Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold445
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: 297477
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 2 of 2
Found at i:210678 original size:32 final size:33
Alignment explanation
Indices: 210615--210682 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
210605 CGTTACAAGC
**
210615 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
210648 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
210680 CAA
1 CAA
210683 GTTTAACTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:210778 original size:20 final size:20
Alignment explanation
Indices: 210736--210785 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
210726 TCTTTTTCAA
*
210736 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
210756 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
210776 GTATCGATAC
1 GTATCGATAC
210786 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:211655 original size:2 final size:2
Alignment explanation
Indices: 211648--211690 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
211638 GAAGATTTTA
*
211648 AT AT AT AT AT AT AT AT AT AT AC 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
211690 A
1 A
211691 AAGAAAGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:212025 original size:17 final size:18
Alignment explanation
Indices: 211992--212025 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
211982 CCCAACAGTA
*
211992 AAAAGAAAACTCATACTG
1 AAAAGAAAACACATACTG
212010 AAAAGAAAA-ACATACT
1 AAAAGAAAACACATACT
212026 AGAGTTTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.15, G:0.09, T:0.15
Consensus pattern (18 bp):
AAAAGAAAACACATACTG
Found at i:212276 original size:23 final size:23
Alignment explanation
Indices: 212250--212301 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
212240 ATTTTGAACT
*
212250 AAAAAAAAATAAAGG-AGAAAGA
1 AAAAAAAAAGAAAGGAAGAAAGA
* * *
212272 GAAAATAAAGAATGGAAGAAAGA
1 AAAAAAAAAGAAAGGAAGAAAGA
212295 AAAAAAA
1 AAAAAAA
212302 GAAAGAAGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (23 bp):
AAAAAAAAAGAAAGGAAGAAAGA
Found at i:212312 original size:23 final size:22
Alignment explanation
Indices: 212251--212318 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
212241 TTTTGAACTA
*
212251 AAAAAAAATAAAG-G-AGAAAG
1 AAAAAAAAGAAAGAGAAGAAAG
*
212271 AGAAAATAAAGAATG-GAAGAAAG
1 A-AAAA-AAAGAAAGAGAAGAAAG
212294 AAAAAAAAGAAAGAAGAAG-AAG
1 AAAAAAAAGAAAG-AGAAGAAAG
212316 AAA
1 AAA
212319 TGAGAGGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.03
21 11 0.28
22 17 0.43
23 11 0.28
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (22 bp):
AAAAAAAAGAAAGAGAAGAAAG
Found at i:213798 original size:23 final size:24
Alignment explanation
Indices: 213756--213804 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
213746 TAACACTTTT
213756 ATTCATTTTTATTTTAAATTA-AAA
1 ATTCATTTTTA-TTTAAATTACAAA
213780 ATTCATGTTTTA-TTAAATTACAAA
1 ATTCAT-TTTTATTTAAATTACAAA
213804 A
1 A
213805 AAATAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.35
24 10 0.43
25 5 0.22
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTCATTTTTATTTAAATTACAAA
Found at i:216351 original size:24 final size:24
Alignment explanation
Indices: 216324--216375 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
216314 TGAAAAGATG
216324 AAAAAAA-AA-AACCTAAGAATAGAA
1 AAAAAAAGAATAACC-AA-AATAGAA
*
216348 AAAAAAAGAATTACCAAAATAGAA
1 AAAAAAAGAATAACCAAAATAGAA
216372 AAAA
1 AAAA
216376 TTAAGACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 18 0.72
25 4 0.16
26 3 0.12
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.10
Consensus pattern (24 bp):
AAAAAAAGAATAACCAAAATAGAA
Found at i:216581 original size:16 final size:16
Alignment explanation
Indices: 216544--216602 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
216534 TCATATATTA
* *
216544 ATTTTAATTTTTAATT
1 ATTTTAAGTTTAAATT
216560 -TTTTAAGTTTAAATT
1 ATTTTAAGTTTAAATT
* *
216575 ATTTTAAATTTATATT
1 ATTTTAAGTTTAAATT
*
216591 AATTTAAGTTTA
1 ATTTTAAGTTTA
216603 GATAGGTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
15 13 0.36
16 23 0.64
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTTAAGTTTAAATT
Found at i:216722 original size:15 final size:15
Alignment explanation
Indices: 216702--216734 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
216692 TATGTAATGA
