Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold357
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: 802879
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 4 of 6
Found at i:459957 original size:100 final size:99
Alignment explanation
Indices: 459853--460056 Score: 261
Period size: 100 Copynumber: 2.0 Consensus size: 99
459843 TTATTATTTA
* **
459853 ATATATTAATCACATGAT-ATTAG-AATAATATTTAATTTTTAATTATATAATAACATTTAATTT
1 ATATATTAAT-A-ATGATCATT-GTAATAATATTTAATTGTTAATTATATAATAACATTTAAACT
* *
459916 AAGAGTTAAAGAAATAGATGAT-TTAATTTTAAATTAT
63 AAGAATTAAAAAAATAGATGATGTT-ATTTTAAATTAT
* * * *
459953 ATATATTGATAATTATGCATTGTAATAATATTTTATTGTTAATTATATAATAAGATTTAAACTAA
1 ATATATTAATAATGAT-CATTGTAATAATATTTAATTGTTAATTATATAATAACATTTAAACTAA
460018 GAATTAAAAAAATAGATGATGTTATTTTAAATTAT
65 GAATTAAAAAAATAGATGATGTTATTTTAAATTAT
460053 ATAT
1 ATAT
460057 TGATAGCTAT
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
98 4 0.04
99 2 0.02
100 83 0.91
101 2 0.02
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (99 bp):
ATATATTAATAATGATCATTGTAATAATATTTAATTGTTAATTATATAATAACATTTAAACTAAG
AATTAAAAAAATAGATGATGTTATTTTAAATTAT
Found at i:460337 original size:22 final size:20
Alignment explanation
Indices: 460304--460347 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
460294 TATTCTTTAC
460304 ATTTTC-TCTATA-AGTTGTT
1 ATTTTCTTCTATATAGTT-TT
460323 ATTTTCTTCTATATAGTTTT
1 ATTTTCTTCTATATAGTTTT
460343 ATTTT
1 ATTTT
460348 TTAACATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 13 0.57
21 4 0.17
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (20 bp):
ATTTTCTTCTATATAGTTTT
Found at i:461381 original size:16 final size:16
Alignment explanation
Indices: 461356--461403 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
461346 AATATATTTA
461356 TATATTATA-TTATAT
1 TATATTATATTTATAT
* *
461371 TATATTTATATTTAAAA
1 TATA-TTATATTTATAT
*
461388 TATTTTATATTTATAT
1 TATATTATATTTATAT
461404 AAATTTTGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTATATTTATAT
Found at i:461398 original size:22 final size:23
Alignment explanation
Indices: 461348--461404 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
461338 TATTGTGAAA
* *
461348 TATATTTATATATTATATTATAT
1 TATATTTATATATTAAAATATAT
*
461371 TATATTTATAT-TTAAAATATTT
1 TATATTTATATATTAAAATATAT
461393 TATATTTATATA
1 TATATTTATATA
461405 AATTTTGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATTTATATATTAAAATATAT
Found at i:461785 original size:173 final size:173
Alignment explanation
Indices: 461480--461798 Score: 428
Period size: 173 Copynumber: 1.8 Consensus size: 173
461470 TTGAAGATTT
461480 TTTTCATTTTTTAATGGATAAAATTTTAAATTTAATTAATGCCTTTTCGATGTATTTAATAATTC
1 TTTTCATTTTTTAATGGATAAAATTTTAAATTTAATTAATGCCTTTTC-ATGTATTTAATAATTC
* * * * * * *
461545 AATTTTATTTGTGTTAACAATATTTTAAGTTAATTTATTATTAAATTATGTATTTAATAACTATG
65 AATGTCACTTGGGTTAACAACATATTAAGTTAATTTATTATTAAATTATATATTTAATAACTATG
461610 ATTTTTATGTT-TACAATATATATTAAAGATTATATTAATTATTA
130 ATTTTTAT-TTCTACAATATATATTAAAGATTATATTAATTATTA
* ** **
461654 TTTTCATATTTTTAGTGGATAATTTTTTTTATTTAATTAATGCCTTATT-ATGTATTTAATAATT
1 TTTTCAT-TTTTTAATGGATAAAATTTTAAATTTAATTAATGCCTT-TTCATGTATTTAATAATT
* ** * *
461718 CAATGTCACTTGGGTTAA-AACGTATTAAGTTGGTTTATTATTAAATTATATATTTGATAATTAT
64 CAATGTCACTTGGGTTAACAACATATTAAGTTAATTTATTATTAAATTATATATTTAATAACTAT
461782 GATTTTTATTTCTACAA
129 GATTTTTATTTCTACAA
461799 CAAATCTCTA
Statistics
Matches: 125, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
172 2 0.02
173 52 0.42
174 36 0.29
175 33 0.26
176 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.52
Consensus pattern (173 bp):
TTTTCATTTTTTAATGGATAAAATTTTAAATTTAATTAATGCCTTTTCATGTATTTAATAATTCA
ATGTCACTTGGGTTAACAACATATTAAGTTAATTTATTATTAAATTATATATTTAATAACTATGA
TTTTTATTTCTACAATATATATTAAAGATTATATTAATTATTA
Found at i:462307 original size:20 final size:20
Alignment explanation
Indices: 462284--462324 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
462274 TTAAATTTTT
462284 AATATATTTT-TATATATTAA
1 AATATATTTTAT-TATATTAA
462304 AATATATTTTATTATATTAA
1 AATATATTTTATTATATTAA
462324 A
1 A
462325 TACGTGTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATATTTTATTATATTAA
Found at i:463266 original size:18 final size:18
Alignment explanation
Indices: 463246--463283 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
463236 ATATAATTAA
*
463246 TTTTATATATTTTTATAAT
1 TTTTATATA-ATTTATAAT
463265 TTTTATATAATTTATAAT
1 TTTTATATAATTTATAAT
463283 T
1 T
463284 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATATAATTTATAAT
Found at i:463305 original size:21 final size:21
Alignment explanation
Indices: 463263--463301 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
463253 TATTTTTATA
*
463263 ATTTTTATATAATTTATAATT
1 ATTTTTATATAATTTAAAATT
*
463284 ATTTTTTTA-AATTTAAAA
1 ATTTTTATATAATTTAAAA
463302 ATTAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTTATATAATTTAAAATT
Found at i:463994 original size:18 final size:19
Alignment explanation
Indices: 463971--464012 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
463961 AATAAATTTG
*
463971 AATAATAT-TGAAATTCAA
1 AATAATATATAAAATTCAA
*
463989 AATAATATATAAAATTTAA
1 AATAATATATAAAATTCAA
464008 AATAA
1 AATAA
464013 CTTAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AATAATATATAAAATTCAA
Found at i:465385 original size:2 final size:2
Alignment explanation
Indices: 465380--465416 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
465370 AGACAATTGC
465380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
465417 GAATAAATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:466814 original size:32 final size:32
Alignment explanation
Indices: 466778--466846 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
466768 CTTAAAATAA
466778 GAGATTAAAAAATAAGAGATTTTTTTAAGTGG
1 GAGATTAAAAAATAAGAGATTTTTTTAAGTGG
*
466810 GAGATTAAAAAATAAGAGATTTTTTTGAGTGG
1 GAGATTAAAAAATAAGAGATTTTTTTAAGTGG
466842 GAGAT
1 GAGAT
466847 AAAGGAACGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (32 bp):
GAGATTAAAAAATAAGAGATTTTTTTAAGTGG
Found at i:466982 original size:21 final size:21
Alignment explanation
Indices: 466958--466997 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
466948 ATATACAGTG
466958 TTTTAAGA-ATAATTTTTTATT
1 TTTTAA-ATATAATTTTTTATT
466979 TTTTAAATATAATTTTTTA
1 TTTTAAATATAATTTTTTA
466998 AAATTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTAAATATAATTTTTTATT
Found at i:467692 original size:21 final size:21
Alignment explanation
Indices: 467666--467706 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
467656 TATTAAAATA
467666 ATATTTTA-TATTAATATTTAT
1 ATATTTTATTATTAA-ATTTAT
467687 ATATTTTATTATTAAATTTA
1 ATATTTTATTATTAAATTTA
467707 AATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATTATTAAATTTAT
Found at i:467780 original size:39 final size:38
Alignment explanation
Indices: 467694--467781 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 38
467684 TATATATTTT
*
467694 ATTATTAAATTTAAATAAAATATTAATTATATTATTAA
1 ATTATTAAATTTAAATAAAATATTAATTATATAATTAA
** *
467732 AAAAGTTAAATTTAATTAAAAT-TTAATTTATATAAATTAA
1 ATTA-TTAAATTTAAATAAAATATTAA-TTATAT-AATTAA
467772 ATTATTAAAT
1 ATTATTAAAT
467782 CAAAATCAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
38 6 0.15
39 28 0.68
40 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
ATTATTAAATTTAAATAAAATATTAATTATATAATTAA
Found at i:468012 original size:19 final size:20
Alignment explanation
Indices: 467975--468014 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
467965 AATTTGATTC
467975 AAAAATTTATTTTATTATTA
1 AAAAATTTATTTTATTATTA
467995 AAAAATATT-TTTTA-TATTA
1 AAAAAT-TTATTTTATTATTA
468014 A
1 A
468015 TATTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 11 0.58
21 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAAATTTATTTTATTATTA
Found at i:468121 original size:46 final size:48
Alignment explanation
Indices: 468032--468124 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 48
468022 ATTTTTATAA
*
468032 TTAAACTTAAATAATTTTTTAATAAATAATAATTTAAATTAAATTAAC
1 TTAAACTTAAATAATTTTTTAATAAATAATAATCTAAATTAAATTAAC
* *
468080 TTAAAC-TAAA-AATTTTTTATTTAAAT-TTAATCT-AATATAAATTAA
1 TTAAACTTAAATAATTTTTTA-ATAAATAATAATCTAAAT-TAAATTAA
468125 ATAAATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
45 3 0.08
46 22 0.55
47 9 0.22
48 6 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (48 bp):
TTAAACTTAAATAATTTTTTAATAAATAATAATCTAAATTAAATTAAC
Found at i:468445 original size:23 final size:22
Alignment explanation
Indices: 468417--468471 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
468407 AAAAAATTAT
*
468417 TTTTAT-ATTAATATTTATATATA
1 TTTTATAATTAA-ATTTAAATA-A
468440 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
468462 TTTT-TAATTA
1 TTTTATAATTA
468472 TTAAATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 6 0.20
22 5 0.17
23 14 0.47
24 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:468474 original size:24 final size:22
Alignment explanation
Indices: 468414--468482 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
468404 ATTAAAAAAT
*
468414 TATTTTTA-TATTAATATTTATA
1 TATTTTTATTATTAA-ATTTAAA
*
468436 TATATTTTATAATTAAATTTAAA
1 TAT-TTTTATTATTAAATTTAAA
468459 TAATTTTTAATTATTAAATATTAA
1 T-ATTTTT-ATTATTAAAT-TTAA
468483 TTTAGATTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.08
23 16 0.41
24 16 0.41
25 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTTTTATTATTAAATTTAAA
Found at i:468959 original size:2 final size:2
Alignment explanation
Indices: 468952--468982 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
468942 AGACAGTTGC
468952 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
468983 GAATAAATCT
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:470927 original size:2 final size:2
Alignment explanation
Indices: 470920--470951 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
470910 AATTAATTAA
470920 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
470952 GTACATAAGT
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):
AT
Found at i:471277 original size:21 final size:21
Alignment explanation
Indices: 471251--471291 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
471241 TATTAAAATA
471251 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
471272 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
471292 AATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:471387 original size:14 final size:14
Alignment explanation
Indices: 471333--471392 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 14
471323 AGTTAAATTG
471333 AATTCAAATTT-TTA
1 AATT-AAATTTATTA
471347 AA--AAATTTA--A
1 AATTAAATTTATTA
*
471357 AATTTAATTTATATA
1 AATTAAATTTAT-TA
471372 AATTAAATTTATTA
1 AATTAAATTTATTA
471386 AATTAAA
1 AATTAAA
471393 ATTGAAGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
10 3 0.08
11 6 0.16
12 6 0.16
14 11 0.29
15 12 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTAAATTTATTA
Found at i:472068 original size:25 final size:25
Alignment explanation
Indices: 472021--472077 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
472011 TACTAAATAA
*
472021 AAAATAAATTATTAAAGAATAAATT
1 AAAATAAATTATTAAAGAATAAAAT
472046 AAAATAACATT-TTAAA-AATTAAAAT
1 AAAATAA-ATTATTAAAGAA-TAAAAT
*
472071 AATATAA
1 AAAATAA
472078 TATAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 2 0.07
25 23 0.82
26 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATAAATTATTAAAGAATAAAAT
Found at i:472321 original size:22 final size:21
Alignment explanation
Indices: 472283--472326 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
472273 TTTATGAAAA
* *
472283 TAAATATAACTTTATAATAAT
1 TAAATAGAACTTGATAATAAT
472304 TAAATAGATACTTGATAATAAT
1 TAAATAGA-ACTTGATAATAAT
472326 T
1 T
472327 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAATAGAACTTGATAATAAT
Found at i:473013 original size:31 final size:30
Alignment explanation
Indices: 472952--473013 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
472942 TGTTATATAT
*
472952 TTATATAATTTTGATACATTATAATTTTTA
1 TTATATAATTTTGATACATTATAATATTTA
*
472982 TTATATAAATTTTGATATATT-TATATATTTA
1 TTATAT-AATTTTGATACATTATA-ATATTTA
473013 T
1 T
473014 ATCGATTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (30 bp):
TTATATAATTTTGATACATTATAATATTTA
Found at i:473920 original size:22 final size:22
Alignment explanation
Indices: 473895--473950 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
473885 TAAAAAAAAT
*
473895 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTAAA
473917 TA-TTTTATAATTAAATTTAAA
1 TATTTTTATAATTAAATTTAAA
473938 TATTTTT-TAATTA
1 TATTTTTATAATTA
473951 TTAAATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTAAA
Found at i:475477 original size:15 final size:16
Alignment explanation
Indices: 475457--475491 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
475447 TATTAAAAAA
475457 ATTAAAT-ATATTTAT
1 ATTAAATAATATTTAT
475472 ATTAAATACATATTTAT
1 ATTAAATA-ATATTTAT
475489 ATT
1 ATT
475492 CGATATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
17 11 0.61
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAAATAATATTTAT
Found at i:477800 original size:1 final size:1
Alignment explanation
Indices: 477794--477886 Score: 69
Period size: 1 Copynumber: 93.0 Consensus size: 1
477784 AAATCTTCAC
* * * ** * * * **
477794 TTTTTTTTTTGTTTTTTTTCTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTCTTTTTCCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
477859 TTTTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
