Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009078.1 Hibiscus syriacus cultivar Beakdansim tig00112517_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: 829977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:217443 original size:21 final size:23
Alignment explanation
Indices: 217397--217444 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
217387 ATCAAGTGTA
*
217397 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
217420 ATAATATAATAGGTAGCGTTTAT
1 ATAATATAATAGGTAGCGCTTAT
217443 AT
1 AT
217445 TGATCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:218389 original size:182 final size:182
Alignment explanation
Indices: 218077--218534 Score: 711
Period size: 182 Copynumber: 2.5 Consensus size: 182
218067 ACTTCTTTAC
*
218077 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
* * * * *
218142 TACATTTTTATAAAGTATCGATACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTTCAAAAG
66 TACATTTTTATAAAGTATCGACATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
*
218207 TGTCGATACTTAAAATAAAGTATCGACACTTTCAACATATCCGGTAGC-TCTT
131 TGTCGATACTTAAAATAAAGTATCGACACTATCAACATATCCGGTAGCGT-TT
* * *
218259 TACCGGTTTTGTCATTTCGAAACCGGTTTTGTCATATTTTTACATATTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
*
218324 TACATTTTTATAAAGTATCGACATTTTATTAGCGCTATAATTTCTTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* *
218389 TGTCGATACTTATAATAAAGTATTGACACTATCAACATATCCGGTAGCGTTT
131 TGTCGATACTTAAAATAAAGTATCGACACTATCAACATATCCGGTAGCGTTT
** ** * * *
218441 TACTTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
218506 TACATTTTTATAAAGTATCGACACTTTTA
66 TACATTTTTATAAAGTATCGACA-TTTTA
218535 ATATATCCGA
Statistics
Matches: 251, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
182 245 0.98
183 6 0.02
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTAAAATAAAGTATCGACACTATCAACATATCCGGTAGCGTTT
Found at i:218642 original size:113 final size:113
Alignment explanation
Indices: 218403--218979 Score: 872
Period size: 112 Copynumber: 5.1 Consensus size: 113
218393 GATACTTATA
* * * * *
218403 ATAAAGTATTGACACTATCAACATATCCGGTAGCGTTTTACTTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
* *
218468 TTTGTCA-TTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
* * * **
218515 ATAAAGTATCGACACTTTTAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGAGTGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
* *
218580 TTTGTCATTTTTTTTACATATTATATTGTTATGGATCGATATATTTTT
66 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
*
218628 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
* * *
218693 TTTGTCATTTTTTTTACCTTTTATATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
* *
218741 ATAAAGTATGGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
* * *
218806 TTTGTC-TTTTTTTTATCTGTTATATTGTTATGGATCAACATATTTTT
66 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
* * * *
218853 ATAAAGTATTGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTATCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
**
218918 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
218965 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
218980 AAACCGACAA
Statistics
Matches: 421, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
112 214 0.51
113 207 0.49
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (113 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
Found at i:218818 original size:225 final size:225
Alignment explanation
Indices: 218403--218979 Score: 906
Period size: 225 Copynumber: 2.6 Consensus size: 225
218393 GATACTTATA
* * * *
218403 ATAAAGTATTGACACTATCAACATATCCGGTAGCGTTTTACTTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
218468 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTT
* * **
218533 TAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGAGTGGTTTTGTCATTTTTTTTA-C
131 CAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTTATC
* *
218597 ATATTATATTGTTATGGATCGATATATTTTT
196 -TATTATATTGTTATGGATCAACATATTTTT
* *
218628 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
* *
218693 TTTGTCATTTTTTTTACCTTTTATATTGTTATAGATCGATACATTTTTATAAAGTATGGACACTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTT
* *
218758 TCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAAACCGGTTTTGTC-TTTTTTTTAT
130 TCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTTAT
*
218822 CTGTTATATTGTTATGGATCAACATATTTTT
195 CTATTATATTGTTATGGATCAACATATTTTT
* * *
218853 ATAAAGTATTGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTATCATTTATAGACCGGT
1 ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
* ** *
218918 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTAATATATTTTTATAAAGTATCGACAC
66 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACAC
218980 AAACCGACAA
Statistics
Matches: 322, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
224 49 0.15
225 169 0.52
226 104 0.32
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (225 bp):
ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTTATC
TATTATATTGTTATGGATCAACATATTTTT
Found at i:225579 original size:46 final size:46
Alignment explanation
Indices: 225512--225599 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
225502 ACAGGAGGTT
* *
225512 AATGCTAAGCAATATCGTAAATGATGCATGCAAAGTATTAAAAGTC
1 AATGCTAAGCAATACCATAAATGATGCATGCAAAGTATTAAAAGTC
*
225558 AATGCTAAGTAATACCATAAATGATGCATGCAAAGTATTAAA
1 AATGCTAAGCAATACCATAAATGATGCATGCAAAGTATTAAA
225600 GGTCTGGATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.26
Consensus pattern (46 bp):
AATGCTAAGCAATACCATAAATGATGCATGCAAAGTATTAAAAGTC
Found at i:230250 original size:16 final size:16
Alignment explanation
Indices: 230215--230257 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
230205 GTTTACTTCA
230215 GAATGATTC-AACGAT
1 GAATGATTCAAACGAT
* *
230230 GAATGATTCAAATGTT
1 GAATGATTCAAACGAT
230246 GAATGATTCAAA
1 GAATGATTCAAA
230258 GGCTCTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (16 bp):
GAATGATTCAAACGAT
Found at i:231954 original size:6 final size:6
Alignment explanation
Indices: 231945--231969 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
231935 ACAACACGCA
231945 CGCACG CGCACG CGCACG CGCACG C
1 CGCACG CGCACG CGCACG CGCACG C
231970 ACACAAACAC
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:0.16, C:0.52, G:0.32, T:0.00
Consensus pattern (6 bp):
CGCACG
Found at i:234231 original size:199 final size:197
Alignment explanation
Indices: 233880--234278 Score: 606
Period size: 199 Copynumber: 2.0 Consensus size: 197
233870 TTTATGGCAC
*
233880 TACAGTGGTTCTGTCTCTTCTTTTGTTCTTTCATTTTGCCTCACGTCAAGAGATGTTTAATTTAC
1 TACAGTGGTTCTGTCTCTTCTTTTGTTCTTTCATTTTGCCTCACGTCAAGAGATGATTAATTTAC
* * *
233945 TAATGAAACATGTTCTCCGGATACATAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCTTGT
66 TAATGAAACAGGTTCTCCAGAAACATAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCTTGT
* *
234010 TCCTGGAGGTCATAGTGTATATATGTATACATGTA-CCTGATTTGTTTTGCTTTTCCACCTTTGC
131 TCCTGGAGGTCATAG-GTATATA--TATACACGTAGCCTGATCTGTTTTGCTTTTCCACCTTTGC
234074 TCACT
193 TCACT
* * *
234079 TACAGTGGTTGTGTCTCTTCTTTTGTTCTTTCGTTTTGCCTCACGTCAAGAGAT-ATTCATCTTA
1 TACAGTGGTTCTGTCTCTTCTTTTGTTCTTTCATTTTGCCTCACGTCAAGAGATGATTAAT-TTA
*
234143 CTAATGAAACGGGGTTCTCCAGAAACATAAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCT
65 CTAATGAAAC-AGGTTCTCCAGAAACAT-AAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCT
* *
234208 TGTTCCTGGAGGTCATA-GTATATATATACACGTATGTCTGATCTGTTTTTCTTTTCCACCTTTG
128 TGTTCCTGGAGGTCATAGGTATATATATACACGTA-GCCTGATCTGTTTTGCTTTTCCACCTTTG
234272 CTCACT
192 CTCACT
234278 T
1 T
234279 GCAGGATGGA
Statistics
Matches: 183, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
197 9 0.05
198 4 0.02
199 104 0.57
200 13 0.07
201 53 0.29
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (197 bp):
TACAGTGGTTCTGTCTCTTCTTTTGTTCTTTCATTTTGCCTCACGTCAAGAGATGATTAATTTAC
TAATGAAACAGGTTCTCCAGAAACATAAGGAGCATTGCTGATTCTTTTCCGTTTCTTTATCTTGT
TCCTGGAGGTCATAGGTATATATATACACGTAGCCTGATCTGTTTTGCTTTTCCACCTTTGCTCA
CT
Found at i:240724 original size:2 final size:2
Alignment explanation
Indices: 240717--240742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
240707 AACATTGGTA
240717 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
240743 GAATATGCAA
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:242474 original size:11 final size:11
Alignment explanation
Indices: 242460--242485 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
242450 TACATATTAA
242460 ATAATAATAAT
1 ATAATAATAAT
242471 ATAATAATAAT
1 ATAATAATAAT
242482 ATAA
1 ATAA
242486 AAACGACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:247522 original size:22 final size:22
Alignment explanation
Indices: 247497--247538 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
247487 AAAATTATCC
**
247497 TAAAAAATATCATAAATAAAGT
1 TAAAAAATAAAATAAATAAAGT
247519 TAAAAAATAAAATAAATAAA
