Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 54
Found at i:280711 original size:30 final size:31
Alignment explanation
Indices: 280670--280738 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
280660 ACTTTAATGG
*
280670 AAAAAATATATATGCAATAAAAAGC-AAGA-
1 AAAAAATATATATACAATAAAAAGCAAAGAC
*
280699 AAAAATATATATATATAATAAAAAGCAAAGAC
1 AAAAA-ATATATATACAATAAAAAGCAAAGAC
280731 AAAAAATA
1 AAAAAATA
280739 AGTATTACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 5 0.14
30 18 0.51
31 7 0.20
32 5 0.14
ACGTcount: A:0.68, C:0.06, G:0.07, T:0.19
Consensus pattern (31 bp):
AAAAAATATATATACAATAAAAAGCAAAGAC
Found at i:281021 original size:29 final size:29
Alignment explanation
Indices: 280967--281022 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
280957 AAAAGCTCAA
* **
280967 AAAATTAAAGTAAATAAAATGTAAGGACT
1 AAAATTAAAGTAAAAAAAATAAAAGGACT
280996 AAAATTAAA-TAAAGAAAAATAAAAGGA
1 AAAATTAAAGTAAA-AAAAATAAAAGGA
281023 AGAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (29 bp):
AAAATTAAAGTAAAAAAAATAAAAGGACT
Found at i:281099 original size:30 final size:30
Alignment explanation
Indices: 281065--281132 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
281055 AAATAAAAGA
* *
281065 GCAATAAAAATAAAATGTTAGT-GTTAATAT
1 GCAATAAAAATAAAA-GTTAATAGTTAACAT
*
281095 GCAATAAAAATGAAAGTTAATAGTTAACAT
1 GCAATAAAAATAAAAGTTAATAGTTAACAT
*
281125 GAAATAAA
1 GCAATAAA
281133 TAACATAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.54, C:0.04, G:0.13, T:0.28
Consensus pattern (30 bp):
GCAATAAAAATAAAAGTTAATAGTTAACAT
Found at i:282977 original size:39 final size:38
Alignment explanation
Indices: 282919--283050 Score: 151
Period size: 39 Copynumber: 3.4 Consensus size: 38
282909 CCTGTACACC
*
282919 CAGTAAGGACTTACTCTATGCACAAAGCAGCTGAGCCTG
1 CAGTAAGGACTTAC-CTATGCACAAAGCAGATGAGCCTG
* *
282958 CAGTAAGGTCTTATCCTATGCATAAAGCAGATGAGCCTG
1 CAGTAAGGACTTA-CCTATGCACAAAGCAGATGAGCCTG
* *
282997 CAGTAAGGACTTACCCTGA-GCACAAAG-ATGAGGAACCTG
1 CAGTAAGGACTTA-CCT-ATGCACAAAGCA-GATGAGCCTG
*
283036 CGGTAAGGACTTACC
1 CAGTAAGGACTTACC
283051 CTGAGCGCAA
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.04
39 76 0.94
40 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (38 bp):
CAGTAAGGACTTACCTATGCACAAAGCAGATGAGCCTG
Found at i:283112 original size:39 final size:38
Alignment explanation
Indices: 282981--283112 Score: 104
Period size: 39 Copynumber: 3.4 Consensus size: 38
282971 TCCTATGCAT
* * *
282981 AAAGCAGATGAGCCTGCAGTAAGGACTTACCCTGAGCAC
1 AAAGCAGA-GAGCCTACAATAAAGACTTACCCTGAGCAC
* * ** * *
283020 AAAG-ATGAGGAACCTGCGGTAAGGACTTACCCTGAGCGC
1 AAAGCA-GA-GAGCCTACAATAAAGACTTACCCTGAGCAC
* *
283059 AATGCAAAAGAGCCTACAATAAAGACTTACCCTGAGCAC
1 AAAGC-AGAGAGCCTACAATAAAGACTTACCCTGAGCAC
*
283098 AAAGCCGAGTAGCCT
1 AAAGCAGAG-AGCCT
283113 GCGCAAAACG
Statistics
Matches: 74, Mismatches: 15, Indels: 8
0.76 0.15 0.08
Matches are distributed among these distances:
38 3 0.04
39 69 0.93
40 1 0.01
41 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.24, T:0.15
Consensus pattern (38 bp):
AAAGCAGAGAGCCTACAATAAAGACTTACCCTGAGCAC
Found at i:284513 original size:29 final size:30
Alignment explanation
Indices: 284454--284513 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
284444 TTGGATCCAA
* * *
284454 AATTTAATCAAAATTTCACTTTGGTCCTCG
1 AATTTAATCAAAATTTCAATTTAGTACTCG
284484 AATTTAATCAAAA-TTCAATTTAGTACTCG
1 AATTTAATCAAAATTTCAATTTAGTACTCG
284513 A
1 A
284514 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (30 bp):
AATTTAATCAAAATTTCAATTTAGTACTCG
Found at i:286412 original size:85 final size:83
Alignment explanation
Indices: 286306--286666 Score: 378
Period size: 82 Copynumber: 4.3 Consensus size: 83
286296 TAACTTTGAA
* * * *
286306 AAGAAAAAGATGTGAATAGTATAGATTCTCAGATTTCAATGGAAATTGTATCAGTTTATCTGTGT
1 AAGAAAAGGACGTGAATAGTATAGATTCTCTGATTTCAATGGAAATT-T-TCAGTTTATCTGAGT
286371 TGATGTGAAATATCAATGAC
64 TGATGTGAAATATCAATGAC
* * *
286391 AAGAAAAGGACATGAATAGTATAGATTCCCTGATTCTC--T-AAAATATTTCAGTTTATCTGAGT
1 AAGAAAAGGACGTGAATAGTATAGATTCTCTGATT-TCAATGGAAAT-TTTCAGTTTATCTGAGT
*
286453 TGATGTGAAATGTCAATGAC
64 TGATGTGAAATATCAATGAC
* * *
286473 AAGAAAAGGACGTGAATAGTGTATATTCTCTGATTTCAATGGAAATTATTTTAGTTTATAC-GAG
1 AAGAAAAGGACGTGAATAGTATAGATTCTCTGATTTCAATGGAAA-T-TTTCAGTTTAT-CTGAG
*
286537 TTGATGTTAAATATCAATGAC
63 TTGATGTGAAATATCAATGAC
* * * * *
286558 AAGCAAAGGATGTGAATAGTATAGATAC-CGTGATTCTC--T-AAAATATTTCAGTTTATCTAAG
1 AAGAAAAGGACGTGAATAGTATAGATTCTC-TGATT-TCAATGGAAAT-TTTCAGTTTATCTGAG
*
286619 TTGATGTGAAATGTCAATGAC
63 TTGATGTGAAATATCAATGAC
* ** *
286640 AAGCAAACAACGTGAATAGTGTAGATT
1 AAGAAAAGGACGTGAATAGTATAGATT
286667 ATCTACGAGG
Statistics
Matches: 235, Mismatches: 31, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
81 3 0.01
82 119 0.51
83 9 0.04
84 7 0.03
85 92 0.39
86 5 0.02
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (83 bp):
AAGAAAAGGACGTGAATAGTATAGATTCTCTGATTTCAATGGAAATTTTCAGTTTATCTGAGTTG
ATGTGAAATATCAATGAC
Found at i:286461 original size:82 final size:82
Alignment explanation
Indices: 286356--286666 Score: 392
Period size: 82 Copynumber: 3.8 Consensus size: 82
286346 GGAAATTGTA
* *
286356 TCAGTTTATCTGTGTTGATGTGAAATATCAATGACAAGAAAAGGACATGAATAGTATAGATTCCC
1 TCAGTTTATCTGAGTTGATGTGAAATATCAATGACAAGAAAAGGACGTGAATAGTATAGATTCCC
286421 TGATTCTCTAAAATATT
66 TGATTCTCTAAAATATT
* * * *
286438 TCAGTTTATCTGAGTTGATGTGAAATGTCAATGACAAGAAAAGGACGTGAATAGTGTATATTCTC
1 TCAGTTTATCTGAGTTGATGTGAAATATCAATGACAAGAAAAGGACGTGAATAGTATAGATTCCC
*
286503 TGATT-TCAATGGAAATTATT
66 TGATTCTC--T--AAAATATT
* * * * *
286523 TTAGTTTATAC-GAGTTGATGTTAAATATCAATGACAAGCAAAGGATGTGAATAGTATAGATACC
1 TCAGTTTAT-CTGAGTTGATGTGAAATATCAATGACAAGAAAAGGACGTGAATAGTATAGATTCC
*
286587 GTGATTCTCTAAAATATT
65 CTGATTCTCTAAAATATT
* * * ** *
286605 TCAGTTTATCTAAGTTGATGTGAAATGTCAATGACAAGCAAACAACGTGAATAGTGTAGATT
1 TCAGTTTATCTGAGTTGATGTGAAATATCAATGACAAGAAAAGGACGTGAATAGTATAGATT
286667 ATCTACGAGG
Statistics
Matches: 195, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
81 3 0.02
82 122 0.63
83 1 0.01
84 1 0.01
85 65 0.33
86 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (82 bp):
TCAGTTTATCTGAGTTGATGTGAAATATCAATGACAAGAAAAGGACGTGAATAGTATAGATTCCC
TGATTCTCTAAAATATT
Found at i:286582 original size:167 final size:167
Alignment explanation
Indices: 286306--286666 Score: 537
Period size: 167 Copynumber: 2.2 Consensus size: 167
286296 TAACTTTGAA
* * * *
286306 AAGAAAAAGATGTGAATAGTATAGATTCTCAGATTTCAATGGAAATTGTATCAGTTTATCTGTGT
1 AAGAAAAAGACGTGAATAGTGTAGATTCTCAGATTTCAATGGAAATTATATCAGTTTATCTGAGT
*
286371 TGATGTGAAATATCAATGACAAGAAAAGGACATGAATAGTATAGATTCCCTGATTCTCTAAAATA
66 TGATGTGAAATATCAATGACAAGAAAAGGACATGAATAGTATAGATACCCTGATTCTCTAAAATA
*
286436 TTTCAGTTTATCTGAGTTGATGTGAAATGTCAATGAC
131 TTTCAGTTTATCTAAGTTGATGTGAAATGTCAATGAC
* * * * *
286473 AAGAAAAGGACGTGAATAGTGTATATTCTCTGATTTCAATGGAAATTATTTTAGTTTATAC-GAG
1 AAGAAAAAGACGTGAATAGTGTAGATTCTCAGATTTCAATGGAAATTATATCAGTTTAT-CTGAG
* * ** *
286537 TTGATGTTAAATATCAATGACAAGCAAAGGATGTGAATAGTATAGATACCGTGATTCTCTAAAAT
65 TTGATGTGAAATATCAATGACAAGAAAAGGACATGAATAGTATAGATACCCTGATTCTCTAAAAT
286602 ATTTCAGTTTATCTAAGTTGATGTGAAATGTCAATGAC
130 ATTTCAGTTTATCTAAGTTGATGTGAAATGTCAATGAC
*
286640 AAGCAAACA-ACGTGAATAGTGTAGATT
1 AAG-AAAAAGACGTGAATAGTGTAGATT
286667 ATCTACGAGG
Statistics
Matches: 173, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
167 169 0.98
168 4 0.02
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (167 bp):
AAGAAAAAGACGTGAATAGTGTAGATTCTCAGATTTCAATGGAAATTATATCAGTTTATCTGAGT
TGATGTGAAATATCAATGACAAGAAAAGGACATGAATAGTATAGATACCCTGATTCTCTAAAATA
TTTCAGTTTATCTAAGTTGATGTGAAATGTCAATGAC
Found at i:290864 original size:45 final size:46
Alignment explanation
Indices: 290800--290887 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
290790 TAAGAAAAGA
* *
290800 TGCTACCTAAAATGTTA-TTTTTCTATCGGAAATATTAATATCGGG
1 TGCTACCTAAAATGTTATTTTTTCTACCGAAAATATTAATATCGGG
*
290845 TGCTACCTAAAATGTTATTTTTTCTACCGAAAATGTTAATATC
1 TGCTACCTAAAATGTTATTTTTTCTACCGAAAATATTAATATC
290888 TGAAATATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 17 0.44
46 22 0.56
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (46 bp):
TGCTACCTAAAATGTTATTTTTTCTACCGAAAATATTAATATCGGG
Found at i:290944 original size:22 final size:22
Alignment explanation
Indices: 290897--290952 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
290887 CTGAAATATT
* * *
290897 CATTTTAGGTTG-CAAAATTAA
1 CATTTTAGGTAGAAAAAAATAA
* *
290918 TATTTTCGGTAGAAAAAAATAA
1 CATTTTAGGTAGAAAAAAATAA
290940 CATTTTAGGTAGA
1 CATTTTAGGTAGA
290953 GCTCTACCGA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (22 bp):
CATTTTAGGTAGAAAAAAATAA
Found at i:291401 original size:16 final size:16
Alignment explanation