477887 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (1 bp):
T
Found at i:477834 original size:31 final size:30
Alignment explanation
Indices: 477796--477888 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 30
477786 ATCTTCACTT
477796 TTTTTTTTGTTTTTTTTCTTTTTCTTTTTCC
1 TTTTTTTTGTTTTTTTT-TTTTTCTTTTTCC
477827 TTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTT-TTTTTTTTTCTTTTTCC
477858 TTTTTTTT-TTGTTTTGTTTTTTTCTTTTTCC
1 TTTTTTTTGTT-TTTT-TTTTTTTCTTTTTCC
477889 AATTGCCATG
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
30 4 0.07
31 51 0.86
32 4 0.07
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (30 bp):
TTTTTTTTGTTTTTTTTTTTTTCTTTTTCC
Found at i:477855 original size:37 final size:37
Alignment explanation
Indices: 477794--477887 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
477784 AAATCTTCAC
477794 TTTTTT-TTTTG-TTTTTTTTCTTTTT-CTTTTTCCTT
1 TTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTT-CTT
*
477829 TTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTTTTT
1 TTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTTCTT
*
477866 TTGTTTTGTTTT-TTTCTTTTTC
1 TT-TTTTGTTTTGTTTTTTTTTC
477888 CAATTGCCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
35 6 0.11
36 5 0.09
37 27 0.51
38 15 0.28
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (37 bp):
TTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTTCTT
Found at i:485841 original size:1 final size:1
Alignment explanation
Indices: 485835--485927 Score: 69
Period size: 1 Copynumber: 93.0 Consensus size: 1
485825 AAATCTTCAC
* * * ** * * * **
485835 TTTTTTTTTTTGTTTTTTTTCTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
485900 TTTTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
485928 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (1 bp):
T
Found at i:485888 original size:37 final size:36
Alignment explanation
Indices: 485836--485928 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 36
485826 AATCTTCACT
485836 TTTTTT-TTTTG-TTTTTTTTCTTTTT-CTTTTTCCTT
1 TTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTT--TT
485871 TTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTTTT
1 TTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTTTT
*
485907 TTGTTTTGTTTT-TTTCTTTTTC
1 TT-TTTTGTTTTGTTTTTTTTTC
485929 CAATTGCCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
35 6 0.11
36 18 0.34
37 23 0.43
38 6 0.11
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (36 bp):
TTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTTTT
Found at i:485905 original size:32 final size:32
Alignment explanation
Indices: 485837--485929 Score: 149
Period size: 31 Copynumber: 3.0 Consensus size: 32
485827 ATCTTCACTT
485837 TTTTTTTTTGTTTT-TTTTCTTTTTCTTTTTCC
1 TTTTTTTTTGTTTTGTTTT-TTTTTCTTTTTCC
485869 -TTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
1 TTTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
485900 TTTTTTTTTGTTTTG--TTTTTTTCTTTTTCC
1 TTTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
485930 AATTGCCATG
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
30 15 0.25
31 26 0.44
32 18 0.31
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (32 bp):
TTTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
Found at i:494066 original size:18 final size:17
Alignment explanation
Indices: 494040--494073 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
494030 ATTGATATTT
*
494040 TAAAATATAATAATATG
1 TAAAATATAAAAATATG
494057 TAAAATTATAAAAATAT
1 TAAAA-TATAAAAATAT
494074 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAAATATAAAAATATG
Found at i:494132 original size:8 final size:8
Alignment explanation
Indices: 494119--494190 Score: 55
Period size: 8 Copynumber: 9.4 Consensus size: 8
494109 TCTCGTATGT
494119 ATATATAA
1 ATATATAA
494127 ATATATAA
1 ATATATAA
*
494135 ATATTAATAC
1 ATA-T-ATAA
*
494145 ATATTTAA
1 ATATATAA
494153 AT-T-TAA
1 ATATATAA
*
494159 TTATA-AA
1 ATATATAA
494166 ATATATAA
1 ATATATAA
494174 ATAT-T-A
1 ATATATAA
*
494180 ATATAAAA
1 ATATATAA
494188 ATA
1 ATA
494191 ATTTTTAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
6 9 0.18
7 9 0.18
8 25 0.49
9 2 0.04
10 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATATAA
Found at i:494169 original size:21 final size:21
Alignment explanation
Indices: 494119--494187 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
494109 TCTCGTATGT
494119 ATATATAAATATATAAATATT-
1 ATATA-AAATATATAAATATTA
* *
494140 A-AT-ACATATTTAAAT-TTA
1 ATATAAAATATATAAATATTA
494158 ATTATAAAATATATAAATATTA
1 A-TATAAAATATATAAATATTA
494180 ATATAAAA
1 ATATAAAA
494188 ATAATTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
17 2 0.05
18 11 0.28
20 4 0.10
21 18 0.46
22 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATAAAATATATAAATATTA
Found at i:494223 original size:17 final size:18
Alignment explanation
Indices: 494177--494224 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
494167 TATATAAATA
*
494177 TTAATATAAAAATAATTT
1 TTAATATAATAATAATTT
* *
494195 TTAATATTATAATATTTT
1 TTAATATAATAATAATTT
494213 TTAA-ATAATAAT
1 TTAATATAATAAT
494225 TTGAGCTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATATAATAATAATTT
Found at i:495386 original size:22 final size:22
Alignment explanation
Indices: 495351--495426 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 22
495341 CATAGTTTAT
* *
495351 AATTAAAAAAATTTTTATATTA
1 AATTTAAATAATTTTTATATTA
*
495373 ATATTTATAT-A-TTTTATAATTA
1 A-ATTTAAATAATTTTTAT-ATTA
495395 AATTTAAATAATTTTTAATTATTA
1 AATTTAAATAATTTTT-A-TATTA
495419 AATATTAA
1 AAT-TTAA
495427 TTTAGATTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
21 13 0.30
22 8 0.19
23 9 0.21
24 8 0.19
25 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTAAATAATTTTTATATTA
Found at i:495387 original size:21 final size:22
Alignment explanation
Indices: 495363--495415 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
495353 TTAAAAAAAT
*
495363 TTTTAT-ATTAATATTTATAT-A
1 TTTTATAATTAA-ATTTAAATAA
495384 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
495406 TTTT-TAATTA
1 TTTTATAATTA
495416 TTAAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:495959 original size:2 final size:2
Alignment explanation
Indices: 495952--495992 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
495942 ATACAGTTGC
495952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
495993 GAATAAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:497494 original size:32 final size:32
Alignment explanation
Indices: 497427--497494 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
497417 TTTAATTTTG
* * * *
497427 ATTTAATAATATTAGAATGAATATTATTTTTA
1 ATTTAATAATATTAAAATAAAAATTATTTTAA
497459 ATTTAATAATATTAAAAATAAAAATTA-TTTAA
1 ATTTAATAATATT-AAAATAAAAATTATTTTAA
497491 ATTT
1 ATTT
