original size:25 final size:25
Alignment explanation
Indices: 704478--704527 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
704468 ATAATTCTTG
704478 CTGATAGAAACAGGCGGCCCTGCAT
1 CTGATAGAAACAGGCGGCCCTGCAT
704503 CTGATAGAAACAGGCGGCCCTGCAT
1 CTGATAGAAACAGGCGGCCCTGCAT
704528 AGATGCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (25 bp):
CTGATAGAAACAGGCGGCCCTGCAT
Found at i:708074 original size:34 final size:32
Alignment explanation
Indices: 708014--708083 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
708004 ATCTTACAAC
* *
708014 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGAGCTAAACTAGAACCTT
*
708046 TCCCTAGCTTTTACACGAGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGAGCTAAACTAGAACCTT
708080 TCCC
1 TCCC
708084 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGAGCTAAACTAGAACCTT
Found at i:708323 original size:20 final size:22
Alignment explanation
Indices: 708298--708337 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
708288 TGTTGTATAT
708298 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
708318 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
708338 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:708473 original size:20 final size:20
Alignment explanation
Indices: 708440--708512 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
708430 GCAGTCTTCG
* *
708440 TGCATGGATACACAGCAGGA
1 TGCATCGATGCACAGCAGGA
708460 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
708480 TGCATCGATGCACAGCAAGA
1 TGCATCGATGCACAGCAGGA
*
708500 TGTATCGATGCAC
1 TGCATCGATGCAC
708513 TAAGTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:710004 original size:19 final size:20
Alignment explanation
Indices: 709961--710008 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
709951 TCTAAATCCT
*
709961 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
709981 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
710000 TTTTCAAAA
1 TTTTCAAAA
710009 GAAAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:711177 original size:20 final size:22
Alignment explanation
Indices: 711152--711191 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
711142 TGTTGTATAT
711152 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
711172 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
711192 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:711423 original size:21 final size:21
Alignment explanation
Indices: 711356--711454 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
711346 TCGAAATGGA
*
711356 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* *
711376 GTGCCTCGATGCACT--AGTGCAG
1 GTGCATGGATGCACTGCAG-G--G
*
711398 GTGCATGGATACACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
711419 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
711440 GTGCATGGATGCACT
1 GTGCATGGATGCACT
711455 TTGACACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
20 13 0.20
21 36 0.55
22 13 0.20
23 1 0.02
24 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.36, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:723672 original size:35 final size:35
Alignment explanation
Indices: 723633--723703 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
723623 CCTTCAATGC
*
723633 AGAAAGTGGATTATACCTTTCATCCCAGATGAACA
1 AGAAAGTGAATTATACCTTTCATCCCAGATGAACA
*
723668 AGAAAGTGAATTTTACCTTTCATCCCAGATGAACA
1 AGAAAGTGAATTATACCTTTCATCCCAGATGAACA
723703 A
1 A
723704 ACTTTGTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (35 bp):
AGAAAGTGAATTATACCTTTCATCCCAGATGAACA
Found at i:724448 original size:2 final size:2
Alignment explanation
Indices: 724441--724505 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
724431 GATAGCTTTG
724441 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
*
724483 AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
724506 CAGAGAGAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 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):
