Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 7 of 204
Found at i:2672793 original size:42 final size:42
Alignment explanation
Indices: 2672747--2672878 Score: 117
Period size: 42 Copynumber: 3.1 Consensus size: 42
2672737 TGGTGAAGGC
2672747 GGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGTGGAGAT
1 GGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGTGGAGAT
* * * * **** * *
2672789 GGAGGAGACGAGGCAATAGT--A-GTTGAAAAGGGTGGTGAAAAT
1 GGAGGA-A-GTGG-AGTACTACACATTGGTGGGGGTGGTGGAGAT
*
2672831 GGAGGAAGTGGAGTACTACACATTGGTGGAGGTGGTGGAGAT
1 GGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGTGGAGAT
2672873 GGAGGA
1 GGAGGA
2672879 GACGAGGCAA
Statistics
Matches: 63, Mismatches: 21, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
39 4 0.06
40 3 0.05
41 2 0.03
42 45 0.71
43 2 0.03
44 3 0.05
45 4 0.06
ACGTcount: A:0.30, C:0.06, G:0.45, T:0.19
Consensus pattern (42 bp):
GGAGGAAGTGGAGTACTACACATTGGTGGGGGTGGTGGAGAT
Found at i:2672906 original size:42 final size:42
Alignment explanation
Indices: 2672777--2672909 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 42
2672767 CATTGGTGGG
*
2672777 GGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAG
1 GGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAA
* * * * * * ****
2672819 GGTGGTGAAAATGGAGGA-A-GTGG-AGTACTACACATTGGTGGA
1 GGTGGTGGAGATGGAGGAGACGAGGCAATAGT--A-GTTGAAAAA
2672861 GGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAA
1 GGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAA
2672903 GGTGGTG
1 GGTGGTG
2672910 AGGTTAGAGG
Statistics
Matches: 64, Mismatches: 21, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
39 4 0.06
40 3 0.05
41 2 0.03
42 46 0.72
43 2 0.03
44 3 0.05
45 4 0.06
ACGTcount: A:0.32, C:0.05, G:0.44, T:0.19
Consensus pattern (42 bp):
GGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAA
Found at i:2672949 original size:84 final size:83
Alignment explanation
Indices: 2672776--2673041 Score: 248
Period size: 84 Copynumber: 3.1 Consensus size: 83
2672766 ACATTGGTGG
*** *
2672776 GGGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAGGGTGGTGAAAATGGAGGAAGTG
1 GGGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAGGGTGGTGAGGTTAGAGGAAGTG
** * **
2672841 GAGTAC-TACACATTGGTG-
66 G-G-ACATAGTCGTTGAAGA
*
2672859 GAGGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAAGGTGGTGAGGTTAGAGGAAGT
1 G-GGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAGGGTGGTGAGGTTAGAGGAAGT
2672924 GGGACAGTAGTCGTTGAAGA
65 GGGACA-TAGTCGTTGAAGA
* * * * * * *
2672944 GGGTGGTGAAGGTGGAGGAGGATGTGGGGCAATAGTTGCTGAAAAGGGTGGTGAAGGTGGAGGAG
1 GGGTGGTGGAGATGGAGGA-GA--CGAGGCAATAGTAGTTGAAAAGGGTGGTG-AGGT-TA-GAG
*
2673009 GAAGTGGGACACTAGTTGTTGAAGA
60 GAAGTGGGACA-TAGTCGTTGAAGA
*
2673034 GGATGGTG
1 GGGTGGTG
2673042 AAGGCGGAGA
Statistics
Matches: 152, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
82 2 0.01
83 2 0.01
84 83 0.55
85 3 0.02
87 24 0.16
88 4 0.03
89 1 0.01
90 33 0.22
ACGTcount: A:0.29, C:0.05, G:0.46, T:0.20
Consensus pattern (83 bp):
GGGTGGTGGAGATGGAGGAGACGAGGCAATAGTAGTTGAAAAGGGTGGTGAGGTTAGAGGAAGTG
GGACATAGTCGTTGAAGA
Found at i:2672992 original size:45 final size:45
Alignment explanation
Indices: 2672886--2673190 Score: 199
Period size: 45 Copynumber: 6.8 Consensus size: 45
2672876 GGAGACGAGG
* * *
2672886 CAATAGTAGTTGAAAAAGGTGGTG-AGGT-TA-GAGGAAGTGGGA
1 CAATAGTTGTTGAAAAGGGTGGTGAAGGTGGAGGAGGAAGTGGGA
* * * * *
2672928 CAGTAGTCGTTGAAGAGGGTGGTGAAGGTGGAGGAGGATGTGGGG
1 CAATAGTTGTTGAAAAGGGTGGTGAAGGTGGAGGAGGAAGTGGGA
*
2672973 CAATAGTTGCTGAAAAGGGTGGTGAAGGTGGAGGAGGAAGTGGGA
1 CAATAGTTGTTGAAAAGGGTGGTGAAGGTGGAGGAGGAAGTGGGA
* * * * * *
2673018 CACTAGTTGTTGAAGAGGATGGTGAAGGCGGAGAAGGAA-TTGGA
1 CAATAGTTGTTGAAAAGGGTGGTGAAGGTGGAGGAGGAAGTGGGA
* * * ** * ** * *
2673062 GCACTAGATG-TCAATTGGGGAGGTAGAGATGAAGGTGGAGGAGGTGGGA
1 -CAATAGTTGTTGAA-AAGGGTGGT-GA-A-GGTGGAGGAGGAAGTGGGA
* ** * * ** *
2673111 CACTAGTCATTGAAAAGGATGGTGAAGGTAGAAAAGGAAGTGGGG
1 CAATAGTTGTTGAAAAGGGTGGTGAAGGTGGAGGAGGAAGTGGGA
* *
2673156 CAATAGTCG-TCAAAGAGGGTGGTGAAGGTGGAGGA
1 CAATAGTTGTTGAAA-AGGGTGGTGAAGGTGGAGGA
2673191 AGTAGGGCAT
Statistics
Matches: 197, Mismatches: 55, Indels: 19
0.73 0.20 0.07
Matches are distributed among these distances:
42 20 0.10
43 4 0.02
44 12 0.06
45 129 0.65
46 3 0.02
47 3 0.02
48 19 0.10
49 7 0.04
ACGTcount: A:0.31, C:0.06, G:0.44, T:0.19
Consensus pattern (45 bp):
CAATAGTTGTTGAAAAGGGTGGTGAAGGTGGAGGAGGAAGTGGGA
Found at i:2673579 original size:48 final size:45
Alignment explanation
Indices: 2673484--2673579 Score: 102
Period size: 48 Copynumber: 2.1 Consensus size: 45
2673474 GGGGTGCTGA
* * ** * *
2673484 AGGTGGAGGAGGGAGGGCACTAGACATCAATGGGGGTTGTGATGG
1 AGGTGGAGGAGGAAGGGCACTACACATCAATAAGGGTGGTGAAGG
*
2673529 AGGTGGAGGAGGAATTGTGGCACTACAGATCAATAAGGGTGGTGAAGG
1 AGGTGGAGGAGGAA--G-GGCACTACACATCAATAAGGGTGGTGAAGG
2673577 AGG
1 AGG
2673580 AATTGAGGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
45 13 0.32
47 1 0.02
48 27 0.66
ACGTcount: A:0.28, C:0.08, G:0.46, T:0.18
Consensus pattern (45 bp):
AGGTGGAGGAGGAAGGGCACTACACATCAATAAGGGTGGTGAAGG
Found at i:2674625 original size:54 final size:54
Alignment explanation
Indices: 2674543--2674654 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
2674533 TTGGAGAGCC
* *
2674543 TGAAGGCTTTGTAAGGTCAACCTTCTGACCTTTTTGCTCGGATGAAAAATCCTT
1 TGAAGGCTTTGTAACGTCAACCTTCTGACATTTTTGCTCGGATGAAAAATCCTT
* * * *
2674597 TGAAGTCTTTGTATCGTCAACCTTCTGACATTTTTGCTTGGATGAAACATCCTT
1 TGAAGGCTTTGTAACGTCAACCTTCTGACATTTTTGCTCGGATGAAAAATCCTT
2674651 TGAA
1 TGAA
2674655 ATCACAGCTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (54 bp):
TGAAGGCTTTGTAACGTCAACCTTCTGACATTTTTGCTCGGATGAAAAATCCTT
Found at i:2675426 original size:93 final size:93
Alignment explanation
Indices: 2675293--2675573 Score: 463
Period size: 93 Copynumber: 3.0 Consensus size: 93
2675283 CTTGAATTCT
*
2675293 ATGGGGATCTACATCTTCCCTCAAGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGAC
1 ATGGGGATCTACATCCTCCCTCAAGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGAC
* *
2675358 TGTCATAATCCACCTTTCCATCCAGTGC
66 TGTCGTAATCCACCTTTCCATCCAGCGC
** *
2675386 ATGGGGATCTACATCCTCCCTTGAGATATCTTTCTGCTCTGGCTTGTTTTCATGGACTATCTGAC
1 ATGGGGATCTACATCCTCCCTCAAGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGAC
* **
2675451 TGTTGTAATCCACCTTTCCATCCAGCAA
66 TGTCGTAATCCACCTTTCCATCCAGCGC
* *
2675479 ATGGGAATCTACATCCTCTCTCAAGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGAC
1 ATGGGGATCTACATCCTCCCTCAAGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGAC
2675544 TGTCGTAATCCACCTTTCCATCCAGCGC
66 TGTCGTAATCCACCTTTCCATCCAGCGC
2675572 AT
1 AT
2675574 CGACTTTTCC
Statistics
Matches: 171, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 171 1.00
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (93 bp):
ATGGGGATCTACATCCTCCCTCAAGATATCTTTCTGCTCTGGCTTGTTTTCATGAACTATCTGAC
TGTCGTAATCCACCTTTCCATCCAGCGC
Found at i:2675582 original size:21 final size:21
Alignment explanation
Indices: 2675555--2675619 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
2675545 GTCGTAATCC
*
2675555 ACCTTTCCATCCAGCGCATCG
1 ACCTTTCCATCCAGCGCATCA
* *
2675576 ACTTTTCCATCCAGCACATCA
1 ACCTTTCCATCCAGCGCATCA
* *
2675597 ACCTTTCCCTCCACCGCATCA
1 ACCTTTCCATCCAGCGCATCA
2675618 AC
1 AC
2675620 TGCATTGCTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.23, C:0.45, G:0.08, T:0.25
Consensus pattern (21 bp):
ACCTTTCCATCCAGCGCATCA
Found at i:2685698 original size:28 final size:28
Alignment explanation
Indices: 2685643--2685715 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
2685633 ATTTAGAAAT
* *** *
2685643 ATAATAATATATGATCTTACTTTCAAAA
1 ATAATAATATATGATATTAAAATAAAAA
2685671 ATAATAATATATGATATTAAAATAAAAA
1 ATAATAATATATGATATTAAAATAAAAA
*
2685699 TTAATATATATAT-ATAT
1 ATAATA-ATATATGATAT
2685716 ATATATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 32 0.84
29 6 0.16
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (28 bp):
ATAATAATATATGATATTAAAATAAAAA
Found at i:2686164 original size:18 final size:19
Alignment explanation
Indices: 2686143--2686180 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2686133 TTATAAATGA
