Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 4 of 16
Found at i:503979 original size:2 final size:2
Alignment explanation
Indices: 503972--503996 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
503962 GTTTCAAAAC
503972 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
503997 GAGATTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:505704 original size:16 final size:16
Alignment explanation
Indices: 505685--505723 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
505675 ATATTATTTA
*
505685 TAAATTTTATAAAATT
1 TAAATTTAATAAAATT
* *
505701 TAAAATAAATAAAATT
1 TAAATTTAATAAAATT
505717 TAAATTT
1 TAAATTT
505724 GTCCACTTTT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAATAAAATT
Found at i:507438 original size:17 final size:19
Alignment explanation
Indices: 507416--507451 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
507406 ATAAAGGAGG
507416 TTTTTC-CTTTTTT-TTTT
1 TTTTTCTCTTTTTTCTTTT
507433 TTTTTCTCTTTTTTCTTTT
1 TTTTTCTCTTTTTTCTTTT
507452 AATCCCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTCTCTTTTTTCTTTT
Found at i:510746 original size:56 final size:56
Alignment explanation
Indices: 510660--510771 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
510650 ATAATTATCA
510660 ACTTCAAGGCACAATGATCTGGTGCTCTAAATCATAAATCAAGGTTAAATTGGCTG
1 ACTTCAAGGCACAATGATCTGGTGCTCTAAATCATAAATCAAGGTTAAATTGGCTG
510716 ACTTCAAGGCACAATGATCTGGTGCTCTAAATCATAAATCAAGGTTAAATTGGCTG
1 ACTTCAAGGCACAATGATCTGGTGCTCTAAATCATAAATCAAGGTTAAATTGGCTG
510772 GGATTTGTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (56 bp):
ACTTCAAGGCACAATGATCTGGTGCTCTAAATCATAAATCAAGGTTAAATTGGCTG
Found at i:512580 original size:30 final size:26
Alignment explanation
Indices: 512544--512599 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 26
512534 TATTTTTAAC
512544 TAAATATTAAGATAGTAAATAAATATTTTT
1 TAAATATTAA-A-AGT-AA-AAATATTTTT
512574 TAAATATTAAAAGTAAAAATATTTTT
1 TAAATATTAAAAGTAAAAATATTTTT
512600 CATAAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 10 0.38
27 2 0.08
28 3 0.12
29 1 0.04
30 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (26 bp):
TAAATATTAAAAGTAAAAATATTTTT
Found at i:512841 original size:19 final size:19
Alignment explanation
Indices: 512817--512854 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
512807 ATGAATAATA
512817 TTATTATATTTTATATTAT
1 TTATTATATTTTATATTAT
512836 TTATTATATTTTATATTAT
1 TTATTATATTTTATATTAT
512855 AATCTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATATTTTATATTAT
Found at i:513180 original size:24 final size:24
Alignment explanation
Indices: 513146--513194 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
513136 TAAATAAGTT
*
513146 AATTAATTAATAATAA-TAAATAAA
1 AATTAAATAAT-ATAATTAAATAAA
*
513170 AATTAAATAATATAATTTAATAAA
1 AATTAAATAATATAATTAAATAAA
513194 A
1 A
513195 TAAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AATTAAATAATATAATTAAATAAA
Found at i:513191 original size:13 final size:13
Alignment explanation
Indices: 513124--513197 Score: 55
Period size: 13 Copynumber: 5.7 Consensus size: 13
513114 TAATTACTTG
513124 ATAAAATTAATTTAA
1 ATAAAA-TAA-TTAA
**
513139 ATAAGTTAATTAA
1 ATAAAATAATTAA
*
513152 TTAATAATAA-TAA
1 ATAA-AATAATTAA
513165 AT-AAA-AATTAA
1 ATAAAATAATTAA
* *
513176 ATAATATAATTTA
1 ATAAAATAATTAA
513189 ATAAAATAA
1 ATAAAATAA
513198 AAATTTATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
10 2 0.04
11 7 0.15
12 3 0.07
13 24 0.52
14 6 0.13
15 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (13 bp):
ATAAAATAATTAA
Found at i:514483 original size:26 final size:26
Alignment explanation
Indices: 514448--514504 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
514438 TATTTGTAAA
*
514448 TTTTATTATTTTAA-AATTAAATATAT
1 TTTTAATATTTTAATAATTAAATAT-T
**
514474 TTTTAATATTTTAATTTTTAAATATT
1 TTTTAATATTTTAATAATTAAATATT
514500 TTTTA
1 TTTTA
514505 TTTTTTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTAATATTTTAATAATTAAATATT
Found at i:514487 original size:8 final size:8
Alignment explanation
Indices: 514425--514501 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
514415 ATAAAATAAC
*
514425 TTTATTAT
1 TTTAATAT
*
514433 TTTTATAT
1 TTTAATAT
514441 TTGTAA-AT
1 TT-TAATAT
*
514449 TTTATTAT
1 TTTAATAT
*
514457 TTTAAAAT
1 TTTAATAT
**
514465 TAAATATATT
1 TTTA-ATA-T
514475 TTTAATAT
1 TTTAATAT
514483 TTTAAT-T
1 TTTAATAT
514490 TTTAAATAT
1 TTT-AATAT
514499 TTT
1 TTT
514502 TTATTTTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
7 6 0.12
8 32 0.62
9 11 0.21
10 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (8 bp):
TTTAATAT
Found at i:514560 original size:28 final size:28
Alignment explanation
Indices: 514504--514561 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
514494 AATATTTTTT
* *
514504 ATTTTTTACAATAATAATAAATATATAA
1 ATTTTTTAAAATAATAATAAAAATATAA
*
514532 ATTTTTTAAAATAATTAA-AAAAATTTAA
1 ATTTTTTAAAATAA-TAATAAAAATATAA
514560 AT
1 AT
514562 GATCGATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTTTTTAAAATAATAATAAAAATATAA
Found at i:515081 original size:2 final size:2
Alignment explanation
Indices: 515074--515113 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
515064 CCACCAGGTT
515074 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
515114 AGGTGAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:515766 original size:2 final size:2
Alignment explanation
Indices: 515759--515797 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
515749 CTTCTTTGTG
515759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
515798 GGTTACGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:519681 original size:31 final size:31
Alignment explanation
Indices: 519635--519707 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
519625 ATATTTAAGA
519635 TTTTTAAT-AATTTTTA-T-TAAAAAAAGCTC
1 TTTTTAATAAATTTTTACTGT-AAAAAAGCTC
* *
519664 TTTTTAAATAAATTTTTACTGTTAAAAAGCTTT
1 TTTTT-AATAAATTTTTACTGTAAAAAAGC-TC
519697 TTTTTAATAAA
1 TTTTTAATAAA
519708 AAAATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 5 0.14
30 3 0.08
31 8 0.22
32 14 0.38
33 7 0.19
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (31 bp):
TTTTTAATAAATTTTTACTGTAAAAAAGCTC
Found at i:521751 original size:3 final size:3
Alignment explanation
Indices: 521743--521779 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
521733 TTTTATTTAT
*
521743 TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
521780 GTTCCTCGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:522479 original size:20 final size:20
Alignment explanation
Indices: 522456--522515 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
522446 ATTAAAAACT
*
522456 TATTTTATTATTTAAAATAA
1 TATTTTAATATTTAAAATAA
* *
522476 TA-TTTAAAATTTTAAAATTA
1 TATTTTAATA-TTTAAAATAA
* *
522496 TTTTTTACTATTTAAAATAA
1 TATTTTAATATTTAAAATAA
522516 AATAGTTTCG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTTAATATTTAAAATAA
Found at i:522869 original size:10 final size:10
Alignment explanation
Indices: 522856--522955 Score: 50
Period size: 10 Copynumber: 10.2 Consensus size: 10
522846 TGTATAAAAA
522856 ATTTATTTAT
1 ATTTATTTAT
*
522866 ATTTATGTA-
1 ATTTATTTAT
522875 A-TT-TTTAT
1 ATTTATTTAT
*
522883 AATTT-TTTAC
1 -ATTTATTTAT
*
522893 A-TAATTTAT
1 ATTTATTTAT
522902 ATTTATTTA-
1 ATTTATTTAT
*
522911 ATTTAATTAT
1 ATTTATTTAT
* * *
522921 CGTATATTAAT
1 -ATTTATTTAT
522932 ATTTATATTAGT
1 ATTTAT-TTA-T
*
522944 ATTTATATAT
1 ATTTATTTAT
522954 AT
