Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 67 of 147
Found at i:12687426 original size:35 final size:35
Alignment explanation
Indices: 12687386--12687477 Score: 100
Period size: 35 Copynumber: 2.6 Consensus size: 35
12687376 ATTTTTTATT
12687386 TAAAGA-AAATAGAATAATAAAAAAGTAAAA-ATAAA
1 TAAAGATAAA-AGAATAATAAAAAAGTAAAACA-AAA
* *
12687421 TAAAGATAAAAAAATAA-AAGAAAGTAAAACCAAAA
1 TAAAGATAAAAGAATAATAAAAAAGTAAAA-CAAAA
*
12687456 TAAAGATAAAAAGAATATTAAA
1 TAAAGAT-AAAAGAATAATAAA
12687478 TAAACCTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
34 11 0.23
35 22 0.47
36 12 0.26
37 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (35 bp):
TAAAGATAAAAGAATAATAAAAAAGTAAAACAAAA
Found at i:12687444 original size:19 final size:17
Alignment explanation
Indices: 12687386--12687449 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
12687376 ATTTTTTATT
* * *
12687386 TAAAGAAAATAGAATAA
1 TAAAGAAAGTAAAAAAA
12687403 TAAA-AAAGT--AAAAA
1 TAAAGAAAGTAAAAAAA
*
12687417 TAAATAAAGATAAAAAAA
1 TAAAGAAAG-TAAAAAAA
12687435 TAAAAGAAAGTAAAA
1 T-AAAGAAAGTAAAA
12687450 CCAAAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.21
15 4 0.10
16 5 0.13
17 4 0.10
18 11 0.28
19 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (17 bp):
TAAAGAAAGTAAAAAAA
Found at i:12687571 original size:5 final size:5
Alignment explanation
Indices: 12687563--12687587 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12687553 AAACCTAGAG
12687563 CGGCT CGGCT CGGCT CGGCT CGGCT
1 CGGCT CGGCT CGGCT CGGCT CGGCT
12687588 TAAGGAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.40, T:0.20
Consensus pattern (5 bp):
CGGCT
Found at i:12687909 original size:20 final size:19
Alignment explanation
Indices: 12687873--12687924 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
12687863 CTCCGGTGGG
* *
12687873 AATTTCGTCGGATTCTGGA
1 AATTTCGCCGGAATCTGGA
12687892 AATTATCGCCGGAATCTGGA
1 AATT-TCGCCGGAATCTGGA
*
12687912 AATTTCGTCGGAA
1 AATTTCGCCGGAA
12687925 GTTCGTCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (19 bp):
AATTTCGCCGGAATCTGGA
Found at i:12688813 original size:1 final size:1
Alignment explanation
Indices: 12688803--12688869 Score: 71
Period size: 1 Copynumber: 67.0 Consensus size: 1
12688793 AACATTGTCA
* * * * * * *
12688803 TTTTTGTTTTTTTTTTTTCTGTTTTTTTTTTATTCTTTTTGTTTTTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12688868 TT
1 TT
12688870 ACCAAAGCTC
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.01, C:0.03, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:12688849 original size:35 final size:36
Alignment explanation
Indices: 12688803--12688870 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
12688793 AACATTGTCA
12688803 TTTTTGTTTTTTTTTTT-TCTGTTTTTTTTTTATTC
1 TTTTTGTTTTTTTTTTTGTCTGTTTTTTTTTTATTC
* *
12688838 TTTTTGTTTTTTTTTTTGTTTTTTTTTTTTTTA
1 TTTTTGTTTTTTTTTTTGTCTGTTTTTTTTTTA
12688871 CCAAAGCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.88
Consensus pattern (36 bp):
TTTTTGTTTTTTTTTTTGTCTGTTTTTTTTTTATTC
Found at i:12688971 original size:42 final size:42
Alignment explanation
Indices: 12688876--12689413 Score: 846
Period size: 42 Copynumber: 13.0 Consensus size: 42
12688866 TTTTACCAAA
* * * *
12688876 GCTCCTCTAAACAAAGGCTCAACGACTTTGAGAAACGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAAGTAAATT
* *
12688919 ACTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
12688961 GCTCCTCTAAACAGAGGCACCACGACTTTTGG-AAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAAGTAAATT
*
12689003 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
12689045 GCTCCTCTAAATAGAGGCACCACGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
12689086 GATCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
12689128 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
12689170 GCTCCTCTAAACAGAGGCACCACGAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
12689211 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
12689253 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
12689294 GCTCTTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
12689336 GCTCCTCTAAACAAAGGCA--ACGAAC-TTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATT
*
12689375 GCTCCTCTAAACAGAGGCA--ACGAAC-TTGGAAAGGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAAT
12689414 ACTCCTAGAC
Statistics
Matches: 467, Mismatches: 21, Indels: 17
0.92 0.04 0.03
Matches are distributed among these distances:
39 38 0.08
40 15 0.03
41 127 0.27
42 257 0.55
43 30 0.06
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
Found at i:12689114 original size:125 final size:126
Alignment explanation
Indices: 12688876--12689413 Score: 846
Period size: 125 Copynumber: 4.3 Consensus size: 126
12688866 TTTTACCAAA
* * * * * *
12688876 GCTCCTCTAAACAAAGGCTCAACGACTTTGAGAAACGTAAATTACTCCTCTAAACAGAGGTACCA
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
*
12688941 CGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGG-AAATTAAATT
65 CGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAAGTAAATT
* *
12689003 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
12689068 GACTTTGG-AAAGTAAATTGATCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
66 GACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
12689128 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
12689193 GAC-TTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
66 GACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
12689253 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCTTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
12689317 GACTTTGGAAAAGTAAATTGCTCCTCTAAACAAAGGCA--ACGAAC-TTGG-AAAGTAAATT
66 GACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATT
*
12689375 GCTCCTCTAAACAGAGGCA--ACGAAC-TTGGAAAGGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAAT
12689414 ACTCCTAGAC
Statistics
Matches: 389, Mismatches: 16, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
120 5 0.01
121 12 0.03
122 29 0.07
123 7 0.02
124 48 0.12
125 223 0.57
126 39 0.10
127 26 0.07
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (126 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
GACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
Found at i:12689120 original size:83 final size:83
Alignment explanation
Indices: 12688876--12689413 Score: 833
Period size: 83 Copynumber: 6.5 Consensus size: 83
12688866 TTTTACCAAA
* * * * *
12688876 GCTCCTCTAAACAAAGGCTCAACGACTTTGAGAAACGTAAATTACTCCTCTAAACAGAGGTACCA
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-GTAAATTGCTCCTCTAAACAGAGGCACCA
12688941 CGACTTTGGAAAAGTAAATT
64 CGACTTTGGAAAAGTAAATT
* *
12688961 GCTCCTCTAAACAGAGGCACCACGACTTTTGGAAATTAAATTGCTCCTCTAAACAGAGGCACCAT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
12689026 GACTTTGGAAAAGTAAATT
65 GACTTTGGAAAAGTAAATT
* *
12689045 GCTCCTCTAAATAGAGGCACCACGACTTTGGAAAGTAAATTGATCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
12689110 ACTTTGGAAAAGTAAATT
66 ACTTTGGAAAAGTAAATT
12689128 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
12689193 GAC-TTGGAAAAGTAAATT
65 GACTTTGGAAAAGTAAATT
12689211 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
12689276 GACTTT-GAAAAGTAAATT
65 GACTTTGGAAAAGTAAATT
* *
12689294 GCTCTTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAAAGGCA--AC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
12689357 GAAC-TTGG-AAAGTAAATT
65 G-ACTTTGGAAAAGTAAATT
12689375 GCTCCTCTAAACAGAGGCA--ACGAAC-TTGGAAAGGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAA-GTAAAT
12689414 ACTCCTAGAC
Statistics
Matches: 430, Mismatches: 16, Indels: 20
0.92 0.03 0.04
Matches are distributed among these distances:
78 3 0.01
79 13 0.03
80 2 0.00
81 33 0.08
82 3 0.01
83 238 0.55
84 107 0.25
85 27 0.06
86 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (83 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGGAAAAGTAAATT
Found at i:12694837 original size:60 final size:60
Alignment explanation
Indices: 12694498--12694847 Score: 432
Period size: 60 Copynumber: 5.9 Consensus size: 60
12694488 TCTTGTATAG
* * * *
12694498 GGAAAATTGATACTTTCACCTTTTCCCCAAAAATA--TTTTTTGGAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTATTTTCAA
* ** *
12694555 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATA-TTTTTTCAAAAATTTTGGTTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTT-ATTTTCAA
*
12694615 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAATATTTTTTTTCG-AAACTTTATTCTT-AA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTT-GAAAATTTTATT-TTCAA
* ** *
12694675 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCT-TTTTTTTTTTAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAA--TATTTTTTTTGAAAATTTTATTTTCAA
12694735 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGAAAATTTT-ATTTTCAA
*
12694797 GGAAAATTGATA-TTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTT
12694848 GATTGTTTAT
Statistics
Matches: 257, Mismatches: 20, Indels: 29
0.84 0.07 0.09
Matches are distributed among these distances:
57 32 0.12
58 9 0.04
59 7 0.03
60 137 0.53
61 52 0.20
62 20 0.08
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTATTTTCAA
Found at i:12695565 original size:25 final size:24
Alignment explanation
Indices: 12695528--12695576 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
12695518 CGAAATCTGG
* *
12695528 AATTTCCAGAAATTCCCAGAAAAAA
1 AATTTCAAAAAATTCCCA-AAAAAA
12695553 AATTTCAAAAAATTCCCAAAAAAA
1 AATTTCAAAAAATTCCCAAAAAAA
12695577 TTTTTGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.57, C:0.18, G:0.04, T:0.20
Consensus pattern (24 bp):
AATTTCAAAAAATTCCCAAAAAAA
Found at i:12695927 original size:34 final size:33
Alignment explanation
Indices: 12695852--12695930 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 33
12695842 TCCAAAAATC
* *
12695852 AAATAAAAAAATA-CTAGATAATTAGAAAAGAT
1 AAATAAAAAAATATCTAGATAAATAGAAAAGAA
* *
12695884 AAAT-CAAAAATATCATAGGATAAATA-AAAATAA
