Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 24
Found at i:3048339 original size:20 final size:20
Alignment explanation
Indices: 3048267--3048353 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
3048257 GATTCTCTCG
3048267 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-AATTTCGCA
*
3048287 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAATTTCGCA
*
3048307 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAATTTCGCA
* *
3048327 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAATTTCGCA
3048347 TTGCGAT
1 TTGCGAT
3048354 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 4 0.06
20 58 0.94
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCA
Found at i:3048928 original size:21 final size:20
Alignment explanation
Indices: 3048833--3048940 Score: 58
Period size: 21 Copynumber: 5.2 Consensus size: 20
3048823 GCCCGACTCA
3048833 CCTGTCATCGTTCAAGAGG-
1 CCTGTCATCGTTCAAGAGGC
** *
3048852 CCTCCCCTATCATTCAAGAGGCC
1 CCT-GTC-ATCGTTCAAGAGG-C
* ** *
3048875 CCTATCATCCCTCAAGAGTC
1 CCTGTCATCGTTCAAGAGGC
*
3048895 CCT-TCCCACCGTTCAAGAGGC
1 CCTGT--CATCGTTCAAGAGGC
*
3048916 CACTGTCATCGTTGAAGAGGTC
1 C-CTGTCATCGTTCAAGAGG-C
3048938 CCT
1 CCT
3048941 CCCAACATTC
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
19 4 0.06
20 5 0.08
21 48 0.73
22 5 0.08
23 4 0.06
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (20 bp):
CCTGTCATCGTTCAAGAGGC
Found at i:3048934 original size:42 final size:42
Alignment explanation
Indices: 3048864--3048944 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
3048854 TCCCCTATCA
*
3048864 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCTTCCCACCG
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCC-TCCCACCG
* ** *
3048906 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
3048945 ACATTCTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 28 0.85
43 5 0.15
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACCG
Found at i:3050558 original size:20 final size:19
Alignment explanation
Indices: 3050529--3050595 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
3050519 CGAAACTAAA
*
3050529 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
3050549 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
3050565 TTCG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
3050582 TTCGCATTGCGATT
1 TTCGCATTGCGATT
3050596 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 5 0.12
18 3 0.08
19 8 0.20
20 11 0.28
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.49
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3050576 original size:34 final size:34
Alignment explanation
Indices: 3050533--3050628 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
3050523 ACTAAATTCG
*
3050533 CGTTGCGATTTTCATTTTCGCATTGCGATTCTTT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
3050567 CGTTGCGATTTTTA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** *
3050600 CGTTGCGATAGTCATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
3050629 AGTCATTCCT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:3050627 original size:20 final size:20
Alignment explanation
Indices: 3050600--3050673 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 20
3050590 GCGATTCTCT
3050600 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
3050620 CATTGCGATAGTCA-TTCCTG
1 CGTTGCGATAGTCATTTCC-G
*
3050640 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
3050660 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
3050674 AATGAATGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.09
20 40 0.85
21 1 0.02
22 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:3053623 original size:23 final size:23
Alignment explanation
Indices: 3053556--3053642 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
3053546 TCATATAAAT
*
3053556 TTGCACCGTAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
3053579 TTTTGTC-CCGAAG-GACCGCGTAGAA
1 --TTG-CACCGAAGTG-CCACGTAGAA
*
3053604 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
3053627 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
3053643 TATAATATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.02
23 31 0.60
24 2 0.04
25 17 0.33
26 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:3065046 original size:16 final size:16
Alignment explanation
Indices: 3065025--3065060 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3065015 TCGAACATCC
**
3065025 ATACATTAAGGAGAAA
1 ATACATTAAAAAGAAA
3065041 ATACATTAAAAAGAAA
1 ATACATTAAAAAGAAA
3065057 ATAC
1 ATAC
3065061 GCTTTAGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.19
Consensus pattern (16 bp):
ATACATTAAAAAGAAA
Found at i:3068290 original size:23 final size:24
Alignment explanation
Indices: 3068261--3068310 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3068251 TAGCATACAC
*
3068261 AAAATAT-ATAACAA-ACAAAAAGA
1 AAAATATAAAAACAACA-AAAAAGA
3068284 AAAATATAAAAACAACAAAAAAGA
1 AAAATATAAAAACAACAAAAAAGA
3068308 AAA
1 AAA
3068311 TTAAGGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 16 0.67
25 1 0.04
ACGTcount: A:0.78, C:0.08, G:0.04, T:0.10
Consensus pattern (24 bp):
AAAATATAAAAACAACAAAAAAGA
Found at i:3068311 original size:23 final size:23
Alignment explanation
Indices: 3068261--3068310 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
3068251 TAGCATACAC
*
3068261 AAAATATATAACAAACAAAAAGA
1 AAAATATAAAACAAACAAAAAGA
3068284 AAAATATAAAA-ACAACAAAAAAGA
1 AAAATATAAAACA-AAC-AAAAAGA
3068308 AAA
1 AAA
3068311 TTAAGGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 1 0.04
23 13 0.54
24 10 0.42
ACGTcount: A:0.78, C:0.08, G:0.04, T:0.10
Consensus pattern (23 bp):
AAAATATAAAACAAACAAAAAGA
Found at i:3068797 original size:2 final size:2
Alignment explanation
Indices: 3068790--3068827 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3068780 ACAACTTGGG
* *
3068790 GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3068828 TTTTAGGCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3073105 original size:15 final size:15
Alignment explanation
Indices: 3073083--3073124 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3073073 ACTTTTTTAT
3073083 TATT-TTTATTATTA
1 TATTATTTATTATTA
* *
3073097 TTTTATTTAGTATTA
1 TATTATTTATTATTA
*
3073112 TATTATATATTAT
1 TATTATTTATTAT
3073125 AATAAATAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTTATTATTA
Found at i:3074209 original size:75 final size:75
Alignment explanation
Indices: 3074130--3074473 Score: 296
Period size: 75 Copynumber: 4.6 Consensus size: 75
3074120 CTGCATATCA
* * *
3074130 ATTTGTTTTAAGATTACTAATAATGTAAAAGATAAAATAAAATAGACGCTAACTATTACGTTTAA
1 ATTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAAATAAAATAGACGCTAACTATTACG-TTAA
*
3074195 A-TATCTACTG
65 ACTACCTACTG
* * * *
3074205 ATTTGTTTAAAGGTTACTAATAATATAAACGGTAAAAT---A-A-ACACTATCTATTACGTTAAA
1 ATTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAAATAAAATAGACGCTAACTATTACGTTAAA
* *
3074265 TTACCTACCG
66 CTACCTACTG
* *
3074275 -TTTGTTTAAAGGTTACTAATATTGTAAACGGTAAAATAAAATAGACGCT-ACATATTACGTTAA
1 ATTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAAATAAAATAGACGCTAAC-TATTACGTTAA
*
3074338 ACTAGCTA-TCG
65 ACTACCTACT-G
* * * * * * * *
3074349 ATTTGTTTAAAGGTTAATAATAATGTAAACA-GTAATATAAAACAGGCACTACCCATTACATTAA
1 ATTTGTTTAAAGGTTACTAATAATGTAAA-AGGTAAAATAAAATAGACGCTAACTATTACGTTAA
*
3074413 A-TAAACACTATATG
65 ACT--AC-CTA-CTG
* *
3074427 CCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAATA
1 --A-TTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAAATAAAATA
3074474 AACGTTACTT
Statistics
Matches: 219, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
69 40 0.18
70 20 0.09
71 1 0.00
72 2 0.01
73 2 0.01
74 23 0.11
75 84 0.38
76 2 0.01
77 3 0.01
78 1 0.00
79 1 0.00
80 1 0.00
81 39 0.18
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (75 bp):
ATTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAAATAAAATAGACGCTAACTATTACGTTAAA
CTACCTACTG
Found at i:3074444 original size:156 final size:144
Alignment explanation
Indices: 3074131--3074487 Score: 396
Period size: 144 Copynumber: 2.4 Consensus size: 144
3074121 TGCATATCAA
* * * *
3074131 TTTGTTTTAAGATTACTAATAATGTAAAAGATAAAATAAAATAGACGCTA-ACTATTACGTTTAA
1 TTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGACGCTACA-TATTACGTTTAA
* * * * * * *
3074195 ATATCTACTGATTTGTTTAAAGGTTACTAATAATATAAACGGTAAAATAAACACTATCTATTACG
65 ATAGCTACTGATTTGTTTAAAGGTTAATAATAATATAAACAGTAAAAAAAACACTACCCATTACA
*
3074260 TTAAATTACCTACCG
130 TTAAATAACCTACCG
*
3074275 TTTGTTTAAAGGTTACTAATATTGTAAACGGTAAAATAAAATAGACGCTACATATTACG-TTAAA
1 TTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGACGCTACATATTACGTTTAAA
*
3074339 CTAGCTA-TCGATTTGTTTAAAGGTTAATAATAATGTAAACAGTAATATAAAACAGGCACTACCC
66 -TAGCTACT-GATTTGTTTAAAGGTTAATAATAATATAAACAGTAA-A-AAAA-A--CACTACCC
