Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 86 of 93
Found at i:33449023 original size:23 final size:25
Alignment explanation
Indices: 33448975--33449023 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
33448965 ATATTTCAAA
33448975 AATTAATAAATTTAAATAAAATTAT
1 AATTAATAAATTTAAATAAAATTAT
33449000 AATTAA-AAA-TTAAA-AAAATATAT
1 AATTAATAAATTTAAATAAAAT-TAT
33449023 A
1 A
33449024 TTTTACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.22
23 9 0.39
24 3 0.13
25 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAATAAATTTAAATAAAATTAT
Found at i:33449899 original size:46 final size:45
Alignment explanation
Indices: 33449817--33449917 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 45
33449807 ATTAAATTTA
* * * *
33449817 AATAATACTAAATAATATTCTTTATCACATTTATTATA-TTCAAAT
1 AATAATACTAAATAAGATGCTTTATAACATTCATTATAGTT-AAAT
* *
33449862 AATAATATTGAAATAAGATGCTTTATAATATTCATTATAGTTAAAT
1 AATAATACT-AAATAAGATGCTTTATAACATTCATTATAGTTAAAT
*
33449908 AATATTACTA
1 AATAATACTA
33449918 TATTAAATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
45 9 0.20
46 35 0.76
47 2 0.04
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (45 bp):
AATAATACTAAATAAGATGCTTTATAACATTCATTATAGTTAAAT
Found at i:33449925 original size:18 final size:20
Alignment explanation
Indices: 33449886--33449931 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
33449876 AAGATGCTTT
*
33449886 ATAATATTCATTATAGTTAA
1 ATAATATTCACTATAGTTAA
33449906 ATAATATT-ACTATA-TTAA
1 ATAATATTCACTATAGTTAA
33449924 ATAATATT
1 ATAATATT
33449932 TAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 5 0.20
20 8 0.32
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATATTCACTATAGTTAA
Found at i:33453204 original size:2 final size:2
Alignment explanation
Indices: 33453192--33453275 Score: 136
Period size: 2 Copynumber: 42.5 Consensus size: 2
33453182 TGCAAGTTAT
*
33453192 TA TA TA AA 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 TA TA TA TA
33453233 TA TNA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33453275 T
1 T
33453276 TATTCGAACT
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.03
2 73 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:33453884 original size:22 final size:22
Alignment explanation
Indices: 33453849--33453890 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
33453839 AGTCAAGTTT
*
33453849 ATTTGTAAATTATTTGAATTGG
1 ATTTGTAAATTATTTAAATTGG
33453871 ATTTGATAAA-TATTTAAATT
1 ATTTG-TAAATTATTTAAATT
33453891 TAATTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTGTAAATTATTTAAATTGG
Found at i:33453896 original size:22 final size:22
Alignment explanation
Indices: 33453849--33453898 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
33453839 AGTCAAGTTT
* *
33453849 ATTTGTAAATTATTTGAATTGG
1 ATTTGTAAATTATTTAAATTGA
*
33453871 ATTTGATAAA-TATTTAAATTTA
1 ATTTG-TAAATTATTTAAATTGA
33453893 ATTTGT
1 ATTTGT
33453899 TTATTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
ATTTGTAAATTATTTAAATTGA
Found at i:33464400 original size:2 final size:2
Alignment explanation
Indices: 33464395--33464425 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33464385 CTCCTCTACA
33464395 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
33464426 CATACATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:33466676 original size:91 final size:92
Alignment explanation
Indices: 33466542--33466715 Score: 253
Period size: 91 Copynumber: 1.9 Consensus size: 92
33466532 CTTTTAATTT
* * *
33466542 TATTTTCTTTAAAATTTTAAAATATTAATAATTTATTATTAAATTATTAATATAATTTTTATTTC
1 TATTTTCATTAAAAATTTAAAACATTAATAATTTATTATTAAATTATTAATATAATTTTTATTTC
*
33466607 AATTTCTTTTTATTTTTTCTCTACTTG
66 AATTTCTTGTTATTTTTTCTCTACTTG
* * *
33466634 TATTTTCATTAAAAATTT-AAACATTAATTAA-TTATTTTTAAATTATTAATATATTTTTTGTTT
1 TATTTTCATTAAAAATTTAAAACATTAA-TAATTTATTATTAAATTATTAATATAATTTTTATTT
*
33466697 TAATTTCTTGTTATTTTTT
65 CAATTTCTTGTTATTTTTT
33466716 ATTTATAGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
91 54 0.74
92 19 0.26
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (92 bp):
TATTTTCATTAAAAATTTAAAACATTAATAATTTATTATTAAATTATTAATATAATTTTTATTTC
AATTTCTTGTTATTTTTTCTCTACTTG
Found at i:33467977 original size:2 final size:2
Alignment explanation
Indices: 33467970--33468011 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
33467960 CTTGGAATCT
33467970 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
33468012 ATCTGTGATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33470455 original size:56 final size:56
Alignment explanation
Indices: 33470394--33470508 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
33470384 GCAAGGAATG
33470394 ATCTAAACTTGATATTTTCTCTTAAAGAAAAATTGTAATTGTCACGTAAGTAATAA
1 ATCTAAACTTGATATTTTCTCTTAAAGAAAAATTGTAATTGTCACGTAAGTAATAA
33470450 ATCTAAACTTGATATTTTCTCTTAAAGAAAAATTGTAATTGTCACGTAAGTAATAA
1 ATCTAAACTTGATATTTTCTCTTAAAGAAAAATTGTAATTGTCACGTAAGTAATAA
33470506 ATC
1 ATC
33470509 AACACCAGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.37
Consensus pattern (56 bp):
ATCTAAACTTGATATTTTCTCTTAAAGAAAAATTGTAATTGTCACGTAAGTAATAA
Found at i:33471850 original size:15 final size:16
Alignment explanation
Indices: 33471832--33471861 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33471822 TTATTATGTG
33471832 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
33471847 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
33471862 AAATTAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:33474873 original size:95 final size:94
Alignment explanation
Indices: 33474693--33474881 Score: 224
Period size: 95 Copynumber: 2.0 Consensus size: 94
33474683 CACATCTATT
*
33474693 ATATTAAGAATATCTTAATATATATAAATACATAGAAAAATCTTTTCATTTATTATCAATTGATT
1 ATATTAAGAATATCTTAATATATATAAATACATAGAAAAATCTTTTCACTTATTATCAATTGATT
* **
33474758 TTAAGTTAAATATATGTCTTAAAAATTTAA
66 TTAAATTAAATATACATCTT-AAAATTTAA
** * *
33474788 ATATT-AGAGATATCTTAAATATATATAAATGTATA-AAAAA-CATTTTCACTTATTGTTAATTG
1 ATATTAAGA-ATATCTT-AATATATATAAATACATAGAAAAATC-TTTTCACTTATTATCAATTG
*
33474850 ATTTTAAATTGAATA-ACCATCTTAAAATTTAA
63 ATTTTAAATTAAATATA-CATCTTAAAATTTAA
33474882 CACAATCTCT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
94 14 0.17
95 51 0.63
96 16 0.20
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (94 bp):
ATATTAAGAATATCTTAATATATATAAATACATAGAAAAATCTTTTCACTTATTATCAATTGATT
TTAAATTAAATATACATCTTAAAATTTAA
Found at i:33492973 original size:24 final size:23
Alignment explanation
Indices: 33492939--33493091 Score: 137
Period size: 24 Copynumber: 6.4 Consensus size: 23
33492929 CCAAAATAGT
33492939 GGAAGAGCGGTAGAGAGAAAGAGG
1 GGAAGAGCGGT-GAGAGAAAGAGG
* *
33492963 GGAAGAACGGTTGAAAGAAAGAGG
1 GGAAGAGCGG-TGAGAGAAAGAGG
* *
33492987 GGACGAGCGGTGGAGAGAGAGAGG
1 GGAAGAGCGGT-GAGAGAAAGAGG
* *
33493011 GGACGAGCTGCG-GAGAGAAAGTGG
1 GGAAGAGC-G-GTGAGAGAAAGAGG
* *
33493035 GGAAGATCGGCTGAGAGAAAGAGA
1 GGAAGAGCGG-TGAGAGAAAGAGG
* *
33493059 AGAAGAACGGCTGAGAGAAAGAGG
1 GGAAGAGCGG-TGAGAGAAAGAGG
*
33493083 GGAAAAGCG
1 GGAAGAGCG
33493092 AGGAAGAGTA
Statistics
Matches: 105, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.01
23 2 0.02
24 99 0.94
25 2 0.02
26 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.47, T:0.06
Consensus pattern (23 bp):
GGAAGAGCGGTGAGAGAAAGAGG
Found at i:33493075 original size:48 final size:48
Alignment explanation
Indices: 33492939--33493091 Score: 164
Period size: 48 Copynumber: 3.2 Consensus size: 48
33492929 CCAAAATAGT
* * *
33492939 GGAAGAGCGGTAGAGAGAAAGAGGGGAAGAACGGTTGAAAGAAAGAGG
1 GGAAGAGCGGTGGAGAGAAAGAGGGGAAGAACGGCTGAGAGAAAGAGG
* * * * * * *
33492987 GGACGAGCGGTGGAGAGAGAGAGGGGACGAGCTGCGGAGAGAAAGTGG
1 GGAAGAGCGGTGGAGAGAAAGAGGGGAAGAACGGCTGAGAGAAAGAGG
* **
33493035 GGAAGATCGGCT-GAGAGAAAGAGAAGAAGAACGGCTGAGAGAAAGAGG
1 GGAAGAGCGG-TGGAGAGAAAGAGGGGAAGAACGGCTGAGAGAAAGAGG
*
33493083 GGAAAAGCG
1 GGAAGAGCG
33493092 AGGAAGAGTA
Statistics
Matches: 82, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
48 81 0.99
49 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.47, T:0.06
Consensus pattern (48 bp):
GGAAGAGCGGTGGAGAGAAAGAGGGGAAGAACGGCTGAGAGAAAGAGG
Found at i:33493075 original size:72 final size:72
Alignment explanation
Indices: 33492951--33493085 Score: 173
Period size: 72 Copynumber: 1.9 Consensus size: 72
33492941 AAGAGCGGTA
* ** * * *
33492951 GAGAGAAAGAGGGGAAGAACGGTTGAAAGAAAGAGGGGACGAGCGGTGGAGAGAGAGAGGGGACG
1 GAGAGAAAGAGGGGAAGAACGGCTGAAAGAAAGAGAAGAAGAACGGTGGAGAGAAAGAGGGGACG
33493016 AGCTGCG
66 AGCTGCG
* * *
33493023 GAGAGAAAGTGGGGAAGATCGGCTGAGAGAAAGAGAAGAAGAACGGCT-GAGAGAAAGAGGGGA
1 GAGAGAAAGAGGGGAAGAACGGCTGAAAGAAAGAGAAGAAGAACGG-TGGAGAGAAAGAGGGGA
33493086 AAAGCGAGGA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 52 0.98
73 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.47, T:0.06
Consensus pattern (72 bp):
GAGAGAAAGAGGGGAAGAACGGCTGAAAGAAAGAGAAGAAGAACGGTGGAGAGAAAGAGGGGACG
AGCTGCG
Found at i:33493134 original size:24 final size:24
Alignment explanation
