Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold311
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: 800152
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 7
Found at i:427549 original size:16 final size:17
Alignment explanation
Indices: 427523--427554 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
427513 CAATTTTCAA
427523 TAAATATTAAAATTTAT
1 TAAATATTAAAATTTAT
427540 TAAA-ATTAAAATTTA
1 TAAATATTAAAATTTA
427555 ATAATTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATATTAAAATTTAT
Found at i:427551 original size:24 final size:24
Alignment explanation
Indices: 427524--427585 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
427514 AATTTTCAAT
*
427524 AAATATTAAAATTTATTAAAATTA
1 AAATATTAAAATTTACTAAAATTA
* *
427548 AAAT-TTAATAATTAACTAACATTA
1 AAATATTAA-AATTTACTAAAATTA
427572 AAA-ATTAAAATTTA
1 AAATATTAAAATTTA
427586 ATTTTTATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATATTAAAATTTACTAAAATTA
Found at i:427689 original size:14 final size:14
Alignment explanation
Indices: 427670--427704 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
427660 TAGATAATAA
*
427670 AAATTTAAATATTT
1 AAATTTAAAAATTT
*
427684 ATATTTAAAAATTT
1 AAATTTAAAAATTT
427698 AAATTTA
1 AAATTTA
427705 TTATAAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTTAAAAATTT
Found at i:427719 original size:23 final size:22
Alignment explanation
Indices: 427665--427719 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
427655 TAAATTAGAT
427665 AATAAAAATTTAAATATTTATA
1 AATAAAAATTTAAATATTTATA
** *
427687 TTTAAAAATTTAAATTTATTATA
1 AATAAAAATTTAAATAT-TTATA
*
427710 AATAACAATT
1 AATAAAAATT
427720 GTTAAAATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAAAAATTTAAATATTTATA
Found at i:427772 original size:10 final size:9
Alignment explanation
Indices: 427749--427806 Score: 55
Period size: 10 Copynumber: 6.0 Consensus size: 9
427739 AATTTTAAAA
*
427749 AAATAAATT
1 AAATAATTT
427758 AAATAATTAT
1 AAATAATT-T
427768 AAAT-ATTT
1 AAATAATTT
427776 AAATATATATT
1 AAATA-AT-TT
427787 AAATTAATTT
1 AAA-TAATTT
427797 AATATAATTT
1 AA-ATAATTT
427807 TTTGTTAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
8 5 0.12
9 10 0.24
10 17 0.40
11 8 0.19
12 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AAATAATTT
Found at i:428537 original size:22 final size:22
Alignment explanation
Indices: 428497--428540 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
428487 TTTTAATATG
* * *
428497 ATATAATTATTATATAAAAATA
1 ATATAAATATAATAAAAAAATA
428519 ATATAAATATAATAAAAAAATA
1 ATATAAATATAATAAAAAAATA
428541 CAAATTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATATAAATATAATAAAAAAATA
Found at i:429366 original size:17 final size:18
Alignment explanation
Indices: 429344--429377 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
429334 TTAAAAATGC
429344 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
429361 AATTATATTATTTATTT
1 AATTATATTATTTATTT
429378 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:429378 original size:17 final size:17
Alignment explanation
Indices: 429344--429395 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
429334 TTAAAAATGC
429344 AATTATATT-TTTATTTT
1 AATTATATTATTTA-TTT
429361 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
429378 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
429392 AATT
1 AATT
429396 CGAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:434517 original size:17 final size:18
Alignment explanation
Indices: 434495--434528 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
434485 TTAAAGATGC
434495 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
434512 AATTATATTATTTATTT
1 AATTATATTATTTATTT
434529 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:434529 original size:17 final size:17
Alignment explanation
Indices: 434495--434546 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
434485 TTAAAGATGC
434495 AATTATATT-TTTATTTT
1 AATTATATTATTTA-TTT
434512 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
434529 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
434543 AATT
1 AATT
434547 CGAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:434617 original size:28 final size:29
Alignment explanation
Indices: 434581--434640 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
434571 TATTGCATCA
434581 AAAAGTTG-TAT-TGAAAGAACACAACATTT
1 AAAAGTTGTTATGT-AAAG-ACACAACATTT
*
434610 AAAA-TTGTTATGTAAAGACATAACATTT
1 AAAAGTTGTTATGTAAAGACACAACATTT
434638 AAA
1 AAA
434641 TAAAGACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 16 0.57
29 11 0.39
30 1 0.04
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (29 bp):
AAAAGTTGTTATGTAAAGACACAACATTT
Found at i:439519 original size:16 final size:16
Alignment explanation
Indices: 439498--439529 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
439488 TTTGAATCAT
439498 TTTTAGATTTGGATTA
1 TTTTAGATTTGGATTA
*
439514 TTTTAGATTTTGATTA
1 TTTTAGATTTGGATTA
439530 CTTCGGATTT
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:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (16 bp):
TTTTAGATTTGGATTA
Found at i:439562 original size:16 final size:16
Alignment explanation
Indices: 439543--439573 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
439533 CGGATTTAAA
*
439543 TCATTTCGGATTCGGG
1 TCATTTCAGATTCGGG
439559 TCATTTCAGATTCGG
1 TCATTTCAGATTCGG
439574 ATTAATTAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (16 bp):
TCATTTCAGATTCGGG
Found at i:442165 original size:17 final size:18
Alignment explanation
Indices: 442143--442180 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
442133 ATATTTTAAT
442143 ATTTAAATTTATTAAA-A
1 ATTTAAATTTATTAAATA
*
442160 ATTTAAATTTTTTAAATA
1 ATTTAAATTTATTAAATA
442178 ATT
1 ATT
442181 AGCTAACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAATTTATTAAATA
Found at i:442287 original size:7 final size:7
Alignment explanation
Indices: 442275--442323 Score: 50
Period size: 6 Copynumber: 7.3 Consensus size: 7
442265 TAATGTAAAG
442275 TTAAATA
1 TTAAATA
442282 TTAAAT-
1 TTAAATA
*
442288 TTTAATA
1 TTAAATA
442295 -TAAAT-
1 TTAAATA
442300 TTAAATA
1 TTAAATA
*
442307 ATAAATA
1 TTAAATA
442314 TTTAAATA
1 -TTAAATA
442322 TT
1 TT
442324 TATATTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
6 14 0.41
7 14 0.41
8 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTAAATA
Found at i:442293 original size:25 final size:26
Alignment explanation
Indices: 442265--442318 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
442255 TATGTAAAAA
* *
442265 TAATGTAAAGTTAAATATTAAAT-TT
1 TAATATAAAGTTAAATAATAAATATT
*
442290 TAATATAAATTTAAATAATAAATATT
1 TAATATAAAGTTAAATAATAAATATT
442316 TAA
1 TAA
442319 ATATTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
TAATATAAAGTTAAATAATAAATATT
Found at i:442316 original size:15 final size:15
Alignment explanation
Indices: 442275--442321 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
442265 TAATGTAAAG
*
442275 TTAAATATTAAAT-T
1 TTAAATAATAAATAT
442289 TT-AAT-AT-AA-AT
1 TTAAATAATAAATAT
442300 TTAAATAATAAATAT
1 TTAAATAATAAATAT
442315 TTAAATA
1 TTAAATA
442322 TTTATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 5 0.19
14 4 0.15
15 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATAATAAATAT
Found at i:442366 original size:15 final size:15
Alignment explanation
Indices: 442314--442366 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
442304 ATAATAAATA
442314 TTTA-AATATTTATAT
1 TTTATAATATTTA-AT
* *
442329 TTATATACTATTTAAG
1 TT-TATAATATTTAAT
*
442345 TTAATAATATTTAAT
1 TTTATAATATTTAAT
442360 TTTATAA
1 TTTATAA
442367 AAAATGAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 18 0.60
16 5 0.17
17 7 0.23
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTATAATATTTAAT
Found at i:444123 original size:15 final size:16
Alignment explanation
Indices: 444103--444133 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
444093 GAGTATATTA
444103 AAATTTATA-TAAAAT
1 AAATTTATATTAAAAT
444118 AAATTTATATTAAAAT
1 AAATTTATATTAAAAT
444134 TTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTTATATTAAAAT
Found at i:444135 original size:12 final size:12
Alignment explanation
Indices: 444096--444141 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
444086 AATATGTGAG
444096 TATATTAAAATT
1 TATATTAAAATT
*
444108 TATATAAAATAAATT
1 TATAT--TA-AAATT
444123 TATATTAAAATT
1 TATATTAAAATT
444135 TATATTA
1 TATATTA
444142 TATTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 17 0.59
13 1 0.03
14 1 0.03
15 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TATATTAAAATT
Found at i:445091 original size:13 final size:13
Alignment explanation
Indices: 445073--445111 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
445063 TATTTTTTTA
445073 AATATTTATATTT
1 AATATTTATATTT
*
445086 AATATTTTTATTT
1 AATATTTATATTT
445099 AATA--TATATTT
1 AATATTTATATTT
445110 AA
1 AA
445112 ATATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 8 0.33
13 16 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:445155 original size:19 final size:18
Alignment explanation
Indices: 445133--445181 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
445123 AAAATATAAG
445133 TAAAATATTTTAAAAAAT
1 TAAAATATTTTAAAAAAT
*
445151 ATAAAAAATTTTAAAAAAT
1 -TAAAATATTTTAAAAAAT
445170 TAAATATATTTT
1 TAAA-ATATTTT
445182 TATTGAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATATTTTAAAAAAT
Found at i:445169 original size:10 final size:10
Alignment explanation
Indices: 445133--445170 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
445123 AAAATATAAG
*
445133 TAAAATATTT
1 TAAAAAATTT
*
445143 TAAAAAA-TA
1 TAAAAAATTT
445152 TAAAAAATTT
1 TAAAAAATTT
445162 TAAAAAATT
1 TAAAAAATT
445171 AAATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:446338 original size:15 final size:16
Alignment explanation
Indices: 446318--446358 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
446308 TAGATATAAT
446318 TATATATTTAAT-ATG
1 TATATATTTAATGATG
* *
446333 TATATATTTAATGTTT
1 TATATATTTAATGATG
446349 TATATATTTA
1 TATATATTTA
446359 TAAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TATATATTTAATGATG
Found at i:446358 original size:8 final size:8
Alignment explanation
Indices: 446311--446360 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
446301 TAATTATTAG
*
446311 ATATAATT
1 ATATATTT
446319 ATATATTT
1 ATATATTT
*
446327 A-ATATGT
1 ATATATTT
446334 ATATATTT
1 ATATATTT
*
446342 A-ATGTTTT
1 ATAT-ATTT
446350 ATATATTT
1 ATATATTT
446358 ATA
1 ATA
446361 AAATTATATC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 8 0.24
8 24 0.71
9 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (8 bp):
ATATATTT
Found at i:447850 original size:88 final size:88
Alignment explanation
Indices: 447507--447983 Score: 587
Period size: 88 Copynumber: 5.4 Consensus size: 88
447497 AATAAATATG
* * * *
447507 ATTATATCTAAGAATC-GATT-TTTTTTATAAAAAAAGAAAAGTTGATTAATTGTAAATGTCAAA
1 ATTATATCTGAGAATCAGATTCTTTTTTAT-AGAAAA-AAAAGTTGATTGATTGTAAATGTCATA
* * *
447570 CTGTAAAGATTAGACTAATGTATGC
64 CTGCAAAGATTAGACTAATGCATGA
* *
447595 ATTATACCTGAGAATCAGATT-TTTTTTTTATG-AAAAAAAGTTGATTGATTGT-AA-GT-AT-C
1 ATTATATCTGAGAATCAGATTCTTTTTTATA-GAAAAAAAAGTTGATTGATTGTAAATGTCATAC
* * *
447654 TGCAAAGATTAGACTCATACATAA
65 TGCAAAGATTAGACTAATGCATGA
*
447678 ATTATATCTGAAAATCAGATTCTTTTTTATAGAAAAAAGAAAAGTTGATTGATTGTAAATGTCAT
1 ATTATATCTGAGAATCAGATTCTTTTTTATAG--AAAA-AAAAGTTGATTGATTGTAAATGTCAT
* *
447743 ACTGTAAGGATTAGACTAATGCATGA
63 ACTGCAAAGATTAGACTAATGCATGA
447769 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAAGTTGATTGATTGTAAATGTCATACT
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAAGTTGATTGATTGTAAATGTCATACT
*
447834 GCAAGGATTAGACTAATGCATGA
66 GCAAAGATTAGACTAATGCATGA
* * *
447857 ATTATATCTTAGAATCAGATTCTTTTTTATAGAAAAAAAAGAGTTGATTGATTGTAAATTTCAGA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAG-AAAAAAA-AGTTGATTGATTGTAAATGTCATA
* *
447922 CTGCAAAAATTAGACTAATGCATAA
64 CTGCAAAGATTAGACTAATGCATGA
* * *
447947 ATTATATCTGAAAATC-GAATTATTTTTTTTA-AAAAAA
1 ATTATATCTGAGAATCAG-ATTCTTTTTTATAGAAAAAA
447984 GACTACAAGG
Statistics
Matches: 343, Mismatches: 32, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
83 39 0.11
84 9 0.03
85 2 0.01
86 5 0.01
87 33 0.10
88 108 0.31
89 25 0.07
90 71 0.21
91 51 0.15
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (88 bp):
ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAAGTTGATTGATTGTAAATGTCATACT
GCAAAGATTAGACTAATGCATGA
Found at i:447906 original size:174 final size:170
Alignment explanation
Indices: 447507--447983 Score: 552
Period size: 174 Copynumber: 2.7 Consensus size: 170
447497 AATAAATATG
* * *
447507 ATTATATCTAAGAATC-GATT-TTTTTTATAAAAAAAGAAAAGTTGATTAATTGTAAATGTCAAA
1 ATTATATCTAAGAATCAGATTCTTTTTTAT-AGAAAA-AAAAG-AGATTGATTGTAAATGTCAAA
* * *
447570 CTGTAAAGATTAGACTAATGTATGCATTATACCTGAGAATCAGATTTTTTTTTTATG-AAAAAAA
63 CTGTAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTTTTTTA-GAAAAAAAA
*
447634 GTTGATTGATTGTAAGTATCTGCAAAGATTAGACTCATACATAA
127 GTTGATTGATTGTAAGTATCTGCAAAGATTAGACTAATACATAA
*
447678 ATTATATCTGAA-AATCAGATTCTTTTTTATAGAAAAAAGAAAAGTTGATTGATTGTAAATGTCA
1 ATTATATCT-AAGAATCAGATTCTTTTTTATAG--AAAA-AAAAG-AGATTGATTGTAAATGTCA
* * *
447742 TACTGTAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAA
61 AACTGTAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATT-TTTTTTTTAGAAAAAA
* * *
447807 AAGTTGATTGATTGTAAATGTCATACTGCAAGGATTAGACTAATGCATGA
125 AAGTTGATTGATTGT-AA-GT-AT-CTGCAAAGATTAGACTAATACATAA
* * *
447857 ATTATATCTTAGAATCAGATTCTTTTTTATAGAAAAAAAAGAGTTGATTGATTGTAAATTTCAGA
1 ATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAAAAGA---GATTGATTGTAAATGTCAAA
* * * *
447922 CTGCAAAAATTAGACTAATGCATAAATTATATCTGAAAATC-GAATTATTTTTTTTA-AAAAAA
63 CTGTAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAG-ATT-TTTTTTTTAGAAAAAA
447984 GACTACAAGG
Statistics
Matches: 267, Mismatches: 23, Indels: 26
0.84 0.07 0.08
Matches are distributed among these distances:
171 13 0.05
172 7 0.03
173 8 0.03
174 73 0.27
175 28 0.10
176 7 0.03
177 13 0.05
178 68 0.25
179 50 0.19
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (170 bp):
ATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAAAAGAGATTGATTGTAAATGTCAAACTG
TAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTTTTTTAGAAAAAAAAGTTG
ATTGATTGTAAGTATCTGCAAAGATTAGACTAATACATAA
Found at i:448126 original size:91 final size:92
Alignment explanation
Indices: 447994--448168 Score: 253
Period size: 91 Copynumber: 1.9 Consensus size: 92
447984 GACTACAAGG
* * * * *
447994 ATTAGACTAATGCATGAATTGTACCTCAGAATCGGATTCCTTTTGGTAGAAAAA-AGAAAAGTTA
1 ATTAGACTAATGCATAAATTATACCTAAGAATCAGATTCCTTTTGATAGAAAAACAGAAAAGTTA
*
448058 ATTGATTATAAGTATCATACTATAAAT
66 ATTGATTATAAATATCATACTATAAAT
** *
448085 ATTAGACTAATGCATAAATTATATTTAAGAATCAGATTCCTTTTGATAGAAAAACTGAAAAGTTA
1 ATTAGACTAATGCATAAATTATACCTAAGAATCAGATTCCTTTTGATAGAAAAACAGAAAAGTTA
*
448150 ATTGATTTTAAATATCATA
66 ATTGATTATAAATATCATA
448169 GTTGAAATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
91 47 0.64
92 26 0.36
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (92 bp):
ATTAGACTAATGCATAAATTATACCTAAGAATCAGATTCCTTTTGATAGAAAAACAGAAAAGTTA
ATTGATTATAAATATCATACTATAAAT
Found at i:448138 original size:155 final size:154
Alignment explanation
Indices: 447835--448138 Score: 369
Period size: 155 Copynumber: 2.0 Consensus size: 154
447825 TGTCATACTG
* * * * *
447835 CAAGGATTAGACTAATGCATGAATTATATCTTAGAATCAGATTCTTTTTTATAGAAAAAAAAGAG
1 CAAGGATTAGACTAATGCATGAATTATACCTCAGAATCAGATTCCTTTTGATAGAAAAAAAAAAG
* * * *
447900 TTGATTGATTGTAAATTTCAGACTGCAAAAATTAGACTAATGCATAAATTATATCTGAAAATCGA
66 TTAATTGATTATAAATATCAGACTACAAAAATTAGACTAATGCATAAATTATATCTGAAAATCGA
* **
447965 ATTATTTTTTTTAAAAAAAGACTA
131 ATTACTTTTGATAAAAAAAGACTA
* * *
447989 CAAGGATTAGACTAATGCATGAATTGTACCTCAGAATCGGATTCCTTTTGGTAGAAAAAAGAAAA
1 CAAGGATTAGACTAATGCATGAATTATACCTCAGAATCAGATTCCTTTTGATAGAAAAAA-AAAA
* * * * *
448054 GTTAATTGATTATAAGTATCATACTATAAATATTAGACTAATGCATAAATTATAT-TTAAGAATC
65 GTTAATTGATTATAAATATCAGACTACAAAAATTAGACTAATGCATAAATTATATCTGAA-AATC
* *
448118 -AGATTCCTTTTGATAGAAAAA
129 GA-ATTACTTTTGATAAAAAAA
448139 CTGAAAAGTT
Statistics