3074403 ATTACATTAAATAAACACTATATGCCAG
124 ATTACATTAAAT-AAC-C--TA--CC-G
* * * *
3074431 TTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAATAAACGTTACTTATTA
1 TTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGACGCTACATATTA
3074488 TATTAAATAA
Statistics
Matches: 179, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
143 6 0.03
144 90 0.50
145 2 0.01
146 3 0.02
147 1 0.01
149 17 0.09
150 2 0.01
151 1 0.01
153 2 0.01
155 2 0.01
156 53 0.30
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (144 bp):
TTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGACGCTACATATTACGTTTAAA
TAGCTACTGATTTGTTTAAAGGTTAATAATAATATAAACAGTAAAAAAAACACTACCCATTACAT
TAAATAACCTACCG
Found at i:3074496 original size:23 final size:23
Alignment explanation
Indices: 3074469--3074520 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3074459 CGGTAAAATA
* *
3074469 AAATAAACGTTACTTATTA-TATT
1 AAATAAACGATACCTATTACT-TT
*
3074492 AAATAAGCGATACCTATTACTTT
1 AAATAAACGATACCTATTACTTT
3074515 AAATAA
1 AAATAA
3074521 GTATTATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.37
Consensus pattern (23 bp):
AAATAAACGATACCTATTACTTT
Found at i:3078623 original size:2 final size:2
Alignment explanation
Indices: 3078616--3078651 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3078606 TTAACAAATC
3078616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3078652 CAATAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3087420 original size:29 final size:29
Alignment explanation
Indices: 3087368--3087449 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
3087358 ACATAGGGAT
* * * * *
3087368 AATTAATCACATGCAATGTTAGAACGGGG
1 AATTAATCCCATGCAGTGTCAGAACGAGA
* *
3087397 AATTAATCCCATACAGTGTCAGAATGAGA
1 AATTAATCCCATGCAGTGTCAGAACGAGA
*
3087426 AATTAATCCCATGTAGTGTCAGAA
1 AATTAATCCCATGCAGTGTCAGAA
3087450 TGAGGAACGC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (29 bp):
AATTAATCCCATGCAGTGTCAGAACGAGA
Found at i:3087450 original size:29 final size:29
Alignment explanation
Indices: 3087397--3087453 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3087387 TAGAACGGGG
3087397 AATTAATCCCATACAGTGTCAGAATGAGA
1 AATTAATCCCATACAGTGTCAGAATGAGA
**
3087426 AATTAATCCCATGTAGTGTCAGAATGAG
1 AATTAATCCCATACAGTGTCAGAATGAG
3087454 GAACGCGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (29 bp):
AATTAATCCCATACAGTGTCAGAATGAGA
Found at i:3088048 original size:21 final size:20
Alignment explanation
Indices: 3088018--3088059 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3088008 AAAACAATGG
3088018 TCAAAGTCAACGATCAACAA
1 TCAAAGTCAACGATCAACAA
* *
3088038 TCAATAGTCAATGGTCAACAA
1 TCAA-AGTCAACGATCAACAA
3088059 T
1 T
3088060 TATCATTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (20 bp):
TCAAAGTCAACGATCAACAA
Found at i:3093832 original size:23 final size:24
Alignment explanation
Indices: 3093806--3093855 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
3093796 TATTATCAAG
*
3093806 TATAATAATAT-ATAGGTAGCGCT
1 TATAATAATATAATAGATAGCGCT
3093829 TAT-ATAATATAATAGATAGCGCT
1 TATAATAATATAATAGATAGCGCT
3093852 TATA
1 TATA
3093856 TTGACATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (24 bp):
TATAATAATATAATAGATAGCGCT
Found at i:3093894 original size:12 final size:12
Alignment explanation
Indices: 3093877--3093901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3093867 TCTAATACAA
3093877 ACAGGTATATTT
1 ACAGGTATATTT
3093889 ACAGGTATATTT
1 ACAGGTATATTT
3093901 A
1 A
3093902 AACCGTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ACAGGTATATTT
Found at i:3094638 original size:178 final size:178
Alignment explanation
Indices: 3094332--3094734 Score: 650
Period size: 178 Copynumber: 2.3 Consensus size: 178
3094322 ATTTTGTTAT
* * *
3094332 ATTTTTACA--TTATATTGTTATAGATCGATACATTTTTATAAAATATCGACATTTTTTGACGCT
1 ATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTTTTAGACGCT
* * * *
3094395 ATAACTTCTTTTCTTTTAAAATCCAAAAGTGTCGATACTTATAATAAATATCTACACTGTCAACA
66 ATAACTTATTCTCTTTTAAAATCCAAAAGTGTCGATACTTATAATAAATATCGACACTATCAACA
* *
3094460 TATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGGTTTTGTC
131 TATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCGGTTTTGTC
3094508 ATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTTTTAG-CGCT
1 ATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTTTTAGACGCT
* *
3094572 ATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAAC
66 ATAACTTATTCTCTTTTAAAATCCAAAAGTGTCGATACTTATAATAAA-TATCGACACTATCAAC
* * *
3094637 ATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGGTTTTGTC
130 ATATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCGGTTTTGTC
3094686 ATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
1 ATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
3094735 AACACTTTCA
Statistics
Matches: 210, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
176 9 0.04
177 48 0.23
178 153 0.73
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (178 bp):
ATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTTTTAGACGCT
ATAACTTATTCTCTTTTAAAATCCAAAAGTGTCGATACTTATAATAAATATCGACACTATCAACA
TATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCGGTTTTGTC
Found at i:3094854 original size:111 final size:110
Alignment explanation
Indices: 3094615--3094890 Score: 455
Period size: 111 Copynumber: 2.5 Consensus size: 110
3094605 GATACTTATA
* * *
3094615 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
3094680 TTTGTCATTTTTACATGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTACATGTTATATTGTTATGGATCAATACATTTTT
*
3094725 ATAAAGTATCAACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
3094790 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
66 TTTGTCA-TTTTTACATGTTATATTGTTATGGATCAATACATTTTT
* *
3094836 ATAAAGTATCGACACTTTCAATATATCCGGT-GATGCTTTACCTATTTTGTCATTT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAG-CGCTTTACCTGTTTTGTCATTT
3094891 TTTACCTGTT
Statistics
Matches: 155, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
110 69 0.45
111 86 0.55
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (110 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTACATGTTATATTGTTATGGATCAATACATTTTT
Found at i:3094964 original size:90 final size:91
Alignment explanation
Indices: 3094789--3094973 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 91
3094779 TATAGACCGG
3094789 TTTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTTT
1 TTTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTTT
*
3094854 CAATATATCCGGTGATGCTTTACCTA
66 CAATATATCCGGTGACGCTTTACCTA
* *
3094880 TTTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATATA-TTTTATAAAGTATCGACACTTT
1 TTTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTTT
* *
3094944 CAATATATCTGGT-AGCGCTTTACCTG
66 CAATATATCCGGTGA-CGCTTTACCTA
3094970 TTTT
1 TTTT
3094974 ATCTTTATAG
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
89 1 0.01
90 47 0.53
91 40 0.45
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.48
Consensus pattern (91 bp):
TTTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTGACGCTTTACCTA
Found at i:3095144 original size:111 final size:111
Alignment explanation
Indices: 3094880--3095160 Score: 464
Period size: 108 Copynumber: 2.6 Consensus size: 111
3094870 GCTTTACCTA
3094880 TTTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATATA-TTTTATAAAGTATCGACACTT
1 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCGACACTT
*
3094943 TCAATATATCTGGTAGCGCTTTACCTGTTTTATCTTTATAGACCGG
66 TCAATATATCGGGTAGCGCTTTACCTGTTTTATCTTTATAGACCGG
* *
3094989 --TTGTCATTTTTTTATCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC-ACACTT
1 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCGACACTT
* *
3095051 TCAATATATCGGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGG
66 TCAATATATCGGGTAGCGCTTTACCTGTTTTATC-TTTATAGACCGG
*
3095098 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACAC
1 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCGACAC
3095161 AAACCGACAA
Statistics
Matches: 158, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
107 6 0.04
108 69 0.44
109 26 0.16
111 53 0.34
112 4 0.03
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.48
Consensus pattern (111 bp):
TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCGACACTT
TCAATATATCGGGTAGCGCTTTACCTGTTTTATCTTTATAGACCGG
Found at i:3100816 original size:3 final size:3
Alignment explanation
Indices: 3100808--3100836 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3100798 ATTAGGTTTT
3100808 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3100837 TGTGTTACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3101373 original size:45 final size:44
Alignment explanation
Indices: 3101324--3101420 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
3101314 AATATTTACG
* *