216702 TAAAATTATT-AAAAT
1 TAAAATT-TTAAAAAT
216717 TAAAATTTTAAAAAT
1 TAAAATTTTAAAAAT
216732 TAA
1 TAA
216735 TAAGTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAATTTTAAAAAT
Found at i:216813 original size:23 final size:23
Alignment explanation
Indices: 216787--216836 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
216777 ATATATTGAA
*
216787 TATTAATATATTATA-TTTAATAT
1 TATTAATA-ATTATAGTATAATAT
* *
216810 TATTTATAATTTTAGTATAATAT
1 TATTAATAATTATAGTATAATAT
216833 TATT
1 TATT
216837 TAAATTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTAATAATTATAGTATAATAT
Found at i:217305 original size:19 final size:19
Alignment explanation
Indices: 217281--217317 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
217271 CTGCTTTGGA
*
217281 AATTTGTATTTCAAAAATG
1 AATTTGAATTTCAAAAATG
217300 AATTTGAATTTCAAAAAT
1 AATTTGAATTTCAAAAAT
217318 AATGTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
AATTTGAATTTCAAAAATG
Found at i:217830 original size:37 final size:37
Alignment explanation
Indices: 217789--217859 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
217779 AAGCGCCTGA
*
217789 TGTGCTTTAATGGTTTGGTCA-AGAAACGGCCGCCCAC
1 TGTGCTTCAATGGTTTGGT-ATAGAAACGGCCGCCCAC
*
217826 TGTGCTTCAATGGTTTGGTATAGAAATGGCCGCC
1 TGTGCTTCAATGGTTTGGTATAGAAACGGCCGCC
217860 TCCTGCTCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 1 0.03
37 30 0.97
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (37 bp):
TGTGCTTCAATGGTTTGGTATAGAAACGGCCGCCCAC
Found at i:218015 original size:18 final size:17
Alignment explanation
Indices: 217980--218023 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
217970 TTTTGGTCAA
217980 TGGTTTGGGTTAACAAAT
1 TGGTTT-GGTTAACAAAT
217998 TGGGTTTGGTTATA-AAAT
1 T-GGTTTGGTTA-ACAAAT
218016 TGGTTTGG
1 TGGTTTGG
218024 ACTAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.29
18 11 0.46
19 6 0.25
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.43
Consensus pattern (17 bp):
TGGTTTGGTTAACAAAT
Found at i:218115 original size:16 final size:16
Alignment explanation
Indices: 218086--218117 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
218076 TTGATTTAAA
218086 TTATTTTTTATTTTTT
1 TTATTTTTTATTTTTT
218102 TTATTTTTTATTTTTT
1 TTATTTTTTATTTTTT
218118 AGATTTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTATTTTTTATTTTTT
Found at i:218123 original size:16 final size:16
Alignment explanation
Indices: 218088--218124 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
218078 GATTTAAATT
**
218088 ATTTTTTATTTTTTTT
1 ATTTTTTATTTTTTAG
218104 ATTTTTTATTTTTTAG
1 ATTTTTTATTTTTTAG
218120 ATTTT
1 ATTTT
218125 GGACAGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
ATTTTTTATTTTTTAG
Found at i:219468 original size:15 final size:15
Alignment explanation
Indices: 219448--219488 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
219438 TTTCGAGTTT
*
219448 TTTTTTTAATTCAAA
1 TTTTTTTAATTAAAA
*
219463 TTTTTTAAATTAAAA
1 TTTTTTTAATTAAAA
219478 TTTTTTTAATT
1 TTTTTTTAATT
219489 TTAATGATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTTAATTAAAA
Found at i:219805 original size:24 final size:24
Alignment explanation
Indices: 219777--219822 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
219767 AATAAAAATT
*
219777 AGCCATCAA-TTTTGACAAACAACA
1 AGCCACCAATTTTTG-CAAACAACA
219801 AGCCACCAATTTTTGCAAACAA
1 AGCCACCAATTTTTGCAAACAA
219823 AAATAACCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTTGCAAACAACA
Found at i:219850 original size:28 final size:28
Alignment explanation
Indices: 219819--219907 Score: 153
Period size: 28 Copynumber: 3.2 Consensus size: 28
219809 ATTTTTGCAA
219819 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAAGAA-AACCACCATATTTGACAAAT
*
219847 ACAAAGGAAACCACCATATTTGACAAAT
1 ACAAAGAAAACCACCATATTTGACAAAT
219875 ACAAAGAAAACCACCATATTTGACAAAT
1 ACAAAGAAAACCACCATATTTGACAAAT
219903 ACAAA
1 ACAAA
219908 AGGTGGCATT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
28 57 0.98
29 1 0.02
ACGTcount: A:0.54, C:0.21, G:0.07, T:0.18
Consensus pattern (28 bp):
ACAAAGAAAACCACCATATTTGACAAAT
Found at i:224453 original size:28 final size:27
Alignment explanation
Indices: 224422--224484 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 27
224412 ATTTTTGTAA
*
224422 ACAAAAATAACCATCATATTTAACAAAT
1 ACAAAAA-AACCACCATATTTAACAAAT
*
224450 ACAAAGAAAACCACCATATTTGACAAAT
