Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold356
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: 432500
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 4
Found at i:357423 original size:16 final size:15
Alignment explanation
Indices: 357321--357426 Score: 62
Period size: 16 Copynumber: 7.1 Consensus size: 15
357311 TATAATATAA
*
357321 ATAAAATAT-TAAAT
1 ATAAAATTTATAAAT
*
357335 ATATAAA-TAATATAAT
1 ATA-AAATTTATA-AAT
* *
357351 AT-AAATATATATAT
1 ATAAAATTTATAAAT
*
357365 -TAAAATTTATATAAA
1 ATAAAATTTATA-AAT
*
357380 AT-AAA-TTATTAAT
1 ATAAAATTTATAAAT
357393 ATTAAAATTTATAAAT
1 A-TAAAATTTATAAAT
*
357409 ATAAAATATTTTAAAT
1 ATAAAAT-TTATAAAT
357425 AT
1 AT
357427 GTGTTAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
13 4 0.06
14 21 0.30
15 21 0.30
16 23 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAAATTTATAAAT
Found at i:358293 original size:16 final size:16
Alignment explanation
Indices: 358272--358303 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
358262 TTTTATATAC
358272 TTTTAATCATAATTCA
1 TTTTAATCATAATTCA
*
358288 TTTTAATTATAATTCA
1 TTTTAATCATAATTCA
358304 CATGTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAATCATAATTCA
Found at i:361677 original size:16 final size:15
Alignment explanation
Indices: 361650--361687 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
361640 ATTTTAAATA
361650 TGTTTT-AATTTTTAT
1 TGTTTTGAATTTTT-T
*
361665 TTTTTTGAATTTTTT
1 TGTTTTGAATTTTTT
361680 TGTTTTGA
1 TGTTTTGA
361688 TAATGATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.74
Consensus pattern (15 bp):
TGTTTTGAATTTTTT
Found at i:362732 original size:48 final size:48
Alignment explanation
Indices: 362662--362757 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
362652 TTTGGCATTT
362662 TTTTTCTTATTCTTTATTTGTATTTTAGCATGTTTATTAAACAAGCAA
1 TTTTTCTTATTCTTTATTTGTATTTTAGCATGTTTATTAAACAAGCAA
362710 TTTTTCTTATTCTTTATTTGTATTTTAGCATGTTTATTAAACAAGCAA
1 TTTTTCTTATTCTTTATTTGTATTTTAGCATGTTTATTAAACAAGCAA
362758 ACAATATGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (48 bp):
TTTTTCTTATTCTTTATTTGTATTTTAGCATGTTTATTAAACAAGCAA
Found at i:368684 original size:16 final size:16
Alignment explanation
Indices: 368663--368723 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
368653 AATTCGAGTA
368663 AATATATATTTAATAT
1 AATATATATTTAATAT
* *
368679 AATATATATTAAATTT
1 AATATATATTTAATAT
*
368695 AA-ATAATAATTAATAT
1 AATAT-ATATTTAATAT
*
368711 TATA-ATTATTTAA
1 AATATA-TATTTAA
368724 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 3 0.09
16 31 0.89
17 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATATATTTAATAT
Found at i:368777 original size:13 final size:12
Alignment explanation
Indices: 368738--368795 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
368728 TTAAAATTTT
*
368738 TTATTATTAATAT
1 TTATTA-TAATAA
*
368751 TTATCATTAATAA
1 TTATTA-TAATAA
368764 TTATTATAATTAA
1 TTATTATAA-TAA
* *
368777 TTATAATAATAT
1 TTATTATAATAA
368789 TTATTAT
1 TTATTAT
368796 TTAAATCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TTATTATAATAA
Found at i:369239 original size:17 final size:18
Alignment explanation
Indices: 369204--369242 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
369194 ATATTTTAAT
* *
369204 AAATACAAATATTTTAAA
1 AAATACAAAAATTTAAAA
369222 AAATA-AAAAATTTAAAA
1 AAATACAAAAATTTAAAA
369239 AAAT
1 AAAT
369243 TATATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATACAAAAATTTAAAA
Found at i:369266 original size:17 final size:17
Alignment explanation
Indices: 369194--369266 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 17
369184 ATTTATATCT
369194 ATATTTTAATAAATACAA
1 ATATTTTAATAAATA-AA
*
369212 ATATTTTAAAAAATAAA
1 ATATTTTAATAAATAAA
* *
369229 A-AATTTAA-AAA-AATT
1 ATATTTTAATAAATAA-A
369244 ATATTTT-ATAAATACAA
1 ATATTTTAATAAATA-AA
369261 ATATTT
1 ATATTT
369267 AAAAATATAC
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.04
15 5 0.11
16 13 0.29
17 10 0.22
18 15 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATTTTAATAAATAAA
Found at i:369267 original size:16 final size:16
Alignment explanation
Indices: 369194--369273 Score: 67
Period size: 16 Copynumber: 4.9 Consensus size: 16
369184 ATTTATATCT
369194 ATATTTTAATAAATACAA
1 ATATTTTAA-AAATA-AA
369212 ATATTTTAAAAAATAAA
1 ATATTTT-AAAAATAAA
* *
369229 A-AATTTAAAAA-AATT
1 ATATTTTAAAAATAA-A
*
369244 ATATTTTATAAATACAA
1 ATATTTTAAAAATA-AA
369261 ATA-TTTAAAAATA
1 ATATTTTAAAAATA
369274 TACATTCAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.04
15 6 0.12
16 21 0.41
17 7 0.14
18 13 0.25
19 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATTTTAAAAATAAA
Found at i:369856 original size:23 final size:26
Alignment explanation
Indices: 369825--369881 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
369815 ATATATATTT
369825 TTTTAATATATTAAT-AAAAT-TATA
1 TTTTAATATATTAATCAAAATATATA
* *
369849 TTTT-ATATTTTTATCAAAATATATA
1 TTTTAATATATTAATCAAAATATATA
369874 TTGTTAAT
1 TT-TTAAT
369882 GGCTGTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.30
24 9 0.33
25 6 0.22
26 2 0.07
27 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTTAATATATTAATCAAAATATATA
Found at i:372586 original size:16 final size:16
Alignment explanation
Indices: 372549--372586 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
372539 TTATTTTTTT
*
372549 ATTTAAGTTTGAATTA
1 ATTTAAGTTTGAACTA
*
372565 AATTAAGTTTGAACTA
1 ATTTAAGTTTGAACTA
372581 ATTTAA
1 ATTTAA
372587 AAAATTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (16 bp):
ATTTAAGTTTGAACTA
Found at i:372637 original size:26 final size:26
Alignment explanation
Indices: 372608--372661 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
372598 ATTATTTAAA
372608 AAATATAAAAAATATTTTTAAT-AATT
1 AAATATAAAAAAT-TTTTTAATCAATT
* * *
372634 AAATTTAAATAATTTTTTTATCAATT
1 AAATATAAAAAATTTTTTAATCAATT
372660 AA
1 AA
372662 TAATAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATATAAAAAATTTTTTAATCAATT
Found at i:377653 original size:23 final size:25
Alignment explanation
Indices: 377627--377729 Score: 65
Period size: 23 Copynumber: 4.2 Consensus size: 25
377617 GTAATTCGTG
377627 TATTTATAT-TATAAAA-ATTATTA
1 TATTTATATATATAAAATATTATTA
* *
377650 TATTATAATTATATTTAAAATATTTTTA
1 TATT-T-A-TATATATAAAATATTATTA
**
377678 TATTTATATAATATTTAAT-TTATTA
1 TATTTATAT-ATATAAAATATTATTA
* *
377703 TA--TAAAT-TTTAAAATATTATTTA
1 TATTTATATATATAAAATATTA-TTA
377726 TATT
1 TATT
377730 ATTTTATATT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
21 5 0.08
22 3 0.05
23 13 0.22
24 1 0.02
25 11 0.18
26 10 0.17
27 7 0.12
28 10 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTATATATATAAAATATTATTA
Found at i:377678 original size:28 final size:27
Alignment explanation
Indices: 377630--377695 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
377620 ATTCGTGTAT
377630 TTATATTATAAAAATTATTATA-TTATAA
1 TTATATT-TAAAAATTATTATATTTAT-A
*
377658 TTATATTTAAAATATTTTTATATTTATA
1 TTATATTTAAAA-ATTATTATATTTATA
