Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 104 of 295
Found at i:30938994 original size:15 final size:15
Alignment explanation
Indices: 30938976--30939026 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
30938966 TTATAGTGTA
30938976 TTTAATTGTATATAT
1 TTTAATTGTATATAT
*
30938991 TTTAAATT-TTTATA-
1 TTT-AATTGTATATAT
*
30939005 TTTAATTGTGTAATAT
1 TTTAATTGTAT-ATAT
30939021 TTTAAT
1 TTTAAT
30939027 AGTGTGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 4 0.13
14 5 0.17
15 11 0.37
16 10 0.33
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTAATTGTATATAT
Found at i:30941820 original size:22 final size:23
Alignment explanation
Indices: 30941782--30941829 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
30941772 TTCAAGTATT
30941782 TTAAAAGACATGATACAAAAATA
1 TTAAAAGACATGATACAAAAATA
30941805 TTAAAA-ACATTG-TACAAAAATA
1 TTAAAAGACA-TGATACAAAAATA
30941827 TTA
1 TTA
30941830 CATGACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (23 bp):
TTAAAAGACATGATACAAAAATA
Found at i:30947044 original size:30 final size:30
Alignment explanation
Indices: 30947005--30947061 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
30946995 ACCTAGCTCC
30947005 CTCTCTCCTTTTCCTTT-TTCCTTCCCCTTT
1 CTCTCTCCTTTT-CTTTCTTCCTTCCCCTTT
* *
30947035 CTCTTTCCTTTTTTTTCTTCCTTCCCC
1 CTCTCTCCTTTTCTTTCTTCCTTCCCC
30947062 CACCCTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (30 bp):
CTCTCTCCTTTTCTTTCTTCCTTCCCCTTT
Found at i:30948946 original size:5 final size:6
Alignment explanation
Indices: 30948897--30948956 Score: 79
Period size: 6 Copynumber: 9.8 Consensus size: 6
30948887 TTGAGTCCAA
30948897 TTATTT TTATGTT TATATTT TTA--T TTATTT TTATCTT TTATTT TTATTT
1 TTATTT TTAT-TT T-TATTT TTATTT TTATTT TTAT-TT TTATTT TTATTT
30948946 TTATTT TTATT
1 TTATTT TTATT
30948957 CTTCTTGTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.08
6 30 0.61
7 12 0.24
8 3 0.06
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:30948967 original size:18 final size:19
Alignment explanation
Indices: 30948921--30948967 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
30948911 ATATTTTTAT
* *
30948921 TTATTTTTATCTTTTATTT
1 TTATTGTTATCTTTTATTC
*
30948940 TTATTTTTAT-TTTTATTC
1 TTATTGTTATCTTTTATTC
*
30948958 TTCTTGTTAT
1 TTATTGTTAT
30948968 GTCTATTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (19 bp):
TTATTGTTATCTTTTATTC
Found at i:30954612 original size:24 final size:24
Alignment explanation
Indices: 30954579--30954630 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
30954569 TTTCTAGAAG
* *
30954579 ATTTAGTATTTATGAATATAATAT
1 ATTTAATATTTATGAACATAATAT
*
30954603 ATTTAATATTTATTAACATAATAT
1 ATTTAATATTTATGAACATAATAT
30954627 ATTT
1 ATTT
30954631 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTAATATTTATGAACATAATAT
Found at i:30958692 original size:15 final size:17
Alignment explanation
Indices: 30958672--30958713 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
30958662 AATTTTAATC
30958672 TTTCTT-TT-ATTTTTT
1 TTTCTTGTTGATTTTTT
*
30958687 TTTCTTGTTGCTTTTTT
1 TTTCTTGTTGATTTTTT
*
30958704 TTTCTGGTTG
1 TTTCTTGTTG
30958714 TAATTGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 2 0.09
17 15 0.65
ACGTcount: A:0.02, C:0.10, G:0.12, T:0.76
Consensus pattern (17 bp):
TTTCTTGTTGATTTTTT
Found at i:30958701 original size:17 final size:17
Alignment explanation
Indices: 30958681--30958713 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30958671 CTTTCTTTTA
*
30958681 TTTTTTTTTCTTGTTGC
1 TTTTTTTTTCTGGTTGC
30958698 TTTTTTTTTCTGGTTG
1 TTTTTTTTTCTGGTTG
30958714 TAATTGCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.15, T:0.76
Consensus pattern (17 bp):
TTTTTTTTTCTGGTTGC
Found at i:30965078 original size:22 final size:22
Alignment explanation
Indices: 30965014--30965080 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
30965004 TTAATTATAA
30965014 AATATTTTAATAT--TGTCGTTT
1 AATATTTTAATATCATGTC-TTT
* *
30965035 AATATTTTTATA-CAATGCCTTT
1 AATATTTTAATATC-ATGTCTTT
*
30965057 AATAATTTAATATCATGTCTTT
1 AATATTTTAATATCATGTCTTT
30965079 AA
1 AA
30965081 AAATACTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (22 bp):
AATATTTTAATATCATGTCTTT
Found at i:30969701 original size:26 final size:27
Alignment explanation
Indices: 30969663--30969716 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
30969653 ATTGTTTAGA
30969663 TATATTATTTTAAATTATTTCATACAT
1 TATATTATTTTAAATTATTTCATACAT
* *
30969690 TATA-TATTTTAAATTGTTTTATACAT
1 TATATTATTTTAAATTATTTCATACAT
30969716 T
1 T
30969717 GTTTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (27 bp):
TATATTATTTTAAATTATTTCATACAT
Found at i:30969935 original size:17 final size:16
Alignment explanation
Indices: 30969913--30969976 Score: 76
Period size: 17 Copynumber: 3.9 Consensus size: 16
30969903 AAACTCATTT
30969913 ATATATTATTATTTTAC
1 ATATATTATTATTTT-C
30969930 ATATATTACTTATTTTC
1 ATATATTA-TTATTTTC
* *
30969947 AT-TTTTATTTTTTTC
1 ATATATTATTATTTTC
30969962 ATATATTATCTATTT
1 ATATATTAT-TATTT
30969977 CAAACTTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.22
16 9 0.22
17 15 0.38
18 7 0.17
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATATTATTATTTTC
Found at i:30971260 original size:20 final size:19
Alignment explanation
Indices: 30971209--30971355 Score: 75
Period size: 20 Copynumber: 7.2 Consensus size: 19
30971199 ATTATAGAAA
30971209 TTTTAAAATTTTTT-AACTT
1 TTTTAAAATTTTTTGAA-TT
* *
30971228 TCTCTATACATTTTTTAGAATT
1 T-TTTA-AAATTTTTT-GAATT
*
30971250 TTTTAAAATTTTTAT-AAAT
1 TTTTAAAATTTTT-TGAATT
*
30971269 TTTAAAAATATAAATTTTGGAA-T
1 TTTTAAAAT-T---TTTT-GAATT
**
30971292 TTTTATAAATACTTTGAATT
1 TTTTA-AAATTTTTTGAATT
* *
30971312 TTTTAAAATTATTTTCAACT
1 TTTTAAAATT-TTTTGAATT
*
30971332 TTTGAAAATTATTTTGAATT
1 TTTTAAAATT-TTTTGAATT
30971352 TTTT
1 TTTT
30971356 TTTGTAATTT
Statistics
Matches: 97, Mismatches: 17, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
19 19 0.20
20 46 0.47
21 12 0.12
22 4 0.04
23 10 0.10
24 6 0.06
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTAAAATTTTTTGAATT
Found at i:30971263 original size:19 final size:19
Alignment explanation
Indices: 30971239--30971277 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30971229 CTCTATACAT
* *
30971239 TTTTTAGAATTTTTTAAAA
1 TTTTTAGAAATTTTAAAAA
*
30971258 TTTTTATAAATTTTAAAAA
1 TTTTTAGAAATTTTAAAAA
30971277 T
1 T
30971278 ATAAATTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTTAGAAATTTTAAAAA
Found at i:30974344 original size:13 final size:13
Alignment explanation
Indices: 30974305--30974344 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
30974295 GCTCGACAGG
* *
30974305 GACACGCCCATAT
1 GACATGCCCATGT
*
30974318 GACATGCCCGTGT
1 GACATGCCCATGT
30974331 GACATGCCCATGT
1 GACATGCCCATGT
30974344 G
1 G
30974345 CGATTACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (13 bp):
GACATGCCCATGT
Found at i:30976444 original size:22 final size:23
Alignment explanation
Indices: 30976390--30976441 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
30976380 TATAAAACCT
30976390 AATAAAAA-TAAG-CTTAAAGAAA
1 AATAAAAAGT-AGTCTTAAAGAAA
* *
30976412 AATAAAAAGTAGTCTTAAAGTAG
1 AATAAAAAGTAGTCTTAAAGAAA
30976435 AATAAAA
1 AATAAAA
30976442 GTAAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.63, C:0.04, G:0.12, T:0.21
Consensus pattern (23 bp):
AATAAAAAGTAGTCTTAAAGAAA
Found at i:30976978 original size:18 final size:18
Alignment explanation
Indices: 30976955--30976996 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
30976945 GTGGCGAATG
30976955 GCGAGGGCAATAAAGTAA
1 GCGAGGGCAATAAAGTAA
30976973 GCGAGGGCAATAAAGTAA
1 GCGAGGGCAATAAAGTAA
30976991 GCGAGG
1 GCGAGG
30976997 TCGAAGGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.38, T:0.10
Consensus pattern (18 bp):
GCGAGGGCAATAAAGTAA
Found at i:30978554 original size:55 final size:54
Alignment explanation
Indices: 30978490--30978620 Score: 147
Period size: 55 Copynumber: 2.4 Consensus size: 54
30978480 CCCGTGTTTT
*
30978490 TTTGGCAGGTTCGTCCACGGTTGCTT-GGCACAGGCGTGTCGCACGCCAGTGTCAA
1 TTTGGCAGGTTCGCCCACGGTT--TTAGGCACAGGCGTGTCGCACGCCAGTGTCAA
* * * * * ***
30978545 TTTGACAGGTTTGGCCACGGTTTTAAGGCACGGGCGTGTCGCACGCCTGTGTTGT
1 TTTGGCAGGTTCGCCCACGGTTTT-AGGCACAGGCGTGTCGCACGCCAGTGTCAA
30978600 TTTGGCAGGTTCGCCCACGGT
1 TTTGGCAGGTTCGCCCACGGT
30978621 CATGTCGCAT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
53 2 0.03
55 61 0.97
ACGTcount: A:0.13, C:0.25, G:0.34, T:0.28
Consensus pattern (54 bp):
TTTGGCAGGTTCGCCCACGGTTTTAGGCACAGGCGTGTCGCACGCCAGTGTCAA
Found at i:30987993 original size:18 final size:18
Alignment explanation
Indices: 30987970--30988004 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30987960 AATTCAAGAA
30987970 AAGCATCAAAATAGTTTC
1 AAGCATCAAAATAGTTTC
*
30987988 AAGCATGAAAATAGTTT
1 AAGCATCAAAATAGTTT
30988005 GGCACATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:31001449 original size:86 final size:86
Alignment explanation
Indices: 31001300--31001469 Score: 313
Period size: 86 Copynumber: 2.0 Consensus size: 86
31001290 AGTAAAATCG
31001300 TATGAAATAAAATCAATCTTAACATAAATATACAAATCACCAATTTGAACATATCAACATGTAGT
1 TATGAAATAAAATCAATCTTAACATAAATATACAAATCACCAATTTGAACATATCAACATGTAGT
