Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 20 of 26
Found at i:3169629 original size:23 final size:23
Alignment explanation
Indices: 3169585--3169634 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3169575 TTTTTAAATT
* **
3169585 ATTTAATTTTTAATTTTTATATTA
1 ATTTAATTTTTAATATGAATA-TA
3169609 ATTT-ATTTTTAATATGAATATA
1 ATTTAATTTTTAATATGAATATA
3169631 ATTT
1 ATTT
3169635 TTAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 6 0.26
23 13 0.57
24 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTAATTTTTAATATGAATATA
Found at i:3169705 original size:24 final size:24
Alignment explanation
Indices: 3169670--3169734 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
3169660 TCATAATTTT
3169670 TAATTATT-ATTTAATATAAATATA
1 TAATT-TTAATTTAATATAAATATA
** *
3169694 TAATTTTAATTTTTTATATATATA
1 TAATTTTAATTTAATATAAATATA
*
3169718 T-TTTTTAATTTAATATA
1 TAATTTTAATTTAATATA
3169735 TTTAATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATTTTAATTTAATATAAATATA
Found at i:3170603 original size:21 final size:23
Alignment explanation
Indices: 3170560--3170603 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3170550 ATTTTTAATA
*
3170560 TTTAAAATTATATAATAATATTT
1 TTTAAAATTATATAATAAAATTT
3170583 TTTAAAATTAT-T-ATAAAATTT
1 TTTAAAATTATATAATAAAATTT
3170604 ATGTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAAATTATATAATAAAATTT
Found at i:3170888 original size:12 final size:12
Alignment explanation
Indices: 3170871--3170904 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3170861 TTTATTGTTA
3170871 ATTTTTTATAAT
1 ATTTTTTATAAT
3170883 ATTTTTTATAAT
1 ATTTTTTATAAT
*
3170895 TTTTATTTAT
1 ATTT-TTTAT
3170905 GTATTGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTTATAAT
Found at i:3171954 original size:22 final size:20
Alignment explanation
Indices: 3171916--3171955 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
3171906 AAGTTTTATT
3171916 TAAATTTAATTAAAAATATA
1 TAAATTTAATTAAAAATATA
3171936 TAAATATTAATATAAAAATA
1 TAAAT-TTAAT-TAAAAATA
3171956 AATTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTAAAAATATA
Found at i:3172102 original size:176 final size:176
Alignment explanation
Indices: 3171808--3172166 Score: 664
Period size: 176 Copynumber: 2.0 Consensus size: 176
3171798 AGACCTCTTC
*
3171808 ATAAATTGAGCTATTCATCTAATTTATTTGAGTTAGATTTTAATTACGAATTTTTTTTATTTGAA
1 ATAAATTAAGCTATTCATCTAATTTATTTGAGTTAGATTTTAATTACGAATTTTTTTTATTTGAA
*
3171873 TCGATCTAATTTAAATTACCATTTAATAATAAAAAGTTTTATTTAAATTTAATTAAAAATATATA
66 TCGATCTAACTTAAATTACCATTTAATAATAAAAAGTTTTATTTAAATTTAATTAAAAATATATA
3171938 AATATTAATATAAAAATAAATTTTAAATTTTTATTAATTTATTAAT
131 AATATTAATATAAAAATAAATTTTAAATTTTTATTAATTTATTAAT
* *
3171984 ATAAATTAAGCTATTCATCTAATTTATTTGAGTTAGATTTTAGTTACGAGTTTTTTTTATTTGAA
1 ATAAATTAAGCTATTCATCTAATTTATTTGAGTTAGATTTTAATTACGAATTTTTTTTATTTGAA
3172049 TCGATCTAACTTAAATTACCATTTAATAATAAAAAGTTTTATTTAAATTTAATTAAAAATATATA
66 TCGATCTAACTTAAATTACCATTTAATAATAAAAAGTTTTATTTAAATTTAATTAAAAATATATA
* *
3172114 AATATTAATATAAAAGTCAATTTTAAATTTTTATTAATTTATTAAT
131 AATATTAATATAAAAATAAATTTTAAATTTTTATTAATTTATTAAT
3172160 ATAAATT
1 ATAAATT
3172167 TTGGTTTAAG
Statistics
Matches: 177, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 177 1.00
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (176 bp):
ATAAATTAAGCTATTCATCTAATTTATTTGAGTTAGATTTTAATTACGAATTTTTTTTATTTGAA
TCGATCTAACTTAAATTACCATTTAATAATAAAAAGTTTTATTTAAATTTAATTAAAAATATATA
AATATTAATATAAAAATAAATTTTAAATTTTTATTAATTTATTAAT
Found at i:3177041 original size:14 final size:15
Alignment explanation
Indices: 3177005--3177054 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3176995 ATGATATTAA
3177005 ATATATTAAAT-TAATT
1 ATAT-TTAAATAT-ATT
3177021 ATATTTAAATATATT
1 ATATTTAAATATATT
* *
3177036 AT-TTTATATTTATT
1 ATATTTAAATATATT
3177050 ATATT
1 ATATT
3177055 ATTTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.40
15 13 0.43
16 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTAAATATATT
Found at i:3177044 original size:20 final size:21
Alignment explanation
Indices: 3177001--3177067 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 21
3176991 AAATATGATA
*
3177001 TTAAATATATTAAATTAATTATAT
1 TTAAATATATT--ATT-TTTATAT
3177025 TTAAATATATTA-TTTTATAT
1 TTAAATATATTATTTTTATAT
*
3177045 TT-ATTATATTATTTTTATAT
1 TTAAATATATTATTTTTATAT
3177065 TTA
1 TTA
3177068 CTAACATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 8 0.21
20 18 0.46
21 1 0.03
22 1 0.03
24 11 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAATATATTATTTTTATAT
Found at i:3177056 original size:14 final size:14
Alignment explanation
Indices: 3177006--3177055 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
3176996 TGATATTAAA
*
3177006 TATATTAAATTAAT
1 TATATTAAATTTAT
*
3177020 TATATTTAAATATAT
1 TATA-TTAAATTTAT
* *
3177035 TATTTTATATTTAT
1 TATATTAAATTTAT
3177049 TATATTA
1 TATATTA
3177056 TTTTTATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATTAAATTTAT
Found at i:3177061 original size:14 final size:14
Alignment explanation
Indices: 3177006--3177062 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
3176996 TGATATTAAA
* *
3177006 TATATTAAATTAAT
1 TATATTATATTTAT
* *
3177020 TATATTTAAATATAT
1 TATA-TTATATTTAT
*
3177035 TATTTTATATTTAT
1 TATATTATATTTAT
*
3177049 TATATTATTTTTAT
1 TATATTATATTTAT
3177063 ATTTACTAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
14 24 0.69
15 11 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTATATTTAT
Found at i:3177499 original size:2 final size:2
Alignment explanation
Indices: 3177492--3177517 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3177482 AGCAAATACA
3177492 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
3177518 GAAAGAGTTA
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:3180816 original size:29 final size:29
Alignment explanation
Indices: 3180782--3180839 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3180772 TTATGAACAT
3180782 AATATACA-TACTAAAATTACCAAGTCTAC
1 AATATA-ATTACTAAAATTACCAAGTCTAC
3180811 AATATAATTACTAAAATTACCAAGTCTAC
1 AATATAATTACTAAAATTACCAAGTCTAC
3180840 CCCGGTAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.29
Consensus pattern (29 bp):
AATATAATTACTAAAATTACCAAGTCTAC
Found at i:3185404 original size:12 final size:12
Alignment explanation
Indices: 3185387--3185454 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 12
3185377 ATTTATTTAA
3185387 ATTTTTTATATT
1 ATTTTTTATATT
3185399 ATTTTTTTAAATATT
1 A-TTTTTT--ATATT
3185414 A-TTTTTAT-TT
1 ATTTTTTATATT
*
3185424 AATTTTTTATA-A
1 -ATTTTTTATATT
3185436 ATTTTTTAT-TT
1 ATTTTTTATATT
*
3185447 AATTTTTA
1 ATTTTTTA
3185455 AACGTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.04
11 19 0.41
12 8 0.17
13 11 0.24
15 6 0.13
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:3185404 original size:13 final size:13
Alignment explanation
Indices: 3185388--3185434 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
3185378 TTTATTTAAA
3185388 TTTTTTATATTAT
1 TTTTTTATATTAT
*
3185401 TTTTTTA-AATAT
1 TTTTTTATATTAT
*
3185413 TATTTTTAT-TTAA
1 T-TTTTTATATTAT
3185426 TTTTTTATA
1 TTTTTTATA
3185435 AATTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 12 0.43
13 16 0.57
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTATATTAT
Found at i:3185527 original size:30 final size:27