497495 TTTTTAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
ATTTAATAATATTAAAATAAAAATTATTTTAA
Found at i:497726 original size:71 final size:67
Alignment explanation
Indices: 497651--497791 Score: 158
Period size: 67 Copynumber: 2.0 Consensus size: 67
497641 ATTTTTGCTC
* *
497651 ATATAAATTACATATCAAATTTTGAGTAAATAAAAAAAT-TAATTATTAATTTAATTTAAAAGTT
1 ATATAAA--ACATATCAAATTTT---TAAATAAAAAAATATAATTATTAAATTAATTTAAAAATT
497715 TAAATAT
61 TAAATAT
* * * * * *
497722 ATATAAAATATATGATATTTTTAATTAAAATAATATAATTATTAAATTAATTTAAAAATTTACAT
1 ATATAAAACATATCAAATTTTTAAATAAAAAAATATAATTATTAAATTAATTTAAAAATTTAAAT
497787 AT
66 AT
497789 ATA
1 ATA
497792 ACAAGTGTGA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
66 11 0.18
67 32 0.52
69 11 0.18
71 7 0.11
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (67 bp):
ATATAAAACATATCAAATTTTTAAATAAAAAAATATAATTATTAAATTAATTTAAAAATTTAAAT
AT
Found at i:498207 original size:21 final size:21
Alignment explanation
Indices: 498181--498221 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
498171 TATTAAAATA
498181 ATATTTTA-TATTAATATTTAT
1 ATATTTTATTATTAA-ATTTAT
498202 ATATTTTATTATTAAATTTA
1 ATATTTTATTATTAAATTTA
498222 AATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATTATTAAATTTAT
Found at i:498253 original size:17 final size:18
Alignment explanation
Indices: 498239--498278 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
498229 TATTAATTAT
498239 ATTATTAAAAAAATTAAA
1 ATTATTAAAAAAATTAAA
* *
498257 ATTTTTAAAAAATTTTAAA
1 ATTATTAAAAAA-ATTAAA
498276 ATT
1 ATT
498279 TAAATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATTAAAAAAATTAAA
Found at i:498274 original size:19 final size:18
Alignment explanation
Indices: 498243--498279 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
498233 AATTATATTA
498243 TTAAAAAAATTAAAATTT
1 TTAAAAAAATTAAAATTT
*
498261 TTAAAAAATTTTAAAATTT
1 TTAAAAAA-ATTAAAATTT
498280 AAATTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAAAAATTAAAATTT
Found at i:499718 original size:2 final size:2
Alignment explanation
Indices: 499711--499750 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
499701 TTGGCGTAGA
499711 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
499751 GATAATAGAA
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:500038 original size:22 final size:19
Alignment explanation
Indices: 500007--500048 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
499997 ATTTTTTATT
500007 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
500028 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
500048 T
1 T
500049 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:500301 original size:31 final size:31
Alignment explanation
Indices: 500239--500371 Score: 102
Period size: 31 Copynumber: 4.3 Consensus size: 31
500229 TTTATTATTT
*
500239 TTTATCATAATTTTATT-TA-AAATATTATATA
1 TTTAT-ATAATTTTATTATATTAATATT-TATA
500270 TTTATATAATTTTATTA-ATTAATAATTTATA
1 TTTATATAATTTTATTATATTAAT-ATTTATA
*
500301 -TTATATAAATTTTGA-TATATTTATATTT-TA
1 TTTATAT-AATTTT-ATTATATTAATATTTATA
* * *
500331 TTAATATTATTTTTTTATATT-ATATTT-TA
1 TTTATATAATTTTATTATATTAATATTTATA
500360 TTTTAATATAAT
1 -TTT-ATATAAT
500372 GATATGACGT
Statistics
Matches: 85, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
29 8 0.09
30 33 0.39
31 35 0.41
32 9 0.11
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (31 bp):
TTTATATAATTTTATTATATTAATATTTATA
Found at i:500771 original size:17 final size:19
Alignment explanation
Indices: 500744--500782 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
500734 ATTTTTTATC
500744 AAATTTAATTTAATT-TAA
1 AAATTTAATTTAATTATAA
*
500762 AAATTT-ATTTTATTATAA
1 AAATTTAATTTAATTATAA
500780 AAA
1 AAA
500783 AGTATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTAATTTAATTATAA
Found at i:501217 original size:22 final size:21
Alignment explanation
Indices: 501192--501258 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
501182 AATAAAAAAT
*
501192 TATTTTTATATTAATATTTATA
1 TATTTTTATATTAA-ATTTAAA
501214 TA-TTTTATAATTAAATTTAAA
1 TATTTTTAT-ATTAAATTTAAA
501235 TAATTTTTAATTATTAAATATTAA
1 T-ATTTTT-A-TATTAAAT-TTAA
501259 TTCAGATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 13 0.34
22 8 0.21
23 4 0.11
24 8 0.21
25 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTATATTAAATTTAAA
Found at i:501221 original size:21 final size:22
Alignment explanation
Indices: 501195--501247 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
501185 AAAAAATTAT
*
501195 TTTTAT-ATTAATATTTATAT-A
1 TTTTATAATTAA-ATTTAAATAA
501216 TTTTATAATTAAATTTAAATAA
1 TTTTATAATTAAATTTAAATAA
501238 TTTT-TAATTA
1 TTTTATAATTA
501248 TTAAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATAATTAAATTTAAATAA
Found at i:501982 original size:18 final size:19
Alignment explanation
Indices: 501939--501983 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
501929 TACAAACGAA
*
501939 ATAAACTTTAATTATTAAT
1 ATAAATTTTAATTATTAAT
*
501958 CTAAATTTTAATTATT-AT
1 ATAAATTTTAATTATTAAT
501976 ATAAATTT
1 ATAAATTT
501984 ATATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAATTTTAATTATTAAT
Found at i:502002 original size:25 final size:24
Alignment explanation
Indices: 501947--502013 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
501937 AAATAAACTT
501947 TAATTAT-TAATCTA-A-ATTTTAA
1 TAATTATATAAT-TATATATTTTAA
*
501969 TTATTATATAAATTTATATATTTTAA
1 TAATTATAT-AA-TTATATATTTTAA
501995 -AATTATATAATTATATATT
1 TAATTATATAATTATATATT
502014 CAAAAAGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 6 0.16
23 10 0.26
24 6 0.16
25 9 0.24
26 7 0.18
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (24 bp):
TAATTATATAATTATATATTTTAA
Found at i:502019 original size:23 final size:25
Alignment explanation
Indices: 501971--502019 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
501961 AATTTTAATT
**
501971 ATTATATAAATTTATATATTTTAAA
1 ATTATATAAATTTATATATTCAAAA
501996 ATTATAT-AA-TTATATATTCAAAA
1 ATTATATAAATTTATATATTCAAAA
502019 A
1 A
502020 GTGAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 2 0.09
25 7 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATATAAATTTATATATTCAAAA
Found at i:502599 original size:28 final size:25
Alignment explanation
Indices: 502547--502599 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
502537 AATACTGATT
*
502547 AAAAATTATTTTATTATTAATTTTA
1 AAAAATTATTTTATCATTAATTTTA
*
502572 AAAAATTATATTTAATACATTACTTTTA
1 AAAAATTAT-TTT-AT-CATTAATTTTA
502600 TTGAATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.39
26 3 0.13
27 2 0.09
28 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAAATTATTTTATCATTAATTTTA
Found at i:503094 original size:2 final size:2
Alignment explanation
Indices: 503087--503114 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
