Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008199.1 Hibiscus syriacus cultivar Beakdansim tig00110819_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2638622
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:995 original size:16 final size:16
Alignment explanation
Indices: 974--1008 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
964 TGGATATTAT
* *
974 TTTTAGTTTTATTTCA
1 TTTTAGTCTCATTTCA
990 TTTTAGTCTCATTTCA
1 TTTTAGTCTCATTTCA
1006 TTT
1 TTT
1009 GTTATCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTTAGTCTCATTTCA
Found at i:1706 original size:15 final size:15
Alignment explanation
Indices: 1688--1717 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1678 TATTTTTCTT
*
1688 AAAATTATTTTAAAA
1 AAAATAATTTTAAAA
1703 AAAATAATTTTAAAA
1 AAAATAATTTTAAAA
1718 GGTATTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATAATTTTAAAA
Found at i:6677 original size:24 final size:24
Alignment explanation
Indices: 6650--6736 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 24
6640 GATATCAGAA
*
6650 ATCAAAACAGAATTCAGAACATAT
1 ATCAGAACAGAATTCAGAACATAT
* * *
6674 ATCAGAACA-AATCCA-AATCAGAA
1 ATCAGAACAGAATTCAGAA-CATAT
* ** *
6697 ATCAGAACAAAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGAACATAT
6721 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
6737 AGTCGAAAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
22 2 0.04
23 17 0.35
24 30 0.61
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGAACATAT
Found at i:6748 original size:24 final size:23
Alignment explanation
Indices: 6674--6750 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
6664 CAGAACATAT
* *
6674 ATCAGAACAAATCCAAATCAGAA
1 ATCAGAACAAATTCAAGTCAGAA
* *
6697 ATCAGAACAAAATTCAGGTCATG-T
1 ATCAGAAC-AAATTCAAGTCA-GAA
6721 ATCAGAACAGAATTCAAGTC-GAAA
1 ATCAGAACA-AATTCAAGTCAG-AA
6745 ATCAGA
1 ATCAGA
6751 TAAAATATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
22 1 0.02
23 9 0.21
24 32 0.74
25 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.18
Consensus pattern (23 bp):
ATCAGAACAAATTCAAGTCAGAA
Found at i:8028 original size:15 final size:15
Alignment explanation
Indices: 8008--8043 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
7998 TAATGAAGTT
8008 AAGTACAAATCTTCA
1 AAGTACAAATCTTCA
8023 AAGTACAAATCTTCA
1 AAGTACAAATCTTCA
8038 AAGTAC
1 AAGTAC
8044 TTTTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.25
Consensus pattern (15 bp):
AAGTACAAATCTTCA
Found at i:8498 original size:36 final size:36
Alignment explanation
Indices: 8451--8523 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
8441 GATAAATTAT
*
8451 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCAATGGCTGATTCTTTTATCACTTA
*
8487 AATCTACATATCAATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCAATGGCTGATTCTTTTATCACTTA
8523 A
1 A
8524 TTCCAGAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCAATGGCTGATTCTTTTATCACTTA
Found at i:11727 original size:18 final size:19
Alignment explanation
Indices: 11704--11740 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11694 CGCATAACAC
11704 CCGTCATT-GTATAAAGCA
1 CCGTCATTGGTATAAAGCA
11722 CCGTCATTGGTATAAAGCA
1 CCGTCATTGGTATAAAGCA
11741 ATTGCAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (19 bp):
CCGTCATTGGTATAAAGCA
Found at i:24875 original size:22 final size:22
Alignment explanation
Indices: 24847--24892 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
24837 AAATTTAATA
*
24847 TTAAGGGTGAATTTATAAAATT
1 TTAAGGGTGAACTTATAAAATT
* *
24869 TTAAGGGTGGACTTGTAAAATT
1 TTAAGGGTGAACTTATAAAATT
24891 TT
1 TT
24893 TAGAGATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (22 bp):
TTAAGGGTGAACTTATAAAATT
Found at i:27064 original size:17 final size:18
Alignment explanation
Indices: 27044--27081 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
27034 ATTAGCATGC
*
27044 CTTTCAAATAAGGTTA-G
1 CTTTCAAAGAAGGTTATG
*
27061 CTTTTAAAGAAGGTTATG
1 CTTTCAAAGAAGGTTATG
27079 CTT
1 CTT
27082 AAAGCTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (18 bp):
CTTTCAAAGAAGGTTATG
Found at i:34628 original size:15 final size:15
Alignment explanation
Indices: 34608--34642 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
34598 ATATATATTT
34608 ATATATATATTAGTA
1 ATATATATATTAGTA
34623 ATATATATATTAGTA
1 ATATATATATTAGTA
34638 ATATA
1 ATATA
34643 AAAATGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
ATATATATATTAGTA
Found at i:38856 original size:56 final size:56
Alignment explanation
Indices: 38791--38903 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
38781 TGTGGAGTGC
*
38791 ACACTTGTTTGAATTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
1 ACACTTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
38847 ACACTTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
1 ACACTTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
38903 A
1 A
38904 ATTTTAGTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.47
Consensus pattern (56 bp):
ACACTTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
Found at i:43868 original size:56 final size:56
Alignment explanation
Indices: 43798--43907 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
43788 GAGTGCACAT
*
43798 TTGTTTGAATTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTACAC
1 TTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTACAC
43854 TTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTAC
1 TTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTAC
43908 TTTTAGTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.48
Consensus pattern (56 bp):
TTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTACAC
Found at i:50286 original size:190 final size:190
Alignment explanation
Indices: 49958--50338 Score: 600
Period size: 190 Copynumber: 2.0 Consensus size: 190
49948 CATTAAAAAG
* *
49958 ACCCTCCACACAAAATTCGGATTGTGTCTCTCTTCTACCTTGATCACCCAGAAATCTTATTTACT
1 ACCCTCCACACAAAATTCGGATTGTATCTCTCTTCTACCTTGATCACCAAGAAATCTTATTTACT
* *
50023 AAGACTTATTACCTATTAAGAATATGTACTTCATTAATAACTTGATTCTCAAGTTACCACAACAG
66 AAGACTTATTACCTATTAAGAATACGTACTTCATTAATAACTTGATTCTCAAGTTACCACAACAA
* * * * *
50088 ACTCCAAACTACACACTACCAGCTACAATTTCGTTCAATATCGAACACATAGTTCCTAGA
131 AATCCAAACTACACACTACCAGCTAAAATTTCGGTCAATATCCAACACATAGTTACTAGA
*
50148 ACCCTCCACACAAAATTCGGATTGTATCTCTCTTCTACCTTGATCACCAAGAAATCTTATTTATT
1 ACCCTCCACACAAAATTCGGATTGTATCTCTCTTCTACCTTGATCACCAAGAAATCTTATTTACT
* * * * **
50213 AAGATTTATTGCCTATTAAGAATACGTGCTTCATTAATAACTTGATTCTTAAGTTACCACGGCAA
66 AAGACTTATTACCTATTAAGAATACGTACTTCATTAATAACTTGATTCTCAAGTTACCACAACAA
* *
50278 AATCCAAACTACACGCTACCAGTTAAAATTTCGGTCAATATCCAACACATAGTTACTAGA
131 AATCCAAACTACACACTACCAGCTAAAATTTCGGTCAATATCCAACACATAGTTACTAGA
50338 A
1 A
50339 ACCTTATGAA
Statistics
Matches: 173, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
190 173 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (190 bp):
ACCCTCCACACAAAATTCGGATTGTATCTCTCTTCTACCTTGATCACCAAGAAATCTTATTTACT
AAGACTTATTACCTATTAAGAATACGTACTTCATTAATAACTTGATTCTCAAGTTACCACAACAA
AATCCAAACTACACACTACCAGCTAAAATTTCGGTCAATATCCAACACATAGTTACTAGA
Found at i:69801 original size:31 final size:32
Alignment explanation
Indices: 69766--69840 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
69756 AAGTTATTTT
69766 TAAATATATATATATATAACTCTTT-AT-AAAA
1 TAAATATATATATATATAACT-TTTAATCAAAA
*
69797 TAAAT-TAT-TATATTTAACTTTTAATCCAAAA
1 TAAATATATATATATATAACTTTTAAT-CAAAA
69828 -AAATATA-ATATAT
1 TAAATATATATATAT
69841 TATATTAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
28 3 0.08
29 12 0.32
30 7 0.18
31 16 0.42
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (32 bp):
TAAATATATATATATATAACTTTTAATCAAAA
Found at i:73205 original size:8 final size:8
Alignment explanation
Indices: 73194--73227 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
73184 CCAAATTTAA
73194 TCCCTCTC
1 TCCCTCTC
73202 TCCCTCTC
1 TCCCTCTC
73210 TCCCTCTC
1 TCCCTCTC
73218 TCCCTCTC
1 TCCCTCTC
73226 TC
1 TC
73228 TCCAGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (8 bp):
TCCCTCTC
Found at i:85146 original size:31 final size:31
Alignment explanation
Indices: 85108--85168 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
85098 ACATGCAAAG
*
85108 CTTATCAACTAAATTGTAAAATTGAAGTAAT
1 CTTATCAACTAAATTGCAAAATTGAAGTAAT
85139 CTTATCAACTAAATTGCAAAATTGAAGTAA
1 CTTATCAACTAAATTGCAAAATTGAAGTAA
85169 AGCACGGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (31 bp):
CTTATCAACTAAATTGCAAAATTGAAGTAAT
Found at i:97999 original size:21 final size:21
Alignment explanation
Indices: 97974--98017 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
97964 AATTTAGTTA
*
97974 ATTAGTTTGTTAGTATAAATT
1 ATTAGCTTGTTAGTATAAATT
* *
97995 ATTAGCTTGTTAGTTTAAGTT
1 ATTAGCTTGTTAGTATAAATT
98016 AT
1 AT
98018 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (21 bp):
ATTAGCTTGTTAGTATAAATT
Found at i:98091 original size:44 final size:49
Alignment explanation
Indices: 97995--98102 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 49
97985 AGTATAAATT
* *
97995 ATTAGCTTGTTAGTTTAAGTTATATATTATATTATATAAAAAATTAGTTA
1 ATTAGTTTGTTAGTTTAAGTTATATA-TATATTATATAAAAAAATAGTTA
* *
98045 ATTAGTTTCTTAGTTTAAGTTAT-TA-A-A-TATA-AAAAAAATATTTA
1 ATTAGTTTGTTAGTTTAAGTTATATATATATTATATAAAAAAATAGTTA
*
98089 ATTAATTTGTTAGT
1 ATTAGTTTGTTAGT
98103 GTCTTTAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
44 23 0.44
45 4 0.08
46 1 0.02
47 1 0.02
49 2 0.04
50 21 0.40
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (49 bp):
ATTAGTTTGTTAGTTTAAGTTATATATATATTATATAAAAAAATAGTTA
Found at i:98541 original size:17 final size:17
Alignment explanation
Indices: 98519--98579 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
98509 GATAATTTCC
98519 GTTTAAAAAAATATTGT
1 GTTTAAAAAAATATTGT
* *
98536 GTTTAAAAATATTTAGTGTT
1 GTTTAAAAA-A-ATATTG-T
*
98556 GTTTTAAAAAAATATTTT
1 G-TTTAAAAAAATATTGT
98574 GTTTAA
1 GTTTAA
98580 TTTATATTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.40
18 3 0.09
19 7 0.20
20 3 0.09
21 8 0.23
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:98583 original size:22 final size:23
Alignment explanation
Indices: 98540--98583 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
98530 TATTGTGTTT
**
98540 AAAAATATTTAGTGTTGTTTTAA
1 AAAAATATTTAGTGTTAATTTAA
*
98563 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
98584 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTAATTTAA
Found at i:100531 original size:15 final size:16
Alignment explanation
Indices: 100511--100544 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
100501 CAAAAAAATT
100511 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
100526 TAATATAATAAACTTA
1 TAATATAATAAACTTA
100542 TAA
1 TAA
100545 AGTAAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:101088 original size:26 final size:26
Alignment explanation
Indices: 101042--101099 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
101032 TTCTTTCTTT
* *
101042 CTTTC-TCGGGTGCACTATATTCTCC
1 CTTTCTTCGGCTGCAATATATTCTCC
*
101067 CTTTCTTCGGCTGCAATCTATTCTCC
1 CTTTCTTCGGCTGCAATATATTCTCC
101093 CTTTCTT
1 CTTTCTT
101100 TCTTTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.10, C:0.33, G:0.12, T:0.45
Consensus pattern (26 bp):
CTTTCTTCGGCTGCAATATATTCTCC
Found at i:101298 original size:27 final size:27
Alignment explanation
Indices: 101268--101323 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
101258 ATAGTTGCAG
* *
101268 CGACATACAGCGAGGAGCAGGAGGGGA
1 CGACATACAACGAGGAGCAAGAGGGGA
* *
101295 CGACATGCAACGGGGAGCAAGAGGGGA
1 CGACATACAACGAGGAGCAAGAGGGGA
101322 CG
1 CG
101324 TGCAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.45, T:0.04
Consensus pattern (27 bp):
CGACATACAACGAGGAGCAAGAGGGGA
Found at i:103744 original size:34 final size:34
Alignment explanation
Indices: 103649--103744 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 34
103639 AACACAATAA
*
103649 TCAATTACATTCTAAACCCCAAATTCTAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTC-AAAATACT
*
103684 TCAATTACATTCTAAACCTCAAATTCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCAAAATACT
* **
103718 TCAATTACATGCCCAACCCCAAATTCA
1 TCAATTACATTCTAAACCCCAAATTCA
103745 TAATCCATTC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
34 30 0.55
35 25 0.45
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.29
Consensus pattern (34 bp):
TCAATTACATTCTAAACCCCAAATTCAAAATACT
Found at i:104382 original size:148 final size:148
Alignment explanation
Indices: 104222--104509 Score: 488
Period size: 148 Copynumber: 1.9 Consensus size: 148
104212 AAACTATTTA
* * * *
104222 AATTAGAATCAAATATTATTATAGTATTATAAATATTTATAATTAAATTTAAATAGAAACTTGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTTGAA
* * **
104287 AATTCAATTCAATTTGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAAAT-TTAGTCAAC
66 AATTCAATTCAATTCGACTTCATTTAAATTTTATAAACTCAAATCG-AAAAAAATCCGAGTCAAC
104351 TATTTTATAAATTGAACTG
130 TATTTTATAAATTGAACTG
104370 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTTGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTTGAA
104435 AATTCAATTCAATTCGACTTCATTTAAATTTTATAAACTCAAATCGAAAAAAATCCGAGTCAACT
66 AATTCAATTCAATTCGACTTCATTTAAATTTTATAAACTCAAATCGAAAAAAATCCGAGTCAACT
104500 ATTTTATAAA
131 ATTTTATAAA
104510 CTAAATTGAG
Statistics
Matches: 131, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
147 8 0.06
148 123 0.94
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTTGAA
AATTCAATTCAATTCGACTTCATTTAAATTTTATAAACTCAAATCGAAAAAAATCCGAGTCAACT
ATTTTATAAATTGAACTG
Found at i:104724 original size:35 final size:35
Alignment explanation
Indices: 104669--104764 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
104659 AATGGACTAT
* * * *
104669 GAATTTGTGGTTGAGCATGTAATTGAAGTATTTTA
1 GAATTTGAGGTTTAGAATGTAATTGAAATATTTTA
*
104704 GAATTTGAGGTTTAGAATGTAATTGAAATATTTTG
1 GAATTTGAGGTTTAGAATGTAATTGAAATATTTTA
* * *
104739 GATTTTGGGGTTTAAAATGTAATTGA
1 GAATTTGAGGTTTAGAATGTAATTGA
104765 TGACTGTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.43
Consensus pattern (35 bp):
GAATTTGAGGTTTAGAATGTAATTGAAATATTTTA
Found at i:110481 original size:105 final size:105
Alignment explanation
Indices: 110232--111532 Score: 2133
Period size: 105 Copynumber: 12.4 Consensus size: 105
110222 AATTTGCTCG
* * * * *
110232 AGAGTAAATTTCAACTTCTCAACGAAGGATCTT-GAATCCAAGACAACACAAGTTCAACTTCACG
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACG
*
110296 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCGATTTC
65 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTC
*
110338 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
110403 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
*
110443 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
110508 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
*
110548 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
110613 CGAAGGGACCGCTGGTTGTCAACAAACATTTC-CCAATTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
*
110652 AGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
110716 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTC
* *
110757 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
110822 CGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
*
110862 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
110927 CGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
* *
110967 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
111032 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCGATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTC
*
111073 AGAGTCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
111138 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
*
111178 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
111243 CAAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
*
111283 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
111348 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTC
* *
111389 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
111454 CGAAGGGATCGCTGGTTGTCAACAAACAATTT-TCCAGTTCC
66 CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCGA-TTTC
* * ** *
111495 ATAGCCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACT
111533 TGGAACAATA
Statistics
Matches: 1139, Mismatches: 49, Indels: 14
0.95 0.04 0.01
Matches are distributed among these distances:
103 70 0.06
104 28 0.02
105 648 0.57
106 388 0.34
107 5 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTC
Found at i:111074 original size:211 final size:211
Alignment explanation
Indices: 110238--111532 Score: 2154
Period size: 211 Copynumber: 6.2 Consensus size: 211
110228 CTCGAGAGTA
* * * *
110238 AATTTCAACTTCTCAACGAAGGATCTT-GAATCCAAGACAACACAAGTTCAACTTCACGACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
110302 GGACCGCTGGTTGTCAATAAACAATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGA
65 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
110367 TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
130 TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAT
*
110432 TTCTCGATTTCAGAGTC
195 TTCTCGATTTCAGAGCC
*
110449 AATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
110514 GACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGAT
66 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
110578 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
131 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
* *
110643 TC-CCAATTCAGAGCC
196 TCTCGATTTCAGAGCC
110658 AATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
110722 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
110787 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
131 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
* *
110852 TCCCAATTTCAGAGCC
196 TCTCGATTTCAGAGCC
110868 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
110933 GACCGCTGGTTGTCAACAAAC-ATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
110997 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
131 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
*
111062 TTCTCGATTTCAGAGTC
195 TTCTCGATTTCAGAGCC
*
111079 AATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
111144 GACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGAT
66 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* * *
111208 ATTGGACTCTAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACATT
131 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
*
111273 TCTCGATTTCAGAGTC
196 TCTCGATTTCAGAGCC
*
111289 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
111354 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGAT
66 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
111419 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAAT
131 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
* * *
111484 TT-TCCAGTTCCATAGCC
195 TTCTCGA-TTTCAGAGCC
** *
111501 AATTTCAACTTCACGGCGGAGGATATTGGACT
1 AATTTCAACTTCACAACGAAGGATATTGGACT
111533 TGGAACAATA
Statistics
Matches: 1030, Mismatches: 46, Indels: 15
0.94 0.04 0.01
Matches are distributed among these distances:
208 70 0.07
209 130 0.13
210 341 0.33
211 445 0.43
212 44 0.04
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (211 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
TCTCGATTTCAGAGCC
Found at i:111166 original size:316 final size:316
Alignment explanation
Indices: 110238--111532 Score: 2139
Period size: 316 Copynumber: 4.1 Consensus size: 316
110228 CTCGAGAGTA
* * *
110238 AATTTCAACTTCTCAACGAAGGATCTT-GAATCCAAGACAACACAAGTTCAACTTCACGACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACACAAGTTCAACTTCACGACGAAG
* * * *
110302 GGACCGCTGGTTGTCAATAAACAATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGA
65 GGACCGCTGGTTGTCAACAAAC-ATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
110367 TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-A
129 TATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA
* * * * *
110431 TTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGT
194 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* * *
110496 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTC
259 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCC
110554 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
110619 GACCGCTGGTTGTCAACAAACATTTCCCAA-TTCAGAGCCAATTTCAACTTCAC-ACGAAGGATA
66 GACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
*
110682 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACT
131 TTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACT
*
110747 TCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTC
196 TCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
110812 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCC
261 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCC
*
