Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold127
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: 3416254
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 147187 characters in sequence are not A, C, G, or T
File 2 of 10
Found at i:339178 original size:43 final size:43
Alignment explanation
Indices: 339130--339213 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
339120 ACCCCAAAAC
* *
339130 GACTCCAAGCCAACGCGCTTTTTGAATTGAAATCAAGTTAAAT
1 GACTCCAAGCCAACACACTTTTTGAATTGAAATCAAGTTAAAT
* *
339173 GACTCCAAGCCAACACACTTTTTGAATTTAAATCGAGTTAA
1 GACTCCAAGCCAACACACTTTTTGAATTGAAATCAAGTTAA
339214 CTTTAAGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (43 bp):
GACTCCAAGCCAACACACTTTTTGAATTGAAATCAAGTTAAAT
Found at i:343931 original size:28 final size:29
Alignment explanation
Indices: 343859--343940 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 29
343849 CATCCACCAT
*
343859 CGGTACATAGTACATGGAACTGTAAAAAC
1 CGGTACATAGTACCTGGAACTGTAAAAAC
* *
343888 CGG--CATAGGGTGCCTGGAACTG-AAACAC
1 CGGTACATA--GTACCTGGAACTGTAAAAAC
343916 CGGTACATAGTACCTGGAACTGTAA
1 CGGTACATAGTACCTGGAACTGTAA
343941 TCATTGGCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
27 4 0.09
28 20 0.45
29 16 0.36
30 4 0.09
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.20
Consensus pattern (29 bp):
CGGTACATAGTACCTGGAACTGTAAAAAC
Found at i:348479 original size:23 final size:23
Alignment explanation
Indices: 348446--348492 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
348436 AAACAAGTCA
*
348446 AACTAAACAGGATTCATCACACT
1 AACTAAACAGGACTCATCACACT
*
348469 AACTAAGCAGGACTCATCACACT
1 AACTAAACAGGACTCATCACACT
348492 A
1 A
348493 TCACATGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.19
Consensus pattern (23 bp):
AACTAAACAGGACTCATCACACT
Found at i:349895 original size:43 final size:44
Alignment explanation
Indices: 349842--349926 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 44
349832 CCCGAGGTGT
* *
349842 GATTTCGTGTAAGACCATGTCTAGGACGTTGGCATCA-ATATGA
1 GATTACGTGTAAGACCATGTCTAGGACATTGGCATCATATATGA
*
349885 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCATATAT
1 GATTACGTGTAAGACCATGTCTAGGACATTGGCATCATATAT
349927 AATTTCTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 34 0.89
44 4 0.11
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
GATTACGTGTAAGACCATGTCTAGGACATTGGCATCATATATGA
Found at i:357481 original size:43 final size:44
Alignment explanation
Indices: 357428--357514 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 44
357418 CCCGAGGTGT
*
357428 GATTTCGTGTAAGACCATGTCTGAGACATTGGCATCG-ATATGA
1 GATTACGTGTAAGACCATGTCTGAGACATTGGCATCGTATATGA
* *
357471 GATTACGTGTAAGACCATGTTTGCGACATTGGCATCGTATATGA
1 GATTACGTGTAAGACCATGTCTGAGACATTGGCATCGTATATGA
357515 TTTCATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 34 0.85
44 6 0.15
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
GATTACGTGTAAGACCATGTCTGAGACATTGGCATCGTATATGA
Found at i:368664 original size:11 final size:10
Alignment explanation
Indices: 368643--368667 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
368633 CTAATGTTAT
368643 AAAAGAAAAA
1 AAAAGAAAAA
368653 AAAAGAAAAA
1 AAAAGAAAAA
368663 AAAAG
1 AAAAG
368668 TACAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:385086 original size:17 final size:17
Alignment explanation
Indices: 385051--385091 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
385041 GATAAGTATA
*
385051 CATTGTCATTGAATTTT
1 CATTGTCATTGAATATT
385068 CATTGTCATT-ACATATT
1 CATTGTCATTGA-ATATT
385085 CA-TGTCA
1 CATTGTCA
385092 GTGCATTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (17 bp):
CATTGTCATTGAATATT
Found at i:387691 original size:24 final size:23
Alignment explanation
Indices: 387664--387709 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
387654 TTTAGAGAAT
387664 TTTGTGTTT-ACGTTTTGAGGGTTC
1 TTTGTGTTTGA-GTTTTG-GGGTTC
*
387688 TTTGTTTTTGAGTTTTGGGGTT
1 TTTGTGTTTGAGTTTTGGGGTT
387710 TAACTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 14 0.70
25 1 0.05
ACGTcount: A:0.07, C:0.04, G:0.30, T:0.59
Consensus pattern (23 bp):
TTTGTGTTTGAGTTTTGGGGTTC
Found at i:398117 original size:20 final size:21
Alignment explanation
Indices: 398084--398130 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
398074 TATATAAATA
* *
398084 ATTTT-TTATTACAA-ATTTG
1 ATTTTCTTATAACAATACTTG
398103 ATTTTCTTATAACAATACTTG
1 ATTTTCTTATAACAATACTTG
398124 -TTTTCTT
1 ATTTTCTT
398131 TACATGTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 15 0.62
21 4 0.17
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTTCTTATAACAATACTTG
Found at i:406343 original size:30 final size:30
Alignment explanation
Indices: 406309--406371 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
406299 ACTTATTTTA
* *
406309 TTGTTAATTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
*
406339 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
406369 TTG
1 TTG
406372 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:406545 original size:74 final size:75
Alignment explanation
Indices: 406445--406596 Score: 297
Period size: 74 Copynumber: 2.0 Consensus size: 75
406435 ATTTGTTAGG
406445 AAATATTTATTTTGATATTTTTAGTATTTTTGATGTATTATATATAATTTTTAAAATTATATAAA
1 AAATATTTATTTTGATATTTTTAGTATTTTTGATGTATTATATATAATTTTTAAAATTATATAAA
406510 AAATAATATA
66 AAATAATATA
406520 AAATATTTATTTT-ATATTTTTAGTATTTTTGATGTATTATATATAATTTTTAAAATTATATAAA
1 AAATATTTATTTTGATATTTTTAGTATTTTTGATGTATTATATATAATTTTTAAAATTATATAAA
406584 AAATAATATA
66 AAATAATATA
406594 AAA
1 AAA
406597 AATAATATGG
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 64 0.83
75 13 0.17
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (75 bp):
AAATATTTATTTTGATATTTTTAGTATTTTTGATGTATTATATATAATTTTTAAAATTATATAAA
AAATAATATA
Found at i:406592 original size:12 final size:12
Alignment explanation
Indices: 406571--406604 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
406561 TATAATTTTT
*
406571 AAAATTATATAA
1 AAAATAATATAA
406583 AAAATAATATAA
1 AAAATAATATAA
406595 AAAATAATAT
1 AAAATAATAT
406605 GGGCAGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:414188 original size:74 final size:74
Alignment explanation
Indices: 414053--414204 Score: 209
Period size: 74 Copynumber: 2.1 Consensus size: 74
414043 CCCAGCCCTC
* *
414053 GTGTCTTTCAAAATCTTAAAAAATTAAGCTCTAGGACTCACATAGACTAGGACACTCCCTTGTGT
1 GTGTCTTTCAAAATCTTAAAAAATTAAGCTCTAGGACTCACATAGACTAGGACACGCCCTTGTAT
*
414118 CCTTGCCGT
66 CCTGGCCGT
* * * *
414127 GTGTCTTTCAAAATCTTAAAAAATTAAGCT-TCAGGACTCGCATGGCCTAAGG-CACGGCCTTGT
1 GTGTCTTTCAAAATCTTAAAAAATTAAGCTCT-AGGACTCACATAGACT-AGGACACGCCCTTGT
414190 ATCCTGGCCGT
64 ATCCTGGCCGT
414201 GTGT
1 GTGT
414205 AATCATTCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
73 1 0.01
74 65 0.94
75 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (74 bp):
GTGTCTTTCAAAATCTTAAAAAATTAAGCTCTAGGACTCACATAGACTAGGACACGCCCTTGTAT
CCTGGCCGT
Found at i:418739 original size:11 final size:11
Alignment explanation
Indices: 418723--418748 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
418713 AATAAAATCC
418723 TTTTTTAATAT
1 TTTTTTAATAT
418734 TTTTTTAATAT
1 TTTTTTAATAT
418745 TTTT
1 TTTT
418749 ATATATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTAATAT
Found at i:420882 original size:18 final size:18
Alignment explanation
Indices: 420859--420898 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
420849 TTAAACCCTT
* *
420859 AAAAACCCTAACCCTAAC
1 AAAAACCCCAAACCTAAC
420877 AAAAACCCCAAACCTAAC
1 AAAAACCCCAAACCTAAC
420895 AAAA
1 AAAA
420899 TTAAAAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.35, G:0.00, T:0.07
Consensus pattern (18 bp):
AAAAACCCCAAACCTAAC
Found at i:425451 original size:3 final size:3
Alignment explanation
Indices: 425443--425479 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
425433 TCATTCTTGC
425443 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
425480 GAAGTTCAAG
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:425888 original size:31 final size:31
Alignment explanation
Indices: 425846--425913 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
425836 TTGATATTTC
* * *
425846 CAAGTTTAGGCCTCAATTTGGGAGCAATTGT
1 CAAGTTCAGGCCTCAATGTGGGAACAATTGT
425877 CAAGTTCAGGCCTCAATGTGGGAACAATTGT
1 CAAGTTCAGGCCTCAATGTGGGAACAATTGT
425908 CAAGTT
1 CAAGTT
425914 TAAGGACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (31 bp):
CAAGTTCAGGCCTCAATGTGGGAACAATTGT
Found at i:426013 original size:58 final size:58
Alignment explanation
Indices: 425890--426015 Score: 146
Period size: 58 Copynumber: 2.2 Consensus size: 58
425880 GTTCAGGCCT
* ** * *
425890 CAATGTGGGAACAATTGTCAAGTTTAAGGACTAACTTGGACAAAAAGAGCTCAAGCCC
1 CAATGTGGGAACAATTATCAAGTACAAGGACTAACTTGGACAAAAAAAGCTCAAGACC
* * * **
425948 CAGTGTGGGAATAATTATCAAGTACAAGGACTAATTTGGACAAAAAAAG-TTTAGAACC
1 CAATGTGGGAACAATTATCAAGTACAAGGACTAACTTGGACAAAAAAAGCTCAAG-ACC
426006 CAATGTGGGA
1 CAATGTGGGA
426016 GTTATTCCCA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
57 3 0.05
58 53 0.95
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (58 bp):
CAATGTGGGAACAATTATCAAGTACAAGGACTAACTTGGACAAAAAAAGCTCAAGACC
Found at i:426715 original size:13 final size:13
Alignment explanation