Alignment explanation
Indices: 3185473--3185535 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 27
3185463 TTACTTCACG
*
3185473 TATATTTTTAATTTTTATATTATAATAA
1 TATATATTTAATTTTTATATTATAA-AA
*
3185501 TATATATTTAATTTTTATATAATATAAAT
1 TATATATTTAATTTTTATAT--TATAAAA
3185530 TATATA
1 TATATA
3185536 ATATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 19 0.61
29 7 0.23
30 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TATATATTTAATTTTTATATTATAAAA
Found at i:3185534 original size:14 final size:14
Alignment explanation
Indices: 3185515--3185550 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
3185505 TATTTAATTT
3185515 TTATATAATATAAA
1 TTATATAATATAAA
*
3185529 TTATATAATATATA
1 TTATATAATATAAA
3185543 TATATATA
1 T-TATATA
3185551 TGAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:3185536 original size:9 final size:11
Alignment explanation
Indices: 3185493--3185551 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
3185483 ATTTTTATAT
3185493 TATA-ATAATA
1 TATATATAATA
* *
3185503 TATATTTAATT
1 TATATATAATA
*
3185514 TTTATATAATA
1 TATATATAATA
3185525 TAAATTATATAATA
1 T--A-TATATAATA
3185539 TATATAT-ATA
1 TATATATAATA
3185549 TAT
1 TAT
3185552 GAAAATAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 10 0.26
11 18 0.46
12 1 0.03
14 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATATATAATA
Found at i:3185546 original size:27 final size:27
Alignment explanation
Indices: 3185515--3185582 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
3185505 TATTTAATTT
* *
3185515 TTATATAATATAAATTATA-TAATATA
1 TTATATAATATAAATAAAAGTAATATA
3185541 -TATATATATATGAAAATAAAAGTAATATA
1 TTATATA-ATAT--AAATAAAAGTAATATA
3185570 TTATATAAT-TAAA
1 TTATATAATATAAA
3185583 AGTTGAAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
25 6 0.17
26 7 0.20
28 7 0.20
29 9 0.26
30 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TTATATAATATAAATAAAAGTAATATA
Found at i:3185664 original size:17 final size:18
Alignment explanation
Indices: 3185644--3185677 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3185634 TCTAAATTTA
3185644 TTTTTTAAA-TTTAATAT
1 TTTTTTAAATTTTAATAT
3185661 TTTTTTAAATTTTAATA
1 TTTTTTAAATTTTAATA
3185678 ATTATCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTTAAATTTTAATAT
Found at i:3190156 original size:34 final size:35
Alignment explanation
Indices: 3190106--3190404 Score: 192
Period size: 34 Copynumber: 8.8 Consensus size: 35
3190096 TCAAGAGAGA
*
3190106 AAGCTTTATAGGTTGAGTTTTTCAACCAA-GAAAG
1 AAGCTTTATAGGTTGAGTATTTCAACCAAGGAAAG
* *
3190140 AGGCTTTATAGCTTGAGTATTTCAACCAAGGAAA-
1 AAGCTTTATAGGTTGAGTATTTCAACCAAGGAAAG
* * *
3190174 AATCTTTATAGGTT---TTTTTCAACTAAGGAAAG
1 AAGCTTTATAGGTTGAGTATTTCAACCAAGGAAAG
* **
3190206 AAGCTTTATAGGTTGAGTATTTCAACAAAAAAAATG
1 AAGCTTTATAGGTTGAGTATTTCAACCAAGGAAA-G
* * * * * * *
3190242 AAGCTTTATATGTTGAATATCTCAACTACGAAAAT
1 AAGCTTTATAGGTTGAGTATTTCAACCAAGGAAAG
* * ** * * *
3190277 AAGTTTTACAGCCTGTGCCA-TTCAACCAAGGAAGG
1 AAGCTTTATAGGTTGAG-TATTTCAACCAAGGAAAG
* * *
3190312 AAGCTTTATAGATTGAATA-TTC--CC-AGAAAAG
1 AAGCTTTATAGGTTGAGTATTTCAACCAAGGAAAG
** *
3190343 AAGCTTTATTTGTTGAATATTTCAACCAA-GAAA-
1 AAGCTTTATAGGTTGAGTATTTCAACCAAGGAAAG
* *
3190376 AA-CAAATTATAGGTTGAGTATCTCAACCA
1 AAGC--TTTATAGGTTGAGTATTTCAACCA
3190405 TGAAGGGAAT
Statistics
Matches: 200, Mismatches: 52, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
31 36 0.18
32 19 0.09
33 2 0.01
34 65 0.32
35 48 0.24
36 30 0.15
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (35 bp):
AAGCTTTATAGGTTGAGTATTTCAACCAAGGAAAG
Found at i:3190212 original size:66 final size:67
Alignment explanation
Indices: 3190091--3190231 Score: 187
Period size: 66 Copynumber: 2.1 Consensus size: 67
3190081 CATTAGATAA
* * *
3190091 TTCAATCAAGAGAGAAAGCTTTATAGGTTGAGTTTTTCAACCAAGAAAGAGGCTTTATAGCTTGA
1 TTCAACCAAGAGAAAAAGCTTTATAGGTT--GTTTTTCAACCAAGAAAGAAGCTTTATAGCTTGA
3190156 GTAT
64 GTAT
* * *
3190160 TTCAACCAAG-GAAAAATCTTTATAGGTT-TTTTTCAACTAAGGAAAGAAGCTTTATAGGTTGAG
1 TTCAACCAAGAGAAAAAGCTTTATAGGTTGTTTTTCAACCAA-GAAAGAAGCTTTATAGCTTGAG
3190223 TAT
65 TAT
3190226 TTCAAC
1 TTCAAC
3190232 AAAAAAAATG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
65 11 0.17
66 29 0.45
68 16 0.25
69 9 0.14
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (67 bp):
TTCAACCAAGAGAAAAAGCTTTATAGGTTGTTTTTCAACCAAGAAAGAAGCTTTATAGCTTGAGT
AT
Found at i:3190549 original size:35 final size:34
Alignment explanation
Indices: 3190497--3190666 Score: 146
Period size: 34 Copynumber: 4.9 Consensus size: 34
3190487 AGTTAGCGTC
*
3190497 TTTCCTTAGTTGAAAAAACTCAACCTATAAAGCTCT
1 TTTCCTTGGTTG-AAAAACTCAACCTATAAAGCT-T
* *
3190533 TTTCCTTAGTTGAAAAACTCAA--TAGCAAAGCTT
1 TTTCCTTGGTTGAAAAACTCAACCTA-TAAAGCTT
* * ** * * *
3190566 TCTTTCTTGGTTGAGATTCTCAACGTAAAAAGTTT
1 T-TTCCTTGGTTGAAAAACTCAACCTATAAAGCTT
* * *
3190601 TTTCCTTGGTTCAAATACTCAACCTATATAGCTT
1 TTTCCTTGGTTGAAAAACTCAACCTATAAAGCTT
* *
3190635 CTTTCCTTGGTTTAAAAACTCAATCTATAAAG
1 -TTTCCTTGGTTGAAAAACTCAACCTATAAAG
3190667 TATTCTTTCT
Statistics
Matches: 109, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
33 4 0.04
34 47 0.43
35 44 0.40
36 14 0.13
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (34 bp):
TTTCCTTGGTTGAAAAACTCAACCTATAAAGCTT
Found at i:3190570 original size:36 final size:35
Alignment explanation
Indices: 3190497--3190564 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
3190487 AGTTAGCGTC
*
3190497 TTTCCTTAGTTGAAAAAACTCAACCTATAAAGCTCT
1 TTTCCTTAGTTGAAAAAACTCAA-CTACAAAGCTCT
3190533 TTTCCTTAGTTG-AAAAACTCAA-TAGCAAAGCT
1 TTTCCTTAGTTGAAAAAACTCAACTA-CAAAGCT
3190565 TTCTTTCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.07
34 6 0.20
35 10 0.33
36 12 0.40
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (35 bp):
TTTCCTTAGTTGAAAAAACTCAACTACAAAGCTCT
Found at i:3192293 original size:29 final size:29
Alignment explanation
Indices: 3192214--3192293 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
3192204 TATATTTTGC
*
3192214 CAAACCTTAAAGGGGTAAGTGCATGTTTTT
1 CAAACCTT-AAGGGGTAAGTGCATGTTTAT
* * *
3192244 TAAA-CTAAAGGGGGCTAAGTGGAT-TTCTAT
1 CAAACCTTAA-GGGG-TAAGTGCATGTT-TAT
3192274 CAAACCTTAAGGGGTAAGTG
1 CAAACCTTAAGGGGTAAGTG
3192294 TCTGTTAGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.05
29 14 0.35
30 20 0.50
31 4 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (29 bp):
CAAACCTTAAGGGGTAAGTGCATGTTTAT
Found at i:3194979 original size:18 final size:18
Alignment explanation
Indices: 3194952--3194993 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3194942 AAATCCCCCT
*
3194952 TGTTTTCTTTCTCTCCTC
1 TGTTTCCTTTCTCTCCTC
*
3194970 TGTTTCCTTTTTCTCCTC
1 TGTTTCCTTTCTCTCCTC
3194988 TGTTTC
1 TGTTTC
3194994 TTAAAGCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.31, G:0.07, T:0.62
Consensus pattern (18 bp):
TGTTTCCTTTCTCTCCTC
Found at i:3195292 original size:19 final size:19
Alignment explanation
Indices: 3195270--3195320 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
3195260 ATTAAAATTT
3195270 TATTTAAATATTAATAAAA
1 TATTTAAATATTAATAAAA
** * *
3195289 TATTTTCATATCAATTAAA
1 TATTTAAATATTAATAAAA
*
3195308 T-TTAAAATATTAA
1 TATTTAAATATTAA
3195321 ATTATTTATG
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTTAAATATTAATAAAA
Found at i:3197290 original size:15 final size:16
Alignment explanation