3101324 TAGAGTTTAATATTAATATTTTTGATAGAAAAAAAATATTTTAGA
1 TAGAGTTTAATATTAATA-TTTAGATAGAAAAAAAATATTTTAAA
* * *
3101369 TAGAGTATAATATTAATATTTAGATAGAAAAATAATGTTTTAAA
1 TAGAGTTTAATATTAATATTTAGATAGAAAAAAAATATTTTAAA
*
3101413 TAGCGTTT
1 TAGAGTTT
3101421 TATCGAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 28 0.62
45 17 0.38
ACGTcount: A:0.45, C:0.01, G:0.12, T:0.41
Consensus pattern (44 bp):
TAGAGTTTAATATTAATATTTAGATAGAAAAAAAATATTTTAAA
Found at i:3101393 original size:24 final size:25
Alignment explanation
Indices: 3101324--3101396 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 25
3101314 AATATTTACG
* *
3101324 TAGAGTTTAATATTAATATTTTTGA
1 TAGAGTATAATATTAATATTTTAGA
*
3101349 TAGA--A-AA-A-AAATATTTTAGA
1 TAGAGTATAATATTAATATTTTAGA
3101369 TAGAGTATAATATTAATA-TTTAGA
1 TAGAGTATAATATTAATATTTTAGA
3101393 TAGA
1 TAGA
3101397 AAAATAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
20 14 0.36
21 1 0.03
22 3 0.08
23 2 0.05
24 11 0.28
25 8 0.21
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (25 bp):
TAGAGTATAATATTAATATTTTAGA
Found at i:3101410 original size:20 final size:20
Alignment explanation
Indices: 3101337--3101415 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
3101327 AGTTTAATAT
*
3101337 TAATATTTTTGATAGAAAAA
1 TAATATTTTAGATAGAAAAA
*
3101357 AAATATTTTAGATAGAGTATAATA
1 TAATATTTTAGATAGA--A-AA-A
3101381 TTAATA-TTTAGATAGAAAAA
1 -TAATATTTTAGATAGAAAAA
* *
3101401 TAATGTTTTAAATAG
1 TAATATTTTAGATAG
3101416 CGTTTTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 4 0.08
20 23 0.48
21 2 0.04
22 2 0.04
23 2 0.04
24 11 0.23
25 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
TAATATTTTAGATAGAAAAA
Found at i:3102952 original size:60 final size:58
Alignment explanation
Indices: 3102828--3102953 Score: 130
Period size: 60 Copynumber: 2.1 Consensus size: 58
3102818 CTTGAGTGGT
* *
3102828 CATTTGATAACTTTTAATAGTCAAGAGACTTAACAAGCAACATTCTATAGTCAAATGAC
1 CATTTG-TAACTTTTAATAGTCAAGAGACTTAACAAGCAACATCCTATAGTCAAAGGAC
* * * **
3102887 TATTTGTAACTTTTAAATAGTCAA-ATGACTTGATA-AAGTAACATCCTATAGTTAGGGGAC
1 CATTTGTAACTTTT-AATAGTCAAGA-GACTT-A-ACAAGCAACATCCTATAGTCAAAGGAC
3102947 CATTTGT
1 CATTTGT
3102954 GTACTTTACC
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
58 9 0.16
59 19 0.35
60 26 0.47
61 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (58 bp):
CATTTGTAACTTTTAATAGTCAAGAGACTTAACAAGCAACATCCTATAGTCAAAGGAC
Found at i:3104955 original size:21 final size:20
Alignment explanation
Indices: 3104909--3104956 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
3104899 GATTCTGACT
3104909 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
3104929 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
3104951 ATCGCA
1 ATCGCA
3104957 ACGCGATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:3104962 original size:21 final size:21
Alignment explanation
Indices: 3104938--3104984 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
3104928 AATTCGCGTT
*
3104938 GCGATTTTCCTAAATCGCAAC
1 GCGATTTACCTAAATCGCAAC
*
3104959 GCGA-TTACGTAAATCGCAAC
1 GCGATTTACCTAAATCGCAAC
*
3104979 GAGATT
1 GCGATT
3104985 CTGACTATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
GCGATTTACCTAAATCGCAAC
Found at i:3105864 original size:24 final size:24
Alignment explanation
Indices: 3105837--3105890 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3105827 GTATTCAAAA
3105837 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
3105861 TTTGATTTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3105885 TTTGAT
1 TTTGAT
3105891 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3108439 original size:33 final size:33
Alignment explanation
Indices: 3108402--3108510 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
3108392 GGAAATTACT
**
3108402 ATCGCAACGAGAGAATCGCAGTGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAAAGCGAAATGAAA
* * *
3108435 ATCGCAACGTGAAAATCGCAACGCGAATATGAAA
1 ATCGCAACGAGAGAATCGCAAAGCGAA-ATGAAA
*
3108469 ATCGCAACAAGAGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAAAGCGAAATGAAA
3108502 ATCGCAACG
1 ATCGCAACG
3108511 CGAATTTAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
33 37 0.56
34 29 0.44
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAAAGCGAAATGAAA
Found at i:3108467 original size:20 final size:19
Alignment explanation
Indices: 3108424--3108514 Score: 85
Period size: 14 Copynumber: 5.3 Consensus size: 19
3108414 GAATCGCAGT
3108424 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
3108442 -CG---TGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
3108457 GCGAATATGAAAATCGCAA-
1 GCGAA-ATGAAAATCGCAAC
* *
3108476 -C--AA-GAGAATCGCAAA
1 GCGAAATGAAAATCGCAAC
3108491 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
3108510 GCGAA
1 GCGAA
3108515 TTTAGTTTCG
Statistics
Matches: 59, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
14 22 0.37
15 1 0.02
16 4 0.07
17 2 0.03
18 3 0.05
19 15 0.25
20 12 0.20
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:3108563 original size:33 final size:33
Alignment explanation
Indices: 3108520--3108599 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
3108510 GCGAATTTAG
* * * *
3108520 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGTATTGCGATTCTCTCATTGCGATTTTCA
3108553 TTTCGTATTGCGATTCTCTCATTGCGATTTTCA
1 TTTCGTATTGCGATTCTCTCATTGCGATTTTCA
3108586 TTTCGTATTGCGAT
1 TTTCGTATTGCGAT
3108600 AGTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTCGTATTGCGATTCTCTCATTGCGATTTTCA
Found at i:3108565 original size:19 final size:19
Alignment explanation
Indices: 3108541--3108599 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
3108531 GATTTTGTCG
3108541 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGTA
*
3108560 TTGCGA--TTC-TCTC--A
1 TTGCGATTTTCATTTCGTA
3108574 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGTA
3108593 TTGCGAT
1 TTGCGAT
3108600 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 7 0.21
16 6 0.18
17 6 0.18
19 14 0.42
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGTA
Found at i:3108607 original size:19 final size:17
Alignment explanation
Indices: 3108549--3108599 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
3108539 CGTTGCGATT
3108549 TTCATTTCGTATTGCGA
1 TTCATTTCGTATTGCGA
*
3108566 TTC-TCTC--ATTGCGA
1 TTCATTTCGTATTGCGA
3108580 TTTTCATTTCGTATTGCGA
1 --TTCATTTCGTATTGCGA
3108599 T
1 T
3108600 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 7 0.26
16 6 0.22
17 7 0.26
19 7 0.26
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.49
Consensus pattern (17 bp):
TTCATTTCGTATTGCGA
Found at i:3108725 original size:14 final size:14
Alignment explanation
Indices: 3108706--3108742 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3108696 CATCAATTAA
3108706 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3108720 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3108734 ACAAATCAA
1 ACAAATCAA
3108743 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3110648 original size:93 final size:95
Alignment explanation
Indices: 3110541--3110773 Score: 407
Period size: 93 Copynumber: 2.5 Consensus size: 95
3110531 ATCGCAACAT
*
3110541 GAATACACAGTTTAGCAGAATTGGTAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-
1 GAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACA
3110605 AAAGACAAATACTAACTTCACAGTGTTAAA
66 AAAGACAAATACTAACTTCACAGTGTTAAA
*
3110635 G-ATACACAGTTTAGCAGAATTGGCAGCAACCAAACAAATTTACTTTCAACCAAAAGACAAAACA
1 GAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACA
3110699 AAAGACAAATACTAACTTCACAGTGTTAAA
66 AAAGACAAATACTAACTTCACAGTGTTAAA
* * *
3110729 GAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATAAATTTACT
1 GAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
3110774 AAGCAATCTA
Statistics
Matches: 131, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
93 60 0.46
94 32 0.24
95 39 0.30
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (95 bp):
GAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACA
AAAGACAAATACTAACTTCACAGTGTTAAA
Found at i:3112321 original size:26 final size:27
Alignment explanation
Indices: 3112292--3112359 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 27
3112282 AAAAAATTTC
*
3112292 TACAAAAACAATAAACAAGT-TAGATA
1 TACAAAAACAATAAACAAGTGAAGATA
* *
3112318 TACAAAAAC--TACAC-TGTGAAGATA
1 TACAAAAACAATAAACAAGTGAAGATA
3112342 TACCAAAAACAATAAACA
1 TA-CAAAAACAATAAACA
3112360 TAAGAGTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.06
24 11 0.33
25 7 0.21
26 9 0.27
27 4 0.12
ACGTcount: A:0.59, C:0.16, G:0.07, T:0.18
Consensus pattern (27 bp):
TACAAAAACAATAAACAAGTGAAGATA
Found at i:3112448 original size:20 final size:20
Alignment explanation
Indices: 3112425--3112480 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3112415 TGAAATGAAA
*
3112425 ATCGCAATGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
