Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 9 of 150
Found at i:2483512 original size:20 final size:20
Alignment explanation
Indices: 2483480--2483598 Score: 70
Period size: 20 Copynumber: 6.2 Consensus size: 20
2483470 CTTTATAAAA
*
2483480 TTTTAT-AATTTTTTATGAT
1 TTTTATAAAATTTTTATGAT
*
2483499 TTTTATAAAATTTTTACGAT
1 TTTTATAAAATTTTTATGAT
* * ** * *
2483519 ATTTGTAATTTTTTTCTAAT
1 TTTTATAAAATTTTTATGAT
* **
2483539 TTTAATAAAATTTAAAT-AT
1 TTTTATAAAATTTTTATGAT
*
2483558 TTTTATTAAAA-TTTAAT-AT
1 TTTTA-TAAAATTTTTATGAT
2483577 TTTT-TATAAATTTTTATG-T
1 TTTTATA-AAATTTTTATGAT
2483596 TTT
1 TTT
2483599 ATTATTTTTT
Statistics
Matches: 75, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
17 2 0.03
18 3 0.04
19 32 0.43
20 38 0.51
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTATAAAATTTTTATGAT
Found at i:2483575 original size:19 final size:20
Alignment explanation
Indices: 2483538--2483586 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
2483528 TTTTTTCTAA
2483538 TTTTAATAAAATTTAAATAT
1 TTTTAATAAAATTTAAATAT
*
2483558 TTTTATTAAAATTT-AATAT
1 TTTTAATAAAATTTAAATAT
*
2483577 TTTTTATAAA
1 TTTTAATAAA
2483587 TTTTTATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAATAAAATTTAAATAT
Found at i:2483850 original size:92 final size:90
Alignment explanation
Indices: 2483669--2483881 Score: 268
Period size: 92 Copynumber: 2.3 Consensus size: 90
2483659 ATTAAGGGCG
* * ** * **
2483669 GTTCAAGTACCCAATTAAGTGCAAAAAAAGGCAGGGCTTAATTGTTTTTTTTTTTGAAAAATTTT
1 GTTCAAGTGCCCAATTGAGTGCAAAAAAAAACAGGGCTTAATTGTATTTTTTTTTGAAAAAAATT
*
2483734 GAGGGCCTTTTTATGCATTTTGAAA
66 GAGGGCCTTTTTATGCATTGTGAAA
*
2483759 GTTCAAGTGCCCAATTGAGTGCAAAAAAGAAACAATGGCTTAATTG-ATTTTTTTTTGAAAAAAA
1 GTTCAAGTGCCCAATTGAGTGCAAAAAA-AAAC-AGGGCTTAATTGTATTTTTTTTTGAAAAAAA
*
2483823 TTGAGGG-TTATTTTGATGCATTGTGAAA
64 TTGAGGGCCT-TTTT-ATGCATTGTGAAA
* *
2483851 GCTCAAGTGCCCAAGTGAGTGCAAAAAAAAA
1 GTTCAAGTGCCCAATTGAGTGCAAAAAAAAA
2483882 ACGCAGGGGC
Statistics
Matches: 107, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
90 27 0.25
91 31 0.29
92 49 0.46
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (90 bp):
GTTCAAGTGCCCAATTGAGTGCAAAAAAAAACAGGGCTTAATTGTATTTTTTTTTGAAAAAAATT
GAGGGCCTTTTTATGCATTGTGAAA
Found at i:2483904 original size:92 final size:91
Alignment explanation
Indices: 2483671--2483912 Score: 251
Period size: 92 Copynumber: 2.7 Consensus size: 91
2483661 TAAGGGCGGT
* * * ** * * **
2483671 TCAAGTACCCAATTAAGTGC-AAAAAAAGGC-AGGGCTTAATTGTTTTTTTTTTTGAAAAATTTT
1 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAACAAGGGCTTAATTG-ATCTTTTTTTGAAAAAAATT
* *
2483734 GAGGGCCTTTTTATGCATTTTGAAAGT
65 GAGGGCCTTTTTATGCATTGTGAAAGC
* * * *
2483761 TCAAGTGCCCAATTGAGTGCAAAAAAGAAACAATGGCTTAATTGATTTTTTTTTGAAAAAAATTG
1 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAACAAGGGCTTAATTGATCTTTTTTTGAAAAAAATTG
*
2483826 AGGG-TTATTTTGATGCATTGTGAAAGC
66 AGGGCCT-TTTT-ATGCATTGTGAAAGC
*
2483853 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAACGCAGGGGCTTAATT-A-CTTTTTTTGAAAAA
1 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAA--CAAGGGCTTAATTGATCTTTTTTTGAAAAA
2483913 GTTTGAAGGC
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
90 19 0.15
91 33 0.26
92 65 0.50
93 1 0.01
94 11 0.09
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (91 bp):
TCAAGTGCCCAAGTGAGTGCAAAAAAAAAACAAGGGCTTAATTGATCTTTTTTTGAAAAAAATTG
AGGGCCTTTTTATGCATTGTGAAAGC
Found at i:2484846 original size:30 final size:32
Alignment explanation
Indices: 2484811--2484894 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 32
2484801 TAGGCTCCCA
*
2484811 AATTTTTTAAAATTCTCATTATA-CTTT-TTA-
1 AATTTTTGAAAATTCTCATTA-AGCTTTCTTAC
* * *
2484841 TATTTTTGAAAATTTTGATTAAGCTTTCTTAC
1 AATTTTTGAAAATTCTCATTAAGCTTTCTTAC
2484873 AATTTTTGAAAATTCTCATTAA
1 AATTTTTGAAAATTCTCATTAA
2484895 TCTCACACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 1 0.02
30 21 0.48
31 3 0.07
32 19 0.43
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (32 bp):
AATTTTTGAAAATTCTCATTAAGCTTTCTTAC
Found at i:2485690 original size:21 final size:21
Alignment explanation
Indices: 2485664--2485705 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2485654 TATATTATAT
* *
2485664 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
*
2485685 AATAAATCAAAAGAAAGAAAG
1 AATAAAACAAAAGAAAGAAAG
2485706 GTAGAAACGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.12
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:2486662 original size:41 final size:40
Alignment explanation
Indices: 2486617--2486742 Score: 125
Period size: 41 Copynumber: 3.2 Consensus size: 40
2486607 CGACTTCGAG
2486617 TCGATGAGACATTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAGACATTGGGTGTCAATTTA-TACTTCGGATTAAT
* * * * *
2486658 TCGATGAGGCATTGGATGCCAA-TT-TACTTCTGTTTAA-
1 TCGATGAGACATTGGGTGTCAATTTATACTTCGGATTAAT
* * * *
2486695 CCGATGAGACACTGGGTGTCAATTTATTATTTCGAATT-AT
1 TCGATGAGACATTGGGTGTCAATTTA-TACTTCGGATTAAT
2486735 TCGATGAG
1 TCGATGAG
2486743 GCACTGGGAG
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
37 17 0.26
38 13 0.20
39 1 0.02
40 16 0.24
41 19 0.29
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (40 bp):
TCGATGAGACATTGGGTGTCAATTTATACTTCGGATTAAT
Found at i:2486718 original size:37 final size:38
Alignment explanation
Indices: 2486618--2486720 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 38
2486608 GACTTCGAGT
*
2486618 CGATGAGACATTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACATTGGGTGTCAA-TT--TACTTCGGATTAATC
* * * * *
2486659 CGATGAGGCATTGGATGCCAATTTACTTCTGTTTAA-C
1 CGATGAGACATTGGGTGTCAATTTACTTCGGATTAATC
*
2486696 CGATGAGACACTGGGTGTCAATTTA
1 CGATGAGACATTGGGTGTCAATTTA
2486721 TTATTTCGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 21 0.40
38 11 0.21
40 2 0.04
41 18 0.35
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (38 bp):
CGATGAGACATTGGGTGTCAATTTACTTCGGATTAATC
Found at i:2494298 original size:73 final size:73
Alignment explanation
Indices: 2494190--2494343 Score: 231
Period size: 73 Copynumber: 2.1 Consensus size: 73
2494180 TGGGTTTAGA
* * *
2494190 GGAAGGAAAAGAAAGGTTTGAAAGGAAACTAGTTTCATTTTTGCTTTTTTTTTTGGTAGAAGGAA
1 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAA-GAA
2494255 A-AT-GAGAG
65 AGATAG-GAG
* *
2494263 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCCTTTTTTCCTTTTTCTTTGGTAGAAGAAA
1 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAAGAAA
2494328 GATAGGAG
66 GATAGGAG
2494336 GGAAGGAA
1 GGAAGGAA
2494344 GGAAAATGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
72 4 0.05
73 69 0.93
74 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (73 bp):
GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAAGAAA
GATAGGAG
Found at i:2495232 original size:17 final size:18
Alignment explanation
Indices: 2495207--2495282 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
2495197 TAAGAGAGAA
*
2495207 AGAAAGAAC-TGAAAAGG
1 AGAAGGAACGTGAAAAGG
2495224 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
* *
2495242 A-AAGGGAGAAG-G-AACGCG
1 AGAA-GGA-ACGTGAAAAG-G
2495260 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
2495278 A-AAGG
1 AGAAGG
2495283 GAGAAGGCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
17 19 0.40
18 21 0.45
19 7 0.15
ACGTcount: A:0.51, C:0.07, G:0.38, T:0.04
Consensus pattern (18 bp):
AGAAGGAACGTGAAAAGG
Found at i:2495249 original size:24 final size:24
Alignment explanation
Indices: 2495217--2495267 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2495207 AGAAAGAACT
*
2495217 GAAAAGGAGAAGGAACGTGAAAAG
1 GAAAAGGAGAAGGAACGCGAAAAG
* *
2495241 GAAAGGGAGAAGGAACGCGAGAAG
1 GAAAAGGAGAAGGAACGCGAAAAG
2495265 GAA
1 GAA
2495268 CGTGAAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.41, T:0.02
Consensus pattern (24 bp):
GAAAAGGAGAAGGAACGCGAAAAG
Found at i:2495289 original size:12 final size:12
Alignment explanation