1 ACAAA-AAAACCACCATATTTAACAAAT
224478 ACAAAAA
1 ACAAAAA
224485 GTGACATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (27 bp):
ACAAAAAAACCACCATATTTAACAAAT
Found at i:225509 original size:3 final size:3
Alignment explanation
Indices: 225501--225538 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
225491 TCTCTTACCT
225501 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
225539 CTATTACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:227621 original size:2 final size:2
Alignment explanation
Indices: 227614--227646 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
227604 TAGAATTGTT
227614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
227647 GTAATTGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:236611 original size:7 final size:7
Alignment explanation
Indices: 236599--236631 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
236589 GAACATGTTT
236599 AATAAAA
1 AATAAAA
236606 AATAAAA
1 AATAAAA
236613 AAT-AAA
1 AATAAAA
236619 AATAAATA
1 AATAAA-A
236627 AATAA
1 AATAA
236632 TTTACTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 12 0.50
8 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AATAAAA
Found at i:236618 original size:14 final size:15
Alignment explanation
Indices: 236599--236631 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
236589 GAACATGTTT
236599 AATAAAAAATAAA-A
1 AATAAAAAATAAATA
236613 AAT-AAAAATAAATA
1 AATAAAAAATAAATA
236627 AATAA
1 AATAA
236632 TTTACTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.53
14 7 0.41
15 1 0.06
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AATAAAAAATAAATA
Found at i:237332 original size:13 final size:13
Alignment explanation
Indices: 237314--237340 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
237304 CACATATTTT
237314 TTTAATTTTTATA
1 TTTAATTTTTATA
237327 TTTAATTTTTATA
1 TTTAATTTTTATA
237340 T
1 T
237341 AATATAGATT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTAATTTTTATA
Found at i:237487 original size:30 final size:30
Alignment explanation
Indices: 237419--237487 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 30
237409 CTTTTTTAAA
* *
237419 TATTAAAA-TTAAATTTAACTTAATTTTTT
1 TATTAAAATTTAAATTTAAATTAATATTTT
* **
237448 TA-AATAAATTTATTTTTAAATTAATATTTT
1 TATTA-AAATTTAAATTTAAATTAATATTTT
237478 TATTAAAATT
1 TATTAAAATT
237488 CTGAGAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.03
29 5 0.16
30 24 0.77
31 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (30 bp):
TATTAAAATTTAAATTTAAATTAATATTTT
Found at i:238232 original size:16 final size:15
Alignment explanation
Indices: 238210--238290 Score: 53
Period size: 16 Copynumber: 5.5 Consensus size: 15
238200 TTTATTTATT
238210 TTTATAAATGCATTA
1 TTTATAAATGCATTA
238225 TGTTATAAAT---TTA
1 T-TTATAAATGCATTA
** **
238238 TTTATTTATTTATT-
1 TTTATAAATGCATTA
238252 TTTATAAATGCATTA
1 TTTATAAATGCATTA
**
238267 TGTTATAAATTTATTTA
1 T-TTATAAATGCA-TTA
238284 TTTATAA
1 TTTATAA
238291 GAAAGATAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
12 6 0.12
13 4 0.08
14 10 0.20
15 4 0.08
16 23 0.45
17 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTATAAATGCATTA
Found at i:238233 original size:42 final size:42
Alignment explanation
Indices: 238185--238288 Score: 208
Period size: 42 Copynumber: 2.5 Consensus size: 42
238175 TTAATGTATC
238185 TTATAAATTTATTTATTTATTTATTTTTATAAATGCATTATG
1 TTATAAATTTATTTATTTATTTATTTTTATAAATGCATTATG
238227 TTATAAATTTATTTATTTATTTATTTTTATAAATGCATTATG
1 TTATAAATTTATTTATTTATTTATTTTTATAAATGCATTATG
238269 TTATAAATTTATTTATTTAT
1 TTATAAATTTATTTATTTAT
238289 AAGAAAGATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (42 bp):
TTATAAATTTATTTATTTATTTATTTTTATAAATGCATTATG
Found at i:247133 original size:18 final size:17
Alignment explanation
Indices: 247100--247133 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
247090 TCAAAAGATA
*
247100 CAGTTATTGTTTCTTTC
1 CAGTTATTGATTCTTTC
247117 CAGTTATTGGATTCTTT
1 CAGTTATT-GATTCTTT
247134 AGTTTTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (17 bp):
CAGTTATTGATTCTTTC
Found at i:251542 original size:21 final size:20
Alignment explanation
Indices: 251492--251542 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
251482 TTAATATCTG
251492 AAAAAATTTTAAAAAATGAA
1 AAAAAATTTTAAAAAATGAA
*
251512 AAAATTATTTTAAAAATAT-ACA
1 AAAA-AATTTTAAAAA-ATGA-A
251534 AAAAAATTT
