Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007803.1 Hibiscus syriacus cultivar Beakdansim tig00110121_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: 468357
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:372217 original size:13 final size:13
Alignment explanation
Indices: 372173--372217 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
372163 TTTAATATTT
372173 ATCGGGTCGGGT-
1 ATCGGGTCGGGTA
* *
372185 ATCGGGCCAGGTA
1 ATCGGGTCGGGTA
372198 ATCGGGTCGGGTA
1 ATCGGGTCGGGTA
372211 ATCGGGT
1 ATCGGGT
372218 AATCAGGGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.16, C:0.18, G:0.44, T:0.22
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:374002 original size:23 final size:23
Alignment explanation
Indices: 373975--374057 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 23
373965 TAATTATTAA
373975 ATTATATTATTATAATATATAAT
1 ATTATATTATTATAATATATAAT
373998 ATTATATTATTATTTTAATA-ATATAT
1 ATTATATTATTA---TAATATATA-AT
* * *
374024 AATAAATTATTAATAAAAT-TAAT
1 ATTATATTATT-ATAATATATAAT
374047 ATTAT-TTATTA
1 ATTATATTATTA
374058 ATTTTATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
21 1 0.02
22 5 0.10
23 17 0.35
24 6 0.12
25 3 0.06
26 16 0.33
27 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATATTATTATAATATATAAT
Found at i:374016 original size:26 final size:26
Alignment explanation
Indices: 373979--374130 Score: 82
Period size: 26 Copynumber: 5.7 Consensus size: 26
373969 TATTAAATTA
*
373979 TATTATTATAATATATAATATTATAT
1 TATTATTTTAATATATAATATTATAT
*
374005 TATTATTTTAATA-AT-ATATAATA-
1 TATTATTTTAATATATAATATTATAT
* * *
374028 AATTATTAATAAAAT-TAATATTAT-T
1 TATTATT-TTAATATATAATATTATAT
* *
374053 TATTAATTTT-ATAAAATAATATTATAGAAA
1 TATT-ATTTTAAT-ATATAATATTAT---AT
* * *
374083 TATTGAATATTAAAATATAATATAATAT
1 TATT--ATTTTAATATATAATATTATAT
*
374111 TATCATTTTAATATTATAAT
1 TATTATTTTAATA-TATAAT
374131 TTTTAATATT
Statistics
Matches: 93, Mismatches: 19, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
23 6 0.06
24 13 0.14
25 13 0.14
26 31 0.33
27 6 0.06
28 4 0.04
30 4 0.04
31 15 0.16
32 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
TATTATTTTAATATATAATATTATAT
Found at i:374124 original size:14 final size:15
Alignment explanation
Indices: 374105--374145 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
374095 AAATATAATA
*
374105 TAATATTATCA-TTT
1 TAATATTATAATTTT
374119 TAATATTATAATTTT
1 TAATATTATAATTTT
*
374134 TAATATTTTAAT
1 TAATATTATAAT
374146 ATCATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATATTATAATTTT
Found at i:374142 original size:8 final size:8
Alignment explanation
Indices: 374115--374163 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
374105 TAATATTATC
374115 ATTTTAAT
1 ATTTTAAT
*
374123 ATTATAAT
1 ATTTTAAT
374131 -TTTTAAT
1 ATTTTAAT
374138 ATTTTAAT
1 ATTTTAAT
* *
374146 ATCATTATT
1 AT-TTTAAT
374155 ATTTTAAT
1 ATTTTAAT
374163 A
1 A
374164 ACATTATCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.18
8 21 0.64
9 6 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTTTAAT
Found at i:374159 original size:17 final size:17
Alignment explanation
Indices: 374137--374170 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
374127 TAATTTTTAA
*
374137 TATTTTAATATCATTAT
1 TATTTTAATAACATTAT
374154 TATTTTAATAACATTAT
1 TATTTTAATAACATTAT
374171 CAACTTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTAATAACATTAT
Found at i:374406 original size:36 final size:39
Alignment explanation
Indices: 374323--374408 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 39
374313 TAAAAAGTTT
* * **
374323 TTTTAATAAGTAATTAATGTAATTAATAATACATTTTTTA
1 TTTTAATAAATAATTAATATAATT-ATAATACATAATTTA
374363 TTTTAATAAATAATTAATATAATT-T-ATAC-TAATTTA
1 TTTTAATAAATAATTAATATAATTATAATACATAATTTA
374399 TTTTAATAAA
1 TTTTAATAAA
374409 ATATAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 15 0.36
37 4 0.10
38 1 0.02
40 22 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (39 bp):
TTTTAATAAATAATTAATATAATTATAATACATAATTTA
Found at i:374495 original size:29 final size:25
Alignment explanation
Indices: 374448--374505 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
374438 AAAATTATAA
374448 ATATAATATATTAATAATTATAT-TG
1 ATATAATATATTAATAATTAT-TCTG
374473 ATATAAATAATATTAAATAAATTATTCTG
1 ATAT-AAT-ATATT-AAT-AATTATTCTG
374502 ATAT
1 ATAT
374506 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.14
26 3 0.11
27 5 0.18
28 4 0.14
29 12 0.43
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (25 bp):
ATATAATATATTAATAATTATTCTG
Found at i:375715 original size:69 final size:70
Alignment explanation
Indices: 375584--375718 Score: 227
Period size: 70 Copynumber: 1.9 Consensus size: 70
375574 TTTTTTTAAC
* *
375584 GATGGATGATAAAAAAAAAATCAAAACGTAACTATATATATTTTAAATATAATTGAGGGACTAAA
1 GATGGATGATAAAAAAAAAATCAAAACCTAACTATATATATTTTAAAAATAATTGAGGGACTAAA
375649 AAAAT
66 AAAAT
* *
375654 GATGGATGATAAAAACAAAATCAAAACCTAACTATATATA-TTTAAAAATAATTGAGTGACTAAA
1 GATGGATGATAAAAAAAAAATCAAAACCTAACTATATATATTTTAAAAATAATTGAGGGACTAAA
375718 A
66 A
375719 TAGAACAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 23 0.38
70 38 0.62
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (70 bp):
GATGGATGATAAAAAAAAAATCAAAACCTAACTATATATATTTTAAAAATAATTGAGGGACTAAA
AAAAT
Found at i:379492 original size:16 final size:17
Alignment explanation
Indices: 379466--379500 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
379456 ATATACATAT
379466 AATACAATTTAAATAAA
1 AATACAATTTAAATAAA
379483 AATA-AATTTAAATAAA
1 AATACAATTTAAATAAA
379499 AA
1 AA
379501 GAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AATACAATTTAAATAAA
Found at i:380193 original size:6 final size:6
Alignment explanation
Indices: 380182--380217 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
380172 ATTGTTTTAT
*
380182 ATATTA ATATTA ATATTA ATATTA TATTTTA ATATT
1 ATATTA ATATTA ATATTA ATATTA -ATATTA ATATT
380218 TTTTAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
ATATTA
Found at i:380197 original size:12 final size:13
Alignment explanation
