Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 3 of 21
Found at i:272174 original size:22 final size:24
Alignment explanation
Indices: 272125--272177 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
272115 AATATGTAAA
* **
272125 AAATATATAAAAATATAATATTTT
1 AAATATAAAAAAATATAATATTAC
272149 AAATATAAAAAAATATAA-A-TAC
1 AAATATAAAAAAATATAATATTAC
272171 AAATATA
1 AAATATA
272178 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 8 0.31
23 1 0.04
24 17 0.65
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATATAAAAAAATATAATATTAC
Found at i:273401 original size:16 final size:16
Alignment explanation
Indices: 273380--273462 Score: 66
Period size: 15 Copynumber: 5.2 Consensus size: 16
273370 AATTTTTCTC
273380 TTATATATAAAATAAA
1 TTATATATAAAATAAA
*
273396 TTATATATAAAA-ATA
1 TTATATATAAAATAAA
*
273411 TATATAAAATAAAATAAA
1 T-TAT-ATATAAAATAAA
*
273429 TTAT-TA-ATATATAAA
1 TTATATATA-AAATAAA
* *
273444 ATATATA-AAAATATA
1 TTATATATAAAATAAA
273459 TTAT
1 TTAT
273463 TTTAAATATA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
14 1 0.02
15 21 0.40
16 18 0.34
17 10 0.19
18 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTATATATAAAATAAA
Found at i:273413 original size:10 final size:10
Alignment explanation
Indices: 273398--273459 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
273388 AAAATAAATT
273398 ATATATAAAA
1 ATATATAAAA
273408 ATATATATAAA
1 ATATATA-AAA
273419 ATA-A-AATAA
1 ATATATAA-AA
*
273428 AT-TAT--TA
1 ATATATAAAA
273435 ATATAT-AAA
1 ATATATAAAA
273444 ATATATAAAA
1 ATATATAAAA
273454 ATATAT
1 ATATAT
273460 TATTTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 13 0.30
10 17 0.40
11 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATATATAAAA
Found at i:273462 original size:30 final size:29
Alignment explanation
Indices: 273421--273488 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
273411 TATATAAAAT
* *
273421 AAAATAAATTA-TTAATATATAAAATATATA
1 AAAATATATTATTTAA-ATATAAAAAAT-TA
273451 AAAATATATTATTTTAAATATAAAAAATTA
1 AAAATATATTA-TTTAAATATAAAAAATTA
*
273481 TAAATATA
1 AAAATATA
273489 AACACATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 19 0.58
31 10 0.30
32 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAATATATTATTTAAATATAAAAAATTA
Found at i:273484 original size:16 final size:16
Alignment explanation
Indices: 273380--273490 Score: 68
Period size: 16 Copynumber: 6.8 Consensus size: 16
273370 AATTTTTCTC
*
273380 TTATATATA-AAATAAA
1 TTATAAATATAAA-AAA
273396 TTAT--ATATAAAAATA
1 TTATAAATATAAAAA-A
273411 TATATAAA-ATAAAATAAA
1 T-TATAAATAT-AAA-AAA
* *
273429 TTATTAATATATAAAA
1 TTATAAATATAAAAAA
* * **
273445 TATATAAAAATATATTA
1 T-TATAAATATAAAAAA
*
273462 TTTTAAATATAAAAAA
1 TTATAAATATAAAAAA
273478 TTATAAATATAAA
1 TTATAAATATAAA
273491 CACATAAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
14 5 0.07
15 5 0.07
16 33 0.45
17 21 0.28
18 8 0.11
19 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTATAAATATAAAAAA
Found at i:273498 original size:46 final size:46
Alignment explanation
Indices: 273402--273498 Score: 103
Period size: 46 Copynumber: 2.1 Consensus size: 46
273392 TAAATTATAT
* *
273402 ATAAAAATATATATAAAATAAAATAAATTATTAATATATAAAATAT
1 ATAAAAATATATATAAAATAAAATAAATTATTAATATATAAAACAC
*
273448 ATAAAAATATATTATTTTAAATATAAA-AAATTA-TAA-ATAT-AAACAC
1 ATAAAAATATA-TA--TAAAATA-AAATAAATTATTAATATATAAAACAC
273494 ATAAA
1 ATAAA
273499 TTTTTTTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
46 20 0.45
47 6 0.14
48 3 0.07
49 12 0.27
50 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (46 bp):
ATAAAAATATATATAAAATAAAATAAATTATTAATATATAAAACAC
Found at i:273516 original size:4 final size:4
Alignment explanation
Indices: 273505--273538 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
273495 TAAATTTTTT
273505 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
273539 TTTACCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:273748 original size:20 final size:20
Alignment explanation
Indices: 273633--273748 Score: 54
Period size: 18 Copynumber: 6.2 Consensus size: 20
273623 ATGTATAGAT
*
273633 AAATAA-ATAA-ATTAATTA
1 AAATAATATAATATAAATTA
*
273651 AAATTTATATAATATAAATT-
1 AAA-TAATATAATATAAATTA
** *
273671 -AATAATATTTTAAAAATT-
1 AAATAATATAATATAAATTA
* * *
273689 ACATAA-A-AATTTTAAATCTT
1 AAATAATATAA-TATAAAT-TA
*
273709 AAAT-ATGTAATATAAA--A
1 AAATAATATAATATAAATTA
273726 AAATAATATAATATAAATTA
1 AAATAATATAATATAAATTA
273746 AAA
1 AAA
273749 ATAACTTGAA
Statistics
Matches: 70, Mismatches: 16, Indels: 22
0.65 0.15 0.20
Matches are distributed among these distances:
17 4 0.06
18 32 0.46
19 10 0.14
20 16 0.23
21 8 0.11
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (20 bp):
AAATAATATAATATAAATTA
Found at i:274797 original size:19 final size:19
Alignment explanation
Indices: 274773--274820 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
274763 ATTAATGATT
274773 TTTATTATATAATTTTATA
1 TTTATTATATAATTTTATA
*
274792 TTTATT-T-TAATTTTCTA
1 TTTATTATATAATTTTATA
274809 TATTA-TATATAA
1 T-TTATTATATAA
274821 AATTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.44
18 5 0.20
19 9 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTATATAATTTTATA
Found at i:277489 original size:48 final size:50
Alignment explanation
Indices: 277402--277495 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
277392 AAATTAAAAT
*
277402 AAAATATTTTTTTATTGATTTGATTAATAGAAAACATAAAAAAATAGTAA
1 AAAATATTTTTTTATTGATTTGAGTAATAGAAAACATAAAAAAATAGTAA
* *
277452 AAAATATTTTTTTATTG-TTTG-GTACATTGAAAA-ATAAAAGAATA
1 AAAATATTTTTTTATTGATTTGAGTA-ATAGAAAACATAAAAAAATA
277496 AAATAGAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
48 12 0.30
49 11 0.28
50 17 0.43
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (50 bp):
AAAATATTTTTTTATTGATTTGAGTAATAGAAAACATAAAAAAATAGTAA
Found at i:277967 original size:17 final size:17
Alignment explanation
Indices: 277937--277977 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
277927 TCCATTAAGC
*
277937 AATTAAATTATAAAGAA
1 AATTAAATTATAAAAAA
* *
277954 AATTATATTTTAAAAAA
1 AATTAAATTATAAAAAA
277971 AATTAAA
1 AATTAAA
277978 AGAACAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTAAATTATAAAAAA
Found at i:278646 original size:16 final size:15
Alignment explanation
Indices: 278625--278668 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
278615 TAATATAAAA
278625 TTTTATAATTTATAAT
1 TTTTAT-ATTTATAAT
278641 TTTTATATATTATAAT
1 TTTTATAT-TTATAAT
278657 TTATTATTATTT
1 TT-TTA-TATTT
278669 TTATTTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 5 0.20
18 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTATATTTATAAT
Found at i:278676 original size:23 final size:22
Alignment explanation
Indices: 278626--278676 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
278616 AATATAAAAT
278626 TTTATAATTTATAATTTTTATA
1 TTTATAATTTATAATTTTTATA
* *
278648 TATTATAATTTATTATTATTTTTA
1 T-TTATAATTTATAATT-TTTATA
278672 TTTAT
1 TTTAT
278677 CACATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 18 0.72
24 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATAATTTATAATTTTTATA
Found at i:278728 original size:21 final size:21
Alignment explanation
Indices: 278704--278744 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
278694 TATATAAATA
