Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold335.1
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: 1266128
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.31
Warning! 68274 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:325797 original size:24 final size:24
Alignment explanation
Indices: 325732--325791 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
325722 AGAGTTTGTC
*
325732 TTCATTTTTAATCAACAGGCTGCT
1 TTCATTTTTAATCAACAGACTGCT
325756 TTCATTTTTAATCAACAGACTGCT
1 TTCATTTTTAATCAACAGACTGCT
325780 TTCATTTTTAAT
1 TTCATTTTTAAT
325792 GGACAGTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (24 bp):
TTCATTTTTAATCAACAGACTGCT
Found at i:329374 original size:49 final size:50
Alignment explanation
Indices: 329313--329582 Score: 176
Period size: 46 Copynumber: 5.6 Consensus size: 50
329303 ACATCAAGTT
* *
329313 CGATGCCATGTCCTAGACATGGTCTTACATTGACTATCGTA-ATC-GAGGC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCATATATCTG-GGC
* * * *
329362 TGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATATCTGTGC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCATATATCTGGGC
* *
329412 CGATGCCATGT-CTCAGACATGGTCTTACACTGAC-A-C--ATCTCAT-AGC
1 CGATGCCATGTCCT-AGACATGGTCTTACACTGACTATCATATATC-TGGGC
* * * * * * * *
329458 CAATTCCATGTCCCAAACATGGTCTTACACT-AGCTCTCGTCTCA-AT--GC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGA-CTATCATAT-ATCTGGGC
* * * * * *
329506 CGATGCCATGCCCAAGACATGGTCTTACACTGGCTCTCAT-GATGT-GGC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCATATATCTGGGC
*
329554 CGATG-CATGTCCCAGACAT-GTCTTACACT
1 CGATGCCATGTCCTAGACATGGTCTTACACT
329583 AGCACACATA
Statistics
Matches: 177, Mismatches: 30, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
45 1 0.01
46 43 0.24
47 15 0.08
48 43 0.24
49 39 0.22
50 35 0.20
51 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (50 bp):
CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCATATATCTGGGC
Found at i:329556 original size:48 final size:47
Alignment explanation
Indices: 329313--329582 Score: 214
Period size: 48 Copynumber: 5.7 Consensus size: 47
329303 ACATCAAGTT
* * * * * *
329313 CGATGCCATGTCCTAGACATGGTCTTACATTGACTATCGTAATCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-AT-GTGGC
* * *
329362 TGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATATCTGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--ATATGTG-GC
* *
329412 CGATGCCATGTCTCAGACATGGTCTTACACTGACACATCTCATA----GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTG--GC-TCTCATATGTGGC
* * * * * * *
329458 CAATTCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTCTCAAT-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAT--GTGGC
329506 CGATGCCATG-CCCAAGACATGGTCTTACACTGGCTCTCATGATGTGGC
1 CGATGCCATGTCCC-AGACATGGTCTTACACTGGCTCTCAT-ATGTGGC
329554 CGATG-CATGTCCCAGACAT-GTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
329583 AGCACACATA
Statistics
Matches: 180, Mismatches: 26, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
43 5 0.03
44 1 0.01
46 39 0.22
47 14 0.08
48 43 0.24
49 36 0.20
50 33 0.18
51 4 0.02
52 1 0.01
53 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGGC
Found at i:329577 original size:94 final size:94
Alignment explanation
Indices: 329266--329585 Score: 276
Period size: 94 Copynumber: 3.4 Consensus size: 94
329256 GTAGAATGCT
* * * *
329266 GATGCCATGTCCCACACATGATCTTACACTAG-T-TCATACATCAA-GTTCGATGCCATGTCCTA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-C-TCAATG-CCGATGCCATG-CCCA
* * * *
329328 GACATGGTCTTACATTGACTATCGTAATCGAGGCT
62 GACATGGTCTTACACTGACTCTC-TAAT-GTGGCC
* * * ** *
329363 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATATATCTGTGCCGATGCCATGTCTCAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATCTCAATGCCGATGCCATG-CCCAG
* * *
329428 ACATGGTCTTACACTGACACATCTCA--TAGCC
63 ACATGGTCTTACACTGACTC-TCTAATGTGGCC
* * * *
329459 AATTCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGCCCAAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGCCC-AGAC
* *
329524 ATGGTCTTACACTGGCTCTCATGATGTGGCC
65 ATGGTCTTACACTGACTCTC-TAATGTGGCC
329555 GATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGC
329586 ACACATATCA
Statistics
Matches: 179, Mismatches: 34, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
93 4 0.02
94 51 0.28
95 13 0.07
96 40 0.22
97 28 0.16
98 1 0.01
99 37 0.21
100 3 0.02
101 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (94 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCCGATGCCATGCCCAGACA
TGGTCTTACACTGACTCTCTAATGTGGCC
Found at i:341304 original size:51 final size:51
Alignment explanation
Indices: 341227--341357 Score: 142
Period size: 51 Copynumber: 2.6 Consensus size: 51
341217 CGGATGCCCG
* *
341227 GTGG-CTTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTCTT-CACAAA
1 GTGGCCTT-CACATAGTACCACACTTGTGA-CCAAAGCTACCTT-TTACACAAA
* *
341278 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTTACACATA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTACCTTTTACACAAA
* * * *
341329 GTGGCCTGCTCTTAGTACCACACATGTGA
1 GTGGCCTTCACATAGTACCACACTTGTGA
341358 TAGAAGCTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
50 2 0.03
51 63 0.91
52 4 0.06
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTACCTTTTACACAAA
Found at i:341365 original size:51 final size:51
Alignment explanation
Indices: 341257--341410 Score: 134
Period size: 51 Copynumber: 3.0 Consensus size: 51
341247 CCCTTGTAGT
* * * * * *
341257 CAAAGCTACCTTCTT-CACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
1 CAAAGCTATCTT-TTACACATAGTGGCCTGCTCTTAGTACCACACATGTGAC
341308 CAAAGCTATCTTTTACACATAGTGGCCTGCTCTTAGTACCACACATGTGA-
1 CAAAGCTATCTTTTACACATAGTGGCCTGCTCTTAGTACCACACATGTGAC
* *** * * * *
341358 TAGAAGCTATCGGGTACGCATAGTAGCCTG-TGCTTAGTACTACACATGCGAC
1 CA-AAGCTATCTTTTACACATAGTGGCCTGCT-CTTAGTACCACACATGTGAC
341410 C
1 C
341411 TAACTATTTG
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
50 4 0.05
51 80 0.95
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (51 bp):
CAAAGCTATCTTTTACACATAGTGGCCTGCTCTTAGTACCACACATGTGAC
Found at i:341444 original size:50 final size:51
Alignment explanation
Indices: 341390--341507 Score: 130
Period size: 52 Copynumber: 2.3 Consensus size: 51
341380 GTAGCCTGTG
* ** *
341390 CTTAGTACTACACATGCGACCT-AACTATTTGGTACACGTAGTAACCTACA
1 CTTAGTACTACACATGCGACCTAAACCATTTGAAACACATAGTAACCTACA
* * * * *
341440 CTTAGTACTGCACACGTGACCTAAAACCATTTTAAACACATAGTAGCCTACA
1 CTTAGTACTACACATGCGACCT-AAACCATTTGAAACACATAGTAACCTACA
*
341492 CATAGTACTACACATG
1 CTTAGTACTACACATG
341508 TGTTCTCACA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
50 19 0.35
52 35 0.65
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (51 bp):
CTTAGTACTACACATGCGACCTAAACCATTTGAAACACATAGTAACCTACA
Found at i:348174 original size:40 final size:40
Alignment explanation
Indices: 348111--348324 Score: 148
Period size: 40 Copynumber: 5.6 Consensus size: 40
348101 GTTGGCCGCA
* * *
348111 ATTATCGTTGGTTTATCCAACTAGAGCTAGGCTCACAATT
1 ATTATCGTCGGTATATCCGACTAGAGCTAGGCTCACAATT
* *
348151 ATTATCGTCGGTAAATCTGACTAGCA-CTAGG-TGCA-AA-T
1 ATTATCGTCGGTATATCCGACTAG-AGCTAGGCT-CACAATT
* * * *
348189 A-T-T-GTTGGTTTATCCAACTAGAGCTGGGCTCACAATT
1 ATTATCGTCGGTATATCCGACTAGAGCTAGGCTCACAATT
*
348226 ATTATCGTCGGTATATCCGACTAGCA-CTAGG-T-GCAA--
1 ATTATCGTCGGTATATCCGACTAG-AGCTAGGCTCACAATT
* * * * * * **
348262 A-TATCGTTGGTTTTTCCAACTAGAACTGGGCTTGCAATT
1 ATTATCGTCGGTATATCCGACTAGAGCTAGGCTCACAATT
348301 ATTATCGTCGGTATATCCGACTAG
1 ATTATCGTCGGTATATCCGACTAG
348325 TACTGGGTGC
Statistics
Matches: 133, Mismatches: 25, Indels: 32
0.70 0.13 0.17
Matches are distributed among these distances:
34 2 0.02
35 41 0.31
36 6 0.05
37 7 0.05
38 6 0.05
39 6 0.05
40 63 0.47
41 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (40 bp):
ATTATCGTCGGTATATCCGACTAGAGCTAGGCTCACAATT
Found at i:348196 original size:75 final size:75
Alignment explanation
Indices: 348079--348372 Score: 410
Period size: 75 Copynumber: 3.9 Consensus size: 75
348069 AATAATTACA
* * * * *
348079 ATCGTCGGTTTATCCGACTAGC-GTTGGCCGCAATTATCGTTGGTTTATCCAACTAGAGCTAGGC
1 ATCGTCGGTATATCCGACTAGCACTAGG-TGCAAATATCGTTGGTTTATCCAACTAGAGCTAGGC
348143 TCACAATTATT
65 TCACAATTATT
* * * *
348154 ATCGTCGGTAAATCTGACTAGCACTAGGTGCAAATATTGTTGGTTTATCCAACTAGAGCTGGGCT
1 ATCGTCGGTATATCCGACTAGCACTAGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTAGGCT
348219 CACAATTATT
66 CACAATTATT
* * *
348229 ATCGTCGGTATATCCGACTAGCACTAGGTGCAAATATCGTTGGTTTTTCCAACTAGAACTGGGCT
1 ATCGTCGGTATATCCGACTAGCACTAGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTAGGCT
**
348294 TGCAATTATT
66 CACAATTATT
* * **
348304 ATCGTCGGTATATCCGACTAGTACTGGGTGCAAATATAATTGGTTTATCCAACTAGAGCTAGGCT
1 ATCGTCGGTATATCCGACTAGCACTAGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTAGGCT
348369 CACA
66 CACA
348373 TTCAATATCA
Statistics
Matches: 193, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
75 190 0.98
76 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (75 bp):
ATCGTCGGTATATCCGACTAGCACTAGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTAGGCT
CACAATTATT
Found at i:348284 original size:35 final size:35
Alignment explanation
Indices: 348170--348359 Score: 139
Period size: 35 Copynumber: 5.1 Consensus size: 35
348160 GGTAAATCTG
* *
348170 ACTAGCACTAGGTGCAAATATTGTTGGTTTATCCA
1 ACTAGCACTGGGTGCAAATATCGTTGGTTTATCCA
* * * *
348205 ACTAG-AGCTGGGCTCACAATTATTATCGTCGGTATATCCG
1 ACTAGCA-CTGGG-T-GCAA--A-TATCGTTGGTTTATCCA
* *
348245 ACTAGCACTAGGTGCAAATATCGTTGGTTTTTCCA
1 ACTAGCACTGGGTGCAAATATCGTTGGTTTATCCA
* * * *
348280 ACTAGAACTGGGCTTGCAATTATTATCGTCGGTATATCCG
1 ACTAGCACTGGG--TGCAA--A-TATCGTTGGTTTATCCA
* **
348320 ACTAGTACTGGGTGCAAATATAATTGGTTTATCCA
1 ACTAGCACTGGGTGCAAATATCGTTGGTTTATCCA
348355 ACTAG
1 ACTAG
348360 AGCTAGGCTC
Statistics
Matches: 119, Mismatches: 24, Indels: 24
0.71 0.14 0.14
Matches are distributed among these distances:
34 1 0.01
35 49 0.41
36 3 0.03
37 8 0.07
38 8 0.07
39 3 0.03
40 46 0.39
41 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (35 bp):
ACTAGCACTGGGTGCAAATATCGTTGGTTTATCCA
Found at i:348402 original size:150 final size:150
Alignment explanation
Indices: 348107--348412 Score: 409
Period size: 150 Copynumber: 2.0 Consensus size: 150
348097 TAGCGTTGGC
* * *
348107 CGCAATTATCGTTGGTTTATCCAACTAGAGCTAGGCTCACAATTATTATCGTCGGTAAATCTGAC
1 CGCAAATATCGTTGGTTTATCCAACTAGAACTAGGCTCACAATTATTATCGTCGGTAAATCCGAC
** * * *
348172 TAGCACTAGGTGCAAATATTGTTGGTTTATCCAACTAGAGCTGGGCTCACAATTATTATCGTCGG