1 TAAAAAATAAAATAAATAAA
247539 AACAAAGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAAATAAAATAAATAAAGT
Found at i:249398 original size:9 final size:9
Alignment explanation
Indices: 249386--249437 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
249376 AAATATTTTA
249386 TATTTAATT
1 TATTTAATT
*
249395 TATTTAA-G
1 TATTTAATT
249403 TATTTAATT
1 TATTTAATT
249412 TATTTAA--
1 TATTTAATT
*
249419 TATTTTATT
1 TATTTAATT
*
249428 TAATTAATT
1 TATTTAATT
249437 T
1 T
249438 TTTTTACAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:249408 original size:17 final size:16
Alignment explanation
Indices: 249379--249435 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
249369 ATATTTTAAA
*
249379 TATTTTATATTTAATT
1 TATTTAATATTTAATT
249395 TATTTAAGTATTTAATT
1 TATTTAA-TATTTAATT
*
249412 TATTTAATATTTTATT
1 TATTTAATATTTAATT
*
249428 TAATTAAT
1 TATTTAAT
249436 TTTTTTTACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:251694 original size:13 final size:13
Alignment explanation
Indices: 251663--251706 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
251653 TATTTAGTAC
*
251663 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* *
251676 TGTTTATTGGAAT
1 TTTTTATTGTAAT
*
251689 TTTTTATTTTAAT
1 TTTTTATTGTAAT
251702 TTTTT
1 TTTTT
251707 TATTATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:263427 original size:20 final size:21
Alignment explanation
Indices: 263368--263436 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 21
263358 AATGGTAATA
263368 AAATGATTATTAAAT-TTTATTT
1 AAAT-ATTATTAAATATTTA-TT
* *
263390 AACTATTA-TAAA-AATTATT
1 AAATATTATTAAATATTTATT
263409 AAAT-TTATTAAATATTTA-T
1 AAATATTATTAAATATTTATT
*
263428 AATTATTAT
1 AAATATTAT
263437 AATATTATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.08
19 13 0.34
20 15 0.39
21 4 0.11
22 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
AAATATTATTAAATATTTATT
Found at i:263431 original size:18 final size:20
Alignment explanation
Indices: 263410--263456 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
263400 AAAATTATTA
263410 AATTTATTAAATATT-TA-T
1 AATTTATTAAATATTATAGT
263428 AA-TTATTATAATATTATAGT
1 AATTTATTA-AATATTATAGT
263448 AATTT-TTAA
1 AATTTATTAA
263457 TAAAAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.24
18 8 0.32
19 3 0.12
20 6 0.24
21 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AATTTATTAAATATTATAGT
Found at i:263436 original size:29 final size:30
Alignment explanation
Indices: 263373--263429 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
263363 TAATAAAATG
*
263373 ATTATTAAATTTTATTTAACTATTATAAAA
1 ATTATTAAATTTTATTTAAATATTATAAAA
263403 ATTATTAAA-TTTA-TTAAATATTTATAA
1 ATTATTAAATTTTATTTAAATA-TTATAA
263430 TTATTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 10 0.40
30 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTATTAAATTTTATTTAAATATTATAAAA
Found at i:263457 original size:18 final size:18
Alignment explanation
Indices: 263413--263497 Score: 57
Period size: 20 Copynumber: 4.4 Consensus size: 18
263403 ATTATTAAAT
263413 TTATTA-AATATTTATAA
1 TTATTATAATATTTATAA
263430 TTATTATAATATTATAGTAA
1 TTATTATAATATT-TA-TAA
* * *
263450 TTTTTAATAAAAGTTAATAA
1 TTATT-ATAATA-TTTATAA
263470 TT-TTAATAATTATTTTATAA
1 TTATT-ATAA-TA-TTTATAA
*
263490 TTTTTATA
1 TTATTATA
263498 GAAGCCATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
17 6 0.11
18 6 0.11
19 9 0.16
20 24 0.44
21 8 0.15
22 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTATTATAATATTTATAA
Found at i:263489 original size:20 final size:19
Alignment explanation
Indices: 263419--263493 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 19
263409 AAATTTATTA
263419 AATA-TTTATAATTATT-AT
1 AATATTTTATAATT-TTAAT
*
263437 AATATTATAGTAATTTTTAAT
1 AATATTTTA-TAA-TTTTAAT
* * *
263458 AAAAGTTAATAATTTTAAT
1 AATATTTTATAATTTTAAT
263477 AATTATTTTATAATTTT
1 AA-TATTTTATAATTTT
263494 TATAGAAGCC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
18 4 0.09
19 12 0.27
20 19 0.43
21 9 0.20
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
AATATTTTATAATTTTAAT
Found at i:268843 original size:153 final size:153
Alignment explanation
Indices: 268565--268871 Score: 605
Period size: 153 Copynumber: 2.0 Consensus size: 153
268555 GGTTGGCTAG
268565 AAGGAGCCCTCGCGAGCAAGCCTCCGAATGACAAGGTAGAAATATCCTACCTGTAATTACTTTTT
1 AAGGAGCCCTCGCGAGCAAGCCTCCGAATGACAAGGTAGAAATATCCTACCTGTAATTACTTTTT
268630 AAGTTTCTCACAATAGCATTGATCCAATAACTCAAACCTGTGACTACAGGTAATGTCAGCAAATC
66 AAGTTTCTCACAATAGCATTGATCCAATAACTCAAACCTGTGACTACAGGTAATGTCAGCAAATC
268695 TGGATATCAAGCAGCAAGGTCTC
131 TGGATATCAAGCAGCAAGGTCTC
268718 AAGGAGCCCTCGCGAGCAAGCCTCCGAATGACAAGGTAGAAATATCCTACCTGTAATTACTTTTT
1 AAGGAGCCCTCGCGAGCAAGCCTCCGAATGACAAGGTAGAAATATCCTACCTGTAATTACTTTTT
*
268783 ATGTTTCTCACAATAGCATTGATCCAATAACTCAAACCTGTGACTACAGGTAATGTCAGCAAATC
66 AAGTTTCTCACAATAGCATTGATCCAATAACTCAAACCTGTGACTACAGGTAATGTCAGCAAATC
268848 TGGATATCAAGCAGCAAGGTCTC
131 TGGATATCAAGCAGCAAGGTCTC
268871 A
1 A
268872 CACTCTCATT
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 153 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (153 bp):
AAGGAGCCCTCGCGAGCAAGCCTCCGAATGACAAGGTAGAAATATCCTACCTGTAATTACTTTTT
AAGTTTCTCACAATAGCATTGATCCAATAACTCAAACCTGTGACTACAGGTAATGTCAGCAAATC
TGGATATCAAGCAGCAAGGTCTC
Found at i:270205 original size:57 final size:57
Alignment explanation
Indices: 270140--270253 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
270130 AATCTTTAAA
270140 GAAATAAGAGGCTGAAAAGAAAATTAGTACCAGGAAAAACAAAAGAACGATCCAGGG
1 GAAATAAGAGGCTGAAAAGAAAATTAGTACCAGGAAAAACAAAAGAACGATCCAGGG
270197 GAAATAAGAGGCTGAAAAGAAAATTAGTACCAGGAAAAACAAAAGAACGATCCAGGG
1 GAAATAAGAGGCTGAAAAGAAAATTAGTACCAGGAAAAACAAAAGAACGATCCAGGG
270254 AACGTAATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.53, C:0.12, G:0.25, T:0.11
Consensus pattern (57 bp):
GAAATAAGAGGCTGAAAAGAAAATTAGTACCAGGAAAAACAAAAGAACGATCCAGGG
Found at i:272922 original size:30 final size:31
Alignment explanation
Indices: 272873--272954 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
272863 ACTAGTGACC
* * **
272873 AAAATGT-AAATTATGAAAGTTTAGGAA-TT
1 AAAATGTAAAATTATAAAAGTTTAAGAACAA
*
272902 AAAATGTAAAATTGTAAAAGTTTAAGAACAA
1 AAAATGTAAAATTATAAAAGTTTAAGAACAA
*
272933 AAAATGTAAAATTTTAAAAGTT
1 AAAATGTAAAATTATAAAAGTT
272955 ATATTTTGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 7 0.16
30 17 0.38
31 21 0.47
ACGTcount: A:0.54, C:0.01, G:0.13, T:0.32
Consensus pattern (31 bp):
AAAATGTAAAATTATAAAAGTTTAAGAACAA
Found at i:275636 original size:12 final size:12
Alignment explanation
Indices: 275619--275643 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
275609 TCATATAAAA
275619 CAAATAATTAAT
1 CAAATAATTAAT
275631 CAAATAATTAAT
1 CAAATAATTAAT
275643 C
1 C
275644 GAATTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (12 bp):
CAAATAATTAAT
Found at i:279992 original size:30 final size:31
Alignment explanation
Indices: 279956--280016 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
279946 GAACTATTCG
279956 AAAGTTGAATAACCAAATT-AAAAAATATTT
1 AAAGTTGAATAACCAAATTAAAAAAATATTT
* *
279986 AAAGTTGAATGACTAAATTAAAAAAATATTT
1 AAAGTTGAATAACCAAATTAAAAAAATATTT
280017 GTTAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (31 bp):
AAAGTTGAATAACCAAATTAAAAAAATATTT
Found at i:285275 original size:19 final size:19
Alignment explanation
Indices: 285253--285294 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
285243 GTTATCTATA
285253 AATCCAAAAAGAAAG-TATG
1 AATCCAAAAA-AAAGTTATG
* *
285272 AATCTAAAAATAAGTTATG
1 AATCCAAAAAAAAGTTATG
285291 AATC
1 AATC
285295 AGAATTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (19 bp):
AATCCAAAAAAAAGTTATG
Found at i:287457 original size:31 final size:31
Alignment explanation
Indices: 287410--287486 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
287400 ATTACATCAG
* *
287410 ATACCACTGAATTTTAGGCGTTGTATCGTTT
1 ATACCACTGAACTTTAGGCGTTATATCGTTT
* *
287441 ATACCATTGAACTTTAGGTGTTATATCGTTT
1 ATACCACTGAACTTTAGGCGTTATATCGTTT
*
287472 ATATCACTGAACTTT
1 ATACCACTGAACTTT
287487 CAATTTTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (31 bp):
ATACCACTGAACTTTAGGCGTTATATCGTTT
Found at i:287508 original size:29 final size:30
Alignment explanation
Indices: 287470--287543 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
287460 GTTATATCGT
* *
287470 TTATATCACTGAACTTTCAATTTTG-TTCA
1 TTATACCACTGAACTTTCAATTTTGTTTAA
* * * *
287499 TTATAGCACTAAACTTTGATTTTTGTTTTAA
1 TTATACCACTGAACTTTCAATTTTG-TTTAA
287530 TTATACCACTGAAC
1 TTATACCACTGAAC
287544 CGTTAAATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 21 0.58
31 15 0.42
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (30 bp):
TTATACCACTGAACTTTCAATTTTGTTTAA
Found at i:288061 original size:33 final size:32
Alignment explanation
Indices: 287990--288126 Score: 102
Period size: 33 Copynumber: 4.2 Consensus size: 32