*
377686 TAATATTTAA
1 TTATATTTAA
377696 TTTATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 5 0.15
28 25 0.74
29 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTATATTTAAAAATTATTATATTTATA
Found at i:377680 original size:17 final size:19
Alignment explanation
Indices: 377658--377693 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
377648 TATATTATAA
377658 TTATATTTA-A-AATATTT
1 TTATATTTATATAATATTT
377675 TTATATTTATATAATATTT
1 TTATATTTATATAATATTT
377694 AATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATTTATATAATATTT
Found at i:377694 original size:17 final size:17
Alignment explanation
Indices: 377647--377700 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
377637 ATAAAAATTA
* *
377647 TTATATTATAATTATAT
1 TTATATAATATTTATAT
377664 TTA-A-AATATTTTTATAT
1 TTATATAATA--TTTATAT
377681 TTATATAATATTTA-AT
1 TTATATAATATTTATAT
377697 TTAT
1 TTAT
377701 TATATAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.10
16 7 0.23
17 16 0.52
18 1 0.03
19 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATAATATTTATAT
Found at i:378766 original size:16 final size:16
Alignment explanation
Indices: 378745--378776 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
378735 TTGAACTTCA
378745 AATTTAATATTTATTT
1 AATTTAATATTTATTT
*
378761 AATTTAATTTTTATTT
1 AATTTAATATTTATTT
378777 CAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTTAATATTTATTT
Found at i:382676 original size:33 final size:31
Alignment explanation
Indices: 382607--382686 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
382597 GTGAAAAAGT
*
382607 TTTATTAAAATATATTATATAAATTAATTAA
1 TTTATAAAAATATATTATATAAATTAATTAA
* * *
382638 TTTATAAAAATATCTTCATAATATATTATTTAA
1 TTTATAAAAATATATT-AT-ATAAATTAATTAA
382671 TTTAT-AAAATAT-TTAT
1 TTTATAAAAATATATTAT
382687 TTTTTATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
30 2 0.05
31 16 0.37
32 9 0.21
33 16 0.37
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (31 bp):
TTTATAAAAATATATTATATAAATTAATTAA
Found at i:382726 original size:20 final size:19
Alignment explanation
Indices: 382694--382749 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
382684 TATTTTTTAT
*
382694 TATT-TTTTAAATTAAGTCAA
1 TATTATTTT-AATTAAAT-AA
382714 TATTATTTTAATTAAATAA
1 TATTATTTTAATTAAATAA
*
382733 TATTAAATTTAATTAAA
1 TATT-ATTTTAATTAAA
382750 ATTTTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.19
20 22 0.69
21 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTATTTTAATTAAATAA
Found at i:384408 original size:21 final size:22
Alignment explanation
Indices: 384384--384438 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
384374 TTTTAAAGCT
**
384384 TTTTCTTTTTTTTTCCTAA-AA
1 TTTTCTTTTTTTTTCAAAATAA
*
384405 TTTTCTCTATTTTTTCAAAATAA
1 TTTTCT-TTTTTTTTCAAAATAA
384428 TTTT-TTTTTTT
1 TTTTCTTTTTTT
384439 CCATAAGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.39
22 11 0.39
23 6 0.21
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTCTTTTTTTTTCAAAATAA
Found at i:385491 original size:15 final size:17
Alignment explanation
Indices: 385473--385520 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
385463 ATTTAAATAA
385473 AAATT-TAAATT-TTTT
1 AAATTATAAATTATTTT
*
385488 AAATTATAATTTATTTT
1 AAATTATAAATTATTTT
385505 -AATTCATAAA-TATTTT
1 AAATT-ATAAATTATTTT
385521 TTTTTACAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 5 0.18
16 15 0.54
17 8 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTATAAATTATTTT
Found at i:386928 original size:15 final size:16
Alignment explanation
Indices: 386904--386938 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
386894 AAATTTTAAA
386904 ATATTCATG-TATATC
1 ATATTCATGTTATATC
*
386919 ATATTTATGTTATATC
1 ATATTCATGTTATATC
386935 ATAT
1 ATAT
386939 GTTGTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (16 bp):
ATATTCATGTTATATC
Found at i:390338 original size:14 final size:14
Alignment explanation
Indices: 390319--390347 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
390309 CATTCACATG
390319 TTGCTCATATATTA
1 TTGCTCATATATTA
390333 TTGCTCATATATTA
1 TTGCTCATATATTA
390347 T
1 T
390348 GATGTTAATT
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:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TTGCTCATATATTA
Found at i:392242 original size:20 final size:20
Alignment explanation
Indices: 392220--392256 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
392210 TTTAATTTAA
392220 AAAATT-TAATTTATTTATT
1 AAAATTATAATTTATTTATT
*
392239 AAAATTATATTTTATTTA
1 AAAATTATAATTTATTTA
392257 ACTCAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAAATTATAATTTATTTATT
Found at i:392449 original size:2 final size:2
Alignment explanation
Indices: 392442--392474 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
392432 ACATACGTAC
392442 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 A
392475 AGGGAAGACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:394593 original size:120 final size:120
Alignment explanation
Indices: 394380--394625 Score: 323
Period size: 120 Copynumber: 2.0 Consensus size: 120
394370 GACAGCAGGG
* * * * * * *
394380 TTCAACCCACGGCTCCTCCTCTTAACGAAAACGCGTCTCATGGCGCTTCCCAAGCAGGATCAGGA
1 TTCAAACCACAGCTCCTCCTCTCAACGAAAACGCGTCGCATAGCGCTGCCCAACCAGGATCAGGA
* * * * *
394445 TCAAGATTTAGTTCTTTTAGAAGGATGCTCAGTAGGTAACGATCGTCAAGCACGA
66 TCAAGATTTAGTTCCTTTAGAAGAATGCTCAGTAGGGAAAGATCATCAAGCACGA
* *
394500 TTCAAACCACAGCTCCTCCTCTCGACGAAAACGCGTCGCATAGTGCTGCCCAACCAGGATCAGGA
1 TTCAAACCACAGCTCCTCCTCTCAACGAAAACGCGTCGCATAGCGCTGCCCAACCAGGATCAGGA
* * *
394565 TCAAGATTT-GATTCCTTTAGAAGAATGCTCTGTAGGGAAAGATCATCATGCAGGA
66 TCAAGATTTAG-TTCCTTTAGAAGAATGCTCAGTAGGGAAAGATCATCAAGCACGA
394620 TTCAAA
1 TTCAAA
394626 GTTGCGCAGA
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
119 1 0.01
120 107 0.99
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (120 bp):
TTCAAACCACAGCTCCTCCTCTCAACGAAAACGCGTCGCATAGCGCTGCCCAACCAGGATCAGGA
TCAAGATTTAGTTCCTTTAGAAGAATGCTCAGTAGGGAAAGATCATCAAGCACGA
Found at i:402156 original size:41 final size:41
Alignment explanation
Indices: 402076--402161 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
402066 ACTCAAATCG
*
402076 ATTTAAATTAAATTATTATTTATATAATAAAAATAATTTTT
1 ATTTAAATTAAATTATTATTTATATAATAAAAATAATTTTA
* *
402117 ATTTAAATTTAATTATAAATATTTATA-AAT-ATAAT-ATTTTA
1 ATTTAAATTAAATTAT---TATTTATATAATAAAAATAATTTTA
402158 ATTT
1 ATTT
402162 TTTAAACTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
41 24 0.62
42 4 0.10
43 3 0.08
44 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (41 bp):
ATTTAAATTAAATTATTATTTATATAATAAAAATAATTTTA
Found at i:402588 original size:21 final size:21
Alignment explanation
Indices: 402536--402603 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 21
402526 TTTTAATATT
402536 TATAATTTTTTTAATCAAATAAGT-
1 TATAA-TTTTTTAAT-AAA-AA-TA
402560 TATAATTTTTTAATAAAAATA
1 TATAATTTTTTAATAAAAATA
*
402581 TATGATTTTTTAAT-AAAATA
1 TATAATTTTTTAATAAAAATA
402601 TAT
1 TAT