Indices: 2495217--2495289 Score: 65
Period size: 12 Copynumber: 6.1 Consensus size: 12
2495207 AGAAAGAACT
*
2495217 GAAAAGGAGAAG
1 GAAAGGGAGAAG
* * *
2495229 GAACGTGAAAAG
1 GAAAGGGAGAAG
2495241 GAAAGGGAGAAG
1 GAAAGGGAGAAG
* *
2495253 GAACGCGAGAAG
1 GAAAGGGAGAAG
* * *
2495265 GAACGTGAAAAG
1 GAAAGGGAGAAG
2495277 GAAAGGGAGAAG
1 GAAAGGGAGAAG
2495289 G
1 G
2495290 CTGAAAGCAA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.49, C:0.05, G:0.42, T:0.03
Consensus pattern (12 bp):
GAAAGGGAGAAG
Found at i:2497054 original size:25 final size:25
Alignment explanation
Indices: 2497020--2497070 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2497010 TTTTCTTGAG
2497020 ATCATATAATGAACCTGATTAGTTT
1 ATCATATAATGAACCTGATTAGTTT
2497045 ATCATATAATGAACCTGATTAGTTT
1 ATCATATAATGAACCTGATTAGTTT
2497070 A
1 A
2497071 GTTGTTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (25 bp):
ATCATATAATGAACCTGATTAGTTT
Found at i:2502829 original size:10 final size:11
Alignment explanation
Indices: 2502798--2502823 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2502788 TTTTAAAAAA
2502798 TAATAACTTTT
1 TAATAACTTTT
2502809 TAATAACTTTT
1 TAATAACTTTT
2502820 TAAT
1 TAAT
2502824 TATTTTCACT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATAACTTTT
Found at i:2504238 original size:4 final size:4
Alignment explanation
Indices: 2504231--2504267 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
2504221 TGCATGCATC
* *
2504231 TATG TATG TATA TATG TATG TCTG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
2504268 TTTGCAGGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2505493 original size:23 final size:23
Alignment explanation
Indices: 2505439--2505495 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2505429 ATATTTTTAA
*
2505439 ATTTTATATTTAATTATAAAAAT
1 ATTTTAAATTTAATTATAAAAAT
* *
2505462 ATATAAAATGTTAA-TATAAAAAT
1 ATTTTAAAT-TTAATTATAAAAAT
2505485 ATTTTAAATTT
1 ATTTTAAATTT
2505496 TTAATAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 2 0.07
23 22 0.79
24 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTTAAATTTAATTATAAAAAT
Found at i:2505499 original size:24 final size:23
Alignment explanation
Indices: 2505447--2505501 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
2505437 AAATTTTATA
2505447 TTTAATTATAAAAATATATAAAAT
1 TTTAA-TATAAAAATATATAAAAT
* * *
2505471 GTTAATATAAAAATATTTTAAATT
1 TTTAATATAAAAATA-TATAAAAT
2505495 TTTAATA
1 TTTAATA
2505502 ATTTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTAATATAAAAATATATAAAAT
Found at i:2508083 original size:5 final size:6
Alignment explanation
Indices: 2508058--2508086 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2508048 TATTTGTATA
2508058 AATTTT AATTTT AATTTT AA-TTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
2508087 CCCATTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:2508083 original size:11 final size:12
Alignment explanation
Indices: 2508058--2508086 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2508048 TATTTGTATA
2508058 AATTTTAATTTT
1 AATTTTAATTTT
2508070 AATTTTAA-TTT
1 AATTTTAATTTT
2508081 AATTTT
1 AATTTT
2508087 CCCATTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
AATTTTAATTTT
Found at i:2511890 original size:3 final size:3
Alignment explanation
Indices: 2511882--2511943 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
2511872 GAAGTTCTGG
2511882 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2511930 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
2511944 ATGCCATCAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2518423 original size:27 final size:27
Alignment explanation
Indices: 2518393--2518459 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
2518383 TAAGTTTCGT
*
2518393 GGGACAGTCCACCATATAGGTGTTTGC
1 GGGACAGTCCACCAAATAGGTGTTTGC
* ** *
2518420 GGGACATTCCATAAAATAGGTGTTTGT
1 GGGACAGTCCACCAAATAGGTGTTTGC
2518447 GGGACAGTCCACC
1 GGGACAGTCCACC
2518460 GTTTAGCCTA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (27 bp):
GGGACAGTCCACCAAATAGGTGTTTGC
Found at i:2521275 original size:27 final size:27
Alignment explanation
Indices: 2521224--2521298 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
2521214 CTTTCTTTAG
* *
2521224 AATATGCCACGAAGGCGTTTCTTTTCATA
1 AATAT-CCACAAAGGC-TTCCTTTTCATA
*
2521253 AATCAT-TACAAAGGCTTCCTTTTCATA
1 AAT-ATCCACAAAGGCTTCCTTTTCATA
*
2521280 GATATCCACAAAGGCTTCC
1 AATATCCACAAAGGCTTCC
2521299 CTTCTTTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.05
27 25 0.64
28 7 0.18
29 3 0.08
30 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (27 bp):
AATATCCACAAAGGCTTCCTTTTCATA
Found at i:2521308 original size:27 final size:26
Alignment explanation
Indices: 2521260--2521323 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
2521250 ATAAATCATT
2521260 ACAAAGGCTTCCTTTTCATAGATAT-CC
1 ACAAAGGCTTCCTTTT-ATAGAT-TGCC
2521287 ACAAAGGCTTCCCTTCTT-TAGATTGCC
1 ACAAAGGCTT-CCTT-TTATAGATTGCC
2521314 ACAAAGGCTT
1 ACAAAGGCTT
2521324 TTATCTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 1 0.03
27 27 0.79
28 4 0.12
29 2 0.06
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (26 bp):
ACAAAGGCTTCCTTTTATAGATTGCC
Found at i:2521534 original size:50 final size:50
Alignment explanation
Indices: 2521439--2521537 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 50
2521429 CTTTTAGTCA
* * * * * *
2521439 TTTCTATATTATGTCATAACCCACCAGTTATGGTATTATATAATATGGTC
1 TTTCCATATGATGCCATAACCCACCAGCTATGGTATTACACAATATGGTC
* * *
2521489 TTTCCATATGATGCCATAGCCCACTAGCTATGGTCTTACACAATATGGT
1 TTTCCATATGATGCCATAACCCACCAGCTATGGTATTACACAATATGGT
2521538 GCCATGGTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (50 bp):
TTTCCATATGATGCCATAACCCACCAGCTATGGTATTACACAATATGGTC
Found at i:2532292 original size:105 final size:105
Alignment explanation
Indices: 2532110--2532323 Score: 410
Period size: 105 Copynumber: 2.0 Consensus size: 105
2532100 CTGGTGCGAG
*
2532110 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
2532175 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
*
2532215 TCAAACAATGTGAAGTTGCCTGATCTTGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
2532280 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
2532320 TCAA
1 TCAA
2532324 CTTATACTCA
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 107 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (105 bp):
TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
Found at i:2542905 original size:106 final size:105
Alignment explanation
Indices: 2542715--2542916 Score: 275
Period size: 106 Copynumber: 1.9 Consensus size: 105
2542705 AAAAATATAT
*
2542715 ATTTTTTTTTACTTTTGGTTTGTCAATGTCCAGCACCAGTATACGAAAAAAGTAAAAAAAAAAAA
1 ATTTTTTTTTACTTTT-GTTTGTCAATGTCCAGCACCAGTATACAAAAAAAGT-AAAAAAAAAAA
* * *
2542780 TTTTGTGGTGGCCTGCCAATTGCCGGCACCACCTTTATTGGA
64 TTTGGTGGTGGCCTACCAATGGCCGGCACCACCTTTATTGGA
*
2542822 ATTTTTTTTTACTTTT-TTCGTGTCAATG-GCAGGGCACCAGTATACAAAAAAAGT-AAAAAAAA
1 ATTTTTTTTTACTTTTGTT--TGTCAATGTCCA--GCACCAGTATACAAAAAAAGTAAAAAAAAA
*
2542884 AATTTGGTGGTGGCCTACCAATGGTCGGCACCA
62 AATTTGGTGGTGGCCTACCAATGGCCGGCACCA
2542917 GTAAATTTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
105 2 0.02
106 39 0.46
107 24 0.28
108 20 0.24
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (105 bp):
ATTTTTTTTTACTTTTGTTTGTCAATGTCCAGCACCAGTATACAAAAAAAGTAAAAAAAAAAATT
TGGTGGTGGCCTACCAATGGCCGGCACCACCTTTATTGGA
Found at i:2543371 original size:13 final size:13
Alignment explanation
Indices: 2543353--2543377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2543343 CGCGACAATT
2543353 TTAATTTTTTCTG
1 TTAATTTTTTCTG
2543366 TTAATTTTTTCT
1 TTAATTTTTTCT
2543378 TTTTTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
TTAATTTTTTCTG
Found at i:2546572 original size:2 final size:2
Alignment explanation
Indices: 2546567--2546594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2546557 TTTAGAAAAC