3112445 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
3112465 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
3112481 CGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:3112460 original size:40 final size:35
Alignment explanation
Indices: 3112416--3112506 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 35
3112406 TCTTTTGGTT
3112416 GAAATGAAAATCGCAATGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAATGAGAG-A-GA--ATCGCAACGC
** *
3112455 GGAAATGACTATCGCAA--CGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAATGAGAGAGAATCGCAACGC
3112489 GAAATGAAAATCGCAATG
1 GAAATGAAAATCGCAATG
3112507 CGATTTTGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
33 14 0.32
34 10 0.23
36 2 0.05
37 1 0.02
38 3 0.07
40 14 0.32
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (35 bp):
GAAATGAAAATCGCAATGAGAGAGAATCGCAACGC
Found at i:3112574 original size:20 final size:19
Alignment explanation
Indices: 3112536--3112600 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
3112526 CGATTCTCTC
3112536 GTTGCGATAGTCATTTCGT
1 GTTGCGATAGTCATTTCGT
3112555 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCA-TTTCGT
* *
3112575 GTTGCGAT-TTCATTTCAT
1 GTTGCGATAGTCATTTCGT
3112593 GTTGCGAT
1 GTTGCGAT
3112601 TTTAAGTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 13 0.30
19 16 0.37
20 14 0.33
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGT
Found at i:3113157 original size:20 final size:20
Alignment explanation
Indices: 3113132--3113325 Score: 194
Period size: 20 Copynumber: 9.6 Consensus size: 20
3113122 CTTTAAAAAT
3113132 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3113152 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3113172 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
3113193 CGCATTGCGATTTATGTATT
1 CGCGTTGCGATTTACGGATA
* * *
3113213 CTCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* * *
3113233 CTCATTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
3113253 CGCGTTGCGATTTTACGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3113275 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
3113294 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
3113315 CTCGTTGCGAT
1 CGCGTTGCGAT
3113326 AGTCAGAATC
Statistics
Matches: 144, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
19 2 0.01
20 90 0.62
21 50 0.35
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3113191 original size:41 final size:40
Alignment explanation
Indices: 3113132--3113325 Score: 205
Period size: 41 Copynumber: 4.8 Consensus size: 40
3113122 CTTTAAAAAT
*
3113132 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTACGGATACTCGTTGCGA-TTTACGTATA
* * * * *
3113172 TGTCGTTGCGATTTACGGATACGCATTGCGATTTATGTATT
1 CG-CGTTGCGATTTACGGATACTCGTTGCGATTTACGTATA
* * * *
3113213 CTCGTTGCGATTTACGTATTCTCATTGCGATTTACAG-ATA
1 CGCGTTGCGATTTACGGATACTCGTTGCGATTTAC-GTATA
* *
3113253 CGCGTTGCGATTTTACGTATTA-TCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGGA-TACTCGTTGCGATTTACGTATA
3113294 CGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGA-TTTACGGATACTCGTTGCGAT
3113326 AGTCAGAATC
Statistics
Matches: 133, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
40 52 0.39
41 80 0.60
42 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (40 bp):
CGCGTTGCGATTTACGGATACTCGTTGCGATTTACGTATA
Found at i:3113339 original size:41 final size:39
Alignment explanation
Indices: 3113129--3113348 Score: 194
Period size: 41 Copynumber: 5.4 Consensus size: 39
3113119 GCGCTTTAAA
*
3113129 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1 AATCGCGTTGCGATTTACGGATACTCGTTGCGA-TTTACG
* * * * *
3113169 TATTGTCGTTGCGATTTACGGATACGCATTGCGATTTATG
1 AATCG-CGTTGCGATTTACGGATACTCGTTGCGATTTACG
* * * * *
3113209 TATTCTCGTTGCGATTTACGTATTCTCATTGCGATTTAC-
1 -AATCGCGTTGCGATTTACGGATACTCGTTGCGATTTACG
*
3113248 AGATACGCGTTGCGATTTTACGTATTA-TCGTTGCGATTTACG
1 A-AT-CGCGTTGCGA-TTTACGGA-TACTCGTTGCGATTTACG
* *
3113290 GATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAG
1 AAT-CGCGTTGCGA-TTTACGGATACTCGTTGCGAT-TTAC-G
3113332 AATCGCGTTGCGATTTA
1 AATCGCGTTGCGATTTA
3113349 TATGTTCGCG
Statistics
Matches: 150, Mismatches: 20, Indels: 20
0.79 0.11 0.11
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 52 0.35
41 91 0.61
42 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (39 bp):
AATCGCGTTGCGATTTACGGATACTCGTTGCGATTTACG
Found at i:3113357 original size:20 final size:20
Alignment explanation
Indices: 3113334--3113386 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
3113324 ATAGTCAGAA
3113334 TCGCGTTGCGATTT-ATATGT
1 TCGCGTTGCGATTTCATAT-T
*
3113354 TCGCGTTCCGATTTTCATATT
1 TCGCGTTGCGA-TTTCATATT
3113375 T-GCGTTGCGATT
1 TCGCGTTGCGATT
3113387 CTGGGAACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 18 0.62
21 5 0.17
22 4 0.14
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTCATATT
Found at i:3114796 original size:23 final size:23
Alignment explanation
Indices: 3114743--3114822 Score: 89
Period size: 22 Copynumber: 3.6 Consensus size: 23
3114733 CACCACAGCT
*
3114743 CGTATAATTGCACC-GAAGTG-CA
1 CGTAGAATTGCACCAG-AGTGCCA
*
3114765 CGTATAATTGCACCAGAGTGCCA
1 CGTAGAATTGCACCAGAGTGCCA
3114788 CGTAGAATTGCA-CAGGAGTGCC-
1 CGTAGAATTGCACCA-GAGTGCCA
3114810 C-TAGAATTGCACC
1 CGTAGAATTGCACC
3114823 GTATTGCCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
21 10 0.19
22 22 0.42
23 21 0.40
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCAGAGTGCCA
Found at i:3114816 original size:21 final size:22
Alignment explanation
Indices: 3114743--3114821 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
3114733 CACCACAGCT
* *
3114743 CGTATAATTGCACCGAAGTG-CA
1 CGTAGAATTGCACAG-AGTGCCA
*
3114765 CGTATAATTGCACCAGAGTGCCA
1 CGTAGAATTGCA-CAGAGTGCCA
3114788 CGTAGAATTGCACAGGAGTGCC-
1 CGTAGAATTGCACA-GAGTGCCA
3114810 C-TAGAATTGCAC
1 CGTAGAATTGCAC
3114822 CGTATTGCCA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
21 11 0.21
22 19 0.37
23 22 0.42
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (22 bp):
CGTAGAATTGCACAGAGTGCCA
Found at i:3115801 original size:2 final size:2
Alignment explanation
Indices: 3115794--3115827 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3115784 TCTTATATTC
3115794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3115828 CAAGATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3119743 original size:22 final size:22
Alignment explanation
Indices: 3119718--3119776 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
3119708 CTCGTATAAT
3119718 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
*
3119740 TGCACC-AGAGTGCCGCGTAGAA
1 TGCACCGA-AGTGCCACGTAGAA
*
3119762 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3119777 TATAATAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (22 bp):
TGCACCGAAGTGCCACGTAGAA
Found at i:3127621 original size:20 final size:21
Alignment explanation
Indices: 3127586--3127629 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3127576 GATTTCTGGG
3127586 CAAGGGGAATCGATACCCATT
1 CAAGGGGAATCGATACCCATT
*
3127607 CAAGGGGAA-CGATACCCCTT
1 CAAGGGGAATCGATACCCATT
3127627 CAA
1 CAA
3127630 ACGAACAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:3128243 original size:21 final size:22
Alignment explanation
Indices: 3128214--3128257 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3128204 TGGGTATGAT
3128214 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
3128235 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
3128257 A
1 A
3128258 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:3129180 original size:146 final size:144
Alignment explanation
Indices: 3128996--3129291 Score: 540
Period size: 146 Copynumber: 2.0 Consensus size: 144
3128986 GAGTCGAGGG
3128996 TCTACGCGTTCTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
1 TCTACGCGTTCTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
*
3129061 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCA-T-TA
3129126 TGGCACTACGGTGCAAT
129 TGGCACTACGG-GCAAT
*
3129143 TCTACGC-TTCTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
1 TCTACGCGTTCTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
3129207 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTATG
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTATG
3129272 GCACTACGGGCAAT
131 GCACTACGGGCAAT
3129286 TCTACG
1 TCTACG
3129292 GGGCACTTCG
Statistics
Matches: 147, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
143 11 0.07
144 13 0.09
145 1 0.01
146 115 0.78
147 7 0.05
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (144 bp):
TCTACGCGTTCTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTATG
GCACTACGGGCAAT
Found at i:3134566 original size:18 final size:17
Alignment explanation
Indices: 3134537--3134577 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
