Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 8 of 160
Found at i:2400980 original size:16 final size:17
Alignment explanation
Indices: 2400961--2401005 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
2400951 CTTATTTCAC
2400961 ATTTTTTTCA-TTTTTT
1 ATTTTTTTCACTTTTTT
2400977 A-TTTTTTCACTTTTTT
1 ATTTTTTTCACTTTTTT
*
2400993 ATTTGTTTCACTT
1 ATTTTTTTCACTT
2401006 CATCTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.31
16 8 0.31
17 10 0.38
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTTCACTTTTTT
Found at i:2401001 original size:17 final size:16
Alignment explanation
Indices: 2400963--2401005 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
2400953 TATTTCACAT
2400963 TTTTTTCA-TTTTTTA
1 TTTTTTCACTTTTTTA
2400978 TTTTTTCACTTTTTTA
1 TTTTTTCACTTTTTTA
2400994 TTTGTTTCACTT
1 TTT-TTTCACTT
2401006 CATCTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.31
16 10 0.38
17 8 0.31
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTTTCACTTTTTTA
Found at i:2404755 original size:115 final size:115
Alignment explanation
Indices: 2404553--2404790 Score: 386
Period size: 115 Copynumber: 2.1 Consensus size: 115
2404543 AACATATAAA
* *
2404553 TCCGTAAATCTATAGCTAAACTTAACAAGATGAGTCACCACCAATCTTTTATTAAGGTGTAATTG
1 TCCGTAAATCTATAGCTAAACTTAACAAGAGGAATCACCACCAATCTTTTATTAAGGTGTAATTG
* *
2404618 GTCACCTAATAAATTTATCCTTTTAAAAAGTTCCTAAGCTTGACTAAGGG
66 GCCACCTAATAAATTTATCCTTTTAAAAAGCTCCTAAGCTTGACTAAGGG
* *
2404668 TCCGTAAATCTATAGCTAAACTTAACAAGAGGAATCGCTACCAATCTTTTATTAAGGTGTAATTG
1 TCCGTAAATCTATAGCTAAACTTAACAAGAGGAATCACCACCAATCTTTTATTAAGGTGTAATTG
* **
2404733 GCCACCTAATGAATTTATCCTTTTAAGGAGCTCCTAAGCTTGACTAAGGG
66 GCCACCTAATAAATTTATCCTTTTAAAAAGCTCCTAAGCTTGACTAAGGG
*
2404783 TCCCTAAA
1 TCCGTAAA
2404791 AAATAGGTTT
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (115 bp):
TCCGTAAATCTATAGCTAAACTTAACAAGAGGAATCACCACCAATCTTTTATTAAGGTGTAATTG
GCCACCTAATAAATTTATCCTTTTAAAAAGCTCCTAAGCTTGACTAAGGG
Found at i:2406822 original size:18 final size:16
Alignment explanation
Indices: 2406786--2406819 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2406776 TATAGTTTTC
2406786 TCACTTGAATAAAATT
1 TCACTTGAATAAAATT
*
2406802 TCACTGTGATTAAAATT
1 TCACT-TGAATAAAATT
2406819 T
1 T
2406820 TCAAATTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (16 bp):
TCACTTGAATAAAATT
Found at i:2407033 original size:11 final size:11
Alignment explanation
Indices: 2407017--2407045 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2407007 AATCCCATAA
2407017 GAGATTTGTTT
1 GAGATTTGTTT
2407028 GAGATTTGTTT
1 GAGATTTGTTT
2407039 GAGATTT
1 GAGATTT
2407046 TTCAGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:2407160 original size:52 final size:53
Alignment explanation
Indices: 2407072--2407198 Score: 186
Period size: 52 Copynumber: 2.4 Consensus size: 53
2407062 TGGACAAGAA
* * *
2407072 GACTTGCAAAAGAAGAATTCT-AAGAGAAAGATGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAAGAAAGATGATTCTTAATAGGCAAGTTT
*
2407124 GACTTGCAAGAGAAGAATTCTAAAAAGAAATA-GATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAAGAAAGATGATTCTTAATAGGCAAGTTT
* *
2407176 GACTTACAGGAGAAGAATTCTAA
1 GACTTGCAAGAGAAGAATTCTAA
2407199 GAGGAGAATT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 60 0.88
53 8 0.12
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.27
Consensus pattern (53 bp):
GACTTGCAAGAGAAGAATTCTAAAAAGAAAGATGATTCTTAATAGGCAAGTTT
Found at i:2407205 original size:17 final size:17
Alignment explanation
Indices: 2407183--2407219 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
2407173 TTTGACTTAC
2407183 AGGAGAAGAATTCTAAG
1 AGGAGAAGAATTCTAAG
2407200 A-G-G-AGAATTCTAAG
1 AGGAGAAGAATTCTAAG
2407214 AGGAGA
1 AGGAGA
2407220 GTGATTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 6
0.74 0.00 0.26
Matches are distributed among these distances:
14 12 0.71
15 2 0.12
16 2 0.12
17 1 0.06
ACGTcount: A:0.46, C:0.05, G:0.32, T:0.16
Consensus pattern (17 bp):
AGGAGAAGAATTCTAAG
Found at i:2407208 original size:14 final size:14
Alignment explanation
Indices: 2407189--2407219 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2407179 TTACAGGAGA
2407189 AGAATTCTAAGAGG
1 AGAATTCTAAGAGG
2407203 AGAATTCTAAGAGG
1 AGAATTCTAAGAGG
2407217 AGA
1 AGA
2407220 GTGATTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.29, T:0.19
Consensus pattern (14 bp):
AGAATTCTAAGAGG
Found at i:2407686 original size:12 final size:12
Alignment explanation
Indices: 2407671--2407714 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
2407661 CTCTTGTGTG
*
2407671 TTTGATTTATTG
1 TTTGATTTATTA
2407683 TTTGATTTATTA
1 TTTGATTTATTA
2407695 TTTGATTTATTA
1 TTTGATTTATTA
2407707 TTTGATTT
1 TTTGATTT
2407715 CGCTTCCGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.68
Consensus pattern (12 bp):
TTTGATTTATTA
Found at i:2408696 original size:2 final size:2
Alignment explanation
Indices: 2408681--2408740 Score: 56
Period size: 2 Copynumber: 31.5 Consensus size: 2
2408671 TAGAACTATG
* *
2408681 TA TA -A TA T- TA TA TA TA TT TA TA T- TCA -A TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
*
2408720 TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2408741 GGTTGTCTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
1 4 0.09
2 43 0.91
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2410306 original size:2 final size:2
Alignment explanation
Indices: 2410299--2410324 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2410289 CATCAATCTT
2410299 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
2410325 GAGAGAGAGA
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):
TA
Found at i:2410329 original size:2 final size:2
Alignment explanation
Indices: 2410324--2410351 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2410314 ATATATATAT
2410324 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2410352 GTGTAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2411952 original size:11 final size:12
Alignment explanation
Indices: 2411915--2411955 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2411905 AGCTCAATAA
*
2411915 AAAATTATTCTA
1 AAAATTATTCTT
*
2411927 AAAATTATCCTT
1 AAAATTATTCTT
2411939 AAAA-TATTCTT
1 AAAATTATTCTT
2411950 AAAATT
1 AAAATT
2411956 GCATCCACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTATTCTT
Found at i:2416371 original size:23 final size:20
Alignment explanation
Indices: 2416345--2416398 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
2416335 TAAAATAATC
2416345 AATTTATTTTTTTATAAATTTAA
1 AATTTATTTTTTT-TAAA--TAA
*
2416368 AATTTGTTCTTTTTTAAATAA
1 AATTTATT-TTTTTTAAATAA
2416389 ATATTTATTT
1 A-ATTTATTT
2416399 ATTAGAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 5 0.19
22 6 0.22
23 11 0.41
24 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
AATTTATTTTTTTTAAATAA
Found at i:2416422 original size:23 final size:23
Alignment explanation
Indices: 2416396--2416439 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2416386 TAAATATTTA
*
2416396 TTTATTAGAATGATAATTAAAAT
1 TTTATAAGAATGATAATTAAAAT
* *
2416419 TTTATAATAATTATAATTAAA
1 TTTATAAGAATGATAATTAAA
2416440 TTGAACTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTATAAGAATGATAATTAAAAT
Found at i:2424480 original size:55 final size:55
Alignment explanation
Indices: 2424406--2424514 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
2424396 ATTATCATGG
*
2424406 TCCTTCGTAAGAAGTTTGTACGTTTACATAAATGTAAACAACATAATATTTTATA
1 TCCTTCGTAAGAAGTTTGTACGTTTACATAAATGCAAACAACATAATATTTTATA