31001365 TATTAAACTAACAAACCTTCA
66 TATTAAACTAACAAACCTTCA
* * *
31001386 TATGAAATAAACTCAATCTTAACATAAATATACAAATCATCAATTTGAACATATCAACTTGTAGT
1 TATGAAATAAAATCAATCTTAACATAAATATACAAATCACCAATTTGAACATATCAACATGTAGT
31001451 TATTAAACTAACAAACCTT
66 TATTAAACTAACAAACCTT
31001470 TCACATTTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.31
Consensus pattern (86 bp):
TATGAAATAAAATCAATCTTAACATAAATATACAAATCACCAATTTGAACATATCAACATGTAGT
TATTAAACTAACAAACCTTCA
Found at i:31005909 original size:43 final size:43
Alignment explanation
Indices: 31005862--31005946 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
31005852 TAAAGCTTAG
31005862 TAAGCTCGTATAGTTAATAAGTAAAACTTACCATTCATTCACT
1 TAAGCTCGTATAGTTAATAAGTAAAACTTACCATTCATTCACT
31005905 TAAGCTCGTATAGTTAATAAGTAAAACTTACCATTCATTCAC
1 TAAGCTCGTATAGTTAATAAGTAAAACTTACCATTCATTCAC
31005947 CATTCAAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (43 bp):
TAAGCTCGTATAGTTAATAAGTAAAACTTACCATTCATTCACT
Found at i:31007376 original size:57 final size:57
Alignment explanation
Indices: 31007288--31007399 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
31007278 TTTTATGTCT
*
31007288 ATAAATGTCCACCCACTATAAAAATGGTCTAATTACCACATAAGGACTTCCACTTCC
1 ATAAATGTCCACCCACTATAAAAATGGTCTAATTACCACATAAGGACCTCCACTTCC
31007345 ATAAATGTCCACCCACTATAAAAATGGTCTAATTACCACATAAGGACCTCCACTT
1 ATAAATGTCCACCCACTATAAAAATGGTCTAATTACCACATAAGGACCTCCACTT
31007400 TAAAGTTCTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.26
Consensus pattern (57 bp):
ATAAATGTCCACCCACTATAAAAATGGTCTAATTACCACATAAGGACCTCCACTTCC
Found at i:31011796 original size:36 final size:36
Alignment explanation
Indices: 31011743--31011844 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
31011733 CGACACCACC
*
31011743 GATATCAAAGTGTTCCACCACTGATATGCATTAACT
1 GATATCAAAGTGTTCCACCACTGATATGCAATAACT
* * *
31011779 GATATCAAAATGATCCACCACTGATATGCAATAATT
1 GATATCAAAGTGTTCCACCACTGATATGCAATAACT
31011815 GATATCAAAGTGTTCCACCACTGATATGCA
1 GATATCAAAGTGTTCCACCACTGATATGCA
31011845 GTATCTCTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (36 bp):
GATATCAAAGTGTTCCACCACTGATATGCAATAACT
Found at i:31035827 original size:20 final size:19
Alignment explanation
Indices: 31035794--31035892 Score: 87
Period size: 20 Copynumber: 5.2 Consensus size: 19
31035784 ATACATGGGA
31035794 TATGATAT--ACATGATTGG
1 TATGATATGCACATGATT-G
*
31035812 TATGATATGCACATGACATG
1 TATGATATGCACATGA-TTG
* *
31035832 TATAAAATGCACATGATATG
1 TATGATATGCACATGAT-TG
31035852 TATGATATGCACATGATATG
1 TATGATATGCACATGAT-TG
* * *
31035872 TATAAAATGCACGTGA-TG
1 TATGATATGCACATGATTG
31035890 TAT
1 TAT
31035893 TCATAAATGC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
18 13 0.19
20 54 0.79
21 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (19 bp):
TATGATATGCACATGATTG
Found at i:31035846 original size:40 final size:40
Alignment explanation
Indices: 31035802--31035888 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
31035792 GATATGATAT
31035802 ACATGAT-TGGTATGATATGCACATGACATGTATAAAATGC
1 ACATGATAT-GTATGATATGCACATGACATGTATAAAATGC
*
31035842 ACATGATATGTATGATATGCACATGATATGTATAAAATGC
1 ACATGATATGTATGATATGCACATGACATGTATAAAATGC
*
31035882 ACGTGAT
1 ACATGAT
31035889 GTATTCATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 43 0.98
41 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (40 bp):
ACATGATATGTATGATATGCACATGACATGTATAAAATGC
Found at i:31035998 original size:25 final size:25
Alignment explanation
Indices: 31035937--31036009 Score: 119
Period size: 26 Copynumber: 2.9 Consensus size: 25
31035927 GGAGGAAGCG
*
31035937 CAAAAGGGCTTATGCCCTAGTTTAC
1 CAAAAGGGCTTATGCCCCAGTTTAC
31035962 CGAAAAGGGCTTATGCCCCAGTTTAC
1 C-AAAAGGGCTTATGCCCCAGTTTAC
*
31035988 CAAAAGGGCTTTTGCCCCAGTT
1 CAAAAGGGCTTATGCCCCAGTT
31036010 ATTAAAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 21 0.47
26 24 0.53
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (25 bp):
CAAAAGGGCTTATGCCCCAGTTTAC
Found at i:31037195 original size:11 final size:11
Alignment explanation
Indices: 31037179--31037205 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31037169 AACAAAGATA
31037179 TTTTTTTCAAT
1 TTTTTTTCAAT
31037190 TTTTTTTCAAT
1 TTTTTTTCAAT
31037201 TTTTT
1 TTTTT
31037206 GTGATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:31043909 original size:20 final size:20
Alignment explanation
Indices: 31043876--31043965 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
31043866 ATACATGGGA
31043876 TATGATAT--ACATGAT-TGG
1 TATGATATGCACATGATAT-G
*
31043894 TATGATATGCACATGACATG
1 TATGATATGCACATGATATG
* *
31043914 TATAAAATGCACATGATATG
1 TATGATATGCACATGATATG
31043934 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
31043954 TATGAAATGCAC
1 TATGATATGCAC
31043966 GTAATGTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.13
20 53 0.85
21 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:31043928 original size:40 final size:40
Alignment explanation
Indices: 31043884--31043965 Score: 130
Period size: 40 Copynumber: 2.0 Consensus size: 40
31043874 GATATGATAT
31043884 ACATGAT-TGGTATGATATGCACATGACATGTATAAAATGC
1 ACATGATAT-GTATGATATGCACATGACATGTATAAAATGC
* *
31043924 ACATGATATGTATGATATGCACATGATATGTATGAAATGC
1 ACATGATATGTATGATATGCACATGACATGTATAAAATGC
31043964 AC
1 AC
31043966 GTAATGTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (40 bp):
ACATGATATGTATGATATGCACATGACATGTATAAAATGC
Found at i:31044080 original size:25 final size:25
Alignment explanation
Indices: 31044019--31044091 Score: 119
Period size: 26 Copynumber: 2.9 Consensus size: 25
31044009 TGAGGAAGTG
31044019 CAAAAGGGCTTATGCCCCAGTTTAC
1 CAAAAGGGCTTATGCCCCAGTTTAC
*
31044044 CGAAAAGGGCTTATGCTCCAGTTTAC
1 C-AAAAGGGCTTATGCCCCAGTTTAC
*
31044070 CAAAAGGGCTTTTGCCCCAGTT
1 CAAAAGGGCTTATGCCCCAGTT
31044092 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 20 0.45
26 24 0.55
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (25 bp):
CAAAAGGGCTTATGCCCCAGTTTAC
Found at i:31047524 original size:14 final size:14
Alignment explanation
Indices: 31047502--31047535 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
31047492 CTCAAGTATA
*
31047502 ACCAATACAAAATG
1 ACCATTACAAAATG
31047516 ACCATTACAAAATG
1 ACCATTACAAAATG
31047530 ACCATT
1 ACCATT
31047536 TTCCCAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.21
Consensus pattern (14 bp):
ACCATTACAAAATG
Found at i:31054035 original size:23 final size:23
Alignment explanation
Indices: 31054000--31054066 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
31053990 TGAAGGTAGG
* *
31054000 ATCTAAATCTGTATCTGTTATAC
1 ATCTGAATATGTATCTGTTATAC
* * *
31054023 ATCTGAATTTGTATCT-ATATGC
1 ATCTGAATATGTATCTGTTATAC
*
31054045 ATCTGAAATATGTATATGTTAT
1 ATCTG-AATATGTATCTGTTAT
31054067 GCATTTGTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
22 9 0.26
23 23 0.66
24 3 0.09
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (23 bp):
ATCTGAATATGTATCTGTTATAC
Found at i:31056760 original size:28 final size:28
Alignment explanation
Indices: 31056710--31056874 Score: 118
Period size: 28 Copynumber: 5.6 Consensus size: 28
31056700 TTACTTACAA
* * *
31056710 TTTAGGGTTTAATGTCTAG-TATTTTAAG
1 TTTAGGGTTTAAGGT-TTGTTATTTTAGG
* *
31056738 TTTATGGTTTAAGGTTTGTTATTTTGGG
1 TTTAGGGTTTAAGGTTTGTTATTTTAGG
* * *
31056766 TTTAGGGTTTAGGGTATATGATATTAGGCTTTAAAG
1 TTTAGGGTTTAAGGT-T-TG---TTA---TTTTAGG
*
31056802 TTTAGGGTTTAATGTTTAG-TATTTTAGG
1 TTTAGGGTTTAAGGTTT-GTTATTTTAGG
* *
31056830 TTTAGGGGTTAAGATTTGTTATTTTAGG
1 TTTAGGGTTTAAGGTTTGTTATTTTAGG
*
31056858 TTTGGGGTTTAAGGTTT
1 TTTAGGGTTTAAGGTTT
31056875 ATAATTTATG
Statistics
Matches: 106, Mismatches: 20, Indels: 22
0.72 0.14 0.15
Matches are distributed among these distances:
27 3 0.03
28 75 0.71
29 1 0.01
30 2 0.02
31 2 0.02
33 3 0.03
34 1 0.01
35 2 0.02
36 17 0.16
ACGTcount: A:0.21, C:0.01, G:0.27, T:0.50
Consensus pattern (28 bp):
TTTAGGGTTTAAGGTTTGTTATTTTAGG
Found at i:31056881 original size:28 final size:27
Alignment explanation
Indices: 31056801--31056888 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 27
31056791 AGGCTTTAAA
* *
31056801 GTTTAGGGTTTAATGTTTAGTATTTTAG
1 GTTTGGGGTTTAAGGTTTA-TATTTTAG
* *
31056829 GTTTAGGGG-TTAAGATTTGTTATTTTAG
1 GTTT-GGGGTTTAAGGTTT-ATATTTTAG
*
31056857 GTTTGGGGTTTAAGGTTTATAATTTATG
1 GTTTGGGGTTTAAGGTTTATATTTTA-G
31056885 GTTT
1 GTTT
31056889 AGTGTTTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
27 10 0.20
28 36 0.73
29 3 0.06
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.52
Consensus pattern (27 bp):
GTTTGGGGTTTAAGGTTTATATTTTAG
Found at i:31057476 original size:40 final size:40
Alignment explanation
Indices: 31057432--31057517 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
31057422 GCACTAGCAC
*
31057432 AAAAACGCCGCAATAGATCGAGAATTAGCAGCGCTTTTTG
1 AAAAACGCCGCAATAGATCGAGAATTAGCAGCACTTTTTG
* * *
31057472 AAAAATGCCGCTATAGATCGAGAATTAGCGGCACTTTTTG
1 AAAAACGCCGCAATAGATCGAGAATTAGCAGCACTTTTTG
31057512 AAAAAC
1 AAAAAC
31057518 TCCACAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCAATAGATCGAGAATTAGCAGCACTTTTTG
Found at i:31059557 original size:22 final size:23
Alignment explanation
Indices: 31059511--31059557 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