Indices: 426697--426724 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
426687 AGTAATCTTC
426697 TTTTCTATGTAAG
1 TTTTCTATGTAAG
426710 TTTTCTATGTAAG
1 TTTTCTATGTAAG
426723 TT
1 TT
426725 CAAGTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (13 bp):
TTTTCTATGTAAG
Found at i:426763 original size:3 final size:3
Alignment explanation
Indices: 426750--426820 Score: 133
Period size: 3 Copynumber: 23.3 Consensus size: 3
426740 TCATTCTTGC
426750 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
426796 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
426821 GAAGTTCAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:430411 original size:37 final size:35
Alignment explanation
Indices: 430360--430430 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
430350 GTTCCAAAAA
*
430360 TAATATTATTTTAATAGT-TTAGTATTTAATTTAATG
1 TAATATTATCTTAATAGTATT-GTA-TTAATTTAATG
*
430396 TAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 TAATA-TTATCTTAATAGTATTGTATTAATTTAAT
430431 ATTAAAGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 15 0.48
37 14 0.45
38 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.55
Consensus pattern (35 bp):
TAATATTATCTTAATAGTATTGTATTAATTTAATG
Found at i:441425 original size:31 final size:31
Alignment explanation
Indices: 441383--441450 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
441373 TTAATATTTC
* * *
441383 CAAGTTTAGGCCCCAATTTAGGAGCAATTGT
1 CAAGTTCAGGCCCCAATGTAGGAACAATTGT
* *
441414 CAAGTTCAGGCCTCAATGTGGGAACAATTGT
1 CAAGTTCAGGCCCCAATGTAGGAACAATTGT
441445 CAAGTT
1 CAAGTT
441451 TAAGGACTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (31 bp):
CAAGTTCAGGCCCCAATGTAGGAACAATTGT
Found at i:442015 original size:23 final size:23
Alignment explanation
Indices: 441988--442035 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
441978 AGTTTTATAG
441988 AACAATTAAATTTATCTACTAAT
1 AACAATTAAATTTATCTACTAAT
*
442011 AACAATTAAATTTATCTACTCAT
1 AACAATTAAATTTATCTACTAAT
442034 AA
1 AA
442036 ATTCTAGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (23 bp):
AACAATTAAATTTATCTACTAAT
Found at i:444542 original size:70 final size:71
Alignment explanation
Indices: 444417--444565 Score: 228
Period size: 70 Copynumber: 2.1 Consensus size: 71
444407 TTGTAGTGCA
*
444417 TTTAATATTGTTAATATGATGCATTTATATGTTTAAATTTCCTTTTACCCGCAATGTAATTAAAT
1 TTTAATATTGTTAATATGATGCATTTATATGTTTAAATTTCCTTTTAACCGCAATGTAATTAAAT
444482 TTTTAT
66 TTTTAT
* * * * * *
444488 TTTTATATTGTTAATGTGATGTATTTATGT-TTTAAATTTCTTTTTAATCGCAATGTAATTAAAT
1 TTTAATATTGTTAATATGATGCATTTATATGTTTAAATTTCCTTTTAACCGCAATGTAATTAAAT
444552 TTTTAT
66 TTTTAT
444558 TTTAATAT
1 TTTAATAT
444566 GATATATATT
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
70 44 0.63
71 26 0.37
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (71 bp):
TTTAATATTGTTAATATGATGCATTTATATGTTTAAATTTCCTTTTAACCGCAATGTAATTAAAT
TTTTAT
Found at i:444556 original size:35 final size:35
Alignment explanation
Indices: 444448--444556 Score: 89
Period size: 35 Copynumber: 3.1 Consensus size: 35
444438 CATTTATATG
* **
444448 TTTAAATTTCCTTTTACCCGCAATGTAATTAAATT
1 TTTAAATTTCTTTTTAATCGCAATGTAATTAAATT
** * ** *
444483 TTTATTTTTATATTGTTAAT-GTGATGT-ATT-TATGT
1 TTTAAATTTCT-TT-TTAATCGCAATGTAATTAAAT-T
444518 TTTAAATTTCTTTTTAATCGCAATGTAATTAAATT
1 TTTAAATTTCTTTTTAATCGCAATGTAATTAAATT
444553 TTTA
1 TTTA
444557 TTTTAATATG
Statistics
Matches: 53, Mismatches: 15, Indels: 12
0.66 0.19 0.15
Matches are distributed among these distances:
33 5 0.09
34 9 0.17
35 27 0.51
36 9 0.17
37 3 0.06
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (35 bp):
TTTAAATTTCTTTTTAATCGCAATGTAATTAAATT
Found at i:445698 original size:13 final size:13
Alignment explanation
Indices: 445680--445709 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
445670 AGCCCAAACT
445680 CAATTACCCAACC
1 CAATTACCCAACC
445693 CAATTACCCAACC
1 CAATTACCCAACC
445706 CAAT
1 CAAT
445710 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:445862 original size:9 final size:9
Alignment explanation
Indices: 445850--445926 Score: 102
Period size: 9 Copynumber: 8.4 Consensus size: 9
445840 AAATAAAAAA
445850 AATTCGGGT
1 AATTCGGGT
445859 AATTCGGGT
1 AATTCGGGT
*
445868 ATTTTTC-GGT
1 A--ATTCGGGT
*
445878 AATTCGGTT
1 AATTCGGGT
*
445887 AATTCGGTT
1 AATTCGGGT
445896 AATTCGGGT
1 AATTCGGGT
445905 AATTCGGGT
1 AATTCGGGT
445914 AATTCGGGT
1 AATTCGGGT
445923 AATT
1 AATT
445927 TTAACCAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
8 3 0.05
9 51 0.84
10 4 0.07
11 3 0.05
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:446385 original size:16 final size:16
Alignment explanation
Indices: 446364--446399 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
446354 TTTGGTTCGC
446364 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
446380 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
446396 TGTA
1 TGTA
446400 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:452077 original size:27 final size:27
Alignment explanation
Indices: 452047--452103 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
452037 GACAACAAAT
* *
452047 GTAGTTTGTCGGGACATTAAACACAGG
1 GTAGTTTGCCAGGACATTAAACACAGG
* *
452074 GTAGTTTGCCAGGACGTTAAACATAGG
1 GTAGTTTGCCAGGACATTAAACACAGG
452101 GTA
1 GTA
452104 AAAATGTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (27 bp):
GTAGTTTGCCAGGACATTAAACACAGG
Found at i:461622 original size:2 final size:2
Alignment explanation
Indices: 461615--461643 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
461605 TGTGTTAAGT
461615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
461644 TCGGATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:461875 original size:37 final size:37
Alignment explanation
Indices: 461830--461944 Score: 176
Period size: 37 Copynumber: 3.1 Consensus size: 37
461820 ATAGATAAAA
* *
461830 ATATATGTATGCATTTGGCATAGGTGAATATAAGGGT
1 ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
*
461867 ATATATGTATGCATTCGGCATAGGTGAAAATAAGTGT
1 ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
* **
461904 ATATATGTATGCATTCGGCATAAGTGGGTATAAGTGT
1 ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
461941 ATAT
1 ATAT
461945 GTGCATTCGG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (37 bp):
ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
Found at i:461955 original size:33 final size:35
Alignment explanation
Indices: 461830--461957 Score: 125
Period size: 37 Copynumber: 3.6 Consensus size: 35
461820 ATAGATAAAA
* * * *
461830 ATATATGTATGCATTTGGCATAGGTGAATATAAGGG
1 ATATATG-ATGCATTCGGCATAAGTGAAAATAAGTG
*
461866 TATATATGTATGCATTCGGCATAGGTGAAAATAAGTG
1 -ATATATG-ATGCATTCGGCATAAGTGAAAATAAGTG
***
461903 TATATATGTATGCATTCGGCATAAGTGGGTATAAGTG
1 -ATATATG-ATGCATTCGGCATAAGTGAAAATAAGTG
461940 -TATATG-TGCATTCGGCAT
1 ATATATGATGCATTCGGCAT
461958 TTATGGTTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
33 12 0.14
35 6 0.07
37 66 0.79
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (35 bp):
ATATATGATGCATTCGGCATAAGTGAAAATAAGTG
Found at i:468455 original size:26 final size:27
Alignment explanation
Indices: 468426--468516 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 27
468416 GATAGAATAC
*
468426 GCCACTAA-GCGATCCTTTTAGAATTT
1 GCCACAAAGGCGATCCTTTTAGAATTT
* * *
468452 GCCACAAAGGCTATTCTTTTAGAGTTT
1 GCCACAAAGGCGATCCTTTTAGAATTT
* * * * *
468479 GCCACAAAGGCTATTCTTTTATAGTTC
1 GCCACAAAGGCGATCCTTTTAGAATTT
468506 GCCACAAAGGC
1 GCCACAAAGGC
468517 TGTTCTTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 7 0.12
27 51 0.88
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (27 bp):
GCCACAAAGGCGATCCTTTTAGAATTT
Found at i:468479 original size:27 final size:27
Alignment explanation
Indices: 468440--468548 Score: 155
Period size: 27 Copynumber: 4.0 Consensus size: 27
468430 CTAAGCGATC
* *
468440 CTTTTAGAATTTGCCACAAAGGCTATT
1 CTTTTAGAGTTCGCCACAAAGGCTATT
*
468467 CTTTTAGAGTTTGCCACAAAGGCTATT
1 CTTTTAGAGTTCGCCACAAAGGCTATT
* *
468494 CTTTTATAGTTCGCCACAAAGGCTGTT
1 CTTTTAGAGTTCGCCACAAAGGCTATT
* *
468521 CTTTTAGAGTTCACCATAAAGGCTATT
1 CTTTTAGAGTTCGCCACAAAGGCTATT
468548 C
1 C
468549 CTTGTTGTCG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (27 bp):
CTTTTAGAGTTCGCCACAAAGGCTATT
Found at i:469417 original size:6 final size:6
Alignment explanation
Indices: 469362--469416 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
469352 TTTCCACTTA
*
469362 AGGAAG AGGAAG AGGAAA AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
*
469410 AAGAAG A
1 AGGAAG A
469417 AAGAAGAACC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (6 bp):
AGGAAG
Found at i:471585 original size:20 final size:18
Alignment explanation
Indices: 471539--471585 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
471529 TGTTTTAACA
471539 TAATTTTTT-TATATTTT
1 TAATTTTTTATATATTTT
**
471556 TAATAATTTATACTTATTTT
1 TAATTTTTTATA--TATTTT
471576 TAATTTTTTA
1 TAATTTTTTA
471586 AAAAATTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.30
18 2 0.09
20 14 0.61
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATTTTTTATATATTTT
Found at i:474905 original size:17 final size:18
Alignment explanation
Indices: 474885--474918 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
474875 TCATTTTTTG