2686143 TTTAATCA-AAATAATTTT
1 TTTAATCATAAATAATTTT
*
2686161 TTTAATTATTAAATAATTTT
1 TTTAATCA-TAAATAATTTT
2686181 ATCATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAATCATAAATAATTTT
Found at i:2690317 original size:19 final size:18
Alignment explanation
Indices: 2690279--2690313 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2690269 TAAATTTTAA
2690279 ATTTTAAATAATATAAAT
1 ATTTTAAATAATATAAAT
2690297 ATTTATAAA-AATATAAA
1 ATTT-TAAATAATATAAA
2690314 ATATAATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTTAAATAATATAAAT
Found at i:2691572 original size:19 final size:19
Alignment explanation
Indices: 2691548--2691605 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
2691538 AATTTTTTCT
2691548 TATAAAAAATAATTAAAAA
1 TATAAAAAATAATTAAAAA
* *
2691567 TATAAAAAATCATCAAAAA
1 TATAAAAAATAATTAAAAA
* * *
2691586 AATATAAAATTTATTAAAAA
1 TATA-AAAAATAATTAAAAA
2691606 AGATAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
TATAAAAAATAATTAAAAA
Found at i:2691606 original size:19 final size:19
Alignment explanation
Indices: 2691582--2691628 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
2691572 AAAATCATCA
*
2691582 AAAAAATATAAAATTTATT
1 AAAAAATATAAAATTTAAT
*
2691601 AAAAAAGATAAAATTTAAT
1 AAAAAATATAAAATTTAAT
*
2691620 AAAACATAT
1 AAAAAATAT
2691629 TTACATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAAATATAAAATTTAAT
Found at i:2691662 original size:21 final size:19
Alignment explanation
Indices: 2691581--2691677 Score: 63
Period size: 21 Copynumber: 4.8 Consensus size: 19
2691571 AAAAATCATC
*
2691581 AAAAAAATATAAAATTTATT
1 AAAAACATATAAAATTTA-T
*
2691601 AAAAA-AGATAAAATTTA-
1 AAAAACATATAAAATTTAT
**
2691618 ATAAAACATATTTACATTTTTAT
1 A-AAAACATA--TA-AAATTTAT
2691641 AAAAACATATTAAAATTCTAT
1 AAAAACATA-TAAAATT-TAT
*
2691662 AAAAATCATAAAAAAT
1 AAAAA-CATATAAAAT
2691678 ATTAAAAGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
17 1 0.02
18 4 0.06
19 13 0.21
20 8 0.13
21 18 0.29
22 17 0.27
23 1 0.02
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAAACATATAAAATTTAT
Found at i:2692192 original size:21 final size:19
Alignment explanation
Indices: 2692168--2692217 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2692158 ATATTTTAAA
2692168 TATTTTTTTACAATTTCTTAT
1 TATTTTTTTACAA-TT-TTAT
* *
2692189 TATTTTTTAAGAATTTTAT
1 TATTTTTTTACAATTTTAT
*
2692208 TACTTTTTTA
1 TATTTTTTTA
2692218 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 12 0.48
20 2 0.08
21 11 0.44
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (19 bp):
TATTTTTTTACAATTTTAT
Found at i:2713314 original size:3 final size:3
Alignment explanation
Indices: 2713306--2713343 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2713296 ACATGATGCT
2713306 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2713344 GTTAAGCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2723506 original size:24 final size:24
Alignment explanation
Indices: 2723462--2723513 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2723452 TTTCTAGAAG
* **
2723462 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTACCATAATAT
*
2723486 ATTTAGCATTTATTACCATAATTT
1 ATTTAGCATTTATTACCATAATAT
2723510 ATTT
1 ATTT
2723514 GACCTACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTACCATAATAT
Found at i:2731957 original size:74 final size:74
Alignment explanation
Indices: 2731836--2731983 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
2731826 TGGACACATG
* *
2731836 TATATTTACTTCTTTGAAGAGTTTTCATGCGTTTTATGAGTCATTGGAAGATCGTATTTCAATGC
1 TATATTTACTTCTTTGAAGAGTTTTCATGCATTTTATGAGTCATTGGAAGATCATATTTCAATGC
2731901 CCTTGTATA
66 CCTTGTATA
*
2731910 TATATTTGCTTCTTTGAAGAGTTTTCATGCATTTTATGAGTCATTGGAAGATCATATTTCAATGC
1 TATATTTACTTCTTTGAAGAGTTTTCATGCATTTTATGAGTCATTGGAAGATCATATTTCAATGC
2731975 CCTTGTATA
66 CCTTGTATA
2731984 GGGTTAAATG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (74 bp):
TATATTTACTTCTTTGAAGAGTTTTCATGCATTTTATGAGTCATTGGAAGATCATATTTCAATGC
CCTTGTATA
Found at i:2741586 original size:30 final size:30
Alignment explanation
Indices: 2741524--2741590 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
2741514 ATTAAAAAAA
* *
2741524 TTTAAAAGTTTATATAATTTTTTTAAAGTT
1 TTTAAAAGTTAATATAATATTTTTAAAGTT
* *
2741554 TTTACAAGTTAATATAA-ATTTTTAATATTT
1 TTTAAAAGTTAATATAATATTTTTAA-AGTT
2741584 TTTAAAA
1 TTTAAAA
2741591 TTAGTAGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (30 bp):
TTTAAAAGTTAATATAATATTTTTAAAGTT
Found at i:2742268 original size:21 final size:21
Alignment explanation
Indices: 2742244--2742323 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
2742234 TCATTTCTGT
* * *
2742244 CATAGCCCCCACCACCACCTC
1 CATAGCCACCACCGCCACCAC
* *
2742265 CATAGCCACCACTGCCCCCAC
1 CATAGCCACCACCGCCACCAC
*
2742286 CATAGCCGCCACCGCCACCAC
1 CATAGCCACCACCGCCACCAC
*
2742307 CATATCCACCACCGCCA
1 CATAGCCACCACCGCCA
2742324 TAACCGCTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.25, C:0.57, G:0.09, T:0.09
Consensus pattern (21 bp):
CATAGCCACCACCGCCACCAC
Found at i:2745780 original size:2 final size:2
Alignment explanation
Indices: 2745773--2745800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2745763 GATTACTTGC
2745773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2745801 TCATATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2745909 original size:2 final size:2
Alignment explanation
Indices: 2745902--2745952 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2745892 GCCATATACT
2745902 TA TA TA TA TA 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
2745944 TA TA TA TA T
1 TA TA TA TA T
2745953 CAAAATGTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2749769 original size:67 final size:67
Alignment explanation
Indices: 2749661--2749792 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
2749651 TTTTCAATTC
2749661 AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGAGATTACCAGTCCACACTAAATCCCCTG
1 AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGAGATTACCAGTCCACACTAAATCCCCTG
2749726 CA
66 CA
* ** *
2749728 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATGCCCTG
1 AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGAGATTACCAGTCCACACTAAATCCCCTG
2749793 TAATATAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGAGATTACCAGTCCACACTAAATCCCCTG
CA
Found at i:2750054 original size:62 final size:57
Alignment explanation
Indices: 2749914--2750060 Score: 154
Period size: 57 Copynumber: 2.5 Consensus size: 57
2749904 ATCCTAATTC
* * *
2749914 GGATTACCCGTCCGGGCTAAATCCATTTTCCACGTATTCTTCGAGAGGGCTATATCAA
1 GGATCACCCGTCCGGGCTAGAT-CATTTTCCACATATTCTTCGAGAGGGCTATATCAA
* * *
2749972 -GATCACCCATCCGGGCTAGAT-ATTTTTCACACATATTCTTTGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCA-TTTTC-CACATATTCTTCGAGAGGGCTATATC---A-A
*
2750033 GGATCACCCGTCCGGGCTAGATCCTTTT
1 GGATCACCCGTCCGGGCTAGATCATTTT
2750061 TACCGTCAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
55 1 0.01
56 5 0.07
57 41 0.56
60 1 0.01
61 1 0.01
62 24 0.33
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (57 bp):
GGATCACCCGTCCGGGCTAGATCATTTTCCACATATTCTTCGAGAGGGCTATATCAA
Found at i:2770856 original size:69 final size:69
Alignment explanation
Indices: 2770745--2770884 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
2770735 CTCTACAAAA
2770745 GAATGCAGCTGAAAGTGCTCAACTCTTGGAAAATGTTGCTCAGAGTCCTGATGTGCAAGTAAGTG
1 GAATGCAGCTGAAAGTGCTCAACTCTTGGAAAATGTTGCTCAGAGTCCTGATGTGCAAGTAAGTG
2770810 CAAG
66 CAAG
2770814 GAATGCAGCTGAAAGTGCTCAACTCTTGGAAAATGTTGCTCAGAGTCCTGATGTGCAAGTAAGTG
1 GAATGCAGCTGAAAGTGCTCAACTCTTGGAAAATGTTGCTCAGAGTCCTGATGTGCAAGTAAGTG
2770879 CAAG
66 CAAG
2770883 GA
1 GA
2770885 GCATTTCAAG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (69 bp):
GAATGCAGCTGAAAGTGCTCAACTCTTGGAAAATGTTGCTCAGAGTCCTGATGTGCAAGTAAGTG
CAAG
Found at i:2775788 original size:4 final size:4
Alignment explanation
Indices: 2775772--2775832 Score: 70
Period size: 4 Copynumber: 15.2 Consensus size: 4
2775762 ATTTCTTGGT
* * **
2775772 TGTA TGCA TGTA TGTA TGTA TG-A TGTA TGCA TGCG TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2775819 TGTAA TGTA TGTA T
1 TGT-A TGTA TGTA T
2775833 CGAAAGAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 3 0.06