Matches: 125, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
154 57 0.46
155 68 0.54
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (154 bp):
CAAGGATTAGACTAATGCATGAATTATACCTCAGAATCAGATTCCTTTTGATAGAAAAAAAAAAG
TTAATTGATTATAAATATCAGACTACAAAAATTAGACTAATGCATAAATTATATCTGAAAATCGA
ATTACTTTTGATAAAAAAAGACTA
Found at i:448208 original size:92 final size:91
Alignment explanation
Indices: 448021--448192 Score: 213
Period size: 92 Copynumber: 1.9 Consensus size: 91
448011 ATTGTACCTC
* * *
448021 AGAATCGGATTCCTTTTGGTAGAAAAAAGAAAAGTTAATTGATTATAAGTATCATACTATAAATA
1 AGAATCAGATTCCTTTTGATAGAAAAAAGAAAAGTTAATTGATTATAAATATCATACTATAAATA
* * * *
448086 TTAGACTAATGCATAAATTATATTTA
66 TTAGACAAATACAGAAATTATATATA
* * *
448112 AGAATCAGATTCCTTTTGATAGAAAAACTGAAAAGTTAATTGATTTTAAATATCATAGT-TGAAA
1 AGAATCAGATTCCTTTTGATAGAAAAA-AGAAAAGTTAATTGATTATAAATATCATACTAT-AAA
448176 TA-TAGGACAAATACAGA
64 TATTA-GACAAATACAGA
448193 TATTTTGAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
91 28 0.41
92 41 0.59
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (91 bp):
AGAATCAGATTCCTTTTGATAGAAAAAAGAAAAGTTAATTGATTATAAATATCATACTATAAATA
TTAGACAAATACAGAAATTATATATA
Found at i:451030 original size:20 final size:20
Alignment explanation
Indices: 451001--451118 Score: 146
Period size: 20 Copynumber: 5.9 Consensus size: 20
450991 TCTTTACCCA
451001 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
451021 AATATATCGATACATGTTTG
1 AATGTATCGATACATTTTTC
* *
451041 AATGTATCGATATATTCTTC
1 AATGTATCGATACATTTTTC
* *
451061 AATGTATCGATACATGTTTG
1 AATGTATCGATACATTTTTC
* * *
451081 AATGTATCAATATATTCTTC
1 AATGTATCGATACATTTTTC
451101 AATGTATCGATACATTTT
1 AATGTATCGATACATTTT
451119 GTCTTTTTAC
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:451062 original size:40 final size:40
Alignment explanation
Indices: 451001--451119 Score: 195
Period size: 40 Copynumber: 3.0 Consensus size: 40
450991 TCTTTACCCA
* * *
451001 AATGTATCGATACATTTTTCAATATATCGATACATGTTTG
1 AATGTATCGATATATTCTTCAATGTATCGATACATGTTTG
451041 AATGTATCGATATATTCTTCAATGTATCGATACATGTTTG
1 AATGTATCGATATATTCTTCAATGTATCGATACATGTTTG
*
451081 AATGTATCAATATATTCTTCAATGTATCGATACAT-TTTG
1 AATGTATCGATATATTCTTCAATGTATCGATACATGTTTG
451120 TCTTTTTACC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 4 0.05
40 71 0.95
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (40 bp):
AATGTATCGATATATTCTTCAATGTATCGATACATGTTTG
Found at i:457692 original size:13 final size:13
Alignment explanation
Indices: 457670--457712 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
457660 AGTCTATTAG
*
457670 ATAAAATTAATAA
1 ATAAATTTAATAA
457683 ATAAATTTAACTAA
1 ATAAATTTAA-TAA
*
457697 A-AAATTAAATAA
1 ATAAATTTAATAA
457709 ATAA
1 ATAA
457713 TAAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAATTTAATAA
Found at i:457722 original size:25 final size:25
Alignment explanation
Indices: 457672--457724 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
457662 TCTATTAGAT
**
457672 AAAATTAATAAATAAATTTAACTAA
1 AAAATTAATAAATAAATAAAACTAA
*
457697 AAAATTAAATAAAT-AATAAAATTAA
1 AAAATT-AATAAATAAATAAAACTAA
457722 AAA
1 AAA
457725 TATATTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAATTAATAAATAAATAAAACTAA
Found at i:458417 original size:28 final size:28
Alignment explanation
Indices: 458385--458441 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
458375 TATACCAAAA
*
458385 AATACTTTAACAATTATAAATAAACCAT
1 AATACTTCAACAATTATAAATAAACCAT
*
458413 AATACTTCAACAATTATAAATAAATCAT
1 AATACTTCAACAATTATAAATAAACCAT
458441 A
1 A
458442 CTTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (28 bp):
AATACTTCAACAATTATAAATAAACCAT
Found at i:458681 original size:22 final size:22
Alignment explanation
Indices: 458645--458707 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
458635 ACTTGTGATC
*
458645 ATTTTTTTAATTTAAAATTTAAA
1 ATTTTTATAA-TTAAAATTTAAA
* *
458668 ATTTTTATAATTAATATTTTAA
1 ATTTTTATAATTAAAATTTAAA
458690 ATTTATATATAA-TAAAAT
1 ATTT-T-TATAATTAAAAT
458708 AAAAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 14 0.41
23 15 0.44
24 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTTATAATTAAAATTTAAA
Found at i:458755 original size:27 final size:24
Alignment explanation
Indices: 458689--458759 Score: 58
Period size: 25 Copynumber: 2.9 Consensus size: 24
458679 TAATATTTTA
458689 AATTTATATATAATAAAATAAAAAAT
1 AATTT-TATA-AATAAAATAAAAAAT
* *
458715 AATTTTA-ATA-AAAATAAATTACATT
1 AATTTTATAAATAAAATAAA--A-AAT
458740 AATTTTATAAATAAAA-AAAA
1 AATTTTATAAATAAAATAAAA
458760 CATACTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
22 8 0.22
23 1 0.03
24 3 0.08
25 11 0.30
26 10 0.27
27 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (24 bp):
AATTTTATAAATAAAATAAAAAAT
Found at i:459036 original size:15 final size:14
Alignment explanation
Indices: 459004--459043 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
458994 ATTTATAAAT
459004 AAAAATTTATTTTG
1 AAAAATTTATTTTG
459018 AAAAATATT-TTTTG
1 AAAAAT-TTATTTTG
*
459032 AAAAACTTATTT
1 AAAAATTTATTT
459044 AAAGAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (14 bp):
AAAAATTTATTTTG
Found at i:459643 original size:22 final size:20
Alignment explanation
Indices: 459615--459657 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
459605 TATTTTTAAT
*
459615 ATAATATAATTATTATATAAAA
1 ATAATATAAATA-TAT-TAAAA
459637 ATAATATAAATATATTAAAA
1 ATAATATAAATATATTAAAA
459657 A
1 A
459658 CGACAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 3 0.15
22 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAATATAAATATATTAAAA
Found at i:460556 original size:13 final size:13
Alignment explanation
Indices: 460538--460570 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
460528 CTCTTATTTT
460538 TTTAATATT-TATA
1 TTTAATATTCT-TA
460551 TTTAATATTCTTA
1 TTTAATATTCTTA
460564 TTTAATA
1 TTTAATA
460571 AATATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATATTCTTA
Found at i:460624 original size:21 final size:21
Alignment explanation
Indices: 460595--460639 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
460585 AATATAAAAC
*
460595 TTTTTAAAT-ATTTATAAATT
1 TTTTTAAATAATTAATAAATT
*
460615 TTTTTAAAATAATTAATATATT
1 TTTTT-AAATAATTAATAAATT
460637 TTT
1 TTT
460640 ATCGAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTAAATAATTAATAAATT
Found at i:461208 original size:29 final size:29
Alignment explanation
Indices: 461147--461208 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 29
461137 TTAAAATTTT
461147 TTATATATTTATAAAAATTTTAAATAATA
1 TTATATATTTATAAAAATTTTAAATAATA
* * *
461176 --ATATCTTTATATACATATTTAAA-AATA
1 TTATATATTTATAAAAAT-TTTAAATAATA
461203 TTATAT
1 TTATAT
461209 GAGTATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
27 17 0.63
28 6 0.22
29 4 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATATATTTATAAAAATTTTAAATAATA
Found at i:462485 original size:22 final size:21
Alignment explanation
Indices: 462455--462507 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
462445 AAAATTATTA
*
462455 TTTTATAAT-TTTAATTTTAAT
1 TTTTATAATATTT-ATTATAAT
462476 TTTTATTAATATTTATTATAAT
1 TTTTA-TAATATTTATTATAAT
*
462498 TAATTATAAT
1 T-TTTATAAT
462508 GTTATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 16 0.59
23 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATAATATTTATTATAAT
Found at i:465095 original size:2 final size:2
Alignment explanation
Indices: 465076--465117 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
465066 GAAAAAACTA
* *
465076 AT AT AC AT AT AC 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
465118 TCTGGATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:468730 original size:15 final size:16
Alignment explanation
Indices: 468710--468742 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
468700 GTGGACATAC
468710 ATATATT-TTATATTT
1 ATATATTATTATATTT
468725 ATATATTCATTATATTT
1 ATATATT-ATTATATTT
468742 A
1 A
468743 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATATTATTATATTT
Found at i:474072 original size:8 final size:8
Alignment explanation
Indices: 474059--474121 Score: 90