503077 TTTCTACTAA
503087 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
503115 TTTGGTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:504249 original size:44 final size:42
Alignment explanation
Indices: 504181--504270 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
504171 GTCAAAGGCC
*
504181 AAAGCACAAAGCAATAATTTATATATATATATATATATATTAAA
1 AAAGCACAAAGCAATAA-TT-TATATACATATATATATATTAAA
* * *
504225 AAAGGACAAAGTAATTATTTATATACATATATATATATTAAA
1 AAAGCACAAAGCAATAATTTATATACATATATATATATTAAA
504267 AAAG
1 AAAG
504271 TAGATCTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 26 0.62
43 2 0.05
44 14 0.33
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (42 bp):
AAAGCACAAAGCAATAATTTATATACATATATATATATTAAA
Found at i:505587 original size:19 final size:19
Alignment explanation
Indices: 505563--505599 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
505553 AATTTTTTTT
* *
505563 AATTTTTTTATATATTTAA
1 AATTTTTTAAAATATTTAA
505582 AATTTTTTAAAATATTTA
1 AATTTTTTAAAATATTTA
505600 TATTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTTTAAAATATTTAA
Found at i:506520 original size:12 final size:14
Alignment explanation
Indices: 506503--506540 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
506493 GCCTTTCATT
506503 TTCCTTTTTT-T-A
1 TTCCTTTTTTATGA
506515 TTCCTTTTTTATGGA
1 TTCCTTTTTTAT-GA
506530 TTCCTTTTTTA
1 TTCCTTTTTTA
506541 AATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 1 0.04
15 12 0.52
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (14 bp):
TTCCTTTTTTATGA
Found at i:507240 original size:2 final size:2
Alignment explanation
Indices: 507233--507268 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
507223 ATTAGACCTT
507233 TA TA 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 TA TA
507269 GTAAATACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:508179 original size:11 final size:12
Alignment explanation
Indices: 508163--508196 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
508153 TCAAATAATT
508163 TTATTTTTTAA-
1 TTATTTTTTAAG
508174 TTATTTTTTAAG
1 TTATTTTTTAAG
*
508186 TAATTTTTTAA
1 TTATTTTTTAA
508197 CTGATATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (12 bp):
TTATTTTTTAAG
Found at i:509035 original size:29 final size:28
Alignment explanation
Indices: 508994--509083 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
508984 ATTTTTATTT
*
508994 AAAATAAGAATTTATTT-GATAAAAATCA
1 AAAATAAAAATTTATTTAGATAAAAAT-A
509022 AAAATCAAAAATTTATTTAGATAAAAATA
1 AAAAT-AAAAATTTATTTAGATAAAAATA
** *
509051 AAAGTATAAGTATTTATTTA-AAAAAAATA
1 AAA--ATAAAAATTTATTTAGATAAAAATA
509080 AAAA
1 AAAA
509084 AATTCAAAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 1 0.02
28 5 0.09
29 26 0.48
30 20 0.37
31 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (28 bp):
AAAATAAAAATTTATTTAGATAAAAATA
Found at i:509456 original size:3 final size:3
Alignment explanation
Indices: 509448--509490 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
509438 ATAAAACGTG
509448 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
509491 ACATATTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:509856 original size:31 final size:32
Alignment explanation
Indices: 509808--509870 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
509798 ATAAGTTAAA
* *
509808 AATAAAAAAATTATAATTTTTCTATGAATTTT
1 AATAAAAAAATTATAATTTTTATATAAATTTT
509840 AATAAAAATAA-T-TAATTTTTATATAAATTTT
1 AATAAAAA-AATTATAATTTTTATATAAATTTT
509871 TTTAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 9 0.32
33 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
AATAAAAAAATTATAATTTTTATATAAATTTT
Found at i:510781 original size:16 final size:15
Alignment explanation
Indices: 510755--510784 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
510745 CTAAACTAGA
510755 TTAAATTTTTAAATT
1 TTAAATTTTTAAATT
510770 TTAAACTTTTTAAAT
1 TTAAA-TTTTTAAAT
510785 ATAATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAAATTTTTAAATT
Found at i:511851 original size:28 final size:31
Alignment explanation
Indices: 511791--511851 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
511781 CATTTAAAAA
*
511791 TTTTAATAAATAATAATATATTAAATATTAT
1 TTTTAATAAATAATAATATATTAAATATAAT
*
511822 TTTTAATAAA-AATAATAT-TTAATTA-AAT
1 TTTTAATAAATAATAATATATTAAATATAAT
511850 TT
1 TT
511852 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 6 0.21
30 8 0.29
31 10 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TTTTAATAAATAATAATATATTAAATATAAT
Found at i:511919 original size:49 final size:51
Alignment explanation
Indices: 511851--511955 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 51
511841 TAATTAAATT
* * *
511851 TAAAAAATTTACATTAACAAAT-TAAAATATTAATTATTA-TATTTTTTAAA
1 TAAAAAATTTACAATAACAAATAAAAAAGATTAATTATTATTATTTTTT-AA
*
511901 TAAAAAATTTA-AATAACAAATAAAAAAGATTTATTATTATTATTTTTTAA
1 TAAAAAATTTACAATAACAAATAAAAAAGATTAATTATTATTATTTTTTAA
511951 TAAAA
1 TAAAA
511956 TAATATTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 9 0.18
50 32 0.65
51 8 0.16
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (51 bp):
TAAAAAATTTACAATAACAAATAAAAAAGATTAATTATTATTATTTTTTAA
Found at i:512094 original size:17 final size:18
Alignment explanation
Indices: 512055--512093 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
512045 TTTAATTGAG
512055 AAAATCACATGTTTTTAT
1 AAAATCACATGTTTTTAT
512073 AAAATCACATGTTTTTAT
1 AAAATCACATGTTTTTAT
512091 AAA
1 AAA
512094 TTAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (18 bp):
AAAATCACATGTTTTTAT
Found at i:517034 original size:2 final size:2
Alignment explanation
Indices: 517027--517057 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
517017 TTGTCCTGTT
*
517027 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
517058 CAGCTGCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:518532 original size:2 final size:2
Alignment explanation
Indices: 518525--518558 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
518515 CTCCACGTTT
518525 TA 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 TA
518559 CCCGAATCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:526447 original size:28 final size:28
Alignment explanation
Indices: 526415--526482 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
526405 TAAAACAATG
* *
526415 ATAAGACAATGTGGATAAACTTGTCTTA
1 ATAAGACAATGTGAATAAACTTGTCCTA
* *
526443 ATAAGACAATGAGAATAAACTTTTCCTA
1 ATAAGACAATGTGAATAAACTTGTCCTA
526471 ATAAGACAATGT
1 ATAAGACAATGT
526483 CTAAAGTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (28 bp):
ATAAGACAATGTGAATAAACTTGTCCTA
Found at i:526540 original size:28 final size:27
Alignment explanation
Indices: 526504--526562 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
526494 ATGGGTTAAA
* * *