278704 TATATATACACAGAGAGAGAT
1 TATATATACACAGAGAGAGAT
* *
278725 TATATATATATAGAGAGAGA
1 TATATATACACAGAGAGAGA
278745 GAGAGAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.27
Consensus pattern (21 bp):
TATATATACACAGAGAGAGAT
Found at i:278728 original size:23 final size:23
Alignment explanation
Indices: 278702--278746 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
278692 ATTATATAAA
278702 TATATATATACACAGAGAGAGAT
1 TATATATATACACAGAGAGAGAT
* *
278725 TATATATATATAGAGAGAGAGA
1 TATATATATACACAGAGAGAGA
278747 GAGAGAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (23 bp):
TATATATATACACAGAGAGAGAT
Found at i:278735 original size:25 final size:25
Alignment explanation
Indices: 278701--278748 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
278691 AATTATATAA
278701 ATATATATATACACAGAGAGAGATT
1 ATATATATATACACAGAGAGAGATT
* *
278726 ATATATATATAGAGAGAGAGAGA
1 ATATATATATACACAGAGAGAGA
278749 GAGAGAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.25
Consensus pattern (25 bp):
ATATATATATACACAGAGAGAGATT
Found at i:278741 original size:2 final size:2
Alignment explanation
Indices: 278736--278770 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
278726 ATATATATAT
278736 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
278771 TTATATGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:279311 original size:34 final size:34
Alignment explanation
Indices: 279268--279332 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
279258 ATATTTTAAT
* * *
279268 TTAAATATAAAATATATAAATAATAATATAATTA
1 TTAAATATAAAAAATAAAAAGAATAATATAATTA
* *
279302 TTAATTATAAAAAATAAAAAGAGTAATATAA
1 TTAAATATAAAAAATAAAAAGAATAATATAA
279333 ATGAATTGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (34 bp):
TTAAATATAAAAAATAAAAAGAATAATATAATTA
Found at i:280753 original size:2 final size:2
Alignment explanation
Indices: 280746--280776 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
280736 TTTAGTGTAA
280746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
280777 ATTTTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:282535 original size:15 final size:15
Alignment explanation
Indices: 282497--282537 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
282487 TTTTGTATTG
282497 AAGTATCAATTTTTTT
1 AAGTAT-AATTTTTTT
*
282513 AAAT-TAATTTTTTT
1 AAGTATAATTTTTTT
282527 AAGTATAATTT
1 AAGTATAATTT
282538 AAAAATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 12 0.55
15 7 0.32
16 3 0.14
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (15 bp):
AAGTATAATTTTTTT
Found at i:283774 original size:6 final size:6
Alignment explanation
Indices: 283763--283829 Score: 79
Period size: 6 Copynumber: 11.8 Consensus size: 6
283753 TATTAATTTA
*
283763 TATATT TATATT TATATC TATATT TATA-T TATA-T TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
**
283809 TA-AGA TAT-TT TATATT TATAT
1 TATATT TATATT TATATT TATAT
283830 AAATTTTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
5 16 0.31
6 36 0.69
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (6 bp):
TATATT
Found at i:283777 original size:22 final size:22
Alignment explanation
Indices: 283750--283827 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 22
283740 TCGTTTAAAA
283750 ATTTATTAATTTATATATTTAT
1 ATTTATTAATTTATATATTTAT
283772 ATTTATATCTATATTTATATTATATTAT
1 A-TT-TAT-TA-ATTTATA-TAT-TTAT
*
283800 ATTTA-T-ATTTAAGATATTTTAT
1 ATTTATTAATTT-ATATA-TTTAT
283822 ATTTAT
1 ATTTAT
283828 ATAAATTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 17
0.72 0.02 0.27
Matches are distributed among these distances:
22 16 0.35
23 5 0.11
24 4 0.09
25 2 0.04
26 9 0.20
27 5 0.11
28 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (22 bp):
ATTTATTAATTTATATATTTAT
Found at i:283828 original size:22 final size:22
Alignment explanation
Indices: 283758--283829 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
283748 AAATTTATTA
283758 ATTTATATATT-T-ATA-TTTAT
1 ATTTATAT-TTATAATATTTTAT
* * *
283778 ATCTATATTTATATTATATTAT
1 ATTTATATTTATAATATTTTAT
283800 ATTTATATTTA-AGATATTTTAT
1 ATTTATATTTATA-ATATTTTAT
283822 ATTTATAT
1 ATTTATAT
283830 AAATTTTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 8 0.19
21 3 0.07
22 29 0.69
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (22 bp):
ATTTATATTTATAATATTTTAT
Found at i:283849 original size:18 final size:17
Alignment explanation
Indices: 283767--283869 Score: 67
Period size: 16 Copynumber: 6.2 Consensus size: 17
283757 AATTTATATA
**
283767 TTTATATTTATATCTAT
1 TTTATATTTATATAAAT
*
283784 ATTTATA-TTATAT-TAT
1 -TTTATATTTATATAAAT
* *
283800 ATTTATATTTA-AGATAT
1 -TTTATATTTATATAAAT
283817 TTTATATTTATATAAAT
1 TTTATATTTATATAAAT
283834 TTTAATATATTA-AT-AA-
1 TTT-ATAT-TTATATAAAT
*
283850 TTAATA-TTATATAAAT
1 TTTATATTTATATAAAT
283866 TTTA
1 TTTA
283870 AAATATCTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 3 0.04
14 2 0.03
15 5 0.07
16 26 0.36
17 21 0.29
18 12 0.17
19 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTATATTTATATAAAT
Found at i:283870 original size:17 final size:17
Alignment explanation
Indices: 283815--283870 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
283805 TATTTAAGAT
283815 ATTTT-ATATTTATATAA
1 ATTTTAATA-TTATATAA
283832 ATTTTAATA-TAT-T-A
1 ATTTTAATATTATATAA
*
283846 ATAATTAATATTATATAA
1 AT-TTTAATATTATATAA
283864 ATTTTAA
1 ATTTTAA
283871 AATATCTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 3 0.09
15 7 0.22
16 6 0.19
17 10 0.31
18 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTAATATTATATAA
Found at i:284091 original size:7 final size:7
Alignment explanation
Indices: 284081--284135 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
284071 TATTTTTTAC
284081 TTATATA
1 TTATATA
284088 TTATATA
1 TTATATA
*
284095 --ATATT
1 TTATATA
*
284100 TTATATT
1 TTATATA
284107 TATATATA
1 T-TATATA
284115 TTATATAA
1 TTATAT-A
284123 TT-TATA
1 TTATATA
284129 TTATATA
1 TTATATA
284136 AAAAATAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 4 0.10
6 3 0.07
7 25 0.61
8 9 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATATA
Found at i:284181 original size:31 final size:30
Alignment explanation
Indices: 284116--284182 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
284106 TTATATATAT
*
284116 TATATAATTTATATTATATAAAAAATAAATA
1 TATATAATTTATA-TATATAAAAAATAAAAA
* *
284147 TATATAATATTATA-ATATAAACATTAAAAAA
1 TATATAAT-TTATATATATAAAAAAT-AAAAA
284178 TATAT
1 TATAT
284183 TACGTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 9 0.29
31 17 0.55
32 5 0.16
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
TATATAATTTATATATATAAAAAATAAAAA
Found at i:284343 original size:26 final size:26
Alignment explanation
Indices: 284313--284372 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
284303 TTTATTTATA
284313 AATATAAATAAATTT-AAATAAAATTT
1 AATATAAATAAATTTAAAAT-AAATTT
** *
284339 AATATTTAT-ATTTTAAAATAAATTT
1 AATATAAATAAATTTAAAATAAATTT
284364 AA-ATAAATA
1 AATATAAATA
284373 TAAATAACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
24 4 0.15
25 12 0.44
26 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATAAATAAATTTAAAATAAATTT
Found at i:285446 original size:23 final size:24
Alignment explanation
Indices: 285420--285467 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
285410 ATTTTTTTAA