Indices: 33493107--33493169 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
33493097 GAGTAGCTAA
* *
33493107 GAGAGAGAGAGGGGACGAGCGACG
1 GAGAGAAAGAGGGGACGAACGACG
* *
33493131 GAGAGAAAGAGGGGATGAACGGCG
1 GAGAGAAAGAGGGGACGAACGACG
33493155 GAGAGAAAGAGGGGA
1 GAGAGAAAGAGGGGA
33493170 AGATTGACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.52, T:0.02
Consensus pattern (24 bp):
GAGAGAAAGAGGGGACGAACGACG
Found at i:33493182 original size:24 final size:24
Alignment explanation
Indices: 33493107--33493190 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
33493097 GAGTAGCTAA
* * *
33493107 GAGAGAGAGAGGGGACGAGCGACG
1 GAGAGAAAGAGGGGAAGAACGACG
* *
33493131 GAGAGAAAGAGGGGATGAACGGCG
1 GAGAGAAAGAGGGGAAGAACGACG
** *
33493155 GAGAGAAAGAGGGGAAGATTGACT
1 GAGAGAAAGAGGGGAAGAACGACG
33493179 GAGAG-AAGAGGG
1 GAGAGAAAGAGGG
33493191 AAAGGAGGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 7 0.14
24 44 0.86
ACGTcount: A:0.38, C:0.07, G:0.50, T:0.05
Consensus pattern (24 bp):
GAGAGAAAGAGGGGAAGAACGACG
Found at i:33495416 original size:94 final size:93
Alignment explanation
Indices: 33495252--33495430 Score: 227
Period size: 94 Copynumber: 1.9 Consensus size: 93
33495242 TGGCGCGCAA
* * * *
33495252 ACAGGCAGAATTGGCGTGCAAGTAGACTGACAGAGCGGGGCACGCAGACAGACAGCTCGAGGCAC
1 ACAGGCAAAATTGGCGCGCAAGTAGACTGACAGAGAGGGG-ACGCAGACAAACAGCTCGAGGCAC
* * *
33495317 TCAAGAAAGGTCCAGACTGCTCCGGAATG
65 CCAAGAAAGGCCCAAACTGCTCCGGAATG
* *
33495346 ACAGGCAAAATTGGCGCGCAGGTAGACTGATATAGAGAGGGG-CGCAGACAAACAG-TGCGAGGC
1 ACAGGCAAAATTGGCGCGCAAGTAGACTG--ACAGAGAGGGGACGCAGACAAACAGCT-CGAGGC
33495409 ACCCAAGAAAGGCCCAAACTGC
63 ACCCAAGAAAGGCCCAAACTGC
33495431 GCTGGAAGGA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
93 1 0.01
94 63 0.86
96 9 0.12
ACGTcount: A:0.33, C:0.24, G:0.32, T:0.11
Consensus pattern (93 bp):
ACAGGCAAAATTGGCGCGCAAGTAGACTGACAGAGAGGGGACGCAGACAAACAGCTCGAGGCACC
CAAGAAAGGCCCAAACTGCTCCGGAATG
Found at i:33514501 original size:78 final size:78
Alignment explanation
Indices: 33514360--33514508 Score: 237
Period size: 78 Copynumber: 1.9 Consensus size: 78
33514350 TCTCTTCACT
* *
33514360 TTCCTTTCTCACTTTCTCTCTCTTGCCGCCACTCTCTCTATCTTCTCCTCAAGCTTTTCTTTTTT
1 TTCCTCTCTCACTTTCTCTCTCTTGCCGCCACTCTCTCTATCTTCTCCTCAAGCCTTTCTTTTTT
*
33514425 TTTTCCCTCCTTC
66 TCTTCCCTCCTTC
* *
33514438 TTCCTCTCTCTCTTTCTCTCTCTTGCCGCCACTCTCTCTATCTTCTCCTTAAGCCCTTT-TTTTT
1 TTCCTCTCTCACTTTCTCTCTCTTGCCGCCACTCTCTCTATCTTCTCCTCAAG-CCTTTCTTTTT
33514502 TTCTTCC
65 TTCTTCC
33514509 TCTCTCTCAC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 61 0.94
79 4 0.06
ACGTcount: A:0.06, C:0.39, G:0.04, T:0.51
Consensus pattern (78 bp):
TTCCTCTCTCACTTTCTCTCTCTTGCCGCCACTCTCTCTATCTTCTCCTCAAGCCTTTCTTTTTT
TCTTCCCTCCTTC
Found at i:33514883 original size:16 final size:16
Alignment explanation
Indices: 33514861--33514900 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
33514851 CCATTATTTA
33514861 TTTATTTATT-ATTAT
1 TTTATTTATTAATTAT
*
33514876 TATTATTTTTTAATTAT
1 T-TTATTTATTAATTAT
33514893 TTTATTTA
1 TTTATTTA
33514901 ATTTAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 14 0.67
17 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTATTTATTAATTAT
Found at i:33515689 original size:69 final size:69
Alignment explanation
Indices: 33515565--33515711 Score: 165
Period size: 69 Copynumber: 2.1 Consensus size: 69
33515555 TAAAAAGTTG
* *
33515565 TGACTATTGAAAAGACATTTTGATTGAAAGATTATGTTTTTTCATATATAAAGTTGTCTCTTGAC
1 TGACTATTGAAAAGACATTTTAATTGAAAGATTATGTTTTTTCATATATAAAGTTGTCACTTGAC
33515630 AAAA
66 AAAA
* * * *
33515634 TGACTATTAGAAAA-AC-TTTTCAATTGAAAGGTTATGTTTTTCTGA-ATGTATAGTTGTCACTT
1 TGACTATT-GAAAAGACATTTT-AATTGAAAGATTATGTTTTT-TCATATATAAAGTTGTCACTT
* *
33515696 GATAAAG
63 GACAAAA
*
33515703 TAACTATTG
1 TGACTATTG
33515712 GGAACACACC
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
68 5 0.08
69 54 0.82
70 7 0.11
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (69 bp):
TGACTATTGAAAAGACATTTTAATTGAAAGATTATGTTTTTTCATATATAAAGTTGTCACTTGAC
AAAA
Found at i:33516389 original size:3 final size:3
Alignment explanation
Indices: 33516381--33516423 Score: 68
Period size: 3 Copynumber: 13.7 Consensus size: 3
33516371 ACCTAAAAAT
33516381 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT-A ATA AT
33516424 TTTAAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33516700 original size:15 final size:15
Alignment explanation
Indices: 33516680--33516710 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33516670 TAGCCACAGG
*
33516680 AAAACAAAAAGAAAA
1 AAAACAAAAACAAAA
33516695 AAAACAAAAACAAAA
1 AAAACAAAAACAAAA
33516710 A
1 A
33516711 GCAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAACAAAAACAAAA
Found at i:33516705 original size:21 final size:22
Alignment explanation
Indices: 33516680--33516720 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
33516670 TAGCCACAGG
33516680 AAAACAAAAAG-AAAAAAAACA
1 AAAACAAAAAGCAAAAAAAACA
33516701 AAAACAAAAAGCAAAAAAAA
1 AAAACAAAAAGCAAAAAAAA
33516721 AGAGGGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (22 bp):
AAAACAAAAAGCAAAAAAAACA
Found at i:33516718 original size:15 final size:14
Alignment explanation
Indices: 33516680--33516721 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
33516670 TAGCCACAGG
33516680 AAAACAAAAAGAAAA
1 AAAACAAAAA-AAAA
*
33516695 AAAAC-AAAAACAA
1 AAAACAAAAAAAAA
*
33516708 AAAGCAAAAAAAAA
1 AAAACAAAAAAAAA
33516722 GAGGGGGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 7 0.30
14 11 0.48
15 5 0.22
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAAAAA
Found at i:33517409 original size:11 final size:11
Alignment explanation
Indices: 33517386--33517428 Score: 56
Period size: 10 Copynumber: 4.1 Consensus size: 11
33517376 AAAAATTAGA
33517386 AAAT-AATAAT
1 AAATAAATAAT
33517396 AAATGAAA-AAT
1 AAAT-AAATAAT
33517407 AAATAAATAAT
1 AAATAAATAAT
33517418 -AATAAATAAT
1 AAATAAATAAT
33517428 A
1 A
33517429 TAATTGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 17 0.59
11 10 0.34
12 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:33517421 original size:14 final size:14
Alignment explanation
Indices: 33517387--33517432 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
33517377 AAAATTAGAA
33517387 AATAAT-AATAAAT
1 AATAATAAATAAAT
*
33517400 GAAAAATAAATAAAT
1 -AATAATAAATAAAT
33517415 AATAATAAATAATAT
1 AATAATAAATAA-AT
33517430 AAT
1 AAT
33517433 TGGAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
AATAATAAATAAAT
Found at i:33517766 original size:13 final size:12
Alignment explanation
Indices: 33517748--33517782 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
33517738 TAGGAAACCA
33517748 AAAAATAAAATAT
1 AAAAATAAAA-AT
33517761 AAAAATAAAAAT
1 AAAAATAAAAAT
33517773 AAATAATAAA
1 AAA-AATAAA
33517783 TAATCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:33519276 original size:20 final size:20
Alignment explanation
Indices: 33519236--33519359 Score: 71
Period size: 21 Copynumber: 6.2 Consensus size: 20
33519226 ATATATAATT
* *
33519236 ATTTAAAAAATAATAATTTTA
1 ATTTAAATATTAAT-ATTTTA
33519257 ATTTAAATATTAATATTTTA
1 ATTTAAATATTAATATTTTA
* **
33519277 ATAT-AAT-TTAAT-TACTA
1 ATTTAAATATTAATATTTTA
* * *
33519294 ATATTTAATAAATAATATTTTT
1 AT-TTAAAT-ATTAATATTTTA
33519316 ATTTATAAT-TTAATATTATT-
1 ATTTA-AATATTAATATT-TTA
*
33519336 A-TTAAATATTAATAATTTTT
1 ATTTAAATATTAAT-ATTTTA
33519356 ATTT
1 ATTT
33519360 TATNNNNNNN
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
17 5 0.06
18 9 0.11
19 16 0.20
20 21 0.26
21 22 0.28
22 7 0.09
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAATATTAATATTTTA
Found at i:33519279 original size:14 final size:14
Alignment explanation
Indices: 33519257--33519354 Score: 50
Period size: 14 Copynumber: 7.4 Consensus size: 14
33519247 AATAATTTTA
*
33519257 ATTTAAATATTAAT
1 ATTTTAATATTAAT
33519271 ATTTTAATA-T-A-
1 ATTTTAATATTAAT
*
33519282 A-TTTAATTACTAAT
1 ATTTTAA-TATTAAT
*
33519296 A-TTTAATAAATAAT
1 ATTTTAAT-ATTAAT
*
33519310 ATTTT--TATTTAT
1 ATTTTAATATTAAT
* *
33519322 AATTTAATATTATT
1 ATTTTAATATTAAT
*
33519336 A-TTAAATATTAAT
1 ATTTTAATATTAAT
33519349 AATTTT
1 -ATTTT
33519355 TATTTTATNN
Statistics
Matches: 64, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
10 5 0.08
11 3 0.05
12 10 0.16
13 14 0.22
14 27 0.42
15 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTTAATATTAAT
Found at i:33519283 original size:25 final size:24
Alignment explanation
Indices: 33519255--33519303 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
33519245 ATAATAATTT
*
33519255 TAATTTAAATATTAATATTTTAATA
1 TAATTTAAATACTAATA-TTTAATA
*
33519280 TAATTTAATTACTAATATTTAATA
1 TAATTTAAATACTAATATTTAATA
33519304 AATAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATTTAAATACTAATATTTAATA
Found at i:33519288 original size:18 final size:21
Alignment explanation
Indices: 33519214--33519282 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 21
33519204 ATTTATTTTT
*
33519214 TAAATATTAATAATATATAATTA