AT
Found at i:759953 original size:31 final size:31
Alignment explanation
Indices: 759918--760005 Score: 142
Period size: 31 Copynumber: 2.8 Consensus size: 31
759908 ATAGACACTT
759918 AAAGTGTAATAGAGAAAACGTTAGACGCCTA
1 AAAGTGTAATAGAGAAAACGTTAGACGCCTA
*
759949 AAAGTGTAATAGAAAAAACGTTAGACGCCTA
1 AAAGTGTAATAGAGAAAACGTTAGACGCCTA
*
759980 AAAGTGTAAT-GCAGAAAACATTAGAC
1 AAAGTGTAATAG-AGAAAACGTTAGAC
760006 ATCTATTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
30 1 0.02
31 52 0.98
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.19
Consensus pattern (31 bp):
AAAGTGTAATAGAGAAAACGTTAGACGCCTA
Found at i:760614 original size:11 final size:11
Alignment explanation
Indices: 760598--760631 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
760588 TCTAGCTCAT
760598 TTAGTTGCATA
1 TTAGTTGCATA
760609 TTAGTTGCAT-
1 TTAGTTGCATA
*
760619 CTAGTTGCATA
1 TTAGTTGCATA
760630 TT
1 TT
760632 TCATGCATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (11 bp):
TTAGTTGCATA
Found at i:760638 original size:21 final size:21
Alignment explanation
Indices: 760599--760639 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
760589 CTAGCTCATT
**
760599 TAGTTGCATATTAGTTGCATC
1 TAGTTGCATATTACATGCATC
*
760620 TAGTTGCATATTTCATGCAT
1 TAGTTGCATATTACATGCAT
760640 GTGGTGGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (21 bp):
TAGTTGCATATTACATGCATC
Found at i:763393 original size:2 final size:2
Alignment explanation
Indices: 763386--763448 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
763376 TTGTGGACAC
763386 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
763428 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
763449 CAAAATGATA
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:764757 original size:14 final size:14
Alignment explanation
Indices: 764720--764760 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
764710 GAAATCTACT
*
764720 TTAACAGTTAATGG
1 TTAACAGTTAACGG
**
764734 TTAATGGTTAACGG
1 TTAACAGTTAACGG
764748 TTAACAGTTAACG
1 TTAACAGTTAACG
764761 TGCATTTAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (14 bp):
TTAACAGTTAACGG
Found at i:776203 original size:19 final size:19
Alignment explanation
Indices: 776179--776217 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
776169 GTTTTACAGA
* *
776179 ATCAAATTCAATTTTTATC
1 ATCAAATTAAAATTTTATC
776198 ATCAAATTAAAATTTTATC
1 ATCAAATTAAAATTTTATC
776217 A
1 A
776218 ATTGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (19 bp):
ATCAAATTAAAATTTTATC
Found at i:776501 original size:79 final size:78
Alignment explanation
Indices: 776406--776560 Score: 249
Period size: 79 Copynumber: 2.0 Consensus size: 78
776396 TCCTCTCGAT
*
776406 TCTCAACTTGATATTAATTTAAGGATAATAATTTA-TCATTCAACTCGAATTTTAGAGTTAAAAT
1 TCTCAACTTGATATTAATTTAAGGATAATAA-TTAGTCACTCAACTCGAATTTTAGAGTT-AAAT
*
776470 TCATCCAGAACCTTA
64 TCACCCAGAACCTTA
*
776485 TCTCAACTTGATATTAATTTAAGGATACTAATTAGTCACTCAACTCGAATTTTAGAGTTAAATTC
1 TCTCAACTTGATATTAATTTAAGGATAATAATTAGTCACTCAACTCGAATTTTAGAGTTAAATTC
*
776550 ACCCATAACCT
66 ACCCAGAACCT
776561 AACTCAGTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
78 18 0.25
79 53 0.75
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (78 bp):
TCTCAACTTGATATTAATTTAAGGATAATAATTAGTCACTCAACTCGAATTTTAGAGTTAAATTC
ACCCAGAACCTTA
Found at i:777924 original size:188 final size:186
Alignment explanation
Indices: 777577--777970 Score: 657
Period size: 188 Copynumber: 2.1 Consensus size: 186
777567 TTTTCTAATT
* * * *
777577 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
777641 ATTATAAAATAAAAATTGTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTGTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
777706 TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
131 TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
777762 TATATAATATATTTAATATTTTTTAATT-AAAAAAACAATTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