474885 TATAT-ACATTATTTTAC
1 TATATAACATTATTTTAC
*
474902 TATATAATATTATTTTA
1 TATATAACATTATTTTA
474919 AGTGTTAACA
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAACATTATTTTAC
Found at i:476611 original size:22 final size:22
Alignment explanation
Indices: 476572--476630 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
476562 TATGGATTGG
* *
476572 TTTATTAAATAATCATAGAAAA
1 TTTATTAAAAAATTATAGAAAA
* *
476594 TTTATAAAAAAATTATAGCAAA
1 TTTATTAAAAAATTATAGAAAA
*
476616 -TTATTTAAAAATTAT
1 TTTATTAAAAAATTAT
476631 TGAGAATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (22 bp):
TTTATTAAAAAATTATAGAAAA
Found at i:476948 original size:21 final size:21
Alignment explanation
Indices: 476923--476976 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
476913 TGGATGTTGA
476923 TTTCAATAAATTTTAAATATT
1 TTTCAATAAATTTTAAATATT
* * *
476944 TTTCAATAAATCTAAAATCTT
1 TTTCAATAAATTTTAAATATT
476965 TTT-AAT-AATTTT
1 TTTCAATAAATTTT
476977 CTATAATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 4 0.14
20 3 0.11
21 21 0.75
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTCAATAAATTTTAAATATT
Found at i:476966 original size:20 final size:21
Alignment explanation
Indices: 476923--476972 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
476913 TGGATGTTGA
*
476923 TTTCAATAAATTTTAAATATT
1 TTTCAATAAATTCTAAATATT
476944 TTTCAATAAA-TCTAAA-ATCT
1 TTTCAATAAATTCTAAATAT-T
*
476964 TTTTAATAA
1 TTTCAATAA
476973 TTTTCTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTCAATAAATTCTAAATATT
Found at i:483872 original size:94 final size:93
Alignment explanation
Indices: 483726--485221 Score: 1538
Period size: 94 Copynumber: 16.0 Consensus size: 93
483716 TTTAGTATCA
* ** * * * * * *
483726 TAGCTTCATCTTGCTCCATTGCAAC-TTAAAGAGATAAGATTTGTTGTTGTAGTTTCATTTCAAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCA-TTCGAC
* *
483790 CCACTACAACTTCAAGGGTATAGGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * *
483819 TAGCTTCATCTTGCTCCACTGCATCTTTAGGGAGATAAGATTCGCTATTGTAGTTTCATTATGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATT-CGAC
* * *
483884 ACACTGCATCTTCAGGGGTATAGGATTTC
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * * * * *
483913 TAGCTTTATCTTGCTCCACTACAACTTCACGAAGATAAGATTCGCTATGGTAACTTCATTCCAGC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTCGA-C
* * * *
483978 CTACTGCATCCTCAGGGGCATAGGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * * *
484007 TAGCTTCATCTTGCTCCATTGCAACTTCAAGGAGATACGATTTGCTATGGTAGCTTCATTTCGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCA-TTCGAC
* * * * *
484072 CTACTTCATCTTCAGGGGCATAGAATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * * * * * ***
484101 TAGCTTTATTTTGTTTCTCTGTAATTTTAGGGAGATAAGATTCGCTATGGTAGCTTCAATAAAAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTC-ATTCGAC
*
484166 CCACTGCAACTTCAGGGGTATATGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * *
484195 TAGCTTCATCTTGCTCCACTACAACTTCAAGGAGATAAGATTTGCTATGGTAGCTTCATTCTGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTC-GAC
* *
484260 CCATTGTAACTTCAGGGGTATAGGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * *
484289 TAGCTCCA-CTTTGCTCCACTGTAACTTTAGGGAGATAAGATTCGCTATCGTAGCTTCATTCCGA
1 TAGCTTCATC-TTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATT-CGA
*
484353 -CCACTGCAAC-TCTAGGGGTATAGGATTTA
64 CCCACTGCAACTTC-AGGGGTATAGGATTTG
* * * * *
484382 TAGCTTCATCTTACTCTACTGTAACTTCAGGGAGATAAGATTCGCTATGGTAGCTTCAATCTGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTC-GAC
* * * *
484447 CTACTGTAACTTCAGAGGTATAAGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * *
484476 TAGCTTCATCTTGCTTCACTTCAACTTTAGGGAGATAAGATTCGCTATTGTAGCTTCAATCTGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTC-GAC
* * *
484541 CCACTGGAACTTCAGGGGTACAAGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * *
484570 TAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAATTCAG-TATGGTAGCTTCAATCTGA
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTC-GCTATGGTAGCTTCATTC-GA
* * * *
484634 CCCGCTACAACTTCAAGGGTATATGATTTG
64 CCCACTGCAACTTCAGGGGTATAGGATTTG
* * *
484664 TAGCTTTATCTTGCTCCACTACAACTTTAGGGAGAT-AGATTCGCTATGGTA---T--TTCCACC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTCGACC
* * * *
484723 CATTGCAACGTCAAGGGTATATGATTTG
66 CACTGCAACTTCAGGGGTATAGGATTTG
* * * * * *
484751 GAGCTTCATCTTACTCCACTGCAACTTTAGGGAGATAGGATTCACTATGGTAGCTTTAATTTGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGC-TTCATTCGAC
** * *
484816 CCACTATAACTTTAGGGGTATAAGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
** * * *
484845 TATTTTCATCTTGCTCCACTGCAAATTTAGGGAGATAAGATTCACTATGGTAGCTTCAATCTGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTC-GAC
* *
484910 CCATTGCAACTTCAGGGGTACAGGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * * *
484939 TGGCTTCATCTTACTCCACTGCAACTTCAGGGAGGTAAGATTCGCTATGGTAGCTTCAATCTGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTC-GAC
* * *
485004 CCACTACAACTTCAGAGGTATAAGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * ** * * * * * *
485033 TAGCTTCATGTTACTCCATTAAAACTTTAAGGAGATAATATTTGTTATTGTAGCTTCAATCTGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTC-GAC
*
485098 CCACTGCAACTTCAGGGGTATAGGATTTC
65 CCACTGCAACTTCAGGGGTATAGGATTTG
* * * * *
485127 TAACTTTATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATGGTAGCTTCAATCCGAC
1 TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTC-ATTCGAC
**
485192 ATACTGCAACTTCAGGGGTATAGGATTTG
65 CCACTGCAACTTCAGGGGTATAGGATTTG
485221 T
1 T
485222 TATTTCACTG
Statistics
Matches: 1168, Mismatches: 211, Indels: 47
0.82 0.15 0.03
Matches are distributed among these distances:
87 59 0.05
88 15 0.01
90 1 0.00
92 5 0.00
93 122 0.10
94 955 0.82
95 11 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (93 bp):
TAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTCATTCGACC
CACTGCAACTTCAGGGGTATAGGATTTG
Found at i:491953 original size:16 final size:15
Alignment explanation
Indices: 491932--491964 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
491922 TAGTGAATAC
491932 AATAACAAGAAATAAT
1 AATAACAAG-AATAAT
491948 AATAACAAGAATAAT
1 AATAACAAGAATAAT
491963 AA
1 AA
491965 AAATATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (15 bp):
AATAACAAGAATAAT
Found at i:493554 original size:16 final size:16
Alignment explanation
Indices: 493529--493563 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
493519 TTTTTTTATA
493529 AATGGAC-TTTTAGTT
1 AATGGACTTTTTAGTT
493544 AATGGACCTTTTTAGTT
1 AATGGA-CTTTTTAGTT
493561 AAT
1 AAT
493564 TGGTGAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 1 0.06
17 11 0.61
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.46
Consensus pattern (16 bp):
AATGGACTTTTTAGTT
Found at i:499644 original size:11 final size:11
Alignment explanation
Indices: 499628--499654 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
499618 AAAAATAGGC
499628 CATTTCCAAGA
1 CATTTCCAAGA
499639 CATTTCCAAGA
1 CATTTCCAAGA
499650 CATTT
1 CATTT
499655 TCTCACCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (11 bp):
CATTTCCAAGA
Found at i:503197 original size:123 final size:124
Alignment explanation
Indices: 502971--503200 Score: 302
Period size: 123 Copynumber: 1.9 Consensus size: 124
502961 GCCGCTCTAG
* * *
502971 CACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAAAAGGTTGGCCGGTTTAAGATCGCAACC
1 CACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAAAAGGTTGGCCGATTTAAGATCACAACA
* * * * *
503036 TCCAAAGCAGCTAGTAGACTTATGTTCTCAACTGACATTATATGATCTCATATCTCCAA
66 TCAAAAGCAGCTAGCAGACCTATGTTCCCAACTAACATTATATGATCTCATATCTCCAA
* * * * *
503095 CACAGCTAGC-AGACTTACGCTCTCAATTGATGTCAT-GAAGGTTTGCCGATTTAAGATCACAAC
1 CACAGCTAGCGA-ACCTACGCTCCCAACTGATGTCATAAAAGGTTGGCCGATTTAAGATCACAAC
* *
503158 ATCAAAAGTAGCTAGCAGACCTATGTTCCCAGCTAACATTATA
65 ATCAAAAGCAGCTAGCAGACCTATGTTCCCAACTAACATTATA
503201 AGACCTGATA
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
123 59 0.66
124 31 0.34
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (124 bp):
CACAGCTAGCGAACCTACGCTCCCAACTGATGTCATAAAAGGTTGGCCGATTTAAGATCACAACA
TCAAAAGCAGCTAGCAGACCTATGTTCCCAACTAACATTATATGATCTCATATCTCCAA
Found at i:506636 original size:44 final size:43
Alignment explanation
Indices: 506587--506767 Score: 118
Period size: 44 Copynumber: 4.0 Consensus size: 43
506577 AGATTTGCTA
* *
506587 TTGTAGTTTCAATCTAT-TCCACTGCAAT-TTCAGGGATATAGGAT
1 TTGTAGTTTC-ATCT-TGTCCACTGC-ATCTTCAGGGAGATAAGAT
506631 TTGTAGTTTCATCTTGGTCCACTGCATCTTCAGGGAGATAAGAT
1 TTGTAGTTTCATCTT-GTCCACTGCATCTTCAGGGAGATAAGAT
* * * *
506675 TCACCATGGTAGCTTTAAT-TTGACCCACTACAACTTCAGGG-GTATAAGAT
1 T-----T-GTAG-TTTCATCTTG-TCCACTGCATCTTCAGGGAG-ATAAGAT
* * * *
506725 TTGTAGCTTCATCTCGCTCCACTGCAACTCCAGGGAGATAAGA
1 TTGTAGTTTCATCTTG-TCCACTGCATCTTCAGGGAGATAAGA
506768 GTCGCTATGG
Statistics
Matches: 110, Mismatches: 13, Indels: 28
0.73 0.09 0.19
Matches are distributed among these distances:
42 1 0.01
43 10 0.09
44 60 0.55
45 2 0.02
49 3 0.03
50 29 0.26
51 5 0.05
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (43 bp):
TTGTAGTTTCATCTTGTCCACTGCATCTTCAGGGAGATAAGAT
Found at i:506675 original size:94 final size:93
Alignment explanation
Indices: 506544--506914 Score: 372