1 TAAATATTAATAAT-TTTAA-TA
* * *
33519237 TTTAAAAAATAATAATTTTAATT
1 --TAAATATTAATAATTTTAATA
33519260 TAAATATTAAT-ATTTTAATA
1 TAAATATTAATAATTTTAATA
33519280 TAA
1 TAA
33519283 TTTAATTACT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 11 0.30
21 9 0.24
23 1 0.03
24 4 0.11
25 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAATATTAATAATTTTAATA
Found at i:33519349 original size:39 final size:40
Alignment explanation
Indices: 33519255--33519359 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
33519245 ATAATAATTT
*
33519255 TAAT-TTAAATATTAATA-TTTTA-ATATAATTTAATTAC
1 TAATATTAAATATTAATATTTTTATTTATAATTTAATTAC
* * *
33519292 TAATATTTAATAAATAATATTTTTATTTATAATTTAA-TAT
1 TAATATTAAAT-ATTAATATTTTTATTTATAATTTAATTAC
*
33519332 TATTATTAAATATTAATAATTTTTATTT
1 TAATATTAAATATTAAT-ATTTTTATTT
33519360 TATNNNNNNN
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
37 4 0.07
38 5 0.09
39 11 0.20
40 26 0.46
41 10 0.18
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (40 bp):
TAATATTAAATATTAATATTTTTATTTATAATTTAATTAC
Found at i:33519359 original size:60 final size:60
Alignment explanation
Indices: 33519207--33519359 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 60
33519197 TTATTTTATT
33519207 TATTTT-TTAAATATTAATAATATATAATTATTTAAAAAATAATAATTTTAATTTAAATATTAA
1 TATTTTATTAAATATTAATAAT-T-T--TTATTTAAAAAATAATAATTTTAATTTAAATATTAA
* * * ** * *
33519270 TATTTTAATATAAT-TTAATTACTAATATTTAATAAATAAT-ATTTTTATTTATAAT-TTAA
1 TATTTTATTA-AATATTAATAATTTTTATTTAAAAAATAATAATTTTAATTTA-AATATTAA
33519329 TATTATTATTAAATATTAATAATTTTTATTT
1 TATT-TTATTAAATATTAATAATTTTTATTT
33519360 TATNNNNNNN
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
59 21 0.29
60 34 0.47
63 7 0.10
64 8 0.11
65 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.54
Consensus pattern (60 bp):
TATTTTATTAAATATTAATAATTTTTATTTAAAAAATAATAATTTTAATTTAAATATTAA
Found at i:33525042 original size:23 final size:22
Alignment explanation
Indices: 33524999--33525042 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
33524989 AAATACAAAC
* **
33524999 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
33525021 ATATTTTGTATTAGAAGATAAT
1 ATATTTT-TATTAGAAGATAAT
33525043 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:33525178 original size:45 final size:45
Alignment explanation
Indices: 33525110--33525203 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
33525100 ATTAAATTTA
* * * *
33525110 AATAATACTAAATAATATTCTTTATTACATTTATTATATTCAAAT
1 AATAATACTAAATAACATGCTTTATAACATTTATTATAGTCAAAT
* * * *
33525155 AATAATATTAAGTAACATGCTTTATAATATTTATTATAGTGAAAT
1 AATAATACTAAATAACATGCTTTATAACATTTATTATAGTCAAAT
33525200 AATA
1 AATA
33525204 TTAATATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (45 bp):
AATAATACTAAATAACATGCTTTATAACATTTATTATAGTCAAAT
Found at i:33528405 original size:47 final size:47
Alignment explanation
Indices: 33528348--33528502 Score: 139
Period size: 47 Copynumber: 3.5 Consensus size: 47
33528338 TTTAAAAAAC
33528348 TCATAACTTGTTTACTCTTCTAGATTTCAAGATAAATTTAAAATAGA
1 TCATAACTTGTTTACTCTTCTAGATTTCAAGATAAATTTAAAATAGA
* * * *
33528395 TCATACCTTGTTTATTGTTCTAGA-TT----AT--ATTTAGAAA-A-C
1 TCATAACTTGTTTACTCTTCTAGATTTCAAGATAAATTTA-AAATAGA
* * * *
33528434 TCACAACTTGTTTACTCTTTTGGATTTCAAGATAAACTTAAAATAGA
1 TCATAACTTGTTTACTCTTCTAGATTTCAAGATAAATTTAAAATAGA
** *
33528481 TCATTCCTTGTTTATTCTTCTA
1 TCATAACTTGTTTACTCTTCTA
33528503 AAATATATTC
Statistics
Matches: 80, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
39 18 0.22
40 8 0.10
41 3 0.04
42 2 0.03
44 2 0.03
45 3 0.04
46 7 0.09
47 37 0.46
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (47 bp):
TCATAACTTGTTTACTCTTCTAGATTTCAAGATAAATTTAAAATAGA
Found at i:33528479 original size:86 final size:86
Alignment explanation
Indices: 33528332--33528545 Score: 329
Period size: 86 Copynumber: 2.5 Consensus size: 86
33528322 ATAGACTTAT
* * * *
33528332 AATATATTTAAAAAACTCATAACTTGTTTACTCTTCTAGATTTCAAGATAAATTTAAAATAGATC
1 AATATATTTAAAAAACTCACAACTTGTTTACTCTTTTGGATTTCAAGATAAACTTAAAATAGATC
* *
33528397 ATACCTTGTTTATTGTTCTAG
66 ATACCTTGTTTATTCTTCTAA
* *
33528418 ATTATATTTAGAAAACTCACAACTTGTTTACTCTTTTGGATTTCAAGATAAACTTAAAATAGATC
1 AATATATTTAAAAAACTCACAACTTGTTTACTCTTTTGGATTTCAAGATAAACTTAAAATAGATC
*
33528483 ATTCCTTGTTTATTCTTCTAA
66 ATACCTTGTTTATTCTTCTAA
* *
33528504 AATATATTCAAAAAACTCACAACTTGTTTATTCTTTTGGATT
1 AATATATTTAAAAAACTCACAACTTGTTTACTCTTTTGGATT
33528546 CTGCTAGATT
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 115 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.43
Consensus pattern (86 bp):
AATATATTTAAAAAACTCACAACTTGTTTACTCTTTTGGATTTCAAGATAAACTTAAAATAGATC
ATACCTTGTTTATTCTTCTAA
Found at i:33528609 original size:30 final size:30
Alignment explanation
Indices: 33528569--33528629 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
33528559 AGGTAAACCT
*
33528569 AAAATTGGTCATACCTTATTTATTTTTTAG
1 AAAATAGGTCATACCTTATTTATTTTTTAG
* *
33528599 AAAATAGGTCATACTTTGTTTATTTTTTAG
1 AAAATAGGTCATACCTTATTTATTTTTTAG
33528629 A
1 A
33528630 TTTTAAGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.49
Consensus pattern (30 bp):
AAAATAGGTCATACCTTATTTATTTTTTAG
Found at i:33531376 original size:34 final size:33
Alignment explanation
Indices: 33531312--33531376 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
33531302 AAATATTTTT
*
33531312 TATTATTTGAATAAATTATCAAAAACATTTTAC
1 TATTATTTGAATAAATTATCAAAAAAATTTTAC
** *
33531345 TATTATTTGAATTATTTTATGAAAAAAATTTT
1 TATTATTTGAA-TAAATTATCAAAAAAATTTT
33531377 CACCACCACC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 11 0.41
34 16 0.59
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (33 bp):
TATTATTTGAATAAATTATCAAAAAAATTTTAC
Found at i:33531815 original size:22 final size:22
Alignment explanation
Indices: 33531771--33531816 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
33531761 AAAATTTTAG
* *
33531771 TTACATATTAATATTTTTTAAA
1 TTACATATTAATATTTATCAAA
33531793 TTACATATTAATATTTATCAAA
1 TTACATATTAATATTTATCAAA
33531815 TT
1 TT
33531817 TATATTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TTACATATTAATATTTATCAAA
Found at i:33547525 original size:3 final size:3
Alignment explanation
Indices: 33547517--33547541 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33547507 CCAAACAAAC
33547517 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
33547542 ATTCATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:33554850 original size:25 final size:26
Alignment explanation
Indices: 33554819--33554881 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
33554809 TTTTTAAATT
*
33554819 TAATTGTTACATGTCAAATTGAAAA-
1 TAATTGTTACACGTCAAATTGAAAAG
* **
33554844 TAATTGTTATACGTCATGTTGAAAATG
1 TAATTGTTACACGTCAAATTGAAAA-G
33554871 TAATTGTTACA
1 TAATTGTTACA
33554882 GGCTATATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 21 0.68
27 10 0.32
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (26 bp):
TAATTGTTACACGTCAAATTGAAAAG
Found at i:33554895 original size:27 final size:27
Alignment explanation
Indices: 33554814--33555047 Score: 197
Period size: 27 Copynumber: 8.7 Consensus size: 27
33554804 TTATATTTTT
* *
33554814 AAATTTAATTGTTACATG-TCAAATTGA
1 AAATTTAATTGTTACATGCT-ATATTAA
* * * *
33554841 AAA--TAATTGTTATACG-TCATGTTGA
1 AAATTTAATTGTTACATGCT-ATATTAA
* *
33554866 AAATGTAATTGTTACAGGCTATATTAA
1 AAATTTAATTGTTACATGCTATATTAA
* ** *
33554893 AAATTTAATTGTTAGATATTATGTTGAA
1 AAATTTAATTGTTACATGCTATATT-AA
* * * *
33554921 AAATATAATTGTTACACGTTATATTGA
1 AAATTTAATTGTTACATGCTATATTAA
*
33554948 AAATTTAGTTGTTACATGCTATATTTAA
1 AAATTTAATTGTTACATGCTATA-TTAA
* * *
33554976 AAATGTAATTGTTATACGCTATATTAA
1 AAATTTAATTGTTACATGCTATATTAA
* *
33555003 AAATTTAGTTGTTACATGCTATGTTAA
1 AAATTTAATTGTTACATGCTATATTAA
*
33555030 AAATTTAATTATTACATG
1 AAATTTAATTGTTACATG
33555048 ACAAAAATTA
Statistics
Matches: 166, Mismatches: 36, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
25 21 0.13
27 100 0.60
28 45 0.27
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (27 bp):
AAATTTAATTGTTACATGCTATATTAA
Found at i:33554944 original size:55 final size:55
Alignment explanation
Indices: 33554859--33555045 Score: 243
Period size: 55 Copynumber: 3.4 Consensus size: 55
33554849 GTTATACGTC
* * * **
33554859 ATGTTG-AAAATGTAATTGTTACAGGCTATATTAAAAATTTAATTGTTAGATATT
1 ATGTTGAAAAATGTAATTGTTACACGCTATATTAAAAATTTAGTTGTTACATGCT
* * *
33554913 ATGTTGAAAAATATAATTGTTACACGTTATATTGAAAATTTAGTTGTTACATGCT
1 ATGTTGAAAAATGTAATTGTTACACGCTATATTAAAAATTTAGTTGTTACATGCT
* * *
33554968 ATATTTAAAAATGTAATTGTTATACGCTATATTAAAAATTTAGTTGTTACATGCT
1 ATGTTGAAAAATGTAATTGTTACACGCTATATTAAAAATTTAGTTGTTACATGCT
* *
33555023 ATGTT-AAAAATTTAATTATTACA
1 ATGTTGAAAAATGTAATTGTTACA
33555046 TGACAAAAAT
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
54 21 0.18
55 93 0.82
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (55 bp):
ATGTTGAAAAATGTAATTGTTACACGCTATATTAAAAATTTAGTTGTTACATGCT
Found at i:33555005 original size:82 final size:82
