Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold355
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: 530098
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
File 4 of 4
Found at i:461343 original size:22 final size:23
Alignment explanation
Indices: 461287--461334 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
461277 GTCCGAGTTA
*
461287 ATTT-AAAATTTTAAATAATATT
1 ATTTAAAAAATTTAAATAATATT
461309 ATTTAAAAAATTTAAA-AATATT
1 ATTTAAAAAATTTAAATAATATT
461331 ATTT
1 ATTT
461335 TATATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAAAAAATTTAAATAATATT
Found at i:463002 original size:2 final size:2
Alignment explanation
Indices: 462995--463034 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
462985 GTTGAACTTG
462995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
463035 TAAAATTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:463344 original size:2 final size:2
Alignment explanation
Indices: 463337--463365 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
463327 GTTATTTATT
463337 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 T
463366 TTGGTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:469564 original size:25 final size:26
Alignment explanation
Indices: 469527--469576 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
469517 ACTTAAAGAA
469527 AATACATATACAA-AAATATATATTT
1 AATACATATACAATAAATATATATTT
*
469552 AATACAT-TGACAATAAATTTATATT
1 AATACATAT-ACAATAAATATATATT
469577 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 11 0.50
26 10 0.45
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (26 bp):
AATACATATACAATAAATATATATTT
Found at i:470274 original size:15 final size:15
Alignment explanation
Indices: 470242--470293 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
470232 TAATTTATTT
*
470242 TATTAAAT-TAAATAA
1 TATTAAATAT-AATTA
470257 TATTAAATATAATTA
1 TATTAAATATAATTA
470272 TA-TAAATATAA-TA
1 TATTAAATATAATTA
*
470285 TATAAAATA
1 TATTAAATA
470294 ATAAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 4 0.12
14 14 0.42
15 14 0.42
16 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATTAAATATAATTA
Found at i:470276 original size:8 final size:7
Alignment explanation
Indices: 470253--470440 Score: 67
Period size: 6 Copynumber: 28.1 Consensus size: 7
470243 ATTAAATTAA
470253 ATAATAT
1 ATAATAT
470260 -TAA-AT
1 ATAATAT
470265 ATAATTAT
1 ATAA-TAT
470273 ATAA-AT
1 ATAATAT
470279 ATAATAT
1 ATAATAT
470286 ATAA-A-
1 ATAATAT
470291 ATAATA-
1 ATAATAT
470297 A-AA-AT
1 ATAATAT
470302 AT-A-AT
1 ATAATAT
470307 ATAATAT
1 ATAATAT
470314 A-ACATAAT
1 ATA-AT-AT
470322 ATAATAT
1 ATAATAT
470329 A-AATAT
1 ATAATAT
470335 AT--TAT
1 ATAATAT
* *
470340 CAAAATTT
1 -ATAATAT
470348 AT-ATGAT
1 ATAAT-AT
470355 ATAA-ATT
1 ATAATA-T
*
470362 ATTAACAT
1 A-TAATAT
*
470370 ATCAAAAT
1 AT-AATAT
470378 -TAATAT
1 ATAATAT
470384 A-AATAT
1 ATAATAT
*
470390 AAAATATT
1 ATAATA-T
*
470398 TTAA-AT
1 ATAATAT
470404 ATAAT-T
1 ATAATAT
470410 ATAATAT
1 ATAATAT
470417 AATAAAATAT
1 -AT--AATAT
470427 ATAA-AT
1 ATAATAT
470433 ATAATAT
1 ATAATAT
470440 A
1 A
470441 AATTATTAAA
Statistics
Matches: 141, Mismatches: 9, Indels: 62
0.67 0.04 0.29
Matches are distributed among these distances:
4 1 0.01
5 17 0.12
6 53 0.38
7 33 0.23
8 28 0.20
9 4 0.03
10 5 0.04
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:470286 original size:5 final size:5
Alignment explanation
Indices: 470262--470441 Score: 85
Period size: 5 Copynumber: 36.4 Consensus size: 5
470252 AATAATATTA
*
470262 AATAT AAT-T -ATAT AAATAT AATAT -ATA- AA-AT AATAAA AATAT AATAT
1 AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AAT-AT AATAT AATAT
* * * * *
470309 AATAT AACAT AATAT AATAT AAATAT ATTAT CAAAATT TATAT GATAT
1 AATAT AATAT AATAT AATAT -AATAT AATAT -AATA-T AATAT AATAT
* * * * * *
470357 AA-AT TAT-T AACAT -ATCAA AAT-T AATAT AAATAT AAAAT ATTTT AAATAT
1 AATAT AATAT AATAT AAT-AT AATAT AATAT -AATAT AATAT AATAT -AATAT
*
470406 AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AA
1 AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AA
470442 ATTATTAAAT
Statistics
Matches: 130, Mismatches: 25, Indels: 40
0.67 0.13 0.21
Matches are distributed among these distances:
3 3 0.02
4 23 0.18
5 71 0.55
6 32 0.25
7 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:470287 original size:21 final size:22
Alignment explanation
Indices: 470245--470309 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
470235 TTTATTTTAT
*
470245 TAAATTAAAT-AATATTAA-ATA
1 TAAATTATATAAATA-TAATATA
470266 T-AATTATATAAATATAATATA
1 TAAATTATATAAATATAATATA
* *
470287 TAAAATAATAAAAATATAATATA
1 T-AAATTATATAAATATAATATA
470310 ATATAACATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 10 0.27
21 9 0.24
23 18 0.49
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATTATATAAATATAATATA
Found at i:470333 original size:31 final size:28
Alignment explanation
Indices: 470245--470443 Score: 123
Period size: 27 Copynumber: 7.2 Consensus size: 28
470235 TTTATTTTAT
470245 TAAAT-TAA-ATAATAT-TAAATATAAT-
1 TAAATATAATATAATATAT-AATATAATA
* *
470270 TATATA-AATATAATATATAAAATAATA
1 TAAATATAATATAATATATAATATAATA
*
470297 AAAATATAATATAATATAACATAATATAATA
1 TAAATATAATATAATAT---ATAATATAATA
* * * *
470328 TAAATATATTATCAAAAT-TTATATGATA
1 TAAATATAATAT-AATATATAATATAATA
* *
470356 TAAAT-T-AT-TAACATATCAAAATTAATA
1 TAAATATAATATAATATAT-AATA-TAATA
* * *
470383 TAAATATAAAATATTTTA-AATATAAT-
1 TAAATATAATATAATATATAATATAATA
*
470409 TATAATATAATAAAATATATAAATATAATA
1 TA-AATATAATATAATATAT-AATATAATA
470439 TAAAT
1 TAAAT
470444 TATTAAATTA
Statistics
Matches: 131, Mismatches: 24, Indels: 34
0.69 0.13 0.18
Matches are distributed among these distances:
24 4 0.03
25 8 0.06
26 19 0.15
27 31 0.24
28 27 0.21