* *
2424461 TCCTTTGTAAGAAGTTTGTACGTTTACATAAATGCAAACAACATAATGTTTTAT
1 TCCTTCGTAAGAAGTTTGTACGTTTACATAAATGCAAACAACATAATATTTTAT
2424515 GTTAGGCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (55 bp):
TCCTTCGTAAGAAGTTTGTACGTTTACATAAATGCAAACAACATAATATTTTATA
Found at i:2426362 original size:17 final size:19
Alignment explanation
Indices: 2426340--2426374 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2426330 TTCTTGACAG
2426340 TGTTGT-GATC-ATCCCTA
1 TGTTGTGGATCAATCCCTA
2426357 TGTTGTGGATCAATCCCT
1 TGTTGTGGATCAATCCCT
2426375 TCAATTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (19 bp):
TGTTGTGGATCAATCCCTA
Found at i:2430311 original size:227 final size:227
Alignment explanation
Indices: 2429910--2430367 Score: 835
Period size: 227 Copynumber: 2.0 Consensus size: 227
2429900 AGTTCATGAG
** *
2429910 TTTGTACTTGGTATAGTCAATGCTGTGTTTCAAATGGTGAGGAGTGAAATATGGTACTTATAACA
1 TTTGTACTTGGTATAGTCAACACTGTGTTTCAAATGGTGAGGAGTGAAATATGATACTTATAACA
* *
2429975 TCCCTTTGATAAAGTTGCATGTCTTATTTAATTAGAGTTTGCACTCAAAATATTTTACCTAGTTT
66 CCCCTTTGATAAAGTTGCATGTCTTATTTAATTAGAGTTTGCACTCAAAATATTTTACCAAGTTT
2430040 TTGCTTCTGAAGTTGGGTATCTTTCTAATGGTCCTCTAATAAAGTAGGAAACAGTATATAATTTA
131 TTGCTTCTGAAGTTGGGTATCTTTCTAATGGTCCTCTAATAAAGTAGGAAACAGTATATAATTTA
2430105 GATGGAATGAGTAGAAACTTTGAGCTTCTGTC
196 GATGGAATGAGTAGAAACTTTGAGCTTCTGTC
*
2430137 TTTGTACTTGGTATAGTCAACACTGTGTTTCAAATGGTGAGGAGTGAAGTATGATACTTATAACA
1 TTTGTACTTGGTATAGTCAACACTGTGTTTCAAATGGTGAGGAGTGAAATATGATACTTATAACA
2430202 CCCCTTTGATAAAGTTGCATGTCTTATTTAATTAGAGTTTGCACTCAAAATATTTTACCAAGTTT
66 CCCCTTTGATAAAGTTGCATGTCTTATTTAATTAGAGTTTGCACTCAAAATATTTTACCAAGTTT
* *
2430267 TTGCTTCTGAAGTTGGGTATCTTTCTAATGGTTCTCTGATAAAGTAGGAAACAGTATATAATTTA
131 TTGCTTCTGAAGTTGGGTATCTTTCTAATGGTCCTCTAATAAAGTAGGAAACAGTATATAATTTA
*
2430332 GATGGAATGAGTTGAAACTTTGAGCTTCTGTC
196 GATGGAATGAGTAGAAACTTTGAGCTTCTGTC
2430364 TTTG
1 TTTG
2430368 ATTAAATAGA
Statistics
Matches: 222, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
227 222 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (227 bp):
TTTGTACTTGGTATAGTCAACACTGTGTTTCAAATGGTGAGGAGTGAAATATGATACTTATAACA
CCCCTTTGATAAAGTTGCATGTCTTATTTAATTAGAGTTTGCACTCAAAATATTTTACCAAGTTT
TTGCTTCTGAAGTTGGGTATCTTTCTAATGGTCCTCTAATAAAGTAGGAAACAGTATATAATTTA
GATGGAATGAGTAGAAACTTTGAGCTTCTGTC
Found at i:2435803 original size:2 final size:2
Alignment explanation
Indices: 2435791--2435823 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2435781 TATTTGATTG
*
2435791 AT AT A- AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2435824 TTTAATTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2441904 original size:17 final size:19
Alignment explanation
Indices: 2441884--2441923 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2441874 AAATCAATTT
*
2441884 TTTATTT-GA-AATAAAAG
1 TTTATTTAGACAATAAAAA
2441901 TTTATTTAGACAATAAAAA
1 TTTATTTAGACAATAAAAA
2441920 TTTA
1 TTTA
2441924 GGGATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (19 bp):
TTTATTTAGACAATAAAAA
Found at i:2445346 original size:17 final size:17
Alignment explanation
Indices: 2445316--2445357 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2445306 TGTGCATCTA
*
2445316 CATCATTGCATTCTATG
1 CATCATTTCATTCTATG
*
2445333 CATTATTTCATTCTATG
1 CATCATTTCATTCTATG
2445350 CATCATTT
1 CATCATTT
2445358 TCATGATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (17 bp):
CATCATTTCATTCTATG
Found at i:2448474 original size:15 final size:16
Alignment explanation
Indices: 2448454--2448483 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2448444 TTTAGAATTA
2448454 TTTGAATAT-TCATTG
1 TTTGAATATCTCATTG
2448469 TTTGAATATCTCATT
1 TTTGAATATCTCATT
2448484 CAGCTCAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (16 bp):
TTTGAATATCTCATTG
Found at i:2449486 original size:25 final size:24
Alignment explanation
Indices: 2449458--2449565 Score: 120
Period size: 21 Copynumber: 4.7 Consensus size: 24
2449448 TTGATTTCTT
*
2449458 AAATAAGAATCTTTAAGATATTTTC
1 AAATGAGAATCTTTAAGA-ATTTTC
*
2449483 AAATGAGAATCTTT--GAATCTT-
1 AAATGAGAATCTTTAAGAATTTTC
2449504 AAATGAGAATCTTTAAGAAGTTTTC
1 AAATGAGAATCTTTAAGAA-TTTTC
*
2449529 AAATGAGAATCTTT--GAATCTT-
1 AAATGAGAATCTTTAAGAATTTTC
*
2449550 AAATGAAAATCTTTAA
1 AAATGAGAATCTTTAA
2449566 AATGTTTTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
21 27 0.38
22 7 0.10
23 8 0.11
24 3 0.04
25 27 0.38
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (24 bp):
AAATGAGAATCTTTAAGAATTTTC
Found at i:2449504 original size:46 final size:46
Alignment explanation
Indices: 2449454--2449589 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 46
2449444 AATCTTGATT
2449454 TCTTAAATAAGAATCTTTAAGATATTTTCAAATGAGAATCTTTGAA
1 TCTTAAATAAGAATCTTTAAGATATTTTCAAATGAGAATCTTTGAA
*
2449500 TCTTAAATGAGAATCTTTAAGA-AGTTTTCAAATGAGAATCTTTGAA
1 TCTTAAATAAGAATCTTTAAGATA-TTTTCAAATGAGAATCTTTGAA
* * * *
2449546 TCTTAAATGAA-AATCTTTAAAATGTTTTTAAATGAAAAT-TTTGA
1 TCTTAAAT-AAGAATCTTTAAGATATTTTCAAATGAGAATCTTTGA
2449590 GGTGTGAAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
45 6 0.07
46 74 0.91
47 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (46 bp):
TCTTAAATAAGAATCTTTAAGATATTTTCAAATGAGAATCTTTGAA
Found at i:2449576 original size:25 final size:24
Alignment explanation
Indices: 2449502--2449584 Score: 82
Period size: 25 Copynumber: 3.5 Consensus size: 24
2449492 TCTTTGAATC
*
2449502 TTAAATGAGAATCTTTAAGAAGTTT
1 TTAAATGAAAATCTTTAA-AAGTTT
* * * *
2449527 TCAAATGAGAATCTTT-GAA--TC
1 TTAAATGAAAATCTTTAAAAGTTT
2449548 TTAAATGAAAATCTTTAAAATGTTT
1 TTAAATGAAAATCTTTAAAA-GTTT
2449573 TTAAATGAAAAT
1 TTAAATGAAAAT
2449585 TTTGAGGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 2 0.04
25 28 0.60
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (24 bp):
TTAAATGAAAATCTTTAAAAGTTT
Found at i:2450221 original size:44 final size:43
Alignment explanation
Indices: 2450058--2450471 Score: 325
Period size: 44 Copynumber: 9.5 Consensus size: 43
2450048 TCAATAAGCC
* * * *
2450058 ATTTATTTTCAAAAGTTGTTGTTGCCTCTGTTTAGAGGAGCATTT
1 ATTTATTTTCTAAAGTCGTTG-AGCCTCTGATTAGAGGAGC-TTT
* * * *
2450103 A-TT-TTTT-AAAAGTTG-TGATGCCTCTGTTTAGAGGAGC--A
1 ATTTATTTTCTAAAGTCGTTGA-GCCTCTGATTAGAGGAGCTTT
* *
2450141 ATTTATTTTCTAAA--AGTTGAGCCTCTGATTAAAGGAGCTTT
1 ATTTATTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
2450182 ATTTATTCTTCTAAAGTCGTTGAGCCTCT-ATTTAGAGGAGCTTT
1 ATTTATT-TTCTAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCTTT
* * *
2450226 GTTTATTTTTTAAAAGTCGTTGAGCCTCTCATTAGAGGAGCTTT
1 ATTTATTTTCT-AAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
* * * **
2450270 GTTTATTTTTTTCAAAATCGTTGAGCCTCTGATTAGATAAGCTTT
1 ATTTA-TTTTCT-AAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
*
2450315 ATTTATTTT-TCAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTGTTT
1 ATTTATTTTCT-AAAGTCGTTGAGCCTCTGATTAGAGGAGC----TTT
* * *
2450362 ATTTGTTATTTCTTGAAGTCGTTGAGCCTCTGATTAGATGAGCTTT
1 ATTT-AT-TTTC-TAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
* * *
2450408 ATTTATTCTT-TCAAATTCGTTGAGCCTTTGTTTAGAGGAG---T
1 ATTTATT-TTCT-AAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
*
2450449 ATTTATTTTTTTAAAGTCGTTGA
1 ATTTA-TTTTCTAAAGTCGTTGA
2450472 ACCTTTATTT
Statistics
Matches: 313, Mismatches: 30, Indels: 56
0.78 0.08 0.14
Matches are distributed among these distances:
38 1 0.00
39 19 0.06
40 7 0.02
41 48 0.15
42 18 0.06
43 37 0.12
44 94 0.30
45 43 0.14
46 7 0.02
47 7 0.02
48 1 0.00
49 3 0.01
50 27 0.09