1 AAATAAAAAAATATC-TA-GATAAATAGAAAAGAA
12695917 AAATAAAAAAATAT
1 AAATAAAAAAATAT
12695931 ATATCAGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
31 7 0.18
32 5 0.13
33 11 0.29
34 15 0.39
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.22
Consensus pattern (33 bp):
AAATAAAAAAATATCTAGATAAATAGAAAAGAA
Found at i:12696719 original size:20 final size:20
Alignment explanation
Indices: 12696673--12696730 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
12696663 TAAAACAATT
*
12696673 TGGGAAAAAGAGAAAGGCATA
1 TGGGAGAAAGA-AAAGGCATA
12696694 TAGGGAGAAAGAAAAGGCATA
1 T-GGGAGAAAGAAAAGGCATA
*
12696715 TGGGAAGAAGGAAAAG
1 TGGG-AGAAAGAAAAG
12696731 CATGGTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 21 0.64
22 9 0.27
ACGTcount: A:0.52, C:0.03, G:0.36, T:0.09
Consensus pattern (20 bp):
TGGGAGAAAGAAAAGGCATA
Found at i:12698838 original size:18 final size:18
Alignment explanation
Indices: 12698815--12698852 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12698805 TCAACAAATG
12698815 AATCAATGAAAAGTTACC
1 AATCAATGAAAAGTTACC
*
12698833 AATCAATGAAAGGTTACC
1 AATCAATGAAAAGTTACC
12698851 AA
1 AA
12698853 AGTGATTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (18 bp):
AATCAATGAAAAGTTACC
Found at i:12700002 original size:2 final size:2
Alignment explanation
Indices: 12699991--12700036 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
12699981 ATTTGACATG
* *
12699991 AT AT -T AT AT AT AT AT GAT AT -T AT CT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
12700032 AT AT A
1 AT AT A
12700037 CTTTTTAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12700009 original size:16 final size:16
Alignment explanation
Indices: 12699988--12700035 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
12699978 ACAATTTGAC
12699988 ATGATATTATATATAT
1 ATGATATTATATATAT
*
12700004 ATGATATTATCTATAT
1 ATGATATTATATATAT
*
12700020 AT-ATA-TATAAATAT
1 ATGATATTATATATAT
12700034 AT
1 AT
12700036 ACTTTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 9 0.31
15 3 0.10
16 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (16 bp):
ATGATATTATATATAT
Found at i:12702862 original size:27 final size:26
Alignment explanation
Indices: 12702813--12702872 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
12702803 AAATAAGATG
* **
12702813 ATATTATTTTATTTTATTTTATTTATA
1 ATATTATCTTATTTTATCATA-TTATA
12702840 ATATTATCTTATTTTATCATATTATA
1 ATATTATCTTATTTTATCATATTATA
*
12702866 ATCTTAT
1 ATATTAT
12702873 ATATCAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATTATCTTATTTTATCATATTATA
Found at i:12702871 original size:21 final size:22
Alignment explanation
Indices: 12702826--12702872 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
12702816 TTATTTTATT
* *
12702826 TTATTTTATTTATAATATTATC
1 TTATTTTATTCATAATATAATC
*
12702848 TTATTTTA-TCATATTATAATC
1 TTATTTTATTCATAATATAATC
12702869 TTAT
1 TTAT
12702873 ATATCAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTTTATTCATAATATAATC
Found at i:12703772 original size:21 final size:22
Alignment explanation
Indices: 12703723--12703779 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
12703713 AAATTAAGTT
12703723 TTTTTTAATATTTAATATTTAA
1 TTTTTTAATATTTAATATTTAA
*
12703745 TATTTTT-AT-TTTTATATTTAAA
1 T-TTTTTAATATTTAATATTT-AA
12703767 TTTTTTTAATATT
1 -TTTTTTAATATT
12703780 AAAAATCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
21 9 0.31
22 10 0.34
23 8 0.28
24 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTTAATATTTAATATTTAA
Found at i:12703827 original size:22 final size:22
Alignment explanation
Indices: 12703770--12703836 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
12703760 ATTTAAATTT
**
12703770 TTTTAATATTAAAAATCATAAA
1 TTTTAATATTAAAAATTTTAAA
* *
12703792 -CTTAATTGTATAAAAATTTTAAA
1 TTTTAA-TAT-TAAAAATTTTAAA
*
12703815 TTTTAATATTAAATATTTTAAA
1 TTTTAATATTAAAAATTTTAAA
12703837 ATTAAAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.11
22 14 0.40
23 13 0.37
24 4 0.11
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (22 bp):
TTTTAATATTAAAAATTTTAAA
Found at i:12703834 original size:15 final size:15
Alignment explanation
Indices: 12703812--12703848 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12703802 TAAAAATTTT
*
12703812 AAATTTTAATATTAA
1 AAATTTTAAAATTAA
*
12703827 ATATTTTAAAATTAA
1 AAATTTTAAAATTAA
12703842 AAATTTT
1 AAATTTT
12703849 TTTCAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTTAAAATTAA
Found at i:12704008 original size:18 final size:16
Alignment explanation
Indices: 12703985--12704019 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
12703975 TTTATTTATG
12703985 TAATTAATAAATTATTAA
1 TAATTAA-AAATT-TTAA
12704003 TAATTAAAAATTTTAA
1 TAATTAAAAATTTTAA
12704019 T
1 T
12704020 GTGCAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 5 0.29
18 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATTAAAAATTTTAA
Found at i:12706574 original size:24 final size:22
Alignment explanation
Indices: 12706544--12706594 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
12706534 TAAAAAAAAA
*
12706544 TTATTAATAAAATGATGATTTATT
1 TTATTAATAAAATAAT-A-TTATT
*
12706568 TTATTAATAAGATAATATTATT
1 TTATTAATAAAATAATATTATT
12706590 TTATT
1 TTATT
12706595 TGTTAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
23 1 0.04
24 14 0.56
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
TTATTAATAAAATAATATTATT
Found at i:12708292 original size:5 final size:5
Alignment explanation
Indices: 12708282--12708306 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12708272 ATTCATAATA
12708282 TTATC TTATC TTATC TTATC TTATC
1 TTATC TTATC TTATC TTATC TTATC
12708307 ATAATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATC
Found at i:12709428 original size:18 final size:17
Alignment explanation
Indices: 12709407--12709462 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
12709397 ATATTAATAA
12709407 TTTAAATAATATAAATTT
1 TTTAAATAA-ATAAATTT
12709425 TTTAAA-AAAT-AATTT
1 TTTAAATAAATAAATTT
12709440 TAATT-AATAAATAAATTAT
1 T--TTAAATAAATAAATT-T
12709459 TTTA
1 TTTA
12709463 TTTTAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 6 0.19
16 4 0.12
17 10 0.31
18 10 0.31
19 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAATAAATAAATTT
Found at i:12709523 original size:17 final size:16
Alignment explanation
Indices: 12709497--12709529 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
12709487 ATAAAATAAA
12709497 ATAAAATAATTTATTT
1 ATAAAATAATTTATTT
12709513 ATAATAATAATTTATTT
1 ATAA-AATAATTTATTT
12709530 TATTCTATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAAAATAATTTATTT
Found at i:12709996 original size:13 final size:12
Alignment explanation
Indices: 12709981--12710073 Score: 76
Period size: 13 Copynumber: 8.1 Consensus size: 12
12709971 TATTTAAAAT
12709981 ATAATATAATAA
1 ATAATATAATAA
12709993 TATAATATAA-AA
1 -ATAATATAATAA
12710005 ATAATATAAATAA
1 ATAATAT-AATAA
*
12710018 AAAATATAA-AA
1 ATAATATAATAA
*
12710029 ATAATATAATTTA
1 ATAATATAA-TAA
12710042 A-AAT-TAA-AA
1 ATAATATAATAA
12710051 A-AAT-T-ATAA
1 ATAATATAATAA
12710060 ATAAATATAATAA
1 AT-AATATAATAA
12710073 A
1 A
12710074 AAATTATATT
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
8 1 0.01
9 9 0.13
11 23 0.34
12 10 0.15
13 24 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATATAATAA
Found at i:12710009 original size:16 final size:16
Alignment explanation
Indices: 12709978--12710020 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
12709968 GGTTATTTAA
12709978 AATATAATATAATAATAT
1 AATATAA-A-AATAATAT
12709996 AATATAAAAATAATAT
1 AATATAAAAATAATAT
12710012 AA-ATAAAAA
1 AATATAAAAA
12710021 ATATAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 1 0.04
18 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATATAAAAATAATAT
Found at i:12710010 original size:24 final size:25
Alignment explanation
Indices: 12709975--12710082 Score: 104
Period size: 24 Copynumber: 4.5 Consensus size: 25
12709965 CTTGGTTATT
*
12709975 TAAAATATAATAT-AATAATATAATA
1 TAAAA-ATAATATAAATAATAAAATA
12710000 TAAAAATAATATAAATAA-AAAATA
1 TAAAAATAATATAAATAATAAAATA
*
12710024 TAAAAATAATAT-AAT-TTAAAAT-
1 TAAAAATAATATAAATAATAAAATA
*
12710046 TAAAAA-AATTATAAATAAATATAATA
1 TAAAAATAA-TATAAAT-AATAAAATA
*
12710072 -AAAAATTATAT
1 TAAAAATAATAT
12710083 TTTATATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.03
22 9 0.13
23 11 0.16
24 24 0.34
25 23 0.33
26 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
TAAAAATAATATAAATAATAAAATA
Found at i:12710021 original size:16 final size:16
Alignment explanation
Indices: 12709988--12710032 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
12709978 AATATAATAT
12709988 AATAATAT-AATATAAA
1 AATAATATAAATA-AAA
12710004 AATAATATAAATAAAA
1 AATAATATAAATAAAA
*
12710020 AAT-ATAAAAATAA
1 AATAATATAAATAA
12710033 TATAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.33
16 14 0.52
17 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAATATAAATAAAA
Found at i:12710067 original size:32 final size:32
Alignment explanation
Indices: 12710016--12710079 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
12710006 TAATATAAAT
**
12710016 AAAAAATATAAAAATAATATAATTTAAAATTA
1 AAAAAATATAAAAATAATATAATAAAAAATTA
*
12710048 AAAAAAT-TATAAATAAATATAATAAAAAATTA
1 AAAAAATATAAAAAT-AATATAATAAAAAATTA
12710080 TATTTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (32 bp):
AAAAAATATAAAAATAATATAATAAAAAATTA
Found at i:12710077 original size:16 final size:16
Alignment explanation
Indices: 12709976--12710077 Score: 52
Period size: 16 Copynumber: 6.3 Consensus size: 16
12709966 TTGGTTATTT
12709976 AAAATATAATATAATAA
1 AAAATA-AATATAATAA
*
12709993 TATAATATAAAAATAAT-A
1 -A-AA-ATAAATATAATAA
*
12710011 TAAATAAA-A-AATATA
1 AAAATAAATATAATA-A
*
12710026 AAAAT-AATATAATTTA
1 AAAATAAATATAA-TAA
* * *
12710042 AAATTAAA-AAAATTA
1 AAAATAAATATAATAA
*
12710057 TAAATAAATATAATAA
1 AAAATAAATATAATAA
12710073 AAAAT
1 AAAAT