3134527 ATTTATTCAG
3134537 AATAATAATTTTTTTAA
1 AATAATAATTTTTTTAA
3134554 AATAATGAATTTTTTTAA
1 AATAAT-AATTTTTTTAA
3134572 AA-AATA
1 AATAATA
3134578 TAAGGATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 9 0.39
18 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATAATAATTTTTTTAA
Found at i:3136745 original size:30 final size:29
Alignment explanation
Indices: 3136700--3136762 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
3136690 TTGTTGGGCG
*
3136700 ACTTTTAAAAACGTCTAGACTATTTAACA
1 ACTTTTAAAAACGTCTAGACTATCTAACA
* * *
3136729 ACTTTTGAAAGACGTCTAGATTATCTAACG
1 ACTTTT-AAAAACGTCTAGACTATCTAACA
3136759 ACTT
1 ACTT
3136763 CTCTAAACAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (29 bp):
ACTTTTAAAAACGTCTAGACTATCTAACA
Found at i:3138730 original size:20 final size:19
Alignment explanation
Indices: 3138707--3138752 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
3138697 CGATATACCA
3138707 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
3138727 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
3138747 GGTAAA
1 GGTAAA
3138753 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:3138894 original size:20 final size:19
Alignment explanation
Indices: 3138871--3138917 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
3138861 CGATATAACA
3138871 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
3138891 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
3138911 GGTAAAA
1 GGTAAAA
3138918 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:3138919 original size:17 final size:18
Alignment explanation
Indices: 3138875--3138922 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
3138865 ATAACAGGTA
3138875 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
3138894 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
3138914 -AAAATGATA
1 AAAAATGATA
3138923 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:3141121 original size:21 final size:21
Alignment explanation
Indices: 3141074--3141138 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
3141064 AAGACAATCA
* * *
3141074 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGATAAACTCGA-G
*
3141096 A-AGTCGTAGATAAACTCGAG
1 AGAGTCGAAGATAAACTCGAG
*
3141116 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGATAAACTCGAG
3141137 AG
1 AG
3141139 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.28, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGATAAACTCGAG
Found at i:3141233 original size:32 final size:33
Alignment explanation
Indices: 3141172--3141236 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3141162 AAATAGATGG
*
3141172 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
3141205 AGTGGTGAAAGAAGTTG-GGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
3141237 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:3142428 original size:4 final size:4
Alignment explanation
Indices: 3142419--3142447 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3142409 TAAGAGATTG
3142419 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
3142448 AAAGGACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:3143043 original size:19 final size:19
Alignment explanation
Indices: 3143019--3143067 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3143009 AATGTAGGGT
3143019 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3143038 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
3143057 TATTTTTGTAT
1 TAATTTTGTAT
3143068 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3144217 original size:199 final size:199
Alignment explanation
Indices: 3143186--3144351 Score: 2150
Period size: 197 Copynumber: 5.9 Consensus size: 199
3143176 CAATATGGCC
* *
3143186 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
3143251 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
3143315 AGAATATGTCT-AATAA--TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
3143377 ATGGAA
194 ATGGAA
3143383 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
3143448 CAAAAGTATAATGTAATAGGTAATTTTTAAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
3143513 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
3143577 GGAA
196 GGAA
*
3143581 AACAGGGTGCACCCACAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
3143646 CAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
3143710 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
3143774 GGAA
196 GGAA
3143778 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
3143843 CAAAAGTATAATGT-ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
3143907 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGACTGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
3143972 GGAA
196 GGAA
*
3143976 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACATCGAAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
3144041 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
3144106 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
3144171 TGGAA
195 TGGAA
3144176 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
3144241 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
3144306 AATGTGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
3144352 CTAATTTAAA
Statistics
Matches: 945, Mismatches: 16, Indels: 14
0.97 0.02 0.01
Matches are distributed among these distances:
195 51 0.05
196 84 0.09
197 251 0.27
198 195 0.21
199 211 0.22
200 153 0.16
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:3145832 original size:18 final size:18
Alignment explanation
Indices: 3145811--3145872 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
3145801 AGCGGTCGCA
3145811 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
3145829 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
3145847 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
3145865 GAAGATGA
1 GAAGATGA
3145873 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:3145835 original size:6 final size:6
Alignment explanation
Indices: 3145811--3145902 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
3145801 AGCGGTCGCA
* * * * * *
3145811 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
3145859 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
3145903 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:3145846 original size:3 final size:3
Alignment explanation
Indices: 3145826--3145906 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
3145816 TGAAGCTGAC
* * * * * ** *
3145826 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
3145874 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3145907 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:3145865 original size:36 final size:36
Alignment explanation
Indices: 3145814--3145890 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
3145804 GGTCGCAGAA
*
3145814 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
3145850 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
3145886 GATGA
1 GATGA
3145891 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:3145906 original size:12 final size:12
Alignment explanation
Indices: 3145814--3145902 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
3145804 GGTCGCAGAA
*
3145814 GATGAAGCTGAC
1 GATGAAGATGAC
3145826 GATGAAGATGAC
1 GATGAAGATGAC
*
3145838 GATGATGATGAC
1 GATGAAGATGAC
* *
3145850 GATGAAGCTGGC
1 GATGAAGATGAC
*
3145862 GATGAAGATGAT
1 GATGAAGATGAC
* * *
3145874 GACGATGATGAT
1 GATGAAGATGAC
* *
3145886 GATGATGATGAA
1 GATGAAGATGAC
3145898 GATGA
1 GATGA
3145903 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:3145906 original size:18 final size:18
Alignment explanation
Indices: 3145811--3145902 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
3145801 AGCGGTCGCA
*
3145811 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
3145829 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
3145847 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
3145865 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
3145883 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
3145901 GA
1 GA
3145903 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:3147699 original size:182 final size:183
Alignment explanation
Indices: 3147364--3147887 Score: 917
Period size: 183 Copynumber: 2.9 Consensus size: 183
3147354 CTTTCAACAT
** * * *
3147364 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
3147429 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
3147493 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
3147546 ATTAT-ATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
3147610 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTAGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
3147675 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
* *
3147728 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