29 12 0.09
30 6 0.05
31 20 0.15
32 4 0.03
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (28 bp):
TAAATATAATATAATATATAATATAATA
Found at i:470417 original size:11 final size:11
Alignment explanation
Indices: 470378--470446 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
470368 ATATCAAAAT
*
470378 TAATATAAATA
1 TAATATAATTA
* *
470389 TAAAAT-ATTT
1 TAATATAATTA
470399 TAAATATAATTA
1 T-AATATAATTA
*
470411 TAATATAATAA
1 TAATATAATTA
* *
470422 AATATATAAATA
1 TA-ATATAATTA
470434 TAATATAAATTA
1 TAATAT-AATTA
470446 T
1 T
470447 TAAATTATTA
Statistics
Matches: 43, Mismatches: 11, Indels: 7
0.70 0.18 0.11
Matches are distributed among these distances:
10 3 0.07
11 23 0.53
12 17 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAATATAATTA
Found at i:470453 original size:43 final size:43
Alignment explanation
Indices: 470262--470454 Score: 111
Period size: 43 Copynumber: 4.5 Consensus size: 43
470252 AATAATATTA
*
470262 AATAT-AATTATATAAA-TATAATATATAAAATAATAAAAATAT
1 AATATAAATTAT-TAAATTATAATATATAAAATAATATAAATAT
* *
470304 AATAT-AA-TA-TAACATAATATAATATA-AATATATTATCAAA-AT
1 AATATAAATTATTAA-AT--TATAATATATAAAATAATAT-AAATAT
* * *
470346 --T-TATATGATATAAATTATTAACATATCAAAATTAATATAAATAT
1 AATATAAATTAT-TAAATTA-TAATATAT-AAAA-TAATATAAATAT
* ** *
470390 AAAATATTTTAAATATAATTATAATATAATAAAAT-ATATAAATAT
1 AATATAAATT-ATTA-AATTATAATAT-ATAAAATAATATAAATAT
470435 AATATAAATTATTAAATTAT
1 AATATAAATTATTAAATTAT
470455 TAAATTTATA
Statistics
Matches: 114, Mismatches: 17, Indels: 39
0.67 0.10 0.23
Matches are distributed among these distances:
39 4 0.04
40 5 0.04
41 9 0.08
42 18 0.16
43 27 0.24
44 10 0.09
45 17 0.15
46 1 0.01
47 15 0.13
48 8 0.07
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.39
Consensus pattern (43 bp):
AATATAAATTATTAAATTATAATATATAAAATAATATAAATAT
Found at i:470459 original size:27 final size:27
Alignment explanation
Indices: 470348--470459 Score: 88
Period size: 27 Copynumber: 4.1 Consensus size: 27
470338 ATCAAAATTT
* *
470348 ATATGATATAAATTATTAACA-TATCAA
1 ATATAATATAAATTATTAA-ATTATTAA
* *
470375 A-ATTAATATAAA-TATAAAATATTTTAA
1 ATA-TAATATAAATTATTAAAT-TATTAA
* *
470402 ATATAAT-TATAATATAATAAAATATATAA
1 ATATAATATA-AAT-TATTAAATTAT-TAA
470431 ATATAATATAAATTATTAAATTATTAA
1 ATATAATATAAATTATTAAATTATTAA
470458 AT
1 AT
470460 TTATATTGTA
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
25 1 0.02
26 8 0.12
27 25 0.38
28 12 0.18
29 18 0.27
30 2 0.03
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (27 bp):
ATATAATATAAATTATTAAATTATTAA
Found at i:470930 original size:31 final size:31
Alignment explanation
Indices: 470859--470931 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
470849 TTAATTTGAC
* * *
470859 TTAAATTTTAATAAAAAATTTAAATTTTTAAT
1 TTAAAATTT-ATAAAAAATTTAAATTATAAAT
* *
470891 TTATAATTTATAAAATATTT-AATTATAAAT
1 TTAAAATTTATAAAAAATTTAAATTATAAAT
470921 ATTAAAATTTA
1 -TTAAAATTTA
470932 AATAATCTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 8 0.24
31 19 0.56
32 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAAAATTTATAAAAAATTTAAATTATAAAT
Found at i:473471 original size:17 final size:16
Alignment explanation
Indices: 473449--473486 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
473439 CAATTATTAT
473449 AAATATTAATAACAA-AA
1 AAATATTAA-AA-AATAA
473466 AAATATTAAAAAATAA
1 AAATATTAAAAAATAA
473482 AAATA
1 AAATA
473487 AACATTACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 9 0.45
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATATTAAAAAATAA
Found at i:473913 original size:68 final size:68
Alignment explanation
Indices: 473804--473940 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
473794 GTTTCCCTGT
*
473804 TTGTAGCAGACGGTGACCGGAGGACTGTTAATCTTATTATCTACGTTACTTCGAGAATACCTTTT
1 TTGTAGCAGACGGTGACCGGAGGACTGTTAATCTTATTATCTACGTTACTTCGAGAATACCCTTT
473869 AAA
66 AAA
473872 TTGTAGCAGACGGTGACCGGAGGACTGTTAATCTTATTATCTACGTTACTTCGAGAATACCCTTT
1 TTGTAGCAGACGGTGACCGGAGGACTGTTAATCTTATTATCTACGTTACTTCGAGAATACCCTTT
473937 AAA
66 AAA
473940 T
1 T
473941 AAATGAAATT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (68 bp):
TTGTAGCAGACGGTGACCGGAGGACTGTTAATCTTATTATCTACGTTACTTCGAGAATACCCTTT
AAA
Found at i:474007 original size:13 final size:13
Alignment explanation
Indices: 473985--474025 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
473975 TATCAAATAC
*
473985 ATATTAATATTTA
1 ATATTTATATTTA
473998 ATATTTATATTT-
1 ATATTTATATTTA
*
474010 ATATTTA-AGTTA
1 ATATTTATATTTA
474022 ATAT
1 ATAT
474026 AAGTTCTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 3 0.12
12 11 0.44
13 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:475859 original size:22 final size:21
Alignment explanation
Indices: 475819--475860 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
475809 ATTACGATCA
475819 TAAATTTATTTTTAATTATAT
1 TAAATTTATTTTTAATTATAT
475840 TAAATATT-TTTTATAATTATA
1 TAAAT-TTATTTT-TAATTATA
475861 AATATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAAATTTATTTTTAATTATAT
Found at i:476137 original size:15 final size:16
Alignment explanation
Indices: 476111--476148 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
476101 CAAAAGTGAA
476111 ATTTTTATAAATAATT
1 ATTTTTATAAATAATT
*
476127 ATTTTTA-AAATATTT
1 ATTTTTATAAATAATT
476142 AGTTTTT
1 A-TTTTT
476149 TTATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTTTATAAATAATT
Found at i:479777 original size:13 final size:13
Alignment explanation
Indices: 479759--479786 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
479749 ATACAAAGAT
479759 CAATGTATCGATA
1 CAATGTATCGATA
479772 CAATGTATCGATA
1 CAATGTATCGATA
479785 CA
1 CA
479787 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:479783 original size:33 final size:33
Alignment explanation