4 42 0.86
5 4 0.08
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (4 bp):
TGTA
Found at i:2775798 original size:23 final size:24
Alignment explanation
Indices: 2775772--2775832 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
2775762 ATTTCTTGGT
2775772 TGTATGCATGTATGTATGTATG-A
1 TGTATGCATGTATGTATGTATGTA
**
2775795 TGTATGCATGCGTGTATGTATGTA
1 TGTATGCATGTATGTATGTATGTA
*
2775819 TGTAATGTATGTAT
1 TGT-ATGCATGTAT
2775833 CGAAAGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 20 0.65
24 4 0.13
25 7 0.23
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (24 bp):
TGTATGCATGTATGTATGTATGTA
Found at i:2775813 original size:27 final size:28
Alignment explanation
Indices: 2775775--2775829 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
2775765 TCTTGGTTGT
2775775 ATGCATGTATGTATGTATG-ATGTATGC
1 ATGCATGTATGTATGTATGAATGTATGC
*
2775802 ATGCGTGTATGTATGTATGTAATGTATG
1 ATGCATGTATGTATGTATG-AATGTATG
2775830 TATCGAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 18 0.72
29 7 0.28
ACGTcount: A:0.25, C:0.05, G:0.27, T:0.42
Consensus pattern (28 bp):
ATGCATGTATGTATGTATGAATGTATGC
Found at i:2779933 original size:46 final size:46
Alignment explanation
Indices: 2779866--2780049 Score: 278
Period size: 46 Copynumber: 4.0 Consensus size: 46
2779856 GGGGATATAG
2779866 ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
1 ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
*
2779912 ATCTATTTATTTACCATATTACTTAGCATGATTGGGAGATTATTAC
1 ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
* * * *
2779958 GTCTATTTATTTTTCCATATTACTTAGCATGATGGAGAGATTATTAG
1 ATCTATTTA-TTTACCATATTACTTAGCATGATTGAGAGATTATTAC
* * *
2780005 ATCTATTCATTTACCATATTACTTGGTATGATTTGAGAGATTATT
1 ATCTATTTATTTACCATATTACTTAGCATGA-TTGAGAGATTATT
2780050 TCCTTCGTAA
Statistics
Matches: 124, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
46 72 0.58
47 52 0.42
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.45
Consensus pattern (46 bp):
ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
Found at i:2781392 original size:23 final size:22
Alignment explanation
Indices: 2781345--2781396 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
2781335 GGCCCGGCCC
**
2781345 TTTTTTAAAAAATAAACACCAA
1 TTTTTTAAAAAATAAACAAAAA
2781367 TTTTTTAAAAATATAAA-AAAATA
1 TTTTTTAAAAA-ATAAACAAAA-A
2781390 TTTTTTA
1 TTTTTTA
2781397 TTATATATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTTTAAAAAATAAACAAAAA
Found at i:2781952 original size:18 final size:18
Alignment explanation
Indices: 2781929--2781964 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2781919 GTTTATTTCG
2781929 TTTAATAAAGAAAAGGAA
1 TTTAATAAAGAAAAGGAA
2781947 TTTAATAAAGAAAAGGAA
1 TTTAATAAAGAAAAGGAA
2781965 AGTGAAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (18 bp):
TTTAATAAAGAAAAGGAA
Found at i:2787080 original size:96 final size:96
Alignment explanation
Indices: 2786916--2787108 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
2786906 CAATGCTCTC
*
2786916 AGTGACCCTTAGCTCCACTGATGAAGTAAATGACCTTGATTTTTCAAGCTTCACCTTGGTGTTTC
1 AGTGACCCTTAGCTCCAATGATGAAGTAAATGACCTTGATTTTTCAAGCTTCACCTTGGTGTTTC
2786981 CGTCCTTGTAATCTGTAATCCGAAATGAGGT
66 CGTCCTTGTAATCTGTAATCCGAAATGAGGT
*
2787012 AGTGACCCTTAGCTCCAATGATGAAGTAAATGACCTTGATTTTTCAAGCTTCATCTTGGTGTTTC
1 AGTGACCCTTAGCTCCAATGATGAAGTAAATGACCTTGATTTTTCAAGCTTCACCTTGGTGTTTC
2787077 CGTCCTTGTAATCTGTAATCCGAAATGAGGT
66 CGTCCTTGTAATCTGTAATCCGAAATGAGGT
2787108 A
1 A
2787109 TTGCTGCTTG
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (96 bp):
AGTGACCCTTAGCTCCAATGATGAAGTAAATGACCTTGATTTTTCAAGCTTCACCTTGGTGTTTC
CGTCCTTGTAATCTGTAATCCGAAATGAGGT
Found at i:2795687 original size:3 final size:3
Alignment explanation
Indices: 2795679--2795715 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2795669 ATAAGCTTTC
2795679 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2795716 ACAGAATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2815930 original size:17 final size:18
Alignment explanation
Indices: 2815908--2815946 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2815898 TGGAGAGTTT
2815908 AATTAA-AAATTTTAAAA
1 AATTAAGAAATTTTAAAA
*
2815925 AATTAATGAGATTTTAAAA
1 AATTAA-GAAATTTTAAAA
2815944 AAT
1 AAT
2815947 ACGGGTCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
AATTAAGAAATTTTAAAA
Found at i:2819782 original size:2 final size:2
Alignment explanation
Indices: 2819775--2819808 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2819765 NNNNNNNNNC
2819775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2819809 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2822341 original size:5 final size:5
Alignment explanation
Indices: 2822328--2822359 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2822318 TTTAAAAAGT
*
2822328 TTTAG TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
2822360 ATATTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:2828011 original size:6 final size:6
Alignment explanation
Indices: 2828000--2828028 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2827990 TTCGAAAGAA
2828000 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
2828029 AATAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:2840958 original size:7 final size:7
Alignment explanation
Indices: 2840940--2840972 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2840930 TAATCATCTA
2840940 TTTATA-
1 TTTATAT
2840946 TTTATAT
1 TTTATAT
2840953 TTTATAT
1 TTTATAT
2840960 TTTATAT
1 TTTATAT
2840967 TTTATA
1 TTTATA
2840973 GAATTAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTATAT
Found at i:2843533 original size:22 final size:21
Alignment explanation
Indices: 2843494--2843537 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
2843484 TATTTTTGAT
*
2843494 TTTTTTTCATCAATCTTTGTTC
1 TTTTTTTCAACAATCTTT-TTC
2843516 TTTTTTTCAAC-ATGCTTTTTC
1 TTTTTTTCAACAAT-CTTTTTC
2843537 T
1 T
2843538 AATAGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.14, C:0.18, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTTTTCAACAATCTTTTTC
Found at i:2843708 original size:20 final size:21
Alignment explanation
Indices: 2843667--2843728 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2843657 GTGGAAATAA
* *
2843667 TAAAATAAATAAATAATACAT
1 TAAATTAAAAAAATAATACAT
2843688 TAAATTAAAAAAATAAT-CAT
1 TAAATTAAAAAAATAATACAT
*
2843708 TAATTTAAAGAAAATAA-ACAT
1 TAAATTAAA-AAAATAATACAT
2843729 AATTATCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 11 0.31
21 25 0.69
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAATTAAAAAAATAATACAT
Found at i:2848268 original size:19 final size:19
Alignment explanation
Indices: 2848244--2848281 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2848234 TTATAAAAAT
2848244 ATATATAAATTTTTTTTCA
1 ATATATAAATTTTTTTTCA
*
2848263 ATATATCAATTTTTTTTCA
1 ATATATAAATTTTTTTTCA
2848282 CTAGAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATATAAATTTTTTTTCA
Found at i:2851528 original size:16 final size:17
Alignment explanation
Indices: 2851500--2851534 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2851490 ATGTAATTGA
*
2851500 AAAAATATAATAAATAT
1 AAAAATATAATAAAAAT
2851517 AAAAATAT-ATAAAAAT
1 AAAAATATAATAAAAAT
2851533 AA
1 AA
2851535 TAGAACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATATAATAAAAAT
Found at i:2852261 original size:21 final size:21
Alignment explanation
Indices: 2852223--2852263 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2852213 ACAACCAAAG
*
2852223 TTAAACTATAATTATTAAAAT
1 TTAAAATATAATTATTAAAAT
2852244 TTAAAATA-AATTATTTAAAA
1 TTAAAATATAATTA-TTAAAA
2852264 GAAGAACCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAATATAATTATTAAAAT
Found at i:2852965 original size:20 final size:19
Alignment explanation
Indices: 2852925--2852964 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2852915 AATTAAGAAA
*
2852925 TTATAAATAATTAATTATT
1 TTATAAATAATAAATTATT
2852944 TTATAAATTAATAAA-TATT
1 TTATAAA-TAATAAATTATT
2852963 TT
1 TT
2852965 TTTATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATAAATAATAAATTATT
Found at i:2856819 original size:19 final size:19
Alignment explanation
Indices: 2856775--2856831 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 19
