Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009238.1 Hibiscus syriacus cultivar Beakdansim tig00112864_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: 1094141
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 5
Found at i:296229 original size:20 final size:20
Alignment explanation
Indices: 296103--296237 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
296093 GATTCTGTAT
*
296103 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
296123 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
296143 AATCGCATTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
296163 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
296183 TATCGCGTTACGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
296204 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
296224 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
296238 TTTCCAAATT
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 80 0.82
21 13 0.13
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:296258 original size:41 final size:40
Alignment explanation
Indices: 296128--296257 Score: 136
Period size: 41 Copynumber: 3.2 Consensus size: 40
296118 GTCAGAATCT
* ***
296128 CGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGAA-TCG
1 CGTTGCGAAAGTCAGTATCGCATTGCGATTTTCA-AATTCG
* * ** *
296168 CGTTGCGAAAGTCAGTATCGCGTTACGATTTTGTATTATCG
1 CGTTGCGAAAGTCAGTATCGCATTGCGATTTTCAAAT-TCG
*
296209 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCG
1 CGTTGCGAAAGTCAGTATCGCATTGCGATTTT-CAAATTCG
296250 CGTTGCGA
1 CGTTGCGA
296258 TTTACTTATT
Statistics
Matches: 72, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 26 0.36
41 43 0.60
42 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (40 bp):
CGTTGCGAAAGTCAGTATCGCATTGCGATTTTCAAATTCG
Found at i:296319 original size:21 final size:22
Alignment explanation
Indices: 296267--296319 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
296257 ATTTACTTAT
*
296267 TCGCATTACG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
296288 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
296309 TCGCATTGCGA
1 TCGCATTGCGA
296320 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:300074 original size:2 final size:2
Alignment explanation
Indices: 300067--300093 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
300057 AATCCATGTA
300067 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
300094 AACAAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:330169 original size:26 final size:26
Alignment explanation
Indices: 330133--330184 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
330123 CTGTAATTGC
330133 TACATGAAGAGGGGGAGTTGCATGGT
1 TACATGAAGAGGGGGAGTTGCATGGT
330159 TACATGAAGAGGGGGAGTTGCATGGT
1 TACATGAAGAGGGGGAGTTGCATGGT
330185 GATCCGGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.42, T:0.23
Consensus pattern (26 bp):
TACATGAAGAGGGGGAGTTGCATGGT
Found at i:330842 original size:17 final size:17
Alignment explanation
Indices: 330820--330853 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
330810 TAAGATATAT
330820 TTTTTTATAAA-ATTTAA
1 TTTTTTA-AAATATTTAA
330837 TTTTTTAAAATATTTAA
1 TTTTTTAAAATATTTAA
330854 AATAATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTTAAAATATTTAA
Found at i:332272 original size:10 final size:10
Alignment explanation
Indices: 332257--332281 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
332247 ACTCAACAAT
332257 ACTAAAACTC
1 ACTAAAACTC
332267 ACTAAAACTC
1 ACTAAAACTC
332277 ACTAA
1 ACTAA
332282 GTTTACGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (10 bp):
ACTAAAACTC
Found at i:333565 original size:19 final size:20
Alignment explanation
Indices: 333541--333578 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
333531 TATTGGGTAT
333541 GTTCTT-AATCATGACAGTG
1 GTTCTTGAATCATGACAGTG
*
333560 GTTCTTGAATCTTGACAGT
1 GTTCTTGAATCATGACAGT
333579 TAGATTCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (20 bp):
GTTCTTGAATCATGACAGTG
Found at i:339708 original size:2 final size:2
Alignment explanation
Indices: 339701--339773 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
339691 GATTTCTCAG
339701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
339743 AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
339774 GGCCTTTGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:344312 original size:28 final size:29
Alignment explanation
Indices: 344268--344322 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
344258 TTAAAAATAT
* *
344268 AAACTAAGGATTAAAATA-TTATTTATTA
1 AAACTAAGGACTAAAATACGTATTTATTA
344296 AAACTAAAGGACT-AAATACGTATTTAT
1 AAACT-AAGGACTAAAATACGTATTTAT
344323 CCTAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (29 bp):
AAACTAAGGACTAAAATACGTATTTATTA
Found at i:345437 original size:3 final size:3
Alignment explanation
Indices: 345431--345471 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
345421 TAATATTTAT
*
345431 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
345472 TTTAAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:345943 original size:116 final size:116
Alignment explanation
Indices: 345700--346615 Score: 1505
Period size: 116 Copynumber: 8.0 Consensus size: 116
345690 TAGAGTCATT
* ** *
345700 CAAAAGGTTGAATAAGCTCTTCTCATTATGAA---CTTCTT-ATTCTTCAGAT---GAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
* ** *** * * * *
345758 TCATTATGAACT-TTCCTGAAAAAACTGATCCATCAAGTGATGGA-TTAAG
66 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
345807 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
*
345872 TCATTATGAACTCTACCTTGCAATGTTAATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
345923 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
345988 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
*
346039 CAAAAGGTTGAACAAATTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
*
346104 TCATTATGAACTATACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
*
346155 CAAAAGCTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
346220 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
346271 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
346336 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
* *
346387 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTCCAGATGACAAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
346452 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
*
346503 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGAT---GAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
* * * ** *
346565 TCATTATGAACTCGACCTGGCAATGCTGATCCATTGAATGATGGATTTAAA
66 TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
346616 TCTTTGCTAA
Statistics
Matches: 767, Mismatches: 33, Indels: 12
0.94 0.04 0.01
Matches are distributed among these distances:
107 29 0.04
110 6 0.01
111 10 0.01
113 53 0.07
114 21 0.03
115 22 0.03
116 626 0.82
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (116 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
TCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAA
Found at i:347041 original size:22 final size:22
Alignment explanation
Indices: 347016--347095 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
347006 CATAAAGCTT
*
347016 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* * *
347038 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTAAAAAGAGAATCTA
* * **
347060 TCATCTCTGAAGTGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
347082 TTATCTTTAAAAAG
1 TCATCTTTAAAAAG
347096 TGTAGATGTA
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:347544 original size:54 final size:53
Alignment explanation
Indices: 347458--347663 Score: 231
Period size: 54 Copynumber: 3.9 Consensus size: 53
347448 AGAATAACTG
* * * *
347458 GTTCGTAAAACATTTGACAACACATTCTTCATCTCATGTGGTTTCAGTTCAGA
1 GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTGCTCAGA
*
347511 TGTTCGTAAAGCATTTGACAACACATTCATCATCTCATGTGGCTTCTGCTCAGA
1 -GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTGCTCAGA
* * *
347565 --T-GTAAAACATTTGACAACACATTCATCGTTTTC-TGTAGCTTCTGCTCAGA
1 GTTCGTAAAACATTTGACAACACATTCATC-ATCTCATGTGGCTTCTGCTCAGA
* * * * **
347615 GGTTCGTAAAGCATTTAACAACACATTCATCCTTTTTTGTGGCTTCTGC
1 -GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTGC
347664 CAAGATTTCT
Statistics
Matches: 132, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
50 41 0.31
51 4 0.03
53 4 0.03
54 83 0.63
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTGCTCAGA
Found at i:347614 original size:104 final size:104
Alignment explanation
Indices: 347462--347663 Score: 271
Period size: 104 Copynumber: 1.9 Consensus size: 104
347452 TAACTGGTTC
* * * * *
347462 GTAAAACATTTGACAACACATTCTTCATCTCATGTGGTTTCAGTTCAGATGTTCGTAAAGCATTT
1 GTAAAACATTTGACAACACATTCATCATCTCATGTAGCTTCAGCTCAGAGGTTCGTAAAGCATTT
*
347527 GACAACACATTCATCATCTCATGTGGCTTCTGCTCAGAT
66 AACAACACATTCATCATCTCATGTGGCTTCTGCTCAGAT
* * *
347566 GTAAAACATTTGACAACACATTCATCGTTTTC-TGTAGCTTCTGCTCAGAGGTTCGTAAAGCATT
1 GTAAAACATTTGACAACACATTCATC-ATCTCATGTAGCTTCAGCTCAGAGGTTCGTAAAGCATT
* * **
347630 TAACAACACATTCATCCTTTTTTGTGGCTTCTGC
65 TAACAACACATTCATCATCTCATGTGGCTTCTGC
347664 CAAGATTTCT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 81 0.96