66 TAGCACTAGGTGCAAATATAATTGGTTTATCCAACTAGAGCTAGGCTCACAATTAATATCATCGG
*
348237 TATATCCGACTAGCACTAGG
131 TATATCCGACAAGCACTAGG
* * * ** *
348257 TGCAAATATCGTTGGTTTTTCCAACTAGAACTGGGCTTGCAATTATTATCGTCGGTATATCCGAC
1 CGCAAATATCGTTGGTTTATCCAACTAGAACTAGGCTCACAATTATTATCGTCGGTAAATCCGAC
* *
348322 TAGTACTGGGTGCAAATATAATTGGTTTATCCAACTAGAGCTAGGCTCAC-ATTCAATATCATCG
66 TAGCACTAGGTGCAAATATAATTGGTTTATCCAACTAGAGCTAGGCTCACAATT-AATATCATCG
* *
348386 GT-TAATCCTACAAGCACTGGG
130 GTAT-ATCCGACAAGCACTAGG
348407 CGCAAA
1 CGCAAA
348413 CTCCTCTGCG
Statistics
Matches: 134, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
149 4 0.03
150 130 0.97
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (150 bp):
CGCAAATATCGTTGGTTTATCCAACTAGAACTAGGCTCACAATTATTATCGTCGGTAAATCCGAC
TAGCACTAGGTGCAAATATAATTGGTTTATCCAACTAGAGCTAGGCTCACAATTAATATCATCGG
TATATCCGACAAGCACTAGG
Found at i:349796 original size:42 final size:42
Alignment explanation
Indices: 349732--349825 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
349722 GAAAATGGCC
* * *
349732 TCTCAGCCGTATGTGACACATGGCCTAACACACGGGCGTGTG
1 TCTCGGCCGTATGTGACACATGGCCTAACACACGGGCATATG
349774 TCTCGGCCGTATGTGACACATGGCCTAACACACGGGCATATG
1 TCTCGGCCGTATGTGACACATGGCCTAACACACGGGCATATG
*
349816 TCTTGGCCGT
1 TCTCGGCCGT
349826 GTGACCCCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (42 bp):
TCTCGGCCGTATGTGACACATGGCCTAACACACGGGCATATG
Found at i:354703 original size:21 final size:20
Alignment explanation
Indices: 354659--354707 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
354649 ATCCTCTGTT
*
354659 AGAAAATTGTAGTACAAGAA
1 AGAAAATTGTAGTACAAAAA
* *
354679 AGAAATTTGTGGTACAATAAA
1 AGAAAATTGTAGTACAA-AAA
354700 AGAAAATT
1 AGAAAATT
354708 AAAAGGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.24
Consensus pattern (20 bp):
AGAAAATTGTAGTACAAAAA
Found at i:355982 original size:3 final size:3
Alignment explanation
Indices: 355974--356008 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
355964 GAAGGAAAAA
355974 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
356009 ATGTTGAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:358928 original size:16 final size:16
Alignment explanation
Indices: 358907--358949 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
358897 TATAACTAAA
358907 TTTAATTAAAAAATAT
1 TTTAATTAAAAAATAT
* *
358923 TTTAATATATAAATTAT
1 TTTAAT-TAAAAAATAT
*
358940 TTGAATTAAA
1 TTTAATTAAA
358950 TTAAAAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTAATTAAAAAATAT
Found at i:359154 original size:19 final size:20
Alignment explanation
Indices: 359130--359186 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
359120 AATAATCACA
359130 AATTATATATATTTAAT-TT
1 AATTATATATATTTAATATT
* *
359149 AATTATA-AAAATTAATATT
1 AATTATATATATTTAATATT
* *
359168 AA-TATATATTTTTATTATT
1 AATTATATATATTTAATATT
359187 TTAACGAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTATATATATTTAATATT
Found at i:362915 original size:23 final size:23
Alignment explanation
Indices: 362827--362916 Score: 62
Period size: 23 Copynumber: 3.9 Consensus size: 23
362817 CGAAATAAGT
*
362827 TAAAAAATTTAAAA-TAAGTAATA
1 TAAACAATTTAAAATTAA-TAATA
* *
362850 -AAATAATTT-TAATTAATATATA
1 TAAACAATTTAAAATTAATA-ATA
* **
362872 AAAACAAGTTTAAAACAAATAATA
1 TAAACAA-TTTAAAATTAATAATA
362896 TATAA-AATTTAAAATTAATAA
1 TA-AACAATTTAAAATTAATAA
362917 AATAGTTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
21 4 0.08
22 14 0.27
23 17 0.33
24 9 0.17
25 8 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAACAATTTAAAATTAATAATA
Found at i:364799 original size:87 final size:88
Alignment explanation
Indices: 364640--364896 Score: 300
Period size: 88 Copynumber: 2.9 Consensus size: 88
364630 GTAACTTGTA
* * * * * * **
364640 GCTTCAATCTGTTCCACTGTAATTTCAGGGAAATGAGATTTGCTATCTTCAGTATGCTCCACTGC
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTCAACATGCTCCACTGC
* *
364705 AATTTCAGGGAGATGAGACTAGTG
65 AACTTCAGGGAGATAAGACTAGTG
* * * *
364729 GTTTCTATCTGCTCCACTGCAA-TTCAGGGAGATAAGATTTGTAACTTCAACCTGCTCCACTACA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAACATGCTCCACTGCA
* ** *
364793 ACTTCAGGGAAATAAGGTTTGTG
66 ACTTCAGGGAGATAAGACTAGTG
* * * *
364816 GCTTCAATTTGCTCTACTGCAACTTCAGGAAGATAAGATTTGTAACTTCAACATGCTCCACTGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAACATGCTCCACTGCA
364881 ACTTCAGGGAGATAAG
66 ACTTCAGGGAGATAAG
364897 GTTTATGGTT
Statistics
Matches: 141, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
87 53 0.38
88 70 0.50
89 18 0.13
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (88 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAACATGCTCCACTGCA
ACTTCAGGGAGATAAGACTAGTG
Found at i:364894 original size:44 final size:43
Alignment explanation
Indices: 364435--364896 Score: 255
Period size: 44 Copynumber: 10.3 Consensus size: 43
364425 CTAATATAAT
* * * *
364435 TTCAGGGAGA-AGAGACTTGTAGCTTCGATCTACTCCACTACAAC
1 TTCAGGGAGATA-AGATTTGTAGCTTC-AACTGCTCCACTGCAAC
* * * * ** * * *
364479 TTCAGTGAGATGAGACTCGTATTTTCAATCTTCTTCTCTGCAAC
1 TTCAGGGAGATAAGATTTGTAGCTTCAA-CTGCTCCACTGCAAC
* ** * * * * *
364523 TTTAGAAAAATAAGATTTGCTATCTTCAGTCTACTCCACTACAAC
1 TTCAGGGAGATAAGATTTG-TAGCTTCA-ACTGCTCCACTGCAAC
* * * * * * *
364568 TTCAGGGAGATAATACTAGTGGTTTTTATCTGCTCCACTGCAAC
1 TTCAGGGAGATAAGATTTGTAG-CTTCAACTGCTCCACTGCAAC
* * *
364612 TTCAGGGAGATAAGACTCGTAACTTGTAGCTTCAATCTGTTCCACTGTAAT
1 TTCAGGGAGATAAGA----T---TTGTAGCTTCAA-CTGCTCCACTGCAAC
* * * *
364663 TTCAGGGAAATGAGATTTGCTATCTTCAGTA-TGCTCCACTGCAAT
1 TTCAGGGAGATAAGATTTG-TAGCTTCA--ACTGCTCCACTGCAAC
* * * * * *
364708 TTCAGGGAGATGAGACTAGTGGTTTCTATCTGCTCCACTGCAA-
1 TTCAGGGAGATAAGATTTGTAGCTTC-AACTGCTCCACTGCAAC
* *
364751 TTCAGGGAGATAAGATTTGTAACTTCAACCTGCTCCACTACAAC
1 TTCAGGGAGATAAGATTTGTAGCTTCAA-CTGCTCCACTGCAAC
* * * * *
364795 TTCAGGGAAATAAGGTTTGTGGCTTCAATTTGCTCTACTGCAAC
1 TTCAGGGAGATAAGATTTGTAGCTTCAA-CTGCTCCACTGCAAC
* * *
364839 TTCAGGAAGATAAGATTTGTAACTTCAACATGCTCCACTGTAAC
1 TTCAGGGAGATAAGATTTGTAGCTTCAAC-TGCTCCACTGCAAC
364883 TTCAGGGAGATAAG
1 TTCAGGGAGATAAG
364897 GTTTATGGTT
Statistics
Matches: 314, Mismatches: 83, Indels: 42
0.72 0.19 0.10
Matches are distributed among these distances:
42 1 0.00
43 34 0.11
44 176 0.56
45 69 0.22
47 2 0.01
50 3 0.01
51 29 0.09
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (43 bp):
TTCAGGGAGATAAGATTTGTAGCTTCAACTGCTCCACTGCAAC
Found at i:365854 original size:6 final size:6
Alignment explanation
Indices: 365845--365879 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
365835 GGCCTCTCCC
*
365845 CTTTTT CTTTTT -TTTTT CTTTTT ATTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
365880 AGGTAAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (6 bp):
CTTTTT
Found at i:365867 original size:12 final size:12
Alignment explanation
Indices: 365846--365880 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
365836 GCCTCTCCCC
365846 TTTTTCTTTTT-
1 TTTTTCTTTTTA
365857 TTTTTCTTTTTA
1 TTTTTCTTTTTA
365869 TTTTTCTTTTTA
1 TTTTTCTTTTTA
365881 GGTAAAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTTTA
Found at i:367586 original size:56 final size:56
Alignment explanation
Indices: 367500--367619 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
367490 ACAAGGGATG
367500 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
367556 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
367612 ATGGGCAA
1 ATGGGCAA
367620 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:369773 original size:50 final size:50
Alignment explanation
Indices: 369713--369816 Score: 201
Period size: 50 Copynumber: 2.1 Consensus size: 50
369703 AGAGTAGTCG
369713 AACC-CAGAATCAGGGGAGATTTTAAATAATAAACTGTACCAATTGGCCC
1 AACCACAGAATCAGGGGAGATTTTAAATAATAAACTGTACCAATTGGCCC
369762 AACCACAGAATCAGGGGAGATTTTAAATAATAAACTGTACCAATTGGCCC
1 AACCACAGAATCAGGGGAGATTTTAAATAATAAACTGTACCAATTGGCCC
369812 AACCA
1 AACCA
369817 AAAATTCTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 4 0.07
50 50 0.93
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (50 bp):
AACCACAGAATCAGGGGAGATTTTAAATAATAAACTGTACCAATTGGCCC
Found at i:371945 original size:36 final size:36
Alignment explanation
Indices: 371898--371969 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
371888 ATATATACAC
371898 TTTCACATTCATCACATCGGCCATTAGGCCTTATCA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCA
371934 TTTCACATTCATCACATCGGCCATTAGGCCTTATCA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCA
371970 CATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33
Consensus pattern (36 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCA
Found at i:371990 original size:49 final size:49
Alignment explanation
Indices: 371934--373013 Score: 2073
Period size: 49 Copynumber: 22.2 Consensus size: 49
371924 GGCCTTATCA
371934 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
371983 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372032 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372081 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372130 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372179 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372228 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372277 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372326 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372375 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372424 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372473 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372522 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372571 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372620 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372669 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372718 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372767 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
372816 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
372865 TTTCATATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
* *
372912 TTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
* *
372959 TTTCACATTCATCATATCGGTCATTAGGCCTTATCACATATATATACA-
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
373007 -TTCACAT
1 TTTCACAT
373014 CACAATTATC
Statistics
Matches: 1021, Mismatches: 8, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
47 94 0.09
49 927 0.91
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (49 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
Found at i:381239 original size:56 final size:56
Alignment explanation