51 1 0.00
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (43 bp):
ATTTATTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
Found at i:2450384 original size:50 final size:46
Alignment explanation
Indices: 2450377--2450497 Score: 78
Period size: 44 Copynumber: 2.8 Consensus size: 46
2450367 TTATTTCTTG
* * *
2450377 AAGTCGTTGAGCCTCTGATTAGATGAGCTTTATTTA--TTCTTTCA
1 AAGTCGTTGAGCCTCTGATTAGAAGAGCTTTGTTTATTTTTTTTCA
* * * * *
2450421 AATTCGTTGAGCCTTTGTTTAGAGGAG---TATTTA-TTTTTTT-A
1 AAGTCGTTGAGCCTCTGATTAGAAGAGCTTTGTTTATTTTTTTTCA
* * *
2450462 AAGTCGTTGAACCT-TTATTTAGAAAAGCTTTGTTTA
1 AAGTCGTTGAGCCTCTGA-TTAGAAGAGCTTTGTTTA
2450498 CTAAAAAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
40 1 0.02
41 26 0.43
42 5 0.08
44 28 0.47
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (46 bp):
AAGTCGTTGAGCCTCTGATTAGAAGAGCTTTGTTTATTTTTTTTCA
Found at i:2450477 original size:41 final size:41
Alignment explanation
Indices: 2450407--2450484 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
2450397 AGATGAGCTT
* * *
2450407 TATTTATTCTTTCAAATTCGTTGAGCCTTTGTTTAGAGGAG
1 TATTTATTCTTTCAAAGTCGTTGAACCTTTATTTAGAGGAG
* *
2450448 TATTTATTTTTTTAAAGTCGTTGAACCTTTATTTAGA
1 TATTTATTCTTTCAAAGTCGTTGAACCTTTATTTAGA
2450485 AAAGCTTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.50
Consensus pattern (41 bp):
TATTTATTCTTTCAAAGTCGTTGAACCTTTATTTAGAGGAG
Found at i:2450926 original size:16 final size:15
Alignment explanation
Indices: 2450901--2450930 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2450891 GGGAGAAGGG
2450901 AACAAAAAAAAGAGA
1 AACAAAAAAAAGAGA
2450916 AACACAAAAAAAGAG
1 AACA-AAAAAAAGAG
2450931 GGAGGCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (15 bp):
AACAAAAAAAAGAGA
Found at i:2451272 original size:39 final size:39
Alignment explanation
Indices: 2451228--2451335 Score: 112
Period size: 39 Copynumber: 2.7 Consensus size: 39
2451218 TTTTTTCTTC
* *
2451228 ATTTTATTTTTATTTTTATT-TTTTGTATTTTACATTTGT
1 ATTTTATTTTTATTTTTATTATTAT-TATTTTACATATGT
* *
2451267 ATTTTATTTTCATTTTTATTATTATTATTTTATATATGT
1 ATTTTATTTTTATTTTTATTATTATTATTTTACATATGT
* * *
2451306 ATATATATTTTTTTCTTTTCTT-TTATTATT
1 AT-TTTATTTTTAT-TTTTATTATTATTATT
2451336 ATTTTTTATC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
39 33 0.57
40 19 0.33
41 6 0.10
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.72
Consensus pattern (39 bp):
ATTTTATTTTTATTTTTATTATTATTATTTTACATATGT
Found at i:2452414 original size:11 final size:10
Alignment explanation
Indices: 2452400--2452447 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
2452390 TTTAATATTC
2452400 TTTTATCTTTA
1 TTTT-TCTTTA
*
2452411 TTTTATTTTTA
1 TTTT-TCTTTA
2452422 TTTTTGCTTTA
1 TTTTT-CTTTA
*
2452433 CTTTTCTTTA
1 TTTTTCTTTA
2452443 TTTTT
1 TTTTT
2452448 TTATTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTTCTTTA
Found at i:2452448 original size:11 final size:11
Alignment explanation
Indices: 2452400--2452458 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
2452390 TTTAATATTC
*
2452400 TTTTATCTTTA
1 TTTTTTCTTTA
2452411 TTTTATT-TTTA
1 TTTT-TTCTTTA
*
2452422 TTTTTGCTTTA
1 TTTTTTCTTTA
*
2452433 -CTTTTCTTTA
1 TTTTTTCTTTA
*
2452443 TTTTTTTATTTA
1 -TTTTTTCTTTA
2452455 TTTT
1 TTTT
2452459 GTTTATCTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 9 0.24
11 20 0.53
12 9 0.24
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTA
Found at i:2452573 original size:58 final size:58
Alignment explanation
Indices: 2452518--2452791 Score: 331
Period size: 58 Copynumber: 4.7 Consensus size: 58
2452508 ATAAAAATAA
* *
2452518 AAAAAATATATTTTTGGGAAAAAGTTGAAAGTAACAATTTTTCTCGAAATTAAAATTTC
1 AAAAAA-ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTC
* * * ** *
2452577 CAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCTATTTTCCTTTAAAATAAAATTTC
1 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTC
* * * *
2452635 AAAAAAA-GTTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTCG-AAATTAAAATTTC
* *
2452693 CAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAATTTC
1 AAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTC
* *
2452751 AAAAGAACATTTTTAGGGAAAAA-TTGAAAGTATCAATTTTC
1 AAAAAAATATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTC
2452792 TCTGCACAAA
Statistics
Matches: 184, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
57 31 0.17
58 109 0.59
59 44 0.24
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (58 bp):
AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTC
Found at i:2454591 original size:58 final size:58
Alignment explanation
Indices: 2454519--2454859 Score: 354
Period size: 59 Copynumber: 5.8 Consensus size: 58
2454509 GCTTTTGTAC
*
2454519 AGGAAAATTAATACTTTCAAC-TTTTCTCCAAAAATATTTTTTGAAAACTTTAATTTCA
1 AGGAAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTTGAAAACTTTAATTTCA
* * * *
2454577 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTGAAAA-TTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA--TTTTTTGAAAACTTTAATTTCA
* * * *
2454636 AAGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTAGAAACTTTAATTTCG
1 AGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGA-AAACTTTAATTTCA
* * *
2454695 AGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAAAAGTTTATTTTCA
1 AGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTGAAAACTTTAATTTCA
** * *
2454754 AAAAAAATTGATATTTTCAA-TTTTTCCTC-AAAATA--TTTT-AAAAATATATATATTTTCA
1 AGGAAAATTGATACTTTCAACTTTTT-CTCAAAAATATTTTTTGAAAACT-T-TA-A-TTTCA
* * *
2454812 AGAAAAATTGGTACTTTCAACTTTTCCTCAAAAATATTATTCTTGAAA
1 AGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATT-TT-TTGAAA
2454860 TTTTATTTTA
Statistics
Matches: 237, Mismatches: 28, Indels: 30
0.80 0.09 0.10
Matches are distributed among these distances:
54 5 0.02
55 5 0.02
56 2 0.01
57 7 0.03
58 66 0.28
59 127 0.54
60 18 0.08
62 2 0.01
63 2 0.01
64 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (58 bp):
AGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAACTTTAATTTCA
Found at i:2454660 original size:117 final size:114
Alignment explanation
Indices: 2454521--2454868 Score: 432
Period size: 117 Copynumber: 3.0 Consensus size: 114
2454511 TTTTGTACAG
*
2454521 GAAAATTAATACTTTCAACTTTTCTCCAAAAATATTTTTTGAAAACTTTAATTTCAAGGAAAATT
1 GAAAATTGATACTTTCAACTTTT-TCCAAAAATATTTTTT-AAAACTTTAATTTCAAGGAAAATT
* *
2454586 GATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTGAAAATTTATTTTTAAA
64 GATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTGAAAATTTATTTTCAAA
*
2454638 GAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTAGAAACTTTAATTTCGAGGAAAAT
1 GAAAATTGATACTTTCAACTTTTT-CCAAAAATA-TTTTTTA-AAACTTTAATTTCAAGGAAAAT
* *
2454703 TGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAAAAGTTTATTTTCAAA
63 TGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAA-TTTATTTTCAAA
* * * * *
2454756 AAAAATTGATATTTTCAA-TTTTTCCTCAAAATA--TTTTAAAAATATATATATTTTCAAGAAAA
1 GAAAATTGATACTTTCAACTTTTTCC-AAAAATATTTTTTAAAACT-T-TA-A-TTTCAAGGAAA
* * *
2454818 ATTGGTACTTTCAACTTTTCCTCAAAAATATTATTCTTGAAATTTTATTTT
61 ATTGATACTTTCAACTTTTCCTCAAAAATATT-TTTTTGAAAATTTATTTT
2454869 ATATTTTTTA
Statistics
Matches: 204, Mismatches: 17, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
113 4 0.02
114 6 0.03
115 2 0.01
116 4 0.02
117 101 0.50
118 87 0.43
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (114 bp):
GAAAATTGATACTTTCAACTTTTTCCAAAAATATTTTTTAAAACTTTAATTTCAAGGAAAATTGA
TACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTCAAA
Found at i:2456306 original size:20 final size:20
Alignment explanation
Indices: 2456278--2456328 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2456268 TAATCATGAA
* *
2456278 AAAAAAAAAACATAAATCAT
1 AAAATAAAAACAAAAATCAT
* *
2456298 AAAATAAAAATAAAAATGAT
1 AAAATAAAAACAAAAATCAT
2456318 AAATATAAAAA
1 AAA-ATAAAAA
2456329 ATTTCTACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATAAAAACAAAAATCAT
Found at i:2456307 original size:27 final size:26
Alignment explanation
Indices: 2456276--2456327 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2456266 GATAATCATG
2456276 AAAAAAAAAAAACATAAATCATAAAAT
1 AAAAAAAAAAAACATAAAT-ATAAAAT
* **
2456303 AAAAATAAAAATGATAAATATAAAA
1 AAAAAAAAAAAACATAAATATAAAA
2456328 AATTTCTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (26 bp):
AAAAAAAAAAAACATAAATATAAAAT
Found at i:2457043 original size:60 final size:60
Alignment explanation
Indices: 2456936--2457198 Score: 311
Period size: 60 Copynumber: 4.4 Consensus size: 60
2456926 CATTTTTAAG
* * * *
2456936 GAAAATAAAAATTTTCAAAAAAACATTTTTGAAAGAAAAGTTGAAAGTCTTAA-TTTTCTTT
1 GAAAATAAAAA-TTTCAAAAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTC-TT
*
2456997 GAAAATGAAAATTTCAAGAAAAATATTTTTGAGA-AAAAGTTGAAAGTATCAA-TTTTCTT
1 GAAAATAAAAATTTCAA-AAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCTT
* * * *
2457056 AAAAAATAAAAATTTAAAAAAATATATTTTTAAG-GAAAAGTTGAACGTATCAATTTTTCTT
1 -GAAAATAAAAATTTCAAAAAA-ATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCTT
* * **
2457117 AAAAATAAAGATTTCAAAAAAGGGATTTTTGA-AGAAAAGTTGAAAGTATCAATTTTTCTT
1 GAAAATAAAAATTTCAAAAAA-ATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCTT
*
2457177 GAAAATAAAAATTTTAAAAAAA
1 GAAAATAAAAATTTCAAAAAAA
2457199 CAATTATGCT
Statistics
Matches: 175, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
59 6 0.03
60 138 0.79
61 31 0.18
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (60 bp):
GAAAATAAAAATTTCAAAAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCTT
Found at i:2462211 original size:21 final size:20
Alignment explanation
Indices: 2462187--2462230 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2462177 TTTTTTATAT
**
2462187 TTAAAATTATCATTTTAATTA
1 TTAAAATTAAAATTTTAA-TA
2462208 TTAAAATTAAAATTTTAATA
1 TTAAAATTAAAATTTTAATA
2462228 TTA
1 TTA
2462231 TATTAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAATTAAAATTTTAATA
Found at i:2463269 original size:33 final size:32
Alignment explanation
Indices: 2463232--2463295 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
2463222 GGCATAAATA
*
2463232 ATTTTTATATTCATAATTT-TTTAATTTATTTTT
1 ATTTTTATATT-ATAATTTATGTAATTT-TTTTT
*
2463265 ATTTTTATCTTATAATTTATGTAATTTTTTT
1 ATTTTTATATTATAATTTATGTAATTTTTTT
2463296 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.69
Consensus pattern (32 bp):
ATTTTTATATTATAATTTATGTAATTTTTTTT
Found at i:2463329 original size:14 final size:14
Alignment explanation
Indices: 2463306--2463335 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2463296 ATAAATAAAT
*
2463306 ATAAATATATATTA
1 ATAAAAATATATTA
2463320 ATAAAAATATATTA
1 ATAAAAATATATTA
2463334 AT
1 AT
2463336 TTTAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAAAATATATTA
Found at i:2463366 original size:23 final size:23
Alignment explanation
Indices: 2463315--2463366 Score: 54
Period size: 23 Copynumber: 2.2 Consensus size: 23
2463305 TATAAATATA
2463315 TATTAATAAAAATATATTAATTT
1 TATTAATAAAAATATATTAATTT
*
2463338 TAATTAATCTAAAATA-A-TAATTT
1 T-ATTAAT-AAAAATATATTAATTT
2463361 CTATTA
1 -TATTA
2463367 TTTAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 11 0.44
24 8 0.32
25 6 0.24
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTAATAAAAATATATTAATTT
Found at i:2464303 original size:14 final size:14
Alignment explanation
Indices: 2464284--2464310 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2464274 TATATTTAAC
2464284 ATATTTAAATATTA
1 ATATTTAAATATTA
2464298 ATATTTAAATATT
1 ATATTTAAATATT
2464311 TTTTTAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTTAAATATTA
Found at i:2464308 original size:8 final size:8
Alignment explanation
Indices: 2464275--2464311 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
2464265 ATTTTAAAAT
2464275 ATATTTAA
1 ATATTTAA
2464283 CATATTTAA
1 -ATATTTAA
2464292 ATA-TT-A
1 ATATTTAA
2464298 ATATTTAA
1 ATATTTAA
2464306 ATATTT
1 ATATTT
2464312 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
6 4 0.15
7 4 0.15
8 10 0.38
9 8 0.31
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (8 bp):
ATATTTAA
Found at i:2473726 original size:37 final size:37
Alignment explanation
Indices: 2473676--2473766 Score: 182
Period size: 37 Copynumber: 2.5 Consensus size: 37
2473666 TTGTTGCTTG
2473676 TAGTATGGTTTTGCAAAGCAATTTATAGAATAAGAAT
1 TAGTATGGTTTTGCAAAGCAATTTATAGAATAAGAAT
2473713 TAGTATGGTTTTGCAAAGCAATTTATAGAATAAGAAT
1 TAGTATGGTTTTGCAAAGCAATTTATAGAATAAGAAT
2473750 TAGTATGGTTTTGCAAA
1 TAGTATGGTTTTGCAAA
2473767 TTCAAGGGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.36
Consensus pattern (37 bp):
TAGTATGGTTTTGCAAAGCAATTTATAGAATAAGAAT
Found at i:2486148 original size:12 final size:12
Alignment explanation
Indices: 2486131--2486159 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2486121 CGGTTCATAC
2486131 TTCATTGTCAGG
1 TTCATTGTCAGG
2486143 TTCATTGTCAGG
1 TTCATTGTCAGG
2486155 TTCAT
1 TTCAT
2486160 AATAAAATAA
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:0.17, C:0.17, G:0.21, T:0.45
Consensus pattern (12 bp):
TTCATTGTCAGG
Found at i:2513926 original size:2 final size:2
Alignment explanation
Indices: 2513919--2513950 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2513909 CTTTTTCATT
2513919 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
2513951 GACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2523358 original size:2 final size:2
Alignment explanation
Indices: 2523346--2523383 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2523336 TTCACAAGTA
*
2523346 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2523384 TGGCTTATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2523557 original size:2 final size:2
Alignment explanation
Indices: 2523539--2523574 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2523529 TGCGTATGCC
*
2523539 CT CT CC CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2523575 ACACACACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:2523579 original size:2 final size:2
Alignment explanation
Indices: 2523574--2523603 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2523564 CTCTCTCTCT
2523574 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2523604 GACAATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2527678 original size:2 final size:2
Alignment explanation
Indices: 2527671--2527707 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2527661 CCACATTCAA
2527671 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2527708 CAAGCTTTTG
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2531122 original size:29 final size:32
Alignment explanation
Indices: 2531069--2531137 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
2531059 ATTTAACAAC
* * *
2531069 TAATCATATTCCAATGC-A-ATTTTTTTTTTA
1 TAATAATATTCCAATGCAAGATTTTATTATTA
2531099 TAA-AATATTCCAATGCAAGATTTTATTATTA
1 TAATAATATTCCAATGCAAGATTTTATTATTA
2531130 TAATAATA
1 TAATAATA
2531138 ACGATGGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 12 0.36
30 4 0.12
31 13 0.39
32 4 0.12
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.46