Indices: 380178--380217 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
380168 AAATATTGTT
380178 TTATATATTAATA
1 TTATATATTAATA
380191 TTA-ATATTAATA
1 TTATATATTAATA
*
380203 TTATATTTTAATA
1 TTATATATTAATA
380216 TT
1 TT
380218 TTTTAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATATTAATA
Found at i:380256 original size:23 final size:23
Alignment explanation
Indices: 380226--380278 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
380216 TTTTTTAATT
380226 AAAATATAATTATAAAATA-TTTA
1 AAAATATAATTAT-AAATACTTTA
* *
380249 AAAATATATTTATCAATACTTTA
1 AAAATATAATTATAAATACTTTA
*
380272 ATAATAT
1 AAAATAT
380279 TATATGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAATATAATTATAAATACTTTA
Found at i:385208 original size:23 final size:23
Alignment explanation
Indices: 385144--385208 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
385134 TTAATAGTAT
385144 ATAATAA-A-TTA-TTAA-TATA
1 ATAATAATATTTATTTAATTATA
385163 ATTAATAATATTTATCATT--TTATA
1 A-TAATAATATTTAT--TTAATTATA
385187 ATAATAATATTTATTTAATTAT
1 ATAATAATATTTATTTAATTAT
385209 TAGTAACGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
19 1 0.03
20 6 0.16
21 3 0.08
22 3 0.08
23 17 0.46
24 5 0.14
25 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATAATATTTATTTAATTATA
Found at i:389540 original size:20 final size:20
Alignment explanation
Indices: 389515--389553 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
389505 GCTACCAATC
*
389515 ATCCCAGACGGGATCTCATT
1 ATCCCAGACAGGATCTCATT
*
389535 ATCCCAGATAGGATCTCAT
1 ATCCCAGACAGGATCTCAT
389554 CATCAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCCCAGACAGGATCTCATT
Found at i:391476 original size:18 final size:18
Alignment explanation
Indices: 391449--391485 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
391439 ATAGCCCTGA
391449 TTTCCTTCTC-TAGCTAT
1 TTTCCTTCTCTTAGCTAT
391466 TTTCACTTCTCTTAGCTAT
1 TTTC-CTTCTCTTAGCTAT
391485 T
1 T
391486 GTTTTTGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTCCTTCTCTTAGCTAT
Found at i:394367 original size:27 final size:27
Alignment explanation
Indices: 394334--394394 Score: 113
Period size: 27 Copynumber: 2.2 Consensus size: 27
394324 TCTCTTTTAA
394334 AAAAACATATTCTTTGGATTTTAAGAG
1 AAAAACATATTCTTTGGATTTTAAGAG
394361 AAAAACATATTCTTTGGATTTTAAGAG
1 AAAAACATATTCTTTGGATTTTAAGAG
394388 AGAAAAC
1 A-AAAAC
394395 GATAATATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (27 bp):
AAAAACATATTCTTTGGATTTTAAGAG
Found at i:394852 original size:263 final size:263
Alignment explanation
Indices: 394385--394870 Score: 767
Period size: 263 Copynumber: 1.8 Consensus size: 263
394375 TGGATTTTAA
** *
394385 GAGAGAAAACGATAATATCTAATTATTTCCAATCGTGAATAAATGACCTCTCATGCCTTAAAGTA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCA
* ** * *
394450 GTCATTTATTACTCCAATTGAAATGAAGAGATATCACTATTTCGTTTTAAAATTCAATATTGATT
66 GTCATTTAATACTCCAATCAAAATGAAGAGATATCACTATTTCGTATTAAAAATCAATATTGATT
** *
394515 CGAGAGAAAACGTTGATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCATTAAAAC
131 CGAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCATTAAAAC
* *
394580 ATTCATTTATTTCTCCAA-TCGAAATGAAGAGATATCATTATTTCATCTTAAAAAATCAATATTG
196 AATCATTTATTACTCCAACT-GAAATGAAGAGATATCATTATTTCATCTTAAAAAATCAATATTG
394644 ATTC
260 ATTC
* *
394648 GAGAGAAAATGATAATATCTAATTATTTCCAATTGAAAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCA
*
394713 TTCATTTAATACTCCAATCAAAATGAAGAGATATCACTATTTCGTATTAAAAATCAATATTGATT
66 GTCATTTAATACTCCAATCAAAATGAAGAGATATCACTATTTCGTATTAAAAATCAATATTGATT
* * * *
394778 CGAGAGAAAACAATAATATGTAATTATTTCCAATCGAGAATAAATGACCTCTCGTGCCTTAAAGC
131 CGAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCATTAAAAC
*
394843 AATCATTTATTACTTCAACTGAAATGAA
196 AATCATTTATTACTCCAACTGAAATGAA
394871 AAAATATTAC
Statistics
Matches: 201, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
263 200 1.00
264 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (263 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCA
GTCATTTAATACTCCAATCAAAATGAAGAGATATCACTATTTCGTATTAAAAATCAATATTGATT
CGAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCATTAAAAC
AATCATTTATTACTCCAACTGAAATGAAGAGATATCATTATTTCATCTTAAAAAATCAATATTGA
TTC
Found at i:394912 original size:131 final size:131
Alignment explanation
Indices: 394385--394870 Score: 731
Period size: 131 Copynumber: 3.7 Consensus size: 131
394375 TGGATTTTAA
* *
394385 GAGAGAAAACGATAATATCTAATTATTTCCAATCGTGAATAAATGACCTCTCATGCCTTAAAGTA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
394450 GTCATTTATTACTCCAATTGAAATGAAGAGATATCACTATTTCGTTTTAAAATTCAATATTGATT
66 TTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATT
394515 C
131 C
* * * *
394516 GAGAGAAAACGTTGATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCATTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
394581 TTCATTTATTTCTCCAATCGAAATGAAGAGATATCATTATTTCATCTTAAAAAATCAATATTGAT
66 TTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTT-AAAAATCAATATTGAT
394646 TC
130 TC
* * *
394648 GAGAGAAAATGATAATATCTAATTATTTCCAATTGAAAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
394713 TTCATTTAATACTCCAATCAAAATGAAGAGATATCACTATTTCGTATTAAAAATCAATATTGATT
66 TTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATT
394778 C
131 C
* * *
394779 GAGAGAAAACAATAATATGTAATTATTTCCAATCGAGAATAAATGACCTCTCGTGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
394844 ATCATTTATTACTTCAA-CTGAAATGAA
66 TTCATTTATTACTCCAATC-GAAATGAA
394871 AAAATATTAC
Statistics
Matches: 317, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
130 1 0.00
131 199 0.63
132 117 0.37
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
TTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATT
C
Found at i:398009 original size:41 final size:40
Alignment explanation
Indices: 397933--398055 Score: 104
Period size: 42 Copynumber: 3.0 Consensus size: 40
397923 CATGTGAAAA
* **
397933 CATCTTGC-CCAAAGGTCTTATGGATGGCCTGAAGGACTTAT
1 CATCTTGCTCAAAAGG-CTTAT-GATGGCCCAAAGGACTTAT
* * *
397974 CATCTTGCTCGAAAGGCTTATAGATGACCCAAAGGATTTAAT
1 CATCTTGCTCAAAAGGCTTAT-GATGGCCCAAAGGACTT-AT
* * * *