2546567 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
2546595 AAAGATAAGG
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):
TA
Found at i:2547272 original size:17 final size:17
Alignment explanation
Indices: 2547252--2547302 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
2547242 CTTTTTTATA
2547252 TAATATATTTGTTTAAT
1 TAATATATTTGTTTAAT
*
2547269 TAATACTAGTTT-TTTTAT
1 TAATA-TA-TTTGTTTAAT
*
2547287 AAATATATTTGTTTAA
1 TAATATATTTGTTTAA
2547303 GTTACTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 11 0.39
19 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (17 bp):
TAATATATTTGTTTAAT
Found at i:2549043 original size:2 final size:2
Alignment explanation
Indices: 2549038--2549066 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2549028 ATTGAACTTT
2549038 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2549067 ACATTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2562283 original size:16 final size:16
Alignment explanation
Indices: 2562262--2562314 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
2562252 TTGGTTCGCT
2562262 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
2562278 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
2562294 ATAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
2562310 GTAAT
1 GTAAT
2562315 AGGTAATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.34, T:0.21
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:2562383 original size:44 final size:46
Alignment explanation
Indices: 2562295--2562384 Score: 157
Period size: 44 Copynumber: 2.0 Consensus size: 46
2562285 AATAGAGGCA
*
2562295 TAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATG
1 TAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATG
2562341 TAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATG
1 TAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATG
2562385 GAATAGAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 20 0.47
45 3 0.07
46 20 0.47
ACGTcount: A:0.27, C:0.04, G:0.30, T:0.39
Consensus pattern (46 bp):
TAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATG
Found at i:2562385 original size:39 final size:44
Alignment explanation
Indices: 2562295--2562401 Score: 143
Period size: 46 Copynumber: 2.5 Consensus size: 44
2562285 AATAGAGGCA
*
2562295 TAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATG
1 TAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATG
2562341 TAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-TG
1 TAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATG
*
2562381 -AATGGAATAGAGGTGTAATAG
1 TAATGGAATAGAGGCGTAATAG
2562402 CATAAGGAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
39 18 0.31
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 20 0.34
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (44 bp):
TAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATG
Found at i:2562553 original size:16 final size:16
Alignment explanation
Indices: 2562545--2562581 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
2562535 TAATTGTTAT
2562545 AAAATATAATTTAATAA
1 AAAATATAATTTAAT-A
2562562 AAATATATAATTTAATA
1 AAA-ATATAATTTAATA
2562579 AAA
1 AAA
2562582 TTNNNNNNNN
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATAATTTAATA
Found at i:2562763 original size:12 final size:12
Alignment explanation
Indices: 2562746--2562797 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2562736 TATAATACTA
2562746 TAAAATATAATT
1 TAAAATATAATT
*
2562758 TAAAATAATTATT
1 TAAAAT-ATAATT
*
2562771 ATTAAATATAATT
1 -TAAAATATAATT
* *
2562784 TATAATATACTT
1 TAAAATATAATT
2562796 TA
1 TA
2562798 TTATTATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 17 0.53
13 10 0.31
14 5 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:2562798 original size:26 final size:26
Alignment explanation
Indices: 2562748--2562800 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2562738 TAATACTATA
*
2562748 AAATATAATTTAAAATAATTATTATT
1 AAATATAATTTAAAATAACTATTATT
*
2562774 AAATATAATTTATAATATACT-TTATT
1 AAATATAATTTAAAATA-ACTATTATT
2562800 A
1 A
2562801 TTATTAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATATAATTTAAAATAACTATTATT
Found at i:2567431 original size:12 final size:12
Alignment explanation
Indices: 2567407--2567440 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2567397 CCGCATTTTA
2567407 AGCAAAAGAACG
1 AGCAAAAGAACG
* *
2567419 AGCCAAAGCACG
1 AGCAAAAGAACG
2567431 AGCAAAAGAA
1 AGCAAAAGAA
2567441 AATAAATAAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.24, T:0.00
Consensus pattern (12 bp):
AGCAAAAGAACG
Found at i:2568552 original size:23 final size:22
Alignment explanation
Indices: 2568508--2568552 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2568498 ATAAAAAATC
*
2568508 TATTTAAAAAAAGGTCAAATTT
1 TATTTAAAAAAAGGTAAAATTT
2568530 TATTTAAAATAAAGG-AAATATTT
1 TATTTAAAA-AAAGGTAAA-ATTT
2568553 CCACTTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (22 bp):
TATTTAAAAAAAGGTAAAATTT
Found at i:2569385 original size:13 final size:13
Alignment explanation
Indices: 2569367--2569391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2569357 AACATTCGGC
2569367 CGGTGGGAATAAT
1 CGGTGGGAATAAT
2569380 CGGTGGGAATAA
1 CGGTGGGAATAA
2569392 ACAAATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (13 bp):
CGGTGGGAATAAT
Found at i:2577721 original size:12 final size:11
Alignment explanation
Indices: 2577682--2577718 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
2577672 TATTTTTTAA
2577682 TTTTAAAATAT
1 TTTTAAAATAT
2577693 TTTTAAAATACT
1 TTTTAAAATA-T
2577705 TTTTAAAA-AT
1 TTTTAAAATAT
2577715 TTTT
1 TTTT
2577719 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.20
11 11 0.44
12 9 0.36
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2578583 original size:61 final size:61
Alignment explanation
Indices: 2578488--2578670 Score: 303
Period size: 61 Copynumber: 3.0 Consensus size: 61
2578478 CTTTGTCTAC
* **
2578488 CCCTTGGCTAGGCTATATTCTATCCACGTGTTTCTGAGCGAATCTAATTCGATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
* *
2578549 CCCTTAGCTAGGCTATAATCTATCCATGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
* *
2578610 CCCTTGGCTGGGCTATAATCTATCCACGTGTTTCTGATTTAATCTAATTCGATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
2578671 TTGTATAACT
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 113 1.00
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (61 bp):
CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
Found at i:2583033 original size:44 final size:44
Alignment explanation
Indices: 2582974--2583059 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
2582964 GTCTTTTTAA
* *
2582974 AATTTGTTGGTAAACATTTGTTTCAATGTTTTTAATGTATTTTT
1 AATTTGTTGGGAAACACTTGTTTCAATGTTTTTAATGTATTTTT
* *
2583018 AATTTGTTGGGAAACACTTGTTTTAATGTTTTTAGTGTATTT
1 AATTTGTTGGGAAACACTTGTTTCAATGTTTTTAATGTATTT
2583060 GATATATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (44 bp):
AATTTGTTGGGAAACACTTGTTTCAATGTTTTTAATGTATTTTT
Found at i:2584802 original size:29 final size:31
Alignment explanation
Indices: 2584760--2584836 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
2584750 TTTACCTCAG
*
2584760 GTTACATTTTAGTCACTTATGTT-TA-AAAT
1 GTTACATTTTAGTCACTTACGTTATAGAAAT
* *
2584789 GTTACATTTTAGTCACTTACGTTATAGTATT
1 GTTACATTTTAGTCACTTACGTTATAGAAAT
*
2584820 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
2584837 GAGTCGTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 22 0.52
30 2 0.05
31 18 0.43
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.47
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTACGTTATAGAAAT
Found at i:2585048 original size:27 final size:26
Alignment explanation
Indices: 2584991--2585050 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
2584981 TTTTAACTTT
* *
2584991 CTTTTTTTCTTCCTTATTTTCCATTCT
1 CTTTTTTTCTCCCTTATTTTCCA-TCC