Indices: 381153--381328 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
381143 ACAAGGGATG
381153 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
381209 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
381265 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
381321 ATGGGCAA
1 ATGGGCAA
381329 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:393259 original size:40 final size:40
Alignment explanation
Indices: 393189--393364 Score: 214
Period size: 40 Copynumber: 4.4 Consensus size: 40
393179 AAGCCAAGTA
* * *
393189 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
393228 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
393268 CCTTCGAGACTTAGCCCGGATATACTAACTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * **
393308 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGTAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
393348 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
393365 AGTTATCATC
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
39 13 0.11
40 106 0.89
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:408249 original size:40 final size:39
Alignment explanation
Indices: 408205--408280 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 39
408195 TACCTCTAAG
*
408205 CATGAAAGGAAGTTGACATAGCTCTGGGCATGTTATGGTT
1 CATGAAAGGAAGTTGACAAAGCTC-GGGCATGTTATGGTT
*
408245 CATGAAAGGAAGTTGGCAAAGCTCGGGCATGTTATG
1 CATGAAAGGAAGTTGACAAAGCTCGGGCATGTTATG
408281 AATAACTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 12 0.35
40 22 0.65
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (39 bp):
CATGAAAGGAAGTTGACAAAGCTCGGGCATGTTATGGTT
Found at i:414659 original size:8 final size:8
Alignment explanation
Indices: 414641--414679 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
414631 CTTTCTTTTC
414641 TTTCTTTTA
1 TTTC-TTTA
414650 TTTCTTTA
1 TTTCTTTA
414658 -TTCTTTA
1 TTTCTTTA
*
414665 TTTTTTTA
1 TTTCTTTA
414673 TTTCTTT
1 TTTCTTT
414680 TATTATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 7 0.26
8 16 0.59
9 4 0.15
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTCTTTA
Found at i:414666 original size:15 final size:16
Alignment explanation
Indices: 414641--414679 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
414631 CTTTCTTTTC
414641 TTTCTTTTATTTCTTTA
1 TTTC-TTTATTTCTTTA
*
414658 -TTCTTTATTTTTTTA
1 TTTCTTTATTTCTTTA
414673 TTTCTTT
1 TTTCTTT
414680 TATTATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTATTTCTTTA
Found at i:414682 original size:9 final size:9
Alignment explanation
Indices: 414632--414683 Score: 67
Period size: 9 Copynumber: 6.2 Consensus size: 9
414622 TTCGTCCTTC
*
414632 TTTCTTTTC
1 TTTCTTTTA
414641 TTTCTTTTA
1 TTTCTTTTA
414650 TTTC-TTTA
1 TTTCTTTTA
414658 -TTC-TTTA
1 TTTCTTTTA
414665 TTT-TTTTA
1 TTTCTTTTA
414673 TTTCTTTTA
1 TTTCTTTTA
414682 TT
1 TT
414684 ATTATAACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
7 7 0.18
8 13 0.33
9 19 0.49
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTA
Found at i:414688 original size:23 final size:23
Alignment explanation
Indices: 414645--414688 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
414635 CTTTTCTTTC
*
414645 TTTTATTTCTTTATTCTTTATTT
1 TTTTATTTCTTTATTCATTATTT
414668 TTTTATTTCTTTTATT-ATTAT
1 TTTTATTTC-TTTATTCATTAT
414689 AACATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTATTTCTTTATTCATTATTT
Found at i:415217 original size:19 final size:18
Alignment explanation
Indices: 415188--415231 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
415178 TAATTTAGTC
*
415188 ATTTTTATTTTTATTTTA
1 ATTTTTATTTTGATTTTA
*
415206 ATATTTTGTTTTGATTTTA
1 AT-TTTTATTTTGATTTTA
415225 ATTTTTA
1 ATTTTTA
415232 CATTCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
ATTTTTATTTTGATTTTA
Found at i:415804 original size:46 final size:46
Alignment explanation
Indices: 415737--415828 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
415727 TTGAGGAGTA
415737 AGGCAAAACAATGGTTGAATTCACTTCCATAGGGTTCTGTTACAAC
1 AGGCAAAACAATGGTTGAATTCACTTCCATAGGGTTCTGTTACAAC
*
415783 AGGCAAAACAATGGTTGAATTCACTTCCATGGGGTTCTGTTACAAC
1 AGGCAAAACAATGGTTGAATTCACTTCCATAGGGTTCTGTTACAAC
415829 TTGGGATCAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (46 bp):
AGGCAAAACAATGGTTGAATTCACTTCCATAGGGTTCTGTTACAAC
Found at i:416387 original size:22 final size:22
Alignment explanation
Indices: 416359--416412 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
416349 ATAAGGTTAT
* *
416359 GCTTAATTAATGGTTTAATT-AG
1 GCTTAATTAATGATTT-ATTAAA
416381 GCTTAATTAATGATTTATTAAA
1 GCTTAATTAATGATTTATTAAA
416403 GCTTAATTAA
1 GCTTAATTAA
416413 GAAAGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (22 bp):
GCTTAATTAATGATTTATTAAA
Found at i:417308 original size:37 final size:37
Alignment explanation
Indices: 417218--417309 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 37
417208 TCTATCGAGC
* * *
417218 CAAATCTTACTGTTCTACTGAATGAAGCTTAATCGAG
1 CAAATCTTACTGTTATATTGAATGAAGCTTAATCAAG
** *
417255 CAAAT-TATACCATTATATTGAATGGAGCTTAA-CTAAG
1 CAAATCT-TACTGTTATATTGAATGAAGCTTAATC-AAG
417292 CAAATCTTACTGTTATAT
1 CAAATCTTACTGTTATAT
417310 GAACTAATGT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
36 2 0.05
37 41 0.93
38 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (37 bp):
CAAATCTTACTGTTATATTGAATGAAGCTTAATCAAG
Found at i:418446 original size:19 final size:18
Alignment explanation
Indices: 418409--418456 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
418399 TCAGGGATCC
*
418409 AATTGAGACAAATCAGAAA
1 AATTGAGA-AAAACAGAAA
**
418428 TTTTGAGAAAAACATGAAA
1 AATTGAGAAAAACA-GAAA
418447 AATTGAGAAA
1 AATTGAGAAA
418457 CAGTGTAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (18 bp):
AATTGAGAAAAACAGAAA
Found at i:419740 original size:23 final size:23
Alignment explanation
Indices: 419703--419757 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
419693 CCGTGTGGCC
*
419703 CACACGACCACACACTCACCCGT
1 CACACGGCCACACACTCACCCGT
* * *
419726 TATACGGCCACACACTCTCCCGT
1 CACACGGCCACACACTCACCCGT
419749 CACACGGCC
1 CACACGGCC
419758 GTGTGTCGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.49, G:0.13, T:0.13
Consensus pattern (23 bp):
CACACGGCCACACACTCACCCGT
Found at i:426284 original size:46 final size:45
Alignment explanation
Indices: 426226--426489 Score: 218
Period size: 46 Copynumber: 5.7 Consensus size: 45
426216 TCACTTGTGT
* * *
426226 GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCTACATTATGG
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCT-CA-GATGA
*
426272 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGC--TCAGATGA
* * *
426320 GTGCTAGTGTAAGA-CATGTCTGGGACATGCATTGGCCTCGAGATGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGG-CTC-AGATG-A
*
426367 -AGCCAGTGTAAGA-CATGTCTGGGACATGCATTGGCT-ATGA-GA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTCA-GATGA
* * *
426409 TATGTCAGTGTAAGACCATGTATGGGACATGGCATCGGCATGGACATG-TGA
1 GA-GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGC-T---CA-GATGA
* *
426460 GAGCTAGTGTAAGACCATGTTTGGGACATG
1 GAGCCAGTGTAAGACCATGTCTGGGACATG
426490 GTGTCAACCT
Statistics
Matches: 183, Mismatches: 17, Indels: 33
0.79 0.07 0.14
Matches are distributed among these distances:
42 1 0.01
43 3 0.02
44 13 0.07
45 16 0.09
46 63 0.34
47 31 0.17
48 23 0.13
49 2 0.01
50 25 0.14
51 6 0.03
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.25
Consensus pattern (45 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTCAGATGA
Found at i:426469 original size:94 final size:93
Alignment explanation
Indices: 426228--426489 Score: 306
Period size: 94 Copynumber: 2.8 Consensus size: 93
426218 ACTTGTGTGA
* *
426228 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCT-ACATTATGGGAGCCAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTGACA-TGTGAGAGCCAGTGTAAGACCATGT
426292 CTGGGACATGGCATCGGCATTGAGATGAGT
65 CTGGGACAT-GCATCGGCATTGAGATGAGT
* *
426322 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGATGT-A-AGCCAGTGTAAGA-CATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-CT-GACATGTGAGAGCCAGTGTAAGACCATG
*
426384 TCTGGGACATGCATTGGC-TATGAGAT-A-T
64 TCTGGGACATGCATCGGCAT-TGAGATGAGT
* *
426412 G-TCAGTGTAAGACCATGTATGGGACATGGCATCGGCATGGACATGTGAGAGCTAGTGTAAGACC
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-T-GACATGTGAGAGCCAGTGTAAGACC
*
426476 ATGTTTGGGACATG
61 ATGTCTGGGACATG
426490 GTGTCAACCT
Statistics
Matches: 146, Mismatches: 11, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
89 1 0.01
90 11 0.08
91 16 0.11
92 26 0.18
93 15 0.10
94 57 0.39
95 16 0.11
96 2 0.01
97 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTGACATGTGAGAGCCAGTGTAAGACCATGTC
TGGGACATGCATCGGCATTGAGATGAGT
Found at i:429718 original size:13 final size:13
Alignment explanation
Indices: 429702--429726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
429692 TTAAATCAGT
429702 TAATTAGTTTAAA
1 TAATTAGTTTAAA
429715 TAATTAGTTTAA
1 TAATTAGTTTAA
429727 TAAACAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:445946 original size:99 final size:96
Alignment explanation
Indices: 445786--446005 Score: 238
Period size: 96 Copynumber: 2.3 Consensus size: 96
445776 TGAGACGAGT
* * **
445786 GCTAGTGTAAGA-CATGTCTGTGACAT-GCATCGG-CTACGAGAT-G-T-GTCAGTGTAAAAACA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCT-CGATTTCGATAGTCAGTGTAAAAACA
* *
445845 TGTCTGGAACATGGCATCAGCATGGACAT-GTTAGA
65 TGTCTGGAACATGGCATCAAC-TGG--ATGGAT-GA
* * * *
445880 GCTTGTGTAGGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGATAGTCAGTGTAAGACCAT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGATAGTCAGTGTAAAAACAT
* *
445945 GTCTGGGACATGGCATCAACTTGATGGATGA
66 GTCTGGAACATGGCATCAACTGGATGGATGA
445976 GCTAGTGTAAGACCATGTCTGGGACATGGC
1 GCTAGTGTAAGACCATGTCTGGGACATGGC
446006 ATCAGCATTA
Statistics
Matches: 105, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
94 10 0.10
95 13 0.12
96 42 0.40
97 5 0.05
98 3 0.03
99 32 0.30
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (96 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGATAGTCAGTGTAAAAACAT
GTCTGGAACATGGCATCAACTGGATGGATGA
Found at i:445998 original size:47 final size:47
Alignment explanation
Indices: 445689--446009 Score: 177
Period size: 47 Copynumber: 6.8 Consensus size: 47
445679 GTCACTTGTG
* *
445689 TGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCATATTATGG-
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-AAC-T-TGATGGA
* *
445736 -GAGCCAGTGTAAGACCATGTCTGGGATATGGCATCAGTA-TTGA-GACGA
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCA--ACTTGATG--GA
