Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_pilon, whole genome shotgun sequence
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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 38
Found at i:395089 original size:38 final size:38
Alignment explanation
Indices: 394995--396089 Score: 1121
Period size: 38 Copynumber: 28.8 Consensus size: 38
394985 ACCAAATCTA
* * *
394995 AAAGATTGAC-TCTTCTTCAAGAGAAAGTCAAGGAAGAA-
1 AAAGATTGACTTC-TCTTCACGAGGAAGTCAA-GAATAAC
* *
395033 AACTGATTGACTTTTCTTCACGAGGAAGTCAAGAATAAC
1 AA-AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
395072 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
395110 AAAGACTGACTCCTCTTCGCGAGGGAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** *
395148 AAAGATTGACTTCTCTTCATAAGGAAGCCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
395186 AAAGATCGACTTCTCTTCACGAGGAAGTCAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
395224 AAAGATCGGCTTCTCTTCACGAGGAAGTCAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
395262 AAAGACTGACTCCTCTTCGCAAGGGAA-TCAGGAATAAC
1 AAAGATTGACTTCTCTTCACGA-GGAAGTCAAGAATAAC
* * * *
395300 AAAGATT-ATTTTTCTTCATGAGGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * **
395337 AAAGATTGACTTCTCTTCACGAGTAAATCACTAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * * *
395375 AAAGACTGAATCCTCTTCGCGAGGGAGTTAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
395413 ATAGATTGAC-TCATCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAAC
* * * *
395451 AAAGATTGA-TTCCTCTTCGCGAATG-AGTCAGGAACAAC
1 AAAGATTGACTT-CTCTTCACG-AGGAAGTCAAGAATAAC
* * * *
395489 AAAGATTGACTTCTCTTAATGAGAAAGTCAAGAACAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
395527 AAAGATTGAATCCTCTTCACGAGGGAGTCAGGAACAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
395565 AAATATTAACTTCTCTTCACAAGGAAGTC-AGAAAAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
395602 AAAGATTAACTTCTCTTCATGAGTAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
395640 AAAGATTGACTTCTCTTCACGAAGAAGTCAAGAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
395678 AAAGATTGACTTTTCTTCACGAGGAAGTCAAGAACAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
395716 AAAGATTGACTTCTCTGCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * ** * *
395754 AAAGACTGACTCCTCTTCGTGAGGGAA-TCAGGAACAAC
1 AAAGATTGACTTCTCTTCACGA-GGAAGTCAAGAATAAC
* *
395792 AAAGATTGACTTCTCTTTACGAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * * *
395830 ATAGATTGAATCCTCTTCGCGAGGGAGTCCATAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
395868 AAAGATTTACTTCTCTTCACAAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * ** * **
395906 AGAGATTGACTCCTCTTCGGGAGGGAGT-TTGAAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG-AATAAC
* * *
395944 AAATATCGACTTCTCTTCACGAAGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * *
395982 AGATATTGACTCCTCTTCATGAGGGAGTCAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
396020 AAAGATTGACTTCTCTTCACGAAGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
396058 AGAGATTGACTCCTCTTCACGATGAAGTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
396090 TTGAAGCTTC
Statistics
Matches: 860, Mismatches: 180, Indels: 34
0.80 0.17 0.03
Matches are distributed among these distances:
36 4 0.00
37 61 0.07
38 755 0.88
39 39 0.05
40 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:398742 original size:31 final size:31
Alignment explanation
Indices: 398704--398828 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
398694 CCCGAAGGAC
* * *
398704 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
398735 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
398766 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
398797 CAGTCCATATGTCCCGAAGAACATAGATAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
398828 C
1 C
398829 CCTCGACCTT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:406388 original size:3 final size:3
Alignment explanation
Indices: 406376--406423 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
406366 TTGGGTCTGC
406376 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
406423 A
1 A
406424 CGGGTCTCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:406956 original size:76 final size:76
Alignment explanation
Indices: 406819--407785 Score: 984
Period size: 76 Copynumber: 12.7 Consensus size: 76
406809 GATTAACTCT
* * * * * * * *
406819 TCTTCAAGAGAAAGTCAAGGAA-AACAACATATTGACTTCTCTTCACGAGGAAGTAAAGAATAAC
1 TCTTCATGAGGAAGTCAA-GAATAACAA-AGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
*
406883 AAAGATTAACTTC
64 AAAGATTGACTTC
* * * *
406896 TTTTCATGAGGAAGTCAAGAATAAAAAAGACTGACTCCTCTTCGCGAGGGAGTTAGGAATAACAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
406961 AGATTGACTTC
66 AGATTGACTTC
* * * * * * *
406972 TCTTCATGAGTAAGTCAAGAATAAAAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
*
407037 AGAAAT-ACTTC
66 AG-ATTGACTTC
* * * * **
407048 TATTCATGAGGAAGTCAAGAATAACAAAGACTAACTCCTCTTTTGTAAGGGAGTCAGGAATAACA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTC-TTCGCGAGGGAGTCAGGAATAACA
*
407113 AAGATTGATTTC
65 AAGATTGACTTC
* * * * *
407125 TCTTCATGAGGAAGTCAAGAATAATAAAGATTGACTCCTCTTCACGAGGAAGTAAAGAATAACAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
* *
407190 AGATTGAGTCC
66 AGATTGACTTC
* * * * * * * * * ** *
407201 TCTTCGTGAGGGAGTTAGGAACAATAAAGATTGACTTCTCTTCACGAGGAAGTCAATAACAACAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
*
407266 AGATTGACTCC
66 AGATTGACTTC
** * * * * * * * *
407277 TCTTCGCGAGGGAGTCAGGAAAAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAACAACAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
* *
407342 AGATTAACTTT
66 AGATTGACTTC
* * * * * * * *
407353 TCTTCACGAGGAAGTCAAGAATAAAAAAGACTGACTCCTCTTTGCGAGGAAATCAGGAACAATAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
407418 AGATTGACTTC
66 AGATTGACTTC
* * *
407429 TCTTCATGAGGAAGTCAAGAATAACATAGATTGACTCCTCCTCGCGAGGGAGTCAGGAATAAAAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
* *
407494 ATATAGACTTC
66 AGATTGACTTC
* * * * * * * * *
407505 TCCTCACGAGGAAGTCAAGAATAGCATAGATTTACTCATCTTCGTGAGGGAATCCGGAATAACAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
* *
407570 ATATTGACTTT
66 AGATTGACTTC
* * * * * * *
407581 TCTTTACGTGGAAGTCAAGAATAACATAGATTGACTCCACTTCGCGAGGGAGTCCGAAATAACAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
*
407646 AGATTGATTTC
66 AGATTGACTTC
* * * *
407657 TCTTCACGAGGAAGTCAAGAATAACAGAGATTGAATCCTCTTCGCGAGGGAGTCAGAAATAACAA
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
407722 AGATTGACTTC
66 AGATTGACTTC
*** *
407733 TCTTCATGAGGAAGTCAAGAATAACAGTTATTGACTCCTCTTCGCGATGGAGT
1 TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGT
407786 TAAGTTAAAG
Statistics
Matches: 757, Mismatches: 129, Indels: 9
0.85 0.14 0.01
Matches are distributed among these distances:
76 675 0.89
77 82 0.11
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (76 bp):
TCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAA
AGATTGACTTC
Found at i:407775 original size:38 final size:38
Alignment explanation
Indices: 406819--407758 Score: 886
Period size: 38 Copynumber: 24.7 Consensus size: 38
406809 GATTAACTCT
* * *
406819 TCTTCAAGAGAAAGTCAAGGAA-AACAACATATTGACTTC
1 TCTTCACGAGGAAGTCAA-GAATAACAA-AGATTGACTTC
* *
406858 TCTTCACGAGGAAGTAAAGAATAACAAAGATTAACTTC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * * * *
406896 TTTTCATGAGGAAGTCAAGAATAAAAAAGACTGACTCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * * *
406934 TCTTCGCGAGGGAGTTAGGAATAACAAAGATTGACTTC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * * *
406972 TCTTCATGAGTAAGTCAAGAATAAAAAAGATTAACTTC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
*
407010 TCTTCACGAGGAAGTCAAGAATAACAAAGAAAT-ACTTC
1 TCTTCACGAGGAAGTCAAGAATAACAAAG-ATTGACTTC
* * * * *
407048 TATTCATGAGGAAGTCAAGAATAACAAAGACTAACTCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
** * * *
407086 TCTT-TTGTAAGGGAGTCAGGAATAACAAAGATTGATTTC
1 TCTTCACG--AGGAAGTCAAGAATAACAAAGATTGACTTC
* * *
407125 TCTTCATGAGGAAGTCAAGAATAATAAAGATTGACTCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * *
407163 TCTTCACGAGGAAGTAAAGAATAACAAAGATTGAGTCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
** * * * * *
407201 TCTTCGTGAGGGAGTTAGGAACAATAAAGATTGACTTC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * *
407239 TCTTCACGAGGAAGTCAATAACAACAAAGATTGACTCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * * *
407277 TCTTCGCGAGGGAGTCAGGAAAAACAAAGATTGACTTC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * *
407315 TCTTCACGAGGAAGTCAAGAACAACAAAGATTAACTTT
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * *
407353 TCTTCACGAGGAAGTCAAGAATAAAAAAGACTGACTCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
** * * * *
407391 TCTTTGCGAGGAAATCAGGAACAATAAAGATTGACTTC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * *
407429 TCTTCATGAGGAAGTCAAGAATAACATAGATTGACTCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * * * * * *
407467 TCCTCGCGAGGGAGTCAGGAATAAAAAATATAGACTTC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * * *
407505 TCCTCACGAGGAAGTCAAGAATAGCATAGATTTAC-TC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
** ** * *
407542 ATCTTCGTGAGGGAA-TCCGGAATAACAAATATTGACTTT
1 -TCTTCACGA-GGAAGTCAAGAATAACAAAGATTGACTTC
* * * *
407581 TCTTTACGTGGAAGTCAAGAATAACATAGATTGACTCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* * * * *
407619 ACTTCGCGAGGGAGTC-CGAAATAACAAAGATTGATTTC
1 TCTTCACGAGGAAGTCAAG-AATAACAAAGATTGACTTC
* * *
407657 TCTTCACGAGGAAGTCAAGAATAACAGAGATTGAATCC
1 TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
* *
407695 TCTTCGCGAGGGAGTC-AGAAATAACAAAGATTGACTTC
1 TCTTCACGAGGAAGTCAAG-AATAACAAAGATTGACTTC
*
407733 TCTTCATGAGGAAGTCAAGAATAACA
1 TCTTCACGAGGAAGTCAAGAATAACA
407759 GTTATTGACT
Statistics