285420 ATTTTAAATTT-A-TATTTAAATTT
1 ATTTT-AATTTGATTATTTAAATTT
*
285443 ATTTTAATTTGATTATTTAAGTTT
1 ATTTTAATTTGATTATTTAAATTT
285467 A
1 A
285468 AATTACTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 6 0.27
24 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
ATTTTAATTTGATTATTTAAATTT
Found at i:285461 original size:30 final size:29
Alignment explanation
Indices: 285403--285471 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
285393 ATTAAGTCAC
*
285403 AGTTTAAATTTTTTTAAATTTTAAATTTA
1 AGTTTAAATTTTTTTAAATTTGAAATTTA
*
285432 TA-TTTAAATTTATTTT-AATTTGATTATTTA
1 -AGTTTAAATTT-TTTTAAATTTGA-AATTTA
285462 AGTTTAAATT
1 AGTTTAAATT
285472 ACTGTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.59
Consensus pattern (29 bp):
AGTTTAAATTTTTTTAAATTTGAAATTTA
Found at i:285564 original size:17 final size:18
Alignment explanation
Indices: 285538--285584 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
285528 TTTGATTAAA
285538 TTTAAATAAAAATATT-T
1 TTTAAATAAAAATATTAT
*
285555 TTTAATTAAAAATATTAT
1 TTTAAATAAAAATATTAT
285573 TTTAAACTAAAA
1 TTTAAA-TAAAA
285585 TAACTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 6 0.23
19 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTAAATAAAAATATTAT
Found at i:286118 original size:2 final size:2
Alignment explanation
Indices: 286111--286135 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
286101 GTGGAGAGTA
286111 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
286136 ATGACATGAT
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:287602 original size:14 final size:14
Alignment explanation
Indices: 287585--287624 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
287575 AAAAATATTA
287585 TAATATTTTAAAT-T
1 TAAT-TTTTAAATAT
287599 TAATTTATTAAATAT
1 TAATTT-TTAAATAT
287614 TAATTTTTAAA
1 TAATTTTTAAA
287625 AATAATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 15 0.62
15 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTTTTAAATAT
Found at i:288679 original size:28 final size:28
Alignment explanation
Indices: 288648--288711 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
288638 AATTTTTTTA
*
288648 ATTTTTTAAAAAAT-TGTAATATGCATAT
1 ATTTTATAAAAAATAT-TAATATGCATAT
** *
288676 ATTTTATATTAAGTATTAATATGCATAT
1 ATTTTATAAAAAATATTAATATGCATAT
288704 ATTTTATA
1 ATTTTATA
288712 TTTAATATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (28 bp):
ATTTTATAAAAAATATTAATATGCATAT
Found at i:290657 original size:20 final size:20
Alignment explanation
Indices: 290632--290669 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
290622 GTATTAAAAA
290632 ATAATTTAAATATTAAATTT
1 ATAATTTAAATATTAAATTT
*
290652 ATAATTTTAATATTAAAT
1 ATAATTTAAATATTAAAT
290670 AAGTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTAAATATTAAATTT
Found at i:297518 original size:67 final size:68
Alignment explanation
Indices: 297440--297574 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 68
297430 AATGAAAGTT
* *
297440 TGAGATAAATTATTATAGAGATAAAATTGAAATCAA-TGGAAAATCAATGTTTAAATAATAAAAT
1 TGAGATAAATTATTATAGAGATAAAATTGAAATCAATTGAAAAATAAATGTTTAAATAATAAAAT
297504 AAA
66 AAA
*
297507 TGAGATTAATTATTATAGAGATAAAATTGAAATCAATTGAAAAATAAATGTTTAAATAATAAAAT
1 TGAGATAAATTATTATAGAGATAAAATTGAAATCAATTGAAAAATAAATGTTTAAATAATAAAAT
297572 AAA
66 AAA
297575 AGTAATTGAG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
67 35 0.55
68 29 0.45
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.31
Consensus pattern (68 bp):
TGAGATAAATTATTATAGAGATAAAATTGAAATCAATTGAAAAATAAATGTTTAAATAATAAAAT
AAA
Found at i:301261 original size:12 final size:12
Alignment explanation
Indices: 301252--301277 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
301242 AAAATTGGTG
301252 GCACAGTTGGCA
1 GCACAGTTGGCA
301264 GCACAGTTGGCA
1 GCACAGTTGGCA
301276 GC
1 GC
301278 CTTTGTTTTC
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:0.27, G:0.35, T:0.15
Consensus pattern (12 bp):
GCACAGTTGGCA
Found at i:307488 original size:2 final size:2
Alignment explanation
Indices: 307483--307522 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
307473 AATCTATGTC
*
307483 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
307523 TTTCTCTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:308363 original size:2 final size:2
Alignment explanation
Indices: 308356--308391 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
308346 ATGTAGAGGA
308356 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
308392 GTAAATTTTA
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:310264 original size:2 final size:2
Alignment explanation
Indices: 310259--310285 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
310249 AACACACTCG
310259 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 T
310286 GAAAAATGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:311531 original size:2 final size:2
Alignment explanation
Indices: 311524--311562 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
311514 AAAATCGAAT
311524 TA TA TA 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 TA TA TA T
311563 TTGGGGGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:313311 original size:16 final size:15
Alignment explanation
Indices: 313273--313317 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
313263 TTAAAAAATT
* *
313273 AAAAACTTAAATTTTA
1 AAAAATTTAAA-TTCA
313289 AAAAATTTAAATTCA
1 AAAAATTTAAATTCA
313304 AAAGAATTTAAATT
1 AAA-AATTTAAATT
313318 TAAGATTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (15 bp):
AAAAATTTAAATTCA
Found at i:314210 original size:2 final size:2
Alignment explanation
Indices: 314205--314240 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
314195 GTATGAGAGA
314205 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
314241 TATCAAGCAA
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:314717 original size:26 final size:25
Alignment explanation
Indices: 314666--314717 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
314656 AAATTTAATC
* *
314666 AAATATTAATTTAATAATAATTAAA
1 AAATATTAAATTAATAATAATCAAA
* *
314691 AAATATTAAAATTAATTATGATCAAA
1 AAATATT-AAATTAATAATAATCAAA
314717 A
1 A
314718 TCTTATACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AAATATTAAATTAATAATAATCAAA
Found at i:319314 original size:17 final size:17
Alignment explanation
Indices: 319292--319341 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
319282 ATTTCCATGA
*
319292 AAAAAATTATTTTTTCT
1 AAAAAATAATTTTTTCT
*
319309 AAAAAA-GATTTATTTCT
1 AAAAAATAATTT-TTTCT
319326 AAAAATATAATTTTTT
1 AAAAA-ATAATTTTTT
319342 TATCAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
18 4 0.14
19 4 0.14
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (17 bp):
AAAAAATAATTTTTTCT
Found at i:320858 original size:14 final size:14
Alignment explanation
Indices: 320839--320865 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
320829 GTTAAAATAT
320839 TATTTATATATTAA
1 TATTTATATATTAA
320853 TATTTATATATTA
1 TATTTATATATTA
320866 TTATAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTATATATTAA
Found at i:324924 original size:25 final size:27
Alignment explanation
Indices: 324872--324928 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
324862 TATCACTATT
324872 TAATTAGTTTTTAAAAATTATATTAAAA
1 TAATTAGTTTTTAAAAATTATA-TAAAA