Indices: 479741--479806 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
479731 AAATTTCCAG
479741 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
479774 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
479807 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:480209 original size:21 final size:21
Alignment explanation
Indices: 480185--480231 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
480175 AATTCATATC
*
480185 ATATTTTA-ATTAATTTTTAAA
1 ATATTTTATA-TAAATTTTAAA
*
480206 ATATTTTATATAAATTTTAAT
1 ATATTTTATATAAATTTTAAA
480227 ATATT
1 ATATT
480232 AATAATTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTATATAAATTTTAAA
Found at i:480492 original size:2 final size:2
Alignment explanation
Indices: 480485--480516 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
480475 TATTTAACAT
480485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
480517 GATGTGTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:480792 original size:15 final size:15
Alignment explanation
Indices: 480768--480799 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
480758 AAAATTAAAT
*
480768 ATAAATATATATTTA
1 ATAAAAATATATTTA
480783 ATAAAAATATATTTA
1 ATAAAAATATATTTA
480798 AT
1 AT
480800 TTTATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAAAATATATTTA
Found at i:480806 original size:20 final size:19
Alignment explanation
Indices: 480775--480827 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
480765 AATATAAATA
*
480775 TATATTTAATAAAAATATATT
1 TATATTTTATAAAAAT-T-TT
480796 TA-ATTTTATAAAAATTTT
1 TATATTTTATAAAAATTTT
480814 TATATTTT-TAAAAA
1 TATATTTTATAAAAA
480828 ATTTATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.33
19 6 0.20
20 12 0.40
21 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATTTTATAAAAATTTT
Found at i:480828 original size:20 final size:22
Alignment explanation
Indices: 480764--480828 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 22
480754 TATAAAAATT
** *
480764 AAATATAAATATATATTTAATAA
1 AAATATATTTATATTTTTAA-AA
*
480787 AAATATATTTA-A-TTTTATAA
1 AAATATATTTATATTTTTAAAA
480807 AAAT-T-TTTATATTTTTAAAA
1 AAATATATTTATATTTTTAAAA
480827 AA
1 AA
480829 TTTATAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 4 0.11
19 2 0.06
20 15 0.43
21 4 0.11
22 1 0.03
23 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATATATTTATATTTTTAAAA
Found at i:481213 original size:20 final size:20
Alignment explanation
Indices: 481188--481261 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
481178 TTAAGTTAGG
*
481188 ATATATTTATATAATTTTTA
1 ATATATTTATATATTTTTTA
481208 ATATATTTATATTATTTTTTA
1 ATATATTTATA-TATTTTTTA
*
481229 TATCATATTTTTATATTTTTTA
1 -AT-ATATTTATATATTTTTTA
*
481251 TTATATCTTAT
1 ATATAT-TTAT
481262 TTAAAATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 15 0.33
21 12 0.26
22 11 0.24
23 8 0.17
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATATTTATATATTTTTTA
Found at i:481228 original size:12 final size:12
Alignment explanation
Indices: 481213--481256 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
481203 TTTTAATATA
481213 TTTATATTATTT
1 TTTATATTATTT
*
481225 TTTATATCATATT
1 TTTATATTAT-TT
481238 TTTATATT-TTT
1 TTTATATTATTT
481249 TATTATAT
1 T-TTATAT
481257 CTTATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 3 0.11
12 16 0.57
13 9 0.32
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:481236 original size:25 final size:25
Alignment explanation
Indices: 481208--481264 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
481198 ATAATTTTTA
481208 ATATATTTATATTATTTT-TTATATC
1 ATATATTTATATT-TTTTATTATATC
*
481233 ATATTTTTATATTTTTTATTATATC
1 ATATATTTATATTTTTTATTATATC
481258 -T-TATTTA
1 ATATATTTA
481265 AAATTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 19 0.66
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (25 bp):
ATATATTTATATTTTTTATTATATC
Found at i:481253 original size:32 final size:32
Alignment explanation
Indices: 481193--481254 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
481183 TTAGGATATA
481193 TTTATATAATTTTTAATATATTTATATTATTT
1 TTTATATAATTTTTAATATATTTATATTATTT
*
481225 TTTATATCATATTTTT-ATAT-TTTTTATTAT
1 TTTATAT-A-ATTTTTAATATATTTATATTAT
481255 ATCTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 16 0.59
33 5 0.19
34 6 0.22
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (32 bp):
TTTATATAATTTTTAATATATTTATATTATTT
Found at i:481651 original size:2 final size:2
Alignment explanation
Indices: 481644--481731 Score: 131
Period size: 2 Copynumber: 44.0 Consensus size: 2
481634 AAATATGTAC
* * * * *
481644 AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT AT AC AC AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
481686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
481728 AT AT
1 AT AT
481732 CAGGGCAGCT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:482148 original size:15 final size:16
Alignment explanation
Indices: 482127--482165 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
482117 AAATCTTAAT
* *
482127 ATAATTAATTACGATA
1 ATAATTAATAACGAAA
482143 AT-ATTAATAACGAAA
1 ATAATTAATAACGAAA
482158 ATAATTAA
1 ATAATTAA
482166 AATTATAAAA
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:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
ATAATTAATAACGAAA
Found at i:484945 original size:15 final size:14
Alignment explanation
Indices: 484925--484957 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
484915 AATGTATAAA
484925 TTTTTTTCTCTTTT
1 TTTTTTTCTCTTTT
484939 CTTTTTTTCTCTTTT
1 -TTTTTTTCTCTTTT
484954 TTTT
1 TTTT
484958 ATATAGACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTCTCTTTT
Found at i:485062 original size:3 final size:3
Alignment explanation