1 AT
522956 AAAATTTATA
Statistics
Matches: 66, Mismatches: 15, Indels: 18
0.67 0.15 0.18
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 16 0.24
10 27 0.41
11 10 0.15
12 7 0.11
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (10 bp):
ATTTATTTAT
Found at i:522964 original size:15 final size:15
Alignment explanation
Indices: 522944--522988 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
522934 TTATATTAGT
522944 ATTTATATATATAAA
1 ATTTATATATATAAA
522959 ATTTATATAT-TAAA
1 ATTTATATATATAAA
* * *
522973 TTTTAAATAAATAAA
1 ATTTATATATATAAA
522988 A
1 A
522989 ATATTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTATATATATAAA
Found at i:526585 original size:17 final size:18
Alignment explanation
Indices: 526542--526578 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
526532 AATAAATATT
*
526542 ATAAAATTTAAATTTTTA
1 ATAAAAATTAAATTTTTA
*
526560 ATAAAAATTAATTTTTTA
1 ATAAAAATTAAATTTTTA
526578 A
1 A
526579 AATAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAAAATTAAATTTTTA
Found at i:526893 original size:12 final size:12
Alignment explanation
Indices: 526878--526905 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
526868 CCAGAAAATT
526878 AAAAGAAAAAGG
1 AAAAGAAAAAGG
526890 AAAAGAAAAAGG
1 AAAAGAAAAAGG
526902 AAAA
1 AAAA
526906 TGGAGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGG
Found at i:531150 original size:108 final size:108
Alignment explanation
Indices: 530959--531176 Score: 400
Period size: 108 Copynumber: 2.0 Consensus size: 108
530949 TTTAATTTAC
*
530959 TTCGAAAAGGGAAAATTGATGTTTATGTGCTGTGCAATGTTGCATCCTTGCAGTGTCGGGATTAC
1 TTCGAAAAGGGAAAATTGATGTTTATGTGCTGTGCAATGTTACATCCTTGCAGTGTCGGGATTAC
*
531024 TTGAATAGATGCTTGGAAATTCAAGTACTTCAAAATATCACAT
66 TTGAATAGATGCTCGGAAATTCAAGTACTTCAAAATATCACAT
*
531067 TTCGAAAAGGGGAAATTGATGTTTATGTGCTGTGCAATGTTACATCCTTGCAGTGTCGGGATTAC
1 TTCGAAAAGGGAAAATTGATGTTTATGTGCTGTGCAATGTTACATCCTTGCAGTGTCGGGATTAC
*
531132 TTGAATAGATGCTCGGAAATTGAAGTACTTCAAAATATCACAT
66 TTGAATAGATGCTCGGAAATTCAAGTACTTCAAAATATCACAT
531175 TT
1 TT
531177 TGAGTTCTAT
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (108 bp):
TTCGAAAAGGGAAAATTGATGTTTATGTGCTGTGCAATGTTACATCCTTGCAGTGTCGGGATTAC
TTGAATAGATGCTCGGAAATTCAAGTACTTCAAAATATCACAT
Found at i:534926 original size:5 final size:5
Alignment explanation
Indices: 534916--534940 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
534906 TGCAAACATT
534916 AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA
534941 TGCACTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:535913 original size:25 final size:25
Alignment explanation
Indices: 535865--535913 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
535855 AATCTCCTTC
* *
535865 TAATAATTTAAAGAAGTTAGGATTA
1 TAATAATTTAAAGAAATTACGATTA
*
535890 TAATAATTTAAAGAAATTTCGATT
1 TAATAATTTAAAGAAATTACGATT
535914 CAATCTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (25 bp):
TAATAATTTAAAGAAATTACGATTA
Found at i:536871 original size:21 final size:21
Alignment explanation
Indices: 536803--536871 Score: 57
Period size: 23 Copynumber: 3.1 Consensus size: 21
536793 TACAATACTT
*
536803 ATATTTAAAAATTTTAAAAATA
1 ATATATAAAAATTTTAAAAA-A
* ***
536825 TATATATAAAAAATAATTATTTAA
1 -ATATAT-AAAAAT-TTTAAAAAA
536849 ATATATAAAAATTTTAAAAAA
1 ATATATAAAAATTTTAAAAAA
536870 AT
1 AT
536872 TAAATATATA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
21 7 0.20
22 6 0.17
23 11 0.31
24 7 0.20
25 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATATAAAAATTTTAAAAAA
Found at i:536893 original size:15 final size:15
Alignment explanation
Indices: 536873--536901 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
536863 TAAAAAAATT
536873 AAATATATATTTATC
1 AAATATATATTTATC
536888 AAATATATATTTAT
1 AAATATATATTTAT
536902 ATTTCACAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATATATTTATC
Found at i:538472 original size:11 final size:10
Alignment explanation
Indices: 538458--538521 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 10
538448 ATGAAAAAAA
538458 TTAAGTTATTT
1 TTAA-TTATTT
538469 TTAATATATTT
1 TTAAT-TATTT
538480 TTAATTATTT
1 TTAATTATTT
* *
538490 AT-ATTGTTTT
1 TTAATT-ATTT
538500 TTAATTTATTT
1 TTAA-TTATTT
*
538511 TTTATTATTT
1 TTAATTATTT
538521 T
1 T
538522 AATAATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
9 3 0.07
10 18 0.41
11 21 0.48
12 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (10 bp):
TTAATTATTT
Found at i:550708 original size:24 final size:22
Alignment explanation
Indices: 550662--550710 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
550652 TTACTTTAAA
*
550662 ATATATAAATATATTTTAACAT
1 ATATATAAATAAATTTTAACAT
*
550684 ATATATAAATTAAATTATTATCAT
1 ATATATAAA-TAAATT-TTAACAT
550708 ATA
1 ATA
550711 AAAATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 5 0.22
24 9 0.39
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATATAAATAAATTTTAACAT
Found at i:550757 original size:11 final size:10
Alignment explanation
Indices: 550735--550790 Score: 57
Period size: 11 Copynumber: 5.8 Consensus size: 10
550725 ATAAAATTAT
550735 TAATTAAATA
1 TAATTAAATA
550745 TAATTATAATA
1 TAATTA-AATA
*
550756 TAATAAAATA
1 TAATTAAATA
550766 T-A-TAAAT-
1 TAATTAAATA
550773 T-ATTAAATA
1 TAATTAAATA
550782 TAAATTAAA
1 T-AATTAAA
550791 GTGCTAGAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 2 0.05
8 9 0.23
9 2 0.05
10 11 0.28
11 15 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATTAAATA
Found at i:550960 original size:12 final size:12
Alignment explanation
Indices: 550945--550982 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
550935 ATATTAAAAA
550945 AATATTTATATT
1 AATATTTATATT
550957 AATATTTATA-T
1 AATATTTATATT
550968 AAT-TTTATAATT
1 AATATTTAT-ATT
550980 AAT
1 AAT
550983 TTATAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.21
11 5 0.21
12 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATATTTATATT
Found at i:550995 original size:12 final size:11
Alignment explanation
Indices: 550948--550998 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
550938 TTAAAAAAAT
*
550948 ATTTATATTAA
1 ATTTATAATAA
550959 TATTTAT-ATAA
1 -ATTTATAATAA
* *
550970 TTTTATAATTA
1 ATTTATAATAA
550981 ATTTATAATAAA
1 ATTTATAAT-AA
550993 ATTTAT
1 ATTTAT
550999 TTTTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
10 5 0.16
11 14 0.44
12 13 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTATAATAA
Found at i:551046 original size:10 final size:10
Alignment explanation
Indices: 551016--551048 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
551006 AAATAAATAA
551016 TAATTTAAATT
1 TAATTTAAA-T
551027 TAATTT-AAT
1 TAATTTAAAT
551036 TAATTTAAAT
1 TAATTTAAAT
551046 TAA
1 TAA
551049 AAAAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.33
10 8 0.38
11 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:557061 original size:14 final size:15
Alignment explanation
Indices: 557042--557072 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
557032 TAGAATCTGC
557042 AAAAAGAAAAA-AAA
1 AAAAAGAAAAAGAAA
557056 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
557071 AA
1 AA
557073 GGAATTAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Found at i:557970 original size:106 final size:107
Alignment explanation
Indices: 557838--558053 Score: 389
Period size: 110 Copynumber: 2.0 Consensus size: 107
557828 TTTATTTTCT
*
557838 TTCACCAACCACAAACAAAAATAATTTTGAAGAAAAAATTTTTC-TTTTTTTTTCTTTTTTTTGG
