Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 22 of 25
Found at i:3184081 original size:25 final size:25
Alignment explanation
Indices: 3184053--3184106 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
3184043 CAAGTGTTTG
3184053 TCTTTGTTGAATTTGGCAAGTTCTT
1 TCTTTGTTGAATTTGGCAAGTTCTT
*
3184078 TCTTTGTTGAATTTGGCAAGTTTTT
1 TCTTTGTTGAATTTGGCAAGTTCTT
3184103 TCTT
1 TCTT
3184107 GTTTATGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.15, C:0.11, G:0.19, T:0.56
Consensus pattern (25 bp):
TCTTTGTTGAATTTGGCAAGTTCTT
Found at i:3189523 original size:22 final size:21
Alignment explanation
Indices: 3189456--3189525 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
3189446 CAGTTTATGA
*
3189456 ATTTCTTTTTTGAAATTTTC-T
1 ATTTTTTTTTTG-AATTTTCAT
* *
3189477 -TTTTTATTTTG-ATTTTGTAT
1 ATTTTTTTTTTGAATTTT-CAT
3189497 AATTTTTTTTTTGAATTTTCAAT
1 -ATTTTTTTTTTGAATTTTC-AT
3189520 ATTTTT
1 ATTTTT
3189526 GAAATAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
18 5 0.13
20 10 0.26
22 16 0.42
23 7 0.18
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (21 bp):
ATTTTTTTTTTGAATTTTCAT
Found at i:3189525 original size:23 final size:22
Alignment explanation
Indices: 3189476--3189525 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
3189466 TGAAATTTTC
**
3189476 TTTTTTATTTTGATTTTGTATAA
1 TTTTTTATTTTGATTTTCAAT-A
3189499 TTTTTT-TTTTGAATTTTCAATA
1 TTTTTTATTTTG-ATTTTCAATA
3189521 TTTTT
1 TTTTT
3189526 GAAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (22 bp):
TTTTTTATTTTGATTTTCAATA
Found at i:3191863 original size:12 final size:13
Alignment explanation
Indices: 3191848--3191885 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3191838 TTATTATTAT
*
3191848 TATTTATAAT-AA
1 TATTAATAATAAA
3191860 TATTAATAATAAA
1 TATTAATAATAAA
*
3191873 TATTAATTATAAA
1 TATTAATAATAAA
3191886 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATTAATAATAAA
Found at i:3191884 original size:16 final size:16
Alignment explanation
Indices: 3191845--3191900 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
3191835 ATATTATTAT
*
3191845 TATTATTTATAAT-AA
1 TATTAATTATAATAAA
3191860 TATT-A--ATAATAAA
1 TATTAATTATAATAAA
3191873 TATTAATTATAA-AAA
1 TATTAATTATAATAAA
*
3191888 AATTAAATTATAA
1 TATT-AATTATAA
3191901 AATAATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 5 0.15
13 6 0.18
14 1 0.03
15 10 0.29
16 12 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAATTATAATAAA
Found at i:3196518 original size:16 final size:17
Alignment explanation
Indices: 3196497--3196528 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3196487 TTATTATATA
3196497 AAAAATAT-AAATAAAT
1 AAAAATATCAAATAAAT
3196513 AAAAATATCAAATAAA
1 AAAAATATCAAATAAA
3196529 ATAGAGCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAATATCAAATAAAT
Found at i:3197994 original size:2 final size:2
Alignment explanation
Indices: 3197989--3198018 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3197979 TGTGTGTGTG
*
3197989 TA TA TA TA TA AA 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
3198019 ATGTCGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3198663 original size:32 final size:33
Alignment explanation
Indices: 3198614--3198675 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
3198604 TAAATCAATG
*
3198614 TAATTATTATATAATT-AAAAATATTATTTTAA
1 TAATTATTATATAATTAAAAAATAATATTTTAA
*
3198646 TAATTATTA-ATTTATTAAAAAATAATATTT
1 TAATTATTATA-TAATTAAAAAATAATATTT
3198676 GATATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 1 0.04
32 13 0.50
33 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
TAATTATTATATAATTAAAAAATAATATTTTAA
Found at i:3198990 original size:15 final size:15
Alignment explanation
Indices: 3198970--3199004 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3198960 CGTTTTGCTG
3198970 AAAAAGAAAGA-AAGA
1 AAAAAGAAA-ACAAGA
3198985 AAAAAGAAAACAAGA
1 AAAAAGAAAACAAGA
3199000 AAAAA
1 AAAAA
3199005 AAATTATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAACAAGA
Found at i:3198999 original size:8 final size:7
Alignment explanation
Indices: 3198970--3199004 Score: 52
Period size: 8 Copynumber: 4.7 Consensus size: 7
3198960 CGTTTTGCTG
3198970 AAAAAGA
1 AAAAAGA
3198977 AAGAAAGA
1 AA-AAAGA
3198985 AAAAAGA
1 AAAAAGA
3198992 AAACAAGA
1 AAA-AAGA
3199000 AAAAA
1 AAAAA
3199005 AAATTATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 12 0.46
8 14 0.54
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:3199070 original size:24 final size:25
Alignment explanation
Indices: 3199017--3199095 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
3199007 ATTATGTGTT
* *
3199017 TATATTTATAATTT-TTTGTATTTAA
1 TATATTAATAATTTATTT-TATTTTA
* *
3199042 AATATT-ATATTTTTATTTT-TTTTA
1 TATATTAATA-ATTTATTTTATTTTA
3199066 TATATTAATAATTTATTTTATTTTA
1 TATATTAATAATTTATTTTATTTTA
3199091 TATAT
1 TATAT
3199096 ATTTTTCTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
24 20 0.44
25 22 0.49
26 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (25 bp):
TATATTAATAATTTATTTTATTTTA
Found at i:3199095 original size:25 final size:24
Alignment explanation
Indices: 3199015--3199095 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
3199005 AAATTATGTG
3199015 TTTATAT-TTATAATTT-TTTGTAT
1 TTTATATATTATAATTTATTT-TAT
* * *
3199038 TTAAAATATTATATTTTTATTTT-T
1 TTTATATATTATA-ATTTATTTTAT
3199062 TTTATATATTAATAATTTATTTTAT
1 TTTATATATT-ATAATTTATTTTAT
3199087 TTTATATAT
1 TTTATATAT
3199096 ATTTTTCTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 5 0.11
24 22 0.47
25 17 0.36
26 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (24 bp):
TTTATATATTATAATTTATTTTAT
Found at i:3199115 original size:17 final size:17
Alignment explanation
Indices: 3199073--3199119 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
3199063 TTATATATTA
*
3199073 ATAATTTATTTTATTTT
1 ATAATTTATTTTATTGT
*
3199090 AT-ATATATTTT-TCTGT
1 ATAATTTATTTTAT-TGT
3199106 ATAATTTATTTTAT
1 ATAATTTATTTTAT
3199120 ATATGGGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.04
16 12 0.50
17 10 0.42
18 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
ATAATTTATTTTATTGT
Found at i:3200324 original size:14 final size:14
Alignment explanation
Indices: 3200305--3200336 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3200295 TACGTGATGG
3200305 AAAAGAAAGAAAGA
1 AAAAGAAAGAAAGA
3200319 AAAAGAAAGAAAGA
1 AAAAGAAAGAAAGA
3200333 AAAA
1 AAAA
3200337 AAATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAGA
Found at i:3200329 original size:18 final size:17
Alignment explanation
Indices: 3200306--3200339 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3200296 ACGTGATGGA
3200306 AAAGAAAGAAAGAAAAAG
1 AAAGAAAGAAA-AAAAAG
3200324 AAAGAAAGAAAAAAAA
1 AAAGAAAGAAAAAAAA
3200340 TTTTATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAAAG
Found at i:3200400 original size:34 final size:37
Alignment explanation
Indices: 3200353--3200437 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 37
3200343 TATATGTTTG
3200353 TTTT-TATATTTTTTTATAT-TTAA-AA-TATTATAT