Matches: 717, Mismatches: 170, Indels: 29
0.78 0.19 0.03
Matches are distributed among these distances:
37 13 0.02
38 644 0.90
39 58 0.08
40 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (38 bp):
TCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTC
Found at i:409059 original size:3 final size:3
Alignment explanation
Indices: 409039--409107 Score: 106
Period size: 3 Copynumber: 23.3 Consensus size: 3
409029 TTGAGCCTAC
*
409039 ATA AAA ATA AT- ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
409084 ATA AT- ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
409108 CAGGTCTTCG
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 55 0.90
4 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:413127 original size:21 final size:21
Alignment explanation
Indices: 413098--413158 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
413088 GACTGTGTAG
413098 AAATGTCCCGAAGGACCACAT
1 AAATGTCCCGAAGGACCACAT
* * *
413119 AAATATCCCAAAGTACCACAT
1 AAATGTCCCGAAGGACCACAT
* * *
413140 AGATGTCTCGAATGACCAC
1 AAATGTCCCGAAGGACCAC
413159 TCCTTAAAGA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.18
Consensus pattern (21 bp):
AAATGTCCCGAAGGACCACAT
Found at i:414151 original size:35 final size:35
Alignment explanation
Indices: 414084--414153 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
414074 CATGGCAATA
*
414084 ATGGTACTGATACTTCCACATTGGTATCGATACCC
1 ATGGTACTGATACTTCCACATTAGTATCGATACCC
*
414119 ATGGTACTGATACTAT-CAC-TTCAGTATTGATACCC
1 ATGGTACTGATACT-TCCACATT-AGTATCGATACCC
414154 CATGAAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 2 0.06
35 28 0.90
36 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (35 bp):
ATGGTACTGATACTTCCACATTAGTATCGATACCC
Found at i:415446 original size:25 final size:26
Alignment explanation
Indices: 415416--415467 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
415406 TTAAAACGTT
* *
415416 AATGTAAAACTTTAGTC-ACATTTAA
1 AATGTAAAACCTTAATCAACATTTAA
415441 AATGTAAAACCTTAATCAACATTTAA
1 AATGTAAAACCTTAATCAACATTTAA
415467 A
1 A
415468 CGTTTCTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (26 bp):
AATGTAAAACCTTAATCAACATTTAA
Found at i:417265 original size:19 final size:19
Alignment explanation
Indices: 417243--417280 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
417233 CATAAAATAC
* *
417243 AATAAATAATATTATTATT
1 AATAAAAAATAATATTATT
417262 AATAAAAAATAATATTATT
1 AATAAAAAATAATATTATT
417281 TTTCAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAAAAATAATATTATT
Found at i:417349 original size:14 final size:14
Alignment explanation
Indices: 417321--417373 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
417311 TATTTATATC
417321 AATATTAAA-ATTAA
1 AATATTAAATA-TAA
*
417335 AATATTATATATAA
1 AATATTAAATATAA
*
417349 AATTTTAAATA-AA
1 AATATTAAATATAA
*
417362 AATTTTAAATAT
1 AATATTAAATAT
417374 TTTATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 13 0.38
14 20 0.59
15 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATTAAATATAA
Found at i:417365 original size:13 final size:13
Alignment explanation
Indices: 417328--417372 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
417318 ATCAATATTA
* *
417328 AAATTAAAATATT
1 AAATAAAAATTTT
*
417341 ATATATAAAATTTT
1 AAATA-AAAATTTT
417355 AAATAAAAATTTT
1 AAATAAAAATTTT
417368 AAATA
1 AAATA
417373 TTTTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATAAAAATTTT
Found at i:417435 original size:42 final size:42
Alignment explanation
Indices: 417380--417469 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
417370 ATATTTTATT
* *
417380 AAAATAA-ATTATTATAAATTATATTAATTATTTATTAAAATA
1 AAAATAATA-TATTATAAATTATATTAATTAATTACTAAAATA
* * *
417422 AGAATAATATATTATTAATTATATTAATTAATTGCTAAAATA
1 AAAATAATATATTATAAATTATATTAATTAATTACTAAAATA
417464 AAAATA
1 AAAATA
417470 TTATTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (42 bp):
AAAATAATATATTATAAATTATATTAATTAATTACTAAAATA
Found at i:417688 original size:32 final size:32
Alignment explanation
Indices: 417650--417728 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 32
417640 ATAACAATAA
417650 AAATATAATATTATATTATTAAAATTATCAAT
1 AAATATAATATTATATTATTAAAATTATCAAT
* * * *
417682 AAATATAAT-TTA-ATAATTAATATTTTCATT
1 AAATATAATATTATATTATTAAAATTATCAAT
*
417712 AAA-ATAATAATATATTA
1 AAATATAATATTATATTA
417729 ATATTAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 5 0.13
30 19 0.49
31 6 0.15
32 9 0.23
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (32 bp):
AAATATAATATTATATTATTAAAATTATCAAT
Found at i:419904 original size:2 final size:2
Alignment explanation
Indices: 419897--419988 Score: 170
Period size: 2 Copynumber: 47.0 Consensus size: 2
419887 CAAAACTAAA
419897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
419938 AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
419979 AT AT AT AT AT
1 AT AT AT AT AT
419989 TATGTTGGTA
Statistics
Matches: 88, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 86 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:423208 original size:2 final size:2
Alignment explanation
Indices: 423201--423294 Score: 62
Period size: 2 Copynumber: 51.0 Consensus size: 2
423191 GACCCGATAC
* * *
423201 AT AT AT AT AT AT AT AT AT AT AT AT CT -T A- AT -T TT AT -T AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
423239 AT AT A- AT AG AG AT AT A- AT -T GA- AA AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
423277 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
423295 TATTGTAGTT
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
1 9 0.12
2 66 0.88
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:423894 original size:24 final size:24
Alignment explanation
Indices: 423867--423912 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
423857 TTAGGAAGGC
423867 CATCCCTAAT-CCTTCCCACTTTTT
1 CATCCCTAATCCCTT-CCACTTTTT
*
423891 CATCCCTAGTCCCTTCCACTTT
1 CATCCCTAATCCCTTCCACTTT
423913 CTCTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.15, C:0.43, G:0.02, T:0.39
Consensus pattern (24 bp):
CATCCCTAATCCCTTCCACTTTTT
Found at i:424746 original size:141 final size:138
Alignment explanation
Indices: 424530--424867 Score: 392
Period size: 141 Copynumber: 2.4 Consensus size: 138
424520 AAATTAAATT
* * * *
424530 TTATCCTAAATTAAAGGACTTATA-TGAAATTAAGCCTAAAATGAAGACTAATATTAAAACCTAG
1 TTATCCTAAATTAAAGGAC-TAAAGTGAAATTAAACCTAAAATGAAGACTAATATTAAAACATAA
** * * *
424594 CCTTTTTTAATAGTTTATTGAATCGAATAATTAATTCAAAACCTCGAGCATAAAAGTGAGGGCCA
65 CCAATTTTAATAGCTTATTGAATCGAATAAATAATTCAAAACCACGAGCATAAAAGTGAGGGCCA
424659 AACTAAAAA
130 AACTAAAAA
* * * *
424668 TTATCCTAAATTAAAGGGCTAAAGGTGAGATTAAACCTAAAATGAATGCTCTAATATTAGAACAT
1 TTATCCTAAATTAAAGGACTAAA-GTGAAATTAAACCTAAAATGAA-G-ACTAATATTAAAACAT
* *
424733 AACCAATTTTAATAGCTTATTGAATCGAATAAATAATTCAGAGCCACGAGCATAAAAGTGAGGGC
63 AACCAATTTTAATAGCTTATTGAATCGAATAAATAATTCAAAACCACGAGCATAAAAGTGAGGGC
* * *
424798 CTAATTAAAAT
128 CAAACTAAAAA
* * * **
424809 TTCTTCTAAATTAAAGAACTAAAGATGAAATT-AATTTAAAATGAAGAATCTAATATTAA
1 TTATCCTAAATTAAAGGACTAAAG-TGAAATTAAACCTAAAATGAAG-A-CTAATATTAA
424868 TCTTAATTAA
Statistics
Matches: 166, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
137 3 0.02
138 18 0.11
139 20 0.12
140 22 0.13
141 103 0.62
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (138 bp):
TTATCCTAAATTAAAGGACTAAAGTGAAATTAAACCTAAAATGAAGACTAATATTAAAACATAAC
CAATTTTAATAGCTTATTGAATCGAATAAATAATTCAAAACCACGAGCATAAAAGTGAGGGCCAA
ACTAAAAA
Found at i:427023 original size:117 final size:117
Alignment explanation
Indices: 426841--427302 Score: 450
Period size: 117 Copynumber: 3.9 Consensus size: 117
426831 CTTTCATCGT
* * * * * * * *
426841 ATGAGTTCTTCTCATTATGAACTCTCTAATAAAAACGTTGATCCACATTCTTTTGTGATAAATTT
1 ATGAGTTCTTCTCATTATGAACTCTC-CATTAAAATGTTGATTCACCTTCTTCTATGATAGATTT
* * *
426906 GAG-TAGAGGTTGAACAAGTTCTTCTCATTATAAACTTTTTCTCCCTCTTTT-G
65 GAGAAAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCT-TTTTGG
* * * * *
426958 ATGAGTTCTTCTCATTATGAACTTTCTATTGGAAATGTTGATTCACCTCCTTCTATGATTGATTT
1 ATGAGTTCTTCTCATTATGAACTCTCCATT-AAAATGTTGATTCACCTTCTTCTATGATAGATTT
* * * *
427023 GAGAAAAATGCTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGG
65 GAGAAAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTTTTTGG
* * * * *** * * *
427076 ATGAATTCTTCTCAATATGAACTCGCCATTAAATATGTTGATACACCAAATTTTCTGATGGATTT
1 ATGAGTTCTTCTCATTATGAACTCTCCATTAAA-ATGTTGATTCACCTTCTTCTATGATAGATTT
* * * *
427141 -A-ACAAAAGGTTTAACAAGTTATTCTCATTATGAACTCCTTCTCCCTTTTTGG
65 GAGA-AAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTTTTTGG
* * * * * *
427193 ATGTGTTTTTCTCATTATGAACTCTCCACTGAAATGGTGATT-ACCTTCTTCTATGATAGACTTG
1 ATGAGTTCTTCTCATTATGAACTCTCCATTAAAATGTTGATTCACCTTCTTCTATGATAGATTTG
* *
427257 AGCAAGAGGTTGAACAAGTTCTTCTCATTATGAAA-TTCTTCTCCCT
66 AGAAAAAGGTTGAACAAGTTCTTCTCATTAT-AAACTTCTTCTCCCT
427303 CATTTCTTCT
Statistics
Matches: 278, Mismatches: 59, Indels: 17
0.79 0.17 0.05
Matches are distributed among these distances:
115 14 0.05
116 46 0.17
117 132 0.47
118 86 0.31
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (117 bp):
ATGAGTTCTTCTCATTATGAACTCTCCATTAAAATGTTGATTCACCTTCTTCTATGATAGATTTG
AGAAAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTTTTTGG
Found at i:427439 original size:24 final size:23
Alignment explanation
Indices: 427412--427528 Score: 115
Period size: 24 Copynumber: 5.3 Consensus size: 23
427402 ATAATACGTG
427412 TATAGTTTTGAAATATATATATAA
1 TATA-TTTTGAAATATATATATAA
427436 TATATTTT--AATATATAT-TATA
1 TATATTTTGAAATATATATATA-A
* * *
427457 TATTTTTTGAAAAATATATATAG
1 TATATTTTGAAATATATATATAA
427480 T-T-TTTT-AAATATATATAT-A
1 TATATTTTGAAATATATATATAA
427499 TATATTATTTGAAATATATATAT-A
1 TATA-T-TTTGAAATATATATATAA
427523 TATATT
1 TATATT
427529 GTTTTCTATT
Statistics
Matches: 79, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
19 1 0.01
20 14 0.18
21 21 0.27
22 3 0.04