398016 TATCATGCTCAAAAGACTTACTGATGGCCCAAAAGACTTA
1 CATCTTGCTCAAAAGGCTTA-TGATGGCCCAAAGGACTTA
398056 CAAAATTTTG
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
41 27 0.41
42 38 0.58
43 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (40 bp):
CATCTTGCTCAAAAGGCTTATGATGGCCCAAAGGACTTAT
Found at i:398155 original size:255 final size:255
Alignment explanation
Indices: 397661--398311 Score: 896
Period size: 255 Copynumber: 2.5 Consensus size: 255
397651 TTTCAAAAAA
* *
397661 AAAAACATGTGAAAA-ATCCTT-CCCGAAGGTCTTATGGATGG-CTCGAATGACTTATCATCTTA
1 AAAAACATGTGAAAACAT-CTTGCCCGAAGGTCTTATGGATGGCCT-GAAGGACTTATCATCTTG
** * * *
397723 CTCGAAATACTTATAGATAACCCAAAGGATTTAAGTATTATCATGCTTGAAATACTTACTGATGG
64 CTCGAAAGGCTTATAGATGACCCAAAGGATTT-A--ATTATCATGCTCGAAAGACTTACTGATGG
* *
397788 CCCAAAGGACTTACTAATTTTGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCATTTTCTTA
126 CCCAAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCATTTCCTTA
397853 CTTTTCAAAAATTTCAATTTTCATATTTAAATCAGAAACCCTGGAAATCATTTTCTCATTTTTAG
191 CTTTTCAAAAATTTCAATTTTCATATTTAAATCAGAAACCCTGGAAATCATTTTCTCATTTTTAG
*
397918 AAAAACATGTGAAAACATCTTGCCCAAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCT
1 AAAAACATGTGAAAACATCTTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCT
*
397983 CGAAAGGCTTATAGATGACCCAAAGGATTTAATTATCATGCTCAAAAGACTTACTGATGGCCCAA
66 CGAAAGGCTTATAGATGACCCAAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCAA
* * * * *
398048 AAGACTTACAAAATTTTGGAAATAGTTTATTAGGTAAGAAACTTTGGAAATCGTTTCCTTATTTT
131 AGGACTTAC-AAATTTTGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCATTTCCTTACTTT
* *** * *
398113 TC-AAAATTTCAATTTTCATATTTAAATGAGAAATTTTGGAAATCGTTTTCTCATTTTTTG
195 TCAAAAATTTCAATTTTCATATTTAAATCAGAAACCCTGGAAATCATTTTCTCATTTTTAG
* * ** *
398173 AAAAACATGAGAAAACATCTTGCTCGAAGGTCTTATGGATGGCCCAAAGAACTTATCATCTTGCT
1 AAAAACATGTGAAAACATCTTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCT
* * * ** * * * *
398238 TGAAAGGCTTATTGATGACCCGAAGGATTTAAGCATCATTCTCGAAAGACATACTGATGGTCCGA
66 CGAAAGGCTTATAGATGACCCAAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCAA
398303 AGGACTTAC
131 AGGACTTAC
398312 TAAGTAAGAA
Statistics
Matches: 351, Mismatches: 39, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
255 213 0.61
256 51 0.15
257 19 0.05
258 66 0.19
259 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (255 bp):
AAAAACATGTGAAAACATCTTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCT
CGAAAGGCTTATAGATGACCCAAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCAA
AGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAAAAACTTTGGAAATCATTTCCTTACTTTT
CAAAAATTTCAATTTTCATATTTAAATCAGAAACCCTGGAAATCATTTTCTCATTTTTAG
Found at i:405908 original size:131 final size:131
Alignment explanation
Indices: 405674--406196 Score: 733
Period size: 131 Copynumber: 4.0 Consensus size: 131
405664 ATTTTAAGAA
* * *
405674 AGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAACGACCTCTCATGCCTTAAAGCAATC
1 AGAAAACAATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* **
405739 ATTTATTACTCCAATCAAAATGAAGAGATATTACTATTTCGTCTTAAAATTCAATATCCATTCGA
66 ATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGATTCGA
405804 G
131 G
* * * * * *
405805 AGAAAAAAATAATATCTAATTATTTCCAGTTAAGAATAAATGACATCTCATGCCTTAAACCATTC
1 AGAAAACAATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* * * *
405870 ATTTATTAATCCAAGCGAAATGAAGAGATATCACTATTTCCTCTTAAAA-TCAATATTGATTCGA
66 ATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGATTCGA
405934 G
131 G
* * * **
405935 AGAAAACGATAATATCTAATTATTTACAATCGAGAATAAATGACCTCTCATAACTTAAAGCAGTC
1 AGAAAACAATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* * *
406000 ATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATTTGA
66 ATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGATTCGA
406065 G
131 G
* ** *
406066 AGGAAACAATAATATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGAAGTC
1 AGAAAACAATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* * * * * *
406131 ATTTATTACTCCAACCAAAATGAAAAGATATTACTATTTCATCCTAAAATTCAATATTAATTCGA
66 ATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGATTCGA
406196 G
131 G
406197 TGTTACTTAT
Statistics
Matches: 345, Mismatches: 46, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
130 114 0.33
131 231 0.67
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (131 bp):
AGAAAACAATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
ATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGATTCGA
G
Found at i:406138 original size:261 final size:262
Alignment explanation
Indices: 405674--406196 Score: 787
Period size: 261 Copynumber: 2.0 Consensus size: 262
405664 ATTTTAAGAA
* **
405674 AGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAACGACCTCTCATGCCTTAAAGCAATC
1 AGAAAACGATAATATCTAATTATTTACAATCAAGAATAAACGACCTCTCATAACTTAAAGCAATC
* *
405739 ATTTATTACTCCAATCAAAATGAAGAGATATTACTATTTCGTCTTAAAATTCAATATCCATTCGA
66 ATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATCCATTCGA
* * *
405804 GAGAAAAAAATAATATCTAATTATTTCCAGTTAAGAATAAATGACATCTCATGCCTTAAACCATT
131 GAGAAAAAAATAATATCTAATTATTTCCAATTAAGAATAAATGACATCTCATGCCTTAAACAAGT
* * * * * *
405869 CATTTATTAATCCAAGCGAAATGAAGAGATATCACTATTTCCTCTTAAAA-TCAATATTGATTCG
196 CATTTATTAATCCAACCAAAATGAAAAGATATCACTATTTCATCCTAAAATTCAATATTAATTCG
405933 AG
261 AG
* * *
405935 AGAAAACGATAATATCTAATTATTTACAATCGAGAATAAATGACCTCTCATAACTTAAAGCAGTC
1 AGAAAACGATAATATCTAATTATTTACAATCAAGAATAAACGACCTCTCATAACTTAAAGCAATC
* ** *
406000 ATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATTTGA
66 ATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATCCATTCGA
* * * * *
406065 GAGGAAACAATAATATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGAAGT
131 GAGAAAAAAATAATATCTAATTATTTCCAATTAAGAATAAATGACATCTCATGCCTTAAACAAGT
* *
406130 CATTTATTACTCCAACCAAAATGAAAAGATATTACTATTTCATCCTAAAATTCAATATTAATTCG
196 CATTTATTAATCCAACCAAAATGAAAAGATATCACTATTTCATCCTAAAATTCAATATTAATTCG
406195 AG
261 AG
406197 TGTTACTTAT
Statistics
Matches: 233, Mismatches: 28, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