31059501 GGAAAGACAG
* *
31059511 TTTTCTATACTTATGTAAGTTCT
1 TTTTCTATACTTAGGTAAGTGCT
31059534 TTTTCTATACTTAGGTAAG-GCT
1 TTTTCTATACTTAGGTAAGTGCT
31059556 TT
1 TT
31059558 GATCCTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (23 bp):
TTTTCTATACTTAGGTAAGTGCT
Found at i:31060484 original size:18 final size:17
Alignment explanation
Indices: 31060444--31060484 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
31060434 TATTTAAAGA
*
31060444 ATAAAAGATAACTTTGG
1 ATAAAACATAACTTTGG
31060461 ACTAAAACATAACTTTGG
1 A-TAAAACATAACTTTGG
31060479 TATAAA
1 -ATAAA
31060485 TGACTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (17 bp):
ATAAAACATAACTTTGG
Found at i:31060668 original size:9 final size:9
Alignment explanation
Indices: 31060629--31060731 Score: 79
Period size: 9 Copynumber: 11.4 Consensus size: 9
31060619 CTTTGGATCT
31060629 TAACTTA-A
1 TAACTTACA
*
31060637 TAACTTATA
1 TAACTTACA
*
31060646 TATATCATATCA
1 TA-A-CTTA-CA
31060658 TAACTTACA
1 TAACTTACA
*
31060667 TAACTCACA
1 TAACTTACA
31060676 TAACTTACA
1 TAACTTACA
31060685 TAACTTACA
1 TAACTTACA
31060694 TAA--TACA
1 TAACTTACA
* *
31060701 TAA-ATATA
1 TAACTTACA
* *
31060709 TACCATATCA
1 TAACTTA-CA
31060719 TAACTTACA
1 TAACTTACA
31060728 TAAC
1 TAAC
31060732 CTAATTATAC
Statistics
Matches: 78, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
7 7 0.09
8 12 0.15
9 42 0.54
10 10 0.13
11 4 0.05
12 3 0.04
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (9 bp):
TAACTTACA
Found at i:31060701 original size:34 final size:34
Alignment explanation
Indices: 31060663--31060730 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
31060653 TATCATAACT
* *
31060663 TACATAACTCACATAACTTA-CATAACTTACATAA
1 TACATAAAT-ACATAACATATCATAACTTACATAA
* *
31060697 TACATAAATATATACCATATCATAACTTACATAA
1 TACATAAATACATAACATATCATAACTTACATAA
31060731 CCTAATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (34 bp):
TACATAAATACATAACATATCATAACTTACATAA
Found at i:31068468 original size:26 final size:26
Alignment explanation
Indices: 31068439--31068488 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
31068429 GACCAGTTCC
*
31068439 TATAAACATTTCACACAACCATTTTG
1 TATAAACAATTCACACAACCATTTTG
* * *
31068465 TATAACCAATTCATATAACCATTT
1 TATAAACAATTCACACAACCATTT
31068489 GTCATCTGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (26 bp):
TATAAACAATTCACACAACCATTTTG
Found at i:31068471 original size:13 final size:13
Alignment explanation
Indices: 31068419--31068488 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
31068409 TTGTACGTAT
*
31068419 ATTTCCATATGACC
1 ATTT-CATATAACC
* * *
31068433 AGTTCCTATAAAC
1 ATTTCATATAACC
* *
31068446 ATTTCACACAACC
1 ATTTCATATAACC
**
31068459 ATTTTGTATAACC
1 ATTTCATATAACC
*
31068472 AATTCATATAACC
1 ATTTCATATAACC
31068485 ATTT
1 ATTT
31068489 GTCATCTGGT
Statistics
Matches: 39, Mismatches: 17, Indels: 1
0.68 0.30 0.02
Matches are distributed among these distances:
13 36 0.92
14 3 0.08
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:31068636 original size:46 final size:46
Alignment explanation
Indices: 31068576--31068798 Score: 313
Period size: 46 Copynumber: 4.8 Consensus size: 46
31068566 TTCAACATGA
* * * * * *
31068576 TGCCATAGTATCTTTCAACTATGGTCTTACTCGTTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACAC-ATTTCATATCAGGT
* * ** * *
31068622 TGCAATGGTATCTTTTAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
31068668 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
31068714 TACCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
31068760 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
31068799 TTTAGAGAGC
Statistics
Matches: 161, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 157 0.98
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:31069208 original size:24 final size:23
Alignment explanation
Indices: 31069176--31069224 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31069166 ATCAGGTAGT
*
31069176 TCACAAAGAACCATATCGTGAAGC
1 TCACAAAGAACC-TATCGGGAAGC
* *
31069200 TCACGAAGAGCCTATCGGGAAGC
1 TCACAAAGAACCTATCGGGAAGC
31069223 TC
1 TC
31069225 TGGATAGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (23 bp):
TCACAAAGAACCTATCGGGAAGC
Found at i:31069221 original size:23 final size:23
Alignment explanation
Indices: 31069189--31069304 Score: 83
Period size: 23 Copynumber: 5.0 Consensus size: 23
31069179 CAAAGAACCA
*
31069189 TATCGTGAAGCTCACGAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* * *
31069212 TATCGGGAAGCTC-TGGATAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* * *
31069234 ATATATCGGGAAGTTCAAG-CGAGCAC
1 ---TATCGGGAAGCTCACGAAGAGC-C
* *
31069260 TATCGGGAGGCTCACAAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* *
31069283 TATCAGGAGGCTCACGAAGAGC
1 TATCGGGAAGCTCACGAAGAGC
31069305 TGTATTTCGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
22 6 0.08
23 45 0.62
24 4 0.06
25 15 0.21
26 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.17
Consensus pattern (23 bp):
TATCGGGAAGCTCACGAAGAGCC
Found at i:31071433 original size:18 final size:18
Alignment explanation
Indices: 31071385--31071433 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
31071375 ATAATATAAT
31071385 TATTTAATTAATAAATATC
1 TATTTAA-TAATAAATATC
*
31071404 TTTTATAAAATAATAAATATC
1 TATT-T--AATAATAAATATC
31071425 TATTTAATA
1 TATTTAATA
31071434 TCTAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 2 0.08
21 14 0.56
22 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTAATAATAAATATC
Found at i:31072951 original size:13 final size:14
Alignment explanation
Indices: 31072935--31072963 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31072925 TTTTAAATAT
31072935 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
31072948 TTATAATGGTTTAA
1 TTATAATGGTTTAA
31072962 TT
1 TT
31072964 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:31073429 original size:21 final size:21
Alignment explanation
Indices: 31073400--31073449 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
31073390 TTACAACATA
* **
31073400 AAGCGGAGGCAGCATTGAGGG
1 AAGCAGAGGCAGCAGCGAGGG
31073421 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAGCGAGGG
31073442 AAGCAGAG
1 AAGCAGAG
31073450 CAGAGCAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGGG
Found at i:31073834 original size:43 final size:43
Alignment explanation
Indices: 31073787--31074038 Score: 223
Period size: 43 Copynumber: 6.0 Consensus size: 43
31073777 CAACGATACT
*
31073787 TTTAGCAGCATTTGTGATAAAAGCGCCGCTAAAGGT-ACTGTTC
1 TTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGGTCA-TGTTC
* * * * *
31073830 TTTAGTGGCATTTGT-AAAAAAACGCCGCTAAAAGTCATGCTC
1 TTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * ** *
31073872 TATAGTGGTGTTTGTTTG-TAAAA-CGCTGCTAAAGGTCATGTTC
1 TTTAGCGGCATTTG--TGATAAAAGCGCCGCTAAAGGTCATGTTC
* * * * *
31073915 TTTAGCGACGTTTATGATAAAAGCGTCGCTAAAGGACATGTTC
1 TTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* **
31073958 TATAGCGGCATTTGT-A-AAAA-AACCGCTAAAGGTCATGTTC
1 TTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * *
31073998 TTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAAGTC-TGTT
1 TTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGGTCATGTT
31074039 TTGCTACATC
Statistics
Matches: 165, Mismatches: 35, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
40 28 0.17
41 7 0.04
42 46 0.28
43 79 0.48
44 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:31074279 original size:21 final size:20
Alignment explanation
Indices: 31074228--31074292 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
31074218 ATATAATGTA
* *
31074228 AAAATATAATCCAATAATTAT
1 AAAATATAATCAAATAA-TAC
* *
31074249 AATATCTAATCAAATTAATAC
1 AAAATATAATCAAA-TAATAC
*
31074270 AAAATATAATAAAAATAAT-C
1 AAAATATAAT-CAAATAATAC
31074290 AAA
1 AAA
31074293 TAAAAATCGA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 4 0.11
21 25 0.71
22 6 0.17
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATATAATCAAATAATAC
Found at i:31074388 original size:56 final size:56
Alignment explanation
Indices: 31074327--31074443 Score: 234
Period size: 56 Copynumber: 2.1 Consensus size: 56
31074317 AACTTATCCA
31074327 TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
1 TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
31074383 TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
1 TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
31074439 TAACA
1 TAACA
31074444 ATGTGAAGGC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (56 bp):
TAACATGTCAATTGTGAACCAAAACATAAACAAAAACTCAAAACCTGAACTTTAAC
Found at i:31076615 original size:15 final size:17
Alignment explanation
Indices: 31076584--31076615 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31076574 ATAATATTAT
31076584 ATAATATCATGTAATAG
1 ATAATATCATGTAATAG
31076601 ATAATAT-AT-TAATAG
1 ATAATATCATGTAATAG
31076616 TTTTGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (17 bp):
ATAATATCATGTAATAG
Found at i:31081767 original size:14 final size:15
Alignment explanation
Indices: 31081736--31081769 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
31081726 TTTTACTTAT
*
31081736 TTATTTCTTTATTTG
1 TTATTTCTTTAATTG