2585018 CTTTTGTTTCTCCCTCTATTTTCC-TCC
1 CTTTT-TTTCTCCCT-TATTTTCCATCC
2585045 CTTTTT
1 CTTTTT
2585051 CATTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 1 0.03
27 12 0.41
28 8 0.28
29 8 0.28
ACGTcount: A:0.05, C:0.30, G:0.02, T:0.63
Consensus pattern (26 bp):
CTTTTTTTCTCCCTTATTTTCCATCC
Found at i:2589698 original size:17 final size:16
Alignment explanation
Indices: 2589676--2589709 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2589666 AAATCCAGGG
2589676 ATTAAAGTGAAAAGAAT
1 ATTAAA-TGAAAAGAAT
*
2589693 ATTAAATTAAAAGAAT
1 ATTAAATGAAAAGAAT
2589709 A
1 A
2589710 AATGTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (16 bp):
ATTAAATGAAAAGAAT
Found at i:2597435 original size:19 final size:20
Alignment explanation
Indices: 2597402--2597449 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
2597392 AAAATTAGTA
* *
2597402 TTTATTTGTG-TTTTTATTT
1 TTTATTTCTGATTTTCATTT
2597421 TTTATTTCTGATTTTCCAATTT
1 TTTATTTCTGATTTT-C-ATTT
2597443 TTTATTT
1 TTTATTT
2597450 TTACTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
22 11 0.46
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTATTTCTGATTTTCATTT
Found at i:2600303 original size:2 final size:2
Alignment explanation
Indices: 2600296--2600326 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2600286 TATTTCTAGA
2600296 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
2600327 AATTGTTAGC
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:2607326 original size:6 final size:6
Alignment explanation
Indices: 2607314--2607351 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
2607304 TATAAACTCT
* *
2607314 GCATCA TCATCA TCATCA GCATCA GCATCA GCATCA GC
1 GCATCA GCATCA GCATCA GCATCA GCATCA GCATCA GC
2607352 TGGATGTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.32, C:0.34, G:0.13, T:0.21
Consensus pattern (6 bp):
GCATCA
Found at i:2609139 original size:14 final size:15
Alignment explanation
Indices: 2609114--2609142 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2609104 TAACTTTCTG
2609114 AATATATATTTATTT
1 AATATATATTTATTT
2609129 AATAT-TATTTATTT
1 AATATATATTTATTT
2609143 TTTATAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATATATATTTATTT
Found at i:2612141 original size:2 final size:2
Alignment explanation
Indices: 2612136--2612169 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2612126 AGTTCTTATC
2612136 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
2612170 TTATCAACTG
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:2617738 original size:27 final size:27
Alignment explanation
Indices: 2617677--2617765 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
2617667 TTTATTTTTG
2617677 TTAAAA-TAATGTCCAAAAACTAAAATT
1 TTAAAATTAAT-TCCAAAAACTAAAATT
2617704 TTAAAATTAATTCCAAAAACTAAAATT
1 TTAAAATTAATTCCAAAAACTAAAATT
* *
2617731 TTAAAATTAA-TACAAAAA--AAAAGT
1 TTAAAATTAATTCCAAAAACTAAAATT
*
2617755 TAAAAATTAAT
1 TTAAAATTAAT
2617766 CTGAATTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
24 14 0.25
26 7 0.12
27 32 0.56
28 4 0.07
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (27 bp):
TTAAAATTAATTCCAAAAACTAAAATT
Found at i:2622363 original size:20 final size:21
Alignment explanation
Indices: 2622326--2622364 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2622316 GGATAGTGGG
2622326 GTCAAATCCATAAACAGTAGA
1 GTCAAATCCATAAACAGTAGA
*
2622347 GTCAAAT-CATGAACAGTA
1 GTCAAATCCATAAACAGTA
2622365 ATAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (21 bp):
GTCAAATCCATAAACAGTAGA
Found at i:2629232 original size:109 final size:109
Alignment explanation
Indices: 2629076--2629276 Score: 316
Period size: 109 Copynumber: 1.8 Consensus size: 109
2629066 TATTTAGTTG
2629076 TTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAAC-GCA
1 TTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGGCA
* *
2629140 AAACAATGCCTTATTTT-AAAATTTTTAAAAGGATATTAAGCCA
66 AAACAATACCTTATTTTGAAAAATTTTAAAAGGATATTAAGCCA
* * *
2629183 TTTGGTTGAACGAGAAAAATCGACACCTAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGG
1 TTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGG
*
2629248 CAAAACATTACCTTATTTTGAAAAATTTT
64 CAAAACAATACCTTATTTTGAAAAATTTT
2629277 CCTTTTTGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 13 0.15
109 45 0.54
110 18 0.21
111 8 0.10
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (109 bp):
TTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGGCA
AAACAATACCTTATTTTGAAAAATTTTAAAAGGATATTAAGCCA
Found at i:2629929 original size:3 final size:3
Alignment explanation
Indices: 2629921--2629989 Score: 111
Period size: 3 Copynumber: 22.3 Consensus size: 3
2629911 ACTAGTGTAG
2629921 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
2629967 GAAA TAA TAA TAA TAA TAA TAA T
1 -TAA TAA TAA TAA TAA TAA TAA T
2629990 GTTAAAAAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 58 0.94
4 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2630612 original size:18 final size:18
Alignment explanation
Indices: 2630589--2630627 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2630579 TGAAAGGAAG
2630589 AAAAATCAA-AAGAAAAAT
1 AAAAAT-AAGAAGAAAAAT
2630607 AAAAATAAGAAGAAAAAT
1 AAAAATAAGAAGAAAAAT
2630625 AAA
1 AAA
2630628 GCTTATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (18 bp):
AAAAATAAGAAGAAAAAT
Found at i:2631410 original size:31 final size:31
Alignment explanation
Indices: 2631370--2631435 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
2631360 AAAATCTCAA
* *
2631370 AATTTGAAAAGTACAATGG-CTAAAATTGACC
1 AATTCGAAAAGCACAA-GGACTAAAATTGACC
* *
2631401 AATTCGAAAAGCATAAGGACTAAAATTGATC
1 AATTCGAAAAGCACAAGGACTAAAATTGACC
2631432 AATT
1 AATT
2631436 AATGTATAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (31 bp):
AATTCGAAAAGCACAAGGACTAAAATTGACC
Found at i:2631732 original size:51 final size:51
Alignment explanation
Indices: 2631651--2631767 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
2631641 TTAGGTATAA
* * *
2631651 TAACAAATTTAGCTCTCAAAATTTACACATTTTGTCAA-TTTGATCTTGATT
1 TAACAAATTTAGCTCACAAAATTTACACATTCTATCAATTTTG-TCTTGATT
* * *
2631702 TAACAAATTTAGC-CAACAATATTTATACATTCTATTAATTTTGTCTTGATT
1 TAACAAATTTAGCTC-ACAAAATTTACACATTCTATCAATTTTGTCTTGATT
2631753 TAACAAATTTAGCTC
1 TAACAAATTTAGCTC
2631768 GTGATATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.02
51 51 0.89
52 5 0.09
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (51 bp):
TAACAAATTTAGCTCACAAAATTTACACATTCTATCAATTTTGTCTTGATT
Found at i:2639945 original size:118 final size:120
Alignment explanation
Indices: 2639698--2640052 Score: 343
Period size: 118 Copynumber: 3.0 Consensus size: 120
2639688 TGTGATGTCT
* * * *** * * * * *
2639698 TGTCCCTTTATTACCTTGAAGGCTAAGATGAGAGGTCTCATCCCCTTTGATAGAATCAACCGAAG
1 TGTCCCTTTATGACCTTGAAGACCAAGGCAAGAGGACTTATCCCCTTAGGTAGAATCAACCAAAG
* * * *
2639763 GCCAATGTGTGAGGTCTCATC-CCTTTGAGGGATTGGC-AAAGTTGTTAGGTCT--
66 GCCAATGTGTGAGGTCTCATCTTCTTTGAGGAATTGGCTAAA-ATGTAAGGTCTCA
* *
2639815 TGTCCCTTTTATGACCTTGAAGGCCAATGCAAGAGGACTTATCCTCCTT-GGTAGAATCAACCAA
1 TGTCCC-TTTATGACCTTGAAGACCAAGGCAAGAGGACTTATCC-CCTTAGGTAGAATCAACCAA
*
2639879 AGGCCAATGTGTGAGGTCTCATCTTCATTGAGGAATTGGCTAAAATGTAAGGTCTCA
64 AGGCCAATGTGTGAGGTCTCATCTTCTTTGAGGAATTGGCTAAAATGTAAGGTCTCA
* * * *
2639936 T-TCCC-TTATGCCCTTGAAGACCAAGGCGAGAGGTCTTATCCCCTTAGGTAGAATCAAACGAAA
1 TGTCCCTTTATGACCTTGAAGACCAAGGCAAGAGGACTTATCCCCTTAGGTAGAATC-AACCAAA
* * * * **
2639999 -GTCAA-GTGTGAGGTCTCAT-TTCCTTTTAGGAAATGACTAAGGTGTAAGGTCTCA
65 GGCCAATGTGTGAGGTCTCATCTT-CTTTGAGGAATTGGCTAAAATGTAAGGTCTCA
2640053 CCCCTATTGG
Statistics
Matches: 201, Mismatches: 28, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
116 2 0.01
117 50 0.25
118 109 0.54
119 32 0.16
120 7 0.03
121 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (120 bp):
TGTCCCTTTATGACCTTGAAGACCAAGGCAAGAGGACTTATCCCCTTAGGTAGAATCAACCAAAG
GCCAATGTGTGAGGTCTCATCTTCTTTGAGGAATTGGCTAAAATGTAAGGTCTCA