261 218 0.94
262 15 0.06
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (262 bp):
AGAAAACGATAATATCTAATTATTTACAATCAAGAATAAACGACCTCTCATAACTTAAAGCAATC
ATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATCCATTCGA
GAGAAAAAAATAATATCTAATTATTTCCAATTAAGAATAAATGACATCTCATGCCTTAAACAAGT
CATTTATTAATCCAACCAAAATGAAAAGATATCACTATTTCATCCTAAAATTCAATATTAATTCG
AG
Found at i:406405 original size:21 final size:21
Alignment explanation
Indices: 406376--406428 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
406366 ATTCTGACTA
406376 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
406397 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
406418 TCGCAATGCGA
1 TCGCATTGCGA
406429 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:406447 original size:20 final size:20
Alignment explanation
Indices: 406422--406460 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
406412 CCTAATTCGC
406422 AATGCGAATATGTAAATCGT
1 AATGCGAATATGTAAATCGT
*
406442 AATGCGAATCTGTAAATCG
1 AATGCGAATATGTAAATCG
406461 CAACGAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (20 bp):
AATGCGAATATGTAAATCGT
Found at i:407371 original size:24 final size:24
Alignment explanation
Indices: 407320--407373 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
407310 AGTATCGAAA
*
407320 TTTGATCTTGGTCAATACGCGGAC
1 TTTGATCTTGGTCAATACGCAGAC
* *
407344 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACGCAGAC
407368 TTTGAT
1 TTTGAT
407374 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACGCAGAC
Found at i:409443 original size:20 final size:20
Alignment explanation
Indices: 409418--409511 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
409408 GACATTCATT
409418 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
409438 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
409458 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
409478 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
409498 TGACTATCGCAACG
1 TGACTATCGCAACG
409512 AGAGAATCGC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 64 0.96
21 3 0.04
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:409533 original size:33 final size:33
Alignment explanation
Indices: 409483--409616 Score: 151
Period size: 33 Copynumber: 3.8 Consensus size: 33
409473 GGAATTGACT
* **
409483 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
409517 ATCGCAATGCGAAATGAAAATCACAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
409550 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGA
409588 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
409617 CGAAATTAGT
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
33 44 0.51
34 9 0.10
35 2 0.02
37 3 0.03
38 13 0.15
39 15 0.17
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:409605 original size:20 final size:19
Alignment explanation
Indices: 409516--409622 Score: 143
Period size: 19 Copynumber: 5.8 Consensus size: 19
409506 GCAACGAGAG
409516 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
409535 AATCACAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
409549 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
409568 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
409587 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
409607 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
409623 TAGTTTCGCG
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
14 7 0.09
16 5 0.06
17 5 0.06
19 42 0.55
20 18 0.23
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:409688 original size:33 final size:33
Alignment explanation
Indices: 409631--409726 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
409621 ATTAGTTTCG
409631 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
409665 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
409698 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
409727 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 32 0.58
34 23 0.42
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:411268 original size:18 final size:19
Alignment explanation
Indices: 411245--411282 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
411235 CTCTTGAGGG
411245 ATGATAGGG-GCCTCTTGA
1 ATGATAGGGAGCCTCTTGA
*
411263 ATGATAGGGAGGCTCTTGA
1 ATGATAGGGAGCCTCTTGA
411282 A
1 A
411283 CGATGACAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.26
Consensus pattern (19 bp):
ATGATAGGGAGCCTCTTGA
Found at i:411795 original size:20 final size:20
Alignment explanation
Indices: 411769--411840 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
411759 GAAACTTAAA
*
411769 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
411789 ATTGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
411809 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
411829 ATCGCAATGCGA
1 ATCGCAATGCGA
411841 TTTTCATTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:411936 original size:20 final size:20
Alignment explanation
Indices: 411911--412020 Score: 157
Period size: 20 Copynumber: 5.5 Consensus size: 20
411901 GATTCTTTCG
* **
411911 TTGCGATAGCCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
411931 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
411951 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
411971 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
411991 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
412011 TTGCGATAGT
1 TTGCGATAGT
412021 AAACTATTCT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:413914 original size:20 final size:20
Alignment explanation
Indices: 413891--413940 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
413881 CTGAAATTTT
413891 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
413911 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
413931 CTATCGCAAC
1 AAATCGCAAC
413941 GTGAATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:414052 original size:20 final size:20
Alignment explanation
Indices: 414004--414052 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
413994 GCGATTCTCT
414004 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * **
414024 CATTACGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
414044 CGTTGCGAT
1 CGTTGCGAT
414053 TCACTCATTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:414708 original size:21 final size:21
Alignment explanation
Indices: 414682--414727 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
414672 TATTCGCATT
*
414682 GCGAATTAGGAAAATTGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
414703 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
414724 GCGA
1 GCGA
414728 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:415352 original size:24 final size:23
Alignment explanation
Indices: 415316--415364 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
415306 TGACTAAAAT
* * *
415316 AAAATAACATAAAGCAACATGCA
1 AAAATAAAATAAAACAAAATGCA
415339 AAAATTAAAATAAAACAAAATGCA
1 AAAA-TAAAATAAAACAAAATGCA
415363 AA
1 AA
415365 TAAGACTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAATAAAATAAAACAAAATGCA
Found at i:423334 original size:21 final size:21
Alignment explanation
Indices: 423296--423339 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
423286 TAATTGATGG
*
423296 TTGTTTTTGTATGTTG-TTAA
1 TTGTTTTTGTATGATGTTTAA
*
423316 TTGTTTTGTTTATGATGTTTAA
1 TTGTTTT-TGTATGATGTTTAA
423338 TT
1 TT
423340 CCTTGAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 7 0.35
22 6 0.30
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.66
Consensus pattern (21 bp):
TTGTTTTTGTATGATGTTTAA
Found at i:423905 original size:21 final size:24
Alignment explanation
Indices: 423854--423908 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 24
423844 CCACAATATC
423854 TCCATTT-ACTTCCACATCACACTA
1 TCCATTTCA-TTCCACATCACACTA
423878 T-CATTTCATTCCA-ATCA-AC-A
1 TCCATTTCATTCCACATCACACTA
423898 TCCATTTCATT
1 TCCATTTCATT
423909 TTGTCATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.07
21 11 0.38
22 4 0.14
23 10 0.34
24 2 0.07
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (24 bp):
TCCATTTCATTCCACATCACACTA
Found at i:424984 original size:16 final size:16
Alignment explanation
Indices: 424960--424991 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
424950 GTGCAATGCA
424960 AAAACAAAAAGAAAAT
1 AAAACAAAAAGAAAAT
*
424976 AAAAGAAAAAGAAAAT
1 AAAACAAAAAGAAAAT
424992 TAGCCAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.03, G:0.09, T:0.06
Consensus pattern (16 bp):
AAAACAAAAAGAAAAT
Found at i:426407 original size:2 final size:2
Alignment explanation
Indices: 426400--426452 Score: 67
Period size: 2 Copynumber: 27.0 Consensus size: 2
426390 GTTCGTTCTT
426400 TA TA TA TA TA TA TA -A TA T- TGA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
426440 GTA TA TA TA TA TA
1 -TA TA TA TA TA TA
426453 CACACACCCC
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.07
2 40 0.87
3 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:426425 original size:15 final size:13
Alignment explanation
Indices: 426401--426452 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
426391 TTCGTTCTTT
426401 ATATATATATATA
1 ATATATATATATA
*
426414 ATAT-TGATATATT
1 ATATAT-ATATATA
426427 ATATATATATATA
1 ATATATATATATA
*
426440 GTATATATATATA
1 ATATATATATATA
426453 CACACACCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 1 0.03
13 32 0.94
14 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:426590 original size:20 final size:21
Alignment explanation
Indices: 426567--426606 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
426557 AACACACACA
* *
426567 TATATAATTTAATTA-ATAAT
1 TATAAAATATAATTATATAAT
426587 TATAAAATATAATTATATAA
1 TATAAAATATAATTATATAA
426607 ATCCAAACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAAAATATAATTATATAAT
Found at i:434351 original size:6 final size:6
Alignment explanation
Indices: 434340--434371 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
434330 AATCAACATT
434340 TTTGCA TTTGCA TTTAGCA TTTGCA TTTGCA T
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA T
434372 GTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
TTTGCA
Found at i:434361 original size:13 final size:12
Alignment explanation
Indices: 434340--434371 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
434330 AATCAACATT
434340 TTTGCATTTGCA
1 TTTGCATTTGCA
434352 TTTAGCATTTGCA
1 TTT-GCATTTGCA
434365 TTTGCAT
1 TTTGCAT
434372 GTATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:436928 original size:18 final size:17
Alignment explanation
Indices: 436905--436946 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
436895 AGAGATATGG
436905 AAAAAAACACAAAAAGA
1 AAAAAAACACAAAAAGA
* *
436922 AAGAAAAAGAGAAAAAGA
1 AA-AAAAACACAAAAAGA
436940 AAAAAAA
1 AAAAAAA
436947 GAAAACGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAACACAAAAAGA
Found at i:436934 original size:8 final size:8
Alignment explanation
Indices: 436923--436983 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
436913 ACAAAAAGAA
436923 AGAAAAAG
1 AGAAAAAG
436931 AGAAAAAG
1 AGAAAAAG
*
436939 A-AAAAAA
1 AGAAAAAG
*
436946 AGAAAACG
1 AGAAAAAG
436954 AGAAAAAG
1 AGAAAAAG
436962 A-AAAGAA-
1 AGAAA-AAG
436969 A-AAAGAAG
1 AGAAA-AAG
436977 AGAAAAA
1 AGAAAAA
436984 AAAGGAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 16 0.36
8 26 0.58
9 3 0.07
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (8 bp):
AGAAAAAG
Found at i:436947 original size:23 final size:23
Alignment explanation
Indices: 436915--436998 Score: 98
Period size: 23 Copynumber: 3.5 Consensus size: 23
436905 AAAAAAACAC
436915 AAAAAGAAAGAAAAAGAGAAAAAG
1 AAAAA-AAAGAAAAAGAGAAAAAG
*
436939 AAAAAAAAGAAAACGAGAAAAAG
1 AAAAAAAAGAAAAAGAGAAAAAG
* *
436962 AAAAGAAAA-AAGAAGAGAAAAAA
1 AAAA-AAAAGAAAAAGAGAAAAAG
436985 AAGGAAAAAAGAAA
1 AA--AAAAAAGAAA
436999 GAAAGAAGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 34 0.67
24 13 0.25
25 4 0.08
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAAAAAAGAAAAAGAGAAAAAG
Found at i:436960 original size:41 final size:41
Alignment explanation
Indices: 436915--436992 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
436905 AAAAAAACAC