* *
777826 ATTATAAAATATAAATTTTATATAAATTTTTAATTAATTAATTAATATTGATTTAGGTTTAAAAG
66 ATTATAAAATAAAAATTGTATATAAA-TTTT--TTAATTAATTAATATTGATTTAGGTTTAAAAG
*
777891 TTATTGGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
128 TTATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
777950 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
777971 AAAATTTTAA
Statistics
Matches: 195, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
185 65 0.33
186 21 0.11
188 109 0.56
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTGTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:777991 original size:9 final size:9
Alignment explanation
Indices: 777977--778009 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
777967 ATTTAAAATT
777977 TTAATTCGG
1 TTAATTCGG
777986 TTAATTCGG
1 TTAATTCGG
777995 TTAATTCGG
1 TTAATTCGG
778004 TTAATT
1 TTAATT
778010 AACCAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (9 bp):
TTAATTCGG
Found at i:778558 original size:23 final size:24
Alignment explanation
Indices: 778531--778577 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
778521 CACACCCGCT
778531 ATAAAAATA-AAATCAAT-AATATA
1 ATAAAAATATAAAT-AATAAATATA
778554 ATAAAAATATAAATAATAAATATA
1 ATAAAAATATAAATAATAAATATA
778578 CGGTGGACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (24 bp):
ATAAAAATATAAATAATAAATATA
Found at i:785227 original size:60 final size:59
Alignment explanation
Indices: 785103--785231 Score: 168
Period size: 60 Copynumber: 2.2 Consensus size: 59
785093 ACTTCAAGAA
* * * * * *
785103 AGTTGAGTGGCCAAATTGATAGCACAATTTTTAAATGGACATATTATTTGGTAGGGTGT
1 AGTTGAGTGGCCAAATTGATAGCAAAATTATTAAATGGACACATTATTTGATAGAGTAT
* * *
785162 GGTTGAGTGGCCAATTTGATAGACAAAATTATTAAATGGGCACATTATTTGATAGAGTAT
1 AGTTGAGTGGCCAAATTGATAG-CAAAATTATTAAATGGACACATTATTTGATAGAGTAT
785222 AGTTGAGTGG
1 AGTTGAGTGG
785232 TGAAAGTGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
59 20 0.34
60 39 0.66
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (59 bp):
AGTTGAGTGGCCAAATTGATAGCAAAATTATTAAATGGACACATTATTTGATAGAGTAT
Found at i:786129 original size:106 final size:106
Alignment explanation
Indices: 786001--786195 Score: 293
Period size: 107 Copynumber: 1.8 Consensus size: 106
785991 GGATTAATTT
*
786001 GCTTAACAGTTTGAGTGGAGTTCTATTTTTAAAATCCTCTGGT-GAAACTGGAATTCGAAATTTT
1 GCTTAACAGTTTGAGTGGAGTTCTATTTTTAAAATCCTCTGGTGGAAACCGGAATTCGAAATTTT
*
786065 AAATCTTGGCCATGGAAAGCTTAGTGGGAGAAGCATAACTA
66 AAATCTTGACCATGGAAAGCTTAGTGGGAGAAGCATAACTA
* * * *
786106 GCTTAAGAGTTTTGAGTGTAGTTCTATTTTTTAAATCTTCTGGTGGAAACCGGAATTCGAAATTT
1 GCTTAACAG-TTTGAGTGGAGTTCTATTTTTAAAATCCTCTGGTGGAAACCGGAATTCGAAATTT
* **
786171 TGAATCTTGACCATTTAAAGCTTAG
65 TAAATCTTGACCATGGAAAGCTTAG
786196 CGAGTATATA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 8 0.10
106 31 0.39
107 40 0.51
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (106 bp):
GCTTAACAGTTTGAGTGGAGTTCTATTTTTAAAATCCTCTGGTGGAAACCGGAATTCGAAATTTT
AAATCTTGACCATGGAAAGCTTAGTGGGAGAAGCATAACTA
Found at i:792920 original size:91 final size:93
Alignment explanation
Indices: 792761--792936 Score: 286
Period size: 92 Copynumber: 1.9 Consensus size: 93
792751 TAAAGTTTAG
792761 AAATCAATTAAATATTATTTATTAAAAACAATTAATCCATTTTCTTGTGTCATTTTTATTTTAAA
1 AAATCAATTAAATATTATTTATTAAAAACAATTAATCCATTTTCTTGTGTCATTTTTATTTTAAA
*
792826 ATAC-AAAATTTATGTATTTATTTAAAA
66 ATACAAAAAATTATGTATTTATTTAAAA
* * *
792853 AAATCAATTAAATATTATTTATTAAAAATAA-TATATCTA-TTTCTTTTGTCATTTTTATTTTAA
1 AAATCAATTAAATATTATTTATTAAAAACAATTA-ATCCATTTTCTTGTGTCATTTTTATTTTAA
792916 AATACAAAAAATTATGTATTT
65 AATACAAAAAATTATGTATTT
792937 TTCCTTCTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
91 30 0.38
92 48 0.62
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (93 bp):
AAATCAATTAAATATTATTTATTAAAAACAATTAATCCATTTTCTTGTGTCATTTTTATTTTAAA
ATACAAAAAATTATGTATTTATTTAAAA