1 AAAAAATTT
251543 CTTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 15 0.58
22 7 0.27
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAAATTTTAAAAAATGAA
Found at i:251552 original size:26 final size:24
Alignment explanation
Indices: 251510--251564 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
251500 TTAAAAAATG
251510 AAAAAATTATTTT-AAAAATATACA
1 AAAAAATTATTTTAAAAAAT-TACA
*
251534 AAAAAATTTCTTTTAAAAAAATTACA
1 AAAAAA-TTATTTT-AAAAAATTACA
251560 AAAAA
1 AAAAA
251565 TAAAATATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 6 0.22
25 6 0.22
26 9 0.33
27 6 0.22
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAAAATTATTTTAAAAAATTACA
Found at i:251565 original size:25 final size:25
Alignment explanation
Indices: 251510--251564 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
251500 TTAAAAAATG
*
251510 AAAAAA-TTATTTTAAAAATATACA
1 AAAAAATTTATTTTAAAAAAATACA
*
251534 AAAAAATTTCTTTTAAAAAAATTACA
1 AAAAAATTTATTTTAAAAAAA-TACA
251560 AAAAA
1 AAAAA
251565 TAAAATATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 6 0.22
25 12 0.44
26 9 0.33
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAAATTTATTTTAAAAAAATACA
Found at i:252415 original size:12 final size:11
Alignment explanation
Indices: 252382--252406 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
252372 ACATTTACCA
252382 AATGGCTTATC
1 AATGGCTTATC
252393 AATGGCTTATC
1 AATGGCTTATC
252404 AAT
1 AAT
252407 AGTCTTATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (11 bp):
AATGGCTTATC
Found at i:254597 original size:2 final size:2
Alignment explanation
Indices: 254590--254625 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
254580 ATTTGTATGG
254590 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
254626 GTTGATCCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:257914 original size:11 final size:11
Alignment explanation
Indices: 257898--257938 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
257888 GATTTTTTCA
257898 ATTTTAAATAT
1 ATTTTAAATAT
257909 ATTTTAAATAT
1 ATTTTAAATAT
257920 A--TT-AATAT
1 ATTTTAAATAT
257928 ATTTTAAATAT
1 ATTTTAAATAT
257939 TAATCGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 6 0.22
9 2 0.07
10 2 0.07
11 17 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTTTAAATAT
Found at i:258218 original size:17 final size:17
Alignment explanation
Indices: 258198--258242 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
258188 AACATGATAT
*
258198 TTATATTTTATAAAAAA
1 TTATATTATATAAAAAA
*
258215 TTAT-TATATATAATAAA
1 TTATAT-TATATAAAAAA
258232 TTATATTATAT
1 TTATATTATAT
258243 TTATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATATTATATAAAAAA
Found at i:259447 original size:12 final size:12
Alignment explanation
Indices: 259416--259493 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 12
259406 TTTTATATAT
* *
259416 TATAATTATTTT
1 TATAAATATTTA
259428 TA-AAATATTTA
1 TATAAATATTTA
*
259439 TATAAATATTAA
1 TATAAATATTTA
259451 TATAGTAATAATTTA
1 TATA--AAT-ATTTA
259466 TATAATATAAATTT-
1 TATAA-AT--ATTTA
259480 TA-AAATATTTA
1 TATAAATATTTA
259491 TAT
1 TAT
259494 TTTGTTAACG
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
10 4 0.07
11 11 0.20
12 16 0.30
13 3 0.06
14 7 0.13
15 13 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (12 bp):
TATAAATATTTA
Found at i:259529 original size:17 final size:17
Alignment explanation
Indices: 259504--259539 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
259494 TTTGTTAACG
*
259504 TTATTTTTTATATTATA
1 TTATATTTTATATTATA
*
259521 TTATATTTTATTTTATA
1 TTATATTTTATATTATA
259538 TT
1 TT
259540 TTTATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATATTTTATATTATA
Found at i:259537 original size:22 final size:22
Alignment explanation
Indices: 259509--259571 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
259499 TAACGTTATT
259509 TTTTATA-TTATATTATATTTTA
1 TTTTATATTTATATTAT-TTTTA
*
259531 TTTTATATTTTTATTATTTTTA
1 TTTTATATTTATATTATTTTTA
* * *
259553 TATAATATTTACATTATTT
1 TTTTATATTTATATTATTT
259572 AATTATATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTATATTTATATTATTTTTA
Found at i:259571 original size:31 final size:31
Alignment explanation
Indices: 259535--259601 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
259525 ATTTTATTTT
* *
259535 ATATTTTTATTAT-TTTTATATAATATTTA-C
1 ATATTTTAATTATATCTTATATAA-ATTTATC