324900 TAATTA-TTTTTAAATAA-TATA-AAAA
1 TAATTAGTTTTTAAA-AATTATATAAAA
324925 TAAT
1 TAAT
324929 ATAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.29
27 12 0.43
28 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TAATTAGTTTTTAAAAATTATATAAAA
Found at i:324927 original size:11 final size:11
Alignment explanation
Indices: 324911--324948 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
324901 AATTATTTTT
324911 AAATAATATAA
1 AAATAATATAA
324922 AAATAATATAA
1 AAATAATATAA
*
324933 TAATAAATATAA
1 AAAT-AATATAA
324945 AAAT
1 AAAT
324949 CTTTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATAATATAA
Found at i:325911 original size:14 final size:13
Alignment explanation
Indices: 325893--325926 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
325883 ATTTTATTAT
*
325893 ATAATTAATGTAA
1 ATAATTAAAGTAA
325906 ATTAATTAAAGTAA
1 A-TAATTAAAGTAA
325920 ATAATTA
1 ATAATTA
325927 CATAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (13 bp):
ATAATTAAAGTAA
Found at i:326659 original size:28 final size:26
Alignment explanation
Indices: 326619--326683 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
326609 TTTTTAATTT
** *
326619 TAAAATTAAATCATATCAAATTTAAA
1 TAAAATTTGATCAAATCAAATTTAAA
* *
326645 TAAATTATTTGATCAAATTAAATTTAAT
1 TAAA--ATTTGATCAAATCAAATTTAAA
326673 TAAAATTTGAT
1 TAAAATTTGAT
326684 TAAAATATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
26 11 0.34
28 21 0.66
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (26 bp):
TAAAATTTGATCAAATCAAATTTAAA
Found at i:326902 original size:22 final size:21
Alignment explanation
Indices: 326877--326926 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
326867 AAATGTATTG
*
326877 TTATAGCACAATGTAAAAATCA
1 TTATAACACAATG-AAAAATCA
* *
326899 TTATAATACAATGCAAAATCA
1 TTATAACACAATGAAAAATCA
326920 TT-TAACA
1 TTATAACA
326927 TATTTTACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 4 0.17
21 9 0.38
22 11 0.46
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (21 bp):
TTATAACACAATGAAAAATCA
Found at i:334553 original size:13 final size:13
Alignment explanation
Indices: 334535--334563 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
334525 AAACCTAACC
334535 TGTTTGCATGCTA
1 TGTTTGCATGCTA
334548 TGTTTGCATGCTA
1 TGTTTGCATGCTA
334561 TGT
1 TGT
334564 GAATTCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (13 bp):
TGTTTGCATGCTA
Found at i:336471 original size:3 final size:3
Alignment explanation
Indices: 336463--336516 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
336453 TGCAGCTATA
* * *
336463 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAC AGT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
336510 AGT AAT A
1 AAT AAT A
336517 TTTTTATGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:336493 original size:23 final size:23
Alignment explanation
Indices: 336466--336510 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
336456 AGCTATAAAT
*
336466 AATAATAATAATAATAATAATAA
1 AATAATAACAATAATAATAATAA
* *
336489 AATAATAACAGTAATAGTAATA
1 AATAATAACAATAATAATAATA
336511 GTAATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
AATAATAACAATAATAATAATAA
Found at i:337855 original size:21 final size:21
Alignment explanation
Indices: 337829--337880 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
337819 TAAAATTTTT
337829 TAATTTTAAT-ATTTGTTTTAA
1 TAATTTTAATAATTT-TTTTAA
* *
337850 TAATTTTATTAATTTTTTTAT
1 TAATTTTAATAATTTTTTTAA
337871 TATATTTTAA
1 TA-ATTTTAA
337881 CTAAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TAATTTTAATAATTTTTTTAA
Found at i:338519 original size:2 final size:2
Alignment explanation
Indices: 338514--338543 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
338504 TCTCTCTCTC
*
338514 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
338544 CGTATGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:338549 original size:16 final size:16
Alignment explanation
Indices: 338518--338566 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
338508 TCTCTCTATA
**
338518 TATATATATATATATG
1 TATATATATACGTATG
338534 TATATATATACGTATG
1 TATATATATACGTATG
* *
338550 TATGTATGTACGTATG
1 TATATATATACGTATG
338566 T
1 T
338567 CTTCATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (16 bp):
TATATATATACGTATG
Found at i:339247 original size:31 final size:31
Alignment explanation
Indices: 339212--339354 Score: 108
Period size: 32 Copynumber: 4.6 Consensus size: 31
339202 CTTTAAAAAA
339212 ATAAAATTAAAATATAATATAATATAAATAT
1 ATAAAATTAAAATATAATATAATATAAATAT
*
339243 ATAAATATATAAAAT-TTATATAATATAAAT-T
1 ATAAA-AT-TAAAATATAATATAATATAAATAT
339274 ATTAATATATTAAAAT-T--T-T--TATAAATAT
1 A-TAA-A-ATTAAAATATAATATAATATAAATAT
*
339302 ATAAAATTTAAATATAATAATAATATATAA-A-
1 ATAAAATTAAAATATAAT-ATAATATA-AATAT
339333 ATAAAATATAAATATATGAATA
1 ATAAAAT-TAAA-ATAT-AATA
339355 GTAAAATCTT
Statistics
Matches: 93, Mismatches: 3, Indels: 30
0.74 0.02 0.24
Matches are distributed among these distances:
25 7 0.08
26 2 0.02
27 10 0.11
28 3 0.03
29 1 0.01
30 2 0.02
31 14 0.15
32 34 0.37
33 17 0.18
34 3 0.03
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (31 bp):
ATAAAATTAAAATATAATATAATATAAATAT
Found at i:339262 original size:9 final size:10
Alignment explanation
Indices: 339223--339349 Score: 58
Period size: 10 Copynumber: 13.2 Consensus size: 10
339213 TAAAATTAAA
339223 ATAT-AATAT
1 ATATAAATAT
339232 A-ATATAA-AT
1 ATATA-AATAT
339241 ATATAAATAT
1 ATATAAATAT
*
339251 ATA-AAATTT
1 ATATAAATAT
*
339260 ATATAATATAA
1 ATATAA-ATAT
*
339271 ATTATTAATAT
1 A-TATAAATAT
*
339282 AT-TAAAATTT
1 ATAT-AAATAT
*
339292 TTATAAATAT
1 ATATAAATAT
*
339302 ATA-AAATTT
1 ATATAAATAT
* *
339311 AAATATA-AT
1 ATATAAATAT
339320 A-AT-AATAT
1 ATATAAATAT
*
339328 ATA-AAATAAA
1 ATATAAAT-AT
339338 ATATAAATAT
1 ATATAAATAT
339348 AT
1 AT
339350 GAATAGTAAA
Statistics
Matches: 86, Mismatches: 17, Indels: 29
0.65 0.13 0.22
Matches are distributed among these distances:
7 1 0.01
8 7 0.08
9 28 0.33
10 34 0.40
11 12 0.14
12 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATAAATAT
Found at i:339295 original size:20 final size:19
Alignment explanation
Indices: 339242--339310 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 19
339232 AATATAAATA
339242 TATAAATATATAAAA--TT
1 TATAAATATATAAAATTTT
* *
339259 TATATA-ATAT-AAATTAT
1 TATAAATATATAAAATTTT
*
339276 TA-ATATAT-TAAAATTTT
1 TATAAATATATAAAATTTT
339293 TATAAATATATAAAATTT
1 TATAAATATATAAAATTT
339311 AAATATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 3 0.07
16 8 0.19
17 18 0.43
18 5 0.12
19 8 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAAATATATAAAATTTT
Found at i:341011 original size:2 final size:2
Alignment explanation
Indices: 341004--341042 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
340994 TTCAATACAA
341004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
341043 GGGTTTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:341757 original size:22 final size:23
Alignment explanation
Indices: 341711--341762 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
341701 TCTCTTTCTC
* *
341711 CTCTTTCTCTCTCTATTCATAAT
1 CTCTTTCTCTCCCTATTCACAAT
*
341734 CTCTTTCTC-CCCTATTCACGAT
1 CTCTTTCTCTCCCTATTCACAAT
*
341756 CTTTTTC
1 CTCTTTC