31081751 TTATTTC-TTAATTG
1 TTATTTCTTTAATTG
31081765 TTATT
1 TTATT
31081770 CTATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATTTCTTTAATTG
Found at i:31085858 original size:115 final size:115
Alignment explanation
Indices: 31085656--31085883 Score: 438
Period size: 115 Copynumber: 2.0 Consensus size: 115
31085646 CAGATCTTAT
31085656 TACTATTTGAATCATATGATAAATACTTGTTCTTATTCTCAATTATGAGTTTTAATCATTGCTTT
1 TACTATTTGAATCATATGATAAATACTTGTTCTTATTCTCAATTATGAGTTTTAATCATTGCTTT
*
31085721 AATATTCTAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAGCA
66 AATATTCCAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAGCA
*
31085771 TACTATTTGAATCATATGATAAATACTTGTTCTTATTTTCAATTATGAGTTTTAATCATTGCTTT
1 TACTATTTGAATCATATGATAAATACTTGTTCTTATTCTCAATTATGAGTTTTAATCATTGCTTT
31085836 AATATTCCAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAG
66 AATATTCCAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAG
31085884 TAAAAGTCCT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (115 bp):
TACTATTTGAATCATATGATAAATACTTGTTCTTATTCTCAATTATGAGTTTTAATCATTGCTTT
AATATTCCAGGATATTAAATCAAGTTTTGATGTGCTTATTCAGTGGAGCA
Found at i:31086537 original size:14 final size:13
Alignment explanation
Indices: 31086518--31086556 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
31086508 ATAGTAGTGC
31086518 ATTATATATTAATT
1 ATTATATATT-ATT
31086532 ATTATATATTATT
1 ATTATATATTATT
31086545 ATT-TATTATTAT
1 ATTATA-TATTAT
31086557 ACTAGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 12 0.50
14 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATATATTATT
Found at i:31087177 original size:240 final size:239
Alignment explanation
Indices: 31086674--31087177 Score: 581
Period size: 240 Copynumber: 2.1 Consensus size: 239
31086664 AATTATTAAT
** * * *
31086674 TATTATATATTATTGTTTATTATTATACTATTTGAAATATGCTCTACGCCCCTATATTTTTCGTA
1 TATTATATATTATTGAATATTATTATACTAGTTGAAATATGCTCTAAGCCCCTATACTTTTCGTA
* *
31086739 CATTTAAAAGTTAGCCCTCCTACTATATTATATAATGTTATATCATATCATATATTAATAATTTC
66 CATTTAAAAGTTAGCCCTCCTACTATATTATATAATGCTATATCATATCATATATTAATAATTTA
* * * * * *
31086804 TATATATGCATAAATGATTAATCATTATAATATCATGTAATGTTGTATCTTTTATTATAATCTAT
131 TATATATGCATAAATGATGAAACACTATAATATAATGTAATCTTATATCTTTTATTATAATCTAT
* * *
31086869 ATCATAATTATAGTTATATATAATAGTAGTACATTATATATTACT
196 ATCATAATAATAGTTATATATAATAGTAG-ACATTATATAGTACA
** * *
31086914 TATTATATATTATTGTTTATTATTATACTAGTTGAAATATGCTCTAAGTCTCTATACTTTTCGTA
1 TATTATATATTATTGAATATTATTATACTAGTTGAAATATGCTCTAAGCCCCTATACTTTTCGTA
* *
31086979 TATTTAAAAGTTAGCCCTCTTACTATATTATATAATGCTATATCATATCATATATTATTTTAATA
66 CATTTAAAAGTTAGCCCTCCTACTATATTATATAATGCTATATCATATC--ATA-TA--TTAATA
* ** * * *
31087044 GTTTATATATATGCAT-TTTTATGAAACACTATAATATAATGTAATACTATATTTTTTTTATTAT
126 ATTTATATATATGCATAAATGATGAAACACTATAATATAATGTAAT-CT-TATATCTTTTATTAT
* * * * *
31087108 AATCTATATTATTATAATAGTTATATAT-GTATTA-ACATT-TTTAGTA-A
189 AATCTATATCATAATAATAGTTATATATAATAGTAGACATTATATAGTACA
31087155 TAGTTATATATTA-T-AATATTATT
1 TA-TTATATATTATTGAATATTATT
31087178 TTATTTATTA
Statistics
Matches: 225, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
240 113 0.50
241 3 0.01
242 18 0.08
243 7 0.03
244 22 0.10
245 25 0.11
246 37 0.16
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (239 bp):
TATTATATATTATTGAATATTATTATACTAGTTGAAATATGCTCTAAGCCCCTATACTTTTCGTA
CATTTAAAAGTTAGCCCTCCTACTATATTATATAATGCTATATCATATCATATATTAATAATTTA
TATATATGCATAAATGATGAAACACTATAATATAATGTAATCTTATATCTTTTATTATAATCTAT
ATCATAATAATAGTTATATATAATAGTAGACATTATATAGTACA
Found at i:31087180 original size:30 final size:29
Alignment explanation
Indices: 31087102--31087181 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
31087092 ATATTTTTTT
*
31087102 TATTATAATCTATATTATTATAATAGTTATA
1 TATTATAATAT-TATT-TTATAATAGTTATA
*
31087133 TATGTATTAACA-T-TTTTAGTAATAGTTATA
1 TAT-TA-TAATATTATTTTA-TAATAGTTATA
31087163 TATTATAATATTATTTTAT
1 TATTATAATATTATTTTAT
31087182 TTATTAGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
28 4 0.10
29 7 0.17
30 21 0.51
31 4 0.10
32 2 0.05
33 3 0.07
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.54
Consensus pattern (29 bp):
TATTATAATATTATTTTATAATAGTTATA
Found at i:31088283 original size:49 final size:49
Alignment explanation
Indices: 31088230--31088324 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
31088220 CTAAATAATT
* *
31088230 ACAAAGTGTAGAATCAAACTATTACAATACAAATAGACTAAAAATTGGA
1 ACAAAGTGTAGAATCAAACAATTACAACACAAATAGACTAAAAATTGGA
* * *
31088279 ACAAAGTGTAGGATTAAACAATTACAACACAAATAGACTAAGAATT
1 ACAAAGTGTAGAATCAAACAATTACAACACAAATAGACTAAAAATT
31088325 AAAATAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.22
Consensus pattern (49 bp):
ACAAAGTGTAGAATCAAACAATTACAACACAAATAGACTAAAAATTGGA
Found at i:31098276 original size:15 final size:15
Alignment explanation
Indices: 31098256--31098305 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
31098246 AGAGCCAGAG
31098256 AAGAAGGAGGAGCCA
1 AAGAAGGAGGAGCCA
* * *
31098271 AAGAAGGAAGAACCC
1 AAGAAGGAGGAGCCA
*
31098286 AAGAAAGAGGAGCCA
1 AAGAAGGAGGAGCCA
31098301 AAGAA
1 AAGAA
31098306 AGAAGAACCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.54, C:0.14, G:0.32, T:0.00
Consensus pattern (15 bp):
AAGAAGGAGGAGCCA
Found at i:31098290 original size:30 final size:30
Alignment explanation
Indices: 31098256--31098389 Score: 146
Period size: 30 Copynumber: 4.4 Consensus size: 30
31098246 AGAGCCAGAG
*
31098256 AAGAAGGAGGAGCCAAAGAAGGAAGAACCC
1 AAGAAGGAGGAGCCAAAGAAAGAAGAACCC
*
31098286 AAGAAAGAGGAGCCAAAGAAAGAAGAACCC
1 AAGAAGGAGGAGCCAAAGAAAGAAGAACCC
* *
31098316 AAGAAGGAAGAAGAG-CAGAAGAAAGAAGAGCCT
1 AAGAAGG-AG--GAGCCA-AAGAAAGAAGAACCC
* *
31098349 AAGAAGGAAGAACCAAA-AAAGGAAGAACCC
1 AAGAAGGAGGAGCCAAAGAAA-GAAGAACCC
*
31098379 AAGAAAGAGGA
1 AAGAAGGAGGA
31098390 AGAGAAGAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
29 3 0.03
30 54 0.62
31 4 0.05
32 3 0.03
33 23 0.26
ACGTcount: A:0.56, C:0.13, G:0.30, T:0.01
Consensus pattern (30 bp):
AAGAAGGAGGAGCCAAAGAAAGAAGAACCC
Found at i:31098319 original size:15 final size:15
Alignment explanation
Indices: 31098271--31098386 Score: 90
Period size: 15 Copynumber: 7.5 Consensus size: 15
31098261 GGAGGAGCCA
*
31098271 AAGAAGGAAGAACCC
1 AAGAAAGAAGAACCC
* * *
31098286 AAGAAAGAGGAGCCA
1 AAGAAAGAAGAACCC
31098301 AAGAAAGAAGAACCC
1 AAGAAAGAAGAACCC
* **
31098316 AAGAAGGAAGAAGAGCAG
1 AAG-A--AAGAAGAACCC
* *
31098334 AAGAAAGAAGAGCCT
1 AAGAAAGAAGAACCC
*
31098349 AAGAAGGAAGAA-CC
1 AAGAAAGAAGAACCC
*
31098363 AAAAAAGGAAGAACCC
1 AAGAAA-GAAGAACCC
31098379 AAGAAAGA
1 AAGAAAGA
31098387 GGAAGAGAAG
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
14 5 0.06
15 53 0.68
16 8 0.10
17 1 0.01
18 11 0.14
ACGTcount: A:0.58, C:0.14, G:0.28, T:0.01
Consensus pattern (15 bp):
AAGAAAGAAGAACCC
Found at i:31098365 original size:63 final size:63
Alignment explanation
Indices: 31098271--31098408 Score: 179
Period size: 63 Copynumber: 2.2 Consensus size: 63
31098261 GGAGGAGCCA
* * * * *
31098271 AAGAAGGAAGAACCCAAGAAAGAGGAGCCAAAGAAA-GAAGAACCCAAGAAGGAAGAAGAGCAG
1 AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAA-AAAGGAAGAACCCAAGAAAGAAGAAGAGAAG
* * * *
31098334 AAGAAAGAAGAGCCTAAGAAGGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAGGAAGAGAAG
1 AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAAGAAGAGAAG
31098397 AAGAAGGAAGAG
1 AAGAAGGAAGAG
31098409 GAGAAAAAGC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 3 0.05
63 61 0.95
ACGTcount: A:0.57, C:0.12, G:0.30, T:0.01
Consensus pattern (63 bp):
AAGAAGGAAGAGCCCAAGAAAGAAGAACCAAAAAAGGAAGAACCCAAGAAAGAAGAAGAGAAG
Found at i:31100390 original size:23 final size:25
Alignment explanation
Indices: 31100364--31100419 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
31100354 AAAAATTTAA
31100364 AAATATTAATTTT-AT-TAAATAAT
1 AAATATTAATTTTAATATAAATAAT
* *
31100387 AAATAATATTTTTAAATGATAAATAAT
1 AAATATTAATTTT-AAT-ATAAATAAT
31100414 AAATAT
1 AAATAT
31100420 GTTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
25 2 0.08
27 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATATTAATTTTAATATAAATAAT
Found at i:31102193 original size:27 final size:25
Alignment explanation
Indices: 31102156--31102207 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
31102146 CTTTACTTAC
31102156 ATTTAAAA-TTTAGTTCCTTATATTT
1 ATTTAAAATTTTA-TTCCTTATATTT
*
31102181 ATTTCAAAGATTTTATTCCTTTTATTT
1 ATTT-AAA-ATTTTATTCCTTATATTT
31102208 TTCAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 12 0.52
28 4 0.17
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.58
Consensus pattern (25 bp):
ATTTAAAATTTTATTCCTTATATTT
Found at i:31107268 original size:10 final size:10
Alignment explanation
Indices: 31107253--31107279 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31107243 GATATAAGTT
31107253 ATAACATATA
1 ATAACATATA
31107263 ATAACATATA
1 ATAACATATA
31107273 ATAACAT
1 ATAACAT
31107280 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAACATATA
Found at i:31112218 original size:21 final size:21
Alignment explanation
Indices: 31112192--31112247 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
31112182 CAAAAATTCT
31112192 AAATAAATAAAAA-ATCTTAAA
1 AAATAAATAAAAATAT-TTAAA
31112213 AAATAAATAAAAATATTTAAA