Indices: 3197271--3197313 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
3197261 AATGAAGTAA
3197271 ATTAATAAAAAATAAT
1 ATTAATAAAAAATAAT
3197287 -TTAATATAAAAAATAAT
1 ATT-A-ATAAAAAATAAT
*
3197304 ATGAATAAAA
1 ATTAATAAAA
3197314 TTTAAATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 2 0.09
16 7 0.30
17 13 0.57
18 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
ATTAATAAAAAATAAT
Found at i:3197310 original size:18 final size:17
Alignment explanation
Indices: 3197275--3197310 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3197265 AAGTAAATTA
*
3197275 ATAAAAAATAATTTAAT
1 ATAAAAAATAATTGAAT
3197292 ATAAAAAATAATATGAAT
1 ATAAAAAATAAT-TGAAT
3197310 A
1 A
3197311 AAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAAAATAATTGAAT
Found at i:3202443 original size:18 final size:18
Alignment explanation
Indices: 3202420--3202456 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3202410 GCTGGAGGGA
*
3202420 TTCCTCGTCTTCGTCTTC
1 TTCCTCATCTTCGTCTTC
*
3202438 TTCCTCATCTTCGTTTTC
1 TTCCTCATCTTCGTCTTC
3202456 T
1 T
3202457 ACTCCATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.35, G:0.08, T:0.54
Consensus pattern (18 bp):
TTCCTCATCTTCGTCTTC
Found at i:3202492 original size:15 final size:15
Alignment explanation
Indices: 3202472--3202542 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
3202462 ATCTTCCTCG
* *
3202472 TCCTCTTCCTCACCA
1 TCCTCATCCTCATCA
*
3202487 TCCTCTTCCTCATCA
1 TCCTCATCCTCATCA
* *
3202502 TCATCATCATCATCA
1 TCCTCATCCTCATCA
* *
3202517 TCCTCCTCATCATCA
1 TCCTCATCCTCATCA
3202532 TCCTCATCCTC
1 TCCTCATCCTC
3202543 TGGGTCTTCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.35
Consensus pattern (15 bp):
TCCTCATCCTCATCA
Found at i:3202504 original size:3 final size:3
Alignment explanation
Indices: 3202496--3202539 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
3202486 ATCCTCTTCC
* * *
3202496 TCA TCA TCA TCA TCA TCA TCA TCC TCC TCA TCA TCA TCC TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
3202540 CTCTGGGTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.25, C:0.41, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:3202540 original size:6 final size:6
Alignment explanation
Indices: 3202485--3202542 Score: 50
Period size: 6 Copynumber: 10.2 Consensus size: 6
3202475 TCTTCCTCAC
* * * * *
3202485 CATCCT CTTCCT CATCAT CATCAT CATCAT CAT-C- C-TCCT CATCAT
1 CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT
3202530 CATCCT CATCCT C
1 CATCCT CATCCT C
3202543 TGGGTCTTCG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 1 0.02
4 2 0.05
5 1 0.02
6 39 0.91
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (6 bp):
CATCCT
Found at i:3203226 original size:19 final size:19
Alignment explanation
Indices: 3203202--3203240 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3203192 TACTCTTTTG
3203202 TAAGAGGAAAATTGAAAAC
1 TAAGAGGAAAATTGAAAAC
3203221 TAAGAGGAAAATTGAAAAC
1 TAAGAGGAAAATTGAAAAC
3203240 T
1 T
3203241 TTAAAACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (19 bp):
TAAGAGGAAAATTGAAAAC
Found at i:3204572 original size:5 final size:5
Alignment explanation
Indices: 3204562--3204595 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3204552 ACATTAAACT
*
3204562 TTTTC TTTTC TTTTC TTTTC TTTTC TGTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
3204596 TCAAATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:3206315 original size:4 final size:4
Alignment explanation
Indices: 3206306--3206377 Score: 62
Period size: 4 Copynumber: 19.0 Consensus size: 4
3206296 ATATAATTTT
* * * *
3206306 TTTC TTTC TTT- TTTT TTTC TTTT TTTC -TTC TTTC ATTC -ATC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
3206350 TTTT TTTC TTAC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
3206378 CCAGCCAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
3 11 0.20
4 44 0.80
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:3206319 original size:11 final size:11
Alignment explanation
Indices: 3206303--3206376 Score: 60
Period size: 11 Copynumber: 6.3 Consensus size: 11
3206293 CACATATAAT
3206303 TTTTTTCTTTC
1 TTTTTTCTTTC
*
3206314 TTTTTTTTTTC
1 TTTTTTCTTTC
3206325 TTTTTT-TCTTC
1 TTTTTTCT-TTC
*
3206336 TTTCATTCATCTTTT
1 TTT--TT--TCTTTC
*
3206351 TTTTTTCTTAC
1 TTTTTTCTTTC
3206362 TTTCTTTCTTTC
1 TTT-TTTCTTTC
3206374 TTT
1 TTT
3206377 CCCAGCCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
10 1 0.02
11 29 0.57
12 10 0.20
13 4 0.08
15 6 0.12
16 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:3206438 original size:3 final size:3
Alignment explanation
Indices: 3206430--3206488 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
3206420 GTATAGATAG
3206430 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3206477 ATA ATA ATA ATA
1 ATA ATA ATA ATA
3206489 CCTTTTTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3206640 original size:23 final size:23
Alignment explanation
Indices: 3206612--3206662 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 23
3206602 TAGATATAAA
3206612 TTTTTTTCTTTCTTTCTTTTTTTTC
1 TTTTTTTC--TCTTTCTTTTTTTTC
3206637 TTTTTTTCTCTTTCTTTTTTTTC
1 TTTTTTTCTCTTTCTTTTTTTTC
3206660 TTT
1 TTT
3206663 CTCTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 18 0.69
25 8 0.31
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTTCTCTTTCTTTTTTTTC
Found at i:3206669 original size:17 final size:17
Alignment explanation
Indices: 3206612--3206672 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 17
3206602 TAGATATAAA
*
3206612 TTTTTTTCTTTCTTTCT
1 TTTTTTTCTTTCTCTCT
3206629 TTTTTTTCTTTTTTTCTCTTTCT
1 TTTTTTTC----TTTCTC--TCT
3206652 TTTTTTTCTTTCTCTCT
1 TTTTTTTCTTTCTCTCT
3206669 TTTT
1 TTTT
3206673 CGGCTGCACC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 15 0.41
19 6 0.16
21 5 0.14
23 11 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTCTCTCT
Found at i:3206673 original size:23 final size:23
Alignment explanation
Indices: 3206622--3206673 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
3206612 TTTTTTTCTT
* *
3206622 TCTTTCTTTTTTTTCTTTTTTTC
1 TCTTTCTTTTTTTTCTTTCTCTC
3206645 TCTTTCTTTTTTTTCTTTCTCTC
1 TCTTTCTTTTTTTTCTTTCTCTC
*
3206668 TTTTTC
1 TCTTTC
3206674 GGCTGCACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
TCTTTCTTTTTTTTCTTTCTCTC
Found at i:3207068 original size:2 final size:2
Alignment explanation
Indices: 3207061--3207096 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3207051 AGCAAATACA
3207061 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
3207097 GAAAGAGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3210375 original size:29 final size:29
Alignment explanation
Indices: 3210341--3210398 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3210331 TTATGAACAT
3210341 AATATACA-TACTAAAATTACCAAGTCTAC
1 AATATA-ATTACTAAAATTACCAAGTCTAC
3210370 AATATAATTACTAAAATTACCAAGTCTAC
1 AATATAATTACTAAAATTACCAAGTCTAC
3210399 CCCGGTAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.29
Consensus pattern (29 bp):
AATATAATTACTAAAATTACCAAGTCTAC
Found at i:3214969 original size:12 final size:12
Alignment explanation
Indices: 3214952--3215019 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 12
3214942 ATTTATTTAA
3214952 ATTTTTTATATT
1 ATTTTTTATATT
3214964 ATTTTTTTAAATATT
1 A-TTTTTT--ATATT
3214979 A-TTTTTAT-TT
