Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 17 of 27
Found at i:2733064 original size:14 final size:14
Alignment explanation
Indices: 2733042--2733106 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
2733032 AAATTTTAAA
*
2733042 AAATGTATTTTATTT
1 AAAT-TATTATATTT
*
2733057 TAATTATTATATTT
1 AAATTATTATATTT
2733071 AAATTA-TA-ATTT
1 AAATTATTATATTT
*
2733083 --ATAATTATATTT
1 AAATTATTATATTT
2733095 AATATTATTATA
1 AA-ATTATTATA
2733107 ATTATGCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.08
11 2 0.05
12 8 0.20
13 2 0.05
14 14 0.35
15 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
AAATTATTATATTT
Found at i:2733102 original size:18 final size:18
Alignment explanation
Indices: 2733051--2733102 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2733041 AAAATGTATT
*
2733051 TTAT-TTTAATTATTATAT
1 TTATATTTAA-TATTATAA
*
2733069 TTAAATTATAAT-TTATAA
1 TTATATT-TAATATTATAA
2733087 TTATATTTAATATTAT
1 TTATATTTAATATTAT
2733103 TATAATTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.14
18 18 0.64
19 3 0.11
20 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTTAATATTATAA
Found at i:2733286 original size:28 final size:28
Alignment explanation
Indices: 2733255--2733326 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
2733245 GTATTAAAAA
* *
2733255 TATATAATATTAATTTAATTGATAAATT
1 TATATAATATTAAATAAATTGATAAATT
* * * *
2733283 TATAAAAAATTAAATAAATTTATAACTT
1 TATATAATATTAAATAAATTGATAAATT
*
2733311 TAAATAATA--AAATAAA
1 TATATAATATTAAATAAA
2733327 AGTTTTAACA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 7 0.20
28 28 0.80
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (28 bp):
TATATAATATTAAATAAATTGATAAATT
Found at i:2733529 original size:17 final size:18
Alignment explanation
Indices: 2733504--2733538 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2733494 ATCAAAATTA
2733504 ATTT-AAAAATAATTAAT
1 ATTTAAAAAATAATTAAT
*
2733521 ATTTTAAAAATAATTAAT
1 ATTTAAAAAATAATTAAT
2733539 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTAAAAAATAATTAAT
Found at i:2733541 original size:33 final size:34
Alignment explanation
Indices: 2733499--2733583 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 34
2733489 GTATTATCAA
2733499 AATTAATTTAAAAATAATTAATATTTTAAA-AA-T
1 AATTAATTTAAAAATAATTAATA-TTTAAATAATT
2733532 AATTAATTTAAAAAT-A--AA-ATTTAAATAATT
1 AATTAATTTAAAAATAATTAATATTTAAATAATT
2733562 AATTTAATTT-AAAATAATTAAT
1 AA-TTAATTTAAAAATAATTAAT
2733584 CTGATTTACA
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
28 6 0.13
29 3 0.07
30 10 0.22
31 8 0.18
32 1 0.02
33 17 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
AATTAATTTAAAAATAATTAATATTTAAATAATT
Found at i:2733555 original size:18 final size:15
Alignment explanation
Indices: 2733499--2733583 Score: 95
Period size: 15 Copynumber: 5.5 Consensus size: 15
2733489 GTATTATCAA
2733499 AATTAATTTAAAAAT
1 AATTAATTTAAAAAT
2733514 AATTAATATTTTAAAAAT
1 AATT-A-A-TTTAAAAAT
2733532 AATTAATTTAAAAAT
1 AATTAATTTAAAAAT
2733547 AA--AATTTAAATAATT
1 AATTAATTTAAA-AA-T
2733562 AATTTAATTT-AAAAT
1 AA-TTAATTTAAAAAT
2733577 AATTAAT
1 AATTAAT
2733584 CTGATTTACA
Statistics
Matches: 62, Mismatches: 0, Indels: 17
0.78 0.00 0.22
Matches are distributed among these distances:
13 8 0.13
14 7 0.11
15 21 0.34
16 4 0.06
17 4 0.06
18 18 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAATTTAAAAAT
Found at i:2733590 original size:19 final size:19
Alignment explanation
Indices: 2733549--2733591 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2733539 TTAAAAATAA
*
2733549 AATTT-AAATAATTAATTT
1 AATTTAAAATAATTAATCT
2733567 AATTTAAAATAATTAATCT
1 AATTTAAAATAATTAATCT
*
2733586 GATTTA
1 AATTTA
2733592 CATGATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
AATTTAAAATAATTAATCT
Found at i:2734056 original size:20 final size:19
Alignment explanation
Indices: 2734016--2734065 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
2734006 ATATCAAATC
* *
2734016 TATATTAAATTTAATTAAT
1 TATATTATATTTAAATAAT
2734035 TATATTATATTTATAATAAT
1 TATATTATATTTA-AATAAT
*
2734055 TAAATTATATT
1 TATATTATATT
2734066 AAAAGAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATTATATTTAAATAAT
Found at i:2734154 original size:2 final size:2
Alignment explanation
Indices: 2734147--2734171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2734137 TGTTTTTCAC
2734147 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
2734172 ATTGATTGGA
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:2746148 original size:37 final size:37
Alignment explanation
Indices: 2746100--2746176 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
2746090 ATATGGAAAC
* *
2746100 AACAATTCTGCCTTATGCATAATCTTTTAGCATTCGA
1 AACAATTCTGCCTTATGCATAACCTTTTAGCATTCAA
* * *
2746137 AACACTTCTGCCTTGTGCATAACCTTTTCGCATTCAA
1 AACAATTCTGCCTTATGCATAACCTTTTAGCATTCAA
2746174 AAC
1 AAC
2746177 CTAAAGTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (37 bp):
AACAATTCTGCCTTATGCATAACCTTTTAGCATTCAA
Found at i:2747291 original size:15 final size:14
Alignment explanation
Indices: 2747264--2747305 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
2747254 ACTAGGAGTG
*
2747264 AAAATGGAAAAAAA
1 AAAAGGGAAAAAAA
2747278 AAAAGGGAAAAAAA
1 AAAAGGGAAAAAAA
2747292 AAAAGGGAAAAAAA
1 AAAAGGGAAAAAAA
2747306 TATTTTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAGGGAAAAAAA
Found at i:2754078 original size:13 final size:14
Alignment explanation
Indices: 2754044--2754088 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
2754034 GATAAATTGA
*
2754044 AGAA-GGATACAAG
1 AGAAGGGATACATG
*
2754057 AGAA-TGATACATG
1 AGAAGGGATACATG
2754070 A-AAGGGATACATG
1 AGAAGGGATACATG
2754083 AGAAGG
1 AGAAGG
2754089 AAGGGGAGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 2 0.07
13 21 0.78
14 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.31, T:0.13
Consensus pattern (14 bp):
AGAAGGGATACATG
Found at i:2754242 original size:26 final size:27
Alignment explanation
Indices: 2754173--2754246 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
2754163 ACAAGCCATA
*
2754173 ATTTTTGACAAATAAAAAGGAACAACC
1 ATTTTTGACAAATACAAAGGAACAACC
* * *
2754200 ATTTTTGACAAATACAAAGTAACCACT
1 ATTTTTGACAAATACAAAGGAACAACC
*
2754227 A-TTTTGACAAACACAAAGGA
1 ATTTTTGACAAATACAAAGGA
2754247 TAGCTTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 17 0.41
27 24 0.59
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAATACAAAGGAACAACC
Found at i:2758718 original size:24 final size:26
Alignment explanation
Indices: 2758691--2758785 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 26
2758681 TAGCCACCAA
*
2758691 TTTTGACAAAC-AACA-AACCACAAT
1 TTTTGACAAACAAAAATAACCACAAT
* *
2758715 TTTTAACAAACAAAAAATAACCACTAT
1 TTTTGACAAAC-AAAAATAACCACAAT
* * **
2758742 TTTTGACAAATACAAAATAATCATTAT
1 TTTTGACAAACA-AAAATAACCACAAT
*
2758769 TTTTTACAAACACAAAA
1 TTTTGACAAACA-AAAA
2758786 AGTAGCTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
24 10 0.17
26 4 0.07
27 44 0.76
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.28
Consensus pattern (26 bp):