402604 TTTTAATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
20 10 0.24
21 15 0.36
22 3 0.07
23 9 0.21
24 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (21 bp):
TATAATTTTTTAATAAAAATA
Found at i:402608 original size:16 final size:16
Alignment explanation
Indices: 402587--402618 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
402577 AATATATGAT
402587 TTTTTAATAAAATATA
1 TTTTTAATAAAATATA
*
402603 TTTTTAATAATATATA
1 TTTTTAATAAAATATA
402619 AGACTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTTAATAAAATATA
Found at i:403175 original size:11 final size:10
Alignment explanation
Indices: 403149--403173 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
403139 AGAAAATTAA
403149 TTTTTAATAT
1 TTTTTAATAT
403159 TTTTTAATAT
1 TTTTTAATAT
403169 TTTTT
1 TTTTT
403174 TATGTTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:404500 original size:16 final size:15
Alignment explanation
Indices: 404492--404521 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
404482 TTTTATTTTA
404492 TTTTATTTTTATAAT
1 TTTTATTTTTATAAT
404507 TTTTATTTTT-TAAT
1 TTTTATTTTTATAAT
404521 T
1 T
404522 AAAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATAAT
Found at i:404814 original size:19 final size:18
Alignment explanation
Indices: 404782--404834 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
404772 TATTTTTATT
*
404782 TAAATTTAATTATATAATA
1 TAAATTTAA-TATATAAAA
404801 TAAATATTAATATA-AAAA
1 TAAAT-TTAATATATAAAA
404819 TAATATTTTAATATAT
1 TAA-A-TTTAATATAT
404835 TTAAATAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 18 0.62
20 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTTAATATATAAAA
Found at i:407543 original size:20 final size:19
Alignment explanation
Indices: 407490--407543 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
407480 ATATTGTGAG
*
407490 TTGATAAAAAATTAATTTAA
1 TTGAT-AAAAATTAATTAAA
**
407510 TAAATAAAATATTAGATTAAA
1 TTGATAAAA-ATTA-ATTAAA
407531 TTGATAAAAATTA
1 TTGATAAAAATTA
407544 TTTTTTATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.15
20 11 0.41
21 12 0.44
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (19 bp):
TTGATAAAAATTAATTAAA
Found at i:408349 original size:14 final size:14
Alignment explanation
Indices: 408330--408357 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
408320 TTAATTATAA
408330 AATATAAAAATATT
1 AATATAAAAATATT
408344 AATATAAAAATATT
1 AATATAAAAATATT
408358 TTTTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:409003 original size:11 final size:11
Alignment explanation
Indices: 408950--409027 Score: 57
Period size: 13 Copynumber: 6.3 Consensus size: 11
408940 TTAATACATA
408950 TATATTTTTATAT
1 TATA-TTTT-TAT
408963 TATATTTTATAT
1 TATATTTT-TAT
*
408975 TAATATTTATAT
1 T-ATATTTTTAT
*
408987 TATATTATATTTT
1 TATATT-T-TTAT
409000 TATTATTTTTACAT
1 TA-TATTTTT--AT
409014 TATATTTTTAT
1 TATATTTTTAT
409025 TAT
1 TAT
409028 CTAACCATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
11 10 0.18
12 16 0.29
13 22 0.40
14 7 0.13
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:409003 original size:22 final size:22
Alignment explanation
Indices: 408956--409025 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
408946 CATATATATT
**
408956 TTTATATTATATTTTATATTAATA
1 TTTATATTATA--TTATATTTTTA
408980 TTTATATTATATTATATTTTTA
1 TTTATATTATATTATATTTTTA
* *
409002 -TTATTTTTACATTATATTTTTA
1 TTTA-TATTATATTATATTTTTA
409024 TT
1 TT
409026 ATCTAACCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.08