1 TTTTGTATATTTTTTTATATATTAATAATTATTATAT
*
3200386 TTTTGTATA-TTTTTTATATATTAATAATTTATTTTAT
1 TTTTGTATATTTTTTTATATATTAATAA-TTATTATAT
3200423 TTTATGTATATTTTT
1 TTT-TGTATATTTTT
3200438 ATGTATTTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
33 14 0.32
34 8 0.18
35 2 0.05
37 10 0.23
38 6 0.14
39 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (37 bp):
TTTTGTATATTTTTTTATATATTAATAATTATTATAT
Found at i:3200437 original size:37 final size:33
Alignment explanation
Indices: 3200353--3200444 Score: 96
Period size: 37 Copynumber: 2.7 Consensus size: 33
3200343 TATATGTTTG
* *
3200353 TTTTTATATTTTTTTATAT-TTAAAATATTATA
1 TTTTTGTATATTTTTATATATTAAAATATTATA
*
3200385 TTTTTGTATATTTTTTATATATTAATAATTTATTTTA
1 TTTTTGTATA-TTTTTATATATTAA-AA--TATTATA
*
3200422 TTTTATGTATATTTTTATGTATT
1 TTTT-TGTATATTTTTATATATT
3200445 TGTTATTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
32 8 0.16
33 9 0.18
34 4 0.08
35 2 0.04
37 21 0.42
38 6 0.12
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (33 bp):
TTTTTGTATATTTTTATATATTAAAATATTATA
Found at i:3200455 original size:38 final size:37
Alignment explanation
Indices: 3200353--3200437 Score: 108
Period size: 38 Copynumber: 2.4 Consensus size: 37
3200343 TATATGTTTG
*
3200353 TTTTTATAT-TTTTTTATAT-TTAA-AA--TATTATA
1 TTTTTGTATATTTTTTATATATTAATAATTTATTATA
*
3200385 TTTTTGTATATTTTTTATATATTAATAATTTATTTTA
1 TTTTTGTATATTTTTTATATATTAATAATTTATTATA
3200422 TTTTATGTATATTTTT
1 TTTT-TGTATATTTTT
3200438 ATGTATTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 8 0.18
33 10 0.22
34 4 0.09
35 2 0.04
37 10 0.22
38 11 0.24
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (37 bp):
TTTTTGTATATTTTTTATATATTAATAATTTATTATA
Found at i:3200744 original size:2 final size:2
Alignment explanation
Indices: 3200737--3200763 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3200727 AATTGAATAA
3200737 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 A
3200764 AATGAGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3204907 original size:33 final size:33
Alignment explanation
Indices: 3204865--3204927 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
3204855 TTAATTGTGA
3204865 AAATAATTATTAAAAAAATAA-AATAATTTTTT
1 AAATAATTATTAAAAAAATAATAATAATTTTTT
** *
3204897 AAATATATTATTTCAAAACTAATAATAATTT
1 AAATA-ATTATTAAAAAAATAATAATAATTT
3204928 CATAATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 5 0.19
33 13 0.50
34 8 0.31
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATAATTATTAAAAAAATAATAATAATTTTTT
Found at i:3205082 original size:14 final size:14
Alignment explanation
Indices: 3205063--3205093 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3205053 AAATAATTAC
*
3205063 TATTATATTTTTAT
1 TATTATAATTTTAT
3205077 TATTATAATTTTAT
1 TATTATAATTTTAT
3205091 TAT
1 TAT
3205094 CTCTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATAATTTTAT
Found at i:3207362 original size:16 final size:16
Alignment explanation
Indices: 3207341--3207372 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3207331 ACACACTTAA
3207341 TATGTTTACCTAATAC
1 TATGTTTACCTAATAC
3207357 TATGTTTACCTAATAC
1 TATGTTTACCTAATAC
3207373 ATTTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
TATGTTTACCTAATAC
Found at i:3211919 original size:34 final size:34
Alignment explanation
Indices: 3211869--3211980 Score: 143
Period size: 34 Copynumber: 3.3 Consensus size: 34
3211859 AAGATATGTT
* * * * * *
3211869 CACCTAATACATTTAATATGCTTACTTGATACAC
1 CACCTAACACACTTAATATGTTTACCTAACACAC
*
3211903 CACCTAACATACTTAATATGTTTACCTAACACAC
1 CACCTAACACACTTAATATGTTTACCTAACACAC
*
3211937 CACCTAACACATTTAATATGTTTACCTAACACAC
1 CACCTAACACACTTAATATGTTTACCTAACACAC
*
3211971 TACCTAACAC
1 CACCTAACAC
3211981 TATATTTACT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.30
Consensus pattern (34 bp):
CACCTAACACACTTAATATGTTTACCTAACACAC
Found at i:3212746 original size:28 final size:28
Alignment explanation
Indices: 3212688--3212746 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3212678 AGATTATAAT
* *
3212688 TTTAATTTTTTTAATATTTTAATTTTAA
1 TTTAATTTATTTAATATTTTAATATTAA
* *
3212716 TTTAATTTATTTAA-ATTATTCATATTCA
1 TTTAATTTATTTAATATT-TTAATATTAA
3212744 TTT
1 TTT
3212747 TTATAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTAATTTATTTAATATTTTAATATTAA
Found at i:3213577 original size:15 final size:17
Alignment explanation
Indices: 3213565--3213602 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
3213555 TATTTTTTAT
3213565 TAAATTATATTTTAATA
1 TAAATTATATTTTAATA
*
3213582 TAAATAATA-TTTAATA
1 TAAATTATATTTTAATA
3213598 TAAAT
1 TAAAT
3213603 ATAAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTATATTTTAATA
Found at i:3213594 original size:16 final size:16
Alignment explanation
Indices: 3213565--3213614 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
3213555 TATTTTTTAT
*
3213565 TAAATTATATTTTAATA
1 TAAATAATA-TTTAATA
3213582 TAAATAATATTTAATA
1 TAAATAATATTTAATA
*
3213598 TAAATATAAATTTAATA
1 TAAATA-ATATTTAATA
3213615 ATTTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATAATATTTAATA
Found at i:3213683 original size:71 final size:67
Alignment explanation
Indices: 3213579--3213755 Score: 196
Period size: 71 Copynumber: 2.6 Consensus size: 67
3213569 TTATATTTTA
* * * * *
3213579 ATATAAATAATATTTAATATAAATATAAATTTAATAATTTTTAAT-ATTATTCAACATAAATGTA
1 ATATATATTATATTTAATATAAATA-AATTTTAATAATTTTTAATGATTATTCAAAATAAATATA
3213643 ATTAT
65 A-T-T
* * *
3213648 ATATATATTTAATTATTTAATATAAATACATTTTAATGA-TTTTAATGATTATTTAAAATAAATA
1 ATATATA-TT-A-TATTTAATATAAATAAATTTTAATAATTTTTAATGATTATTCAAAATAAATA
3213712 TAATT
63 TAATT
*
3213717 ATATATATTATATTTAATATAAATATATTTTTAATAATT
1 ATATATATTATATTTAATATAAATA-AATTTTAATAATT
3213756 AAAATTTATT
Statistics
Matches: 91, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
66 15 0.16
67 9 0.10
68 3 0.03
69 14 0.15
70 9 0.10
71 26 0.29
72 15 0.16
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (67 bp):
ATATATATTATATTTAATATAAATAAATTTTAATAATTTTTAATGATTATTCAAAATAAATATAA
TT
Found at i:3213757 original size:24 final size:25
Alignment explanation
Indices: 3213699--3213757 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 25
3213689 TTAATGATTA
* *
3213699 TTTAA-AATAAATATAATTATATAT
1 TTTAATAATTAATATAAATATATAT
* *
3213723 ATT-ATATTTAATATAAATATAT-T
1 TTTAATAATTAATATAAATATATAT
3213746 TTTAATAATTAA
1 TTTAATAATTAA
3213758 AATTTATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAATAATTAATATAAATATATAT
Found at i:3215232 original size:20 final size:19
Alignment explanation
Indices: 3215200--3215238 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3215190 AAAATTTAGA
*
3215200 TAAAATTATTTAATTTAAT
1 TAAAATTAATTAATTTAAT
3215219 TAAATATTAATTAATTTAAT
1 TAAA-ATTAATTAATTTAAT
3215239 GATTTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAATTAATTAATTTAAT
Found at i:3215490 original size:29 final size:27
Alignment explanation
Indices: 3215469--3215522 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
3215459 TTTATATTTA
3215469 TTTTTTAATTTTTATAAAATTTTAATT