Consensus pattern (32 bp):
TAATAATATTCCAATGCAAGATTTTATTATTA
Found at i:2531428 original size:15 final size:15
Alignment explanation
Indices: 2531408--2531437 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2531398 TTATTAATAG
2531408 ATTATATAATTATTT
1 ATTATATAATTATTT
*
2531423 ATTATATTATTATTT
1 ATTATATAATTATTT
2531438 TTTACAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATATAATTATTT
Found at i:2531701 original size:11 final size:12
Alignment explanation
Indices: 2531635--2531710 Score: 52
Period size: 13 Copynumber: 6.5 Consensus size: 12
2531625 AAAATACGAT
*
2531635 ATAAAGATTATA
1 ATAAAAATTATA
*
2531647 TTAAAAAATT-T-
1 AT-AAAAATTATA
* *
2531658 ATGAAAATAATA
1 ATAAAAATTATA
*
2531670 ATTTAAAATTATA
1 A-TAAAAATTATA
2531683 ATAAAAATTAT-
1 ATAAAAATTATA
*
2531694 ATATAAATT-TA
1 ATAAAAATTATA
2531705 ATAAAA
1 ATAAAA
2531711 TTAAAAATAT
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
10 6 0.12
11 15 0.31
12 12 0.24
13 16 0.33
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
ATAAAAATTATA
Found at i:2532106 original size:16 final size:16
Alignment explanation
Indices: 2532074--2532130 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2532064 ATTGTTATGC
* *
2532074 ATTTATTATGAATATT
1 ATTTATTATAAAAATT
2532090 ATTTATTATAAAAATT
1 ATTTATTATAAAAATT
* *
2532106 AAATATATTAAAAATAATT
1 --ATTTATTATAAA-AATT
2532125 ATTTAT
1 ATTTAT
2532131 AAATTATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 14 0.42
17 5 0.15
18 10 0.30
19 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTTATTATAAAAATT
Found at i:2532483 original size:20 final size:21
Alignment explanation
Indices: 2532454--2532498 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2532444 TTTTGAAATC
2532454 AAAATCAAA-TATAATGTT-TT
1 AAAATCAAATTATAAT-TTATT
*
2532474 AAAATTAAATTATAATTTATT
1 AAAATCAAATTATAATTTATT
2532495 AAAA
1 AAAA
2532499 AAATTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATCAAATTATAATTTATT
Found at i:2544720 original size:20 final size:20
Alignment explanation
Indices: 2544673--2544720 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2544663 ATGTATTCTA
*
2544673 TATATTTAATAAATTAATTT
1 TATATTTAATAAATTAACTT
*
2544693 TGTATTTAATAAATTAAACTT
1 TATATTTAATAAATT-AACTT
2544714 TAT-TTTA
1 TATATTTA
2544721 GATTTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TATATTTAATAAATTAACTT
Found at i:2544772 original size:17 final size:18
Alignment explanation
Indices: 2544750--2544783 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2544740 ATTTGTATTT
2544750 AAAAATACATAT-TTATA
1 AAAAATACATATCTTATA
2544767 AAAAATACATATCTTAT
1 AAAAATACATATCTTAT
2544784 TTTTTATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATACATATCTTATA
Found at i:2559334 original size:2 final size:2
Alignment explanation
Indices: 2559327--2559357 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2559317 CTCTATAGAC
2559327 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2559358 TCAGCTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2565843 original size:29 final size:27
Alignment explanation
Indices: 2565793--2565866 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 27
2565783 TCTCAGCATT
* *
2565793 AATTATTATCTTA-TAAATTATCAATAA
1 AATTTTTAT-TTATTAAAATATCAATAA
* *
2565820 AATTTTTAATTATATTAAAATATCATTGA
1 AATTTTT-ATT-TATTAAAATATCAATAA
*
2565849 AGTTTTTATTTATTAAAA
1 AATTTTTATTTATTAAAA
2565867 GTTTAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 15 0.38
28 7 0.18
29 17 0.44
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (27 bp):
AATTTTTATTTATTAAAATATCAATAA
Found at i:2580942 original size:29 final size:31
Alignment explanation
Indices: 2580896--2580955 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
2580886 ATAAATAACT
*
2580896 TTTAAATTTTAATAAAATATTTAATATGATA
1 TTTAAATTTTAATAAAATATTTAACATGATA
*
2580927 TTTAAATTTT-A-AAAATTTTTAACATGATA
1 TTTAAATTTTAATAAAATATTTAACATGATA
2580956 CTATAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 1 0.04
31 10 0.37
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTAAATTTTAATAAAATATTTAACATGATA
Found at i:2580968 original size:29 final size:29
Alignment explanation
Indices: 2580909--2580974 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
2580899 AAATTTTAAT
* * *
2580909 AAAATATTTAATATGATATTTAAATTTTA
1 AAAATATTTAACATGATATATAAATTATA
*
2580938 AAAATTTTTAACATGATACTATAAA-TATA
1 AAAATATTTAACATGATA-TATAAATTATA
*
2580967 AATATATT
1 AAAATATT
2580975 AATTAATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (29 bp):
AAAATATTTAACATGATATATAAATTATA
Found at i:2589362 original size:23 final size:23
Alignment explanation
Indices: 2589311--2589362 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2589301 AAATCGATTG
* * * *
2589311 TAAATATTAAATATATATTAATT
1 TAAATTTTAAATAAAAATTAAAT
*
2589334 TTAATTTTAAATAAAAATTAAAT
1 TAAATTTTAAATAAAAATTAAAT
2589357 TAAATT
1 TAAATT
2589363 ATATATGTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAATTTTAAATAAAAATTAAAT
Found at i:2596452 original size:2 final size:2
Alignment explanation
Indices: 2596447--2596481 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2596437 AGAAGTGATC
*
2596447 AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2596482 ATGAGTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2600353 original size:6 final size:6
Alignment explanation
Indices: 2600307--2600365 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
2600297 TTAAATACTC
* * **
2600307 ATAAAT ATAAAA ATAAA- AGTAAAT TTAAA- ATATTT ATTAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT A-TAAAT ATAAAT ATAAAT A-TAAAT ATAAAT
2600355 ATAAAT ATAAA
1 ATAAAT ATAAA
2600366 AAATGCTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 3 0.07
6 35 0.83
7 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:2602273 original size:26 final size:26
Alignment explanation
Indices: 2602248--2602303 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
2602238 TCAATTAATT
2602248 ATTTA-ATTT-TTAAAAATTTT-AAA
1 ATTTATATTTATTAAAAATTTTCAAA
*
2602271 ATTTATATTTATTCAAAATTTTCAAA
1 ATTTATATTTATTAAAAATTTTCAAA
*
2602297 ATATATA
1 ATTTATA
2602304 AATTTTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 4 0.14
25 10 0.36
26 9 0.32
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTATATTTATTAAAAATTTTCAAA
Found at i:2604791 original size:28 final size:29
Alignment explanation
Indices: 2604760--2604814 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
2604750 ATAATATGTA
*
2604760 AAAAATATTTAA-ATATTATTT-ATAATTT
1 AAAAATAATTAATAT-TTATTTAATAATTT
*
2604788 AAAATTAATTAATATTTATTTAATAAT
1 AAAAATAATTAATATTTATTTAATAAT
2604815 AAAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AAAAATAATTAATATTTATTTAATAATTT
Found at i:2604804 original size:17 final size:17
Alignment explanation
Indices: 2604763--2604805 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2604753 ATATGTAAAA
2604763 AATATTTAAATATTATT
1 AATATTTAAATATTATT
*
2604780 TATAATTTAAA-ATTAATT
1 AAT-ATTTAAATATT-ATT
2604798 AATATTTA
1 AATATTTA
2604806 TTTAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTTAAATATTATT
Found at i:2604813 original size:29 final size:30
Alignment explanation
Indices: 2604771--2604847 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
2604761 AAAATATTTA
2604771 AATA-TTATTT-ATAATTTAAAA-TTAATT
1 AATATTTATTTAATAATTTAAAATTTAATT
* *
2604798 AATATTTATTTAATAA-TAAAAATTTTATT
1 AATATTTATTTAATAATTTAAAATTTAATT
* *
2604827 AATATTTTATTAAAAAATTTA