TTTTGACAAACAAAAATAACCACAAT
Found at i:2758743 original size:27 final size:27
Alignment explanation
Indices: 2758706--2758786 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
2758696 ACAAACAACA
*
2758706 AACCACAATTTTTAACAAACAAAAAAT
1 AACCACTATTTTTAACAAACAAAAAAT
* * *
2758733 AACCACTATTTTTGACAAATACAAAAT
1 AACCACTATTTTTAACAAACAAAAAAT
* * *
2758760 AATCATTATTTTTTACAAACACAAAAA
1 AACCACTATTTTTAACAAACA-AAAAA
2758787 GTAGCTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 40 0.91
28 4 0.09
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.28
Consensus pattern (27 bp):
AACCACTATTTTTAACAAACAAAAAAT
Found at i:2759349 original size:12 final size:13
Alignment explanation
Indices: 2759326--2759354 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2759316 ATGCATTCAA
2759326 GCATTCCATGCAT
1 GCATTCCATGCAT
2759339 GCATT-CATGCAT
1 GCATTCCATGCAT
2759351 GCAT
1 GCAT
2759355 AAATTTATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (13 bp):
GCATTCCATGCAT
Found at i:2762008 original size:3 final size:3
Alignment explanation
Indices: 2762000--2762028 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2761990 TTTTCAGGGT
2762000 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2762029 GGGTGGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2762210 original size:38 final size:37
Alignment explanation
Indices: 2762134--2762215 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 37
2762124 AACAACATAT
*
2762134 TTTTTAAAAAAAAACGTAATTAAATAATTATTTTTAAA
1 TTTTTAAAAAAAAAC-TAATTAAATAATTATTTATAAA
*
2762172 TTTTTAATAAAAATAA-TAATTTAATAATT-TTTAATAAA
1 TTTTTAA-AAAAA-AACTAATTAAATAATTATTT-ATAAA
*
2762210 TATTTA
1 TTTTTA
2762216 GTTGCATCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
37 3 0.08
38 28 0.74
39 5 0.13
40 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (37 bp):
TTTTTAAAAAAAAACTAATTAAATAATTATTTATAAA
Found at i:2762772 original size:17 final size:17
Alignment explanation
Indices: 2762750--2762785 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2762740 ATAATTATAT
*
2762750 TAATTAAATTACTAAAA
1 TAATTAAATTAATAAAA
*
2762767 TAATTAATTTAATAAAA
1 TAATTAAATTAATAAAA
2762784 TA
1 TA
2762786 TAAATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATTAAATTAATAAAA
Found at i:2762951 original size:22 final size:19
Alignment explanation
Indices: 2762920--2762964 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 19
2762910 TATTTTTATT
2762920 TAAATTTAATTATAAAATATA
1 TAAATTTAATTAT-AAATA-A
2762941 TAAATATTAATTATAAATAA
1 TAAAT-TTAATTATAAATAA
2762961 TAAA
1 TAAA
2762965 CATAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATTATAAATAA
Found at i:2763580 original size:25 final size:26
Alignment explanation
Indices: 2763552--2763606 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
2763542 ATCTCACCTT
2763552 ATAATATATAAATATTAATATAAA-A
1 ATAATATATAAATATTAATATAAATA
* * *
2763577 ATAATATTTTAATATTATTATAAATA
1 ATAATATATAAATATTAATATAAATA
2763603 ATAA
1 ATAA
2763607 AATAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAATATATAAATATTAATATAAATA
Found at i:2763796 original size:20 final size:20
Alignment explanation
Indices: 2763771--2763813 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2763761 TTCCCTTAAC
*
2763771 ATTTATTCTTTATAATATAT
1 ATTTATGCTTTATAATATAT
* *
2763791 ATTTATGCTTTTTAATATTT
1 ATTTATGCTTTATAATATAT
2763811 ATT
1 ATT
2763814 AATTATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTATGCTTTATAATATAT
Found at i:2769614 original size:20 final size:20
Alignment explanation
Indices: 2769589--2769627 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2769579 AAGAGTTTGT
2769589 TTAAAGATTTACTAGTGAAA
1 TTAAAGATTTACTAGTGAAA
2769609 TTAAAGATTTACTAGTGAA
1 TTAAAGATTTACTAGTGAA
2769628 GACAGTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (20 bp):
TTAAAGATTTACTAGTGAAA
Found at i:2774889 original size:20 final size:21
Alignment explanation
Indices: 2774864--2774902 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2774854 GAGGATCAGT
*
2774864 TATTAC-ATTTAATAAAATAA
1 TATTACTATTTAACAAAATAA
2774884 TATTACTATTTAACAAAAT
1 TATTACTATTTAACAAAAT
2774903 CCTTTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTACTATTTAACAAAATAA
Found at i:2784138 original size:3 final size:3
Alignment explanation
Indices: 2784130--2784179 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2784120 CTTTACTTTT
2784130 ATA ATA 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
2784178 AT
1 AT
2784180 TATTATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2784184 original size:3 final size:3
Alignment explanation
Indices: 2784178--2784206 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2784168 AATAATAATA
2784178 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2784207 GATGTATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2785323 original size:2 final size:2
Alignment explanation
Indices: 2785316--2785370 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2785306 AGCCAAAGCC
2785316 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
2785358 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2785371 CGTTTTTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2785434 original size:4 final size:4
Alignment explanation
Indices: 2785425--2785452 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2785415 ATTTTGGGCT
2785425 CTTC CTTC CTTC CTTC CTTC CTTC CTTC
1 CTTC CTTC CTTC CTTC CTTC CTTC CTTC
2785453 TCTCCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (4 bp):
CTTC
Found at i:2786208 original size:2 final size:2
Alignment explanation
Indices: 2786201--2786228 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2786191 TCGTATGAAA
2786201 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
2786229 TCATTCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2787331 original size:2 final size:2
Alignment explanation
Indices: 2787324--2787356 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2787314 AATTAGGGTG
2787324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2787357 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2787375 original size:4 final size:4
Alignment explanation
Indices: 2787354--2787441 Score: 68
Period size: 4 Copynumber: 21.5 Consensus size: 4
2787344 ATATATATAT
* * * * *
2787354 ATAC ACAC ACAC ACAC ATAC ATAT ATATGC ATAC ATAC ATAC ATAA ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA--C ATAC ATAC ATAC ATAC ATAC
* * * * *
2787404 ATAC ATAC ATAT ATAT AGAC ATAC ATAT ATAT ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
2787442 GCAGCAGCAA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
4 67 0.96
6 3 0.04
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:2787392 original size:34 final size:34
Alignment explanation
Indices: 2787340--2787416 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 34
2787330 ATATATATAT
* * *
2787340 ATATATATATATATATACACACACACACACATAC
1 ATATATATACATACATACACACACAAACACATAC
* * * *
2787374 ATATATATGCATACATACATACATAAATACATAC
1 ATATATATACATACATACACACACAAACACATAC
*
2787408 ATACATATA
1 ATATATATA