1 TTCACCAACCACAAACAAAAATAATTTTGAAGAAAAAATTTTTCTTTTTTTTTTCTTGTTTTTGG
557902 CCTGAGCGAATGAGTTTACCTCAGAAGGGAACTCCGCGCAGA
66 CCTGAGCGAATGAGTTTACCTCAGAAGGGAACTCCGCGCAGA
557944 TTCACCAACCACAAACAAAAATAATTTTGAAGAAAAAATTTTTCTTTTTTTTTTTTTCTTGTTTT
1 TTCACCAACCACAAACAAAAATAATTTTGAAGAAAAAATTTTTC---TTTTTTTTTTCTTGTTTT
558009 TGGCCTGAGCGAATGAGTTTACCTCAGAAGGGAACTCCGCGCAGA
63 TGGCCTGAGCGAATGAGTTTACCTCAGAAGGGAACTCCGCGCAGA
558054 GGCGCTCGCA
Statistics
Matches: 105, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
106 44 0.42
110 61 0.58
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (107 bp):
TTCACCAACCACAAACAAAAATAATTTTGAAGAAAAAATTTTTCTTTTTTTTTTCTTGTTTTTGG
CCTGAGCGAATGAGTTTACCTCAGAAGGGAACTCCGCGCAGA
Found at i:558200 original size:5 final size:5
Alignment explanation
Indices: 558163--558208 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
558153 TTTAGATTGG
* * *
558163 GAAACA GAAAA GAAAG GAAAA GGAAA GAAAA GAAAA GAAGA GAAAA
1 GAAA-A GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
558209 ATATGGAAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:558787 original size:14 final size:15
Alignment explanation
Indices: 558744--558793 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
558734 TAAAAACTAT
558744 ATTT-TTTATTATTA
1 ATTTATTTATTATTA
*
558758 ATGTAACTTTATTATTA
1 AT-TTA-TTTATTATTA
558775 ATTTATTTA-TATTA
1 ATTTATTTATTATTA
558789 ATTTA
1 ATTTA
558794 ATAATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 12 0.39
15 5 0.16
16 2 0.06
17 12 0.39
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
ATTTATTTATTATTA
Found at i:558825 original size:15 final size:16
Alignment explanation
Indices: 558807--558836 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
558797 ATAAAAAATT
558807 TTATATA-TTATTTTA
1 TTATATATTTATTTTA
558822 TTATATATTTATTTT
1 TTATATATTTATTTT
558837 CTAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATATATTTATTTTA
Found at i:563188 original size:18 final size:17
Alignment explanation
Indices: 563145--563191 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
563135 ATTAGTTATT
563145 ATTTA-TTTAATATTAA
1 ATTTATTTTAATATTAA
**
563161 AAATATTTTTAATATTTAA
1 ATTTA-TTTTAATA-TTAA
563180 ATTTATTTTAAT
1 ATTTATTTTAAT
563192 TCAGATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
18 14 0.58
19 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTATTTTAATATTAA
Found at i:566013 original size:5 final size:5
Alignment explanation
Indices: 566003--566130 Score: 54
Period size: 5 Copynumber: 26.0 Consensus size: 5
565993 TATCATATTA
* * * * * * *
566003 TATAT TTTAT TATAT TATAAT TATTT TTTAT T-TAT ATAAAT TTTAA TATTT
1 TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT -TATAT TATAT TATAT
* * *
566054 TA-AT AAT-T TATAT TATA- TATATT TAAAAT TAT-T TATAT TATAT TTTA-
1 TATAT TATAT TATAT TATAT TATA-T T-ATAT TATAT TATAT TATAT TATAT
* *
566101 TATTT TA-AT TATTT TATAT TATAT TCATAT
1 TATAT TATAT TATAT TATAT TATAT T-ATAT
566131 CGCATATTAA
Statistics
Matches: 88, Mismatches: 23, Indels: 23
0.66 0.17 0.17
Matches are distributed among these distances:
4 21 0.24
5 51 0.58
6 14 0.16
7 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:566019 original size:17 final size:18
Alignment explanation
Indices: 565997--566096 Score: 73
Period size: 17 Copynumber: 5.5 Consensus size: 18
565987 CCAACGTATC
565997 ATATTATAT-ATTTTATT
1 ATATTATATAATTTTATT
*
566014 ATATTATAATTATTTT-TT
1 ATATTAT-ATAATTTTATT
*
566032 AT-TTATATAAATTTTAAT
1 ATATTATAT-AATTTTATT
*
566050 ATTTTA-ATAATTTATATT
1 ATATTATATAATTT-TATT
* **
566068 ATATATATTTAAAATTATTT
1 ATAT-TATATAATTTTA-TT
566088 ATATTATAT
1 ATATTATAT
566097 TTTATATTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.03
17 21 0.32
18 17 0.26
19 16 0.24
20 10 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTATATAATTTTATT
Found at i:566101 original size:16 final size:17
Alignment explanation
Indices: 565997--566130 Score: 75
Period size: 16 Copynumber: 7.8 Consensus size: 17
565987 CCAACGTATC
*
565997 ATATTATA-TATTTTATT
1 ATATTATATTATATT-TT
*
566014 ATATTATAATTATTTTTT
1 ATATTAT-ATTATATTTT
*
566032 AT-TTATA-TAAATTTT
1 ATATTATATTATATTTT
* *
566047 AATATT-T-TAATAATTT
1 -ATATTATATTATATTTT
*
566063 ATATTATA-TATATTTAAA
1 ATATTATATTATATTT--T
566081 ATTATTTATATTATATTTT
1 A-TA-TTATATTATATTTT
* *
566100 ATATTTTAAT-TATTTT
1 ATATTATATTATATTTT
566116 ATATTATATTCATAT
1 ATATTATATT-ATAT
566131 CGCATATTAA
Statistics
Matches: 90, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
15 11 0.12
16 29 0.32
17 18 0.20
18 11 0.12
19 9 0.10
20 5 0.06
21 7 0.08
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTATATTATATTTT
Found at i:566112 original size:23 final size:23
Alignment explanation
Indices: 566048--566120 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
566038 ATAAATTTTA
566048 ATATTTTAATAATTTATATTATA-T
1 ATATTTT-ATAATTTA-ATTATATT
* *
566072 ATA-TTTA-AAATTATTTATATT
1 ATATTTTATAATTTAATTATATT
* *
566093 ATATTTTATATTTTAATTATTTT
1 ATATTTTATAATTTAATTATATT
566116 ATATT
1 ATATT
566121 ATATTCATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
20 5 0.12
21 9 0.22
22 5 0.12
23 18 0.45
24 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTTTATAATTTAATTATATT
Found at i:566951 original size:27 final size:27
Alignment explanation
Indices: 566910--566965 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
566900 AAGTAACATC
* *
566910 AATATTTTATATTAATTTTTAAATTTTA
1 AATATATTATATTAAATTTT-AATTTTA
566938 AATATATTA-ATTAAATTTTAATTTTA
1 AATATATTATATTAAATTTTAATTTTA
566964 AA
1 AA
566966 ACTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 9 0.35
27 9 0.35
28 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AATATATTATATTAAATTTTAATTTTA
Found at i:566975 original size:26 final size:27
Alignment explanation
Indices: 566910--566977 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
566900 AAGTAACATC
* *
566910 AATATTTTATATTAATTTTTAAATTTTA
1 AATA-TTTAAATTAAATTTTAAATTTTA
566938 AATATATT-AATTAAATTTT-AATTTTA
1 AATAT-TTAAATTAAATTTTAAATTTTA
566964 AA-ACTTTAAATTAA
1 AATA-TTTAAATTAA
566978 TTAAGTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
25 3 0.09
26 16 0.46
27 10 0.29
28 6 0.17
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
AATATTTAAATTAAATTTTAAATTTTA
Found at i:567162 original size:31 final size:27
Alignment explanation
Indices: 567124--567190 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 27
567114 AATTTAATTG
*
567124 ATATATTTTAAAAGTTTTAAATTAATATAAA
1 ATATA-TTTAAAA--TTTAAA-AAATATAAA
567155 ATATATTTAAAATTTAAAAAATATAAA
1 ATATATTTAAAATTTAAAAAATATAAA
* *
567182 TTAAATTTA
1 ATATATTTA
567191 GTAAAATCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 15 0.45
28 6 0.18
30 7 0.21
31 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATATTTAAAATTTAAAAAATATAAA
Found at i:567196 original size:21 final size:20
Alignment explanation
Indices: 567149--567197 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
567139 TTTAAATTAA
*
567149 TATAAAATATATTTAAAATT
1 TATAAAATATAATTAAAATT
*
567169 TAAAAAATATAAATT-AAATT
1 TATAAAATAT-AATTAAAATT
567189 TAGTAAAAT
1 TA-TAAAAT
567198 CCCGAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TATAAAATATAATTAAAATT
Found at i:576886 original size:17 final size:18
Alignment explanation
Indices: 576841--576902 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 18
576831 ATCTTTAAAG
576841 TTAATTATAAAAATATATAAAT
1 TTAA-TATAAAAATATAT---T