1 TTTTTTAATTTTTATAAAATTTTAATT
* *
3215496 TTTTTT-ATTTCT-TAAATTTTTAATT
1 TTTTTTAATTTTTATAAAATTTTAATT
3215521 TT
1 TT
3215523 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.56
26 5 0.20
27 6 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTTTAATTTTTATAAAATTTTAATT
Found at i:3215665 original size:27 final size:25
Alignment explanation
Indices: 3215635--3215687 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
3215625 AAAGTGAAAA
*
3215635 TGAAAATAAAAAAATTATTTATATATT
1 TGAAAA-AAAAAAA-GATTTATATATT
*
3215662 TGAAAAATAAAAAGATTTATATATT
1 TGAAAAAAAAAAAGATTTATATATT
3215687 T
1 T
3215688 TTTAAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.50
26 6 0.25
27 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
TGAAAAAAAAAAAGATTTATATATT
Found at i:3215742 original size:16 final size:15
Alignment explanation
Indices: 3215721--3215789 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
3215711 TTGATTATTA
3215721 ATTATTTATATATAAT
1 ATTATTTATA-ATAAT
3215737 ATTA-TTA-AA-AAT
1 ATTATTTATAATAAT
* *
3215749 ATTATTTTTAAATCAT
1 ATTATTTAT-AATAAT
* *
3215765 ATTATTTTTAAAAAT
1 ATTATTTATAATAAT
*
3215780 GTTATTTATA
1 ATTATTTATA
3215790 TACTTTGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
12 7 0.16
13 3 0.07
14 1 0.02
15 17 0.40
16 15 0.35
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (15 bp):
ATTATTTATAATAAT
Found at i:3215759 original size:15 final size:15
Alignment explanation
Indices: 3215736--3215786 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
3215726 TTATATATAA
*
3215736 TATTATTAAAAATAT
1 TATTTTTAAAAATAT
*
3215751 TATTTTTAAATCATAT
1 TATTTTTAAA-AATAT
*
3215767 TATTTTTAAAAATGT
1 TATTTTTAAAAATAT
3215782 TATTT
1 TATTT
3215787 ATATACTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 17 0.55
16 14 0.45
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
TATTTTTAAAAATAT
Found at i:3215919 original size:13 final size:13
Alignment explanation
Indices: 3215881--3215936 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
3215871 ATTTTCAATA
*
3215881 TTTTAAAAATAA-
1 TTTTAAATATAAT
*
3215893 TTATAAATATTAAT
1 TTTTAAATA-TAAT
3215907 TTTTAAATATAAT
1 TTTTAAATATAAT
3215920 TTATTAAA-AT-AT
1 TT-TTAAATATAAT
3215932 TTTTA
1 TTTTA
3215937 TTAAATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.08
12 11 0.29
13 11 0.29
14 13 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTAAATATAAT
Found at i:3215946 original size:23 final size:23
Alignment explanation
Indices: 3215917--3215963 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3215907 TTTTAAATAT
* *
3215917 AATTTATTAAAATATTTTTATTA
1 AATTTATTAAAATATATGTATTA
*
3215940 AATTTATTTAAATATATGTATTA
1 AATTTATTAAAATATATGTATTA
3215963 A
1 A
3215964 TAATATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTTATTAAAATATATGTATTA
Found at i:3215949 original size:13 final size:14
Alignment explanation
Indices: 3215896--3215949 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
3215886 AAAATAATTA
3215896 TAAATATTAATTT-T
1 TAAATATT-ATTTAT
*
3215910 TAAATATAATTTAT
1 TAAATATTATTTAT
3215924 TAAAATATT-TTTAT
1 T-AAATATTATTTAT
3215938 TAAAT-TTATTTA
1 TAAATATTATTTA
3215950 AATATATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
12 2 0.06
13 12 0.34
14 15 0.43
15 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAATATTATTTAT
Found at i:3216308 original size:21 final size:20
Alignment explanation
Indices: 3216276--3216317 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
3216266 AGCCCAAAGG
3216276 CTCTCCCTCTCCTACCACCTC
1 CTCTCCCTCTCCT-CCACCTC
*
3216297 CTCT-CCTCCTCCTCCTCCTC
1 CTCTCCCT-CTCCTCCACCTC
3216317 C
1 C
3216318 AACGCCTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.05, C:0.64, G:0.00, T:0.31
Consensus pattern (20 bp):
CTCTCCCTCTCCTCCACCTC
Found at i:3221977 original size:14 final size:16
Alignment explanation
Indices: 3221949--3221981 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3221939 AAAATAAAAC
3221949 ATTTATAAATATTAAA
1 ATTTATAAATATTAAA
3221965 ATTTA-AAAT-TTAAA
1 ATTTATAAATATTAAA
3221979 ATT
1 ATT
3221982 ATTAGATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTATAAATATTAAA
Found at i:3222281 original size:20 final size:22
Alignment explanation
Indices: 3222239--3222285 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
3222229 TTTTAGGTTT
*
3222239 AATT-TATTAATTTTAAAATTA
1 AATTATATTAAATTTAAAATTA
3222260 AATTATATTAAATTT-AAA-TA
1 AATTATATTAAATTTAAAATTA
3222280 AATTAT
1 AATTAT
3222286 CTGATTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 7 0.29
22 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTATATTAAATTTAAAATTA
Found at i:3222762 original size:9 final size:9
Alignment explanation
Indices: 3222743--3222780 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
3222733 TTTTTTTTTT
*
3222743 AAAAAAAAG
1 AAAAGAAAG
*
3222752 AAGAGAAAG
1 AAAAGAAAG
3222761 AAAAGAAAG
1 AAAAGAAAG
3222770 AAAAGAAAG
1 AAAAGAAAG
3222779 AA
1 AA
3222781 TAGAGTCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:3223053 original size:22 final size:22
Alignment explanation
Indices: 3223028--3223088 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
3223018 ATGGGGTTTT
3223028 TTTTTTAAAAA-AAAAGAAATAA
1 TTTTTTAAAAATAAAA-AAATAA
*
3223050 TTTTTTAAAAATTAAAAAAATTA
1 TTTTTTAAAAA-TAAAAAAATAA
*
3223073 -TTTTTAAATATAAAAA
1 TTTTTTAAAAATAAAAA
3223089 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 6 0.17
22 20 0.57
23 5 0.14
24 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTTTTAAAAATAAAAAAATAA
Found at i:3224006 original size:17 final size:17
Alignment explanation
Indices: 3223986--3224019 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3223976 ATATTAAAAT
3223986 ATTAAAAAATATTTTTA
1 ATTAAAAAATATTTTTA
* *
3224003 ATTAATATATATTTTTA
1 ATTAAAAAATATTTTTA
3224020 TAATTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAAAAATATTTTTA
Found at i:3224032 original size:29 final size:25
Alignment explanation
Indices: 3223995--3224063 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 25
3223985 TATTAAAAAA
3223995 TATT-TTTAATTAATATATATTTTT
1 TATTATTTAATTAATATATATTTTT
* * *
3224019 ATAATTAAATTTAAATAAAATTTATTTTT
1 -T-ATT--ATTTAATTAATATATATTTTT
3224048 TATTATTTAATTAATA
1 TATTATTTAATTAATA
3224064 ATAATTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
25 11 0.31
26 3 0.09
27 3 0.09
28 1 0.03
29 17 0.49
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATTTAATTAATATATATTTTT
Found at i:3224069 original size:29 final size:32
Alignment explanation
Indices: 3224005--3224075 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 32
3223995 TATTTTTAAT
*
3224005 TAATATATATTTTTATAATTAAATTTAAATAA
1 TAATTTATATTTTTATAATTAAATTTAAATAA
* *
3224037 -AATTTAT-TTTTTATTATTTAA-TT-AATAA
1 TAATTTATATTTTTATAATTAAATTTAAATAA
3224065 TAATTTA-ATTT
1 TAATTTATATTT
3224076 AAATCGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 5 0.15
29 11 0.32
30 12 0.35
31 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TAATTTATATTTTTATAATTAAATTTAAATAA