Indices: 291364--291401 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
291354 CCGATTCTCC
291364 TTTTTTATTTTATTAT
1 TTTTTTATTTTATTAT
*
291380 TATTTTATTTTAATT-T
1 TTTTTTATTTT-ATTAT
291396 TTTTTT
1 TTTTTT
291402 TTCATTTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTATTTTATTAT
Found at i:292096 original size:62 final size:62
Alignment explanation
Indices: 292022--292145 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
292012 AAAGGTGTTC
*
292022 TTGAAAGTAAAAAGAATATTGAATGAAAATAGGCATGAAATGCTCAAACAACAAGTTTAAGG
1 TTGAAAGCAAAAAGAATATTGAATGAAAATAGGCATGAAATGCTCAAACAACAAGTTTAAGG
292084 TTGAAAGCAAAAAGAATATTGAATGAAAATAGGCATGAAATGCTCAAACAACAAGTTTAAGG
1 TTGAAAGCAAAAAGAATATTGAATGAAAATAGGCATGAAATGCTCAAACAACAAGTTTAAGG
292146 CTTTCTTTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (62 bp):
TTGAAAGCAAAAAGAATATTGAATGAAAATAGGCATGAAATGCTCAAACAACAAGTTTAAGG
Found at i:293193 original size:23 final size:24
Alignment explanation
Indices: 293153--293202 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
293143 CAAACCATTC
293153 AAACACAAATATCCAAAACATCCA
1 AAACACAAATATCCAAAACATCCA
*
293177 AAACAC-AA-ATCCAAAAACTTCCA
1 AAACACAAATATCC-AAAACATCCA
293200 AAA
1 AAA
293203 TGTTTTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.58
24 6 0.25
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (24 bp):
AAACACAAATATCCAAAACATCCA
Found at i:294603 original size:21 final size:21
Alignment explanation
Indices: 294574--294614 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
294564 CAACATAATT
294574 AAATCAAAAACAATA-ATTTTA
1 AAAT-AAAAACAATATATTTTA
294595 AAATAAAAACAATATATTTT
1 AAATAAAAACAATATATTTT
294615 TATTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAAAAACAATATATTTTA
Found at i:298751 original size:28 final size:28
Alignment explanation
Indices: 298719--298775 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
298709 TTCTAACTTT
298719 TAAGATCATCAATTCTTTTTGATGATCA
1 TAAGATCATCAATTCTTTTTGATGATCA
298747 TAAGATCATCAATTCTTTTTGATGATCA
1 TAAGATCATCAATTCTTTTTGATGATCA
298775 T
1 T
298776 CATTGACCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (28 bp):
TAAGATCATCAATTCTTTTTGATGATCA
Found at i:301723 original size:21 final size:21
Alignment explanation
Indices: 301684--301723 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
301674 AAGGAAGATT
*
301684 AATGAAATGATAAAGATAAGA
1 AATGAAATGATAAAAATAAGA
301705 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
301724 AAGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGA
Found at i:305699 original size:21 final size:21
Alignment explanation
Indices: 305660--305699 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
305650 AAAGAAGATT
*
305660 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
305681 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
305700 ATGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:305748 original size:22 final size:21
Alignment explanation
Indices: 305722--305762 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
305712 GCTGCATAAT
305722 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
305744 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
305763 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:307841 original size:16 final size:16
Alignment explanation
Indices: 307791--307861 Score: 79
Period size: 16 Copynumber: 4.4 Consensus size: 16
307781 TGGATTAAAA
* **
307791 TTCAGTTCAGGTTTCT
1 TTCAGTTCGGGTTAAT
**
307807 TTCAGTTCGGGTTGCT
1 TTCAGTTCGGGTTAAT
*
307823 TTCAATTCGGGTTAAT
1 TTCAGTTCGGGTTAAT
*
307839 TTCGGTTCGGGTTAAT
1 TTCAGTTCGGGTTAAT
307855 TTCAGTT
1 TTCAGTT
307862 TTAGTTCGAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.14, C:0.15, G:0.24, T:0.46
Consensus pattern (16 bp):
TTCAGTTCGGGTTAAT
Found at i:307895 original size:38 final size:39
Alignment explanation
Indices: 307828--307901 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 39
307818 TTGCTTTCAA
* * *
307828 TTCGGGTTAATTTCGGTTCGGGTTAATTTC-AGTTTTAG
1 TTCGAGTTAATTTAGGCTCGGGTTAATTTCAAGTTTTAG
* *
307866 TTCGAGTTAATTTAGGCTCTGGTTGATTTCAAGTTT
1 TTCGAGTTAATTTAGGCTCGGGTTAATTTCAAGTTT
307902 GCTAAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 25 0.83
39 5 0.17
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (39 bp):
TTCGAGTTAATTTAGGCTCGGGTTAATTTCAAGTTTTAG
Found at i:318672 original size:24 final size:22
Alignment explanation
Indices: 318635--318700 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 22
318625 GGCACTTAGA
318635 GAGAA-AAATAGAAGATAAGAAATT
1 GAGAAGAAAT-GAAGA-AAGAAA-T
*
318659 GAGAAGAAATGAAGAAATAAAT
1 GAGAAGAAATGAAGAAAGAAAT
318681 -AGAAGAAGATGAA-AAA-AAAT
1 GAGAAGAA-ATGAAGAAAGAAAT
318701 AAATGGTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
20 4 0.10
21 10 0.26
22 6 0.15
23 5 0.13
24 10 0.26
25 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (22 bp):
GAGAAGAAATGAAGAAAGAAAT
Found at i:320819 original size:19 final size:19
Alignment explanation
Indices: 320795--320858 Score: 119
Period size: 19 Copynumber: 3.4 Consensus size: 19
320785 TTCTAGGTCA
320795 AGTATCGATACCTCTTTTG
1 AGTATCGATACCTCTTTTG
320814 AGTATCGATACCTCTTTTG
1 AGTATCGATACCTCTTTTG
*
320833 AGTATCGATACCTCTTTTA
1 AGTATCGATACCTCTTTTG
320852 AGTATCG
1 AGTATCG
320859 GTACAAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (19 bp):
AGTATCGATACCTCTTTTG
Found at i:321547 original size:17 final size:17
Alignment explanation
Indices: 321513--321550 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
321503 AAGAAAATGA
321513 GAAG-GAATGAAGAAAT
1 GAAGAGAATGAAGAAAT
321529 GAAGAGAAT-AAGAAGAT
1 GAAGAGAATGAAGAA-AT
321546 GAAGA
1 GAAGA
321551 TGAAGAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.11
Consensus pattern (17 bp):
GAAGAGAATGAAGAAAT
Found at i:326140 original size:64 final size:65
Alignment explanation
Indices: 326027--326169 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 65
326017 TGCACTAAGA
* * *
326027 GTGCATCGATGCATAAAATGCATTCTATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTT-
1 GTGCATCGATGCATAAAATGAATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGATTG
** * *
326091 GTGCATCGATGCATAAAATGAATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGAATTCGATGTTTCAAAATA-GCCA-GAGTGCATCGATGCATAGAT
326154 TG
64 TG
*
326156 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
326170 CACTTTGAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 7 0.10
64 47 0.69
65 14 0.21
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGAATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGATTG
Found at i:328408 original size:23 final size:23
Alignment explanation
Indices: 328378--328459 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
328368 GCATGGCCTT
328378 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
328401 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
328423 -TGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
328445 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
328460 TGTTAAGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 3 0.06
23 17 0.36
24 13 0.28
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:328471 original size:44 final size:44
Alignment explanation
Indices: 328382--328478 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
328372 GGCCTTGTGC
* *
328382 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGATGCATCTTCAAGATGT
*
328426 ATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTGTTAAG-TGT
1 ATCGATGCACATTC-AAGGAG-TGCATCGATGCATCT-TCAAGATGT
328470 ATCGATGCA
1 ATCGATGCA
328479 TTAAGCAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 29 0.62
45 18 0.38
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGATGCATCTTCAAGATGT
Found at i:334278 original size:19 final size:19
Alignment explanation
Indices: 334254--334305 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
334244 TTGGACCCTT
334254 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
334273 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
334292 AGTGCATCGATGCA
1 AGTGCATCGGTGCA
334306 TAAAATGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:334385 original size:45 final size:45
Alignment explanation
Indices: 334336--334423 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
334326 AAAATAGCCA
*
334336 GAGTGCATCGATGCATAGCT-TGTGCATCAATGCATCAAATGCACT
1 GAGTGCATCGATGCAT-GCTATGTGCATCAATGCATAAAATGCACT
* *
334381 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATGCTATGTGCATCAATGCATAAAATGCA
334424 TTCGATGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 2 0.05
45 37 0.95
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (45 bp):
GAGTGCATCGATGCATGCTATGTGCATCAATGCATAAAATGCACT
Found at i:334494 original size:45 final size:45
Alignment explanation