110868 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
110933 GACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 GACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* *
110998 TTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATT
131 TTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACT
* * * *
111063 TCTCGATTTCAGAGTCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
196 TCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * *
111128 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTC
261 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCC
* * *
111184 AATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACAAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
* * *
111249 GACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATA
66 GACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* *
111314 TTGGACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACT
131 TTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACT
*
111379 TCCCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTC
196 TCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * * * *
111444 AACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAATTTTCCAGTTCCATAGCC
261 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAATTTCAGAGCC
** *
111501 AATTTCAACTTCACGGCGGAGGATATTGGACT
1 AATTTCAACTTCACAACGAAGGATATTGGACT
111533 TGGAACAATA
Statistics
Matches: 920, Mismatches: 54, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
313 70 0.08
314 231 0.25
315 30 0.03
316 543 0.59
317 46 0.05
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (316 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
TTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACT
TCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCC
Found at i:111855 original size:83 final size:83
Alignment explanation
Indices: 111723--111892 Score: 218
Period size: 83 Copynumber: 2.0 Consensus size: 83
111713 AGAAGGAGTG
* *
111723 TCTGCCAACAAAAGACCTTTGAATTCGACTACGCTCAGCTCAATGGCACATCATTTGCAGCATAA
1 TCTGCCAACAAAAGACCTTCGAATTCGACTACGCTCAGCTCAA-GGCACATCATTTACAGCATAA
* * * *
111788 CTCAAGTCGAGAAGGGTTA
65 CCCAAGGCAAGAAGGGCTA
* *
111807 TCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTTAGCTCTTAA-GCACATCATTTACAGCATA
1 TCTGCCAACAAAAGACCTTCGAATTCGACTACGCTCAGCTC--AAGGCACATCATTTACAGCATA
*
111870 GCCCAAGGCAAGAAGGGCTA
64 ACCCAAGGCAAGAAGGGCTA
111890 TCT
1 TCT
111893 ATCAATAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
83 64 0.85
84 9 0.12
85 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (83 bp):
TCTGCCAACAAAAGACCTTCGAATTCGACTACGCTCAGCTCAAGGCACATCATTTACAGCATAAC
CCAAGGCAAGAAGGGCTA
Found at i:114906 original size:70 final size:68
Alignment explanation
Indices: 114775--114911 Score: 195
Period size: 70 Copynumber: 2.0 Consensus size: 68
114765 ATCTGCTCTG
*
114775 CTCAGGCTTTTGCAGGTAATGATATTGGCGAAGGAGAAGCGATAGCCCCTTTCACTAAGGTAAAA
1 CTCAGGCTTTTGCAGGTAATGATATTGGCAAAGGAGAAGCGATAGCCCCTTTCACTAAGGTAAAA
114840 TAA
66 TAA
* * * *
114843 CTCAGGCTTTTGCAGGTAATGGTGATTGGTAAAGGAGAAAGCGAT-GATCCCTTTCACTCAGGTA
1 CTCAGGCTTTTGCAGGTAATGAT-ATTGGCAAAGGAG-AAGCGATAG-CCCCTTTCACTAAGGTA
114907 AAATA
63 AAATA
114912 GAGCACTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 22 0.36
69 12 0.20
70 27 0.44
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (68 bp):
CTCAGGCTTTTGCAGGTAATGATATTGGCAAAGGAGAAGCGATAGCCCCTTTCACTAAGGTAAAA
TAA
Found at i:114990 original size:6 final size:6
Alignment explanation
Indices: 114979--115359 Score: 228
Period size: 6 Copynumber: 66.5 Consensus size: 6
114969 CTTCTTAGCC
* * * * * *
114979 CTCTCT CTCTCT CTCCCT CTCCCT CTCCCC CTCTCC CTCTC- CTCCCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * * * * * * *
115026 CCCTCT CTCACA CTCTCT CTCCCT ATC-CC CTCTCT CTCTCC CCCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * * * * *
115073 CTCCCT CCCTCT CTCTCT CTCTCT CCCTCT CTCTCC CTCCCT CTCCCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
*
115121 CTCTCT CTCTCT CTC-CT -TCTCT C-CTCT CTCCCT CT-TC- CTCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* *
115164 CTATCT C-CATCT CTCTCT CTCT-T C-CTCT CTC-CT -TCTCT CCCTCT
1 CTCTCT CTC-TCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * * * * *
115208 CCCTCC CTCTCT CCCTCT CTCTCT -TCTC- CTCTCT CCCTCC CCCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * * * *
115254 CTTTCT CCCTCT CCCTCT CCCTC- CT-TCT CTCCCT CTCTCT CTCTC-
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * * *
115299 CTCT-T CTCCCT CTC-CT CCCTCT CCCTCT CCCTCT C-CATCT C-CATCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTC-TCT CTC-TCT
* *
115345 CTCTCA CTTTCT CTC
1 CTCTCT CTCTCT CTC
115360 CCTCCCCCCT
Statistics
Matches: 297, Mismatches: 56, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
4 10 0.03
5 50 0.17
6 235 0.79
7 2 0.01
ACGTcount: A:0.02, C:0.58, G:0.00, T:0.40
Consensus pattern (6 bp):
CTCTCT
Found at i:115004 original size:14 final size:14
Alignment explanation
Indices: 114981--115333 Score: 250
Period size: 14 Copynumber: 24.8 Consensus size: 14
114971 TCTTAGCCCT
*
114981 CTCTCTCTCTCTCC
1 CTCTCCCTCTCTCC
*
114995 CTCTCCCTCTCCCC
1 CTCTCCCTCTCTCC
115009 CTCTCCCTCTC-CTC
1 CTCTCCCTCTCTC-C
*
115023 C-CTCCCTCTCTCA
1 CTCTCCCTCTCTCC
*
115036 CACT--CTCTCTCC
1 CTCTCCCTCTCTCC
* *
115048 CTATCCCCTCTCTCT
1 CTCT-CCCTCTCTCC
*
115063 CTCCCCCTCTCTCC
1 CTCTCCCTCTCTCC
115077 CTC-CCTCTCTCTCTC
1 CTCTCC-CTCTCTC-C
115092 TCTCTCCCTCTCTCTC
1 -CTCTCCCTCTCTC-C
115108 C-CTCCCTCTC-CC
1 CTCTCCCTCTCTCC
115120 TCTCTCTCTCTCTCTCC
1 -CTCTC-C-CTCTCTCC
*
115137 TTCTCTCCTCTCTCC
1 CTCTC-CCTCTCTCC
* *
115152 CTCTTCCTCTCTCT
1 CTCTCCCTCTCTCC
* *
115166 ATCTCCATCTCTCTCT
1 CTCTCC--CTCTCTCC
*
115182 CTCTTCCTCTCTCC
1 CTCTCCCTCTCTCC
*
115196 TTCTCTCC-CTCT-C
1 CTCTC-CCTCTCTCC
115209 C-CTCCCTCTCTCC
1 CTCTCCCTCTCTCC
*
115222 CTCTCTCTCTTCTCC
1 CTCTCCCTC-TCTCC
115237 TCTCTCCCTC-C-CC
1 -CTCTCCCTCTCTCC
*
115250 CTCT--CTTTCTCC
1 CTCTCCCTCTCTCC
115262 CTCTCCCTCTCCCTCC
1 CTCTCCCTCT--CTCC
*
115278 TTCTCTCCCTCTCTCT
1 --CTCTCCCTCTCTCC
115294 CTCT-CCTCTTCTCC
1 CTCTCCCTC-TCTCC
*
115308 CTCTCCTCCCTCTCC
1 CTCTCC-CTCTCTCC
115323 CTCTCCCTCTC
1 CTCTCCCTCTC
115334 CATCTCCATC
Statistics
Matches: 275, Mismatches: 30, Indels: 68
0.74 0.08 0.18
Matches are distributed among these distances:
10 2 0.01
11 3 0.01
12 27 0.10
13 24 0.09
14 111 0.40
15 42 0.15
16 52 0.19
17 4 0.01
18 10 0.04
ACGTcount: A:0.01, C:0.59, G:0.00, T:0.39
Consensus pattern (14 bp):
CTCTCCCTCTCTCC
Found at i:118425 original size:60 final size:61
Alignment explanation
Indices: 118319--118464 Score: 149
Period size: 60 Copynumber: 2.4 Consensus size: 61
118309 TTAATTTTAT
* * *
118319 TTTTGAAACA-TTCTAATTTT-ATCCCTAAACTATGACTATCAATCTAAATT-AGTCCTTAAAC
1 TTTT-AAACATTTCT-ATTTTCATCCTTAAAATATGACTATCAATCTAAATTGAGTCC-CAAAC
* * *
118380 TTTTAAATATTTC-ATTTTCATCCTTAAAATATGACCT-TCATTCTAAATTGATTCCCAAAC
1 TTTTAAACATTTCTATTTTCATCCTTAAAATATGA-CTATCAATCTAAATTGAGTCCCAAAC
**
118440 TTTTGTACATTTCTATTTTCATCCT
1 TTTTAAACATTTCTATTTTCATCCT
118465 AAACTATACA
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
59 5 0.07
60 42 0.59
61 24 0.34
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.45
Consensus pattern (61 bp):
TTTTAAACATTTCTATTTTCATCCTTAAAATATGACTATCAATCTAAATTGAGTCCCAAAC
Found at i:124089 original size:6 final size:6
Alignment explanation
Indices: 124078--124104 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
124068 ATCTATAAGA
124078 CTATAT CTATAT CTATAT CTATAT CTA
1 CTATAT CTATAT CTATAT CTATAT CTA
124105 CATTAACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (6 bp):
CTATAT
Found at i:124922 original size:18 final size:19
Alignment explanation
Indices: 124890--124926 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
124880 GAGAAGATGA
124890 CATGGTAAACCCAACACAC
1 CATGGTAAACCCAACACAC
*
124909 CATGG-AAACGCAACACAC
1 CATGGTAAACCCAACACAC
124927 ATGATATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.43, C:0.35, G:0.14, T:0.08
Consensus pattern (19 bp):
CATGGTAAACCCAACACAC
Found at i:130064 original size:45 final size:45
Alignment explanation
Indices: 130000--130092 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
129990 ACACATACAA
130000 AATAAGACATAGACATGAACCTCATTTAAAAAACCCCATAAACCT
1 AATAAGACATAGACATGAACCTCATTTAAAAAACCCCATAAACCT
130045 AATAAGACATAGACATGAACCTCATTTAAAAAACCCCATAAACCT
1 AATAAGACATAGACATGAACCTCATTTAAAAAACCCCATAAACCT
130090 AAT
1 AAT
130093 GGAAGAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.49, C:0.24, G:0.06, T:0.20
Consensus pattern (45 bp):
AATAAGACATAGACATGAACCTCATTTAAAAAACCCCATAAACCT
Found at i:140711 original size:93 final size:93
Alignment explanation
Indices: 140552--140738 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
140542 GAGTGGATGG
140552 TGGTAATGAGTTGGCTGGCACTGAATATGTGGATGATATCTACAAGTTCTACAAACGGACGGAAG
1 TGGTAATGAGTTGGCTGGCACTGAATATGTGGATGATATCTACAAGTTCTACAAACGGACGGAAG
140617 TAATAATCTTTCACTTTTTCTTAATAAT
66 TAATAATCTTTCACTTTTTCTTAATAAT
140645 TGGTAATGAGTTGGCTGGCACTGAATATGTGGATGATATCTACAAGTTCTACAAACGGACGGAAG
1 TGGTAATGAGTTGGCTGGCACTGAATATGTGGATGATATCTACAAGTTCTACAAACGGACGGAAG
140710 TAATAATCTTTCACTTTTTCTTAATAAT
66 TAATAATCTTTCACTTTTTCTTAATAAT
140738 T
1 T
140739 TTTTTCCCTG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (93 bp):
TGGTAATGAGTTGGCTGGCACTGAATATGTGGATGATATCTACAAGTTCTACAAACGGACGGAAG
TAATAATCTTTCACTTTTTCTTAATAAT
Found at i:141940 original size:35 final size:38
Alignment explanation
Indices: 141873--141942 Score: 110
Period size: 35 Copynumber: 1.9 Consensus size: 38
141863 GCAAAGGGGT
*
141873 GATCATGTTTCTTTTATGATCCTTTTGGAGTAGGATTC
1 GATCATGTTTCTTTTATGATCCTTTTGAAGTAGGATTC
141911 GATCATG-TT-TTTTATGAT-CTTTTGAAGTAGGA
1 GATCATGTTTCTTTTATGATCCTTTTGAAGTAGGA
141943 CTTACTAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 13 0.42
36 9 0.29
37 2 0.06
38 7 0.23
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.47
Consensus pattern (38 bp):
GATCATGTTTCTTTTATGATCCTTTTGAAGTAGGATTC
Found at i:147134 original size:23 final size:23
Alignment explanation
Indices: 147107--147155 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
147097 AGATTACAAC
147107 TTTTTAATATAAATTTTGAATTT
1 TTTTTAATATAAATTTTGAATTT
** *
147130 TTTTTGTTATTAATTTTGAATTT
1 TTTTTAATATAAATTTTGAATTT
147153 TTT
1 TTT
147156 ATTTATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (23 bp):