Period size: 94 Copynumber: 4.0 Consensus size: 93
506534 GTGTTAGAGT
* * * * * * *
506544 TTCATCTTGCTCTATTGCAACTTTAAGGAGATAAGATTTGCTATTGTAGTTTCAATCT-ATTCCA
1 TTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAGCTTCAATCTGA--CCA
* *
506608 CTGCAATTTCAGGGATATAGGATTTGTAGT
64 CTGCAACTTCAGGGATATAGGATTTGTAGC
* * * * * *
506638 TTCATCTTGGTCCACTGCATCTTCAGGGAGATAAGATTCACCATGGTAGCTTTAATTTGACCCAC
1 TTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAGCTTCAATCTGA-CCAC
* * *
506703 TACAACTTCAGGGGTATAAGATTTGTAGC
65 TGCAACTTCAGGGATATAGGATTTGTAGC
* * * *
506732 TTCATCTCGCTCCACTGCAACTCCAGGGAGATAAGAGTCGCTATGGTAGCTTCAATCTGACCGAT
1 TTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAGCTTCAATCTGACC-AC
**
506797 TGCAACTTCA-CAATATAGGATTTGTAGC
65 TGCAACTTCAGGGATATAGGATTTGTAGC
* * * * *
506825 TTCATCTTGCACCATTGCAATTTCAGGGAGATAAGATTTGCTATTGTAGCTTCAAT-TCGACCCA
1 TTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAGCTTCAATCT-GA-CCA
* *
506889 CTACAACTTCAAAGG-TATAGGATTTG
64 CTGCAACTTC-AGGGATATAGGATTTG
506915 AGGTTTCACT
Statistics
Matches: 225, Mismatches: 46, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
92 1 0.00
93 75 0.33
94 148 0.66
95 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (93 bp):
TTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTAGCTTCAATCTGACCACT
GCAACTTCAGGGATATAGGATTTGTAGC
Found at i:514687 original size:24 final size:24
Alignment explanation
Indices: 514628--514677 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
514618 GAAATTAAAC
**
514628 ATAAAATATTAAATAACATAAAGG
1 ATAAAATAAAAAATAACATAAAGG
514652 ATAAAATAAAAAATAACATAAAGG
1 ATAAAATAAAAAATAACATAAAGG
514676 AT
1 AT
514678 CGAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.22
Consensus pattern (24 bp):
ATAAAATAAAAAATAACATAAAGG
Found at i:519540 original size:40 final size:40
Alignment explanation
Indices: 519496--519634 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
519486 TTACACTTTT
* * * *
519496 TGTCTAGCGTGTTTCGATTAGATTAGCTCTTATCAGCTTC
1 TGTCTAGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTC
* * *
519536 TGTCT-GAAGTGTTTCGGGTGGATTAGTTCTTATGAGCTTC
1 TGTCTAG-TGTGTTTCGGTTGGATTAGCTCTTATGAGCTTC
* * *
519576 TTTTTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTC
1 TGTCTAGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTC
519616 -GTTCTAGTGTG-TTCGGTTG
1 TG-TCTAGTGTGTTTCGGTTG
519635 ATCTAACGAT
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
39 9 0.11
40 72 0.88
41 1 0.01
ACGTcount: A:0.13, C:0.14, G:0.27, T:0.45
Consensus pattern (40 bp):
TGTCTAGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTC
Found at i:521353 original size:43 final size:43
Alignment explanation
Indices: 521241--521354 Score: 108
Period size: 43 Copynumber: 2.7 Consensus size: 43
521231 TGTGTTTTCG
* * * * * * *
521241 TGTAAGACAACGTCTAGTACGTTGGCATTGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGAAGTTGGCATCGACTTGTGATTACA
521284 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTGATTACA
1 TGTAAGACCAC-GTCTGGGA-AGTTGGCATCGACT-TGTGATTACA
*
521327 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGAAGTTGGCAT
521355 TGTACGAGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
42 3 0.05
43 53 0.91
44 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGAAGTTGGCATCGACTTGTGATTACA
Found at i:534186 original size:73 final size:73
Alignment explanation
Indices: 534101--534239 Score: 183
Period size: 73 Copynumber: 1.9 Consensus size: 73
534091 TACCTTCCCA
* * *
534101 AAAAAATTTACTTCCCCCCACATCC-CCAAAACTTTTTTCCTTTTACTTT-TCCCAAGACATTTA
1 AAAAAATTTACTT--CCCCAAAACCTCCAAAACTTTTTTCCTTTTACTTTCTCCCAAAACATTTA
534164 CTTCTCCCTC
64 CTTCTCCCTC
* * **
534174 AAAAATTTTACTTCCCCAAAACCTCCAAAATTTTTTTCCTTTTGTTTTCTCCCAAAACATTTACT
1 AAAAAATTTACTTCCCCAAAACCTCCAAAACTTTTTTCCTTTTACTTTCTCCCAAAACATTTACT
534239 T
66 T
534240 TACTCAAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 8 0.14
72 21 0.37
73 28 0.49
ACGTcount: A:0.28, C:0.31, G:0.01, T:0.40
Consensus pattern (73 bp):
AAAAAATTTACTTCCCCAAAACCTCCAAAACTTTTTTCCTTTTACTTTCTCCCAAAACATTTACT
TCTCCCTC
Found at i:535091 original size:12 final size:13
Alignment explanation
Indices: 535060--535098 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
535050 AATTTAGTAT
* *
535060 TATTTTTGAGAAA
1 TATTTTTAAAAAA
535073 TATTTTTAAAAAA
1 TATTTTTAAAAAA
535086 TA-TTTTAAAAAA
1 TATTTTTAAAAAA
535098 T
1 T
535099 TGATTTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (13 bp):
TATTTTTAAAAAA
Found at i:549670 original size:2 final size:2
Alignment explanation
Indices: 549659--549688 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
549649 TACGATTGAT
549659 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
549689 CATGTAAACG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:561621 original size:26 final size:25
Alignment explanation
Indices: 561592--561686 Score: 106
Period size: 26 Copynumber: 3.8 Consensus size: 25
561582 AGACTTACCA
*
561592 CAGCTCGTATGATCTTACCGTTATAT
1 CAGCTCGTATGAGCTTACCGTT-TAT
*
561618 CAGCTCTTATGAGCTTACCG-TT-T
1 CAGCTCGTATGAGCTTACCGTTTAT
561641 CAGCTCG-ATAGAGCTTACCGTTTAT
1 CAGCTCGTAT-GAGCTTACCGTTTAT
* *
561666 CAGCTTGGAATGAGCTTACCG
1 CAGC-TCGTATGAGCTTACCG
561687 ATCATGGCTC
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
22 2 0.03
23 17 0.28
24 3 0.05
25 6 0.10
26 30 0.50
27 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCGTTTAT
Found at i:561679 original size:49 final size:49
Alignment explanation
Indices: 561592--561686 Score: 124
Period size: 49 Copynumber: 1.9 Consensus size: 49
561582 AGACTTACCA
* *
561592 CAGCTCGTATGATCTTACCGTTATATCAGCTCTTATGAGCTTACCGTTT
1 CAGCTCGTATGAGCTTACCGTTATATCAGCTCTAATGAGCTTACCGTTT
561641 CAGCTCG-ATAGAGCTTACCGTT-TATCAGCT-TGGAATGAGCTTACCG
1 CAGCTCGTAT-GAGCTTACCGTTATATCAGCTCT--AATGAGCTTACCG
561687 ATCATGGCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
47 1 0.02
48 10 0.24
49 30 0.73
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (49 bp):
CAGCTCGTATGAGCTTACCGTTATATCAGCTCTAATGAGCTTACCGTTT
Found at i:568048 original size:7 final size:7
Alignment explanation
Indices: 568038--568071 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
568028 GTCCAAAAGT
568038 CCACAAA
1 CCACAAA
568045 CCACAAA
1 CCACAAA
568052 CCACAAA
1 CCACAAA
*
568059 CCAGAAA
1 CCACAAA
568066 CC-CAAA
1 CCACAAA
568072 ATTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 3 0.12
7 22 0.88
ACGTcount: A:0.56, C:0.41, G:0.03, T:0.00
Consensus pattern (7 bp):
CCACAAA
Found at i:570696 original size:15 final size:15
Alignment explanation
Indices: 570676--570709 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
570666 TATCCACATT
570676 TAATCATAATTTAAA
1 TAATCATAATTTAAA
* *
570691 TAATCATGATTTTAA
1 TAATCATAATTTAAA
570706 TAAT
1 TAAT
570710 AAAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
TAATCATAATTTAAA
Found at i:573803 original size:23 final size:23
Alignment explanation
Indices: 573760--573803 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
573750 TACATTTAAA
* *
573760 TAAAGATAATAAAAATCAAATTG
1 TAAACATAATAAAAATAAAATTG
*
573783 TAAACATAATAAACATAAAAT
1 TAAACATAATAAAAATAAAAT
573804 AATTATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (23 bp):
TAAACATAATAAAAATAAAATTG
Found at i:580666 original size:33 final size:33
Alignment explanation
Indices: 580602--580666 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
580592 TCTTTATGGC
* *
580602 TTAAATTGAAAATGATTTTTATATAGGGGGAGT
1 TTAAATTGAAAATGACTTTTATATAGAGGGAGT
580635 TTAAATTGAAAATGACTTTTAT-TAAGAGGGAG
1 TTAAATTGAAAATGACTTTTATAT-AGAGGGAG
580667 CAACCTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (33 bp):
TTAAATTGAAAATGACTTTTATATAGAGGGAGT
Found at i:581014 original size:20 final size:20
Alignment explanation
Indices: 580991--581029 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
580981 TATCGGTACT
*
580991 TTTCTTAAGGTATCGATATA
1 TTTCCTAAGGTATCGATATA
*
581011 TTTCCTAAGGTATTGATAT
1 TTTCCTAAGGTATCGATAT
581030 TTCATGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTCCTAAGGTATCGATATA
Found at i:588912 original size:45 final size:45
Alignment explanation
Indices: 588852--588945 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
588842 TAGAATTTTT
588852 ATCATAATTGCCAAGGAGAGTTCAATTATAGTCTTGCAAATTTGA
1 ATCATAATTGCCAAGGAGAGTTCAATTATAGTCTTGCAAATTTGA
* *
588897 ATCATAATTGTCAAGGAGAGTTCAATTATAGTCTTGCAAATTTGT
1 ATCATAATTGCCAAGGAGAGTTCAATTATAGTCTTGCAAATTTGA
588942 ATCA
1 ATCA
588946 CAAATACTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (45 bp):
ATCATAATTGCCAAGGAGAGTTCAATTATAGTCTTGCAAATTTGA
Found at i:589827 original size:4 final size:4
Alignment explanation
Indices: 589820--589845 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
589810 CCATATGATC
589820 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
589846 AATGTACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:597514 original size:52 final size:49
Alignment explanation
Indices: 597408--597561 Score: 159
Period size: 49 Copynumber: 3.1 Consensus size: 49
597398 ATGATGCTTA
* * * * *
597408 AATGCATGATATAATTAAGATGCAAAC-TAAATGAACA-AATGAGTTACTT
1 AATGCATGACATATTTATGATGCAAACTTAACT-AACATAA-GAGTTACAT
* * **
597457 AATGCATGACTTAATTTAATGATGCAGACTTAAACTAACATGGGAGTTACAT