23 17 0.22
24 23 0.29
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TATATTTTGAAATATATATATAA
Found at i:427467 original size:44 final size:46
Alignment explanation
Indices: 427417--427528 Score: 162
Period size: 44 Copynumber: 2.5 Consensus size: 46
427407 ACGTGTATAG
427417 TTTTGAAATATATATATAATATATTTT-AATATATAT-TATATATT
1 TTTTGAAATATATATATAATATATTTTAAATATATATATATATATT
* *
427461 TTTTGAAAAATATATATAGT-T-TTTTAAATATATATATATATATT
1 TTTTGAAATATATATATAATATATTTTAAATATATATATATATATT
*
427505 ATTTGAAATATATATAT-ATATATT
1 TTTTGAAATATATATATAATATATT
427529 GTTTTCTATT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
42 4 0.07
43 11 0.19
44 42 0.71
45 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (46 bp):
TTTTGAAATATATATATAATATATTTTAAATATATATATATATATT
Found at i:427484 original size:22 final size:22
Alignment explanation
Indices: 427417--427525 Score: 129
Period size: 21 Copynumber: 5.0 Consensus size: 22
427407 ACGTGTATAG
*
427417 TTTTGAAATATATATATAATATA
1 TTTTGAAATATATATAT-ATATT
427440 TTTT--AATATATATTATATATT
1 TTTTGAAATATATA-TATATATT
427461 TTTTGAAA-A-ATATATATAGTT
1 TTTTGAAATATATATATATA-TT
427482 TTTT-AAATATATATATATATAT
1 TTTTGAAATATATATATATAT-T
427504 TATTTGAAATATATATATATAT
1 T-TTTGAAATATATATATATAT
427526 ATTGTTTTCT
Statistics
Matches: 76, Mismatches: 1, Indels: 17
0.81 0.01 0.18
Matches are distributed among these distances:
20 9 0.12
21 27 0.36
22 15 0.20
23 9 0.12
24 16 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTTGAAATATATATATATATT
Found at i:427543 original size:3 final size:3
Alignment explanation
Indices: 427535--427565 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
427525 TATTGTTTTC
427535 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
427566 TTAGGTCTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:429083 original size:17 final size:19
Alignment explanation
Indices: 429063--429099 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
429053 TTCAGATCGA
429063 ATTTAAA-TTT-AATTTTT
1 ATTTAAATTTTAAATTTTT
429080 ATTTAAATTTTAAATTTTT
1 ATTTAAATTTTAAATTTTT
429099 A
1 A
429100 CGACTAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTAAATTTTAAATTTTT
Found at i:429782 original size:18 final size:17
Alignment explanation
Indices: 429734--429774 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
429724 TAGTTTTTTA
429734 TTTCATTTCT-TTTCATT
1 TTTCATTTCTCTTT-ATT
429751 TTTCATTTCTCTTTATT
1 TTTCATTTCTCTTTATT
429768 TCTTCAT
1 T-TTCAT
429775 GTTTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCATTTCTCTTTATT
Found at i:441270 original size:30 final size:29
Alignment explanation
Indices: 441214--441317 Score: 104
Period size: 30 Copynumber: 3.4 Consensus size: 29
441204 TAATTTTAAA
441214 ATATATATAT-TACATATTTT-AATATATAT
1 ATATATATATATA-AT-TTTTAAATATATAT
* *
441243 ATATATATATATAGGTTTTTAAATATATAC
1 ATATATATATATA-ATTTTTAAATATATAT
* *
441273 ATATACATAATATAATTTTGAAATATATATT
1 ATATATAT-ATATAATTTTTAAATATATA-T
441304 ATATATGATATATA
1 ATATAT-ATATATA
441318 TGTGTGTATG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
29 14 0.23
30 31 0.50
31 15 0.24
32 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (29 bp):
ATATATATATATAATTTTTAAATATATAT
Found at i:441277 original size:59 final size:58
Alignment explanation
Indices: 441169--441322 Score: 139
Period size: 59 Copynumber: 2.6 Consensus size: 58
441159 CTTGTCTAAT
* * * * * * *
441169 TATTTTAAGATATATTTATATATATAATATGTGTATAATTTTAAAATATATATATTACA
1 TATTTTAATATATATATATATATAT-ATAGGTGTATAAATATAAAATATACATAATACA
* * * *
441228 TATTTTAATATATATATATATATATATAGGTTTTTAAATATATACATATACATAATATA
1 TATTTTAATATATATATATATATATATAGGTGTATAAATATA-AAATATACATAATACA
*
441287 -ATTTTGAAATATATATTATATATGATATATATGTGT
1 TATTTT--AATATATA-TATATAT-ATATATAGGTGT
441323 GTATGTGTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
58 17 0.22
59 35 0.45
60 8 0.10
61 7 0.09
62 10 0.13
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.49
Consensus pattern (58 bp):
TATTTTAATATATATATATATATATATAGGTGTATAAATATAAAATATACATAATACA
Found at i:441364 original size:13 final size:13
Alignment explanation
Indices: 441348--441396 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
441338 TTGAAAAATA
*
441348 TATATTGTTTTAT
1 TATATTATTTTAT
*
441361 TATATTATTATAT
1 TATATTATTTTAT
*
441374 TATTTTATTTTAT
1 TATATTATTTTAT
*
441387 T-TTTTATTTT
1 TATATTATTTT
441397 TTTAGGTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (13 bp):
TATATTATTTTAT
Found at i:441397 original size:13 final size:13
Alignment explanation
Indices: 441355--441396 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
441345 ATATATATTG
*
441355 TTTTATTATATTA
1 TTTTATTATTTTA
*
441368 TTATATTATTTTA
1 TTTTATTATTTTA
441381 TTTTATT-TTTTA
1 TTTTATTATTTTA
441393 TTTT
1 TTTT
441397 TTTAGGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:442909 original size:12 final size:12
Alignment explanation
Indices: 442894--442918 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
442884 TTGAATTTAA
442894 ATTTAAATTTTT
1 ATTTAAATTTTT
442906 ATTTAAATTTTT
1 ATTTAAATTTTT
442918 A
1 A
442919 AATTTTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTAAATTTTT
Found at i:443452 original size:117 final size:116
Alignment explanation
Indices: 443202--443651 Score: 390
Period size: 117 Copynumber: 3.9 Consensus size: 116
443192 TATTTGTATG
* * * * * *
443202 ATGGATTTGA-TAAAAGGTTAAACAAGTTCTTATCATTATAAACTTTTTCTCCCTTTTTGGATGA
1 ATGGATTTGAGAAAAAGG-TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGACGA
* * * * * ** * ** * * *
443266 GTTATTCCCATTATGAACTCTACACT-GAAATGGTAATTTTCCTCGTTTTGTG
65 ATTCTTCTCATTATGAACTCTCCATTGGAAATATTGATCATCCTC-TTCTATA
** * ** * **
443318 GCGGACTTGAGCGAAAGGATGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCCTTGGACGA
1 ATGGATTTGAGAAAAAGG-TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGACGA
* *
443383 TTTCTTCTCATTATGAATTCTCCATTGGAAATATTGAT-ATACCTCATTCTATA
65 ATTCTTCTCATTATGAACTCTCCATTGGAAATATTGATCAT-CCTC-TTCTATA
** *
443436 ATGGATTTGA-TTAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGAAGA
1 ATGGATTTGAGAAAAAGG-TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGACGA
* * * * * * * *
443500 GTTCTTCTCATTTTGAACTCTCCATTGGAAATGTTAATCCATCTTCTTTTGTG
65 ATTCTTCTCATTATGAACTCTCCATTGGAAATATTGAT-CATCCTCTTCTATA
* *
443553 ATGGATTTGAGAAAAATGTCGAACAAGTTCTTTTCA-T-TGAACTTCTTCTCCCTTTTTGGACGA
1 ATGGATTTGAGAAAAAGGT-GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGACGA
* *
443616 ATTCTTCTCATTATGAACTCTCTATTAGAAATATTG
65 ATTCTTCTCATTATGAACTCTCCATTGGAAATATTG
443652 GTTTGTTTTC
Statistics
Matches: 269, Mismatches: 58, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
116 62 0.23
117 160 0.59
118 45 0.17
119 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (116 bp):
ATGGATTTGAGAAAAAGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGACGAA
TTCTTCTCATTATGAACTCTCCATTGGAAATATTGATCATCCTCTTCTATA
Found at i:444134 original size:8 final size:8
Alignment explanation
Indices: 444109--444190 Score: 51
Period size: 8 Copynumber: 10.2 Consensus size: 8
444099 AGATTTTCAC
*
444109 TTTATATT
1 TTTATTTT
* *
444117 TCTATATT
1 TTTATTTT
444125 TTTATTTTT
1 TTTA-TTTT
444134 TTTATTTT
1 TTTATTTT
444142 TTTATTTT
1 TTTATTTT
**
444150 TTCGTTTCT
1 TTTATTT-T
*
444159 TTTA-ATT
1 TTTATTTT
**
444166 TTT-TCCT
1 TTTATTTT
*
444173 TTTAATTT
1 TTTATTTT
444181 TTTATTTT
1 TTTATTTT
444189 TT
1 TT
444191 CTTCTTTCTT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
7 8 0.14
8 38 0.68
9 10 0.18
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTATTTT
Found at i:444137 original size:9 final size:9
Alignment explanation
Indices: 444123--444151 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
444113 TATTTCTATA
444123 TTTTTATTT
1 TTTTTATTT
444132 TTTTTA-TT
1 TTTTTATTT
444140 TTTTTATTT
1 TTTTTATTT
444149 TTT
1 TTT
444152 CGTTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:444176 original size:14 final size:14
Alignment explanation
Indices: 444157--444183 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
444147 TTTTTCGTTT
444157 CTTTTAATTTTTTC
1 CTTTTAATTTTTTC
444171 CTTTTAATTTTTT
1 CTTTTAATTTTTT
444184 ATTTTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (14 bp):
CTTTTAATTTTTTC
Found at i:444213 original size:46 final size:47
Alignment explanation
Indices: 444131--444221 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 47
444121 TATTTTTATT
* *
444131 TTTTTTATTTTTTTATTTTTTCGTTTCTTTTAATTTTTTCCTTTTAA
1 TTTTTTATTTTTTTATTCTTTCGTTTCTTTTAATTTTTTCATTTTAA
* * *
444178 TTTTTTA-TTTTTTCTTCTTTC-TTTTTCTTTCATTTTTTCATTTT
1 TTTTTTATTTTTTTATTCTTTCGTTTCT-TTTAATTTTTTCATTTT
444222 TCATTACAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 4 0.11
46 27 0.71
47 7 0.18
ACGTcount: A:0.10, C:0.11, G:0.01, T:0.78
Consensus pattern (47 bp):
TTTTTTATTTTTTTATTCTTTCGTTTCTTTTAATTTTTTCATTTTAA
Found at i:444218 original size:8 final size:8
Alignment explanation
Indices: 444130--444226 Score: 51
Period size: 8 Copynumber: 12.2 Consensus size: 8
444120 ATATTTTTAT
*
444130 TTTTTTTA
1 TTTTTTCA
*
444138 TTTTTTTA
1 TTTTTTCA
*
444146 TTTTTTCGT
1 TTTTTTC-A
*
444155 TTCTTTTAA
1 TT-TTTTCA
444164 TTTTTTC-
1 TTTTTTCA
* *
444171 -CTTTTAA
1 TTTTTTCA
444178 TTTTTT-A
1 TTTTTTCA
444185 TTTTTTC-
1 TTTTTTCA
* *
444192 TTCTTTCTT
1 TTTTTTC-A
444201 TTTCTTTCA
1 TTT-TTTCA
444210 TTTTTTCA
1 TTTTTTCA
444218 -TTTTTCA
1 TTTTTTCA
444225 TT
1 TT
444227 ACAACAGTTG
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
6 4 0.06
7 20 0.29
8 28 0.41
9 9 0.13
10 8 0.12
ACGTcount: A:0.10, C:0.11, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:444915 original size:15 final size:15
Alignment explanation
Indices: 444897--444954 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
444887 CTTTTATTGG
444897 TTTTCTTTTTTTCTT
1 TTTTCTTTTTTTCTT
* *
444912 TTTTCCATTTTTCCTT
1 TTTT-CTTTTTTTCTT
* *