12710078 TATATTTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
13 3 0.05
14 3 0.05
15 20 0.31
16 21 0.33
17 3 0.05
18 2 0.03
19 9 0.14
20 3 0.05
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAAATATAATAA
Found at i:12710503 original size:42 final size:42
Alignment explanation
Indices: 12710417--12710504 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
12710407 AATTATATAG
* * * * **
12710417 AATATTAAACTTTTAATTTTAATGATCATAATTTATTAACAA
1 AATACTAAAATTTTAATTTTAATAATCAAAATTTAAAAACAA
* *
12710459 AATACTAAAATTTTAATTTTGATAATCAAAATTTAAAAATAA
1 AATACTAAAATTTTAATTTTAATAATCAAAATTTAAAAACAA
12710501 AATA
1 AATA
12710505 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (42 bp):
AATACTAAAATTTTAATTTTAATAATCAAAATTTAAAAACAA
Found at i:12719501 original size:62 final size:62
Alignment explanation
Indices: 12719380--12719552 Score: 176
Period size: 62 Copynumber: 2.8 Consensus size: 62
12719370 AGAAAACACA
* * * *
12719380 TTTAATAATCCCTTATAAAAAATTGAA-GAAGATTATTGAAGGCG-TTTTTGGTCAAAAACG-C
1 TTTAATAATCCCTCATAAAAAATT-AAGGGA-ATTATTGAAAGCGTTTTTTGCTCAAAAACGTC
**
12719441 TTTTAATAATCTCCTCATAAAAAATTAAGGGAATTATTGAAAGCGTTTTTTGCT-TGAAACGTC
1 -TTTAATAATC-CCTCATAAAAAATTAAGGGAATTATTGAAAGCGTTTTTTGCTCAAAAACGTC
* * *
12719504 TTTAATAATCCTCTCATAAAAAATAGAAGGG-ATCATTAAAAGCGTTTTT
1 TTTAATAATCC-CTCATAAAAAAT-TAAGGGAATTATTGAAAGCGTTTTT
12719553 CGCAGAAATA
Statistics
Matches: 96, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
61 1 0.01
62 67 0.70
63 28 0.29
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (62 bp):
TTTAATAATCCCTCATAAAAAATTAAGGGAATTATTGAAAGCGTTTTTTGCTCAAAAACGTC
Found at i:12723938 original size:4 final size:4
Alignment explanation
Indices: 12723929--12723982 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
12723919 GAGTAAAACC
* *
12723929 TAAA TAAA T-AA TAAA T-AA TGAA TAAA TAAA TATAA -AAA TAAA CAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAAA
*
12723975 TAAG TAAA
1 TAAA TAAA
12723983 AAAAATAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
3 8 0.20
4 31 0.76
5 2 0.05
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:12723943 original size:11 final size:11
Alignment explanation
Indices: 12723929--12723970 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
12723919 GAGTAAAACC
12723929 TAAATAAATAA
1 TAAATAAATAA
12723940 TAAAT-AATGAA
1 TAAATAAAT-AA
12723951 TAAATAAATATA
1 TAAATAAATA-A
*
12723963 AAAATAAA
1 TAAATAAA
12723971 CAAATAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 3 0.11
11 13 0.48
12 11 0.41
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:12724851 original size:22 final size:22
Alignment explanation
Indices: 12724809--12724856 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
12724799 GCACACTTTT
* *
12724809 CAAAAGTTTTCAACTTGAAATC
1 CAAAAGTTTACAACTTAAAATC
* *
12724831 CAAAAGTTTACAATTTAAAATT
1 CAAAAGTTTACAACTTAAAATC
12724853 CAAA
1 CAAA
12724857 GATTTGCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (22 bp):
CAAAAGTTTACAACTTAAAATC
Found at i:12724873 original size:20 final size:20
Alignment explanation
Indices: 12724848--12724885 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12724838 TTACAATTTA
12724848 AAATTCAAAGATTTGCAATT
1 AAATTCAAAGATTTGCAATT
*
12724868 AAATTCAAAGGTTTGCAA
1 AAATTCAAAGATTTGCAA
12724886 AAGATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
AAATTCAAAGATTTGCAATT
Found at i:12724894 original size:19 final size:19
Alignment explanation
Indices: 12724848--12724895 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
12724838 TTACAATTTA
12724848 AAATTCAAAGATTTGCAATT
1 AAATTCAAAGATTTGCAA-T
*
12724868 AAATTCAAAGGTTTGCAA-
1 AAATTCAAAGATTTGCAAT
12724886 AAGATTCAAA
1 AA-ATTCAAA
12724896 ATTCATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 7 0.27
20 17 0.65
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.29
Consensus pattern (19 bp):
AAATTCAAAGATTTGCAAT
Found at i:12724907 original size:18 final size:17
Alignment explanation
Indices: 12724884--12725227 Score: 119
Period size: 18 Copynumber: 18.9 Consensus size: 17
12724874 AAAGGTTTGC
12724884 AAAAGATTCAAAATTCAT
1 AAAA-ATTCAAAATTCAT
*
12724902 AAAAGACTT-AAGATTCAT
1 AAAA-A-TTCAAAATTCAT
12724920 AAAAATTCAAAAGTTCGCA-
1 AAAAATTCAAAA-TT--CAT
*
12724939 AAAAATTCAAAATTCAC
1 AAAAATTCAAAATTCAT
* *
12724956 AAAAATTGAAAGGTTCAT
1 AAAAATTCAAA-ATTCAT
* * *
12724974 AAAGGACTCAAGATTTGCA-
1 AAA-AATTCAA-AATT-CAT
*
12724993 AAGAAATTCAAAAATTCAC
1 AA-AAATTC-AAAATTCAT
* *
12725012 AAAAGATTCAAGATTCGT
1 AAAA-ATTCAAAATTCAT
*
12725030 AAAAATTCAAAAATTCGT
1 AAAAATTC-AAAATTCAT
* *
12725048 AAAAAATC--ATTTGC--
1 AAAAATTCAAAATT-CAT
* * *
12725062 AAAGATGCAAAAATTCGT
1 AAAAATTC-AAAATTCAT
*
12725080 AAAAAATTCAAAATTCGT
1 -AAAAATTCAAAATTCAT
* *
12725098 AAATATTTAAAAATTCAT
1 AAA-AATTCAAAATTCAT
12725116 AAAAAATTCAAAATTCGCA-
1 -AAAAATTCAAAATT--CAT
*
12725135 AGATTCAAGGATTCAAAGATTCAC
1 A-A---AA--ATTCAAA-ATTCAT
* * *
12725159 AAACAATTCAAGATTTAC
1 AAA-AATTCAAAATTCAT
* *
12725177 AAGAATTCAAAATTCAC
1 AAAAATTCAAAATTCAT
12725194 AAAAATTCTAAAATTCAT
1 AAAAATTC-AAAATTCAT
*
12725212 AAAAGATTCAAGATTC
1 AAAA-ATTCAAAATTC
12725228 GCAAAAGAAA
Statistics
Matches: 252, Mismatches: 37, Indels: 74
0.69 0.10 0.20
Matches are distributed among these distances:
14 5 0.02
15 3 0.01
16 6 0.02
17 43 0.17
18 113 0.45
19 54 0.21
20 11 0.04
21 1 0.00
22 2 0.01
23 3 0.01
24 8 0.03
25 3 0.01
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAAATTCAAAATTCAT
Found at i:12724926 original size:54 final size:54
Alignment explanation
Indices: 12724868--12725040 Score: 190
Period size: 54 Copynumber: 3.2 Consensus size: 54
12724858 ATTTGCAATT
* *
12724868 AAATTCAAAGGTTTGCAAAAGATTCAAAATTCATAAAAGACTT-AAGATTCATAA
1 AAATTCAAAGGTTTGCAAAAAATTCAAAATTCACAAAAGA-TTAAAGATTCATAA
* * *
12724922 AAATTCAAAAGTTCGCAAAAAATTCAAAATTCACAAAA-ATTGAAAGGTTCATAA
1 AAATTCAAAGGTTTGCAAAAAATTCAAAATTCACAAAAGATT-AAAGATTCATAA
* * * * *
12724976 AGGACTC-AAGATTTGCAAAGAAATTCAAAAATTCACAAAAGATTCAAGATTCGTAA
1 A-AATTCAAAGGTTTGCAAA-AAATTC-AAAATTCACAAAAGATTAAAGATTCATAA
12725032 AAATTCAAA
1 AAATTCAAA
12725041 AATTCGTAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 54 0.56
55 12 0.12
56 25 0.26
57 3 0.03
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (54 bp):
AAATTCAAAGGTTTGCAAAAAATTCAAAATTCACAAAAGATTAAAGATTCATAA
Found at i:12724960 original size:36 final size:36
Alignment explanation
Indices: 12724883--12725222 Score: 149
Period size: 36 Copynumber: 9.3 Consensus size: 36
12724873 CAAAGGTTTG
* * *
12724883 CAAAAGATTC-AAAATTCATAAAAGACTT-AAGATTCA
1 CAAAA-ATTCAAAAATTCACAAAA-AATTCAAAATTCA
* * *
12724919 TAAAAATTCAAAAGTTCGCAAAAAATTCAAAATTCA
1 CAAAAATTCAAAAATTCACAAAAAATTCAAAATTCA
* ** * ** * *
12724955 CAAAAATTGAAAGGTTCATAAAGGACTCAAGATTTGCA
1 CAAAAATTCAAAAATTCACAAAAAATTCAA-AATT-CA
* * *
12724993 -AAGAAATTCAAAAATTCACAAAAGATTCAAGATTCG
1 CAA-AAATTCAAAAATTCACAAAAAATTCAAAATTCA
* ** **
12725029 TAAAAATTCAAAAATTCGTAAAAAA-TC---ATTTG
1 CAAAAATTCAAAAATTCACAAAAAATTCAAAATTCA
* * ** *
12725061 CAAAGATGCAAAAATTCGTAAAAAATTCAAAATTCG
1 CAAAAATTCAAAAATTCACAAAAAATTCAAAATTCA
* * * * *
12725097 TAAATATTTAAAAATTCATAAAAAATTCAAAATTCG
1 CAAAAATTCAAAAATTCACAAAAAATTCAAAATTCA
* * * *
12725133 CAAGATTCAAGGATTCAAAGATTCACAAACAATTCAAGATTTA
1 C-A-A---AA--ATTCAAAAATTCACAAAAAATTCAAAATTCA
*
12725176 CAAGAATTC-AAAATTCAC-AAAAATTCTAAAATTCA
1 CAAAAATTCAAAAATTCACAAAAAATTC-AAAATTCA
*
12725211 TAAAAGATTCAA
1 CAAAA-ATTCAA
12725223 GATTCGCAAA
Statistics
Matches: 231, Mismatches: 53, Indels: 39
0.72 0.16 0.12
Matches are distributed among these distances:
32 26 0.11
33 2 0.01
34 7 0.03
35 26 0.11
36 106 0.46
37 11 0.05
38 25 0.11
41 2 0.01
42 1 0.00
43 25 0.11
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (36 bp):
CAAAAATTCAAAAATTCACAAAAAATTCAAAATTCA
Found at i:12725021 original size:74 final size:72
Alignment explanation
Indices: 12724897--12725036 Score: 174
Period size: 74 Copynumber: 1.9 Consensus size: 72
12724887 AGATTCAAAA
* * *
12724897 TTCATAAAAGACTTAAGATTCATAAAAATTCAAAAGTTCGCAAAAAATTCAAAATTCACAAAAAT
1 TTCATAAAAGACTCAAGATTCATAAAAATTCAAAAATTCACAAAAAATTCAAAATTCACAAAAAT
12724962 TGAAAGG
66 TGAAAGG
* * * **
12724969 TTCATAAAGGACTCAAGATTTGCA-AAGAAATTCAAAAATTCACAAAAGATTCAAGATTCGTAAA
1 TTCATAAAAGACTCAAGA-TT-CATAA-AAATTCAAAAATTCACAAAAAATTCAAAATTCACAAA
12725033 AATT
63 AATT
12725037 CAAAAATTCG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
72 16 0.28
73 4 0.07
74 37 0.65
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.26
Consensus pattern (72 bp):
TTCATAAAAGACTCAAGATTCATAAAAATTCAAAAATTCACAAAAAATTCAAAATTCACAAAAAT
TGAAAGG
Found at i:12725097 original size:68 final size:69
Alignment explanation
Indices: 12724927--12725122 Score: 187
Period size: 68 Copynumber: 2.8 Consensus size: 69
12724917 CATAAAAATT
* * ** * ** * *
12724927 CAAAAGTTCGCAAAAAATTCAAAATTCACAAAAATTGAAAGGTTCATAAAGGACTCAAGATTTGC
1 CAAAAATTCACAAAAAATTCAAAATTCGTAAAAATTCAAAAATTCATAAA-AAATC---ATTTGC
*
12724992 AAAGAAATT
62 AAAG-AATG
* * *
12725001 CAAAAATTCACAAAAGATTCAAGATTCGTAAAAATTCAAAAATTCGTAAAAAATCATTTGCAAAG
1 CAAAAATTCACAAAAAATTCAAAATTCGTAAAAATTCAAAAATTCATAAAAAATCATTTGCAAAG
12725066 -ATG
66 AATG
** * *
12725069 CAAAAATTCGTAAAAAATTCAAAATTCGTAAATATTTAAAAATTCATAAAAAAT
1 CAAAAATTCACAAAAAATTCAAAATTCGTAAAAATTCAAAAATTCATAAAAAAT
12725123 TCAAAATTCG
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
68 49 0.48
70 10 0.10
73 3 0.03
74 40 0.39
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.26
Consensus pattern (69 bp):
CAAAAATTCACAAAAAATTCAAAATTCGTAAAAATTCAAAAATTCATAAAAAATCATTTGCAAAG
AATG
Found at i:12725192 original size:43 final size:43
Alignment explanation
Indices: 12725110--12725192 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 43
12725100 ATATTTAAAA
* * *
12725110 ATTCATAAAAAATTCAAAATTCGCAAGATTCAAGGATTCAAAG
1 ATTCACAAAAAATTCAAAATTCACAAGATTCAAGAATTCAAAG
* * *
12725153 ATTCACAAACAATTCAAGATTTACAAGAATTCAA-AATTCA
1 ATTCACAAAAAATTCAAAATTCACAAG-ATTCAAGAATTCA