Found at i:2644767 original size:122 final size:122
Alignment explanation
Indices: 2644558--2644852 Score: 353
Period size: 122 Copynumber: 2.4 Consensus size: 122
2644548 ACCTAATGGC
* * * *
2644558 TTAAATGAAAACTTTTGATTAGTTTAGTGACCATTTTGTAACTTTTTAAAGTTACAAATAACGAT
1 TTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAAGCTACAAATAACGAT
* * * *
2644623 TTTAACTTTCTGCGAAGAGAGAAGGCTATATAACAATAATTTTAACA-ATCTAATGAA-
66 TTTAAATTTCTGCGAAGAGAGAAGGCTATACAACAACAATTTTAACAGCT-TAAT-AAT
** * * ** *
2644680 TTAAATAAAAACTTTAAAATAGTTTAATGATCATTTTGTAACTTTTTGAAGCTGTAAATAATGAT
1 TTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAAGCTACAAATAACGAT
* * * *
2644745 TTTAAATTTTTGC-AGATAGAGAAGGCTATACAATAACGATTTTAACAGCTTAATAAT
66 TTTAAATTTCTGCGA-AGAGAGAAGGCTATACAACAACAATTTTAACAGCTTAATAAT
**
2644802 TTAAATAAAATTTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAAG
1 TTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAAG
2644853 TTGAATAACC
Statistics
Matches: 145, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
121 3 0.02
122 141 0.97
123 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (122 bp):
TTAAATAAAAACTTTTGAATAGTTTAGTGACCATTTTGTAACTTTTTGAAGCTACAAATAACGAT
TTTAAATTTCTGCGAAGAGAGAAGGCTATACAACAACAATTTTAACAGCTTAATAAT
Found at i:2656898 original size:2 final size:2
Alignment explanation
Indices: 2656891--2656918 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2656881 CCTTCTAGAA
2656891 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2656919 ATTTGACCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2659353 original size:2 final size:2
Alignment explanation
Indices: 2659319--2659343 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2659309 ACATACATAC
2659319 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 A
2659344 CACCTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2661452 original size:44 final size:43
Alignment explanation
Indices: 2661356--2661477 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 43
2661346 ACTTGATGCG
* * * * *
2661356 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATGAATTCA
* * *
2661400 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGAATTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-GAATTCA
*
2661444 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
2661478 TACTTCTCCA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 3 0.05
44 62 0.95
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATGAATTCA
Found at i:2661499 original size:44 final size:44
Alignment explanation
Indices: 2661451--2661565 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
2661441 TCAATCTGCT
*
2661451 CCACTGCAACCTCAGGGAGATAAGA-TT-TACTTCTCCAGTCGGCC
1 CCACTGCAACCTCAGGGAGATAAGACTTGT-CTTCT-CAGTCGACC
** * * * *
2661495 CCACTGTGACTTCAAGGG-GATAAGACTTGTTTTCTCAGTCTACT
1 CCACTGCAACCTC-AGGGAGATAAGACTTGTCTTCTCAGTCGACC
2661539 CCACTGCAACCTCAGGGAGATAAGACT
1 CCACTGCAACCTCAGGGAGATAAGACT
2661566 ATTGTTTTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
43 4 0.07
44 42 0.74
45 10 0.18
46 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (44 bp):
CCACTGCAACCTCAGGGAGATAAGACTTGTCTTCTCAGTCGACC
Found at i:2661730 original size:87 final size:88
Alignment explanation
Indices: 2661619--2661829 Score: 345
Period size: 87 Copynumber: 2.4 Consensus size: 88
2661609 TGTAATCTTC
* * *
2661619 GATCTGCTTCACTGTTAACGCAGGAAAGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
2661684 ATGGAGGCAAGGCTTTG-TTTTT
66 ATGGAGGCAAGGCTTTGTTTTTT
*
2661706 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCTCTGCAACCG
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
2661771 ATGGAGGCAAGGCTTTGTTTTTT
66 ATGGAGGCAAGGCTTTGTTTTTT
* *
2661794 GATATGCTTCGCTGTTAACT-CAAGAAGGCAAGATCT
1 GATCTGCTTCGCTGTTAA-TGCAGGAAGGCAAGATCT
2661830 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
87 78 0.67
88 37 0.32
89 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (88 bp):
GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
ATGGAGGCAAGGCTTTGTTTTTT
Found at i:2663327 original size:13 final size:13
Alignment explanation
Indices: 2663309--2663376 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
2663299 TTAGCCTCTC
*
2663309 CATTTTTATTTTT
1 CATTTTTATTCTT
*
2663322 CATTTTCATTCTT
1 CATTTTTATTCTT
2663335 CATTTTTCATTCTT
1 CATTTTT-ATTCTT
2663349 -ATTTTTATT-TT
1 CATTTTTATTCTT
*
2663360 --TTTTCATT-TT
1 CATTTTTATTCTT
2663370 CATTTTT
1 CATTTTT
2663377 TGACTCAGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
10 9 0.19
11 2 0.04
12 7 0.15
13 23 0.49
14 6 0.13
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (13 bp):
CATTTTTATTCTT
Found at i:2663369 original size:6 final size:6
Alignment explanation
Indices: 2663318--2663375 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
2663308 CCATTTTTAT
*
2663318 TTTTCA TTTTCA TTCTTCA TTTTTCA TTCTT-A TTTTTA TTTT-- TTTTCA
1 TTTTCA TTTTCA TT-TTCA -TTTTCA TT-TTCA TTTTCA TTTTCA TTTTCA
2663366 TTTTCA TTTT
1 TTTTCA TTTT
2663376 TTGACTCAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.09
5 2 0.04
6 28 0.61
7 10 0.22
8 2 0.04
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCA
Found at i:2663376 original size:7 final size:7
Alignment explanation
Indices: 2663309--2663360 Score: 58
Period size: 6 Copynumber: 8.0 Consensus size: 7
2663299 TTAGCCTCTC
2663309 CATTTTT
1 CATTTTT
2663316 -ATTTTT
1 CATTTTT
2663322 CA-TTTT
1 CATTTTT
*
2663328 CATTCTT
1 CATTTTT
2663335 CATTTTT
1 CATTTTT
*
2663342 CATTCTT
1 CATTTTT
2663349 -ATTTTT
1 CATTTTT
2663355 -ATTTTT
1 CATTTTT
2663361 TTTCATTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
6 23 0.59
7 16 0.41
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:2679016 original size:16 final size:18
Alignment explanation
Indices: 2678995--2679031 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2678985 GCAATATACC
2678995 AAATATTA-T-TCTTTAA
1 AAATATTATTATCTTTAA
2679011 AAATATTATTATCTTTAA
1 AAATATTATTATCTTTAA
2679029 AAA
1 AAA
2679032 AAACTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATTATTATCTTTAA
Found at i:2679998 original size:4 final size:4
Alignment explanation
Indices: 2679991--2680016 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2679981 AGATTCTCTC
2679991 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
2680017 CCTTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:2682743 original size:11 final size:11
Alignment explanation
Indices: 2682729--2682769 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2682719 AATATGGTAA
2682729 AAAAATAAAAT
1 AAAAATAAAAT
2682740 -AAAATAAAAT
1 AAAAATAAAAT
*
2682750 AAAAATATTAA-
1 AAAAATA-AAAT
2682761 AAAAATAAA
1 AAAAATAAA
2682770 CATGTGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 11 0.42
11 13 0.50
12 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2691180 original size:40 final size:40
Alignment explanation
Indices: 2691110--2691185 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
2691100 ATTTCAACAC
* * *
2691110 TTATATGCACGAAATTAACAAAATTGAATAATCCAACAAT
1 TTATATGCACGAAATTAACAAAAATAAATAACCCAACAAT
*
2691150 TTATATGCAAC-AAATTAATAAAAATAAATAACCCAA
1 TTATATGC-ACGAAATTAACAAAAATAAATAACCCAA
2691186 AGGCAAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.26
Consensus pattern (40 bp):
TTATATGCACGAAATTAACAAAAATAAATAACCCAACAAT
Found at i:2694206 original size:28 final size:30
Alignment explanation
Indices: 2694150--2694226 Score: 113
Period size: 28 Copynumber: 2.6 Consensus size: 30
2694140 CACAGGAATA
2694150 AGTTGCTCACACAAGCTAACAGTATATTAG
1 AGTTGCTCACACAAGCTAACAGTATATTAG
* * *
2694180 GGTTGCTCACACAAGTTGACA-T-TATTAG
1 AGTTGCTCACACAAGCTAACAGTATATTAG
2694208 AGTTGCTCACACAAGCTAA
1 AGTTGCTCACACAAGCTAA
2694227 ACCTACGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 22 0.54
29 1 0.02
30 18 0.44
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (30 bp):