Found at i:792996 original size:22 final size:22
Alignment explanation
Indices: 792971--793013 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
792961 TTAAAGTTGA
792971 TGACTTCAATAAAATTATAAAG
1 TGACTTCAATAAAATTATAAAG
*
792993 TGACTTTAATAAAATTATAAA
1 TGACTTCAATAAAATTATAAA
793014 ATGTTTCATC
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:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (22 bp):
TGACTTCAATAAAATTATAAAG
Found at i:795166 original size:39 final size:39
Alignment explanation
Indices: 795109--795214 Score: 133
Period size: 39 Copynumber: 2.7 Consensus size: 39
795099 CATAATTTTC
* * * *
795109 AAATTAATTT-ACCCTAACATTATAAATTCTCAATCTGTT
1 AAATT-ATTTCACCATAACATTCTAAATTCTAAATCTCTT
*
795148 AAATTATTTCACCATAACATTCTAAATTCTAAATTTCTT
1 AAATTATTTCACCATAACATTCTAAATTCTAAATCTCTT
* *
795187 AAATTATTTCATCATAAGATTCTAAATT
1 AAATTATTTCACCATAACATTCTAAATT
795215 GTTTCTCAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 4 0.07
39 55 0.93
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (39 bp):
AAATTATTTCACCATAACATTCTAAATTCTAAATCTCTT
Found at i:801830 original size:25 final size:26
Alignment explanation
Indices: 801798--801873 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 26
801788 TTGAATGTTA
801798 AATA-AATTAGTA-ATATAATTTTTT
1 AATATAATTAGTAGATATAATTTTTT
*
801822 AATATAATTAAG-AGGT-T-ATTTGTTT
1 AATATAATT-AGTAGATATAATTT-TTT
* *
801847 AATATAATTAGTAGTTATAATTATTT
1 AATATAATTAGTAGATATAATTTTTT
801873 A
1 A
801874 TTGCAACATT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
24 10 0.24
25 21 0.50
26 8 0.19
27 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (26 bp):
AATATAATTAGTAGATATAATTTTTT
Found at i:812205 original size:160 final size:159
Alignment explanation
Indices: 811950--812264 Score: 621
Period size: 160 Copynumber: 2.0 Consensus size: 159
811940 ATTCTTCGAG
811950 TTACCTTTGTATGATGAAAGATTTAATTAAGCAAACACAACACAAAGTTTTATATGTGAATGTGA
1 TTACCTTTGTATGATGAAAGATTTAATTAAGCAAACACAACACAAAGTTTTATATGTGAATGTGA
812015 TACAATAATATATTTTATAATAATTGTTTTTTTTAACGGTGACTATATTATAATCTTACTTTTTT
66 TACAATAATATATTTTATAATAATTGTTTTTTTTAACGGTGACTATATTATAATCTTAC-TTTTT
812080 GCAATTAAAATGAAAGTTTATTAAAGGAGT
130 GCAATTAAAATGAAAGTTTATTAAAGGAGT
812110 TTACCTTTGTATGATGAAAGATTTAATTAAGCAAACACAACACAAAGTTTTATATGTGAATGTGA
1 TTACCTTTGTATGATGAAAGATTTAATTAAGCAAACACAACACAAAGTTTTATATGTGAATGTGA
812175 TACAATAATATATTTTATAATAATTGTTTTTTTTAACGGTGACTATATTATAATCTTACTTTTTG
66 TACAATAATATATTTTATAATAATTGTTTTTTTTAACGGTGACTATATTATAATCTTACTTTTTG
812240 CAATTAAAATGAAAGTTTATTAAAG
131 CAATTAAAATGAAAGTTTATTAAAG
812265 TTGCGTGGCT
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 31 0.20
160 124 0.80
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.41
Consensus pattern (159 bp):
TTACCTTTGTATGATGAAAGATTTAATTAAGCAAACACAACACAAAGTTTTATATGTGAATGTGA
TACAATAATATATTTTATAATAATTGTTTTTTTTAACGGTGACTATATTATAATCTTACTTTTTG
CAATTAAAATGAAAGTTTATTAAAGGAGT
Found at i:820660 original size:14 final size:14
Alignment explanation
Indices: 820643--820689 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
820633 TGTAATAGTA
820643 AATTTGTAC-TGTTT
1 AATTTG-ACTTGTTT
820657 AATTTGACTTGTTT
1 AATTTGACTTGTTT
820671 AATTTGACTTGTTT
1 AATTTGACTTGTTT
820685 AATTT
1 AATTT
820690 ATCAGTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 2 0.06
14 30 0.94
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.57
Consensus pattern (14 bp):
AATTTGACTTGTTT
Found at i:827331 original size:16 final size:16
Alignment explanation
Indices: 827310--827350 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
827300 ACTAAATCAT
*
827310 GTTTGCTTTCGATTGG
1 GTTTGCTTTCGATTCG
*
827326 GTTTGCTTTCGGTTCG
1 GTTTGCTTTCGATTCG
827342 GTTTGCTTT
1 GTTTGCTTT
827351 TGGTCCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.02, C:0.15, G:0.29, T:0.54
Consensus pattern (16 bp):
GTTTGCTTTCGATTCG
Found at i:827642 original size:17 final size:18
Alignment explanation