Period size: 8 Copynumber: 7.9 Consensus size: 8
474049 AAAGACTGAC
474059 ATATATAT
1 ATATATAT
474067 ATATATAT
1 ATATATAT
*
474075 ATGTATAT
1 ATATATAT
*
474083 ATATGTAT
1 ATATATAT
*
474091 ATATGTAT
1 ATATATAT
474099 ATATATAT
1 ATATATAT
*
474107 ATATATGT
1 ATATATAT
474115 ATATATA
1 ATATATA
474122 GTTGCATGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 49 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (8 bp):
ATATATAT
Found at i:474074 original size:10 final size:10
Alignment explanation
Indices: 474059--474121 Score: 90
Period size: 10 Copynumber: 6.3 Consensus size: 10
474049 AAAGACTGAC
474059 ATATATATAT
1 ATATATATAT
*
474069 ATATATATGT
1 ATATATATAT
*
474079 ATATATATGT
1 ATATATATAT
*
474089 ATATATGTAT
1 ATATATATAT
474099 ATATATATAT
1 ATATATATAT
*
474109 ATATGTATAT
1 ATATATATAT
474119 ATA
1 ATA
474122 GTTGCATGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 48 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (10 bp):
ATATATATAT
Found at i:474083 original size:18 final size:18
Alignment explanation
Indices: 474060--474121 Score: 115
Period size: 18 Copynumber: 3.4 Consensus size: 18
474050 AAGACTGACA
474060 TATATATATATATATATG
1 TATATATATATATATATG
*
474078 TATATATATGTATATATG
1 TATATATATATATATATG
474096 TATATATATATATATATG
1 TATATATATATATATATG
474114 TATATATA
1 TATATATA
474122 GTTGCATGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TATATATATATATATATG
Found at i:474812 original size:28 final size:29
Alignment explanation
Indices: 474781--474837 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
474771 TATTTAGCTT
*
474781 AATATTTAGAT-TTATTTTT-TAATATAAA
1 AATATTAAGATATTATTTTTATAAT-TAAA
474809 AATATTAAGATATTATTTTTATAATTAAA
1 AATATTAAGATATTATTTTTATAATTAAA
474838 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 10 0.38
29 12 0.46
30 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (29 bp):
AATATTAAGATATTATTTTTATAATTAAA
Found at i:475107 original size:3 final size:3
Alignment explanation
Indices: 475099--475127 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
475089 CCTCTGCTTA
475099 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
475128 ATTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:475132 original size:3 final size:3
Alignment explanation
Indices: 475126--475162 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
475116 CTTCTTCTTC
475126 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
475163 AATCATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:479257 original size:19 final size:21
Alignment explanation
Indices: 479216--479257 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
479206 TTTGTATAAG
*
479216 TGTTTTCAAGTCTTAAATCTAA
1 TGTTTTCAAG-CTAAAATCTAA
479238 TGTTTTCAAG-TAAAAT-TAA
1 TGTTTTCAAGCTAAAATCTAA
479257 T
1 T
479258 CCAAAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
22 10 0.53
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (21 bp):
TGTTTTCAAGCTAAAATCTAA
Found at i:479446 original size:20 final size:20
Alignment explanation
Indices: 479421--479473 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
479411 CTAAGTGAAA
*
479421 TGTATCGATACATG-GGACAT
1 TGTATCGATACATGAAGA-AT
*
479441 TGTATCAATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
479461 TGTATCGATACAT
1 TGTATCGATACAT
479474 TATGCCCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:481078 original size:3 final size:3
Alignment explanation
Indices: 481063--481103 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
481053 AAGCATCAAA
* * *
481063 GAT GAT GAA GAT GAT GAA GAT GAT GAT GAT GAT AAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
481104 GGTTGACTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:481103 original size:9 final size:9
Alignment explanation
Indices: 481061--481095 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
481051 TCAAGCATCA
481061 AAGATGATG
1 AAGATGATG
481070 AAGATGATG
1 AAGATGATG
481079 AAGATGATG
1 AAGATGATG
*
481088 ATGATGAT
1 AAGATGAT
481096 AATGATGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.26
Consensus pattern (9 bp):
AAGATGATG
Found at i:481674 original size:19 final size:19
Alignment explanation
Indices: 481645--481715 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
481635 ATAAAAAATC
481645 AAAAATC-AAAAATTAATA
1 AAAAATCAAAAAATTAATA
* *
481663 AAAAATCAAAAAAAATATATC
1 AAAAATC-AAAAAATTA-ATA
* *
481684 AAAAATAAAAAAATAAAATA
1 AAAAATCAAAAAAT-TAATA
*
481704 AAACA-CAAAAAA
1 AAAAATCAAAAAA
481716 GAAATGGTCA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
18 7 0.17
19 6 0.15
20 19 0.46
21 9 0.22
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAATCAAAAAATTAATA
Found at i:482337 original size:44 final size:44
Alignment explanation
Indices: 482263--482352 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
482253 CAATAGAGAT
* *
482263 GCTGTAGCAAATTAACAAATGGCAATAATGATGGATAAGCACCA
1 GCTGCAGCAAATTAACAAATGGCAACAATGATGGATAAGCACCA
* * *
482307 GCTGCAGCAAATTTACAAATGGCAGCAATGATGGATGAGCACCA
1 GCTGCAGCAAATTAACAAATGGCAACAATGATGGATAAGCACCA
482351 GC
1 GC
482353 AACACGTGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (44 bp):
GCTGCAGCAAATTAACAAATGGCAACAATGATGGATAAGCACCA
Found at i:482732 original size:35 final size:36
Alignment explanation
Indices: 482657--482737 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 36
482647 AAACTCAAAG
*
482657 AAAAAAACCAGATTCCAGTAGCATCCAATCCACGAT
1 AAAAAAACCAGATTCCAGCAGCATCCAATCCACGAT
* * * * *
482693 AAAAAAACTAGCTTCGAGCAGCCTCCAGTCCACGA-
1 AAAAAAACCAGATTCCAGCAGCATCCAATCCACGAT
482728 AAAAAAACCA
1 AAAAAAACCA
482738 ACACCAATAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 9 0.24
36 29 0.76
ACGTcount: A:0.46, C:0.28, G:0.12, T:0.14
Consensus pattern (36 bp):
AAAAAAACCAGATTCCAGCAGCATCCAATCCACGAT
Found at i:483775 original size:5 final size:5
Alignment explanation
Indices: 483734--483762 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
483724 ATTTTAAAAT
483734 TTTTA TTTTA TTTTA TTTTA TTTT- TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
483763 AATCTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:484052 original size:13 final size:14
Alignment explanation
Indices: 484031--484059 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
484021 AAATTTTCGT
484031 AAATAAAAATAATA
1 AAATAAAAATAATA
484045 AAAT-AAAATAATA
1 AAATAAAAATAATA
484058 AA
1 AA
484060 TAGATTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAATA
Found at i:492193 original size:20 final size:20
Alignment explanation
Indices: 492170--492223 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
492160 CACACCCAGA
492170 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
*
492190 TGTATCAATACATTATGCTT
1 TGTATCGATACATTATGCTT
492210 TGTATCGATACATT
1 TGTATCGATACATT
492224 GTATCGATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:492227 original size:13 final size:13
Alignment explanation
Indices: 492209--492235 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
492199 ACATTATGCT
492209 TTGTATCGATACA
1 TTGTATCGATACA
492222 TTGTATCGATACA
1 TTGTATCGATACA
492235 T
1 T
492236 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:492244 original size:19 final size:20
Alignment explanation
Indices: 492220--492275 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
492210 TGTATCGATA
492220 CATTGTATCGATACATGC-T
1 CATTGTATCGATACATGCGT
*
492239 CATTGTATCGATACATACGT
1 CATTGTATCGATACATGCGT
*
492259 AATTGTATCGATACATG
1 CATTGTATCGATACATG
492276 AAACTAGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (20 bp):
CATTGTATCGATACATGCGT
Found at i:492353 original size:20 final size:20
Alignment explanation
Indices: 492306--492356 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
492296 AAGTGAACTG
* *
492306 TATCGATACATGGGACATTG
1 TATCGATACATGAGACATTA
*
492326 TATTGATACATGAAGA-ATTA
1 TATCGATACATG-AGACATTA
492346 TATCGATACAT
1 TATCGATACAT
492357 TATGCCCAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
TATCGATACATGAGACATTA
Found at i:493193 original size:18 final size:18
Alignment explanation
Indices: 493166--493201 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