1 AATA-TTTATTTAATAATTTA
2604848 TTTAATAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 13 0.32
30 10 0.25
31 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AATATTTATTTAATAATTTAAAATTTAATT
Found at i:2604842 original size:24 final size:25
Alignment explanation
Indices: 2604814--2604865 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
2604804 TATTTAATAA
* *
2604814 TAAAAATTTTA-TTAAT-ATTTTAT
1 TAAAAAATTTATTTAATAAATTTAT
2604837 TAAAAAATTTATTTAATAAATTTAT
1 TAAAAAATTTATTTAATAAATTTAT
2604862 TAAA
1 TAAA
2604866 TTTTACTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 5 0.20
25 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAAAAATTTATTTAATAAATTTAT
Found at i:2604843 original size:25 final size:26
Alignment explanation
Indices: 2604805--2604865 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
2604795 ATTAATATTT
*
2604805 ATTTAATAATAAAAATTT-TATTAAT-A
1 ATTTATTAA-AAAAATTTAT-TTAATAA
*
2604831 TTTTATT-AAAAAATTTATTTAATAA
1 ATTTATTAAAAAAATTTATTTAATAA
2604856 ATTTATTAAA
1 ATTTATTAAA
2604866 TTTTACTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 13 0.45
25 9 0.31
26 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTATTAAAAAAATTTATTTAATAA
Found at i:2604849 original size:12 final size:12
Alignment explanation
Indices: 2604814--2604865 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
2604804 TATTTAATAA
*
2604814 TAAAAATTTTAT
1 TAAAAAATTTAT
* *
2604826 T-AATATTTTAT
1 TAAAAAATTTAT
2604837 TAAAAAATTTATT
1 TAAAAAATTTA-T
*
2604850 TAATAAATTTAT
1 TAAAAAATTTAT
2604862 TAAA
1 TAAA
2604866 TTTTACTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 10 0.30
12 12 0.36
13 11 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAAAAATTTAT
Found at i:2604921 original size:20 final size:20
Alignment explanation
Indices: 2604896--2604936 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2604886 CGATAAGATC
*
2604896 TTTTAATTTATAAATTTTAA
1 TTTTAAGTTATAAATTTTAA
* *
2604916 TTTTAAGTTATTATTTTTAA
1 TTTTAAGTTATAAATTTTAA
2604936 T
1 T
2604937 AAAAAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAAGTTATAAATTTTAA
Found at i:2605161 original size:2 final size:2
Alignment explanation
Indices: 2605154--2605178 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2605144 TTTTTCTCCT
2605154 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2605179 CTTCATGTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2610155 original size:27 final size:26
Alignment explanation
Indices: 2610125--2610190 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 26
2610115 ACGGGAAGAA
2610125 CAGAGTGTGCTGGCTGAGTAGGA-ACCG
1 CAGA-TGTGCTGGCTGAG-AGGATACCG
* * *
2610152 CAGATGCTGGTGGCTGTGGGGATACCG
1 CAGATG-TGCTGGCTGAGAGGATACCG
2610179 CAGATTGTGCTG
1 CAGA-TGTGCTG
2610191 AACGTGGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.16
27 25 0.78
28 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.41, T:0.23
Consensus pattern (26 bp):
CAGATGTGCTGGCTGAGAGGATACCG
Found at i:2617585 original size:2 final size:2
Alignment explanation
Indices: 2617573--2617608 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2617563 GCAAAGCTAA
*
2617573 TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2617609 AGAGAGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:2617613 original size:2 final size:2
Alignment explanation
Indices: 2617608--2617636 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2617598 GTGTGTGTGT
2617608 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2617637 TAACCATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2623317 original size:31 final size:32
Alignment explanation
Indices: 2623257--2623317 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
2623247 CCAACCCGAA
** *
2623257 TTAATATATATATAAATTTTTTTATATATACG
1 TTAATATATATATAAATTAATTTACATATACG
2623289 TTAAT-TATATATAAATTAATTTACATATA
1 TTAATATATATATAAATTAATTTACATATA
2623318 ATTAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (32 bp):
TTAATATATATATAAATTAATTTACATATACG
Found at i:2627966 original size:2 final size:2
Alignment explanation
Indices: 2627959--2627989 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2627949 TAGCTTCTTT
2627959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2627990 GTTCCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2629704 original size:22 final size:21
Alignment explanation
Indices: 2629679--2629731 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 21
2629669 TCAGAAATTA
2629679 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTT-AAAT
2629701 ATAAAAATATTATTTTTTAAAT
1 AT-AAAATATTATTTTTTAAAT
2629723 AT-AAATATT
1 ATAAAATATT
2629732 TAAAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.23
22 8 0.27
23 15 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:2629709 original size:23 final size:22
Alignment explanation
Indices: 2629681--2629727 Score: 85
Period size: 23 Copynumber: 2.1 Consensus size: 22
2629671 AGAAATTAAT
2629681 AAAATATTATTTTTTAAAATATA
1 AAAATATTATTTTTT-AAATATA
2629704 AAAATATTATTTTTTAAATATA
1 AAAATATTATTTTTTAAATATA
2629726 AA
1 AA
2629728 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATATTATTTTTTAAATATA
Found at i:2629733 original size:14 final size:14
Alignment explanation
Indices: 2629716--2629767 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2629706 AATATTATTT
2629716 TTTAAATATAAATA
1 TTTAAATATAAATA
*
2629730 TTTAAAAATATAATTA
1 TTT--AAATATAAATA
* *
2629746 TATAAATATATATA
1 TTTAAATATAAATA
*
2629760 ATTAAATA
1 TTTAAATA
2629768 ATTAATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 18 0.60
16 12 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAATATAAATA
Found at i:2629738 original size:16 final size:16
Alignment explanation
Indices: 2629719--2629757 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2629709 ATTATTTTTT
*
2629719 AAATATAAATATTTAA
1 AAATATAAATATATAA
*
2629735 AAATATAATTATATAA
1 AAATATAAATATATAA
*
2629751 ATATATA
1 AAATATA
2629758 TAATTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATAAATATATAA
Found at i:2629738 original size:30 final size:30
Alignment explanation
Indices: 2629702--2629775 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
2629692 TTTTAAAATA
* * * *
2629702 TAAAAATATTATTTTTTAAATATAAATATT
1 TAAAAATATAATTATATAAATATAAATAAT
*
2629732 TAAAAATATAATTATATAAATATATATAAT
1 TAAAAATATAATTATATAAATATAAATAAT
2629762 TAAATAAT-TAATTA
1 TAAA-AATATAATTA
2629776 AAAAATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 35 0.92
31 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAAAATATAATTATATAAATATAAATAAT
Found at i:2632794 original size:28 final size:29
Alignment explanation
Indices: 2632756--2632813 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
2632746 AAAATTGATA
2632756 TTTAAAAAATATA-A-TTTATATTTAAATT
1 TTTAAAAAATATACATTTTA-ATTTAAATT
*
2632784 TTTAAATAATATATCATTTTAATTTAAATT
1 TTTAAAAAATATA-CATTTTAATTTAAATT
2632814 ATAATATCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 12 0.46
30 10 0.38
31 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAAAAAATATACATTTTAATTTAAATT
Found at i:2637109 original size:22 final size:24
Alignment explanation
Indices: 2637076--2637122 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
2637066 AAATAATTAT
2637076 TTATATATAAAT-ATAT-TAAAAA
1 TTATATATAAATAATATATAAAAA
2637098 TTATAT-TAAAATAATATATAAAAA
1 TTATATAT-AAATAATATATAAAAA
2637122 T
1 T
2637123 AAAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.05
22 10 0.45
23 4 0.18