105 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (104 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTAGCTTCAGCTCAGAGGTTCGTAAAGCATTT
AACAACACATTCATCATCTCATGTGGCTTCTGCTCAGAT
Found at i:349871 original size:115 final size:114
Alignment explanation
Indices: 349670--349896 Score: 346
Period size: 115 Copynumber: 2.0 Consensus size: 114
349660 GATCATGCAG
* * * * * *
349670 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATCGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
349735 ACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* *
349784 TTCATCTTTAAAATCCAATGATTGGTTTTTGAGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATCGG-TTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
349849 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
349897 CATGGAACTT
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
114 22 0.22
115 79 0.78
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTAAAATCCAATGATCGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:352170 original size:12 final size:12
Alignment explanation
Indices: 352155--352188 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
352145 TCAATTTTCC
352155 TTTTTCTTTTTT
1 TTTTTCTTTTTT
*
352167 TTTTCCTTTTTT
1 TTTTTCTTTTTT
352179 TTTCTTCTTT
1 TTT-TTCTTT
352189 CTTTATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:352171 original size:11 final size:11
Alignment explanation
Indices: 352155--352184 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
352145 TCAATTTTCC
352155 TTTTTCTTTTT
1 TTTTTCTTTTT
*
352166 TTTTTCCTTTT
1 TTTTTCTTTTT
352177 TTTTTCTT
1 TTTTTCTT
352185 CTTTCTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:352189 original size:18 final size:18
Alignment explanation
Indices: 352150--352189 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
352140 TTGATTCAAT
*
352150 TTTCCTTTTTCTTTTTTT
1 TTTCCTTTTTCTTTTTTC
352168 TTTCCTTTTT-TTTTCTTC
1 TTTCCTTTTTCTTTT-TTC
352186 TTTC
1 TTTC
352190 TTTATTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCCTTTTTCTTTTTTC
Found at i:355497 original size:14 final size:14
Alignment explanation
Indices: 355463--355516 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
355453 TTGTGCAATA
* *
355463 CAAATGCAAAGATG
1 CAAATGTAAATATG
355477 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
355492 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
355506 TAAATGTAAAT
1 CAAATGTAAAT
355517 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:357843 original size:13 final size:13
Alignment explanation
Indices: 357806--357845 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
357796 TCGATATTGA
357806 AAAATAAATA-TT
1 AAAATAAATATTT
*
357818 AAAATAATTTATTT
1 AAAATAA-ATATTT
357832 AAAATAAATATTT
1 AAAATAAATATTT
357845 A
1 A
357846 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:357846 original size:17 final size:17
Alignment explanation
Indices: 357819--357863 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
357809 ATAAATATTA
357819 AAATAATTTATTTAAAAT
1 AAAT-ATTTATTTAAAAT
**
357837 AAATATTTATTTATTAT
1 AAATATTTATTTAAAAT
*
357854 ATATATTTAT
1 AAATATTTAT
357864 GACTACATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATTTATTTAAAAT
Found at i:358160 original size:28 final size:29
Alignment explanation
Indices: 358116--358170 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
358106 TTAAAAATAT
* *
358116 AAACTAAGGATTAAAATA-TTATTTATTA
1 AAACTAAGGACTAAAATACGTATTTATTA
358144 AAACTAAAGGACT-AAATACGTATTTAT
1 AAACT-AAGGACTAAAATACGTATTTAT
358171 CCTAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (29 bp):
AAACTAAGGACTAAAATACGTATTTATTA
Found at i:359285 original size:3 final size:3
Alignment explanation
Indices: 359279--359322 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
359269 TAATATTTAT
*
359279 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
359323 TTTAAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:360501 original size:28 final size:31
Alignment explanation
Indices: 360434--360501 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 31
360424 GATGTTATTC
360434 TTAAATTCTTAAATTTATGATGAAGAAATAAA
1 TTAAA-TCTTAAATTTATGATGAAGAAATAAA
360466 -TAAA--TTAAA-TT-T-ATGAAGAAATAAA
1 TTAAATCTTAAATTTATGATGAAGAAATAAA
360491 TTAAATCTTAA
1 TTAAATCTTAA
360502 GTTTGAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
25 13 0.39
26 5 0.15
27 2 0.06
28 9 0.27
31 4 0.12
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (31 bp):
TTAAATCTTAAATTTATGATGAAGAAATAAA
Found at i:360783 original size:33 final size:33
Alignment explanation
Indices: 360732--360794 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
360722 AGATTACATC
360732 AAAGGTTAACTGTCGAGATTAATTTGAAAATAA
1 AAAGGTTAACTGTCGAGATTAATTTGAAAATAA
* *
360765 AAAGGTTAATTGTTGAGATTAATTTGAAAA
1 AAAGGTTAACTGTCGAGATTAATTTGAAAA
360795 CAAAGACTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (33 bp):
AAAGGTTAACTGTCGAGATTAATTTGAAAATAA
Found at i:366178 original size:33 final size:34
Alignment explanation
Indices: 366141--366205 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
366131 TGGAAATTTC
*
366141 ATCTTGGTTGATGGCCAACTTATT-GAAAAATTA
1 ATCTTGGTTGATGGCCAACTCATTGGAAAAATTA
*
366174 ATCTTGGTTGGTGGCCAACTCATTGGAAAAAT
1 ATCTTGGTTGATGGCCAACTCATTGGAAAAAT
366206 CTTTGGTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (34 bp):
ATCTTGGTTGATGGCCAACTCATTGGAAAAATTA
Found at i:369908 original size:57 final size:58
Alignment explanation
Indices: 369808--369921 Score: 149
Period size: 57 Copynumber: 1.9 Consensus size: 58
369798 ACAAGAAGAA
* * * **
369808 GAATACTCAATCGTGCAATCTTCATTTCAACCACCACCACCAACAGTTGAAGAAGAATAT
1 GAATACTCAAGCATGCAATCATCATTT--ACCACCACCACCAACAACTGAAGAAGAATAT
*
369868 GAATACTCAAGCATGCAATCATCATTT-CCACCACCGCCAACAACTGAAGAAGAA
1 GAATACTCAAGCATGCAATCATCATTTACCACCACCACCAACAACTGAAGAAGAA
369922 GAAGAAGAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 24 0.50
60 24 0.50
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.20
Consensus pattern (58 bp):
GAATACTCAAGCATGCAATCATCATTTACCACCACCACCAACAACTGAAGAAGAATAT
Found at i:369932 original size:60 final size:60
Alignment explanation
Indices: 369800--369932 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
369790 GAAGGGGAAC
* * * * **
369800 AAGAAGAAGAATACTCAATCGTGCAATCTTCATTTCAACCACCACCACCAACAGTTGAAG
1 AAGAAGAAGAATACTCAAGCATGCAATCATCATTTCAACCACCACCAACAACAGAAGAAG
* * * * *
369860 AAGAATATGAATACTCAAGCATGCAATCATCATTTCCACCACCGCCAACAACTGAAGAAG
1 AAGAAGAAGAATACTCAAGCATGCAATCATCATTTCAACCACCACCAACAACAGAAGAAG
369920 AAGAAGAAGAATA
1 AAGAAGAAGAATA
369933 TTCACAAATG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.18
Consensus pattern (60 bp):
AAGAAGAAGAATACTCAAGCATGCAATCATCATTTCAACCACCACCAACAACAGAAGAAG
Found at i:370200 original size:4 final size:4
Alignment explanation
Indices: 370191--370221 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
370181 GAGAGAAGAA
370191 GAAG GAAG GAAG GAA- GAAG GAAG GAAG GAAG
1 GAAG GAAG GAAG GAAG GAAG GAAG GAAG GAAG
370222 AAAGAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (4 bp):
GAAG
Found at i:370202 original size:11 final size:11
Alignment explanation
Indices: 370188--370238 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
370178 AGGGAGAGAA
370188 GAAGAAGGAAG
1 GAAGAAGGAAG
370199 GAAGGAA-GAAG
1 GAA-GAAGGAAG
370210 GAAGGAAGGAAG
1 GAA-GAAGGAAG
*
370222 AAAGAA-GAA-
1 GAAGAAGGAAG
370231 GAAGAAGG
1 GAAGAAGG
370239 GTTAACTGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 5 0.14
10 4 0.11
11 17 0.49
12 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (11 bp):
GAAGAAGGAAG
Found at i:370206 original size:15 final size:15
Alignment explanation
Indices: 370188--370238 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
370178 AGGGAGAGAA
370188 GAAGAAGGAAGGAAG
1 GAAGAAGGAAGGAAG
370203 GAAGAAGGAAGGAAG
1 GAAGAAGGAAGGAAG
*
370218 GAAGAAAGAA-GAA-
1 GAAGAAGGAAGGAAG
370231 GAAGAAGG
1 GAAGAAGG
370239 GTTAACTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 7 0.21
14 3 0.09
15 24 0.71
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAAGGAAG
Found at i:370738 original size:17 final size:16
Alignment explanation
Indices: 370716--370747 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
370706 TTACCATATT
370716 AAAAATCGATTTTTTTA
1 AAAAAT-GATTTTTTTA
370733 AAAAATGATTTTTTT
1 AAAAATGATTTTTTT
370748 CAAACCGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
AAAAATGATTTTTTTA
Found at i:374604 original size:65 final size:65
Alignment explanation
Indices: 374500--374630 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
374490 TTAGTTGTTG
* *
374500 ATTTTCTTAGAGGTCATGGGTTCGAACACAAACGGTTGCAACATGGTGATTGAGCGTTTATTATC
1 ATTTTCATAGAGGTCATGGGTTCGAACACAAACGGTTGCAACAGGGTGATTGAGCGTTTATTATC
*
374565 ATTTTCATAGAGGTCATGGGTTCGAACACAAACGGTTGCAATAGGGTGATTGAGCGTTTATTATC
1 ATTTTCATAGAGGTCATGGGTTCGAACACAAACGGTTGCAACAGGGTGATTGAGCGTTTATTATC
374630 A
1 A
374631 AATGATTGAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (65 bp):
ATTTTCATAGAGGTCATGGGTTCGAACACAAACGGTTGCAACAGGGTGATTGAGCGTTTATTATC
Found at i:375886 original size:30 final size:29
Alignment explanation
Indices: 375850--375925 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
375840 ACTAAGCGAT
*
375850 TTTCCCGATATATCACCGGTGAACAGTATA
1 TTTCCCGATATAACACCGGT-AACAGTATA
* * * *
375880 TTTCCCGATCTAACACCGGTCAGATTATA