Indices: 334445--334532 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
334435 AAAATAGCCA
*
334445 GAGTGCATCGATGCATAGCT-TGTGCATCAATGCATCAAATGCACT
1 GAGTGCATCGATGCAT-GCTATGTGCATCAATGCATAAAATGCACT
* *
334490 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATGCTATGTGCATCAATGCATAAAATGCA
334533 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 2 0.05
45 37 0.95
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (45 bp):
GAGTGCATCGATGCATGCTATGTGCATCAATGCATAAAATGCACT
Found at i:334569 original size:109 final size:109
Alignment explanation
Indices: 334293--334541 Score: 498
Period size: 109 Copynumber: 2.3 Consensus size: 109
334283 TGCACTAAGA
334293 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTTG
334358 TGCATCAATGCATCAAATGCACTGAGTGCATCGATGCATGGTAT
66 TGCATCAATGCATCAAATGCACTGAGTGCATCGATGCATGGTAT
334402 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTTG
334467 TGCATCAATGCATCAAATGCACTGAGTGCATCGATGCATGGTAT
66 TGCATCAATGCATCAAATGCACTGAGTGCATCGATGCATGGTAT
334511 GTGCATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
334542 CAATTTATTC
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 140 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (109 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTTG
TGCATCAATGCATCAAATGCACTGAGTGCATCGATGCATGGTAT
Found at i:336587 original size:17 final size:17
Alignment explanation
Indices: 336565--336598 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
336555 TGCATATCGA
336565 TTTATTCAAATT-TTTAC
1 TTTATT-AAATTATTTAC
336582 TTTATTAAATTATTTAC
1 TTTATTAAATTATTTAC
336599 AAAATTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATTAAATTATTTAC
Found at i:336836 original size:36 final size:36
Alignment explanation
Indices: 336772--336841 Score: 106
Period size: 38 Copynumber: 1.9 Consensus size: 36
336762 AATGATATTT
*
336772 TGTAACGAAACATGTACAATTATATAATACTTTTTTGA
1 TGTAACAAAACATGTA-AATTATATAATA-TTTTTTGA
336810 TGTAACAAAACATGT-AATTATATAATATTTTT
1 TGTAACAAAACATGTAAATTATATAATATTTTT
336842 AATGTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 5 0.16
36 12 0.39
38 14 0.45
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (36 bp):
TGTAACAAAACATGTAAATTATATAATATTTTTTGA
Found at i:337840 original size:17 final size:17
Alignment explanation
Indices: 337818--337902 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 17
337808 TTAATTATCC
337818 TAATATTTAAGTAGTGT
1 TAATATTTAAGTAGTGT
337835 TAATATTTAAACTCATGTAGTGGTTT
1 TAATATTT--A---A-GTAGT-G--T
* *
337861 TAATCATTTAATTA-TCT
1 TAAT-ATTTAAGTAGTGT
337878 TAATATTTAAGTAGTGT
1 TAATATTTAAGTAGTGT
337895 TAATATTT
1 TAATATTT
337903 GAACTCATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 22
0.67 0.05 0.28
Matches are distributed among these distances:
16 8 0.15
17 23 0.43
19 1 0.02
20 1 0.02
21 2 0.04
22 2 0.04
23 5 0.09
24 1 0.02
25 1 0.02
26 5 0.09
27 4 0.08
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (17 bp):
TAATATTTAAGTAGTGT
Found at i:337922 original size:60 final size:60
Alignment explanation
Indices: 337806--337922 Score: 191
Period size: 60 Copynumber: 1.9 Consensus size: 60
337796 ATGAATGATT
*
337806 ATTTAATTATCCTAATATTTAAGTAGTGTTAATATTTAAACTCATGTAGTGGTTTTAATC
1 ATTTAATTATCCTAATATTTAAGTAGTGTTAATATTTAAACTCATGTAGTGATTTTAATC
* *
337866 ATTTAATTATCTTAATATTTAAGTAGTGTTAATATTTGAACTCAT-TAAGTGATTTTA
1 ATTTAATTATCCTAATATTTAAGTAGTGTTAATATTTAAACTCATGT-AGTGATTTTA
337923 GTAGTAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (60 bp):
ATTTAATTATCCTAATATTTAAGTAGTGTTAATATTTAAACTCATGTAGTGATTTTAATC
Found at i:351282 original size:13 final size:13
Alignment explanation
Indices: 351264--351293 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
351254 TCGTCATGAA
351264 TCGTCGCCATTCG
1 TCGTCGCCATTCG
351277 TCGTCGCCATTCG
1 TCGTCGCCATTCG
351290 TCGT
1 TCGT
351294 TAATTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.37, G:0.23, T:0.33
Consensus pattern (13 bp):
TCGTCGCCATTCG
Found at i:351716 original size:17 final size:18
Alignment explanation
Indices: 351686--351724 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
351676 GTCATAACCC
351686 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
351704 GACCCGA-CCGACCCGTT
1 GACCCGACCCGACCCGTT
351721 GACC
1 GACC
351725 GTTGACCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.10
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:353033 original size:19 final size:19
Alignment explanation
Indices: 353009--353048 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
352999 GTAACATTCA
*
353009 CTTACGGTCAATTTTCATT
1 CTTACGATCAATTTTCATT
**
353028 CTTACGATTGATTTTCATT
1 CTTACGATCAATTTTCATT
353047 CT
1 CT
353049 AAAGGTTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (19 bp):
CTTACGATCAATTTTCATT
Found at i:356760 original size:65 final size:65
Alignment explanation
Indices: 356673--356828 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 65
356663 CACACCCATT
* * ** *
356673 TCGAATGCACTTTGTGTACCGATGCACAAG-TTATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGTACTTTATGTACCGATGCA-AAGACCATGCATCGATGCACTCCTGAATATTTTGAAAC
356737 A
65 A
* * * ** *
356738 TCGAATGTATTTTATGTTCCGATGCATAGACCATGCATCGATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGTACTTTATGTACCGATGCAAAGACCATGCATCGATGCACTCCTGAATATTTTGAAACA
* *
356803 TCGAATGTA-ATTAGTGTATCGATGCA
1 TCGAATGTACTTTA-TGTACCGATGCA
356829 CCTCCACTAA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 5 0.07
65 70 0.93
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (65 bp):
TCGAATGTACTTTATGTACCGATGCAAAGACCATGCATCGATGCACTCCTGAATATTTTGAAACA
Found at i:365409 original size:65 final size:64
Alignment explanation
Indices: 365339--365493 Score: 179
Period size: 65 Copynumber: 2.4 Consensus size: 64
365329 CACACCCATT
* * * * *
365339 TCGAATGCATTTTGTGTACTGGTGCATAAG-TCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTATGTACCGATGCA-AAGACCATGCATCGATGCACTCCTGAAT-TTTTGAAAC
365403 A
64 A
* *
365404 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATTTTTGAAACA
1 TCGAATGCATTTTATGTACCGATGCAAAGACCATGCATCGATGCACTCCTGAATTTTTGAAACA
* * *
365468 TCAAATGTA-ATTAGTGTACCGATGCA
1 TCGAATGCATTTTA-TGTACCGATGCA
365494 CCTCTAGTGT
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 3 0.04
64 31 0.40
65 44 0.56
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCAAAGACCATGCATCGATGCACTCCTGAATTTTTGAAACA
Found at i:365487 original size:64 final size:65
Alignment explanation
Indices: 365370--365494 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 65
365360 GTGCATAAGT
* * *
365370 CATGCATCGATGCACTCTTGAATATTTTGAAACATCGAATGCATTTTATGTACCGATGCACAGAC
1 CATGCATCGATGCACTCCTGAATATTTTGAAACATCAAATGCATATTATGTACCGATGCACAGAC
* *
365435 CATGCATCGATGCACTCCTGGAT-TTTTGAAACATCAAATGTA-ATTAGTGTACCGATGCAC
1 CATGCATCGATGCACTCCTGAATATTTTGAAACATCAAATGCATATTA-TGTACCGATGCAC
365495 CTCTAGTGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 3 0.06
64 30 0.56
65 21 0.39
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (65 bp):
CATGCATCGATGCACTCCTGAATATTTTGAAACATCAAATGCATATTATGTACCGATGCACAGAC
Found at i:365503 original size:19 final size:19
Alignment explanation
Indices: 365479--365532 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
365469 CAAATGTAAT
365479 TAGTGTACCGATGCACCTC
1 TAGTGTACCGATGCACCTC
* *
365498 TAGTGTATCGATGCATCTC
1 TAGTGTACCGATGCACCTC
365517 TAGTGTACCGATGCAC
1 TAGTGTACCGATGCAC
365533 TAAGCCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (19 bp):
TAGTGTACCGATGCACCTC
Found at i:366855 original size:3 final size:3
Alignment explanation
Indices: 366847--366913 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
366837 CTCCTCATTT
366847 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
366895 TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC T
366914 ATCGTCGTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:372551 original size:11 final size:11
Alignment explanation
Indices: 372537--372562 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
372527 TTTCCTTGGC
372537 TTTTCTTTTCT
1 TTTTCTTTTCT
372548 TTTTCTTTTCT
1 TTTTCTTTTCT
372559 TTTT
1 TTTT
372563 TGAAATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:372574 original size:23 final size:23
Alignment explanation
Indices: 372548--372603 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
372538 TTTCTTTTCT
372548 TTTTCTTTTCTTTTT-TGAAATTC
1 TTTTCTTTTCTTTTTCTG-AATTC
* * *
372571 TTTTCTTCTTGTTTTTCTGATTTT
1 TTTTCTT-TTCTTTTTCTGAATTC
372595 TTTTCTTTT
1 TTTTCTTTT
372604 TGTATTTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.32
24 17 0.61
25 2 0.07
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.75
Consensus pattern (23 bp):
TTTTCTTTTCTTTTTCTGAATTC
Found at i:377190 original size:42 final size:42
Alignment explanation