Indices: 485054--485094 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
485044 TCTAATACAC
485054 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
485095 TAAAAAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:486436 original size:20 final size:21
Alignment explanation
Indices: 486411--486455 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
486401 GCCCTTCTTT
*
486411 TCTTCTCCTG-CCAAGCCCAC
1 TCTTCTCCCGCCCAAGCCCAC
*
486431 TCTTCTCCCGCCCAGGCCCAC
1 TCTTCTCCCGCCCAAGCCCAC
486452 TCTT
1 TCTT
486456 TCTTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.11, C:0.51, G:0.11, T:0.27
Consensus pattern (21 bp):
TCTTCTCCCGCCCAAGCCCAC
Found at i:486912 original size:18 final size:17
Alignment explanation
Indices: 486891--486929 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
486881 ATAGATTAAA
486891 ATAATTAATTTAATATGG
1 ATAATTAATTTAATAT-G
* *
486909 ATAATTTATTTGATATG
1 ATAATTAATTTAATATG
486926 ATAA
1 ATAA
486930 ATATATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (17 bp):
ATAATTAATTTAATATG
Found at i:486973 original size:20 final size:21
Alignment explanation
Indices: 486948--486987 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
486938 AAATTGAGTT
486948 TTAATTAAATTAA-TAAAAAA
1 TTAATTAAATTAATTAAAAAA
*
486968 TTAATTCAATTAATTAAAAA
1 TTAATTAAATTAATTAAAAA
486988 CTGATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAATTAAATTAATTAAAAAA
Found at i:487183 original size:3 final size:3
Alignment explanation
Indices: 487175--487221 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
487165 ACAATTTTTT
487175 ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
487222 TTTTTAATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:487277 original size:15 final size:14
Alignment explanation
Indices: 487232--487278 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 14
487222 TTTTTAATTC
487232 TTAAAATAATTTTT
1 TTAAAATAATTTTT
*
487246 TTAAAAAAATATTTT
1 TTAAAATAAT-TTTT
487261 TTAAAATATATTTTT
1 TTAAAATA-ATTTTT
487276 TTA
1 TTA
487279 CATAAAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.31
15 18 0.62
16 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAAATAATTTTT
Found at i:487520 original size:15 final size:14
Alignment explanation
Indices: 487482--487520 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
487472 TTATTTTTAA
487482 TAAAATAAAAATTT
1 TAAAATAAAAATTT
*
487496 TAAATTTAAAAATTT
1 TAAA-ATAAAAATTT
487511 TAAAAGTAAA
1 TAAAA-TAAA
487521 TTGAAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TAAAATAAAAATTT
Found at i:489344 original size:72 final size:71
Alignment explanation
Indices: 489252--489502 Score: 231
Period size: 72 Copynumber: 3.5 Consensus size: 71
489242 TTTTAAATAA
*
489252 AAATTTAAACTTCTACAAATAAAGATAAATAATACCTTAAAAATTTAAACTCATGTAATAAATCC
1 AAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTC-TGTAATAAATCC
489317 AAAAAAT
65 AAAAAAT
* * * * * * * *
489324 AAATTTAAATTTTTATAAATAAAAATGAATTATACGATCAAAAATATAAACT-TGT-ATAATTAT
1 AAATTTAAACTTCTACAAATAAAAATAAATAATAC-CTTAAAAATTTAAACTCTGTAATAA--AT
*
489387 ACCTAAAAAAC
63 -CC-AAAAAAT
* * * * * *
489398 ATATTTAAACTTTTACAAATAAAAATAAAT-TTACCTTAAAAATTTTAACTCGTATAATCATAT-
1 AAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTC-TGTAAT-AAATC
*
489461 CTAAAAAT
64 CAAAAAAT
* *
489469 AAATTTAAACTTCTACAAATATAGATAAATAATA
1 AAATTTAAACTTCTACAAATAAAAATAAATAATA
489503 TCCTAATTTT
Statistics
Matches: 141, Mismatches: 28, Indels: 20
0.75 0.15 0.11
Matches are distributed among these distances:
70 4 0.03
71 34 0.24
72 46 0.33
73 18 0.13
74 36 0.26
75 2 0.01
76 1 0.01
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (71 bp):
AAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCTGTAATAAATCCA
AAAAAT
Found at i:489687 original size:16 final size:15
Alignment explanation
Indices: 489670--489718 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
489660 TCAACATATA
489670 TTTATTAAAAATTAT
1 TTTATTAAAAATTAT
* *
489685 ATT-TTAAAAAATAT
1 TTTATTAAAAATTAT
*
489699 TTTTTTAAAAAATTAT
1 TTTATT-AAAAATTAT
489715 TTTA
1 TTTA
489719 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 12 0.44
15 4 0.15
16 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTATTAAAAATTAT
Found at i:489691 original size:14 final size:14
Alignment explanation
Indices: 489674--489722 Score: 64
Period size: 15 Copynumber: 3.5 Consensus size: 14
489664 CATATATTTA
*
489674 TTAAAAATTATATT
1 TTAAAAAATATATT
*
489688 TTAAAAAATATTTTT
1 TTAAAAAATA-TATT
489703 TTAAAAAAT-TATT
1 TTAAAAAATATATT
489716 TTAAAAA
1 TTAAAAA
489723 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.32
14 9 0.29
15 12 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAAAAATATATT
Found at i:489699 original size:28 final size:28
Alignment explanation
Indices: 489665--489722 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
489655 ATTTTTCAAC
*
489665 ATATATTTATTAAAAATTATATTTTAAAAA
1 ATAT-TTTATTAAAAAAT-TATTTTAAAAA
*
489695 ATATTTTTTTAAAAAATTATTTTAAAAA
1 ATATTTTATTAAAAAATTATTTTAAAAA
489723 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 11 0.42
29 11 0.42
30 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATTTTATTAAAAAATTATTTTAAAAA
Found at i:492758 original size:2 final size:2
Alignment explanation
Indices: 492753--492796 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
492743 GTGAATTCAA
492753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
492795 AT
1 AT
492797 CACTACTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493302 original size:26 final size:25
Alignment explanation
Indices: 493245--493303 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
493235 TAACTAATAA
*
493245 AATTAT-ATTAAATTATATTTGTTG
1 AATTATAATTAAATTATATTAGTTG
*
493269 AATAATAATTGAAATTATATTAGTT-