* * ** *
445784 -GTGCTAGTGTAAGA-CATGTCTGTGACAT-GCATCGGC-T-ACGAGA
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATG-GA
* * * * * * *
445827 TGTG-TCAGTGTAAAAACATGTCTGGAACATGGCATCAGCATGGACAT-GT
1 TGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCAAC-TTG--ATGGA
* * * ** * *
445876 TAGAGCTTGTGTAGGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGA
1 T-GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-AACTTGA--TGGA
445927 T-AG-TCAGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATGGA
1 TGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATGGA
445973 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCA
1 TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCA
446010 GCATTATACC
Statistics
Matches: 211, Mismatches: 36, Indels: 54
0.70 0.12 0.18
Matches are distributed among these distances:
43 4 0.02
44 13 0.06
45 13 0.06
46 31 0.15
47 61 0.29
48 24 0.11
49 31 0.15
50 29 0.14
51 5 0.02
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (47 bp):
TGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATGGA
Found at i:449077 original size:13 final size:13
Alignment explanation
Indices: 449059--449083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
449049 TAATTTATAT
449059 GTGTGAAAATTTC
1 GTGTGAAAATTTC
449072 GTGTGAAAATTT
1 GTGTGAAAATTT
449084 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:449552 original size:136 final size:136
Alignment explanation
Indices: 449308--449578 Score: 524
Period size: 136 Copynumber: 2.0 Consensus size: 136
449298 TACGTATTAA
*
449308 ATTAAACAAAAACAAATGGCCATGCAAGTGTTCATCTTTCTTGGCTGAACCTAAGAAGAAAATAA
1 ATTAAACAAAAACAAATGGCCATGCAAGTGTTCATCTTTCTTGGCCGAACCTAAGAAGAAAATAA
449373 AGCTTTTGAAAGCTTTAAACATTCAAAACTTTGGGAAGCTTAATTCGGGTATGTATTTTGCTCTG
66 AGCTTTTGAAAGCTTTAAACATTCAAAACTTTGGGAAGCTTAATTCGGGTATGTATTTTGCTCTG
449438 TTTTTT
131 TTTTTT
449444 ATTAAACAAAAACAAATGGCCATGCAAGTGTTCATCTTTCTTGGCCGAACCTAAGAAGAAAATAA
1 ATTAAACAAAAACAAATGGCCATGCAAGTGTTCATCTTTCTTGGCCGAACCTAAGAAGAAAATAA
*
449509 AGCTTTTGAAAGCTTTAAACATTCGAAACTTTGGGAAGCTTAATTCGGGTATGTATTTTGCTCTG
66 AGCTTTTGAAAGCTTTAAACATTCAAAACTTTGGGAAGCTTAATTCGGGTATGTATTTTGCTCTG
449574 TTTTT
131 TTTTT
449579 GATGATTTTT
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 133 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (136 bp):
ATTAAACAAAAACAAATGGCCATGCAAGTGTTCATCTTTCTTGGCCGAACCTAAGAAGAAAATAA
AGCTTTTGAAAGCTTTAAACATTCAAAACTTTGGGAAGCTTAATTCGGGTATGTATTTTGCTCTG
TTTTTT
Found at i:451873 original size:12 final size:12
Alignment explanation
Indices: 451856--451881 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
451846 ACTATCATGG
451856 TATAATGGTAAT
1 TATAATGGTAAT
451868 TATAATGGTAAT
1 TATAATGGTAAT
451880 TA
1 TA
451882 AAGCATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (12 bp):
TATAATGGTAAT
Found at i:456055 original size:61 final size:61
Alignment explanation
Indices: 455980--456104 Score: 214
Period size: 61 Copynumber: 2.0 Consensus size: 61
455970 TTTGTTAGAG
* *
455980 TTCCTAGTGAGCGAGATGATATTCGTTATTCTGCTAATGTCAGTAATCATGCAACTAGACA
1 TTCCTAGTGAGCGAGATGATATTCATTATTCTACTAATGTCAGTAATCATGCAACTAGACA
* *
456041 TTCCTAGTGAGCGAGATGATATTCATTATTCTATTAATGTTAGTAATCATGCAACTAGACA
1 TTCCTAGTGAGCGAGATGATATTCATTATTCTACTAATGTCAGTAATCATGCAACTAGACA
456102 TTC
1 TTC
456105 TTTGCAGGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (61 bp):
TTCCTAGTGAGCGAGATGATATTCATTATTCTACTAATGTCAGTAATCATGCAACTAGACA
Found at i:456616 original size:5 final size:5
Alignment explanation
Indices: 456606--456647 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
456596 ACCCGAGTGT
*
456606 TTTTA TTTTA TTTTA -TTTA -TTTA TTTTA CTTTTA TGTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTT
456648 CAAAAAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 8 0.24
5 20 0.61
6 5 0.15
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:456885 original size:15 final size:16
Alignment explanation
Indices: 456865--456903 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
456855 AATGATAATC
456865 ATGACCTG-GAGACAT
1 ATGACCTGTGAGACAT
456880 ATGACCCTGTGAGACAT
1 ATGA-CCTGTGAGACAT
*
456897 ACGACCT
1 ATGACCT
456904 AGCACACGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (16 bp):
ATGACCTGTGAGACAT
Found at i:457571 original size:22 final size:21
Alignment explanation
Indices: 457543--457585 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
457533 CCTCAGGCGA
457543 CCGCCTAGCACAACCACTCTT
1 CCGCCTAGCACAACCACTCTT
*
457564 NCCGCCTAGCACAACCCCTCTT
1 -CCGCCTAGCACAACCACTCTT
457586 TCCTTCCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.49, G:0.09, T:0.19
Consensus pattern (21 bp):
CCGCCTAGCACAACCACTCTT
Found at i:457838 original size:22 final size:21
Alignment explanation
Indices: 457790--457847 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
457780 CTTTTTTCTG
* *
457790 TTGTTTATTTTATTATTATCT
1 TTGTTTATTATATTATTATAT
* *
457811 TAGTTTATTATAGTTCTTATAT
1 TTGTTTATTATA-TTATTATAT
457833 TTG-TT-TTATATTATT
1 TTGTTTATTATATTATT
457848 GGCCCTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 12 0.40
22 9 0.30
ACGTcount: A:0.22, C:0.03, G:0.07, T:0.67
Consensus pattern (21 bp):
TTGTTTATTATATTATTATAT
Found at i:467616 original size:9 final size:9
Alignment explanation
Indices: 467598--467633 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
467588 AAAACAGTCC
467598 TCAA-ATGT
1 TCAACATGT
467606 TCAACATGT
1 TCAACATGT
467615 TCAACATGT
1 TCAACATGT
467624 TCAACATGT
1 TCAACATGT
467633 T
1 T
467634 TGAACTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.15
9 23 0.85
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (9 bp):
TCAACATGT
Found at i:473733 original size:43 final size:43
Alignment explanation
Indices: 473677--473791 Score: 108
Period size: 43 Copynumber: 2.7 Consensus size: 43
473667 CTTACATGTT
* * * * **
473677 ATCACATATCGATGTCATTGTCCTAGACAGGGTCTTACACGAA
1 ATCACATAACGATGCCAATGTCCCAGACAGCATCTTACACGAA
* * *
473720 ATCATATAACGATGCCAATGTCCCAGACATCATCTTACACGTA
1 ATCACATAACGATGCCAATGTCCCAGACAGCATCTTACACGAA
*
473763 ATCACA-ATACAATGCCAACT-TCCCAGACA
1 ATCACATA-ACGATGCCAA-TGTCCCAGACA
473792 TGGTCTTACA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 57 0.97
44 1 0.02
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (43 bp):
ATCACATAACGATGCCAATGTCCCAGACAGCATCTTACACGAA
Found at i:473792 original size:43 final size:43
Alignment explanation
Indices: 473709--473810 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
473699 CTAGACAGGG
* * *
473709 TCTTACACGAAATCATATAACGATGCCAATGTCCCAGACATCA
1 TCTTACACGTAATCAAATAACAATGCCAATGTCCCAGACATCA
**
473752 TCTTACACGTAATCACAAT-ACAATGCCAACT-TCCCAGACATGG
1 TCTTACACGTAATCA-AATAACAATGCCAA-TGTCCCAGACATCA
*
473795 TCTTACATGTAATCAA
1 TCTTACACGTAATCAA
473811 TCTTGATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.02
43 47 0.92
44 3 0.06
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.25
Consensus pattern (43 bp):
TCTTACACGTAATCAAATAACAATGCCAATGTCCCAGACATCA
Found at i:481964 original size:30 final size:30
Alignment explanation
Indices: 481928--481987 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
481918 ATTTAATCTA
481928 AGACTTAAACATGCACATTAACCACACCTT
1 AGACTTAAACATGCACATTAACCACACCTT
*
481958 AGACTTAAACATGCACATTAACTACACCTT
1 AGACTTAAACATGCACATTAACCACACCTT
481988 TCGATAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (30 bp):
AGACTTAAACATGCACATTAACCACACCTT
Found at i:482968 original size:19 final size:18
Alignment explanation
Indices: 482922--482968 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
482912 AGTATTTTTA
482922 TTTTTATTTTTTTAGTTG
1 TTTTTATTTTTTTAGTTG
** *
482940 TACTTCTTTTTGTTAGTTG
1 TTTTTATTTTT-TTAGTTG
482959 TTTTTATTTT
1 TTTTTATTTT
482969 ATTTTTCAGG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.11, C:0.04, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTTTATTTTTTTAGTTG
Found at i:483950 original size:15 final size:14
Alignment explanation
Indices: 483930--483959 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
483920 ACTTTGTTCT
483930 TAAAAAACAAAAAAA
1 TAAAAAA-AAAAAAA
483945 TAAAAAAAAAAAAA
1 TAAAAAAAAAAAAA
483959 T
1 T
483960 TGAGCTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (14 bp):
TAAAAAAAAAAAAA
Found at i:488704 original size:42 final size:42
Alignment explanation
Indices: 488605--488872 Score: 448
Period size: 42 Copynumber: 6.3 Consensus size: 42
488595 TTATTTGAAA
*
488605 AAACACCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGATCACGACCTTTAGCGGCGC-TTTTCCAC
*
488648 AAACGCCACTAAAGATCACGACCTTTAGCGGCGC-TTTCTCAC
1 AAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTC-CAC
488690 AAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTCCAC
1 AAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTCCAC
*
488732 AAACACCGCTAAAGATCACGACCTTTAGCGGCGCTTTTCCAC
1 AAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTCCAC
*
488774 AAACACCGCTAAAGATCACGACCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTCC-AC
*
488817 AAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTCTCAA
1 AAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTC-CAC
488860 AAACGCCGCTAAA
1 AAACGCCGCTAAA
488873 AGTATGAAAT
Statistics
Matches: 215, Mismatches: 6, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
41 4 0.02
42 120 0.56
43 90 0.42
44 1 0.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTCCAC
Found at i:489479 original size:18 final size:18
Alignment explanation
Indices: 489456--489496 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
489446 TGTGCCTCCT
489456 GCAAATTGTTCTTGGACC
1 GCAAATTGTTCTTGGACC
489474 GCAAATTGTTCTTGGACC
1 GCAAATTGTTCTTGGACC
489492 GCAAA
1 GCAAA
489497 GTGTAGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (18 bp):
GCAAATTGTTCTTGGACC
Found at i:489506 original size:18 final size:18
Alignment explanation
Indices: 489456--489506 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
489446 TGTGCCTCCT
* *
489456 GCAAATTGTTCTTGGACC
1 GCAAAGTGTACTTGGACC
* *
489474 GCAAATTGTTCTTGGACC
1 GCAAAGTGTACTTGGACC
*
489492 GCAAAGTGTAGTTGG
1 GCAAAGTGTACTTGG
489507 TTTTTCCTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (18 bp):
GCAAAGTGTACTTGGACC
Found at i:493541 original size:14 final size:14
Alignment explanation
Indices: 493515--493559 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
493505 TAAACCTGTT
*
493515 TAAACCCTAAACCA
1 TAAACCTTAAACCA
* *
493529 TATATCTTAAACCA
1 TAAACCTTAAACCA
*
493543 TAAACCTTAAACTA
1 TAAACCTTAAACCA
493557 TAA
1 TAA