Found at i:3225456 original size:2 final size:2
Alignment explanation
Indices: 3225449--3225474 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3225439 AAACATATGA
3225449 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
3225475 GAAGAGAGAG
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:3226561 original size:17 final size:16
Alignment explanation
Indices: 3226514--3226608 Score: 61
Period size: 15 Copynumber: 5.8 Consensus size: 16
3226504 TAAATTAAAA
3226514 TAAATTAATAATTTTCTT
1 TAAATTAAT-ATTTT-TT
*
3226532 TATAATTATTATTTTTAT
1 TA-AATTAATATTTTT-T
3226550 TAAATTAATA-TTTTT
1 TAAATTAATATTTTTT
* * **
3226565 TAAA-AAATATATACT
1 TAAATTAATATTTTTT
*
3226580 TAATTTAA-ATTTTTT
1 TAAATTAATATTTTTT
*
3226595 AAAATTAATTATTT
1 TAAATTAA-TATTT
3226609 AAATTATTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
14 4 0.07
15 20 0.34
16 6 0.10
17 12 0.21
18 10 0.17
19 6 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATTAATATTTTTT
Found at i:3226564 original size:18 final size:18
Alignment explanation
Indices: 3226514--3226566 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
3226504 TAAATTAAAA
*
3226514 TAAATTAATAATTTTCT-T
1 TAAATTAAT-ATTTTTTAT
*
3226532 TATAATTATTA-TTTTTAT
1 TA-AATTAATATTTTTTAT
3226550 TAAATTAATATTTTTTA
1 TAAATTAATATTTTTTA
3226567 AAAAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.38
18 12 0.41
19 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATTAATATTTTTTAT
Found at i:3226602 original size:20 final size:21
Alignment explanation
Indices: 3226579--3226650 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 21
3226569 AAATATATAC
3226579 TTAATTTAAATT-TTTTAAAA
1 TTAATTTAAATTATTTTAAAA
*
3226599 TTAATTATTTAAATTATTTTAAAT
1 TT-A--ATTTAAATTATTTTAAAA
* *
3226623 TTAAATT-AATTAATTTAAATA
1 TTAATTTAAATTATTTTAAA-A
3226644 TTAATTT
1 TTAATTT
3226651 TTAATTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 13 0.31
21 10 0.24
23 10 0.24
24 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATTTAAATTATTTTAAAA
Found at i:3226648 original size:12 final size:14
Alignment explanation
Indices: 3226596--3226668 Score: 68
Period size: 14 Copynumber: 5.5 Consensus size: 14
3226586 AAATTTTTTA
3226596 AAATTAATT-ATTT
1 AAATTAATTAATTT
*
3226609 AAATTATTTTAAATTT
1 AAATTA-ATT-AATTT
3226625 AAATTAATTAATTT
1 AAATTAATTAATTT
3226639 AAA-T-ATTAATTT
1 AAATTAATTAATTT
*
3226651 ---TTAATTAAATT
1 AAATTAATTAATTT
3226662 AAATTAA
1 AAATTAA
3226669 ATAAATTGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
10 1 0.02
11 7 0.14
12 8 0.16
13 7 0.14
14 14 0.29
15 2 0.04
16 10 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATTAATTAATTT
Found at i:3226651 original size:33 final size:29
Alignment explanation
Indices: 3226596--3226668 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 29
3226586 AAATTTTTTA
3226596 AAATTAATT-ATTTAAATTATTTTAAATTT
1 AAATTAATTAATTTAAATTATTTTAAA-TT
*
3226625 AAATTAATTAATTTAAATATTAATTTTTAATT
1 AAATTAATTAATTT-AA-ATT-ATTTTAAATT
3226657 AAATTAAATTAA
1 AAATT-AATTAA
3226669 ATAAATTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
29 9 0.24
30 4 0.11
31 2 0.05
32 10 0.26
33 13 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AAATTAATTAATTTAAATTATTTTAAATT
Found at i:3226662 original size:28 final size:27
Alignment explanation
Indices: 3226593--3226671 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
3226583 TTTAAATTTT
* * *
3226593 TTAAAATT-AATTATTTAAATT--ATT
1 TTAAATTTAAATTAATTAAATTAAATA
*
3226617 TTAAATTTAAATTAATTAATTTAAATA
1 TTAAATTTAAATTAATTAAATTAAATA
* *
3226644 TTAATTTTTAATTAAATTAAATTAAATA
1 TTAAATTTAAATT-AATTAAATTAAATA
3226672 AATTGATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 7 0.16
25 11 0.25
27 13 0.30
28 13 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAAATTTAAATTAATTAAATTAAATA
Found at i:3231613 original size:22 final size:22
Alignment explanation
Indices: 3231588--3231630 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3231578 ATTTATATTA
* *
3231588 TTTATATATTTTTAAATTTAAT
1 TTTAAATATTATTAAATTTAAT
3231610 TTTAAATATTATTAAATTTAA
1 TTTAAATATTATTAAATTTAA
3231631 GTATATTTAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAATATTATTAAATTTAAT
Found at i:3231695 original size:22 final size:23
Alignment explanation
Indices: 3231655--3231710 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
3231645 AGTAGTTTAA
3231655 ATTTATTTAAATTTATTAAAAT-T
1 ATTT-TTTAAATTTATTAAAATAT
* *
3231678 ATTTTTTAATTTTTTTAAAATAT
1 ATTTTTTAAATTTATTAAAATAT
3231701 ATTTTTTAAA
1 ATTTTTTAAA
3231711 AATATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTTAAATTTATTAAAATAT
Found at i:3231706 original size:15 final size:15
Alignment explanation
Indices: 3231686--3231724 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3231676 TTATTTTTTA
*
3231686 ATTTTTTTAAAATAT
1 ATTTTTTAAAAATAT
3231701 ATTTTTTAAAAATAT
1 ATTTTTTAAAAATAT
*
3231716 AATTTTTAA
1 ATTTTTTAA
3231725 TAATTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTTTAAAAATAT
Found at i:3231733 original size:15 final size:14
Alignment explanation
Indices: 3231689--3231738 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
3231679 TTTTTTAATT
*
3231689 TTTTTAAAATATAT
1 TTTTTAAAATATAA
3231703 TTTTTAAAAATATAA
1 TTTTT-AAAATATAA
*
3231718 TTTTTAATAATTTAA
1 TTTTTAA-AATATAA
3231733 TATTTT
1 T-TTTT
3231739 TAATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.23
15 20 0.65
16 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTAAAATATAA
Found at i:3231755 original size:24 final size:24
Alignment explanation
Indices: 3231715--3231761 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3231705 TTTAAAAATA
*
3231715 TAATTTTTAATAATTTAATATTTT
1 TAATTTTTAATAATTTAAAATTTT
*
3231739 TAATTTATTAA-ATTTTAAAATTT
1 TAATTT-TTAATAATTTAAAATTT
3231762 AAATAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATTTTTAATAATTTAAAATTTT
Found at i:3231801 original size:14 final size:13
Alignment explanation
Indices: 3231782--3231822 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3231772 ACATATTTTT
3231782 TAATATTTATATTA
1 TAATATTTAT-TTA
3231796 TAATA-TTATTTA
1 TAATATTTATTTA
3231808 TATATATTT-TTTA
1 TA-ATATTTATTTA
3231821 TA
1 TA
3231823 TAATAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 13 0.52
14 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TAATATTTATTTA
Found at i:3231843 original size:30 final size:30
Alignment explanation
Indices: 3231787--3231845 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3231777 TTTTTTAATA
* * *
3231787 TTTATATTATAATATTATTTATATATATTT
1 TTTATATAATAAAATTACTTATATATATTT
3231817 TTTATATAATAAAAATTACTTAATATATA
1 TTTATATAAT-AAAATTACTT-ATATATA
3231846 AAATATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
31 8 0.33
32 7 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTATATAATAAAATTACTTATATATATTT
Found at i:3232928 original size:37 final size:34
Alignment explanation
Indices: 3232862--3232930 Score: 84
Period size: 37 Copynumber: 1.9 Consensus size: 34
3232852 ATTCAGATAT
*
3232862 TTATTATTATTTATTATTTTAAATATATTTATTA