1 AATTATAATT-AAATTATATTAGTTG
493294 ATATTATAAT
1 A-ATTATAAT
493304 ACACTCACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 5 0.17
25 4 0.14
26 20 0.69
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (25 bp):
AATTATAATTAAATTATATTAGTTG
Found at i:493633 original size:197 final size:197
Alignment explanation
Indices: 493216--493747 Score: 589
Period size: 197 Copynumber: 2.7 Consensus size: 197
493206 ATTATAAAAT
* * *
493216 ATTAAAATTATATTTATTTTAACTAATAAAATTATATTAAATTATATTTGTTGAATAATAATTGA
1 ATTAAAATTATATTTATATTAAATAATAAAAATATATTAAATTATATTTGTTGAATAATAATTGA
* * * * * * *
493281 AATTATATTAGTTATATTATAATACACTCACCAT-G-TAAGT-AGTTAAAAAAATGTGAATAAAA
66 AATTATTTTA-ATATATTATGATACACCCACTATGGATAACTAAG--AAAAATATGT-AATAAAA
* * * * *
493343 ATTTA-CTTTTAAAAAATTTTAATTAGTAAGTAGTTTTTATTTTTTTATAAAAATTAGAAACTCA
127 ATTTATTTTTTAAAAAACTTTAATTAATAAGTAGTTTTTATTTTTTTATAAAAAATAAAAACTCA
493407 GTTGTG
192 GTTGTG
*
493413 -TTAAAATTATATTTATATTAAATAGTAAAAATATATTAAATTATATTTGTTGAATAATAATTGA
1 ATTAAAATTATATTTATATTAAATAATAAAAATATATTAAATTATATTTGTTGAATAATAATTGA
* * *
493477 AATTATTTTACTATATTATGATACACCCACTTTTGGATAATTAAGAAAAATATGTTAATAAAAAT
66 AATTATTTTAATATATTATGATACACCCAC-TATGGATAACTAAGAAAAATATG-TAATAAAAAT
* * * *
493542 TTATTTTTTAAAAAACTTTAATTAATGAGTATTTTTTA-TTTTTTATAAAAAATAAAAATTTA-T
129 TTATTTTTTAAAAAACTTTAATTAATAAGTAGTTTTTATTTTTTTATAAAAAATAAAAACTCAGT
493605 TG-G
194 TGTG
* * * * * * * *
493608 AATTAAAATTATGTTTGTGTTAAATAATAAAAATATATTAATTTAAATTTATTAAATAACAATTG
1 -ATTAAAATTATATTTATATTAAATAATAAAAATATATTAAATTATATTTGTTGAATAATAATTG
* * *
493673 AAATTATATTTAATATATTATGACATACTCC-CTATGCGAGTAGCTAAGAAAAATATG-AATAAA
65 AAATTAT-TTTAATATATTATGATACAC-CCACTATG-GA-TAACTAAGAAAAATATGTAATAAA
493736 AATTTATTTTTT
126 AATTTATTTTTT
493748 TTAAAAAAAC
Statistics
Matches: 287, Mismatches: 36, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
195 18 0.06
196 73 0.25
197 123 0.43
198 54 0.19
199 19 0.07
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (197 bp):
ATTAAAATTATATTTATATTAAATAATAAAAATATATTAAATTATATTTGTTGAATAATAATTGA
AATTATTTTAATATATTATGATACACCCACTATGGATAACTAAGAAAAATATGTAATAAAAATTT
ATTTTTTAAAAAACTTTAATTAATAAGTAGTTTTTATTTTTTTATAAAAAATAAAAACTCAGTTG
TG
Found at i:493687 original size:22 final size:21
Alignment explanation
Indices: 493647--493687 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
493637 AAAATATATT
*
493647 AATTTAAATTTATTAAATAAC
1 AATTGAAATTTATTAAATAAC
*
493668 AATTGAAATTATATTTAATA
1 AATTGAAATT-TATTAAATA
493688 TATTATGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTGAAATTTATTAAATAAC
Found at i:494163 original size:16 final size:17
Alignment explanation
Indices: 494125--494173 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
494115 TAATTATTTA
494125 AAAATAAATTAAAAATT
1 AAAATAAATTAAAAATT
*
494142 AAAATAATTTAAAAATT
1 AAAATAAATTAAAAATT
*
494159 -CAATAAAATTAAAAA
1 AAAAT-AAATTAAAAA
494174 ATAATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 3 0.11
17 25 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAATTAAAAATT
Found at i:494165 original size:28 final size:27
Alignment explanation
Indices: 494120--494172 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
494110 TAATATAATT
494120 ATTTAAAAATAAATTAAAAATTAAAATA
1 ATTTAAAAATAAATT-AAAATTAAAATA
*
494148 ATTTAAAAATTCAA-TAAAATTAAAA
1 ATTTAAAAA-TAAATTAAAATTAAAA
494173 AATAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 10 0.43
29 3 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
ATTTAAAAATAAATTAAAATTAAAATA
Found at i:494179 original size:16 final size:16
Alignment explanation
Indices: 494130--494179 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
494120 ATTTAAAAAT
494130 AAATTAAAAATTAA-A
1 AAATTAAAAATTAATA
494145 ATAATTTAAAAATTCAATA
1 A-AA-TTAAAAATT-AATA
*
494164 AAATTAAAAAATAATA
1 AAATTAAAAATTAATA
494180 TTTTATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.03
16 6 0.20
17 17 0.57
18 4 0.13
19 2 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTAAAAATTAATA
Found at i:494587 original size:1 final size:1
Alignment explanation
Indices: 494581--494610 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
494571 CCGTACGAAT
494581 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
494611 CCAAAGCCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:494738 original size:2 final size:2
Alignment explanation
Indices: 494733--494784 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
494723 GTTCAAGCAT
* *
494733 TA TA TA CA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
494774 TA TA TA TA TA T
1 TA TA TA TA TA T
494785 GAAAAATCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:497217 original size:142 final size:142
Alignment explanation
Indices: 496961--497242 Score: 521
Period size: 142 Copynumber: 2.0 Consensus size: 142
496951 CCAACGAAAT
* * *
496961 CCCAATTCCTTTATGTAGATGGGTGGAGAAAAAGGTTCAGTCAATTATCCTCCAAACTGAAGATA
1 CCCAATTCCTTTATATAGATGGGTGGAGAAAAAGGATCAGTCAATTATCCTCCAAACTAAAGATA
497026 AAATAGGTGAAAATAAAATTATGGTTCACAACCTAATATCATTCGAAGATGGTAAAAACATGAAG
66 AAATAGGTGAAAATAAAATTATGGTTCACAACCTAATATCATTCGAAGATGGTAAAAACATGAAG
497091 ATAAGACTTGCA
131 ATAAGACTTGCA
497103 CCCAATTCCTTTATATAGATGGGTGGCA-AAAAAGGATCAGTCAATTATCCTCCAAACTAAAGAT
1 CCCAATTCCTTTATATAGATGGGTGG-AGAAAAAGGATCAGTCAATTATCCTCCAAACTAAAGAT
497167 AAAATAGGTGAAAATAAAATTATGGTTCACAACCTAATATCATTCGAAGATGGTAAAAACATGAA
65 AAAATAGGTGAAAATAAAATTATGGTTCACAACCTAATATCATTCGAAGATGGTAAAAACATGAA
497232 GATAAGACTTG
130 GATAAGACTTG
497243 TATCGACTCC
Statistics
Matches: 136, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
142 135 0.99
143 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (142 bp):
CCCAATTCCTTTATATAGATGGGTGGAGAAAAAGGATCAGTCAATTATCCTCCAAACTAAAGATA