436915 AAAAAG-AAAGAAAAAGAGAAAAAGAAAAAAAA-GAAAACGAG
1 AAAAAGAAAAGAAAAA-AG-AAAAGAAAAAAAAGGAAAACGAG
*
436956 AAAAAGAAAAGAAAAAAGAAGAGAAAAAAAAGGAAAA
1 AAAAAGAAAAGAAAAAAGAAAAGAAAAAAAAGGAAAA
436993 AAGAAAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
40 12 0.35
41 13 0.38
42 9 0.26
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (41 bp):
AAAAAGAAAAGAAAAAAGAAAAGAAAAAAAAGGAAAACGAG
Found at i:437000 original size:23 final size:22
Alignment explanation
Indices: 436917--437009 Score: 93
Period size: 23 Copynumber: 4.1 Consensus size: 22
436907 AAAAACACAA
*
436917 AAAGAAAGAAAAAGAGAAAAAG
1 AAAGAAAAAAAAAGAGAAAAAG
436939 AAA-AAAAAGAAAACGAGAAAAAG
1 AAAGAAAAA-AAAA-GAGAAAAAG
*
436962 AAAAGAAAAAAGAAGAGAAAAA-
1 -AAAGAAAAAAAAAGAGAAAAAG
*
436984 AAAGGAAAAAAGAAAGA-AAGAAG
1 AAA-GAAAAAA-AAAGAGAAAAAG
437007 AAA
1 AAA
437010 ATAGACAGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
21 7 0.12
22 18 0.30
23 24 0.40
24 6 0.10
25 5 0.08
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAAAAGAGAAAAAG
Found at i:437008 original size:40 final size:41
Alignment explanation
Indices: 436915--437010 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 41
436905 AAAAAAACAC
*
436915 AAAAAGAAAGAAAAAGAGAAAAAGAAAAAAAAGAAAACGAGA
1 AAAAAG-AAGAAAAAGAGAAAAAGAAAAAAAAGAAAACAAGA
* *
436957 AAAAGAAAAGAAAAA-AG-AAGAGAAAAAAAAGGAAAA-AAGA
1 AAAA-AGAAGAAAAAGAGAAAAAGAAAAAAAA-GAAAACAAGA
436997 AAGAAAGAAGAAAA
1 AA-AAAGAAGAAAA
437011 TAGACAGATC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
40 25 0.53
41 9 0.19
42 12 0.26
43 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (41 bp):
AAAAAGAAGAAAAAGAGAAAAAGAAAAAAAAGAAAACAAGA
Found at i:437687 original size:28 final size:28
Alignment explanation
Indices: 437647--437709 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
437637 GCAAGAAGCC
*
437647 AACCTGAAACACATTACCTCCCCAAATT
1 AACCTGAAACACACTACCTCCCCAAATT
* *
437675 AACCTGAAACACACTACCTTCCCAAGTT
1 AACCTGAAACACACTACCTCCCCAAATT
*
437703 AGCCTGA
1 AACCTGA
437710 GCCTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.35, G:0.08, T:0.21
Consensus pattern (28 bp):
AACCTGAAACACACTACCTCCCCAAATT
Found at i:439476 original size:20 final size:19
Alignment explanation
Indices: 439451--439511 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 19
439441 TTCTTGATTT
439451 GTAAGTCCTCCGGGCCATC
1 GTAAGTCCTCCGGGCCATC
* *
439470 GGTAAGTCTTCCGAGCATCATAC
1 -GTAAGTCCTCCGGGC--CAT-C
439493 GTAAGTCCTCCGGGCCATC
1 GTAAGTCCTCCGGGCCATC
439512 CATAAGACCT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 1 0.03
20 16 0.47
22 16 0.47
23 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (19 bp):
GTAAGTCCTCCGGGCCATC
Found at i:439498 original size:132 final size:132
Alignment explanation
Indices: 439097--439783 Score: 1083
Period size: 132 Copynumber: 5.2 Consensus size: 132
439087 TTTCTTAATG
* * *
439097 CGTAAGTCATCCGGGCCATCCATAAGACCTTTAGTGCAGGATTTTTTCAAATGAGATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* *
439162 CTAAGCCTTCGGGAGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAACTCTTCCGAGCAAT-
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGC-ATC
*
439226 ATT
130 ATA
*
439229 CGTAAGTCCTCTGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* *
439294 CTAAGCCTT-TGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGA
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATCA
439358 TGA
131 T-A
** **
439361 -GTAAGTTTTCTTGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* *
439425 CTAAGACTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCGGTAAGTCTTCCGAGCATCA
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATCA
439490 TA
131 TA
* *
439492 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAAATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* **
439557 CTAAGCCTTTGGGGGTTTCTTGATTTGTAAGTCCTCCAAGCCATCAGTAAGTCTTCCGAGCATCA
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATCA
*
439622 TG
131 TA
439624 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* * *
439689 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCAGGCCATCAGTAAGTCTTCCGAGCATGA
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATCA
*
439754 TG
131 TA
* * *
439756 CGTAAGTCCTTCAGGCCATCTATAAGAC
1 CGTAAGTCCTCCGGGCCATCCATAAGAC
439784 ATTTGGGCAG
Statistics
Matches: 515, Mismatches: 36, Indels: 8
0.92 0.06 0.01
Matches are distributed among these distances:
130 2 0.00
131 120 0.23
132 393 0.76
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (132 bp):
CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATCA
TA
Found at i:441740 original size:26 final size:29
Alignment explanation
Indices: 441711--441779 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
441701 TAATGTTCAT
*
441711 TTTA-GTAAT-TATAT-TTTGTTTGCTTA
1 TTTACGTAATATATATGCTTGTTTGCTTA
*
441737 TTTAACGTAATATTTATGCTTGTTTGCTTA
1 TTT-ACGTAATATATATGCTTGTTTGCTTA
441767 TTTAACGTAATAT
1 TTT-ACGTAATAT
441780 TTATTCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 3 0.08
27 1 0.03
28 5 0.14
29 4 0.11
30 24 0.65
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (29 bp):
TTTACGTAATATATATGCTTGTTTGCTTA
Found at i:441760 original size:30 final size:30
Alignment explanation
Indices: 441726--441783 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
441716 TAATTATATT
441726 TTGTTTGCTTATTTAACGTAATATTTATGC
1 TTGTTTGCTTATTTAACGTAATATTTATGC
441756 TTGTTTGCTTATTTAACGTAATATTTAT
1 TTGTTTGCTTATTTAACGTAATATTTAT
441784 TCTTAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (30 bp):
TTGTTTGCTTATTTAACGTAATATTTATGC
Found at i:443879 original size:22 final size:22
Alignment explanation
Indices: 443852--443897 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
443842 ATTATATTTG
443852 TTATTT-TTCATTTTATTTGGTT
1 TTATTTATTCA-TTTATTTGGTT
* *
443874 TTATTTATTTATTTATTTTGTT
1 TTATTTATTCATTTATTTGGTT
443896 TT
1 TT
443898 TTCGCATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (22 bp):
TTATTTATTCATTTATTTGGTT
Found at i:445484 original size:3 final size:3
Alignment explanation
Indices: 445478--445524 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