AGTTGCTCACACAAGCTAACAGTATATTAG
Found at i:2703388 original size:2 final size:2
Alignment explanation
Indices: 2703381--2703406 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2703371 AAATATTGTA
2703381 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
2703407 GAAAATCTTT
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:2706805 original size:19 final size:20
Alignment explanation
Indices: 2706718--2706816 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 20
2706708 TCTAACTTTC
*
2706718 TTTATATATATTTTTAGATATT
1 TTTATAAATATTTTTA-A-ATT
* *
2706740 TTT-TAAAT-TTATTATATT
1 TTTATAAATATTTTTAAATT
2706758 TTT-TAAAATATAAATTTTGAAATT
1 TTTAT-AAATAT---TTTT-AAATT
2706782 TTTATAAATATTTTTAAA-T
1 TTTATAAATATTTTTAAATT
2706801 TTTATAAATATTTTTA
1 TTTATAAATATTTTTA
2706817 TTTTATTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
18 7 0.11
19 21 0.32
20 9 0.14
21 8 0.12
22 3 0.05
23 3 0.05
24 13 0.20
25 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTATAAATATTTTTAAATT
Found at i:2706821 original size:17 final size:18
Alignment explanation
Indices: 2706781--2706822 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
2706771 ATTTTGAAAT
2706781 TTTTATAAATATTTTTAAA
1 TTTTATAAATATTTTT-AA
2706800 TTTTATAAATATTTTT-A
1 TTTTATAAATATTTTTAA
2706817 TTTTAT
1 TTTTAT
2706823 TTTTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.30
19 16 0.70
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATAAATATTTTTAA
Found at i:2707960 original size:29 final size:29
Alignment explanation
Indices: 2707896--2707974 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
2707886 GTGAATGTTT
* *
2707896 TCAATTTAGTCTTTATA-TTTTAATTTGA
1 TCAATTTAGTTTTTGTATTTTTAATTTGA
*
2707924 TCATATTTAGTTTTTGTATTTTTCAA-TTGG
1 TCA-ATTTAGTTTTTGTATTTTT-AATTTGA
*
2707954 TCAATTTTAGTTTATGTATTT
1 TCAA-TTTAGTTTTTGTATTT
2707975 AAAAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 3 0.07
29 13 0.30
30 25 0.58
31 2 0.05
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.59
Consensus pattern (29 bp):
TCAATTTAGTTTTTGTATTTTTAATTTGA
Found at i:2711242 original size:53 final size:53
Alignment explanation
Indices: 2711150--2711251 Score: 136
Period size: 52 Copynumber: 1.9 Consensus size: 53
2711140 AGTTAGGCCT
*
2711150 TGAAATTGGTAATTATTCCCCATTGAGGTCTGAA-CTTTTTTGTCCAAGATTC
1 TGAAATTGGCAATTATTCCCCATTGAGGTCTGAATCTTTTTTGTCCAAGATTC
* * *
2711202 TGAACTTGGCAATTTTTCCCACATTGAGG-CTTGAATTTTTTTTGTCCAAG
1 TGAAATTGGCAATTATTCCC-CATTGAGGTC-TGAATCTTTTTTGTCCAAG
2711252 TTAGTCCCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
52 18 0.42
53 12 0.28
54 13 0.30
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (53 bp):
TGAAATTGGCAATTATTCCCCATTGAGGTCTGAATCTTTTTTGTCCAAGATTC
Found at i:2713555 original size:18 final size:18
Alignment explanation
Indices: 2713529--2713564 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2713519 TTTTTTTTCA
* *
2713529 GGAATAATATAGAAAAAT
1 GGAACAATAAAGAAAAAT
2713547 GGAACAATAAAGAAAAAT
1 GGAACAATAAAGAAAAAT
2713565 TTTTTAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.03, G:0.17, T:0.17
Consensus pattern (18 bp):
GGAACAATAAAGAAAAAT
Found at i:2714514 original size:27 final size:27
Alignment explanation
Indices: 2714461--2714515 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2714451 AATAAAAAAT
* * *
2714461 ATAAAACTTTAAAAATTATAATTTTTA
1 ATAAAAATTTAAAAATGATAATCTTTA
2714488 ATAAAAATTATAAAAATGA-AATCTTTA
1 ATAAAAATT-TAAAAATGATAATCTTTA
2714515 A
1 A
2714516 AATTCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (27 bp):
ATAAAAATTTAAAAATGATAATCTTTA
Found at i:2717602 original size:16 final size:18
Alignment explanation
Indices: 2717571--2717608 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2717561 AAAATTCACG
2717571 AAATTGAAACATTAAAAA
1 AAATTGAAACATTAAAAA
*
2717589 AAATT-AAA-ATTAAAAC
1 AAATTGAAACATTAAAAA
2717605 AAAT
1 AAAT
2717609 CTTCACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATTGAAACATTAAAAA
Found at i:2717675 original size:23 final size:23
Alignment explanation
Indices: 2717648--2717696 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2717638 AACTAAACGA
2717648 AATACGGAAACGCAAAATTCAAT
1 AATACGGAAACGCAAAATTCAAT
2717671 AATACGGAAACGCAAAATTCAAT
1 AATACGGAAACGCAAAATTCAAT
2717694 AAT
1 AAT
2717697 GACTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.18
Consensus pattern (23 bp):
AATACGGAAACGCAAAATTCAAT
Found at i:2721306 original size:14 final size:15
Alignment explanation
Indices: 2721270--2721306 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2721260 AATGTTTTAC
2721270 TTTTCTGGAAAATGA
1 TTTTCTGGAAAATGA
*
2721285 TTTACTGGAAAAT-A
1 TTTTCTGGAAAATGA
2721299 TTTTCTGG
1 TTTTCTGG
2721307 TGTTTGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (15 bp):
TTTTCTGGAAAATGA
Found at i:2724879 original size:17 final size:17
Alignment explanation
Indices: 2724857--2724894 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2724847 TAAGGGTGGG
2724857 TTTAGATGGACAGTGCA
1 TTTAGATGGACAGTGCA
* *
2724874 TTTAGATGGATAGTGCG
1 TTTAGATGGACAGTGCA
2724891 TTTA
1 TTTA
2724895 TTTGCGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (17 bp):
TTTAGATGGACAGTGCA
Found at i:2725102 original size:12 final size:12
Alignment explanation
Indices: 2725085--2725110 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2725075 TTTTATCATA
2725085 AAATGGTTAAGT
1 AAATGGTTAAGT
2725097 AAATGGTTAAGT
1 AAATGGTTAAGT
2725109 AA
1 AA
2725111 TTTCCTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (12 bp):
AAATGGTTAAGT
Found at i:2728255 original size:17 final size:17
Alignment explanation
Indices: 2728233--2728266 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2728223 AACAAATTAT
2728233 TAAAAAACT-TATTAAAA
1 TAAAAAA-TATATTAAAA
2728250 TAAAAAATATATTAAAA
1 TAAAAAATATATTAAAA
2728267 AATCTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATATATTAAAA
Found at i:2728358 original size:2 final size:2
Alignment explanation
Indices: 2728345--2728385 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
2728335 CGATTCAATC
* *
2728345 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT GAT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
2728386 CGTAAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2738461 original size:47 final size:47
Alignment explanation
Indices: 2738392--2738513 Score: 163
Period size: 47 Copynumber: 2.6 Consensus size: 47
2738382 AGTCCAACTT
* *
2738392 TGGTCTTACACGGAATCACATATCACACCAATATCATATCCCAGATA
1 TGGTCTTACACAGAAGCACATATCACACCAATATCATATCCCAGATA
* * * *
2738439 TGGTCTTACACAGTAGCACATATCACATCGATGTCATATCCCAGATA
1 TGGTCTTACACAGAAGCACATATCACACCAATATCATATCCCAGATA
* *
2738486 TGGTCTTACACGGAAATCACATATCACA
1 TGGTCTTACACAG-AAGCACATATCACA
2738514 TATTGCCATG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 53 0.82
48 12 0.18
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (47 bp):
TGGTCTTACACAGAAGCACATATCACACCAATATCATATCCCAGATA
Found at i:2740781 original size:24 final size:24
Alignment explanation
Indices: 2740753--2740800 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2740743 CAAGTATGCC
2740753 TACTTTAAATTTTCCATTCTTCAT
1 TACTTTAAATTTTCCATTCTTCAT
2740777 TACTTTAAATTTTCCATTCTTCAT
1 TACTTTAAATTTTCCATTCTTCAT
2740801 AAGAGACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (24 bp):
TACTTTAAATTTTCCATTCTTCAT
Found at i:2747394 original size:16 final size:16
Alignment explanation
Indices: 2747373--2747408 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2747363 CTCATAAAAA
*
2747373 TTAATTTAATTATTTT
1 TTAATTAAATTATTTT
*
2747389 TTAATTAAATTTTTTT
1 TTAATTAAATTATTTT
2747405 TTAA
1 TTAA
2747409 AAATCTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATTAAATTATTTT
Found at i:2751767 original size:20 final size:20
Alignment explanation
Indices: 2751729--2751767 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2751719 TGAACCAAAA
*