22 25 0.62
23 1 0.03
24 11 0.28
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATATTATATTATATTTTTA
Found at i:414548 original size:19 final size:20
Alignment explanation
Indices: 414497--414548 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
414487 AAATTCCATG
*
414497 AAATAAAAAAATAATAATAAA
1 AAAT-AAAAAATGATAATAAA
** *
414518 AAAGGAATAATGAT-ATAAA
1 AAATAAAAAATGATAATAAA
414537 AAATAAAAAATG
1 AAATAAAAAATG
414549 CAATATAAGT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 14 0.58
20 7 0.29
21 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (20 bp):
AAATAAAAAATGATAATAAA
Found at i:414608 original size:24 final size:24
Alignment explanation
Indices: 414575--414642 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
414565 ATAATTTTAA
*
414575 AAATATATAAATAATA-ATAATAAT
1 AAATAAATAAATAATATAT-ATAAT
*
414599 AAATAAATAAATAATATATATCAT
1 AAATAAATAAATAATATATATAAT
* *
414623 AATTAAATAAAATGATATAT
1 AAATAAAT-AAATAATATAT
414643 TTTTTTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 26 0.68
25 12 0.32
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (24 bp):
AAATAAATAAATAATATATATAAT
Found at i:414816 original size:10 final size:9
Alignment explanation
Indices: 414769--414874 Score: 53
Period size: 8 Copynumber: 12.0 Consensus size: 9
414759 TTTTTCAATA
414769 ATTTTA-AT
1 ATTTTATAT
* *
414777 AATTTATGT
1 ATTTTATAT
414786 ATTTGTAT-T
1 ATTT-TATAT
414795 ATTTTATAT
1 ATTTTATAT
414804 ATTTTATTAT
1 ATTTTA-TAT
*
414814 ATTATAATCAT
1 ATT-TTAT-AT
* *
414825 ATTTAAAAT
1 ATTTTATAT
414834 A-TTTATAT
1 ATTTTATAT
* *
414842 -TTATATAA
1 ATTTTATAT
414850 ATTTTA-AT
1 ATTTTATAT
*
414858 ATATTA-AT
1 ATTTTATAT
*
414866 AATTTATAT
1 ATTTTATAT
414875 CATATAAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
8 30 0.40
9 25 0.33
10 13 0.17
11 7 0.09
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (9 bp):
ATTTTATAT
Found at i:414859 original size:18 final size:17
Alignment explanation
Indices: 414830--414892 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
414820 ATCATATTTA
414830 AAATATTTATATTTATAT
1 AAAT-TTTATATTTATAT
414848 AAATTTTAATATATTA-AT
1 AAATTTT-ATAT-TTATAT
*
414866 -AA-TTTATA-TCATAT
1 AAATTTTATATTTATAT
414880 AAATTTTATATTT
1 AAATTTTATATTT
414893 TAATTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 5 0.14
16 9 0.24
17 6 0.16
18 10 0.27
19 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATTTTATATTTATAT
Found at i:414887 original size:16 final size:15
Alignment explanation
Indices: 414843--414890 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
414833 TATTTATATT
414843 TATATAAATTTTA-A
1 TATATAAATTTTATA
*
414857 TATATTAATAATTTATA
1 TATA-TAA-ATTTTATA
414874 TCATATAAATTTTATA
1 T-ATATAAATTTTATA
414890 T
1 T
414891 TTTAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 4 0.14
15 3 0.11
16 13 0.46
17 5 0.18
18 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATAAATTTTATA
Found at i:418658 original size:21 final size:20
Alignment explanation
Indices: 418616--418659 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
418606 TATTACTAAA
*
418616 TTATTATTTTATATTAATAT
1 TTATTATTTTATATTAAAAT
418636 TTATATATTTTA-ATATAAAAT
1 TTAT-TATTTTATAT-TAAAAT
418657 TTA
1 TTA
418660 AATAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTATTTTATATTAAAAT
Found at i:419141 original size:15 final size:15
Alignment explanation
Indices: 419121--419150 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
419111 ATTCGTTTGT