2856765 AAGAATAAAT
2856775 AAAAAGAAAGAAAGATAGGAACG
1 AAAAAGAAAGAAAGA-A--AA-G
*
2856798 AAACAGAAAGAAAGAAAAG
1 AAAAAGAAAGAAAGAAAAG
2856817 AAAAAGGAAAGAAAG
1 AAAAA-GAAAGAAAG
2856832 GAAGGAGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.16
20 11 0.35
22 1 0.03
23 14 0.45
ACGTcount: A:0.70, C:0.04, G:0.25, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGAAAGAAAAG
Found at i:2857528 original size:24 final size:24
Alignment explanation
Indices: 2857496--2857555 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
2857486 GTGTTTTGCA
*
2857496 ATTGAAATTGATTG-ATTTAGTATGTG
1 ATTG-AATTGATTGAATTGA-TAT-TG
*
2857522 A-TGAATTTATTGAATTGATATTG
1 ATTGAATTGATTGAATTGATATTG
2857545 ATTGAATTGAT
1 ATTGAATTGAT
2857556 ATATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 3 0.10
24 19 0.66
25 6 0.21
26 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (24 bp):
ATTGAATTGATTGAATTGATATTG
Found at i:2857824 original size:40 final size:39
Alignment explanation
Indices: 2857714--2857845 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 39
2857704 TGACTTCGAG
*
2857714 TCGATGAGACACTGGGTGTCAATTTACTACTTCAGATTAA
1 TCGATGAGACACTGGGTGTCAATTTATTACTTC-GATTAA
* * *
2857754 TTCGATGAGGCACTAGGTGCCAA---ATTACTTCGATTTAA
1 -TCGATGAGACACTGGGTGTCAATTTATTACTTCGA-TTAA
2857792 TCGATGAGACACTGGGTGTCAATTTATTACTTCGAATT-A
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCG-ATTAA
*
2857831 TCCGATGAGGCACTG
1 T-CGATGAGACACTG
2857846 AGTGCCAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
37 21 0.27
38 11 0.14
39 2 0.03
40 23 0.30
41 20 0.26
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTTATTACTTCGATTAA
Found at i:2860310 original size:16 final size:16
Alignment explanation
Indices: 2860273--2860314 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2860263 AAATTAAACG
*
2860273 TTATTTTTTAATTTAA
1 TTATTATTTAATTTAA
2860289 TGTATTATTT-ATTTATA
1 T-TATTATTTAATTTA-A
2860306 TTATTATTT
1 TTATTATTT
2860315 TTCACATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTATTTAATTTAA
Found at i:2873419 original size:18 final size:17
Alignment explanation
Indices: 2873386--2873419 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2873376 ATACACGGAG
*
2873386 CCTATAACATATTTTAA
1 CCTATAACAAATTTTAA
2873403 CCTATAACAAAATTTTA
1 CCTATAAC-AAATTTTA
2873420 GGATGGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
CCTATAACAAATTTTAA
Found at i:2879320 original size:18 final size:20
Alignment explanation
Indices: 2879295--2879338 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2879285 TCAAATTTTT
2879295 ACTTTAA-TTTATT-TATAC
1 ACTTTAATTTTATTATATAC
*
2879313 ATTTTAATTTTATTATATAC
1 ACTTTAATTTTATTATATAC
2879333 ACTTTA
1 ACTTTA
2879339 TTACTTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 6 0.27
20 10 0.45
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (20 bp):
ACTTTAATTTTATTATATAC
Found at i:2890611 original size:37 final size:38
Alignment explanation
Indices: 2890566--2890671 Score: 160
Period size: 37 Copynumber: 2.8 Consensus size: 38
2890556 ACTTAAGAGT
* *
2890566 TAGACTTTAGTTTTATTTTTATTGGGTTGGTAATTGGG
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGTAATTGGA
*
2890604 T-GACTTTAGTTTTAATTTTATTGTGTTGGGTAATTGGA
1 TAGACTTTAGTTTTAATTTTATTGGGTT-GGTAATTGGA
*
2890642 TAGACTTTAGTTTTAGTTTTATTGGGTTGG
1 TAGACTTTAGTTTTAATTTTATTGGGTTGG
2890672 GTTGGATAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
37 24 0.39
38 13 0.21
39 24 0.39
ACGTcount: A:0.19, C:0.03, G:0.25, T:0.53
Consensus pattern (38 bp):
TAGACTTTAGTTTTAATTTTATTGGGTTGGTAATTGGA
Found at i:2890662 original size:39 final size:39
Alignment explanation
Indices: 2890566--2890673 Score: 166
Period size: 39 Copynumber: 2.8 Consensus size: 39
2890556 ACTTAAGAGT
* *
2890566 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGA
*
2890604 T-GACTTTAGTTTTAATTTTATTGTGTTGGGTAATTGGA
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGA
*
2890642 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGT
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGT
2890674 TGGATAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
37 24 0.38
38 11 0.17
39 28 0.44
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.53
Consensus pattern (39 bp):
TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGA
Found at i:2891500 original size:44 final size:44
Alignment explanation
Indices: 2891442--2891536 Score: 167
Period size: 44 Copynumber: 2.2 Consensus size: 44
2891432 TGAAACAATT
*
2891442 ATAAAG-A-AAAATTCATTATTTAATTAATATAAAGTATAATGA
1 ATAAAGAACAAAATTCATTATTTAACTAATATAAAGTATAATGA
2891484 ATAAAGAACAAAATTCATTATTTAACTAATATAAAGTATAATGA
1 ATAAAGAACAAAATTCATTATTTAACTAATATAAAGTATAATGA
2891528 ATAAAGAAC
1 ATAAAGAAC
2891537 CGGAAAGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 6 0.12
43 1 0.02
44 43 0.86
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (44 bp):
ATAAAGAACAAAATTCATTATTTAACTAATATAAAGTATAATGA
Found at i:2891871 original size:20 final size:21
Alignment explanation
Indices: 2891834--2891873 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2891824 TATATGATTA
*
2891834 AATCAAAATTTACCATTTTAAG
1 AATCAAAATATA-CATTTTAAG
2891856 AATCAAAATATA-ATTTTA
1 AATCAAAATATACATTTTA
2891874 TCATTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
AATCAAAATATACATTTTAAG
Found at i:2901624 original size:2 final size:2
Alignment explanation
Indices: 2901617--2901649 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2901607 AATCTCTAAC
2901617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2901650 GGGTGGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2910153 original size:15 final size:14
Alignment explanation
Indices: 2910129--2910158 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2910119 ATAACTTTCA
2910129 TTTTATTTTATTTT
1 TTTTATTTTATTTT
2910143 TTTTCATTTTATTTT
1 TTTT-ATTTTATTTT
2910158 T
1 T
2910159 ACATGTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATTTTATTTT
Found at i:2916440 original size:6 final size:6
Alignment explanation
Indices: 2916429--2916454 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2916419 TATAATATGA
2916429 ATCTAT ATCTAT ATCTAT ATCTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT AT
2916455 ATAGAGAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:2923897 original size:19 final size:16
Alignment explanation
Indices: 2923856--2923912 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
2923846 ACATGTCAAC
2923856 ATTTAATTATTTTTAT
1 ATTTAATTATTTTTAT
2923872 ATTTAATTATTTTTGAT
1 ATTTAATTATTTTT-AT
*
2923889 AATTTTAATGATTTTTAT
1 -A-TTTAATTATTTTTAT
*
2923907 TTTTAA
1 ATTTAA
2923913 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 19 0.53
17 2 0.06
18 3 0.08
19 12 0.33
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
ATTTAATTATTTTTAT
Found at i:2925856 original size:23 final size:26
Alignment explanation
Indices: 2925825--2925874 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
2925815 CATTTAATAT
2925825 TTATATTTTT-A-TTAAA-TTGATTA
1 TTATATTTTTGAGTTAAATTTGATTA
*
2925848 TTATTTTTTTGAGTTAAATTTGATTA
1 TTATATTTTTGAGTTAAATTTGATTA
2925874 T
1 T
2925875 CAACTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 1 0.04
25 5 0.22
26 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TTATATTTTTGAGTTAAATTTGATTA
Found at i:2937696 original size:4 final size:4
Alignment explanation
Indices: 2937687--2937721 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
2937677 AATGTTTATA
* *
2937687 TATG TATG TATG TATA TATG TATG TATG CATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
2937722 ATTTGGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:2937704 original size:16 final size:16
Alignment explanation
Indices: 2937683--2937714 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2937673 GTCAAATGTT
2937683 TATATATGTATGTATG
1 TATATATGTATGTATG
2937699 TATATATGTATGTATG
1 TATATATGTATGTATG
2937715 CATGTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (16 bp):
TATATATGTATGTATG
Found at i:2939746 original size:33 final size:33
Alignment explanation
Indices: 2939707--2939772 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2939697 TTCATCGCAG