341763 GCTGTTGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.13, C:0.35, G:0.02, T:0.50
Consensus pattern (23 bp):
CTCTTTCTCTCCCTATTCACAAT
Found at i:342942 original size:16 final size:17
Alignment explanation
Indices: 342917--342952 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
342907 TTATTTATTT
*
342917 TTACTAATTTTTAAAAA
1 TTACTAATTTATAAAAA
342934 TTACT-ATTTATAAAAA
1 TTACTAATTTATAAAAA
342950 TTA
1 TTA
342953 TTAAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TTACTAATTTATAAAAA
Found at i:342977 original size:19 final size:20
Alignment explanation
Indices: 342941--342991 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
342931 AAATTACTAT
**
342941 TTATAAAAATTATTAAATAA
1 TTATAAAAATTAAAAAATAA
342961 TTATAAAAA-TAAAAAAT-A
1 TTATAAAAATTAAAAAATAA
*
342979 TATATAATAATTA
1 T-TATAAAAATTA
342992 GAAAGCAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTATAAAAATTAAAAAATAA
Found at i:343171 original size:22 final size:27
Alignment explanation
Indices: 343131--343183 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 27
343121 AAATAAATAA
343131 AAATTATTTATTTTGATTAA-TT-ATT
1 AAATTATTTATTTTGATTAATTTGATT
343156 AAATTA-TT-TTTT-ATTAATTTGATT
1 AAATTATTTATTTTGATTAATTTGATT
343180 AAAT
1 AAAT
343184 AATTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.19
23 6 0.23
24 9 0.35
25 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
AAATTATTTATTTTGATTAATTTGATT
Found at i:343423 original size:39 final size:39
Alignment explanation
Indices: 343378--343468 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 39
343368 ATTTAATTTT
*
343378 TAAATTA-ATAAATTTAAAATAAAAATTAA-ATA-AATATAA
1 TAAATTATA-AAATATAAAAT--AAATTAAGATATAATATAA
343417 TAAATTATAAAATATAAAATAAATTAAGATATAATATAAA
1 TAAATTATAAAATATAAAATAAATTAAGATATAATAT-AA
343457 TATAA-TATAAAA
1 TA-AATTATAAAA
343469 AACAATTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
37 7 0.15
38 3 0.07
39 22 0.48
40 12 0.26
41 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (39 bp):
TAAATTATAAAATATAAAATAAATTAAGATATAATATAA
Found at i:343437 original size:28 final size:27
Alignment explanation
Indices: 343395--343467 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
343385 ATAAATTTAA
* *
343395 AATAAAA-ATTAAATAAATATAATAAAT
1 AATAAAATATAAAATAAAT-TAAGAAAT
* *
343422 TATAAAATATAAAATAAATTAAGATAT
1 AATAAAATATAAAATAAATTAAGAAAT
*
343449 AATATAAATATAATATAAA
1 AATA-AAATATAAAATAAA
343468 AAACAATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 15 0.39
28 23 0.61
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (27 bp):
AATAAAATATAAAATAAATTAAGAAAT
Found at i:343449 original size:34 final size:33
Alignment explanation
Indices: 343377--343492 Score: 118
Period size: 33 Copynumber: 3.5 Consensus size: 33
343367 AATTTAATTT
343377 TTAAAT-TAATAAATT-TAAAATA-AAAATTAAA
1 TTAAATATAATAAATTATAAAATATAAAA-TAAA
343408 -TAAATATAATAAATTATAAAATATAAAATAAA
1 TTAAATATAATAAATTATAAAATATAAAATAAA
* *
343440 TTAAGATATAATATAA--ATATAATATAAAAAACAA
1 TTAA-ATATAATA-AATTATAAAATATAAAATA-AA
*
343474 TTAAAATATAATATATTAT
1 TT-AAATATAATAAATTAT
343493 CAAGCTTAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
30 5 0.07
31 9 0.12
32 11 0.15
33 21 0.29
34 20 0.28
35 6 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (33 bp):
TTAAATATAATAAATTATAAAATATAAAATAAA
Found at i:344272 original size:19 final size:22
Alignment explanation
Indices: 344235--344280 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
344225 AAATAATTTT
344235 TTTATTATATTTCTAAATATAA
1 TTTATTATATTTCTAAATATAA
344257 TTTATTAT-TTT-TAATATATCAA
1 TTTATTATATTTCTAA-ATAT-AA
344279 TT
1 TT
344281 AACTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.14
21 7 0.32
22 12 0.55
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTATATTTCTAAATATAA
Found at i:344317 original size:17 final size:17
Alignment explanation
Indices: 344287--344338 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
344277 AATTAACTTA
344287 AAATATTAAT-TATTTAT
1 AAATA-TAATATATTTAT
344304 AAATATAATATA-TTA-
1 AAATATAATATATTTAT
*
344319 AAATATAGTATATTT-T
1 AAATATAATATATTTAT
344335 AAAT
1 AAAT
344339 GTTATTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 11 0.35
16 13 0.42
17 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AAATATAATATATTTAT
Found at i:344324 original size:15 final size:15
Alignment explanation
Indices: 344284--344332 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
344274 ATCAATTAAC
344284 TTAAAATATTAAT-TA
1 TTAAAATA-TAATATA
344299 TTTATAAATATAATATA
1 -TTA-AAATATAATATA
*
344316 TTAAAATATAGTATA
1 TTAAAATATAATATA
344331 TT
1 TT
344333 TTAAATGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 13 0.43
16 10 0.33
17 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TTAAAATATAATATA
Found at i:344538 original size:46 final size:46
Alignment explanation
Indices: 344469--344574 Score: 171
Period size: 46 Copynumber: 2.3 Consensus size: 46
344459 TATTCTTTTT
*
344469 TTTATTTCA-TTT-AATGAATCAAATTAAATAATACTTATTAAATC
1 TTTATTTAATTTTCAATGAATCAAATTAAATAATACTTATTAAATC
*
344513 TTTATTTAATTTTCAATGAATCAAATTAAATAATACTTATTAAATT
1 TTTATTTAATTTTCAATGAATCAAATTAAATAATACTTATTAAATC
*
344559 TTTATTTAATTCTCAA
1 TTTATTTAATTTTCAA
344575 CAAATACTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 8 0.14
45 3 0.05
46 46 0.81
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (46 bp):
TTTATTTAATTTTCAATGAATCAAATTAAATAATACTTATTAAATC
Found at i:345946 original size:19 final size:18
Alignment explanation
Indices: 345922--345957 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
345912 CTCTAAGAAT
345922 CTTTTTAACTTTTTTTTTC
1 CTTTTT-ACTTTTTTTTTC
*
345941 CTTTTTTCTTTTTTTTT
1 CTTTTTACTTTTTTTTT
345958 TTTTGTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
CTTTTTACTTTTTTTTTC
Found at i:350741 original size:15 final size:14
Alignment explanation
Indices: 350721--350750 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
350711 TTATTAATAT
350721 ATTTATTTAAACTTA
1 ATTTATTTAAA-TTA
350736 ATTTATTTAAATTA
1 ATTTATTTAAATTA
350750 A
1 A
350751 ATAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATTTAAATTA
Found at i:351120 original size:30 final size:30
Alignment explanation
Indices: 351085--351146 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
351075 ATTTTTATTT
*
351085 TAAAAATTAAAATT-TTAAAAAAATATAAA
1 TAAAAAATAAAATTATTAAAAAAATATAAA
* * *
351114 TAAAAAATAACATTATTCAAAAATTATAAA
1 TAAAAAATAAAATTATTAAAAAAATATAAA
351144 TAA
1 TAA
351147 TTGATACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (30 bp):
TAAAAAATAAAATTATTAAAAAAATATAAA
Found at i:352168 original size:14 final size:13
Alignment explanation
Indices: 352151--352200 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
352141 TATAATTTCA
352151 AAAATATAAGAATT
1 AAAATATAA-AATT
*
352165 AAAATATTAAATTT
1 AAAATA-TAAAATT
352179 AATAATATACAAATT
1 AA-AATATA-AAATT
352194 AAAATAT
1 AAAATAT
352201 TTATTTCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:352186 original size:29 final size:31
Alignment explanation
Indices: 352138--352208 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
352128 ATTTCTTATT
352138 TATTATAATTTCAAAAATATA-AGAATTAAAA
1 TATTATAATTTCAAAAATATACA-AATTAAAA
*
352169 TATTA-AATTT-AATAATATACAAATTAAAA
1 TATTATAATTTCAAAAATATACAAATTAAAA
352198 TATT-T-ATTTCA
1 TATTATAATTTCA