287980 ATATGATAAT
* * *
287990 AAAAAATAAAT-AAAATAGAAAAAAAGGATATATA
1 AAAAAAGAAATAAAAATA-AAAAATA--ATAAATA
* **
288024 AAAAAAGATAATAAAAATGAAAAATAATATTTTA
1 AAAAAAGA-AATAAAAATAAAAAATAATA-AATA
* *
288058 AAAAATACAAA-AATAATAAAAAATAATAAATA
1 AAAAA-AGAAATAAAAATAAAAAATAATAAATA
*
288090 AAAAAAGAAAT-AAAGTAAAAAATAAT-AATA
1 AAAAAAGAAATAAAAATAAAAAATAATAAATA
*
288120 ACAAAAG
1 AAAAAAG
288127 GTTAAGTTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
30 10 0.12
31 17 0.20
32 7 0.08
33 18 0.21
34 17 0.20
35 11 0.13
36 5 0.06
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (32 bp):
AAAAAAGAAATAAAAATAAAAAATAATAAATA
Found at i:288061 original size:66 final size:64
Alignment explanation
Indices: 287989--288116 Score: 159
Period size: 66 Copynumber: 2.0 Consensus size: 64
287979 AATATGATAA
* * *
287989 TAAAAAATAAATAAAATAGA-AAAAAAGGATATATAAAAAAAGATAATAAAAATGAAAAATAATA
1 TAAAAAATAAA-AAAATA-ATAAAAAAGAATAAATAAAAAAAGA-AAT-AAAATAAAAAATAATA
288053 TTT
62 TTT
* * *
288056 TAAAAAATACAAAAATAATAAAAAATAATAAATAAAAAAAGAAATAAAGTAAAAAATAATA
1 TAAAAAATAAAAAAATAATAAAAAAGAATAAATAAAAAAAGAAATAAAATAAAAAATAATA
288117 ATAACAAAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
64 14 0.26
65 4 0.07
66 26 0.48
67 10 0.19
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.20
Consensus pattern (64 bp):
TAAAAAATAAAAAAATAATAAAAAAGAATAAATAAAAAAAGAAATAAAATAAAAAATAATATTT
Found at i:288079 original size:18 final size:17
Alignment explanation
Indices: 288056--288095 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
288046 AATAATATTT
288056 TAAAAAATACAAAAATAA
1 TAAAAAATA-AAAAATAA
*
288074 TAAAAAATAATAAATAA
1 TAAAAAATAAAAAATAA
288091 -AAAAA
1 TAAAAA
288096 GAAATAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 9 0.43
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (17 bp):
TAAAAAATAAAAAATAA
Found at i:288109 original size:31 final size:31
Alignment explanation
Indices: 287990--288126 Score: 107
Period size: 34 Copynumber: 4.2 Consensus size: 31
287980 ATATGATAAT
* * *
287990 AAAAAATAAATAAAATAGAAAAAAAGGATATATA
1 AAAAAAGAAATAAAATA-AAAAATA--ATAAATA
* **
288024 AAAAAAGATAATAAAAATGAAAAATAATATTTTA
1 AAAAAAGA-AAT-AAAATAAAAAATAATA-AATA
*
288058 AAAAATACAAA-AATAATAAAAAATAATAAATA
1 AAAAA-AGAAATAA-AATAAAAAATAATAAATA
*
288090 AAAAAAGAAATAAAGTAAAAAATAAT-AATA
1 AAAAAAGAAATAAAATAAAAAATAATAAATA
*
288120 ACAAAAG
1 AAAAAAG
288127 GTTAAGTTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
30 10 0.12
31 16 0.19
32 11 0.13
33 16 0.19
34 17 0.20
35 11 0.13
36 5 0.06
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (31 bp):
AAAAAAGAAATAAAATAAAAAATAATAAATA
Found at i:289378 original size:16 final size:17
Alignment explanation
Indices: 289362--289401 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
289352 AAATAAAATA
289362 AAATAAAT-AAAT-GAT
1 AAATAAATAAAATAGAT
289377 AAATGAAATAAAATAGAT
1 AAAT-AAATAAAATAGAT
289395 AAATAAA
1 AAATAAA
289402 AACATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 4 0.18
17 7 0.32
18 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AAATAAATAAAATAGAT
Found at i:289464 original size:37 final size:37
Alignment explanation
Indices: 289413--289739 Score: 340
Period size: 37 Copynumber: 8.8 Consensus size: 37
289403 ACATTTTTTT
* * *
289413 AAACTATACAATATATGTTTTAAAAAAGTAATTTTCA
1 AAACTATATAATATATATTTTAAAAAACTAATTTTCA
* * *
289450 AAA-TCATATAATATATATTTAAAAAAAATAATTTTTA
1 AAACT-ATATAATATATATTTTAAAAAACTAATTTTCA
* *
289487 AAACTCTATAATATATA-TTT-AAAATCTAATTTTCA
1 AAACTATATAATATATATTTTAAAAAACTAATTTTCA
*
289522 AAACTATATAATATATATATTTTTAAAAACTAATTTTCA
1 AAACTATAT-A-ATATATATTTTAAAAAACTAATTTTCA
* *
289561 AAACTATATAATATATATTTTTAAAAACTAATTTTTA
1 AAACTATATAATATATATTTTAAAAAACTAATTTTCA
** *
289598 AAACTATAT-ATATATATTTTTTAAAACTAATTTTTA
1 AAACTATATAATATATATTTTAAAAAACTAATTTTCA
* ** * ** *
289634 AAACTATATAATACATATGTTTTCAAAATTGTTTTTAA
1 AAACTATATAATATATAT-TTTAAAAAACTAATTTTCA
* *
289672 AAACTATATATTATATATATTTTAAAAAAAT-GTTTTCA
1 AAACTATATA--ATATATATTTTAAAAAACTAATTTTCA
* *
289710 AAACTATATAATATATGTTTTCAAAAACTA
1 AAACTATATAATATATATTTTAAAAAACTA
289740 TATATTATAT
Statistics
Matches: 250, Mismatches: 29, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
35 20 0.08
36 55 0.22
37 93 0.37
38 44 0.18
39 31 0.12
40 7 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (37 bp):
AAACTATATAATATATATTTTAAAAAACTAATTTTCA
Found at i:289474 original size:22 final size:22
Alignment explanation
Indices: 289449--289510 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 22
289439 AGTAATTTTC
289449 AAAATCATATAATATATATTT-
1 AAAATCATATAATATATATTTA
*
289470 AAAA--A-A-AATA-ATTTTTA
1 AAAATCATATAATATATATTTA
*
289487 AAACTC-TATAATATATATTTA
1 AAAATCATATAATATATATTTA
289508 AAA
1 AAA
289511 TCTAATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
16 5 0.16
17 7 0.22
18 1 0.03
19 2 0.06
20 4 0.12
21 13 0.41
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATCATATAATATATATTTA
Found at i:289632 original size:14 final size:13
Alignment explanation
Indices: 289540--289639 Score: 61
Period size: 13 Copynumber: 8.0 Consensus size: 13
289530 TAATATATAT
289540 ATTTTTAAAAACTA
1 ATTTTT-AAAACTA
*
289554 ATTTTCAAAACT-
1 ATTTTTAAAACTA
* *
289566 A--TATAATA-TA
1 ATTTTTAAAACTA
289576 TATTTTTAAAAACTA
1 -ATTTTT-AAAACTA
289591 ATTTTTAAAACT-
1 ATTTTTAAAACTA
* * *
289603 ATATAT-ATA-TA
1 ATTTTTAAAACTA
*
289614 TTTTTTAAAACTA
1 ATTTTTAAAACTA
289627 ATTTTTAAAACTA
1 ATTTTTAAAACTA
289640 TATAATACAT
Statistics
Matches: 63, Mismatches: 14, Indels: 19
0.66 0.15 0.20
Matches are distributed among these distances:
9 1 0.02
10 5 0.08
11 6 0.10
12 7 0.11
13 28 0.44
14 14 0.22
15 2 0.03
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTTAAAACTA
Found at i:289741 original size:24 final size:24
Alignment explanation
Indices: 289701--289759 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
289691 TTTTAAAAAA
289701 ATGTTTTC-AAAACTATATAATAT
1 ATGTTTTCAAAAACTATATAATAT
*
289724 ATGTTTTCAAAAACTATATATTAT
1 ATGTTTTCAAAAACTATATAATAT
*
289748 ATATTTTCAAAA
1 ATGTTTTCAAAA
289760 TATTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 8 0.24
24 25 0.76
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (24 bp):
ATGTTTTCAAAAACTATATAATAT
Found at i:289791 original size:60 final size:61
Alignment explanation
Indices: 289665--289795 Score: 142
Period size: 60 Copynumber: 2.1 Consensus size: 61
289655 TTCAAAATTG
* * ** * *
289665 TTTTTAAAAACTATATATTATATATATTTTAAAAAAATGTTTTCAAAACTATATAATATATG
1 TTTTCAAAAACTATATATTATATATATTTT-AAAAAATATTTAAAAAACCATATAATATATA
* *
289727 TTTTCAAAAACTATATA-T-TATATATTTT-CAAAATATTTAAAAAACCCATATATTATATAA
1 TTTTCAAAAACTATATATTATATATATTTTAAAAAATATTTAAAAAA-CCATATAATATAT-A
289787 TTTTCAAAA
1 TTTTCAAAA
289796 TGATTTCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
58 12 0.20
59 11 0.19
60 19 0.32
61 1 0.02
62 16 0.27
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (61 bp):
TTTTCAAAAACTATATATTATATATATTTTAAAAAATATTTAAAAAACCATATAATATATA
Found at i:289819 original size:35 final size:34
Alignment explanation
Indices: 289732--289820 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 34
289722 ATATGTTTTC
289732 AAAAACTATATATTATAT-ATTTTCAAAATATTT
1 AAAAACTATATATTATATAATTTTCAAAATATTT
*
289765 AAAAAACCCATATATTATATAATTTTCAAAATGATTT
1 -AAAAA-CTATATATTATATAATTTTCAAAAT-ATTT
*
289802 -CAAACTATATATGTATATA
1 AAAAACTATATAT-TATATA
289821 TATATAAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
34 12 0.25
35 21 0.44
36 11 0.23
37 4 0.08
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.40
Consensus pattern (34 bp):
AAAAACTATATATTATATAATTTTCAAAATATTT
Found at i:290080 original size:19 final size:19
Alignment explanation
Indices: 290053--290101 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
290043 ATTTATTGCT
*
290053 ATTTTATAATAAATCTATA
1 ATTTAATAATAAATCTATA
* * *
290072 ATTTAATAATTATTTTATA
1 ATTTAATAATAAATCTATA
290091 ATTCTAATAAT
1 ATT-TAATAAT
290102 TTAATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTAATAATAAATCTATA
Found at i:290648 original size:33 final size:33
Alignment explanation
Indices: 290607--290673 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
290597 ATTAAAAGTT
290607 AAAAAATGGTCGTTTGAGAATGTTGTTTTGTTA
1 AAAAAATGGTCGTTTGAGAATGTTGTTTTGTTA
290640 AAAAAATGGTCGTTTGAGAATGTTGTTTTGTTA
1 AAAAAATGGTCGTTTGAGAATGTTGTTTTGTTA
290673 A
1 A
290674 GTCTCTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.42
Consensus pattern (33 bp):
AAAAAATGGTCGTTTGAGAATGTTGTTTTGTTA
Found at i:291110 original size:14 final size:13
Alignment explanation
Indices: 291082--291108 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
291072 TAATTATCTC
291082 ATATCATTAAAAA
1 ATATCATTAAAAA
291095 ATATCATTAAAAA
1 ATATCATTAAAAA
291108 A
1 A
291109 ATTAAGGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATCATTAAAAA
Found at i:293894 original size:53 final size:53