Indices: 827620--827653 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
827610 AAAAGATAAA
827620 AAAATATATT-ATTATTC
1 AAAATATATTGATTATTC
*
827637 AAAATATTTTGATTATT
1 AAAATATATTGATTATT
827654 TCCGGTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
AAAATATATTGATTATTC
Found at i:828306 original size:22 final size:22
Alignment explanation
Indices: 828281--828328 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
828271 CTACTCATAC
*
828281 TTTAAAGCATCAAAATAGTTTT
1 TTTAAAGCATCAAAATAATTTT
828303 TTTAAAGCATCAAAATAATTTT
1 TTTAAAGCATCAAAATAATTTT
828325 TTTA
1 TTTA
828329 TTGATGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (22 bp):
TTTAAAGCATCAAAATAATTTT
Found at i:833646 original size:23 final size:23
Alignment explanation
Indices: 833616--833667 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
833606 ATATTTTTAG
833616 TAACATATTCATTTAACATCTGC
1 TAACATATTCATTTAACATCTGC
* *
833639 TAACATATTCATTTAACGTTTGC
1 TAACATATTCATTTAACATCTGC
833662 TAACAT
1 TAACAT
833668 GTTCCCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (23 bp):
TAACATATTCATTTAACATCTGC
Found at i:833677 original size:23 final size:23
Alignment explanation
Indices: 833616--833700 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
833606 ATATTTTTAG
* *
833616 TAACATATTCATTTAACA-TCTGC
1 TAACATATTCACTTAA-AGTTTGC
* *
833639 TAACATATTCATTTAACGTTTGC
1 TAACATATTCACTTAAAGTTTGC
* *
833662 TAACATGTTCCCTTAAAAGTTTGC
1 TAACATATTCACTT-AAAGTTTGC
* *
833686 TAACATCTTCGCTTA
1 TAACATATTCACTTA
833701 TATGGTCTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
23 32 0.62
24 20 0.38
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (23 bp):
TAACATATTCACTTAAAGTTTGC
Found at i:842554 original size:16 final size:16
Alignment explanation
Indices: 842535--842568 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
842525 GCATCCAAGA
842535 GAAACATGA-CATATTC
1 GAAA-ATGAGCATATTC
842551 GAAAATGAGCATATTC
1 GAAAATGAGCATATTC
842567 GA
1 GA
842569 GTATACCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (16 bp):
GAAAATGAGCATATTC
Found at i:845321 original size:78 final size:79
Alignment explanation
Indices: 845237--845492 Score: 268
Period size: 77 Copynumber: 3.2 Consensus size: 79
845227 ATAAAAATTC
* *
845237 AAAATTTTGACTCGACTCGA-AAAAATTTTAAGTCAACTCTAAGTTATAAAATAAAACTCATCAA
1 AAAATTTTGACTCGACTCGACAAAAATTTTAAGTCAACTCTAAGTTATAAAATAAGACTCGTCAA
845301 CTCGAATAACTCAA
66 CTCGAATAACTCAA
* * * ** *
845315 AAAATTTTGACTCGACTC-ATAAAAA-TTCAAGTCCACTCCGAGTTATAAAATAAGACCCGTCAA
1 AAAATTTTGACTCGACTCGACAAAAATTTTAAGTCAACTCTAAGTTATAAAATAAGACTCGTCAA
845378 CTCGAATAACTCAA
66 CTCGAATAACTCAA
** * * * *
845392 AATTTTTTTGACTCAACTCGACTCAAAAATTTTTTTAAGTCTACTCTAAATTATAAAATAGGACT
1 AA-AATTTTGACTCGACTCGA--CAAAAA---TTTTAAGTCAACTCTAAGTTATAAAATAAGACT
* *
845457 TGTCAGCTCGAATAACTC-A
60 CGTCAACTCGAATAACTCAA
**
845476 AATTTTTTGACTCGACT
1 AAAATTTTGACTCGACT
845493 TGATTGAACA
Statistics
Matches: 148, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
77 48 0.32
78 36 0.24
79 1 0.01
81 5 0.03
83 14 0.09
84 3 0.02
85 41 0.28
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (79 bp):
AAAATTTTGACTCGACTCGACAAAAATTTTAAGTCAACTCTAAGTTATAAAATAAGACTCGTCAA
CTCGAATAACTCAA
Found at i:847715 original size:17 final size:17
Alignment explanation
Indices: 847693--847737 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
847683 GTTTATTTTT
847693 TTAATTTCAAATTACTC
1 TTAATTTCAAATTACTC
*
847710 TTAATTT--AATCACTC
1 TTAATTTCAAATTACTC
847725 -TAACTTTCAAATT
1 TTAA-TTTCAAATT
847738 TATTTTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
17 10 0.43
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTTCAAATTACTC
Found at i:852885 original size:15 final size:15
Alignment explanation
Indices: 852865--852896 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
852855 AAAATATTTC
*
852865 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