1 ATTTTTTATATT
*
3214989 AATTTTTTATA-A
1 -ATTTTTTATATT
3215001 ATTTTTTAT-TT
1 ATTTTTTATATT
*
3215012 AATTTTTA
1 ATTTTTTA
3215020 AACGTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.04
11 19 0.41
12 8 0.17
13 11 0.24
15 6 0.13
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:3214969 original size:13 final size:13
Alignment explanation
Indices: 3214953--3214999 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
3214943 TTTATTTAAA
3214953 TTTTTTATATTAT
1 TTTTTTATATTAT
*
3214966 TTTTTTA-AATAT
1 TTTTTTATATTAT
*
3214978 TATTTTTAT-TTAA
1 T-TTTTTATATTAT
3214991 TTTTTTATA
1 TTTTTTATA
3215000 AATTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 12 0.43
13 16 0.57
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTATATTAT
Found at i:3215100 original size:14 final size:14
Alignment explanation
Indices: 3215081--3215116 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
3215071 TATTTAATTT
3215081 TTATATAATATAAA
1 TTATATAATATAAA
*
3215095 TTATATAATATATA
1 TTATATAATATAAA
3215109 TATATATA
1 T-TATATA
3215117 TGAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:3215102 original size:9 final size:11
Alignment explanation
Indices: 3215059--3215117 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
3215049 ATTTTTATAT
3215059 TATA-ATAATA
1 TATATATAATA
* *
3215069 TATATTTAATT
1 TATATATAATA
*
3215080 TTTATATAATA
1 TATATATAATA
3215091 TAAATTATATAATA
1 T--A-TATATAATA
3215105 TATATAT-ATA
1 TATATATAATA
3215115 TAT
1 TAT
3215118 GAAAATAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 10 0.26
11 18 0.46
12 1 0.03
14 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATATATAATA
Found at i:3215112 original size:27 final size:27
Alignment explanation
Indices: 3215081--3215148 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
3215071 TATTTAATTT
* *
3215081 TTATATAATATAAATTATA-TAATATA
1 TTATATAATATAAATAAAAGTAATATA
3215107 -TATATATATATGAAAATAAAAGTAATATA
1 TTATATA-ATAT--AAATAAAAGTAATATA
3215136 TTATATAAT-TAAA
1 TTATATAATATAAA
3215149 AGTTAAAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
25 6 0.17
26 7 0.20
28 7 0.20
29 9 0.26
30 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TTATATAATATAAATAAAAGTAATATA
Found at i:3219698 original size:34 final size:34
Alignment explanation
Indices: 3219654--3219966 Score: 153
Period size: 34 Copynumber: 9.2 Consensus size: 34
3219644 CATTAGATAA
* * *
3219654 TTCAATCAAGAGAGAAACTTTATAGGTTGAGTTT
1 TTCAACCAAGAAAGAAACTTTATAGGTTGAGTAT
** *
3219688 TTCAACCAAGAAAGAGGCTTTATAGCTTGAGTAT
1 TTCAACCAAGAAAGAAACTTTATAGGTTGAGTAT
* *
3219722 TTCAACCAAGGAAA-AATCTTTATAGGTT---TTT
1 TTCAACCAA-GAAAGAAACTTTATAGGTTGAGTAT
* *
3219753 TTCAACTAAGGAAAGAAGCTTTATAGGTTGAGTAT
1 TTCAACCAA-GAAAGAAACTTTATAGGTTGAGTAT
* * * * *
3219788 TTCAACAAAAAAAATGAAGCTTTATATGTTGAATAT
1 TTCAAC-CAAGAAA-GAAACTTTATAGGTTGAGTAT
* * * * * ** *
3219824 CTCAACTACGAAA-ATAAGTTTTACAGCCTGTGTCA-
1 TTCAACCAAGAAAGA-AA-CTTTATAGGTTGAGT-AT
* * * *
3219859 TTCAACCAAGGAAGGAAGCTTTATAGATTGAATA-
1 TTCAACCAA-GAAAGAAACTTTATAGGTTGAGTAT
* ** *
3219893 TTC--CC-AGAAAAGAAGCTTTATTTGTTGAATAT
1 TTCAACCAAG-AAAGAAACTTTATAGGTTGAGTAT
**
3219925 TTCAACCAAGAAA-AACAAATTATAGGTTGAGTAT
1 TTCAACCAAGAAAGAA-ACTTTATAGGTTGAGTAT
*
3219959 CTCAACCA
1 TTCAACCA
3219967 TGAAGGGAAT
Statistics
Matches: 210, Mismatches: 51, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
30 1 0.00
31 35 0.17
32 18 0.09
33 3 0.01
34 77 0.37
35 44 0.21
36 31 0.15
37 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (34 bp):
TTCAACCAAGAAAGAAACTTTATAGGTTGAGTAT
Found at i:3219784 original size:66 final size:66
Alignment explanation
Indices: 3219654--3219793 Score: 185
Period size: 66 Copynumber: 2.1 Consensus size: 66
3219644 CATTAGATAA
* * *
3219654 TTCAATCAAGAGAGAAACTTTATAGGTTGAGTTTTTCAACCAAGAAAGAGGCTTTATAGCTTGAG
1 TTCAACCAAGAGAAAAACTTTATAGGTT--GTTTTTCAACCAAGAAAGAAGCTTTATAGCTTGAG
3219719 TAT
64 TAT
* *
3219722 TTCAACCAAG-GAAAAATCTTTATAGGTT-TTTTTCAACTAAGGAAAGAAGCTTTATAGGTTGAG
1 TTCAACCAAGAGAAAAA-CTTTATAGGTTGTTTTTCAACCAA-GAAAGAAGCTTTATAGCTTGAG
3219785 TAT
64 TAT
3219788 TTCAAC
1 TTCAAC
3219794 AAAAAAAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
65 11 0.17
66 29 0.45
67 5 0.08
68 20 0.31
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (66 bp):
TTCAACCAAGAGAAAAACTTTATAGGTTGTTTTTCAACCAAGAAAGAAGCTTTATAGCTTGAGTA
T
Found at i:3220111 original size:35 final size:34
Alignment explanation
Indices: 3220059--3220228 Score: 146
Period size: 34 Copynumber: 4.9 Consensus size: 34
3220049 AGTTAGCGTC
*
3220059 TTTCCTTAGTTGAAAAAACTCAACCTATAAAGCTCT
1 TTTCCTTGGTTG-AAAAACTCAACCTATAAAGCT-T
* *
3220095 TTTCCTTAGTTGAAAAACTCAA--TAGCAAAGCTT
1 TTTCCTTGGTTGAAAAACTCAACCTA-TAAAGCTT
* * ** * * *
3220128 TCTTTCTTGGTTGAGATTCTCAACGTAAAAAGTTT
1 T-TTCCTTGGTTGAAAAACTCAACCTATAAAGCTT
* * *
3220163 TTTCCTTGGTTCAAATACTCAACCTATATAGCTT
1 TTTCCTTGGTTGAAAAACTCAACCTATAAAGCTT
* *
3220197 CTTTCCTTGGTTTAAAAACTCAATCTATAAAG
1 -TTTCCTTGGTTGAAAAACTCAACCTATAAAG
3220229 TATTCTTTCT
Statistics
Matches: 109, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
33 4 0.04
34 47 0.43
35 44 0.40
36 14 0.13
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (34 bp):
TTTCCTTGGTTGAAAAACTCAACCTATAAAGCTT
Found at i:3220132 original size:36 final size:35
Alignment explanation
Indices: 3220059--3220126 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
3220049 AGTTAGCGTC
*
3220059 TTTCCTTAGTTGAAAAAACTCAACCTATAAAGCTCT
1 TTTCCTTAGTTGAAAAAACTCAA-CTACAAAGCTCT
3220095 TTTCCTTAGTTG-AAAAACTCAA-TAGCAAAGCT
1 TTTCCTTAGTTGAAAAAACTCAACTA-CAAAGCT
3220127 TTCTTTCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.07
34 6 0.20
35 10 0.33
36 12 0.40
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (35 bp):
TTTCCTTAGTTGAAAAAACTCAACTACAAAGCTCT
Found at i:3221854 original size:29 final size:29
Alignment explanation
Indices: 3221775--3221854 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
3221765 TATATTTTGC
*
3221775 CAAACCTTAAAGGGGTAAGTGCATGTTTTT
1 CAAACCTT-AAGGGGTAAGTGCATGTTTAT
* * *
3221805 TAAA-CTAAAGGGGGCTAAGTGGAT-TTCTAT
1 CAAACCTTAA-GGGG-TAAGTGCATGTT-TAT
3221835 CAAACCTTAAGGGGTAAGTG
1 CAAACCTTAAGGGGTAAGTG
3221855 TCTGTTAGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.05
29 14 0.35
30 20 0.50
31 4 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (29 bp):
CAAACCTTAAGGGGTAAGTGCATGTTTAT
Found at i:3224533 original size:18 final size:18
Alignment explanation
Indices: 3224506--3224547 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3224496 AAATCCCCCT
*
3224506 TGTTTTCTTTCTCTCCTC
1 TGTTTCCTTTCTCTCCTC
*
3224524 TGTTTCCTTTTTCTCCTC
1 TGTTTCCTTTCTCTCCTC
3224542 TGTTTC
1 TGTTTC
3224548 TTAAAGCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.31, G:0.07, T:0.62
Consensus pattern (18 bp):
TGTTTCCTTTCTCTCCTC
Found at i:3224777 original size:30 final size:28
Alignment explanation
Indices: 3224734--3224790 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
3224724 CGAAGGAATC
*
3224734 ATTTTAATTTATATATTATTAAAATTATT
1 ATTTTAATTTATATATTA-AAAAATTATT
*
3224763 ATTTTAATTTTATATTTTAAAAAATTAT
1 ATTTTAA-TTTATATATTAAAAAATTAT
3224791 AATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTAATTTATATATTAAAAAATTATT
Found at i:3224845 original size:19 final size:19
Alignment explanation