12725193 CAAAAATTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
43 27 0.82
44 6 0.18
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (43 bp):
ATTCACAAAAAATTCAAAATTCACAAGATTCAAGAATTCAAAG
Found at i:12725931 original size:34 final size:34
Alignment explanation
Indices: 12725887--12725952 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
12725877 AAGATTAATG
* *
12725887 TCACCTATCACCACATTTTCACATGGGACTCCAC
1 TCACCGATCACCACATGTTCACATGGGACTCCAC
12725921 TCACCGATCACCACATGTTCACATGGGACTCC
1 TCACCGATCACCACATGTTCACATGGGACTCC
12725953 GCTGCTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.26, C:0.38, G:0.12, T:0.24
Consensus pattern (34 bp):
TCACCGATCACCACATGTTCACATGGGACTCCAC
Found at i:12727920 original size:59 final size:58
Alignment explanation
Indices: 12727860--12728246 Score: 440
Period size: 59 Copynumber: 6.5 Consensus size: 58
12727850 TTGCGTAGGA
* * *
12727860 AAAATTGATACTTTCAACTTTTCTCAAAAAATATTCTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCTCAAAAAATATTCTTTTGAAAATTTATTTTCAAGG
* * * *
12727918 AAAATTGATACTTTCGACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTT-CTCAAAAA-ATATTCTTTTGAAAATTTATTTTCAAGG
* * * * *
12727978 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGT
1 AAAATTGATACTTTCAACTTTTCTCAAAAAATA-TTCTTTTGAAAATTTATTTTCAAGG
* * * *
12728037 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCTCAAAAAATATTCTTTTGAAAATTT-ATTTTCAAGG
* * *
12728096 AAAATTGATACGTTT-AACTTTTCCTCAAAAACCT-TTTTTTTGAAAATTTATTTTTTAAGG
1 AAAATTGATAC-TTTCAACTTTT-CTCAAAAA-ATATTCTTTTGAAAATTTA-TTTTCAAGG
* *
12728156 AAAATTGATACTTTCAACTTTT-TCCCAAAAATATTC-TTTGAAAACTTTGATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTCT-CAAAAAATATTCTTTTGAAAA-TTT-ATTTTCAAGG
*
12728215 AAAATTGATACTTTCAACTTTTCCCCAAAAAA
1 AAAATTGATACTTTCAACTTTT-CTCAAAAAA
12728247 ATATATTTTT
Statistics
Matches: 283, Mismatches: 31, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
58 45 0.16
59 140 0.49
60 97 0.34
61 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCTCAAAAAATATTCTTTTGAAAATTTATTTTCAAGG
Found at i:12727980 original size:17 final size:16
Alignment explanation
Indices: 12727945--12727983 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12727935 CTTTTCCTCA
**
12727945 AAAATTTATTTTTTTG
1 AAAATTTATTTTTAGG
12727961 AAAATTTATTTTTAAGG
1 AAAATTTATTTTT-AGG
12727978 AAAATT
1 AAAATT
12727984 GATACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
AAAATTTATTTTTAGG
Found at i:12728042 original size:119 final size:117
Alignment explanation
Indices: 12727860--12728245 Score: 510
Period size: 119 Copynumber: 3.3 Consensus size: 117
12727850 TTGCGTAGGA
* * * * * **
12727860 AAAATTGATACTTTCAACTTTTCTCAAAAAATA-TTCTTTTGAAACTTTAATTTCGAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGAAAATT
* *
12727924 GATACTTTCGACTTTTCCTCAAAAATTTATTTTTTTGAAAATTT-ATTTTTAAGG
66 GATACTTTCAACTTTTCC-CAAAAA--TATTTTTTTGAAAATTTGATTTTCAAGG
*
12727978 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGTAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGAAAATT
* * *
12728043 GATACTTTCAACTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAAGG
66 GATACTTTCAACTTTT-CCCAAAAATATTTTTTTGAAAATTTGATTTTCAAGG
* **
12728096 AAAATTGATACGTTT-AACTTTTCCTCAAAAACCTTTTTTTTGAAAATTTATTTTTTAAGGAAAA
1 AAAATTGATAC-TTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTA-TTTTTAAGGAAAA
* *
12728160 TTGATACTTTCAACTTTTTCCCAAAAATA-TTCTTTGAAAACTTTGATTTTCAAAG
64 TTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTGAAAA-TTTGATTTTCAAGG
12728215 AAAATTGATACTTTCAACTTTTCCCCAAAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAA
12728246 AATATATTTT
Statistics
Matches: 237, Mismatches: 23, Indels: 15
0.86 0.08 0.05
Matches are distributed among these distances:
117 14 0.06
118 93 0.39
119 124 0.52
120 6 0.03
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (117 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGAAAATT
GATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAAATTTGATTTTCAAGG
Found at i:12728185 original size:178 final size:177
Alignment explanation
Indices: 12727860--12728245 Score: 584
Period size: 178 Copynumber: 2.2 Consensus size: 177
12727850 TTGCGTAGGA
* * * *
12727860 AAAATTGATACTTTCAACTTTTCTCAAAAAATATTCTTTTGAAACTTTAATTTCGAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGGAAACTTTAATTTCAAGGAAAATTG
* **
12727925 ATACTTTCGACTTTTCCTCAAAAATTTATTTTTTTGAAAATTTATTTTTAAGGAAAATTGATACT
66 ATACTTTCAACTTTTCCTCAAAAACCTATTTTTTTGAAAATTTATTTTTAAGGAAAATTGATACT
* *
12727990 TTCAACTTTTCCCCAAAAATATTTTTTTTGAAAA-TTT-ATTTT-TAAG
131 TTCAACTTTTCCCCAAAAATA--TTCTTTGAAAACTTTGATTTTCAAAG
*
12728036 TAAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAAGGAAAAT
1 -AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGGAAACTTT-AATTTCAAGGAAAAT
12728101 TGATACGTTT-AACTTTTCCTCAAAAACCT-TTTTTTTGAAAATTTATTTTTTAAGGAAAATTGA
64 TGATAC-TTTCAACTTTTCCTCAAAAACCTATTTTTTTGAAAATTTA-TTTTTAAGGAAAATTGA
*
12728164 TACTTTCAACTTTTTCCCAAAAATATTCTTTGAAAACTTTGATTTTCAAAG
127 TACTTTCAACTTTTCCCCAAAAATATTCTTTGAAAACTTTGATTTTCAAAG
12728215 AAAATTGATACTTTCAACTTTTCCCCAAAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAA
12728246 AATATATTTT
Statistics
Matches: 192, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
176 10 0.05
177 64 0.33
178 112 0.58
179 6 0.03
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (177 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGGAAACTTTAATTTCAAGGAAAATTG
ATACTTTCAACTTTTCCTCAAAAACCTATTTTTTTGAAAATTTATTTTTAAGGAAAATTGATACT
TTCAACTTTTCCCCAAAAATATTCTTTGAAAACTTTGATTTTCAAAG
Found at i:12728293 original size:5 final size:5
Alignment explanation
Indices: 12728282--12728355 Score: 71
Period size: 5 Copynumber: 14.4 Consensus size: 5
12728272 AAAATAGAAT
* * *
12728282 AATAA AACAA AATAA AAGAA AA-AA AATAA AATAA AA-AA AAGTAA AACAAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA-TAA AA-TAA
12728332 AATAAA AATAA AATAA AGATAA AA
1 AAT-AA AATAA AATAA A-ATAA AA
12728356 AGAATATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
4 8 0.14
5 32 0.55
6 18 0.31
ACGTcount: A:0.81, C:0.03, G:0.04, T:0.12
Consensus pattern (5 bp):
AATAA
Found at i:12728309 original size:14 final size:14
Alignment explanation
Indices: 12728268--12728333 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
12728258 ATTTTTATTT
*
12728268 AAAGAAAATAGAATA
1 AAAGAAAA-AAAATA
* *
12728283 ATA-AAACAAAATA
1 AAAGAAAAAAAATA
12728296 AAAGAAAAAAAATA
1 AAAGAAAAAAAATA
*
12728310 AAATAAAAAAAAGTA
1 AAAGAAAAAAAA-TA
*
12728325 AAACAAAAA
1 AAAGAAAAA
12728334 TAAAAATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
13 7 0.17
14 23 0.55
15 12 0.29
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (14 bp):
AAAGAAAAAAAATA
Found at i:12728309 original size:27 final size:26
Alignment explanation
Indices: 12728268--12728355 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 26
12728258 ATTTTTATTT
*
12728268 AAAGAAAATAGAATAATAAAACAAAATA
1 AAAGAAAA-AAAATAATAAAA-AAAATA
12728296 AAAGAAAAAAAATAAAATAAAAAAAAGTA
1 AAAGAAAAAAAAT--AATAAAAAAAA-TA
*
12728325 AAACAAAAATAAA-AATAAAATAAAGATA
1 AAAGAAAAA-AAATAATAAAA-AAA-ATA
12728353 AAA
1 AAA
12728356 AGAATATTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
27 11 0.21
28 20 0.38
29 18 0.35
30 3 0.06
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (26 bp):
AAAGAAAAAAAATAATAAAAAAAATA
Found at i:12728312 original size:19 final size:18
Alignment explanation
Indices: 12728285--12728344 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
12728275 ATAGAATAAT
12728285 AAAACAAAATAAAAGAAAA
1 AAAACAAAATAAAA-AAAA
*
12728304 AAAATAAAATAAAAAAAA
1 AAAACAAAATAAAAAAAA
12728322 GTAAAACAAAAATAAAAATAAA
1 --AAAAC-AAAATAAAAA-AAA
12728344 A
1 A
12728345 TAAAGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 4 0.11
19 13 0.37
20 5 0.14
21 10 0.29
22 3 0.09
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.10
Consensus pattern (18 bp):
AAAACAAAATAAAAAAAA
Found at i:12728317 original size:11 final size:11
Alignment explanation
Indices: 12728303--12728355 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
12728293 ATAAAAGAAA
12728303 AAAAATAAAAT
1 AAAAATAAAAT
*
12728314 AAAAA-AAAGT
1 AAAAATAAAAT
12728324 AAAACA-AAAAT
1 AAAA-ATAAAAT
12728335 AAAAATAAAAT
1 AAAAATAAAAT
*
12728346 AAAGATAAAA
1 AAAAATAAAA
12728356 AGAATATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 9 0.24
11 28 0.76
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:12728367 original size:27 final size:25
Alignment explanation
Indices: 12728267--12728370 Score: 79
Period size: 27 Copynumber: 4.0 Consensus size: 25
12728257 TATTTTTATT
* *
12728267 TAAAGAAAATAGAATAATAAAACAAAA
1 TAAAGAAAA-AAAAT-ATAAAATAAAA
12728294 TAAA-AGAAAAAAA-ATAAAATAAAA
1 TAAAGA-AAAAAAATATAAAATAAAA
*
12728318 AAAAGTAAAACAAAA-ATAAAAATAAAA
1 TAAAG-AAAA-AAAATAT-AAAATAAAA
*
12728345 TAAAGATAAAAAGAATATTAAATAAA
1 TAAAGA-AAAAA-AATATAAAATAAA
12728371 CCTAATCTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
24 13 0.20
25 3 0.05
26 14 0.22
27 32 0.50
28 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (25 bp):
TAAAGAAAAAAAATATAAAATAAAA
Found at i:12729322 original size:6 final size:6
Alignment explanation
Indices: 12729311--12729400 Score: 51
Period size: 6 Copynumber: 14.5 Consensus size: 6
12729301 TTATAAGATA
* * * *
12729311 AAAAAT AAAAAT AAAAAT AACAGAT AAATAT GAGATAAAT AAAAAT ACATAT
1 AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT -A-A-AAAT AAAAAT AAAAAT
* *
12729363 -AAAAT -AAAAT GAAAAAA AAGAAAA AAAAAT -AAAAT AAA
1 AAAAAT AAAAAT -AAAAAT AA-AAAT AAAAAT AAAAAT AAA
12729401 GAAAGGGAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 13 0.19
6 32 0.48
7 17 0.25
8 2 0.03
9 3 0.04
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:12729495 original size:25 final size:25
Alignment explanation
Indices: 12729444--12729516 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
12729434 ATAAATAAAT