1 AAATAAATAAAAATATTTAAA
*
31112234 AAAT-TATAAAAATA
1 AAATAAATAAAAATA
31112248 ATTATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 9 0.27
21 22 0.67
22 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAATAAAAATATTTAAA
Found at i:31113831 original size:14 final size:15
Alignment explanation
Indices: 31113820--31113874 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
31113810 ACTTAAAATT
31113820 TTAAA-TTTAAAAGA
1 TTAAATTTTAAAAGA
31113834 TTAAATTTTAAAA-A
1 TTAAATTTTAAAAGA
* * * *
31113848 ATAACTGTAAAAAGA
1 TTAAATTTTAAAAGA
*
31113863 CTAAATTTTAAA
1 TTAAATTTTAAA
31113875 TATGGAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
14 15 0.48
15 16 0.52
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (15 bp):
TTAAATTTTAAAAGA
Found at i:31115509 original size:31 final size:31
Alignment explanation
Indices: 31115471--31115601 Score: 110
Period size: 31 Copynumber: 4.3 Consensus size: 31
31115461 TTAAGATATT
*
31115471 ATTTGGTACTTGAGTTTGACTTTAATGTTTA
1 ATTTGGTACTTGAATTTGACTTTAATGTTTA
* * *
31115502 ATTTGGTACCTTTAATTT---TTT-TTGTCCTA
1 ATTTGGTA-CTTGAATTTGACTTTAATGT-TTA
* *
31115531 ATTTGGTACTTGAATTTGGCTTTAGTGTTTA
1 ATTTGGTACTTGAATTTGACTTTAATGTTTA
* * * *
31115562 CTTTGGTACATAAATTTGAC-TTAACTGTTCA
1 ATTTGGTACTTGAATTTGACTTTAA-TGTTTA
31115593 ATTTGGTAC
1 ATTTGGTAC
31115602 CTAAGCTTCT
Statistics
Matches: 79, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
28 11 0.14
29 13 0.16
30 3 0.04
31 42 0.53
32 10 0.13
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (31 bp):
ATTTGGTACTTGAATTTGACTTTAATGTTTA
Found at i:31116332 original size:17 final size:20
Alignment explanation
Indices: 31116290--31116329 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31116280 TTATGTTTAA
31116290 ATGTTTTTTAAAAAACTATG
1 ATGTTTTTTAAAAAACTATG
*
31116310 ATGTTTTTTAAAAAATTATG
1 ATGTTTTTTAAAAAACTATG
31116330 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (20 bp):
ATGTTTTTTAAAAAACTATG
Found at i:31117003 original size:14 final size:14
Alignment explanation
Indices: 31116959--31117005 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
31116949 TTTTAAAATT
31116959 ATATATGAACTTTG
1 ATATATGAACTTTG
31116973 ATTTAATATGTAA-TTTG
1 A--T-ATATG-AACTTTG
31116990 ATATATGAACTTTG
1 ATATATGAACTTTG
31117004 AT
1 AT
31117006 TTGATACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.07
14 12 0.43
15 1 0.04
16 1 0.04
17 10 0.36
18 2 0.07
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (14 bp):
ATATATGAACTTTG
Found at i:31126852 original size:27 final size:27
Alignment explanation
Indices: 31126822--31126876 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
31126812 CTTTTCTTTT
*
31126822 TGTGTTCTGCCAATTTTTTACTCTCCA
1 TGTGTTCTGCCAATTTTCTACTCTCCA
31126849 TGTGTTCTGCCAATTTTCTACTCTCCA
1 TGTGTTCTGCCAATTTTCTACTCTCCA
31126876 T
1 T
31126877 CTTTTCTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.27, G:0.11, T:0.47
Consensus pattern (27 bp):
TGTGTTCTGCCAATTTTCTACTCTCCA
Found at i:31126883 original size:27 final size:27
Alignment explanation
Indices: 31126824--31126883 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
31126814 TTTCTTTTTG
* *
31126824 TGTTCTGCCAATTTTTTACTCTCCATG
1 TGTTCTGCCAATTTTCTACTCTCCATC
31126851 TGTTCTGCCAATTTTCTACTCTCCATC
1 TGTTCTGCCAATTTTCTACTCTCCATC
*
31126878 TTTTCT
1 TGTTCT
31126884 TTCTCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.13, C:0.28, G:0.08, T:0.50
Consensus pattern (27 bp):
TGTTCTGCCAATTTTCTACTCTCCATC
Found at i:31136465 original size:28 final size:28
Alignment explanation
Indices: 31136434--31136492 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
31136424 AAATCCATTA
* *
31136434 ATATTATGTAA-AATAAAGACATGCATAT
1 ATATTATATAAGAA-AAAGACATGCACAT
*
31136462 ATATTATATAAGAAAAAGTCATGCACAT
1 ATATTATATAAGAAAAAGACATGCACAT
31136490 ATA
1 ATA
31136493 AATAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (28 bp):
ATATTATATAAGAAAAAGACATGCACAT
Found at i:31138018 original size:22 final size:24
Alignment explanation
Indices: 31137985--31138039 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
31137975 CTTAACCTAA
* *
31137985 AATTA-TTAATTTTATTAA-TTTT
1 AATTATTTTATTTAATTAATTTTT
31138007 AA-TATTTTATTTAATTAATTTTT
1 AATTATTTTATTTAATTAATTTTT
31138030 AATTATTTTA
1 AATTATTTTA
31138040 ATGATCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 13 0.46
23 6 0.21
24 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
AATTATTTTATTTAATTAATTTTT
Found at i:31145105 original size:28 final size:28
Alignment explanation
Indices: 31145057--31145111 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
31145047 AACCGATCCA
*
31145057 AAAACCTCAATTAACATACAAATTAAAG
1 AAAACCTCAATTAACATACAAAATAAAG
* *
31145085 AAAACTTCAATTCA-ATAACAAAATAAA
1 AAAACCTCAATTAACAT-ACAAAATAAA
31145112 AAACGAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (28 bp):
AAAACCTCAATTAACATACAAAATAAAG
Found at i:31145737 original size:45 final size:45
Alignment explanation
Indices: 31145688--31145860 Score: 240
Period size: 45 Copynumber: 3.8 Consensus size: 45
31145678 CCATACAAGA
31145688 AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTCT
1 AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTCT
**
31145733 AACGAGTAAGACCATAGCT-AAAGAACGTTATGGCATCACAATTCT
1 AACGAGTAAGACCATAGCTGAAAG-ACGTTATGGCATCATGATTCT
** * * *
31145778 ATTGAGTAAGACCATAACTGAAAGACGTCATGGTATCATGATTCT
1 AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTCT
* * *
31145823 AATGAGTAAAACCATAGCTGAAAGATGTTATGGCATCA
1 AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCA
31145861 CAAATCAAAT
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
44 4 0.04
45 103 0.93
46 4 0.04
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (45 bp):
AACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTCT
Found at i:31145802 original size:90 final size:90
Alignment explanation
Indices: 31145691--31145863 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 90
31145681 TACAAGAAAC
* * *
31145691 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTCTAACGAGTAAGACCATAGCT-AAA
1 GAGTAAGACCATAACTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTGAAA
31145755 GAACGTTATGGCATCACAATTCTATT
66 G-ACGTTATGGCATCACAATTCTATT
* *
31145781 GAGTAAGACCATAACTGAAAGACGTCATGGTATCATGATTCTAATGAGTAAAACCATAGCTGAAA
1 GAGTAAGACCATAACTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTGAAA
*
31145846 GATGTTATGGCATCACAA
66 GACGTTATGGCATCACAA
31145864 ATCAAATGAA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
90 72 0.95
91 4 0.05
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (90 bp):
GAGTAAGACCATAACTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTGAAA
GACGTTATGGCATCACAATTCTATT
Found at i:31145872 original size:45 final size:45
Alignment explanation
Indices: 31145691--31145893 Score: 237
Period size: 45 Copynumber: 4.5 Consensus size: 45
31145681 TACAAGAAAC
** *
31145691 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTCTAAC
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTAAT
*
31145736 GAGTAAGACCATAGCT-AAAGAACGTTATGGCATCACAATTCTATT
1 GAGTAAGACCATAGCTGAAAG-ACGTTATGGCATCACAATTCTAAT
* * * **
31145781 GAGTAAGACCATAACTGAAAGACGTCATGGTATCATGATTCTAAT
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTAAT
* * * *
31145826 GAGTAAAACCATAGCTGAAAGATGTTATGGCATCACAAATCAAAT
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTAAT
** * *
31145871 GAACAAGACCGTAGTTGAAAGAC
1 GAGTAAGACCATAGCTGAAAGAC
31145894 ACTATAGCAA
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
44 4 0.03
45 123 0.94
46 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (45 bp):
GAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAATTCTAAT
Found at i:31145890 original size:90 final size:90
Alignment explanation
Indices: 31145695--31145893 Score: 265
Period size: 90 Copynumber: 2.2 Consensus size: 90
31145685 AGAAACGAGT
* *
31145695 AAGACCATAGCTGAAAGACGTTATGGCATCATGATTCTAACGAGTAAGACCATAGCTAAAGAACG
1 AAGACCATAGCTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTAAAGAACG
* * * **
31145760 TTATGGCATCACAATTCTATTGAGT
66 TTATGGCATCACAAATCAAATGAAC
* * * *
31145785 AAGACCATAACTGAAAGACGTCATGGTATCATGATTCTAATGAGTAAAACCATAGCTGAAAG-AT
1 AAGACCATAGCTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCT-AAAGAAC
31145849 GTTATGGCATCACAAATCAAATGAAC
65 GTTATGGCATCACAAATCAAATGAAC
* *
31145875 AAGACCGTAGTTGAAAGAC
1 AAGACCATAGCTGAAAGAC
31145894 ACTATAGCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 90 0.96
91 4 0.04
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (90 bp):
AAGACCATAGCTGAAAGACGTCATGGCATCATGATTCTAACGAGTAAAACCATAGCTAAAGAACG
TTATGGCATCACAAATCAAATGAAC
Found at i:31149165 original size:3 final size:3
Alignment explanation
Indices: 31149157--31149182 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31149147 AAACCAATTC
31149157 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
31149183 ACATTAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31153055 original size:22 final size:19
Alignment explanation
Indices: 31153013--31153066 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 19
31153003 TGTTTCAAAA
31153013 TTTTTTATTTTT-AAATAT
1 TTTTTTATTTTTAAAATAT