Indices: 3224823--3224873 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
3224813 ATTAAAATTT
3224823 TATTTAAATATTAATAAAA
1 TATTTAAATATTAATAAAA
** * *
3224842 TATTTTCATATCAATTAAA
1 TATTTAAATATTAATAAAA
*
3224861 T-TTAAAATATTAA
1 TATTTAAATATTAA
3224874 ATTATTTATA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTTAAATATTAATAAAA
Found at i:3226844 original size:15 final size:15
Alignment explanation
Indices: 3226826--3226874 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
3226816 AATAATAATG
3226826 AAATAAATTAATAAA
1 AAATAAATTAATAAA
*
3226841 AAATAATTTAATATAAA
1 AAATAAATT-A-ATAAA
*
3226858 AAATAATATGAATAAA
1 AAATAA-ATTAATAAA
3226874 A
1 A
3226875 TTTAAATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 12 0.43
18 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AAATAAATTAATAAA
Found at i:3226871 original size:18 final size:17
Alignment explanation
Indices: 3226836--3226871 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3226826 AAATAAATTA
*
3226836 ATAAAAAATAATTTAAT
1 ATAAAAAATAATTGAAT
3226853 ATAAAAAATAATATGAAT
1 ATAAAAAATAAT-TGAAT
3226871 A
1 A
3226872 AAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAAAATAATTGAAT
Found at i:3232013 original size:18 final size:18
Alignment explanation
Indices: 3231990--3232026 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3231980 GCTGGAGGGA
*
3231990 TTCCTCGTCTTCGTCTTC
1 TTCCTCATCTTCGTCTTC
*
3232008 TTCCTCATCTTCGTTTTC
1 TTCCTCATCTTCGTCTTC
3232026 T
1 T
3232027 ACTCCATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.35, G:0.08, T:0.54
Consensus pattern (18 bp):
TTCCTCATCTTCGTCTTC
Found at i:3232062 original size:15 final size:15
Alignment explanation
Indices: 3232042--3232073 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3232032 ATCTTCCTCG
3232042 TCCTCTTCCTCACCA
1 TCCTCTTCCTCACCA
*
3232057 TCCTCTTCCTCATCA
1 TCCTCTTCCTCACCA
3232072 TC
1 TC
3232074 ATCATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (15 bp):
TCCTCTTCCTCACCA
Found at i:3232074 original size:3 final size:3
Alignment explanation
Indices: 3232066--3232109 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
3232056 ATCCTCTTCC
* * * *
3232066 TCA TCA TCA TCA TCA TCA TCC TCC TCC TCA TCA TCA TCC TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
3232110 CTCTGGGTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.23, C:0.43, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:3232090 original size:24 final size:24
Alignment explanation
Indices: 3232063--3232112 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
3232053 ACCATCCTCT
3232063 TCCTCATCATCATCATCATCATCC
1 TCCTCATCATCATCATCATCATCC
* *
3232087 TCCTCCTCATCATCATCCTCATCC
1 TCCTCATCATCATCATCATCATCC
3232111 TC
1 TC
3232113 TGGGTCTTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (24 bp):
TCCTCATCATCATCATCATCATCC
Found at i:3232098 original size:18 final size:18
Alignment explanation
Indices: 3232069--3232112 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
3232059 CTCTTCCTCA
*
3232069 TCATCATCATCATCATCC
1 TCATCCTCATCATCATCC
*
3232087 TCCTCCTCATCATCATCC
1 TCATCCTCATCATCATCC
3232105 TCATCCTC
1 TCATCCTC
3232113 TGGGTCTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.45, G:0.00, T:0.34
Consensus pattern (18 bp):
TCATCCTCATCATCATCC
Found at i:3232110 original size:6 final size:6
Alignment explanation
Indices: 3232055--3232112 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
3232045 TCTTCCTCAC
* * * *
3232055 CATCCT CTTCCT CATCATCAT CATCAT CATCCT CCTCCT CATCAT CATCCT
1 CATCCT CATCCT CATC--C-T CATCCT CATCCT CATCCT CATCCT CATCCT
3232106 CATCCT C
1 CATCCT C
3232113 TGGGTCTTCG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
6 35 0.85
8 1 0.02
9 5 0.12
ACGTcount: A:0.19, C:0.47, G:0.00, T:0.34
Consensus pattern (6 bp):
CATCCT
Found at i:3234797 original size:2 final size:2
Alignment explanation
Indices: 3234785--3234815 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3234775 TAATAGTGCA
*
3234785 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3234816 AAATAGCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3235843 original size:20 final size:20
Alignment explanation
Indices: 3235784--3235843 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
3235774 TTATTTATAA
*
3235784 ATTTTATTTTTATGTGTAAATT
1 ATTTTATATTTA--TGTAAATT
* * * *
3235806 ATATTAAATTAATATAAATT
1 ATTTTATATTTATGTAAATT
3235826 ATTTTATATTTATGTAAA
1 ATTTTATATTTATGTAAA
3235844 ATTAAATTAT
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 21 0.72
22 8 0.28
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTTATATTTATGTAAATT
Found at i:3237361 original size:18 final size:20
Alignment explanation
Indices: 3237334--3237371 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
3237324 TATTTGACTA
*
3237334 TAATATATTT-TA-AAAAAT
1 TAATAAATTTATATAAAAAT
3237352 TAATAAATTTATATAAAAAT
1 TAATAAATTTATATAAAAAT
3237372 AACGTGACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATAAATTTATATAAAAAT
Found at i:3240616 original size:2 final size:2
Alignment explanation
Indices: 3240609--3240640 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3240599 TGCTCTGAGA
3240609 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
3240641 TGGCCTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3241152 original size:24 final size:23
Alignment explanation
Indices: 3241087--3241152 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
3241077 ATAATTTTTG
** *
3241087 ATTAATTAATAATAAAAATAATT
1 ATTAATTAATTTTATAAATAATT
*
3241110 -TTAAAATAATTTTATTAAATAATT
1 ATT-AATTAATTTTA-TAAATAATT
3241134 ATTAATTAATTTTTATAAA
1 ATTAATTAA-TTTTATAAA
3241153 AAAATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
22 2 0.06
23 8 0.24
24 17 0.50
25 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTAATTAATTTTATAAATAATT
Found at i:3241415 original size:16 final size:17
Alignment explanation
Indices: 3241394--3241425 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3241384 CTTTATCAAT
3241394 TTAAAACTAA-AAAAAA
1 TTAAAACTAATAAAAAA
3241410 TTAAAACTAATAAAAA
1 TTAAAACTAATAAAAA
3241426 CAAGACTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
TTAAAACTAATAAAAAA
Found at i:3242780 original size:24 final size:24
Alignment explanation
Indices: 3242759--3242808 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
3242749 AGTTAAATTT
*
3242759 ATTTAATCAATAATTAAAAAATAA
1 ATTTAATAAATAATTAAAAAATAA
* * *
3242783 ATTTAATAAATTATTAAGAGATAA
1 ATTTAATAAATAATTAAAAAATAA
3242807 AT
1 AT
3242809 GTATAATGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATTTAATAAATAATTAAAAAATAA
Found at i:3244061 original size:20 final size:19
Alignment explanation
Indices: 3244029--3244080 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3244019 TATATAATTA
*
3244029 AATAGTTAATATTTATTTT
1 AATAATTAATATTTATTTT
3244048 AATAATTAATTATTTATTTT
1 AATAATTAA-TATTTATTTT
3244068 -ATATATT-ATATTT
1 AATA-ATTAATATTT
3244081 TGTGAAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 12 0.40
20 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AATAATTAATATTTATTTT
Found at i:3244281 original size:2 final size:2
Alignment explanation
Indices: 3244276--3244301 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3244266 TATATTCTCA
3244276 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