Alignment explanation
Indices: 293809--293918 Score: 184
Period size: 53 Copynumber: 2.1 Consensus size: 53
293799 AAAATAATAC
* * *
293809 AGTATCAAATACAAATCAAAGTTACAACTGAATATACATATGGGTTTATATAT
1 AGTACCAAATACAAATCAAAGTTACAACTGAATATACATAAGGGTTCATATAT
*
293862 AGTACCAAATACAAATCAGAGTTACAACTGAATATACATAAGGGTTCATATAT
1 AGTACCAAATACAAATCAAAGTTACAACTGAATATACATAAGGGTTCATATAT
293915 AGTA
1 AGTA
293919 TATGCCCTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (53 bp):
AGTACCAAATACAAATCAAAGTTACAACTGAATATACATAAGGGTTCATATAT
Found at i:295265 original size:65 final size:64
Alignment explanation
Indices: 295064--295273 Score: 166
Period size: 65 Copynumber: 3.2 Consensus size: 64
295054 TGCACTAAGA
* * * * *
295064 GTGCATCGATGCATCAAGTGTATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGG-C
1 GTGCATCGATGCATCAAATGCATTCAATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGAT
295126 TG
63 TG
* *
295128 GTGCATCAATGCATCAAATGCATTCAATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCAATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGG-AT
295193 AT-
63 -TG
* * **
295195 -T-CATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCAATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGGAT
295256 TG
63 TG
*
295258 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
295274 CTCTGAAAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
62 4 0.03
63 5 0.04
64 46 0.39
65 56 0.47
66 5 0.04
67 1 0.01
68 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCAATGTTTCATAAAATCTCAGTGCATCGATGCATGGATTG
Found at i:298159 original size:35 final size:35
Alignment explanation
Indices: 298113--298184 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
298103 TTCACCAAAT
298113 AACATAAACTCCCCCTAACTAATAGCAAAGAATGC
1 AACATAAACTCCCCCTAACTAATAGCAAAGAATGC
298148 AACATAAACTCCCCCTAACTAATAGCAAAGAATGC
1 AACATAAACTCCCCCTAACTAATAGCAAAGAATGC
298183 AA
1 AA
298185 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.47, C:0.28, G:0.08, T:0.17
Consensus pattern (35 bp):
AACATAAACTCCCCCTAACTAATAGCAAAGAATGC
Found at i:301288 original size:55 final size:56
Alignment explanation
Indices: 301204--301314 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 56
301194 TTTTGAATCA
301204 TCACCAAAAGTCACTTCTCCTCCATTTTTGGCTTTAAACTCA-TGAACTGGTTTTT
1 TCACCAAAAGTCACTTCTCCTCCATTTTTGGCTTTAAACTCACTGAACTGGTTTTT
301259 TCACCAAAAGTCACTTCTCCTCCATTTTTGGCTTTAAACTCACTGAACTGGTTTTT
1 TCACCAAAAGTCACTTCTCCTCCATTTTTGGCTTTAAACTCACTGAACTGGTTTTT
301315 GTCTCCGGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 42 0.76
56 13 0.24
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (56 bp):
TCACCAAAAGTCACTTCTCCTCCATTTTTGGCTTTAAACTCACTGAACTGGTTTTT
Found at i:301882 original size:22 final size:21
Alignment explanation
Indices: 301840--301879 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
301830 GAGTTTATTT
*
301840 TCATTTTTAAATTTTGAAACA
1 TCATTTTTAAATTTTAAAACA
*
301861 TCATTTTTATATTTTAAAA
1 TCATTTTTAAATTTTAAAA
301880 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTAAATTTTAAAACA
Found at i:304001 original size:18 final size:17
Alignment explanation
Indices: 303947--303995 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
303937 TTGAACCCTT
* *
303947 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
303965 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
303983 AGTGCATTCGATG
1 AGTGCA-TCGATG
303996 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:304064 original size:46 final size:45
Alignment explanation
Indices: 303966--304071 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
303956 GTGCACTAAG
* *
303966 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
304011 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
304057 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
304072 GGTATGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 29 0.54
46 22 0.41
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:304146 original size:65 final size:63
Alignment explanation
Indices: 304012--304157 Score: 163
Period size: 65 Copynumber: 2.3 Consensus size: 63
304002 AATAGCCAGA
*
304012 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTAT
* **
304077 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGGTA
304139 TT
63 -T
*
304141 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
304158 CTCTGAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.04
63 4 0.06
64 21 0.30
65 42 0.60
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTAT
Found at i:316464 original size:21 final size:20
Alignment explanation
Indices: 316440--316538 Score: 69
Period size: 20 Copynumber: 5.4 Consensus size: 20
316430 AACTTTGAAA
316440 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
316461 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
316475 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
*
316496 AAATGTTTT-----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
316510 AAATAGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
316531 AAATGTTT
1 AAATGTTT
316539 CTTTGAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 29
0.65 0.04 0.31
Matches are distributed among these distances:
14 10 0.17
15 12 0.20
16 4 0.07
19 4 0.07
20 15 0.25
21 15 0.25
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.46
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:316581 original size:36 final size:37
Alignment explanation
Indices: 316432--316585 Score: 212
Period size: 35 Copynumber: 4.3 Consensus size: 37
316422 TGGCAACTAA
316432 CTTTGAAAAAATGA-TTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGAGTTTTCAAAGTTTGGTAAATGTTT
316469 CTTTG-AAAATG-GTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGAGTTTTCAAAGTTTGGTAAATGTTT
*
316504 TTTTG-AAAAT-AGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGAGTTTTCAAAGTTTGGTAAATGTTT
* * *
316539 CTTTGAAAAATGATTTTTAAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGAGTTTTCAAAGTTTGGTAAATGTTT
*
316576 -GTTGAAAAAT
1 CTTTGAAAAAT
316586 TGTAATGGGA
Statistics
Matches: 107, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
35 66 0.62
36 14 0.13
37 27 0.25
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATGAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:321035 original size:35 final size:36
Alignment explanation
Indices: 320996--321073 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
320986 ACCAACTTTG
*
320996 GAAAAAT-GATTTTCAAAGTTTGGTAAATGTTTTTT
1 GAAAAATGGATTTTCAAAGTTTGGTAAATGTTTGTT
* *
321031 GAAAAATGGTTTTTCAAAGTTTGGTAGATGTTTGTT
1 GAAAAATGGATTTTCAAAGTTTGGTAAATGTTTGTT
321067 GAAAAAT
1 GAAAAAT
321074 TATAATGGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 7 0.18
36 32 0.82
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.42
Consensus pattern (36 bp):
GAAAAATGGATTTTCAAAGTTTGGTAAATGTTTGTT
Found at i:324110 original size:16 final size:17
Alignment explanation
Indices: 324075--324106 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
324065 GTTCCTTTGC
324075 ATTTTCTTTTATCATTT
1 ATTTTCTTTTATCATTT
324092 ATTTT-TTTTAT-ATTT
1 ATTTTCTTTTATCATTT
324107 TATTCTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 6 0.40
17 5 0.33
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTCTTTTATCATTT
Found at i:325879 original size:24 final size:24
Alignment explanation
Indices: 325847--325898 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
325837 TCCTCTCTCT
**
325847 TTCTCCTCCTTTTCCTTTTTCTTC
1 TTCTCCTCCTTTTCCTCCTTCTTC
*
325871 TTCTCCTCCTTTTTCTCCTTCTTC
1 TTCTCCTCCTTTTCCTCCTTCTTC
325895 TTCT
1 TTCT
325899 TGTTCGTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (24 bp):
TTCTCCTCCTTTTCCTCCTTCTTC
Found at i:325880 original size:18 final size:18
Alignment explanation
Indices: 325859--325915 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
325849 CTCCTCCTTT
325859 TCCTTTTTCTTCTTCTCC
1 TCCTTTTTCTTCTTCTCC
* *
325877 TCCTTTTTCTCCTTCTTC
1 TCCTTTTTCTTCTTCTCC
* * *
325895 TTCTTGTTCGTCTTCCTCC
1 TCCTTTTTCTTCTT-CTCC
325914 TC
1 TC
325916 TATTAAAATA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.00, C:0.39, G:0.04, T:0.58
Consensus pattern (18 bp):
TCCTTTTTCTTCTTCTCC
Found at i:325898 original size:12 final size:12
Alignment explanation
Indices: 325865--325898 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
325855 CTTTTCCTTT
325865 TTCTTCTTCTCC
1 TTCTTCTTCTCC
* *
325877 TCCTTTTTCTCC
1 TTCTTCTTCTCC
325889 TTCTTCTTCT
1 TTCTTCTTCT
325899 TGTTCGTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCTTCTCC
Found at i:327546 original size:28 final size:28
Alignment explanation
Indices: 327463--327536 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 28
327453 TTTTTTTAAT
327463 AATG-TAGGTACCTATTTTGATCAAAAA
1 AATGTTAGGTACCTATTTTGATCAAAAA
327490 ATATGTTAGGTACCTATTTTGATCAAAAA
1 A-ATGTTAGGTACCTATTTTGATCAAAAA
327519 AATGTTAGGTACCTATTT
1 AATGTTAGGTACCTATTT