1 TTTCCCGATATAACACCGGTAACAGTATA
*
375909 TTTCCCGATCTAACACC
1 TTTCCCGATATAACACC
375926 CTTAGCAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (29 bp):
TTTCCCGATATAACACCGGTAACAGTATA
Found at i:376013 original size:51 final size:51
Alignment explanation
Indices: 375937--376065 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
375927 TTAGCAGTAA
* * *
375937 AGCGCGCCCCCTGCACTGCGCTATACGATGATTTGGC-GCCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGATCTGGCAGACACGT-GGGTAT
* *
375988 AGCGCGCCCCCTGCACCGCGCTATACGGTGATCTGGCATACACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGATCTGGCAGACACGTGGGTAT
* * *
376039 AGCGCGGCCCCTGCAGCGCGTTATACG
1 AGCGCGCCCCCTGCACCGCGCTATACG
376066 CCACGTAGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 64 0.93
52 5 0.07
ACGTcount: A:0.16, C:0.33, G:0.31, T:0.19
Consensus pattern (51 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGATCTGGCAGACACGTGGGTAT
Found at i:379805 original size:50 final size:50
Alignment explanation
Indices: 379711--379805 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
379701 AAGTCTAACA
* * * *
379711 AATTTAACAAAATAAAGTAAGTATTAAATGAGAAATAATAAAAAAATTAC
1 AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAAAAAAAAAAATTAC
* *
379761 AATTTAACAAAATAAAGTAAATA-CAAAT-ATAATAAAAAACAAAAA
1 AATTTAACAAAATAAAGTAAATATCAAATGAGAA-AAAAAAAAAAAA
379806 CTATCGATGC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
48 3 0.08
49 13 0.34
50 22 0.58
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.23
Consensus pattern (50 bp):
AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAAAAAAAAAAATTAC
Found at i:382086 original size:12 final size:10
Alignment explanation
Indices: 382072--382112 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
382062 ACCTTAAAAA
*
382072 GAGAGTATTT
1 GAGAGAATTT
382082 GAGAGAAATTT
1 GAGAG-AATTT
382093 -AGAGAATTT
1 GAGAGAATTT
382102 GAGAGAATTT
1 GAGAGAATTT
382112 G
1 G
382113 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:382355 original size:29 final size:30
Alignment explanation
Indices: 382313--382388 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 30
382303 TACTTCTAAG
382313 GGTGTTAGATCGGGAAATATAAT-TTGACC
1 GGTGTTAGATCGGGAAATATAATGTTGACC
*
382342 GGTGTTAGATCGGGAAATATAATGTTTACC
1 GGTGTTAGATCGGGAAATATAATGTTGACC
* *
382372 GGTGATATATCGGGAAA
1 GGTGTTAGATCGGGAAA
382389 ATCACCCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
29 23 0.53
30 20 0.47
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (30 bp):
GGTGTTAGATCGGGAAATATAATGTTGACC
Found at i:383194 original size:15 final size:15
Alignment explanation
Indices: 383174--383202 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
383164 ATTTAATAGT
383174 AATAATTAAATAATC
1 AATAATTAAATAATC
383189 AATAATTAAATAAT
1 AATAATTAAATAAT
383203 AAAATCAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATTAAATAATC
Found at i:383388 original size:2 final size:2
Alignment explanation
Indices: 383381--383422 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
383371 ATGAAAACAA
383381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
383423 TTTAGTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:395011 original size:29 final size:29
Alignment explanation
Indices: 394976--395057 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
394966 AAACTAAATT
*
394976 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
395005 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
395034 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
395058 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:399467 original size:29 final size:29
Alignment explanation
Indices: 399432--399513 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
399422 AAACTAAATT
*
399432 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
399461 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
399490 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
399514 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:408190 original size:31 final size:31
Alignment explanation
Indices: 408153--408221 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
408143 TCACCAAAAA
* *
408153 TATTAGATTTACCGTTTACCCAAAAAATAAC
1 TATTAGATTGACCATTTACCCAAAAAATAAC
* **
408184 TATTAGATTGACTATTTACCGGAAAAATAAC
1 TATTAGATTGACCATTTACCCAAAAAATAAC
408215 TATTAGA
1 TATTAGA
408222 CGAAGAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (31 bp):
TATTAGATTGACCATTTACCCAAAAAATAAC
Found at i:408674 original size:26 final size:26
Alignment explanation
Indices: 408640--408722 Score: 157
Period size: 26 Copynumber: 3.2 Consensus size: 26
408630 AGCGGAGTTA
408640 ATTATGTAATTATGTATCAGGTTTTT
1 ATTATGTAATTATGTATCAGGTTTTT
408666 ATTATGTAATTATGTATCAGGTTTTT
1 ATTATGTAATTATGTATCAGGTTTTT
*
408692 ATTATGTAATTATGTACCAGGTTTTT
1 ATTATGTAATTATGTATCAGGTTTTT
408718 ATTAT
1 ATTAT
408723 AAACAGAGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (26 bp):
ATTATGTAATTATGTATCAGGTTTTT
Found at i:410591 original size:38 final size:36
Alignment explanation
Indices: 410515--410591 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
410505 TTTTTATATT
*
410515 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
410551 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
410589 TTT
1 TTT
410592 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 5 0.14
37 21 0.60
38 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:421681 original size:29 final size:29
Alignment explanation
Indices: 421646--421727 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
421636 AAACTAAATT
*
421646 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
421675 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
421704 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
421728 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:423038 original size:15 final size:15
Alignment explanation
Indices: 423015--423044 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
423005 ACGAGGCTGG
423015 AATTACAACAATAAC
1 AATTACAACAATAAC
*
423030 AATTCCAACAATAAC
1 AATTACAACAATAAC
423045 TATGAGAAAG
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:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:426448 original size:29 final size:29
Alignment explanation
Indices: 426413--426494 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
426403 AAACTAAATT
*
426413 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
426442 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
426471 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
426495 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:434293 original size:15 final size:17
Alignment explanation
Indices: 434265--434308 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
434255 CATTTTCGTA
*
434265 GTTTGAGCGTTTTGAA-
1 GTTTGAGAGTTTTGAAC
434281 GTTTGA-AGTTTTGAAC
1 GTTTGAGAGTTTTGAAC
434297 GTTTGAGAGTTT
1 GTTTGAGAGTTT
434309 AGAGTTACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 12 0.48
17 5 0.20
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (17 bp):
GTTTGAGAGTTTTGAAC
Found at i:434526 original size:83 final size:81
Alignment explanation
Indices: 434384--434910 Score: 397
Period size: 83 Copynumber: 6.4 Consensus size: 81
434374 TTATGTGAAG
* *
434384 TGGCAGAA-ATTCTCTGAATAATAATGGAAAACACTTTCTCC-AAA-ATGCACATTTCATTTCGG
1 TGGCA-AAGATTCTCTGAATAATAATGG-AAA-TCTTTCCCCGAAACATGC-C-TTTCATTTCGG
*
434446 ATGTGATAGAACACTCTGACA
61 ATGGGATAGAACACTCTGACA
* * * **
434467 TGGCAGAGATTCTCTGAATAATAATGGAAATCGTTTTCCCCGAAGCATGCCTTTTATTTCAAATG
1 TGGCAAAGATTCTCTGAATAATAATGGAAATC--TTTCCCCGAAACATGCCTTTCATTTCGGATG
434532 GGATAGAACACTCTGACA
64 GGATAGAACACTCTGACA
* * * * * **
434550 TGGCAAATATTATCTGAATAATAATGGAAAATACTTTCCCTGAAGCACGCCTTTCATTTCAAATG
1 TGGCAAAGATTCTCTGAATAATAATGG-AAAT-CTTTCCCCGAAACATGCCTTTCATTTCGGATG
*
434615 GGATGGAACACTCTGACA
64 GGATAGAACACTCTGACA
* * * * * *
434633 TGGTAAATATTCTTTGAATAATAATGGAAAATACTTTCCCCAAAACACGCTTTTCATTTCGGATG
1 TGGCAAAGATTCTCTGAATAATAATGG-AAAT-CTTTCCCCGAAACATGCCTTTCATTTCGGATG
* *
434698 TGATGGAACACT-TGGACA
64 GGATAGAACACTCT-GACA
* * * * * *** *
434716 TGCCAGAGATTCGCTAAATAATAATGGAAAAAGCTTTCATTGAAACATGCCTTTCATTTTGGATG
1 TGGCAAAGATTCTCTGAATAATAATGG--AAATCTTTCCCCGAAACATGCCTTTCATTTCGGATG
434781 GGAT-GAAACACTCTGACA
64 GGATAG-AACACTCTGACA
* * * * * * *
434799 TGACAAAGATTAC-CTAAATAATAATGGAAAACACTTCTCTCGAAACACGCCTTTCATTTCAGAT
1 TGGCAAAGATT-CTCTGAATAATAATGGAAATC-TTTC-CCCGAAACATGCCTTTCATTTCGGAT
* * * * *
434863 GAGATTA-ATCACTATTATAA
63 GGGA-TAGAACACTCTGA-CA
*
434883 T-TC-AAGATTCTCTGAATAATAATGGAAA
1 TGGCAAAGATTCTCTGAATAATAATGGAAA
434911 AATGCATCCC
Statistics
Matches: 369, Mismatches: 57, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
81 6 0.02
82 31 0.08
83 311 0.84
84 16 0.04
85 5 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (81 bp):
TGGCAAAGATTCTCTGAATAATAATGGAAATCTTTCCCCGAAACATGCCTTTCATTTCGGATGGG
ATAGAACACTCTGACA
Found at i:434829 original size:166 final size:165
Alignment explanation
Indices: 434400--434863 Score: 460
Period size: 166 Copynumber: 2.8 Consensus size: 165
434390 AAATTCTCTG
** *
434400 AATAATAATGGAAAACACTTTCTCCAAA-ATGCACATTTCATTTCGGATGTGAT-AGAACACTCT
1 AATAATAATGGAAAACACTTTCTTGAAACATGC-C-TTTCATTTCGGATGGGATGA-AACACTCT
* * *
434463 GACATGGCAGAGATTCTCTGAATAATAATGG-AAAT-CGTTTTCCCCGAAGCATGCCTTTT-ATT