2787417 TATAGACATA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.29
Consensus pattern (34 bp):
ATATATATACATACATACACACACAAACACATAC
Found at i:2787405 original size:16 final size:16
Alignment explanation
Indices: 2787330--2787441 Score: 89
Period size: 16 Copynumber: 6.9 Consensus size: 16
2787320 GGTGATATAT
* * *
2787330 ATATATATATATATAT
1 ATATATACATACATAC
* *
2787346 ATATATATATACACAC
1 ATATATACATACATAC
* * * *
2787362 ACACACACATACATAT
1 ATATATACATACATAC
2787378 ATATGCATACATACATAC
1 ATAT--ATACATACATAC
*
2787396 ATAAATACATACATAC
1 ATATATACATACATAC
* *
2787412 ATATATATAGACATAC
1 ATATATACATACATAC
*
2787428 ATATATATATACAT
1 ATATATACATACAT
2787442 GCAGCAGCAA
Statistics
Matches: 76, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
16 63 0.83
18 13 0.17
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (16 bp):
ATATATACATACATAC
Found at i:2793386 original size:20 final size:20
Alignment explanation
Indices: 2793361--2793403 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2793351 AATTGAAGAA
*
2793361 GGATACAAGAGAGGGATGAG
1 GGATACAAGAGAGGGAGGAG
**
2793381 GGATACTTGAGAGGGAGGAG
1 GGATACAAGAGAGGGAGGAG
2793401 GGA
1 GGA
2793404 GCTTCTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.49, T:0.12
Consensus pattern (20 bp):
GGATACAAGAGAGGGAGGAG
Found at i:2793520 original size:28 final size:27
Alignment explanation
Indices: 2793485--2793550 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
2793475 AGCCTACATA
* *
2793485 TTTGACAAATACAAAGGA-AACTACCATT
1 TTTGACAAACACAAA--ATAACCACCATT
2793513 TTTGACAAACACAAAATAACCACCATT
1 TTTGACAAACACAAAATAACCACCATT
*
2793540 TTTTACAAACA
1 TTTGACAAACA
2793551 AATGGGTGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.56
28 14 0.41
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (27 bp):
TTTGACAAACACAAAATAACCACCATT
Found at i:2795469 original size:21 final size:22
Alignment explanation
Indices: 2795431--2795476 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2795421 ATTTGTTGAA
* **
2795431 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
2795452 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
2795474 ACT
1 ACT
2795477 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:2797956 original size:20 final size:20
Alignment explanation
Indices: 2797931--2797968 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2797921 AGAATTGAAG
2797931 AGGGATACAAGAGAGGGATA
1 AGGGATACAAGAGAGGGATA
**
2797951 AGGGATACTTGAGAGGGA
1 AGGGATACAAGAGAGGGA
2797969 GGAGGGAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.42, T:0.13
Consensus pattern (20 bp):
AGGGATACAAGAGAGGGATA
Found at i:2797974 original size:20 final size:20
Alignment explanation
Indices: 2797930--2797975 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2797920 AAGAATTGAA
*
2797930 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
2797950 AAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
2797970 GAGGGA
1 GAGGGA
2797976 GCTTCTATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.48, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:2798113 original size:27 final size:28
Alignment explanation
Indices: 2798057--2798122 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 28
2798047 AGCCTTCATA
*
2798057 TTTGACAAATACAAAGAAAACCACCATT
1 TTTGACAAACACAAAGAAAACCACCATT
*
2798085 TTTGACAAACACAAA-ATAACCACCATT
1 TTTGACAAACACAAAGAAAACCACCATT
2798112 TTTGACAAACA
1 TTTGACAAACA
2798123 AATAGGTGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (28 bp):
TTTGACAAACACAAAGAAAACCACCATT
Found at i:2799109 original size:19 final size:21
Alignment explanation
Indices: 2799085--2799129 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
2799075 GTTAACTTGA
2799085 TTTAATTTTA-TA-TTAATCT
1 TTTAATTTTATTATTTAATCT
*
2799104 TTTAA-TTTATTATTTAATTT
1 TTTAATTTTATTATTTAATCT
2799124 TTTAAT
1 TTTAAT
2799130 AGTAATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 11 0.50
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTAATTTTATTATTTAATCT
Found at i:2799347 original size:20 final size:20
Alignment explanation
Indices: 2799320--2799359 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2799310 ATATAATACA
*
2799320 AATAAAATA-ATTAAAATTT
1 AATAAAATATATAAAAATTT
2799339 AATATAAATATATAAAAATTT
1 AATA-AAATATATAAAAATTT
2799360 TTAAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAAATATATAAAAATTT
Found at i:2801388 original size:41 final size:41
Alignment explanation
Indices: 2801308--2801390 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
2801298 TTCATCACAT
*
2801308 AAATCAAAACTATTGTTCATTCCACCATAGCAATATGACAA
1 AAATCAAAACTATTGTTCATTCCACCATAACAATATGACAA
* * * *
2801349 AAATTAAAACTATTGTTTATTCCACCATAACCATGTGACAA
1 AAATCAAAACTATTGTTCATTCCACCATAACAATATGACAA
2801390 A
1 A
2801391 GTGTCGACAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.29
Consensus pattern (41 bp):
AAATCAAAACTATTGTTCATTCCACCATAACAATATGACAA
Found at i:2802964 original size:29 final size:28
Alignment explanation
Indices: 2802931--2802995 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
2802921 TTTCATTTGA
*
2802931 AATAAACGCATATTTAAGTACAAATAAAG
1 AATAAAAGCATATTTAAGTAC-AATAAAG
** *
2802960 AATAAAAGTTTATTTAAGTTCAATAAAG
1 AATAAAAGCATATTTAAGTACAATAAAG
2802988 ATATAAAA
1 A-ATAAAA
2802996 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.29
Consensus pattern (28 bp):
AATAAAAGCATATTTAAGTACAATAAAG
Found at i:2803471 original size:7 final size:7
Alignment explanation
Indices: 2803459--2803485 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2803449 ACTTGTAGAT
2803459 AAATTTA
1 AAATTTA
2803466 AAATTTA
1 AAATTTA
2803473 AAATTTA
1 AAATTTA
2803480 AAATTT
1 AAATTT
2803486 TAATATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:2806631 original size:20 final size:20
Alignment explanation
Indices: 2806563--2806634 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
2806553 AATTAATTTT
* *
2806563 TATAAAATTAAAAATAACAA
1 TATAAAATTAAAATTAATAA
*
2806583 TA-ATAATTAAATTATTATCATAA
1 TATAAAATTAAA--ATTA--ATAA
2806606 TAATAAAATTAAAATTAATAA
1 T-ATAAAATTAAAATTAATAA
2806627 TATAAAAT
1 TATAAAAT
2806635 ATATATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 8 0.19
20 9 0.21
21 8 0.19
23 8 0.19
24 1 0.02
25 8 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TATAAAATTAAAATTAATAA
Found at i:2806644 original size:21 final size:21
Alignment explanation
Indices: 2806550--2806634 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
2806540 AAATGGATAA
** *
2806550 TAAAATTAATTTTTATAAAAT
1 TAAAATTAATAATAATAAAAT
* *
2806571 TAAAAATAACAATAAT--AAT
1 TAAAATTAATAATAATAAAAT
2806590 TAAATTATTATCATAATAATAAAAT
1 TAAA--ATTA--ATAATAATAAAAT
2806615 TAAAATTAATAAT-ATAAAAT
1 TAAAATTAATAATAATAAAAT
2806635 ATATATTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
19 7 0.14
20 7 0.14
21 19 0.37
23 11 0.22
25 7 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATTAATAATAATAAAAT
Found at i:2806776 original size:34 final size:34
Alignment explanation
Indices: 2806692--2806784 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 34