259565 AT-TATTTAATTATATCTTATATAAATTTATC
1 ATAT-TTTAATTATATCTTATATAAATTTATC
259596 ATATTT
1 ATATTT
259602 AACATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
29 1 0.03
30 15 0.48
31 14 0.45
32 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (31 bp):
ATATTTTAATTATATCTTATATAAATTTATC
Found at i:260249 original size:16 final size:16
Alignment explanation
Indices: 260208--260257 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
260198 TAAAATTTAA
* *
260208 ATATTA-ATATTTGTA
1 ATATTATATATTTTTC
260223 ATATATATATATTTTTC
1 ATAT-TATATATTTTTC
*
260240 ATATTATATATCTTTC
1 ATATTATATATTTTTC
260256 AT
1 AT
260258 TGTACTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 4 0.13
16 15 0.50
17 11 0.37
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (16 bp):
ATATTATATATTTTTC
Found at i:262254 original size:28 final size:28
Alignment explanation
Indices: 262222--262283 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
262212 ATTCAATCGA
262222 ATATAACATTAAAAATA-ATA-AAAATAT
1 ATATAACA-TAAAAATATATACAAAATAT
* *
262249 ATTATAATATAAAAATATATACATAATAT
1 A-TATAACATAAAAATATATACAAAATAT
262278 ATATAA
1 ATATAA
262284 TATTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.30
28 14 0.47
29 7 0.23
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (28 bp):
ATATAACATAAAAATATATACAAAATAT
Found at i:262263 original size:19 final size:19
Alignment explanation
Indices: 262239--262278 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
262229 ATTAAAAATA
*
262239 ATAAAAATATAT-TATAAT
1 ATAAAAATATATACATAAT
262257 ATAAAAATATATACATAAT
1 ATAAAAATATATACATAAT
262276 ATA
1 ATA
262279 TATAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAAATATATACATAAT
Found at i:262304 original size:22 final size:21
Alignment explanation
Indices: 262272--262332 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
262262 AATATATACA
262272 TAATATATATAATATTTATTAT
1 TAATATATATAATATTTA-TAT
* *
262294 TAATATTTATAATAAATTATAT
1 TAATATATATAAT-ATTTATAT
*
262316 AAATATATATAAT-TTTA
1 TAATATATATAATATTTA
262333 AATATAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 3 0.09
22 26 0.79
23 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATATATATAATATTTATAT
Found at i:262329 original size:18 final size:18
Alignment explanation
Indices: 262243--262348 Score: 62
Period size: 18 Copynumber: 5.8 Consensus size: 18
262233 AAAATAATAA
*
262243 AAATATATTATAA-TATAA
1 AAATATA-TATAATTATAT
262261 AAATATATACATAA-TATAT
1 AAATATAT--ATAATTATAT
* *
262280 ATAATATTTATTATTA-AT
1 A-AATATATATAATTATAT
**
262298 ATTTATA-ATAAATTATAT
1 AAATATATAT-AATTATAT
262316 AAATATATATAATT-T-T
1 AAATATATATAATTATAT
262332 AAATATAAATATAATTA
1 AAATAT--ATATAATTA
262349 AAAAAATTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
16 9 0.13
17 9 0.13
18 32 0.46
19 13 0.19
20 6 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATATATAATTATAT
Found at i:262343 original size:44 final size:45
Alignment explanation
Indices: 262256--262343 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
262246 TATATTATAA
* *
262256 TATAAAAATATATACATAATATATATAATATTTATTATTAATATT
1 TATAAAAATATATACATAATATATATAATATTTAATATAAATATT
*
262301 TATAATAAAT-TATATA-AATATATATAAT-TTTAAATATAAATAT
1 TATAA-AAATATATACATAATATATATAATATTT-AATATAAATAT
262344 AATTAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
43 3 0.08
44 21 0.55
45 10 0.26
46 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (45 bp):
TATAAAAATATATACATAATATATATAATATTTAATATAAATATT
Found at i:266681 original size:3 final size:3
Alignment explanation
Indices: 266673--266710 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
266663 CACTTAAAGG
*
266673 TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
266711 GTTTTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:267111 original size:21 final size:21
Alignment explanation
Indices: 267079--267127 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
267069 TATAATTTTA
* *
267079 ATTAAATTAAATTAATTAAGAG
1 ATTAAA-TAAAATAATAAAGAG
267101 A-TAAATAAAATAATAAAGAG
1 ATTAAATAAAATAATAAAGAG
267121 ATTAAAT
1 ATTAAAT
267128 TTTTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.58
21 9 0.38
22 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (21 bp):
ATTAAATAAAATAATAAAGAG
Found at i:268642 original size:26 final size:29
Alignment explanation