63 GACATGGCAAAGATTCTCTGAATAATAATGGAAAATAC--TTTCCCCGAAACACG-CTTTTCATT
* * * * *
434525 TCAAATGGGATAGAACACTCTGACATGGCAAATATTATCTG
125 TCAGATGGGATAGAACACTCTGACATGCCAAAGATTAGCTA
* * * * ** *
434566 AATAATAATGGAAAATACTTTCCCTGAAGCACGCCTTTCATTTCAAATGGGATGGAACACTCTGA
1 AATAATAATGGAAAACACTTT-CTTGAAACATGCCTTTCATTTCGGATGGGATGAAACACTCTGA
* * * * *
434631 CATGGTAAATATTCTTTGAATAATAATGGAAAATACTTTCCCCAAAACACGCTTTTCATTTCGGA
65 CATGGCAAAGATTCTCTGAATAATAATGGAAAATACTTTCCCCGAAACACGCTTTTCATTTCAGA
* * * *
434696 TGTGATGGAACACT-TGGACATGCCAGAGATTCGCTA
130 TGGGATAGAACACTCT-GACATGCCAAAGATTAGCTA
*
434732 AATAATAATGGAAAA-AGCTTTCATTGAAACATGCCTTTCATTTTGGATGGGATGAAACACTCTG
1 AATAATAATGGAAAACA-CTTTC-TTGAAACATGCCTTTCATTTCGGATGGGATGAAACACTCTG
* * * * *
434796 ACATGACAAAGATTAC-CTAAATAATAATGGAAAACAC-TTCTCTCGAAACACGCCTTTCATTTC
64 ACATGGCAAAGATT-CTCTGAATAATAATGGAAAATACTTTC-CCCGAAACACGCTTTTCATTTC
434859 AGATG
127 AGATG
434864 AGATTAATCA
Statistics
Matches: 243, Mismatches: 44, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
165 11 0.05
166 219 0.90
167 9 0.04
168 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (165 bp):
AATAATAATGGAAAACACTTTCTTGAAACATGCCTTTCATTTCGGATGGGATGAAACACTCTGAC
ATGGCAAAGATTCTCTGAATAATAATGGAAAATACTTTCCCCGAAACACGCTTTTCATTTCAGAT
GGGATAGAACACTCTGACATGCCAAAGATTAGCTA
Found at i:434850 original size:249 final size:249
Alignment explanation
Indices: 434392--434859 Score: 627
Period size: 249 Copynumber: 1.9 Consensus size: 249
434382 AGTGGCAGAA
* **
434392 ATTCTCTGAATAATAATGGAAAACACTTTCTCCAAAATGCACATTTCATTTCGGATGTGATAGAA
1 ATTCTCTGAATAATAATGGAAAACACTTTCCCCAAAACACACATTTCATTTCGGATGTGATAGAA
* * * ** * * * *
434457 CACTCTGACATGGCAGAGATTCTCTGAATAATAATGGAAATCGTTTTCCCCGAAGCATGCCTTTT
66 CACTCTGACATGCCAGAGATTCGCTAAATAATAATGGAAAAAGCTTTCACCGAAACATGCCTTTC
* * * * *
434522 ATTTCAAATGGGATAGAACACTCTGACATGGCAAATATTATCTGAATAATAATGGAAAATACTTT
131 ATTTCAAATGGGATAGAACACTCTGACATGACAAAGATTACCTAAATAATAATGGAAAACACTTT
*
434587 CCCTGAAGCACGCCTTTCATTTCAAATGGGATGGAACACTCTGACATGGTAAAT
196 CCCTGAAACACGCCTTTCATTTCAAATGGGATGGAACACTCTGACATGGTAAAT
* * * * *
434641 ATTCTTTGAATAATAATGGAAAATACTTTCCCCAAAACACGCTTTTCATTTCGGATGTGATGGAA
1 ATTCTCTGAATAATAATGGAAAACACTTTCCCCAAAACACACATTTCATTTCGGATGTGATAGAA
**
434706 CACT-TGGACATGCCAGAGATTCGCTAAATAATAATGGAAAAAGCTTTCATTGAAACATGCCTTT
66 CACTCT-GACATGCCAGAGATTCGCTAAATAATAATGGAAAAAGCTTTCACCGAAACATGCCTTT
***
434770 CATTTTGGATGGGAT-GAAACACTCTGACATGACAAAGATTACCTAAATAATAATGGAAAACAC-
130 CATTTCAAATGGGATAG-AACACTCTGACATGACAAAGATTACCTAAATAATAATGGAAAACACT
*
434833 TTCTCTCGAAACACGCCTTTCATTTCA
194 TTCCCT-GAAACACGCCTTTCATTTCA
434860 GATGAGATTA
Statistics
Matches: 187, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
248 7 0.04
249 180 0.96
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (249 bp):
ATTCTCTGAATAATAATGGAAAACACTTTCCCCAAAACACACATTTCATTTCGGATGTGATAGAA
CACTCTGACATGCCAGAGATTCGCTAAATAATAATGGAAAAAGCTTTCACCGAAACATGCCTTTC
ATTTCAAATGGGATAGAACACTCTGACATGACAAAGATTACCTAAATAATAATGGAAAACACTTT
CCCTGAAACACGCCTTTCATTTCAAATGGGATGGAACACTCTGACATGGTAAAT
Found at i:435749 original size:31 final size:31
Alignment explanation
Indices: 435711--435835 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
435701 CCCGAAGGAC
* * *
435711 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
435742 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
435773 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
435804 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
435835 C
1 C
435836 CCTCGACCCT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:440437 original size:31 final size:31
Alignment explanation
Indices: 440402--440482 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
440392 TCCATAGATT
* * *
440402 CCGAAAAACCTAGGTAATCACTCCATATGTC
1 CCGAAGAACATAGGTAAACACTCCATATGTC
*
440433 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACACTCCATATGTC
440464 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
440483 CCTCGACCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACACTCCATATGTC
Found at i:442780 original size:26 final size:27
Alignment explanation
Indices: 442749--442799 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
442739 CTATAAAAAT
*
442749 AACAAACCATGAAT-ATTACATTAAAC
1 AACAAACCATGAATCATGACATTAAAC
* *
442775 AACAAACTATTAATCATGACATTAA
1 AACAAACCATGAATCATGACATTAA
442800 GAATACCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.25
Consensus pattern (27 bp):
AACAAACCATGAATCATGACATTAAAC
Found at i:444780 original size:13 final size:13
Alignment explanation
Indices: 444742--444783 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
444732 AATGAGATTC
444742 AAATTAT-ATCAATA
1 AAATTATAAT-AA-A
444756 AAATTA-AATAAA
1 AAATTATAATAAA
444768 AAATTATAATAAA
1 AAATTATAATAAA
444781 AAA
1 AAA
444784 CATACTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.27
13 11 0.42
14 8 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATTATAATAAA
Found at i:448255 original size:78 final size:78
Alignment explanation
Indices: 448166--448315 Score: 291
Period size: 78 Copynumber: 1.9 Consensus size: 78
448156 TATACTTCCT
448166 TGTAATCATCTTATACTATTACAAAAACTTGTATATTTTACTATTCTCTCTCTCTATTTATATAT
1 TGTAATCATCTTATACTATTACAAAAACTTGTATATTTTACTATTCTCTCTCTCTATTTATATAT
448231 ATATATATATAAC
66 ATATATATATAAC
*
448244 TGTAATCATCTTATACTATTACAAAAACTTGTATATTTTACTATTCTCTCTCTCTCTTTATATAT
1 TGTAATCATCTTATACTATTACAAAAACTTGTATATTTTACTATTCTCTCTCTCTATTTATATAT
448309 ATATATA
66 ATATATA
448316 GTTAGTTAGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (78 bp):
TGTAATCATCTTATACTATTACAAAAACTTGTATATTTTACTATTCTCTCTCTCTATTTATATAT
ATATATATATAAC
Found at i:448641 original size:36 final size:36
Alignment explanation
Indices: 448549--448642 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
448539 TCGGAGATGA
* *
448549 TAAATGGGGACGGGGACGGGAAAAAACCGCATGTTT
1 TAAATGGGGACGGGGACGGGGAAAAACCGAATGTTT
*
448585 TAAATGGGGACGGGGACGGGGAAAAACTGAATGTTT
1 TAAATGGGGACGGGGACGGGGAAAAACCGAATGTTT
*
448621 TAAATGGGGACGGAGACGGGGA
1 TAAATGGGGACGGGGACGGGGA
448643 CGAGTTTGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.33, C:0.11, G:0.40, T:0.16
Consensus pattern (36 bp):
TAAATGGGGACGGGGACGGGGAAAAACCGAATGTTT
Found at i:448727 original size:2 final size:2
Alignment explanation
Indices: 448720--448829 Score: 65
Period size: 2 Copynumber: 58.5 Consensus size: 2
448710 AAATAATTAT
* *
448720 TA TA TA TA TA TA TA TT TA TA TA TA TA TA -A TA T- TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
448759 TT TA -A TT TA -A GT- TA AA AA 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
* * * *
448799 -A TA TT TA TA TA TT TA -A TT TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
448830 TCGGCCTGAT
Statistics
Matches: 81, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
1 8 0.10
2 73 0.90
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:451254 original size:24 final size:27
Alignment explanation
Indices: 451203--451254 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
451193 CGTTTTTGGA
451203 GTATTATGCATGTATTAAATATACTTAT
1 GTATTATGCATGTATTAAATATA-TTAT
*
451231 GTATTATGTA-GTA-TAAATAT-TTAT
1 GTATTATGCATGTATTAAATATATTAT
451255 ATGTGTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.17
26 7 0.30
27 3 0.13
28 9 0.39
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (27 bp):
GTATTATGCATGTATTAAATATATTAT
Found at i:461107 original size:19 final size:19
Alignment explanation
Indices: 461083--461119 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
461073 ATGACCAACA
461083 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
461102 AAATCGCAATGCGATCTC
1 AAATCGCAATGCGATCTC
461120 CAGTATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:461218 original size:21 final size:21
Alignment explanation
Indices: 461192--461247 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
461182 ACTATCGCAA
*
461192 TGCGATAGTCCAAATTTGCGT
1 TGCGATAGTCCAAATTCGCGT
*
461213 TGCGATAGTCCGAATTCGCGT
1 TGCGATAGTCCAAATTCGCGT
461234 TGCGATAGTCCAAA
1 TGCGATAGTCCAAA
461248 ATCATTGCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCCAAATTCGCGT
Found at i:461285 original size:21 final size:21
Alignment explanation
Indices: 461255--461302 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
461245 AAAATCATTG
*
461255 CGATAACACTGTTCACCGTTA
1 CGATAGCACTGTTCACCGTTA
* *
461276 CGATAGCACTGTTCACTGTTG
1 CGATAGCACTGTTCACCGTTA
461297 CGATAG
1 CGATAG
461303 TCTGAATTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (21 bp):
CGATAGCACTGTTCACCGTTA
Found at i:461299 original size:42 final size:42
Alignment explanation
Indices: 461252--461478 Score: 178
Period size: 42 Copynumber: 5.5 Consensus size: 42
461242 TCCAAAATCA
* *
461252 TTGCGATAACACTGTTCACCGTTACGATAGCACTGTTCACTG
1 TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCACCG
** * ***
461294 TTGCGAT-AGTCTGAATTC-GCGTTGCGATAGTC-CAAAATCA---
1 TTGCGATAACACTG--TTCACCGTTGCGATAG-CAC-TGTTCACCG
* * *
461334 TTGCGATAGCATTGTTCACAGTTGCGATAGCACTGTTCACCG
1 TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCACCG
* * * *
461376 TTGCGATAGCACTGTTCACCGTTGCGATAACAATGTTCACTG
1 TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCACCG
** ** * *
461418 TTGCGATAACACTGTTCACTTTTGCGATAATATTGTTCACCA