3244302 TCTCAAGTCC
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:3245086 original size:30 final size:30
Alignment explanation
Indices: 3245045--3245135 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
3245035 TTTTTAATTT
*
3245045 TTAAACATAATTAATTAATAAAAATTATTA
1 TTAATCATAATTAATTAATAAAAATTATTA
* *
3245075 TTAATCATAATTGATTAATGAAAA--A-TA
1 TTAATCATAATTAATTAATAAAAATTATTA
* *
3245102 TTAATTATGATTAATT-A-AAAAATTAATTA
1 TTAATCATAATTAATTAATAAAAATT-ATTA
3245131 TTAAT
1 TTAAT
3245136 TAAGTTCCTT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
25 4 0.08
26 1 0.02
27 15 0.30
28 2 0.04
29 7 0.14
30 21 0.42
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (30 bp):
TTAATCATAATTAATTAATAAAAATTATTA
Found at i:3245126 original size:22 final size:23
Alignment explanation
Indices: 3245086--3245131 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3245076 TAATCATAAT
3245086 TGATTAATGAAAAATATTAATTA
1 TGATTAATGAAAAATATTAATTA
*
3245109 TGATTAATTAAAAA-ATTAATTA
1 TGATTAATGAAAAATATTAATTA
3245131 T
1 T
3245132 TAATTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
TGATTAATGAAAAATATTAATTA
Found at i:3245137 original size:23 final size:23
Alignment explanation
Indices: 3245088--3245138 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
3245078 ATCATAATTG
*
3245088 ATTAATGAAAAATATTAATTATG
1 ATTAATGAAAAATATTAATTATA
*
3245111 ATTAATTAAAAA-ATTAATTATTA
1 ATTAATGAAAAATATTAATTA-TA
3245134 ATTAA
1 ATTAA
3245139 GTTCCTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTAATGAAAAATATTAATTATA
Found at i:3248595 original size:7 final size:7
Alignment explanation
Indices: 3248583--3248608 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3248573 ATTGTATCTA
3248583 TTTTTAT
1 TTTTTAT
3248590 TTTTTAT
1 TTTTTAT
3248597 TTTTTAT
1 TTTTTAT
3248604 TTTTT
1 TTTTT
3248609 TGTCCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:3253787 original size:32 final size:32
Alignment explanation
Indices: 3253751--3253813 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3253741 TATTCAAGAT
3253751 AACATCTTTCATATTACTCTAACCTCCATTAC
1 AACATCTTTCATATTACTCTAACCTCCATTAC
*
3253783 AACATCTTTCATGTTACTCTAACCTCCATTA
1 AACATCTTTCATATTACTCTAACCTCCATTA
3253814 TTTTTCACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.02, T:0.38
Consensus pattern (32 bp):
AACATCTTTCATATTACTCTAACCTCCATTAC
Found at i:3259000 original size:20 final size:19
Alignment explanation
Indices: 3258977--3259043 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
3258967 CCTAAATAAG
3258977 ATTTTAAATAATTAAAATT
1 ATTTTAAATAATTAAAATT
* ** *
3258996 AATTTATCTAATTTAAATT
1 ATTTTAAATAATTAAAATT
* *
3259015 ATTATTTAATAATAAAAATTT
1 ATT-TTAAATAATTAAAA-TT
3259036 ATTTTAAA
1 ATTTTAAA
3259044 ATTTATAAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 3
0.71 0.22 0.06
Matches are distributed among these distances:
19 17 0.49
20 13 0.37
21 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTAAATAATTAAAATT
Found at i:3259086 original size:30 final size:28
Alignment explanation
Indices: 3259012--3259088 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 28
3259002 TCTAATTTAA
3259012 ATTATTATTTAATAATAAAAATTTATTTT
1 ATTATT-TTTAATAATAAAAATTTATTTT
** *
3259041 AAAATTTATAAATAATATAAAATATTA-TTT
1 ATTATTT-TTAATAATA-AAAAT-TTATTTT
3259071 ATTATTTTTATATAATAA
1 ATTATTTTTA-ATAATAA
3259089 TTTATGTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.03
29 15 0.39
30 19 0.50
31 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTATTTTTAATAATAAAAATTTATTTT
Found at i:3259093 original size:21 final size:21
Alignment explanation
Indices: 3259067--3259106 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3259057 ATAAAATATT
*
3259067 ATTTAT-TATTTTTATATAATA
1 ATTTATGT-TTTTTAAATAATA
3259088 ATTTATGTTTTTTAAATAA
1 ATTTATGTTTTTTAAATAA
3259107 ATCATGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTATGTTTTTTAAATAATA
Found at i:3259999 original size:22 final size:22
Alignment explanation
Indices: 3259972--3260013 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3259962 AAATTAAAAT
3259972 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
3259994 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
3260014 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:3264471 original size:2 final size:2
Alignment explanation
Indices: 3264464--3264496 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3264454 AGCAGGTCGC
3264464 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
3264497 TATGGAACAT
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:3265400 original size:15 final size:14
Alignment explanation
Indices: 3265379--3265416 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
3265369 TTAGCTTATT
*
3265379 ATTTTTTTTAAATA
1 ATTTTTTTTAAAAA
3265393 ATTTTTTTTAAAAA
1 ATTTTTTTTAAAAA
3265407 ATTTATTTTT
1 ATTT-TTTTT
3265417 TCACCCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTTTTTAAAAA
Found at i:3265637 original size:13 final size:14
Alignment explanation
Indices: 3265612--3265645 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3265602 TACTATTCGT
3265612 AAATATATATATAA
1 AAATATATATATAA
*
3265626 AATTATAT-TATAA
1 AAATATATATATAA
3265639 AAATATA
1 AAATATA
3265646 AATTATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATATATATAA
Found at i:3266452 original size:12 final size:12
Alignment explanation
Indices: 3266420--3266463 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3266410 AACTAAAAAA
*
3266420 TAAAAAAAAATT
1 TAAAAAAATATT
3266432 ATAATAAAAATATT
1 -TAA-AAAAATATT
*
3266446 TAAAAAATTATT
1 TAAAAAAATATT
3266458 TAAAAA
1 TAAAAA
3266464 TTTAACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 14 0.50
13 6 0.21
14 8 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAAAAATATT
Found at i:3271444 original size:2 final size:2
Alignment explanation
Indices: 3271437--3271469 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3271427 AGCAGGTCGC
3271437 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
3271470 TATGGAACAT
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:3272608 original size:13 final size:14
Alignment explanation
Indices: 3272583--3272616 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3272573 TACTATTCGT
3272583 AAATATATATATAA
1 AAATATATATATAA
*
3272597 AATTATAT-TATAA
1 AAATATATATATAA
3272610 AAATATA
1 AAATATA
3272617 AATTATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATATATATAA
Found at i:3273425 original size:12 final size:12
Alignment explanation
Indices: 3273393--3273436 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3273383 AACTAAAAAA
*
3273393 TAAAAAAAAATT
1 TAAAAAAATATT
3273405 ATAATAAAAATATT
1 -TAA-AAAAATATT
*
3273419 TAAAAAATTATT
1 TAAAAAAATATT
3273431 TAAAAA
1 TAAAAA
3273437 TTTAACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 14 0.50
13 6 0.21
14 8 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAAAAATATT
Found at i:3278421 original size:2 final size:2
Alignment explanation
Indices: 3278414--3278446 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3278404 AGCAGGTCGC
3278414 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
3278447 TATGGAACAT
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:3279362 original size:17 final size:16
Alignment explanation