493560 TGATAATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:493811 original size:40 final size:40
Alignment explanation
Indices: 493717--493844 Score: 175
Period size: 40 Copynumber: 3.2 Consensus size: 40
493707 TTATATAACT
* * *
493717 TTTAGCGGCGTTTTACTAAAAGCGTCGCTAATGCCCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTC-AGTC
*
493758 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCAGTC
1 TTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCAGTC
* * * *
493798 TTTAACGGTGTTTTACCAAAAGCGTCGCTAATGATCAGTT
1 TTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCAGTC
493838 TTTAGCG
1 TTTAGCG
493845 ACGCCGCTGT
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 44 0.57
41 33 0.43
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (40 bp):
TTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCAGTC
Found at i:494216 original size:13 final size:12
Alignment explanation
Indices: 494187--494229 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
494177 AGCAAAATAG
**
494187 GTTTTTAGTAGC
1 GTTTTTAGCGGC
494199 GTTTTTAGCGGC
1 GTTTTTAGCGGC
494211 GTTTTTAGCGGC
1 GTTTTTAGCGGC
494223 GTTTTTA
1 GTTTTTA
494230 ATAAAAGCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.12, C:0.12, G:0.28, T:0.49
Consensus pattern (12 bp):
GTTTTTAGCGGC
Found at i:495325 original size:14 final size:14
Alignment explanation
Indices: 495306--495425 Score: 73
Period size: 14 Copynumber: 8.5 Consensus size: 14
495296 GTTATGGGCC
*
495306 AGTTTAGGGTTTAA
1 AGTTTAGGGTTTAG
* *
495320 AGTTTA-TGTGTA-
1 AGTTTAGGGTTTAG
*
495332 AGGTTTATGGTTTTAG
1 A-GTTTA-GGGTTTAG
* * *
495348 GGTTTATGGTTTTAA
1 AGTTTA-GGGTTTAG
*
495363 AGTTTATGGTTTAG
1 AGTTTAGGGTTTAG
* * *
495377 GGGTTAAGGTTTAG
1 AGTTTAGGGTTTAG
495391 AGTTTAGGGTTTAG
1 AGTTTAGGGTTTAG
* *
495405 GGTTTATGGTTTAG
1 AGTTTAGGGTTTAG
*
495419 GGTTTAG
1 AGTTTAG
495426 TGTTAATAAA
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
12 1 0.01
13 9 0.11
14 51 0.62
15 21 0.26
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.47
Consensus pattern (14 bp):
AGTTTAGGGTTTAG
Found at i:495415 original size:28 final size:28
Alignment explanation
Indices: 495306--495425 Score: 118
Period size: 28 Copynumber: 4.2 Consensus size: 28
495296 GTTATGGGCC
** *
495306 AGTTTAGGGTTTAAAGTTTAT-GTGTA-
1 AGTTTAGGGTTTAGGGTTTATGGTTTAG
* *
495332 AGGTTTATGGTTTTAGGGTTTATGGTTTTAA
1 A-GTTTA-GGGTTTAGGGTTTATGG-TTTAG
* * *
495363 AGTTTATGGTTTAGGGGTTAAGGTTTAG
1 AGTTTAGGGTTTAGGGTTTATGGTTTAG
495391 AGTTTAGGGTTTAGGGTTTATGGTTTAG
1 AGTTTAGGGTTTAGGGTTTATGGTTTAG
*
495419 GGTTTAG
1 AGTTTAG
495426 TGTTAATAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
27 5 0.07
28 47 0.62
29 14 0.18
30 8 0.11
31 1 0.01
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.47
Consensus pattern (28 bp):
AGTTTAGGGTTTAGGGTTTATGGTTTAG
Found at i:495458 original size:6 final size:7
Alignment explanation
Indices: 495333--495459 Score: 80
Period size: 7 Copynumber: 18.0 Consensus size: 7
495323 TTATGTGTAA
495333 GGTTTAT
1 GGTTTAT
*
495340 GGTTTTAG
1 GG-TTTAT
495348 GGTTTAT
1 GGTTTAT
*
495355 GGTTTTAA
1 GG-TTTAT
*
495363 AGTTTAT
1 GGTTTAT
*
495370 GGTTTAG
1 GGTTTAT
* *
495377 GGGTTAA
1 GGTTTAT
495384 GGTTTA-
1 GGTTTAT
*
495390 GAGTTTAG
1 G-GTTTAT
*
495398 GGTTTAG
1 GGTTTAT
495405 GGTTTAT
1 GGTTTAT
*
495412 GGTTTAG
1 GGTTTAT
495419 GGTTTA-
1 GGTTTAT
*
495425 GTGTTAAT
1 G-GTTTAT
***
495433 AAATTAT
1 GGTTTAT
495440 GGTTTAT
1 GGTTTAT
495447 GGTTTA-
1 GGTTTAT
495453 GGTTTAT
1 GGTTTAT
495460 ATGGTTAATG
Statistics
Matches: 93, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
6 8 0.09
7 73 0.78
8 12 0.13
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (7 bp):
GGTTTAT
Found at i:495705 original size:14 final size:14
Alignment explanation
Indices: 495669--495705 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
495659 GAAAAAAATG
495669 AAATTATTTAGATT
1 AAATTATTTAGATT
495683 AAATT-TTTAGATT
1 AAATTATTTAGATT
495696 AAATTATTTA
1 AAATTATTTA
495706 AGGGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
AAATTATTTAGATT
Found at i:498712 original size:19 final size:19
Alignment explanation
Indices: 498688--498727 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
498678 ATTGGATTTG
498688 ACTATAATTTGATATACCA
1 ACTATAATTTGATATACCA
498707 ACTATAATTTGATATACCA
1 ACTATAATTTGATATACCA
498726 AC
1 AC
498728 GAGCTTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (19 bp):
ACTATAATTTGATATACCA
Found at i:499591 original size:15 final size:13
Alignment explanation
Indices: 499559--499593 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
499549 TTACATAATA
499559 CATAAATATATAT
1 CATAAATATATAT
499572 CATAAATATATAT
1 CATAAATATATAT
499585 CATATAATA
1 CATA-AATA
499594 ACTTACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (13 bp):
CATAAATATATAT
Found at i:499646 original size:43 final size:43
Alignment explanation
Indices: 499599--499800 Score: 183
Period size: 43 Copynumber: 4.5 Consensus size: 43
499589 TAATAACTTA
* * *
499599 CATAACTTATATACCTTACAAAATACATAAATATATATCATAT
1 CATAACTTACAAAACTTACAAAATACATAAATATATATCATAT
* *
499642 CATAACTTACACAACTTACATAATACATAAATATATATCATAT
1 CATAACTTACAAAACTTACAAAATACATAAATATATATCATAT
*
499685 AATAACTTACAAAACTTA-AATAATACATAAATATATATATCATAAAT
1 CATAACTTACAAAACTTACAA-AATACAT-AA-ATATATATCAT--AT
* * ** * *
499732 -ATATATCATATCATAACTTACATACCTTACATAAATGTATATCATAA
1 CATA-A-CTTA-CAAAACTTACA-A-AATACATAAATATATATCATAT
*
499779 CATAACTTACATAACTTACAAA
1 CATAACTTACAAAACTTACAAA
499801 GCTTACTTAA
Statistics
Matches: 132, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
42 1 0.01
43 62 0.47
44 3 0.02
45 22 0.17
46 6 0.05
47 5 0.04
48 6 0.05
49 18 0.14
50 3 0.02
51 6 0.05
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.33
Consensus pattern (43 bp):
CATAACTTACAAAACTTACAAAATACATAAATATATATCATAT
Found at i:499735 original size:13 final size:13
Alignment explanation
Indices: 499717--499741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
499707 ATACATAAAT
499717 ATATATATCATAA
1 ATATATATCATAA
499730 ATATATATCATA
1 ATATATATCATA
499742 TCATAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATATCATAA
Found at i:499755 original size:9 final size:9
Alignment explanation
Indices: 499743--499815 Score: 60
Period size: 9 Copynumber: 8.1 Consensus size: 9
499733 TATATCATAT
499743 CATAACTTA
1 CATAACTTA
*
499752 CATACCTTA
1 CATAACTTA
*
499761 CATAAATGTA
1 CATAACT-TA
* * *
499771 TATCA-TAA
1 CATAACTTA
499779 CATAACTTA
1 CATAACTTA
499788 CATAACTTA
1 CATAACTTA
499797 CA-AAGCTTA
1 CATAA-CTTA
*
499806 CTTAACTTA
1 CATAACTTA
499815 C
1 C
499816 GTAATACATA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
8 6 0.12
9 37 0.74
10 7 0.14
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Found at i:504936 original size:13 final size:14
Alignment explanation
Indices: 504920--504948 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
504910 TTCTAAATAT
504920 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
504933 TTATAATTGTTTAA
1 TTATAATTGTTTAA
504947 TT
1 TT
504949 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:505382 original size:15 final size:15
Alignment explanation
Indices: 505357--505399 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
505347 GCAACAACTT
505357 AGAGCGGAGGCAGCAG
1 AGAG-GGAGGCAGCAG
505373 AGAGGGAGGCAGCAG
1 AGAGGGAGGCAGCAG
*
505388 CGAGGGAGGCAG
1 AGAGGGAGGCAG
505400 AGGCACGAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.30, C:0.16, G:0.53, T:0.00
Consensus pattern (15 bp):
AGAGGGAGGCAGCAG
Found at i:505403 original size:21 final size:21
Alignment explanation
Indices: 505366--505432 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
505356 TAGAGCGGAG
505366 GCAGC-AGAGAGG--GAGGCA
1 GCAGCGAGAGAGGCAGAGGCA
*
505384 GCAGCGAGGGAGGCAGAGGCA
1 GCAGCGAGAGAGGCAGAGGCA
*
505405 -CGAGCGAGAGAGGCAGAGGTA
1 GC-AGCGAGAGAGGCAGAGGCA
505426 GCAGCGA
1 GCAGCGA
505433 TGGCAGCAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.12
19 6 0.15
20 1 0.02
21 28 0.68
22 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.49, T:0.01
Consensus pattern (21 bp):
GCAGCGAGAGAGGCAGAGGCA
Found at i:509542 original size:24 final size:24
Alignment explanation
Indices: 509505--509551 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
509495 TAAATTTAGG
* * *
509505 TTTTTTCTATTTTAGTTACTTTAA
1 TTTTTTCTAATTTAATAACTTTAA
*
509529 TTTTTTTTAATTTAATAACTTTA
1 TTTTTTCTAATTTAATAACTTTA
509552 GATAAGATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTTTCTAATTTAATAACTTTAA
Found at i:514138 original size:43 final size:43
Alignment explanation
Indices: 514074--514336 Score: 395
Period size: 43 Copynumber: 6.1 Consensus size: 43
514064 CCAGCATTAC
*
514074 GCCTGCTAGGCACGAAGGCCCGAATACACATCAACGGCACGAA
1 GCCTGCTAGGCACGAAAGCCCGAATACACATCAACGGCACGAA
* *
514117 GCCTGCTAGGCACGAAAGCCCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAAGCCCGAATACACATCAACGGCACGAA
*
514160 GCCTGCTAGGCACGAAGGCCCGAATACACATCAACGGCACGAA
1 GCCTGCTAGGCACGAAAGCCCGAATACACATCAACGGCACGAA
* *
514203 GCCTGCTAGGCACGAAAGCCCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAAGCCCGAATACACATCAACGGCACGAA
*
514246 GCCTGCTAGGCACG-AAGACCCGAATACACATC-ACTGGCATGAA
1 GCCTGCTAGGCACGAAAG-CCCGAATACACATCAAC-GGCACGAA
* * * *
514289 TCCTGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAAGCCCGAATACACATCAACGGCACGAA
514332 GCCTG
1 GCCTG
514337 TGGGATTTAA
Statistics
Matches: 198, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
42 4 0.02
43 191 0.96
44 3 0.02
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAAGCCCGAATACACATCAACGGCACGAA
Found at i:514206 original size:86 final size:86
Alignment explanation
Indices: 514074--514336 Score: 474
Period size: 86 Copynumber: 3.1 Consensus size: 86
514064 CCAGCATTAC
514074 GCCTGCTAGGCACGAAGGCCCGAATACACATCAACGGCACGAAGCCTGCTAGGCACGAAAGCCCG
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCAACGGCACGAAGCCTGCTAGGCACGAAAGCCCG
514139 AATATACATCACCGGCACGAA
66 AATATACATCACCGGCACGAA
514160 GCCTGCTAGGCACGAAGGCCCGAATACACATCAACGGCACGAAGCCTGCTAGGCACGAAAGCCCG
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCAACGGCACGAAGCCTGCTAGGCACGAAAGCCCG
514225 AATATACATCACCGGCACGAA
66 AATATACATCACCGGCACGAA
* * * *
514246 GCCTGCTAGGCACGAAGACCCGAATACACATC-ACTGGCATGAATCCTGCTAGGCACGAAGGCCC
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCAAC-GGCACGAAGCCTGCTAGGCACGAAAGCCC
514310 GAATATACATCACCGGCACGAA
65 GAATATACATCACCGGCACGAA
514332 GCCTG
1 GCCTG
514337 TGGGATTTAA
Statistics
Matches: 172, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