327537 AAACCAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 1 0.02
28 20 0.44
29 24 0.53
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (28 bp):
AATGTTAGGTACCTATTTTGATCAAAAA
Found at i:327546 original size:29 final size:29
Alignment explanation
Indices: 327463--327536 Score: 125
Period size: 28 Copynumber: 2.6 Consensus size: 29
327453 TTTTTTTAAT
327463 AATG-TAGGTACCTATTTTGATCAAAAAA
1 AATGTTAGGTACCTATTTTGATCAAAAAA
*
327491 TATGTTAGGTACCTATTTTGATC-AAAAA
1 AATGTTAGGTACCTATTTTGATCAAAAAA
327519 AATGTTAGGTACCTATTT
1 AATGTTAGGTACCTATTT
327537 AAACCAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 25 0.58
29 18 0.42
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (29 bp):
AATGTTAGGTACCTATTTTGATCAAAAAA
Found at i:327991 original size:9 final size:9
Alignment explanation
Indices: 327979--328030 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
327969 TAATATTTTG
327979 TATTTAATT
1 TATTTAATT
*
327988 TATTTAA-G
1 TATTTAATT
327996 TATTTAATT
1 TATTTAATT
328005 TATTTAA--
1 TATTTAATT
* *
328012 TATTTTACT
1 TATTTAATT
328021 TATTTAATT
1 TATTTAATT
328030 T
1 T
328031 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:328000 original size:17 final size:17
Alignment explanation
Indices: 327978--328027 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
327968 TTAATATTTT
327978 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
327995 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
328012 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
328028 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:328023 original size:16 final size:16
Alignment explanation
Indices: 327987--328032 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
327977 TGTATTTAAT
* *
327987 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
328004 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
328020 TTATTTAAT-TTTT
1 TTATTTAATATTTT
328033 TTGCAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:329486 original size:65 final size:63
Alignment explanation
Indices: 329279--329488 Score: 194
Period size: 65 Copynumber: 3.3 Consensus size: 63
329269 TGCACTAAGA
* * * * *
329279 GTGCATCGATGCATTAAGTGCATTCAATGTTTCA-AAATAGCTAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCT-CAGTGCATCGATGCATGGTTG
* * *
329343 GTTCATCGATGCATCAAATGTATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
329408 -
63 G
* * **
329408 GTGTATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
329471 TG
62 TG
*
329473 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
329489 CTCTGAAAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 45 0.38
65 62 0.52
66 6 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:329949 original size:2 final size:2
Alignment explanation
Indices: 329942--329992 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
329932 AATTGATTAA
329942 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
329984 AT AT AT AT A
1 AT AT AT AT A
329993 GCTTAAGCTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:337697 original size:64 final size:64
Alignment explanation
Indices: 337609--337818 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 64
337599 TGCACTAAGA
* * *
337609 GTGCATCGATGCATTAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGATG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGATG
* ** *
337673 GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGG-A
337737 T-
63 TG
* * * ** *
337738 GTGCATCGATGGATGAAATGTATTCGATGTTT-AATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGGA-
337801 TG
63 TG
* *
337803 ATGCATCGGTGCATCA
1 GTGCATCGATGCATCA
337819 CTCTGAAAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 48 0.41
65 61 0.52
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGATG
Found at i:339507 original size:44 final size:47
Alignment explanation
Indices: 339455--339572 Score: 136
Period size: 47 Copynumber: 2.6 Consensus size: 47
339445 GTCGCTATAC
* *
339455 AAGGCGCGGTACCTGCATCGCGCCT-TATATAATT-AT-A-TAAAGGT
1 AAGGCGCGGCACCTGCACCGCG-CTATATATAATTCATAATTAAAGGT
* * *
339499 ATGGCGCGGCCCCTGCCCCGCGCTATATATAATTCATAATTAAAGGT
1 AAGGCGCGGCACCTGCACCGCGCTATATATAATTCATAATTAAAGGT
* *
339546 AAGGCGCGGCCCCTGCCCCGCGCTATA
1 AAGGCGCGGCACCTGCACCGCGCTATA
339573 CCAACGTGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
43 2 0.03
44 26 0.41
45 2 0.03
46 1 0.02
47 33 0.52
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (47 bp):
AAGGCGCGGCACCTGCACCGCGCTATATATAATTCATAATTAAAGGT
Found at i:339558 original size:47 final size:44
Alignment explanation
Indices: 339480--339572 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 44
339470 CATCGCGCCT
*
339480 TATATAATTATATAAAGGTATGGCGCGGCCCCTGCCCCGCGCTA
1 TATATAATTATATAAAGGTAAGGCGCGGCCCCTGCCCCGCGCTA
339524 TATATAATTCATAATTAAAGGTAAGGCGCGGCCCCTGCCCCGCGCTA
1 TATATAATT-AT-A-TAAAGGTAAGGCGCGGCCCCTGCCCCGCGCTA
339571 TA
1 TA
339573 CCAACGTGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 9 0.20
45 2 0.04
46 1 0.02
47 33 0.73
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (44 bp):
TATATAATTATATAAAGGTAAGGCGCGGCCCCTGCCCCGCGCTA
Found at i:340176 original size:18 final size:17
Alignment explanation
Indices: 340149--340183 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
340139 AAAAAAATGC
340149 TTGCCCACTACCACCGA
1 TTGCCCACTACCACCGA
340166 TTGCTCCACTACCACCGA
1 TTGC-CCACTACCACCGA
340184 ATTCCAGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.23, C:0.46, G:0.11, T:0.20
Consensus pattern (17 bp):
TTGCCCACTACCACCGA
Found at i:344752 original size:10 final size:10
Alignment explanation
Indices: 344731--344762 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
344721 TAAGACAAAG
344731 AAAATAAGAAA
1 AAAATAA-AAA
344742 AAAATAAAAA
1 AAAATAAAAA
344752 AAAATAAAAA
1 AAAATAAAAA
344762 A
1 A
344763 TAAAAAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:346837 original size:43 final size:43
Alignment explanation
Indices: 346776--347031 Score: 426
Period size: 43 Copynumber: 6.0 Consensus size: 43
346766 ATAAGAAACT
346776 AAGCTTGAGGGACCAACGTGATATGTTA-GGGTTCCTTGATGAG
1 AAGCTTGAGGGACCAACGTGATATG-TAGGGGTTCCTTGATGAG
*
346819 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCTTTGATGAG
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAG
346862 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAG
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAG
* *
346905 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATAAT
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAG
* *
346948 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCTTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAG
* *
346991 AA-CTAGAGGGACCAACGTGATATTTAGGGGTTCCTTGATGA
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGA
347032 CAACTAAGAA
Statistics
Matches: 202, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
42 38 0.19
43 164 0.81
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (43 bp):
AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAG
Found at i:347114 original size:42 final size:41
Alignment explanation
Indices: 347068--347181 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 41
347058 AAGGGTTTCT
347068 TGATGAGTAAGTCCTTCGGGCCATC-AGTAAGTCTTTCGAGCA
1 TGATGA-TAAGTCCTTCGGGCCATCTA-TAAGTCTTTCGAGCA
* * * * *
347110 TGATGCTTAAATCCTTCGGGTCATCTATAAGTTTTTCGAGTA
1 TGATG-ATAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
* * *
347152 AGATGATAAGACCTTCGGGCCATCCATAAG
1 TGATGATAAGTCCTTCGGGCCATCTATAAG
347182 ACCTTTGGGC
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
41 20 0.34
42 38 0.64
43 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
TGATGATAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
Found at i:347813 original size:20 final size:19
Alignment explanation
Indices: 347750--347814 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
347740 TTAATGGAGA
347750 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* *
347769 CATCCGATAAATGGAGAAGAA--
1 -GTTC-AT-AAT-GAGAAGAACT
347790 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
347810 GTTCA
1 GTTCA
347815 ACCTTGGTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
17 8 0.23
18 3 0.09
19 2 0.06
20 9 0.26
21 2 0.06
22 3 0.09
23 8 0.23
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:348582 original size:11 final size:11
Alignment explanation
Indices: 348566--348599 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
348556 AACATTTTTG
348566 AAGAAAAAAAC
1 AAGAAAAAAAC
348577 AAGAAAAAAAC
1 AAGAAAAAAAC
*
348588 AAGTAAAAAAC
1 AAGAAAAAAAC
348599 A
1 A
348600 GTGTAAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.79, C:0.09, G:0.09, T:0.03
Consensus pattern (11 bp):
AAGAAAAAAAC
Found at i:361803 original size:22 final size:21
Alignment explanation
Indices: 361758--361803 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
361748 TAGAAATTTG
* *
361758 TCCCGAAGACCACGTAGAATT