419121 GTGTATATATATATA
1 GTGTATATATATATA
419136 GTGTATATATATATA
1 GTGTATATATATATA
419151 TATAGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
GTGTATATATATATA
Found at i:419144 original size:17 final size:17
Alignment explanation
Indices: 419119--419152 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
419109 GTATTCGTTT
*
419119 GTGTGTATATATATATA
1 GTGTATATATATATATA
419136 GTGTATATATATATATA
1 GTGTATATATATATATA
419153 TAGTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (17 bp):
GTGTATATATATATATA
Found at i:420288 original size:24 final size:23
Alignment explanation
Indices: 420254--420300 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
420244 ATTTTATACA
420254 AATTTTAAAATAATTA-TTTAAT
1 AATTTTAAAATAATTACTTTAAT
420276 AATTTTATTAAATAATTACTTTAAT
1 AATTTTA--AAATAATTACTTTAAT
420301 TTTAAACGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
24 9 0.41
25 6 0.27
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTTAAAATAATTACTTTAAT
Found at i:420301 original size:22 final size:21
Alignment explanation
Indices: 420254--420306 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
420244 ATTTTATACA
*
420254 AATTTTAAAATAATTATTTAAT
1 AATTTTAAAATAATTACTT-AT
420276 AATTTTATTAAATAATTACTT-T
1 AATTTTA--AAATAATTACTTAT
420298 AATTTTAAA
1 AATTTTAAA
420307 CGAAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
22 15 0.54
24 11 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTAAAATAATTACTTAT
Found at i:420642 original size:25 final size:25
Alignment explanation
Indices: 420614--420665 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
420604 TAACTTACGC
*
420614 TAAACATAATTAAAT-AAATATAATA
1 TAAACA-AAATAAATAAAATATAATA
*
420639 TAAATAAAATAAATAAAATATAATA
1 TAAACAAAATAAATAAAATATAATA
420664 TA
1 TA
420666 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
TAAACAAAATAAATAAAATATAATA
Found at i:420645 original size:9 final size:9
Alignment explanation
Indices: 420625--420663 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
420615 AAACATAATT
420625 AAATAAATA
1 AAATAAATA
420634 TAATATAAATA
1 -AA-ATAAATA
420645 AAATAAATA
1 AAATAAATA
420654 AAATATAATA
1 AAATA-AATA
420664 TATATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 12 0.44
10 8 0.30
11 7 0.26
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAATAAATA
Found at i:421002 original size:26 final size:26
Alignment explanation
Indices: 420948--421010 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
420938 TAAAATTTTT
* *
420948 ATAAATATAAAATATTTTAATATATA
1 ATAAATATAAAATAGTATAATATATA
420974 ATAAATATAAATTATAGTATAA-ATA-A
1 ATAAATATAAA--ATAGTATAATATATA
421000 ATAAATTATAA
1 ATAAA-TATAA
421011 TATTTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 17 0.53
27 8 0.25
28 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
ATAAATATAAAATAGTATAATATATA
Found at i:421860 original size:21 final size:20
Alignment explanation
Indices: 421818--421860 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
421808 ATATAAATTT
*
421818 ATAAATTATTAATTTATCAA
1 ATAAATTATTAATTAATCAA
* *
421838 ATAAATTTATTTATTAATTAA
1 ATAAA-TTATTAATTAATCAA
421859 AT
1 AT
421861 TATTTTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAATTATTAATTAATCAA
Found at i:422993 original size:20 final size:21
Alignment explanation
Indices: 422947--423003 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
422937 ACCAAGGAAA
*
422947 TGTATCGATACATGCTTTAAGT
1 TGTATCGATACAT-TTTTAAGT
*
422969 TGTATCGATACATTTTTCA-T