Alignment explanation
Indices: 33554843--33555047 Score: 232
Period size: 82 Copynumber: 2.5 Consensus size: 82
33554833 CAAATTGAAA
* * * * *
33554843 ATAATTGTTATACGTCATGTTGAAAATGTAATTGTTACAGGCTATATTAAAAATTTAATTGTTAG
1 ATAATTGTTACACGTTATGTTGAAAATTTAATTGTTACATGCTATATTAAAAATGTAATTGTTAG
* * *
33554908 ATATTATGTTGAAAAAT
66 ACACTATATTGAAAAAT
* *
33554925 ATAATTGTTACACGTTATATTGAAAATTTAGTTGTTACATGCTATATTTAAAAATGTAATTGTTA
1 ATAATTGTTACACGTTATGTTGAAAATTTAATTGTTACATGCTATA-TTAAAAATGTAATTGTTA
* *
33554990 TACGCTATATT-AAAAAT
65 GACACTATATTGAAAAAT
* * * * * *
33555007 TTAGTTGTTACATGCTATGTTAAAAATTTAATTATTACATG
1 ATAATTGTTACACGTTATGTTGAAAATTTAATTGTTACATG
33555048 ACAAAAATTA
Statistics
Matches: 102, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
82 79 0.77
83 23 0.23
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (82 bp):
ATAATTGTTACACGTTATGTTGAAAATTTAATTGTTACATGCTATATTAAAAATGTAATTGTTAG
ACACTATATTGAAAAAT
Found at i:33555221 original size:28 final size:26
Alignment explanation
Indices: 33555172--33555347 Score: 77
Period size: 27 Copynumber: 6.5 Consensus size: 26
33555162 ACCATGTTGA
* * *
33555172 AAAATGTAG-TGTTGCACATCAAATTCT
1 AAAAT-TAGTTGTTACACGTCAAATT-G
*
33555199 AAAATTTAGTTGTTACACGTCAAGTTG
1 AAAA-TTAGTTGTTACACGTCAAATTG
* ** *
33555226 AAAA-TAATTGTTACACGTCATGTTA
1 AAAATTAGTTGTTACACGTCAAATTG
* * ** *
33555251 AAAATATAATTATTACACACCATATTG
1 AAAAT-TAGTTGTTACACGTCAAATTG
* * * **
33555278 AAAATTTAGTTTTTACACATTATGTTG
1 AAAA-TTAGTTGTTACACGTCAAATTG
* * *
33555305 AAAAATGTAGTTATTACACGTTAGATTG
1 -AAAAT-TAGTTGTTACACGTCAAATTG
33555333 AAAATTTAGTTGTTA
1 AAAA-TTAGTTGTTA
33555348 AACATAATGT
Statistics
Matches: 119, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
25 22 0.18
27 60 0.50
28 37 0.31
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (26 bp):
AAAATTAGTTGTTACACGTCAAATTG
Found at i:33555240 original size:25 final size:25
Alignment explanation
Indices: 33555208--33555256 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
33555198 TAAAATTTAG
*
33555208 TTGTTACACGTCAAGTTGAAAATAA
1 TTGTTACACGTCAAGTTAAAAATAA
*
33555233 TTGTTACACGTCATGTTAAAAATA
1 TTGTTACACGTCAAGTTAAAAATA
33555257 TAATTATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (25 bp):
TTGTTACACGTCAAGTTAAAAATAA
Found at i:33555320 original size:55 final size:55
Alignment explanation
Indices: 33555233--33555375 Score: 180
Period size: 55 Copynumber: 2.6 Consensus size: 55
33555223 TTGAAAATAA
* * *
33555233 TTGTTACACGTCATGTT-AAAAATATAATTATTACACACCATATTGAAAATTTAG
1 TTGTTACACATAATGTTGAAAAATATAATTATTACACACCAGATTGAAAATTTAG
* * * * ***
33555287 TTTTTACACATTATGTTGAAAAATGTAGTTATTACACGTTAGATTGAAAATTTAG
1 TTGTTACACATAATGTTGAAAAATATAATTATTACACACCAGATTGAAAATTTAG
*
33555342 TTGTTAAACATAATGTTGAAAAATATAATTATTA
1 TTGTTACACATAATGTTGAAAAATATAATTATTA
33555376 TATCTCATGT
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
54 14 0.19
55 60 0.81
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (55 bp):
TTGTTACACATAATGTTGAAAAATATAATTATTACACACCAGATTGAAAATTTAG
Found at i:33555389 original size:55 final size:55
Alignment explanation
Indices: 33555211--33555402 Score: 169
Period size: 55 Copynumber: 3.5 Consensus size: 55
33555201 AATTTAGTTG
* * * * * *
33555211 TTACACGTCAAGTTGAAAA--TAATTGTTACACGTCATGTT-AAAAATATAATTA
1 TTACACATCATGTTGAAAATTTAGTTGTTAAACATAATGTTGAAAAATATAATTA
* * * * * * *
33555263 TTACACACCATATTGAAAATTTAGTTTTTACACATTATGTTGAAAAATGTAGTTA
1 TTACACATCATGTTGAAAATTTAGTTGTTAAACATAATGTTGAAAAATATAATTA
* *
33555318 TTACACGTTA-GATTGAAAATTTAGTTGTTAAACATAATGTTGAAAAATATAATTA
1 TTACACATCATG-TTGAAAATTTAGTTGTTAAACATAATGTTGAAAAATATAATTA
* * *
33555373 TTATATC-TCATGTTGAATATTTAATTGTTA
1 TTACA-CATCATGTTGAAAATTTAGTTGTTA
33555403 CACGTTATAT
Statistics
Matches: 111, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
52 15 0.14
54 16 0.14
55 78 0.70
56 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (55 bp):
TTACACATCATGTTGAAAATTTAGTTGTTAAACATAATGTTGAAAAATATAATTA
Found at i:33555403 original size:386 final size:385
Alignment explanation
Indices: 33554665--33555422 Score: 986
Period size: 386 Copynumber: 2.0 Consensus size: 385
33554655 ACACGCGATA
* *
33554665 AAAAATCACGTGAGCTGATGACATGGCAACTTAAAAATATTTTCTAAATATTTGTTACACGGCAT
1 AAAAATCACGTGAGCTGATGACATGACAACTTAAAAATATTTTCTAAATATTTGTTACACGACAT
* * * *
33554730 ATTGAGAAATGTTATTATTACTTTTTATGCAAAAAATGTTGTTAACATCATGTTGAAAAATGTAG
66 ATTGAGAAATCTTATTATTACTTTTTATGAAAAAAATATTGTTAACACCATGTTGAAAAATGTAG
* * * * * * *
33554795 TGTTACACGTTATATTTTTAAATTTAATTGTTACATGTCAAATTGAAAATAATTGTTATACGTCA
131 TGTTACACATCAAATTCTAAAATTTAATTGTTACACGTCAAATTGAAAATAATTGTTACACGTCA
* * * ** * * *
33554860 TGTTGAAAATGTAATTGTTACAGGCTATATTAAAAATTTAATTGTTAGATATTATGTTGAAAAAT
196 TGTTAAAAATATAATTATTACACACCATATTAAAAATTTAATTGTTACACATTATGTTGAAAAAT
* * * * *
33554925 ATAATTGTTACACGTTATATTGAAAATTTAGTTGTTACATGCTATATTTAAAAATGTAATTGTTA
261 ATAATTATTACACGTTAGATTGAAAATTTAGTTGTTACATACTATATTTAAAAATATAATTATTA
* * *
33554990 TACGCTATATTAAAAATTTAGTTGTTACATGCTATGTTAAAAATTTAATTATTACATGAC
326 TACGCTATATTAAAAATTTAATTGTTACACGCTATATTAAAAATTTAATTATTACATGAC
* * *
33555050 AAAAATTACGTGAGTTGATGACATGAC-AGTTAAAAAATATTTTCTAAATATTTGTTACACGACA
1 AAAAATCACGTGAGCTGATGACATGACAACTT-AAAAATATTTTCTAAATATTTGTTACACGACA
* * * *
33555114 TGTTGGGAAATCTTATTGTTACTTTTTTGTGAAAAAAATATTGTTAACACCATGTTGAAAAATGT
65 TATTGAGAAATCTTATTATTAC-TTTTTATGAAAAAAATATTGTTAACACCATGTTGAAAAATGT
* * *
33555179 AGTGTTGCACATCAAATTCTAAAATTTAGTTGTTACACGTCAAGTTGAAAATAATTGTTACACGT
129 AGTGTTACACATCAAATTCTAAAATTTAATTGTTACACGTCAAATTGAAAATAATTGTTACACGT
* * *
33555244 CATGTTAAAAATATAATTATTACACACCATATTGAAAATTTAGTTTTTACACATTATGTTGAAAA
194 CATGTTAAAAATATAATTATTACACACCATATTAAAAATTTAATTGTTACACATTATGTTGAAAA
* *
33555309 ATGTAGTTATTACACGTTAGATTGAAAATTTAGTTGTTA-A-AC-ATAATGTTGAAAAATATAAT
259 ATATAATTATTACACGTTAGATTGAAAATTTAGTTGTTACATACTAT-AT-TT-AAAAATATAAT
* * * * *
33555371 TATTATA-TCTCATGTTGAATATTTAATTGTTACACGTTATATTAAAAATTTA
321 TATTATACGCT-ATATTAAAAATTTAATTGTTACACGCTATATTAAAAATTTA
33555423 GATGTTGTAT
Statistics
Matches: 318, Mismatches: 49, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
383 2 0.01
384 6 0.02
385 78 0.25
386 232 0.73
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (385 bp):
AAAAATCACGTGAGCTGATGACATGACAACTTAAAAATATTTTCTAAATATTTGTTACACGACAT
ATTGAGAAATCTTATTATTACTTTTTATGAAAAAAATATTGTTAACACCATGTTGAAAAATGTAG
TGTTACACATCAAATTCTAAAATTTAATTGTTACACGTCAAATTGAAAATAATTGTTACACGTCA
TGTTAAAAATATAATTATTACACACCATATTAAAAATTTAATTGTTACACATTATGTTGAAAAAT
ATAATTATTACACGTTAGATTGAAAATTTAGTTGTTACATACTATATTTAAAAATATAATTATTA
TACGCTATATTAAAAATTTAATTGTTACACGCTATATTAAAAATTTAATTATTACATGAC
Found at i:33555544 original size:27 final size:27
Alignment explanation
Indices: 33555199--33555546 Score: 213
Period size: 27 Copynumber: 12.9 Consensus size: 27
33555189 ATCAAATTCT
* * *
33555199 AAAATTTAGTTGTTACACGTCAAGTTG
1 AAAATTTAGTTATTACACGTCATGTTA
* *
33555226 AAAA--TAATTGTTACACGTCATGTTA
1 AAAATTTAGTTATTACACGTCATGTTA
* * ** * *
33555251 AAAATATAATTATTACACACCATATTG
1 AAAATTTAGTTATTACACGTCATGTTA
* * *
33555278 AAAATTTAGTTTTTACACATTATGTTGA
1 AAAATTTAGTTATTACACGTCATGTT-A
* * *
33555306 AAAATGTAGTTATTACACGTTA-GATTG
1 AAAATTTAGTTATTACACGTCATG-TTA
* * * *
33555333 AAAATTTAGTTGTTAAACATAATGTTGA
1 AAAATTTAGTTATTACACGTCATGTT-A
* * * *
33555361 AAAATATAATTATTATATC-TCATGTTG
1 AAAATTTAGTTATTACA-CGTCATGTTA
* * * * *
33555388 AATATTTAATTGTTACACGTTATATTA
1 AAAATTTAGTTATTACACGTCATGTTA
* * ** * * *
33555415 AAAATTTAGATGTTGTATGTCGTATTAA
1 AAAATTTAGTTATTACACGTCATGTT-A
33555443 AAAATTTAGTTATTACACGTCATG--A
1 AAAATTTAGTTATTACACGTCATGTTA
*
33555468 AAAATTTAGTTATTACACGTCATGTTG
1 AAAATTTAGTTATTACACGTCATGTTA
* * *
33555495 AAGATTTAATTATTACTCGTCATGTTA
1 AAAATTTAGTTATTACACGTCATGTTA
* * *
33555522 AATATTTAGTTGTTGCACGTCATGT
1 AAAATTTAGTTATTACACGTCATGT
33555547 CATAATTTGA
Statistics
Matches: 247, Mismatches: 63, Indels: 22
0.74 0.19 0.07
Matches are distributed among these distances:
25 47 0.19
26 1 0.00
27 139 0.56
28 59 0.24
29 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (27 bp):
AAAATTTAGTTATTACACGTCATGTTA
Found at i:33573299 original size:31 final size:31
Alignment explanation
Indices: 33573240--33573330 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
33573230 TTAAAAAATT
** **
33573240 AAAATAAAATATATAATATACAAAATTATGTTA
1 AAAATAAAATA-A-AATATATGAAATTATAATA
*
33573273 AAAATAAAATAAAATATATGAGATTATAATA
1 AAAATAAAATAAAATATATGAAATTATAATA
*
33573304 AAAATAAAAATAAAATATATGATATTA
1 AAAAT-AAAATAAAATATATGAAATTA
33573331 CAAATATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 19 0.37
32 21 0.41
33 11 0.22
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (31 bp):
AAAATAAAATAAAATATATGAAATTATAATA
Found at i:33573319 original size:32 final size:31
Alignment explanation
Indices: 33573271--33573330 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
33573261 AAAATTATGT
33573271 TAAAAATAAAATAAAATATATGAGATTATAA
1 TAAAAATAAAATAAAATATATGAGATTATAA
*