1 TCCCGAAGACCACATAGAAAT
*
361779 TCCCGAATGACCACATATAAAT
1 TCCCGAA-GACCACATAGAAAT
361801 TCC
1 TCC
361804 TTAAGAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (21 bp):
TCCCGAAGACCACATAGAAAT
Found at i:362029 original size:31 final size:30
Alignment explanation
Indices: 361980--362045 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
361970 ATTTATATCG
*
361980 CATAGACATATCATTTCCATACCTTTACCA
1 CATAAACATATCATTTCCATACCTTTACCA
* * *
362010 CATAAACATTTCATTTTCCATACTTTTATCA
1 CATAAACATATCA-TTTCCATACCTTTACCA
362041 CATAA
1 CATAA
362046 TTCATATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.38
Consensus pattern (30 bp):
CATAAACATATCATTTCCATACCTTTACCA
Found at i:362469 original size:21 final size:21
Alignment explanation
Indices: 362445--362487 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
362435 TCACATTCGT
* *
362445 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
362466 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
362487 T
1 T
362488 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:369024 original size:31 final size:30
Alignment explanation
Indices: 368962--369040 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
368952 TTACAATTCA
* *
368962 CATA-ATTATATCGCATAGACATATCATTTC
1 CATACATT-TATCACATAAACATATCATTTC
*
368992 CATACATTTATCACATAAACATTTCATTTTC
1 CATACATTTATCACATAAACATATCA-TTTC
*
369023 CATACCTTTATCACATAA
1 CATACATTTATCACATAA
369041 TTCATATAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 19 0.44
31 24 0.56
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
CATACATTTATCACATAAACATATCATTTC
Found at i:369475 original size:21 final size:21
Alignment explanation
Indices: 369451--369493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
369441 TCACATTCGT
*
369451 TTGAGGGGGTATCGATTCCCC
1 TTGAGGGGGTACCGATTCCCC
**
369472 TTGATTGGGTACCGATTCCCC
1 TTGAGGGGGTACCGATTCCCC
369493 T
1 T
369494 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAGGGGGTACCGATTCCCC
Found at i:370574 original size:27 final size:28
Alignment explanation
Indices: 370544--370601 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
370534 CTATCAACTT
*
370544 TATTTACTTTTAGATGATTAAAATAAA-
1 TATTTACTTTTAGATAATTAAAATAAAC
*
370571 TA-TTATTTTTAGATAATTAAAATAAAC
1 TATTTACTTTTAGATAATTAAAATAAAC
370598 TATT
1 TATT
370602 AAATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 22 0.81
27 4 0.15
28 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (28 bp):
TATTTACTTTTAGATAATTAAAATAAAC
Found at i:370581 original size:26 final size:27
Alignment explanation
Indices: 370551--370602 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
370541 CTTTATTTAC
*
370551 TTTTAGATGATTAAAATAAA-TATTAT
1 TTTTAGATAATTAAAATAAACTATTAT
370577 TTTTAGATAATTAAAATAAACTATTA
1 TTTTAGATAATTAAAATAAACTATTA
370603 AATAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (27 bp):
TTTTAGATAATTAAAATAAACTATTAT
Found at i:371018 original size:46 final size:46
Alignment explanation
Indices: 370967--371108 Score: 141
Period size: 46 Copynumber: 3.1 Consensus size: 46
370957 ACTATTAAAT
370967 AATAAATTATATTTTTAAGGATGTTATTATTAAGTTGTTAAAATAA
1 AATAAATTATATTTTTAAGGATGTTATTATTAAGTTGTTAAAATAA
* * * * ** *
371013 AATAAATTATTATTTATTTTTA-GATAATTA-AAATAAACTATT-AAAT--
1 AATAAATTA-TA--T-TTTTAAGGAT-GTTATTATTAAGTTGTTAAAATAA
371059 AATAAATTATATTTTTAAGGATGTTATTATTAAGTTGTTAAAATAA
1 AATAAATTATATTTTTAAGGATGTTATTATTAAGTTGTTAAAATAA
371105 AATA
1 AATA
371109 TAAATACATA
Statistics
Matches: 72, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
42 8 0.11
43 11 0.15
44 4 0.06
45 2 0.03
46 22 0.31
47 2 0.03
48 4 0.06
49 11 0.15
50 8 0.11
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (46 bp):
AATAAATTATATTTTTAAGGATGTTATTATTAAGTTGTTAAAATAA
Found at i:372779 original size:33 final size:34
Alignment explanation
Indices: 372702--372779 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 34
372692 TATGTTAAAA
* *
372702 ATAAATTTATAAAATATTAAAAATATATAAATATT
1 ATAAATTTA-AAAATATAAAAAAAATATAAATATT
* *
372737 TTTAA-TTAAAAATATAAAAAAAAT-TAAA-ATAT
1 ATAAATTTAAAAATATAAAAAAAATATAAATAT-T
372769 ATAAATTTAAA
1 ATAAATTTAAA
372780 GATAATGAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
31 2 0.06
32 8 0.23
33 19 0.54
34 3 0.09
35 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (34 bp):
ATAAATTTAAAAATATAAAAAAAATATAAATATT
Found at i:373222 original size:19 final size:19
Alignment explanation
Indices: 373200--373236 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
373190 ATAGTTTATT
373200 TATTTTAACTTAAAATATA
1 TATTTTAACTTAAAATATA
**
373219 TATTTTATGTTAAAATAT
1 TATTTTAACTTAAAATAT
373237 TTGAAGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TATTTTAACTTAAAATATA
Found at i:374362 original size:8 final size:8
Alignment explanation
Indices: 374351--374377 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
374341 ATAATATTAT
374351 TTTTAAAA
1 TTTTAAAA
374359 TTTTAAAA
1 TTTTAAAA
374367 TTTTAAAA
1 TTTTAAAA
374375 TTT
1 TTT
374378 AGCAACACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Found at i:375547 original size:6 final size:6
Alignment explanation
Indices: 375506--375639 Score: 67
Period size: 6 Copynumber: 24.3 Consensus size: 6
375496 TCAGGTCGGG
* * * * *
375506 TATATA TATATT TAAAT- TAAATA TATAAA TAT-TA TATATA TAT-TT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
375551 TA-ATT TAAAT- TAAATA TATAAA TAT-TA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
375596 TAT-TA -ATTTA AAT-TA AATTTA T-TA-A TAT-TA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
375638 TA
1 TA
375640 ATAATTATTT
Statistics
Matches: 105, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.04
5 40 0.38
6 61 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:375601 original size:38 final size:38
Alignment explanation
Indices: 375506--375640 Score: 146
Period size: 38 Copynumber: 3.4 Consensus size: 38
375496 TCAGGTCGGG
*
375506 TATATATATATTTAAATTAAATATATAAATATTATATA
1 TATATATATATATAAATTAAATATATAAATATTATATA
* *
375544 TATAT-TTTAATTTAAATTAAATATATAAATATTATATA
1 TATATATAT-ATATAAATTAAATATATAAATATTATATA
* * *
375582 TATATATATATATATATTAATTTAAATTAAATTTATTAATATTA
1 TATATATATATATAAATTAA-ATATA-TAAA--TATT-ATA-TA
375626 TATATATATATATAA
1 TATATATATATATAA
375641 TAATTATTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
37 2 0.02
38 48 0.59
39 5 0.06
40 4 0.05
42 4 0.05
43 3 0.04
44 16 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
TATATATATATATAAATTAAATATATAAATATTATATA
Found at i:375604 original size:48 final size:48
Alignment explanation
Indices: 375523--375646 Score: 184
Period size: 48 Copynumber: 2.7 Consensus size: 48
375513 ATATTTAAAT
* *
375523 TAAATA-TATAAATAT-TATATATATATTTTAATTTAAATTAAATATA
1 TAAATATTATATATATATATATATATATATTAATTTAAATTAAATATA
*
375569 TAAATATTATATATATATATATATATATATTAATTTAAATTAAATTTA
1 TAAATATTATATATATATATATATATATATTAATTTAAATTAAATATA
*
375617 TTAATATTATATATATATATATA-ATA-ATTA
1 TAAATATTATATATATATATATATATATATTA
375647 TTTTTAATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
46 10 0.14
47 11 0.15
48 51 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (48 bp):
TAAATATTATATATATATATATATATATATTAATTTAAATTAAATATA
Found at i:375782 original size:36 final size:36
Alignment explanation
Indices: 375704--375786 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
375694 GATTATCAAA
***
375704 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTC
1 CCCGTCCCCGTCCCCGTTTAACATAAACAAATTTTC
* *
375740 CCCGTCCTCGTCCCCGTTTAGCATAAA-AAATTTTC
1 CCCGTCCCCGTCCCCGTTTAACATAAACAAATTTTC
*
375775 CTTCGTCCCCGT
1 C-CCGTCCCCGT
375787 TTAATTCGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 6 0.15
36 33 0.85
ACGTcount: A:0.17, C:0.39, G:0.13, T:0.31
Consensus pattern (36 bp):
CCCGTCCCCGTCCCCGTTTAACATAAACAAATTTTC
Found at i:382894 original size:50 final size:51
Alignment explanation
Indices: 382802--382907 Score: 198
Period size: 50 Copynumber: 2.1 Consensus size: 51
382792 TTTGTTTTAT
382802 TCTA-AATTGGCACTTTTAGTACATAGAGATAATACCATTCTAGTCGTACG
1 TCTATAATTGGCACTTTTAGTACATAGAGATAATACCATTCTAGTCGTACG
382852 TCTATAATTGGCACTTTTAGTACA-AGAGATAATACCATTCTAGTCGTACG
1 TCTATAATTGGCACTTTTAGTACATAGAGATAATACCATTCTAGTCGTACG
382902 TCTATA
1 TCTATA
382908 TTTATGATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 36 0.65
51 19 0.35
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (51 bp):
TCTATAATTGGCACTTTTAGTACATAGAGATAATACCATTCTAGTCGTACG
Found at i:384519 original size:2 final size:2
Alignment explanation
Indices: 384512--384547 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
384502 TCCATCGTTC
384512 CT CT CT 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
384548 GCTTTCTCGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:385959 original size:15 final size:14
Alignment explanation
Indices: 385939--385979 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