Indices: 377103--377199 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
377093 GATAAAAACA
* * * * **
377103 TTTTGTCACTAGTCTTAGTTGGTGATTTGGGATGATAATTGT
1 TTTTGTCACTATTCTTAGTTGATGATTTGGGACGACAATAAT
*
377145 TTTTGTCACTATTCTTAGTTGATGATTTGTGACGACAATAAT
1 TTTTGTCACTATTCTTAGTTGATGATTTGGGACGACAATAAT
*
377187 TTTTATCACTATT
1 TTTTGTCACTATT
377200 GAAGTGAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (42 bp):
TTTTGTCACTATTCTTAGTTGATGATTTGGGACGACAATAAT
Found at i:380254 original size:9 final size:9
Alignment explanation
Indices: 380236--380271 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
380226 TTAATATTAT
380236 ATATATTAAA
1 ATATA-TAAA
380246 ATATATAAA
1 ATATATAAA
380255 ATATATAAA
1 ATATATAAA
380264 ATATATAA
1 ATATATAA
380272 TTATGTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 21 0.81
10 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATATAAA
Found at i:382306 original size:23 final size:23
Alignment explanation
Indices: 382271--382324 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
382261 ATGTAAAATG
* *
382271 ATTTAAATATTTTTGAATTAATA
1 ATTTATATATTTTAGAATTAATA
* *
382294 ATTTATATCTTTTAGAATTTATA
1 ATTTATATATTTTAGAATTAATA
*
382317 ATTGATAT
1 ATTTATAT
382325 TACAAAGTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.54
Consensus pattern (23 bp):
ATTTATATATTTTAGAATTAATA
Found at i:384849 original size:21 final size:21
Alignment explanation
Indices: 384823--384881 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
384813 TTTCTAAAAA
*
384823 AAAAGGATTGATCCCTTTAGG
1 AAAAGGATCGATCCCTTTAGG
384844 AAAAGGATCGATCCCTTTAGG
1 AAAAGGATCGATCCCTTTAGG
*
384865 GAAAGGATCGATCCCTT
1 AAAAGGATCGATCCCTT
384882 CTGAATAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTTAGG
Found at i:384891 original size:21 final size:20
Alignment explanation
Indices: 384823--384901 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 20
384813 TTTCTAAAAA
*
384823 AAAAGGATTGATCCCTTTAGG
1 AAAAGGATCGATCCCTTTA-G
384844 AAAAGGATCGATCCCTTTAGG
1 AAAAGGATCGATCCCTTTA-G
*
384865 GAAAGGATCGATCCCTTCT-G
1 AAAAGGATCGATCCCTT-TAG
*
384885 AATAAGGATCGGTCCCT
1 AA-AAGGATCGATCCCT
384902 GGGCCAGAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 49 0.94
22 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (20 bp):
AAAAGGATCGATCCCTTTAG
Found at i:392215 original size:19 final size:20
Alignment explanation
Indices: 392176--392227 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
392166 GAAAGTTTCT
392176 AGAAAATTAAGATAAAAACA
1 AGAAAATTAAGATAAAAACA
*
392196 A-AAAATTAAGA-ACAAGACA
1 AGAAAATTAAGATA-AAAACA
392215 ATGAAAATTAAGA
1 A-GAAAATTAAGA
392228 GAATGAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 16 0.57
20 1 0.04
21 10 0.36
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (20 bp):
AGAAAATTAAGATAAAAACA
Found at i:394509 original size:14 final size:14
Alignment explanation
Indices: 394490--394540 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
394480 AAACTAAGTC
*
394490 AACTCGTATGAGTT
1 AACTCGTCTGAGTT
*
394504 AACTCGTCTG-TTT
1 AACTCGTCTGAGTT
*
394517 AACTCATCTGAGTT
1 AACTCGTCTGAGTT
394531 AACTCGTCTG
1 AACTCGTCTG
394541 TGTCAACCCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (14 bp):
AACTCGTCTGAGTT
Found at i:394520 original size:13 final size:13
Alignment explanation
Indices: 394502--394541 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
394492 CTCGTATGAG
394502 TTAACTCGTCTGT
1 TTAACTCGTCTGT
* *
394515 TTAACTCATCTGAG
1 TTAACTCGTCTG-T
394529 TTAACTCGTCTGT
1 TTAACTCGTCTGT
394542 GTCAACCCGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (13 bp):
TTAACTCGTCTGT
Found at i:394520 original size:27 final size:27
Alignment explanation
Indices: 394490--394541 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
394480 AAACTAAGTC
*
394490 AACTCGTATGAGTTAACTCGTCTGTTT
1 AACTCATATGAGTTAACTCGTCTGTTT
*
394517 AACTCATCTGAGTTAACTCGTCTGT
1 AACTCATATGAGTTAACTCGTCTGT
394542 GTCAACCCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (27 bp):
AACTCATATGAGTTAACTCGTCTGTTT
Found at i:397052 original size:46 final size:45
Alignment explanation
Indices: 396996--397102 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
396986 TGAACTTACC
* * *
396996 ATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGTAATTG
1 ATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAATTG
* * *
397042 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCAATTG
397087 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
397103 TTAGGGCACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 32 0.59
46 19 0.35
47 3 0.06
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCAATTG
Found at i:405022 original size:18 final size:18
Alignment explanation
Indices: 404999--405036 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
404989 TGTTTGTTTG
404999 ATGGATATTTGAACTTTT
1 ATGGATATTTGAACTTTT
405017 ATGGATATTTGAACTTTT
1 ATGGATATTTGAACTTTT
405035 AT
1 AT
405037 TTCATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (18 bp):
ATGGATATTTGAACTTTT
Found at i:405784 original size:65 final size:64
Alignment explanation
Indices: 405680--405836 Score: 167
Period size: 65 Copynumber: 2.4 Consensus size: 64
405670 AATTAAATTG
* *
405680 AACATCGAATGCATTTAATGCATCGATGAACATATCATGCA-CTGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGAACATACCATGCATC-GATGCACTGAGGATATTT-TG
405743 AA
64 -A
* * * ** *
405745 AACATCGAATGCATTTGATGTATCGATGTACCA-GCCATGCATCGATGCACTTTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATG-AACATACCATGCATCGATGCACTGAGGATATTTTGA
* *
405809 AACATCGAATGCAATTGATGCATTGATG
1 AACATCGAATGCATTTGATGCATCGATG
405837 CACTCTTAGT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
64 26 0.33
65 45 0.58
66 7 0.09
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGAACATACCATGCATCGATGCACTGAGGATATTTTGA
Found at i:406956 original size:30 final size:30
Alignment explanation
Indices: 406856--406974 Score: 139
Period size: 31 Copynumber: 3.9 Consensus size: 30
406846 TAGACTCTGA
406856 GGCCCCGAGATCTTTCTTGGGTAGGCCATAC
1 GGCCCCGAGATCTTTCTTGGGTAGGCC-TAC
*
406887 GGCCCCAAGATCTTTCTTGGGTAGGCCCTAC
1 GGCCCCGAGATCTTTCTTGGGTAGG-CCTAC
* * **
406918 GACCCCGAGATCTTTCTTGTGTAGGCCTGT
1 GGCCCCGAGATCTTTCTTGGGTAGGCCTAC
* * *
406948 GGCCCCGAGTAACCTTCTTGGGGAGGC
1 GGCCCCGAG-ATCTTTCTTGGGTAGGC
406975 TCTCGGGCCC
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
30 11 0.15
31 62 0.83
32 2 0.03
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.26
Consensus pattern (30 bp):
GGCCCCGAGATCTTTCTTGGGTAGGCCTAC
Found at i:406966 original size:62 final size:62
Alignment explanation
Indices: 406858--406974 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 62
406848 GACTCTGAGG
* * *
406858 CCCCGAGATCTTTCTTGGGTAGGCCATACGGCCCCAAGATCTTTCTTGGGTAGGCCCTACGA
1 CCCCGAGATCTTTCTTGGGTAGGCCATACGGCCCCAAGAACCTTCTTGGGGAGGCCCTACGA
* ** *
406920 CCCCGAGATCTTTCTTGTGTAGGCC-TGTGGCCCCGAGTAACCTTCTTGGGGAGGC
1 CCCCGAGATCTTTCTTGGGTAGGCCATACGGCCCCAAG-AACCTTCTTGGGGAGGC
406975 TCTCGGGCCC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 9 0.19
62 38 0.81
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.26
Consensus pattern (62 bp):
CCCCGAGATCTTTCTTGGGTAGGCCATACGGCCCCAAGAACCTTCTTGGGGAGGCCCTACGA
Found at i:418724 original size:27 final size:27
Alignment explanation
Indices: 418694--418751 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
418684 GTATATCAAG
* * *
418694 ATGAATGAAAT-ACCCTCGAGTCCTTAA
1 ATGAAT-AAATAAACCTCAAGTACTTAA
418721 ATGAATAAATAAACCTCAAGTACTTAA
1 ATGAATAAATAAACCTCAAGTACTTAA
418748 ATGA
1 ATGA
418752 TCTAAATACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (27 bp):
ATGAATAAATAAACCTCAAGTACTTAA
Found at i:418766 original size:27 final size:25
Alignment explanation
Indices: 418694--418767 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 25
418684 GTATATCAAG
* *
418694 ATGAATGAAATACCCTCGAGTCCTTAA
1 ATGAAT-AAATA-CCTCAAGTACTTAA
418721 ATGAATAAATAAACCTCAAGTACTTAA
1 ATGAATAAAT--ACCTCAAGTACTTAA
*
418748 ATGATCTAAATACCTTCAAG
1 ATGA-ATAAATACC-TCAAG
418768 GTCTAGAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 7 0.17
27 27 0.68
28 6 0.15
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (25 bp):
ATGAATAAATACCTCAAGTACTTAA
Found at i:424134 original size:29 final size:30
Alignment explanation
Indices: 424080--424137 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
424070 TACCTTTCCA
*
424080 TGAGGCACCCAAAGTCATGCTACCTCTCTC
1 TGAGGCACCCAAAGTCATACTACCTCTCTC
* *
424110 TGAGGCA-CTAAATTCATACTACCTCTCT
1 TGAGGCACCCAAAGTCATACTACCTCTCT
424138 TCGAGGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.28
Consensus pattern (30 bp):
TGAGGCACCCAAAGTCATACTACCTCTCTC
Found at i:424150 original size:29 final size:29
Alignment explanation