1 TTATTATTATTTATTATTTAAAATATATTTATTA
* *
3232896 TTATTATTATTTTTTTATGTGTAAAATTTATTTAT
1 TTATTATTA-TTTATTAT-T-TAAAATATATTTAT
3232931 AAATTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 9 0.31
35 7 0.24
36 1 0.03
37 12 0.41
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (34 bp):
TTATTATTATTTATTATTTAAAATATATTTATTA
Found at i:3232952 original size:22 final size:21
Alignment explanation
Indices: 3232918--3232988 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 21
3232908 TTTTATGTGT
*
3232918 AAAATTTATTTATAAATTATA
1 AAAATTTATTTATAAATAATA
3232939 AAAATTATATTTATAAATAATA
1 AAAATT-TATTTATAAATAATA
*
3232961 ATTAAATTTATAT-TAAATAATA
1 A--AAATTTATTTATAAATAATA
3232983 ATAAAT
1 A-AAAT
3232989 ATAAAGAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.24
22 25 0.56
23 4 0.09
24 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATTTATTTATAAATAATA
Found at i:3232963 original size:19 final size:19
Alignment explanation
Indices: 3232936--3232972 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3232926 TTTATAAATT
*
3232936 ATAAAAATTATATTTATAA
1 ATAAAAATTAAATTTATAA
*
3232955 ATAATAATTAAATTTATA
1 ATAAAAATTAAATTTATA
3232973 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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAAAATTAAATTTATAA
Found at i:3235063 original size:12 final size:12
Alignment explanation
Indices: 3235013--3235088 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
3235003 ACGTTTGATG
*
3235013 AAAAAGAAAG-A
1 AAAAAGGAAGAA
3235024 AAAAA--AAGAA
1 AAAAAGGAAGAA
*
3235034 AAAAAGAAAGAA
1 AAAAAGGAAGAA
**
3235046 GGAAAGGAAGAA
1 AAAAAGGAAGAA
*
3235058 ATAAAGG-AGATA
1 AAAAAGGAAGA-A
3235070 AAAAAGGGAAGAA
1 AAAAA-GGAAGAA
3235083 AGAAAA
1 A-AAAA
3235089 AAAAATTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
9 3 0.06
10 6 0.12
11 8 0.15
12 24 0.46
13 4 0.08
14 7 0.13
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
AAAAAGGAAGAA
Found at i:3235183 original size:20 final size:20
Alignment explanation
Indices: 3235109--3235184 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 20
3235099 TATTGATATT
**
3235109 TATATTTTTA-TTTAAAATA
1 TATATTTTTATTTTATTATA
*
3235128 TTATATTTTTATATATTTTTATA
1 -TATATTTTTAT-T-TTATTATA
*
3235151 TATTAATAATTTATTTTATTATA
1 TA-T-AT-TTTTATTTTATTATA
3235174 TATATTTTTAT
1 TATATTTTTAT
3235185 ATATACATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 15 0.34
21 2 0.05
22 4 0.09
23 15 0.34
24 3 0.07
25 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATTTTTATTTTATTATA
Found at i:3235188 original size:10 final size:10
Alignment explanation
Indices: 3235129--3235154 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3235119 TTTAAAATAT
3235129 TATATTTTTA
1 TATATTTTTA
3235139 TATATTTTTA
1 TATATTTTTA
3235149 TATATT
1 TATATT
3235155 AATAATTTAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATATTTTTA
Found at i:3235213 original size:37 final size:35
Alignment explanation
Indices: 3235094--3235219 Score: 104
Period size: 35 Copynumber: 3.6 Consensus size: 35
3235084 GAAAAAAAAA
*
3235094 TTATA-TATTGATATTTATATTTT-TAT-TTAA-AAT
1 TTATATTATT-ATATATAT-TTTTATATATTAATAAT
3235127 ATTATATT-TT-TATATATTTTTATATATTAATAAT
1 -TTATATTATTATATATATTTTTATATATTAATAAT
*
3235161 TTATTTTATTATATATATTTTTATATA-TACATATAT
1 TTATATTATTATATATATTTTTATATATTA-ATA-AT
* *
3235197 TTGTATTATGTGTATATTATTTT
1 TTATATTAT-TATATA-TATTTT
3235220 CATGTTATGT
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
31 4 0.05
32 9 0.12
33 10 0.13
34 14 0.18
35 20 0.26
36 9 0.12
37 5 0.06
38 6 0.08
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (35 bp):
TTATATTATTATATATATTTTTATATATTAATAAT
Found at i:3235538 original size:17 final size:17
Alignment explanation
Indices: 3235508--3235549 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3235498 CGTTCAGGAG
*
3235508 AGAAAAAAGAAAAAGAA
1 AGAAAAAAGAAAAAAAA
* *
3235525 AGAAAGAAGGAAAAAAA
1 AGAAAAAAGAAAAAAAA
3235542 AGAAAAAA
1 AGAAAAAA
3235550 ACGAAAGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AGAAAAAAGAAAAAAAA
Found at i:3235547 original size:26 final size:27
Alignment explanation
Indices: 3235510--3235565 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
3235500 TTCAGGAGAG
*
3235510 AAAAAAGAAAAAGAAA-GAAAGAAGGAA
1 AAAAAAGAAAAA-AAACGAAAGAAAGAA
3235537 AAAAAAG-AAAAAAACGAAAGAAAGAA
1 AAAAAAGAAAAAAAACGAAAGAAAGAA
3235563 AAA
1 AAA
3235566 GAGAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 3 0.11
26 17 0.63
27 7 0.26
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAAAAAAACGAAAGAAAGAA
Found at i:3236522 original size:15 final size:14
Alignment explanation
Indices: 3236498--3236534 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
3236488 TAAATTTTAT
3236498 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
3236512 AAAAGAAAGAAAAAG
1 AAAA-AAAGAAAAAG
3236527 AGAAAAAA
1 A-AAAAAA
3236535 TTTATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 14 0.67
16 3 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:3240627 original size:79 final size:79
Alignment explanation
Indices: 3240496--3240657 Score: 279
Period size: 79 Copynumber: 2.1 Consensus size: 79
3240486 CTTAACAAGG
* * *
3240496 CATGCCAAAAGGATAGTTATCTGCTTCCTAGTGTTGATCGCCTAGTCGATGCCTCGGCTGGACAT
1 CATGCCAAAAGAATAGTTATCCGCTTCCTAGCGTTGATCGCCTAGTCGATGCCTCGGCTGGACAT
3240561 CAACTTTTGACATT
66 CAACTTTTGACATT
*
3240575 CATGCCCAAAGAATAGTTATCCGCTTCCTAGCGTTGATCGCCTAGTCGATGCCTCGGCTGGACAT
1 CATGCCAAAAGAATAGTTATCCGCTTCCTAGCGTTGATCGCCTAGTCGATGCCTCGGCTGGACAT
*
3240640 CAACTTTTGATATT
66 CAACTTTTGACATT
3240654 CATG
1 CATG
3240658 GATGTCTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (79 bp):
CATGCCAAAAGAATAGTTATCCGCTTCCTAGCGTTGATCGCCTAGTCGATGCCTCGGCTGGACAT
CAACTTTTGACATT
Found at i:3243616 original size:43 final size:43
Alignment explanation
Indices: 3243523--3243650 Score: 157
Period size: 43 Copynumber: 3.0 Consensus size: 43
3243513 TAATTCTTTG
* * **
3243523 GCAAGCATACAAGTGAGTAACTAAGTTACCACACATAGATTAT
1 GCAAGCATACAAGCGAGTAACTAAGTTACCACGCATAGATGCT
* * *
3243566 ACCAGCATACAAGCCAGTAACTAAGTTACCACGCATAGATGCT
1 GCAAGCATACAAGCGAGTAACTAAGTTACCACGCATAGATGCT
* * * *
3243609 GCAAGCATACAAGCGAGCAACAAAGTTGCCACGCATACATGC
1 GCAAGCATACAAGCGAGTAACTAAGTTACCACGCATAGATGC
3243651 CTACTCAACA
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (43 bp):
GCAAGCATACAAGCGAGTAACTAAGTTACCACGCATAGATGCT
Found at i:3247391 original size:9 final size:9
Alignment explanation
Indices: 3247377--3247409 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
3247367 TTTATTTGAT
3247377 AAAAAAAGA
1 AAAAAAAGA
3247386 AAAAAAAGA
1 AAAAAAAGA
3247395 AAGAAAAAGA
1 AA-AAAAAGA
3247405 AAAAA
1 AAAAA
3247410 TGTATGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:3247392 original size:10 final size:10
Alignment explanation
Indices: 3247377--3247409 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3247367 TTTATTTGAT
3247377 AAAAAAAG-A
1 AAAAAAAGAA
3247386 AAAAAAAGAA
1 AAAAAAAGAA
*
3247396 AGAAAAAGAA
1 AAAAAAAGAA
3247406 AAAA