24 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTATATATAAATAATATATAAAAA
Found at i:2645634 original size:67 final size:67
Alignment explanation
Indices: 2645520--2645650 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 67
2645510 GCTCTCGACC
* *
2645520 AGGTCATGGCATTGCTCTAGCAATACCCACGAACAAAATAACGAACACAAATCAAGAATAAGAAA
1 AGGTCATGGCATTACTCTAGCAATACCCACGAACAAAATAACAAACACAAATCAAGAATAAGAAA
2645585 TT
66 TT
* * *
2645587 AGGTCATGGCATTACTCTGGCAATACCCACGAACAAAATAGCAAACACAAATCAATAATAAGAA
1 AGGTCATGGCATTACTCTAGCAATACCCACGAACAAAATAACAAACACAAATCAAGAATAAGAA
2645651 TATACAAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.18
Consensus pattern (67 bp):
AGGTCATGGCATTACTCTAGCAATACCCACGAACAAAATAACAAACACAAATCAAGAATAAGAAA
TT
Found at i:2651561 original size:14 final size:15
Alignment explanation
Indices: 2651542--2651572 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2651532 CAACCCCTTG
2651542 ATATATATTAT-ATT
1 ATATATATTATAATT
2651556 ATATATATTATAATT
1 ATATATATTATAATT
2651571 AT
1 AT
2651573 TTTATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATATATTATAATT
Found at i:2651577 original size:20 final size:21
Alignment explanation
Indices: 2651543--2651581 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2651533 AACCCCTTGA
2651543 TATATATTATATTATATATAT
1 TATATATTATATTATATATAT
*
2651564 TATA-ATTATTTTATATAT
1 TATATATTATATTATATAT
2651582 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATATTATATTATATATAT
Found at i:2651594 original size:20 final size:18
Alignment explanation
Indices: 2651552--2651588 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2651542 ATATATATTA
*
2651552 TATTATATATATTATAAT
1 TATTTTATATATTATAAT
*
2651570 TATTTTATATATTTTAAT
1 TATTTTATATATTATAAT
2651588 T
1 T
2651589 TAATTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTATATATTATAAT
Found at i:2652014 original size:31 final size:31
Alignment explanation
Indices: 2651962--2652027 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
2651952 AATTTAAAGA
2651962 TTAAAAAAATTAAAATTATT-AAATAATATTT
1 TTAAAAAAATTAAAA-TATTAAAATAATATTT
*
2651993 TTAAAAAAATTAATTAA-ATTAAAATTATATTT
1 TTAAAAAAATTAA--AATATTAAAATAATATTT
2652025 TTA
1 TTA
2652028 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 16 0.52
32 13 0.42
33 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAAAAAAATTAAAATATTAAAATAATATTT
Found at i:2652023 original size:32 final size:30
Alignment explanation
Indices: 2651962--2652027 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 30
2651952 AATTTAAAGA
2651962 TTAAAAAAATTAAAATTATTAAATAATATTT
1 TTAAAAAAATTAAAATTA-TAAATAATATTT
*
2651993 TTAAAAAAATTAATTAAATTA-AAATTATATTT
1 TTAAAAAAATT-A--AAATTATAAATAATATTT
2652025 TTA
1 TTA
2652028 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 11 0.35
32 14 0.45
34 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TTAAAAAAATTAAAATTATAAATAATATTT
Found at i:2653348 original size:13 final size:13
Alignment explanation
Indices: 2653330--2653354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2653320 TATTTAATAG
2653330 ATTTAAAATTTAA
1 ATTTAAAATTTAA
2653343 ATTTAAAATTTA
1 ATTTAAAATTTA
2653355 TATATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAAATTTAA
Found at i:2653618 original size:18 final size:17
Alignment explanation
Indices: 2653586--2653619 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2653576 TGGACATCTT
2653586 AAAATTAAAAAAAAAAA
1 AAAATTAAAAAAAAAAA
*
2653603 AAAATCTAAAAGAAAAA
1 AAAAT-TAAAAAAAAAA
2653620 TTTTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAATTAAAAAAAAAAA
Found at i:2654263 original size:8 final size:8
Alignment explanation
Indices: 2654250--2654274 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2654240 ACAATCTCAA
2654250 ATTTATAT
1 ATTTATAT
2654258 ATTTATAT
1 ATTTATAT
2654266 ATTTATAT
1 ATTTATAT
2654274 A
1 A
2654275 AAATTACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTATAT
Found at i:2656574 original size:19 final size:19
Alignment explanation
Indices: 2656550--2656589 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2656540 ATAACAGGAG
* *
2656550 AAAGCAATACAAAGTTTAT
1 AAAGCAAAACAAAATTTAT
2656569 AAAGCAAAACAAAATTTAT
1 AAAGCAAAACAAAATTTAT
2656588 AA
1 AA
2656590 GAAATTTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (19 bp):
AAAGCAAAACAAAATTTAT
Found at i:2665054 original size:2 final size:2
Alignment explanation
Indices: 2665047--2665073 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2665037 GATAAACCAA
2665047 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 A
2665074 AATCTAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2670991 original size:21 final size:21
Alignment explanation
Indices: 2670943--2670991 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
2670933 TGATTTTTAA
2670943 ATTTTAT-TTTAATAAAATTT
1 ATTTTATATTTAATAAAATTT
*
2670963 -TTAATATATTTAA-ATAAATTT
1 ATT-TTATATTTAATA-AAATTT
2670984 ATTTTATA
1 ATTTTATA
2670992 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
19 2 0.09
20 4 0.17
21 15 0.65
22 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTATATTTAATAAAATTT
Found at i:2671035 original size:18 final size:18
Alignment explanation
Indices: 2670988--2671036 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2670978 AAATTTATTT
2670988 TATAAAAATTTTAA-AAAA
1 TATAAAAA-TTTAATAAAA
2671006 TATAAAAA-TTAATAAAA
1 TATAAAAATTTAATAAAA
2671023 -ATAAATAATTTAAT
1 TATAAA-AATTTAAT
2671037 TTAATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.32
17 6 0.21
18 13 0.46
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAAAAATTTAATAAAA
Found at i:2671081 original size:6 final size:6
Alignment explanation
Indices: 2671060--2671121 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
2671050 TTATATTTCG
* * * *
2671060 ATTTAA AATTAG ATTTAA ATTTAA TATATAC ATTTAA TATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA -ATTTAA ATTTAA
2671109 ATTTAA A-TTAA AT
1 ATTTAA ATTTAA AT
2671122 AAAAAATAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
5 10 0.23
6 24 0.55
7 10 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:2671096 original size:13 final size:13
Alignment explanation
Indices: 2671075--2671122 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
2671065 AAATTAGATT
2671075 TAAATTTAATATA
1 TAAATTTAATATA
* *
2671088 TACATTTAATATT
1 TAAATTTAATATA
2671101 TAAATTTAAT-T-
1 TAAATTTAATATA
*
2671112 TAAATTAAATA
1 TAAATTTAATA
2671123 AAAAATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 20 0.67
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTTAATATA
Found at i:2671112 original size:11 final size:12
Alignment explanation
Indices: 2671049--2671117 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
2671039 AATTTGATTT
* *
2671049 TTTATATTTCGA
1 TTTAAATTTAGA
*
2671061 TTTAAAATTAGA
1 TTTAAATTTAGA
2671073 TTTAAATTTA-A
1 TTTAAATTTAGA
* *
2671084 TATATACATTTAATA
1 T-T-TAAATTT-AGA
2671099 TTTAAATTTA-A
1 TTTAAATTTAGA
2671110 TTTAAATT
1 TTTAAATT
2671118 AAATAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
11 11 0.23
12 20 0.43
13 12 0.26
14 2 0.04
15 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (12 bp):
TTTAAATTTAGA
Found at i:2671917 original size:30 final size:28
Alignment explanation
Indices: 2671872--2671931 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
2671862 TAAATGGGTC
*
2671872 TAAATCATTAATTTTTTAAATAACTAAAAT
1 TAAAACATT-ATTTTTT-AATAACTAAAAT
*
2671902 TAAAACATTATTTTTTAATACCTAAAAT
1 TAAAACATTATTTTTTAATAACTAAAAT