Indices: 424094--424150 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
424084 GCACCCAAAG
* *
424094 TCATGCTACCTCTCTCTGAGGCACTAAAT
1 TCATACTACCTCTCTCTGAGGCAATAAAT
*
424123 TCATACTACCTCTCT-TCGAGGTAATAAA
1 TCATACTACCTCTCTCT-GAGGCAATAAA
424151 GTCACACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (29 bp):
TCATACTACCTCTCTCTGAGGCAATAAAT
Found at i:424787 original size:19 final size:18
Alignment explanation
Indices: 424752--424805 Score: 81
Period size: 19 Copynumber: 2.9 Consensus size: 18
424742 AGAGAAAGAA
424752 AAAGGAAAAAATAAAAAT
1 AAAGGAAAAAATAAAAAT
* *
424770 AAAGTAAAAATTAGAAAAT
1 AAAGGAAAAAATA-AAAAT
424789 AAAGGAAAAAATAAAAA
1 AAAGGAAAAAATAAAAA
424806 GAGAGAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (18 bp):
AAAGGAAAAAATAAAAAT
Found at i:424826 original size:37 final size:37
Alignment explanation
Indices: 424752--424828 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
424742 AGAGAAAGAA
* *
424752 AAAGGAAAAAATAAAAATAAAGTAAAAATTAGAAAAT
1 AAAGGAAAAAATAAAAAGAAAGTAAAAATTAAAAAAT
*
424789 AAAGGAAAAAATAAAAAGAGAG-AGAAAA-TAAATAAAT
1 AAAGGAAAAAATAAAAAGAAAGTA-AAAATTAAA-AAAT
424826 AAA
1 AAA
424829 TAAATGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 4 0.11
37 31 0.89
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (37 bp):
AAAGGAAAAAATAAAAAGAAAGTAAAAATTAAAAAAT
Found at i:425752 original size:25 final size:25
Alignment explanation
Indices: 425720--425768 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
425710 TTTCAAAAAC
425720 TTCATCAAACGTTTTTCAAAATTCT
1 TTCATCAAACGTTTTTCAAAATTCT
*
425745 TTCATCAAATGTTTTTCAAAATTC
1 TTCATCAAACGTTTTTCAAAATTC
425769 AAACATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (25 bp):
TTCATCAAACGTTTTTCAAAATTCT
Found at i:426903 original size:3 final size:3
Alignment explanation
Indices: 426895--426991 Score: 194
Period size: 3 Copynumber: 32.3 Consensus size: 3
426885 TTTTCAACCA
426895 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
426943 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
426991 T
1 T
426992 TTAGAAACCC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:440680 original size:36 final size:36
Alignment explanation
Indices: 440633--440717 Score: 152
Period size: 36 Copynumber: 2.4 Consensus size: 36
440623 GGTCTGACCA
440633 GTTGACTTTGACCCGAACGTTGACTTGACCCTACCC
1 GTTGACTTTGACCCGAACGTTGACTTGACCCTACCC
* *
440669 GTTGACTTTGACCCGAACGTTGACTTGACCTTACCT
1 GTTGACTTTGACCCGAACGTTGACTTGACCCTACCC
440705 GTTGACTTTGACC
1 GTTGACTTTGACC
440718 TGACCCTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (36 bp):
GTTGACTTTGACCCGAACGTTGACTTGACCCTACCC
Found at i:440727 original size:18 final size:18
Alignment explanation
Indices: 440626--440727 Score: 93
Period size: 18 Copynumber: 5.6 Consensus size: 18
440616 TCGAATCGGT
440626 CTGACCAGTTGACTTTGAC
1 CTGACC-GTTGACTTTGAC
* *
440645 CCGAACGTTGAC-TTGACC
1 CTGACCGTTGACTTTGA-C
440663 CT-ACCCGTTGACTTTGAC
1 CTGA-CCGTTGACTTTGAC
* *
440681 CCGAACGTTGAC-TTGAC
1 CTGACCGTTGACTTTGAC
*
440698 CTTACCTGTTGACTTTGAC
1 CTGACC-GTTGACTTTGAC
*
440717 CTGACCCTTGA
1 CTGACCGTTGA
440728 TATTGACTAG
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
17 13 0.20
18 34 0.52
19 19 0.29
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (18 bp):
CTGACCGTTGACTTTGAC
Found at i:448802 original size:2 final size:2
Alignment explanation
Indices: 448795--448829 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
448785 AACCCACCAT
448795 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
448830 TTGTAAGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:449837 original size:13 final size:13
Alignment explanation
Indices: 449819--449843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
449809 CAAACCTCTT
449819 GTCGTGAATCGTC
1 GTCGTGAATCGTC
449832 GTCGTGAATCGT
1 GTCGTGAATCGT
449844 TAATTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (13 bp):
GTCGTGAATCGTC
Found at i:452598 original size:24 final size:24
Alignment explanation
Indices: 452550--452641 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
452540 TTCGATTTGA
* *
452550 ATTCTGTTATGATACCTGATC-TGG
1 ATTCTGATATGATACTTGA-CATGG
* *
452574 ATTTTGATATGATATTTGACATGG
1 ATTCTGATATGATACTTGACATGG
* *
452598 ATTCTGATTTGTTACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
452622 ATTCTGATATAATACTTGAC
1 ATTCTGATATGATACTTGAC
452642 CTGAATTATG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 1 0.02
24 55 0.98
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:453414 original size:14 final size:14
Alignment explanation
Indices: 453395--453423 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
453385 CATGTGATTA
453395 GGGGGCATATAATT
1 GGGGGCATATAATT
453409 GGGGGCATATAATT
1 GGGGGCATATAATT
453423 G
1 G
453424 TATTTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (14 bp):
GGGGGCATATAATT
Found at i:454932 original size:16 final size:15
Alignment explanation
Indices: 454907--454941 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
454897 CCGACTGCCC
454907 GACCCGTTGACCATT
1 GACCCGTTGACCATT
*
454922 GACCGCGTTGACCGTT
1 GACC-CGTTGACCATT
454938 GACC
1 GACC
454942 AGAACTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.17, C:0.34, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCATT
Found at i:457274 original size:24 final size:24
Alignment explanation
Indices: 457233--457327 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
457223 TGAATTTTGT
* *
457233 TATGATACCTGA-TCTGGATTTTGA
1 TATGATACTTGACT-TGGATTATGA
*
457257 TATGATATTTGACTTGGATTATGA
1 TATGATACTTGACTTGGATTATGA
* * *
457281 TCTGTTACTTGA-TATGGATTCTGA
1 TATGATACTTGACT-TGGATTATGA
*
457305 TATGATACTTGACTTGAATTATG
1 TATGATACTTGACTTGGATTATG
457328 TTTTGATTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.02
24 54 0.95
25 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.44
Consensus pattern (24 bp):
TATGATACTTGACTTGGATTATGA
Found at i:459090 original size:39 final size:39
Alignment explanation
Indices: 459035--459128 Score: 136
Period size: 39 Copynumber: 2.4 Consensus size: 39
459025 ATTGATTGTC
*
459035 CATGCTTTAAGGAAGGAC-GGAGGATTGAATACGATCGTT
1 CATGCTTTAAGGAAGGACAGG-GGATTGAATACGAACGTT
* * *
459074 CATGCTCTAAGCAAGGACAGGGGATTGAATATGAACGTT
1 CATGCTTTAAGGAAGGACAGGGGATTGAATACGAACGTT
459113 CATGCTTTAAGGAAGG
1 CATGCTTTAAGGAAGG
459129 GACTCAAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 46 0.96
40 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (39 bp):
CATGCTTTAAGGAAGGACAGGGGATTGAATACGAACGTT
Found at i:460567 original size:23 final size:22
Alignment explanation
Indices: 460516--460570 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
460506 GTAATTTTCT
*
460516 TTTTTTTCTTTTTTTACAAAAG
1 TTTTTTTGTTTTTTTACAAAAG
* *
460538 TTCTTTTGTTTTTTTATTAACAA-
1 TTTTTTTGTTTTTTTA-CAA-AAG
460561 TTTTTTTGTT
1 TTTTTTTGTT
460571 AAAAATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 14 0.52
23 11 0.41
24 2 0.07
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTTTTTGTTTTTTTACAAAAG
Found at i:465574 original size:27 final size:27
Alignment explanation
Indices: 465544--465600 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
465534 AGATTTATAA
465544 TCCTAATAAAAAGTTGCAAGAATAGTT
1 TCCTAATAAAAAGTTGCAAGAATAGTT
465571 TCCTAATAAAAAGTTGCAAGAATAGTT
1 TCCTAATAAAAAGTTGCAAGAATAGTT
465598 TCC
1 TCC
465601 ATGTTAGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (27 bp):
TCCTAATAAAAAGTTGCAAGAATAGTT
Found at i:465828 original size:25 final size:24
Alignment explanation
Indices: 465765--465828 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
465755 ACAATTTAAA
*
465765 CTAAAAAACCCAAAACCATTTTACT
1 CTAAAAAACCC-TAACCATTTTACT
**
465790 CTAAAAAAATCTAACCATTTTAACAT
1 CTAAAAAACCCTAACCATTTT-AC-T
465816 -TAAAAAACCCTAA
1 CTAAAAAACCCTAA
465829 TCAGTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 9 0.28
25 22 0.69
26 1 0.03
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (24 bp):
CTAAAAAACCCTAACCATTTTACT
Found at i:469182 original size:20 final size:20
Alignment explanation
Indices: 469142--469180 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
469132 CATTGCAGGA
*
469142 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
469162 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
469181 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:479106 original size:6 final size:6
Alignment explanation
Indices: 479095--479659 Score: 1074
Period size: 6 Copynumber: 95.5 Consensus size: 6
479085 CAAACACTAA