TTTTTAATATAAATTTTGAATTT
Found at i:155079 original size:97 final size:99
Alignment explanation
Indices: 154970--155165 Score: 378
Period size: 97 Copynumber: 2.0 Consensus size: 99
154960 TTTGTGTTGC
154970 GATCCAATTGAATTGGTTTTAAAGATTAATTTATTATTTGATTTGAAATTAAAAATAAAATGTCC
1 GATCCAATTGAATTGGTTTTAAAGATTAATTTATTATTTGATTTGAAATTAAAAATAAAATGTCC
155035 AAATG-TTTTTTAATTAC-AAAAAATGAATAATA
66 AAATGTTTTTTTAATTACAAAAAAATGAATAATA
155067 GATCCAATTGAATTGGTTTTAAAGATTAATTTATTATTTGATTTGAAATTAAAAATAAAATGTCC
1 GATCCAATTGAATTGGTTTTAAAGATTAATTTATTATTTGATTTGAAATTAAAAATAAAATGTCC
155132 AAATGTTTTTTTAATTACAAAAAAATGAATAATA
66 AAATGTTTTTTTAATTACAAAAAAATGAATAATA
155166 CGAATTACTA
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
97 70 0.72
98 12 0.12
99 15 0.15
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.40
Consensus pattern (99 bp):
GATCCAATTGAATTGGTTTTAAAGATTAATTTATTATTTGATTTGAAATTAAAAATAAAATGTCC
AAATGTTTTTTTAATTACAAAAAAATGAATAATA
Found at i:165212 original size:31 final size:31
Alignment explanation
Indices: 165174--165238 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
165164 ATATATTTAA
*
165174 ATATTTTATTATTAATTT-AATATAAAAATAT
1 ATATTTTACTATTAATTTAAAT-TAAAAATAT
* *
165205 ATATTTTACTCTTATTTTAAATTAAAAATAT
1 ATATTTTACTATTAATTTAAATTAAAAATAT
165236 ATA
1 ATA
165239 ATATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATTTTACTATTAATTTAAATTAAAAATAT
Found at i:165243 original size:34 final size:32
Alignment explanation
Indices: 165174--165295 Score: 112
Period size: 34 Copynumber: 3.9 Consensus size: 32
165164 ATATATTTAA
* *
165174 ATATTTTATTATTAATTT-AA-TATAAAAATAT
1 ATATTTTATTCTTATTTTAAATTA-AAAAATAT
*
165205 ATATTTTACTCTTATTTTAAATTAAAAATATAT
1 ATATTTTATTCTTATTTTAAATTAAAAA-ATAT
* *
165238 AATATTTTATTTTTATCTTT-ACTT-AAAAATAT
1 -ATATTTTATTCTTAT-TTTAAATTAAAAAATAT
*
165270 -T-TTTTATTCATATTTTAAATTAAAAA
1 ATATTTTATTCTTATTTTAAATTAAAAA
165296 TATTTTTTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
28 3 0.04
29 13 0.17
30 5 0.07
31 15 0.20
32 10 0.13
33 10 0.13
34 16 0.21
35 3 0.04
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (32 bp):
ATATTTTATTCTTATTTTAAATTAAAAAATAT
Found at i:165270 original size:100 final size:100
Alignment explanation
Indices: 165089--165271 Score: 228
Period size: 100 Copynumber: 1.8 Consensus size: 100
165079 AATTTTTTAT
* * * *
165089 TTTAATGTAAAAATATGTATTTTATCTTTATCATCACTTAAAAATATATATATTTTTTAAATATC
1 TTTAATATAAAAATATATATTTTATCTTTATCATAAATTAAAAATATATATATTTTTTAAATATC
*
165154 TTAACTTGAAATATATTTAAATATTTTATTATTAA
66 TTAACTTGAAAAATATTTAAATATTTTATTATTAA
** **
165189 TTTAATATAAAAATATATATTTTA-CTCTTATTTTAAATTAAAAATATATAATATTTTATT-TTT
1 TTTAATATAAAAATATATATTTTATCT-TTATCATAAATTAAAAATATAT-ATATTTT-TTAAAT
*
165252 ATCTTTACTT-AAAAATATTT
63 ATCTTAACTTGAAAAATATTT
165272 TTTATTCATA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
99 2 0.03
100 49 0.70
101 17 0.24
102 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (100 bp):
TTTAATATAAAAATATATATTTTATCTTTATCATAAATTAAAAATATATATATTTTTTAAATATC
TTAACTTGAAAAATATTTAAATATTTTATTATTAA
Found at i:165274 original size:29 final size:29
Alignment explanation
Indices: 165172--165304 Score: 96
Period size: 29 Copynumber: 4.4 Consensus size: 29
165162 AAATATATTT
165172 AAATATTTTATTATT-A-A-TTT-AATATAA
1 AAATATTTT-TTATTCATATTTTAAAT-TAA
* *
165199 AAATATATATTTTACTCTTATTTTAAATTAAA
1 AAATAT-T-TTTTATTCATATTTTAAATT-AA
** *
165231 AATATATAATATTTTATTTTTATCTTT-ACTTAA
1 AA-ATAT--T-TTTTATTCATAT-TTTAAATTAA
165264 AAATATTTTTTATTCATATTTTAAATTAA
1 AAATATTTTTTATTCATATTTTAAATTAA
165293 AAATATTTTTTA
1 AAATATTTTTTA
165305 AATTAATAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
27 6 0.07
28 8 0.09
29 29 0.33
30 2 0.02
31 4 0.05
32 11 0.13
33 8 0.09
34 16 0.18
35 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
AAATATTTTTTATTCATATTTTAAATTAA
Found at i:165294 original size:63 final size:65
Alignment explanation
Indices: 165173--165298 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 65
165163 AATATATTTA
*
165173 AATATTTTATTATTAATTTAATATAAAAATATATATTTTACTCTTATTTTAAATTAAAAATATAT
1 AATATTTTATTATTAATTTAATATAAAAATATATATTTTACTCATATTTTAAATTAAAAATATAT
* * * *
165238 AATATTTTATTTTTATCTTTACT-TAAAAATAT-T-TTTTATTCATATTTTAAATTAAAAATAT
1 AATATTTTATTATTA-ATTTAATATAAAAATATATATTTTACTCATATTTTAAATTAAAAATAT
165299 TTTTTAAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
63 26 0.47
64 1 0.02
65 23 0.42
66 5 0.09
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (65 bp):
AATATTTTATTATTAATTTAATATAAAAATATATATTTTACTCATATTTTAAATTAAAAATATAT
Found at i:165300 original size:16 final size:17
Alignment explanation
Indices: 165282--165315 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
165272 TTTATTCATA
165282 TTTTAAATTAAAAATATT
1 TTTTAAATTAAAAATA-T
*
165300 TTTTAAATTAATAATA
1 TTTTAAATTAAAAATA
165316 AGCTTGTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAATTAAAAATAT
Found at i:167143 original size:21 final size:22
Alignment explanation
Indices: 167117--167158 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
167107 AAATTTTAAT
* *
167117 TTATTTGATTTATTAA-ATTGA
1 TTATTTAATTAATTAATATTGA
167138 TTATTTAATTAATTAATATTG
1 TTATTTAATTAATTAATATTG
167159 TTTAAATTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
TTATTTAATTAATTAATATTGA
Found at i:167717 original size:18 final size:18
Alignment explanation
Indices: 167694--167739 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
167684 TCGATGGTGT
167694 TATTATTATTTAATAAAA
1 TATTATTATTTAATAAAA
*
167712 TATTATTATTTGATAAAA
1 TATTATTATTTAATAAAA
* *
167730 AATAATTATT
1 TATTATTATT
167740 ATTAAATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TATTATTATTTAATAAAA
Found at i:167719 original size:21 final size:22
Alignment explanation
Indices: 167693--167743 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
167683 ATCGATGGTG
*
167693 TTATTATTAT-TTAATAAAAT-A
1 TTATTATTATGATAA-AAAATAA
167714 TTATTATT-TGATAAAAAATAA
1 TTATTATTATGATAAAAAATAA
167735 TTATTATTA
1 TTATTATTA
167744 AATGGTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATTATTATGATAAAAAATAA
Found at i:169978 original size:16 final size:16
Alignment explanation
Indices: 169939--169984 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
169929 AACTTGAAAA
* *
169939 TATAGTTTTAATATTT
1 TATAATTTTAATATTC
169955 TAATAATTTTAATATTC
1 T-ATAATTTTAATATTC
169972 TATAATTTTAATA
1 TATAATTTTAATA
169985 CTATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
TATAATTTTAATATTC
Found at i:170435 original size:32 final size:32
Alignment explanation
Indices: 170390--170541 Score: 131
Period size: 31 Copynumber: 4.9 Consensus size: 32
170380 TTAAAAGTTA
* *
170390 AAATAAG-AT-AAAAATATATATTTTTATCTT
1 AAATAAGAATAAAAAATATATATTTTAAACTT
*
170420 AGATAAGAATAAAAAATATAT-TTTTAAACTT
1 AAATAAGAATAAAAAATATATATTTTAAACTT
170451 AAATAAGAATAATAAAATATATATTTT-AA-TT
1 AAATAAGAATAA-AAAATATATATTTTAAACTT
* ** * * *
170482 TAATTTG-ATAATAAA-ATATATTTAATAAGTT
1 AAATAAGAATAAAAAATATATATTTTA-AACTT
*
170513 AATATAAAAAT-AAAAATATATATTTTAAA
1 AA-ATAAGAATAAAAAATATATATTTTAAA
170542 GTAAAAATAA
Statistics
Matches: 97, Mismatches: 15, Indels: 18
0.75 0.12 0.14
Matches are distributed among these distances:
28 8 0.08
29 3 0.03
30 12 0.12
31 30 0.31
32 29 0.30
33 15 0.15
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (32 bp):
AAATAAGAATAAAAAATATATATTTTAAACTT
Found at i:170453 original size:62 final size:60
Alignment explanation
Indices: 170377--170540 Score: 172
Period size: 61 Copynumber: 2.6 Consensus size: 60
170367 ATTTTATTAA
*
170377 ATTTTAAAAGTTAAAATAAGATAAAAATATATATTTTTATCTTAGATAAGAATAA-AAAATAT
1 ATTTTAAAAGTTAAAATAAGATAAAAATATATATTTTAAT-TTA-ATAAG-ATAATAAAATAT
* * **
170439 ATTTTTAAACTT-AAATAAGAATAATAAAATATATATTTTAATTTAATTTGATAATAAAATAT
1 ATTTTAAAAGTTAAAATAAG-AT-A-AAAATATATATTTTAATTTAATAAGATAATAAAATAT
* *
170501 A-TTTAATAAGTTAATATAAAAATAAAAATATATATTTTAA
1 ATTTTAA-AAGTTAAAAT-AAGATAAAAATATATATTTTAA
170541 AGTAAAAATA
Statistics
Matches: 86, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
61 31 0.36
62 28 0.33
63 9 0.10
64 18 0.21
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (60 bp):
ATTTTAAAAGTTAAAATAAGATAAAAATATATATTTTAATTTAATAAGATAATAAAATAT
Found at i:170473 original size:34 final size:31
Alignment explanation
Indices: 170390--170538 Score: 130
Period size: 30 Copynumber: 4.8 Consensus size: 31
170380 TTAAAAGTTA
*
170390 AAATAAG-ATAAAAATATATATTTTTATCTT
1 AAATAAGAATAAAAATATATATTTTTAACTT
*
170420 AGATAAGAATAAAAA-ATATATTTTTAAACTT
1 AAATAAGAATAAAAATATATATTTTT-AACTT
170451 AAATAAGAATAATAAA-ATATATATTTTAA-TT
1 AAATAAGAATAA-AAATATATAT-TTTTAACTT
* ** * *
170482 TAATTTG-ATAATAAA-ATATATTTAATAAGTT
1 AAATAAGAATAA-AAATATATATTT-TTAACTT
*
170513 AATATAAAAATAAAAATATATATTTT
1 AA-ATAAGAATAAAAATATATATTTT
170539 AAAGTAAAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 16
0.78 0.10 0.13
Matches are distributed among these distances:
29 2 0.02
30 33 0.34
31 31 0.32
32 16 0.16
33 16 0.16
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (31 bp):
AAATAAGAATAAAAATATATATTTTTAACTT
Found at i:177028 original size:42 final size:42
Alignment explanation
Indices: 176968--177051 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
176958 CAAAACCACA
176968 CAATATGTTTTCAATCATTTTTCTTACTTCATTGGTGCTAGC
1 CAATATGTTTTCAATCATTTTTCTTACTTCATTGGTGCTAGC
*
177010 CAATATGTTTTCATTCATTTTTCTTACTTCATTGGTGCTAGC
1 CAATATGTTTTCAATCATTTTTCTTACTTCATTGGTGCTAGC
177052 TTCATCTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (42 bp):
CAATATGTTTTCAATCATTTTTCTTACTTCATTGGTGCTAGC
Found at i:182921 original size:2 final size:2
Alignment explanation
Indices: 182914--182959 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
182904 TTACATTTGC
* *
182914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
182956 AT AT
1 AT AT
182960 TAAATATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:183040 original size:30 final size:30
Alignment explanation
Indices: 183004--183068 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
182994 AAATATGTAT
* * *
183004 AATTAAATTGAAATTAAAATTTATATATAC
1 AATTAAATTAAAACTAAAATTCATATATAC
*
183034 AATTAAATTAAAACTAAAATTCATGTATAC
1 AATTAAATTAAAACTAAAATTCATATATAC
*
183064 TATTA
1 AATTA
183069 CACAATATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (30 bp):
AATTAAATTAAAACTAAAATTCATATATAC