3147793 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
3147858 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
3147888 GTAATTTGAA
Statistics
Matches: 325, Mismatches: 15, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
181 76 0.23
182 101 0.31
183 148 0.46
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
Found at i:3150802 original size:22 final size:23
Alignment explanation
Indices: 3150746--3150808 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
3150736 ATAGGTAAAC
*
3150746 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
3150769 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
3150792 ATAT-ATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
3150809 TGGTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 12 0.34
23 23 0.66
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:3150815 original size:22 final size:23
Alignment explanation
Indices: 3150746--3150817 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
3150736 ATAGGTAAAC
* **
3150746 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
3150769 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
3150792 ATAT-ATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
3150814 ATAT
1 ATAT
3150818 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:3151205 original size:23 final size:23
Alignment explanation
Indices: 3151174--3151237 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
3151164 ATAGGTAAAC
*
3151174 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
3151197 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
3151220 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
3151238 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:3151244 original size:23 final size:23
Alignment explanation
Indices: 3151174--3151246 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
3151164 ATAGGTAAAC
* **
3151174 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
3151197 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
3151220 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
3151243 ATAT
1 ATAT
3151247 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:3151342 original size:429 final size:425
Alignment explanation
Indices: 3150544--3151475 Score: 1744
Period size: 429 Copynumber: 2.2 Consensus size: 425
3150534 GTTAATGTTG
* * *
3150544 TTAAATT-TAAATTCTAAATAATA-TTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA-TTTTTGTGCAA
3150607 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATA
65 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATA
3150672 AATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
130 AATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
3150737 TAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATATGTAA
195 TAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATATGTAA
3150802 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
*
3150867 GGAAAATATTAATTTAAGGTTATGTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
325 GGAAAACATTAATTTAAGGTTATGTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
3150932 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
390 GTCTAATGATTTATTTTTTACGTTACG--ATATA-TA-TA
3150972 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAA
3151037 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAA
3151102 ATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT-AT
131 ATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
3151166 AGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
196 AGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATAT-ATGTAA
3151231 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
*
3151296 GGAAAACATTAATTTAATGTTATGTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
325 GGAAAACATTAATTTAAGGTTATGTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
3151361 GTCTAATGATTTATTTTTTACGTTACGATATATATA
390 GTCTAATGATTTATTTTTTACGTTACGATATATATA
3151397 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAA
3151462 TGAAATTATTAAAT
66 TGAAATTATTAAAT
3151476 CAAATAATTC
Statistics
Matches: 496, Mismatches: 5, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
425 81 0.16
426 2 0.00
427 5 0.01
428 67 0.14
429 313 0.63
430 28 0.06
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (425 bp):
TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAA
TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAA
ATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
AGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATATATGTAAT
AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
GAAAACATTAATTTAAGGTTATGTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
TCTAATGATTTATTTTTTACGTTACGATATATATA
Found at i:3151544 original size:25 final size:25
Alignment explanation
Indices: 3151510--3151560 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
3151500 ACAACAAATC
*
3151510 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
3151535 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
3151560 A
1 A
3151561 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:3151969 original size:18 final size:18
Alignment explanation
Indices: 3151948--3151984 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3151938 GTAATTGGAG
3151948 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3151966 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3151984 T
1 T
3151985 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3151992 original size:24 final size:24
Alignment explanation
Indices: 3151940--3151986 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3151930 TTTCATATGT
* *
3151940 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
3151964 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
3151987 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:3152285 original size:39 final size:39
Alignment explanation
Indices: 3152242--3152328 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
3152232 TCCGATGCTC
*
3152242 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
3152281 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
3152320 ATCAAAATC
1 ATCAAAATC
3152329 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:3152758 original size:23 final size:23
Alignment explanation
Indices: 3152727--3152799 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
3152717 ATAGGTAAAC
*
3152727 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3152750 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3152773 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
3152796 ATAT
1 ATAT
3152800 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3159012 original size:2 final size:2
Alignment explanation
Indices: 3159005--3159037 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3158995 ATTATATCAT
3159005 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 T
3159038 TAATGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3159906 original size:23 final size:24
Alignment explanation
Indices: 3159862--3159911 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
3159852 TAAGTCTACC
* *
3159862 TTTATGACATATTTTTAATTGT-T
1 TTTATAACACATTTTTAATTGTCT
**
3159885 TTTATAACACATTTTTCTTTGTCT
1 TTTATAACACATTTTTAATTGTCT
3159909 TTT
1 TTT
3159912 GACTCGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.62
Consensus pattern (24 bp):
TTTATAACACATTTTTAATTGTCT
Found at i:3164327 original size:46 final size:45
Alignment explanation
Indices: 3164275--3164375 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 45
3164265 AAACAGAGAT
*
3164275 ATCAGAAAT-AAAAAGAATTCAGATCATATATCATAACAGAATCCA
1 ATCAGAAATGAAAAA-AATTCAGATCATATATCAAAACAGAATCCA
* * * * *
3164320 GATCAGAAATGAACAAAATTCAGGTCATGTATCAAAACTGAATTCA
1 -ATCAGAAATGAAAAAAATTCAGATCATATATCAAAACAGAATCCA
3164366 AGTCAGAAAT
1 A-TCAGAAAT
3164376 CAGATGAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 1 0.02
46 42 0.89
47 4 0.09
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.23
Consensus pattern (45 bp):
ATCAGAAATGAAAAAAATTCAGATCATATATCAAAACAGAATCCA
Found at i:3169656 original size:18 final size:18
Alignment explanation
Indices: 3169633--3169667 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3169623 TTCCATCCGG
*
3169633 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
3169651 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
3169668 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:3170841 original size:19 final size:19
Alignment explanation
Indices: 3170819--3170901 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
3170809 CTAGGCGGCT
*
3170819 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
3170838 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
3170857 CGGCTCGGCT----T-AAA
1 CGGCTCGGCTCAGCTCAAA
*