Indices: 3279323--3279365 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
3279313 ACTTGTTAGC
3279323 TTATTATTTTTTTTAAA
1 TTATT-TTTTTTTTAAA
*
3279340 TAATTTTTTTTTTAAA
1 TTATTTTTTTTTTAAA
3279356 TTTATTTTTT
1 -TTATTTTTT
3279366 CACCCACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTTTTTTTAAA
Found at i:3279585 original size:13 final size:14
Alignment explanation
Indices: 3279560--3279593 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3279550 TACTATTCGT
3279560 AAATATATATATAA
1 AAATATATATATAA
*
3279574 AATTATAT-TATAA
1 AAATATATATATAA
3279587 AAATATA
1 AAATATA
3279594 AATTATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATATATATAA
Found at i:3280401 original size:12 final size:12
Alignment explanation
Indices: 3280369--3280412 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3280359 AACTAAAAAA
*
3280369 TAAAAAAAAATT
1 TAAAAAAATATT
3280381 ATAATAAAAATATT
1 -TAA-AAAAATATT
*
3280395 TAAAAAATTATT
1 TAAAAAAATATT
3280407 TAAAAA
1 TAAAAA
3280413 TTTAACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 14 0.50
13 6 0.21
14 8 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAAAAATATT
Found at i:3285391 original size:2 final size:2
Alignment explanation
Indices: 3285384--3285418 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3285374 AGCAGGTCGC
3285384 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
3285419 TATGGAACAT
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:3287164 original size:129 final size:129
Alignment explanation
Indices: 3287005--3287261 Score: 426
Period size: 129 Copynumber: 2.0 Consensus size: 129
3286995 TTTTTTTTGG
** *
3287005 GGGGGGGGGGGGGGCGGGGGAGGGTGTGGGTGGAGTGGTGGCTGAACTAAAGTTTCAAATGATAA
1 GGGGGGGGGGGGGGCGGGCAAGGGTGTGGGTGGAGTGATGGCTGAACTAAAGTTTCAAATGATAA
*
3287070 TTTTAAGGTTTGAATTATGGTTATATCAAAATCAATACGAAAATGGACAAAGGAAAATGATTATT
66 TTTTAAGGTTTGAA-TATGCTTATATCAAAATCAATACGAAAATGGACAAAGGAAAATGATTATT
* *
3287135 GGGGGGGGGGGGGG-GGGCAAGGGTGTGGGTGGAGTGATGGCTGAGCTAAAGTTTCATATGATAA
1 GGGGGGGGGGGGGGCGGGCAAGGGTGTGGGTGGAGTGATGGCTGAACTAAAGTTTCAAATGATAA
* *
3287199 TTTTAAGGTTTGAATATGCTTATATTAAAATCAATATGAAAATGGACAAAGGAAAATGATTAT
66 TTTTAAGGTTTGAATATGCTTATATCAAAATCAATACGAAAATGGACAAAGGAAAATGATTAT
3287262 ACGATAAAGA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
128 46 0.39
129 59 0.50
130 14 0.12
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.27
Consensus pattern (129 bp):
GGGGGGGGGGGGGGCGGGCAAGGGTGTGGGTGGAGTGATGGCTGAACTAAAGTTTCAAATGATAA
TTTTAAGGTTTGAATATGCTTATATCAAAATCAATACGAAAATGGACAAAGGAAAATGATTATT
Found at i:3289382 original size:16 final size:16
Alignment explanation
Indices: 3289359--3289420 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
3289349 ATTTTAATAA
3289359 TAAA-TTAAATTAACT
1 TAAATTTAAATTAACT
* *
3289374 TAAATTTAAAATAATT
1 TAAATTTAAATTAACT
* *
3289390 TAACTAGTAAA-TAACT
1 TAAAT-TTAAATTAACT
3289406 TAAATTTAAAATTAA
1 TAAATTT-AAATTAA
3289421 ATTTTTAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 5 0.14
16 24 0.67
17 7 0.19
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTAACT
Found at i:3293064 original size:18 final size:18
Alignment explanation
Indices: 3293025--3293071 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3293015 TAAGTCAATT
*
3293025 TTAATTGATTTTAATTGA
1 TTAATTGATTCTAATTGA
*
3293043 TTAATTGA-TCTAATTTA
1 TTAATTGATTCTAATTGA
3293060 GTTAATTTGATT
1 -TTAA-TTGATT
3293072 TAGTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 12 0.50
19 4 0.17
20 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (18 bp):
TTAATTGATTCTAATTGA
Found at i:3293317 original size:5 final size:5
Alignment explanation
Indices: 3293300--3293336 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
3293290 ATCTCATTTT
3293300 ATATA ATTATA ATATA ATATA ATATA ATAATA ATATA
1 ATATA A-TATA ATATA ATATA ATATA AT-ATA ATATA
3293337 TCTCATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 20 0.67
6 10 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:3293321 original size:16 final size:16
Alignment explanation
Indices: 3293300--3293336 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3293290 ATCTCATTTT
3293300 ATATAATTATAAT-ATA
1 ATATAA-TATAATAATA
3293316 ATATAATATAATAATA
1 ATATAATATAATAATA
3293332 ATATA
1 ATATA
3293337 TCTCATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAATATAATAATA
Found at i:3293399 original size:24 final size:27
Alignment explanation
Indices: 3293341--3293399 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 27
3293331 AATATATCTC
3293341 ATTTTAACATATAATTATTTTTATAATA
1 ATTTTAA-ATATAATTATTTTTATAATA
* *
3293369 A-TATAAATA-ATTTATTTTT-TAA-A
1 ATTTTAAATATAATTATTTTTATAATA
3293392 ATTTTAAA
1 ATTTTAAA
3293400 ACCGATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.07
24 8 0.30
25 9 0.33
26 3 0.11
27 4 0.15
28 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTTAAATATAATTATTTTTATAATA
Found at i:3293616 original size:15 final size:17
Alignment explanation
Indices: 3293592--3293623 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3293582 CTCCCCCCTC
3293592 AAAAGAAGAAA-AAAAA
1 AAAAGAAGAAAGAAAAA
3293608 AAAAG-AGAAAGAAAAA
1 AAAAGAAGAAAGAAAAA
3293624 GCCTCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAGAAGAAAGAAAAA
Found at i:3301196 original size:15 final size:14
Alignment explanation
Indices: 3301176--3301229 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
3301166 ATTATTTAGC
3301176 ATAAATATAATTTT
1 ATAAATATAATTTT
* *
3301190 AATAAATATTAAATAT
1 -ATAAATA-TAATTTT
*
3301206 ATATATATAATTTT
1 ATAAATATAATTTT
3301220 ATAAAATATA
1 AT-AAATATA
3301230 TACATTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 7 0.23
15 19 0.61
16 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAATATAATTTT
Found at i:3301353 original size:21 final size:21
Alignment explanation
Indices: 3301324--3301402 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 21
3301314 ACACATTTAT
*
3301324 AATAGTTAATCTCACCATTAA
1 AATATTTAATCTCACCATTAA
* * * *
3301345 AATATTTAATTTTATCATTAT
1 AATATTTAATCTCACCATTAA
* * ** *
3301366 AATATTTAATTTTATTATTAC
1 AATATTTAATCTCACCATTAA
*
3301387 AATAATTAATCTCACC
1 AATATTTAATCTCACC
3301403 GTTACTATTA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.46
Consensus pattern (21 bp):
AATATTTAATCTCACCATTAA
Found at i:3301841 original size:14 final size:14
Alignment explanation
Indices: 3301825--3301860 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
3301815 GGTGAAAATT
3301825 AAATAATAAATATTA
1 AAAT-ATAAATATTA
3301840 AAATATAAATATTA
1 AAATATAAATATTA
3301854 AACATAT
1 AA-ATAT
3301861 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATAAATATTA
Found at i:3301849 original size:21 final size:22
Alignment explanation
Indices: 3301819--3301865 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
3301809 TTCTTTGGTG
3301819 AAAATTAAATAAT-AA-ATATT
1 AAAATTAAATAATAAACATATT
*
3301839 AAAATATAAATATTAAACATATT
1 AAAAT-TAAATAATAAACATATT
3301862 AAAA
1 AAAA
3301866 AAATTAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 2 0.09
23 9 0.39
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATTAAATAATAAACATATT
Found at i:3302119 original size:41 final size:40
Alignment explanation
Indices: 3302063--3302154 Score: 166
Period size: 41 Copynumber: 2.2 Consensus size: 40
3302053 TAAAGTAATA
3302063 ATAAAAAAAATAAAAAGACATTTACATAGACTTAATTTTG