2806682 TTGAATATTA
* *
2806692 AAAATATTATA-TTATA-TATATAAT-AAATAATT
1 AAAAT-TTATATTTATATTAAATAATAAAATAAAT
*
2806724 AAAATTTATATTTATATTACATAATAAATATAAAT
1 AAAATTTATATTTATATTAAATAATAAA-ATAAAT
*
2806759 AAAA-TTATATTTTTATTAAATAATAA
1 AAAATTTATATTTATATTAAATAATAA
2806785 TTAAAATTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.09
32 10 0.19
33 7 0.13
34 22 0.42
35 9 0.17
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (34 bp):
AAAATTTATATTTATATTAAATAATAAAATAAAT
Found at i:2807046 original size:39 final size:38
Alignment explanation
Indices: 2806956--2807046 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 38
2806946 TTTGATGTTA
2806956 AATAATAA-TTAAAATTATATTTATATTAAATAATAATT
1 AATAA-AACTTAAAATTATATTTATATTAAATAATAATT
2806994 AA-AGAATAC-TAAAATTATATTTATATTTAAA-AATAAATT
1 AATA-AA-ACTTAAAATTATATTTATA-TTAAATAAT-AATT
2807033 AATAAAACTTAAAA
1 AATAAAACTTAAAA
2807047 ATTAAAAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
37 2 0.04
38 25 0.54
39 18 0.39
40 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (38 bp):
AATAAAACTTAAAATTATATTTATATTAAATAATAATT
Found at i:2807339 original size:33 final size:33
Alignment explanation
Indices: 2807299--2807361 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
2807289 GAATAACAAA
*
2807299 CTGGGTCATGCAAAACTGCGGTTAGTAAACTAG
1 CTGGGTCATGCAAAACTGAGGTTAGTAAACTAG
2807332 CTGGGTCATGCAAAACTGAGGTTAGTAAAC
1 CTGGGTCATGCAAAACTGAGGTTAGTAAAC
2807362 CAGTATAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (33 bp):
CTGGGTCATGCAAAACTGAGGTTAGTAAACTAG
Found at i:2811899 original size:3 final size:3
Alignment explanation
Indices: 2811883--2811917 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2811873 TGGTGGCTGC
* *
2811883 TGT TGC TGT GGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
2811918 CCGCTGCTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.37, T:0.60
Consensus pattern (3 bp):
TGT
Found at i:2815773 original size:15 final size:15
Alignment explanation
Indices: 2815753--2815786 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2815743 ATGTAATGTC
2815753 AAAATAAAAAGAAAA
1 AAAATAAAAAGAAAA
* *
2815768 AAAATAATAATAAAA
1 AAAATAAAAAGAAAA
2815783 AAAA
1 AAAA
2815787 GGTTCGGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAATAAAAAGAAAA
Found at i:2816828 original size:17 final size:17
Alignment explanation
Indices: 2816806--2816843 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2816796 TTTAAGTGAT
2816806 TATTGAATATAAATATA
1 TATTGAATATAAATATA
*
2816823 TATTGAATATAATTATA
1 TATTGAATATAAATATA
2816840 TATT
1 TATT
2816844 TATATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
TATTGAATATAAATATA
Found at i:2822556 original size:25 final size:25
Alignment explanation
Indices: 2822516--2822564 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2822506 TATAATAAGT
2822516 ATAATATAATATATTTTAA-ATATAA
1 ATAATATAATATA-TTTAATATATAA
2822541 ATAATATAAT-TCATTTAATATATA
1 ATAATATAATAT-ATTTAATATATA
2822565 TCATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAATATAATATATTTAATATATAA
Found at i:2823214 original size:27 final size:25
Alignment explanation
Indices: 2823184--2823240 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
2823174 AATAATCATA
2823184 TAATTT-ATTAATAAAATATTAAAATTT
1 TAATTTAATT-ATAAAA-ATT-AAATTT
2823211 TAATTTAAATTATAAAAATTAAATTT
1 TAATTT-AATTATAAAAATTAAATTT
2823237 TAAT
1 TAAT
2823241 AATCTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 10 0.36
27 9 0.32
28 6 0.21
29 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TAATTTAATTATAAAAATTAAATTT
Found at i:2823234 original size:14 final size:14
Alignment explanation
Indices: 2823215--2823257 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2823205 AAATTTTAAT
2823215 TTAAATTATAAAAA
1 TTAAATTATAAAAA
* *
2823229 TTAAATTTTAATAA
1 TTAAATTATAAAAA
*
2823243 TCTTAATTATAAAAA
1 T-TAAATTATAAAAA
2823258 AATTTAACAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAATTATAAAAA
Found at i:2823243 original size:29 final size:27
Alignment explanation
Indices: 2823194--2823257 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
2823184 TAATTTATTA
2823194 ATAAAATATTAAAATTTTAAT-TTAAATT
1 ATAAAA-ATTAAAATTTTAATCTT-AATT
*
2823222 ATAAAAATTAAATTTTAATAATCTTAATT
1 ATAAAAATTAAAATTT--TAATCTTAATT
2823251 ATAAAAA
1 ATAAAAA
2823258 AATTTAACAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 9 0.28
28 6 0.19
29 15 0.47
30 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAAAAATTAAAATTTTAATCTTAATT
Found at i:2824539 original size:15 final size:14
Alignment explanation
Indices: 2824510--2824544 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2824500 AATTTTTTTA
2824510 TATATTAAACATAT
1 TATATTAAACATAT
*
2824524 TATATTAATTCATAT
1 TATATTAA-ACATAT
2824539 TATATT
1 TATATT
2824545 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATTAAACATAT
Found at i:2830061 original size:22 final size:20
Alignment explanation
Indices: 2830036--2830077 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2830026 TTGATAAGAT
*
2830036 GGAAGAGGAAAGAAAAATAAAA
1 GGAAGA-GAAA-AAAAAGAAAA
2830058 GGAAGAGAAAAAAAAGAAAA
1 GGAAGAGAAAAAAAAGAAAA
2830078 TTTATGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (20 bp):
GGAAGAGAAAAAAAAGAAAA
Found at i:2830196 original size:29 final size:29
Alignment explanation
Indices: 2830143--2830202 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
2830133 ATATTATAAA
* * *
2830143 TTTATATAAATTTTTACATAATAATTTAT
1 TTTATAAAAATTTTAACATAATAATATAT
* *
2830172 TTTATAAAAATTTTAATATATTAATATAT
1 TTTATAAAAATTTTAACATAATAATATAT
2830201 TT
1 TT
2830203 ATTTTTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTATAAAAATTTTAACATAATAATATAT
Found at i:2830214 original size:11 final size:11
Alignment explanation
Indices: 2830200--2830259 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 11
2830190 TATTAATATA
2830200 TTTATTT-TTT
1 TTTATTTATTT
2830210 ATTTATATTATTT
1 -TTTAT-TTATTT
* *
2830223 TTAATATTATGT
1 TTTAT-TTATTT
*
2830235 TTTAATTATTT
1 TTTATTTATTT
2830246 TTTATTTTATTT
1 TTTA-TTTATTT
2830258 TT
1 TT
2830260 AATGACATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 14 0.35
12 23 0.57
13 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:2830237 original size:13 final size:12
Alignment explanation
Indices: 2830214--2830262 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
2830204 TTTTTTATTT
2830214 ATATTATTTTTA
1 ATATTATTTTTA
2830226 ATATTATGTTTT-
1 ATATTAT-TTTTA
*
2830238 A-ATTATTTTTT
1 ATATTATTTTTA
*
2830249 ATTTTATTTTTA
1 ATATTATTTTTA
2830261 AT
1 AT
2830263 GACATCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 4 0.12
11 6 0.19
12 18 0.56
13 4 0.12
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
ATATTATTTTTA
Found at i:2830244 original size:23 final size:22
Alignment explanation
Indices: 2830211--2830262 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
2830201 TTATTTTTTA
2830211 TTTATATTATTTTTAATATTATGT
1 TTTA-ATTATTTTTAATATTAT-T
* *
2830235 TTTAATTATTTTTTATTTTATT
1 TTTAATTATTTTTAATATTATT
2830257 TTTAAT
1 TTTAAT