352209 CTATAATACA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
28 4 0.11
29 21 0.58
30 6 0.17
31 5 0.14
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (31 bp):
TATTATAATTTCAAAAATATACAAATTAAAA
Found at i:352272 original size:2 final size:2
Alignment explanation
Indices: 352267--352294 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
352257 TATTTCTACC
352267 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
352295 TCATGATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:353640 original size:36 final size:37
Alignment explanation
Indices: 353567--353647 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
353557 TGCATATGTA
* * * *
353567 TTAAATTTTTTATATTTTATTATATTATAATAGTATT
1 TTAATTTTTTTATATTTAACTATATTATAATAATATT
353604 TTAATTTTTTTATATTATAACTATATT-TAA-AATATT
1 TTAATTTTTTTATATT-TAACTATATTATAATAATATT
353640 TTATATTT
1 TTA-ATTT
353648 ATAAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 8 0.21
37 22 0.58
38 8 0.21
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (37 bp):
TTAATTTTTTTATATTTAACTATATTATAATAATATT
Found at i:353659 original size:27 final size:27
Alignment explanation
Indices: 353586--353666 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
353576 TTATATTTTA
* * * * *
353586 TTATATTATAATAGTATTTTAATTTTT
1 TTATATTATAAAAATATTTAAAATATT
**
353613 TTATATTATAACTATATTTAAAATATT
1 TTATATTATAAAAATATTTAAAATATT
*
353640 TTATATTTATAAAAAT-TTTAATATATT
1 TTATA-TTATAAAAATATTTAAAATATT
353667 AATAATTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 36 0.82
28 8 0.18
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
TTATATTATAAAAATATTTAAAATATT
Found at i:353663 original size:18 final size:16
Alignment explanation
Indices: 353625--353690 Score: 55
Period size: 16 Copynumber: 4.0 Consensus size: 16
353615 ATATTATAAC
*
353625 TATATTTAAAATATTT
1 TATATTTAAAAAATTT
353641 TATATTTATAAAAATTT
1 TATATTTA-AAAAATTT
*
353658 TAATATATT-AATAA-TT
1 T-ATAT-TTAAAAAATTT
*
353674 TATATTTTATAAAATTT
1 TATA-TTTAAAAAATTT
353691 AAAATAATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 5 0.12
16 15 0.38
17 14 0.35
18 4 0.10
19 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTTAAAAAATTT
Found at i:354050 original size:19 final size:18
Alignment explanation
Indices: 354026--354080 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
354016 TGTGCGTGGG
354026 TTAAAATATATATTAAAAT
1 TTAAAA-ATATATTAAAAT
* * *
354045 TTAAAAATTTATTTGATAT
1 TTAAAAATATA-TTAAAAT
354064 TTAAAAATA-ATTAAAAT
1 TTAAAAATATATTAAAAT
354081 ATATATTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 5 0.17
18 5 0.17
19 19 0.66
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAAAAATATATTAAAAT
Found at i:354427 original size:21 final size:20
Alignment explanation
Indices: 354399--354448 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
354389 TTATTCATTT
*
354399 ATAAATATAATTAAATTTAAA
1 ATAAATATAATTAAACTT-AA
* *
354420 ATTAATATTATTAAACTTAA
1 ATAAATATAATTAAACTTAA
354440 ATAAATATA
1 ATAAATATA
354449 TAATTTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAATATAATTAAACTTAA
Found at i:354932 original size:22 final size:20
Alignment explanation
Indices: 354907--354957 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
354897 TACACTTTAT
*
354907 TTTTTTATTAATTATTAATATA
1 TTTTTTATTAA-TATT-ATAAA
*
354929 TTTTTAATTTAATATTATAAA
1 TTTTTTA-TTAATATTATAAA
354950 TTTTTTAT
1 TTTTTTAT
354958 AAACCTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 10 0.40
22 10 0.40
23 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTATTAATATTATAAA
Found at i:354955 original size:23 final size:21
Alignment explanation
Indices: 354905--354955 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
354895 TTTACACTTT
*
354905 ATTTTTTTATTAATTATTAAT
1 ATTTTTTTATTAATTATTAAA
*
354926 ATATTTTTAATTTAA-TATTATAA
1 AT-TTTTTTA-TTAATTATTA-AA
354949 ATTTTTT
1 ATTTTTT
354956 ATAAACCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.08
22 16 0.64
23 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTTTTATTAATTATTAAA
Found at i:354984 original size:8 final size:8
Alignment explanation
Indices: 354971--355011 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
354961 CCTAATTTTA
354971 ATATATAC
1 ATATATAC
354979 ATATAT--
1 ATATATAC
354985 A-ATATAC
1 ATATATAC
*
354992 ATATATAT
1 ATATATAC
355000 ATATATAC
1 ATATATAC
355008 ATAT
1 ATAT
355012 TAAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
5 4 0.14
6 1 0.04
7 1 0.04
8 22 0.79
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATATAC
Found at i:354987 original size:21 final size:21
Alignment explanation
Indices: 354971--355011 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
354961 CCTAATTTTA
354971 ATATATACATATATAATATAC
1 ATATATACATATATAATATAC
*
354992 ATATATATATATATACATAT
1 ATATATACATATATA-ATAT
355012 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATATACATATATAATATAC
Found at i:354991 original size:13 final size:14
Alignment explanation
Indices: 354971--355004 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
354961 CCTAATTTTA
354971 ATATATACATATAT
1 ATATATACATATAT
354985 A-ATATACATATAT
1 ATATATACATATAT
354998 ATATATA
1 ATATATA
355005 TACATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:355039 original size:17 final size:17
Alignment explanation
Indices: 355019--355080 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
355009 TATTAAAAAA
355019 ATATATAAAATATTAAT
1 ATATATAAAATATTAAT
** *
355036 ATATATATGATTTTAAT
1 ATATATAAAATATTAAT
*
355053 ATATATTTAATATATTAA-
1 ATATA--TAAAATATTAAT
*
355071 AAATATAAAA
1 ATATATAAAA
355081 AAAAGTATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
16 4 0.11
17 19 0.54
18 4 0.11
19 8 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATATATAAAATATTAAT
Found at i:355053 original size:65 final size:64
Alignment explanation
Indices: 354968--355093 Score: 148
Period size: 65 Copynumber: 2.0 Consensus size: 64
354958 AAACCTAATT
* * *
354968 TTAATATATACATATATAATATACATAT-ATATATATATACATATTAAAAAAA-TATATAAAATA
1 TTAATATATACATATATAATATACATATAATATAT-TAAAAATATAAAAAAAAGTATATAAAATA
* * * *
355031 TTAATATATATATGATTTTAATATATATTTAATATATTAAAAATATAAAAAAAAGTATATAAA
1 TTAATATATACAT-A-TATAATATACATATAATATATTAAAAATATAAAAAAAAGTATATAAA
355094 TTTTTTTTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
63 12 0.23
64 1 0.02
65 25 0.48
66 14 0.27
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (64 bp):
TTAATATATACATATATAATATACATATAATATATTAAAAATATAAAAAAAAGTATATAAAATA
Found at i:355394 original size:22 final size:22
Alignment explanation
Indices: 355368--355409 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
355358 TGTAACTTAT
* * *
355368 AAATTACTAATTAATTAAAATA
1 AAATTAATAATAAAATAAAATA
355390 AAATTAATAATAAAATAAAA
1 AAATTAATAATAAAATAAAA
355410 AGTAATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATTAATAATAAAATAAAATA
Found at i:355403 original size:17 final size:18
Alignment explanation
Indices: 355383--355419 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
355373 ACTAATTAAT
*
355383 TAAAAT-AAAATTAATAA
1 TAAAATAAAAAGTAATAA
355400 TAAAATAAAAAGTAATAA
1 TAAAATAAAAAGTAATAA
355418 TA
1 TA
355420 TTTTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
TAAAATAAAAAGTAATAA