444928 TTTTC-GTTTTTCGT
1 TTTTCTTTTTTTCTT
444942 TTTTCATTTTTTT
1 TTTTC-TTTTTTT
444955 TGTTCTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 11 0.32
15 5 0.15
16 18 0.53
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTCTTTTTTTCTT
Found at i:444945 original size:8 final size:8
Alignment explanation
Indices: 444897--444938 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
444887 CTTTTATTGG
444897 TTTT-CTT
1 TTTTCCTT
*
444904 TTTTTCTT
1 TTTTCCTT
*
444912 TTTTCCAT
1 TTTTCCTT
444920 TTTTCCTT
1 TTTTCCTT
*
444928 TTTTCGTT
1 TTTTCCTT
444936 TTT
1 TTT
444939 CGTTTTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 4 0.13
8 26 0.87
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTCCTT
Found at i:444952 original size:8 final size:7
Alignment explanation
Indices: 444897--444966 Score: 61
Period size: 7 Copynumber: 9.7 Consensus size: 7
444887 CTTTTATTGG
444897 TTTTCTTT
1 TTTTC-TT
444905 TTTTCTT
1 TTTTCTT
444912 TTTTCCATT
1 TTTT-C-TT
*
444921 TTTCCTT
1 TTTTCTT
*
444928 TTTTCGT
1 TTTTCTT
*
444935 TTTTCGT
1 TTTTCTT
*
444942 TTTTCAT
1 TTTTCTT
444949 TTTT-TT
1 TTTTCTT
*
444955 TGTTCTT
1 TTTTCTT
444962 TTTTC
1 TTTTC
444967 CAAGCGTAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
6 4 0.08
7 36 0.69
8 7 0.13
9 5 0.10
ACGTcount: A:0.03, C:0.16, G:0.04, T:0.77
Consensus pattern (7 bp):
TTTTCTT
Found at i:448623 original size:19 final size:20
Alignment explanation
Indices: 448573--448623 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
448563 TAGCAAAAGT
448573 ATCGATCCCTTTGACAAAATG
1 ATCGATCCC-TTGACAAAATG
* *
448594 ATTGATGCCTTGA-AAAATG
1 ATCGATCCCTTGACAAAATG
448613 ATCGATCCCTT
1 ATCGATCCCTT
448624 TGTTACAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 15 0.58
20 4 0.15
21 7 0.27
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (20 bp):
ATCGATCCCTTGACAAAATG
Found at i:454674 original size:21 final size:21
Alignment explanation
Indices: 454644--454683 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
454634 CATATTCCTA
* *
454644 AAAAATGATCAATCTCTTTAC
1 AAAAAGGATCAATCCCTTTAC
*
454665 AAAAAGGATCGATCCCTTT
1 AAAAAGGATCAATCCCTTT
454684 TTGCGAAGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGGATCAATCCCTTTAC
Found at i:456591 original size:21 final size:21
Alignment explanation
Indices: 456545--456642 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 21
456535 GTTTTGGCTC
* *
456545 AAAGGATCGATCCCCTAG-CA
1 AAAGGATCGATCCCTTTGACA
*
456565 AAAGGATCGATCCCTTTGACT
1 AAAGGATCGATCCCTTTGACA
* *
456586 AAAGGATCGATCCTTTTGACT
1 AAAGGATCGATCCCTTTGACA
*
456607 AAAGGATCGATCCCCTTGA-A
1 AAAGGATCGATCCCTTTGACA
* *
456627 AAAAGATCGATTCCTT
1 AAAGGATCGATCCCTT
456643 GGATAACAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
20 29 0.43
21 38 0.57
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (21 bp):
AAAGGATCGATCCCTTTGACA
Found at i:462249 original size:18 final size:19
Alignment explanation
Indices: 462206--462252 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
462196 AAATTTGATT
* *
462206 TTTATATTAATTCTAATTC
1 TTTATATTATTTATAATTC
462225 TTTATATTATTTATAATTC
1 TTTATATTATTTATAATTC
462244 -TTATATTAT
1 TTTATATTAT
462253 AAATTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATTATTTATAATTC
Found at i:462265 original size:13 final size:14
Alignment explanation
Indices: 462231--462267 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
462221 ATTCTTTATA
462231 TTATTTAT-AATTC
1 TTATTTATAAATTC
462244 TTATATTATAAATT-
1 TTAT-TTATAAATTC
462258 TTATTTATAA
1 TTATTTATAA
462268 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:462858 original size:23 final size:23
Alignment explanation
Indices: 462828--462882 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
462818 GCAGCAACCG
*
462828 ACAAGCATCAATGTACCAATTCA
1 ACAAGCATCAATGCACCAATTCA
* *
462851 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCAATGCACCAATTCA
*
462874 GCAAGCATC
1 ACAAGCATC
462883 CTGCATTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (23 bp):
ACAAGCATCAATGCACCAATTCA
Found at i:465481 original size:31 final size:31
Alignment explanation
Indices: 465443--465505 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
465433 TATAATTTGT
465443 AATTAATATTAATATAAAATATA-GTATATAA
1 AATTAATATTAATATAAAATATATGT-TATAA
*
465474 AATTAATATTAATATAAACTATATGTTATAA
1 AATTAATATTAATATAAAATATATGTTATAA
465505 A
1 A
465506 TTATATAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (31 bp):
AATTAATATTAATATAAAATATATGTTATAA
Found at i:465517 original size:21 final size:22
Alignment explanation
Indices: 465493--465539 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
465483 TAATATAAAC
*
465493 TATATG-TTATAAATTATATAG
1 TATATGTTTATAAACTATATAG
*
465514 TATA-GTTTATAAACTATATAT
1 TATATGTTTATAAACTATATAG
465535 TATAT
1 TATAT
465540 TAATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (22 bp):
TATATGTTTATAAACTATATAG
Found at i:465541 original size:88 final size:89
Alignment explanation
Indices: 465416--465585 Score: 224
Period size: 88 Copynumber: 1.9 Consensus size: 89
465406 ATTAACTTAT
** *
465416 ATTACTATAATATAGTTTATAATTTGTAATTAATATTAATATAAAAT-ATAGTATATA-A-AATT
1 ATTACTATAATATAGTTTATAAACTATAATTAATATTAATAT-AAATCATAGT-TA-AGATAATT
*
465478 AATATTAATATAAACTATATGTTATAA
63 AACATTAATATAAACTATATGTTATAA
*
465505 ATTA-TATAGTATAGTTTATAAACTATATATT-ATATTAATATAAATCATAGTTAAGATAATTAA
1 ATTACTATAATATAGTTTATAAACTATA-ATTAATATTAATATAAATCATAGTTAAGATAATTAA
465568 CATTAATATAAACTATAT
65 CATTAATATAAACTATAT
465586 AGTACATTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
86 1 0.01
87 7 0.10
88 57 0.79
89 7 0.10
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.43
Consensus pattern (89 bp):
ATTACTATAATATAGTTTATAAACTATAATTAATATTAATATAAATCATAGTTAAGATAATTAAC
ATTAATATAAACTATATGTTATAA
Found at i:465718 original size:20 final size:21
Alignment explanation
Indices: 465691--465822 Score: 139
Period size: 20 Copynumber: 6.3 Consensus size: 21
465681 TATAGTTTAC
465691 ATATATAGTTTATATA-ACAT
1 ATATATAGTTTATATATACAT
*
465711 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATATACAT
*
465734 ATACTATAGGTTATATAT--AT
1 ATA-TATAGTTTATATATACAT
* *
465754 ATATATA-TATATATATATAT
1 ATATATAGTTTATATATACAT
465774 ATATATAGTTTATATATAC-T
1 ATATATAGTTTATATATACAT
* *
465794 ATACATAGTTTATACATACAT
1 ATATATAGTTTATATATACAT
465815 ATACTATA
1 ATA-TATA
465823 AGTTACATAT
Statistics
Matches: 93, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
18 7 0.08
19 4 0.04
20 39 0.42
21 15 0.16
22 16 0.17
23 8 0.09
24 4 0.04
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (21 bp):
ATATATAGTTTATATATACAT
Found at i:465730 original size:2 final size:2
Alignment explanation
Indices: 465723--465796 Score: 78
Period size: 2 Copynumber: 36.0 Consensus size: 2
465713 AAATAGATTG
* **
465723 TA TA TA TA CA TA TA CTA TA GG T- 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
*
465765 TA TA TA TA TA TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
465797 CATAGTTTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 55 0.90
3 5 0.08
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:465742 original size:24 final size:23
Alignment explanation
Indices: 465691--465778 Score: 92
Period size: 24 Copynumber: 3.9 Consensus size: 23
465681 TATAGTTTAC
465691 ATATATAG-TT-TATATA-ACAT
1 ATATATAGATTATATATATACAT
* *
465711 ATAAATAGATTGTATATATACAT
1 ATATATAGATTATATATATACAT
* *
465734 ATACTATAGGTTATATATATATAT
1 ATA-TATAGATTATATATATACAT
*
465758 ATATATATATATATATATATA
1 ATATATAGAT-TATATATATA
465779 TAGTTTATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 7 0.12
21 2 0.04
22 6 0.11
23 12 0.21
24 29 0.52
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (23 bp):
ATATATAGATTATATATATACAT
Found at i:465931 original size:17 final size:17
Alignment explanation
Indices: 465909--465947 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
465899 GGTTTAGGGT
465909 TTTATTAAATTATATAC
1 TTTATTAAATTATATAC
** *
465926 TTTATTACTTTATATAG
1 TTTATTAAATTATATAC
465943 TTTAT
1 TTTAT
465948 GTATAGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATTAAATTATATAC
Found at i:465974 original size:2 final size:2
Alignment explanation
Indices: 465967--466079 Score: 226
Period size: 2 Copynumber: 56.5 Consensus size: 2
465957 TTCTATAAAC
465967 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
466009 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
466051 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
466080 CGTATAGATT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 111 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:466190 original size:13 final size:13
Alignment explanation
Indices: 466162--466268 Score: 62
Period size: 13 Copynumber: 8.2 Consensus size: 13
466152 TATATTTTTT
466162 TATAGTTTATACATA
1 TATAGTTTAT--ATA
466177 TATAGTTTATATA
1 TATAGTTTATATA
*
466190 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
466205 CATAATTTATATA
1 TATAGTTTATATA
*
466218 TATAG-CTA-ATA
1 TATAGTTTATATA
*
466229 AATA--TTATATA
1 TATAGTTTATATA
* *
466240 GTTTA-TATTATAAA
1 -TATAGT-TTATATA
466254 TATAGTTTATATA
1 TATAGTTTATATA
466267 TA
1 TA
466269 AACTTATATT
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
10 2 0.03
11 9 0.13
12 4 0.06
13 29 0.41
14 7 0.10
15 20 0.28
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:466191 original size:26 final size:26
Alignment explanation
Indices: 465960--466219 Score: 85
Period size: 24 Copynumber: 9.9 Consensus size: 26
465950 ATAGTATTTC
* *
465960 TATAAACTATATATATATATAT-ATA
1 TATAAACTATATATTTATATATAATT
* * *
465985 TATATA-TATATATATATATAT-ATA
1 TATAAACTATATATTTATATATAATT
* * *
466009 TATATA-TATATATATATATAT-ATA
1 TATAAACTATATATTTATATATAATT
* * *
466033 TATATA-TATATATATATATAT-ATA
1 TATAAACTATATATTTATATATAATT
* * *
466057 TATATA-TATATATATATATAT-ATCG
1 TATAAACTATATATTTATATATAAT-T
* * *