576863 ATTAATATAAAAATAT-TT
1 -TTAATATAAAAATATATT
**
576881 TTAATATATTAATATATT
1 TTAATATAAAAATATATT
576899 TTAA
1 TTAA
576903 ATAGTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 13 0.36
18 7 0.19
21 1 0.03
22 11 0.31
23 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATATAAAAATATATT
Found at i:576910 original size:18 final size:17
Alignment explanation
Indices: 576864--576914 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
576854 TATATAAATA
**
576864 TTAATATAAAAATATTT
1 TTAATATATTAATATTT
576881 TTAATATATTAATATATT
1 TTAATATATTAATAT-TT
576899 TTAA-ATAGTTAA-ATTT
1 TTAATATA-TTAATATTT
576915 GTTTTTTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 2 0.07
17 18 0.60
18 10 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTAATATATTAATATTT
Found at i:577722 original size:3 final size:3
Alignment explanation
Indices: 577714--577747 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
577704 TACCGCCATG
577714 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
577748 CAAATTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:577879 original size:2 final size:2
Alignment explanation
Indices: 577872--577905 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
577862 CAGAAAAAGA
577872 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
577906 TAAAGCAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:582717 original size:15 final size:16
Alignment explanation
Indices: 582697--582726 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
582687 ATTTTTTTAA
582697 ATAATAAAA-AATTTC
1 ATAATAAAATAATTTC
582712 ATAATAAAATAATTT
1 ATAATAAAATAATTT
582727 TAATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATAAAATAATTTC
Found at i:582814 original size:21 final size:22
Alignment explanation
Indices: 582772--582819 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
582762 TAATTTATAA
582772 TTTATAATATAAATTAAAAAATT
1 TTTATAATATAAATT-AAAAATT
582795 TTTATGAA-ATAAATT-AAAATT
1 TTTAT-AATATAAATTAAAAATT
582816 TTTA
1 TTTA
582820 GATTCCAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.42
23 12 0.50
24 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TTTATAATATAAATTAAAAATT
Found at i:584326 original size:20 final size:19
Alignment explanation
Indices: 584294--584333 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
584284 TAATTGAAAT
* *
584294 TAATTTTATAAATATTAAA
1 TAATTTTAAAAATAATAAA
584313 TAATTTATAAAAATAATAAA
1 TAATTT-TAAAAATAATAAA
584333 T
1 T
584334 TTTTATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTTTAAAAATAATAAA
Found at i:584354 original size:17 final size:15
Alignment explanation
Indices: 584334--584368 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
584324 AATAATAAAT
584334 TTTTATTTATATTTATA
1 TTTTA-TTATATTT-TA
584351 TTTTATTATATTTTA
1 TTTTATTATATTTTA
584366 TTT
1 TTT
584369 CTCCTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 8 0.44
17 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTATATTTTA
Found at i:585403 original size:29 final size:30
Alignment explanation
Indices: 585368--585446 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
585358 ACAAATTATT
*
585368 AAAATTAAAATTTTAAT-T-AATATATTTTA
1 AAAATTAAAA-ATTAATATAAATATATTTTA
585397 AAAATTAAAAATTAATATAAAATATATTTTA
1 AAAATTAAAAATTAATAT-AAATATATTTTA
*
585428 AAATTTAAAAATTATATAT
1 AAAATTAAAAATTA-ATAT
585447 TAGATAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 5 0.11
29 11 0.25
31 24 0.55
32 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AAAATTAAAAATTAATATAAATATATTTTA
Found at i:585408 original size:30 final size:30
Alignment explanation
Indices: 585368--585458 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 30
585358 ACAAATTATT
585368 AAAATT-AAAATTTTAATTAATATATTTTA
1 AAAATTAAAAATTTTAATTAATATATTTTA
585397 AAAATTAAAAA--TTAATATAAAATATATTTTA
1 AAAATTAAAAATTTTAAT-T--AATATATTTTA
* *
585428 AAATTTAAAAATTATATATTAGATAATATTT
1 AAAATTAAAAATTTTA-ATTA-AT-ATATTT
585459 AATTAATATG
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
28 5 0.10
29 7 0.14
30 4 0.08
31 22 0.43
32 2 0.04
33 9 0.18
34 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (30 bp):
AAAATTAAAAATTTTAATTAATATATTTTA
Found at i:585424 original size:31 final size:32
Alignment explanation
Indices: 585386--585446 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
585376 AATTTTAATT
585386 AATATATTTTAAAAATTAAAAATTA-ATATAA
1 AATATATTTTAAAAATTAAAAATTATATATAA
*
585417 AATATATTTTAAAATTTAAAAATTATATAT
1 AATATATTTTAAAAATTAAAAATTATATAT
585447 TAGATAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AATATATTTTAAAAATTAAAAATTATATATAA
Found at i:586525 original size:2 final size:2
Alignment explanation
Indices: 586518--586543 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
586508 TAGCTTAATA
586518 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
586544 TTGTTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:587063 original size:17 final size:16
Alignment explanation
Indices: 587026--587069 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
587016 TGAGTTAAAA
587026 AATTATAAAA-ATAAT
1 AATTATAAAATATAAT
**
587041 TTTTATAAAATTATAAT
1 AATTATAAAA-TATAAT
587058 AATTATAAAATA
1 AATTATAAAATA
587070 AGGAATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTATAAAATATAAT
Found at i:587309 original size:19 final size:19
Alignment explanation
Indices: 587287--587323 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
587277 ATATCAAATC
587287 AATTAAAAAATTACAATAA
1 AATTAAAAAATTACAATAA
* *
587306 AATTAATAAATTATAATA
1 AATTAAAAAATTACAATA
587324 TTAAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTAAAAAATTACAATAA
Found at i:587506 original size:18 final size:18
Alignment explanation
Indices: 587483--587538 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 18
587473 TATTTAAAAT
587483 ATTTTATATTTATTATAA
1 ATTTTATATTTATTATAA
*
587501 ATTTTA-ATATATTA-ATA
1 ATTTTATATTTATTATA-A
587518 A-TTTATA-TTA-TATAA
1 ATTTTATATTTATTATAA
587533 ATTTTA
1 ATTTTA
587539 AAAATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 4 0.12
16 12 0.38
17 10 0.31
18 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTATATTTATTATAA
Found at i:588523 original size:28 final size:27
Alignment explanation
Indices: 588483--588537 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
588473 AACAATTCAA
*
588483 AAAAATTATGACAAAATTCAACAAAAT
1 AAAAATTATGACAAAATTAAACAAAAT
* *
588510 AAAATTTAGTGACAAAATTAAATAAAAT
1 AAAAATTA-TGACAAAATTAAACAAAAT
588538 CAAACTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (27 bp):
AAAAATTATGACAAAATTAAACAAAAT
Found at i:589310 original size:15 final size:14
Alignment explanation
Indices: 589283--589339 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
589273 TGTATTTGTT
*
589283 TTAATTAAAATTT-
1 TTAATTTAAATTTA
589296 TTAAATTTTAAATTTA
1 TT-AA-TTTAAATTTA
*
589312 TTAATTTAAATTAA
1 TTAATTTAAATTTA
589326 TTCAATTT-AATTTA
1 TT-AATTTAAATTTA
589340 AATTAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.05
14 18 0.49
15 15 0.41
16 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAATTTAAATTTA
Found at i:589326 original size:10 final size:10
Alignment explanation
Indices: 589311--589361 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
589301 TTTTAAATTT
589311 ATTAATTTAA
1 ATTAATTTAA
*
589321 ATTAATTCAA
1 ATTAATTTAA
*
589331 TTTAATTTAA
1 ATTAATTTAA
589341 ATTAA-TTAA
1 ATTAATTTAA
* *
589350 TTTATTTTAA
1 ATTAATTTAA
589360 AT
1 AT