479095 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479143 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479191 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479239 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479287 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479335 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479383 TATATG TATATG TATATG TATATG TATATG --TATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479429 TATATG TATATG TATATG TATATG TATATG TATATG --TATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479475 TATATG TATATG TATATG TATATG TATATG --TATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479521 TATATG TATATG TATATG TATA-- TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479567 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
479615 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TAT
479660 CGAATAATAA
Statistics
Matches: 551, Mismatches: 0, Indels: 16
0.97 0.00 0.03
Matches are distributed among these distances:
4 16 0.03
6 535 0.97
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:485103 original size:75 final size:76
Alignment explanation
Indices: 484952--485215 Score: 342
Period size: 75 Copynumber: 3.5 Consensus size: 76
484942 ATCTCACTTG
* *
484952 AGATTGTTTTTCTTTAAAA-ACATATTTGTCTCGCTTGAGACA-ATTTTTACTGGAAATAAGATA
1 AGATTGTTTTTC-TTAAAACA-AGATTTGTCTCGCTTGAGACAGA-TTTTACTCGAAATAAGATA
485015 TTTCATTTCACTCA
63 TTTCATTTCACTCA
* *
485029 ATATTGTTTTTCTTAAAACAAGATTCGTCTCGCTTGAGACAGATTTTACTCG-AATAAGATATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGATTTTACTCGAAATAAGATATTT
*
485093 CATTTAACTCA
66 CATTTCACTCA
* * * * * *
485104 AGATTATTTTTCTTAAAACAATATTTGTCTCGCCTGAGACAGTTTTTACTCGAAAGAAGACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGATTTTACTCGAAATAAGATATTT
485169 CATTTCACTCA
66 CATTTCACTCA
* *
485180 AGATTG--TTT-TTAAAACAAGATTTATCTCACTTGAGA
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGA
485216 TTGTTTCACT
Statistics
Matches: 165, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
73 23 0.14
74 3 0.02
75 68 0.41
76 58 0.35
77 13 0.08
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGATTTTACTCGAAATAAGATATTT
CATTTCACTCA
Found at i:485248 original size:39 final size:39
Alignment explanation
Indices: 485196--485651 Score: 594
Period size: 39 Copynumber: 11.7 Consensus size: 39
485186 TTTTTAAAAC
*
485196 AAGA-TTTATCTCACTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * * *
485234 AAGATTTCATCTCACTTGAGATAGTTTCACTAGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
*
485273 AAGATTTTATCTCGCTTGAGATTGTTTCACTCAAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
485312 AAGATTTTATCTCGCTTTAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * * * *
485351 AAGATTTCATATCGCTTGAGATAGTTTCACTTGAAATAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * *
485390 AAGATTTCATCTTGCTTGAGATTGTTTCATTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * ** *
485429 AAGATTTTATATCGCTTGAGATAGTTTCACTAAAAAACAT
1 AAGATTTTATCTCGCTTGAGATTGTTTCACT-CGAAACAG
*
485469 AAGATTTTATCTCGCTTGAGATTATTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
485508 AAGATTTTATCTCGCTTGAGATTATTTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
485547 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * *
485586 AAGATTTTATCTCACTTGAGATAT-TTTCACTTGAAACCAA
1 AAGATTTTATCTCGCTTGAGAT-TGTTTCACTCGAAA-CAG
* * *
485626 AAGA-TTTAACTCACTTAAGATTGTTT
1 AAGATTTTATCTCGCTTGAGATTGTTT
485652 TTCTTAAAAC
Statistics
Matches: 369, Mismatches: 44, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
38 5 0.01
39 324 0.88
40 40 0.11
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
Found at i:485534 original size:20 final size:20
Alignment explanation
Indices: 485472--485534 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
485462 AAAACATAAG
485472 ATTTTATCTCGCTTGAGATT
1 ATTTTATCTCGCTTGAGATT
* **** **
485492 ATTTCA-CTCGAAACAGAAG
1 ATTTTATCTCGCTTGAGATT
485511 ATTTTATCTCGCTTGAGATT
1 ATTTTATCTCGCTTGAGATT
485531 ATTT
1 ATTT
485535 CACTTGAAAC
Statistics
Matches: 28, Mismatches: 14, Indels: 2
0.64 0.32 0.05
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
ATTTTATCTCGCTTGAGATT
Found at i:485929 original size:135 final size:135
Alignment explanation
Indices: 485693--485949 Score: 379
Period size: 135 Copynumber: 1.9 Consensus size: 135
485683 TTAACACTTC
* *
485693 AAATGGAGAGTTCATTATGAGAAGAGCTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
1 AAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
* * ** * * *
485758 ACTTGTTCGACCTATCGCTCGATTCACGGTATTTCGAATCATCGATGCCTCACTTGACGATTAGG
66 ACTTGTTCAACCTATCGCTCAATTCACAATACTTCGAATCAGCAATGCCTCACTTGACGATTAGG
485823 ATTTT
131 ATTTT
* * * *
485828 AAATGGAGTGTTCATAATTAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCGTACTGAGAAGA
1 AAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
* *
485893 ACTTGTTCAACCTATTGCTCAATTCACAATACTTCGAATCAGCAATGCCTCGCTTGA
66 ACTTGTTCAACCTATCGCTCAATTCACAATACTTCGAATCAGCAATGCCTCACTTGA
485950 GGGATTGACA
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
135 107 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (135 bp):
AAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGA
ACTTGTTCAACCTATCGCTCAATTCACAATACTTCGAATCAGCAATGCCTCACTTGACGATTAGG
ATTTT
Found at i:487409 original size:16 final size:14
Alignment explanation
Indices: 487388--487426 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
487378 GGTCCTCATA
*
487388 TTTTATTTTATGTTGT
1 TTTTATTTTA-CTT-T
487404 TTTTATTTTACTTT
1 TTTTATTTTACTTT
487418 TTTTATTTT
1 TTTTATTTT
487427 TTGATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 2 0.09
16 10 0.45
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTTATTTTACTTT
Found at i:501415 original size:132 final size:131
Alignment explanation
Indices: 501190--502078 Score: 1382
Period size: 132 Copynumber: 6.7 Consensus size: 131
501180 TGGTCCGAAT
501190 GACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
1 GACTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
* *
501255 TGAAGGTCTTATGGATGGCCTGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCAG
65 TGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGG
501320 AG
130 AG
* *
501322 GACTTACAAATCAAGAAATCTCCGAAGGCTTAGTCTCTAAAATCTCATTTGAAAACATCCTGCAC
1 GACTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
* * * * * * *
501387 TGAAAGTCATATAGATGGCCCGGAGGACTTAAGTATCATGCTCGAAAGACTTACCGATGGCCCGG
65 TGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGG
501452 AG
130 AG
* *
501454 GACTTACAAATCAAGAAATCCCGGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACAACCTGCAC
1 GACTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
*
501519 TGAAGGTCTTATGGATGGCTCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGG
65 TGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGG
501584 AG
130 AG
* *
501586 GACTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTTCTAAAATTTCATTTGAAAACATCCTGCAC
1 GACTTACAAATCAAGAAACCCC-GAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
* * * * **
501651 TGAAAGTCTTATGGATGGCCCGGAGGACTTATGCATCATGCTTGGAAGACTTAATGATATCCCGG
65 TGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGG
501716 AG
130 AG
*
501718 GACTTACAAATCAAGAAACCCCTGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCATGCAC
1 GACTTACAAATCAAGAAACCCC-GAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
* * * * *
501783 TGAAAGTCTTATGTATGGCCCGGAAGACTTATGCATCATGCTCGGAAGACTTACTGATGGCCCGA
65 TGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGG
501848 AG
130 AG
*
501850 GACTTACCAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
1 GACTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
* * * * *
501915 TGAAGGTCTTATGGATGGTCCGGAGGACTTACGTATCATGCTCGTAAGATTTACTGATGGCCTGG
65 TGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGG
501980 AG
130 AG
*
501982 GACTTACAAATCAAGAAACTCCCGAAGGCTTAGTTTCTAAAATCGCATTTGAAAACATCCTGCAC
1 GACTTACAAATCAAGAAAC-CCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCAC
* *
502047 TGAAGGTCTTATGGATGGCCTGGATGACTTAC
65 TGAAGGTCTTATGGATGGCCCGGAGGACTTAC
502079 AACTCAATAA
Statistics
Matches: 692, Mismatches: 62, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
131 4 0.01
132 684 0.99
133 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (131 bp):
GACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACT
GAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGGA
G
Found at i:501815 original size:20 final size:20
Alignment explanation
Indices: 501790--501855 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
501780 CACTGAAAGT
501790 CTTATGTATGGCCCGGAAGA
1 CTTATGTATGGCCCGGAAGA
*
501810 CTTATGCATCAT-GCTCGGAAGA
1 CTTATG--T-ATGGCCCGGAAGA
501832 CTTACTG-ATGGCCC-GAAGGA
1 CTTA-TGTATGGCCCGGAA-GA
501852 CTTA
1 CTTA
501856 CCAATCAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
19 5 0.13
20 15 0.39
22 14 0.37
23 4 0.11
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (20 bp):