1 AATGCATGACAT-ATTT-ATGATGCAAACTT-AACTAACATAAGAGTTACAT
*
597509 AATGCATGTCATATTTATGATGCAAACTTAACTAACATAAGAGTTACAT
1 AATGCATGACATATTTATGATGCAAACTTAACTAACATAAGAGTTACAT
597558 AATG
1 AATG
597562 ATACGAGCTC
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
49 32 0.37
50 15 0.17
51 13 0.15
52 23 0.27
53 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (49 bp):
AATGCATGACATATTTATGATGCAAACTTAACTAACATAAGAGTTACAT
Found at i:598232 original size:52 final size:51
Alignment explanation
Indices: 598167--598297 Score: 176
Period size: 50 Copynumber: 2.6 Consensus size: 51
598157 TGAGCAAATT
* * *
598167 AGTTACTTAATGCATGACTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATGACTTAATTTAATGATGCAAACTT-AACTAACATGAG
*
598219 AGTTACATAATGCATGTA-ATAATTT-ATGATGCAAACTTAACTAACATGAG
1 AGTTACATAATGCATG-ACTTAATTTAATGATGCAAACTTAACTAACATGAG
* *
598269 AGTTACATAATGCATGACTTTATTAAATG
1 AGTTACATAATGCATGACTTAATTTAATG
598298 CAAAACACAT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
49 1 0.01
50 31 0.45
51 15 0.22
52 21 0.30
53 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (51 bp):
AGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAG
Found at i:598403 original size:30 final size:31
Alignment explanation
Indices: 598345--598404 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
598335 ACCAATAATG
*
598345 CAAGACATTAATTAAAGATGCATTTAATAAA
1 CAAGACATTAATTAAAGATGCATATAATAAA
598376 CAAGACA-TAATTAAAGACT-CATATAATAA
1 CAAGACATTAATTAAAGA-TGCATATAATAA
598405 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (31 bp):
CAAGACATTAATTAAAGATGCATATAATAAA
Found at i:600362 original size:5 final size:5
Alignment explanation
Indices: 600352--600377 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
600342 TGAGCATTCG
600352 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
600378 AATTTTCGAG
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:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:601022 original size:17 final size:17
Alignment explanation
Indices: 600995--601027 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
600985 AAAGTTTAGG
600995 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
601013 GGGG-AATAAAAGTTT
1 GGGGAAATAAAAGTTT
601028 GAAGGAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 3 0.20
18 4 0.27
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:601402 original size:9 final size:9
Alignment explanation
Indices: 601388--601422 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
601378 TAGTTTGATG
601388 TTCGAATTA
1 TTCGAATTA
601397 TTCGAATTA
1 TTCGAATTA
*
601406 TTCGAGTTA
1 TTCGAATTA
601415 TTCGAATT
1 TTCGAATT
601423 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TTCGAATTA
Found at i:602100 original size:23 final size:23
Alignment explanation
Indices: 602048--602100 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
602038 ATATCAATTT
*
602048 TAAAAAATTATAAATATATATAA
1 TAAAAAATTATAAATATATAAAA
*
602071 TAGAAAA-TATACAATA-ATAAAA
1 TAAAAAATTATA-AATATATAAAA
602093 GTAAAAAA
1 -TAAAAAA
602101 ATCATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (23 bp):
TAAAAAATTATAAATATATAAAA
Found at i:602321 original size:15 final size:15
Alignment explanation
Indices: 602283--602322 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
602273 AATATCCTTC
602283 AATTAATTTT--TTT
1 AATTAATTTTAATTT
602296 AATTACA-TTTAATTT
1 AATTA-ATTTTAATTT
602311 AATTAATTTTAA
1 AATTAATTTTAA
602323 ATTCAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 2 0.09
15 13 0.57
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTAATTTTAATTT
Found at i:608240 original size:16 final size:17
Alignment explanation
Indices: 608209--608247 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
608199 TGGAGTAAAT
*
608209 AAGAATATGAAATGGGG
1 AAGAAGATGAAATGGGG
608226 AAGAAGATG-AATGGGG
1 AAGAAGATGAAATGGGG
608242 AGAGAA
1 A-AGAA
608248 AGAAAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (17 bp):
AAGAAGATGAAATGGGG
Found at i:612035 original size:43 final size:43
Alignment explanation
Indices: 611966--612248 Score: 245
Period size: 43 Copynumber: 6.6 Consensus size: 43
611956 TTTATGTGAA
* * * *
611966 AAACGCCACTAAAGGTCATGACCTTTAGCGGCGCTTTAGTCAC
1 AAACGCCGCTAAAGATCGTAACCTTTAGCGGCGCTTTAGTCAC
* * * *
612009 AAATGCCGCTAAAGATCGTGACCTTTAGCGGC-ATTT-GTGAC
1 AAACGCCGCTAAAGATCGTAACCTTTAGCGGCGCTTTAGTCAC
* * *
612050 TAAAACGCTGCTAAAGATCGTAACCTTTAGCGGCGCTATAGCCAC
1 --AAACGCCGCTAAAGATCGTAACCTTTAGCGGCGCTTTAGTCAC
* * * * *
612095 AAATGCCGCTAAAGATTGTGACCTTTAGCGGCGCTTTAGCCGC
1 AAACGCCGCTAAAGATCGTAACCTTTAGCGGCGCTTTAGTCAC
* * * * *
612138 AAACGCCGCTAAAGAAT-ATAACCTTTAGTGGCGCTTTTGTTAA
1 AAACGCCGCTAAAG-ATCGTAACCTTTAGCGGCGCTTTAGTCAC
* * * *
612181 AAACGCCGCTAAAGAAC-AAACCTTTAGCGGCGCTTCT-GACAA
1 AAACGCCGCTAAAGATCGTAACCTTTAGCGGCGCTT-TAGTCAC
* *
612223 AAACGCCGCTAAA-AACATAACCTTTA
1 AAACGCCGCTAAAGATCGTAACCTTTA
612249 AAAAAATTAT
Statistics
Matches: 198, Mismatches: 34, Indels: 17
0.80 0.14 0.07
Matches are distributed among these distances:
41 7 0.04
42 44 0.22
43 140 0.71
44 4 0.02
45 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCGTAACCTTTAGCGGCGCTTTAGTCAC
Found at i:613593 original size:20 final size:20
Alignment explanation
Indices: 613528--613604 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 20
613518 GTAAAAAATA
* * *
613528 ATAAATTAAATAAATAATAC
1 ATAATTTAAAAAAATAACAC
*
613548 ATGAAATTAAAAAAATAACAC
1 AT-AATTTAAAAAAATAACAC
*
613569 TTAATTTAAAGAAAATAA-AC
1 ATAATTTAAA-AAAATAACAC
613589 ATAATTATCAAAAAAA
1 ATAATT-T-AAAAAAA
613605 ATTAACTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 16 0.33
21 29 0.60
22 3 0.06
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (20 bp):
ATAATTTAAAAAAATAACAC
Found at i:615816 original size:7 final size:7
Alignment explanation
Indices: 615806--615848 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
615796 AATTAATCTT
615806 TAACCCC
1 TAACCCC
615813 TAACCCC
1 TAACCCC
*
615820 TAATCCC
1 TAACCCC
*
615827 TAACCTC
1 TAACCCC
615834 TAACCCC
1 TAACCCC
*
615841 TAAGCCC
1 TAACCCC
615848 T
1 T
615849 CTTTTACAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.28, C:0.49, G:0.02, T:0.21
Consensus pattern (7 bp):
TAACCCC
Found at i:615830 original size:21 final size:21
Alignment explanation
Indices: 615806--615848 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
615796 AATTAATCTT
*
615806 TAACCCCTAACCCCTAATCCC
1 TAACCCCTAACCCCTAAGCCC
*
615827 TAACCTCTAACCCCTAAGCCC
1 TAACCCCTAACCCCTAAGCCC
615848 T
1 T
615849 CTTTTACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.49, G:0.02, T:0.21
Consensus pattern (21 bp):
TAACCCCTAACCCCTAAGCCC
Found at i:616184 original size:14 final size:14
Alignment explanation
Indices: 616162--616205 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
616152 ATAAACCTTA
* *
616162 AATCCCTAACTCTT
1 AATCCCTAACCCCT
*
616176 AATCTCTAACCCCT
1 AATCCCTAACCCCT
*
616190 AATCCCTAACGCCT
1 AATCCCTAACCCCT
616204 AA
1 AA
616206 ATCACAACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.32, C:0.39, G:0.02, T:0.27
Consensus pattern (14 bp):
AATCCCTAACCCCT
Found at i:616244 original size:14 final size:15
Alignment explanation
Indices: 616225--616257 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
616215 CTTAAACCAG
616225 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
616239 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
616254 AATC
1 AATC
616258 TATAAACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:616588 original size:41 final size:42
Alignment explanation
Indices: 616526--616786 Score: 309
Period size: 41 Copynumber: 6.4 Consensus size: 42
616516 CGAGCATTAG
* * * *
616526 AAAAATGCTGCTAAAAGC-CCGAGCATTAGCGGCGCTTTCTC
1 AAAAACGCCGCTAAAAGCTCCGAGCATTAGCGGCGCTTTTTT
* * *
616567 AAAAACGCCGCTAAAATC-CCGAGCATTAGCGGCGCTTTCTC
1 AAAAACGCCGCTAAAAGCTCCGAGCATTAGCGGCGCTTTTTT
* *
616608 AAAAACACCGCTAAAAGC-CCAAGCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAAGCTCCGAGCATTAGCGGCGCTTTTTT
* *
616649 AAAAACGCCACT-AAAGCTCTGAGCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAAGCTCCGAGCATTAGCGGCGCTTTTTT
* * *
616690 AGAAACACCGCT-AAAGCTCTGAGCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAAGCTCCGAGCATTAGCGGCGCTTTTTT
* * * *
616731 AGAAACGCCGCT-AAATCTCTGAGCATTAGCGGCCCTTTTTT
1 AAAAACGCCGCTAAAAGCTCCGAGCATTAGCGGCGCTTTTTT
*
616772 AGAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
616787 GCCCTGAAAG
Statistics
Matches: 200, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
40 5 0.03
41 193 0.96
42 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAAGCTCCGAGCATTAGCGGCGCTTTTTT
Found at i:616663 original size:82 final size:81
Alignment explanation
Indices: 616539--616790 Score: 353
Period size: 82 Copynumber: 3.1 Consensus size: 81
616529 AATGCTGCTA
* * *
616539 AAAGCCCGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAATC-CCGAGCATTAGCGGCGCT
1 AAAGCCCGAGCATTAGCGGCGCTTTTTTAAAAACGCCGCT-AAATCTCTGAGCATTAGCGGCGCT
* * *
616603 TTCTCAAAAACACCGCT
65 TTTTTAGAAACACCGCT
* * *
616620 AAAAGCCCAAGCATTAGCGGCGCTTTTTTAAAAACGCCACTAAAGCTCTGAGCATTAGCGGCGCT
1 -AAAGCCCGAGCATTAGCGGCGCTTTTTTAAAAACGCCGCTAAATCTCTGAGCATTAGCGGCGCT
616685 TTTTTAGAAACACCGCT
65 TTTTTAGAAACACCGCT
* * *