33573302 TAAAAATAAAAATAAAATATATGATATTA
1 TAAAAAT-AAAATAAAATATATGAGATTA
33573331 CAAATATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (31 bp):
TAAAAATAAAATAAAATATATGAGATTATAA
Found at i:33573335 original size:27 final size:30
Alignment explanation
Indices: 33573271--33573381 Score: 83
Period size: 27 Copynumber: 3.8 Consensus size: 30
33573261 AAAATTATGT
33573271 TAAAAAT-AAAATAAAATATATGAGATTATAA
1 TAAAAATAAAAATAAAATATAT-AGATTAT-A
33573302 TAAAAATAAAAATAAAATATAT-GA-TAT-
1 TAAAAATAAAAATAAAATATATAGATTATA
* * * *
33573329 TACAAATATAATTAAGATATGAT--ATTATA
1 TAAAAATAAAAATAAAATAT-ATAGATTATA
*
33573358 TAAAAATTAATAATGAAAA-ATATA
1 TAAAAA-TAAAAAT-AAAATATATA
33573382 AATATATTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
27 17 0.27
28 5 0.08
29 10 0.16
30 8 0.12
31 10 0.16
32 14 0.22
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (30 bp):
TAAAAATAAAAATAAAATATATAGATTATA
Found at i:33573549 original size:15 final size:15
Alignment explanation
Indices: 33573529--33573571 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
33573519 TATTATCTTC
33573529 TTATAATCATATTAT
1 TTATAATCATATTAT
33573544 TTATAATCA-AGTTAT
1 TTATAATCATA-TTAT
33573559 TTATAATCATATT
1 TTATAATCATATT
33573572 GTATTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (15 bp):
TTATAATCATATTAT
Found at i:33574372 original size:21 final size:22
Alignment explanation
Indices: 33574346--33574389 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
33574336 AAGTTTTTTG
33574346 TTTTTTAAT-GTAAATTTGACT
1 TTTTTTAATGGTAAATTTGACT
*
33574367 TTTTTTCATGGGTAAATTTGACT
1 TTTTTTAAT-GGTAAATTTGACT
33574390 ATTCGGGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.55
Consensus pattern (22 bp):
TTTTTTAATGGTAAATTTGACT
Found at i:33593802 original size:23 final size:25
Alignment explanation
Indices: 33593775--33593828 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
33593765 TATTAATATG
33593775 ATTTTTTATT-TCAATTTCT-TTTT-
1 ATTTTTT-TTCTCAATTTCTATTTTC
*
33593798 ATTTTTTTTCTCAATTTGTATTTTC
1 ATTTTTTTTCTCAATTTCTATTTTC
33593823 ATTTTT
1 ATTTTT
33593829 CATCTTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 15 0.56
24 4 0.15
25 6 0.22
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (25 bp):
ATTTTTTTTCTCAATTTCTATTTTC
Found at i:33603505 original size:2 final size:2
Alignment explanation
Indices: 33603492--33603616 Score: 112
Period size: 2 Copynumber: 61.0 Consensus size: 2
33603482 TATGTGTAGA
*
33603492 AT AT AC 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
* * * * *
33603534 CAT AT AT GT ACT AT -T AT GAA AA ACT CT -T A- ACN AT AT AT AT AT
1 -AT AT AT AT A-T AT AT AT -AT AT A-T AT AT AT A-T AT AT AT AT AT
*
33603576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
33603617 GTACTATTAT
Statistics
Matches: 104, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
1 3 0.03
2 93 0.89
3 8 0.08
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:33603616 original size:76 final size:75
Alignment explanation
Indices: 33603492--33603640 Score: 271
Period size: 76 Copynumber: 2.0 Consensus size: 75
33603482 TATGTGTAGA
33603492 ATATACATATATATATATATATATATATATATATATATATATCATATATGTACTATTATGAAAAA
1 ATATACATATATATATATATATATATATATATATATATATATCATATATGTACTATTATGAAAAA
33603557 CTCTTAACNAT
66 CTCTTAAC-AT
* *
33603568 ATATATATATATATATATATATATATATATATATATGTATATCATATATGTACTATTATGAAAAA
1 ATATACATATATATATATATATATATATATATATATATATATCATATATGTACTATTATGAAAAA
33603633 CTCTTAAC
66 CTCTTAAC
33603641 CTTTTTGTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (75 bp):
ATATACATATATATATATATATATATATATATATATATATATCATATATGTACTATTATGAAAAA
CTCTTAACAT
Found at i:33606915 original size:2 final size:2
Alignment explanation
Indices: 33606908--33606948 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
33606898 NNGAACATTC
33606908 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33606947 AT
1 AT
33606949 TATTTTATCG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:33606928 original size:15 final size:15
Alignment explanation
Indices: 33606908--33606948 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
33606898 NNGAACATTC
33606908 ATATATATATATATA
1 ATATATATATATATA
33606923 ATATATATATATATA
1 ATATATATATATATA
33606938 ATA-ATATATAT
1 ATATATATATAT
33606949 TATTTTATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:33640572 original size:42 final size:42
Alignment explanation
Indices: 33640499--33640583 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
33640489 TTGACAAACC
* ** *
33640499 TAGTACATGTGTTCATGTCCCATTGACCCTTGATTTACATTA
1 TAGTACATGTATTCATGTCCCAAGGAACCTTGATTTACATTA
*
33640541 TAGTGCATGTATTCATGTCCCAAGGAACCTTGATTTACATTA
1 TAGTACATGTATTCATGTCCCAAGGAACCTTGATTTACATTA
33640583 T
1 T
33640584 CAAAAAGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (42 bp):
TAGTACATGTATTCATGTCCCAAGGAACCTTGATTTACATTA
Found at i:33651227 original size:2 final size:2
Alignment explanation
Indices: 33651220--33651272 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
33651210 GTGACACCAT
33651220 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC ATC T- TC TC T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC
33651261 TC T- TC TC TC TC T
1 TC TC TC TC TC TC T
33651273 GGAGCCAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:33651613 original size:9 final size:9
Alignment explanation
Indices: 33651599--33651629 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33651589 GATGAGATCC
33651599 ATCATCATA
1 ATCATCATA
*
33651608 ATCATCATC
1 ATCATCATA
33651617 ATCATCATA
1 ATCATCATA
33651626 ATCA
1 ATCA
33651630 GTTGTCTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (9 bp):
ATCATCATA
Found at i:33664032 original size:2 final size:2
Alignment explanation
Indices: 33664027--33664052 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33664017 AGAAAAAAAA
33664027 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
33664053 TACGAAAGAG
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:33686057 original size:12 final size:12
Alignment explanation
Indices: 33686008--33686060 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
33685998 TCACTACCTG
33686008 CAGCCCCAGTCC
1 CAGCCCCAGTCC
* *
33686020 CAGTCCCAGTTC
1 CAGCCCCAGTCC
* * *
33686032 CGGCCCCCGGCC
1 CAGCCCCAGTCC
*
33686044 CAGCCCCAGCCC
1 CAGCCCCAGTCC
33686056 CAGCC
1 CAGCC
33686061 TCCTGAAACA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.13, C:0.58, G:0.21, T:0.08
Consensus pattern (12 bp):
CAGCCCCAGTCC
Found at i:33687126 original size:24 final size:24
Alignment explanation
Indices: 33687090--33687136 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
33687080 TATATTATTG
*
33687090 TTTTATTTATATT-TGTTTATTTT
1 TTTTATTTATATTCTCTTTATTTT
*
33687113 TTTTCATTTCTATTCTCTTTATTT
1 TTTT-ATTTATATTCTCTTTATTT
33687137 ATATGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 8 0.40
25 8 0.40
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTTATTTATATTCTCTTTATTTT
Found at i:33687554 original size:15 final size:14
Alignment explanation
Indices: 33687519--33687566 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
33687509 TTATCAATCC
*
33687519 TATATATTGTATTT
1 TATATATTATATTT
*
33687533 AAT-TATTTATATTT
1 TATATA-TTATATTT
33687547 TATATATTATAATTT
1 TATATATTAT-ATTT
33687562 TATAT
1 TATAT
33687567 TTAGTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.07
14 15 0.54
15 11 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TATATATTATATTT
Found at i:33687567 original size:28 final size:29
Alignment explanation
Indices: 33687519--33687574 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
33687509 TTATCAATCC
*
33687519 TATATATTGTATTTAATTATTTA-TATTT
1 TATATATTATATTTAATTATTTAGTATTT
*
33687547 TATATATTATAATTTTA-TATTTAGTATT
1 TATATATTAT-ATTTAATTATTTAGTATT
33687575 ATAAGTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (29 bp):
TATATATTATATTTAATTATTTAGTATTT
Found at i:33691019 original size:2 final size:2
Alignment explanation
Indices: 33691012--33691041 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
33691002 CTTGTTTTTA
*
33691012 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33691042 GAAGTGCAAA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33694780 original size:45 final size:45
Alignment explanation
Indices: 33694716--33694918 Score: 194
Period size: 45 Copynumber: 4.4 Consensus size: 45
33694706 CACGCTATAA
* * *
33694716 TGTTATACACCATATACAAAAATCTGTGACAAGCCATGGTTAACG
1 TGTTACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAACG
* * * *
33694761 TGTTACACGCCATATACAAAAATCTGTGACAAGTCAT-GTACAAAAACA
1 TGTTACACGCCATGTACAAAAATCTGTGACAAGCCATGGT----TAACG
* * *
33694809 TGTGACACGCCATGTACAAAAATTTGTGACAAGCCATGGTTAGCG
1 TGTTACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAACG
* ** * * *
33694854 TGTGACACTTCATGTACAAAAA-CTTGTGATAAGTCATGGTTAGCG
1 TGTTACACGCCATGTACAAAAATC-TGTGACAAGCCATGGTTAACG
*
33694899 TGTTACACGTCATGTACAAA
1 TGTTACACGCCATGTACAAA
33694919 TACATGTGAC
Statistics