AAATAGGTGAAAATAAAATTATGGTTCACAACCTAATATCATTCGAAGATGGTAAAAACATGAAG
ATAAGACTTGCA
Found at i:503364 original size:27 final size:25
Alignment explanation
Indices: 503334--503397 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
503324 ATAAATTTTA
503334 TTATA-TTATAATTATATTTAAAATATG
1 TTATATTTAT-ATTA-ATTT-AAATATG
*
503361 TTATATTTATATTAATTTTAATATG
1 TTATATTTATATTAATTTAAATATG
503386 TTAATAATTTAT
1 TT-AT-ATTTAT
503398 TTTATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.24
26 6 0.18
27 15 0.45
28 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
TTATATTTATATTAATTTAAATATG
Found at i:505508 original size:20 final size:20
Alignment explanation
Indices: 505470--505508 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
505460 AAAATCATAA
*
505470 TTTTTAAAGTTAAAGGAATT
1 TTTTTAAAGTTAAAAGAATT
505490 TTTTTAAA-TTCAAAAGAAT
1 TTTTTAAAGTT-AAAAGAAT
505509 CACTATTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTTTAAAGTTAAAAGAATT
Found at i:509371 original size:13 final size:13
Alignment explanation
Indices: 509353--509377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
509343 CATAAAATGT
509353 TGTATCGATACAA
1 TGTATCGATACAA
509366 TGTATCGATACA
1 TGTATCGATACA
509378 TGTTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:509458 original size:13 final size:13
Alignment explanation
Indices: 509440--509464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
509430 ATCACTTAAA
509440 TGTATCGATACAT
1 TGTATCGATACAT
509453 TGTATCGATACA
1 TGTATCGATACA
509465 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:509529 original size:52 final size:52
Alignment explanation
Indices: 509473--509653 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
509463 CACTGATCTT
*
509473 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
509525 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
509577 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
509629 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
509654 TCATATTTCG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:523521 original size:1 final size:1
Alignment explanation
Indices: 523515--523613 Score: 72
Period size: 1 Copynumber: 99.0 Consensus size: 1
523505 GGCGTCCTCC
** ** ** **
523515 AAAAAAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAAAAGGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
523580 CAAAAACAATAAAAAAACAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
523614 GGGGGTCCGG
Statistics
Matches: 76, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:523541 original size:17 final size:16
Alignment explanation
Indices: 523515--523613 Score: 94
Period size: 17 Copynumber: 6.1 Consensus size: 16
523505 GGCGTCCTCC
523515 AAAAAA-AAAAAAAAA
1 AAAAAACAAAAAAAAA
**
523530 AAAAAACGAAAAAAATG
1 AAAAAAC-AAAAAAAAA
*
523547 AAAAACCAAAAAAAAA
1 AAAAAACAAAAAAAAA
*
523563 AAAAAAGGAAAAAAAAA
1 AAAAAA-CAAAAAAAAA
* *
523580 CAAAAAC-AATAAAAA
1 AAAAAACAAAAAAAAA
*
523595 AACAAACAAAAACAAAA
1 AAAAAACAAAAA-AAAA
523612 AA
1 AA
523614 GGGGGTCCGG
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
15 18 0.27
16 15 0.23
17 33 0.50
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (16 bp):
AAAAAACAAAAAAAAA
Found at i:523577 original size:27 final size:26
Alignment explanation
Indices: 523514--523613 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 26
523504 CGGCGTCCTC
* *
523514 CAAAAAAAAAAAAAAAAAAAAACGAAAA
1 CAAACAAAAACAAAAAAAAAAA--AAAA
*
523542 -AAATGAAAAACCAAAAAAAAAAAAAAA
1 CAAA-CAAAAA-CAAAAAAAAAAAAAAA
* * *
523569 GGAAAAAAAAACAAAAACAATAAAAAAA
1 -CAAACAAAAACAAAAA-AAAAAAAAAA
523597 CAAACAAAAACAAAAAA
1 CAAACAAAAACAAAAAA
523614 GGGGGTCCGG
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.02
27 27 0.44
28 19 0.31
29 14 0.23
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.02
Consensus pattern (26 bp):
CAAACAAAAACAAAAAAAAAAAAAAA
Found at i:523578 original size:44 final size:45
Alignment explanation
Indices: 523514--523615 Score: 140
Period size: 44 Copynumber: 2.3 Consensus size: 45
523504 CGGCGTCCTC
* *
523514 CAAAAAAAAAAAA--AAAAAAAAACGAAAAA-AATGAAAAACCAAA
1 CAAAAAAAAAAAAGGAAAAAAAAAC-AAAAACAATAAAAAAACAAA
523557 -AAAAAAAAAAAAGGAAAAAAAAACAAAAACAATAAAAAAACAAA
1 CAAAAAAAAAAAAGGAAAAAAAAACAAAAACAATAAAAAAACAAA
*
523601 CAAAAACAAAAAAGG
1 CAAAAAAAAAAAAGG
523616 GGGTCCGGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
42 12 0.23
43 5 0.10
44 22 0.42
45 13 0.25
ACGTcount: A:0.83, C:0.09, G:0.06, T:0.02
Consensus pattern (45 bp):
CAAAAAAAAAAAAGGAAAAAAAAACAAAAACAATAAAAAAACAAA
Found at i:523594 original size:33 final size:34
Alignment explanation
Indices: 523514--523596 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
523504 CGGCGTCCTC
* *
523514 CAAAAAAAAAAAAAAAAAAAAACGAAAAAAATGA
1 CAAAAACAAAAAAAAAAAAAAACGAAAAAAATAA
* *
523548 -AAAACCAAAAAAAAAAAAAAAGGAAAAAAA-AA
1 CAAAAACAAAAAAAAAAAAAAACGAAAAAAATAA
*
523580 CAAAAACAATAAAAAAA
1 CAAAAACAAAAAAAAAA
523597 CAAACAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.02
33 41 0.98
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (34 bp):
CAAAAACAAAAAAAAAAAAAAACGAAAAAAATAA
Found at i:525090 original size:29 final size:27
Alignment explanation
Indices: 525051--525174 Score: 122
Period size: 27 Copynumber: 4.4 Consensus size: 27
525041 TCACCCTTCA
*
525051 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA--TTTTTC
*
525080 AAAGCCCACAAGTCGGTGGCATTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTC
* ***
525107 GAAAGCCCACAAGTTAGTGGCAACCTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTC
* *
525135 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA---TTTTTC
525165 AAAGCCCACA
1 AAAGCCCACA
525175 CAAGTCGGTG
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
27 25 0.32
28 22 0.28
29 19 0.24