Found at i:355415 original size:15 final size:14
Alignment explanation
Indices: 355395--355447 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
355385 AAATAAAATT
355395 AATAATAAAATAAA
1 AATAATAAAATAAA
* **
355409 AAGTAATAATATTTTA
1 AA-TAATAA-AATAAA
355425 AATAATAAAATTAAA
1 AATAATAAAA-TAAA
355440 AATAATAA
1 AATAATAA
355448 TATTTTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 3 0.10
15 22 0.73
16 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
AATAATAAAATAAA
Found at i:355426 original size:18 final size:17
Alignment explanation
Indices: 355405--355456 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
355395 AATAATAAAA
355405 TAAAAAGTAATAATATTT
1 TAAAAA-TAATAATATTT
*
355423 T--AAATAATAA-A-AT
1 TAAAAATAATAATATTT
355436 TAAAAATAATAATATTT
1 TAAAAATAATAATATTT
355453 TAAA
1 TAAA
355457 TTGAGAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
13 2 0.07
14 1 0.04
15 15 0.54
16 4 0.14
17 5 0.18
18 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAAAATAATAATATTT
Found at i:355431 original size:30 final size:30
Alignment explanation
Indices: 355395--355457 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
355385 AAATAAAATT
355395 AATAATAAAA-TAAAAAGTAATAATATTTTA
1 AATAATAAAATTAAAAA-TAATAATATTTTA
355425 AATAATAAAATTAAAAATAATAATATTTTA
1 AATAATAAAATTAAAAATAATAATATTTTA
355455 AAT
1 AAT
355458 TGAGAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AATAATAAAATTAAAAATAATAATATTTTA
Found at i:355457 original size:15 final size:15
Alignment explanation
Indices: 355412--355457 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
355402 AAATAAAAAG
355412 TAATAATATTTTAAA
1 TAATAATATTTTAAA
* **
355427 TAATAAAATTAAAAA
1 TAATAATATTTTAAA
355442 TAATAATATTTTAAA
1 TAATAATATTTTAAA
355457 T
1 T
355458 TGAGAATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATATTTTAAA
Found at i:356308 original size:26 final size:26
Alignment explanation
Indices: 356279--356332 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
356269 TTTTTAAACT
*
356279 ATCATTAAAAATGATATTA-TTAAAAA
1 ATCATCAAAAAT-ATATTATTTAAAAA
*
356305 ATCATCAAATATATATTATTTAAAAA
1 ATCATCAAAAATATATTATTTAAAAA
356331 AT
1 AT
356333 ATATTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (26 bp):
ATCATCAAAAATATATTATTTAAAAA
Found at i:356349 original size:19 final size:17
Alignment explanation
Indices: 356310--356351 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
356300 AAAAAATCAT
*
356310 CAAATATATATTATTTA
1 CAAAAATATATTATTTA
356327 -AAAAATATATTATTAATA
1 CAAAAATATATTATT--TA
356345 CAAAAAT
1 CAAAAAT
356352 CGTCAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 13 0.62
18 2 0.10
19 6 0.29
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
CAAAAATATATTATTTA
Found at i:356718 original size:34 final size:34
Alignment explanation
Indices: 356679--356777 Score: 100
Period size: 33 Copynumber: 3.0 Consensus size: 34
356669 TAAAAAATTT
*
356679 TTAAAATATATTATATAAAAATATTATAAATATA
1 TTAAAATATATTATATAATAATATTATAAATATA
356713 TT-AAA-AT-TTATATAATAATAATTATTAAAT-TA
1 TTAAAATATATTATATAATAAT-ATTA-TAAATATA
* * * *
356745 TTAAAATTTA-TAAATAATATTATTTTAAATATA
1 TTAAAATATATTATATAATAATATTATAAATATA
356778 AAATTTAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
31 11 0.20
32 15 0.28
33 16 0.30
34 12 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
TTAAAATATATTATATAATAATATTATAAATATA
Found at i:356747 original size:32 final size:31
Alignment explanation
Indices: 356689--356790 Score: 122
Period size: 32 Copynumber: 3.3 Consensus size: 31
356679 TTAAAATATA
*
356689 TTATATAAAAATATTA-TAAATATATTAAAAT
1 TTATATAATAATATTATTAAAT-TATTAAAAT
356720 TTATATAATAATAATTATTAAATTATTAAAAT
1 TTATATAATAAT-ATTATTAAATTATTAAAAT
356752 TTATA-AATAATATTATTTTAAA-TA-TAAAAT
1 TTATATAATAATATTA--TTAAATTATTAAAAT
356782 TTAATATAA
1 TT-ATATAA
356791 ATATACAAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 11
0.84 0.01 0.14
Matches are distributed among these distances:
30 12 0.19
31 22 0.34
32 25 0.39
33 5 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TTATATAATAATATTATTAAATTATTAAAAT
Found at i:356758 original size:17 final size:17
Alignment explanation
Indices: 356696--356759 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
356686 ATATTATATA
356696 AAAATATTATAAATATATT
1 AAAAT-TTATAAAT-TATT
356715 AAAATTTATATAA-TA--
1 AAAATTTATA-AATTATT
*
356730 ATAA-TTATTAAATTATT
1 AAAATTTA-TAAATTATT
356747 AAAATTTATAAAT
1 AAAATTTATAAAT
356760 AATATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
14 5 0.14
15 7 0.19
17 10 0.27
18 8 0.22
19 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTTATAAATTATT
Found at i:357285 original size:14 final size:15
Alignment explanation
Indices: 357266--357303 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
357256 ATTTTATAAA
357266 TTAAATA-AAAAATT
1 TTAAATATAAAAATT
* *
357280 TTAAATATATAATTT
1 TTAAATATAAAAATT
357295 TTAAATATA
1 TTAAATATA
357304 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAAAAATT
Found at i:357537 original size:15 final size:15
Alignment explanation
Indices: 357495--357570 Score: 66
Period size: 15 Copynumber: 5.0 Consensus size: 15
357485 TATATAGTAT
*
357495 ATATAAATTTATATAA
1 ATATAAATAT-TATAA
* *
357511 ATATGTAATATTTTAA
1 ATAT-AAATATTATAA
*
357527 ATATAAATATTATAC
1 ATATAAATATTATAA
*
357542 ATAAAAATA-TATAA
1 ATATAAATATTATAA
357556 ATAT-AATATATATAA
1 ATATAAATAT-TATAA
357571 TATTTTCTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
13 4 0.08
14 7 0.15
15 21 0.44
16 12 0.25
17 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (15 bp):
ATATAAATATTATAA
Found at i:357879 original size:19 final size:19
Alignment explanation
Indices: 357844--357903 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
357834 AAATTATGAT
*
357844 ATAAAAAATAATGTAAATA
1 ATAAAAAATAATATAAATA
357863 ATAAATAAAT-ATATAAATA
1 ATAAA-AAATAATATAAATA
* * *
357882 TATTAAAATTTATATAAA-A
1 -ATAAAAAATAATATAAATA
357901 ATA
1 ATA
357904 TATTATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 2 0.06
19 17 0.50
20 15 0.44
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAAAAAATAATATAAATA
Found at i:357895 original size:12 final size:11
Alignment explanation
Indices: 357880--357945 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
357870 AATATATAAA
357880 TATATTAAAAT
1 TATATTAAAAT
*
357891 T-TATATAAAAA
1 TATAT-TAAAAT
*
357902 TATATTATTAA-
1 TATATTA-AAAT
357913 TATATTAAAAT
1 TATATTAAAAT
357924 T-TA-TAAAAT
1 TATATTAAAAT
*
357933 TATAATAAAAT
1 TATATTAAAAT
357944 TA
1 TA
357946 AAATATGACA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 7 0.15
10 9 0.20
11 25 0.54
12 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATTAAAAT
Found at i:357897 original size:20 final size:20
Alignment explanation
Indices: 357872--357944 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
357862 AATAAATAAA
357872 TATATAAATATATTAAAATT
1 TATATAAATATATTAAAATT
*
357892 TATATAAA-A-A-T-ATA-T
1 TATATAAATATATTAAAATT
357907 TAT-T-AATATATTAAAATT
1 TATATAAATATATTAAAATT
*
357925 TATA-AAATTATAATAAAATT
1 TATATAAA-TATATTAAAATT
357945 AAAATATGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 5 0.12
16 3 0.07
17 3 0.07
18 5 0.12
19 3 0.07
20 19 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATAAATATATTAAAATT
Found at i:357918 original size:33 final size:35