616702 AAAGCTCTGAGCATTAGCGGCGCTTTTTTAGAAACGCCGCTAAATCTCTGAGCATTAGCGGCCCT
1 AAAGC-CCGAGCATTAGCGGCGCTTTTTTAAAAACGCCGCTAAATCTCTGAGCATTAGCGGCGCT
*
616767 TTTTTAGAAACGCCGCT
65 TTTTTAGAAACACCGCT
616784 AAAGCCC
1 AAAGCCC
616791 TGAAAGTTCA
Statistics
Matches: 151, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
81 10 0.07
82 141 0.93
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (81 bp):
AAAGCCCGAGCATTAGCGGCGCTTTTTTAAAAACGCCGCTAAATCTCTGAGCATTAGCGGCGCTT
TTTTAGAAACACCGCT
Found at i:616868 original size:40 final size:39
Alignment explanation
Indices: 616837--616959 Score: 120
Period size: 40 Copynumber: 3.1 Consensus size: 39
616827 TTTGCGGCAT
616837 TTTTCCAAAAAACGCCGCTAATGCTCATTTTTAGCGGCC
1 TTTTCCAAAAAACGCCGCTAATGCTCATTTTTAGCGGCC
* * * **
616876 TTTTCCTAAAAACGTCGCTAATGCTCGATCTTTAGCGGTG
1 TTTTCCAAAAAACGCCGCTAATGCTC-ATTTTTAGCGGCC
** * * * * *
616916 TTTTGTATAAAGCGCCGCTAATGCTTGATTTTTAGTGGCG
1 TTTTCCAAAAAACGCCGCTAATGC-TCATTTTTAGCGGCC
616956 TTTT
1 TTTT
616960 TTGTCCAAAC
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
39 24 0.36
40 42 0.63
41 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (39 bp):
TTTTCCAAAAAACGCCGCTAATGCTCATTTTTAGCGGCC
Found at i:630772 original size:20 final size:20
Alignment explanation
Indices: 630749--630798 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
630739 GCTTATGGTT
630749 AATTAATTAAAGTTTAATTA
1 AATTAATTAAAGTTTAATTA
*
630769 AATTAATT-AAGATTAATTA
1 AATTAATTAAAGTTTAATTA
630788 AA--AATTAAAGT
1 AATTAATTAAAGT
630799 AAGTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 3 0.11
19 12 0.44
20 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (20 bp):
AATTAATTAAAGTTTAATTA
Found at i:630785 original size:10 final size:10
Alignment explanation
Indices: 630750--630788 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
630740 CTTATGGTTA
630750 ATTAATTAAAG
1 ATTAATT-AAG
*
630761 TTTAATTAA-
1 ATTAATTAAG
630770 ATTAATTAAG
1 ATTAATTAAG
630780 ATTAATTAA
1 ATTAATTAA
630789 AAATTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 11 0.44
11 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (10 bp):
ATTAATTAAG
Found at i:631579 original size:62 final size:62
Alignment explanation
Indices: 631503--631622 Score: 222
Period size: 62 Copynumber: 1.9 Consensus size: 62
631493 TAAATTATTT
*
631503 TTTGAATTGCATTTGTTTCAATTTTATGTTTATATTTAAGTGACTTTATGGAAATTGAATAA
1 TTTGAATTGCATTTGTTTCAATTTTATGTTTATATTTAAATGACTTTATGGAAATTGAATAA
*
631565 TTTGAATTGTATTTGTTTCAATTTTATGTTTATATTTAAATGACTTTATGGAAATTGA
1 TTTGAATTGCATTTGTTTCAATTTTATGTTTATATTTAAATGACTTTATGGAAATTGA
631623 CTTATTTAGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (62 bp):
TTTGAATTGCATTTGTTTCAATTTTATGTTTATATTTAAATGACTTTATGGAAATTGAATAA
Found at i:633860 original size:6 final size:6
Alignment explanation
Indices: 633846--633875 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
633836 CTATTAACAT
*
633846 GACTCA GACTTA GACTCA GACTCA GACTCA
1 GACTCA GACTCA GACTCA GACTCA GACTCA
633876 AACAAATACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (6 bp):
GACTCA
Found at i:638024 original size:26 final size:27
Alignment explanation
Indices: 637972--638024 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
637962 ACCATAGCAC
*
637972 AAATCAGTCATTTACCCTCGAGGGGCA
1 AAATCAGTCATTTACCCTCGAGAGGCA
637999 AAAT-AGTCATTTACCCTTC-AGAGGCA
1 AAATCAGTCATTTACCC-TCGAGAGGCA
638025 TTAGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (27 bp):
AAATCAGTCATTTACCCTCGAGAGGCA
Found at i:648065 original size:44 final size:46
Alignment explanation
Indices: 648015--648107 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
648005 TTATACCTCT
* *
648015 ATTCCATTCAACCAAACACAAGAA-TACC-ATTATGCCTATATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCC
*
648059 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCC
648105 ATT
1 ATT
648108 ACGCATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.52
45 4 0.09
46 17 0.39
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCC
Found at i:648110 original size:16 final size:16
Alignment explanation
Indices: 648089--648141 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
648079 AGAATTACCT
648089 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
648105 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
* *
648121 ATTACACCTCTATTCA
1 ATTACGCCTCTATTCC
648137 ATTAC
1 ATTAC
648142 AGCGAACCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.26, C:0.32, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:655403 original size:15 final size:16
Alignment explanation
Indices: 655378--655414 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
655368 GCGAGTTTTC
655378 TTTAT-AAAAATCA-T
1 TTTATAAAAAATCATT
655392 TTTATAAAAAATCATT
1 TTTATAAAAAATCATT
655408 TTTATAA
1 TTTATAA
655415 GTATAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTATAAAAAATCATT
Found at i:664018 original size:21 final size:21
Alignment explanation
Indices: 663978--664018 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
663968 TGAGTCAAAA
* * *
663978 ATTTTCAAATATGTTTTAATC
1 ATTTTCAAACAAGTTATAATC
663999 ATTTTCAAACAAGTTATAAT
1 ATTTTCAAACAAGTTATAAT
664019 TGCTCCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTTTCAAACAAGTTATAATC
Found at i:666215 original size:36 final size:36
Alignment explanation
Indices: 666159--666243 Score: 152
Period size: 36 Copynumber: 2.3 Consensus size: 36
666149 ACTTGGAGAG
666159 AAAGTAAACAAAATGCAAGAAATTAATAATGACTTTGA
1 AAAG-AAA-AAAATGCAAGAAATTAATAATGACTTTGA
666197 AAAGAAAAAAATGCAAGAAATTAATAATGACTTTGA
1 AAAGAAAAAAATGCAAGAAATTAATAATGACTTTGA
666233 AAAGAAAAAAA
1 AAAGAAAAAAA
666244 ATTAGACTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 40 0.85
37 3 0.06
38 4 0.09
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.20
Consensus pattern (36 bp):
AAAGAAAAAAATGCAAGAAATTAATAATGACTTTGA
Found at i:666924 original size:33 final size:33
Alignment explanation
Indices: 666858--666920 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
666848 ATCTTTATGC
* * *
666858 CTTAAATTGAAAATTATTTTTATATAAGGGGAG
1 CTTAAATCGAAAATGAATTTTATATAAGGGGAG
666891 CTTAAATCGAAAATGAATTTTAT-TAAGGGG
1 CTTAAATCGAAAATGAATTTTATATAAGGGG
666921 GAGCAATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (33 bp):
CTTAAATCGAAAATGAATTTTATATAAGGGGAG
Found at i:672004 original size:19 final size:19
Alignment explanation
Indices: 671936--672074 Score: 75
Period size: 21 Copynumber: 7.0 Consensus size: 19
671926 GTATTTTATA
671936 ATTAAAATTATAAAAAAATT
1 ATTAAAATTATAAAAAAA-T
* * ***
671956 ATACAAAATCATAAAGTTTAT
1 AT-TAAAATTATAAA-AAAAT
* *
671977 ATAAAAATTATAAAGAAAT
1 ATTAAAATTATAAAAAAAT
*
671996 TTTAAAATTATAAAAAAAT
1 ATTAAAATTATAAAAAAAT
* **
672015 ATT-AAAGT-GCAAAAAAT
1 ATTAAAATTATAAAAAAAT
672032 ATATAGAAATTTATAAAAAAATT
1 AT-TA-AAA-TTATAAAAAAA-T
* *
672055 ATTATAAATGAAAAAAAAAT
1 ATTA-AAATTATAAAAAAAT
672075 TATAAACTNN
Statistics
Matches: 88, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
17 9 0.10
18 5 0.06
19 20 0.23
20 16 0.18
21 23 0.26
22 12 0.14
23 3 0.03
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
ATTAAAATTATAAAAAAAT
Found at i:672021 original size:30 final size:30
Alignment explanation
Indices: 671937--672014 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
671927 TATTTTATAA
*
671937 TTAAAATTATAAAAAAATTATACA-AAATC
1 TTAAAATTATAAAAAAATTATAAAGAAATC
* * * *
671966 ATAAAGTTTATATAAAAATTATAAAGAAATT
1 TTAAA-ATTATAAAAAAATTATAAAGAAATC
671997 TTAAAATTATAAAAAAAT
1 TTAAAATTATAAAAAAAT
672015 ATTAAAGTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 4 0.10
30 27 0.69
31 8 0.21
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (30 bp):
TTAAAATTATAAAAAAATTATAAAGAAATC
Found at i:672606 original size:25 final size:22
Alignment explanation
Indices: 672571--672626 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 22
672561 AAAAATTATA
*
672571 TTATTATTTTATATTTTTTACATT
1 TTATAATTTTATATTTTTT-CA-T
672595 TTCATAATTTTATATTTTTTCAT
1 TT-ATAATTTTATATTTTTTCAT
672618 TTATAATTT
1 TTATAATTT
672627 GTTTTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 7 0.23
23 3 0.10
24 4 0.13
25 16 0.53
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATAATTTTATATTTTTTCAT
Found at i:672711 original size:20 final size:21
Alignment explanation
Indices: 672668--672723 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
672658 TCACCTTAAT
672668 TTTTTTATAATTCTTAGAAGTA
1 TTTTTTATAATT-TTAGAAGTA
* *
672690 TTTTTTATAATTTTA-TATTA
1 TTTTTTATAATTTTAGAAGTA
*
672710 TTTTTAATAATTTT
1 TTTTTTATAATTTT
672724 TAATGATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 16 0.52
21 3 0.10
22 12 0.39
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTTATAATTTTAGAAGTA
Found at i:672732 original size:20 final size:19
Alignment explanation
Indices: 672691--672753 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
672681 TTAGAAGTAT
*
672691 TTTTTATAA-TTTTATATTA
1 TTTTTATAATTTTTA-ATGA
672710 TTTTTAATAATTTTTAATGA
1 TTTTT-ATAATTTTTAATGA
**
672730 TTTTTATGGTTTTTTAATGA
1 TTTTTAT-AATTTTTAATGA
672750 TTTT
1 TTTT
672754 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 7 0.18
20 26 0.68
21 5 0.13
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTTATAATTTTTAATGA
Found at i:672735 original size:10 final size:10