Matches: 133, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
44 2 0.02
45 93 0.70
48 36 0.27
49 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAACG
Found at i:33694812 original size:24 final size:23
Alignment explanation
Indices: 33694775--33694960 Score: 82
Period size: 24 Copynumber: 8.0 Consensus size: 23
33694765 ACACGCCATA
33694775 TACAAAAATCTGTGACAAGTCATG
1 TACAAAAA-CTGTGACAAGTCATG
* *
33694799 TACAAAAACATGTGACACGCCATG
1 TACAAAAAC-TGTGACAAGTCATG
* *
33694823 TACAAAAATTTGTGACAAGCCATGG
1 TACAAAAA-CTGTGACAAGTCAT-G
* * **
33694848 T----TAGCGTGTGACACTTCATG
1 TACAAAAAC-TGTGACAAGTCATG
*
33694868 TACAAAAACTTGTGATAAGTCATGG
1 TACAAAAAC-TGTGACAAGTCAT-G
* * * *
33694893 T----TAGCGTGTTACACGTCATG
1 TACAAAAAC-TGTGACAAGTCATG
* *
33694913 TACAAATACATGTGACACGTCATG
1 TACAAAAAC-TGTGACAAGTCATG
*
33694937 TATAAAAATCTGTGACAAGTCATG
1 TACAAAAA-CTGTGACAAGTCATG
33694961 GTTAGCGTGT
Statistics
Matches: 118, Mismatches: 30, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
20 4 0.03
21 23 0.19
23 1 0.01
24 85 0.72
25 5 0.04
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (23 bp):
TACAAAAACTGTGACAAGTCATG
Found at i:33694951 original size:114 final size:114
Alignment explanation
Indices: 33694793--33695019 Score: 357
Period size: 114 Copynumber: 2.0 Consensus size: 114
33694783 TCTGTGACAA
*
33694793 GTCATGTACAAAAACATGTGACACGCCATGTACAAAAATTTGTGACAAGCCATGGTTAGCGTGTG
1 GTCATGTACAAAAACATGTGACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAGCGTGTG
* * *
33694858 ACACT-TCATGTACAAAAACTTGTGATAAGTCATGGTTAGCGTGTTACAC
66 ACA-TGTCATGTACAAAAACCTGTGACAAATCATGGTTAGCGTGTTACAC
* * * *
33694907 GTCATGTACAAATACATGTGACACGTCATGTATAAAAATCTGTGACAAGTCATGGTTAGCGTGTG
1 GTCATGTACAAAAACATGTGACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAGCGTGTG
*
33694972 ACATGTCATGTACAAAAGCCTGTGACAAATCATGGTTAGCGTGTTACA
66 ACATGTCATGTACAAAAACCTGTGACAAATCATGGTTAGCGTGTTACA
33695020 TGCCATATGC
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 1 0.01
114 102 0.99
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (114 bp):
GTCATGTACAAAAACATGTGACACGCCATGTACAAAAATCTGTGACAAGCCATGGTTAGCGTGTG
ACATGTCATGTACAAAAACCTGTGACAAATCATGGTTAGCGTGTTACAC
Found at i:33694972 original size:45 final size:44
Alignment explanation
Indices: 33694923--33695178 Score: 215
Period size: 45 Copynumber: 5.7 Consensus size: 44
33694913 TACAAATACA
* * *
33694923 TGTGACACGTCATGTATAAAAATCTGTGACAAGTCATGGTTAGCG
1 TGTGACACGCCATGTA-AAAAACCTGTGACAAGCCATGGTTAGCG
* * * **
33694968 TGTGACATGTCATGTACAAAAGCCTGTGACAAATCATGGTTAGCG
1 TGTGACACGCCATGTA-AAAAACCTGTGACAAGCCATGGTTAGCG
* * * * * * *
33695013 TGTTACATGCCATATGCAAAAACCTATGATAAGCCATGGTTAGTG
1 TGTGACACGCCATGT-AAAAAACCTGTGACAAGCCATGGTTAGCG
* * *
33695058 TGTGACACGCCATGTACAAAAGCATGTGACAAGCCATAGTTAGCG
1 TGTGACACGCCATGTA-AAAAACCTGTGACAAGCCATGGTTAGCG
* * * * *
33695103 TGTGACACGCTATGTACAAAAGCTTGTGACAAGCCATGATAAGCG
1 TGTGACACGCCATGTA-AAAAACCTGTGACAAGCCATGGTTAGCG
* * * *
33695148 TGTTACATGCCATGTGCAAAAACCTATGACA
1 TGTGACACGCCATGT-AAAAAACCTGTGACA
33695179 CGTCATGCAC
Statistics
Matches: 171, Mismatches: 37, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
45 171 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (44 bp):
TGTGACACGCCATGTAAAAAACCTGTGACAAGCCATGGTTAGCG
Found at i:33694998 original size:69 final size:69
Alignment explanation
Indices: 33694854--33694987 Score: 207
Period size: 69 Copynumber: 1.9 Consensus size: 69
33694844 ATGGTTAGCG
* * *
33694854 TGTGACACTTCATGTACAAAAACTTGTGATAAGTCATGGTTAGCGTGTTACACGTCATGTACAAA
1 TGTGACACGTCATGTACAAAAACTTGTGACAAGTCATGGTTAGCGTGTGACACGTCATGTACAAA
33694919 TACA
66 TACA
* *
33694923 TGTGACACGTCATGTATAAAAA-TCTGTGACAAGTCATGGTTAGCGTGTGACATGTCATGTACAA
1 TGTGACACGTCATGTACAAAAACT-TGTGACAAGTCATGGTTAGCGTGTGACACGTCATGTACAA
33694987 A
65 A
33694988 AGCCTGTGAC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 1 0.02
69 58 0.98
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (69 bp):
TGTGACACGTCATGTACAAAAACTTGTGACAAGTCATGGTTAGCGTGTGACACGTCATGTACAAA
TACA
Found at i:33695005 original size:69 final size:69
Alignment explanation
Indices: 33694854--33695005 Score: 200
Period size: 69 Copynumber: 2.2 Consensus size: 69
33694844 ATGGTTAGCG
* * *
33694854 TGTGACACTTCATGTACAAAAACTTGTGATAAGTCATGGTTAGCGTGTTACACGTCATGTACAAA
1 TGTGACACATCATGTACAAAAACTTGTGACAAGTCATGGTTAGCGTGTGACACGTCATGTACAAA
33694919 TACA
66 TACA
* * *
33694923 TGTGACACGTCATGTATAAAAA-TCTGTGACAAGTCATGGTTAGCGTGTGACATGTCATGTACAA
1 TGTGACACATCATGTACAAAAACT-TGTGACAAGTCATGGTTAGCGTGTGACACGTCATGTACAA
*
33694987 A-AGCC
65 ATA-CA
*
33694992 TGTGACAAATCATG
1 TGTGACACATCATG
33695006 GTTAGCGTGT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
68 2 0.03
69 71 0.97
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (69 bp):
TGTGACACATCATGTACAAAAACTTGTGACAAGTCATGGTTAGCGTGTGACACGTCATGTACAAA
TACA
Found at i:33695087 original size:24 final size:24
Alignment explanation
Indices: 33695058--33695140 Score: 75
Period size: 24 Copynumber: 3.6 Consensus size: 24
33695048 ATGGTTAGTG
*
33695058 TGTGACACGCCATGTACAAAAGCA
1 TGTGACAAGCCATGTACAAAAGCA
* *
33695082 TGTGACAAGCCATAGT----TAGCG
1 TGTGACAAGCCAT-GTACAAAAGCA
* * *
33695103 TGTGACACGCTATGTACAAAAGCT
1 TGTGACAAGCCATGTACAAAAGCA
33695127 TGTGACAAGCCATG
1 TGTGACAAGCCATG
33695141 ATAAGCGTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
20 2 0.04
21 14 0.31
24 27 0.60
25 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (24 bp):
TGTGACAAGCCATGTACAAAAGCA
Found at i:33695108 original size:135 final size:135
Alignment explanation
Indices: 33694923--33695176 Score: 368
Period size: 135 Copynumber: 1.9 Consensus size: 135
33694913 TACAAATACA
* * * * *
33694923 TGTGACACGTCATGTATAAAAATCTGTGACAAGTCATGGTTAGCGTGTGACATG-TCATGTACAA
1 TGTGACACGCCATGTATAAAAAGCTGTGACAAGCCATAGTTAGCGTGTGACACGCT-ATGTACAA
* * *
33694987 AAGCCTGTGACAAATCATGGTTAGCGTGTTACATGCCATATGCAAAAACCTATGATAAGCCATGG
65 AAGCCTGTGACAAACCATGATAAGCGTGTTACATGCCATATGCAAAAACCTATGATAAGCCATGG
33695052 TTAGTG
130 TTAGTG
*
33695058 TGTGACACGCCATGTA-CAAAAGCATGTGACAAGCCATAGTTAGCGTGTGACACGCTATGTACAA
1 TGTGACACGCCATGTATAAAAAGC-TGTGACAAGCCATAGTTAGCGTGTGACACGCTATGTACAA
* * *
33695122 AAGCTTGTGACAAGCCATGATAAGCGTGTTACATGCCATGTGCAAAAACCTATGA
65 AAGCCTGTGACAAACCATGATAAGCGTGTTACATGCCATATGCAAAAACCTATGA
33695177 CACGTCATGC
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
134 5 0.05
135 99 0.94
136 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (135 bp):
TGTGACACGCCATGTATAAAAAGCTGTGACAAGCCATAGTTAGCGTGTGACACGCTATGTACAAA
AGCCTGTGACAAACCATGATAAGCGTGTTACATGCCATATGCAAAAACCTATGATAAGCCATGGT
TAGTG
Found at i:33695178 original size:90 final size:90
Alignment explanation
Indices: 33694923--33695178 Score: 269
Period size: 90 Copynumber: 2.8 Consensus size: 90
33694913 TACAAATACA
* * * * * *
33694923 TGTGACACGTCATGTATAAAAATCTGTGACAAGTCATGGTTAGCGTGTGACATGTCATGTACAAA
1 TGTGACACGCCATATACAAAAACCTGTGACAAGCCATGGTTAGCGTGTGACATGCCATGTACAAA
* *
33694988 AGCCTGTGACAAATCATGGTTAGCG
66 AGCCTGTGACAAACCATAGTTAGCG
* * * * * * *
33695013 TGTTACATGCCATATGCAAAAACCTATGATAAGCCATGGTTAGTGTGTGACACGCCATGTACAAA
1 TGTGACACGCCATATACAAAAACCTGTGACAAGCCATGGTTAGCGTGTGACATGCCATGTACAAA
* *
33695078 AGCATGTGACAAGCCATAGTTAGCG
66 AGCCTGTGACAAACCATAGTTAGCG
* * * * * * * *
33695103 TGTGACACGCTATGTACAAAAGCTTGTGACAAGCCATGATAAGCGTGTTACATGCCATGTGCAAA
1 TGTGACACGCCATATACAAAAACCTGTGACAAGCCATGGTTAGCGTGTGACATGCCATGTACAAA
* *
33695168 AACCTATGACA
66 AGCCTGTGACA
33695179 CGTCATGCAC
Statistics
Matches: 131, Mismatches: 35, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
90 131 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (90 bp):
TGTGACACGCCATATACAAAAACCTGTGACAAGCCATGGTTAGCGTGTGACATGCCATGTACAAA
AGCCTGTGACAAACCATAGTTAGCG
Found at i:33695546 original size:23 final size:23
Alignment explanation
Indices: 33695506--33695555 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
33695496 TTTGGTGTCT
*
33695506 TGAAAGCGTAAGAAAGAGAAATC
1 TGAAAACGTAAGAAAGAGAAATC
* *
33695529 TGAAAACGTGAGAGAGAGAAATC
1 TGAAAACGTAAGAAAGAGAAATC
33695552 -GAAA
1 TGAAA
33695556 GCATAGCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.12
Consensus pattern (23 bp):
TGAAAACGTAAGAAAGAGAAATC
Found at i:33696924 original size:14 final size:14
Alignment explanation
Indices: 33696905--33696933 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33696895 AAATTTTAGG
33696905 ATTGTTAATATGAT
1 ATTGTTAATATGAT
33696919 ATTGTTAATATGAT
1 ATTGTTAATATGAT
33696933 A
1 A
33696934 GTTTGATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (14 bp):
ATTGTTAATATGAT
Found at i:33700810 original size:14 final size:15
Alignment explanation
Indices: 33700793--33700833 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
33700783 TTCTGTTTCT
33700793 TTTGTGTGG-GTGGG
1 TTTGTGTGGTGTGGG
33700807 TTTGTGTGGTGTGGG
1 TTTGTGTGGTGTGGG
33700822 --TGTG-GGTGTGGG
1 TTTGTGTGGTGTGGG
33700834 GACGACAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.31
13 4 0.15