1 TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCACCG
*
461460 TTGCGATAGCACTGTTCAC
1 TTGCGATAACACTGTTCAC
461479 ATTGCGAATT
Statistics
Matches: 146, Mismatches: 29, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
39 7 0.05
40 18 0.12
41 6 0.04
42 108 0.74
43 7 0.05
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (42 bp):
TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCACCG
Found at i:461331 original size:82 final size:82
Alignment explanation
Indices: 461210--461384 Score: 296
Period size: 82 Copynumber: 2.1 Consensus size: 82
461200 TCCAAATTTG
*
461210 CGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTT
1 CGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACAGTT
461275 ACGATAGCACTGTTCAC
66 ACGATAGCACTGTTCAC
* * * *
461292 TGTTGCGATAGTCTGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAGCATTGTTCACAGTT
1 CGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACAGTT
*
461357 GCGATAGCACTGTTCAC
66 ACGATAGCACTGTTCAC
461374 CGTTGCGATAG
1 CGTTGCGATAG
461385 CACTGTTCAC
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (82 bp):
CGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACAGTT
ACGATAGCACTGTTCAC
Found at i:461360 original size:21 final size:21
Alignment explanation
Indices: 461334--461485 Score: 173
Period size: 21 Copynumber: 7.3 Consensus size: 21
461324 TCCAAAATCA
*
461334 TTGCGATAGCATTGTTCACAG
1 TTGCGATAGCACTGTTCACAG
*
461355 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACAG
*
461376 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACAG
* * *
461397 TTGCGATAACAATGTTCACTG
1 TTGCGATAGCACTGTTCACAG
* **
461418 TTGCGATAACACTGTTCACTT
1 TTGCGATAGCACTGTTCACAG
** *
461439 TTGCGATAATATTGTTCACCA-
1 TTGCGATAGCACTGTTCA-CAG
461460 TTGCGATAGCACTGTTCACA-
1 TTGCGATAGCACTGTTCACAG
461480 TTGCGA
1 TTGCGA
461486 ATTTACGATA
Statistics
Matches: 117, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
20 8 0.07
21 108 0.92
22 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACAG
Found at i:461399 original size:82 final size:81
Alignment explanation
Indices: 461210--461404 Score: 257
Period size: 82 Copynumber: 2.4 Consensus size: 81
461200 TCCAAATTTG
* * * *
461210 CGTTGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTT
1 CGTTGCGATAGACTG-ATTCCCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACAGTT
461275 ACGATAGCACTGTTCAC
65 ACGATAGCACTGTTCAC
* * * * *
461292 TGTTGCGATAGTCTGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAGCATTGTTCACAGTT
1 CGTTGCGATAGACTG-ATTCCCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACAGTT
*
461357 GCGATAGCACTGTTCAC
65 ACGATAGCACTGTTCAC
461374 CGTTGCGATAGCACTG-TTCACCGTTGCGATA
1 CGTTGCGATAG-ACTGATTC-CCGTTGCGATA
461405 ACAATGTTCA
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
81 3 0.03
82 96 0.94
83 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (81 bp):
CGTTGCGATAGACTGATTCCCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACAGTTA
CGATAGCACTGTTCAC
Found at i:461422 original size:63 final size:63
Alignment explanation
Indices: 461252--461478 Score: 214
Period size: 63 Copynumber: 3.6 Consensus size: 63
461242 TCCAAAATCA
* * *
461252 TTGCGATAACACTGTTCACCGTTACGATAGCACTGTTCACTGTTGCGATAG-TCTGAATTC-GCG
1 TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCACTGTTGCGATAGCACTG--TTCACCG
* *** * *
461315 TTGCGATAGTC-CAAAATCA---TTGCGATAGCATTGTTCACAGTTGCGATAGCACTGTTCACCG
1 TTGCGATA-ACAC-TGTTCACCGTTGCGATAGCACTGTTCACTGTTGCGATAGCACTGTTCACCG
* * * * **
461376 TTGCGATAGCACTGTTCACCGTTGCGATAACAATGTTCACTGTTGCGATAACACTGTTCACTT
1 TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCACTGTTGCGATAGCACTGTTCACCG
* * *
461439 TTGCGATAATATTGTTCACCATTGCGATAGCACTGTTCAC
1 TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCAC
461479 ATTGCGAATT
Statistics
Matches: 131, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
60 7 0.05
61 38 0.29
62 3 0.02
63 79 0.60
64 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (63 bp):
TTGCGATAACACTGTTCACCGTTGCGATAGCACTGTTCACTGTTGCGATAGCACTGTTCACCG
Found at i:461662 original size:16 final size:17
Alignment explanation
Indices: 461635--461686 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
461625 TTTATTTATG
461635 ATAAACTATAAATTTTAA
1 ATAAA-TATAAATTTTAA
*
461653 AT-AATATAAA-ATTAA
1 ATAAATATAAATTTTAA
*
461668 ATAAATATAAATTCTAA
1 ATAAATATAAATTTTAA
461685 AT
1 AT
461687 TATTTATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 14 0.48
17 7 0.24
18 2 0.07
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAATATAAATTTTAA
Found at i:462164 original size:21 final size:21
Alignment explanation
Indices: 462133--462264 Score: 187
Period size: 21 Copynumber: 6.4 Consensus size: 21
462123 TATCGCAAAT
462133 TCGCAAT-GTGAACAGTGTTA
1 TCGCAATGGTGAACAGTGTTA
*
462153 TCGTAATGGTGAACAGTGTTA
1 TCGCAATGGTGAACAGTGTTA
* *
462174 TCGTAACGGTGAACAGTGTTA
1 TCGCAATGGTGAACAGTGTTA
* *
462195 TCGCAAT-GTGAACAATGCTA
1 TCGCAATGGTGAACAGTGTTA
*
462215 TCGCAATGGTGAACAGTATTA
1 TCGCAATGGTGAACAGTGTTA
*
462236 TCGCAACGGTGAACAGTGTTA
1 TCGCAATGGTGAACAGTGTTA
462257 TCGCAATG
1 TCGCAATG
462265 ATTTTGGACT
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
20 24 0.24
21 74 0.76
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (21 bp):
TCGCAATGGTGAACAGTGTTA
Found at i:462230 original size:62 final size:62
Alignment explanation
Indices: 462133--462264 Score: 219
Period size: 62 Copynumber: 2.1 Consensus size: 62
462123 TATCGCAAAT
* * * * *
462133 TCGCAATGTGAACAGTGTTATCGTAATGGTGAACAGTGTTATCGTAACGGTGAACAGTGTTA
1 TCGCAATGTGAACAATGCTATCGCAATGGTGAACAGTATTATCGCAACGGTGAACAGTGTTA
462195 TCGCAATGTGAACAATGCTATCGCAATGGTGAACAGTATTATCGCAACGGTGAACAGTGTTA
1 TCGCAATGTGAACAATGCTATCGCAATGGTGAACAGTATTATCGCAACGGTGAACAGTGTTA
462257 TCGCAATG
1 TCGCAATG
462265 ATTTTGGACT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (62 bp):
TCGCAATGTGAACAATGCTATCGCAATGGTGAACAGTATTATCGCAACGGTGAACAGTGTTA
Found at i:462261 original size:42 final size:41
Alignment explanation
Indices: 462133--462264 Score: 176
Period size: 41 Copynumber: 3.2 Consensus size: 41
462123 TATCGCAAAT
*
462133 TCGCAAT-GTGAACAGTGTTATCGTAATGGTGAACAGTGTTA
1 TCGCAATGGTGAACAGTGTTATCGCAA-GGTGAACAGTGTTA
* * * * *
462174 TCGTAACGGTGAACAGTGTTATCGCAATGTGAACAATGCTA
1 TCGCAATGGTGAACAGTGTTATCGCAAGGTGAACAGTGTTA
*
462215 TCGCAATGGTGAACAGTATTATCGCAACGGTGAACAGTGTTA
1 TCGCAATGGTGAACAGTGTTATCGCAA-GGTGAACAGTGTTA
462257 TCGCAATG
1 TCGCAATG
462265 ATTTTGGACT
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 40 0.52
42 37 0.48
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (41 bp):
TCGCAATGGTGAACAGTGTTATCGCAAGGTGAACAGTGTTA
Found at i:462345 original size:21 final size:21
Alignment explanation
Indices: 462294--462346 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
462284 CAAATTCGGA
* *
462294 CTATCGCAACGGTGAACAGTG
1 CTATCGCAATGGCGAACAGTG
462315 CTATCGCAATGGCGAACAGTG
1 CTATCGCAATGGCGAACAGTG
*
462336 TTATCGCAATG
1 CTATCGCAATG
462347 ATTTTGGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
CTATCGCAATGGCGAACAGTG
Found at i:462356 original size:61 final size:61
Alignment explanation
Indices: 462291--462447 Score: 232
Period size: 61 Copynumber: 2.6 Consensus size: 61
462281 ACGCAAATTC
* *
462291 GGACTATCGCAACGGTGAA-CAGTG-CTATCGCAATGGCGAACAGTGTTATCGCAATGATTTT
1 GGACTATCGCAACGGCGAATC-G-GACTATCGCAACGGCGAACAGTGTTATCGCAATGATTTT
462352 GGACTATCGCAAC-GCGAATTCGGACTATCGCAACGGCGAACAGTGTTATCGCAATGATTTT
1 GGACTATCGCAACGGCGAA-TCGGACTATCGCAACGGCGAACAGTGTTATCGCAATGATTTT
462413 GGACTATCGCAAC-GCGAATTCGGACTATCGCAACG
1 GGACTATCGCAACGGCGAA-TCGGACTATCGCAACG
462448 TGAATTTGGA
Statistics
Matches: 91, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
60 5 0.05
61 85 0.93
62 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (61 bp):
GGACTATCGCAACGGCGAATCGGACTATCGCAACGGCGAACAGTGTTATCGCAATGATTTT
Found at i:462378 original size:21 final size:21
Alignment explanation
Indices: 462352--462465 Score: 112
Period size: 21 Copynumber: 5.5 Consensus size: 21
462342 CAATGATTTT
462352 GGACTATCGCAACGCGAATTC
1 GGACTATCGCAACGCGAATTC
462373 GGACTATCGCAACGGCGAA--C
1 GGACTATCGCAAC-GCGAATTC
* * * *
462393 AGTG-TTATCGCAA--TGATTTT
1 -G-GACTATCGCAACGCGAATTC
462413 GGACTATCGCAACGCGAATTC
1 GGACTATCGCAACGCGAATTC
* *
462434 GGACTATCGCAACGTGAATTT
1 GGACTATCGCAACGCGAATTC
462455 GGACTATCGCA
1 GGACTATCGCA
462466 TTGCGATAGT
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
18 3 0.04
19 9 0.12
20 1 0.01
21 56 0.75
22 6 0.08
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (21 bp):
GGACTATCGCAACGCGAATTC
Found at i:462406 original size:82 final size:82
Alignment explanation
Indices: 462212--462407 Score: 329
Period size: 82 Copynumber: 2.4 Consensus size: 82
462202 GTGAACAATG
* * * *
462212 CTATCGCAATGGTGAACAGTATTATCGCAACGGTGAACAGTGTTATCGCAATGATTTTGGACTAT
1 CTATCGCAACGGTGAACAGTGTTATCGCAATGGCGAACAGTGTTATCGCAATGATTTTGGACTAT
462277 CGCAACGCAAATTCGGA
66 CGCAACGCAAATTCGGA
*
462294 CTATCGCAACGGTGAACAGTGCTATCGCAATGGCGAACAGTGTTATCGCAATGATTTTGGACTAT
1 CTATCGCAACGGTGAACAGTGTTATCGCAATGGCGAACAGTGTTATCGCAATGATTTTGGACTAT
*
462359 CGCAACGCGAATTCGGA
66 CGCAACGCAAATTCGGA
*
462376 CTATCGCAACGGCGAACAGTGTTATCGCAATG
1 CTATCGCAACGGTGAACAGTGTTATCGCAATG
462408 ATTTTGGACT
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 106 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (82 bp):