445468 TATTTAATAT
** *
445478 TTA TTA TTA TCG TTA -TA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
445525 ATTTACATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:446735 original size:19 final size:19
Alignment explanation
Indices: 446689--446735 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
446679 CATTAATTTG
*
446689 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
446709 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
446729 TATATTT
1 TATATTT
446736 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:449234 original size:32 final size:32
Alignment explanation
Indices: 449185--449246 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
449175 TCTTACCTGT
*
449185 ACTAACTAATTTCTTTTCTGTTCTTTGTGTGC
1 ACTAACTAATTTATTTTCTGTTCTTTGTGTGC
* *
449217 ACTAACTTATTTATTTTCTGTTGTTTGTGT
1 ACTAACTAATTTATTTTCTGTTCTTTGTGT
449247 CTTTTTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.15, G:0.13, T:0.56
Consensus pattern (32 bp):
ACTAACTAATTTATTTTCTGTTCTTTGTGTGC
Found at i:453566 original size:103 final size:102
Alignment explanation
Indices: 453381--453685 Score: 373
Period size: 103 Copynumber: 2.9 Consensus size: 102
453371 TTTTGAGAAA
453381 TTTAAAACAAATTGCGTCTCGCTTGAGACATTTTTTCCTTTGATATACAAATTTCGAATTTGCTT
1 TTTAAAACAAATT-CGTCTCGCTTGAGACA-TTTTTCCTTTGA-ATACAAATTTCGAATTTGCTT
*
453446 CACTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
63 CACTTAAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
* * *
453486 -TTAAAACAAACTTCATCTCGCTTTAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTC
1 TTTAAAACAAA-TTCGTCTCGCTTGAGACATTTTTCCTTTGA-ATACAAATTTCGAATTTGCTTC
* *
453550 ACTTAAAACAATATTAATCTCAATTGAGATTGTTGTTTC
64 ACTTAAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
* * * * *
453589 TTTCAAAAAAAAAATTCGTCTCGCTTGAGACATTTTCCCTCAT-AATACAAATTTCAAAGTTG-T
1 TTT---AAAACAAATTCGTCTCGCTTGAGACATTTTTCCT-TTGAATACAAATTTCGAATTTGCT
* * *
453652 TGTATTTAAAACAAAATTAATATCACTTGAGATT
62 T-CACTTAAAACAAAATTAATCTCACTTGAGATT
453686 TTCAAAGATG
Statistics
Matches: 173, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
103 69 0.40
104 28 0.16
105 44 0.25
106 24 0.14
107 8 0.05
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.40
Consensus pattern (102 bp):
TTTAAAACAAATTCGTCTCGCTTGAGACATTTTTCCTTTGAATACAAATTTCGAATTTGCTTCAC
TTAAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
Found at i:453912 original size:29 final size:31
Alignment explanation
Indices: 453858--453943 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 31
453848 TTTCTCTTGA
*
453858 AACAAATCTTTGAGTT-TGTTCCTTTTAAAT-
1 AACAAATCTTTGAGTTAT-TTCTTTTTAAATG
***
453888 AA-AAATCTTTGAGTTATTTCTTTTTTTTTG
1 AACAAATCTTTGAGTTATTTCTTTTTAAATG
453918 AACAAATCTTTGAGTCTATTTCTTTT
1 AACAAATCTTTGAGT-TATTTCTTTT
453944 GAAACAAAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 21 0.44
30 5 0.10
31 12 0.25
32 10 0.21
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (31 bp):
AACAAATCTTTGAGTTATTTCTTTTTAAATG
Found at i:454017 original size:29 final size:30
Alignment explanation
Indices: 453981--454042 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
453971 AATTTCGTGA
*
453981 AAAAATCTTTGAGTC-GTTTCTTTTGAAAC
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
454010 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
454040 AAA
1 AAA
454043 TTTTTGTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (30 bp):
AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
Found at i:454048 original size:91 final size:93
Alignment explanation
Indices: 453921--454097 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 93
453911 TTTTTTGAAC
* *
453921 AAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC-GTGAAAAA
1 AAATCTTTGAGTCTATTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTGAGAAAAA
453985 ATCTTTGAGTC-GTTTCTTTTGAAACAA
66 ATCTTTGAGTCTGTTTCTTTTGAAACAA
* *
454012 AAATCTTTGAGTCTGTTTCTTTGGAAACAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAA
1 AAATCTTTGAGTCTATTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC---TGAGAA
454077 AAAATCTTTGAGTCTGTTTCT
63 AAAATCTTTGAGTCTGTTTCT
454098 CTTAAAATGA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
91 53 0.69
95 18 0.23
96 6 0.08
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (93 bp):
AAATCTTTGAGTCTATTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTGAGAAAAA
ATCTTTGAGTCTGTTTCTTTTGAAACAA
Found at i:454111 original size:66 final size:66
Alignment explanation
Indices: 453997--454121 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
453987 CTTTGAGTCG
*
453997 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAATTTTTGTCTCTCTTGAGAC
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGAAAACAAA-TTTTGTCTCTCTTGAGAC
454062 AA
65 AA
* **
454064 TTTCTTTTGAGA-AAAAATCTTTGAGTCTGTTTCTCTT-AAAATGAATTTTGTCTCTCTT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT-TTGAAAACAAATTTTGTCTCTCTT
454122 AAAACAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
65 13 0.25
66 27 0.51
67 13 0.25
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.46
Consensus pattern (66 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGAAAACAAATTTTGTCTCTCTTGAGACA
A
Found at i:454184 original size:28 final size:26
Alignment explanation
Indices: 454075--454196 Score: 87
Period size: 28 Copynumber: 4.6 Consensus size: 26
454065 TTCTTTTGAG
454075 AAAAAATCTTTGAGTCTGTTTCTCTTA
1 AAAAAATCTTTGAGTCTG-TTCTCTTA
*
454102 AAATGAAT-TTT--GTC---TCTCTTA
1 AAA-AAATCTTTGAGTCTGTTCTCTTA
*
454123 AAACAAATTTTTGAGTCTGTTCAT-TTAAA
1 AAA-AAATCTTTGAGTCTGTTC-TCTT--A
454152 AAAAAATCTTTGAGTCTGTTTCTCTTA
1 AAAAAATCTTTGAGTCTG-TTCTCTTA
454179 ACAAAATCATCTTTGAGT
1 A-AAAA--ATCTTTGAGT
454197 TTATTTCTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 27
0.71 0.04 0.25
Matches are distributed among these distances:
21 13 0.17
22 3 0.04
24 3 0.04
25 3 0.04
27 12 0.16
28 23 0.30
29 9 0.12
30 10 0.13
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (26 bp):
AAAAAATCTTTGAGTCTGTTCTCTTA
Found at i:454341 original size:118 final size:118