3170871 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
3170890 CGGCTCGGCTCA
1 CGGCTCGGCTCA
3170902 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:3170848 original size:14 final size:14
Alignment explanation
Indices: 3170843--3170909 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
3170833 TCAAACGGCT
*
3170843 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
3170857 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
3170871 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
3170889 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
3170904 CGGCTC
1 CGGCTC
3170910 CTCAGGCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.16
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:3170872 original size:33 final size:33
Alignment explanation
Indices: 3170825--3170909 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
3170815 GGCTCGGCTT
*
3170825 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
3170858 GGCTCGGCTTAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
3170891 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
3170910 CTCAGGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.16
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:3174664 original size:18 final size:18
Alignment explanation
Indices: 3174641--3174675 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3174631 TTCCATCCGG
*
3174641 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
3174659 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
3174676 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:3175850 original size:19 final size:19
Alignment explanation
Indices: 3175828--3175910 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
3175818 CTAGGCGGCT
*
3175828 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
3175847 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
3175866 CGGCTCGGCT----T-AAA
1 CGGCTCGGCTCAGCTCAAA
*
3175880 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
3175899 CGGCTCGGCTCA
1 CGGCTCGGCTCA
3175911 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:3175857 original size:14 final size:14
Alignment explanation
Indices: 3175852--3175918 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
3175842 TCAAACGGCT
*
3175852 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
3175866 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
3175880 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
3175898 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
3175913 CGGCTC
1 CGGCTC
3175919 CTCAGGCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.16
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:3175881 original size:33 final size:33
Alignment explanation
Indices: 3175834--3175918 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
3175824 GGCTCGGCTT
*
3175834 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
3175867 GGCTCGGCTTAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
3175900 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
3175919 CTCAGGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.16
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:3177897 original size:60 final size:60
Alignment explanation
Indices: 3177789--3177901 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
3177779 TCAGGGGACC
* * * **
3177789 ATTTTATAACTTTTGATAGGCGATGGACTTAATAAAGAAACATTCTATAGTCATAAGACT
1 ATTTTATAACTTTTAATAAGCGAGGGACTTAATAAAGAAACACCCTATAGTCATAAGACT
* *
3177849 ATTTTATAACTTTTAATAATCGAGGGACTTAATAAA-ATAATACCCTATAGTCA
1 ATTTTATAACTTTTAATAAGCGAGGGACTTAATAAAGA-AACACCCTATAGTCA
3177902 GGGACCATTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 44 0.98
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAAGCGAGGGACTTAATAAAGAAACACCCTATAGTCATAAGACT
Found at i:3200393 original size:22 final size:23
Alignment explanation
Indices: 3200362--3200408 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3200352 AAAATATTTT
3200362 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
3200385 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
3200407 TA
1 TA
3200409 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:3200408 original size:27 final size:26
Alignment explanation
Indices: 3200376--3200466 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
3200366 AATATTTCTA
3200376 ATAATATAATATTATATTTTTAATATT
1 ATAATATAATATTATA-TTTTAATATT
* * * * *
3200403 ATAATAAAATAATCA-ATTATATTATA
1 ATAATATAAT-ATTATATTTTAATATT
*
3200429 ATAATATAAATATTATATTTT-ATTTT
1 ATAATAT-AATATTATATTTTAATATT
3200455 AATAATATAATA
1 -ATAATATAATA
3200467 AATTATTAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
26 22 0.45
27 24 0.49
28 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAATATAATATTATATTTTAATATT
Found at i:3200430 original size:50 final size:50
Alignment explanation
Indices: 3200374--3200584 Score: 139
Period size: 53 Copynumber: 4.1 Consensus size: 50
3200364 TTAATATTTC
*
3200374 TAATAATAT-AATATTATATTTTTAATATTATAATAAAATAATCAATTATATTA
1 TAATAATATAAATATTATA-TTTT-AT-TT-TAATAAAATAATAAATTATATTA
* *
3200427 TAATAATATAAATATTATATTTTATTTTAATAATATAATAAATTAT-TAA
1 TAATAATATAAATATTATATTTTATTTTAATAAAATAATAAATTATATTA
* * * * *
3200476 TAA-AA-ATATATATTAT-TTATTAATTTCATAGAAATAA-ATTATTAAATTA
1 TAATAATATAAATATTATATT-TTATTTTAATA-AAATAATA-AATTATATTA
* * * * * *
3200525 TTAATAATGA-ATATATTATATATTTAATATTAATATAATAATCTAATAATATTT
1 -TAATAAT-ATAAATATTATAT-TTT-ATTTTAATAAAATAAT-AAATTATATTA
3200579 TAATAA
1 TAATAA
3200585 AGATATTTAA
Statistics
Matches: 125, Mismatches: 19, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
46 2 0.02
47 20 0.16
48 11 0.09
49 7 0.06
50 20 0.16
51 4 0.03
52 11 0.09
53 28 0.22
54 22 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (50 bp):
TAATAATATAAATATTATATTTTATTTTAATAAAATAATAAATTATATTA
Found at i:3200497 original size:26 final size:26
Alignment explanation
Indices: 3200468--3200559 Score: 71
Period size: 26 Copynumber: 3.4 Consensus size: 26
3200458 AATATAATAA
3200468 ATTATTAATAAAAATATATATTATTT
1 ATTATTAATAAAAATATATATTATTT
* * *
3200494 ATTAATTTCATAGAAATA-A-ATTATTAA
1 ATT-A-TTAATAAAAATATATATTATT-T
*
3200521 ATTATTAATAATGAATATATTATATATTT
1 ATTATTAATAA-AAATATA-TAT-TATTT
*
3200550 AATATTAATA
1 ATTATTAATA
3200560 TAATAATCTA
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
25 5 0.10
26 14 0.28
27 6 0.12
28 10 0.20
29 11 0.22
30 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTATTAATAAAAATATATATTATTT
Found at i:3200512 original size:53 final size:54
Alignment explanation
Indices: 3200455--3200590 Score: 147
Period size: 53 Copynumber: 2.6 Consensus size: 54
3200445 ATTTTATTTT
* * *
3200455 AATAATATAATAAATTATTAATAAAAATATATATTATTTA-TTAAT-TTCATAGA
1 AATAATATAATAAATTATTAATAAAGATATATATTATATATTTAATATTAATA-A
* * *
3200508 AATAA-ATTATTAAATTATTAATAATGA-ATATATTATATATTTAATATTAATAT
1 AATAATA-TAATAAATTATTAATAAAGATATATATTATATATTTAATATTAATAA
*
3200561 AATAATCTAATAATATT-TTAATAAAGATAT
1 AATAATATAATAA-ATTATTAATAAAGATAT
3200591 TTAAAATATA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
52 12 0.18
53 46 0.68
54 10 0.15
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (54 bp):
AATAATATAATAAATTATTAATAAAGATATATATTATATATTTAATATTAATAA
Found at i:3200605 original size:23 final size:23
Alignment explanation
Indices: 3200579--3200623 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3200569 AATAATATTT
3200579 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3200602 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3200624 TTATAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3200644 original size:35 final size:34
Alignment explanation
Indices: 3200571--3200645 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 34
3200561 AATAATCTAA
3200571 TAATATTTTAATAAAGATATTTAAAATATACTAAT
1 TAATATTTTAATAAAGATATTTAAAATATACT-AT
* *
3200606 TAATATTTTTA-AAATATATTATAAAACTATTACT-T
1 TAATATTTTAATAAAGATATT-TAAAA-TA-TACTAT
3200641 TAATA
1 TAATA
3200646 AATAATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 8 0.23
35 21 0.60
36 2 0.06
37 4 0.11
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (34 bp):
TAATATTTTAATAAAGATATTTAAAATATACTAT
Found at i:3201268 original size:7 final size:7
Alignment explanation
Indices: 3201247--3201278 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
3201237 TCAATTAGTG
3201247 AATTTTA
1 AATTTTA
3201254 ATATTTTA
1 A-ATTTTA
3201262 AATTTTA
1 AATTTTA
3201269 AATTTTA
1 AATTTTA
3201276 AAT
1 AAT
3201279 CTAGACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:3210059 original size:20 final size:20
Alignment explanation
Indices: 3210034--3210071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3210024 TAATAAATTG
*
3210034 AAGATTAATAATAATAAAAA
1 AAGATTAACAATAATAAAAA
*
3210054 AAGATTAACAATTATAAA
1 AAGATTAACAATAATAAA