CTATCGCAACGGTGAACAGTGTTATCGCAATGGCGAACAGTGTTATCGCAATGATTTTGGACTAT
CGCAACGCAAATTCGGA
Found at i:462438 original size:82 final size:80
Alignment explanation
Indices: 462212--462465 Score: 233
Period size: 82 Copynumber: 3.1 Consensus size: 80
462202 GTGAACAATG
* * ** * * * * *
462212 CTATCGCAATGGTGAACAGTATTATCGCAACGGTGAACAGTGTTATCGCAATGATTTTGGACTAT
1 CTATCGCAACGGCGAACAGTGCTATCGCAA-TG-GAACAGTGCTATCGCAACGAATTCGGACTAT
*
462277 CGCAACGCAAATTCGGA
64 CGCAACGCGAATTCGGA
* * * * *
462294 CTATCGCAACGGTGAACAGTGCTATCGCAATGGCGAACAGTGTTATCGCAATGATTTTGGACTAT
1 CTATCGCAACGGCGAACAGTGCTATCGCAAT-G-GAACAGTGCTATCGCAACGAATTCGGACTAT
462359 CGCAACGCGAATTCGGA
64 CGCAACGCGAATTCGGA
* ***
462376 CTATCGCAACGGCGAACAGTGTTATCGCAAT-G-ATTTTGGACTATCGCAACGCGAATTCGGACT
1 CTATCGCAACGGCGAACAGTGCTATCGCAATGGAACAGT-G-CTATCGCAA--CGAATTCGGACT
* *
462439 ATCGCAACGTGAATTTGGA
62 ATCGCAACGCGAATTCGGA
462458 CTATCGCA
1 CTATCGCA
462466 TTGCGATAGT
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
78 2 0.01
79 2 0.01
80 8 0.05
82 138 0.92
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (80 bp):
CTATCGCAACGGCGAACAGTGCTATCGCAATGGAACAGTGCTATCGCAACGAATTCGGACTATCG
CAACGCGAATTCGGA
Found at i:462465 original size:61 final size:61
Alignment explanation
Indices: 462315--462447 Score: 239
Period size: 61 Copynumber: 2.2 Consensus size: 61
462305 GTGAACAGTG
* *
462315 CTATCGCAATGGCGAACAGTGTTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGA
1 CTATCGCAACGGCGAACAGTGCTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGA
*
462376 CTATCGCAACGGCGAACAGTGTTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGA
1 CTATCGCAACGGCGAACAGTGCTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGA
462437 CTATCGCAACG
1 CTATCGCAACG
462448 TGAATTTGGA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (61 bp):
CTATCGCAACGGCGAACAGTGCTATCGCAATGATTTTGGACTATCGCAACGCGAATTCGGA
Found at i:462485 original size:20 final size:20
Alignment explanation
Indices: 462460--462512 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
462450 AATTTGGACT
462460 ATCGCATTGCGATAGTTAGA
1 ATCGCATTGCGATAGTTAGA
462480 ATCGCATTGCGATAGTTAGA
1 ATCGCATTGCGATAGTTAGA
*
462500 ATCGTATTGCGAT
1 ATCGCATTGCGAT
462513 TTTCCAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTTAGA
Found at i:462582 original size:19 final size:19
Alignment explanation
Indices: 462558--462594 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
462548 TGCGATACTG
*
462558 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
462577 GAGATCGCATTGCGATTT
1 GAGATCACATTGCGATTT
462595 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Found at i:468909 original size:262 final size:264
Alignment explanation
Indices: 468444--468969 Score: 1038
Period size: 262 Copynumber: 2.0 Consensus size: 264
468434 CTTCATCTTC
468444 AATTTCCACAATGAGAAATTTCTTCCATTAAATTTTTCAATATTAAATTTCGTTGCCATAGCTTC
1 AATTTCCACAATGAGAAATTTCTTCCATTAAATTTTTCAATATTAAATTTCGTTGCCATAGCTTC
468509 TATTACGGATAGCTCCCACTATTTCACCATCGTGAATAGTTCTCTAGAACCTTTAAAGAATGGGT
66 TATTACGGATAGCTCCCACTATTTCACCATCGTGAATAGTTCTCTAGAACCTTTAAAGAATGGGT
468574 AATACCTTCTTACTTTCTTATGTTGGAGGATCCACCTTTTGGTGGCAACCACAAAGACAATAAGT
131 AATACCTTCTTACTTTCTTATGTTGGAGGATCCACCTTTTGGTGGCAACCACAAAGACAATAAGT
468639 AGATATTACACACTCAAATCTAG-TTTGATACCAATTGTTGC-GAAGACGGCTATCGAATAGAGC
196 AGATATTACACACTCAAATCTAGTTTTGATACCAATTGTTGCGGAAGACGGCTATCGAATAGAGC
468702 AAAA
261 AAAA
468706 AATTTCCACAATGAGAAATTTCTTCCATTAAATTTTTCAATATTAAATTTCGTTGCCATAGCTTC
1 AATTTCCACAATGAGAAATTTCTTCCATTAAATTTTTCAATATTAAATTTCGTTGCCATAGCTTC
468771 TATTACGGATAGCTCCCACTATTTCACCATCGTGAATAGTTCTCTAGAACCTTTAAAGAATGGGT
66 TATTACGGATAGCTCCCACTATTTCACCATCGTGAATAGTTCTCTAGAACCTTTAAAGAATGGGT
468836 AATACCTTCTTACTTTCTTATGTTGGAGGATCCACCTTTTGGTGGCAACCACAAAGACAATAAGT
131 AATACCTTCTTACTTTCTTATGTTGGAGGATCCACCTTTTGGTGGCAACCACAAAGACAATAAGT
468901 AGATATTACACACTCAAATCTAGTTTTGATACCAATTGTTGCGGAAGACGGCTATCGAATAGAGC
196 AGATATTACACACTCAAATCTAGTTTTGATACCAATTGTTGCGGAAGACGGCTATCGAATAGAGC
468966 AAAA
261 AAAA
468970 TCGCAACTGA
Statistics
Matches: 262, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
262 218 0.83
263 18 0.07
264 26 0.10
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (264 bp):
AATTTCCACAATGAGAAATTTCTTCCATTAAATTTTTCAATATTAAATTTCGTTGCCATAGCTTC
TATTACGGATAGCTCCCACTATTTCACCATCGTGAATAGTTCTCTAGAACCTTTAAAGAATGGGT
AATACCTTCTTACTTTCTTATGTTGGAGGATCCACCTTTTGGTGGCAACCACAAAGACAATAAGT
AGATATTACACACTCAAATCTAGTTTTGATACCAATTGTTGCGGAAGACGGCTATCGAATAGAGC
AAAA
Found at i:470008 original size:21 final size:21
Alignment explanation
Indices: 469984--470042 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
469974 GTCCGAGTTA
469984 TCCGCGACGGCCGCAATAGCG
1 TCCGCGACGGCCGCAATAGCG
*
470005 TCCGCGACGACCGCAATAGCG
1 TCCGCGACGGCCGCAATAGCG
* *
470026 CCCACGACGGCCGCAAT
1 TCCGCGACGGCCGCAAT
470043 CACGGTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.41, G:0.29, T:0.08
Consensus pattern (21 bp):
TCCGCGACGGCCGCAATAGCG
Found at i:474845 original size:11 final size:11
Alignment explanation
Indices: 474829--474884 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
474819 ATATTTTATA
474829 ATTTAAATTTT
1 ATTTAAATTTT
474840 ATTTAAATTTT
1 ATTTAAATTTT
*
474851 -TTTGAATTGAATT
1 ATTTAAATT---TT
474864 ATTTAAACTTTT
1 ATTTAAA-TTTT
474876 ATTTAAATT
1 ATTTAAATT
474885 ATAATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 7 0.18
11 13 0.34
12 9 0.24
13 2 0.05
14 5 0.13
15 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (11 bp):
ATTTAAATTTT
Found at i:474869 original size:24 final size:27
Alignment explanation
Indices: 474838--474894 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 27
474828 AATTTAAATT
*
474838 TTATTTAAA-TTTT-TTTGAATT-GAA
1 TTATTTAAACTTTTATTTAAATTAGAA
*
474862 TTATTTAAACTTTTATTTAAATTATAA
1 TTATTTAAACTTTTATTTAAATTAGAA
474889 TTATTT
1 TTATTT
474895 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 9 0.32
25 4 0.14
26 7 0.25
27 8 0.29
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (27 bp):
TTATTTAAACTTTTATTTAAATTAGAA
Found at i:483911 original size:22 final size:21
Alignment explanation
Indices: 483859--483934 Score: 56
Period size: 20 Copynumber: 3.8 Consensus size: 21
483849 ATATCCCAAA
483859 TTAATAAAAA-ATTTATAGTT
1 TTAATAAAAATATTTATAGTT
* ** *
483879 ATAATTTAAATATTTAATATTT
1 TTAATAAAAATATTT-ATAGTT
483901 TTAAT-AAAA-A-TTATA-TT
1 TTAATAAAAATATTTATAGTT
483918 TT-ATAAAAATAATTTAT
1 TTAATAAAAAT-ATTTAT
483935 GAATTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.05
17 8 0.18
18 3 0.07
19 3 0.07
20 12 0.27
21 7 0.16
22 9 0.20
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TTAATAAAAATATTTATAGTT
Found at i:485190 original size:17 final size:17
Alignment explanation
Indices: 485165--485201 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
485155 CTCAATGAAT
485165 AATTGTAAATTAGTTAA
1 AATTGTAAATTAGTTAA
* *
485182 AATTTTAAATTATTTAA
1 AATTGTAAATTAGTTAA
485199 AAT
1 AAT
485202 AAAGGGTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
AATTGTAAATTAGTTAA
Found at i:485230 original size:127 final size:127
Alignment explanation
Indices: 485082--485336 Score: 494
Period size: 127 Copynumber: 2.0 Consensus size: 127
485072 TTTATAGTGC
485082 ACGACGAGCAGAGATGAACACTACTAACAACGAGACCATTAATTTAATTTATAAGAATTTAAATT
1 ACGACGAGCAGAGATGAACACTACTAACAACGAGACCATTAATTTAATTTATAAGAATTTAAATT
485147 CTAAATGGCTCAATGAATAATTGTAAATTAGTTAAAATTTTAAATTATTTAAAATAAAGGGT
66 CTAAATGGCTCAATGAATAATTGTAAATTAGTTAAAATTTTAAATTATTTAAAATAAAGGGT
485209 ACGACGAGCATG-GATGAACACTACTAACAACGAGACCATTAATTTAATTTATAAGAATTTAAAT
1 ACGACGAGCA-GAGATGAACACTACTAACAACGAGACCATTAATTTAATTTATAAGAATTTAAAT
485273 TCTAAATGGCTCAATGAATAATTGTAAATTAGTTAAAATTTTAAATTATTTAAAATAAAGGGT
65 TCTAAATGGCTCAATGAATAATTGTAAATTAGTTAAAATTTTAAATTATTTAAAATAAAGGGT
485336 A
1 A
485337 AAATATATTA
Statistics
Matches: 127, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
127 126 0.99
128 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (127 bp):
ACGACGAGCAGAGATGAACACTACTAACAACGAGACCATTAATTTAATTTATAAGAATTTAAATT
CTAAATGGCTCAATGAATAATTGTAAATTAGTTAAAATTTTAAATTATTTAAAATAAAGGGT
Found at i:485317 original size:17 final size:17
Alignment explanation
Indices: 485292--485328 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
485282 CTCAATGAAT
485292 AATTGTAAATTAGTTAA
1 AATTGTAAATTAGTTAA
* *
485309 AATTTTAAATTATTTAA
1 AATTGTAAATTAGTTAA
485326 AAT
1 AAT
485329 AAAGGGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
AATTGTAAATTAGTTAA
Found at i:486551 original size:23 final size:23
Alignment explanation
Indices: 486525--486664 Score: 172
Period size: 23 Copynumber: 6.1 Consensus size: 23
486515 TACCATGTAA
* *
486525 AAATGTCCCGAAGGACCACATAG
1 AAATGTCCCGAAGGACCGCGTAG
*
486548 AAATGTCCTGAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCGCGTAG
* *
486571 AAATGTCCCTAAGGAACGCGTAG
1 AAATGTCCCGAAGGACCGCGTAG
*
486594 AAATGTCCCTAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCGCGTAG
* * * *
486617 AAATGTCCTGAAGAACCACATAG
1 AAATGTCCCGAAGGACCGCGTAG
* *
486640 AATTATCCCGAAGGACCGCGTAG
1 AAATGTCCCGAAGGACCGCGTAG
486663 AA
1 AA
486665 CCCTCGACTC
Statistics
Matches: 99, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 99 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (23 bp):