Found at i:184752 original size:17 final size:17
Alignment explanation
Indices: 184726--184768 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
184716 GCCCATGTAC
*
184726 ATATGCGAGAACTATAT
1 ATATGTGAGAACTATAT
184743 ATATGTGAGAACTATAT
1 ATATGTGAGAACTATAT
184760 ATATGTGAG
1 ATATGTGAG
184769 TACATTGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (17 bp):
ATATGTGAGAACTATAT
Found at i:184886 original size:18 final size:18
Alignment explanation
Indices: 184859--184910 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
184849 CATTGTATAT
184859 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCACTAC
* *
184877 GTCCCAAAGGACCACTAT
1 GTCCCGAAGGACCACTAC
*
184895 GTCCCGAATGACCACT
1 GTCCCGAAGGACCACT
184911 GATAATCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.37, G:0.19, T:0.15
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAC
Found at i:188969 original size:18 final size:18
Alignment explanation
Indices: 188946--189038 Score: 114
Period size: 18 Copynumber: 4.9 Consensus size: 18
188936 GCGTAGAATT
*
188946 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
188964 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
188986 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
189004 CGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
189022 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
189039 GATAATCCCT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
18 47 0.72
22 18 0.28
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:191794 original size:21 final size:20
Alignment explanation
Indices: 191770--191884 Score: 97
Period size: 23 Copynumber: 5.3 Consensus size: 20
191760 ACCGAAGTGT
191770 CACATAATTGTCCCGAAGGAC
1 CACATAATT-TCCCGAAGGAC
*
191791 CACATAGGTTTGCACCGAAGTG-C
1 CACATA-ATTT-C-CCGAAG-GAC
*
191814 CACATAGATTTGCACCGAAGTAC
1 CACATA-ATTT-C-CCGAAGGAC
* *
191837 CACATATTTTCTCGAAGGAC
1 CACATAATTTCCCGAAGGAC
191857 CACATAATTATCCCGAAGGAC
1 CACATAATT-TCCCGAAGGAC
*
191878 CATATAA
1 CACATAA
191885 AACCCTCGAC
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
20 15 0.19
21 24 0.30
22 6 0.08
23 33 0.42
24 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (20 bp):
CACATAATTTCCCGAAGGAC
Found at i:191858 original size:20 final size:21
Alignment explanation
Indices: 191828--191884 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
191818 TAGATTTGCA
* *
191828 CCGAAGTACCACAT-ATTTTC
1 CCGAAGGACCACATAATTATC
*
191848 TCGAAGGACCACATAATTATC
1 CCGAAGGACCACATAATTATC
*
191869 CCGAAGGACCATATAA
1 CCGAAGGACCACATAA
191885 AACCCTCGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (21 bp):
CCGAAGGACCACATAATTATC
Found at i:192499 original size:19 final size:20
Alignment explanation
Indices: 192452--192502 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
192442 CTAGTACCGA
*
192452 TACCGATACTTCTCTTCAAGGG
1 TACCGATAC--CTCCTCAAGGG
*
192474 TATCGATACCTCCTCAA-GG
1 TACCGATACCTCCTCAAGGG
192493 TACCGATACC
1 TACCGATACC
192503 AATTTGGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 7 0.27
22 8 0.31
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (20 bp):
TACCGATACCTCCTCAAGGG
Found at i:192571 original size:21 final size:21
Alignment explanation
Indices: 192536--192588 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
192526 CTTAAAAATG
192536 GTATCGATA-CTACCCTTACA
1 GTATCGATACCTACCCTTACA
192556 GTATCGATACCTACCCTTACA
1 GTATCGATACCTACCCTTACA
* *
192577 GTGTTGATACCT
1 GTATCGATACCT
192589 CTTCAACAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 9 0.30
21 21 0.70
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.32
Consensus pattern (21 bp):
GTATCGATACCTACCCTTACA
Found at i:193383 original size:16 final size:17
Alignment explanation
Indices: 193362--193396 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
193352 GAAGTATTGG
193362 TATGTGAAAATG-TTTA
1 TATGTGAAAATGCTTTA
*
193378 TATGTGAATATGCTTTA
1 TATGTGAAAATGCTTTA
193395 TA
1 TA
193397 CAAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (17 bp):
TATGTGAAAATGCTTTA
Found at i:193583 original size:23 final size:23
Alignment explanation
Indices: 193557--193611 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
193547 ACGGTCCTTT
*
193557 GGGACAAATCTATGTGTTCATTC
1 GGGACAAATCTATGTGGTCATTC
* * *
193580 GGGACAATTCTATGTGGTCCTTT
1 GGGACAAATCTATGTGGTCATTC
193603 GGGACAAAT
1 GGGACAAAT
193612 TCTTAACAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (23 bp):
GGGACAAATCTATGTGGTCATTC
Found at i:201279 original size:19 final size:20
Alignment explanation
Indices: 201242--201291 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
201232 ACGTGAGAAT
*
201242 AATAAATAA-AACAAGAACA
1 AATAAAAAATAACAAGAACA
*
201261 AATAGAAAATAACAA-AACA
1 AATAAAAAATAACAAGAACA
*
201280 CATAAAAAATAA
1 AATAAAAAATAA
201292 TAATAAAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.74, C:0.10, G:0.04, T:0.12
Consensus pattern (20 bp):
AATAAAAAATAACAAGAACA
Found at i:201594 original size:34 final size:36
Alignment explanation
Indices: 201556--201628 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
201546 TAATATATAT
201556 AAATAAATAAAAAC-A-AAAATAGAATATTAAGAAA
1 AAATAAATAAAAACGATAAAATAGAATATTAAGAAA
* *
201590 AAATATATAAAAACGTATAAAATATAATATTAAGAAA
1 AAATAAATAAAAACG-ATAAAATAGAATATTAAGAAA
201627 AA
1 AA
201629 TATATATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 13 0.38
36 1 0.03
37 20 0.59
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (36 bp):
AAATAAATAAAAACGATAAAATAGAATATTAAGAAA
Found at i:201628 original size:17 final size:17
Alignment explanation
Indices: 201570--201632 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
201560 AAATAAAAAC
*
201570 AAAAATAGAATATTAAG
1 AAAAATATAATATTAAG
**
201587 AAAAA-ATATATAAAAACG
1 AAAAATATA-ATATTAA-G
201605 TATAAAATATAATATTAAG
1 -A-AAAATATAATATTAAG
201624 AAAAATATA
1 AAAAATATA
201633 TATACATAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
16 2 0.06
17 18 0.50
18 2 0.06
19 2 0.06
20 9 0.25
21 3 0.08
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (17 bp):
AAAAATATAATATTAAG
Found at i:201632 original size:34 final size:33
Alignment explanation
Indices: 201531--201632 Score: 95
Period size: 37 Copynumber: 3.0 Consensus size: 33
201521 AAATAATAGA
* *
201531 AAAAAAGTAAAAATATAATATATATA-AATAA-AT
1 AAAAACGTAAAAATATAATAT-TA-AGAAAAATAT
*
201564 AAAAAC--AAAAATAGAATATTAAGAAAAAATATAT
1 AAAAACGTAAAAATATAATATTAAG--AAAA-ATAT
201598 AAAAACGTATAAAATATAATATTAAGAAAAATAT
1 AAAAACGTA-AAAATATAATATTAAGAAAAATAT
201632 A
1 A
201633 TATACATAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
29 1 0.02
30 2 0.04
31 12 0.21
32 3 0.05
33 6 0.11
34 13 0.23
35 4 0.07
36 1 0.02
37 15 0.26
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (33 bp):
AAAAACGTAAAAATATAATATTAAGAAAAATAT
Found at i:201678 original size:2 final size:2
Alignment explanation
Indices: 201666--201811 Score: 151
Period size: 2 Copynumber: 76.0 Consensus size: 2
201656 TTAATACATC
*
201666 TA TA CA 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
* *
201708 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA -A TA AA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
201748 AA TA TA TA AA TA -A AA AA TA TA AA TA AA TA -A AA AA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
201787 -A 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
201812 GGACGAAATT
Statistics
Matches: 124, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
1 6 0.05
2 118 0.95
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (2 bp):
TA
Found at i:202962 original size:85 final size:83
Alignment explanation
Indices: 202848--203033 Score: 241
Period size: 83 Copynumber: 2.2 Consensus size: 83
202838 TAATTTTCGT
* * * * *
202848 TGACAGATAGCCCTTCTTGCCTTGAGTTATGCTGTAAATT-TGATTTACCTCT-GAGTTGAATGT
1 TGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATTATG-TGT--CT-TGGAGCTGAACGT
202911 AATCGAACTCGAAGGTCTTTGA
62 AATCGAACTCGAAGGTCTTTGA
* * *
202933 TGATAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATTATGTGTCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATTATGTGTCTTGGAGCTGAACGTAATC
*
202998 GAACTCGAAGGTCTTTGT
66 GAACTCGAAGGTCTTTGA
203016 TGACAGATAACCCTTCTT
1 TGACAGATAACCCTTCTT
203034 TAAGTTGGAT
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
82 1 0.01
83 47 0.53
85 39 0.44
86 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (83 bp):
TGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATTATGTGTCTTGGAGCTGAACGTAATC
GAACTCGAAGGTCTTTGA
Found at i:203029 original size:83 final size:84
Alignment explanation
Indices: 202815--203033 Score: 250
Period size: 85 Copynumber: 2.6 Consensus size: 84
202805 AGGTGTCATC
* * * *
202815 GAGCTGAATGGAATCGAACTCGATA-AT-TTTCGTTGACAGATAGCCCTTCTTGCCTTGAGTTAT
1 GAGCTGAACGTAATCGAACTCGA-AGGTCTTT-GTTGACAGATAACCCTTCTTGCCTTGAGTTAT
* *
202878 GCTGTAAATTTGATTTACCTCT
64 GCTGCAAATTTGATGTA-CTCT
* * * *
202900 GAGTTGAATGTAATCGAACTCGAAGGTCTTTGATGATAGATAACCCTTCTTGCCTTGAGTTATGC
1 GAGCTGAACGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGC
202965 TGCAAATTATG-TGT-CT-T
66 TGCAAATT-TGATGTACTCT
* *
202982 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTT
1 -GAGCTGAACGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTT
203034 TAAGTTGGAT
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
82 1 0.01
83 47 0.41
84 1 0.01
85 62 0.53
86 5 0.04
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (84 bp):
GAGCTGAACGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGC
TGCAAATTTGATGTACTCT
Found at i:203418 original size:110 final size:110
Alignment explanation
Indices: 203265--203463 Score: 272
Period size: 110 Copynumber: 1.8 Consensus size: 110
203255 AACTGGGAAA
* * **
203265 TTGTTTGTTGACAGCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTTTAATA
1 TTGTTTGTTGACAACCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGTTATCTCGAGTCCAATA
* *
203330 TCATTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAG
66 TCACTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAG
* * * * * *
203375 TTGTTTGTTGACAATCAGTCGCCCCTTCGTTATGAATTTGAGCTTGTGTTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAACCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGTTATCTCGAGTCCAATA
* *
203440 TCCCTCGCTGTGAAGTTGAAATTG
66 TCACTCGCTGTGAAGTTAAAATTG
203464 GCTATGAAAC
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