526504 ACAAAATGGATAAGGTTGTCTTAATAAG
1 ACAAAATGGATAAAGTTATCTT-ACAAG
*
526532 ACAATATGGATAAAGTTATCTTACAAG
1 ACAAAATGGATAAAGTTATCTTACAAG
526559 ACAA
1 ACAA
526563 CATCCAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (27 bp):
ACAAAATGGATAAAGTTATCTTACAAG
Found at i:526696 original size:82 final size:82
Alignment explanation
Indices: 526601--526756 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 82
526591 AATGGATAAG
* *
526601 CTTAATAAGACAATGTGGATAAACTTGTCTTAAAAAGACAATG-TCTAAAATAGACATATCTTAA
1 CTTAATAAAACAATGTAGATAAACTTGTCTTAAAAAGACAA-GATCTAAAATAGACATATCTTAA
526665 GATAAGTTGTCTTAATGC
65 GATAAGTTGTCTTAATGC
* * * * *
526683 CTTAATAAAACAATGTAGATAAGCTTGTCTTAACAAGACAAGATCTACAATATACATGTCTTAAG
1 CTTAATAAAACAATGTAGATAAACTTGTCTTAAAAAGACAAGATCTAAAATAGACATATCTTAAG
526748 ATAAGTTGT
66 ATAAGTTGT
526757 TTTGGCCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.02
82 65 0.98
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (82 bp):
CTTAATAAAACAATGTAGATAAACTTGTCTTAAAAAGACAAGATCTAAAATAGACATATCTTAAG
ATAAGTTGTCTTAATGC
Found at i:527489 original size:27 final size:27
Alignment explanation
Indices: 527451--527505 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
527441 ATCCGTGAGA
527451 TAGTATTGCCACAATTACTCCACAACC
1 TAGTATTGCCACAATTACTCCACAACC
527478 TAGTATTGCCACAATTACTCCACAACC
1 TAGTATTGCCACAATTACTCCACAACC
527505 T
1 T
527506 TCTCGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.27
Consensus pattern (27 bp):
TAGTATTGCCACAATTACTCCACAACC
Found at i:528175 original size:13 final size:13
Alignment explanation
Indices: 528157--528185 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
528147 CACCACCACC
528157 CTTTCCACAACAT
1 CTTTCCACAACAT
528170 CTTTCCACAACAT
1 CTTTCCACAACAT
528183 CTT
1 CTT
528186 CAAAAGCATG
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:0.28, C:0.38, G:0.00, T:0.34
Consensus pattern (13 bp):
CTTTCCACAACAT
Found at i:534289 original size:5 final size:5
Alignment explanation
Indices: 534281--534306 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
534271 AAGATATGAT
534281 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
534307 TTTATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:534500 original size:25 final size:27
Alignment explanation
Indices: 534472--534521 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
534462 TTTATTTTAA
*
534472 TTTTTAATTTC-A-TTTTTTAAAAAGC
1 TTTTCAATTTCAATTTTTTTAAAAAGC
534497 TTTTCAATTTCAATTTTTTTAAAAA
1 TTTTCAATTTCAATTTTTTTAAAAA
534522 AAATTTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 11 0.50
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTCAATTTCAATTTTTTTAAAAAGC
Found at i:535097 original size:2 final size:2
Alignment explanation
Indices: 535090--535123 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
535080 AGTCTTAGTT
535090 TA 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 TA
535124 ATTATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:536458 original size:22 final size:21
Alignment explanation
Indices: 536425--536465 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
536415 CGAGTTTGAT
* *
536425 TTTTGTATATTAATATTTTTA
1 TTTTGTAAATTAAAATTTTTA
536446 TTTTGTAAAATTAAAATTTT
1 TTTTGT-AAATTAAAATTTT
536466 CATTGAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTGTAAATTAAAATTTTTA
Found at i:537477 original size:2 final size:2
Alignment explanation
Indices: 537464--537497 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
537454 TTTTCACTGC
* *
537464 AT AT AA AT AT AT AT AT AT CT 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
537498 TACGTGATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:537728 original size:2 final size:2
Alignment explanation
Indices: 537721--537754 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
537711 TCTGATATTG
537721 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
537755 TTAAACAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:538196 original size:16 final size:15
Alignment explanation
Indices: 538175--538221 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
538165 AGTGAAAATA
538175 AAAAATATATATAATT
1 AAAAATATAT-TAATT
538191 AAAAATATACTTAATTT
1 AAAAATATA-TTAA-TT
*
538208 AAAAAGATATTAAT
1 AAAAATATATTAAT
538222 AAATTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.04
16 16 0.57
17 11 0.39
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
AAAAATATATTAATT
Found at i:538335 original size:22 final size:21
Alignment explanation
Indices: 538291--538335 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
538281 ATTAATTAAA
* *
538291 TATTATATAACTACATAAATT
1 TATTATATAAATAAATAAATT
*
538312 TATTATATTAAATAAATAATTT
1 TATTATA-TAAATAAATAAATT
538334 TA
1 TA
538336 AAACTTTCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTATATAAATAAATAAATT
Found at i:538423 original size:18 final size:18
Alignment explanation
Indices: 538383--538424 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
538373 AAAATTTTAT
538383 AAAAAATTAATAAAATGA
1 AAAAAATTAATAAAATGA
* * *
538401 TAAAAATTATTAAAATTA
1 AAAAAATTAATAAAATGA
538419 AAAAAA
1 AAAAAA
538425 AAGAGATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAAATTAATAAAATGA
Found at i:538740 original size:25 final size:24
Alignment explanation
Indices: 538702--538760 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
538692 TTTAATATTA
*
538702 ATTTAATAAATAAAATTTGTCATT
1 ATTTAATAAATAAAATTTATCATT
*
538726 ATTTAATATATTAAAATTTATCATT
1 ATTTAATA-AATAAAATTTATCATT
*
538751 ATATAATAAA
1 ATTTAATAAA
538761 ATAATATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTTAATAAATAAAATTTATCATT
Found at i:542443 original size:19 final size:18
Alignment explanation
Indices: 542410--542446 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
542400 ATGAAAATTC
542410 ATAATAATGAATAATTTA
1 ATAATAATGAATAATTTA
*
542428 ATAATAAATTAATAATTTA
1 ATAAT-AATGAATAATTTA
542447 TTAAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAATAATGAATAATTTA
Found at i:543169 original size:23 final size:22
Alignment explanation
Indices: 543143--543198 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
543133 TATGTAAATT
543143 TTTTTATTTA-TTATTTATTATAC
1 TTTTTATTTAGTT-TTT-TTATAC
*
543166 TTTTTAGTTTAGTTTTTTTATAT
1 TTTTTA-TTTAGTTTTTTTATAC
543189 TTTTCTATTT
1 TTTT-TATTT
543199 TGGTCAGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 18 0.62
24 9 0.31
25 2 0.07
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTTATTTAGTTTTTTTATAC
Found at i:547420 original size:20 final size:20
Alignment explanation
Indices: 547379--547418 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
547369 AGTTGCATAT
547379 ATCTATATTCTATATAATAA
1 ATCTATATTCTATATAATAA
547399 ATCTATA-TCTATATAATAA
1 ATCTATATTCTATATAATAA
547418 A
1 A