2830263 GACATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 7 0.27
23 15 0.58
24 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTAATTATTTTTAATATTATT
Found at i:2830260 original size:11 final size:11
Alignment explanation
Indices: 2830211--2830260 Score: 57
Period size: 11 Copynumber: 4.4 Consensus size: 11
2830201 TTATTTTTTA
2830211 TTTATATTATT
1 TTTATATTATT
2830222 TTTAATATTATGT
1 TTT-ATATTAT-T
2830235 TTTA-ATTATTT
1 TTTATATTA-TT
*
2830246 TTTATTTTATT
1 TTTATATTATT
2830257 TTTA
1 TTTA
2830261 ATGACATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 18 0.53
12 12 0.35
13 4 0.12
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2831141 original size:21 final size:21
Alignment explanation
Indices: 2831115--2831156 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2831105 AAAATATTAT
* *
2831115 TTTTATATTAATATTTATATA
1 TTTTATAATAAAATTTATATA
2831136 TTTTATAATAAAATTTATATA
1 TTTTATAATAAAATTTATATA
2831157 AAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATAATAAAATTTATATA
Found at i:2831334 original size:28 final size:29
Alignment explanation
Indices: 2831289--2831347 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
2831279 GTACTTAAAA
2831289 ATAAATATAAAATAT-AAAATATTTAATAT
1 ATAAATATAAAATATAAAAAT-TTTAATAT
* *
2831318 ATAAATA-AAATTTTAAAAATTTTAATAT
1 ATAAATATAAAATATAAAAATTTTAATAT
2831346 AT
1 AT
2831348 TTATACGACG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAAATATAAAATATAAAAATTTTAATAT
Found at i:2833432 original size:2 final size:2
Alignment explanation
Indices: 2833425--2833457 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2833415 AACAGGGTCA
2833425 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2833458 ACATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2835174 original size:11 final size:12
Alignment explanation
Indices: 2835148--2835199 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
2835138 ATTAATTTTT
2835148 TATTATTTATAA
1 TATTATTTATAA
2835160 TATTATTTA-AA
1 TATTATTTATAA
*
2835171 TATTAATTTTATAT
1 TATT-A-TTTATAA
*
2835185 TAATATTTAT-A
1 TATTATTTATAA
2835196 TATT
1 TATT
2835200 TAAATAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 9 0.27
12 15 0.45
13 5 0.15
14 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTATTTATAA
Found at i:2835177 original size:34 final size:34
Alignment explanation
Indices: 2835137--2835210 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
2835127 AATTAAATTA
*
2835137 AATTAATTTTTTATT-AT-TTATAATATTATTTAAAT
1 AATTAATTTTATATTAATATT-T-ATA-TATTTAAAT
2835172 -ATTAATTTTATATTAATATTTATATATTTAAAT
1 AATTAATTTTATATTAATATTTATATATTTAAAT
2835205 AATTAA
1 AATTAA
2835211 AATTTAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
33 9 0.26
34 21 0.60
35 3 0.09
36 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
AATTAATTTTATATTAATATTTATATATTTAAAT
Found at i:2835191 original size:25 final size:25
Alignment explanation
Indices: 2835153--2835227 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
2835143 TTTTTTATTA
* *
2835153 TTTATAATATTATTTAAATATTAAT
1 TTTATATTAATATTTAAATATTAAT
*
2835178 TTTATATTAATATTTATATATTTAA-
1 TTTATATTAATATTTAAATA-TTAAT
* *
2835203 -ATA-ATTAAAATTTAAATA-TAAT
1 TTTATATTAATATTTAAATATTAAT
2835225 TTT
1 TTT
2835228 TTTATTATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
21 3 0.08
23 14 0.35
24 2 0.05
25 17 0.43
26 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTATATTAATATTTAAATATTAAT
Found at i:2836345 original size:5 final size:5
Alignment explanation
Indices: 2836327--2836480 Score: 69
Period size: 5 Copynumber: 32.0 Consensus size: 5
2836317 TAATTTATTT
* * * * *
2836327 ATATG ATATAA ATATA ATATA AAAAA ATTAAA ATATA TTATA A-AT- ATATA
1 ATATA ATAT-A ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA
* * * * * *
2836377 ATTTT ATATA ATATA A-ATT AT-TA ATATTA AAATT AT-TA ATATA AAATA
1 ATATA ATATA ATATA ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA
* *
2836425 ATTTAA ATATA ATTATA ATATA ATA-A A-ATA ATAT- ATA-A AT-TA TTA-A
1 ATAT-A ATATA A-TATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2836471 ATATA ATATA
1 ATATA ATATA
2836481 TGTTAAAATA
Statistics
Matches: 110, Mismatches: 23, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
3 2 0.02
4 27 0.25
5 60 0.55
6 21 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:2836364 original size:2 final size:2
Alignment explanation
Indices: 2836266--2836347 Score: 59
Period size: 2 Copynumber: 43.0 Consensus size: 2
2836256 CTTTACCTTT
* *
2836266 TA TA TA TA TA TA TA TA TA TA TA TGA T- TC GA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
* * *
2836306 TA TA T- TA TA TA TA -A TT TA TT TA TA TGA TA TA AA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
2836346 TA
1 TA
2836348 AAAAAATTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
1 6 0.10
2 53 0.84
3 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2836385 original size:23 final size:24
Alignment explanation
Indices: 2836359--2836419 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 24
2836349 AAAAATTAAA
*
2836359 ATATATTATAAATATA-TAATTTT
1 ATATATTATAAATATATTAATATT
*
2836382 ATATAATATAAAT-TATTAATATT
1 ATATATTATAAATATATTAATATT
* *
2836405 A-AAATTATTAATATA
1 ATATATTATAAATATA
2836420 AAATAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATTATAAATATATTAATATT
Found at i:2836403 original size:30 final size:30
Alignment explanation
Indices: 2836363--2836453 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
2836353 ATTAAAATAT
*
2836363 ATTATAAATATATAATTTTATATAATATAA
1 ATTATTAATATATAATTTTATATAATATAA
**
2836393 ATTATTAATAT-TAAAATTAT-TAATATAAA
1 ATTATTAATATATAATTTTATATAATAT-AA
* *
2836422 ATAATTTAA-ATATAATTATAATATAATA-AA
1 ATTA-TTAATATATAATT-TTATATAATATAA
2836452 AT
1 AT
2836454 AATATATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
28 6 0.12
29 14 0.29
30 21 0.43
31 3 0.06
32 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATTATTAATATATAATTTTATATAATATAA
Found at i:2838163 original size:2 final size:2
Alignment explanation
Indices: 2838156--2838190 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2838146 GGGGAAAGAA
2838156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2838191 GAGAGAGAGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2838195 original size:2 final size:2
Alignment explanation
Indices: 2838190--2838231 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2838180 ATATATATAT
2838190 AG AG AG AG AG AG AG AG AG AG AG AG AG 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 AG AG AG AG
2838232 GGAAGCAAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2841842 original size:18 final size:18
Alignment explanation
Indices: 2841811--2841845 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2841801 CCCAGGCTGG
**
2841811 AGGGCACATTCTCTGTTA
1 AGGGCACAAACTCTGTTA
2841829 AGGGCACAAACTCTGTT
1 AGGGCACAAACTCTGTT
2841846 GGTGTCTGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
AGGGCACAAACTCTGTTA
Found at i:2843610 original size:21 final size:21
Alignment explanation