1 AAAA
3247410 TGTATGCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:3247957 original size:16 final size:15
Alignment explanation
Indices: 3247930--3247971 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
3247920 ATTTTTAAAT
3247930 AAATTTTATTAATTA
1 AAATTTTATTAATTA
*
3247945 TAATTTTATTTAATTA
1 AAATTTTA-TTAATTA
3247961 AAATTTT-TTAA
1 AAATTTTATTAA
3247972 AATATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATTTTATTAATTA
Found at i:3248105 original size:16 final size:17
Alignment explanation
Indices: 3248084--3248116 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3248074 ACAAAAATTG
3248084 TAAAA-TTATTATATCA
1 TAAAATTTATTATATCA
*
3248100 TAAAATTTATTTTATCA
1 TAAAATTTATTATATCA
3248117 CGTTGTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAATTTATTATATCA
Found at i:3248683 original size:20 final size:21
Alignment explanation
Indices: 3248658--3248718 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
3248648 TAGTGAAAAA
3248658 ATTATTTTAAT-TTTT-ATATT
1 ATTA-TTTAATATTTTAATATT
3248678 ATTATTTAATATTTTAATATTT
1 ATTATTTAATATTTTAATA-TT
*
3248700 ATATTTTTAA-ATTTTAATA
1 AT-TATTTAATATTTTAATA
3248719 AATAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 6 0.17
20 8 0.22
21 3 0.08
22 13 0.36
23 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTTAATATTTTAATATT
Found at i:3248760 original size:23 final size:21
Alignment explanation
Indices: 3248713--3248769 Score: 55
Period size: 23 Copynumber: 2.7 Consensus size: 21
3248703 TTTTTAAATT
3248713 TTAATAA--ATAAAAAAATAA
1 TTAATAATGATAAAAAAATAA
* *
3248732 TTAATAATGTTAAAAAAATTAT
1 TTAATAATGATAAAAAAA-TAA
*
3248754 TTAAATACTGATAAAA
1 TT-AATAATGATAAAA
3248770 TATTTGATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.23
21 8 0.27
22 4 0.13
23 11 0.37
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TTAATAATGATAAAAAAATAA
Found at i:3252863 original size:13 final size:14
Alignment explanation
Indices: 3252845--3252873 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3252835 GATTTAACTC
3252845 TTTTTAAATA-ATT
1 TTTTTAAATATATT
3252858 TTTTTAAATATATT
1 TTTTTAAATATATT
3252872 TT
1 TT
3252874 AATGATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTAAATATATT
Found at i:3254403 original size:15 final size:14
Alignment explanation
Indices: 3254373--3254420 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
3254363 TGAAAGAGTA
*
3254373 ATTTTAATTTTTAT
1 ATTTTAATATTTAT
3254387 ATTATTAA-ATTTAAT
1 ATT-TTAATATTT-AT
3254402 ATTTTAATATTTAT
1 ATTTTAATATTTAT
3254416 ATTTT
1 ATTTT
3254421 TTTAAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTAATATTTAT
Found at i:3254421 original size:15 final size:15
Alignment explanation
Indices: 3254374--3254421 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3254364 GAAAGAGTAA
*
3254374 TTTTAATTTTTATAT
1 TTTTAATATTTATAT
*
3254389 TATTAA-ATTTA-AT
1 TTTTAATATTTATAT
3254402 ATTTTAATATTTATAT
1 -TTTTAATATTTATAT
3254418 TTTT
1 TTTT
3254422 TTAAATTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 14 0.52
16 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATATTTATAT
Found at i:3255445 original size:14 final size:13
Alignment explanation
Indices: 3255421--3255455 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3255411 TGTTTAAGAG
3255421 TATAATATATTTC
1 TATAATATATTTC
3255434 TATAATTATATTTC
1 TATAA-TATATTTC
*
3255448 TAAAATAT
1 TATAATAT
3255456 GTATAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (13 bp):
TATAATATATTTC
Found at i:3255499 original size:17 final size:17
Alignment explanation
Indices: 3255474--3255507 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3255464 TAAGTCGAGC
3255474 TTTGAAAAAAAATTATA
1 TTTGAAAAAAAATTATA
*
3255491 TTTGTAAAAAAATTATA
1 TTTGAAAAAAAATTATA
3255508 ACTATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
TTTGAAAAAAAATTATA
Found at i:3256201 original size:3 final size:3
Alignment explanation
Indices: 3256193--3256234 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3256183 ATTTGGCTTA
3256193 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3256235 GCTGAATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3256841 original size:93 final size:94
Alignment explanation
Indices: 3256679--3256865 Score: 308
Period size: 93 Copynumber: 2.0 Consensus size: 94
3256669 CTTGGAAAGA
** *
3256679 AAACCAGAACTGCTGCGCCCCCACGCCTTTCTCTTGTAAGGGTAGTTTCGTTGAGTTGGTGGATT
1 AAACCAGAACTGCTGCGCCCCCACGCCTTTCAATTGTAAGGGTAGTTTCGTTGAGTTGGTGGATC
3256744 CTATGGCTGAAA-TTTTTTGTTTGGCTGT
66 CTATGGCTGAAATTTTTTTGTTTGGCTGT
3256772 AAACCAGAACT-CATGCGCCCCCATC-CCTTTCAATTGTAAGGGTAGTTTCGTTGAGTTGGTGGA
1 AAACCAGAACTGC-TGCGCCCCCA-CGCCTTTCAATTGTAAGGGTAGTTTCGTTGAGTTGGTGGA
3256835 TCCTATGGCTGAAATTTTTTTGTTTGGCTGT
64 TCCTATGGCTGAAATTTTTTTGTTTGGCTGT
3256866 GTCGGTGTGA
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
92 1 0.01
93 70 0.80
94 17 0.19
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (94 bp):
AAACCAGAACTGCTGCGCCCCCACGCCTTTCAATTGTAAGGGTAGTTTCGTTGAGTTGGTGGATC
CTATGGCTGAAATTTTTTTGTTTGGCTGT
Found at i:3257060 original size:26 final size:26
Alignment explanation
Indices: 3257024--3257077 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
3257014 ATTTAAAATT
*
3257024 TTTAAATATTTGATAATTATA-TTAAA
1 TTTAAATATTTGAAAATTA-AGTTAAA
* *
3257050 TTTAATTATTTTAAAATTAAGTTAAA
1 TTTAAATATTTGAAAATTAAGTTAAA
3257076 TT
1 TT
3257078 ACTTTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
TTTAAATATTTGAAAATTAAGTTAAA
Found at i:3257445 original size:28 final size:28
Alignment explanation
Indices: 3257382--3257451 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
3257372 AAATATTATT
3257382 ATAAAAAATGATA-TTAAGAATTAAAATA
1 ATAAAAAAT-ATATTTAAGAATTAAAATA
*
3257410 TTAAAAAATATATTTAA-AATTATAAA-A
1 ATAAAAAATATATTTAAGAATTA-AAATA
3257437 ATAATAAAAT-TATTT
1 ATAA-AAAATATATTT
3257452 TATTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
ATAAAAAATATATTTAAGAATTAAAATA
Found at i:3259578 original size:19 final size:19
Alignment explanation
Indices: 3259554--3259593 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3259544 ATTTTTTTTT
* *
3259554 TATATTTTATAATTAAAAA
1 TATATTTTAAAAATAAAAA
3259573 TATATTTTAAAAATAAAAA
1 TATATTTTAAAAATAAAAA
3259592 TA
1 TA
3259594 ATTAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATTTTAAAAATAAAAA
Found at i:3259656 original size:22 final size:20
Alignment explanation
Indices: 3259631--3259673 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
3259621 AATACATTAG
3259631 AAAAGAAAATAAAATAGTATTT
1 AAAAGAAAATAAAA-A-TATTT
* *
3259653 AAAATATAATAAAAATATTT
1 AAAAGAAAATAAAAATATTT
3259673 A
1 A
3259674 TATATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAGAAAATAAAAATATTT
Found at i:3259711 original size:23 final size:19
Alignment explanation
Indices: 3259667--3259703 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3259657 TATAATAAAA
3259667 ATATTTATATATTTATATC
1 ATATTTATATATTTATATC
3259686 ATATTTATATATTT-TATC
1 ATATTTATATATTTATATC
3259704 GTATCATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTATATATTTATATC
Found at i:3260834 original size:18 final size:18
Alignment explanation
Indices: 3260811--3260868 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
3260801 TATAATAGAG
*
3260811 TTTCTTTTTTTCTTTTTT
1 TTTCTTTTTTTCTTTTTC
*
3260829 TTTCTTTTATTCTATTTTC
1 TTTCTTTTTTTCT-TTTTC
*
3260848 TTTCTTGTTTATC-TTTTC
1 TTTCTT-TTTTTCTTTTTC
3260866 TTT
1 TTT
3260869 ATGAATCAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 20 0.59
19 10 0.29
20 4 0.12
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTTTCTTTTTC
Found at i:3263283 original size:2 final size:2
Alignment explanation
Indices: 3263278--3263336 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
3263268 ATATATATGT
*
3263278 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3263320 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
3263337 TCTGTTAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3263842 original size:20 final size:19
Alignment explanation
Indices: 3263780--3263831 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3263770 AAAACAATTT
* *
3263780 TTTTAAAA-TTTTATTTTT
1 TTTTAAAATTTTTATATTA
*
3263798 TATTTGAAATTTTTATATTA
1 T-TTTAAAATTTTTATATTA
3263818 TTTTAAAATTTTTA
1 TTTTAAAATTTTTA
3263832 ATTCTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.04
19 18 0.64
20 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTAAAATTTTTATATTA
Found at i:3267706 original size:21 final size:21
Alignment explanation
Indices: 3267682--3267723 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3267672 TGAAATGATG
*
3267682 CATTAGTTGGATGAAAGAATA
1 CATTAGTTGGATGAAAAAATA
**
3267703 CATTTTTTGGATGAAAAAATA
1 CATTAGTTGGATGAAAAAATA
3267724 TAACTTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (21 bp):
CATTAGTTGGATGAAAAAATA
Found at i:3267731 original size:21 final size:21
Alignment explanation
Indices: 3267688--3267731 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3267678 GATGCATTAG
* **
3267688 TTGGATGAAAGAATACATTTT
1 TTGGATGAAAAAATACAACTT
*
3267709 TTGGATGAAAAAATATAACTT
1 TTGGATGAAAAAATACAACTT
3267730 TT
1 TT
3267732 ATCACCAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (21 bp):
TTGGATGAAAAAATACAACTT
Found at i:3268764 original size:14 final size:15
Alignment explanation
Indices: 3268745--3268780 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3268735 ATATGTGTTT
3268745 TTATAAAAAATAA-A
1 TTATAAAAAATAATA
3268759 TTATAAAAAATAATA
1 TTATAAAAAATAATA
3268774 TT-TAAAA
1 TTATAAAA
3268781 TTTAAACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTATAAAAAATAATA
Found at i:3269038 original size:6 final size:6
Alignment explanation
Indices: 3269029--3269053 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3269019 ACTTGCCGGT
3269029 CTTGCC CTTGCC CTTGCC CTTGCC C
1 CTTGCC CTTGCC CTTGCC CTTGCC C
3269054 AGATAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.16, T:0.32
Consensus pattern (6 bp):
CTTGCC
Found at i:3272653 original size:2 final size:2
Alignment explanation
Indices: 3272646--3272680 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3272636 TGTGCCACTC
3272646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3272681 TTAAATATTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3279464 original size:3 final size:3
Alignment explanation
Indices: 3279456--3279495 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
3279446 ATCTGTCCAA
* *
3279456 TAT TAT TAT TAT TAT TAT TAT TAT TCT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3279496 TCATCTTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3279875 original size:22 final size:23
Alignment explanation
Indices: 3279836--3279880 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3279826 TTTTTTTTGG
*
3279836 TTATTTTAAAATCGC-AAATAAA
1 TTATTATAAAATCGCAAAATAAA
3279858 TTATTATAAAAT-GTCAAAATAAA
1 TTATTATAAAATCG-CAAAATAAA
3279881 AAAATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 12 0.60
23 7 0.35
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (23 bp):
TTATTATAAAATCGCAAAATAAA
Found at i:3279959 original size:2 final size:2
Alignment explanation
Indices: 3279952--3279984 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3279942 AGTGTTACGT
3279952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3279985 TTCTTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3280921 original size:20 final size:20
Alignment explanation
Indices: 3280880--3280922 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3280870 ACTATTTAAA
*
3280880 TTTAAAATAATTTTTCCTTG
1 TTTAAAATAATTTTTCATTG
3280900 TTTAAAAT-ATTTTTCATGTG
1 TTTAAAATAATTTTTCAT-TG
3280920 TTT
1 TTT
3280923 TTTTTATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTAAAATAATTTTTCATTG
Found at i:3282006 original size:47 final size:47
Alignment explanation
Indices: 3281953--3282043 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
3281943 CCAAAAGAAC
*
3281953 AAAAGATTTAGTTATTAACTACTAAAGACTTAAAGCAATTTAGGAAA
1 AAAAGATTTAGTTACTAACTACTAAAGACTTAAAGCAATTTAGGAAA
* *
3282000 AAAAGATTTGGTTACTAACTACTAAAGACTTTAAGCAATTTAGG
1 AAAAGATTTAGTTACTAACTACTAAAGACTTAAAGCAATTTAGG
3282044 TAGGTGTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (47 bp):
AAAAGATTTAGTTACTAACTACTAAAGACTTAAAGCAATTTAGGAAA
Found at i:3283339 original size:213 final size:216
Alignment explanation
Indices: 3282930--3283344 Score: 527
Period size: 213 Copynumber: 1.9 Consensus size: 216
3282920 AAACTTCTTA
* *
3282930 GAATAATTCAACATGGTAAAACATAAGATTAATAATTTTGAACTACTTTTAAATGCCTTTTCAAA
1 GAATAATTCAACATGGTAAAACACAAGATTAATAATGTTGAACTACTTTTAAATGCCTTTTCAAA
* * **
3282995 CAAAAATGGAGTTTAAGGCATTACAAAAAAATAAAAACCTTGAATATATTAAGCTATGGTTGATC
66 CAAAAATAGAGTTTAAGG-ATTAC-AAAAAATAAAAACCTTAAATATATTAAGCTATGACTGATC
* * * * *
3283060 TATTATTATGTTGTGTGTACATAATCTTACTTGAGTGAATTTGGTGTTCTAAATATGAACTTAAT
129 CATTATTATGTTGTGTATAAATAATCTTACTTGAATGAATTTAGTGTTCTAAATATGAACTTAAT
3283125 GGATTTTATTTAAAACTTGTAGG
194 GGATTTTATTTAAAACTTGTAGG
* * * * *
3283148 GAATAGTTCAAGATGGTAAAACACGATATTAATAA-GTTGGACTACTTTTAAATGCCTTTTCAAA
1 GAATAATTCAACATGGTAAAACACAAGATTAATAATGTTGAACTACTTTTAAATGCCTTTTCAAA
* **
3283212 CAAAATTAGAGTTTAA-G-TTATC-AAAAATAAAAATGTTAAAATATATTAAGCTATGACTGA-C
66 CAAAAATAGAGTTTAAGGATTA-CAAAAAATAAAAACCTT-AAATATATTAAGCTATGACTGATC
* * * **
3283273 CCTTGTTATGTTGTGTATAAATAATCTTGCTTGAATGAATTTAGT-TTACTAAATATGATGTTAA
129 CATTATTATGTTGTGTATAAATAATCTTACTTGAATGAATTTAGTGTT-CTAAATATGAACTTAA
3283337 TGGATTTT
193 TGGATTTT
3283345 GTGCCTCTTT
Statistics
Matches: 170, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
212 2 0.01
213 73 0.43
214 22 0.13
215 1 0.01
216 1 0.01
217 41 0.24
218 30 0.18
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (216 bp):
GAATAATTCAACATGGTAAAACACAAGATTAATAATGTTGAACTACTTTTAAATGCCTTTTCAAA
CAAAAATAGAGTTTAAGGATTACAAAAAATAAAAACCTTAAATATATTAAGCTATGACTGATCCA
TTATTATGTTGTGTATAAATAATCTTACTTGAATGAATTTAGTGTTCTAAATATGAACTTAATGG
ATTTTATTTAAAACTTGTAGG
Found at i:3288398 original size:2 final size:2
Alignment explanation