2671930 TA
1 TA
2671932 TTAGAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 13 0.46
29 7 0.25
30 8 0.29
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAAACATTATTTTTTAATAACTAAAAT
Found at i:2683704 original size:13 final size:13
Alignment explanation
Indices: 2683688--2683712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2683678 TTCATAGAAG
2683688 TATTTAAAATTTT
1 TATTTAAAATTTT
2683701 TATTTAAAATTT
1 TATTTAAAATTT
2683713 CAAATATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTAAAATTTT
Found at i:2683748 original size:15 final size:16
Alignment explanation
Indices: 2683728--2683760 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2683718 ATTAATTTTA
2683728 TTTTAT-TTATAAATT
1 TTTTATATTATAAATT
2683743 TTTTATAATTATAAATT
1 TTTTAT-ATTATAAATT
2683760 T
1 T
2683761 ATGACTTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTATATTATAAATT
Found at i:2684402 original size:3 final size:3
Alignment explanation
Indices: 2684394--2684424 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2684384 TTGCAAACTA
2684394 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
2684425 CTGACCAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:2690097 original size:21 final size:21
Alignment explanation
Indices: 2690034--2690094 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
2690024 GGGATTGAAA
* *
2690034 ATTATAATGATAAAATTAATT
1 ATTATAATAATAAAATTAAAT
*
2690055 ATTATACTAATAAAATTAAAT
1 ATTATAATAATAAAATTAAAT
*
2690076 ATTATAAT-ATATAATTAAA
1 ATTATAATAATAAAATTAAA
2690095 ATAATTTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 10 0.29
21 25 0.71
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTATAATAATAAAATTAAAT
Found at i:2698547 original size:6 final size:6
Alignment explanation
Indices: 2698536--2698560 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2698526 ATAATTTTTT
2698536 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
2698561 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:2710555 original size:27 final size:27
Alignment explanation
Indices: 2710505--2710557 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2710495 TTATTATTTT
* *
2710505 TTAAAAATAATTGTATAAATTAATTAG
1 TTAAAAATAATTGAATAAACTAATTAG
* *
2710532 TTAAAAATGATTGAATGAACTAATTA
1 TTAAAAATAATTGAATAAACTAATTA
2710558 AATTATATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (27 bp):
TTAAAAATAATTGAATAAACTAATTAG
Found at i:2712507 original size:26 final size:26
Alignment explanation
Indices: 2712478--2712531 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2712468 ATTATTTTGA
2712478 ATAGGTTATCTATTTTGATAATTATT
1 ATAGGTTATCTATTTTGATAATTATT
2712504 ATAGGTTATCTATTTTGATAATTATT
1 ATAGGTTATCTATTTTGATAATTATT
2712530 AT
1 AT
2712532 GTACAAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (26 bp):
ATAGGTTATCTATTTTGATAATTATT
Found at i:2715564 original size:24 final size:24
Alignment explanation
Indices: 2715532--2715592 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2715522 GAGCAACTAC
* *
2715532 AAGAAGTGGAGGAGGAAGTAGAAG
1 AAGAAGTGGAAGAGGAAATAGAAG
* *
2715556 AAGAGGTGGAAGAGGAAATTGAAG
1 AAGAAGTGGAAGAGGAAATAGAAG
*
2715580 AAGAAGTAGAAGA
1 AAGAAGTGGAAGA
2715593 AGAAGAGGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.41, T:0.10
Consensus pattern (24 bp):
AAGAAGTGGAAGAGGAAATAGAAG
Found at i:2715584 original size:3 final size:3
Alignment explanation
Indices: 2715576--2715628 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
2715566 AGAGGAAATT
* * *
2715576 GAA GAA GAA GTA GAA GAA GAA GAG GAA GAG GAA GAA GAA G-A GAA CGAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA
2715624 GAA GA
1 GAA GA
2715629 CGATGATGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.58, C:0.02, G:0.38, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:2715591 original size:12 final size:12
Alignment explanation
Indices: 2715532--2715616 Score: 64
Period size: 12 Copynumber: 7.1 Consensus size: 12
2715522 GAGCAACTAC
* *
2715532 AAGAAGTGGAGG
1 AAGAAGTAGAAG
*
2715544 AGGAAGTAGAAG
1 AAGAAGTAGAAG
* *
2715556 AAGAGGTGGAAG
1 AAGAAGTAGAAG
* * *
2715568 AGGAAATTGAAG
1 AAGAAGTAGAAG
2715580 AAGAAGTAGAAG
1 AAGAAGTAGAAG
2715592 AAGAAG-AGGAAG
1 AAGAAGTA-GAAG
* *
2715604 AGGAAGAAGAAG
1 AAGAAGTAGAAG
2715616 A
1 A
2715617 GAACGAAGAA
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
11 1 0.02
12 55 0.96
13 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.41, T:0.07
Consensus pattern (12 bp):
AAGAAGTAGAAG
Found at i:2716593 original size:30 final size:27
Alignment explanation
Indices: 2716571--2716624 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2716561 CTGCAGTGGG
2716571 GTTCAACCCCGGGGTGGCTGCTGCTGC
1 GTTCAACCCCGGGGTGGCTGCTGCTGC
*
2716598 GTTTAACCCCGGGGTGGCTGCTGCTGC
1 GTTCAACCCCGGGGTGGCTGCTGCTGC
2716625 ACCGGCTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.07, C:0.31, G:0.37, T:0.24
Consensus pattern (27 bp):
GTTCAACCCCGGGGTGGCTGCTGCTGC
Found at i:2724531 original size:2 final size:2
Alignment explanation
Indices: 2724524--2724552 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2724514 TTCAAAAAGA
2724524 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 A
2724553 ATACCCCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2729999 original size:30 final size:30
Alignment explanation
Indices: 2729963--2730024 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2729953 CATGTGGTCG
2729963 TAGTGCATTAGCCTTGTTATCAAGAAAGAC
1 TAGTGCATTAGCCTTGTTATCAAGAAAGAC
2729993 TAGTGCATTAGCCTTGTTATCAAGAAAGAC
1 TAGTGCATTAGCCTTGTTATCAAGAAAGAC
2730023 TA
1 TA
2730025 TGTTTTGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (30 bp):
TAGTGCATTAGCCTTGTTATCAAGAAAGAC
Found at i:2737940 original size:30 final size:31
Alignment explanation
Indices: 2737906--2737986 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 31
2737896 GTGAAAACAA
*
2737906 CAAAATGAGATTTTTTTTT-ACTAATATACT
1 CAAAATGAGATTTTTTTTTCACCAATATACT
* * *
2737936 CAAAATAAGATTTTTTTTTCGACCGATATATT
1 CAAAATGAGATTTTTTTTTC-ACCAATATACT
2737968 CAAAATGAGATTTTTTTTT
1 CAAAATGAGATTTTTTTTT
2737987 TAACAATACG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 18 0.41
32 26 0.59
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.47
Consensus pattern (31 bp):
CAAAATGAGATTTTTTTTTCACCAATATACT
Found at i:2743286 original size:3 final size:3
Alignment explanation
Indices: 2743280--2743311 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2743270 TAAAAACATA
2743280 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2743312 CAACAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2743316 original size:3 final size:3
Alignment explanation
Indices: 2743310--2743362 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
2743300 TAATAATAAT
* * * *
2743310 AAC AAC AAC AAC AGC AGC AGC AAC AAC AAC AGC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
*
2743358 GAC AA
1 AAC AA
2743363 TAATAATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.58, C:0.32, G:0.09, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2743335 original size:15 final size:15
Alignment explanation
Indices: 2743312--2743355 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2743302 ATAATAATAA
*
2743312 CAACAACAACAGCAG
1 CAACAACAACAACAG
*
2743327 CAGCAACAACAACAG
1 CAACAACAACAACAG
2743342 CAACAACAACAACA
1 CAACAACAACAACA
2743356 ACGACAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.57, C:0.34, G:0.09, T:0.00
Consensus pattern (15 bp):
CAACAACAACAACAG
Done.