589362 AAAATTCTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
9 7 0.21
10 26 0.79
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:589337 original size:20 final size:19
Alignment explanation
Indices: 589312--589361 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 19
589302 TTTAAATTTA
589312 TTAATTTAAATTAATTCAAT
1 TTAATTTAAATTAATT-AAT
589332 TTAATTTAAATTAATTAAT
1 TTAATTTAAATTAATTAAT
*
589351 TTATTTTAAAT
1 TTAATTTAAAT
589362 AAAATTCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATTTAAATTAATTAAT
Found at i:589359 original size:14 final size:14
Alignment explanation
Indices: 589302--589347 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
589292 ATTTTTAAAT
*
589302 TTTAAATTTATTAA
1 TTTAAATTAATTAA
589316 TTTAAATTAATTCAA
1 TTTAAATTAATT-AA
*
589331 TTTAATTTAAATTAA
1 TTTAAATT-AATTAA
589346 TT
1 TT
589348 AATTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.39
15 13 0.46
16 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTAAATTAATTAA
Found at i:589366 original size:24 final size:24
Alignment explanation
Indices: 589320--589367 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
589310 TATTAATTTA
* *
589320 AATTAATTCAATTTAATTTAAATT
1 AATTAATTCAATTTAAATAAAATT
* *
589344 AATTAATTTATTTTAAATAAAATT
1 AATTAATTCAATTTAAATAAAATT
589368 CTCATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTAATTCAATTTAAATAAAATT
Found at i:589676 original size:16 final size:18
Alignment explanation
Indices: 589655--589688 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
589645 TTAATTTTAT
589655 TATTAATT-TA-TTAAAA
1 TATTAATTATATTTAAAA
589671 TATTAATTATATTTAAAA
1 TATTAATTATATTTAAAA
589689 ATATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTAATTATATTTAAAA
Found at i:597324 original size:2 final size:2
Alignment explanation
Indices: 597319--597343 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
597309 ATCTCCTCTC
597319 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 T
597344 GACATTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:597882 original size:12 final size:12
Alignment explanation
Indices: 597865--597897 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
597855 TAATAATTTT
*
597865 AAATATGATATA
1 AAATATAATATA
597877 AAATATAATAT-
1 AAATATAATATA
597888 AAATATAATA
1 AAATATAATA
597898 CATTTAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
AAATATAATATA
Found at i:598012 original size:17 final size:17
Alignment explanation
Indices: 597984--598033 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 17
597974 TATATTATTA
597984 TAATTATATTTAAAATTT
1 TAATTATATTTAAAA-TT
598002 TAATT-TATTTAATAATT
1 TAATTATATTTAA-AATT
598019 TATATTATATTTAAA
1 TA-ATTATATTTAAA
598034 TTACACACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 11 0.38
18 11 0.38
19 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTATATTTAAAATT
Found at i:598035 original size:17 final size:19
Alignment explanation
Indices: 597981--598033 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
597971 ATATATATTA
597981 TTATAATTATATTTAAAAT
1 TTATAATTATATTTAAAAT
598000 TT-TAATT-TATTTAATAAT
1 TTATAATTATATTTAA-AAT
598018 TTAT-ATTATATTTAAA
1 TTATAATTATATTTAAA
598034 TTACACACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.23
18 14 0.45
19 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATAATTATATTTAAAAT
Found at i:598747 original size:31 final size:30
Alignment explanation
Indices: 598697--598759 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
598687 ATAATTATTT
*
598697 AATATTTAATATTATTTTAAATAATAAA-ATA
1 AATATTTAATATTAATTT-AAT-ATAAATATA
598728 AATATTTAA-ATATAATTTAATATAAATATA
1 AATATTTAATAT-TAATTTAATATAAATATA
598758 AA
1 AA
598760 AAATAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 14 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AATATTTAATATTAATTTAATATAAATATA
Found at i:599448 original size:10 final size:10
Alignment explanation
Indices: 599423--599460 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
599413 TGTTTATATT
599423 ATTTATAA-A
1 ATTTATAATA
599432 ATTTATAATA
1 ATTTATAATA
*
599442 TTTTATAATA
1 ATTTATAATA
599452 ATTTATAAT
1 ATTTATAAT
599461 TTATAATCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTATAATA
Found at i:599467 original size:17 final size:19
Alignment explanation
Indices: 599415--599460 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
599405 TTATTTATTG
*
599415 TTTATATTATTTATAA-AA
1 TTTATAATATTTATAATAA
599433 TTTATAATATTTTATAATAA
1 TTTATAATA-TTTATAATAA
599453 TTTATAAT
1 TTTATAAT
599461 TTATAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.32
19 7 0.28
20 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATAATATTTATAATAA
Found at i:600741 original size:16 final size:16
Alignment explanation
Indices: 600722--600755 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
600712 AATACTTGAC
*
600722 TATTTTATGAAATAAA
1 TATTTAATGAAATAAA
*
600738 TATTTAATGAATTAAA
1 TATTTAATGAAATAAA
600754 TA
1 TA
600756 ATTATATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TATTTAATGAAATAAA
Found at i:601199 original size:6 final size:6
Alignment explanation
Indices: 601188--601213 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
601178 ACTTTGACCC
601188 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
601214 TAACAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:601959 original size:14 final size:14
Alignment explanation
Indices: 601942--601984 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
601932 AAAAATAATT
*
601942 AATTAAATATAAAA
1 AATTTAATATAAAA
*
601956 AATTTACTA-AAAA
1 AATTTAATATAAAA
601969 TAATTTAATATAAAA
1 -AATTTAATATAAAA
601984 A
1 A
601985 CTTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.17
14 16 0.67
15 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTTAATATAAAA
Found at i:603486 original size:21 final size:20
Alignment explanation
Indices: 603449--603491 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
603439 GTTAATTTAG
* *
603449 TTTTATATATTTTTATTAAT
1 TTTTATAAATTTATATTAAT
*
603469 TTTTATAAAATTTATATTTAT
1 TTTTAT-AAATTTATATTAAT
603490 TT
1 TT
603492 ATTTCGATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATAAATTTATATTAAT
Found at i:603917 original size:2 final size:2
Alignment explanation
Indices: 603901--603948 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
603891 ATTTAGCCCT
* *
603901 TA TA TA CA TA CA 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
603943 TA TA TA
1 TA TA TA
603949 GCTAGGTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:604389 original size:120 final size:114
Alignment explanation
Indices: 604175--604408 Score: 378
Period size: 120 Copynumber: 2.0 Consensus size: 114
604165 AATTAAGGCC
*
604175 AAATTAATTAAATGTTTATTCACATAATTTGATGCATATATATATATACATAAGTACAAATAAAT
1 AAATTAATTAAATGTTTATTCACATAATTTGATGCATATATATATATACATAAATACAAATAAAT
*
604240 GACAAGCTACTATTTCATTAATGAATACATTTAAAAATATGAGGTTTTT
66 GACAAGCTACTATTTCATTAATGAATACATTTAAAAATATGAAGTTTTT
*
604289 AAATTAATTAAATGTTTATTCACATAATTTGATGCATATATATATATATATATATATAGACACAA
1 AAATTAATTAAATGTTTATTCACATAATTTGATGCATATATATATATACATA-A-AT--ACA-AA
*
604354 GTAAATGACAAGCTACTATTTCATTAATGAATACATTTAAAAATTTGAAGTTTTT
61 -TAAATGACAAGCTACTATTTCATTAATGAATACATTTAAAAATATGAAGTTTTT
604409 TTTAAAAGAA
Statistics
Matches: 110, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
114 51 0.46
115 1 0.01
116 1 0.01
118 3 0.03
119 2 0.02
120 52 0.47