493156 TAATGCATAA
*
493166 TTTTATAATTTATAATAT
1 TTTTAAAATTTATAATAT
*
493184 TTTTAAAATTTGTAATAT
1 TTTTAAAATTTATAATAT
493202 AGTGAGGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTAAAATTTATAATAT
Found at i:496613 original size:80 final size:79
Alignment explanation
Indices: 496453--496915 Score: 331
Period size: 80 Copynumber: 5.9 Consensus size: 79
496443 AACACCGAAT
* * * * * * *
496453 TTTTCATCTCGGAGATACTTCAATCCCATTATTTTTGAA-GAGATACTCTAACACTCGTTTTTAC
1 TTTTCATCTCGGGGATACTTCAACCCCATTATTTCTCAAGGAGATACTCCAAC-CCCATTTTTAC
*
496517 TTCTAAAATATCAAA
65 TTCCAAAATATCAAA
* * * *
496532 TTTTTCATCTTGGGGGTACTTTAACCCCATTATTTCT-AAGGAGAAACTCCAACCCCATTTTTAC
1 -TTTTCATCTCGGGGATACTTCAACCCCATTATTTCTCAAGGAGATACTCCAACCCCATTTTTAC
496596 TTCCAAAATATCAAAA
65 TTCCAAAATATC-AAA
** ** * * *
496612 TTTTCATCTTTGGGATACTGAAACCCCATTATTT-TCGAGGGGATACTCCAA-CCCGTTTTTACT
1 TTTTCATCTCGGGGATACTTCAACCCCATTATTTCTCAAGGAGATACTCCAACCCCATTTTTACT
496675 TCCAAAATATCAAA
66 TCCAAAATATCAAA
* * * * * * *
496689 TTTTCATCTCGGGGATACTCCAACTCCATTATAT-TCGAGGAGATACTCTAATCCCATTTTTTCT
1 TTTTCATCTCGGGGATACTTCAACCCCATTATTTCTCAAGGAGATACTCCAACCCCATTTTTACT
** ***
496753 TTTAAAATAT-TTT
66 TCCAAAATATCAAA
* * * * * * *
496766 TTTTCCAT-T-GGGAATACTCCAACCCCATCATTT-TCAAGG-GAATACTCCAAACCCGTTTCTC
1 TTTT-CATCTCGGGGATACTTCAACCCCATTATTTCTCAAGGAG-ATACTCCAACCCCATTTTTA
*
496827 CTTCCAAAAGCT-TCCAAT
64 CTTCCAAAA--TAT-CAAA
* * * * * * *
496845 TTTTCACCATC-GGAATACTCCAACCCTATTATTT-TCATGGAGATACTCCAATCCCATTTTTAT
1 TTTTCATC-TCGGGGATACTTCAACCCCATTATTTCTCAAGGAGATACTCCAACCCCATTTTTAC
*
496908 TTTCAAAA
65 TTCCAAAA
496916 GCATCGATTT
Statistics
Matches: 311, Mismatches: 58, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
75 1 0.00
76 47 0.15
77 52 0.17
78 47 0.15
79 69 0.22
80 94 0.30
81 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (79 bp):
TTTTCATCTCGGGGATACTTCAACCCCATTATTTCTCAAGGAGATACTCCAACCCCATTTTTACT
TCCAAAATATCAAA
Found at i:496621 original size:79 final size:78
Alignment explanation
Indices: 496453--496749 Score: 305
Period size: 79 Copynumber: 3.8 Consensus size: 78
496443 AACACCGAAT
* * * * * * *
496453 TTTTCATCTCGGAGATACTTC-AATCCCATTATTTTTGAAGAGATACTCTAACACTCGTTTTTAC
1 TTTTCATCTTGGGGATAC-TCAAACCCCATTATTTCTGAGGAGATACTCCAAC-C-CATTTTTAC
* *
496517 TTCTAAAATATCAAAT
63 TTCCAAAATATCAAAA
* ** * *
496533 TTTTCATCTTGGGGGTACTTTAACCCCATTATTTCTAAGGAGAAACTCCAACCCCATTTTTACTT
1 TTTTCATCTTGGGGATACTCAAACCCCATTATTTCTGAGGAGATACTCCAA-CCCATTTTTACTT
496598 CCAAAATATCAAAA
65 CCAAAATATCAAAA
* * * *
496612 TTTTCATCTTTGGGATACTGAAACCCCATTATTT-TCGAGGGGATACTCCAACCCGTTTTTACTT
1 TTTTCATCTTGGGGATACTCAAACCCCATTATTTCT-GAGGAGATACTCCAACCCATTTTTACTT
496676 CCAAAATATC-AAA
65 CCAAAATATCAAAA
* * * *
496689 TTTTCATCTCGGGGATACTCCAACTCCATTATATTC-GAGGAGATACTCTAATCCCATTTTT
1 TTTTCATCTTGGGGATACTCAAACCCCATTAT-TTCTGAGGAGATACTCCAA-CCCATTTTT
496750 TCTTTTAAAA
Statistics
Matches: 182, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
77 43 0.24
78 33 0.18
79 65 0.36
80 40 0.22
81 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (78 bp):
TTTTCATCTTGGGGATACTCAAACCCCATTATTTCTGAGGAGATACTCCAACCCATTTTTACTTC
CAAAATATCAAAA
Found at i:496760 original size:156 final size:150
Alignment explanation
Indices: 496477--496915 Score: 389
Period size: 156 Copynumber: 2.8 Consensus size: 150
496467 ATACTTCAAT
* * * * *
496477 CCCATTATTTTTGAAGAGATACTCTAACACTCGTTTTTACTTCTAAAATATCAAATTTTTCATCT
1 CCCATTATTTTCGAGGGGATACTCCAAC-C-CGTTTTTACTTCCAAAATATCAAA-TTTTCATCT
* * ** * *
496542 TGGGGGTACTTTAACCCCATTATTTCTAAGGAGAAACTCCAACCCCATTTTTACTTCCAAAATAT
63 CGGGGATACTCCAA-CCCATTATTTC--AGGAGATACTCCAATCCCATTTTTACTTCCAAAATAT
* *
496607 CAAAATTTTCATCTTTGGG-ATACTGAAAC
125 --AAATTTTC--CATTGGGAATACTCAAAC
496636 CCCATTATTTTCGAGGGGATACTCCAACCCGTTTTTACTTCCAAAATATCAAATTTTCATCTCGG
1 CCCATTATTTTCGAGGGGATACTCCAACCCGTTTTTACTTCCAAAATATCAAATTTTCATCTCGG
* * ** ***
496701 GGATACTCCAACTCCATTATATTCGAGGAGATACTCTAATCCCATTTTTTCTTTTAAAATATTTT
66 GGATACTCCAAC-CCATTAT-TTC-AGGAGATACTCCAATCCCATTTTTACTTCCAAAATATAAA
*
496766 TTTTCCATTGGGAATACTCCAAC
128 TTTTCCATTGGGAATACTCAAAC
* * * * * * *
496789 CCCATCATTTTCAAGGGAATACTCCAAACCCGTTTCTCCTTCCAAAAGCT-TCCAATTTTTCACC
1 CCCATTATTTTCGAGGGGATACTCC-AACCCGTTTTTACTTCCAAAA--TAT-CAAATTTTCATC
* * *
496853 ATC-GGAATACTCCAACCCTATTATTTTCATGGAGATACTCCAATCCCATTTTTATTTTCAAAA
62 -TCGGGGATACTCCAACCC-ATTA-TTTCA-GGAGATACTCCAATCCCATTTTTACTTCCAAAA
496916 GCATCGATTT
Statistics
Matches: 235, Mismatches: 34, Indels: 25
0.80 0.12 0.09
Matches are distributed among these distances:
152 6 0.03
153 30 0.13
154 24 0.10
155 5 0.02
156 116 0.49
157 29 0.12
158 1 0.00
159 24 0.10
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.36
Consensus pattern (150 bp):
CCCATTATTTTCGAGGGGATACTCCAACCCGTTTTTACTTCCAAAATATCAAATTTTCATCTCGG
GGATACTCCAACCCATTATTTCAGGAGATACTCCAATCCCATTTTTACTTCCAAAATATAAATTT
TCCATTGGGAATACTCAAAC
Found at i:496916 original size:80 final size:79
Alignment explanation
Indices: 496554--496958 Score: 204
Period size: 80 Copynumber: 5.2 Consensus size: 79
496544 GGGGTACTTT
* * * * *
496554 AACCCCATTA-TTTCTAAGGAGAA-ACTCCAACCCCATTTTTACTTCCAAAA-TATCAAAATTTT
1 AACCCCATCATTTTC-AAGG-GAATACTCCAAACCCATTTCTACTTCCAAAAGCATC-AATTTTT
* * * * **
496616 CATCTTTGGGATACTGA
63 CACCATCGGAATACTCC
* * * * * * * *
496633 AACCCCATTATTTTCGAGGGGATACTCC-AACCCGTTTTTACTTCCAAAA-TATCAAATTTTCAT
1 AACCCCATCATTTTCAAGGGAATACTCCAAACCCATTTCTACTTCCAAAAGCATCAATTTTTCAC
*
496696 C-TCGGGGATACTCC
66 CATC-GGAATACTCC
* * * * * * * * ** * **
496710 AACTCCATTATATTCGA-GGAGATACTCTAATCCCATTTTTTCTT-TTAAA--AT-ATTTTTTTT
1 AACCCCATCATTTTCAAGGGA-ATACTCCAAACCCATTTCTACTTCCAAAAGCATCAATTTTTCA
*
496770 CCATTGGGAATACTCC
65 CCA-TCGGAATACTCC
* * *
496786 AACCCCATCATTTTCAAGGGAATACTCCAAACCCGTTTCTCCTTCCAAAAGCTTCCAATTTTTCA
1 AACCCCATCATTTTCAAGGGAATACTCCAAACCCATTTCTACTTCCAAAAGCAT-CAATTTTTCA
496851 CCATCGGAATACTCC
65 CCATCGGAATACTCC
* * * * * * * *
496866 AACCCTATTATTTTC-ATGGAGATACTCCAATCCCATTTTTATTTTCAAAAGCATCGATTTTTCA
1 AACCCCATCATTTTCAAGGGA-ATACTCCAAACCCATTTCTACTTCCAAAAGCATCAATTTTTCA
* *
496930 CTATCGTGGATACTCC
65 CCATCG-GAATACTCC
* *
496946 AATCTCATCATTT
1 AACCCCATCATTT
496959 ATGAGGGGAT
Statistics
Matches: 255, Mismatches: 56, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
75 6 0.02
76 45 0.18
77 50 0.20
78 37 0.15
79 37 0.15
80 71 0.28
81 9 0.04
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36
Consensus pattern (79 bp):
AACCCCATCATTTTCAAGGGAATACTCCAAACCCATTTCTACTTCCAAAAGCATCAATTTTTCAC
CATCGGAATACTCC
Found at i:498984 original size:3 final size:3
Alignment explanation
Indices: 498976--499016 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
498966 CGTTTACATC
498976 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
499017 CAGTAGAACT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:499396 original size:13 final size:13
Alignment explanation
Indices: 499378--499402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
499368 AAGTAGTAGA
499378 TGTATCGATACAG
1 TGTATCGATACAG
499391 TGTATCGATACA
1 TGTATCGATACA
499403 TGCTTAAAAT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:499503 original size:22 final size:20
Alignment explanation
Indices: 499473--499526 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
499463 TTAGTAAGTG
*
499473 TATCAATACATGCTTACAATTC
1 TATCGATACATGCTT-CAA-TC
* * *
499495 TATCGATACATTCTTTAATG
1 TATCGATACATGCTTCAATC
499515 TATCGATACATG
1 TATCGATACATG
499527 GAGGTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 12 0.44
21 2 0.07
22 13 0.48
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (20 bp):
TATCGATACATGCTTCAATC
Found at i:499520 original size:20 final size:21
Alignment explanation
Indices: 499451--499525 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
499441 GCCAAGGAAA
**
499451 TGTATCGATACATT-AGTAAG
1 TGTATCGATACATTCTTTAAG
* * * *
499471 TGTATCAATACATGCTTACAAT
1 TGTATCGATACATTCTT-TAAG
*
499493 TCTATCGATACATTCTTTAA-
1 TGTATCGATACATTCTTTAAG
499513 TGTATCGATACAT
1 TGTATCGATACAT
499526 GGAGGTAAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 24 0.57