2751729 TTTTAATATTTTTTATAATT
1 TTTTAATATTTATTATAATT
2751749 TTTTAATGATTTATT-TAAT
1 TTTTAAT-ATTTATTATAAT
2751768 CAAATCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTAATATTTATTATAATT
Found at i:2757785 original size:31 final size:31
Alignment explanation
Indices: 2757750--2757808 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2757740 TAATCCAATA
*
2757750 ACTTAAATAAAAACTTTCGAATAATTTAATG
1 ACTTAAATAAAAACTTTCAAATAATTTAATG
* * *
2757781 ACTTAAATGAGAACTTTTAAATAATTTA
1 ACTTAAATAAAAACTTTCAAATAATTTA
2757809 CTGATCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTTAATG
Found at i:2758371 original size:20 final size:19
Alignment explanation
Indices: 2758318--2758371 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
2758308 TTTTATTTTT
2758318 ATTTTTTAATTTTAAAATA
1 ATTTTTTAATTTTAAAATA
*
2758337 ATTTTTTTATTTTTAAAATA
1 A-TTTTTTAATTTTAAAATA
2758357 ATTTTTTAATGTTTA
1 ATTTTTTAAT-TTTA
2758372 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTTAATTTTAAAATA
Found at i:2763646 original size:29 final size:29
Alignment explanation
Indices: 2763579--2763636 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2763569 AGAATATTGA
*
2763579 AAATTCTTTTATTCTTTCACTAATTTTTG
1 AAATTCTTTTATTCTTTCACTAACTTTTG
2763608 AAATTCTTTTATTCTTTCACTAACTTTTG
1 AAATTCTTTTATTCTTTCACTAACTTTTG
2763637 TCTTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.03, T:0.57
Consensus pattern (29 bp):
AAATTCTTTTATTCTTTCACTAACTTTTG
Found at i:2763854 original size:25 final size:25
Alignment explanation
Indices: 2763820--2763881 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
2763810 CGTTAATTGC
2763820 AAACTTAATTGGGTCCTCCACTTGA
1 AAACTTAATTGGGTCCTCCACTTGA
2763845 AAACTTAATTGGGTCCTCCACTTGA
1 AAACTTAATTGGGTCCTCCACTTGA
2763870 AAACTTAATTGG
1 AAACTTAATTGG
2763882 TTTGACTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (25 bp):
AAACTTAATTGGGTCCTCCACTTGA
Found at i:2770042 original size:24 final size:25
Alignment explanation
Indices: 2769981--2770042 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
2769971 GACACACCAT
2769981 AGCTCGTATGAGCTTACCGATATTC
1 AGCTCGTATGAGCTTACCGATATTC
* * *
2770006 AGCTCGGAGGAGCTTACCG-TTTATC
1 AGCTCGTATGAGCTTACCGATAT-TC
2770031 -GCTCGTATGAGC
1 AGCTCGTATGAGC
2770043 ATACATGTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATATTC
Found at i:2771260 original size:12 final size:12
Alignment explanation
Indices: 2771245--2771275 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2771235 TACACGAGCT
*
2771245 AGGACACGGGTA
1 AGGACACGGGCA
2771257 AGGACACGGGCA
1 AGGACACGGGCA
2771269 AGGACAC
1 AGGACAC
2771276 AGACGTGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.39, T:0.03
Consensus pattern (12 bp):
AGGACACGGGCA
Found at i:2777659 original size:12 final size:12
Alignment explanation
Indices: 2777642--2777670 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2777632 AAAAAAATTC
2777642 CATTCTTTTTAG
1 CATTCTTTTTAG
2777654 CATTCTTTTTAG
1 CATTCTTTTTAG
2777666 CATTC
1 CATTC
2777671 ATATGAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (12 bp):
CATTCTTTTTAG
Found at i:2779382 original size:29 final size:30
Alignment explanation
Indices: 2779326--2779382 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
2779316 AAATTGAATC
* *
2779326 AAATCAAAATTTCATGTAAAAAATTACATA
1 AAATCAAAATTTCATGCAAAAAACTACATA
*
2779356 AAATCAAAA-TTCATGCATAAAACTACA
1 AAATCAAAATTTCATGCAAAAAACTACA
2779383 CATCGGACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (30 bp):
AAATCAAAATTTCATGCAAAAAACTACATA
Found at i:2783532 original size:283 final size:283
Alignment explanation
Indices: 2783025--2783592 Score: 1109
Period size: 283 Copynumber: 2.0 Consensus size: 283
2783015 ATTTTACTTT
* *
2783025 TATATAAAAATTAATTTAAACCAAGTTTAATATTATTATATTGATAATAAATTTTATTTTTATTT
1 TATATAAAAATTAACTTAAACCAAGTTTAATATTATTATATTGATAATAAATTTTATTTATATTT
*
2783090 TTAAAAATATTTAAAATATTAATATAAAATATTATATTTTTTAATATTATTAAATATACGTATTT
66 TTAAAAATATTTAAAATATTAATATAAAATATTATATTTTTTAATATTATTAAATATACATATTT
2783155 AATTATTTATATTTATTCATATAATTAATATAATTTATTATTTTTAATAAATTATTTAATATTTA
131 AATTATTTATATTTATTCATATAATTAATATAATTTATTATTTTTAATAAATTATTTAATATTTA
2783220 AATTTTATTTTAATAGTAAATTTTAAAAATAATAATTTTAAATAATATTATTCACATATTATTGA
196 AATTTTATTTTAATAGTAAATTTTAAAAATAATAATTTTAAATAATATTATTCACATATTATTGA
2783285 AAATATCAATATTAATTTTTTAA
261 AAATATCAATATTAATTTTTTAA
2783308 TATATAAAAATTAACTTAAACCAAGTTTAATATTATTATATTGATAATAAATTTTATTTATATTT
1 TATATAAAAATTAACTTAAACCAAGTTTAATATTATTATATTGATAATAAATTTTATTTATATTT
2783373 TTAAAAATATTTAAAATATTAATATAAAATATTATATTTTTTAATATTATTAAATATACATATTT
66 TTAAAAATATTTAAAATATTAATATAAAATATTATATTTTTTAATATTATTAAATATACATATTT
2783438 AATTATTTATATTTATTCATATAATTAATATAATTTATTATTTTTAATAAATTATTTAATATTTA
131 AATTATTTATATTTATTCATATAATTAATATAATTTATTATTTTTAATAAATTATTTAATATTTA
2783503 AATTTTATTTTAATAGTAAATTTTAAAAATAATAATTTTAAATAATATTATTCACATATTATTGA
196 AATTTTATTTTAATAGTAAATTTTAAAAATAATAATTTTAAATAATATTATTCACATATTATTGA
2783568 AAATATCAATATTAATTTTTTAA
261 AAATATCAATATTAATTTTTTAA
2783591 TA
1 TA
2783593 CTAAATATTT
Statistics
Matches: 282, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
283 282 1.00
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (283 bp):
TATATAAAAATTAACTTAAACCAAGTTTAATATTATTATATTGATAATAAATTTTATTTATATTT
TTAAAAATATTTAAAATATTAATATAAAATATTATATTTTTTAATATTATTAAATATACATATTT
AATTATTTATATTTATTCATATAATTAATATAATTTATTATTTTTAATAAATTATTTAATATTTA
AATTTTATTTTAATAGTAAATTTTAAAAATAATAATTTTAAATAATATTATTCACATATTATTGA
AAATATCAATATTAATTTTTTAA
Found at i:2789763 original size:2 final size:2
Alignment explanation
Indices: 2789756--2789785 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2789746 ACTTTGGTGC
2789756 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2789786 CTTCTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2794319 original size:6 final size:6
Alignment explanation
Indices: 2794310--2794335 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2794300 CTTAATTCTA
2794310 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
2794336 AAAACCCAAT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:2798899 original size:61 final size:60
Alignment explanation
Indices: 2798829--2798954 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
2798819 AATATTCAAC
* * *
2798829 AAATATAGCCCTC-AATGTTTACAAAAAAATTT-ATTTTAGTTTGAATTCTAAAAAAATTAAT
1 AAATTTAGCCCTCAAAT-TTT--AAAAAAATTTCAATTTAGTTTCAATTCTAAAAAAATTAAT
* * **
2798890 AAATTTAGCCCTCAAATTTTATAAAATTTTCAATTTAGTTTCAATTCTAAAAATTTTAAT
1 AAATTTAGCCCTCAAATTTTAAAAAAATTTCAATTTAGTTTCAATTCTAAAAAAATTAAT
2798950 AAATT
1 AAATT
2798955 AATTTTTGGT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
59 8 0.14
60 30 0.54
61 15 0.27
62 3 0.05
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (60 bp):
AAATTTAGCCCTCAAATTTTAAAAAAATTTCAATTTAGTTTCAATTCTAAAAAAATTAAT
Found at i:2810431 original size:8 final size:8
Alignment explanation
Indices: 2810420--2810454 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2810410 TAAATGATGA
*
2810420 TATGTATG
1 TATGCATG
2810428 TATGCATG
1 TATGCATG
2810436 TATGCATG
1 TATGCATG
*
2810444 CATGCATG
1 TATGCATG
2810452 TAT
1 TAT
2810455 TCCTTCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (8 bp):
TATGCATG
Found at i:2810438 original size:12 final size:12
Alignment explanation
Indices: 2810421--2810454 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2810411 AAATGATGAT
2810421 ATGTATGTATGC
1 ATGTATGTATGC
*
2810433 ATGTATGCATGC
1 ATGTATGTATGC
*
2810445 ATGCATGTAT
1 ATGTATGTAT
2810455 TCCTTCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (12 bp):
ATGTATGTATGC
Found at i:2814359 original size:13 final size:13
Alignment explanation
Indices: 2814341--2814367 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2814331 GACTTTAGCC
2814341 TACGTGCTTTTCT
1 TACGTGCTTTTCT
2814354 TACGTGCTTTTCT
1 TACGTGCTTTTCT
2814367 T
1 T