Indices: 3288391--3288434 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3288381 TTTAATAATG
3288391 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
3288433 AT
1 AT
3288435 GTAAGCAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3291592 original size:25 final size:24
Alignment explanation
Indices: 3291517--3291594 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
3291507 ATATTAAAAA
*
3291517 AAATT-AATTTTTCATATTATTAT
1 AAATTAAAATTTTCATATTATTAT
* * *
3291540 AAAGTTTAAA-TTT-ATAGTGAATTTT
1 AAA-TTAAAATTTTCATA-T-TATTAT
3291565 AAATATAAAATTTTCATATTATTAT
1 AAAT-TAAAATTTTCATATTATTAT
3291590 AAATT
1 AAATT
3291595 TTAAAGTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
23 6 0.14
24 8 0.19
25 21 0.50
26 4 0.10
27 3 0.07
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (24 bp):
AAATTAAAATTTTCATATTATTAT
Found at i:3292295 original size:2 final size:2
Alignment explanation
Indices: 3292282--3292316 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3292272 AAGTTTTGCC
*
3292282 AT AT AC 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
3292317 GGCAATCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3293665 original size:24 final size:23
Alignment explanation
Indices: 3293592--3293665 Score: 55
Period size: 24 Copynumber: 3.2 Consensus size: 23
3293582 GAGGATTTGT
* *
3293592 AATTTTATCTGTATAAAAGTTATA
1 AATTTTATCT-TGTAAAAGTTTTA
* *
3293616 AATTATT-TGTTG-AAGAGTTTGT-
1 AATT-TTATCTTGTAAAAGTTT-TA
3293638 AATTTTATCTATGTAAAAGTTTTA
1 AATTTTATCT-TGTAAAAGTTTTA
3293662 AATT
1 AATT
3293666 GTAATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 2 0.05
22 12 0.32
23 5 0.13
24 17 0.45
25 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (23 bp):
AATTTTATCTTGTAAAAGTTTTA
Found at i:3299648 original size:24 final size:23
Alignment explanation
Indices: 3299575--3299648 Score: 55
Period size: 24 Copynumber: 3.2 Consensus size: 23
3299565 GAGGATTTGT
* *
3299575 AATTTTATCTGTATAAAAGTTATA
1 AATTTTATCT-TGTAAAAGTTTTA
* *
3299599 AATTATT-TGTTG-AAGAGTTTGT-
1 AATT-TTATCTTGTAAAAGTTT-TA
3299621 AATTTTATCTATGTAAAAGTTTTA
1 AATTTTATCT-TGTAAAAGTTTTA
3299645 AATT
1 AATT
3299649 GTAATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 2 0.05
22 12 0.32
23 5 0.13
24 17 0.45
25 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (23 bp):
AATTTTATCTTGTAAAAGTTTTA
Found at i:3301462 original size:21 final size:20
Alignment explanation
Indices: 3301432--3301476 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3301422 CGAATAGATA
3301432 TTATTCAATATAAATAA-TTAT
1 TTATTCAATA-AAA-AATTTAT
*
3301453 TTATTTAATAAAAAATTTAT
1 TTATTCAATAAAAAATTTAT
3301473 TTAT
1 TTAT
3301477 AAAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 11 0.50
21 9 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTCAATAAAAAATTTAT
Found at i:3301478 original size:15 final size:16
Alignment explanation
Indices: 3301451--3301481 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3301441 ATAAATAATT
3301451 ATTTATTTAATAAAAA
1 ATTTATTTAATAAAAA
3301467 ATTTATTT-ATAAAAA
1 ATTTATTTAATAAAAA
3301482 TATATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTATTTAATAAAAA
Found at i:3304449 original size:18 final size:17
Alignment explanation
Indices: 3304423--3304456 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3304413 TAAGAGAAGA
*
3304423 AGAAAGAAGGAAAGAAT
1 AGAAAGAAGAAAAGAAT
3304440 AGAAATGAAGAAAAGAA
1 AGAAA-GAAGAAAAGAA
3304457 AAGGGAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (17 bp):
AGAAAGAAGAAAAGAAT
Found at i:3315371 original size:21 final size:23
Alignment explanation
Indices: 3315346--3315393 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
3315336 GGTATAACAA
3315346 TATT-AATAAT-TTATTATTTAT
1 TATTAAATAATATTATTATTTAT
*
3315367 TATTAAAATAATATTATTATTTTT
1 TATT-AAATAATATTATTATTTAT
3315391 TAT
1 TAT
3315394 GTTGTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
23 6 0.26
24 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTAAATAATATTATTATTTAT
Found at i:3587272 original size:13 final size:13
Alignment explanation
Indices: 3587254--3587279 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3587244 TCATTTCAAG
3587254 TTTTATTTTTTAT
1 TTTTATTTTTTAT
3587267 TTTTATTTTTTAT
1 TTTTATTTTTTAT
3587280 CAAATTAGGA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:3587559 original size:23 final size:24
Alignment explanation
Indices: 3587526--3587576 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
3587516 GGGAAAGGAA
* **
3587526 AATTTGAGATGAAATATTTTTAAT
1 AATTTGAGATGAAAAATAATTAAT
3587550 AATTT-AGATGAAAAATAATTAAT
1 AATTTGAGATGAAAAATAATTAAT
3587573 AATT
1 AATT
3587577 GATAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (24 bp):
AATTTGAGATGAAAAATAATTAAT
Found at i:3588402 original size:2 final size:2
Alignment explanation
Indices: 3588395--3588427 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3588385 TTTAAATGAT
3588395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3588428 GTCAAAATCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3588768 original size:6 final size:6
Alignment explanation
Indices: 3588743--3588776 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
3588733 AAACATCGTA
*
3588743 AAAAAG AAAGAAG GAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAA
3588777 TGCTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3590131 original size:2 final size:2
Alignment explanation
Indices: 3590124--3590149 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3590114 GCGTGGCCTC
3590124 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
3590150 GTGAGTGGGT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3592856 original size:2 final size:2
Alignment explanation
Indices: 3592849--3592878 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3592839 CCCTCCAAAC
3592849 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3592879 AATATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3593489 original size:2 final size:2
Alignment explanation
Indices: 3593445--3593470 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3593435 CACAAAACAA
3593445 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
3593471 TATCAATTCT
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:3593489 original size:23 final size:21
Alignment explanation
Indices: 3593463--3593506 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3593453 ATATATATAT
*
3593463 ATATATATTATCAATTCTACA
1 ATATATATAATCAATTCTACA
*
3593484 ATATATATAATCAATTCTCCA
1 ATATATATAATCAATTCTACA
3593505 AT
1 AT
3593507 TTACTGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATATATAATCAATTCTACA
Found at i:3594129 original size:19 final size:19
Alignment explanation
Indices: 3594083--3594130 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3594073 GTAAATTATT
* *
3594083 AATATATCAACATTTATATA
1 AATATAT-AAGATTTAAATA
3594103 AATATATAAGATTTAAATA
1 AATATATAAGATTTAAATA
3594122 TAAT-TATAA
1 -AATATATAA
3594131 TATAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
AATATATAAGATTTAAATA
Done.