85 2 0.01
86 170 0.99
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (86 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCAACGGCACGAAGCCTGCTAGGCACGAAAGCCCG
AATATACATCACCGGCACGAA
Found at i:518045 original size:28 final size:27
Alignment explanation
Indices: 517981--518045 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
517971 ACACAAATTG
* * *
517981 AAAATATAATAAAAAGTGATTATATTA
1 AAAATAAAATAAAAAGTAAATATATTA
* *
518008 AAATTGAAAATAAAATGTAAATATGATTA
1 AAAAT-AAAATAAAAAGTAAATAT-ATTA
518037 AAAATAAAA
1 AAAATAAAA
518046 AATATATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 18 0.60
29 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAATAAAATAAAAAGTAAATATATTA
Found at i:525723 original size:46 final size:46
Alignment explanation
Indices: 525558--525732 Score: 149
Period size: 46 Copynumber: 3.8 Consensus size: 46
525548 ATTTAGGCAT
* ** * * * *
525558 CCGAACTCGTTGAGTTGAGTTTGAGTTAACTTATGGATGCGAATGT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGAAGCGAACGC
* * * * *
525604 TCGAGCTCGTTGAGTTGAGTCCGAGTTCA-TGAGATGTAA-C-TAGGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT--TATGGAAGCGAACGC
*
525649 ATCCGAGCTCGTTGAGTTGACTCCGAGTTCACTTATGGAAGCGAACGC
1 --CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGAAGCGAACGC
** *
525697 CCGAGCTCGTTGAGTTGAGTTTGAGTTCGCTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
525733 GCGGGTTACA
Statistics
Matches: 101, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
45 3 0.03
46 62 0.61
47 32 0.32
48 4 0.04
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGAAGCGAACGC
Found at i:531630 original size:40 final size:40
Alignment explanation
Indices: 531576--531889 Score: 450
Period size: 40 Copynumber: 7.8 Consensus size: 40
531566 CATTTGAATG
531576 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * *
531616 ATATCCGGGATAAGACCCGAAGGCATTTGTGTGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
531656 ATATCCGGGCTAAGACCCGACGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
531696 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
531736 ATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTG--AT
*
531778 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
531818 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
** * *
531858 ATGCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
531890 TTGTGGTTAT
Statistics
Matches: 246, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
40 209 0.85
41 2 0.01
42 35 0.14
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:531840 original size:122 final size:120
Alignment explanation
Indices: 531576--531889 Score: 452
Period size: 122 Copynumber: 2.6 Consensus size: 120
531566 CATTTGAATG
* *
531576 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGATAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATATCCGGGATAAGACCCGAAGGCA
* * *
531641 TTTGTGTGAACTGATATATCCGGGCTAAGACCCGACGGCATTTGTGCGAATTGAT
66 TTTGTGCGAACTGATATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAATTGAT
* *
531696 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATATCCGGGATAAGACCCGAAGGCA
**
531761 TTTGTGCGAGTTGATATATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
66 TTTGTGCGAACTG--ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAA-TTGAT
* ** *
531818 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGCTATGCCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTTGATATATCCGGGATAAGACCCGAAGGC
*
531882 AATTGTGC
65 ATTTGTGC
531890 TTGTGGTTAT
Statistics
Matches: 175, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
120 71 0.41
121 5 0.03
122 99 0.57
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (120 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATATCCGGGATAAGACCCGAAGGCA
TTTGTGCGAACTGATATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAATTGAT
Found at i:531903 original size:162 final size:160
Alignment explanation
Indices: 531576--531909 Score: 474
Period size: 162 Copynumber: 2.1 Consensus size: 160
531566 CATTTGAATG
531576 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGATAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGATAAGACCCGAAGGCA
* * * * *
531641 TTTGTGTGAACTGATATATCCGGGCTAAGACCCGACGGCATTTGTGCGAATTGATATATCCGGGC
66 ATTGTGTCAACTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAATTGATATACCCGGGC
*
531706 TAAGACCCGAAGGCAATTGTGCGAGTTGAT
131 TAAGACCCGAAGGCAATTGTGCGAGTGGAT
* * *
531736 ATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATATATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTG--ATATATCCGGGATAAGACCCGAAGG
* * * *
531801 CAATTGTG-CAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATGCCCG
64 CAATTGTGTCAA-CTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAATTGATATACCCG
* ** *
531865 GGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
128 GGCTAAGACCCGAAGGCAATTGTGCGAGTGGAT
531898 ATATCC-GGCTAA
1 ATATCCGGGCTAA
531910 ATTCCGAAGA
Statistics
Matches: 154, Mismatches: 17, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
160 36 0.23
161 8 0.05
162 110 0.71
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (160 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGATAAGACCCGAAGGCA
ATTGTGTCAACTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAATTGATATACCCGGGC
TAAGACCCGAAGGCAATTGTGCGAGTGGAT
Found at i:537810 original size:49 final size:49
Alignment explanation
Indices: 537754--537876 Score: 155
Period size: 47 Copynumber: 2.6 Consensus size: 49
537744 TATTTGAATA
* * *
537754 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAACGTGATG
* * *
537803 AATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAACGTGATG
*
537850 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
537877 TCCCGAAGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
47 48 0.76
48 1 0.02
49 14 0.22
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAACGTGATG
Found at i:565696 original size:49 final size:50
Alignment explanation
Indices: 565511--565708 Score: 184
Period size: 50 Copynumber: 4.0 Consensus size: 50
565501 TGATCTATTG
* * * * * *
565511 TGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAGC
1 TGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATGA
* * * ** *
565562 TGTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGG
1 TGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGA
* *
565612 TGAGGTCACGTGTGTAGTACTAAGTGCAGGTTACTACGTGTACCAGACT-A
1 TGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TGA
* * * * * *
565662 T-TGGTCGCATTTGTAGTACTAAGTGGAGGCTACTATGCGTACCAGAT
1 TGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
565709 AGCTTCGGCT
Statistics
Matches: 121, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
48 1 0.01
49 37 0.31
50 45 0.37
51 38 0.31
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (50 bp):
TGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGA
Found at i:568735 original size:15 final size:15
Alignment explanation
Indices: 568715--568779 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
568705 GTGTCTTGGG
568715 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
568730 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
568745 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
568760 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
568774 TTTCTT
1 TTTCTT
568780 ATTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.28
15 27 0.63
16 4 0.09
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:568747 original size:30 final size:31
Alignment explanation
Indices: 568711--568779 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
568701 TATCGTGTCT
568711 TGGGTTTCTT-TAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCT-TGGATTTCTTTATTC
568741 TGGGTTT-TTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCTTGGATTTCTTTATTC
*
568771 -GGTTTTCTT
1 TGGGTTTCTT
568780 ATTATCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.61
Consensus pattern (31 bp):
TGGGTTTCTTCTATCTTGGATTTCTTTATTC
Found at i:575345 original size:37 final size:36
Alignment explanation
Indices: 575291--575363 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
575281 TCAATGATGA
575291 ATCAATATAAATACAAACTCTTTACCCGAGTTAGGT
1 ATCAATATAAATACAAACTCTTTACCCGAGTTAGGT
* * *
575327 ATCACTATAAATTACAAACTCTTTCCCCGATTTAGGT
1 ATCAATATAAA-TACAAACTCTTTACCCGAGTTAGGT
575364 TGTACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (36 bp):
ATCAATATAAATACAAACTCTTTACCCGAGTTAGGT
Found at i:578010 original size:52 final size:50
Alignment explanation
Indices: 577891--578067 Score: 248
Period size: 51 Copynumber: 3.5 Consensus size: 50
577881 GGATACCAGA
* * * *
577891 TGGCCTGCACATAGTACCACCCTTGTAGTCAAAGCTACCTTCTTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTA-ACAAAGCTATCTTCTTCACAAAG
577942 TGGCCTTCACATAGTACCACACTTGTAACCAAAGCTATCTTTCTTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTAA-CAAAGCTATC-TTCTTCACAAAG
* * * *
577994 TGGCCTTCACAAAGTACCACACTTGTGACTAAGCTATC-TCTTCTCAAAG
1 TGGCCTTCACATAGTACCACACTTGTAACAAAGCTATCTTCTTCACAAAG
578043 TGGCCTTCACATAGTACCACACTTG
1 TGGCCTTCACATAGTACCACACTTG
578068 AGTTACTAGT
Statistics
Matches: 115, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
49 34 0.30
51 43 0.37
52 38 0.33
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (50 bp):
TGGCCTTCACATAGTACCACACTTGTAACAAAGCTATCTTCTTCACAAAG
Found at i:590604 original size:47 final size:46
Alignment explanation
Indices: 590535--590848 Score: 189
Period size: 47 Copynumber: 6.7 Consensus size: 46
590525 GGTATAATAC
590535 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATC-AAGT
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTC-TCCATCGAAGT
** * * * *
590582 CGATGCTATGTCCCAGACATGGTCTTACACTAACTATCAAAATCGAGGC
1 CGATGC-ATGTCCCAGACATGGTCTTACACTGGCTCTC--CATCGAAGT
* * * *
590631 CGACGCCATGTCCCAGACATGGTATTACACTAGCTCTCACATATCCG-TGT
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTCTC-C--AT-CGAAGT
* * * * *
590681 CGATGCCATGTCCCAGACATGGTCTTACACTGACACAT--TTCGTAGC
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTC-TCCATCGAAGT
* * * *
590727 CGATACATGTCCCAGACAT-GTCTTACACTGGCT-TACATCAAGAGGA
1 CGATGCATGTCCCAGACATGGTCTTACACTGGCTCTCCATC--GAAGT
* * * *
590773 CGATGCATGTCCCGGACATGATATTACATTGGCTCT-CAT--AATGT
1 CGATGCATGTCCCAGACATGGTCTTACACTGGCTCTCCATCGAA-GT
590817 GGCCGATGCATGTCCCAGACAT-GTCTTACACT
1 ---CGATGCATGTCCCAGACATGGTCTTACACT
590849 AGCACACAAA
Statistics
Matches: 208, Mismatches: 39, Indels: 41
0.72 0.14 0.14
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 15 0.07