21 2 0.05
22 16 0.38
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTCTTTAAG
Found at i:499825 original size:43 final size:43
Alignment explanation
Indices: 499755--499847 Score: 132
Period size: 43 Copynumber: 2.2 Consensus size: 43
499745 GTATTTTCAG
* * *
499755 CCACCCTATTTTCCTCTGAACCCTGGCAAGCATTCATTTCCAA
1 CCACCTTATTTTCCTATAAACCCTGGCAAGCATTCATTTCCAA
* * *
499798 CCACCTTATTTTGCTATAAACCTTGGCAAGCATTCATTTCCAG
1 CCACCTTATTTTCCTATAAACCCTGGCAAGCATTCATTTCCAA
499841 CCACCTT
1 CCACCTT
499848 TCTCAACCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.24, C:0.34, G:0.10, T:0.32
Consensus pattern (43 bp):
CCACCTTATTTTCCTATAAACCCTGGCAAGCATTCATTTCCAA
Found at i:502864 original size:19 final size:19
Alignment explanation
Indices: 502840--502876 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
502830 CTACGGATCT
502840 TCCACCTTCAATCAATATC
1 TCCACCTTCAATCAATATC
502859 TCCACCTTCAATCAATAT
1 TCCACCTTCAATCAATAT
502877 GTTTCTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (19 bp):
TCCACCTTCAATCAATATC
Found at i:503552 original size:22 final size:23
Alignment explanation
Indices: 503526--503583 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
503516 TGTAAGATAC
***
503526 TTTTATATTTATTTTATTA-ATT
1 TTTTATATTTATAAAATTATATT
*
503548 TTTTATATTTAAAAAATTATATT
1 TTTTATATTTATAAAATTATATT
503571 TTTTATATTTATA
1 TTTTATATTTATA
503584 TTAAAATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTATATTTATAAAATTATATT
Found at i:503592 original size:23 final size:23
Alignment explanation
Indices: 503526--503594 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
503516 TGTAAGATAC
* **
503526 TTTTATATTTATTTTATTA-ATT
1 TTTTATATTTATATTAAAATATT
*
503548 TTTTATATTTA-A-AAAATTATATT
1 TTTTATATTTATATTAAA--ATATT
503571 TTTTATATTTATATTAAAATATT
1 TTTTATATTTATATTAAAATATT
503594 T
1 T
503595 ATTAAATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
20 1 0.03
22 12 0.32
23 20 0.54
24 1 0.03
25 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTATATTTATATTAAAATATT
Found at i:503616 original size:13 final size:13
Alignment explanation
Indices: 503598--503622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
503588 AATATTTATT
503598 AAATATAAATATC
1 AAATATAAATATC
503611 AAATATAAATAT
1 AAATATAAATAT
503623 TTAAAAAAAT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAAATATC
Found at i:503805 original size:28 final size:28
Alignment explanation
Indices: 503765--503820 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
503755 GTTTGTAAAC
503765 TATCATTGTAATCTTATTTCTTAATGCA
1 TATCATTGTAATCTTATTTCTTAATGCA
503793 TATCATTGTAATCTTATTTCTTAATGCA
1 TATCATTGTAATCTTATTTCTTAATGCA
503821 ATGTTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (28 bp):
TATCATTGTAATCTTATTTCTTAATGCA
Found at i:505581 original size:22 final size:23
Alignment explanation
Indices: 505548--505612 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
505538 TGTTAAAATT
505548 TTTAA-AATTATTTTTATTTTAATA
1 TTTAATAA-TATTTTTATTTTAA-A
*
505572 TTT-AT-ATATTTTTATAATTAAA
1 TTTAATAATATTTTTAT-TTTAAA
505594 TTTAGATAATATTTTTATT
1 TTTA-ATAATATTTTTATT
505613 AATGAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
22 13 0.38
23 6 0.18
24 5 0.15
25 10 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTAATAATATTTTTATTTTAAA
Found at i:518308 original size:25 final size:25
Alignment explanation
Indices: 518271--518323 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
518261 CTAAATTTAA
* *
518271 ATTTTAAATTTTAAATTTTGATT-AG
1 ATTTTAAACTTTAAAATTT-ATTCAG
*
518296 ATTTTATACTTTAAAATTTATTCAG
1 ATTTTAAACTTTAAAATTTATTCAG
518321 ATT
1 ATT
518324 ATTTTTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.55
Consensus pattern (25 bp):
ATTTTAAACTTTAAAATTTATTCAG
Found at i:519381 original size:21 final size:22
Alignment explanation
Indices: 519363--519404 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
519353 ATTTATTTTT
519363 AAATTT-TTTTTTTATATTTAA
1 AAATTTATTTTTTTATATTTAA
*
519384 AAATTTATTTTTTTAGATTTA
1 AAATTTATTTTTTTATATTTA
519405 TATTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
AAATTTATTTTTTTATATTTAA
Found at i:521068 original size:21 final size:21
Alignment explanation
Indices: 521044--521104 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
521034 TATAACTAAT
521044 ATAATTATATTATTAAATTAA
1 ATAATTATATTATTAAATTAA
*
521065 ATAATTA-ATTTATTAAAATAA
1 ATAATTATA-TTATTAAATTAA
* *
521086 AAAATATATATTATAAAAT
1 ATAAT-TATATTATTAAAT
521105 ATATAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 22 0.67
22 9 0.27
23 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTATATTATTAAATTAA
Found at i:526174 original size:20 final size:20
Alignment explanation
Indices: 526139--526184 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
526129 TTAGCATGCT
526139 AAAA-AACAAAAGGACAAAG
1 AAAAGAACAAAAGGACAAAG
526158 AAAAGAACAGAAA-GACAAAG
1 AAAAGAACA-AAAGGACAAAG
526178 AAAAGAA
1 AAAAGAA
526185 TAACATGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.16
20 18 0.72
21 3 0.12
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAGAACAAAAGGACAAAG
Found at i:531837 original size:20 final size:20
Alignment explanation
Indices: 531812--531886 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
531802 TTTTACCCAG
531812 ATATATCGATACATTTTTCA
1 ATATATCGATACATTTTTCA
* * *
531832 ATATATCGATACATATATGA
1 ATATATCGATACATTTTTCA
* * * *
531852 ATGTATTGATATATTCTTCA
1 ATATATCGATACATTTTTCA
*
531872 ATGTATCGATACATT
1 ATATATCGATACATT
531887 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (20 bp):
ATATATCGATACATTTTTCA
Found at i:532826 original size:20 final size:19
Alignment explanation
Indices: 532794--532839 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
532784 AGCCTTTGAC
*
532794 CATGCATTTTTTATTATGTTT
1 CATGCA-TTTTTAATAT-TTT
532815 CATGCATTTTTAATATTTT
1 CATGCATTTTTAATATTTT
532834 CA-GCAT
1 CATGCAT
532840 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 5 0.21
20 9 0.38
21 6 0.25
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (19 bp):
CATGCATTTTTAATATTTT
Found at i:536167 original size:26 final size:25
Alignment explanation
Indices: 536138--536186 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
536128 TTTCTAGATA
*
536138 TGTTTTGACTCAATATTGATTTCATT
1 TGTTTCGACTCAATATT-ATTTCATT
*
536164 TGTTTCGACTCGATATTATTTCA
1 TGTTTCGACTCAATATTATTTCA
536187 ATATAATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.51
Consensus pattern (25 bp):
TGTTTCGACTCAATATTATTTCATT
Found at i:545192 original size:78 final size:78
Alignment explanation
Indices: 545087--545237 Score: 268
Period size: 79 Copynumber: 1.9 Consensus size: 78
545077 ACATATAATA
*
545087 GGTTTATGATTTGAATTTTAATATTTGTAA-TTTTTATTTTATTTCAAGTTACTATTAAACATGT
1 GGTTTATGATTTAAATTTTAATATTTGTAATTTTTTATTTTATTTCAAGTTACTATTAAACATGT
545151 TTATGAGTTAGAC
66 TTATGAGTTAGAC
*
545164 GGTTTATGATTTTAAATTTTAATATTTGTAATTTTTTATTTTATTTCAAGTTACTATTAAACTTG
1 GGTTTATGA-TTTAAATTTTAATATTTGTAATTTTTTATTTTATTTCAAGTTACTATTAAACATG
545229 TTTATGAGT
65 TTTATGAGT
545238 ATTTCAAACG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 9 0.13
78 20 0.29
79 41 0.59
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (78 bp):
GGTTTATGATTTAAATTTTAATATTTGTAATTTTTTATTTTATTTCAAGTTACTATTAAACATGT
TTATGAGTTAGAC
Found at i:545299 original size:13 final size:13
Alignment explanation
Indices: 545281--545306 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
545271 GGCCGATCAA
545281 ACATAAGTTAATT
1 ACATAAGTTAATT
545294 ACATAAGTTAATT
1 ACATAAGTTAATT
545307 TGAAATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ACATAAGTTAATT
Found at i:546863 original size:2 final size:2
Alignment explanation
Indices: 546856--546886 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
546846 CACTAAGAAC
546856 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
546887 AGTCAAAACT
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:547808 original size:125 final size:124
Alignment explanation
Indices: 547643--547892 Score: 374
Period size: 125 Copynumber: 2.0 Consensus size: 124
547633 TTTTAAAATG
* *