CTTATGTATGGCCCGGAAGA
Found at i:502123 original size:90 final size:90
Alignment explanation
Indices: 501970--502168 Score: 308
Period size: 90 Copynumber: 2.2 Consensus size: 90
501960 AAGATTTACT
* *
501970 GATGGCCTGGAGGACTTACAAATCAAGAAACTCCCGAAGGCTTAGTTTCTAAAATCGCATTTGAA
1 GATGGCCTGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATAGCATTTGAA
*
502035 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATA
* * * * * *
502060 GATGGCCTGGATGACTTACAACTCAATAAACCCCCGATGGCTTAGTTTCTAAAATATCGTTTGAA
1 GATGGCCTGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATAGCATTTGAA
502125 AACATCCTGCACTGAAGGTCTTATA
66 AACATCCTGCACTGAAGGTCTTATA
*
502150 GATGGCCCGGAGGACTTAC
1 GATGGCCTGGAGGACTTAC
502169 GCATCATGCT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 98 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (90 bp):
GATGGCCTGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATAGCATTTGAA
AACATCCTGCACTGAAGGTCTTATA
Found at i:502313 original size:43 final size:43
Alignment explanation
Indices: 502250--502397 Score: 197
Period size: 43 Copynumber: 3.4 Consensus size: 43
502240 AGTTTCTTAG
* * * * *
502250 TTGTCACCAAGTAACGCCTACATATCACGTTGGTCCCTCAAGT
1 TTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAGC
* *
502293 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAAC
1 TTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAGC
* * **
502336 TTGTCCTCAAGAAACCTCTACATATCACGATGGTTTCTCAAGC
1 TTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAGC
502379 TTGTCATCAAGAAACCCCT
1 TTGTCATCAAGAAACCCCT
502398 GAAAATCAGG
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.27
Consensus pattern (43 bp):
TTGTCATCAAGAAACCCCTACATATCACGATGGTCCCTCAAGC
Found at i:503685 original size:28 final size:27
Alignment explanation
Indices: 503653--503715 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
503643 GATAAATGGC
*
503653 TCAGGTTGACATGGGAATGTAATGTGTT
1 TCAGGTTGACATGGG-AGGTAATGTGTT
* **
503681 TCAGGTTAATTTGGGAGGTAATGTGTT
1 TCAGGTTGACATGGGAGGTAATGTGTT
*
503708 TGAGGTTG
1 TCAGGTTG
503716 GCTTCTTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38
Consensus pattern (27 bp):
TCAGGTTGACATGGGAGGTAATGTGTT
Found at i:504374 original size:25 final size:24
Alignment explanation
Indices: 504346--504431 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
504336 GATTTGTATA
*
504346 TTTTCTTCTTTCTTCTTTCTTCTTT
1 TTTTCTT-TTTCTTCTTTCTTCTTC
* * *
504371 TTTTATTTTTTTCTCTTTTTTCTTC
1 TTTTCTTTTTCT-TCTTTCTTCTTC
*
504396 TTTTCTTTTTC-TCATTTTCTTC-TG
1 TTTTCTTTTTCTTC--TTTCTTCTTC
504420 TTTTCTTTTTCT
1 TTTTCTTTTTCT
504432 CATTTTCTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
23 2 0.04
24 16 0.33
25 31 0.63
ACGTcount: A:0.02, C:0.20, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTCTTTTTCTTCTTTCTTCTTC
Found at i:504381 original size:8 final size:8
Alignment explanation
Indices: 504346--504447 Score: 73
Period size: 8 Copynumber: 12.2 Consensus size: 8
504336 GATTTGTATA
504346 TTTTCTTCT
1 TTTTCTT-T
504355 TTCTTC-TT
1 TT-TTCTTT
*
504363 TCTTCTTT
1 TTTTCTTT
*
504371 TTTTATTT
1 TTTTCTTT
504379 TTTTCTCTT
1 TTTTCT-TT
*
504388 TTTTCTTC
1 TTTTCTTT
504396 TTTTCTTT
1 TTTTCTTT
*
504404 TTCTCATTT
1 TTTTC-TTT
* *
504413 TCTTC-TG
1 TTTTCTTT
504420 TTTTCTTT
1 TTTTCTTT
*
504428 TTCTCATTT
1 TTTTC-TTT
504437 TCTTTCTTT
1 T-TTTCTTT
504446 TT
1 TT
504448 GTGTTTTTTC
Statistics
Matches: 72, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
7 8 0.11
8 33 0.46
9 25 0.35
10 6 0.08
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTCTTT
Found at i:504394 original size:32 final size:33
Alignment explanation
Indices: 504346--504439 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 33
504336 GATTTGTATA
* *
504346 TTTTCTTCTTTCTTCTTTCTTCTTTTT-TTATTT
1 TTTTC-TCTTTTTTCTTTCTTCTTTTTCTCATTT
*
504379 TTTTCTCTTTTTTCTTCTTTTCTTTTTCTCATTT
1 TTTTCTCTTTTTTCTT-TCTTCTTTTTCTCATTT
* * *
504413 TCTTCTGTTTTCTT-TTTC-TCATTTTCT
1 TTTTCTCTTTT-TTCTTTCTTCTTTTTCT
504440 TTCTTTTTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
32 18 0.35
33 15 0.29
34 16 0.31
35 2 0.04
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (33 bp):
TTTTCTCTTTTTTCTTTCTTCTTTTTCTCATTT
Found at i:504439 original size:14 final size:14
Alignment explanation
Indices: 504387--504441 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
504377 TTTTTTCTCT
504387 TTTTTCTTC-TTTTC
1 TTTTTC-TCATTTTC
504401 TTTTTCTCATTTTC
1 TTTTTCTCATTTTC
*
504415 ---TTCT-GTTTTC
1 TTTTTCTCATTTTC
504425 TTTTTCTCATTTTC
1 TTTTTCTCATTTTC
504439 TTT
1 TTT
504442 CTTTTTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 5 0.15
11 4 0.12
13 6 0.18
14 19 0.56
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTTCTCATTTTC
Found at i:504447 original size:24 final size:24
Alignment explanation
Indices: 504346--504447 Score: 95
Period size: 24 Copynumber: 4.2 Consensus size: 24
504336 GATTTGTATA
*
504346 TTTTCTTCTTTCTTCTTTCTTCTTT-T
1 TTTTCTT-TTTC-TCATT-TTCTTTCT
* *
504372 TTTATTTTTTTCTC-TTTTTTCTTC-
1 TTT-TCTTTTTCTCATTTTCT-TTCT
504396 TTTTCTTTTTCTCATTTTC-TTCT
1 TTTTCTTTTTCTCATTTTCTTTCT
504419 GTTTTCTTTTTCTCATTTTCTTTCT
1 -TTTTCTTTTTCTCATTTTCTTTCT
504444 TTTT
1 TTTT
504448 GTGTTTTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
22 3 0.05
23 12 0.18
24 34 0.52
25 6 0.09
26 7 0.11
27 3 0.05
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTCTTTTTCTCATTTTCTTTCT
Found at i:504457 original size:57 final size:57
Alignment explanation
Indices: 504354--504467 Score: 135
Period size: 57 Copynumber: 2.0 Consensus size: 57
504344 TATTTTCTTC
* * * *
504354 TTTCTTCTTTCTTCTTTTTTTATTTTTTTCTCTTTTTTCTTCTTTTCTTTTTCTCAT
1 TTTCTTCTTTCTTCTTTTTTCATTTTTTTCTCTTTTGTCTTCTTTTCTATATCTCAT
*
504411 TTTCTTCTGTT-TTCTTTTTCTCATTTTCTTTCT-TTTTGTGTT-TTTTCTATATCTCAT
1 TTTCTTCT-TTCTTCTTTTT-TCATTTT-TTTCTCTTTTGTCTTCTTTTCTATATCTCAT
504468 CCTTTTCTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
57 29 0.59
58 15 0.31
59 5 0.10
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (57 bp):
TTTCTTCTTTCTTCTTTTTTCATTTTTTTCTCTTTTGTCTTCTTTTCTATATCTCAT
Found at i:509209 original size:13 final size:13
Alignment explanation
Indices: 509176--509211 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
509166 ATAATAAAGT
*
509176 AATATGTATAATA
1 AATATGTAAAATA
509189 ATATATGTAAAATA
1 A-ATATGTAAAATA
509203 AATATGTAA
1 AATATGTAA
509212 TACATAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AATATGTAAAATA
Found at i:511842 original size:13 final size:13
Alignment explanation
Indices: 511814--511862 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
511804 TGGGGATTTA
*
511814 AAATTAATACAAAT
1 AAATAAATA-AAAT
*
511828 AAATGAATAAAAT
1 AAATAAATAAAAT
511841 AAATAAATAAATACT
1 AAATAAATAAA-A-T
511856 AAATAAA
1 AAATAAA
511863 AATAATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 14 0.45
14 9 0.29
15 8 0.26
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:514016 original size:19 final size:19
Alignment explanation
Indices: 513992--514032 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
513982 ATGTTTGCAC
513992 TTTATTTTATTTTATTC-TT
1 TTTATTTTATTTT-TTCATT
514011 TTTATTTTATTTTTTCATT
1 TTTATTTTATTTTTTCATT
514030 TTT
1 TTT
514033 TCTCTCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTATTTTATTTTTTCATT
Found at i:514110 original size:31 final size:31
Alignment explanation
Indices: 514044--514117 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
514034 CTCTCATTAT
514044 TTTATTTTG-TTTTAATTTTCTGTTTTTTAG
1 TTTATTTTGTTTTTAATTTTCTGTTTTTTAG
* * *
514074 GTTATTTTGTTTTTTATTTTC-GTTATTTTTG
1 TTTATTTTGTTTTTAATTTTCTGTT-TTTTAG
*
514105 TTTATTTTATTTT
1 TTTATTTTGTTTT
514118 ATTCCTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (31 bp):
TTTATTTTGTTTTTAATTTTCTGTTTTTTAG
Found at i:524893 original size:6 final size:6
Alignment explanation
Indices: 524884--524940 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
524874 TTGAAAAAAT
* * *
524884 AAAATA AAAAGA AAAAG- AAAAGG AAACGA AAGAGAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA-A-AGA AAAAGA AAAAGA
*
524933 AAAGGA AA
1 AAAAGA AA
524941 GAAATAAGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 5 0.12
6 32 0.74
7 2 0.05
8 4 0.09
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:525565 original size:21 final size:21
Alignment explanation
Indices: 525541--525593 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
525531 AACATTTGAA
525541 AAATTCAAGATCAGGAATCAG
1 AAATTCAAGATCAGGAATCAG
* *
525562 AAATTCAAGATCGGGAATTAG
1 AAATTCAAGATCAGGAATCAG
525583 AAATTCAAGAT
1 AAATTCAAGAT
525594 TCCAGAACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (21 bp):
AAATTCAAGATCAGGAATCAG
Found at i:528456 original size:12 final size:12
Alignment explanation