45 16 0.08
46 35 0.17
47 63 0.30
48 5 0.02
49 34 0.16
50 35 0.17
51 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGGTCTTACACTGGCTCTCCATCGAAGT
Found at i:590661 original size:49 final size:50
Alignment explanation
Indices: 590534--590711 Score: 161
Period size: 49 Copynumber: 3.6 Consensus size: 50
590524 GGGTATAATA
* ** **
590534 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-C--AT-CAAG
1 CCGACGCCATGTCCCAGACATGGTCTTACACTAACT-ATCACAAATCCGGG
* * *
590581 TCGATGCTATGTCCCAGACATGGTCTTACACTAACTATCA-AAAT-CGAGG
1 CCGACGCCATGTCCCAGACATGGTCTTACACTAACTATCACAAATCCG-GG
* * * * *
590630 CCGACGCCATGTCCCAGACATGGTATTACACTAGCTCTCACATATCCGTG
1 CCGACGCCATGTCCCAGACATGGTCTTACACTAACTATCACAAATCCGGG
* *
590680 TCGATGCCATGTCCCAGACATGGTCTTACACT
1 CCGACGCCATGTCCCAGACATGGTCTTACACT
590712 GACACATTTC
Statistics
Matches: 108, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
46 3 0.03
47 32 0.30
48 3 0.03
49 35 0.32
50 33 0.31
51 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (50 bp):
CCGACGCCATGTCCCAGACATGGTCTTACACTAACTATCACAAATCCGGG
Found at i:590707 original size:99 final size:96
Alignment explanation
Indices: 590534--590711 Score: 259
Period size: 96 Copynumber: 1.8 Consensus size: 96
590524 GGGTATAATA
* * * *
590534 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGTCGATGCTATGTCCCAGA
1 CCGACGCCATGTCCCAGACATGGTATTACACTAGCTCATCCATCAAGTCGATGCCATGTCCCAGA
590599 CATGGTCTTACACTAACTATCAAAATCGAGG
66 CATGGTCTTACACTAACTATCAAAATCGAGG
**
590630 CCGACGCCATGTCCCAGACATGGTATTACACTAGCTC-TCACATATCCGTGTCGATGCCATGTCC
1 CCGACGCCATGTCCCAGACATGGTATTACACTAGCTCATC-C--AT-CAAGTCGATGCCATGTCC
590694 CAGACATGGTCTTACACT
62 CAGACATGGTCTTACACT
590712 GACACATTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
95 2 0.03
96 35 0.49
98 2 0.03
99 33 0.46
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (96 bp):
CCGACGCCATGTCCCAGACATGGTATTACACTAGCTCATCCATCAAGTCGATGCCATGTCCCAGA
CATGGTCTTACACTAACTATCAAAATCGAGG
Found at i:601958 original size:55 final size:55
Alignment explanation
Indices: 601840--601943 Score: 127
Period size: 55 Copynumber: 1.9 Consensus size: 55
601830 TGGGTCAATG
* * * ** *
601840 TTGAATACGAGCAAGCCACACAGGCATGTGCCTTGGCCATGTTTAAAAGATAGTA
1 TTGAACACGAGTAGGCCACACAGGCATGTGCCAAGGCCATGTTGAAAAGATAGTA
* * *
601895 TTGAACACGAGTAGGCCACACGGGCGTGTGCCAAGGCCGTGTTGAAAAG
1 TTGAACACGAGTAGGCCACACAGGCATGTGCCAAGGCCATGTTGAAAAG
601944 TCAGTGTTGC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (55 bp):
TTGAACACGAGTAGGCCACACAGGCATGTGCCAAGGCCATGTTGAAAAGATAGTA
Found at i:606505 original size:66 final size:66
Alignment explanation
Indices: 606428--606560 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
606418 ACTAAATTGT
*
606428 AAAAGTTATAAAATATGTAGTAAAAGTGTGTTTTAATGGAAACTGTGGGCTGTTATAGTTATGAA
1 AAAAGTTATAAAATATGTAGTAAAAGTGTGTTTTAATGGAAACTGTGGGCTGTTATAGCTATGAA
606493 A
66 A
* *
606494 AAAAGTTATAAAATATGTAGTAAAAGTGTGTTTTAATGGAAATTGTGGGCTGTTATGGCTATGAA
1 AAAAGTTATAAAATATGTAGTAAAAGTGTGTTTTAATGGAAACTGTGGGCTGTTATAGCTATGAA
606559 A
66 A
606560 A
1 A
606561 TGATCCGGGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (66 bp):
AAAAGTTATAAAATATGTAGTAAAAGTGTGTTTTAATGGAAACTGTGGGCTGTTATAGCTATGAA
A
Found at i:631267 original size:28 final size:28
Alignment explanation
Indices: 631235--631304 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
631225 ATAGTAAGTC
631235 CGCACACTTAGTGCT-TA-ATAGTCAAACT
1 CGCACACTTAGTGCTATACA-A-TCAAACT
*
631263 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
631291 CGCACACTTAGTGC
1 CGCACACTTAGTGC
631305 CAATCTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 35 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:639130 original size:13 final size:12
Alignment explanation
Indices: 639110--639140 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
639100 ATTTTGAATA
639110 TTTTATTTTATT
1 TTTTATTTTATT
639122 TTATTATTTTATT
1 TT-TTATTTTATT
639135 TTTTAT
1 TTTTAT
639141 AAAGAACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:646216 original size:15 final size:15
Alignment explanation
Indices: 646196--646264 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 15
646186 ATATCTTGGG
646196 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* * *
646211 TCTCTTTATTCTAGA
1 TTTCTTTATCCTGGA
* *
646226 ATTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
646241 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
646256 TTTCTTTAT
1 TTTCTTTAT
646265 TCAGTTTCCT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.16, C:0.17, G:0.10, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:646261 original size:30 final size:30
Alignment explanation
Indices: 646187--646266 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
646177 CATAGTATCA
* * *
646187 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* * *
646217 TAT-TCTAGAATTCTTTATTCTGGATTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
646247 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
646267 AGTTTCCTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.03
30 38 0.95
31 1 0.03
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.55
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:648823 original size:93 final size:93
Alignment explanation
Indices: 648663--648835 Score: 220
Period size: 93 Copynumber: 1.9 Consensus size: 93
648653 AGGATGTTTG
* * * * * * *** * *
648663 GGCATCCGAACTCTTTGAGTTGAGTCTGAGTTCATTTATGGATGCGAATGTCCGAATTCGTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCGTTAAG
648728 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
648756 GGCATCCAAACTCGTTGAGTTGAGTCCGATTTCACTCATGGATGCAAACACCCGAGCTCGTTAAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCGTTAAG
*
648821 TTGAGTTCGAGTTCG
66 TTGAGTCCGAGTTCG
648836 CTTATGGGCG
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
93 66 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.31
Consensus pattern (93 bp):
GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCGTTAAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:661575 original size:48 final size:45
Alignment explanation
Indices: 661380--661580 Score: 176
Period size: 46 Copynumber: 4.3 Consensus size: 45
661370 TATAAGAGCC
* * *
661380 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCACTGAGA-G-GTGCT
* * *
661428 AGTGTAAGA-CATGTCTGGGACATGCATCAGC-CATGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCAC-TGAGAGGT--GCT
* ** *
661474 AGTGTAAGA-TATGTCTGGGACATGCATCGGCTAC-GAGATTTGTT
1 AGTGTAAGACCATGTCTGGGACATGCATCGGC-ACTGAGAGGTGCT
* *
661518 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCAC-T-GAGAGGTGCT
661566 AGTGTAAGACCATGT
1 AGTGTAAGACCATGT
661581 ATAGGACAAG
Statistics
Matches: 128, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
44 11 0.09
45 15 0.12
46 56 0.44
47 14 0.11
48 32 0.25
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (45 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCACTGAGAGGTGCT
Found at i:671316 original size:25 final size:25
Alignment explanation
Indices: 671279--671331 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
671269 TGTTAGAGTG
671279 TACCATCCCTCTTAACTACCCATTC
1 TACCATCCCTCTTAACTACCCATTC
*
671304 TACCATCCTTCTTAACTACCCATTC
1 TACCATCCCTCTTAACTACCCATTC
671329 TAC
1 TAC
671332 TTTAGAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.34
Consensus pattern (25 bp):
TACCATCCCTCTTAACTACCCATTC
Found at i:675431 original size:42 final size:41
Alignment explanation
Indices: 675318--675415 Score: 126
Period size: 41 Copynumber: 2.3 Consensus size: 41
675308 ATGTATGAAT
* *
675318 TCATGTAAGACCATGTCTGGGACATTGGCATCGTATATGAC
1 TCATGTAAGACCATGTCTGGGACAGTGGCATCATATATGAC
* *
675359 TCATGTAAAACCTTGTCTGGGACAGTGGCATCAATATATGA-
1 TCATGTAAGACCATGTCTGGGACAGTGGCATC-ATATATGAC
675400 TAACATGTAAGACCAT
1 T--CATGTAAGACCAT
675416 ATCTAGGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 30 0.62
42 7 0.15
43 11 0.23
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (41 bp):
TCATGTAAGACCATGTCTGGGACAGTGGCATCATATATGAC
Found at i:677217 original size:15 final size:15
Alignment explanation
Indices: 677197--677226 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
677187 CAACACTTGT
677197 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
677212 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
677227 AATACATTAG
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:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:686257 original size:69 final size:69
Alignment explanation
Indices: 686142--686330 Score: 189
Period size: 69 Copynumber: 2.7 Consensus size: 69
686132 AATATTTATG
* * * * * * * * *
686142 TCACATTAAGGCTCACAAGAAAAGAGCCCCAGCCTCTAACACAGTTAGTGAGAGCAAAGTTCCCA
1 TCACACTAAGGCTCATAGGCAAAGAGTCACAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCA
* *
686207 GCTT
66 ACTA
** *
686211 TCACACTAAGGCTCATAGGCAAAGAGTCACAGCCTCCAACATAGTTAGCAAGAGCAAAGCTCTCA
1 TCACACTAAGGCTCATAGGCAAAGAGTCACAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCA
686276 ACTA
66 ACTA
* ** * * * *
686280 TAATTCTAAGGCTCGTAGGCGAAGAGTCGCAACCTCCAACATAGTTAGTGA
1 TCACACTAAGGCTCATAGGCAAAGAGTCACAGCCTCCAACATAGTTAGTGA
686331 AAGAAAAACT
Statistics
Matches: 97, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 97 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (69 bp):
TCACACTAAGGCTCATAGGCAAAGAGTCACAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCA
ACTA
Found at i:686343 original size:69 final size:69
Alignment explanation
Indices: 686216--686344 Score: 179
Period size: 69 Copynumber: 1.9 Consensus size: 69
686206 AGCTTTCACA
* * *
686216 CTAAGGCTCATAGGCAAAGAGTCACAGCCTCCAACATAGTTAGCAAGAGCAAAGCTCTCAACTAT
1 CTAAGGCTCATAGGCAAAGAGTCACAACCTCCAACATAGTTAGCAAGAGAAAAACTCTCAACTAT
686281 AATT
66 AATT
* * * *
686285 CTAAGGCTCGTAGGCGAAGAGTCGCAACCTCCAACATAGTTAGTGAA-AGAAAAACTCTCA
1 CTAAGGCTCATAGGCAAAGAGTCACAACCTCCAACATAGTTAG-CAAGAGAAAAACTCTCA
686345 GCTGTCATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
69 50 0.96
70 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (69 bp):
CTAAGGCTCATAGGCAAAGAGTCACAACCTCCAACATAGTTAGCAAGAGAAAAACTCTCAACTAT
AATT
Found at i:686372 original size:69 final size:68
Alignment explanation
Indices: 686216--686406 Score: 170
Period size: 69 Copynumber: 2.8 Consensus size: 68
686206 AGCTTTCACA
* * * * * * *
686216 CTAAGGCTCATAGGCAAAGAGTCACAGCCTCCAACATAGTTAGCAAGAGCAAAGCTCTCAACTAT
1 CTAAGGCTCGTAGCCGAAGAGTCGCAGCCTCCAACATAGTTAG-AAAAGAAAAACTCTCAACTAT
686281 AATT
65 AATT
* * * * *
686285 CTAAGGCTCGTAGGCGAAGAGTCGCAACCTCCAACATAGTTAGTGAAAGAAAAACTCTCAGCTGT