466082 TATAGATTACTTATATTAGTTATACATACATA
1 TATA-A--AC-TATA-TATTTATATATA-ATT
* * *
466114 TATATACTATATTAATATAATTTATAATT
1 TATAAACTATA-T-AT-TTATATATAATT
* * *
466143 TATAAACTATATATTTTTTTATAGTT
1 TATAAACTATATATTTATATATAATT
*
466169 TATACA-TATATAGTTTATATATATAGTT
1 TATAAACTATATA-TTTATATATA-A-TT
466197 CATATAAAC-ATA-ATTTATATATA
1 --TATAAACTATATATTTATATATA
466220 TAGCTAATAA
Statistics
Matches: 196, Mismatches: 22, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
24 89 0.45
25 15 0.08
26 22 0.11
27 2 0.01
28 20 0.10
29 16 0.08
30 18 0.09
31 8 0.04
32 4 0.02
33 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.48
Consensus pattern (26 bp):
TATAAACTATATATTTATATATAATT
Found at i:466256 original size:18 final size:17
Alignment explanation
Indices: 466235--466270 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
466225 AATAAATATT
466235 ATATAGTTTATATTATAA
1 ATATAGTTTATA-TATAA
466253 ATATAGTTTATATATAA
1 ATATAGTTTATATATAA
466270 A
1 A
466271 CTTATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
ATATAGTTTATATATAA
Found at i:466368 original size:18 final size:18
Alignment explanation
Indices: 466345--466543 Score: 105
Period size: 18 Copynumber: 10.8 Consensus size: 18
466335 TGTAAATATC
466345 AACTATAGTTTATATGTA
1 AACTATAGTTTATATGTA
*
466363 AACTATAG-TTAGTATATA
1 AACTATAGTTTA-TATGTA
466381 AACTATATAGTTTATATGTA
1 AAC--TATAGTTTATATGTA
* *
466401 AACTATAGTTCATATATA
1 AACTATAGTTTATATGTA
**
466419 AA-TATCA-ACTATAT-TA
1 AACTAT-AGTTTATATGTA
*
466435 TATA-TATAGTTCATATGTA
1 -A-ACTATAGTTTATATGTA
466454 AACTGAATAGTTTATA--T-
1 AACT--ATAGTTTATATGTA
*
466471 -A-TATAGTTCATATGTA
1 AACTATAGTTTATATGTA
466487 AACTGAATAGTTTATATAGTTTA
1 AACT--ATAGTTTATAT-G--TA
*
466510 TATA-TATAGTTCATATGTA
1 -A-ACTATAGTTTATATGTA
*
466529 AACTATAGTTCATAT
1 AACTATAGTTTATAT
466544 ATATAGTATA
Statistics
Matches: 142, Mismatches: 14, Indels: 50
0.69 0.07 0.24
Matches are distributed among these distances:
13 9 0.06
15 2 0.01
16 3 0.02
17 15 0.11
18 57 0.40
19 4 0.03
20 32 0.23
21 5 0.04
22 10 0.07
23 2 0.01
24 2 0.01
25 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (18 bp):
AACTATAGTTTATATGTA
Found at i:466392 original size:38 final size:38
Alignment explanation
Indices: 466348--466535 Score: 141
Period size: 38 Copynumber: 5.1 Consensus size: 38
466338 AAATATCAAC
466348 TATAGTTTATATGTAAACTATAGTT-AGTATATAAACTA
1 TATAGTTTATATGTAAACTATAGTTCA-TATATAAACTA
466386 TATAGTTTATATGTAAACTATAGTTCATATATAAA-TA
1 TATAGTTTATATGTAAACTATAGTTCATATATAAACTA
* * * * *
466423 TCA-ACTATAT-TATATA-TATAGTTCATATGTAAACTGA
1 T-ATAGTTTATATGTAAACTATAGTTCATATATAAACT-A
*
466460 -ATAGTTTATA--T--A-TATAGTTCATATGTAAACTGA
1 TATAGTTTATATGTAAACTATAGTTCATATATAAACT-A
*
466493 -ATAGTTTATATAGTTTATATA-TATAGTTCATATGTAAACTA
1 TATAGTTTATAT-G--TA-A-ACTATAGTTCATATATAAACTA
466534 TA
1 TA
466536 GTTCATATAT
Statistics
Matches: 127, Mismatches: 7, Indels: 28
0.78 0.04 0.17
Matches are distributed among these distances:
33 32 0.25
35 18 0.14
36 10 0.08
37 9 0.07
38 35 0.28
39 1 0.01
41 1 0.01
42 21 0.17
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (38 bp):
TATAGTTTATATGTAAACTATAGTTCATATATAAACTA
Found at i:466443 original size:35 final size:33
Alignment explanation
Indices: 466404--466504 Score: 123
Period size: 33 Copynumber: 3.0 Consensus size: 33
466394 ATATGTAAAC
*
466404 TATAGTTCATATATAAATATCAACTA-TATTATATA
1 TATAGTTCATATGTAAA-ATCAA-TAGT-TTATATA
* *
466439 TATAGTTCATATGTAAACTGAATAGTTTATATA
1 TATAGTTCATATGTAAAATCAATAGTTTATATA
* *
466472 TATAGTTCATATGTAAACTGAATAGTTTATATA
1 TATAGTTCATATGTAAAATCAATAGTTTATATA
466505 GTTTATATAT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
33 42 0.68
34 4 0.06
35 16 0.26
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.43
Consensus pattern (33 bp):
TATAGTTCATATGTAAAATCAATAGTTTATATA
Found at i:466474 original size:33 final size:33
Alignment explanation
Indices: 466432--466504 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
466422 ATCAACTATA
466432 TTATATATATAGTTCATATGTAAACTGAATAGT
1 TTATATATATAGTTCATATGTAAACTGAATAGT
466465 TTATATATATAGTTCATATGTAAACTGAATAGT
1 TTATATATATAGTTCATATGTAAACTGAATAGT
466498 TTATATA
1 TTATATA
466505 GTTTATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (33 bp):
TTATATATATAGTTCATATGTAAACTGAATAGT
Found at i:466546 original size:42 final size:41
Alignment explanation
Indices: 466460--466544 Score: 145
Period size: 42 Copynumber: 2.1 Consensus size: 41
466450 TGTAAACTGA
466460 ATAGTTTATATATATAGTTCATATGTAAACTGAATAGTTTAT
1 ATAGTTTATATATATAGTTCATATGTAAACT-AATAGTTTAT
*
466502 ATAGTTTATATATATAGTTCATATGTAAACT-ATAGTTCAT
1 ATAGTTTATATATATAGTTCATATGTAAACTAATAGTTTAT
466542 ATA
1 ATA
466545 TATAGTATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 11 0.26
42 31 0.74
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.45
Consensus pattern (41 bp):
ATAGTTTATATATATAGTTCATATGTAAACTAATAGTTTAT
Found at i:466553 original size:18 final size:17
Alignment explanation
Indices: 466508--466553 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
466498 TTATATAGTT
466508 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
466525 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
466543 TATATAGTATA
1 TATATA-TATA
466554 TACTATATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:467275 original size:207 final size:204
Alignment explanation
Indices: 466848--467227 Score: 571
Period size: 207 Copynumber: 1.8 Consensus size: 204
466838 CATAGTTATC
* *
466848 ACTTATTTATATTTTTTACTTGGCCCATAACTTTTTAAATGTGTATAATTTAGTACTTTTTGTAT
1 ACTTATTTATA-TTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTGTAT
* *
466913 TAATTTAAATCTCACAATTTAAAATTATTTCGATTTGATCCCTTTGTGTTGTTTAATTTATTTAA
65 TAATTTAAACCTAACAATTTAAAATTATTTCGATTTGATCCCTTTGTGTTGTTTAATTTATTTAA
* * * *
466978 ATTTTTATTTGTAATTTCATTTTTGTTCAATTTAGTCCTCCAAACTATATTTGCATCTGAAATTG
130 ATTTTAATTTGTAATTTCATATTTGTTCAATTTAATCCTCCAAACTATATTTGCATCTAAAATTG
*
467043 ACACATACTTATT
195 ACAC--AC-TATG
467056 ACTTATTTATATTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTGTATT
1 ACTTATTTATATTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTGTATT
*
467121 AATTTCAACCTAACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAATTT
66 AATTTAAACCTAACAATTTAAAATTATTTCGATTTGAT-CC-C-T---T-TGTGTTGTTTAATTT
467186 ATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAAT
124 ATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAAT
467228 TCTTAAATTT
Statistics
Matches: 157, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
207 87 0.55
208 13 0.08
209 1 0.01
210 1 0.01
213 1 0.01
214 54 0.34
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (204 bp):
ACTTATTTATATTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTGTATT
AATTTAAACCTAACAATTTAAAATTATTTCGATTTGATCCCTTTGTGTTGTTTAATTTATTTAAA
TTTTAATTTGTAATTTCATATTTGTTCAATTTAATCCTCCAAACTATATTTGCATCTAAAATTGA
CACACTATG
Found at i:467997 original size:12 final size:13
Alignment explanation
Indices: 467972--468024 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 13
467962 GGGTCTTTTA
467972 TATTGATTTT-TTT
1 TATT-ATTTTATTT
467985 TATT-TTTTATTT
1 TATTATTTTATTT
467997 TATTATTATTATTAT
1 TATTATT-TTATT-T
468012 TATTATTATTATT
1 TATTATT-TTATT
468025 ATTACTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.11
12 7 0.19
13 6 0.17
14 5 0.14
15 14 0.39
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TATTATTTTATTT
Found at i:468002 original size:3 final size:3
Alignment explanation
Indices: 467991--468028 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
467981 TTTTTATTTT
467991 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
468029 CTAATTACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:469920 original size:21 final size:22
Alignment explanation
Indices: 469879--469920 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
469869 CTTTATGCAT
*
469879 ATATAGTAAATGTTCTTATTTA
1 ATATAGTAAATATTCTTATTTA
*
469901 ATATTGTAAATATT-TTATTT
1 ATATAGTAAATATTCTTATTT
469921 GTCATTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
ATATAGTAAATATTCTTATTTA
Found at i:483019 original size:146 final size:147
Alignment explanation
Indices: 482745--483020 Score: 428
Period size: 146 Copynumber: 1.9 Consensus size: 147
482735 AACATCAACT
482745 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
1 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
* ** * *
482810 AGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
66 AGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTACGAACCATGTCAT
482875 GTCATCTACCCTTAGAC
131 GTCATCTACCCTTAGAC
* * *
482892 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATCAGCCGTCCTCATTACGT
1 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
* * * * *
482956 AGGAACCTAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTACGAGCCGTGTCAT
66 AGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTACGAACCATGTCAT
483021 CCCTTGACCA
Statistics
Matches: 116, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
146 77 0.66
147 39 0.34
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (147 bp):
GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
AGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTACGAACCATGTCAT
GTCATCTACCCTTAGAC
Found at i:483277 original size:12 final size:13
Alignment explanation
Indices: 483252--483304 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 13
483242 GAGTCTTTTA
483252 TATTGATTTT-TTT
1 TATT-ATTTTATTT
483265 TATT-TTTTATTT
1 TATTATTTTATTT
483277 TATTATTATTATTAT
1 TATTATT-TTATT-T
483292 TATTATTATTATT
1 TATTATT-TTATT
483305 ATTACTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.11
12 7 0.19
13 6 0.17
14 5 0.14
15 14 0.39
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TATTATTTTATTT
Found at i:483282 original size:3 final size:3
Alignment explanation
Indices: 483271--483308 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