852880 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
852895 TT
1 TT
852897 GGATCTGCCA
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:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:854123 original size:21 final size:21
Alignment explanation
Indices: 854099--854159 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
854089 AAACATCTAC
854099 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
**
854120 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
854135 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
854156 CAAA
1 CAAA
854160 GTTGGTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 12 0.40
17 1 0.03
19 1 0.03
21 16 0.53
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:854136 original size:36 final size:36
Alignment explanation
Indices: 854081--854160 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
854071 CCCATTCTTA
*
854081 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
*
854116 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
854152 TTTTCAAAG
1 TTTTCAAAG
854161 TTGGTTGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 5 0.12
36 37 0.88
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
Found at i:854949 original size:2 final size:2
Alignment explanation
Indices: 854942--854972 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
854932 TTGAACAATG
854942 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
854973 GTTGATTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:869356 original size:2 final size:2
Alignment explanation
Indices: 869349--869444 Score: 63
Period size: 2 Copynumber: 54.0 Consensus size: 2
869339 GAAAATATTT
* *
869349 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA -A AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
869385 TA TA TA TA -A T- TA -A TA TA -A AA AA TA TA -A AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
869421 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
869445 ATCGGGGCGG
Statistics
Matches: 78, Mismatches: 4, Indels: 24
0.74 0.04 0.23
Matches are distributed among these distances:
1 12 0.15
2 66 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:869396 original size:36 final size:36
Alignment explanation
Indices: 869340--869428 Score: 155
Period size: 36 Copynumber: 2.5 Consensus size: 36
869330 TCCGAACCCG
*
869340 AAAATATT-T-TATATATAATTAATATAAAATATAT
1 AAAATATTATATATATATAATTAATATAAAAAATAT
869374 AAAATATTATATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATATAATTAATATAAAAAATAT
869410 AAAATATTATATATATATA
1 AAAATATTATATATATATA
869429 TATATATATA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
34 8 0.15
35 1 0.02
36 43 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
AAAATATTATATATATATAATTAATATAAAAAATAT
Found at i:869444 original size:34 final size:36
Alignment explanation
Indices: 869340--869445 Score: 141
Period size: 36 Copynumber: 3.1 Consensus size: 36
869330 TCCGAACCCG
*
869340 AAAATATTTTATATATA-AT-TAATATAAAATATAT
1 AAAATATTATATATATATATATAATATAAAATATAT
*
869374 AAAATATTATATATATATA-ATTAATATAAAAAATAT
1 AAAATATTATATATATATATA-TAATATAAAATATAT
*
869410 AAAATATTATATATATATATAT-ATAT-ATATATAT
1 AAAATATTATATATATATATATAATATAAAATATAT
869444 AA
1 AA
869446 TCGGGGCGGG
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
34 24 0.38
35 5 0.08
36 34 0.53
37 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
AAAATATTATATATATATATATAATATAAAATATAT
Found at i:870460 original size:5 final size:5
Alignment explanation
Indices: 870450--870475 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
870440 TGACTTAGAA
870450 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
870476 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:873166 original size:2 final size:2
Alignment explanation
Indices: 873159--873206 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
873149 AAATTGAAAG
873159 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