* * *
2939707 ACCTTCAAATTTTTCTCTTAGATTATGTTTGTT
1 ACCTTCAAATTGTACTCTTAGATTAAGTTTGTT
*
2939740 ACCTTCATATTGTACTCTTAGATTAAGTTTGTT
1 ACCTTCAAATTGTACTCTTAGATTAAGTTTGTT
2939773 TTGTCGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.52
Consensus pattern (33 bp):
ACCTTCAAATTGTACTCTTAGATTAAGTTTGTT
Found at i:2953514 original size:15 final size:16
Alignment explanation
Indices: 2953486--2953517 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2953476 ATAATAAATG
2953486 ACTAAAACATAAAGTA
1 ACTAAAACATAAAGTA
2953502 ACTAAAACA-AAAGTA
1 ACTAAAACATAAAGTA
2953517 A
1 A
2953518 TAGTTTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.12, G:0.06, T:0.16
Consensus pattern (16 bp):
ACTAAAACATAAAGTA
Found at i:2958274 original size:21 final size:21
Alignment explanation
Indices: 2958235--2958275 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2958225 TGTTTCACTT
*
2958235 ATTCAAAACATGATTAAACAC
1 ATTCAAAACATGATAAAACAC
2958256 ATTCAAAACATG-TCAAAACA
1 ATTCAAAACATGAT-AAAACA
2958276 ACCATCCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.54, C:0.20, G:0.05, T:0.22
Consensus pattern (21 bp):
ATTCAAAACATGATAAAACAC
Found at i:2959121 original size:40 final size:39
Alignment explanation
Indices: 2959066--2959201 Score: 159
Period size: 40 Copynumber: 3.5 Consensus size: 39
2959056 ACCAGTTTGG
*
2959066 CACCCAGTGCCTCATCGAATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATAATCCGAAGT-ATAAATTGA
* ** * *
2959106 CACCCAGTGTCTCATCGTCTAAACCGAAGT-T-AATTGG
1 CACCCAGTGCCTCATCGAATAATCCGAAGTATAAATTGA
2959143 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAGTA-TAAATTGA
* *
2959184 CACCTAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
2959202 CTCGAAGTCG
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
37 21 0.27
38 11 0.14
40 26 0.33
41 21 0.27
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGTATAAATTGA
Found at i:2961299 original size:17 final size:17
Alignment explanation
Indices: 2961262--2961307 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2961252 AAATAAGTAC
***
2961262 TTTTATAATTTTATTTT
1 TTTTATAATTTTATAAA
2961279 TTTTATAATTTTATAAA
1 TTTTATAATTTTATAAA
2961296 TTTTAATAATTT
1 TTTT-ATAATTT
2961308 ATTCAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATAATTTTATAAA
Found at i:2972837 original size:43 final size:43
Alignment explanation
Indices: 2972771--2972867 Score: 185
Period size: 43 Copynumber: 2.2 Consensus size: 43
2972761 AATATATATG
2972771 ATCTGTTTGTTTTTTTCTGGCCAAGAGGATAATTGCTAATGGAC
1 ATCT-TTTGTTTTTTTCTGGCCAAGAGGATAATTGCTAATGGAC
2972815 ATCTTTTGTTTTTTTCTGGCCAAGAGGATAATTGCTAATGGAC
1 ATCTTTTGTTTTTTTCTGGCCAAGAGGATAATTGCTAATGGAC
2972858 ATCTTTTGTT
1 ATCTTTTGTT
2972868 GTTAGGTTGC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 49 0.92
44 4 0.08
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.44
Consensus pattern (43 bp):
ATCTTTTGTTTTTTTCTGGCCAAGAGGATAATTGCTAATGGAC
Found at i:2987293 original size:2 final size:2
Alignment explanation
Indices: 2987286--2987311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2987276 AAAGGACCAA
2987286 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2987312 GTATTACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2990165 original size:2 final size:2
Alignment explanation
Indices: 2990152--2990181 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
2990142 AATTAGCTAT
2990152 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
2990182 TTTACTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2991223 original size:21 final size:21
Alignment explanation
Indices: 2991182--2991223 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2991172 TGTAATTCGA
* *
2991182 TTTATTAAAAATTATTTACAT
1 TTTATTAAAAATGATTAACAT
2991203 TTTA-TAAAATATGATTAACAT
1 TTTATTAAAA-ATGATTAACAT
2991224 GTTTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTATTAAAAATGATTAACAT
Found at i:2993744 original size:2 final size:2
Alignment explanation
Indices: 2993737--2993768 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2993727 CTTATTCTTT
*
2993737 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2993769 GTTTGATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2994897 original size:12 final size:12
Alignment explanation
Indices: 2994880--2994913 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2994870 AGGCCCGCCC
2994880 ATATTAATTTTT
1 ATATTAATTTTT
*
2994892 ATATTATTTTTT
1 ATATTAATTTTT
2994904 ATA-TAATTTT
1 ATATTAATTTT
2994914 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:2996650 original size:18 final size:17
Alignment explanation
Indices: 2996614--2996652 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2996604 GGGTCAATGT
* *
2996614 ATTAGTTTATGGGTTTA
1 ATTAGTTTATCGATTTA
2996631 ATTAGTTTAATCGATTTA
1 ATTAGTTT-ATCGATTTA
2996649 ATTA
1 ATTA
2996653 AATAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (17 bp):
ATTAGTTTATCGATTTA
Found at i:3000129 original size:35 final size:35
Alignment explanation
Indices: 3000083--3000152 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3000073 AGTCATGAGT
3000083 AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
1 AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
3000118 AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
1 AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
3000153 CTACTGCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (35 bp):
AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
Found at i:3001782 original size:13 final size:12
Alignment explanation
Indices: 3001763--3001801 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3001753 TGAGTATGTA
3001763 TTTTTTATATAT
1 TTTTTTATATAT
3001775 TATTTTTATA-AT
1 T-TTTTTATATAT
*
3001787 TTTTTCATATAT
1 TTTTTTATATAT
3001799 TTT
1 TTT
3001802 AATGATCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 7 0.29
12 9 0.38
13 8 0.33
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTTATATAT
Found at i:3002714 original size:30 final size:31
Alignment explanation
Indices: 3002675--3002734 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3002665 AGAGGTGGAA
*
3002675 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
3002706 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
3002735 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:3013991 original size:31 final size:31
Alignment explanation
Indices: 3013953--3014012 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
3013943 AGAAATCAAA
3013953 TATTTCATGTTATTTAAGATATTTAATATGG
1 TATTTCATGTTATTTAAGATATTTAATATGG
*
3013984 TATTTCATTTTATTTAAGATATTTAATAT
1 TATTTCATGTTATTTAAGATATTTAATAT
3014013 AAAAGAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.55
Consensus pattern (31 bp):
TATTTCATGTTATTTAAGATATTTAATATGG
Found at i:3016496 original size:30 final size:30
Alignment explanation
Indices: 3016462--3016520 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
3016452 AATTTGACTA
** * *
3016462 TTTTTGAAAAGGTTGATGGTTAAATTTAAC
1 TTTTTGAAAAAATTGAGGGTCAAATTTAAC
*
3016492 TTTTTTAAAAAATTGAGGGTCAAATTTAA
1 TTTTTGAAAAAATTGAGGGTCAAATTTAA
3016521 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.42
Consensus pattern (30 bp):
TTTTTGAAAAAATTGAGGGTCAAATTTAAC
Found at i:3016960 original size:31 final size:30
Alignment explanation
Indices: 3016899--3016961 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
3016889 AGATAATTGG
* *
3016899 GTGATCAAAAAGACAAAATTAAATAATTAA
1 GTGACCAAAAAGACAAAATAAAATAATTAA
*
3016929 GTGACCAAAAA-ATAAAATAAAATATAGTTAA
1 GTGACCAAAAAGACAAAATAAAATA-A-TTAA
3016960 GT
1 GT
3016962 TACTACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.24
Consensus pattern (30 bp):
GTGACCAAAAAGACAAAATAAAATAATTAA
Found at i:3035279 original size:30 final size:30
Alignment explanation
Indices: 3035225--3035288 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
3035215 AGATCACTCA
3035225 ATATCTTGTTCAGGAGTTTAGGAAGA-CTGG
1 ATATCTTGTTCAGGAGTTTAGGAAGATCT-G
*
3035255 ATATCTTGTTCAGGA-TCTTGGGAAGATCTG
1 ATATCTTGTTCAGGAGT-TTAGGAAGATCTG
3035285 ATAT
1 ATAT
3035289 TTGATTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.90
31 2 0.06