AAATGTCCCGAAGGACCGCGTAG
Found at i:486618 original size:69 final size:69
Alignment explanation
Indices: 486525--486664 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 69
486515 TACCATGTAA
* * * * *
486525 AAATGTCCCGAAGGACCACATAGAAATGTCCTGAAGGACCGCGTAGAAATGTCCCTAAGGAACGC
1 AAATGTCCCGAAGGACCACATAGAAATGTCCTGAAGAACCACATAGAAATATCCCGAAGGAACGC
486590 GTAG
66 GTAG
* * * * *
486594 AAATGTCCCTAAGGACCGCGTAGAAATGTCCTGAAGAACCACATAGAATTATCCCGAAGGACCGC
1 AAATGTCCCGAAGGACCACATAGAAATGTCCTGAAGAACCACATAGAAATATCCCGAAGGAACGC
486659 GTAG
66 GTAG
486663 AA
1 AA
486665 CCCTCGACTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (69 bp):
AAATGTCCCGAAGGACCACATAGAAATGTCCTGAAGAACCACATAGAAATATCCCGAAGGAACGC
GTAG
Found at i:488738 original size:65 final size:65
Alignment explanation
Indices: 488540--488749 Score: 234
Period size: 65 Copynumber: 3.2 Consensus size: 65
488530 TGGACCCTTA
* * ** *
488540 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCA-GAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCATG-GTGCATCGATGCATGGTT
488603 G
65 G
* * *
488604 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATTC-TCAGTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAATTCAT-GGTGCATCGATGCATGGT
488667 AT-
64 -TG
* *
488669 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCATGGTGCATCGATGCATGG-TT
488733 G
65 G
*
488734 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
488750 CTCTGAAAAT
Statistics
Matches: 122, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
63 3 0.02
64 53 0.43
65 65 0.53
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCATGGTGCATCGATGCATGGTTG
Found at i:489151 original size:16 final size:16
Alignment explanation
Indices: 489104--489152 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
489094 CACCTTACTA
*
489104 TAACACTTCTCCCCTT
1 TAACACTTCTCCCCCT
* * **
489120 TAAAACTTTTAACCCT
1 TAACACTTCTCCCCCT
489136 TAACACTTCTCCCCCT
1 TAACACTTCTCCCCCT
489152 T
1 T
489153 TTTGTTAAAT
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (16 bp):
TAACACTTCTCCCCCT
Found at i:493798 original size:15 final size:15
Alignment explanation
Indices: 493778--493807 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
493768 ACTAATTGCA
493778 CATATAAACAATTAC
1 CATATAAACAATTAC
*
493793 CATATAAACACTTAC
1 CATATAAACAATTAC
493808 ACGCTAAGTC
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:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (15 bp):
CATATAAACAATTAC
Found at i:495209 original size:23 final size:23
Alignment explanation
Indices: 495183--495354 Score: 146
Period size: 23 Copynumber: 7.3 Consensus size: 23
495173 CACCACAGCT
*
495183 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
495206 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* * *
495229 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* * *
495252 TATAATAATTGCACCGGAGTACCG
1 CAT-ATAATTGCACCGGAGTGCCA
* * **
495276 CGTAGAATTGCACCGTTGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* *
495299 TATAATAATTGCACCGGAGTGCCG
1 CAT-ATAATTGCACCGGAGTGCCA
* * **
495323 CGTAGAATTGCACCATAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
495346 TATAATAAT
1 CAT-ATAAT
495355 GACCATAAGG
Statistics
Matches: 112, Mismatches: 34, Indels: 5
0.74 0.23 0.03
Matches are distributed among these distances:
23 74 0.66
24 38 0.34
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:495277 original size:47 final size:47
Alignment explanation
Indices: 495188--495354 Score: 282
Period size: 47 Copynumber: 3.6 Consensus size: 47
495178 CAGCTCATAT
* *
495188 AATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
*
495234 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTACCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
*
495281 AATTGCACCGTTGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
*
495328 AATTGCACCATAGTGCCATATAATAAT
1 AATTGCACCGTAGTGCCATATAATAAT
495355 GACCATAAGG
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 19 0.17
47 94 0.83
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (47 bp):
AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
Found at i:495495 original size:103 final size:103
Alignment explanation
Indices: 495361--495578 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
495351 TAATGACCAT
* *
495361 AAGGATCACATATCATTCCTTAAGAATCATATACATAT-ACAAGGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGACAA-GGATCAAGTATGTGTCTAACC
495425 AGACTTCACACATGTTCCAAATAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAATAATACATATATGTCCCG
*
495464 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTAACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGACAAGGATCAAGTATGTGTCTAACCA
495529 GACTTCACACATGTTCCAAATAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAATAATACATATATGTCCCG
495567 AAGGACCACATA
1 AAGGACCACATA
495579 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 108 0.97
104 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGACAAGGATCAAGTATGTGTCTAACCA
GACTTCACACATGTTCCAAATAATACATATATGTCCCG
Found at i:496292 original size:21 final size:22
Alignment explanation
Indices: 496254--496294 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
496244 TTTTCCTTTA
496254 GGGGGAATCGGTTCCCTCCTGT
1 GGGGGAATCGGTTCCCTCCTGT
* *
496276 GGGGGTATTGGTT-CCTCCT
1 GGGGGAATCGGTTCCCTCCT
496295 TGATATTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.07, C:0.24, G:0.37, T:0.32
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTCCTGT
Found at i:497125 original size:23 final size:23
Alignment explanation
Indices: 497099--497167 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
497089 CACCACAACT
*
497099 CATATAATTGCGCCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
497122 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * * *
497145 CGTAGAATTGCACTGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
497168 TACAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:497346 original size:103 final size:102
Alignment explanation
Indices: 497186--497400 Score: 367
Period size: 103 Copynumber: 2.1 Consensus size: 102
497176 TGTCCATAAG
* * *
497186 GACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
497251 TTCACACATGTTCCAAAGAATACATATATATCCCGAA
66 TTCACACATGTTCCAAAGAATACATATATATCCCGAA
*
497288 TGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGA
1 -GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGA
*
497353 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
65 CTTCACACATGTTCCAAAGAATACATATATATCCCGAA
497391 GAACCACATA
1 G-ACCACATA
497401 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 105 0.99
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (102 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATATCCCGAA
Found at i:498339 original size:64 final size:63
Alignment explanation
Indices: 498187--498348 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 63
498177 TTCCCTATCG
* * ** * ** *
498187 GTGCATCGATGTACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTTTATTACTGG
1 GTGCATCGATGCACTACCTGTGCATCGATGCACCAAATACATTCGATGTTTGTTGATTAAAGA
* * * *
498250 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGCATTCGATGTTT-TTAGATTAAAA
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACCAAATACATTCGATGTTTGTT-GATT-AAA
498313 GA
62 GA
*
498315 GTGCATCGATGCACTACCTGTGCATCGATACACC
1 GTGCATCGATGCACTACCTGTGCATCGATGCACC
498349 TTCAAACAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
63 6 0.08
64 67 0.85
65 6 0.08
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACCAAATACATTCGATGTTTGTTGATTAAAGA
Found at i:502993 original size:23 final size:23
Alignment explanation
Indices: 502967--503044 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
502957 CACCACAGCT
502967 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
502990 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
503013 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
503036 TATAATAAT
1 CAT-ATAAT
503045 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:503222 original size:103 final size:103
Alignment explanation
Indices: 503051--503268 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
503041 TAATGTCCAT
*
503051 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
*
503116 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
503154 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGAGATCAAGTATGTGTCTCACC
503218 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
503257 AAGGACCACATA
1 AAGGACCACATA
503269 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 108 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:507539 original size:64 final size:65
Alignment explanation
Indices: 507471--507630 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
507461 TGAACCCTTA
* *
507471 GTGCATCGATGCATCAAGTGCATTCGATGTTTT-A-AAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCACAAA-AGCCACAGTGCATCGATGCATGG-T
507534 -G
64 AG
* * * *
507535 GTGCATCGATGCATCAAATGCATTCGATGTTTTCACAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCACAAAAGCCACAGTGCATCGATGCATGGTAG
*
507600 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
507631 CAATTTAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 33 0.38
65 50 0.58
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCACAAAAGCCACAGTGCATCGATGCATGGTAG