110 75 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (110 bp):
TTGTTTGTTGACAACCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGTTATCTCGAGTCCAATA
TCACTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAG
Found at i:204280 original size:68 final size:65
Alignment explanation
Indices: 204190--204577 Score: 262
Period size: 65 Copynumber: 5.8 Consensus size: 65
204180 AAGATATCTG
* * * * **
204190 TTGTTTCATGAAAAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-
204255 TT
64 TT
204257 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTT-AGGAGAAATAAATTCAAAGA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGG-GAAATAAATTCAAAGA
204321 TT
64 TT
* * * * *
204323 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
204388 ACAAA-ACT
57 TCAAAGATT
* * * * * * *** * * *
204396 TAGTTCCAAAAGAAACTGTCTTAAGGGAGACGAAATTTGTTTCAAATAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * * *** *
204461 TTGTTTCAAG-GAAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGCGAAATGTTTTCAATG-T
1 TTGTTTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
204524 T
65 T
** * *
204525 TATGTTTTGAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAA
204578 CTATCTCAAG
Statistics
Matches: 257, Mismatches: 47, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
64 9 0.04
65 118 0.46
66 24 0.09
67 23 0.09
68 30 0.12
70 1 0.00
72 1 0.00
73 46 0.18
74 5 0.02
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:204307 original size:36 final size:36
Alignment explanation
Indices: 204259--204669 Score: 214
Period size: 36 Copynumber: 12.0 Consensus size: 36
204249 GAAGATTTTG
*
204259 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * **
204295 TGTTTTAGGAGAAA-----T--A-A-ATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-AT-T
*
204324 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
204360 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
204397 AGTTCCAAAAGAAACTGTCTTAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
204433 TGTTTCAA-ATAAAACATAT-TC-----A-A-ATATTT
1 TGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACAAAATT
*
204462 TGTTTCAAG-GAAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATT
* * * * *
204498 TATTTCAAGCGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
** * *
204526 ATGTTTTGAGAGAAACTGTCTCAAGGGAGGCAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
204564 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** * *
204600 CATTTCAAGAGAAACTGTCTCAAGGGAGAC-AATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
204635 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
204670 CTTCTTTTTA
Statistics
Matches: 276, Mismatches: 61, Indels: 76
0.67 0.15 0.18
Matches are distributed among these distances:
27 5 0.02
28 6 0.02
29 44 0.16
30 4 0.01
31 2 0.01
32 1 0.00
33 1 0.00
34 3 0.01
35 33 0.12
36 107 0.39
37 64 0.23
38 6 0.02
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:204483 original size:203 final size:202
Alignment explanation
Indices: 204259--204642 Score: 506
Period size: 203 Copynumber: 1.9 Consensus size: 202
204249 GAAGATTTTG
* * * *
204259 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAAATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAATAAATTCAAAG-TTT
* *
204324 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGA
*
204387 GACAAAACTT-AGTTCCAAAAGAAACTGTCTTAAGGGAGACGAAATTTGTTTCAAATAAAACATA
130 GACAAAA-TTCA-TTCCAAAAGAAACTGTCTCAAGGGAGAC-AAATTTGTTTCAAATAAAACATA
204451 TTCAAATATTT
192 TTCAAATATTT
* * *** *
204462 TGTTTCAAG-GAAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGCGAAATGTTTTCAATGTTT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAATAAATTCAAAGTTT
** * * *
204526 ATGTTTTGAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGA
* * *
204591 GACAAAATTCATTTCAAGAGAAACTGTCTCAAGGGAGACAATTTTGTTTCAA
130 GACAAAATTCATTCCAAAAGAAACTGTCTCAAGGGAGACAAATTTGTTTCAA
204643 GGGAAACTAT
Statistics
Matches: 156, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
202 16 0.10
203 105 0.67
204 35 0.22
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (202 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAATAAATTCAAAGTTTA
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAG
ACAAAATTCATTCCAAAAGAAACTGTCTCAAGGGAGACAAATTTGTTTCAAATAAAACATATTCA
AATATTT
Found at i:204652 original size:71 final size:73
Alignment explanation
Indices: 204534--204669 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 73
204524 TTATGTTTTG
204534 AGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
1 AGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
204599 TCATTTCA
66 TCATTTCA
* * *
204607 AGAGAAACTGTCTCAAGGGA-G-ACAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 AGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
204670 CTTCTTTTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 39 0.65
72 1 0.02
73 20 0.33
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (73 bp):
AGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
TCATTTCA
Found at i:205274 original size:10 final size:11
Alignment explanation
Indices: 205249--205274 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
205239 ATATCAATTA
205249 AAAAAGTTTTG
1 AAAAAGTTTTG
205260 AAAAAGTTTTG
1 AAAAAGTTTTG
205271 AAAA
1 AAAA
205275 TATTGCCCCT
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (11 bp):
AAAAAGTTTTG
Found at i:206115 original size:69 final size:69
Alignment explanation
Indices: 206000--206137 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
205990 TGTCTCTATC
**
206000 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
206065 TCAT
66 TCAT
* *
206069 TTGATGCTCTATGATCTTCGAGTAAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
206134 TCAT
66 TCAT
206138 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:206230 original size:12 final size:12
Alignment explanation
Indices: 206210--206267 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
206200 TTTTCTTCAA
206210 TTTTC-CTTTGT
1 TTTTCTCTTTGT
*
206221 TTTTCTCTTTTT
1 TTTTCTCTTTGT
*
206233 ATTTTATCTTTGCT
1 -TTTTCTCTTTG-T
206247 TTTT-TCTCTT-T
1 TTTTCTCT-TTGT
206258 TTTTCTCTTT
1 TTTTCTCTTT
206268 TTATTCTGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 12 0.31
12 11 0.28
13 15 0.38
14 1 0.03
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTCTTTGT
Found at i:206249 original size:25 final size:24
Alignment explanation
Indices: 206215--206267 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
206205 TTCAATTTTC
* *
206215 CTTTGTTTTTCTCTTTTTATTTTAT
1 CTTTGCTTTTCTCTCTTT-TTTTAT
* *
206240 CTTTGCTTTTTTCTCTTTTTTTCT
1 CTTTGCTTTTCTCTCTTTTTTTAT
206264 CTTT
1 CTTT
206268 TTATTCTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (24 bp):
CTTTGCTTTTCTCTCTTTTTTTAT
Found at i:208389 original size:30 final size:30
Alignment explanation
Indices: 208353--208421 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
208343 TTATTTGAGT
*
208353 TATGTGATAAAGGTATGG-AAATGATATGTC
1 TATGTGATAAAGGTA-GGAAAATAATATGTC
208383 TATGTGATAAAGGTAGGAAAATAATATGTC
1 TATGTGATAAAGGTAGGAAAATAATATGTC
*
208413 TACGTGATA
1 TATGTGATA
208422 CAAATTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGTGATAAAGGTAGGAAAATAATATGTC
Found at i:208669 original size:23 final size:23
Alignment explanation
Indices: 208632--208699 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
208622 ATTATTATAT
* *
208632 GGCACTACGGTGCAATTGTACGC
1 GGCACTCCGGTGCAATTATACGC
* * * *
208655 GGTACTCCGGTGCAATTCTATGT
1 GGCACTCCGGTGCAATTATACGC
*
208678 GGCACTTCGGTGCAATTATACG
1 GGCACTCCGGTGCAATTATACG
208700 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATACGC
Found at i:209447 original size:15 final size:15
Alignment explanation
Indices: 209423--209456 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
209413 CCGTAGGACC
209423 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
* *
209438 ACTACGTCCCGAATG
1 ACTACATCCCGAAGG
209453 ACTA
1 ACTA
209457 TTATACCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:209584 original size:29 final size:29
Alignment explanation
Indices: 209541--209650 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
209531 TTTCATATGC
209541 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
209569 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
209598 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
209627 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
209651 ATATCACATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:217641 original size:20 final size:20
Alignment explanation
Indices: 217618--217660 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
217608 AATCCACCAC
*
217618 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
217638 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
217658 ATG
1 ATG
217661 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:218211 original size:2 final size:2
Alignment explanation
Indices: 218204--218244 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
218194 CCAAGGCATT
218204 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
218245 TATGTGGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:228029 original size:20 final size:20
Alignment explanation
Indices: 228006--228048 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
227996 AATCCACCAC
*
228006 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
228026 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
228046 ATG
1 ATG
228049 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:233188 original size:29 final size:29
Alignment explanation
Indices: 233145--233280 Score: 211
Period size: 29 Copynumber: 4.7 Consensus size: 29
233135 TCATATGCTA
*
233145 ATGTA-CTCATGTCATTTCTCTTGTCATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
* *
233173 ATGTAGTTCATTTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
* *
233202 ATGTAGTTCATTTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
233231 ATGTAGCTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
233260 ATGTAGCTCATGTCATGTTCT
1 ATGTAGCTCATGTCAT-TTCT
233281 ATATCACATA
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
28 5 0.05
29 92 0.91
30 4 0.04
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.48
Consensus pattern (29 bp):
ATGTAGCTCATGTCATTTCTCTTGTGATC
Found at i:241166 original size:30 final size:30
Alignment explanation
Indices: 241132--241200 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