1 CTAAGGCTCGTAGCCGAAGAGTCGCAGCCTCCAACATAGTTAG-AAAAGAAAAACTCTCAACTAT
*
686350 CATAT
65 AAT-T
* * * *
686355 C-AAGGTTTGTAGCCGAAGAG-CAGCAGCCTCTAACACAGTTAGAAAAAGAAAA
1 CTAAGGCTCGTAGCCGAAGAGTC-GCAGCCTCCAACATAGTTAG-AAAAGAAAA
686407 GTTCCAAGCT
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
68 1 0.01
69 97 0.97
70 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (68 bp):
CTAAGGCTCGTAGCCGAAGAGTCGCAGCCTCCAACATAGTTAGAAAAGAAAAACTCTCAACTATA
ATT
Found at i:688213 original size:18 final size:18
Alignment explanation
Indices: 688190--688225 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
688180 AATAAGAAAT
688190 AAAAATAAGTCATTCTAG
1 AAAAATAAGTCATTCTAG
688208 AAAAATAAGTCATTCTAG
1 AAAAATAAGTCATTCTAG
688226 GGTTCTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAAATAAGTCATTCTAG
Found at i:689707 original size:11 final size:11
Alignment explanation
Indices: 689669--689708 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
689659 ATATAATGCC
689669 TTATATGTTGG
1 TTATATGTTGG
689680 CTTATATGGTATGG
1 -TTATAT-GT-TGG
689694 TTATATGTTGG
1 TTATATGTTGG
689705 TTAT
1 TTAT
689709 TTTGGATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.27
12 8 0.31
13 8 0.31
14 3 0.12
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.53
Consensus pattern (11 bp):
TTATATGTTGG
Found at i:695672 original size:100 final size:100
Alignment explanation
Indices: 695499--695697 Score: 380
Period size: 100 Copynumber: 2.0 Consensus size: 100
695489 CCCCTCTTCC
*
695499 AGGCCCGTCACAAGGGAAACGAAAACCGAGATTTGCTTTATCCGGTATCAAACGCGAGCTGCGAG
1 AGGCCCGTCACAAGGGAAACAAAAACCGAGATTTGCTTTATCCGGTATCAAACGCGAGCTGCGAG
695564 CAAATAGAACACCTTTCAGGAGTATCAATACCGTT
66 CAAATAGAACACCTTTCAGGAGTATCAATACCGTT
*
695599 AGGCCCGTCACAAGGGAAACAAAAACTGAGATTTGCTTTATCCGGTATCAAACGCGAGCTGCGAG
1 AGGCCCGTCACAAGGGAAACAAAAACCGAGATTTGCTTTATCCGGTATCAAACGCGAGCTGCGAG
695664 CAAATAGAACACCTTTCAGGAGTATCAATACCGT
66 CAAATAGAACACCTTTCAGGAGTATCAATACCGT
695698 CACATGAATC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.20
Consensus pattern (100 bp):
AGGCCCGTCACAAGGGAAACAAAAACCGAGATTTGCTTTATCCGGTATCAAACGCGAGCTGCGAG
CAAATAGAACACCTTTCAGGAGTATCAATACCGTT
Found at i:697456 original size:15 final size:15
Alignment explanation
Indices: 697438--697468 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
697428 ATCTCTCATC
697438 TATCTATCTATTTTT
1 TATCTATCTATTTTT
697453 TATCTATCTATTTTT
1 TATCTATCTATTTTT
697468 T
1 T
697469 CTTTAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TATCTATCTATTTTT
Found at i:698170 original size:16 final size:17
Alignment explanation
Indices: 698143--698176 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
698133 AAATGGATTT
698143 AATAGAAATTAAATAGA
1 AATAGAAATTAAATAGA
698160 AATAG-AATTAAATAGA
1 AATAGAAATTAAATAGA
698176 A
1 A
698177 TTCTCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (17 bp):
AATAGAAATTAAATAGA
Found at i:699106 original size:15 final size:15
Alignment explanation
Indices: 699077--699138 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
699067 GTAGAAAGCC
* *
699077 TATTTTTTTTTCTAG
1 TATTTTATTTACTAG
699092 TATTTTATTTACTAG
1 TATTTTATTTACTAG
**
699107 CGTGTTTATTTACTAGCG
1 TAT-TTTATTTACTA--G
699125 TA-TTTATTTACTAG
1 TATTTTATTTACTAG
699139 CGTATTTGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
14 1 0.03
15 14 0.37
16 22 0.58
18 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.11, T:0.58
Consensus pattern (15 bp):
TATTTTATTTACTAG
Found at i:699116 original size:16 final size:16
Alignment explanation
Indices: 699095--699145 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
699085 TTTCTAGTAT
*
699095 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTA
699111 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
699127 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
699143 TTT
1 TTT
699146 GCTCTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:707364 original size:93 final size:93
Alignment explanation
Indices: 707251--707422 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
707241 CGCCCATAAG
* *
707251 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
707316 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
707344 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
707409 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
707423 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:707419 original size:46 final size:46
Alignment explanation
Indices: 707244--707419 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
707234 TGTAACCCGC
* * *
707244 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
707290 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
707340 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
707383 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
707420 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:708874 original size:40 final size:40
Alignment explanation
Indices: 708824--708939 Score: 153
Period size: 40 Copynumber: 2.9 Consensus size: 40
708814 GATATATTAA
*
708824 ATATCCGGGTTAAATCCCGCAGGCTTTATGCTGGTAATGT
1 ATATCCGGGTTAAATCCCGTAGGCTTTATGCTGGTAATGT
* ** * **
708864 ATCTTTGGGTTAAATCACGTAGGCTTCGTGCTGGTAATGT
1 ATATCCGGGTTAAATCCCGTAGGCTTTATGCTGGTAATGT
708904 ATATCCGGGTTAAATCCCGTAGGC-TTAGTGCTGGTA
1 ATATCCGGGTTAAATCCCGTAGGCTTTA-TGCTGGTA
708940 CTATATCTGA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
39 1 0.02
40 61 0.98
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (40 bp):
ATATCCGGGTTAAATCCCGTAGGCTTTATGCTGGTAATGT
Found at i:710767 original size:224 final size:224
Alignment explanation
Indices: 710377--710826 Score: 900
Period size: 224 Copynumber: 2.0 Consensus size: 224
710367 ATTATTGGTG
710377 GAATACATTGGTTTTTGTTGTACCCAGAGAGCGGGTGACGTGGGAGTTCTTCCAAACTGAATTCC
1 GAATACATTGGTTTTTGTTGTACCCAGAGAGCGGGTGACGTGGGAGTTCTTCCAAACTGAATTCC
710442 GAAAAAAGTATATCAGTCAGAGGTTCATCGATCAAAAACAAAAAGAATTTCTTGAGCTTAAGCAA
66 GAAAAAAGTATATCAGTCAGAGGTTCATCGATCAAAAACAAAAAGAATTTCTTGAGCTTAAGCAA
710507 GGTTCTATGTCAGTTACTGATTATGAACGGAAGTTTGTCAGACTTAGTAGATATGCTCAGAAATG
131 GGTTCTATGTCAGTTACTGATTATGAACGGAAGTTTGTCAGACTTAGTAGATATGCTCAGAAATG
710572 TGTATCGTCTGAGGCTATTATGTGTAAAC
196 TGTATCGTCTGAGGCTATTATGTGTAAAC
710601 GAATACATTGGTTTTTGTTGTACCCAGAGAGCGGGTGACGTGGGAGTTCTTCCAAACTGAATTCC
1 GAATACATTGGTTTTTGTTGTACCCAGAGAGCGGGTGACGTGGGAGTTCTTCCAAACTGAATTCC
710666 GAAAAAAGTATATCAGTCAGAGGTTCATCGATCAAAAACAAAAAGAATTTCTTGAGCTTAAGCAA
66 GAAAAAAGTATATCAGTCAGAGGTTCATCGATCAAAAACAAAAAGAATTTCTTGAGCTTAAGCAA
710731 GGTTCTATGTCAGTTACTGATTATGAACGGAAGTTTGTCAGACTTAGTAGATATGCTCAGAAATG
131 GGTTCTATGTCAGTTACTGATTATGAACGGAAGTTTGTCAGACTTAGTAGATATGCTCAGAAATG
710796 TGTATCGTCTGAGGCTATTATGTGTAAAC
196 TGTATCGTCTGAGGCTATTATGTGTAAAC
710825 GA
1 GA
710827 TTTGAAGATG
Statistics
Matches: 226, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 226 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (224 bp):
GAATACATTGGTTTTTGTTGTACCCAGAGAGCGGGTGACGTGGGAGTTCTTCCAAACTGAATTCC
GAAAAAAGTATATCAGTCAGAGGTTCATCGATCAAAAACAAAAAGAATTTCTTGAGCTTAAGCAA
GGTTCTATGTCAGTTACTGATTATGAACGGAAGTTTGTCAGACTTAGTAGATATGCTCAGAAATG
TGTATCGTCTGAGGCTATTATGTGTAAAC
Found at i:720349 original size:40 final size:40
Alignment explanation
Indices: 720299--720414 Score: 160
Period size: 40 Copynumber: 2.9 Consensus size: 40
720289 GATATATTAA
*
720299 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTTGTAATGT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATGT
* * * * *
720339 ATCTCTGGGTTAAATCACGTAGGCTTCATGCTGGTAATGT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATGT
* *
720379 ATATCCGGGTTAAATCCCACAGGCTTAGTGCTGGTA
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
720415 CTATATCCGA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (40 bp):
ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATGT
Found at i:721344 original size:47 final size:46
Alignment explanation
Indices: 721267--721583 Score: 233
Period size: 47 Copynumber: 6.9 Consensus size: 46
721257 GGTGTTACAG
*
721267 TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGA
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGA
* * * * *
721315 CGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGC-CT--GA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
* *
721358 T---AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGA
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGA
* * *** * *
721403 TGAGTGCCAGTATAAGACATGTCTGGGACCCACATCGGCCTCGATGA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGA-GA
* *
721450 TG-GTAGCCAGTGTAAGACGTGTCTGGGACATGCATCGGC--TAAG-
1 TGAG-AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
* * * ** *
721493 CGTA-ATGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGTACATA
1 TG-AGA-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCA--TTGAGA
*
721542 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
721584 ACCTAACCCA
Statistics
Matches: 212, Mismatches: 36, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
40 11 0.05
41 14 0.07
42 7 0.03
43 4 0.02
44 32 0.15
45 5 0.02
46 18 0.08
47 58 0.27
48 39 0.18
49 16 0.08
50 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (46 bp):
TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
Found at i:721420 original size:88 final size:90
Alignment explanation
Indices: 721271--721582 Score: 341
Period size: 88 Copynumber: 3.4 Consensus size: 90
721261 TTACAGTGAG
* * *
721271 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TAGAGACGAGTGCTAGTGTAAGACATG
721336 TCTGGGACATGCATCAG-C-C-TGAT
65 TCTGGGACATGCATCAGCCTCATGAT
* * *
721359 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGAGTGCCAGTATAAGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TAGAGACGAGTGCTAGTGTAAGACATG
*** *
721424 TCTGGGACCCACATCGGCCTCGATGATGGT
65 TCTGGGACATGCATCAGCCTC-ATGA---T
* *
721454 AGCCAGTGTAAGA-CGTGTCTGGGACAT-GCATCGGCTA-AG-CGTAATGCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTAGAGACG-AGTGCTAGTGTAAGACATG
*
721515 TCTGGGACATGCATCAGCACGTACATATGAG
65 TCTGGGACATGCATCAGC-C-T-C--ATGAT
*
721546 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
721583 AACCTAACCC
Statistics
Matches: 186, Mismatches: 24, Indels: 22
0.80 0.10 0.09
Matches are distributed among these distances:
88 71 0.38
89 1 0.01
90 2 0.01
91 32 0.17
92 18 0.10
93 22 0.12
94 22 0.12
95 18 0.10
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (90 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTAGAGACGAGTGCTAGTGTAAGACATGT
CTGGGACATGCATCAGCCTCATGAT
Done.