30 12 0.15
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23
Consensus pattern (27 bp):
AAAGCCCACAAGTCAGTGGCATTTTTC
Found at i:525152 original size:27 final size:27
Alignment explanation
Indices: 525077--525202 Score: 99
Period size: 27 Copynumber: 4.4 Consensus size: 27
525067 TGGCATTTTT
* * ***
525077 TTCAAAGCCCACAAGTCGGTGGCATTT
1 TTCAAAGCCCACAAATCAGTGGCAACC
* *
525104 TTCGAAAGCCCACAAGTTAGTGGCAACC
1 TTC-AAAGCCCACAAATCAGTGGCAACC
*
525132 TTCAAAGCCCACAAATCAGTGGCACCC
1 TTCAAAGCCCACAAATCAGTGGCAACC
*
525159 TTTTCCAAAGCCCACACAAGTCGGTGGCAACCC
1 --TT-CAAAGCCCACA-AA-TCAGTGGCAA-CC
*
525192 TTCTAAGCCCA
1 TTCAAAGCCCA
525203 ATATAGCTGG
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
27 24 0.30
28 22 0.27
29 2 0.02
30 19 0.23
31 4 0.05
32 8 0.10
33 2 0.02
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (27 bp):
TTCAAAGCCCACAAATCAGTGGCAACC
Found at i:525154 original size:55 final size:59
Alignment explanation
Indices: 525077--525202 Score: 152
Period size: 55 Copynumber: 2.2 Consensus size: 59
525067 TGGCATTTTT
* * * * *
525077 TTCAAAGCCCACAAGTCGGTGGCA-TTTTTCGAAAG-CC-CACAAGTTAGTGGCAA-CC
1 TTCAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
*
525132 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACACAAGTCGGTGGCAACCC
1 TTCAAAGCCCACAAATCAGTGGCA-CCTTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
*
525192 TTCTAAGCCCA
1 TTCAAAGCCCA
525203 ATATAGCTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
55 22 0.37
57 9 0.15
58 2 0.03
59 14 0.24
60 12 0.20
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (59 bp):
TTCAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
Found at i:525200 original size:30 final size:30
Alignment explanation
Indices: 525114--525202 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
525104 TTCGAAAGCC
*
525114 CACAAGTTAGTGGCAA-CCTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
525143 CA-AA-TCAGTGGC-ACCCTTTTCCAAAGCCCA
1 CACAAGTCAGTGGCAACCC--TT-CAAAGCCCA
* *
525173 CACAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
525203 ATATAGCTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
26 1 0.02
27 9 0.18
28 2 0.04
29 4 0.08
30 19 0.38
31 4 0.08
32 7 0.14
33 4 0.08
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.18
Consensus pattern (30 bp):
CACAAGTCAGTGGCAACCCTTCAAAGCCCA
Found at i:525314 original size:48 final size:46
Alignment explanation
Indices: 525195--525465 Score: 297
Period size: 43 Copynumber: 5.8 Consensus size: 46
525185 GCAACCCTTC
* * *
525195 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TTA-C-T
*
525244 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-A-CT
525292 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-T--T
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTACT
* *
525335 TAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACC-T--T
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTACT
*
525378 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC---TT--A-C-T
*
525430 TAAGGT-CAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAA-GTCCAATATAGCTGGCCTTGAATCAGCACATTG
525466 ACATCCTTTT
Statistics
Matches: 198, Mismatches: 11, Indels: 22
0.86 0.05 0.10
Matches are distributed among these distances:
42 30 0.15
43 49 0.25
46 1 0.01
47 1 0.01
48 43 0.22
49 41 0.21
52 5 0.03
53 28 0.14
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (46 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTACT
Found at i:525334 original size:21 final size:21
Alignment explanation
Indices: 525310--525377 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
525300 ATATAGCTGG
525310 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* *
525331 CCTTTAAGTC--CA-ATGTAGCTGA
1 CCTTGAA-TCAGCACAT-TGGC--A
525353 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
525374 CCTT
1 CCTT
525378 TAAGTCCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:525454 original size:53 final size:53
Alignment explanation
Indices: 525375--525527 Score: 182
Period size: 53 Copynumber: 2.9 Consensus size: 53
525365 ACATTGGCAC
* *
525375 CTTTAAGTCCATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTC-CAT
1 CTTTAAGTCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCAG
* * *
525427 CTTTAAGGTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAA-GTCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTTCTCAG
* * * * * *
525482 CTTTAAGCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
525528 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 14, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
52 6 0.07
53 35 0.42
54 35 0.42
55 8 0.10
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTCAG
Found at i:525663 original size:165 final size:170
Alignment explanation
Indices: 525376--525695 Score: 474
Period size: 165 Copynumber: 1.9 Consensus size: 170
525366 CATTGGCACC
*
525376 TTTAAGTCCATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCCATCTTTAAGGTCAATG
1 TTTAAGTCCATATAGCTGGCCTTGAATCAGCATATTGGCA-C--TCTCCATCTTTAAGGTCAATG
525441 TAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCAATATCGTTGGCCGT
63 TAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCAATATCGTTGGCCGT
*
525506 GAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
128 GAATCAACATATTGGCACCTTTATCACTTTTCTCATCATCATT
* *
525549 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT-GCA-TCT-CATC-TTAAGTTCAATGTA
1 TTTAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACTCTCCATCTTTAAGGTCAATGTA
* * *
525610 GCTGGCCTTG-ATCAGCA-GTTGACATCC-TTTTCTCATCTTTAAGCCCAATATCGTTGGCCTTG
65 GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAG-CCAATATCGTTGGCCGTG
*
525672 AATCACCATATTGGCACCTTTATC
129 AATCAACATATTGGCACCTTTATC
525696 TTTAAGTCCA
Statistics