547643 ATATATCTTTAAATATATTAATTTAAAATTTAAAATTTAATATTTGTAATTAGATTTATTTATAA
1 ATATATCTTTAAATACATTAATTTAAAATTTAAAATTTAATATTTATAATTAGATTTATTTATAA
* * * * * *
547708 ATTAAATTCATCGTTATTGAAAATTTTAAAAAAAATTTTTCTTAAGTTTAGGTCAAGTTA
66 ATCAAATTAATCATGATTGAAAATTTT-AAAAAAATTTTGCTTAAGCTTAGGTCAAGTTA
* *
547768 ATATATCTTTAAATACGTTAATTTAAAATTTAAATTTTAATATTTATAATTAGATTTATTTATAA
1 ATATATCTTTAAATACATTAATTTAAAATTTAAAATTTAATATTTATAATTAGATTTATTTATAA
* * *
547833 ATCAAATTAATTATGATTGAAAATTTTTAAAATATTTTGCTTAAGCTTAGGTCAAGTTA
66 ATCAAATTAATCATGATTGAAAATTTTAAAAAAATTTTGCTTAAGCTTAGGTCAAGTTA
547892 A
1 A
547893 CTAAAAAACT
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
124 29 0.26
125 83 0.74
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (124 bp):
ATATATCTTTAAATACATTAATTTAAAATTTAAAATTTAATATTTATAATTAGATTTATTTATAA
ATCAAATTAATCATGATTGAAAATTTTAAAAAAATTTTGCTTAAGCTTAGGTCAAGTTA
Found at i:547956 original size:23 final size:23
Alignment explanation
Indices: 547903--547975 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
547893 CTAAAAAACT
*
547903 TATTT-TATTATTTATTATATTAT
1 TATTTATATTATTT-TTATATTAA
**
547926 TA-AAATATTATTTTTATATTAA
1 TATTTATATTATTTTTATATTAA
547948 TATTTATA-TATTTTTATAATTAA
1 TATTTATATTATTTTTAT-ATTAA
547971 -ATTTA
1 TATTTA
547976 AATAAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 24 0.57
23 18 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTATATTATTTTTATATTAA
Found at i:553002 original size:37 final size:36
Alignment explanation
Indices: 552950--553048 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 36
552940 TTTATTTTTC
** *
552950 GTGGATTGGCGCTGCCACCCAAATTTTGACAATCATA
1 GTGGATTGGC-CTGCCACCCAAATACTAACAATCATA
* *
552987 GTGGATTAGCACTGCCACTCAAATACTAACAATCATA
1 GTGGATTGGC-CTGCCACCCAAATACTAACAATCATA
*
553024 GTGGATTGGCCAAGCCACCCAAATA
1 GTGGATTGGCC-TGCCACCCAAATA
553049 TTACTTGTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 1 0.02
37 51 0.98
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (36 bp):
GTGGATTGGCCTGCCACCCAAATACTAACAATCATA
Found at i:557751 original size:37 final size:37
Alignment explanation
Indices: 557692--557790 Score: 101
Period size: 37 Copynumber: 2.7 Consensus size: 37
557682 TTTATTTTTC
* * * *
557692 GTGGATTGGCGCTGCCACCCAAATTCTGACAATCATA
1 GTGGATTGACACTGCCACCCAAATACTAACAATCATA
* *
557729 GTGGATTGACACTGTCATCCAAATACTAACAATCATA
1 GTGGATTGACACTGCCACCCAAATACTAACAATCATA
* * *
557766 ATGGATTGGC-CAAGCCACCCAAATA
1 GTGGATTGACAC-TGCCACCCAAATA
557791 TTACTTATCG
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
36 1 0.02
37 49 0.98
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (37 bp):
GTGGATTGACACTGCCACCCAAATACTAACAATCATA
Found at i:559662 original size:20 final size:19
Alignment explanation
Indices: 559622--559685 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
559612 CATTATAATA
*
559622 ATTTTTAAAATATTT-TAT
1 ATTTATAAAATATTTATAT
559640 ATTTATCAAAAT-TTTAATAT
1 ATTTAT-AAAATATTT-ATAT
* *
559660 ATTAATAAAATATTTTTAT
1 ATTTATAAAATATTTATAT
559679 ATTTATA
1 ATTTATA
559686 TTTCATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 8 0.21
19 19 0.50
20 11 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTATAAAATATTTATAT
Found at i:559722 original size:28 final size:27
Alignment explanation
Indices: 559668--559742 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
559658 ATATTAATAA
559668 AATATTTTTATATTTATATTTCATTTAT
1 AATATTTTTATA-TTATATTTCATTTAT
*
559696 ATTATTTTTATATTATATTAT-ATTTTAT
1 AATATTTTTATATTATATT-TCA-TTTAT
559724 AATATATTTTA-ATTA-ATTT
1 AATAT-TTTTATATTATATTT
559743 TTAATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 1 0.02
27 11 0.26
28 25 0.60
29 5 0.12
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (27 bp):
AATATTTTTATATTATATTTCATTTAT
Found at i:559723 original size:17 final size:17
Alignment explanation
Indices: 559675--559731 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
559665 TAAAATATTT
*
559675 TTATATTTATATTTCAT-
1 TTATA-TTATATTTTATA
559692 TTATATTAT-TTTTATA
1 TTATATTATATTTTATA
559708 TTATATTATATTTTATA
1 TTATATTATATTTTATA
*
559725 ATATATT
1 TTATATT
559732 TTAATTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
15 5 0.14
16 13 0.36
17 18 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTATATTTTATA
Found at i:559952 original size:17 final size:16
Alignment explanation
Indices: 559932--559979 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
559922 AAATACATAA
*
559932 AAAATATAAATATTTTT
1 AAAATATAAA-AATTTT
*
559949 AAAAAATTAAAAATTTT
1 AAAATA-TAAAAATTTT
559966 AATAATATAAAAAT
1 AA-AATATAAAAAT
559980 ATTTTTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATATAAAAATTTT
Found at i:559959 original size:18 final size:19
Alignment explanation
Indices: 559929--559984 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
559919 AAAAAATACA
*
559929 TAAAAAATATAAATATTTT
1 TAAAAAATATAAAAATTTT
559948 TAAAAAAT-TAAAAA-TTT
1 TAAAAAATATAAAAATTTT
*
559965 T-AATAATATAAAAATATTT
1 TAAAAAATATAAAAAT-TTT
559984 T
1 T
559985 TTATCTCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 5 0.16
17 10 0.31
18 5 0.16
19 12 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAAATATAAAAATTTT
Found at i:560406 original size:2 final size:2
Alignment explanation
Indices: 560339--560390 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
560329 TTAGACACAT
* * *
560339 TA TA AA TA TA AA TA TA AA TA TA TA -A 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
560380 TA TA TA TA TA T
1 TA TA TA TA TA T
560391 TCTATACTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:561587 original size:27 final size:27
Alignment explanation
Indices: 561548--561599 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
561538 TTTAAAAGAT
*
561548 AAAAAAAATTTATACCTAATAGATAAA
1 AAAAAAAAATTATACCTAATAGATAAA
561575 AAAAAAAAATTATACCTAATAGATA
1 AAAAAAAAATTATACCTAATAGATA
561600 TAGGAGTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAAAAAAATTATACCTAATAGATAAA
Found at i:565833 original size:13 final size:12
Alignment explanation
Indices: 565793--565846 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
565783 TATGTATATA
565793 ATAAATATTAAT
1 ATAAATATTAAT
* *
565805 ATAATTAATT-AG
1 ATAAAT-ATTAAT
565817 ATAAATATTAAAT
1 ATAAATATT-AAT
565830 ATAAATATTAAT
1 ATAAATATTAAT
565842 ATAAA
1 ATAAA
565847 AAATTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 3 0.09
12 19 0.54
13 13 0.37
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
ATAAATATTAAT
Found at i:567782 original size:19 final size:20
Alignment explanation
Indices: 567749--567787 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
567739 TGTGTACGTG
567749 TATATATATATATAA-ATTT
1 TATATATATATATAATATTT
567768 TATATAT-TATAATAATATTT
1 TATATATATAT-ATAATATTT
567788 AAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 11 0.61
20 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATATATATATAATATTT
Found at i:567852 original size:6 final size:6
Alignment explanation
Indices: 567841--567886 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
567831 AATTTTAAAA
* *
567841 TATTTT TATTTT TATTTT TATATTA TATTTT TATATT TATATTT TA
1 TATTTT TATTTT TATTTT TAT-TTT TATTTT TATTTT TAT-TTT TA
567887 GATTATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 25 0.74
7 9 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:567871 original size:19 final size:19
Alignment explanation
Indices: 567847--567913 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
567837 AAAATATTTT
567847 TATTTTTATTTTTATATTA
1 TATTTTTATTTTTATATTA
* *
567866 TATTTTTATATTTATATTT
1 TATTTTTATTTTTATATTA
**
567885 TA-GATTATATTTTA-ATTA
1 TATTTTTAT-TTTTATATTA
567903 T-TTTTTATTTT
1 TATTTTTATTTT
567914 ATGTTTATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 23 0.61
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (19 bp):
TATTTTTATTTTTATATTA
Found at i:567915 original size:12 final size:12
Alignment explanation
Indices: 567855--567915 Score: 61
Period size: 12 Copynumber: 5.0 Consensus size: 12
567845 TTTATTTTTA
567855 TTTTTATATTAT
1 TTTTTATATTAT
567867 ATTTTTATATTTAT
1 -TTTTTATA-TTAT