Indices: 528441--528494 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
528431 TATGTATATA
528441 TTATTTTTGTT-T
1 TTATTTTT-TTAT
528453 TTATTTTTTTAT
1 TTATTTTTTTAT
*
528465 TTA-TTTTCT-T
1 TTATTTTTTTAT
528475 TTATTTTTATTAT
1 TTATTTTT-TTAT
*
528488 TTCTTTT
1 TTATTTT
528495 CCTTTCGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 4 0.11
11 11 0.31
12 13 0.37
13 7 0.20
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:528479 original size:22 final size:23
Alignment explanation
Indices: 528439--528582 Score: 75
Period size: 23 Copynumber: 6.0 Consensus size: 23
528429 TATATGTATA
*
528439 TATTATTT-TTGT-TTTTATTTT
1 TATTATTTATTTTCTTTTATTTT
528460 T-TTATTTATTTTCTTTTATTTT
1 TATTATTTATTTTCTTTTATTTT
* **
528482 TATTATTTCTTTTCCTTTCGGTTCTGT
1 TATTATTTATTTT-CTTT-TATT-T-T
* *
528509 T-TTCACTTTATTTTATTTTATTAT
1 TATT-A-TTTATTTTCTTTTATTTT
*
528533 TATTGTTT-TTTTCATTTT-TTTCT
1 TATTATTTATTTTC-TTTTATTT-T
*
528556 CTCATTATTTTATTTTGTTTTATTTT
1 -T-ATTA-TTTATTTTCTTTTATTTT
528582 T
1 T
528583 CTATTTTTTA
Statistics
Matches: 92, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
20 6 0.07
21 4 0.04
22 16 0.17
23 18 0.20
24 7 0.08
25 8 0.09
26 13 0.14
27 13 0.14
28 7 0.08
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.74
Consensus pattern (23 bp):
TATTATTTATTTTCTTTTATTTT
Found at i:528487 original size:19 final size:19
Alignment explanation
Indices: 528458--528494 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
528448 TGTTTTTATT
528458 TTTTTATTTATTTTCTTTTA
1 TTTTTATTTA-TTTCTTTTA
528478 TTTTTA-TTATTTCTTTT
1 TTTTTATTTATTTCTTTT
528495 CCTTTCGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTATTTATTTCTTTTA
Found at i:528631 original size:20 final size:20
Alignment explanation
Indices: 528594--528631 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
528584 TATTTTTTAG
*
528594 GTTATTTGTTTTTTATTTTC
1 GTTATTTGTTTTTAATTTTC
528614 GTTATTT-TTGTTTAATTT
1 GTTATTTGTT-TTTAATTT
528632 ATTTTATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.13, C:0.03, G:0.11, T:0.74
Consensus pattern (20 bp):
GTTATTTGTTTTTAATTTTC
Found at i:530547 original size:3 final size:3
Alignment explanation
Indices: 530529--530561 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
530519 TTAAAACTAA
530529 AAT AA- AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
530562 AATGGATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:531764 original size:19 final size:19
Alignment explanation
Indices: 531740--531780 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
531730 AAGTAAAATG
531740 AAAGAATATAAAGAATG-AT
1 AAAGAATATAAA-AATGTAT
*
531759 AAAGAATATGAAAATGTAT
1 AAAGAATATAAAAATGTAT
531778 AAA
1 AAA
531781 ATGATTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (19 bp):
AAAGAATATAAAAATGTAT
Found at i:537506 original size:40 final size:40
Alignment explanation
Indices: 537449--537570 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
537439 TGCAGGTTTA
537449 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
537489 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
537529 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
537569 TA
1 TA
537571 GCACTACGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:539522 original size:6 final size:6
Alignment explanation
Indices: 539511--539535 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
539501 AAGACCCATA
539511 GGTCAT GGTCAT GGTCAT GGTCAT G
1 GGTCAT GGTCAT GGTCAT GGTCAT G
539536 ATACAAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.36, T:0.32
Consensus pattern (6 bp):
GGTCAT
Found at i:539887 original size:31 final size:31
Alignment explanation
Indices: 539849--539908 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
539839 CTGAAGTAAG
*
539849 ATTATATGCTATTTCTATAACTTGGGAATAA
1 ATTATATGCTATTTCCATAACTTGGGAATAA
539880 ATTATATGCTATTTCCATAACTTGGGAAT
1 ATTATATGCTATTTCCATAACTTGGGAAT
539909 TTCCATAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (31 bp):
ATTATATGCTATTTCCATAACTTGGGAATAA
Found at i:540680 original size:16 final size:17
Alignment explanation
Indices: 540656--540717 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 17
540646 TATTATTATA
*
540656 AGAAGAAGAAAAAA-AC
1 AGAAAAAGAAAAAATAC
*
540672 AGAAAAAGAAAAAAATAT
1 AGAAAAAG-AAAAAATAC
* *
540690 AGAAAAAGAAAATATAG
1 AGAAAAAGAAAAAATAC
540707 A-AAAAAGAAAA
1 AGAAAAAGAAAA
540718 TGAAAATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
16 17 0.43
17 14 0.35
18 9 0.22
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (17 bp):
AGAAAAAGAAAAAATAC
Found at i:540681 original size:6 final size:6
Alignment explanation
Indices: 540658--540775 Score: 53
Period size: 6 Copynumber: 18.3 Consensus size: 6
540648 TTATTATAAG
*
540658 AAGAAGA AA-AAA ACAGAAA AAGAAA AA-AATA TAGAAA AAGAAAA TATAGAAAA
1 AAGAA-A AAGAAA A-AGAAA AAGAAA AAGAA-A AAGAAA AAG-AAA -A-AG-AAA
* * * * * *
540711 AAGAAA ATGAAA ATGAAA ACGAAGA AGAAAAA AATGAAA ACGAGA AAG-AA
1 AAGAAA AAGAAA AAGAAA AAGAA-A A-AGAAA AA-GAAA AAGAAA AAGAAA
540761 AAGAAA AAGAGAA AA
1 AAGAAA AAGA-AA AA
540776 AATGAGAGAT
Statistics
Matches: 88, Mismatches: 11, Indels: 24
0.72 0.09 0.20
Matches are distributed among these distances:
5 8 0.09
6 45 0.51
7 25 0.28
8 4 0.05
9 6 0.07
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:540685 original size:15 final size:15
Alignment explanation
Indices: 540665--540729 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
540655 AAGAAGAAGA
*
540665 AAAAAACAGAAAAAG
1 AAAAAATAGAAAAAG
540680 AAAAAAATATAGAAAAAG
1 --AAAAA-ATAGAAAAAG
*
540698 AAAATATAGAAAAA-
1 AAAAAATAGAAAAAG
* *
540712 AGAAAAT-GAAAATG
1 AAAAAATAGAAAAAG
540726 AAAA
1 AAAA
540730 CGAAGAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 5 0.12
14 8 0.20
15 9 0.22
16 4 0.10
17 5 0.12
18 9 0.22
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (15 bp):
AAAAAATAGAAAAAG
Found at i:540686 original size:17 final size:18
Alignment explanation
Indices: 540658--540701 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
540648 TTATTATAAG
*
540658 AAGAAGAAAAAAACAGAAA
1 AAGAA-AAAAATACAGAAA
*
540677 AAGAAAAAAATATAGAAA
1 AAGAAAAAAATACAGAAA
540695 AAGAAAA
1 AAGAAAA
540702 TATAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (18 bp):
AAGAAAAAAATACAGAAA
Found at i:540750 original size:33 final size:33
Alignment explanation
Indices: 540693--540780 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
540683 AAAATATAGA
* *
540693 AAAAGAAAATATAGAAAAAA-GAAAATGA-AAATG
1 AAAAGAAAA-AGAGAAAAAATGAAAACGAGAAA-G
*
540726 AAAACGAAGAAGA-AAAAAATGAAAACGAGAAAG
1 AAAA-GAAAAAGAGAAAAAATGAAAACGAGAAAG
540759 AAAAGAAAAAGAGAAAAAATGA
1 AAAAGAAAAAGAGAAAAAATGA
540781 GAGATGGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
32 13 0.28
33 27 0.57
34 7 0.15
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (33 bp):
AAAAGAAAAAGAGAAAAAATGAAAACGAGAAAG
Found at i:540756 original size:20 final size:22
Alignment explanation
Indices: 540720--540762 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
540710 AAAGAAAATG
540720 AAAATGAAAACGAAG-AAGAAA
1 AAAATGAAAACGAAGAAAGAAA
540741 AAAATGAAAACG-AGAAAGAAA
1 AAAATGAAAACGAAGAAAGAAA
540762 A
1 A
540763 GAAAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.72, C:0.05, G:0.19, T:0.05
Consensus pattern (22 bp):
AAAATGAAAACGAAGAAAGAAA
Found at i:540768 original size:27 final size:27
Alignment explanation
Indices: 540663--540768 Score: 85
Period size: 28 Copynumber: 3.9 Consensus size: 27
540653 ATAAGAAGAA
* *
540663 GAAAAA-AACAGAAAAAGAAAAAAATAT
1 GAAAAAGAAAAGAAGAAGAAAAAAA-AT
*
540690 AGAAAAAGAAAATATAGAA-AAAAGAAAAT
1 -GAAAAAGAAAAGA-AGAAGAAAA-AAAAT
*
540719 GAAAATGAAAACGAAGAAG-AAAAAAAT
1 GAAAAAGAAAA-GAAGAAGAAAAAAAAT
*
540746 GAAAACGAGAAAGAA-AAGAAAAA
1 GAAAAAGA-AAAGAAGAAGAAAAA
540769 GAGAAAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
26 3 0.05
27 19 0.29
28 26 0.40
29 11 0.17
30 6 0.09
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.07
Consensus pattern (27 bp):
GAAAAAGAAAAGAAGAAGAAAAAAAAT
Found at i:540774 original size:17 final size:16
Alignment explanation
Indices: 540655--540770 Score: 60
Period size: 16 Copynumber: 6.9 Consensus size: 16
540645 ATATTATTAT
540655 AAGAAGAAGAAAAA-AA
1 AAGAA-AAGAAAAAGAA
*
540671 CAGAAAAAGAAAAA-AA
1 AAG-AAAAGAAAAAGAA
* *
540687 TATAGAAAAAGAAAATATAG
1 -A-AG-AAAAGAAAA-AGAA
*
540707 AA-AAAAGAAAATGAA
1 AAGAAAAGAAAAAGAA
*
540722 AATGAAAACGAAGAAGAA
1 AA-GAAAA-GAAAAAGAA
* *
540740 AA-AAATGAAAACGAGA
1 AAGAAAAGAAAAAGA-A
540756 AAGAAAAGAAAAAGA
1 AAGAAAAGAAAAAGA
540771 GAAAAAATGA
Statistics
Matches: 77, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
15 9 0.12
16 27 0.35
17 16 0.21
18 22 0.29
19 2 0.03
20 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (16 bp):
AAGAAAAGAAAAAGAA
Done.