241122 TTATATGAGT
*
241132 TATGTGATAAAGGTATGG-AAATGATATGTC
1 TATGTGATAAAGGTA-GGAAAATAATATGTC
241162 TATGTGATAAAGGTAGGAAAATAATATGTC
1 TATGTGATAAAGGTAGGAAAATAATATGTC
*
241192 TACGTGATA
1 TATGTGATA
241201 CAAATTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGTGATAAAGGTAGGAAAATAATATGTC
Found at i:241458 original size:23 final size:23
Alignment explanation
Indices: 241432--241486 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
241422 ACTACAGTGT
241432 AATTCTACGCGGCACTCCGGTGC
1 AATTCTACGCGGCACTCCGGTGC
* * *
241455 AATTCTAAGTGGCACTTCGGTGC
1 AATTCTACGCGGCACTCCGGTGC
*
241478 AATTATACG
1 AATTCTACG
241487 AGCTGTGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (23 bp):
AATTCTACGCGGCACTCCGGTGC
Found at i:244373 original size:12 final size:12
Alignment explanation
Indices: 244356--244381 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
244346 AACACGTAAA
244356 AATAATAAAAAT
1 AATAATAAAAAT
244368 AATAATAAAAAT
1 AATAATAAAAAT
244380 AA
1 AA
244382 ACAAAATGAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:244616 original size:14 final size:15
Alignment explanation
Indices: 244587--244616 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
244577 CATGATATTA
244587 AGAAAAAATAATAAT
1 AGAAAAAATAATAAT
244602 AGAAAAAATAA-AAT
1 AGAAAAAATAATAAT
244616 A
1 A
244617 AAGTAAAAAT
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:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AGAAAAAATAATAAT
Found at i:244627 original size:25 final size:24
Alignment explanation
Indices: 244592--244649 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
244582 TATTAAGAAA
*
244592 AAATAATAATAGAAAAAATAAAAT
1 AAATAAAAATAGAAAAAATAAAAT
* * * *
244616 AAAGTAAAAATATAATATATATAAT
1 AAA-TAAAAATAGAAAAAATAAAAT
244641 AAATAAAAA
1 AAATAAAAA
244650 CAAAAATAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (24 bp):
AAATAAAAATAGAAAAAATAAAAT
Found at i:244642 original size:30 final size:30
Alignment explanation
Indices: 244590--244647 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
244580 GATATTAAGA
244590 AAAAATAATAATAGAAAAAATAAAATAAAGT
1 AAAAATAATAATAGAAAAAAT-AAATAAAGT
* * *
244621 AAAAAT-ATAATATATATAATAAATAAA
1 AAAAATAATAATAGAAAAAATAAATAAA
244648 AACAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 11 0.46
31 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (30 bp):
AAAAATAATAATAGAAAAAATAAATAAAGT
Found at i:244740 original size:40 final size:39
Alignment explanation
Indices: 244659--244741 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
244649 ACAAAAATAG
* * * *
244659 AATATTAAGAAAATATATATATAAAAATGTATAAAGTAT
1 AATATTAAGAAAATATATACATAAAAATGGAGAAAGAAT
*
244698 AATATTAAGAAAAATATATACATAGTAAATGGAGAAA-AAT
1 AATATTAAG-AAAATATATACATA-AAAATGGAGAAAGAAT
244738 AATA
1 AATA
244742 CATCTATACA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 9 0.24
40 19 0.51
41 9 0.24
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.29
Consensus pattern (39 bp):
AATATTAAGAAAATATATACATAAAAATGGAGAAAGAAT
Found at i:244805 original size:21 final size:20
Alignment explanation
Indices: 244776--244842 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
244766 TAAGATATAT
*
244776 ATAATAAAAATAATAAAATAA
1 ATAA-AAAAAAAATAAAATAA
* * *
244797 ATAAAAAAAGGAATATAGTAA
1 ATAAAAAAA-AAATAAAATAA
*
244818 ATAAATAAAAAAATATAATTAA
1 ATAAA-AAAAAAATA-AAATAA
244840 ATA
1 ATA
244843 TATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
20 5 0.14
21 21 0.57
22 11 0.30
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (20 bp):
ATAAAAAAAAAATAAAATAA
Found at i:256462 original size:27 final size:27
Alignment explanation
Indices: 256420--256487 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
256410 AGTGTAGGAA
256420 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
256445 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
256472 TATAGAGATATGATTT
1 TATAGAGATATGATTT
256488 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:258372 original size:21 final size:21
Alignment explanation
Indices: 258356--258409 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
258346 GCGTTGCATT
258356 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
258377 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
258398 TCGCGTTGCGAT
1 TCGCGTTGCGAT
258410 TTTCCATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:258447 original size:42 final size:40
Alignment explanation
Indices: 258380--258491 Score: 113
Period size: 41 Copynumber: 2.8 Consensus size: 40
258370 TTGAAAATCG
* *
258380 CGTTGCGATAGT-TGA-AAATCGCGTTGCGATTTTCC-ATTT
1 CGTTGCGATAGTCT-ACAAAT-TCGTTGCGATTTTCCAAATT
**
258419 CGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 --CGTTGCGATAGTCTACAAAT-TCGTTGCGATTTTCCAAATT
*
258462 CGTTGCGATAGTTTACAAATTCGTTGCGAT
1 CGTTGCGATAGTCTACAAATTCGTTGCGAT
258492 AGTCTACAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 10 0.17
41 30 0.50
42 17 0.28
43 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATAGTCTACAAATTCGTTGCGATTTTCCAAATT
Found at i:258449 original size:22 final size:21
Alignment explanation
Indices: 258421--258535 Score: 94
Period size: 21 Copynumber: 5.6 Consensus size: 21
258411 TTCCATTTCG
**
258421 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAAAT-T
* *
258443 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAAATT
*
258462 CGTTGCGATAGTTTACAAATT
1 CGTTGCGATAGTCTACAAATT
**
258483 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAAAT-T
* *
258505 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAAATT
*
258524 CGTTGTGATAGT
1 CGTTGCGATAGT
258536 TAAAAAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 19 0.25
20 10 0.13
21 27 0.36
22 19 0.25
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAAATT
Found at i:259653 original size:41 final size:42
Alignment explanation
Indices: 259608--259700 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 42
259598 CAACGAATTT
* *
259608 TCGCAACGAATTTGGAAA-ATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAACATCACAACAACAACTGTAGACTA
*
259649 TCGCAACGAATTTGTAAACTATCACAACAACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAC-ATCACAACAACAACTGTAGACTA
259692 TCGCAACGA
1 TCGCAACGA
259701 CAACTGTAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 17 0.36
43 30 0.64
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (42 bp):
TCGCAACGAATTTGGAAACATCACAACAACAACTGTAGACTA
Found at i:259654 original size:22 final size:22
Alignment explanation
Indices: 259626--259721 Score: 131
Period size: 22 Copynumber: 4.4 Consensus size: 22
259616 AATTTGGAAA
259626 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
** *
259648 ATCGCAACGA-ATTTGTAAACT
1 ATCGCAACGACAACTGTAGACT
* *
259669 ATCACAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
259691 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
259713 ATCGTAACG
1 ATCGCAACG
259722 CGATTTTCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
21 16 0.26
22 46 0.74
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:261801 original size:2 final size:2
Alignment explanation
Indices: 261786--261841 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
261776 GATTTTTATC
261786 TA TA -A TA TA T- 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
261826 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
261842 CACGTATGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:270837 original size:13 final size:13
Alignment explanation
Indices: 270819--270843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
270809 TAGTAATAAA
270819 AAAACTAAAAATG
1 AAAACTAAAAATG
270832 AAAACTAAAAAT
1 AAAACTAAAAAT
270844 ACTTCGATTA
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:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAACTAAAAATG
Found at i:271156 original size:2 final size:2
Alignment explanation
Indices: 271149--271253 Score: 57
Period size: 2 Copynumber: 57.0 Consensus size: 2
271139 ATCGGGGCGG
* * * *
271149 AT AT AT AT AT TT AA AT -T AA AT AT AT AA AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
271189 AT AT AT AT AT -T TT A- AT TT A- AT TT AA AT TT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
271226 -T AT TT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
271254 TTATTTTTAA
Statistics
Matches: 75, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
1 9 0.12
2 66 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:271214 original size:46 final size:46
Alignment explanation
Indices: 271157--271244 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
271147 GGATATATAT
271157 ATTTAAATTAAATATATAAATATTATATATATATATATATATTTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATATATATTTTA
* * * *
271203 ATTTAATTTAAATTTATTAATATTATTTATATATATATATAT
1 ATTTAAATTAAATATATAAATATTATATATATATATATATAT
271245 ATATAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (46 bp):
ATTTAAATTAAATATATAAATATTATATATATATATATATATTTTA
Found at i:276440 original size:29 final size:30
Alignment explanation
Indices: 276407--276482 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
276397 ATCCTAAGAT
*
276407 TATTATAAGTTATAAAATG-GTCACTTGAC
1 TATTAAAAGTTATAAAATGAGTCACTTGAC
*
276436 TATTAAAAGTTATAAAATGAGTCCCTTGAC
1 TATTAAAAGTTATAAAATGAGTCACTTGAC
*
276466 TATTAAAAGTTACAAAA
1 TATTAAAAGTTATAAAA
276483 ATTTCATCAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
29 18 0.42
30 25 0.58
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (30 bp):
TATTAAAAGTTATAAAATGAGTCACTTGAC
Found at i:277620 original size:2 final size:2
Alignment explanation
Indices: 277613--277665 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
277603 TTTCTTGAAT
277613 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
277655 TA TA TA TA TA T
1 TA TA TA TA TA T
277666 TTCTAAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:279448 original size:6 final size:6
Alignment explanation
Indices: 279440--279798 Score: 196
Period size: 6 Copynumber: 59.8 Consensus size: 6
279430 GGGTGGCAAC
* * * * * * *
279440 GGAAAC GGAAAT GGAAAT GGCAAC GGCAAC GGAAAT GGAAAT GGCAAC
1 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT
* * * * * * * *
279488 GGGAAC GGAAAT GGAAAT GGAAAC GGAAAC GGCAAC GGCAAT GGTAAT
1 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT
* * * * * * * *
279536 GGCAAC GGGAAC GGGAAC GGAAAT GGAAAT GGAAAC GGAAAC GGAAAT