1 TGTATCGATACATTTTTAAGT
422989 TGTATCGATACATTT
1 TGTATCGATACATTT
423004 GGGTTTTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 16 0.48
21 4 0.12
22 13 0.39
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATTTTTAAGT
Found at i:424943 original size:282 final size:280
Alignment explanation
Indices: 424428--424969 Score: 951
Period size: 282 Copynumber: 1.9 Consensus size: 280
424418 CCCCTGTTTC
*
424428 AAGTTGGCAGCAACACTGTTACATGTTGAAAAATCACTTTAAATAATAAAAGATTTTTTCAGAAT
1 AAGTTGGCAGCAACACTATTACATGTTGAAAAATCACTTTAAATAATAAAAGATTTTTTCAGAAT
* *
424493 TTTTTAGTATTTTCTCATAAATTGTGTCAATTTTTAACGGTATCTTATTTGTCTTCGAACTAGTC
66 TTTTTAGTATTTTCTCATAAATTGTGTCAATTTCTAACGGTATCTTATTTGCCTTCGAACTAGTC
** *
424558 CGGATTTGGGAGTTACGATTTTACGAACCCAAGCTGTCAAGAACCCACGGAATCAACGAAATGCA
131 CGGATGAGGGAGTTACGATTTTACGAACCCAAGCTGTCAAGAACCCACGAAATCAACGAAATGCA
424623 TTCAAGTTAGGCCATTCAGGCCCACTAGACGATTTTTTTTC-AAATTTTCTCAACATTTTTCATA
196 TTCAAGTTAGGCCATTCAGGCCCACTAGACGA-TTTTTTTCAAAATTTT-TCAACATTTTTCATA
424687 AATGTTACACTGTTACATGTTG
259 AATGTTACACTGTTACATGTTG
* * *
424709 AAGTTGGCAGCAACACTATTACATGTTGAATAATTATTTTAAAATAATAAAAGATTTTTTCAGAA
1 AAGTTGGCAGCAACACTATTACATGTTGAAAAATCACTTT-AAATAATAAAAGATTTTTTCAGAA
*
424774 TTTTTTAGTATTTTCTCATAAATTTTGTCAATTTCTAACGGTATCTTATTTGCCTTCGAACTAGT
65 TTTTTTAGTATTTTCTCATAAATTGTGTCAATTTCTAACGGTATCTTATTTGCCTTCGAACTAGT
424839 CCGGATGAGGGAGTTACGATTTTACGAACCCAAGCTGTCAAGAACCCACGAAATCAACGAAATGC
130 CCGGATGAGGGAGTTACGATTTTACGAACCCAAGCTGTCAAGAACCCACGAAATCAACGAAATGC
*
424904 ATTCAAGTTGGGCCATTCAGGCCCACTAGACGATTTTTTTCAAAATTTTTCAACATTTTTCATAA
195 ATTCAAGTTAGGCCATTCAGGCCCACTAGACGATTTTTTTCAAAATTTTTCAACATTTTTCATAA
424969 A
260 A
424970 AGGTTCTTGA
Statistics
Matches: 248, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
281 61 0.25
282 187 0.75
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (280 bp):
AAGTTGGCAGCAACACTATTACATGTTGAAAAATCACTTTAAATAATAAAAGATTTTTTCAGAAT
TTTTTAGTATTTTCTCATAAATTGTGTCAATTTCTAACGGTATCTTATTTGCCTTCGAACTAGTC
CGGATGAGGGAGTTACGATTTTACGAACCCAAGCTGTCAAGAACCCACGAAATCAACGAAATGCA
TTCAAGTTAGGCCATTCAGGCCCACTAGACGATTTTTTTCAAAATTTTTCAACATTTTTCATAAA
TGTTACACTGTTACATGTTG
Found at i:427376 original size:2 final size:2
Alignment explanation
Indices: 427369--427400 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
427359 TGCTTTCGAC
*
427369 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
427401 TCTTGGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:428184 original size:2 final size:2
Alignment explanation
Indices: 428177--428219 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
428167 TGAATACTCA
*
428177 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
428219 A
1 A
428220 ACCCATACTA
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:428473 original size:55 final size:57
Alignment explanation
Indices: 428366--428482 Score: 186
Period size: 55 Copynumber: 2.1 Consensus size: 57
428356 ACATGAACCT
*
428366 TATTAAAGATCTATATATATATATACTATAATAATTCTATACATGAATTACATTGATG
1 TATTAAAGATCTATATATATATATA-TATAATAATTCTATACATAAATTACATTGATG
428424 TATTAAAGATCTATATATATA-AT-TATAATTAATT-TATACATAAATTACATTGATG
1 TATTAAAGATCTATATATATATATATATAA-TAATTCTATACATAAATTACATTGATG
428479 TATT
1 TATT
428483 TCTTTAATCC
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
55 29 0.51
56 5 0.09
57 2 0.04
58 21 0.37
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (57 bp):
TATTAAAGATCTATATATATATATATATAATAATTCTATACATAAATTACATTGATG
Done.