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (30 bp):
ATATCTTGTTCAGGAGTTTAGGAAGATCTG
Found at i:3036806 original size:43 final size:43
Alignment explanation
Indices: 3036743--3037153 Score: 612
Period size: 43 Copynumber: 9.7 Consensus size: 43
3036733 AACTTGCACA
* * *
3036743 ATGCC-ATATCCCAGATATGGTCTTACATGCT-ATCAT-ATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-TAATC-TCATATCG
3036785 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
3036828 ATGCCAATGTCCCAGACATGGTCTTACACG-AA--TCATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATAT-CG
3036869 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
*
3036912 ATGCCAATGTCCCGGACATGGTCTTACACG-AA--TCATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATAT-CG
3036953 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
3036996 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
*
3037039 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
* *
3037082 ATGCCCATGTCCTAGACATGGTCTTACACG-AA--TCATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATAT-CG
**
3037123 ATGCCAATGTATCAGACATGGTCTTACACGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGT
3037154 TCGAAGTTCT
Statistics
Matches: 343, Mismatches: 13, Indels: 26
0.90 0.03 0.07
Matches are distributed among these distances:
40 18 0.05
41 90 0.26
42 17 0.05
43 206 0.60
44 12 0.03
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
Found at i:3036885 original size:84 final size:84
Alignment explanation
Indices: 3036743--3037153 Score: 673
Period size: 84 Copynumber: 4.9 Consensus size: 84
3036733 AACTTGCACA
* * * *
3036743 ATGCC-ATATCCCAGATATGGTCTTACATGCTATCATATATCGATGCCAATGTCCCAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCATATA-CGATGCCAATGTCCCAGACATGGT
3036807 CTTACACGTAATCTCATATCG
64 CTTACACGTAATCTCATATCG
3036828 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGTCT
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGTCT
3036893 TACACGTAATCTCATATCG
66 TACACGTAATCTCATATCG
*
3036912 ATGCCAATGTCCCGGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGTCT
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGTCT
3036977 TACACGTAATCTCATATCG
66 TACACGTAATCTCATATCG
3036996 ATGCCAATGTCCCAGACATGGTCTTACACGTAATC-TCATATCGATGCCAATGTCCCAGACATGG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCAT-ATA-CGATGCCAATGTCCCAGACATGG
*
3037060 TCTTACACGTAATCTCATATCA
63 TCTTACACGTAATCTCATATCG
* * **
3037082 ATGCCCATGTCCTAGACATGGTCTTACACGAATCATATACGATGCCAATGTATCAGACATGGTCT
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGTCT
3037147 TACACGT
66 TACACGT
3037154 TCGAAGTTCT
Statistics
Matches: 310, Mismatches: 11, Indels: 11
0.93 0.03 0.03
Matches are distributed among these distances:
84 189 0.61
85 27 0.09
86 94 0.30
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (84 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGTCT
TACACGTAATCTCATATCG
Found at i:3036998 original size:127 final size:127
Alignment explanation
Indices: 3036743--3037153 Score: 638
Period size: 127 Copynumber: 3.2 Consensus size: 127
3036733 AACTTGCACA
* * *
3036743 ATGCC-ATATCCCAGATATGGTCTTACATGCT-ATCAT-ATATCGATGCCAATGTCCCAGACATG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-TAATC-TCATATCGATGCCAATGTCCCAGACATG
3036805 GTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACG
64 GTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACG
*
3036869 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCGGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
3036934 CTTACACG-AA--TCATATACGATGCCAATGTCCCAGACATGGTCTTACACGTAATC-TCATATC
66 CTTACACGTAATCTCATAT-CGATGCCAATGTCCCAGACATGGTCTTACACG-AATCAT-ATA-C
3036995 G
127 G
3036996 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
* * *
3037061 CTTACACGTAATCTCATATCAATGCCCATGTCCTAGACATGGTCTTACACGAATCATATACG
66 CTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACG
**
3037123 ATGCCAATGTATCAGACATGGTCTTACACGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGT
3037154 TCGAAGTTCT
Statistics
Matches: 264, Mismatches: 10, Indels: 21
0.89 0.03 0.07
Matches are distributed among these distances:
124 6 0.02
125 33 0.12
126 16 0.06
127 164 0.62
128 9 0.03
129 30 0.11
130 6 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (127 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
CTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACG
Found at i:3037338 original size:31 final size:31
Alignment explanation
Indices: 3037295--3037495 Score: 174
Period size: 31 Copynumber: 6.5 Consensus size: 31
3037285 TATATATATA
* *
3037295 TATATTCATATACGAATCAAATTCGGCAACG
1 TATAATCATATACGAATCAAATTCGGCAATG
* *
3037326 TATAATCATATACAAATC-AATTTGGCAATG
1 TATAATCATATACGAATCAAATTCGGCAATG
* * *
3037356 TATAACCATATATGAATCAAATTCGACAATG
1 TATAATCATATACGAATCAAATTCGGCAATG
**
3037387 TATAATCATATACGAATC-AATTCGGCAACC
1 TATAATCATATACGAATCAAATTCGGCAATG
** * ** * **
3037417 TATTTTCTTATATAAATCAACTTCGATAATG
1 TATAATCATATACGAATCAAATTCGGCAATG
* * **
3037448 TATAACCATATACAAAT-AAATTTTAGCAATG
1 TATAATCATATACGAATCAAA-TTCGGCAATG
*
3037479 TATAATTATATACGAAT
1 TATAATCATATACGAAT
3037496 TAATTCAGCA
Statistics
Matches: 130, Mismatches: 37, Indels: 6
0.75 0.21 0.03
Matches are distributed among these distances:
30 49 0.38
31 81 0.62
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (31 bp):
TATAATCATATACGAATCAAATTCGGCAATG
Found at i:3037377 original size:61 final size:61
Alignment explanation
Indices: 3037295--3037495 Score: 204
Period size: 61 Copynumber: 3.3 Consensus size: 61
3037285 TATATATATA
* *
3037295 TATATTCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATG
1 TATAATCATATACGAATCAAATTCGACAACGTATAATCATATACAAATCAATTTGGCAATG
* * * * * **
3037356 TATAACCATATATGAATCAAATTCGACAATGTATAATCATATACGAATCAATTCGGCAACC
1 TATAATCATATACGAATCAAATTCGACAACGTATAATCATATACAAATCAATTTGGCAATG
** * ** * * * * * *
3037417 TATTTTCTTATATAAATCAACTTCGATAATGTATAACCATATACAAATAAATTTTAGCAATG
1 TATAATCATATACGAATCAAATTCGACAACGTATAATCATATACAAATCAA-TTTGGCAATG
*
3037479 TATAATTATATACGAAT
1 TATAATCATATACGAAT
3037496 TAATTCAGCA
Statistics
Matches: 110, Mismatches: 29, Indels: 1
0.79 0.21 0.01
Matches are distributed among these distances:
61 93 0.85
62 17 0.15
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (61 bp):
TATAATCATATACGAATCAAATTCGACAACGTATAATCATATACAAATCAATTTGGCAATG
Found at i:3037448 original size:92 final size:91
Alignment explanation
Indices: 3037295--3037530 Score: 251
Period size: 92 Copynumber: 2.6 Consensus size: 91
3037285 TATATATATA
* * * *
3037295 TATATTCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATGTATA
1 TATAATCATATACGAATC-AATTCGGCAACCTATAATCATATACAAATCAATTCGACAATGTATA
**
3037360 ACCATATATGAATCAAATTCGA-CAATG
65 ACCATATACAAAT-AAATTCGAGCAATG
** * * *
3037387 TATAATCATATACGAATCAATTCGGCAACCTATTTTCTTATATAAATCAACTTCGATAATGTATA
1 TATAATCATATACGAATCAATTCGGCAACCTATAATCATATACAAATCAA-TTCGACAATGTATA
**
3037452 ACCATATACAAATAAATTTTAGCAATG
65 ACCATATACAAATAAATTCGAGCAATG
* * * * * *
3037479 TATAATTATATACGAATTAATTCAGCAACTTAT-ATCCACATACAATTCAATT
1 TATAATCATATACGAATCAATTCGGCAACCTATAAT-CATATACAAATCAATT
3037531 TCAACAACTT
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
91 36 0.30
92 83 0.70
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (91 bp):
TATAATCATATACGAATCAATTCGGCAACCTATAATCATATACAAATCAATTCGACAATGTATAA
CCATATACAAATAAATTCGAGCAATG
Found at i:3046956 original size:19 final size:19
Alignment explanation
Indices: 3046932--3046968 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3046922 TTATATTAAT
*
3046932 ATATTTATAATTGAAATAA
1 ATATTTATAATTAAAATAA
*
3046951 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
3046969 TTAATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:3047091 original size:22 final size:22
Alignment explanation
Indices: 3047051--3047106 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
3047041 AATAAAATTG
*
3047051 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
3047071 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* *
3047093 TATTAATAAATTAT
1 AAATAATAAATTAT
3047107 TATATGACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 9 0.29
21 2 0.06
22 20 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:3047189 original size:25 final size:25