Indices: 268594--268655 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 29
268584 ATTCATATAC
268594 TTATAATTAATAAAAAATAAAAAA-TA-TT
1 TTAT-ATTAATAAAAAATAAAAAATTATTT
268622 TTATATTAAT-AAAAATAAAAAATTATTT
1 TTATATTAATAAAAAATAAAAAATTATTT
268650 TTATAT
1 TTATAT
268656 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 12 0.38
27 8 0.25
28 12 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TTATATTAATAAAAAATAAAAAATTATTT
Found at i:270393 original size:18 final size:16
Alignment explanation
Indices: 270372--270410 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
270362 CATATCCAAT
*
270372 TTTTTTTCAGATTTAAA
1 TTTTTTT-AAATTTAAA
270389 CTTTTTTTAAATTTAAA
1 -TTTTTTTAAATTTAAA
270406 TTTTT
1 TTTTT
270411 GACAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 8 0.40
18 7 0.35
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTTTTAAATTTAAA
Found at i:270551 original size:2 final size:2
Alignment explanation
Indices: 270544--270568 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
270534 CTTTTTAAGA
270544 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
270569 CTTTTAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:271327 original size:2 final size:2
Alignment explanation
Indices: 271320--271348 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
271310 CTTTTTAAGA
271320 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
271349 CTTTTAATGA
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:271554 original size:65 final size:65
Alignment explanation
Indices: 271450--271579 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
271440 TTAGACTTCG
271450 ACGCACGCTTCGATACTTAAATCAAAATCTTTTCGAAAAAGCAGGATCCTCACTTTAACTTAGGT
1 ACGCACGCTTCGATACTTAAATCAAAATCTTTTCGAAAAAGCAGGATCCTCACTTTAACTTAGGT
271515 ACGCACGCTTCGATACTTAAATCAAAATCTTTTCGAAAAAGCAGGATCCTCACTTTAACTTAGGT
1 ACGCACGCTTCGATACTTAAATCAAAATCTTTTCGAAAAAGCAGGATCCTCACTTTAACTTAGGT
271580 TTAGGGTCTG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (65 bp):
ACGCACGCTTCGATACTTAAATCAAAATCTTTTCGAAAAAGCAGGATCCTCACTTTAACTTAGGT
Found at i:272605 original size:17 final size:20
Alignment explanation
Indices: 272563--272606 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
272553 AAATTTATCA
*
272563 ATTATTATATTTAATATAAT
1 ATTATTATATTGAATATAAT
272583 ATTATTAT-TTGAAT-TAAT
1 ATTATTATATTGAATATAAT
272601 -TTATTA
1 ATTATTA
272607 ATTAACTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 4 0.17
19 5 0.22
20 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATATTGAATATAAT
Found at i:272989 original size:3 final size:3
Alignment explanation
Indices: 272981--273019 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
272971 AAACTCGTAT
272981 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
273020 TTGTTAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:273896 original size:2 final size:2
Alignment explanation
Indices: 273889--273918 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
273879 ATCTATACTT
273889 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
273919 GCATTATAAA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:276139 original size:2 final size:2
Alignment explanation
Indices: 276132--276158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
276122 ATATACGTAC
276132 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
276159 AACATTCAAT
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:279241 original size:80 final size:79
Alignment explanation
Indices: 279134--279341 Score: 231
Period size: 79 Copynumber: 2.6 Consensus size: 79
279124 GAGATAATAA
* * * * *
279134 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
279198 A-TTAGAAAAAAAAAAT
64 ATTTAG-AAAAAAAAAC
* * *
279214 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTTGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
279279 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* *
279293 CGGGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
279342 GAAATAACGA
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
79 56 0.52
80 51 0.48
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:279326 original size:28 final size:27
Alignment explanation
Indices: 279293--279364 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
279283 GGAATAAAGC
279293 CGGGGTTGGAGTATCCCC-TCGAAAGTAA
1 CGGGGTTGGAGTATCCCCAT-GAAA-TAA