873201 AT AT AT
1 AT AT AT
873207 GATGGATGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:887384 original size:15 final size:16
Alignment explanation
Indices: 887359--887390 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
887349 TATCGTCGAC
887359 CGAATTTCACTATTCA
1 CGAATTTCACTATTCA
887375 CGAA-TTCACTATTCA
1 CGAATTTCACTATTCA
887390 C
1 C
887391 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAATTTCACTATTCA
Found at i:887851 original size:23 final size:22
Alignment explanation
Indices: 887824--887877 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
887814 CTACCAAAAT
887824 TTTACCAAACTTTCAAAGAAACA
1 TTTACCAAACTTTCAAA-AAACA
* *
887847 TTTACCAAACTTTGAAAAAATA
1 TTTACCAAACTTTCAAAAAACA
*
887869 TTTTCCAAA
1 TTTACCAAA
887878 GTTGGTTGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (22 bp):
TTTACCAAACTTTCAAAAAACA
Found at i:887876 original size:22 final size:23
Alignment explanation
Indices: 887822--887877 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
887812 ATCTACCAAA
887822 ATTTTACCAAACTTTCAAAGAAAC
1 ATTTT-CCAAACTTTCAAAGAAAC
* * *
887846 ATTTACCAAACTTTGAAA-AAAT
1 ATTTTCCAAACTTTCAAAGAAAC
887868 ATTTTCCAAA
1 ATTTTCCAAA
887878 GTTGGTTGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 12 0.43
23 12 0.43
24 4 0.14
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (23 bp):
ATTTTCCAAACTTTCAAAGAAAC
Found at i:890106 original size:19 final size:19
Alignment explanation
Indices: 890082--890136 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
890072 TGATAGTGGT
*
890082 TTTAATTCAATCTAATATC
1 TTTAATTAAATCTAATATC
*
890101 TTTAATTTAAT-TCAATATC
1 TTTAATTAAATCT-AATATC
890120 TTTAATTAATATCTAAT
1 TTTAATTAA-ATCTAAT
890137 CAAATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 1 0.03
19 24 0.77
20 5 0.16
21 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAATTAAATCTAATATC
Found at i:890512 original size:2 final size:2
Alignment explanation
Indices: 890505--890540 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
890495 GTACGAATGC
890505 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
890541 CTCATAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:902126 original size:27 final size:27
Alignment explanation
Indices: 902096--902150 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
902086 CGTCGTCGTT
902096 GATTAGTTGTGGATCGTACTCACTGTC
1 GATTAGTTGTGGATCGTACTCACTGTC
902123 GATTAGTTGTGGATCGTACTCACTGTC
1 GATTAGTTGTGGATCGTACTCACTGTC
902150 G
1 G
902151 TCTAGACCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (27 bp):
GATTAGTTGTGGATCGTACTCACTGTC
Found at i:902339 original size:24 final size:24
Alignment explanation
Indices: 902312--902364 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
902302 ACGCTCGTGA
*
902312 ATGTTCGTGAATGTTCGTTCGGTT
1 ATGTTCGTGAATGTTCGTTCAGTT
** *
902336 ATGTTCGTTTATGTTCGTTCATTT
1 ATGTTCGTGAATGTTCGTTCAGTT
902360 ATGTT
1 ATGTT
902365 TAACTCAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
ATGTTCGTGAATGTTCGTTCAGTT
Found at i:920659 original size:36 final size:38
Alignment explanation
Indices: 920561--920683 Score: 112
Period size: 37 Copynumber: 3.3 Consensus size: 38
920551 GAAAAAAAAG
* **
920561 AAATAATA-ATAATATATTATATATAAAAAAATATTTTCCA
1 AAATTATATATAATATATTAT-T-TTTAAAAATATTTT-CA
**
920601 AAA-CCTATATAATATA-TATTTTTAAAAATATTTT-A
1 AAATTATATATAATATATTATTTTTAAAAATATTTTCA
* *
920636 CAATTATATATTAA-ATATTTTTTTTAAAAATATTTTCA
1 AAATTATATA-TAATATATTATTTTTAAAAATATTTTCA
920674 AAATTATATA
1 AAATTATATA
920684 GTTTTCAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
35 3 0.04
36 7 0.10
37 32 0.46
38 11 0.16
39 5 0.07
40 11 0.16
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (38 bp):
AAATTATATATAATATATTATTTTTAAAAATATTTTCA
Found at i:920688 original size:29 final size:29
Alignment explanation
Indices: 920656--920712 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