Alignment explanation
Indices: 357860--357928 Score: 106
Period size: 33 Copynumber: 2.0 Consensus size: 35
357850 AATAATGTAA
357860 ATAATAAATAAATATATAAATATATTAAAATTTAT
1 ATAATAAATAAATATATAAATATATTAAAATTTAT
* *
357895 ATAA-AAATATAT-TATTAATATATTAAAATTTAT
1 ATAATAAATAAATATATAAATATATTAAAATTTAT
357928 A
1 A
357929 AAATTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 21 0.66
34 7 0.22
35 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
ATAATAAATAAATATATAAATATATTAAAATTTAT
Found at i:357921 original size:22 final size:22
Alignment explanation
Indices: 357865--357942 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
357855 TGTAAATAAT
* *
357865 AAATAAATATATAAATATATTA
1 AAATATATATAAAAATATATTA
*
357887 AAATTTATATAAAAATATATTA
1 AAATATATATAAAAATATATTA
* *
357909 TTAATATAT-T-AAAATTTA-TA
1 -AAATATATATAAAAATATATTA
357929 AAAT-TATAATAAAA
1 AAATATAT-ATAAAA
357943 TTAAAATATG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.07
19 3 0.07
20 3 0.07
21 10 0.22
22 20 0.44
23 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATATATAAAAATATATTA
Found at i:358883 original size:20 final size:21
Alignment explanation
Indices: 358848--358886 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
358838 AGATAAATAT
358848 AAATATAGTAAATAATTTAAC
1 AAATATAGTAAATAATTTAAC
*
358869 AAATAT-GTAATTAATTTA
1 AAATATAGTAAATAATTTA
358887 GTGGTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
AAATATAGTAAATAATTTAAC
Found at i:359895 original size:15 final size:15
Alignment explanation
Indices: 359875--359952 Score: 52
Period size: 15 Copynumber: 5.1 Consensus size: 15
359865 TTATATAATA
*
359875 ATTAAATTTTAATTT
1 ATTAAATTTAAATTT
359890 ATTAAATTTAAATTTTT
1 ATTAAATTTAAA--TTT
* *
359907 TTATAAATTTAAATAT
1 AT-TAAATTTAAATTT
**
359923 -TTAAAGATAACA-TT
1 ATTAAATTTAA-ATTT
*
359937 ATTTAATTTAAATTT
1 ATTAAATTTAAATTT
359952 A
1 A
359953 AATAATAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
14 9 0.19
15 23 0.48
16 2 0.04
17 4 0.08
18 10 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (15 bp):
ATTAAATTTAAATTT
Found at i:359915 original size:18 final size:20
Alignment explanation
Indices: 359876--359925 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
359866 TATATAATAA
359876 TTAAATTTTAATTTATTAAAT
1 TTAAATTTT-ATTTATTAAAT
359897 TTAAATTTT-TTTA-TAAAT
1 TTAAATTTTATTTATTAAAT
359915 TTAAATATTTA
1 TTAAAT-TTTA
359926 AAGATAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.41
19 7 0.26
21 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAAATTTTATTTATTAAAT
Found at i:359952 original size:53 final size:51
Alignment explanation
Indices: 359891--360025 Score: 141
Period size: 53 Copynumber: 2.6 Consensus size: 51
359881 TTTTAATTTA
** *
359891 TTAAATTTAAAT-TTTTTTATAAATTTAAATATTTAAAGATAACATTATTTAAT
1 TTAAATTTAAATATAATATATAAATTTAAAT-TTTAAA-ATAACATTA-TTAAT
* **
359944 TTAAATTTAAATAATAATATATGAATTTAAATTTTAAAATAATTTTATTAAT
1 TTAAATTTAAAT-ATAATATATAAATTTAAATTTTAAAATAACATTATTAAT
*
359996 TTAAATTTAAATAT--TATAAAAATTATAAAT
1 TTAAATTTAAATATAATATATAAATT-TAAAT
360026 AACTGTTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
49 8 0.11
50 5 0.07
51 2 0.03
52 17 0.24
53 19 0.27
54 6 0.08
55 14 0.20
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
TTAAATTTAAATATAATATATAAATTTAAATTTTAAAATAACATTATTAAT
Found at i:359975 original size:26 final size:27
Alignment explanation
Indices: 359941--360008 Score: 95
Period size: 26 Copynumber: 2.6 Consensus size: 27
359931 AACATTATTT
359941 AATTTAAATTTAAATAATAA-TATATG
1 AATTTAAATTTAAATAATAATTATATG
* * *
359967 AATTTAAATTTTAA-AATAATTTTATT
1 AATTTAAATTTAAATAATAATTATATG
359993 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
360009 TTATAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 5 0.14
26 30 0.83
27 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
AATTTAAATTTAAATAATAATTATATG
Found at i:361074 original size:22 final size:20
Alignment explanation
Indices: 361048--361094 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
361038 AAATTTAAAA
*
361048 TAATTATCTTGAATCATTTATT
1 TAATTATCTTAAAT--TTTATT
*
361070 TAATTATTTTAAATTTTATT
1 TAATTATCTTAAATTTTATT
361090 TAATT
1 TAATT
361095 TAAGATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TAATTATCTTAAATTTTATT
Found at i:361102 original size:24 final size:26
Alignment explanation
Indices: 361075--361136 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 26
361065 TTATTTAATT
*
361075 ATTTTAAATTTTATTTA-AT-TTAAG
1 ATTTTAAATTTTATTTAGATATTAAA
*
361099 A-TTTAAATATT-TTTAGATATTAAA
1 ATTTTAAATTTTATTTAGATATTAAA
*
361123 ATTAT-AATTTTATT
1 ATTTTAAATTTTATT
361137 ACGTTACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
22 4 0.13
23 11 0.37
24 11 0.37
25 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
ATTTTAAATTTTATTTAGATATTAAA
Found at i:361349 original size:14 final size:14
Alignment explanation
Indices: 361332--361360 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
361322 TATCTTCTTT
361332 TTATATTTTGTTCA
1 TTATATTTTGTTCA
361346 TTATATTTTGTTCA
1 TTATATTTTGTTCA
361360 T
1 T
361361 GTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
TTATATTTTGTTCA
Found at i:362614 original size:18 final size:19
Alignment explanation
Indices: 362593--362643 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
362583 TTATTTTATT
362593 ATTTAAATATATTTTT-AA
1 ATTTAAATATATTTTTAAA
362611 ATTT-AATATTATTTTTAAA
1 ATTTAAATA-TATTTTTAAA
*
362630 ATTTTAAAAATATT
1 A-TTTAAATATATT
362644 AAAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 3 0.11
20 7 0.25
21 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAAATATATTTTTAAA
Found at i:363747 original size:23 final size:23
Alignment explanation
Indices: 363721--363764 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
363711 GCTGGACGAA
*
363721 AAAATGAAAAAATATTTTAAAAG
1 AAAAGGAAAAAATATTTTAAAAG
*
363744 AAAAGGAAAAATTATTTTAAA
1 AAAAGGAAAAAATATTTTAAA
363765 TCCTACGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (23 bp):
AAAAGGAAAAAATATTTTAAAAG
Found at i:364860 original size:62 final size:62
Alignment explanation
Indices: 364765--364887 Score: 246
Period size: 62 Copynumber: 2.0 Consensus size: 62
364755 ACTTTTTCTT
364765 TTTTTTTTTTTTACCAGATAGGTTAAGAGAATGAATTCTCCAAATGCAATTTCAGGGGAATC
1 TTTTTTTTTTTTACCAGATAGGTTAAGAGAATGAATTCTCCAAATGCAATTTCAGGGGAATC
364827 TTTTTTTTTTTTACCAGATAGGTTAAGAGAATGAATTCTCCAAATGCAATTTCAGGGGAAT
1 TTTTTTTTTTTTACCAGATAGGTTAAGAGAATGAATTCTCCAAATGCAATTTCAGGGGAAT
364888 GCATTCATTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (62 bp):
TTTTTTTTTTTTACCAGATAGGTTAAGAGAATGAATTCTCCAAATGCAATTTCAGGGGAATC
Found at i:370188 original size:51 final size:51
Alignment explanation
Indices: 370130--370231 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 51
370120 ATTATTATAT
370130 TTTTAATAAAATATTT-A-ATAAATCA-AATATGATAATATAATTTTTTTAATA
1 TTTTAATAAAAT-TTTCATATAAATCATAA-ATGATAATATAA-TTTTTTAATA
* * * *
370181 TTTTAATAATATTTTCATATATATCATAAATTATAATATTATTTTTTAATA
1 TTTTAATAAAATTTTCATATAAATCATAAATGATAATATAATTTTTTAATA
370232 ATTATATTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
50 3 0.07
51 22 0.50
52 17 0.39
53 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (51 bp):
TTTTAATAAAATTTTCATATAAATCATAAATGATAATATAATTTTTTAATA
Done.