483261 TTTTTATTTT
483271 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
483309 CTAATTACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:485189 original size:21 final size:22
Alignment explanation
Indices: 485148--485189 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
485138 CTTTATGCAT
*
485148 ATATAGTAAATGTTCTTATTTA
1 ATATAGTAAATATTCTTATTTA
*
485170 ATATTGTAAATATT-TTATTT
1 ATATAGTAAATATTCTTATTT
485190 GTCATTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
ATATAGTAAATATTCTTATTTA
Found at i:488714 original size:23 final size:24
Alignment explanation
Indices: 488662--488727 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 24
488652 TGGAACTTGA
*
488662 TTTTTAAGTT-GAAACCTGAA---
1 TTTTTAAGTTGGAAACCTAAATTC
488682 TTTTTAAGTTGG-AACCTAAATTC
1 TTTTTAAGTTGGAAACCTAAATTC
* *
488705 TTTTTTAGTTGGAAACCTTAATT
1 TTTTTAAGTTGGAAACCTAAATT
488728 TTAAGGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 17 0.45
21 1 0.03
23 11 0.29
24 9 0.24
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (24 bp):
TTTTTAAGTTGGAAACCTAAATTC
Found at i:488767 original size:19 final size:20
Alignment explanation
Indices: 488725--488768 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
488715 GGAAACCTTA
* *
488725 ATTTTAAGGTTGCAAGCTAG
1 ATTTTAAGGTTGCAACCCAG
*
488745 ATTTT-AGGTTGCAACCCAT
1 ATTTTAAGGTTGCAACCCAG
488764 ATTTT
1 ATTTT
488769 CATATTACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTTTAAGGTTGCAACCCAG
Found at i:488948 original size:26 final size:26
Alignment explanation
Indices: 488914--488977 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
488904 TTAAAAAACA
* *
488914 TTTTAAAAATATATATAATATATAGT
1 TTTTGAAAACATATATAATATATAGT
*
488940 TTTTGAAAACATTTATAATATATAGT
1 TTTTGAAAACATATATAATATATAGT
*
488966 TTTCGAAAACAT
1 TTTTGAAAACAT
488978 TTTGAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (26 bp):
TTTTGAAAACATATATAATATATAGT
Found at i:488990 original size:2 final size:2
Alignment explanation
Indices: 488983--489012 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
488973 AACATTTTGA
488983 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
489013 GGTTTTGAAA
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:488990 original size:28 final size:26
Alignment explanation
Indices: 488927--488989 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
488917 TAAAAATATA
*
488927 TATAATATATAGTTTTTGAAAACATT
1 TATAATATATAGTTTTCGAAAACATT
488953 TATAATATATAGTTTTCGAAAACATT
1 TATAATATATAGTTTTCGAAAACATT
488979 T-TGAATATATA
1 TAT-AATATATA
488990 TATATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (26 bp):
TATAATATATAGTTTTCGAAAACATT
Found at i:489001 original size:38 final size:37
Alignment explanation
Indices: 488993--489215 Score: 242
Period size: 38 Copynumber: 5.9 Consensus size: 37
488983 ATATATATAT
488993 ATATATATATATATAATATAGGTTTTGAAAACATTTTGA
1 ATATATATATATAT-ATATA-GTTTTGAAAACATTTTGA
* *
489032 AAATATATATATAATATATAGCTTTGAAAACATTTTGA
1 ATATATATATAT-ATATATAGTTTTGAAAACATTTTGA
*
489070 ATATATATATA-ATATATAGTTTTTGAAAATATTTTGAA
1 ATATATATATATATATATAG-TTTTGAAAACATTTTG-A
489108 ATATATATATAATATATATAGTTTTGAAAACATTTTGA
1 ATATATATAT-ATATATATAGTTTTGAAAACATTTTGA
* * * *
489146 AAATATATATA-ATATATAATTTT--AAGCATTTTTTA
1 ATATATATATATATATATAGTTTTGAAAACA-TTTTGA
* *
489181 A-A-ATATATCATATGTATAGATTTAGAAAACATTTT
1 ATATATATAT-ATATATATAG-TTTTGAAAACATTTT
489216 TTGAAAAATA
Statistics
Matches: 159, Mismatches: 14, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
33 6 0.04
34 6 0.04
35 12 0.08
36 22 0.14
37 19 0.12
38 52 0.33
39 32 0.20
40 10 0.06
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATATATATATATATAGTTTTGAAAACATTTTGA
Found at i:489008 original size:114 final size:111
Alignment explanation
Indices: 488882--489168 Score: 314
Period size: 114 Copynumber: 2.5 Consensus size: 111
488872 GGGTATTTTT
*
488882 AATATATATATAATATAATATTTTAAAAAACATTTTAAAAATATATATAATATATAGTTTTTGAA
1 AATATATATATAATATAATATTTT-GAAAACATTTTAAAAATATATATAATATATAGTTTTTGAA
* **
488947 AACATTTAT-AATATATAGTTTTCGA-AAACATTTTGAATATATATATAT-A
65 AACATTT-TGAATATATA-TATAAGATAAACATTTTGAA-A-ATAT-TATGA
* ** *
488996 TATATATATATAATAT-AGGTTTTGAAAACATTTTGAAAATATATATATAATATATAG-CTTTGA
1 AATATATATATAATATAATATTTTGAAAACATTTT-AAAA-ATATATATAATATATAGTTTTTGA
* * ** *
489059 AAACATTTTGAATATATATATAATATATAGTTTTTGAAAATATTTTGA
64 AAACATTTTGAATATATATATAAGATAAACATTTTGAAAATATTATGA
* *
489107 AATATATATATAATATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAATTTT
1 AATATATATATAATATA-ATA-TTTTGAAAACATTTTAAAAATATATATAATATATAGTTTT
489169 AAGCATTTTT
Statistics
Matches: 145, Mismatches: 19, Indels: 19
0.79 0.10 0.10
Matches are distributed among these distances:
110 2 0.01
111 20 0.14
112 31 0.21
113 45 0.31
114 47 0.32
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (111 bp):
AATATATATATAATATAATATTTTGAAAACATTTTAAAAATATATATAATATATAGTTTTTGAAA
ACATTTTGAATATATATATAAGATAAACATTTTGAAAATATTATGA
Found at i:489023 original size:49 final size:50
Alignment explanation
Indices: 488953--489051 Score: 157
Period size: 49 Copynumber: 2.0 Consensus size: 50
488943 TGAAAACATT
*
488953 TATAATATATAGTTTTCGAAAACATTTTGAATATATATATATATATATATA
1 TATAATATATAGTTTTCGAAAACATTTTGAAAATATATATATA-ATATATA
*
489004 TATAATATA-GGTTTT-GAAAACATTTTGAAAATATATATATAATATATA
1 TATAATATATAGTTTTCGAAAACATTTTGAAAATATATATATAATATATA
489052 GCTTTGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 7 0.15
49 25 0.54
50 5 0.11
51 9 0.20
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (50 bp):
TATAATATATAGTTTTCGAAAACATTTTGAAAATATATATATAATATATA
Found at i:489254 original size:23 final size:22
Alignment explanation
Indices: 489228--489294 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
489218 GAAAAATATT
489228 TTATATACTTTTTTATTATTTAA
1 TTATATACTTTTTTATT-TTTAA
* * *
489251 TTATTTATTTTTTTATTTTTATT
1 TTATATACTTTTTTATTTTTA-A
* **
489274 TTTTATTTTTTTTTATTTTTA
1 TTATATACTTTTTTATTTTTA
489295 TTTAGGTCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.78
Consensus pattern (22 bp):
TTATATACTTTTTTATTTTTAA
Found at i:489265 original size:8 final size:8
Alignment explanation
Indices: 489236--489297 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 8
489226 TTTTATATAC
489236 TTTTTTA-
1 TTTTTTAT
* *
489243 TTATTTAA
1 TTTTTTAT
*
489251 TTATTTAT
1 TTTTTTAT
489259 TTTTTTA-
1 TTTTTTAT
489266 -TTTTTA-
1 TTTTTTAT
489272 TTTTTTAT
1 TTTTTTAT
489280 TTTTTT-T
1 TTTTTTAT
489287 TATTTTTAT
1 T-TTTTTAT
489296 TT
1 TT
489298 AGGTCCAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.13
7 14 0.30
8 25 0.53
9 2 0.04
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:489266 original size:12 final size:12
Alignment explanation
Indices: 489226--489297 Score: 58
Period size: 12 Copynumber: 6.0 Consensus size: 12
489216 TTGAAAAATA
* *
489226 TTTTATATACTT
1 TTTTATTTATTT
489238 TTTTA-TTATTT
1 TTTTATTTATTT
**
489249 AATTATTTATTT
1 TTTTATTTATTT
*
489261 TTTTATTTTTATT
1 TTTTATTTAT-TT
489274 TTTTATTT-TTT
1 TTTTATTTATTT
*
489285 TTTATTTTTATTT
1 TTT-TATTTATTT
489298 AGGTCCAAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
11 12 0.25
12 23 0.48
13 13 0.27
ACGTcount: A:0.19, C:0.01, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:489271 original size:6 final size:6
Alignment explanation
Indices: 489251--489297 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
489241 TATTATTTAA
489251 TTATTT ATT-TTT TTATTT TTATTT TT-TATT TT-TTT TTATTT TTATTT
1 TTATTT -TTATTT TTATTT TTATTT TTAT-TT TTATTT TTATTT TTATTT
489298 AGGTCCAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 7 0.19
6 28 0.76
7 2 0.05
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:489278 original size:29 final size:29
Alignment explanation
Indices: 489237--489297 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
489227 TTTATATACT
489237 TTTTTATTATTTAATTATTTATT-TTTTTA
1 TTTTTATTATTT-ATTATTTATTATTTTTA
* * *
489266 TTTTTATTTTTTATTTTTTTTTATTTTTA
1 TTTTTATTATTTATTATTTATTATTTTTA
489295 TTT
1 TTT
489298 AGGTCCAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTTATTATTTATTATTTATTATTTTTA
Found at i:489295 original size:23 final size:21
Alignment explanation
Indices: 489236--489297 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 21
489226 TTTTATATAC
*
489236 TTTTTTATTATTTAATTATTTAT
1 TTTTTTATT-TTT-ATTTTTTAT
489259 TTTTTTATTTTTATTTTTTATTT
1 TTTTTTATTTTTATTTTTTA--T
489282 TTTTTTATTTTTATTT
1 TTTTTTATTTTTATTT
489298 AGGTCCAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 7 0.19
22 3 0.08
23 26 0.72
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTATTTTTATTTTTTAT
Found at i:489811 original size:23 final size:23
Alignment explanation
Indices: 489775--489825 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
489765 AACATCCCTG
* *
489775 GAAAAACCAGAACAC-CAACCAA
1 GAAAAAACAAAACACACAACCAA
*
489797 GTAAAAAACAAAACACACAACGAA
1 G-AAAAAACAAAACACACAACCAA
489821 GAAAA
1 GAAAA
489826 CGAAGCATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 16 0.67
24 7 0.29
ACGTcount: A:0.65, C:0.24, G:0.10, T:0.02
Consensus pattern (23 bp):
GAAAAAACAAAACACACAACCAA
Found at i:494765 original size:2 final size:2
Alignment explanation
Indices: 494754--494812 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
494744 TAAAGGTGAT
494754 TA TA -A TA TA TA TA TA TA T- 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
494794 TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
494813 AAGCTTGAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:496611 original size:201 final size:201
Alignment explanation
Indices: 496262--496676 Score: 652
Period size: 201 Copynumber: 2.1 Consensus size: 201
496252 GAACTGTTCG
* * * * *
496262 CAGCATAGCTCAAGGCGAGAAGGGTTATCTATCCATAAAAACTTTCGAGTTCGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAAGGCTATATATCAATAAAAACTTTCGAGCTCGATTCCATTCAGC