* ** *
12729444 AATAAATACATAGGATATAAAGGAA
1 AATATATACATAAAATATAAAAGAA
*
12729469 AATATATACATAAAATATAAAATAA
1 AATATATACATAAAATATAAAAGAA
12729494 AA-ATA-AC--AAAATATAAAACGAA
1 AATATATACATAAAATATAAAA-GAA
12729516 A
1 A
12729517 TTGGGCTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
21 11 0.27
22 3 0.07
23 2 0.05
24 3 0.07
25 22 0.54
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (25 bp):
AATATATACATAAAATATAAAAGAA
Found at i:12729703 original size:40 final size:40
Alignment explanation
Indices: 12729593--12729745 Score: 261
Period size: 41 Copynumber: 3.8 Consensus size: 40
12729583 GCCCCTCTTT
**
12729593 GCACCACGACTTTGAAAAGTAAATTGCTTTTCTAAACAGAG
1 GCACCACGACTTTGAAAA-TAAATTGCTCCTCTAAACAGAG
12729634 GCACCACGACTTTGGAAAATAAATTGCTCCTCTAAACAGAG
1 GCACCACGACTTT-GAAAATAAATTGCTCCTCTAAACAGAG
12729675 GCACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAG
1 GCACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAG
12729715 GCACCACGACTTTGAAAAATAAATTGCTCCT
1 GCACCACGACTTTG-AAAATAAATTGCTCCT
12729746 TGACAATTAT
Statistics
Matches: 108, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
40 41 0.38
41 62 0.57
42 5 0.05
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (40 bp):
GCACCACGACTTTGAAAATAAATTGCTCCTCTAAACAGAG
Found at i:12729734 original size:81 final size:82
Alignment explanation
Indices: 12729593--12729745 Score: 272
Period size: 81 Copynumber: 1.9 Consensus size: 82
12729583 GCCCCTCTTT
** *
12729593 GCACCACGACTTTGAAAAGTAAATTGCTTTTCTAAACAGAGGCACCACGACTTTGGAAAATAAAT
1 GCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAAT
12729658 TGCTCCTCTAAACAGAG
66 TGCTCCTCTAAACAGAG
12729675 GCACCACGACTTTGAAAA-TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAAT
1 GCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAAT
12729739 TGCTCCT
66 TGCTCCT
12729746 TGACAATTAT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
81 50 0.74
82 18 0.26
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (82 bp):
GCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAAT
TGCTCCTCTAAACAGAG
Found at i:12730763 original size:16 final size:16
Alignment explanation
Indices: 12730742--12730826 Score: 54
Period size: 17 Copynumber: 5.3 Consensus size: 16
12730732 AGTCCTCCTG
12730742 TTTCATTCATTTTTTT
1 TTTCATTCATTTTTTT
12730758 TTTCATTATCATTTTTTT
1 TTTCA-T-TCATTTTTTT
*
12730776 ATTT--TTTA-TTTTTT
1 -TTTCATTCATTTTTTT
*
12730790 TTT-ATT-TTTTTATTT
1 TTTCATTCATTTT-TTT
**
12730805 TTTCATTTTTTTATTTT
1 TTTCATTCATTT-TTTT
12730822 TTTCA
1 TTTCA
12730827 AGCATAGTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
13 3 0.05
14 11 0.19
15 8 0.14
16 9 0.16
17 13 0.22
18 11 0.19
19 3 0.05
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCATTCATTTTTTT
Found at i:12730781 original size:8 final size:8
Alignment explanation
Indices: 12730768--12730824 Score: 87
Period size: 8 Copynumber: 7.0 Consensus size: 8
12730758 TTTCATTATC
12730768 ATTTTTTT
1 ATTTTTTT
12730776 ATTTTTTAT
1 ATTTTTT-T
*
12730785 TTTTTTTT
1 ATTTTTTT
12730793 ATTTTTTT
1 ATTTTTTT
*
12730801 ATTTTTTC
1 ATTTTTTT
12730809 ATTTTTTT
1 ATTTTTTT
12730817 ATTTTTTT
1 ATTTTTTT
12730825 CAAGCATAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
8 37 0.84
9 7 0.16
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.86
Consensus pattern (8 bp):
ATTTTTTT
Found at i:12730782 original size:7 final size:7
Alignment explanation
Indices: 12730770--12730823 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
12730760 TCATTATCAT
12730770 TTTTTTA
1 TTTTTTA
12730777 TTTTTTA
1 TTTTTTA
12730784 -TTTTT-
1 TTTTTTA
*
12730789 TTTTAT-
1 TTTTTTA
12730795 TTTTTTA
1 TTTTTTA
12730802 TTTTTTCA
1 TTTTTT-A
12730810 TTTTTTTA
1 -TTTTTTA
12730818 TTTTTT
1 TTTTTT
12730824 TCAAGCATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 14 0.34
7 19 0.46
8 2 0.05
9 6 0.15
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:12730787 original size:33 final size:34
Alignment explanation
Indices: 12730750--12730824 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
12730740 TGTTTCATTC
*
12730750 ATTTTTTTTT-TCATTATCATTTTTTTA-TTTTTT
1 ATTTTTTTTTAT-ATTATCATTTTTTCATTTTTTT
* * *
12730783 ATTTTTTTTTATTTTTTTATTTTTTCATTTTTTT
1 ATTTTTTTTTATATTATCATTTTTTCATTTTTTT
12730817 ATTTTTTT
1 ATTTTTTT
12730825 CAAGCATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 21 0.58
34 15 0.42
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (34 bp):
ATTTTTTTTTATATTATCATTTTTTCATTTTTTT
Found at i:12733995 original size:501 final size:501
Alignment explanation
Indices: 12733053--12734047 Score: 1882
Period size: 501 Copynumber: 2.0 Consensus size: 501
12733043 ATTATTTAGT
*
12733053 AAAAGAAAAAGGGTTGAAGTATTAGATAAAAGGAAAACCTACCTATCGTGAAACAGAAAGAAAAT
1 AAAAGAAAAAGGGTTGAAGTATTAGATAAAAAGAAAACCTACCTATCGTGAAACAGAAAGAAAAT
12733118 AGAGTTCTTCTTCTTCATCTTCTTTAGGGTTAGAGAATATGAAAAATCAAGTTGGAGATTCACAA
66 AGAGTTCTTCTTCTTCATCTTCTTTAGGGTTAGAGAATATGAAAAATCAAGTTGGAGATTCACAA
12733183 TCAGAAGCTACAATCAAGTTAATCCCTTAAAGGTGAGTACATGCCCTCTTTTTATTTAAGAATAA
131 TCAGAAGCTACAATCAAGTTAATCCCTTAAAGGTGAGTACATGCCCTCTTTTTATTTAAGAATAA
12733248 ATATCAAGTTGATTGTTATTATTTGGAGTTGAAGTTTTGAGAGAAAAATCAAGAAAAATCATGAA
196 ATATCAAGTTGATTGTTATTATTTGGAGTTGAAGTTTTGAGAGAAAAATCAAGAAAAATCATGAA
*
12733313 ATCCTTCATTAATCTTGATGATATATATGGGTAAATTATTGGGCTTTGTTTATTTCATGTTCTTA
261 ATCCTTCATTAATCTTGATGATATATATGGGTAAATTATTGGGATTTGTTTATTTCATGTTCTTA
12733378 AGAGTTATTGATGATTATTGAATAGAGTTTGAAGGCTGAAAGTAAGGATTTGAGTTTTTAAAGAT
326 AGAGTTATTGATGATTATTGAATAGAGTTTGAAGGCTGAAAGTAAGGATTTGAGTTTTTAAAGAT
* *
12733443 TGAAGGAGAAATTCTATTTTTGGATGAGATGTTGTGATCTGTAATAATGAATTAAAATAGAATTT
391 TGAAGGAGAAATTCTATTTTTGGATGAGATGTTATGATCTATAATAATGAATTAAAATAGAATTT
12733508 TGTATTAATGGATAGATTATTACTGTGATTATTATATATCATCAGA
456 TGTATTAATGGATAGATTATTACTGTGATTATTATATATCATCAGA
* *
12733554 AAAAGAAAAAGGGTTGAAGTATTAGATAAAAAGAAAACCTACCTATCGTGAAATAGAAAGGAAAT
1 AAAAGAAAAAGGGTTGAAGTATTAGATAAAAAGAAAACCTACCTATCGTGAAACAGAAAGAAAAT
* *
12733619 AGAGTTCTTCTTCTTTATCTTTTTTAGGGTTAGAGAATATGAAAAATCAAGTTGGAGATTCACAA
66 AGAGTTCTTCTTCTTCATCTTCTTTAGGGTTAGAGAATATGAAAAATCAAGTTGGAGATTCACAA
* *
12733684 TCAGAAGCTATAATCAAGTTAATCCCTTAAAGGTGAGTACATGCCTTCTTTTTATTTAAGAATAA
131 TCAGAAGCTACAATCAAGTTAATCCCTTAAAGGTGAGTACATGCCCTCTTTTTATTTAAGAATAA
12733749 ATATCAAGTTGATTGTTATTATTTGGAGTTGAAGTTTTGAGAGAAAAATCAAGAAAAATCATGAA
196 ATATCAAGTTGATTGTTATTATTTGGAGTTGAAGTTTTGAGAGAAAAATCAAGAAAAATCATGAA
*
12733814 ATCCTTCATTAATCTTGATGATATATATGGGTAAATTATTGGGATTTGTTTATTTGATGTTCTTA
261 ATCCTTCATTAATCTTGATGATATATATGGGTAAATTATTGGGATTTGTTTATTTCATGTTCTTA
12733879 AGAGTTATTGATGATTATTGAATAGAGTTTGAAGGCTGAAAGTAAGGATTTGAGTTTTTAAAGAT
326 AGAGTTATTGATGATTATTGAATAGAGTTTGAAGGCTGAAAGTAAGGATTTGAGTTTTTAAAGAT
12733944 TGAAGGAGAAATTCTATTTTTGGATGAGATGTTATGATCTATAATAATGAATTAAAATAGAATTT
391 TGAAGGAGAAATTCTATTTTTGGATGAGATGTTATGATCTATAATAATGAATTAAAATAGAATTT
*
12734009 TGTATTAATGGATAGATTATTGCTGTGATTATTATATAT
456 TGTATTAATGGATAGATTATTACTGTGATTATTATATAT
12734048 TATTGGAAAG
Statistics
Matches: 482, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
501 482 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (501 bp):
AAAAGAAAAAGGGTTGAAGTATTAGATAAAAAGAAAACCTACCTATCGTGAAACAGAAAGAAAAT
AGAGTTCTTCTTCTTCATCTTCTTTAGGGTTAGAGAATATGAAAAATCAAGTTGGAGATTCACAA
TCAGAAGCTACAATCAAGTTAATCCCTTAAAGGTGAGTACATGCCCTCTTTTTATTTAAGAATAA
ATATCAAGTTGATTGTTATTATTTGGAGTTGAAGTTTTGAGAGAAAAATCAAGAAAAATCATGAA
ATCCTTCATTAATCTTGATGATATATATGGGTAAATTATTGGGATTTGTTTATTTCATGTTCTTA
AGAGTTATTGATGATTATTGAATAGAGTTTGAAGGCTGAAAGTAAGGATTTGAGTTTTTAAAGAT
TGAAGGAGAAATTCTATTTTTGGATGAGATGTTATGATCTATAATAATGAATTAAAATAGAATTT
TGTATTAATGGATAGATTATTACTGTGATTATTATATATCATCAGA
Found at i:12735107 original size:19 final size:16
Alignment explanation
Indices: 12735068--12735100 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12735058 AACGATTTGA
12735068 ATGATAATGATGATTT
1 ATGATAATGATGATTT
12735084 ATGATAATGATGATTT
1 ATGATAATGATGATTT
12735100 A
1 A
12735101 CGATGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:12738981 original size:16 final size:16
Alignment explanation
Indices: 12738962--12738992 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12738952 TCAAGATTAT
*
12738962 TTTATCTTTCTCTTTC
1 TTTAGCTTTCTCTTTC
12738978 TTTAGCTTTCTCTTT
1 TTTAGCTTTCTCTTT
12738993 TCTAGCCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.23, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTAGCTTTCTCTTTC
Found at i:12744634 original size:60 final size:57
Alignment explanation
Indices: 12744504--12745134 Score: 685
Period size: 60 Copynumber: 10.7 Consensus size: 57
12744494 TATGACAGGA
* * * * **
12744504 AAAATTGATACTTTCAACTTTTCC-CAAAAAATATTCTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAAT-TTTTTTTAAAAATTTATTTTTAAGG
*
12744562 AAAATTGATACTTTCGACTTCTT-CTCAAAAATTTATTTTTTTAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTT-TTCCTCAAAAA--T-TTTTTTTAAAAATTTATTTTTAAGG
* * *
12744622 AAAATTGATACTTTTAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAA-ATTTTTTTTAAAAATTTATTTTTAAGG
* * * * * * *
12744681 AAAATTGATACTTTCAATTTTTCCCCAAAAATATTCTTTGAAAACTTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTTAAAAATTT-ATTTTTAAGG
** *
12744740 AAAATTGATAAGTTCAACTTTTCTTCAAAAACCTTTTTTTTAAAAATTTATTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TTTTTTTTAAAAATTTA-TTTTTAAGG
* * ** * *
12744800 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTTAAAAATTT-ATTTTTAAGG
* * * *
12744859 -AAATTGATACTTTCAACTTTTCCTCAAAAATATTCTTTGAAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTTAAAAATTT-ATTTTTAAGG
* *
12744917 AAAATTGATACTTTCAACTTTTCTTCAAAAACCTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TTTTTTTTAAAAATTTATTTTTAAGG
* *
12744976 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA---TTTTTTTTAAAAATTTATTTTTAAGG
12745036 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTAAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TTTTTTTT-AAAAATTTATTTTTAAGG