31153031 TTTTTTATTTTTAATTAATATT
1 TTTTTTATTTTTAA--AATA-T
31153053 TTTTTTATTTTTAA
1 TTTTTTATTTTTAA
31153067 CTCTTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.38
19 1 0.03
21 4 0.12
22 15 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTATTTTTAAAATAT
Found at i:31153168 original size:22 final size:20
Alignment explanation
Indices: 31153143--31153200 Score: 91
Period size: 19 Copynumber: 2.9 Consensus size: 20
31153133 CTTATAAAAA
31153143 TAATTAAAAATAAAAAATACAT
1 TAATTAAAAATAAAAAAT--AT
31153165 TAATTAAAAAT-AAAAATAT
1 TAATTAAAAATAAAAAATAT
31153184 TAATTAAAAATAAAAAA
1 TAATTAAAAATAAAAAA
31153201 ACTTGAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.37
20 5 0.14
21 6 0.17
22 11 0.31
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
TAATTAAAAATAAAAAATAT
Found at i:31153407 original size:141 final size:141
Alignment explanation
Indices: 31153262--31153692 Score: 523
Period size: 142 Copynumber: 3.0 Consensus size: 141
31153252 GGAACATCAT
* *
31153262 ACTCAA-GAATGTAATCGCAATTATCTAACCATCTAACGAAAGGAGCTAATATGTT-AAAAATAT
1 ACTCAACG-ATGTAATTGCAATTATCTAACCATCTAACGAAAGGA-CTAATATGTTAAAAAAAAT
* * * *
31153325 TAATTAATAATAATT-ATAAGCTTGAAGCAACATAAAATAAAAAATACGAATGTGAGT-AGTAGA
64 TAATTAA-AATATTTAAAAAGCTTGAAGCAACATAAAATAAAAAATACAAATATGAGTAAG-AGA
*
31153388 GGAATCAAACTCGAG
127 GAAATCAAACTCGAG
* * *
31153403 ACTCAACGATGTAATTACAATTATCTAGCCATCTAACGAAAGGACTAATATGTTAAAAGAACATT
1 ACTCAACGATGTAATTGCAATTATCTAACCATCTAACGAAAGGACTAATATGTTAAAA-AAAATT
* *
31153468 AATTAAAAT-TTTAAAAAACTTGAAGCAACATGAAATAAAAAAATACAAATATGAGTAAGAGAGA
65 AATTAAAATATTTAAAAAGCTTGAAGCAACATAAAAT-AAAAAATACAAATATGAGTAAGAGAGA
*
31153532 AATCGAACTCGAG
129 AATCAAACTCGAG
* * * * * *
31153545 ACTCAATGATGTAATTGGAACTATCTAATCATCTAACAAAAGAACTAATATGTTAAAAAAAATTA
1 ACTCAACGATGTAATTGCAATTATCTAACCATCTAACGAAAGGACTAATATGTTAAAAAAAATTA
** * *
31153610 ATTAAAA-ATTTAAAAAGCTTGAAGTGACATGAAATAAAAAAAATATAAATATGAGTAAGAGAGA
66 ATTAAAATATTTAAAAAGCTTGAAGCAACAT-AAA-ATAAAAAATACAAATATGAGTAAGAGAGA
* *
31153674 AATTAAAGTCGAG
129 AATCAAACTCGAG
31153687 ACTCAA
1 ACTCAA
31153693 GAATAAAAGC
Statistics
Matches: 251, Mismatches: 30, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
140 12 0.05
141 97 0.39
142 139 0.55
143 3 0.01
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (141 bp):
ACTCAACGATGTAATTGCAATTATCTAACCATCTAACGAAAGGACTAATATGTTAAAAAAAATTA
ATTAAAATATTTAAAAAGCTTGAAGCAACATAAAATAAAAAATACAAATATGAGTAAGAGAGAAA
TCAAACTCGAG
Found at i:31158625 original size:3 final size:3
Alignment explanation
Indices: 31158617--31158657 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31158607 TTTGTCAAGC
31158617 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31158658 TTCAAATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31163451 original size:47 final size:48
Alignment explanation
Indices: 31163398--31163749 Score: 240
Period size: 47 Copynumber: 7.5 Consensus size: 48
31163388 TAGTGAACAA
31163398 CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGAC
*
31163445 CATGTCTGGGACATGGCATCGG---CATTGGGATGAGAGCTAGTGTAAGA-
1 CATGTCTGGGACATGGCATCGGCCACATT---ATGAGAGCCAGTGTAAGAC
* * *
31163492 CATGTCTGGGACAT-GCATCGGCCCCATGACGTA-AGCCAGTGTAAGA-
1 CATGTCTGGGACATGGCATCGGCCACATTATG-AGAGCCAGTGTAAGAC
* * * * *
31163538 CATGTATGGGACAT-GCATCGGCTAC--GA-GATTAGTCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCACATTATGA-GAGCCAGTGTAAGAC
* * * * * *
31163583 CCTGTCT-GAACATGGAATC-GACACGAATATGTGAGAGCTAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCAC--AT-TATGAGAGCCAGTGTAAGAC
* * * * * *
31163632 CATGTCTGGGACATGGCGTTGGTCTCGATT-TCGATAGTCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCAC-ATTAT-GAGAGCCAGTGTAAGAC
*
31163681 CATGTCTGGGATC-TGGCATC-G--AC-TTGATGAATGAGCCAATGTAAGAC
1 CATGTCTGGGA-CATGGCATCGGCCACATT-ATG-A-GAGCCAGTGTAAGAC
31163728 CATGTCTGGGACATGGCATCGG
1 CATGTCTGGGACATGGCATCGG
31163750 TATTATACCC
Statistics
Matches: 241, Mismatches: 36, Indels: 55
0.73 0.11 0.17
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 24 0.10
45 14 0.06
46 47 0.20
47 59 0.24
48 27 0.11
49 52 0.22
50 13 0.05
51 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (48 bp):
CATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAGAC
Found at i:31163533 original size:46 final size:46
Alignment explanation
Indices: 31163397--31163559 Score: 206
Period size: 46 Copynumber: 3.5 Consensus size: 46
31163387 CTAGTGAACA
*
31163397 ACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAG
1 ACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAG
* *
31163443 ACCATGTCTGGGACATGGCATCGG-CA-TTGGGATGAGAGCTAGTGTAAG
1 A-CATGTCTGGGACAT-GCATCGGCCACAT--GATGAGAGCCAGTGTAAG
* *
31163491 ACATGTCTGGGACATGCATCGGCCCCATGACGTA-AGCCAGTGTAAG
1 ACATGTCTGGGACATGCATCGGCCACATGATG-AGAGCCAGTGTAAG
*
31163537 ACATGTATGGGACATGCATCGGC
1 ACATGTCTGGGACATGCATCGGC
31163560 TACGAGATTA
Statistics
Matches: 102, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
46 45 0.44
47 32 0.31
48 25 0.25
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (46 bp):
ACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAG
Found at i:31172246 original size:40 final size:40
Alignment explanation
Indices: 31172202--31172281 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
31172192 AATTATTGAC
*
31172202 ACAAGATTCCCGAACCGAATCCAAGAAACAAACGAAGGTT
1 ACAAGATTCCCAAACCGAATCCAAGAAACAAACGAAGGTT
* *
31172242 ACAAGATTCCCAAACCGAATCCAAGGAACGAACGAAGGTT
1 ACAAGATTCCCAAACCGAATCCAAGAAACAAACGAAGGTT
31172282 TACCAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (40 bp):
ACAAGATTCCCAAACCGAATCCAAGAAACAAACGAAGGTT
Found at i:31172396 original size:25 final size:26
Alignment explanation
Indices: 31172359--31172407 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
31172349 GAAATGAGAG
31172359 AAAAGAAACTAAAATAAAATAAAAAT
1 AAAAGAAACTAAAATAAAATAAAAAT
* *
31172385 AAAAGGAA-TAAAGTAAAATAAAA
1 AAAAGAAACTAAAATAAAATAAAA
31172408 TATTTCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (26 bp):
AAAAGAAACTAAAATAAAATAAAAAT
Found at i:31185097 original size:14 final size:14
Alignment explanation
Indices: 31185078--31185110 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
31185068 ACGCCTAACT
31185078 TGGCCTAGCCCGTA
1 TGGCCTAGCCCGTA
31185092 TGGCCTAGCCCGTA
1 TGGCCTAGCCCGTA
31185106 TGGCC
1 TGGCC
31185111 CACACAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (14 bp):
TGGCCTAGCCCGTA
Found at i:31185704 original size:6 final size:5
Alignment explanation
Indices: 31185682--31185728 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
31185672 GAGAAAATTT
* *
31185682 TAAAA TAAAA TAAAA TAAAAA TAAAA -CAAA TAAAG TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
31185729 TTTCAACTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 3 0.08
5 28 0.78
6 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:31185714 original size:20 final size:19
Alignment explanation
Indices: 31185689--31185726 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
31185679 TTTTAAAATA
31185689 AAATAAAATAAAAATAAAAC
1 AAATAAAAT-AAAATAAAAC
*
31185709 AAATAAAGTAAAATAAAA
1 AAATAAAATAAAATAAAA
31185727 TATTTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAC
Found at i:31192732 original size:39 final size:38
Alignment explanation
Indices: 31192683--31192782 Score: 121
Period size: 39 Copynumber: 2.6 Consensus size: 38
31192673 CAAATATAAT
* *
31192683 AATTATAATTACCATAATTATAATAATATTTGA-CCAAAA
1 AATTATAATTACAATAATTATAATAATATGTGATCC--AA
* * * *
31192722 AATTACAATTATAGTAATTATAATAATATGTGATCCTA
1 AATTATAATTACAATAATTATAATAATATGTGATCCAA
31192760 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
31192783 CAAAGGTTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 21 0.41
39 28 0.55
40 2 0.04
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATGTGATCCAA
Found at i:31196097 original size:42 final size:43
Alignment explanation
Indices: 31196043--31196139 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 43
31196033 CTGTCCTAGG
*
31196043 CATGGTCTTACACGA-AATCA-AATAACGACGCCAATGT-CCAAA
1 CATGGTCTTACAC-ATAATCACAAT-ACAACGCCAATGTCCCAAA
* *
31196085 CATGGTCTTACACATAATCACAATACAATGCCAATGTCCCAGA
1 CATGGTCTTACACATAATCACAATACAACGCCAATGTCCCAAA
31196128 CATGGTCTTACA
1 CATGGTCTTACA
31196140 TGTAATCGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 1 0.02
42 29 0.59
43 19 0.39
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (43 bp):
CATGGTCTTACACATAATCACAATACAACGCCAATGTCCCAAA
Found at i:31196146 original size:43 final size:43
Alignment explanation
Indices: 31196001--31196146 Score: 154
Period size: 43 Copynumber: 3.4 Consensus size: 43
31195991 TATCCCAAAT
* * * * *
31196001 ATGGTCTTACATGTTATCAC-ATATCGATGCCACTGTCCTAGGC
1 ATGGTCTTACACGTAATCACAATA-CGATGCCAATGTCCCAGAC
* * *
31196044 ATGGTCTTACACGAAATCA-AATAACGACGCCAATGT-CCAAAC
1 ATGGTCTTACACGTAATCACAAT-ACGATGCCAATGTCCCAGAC
* *
31196086 ATGGTCTTACACATAATCACAATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACGATGCCAATGTCCCAGAC
*
31196129 ATGGTCTTACATGTAATC
1 ATGGTCTTACACGTAATC
31196147 GCATCTCAGT
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 31 0.37
43 52 0.62
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACAATACGATGCCAATGTCCCAGAC
Found at i:31198009 original size:33 final size:33
Alignment explanation
Indices: 31197967--31198034 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
31197957 TCACTAAGTT
*
31197967 CAGTCCAGTACAATGGTGTTTGACACTTCTGAC
1 CAGTCCAGTACAACGGTGTTTGACACTTCTGAC
31198000 CAGTCCAGTACAACGGTGTTTGACACTTCTGAC
1 CAGTCCAGTACAACGGTGTTTGACACTTCTGAC
31198033 CA
1 CA
31198035 TATAAAGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (33 bp):
CAGTCCAGTACAACGGTGTTTGACACTTCTGAC
Found at i:31204215 original size:43 final size:44
Alignment explanation
Indices: 31204166--31204292 Score: 150
Period size: 43 Copynumber: 2.9 Consensus size: 44
31204156 GGTTACTGAG
*
31204166 ATGTGATTACATGTAAGACAATGTCTGGGACATTGGCATTG-TA
1 ATGTGATTACATGTAAGACAATGTCTGGGACATTGGCATCGTTA
* * * * *
31204209 TTGTGATTACCTATAAGACCATGTCTGGGACATTAGCATCGTTA
1 ATGTGATTACATGTAAGACAATGTCTGGGACATTGGCATCGTTA
* * * *
31204253 AT-TGATTACGTGTAAGACATTGTCTGAGACAGTGGCATCG
1 ATGTGATTACATGTAAGACAATGTCTGGGACATTGGCATCG
31204293 ATATGTTATA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
43 66 0.96
44 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACAATGTCTGGGACATTGGCATCGTTA
Found at i:31216121 original size:20 final size:20
Alignment explanation
Indices: 31216093--31216144 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
31216083 AATGGCTAAG
*
31216093 CACATGGGCATGTCCCAAGC
1 CACACGGGCATGTCCCAAGC
31216113 CACACGGGCATGTCCCAAGC
1 CACACGGGCATGTCCCAAGC
31216133 CACACGGGCATG
1 CACACGGGCATG
31216145 CGTGACCACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.37, G:0.27, T:0.12
Consensus pattern (20 bp):
CACACGGGCATGTCCCAAGC
Found at i:31221806 original size:33 final size:33
Alignment explanation
Indices: 31221742--31221807 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
31221732 AAAAAATTAA
* * *
31221742 TTACGAAAATTGGTTGAGATAAAATTTATTTAC
1 TTACGAAAATGGGTTGAGATAAAAATGATTTAC
*
31221775 TTACGGAAATGGGTTGAGCA-AAAAATGATTTAC
1 TTACGAAAATGGGTTGAG-ATAAAAATGATTTAC
31221808 GAGAATGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (33 bp):
TTACGAAAATGGGTTGAGATAAAAATGATTTAC
Found at i:31222814 original size:129 final size:132
Alignment explanation
Indices: 31222401--31222891 Score: 498
Period size: 131 Copynumber: 3.8 Consensus size: 132
31222391 AGGGATCTTT
* ** ** * * * *
31222401 GATTGTTTTGAGCAAATGAAAAAGCGCAACCCAGCACGATAGGGC-TCGATT-CTCAAATTGCCA
1 GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAT-GATTCCGCGAATTGCCA
* * * ** * *
31222464 AACATCGAA-CGTCGCCTTCGTTTTGAAAA-ATTTTTAATAA-ACATGAGTGAAAACCTAAAGGA
65 AACATCAAATC-TCGTCTTCGTTTT-AAAAGATTTTTAA-AAGACATGAGTGGAAATTTGAAGTA
31222526 ATATTC
127 ATATTC
* * ** * * * *
31222532 GATTGTTTTGAGCAAATGAGAAATCACAACCCAGCACGATAAGGCATGATTCC-CGAATTACCAA
1 GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCAA
* * * * * * * *
31222596 ACACCGAGTATCGCCTTTGTTTTAAAAGATTTTTAGAAGACATGAGTGGAATTTTGAAGTAATAT
66 ACATCAAATCTCGTCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGGAAATTTGAAGTAATAT
31222661 TC
131 TC
31222663 GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCAA
1 GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCAA
** * *
31222728 ACATCAAATCTCGTCTTCG-TTTAAGGGA-TTTTAAAAGATATGAGT-GAAATTTGAAGTGATAT
66 ACATCAAATCTCGTCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGGAAATTTGAAGTAATAT
31222790 TC
131 TC
*
31222792 GATTATTTCGAGC-AATCGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCA
1 GATTATTTTGAGCAAAT-GCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCA
* * *
31222856 AATATCAAATCTCGTCTTCATTTTAAAGAGTTTTTT
65 AACATCAAATCTCGTCTTCGTTTTAAA-AGATTTTT
31222892 TTTAAATGTG
Statistics
Matches: 307, Mismatches: 43, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
128 3 0.01
129 94 0.31
130 26 0.08
131 155 0.50
132 29 0.09
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (132 bp):
GATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCATGATTCCGCGAATTGCCAA
ACATCAAATCTCGTCTTCGTTTTAAAAGATTTTTAAAAGACATGAGTGGAAATTTGAAGTAATAT
TC
Found at i:31234570 original size:124 final size:125
Alignment explanation
Indices: 31234413--31234660 Score: 347
Period size: 124 Copynumber: 2.0 Consensus size: 125
31234403 TAATCGATCA
* *
31234413 TATTGCTTTCATAATTAATTTTCCAGTAAAAAAATTTATTGCTACTTGCTATTTATTTAAATAGG
1 TATTGCTTTCATAATTAATTGTCCAGTAAAAAAATTTATTGCTACTTGCTAGTTATTTAAATAGG
* * * ** * *
31234478 AATGTTGTTTATTTAAAT-AGAAAAACATATTTTCTATTCATGGTTAACTTATAAAATCG
66 AATGTTATTTATTTAAATGAAAAAAACATATCTGATATTAATGATTAACTTATAAAATCG
* * * *
31234537 TATTGCTTTGATGATTAATGTGTCGA-TAAAAAAATTTGTTGCTACTTGCTAGTTATTTAAATAG
1 TATTGCTTTCATAATTAAT-TGTCCAGTAAAAAAATTTATTGCTACTTGCTAGTTATTTAAATAG
31234601 GAATGTTATTTATTTAAATGGAAAAAAACATATCTGATATTAATGATTAACTTATAAAAT
65 GAATGTTATTTATTTAAAT-GAAAAAAACATATCTGATATTAATGATTAACTTATAAAAT
31234661 TGCATGTCAT
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
124 71 0.66
125 4 0.04
126 33 0.31
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.43
Consensus pattern (125 bp):
TATTGCTTTCATAATTAATTGTCCAGTAAAAAAATTTATTGCTACTTGCTAGTTATTTAAATAGG
AATGTTATTTATTTAAATGAAAAAAACATATCTGATATTAATGATTAACTTATAAAATCG
Found at i:31236979 original size:44 final size:44
Alignment explanation
Indices: 31236925--31237012 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
31236915 AAATACAACA
* * *
31236925 GATAACTTTTAAAATGCATTCGAACTTATGGTACATATGATGTT
1 GATAAATTTTAAAATGCATTCGAACCTAGGGTACATATGATGTT
31236969 GATAAATTTTAAAATGCATTCGAACCTAGGGTACATATGATGTT
1 GATAAATTTTAAAATGCATTCGAACCTAGGGTACATATGATGTT
31237013 TACCTTGGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (44 bp):
GATAAATTTTAAAATGCATTCGAACCTAGGGTACATATGATGTT
Found at i:31240053 original size:33 final size:33
Alignment explanation
Indices: 31240016--31240176 Score: 103
Period size: 33 Copynumber: 4.9 Consensus size: 33
31240006 ACTTACCCTC
* * *
31240016 TGTTTACTATCCCAGCGGACTATCTTTATTTTG
1 TGTTTACTATCCCAGCAGACTATCTCTATTCTG
* *
31240049 TGTTTACTATTCCAGCAGATTATCTCTATTCTG
1 TGTTTACTATCCCAGCAGACTATCTCTATTCTG
* ** * * * * *
31240082 TGTTTACT-GCCTTGGCAAATTATCTATGTTTTG
1 TGTTTACTATCC-CAGCAGACTATCTCTATTCTG
* *
31240115 TGTTTACTGTCCCAGC-GAACTAT-TATTATTCTG
1 TGTTTACTATCCCAGCAG-ACTATCT-CTATTCTG
* * * *
31240148 TGTTTATTGTCCTAGCAAACTATCTCTAT
1 TGTTTACTATCCCAGCAGACTATCTCTAT
31240177 GGATGCCATG
Statistics
Matches: 97, Mismatches: 25, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
32 2 0.02
33 92 0.95
34 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTTTACTATCCCAGCAGACTATCTCTATTCTG
Found at i:31242768 original size:10 final size:10
Alignment explanation
Indices: 31242753--31242791 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
31242743 AATTTTAGCT
31242753 TTTATCTTTA
1 TTTATCTTTA
*
31242763 TTTATCCTTA
1 TTTATCTTTA
31242773 TTTATCTTTA
1 TTTATCTTTA
31242783 TTTATCTTT
1 TTTATCTTT
31242792 TAGAATTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:31246422 original size:14 final size:14
Alignment explanation
Indices: 31246371--31246422 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
31246361 TAGAATTGAG
31246371 TTAATAAAATT-AT
1 TTAATAAAATTAAT
31246384 TTAATGGAAAAATTAA-
1 TTAAT---AAAATTAAT
31246400 TTAATTAAAATTAAT
1 TTAA-TAAAATTAAT
31246415 TTAATAAA
1 TTAATAAA
31246423 TAATGTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.15
14 12 0.36
15 4 0.12
16 10 0.30
17 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (14 bp):
TTAATAAAATTAAT
Found at i:31252799 original size:33 final size:32
Alignment explanation
Indices: 31252728--31252808 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
31252718 ACTTGAGCTG
* *
31252728 GGAGGAGTAGAATACGACGGTGGATACAGGCC
1 GGAGGAGTAGAGTACGACGGTGGATACAGACC
*
31252760 GAGAGGAGTAGAGTGCGACGGTGGATAC-GACTC
1 G-GAGGAGTAGAGTACGACGGTGGATACAGAC-C
*
31252793 TGGAGGAGTTGAGTAC
1 -GGAGGAGTAGAGTAC
31252809 ATGGGTGGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 3 0.07
33 37 0.90
34 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.42, T:0.16
Consensus pattern (32 bp):
GGAGGAGTAGAGTACGACGGTGGATACAGACC
Found at i:31254883 original size:15 final size:16
Alignment explanation
Indices: 31254863--31254894 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31254853 ATAAATAATA
31254863 ATAT-AAAATTACATT
1 ATATAAAAATTACATT
31254878 ATATAAAAATTACATT
1 ATATAAAAATTACATT
31254894 A
1 A
31254895 AAAAATCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:31255259 original size:115 final size:115
Alignment explanation
Indices: 31254935--31255369 Score: 618
Period size: 115 Copynumber: 3.8 Consensus size: 115
31254925 TAACGATTTA
* ** * *
31254935 TAATCATAAATTACTAACACAAAATAACTAT-AAATT-TTTTTAAAAAAAATACATTACTAAATA
1 TAATCTTAAATTACT-A-ACAAAATAACTATAAAATTATTTTT-TTAAAAATATATTACTAAAAA
*
31254998 AA--A-AAT-CA-TAATACACTAAACCACTAAACACTACCAATTTATATAACC
63 AATCACAATACACTAATACACTAAACCACTAAACACTAACAATTTATATAACC
* * * *
31255046 TAATCTTAAATTACTAATAAAATAGCTATAAAAATA-TTTTTTAAAATTATATTACTAAAAAAAT
1 TAATCTTAAATTACTAACAAAATAACTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAAT
31255110 CACAATACACTAATACACTAAACCACTAAACACTAACAATTTATATAACC
66 CACAATACACTAATACACTAAACCACTAAACACTAACAATTTATATAACC
* *
31255160 TAATCTTAAATTACTAATAAAATAGCTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAAT
1 TAATCTTAAATTACTAACAAAATAACTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAAT
*
31255225 CACAATACACTAATACACTAAACTACTAAACACTAACAATTTATATAACC
66 CACAATACACTAATACACTAAACCACTAAACACTAACAATTTATATAACC
* *
31255275 TAATCTTAAATTACTAACAGAATAACTATAAAATTATTTTTTTTAAATATATTATTACTAAAAAA
1 TAATCTTAAATTACTAACAAAATAACTATAAAATTA-TTTTTTTAAAAATA-TATTACTAAAAAA
*
31255340 ATCACAATACACTAATACATTAAA-CACTAA
64 ATCACAATACACTAATACACTAAACCACTAA
31255370 CAATTTGTAA
Statistics
Matches: 295, Mismatches: 19, Indels: 15
0.90 0.06 0.05
Matches are distributed among these distances:
109 29 0.10
110 9 0.03
111 15 0.05
112 3 0.01
113 2 0.01
114 74 0.25
115 109 0.37
116 18 0.06
117 36 0.12
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (115 bp):
TAATCTTAAATTACTAACAAAATAACTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAAT
CACAATACACTAATACACTAAACCACTAAACACTAACAATTTATATAACC
Found at i:31255271 original size:229 final size:227
Alignment explanation
Indices: 31254935--31255369 Score: 621
Period size: 229 Copynumber: 1.9 Consensus size: 227
31254925 TAACGATTTA
*
31254935 TAATCATAAATTACTAACACAAAATAACTATAAATTTTTTTAAAAAAAATACATTACTAAATAAA
1 TAATCATAAATTACTAACACAAAATAACTATAAATTTTTTTAAAAAAAATACATTACTAAAAAAA
* *
31255000 AAATCATAATACACTAAACCACTAAACACTACCAATTTATATAACCTAATCTTAAATTACTAATA
66 AAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAACA
*
31255065 AAATAGCTATAAAAATA-TTTTTTAAAAT-TA-TATTACTAAAAAAATCACAATACACTAATACA
131 AAATAACTATAAAAATATTTTTTTAAAATATATTATTACTAAAAAAATCACAATACACTAATACA
31255127 CTAAACCACTAAACACTAACAATTTATATAACC
196 CTAAA-CACTAAACACTAACAATTTATATAACC
* * * ** *
31255160 TAATCTTAAATTACT-A-ATAAAATAGCTATAAAATTATTTTT-TTAAAAATATATTACTAAAAA
1 TAATCATAAATTACTAACACAAAATAACTAT-AAATT-TTTTTAAAAAAAATACATTACTAAAAA
*
31255222 AATCACAATACACTAATACACTAAACTACTAAACACTAACAATTTATATAACCTAATCTTAAATT
64 AA--A-AAT-CA-TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATT
* * *
31255287 ACTAACAGAATAACTATAAAATTATTTTTTTTAAATATATTATTACTAAAAAAATCACAATACAC
124 ACTAACAAAATAACTATAAAAATATTTTTTTAAAATATATTATTACTAAAAAAATCACAATACAC
*
31255352 TAATACATTAAACACTAA
189 TAATACACTAAACACTAA
31255370 CAATTTGTAA
Statistics
Matches: 185, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
223 11 0.06
224 25 0.14
225 19 0.10
226 1 0.01
227 3 0.02
228 2 0.01
229 70 0.38
230 10 0.05
231 8 0.04
232 36 0.19
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (227 bp):
TAATCATAAATTACTAACACAAAATAACTATAAATTTTTTTAAAAAAAATACATTACTAAAAAAA
AAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAACA
AAATAACTATAAAAATATTTTTTTAAAATATATTATTACTAAAAAAATCACAATACACTAATACA
CTAAACACTAAACACTAACAATTTATATAACC
Found at i:31255573 original size:3 final size:3
Alignment explanation
Indices: 31255567--31255604 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
31255557 TACCCTTTTT
*
31255567 TTC TTC TTC TTC TTC TTC TTCC TTC TTC TTC TCC TTC T
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC T
31255605 GATTTCCCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:31263053 original size:20 final size:20
Alignment explanation
Indices: 31263020--31263113 Score: 70
Period size: 20 Copynumber: 4.7 Consensus size: 20
31263010 TGAAAAATAA
*
31263020 TAAAATAAATAAATAATACAT
1 TAAATTAAA-AAATAATACAT
*
31263041 TAAATTAAAAAATAATTC-T
1 TAAATTAAAAAATAATACAT
31263060 TAAATTAAAGAAAATAA-ACA-
1 TAAATT-AA-AAAATAATACAT
*
31263080 TAATTATTTAAAAATAATA-AT
1 TAA--ATTAAAAAATAATACAT
* *
31263101 TTAATAAAAAAAT
1 TAAATTAAAAAAT
31263114 TATCAGTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
19 15 0.25
20 22 0.37
21 19 0.32
22 3 0.05
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (20 bp):
TAAATTAAAAAATAATACAT
Found at i:31263064 original size:19 final size:21
Alignment explanation
Indices: 31263020--31263068 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
31263010 TGAAAAATAA
*
31263020 TAAAATAAATAAATAATACAT
1 TAAATTAAATAAATAATACAT
*
31263041 TAAATTAAA-AAATAATTC-T
1 TAAATTAAATAAATAATACAT
31263060 TAAATTAAA
1 TAAATTAAA
31263069 GAAAATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
20 8 0.31
21 8 0.31
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATTAAATAAATAATACAT
Found at i:31266660 original size:16 final size:16
Alignment explanation
Indices: 31266639--31266673 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31266629 GAAATTATTA
31266639 AAATATTATAAAATTG
1 AAATATTATAAAATTG
31266655 AAATATTATAAAATTG
1 AAATATTATAAAATTG
31266671 AAA
1 AAA
31266674 GAATTACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AAATATTATAAAATTG
Found at i:31268038 original size:24 final size:24
Alignment explanation
Indices: 31268011--31268057 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
31268001 TTATTATTTT
*
31268011 AATTATTTTCTAATAATTCTTATA
1 AATTATTTTCTAAAAATTCTTATA
* *
31268035 AATTATTTTTTAAAAATTTTTAT
1 AATTATTTTCTAAAAATTCTTAT
31268058 GATTTTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTATTTTCTAAAAATTCTTATA
Found at i:31270066 original size:35 final size:35
Alignment explanation
Indices: 31270026--31270110 Score: 161
Period size: 35 Copynumber: 2.4 Consensus size: 35
31270016 CTATAAAGTG
*
31270026 CATCTATGACAACCTAGAGAAATATAAAAGGAAAT
1 CATCTATGATAACCTAGAGAAATATAAAAGGAAAT
31270061 CATCTATGATAACCTAGAGAAATATAAAAGGAAAT
1 CATCTATGATAACCTAGAGAAATATAAAAGGAAAT
31270096 CATCTATGATAACCT
1 CATCTATGATAACCT
31270111 GCATATTAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (35 bp):
CATCTATGATAACCTAGAGAAATATAAAAGGAAAT
Found at i:31273682 original size:23 final size:25
Alignment explanation
Indices: 31273637--31273684 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
31273627 TATTTTAGTT
**
31273637 TTTATTACTTTTTTAACTTTAATCA
1 TTTATTACTTTTTTAACCCTAATCA
31273662 TTTATT-CTTTTTT-ACCCTAATCA
1 TTTATTACTTTTTTAACCCTAATCA
31273685 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 7 0.33
25 6 0.29
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTATTACTTTTTTAACCCTAATCA
Found at i:31274902 original size:14 final size:15
Alignment explanation
Indices: 31274883--31274913 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31274873 TTTATATATT
31274883 TTTAT-AATTTTAAA
1 TTTATAAATTTTAAA
31274897 TTTATAAATTTTAAA
1 TTTATAAATTTTAAA
31274912 TT
1 TT
31274914 CTTTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATAAATTTTAAA
Found at i:31274968 original size:49 final size:49
Alignment explanation
Indices: 31274881--31274974 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
31274871 CTTTTATATA
* *
31274881 TTTTTATAATTTTAAATTTATAAATTTTAAATTCTTTATAAATTTTGTT
1 TTTTTATAAATTTAAATGTATAAATTTTAAATTCTTTATAAATTTTGTT
* * * *
31274930 TTTTTATAAATTTATATGT-TACATTTTATAATTTTTTATACATTT
1 TTTTTATAAATTTAAATGTATAAATTTTA-AATTCTTTATAAATTT
31274975 CCGAAATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 8 0.21
49 30 0.79
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (49 bp):
TTTTTATAAATTTAAATGTATAAATTTTAAATTCTTTATAAATTTTGTT
Found at i:31275805 original size:13 final size:13
Alignment explanation
Indices: 31275787--31275812 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31275777 CACTAATTCT
31275787 ATCACCCCACTAA
1 ATCACCCCACTAA
31275800 ATCACCCCACTAA
1 ATCACCCCACTAA
31275813 TCTCATTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCCCACTAA
Found at i:31276370 original size:21 final size:20
Alignment explanation
Indices: 31276344--31276382 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31276334 TTATGAACAT
31276344 TTTTTAAATATTATATTATTA
1 TTTTTAAATATTAT-TTATTA
*
31276365 TTTTTATATATTATTTAT
1 TTTTTAAATATTATTTAT
31276383 ATTAAGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAAATATTATTTATTA
Found at i:31276459 original size:21 final size:20
Alignment explanation
Indices: 31276422--31276460 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
31276412 TTTATTCGTA
*
31276422 TATATATATATATTGTTTTG
1 TATATATATATACTGTTTTG
*
31276442 TATATCATTTATACTGTTT
1 TATAT-ATATATACTGTTT
31276461 CGTTACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (20 bp):
TATATATATATACTGTTTTG
Found at i:31276763 original size:25 final size:25
Alignment explanation
Indices: 31276734--31276785 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
31276724 GATAGATCAA
*
31276734 TATTT-TGTATTTTATGCATTAATTT
1 TATTTATGTATTTTAT-AATTAATTT
*
31276759 TATTTATTTATTTTATAATTAATTT
1 TATTTATGTATTTTATAATTAATTT
31276784 TA
1 TA
31276786 AAATTTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (25 bp):
TATTTATGTATTTTATAATTAATTT
Found at i:31283060 original size:64 final size:64
Alignment explanation
Indices: 31282980--31283106 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 64
31282970 CATTCATAGT
* ** *
31282980 ACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGGCATAAGCATC
1 ACATCTAGCTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAACTATTTGGCATAAGCATC
* *
31283044 ACATCTAGCTAGGAGCATTTGATTTATTTCAATCATAGCATCCTAACTGTTTGGCATAAGCAT
1 ACATCTAGCTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAACTATTTGGCATAAGCAT
31283107 ATATACATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (64 bp):
ACATCTAGCTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAACTATTTGGCATAAGCATC
Done.