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (114 bp):
AAATTAATTAAATGTTTATTCACATAATTTGATGCATATATATATATACATAAATACAAATAAAT
GACAAGCTACTATTTCATTAATGAATACATTTAAAAATATGAAGTTTTT
Found at i:604605 original size:2 final size:2
Alignment explanation
Indices: 604600--604647 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
604590 CATATATGTG
*
604600 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA 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
604642 TA -A TA T
1 TA TA TA T
604648 TCTTTCACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:605952 original size:2 final size:2
Alignment explanation
Indices: 605945--605973 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
605935 ATGCACTTCA
605945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
605974 ATAATTTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:608057 original size:12 final size:12
Alignment explanation
Indices: 608040--608066 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
608030 ATGAACAGTC
608040 ATACATATATAT
1 ATACATATATAT
608052 ATACATATATAT
1 ATACATATATAT
608064 ATA
1 ATA
608067 TATTTACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATACATATATAT
Found at i:608865 original size:2 final size:2
Alignment explanation
Indices: 608858--608883 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
608848 TCACATTATT
608858 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
608884 GTCATAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:609062 original size:10 final size:10
Alignment explanation
Indices: 609049--609074 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
609039 TCTTTTTTAT
609049 TAAAAAAATA
1 TAAAAAAATA
609059 TAAAAAAATA
1 TAAAAAAATA
609069 TAAAAA
1 TAAAAA
609075 TCAAGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:610392 original size:1 final size:1
Alignment explanation
Indices: 610386--610410 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
610376 TGAAATTTGC
610386 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
610411 CTGATGGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:612041 original size:12 final size:12
Alignment explanation
Indices: 612014--612094 Score: 60
Period size: 12 Copynumber: 6.7 Consensus size: 12
612004 ATTTATAAAA
*
612014 AAATATAATTAAT
1 AAAT-TAATTATT
*
612027 AAATTAATTTTT
1 AAATTAATTATT
*
612039 AAAATAATATATT
1 AAATTAAT-TATT
*
612052 AAATAAAAATT-TT
1 AAAT--TAATTATT
*
612065 AAATTAATAATT
1 AAATTAATTATT
612077 AAA-TAATTATT
1 AAATTAATTATT
612088 -AATTAAT
1 AAATTAAT
612095 GTCTGTGTGC
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
10 2 0.04
11 14 0.26
12 18 0.33
13 16 0.30
14 1 0.02
15 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATTAATTATT
Found at i:613006 original size:34 final size:33
Alignment explanation
Indices: 612958--613178 Score: 248
Period size: 34 Copynumber: 6.5 Consensus size: 33
612948 TGGTAAAAAC
*
612958 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
612991 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
613025 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
613059 TTCTCATTTAATCAACAATTGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
613093 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
613127 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
613161 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
613179 TCTCCCACTT
Statistics
Matches: 158, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
33 22 0.14
34 130 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:613074 original size:68 final size:67
Alignment explanation
Indices: 612960--613178 Score: 278
Period size: 68 Copynumber: 3.2 Consensus size: 67
612950 GTAAAAACCA
* * *
612960 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
613025 CAC
65 CAC
* * * * *
613028 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATTGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
613093 CTC
65 CAC
* * * * *
613096 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
613161 CA-
65 CAC
613163 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
613179 TCTCCCACTT
Statistics
Matches: 129, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
67 17 0.13
68 111 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:613102 original size:102 final size:101
Alignment explanation
Indices: 612958--613179 Score: 354
Period size: 102 Copynumber: 2.2 Consensus size: 101
612948 TGGTAAAAAC
* * *
612958 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATTGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
613023 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * *
613059 TTCTCATTTAATCAACAATTGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATTGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
613124 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
613161 CACCATTTAATCAACAATT
1 CACCATTTAATCAACAATT
613180 CTCCCACTTG
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 17 0.16
102 92 0.84
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATTGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:617633 original size:34 final size:33
Alignment explanation
Indices: 617585--617803 Score: 244
Period size: 34 Copynumber: 6.5 Consensus size: 33
617575 TGGTAAAAAC
*
617585 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
617618 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
617652 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
617686 TTCTCATTTAATCAACAATTGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
617720 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
617754 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
617788 CACCATTTAATCAACA
1 CACCATTTAATCAACA
617804 GTTTTTGGTA
Statistics
Matches: 156, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
33 20 0.13
34 130 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:617701 original size:68 final size:67
Alignment explanation
Indices: 617587--617803 Score: 274
Period size: 68 Copynumber: 3.2 Consensus size: 67
617577 GTAAAAACCA
* * *
617587 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
617652 CAC
65 CAC
* * * * *
617655 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATTGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
617720 CTC
65 CAC
* * * * *
617723 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
617788 CA-
65 CAC
617790 CCATTTAATCAACA
1 CCATTTAATCAACA
617804 GTTTTTGGTA
Statistics
Matches: 127, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
67 15 0.12
68 111 0.87
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:617729 original size:102 final size:101
Alignment explanation
Indices: 617585--617803 Score: 348
Period size: 102 Copynumber: 2.2 Consensus size: 101
617575 TGGTAAAAAC
* *
617585 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
617650 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * * *
617686 TTCTCATTTAATCAACAATTGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
617751 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
617788 CACCATTTAATCAACA
1 CACCATTTAATCAACA
617804 GTTTTTGGTA
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 14 0.13
102 92 0.87
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:618400 original size:18 final size:19
Alignment explanation
Indices: 618353--618400 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
618343 TTATTTATTT
*
618353 TTTAAAATAA-TGATAATT