Matches: 137, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
164 15 0.11
165 48 0.35
166 7 0.05
167 23 0.17
168 4 0.03
169 2 0.01
173 12 0.09
174 26 0.19
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (170 bp):
TTTAAGTCCATATAGCTGGCCTTGAATCAGCATATTGGCACTCTCCATCTTTAAGGTCAATGTAG
CTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCAATATCGTTGGCCGTGAA
TCAACATATTGGCACCTTTATCACTTTTCTCATCATCATT
Found at i:525707 original size:49 final size:49
Alignment explanation
Indices: 525549--525899 Score: 400
Period size: 49 Copynumber: 7.3 Consensus size: 49
525539 CATCATCATT
* * * *
525549 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT-GCATC-TCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * * *
525596 -TTAAGTTCAATGTAGCTGGCCTTG-ATCAGCA-GTTGACATCCTTTTCTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CC--TT-T-ATC
* * * * *
525647 TTTAAGCCCAATATCGTTGGCCTTGAATCACCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
*
525696 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
525745 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
*
525794 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C----T-
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* *
525837 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
525886 TTTAAGTCCAATAT
1 TTTAAGTCCAATAT
525900 CGCTAGCCGC
Statistics
Matches: 262, Mismatches: 26, Indels: 30
0.82 0.08 0.09
Matches are distributed among these distances:
43 40 0.15
44 4 0.02
45 9 0.03
46 22 0.08
48 2 0.01
49 147 0.56
50 1 0.00
51 5 0.02
52 19 0.07
53 8 0.03
54 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
Found at i:525816 original size:147 final size:142
Alignment explanation
Indices: 525548--525897 Score: 442
Period size: 147 Copynumber: 2.4 Consensus size: 142
525538 TCATCATCAT
* * *
525548 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT-GCATC-TCATC-TTAAGTTCAATGTA
1 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* * *
525610 GCTGGCCTTGATCAGCAGTTGACATCCTTTTCTCATCTTTAAGCCCAATATCGTTGGCCTTGAAT
66 GCTGGCCTTGATCAGCAATTGACATCC--TTCTCATCTTTAAGCCCAATATAGCTGGCCTTGAAT
*
525675 CACCATATTGGCACC
129 CACCACATTGGCA-C
*
525690 TTTATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCA
1 ----T-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCA
* * *
525755 ATGTAGCTGGCCTTGACTCAGCACATTGGCA-CC-T-TCATCTTTAAGTCCAATGTAGCTGGCCT
61 ATGTAGCTGGCCTTGA-TCAGCA-ATTGACATCCTTCTCATCTTTAAGCCCAATATAGCTGGCCT
*
525817 TGAATCAGCACATTGGCAC
124 TGAATCACCACATTGGCAC
* *
525836 TTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAAT
1 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
525898 ATCGCTAGCC
Statistics
Matches: 183, Mismatches: 15, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
141 58 0.32
142 1 0.01
146 2 0.01
147 76 0.42
148 5 0.03
149 4 0.02
150 24 0.13
151 8 0.04
152 5 0.03
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (142 bp):
TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
GCTGGCCTTGATCAGCAATTGACATCCTTCTCATCTTTAAGCCCAATATAGCTGGCCTTGAATCA
CCACATTGGCAC
Found at i:525856 original size:43 final size:43
Alignment explanation
Indices: 525793--525883 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
525783 GCACCTTCAT
525793 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
525836 TTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
525879 CTTTA
1 CTTTA
525884 TCTTTAAGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:525931 original size:92 final size:92
Alignment explanation
Indices: 525726--525931 Score: 233
Period size: 92 Copynumber: 2.2 Consensus size: 92
525716 CCTTGAATCA
*
525726 GCATATTGGCACCTTTAT-C-TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
1 GCATATTGGC-CCTTTATCCTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* *
525789 TCATCTTTAAGTCCAATGTAGCTGGCCTT
65 TCATCTTTAAGTCCAATATAGCTAGCC-T
** * * ** *
525818 G-A-ATCAGCACATTGGCACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
1 GCATATTGGCCCTTTATC-CTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* *
525881 TTATCTTTAAGTCCAATATCGCTAGCC-
65 TCATCTTTAAGTCCAATATAGCTAGCCT
525908 GCATATTGGCTCCTTTATCCTTTT
1 GCATATTGGC-CCTTTATCCTTTT
525932 TCTCATCTCT
Statistics
Matches: 90, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
89 3 0.03
90 5 0.06
91 3 0.03
92 75 0.83
93 4 0.04
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (92 bp):
GCATATTGGCCCTTTATCCTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
CATCTTTAAGTCCAATATAGCTAGCCT
Found at i:526656 original size:13 final size:13
Alignment explanation
Indices: 526638--526662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
526628 CATAAAATGT
526638 TGTATCGATACAA
1 TGTATCGATACAA
526651 TGTATCGATACA
1 TGTATCGATACA
526663 TGTTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:526743 original size:13 final size:13
Alignment explanation
Indices: 526725--526749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
526715 ATCACTTAAA
526725 TGTATCGATACAT
1 TGTATCGATACAT
526738 TGTATCGATACA
1 TGTATCGATACA
526750 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:526814 original size:52 final size:52
Alignment explanation
Indices: 526758--526937 Score: 344
Period size: 52 Copynumber: 3.5 Consensus size: 52
526748 CACTGATCTT
*
526758 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
526810 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
526862 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTAT-AAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
526913 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
526938 TCATATTTCG
Statistics
Matches: 127, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
51 28 0.22
52 99 0.78
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.