*
496327 TCGATGACATATCAACTGCATGGTAGCAGCGAGGAACTACTTTCCGGTTAAAGTTTAAACTAAGG
66 TCGATGACATATCAACTGCATGGTAGCAGCAAGGAACTACTTTCCGGTTAAAGTTTAAACTAAGG
* * * *
496392 TCTTTGAGTCAAGAAGAAGACCTAGGTGGGTTGTGATTTAGCAACAATGAACTATCTCCCAG-CT
131 TCTTTAAGTCAAGAAGAAGACCTAGGTGGGTTGTGATCTAGCAACAAGGAACTATATCCCAGTC-
496456 AAAATTA
195 AAAATTA
* *
496463 CAGTATAGCTCAAGGCGAGAAAGGCTATATGTCAATAAAAACTTTCGAGCTCGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAAGGCTATATATCAATAAAAACTTTCGAGCTCGATTCCATTCAGC
* * *
496528 TCGATGACATATCAACTGCATGGTAGCAGCAAGGAATTACTTTCCGGTTGAAGTTTTAACTAAGG
66 TCGATGACATATCAACTGCATGGTAGCAGCAAGGAACTACTTTCCGGTTAAAGTTTAAACTAAGG
* *
496593 TCTTTAAGTCAAGAAGAAGACCTGGGTTGGTTGTGATCTAGCAACAAGGAACTATATCCCAGTCA
131 TCTTTAAGTCAAGAAGAAGACCTAGGTGGGTTGTGATCTAGCAACAAGGAACTATATCCCAGTCA
*
496658 AATTTA
196 AAATTA
496664 CAGCATAGCTCAA
1 CAGCATAGCTCAA
496677 AGGGCTATCT
Statistics
Matches: 194, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
201 193 0.99
202 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (201 bp):
CAGCATAGCTCAAGGCGAGAAAGGCTATATATCAATAAAAACTTTCGAGCTCGATTCCATTCAGC
TCGATGACATATCAACTGCATGGTAGCAGCAAGGAACTACTTTCCGGTTAAAGTTTAAACTAAGG
TCTTTAAGTCAAGAAGAAGACCTAGGTGGGTTGTGATCTAGCAACAAGGAACTATATCCCAGTCA
AAATTA
Found at i:497266 original size:36 final size:36
Alignment explanation
Indices: 497192--497319 Score: 144
Period size: 34 Copynumber: 3.7 Consensus size: 36
497182 CTATATATAT
* *
497192 ACATATATAATAT-T--TTTTGAAAAACATTTTGAAA
1 ACATATATAATATATAGTTTTG-GAAACATTTTCAAA
*
497226 ATATATAT-A-ATATAGTTTTGGAAACA-TTTCAAA
1 ACATATATAATATATAGTTTTGGAAACATTTTCAAA
* *
497259 A-ATATATAATATATAGTTTTGAAAACATTTTGAAA
1 ACATATATAATATATAGTTTTGGAAACATTTTCAAA
*
497294 ACATATATAATATATAGTTTTCGAAA
1 ACATATATAATATATAGTTTTGGAAA
497320 ATATTTTGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
32 8 0.10
33 10 0.12
34 28 0.35
35 12 0.15
36 22 0.28
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (36 bp):
ACATATATAATATATAGTTTTGGAAACATTTTCAAA
Found at i:497367 original size:2 final size:2
Alignment explanation
Indices: 497360--497435 Score: 110
Period size: 2 Copynumber: 41.0 Consensus size: 2
497350 TATTTTGAAA
497360 AT AT AT AT AT AT -T AT -T AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
497399 AT AT A- AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
497436 TTTTGAAATA
Statistics
Matches: 68, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
1 6 0.09
2 62 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:497381 original size:29 final size:29
Alignment explanation
Indices: 497320--497443 Score: 102
Period size: 29 Copynumber: 4.4 Consensus size: 29
497310 GTTTTCGAAA
*
497320 ATATTTTGAAAATATAT-TATAGTTTTGAA-
1 ATATTTTGAAAATATATATATA-TTAT-AAT
497349 ATATTTTGAAAATATATATATATTATTATAT
1 ATATTTTGAAAATATATATATATTA-TA-AT
* *
497380 ATATATT--ATATATATATATA-TATAAT
1 ATATTTTGAAAATATATATATATTATAAT
* *
497406 ATA-TAT--ATATATATATATATTATAAT
1 ATATTTTGAAAATATATATATATTATAAT
497432 ATATTTTTGAAA
1 ATA-TTTTGAAA
497444 TATTTTGAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 17
0.77 0.07 0.17
Matches are distributed among these distances:
25 14 0.18
26 14 0.18
27 2 0.03
28 4 0.05
29 32 0.41
30 7 0.09
31 6 0.08
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
ATATTTTGAAAATATATATATATTATAAT
Found at i:497391 original size:21 final size:20
Alignment explanation
Indices: 497360--497436 Score: 106
Period size: 19 Copynumber: 3.9 Consensus size: 20
497350 TATTTTGAAA
497360 ATATATA-TATAT-TATTAT
1 ATATATATTATATATATTAT
497378 ATATATATTATATATA-TAT
1 ATATATATTATATATATTAT
*
497397 ATATATAATATATATATATAT
1 ATATATATTATATATAT-TAT
497418 ATATATATTATAATATATT
1 ATATATATTAT-ATATATT
497437 TTTGAAATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
18 7 0.13
19 23 0.44
20 2 0.04
21 14 0.27
22 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATATATTATATATATTAT
Found at i:497475 original size:36 final size:36
Alignment explanation
Indices: 497418--497567 Score: 200
Period size: 36 Copynumber: 4.2 Consensus size: 36
497408 ATATATATAT
* *
497418 ATATATATTATAATATATTTTTG-AAATATTTTGAAA
1 ATATATATAAT-ATATATTTTTGAAAACATTTTGAAA
497454 ATATATATAATATATAGTTTTTGAAAACATTTTG-AA
1 ATATATATAATATATA-TTTTTGAAAACATTTTGAAA
*
497490 ATATATA-ATATATATAGTTTTGAAAACATTTTGAAA
1 ATATATATA-ATATATATTTTTGAAAACATTTTGAAA
*
497526 ATATATATAATATATAATTTT-AAAACATTTTTGAAA
1 ATATATATAATATATATTTTTGAAAACA-TTTTGAAA
497562 ATATAT
1 ATATAT
497568 CATGTGTATA
Statistics
Matches: 104, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
35 28 0.27
36 66 0.63
37 10 0.10
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATATAATATATATTTTTGAAAACATTTTGAAA
Found at i:497602 original size:38 final size:36
Alignment explanation
Indices: 497416--497613 Score: 194
Period size: 36 Copynumber: 5.4 Consensus size: 36
497406 ATATATATAT
* *
497416 ATATATATATTATAATATATTTTTG-AAATATTTTGAAA
1 ATATATATA-TAT-ATAGA-TTTTGAAAACATTTTGAAA
*
497454 ATATATATAATATATAGTTTTTGAAAACATTTTG-AA
1 ATATATAT-ATATATAGATTTTGAAAACATTTTGAAA
497490 ATATATAATATATATAG-TTTTGAAAACATTTTGAAA
1 ATATAT-ATATATATAGATTTTGAAAACATTTTGAAA
497526 ATATATATAATATATA-ATTTT-AAAACATTTTTGAAA
1 ATATATAT-ATATATAGATTTTGAAAACA-TTTTGAAA
* * *
497562 ATATATCATGTGTATAGATTTCGAAAACGATTTTTG-AA
1 ATATAT-ATATATATAGATTTTGAAAAC-A-TTTTGAAA
*
497600 ATATAT-TTTATATA
1 ATATATATATATATA
497614 CTTTTTTATT
Statistics
Matches: 141, Mismatches: 8, Indels: 24
0.82 0.05 0.14
Matches are distributed among these distances:
35 24 0.17
36 65 0.46
37 20 0.14
38 24 0.17
39 8 0.06
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (36 bp):
ATATATATATATATAGATTTTGAAAACATTTTGAAA
Found at i:497613 original size:72 final size:71
Alignment explanation
Indices: 497194--497605 Score: 240
Period size: 72 Copynumber: 6.1 Consensus size: 71
497184 ATATATATAC
* *
497194 ATATATAATAT-T--TTTTGAAAAACATTTTGAAA-ATAT-ATATAATATAGTTTTGGAAACA-T
1 ATATATAATATATAATTTTG-AAAACATTTTGAAATATATAATAT-ATATAGTTTCGAAAACATT
*
497253 TTCAAAA-
64 TTGAAAAT
* * *
497260 ATATATAATATATAGTTTTGAAAACATTTTGAAA-ACATATATAATATATAGTTTTCGAAAATAT
1 ATATATAATATATAATTTTGAAAACATTTTGAAATATATA-AT-ATATATAG-TTTCGAAAACAT
497324 TTTG--AA-
63 TTTGAAAAT
* * * * *
497330 A-ATAT-AT-TATAGTTTTG-AAATATTTTGAAA-ATATATATATAT-TA--TT--ATATATATA
1 ATATATAATATATAATTTTGAAAACATTTTGAAATATATA-ATATATATAGTTTCGA-AAACATT
*
497385 TT--ATAT
64 TTGAAAAT
* * * * * * * * *
497391 ATATAT-ATATATAA-TAT--ATATA-TAT-ATATATATATTATAATATATTTTTG-AAATATTT
1 ATATATAATATATAATTTTGAAAACATTTTGAAATATATAATAT-ATATAGTTTCGAAAACATTT
497449 TGAAAAT
65 TGAAAAT
* *
497456 ATATATAATATATAGTTTTTGAAAACATTTTGAAATATATAATATATATAGTTTTGAAAACATTT
1 ATATATAATATATA-ATTTTGAAAACATTTTGAAATATATAATATATATAGTTTCGAAAACATTT
497521 TGAAAAT
65 TGAAAAT
* * *
497528 ATATATAATATATAATTTT-AAAACATTTTTGAAAATATATCATGTGTATAGATTTCGAAAACGA
1 ATATATAATATATAATTTTGAAAACA-TTTTG-AAATATATAATATATATAG-TTTCGAAAAC-A
497592 TTTTTG-AAAT
62 -TTTTGAAAAT
497602 ATAT
1 ATAT
497606 TTTATATACT
Statistics
Matches: 278, Mismatches: 33, Indels: 62
0.75 0.09 0.17
Matches are distributed among these distances:
59 6 0.02
60 17 0.06
61 9 0.03
62 8 0.03
63 13 0.05
64 2 0.01
65 13 0.05
66 37 0.13
67 11 0.04
68 21 0.08
69 9 0.03
70 20 0.07
71 31 0.11
72 58 0.21
73 9 0.03
74 9 0.03
75 5 0.02
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (71 bp):
ATATATAATATATAATTTTGAAAACATTTTGAAATATATAATATATATAGTTTCGAAAACATTTT
GAAAAT
Found at i:497641 original size:12 final size:12
Alignment explanation
Indices: 497626--497666 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
497616 TTTTTATTAT
497626 TTATTTATTTTC
1 TTATTTATTTTC
*
497638 TTATTT-TTATTT
1 TTATTTATT-TTC
497650 TTATTTATTTTC
1 TTATTTATTTTC
497662 -TATTT
1 TTATTT
497667 TCTATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.28
12 16 0.64
13 2 0.08
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (12 bp):
TTATTTATTTTC
Found at i:497644 original size:24 final size:23
Alignment explanation
Indices: 497616--497688 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 23
497606 TTTATATACT
497616 TTTTTATTATTTATTTATTTTCTTA
1 TTTTTATT-TTTATTTATTTTC-TA
497641 TTTTTATTTTTATTTATTTTCTA
1 TTTTTATTTTTATTTATTTTCTA
**
497664 TTTTCTATTAAT-TTTATTTT-TA
1 TTTT-TATTTTTATTTATTTTCTA
497686 TTT
1 TTT
497689 AGGTCCAAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
22 5 0.11
23 14 0.31
24 18 0.40
25 8 0.18
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTATTTTTATTTATTTTCTA
Found at i:497660 original size:16 final size:16
Alignment explanation
Indices: 497618--497689 Score: 74
Period size: 16 Copynumber: 4.2 Consensus size: 16
497608 TATATACTTT
*
497618 TTTATTATTTATTTATTT
1 TTTATT-TTTATTT-TTA
497636 TCTTATTTTTATTTTTA
1 T-TTATTTTTATTTTTA
497653 TTTATTTTCTATTTTCTA
1 TTTATTTT-TATTTT-TA
*
497671 -TTAATTTTATTTTTA
1 TTTATTTTTATTTTTA
497686 TTTA
1 TTTA
497690 GGTCCAAGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
15 2 0.04
16 16 0.33
17 15 0.31
18 10 0.21
19 5 0.10
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:497684 original size:33 final size:32
Alignment explanation
Indices: 497616--497689 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
497606 TTTATATACT
* *
497616 TTTTTA-TTATTTATTTATTTTCTTATTTTTA
1 TTTTTATTTATTTATCTATTTTCTTAATTTTA
497647 TTTTTATTTATTT-TCTATTTTCTATTAATTTTA
1 TTTTTATTTATTTATCTATTTTC--TTAATTTTA
497680 TTTTTATTTA
1 TTTTTATTTA
497690 GGTCCAAGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 14 0.37
32 6 0.16
33 18 0.47
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTTATTTATTTATCTATTTTCTTAATTTTA
Found at i:498208 original size:24 final size:23
Alignment explanation
Indices: 498165--498216 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
498155 GAATATCATT
*
498165 GAAAAAATCAGAACACCAACCAA
1 GAAAAAATCACAACACCAACCAA
*
498188 GCAAAAAA-CACAACACACAACGAA