Indices: 2843586--2843625 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2843576 AATTAAGATC
2843586 TTAA-TTAATTGAGTCTATAAT
1 TTAATTTAATT-AGTCTATAAT
*
2843607 TTAATTTAATTAGTTTATA
1 TTAATTTAATTAGTCTATA
2843626 CAATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (21 bp):
TTAATTTAATTAGTCTATAAT
Found at i:2844583 original size:2 final size:2
Alignment explanation
Indices: 2844576--2844613 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2844566 TATAGCACGG
2844576 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
2844614 GGAGATTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2845666 original size:7 final size:7
Alignment explanation
Indices: 2845654--2845696 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
2845644 TTGGTTAAAC
2845654 AAAAAAT
1 AAAAAAT
2845661 AAAAAA-
1 AAAAAAT
2845667 AGAGAAAAT
1 A-A-AAAAT
2845676 AAAAAAT
1 AAAAAAT
2845683 AAAAAAAT
1 -AAAAAAT
2845691 AAAAAA
1 AAAAAA
2845697 AATATTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 1 0.03
7 18 0.56
8 12 0.38
9 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (7 bp):
AAAAAAT
Found at i:2845667 original size:8 final size:8
Alignment explanation
Indices: 2845654--2845697 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
2845644 TTGGTTAAAC
2845654 AAAAAATA
1 AAAAAATA
*
2845662 AAAAAA-G
1 AAAAAATA
*
2845669 AGAAAAT-
1 AAAAAATA
2845676 AAAAAATA
1 AAAAAATA
2845684 AAAAAATA
1 AAAAAATA
2845692 AAAAAA
1 AAAAAA
2845698 ATATTTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 11 0.35
8 20 0.65
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (8 bp):
AAAAAATA
Found at i:2845676 original size:15 final size:14
Alignment explanation
Indices: 2845654--2845698 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
2845644 TTGGTTAAAC
2845654 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
*
2845668 GAGAAAATAAAAAATA
1 -AAAAAATAAAAAA-A
2845684 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
2845698 A
1 A
2845699 TATTTTATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 24 0.89
16 1 0.04
ACGTcount: A:0.87, C:0.00, G:0.04, T:0.09
Consensus pattern (14 bp):
AAAAAATAAAAAAA
Found at i:2845696 original size:22 final size:22
Alignment explanation
Indices: 2845654--2845696 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2845644 TTGGTTAAAC
*
2845654 AAAAAATAAAAAAAGAGAAAAT
1 AAAAAATAAAAAAAGAAAAAAT
*
2845676 AAAAAATAAAAAAATAAAAAA
1 AAAAAATAAAAAAAGAAAAAA
2845697 AATATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAAATAAAAAAAGAAAAAAT
Found at i:2845880 original size:23 final size:24
Alignment explanation
Indices: 2845854--2845904 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
2845844 TTTTAAATAA
2845854 AAATAAT-ATAATAT-ATTAACATT
1 AAATAATAATAATATAATTAA-ATT
*
2845877 AAAT-TTAATAATATAATTAAATT
1 AAATAATAATAATATAATTAAATT
2845900 AAATA
1 AAATA
2845905 TAAGCTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 1 0.04
23 18 0.75
24 5 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATAATAATAATATAATTAAATT
Found at i:2853289 original size:22 final size:22
Alignment explanation
Indices: 2853240--2853311 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
2853230 TAAATTTTAT
* *
2853240 TATTTAAAATAATTTTTAAAAA
1 TATTTAAAAAAATTTATAAAAA
* **
2853262 TTTTTAAAAAAATTTATATTAA
1 TATTTAAAAAAATTTATAAAAA
2853284 TATTTATAAATAAATTTAAATAAAAA
1 TATTTA-AAA-AAATTT--ATAAAAA
2853310 TA
1 TA
2853312 CAATAAATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 22 0.58
23 3 0.08
24 6 0.16
26 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTTAAAAAAATTTATAAAAA
Found at i:2854164 original size:23 final size:24
Alignment explanation
Indices: 2854123--2854179 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
2854113 ATATAAAATG
2854123 AAATTATAATTTAAATTTAAATATT
1 AAATTATAATTT-AATTTAAATATT
* *
2854148 TAATTATAATTT-TTTTAAATATT
1 AAATTATAATTTAATTTAAATATT
2854171 AAATTATAA
1 AAATTATAA
2854180 ATTATGTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 18 0.62
25 11 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATTATAATTTAATTTAAATATT
Found at i:2856459 original size:2 final size:2
Alignment explanation
Indices: 2856452--2856477 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2856442 TTTTAAACGT
2856452 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
2856478 AACAGAGCGC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2856602 original size:3 final size:3
Alignment explanation
Indices: 2856596--2856622 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2856586 TTAATGTATT
2856596 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2856623 CATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2857616 original size:42 final size:44
Alignment explanation
Indices: 2857560--2857671 Score: 131
Period size: 47 Copynumber: 2.5 Consensus size: 44
2857550 AACAATAAAC
*
2857560 TTTTATAATAAAATTAAGTTGAAT-A-TC-TTTAAATTATTGACT
1 TTTTATAATAAAATTAA-TTAAATAATTCATTTAAATTATTGACT
*
2857602 TTTTATTATAAAATTGAATTAAATAAATTCAATTTAAATTATTGACT
1 TTTTATAATAAAATT-AATTAAAT-AATTC-ATTTAAATTATTGACT
*
2857649 TTTTATGATAAAATTAAATTAAA
1 TTTTATAATAAAATT-AATTAAA
2857672 ATTCCTTCTT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
42 19 0.32
43 2 0.03
44 1 0.02
45 2 0.03
47 36 0.60
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (44 bp):
TTTTATAATAAAATTAATTAAATAATTCATTTAAATTATTGACT
Found at i:2861017 original size:20 final size:19
Alignment explanation
Indices: 2860994--2861056 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 19
2860984 TTTAAATACA
*
2860994 TTATATTAATTATATT-AT
1 TTATATTAAATATATTAAT
*
2861012 TTTTATTAAATATATTATAT
1 TTATATTAAATATATTA-AT
*
2861032 TTATATTTAA-A-ATTAATT
1 TTATATTAAATATATTAA-T
2861050 TTATATT
1 TTATATT
2861057 TATTAAAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 1 0.03
18 26 0.68
19 1 0.03
20 10 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTAAATATATTAAT
Found at i:2861088 original size:19 final size:19
Alignment explanation
Indices: 2861031--2861089 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
2861021 ATATATTATA
* *
2861031 TTTATATTTAAAATTAA-T
1 TTTATATTTATATTTAATT
**
2861049 TTTATATTTAT-TAAAAGTT
1 TTTATATTTATATTTAA-TT
2861068 TTTATATTTATATTTAATT
1 TTTATATTTATATTTAATT
2861087 TTT
1 TTT
2861090 TTTTTGGGCC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 2 0.06
18 10 0.31
19 17 0.53
20 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATATTTATATTTAATT
Found at i:2861374 original size:4 final size:5
Alignment explanation
Indices: 2861347--2861395 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
2861337 GGAAATTATC
* *
2861347 ATATT ATATT ATATT ATATT AT-TT AT-TT AT-TT AAAATA ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT -ATATT ATATT ATATT
2861395 A
1 A
2861396 AATACAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 10 0.26
5 27 0.71
6 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:2869197 original size:2 final size:2
Alignment explanation
Indices: 2869190--2869214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2869180 TAGAGGTAAC