14 9 0.35
15 5 0.19
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (15 bp):
TTTGTGTGGTGTGGG
Found at i:33709859 original size:15 final size:15
Alignment explanation
Indices: 33709836--33709865 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33709826 ATTTCTGATA
*
33709836 ATAATATTATTATTT
1 ATAAAATTATTATTT
33709851 ATAAAATTATTATTT
1 ATAAAATTATTATTT
33709866 TATTACATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAAAATTATTATTT
Found at i:33713280 original size:2 final size:2
Alignment explanation
Indices: 33713273--33713330 Score: 100
Period size: 2 Copynumber: 29.0 Consensus size: 2
33713263 TGAATACAAT
33713273 TA TA TA TA TA TA NTA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33713315 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
33713331 GTGATAGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 51 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33714314 original size:22 final size:22
Alignment explanation
Indices: 33714287--33714328 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33714277 AAGGAGGAAA
33714287 AAAATTATTTGATTGATTCACG
1 AAAATTATTTGATTGATTCACG
* *
33714309 AAAATTGTTTTATTGATTCA
1 AAAATTATTTGATTGATTCA
33714329 TAAAAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (22 bp):
AAAATTATTTGATTGATTCACG
Found at i:33714334 original size:22 final size:22
Alignment explanation
Indices: 33714286--33714334 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
33714276 AAAGGAGGAA
33714286 AAAAATTATTTGATTGATTCAC
1 AAAAATTATTTGATTGATTCAC
* * * *
33714308 GAAAATTGTTTTATTGATTCAT
1 AAAAATTATTTGATTGATTCAC
33714330 AAAAA
1 AAAAA
33714335 AAGAAAATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (22 bp):
AAAAATTATTTGATTGATTCAC
Found at i:33716708 original size:17 final size:18
Alignment explanation
Indices: 33716675--33716709 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33716665 AGAACAAAAT
*
33716675 TAAAAAAATATATATAAA
1 TAAAAAAATATAAATAAA
33716693 TAAAAAAAT-TAAATAAA
1 TAAAAAAATATAAATAAA
33716710 AACTTTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAAATATAAATAAA
Found at i:33718695 original size:54 final size:54
Alignment explanation
Indices: 33718615--33718726 Score: 217
Period size: 54 Copynumber: 2.1 Consensus size: 54
33718605 AATAAAGTGA
33718615 TTCT-TCTTATAACATTATAGTATACATTGCACCATTTCGAGTTCCCTGTTTAC
1 TTCTCTCTTATAACATTATAGTATACATTGCACCATTTCGAGTTCCCTGTTTAC
33718668 TTCTCTCTTATAACATTATAGTATACATTGCACCATTTCGAGTTCCCTGTTTAC
1 TTCTCTCTTATAACATTATAGTATACATTGCACCATTTCGAGTTCCCTGTTTAC
33718722 TTCTC
1 TTCTC
33718727 GGATCTTGCC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 4 0.07
54 54 0.93
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (54 bp):
TTCTCTCTTATAACATTATAGTATACATTGCACCATTTCGAGTTCCCTGTTTAC
Found at i:33727428 original size:42 final size:42
Alignment explanation
Indices: 33727368--33727452 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
33727358 AATTGTTGCT
33727368 GCTGCTGCCGGCTACTTTTGTTTGGTTACTGGTTTTTAATGA
1 GCTGCTGCCGGCTACTTTTGTTTGGTTACTGGTTTTTAATGA
*
33727410 GCTGCTGCCGGCTGCTTTTGTTTGGTTACTGGTTTTTAATGA
1 GCTGCTGCCGGCTACTTTTGTTTGGTTACTGGTTTTTAATGA
33727452 G
1 G
33727453 TATTCAACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.11, C:0.16, G:0.28, T:0.45
Consensus pattern (42 bp):
GCTGCTGCCGGCTACTTTTGTTTGGTTACTGGTTTTTAATGA
Found at i:33760319 original size:18 final size:18
Alignment explanation
Indices: 33760298--33760351 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
33760288 GATATAATAC
*
33760298 TTTAATTTTTTTTAATTA
1 TTTAATTATTTTTAATTA
*
33760316 TTTAAAATATTTTT-ATTA
1 TTT-AATTATTTTTAATTA
* *
33760334 TTTTATTATGTTTAATTA
1 TTTAATTATTTTTAATTA
33760352 AATTTTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.24
18 14 0.48
19 8 0.28
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTAATTATTTTTAATTA
Found at i:33760380 original size:26 final size:29
Alignment explanation
Indices: 33760324--33760380 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 29
33760314 TATTTAAAAT
*
33760324 ATTTTTATTATTTTATTATGTTTAATTAA
1 ATTTTTATTATTTTATTATGTTTAATCAA
33760353 ATTTTTA-TA-TTT-TTAT-TTTAAATCAA
1 ATTTTTATTATTTTATTATGTTT-AATCAA
33760379 AT
1 AT
33760381 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 3 0.12
26 11 0.42
27 3 0.12
28 2 0.08
29 7 0.27
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (29 bp):
ATTTTTATTATTTTATTATGTTTAATCAA
Found at i:33770400 original size:15 final size:15
Alignment explanation
Indices: 33770380--33770410 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33770370 TTTTAGACAA
33770380 TTTCAATTGTAAGTC
1 TTTCAATTGTAAGTC
33770395 TTTCAATTGTAAGTC
1 TTTCAATTGTAAGTC
33770410 T
1 T
33770411 ATTTTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (15 bp):
TTTCAATTGTAAGTC
Found at i:33775142 original size:9 final size:9
Alignment explanation
Indices: 33775130--33775154 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
33775120 TGATATTAAT
33775130 GATGATGAA
1 GATGATGAA
33775139 GATGATGAA
1 GATGATGAA
33775148 GATGATG
1 GATGATG
33775155 TAATTTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (9 bp):
GATGATGAA
Found at i:33787757 original size:20 final size:22
Alignment explanation
Indices: 33787719--33787758 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33787709 AATCTCTGGC
*
33787719 AGAGAGAGAGAGAAGAAAGAGA
1 AGAGAGAGACAGAAGAAAGAGA
33787741 AGAGAGA-ACAGAA-AAAGA
1 AGAGAGAGACAGAAGAAAGA
33787759 CGAATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (22 bp):
AGAGAGAGACAGAAGAAAGAGA
Found at i:33795213 original size:13 final size:14
Alignment explanation
Indices: 33795188--33795225 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
33795178 CAAAAATTAT
33795188 AACTTATTAAAAAG
1 AACTTATTAAAAAG
*
33795202 AACTTA-TAAAAAA
1 AACTTATTAAAAAG
*
33795215 AATTTATTAAA
1 AACTTATTAAA
33795226 TAATTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (14 bp):
AACTTATTAAAAAG
Found at i:33797881 original size:2 final size:2
Alignment explanation
Indices: 33797874--33797901 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33797864 AGCATCCATA
33797874 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
33797902 TNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33799302 original size:23 final size:22
Alignment explanation
Indices: 33799245--33799319 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
33799235 TTTTAATATT
*
33799245 AAAATATTATTTAATTATAATA
1 AAAATATTATTAAATTATAATA
** *
33799267 AAAAGT-TTAATTATCTTCTAATA
1 AAAA-TATT-ATTAAATTATAATA
33799290 CAAAATATTATTAAATTATAATA
1 -AAAATATTATTAAATTATAATA
33799313 AAAATAT
1 AAAATAT
33799320 GTTTGTGTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
22 13 0.31
23 23 0.55
24 6 0.14
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (22 bp):
AAAATATTATTAAATTATAATA
Found at i:33799410 original size:23 final size:23
Alignment explanation
Indices: 33799383--33799438 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
33799373 TACTTAGAAT
33799383 ATTTTTATCTTTTAACAAAATAA
1 ATTTTTATCTTTTAACAAAATAA
* * * *
33799406 ATTTTTTTATTTTAATAAAATAT
1 ATTTTTATCTTTTAACAAAATAA
*
33799429 ATATTTATCT
1 ATTTTTATCT
33799439 CATCATAGTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTTATCTTTTAACAAAATAA
Found at i:33802871 original size:25 final size:25
Alignment explanation
Indices: 33802836--33802883 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
33802826 TCAAGTGATC
*
33802836 ATTATATTATATT-ATATTATTATTG
1 ATTATAATATATTAATA-TATTATTG
33802861 ATTATAATATATTAATATATTAT
1 ATTATAATATATTAATATATTAT
33802884 GTTAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTATAATATATTAATATATTATTG
Found at i:33802939 original size:28 final size:29
Alignment explanation
Indices: 33802898--33802953 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
33802888 AAATTATATG
33802898 ATATATAATGATAAATAATAT-TTTAATTA
1 ATATATAATGATAAA-AATATATTTAATTA
* *
33802927 ATAT-TAATTATAAAAATTTATTTAATT
1 ATATATAATGATAAAAATATATTTAATT
33802954 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.17
28 16 0.67
29 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
ATATATAATGATAAAAATATATTTAATTA
Found at i:33811025 original size:13 final size:13
Alignment explanation
Indices: 33811007--33811050 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
33810997 TTTATTTTAA
33811007 AATATTAATAATT
1 AATATTAATAATT
*
33811020 AATATT-TTAATAT
1 AATATTAATAAT-T
33811033 AAT-TTAATAATT
1 AATATTAATAATT
33811045 AATATT
1 AATATT
33811051 TTATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATTAATAATT
Found at i:33811025 original size:28 final size:26
Alignment explanation
Indices: 33810994--33811078 Score: 109
Period size: 25 Copynumber: 3.2 Consensus size: 26
33810984 TATTTATTTT
*
33810994 TATTTTATTTTAAAATATTAATAATTAA
1 TATTTTA-TTTATAAT-TTAATAATTAA
*
33811022 TATTTTA-ATATAATTTAATAATTAA
1 TATTTTATTTATAATTTAATAATTAA
33811047 TATTTTATTTATAATTTAATATTATTAA
1 TATTTTATTTATAATTTAATA--ATTAA