920646 TTAAATATTT
* *
920656 TTTTTAAAAATATTTTCAAAATTATATAG
1 TTTTCAAAAATATTTTCAAAACTATATAG
* *
920685 TTTTCAAAAATGTTTTTAAAACTATATA
1 TTTTCAAAAATATTTTCAAAACTATATA
920713 TTATATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (29 bp):
TTTTCAAAAATATTTTCAAAACTATATAG
Found at i:920740 original size:34 final size:36
Alignment explanation
Indices: 920676--921017 Score: 141
Period size: 37 Copynumber: 9.2 Consensus size: 36
920666 TATTTTCAAA
* *
920676 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAGTTTTCAAAAATGATTTCAAAACTATAT
920712 ATTATAT-GTTTTC-AAAATGATTTCAAAACTATATAATATAT
1 ATTATATAGTTTTCAAAAATGATTTCAAAAC-------TATAT
* *** *
920753 ATATATATATGTTTTC-AAAATGTTTTTTTTAA-AACTAT
1 AT-TATATA-GTTTTCAAAAATG-ATTTCAAAACTA-TAT
* * * *
920791 A-TATATA-TTTT-TAAAATGTTTTAAAAATTATAT
1 ATTATATAGTTTTCAAAAATGATTTCAAAACTATAT
* *
920824 AATATATATA-TTTTCAAAAATGTTTTAAAAACTATAT
1 -AT-TATATAGTTTTCAAAAATGATTTCAAAACTATAT
* * * *
920861 ATTATATTAATTTTC-AAAATGTTTTTAAAAATTATAT
1 ATTATA-TAGTTTTCAAAAATG-ATTTCAAAACTATAT
** * * *
920898 AATATATATA-TTTTCAAAAAAAAATTGAAAATTATAT
1 -AT-TATATAGTTTTCAAAAATGATTTCAAAACTATAT
* ** *
920935 ATTATATTAATTTTC-AAAATGCCTTAAAAACTATAT
1 ATTATA-TAGTTTTCAAAAATGATTTCAAAACTATAT
* * *
920971 AATATATAAATGTTTTGAAACAT-ATTTTCAAAACTATAT
1 -AT-TATATA-GTTTTCAAAAATGA-TTTCAAAACTATAT
921010 ATTATATA
1 ATTATATA
921018 TATATAAAAT
Statistics
Matches: 242, Mismatches: 33, Indels: 61
0.72 0.10 0.18
Matches are distributed among these distances:
33 9 0.04
34 26 0.11
35 14 0.06
36 52 0.21
37 70 0.29
38 22 0.09
39 20 0.08
41 7 0.03
42 5 0.02
44 12 0.05
45 5 0.02
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
ATTATATAGTTTTCAAAAATGATTTCAAAACTATAT
Found at i:920852 original size:37 final size:37
Alignment explanation
Indices: 920789--921020 Score: 213
Period size: 37 Copynumber: 6.3 Consensus size: 37
920779 TTTTAAAACT
* *
920789 ATATATATATTTT-TAAAATGTTTTAAAAATTATATA
1 ATATATATATTTTCAAAAATGTTTTAAAAACTATATA
920825 ATATATATATTTTCAAAAATGTTTTAAAAACTATATA
1 ATATATATATTTTCAAAAATGTTTTAAAAACTATATA
* *
920862 TTATAT-TAATTTTC-AAAATGTTTTTAAAAATTATATA
1 ATATATAT-ATTTTCAAAAATG-TTTTAAAAACTATATA
**** * *
920899 ATATATATATTTTCAAAAAAAAATTGAAAATTATATA
1 ATATATATATTTTCAAAAATGTTTTAAAAACTATATA
* **
920936 TTATAT-TAATTTTC-AAAATGCCTTAAAAACTATATA
1 ATATATAT-ATTTTCAAAAATGTTTTAAAAACTATATA
* * * * *
920972 ATATATAAATGTTTTGAAACATATTTTCAAAACTATATA
1 ATATAT--ATATTTTCAAAAATGTTTTAAAAACTATATA
*
921011 TTATATATAT
1 ATATATATAT
921021 ATAAAATTAA
Statistics
Matches: 159, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
36 42 0.26
37 85 0.53
38 9 0.06
39 23 0.14
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (37 bp):
ATATATATATTTTCAAAAATGTTTTAAAAACTATATA
Found at i:924030 original size:132 final size:131
Alignment explanation
Indices: 923790--924055 Score: 406
Period size: 132 Copynumber: 2.0 Consensus size: 131
923780 TTCTCTCGGG
* * * * * *
923790 TGTGAGTGTCGAATACGAGTATGTTATCTTACATGGGTATGGTTAGACCTTTTGAAGGTTCTCCA
1 TGTGAGTGTCAAATACGAGTATGTTATCTGACATGAGTACGGTTAGACCTTTTGAAGGCTATCCA
**
923855 TGTATTTGGAGGAAGGAATAATGGATTGTTGAGAGCTTCTGTTTCCTTATCTTGATAGATTTCCT
66 TGTATTTGGAGGAAGGAATAATGGATTGTTGAGAGCTGATGTTTCCTTATCTTGATAGATTTCC-
923920 AT
130 AT
* * *
923922 TGTGAGTGTCAAATACGAGTATGTTATCTGACGTGAGTACGTTTAGACTTTTTGAAGGCTATCCA
1 TGTGAGTGTCAAATACGAGTATGTTATCTGACATGAGTACGGTTAGACCTTTTGAAGGCTATCCA
* *
923987 TGTATTTGGAGGAAGGTATAATGGATTGTTGAGAGCTGATGTTTCCTTGTCTTGATAGATTTCCA
66 TGTATTTGGAGGAAGGAATAATGGATTGTTGAGAGCTGATGTTTCCTTATCTTGATAGATTTCCA
924052 T
131 T
924053 TGT
1 TGT
924056 TTTTTCTTTT
Statistics
Matches: 121, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
131 5 0.04
132 116 0.96
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.39
Consensus pattern (131 bp):
TGTGAGTGTCAAATACGAGTATGTTATCTGACATGAGTACGGTTAGACCTTTTGAAGGCTATCCA
TGTATTTGGAGGAAGGAATAATGGATTGTTGAGAGCTGATGTTTCCTTATCTTGATAGATTTCCA
T
Done.