Alignment explanation
Indices: 672709--672753 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
672699 ATTTTATATT
*
672709 ATTTTTAATA
1 ATTTTTAATG
672719 ATTTTTAATG
1 ATTTTTAATG
672729 ATTTTT-ATGG
1 ATTTTTAAT-G
*
672739 TTTTTTAATG
1 ATTTTTAATG
672749 ATTTT
1 ATTTT
672754 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.87
11 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (10 bp):
ATTTTTAATG
Found at i:680813 original size:20 final size:20
Alignment explanation
Indices: 680790--680973 Score: 83
Period size: 20 Copynumber: 9.2 Consensus size: 20
680780 TGGGATTAGA
*
680790 GGCACCGAAGTGCAAATAGG
1 GGCACCGAAGTACAAATAGG
* * * *
680810 GGCACAGATGTGC-ATTCAGG
1 GGCACCGAAGTACAAAT-AGG
*
680830 GGTACCGAAGTACAAATAGG
1 GGCACCGAAGTACAAATAGG
680850 GGCA-CGTAAGTAC-AATAAGG
1 GGCACCG-AAGTACAAAT-AGG
* * * *
680870 GGTACCAAAGTACAAACAAG
1 GGCACCGAAGTACAAATAGG
* * * *
680890 GGCA-TGTAAGTGCCATTAGG
1 GGCACCG-AAGTACAAATAGG
* * *
680910 GGTACCAAAGAACAAATAGG
1 GGCACCGAAGTACAAATAGG
* *
680930 GGCA-CGTAAATGC-AATAAGG
1 GGCACCG-AAGTACAAAT-AGG
* *
680950 GGTACCGAAGTACAAACAGG
1 GGCACCGAAGTACAAATAGG
680970 GGCA
1 GGCA
680974 TGTAAGTGTA
Statistics
Matches: 114, Mismatches: 38, Indels: 24
0.65 0.22 0.14
Matches are distributed among these distances:
19 11 0.10
20 94 0.82
21 9 0.08
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.14
Consensus pattern (20 bp):
GGCACCGAAGTACAAATAGG
Found at i:680815 original size:40 final size:40
Alignment explanation
Indices: 680750--680854 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
680740 GCATAATAGG
* * *
680750 GGCACCAAAGTGC-AATAAGGAGCACAAATGTGGGATT-AGA
1 GGCACCGAAGTGCAAAT-AGGGGCACAAATGT-GCATTCAGA
* *
680790 GGCACCGAAGTGCAAATAGGGGCACAGATGTGCATTCAGG
1 GGCACCGAAGTGCAAATAGGGGCACAAATGTGCATTCAGA
* *
680830 GGTACCGAAGTACAAATAGGGGCAC
1 GGCACCGAAGTGCAAATAGGGGCAC
680855 GTAAGTACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 4 0.07
40 49 0.88
41 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.14
Consensus pattern (40 bp):
GGCACCGAAGTGCAAATAGGGGCACAAATGTGCATTCAGA
Found at i:680871 original size:40 final size:40
Alignment explanation
Indices: 680793--680987 Score: 221
Period size: 40 Copynumber: 4.9 Consensus size: 40
680783 GATTAGAGGC
* * * *
680793 ACCGAAGTGCAAATAGGGGCACAG-ATGTGCATTCAGGGGT
1 ACCGAAGTACAAATAGGGGCAC-GTAAGTGCAATAAGGGGT
*
680833 ACCGAAGTACAAATAGGGGCACGTAAGTACAATAAGGGGT
1 ACCGAAGTACAAATAGGGGCACGTAAGTGCAATAAGGGGT
* * * * * *
680873 ACCAAAGTACAAACAAGGGCATGTAAGTGCCATTAGGGGT
1 ACCGAAGTACAAATAGGGGCACGTAAGTGCAATAAGGGGT
* * *
680913 ACCAAAGAACAAATAGGGGCACGTAAATGCAATAAGGGGT
1 ACCGAAGTACAAATAGGGGCACGTAAGTGCAATAAGGGGT
* * *
680953 ACCGAAGTACAAACAGGGGCATGTAAGTGTAATAA
1 ACCGAAGTACAAATAGGGGCACGTAAGTGCAATAA
680988 TTTAATAATT
Statistics
Matches: 129, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 1 0.01
40 128 0.99
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16
Consensus pattern (40 bp):
ACCGAAGTACAAATAGGGGCACGTAAGTGCAATAAGGGGT
Found at i:680946 original size:80 final size:81
Alignment explanation
Indices: 680822--680981 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 81
680812 CACAGATGTG
* * *
680822 CATTCAGGGGTACCGAAGTACAAATAGGGGCACGTAAGTACAATAAGGGGTACCAAAGTACAAAC
1 CATTCAGGGGTACCAAAGAACAAATAGGGGCACGTAAATACAATAAGGGGTACCAAAGTACAAAC
680887 AAGGGCATGTAAGTGC
66 AAGGGCATGTAAGTGC
* *
680903 CATT-AGGGGTACCAAAGAACAAATAGGGGCACGTAAATGCAATAAGGGGTACCGAAGTACAAAC
1 CATTCAGGGGTACCAAAGAACAAATAGGGGCACGTAAATACAATAAGGGGTACCAAAGTACAAAC
*
680967 AGGGGCATGTAAGTG
66 AAGGGCATGTAAGTG
680982 TAATAATTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 69 0.95
81 4 0.05
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16
Consensus pattern (81 bp):
CATTCAGGGGTACCAAAGAACAAATAGGGGCACGTAAATACAATAAGGGGTACCAAAGTACAAAC
AAGGGCATGTAAGTGC
Found at i:691954 original size:14 final size:13
Alignment explanation
Indices: 691928--691952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
691918 ATTACATCAA
691928 AATTTTTAAAAAT
1 AATTTTTAAAAAT
691941 AATTTTTAAAAA
1 AATTTTTAAAAA
691953 ATCATAGTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:691997 original size:23 final size:23
Alignment explanation
Indices: 691965--692011 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
691955 CATAGTTATC
* *
691965 AATGAGAATGG-TGGAGGTTGCAT
1 AATGACAATGGAT-GAGGTTCCAT
691988 AATGACAATGGATGAGGTTCCAT
1 AATGACAATGGATGAGGTTCCAT
692011 A
1 A
692012 GTTTCCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.34, C:0.09, G:0.32, T:0.26
Consensus pattern (23 bp):
AATGACAATGGATGAGGTTCCAT
Found at i:693630 original size:6 final size:6
Alignment explanation
Indices: 693619--693651 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
693609 CATTGTAGCC
693619 ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATG
1 ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATG
693652 ATCAGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.18
Consensus pattern (6 bp):
ATGGCA
Found at i:699105 original size:22 final size:22
Alignment explanation
Indices: 699075--699117 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
699065 ATTATAAACT
699075 AAGTCGTTAATTACCCTTAACA
1 AAGTCGTTAATTACCCTTAACA
*
699097 AAGTTGTTAATTACCCTTAAC
1 AAGTCGTTAATTACCCTTAAC
699118 TATGAATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (22 bp):
AAGTCGTTAATTACCCTTAACA
Found at i:705124 original size:13 final size:13
Alignment explanation
Indices: 705106--705131 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
705096 GTTATTAGGC
705106 TATTTTTTATTAT
1 TATTTTTTATTAT
705119 TATTTTTTATTAT
1 TATTTTTTATTAT
705132 CGGGCCGGGC
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTTATTAT
Found at i:705506 original size:44 final size:44
Alignment explanation
Indices: 705410--705514 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
705400 ACTTGATGCG
* * * *
705410 ATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTTAGAGAGATAAGATCTATGAATTCA
* * *
705454 ATCCGCTCCACTACAACTTTA-AGGAGATAGGAT-TATCGAATTCA
1 ATCTGCTCCACTGCAACTTTAGA-GAGATAAGATCTAT-GAATTCA
705498 ATCTGCTCCACTGCAAC
1 ATCTGCTCCACTGCAAC
705515 CTCAGGGAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
43 4 0.08
44 46 0.92
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTTAGAGAGATAAGATCTATGAATTCA
Found at i:705605 original size:44 final size:44
Alignment explanation
Indices: 705494--705606 Score: 120
Period size: 44 Copynumber: 2.6 Consensus size: 44
705484 GATTATCGAA
* * *
705494 TTCAATCTGCTCCACTGCAACCTCAGGGAGTTAAGATTTGCTTC
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACTTGCTTC
* *** * *
705538 TTCAGTCTGCCCCACTATGACTTCAGGGGGTTAAGACTTG-TTT
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACTTGCTTC
*
705581 TCTCAGTCTGCTCCGCTGCAACTTCA
1 T-TCAGTCTGCTCCACTGCAACTTCA
705607 AAGAGATAAG
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
43 3 0.06
44 51 0.94
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.33
Consensus pattern (44 bp):
TTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACTTGCTTC
Found at i:708747 original size:32 final size:32
Alignment explanation
Indices: 708685--708747 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
708675 TTCATTTTCA
*
708685 TTTTGACCTTGATTTTTGATTTTTCTTTTTTG
1 TTTTGACCTTGATTTTTGATTTTGCTTTTTTG
* *
708717 TTTTGATCTTGA-TTTTGCTTTTGCTCTTTTT
1 TTTTGACCTTGATTTTTGATTTTGCT-TTTTT
708748 TTTAATCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.08, C:0.11, G:0.13, T:0.68
Consensus pattern (32 bp):
TTTTGACCTTGATTTTTGATTTTGCTTTTTTG
Found at i:713630 original size:23 final size:23
Alignment explanation
Indices: 713581--713630 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
713571 ACAAATATGC
* *
713581 TAAATTTAAATAATGATACCTAG
1 TAAATTTAAATAATAATACATAG
713604 TAAATTTCAAATAATAATACATA-
1 TAAATTT-AAATAATAATACATAG
713627 TAAA
1 TAAA
713631 ACTTAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (23 bp):
TAAATTTAAATAATAATACATAG
Found at i:716433 original size:15 final size:15
Alignment explanation
Indices: 716415--716447 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
716405 AAATAATAAG
716415 AAAGGAAATAAATGA
1 AAAGGAAATAAATGA
*
716430 AAAGTAAATAAATGA
1 AAAGGAAATAAATGA
716445 AAA
1 AAA
716448 ACAAGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAGGAAATAAATGA
Found at i:718913 original size:31 final size:30
Alignment explanation
Indices: 718878--718992 Score: 131
Period size: 31 Copynumber: 3.7 Consensus size: 30
718868 CATCAAATAC
* *
718878 TCATATTTGCATTATCATACTCTGTAATCAT
1 TCATATTTTCA-TATCATACCCTGTAATCAT
**
718909 TCATATTTTCATATTCATACCCTGTCTTCAT
1 TCATATTTTCATA-TCATACCCTGTAATCAT
* *
718940 TCATATTTACATATCATACCCTATAATCAT
1 TCATATTTTCATATCATACCCTGTAATCAT
* *
718970 TCACATTTTCATTTTCATACCCT
1 TCATATTTTCA-TATCATACCCT
718993 TTACACTGTA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
30 25 0.35
31 46 0.65
ACGTcount: A:0.28, C:0.24, G:0.03, T:0.45
Consensus pattern (30 bp):
TCATATTTTCATATCATACCCTGTAATCAT
Found at i:720818 original size:17 final size:18
Alignment explanation
Indices: 720796--720835 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
720786 AAACTATAAT
720796 CATTTCCA-TATTTTTC-C
1 CATTTCCACTA-TTTTCAC