*
12745096 AAAATTGATACTTTCAATTTTTCC-CAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTT
12745135 TATTTTTATT
Statistics
Matches: 500, Mismatches: 53, Indels: 40
0.84 0.09 0.07
Matches are distributed among these distances:
57 3 0.01
58 104 0.21
59 190 0.38
60 196 0.39
61 6 0.01
62 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTAAAAATTTATTTTTAAGG
Found at i:12744686 original size:59 final size:59
Alignment explanation
Indices: 12744504--12745135 Score: 755
Period size: 59 Copynumber: 10.7 Consensus size: 59
12744494 TATGACAGGA
* * * **
12744504 AAAATTGATACTTTCAACTTTTCC-CAAAAA-ATATTCTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTTGAAAATTTATTTTTAAGG
* * *
12744562 AAAATTGATACTTTCGACTTCTT-CTCAAAAATTTATTTTTTTAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTT-TTCCTCAAAAATAT-TTTTTTTGAAAATTTATTTTTAAGG
* *
12744622 AAAATTGATACTTTTAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
* * * * *
12744681 AAAATTGATACTTTCAATTTTTCCCCAAAAATA--TTCTTTGAAAACTTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAA-TTT-ATTTTTAAGG
** * ** *
12744740 AAAATTGATAAGTTCAACTTTTCTTCAAAAACCTTTTTTTTAAAAATTTATTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTA-TTTTTAAGG
* * * * *
12744800 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTCTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTT-ATTTTTAAGG
* *
12744859 -AAATTGATACTTTCAACTTTTCCTCAAAAATA--TTCTTTGAAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAA-TTT-ATTTTTAAGG
* **
12744917 AAAATTGATACTTTCAACTTTTCTTCAAAAACCTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
*
12744976 AAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTTGAAAATTTATTTTTAAGG
** *
12745036 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTAAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTT-GAAAATTTATTTTTAAGG
*
12745096 AAAATTGATACTTTCAATTTTTCC-CAAAAATATTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTT
12745136 ATTTTTATTT
Statistics
Matches: 497, Mismatches: 59, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
57 17 0.03
58 68 0.14
59 209 0.42
60 184 0.37
61 19 0.04
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
Found at i:12744865 original size:177 final size:173
Alignment explanation
Indices: 12744505--12745136 Score: 843
Period size: 177 Copynumber: 3.6 Consensus size: 173
12744495 ATGACAGGAA
* * *
12744505 AAATTGATACTTTCAACTTTTCCCAAAAAATATTCTTTTG-AAACTTTAATTTCGAGGAAAATTG
1 AAATTGATACTTTCAACTTTTCCCCAAAAATATTC-TTTGAAAACTTTATTTTCAAGGAAAATTG
* **
12744569 ATACTTTCGACTTCTTCTCAAAAATTTATTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACT
65 ATACTTTCAACTT-TTCTCAAAAACCT-TTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACT
*
12744634 TTTAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
128 TTCAACTTTTCCCCAAAAATA-TTTTTTTGAAAATTTATTTTTAAGG
* *
12744681 AAAATTGATACTTTCAATTTTTCCCCAAAAATATTCTTTGAAAACTTTGATTTTCAAGAAAAATT
1 -AAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGAAAACTTT-ATTTTCAAGGAAAATT
**
12744746 GATAAGTTCAACTTTTCTTCAAAAACCTTTTTTTTAAAAATTTATTTTTTAAGGAAAATTGATAC
64 GATACTTTCAACTTTTC-TCAAAAACCTTTTTTTTAAAAATTTA-TTTTTAAGGAAAATTGATAC
* * * *
12744811 TTTCAACTTTTCCCCAAAAATATTCTTTGGAAACTTTGATTTTCAAGG
127 TTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTT-ATTTTTAAGG
*
12744859 AAATTGATACTTTCAACTTTTCCTCAAAAATATTCTTTGAAAACTTTGATTTTCAAGGAAAATTG
1 AAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGAAAACTTT-ATTTTCAAGGAAAATTG
*
12744924 ATACTTTCAACTTTTCTTCAAAAACCTTTTTTTTGAAAATTTATTTTTAAGGAAAATTGATACTT
65 ATACTTTCAACTTTTC-TCAAAAACCTTTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACTT
* * *
12744989 TCAACTTTTCCTCAAAAACCTTTTTTTTTGAAAATTTATTTTTAAGAA
129 TCAACTTTTCCCCAAAAA--TATTTTTTTGAAAATTTATTTTTAAG-G
* * * * * *
12745037 AAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTAAAAAATTTATTTTTAAGGAAAATT
1 AAATTGATACTTTCAACTTTTCCCCAAAAA--TATTCTTTGAAAACTTTATTTTCAAGGAAAATT
* * **
12745102 GATACTTTCAATTTTTCCCAAAAATATTTTTTTTA
64 GATACTTTCAACTTTTCTCAAAAACCTTTTTTTTA
12745137 TTTTTATTTA
Statistics
Matches: 407, Mismatches: 38, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
176 43 0.11
177 181 0.44
178 139 0.34
179 31 0.08
180 13 0.03
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (173 bp):
AAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTGAAAACTTTATTTTCAAGGAAAATTGA
TACTTTCAACTTTTCTCAAAAACCTTTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTC
AACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
Found at i:12745218 original size:11 final size:11
Alignment explanation
Indices: 12745150--12745229 Score: 78
Period size: 11 Copynumber: 7.4 Consensus size: 11
12745140 TTATTTAAAG
12745150 AAAATAGAATAAT
1 AAAATA-AA-AAT
*
12745163 AAAA-CAAAAT
1 AAAATAAAAAT
12745173 AAAAT-AAAAT
1 AAAATAAAAAT
12745183 AAAATAAAAA-
1 AAAATAAAAAT
*
12745193 AAAGTAAAACA-
1 AAAATAAAA-AT
12745204 AAAATAAAAAT
1 AAAATAAAAAT
*
12745215 AAAATAAAGAT
1 AAAATAAAAAT
12745226 AAAA
1 AAAA
12745230 AGAATATTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
10 26 0.44
11 29 0.49
13 4 0.07
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:12745227 original size:6 final size:5
Alignment explanation
Indices: 12745160--12745229 Score: 79
Period size: 5 Copynumber: 13.4 Consensus size: 5
12745150 AAAATAGAAT
* *
12745160 AATAA AACAA AATAA AATAA AATAA AATAA AA-AA AAGTAA AACAAA AATAAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA-TAA AA-TAA AAT-AA
12745212 AATAA AATAA AGATAA AA
1 AATAA AATAA A-ATAA AA
12745230 AGAATATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
4 4 0.07
5 34 0.61
6 18 0.32
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:12745274 original size:8 final size:8
Alignment explanation
Indices: 12745261--12745289 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12745251 CTAATAAATA
12745261 AAATAAAC
1 AAATAAAC
12745269 AAATAAAC
1 AAATAAAC
12745277 AAATAAAC
1 AAATAAAC
12745285 AAATA
1 AAATA
12745290 TAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATAAAC
Found at i:12746394 original size:13 final size:12
Alignment explanation
Indices: 12746376--12746419 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
12746366 GATATAAAAG
12746376 AAAATATATACAT
1 AAAATATA-ACAT
*
12746389 AAAATATAAAAT
1 AAAATATAACAT
12746401 AAAA-ATAACA-
1 AAAATATAACAT
12746411 AAAATATAA
1 AAAATATAA
12746420 AACAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.14
11 9 0.32
12 7 0.25
13 8 0.29
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATATAACAT
Found at i:12746417 original size:22 final size:25
Alignment explanation
Indices: 12746353--12746427 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
12746343 ATAAATAAAT
* ** *
12746353 AATAAATACATAGGATATAAAAGAA
1 AATATATACATAAAATATAAAACAA
*
12746378 AATATATACATAAAATATAAAATAA
1 AATATATACATAAAATATAAAACAA
12746403 AA-ATA-ACA-AAAATATAAAACAA
1 AATATATACATAAAATATAAAACAA
12746425 AAT
1 AAT
12746428 TGGGCTTACC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 15 0.34
23 3 0.07
24 3 0.07
25 23 0.52
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.21
Consensus pattern (25 bp):
AATATATACATAAAATATAAAACAA
Found at i:12748608 original size:6 final size:6
Alignment explanation
Indices: 12748597--12748640 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
12748587 TTTTATTAAT
*
12748597 ATATAA ATATAA ATATAA CTATAA ATATAA ATATATA AT-TAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA-A ATATAA AT
12748641 GAAATAATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
5 3 0.09
6 29 0.83
7 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:12749091 original size:23 final size:24
Alignment explanation
Indices: 12749065--12749110 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12749055 TTATGAATTA
*
12749065 AAAAAAAACTAAAAAAA-AAAAAG
1 AAAAAAAACCAAAAAAAGAAAAAG
*
12749088 AAAAAAGACCAAAAAAAGAAAAA
1 AAAAAAAACCAAAAAAAGAAAAA
12749111 AATTCGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.02
Consensus pattern (24 bp):
AAAAAAAACCAAAAAAAGAAAAAG
Found at i:12749190 original size:17 final size:18
Alignment explanation
Indices: 12749165--12749198 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12749155 ATTATCAAAT
*
12749165 TAAAGAAAAAGA-AAAAG
1 TAAAAAAAAAGATAAAAG
12749182 TAAAAAAAAAGATAAAA
1 TAAAAAAAAAGATAAAA
12749199 ACATATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (18 bp):
TAAAAAAAAAGATAAAAG
Found at i:12749816 original size:2 final size:2
Alignment explanation
Indices: 12749809--12749839 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12749799 GTAATAAACA
12749809 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 A
12749840 AATCAAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12750718 original size:3 final size:3
Alignment explanation
Indices: 12750693--12750740 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
12750683 ATCGTTACCA
* * * * *
12750693 TCT TCC TCT TCT CCT CCT CCT TCT TCT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12750741 CCACATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:12753823 original size:19 final size:19
Alignment explanation
Indices: 12753799--12753836 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12753789 AAACTGCATG
12753799 TATCTCTAACTAGAGTTAT
1 TATCTCTAACTAGAGTTAT
12753818 TATCTCTAACTAGAGTTAT
1 TATCTCTAACTAGAGTTAT
12753837 AGTCAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
TATCTCTAACTAGAGTTAT
Found at i:12756002 original size:16 final size:14
Alignment explanation
Indices: 12755968--12755999 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12755958 AATATTTAAA
12755968 ATTATAAATTCATC
1 ATTATAAATTCATC
12755982 ATTATAAATT-ATC
1 ATTATAAATTCATC
12755995 ATTAT
1 ATTAT
12756000 TATTATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATAAATTCATC
Found at i:12758548 original size:26 final size:26
Alignment explanation