2869190 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
2869215 ACCCATTTCA
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:2876818 original size:16 final size:16
Alignment explanation
Indices: 2876797--2876852 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
2876787 TAATGACCGT
*
2876797 GGATCATAAACCTGAC
1 GGATCATAAACCCGAC
* *
2876813 GGATCATATACCCGAT
1 GGATCATAAACCCGAC
** *
2876829 GGATCATATTCCCGAT
1 GGATCATAAACCCGAC
2876845 GGATCATA
1 GGATCATA
2876853 TTCATAACCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (16 bp):
GGATCATAAACCCGAC
Found at i:2876853 original size:16 final size:16
Alignment explanation
Indices: 2876813--2876855 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
2876803 TAAACCTGAC
*
2876813 GGATCATATACCCGAT
1 GGATCATATTCCCGAT
2876829 GGATCATATTCCCGAT
1 GGATCATATTCCCGAT
2876845 GGATCATATTC
1 GGATCATATTC
2876856 ATAACCGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (16 bp):
GGATCATATTCCCGAT
Found at i:2887707 original size:200 final size:200
Alignment explanation
Indices: 2887360--2887759 Score: 764
Period size: 200 Copynumber: 2.0 Consensus size: 200
2887350 AAATCAAGCG
* *
2887360 CAGAAAAAGGGATATAACCATGAGAAAGCAATTGAATACTAAACAATTTAGAGAACAAGAGAATA
1 CAGAAAAAGGGATATAACCATGAGAAAGCAAATGAATACTAAACAATTTAAAGAACAAGAGAATA
2887425 TTGCCCTTAGTTATACTCCATATTTAATTAATACCCTTACCAAGAACCCCTAATTGCAAAGGCGC
66 TTGCCCTTAGTTATACTCCATATTTAATTAATACCCTTACCAAGAACCCCTAATTGCAAAGGCGC
*
2887490 ACTCAAAACCTAGAGCCTCATGTGTCTATGACAAAAAACTTGCACTCTACTCTTACAATATTGCT
131 ACTCAAAACCCAGAGCCTCATGTGTCTATGACAAAAAACTTGCACTCTACTCTTACAATATTGCT
2887555 ACTTT
196 ACTTT
*
2887560 CAGAAAAAGGGATATAACCATGAGAAAGCAAATGAATACTAAACAATTTAAAGAACATGAGAATA
1 CAGAAAAAGGGATATAACCATGAGAAAGCAAATGAATACTAAACAATTTAAAGAACAAGAGAATA
2887625 TTGCCCTTAGTTATACTCCATATTTAATTAATACCCTTACCAAGAACCCCTAATTGCAAAGGCGC
66 TTGCCCTTAGTTATACTCCATATTTAATTAATACCCTTACCAAGAACCCCTAATTGCAAAGGCGC
2887690 ACTCAAAACCCAGAGCCTCATGTGTCTATGACAAAAAACTTGCACTCTACTCTTACAATATTGCT
131 ACTCAAAACCCAGAGCCTCATGTGTCTATGACAAAAAACTTGCACTCTACTCTTACAATATTGCT
2887755 ACTTT
196 ACTTT
2887760 TATCTAAAAG
Statistics
Matches: 196, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 196 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (200 bp):
CAGAAAAAGGGATATAACCATGAGAAAGCAAATGAATACTAAACAATTTAAAGAACAAGAGAATA
TTGCCCTTAGTTATACTCCATATTTAATTAATACCCTTACCAAGAACCCCTAATTGCAAAGGCGC
ACTCAAAACCCAGAGCCTCATGTGTCTATGACAAAAAACTTGCACTCTACTCTTACAATATTGCT
ACTTT
Found at i:2891132 original size:3 final size:3
Alignment explanation
Indices: 2891126--2891159 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2891116 TATAATATCA
2891126 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2891160 TAAATTTTTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2891361 original size:20 final size:20
Alignment explanation
Indices: 2891337--2891389 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2891327 AATACGAATT
2891337 AATAATATATAAAAATTTTA
1 AATAATATATAAAAATTTTA
* *
2891357 TATAA-ATATATAATATTTTA
1 AATAATATATA-AAAATTTTA
2891377 AATAATATTATAA
1 AATAATA-TATAA
2891390 TACGTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.19
20 16 0.59
21 2 0.07
22 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATAATATATAAAAATTTTA
Found at i:2900445 original size:13 final size:13
Alignment explanation
Indices: 2900429--2900454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2900419 AAGTATAGTA
2900429 CATCTATGTTACT
1 CATCTATGTTACT
2900442 CATCTATGTTACT
1 CATCTATGTTACT
2900455 TGAACTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
CATCTATGTTACT
Found at i:2901530 original size:19 final size:21
Alignment explanation
Indices: 2901495--2901535 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2901485 CTAGGAATAA
*
2901495 ATTACATAAAATGAGCT-ATT
1 ATTACATAAAATCAGCTGATT
2901515 ATTACAT-AAATCAGCTGATT
1 ATTACATAAAATCAGCTGATT
2901535 A
1 A
2901536 GGCCTTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
ATTACATAAAATCAGCTGATT
Found at i:2904161 original size:16 final size:16
Alignment explanation
Indices: 2904134--2904185 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2904124 ATTATTTCAT
*
2904134 AATATTAAATAATTAA
1 AATATAAAATAATTAA
*
2904150 AA-ATAAAAATAAGTAA
1 AATAT-AAAATAATTAA
2904166 AATATAAAATAATTTAA
1 AATATAAAATAA-TTAA
2904183 AAT
1 AAT
2904186 TTTAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.07
16 20 0.67
17 8 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AATATAAAATAATTAA
Found at i:2904191 original size:41 final size:39
Alignment explanation
Indices: 2904146--2904223 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 39
2904136 TATTAAATAA
*
2904146 TTAAAAATAAAAATAAGTAAAATATAAAATAATTTAAAATT
1 TTAAAAATAAAAATAAATAAAATATAAAAT--TTTAAAATT
* *
2904187 TTAAAAATAAAAATAAATAAATTTTAAAATTTTAAAA
1 TTAAAAATAAAAATAAATAAAATATAAAATTTTAAAA
2904224 ATAAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 7 0.21
41 27 0.79
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (39 bp):
TTAAAAATAAAAATAAATAAAATATAAAATTTTAAAATT
Found at i:2904207 original size:24 final size:25
Alignment explanation
Indices: 2904164--2904215 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 25
2904154 AAAAATAAGT
*
2904164 AAAATATAAAATAATTTAAAATTTTA
1 AAAATATAAAATAATAT-AAATTTTA
2904190 AAAATA-AAAATAA-ATAAATTTTA
1 AAAATATAAAATAATATAAATTTTA
2904213 AAA
1 AAA
2904216 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 11 0.44
24 1 0.04
25 7 0.28
26 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATATAAAATAATATAAATTTTA
Found at i:2904210 original size:30 final size:32
Alignment explanation
Indices: 2904163--2904230 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
2904153 TAAAAATAAG
2904163 TAAAATATAAAATAA-TTTAAAATTTTAAAAA
1 TAAAATATAAAATAATTTTAAAATTTTAAAAA
2904194 TAAAA-AT-AAATAAATTTTAAAATTTTAAAAA
1 TAAAATATAAAAT-AATTTTAAAATTTTAAAAA
2904225 TAAAAT
1 TAAAAT
2904231 TATGATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.12
30 4 0.12
31 26 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (32 bp):
TAAAATATAAAATAATTTTAAAATTTTAAAAA
Found at i:2904499 original size:23 final size:24
Alignment explanation
Indices: 2904471--2904517 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2904461 AAATTATTTT
2904471 TAATTAA-AATTTTTTAAA-ATTAG
1 TAATTAATAA-TTTTTAAATATTAG
2904494 TAATTAATTAATTTTTAAATATTA
1 TAATTAA-TAATTTTTAAATATTA
2904518 TTTATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
24 8 0.38
25 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAATTAATAATTTTTAAATATTAG
Found at i:2904721 original size:29 final size:29
Alignment explanation
Indices: 2904689--2904779 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 29
2904679 TTAATATACT
*
2904689 AATAATATTTATTAATTATTAATAAAATA
1 AATAATATTTATTAATTTTTAATAAAATA
2904718 AATAATATTTTTATTAAATTTTTTAA-AAAATA
1 AATAATA--TTTATT-AA-TTTTTAATAAAATA
*
2904750 ATATAAATAATT-TT-ATTTTTAATAAAATA
1 A-AT-AATATTTATTAATTTTTAATAAAATA
2904779 A
1 A
2904780 TATTATACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
28 7 0.13
29 15 0.28
31 8 0.15
32 11 0.21