33811075 TATT
1 TATT
33811079 AAAATATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
25 18 0.35
26 17 0.33
28 16 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTTTATTTATAATTTAATAATTAA
Found at i:33811036 original size:17 final size:17
Alignment explanation
Indices: 33811014--33811078 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
33811004 TAAAATATTA
33811014 ATAATTAATATTTTAAT
1 ATAATTAATATTTTAAT
*
33811031 ATAATTTAATA-ATTAAT
1 ATAA-TTAATATTTTAAT
* * *
33811048 ATTTTATTTATAATTTAAT
1 A--TAATTAATATTTTAAT
*
33811067 ATTATTAATATT
1 ATAATTAATATT
33811079 AAAATATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
17 19 0.50
18 11 0.29
19 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAATTAATATTTTAAT
Found at i:33811051 original size:59 final size:56
Alignment explanation
Indices: 33810991--33811103 Score: 140
Period size: 59 Copynumber: 2.0 Consensus size: 56
33810981 GATTATTTAT
* * *
33810991 TTTTATTT-TATTTTAA-AATATTAATAATTAATATTTTAATATAATTTAATAATTAATA
1 TTTTATTTATAATTTAATAATATTAAT-ATTAAAATATTAA-ATAATTT--TAATTAATA
*
33811049 TTTTATTTATAATTTAATATTATTAATATTAAAATATTAAATAATTTTAATTAAT
1 TTTTATTTATAATTTAATAATATTAATATTAAAATATTAAATAATTTTAATTAAT
33811104 TTCCAAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
56 8 0.16
58 15 0.31
59 18 0.37
60 8 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (56 bp):
TTTTATTTATAATTTAATAATATTAATATTAAAATATTAAATAATTTTAATTAATA
Found at i:33811306 original size:15 final size:16
Alignment explanation
Indices: 33811275--33811308 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
33811265 TTTATTTTCA
33811275 TTAAAATTTTAAAAAT
1 TTAAAATTTTAAAAAT
*
33811291 TTAAAA-TTTAATAAT
1 TTAAAATTTTAAAAAT
33811306 TTA
1 TTA
33811309 TTATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATTTTAAAAAT
Found at i:33811342 original size:7 final size:7
Alignment explanation
Indices: 33811330--33811367 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
33811320 TTAGTATAAT
33811330 TTTTTTA
1 TTTTTTA
33811337 TTTTTT-
1 TTTTTTA
*
33811343 TATTTGTA
1 T-TTTTTA
33811351 TTTTTTA
1 TTTTTTA
33811358 TTTTTTA
1 TTTTTTA
33811365 TTT
1 TTT
33811368 ATACTCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 1 0.04
7 25 0.93
8 1 0.04
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:33811394 original size:8 final size:8
Alignment explanation
Indices: 33811383--33811486 Score: 61
Period size: 8 Copynumber: 12.6 Consensus size: 8
33811373 CATTAAAAAT
33811383 TTAATATA
1 TTAATATA
33811391 TTAATA-A
1 TTAATATA
*
33811398 TTTAATAAA
1 -TTAATATA
* *
33811407 TAAAAATA
1 TTAATATA
*
33811415 TTAATATT
1 TTAATATA
33811423 TTAATCATA
1 TTAAT-ATA
33811432 TTAATATTA
1 TTAATA-TA
* *
33811441 ATAATGT-
1 TTAATATA
33811448 TTAAATTATA
1 TT-AA-TATA
33811458 TATAA-ATA
1 T-TAATATA
*
33811466 TTAATATT
1 TTAATATA
*
33811474 TTAAAATA
1 TTAATATA
33811482 TTAAT
1 TTAAT
33811487 TTTTTATAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
7 5 0.07
8 47 0.65
9 16 0.22
10 3 0.04
11 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (8 bp):
TTAATATA
Found at i:33811458 original size:26 final size:23
Alignment explanation
Indices: 33811388--33811486 Score: 85
Period size: 24 Copynumber: 4.1 Consensus size: 23
33811378 AAAATTTAAT
* * **
33811388 ATATTAATAATTTAATAAATAAAA
1 ATATTAATATTTTAA-ATATATTA
33811412 ATATTAATATTTT-AATCATATTA
1 ATATTAATATTTTAAAT-ATATTA
33811435 ATATTAATAATGTTTAAATTATATATAA
1 ATATTAAT-AT-TTTAAA-TATAT-T-A
33811463 ATATTAATATTTTAAA-ATATTA
1 ATATTAATATTTTAAATATATTA
33811485 AT
1 AT
33811487 TTTTTATAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
22 4 0.06
23 14 0.22
24 18 0.28
25 3 0.05
26 12 0.19
27 4 0.06
28 9 0.14
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATTAATATTTTAAATATATTA
Found at i:33811491 original size:16 final size:16
Alignment explanation
Indices: 33811461--33811508 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
33811451 AATTATATAT
*
33811461 AAATATTAATATTTTA
1 AAATATTAATTTTTTA
33811477 AAATATTAATTTTTTA
1 AAATATTAATTTTTTA
* *
33811493 TAATTTATAATTTTTT
1 AAATAT-TAATTTTTT
33811509 TCTCCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATATTAATTTTTTA
Found at i:33821885 original size:30 final size:30
Alignment explanation
Indices: 33821849--33821908 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
33821839 ATACATTCTA
* *
33821849 GTTGTAACTATAACCTGAAAATTGCTCTCT
1 GTTGTAAATATAAACTGAAAATTGCTCTCT
*
33821879 GTTGTAAATATAAACTGAGAATTGCTCTCT
1 GTTGTAAATATAAACTGAAAATTGCTCTCT
33821909 CTCTCTCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (30 bp):
GTTGTAAATATAAACTGAAAATTGCTCTCT
Found at i:33824438 original size:2 final size:2
Alignment explanation
Indices: 33824431--33824515 Score: 147
Period size: 2 Copynumber: 43.0 Consensus size: 2
33824421 ACTGGCTAAA
33824431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33824472 ANT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33824514 AT
1 AT
33824516 TAAAAATAAG
Statistics
Matches: 80, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.03
2 77 0.96
3 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33829460 original size:2 final size:2
Alignment explanation
Indices: 33829453--33829488 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
33829443 TCCCAAAAAG
*
33829453 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
33829489 AGCTAGCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33836197 original size:21 final size:21
Alignment explanation
Indices: 33836172--33836223 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
33836162 AGTTTTTTAT
33836172 TTTAAAATATA-AATATAAAAA
1 TTTAAAATATATAATA-AAAAA
33836193 TTTAATTAA-ATATAATAAAAAA
1 TTTAA--AATATATAATAAAAAA
*
33836215 TTAAAAATA
1 TTTAAAATA
33836224 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
20 2 0.08
21 6 0.23
22 12 0.46
23 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TTTAAAATATATAATAAAAAA
Found at i:33837982 original size:25 final size:25
Alignment explanation
Indices: 33837947--33837995 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
33837937 TTTAAATAAA
33837947 TTTTTATTTTTTATTGTA-ATCAAG
1 TTTTTATTTTTTATTGTATATCAAG
*
33837971 TTTTTATATTTTTATTTTATATCAA
1 TTTTTAT-TTTTTATTGTATATCAA
33837996 ATAAATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 10 0.45
26 5 0.23
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTTTATTTTTTATTGTATATCAAG
Found at i:33838322 original size:30 final size:29
Alignment explanation
Indices: 33838270--33838364 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
33838260 AATTATTAGT
*
33838270 TATAAGAGCTTGTTT-AACTCAAAATAAAA
1 TATAAGAGCTTATTTGAA-TCAAAATAAAA
* *
33838299 GTATATGAGCTTATTTGATTCAAAATGAAAA
1 -TATAAGAGCTTATTTGAATCAAAAT-AAAA
* **
33838330 TATAAAAATTTATTTGAATCAAAATAAAAA
1 TATAAGAGCTTATTTGAATCAAAAT-AAAA
33838360 TATAA
1 TATAA
33838365 AAATTTATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 49 0.91
31 5 0.09
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (29 bp):
TATAAGAGCTTATTTGAATCAAAATAAAA
Found at i:33838365 original size:30 final size:30
Alignment explanation
Indices: 33838309--33838374 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
33838299 GTATATGAGC
* *
33838309 TTATTTGATTCAAAATGAAAATATAAAAAT
1 TTATTTGAATCAAAATAAAAATATAAAAAT
33838339 TTATTTGAATCAAAATAAAAATATAAAAAT
1 TTATTTGAATCAAAATAAAAATATAAAAAT
33838369 TTATTT
1 TTATTT
33838375 AAGTTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (30 bp):
TTATTTGAATCAAAATAAAAATATAAAAAT
Found at i:33839544 original size:5 final size:5
Alignment explanation
Indices: 33839510--33839556 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
33839500 CACGAAGGGG
***
33839510 AAAGA AAAGGA AAAGA TTGGA AAA-A AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAA-GA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
33839557 GCACCTGCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.12
5 25 0.74
6 5 0.15
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:33844477 original size:15 final size:15
Alignment explanation
Indices: 33844459--33844519 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
33844449 TATTTTATTT
33844459 TTTAAATATTAATAA
1 TTTAAATATTAATAA
*
33844474 TTT--ATA--ATTAA
1 TTTAAATATTAATAA
*
33844485 TTAAAATATTAATAA
1 TTTAAATATTAATAA
* *
33844500 TTTAAATATCAATAT
1 TTTAAATATTAATAA
33844515 TTTAA
1 TTTAA
33844520 TATAATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 6 0.17
13 6 0.17
15 24 0.67
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:33845126 original size:23 final size:23
Alignment explanation
Indices: 33845076--33845128 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
33845066 AGTTCCAGTT
* * *
33845076 AGAGAGAGAATGAGAGAGGGAGA
1 AGAGAGAGAAAGAGAAAGGGAAA
33845099 AGAGAGAGAAAGA-AAAGGGAAA
1 AGAGAGAGAAAGAGAAAGGGAAA
33845121 ATGAGAGA
1 A-GAGAGA
33845129 AAAAAAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.04
Consensus pattern (23 bp):
AGAGAGAGAAAGAGAAAGGGAAA
Done.