1 TTTAAAATAATTGATAATA
* *
618371 TTTAAATTAATTTATAA-A
1 TTTAAAATAATTGATAATA
618389 TTTAAAATAATT
1 TTTAAAATAATT
618401 AATTGTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTAAAATAATTGATAATA
Found at i:623371 original size:24 final size:23
Alignment explanation
Indices: 623309--623371 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
623299 AGAGTGAATT
623309 TAAACAAATATCAT-AATATTTAAA
1 TAAA-AAATAT-ATAAATATTTAAA
** *
623333 T-AATGATATAAAAATATTTTAAA
1 TAAAAAATATATAAATA-TTTAAA
623356 TAAAAAATATATAAAT
1 TAAAAAATATATAAAT
623372 TATATGAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
21 1 0.03
22 8 0.27
23 9 0.30
24 12 0.40
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAAATATATAAATATTTAAA
Found at i:633073 original size:31 final size:30
Alignment explanation
Indices: 633036--633107 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
633026 ATTAAATAGA
633036 TTAAATTAATTTAAATT-AATT-TGTTTAAGTT
1 TTAAATT-ATTTAAATTGAATTAT-TTT-AGTT
* *
633067 TTAAATTTTTTAATTTGAATTATTTTAGTT
1 TTAAATTATTTAAATTGAATTATTTTAGTT
*
633097 TTAAATCATTT
1 TTAAATTATTT
633108 TAGTTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 20 0.57
31 14 0.40
32 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (30 bp):
TTAAATTATTTAAATTGAATTATTTTAGTT
Found at i:633078 original size:16 final size:16
Alignment explanation
Indices: 633053--633142 Score: 62
Period size: 16 Copynumber: 5.7 Consensus size: 16
633043 AATTTAAATT
633053 AATTTGTTTAAGTTTTA
1 AATTT-TTTAAGTTTTA
*
633070 AATTTTTTAA--TTTG
1 AATTTTTTAAGTTTTA
633084 AATTATTTT-AGTTTTA
1 AATT-TTTTAAGTTTTA
*
633100 AATCATTTT-AGTTTTA
1 AAT-TTTTTAAGTTTTA
* ** *
633116 AATTATTTCGGATTTA
1 AATTTTTTAAGTTTTA
*
633132 AATTATTTAAG
1 AATTTTTTAAG
633143 AATCGAATCA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
14 8 0.14
15 7 0.12
16 39 0.66
17 5 0.08
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (16 bp):
AATTTTTTAAGTTTTA
Found at i:633222 original size:37 final size:37
Alignment explanation
Indices: 633150--633222 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
633140 AAGAATCGAA
* * * *
633150 TCAATTAAGTTTAATATTTGAATTAATTTATTTTGAG
1 TCAATTAAGTTTAACATTTGAATTAACTGAGTTTGAG
*
633187 TCAATT-AGATTTAACATTTGAATTTACTGAGTTTGA
1 TCAATTAAG-TTTAACATTTGAATTAACTGAGTTTGA
633223 TCATTTTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 2 0.07
37 28 0.93
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (37 bp):
TCAATTAAGTTTAACATTTGAATTAACTGAGTTTGAG
Found at i:635121 original size:6 final size:6
Alignment explanation
Indices: 635110--635135 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
635100 AATTTTGTAC
635110 TCAACT TCAACT TCAACT TCAACT TC
1 TCAACT TCAACT TCAACT TCAACT TC
635136 TTGCTGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (6 bp):
TCAACT
Found at i:635663 original size:38 final size:38
Alignment explanation
Indices: 635621--635693 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
635611 TTCATTATTT
635621 ATTTTTG-ATATATTTTTAAATATA-AATATAAAAATATA
1 ATTTTTGAATA-ATTTTTAAATATATAATA-AAAAATATA
*
635659 ATTTTTTAATAATTTTTAAATATATAATAAAAAAT
1 ATTTTTGAATAATTTTTAAATATATAATAAAAAAT
635694 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
ATTTTTGAATAATTTTTAAATATATAATAAAAAATATA
Found at i:635817 original size:411 final size:414
Alignment explanation
Indices: 635016--635849 Score: 1028
Period size: 411 Copynumber: 2.0 Consensus size: 414
635006 GCTTTCTTTA
*
635016 TCAGTAAAATATTGTTCAACTAGCACTTCTATTTGACTGCTCAGCTTAGCCTAATGGGTATTTTT
1 TCAGTAAAATATTGTTCAACTAGCACTTCTATTTGACTGCTCAGCTTAGCCTAATGAGTA-TTTT
635081 TTTTTTTAACGCCCCATAGAATTTTGTACTCAACTTCAACTTCAACTTCAACTTCTTGCTGTTTG
65 TTTTTTTAACGCCCCATAGAATTTTGTACT-AACTTCAACTTCAACTTCAA----TTGCTGTTTG
* ** ** *
635146 GAGTAATTTTAACCAATGTTGCTCCCATTTTCAATTTTTTCTTAAAATATCTATGTTTGTCGTTT
125 GAGTAATTTTAACCAATGTTGCTCCCATTTTCAATTTGTTCTTAAAATATCTACATTCATCATTT
* *
635211 AATTCTGATATATTTTTAAATAAGTATACATATATATAATTTTTCAATAATTTTTAAATATATAA
190 AATTCTGATATATTTTTAAATAAATATACATAAATATAATTTTTCAATAATTTTTAAATATATAA
* * * * *
635276 AAAATTTTAAAAATAAATATATTTTTATTAAACACATATTCATATCTCATATTTACATTTAAATT
255 AAAATTTAAAAAATAAATATATTTATATTAAACACATAATCAAATCTCATACTTACATTTAAATT
* * * * *
635341 CGAATAACATAAATTTTAACTCATGTATTTTTATATAAAGACAGACCAGGGCAAATGAACATAGG
320 CAAATAACATAAATTTTAACACATATATTTTTATATAAAGAAAGACCAGGACAAATGAACATAGG
* *
635406 TTGACTCTCTTCCTTTCCTCGTAAATTTCT
385 TTGACTCTCCTCATTTCCTCGTAAATTTCT
*
635436 TCAGTAAAATATTGTTCAACTAGCACTTAAATTCTATTTGACTGCTCAGCTTAGCCTTATGAGTA
1 TCAGTAAAATATTGTTCAACTAGCAC-----TTCTATTTGACTGCTCAGCTTAGCCTAATGAGTA
* * * *
635501 -TTTTTTTTTTAATGCCCCTTA-TATTTT-T-GT-ACTT-AACTTCAACTT-AA-TGCTGTTTGG
61 TTTTTTTTTTTAACGCCCCATAGAATTTTGTACTAACTTCAACTTCAACTTCAATTGCTGTTTGG
* * * ** * *
635558 AGTTATTTTAATCAATGTTGCTCTCATTTTTTATTTGTT-TTAAAATATTTACATTCATTATTTA
126 AGTAATTTTAACCAATGTTGCTCCCATTTTCAATTTGTTCTTAAAATATCTACATTCATCATTTA
* * *
635622 TTTTTGATATATTTTTAAATATAAATATA-A-AAATATAATTTTTTAATAATTTTTAAATATATA
191 ATTCTGATATATTTTT-AA-ATAAATATACATAAATATAATTTTTCAATAATTTTT-AA-ATAT-
* * * ** *
635685 ATAAAAAATTTAAAAAATAAATATATTTATATTAGATATATAATCAAATCTTGTACTTATATTTA
251 ATAAAAAATTTAAAAAATAAATATATTTATATTAAACACATAATCAAATCTCATACTTACATTTA
* * *
635750 AATTCAAATAATATAAATTTTAACACATATA-TTTT-TGTAAAGAAAGACTAGGACAAATGAACA
316 AATTCAAATAACATAAATTTTAACACATATATTTTTATATAAAGAAAGACCAGGACAAATGAACA
635813 TAGGTTGACTCTCCTCATTTCCTCGTAAATTTCT
381 TAGGTTGACTCTCCTCATTTCCTCGTAAATTTCT
635847 TCA
1 TCA
635850 TGCTCATTAA
Statistics
Matches: 359, Mismatches: 45, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
410 54 0.15
411 107 0.30
412 16 0.04
413 81 0.23
416 2 0.01
417 11 0.03
418 4 0.01
420 27 0.08
421 1 0.00
422 5 0.01
423 19 0.05
425 32 0.09
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (414 bp):
TCAGTAAAATATTGTTCAACTAGCACTTCTATTTGACTGCTCAGCTTAGCCTAATGAGTATTTTT
TTTTTTAACGCCCCATAGAATTTTGTACTAACTTCAACTTCAACTTCAATTGCTGTTTGGAGTAA
TTTTAACCAATGTTGCTCCCATTTTCAATTTGTTCTTAAAATATCTACATTCATCATTTAATTCT
GATATATTTTTAAATAAATATACATAAATATAATTTTTCAATAATTTTTAAATATATAAAAAATT
TAAAAAATAAATATATTTATATTAAACACATAATCAAATCTCATACTTACATTTAAATTCAAATA
ACATAAATTTTAACACATATATTTTTATATAAAGAAAGACCAGGACAAATGAACATAGGTTGACT
CTCCTCATTTCCTCGTAAATTTCT
Found at i:636377 original size:2 final size:2
Alignment explanation
Indices: 636370--636404 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
636360 ATTCAGGTAA
636370 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
636405 CCTTCCTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:640163 original size:20 final size:18
Alignment explanation
Indices: 640140--640184 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
640130 CAATTATATT
640140 TAAAATATTATATATATTTA
1 TAAAAT-TTA-ATATATTTA
640160 TAAAATTTAATATATTTA
1 TAAAATTTAATATATTTA
*
640178 TATAATT
1 TAAAATT
640185 CATATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 15 0.62
19 3 0.12
20 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAAATTTAATATATTTA
Found at i:640999 original size:2 final size:2
Alignment explanation
Indices: 640992--641025 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
640982 TGGGAAAATA
640992 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
641026 TGCTGCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:652793 original size:16 final size:16
Alignment explanation
Indices: 652772--652819 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
652762 ATAAAATAAA