* *
567881 ATTTTAGATTAT
1 TTTTTATATTAT
*
567893 ATTTTA-ATTAT
1 TTTTTATATTAT
*
567904 TTTTTATTTTAT
1 TTTTTATATTAT
567916 GTTTATTACT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 10 0.24
12 14 0.33
13 14 0.33
14 4 0.10
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (12 bp):
TTTTTATATTAT
Found at i:568277 original size:7 final size:7
Alignment explanation
Indices: 568265--568308 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
568255 ATATATTTTT
568265 TTATTAA
1 TTATTAA
568272 TTATTAA
1 TTATTAA
568279 TTATTAA
1 TTATTAA
568286 TTATTAA
1 TTATTAA
568293 TTATTAA
1 TTATTAA
568300 TTATTAA
1 TTATTAA
568307 TT
1 TT
568309 TTTCATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTATTAA
Found at i:569482 original size:13 final size:13
Alignment explanation
Indices: 569464--569493 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
569454 TACAAGCCAA
*
569464 TGTATCGATACAT
1 TGTATCAATACAT
569477 TGTATCAATACAT
1 TGTATCAATACAT
569490 TGTA
1 TGTA
569494 CCATGTATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:569564 original size:21 final size:21
Alignment explanation
Indices: 569538--569593 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
569528 CTGCCAATTT
**
569538 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
569559 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
569578 CATGTATCGATACAAT
1 CATGTATCGATACAAT
569594 GTATCGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:569597 original size:13 final size:13
Alignment explanation
Indices: 569579--569605 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
569569 TACATTGAAC
569579 ATGTATCGATACA
1 ATGTATCGATACA
569592 ATGTATCGATACA
1 ATGTATCGATACA
569605 A
1 A
569606 GGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:570165 original size:15 final size:17
Alignment explanation
Indices: 570145--570178 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
570135 ATTTTCGTTT
570145 TTCT-CCCCTTAAA-AA
1 TTCTCCCCCTTAAACAA
570160 TTCTCCCCCTTAAACAA
1 TTCTCCCCCTTAAACAA
570177 TT
1 TT
570179 ATCTTCTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (17 bp):
TTCTCCCCCTTAAACAA
Found at i:572118 original size:13 final size:13
Alignment explanation
Indices: 572100--572128 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
572090 AAATAGTACC
572100 CAATGTATCGATA
1 CAATGTATCGATA
572113 CAATGTATCGATA
1 CAATGTATCGATA
572126 CAA
1 CAA
572129 GAAATGTTGT
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:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:572289 original size:19 final size:19
Alignment explanation
Indices: 572254--572294 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
572244 CTATAGACCC
572254 TAATTCATATCAAACAACCA
1 TAATTCATATCAAACAA-CA
*
572274 TAATTCA-ATCATACAACA
1 TAATTCATATCAAACAACA
572292 TAA
1 TAA
572295 CAAATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 8 0.40
20 7 0.35
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (19 bp):
TAATTCATATCAAACAACA
Found at i:573762 original size:13 final size:13
Alignment explanation
Indices: 573744--573768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
573734 CATAAAGTGT
573744 TGTATCGATACAA
1 TGTATCGATACAA
573757 TGTATCGATACA
1 TGTATCGATACA
573769 TATTTTTTTG
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:573762 original size:33 final size:33
Alignment explanation
Indices: 573724--573790 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
573714 TTCAACAATT
573724 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
573757 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
573790 T
1 T
573791 TTAAGCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:573849 original size:13 final size:13
Alignment explanation
Indices: 573831--573855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
573821 ATTACTCAAA
573831 TGTATCGATACAT
1 TGTATCGATACAT
573844 TGTATCGATACA
1 TGTATCGATACA
573856 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:573920 original size:52 final size:52
Alignment explanation
Indices: 573864--573988 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
573854 CACTGATCTT
*
573864 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
* *
573916 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
*
573968 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
573989 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
Found at i:580887 original size:51 final size:50
Alignment explanation
Indices: 580765--580900 Score: 148
Period size: 51 Copynumber: 2.6 Consensus size: 50
580755 AAAATTAGTA
* * *
580765 TTTTAGAGATAACAACGGGGCTAGAGTATCCCCGATTACGGAAAAACGGTG
1 TTTTAGAAATAA-AACGGGGTTAGAGTATCCCCGATTACGGAAAAACGATG
* * * *
580816 TTCTAAAGAATAAAATCGGGGTTAGAGTATCCCCGATTA-TGAAAAATTGATG
1 TTTTAGA-AATAAAA-CGGGGTTAGAGTATCCCCGATTACGGAAAAA-CGATG
*
580868 TTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 TTTTAGAAATAAAA-CGGGGTTAGAGTATCCCC
580901 TCGAAAATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
51 37 0.52
52 34 0.48
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (50 bp):
TTTTAGAAATAAAACGGGGTTAGAGTATCCCCGATTACGGAAAAACGATG
Found at i:580924 original size:79 final size:79
Alignment explanation
Indices: 580832--581338 Score: 811
Period size: 79 Copynumber: 6.4 Consensus size: 79
580822 AGAATAAAAT
*
580832 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
580897 CCCCTCGAAAATAA
66 CCCCTCGAAAATAA
580911 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
580976 CCCCTC-AGAAATAA
66 CCCCTCGA-AAATAA
* * * *
580990 CAGGGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
581055 CACCTCGAAAATAA
66 CCCCTCGAAAATAA
* * * * *
581069 CGAGGTTTGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAGATAAAACCGGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
581134 -CCCTCGGAAATAA
66 CCCCTCGAAAATAA
* *
581147 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
581212 CCCCTCAAAAATAA
66 CCCCTCGAAAATAA
* *
581226 CGGGGTTGGAGTATCTCCGATTATGAAAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
581291 CCCCTCGGAAATAA
66 CCCCTCGAAAATAA
* *
581305 AGGGGTTGGAGTATCCCCGATTGTGAAAAATTGA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGA
581339 GAAACTTAAC
Statistics
Matches: 392, Mismatches: 33, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
78 72 0.18
79 319 0.81
80 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGAAAATAA
Found at i:581255 original size:236 final size:237
Alignment explanation
Indices: 580835--581338 Score: 821
Period size: 236 Copynumber: 2.1 Consensus size: 237
580825 ATAAAATCGG
*
580835 GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCC
*
580900 CTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGG
66 CTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCAG
* *
580965 GGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTT
131 GGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTT
*
581030 AGAAATAAAACCGGGGTTGGAGTATCACCTCGAAAATAACGA
196 AGAAATAAAACCGGGGTTGGAGTATCACCTCGAAAATAAAGA
* * *
581072 GGTTTGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAGATAAAACCGGGGTTAGAGTAT-CC
1 GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCC
* *
581136 CTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCAG
66 CTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCAG
* * * *
581201 GGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCTCCGATTATGAAAAATTGATGTTTT
131 GGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTT
* * * *
581266 AGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAATAAAGG
196 AGAAATAAAACCGGGGTTGGAGTATCACCTCGAAAATAAAGA
* *
581308 GGTTGGAGTATCCCCGATTGTGAAAAATTGA
1 GGTTAGAGTATCCCCGATTATGAAAAATTGA
581339 GAAACTTAAC
Statistics
Matches: 246, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
236 188 0.76
237 58 0.24
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (237 bp):
GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCC
CTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCAG
GGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTT
AGAAATAAAACCGGGGTTGGAGTATCACCTCGAAAATAAAGA
Done.