1 G-AAAAAATCACAACAC-CAACCAA
498212 GAAAA
1 GAAAA
498217 CGAAGCATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.63, C:0.25, G:0.10, T:0.02
Consensus pattern (23 bp):
GAAAAAATCACAACACCAACCAA
Found at i:499404 original size:39 final size:41
Alignment explanation
Indices: 499361--499469 Score: 109
Period size: 39 Copynumber: 2.7 Consensus size: 41
499351 TTACAAGTAG
*
499361 GGTGATGTATCGTACGAGATACACACCTAAATTGA-AAG-T
1 GGTGATGTATCGTACGAGATACACACCTAAATTGACAAGAA
* * * * *
499400 GGTGATATATTGTACGTGATACACACC--CATTTACAAGCAA
1 GGTGATGTATCGTACGAGATACACACCTAAATTGACAAG-AA
* *
499440 GGTGATGTATCGTACGGGGTACACACCTAA
1 GGTGATGTATCGTACGAGATACACACCTAA
499470 TTAATAGAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
37 4 0.07
38 3 0.06
39 24 0.44
40 23 0.43
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (41 bp):
GGTGATGTATCGTACGAGATACACACCTAAATTGACAAGAA
Found at i:499455 original size:40 final size:39
Alignment explanation
Indices: 499343--499466 Score: 108
Period size: 40 Copynumber: 3.1 Consensus size: 39
499333 GGTTGCGACA
* *
499343 ACACCCAATTACAAGTAGGGTGATGTATCGTACGAGATAC
1 ACACCCATTTACAAG-AAGGTGATGTATCGTACGAGATAC
* * * * * *
499383 ACACCTAAATTGA-AAG-TGGTGATATATTGTACGTGATAC
1 ACACC--CATTTACAAGAAGGTGATGTATCGTACGAGATAC
* *
499422 ACACCCATTTACAAGCAAGGTGATGTATCGTACGGGGTAC
1 ACACCCATTTACAAG-AAGGTGATGTATCGTACGAGATAC
499462 ACACC
1 ACACC
499467 TAATTAATAG
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
37 4 0.06
38 3 0.05
39 24 0.37
40 28 0.43
41 3 0.05
42 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (39 bp):
ACACCCATTTACAAGAAGGTGATGTATCGTACGAGATAC
Found at i:506316 original size:18 final size:18
Alignment explanation
Indices: 506289--506360 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
506279 TAACCAAGTC
506289 TCCA-TGCATCACTAGTA
1 TCCACTGCATCACTAGTA
*
506306 TCCACTGCATCACTACTA
1 TCCACTGCATCACTAGTA
* *
506324 -CGACAC-GATTATCAATAGTA
1 TC--CACTG--CATCACTAGTA
506344 TCCACTGCATCACTAGT
1 TCCACTGCATCACTAGT
506361 GTTCACTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
17 5 0.12
18 21 0.50
19 6 0.14
20 9 0.21
21 1 0.02
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.28
Consensus pattern (18 bp):
TCCACTGCATCACTAGTA
Found at i:510574 original size:2 final size:2
Alignment explanation
Indices: 510567--510597 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
510557 ATGTACCATT
510567 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
510598 ATATATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:511354 original size:2 final size:2
Alignment explanation
Indices: 511347--511415 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
511337 AAACATAAAA
511347 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
511389 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
511416 TATATATATA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:511473 original size:2 final size:2
Alignment explanation
Indices: 511415--511456 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
511405 ACACACACAC
511415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
511457 CATACCGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:511758 original size:23 final size:23
Alignment explanation
Indices: 511732--511782 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
511722 CACCACAGCT
*
511732 CGTATAAATGCATCGAAGTGCCA
1 CGTATAAATGCATCGAAGTACCA
** * *
511755 CGTAGGATTGCATCGAAGTACCG
1 CGTATAAATGCATCGAAGTACCA
511778 CGTAT
1 CGTAT
511783 TTAACACCCC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (23 bp):
CGTATAAATGCATCGAAGTACCA
Found at i:512412 original size:18 final size:18
Alignment explanation
Indices: 512389--512423 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
512379 CTGAATATTT
512389 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
512407 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
512424 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:519971 original size:19 final size:19
Alignment explanation
Indices: 519947--519992 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
519937 TTAAGGGGCC
*
519947 ATCGATATACTACCTAAGT
1 ATCGATACACTACCTAAGT
* *
519966 ATCGATACCCTACCTAGGT
1 ATCGATACACTACCTAAGT
519985 ATCGATAC
1 ATCGATAC
519993 CCAAATTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (19 bp):
ATCGATACACTACCTAAGT
Found at i:519993 original size:19 final size:19
Alignment explanation
Indices: 519956--519994 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
519946 CATCGATATA
519956 CTACCTAAGTATCGATACC
1 CTACCTAAGTATCGATACC
*
519975 CTACCTAGGTATCGATACC
1 CTACCTAAGTATCGATACC
519994 C
1 C
519995 AAATTACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.26
Consensus pattern (19 bp):
CTACCTAAGTATCGATACC
Found at i:524494 original size:21 final size:21
Alignment explanation
Indices: 524440--524509 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
524430 CAAATATTCA
524440 AAAAAAATTAAATATAAATACT
1 AAAAAAA-TAAATATAAATACT
524462 AAAAACAA-AAAT-TAAATTACT
1 AAAAA-AATAAATATAAA-TACT
* **
524483 AAAAAAATAAATGTTTATACT
1 AAAAAAATAAATATAAATACT
524504 AAAAAA
1 AAAAAA
524510 TACAAAACCT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 6 0.14
21 27 0.64
22 7 0.17
23 2 0.05
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.26
Consensus pattern (21 bp):
AAAAAAATAAATATAAATACT
Found at i:526278 original size:24 final size:24
Alignment explanation
Indices: 526251--526312 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
526241 CGTTCATGAA
*
526251 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
526275 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
526299 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
526313 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:527802 original size:16 final size:16
Alignment explanation
Indices: 527779--527833 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
527769 GGGTCTCCAA
527779 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
527795 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
527811 CGTTTATGTTTGTGTT
1 CGTTTATGTTCGTGTT
527827 CGTTTAT
1 CGTTTAT
527834 TTATTAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:527921 original size:16 final size:16
Alignment explanation
Indices: 527900--527947 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
527890 AAAAAAAATT
527900 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
527916 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
527932 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
527948 CTTATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:528564 original size:26 final size:23
Alignment explanation
Indices: 528507--528567 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 23
528497 TAAATATAAA
528507 TATTTATTGTGTTTTTTATTTATT
1 TATTTATT-TGTTTTTTATTTATT
*
528531 TGA-GTATTTCGTTATTTTATTTTATT
1 T-ATTTATTT-GTT-TTTTA-TTTATT
528557 TATTTATTTGT
1 TATTTATTTGT
528568 CATATGACGT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
23 1 0.03
24 8 0.27
25 9 0.30
26 12 0.40
ACGTcount: A:0.18, C:0.02, G:0.10, T:0.70
Consensus pattern (23 bp):
TATTTATTTGTTTTTTATTTATT
Found at i:530110 original size:23 final size:22
Alignment explanation
Indices: 530054--530110 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
530044 ATAGTTGAAA
* *
530054 TATTTATAAAATTAAACTTTAT
1 TATTTATAAAATTAAAATTAAT
*
530076 T-TCTTATCAAATTAAAGATTAAT
1 TAT-TTATAAAATTAAA-ATTAAT
*
530099 TATTTATTAAAT
1 TATTTATAAAAT
530111 CTCTATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 1 0.04
22 13 0.46
23 13 0.46
24 1 0.04
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTATAAAATTAAAATTAAT
Found at i:532143 original size:15 final size:15
Alignment explanation
Indices: 532125--532180 Score: 76
Period size: 15 Copynumber: 3.6 Consensus size: 15
532115 TAACCGGTTT
532125 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
532140 CGGTTTTTTAAAAAAAC
1 CGG--TTTTAAAAAAAC
*
532157 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
532172 CGATTTTAA
1 CGGTTTTAA
532181 TATTCCAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 21 0.58
17 15 0.42
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:532150 original size:17 final size:17
Alignment explanation
Indices: 532128--532178 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
532118 CCGGTTTCGG
532128 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
532145 TTTTAAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
532160 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
532177 TT
1 TT
532179 AATATTCCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:532596 original size:13 final size:13
Alignment explanation
Indices: 532575--532629 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
532565 AAGTTCGATA
*
532575 AATTCAAATACTT
1 AATTGAAATACTT
532588 AATTGAAATACTT
1 AATTGAAATACTT
* *
532601 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
532615 AATTGAAATACTT
1 AATTGAAATACTT
532628 AA
1 AA
532630 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:532711 original size:32 final size:33
Alignment explanation
Indices: 532615--532713 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
532605 AACTCAACAT
* * *
532615 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
532648 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
532681 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
532713 A
1 A
532714 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:532732 original size:21 final size:21
Alignment explanation
Indices: 532708--532747 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
532698 ACTTCAAGTT
532708 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
532729 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
532748 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Done.