Found at i:507669 original size:65 final size:63
Alignment explanation
Indices: 507471--507672 Score: 214
Period size: 65 Copynumber: 3.1 Consensus size: 63
507461 TGAACCCTTA
* * * * *
507471 GTGCATCGATGCATCAAGTGCATTCGATGTTTTAA-AATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAA-A-TCATAGTGCATCGATGCATGGTTG
* *
507535 GTGCATCGATGCATCAAATGCATTCGATGTTTTCACA-AAATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-ATAAATCAT-AGTGCATCGATGCATGGT-
507599 T-
62 TG
* *
507600 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA--TAAATCATAGTGCATCGATGCATGG-TT
507664 G
63 G
507665 GTGCATCG
1 GTGCATCG
507673 GTGCCTCACT
Statistics
Matches: 118, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.39
65 63 0.53
66 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAATCATAGTGCATCGATGCATGGTTG
Found at i:513371 original size:6 final size:6
Alignment explanation
Indices: 513360--513469 Score: 197
Period size: 6 Copynumber: 18.7 Consensus size: 6
513350 TGTCTATATG
513360 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TG--TA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
*
513406 TGTATA TGTATA TGTATA TGTATA TGTATA TATATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
513454 TGTATA TGTATA TGTA
1 TGTATA TGTATA TGTA
513470 ATTGTTTGAG
Statistics
Matches: 100, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
4 4 0.04
6 96 0.96
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:529277 original size:75 final size:75
Alignment explanation
Indices: 529127--529334 Score: 274
Period size: 75 Copynumber: 2.8 Consensus size: 75
529117 CAAAGCCAAA
* ** * **
529127 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
529192 TTGGCTCCGAG
65 TTGGCTCCGAG
*
529203 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
529268 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
529278 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
529335 TGTACAACGG
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
75 86 0.74
76 31 0.26
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:532385 original size:2 final size:2
Alignment explanation
Indices: 532378--532418 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
532368 TAGAAAATCA
*
532378 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
532419 TGATACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:535730 original size:280 final size:281
Alignment explanation
Indices: 535214--535772 Score: 906
Period size: 281 Copynumber: 2.0 Consensus size: 281
535204 ATGGATTTTC
*
535214 ACATCACATGCTCATGGGATCTCTCGCCATGTGTTCTACGCAATTGAGTTTAGAATTGAAAAAAA
1 ACATCACATGCTCATGGGATCTCTCGCCATGCGTTCTACGCAATTGAGTTTAGAATTGAAAAAAA
* *
535279 TAAGGGTAAAGTACACAAATGGTCCCATGATTACAGGATACTAGTTTATTGAGTCACTAGATTAT
66 TAAGGGCAAAGTACACAAATGGTCCCATGATTACAGGATACTAGTTTATTAAGTCACTAGATTAT
* * *
535344 TAAAAGTTACAAAATGATCCTTCGACTATATGACATTGCTTTGTCGAGTCCATCGACTATTAAAA
131 TAAAAGTTACAAAATGATCCCTCGACTATATGACATTACTTTGTCGAGTCCATCGACAATTAAAA
*
535409 ATAAAAAAAATGGTAATTTGACTATTTATTGTGTTCTAAACGCATCATTTTTCGTT-AAAAAATG
196 ATAAAAAAAATGGTAATTTGACTATTCATTGTGTTCTAAACGCATCATTTTTCGTTAAAAAAATG
*
535473 ATAGTAGTTTGAGCTAGATGT
261 ATAGCAGTTTGAGCTAGATGT
* * *
535494 ACATCACATGCTTATGGGATCTTTCGCCATGCGTTCTATGCAATTGAGTTTAGAATTGAAAAAAA
1 ACATCACATGCTCATGGGATCTCTCGCCATGCGTTCTACGCAATTGAGTTTAGAATTG-AAAAAA
* * * *
535559 ATAAGGGCAAAGTACACAAATGGTCCCGTGGTTATAGGATACTAGTTTATTAAGTTACTAGATTA
65 ATAAGGGCAAAGTACACAAATGGTCCCATGATTACAGGATACTAGTTTATTAAGTCACTAGATTA
* *
535624 TTAAAAGTTACAAAATGATCCCTCGACTATATGACATTACTTTGTTGAGTCCCTCGACAATTAAA
130 TTAAAAGTTACAAAATGATCCCTCGACTATATGACATTACTTTGTCGAGTCCATCGACAATTAAA
* * * *
535689 AAT-TACAAAATGGTCATTTGACTATTCATTGTGTTCTAAACGCATCCTTTTTCGTTAAAAAAAT
195 AATAAAAAAAATGGTAATTTGACTATTCATTGTGTTCTAAACGCATCATTTTTCGTTAAAAAAAT
535753 GATAGCAGTTTGAGCTAGAT
260 GATAGCAGTTTGAGCTAGAT
535773 TTTAACCTAC
Statistics
Matches: 256, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
280 102 0.40
281 154 0.60
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (281 bp):
ACATCACATGCTCATGGGATCTCTCGCCATGCGTTCTACGCAATTGAGTTTAGAATTGAAAAAAA
TAAGGGCAAAGTACACAAATGGTCCCATGATTACAGGATACTAGTTTATTAAGTCACTAGATTAT
TAAAAGTTACAAAATGATCCCTCGACTATATGACATTACTTTGTCGAGTCCATCGACAATTAAAA
ATAAAAAAAATGGTAATTTGACTATTCATTGTGTTCTAAACGCATCATTTTTCGTTAAAAAAATG
ATAGCAGTTTGAGCTAGATGT
Found at i:537598 original size:18 final size:17
Alignment explanation
Indices: 537575--537609 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
537565 CATTGGCGTA
537575 TAACAACATCTACAACAT
1 TAACAACATC-ACAACAT
*
537593 TAACAATATCACAACAT
1 TAACAACATCACAACAT
537610 CAGGGTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (17 bp):
TAACAACATCACAACAT
Found at i:539992 original size:16 final size:16
Alignment explanation
Indices: 539964--540015 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
539954 CGTATCGACG
539964 ACAAAATTTTACTATTC
1 ACAAAA-TTTACTATTC
539981 ACAAAATTTACTATTC
1 ACAAAATTTACTATTC
539997 ACAAAATTTACTATTC
1 ACAAAATTTACTATTC
540013 ACA
1 ACA
540016 TGAATAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 29 0.83
17 6 0.17
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (16 bp):
ACAAAATTTACTATTC
Found at i:540724 original size:15 final size:16
Alignment explanation
Indices: 540704--540744 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
540694 CTCCGTGGTT
540704 GTCTTGTCCC-TCAAC
1 GTCTTGTCCCTTCAAC
540719 GTCTTGGCTCCCTTCAAC
1 GTCTT-G-TCCCTTCAAC
540737 -TCTTGTCC
1 GTCTTGTCC
540745 ACTAGTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 8 0.35
18 5 0.22
ACGTcount: A:0.10, C:0.39, G:0.15, T:0.37
Consensus pattern (16 bp):
GTCTTGTCCCTTCAAC
Found at i:540989 original size:33 final size:33
Alignment explanation
Indices: 540947--541023 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
540937 CAACGTCTTT
540947 TCGATCCTGGGTTCGTCCTCTTCTCTGGACAAC
1 TCGATCCTGGGTTCGTCCTCTTCTCTGGACAAC
540980 TCGATCCTGGGTTCGTCCTCTTCTCTGGACAAC
1 TCGATCCTGGGTTCGTCCTCTTCTCTGGACAAC
*
541013 TCGATCATGGG
1 TCGATCCTGGG
541024 CTCATCCATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.13, C:0.31, G:0.23, T:0.32
Consensus pattern (33 bp):
TCGATCCTGGGTTCGTCCTCTTCTCTGGACAAC
Found at i:541547 original size:17 final size:17
Alignment explanation
Indices: 541525--541557 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
541515 TATGCCTAAG
541525 ACGCCTCAACTTGGACT
1 ACGCCTCAACTTGGACT
541542 ACGCCTCAACTTGGAC
1 ACGCCTCAACTTGGAC
541558 CACACTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.21
Consensus pattern (17 bp):
ACGCCTCAACTTGGACT
Found at i:541567 original size:17 final size:17
Alignment explanation
Indices: 541528--541567 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
541518 GCCTAAGACG
* *
541528 CCTCAACTTGGACTACG
1 CCTCAACTTGGACCACA
541545 CCTCAACTTGGACCACA
1 CCTCAACTTGGACCACA
*
541562 CTTCAA
1 CCTCAA
541568 TCCTGGTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.38, G:0.12, T:0.23
Consensus pattern (17 bp):
CCTCAACTTGGACCACA
Found at i:542461 original size:16 final size:17
Alignment explanation
Indices: 542430--542463 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
542420 CGTATCTCCG
*
542430 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
542447 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
542463 A
1 A
542464 TGTGAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:543871 original size:21 final size:21
Alignment explanation
Indices: 543845--543888 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
543835 ATTCTGGGCT
* *
543845 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
543866 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
543887 AG
1 AG
543889 CGAATAAAAT
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:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:544731 original size:31 final size:31
Alignment explanation
Indices: 544647--544770 Score: 119
Period size: 31 Copynumber: 4.0 Consensus size: 31
544637 GAGTCGAGGG
* *
544647 TACCTATGTTCTACGGAAAATATGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* *
544678 TTACCTATG-TCTTTC-GAGACATATGGATAGTA
1 -TACCTATGTTC-TACGGA-ACATATGGACAGTA
*
544710 TACCTATGTTCTAAGGAACATATGGACAGT-
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
544740 TCACCTAGGTTCTTCGGAACCTATGGACAGT
1 T-ACCTATGTTCTACGGAACATATGGACAGT
544771 TGCCGAGGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.01
31 50 0.66
32 25 0.33
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:544809 original size:30 final size:30
Alignment explanation
Indices: 544758--544829 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
544748 GTTCTTCGGA
* * *
544758 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
544788 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
544818 ACCTCTGGATAG
1 ACCTCTGGATAG
544830 GTCCTGCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:549126 original size:21 final size:21
Alignment explanation
Indices: 549100--549143 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
549090 ATTCTGGGCT
* *
549100 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
549121 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
549142 AG
1 AG
549144 CGAATAAAAT
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:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Done.