652772 TATAATTTTTATTAAT
1 TATAATTTTTATTAAT
* **
652788 TATAATTATTATTTTT
1 TATAATTTTTATTAAT
*
652804 TATTATTTTTACTTAA
1 TATAATTTTTA-TTAA
652820 AATATTTTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TATAATTTTTATTAAT
Found at i:652873 original size:22 final size:22
Alignment explanation
Indices: 652848--652889 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
652838 ATAATAAAAA
*
652848 TTTAGTTAATTTTAAAATTATT
1 TTTAATTAATTTTAAAATTATT
* *
652870 TTTAATTATTTTTTAAATTA
1 TTTAATTAATTTTAAAATTA
652890 AATTATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTAATTAATTTTAAAATTATT
Found at i:652918 original size:28 final size:27
Alignment explanation
Indices: 652862--652920 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
652852 GTTAATTTTA
* * *
652862 AAATTATTTTTAATTATTTTTTAAATT
1 AAATTATTATTAATTATATTATAAATT
*
652889 AAATTATTATTATATTATATTATAATTT
1 AAATTATTATTA-ATTATATTATAAATT
652917 AAAT
1 AAAT
652921 ACATATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
AAATTATTATTAATTATATTATAAATT
Found at i:654597 original size:22 final size:23
Alignment explanation
Indices: 654572--654624 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
654562 ATTATCTAAA
*
654572 AATATTAAAATATTTTTTAA-TT
1 AATATTAAAATATTTTATAATTT
* *
654594 AATATTCACATATTTTATAATTT
1 AATATTAAAATATTTTATAATTT
654617 AAT-TTAAA
1 AATATTAAA
654625 TAAAATAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTAAAATATTTTATAATTT
Found at i:656885 original size:18 final size:18
Alignment explanation
Indices: 656828--656892 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 18
656818 TAATATTTAA
*
656828 AATATTAT-TATTTATAT
1 AATATTATATATTAATAT
* * *
656845 TATA-TAAATTTTAATAT
1 AATATTATATATTAATAT
656862 -AT-TTATATATTAATAT
1 AATATTATATATTAATAT
*
656878 AATATTATATTTTAA
1 AATATTATATATTAA
656893 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
16 15 0.41
17 12 0.32
18 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATTATATATTAATAT
Found at i:656888 original size:43 final size:42
Alignment explanation
Indices: 656839--656921 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
656829 ATATTATTAT
*
656839 TTATATTATATAAATTTTAATA-TAT-TTATATATTAATATAATA
1 TTATATTATA-AAATTTTAAAATTATATT-TATATT-ATATAATA
*
656882 TTATATTTTAAAATTTTAAAATTATATTTATATTATATAA
1 TTATATTATAAAATTTTAAAATTATATTTATATTATATAA
656922 CTAAAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
42 16 0.44
43 18 0.50
44 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (42 bp):
TTATATTATAAAATTTTAAAATTATATTTATATTATATAATA
Found at i:657837 original size:2 final size:2
Alignment explanation
Indices: 657830--657863 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
657820 ATGCCCAAAT
*
657830 AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
657864 TCAAGAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:658101 original size:23 final size:23
Alignment explanation
Indices: 658075--658129 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
658065 ATAGTTTATT
658075 TTTTAAAATTAAATTAATTTAAA
1 TTTTAAAATTAAATTAATTTAAA
*
658098 TTTTAAAAAATAAATTAATTTAAA
1 TTTT-AAAATTAAATTAATTTAAA
658122 -TTTAAAAT
1 TTTTAAAAT
658130 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 7 0.24
24 18 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTTAAAATTAAATTAATTTAAA
Found at i:659592 original size:2 final size:2
Alignment explanation
Indices: 659587--659615 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
659577 ATATATATAT
659587 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
659616 CGAAGATGGT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:671661 original size:21 final size:22
Alignment explanation
Indices: 671637--671684 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
671627 TTCAGTGAGC
* *
671637 TTAATATAAATATTTTA-ATAT
1 TTAATATAAATAATTTATAGAT
*
671658 TTAATTTAAATAATTTATAGAT
1 TTAATATAAATAATTTATAGAT
671680 TTAAT
1 TTAAT
671685 CAAAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAATATAAATAATTTATAGAT
Found at i:675632 original size:70 final size:68
Alignment explanation
Indices: 675525--675702 Score: 209
Period size: 70 Copynumber: 2.6 Consensus size: 68
675515 ACTTTCAAAT
* * ** **
675525 TTTTTTAATTTAA--AATTTTTATTTTATTAAAAATTAATAATTAATATTTTAATTTTTTAATAT
1 TTTTTAAATTTAATTAATTTTTATTTTATTAAAATTTAATAATTAATAAGTTAATTTTAAAATAT
675588 AAA
66 AAA
675591 TTTTTAAAAATTTAATTAATTTTTATTTTATTAAAATTTAATAATTAATAAGTTAATTTTAAAAT
1 TTTTT--AAATTTAATTAATTTTTATTTTATTAAAATTTAATAATTAATAAGTTAATTTTAAAAT
*
675656 ATATA
64 ATAAA
* * * * *
675661 TTTTTTAATTTAATTAAATTTTACTTT-TTAAATTTTTATAAT
1 TTTTTAAATTTAATTAATTTTTATTTTATTAAAATTTAATAAT
675703 GAAATCTCAA
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
66 5 0.05
67 13 0.14
68 26 0.27
70 52 0.54
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (68 bp):
TTTTTAAATTTAATTAATTTTTATTTTATTAAAATTTAATAATTAATAAGTTAATTTTAAAATAT
AAA
Found at i:685280 original size:76 final size:77
Alignment explanation
Indices: 685191--685373 Score: 287
Period size: 76 Copynumber: 2.4 Consensus size: 77
685181 TTTTTCTTAT
* *
685191 TTTTGTTACGTCTTATTATTATAAAATAAAAAATTTTCAAAGATGTTAAGCGGTTTC-ATCAGTT
1 TTTTGTTACGTCTTATTATTATAAAATAAAAAATTTTCAAAGAAGTTAAGCGGTTTCGATCAATT
*
685255 TTTTCTTCCTCC
66 TTTTCTTCCTAC
* * *
685267 TTTTGTTATGTCTTATTATCATAAAATAAAAAATTTTCAAAGAAGTTAAGCGGTTTCGGTCAATT
1 TTTTGTTACGTCTTATTATTATAAAATAAAAAATTTTCAAAGAAGTTAAGCGGTTTCGATCAATT
**
685332 TTTTCTTTTTAC
66 TTTTCTTCCTAC
685344 TTTTGTTACGTCTTATTATTATAAAATAAA
1 TTTTGTTACGTCTTATTATTATAAAATAAA
685374 TTTTTTTTAA
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
76 54 0.56
77 42 0.44
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.47
Consensus pattern (77 bp):
TTTTGTTACGTCTTATTATTATAAAATAAAAAATTTTCAAAGAAGTTAAGCGGTTTCGATCAATT
TTTTCTTCCTAC
Found at i:685546 original size:19 final size:18
Alignment explanation
Indices: 685508--685546 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
685498 ATTAGAAATG
*
685508 ATTTTTTTATTTGTATAA
1 ATTTTTTTATTTGTAAAA
*
685526 ATTTTTTTATATTTTAAAA
1 ATTTTTTTAT-TTGTAAAA
685545 AT
1 AT
685547 AATTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTTTTTATTTGTAAAA
Found at i:685924 original size:3 final size:3
Alignment explanation
Indices: 685916--685952 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
685906 TGGACAAACA
685916 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
685953 CTACAAATTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:690241 original size:28 final size:29
Alignment explanation
Indices: 690192--690247 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
690182 ATGAGGAGAG
690192 TATTTTAATTTTATAATATT-AAATTTAA
1 TATTTTAATTTTATAATATTAAAATTTAA
*
690220 TATTTTAATTTT-TATATGTTAAAATTTA
1 TATTTTAATTTTATA-ATATTAAAATTTA
690248 TAATAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 2 0.08
28 16 0.64
29 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TATTTTAATTTTATAATATTAAAATTTAA
Found at i:690297 original size:19 final size:18
Alignment explanation
Indices: 690255--690306 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
690245 TTATAATAAA
*
690255 TAAAAATAATTAATATAT
1 TAAAAATATTTAATATAT
690273 TAAAAATATTTAA-ATAT
1 TAAAAATATTTAATATAT
690290 TAATAAA-ATATTAATAT
1 TAA-AAATAT-TTAATAT
690307 TATGAAAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.30
18 19 0.63
19 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAAATATTTAATATAT
Done.