Indices: 12758498--12758549 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12758488 GACATAAAAA
*
12758498 TAATAAAATAAAATAATTTAAATTTT
1 TAATAAAATAAAATAATATAAATTTT
*
12758524 TAATAAAATTAAAAT-ATATATATTTT
1 TAATAAAA-TAAAATAATATAAATTTT
12758550 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TAATAAAATAAAATAATATAAATTTT
Found at i:12759769 original size:14 final size:14
Alignment explanation
Indices: 12759750--12759791 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
12759740 ATATTATTTG
12759750 ATAATTTAAAATAA
1 ATAATTTAAAATAA
* *
12759764 ATAATTAAAAAT-T
1 ATAATTTAAAATAA
12759777 ATATATTTAAAATAA
1 ATA-ATTTAAAATAA
12759792 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATTTAAAATAA
Found at i:12761255 original size:13 final size:13
Alignment explanation
Indices: 12761237--12761264 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12761227 AAAGTAAAAA
12761237 AATTTTAAAATAT
1 AATTTTAAAATAT
12761250 AATTTTAAAATAT
1 AATTTTAAAATAT
12761263 AA
1 AA
12761265 AAAATAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTTTAAAATAT
Found at i:12762578 original size:25 final size:26
Alignment explanation
Indices: 12762532--12762580 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
12762522 AAATTTAAAG
* *
12762532 AAAATTTATCACTTAGAGATTTCTTA
1 AAAATTTACCACTTAGAAATTTCTTA
*
12762558 AAAATTTACCA-TTTGAAATTTCT
1 AAAATTTACCACTTAGAAATTTCT
12762581 AAGAATCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (26 bp):
AAAATTTACCACTTAGAAATTTCTTA
Found at i:12762815 original size:16 final size:16
Alignment explanation
Indices: 12762796--12762832 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12762786 AAAATTTTTA
* *
12762796 TTTTTATTTTTTTTGT
1 TTTTTATTTTTCTTCT
12762812 TTTTTATTTTTCTTCT
1 TTTTTATTTTTCTTCT
12762828 TTTTT
1 TTTTT
12762833 TTGTTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.05, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTATTTTTCTTCT
Found at i:12762818 original size:22 final size:23
Alignment explanation
Indices: 12762790--12762832 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
12762780 AATTCCAAAA
12762790 TTTTTATTTTTATT-TTTTTTGT
1 TTTTTATTTTTATTCTTTTTTGT
*
12762812 TTTTTATTTTTCTTCTTTTTT
1 TTTTTATTTTTATTCTTTTTT
12762833 TTGTTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.07, C:0.05, G:0.02, T:0.86
Consensus pattern (23 bp):
TTTTTATTTTTATTCTTTTTTGT
Found at i:12763455 original size:14 final size:14
Alignment explanation
Indices: 12763436--12763471 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
12763426 TATATATCCA
12763436 AAAATAAACCATAT
1 AAAATAAACCATAT
12763450 AAAATACAAACCATAT
1 AAAAT--AAACCATAT
12763466 AAAATA
1 AAAATA
12763472 CAAAACTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
16 14 0.70
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAACCATAT
Found at i:12763462 original size:16 final size:16
Alignment explanation
Indices: 12763441--12763475 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12763431 ATCCAAAAAT
12763441 AAACCATATAAAATAC
1 AAACCATATAAAATAC
12763457 AAACCATATAAAATAC
1 AAACCATATAAAATAC
12763473 AAA
1 AAA
12763476 ACTGCCTCTT
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:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (16 bp):
AAACCATATAAAATAC
Found at i:12765640 original size:24 final size:21
Alignment explanation
Indices: 12765593--12765640 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 21
12765583 TTTCATCAGA
12765593 TTTCCTTTTCCTCTCTCTCTC
1 TTTCCTTTTCCTCTCTCTCTC
*
12765614 TTTCCTTTTTTCTCTCATTCTCTC
1 TTTCC-TTTTCCTCTC--TCTCTC
12765638 TTT
1 TTT
12765641 AAAACCCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 9 0.39
24 9 0.39
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTCCTTTTCCTCTCTCTCTC
Found at i:12766396 original size:42 final size:42
Alignment explanation
Indices: 12766350--12766451 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
12766340 GAGGCAAAGT
*
12766350 AACTTTGAAAAAATAAATTACTCATCTAAACAAAGGTACCAC
1 AACTTTGAAAAAATAAATTACTCATCTAAACAAAGGCACCAC
* * * * *
12766392 AACTTTGGAAAAATAAATTGCTCCTCTAAATAAAGGCACTAC
1 AACTTTGAAAAAATAAATTACTCATCTAAACAAAGGCACCAC
* *
12766434 AACTTTGAGAAATTAAAT
1 AACTTTGAAAAAATAAAT
12766452 GCTCCTCGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (42 bp):
AACTTTGAAAAAATAAATTACTCATCTAAACAAAGGCACCAC
Found at i:12767069 original size:22 final size:22
Alignment explanation
Indices: 12766996--12767078 Score: 105
Period size: 22 Copynumber: 3.7 Consensus size: 22
12766986 CTCAAAGGTT
*
12766996 CTCAAAGATTTTCATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
* *
12767018 TGTCTTAAAGATTCTCATTT-AAGA
1 ---CTCAAAGATTCTCATTTGAAAA
12767042 CTCAAAGATTCTCATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
12767064 CTCAAAGATTCTCAT
1 CTCAAAGATTCTCAT
12767079 CAAAGATTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.31
22 18 0.35
24 3 0.06
25 15 0.29
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
CTCAAAGATTCTCATTTGAAAA
Found at i:12767672 original size:64 final size:64
Alignment explanation
Indices: 12767602--12767756 Score: 211
Period size: 64 Copynumber: 2.4 Consensus size: 64
12767592 CATAGGTTTT
* * *
12767602 TCAGCACTAGCTATTTCAGAATAAATTATGTATTTTGATCATTTGATTATCATTCACAAGCTTC
1 TCAGCACTAGCCATTTCAGAATAAATTATGTATTTTGATCATTTAATTACCATTCACAAGCTTC
* * * *
12767666 TCAGCACTAGCCATTTTAGAATAAATTTTGTCTTTTGATCATTTAATTACCATTCACCAGCTTC
1 TCAGCACTAGCCATTTCAGAATAAATTATGTATTTTGATCATTTAATTACCATTCACAAGCTTC
* * * *
12767730 TCAGCATTAACCATTCCAGAATGAATT
1 TCAGCACTAGCCATTTCAGAATAAATT
12767757 TCGTCTACTG
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (64 bp):
TCAGCACTAGCCATTTCAGAATAAATTATGTATTTTGATCATTTAATTACCATTCACAAGCTTC
Found at i:12768353 original size:26 final size:26
Alignment explanation
Indices: 12768324--12768398 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 26
12768314 AATTTGAGTC
*
12768324 TTTTTTTTTTCTTTTTCAATTTTT-A
1 TTTTTTTTTTCTTTTTCATTTTTTCA
*
12768349 -TTTTTTTTTCTTGTTTCATTTTTTCC
1 TTTTTTTTTTCTT-TTTCATTTTTTCA
12768375 TTTTTTTTATT-TTTTTCATTTTTT
1 TTTTTTTT-TTCTTTTTCATTTTTT
12768399 TCCTTTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 12 0.27
25 10 0.23
26 11 0.25
27 9 0.20
28 2 0.05
ACGTcount: A:0.08, C:0.09, G:0.01, T:0.81
Consensus pattern (26 bp):
TTTTTTTTTTCTTTTTCATTTTTTCA
Found at i:12768355 original size:9 final size:9
Alignment explanation
Indices: 12768351--12768405 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
12768341 AATTTTTATT
12768351 TTTTTTTC-
1 TTTTTTTCA
*
12768359 TTGT-TTCA
1 TTTTTTTCA
*
12768367 -TTTTTTCC
1 TTTTTTTCA
*
12768375 TTTTTTTTA
1 TTTTTTTCA
12768384 TTTTTTTCA
1 TTTTTTTCA
*
12768393 TTTTTTTCC
1 TTTTTTTCA
12768402 TTTT
1 TTTT
12768406 ATTATTGATA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 5 0.14
8 6 0.16
9 26 0.70
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:12768405 original size:26 final size:26
Alignment explanation
Indices: 12768323--12768411 Score: 78
Period size: 26 Copynumber: 3.4 Consensus size: 26
12768313 TAATTTGAGT
*
12768323 CTTTTTTTTTTCTTTTTCAATTTTTATT-
1 CTTTTTTTATT-TTTTTC-ATTTTT-TTC
* *
12768351 -TTTTTTT-CTTGTTTCATTT-TTTC
1 CTTTTTTTATTTTTTTCATTTTTTTC
12768374 CTTTTTTTTATTTTTTTCATTTTTTTC
1 C-TTTTTTTATTTTTTTCATTTTTTTC
*
12768401 CTTTTATTATT
1 CTTTTTTTATT
12768412 GATATCTCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
22 2 0.04
23 1 0.02
24 4 0.08
25 12 0.24
26 20 0.39
27 12 0.24
ACGTcount: A:0.09, C:0.11, G:0.01, T:0.79
Consensus pattern (26 bp):
CTTTTTTTATTTTTTTCATTTTTTTC
Found at i:12769955 original size:18 final size:18
Alignment explanation
Indices: 12769932--12769966 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12769922 TTAGTAGATT
12769932 TAAGAAA-AATAAAAATAG
1 TAAGAAAGAA-AAAAATAG
12769950 TAAGAAAGAAAAAAATA
1 TAAGAAAGAAAAAAATA
12769967 TGGCTTTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (18 bp):
TAAGAAAGAAAAAAATAG
Found at i:12778504 original size:15 final size:16
Alignment explanation
Indices: 12778486--12778521 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
12778476 AATTTCAAAA
*
12778486 TTTTTATTTTT-TTGT
1 TTTTTATTTTTCTTCT
12778501 TTTTTATTTTTCTTCT
1 TTTTTATTTTTCTTCT
12778517 TTTTT
1 TTTTT
12778522 TGTTTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTATTTTTCTTCT
Found at i:12778756 original size:16 final size:16
Alignment explanation
Indices: 12778735--12778765 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12778725 TTAATCATGA
12778735 AAGGAAAAAAAAAACT
1 AAGGAAAAAAAAAACT
*
12778751 AAGGAAAAAACAAAC
1 AAGGAAAAAAAAAAC
12778766 ACATAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.13, T:0.03
Consensus pattern (16 bp):
AAGGAAAAAAAAAACT
Found at i:12778814 original size:25 final size:23
Alignment explanation
Indices: 12778768--12778822 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
12778758 AAACAAACAC
* *
12778768 ATAAATAAAATACTAAATAAAATAA
1 ATAAA-AAAATACCAAAGAAAA-AA
12778793 ATAAAAAAATTACCAAAGAAAAAA
1 ATAAAAAAA-TACCAAAGAAAAAA
12778817 ATAAAA
1 ATAAAA
12778823 GAATGGCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (23 bp):
ATAAAAAAATACCAAAGAAAAAA
Found at i:12780492 original size:141 final size:140
Alignment explanation
Indices: 12780238--12780521 Score: 523
Period size: 141 Copynumber: 2.0 Consensus size: 140
12780228 GGCATGAATG
12780238 AATGAATGGCTTAAATTACATTGGAAAATGTGACACTGACCCCTGCAATGTTGCTCAGCCTTGGG
1 AATGAATGGCTTAAATTACATTGGAAAATGTGACACTGACCCCTGCAATGTTGCTCAGCCTTGGG
12780303 GAACTAGTACCCCCCATCACGAACGAATGAAATTTCACTGGTCCCTCCACAAAGCTGGGGTGGAT
66 GAACTAGTACCCCCCATCACGAACGAATGAAATTTCACTGGTCCCTCCACAAAGCTGGGGTGGAT
12780368 TTTTGTTTGCT
131 TTTTG-TTGCT
*
12780379 AATGAATGGCTTAAATTACATTGGAAAATGTGACACTGACCCTTGCAATGTTGCTCAGCCTTGGG
1 AATGAATGGCTTAAATTACATTGGAAAATGTGACACTGACCCCTGCAATGTTGCTCAGCCTTGGG
* * *
12780444 GGAGTAGTACCCCCCATCACGAACGAATGAAATTTCACTGGTCGCTCCACAAAGCTGGGGTGGAT
66 GAACTAGTACCCCCCATCACGAACGAATGAAATTTCACTGGTCCCTCCACAAAGCTGGGGTGGAT
12780509 TTTTGTTGCT