720813 CATTT-CACTATTTTCAC
1 CATTTCCACTATTTTCAC
720830 CATTTC
1 CATTTC
720836 TATAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (18 bp):
CATTTCCACTATTTTCAC
Found at i:722015 original size:31 final size:32
Alignment explanation
Indices: 721981--722120 Score: 162
Period size: 31 Copynumber: 4.5 Consensus size: 32
721971 GTATATGTTT
*
721981 TATACATTGCCAAATTTGATTTGTATATG-GT
1 TATACATTGCCAAATTTGATTTGTATATGAGA
*
722012 TATACATTGTCAAATTTGATTTGTATATG-GA
1 TATACATTGCCAAATTTGATTTGTATATGAGA
* *
722043 TATTCATTGCCGAATTTGATTTGTATA-GAGA
1 TATACATTGCCAAATTTGATTTGTATATGAGA
* ** *
722074 TATACATTGCCGAATTTGATTCATATAT-TGA
1 TATACATTGCCAAATTTGATTTGTATATGAGA
**
722105 TATATGTTGCCAAATT
1 TATACATTGCCAAATT
722121 GGTTTGAGCA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
30 1 0.01
31 94 0.99
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.44
Consensus pattern (32 bp):
TATACATTGCCAAATTTGATTTGTATATGAGA
Found at i:722321 original size:43 final size:43
Alignment explanation
Indices: 722251--722366 Score: 169
Period size: 43 Copynumber: 2.7 Consensus size: 43
722241 TGTGATTTCG
* * *
722251 TGTAAGACCATGTTTGGGACATCGGCATCGAAGTGAGAAAACA
1 TGTAAGACCATGTCTAGGACATTGGCATCGAAGTGAGAAAACA
* * **
722294 TGTAAAACCATGTCTAGGACGTTGGCATCGAAGTGAGAAAATG
1 TGTAAGACCATGTCTAGGACATTGGCATCGAAGTGAGAAAACA
722337 TGTAAGACCATGTCTAGGACATTGGCATCG
1 TGTAAGACCATGTCTAGGACATTGGCATCG
722367 TATATGATTC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATTGGCATCGAAGTGAGAAAACA
Found at i:739932 original size:661 final size:661
Alignment explanation
Indices: 738672--739993 Score: 2635
Period size: 661 Copynumber: 2.0 Consensus size: 661
738662 TTTGAAGAAG
738672 ACCGTGAGATCCCTATTCTACTAGGAAGGCCCTTCTTAGCCACATATAGGTCCATCATTGGCTTA
1 ACCGTGAGATCCCTATTCTACTAGGAAGGCCCTTCTTAGCCACATATAGGTCCATCATTGGCTTA
738737 GAAATAATGAATTGATAATGAGAATAAATGGTGAGACCAAAATATTAAAATGTGGTAATTTACAA
66 GAAATAATGAATTGATAATGAGAATAAATGGTGAGACCAAAATATTAAAATGTGGTAATTTACAA
738802 AATGGGGGATGTGAGGAAATTTTAGGAGGAAATTGTTATGATATATCTATGAGTACCCCTAATAA
131 AATGGGGGATGTGAGGAAATTTTAGGAGGAAATTGTTATGATATATCTATGAGTACCCCTAATAA
738867 ACTTGATCAAGGGACGGTATATTCTGTGATTAGTGCAGGTAGAATAAATAAATCGATGGAGCAGG
196 ACTTGATCAAGGGACGGTATATTCTGTGATTAGTGCAGGTAGAATAAATAAATCGATGGAGCAGG
738932 ACAAATGAAAAGTTGTAGAGTGGCATGATGGAGTTTGGACAAATGAAGATAGACAAATGCCAAAA
261 ACAAATGAAAAGTTGTAGAGTGGCATGATGGAGTTTGGACAAATGAAGATAGACAAATGCCAAAA
738997 TAGACATTCAGACAACGCATAACTGAGCTAGTGGATGAATACGACAGTCATACGTGTAACACCCC
326 TAGACATTCAGACAACGCATAACTGAGCTAGTGGATGAATACGACAGTCATACGTGTAACACCCC
739062 AAATTTTGGTCCTAGAAGAAATAGGTTTTGAACAAGGGAACAGTTAGGAGACTGCACATAAATAT
391 AAATTTTGGTCCTAGAAGAAATAGGTTTTGAACAAGGGAACAGTTAGGAGACTGCACATAAATAT
739127 TTAGTTGTGCAAGGAATTGACATAAATGAATATGTCTGCTTCAGTGGTTAAGTGATTTAGGAGTG
456 TTAGTTGTGCAAGGAATTGACATAAATGAATATGTCTGCTTCAGTGGTTAAGTGATTTAGGAGTG
739192 CTTGGAAGTGTCTGAAAAGTCAAGGGTTCAAGCCTTGGCTTATGCAAAAATTTTATTTTAAGTGA
521 CTTGGAAGTGTCTGAAAAGTCAAGGGTTCAAGCCTTGGCTTATGCAAAAATTTTATTTTAAGTGA
739257 ATAAAATCCTTGGATCTAGATAGTAGGTTCTTAAATTATTGTGGTTAAAATATGATACAAAGGAG
586 ATAAAATCCTTGGATCTAGATAGTAGGTTCTTAAATTATTGTGGTTAAAATATGATACAAAGGAG
*
739322 TTGTTGGTCTA
651 TTGCTGGTCTA
739333 ACCGTGAGATCCCTATTCTACTAGGAAGGCCCTTCTTAGCCACATATAGGTCCATCATTGGCTTA
1 ACCGTGAGATCCCTATTCTACTAGGAAGGCCCTTCTTAGCCACATATAGGTCCATCATTGGCTTA
739398 GAAATAATGAATTGATAATGAGAATAAATGGTGAGACCAAAATATTAAAATGTGGTAATTTACAA
66 GAAATAATGAATTGATAATGAGAATAAATGGTGAGACCAAAATATTAAAATGTGGTAATTTACAA
739463 AATGGGGGATGTGAGGAAATTTTAGGAGGAAATTGTTATGATATATCTATGAGTACCCCTAATAA
131 AATGGGGGATGTGAGGAAATTTTAGGAGGAAATTGTTATGATATATCTATGAGTACCCCTAATAA
739528 ACTTGATCAAGGGACGGTATATTCTGTGATTAGTGCAGGTAGAATAAATAAATCGATGGAGCAGG
196 ACTTGATCAAGGGACGGTATATTCTGTGATTAGTGCAGGTAGAATAAATAAATCGATGGAGCAGG
739593 ACAAATGAAAAGTTGTAGAGTGGCATGATGGAGTTTGGACAAATGAAGATAGACAAATGCCAAAA
261 ACAAATGAAAAGTTGTAGAGTGGCATGATGGAGTTTGGACAAATGAAGATAGACAAATGCCAAAA
739658 TAGACATTCAGACAACGCATAACTGAGCTAGTGGATGAATACGACAGTCATACGTGTAACACCCC
326 TAGACATTCAGACAACGCATAACTGAGCTAGTGGATGAATACGACAGTCATACGTGTAACACCCC
739723 AAATTTTGGTCCTAGAAGAAATAGGTTTTGAACAAGGGAACAGTTAGGAGACTGCACATAAATAT
391 AAATTTTGGTCCTAGAAGAAATAGGTTTTGAACAAGGGAACAGTTAGGAGACTGCACATAAATAT
739788 TTAGTTGTGCAAGGAATTGACATAAATGAATATGTCTGCTTCAGTGGTTAAGTGATTTAGGAGTG
456 TTAGTTGTGCAAGGAATTGACATAAATGAATATGTCTGCTTCAGTGGTTAAGTGATTTAGGAGTG
739853 CTTGGAAGTGTCTGAAAAGTCAAGGGTTCAAGCCTTGGCTTATGCAAAAATTTTATTTTAAGTGA
521 CTTGGAAGTGTCTGAAAAGTCAAGGGTTCAAGCCTTGGCTTATGCAAAAATTTTATTTTAAGTGA
739918 ATAAAATCCTTGGATCTAGATAGTAGGTTCTTAAATTATTGTGGTTAAAATATGATACAAAGGAG
586 ATAAAATCCTTGGATCTAGATAGTAGGTTCTTAAATTATTGTGGTTAAAATATGATACAAAGGAG
739983 TTGCTGGTCTA
651 TTGCTGGTCTA
739994 CTGGTAAGGG
Statistics
Matches: 660, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
661 660 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (661 bp):
ACCGTGAGATCCCTATTCTACTAGGAAGGCCCTTCTTAGCCACATATAGGTCCATCATTGGCTTA
GAAATAATGAATTGATAATGAGAATAAATGGTGAGACCAAAATATTAAAATGTGGTAATTTACAA
AATGGGGGATGTGAGGAAATTTTAGGAGGAAATTGTTATGATATATCTATGAGTACCCCTAATAA
ACTTGATCAAGGGACGGTATATTCTGTGATTAGTGCAGGTAGAATAAATAAATCGATGGAGCAGG
ACAAATGAAAAGTTGTAGAGTGGCATGATGGAGTTTGGACAAATGAAGATAGACAAATGCCAAAA
TAGACATTCAGACAACGCATAACTGAGCTAGTGGATGAATACGACAGTCATACGTGTAACACCCC
AAATTTTGGTCCTAGAAGAAATAGGTTTTGAACAAGGGAACAGTTAGGAGACTGCACATAAATAT
TTAGTTGTGCAAGGAATTGACATAAATGAATATGTCTGCTTCAGTGGTTAAGTGATTTAGGAGTG
CTTGGAAGTGTCTGAAAAGTCAAGGGTTCAAGCCTTGGCTTATGCAAAAATTTTATTTTAAGTGA
ATAAAATCCTTGGATCTAGATAGTAGGTTCTTAAATTATTGTGGTTAAAATATGATACAAAGGAG
TTGCTGGTCTA
Found at i:740911 original size:27 final size:27
Alignment explanation
Indices: 740870--741095 Score: 267
Period size: 27 Copynumber: 8.4 Consensus size: 27
740860 CCCTAAAATA
* *
740870 GGTAAACTGACCGAAATACCCCCATAG
1 GGTAAAATGAACGAAATACCCCCATAG
* * *
740897 GGTAAAATAAACGAAATACCCCCAGAA
1 GGTAAAATGAACGAAATACCCCCATAG
* * *
740924 GGTAAAATGACCGAAATACTCTCATAG
1 GGTAAAATGAACGAAATACCCCCATAG
*
740951 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGAACGAAATACCCCCATAG
*
740978 GGTAAAATG-ACTGAAATACCCCTATAG
1 GGTAAAATGAAC-GAAATACCCCCATAG
* *
741005 GGTAAAATG-ACTGAAATACCACCATAA
1 GGTAAAATGAAC-GAAATACCCCCATAG
*
741032 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGAACGAAATACCCCCATAG
* **
741059 GGTAAAATGATCGAAATACCATCATAG
1 GGTAAAATGAACGAAATACCCCCATAG
*
741086 GTTAAAATGA
1 GGTAAAATGA
741096 CTGTTATACC
Statistics
Matches: 172, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 170 0.99
28 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
GGTAAAATGAACGAAATACCCCCATAG
Found at i:740951 original size:54 final size:54
Alignment explanation
Indices: 740869--741096 Score: 298
Period size: 54 Copynumber: 4.2 Consensus size: 54
740859 ACCCTAAAAT
* * *
740869 AGGTAAACTGACCGAAATACCCCCATAGGGTAAAATAAACGAAATACCCCCAGA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAACGAAATACCCCCATA
* * *
740923 AGGTAAAATGACCGAAATACTCTCATAGGGTAAAATGATCGAAATACCCCCATA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAACGAAATACCCCCATA
* * * *
740977 GGGTAAAATGACTGAAATACCCCTATAGGGTAAAATG-ACTGAAATACCACCATA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAAC-GAAATACCCCCATA
* * **
741031 AGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCATCAT-
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAACGAAATACCCCCATA
741084 AGGTTAAAATGAC
1 AGG-TAAAATGAC
741097 TGTTATACCC
Statistics
Matches: 151, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
53 4 0.03
54 146 0.97
55 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (54 bp):
AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAACGAAATACCCCCATA
Found at i:741086 original size:81 final size:79
Alignment explanation
Indices: 740869--741098 Score: 300
Period size: 81 Copynumber: 2.8 Consensus size: 79
740859 ACCCTAAAAT
* * * * *
740869 AGGTAAACTGACCGAAATACCCCCATAGGGTAAAATAAACGAAATACCCCCAGAAGGTAAAATGA
1 AGGTAAAATGATCGAAATACCCCCATAGGGTAAAAT-GACGAAATA-CCCCATAGGGTAAAATGA
* *
740934 CCGAAATACTCTCATA
64 CTGAAATACTCCCATA
*
740950 GGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGA
1 AGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGAC-GAAATACCCC-ATAGGGTAAAATGA
741015 CTGAAATAC-CACCATA
64 CTGAAATACTC-CCATA
* *
741031 AGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCATCATAGGTTAAAATGA
1 AGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGA-CGAAATACC-CCATAGGGTAAAATGA
741096 CTG
64 CTG
741099 TTATACCCCT
Statistics
Matches: 133, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
80 7 0.05
81 124 0.93
82 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (79 bp):
AGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACGAAATACCCCATAGGGTAAAATGACT
GAAATACTCCCATA
Found at i:746658 original size:27 final size:27
Alignment explanation
Indices: 746582--746659 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
746572 AGCATGTCAA
* ** *
746582 GAAAGGAAAAGCCTTTGTGGAAAATTAT
1 GAAA-GAAAAGCCTTTATGGCGAATCAT
* *
746610 GAAAGAAAAGCCTTTTTAGCGAATCAT
1 GAAAGAAAAGCCTTTATGGCGAATCAT
746637 GAAAGAAAAGCCTTTATGGCGAA
1 GAAAGAAAAGCCTTTATGGCGAA
746660 CTATGAAGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 39 0.91
28 4 0.09
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTATGGCGAATCAT
Done.