385929 TAGTTATTAC
*
385939 TTTTAAAAAAATAA
1 TTTTTAAAAAATAA
385953 TTTTTAAAAAATAA
1 TTTTTAAAAAATAA
* *
385967 TTTGTAATAAATA
1 TTTTTAAAAAATA
385980 TAAGATAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
TTTTTAAAAAATAA
Found at i:393783 original size:12 final size:12
Alignment explanation
Indices: 393768--393793 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
393758 CCAGGCAAGT
393768 GCAGCGGCACCA
1 GCAGCGGCACCA
393780 GCAGCGGCACCA
1 GCAGCGGCACCA
393792 GC
1 GC
393794 TCCGGCTCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.35, T:0.00
Consensus pattern (12 bp):
GCAGCGGCACCA
Found at i:396786 original size:2 final size:2
Alignment explanation
Indices: 396773--396807 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
396763 ATTAATGTGT
*
396773 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
396808 TACATGTGGG
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:397054 original size:8 final size:9
Alignment explanation
Indices: 397041--397096 Score: 51
Period size: 9 Copynumber: 5.7 Consensus size: 9
397031 TGACTGTCGA
397041 TTTTTTTCT
1 TTTTTTTCT
397050 TTTTTTTCT
1 TTTTTTTCT
397059 TTTTTATATCAT
1 TTTTT-T-TC-T
397071 ATATTTTTT-T
1 -T-TTTTTTCT
397081 TCTTTTTTCT
1 T-TTTTTTCT
397091 TTTTTT
1 TTTTTT
397097 AATAAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 26 0.65
10 4 0.10
11 2 0.05
12 2 0.05
13 2 0.05
14 4 0.10
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:400166 original size:16 final size:14
Alignment explanation
Indices: 400131--400165 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
400121 ATATATATTT
*
400131 TATTTTATTATATA
1 TATTTTATTAAATA
400145 TATTTTATTAAATA
1 TATTTTATTAAATA
400159 TGATTTT
1 T-ATTTT
400166 TTTCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TATTTTATTAAATA
Found at i:405024 original size:15 final size:15
Alignment explanation
Indices: 404997--405032 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
404987 TGCAGGGAGA
404997 TTTCTGCTTTATTTG
1 TTTCTGCTTTATTTG
405012 TATTCTG-TTTATTTG
1 T-TTCTGCTTTATTTG
405027 TTTCTG
1 TTTCTG
405033 GTAATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 5 0.25
ACGTcount: A:0.08, C:0.11, G:0.14, T:0.67
Consensus pattern (15 bp):
TTTCTGCTTTATTTG
Found at i:408008 original size:6 final size:6
Alignment explanation
Indices: 407999--408028 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
407989 TAAGGTTTAT
407999 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA
1 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA
408029 AACTTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
GTTTGA
Found at i:417181 original size:42 final size:43
Alignment explanation
Indices: 417067--417291 Score: 285
Period size: 43 Copynumber: 5.3 Consensus size: 43
417057 TAACGATATA
* * * * ** *
417067 TAGCGGCGTTT-TTTCAACAACCGCCGCAAAAGGTGCTGATATT
1 TAGCGGCGTTTGTTT-TACAAACGCAGCAATAGGTTTTGACATT
*** *
417110 TAGCGGCGTTTGTAAGACAAACGCTGCAATAGGTTTTGACATT
1 TAGCGGCGTTTGTTTTACAAACGCAGCAATAGGTTTTGACATT
*
417153 TCGCGGCGTTT-TTTTACAAACGCAGCAATAGGTTTTGACATT
1 TAGCGGCGTTTGTTTTACAAACGCAGCAATAGGTTTTGACATT
417195 TAGCGGCGTTTGTTTTACAAACGCAGCAATAGGTTTTGACATT
1 TAGCGGCGTTTGTTTTACAAACGCAGCAATAGGTTTTGACATT
* *
417238 TAGCGGCGTTTGTTTTATAACCGTC-GCAATAGGTTTTGACATT
1 TAGCGGCGTTTGTTTTACAAACG-CAGCAATAGGTTTTGACATT
417281 TAGCGGCGTTT
1 TAGCGGCGTTT
417292 TTAGGATAAA
Statistics
Matches: 162, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 37 0.23
43 123 0.76
44 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (43 bp):
TAGCGGCGTTTGTTTTACAAACGCAGCAATAGGTTTTGACATT
Found at i:417204 original size:85 final size:84
Alignment explanation
Indices: 417067--417291 Score: 297
Period size: 85 Copynumber: 2.6 Consensus size: 84
417057 TAACGATATA
* * ** *
417067 TAGCGGCGTTTTTTCAACAACCGCCGCAAAAGGTGCTGATATTTAGCGGCGTTTGTAAGACAAAC
1 TAGCGGCGTTTTTT-TACAACCG-CGCAATAGGTTTTGACATTTAGCGGCGTTTGTAAGACAAAC
*
417132 GCTGCAATAGGTTTTGACATT
64 GCAGCAATAGGTTTTGACATT
* * ***
417153 TCGCGGCGTTTTTTTACAAACGCAGCAATAGGTTTTGACATTTAGCGGCGTTTGTTTTACAAACG
1 TAGCGGCGTTTTTTTACAACCGC-GCAATAGGTTTTGACATTTAGCGGCGTTTGTAAGACAAACG
417218 CAGCAATAGGTTTTGACATT
65 CAGCAATAGGTTTTGACATT
*
417238 TAGCGGCGTTTGTTTTATAACCGTCGCAATAGGTTTTGACATTTAGCGGCGTTT
1 TAGCGGCGTTT-TTTTACAACCG-CGCAATAGGTTTTGACATTTAGCGGCGTTT
417292 TTAGGATAAA
Statistics
Matches: 122, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.01
85 69 0.57
86 51 0.42
87 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (84 bp):
TAGCGGCGTTTTTTTACAACCGCGCAATAGGTTTTGACATTTAGCGGCGTTTGTAAGACAAACGC
AGCAATAGGTTTTGACATT
Found at i:417209 original size:22 final size:22
Alignment explanation
Indices: 417184--417253 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
417174 GCAGCAATAG
417184 GTTTTGACATTTAGCGGCGTTT
1 GTTTTGACATTTAGCGGCGTTT
* * * **
417206 GTTTT-ACA--AACGCAGCAATAG
1 GTTTTGACATTTA-GCGGC-GTTT
417227 GTTTTGACATTTAGCGGCGTTT
1 GTTTTGACATTTAGCGGCGTTT
417249 GTTTT
1 GTTTT
417254 ATAACCGTCG
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 9 0.27
22 14 0.42
23 4 0.12
24 1 0.03
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.41
Consensus pattern (22 bp):
GTTTTGACATTTAGCGGCGTTT
Found at i:422348 original size:44 final size:42
Alignment explanation
Indices: 422275--422360 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 42
422265 AAATGTATGG
*
422275 TTAAACCTATTGCGGCGTTTGTTGAAAAAAAATGCCACTATAGA
1 TTAAACCTATTGCGGCGTTTGTTG--AAAAAACGCCACTATAGA
* * *
422319 TTAACCCTTTTGCGGCGTTTGTTGTAAAAACGCCACTATAGA
1 TTAAACCTATTGCGGCGTTTGTTGAAAAAACGCCACTATAGA
422361 CGAACCTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 16 0.42
44 22 0.58
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (42 bp):
TTAAACCTATTGCGGCGTTTGTTGAAAAAACGCCACTATAGA
Found at i:423918 original size:40 final size:41
Alignment explanation
Indices: 423832--423923 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 41
423822 GTTTTTTGTT
* * * *
423832 AAAACGCCACTATATGTCCAATATATTGCAGCGTTTGTACAT
1 AAAACGCCACTAGA-GTACAATATATTGCAGCGTTTATACAA
*
423874 AAAACGCCACTAGA-TACAATAATATTGCGGCGTTTAT-CAA
1 AAAACGCCACTAGAGTACAAT-ATATTGCAGCGTTTATACAA
423914 AAAACGCCAC
1 AAAACGCCAC
423924 ACCATTAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
40 17 0.39
41 14 0.32
42 13 0.30
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (41 bp):
AAAACGCCACTAGAGTACAATATATTGCAGCGTTTATACAA
Found at i:427591 original size:24 final size:23
Alignment explanation
Indices: 427560--427608 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
427550 TTTTTATATA
*
427560 TATTATAATATTACATATTTAAT
1 TATTATAATATTACATATTAAAT
* *
427583 TATTAATAATTTTATATATTAAAT
1 TATT-ATAATATTACATATTAAAT
427607 TA
1 TA
427609 AACTAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTATAATATTACATATTAAAT
Found at i:427734 original size:18 final size:18
Alignment explanation
Indices: 427698--427734 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
427688 AAGTTTTATA
* *
427698 TTTAAAAAAATTAATAAT
1 TTTAAAAAAAATAAAAAT
427716 TTTAAAAAAAATAAAAAT
1 TTTAAAAAAAATAAAAAT
427734 T
1 T
427735 AGATACCCGA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAAAAATAAAAAT
Found at i:428234 original size:15 final size:15
Alignment explanation
Indices: 428208--428279 Score: 126
Period size: 15 Copynumber: 4.7 Consensus size: 15
428198 AAAAAACCCG
428208 ACCCGATCGGGTCGGA
1 ACCCG-TCGGGTCGGA
428224 ACCCGTCGGGTCGGA
1 ACCCGTCGGGTCGGA
*
428239 ACCCGTTGGGTCGGA
1 ACCCGTCGGGTCGGA
428254 ACCCGTCGGGTCGGA
1 ACCCGTCGGGTCGGA
428269 ACCCGTCGGGT
1 ACCCGTCGGGT
428280 TCGAGTTAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
15 49 0.91
16 5 0.09
ACGTcount: A:0.14, C:0.32, G:0.39, T:0.15
Consensus pattern (15 bp):
ACCCGTCGGGTCGGA
Found at i:431709 original size:9 final size:9
Alignment explanation
Indices: 431695--431728 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
431685 TGGTTCGTGC
431695 TATTGTTAT
1 TATTGTTAT
431704 TATTGTTAT
1 TATTGTTAT
* *
431713 TGTTATTAT
1 TATTGTTAT
431722 TATTGTT
1 TATTGTT
431729 GTTGTTGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (9 bp):
TATTGTTAT
Found at i:431712 original size:6 final size:6
Alignment explanation
Indices: 431703--431746 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
431693 GCTATTGTTA
* * * *
431703 TTATTG TTATTG TTATTA TTATTG TTGTTG TTGTTG TTGTTG TT
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TT
431747 TGATAGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.11, C:0.00, G:0.20, T:0.68
Consensus pattern (6 bp):
TTATTG
Found at i:431723 original size:18 final size:18
Alignment explanation
Indices: 431700--431734 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
431690 CGTGCTATTG
431700 TTATTATTGTTATTGTTA
1 TTATTATTGTTATTGTTA
*
431718 TTATTATTGTTGTTGTT
1 TTATTATTGTTATTGTT
431735 GTTGTTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (18 bp):