33 8 0.15
34 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAATATTTATTAATTTTTAATAAAATA
Found at i:2906242 original size:2 final size:2
Alignment explanation
Indices: 2906235--2906259 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2906225 ATTTTTGTAT
2906235 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
2906260 GCAAAGTGCA
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:2906453 original size:18 final size:18
Alignment explanation
Indices: 2906432--2906466 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2906422 AAATATTATA
2906432 ATAA-AAAATAATATAAAG
1 ATAATAAAA-AATATAAAG
2906450 ATAATAAAAAATATAAA
1 ATAATAAAAAATATAAA
2906467 TATGTTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAATAAAAAATATAAAG
Found at i:2906465 original size:9 final size:10
Alignment explanation
Indices: 2906429--2906466 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2906419 TTAAAATATT
2906429 ATAATAAAAA
1 ATAATAAAAA
*
2906439 ATAATATAAAG
1 ATAATA-AAAA
2906450 ATAATAAAAA
1 ATAATAAAAA
2906460 AT-ATAAA
1 ATAATAAA
2906467 TATGTTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 5 0.20
10 11 0.44
11 9 0.36
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:2909382 original size:12 final size:12
Alignment explanation
Indices: 2909365--2909389 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2909355 TTTCGTTGCG
2909365 TTCTTTTTTTTT
1 TTCTTTTTTTTT
2909377 TTCTTTTTTTTT
1 TTCTTTTTTTTT
2909389 T
1 T
2909390 GGGAAAAATT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:2909900 original size:31 final size:31
Alignment explanation
Indices: 2909862--2909928 Score: 127
Period size: 30 Copynumber: 2.2 Consensus size: 31
2909852 CTCTTATCTT
2909862 ATTAATTTTTTTTTTAAAATTTAAAATCATC
1 ATTAATTTTTTTTTTAAAATTTAAAATCATC
2909893 ATTAA-TTTTTTTTTAAAATTTAAAATCATC
1 ATTAATTTTTTTTTTAAAATTTAAAATCATC
2909923 ATTAAT
1 ATTAAT
2909929 CGTAATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTAATTTTTTTTTTAAAATTTAAAATCATC
Found at i:2910440 original size:24 final size:24
Alignment explanation
Indices: 2910413--2910466 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
2910403 CATTTCACTT
*
2910413 TTTTATTATATTAATATTTATAT-A
1 TTTTATTATATTAA-ATTTAAATAA
2910437 TTTTA-TA-ATTAAATTTAAATAA
1 TTTTATTATATTAAATTTAAATAA
2910459 TTTT-TTAT
1 TTTTATTAT
2910467 TAAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 7 0.27
22 12 0.46
23 2 0.08
24 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTATTATATTAAATTTAAATAA
Found at i:2910452 original size:21 final size:21
Alignment explanation
Indices: 2910418--2910524 Score: 84
Period size: 21 Copynumber: 5.2 Consensus size: 21
2910408 CACTTTTTTA
*
2910418 TTATATTAATATTTATAT-ATT
1 TTATATTAA-ATTTAAATAATT
2910439 TTATAATTAAATTTAAATAATT
1 TTAT-ATTAAATTTAAATAATT
*
2910461 TTTTATTAAA--T-AATAA-T
1 TTATATTAAATTTAAATAATT
*
2910478 TTAAATTAAA-TTAAACTAATT
1 TTATATTAAATTTAAA-TAATT
* *
2910499 TTAT-TTAATTTTATAAAAATT
1 TTATATTAAATTTA-AATAATT
2910520 TTATA
1 TTATA
2910525 ATTATTAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
17 9 0.13
18 6 0.09
19 3 0.04
20 7 0.10
21 32 0.46
22 13 0.19
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATATTAAATTTAAATAATT
Found at i:2913070 original size:31 final size:29
Alignment explanation
Indices: 2913035--2913097 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
2913025 TTAAATCGAG
*
2913035 TTTAAATATAAATTTTTATAAT-ATAATATAA
1 TTTAAAT-T-AATTTTTA-AATAATAAAATAA
*
2913066 TTTAAATTATTTTTTAAATAATAAAATAA
1 TTTAAATTAATTTTTAAATAATAAAATAA
2913095 TTT
1 TTT
2913098 TTAAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 18 0.62
30 1 0.03
31 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTAAATTAATTTTTAAATAATAAAATAA
Found at i:2913943 original size:15 final size:14
Alignment explanation
Indices: 2913919--2913961 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2913909 ACTCAAATAC
2913919 ATATTAAAATATAA
1 ATATTAAAATATAA
2913933 ATATATAAAATATAA
1 ATAT-TAAAATATAA
* *
2913948 TTTTTTAAAATATA
1 -ATATTAAAATATA
2913962 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 19 0.76
16 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATTAAAATATAA
Found at i:2914157 original size:13 final size:14
Alignment explanation
Indices: 2914141--2914174 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2914131 ACAAATAATT
2914141 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
2914154 TTATTAAATTTTTA
1 TTATTAAATTTATA
2914168 TTATTAA
1 TTATTAA
2914175 TAAGTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:2914377 original size:22 final size:21
Alignment explanation
Indices: 2914352--2914432 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
2914342 TTTAAATAAC
*
2914352 TTAATTTATTAATAATAAAAAT
1 TTAATTTAATAA-AATAAAAAT
*
2914374 TTAATTTAATAAAATTAAAATT
1 TTAATTTAATAAAA-TAAAAAT
* *
2914396 TTACCATTTAAGTAAAAATTAATAT
1 TTA--ATTTAA-T-AAAATAAAAAT
*
2914421 TAAATTTAATAA
1 TTAATTTAATAA
2914433 TTCAAAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.08
22 21 0.44
23 6 0.12
24 6 0.12
25 7 0.15
26 4 0.08
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (21 bp):
TTAATTTAATAAAATAAAAAT
Found at i:2916692 original size:11 final size:11
Alignment explanation
Indices: 2916676--2916725 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
2916666 CAAAAAAATT
2916676 AAAATATAATA
1 AAAATATAATA
*
2916687 AAAATATGATA
1 AAAATATAATA
*
2916698 TAAATA-AATA
1 AAAATATAATA
2916708 AAAATATAA-A
1 AAAATATAATA
*
2916718 AAATTATA
1 AAAATATA
2916726 TTTTATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAATATAATA
Found at i:2919561 original size:20 final size:20
Alignment explanation
Indices: 2919532--2919593 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
2919522 AAATTAATTT
*
2919532 TATATAAAAATATAAATAAA
1 TATATTAAAATATAAATAAA
* *
2919552 TATATTAAAATTTATATAAA
1 TATATTAAAATATAAATAAA
* *
2919572 TTATTTTATAATATAAA-AAA
1 -TATATTAAAATATAAATAAA
2919592 TA
1 TA
2919594 ATAATACGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.06
20 20 0.59
21 12 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATTAAAATATAAATAAA
Found at i:2920807 original size:17 final size:17
Alignment explanation
Indices: 2920787--2920839 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2920777 ATATATTTTT
2920787 TAAAAATAATTATAAAA
1 TAAAAATAATTATAAAA
* * *
2920804 TAAAATTAATTTTAAAT
1 TAAAAATAATTATAAAA
*
2920821 TATAAAATAAATA-AAAA
1 TA-AAAATAATTATAAAA
2920838 TA
1 TA
2920840 CATAAATAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATAATTATAAAA
Found at i:2923257 original size:14 final size:14
Alignment explanation
Indices: 2923238--2923299 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
2923228 ATTTGTTAAG
2923238 TTAATTTAAATAAT
1 TTAATTTAAATAAT
2923252 TTAATTTATTAATAAT
1 TTAATTTA--AATAAT
** *
2923268 AAAATTTTAATAAT
1 TTAATTTAAATAAT
* * *
2923282 ATAATTTATATAAA
1 TTAATTTAAATAAT
2923296 TTAA
1 TTAA
2923300 AATTTTATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
14 27 0.71
16 11 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATTTAAATAAT
Done.