Alignment explanation
Indices: 454186--454401 Score: 301
Period size: 118 Copynumber: 1.8 Consensus size: 118
454176 TTAACAAAAT
* * *
454186 CATCTTTGAGTTTATTTCTTTAAAAACAAATTGTGTCTCTCTTGAGACAGTTTCTAATGA-AAAA
1 CATCTTTGAGTATATTTATTTAAAAACAAATTGTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
454250 CCAACCTTTGAGATTGTCTCCTTTGAAA-AAAATTGTCTCACTTAAGATGTAATC
66 --AACCTTTGAGATTGTCTCCTTTGAAACAAAATTGTCTCACTTAAGATGTAATC
** * **
454304 CATCTTTGAGTATATTTATTTGGAAACAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAA
1 CATCTTTGAGTATATTTATTTAAAAACAAATTGTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
* * *
454369 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATT
66 AACCTTTGAGATTGTCTCCTTTGAAACAAAATT
454402 TTGTCTCTCG
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
117 23 0.27
118 58 0.68
119 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (118 bp):
CATCTTTGAGTATATTTATTTAAAAACAAATTGTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
AACCTTTGAGATTGTCTCCTTTGAAACAAAATTGTCTCACTTAAGATGTAATC
Found at i:454519 original size:31 final size:30
Alignment explanation
Indices: 454484--454550 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
454474 CCTTGAGGCA
454484 GTTTCTCTAGAAATACAAA-ATCTTTGAGTTT
1 GTTTCTCTAGAAATA-AAACATCTTTGAG-TT
* *
454515 GTTTCTCTTGAAATAAAACCATTTTTGAGTT
1 GTTTCTCTAGAAATAAAA-CATCTTTGAGTT
454546 GTTTC
1 GTTTC
454551 ACTTGAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.09
31 21 0.66
32 8 0.25
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (30 bp):
GTTTCTCTAGAAATAAAACATCTTTGAGTT
Found at i:454570 original size:15 final size:15
Alignment explanation
Indices: 454547--454605 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
454537 TTTTGAGTTG
*
454547 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
454562 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
454577 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
454592 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
454606 AGATCATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:455085 original size:63 final size:65
Alignment explanation
Indices: 454909--455086 Score: 166
Period size: 66 Copynumber: 2.7 Consensus size: 65
454899 CAAAACAAAC
* * *
454909 ATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAATTTCCCATGAAACACC
1 ATCTTTGAGAACGTTTCCTTTGAAACGAATTTTGTCTC-TTTGAGACAATTTCCCATGAAACACC
454974 G
65 G
** * * * **
454975 ATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCT-TGCTTGAGACAA-TTCCCTTTAAATG
1 ATCTTTGAGAACGTTT-CCTTTGAAACGAATTTTGTCTCT--TTGAGACAATTTCCCATGAAACA
455038 CC-
63 CCG
***
455040 ATCTTTG-GGTTGTTTCCTTTGAAACGAATTTTGTCTCTTTCGAGACA
1 ATCTTTGAGAACGTTTCCTTTGAAACGAATTTTGTCTCTTT-GAGACA
455087 GTTGCTTTTG
Statistics
Matches: 91, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
62 2 0.02
63 24 0.26
64 6 0.07
65 8 0.09
66 26 0.29
67 25 0.27
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (65 bp):
ATCTTTGAGAACGTTTCCTTTGAAACGAATTTTGTCTCTTTGAGACAATTTCCCATGAAACACCG
Found at i:455508 original size:43 final size:40
Alignment explanation
Indices: 455410--455508 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 40
455400 CCCTAGATGG
* * *
455410 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGA
1 CCAGAACTCTTCATCACGTAGGAACCGTGTCATCCCACGA
** *
455450 CCAGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAAACGA
1 CCAGAACTCTTCATCACGTAGGAACCGTGTCATCCC----ACGA
455493 CCAGAACTCTTCATCA
1 CCAGAACTCTTCATCA
455509 TGTATAAGCA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
39 3 0.07
40 27 0.59
43 16 0.35
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.23
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTAGGAACCGTGTCATCCCACGA
Found at i:455689 original size:3 final size:3
Alignment explanation
Indices: 455683--455729 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
455673 TATTTAATAT
** *
455683 TTA TTA TTA TCG TTA -TA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
455730 ATTTACATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:456935 original size:19 final size:19
Alignment explanation
Indices: 456889--456935 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
456879 CATTAATTTG
*
456889 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
456909 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
456929 TATATTT
1 TATATTT
456936 ATTTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:457347 original size:7 final size:8
Alignment explanation
Indices: 457322--457349 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
457312 TGAATATAAC
457322 TTTGAATT
1 TTTGAATT
457330 TTTGAATT
1 TTTGAATT
457338 TTTGAATT
1 TTTGAATT
457346 TTTG
1 TTTG
457350 GCTTCAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (8 bp):
TTTGAATT
Found at i:459708 original size:10 final size:10
Alignment explanation
Indices: 459693--459733 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
459683 CATTTAAATA
*
459693 ATAAACGAAT
1 ATAAACGAAC
459703 ATAAACGAAC
1 ATAAACGAAC
**
459713 ACGAACGAAC
1 ATAAACGAAC
459723 ATAAACGAAC
1 ATAAACGAAC
459733 A
1 A
459734 ACACAAACAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:459721 original size:20 final size:20
Alignment explanation
Indices: 459696--459733 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
459686 TTAAATAATA
*
459696 AACGAATATAAACGAACACG
1 AACGAACATAAACGAACACG
459716 AACGAACATAAACGAACA
1 AACGAACATAAACGAACA
459734 ACACAAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.21, G:0.13, T:0.08
Consensus pattern (20 bp):
AACGAACATAAACGAACACG
Found at i:466057 original size:20 final size:20
Alignment explanation
Indices: 466032--466079 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
466022 TTCGTCTGTT
*
466032 GCCCGCTGGCCGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
* *
466052 GCCCGCCGTCTGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
*
466072 GTCCGCCG
1 GCCCGCCG
466080 CCACACTCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.00, C:0.54, G:0.33, T:0.12
Consensus pattern (20 bp):
GCCCGCCGGCCGCTGCCGCC
Done.