547419 ATTAAGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (20 bp):
ATCTATATTCTATATAATAA
Found at i:547922 original size:20 final size:20
Alignment explanation
Indices: 547897--547948 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
547887 GATTTCAAGG
547897 ATTTTTAGAAATCAAAAAGA
1 ATTTTTAGAAATCAAAAAGA
*
547917 ATTTTTAGAAATCGAAAAGA
1 ATTTTTAGAAATCAAAAAGA
547937 ATTTTTAGAAAT
1 ATTTTTAGAAAT
547949 TCACTTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.35
Consensus pattern (20 bp):
ATTTTTAGAAATCAAAAAGA
Found at i:550046 original size:20 final size:19
Alignment explanation
Indices: 549994--550058 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
549984 TATTTATTTT
*
549994 TAATATATTATATATTTATA
1 TAATTTATTATATATTTA-A
*
550014 TAAATT-TTA-ATATATTAA
1 TAATTTATTATATAT-TTAA
550032 TAATTTATTATATATTTTAA
1 TAATTTATTATATA-TTTAA
550052 TATATTT
1 TA-ATTT
550059 CTAATTCTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 10 0.27
19 9 0.24
20 13 0.35
21 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTTATTATATATTTAA
Found at i:550063 original size:28 final size:28
Alignment explanation
Indices: 549971--550064 Score: 104
Period size: 28 Copynumber: 3.4 Consensus size: 28
549961 TAAAATTAAA
*
549971 ATTTATAATTT-TATATTTATTTTTAATAT
1 ATTTATAATTTAT-TATATA-TTTTAATAT
*
550000 A-TTATATATTTA-TATAAATTTTAATAT
1 ATTTATA-ATTTATTATATATTTTAATAT
*
550027 ATTAATAATTTATTATATATTTTAATAT
1 ATTTATAATTTATTATATATTTTAATAT
*
550055 ATTTCTAATT
1 ATTTATAATT
550065 CTTGTATTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
27 15 0.27
28 35 0.64
29 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTATAATTTATTATATATTTTAATAT
Found at i:551330 original size:16 final size:17
Alignment explanation
Indices: 551311--551345 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
551301 TAAATTATAC
*
551311 TTTTGATAATTTTT-TT
1 TTTTGAAAATTTTTATT
551327 TTTTGAAAATTTTTATT
1 TTTTGAAAATTTTTATT
551344 TT
1 TT
551346 AATTACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTGAAAATTTTTATT
Found at i:551970 original size:28 final size:27
Alignment explanation
Indices: 551919--551973 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
551909 GGATATAAGT
* *
551919 TTAAAATTAAAGATTAAATATAAACAA
1 TTAAAATTAAAAAATAAATATAAACAA
*
551946 TTAAAATTATAAAAATAAATTTAAACAA
1 TTAAAATTA-AAAAATAAATATAAACAA
551974 AATATTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (27 bp):
TTAAAATTAAAAAATAAATATAAACAA
Found at i:552504 original size:2 final size:2
Alignment explanation
Indices: 552497--552524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
552487 ATCAAAAGAA
552497 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
552525 TGTTAATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:552946 original size:2 final size:2
Alignment explanation
Indices: 552939--553001 Score: 68
Period size: 2 Copynumber: 35.0 Consensus size: 2
552929 CATCTTTTTA
552939 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
552977 AT AT A- AT AT A- AT AT AA AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
553002 TCTAATGTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
1 7 0.13
2 45 0.87
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:552954 original size:10 final size:10
Alignment explanation
Indices: 552939--553001 Score: 68
Period size: 9 Copynumber: 7.0 Consensus size: 10
552929 CATCTTTTTA
552939 ATATATATAT
1 ATATATATAT
552949 ATATATATAT
1 ATATATATAT
552959 ATA-ATATA-
1 ATATATATAT
552967 ATATA-ATAT
1 ATATATATAT
552976 A-ATATA-AT
1 ATATATATAT
*
552984 ATA-ATATAA
1 ATATATATAT
552993 AT-TATATAT
1 ATATATATAT
553002 TCTAATGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
8 15 0.33
9 17 0.38
10 13 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:552967 original size:5 final size:5
Alignment explanation
Indices: 552937--552992 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
552927 TCCATCTTTT
552937 TAATA TATATA TATATA TATATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TA-ATA TA-ATA TA-ATA TAATA TAATA TAATA TAATA TAATA
552985 TAATA TAA
1 TAATA TAA
552993 ATTATATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 33 0.66
6 17 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:554478 original size:3 final size:3
Alignment explanation
Indices: 554470--554509 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
554460 ATCAGTGTTC
554470 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
554510 TTGCAGCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:555236 original size:21 final size:21
Alignment explanation
Indices: 555186--555237 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
555176 TGAACTCAAA
*
555186 TAATTTAAAATTTTAAATCATT
1 TAATTTAAAA-TTCAAATCATT
*
555208 GAATTTTAAAA-TCAAATCATTT
1 TAA-TTTAAAATTCAAATCA-TT
555230 TAATTTAA
1 TAATTTAA
555238 GATGGTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 12 0.48
22 6 0.24
23 7 0.28
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATTTAAAATTCAAATCATT
Found at i:555763 original size:17 final size:17
Alignment explanation
Indices: 555741--555775 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
555731 TTAGATTAAG
*
555741 TTATTTTAGATTTAAAT
1 TTATTTTAAATTTAAAT
555758 TTATTTTAAATTTAAAT
1 TTATTTTAAATTTAAAT
555775 T
1 T
555776 ATACGGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTATTTTAAATTTAAAT
Found at i:556693 original size:5 final size:5
Alignment explanation
Indices: 556671--556715 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
556661 CAAAAGGGAG
* *
556671 AAAGA AAA-A AACGA AAAGA AAAGA AAAGA CAAG- AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
556716 TCGTCCCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
4 6 0.18
5 28 0.82
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:557640 original size:16 final size:16
Alignment explanation
Indices: 557621--557652 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
557611 AATTATATTT
557621 AATTATTATTAAATTA
1 AATTATTATTAAATTA
*
557637 AATTATTGTTAAATTA
1 AATTATTATTAAATTA
557653 TATTCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:559418 original size:18 final size:18
Alignment explanation
Indices: 559391--559428 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
559381 AATTATTTTA
*
559391 AAAATAATTATATAAGTT
1 AAAATAATTATATAAATT
*
559409 AAAATTATTATATAAATT
1 AAAATAATTATATAAATT
559427 AA
1 AA
559429 TTAAATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAATAATTATATAAATT
Found at i:561825 original size:19 final size:19
Alignment explanation
Indices: 561798--561838 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
561788 TCTTGGTGAA
*
561798 GAGAGAGAACCCATTAGAT
1 GAGAGAGAACCCAATAGAT
* *
561817 GAGATAGAATCCAATAGAT
1 GAGAGAGAACCCAATAGAT
561836 GAG
1 GAG