1 ATAAAAAAAATAAAAAGACATTTACATAGACTTAATTTTG
3302103 ATAAAAAAAATTAAAAAGACATTTACATAGACTTAATTTTG
1 ATAAAAAAAA-TAAAAAGACATTTACATAGACTTAATTTTG
3302144 ATTAAAAAAAA
1 A-TAAAAAAAA
3302155 AAAGCTTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 10 0.20
41 31 0.62
42 9 0.18
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (40 bp):
ATAAAAAAAATAAAAAGACATTTACATAGACTTAATTTTG
Found at i:3302532 original size:27 final size:27
Alignment explanation
Indices: 3302490--3302541 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3302480 AATTTAAATA
**
3302490 ATATAAATTATTAAT-ATATTAAAATTT
1 ATATAAATTAAAAATAAT-TTAAAATTT
3302517 ATATAAATTAAAAATAATTTAAAAT
1 ATATAAATTAAAAATAATTTAAAAT
3302542 AATTATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAAATTAAAAATAATTTAAAATTT
Found at i:3302548 original size:27 final size:27
Alignment explanation
Indices: 3302480--3302549 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
3302470 GAATATGTTA
**
3302480 AATTT-AAATAA-TATAAATTATTAAT
1 AATTTAAAATAATTATAAATTAAAAAT
*
3302505 -ATATTAAAAT-TTATATAAATTAAAAAT
1 AAT-TTAAAATAAT-TATAAATTAAAAAT
3302532 AATTTAAAATAATTATAA
1 AATTTAAAATAATTATAA
3302550 TATATATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
24 2 0.06
25 2 0.06
26 4 0.11
27 24 0.69
28 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATTTAAAATAATTATAAATTAAAAAT
Found at i:3305743 original size:14 final size:15
Alignment explanation
Indices: 3305724--3305754 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3305714 AATATAAATT
3305724 ATTAAT-ATATTAAA
1 ATTAATAATATTAAA
3305738 ATTAATAATATTAAA
1 ATTAATAATATTAAA
3305753 AT
1 AT
3305755 ATTTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAATAATATTAAA
Found at i:3305755 original size:25 final size:26
Alignment explanation
Indices: 3305727--3305794 Score: 68
Period size: 28 Copynumber: 2.6 Consensus size: 26
3305717 ATAAATTATT
3305727 AATATATTAAA-AT-TAATAATATTAA
1 AATATATTAAATATATAATAATA-TAA
* *
3305752 AATATTTTAAATATGATTATAATATAA
1 AATATATTAAATAT-ATAATAATATAA
*
3305779 AATATATATAAGTATA
1 AATATAT-TAAATATA
3305795 ATATAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 10 0.29
26 2 0.06
27 10 0.29
28 13 0.37
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
AATATATTAAATATATAATAATATAA
Found at i:3305993 original size:13 final size:13
Alignment explanation
Indices: 3305974--3306017 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3305964 TAAGATTCAA
3305974 AAAAATAATAAAT
1 AAAAATAATAAAT
* *
3305987 TAAAATAATATAT
1 AAAAATAATAAAT
*
3306000 AAAAATAAAATAAT
1 AAAAATAATA-AAT
3306014 AAAA
1 AAAA
3306018 TTTGAGATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:3307012 original size:19 final size:21
Alignment explanation
Indices: 3306988--3307034 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3306978 TATAACTAAT
*
3306988 TAAAATTT-TTTTAAAT-TAA
1 TAAAATTTATATTAAATATAA
3307007 TAAAATATTATATTAAATATAA
1 TAAAAT-TTATATTAAATATAA
3307029 -AAAATT
1 TAAAATT
3307035 AAAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 12 0.50
22 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATTTATATTAAATATAA
Found at i:3307507 original size:15 final size:13
Alignment explanation
Indices: 3307476--3307513 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
3307466 CTAGGTATTT
3307476 ATTA-AATTTTAA
1 ATTATAATTTTAA
3307488 ATTATAATTTTAA
1 ATTATAATTTTAA
3307501 TATTTATAATTTT
1 -A-TTATAATTTT
3307514 TTTAATATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 8 0.35
14 1 0.04
15 10 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTATAATTTTAA
Found at i:3307656 original size:22 final size:22
Alignment explanation
Indices: 3307619--3307679 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
3307609 TTAAATTATC
* *
3307619 ATTTAATTAATAAAATTATTTAA
1 ATTTAAAT-ATAAAATTATATAA
3307642 ATTTAAATATAAAATTATATAA
1 ATTTAAATATAAAATTATATAA
* *
3307664 ATATCAATA-AAAATTA
1 ATTTAAATATAAAATTA
3307680 ATATTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.21
22 20 0.59
23 7 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTTAAATATAAAATTATATAA
Found at i:3307904 original size:16 final size:15
Alignment explanation
Indices: 3307868--3307906 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3307858 TATGTTTTCG
3307868 TTATTTTAAATAAAA
1 TTATTTTAAATAAAA
* *
3307883 TAATTTTAAATTTAAA
1 TTATTTTAAA-TAAAA
3307899 TTATTTTA
1 TTATTTTA
3307907 TGTTTAGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATTTTAAATAAAA
Found at i:3308748 original size:22 final size:24
Alignment explanation
Indices: 3308710--3308755 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
3308700 TTGAATTATT
3308710 ATTTAATTAGTAAAAATAT-TTAA
1 ATTTAATTAGTAAAAATATATTAA
3308733 ATTTAATTA-TAAAAATATATTAA
1 ATTTAATTAGTAAAAATATATTAA
3308756 TATAAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTAATTAGTAAAAATATATTAA
Found at i:3308763 original size:23 final size:23
Alignment explanation
Indices: 3308714--3308763 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
3308704 ATTATTATTT
*
3308714 AATTAGTAAAAATATTTAAATTT
1 AATTAGTAAAAATATTTAAATTA
3308737 AATTA-TAAAAATATATT-AATATA
1 AATTAGTAAAAATAT-TTAAAT-TA
3308760 AATT
1 AATT
3308764 GATATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AATTAGTAAAAATATTTAAATTA
Found at i:3308958 original size:16 final size:16
Alignment explanation
Indices: 3308934--3308990 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
3308924 GATAAAATTT
*
3308934 TTTTGAGTTTCAG-TTA
1 TTTTAAGTTT-AGATTA
3308950 TTTTAAGTTTAGATTA
1 TTTTAAGTTTAGATTA
*
3308966 TTTTATGTTTAGACTT-
1 TTTTAAGTTTAGA-TTA
3308982 TTTTAAGTT
1 TTTTAAGTT
3308991 CGACTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 2 0.06
16 32 0.89
17 2 0.06
ACGTcount: A:0.23, C:0.04, G:0.14, T:0.60
Consensus pattern (16 bp):
TTTTAAGTTTAGATTA
Found at i:3309001 original size:16 final size:17
Alignment explanation
Indices: 3308947--3309001 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 17
3308937 TGAGTTTCAG
3308947 TTATTTTAAGTTTAGA-
1 TTATTTTAAGTTTAGAC
*
3308963 TTATTTTATGTTTAGAC
1 TTATTTTAAGTTTAGAC
*
3308980 TT-TTTTAAG-TTCGAC
1 TTATTTTAAGTTTAGAC
3308995 TTATTTT
1 TTATTTT
3309002 GAATTAGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.21
16 25 0.74
17 2 0.06
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.60
Consensus pattern (17 bp):
TTATTTTAAGTTTAGAC
Found at i:3310204 original size:21 final size:21
Alignment explanation
Indices: 3310150--3310205 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
3310140 ATTAAAGCTT
*
3310150 TATTATAAAAATTTTTTATTA
1 TATTATAAAATTTTTTTATTA
*
3310171 TAATT-TGATAATTTTTTTATTA
1 T-ATTAT-AAAATTTTTTTATTA
*
3310193 TATTATTAAATTT
1 TATTATAAAATTT
3310206 AAATCATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TATTATAAAATTTTTTTATTA
Found at i:3310305 original size:22 final size:23
Alignment explanation
Indices: 3310263--3310311 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
3310253 TAAGTTTGTA
* *
3310263 CAAAT-TTTAATTTTTTTTAATT
1 CAAATCTTTAATTTTGTATAATT
3310285 CAAATCTTTAA-TTTGTATAATT
1 CAAATCTTTAATTTTGTATAATT
3310307 -AAATC
1 CAAATC
3310312 AGATTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 14 0.58
23 5 0.21
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (23 bp):
CAAATCTTTAATTTTGTATAATT
Done.