Alignment explanation
Indices: 3047141--3047189 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3047131 AATATGTATG
*
3047141 TTTAATAATATTAAAAATATAATAT
1 TTTAATAATATTAAAAATAAAATAT
* **
3047166 TTTAATAATTTTAAATTTAAAATA
1 TTTAATAATATTAAAAATAAAATA
3047190 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTAATAATATTAAAAATAAAATAT
Found at i:3050140 original size:15 final size:15
Alignment explanation
Indices: 3050120--3050150 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3050110 GCATCCTCTG
*
3050120 TTCCAATTATATATA
1 TTCCAATTATACATA
3050135 TTCCAATTATACATA
1 TTCCAATTATACATA
3050150 T
1 T
3050151 ATGGGTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (15 bp):
TTCCAATTATACATA
Found at i:3050816 original size:111 final size:111
Alignment explanation
Indices: 3050608--3050839 Score: 249
Period size: 111 Copynumber: 2.1 Consensus size: 111
3050598 GATTCACAAA
*
3050608 AAGCGCCGCAAAAAAATAAGGCCAACGACGTCGTTTACTGAGTTTTCGGGCCATTAGCGGCGTTT
1 AAGCGCCGCAAAAAAATAAGGCCAACGACGTCGTTTACTGAGTTGTCGGGCCATTAGCGGCGTTT
* *
3050673 TTACAAAAGCGCCGCTAATGCTCCTGTCTTTAGCGGCG-TTTCTGAG
66 TTACAAAAGCGCCACTAATGATCCTGTCTTTAGCGGCGATTTCTG-G
* * * ** * *
3050719 AAGCGCCGCAAAAAACCTAAGGGCAACGACG-CTGTTTTCTTTGTTGT-GGGTCTTTAGCGGCGT
1 AAGCGCCGCAAAAAA-ATAAGGCCAACGACGTC-GTTTACTGAGTTGTCGGGCCATTAGCGGCGT
* * * *
3050782 TTTCT-TAAAAGCGCCACTAATGAT-TTGTTTTTTAGCGGCGATTTTCTGT
64 TTT-TACAAAAGCGCCACTAATGATCCTG-TCTTTAGCGGCGA-TTTCTGG
3050831 AAGCGCCGC
1 AAGCGCCGC
3050840 TAATAGTAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
110 2 0.02
111 60 0.59
112 33 0.33
113 6 0.06
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (111 bp):
AAGCGCCGCAAAAAAATAAGGCCAACGACGTCGTTTACTGAGTTGTCGGGCCATTAGCGGCGTTT
TTACAAAAGCGCCACTAATGATCCTGTCTTTAGCGGCGATTTCTGG
Found at i:3051222 original size:18 final size:21
Alignment explanation
Indices: 3051176--3051224 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
3051166 TAGTTCGACT
3051176 AAATTAATATATAAATCAAAC
1 AAATTAATATATAAATCAAAC
* *
3051197 AAAGTAATATA-AAA-C-ACC
1 AAATTAATATATAAATCAAAC
3051215 AAATTAATAT
1 AAATTAATAT
3051225 CGTGATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 3 0.12
21 10 0.40
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATTAATATATAAATCAAAC
Found at i:3051500 original size:15 final size:16
Alignment explanation
Indices: 3051482--3051512 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3051472 GCTTTAAGAC
3051482 TTAGGGTT-TAGGGGT
1 TTAGGGTTATAGGGGT
3051497 TTAGGGTTATAGGGGT
1 TTAGGGTTATAGGGGT
3051513 CGGGTTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (16 bp):
TTAGGGTTATAGGGGT
Found at i:3053158 original size:230 final size:229
Alignment explanation
Indices: 3052705--3053159 Score: 596
Period size: 230 Copynumber: 2.0 Consensus size: 229
3052695 NNNNCATTGT
*
3052705 TATTAGTGGCGTTACACTCAAAACGCCGCAAATATATTTTAAAGATTACACGAGTTTGCGTTAAA
1 TATTAGTGGCGTTACACCCAAAACGCCGCAAATATATTTTAAAGATTACACGAGTTTGCGTTAAA
*
3052770 CGACTGCGTTTGACCTTATATTTAGTGGCACTTATATATAAACGTCGCAAACTCGAAATGGTGTT
66 CGACTGCGTTTGACCTTATATTTAGTGGCACTTATATATAAACGCCGCAAACTCGAAATGGTGTT
* * *
3052835 ACGAAAAACGGCGCCGTATTCTTATTACATTTAGTGGCGTTTTAGATAAAACGTCGCAAGTATGT
131 ACGAAAAACGACGCCGTATTCTTATTACATTTAGTGGCGTTTTAGATAAAACG-CGCAAATATGC
* * ***
3052900 TTTCTTTGTTACAGAAACGGCATCGTTTTCAAGGA
195 ATTATAACTTACAGAAACGGCATCGTTTTCAAGGA
* * *
3052935 TATTTGTGGCGTTACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCTTTAAA
1 TATTAGTGGCGTTACACCCAAAACGCCGCAAATATATTTTAAAGATTACACGAGTTTGCGTTAAA
* *
3053000 CGATTGCGTTTGACCTTATATTTAGTGGCGCTTATATATAAACGCCGCCAAA-TCGAAATGGTGT
66 CGACTGCGTTTGACCTTATATTTAGTGGCACTTATATATAAACGCCG-CAAACTCGAAATGGTGT
* * *** *
3053064 TACGGAAAACGACGTCGT-TTACTTAGTTGGTTTTAGTGGCGCTTTTA-TTAAACAC-CGCAAAT
130 TACGAAAAACGACGCCGTATT-CTTA-TTACATTTAGTGGCG-TTTTAGATAAA-ACGCGCAAAT
* * *
3053126 TTGCATTATAACTTA-AGGAAACTGCGTCGTTTTC
191 ATGCATTATAACTTACA-GAAACGGCATCGTTTTC
3053160 CATTGTTAGT
Statistics
Matches: 195, Mismatches: 24, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
229 3 0.02
230 165 0.85
231 20 0.10
232 7 0.04
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (229 bp):
TATTAGTGGCGTTACACCCAAAACGCCGCAAATATATTTTAAAGATTACACGAGTTTGCGTTAAA
CGACTGCGTTTGACCTTATATTTAGTGGCACTTATATATAAACGCCGCAAACTCGAAATGGTGTT
ACGAAAAACGACGCCGTATTCTTATTACATTTAGTGGCGTTTTAGATAAAACGCGCAAATATGCA
TTATAACTTACAGAAACGGCATCGTTTTCAAGGA
Found at i:3053473 original size:19 final size:19
Alignment explanation
Indices: 3053451--3053494 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3053441 CAGACATCTC
*
3053451 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* * *
3053470 CCCCTAATTCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
3053489 CCCCAA
1 CCCCAA
3053495 CGTAGTCCAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.41, G:0.02, T:0.25
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:3054640 original size:18 final size:18
Alignment explanation
Indices: 3054580--3054644 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
3054570 TACTCAAAAA
3054580 ATAAATAAATTAGTCTTT
1 ATAAATAAATTAGTCTTT
* ** **
3054598 ATAAAAAAATTTTA-AATAA
1 ATAAATAAA--TTAGTCTTT
3054617 ATAAATAAATTAGTCTTT
1 ATAAATAAATTAGTCTTT
3054635 ATAAATAAAT
1 ATAAATAAAT
3054645 AGATAAAATT
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
17 3 0.09
18 19 0.56
19 9 0.26
20 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAAATAAATTAGTCTTT
Found at i:3055145 original size:12 final size:13
Alignment explanation
Indices: 3055128--3055159 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3055118 AACACTTTGC
3055128 TTAATTTTTAA-T
1 TTAATTTTTAAGT
3055140 TTAA-TTTTAAGT
1 TTAATTTTTAAGT
3055152 TTAATTTT
1 TTAATTTT
3055160 AGATAACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 9 0.50
13 3 0.17
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TTAATTTTTAAGT
Found at i:3055297 original size:9 final size:9
Alignment explanation
Indices: 3055283--3055418 Score: 101
Period size: 9 Copynumber: 16.0 Consensus size: 9
3055273 CAATTTCGAA
3055283 TTACATAAC
1 TTACATAAC
3055292 TTACATAA-
1 TTACATAAC
3055300 -TACATAACC
1 TTACATAA-C
* *
3055309 TT-CCTAGC
1 TTACATAAC
* *
3055317 TTACATTAT
1 TTACATAAC
*
3055326 TTAGATAA-
1 TTACATAAC
*
3055334 -TACATAGC
1 TTACATAAC
*
3055342 CTACATAAC
1 TTACATAAC
*
3055351 TTACATAAA
1 TTACATAAC
*
3055360 TTAAATAAC
1 TTACATAAC
3055369 TTACATAAC
1 TTACATAAC
*
3055378 TCACATAA-
1 TTACATAAC
*
3055386 -TACACAAC
1 TTACATAAC
3055394 TTACATAAC
1 TTACATAAC
3055403 TTACATAA-
1 TTACATAAC
3055411 -TACATAAC
1 TTACATAAC
3055419 CTTCCTATCA
Statistics
Matches: 98, Mismatches: 20, Indels: 19
0.72 0.15 0.14
Matches are distributed among these distances:
7 24 0.24
8 3 0.03
9 70 0.71
10 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (9 bp):
TTACATAAC
Found at i:3055358 original size:25 final size:25
Alignment explanation
Indices: 3055284--3055418 Score: 121
Period size: 25 Copynumber: 5.3 Consensus size: 25
3055274 AATTTCGAAT
3055284 TACATAACTTACATAA--TACATAA
1 TACATAACTTACATAACTTACATAA
* * * * * *
3055307 CCTTCCTAGCTTACATTATTTAGATAA
1 --TACATAACTTACATAACTTACATAA
* *
3055334 TACATAGCCTACATAACTTACATAAA
1 TACATAACTTACATAACTTACAT-AA
* *
3055360 TTAAATAACTTACATAACTCACATAA
1 -TACATAACTTACATAACTTACATAA
*
3055386 TACACAACTTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
3055411 TACATAAC
1 TACATAAC
3055419 CTTCCTATCA
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
25 58 0.67
26 4 0.05
27 25 0.29
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:3056703 original size:21 final size:20
Alignment explanation
Indices: 3056677--3056747 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 20
3056667 GTACAACTTA
3056677 AAGCAGAGGCGACAGCGAGGG
1 AAGCAGAGGCG-CAGCGAGGG
* *
3056698 AAGCAGCGGCGGCAGCTAGGG
1 AAGCAGAGGC-GCAGCGAGGG
* *
3056719 AAGCAGAGGTTGCAGCGAGAG
1 AAGCAGAGG-CGCAGCGAGGG
3056740 AAGCAGAG
1 AAGCAGAG
3056748 CAGAGCAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.45, T:0.04
Consensus pattern (20 bp):
AAGCAGAGGCGCAGCGAGGG
Found at i:3057152 original size:43 final size:43
Alignment explanation
Indices: 3057058--3057195 Score: 197