TTATTATTGTTATTGTTA
Found at i:440753 original size:3 final size:3
Alignment explanation
Indices: 440745--440785 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
440735 TCAGTTCATT
*
440745 TTA TTA TTA TTAA TTA TTA AT- TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
440786 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:441853 original size:2 final size:2
Alignment explanation
Indices: 441846--441871 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
441836 CCTTATCAGA
441846 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
441872 TTAGGTAAAT
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:452162 original size:54 final size:54
Alignment explanation
Indices: 452080--452249 Score: 277
Period size: 54 Copynumber: 3.1 Consensus size: 54
452070 ACTTCAATAA
*
452080 TTACGAACATCTGAATAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTT
1 TTACGAACATCTGAACAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTT
*
452134 TTACGAACATCTAAACAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTT
1 TTACGAACATCTGAACAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTT
* *** *
452188 TTACGAACATCTGAACAGAAGCCACAGGAAAGGATGAATGCACTATCAAATGTT
1 TTACGAACATCTGAACAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTT
452242 TTACGAAC
1 TTACGAAC
452250 CTGCTATTCT
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 108 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (54 bp):
TTACGAACATCTGAACAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTT
Found at i:452642 original size:22 final size:22
Alignment explanation
Indices: 452613--452667 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
452603 ATCTACACTC
*
452613 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
452635 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
452657 TTCAAAGATGA
1 TTCAAAGATGA
452668 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:453386 original size:113 final size:113
Alignment explanation
Indices: 453070--453738 Score: 940
Period size: 113 Copynumber: 6.0 Consensus size: 113
453060 GCAAAGTTCA
** * **
453070 AATCCATCATTCAATGGATCAACA-TTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
453133 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* * * * *
453182 AATCCATCATTCGATGGATTGA-CATTTCTATAG-AAGTTCATAATGAGAAGAACTCATATGAAG
1 AATCCATCATTTGATGGA-TCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
453245 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
*
453294 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
453359 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* *
453407 AATCTATTATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
453472 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACT-TG
* * * * *
453520 AATTCATCACTTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
453584 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
* * * * *
453633 AATCCATCACTTGATGGAACAGCTTTTCTAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
453697 AGGAAGAAGAAGTTCATAATAAGAAGAA-TTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
453739 GCATAATTCT
Statistics
Matches: 510, Mismatches: 38, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
111 15 0.03
112 180 0.35
113 309 0.61
114 6 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
Found at i:454244 original size:76 final size:76
Alignment explanation
Indices: 454144--454858 Score: 1297
Period size: 76 Copynumber: 9.4 Consensus size: 76
454134 ACTATTTCCC
* *
454144 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTT-
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT-TTC
*
454208 AAAGCCTTCAGG
65 AAAGCCTTCGGG
*
454220 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
454285 AAGCCTTCGGG
66 AAGCCTTCGGG
*
454296 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
454361 AAGCCTTAGGG
66 AAGCCTTCGGG
*
454372 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
454437 AAGCCTTCGGG
66 AAGCCTTCGGG
454448 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
454513 AAGCCTTAGGG
66 AAGCCTTCGGG
454524 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
454589 AAGCCTTCGGG
66 AAGCCTTCGGG
454600 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
454665 AAGCCTTCGGG
66 AAGCCTTCGGG
*
454676 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
454741 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
454752 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
454817 AAGCCTTAGGG
66 AAGCCTTCGGG
*
454828 TCATCTGTAAGCCCTTCAGTGCATGATGTTT
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTT
454859 TCAACATTTC
Statistics
Matches: 621, Mismatches: 17, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 2 0.00
76 619 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGG
Found at i:454996 original size:3 final size:3
Alignment explanation
Indices: 454988--455028 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
454978 TCAGTTCATT
*
454988 TTA TTA TTA TTAA TTA TTA AT- TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
455029 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:456475 original size:23 final size:24
Alignment explanation
Indices: 456440--456485 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
456430 ATATATATGA
456440 TAAATAATAA-TTT-ATATTTTTT
1 TAAATAATAATTTTAATATTTTTT
*
456462 TAAATAAATTATTTTAATATTTTT
1 TAAAT-AATAATTTTAATATTTTT
456486 CAATATCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 4 0.20
24 3 0.15
25 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TAAATAATAATTTTAATATTTTTT
Found at i:466007 original size:15 final size:15
Alignment explanation
Indices: 465989--466018 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
465979 TGTAAAAAGT
465989 AATACAATAAAATAA
1 AATACAATAAAATAA
*
466004 AATATAATAAAATAA
1 AATACAATAAAATAA
466019 TATAAACTAT
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:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AATACAATAAAATAA
Found at i:466959 original size:31 final size:30
Alignment explanation
Indices: 466902--466964 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
466892 ATTTTTTTAA
466902 TTATTATATGTTATTATCATTAAATTAATG
1 TTATTATATGTTATTATCATTAAATTAATG
*
466932 TTATTATATGTATTTTTATC-TTAAATTAATG
1 TTATTATATG--TTATTATCATTAAATTAATG
466963 TT
1 TT
466965 TGTTTATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 10 0.33
31 13 0.43
32 7 0.23
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.57
Consensus pattern (30 bp):
TTATTATATGTTATTATCATTAAATTAATG
Found at i:468860 original size:146 final size:149
Alignment explanation
Indices: 468680--469062 Score: 424
Period size: 146 Copynumber: 2.5 Consensus size: 149
468670 TTGTAAAGAC
* *
468680 ATTTATTTATTTAAAAATATCTGAA-AAGTACATCTAGTTGCTTTAAGACTGTATTTTCTTTAAT
1 ATTTATTTATTTTAAAATATCAGAATAAG-ACATCTAGTTGCTTTAAGACTGTATTTTCTTTAAT
* *
468744 TTTAATAAATAAATATTAATAAGAATATAATAATTTTCCTAA-AAAATAA-TGAAGT-A-AATA-
65 TTTAA-AAATAAATAATAATAA-AA-ATAATAATTTTCCTAATAAAATAATTGAAATAACAATAG
*
468804 TA-TAT-ATTTTATAAGCATGAT
127 TATTATGATTTTATAAGCAGGAT
468825 ATTTATTTATTTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGACTGTATTTTCTTTATA
1 ATTTATTTA-TTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGACTGTATTTTCTTTA-A
* * *
468890 TTTGAAAAATAAATAAATATTAAAAATAATAATTTTCCTAATAAAATAATTTAAATAAAACAATA
64 TTTTAAAAATAAAT-AATAATAAAAATAATAATTTTCCTAATAAAATAATTGAAAT--AACAATA
* * *
468955 TGTATTTTTTGGTTTTTATAAGTAGGAT
126 -GTA--TTAT-GATTTTATAAGCAGGAT
* * **
468983 ATTTATTTAATTTTAAAATACCAGAATATGACATCTAGTTGCTTTAAGACTGCCCTTTTC-TTAA
1 ATTTATTT-ATTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGACTG-TATTTTCTTTAA
*
469047 TATTAAAAATAAATAA
64 TTTTAAAAATAAATAA
469063 ATATTATTAT
Statistics
Matches: 202, Mismatches: 17, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
145 25 0.12
146 64 0.32
147 19 0.09
150 1 0.00
151 4 0.02
153 2 0.01
156 4 0.02
157 13 0.06
158 64 0.32
159 6 0.03
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (149 bp):
ATTTATTTATTTTAAAATATCAGAATAAGACATCTAGTTGCTTTAAGACTGTATTTTCTTTAATT
TTAAAAATAAATAATAATAAAAATAATAATTTTCCTAATAAAATAATTGAAATAACAATAGTATT
ATGATTTTATAAGCAGGAT
Found at i:470479 original size:3 final size:3
Alignment explanation
Indices: 470471--470502 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
470461 CTTTTTTATT
*
470471 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
470503 TGATGATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:480706 original size:22 final size:23
Alignment explanation
Indices: 480678--480721 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
480668 AGTTTTATTA
480678 AAGTTTTCT-CTTTTTACTTTTC
1 AAGTTTTCTCCTTTTTACTTTTC
* *
480700 AAGTTTTTTCCTTTTTCCTTTT
1 AAGTTTTCTCCTTTTTACTTTT
480722 ATTTTCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.11, C:0.18, G:0.05, T:0.66
Consensus pattern (23 bp):
AAGTTTTCTCCTTTTTACTTTTC
Done.