279321 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCC-ATGAAATAA
*
279349 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
279365 TCGATTGTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATGAAATAA
Found at i:281689 original size:55 final size:55
Alignment explanation
Indices: 281605--282236 Score: 920
Period size: 55 Copynumber: 11.4 Consensus size: 55
281595 ATAAAGTGTA
* * * * *
281605 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
281660 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
281715 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
281770 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
281825 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
281880 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * **
281940 TCCCGCTTTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
281994 TCCTGCTCTCTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
282049 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
282104 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
282159 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
282214 TCCTGCTCTTTGGGGACTGGAAA
1 TCCTGCTCTTTGAGGACTGGAAA
282237 GCGGATGGAG
Statistics
Matches: 530, Mismatches: 31, Indels: 32
0.89 0.05 0.05
Matches are distributed among these distances:
53 2 0.00
54 27 0.05
55 441 0.83
56 12 0.02
59 26 0.05
60 20 0.04
61 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:281792 original size:26 final size:26
Alignment explanation
Indices: 281763--281847 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
281753 GTGGGCTTTA
281763 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** *
281789 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC--TG
* *
281818 AAAGGCGTCCTGCTCTTTGAGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
281844 AAAG
1 AAAG
281848 ATGCCACCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 16 0.36
27 5 0.11
28 6 0.14
29 11 0.25
30 3 0.07
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:281819 original size:29 final size:29
Alignment explanation
Indices: 281677--281822 Score: 87
Period size: 29 Copynumber: 5.2 Consensus size: 29
281667 CTTTGAGGAC
281677 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** * * *
281706 T-AAGAGGTGTCCTGC-TCTT-TGAGGAC-T
1 TGAA-AGGTG-CCACCAACTTGTGTGGGCTT
* *
281733 GGAAA-ATGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
* ** *
281761 TAAAAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAAAGGTG-CCACCAACTTGTGTGGG-CTT
281787 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
281816 TGAAAGG
1 TGAAAGG
281823 CGTCCTGCTC
Statistics
Matches: 81, Mismatches: 22, Indels: 28
0.62 0.17 0.21
Matches are distributed among these distances:
25 6 0.07
26 16 0.20
27 13 0.16
28 19 0.23
29 21 0.26
30 6 0.07
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:282071 original size:27 final size:27
Alignment explanation
Indices: 282041--282181 Score: 65
Period size: 27 Copynumber: 5.1 Consensus size: 27
282031 TGTGGGCTTT
282041 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
282068 GAAA-ATG-CCACCAACTTATGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
282095 TAAAAGGTGTCCTGCTCTTTGAGGACTG
1 GA-AAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
282123 GAAA-ATG-CCACCAACTTATGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
282151 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
282178 GAAA
1 GAAA
282182 ATGCCACCAA
Statistics
Matches: 74, Mismatches: 30, Indels: 20
0.60 0.24 0.16
Matches are distributed among these distances:
25 6 0.08
26 10 0.14
27 23 0.31
28 19 0.26
29 10 0.14
30 6 0.08
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:282109 original size:279 final size:278
Alignment explanation
Indices: 281605--282237 Score: 955
Period size: 279 Copynumber: 2.3 Consensus size: 278
281595 ATAAAGTGTA
* * * * *
281605 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTT---GAAAGGCGTCCTGC
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAGAAAGGCGTCCCGC
*
281666 TCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGA
65 TCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGGA
* *
281731 CTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTG
130 CTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGAAAGATG
* *
281796 CCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACT
195 CCACCAACTTATGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACT
*
281860 TGTGTGGGCTTT-AAGAGGTG
259 TATGTGGGCTTTGAA-AGGTG
* *
281880 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTGTCCCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAG-AAAGGCGTCCCG
*
281945 CTTTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGG
64 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGG
*
282009 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-A
129 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGA
*
282073 TGCCACCAACTTATGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
193 TGCCACCAACTTATGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAAC
282138 TTATGTGGGCTTTGAAAGGTG
258 TTATGTGGGCTTTGAAAGGTG
* *
282159 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---GAAAGGTGTCCTGCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAGGCGTCCCGCT
*
282221 CTTTGGGGACTGGAAAG
66 CTTTGAGGACT-GAAAG
282238 CGGATGGAGA
Statistics
Matches: 327, Mismatches: 20, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
274 21 0.06
275 40 0.12
276 7 0.02
279 227 0.69
280 32 0.10
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (278 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAGGCGTCCCGCT
CTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGGAC
TGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGAAAGATGC
CACCAACTTATGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTA
TGTGGGCTTTGAAAGGTG
Found at i:283235 original size:17 final size:18
Alignment explanation
Indices: 283213--283251 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
283203 CTTTTCTCTC
283213 TTTTC-TTTG-TTTTGTTT
1 TTTTCTTTTGCTTTT-TTT
283230 TTTTCTTTTGCTTTTTTT
1 TTTTCTTTTGCTTTTTTT
283248 TTTT
1 TTTT
283252 TTGAAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (18 bp):
TTTTCTTTTGCTTTTTTT
Found at i:283247 original size:22 final size:21
Alignment explanation
Indices: 283211--283253 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
283201 TTCTTTTCTC
283211 TCTTTTCTTTGTTTTGTTTTTT
1 TCTTTTCTTTGTTTT-TTTTTT
283233 TCTTTTGCTTT-TTTTTTTTTT
1 TCTTTT-CTTTGTTTTTTTTTT
283254 GAAGAGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (21 bp):
TCTTTTCTTTGTTTTTTTTTT
Found at i:295763 original size:79 final size:79
Alignment explanation
Indices: 295658--295864 Score: 238
Period size: 79 Copynumber: 2.6 Consensus size: 79
295648 GAGATAATAA
* * * * *
295658 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
295722 A-TTAGAAAAAAAAAT
64 ATTTAGAAAAAAAAAC
* *
295737 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
295802 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* * *
295816 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
295865 GAAATAACGA
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 7 0.06
79 101 0.94
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:295856 original size:28 final size:28
Alignment explanation
Indices: 295816--295887 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
295806 GGAATAAAGC
** *
295816 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
295844 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
295872 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
295888 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:295879 original size:107 final size:107
Alignment explanation
Indices: 295737--295941 Score: 252
Period size: 107 Copynumber: 1.9 Consensus size: 107
295727 AAAAAAAAAT
* *
295737 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-
1 CGGGATTGGAGTATCCC-TCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* * *
295801 TTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAA
65 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
* * * * ***
295844 CGGGGTTGGAGTATCCC-CGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTA
1 CGGGATTGGAGTATCCCTCGA--AAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATA
*
295908 TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
64 TTTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
295942 GATTAAAGGA
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
105 3 0.04
107 50 0.61
108 29 0.35
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (107 bp):
CGGGATTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATATT
TTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
Done.