1 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT
* * * * * * * * * *
279584 GGCAAT GGTAAT GGAAAC GGCAAC GGTAAT GGAAAC GGCAAC GGTAAT
1 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT
* * * * * *
279632 GGAAAT GGAAAC GGAAAT GGCAAC GGTAAT GGAAAT GGCAAT GGTAAT
1 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT
* * * * * * * *
279680 GGAAAT GGAAAC GGCAAT GGCAAC GGAAAT GGAAAT GGCAAC GGCAAC
1 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT
* * * * * * * * *
279728 GGTAAT GGCAAT GGCAAC GGCAAC GGTAAT GGAAAT GGCAAT GGCAAT
1 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT
* *
279776 GGTAAT GGAAAT GGCAAT GGAAA
1 GGAAAT GGAAAT GGAAAT GGAAA
279799 CGGCAACGGT
Statistics
Matches: 289, Mismatches: 64, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 289 1.00
ACGTcount: A:0.41, C:0.13, G:0.34, T:0.12
Consensus pattern (6 bp):
GGAAAT
Found at i:279473 original size:18 final size:18
Alignment explanation
Indices: 279440--279818 Score: 221
Period size: 18 Copynumber: 21.4 Consensus size: 18
279430 GGGTGGCAAC
*
279440 GGAAACGGAAATGGAAAT
1 GGAAACGGCAATGGAAAT
* *
279458 GGCAACGGCAACGGAAAT
1 GGAAACGGCAATGGAAAT
* * * *
279476 GGAAATGGCAACGGGAAC
1 GGAAACGGCAATGGAAAT
* * *
279494 GGAAATGGAAATGGAAAC
1 GGAAACGGCAATGGAAAT
* *
279512 GGAAACGGCAACGGCAAT
1 GGAAACGGCAATGGAAAT
* * * * *
279530 GGTAATGGCAACGGGAAC
1 GGAAACGGCAATGGAAAT
* *
279548 GGGAACGGAAATGGAAAT
1 GGAAACGGCAATGGAAAT
*
279566 GGAAA---C---GGAAAC
1 GGAAACGGCAATGGAAAT
* *
279578 GGAAATGGCAATGGTAAT
1 GGAAACGGCAATGGAAAT
* *
279596 GGAAACGGCAACGGTAAT
1 GGAAACGGCAATGGAAAT
* *
279614 GGAAACGGCAACGGTAAT
1 GGAAACGGCAATGGAAAT
* * *
279632 GGAAATGGAAACGGAAAT
1 GGAAACGGCAATGGAAAT
* *
279650 GGCAACGGTAATGGAAAT
1 GGAAACGGCAATGGAAAT
* * *
279668 GGCAATGGTAATGGAAAT
1 GGAAACGGCAATGGAAAT
* *
279686 GGAAACGGCAATGGCAAC
1 GGAAACGGCAATGGAAAT
* * * *
279704 GGAAATGGAAATGGCAAC
1 GGAAACGGCAATGGAAAT
* * *
279722 GGCAACGGTAATGGCAAT
1 GGAAACGGCAATGGAAAT
* * *
279740 GGCAACGGCAACGGTAAT
1 GGAAACGGCAATGGAAAT
* *
279758 GGAAATGGCAATGGCAAT
1 GGAAACGGCAATGGAAAT
* * * *
279776 GGTAATGGAAATGGCAAT
1 GGAAACGGCAATGGAAAT
* *
279794 GGAAACGGCAACGGTAAT
1 GGAAACGGCAATGGAAAT
*
279812 GGCAACG
1 GGAAACG
279819 ACAAGGGCAA
Statistics
Matches: 289, Mismatches: 66, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
12 10 0.03
15 1 0.00
18 278 0.96
ACGTcount: A:0.40, C:0.13, G:0.34, T:0.12
Consensus pattern (18 bp):
GGAAACGGCAATGGAAAT
Found at i:279828 original size:24 final size:24
Alignment explanation
Indices: 279434--279816 Score: 301
Period size: 24 Copynumber: 16.2 Consensus size: 24
279424 TAATAAGGGT
* * *
279434 GGCAACGGAAACGGAAATGGAAAT
1 GGCAATGGCAACGGTAATGGAAAT
* *
279458 GGCAACGGCAACGGAAATGGAAAT
1 GGCAATGGCAACGGTAATGGAAAT
* * *
279482 GGCAACGGGAACGGAAATGGAAAT
1 GGCAATGGCAACGGTAATGGAAAT
* * * * * *
279506 GGAAACGGAAACGGCAACGGCAAT
1 GGCAATGGCAACGGTAATGGAAAT
* * * * *
279530 GGTAATGGCAACGGGAACGGGAAC
1 GGCAATGGCAACGGTAATGGAAAT
* * * * * *
279554 GGAAATGGAAATGGAAACGGAAAC
1 GGCAATGGCAACGGTAATGGAAAT
* *
279578 GGAAATGGCAATGGTAATGGAAA-
1 GGCAATGGCAACGGTAATGGAAAT
*
279601 --C---GGCAACGGTAATGGAAAC
1 GGCAATGGCAACGGTAATGGAAAT
* * * * *
279620 GGCAACGGTAATGGAAATGGAAAC
1 GGCAATGGCAACGGTAATGGAAAT
*
279644 GGAAATGGCAACGGTAATGGAAAT
1 GGCAATGGCAACGGTAATGGAAAT
* * * *
279668 GGCAATGGTAATGGAAATGGAAAC
1 GGCAATGGCAACGGTAATGGAAAT
*
279692 GGCAATGGCAACGGAAATGGAAAT
1 GGCAATGGCAACGGTAATGGAAAT
* *
279716 GGCAACGGCAACGGTAATGGCAAT
1 GGCAATGGCAACGGTAATGGAAAT
*
279740 GGCAACGGCAACGGTAATGGAAAT
1 GGCAATGGCAACGGTAATGGAAAT
*
279764 GGCAATGGCAATGGTAATGGAAAT
1 GGCAATGGCAACGGTAATGGAAAT
* * * *
279788 GGCAATGGAAACGGCAACGGTAAT
1 GGCAATGGCAACGGTAATGGAAAT
279812 GGCAA
1 GGCAA
279817 CGACAAGGGC
Statistics
Matches: 302, Mismatches: 51, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
18 16 0.05
21 1 0.00
24 285 0.94
ACGTcount: A:0.40, C:0.14, G:0.34, T:0.12
Consensus pattern (24 bp):
GGCAATGGCAACGGTAATGGAAAT
Found at i:279831 original size:48 final size:48
Alignment explanation
Indices: 279433--279813 Score: 333
Period size: 48 Copynumber: 7.9 Consensus size: 48
279423 ATAATAAGGG
* * * *
279433 TGGCAACGGAAACGGAAATGGAAATGGCAACGGCAACGGAAATGGAAA
1 TGGCAACGGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGGAAA
* * * *
279481 TGGCAACGGGAACGGAAATGGAAATGGAAACGG--A----AACGGCAA
1 TGGCAACGGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGGAAA
* * * * * * * * * *
279523 CGGCAATGGTAATGGCAACGGGAACGGGAACGGAAATGGAAATGGAAA
1 TGGCAACGGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGGAAA
* * * * *
279571 CGGAAACGGAAATGGCAATGGTAATGGAAACGGCAACGGTAATGGAAA
1 TGGCAACGGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGGAAA
* * *
279619 CGGCAACGGTAATGGAAATGGAAACGGAAATGGCAACGGTAATGGAAA
1 TGGCAACGGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGGAAA
* * * * *
279667 TGGCAATGGTAATGGAAATGGAAACGGCAATGGCAACGGAAATGGAAA
1 TGGCAACGGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGGAAA
* * * * *
279715 TGGCAACGGCAACGGTAATGGCAATGGCAACGGCAACGGTAATGGAAA
1 TGGCAACGGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGGAAA
*
279763 TGGCAATGGCAATGGTAATGGAAATGGCAATGGAAACGGCAACGGTAATGG
1 TGGCAA---C---GGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGG
279814 CAACGACAAG
Statistics
Matches: 274, Mismatches: 47, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
42 30 0.11
44 1 0.00
46 1 0.00
48 207 0.76
51 1 0.00
54 34 0.12
ACGTcount: A:0.40, C:0.13, G:0.34, T:0.12
Consensus pattern (48 bp):
TGGCAACGGTAATGGAAATGGAAATGGAAACGGCAACGGTAATGGAAA
Found at i:283892 original size:2 final size:2
Alignment explanation
Indices: 283885--283912 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
283875 CTTGAATTGC
283885 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
283913 TTAAAATATT
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:287882 original size:19 final size:19
Alignment explanation
Indices: 287854--287915 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
287844 AAAACCAGAA
287854 CCCC-AGGGGGTATCGATT
1 CCCCTAGGGGGTATCGATT
*
287872 CCCCTAGGGGGAATC-AGTT
1 CCCCTAGGGGGTATCGA-TT
*
287891 CCCCTTCAAAGGGGTATCGATT
1 CCCC-T--AGGGGGTATCGATT
287913 CCC
1 CCC
287916 TCTGCCTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.14
19 15 0.43
20 1 0.03
22 13 0.37
23 1 0.03
ACGTcount: A:0.19, C:0.31, G:0.27, T:0.23
Consensus pattern (19 bp):
CCCCTAGGGGGTATCGATT
Found at i:293845 original size:22 final size:22
Alignment explanation
Indices: 293817--293868 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
293807 AATTTTTGGC
*
293817 TTTAAAAT-GGTTCGAAATATTT
1 TTTAAAATCGGTTCGAAAT-TAT
* *
293839 TTTAAAATCGTTTTGAAATTAT
1 TTTAAAATCGGTTCGAAATTAT
293861 TTTAAAAT
1 TTTAAAAT
293869 TAAAACTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTAAAATCGGTTCGAAATTAT
Found at i:295264 original size:6 final size:6
Alignment explanation
Indices: 295250--295628 Score: 164
Period size: 6 Copynumber: 63.2 Consensus size: 6
295240 TAATAAGGGT
* * * * * * *
295250 GGCAAC GGAAAC GGAAAT GGCAAC GGCAAT GGAAAT GGCAAC GGGAAC
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC
* * * * * *
295298 GGGAAC GGAAAT GGCAAC GGCAAC GGCAAC GGCAAT GGTAAT GGCAAC
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC
* * * * * * * * *
295346 GGCAAC GGCAAC GGAAAT GGAAAC GGAAAT GGCAAT GGTAAT GGAAAC
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC
* * ** * * * * * *
295394 GGCAAC GGCAAC GGTAAT GAAAAT GGAAAC GGAAAT GGCAAC GGTAAT
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC
* * * * * * * * * *
295442 GGAAAT GGCAAT GGTAAT GGAAAT GGAAAC GGCAAT GGCAAC GGAAAC
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC
* * * * * * * * * *
295490 GGAAAT GGTAAT GGCAAC GGCAAT GGTAAT GGAAAT GGCAAT GGCAAC
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC
* * * * * * * *
295538 GGTAAC GGTAAC AGTAAC GGCAAT GGAAAC GGCAAC CGCAAC GGTAAC
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC
* * * * * *
295586 GGCAAC GGAAAT GGCAAT GGAAAC GGCAAC GGTAAT GGCAAC G
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC G
295629 ATACCAACCA
Statistics
Matches: 296, Mismatches: 77, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 296 1.00
ACGTcount: A:0.39, C:0.17, G:0.33, T:0.11
Consensus pattern (6 bp):
GGCAAC
Found at i:295283 original size:24 final size:24
Alignment explanation
Indices: 295250--295628 Score: 239
Period size: 24 Copynumber: 16.0 Consensus size: 24
295240 TAATAAGGGT
*
295250 GGCAACGGAAACGGAAATGGCAAC
1 GGCAACGGAAACGGTAATGGCAAC
* * * * *
295274 GGCAATGGAAATGGCAACGGGAAC
1 GGCAACGGAAACGGTAATGGCAAC
* * * *
295298 GGGAACGGAAATGGCAACGGCAAC
1 GGCAACGGAAACGGTAATGGCAAC
* *
295322 GGCAACGGCAATGGTAATGGCAAC
1 GGCAACGGAAACGGTAATGGCAAC
* * *
295346 GGCAACGGCAACGGAAATGGAAAC
1 GGCAACGGAAACGGTAATGGCAAC
* * * * *
295370 GGAAATGGCAATGGTAATGGAAAC
1 GGCAACGGAAACGGTAATGGCAAC
*
295394 GGCAACGGCAACGGTAAT-G-AA-
1 GGCAACGGAAACGGTAATGGCAAC
* *
295415 ---AATGGAAACGGAAATGGCAAC
1 GGCAACGGAAACGGTAATGGCAAC
* * * * * *
295436 GGTAATGGAAATGGCAATGGTAAT
1 GGCAACGGAAACGGTAATGGCAAC
* * *
295460 GGAAATGGAAACGGCAATGGCAAC
1 GGCAACGGAAACGGTAATGGCAAC
* *
295484 GGAAACGGAAATGGTAATGGCAAC
1 GGCAACGGAAACGGTAATGGCAAC
* * * * *
295508 GGCAATGGTAATGGAAATGGCAAT
1 GGCAACGGAAACGGTAATGGCAAC
* ** *
295532 GGCAACGGTAACGGTAACAGTAAC
1 GGCAACGGAAACGGTAATGGCAAC
* * **
295556 GGCAATGGAAACGGCAACCGCAAC
1 GGCAACGGAAACGGTAATGGCAAC
* * * *
295580 GGTAACGGCAACGGAAATGGCAAT
1 GGCAACGGAAACGGTAATGGCAAC
* *
295604 GGAAACGGCAACGGTAATGGCAAC
1 GGCAACGGAAACGGTAATGGCAAC
295628 G
1 G
295629 ATACCAACCA
Statistics
Matches: 286, Mismatches: 63, Indels: 12
0.79 0.17 0.03
Matches are distributed among these distances:
18 12 0.04
19 1 0.00
20 2 0.01
22 2 0.01
23 1 0.00
24 268 0.94
ACGTcount: A:0.39, C:0.17, G:0.33, T:0.11
Consensus pattern (24 bp):
GGCAACGGAAACGGTAATGGCAAC
Found at i:298071 original size:16 final size:16
Alignment explanation
Indices: 298036--298078 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
298026 ATAAAATTTC
*
298036 AAAATAGATACAATTAAT
1 AAAATAGA-A-AACTAAT
298054 AAAATAGAAAACTAAT
1 AAAATAGAAAACTAAT
298070 AAAA-AGAAA
1 AAAATAGAAA
298079 TTCAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 10 0.42
17 1 0.04
18 8 0.33
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.19
Consensus pattern (16 bp):
AAAATAGAAAACTAAT
Done.