Period size: 43 Copynumber: 3.2 Consensus size: 43
3057048 TTTTGTGAAA
* * *
3057058 AAGCGCCACTAAAGACCATGTTCTTTAGCGGCG-TTTTTTTCT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCT
3057100 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCT
* * *
3057143 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTGTTTGT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT-TTTCT
*
3057187 AAACGCCGC
1 AAGCGCCGC
3057196 AAACGTTTGC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 30 0.34
43 45 0.52
44 12 0.14
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCT
Found at i:3059343 original size:3 final size:3
Alignment explanation
Indices: 3059337--3059365 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3059327 CTTTCCATCT
3059337 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3059366 TAATGTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3060260 original size:15 final size:16
Alignment explanation
Indices: 3060225--3060261 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3060215 TAAATACCCC
3060225 AAAGGGGGAAGGACTT
1 AAAGGGGGAAGGACTT
*
3060241 CAAGGGGGAAGGAC-T
1 AAAGGGGGAAGGACTT
3060256 AAAGGG
1 AAAGGG
3060262 TGAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.38, C:0.08, G:0.46, T:0.08
Consensus pattern (16 bp):
AAAGGGGGAAGGACTT
Found at i:3068434 original size:7 final size:7
Alignment explanation
Indices: 3068416--3068450 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
3068406 TTAAATTATT
3068416 ATTTTTA
1 ATTTTTA
3068423 A-TTTTA
1 ATTTTTA
3068429 ATTTTTA
1 ATTTTTA
3068436 ATTTTTA
1 ATTTTTA
3068443 ATTTTTA
1 ATTTTTA
3068450 A
1 A
3068451 AAATAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTTTTA
Found at i:3068538 original size:22 final size:22
Alignment explanation
Indices: 3068513--3068555 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3068503 TTTGAGTCAA
*
3068513 AATAATAA-TTTAATTATTTTGT
1 AATAA-AATTTTAATTAATTTGT
3068535 AATAAAATTTTAATTAATTTG
1 AATAAAATTTTAATTAATTTG
3068556 ACATGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
AATAAAATTTTAATTAATTTGT
Found at i:3070961 original size:22 final size:21
Alignment explanation
Indices: 3070894--3070966 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 21
3070884 ATATTAAATA
3070894 AATTATTAAAATAATAAATCATATT
1 AATTA-TAAAAT-ATAAAT-A-ATT
* * *
3070919 AATTATAACA-ATAATTTATT
1 AATTATAAAATATAAATAATT
3070939 ATATTATAAAATATAAATAATT
1 A-ATTATAAAATATAAATAATT
*
3070961 ACTTAT
1 AATTAT
3070967 GAATGTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 4 0.10
21 12 0.31
22 14 0.36
24 4 0.10
25 5 0.13
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTATAAAATATAAATAATT
Found at i:3071073 original size:20 final size:20
Alignment explanation
Indices: 3071048--3071088 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3071038 TAAAATAAAA
3071048 AATATTATTAATGTAATAAT
1 AATATTATTAATGTAATAAT
*
3071068 AATATTCTTAATGTAATAAT
1 AATATTATTAATGTAATAAT
3071088 A
1 A
3071089 TTAGGCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
AATATTATTAATGTAATAAT
Found at i:3071531 original size:15 final size:15
Alignment explanation
Indices: 3071511--3071541 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3071501 TTTAAAAACC
3071511 AAACCCAATCCAATT
1 AAACCCAATCCAATT
*
3071526 AAACCCAATTCAATT
1 AAACCCAATCCAATT
3071541 A
1 A
3071542 CAAAACCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACCCAATCCAATT
Found at i:3072618 original size:3 final size:3
Alignment explanation
Indices: 3072610--3072678 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
3072600 ATATTTTTAT
3072610 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3072658 TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
3072679 AACTGTTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3080127 original size:32 final size:31
Alignment explanation
Indices: 3080067--3080128 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
3080057 ACTCTTGTAT
*
3080067 AGAAAGCCCTTAATTATAAATGGACTTATTA
1 AGAAAGCCCTTAATTATAAACGGACTTATTA
* * *
3080098 AGAAAGCCCATTAGTTATAAGCGGGCTTATT
1 AGAAAGCCC-TTAATTATAAACGGACTTATT
3080129 CTGACCCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (31 bp):
AGAAAGCCCTTAATTATAAACGGACTTATTA
Found at i:3101226 original size:20 final size:20
Alignment explanation
Indices: 3101190--3101229 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3101180 ATAATATTAT
*
3101190 AATTTAAAGATATATTTAAA
1 AATTTAAAAATATATTTAAA
3101210 AATTTAAAAAT-TAATTTAAA
1 AATTTAAAAATAT-ATTTAAA
3101230 TTAAACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AATTTAAAAATATATTTAAA
Found at i:3117545 original size:18 final size:17
Alignment explanation
Indices: 3117518--3117555 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
3117508 AGAGGTTAGC
3117518 AAAAAAATATTTTTAAA
1 AAAAAAATATTTTTAAA
3117535 AAAATAAATATTTTTAAA
1 AAAA-AAATATTTTTAAA
3117553 AAA
1 AAA
3117556 GAGATACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAAAATATTTTTAAA
Found at i:3149902 original size:40 final size:40
Alignment explanation
Indices: 3149858--3149936 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
3149848 TTTTACTTGA
* *
3149858 CCGGTGATATTTATACTTATATATTAAAGTAAGGTTCAAG
1 CCGGTGATATCTATACTTATATATTAAAGTAAGATTCAAG
* *
3149898 CCGGTGATGTCTATACTTATATATTGAAGTAAGATTCAA
1 CCGGTGATATCTATACTTATATATTAAAGTAAGATTCAA
3149937 AGGTTCTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (40 bp):
CCGGTGATATCTATACTTATATATTAAAGTAAGATTCAAG
Found at i:3155533 original size:11 final size:11
Alignment explanation
Indices: 3155517--3155542 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3155507 GGTTTCAATT
3155517 TTTCTTGAAAA
1 TTTCTTGAAAA
3155528 TTTCTTGAAAA
1 TTTCTTGAAAA
3155539 TTTC
1 TTTC
3155543 GAGTTATTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTTGAAAA
Found at i:3157555 original size:13 final size:13
Alignment explanation
Indices: 3157537--3157563 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3157527 TTCTTGAGAG
3157537 AATATATATATAT
1 AATATATATATAT
3157550 AATATATATATAT
1 AATATATATATAT
3157563 A
1 A
3157564 TTAGATGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:3158766 original size:21 final size:22
Alignment explanation
Indices: 3158723--3158767 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
3158713 ATTTCAACAA
*
3158723 AAATCAAAGTTTCATGTGCATC
1 AAATCAAAGTTTCATATGCATC
*
3158745 AAATCAAAG-TTCATATGTATC
1 AAATCAAAGTTTCATATGCATC
3158766 AA
1 AA
3158768 GTTATACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (22 bp):
AAATCAAAGTTTCATATGCATC
Found at i:3160474 original size:15 final size:14
Alignment explanation
Indices: 3160447--3160473 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3160437 AATTTAGTAT
3160447 TATTTTTAAAAAAG
1 TATTTTTAAAAAAG
3160461 TATTTTTAAAAAA
1 TATTTTTAAAAAA
3160474 ACTTTTGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TATTTTTAAAAAAG
Found at i:3171400 original size:2 final size:2
Alignment explanation
Indices: 3171387--3171419 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3171377 CTAATAGTGA
*
3171387 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3171420 ACCACTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3189431 original size:34 final size:32
Alignment explanation
Indices: 3189365--3189432 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 32
3189355 TTATTTATGG
*
3189365 TTATTTTTAATTATTTAATGATATTTTAGTAA
1 TTATTTTTAATTATTGAATGATATTTTAGTAA
*
3189397 TTATTTTTATATTATTGACAT-ATAATTTTCGTAA
1 TTATTTTTA-ATTATTGA-ATGAT-ATTTTAGTAA
3189431 TT
1 TT
3189433 TTTACCTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 9 0.29
33 9 0.29
34 13 0.42
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (32 bp):
TTATTTTTAATTATTGAATGATATTTTAGTAA
Found at i:3191475 original size:19 final size:19
Alignment explanation
Indices: 3191447--3191485 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3191437 GGGATATGTG
*
3191447 TTAGTGTTGGACATGTGAA
1 TTAGTATTGGACATGTGAA
3191466 TTAGTATTGGACATGTGAA
1 TTAGTATTGGACATGTGAA
3191485 T
1 T
3191486 AATTAAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.38
Consensus pattern (19 bp):
TTAGTATTGGACATGTGAA
Done.