561839 TTGTTGATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.27, T:0.17
Consensus pattern (19 bp):
GAGAGAGAACCCAATAGAT
Found at i:564835 original size:2 final size:2
Alignment explanation
Indices: 564828--564863 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
564818 CAGTCTGAGT
564828 TA TA 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 TA TA
564864 AATTATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:564896 original size:7 final size:7
Alignment explanation
Indices: 564862--564896 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
564852 TATATATATA
*
564862 TAAATTA
1 TAAATTT
564869 TAAATTT
1 TAAATTT
*
564876 TAAAATT
1 TAAATTT
564883 TAAATTT
1 TAAATTT
564890 TAAATTT
1 TAAATTT
564897 ATTAATATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
TAAATTT
Found at i:565527 original size:2 final size:2
Alignment explanation
Indices: 565520--565563 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
565510 CTTAACTAGT
565520 TA TA TA TA TA 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 TA TA TA TA TA
565562 TA
1 TA
565564 GGTTTCAAGA
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):
TA
Found at i:567094 original size:2 final size:2
Alignment explanation
Indices: 567087--567116 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
567077 ACATACATAC
567087 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
567117 CACACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:567302 original size:22 final size:22
Alignment explanation
Indices: 567277--567323 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
567267 TCTACCTTTT
*
567277 CTTTTTTCTTT-TTACTTTTGAA
1 CTTTTTT-TTTCTTACTTTTCAA
*
567299 CTTTTTTTTTCTTTCTTTTCAA
1 CTTTTTTTTTCTTACTTTTCAA
567321 CTT
1 CTT
567324 CCTAACATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70
Consensus pattern (22 bp):
CTTTTTTTTTCTTACTTTTCAA
Found at i:567588 original size:22 final size:22
Alignment explanation
Indices: 567547--567588 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
567537 ATTTAAAAAC
*
567547 TTATTATATAAATTATATAAAT
1 TTATTATATAAATTAAATAAAT
567569 TTATTATATCAAA-TAAATAA
1 TTATTATAT-AAATTAAATAA
567589 TCTAAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATTATATAAATTAAATAAAT
Found at i:568015 original size:25 final size:24
Alignment explanation
Indices: 567968--568015 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
567958 TGATAATTTA
*
567968 ATTTAATAAATAAACTTTATCATC
1 ATTTAATAAATAAAATTTATCATC
* *
567992 ATTTAATATACTAAAATTTGTCAT
1 ATTTAATA-AATAAAATTTATCAT
568016 AATATGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTTAATAAATAAAATTTATCATC
Found at i:568799 original size:16 final size:16
Alignment explanation
Indices: 568780--568813 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
568770 TTATTTTATA
568780 TTTAAATTATGTAAAT
1 TTTAAATTATGTAAAT
* *
568796 TTTAGATTATTTAAAT
1 TTTAAATTATGTAAAT
568812 TT
1 TT
568814 GATACTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAATTATGTAAAT
Found at i:570352 original size:20 final size:20
Alignment explanation
Indices: 570316--570362 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
570306 TAAAGTATAT
570316 TATAAAATTATTATAATTTA
1 TATAAAATTATTATAATTTA
*
570336 TATAATATT-TTATTAATTTA
1 TATAAAATTATTA-TAATTTA
*
570356 TTTAAAA
1 TATAAAA
570363 AATTATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAAAATTATTATAATTTA
Found at i:571003 original size:5 final size:5
Alignment explanation
Indices: 570995--571083 Score: 60
Period size: 5 Copynumber: 17.8 Consensus size: 5
570985 TTATTCGATA
* * *
570995 AATTT AATTT AAATT AATTT AAATTT AAATTT -ATAT AATTT --TTT TATTT
1 AATTT AATTT AATTT AATTT -AATTT -AATTT AATTT AATTT AATTT AATTT
* * *
571044 AAGTA AATTT AATTT AATTT AAATTAT TATTT AA-TT AATT
1 AATTT AATTT AATTT AATTT -AATT-T AATTT AATTT AATT
571084 AAAAAATTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
3 3 0.05
4 7 0.11
5 37 0.56
6 18 0.27
7 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:571077 original size:22 final size:22
Alignment explanation
Indices: 571050--571112 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
571040 ATTTAAGTAA
**
571050 ATTTAATTTAATTTAAATTATT
1 ATTTAATTTAATTTAAAAAATT
571072 ATTTAA-TTAA-TTAAAAAATT
1 ATTTAATTTAATTTAAAAAATT
571092 ATTTAAATTTAATTATAAAAA
1 ATTT-AATTTAATT-TAAAAA
571113 TATATAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 12 0.34
21 6 0.17
22 10 0.29
23 1 0.03
24 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAATTTAATTTAAAAAATT
Found at i:571120 original size:22 final size:23
Alignment explanation
Indices: 571077--571139 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
571067 TTATTATTTA
*
571077 ATTAATTA-AAAAATTATTTAAAT
1 ATTAATTATAAAAA-TATATAAAT
571100 -TTAATTATAAAAATATATAAAT
1 ATTAATTATAAAAATATATAAAT
*
571122 ATT-ATTATAAAATTATAT
1 ATTAATTATAAAAATATAT
571140 TTTAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 29 0.81
23 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTAATTATAAAAATATATAAAT
Found at i:571950 original size:25 final size:25
Alignment explanation
Indices: 571922--571969 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
571912 TTAATATATT
571922 AATA-AATTATATTATATATTTTTAA
1 AATATAATTATATT-TATATTTTTAA
**
571947 AATATTTTTATATTTATATTTTT
1 AATATAATTATATTTATATTTTT
571970 TTTATGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
AATATAATTATATTTATATTTTTAA
Found at i:571951 original size:45 final size:45
Alignment explanation
Indices: 571866--571951 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
571856 ATTAATTTAT
* * *
571866 TTTATTATATTATAATTATATTTTAAAATTTTTATTAATATAAAA
1 TTTAATATATTATAATTATATTATAAAATTTTTATAAATATAAAA
*
571911 TTTAATATATTAATAAATTATATTAT-ATATTTTTA-AAATAT
1 TTTAATATATT-AT-AATTATATTATAAAATTTTTATAAATAT
571952 TTTTATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
45 15 0.43
46 10 0.29
47 10 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (45 bp):
TTTAATATATTATAATTATATTATAAAATTTTTATAAATATAAAA
Found at i:574100 original size:30 final size:30
Alignment explanation
Indices: 574048--574107 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
574038 TTTAAATAAT
*
574048 AATTTTATTTATATTAATTTTAAT-TAAAA
1 AATTTTATTTAAATTAATTTTAATATAAAA
574077 AATTTATATTTAAATTTAA-TTTAATATAAAA
1 AATTT-TATTTAAA-TTAATTTTAATATAAAA
574108 TAAATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 5 0.19
30 13 0.48
31 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTTTATTTAAATTAATTTTAATATAAAA
Found at i:574620 original size:2 final size:2
Alignment explanation
Indices: 574613--574647 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
574603 CATCTTTTGA
*
574613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
574648 ATGTAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.