131 TTTTGTTGCT
12780519 AAT
1 AAT
12780522 CACTAAAATG
Statistics
Matches: 139, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
140 8 0.06
141 131 0.94
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (140 bp):
AATGAATGGCTTAAATTACATTGGAAAATGTGACACTGACCCCTGCAATGTTGCTCAGCCTTGGG
GAACTAGTACCCCCCATCACGAACGAATGAAATTTCACTGGTCCCTCCACAAAGCTGGGGTGGAT
TTTTGTTGCT
Found at i:12789281 original size:3 final size:3
Alignment explanation
Indices: 12789275--12789313 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
12789265 ATCGTCATCA
*
12789275 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12789314 CGACAGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:12793064 original size:6 final size:7
Alignment explanation
Indices: 12793046--12793072 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12793036 TAATAGAAGC
12793046 ATTTTTT
1 ATTTTTT
12793053 ATTTTTT
1 ATTTTTT
12793060 ATTTTTT
1 ATTTTTT
12793067 ATTTTT
1 ATTTTT
12793073 GTTTTAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:12795161 original size:210 final size:211
Alignment explanation
Indices: 12794791--12795257 Score: 726
Period size: 210 Copynumber: 2.2 Consensus size: 211
12794781 CGGAGTTCCA
* * *
12794791 AGCAAGCTTAAACATTTGAATTTAAGAGGCTGCAAAAGTCTTAGGAGTTTTTCAACCAAAATAAT
1 AGCAGGCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTA-GAGTTTTCCAACC-AAATAAT
* ** * *
12794856 TGGAATGAAATCTCTTGAGCATTTAATTCTTTCAGATTGCTCAAAATTTGAAAGGTTTCCAGAGA
64 TGGAATGAAATCTCTTGAGAAAGTAATTCTTTCAGACTGCTCAAAATTTCAAAGGTTTCCAGAGA
* *
12794921 TTGATGGAGAAATGGAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCT
129 TTGATGGACAAATGGAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCC
12794986 TCTTCAATTGGACATCTC
194 TCTTCAATTGGACATCTC
12795004 AGCAGGCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGA-TCTCTTCCAACC-AA-AAT
1 AGCAGGCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGAGT-T-TTCCAACCAAATAAT
* * * *
12795066 TGGAATGGAATCTCTTGATAAAGTAATTCTTTCAGGCTGCTC-AAATCTTCAAAGGTTTCCAGTG
64 TGGAATGAAATCTCTTGAGAAAGTAATTCTTTCAGACTGCTCAAAAT-TTCAAAGGTTTCCAGAG
12795130 ATTGATGGACAAATGGAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCC
128 ATTGATGGACAAATGGAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCC
12795195 CTCTTCAATTGGACATCTC
193 CTCTTCAATTGGACATCTC
*
12795214 AGCAGGCTTAAACTTCTGAATTTAAGAGGCTGCAAAAGTCTTAG
1 AGCAGGCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAG
12795258 GAATTTGCTT
Statistics
Matches: 236, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
209 4 0.02
210 178 0.75
211 3 0.01
212 3 0.01
213 48 0.20
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (211 bp):
AGCAGGCTTAAACTTTTGAATTTAAGAGGCTGCAAAAGTCTTAGAGTTTTCCAACCAAATAATTG
GAATGAAATCTCTTGAGAAAGTAATTCTTTCAGACTGCTCAAAATTTCAAAGGTTTCCAGAGATT
GATGGACAAATGGAATGTTTGCAGGAGCTTCATTTAGATGGAACAGGCATTGAAGAACTTCCCTC
TTCAATTGGACATCTC
Found at i:12797277 original size:2 final size:2
Alignment explanation
Indices: 12797272--12797314 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
12797262 AAAAATATTT
*
12797272 TA TA TA TA TT TA TA TA TA TA TA 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
12797314 T
1 T
12797315 GAAGCATGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12804535 original size:14 final size:14
Alignment explanation
Indices: 12804512--12804546 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12804502 ATCTATCATA
*
12804512 ATAGAAATCCTACC
1 ATAGATATCCTACC
12804526 ATAGATATCCTACC
1 ATAGATATCCTACC
12804540 ATAGATA
1 ATAGATA
12804547 CAGCATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (14 bp):
ATAGATATCCTACC
Found at i:12806403 original size:23 final size:23
Alignment explanation
Indices: 12806364--12806415 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
12806354 TCAAATGATT
**
12806364 TTTATTTTTTAAATTAATTTTTA
1 TTTATTTTTTAAATTAATTTAAA
*
12806387 TTTA-TTTTTATACTTAATTTAAA
1 TTTATTTTTTA-AATTAATTTAAA
12806410 TTTATT
1 TTTATT
12806416 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 6 0.25
23 17 0.71
24 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTATTTTTTAAATTAATTTAAA
Found at i:12815572 original size:41 final size:41
Alignment explanation
Indices: 12815509--12815590 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
12815499 ATTATAACAT
* *
12815509 ATAATTTTTATATAAAATATAATACAAATACATAAATTTTA
1 ATAATTTATATATAAAACATAATACAAATACATAAATTTTA
** *
12815550 ATAATTTATATA-ATAAACATAATATGAATATATAAATTTTA
1 ATAATTTATATATA-AAACATAATACAAATACATAAATTTTA
12815591 TAGGCTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 34 0.97
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (41 bp):
ATAATTTATATATAAAACATAATACAAATACATAAATTTTA
Found at i:12815627 original size:13 final size:13
Alignment explanation
Indices: 12815611--12815640 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12815601 TTAAATTGAG
12815611 TTTTTA-TTTTTA
1 TTTTTACTTTTTA
12815623 TTTTTACTTTTTA
1 TTTTTACTTTTTA
12815636 TTTTT
1 TTTTT
12815641 TAATAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTACTTTTTA
Found at i:12815642 original size:7 final size:6
Alignment explanation
Indices: 12815611--12815640 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
12815601 TTAAATTGAG
12815611 TTTTTA TTTTTA TTTTTA CTTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTT
12815641 TAATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:12816042 original size:20 final size:19
Alignment explanation
Indices: 12816017--12816060 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
12816007 TCGAATCAAA
*
12816017 TTATATATTTTTATTAATTT
1 TTATATATTTTT-TAAATTT
12816037 TTATATATTTTTTAAATTT
1 TTATATATTTTTTAAATTT
12816056 TTATA
1 TTATA
12816061 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATATTTTTTAAATTT
Found at i:12816064 original size:11 final size:10
Alignment explanation
Indices: 12816017--12816062 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
12816007 TCGAATCAAA
*
12816017 TTATATATTT
1 TTATAAATTT
*
12816027 TTATTAATTT
1 TTATAAATTT
*
12816037 TTATATATTT
1 TTATAAATTT
12816047 TT-TAAATTT
1 TTATAAATTT
12816056 TTATAAA
1 TTATAAA
12816063 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATAAATTT
Found at i:12816131 original size:13 final size:12
Alignment explanation
Indices: 12816096--12816134 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12816086 AAATCTATTT
12816096 AAATATATTAAA
1 AAATATATTAAA
* *
12816108 AATTTTATTAAA
1 AAATATATTAAA
12816120 ATAATATATTAAA
1 A-AATATATTAAA
12816133 AA
1 AA
12816135 CAAAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATATTAAA
Found at i:12816563 original size:18 final size:19
Alignment explanation
Indices: 12816541--12816592 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
12816531 TTTAAATTTT
12816541 TATATTAATATAAATTATAA
1 TATA-TAATATAAATTATAA
***
12816561 TATATAAT-TTTTTTATAA
1 TATATAATATAAATTATAA
*
12816579 AATATAATATAAAT
1 TATATAATATAAAT
12816593 ATATCAATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
18 14 0.58
19 6 0.25
20 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATAATATAAATTATAA
Found at i:12816572 original size:31 final size:33
Alignment explanation
Indices: 12816535--12816609 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 33
12816525 ATATATTTTA
*
12816535 AATTTTTATATTAATATA-AAT-TATAATATAT-
1 AATTTTTATATTAAAATATAATATA-AATATATC
*
12816566 AATTTTTTTA-TAAAATATAATATAAATATATC
1 AATTTTTATATTAAAATATAATATAAATATATC
*
12816598 AATTTTAATATT
1 AATTTTTATATT
12816610 TTATTATGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 6 0.17
31 19 0.53
32 10 0.28
33 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (33 bp):
AATTTTTATATTAAAATATAATATAAATATATC
Found at i:12816583 original size:32 final size:33
Alignment explanation
Indices: 12816537--12816603 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
12816527 ATATTTTAAA
*
12816537 TTTTTATATTAATATAA-ATTATAATATAT-AATT
1 TTTTTATATAAATATAATA-TA-AATATATCAATT
12816570 TTTTTATA-AAATATAATATAAATATATCAATT
1 TTTTTATATAAATATAATATAAATATATCAATT
12816602 TT
1 TT
12816604 AATATTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 7 0.23
32 15 0.48
33 9 0.29
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
TTTTTATATAAATATAATATAAATATATCAATT
Found at i:12824879 original size:21 final size:22
Alignment explanation
Indices: 12824855--12824897 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
12824845 TATATATTTA
12824855 TATTTGTATTCC-TAG-ATTAAG
1 TATTTGTA-TCCTTAGAATTAAG
12824876 TATTTGTATCCTTAGAATTAAG
1 TATTTGTATCCTTAGAATTAAG
12824898 AACAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 11 0.55
22 6 0.30
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (22 bp):
TATTTGTATCCTTAGAATTAAG
Found at i:12825071 original size:24 final size:26
Alignment explanation
Indices: 12825043--12825093 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
12825033 ATACATTTAA
12825043 TTTTA-CTCTTAATTTTTC-ATATAG
1 TTTTATCTCTTAATTTTTCTATATAG
* *
12825067 TTTTATTTTTTAATTTTTCTATATAG
1 TTTTATCTCTTAATTTTTCTATATAG
12825093 T
1 T
12825094 ATCAGAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 11 0.48
26 7 0.30
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTATCTCTTAATTTTTCTATATAG
Found at i:12832528 original size:52 final size:52
Alignment explanation
Indices: 12832426--12832530 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
12832416 TGGACAAGAA
* * *
12832426 GACTTGCAAAAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAGATAAGTTT
1 GACTTGCAAAAGAAAAATTCTAAAAGAAAGAGGATTCTTAATAGACAAGTTT
* * * *
12832478 GACTTGCAAGAGAAAAATTTTAAAAAGAAAG-GGATTCTTAATGGGCAAGTTT
1 GACTTGCAAAAGAAAAATTCT-AAAAGAAAGAGGATTCTTAATAGACAAGTTT
12832530 G
1 G
12832531 TATGGTTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 37 0.82
53 8 0.18
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.27
Consensus pattern (52 bp):
GACTTGCAAAAGAAAAATTCTAAAAGAAAGAGGATTCTTAATAGACAAGTTT
Done.