2814368 TTTTCTTTAA
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:0.07, C:0.22, G:0.15, T:0.56
Consensus pattern (13 bp):
TACGTGCTTTTCT
Found at i:2815032 original size:18 final size:19
Alignment explanation
Indices: 2814987--2815038 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
2814977 AAAAACTATA
2814987 TTAAAAATATTTTATTAATTT
1 TTAAAAATA-TTTA-TAATTT
*
2815008 TT-TAAATATTTAT-ATTT
1 TTAAAAATATTTATAATTT
2815025 TTAAAAATATTTAT
1 TTAAAAATATTTAT
2815039 CAATAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 11 0.39
19 4 0.14
20 5 0.18
21 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAAAAATATTTATAATTT
Found at i:2825803 original size:11 final size:11
Alignment explanation
Indices: 2825787--2825831 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
2825777 AAAAAAATTG
2825787 TTGTTTTCTTA
1 TTGTTTTCTTA
* *
2825798 TTGTTTTATTG
1 TTGTTTTCTTA
2825809 TTGTTTTCTTA
1 TTGTTTTCTTA
* *
2825820 CTGTTTTGTTA
1 TTGTTTTCTTA
2825831 T
1 T
2825832 CATTTCAGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.09, C:0.07, G:0.13, T:0.71
Consensus pattern (11 bp):
TTGTTTTCTTA
Found at i:2825811 original size:22 final size:22
Alignment explanation
Indices: 2825783--2825826 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2825773 AAAAAAAAAA
*
2825783 ATTGTTGTTTTCTTATTGTTTT
1 ATTGTTGTTTTCTTACTGTTTT
2825805 ATTGTTGTTTTCTTACTGTTTT
1 ATTGTTGTTTTCTTACTGTTTT
2825827 GTTATCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.07, G:0.14, T:0.70
Consensus pattern (22 bp):
ATTGTTGTTTTCTTACTGTTTT
Found at i:2826053 original size:2 final size:2
Alignment explanation
Indices: 2826046--2826070 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2826036 TTATATTCTA
2826046 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 A
2826071 AATCCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2837276 original size:27 final size:26
Alignment explanation
Indices: 2837239--2837293 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
2837229 AGTTTCATAC
*
2837239 TTTTTTTTCTAAT-GGGTACTTGTAT
1 TTTTTTTTCTAATCGAGTACTTGTAT
*
2837264 TTTTTTTGGTCTAATCTAGTACTTGTAT
1 TTTTTTT--TCTAATCGAGTACTTGTAT
2837292 TT
1 TT
2837294 GACAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.28
27 6 0.24
28 12 0.48
ACGTcount: A:0.16, C:0.09, G:0.15, T:0.60
Consensus pattern (26 bp):
TTTTTTTTCTAATCGAGTACTTGTAT
Found at i:2839123 original size:2 final size:2
Alignment explanation
Indices: 2839116--2839147 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2839106 ATGTAATTAT
2839116 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
2839148 CTGCAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2840032 original size:53 final size:53
Alignment explanation
Indices: 2839956--2840136 Score: 194
Period size: 53 Copynumber: 3.7 Consensus size: 53
2839946 TTATATTTTG
2839956 TTAC-AACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
* * *
2840008 TTACTAACAATTAATACAATTAACAATTAATAATTT--TACTAA---CAAAATG
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATA-TAATTTGATAATT
*
2840057 TTAGTAACAA-T--T--AA-T---AATTAATAATTTGATATAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
* *
2840101 TTAGTAACAATTAATACAATTAAAAATTAATAATTT
1 TTACTAACAATTAATACAATTAACAATTAATAATTT
2840137 TACTAACAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 31
0.74 0.05 0.22
Matches are distributed among these distances:
40 12 0.11
41 3 0.03
42 2 0.02
43 1 0.01
44 16 0.15
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 15 0.14
50 1 0.01
51 2 0.02
52 7 0.07
53 43 0.41
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (53 bp):
TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
Found at i:2840078 original size:93 final size:93
Alignment explanation
Indices: 2839970--2840153 Score: 341
Period size: 93 Copynumber: 2.0 Consensus size: 93
2839960 AACAATTAAT
*
2839970 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAAT
1 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAAAAAT
2840035 TAATAATTTTACTAACAAAATGTTAGTA
66 TAATAATTTTACTAACAAAATGTTAGTA
* *
2840063 ACAATTAATAATTAATAATTTGATATAATTTGATAATTTTAGTAACAATTAATACAATTAAAAAT
1 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAAAAAT
2840128 TAATAATTTTACTAACAAAATGTTAG
66 TAATAATTTTACTAACAAAATGTTAG
2840154 ATTTTACAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (93 bp):
ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAAAAAT
TAATAATTTTACTAACAAAATGTTAGTA
Found at i:2840221 original size:16 final size:16
Alignment explanation
Indices: 2840200--2840240 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
2840190 ATTTTGATAC
2840200 AATTTTAATAACAATT
1 AATTTTAATAACAATT
2840216 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
2840232 AGTTTTAAT
1 AATTTTAAT
2840241 TTTAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:2840242 original size:22 final size:23
Alignment explanation
Indices: 2840214--2840275 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
2840204 TTAATAACAA
* *
2840214 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
2840236 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
*
2840259 TTGATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
2840276 ACAGGCCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 16 0.46
23 13 0.37
24 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:2850389 original size:29 final size:30
Alignment explanation
Indices: 2850331--2850389 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2850321 CTAGGCTTGC
* *
2850331 ATTTTAAAATAAAATATGGTGAGATTAAAT
1 ATTTTAAAATAAAATATGGAGAGACTAAAT
*
2850361 ATTTTAAAATAAAA-ATGGAGTGACTAAAT
1 ATTTTAAAATAAAATATGGAGAGACTAAAT
2850390 TTTAAATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.34
Consensus pattern (30 bp):
ATTTTAAAATAAAATATGGAGAGACTAAAT
Found at i:2858515 original size:13 final size:14
Alignment explanation
Indices: 2858462--2858515 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 14
2858452 ATTTTTTAAT
2858462 TTTTA-ATTATTT-
1 TTTTATATTATTTC
*
2858474 TTTTACATTATTTC
1 TTTTATATTATTTC
* *
2858488 TCTTTATTTTTTTTC
1 T-TTTATATTATTTC
2858503 TTTT-TATTATTTC
1 TTTTATATTATTTC
2858516 CTTATAATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 5 0.15
13 14 0.41
14 4 0.12
15 11 0.32
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATATTATTTC
Found at i:2869938 original size:31 final size:29
Alignment explanation
Indices: 2869903--2869964 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2869893 ATTTGGTATC
*
2869903 TGTACTTTCATAAAATGTTTAATGTGATACA
1 TGTACTTT-A-AAAATGTCTAATGTGATACA
* *
2869934 TGTACTTTAGAAATGTCTAATGTGGTACA
1 TGTACTTTAAAAATGTCTAATGTGATACA
2869963 TG
1 TG
2869965 AACCATCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.68
30 1 0.04
31 8 0.29
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (29 bp):
TGTACTTTAAAAATGTCTAATGTGATACA
Found at i:2870304 original size:29 final size:30
Alignment explanation
Indices: 2870267--2870332 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
2870257 ACATTTTATG
**
2870267 AAAAATACATGTACCACATTAAATATTT-T
1 AAAAATACAAATACCACATTAAATATTTGT
*
2870296 CAAAATACAAATACCACATTAAATATTTGT
1 AAAAATACAAATACCACATTAAATATTTGT
2870326 AAAAATA
1 AAAAATA
2870333 TAAGTACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAAATACAAATACCACATTAAATATTTGT
Found at i:2871162 original size:29 final size:31
Alignment explanation
Indices: 2871102--2871163 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
2871092 ACAATTTAAT
* *
2871102 TTGGTCATTTTGAATTTTTGTATTTTTTGAA
1 TTGGTCATTTTGAATTTCTGTATTTTTCGAA
*
2871133 TTGGTCATTTT-TA-TTCTGTATTTTTCGAA
1 TTGGTCATTTTGAATTTCTGTATTTTTCGAA
2871162 TT
1 TT
2871164 TTAAACTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 16 0.57
30 1 0.04
31 11 0.39
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.61
Consensus pattern (31 bp):
TTGGTCATTTTGAATTTCTGTATTTTTCGAA
Done.