3210072 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
AAGATTAACAATAATAAAAA
Found at i:3211946 original size:20 final size:20
Alignment explanation
Indices: 3211921--3211968 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3211911 ACGCGATATC
*
3211921 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGGTAAAAAG
*
3211941 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTAAAAAG
3211961 AAAATCGC
1 AAAATCGC
3211969 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGGTAAAAAG
Found at i:3212218 original size:20 final size:20
Alignment explanation
Indices: 3211986--3212216 Score: 291
Period size: 20 Copynumber: 11.4 Consensus size: 20
3211976 TTTAGAAGAA
*
3211986 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
3212006 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
3212026 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
3212046 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
3212069 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
3212089 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
3212109 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
* * *
3212129 AATCACAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
3212149 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
3212169 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
3212189 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
3212209 AATCGCAA
1 AATCGCAA
3212217 CGTTAAAAAG
Statistics
Matches: 188, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
20 169 0.90
21 3 0.02
22 2 0.01
23 14 0.07
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:3212403 original size:6 final size:6
Alignment explanation
Indices: 3212392--3212430 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
3212382 GACGCGTATT
3212392 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
3212431 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3213148 original size:6 final size:6
Alignment explanation
Indices: 3213116--3213180 Score: 102
Period size: 6 Copynumber: 11.5 Consensus size: 6
3213106 CGTCGTCTCG
3213116 GGTCG- GGTCGT -GTCGT -GTCGT -GTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3213160 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
3213181 AATACGTGTC
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 20 0.34
6 38 0.66
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
GGTCGT
Found at i:3213465 original size:63 final size:63
Alignment explanation
Indices: 3213368--3213492 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
3213358 CTGTTATGTC
3213368 TGTGTGTATCAGGTCGAGTCAAATACACATTATTACTTTAAAAACCAAAATGATTTTCAAATG
1 TGTGTGTATCAGGTCGAGTCAAATACACATTATTACTTTAAAAACCAAAATGATTTTCAAATG
* *
3213431 TGTGTGTGTCAGGTCGAGTCAAATACACATTATTACTTTAAAAACCAAATTGATTTTCAAAT
1 TGTGTGTATCAGGTCGAGTCAAATACACATTATTACTTTAAAAACCAAAATGATTTTCAAAT
3213493 CAGATAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (63 bp):
TGTGTGTATCAGGTCGAGTCAAATACACATTATTACTTTAAAAACCAAAATGATTTTCAAATG
Found at i:3216641 original size:2 final size:2
Alignment explanation
Indices: 3216634--3216671 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3216624 ATCATATACA
3216634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3216672 TTGTATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3218840 original size:18 final size:18
Alignment explanation
Indices: 3218817--3218853 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3218807 AGACGGCCCC
* *
3218817 TATTAATTTATTTTTATT
1 TATTAAGTTATTATTATT
3218835 TATTAAGTTATTATTATT
1 TATTAAGTTATTATTATT
3218853 T
1 T
3218854 TATCAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTAAGTTATTATTATT
Found at i:3223103 original size:33 final size:33
Alignment explanation
Indices: 3223066--3223146 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
3223056 TCTCAATTCC
*
3223066 AAATGACTCGAACCTGAAACTAATCCATACCTA
1 AAATGACTCGAACCTGAAACGAATCCATACCTA
3223099 AAATGACTC-AATCCTGAAACGAATCCATACCTA
1 AAATGACTCGAA-CCTGAAACGAATCCATACCTA
*
3223132 AAATGACCCGAACCT
1 AAATGACTCGAACCT
3223147 TAAAACCAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 2 0.05
33 40 0.91
34 2 0.05
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (33 bp):
AAATGACTCGAACCTGAAACGAATCCATACCTA
Found at i:3233246 original size:63 final size:64
Alignment explanation
Indices: 3233098--3233258 Score: 186
Period size: 63 Copynumber: 2.5 Consensus size: 64
3233088 ATTGTTCAAG
* *
3233098 GTGTATCGATGCACATGA-AGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATACCATCA
1 GTGTATCGATGCACA-GATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCATCA
* ** ** *
3233162 GTGTATAGATGCACA-AGTAGTGCATCGATGCACCCCCTT-AAATGCAAACATCGAATAGGATTT
1 GTGTATCGATGCACAGA-TAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCA-TC
3233225 A
64 A
*
3233226 -TGTATCGATGCATAGATAGTGCATCGATGCACC
1 GTGTATCGATGCACAGATAGTGCATCGATGCACC
3233259 TGTCAAGGGA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 46 0.55
64 36 0.43
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCATCA
Found at i:3234016 original size:20 final size:20
Alignment explanation
Indices: 3233971--3234065 Score: 76
Period size: 20 Copynumber: 4.9 Consensus size: 20
3233961 CAGATTGCCT
*
3233971 AGGGGGTACAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
*
3233991 AAGGGGAACAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
* *
3234011 AGGGGGTATC-GATT--CCTC
1 AGGGGG-AACAGATTCCCCCC
3234029 ---GGGAACAGATTCCCCCCC
1 AGGGGGAACAGATT-CCCCCC
*
3234047 TAGGGGGTACAGATTCCCC
1 -AGGGGGAACAGATTCCCC
3234066 ACTAAATGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.03
15 7 0.12
18 6 0.10
20 27 0.47
21 6 0.10
22 10 0.17
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (20 bp):
AGGGGGAACAGATTCCCCCC
Found at i:3234034 original size:35 final size:37
Alignment explanation
Indices: 3233994--3234063 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
3233984 TCCCCCCAAG
3233994 GGGAACAGATT-CCCCCC-AGGGGGTATC-GATTCCTC
1 GGGAACAGATTCCCCCCCTAGGGGGTA-CAGATTCCTC
3234029 GGGAACAGATTCCCCCCCTAGGGGGTACAGATTCC
1 GGGAACAGATTCCCCCCCTAGGGGGTACAGATTCC
3234064 CCACTAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 11 0.34
36 7 0.22
37 14 0.44
ACGTcount: A:0.21, C:0.31, G:0.29, T:0.19
Consensus pattern (37 bp):
GGGAACAGATTCCCCCCCTAGGGGGTACAGATTCCTC
Found at i:3234543 original size:34 final size:32
Alignment explanation
Indices: 3234504--3234573 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3234494 TATTGTAAAG
* *
3234504 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCC-TG-AAAAACTA
*
3234538 GGGAAAGGTTCTAGTTTAGCCCTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCTGAAAAACTA
3234570 GGGA
1 GGGA
3234574 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 2 0.06
34 20 0.61
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCTGAAAAACTA
Found at i:3235584 original size:19 final size:20
Alignment explanation
Indices: 3235557--3235596 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3235547 CTTCTTCTAG
* *
3235557 AAATGAAAATGGAAT-TTGA
1 AAATCAAAATGAAATCTTGA
3235576 AAATCAAAATGAAATCTTGA
1 AAATCAAAATGAAATCTTGA
3235596 A
1 A
3235597 GAAGGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
AAATCAAAATGAAATCTTGA
Found at i:3237082 original size:21 final size:21
Alignment explanation
Indices: 3237056--3237136 Score: 119
Period size: 21 Copynumber: 3.9 Consensus size: 21
3237046 CAGATTGCCT
3237056 AGGGGGTACAGATTCCCCCCC
1 AGGGGGTACAGATTCCCCCCC
3237077 AGGGGGTACAGATTCCCCCCC
1 AGGGGGTACAGATTCCCCCCC
* * *
3237098 AGGGGGAATAGATTTCCCCCC
1 AGGGGGTACAGATTCCCCCCC
3237119 AGGGGGTATC-GATTCCCC
1 AGGGGGTA-CAGATTCCCC
3237137 GGGAACAGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (21 bp):
AGGGGGTACAGATTCCCCCCC
Found at i:3237610 original size:34 final size:34
Alignment explanation
Indices: 3237566--3237640 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
3237556 CCTATTGTAA
*
3237566 AGGGGAAGGTTCTAGCTTATCCCGTGTAAAAGAT
1 AGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGAT
*
3237600 AGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCT
1 AGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGAT
3237634 AGGGAAA
1 AGGGAAA
3237641 TGTTATAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (34 bp):
AGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGAT
Found at i:3238675 original size:19 final size:20
Alignment explanation
Indices: 3238653--3238692 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3238643 CTTCTTCTAG
* *
3238653 AAATGAAAATGGAAT-TTGA
1 AAATCAAAATGAAATCTTGA
3238672 AAATCAAAATGAAATCTTGA
1 AAATCAAAATGAAATCTTGA
3238692 A
1 A
3238693 GAAGGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
AAATCAAAATGAAATCTTGA
Found at i:3240178 original size:21 final size:21
Alignment explanation
Indices: 3240152--3240231 Score: 110
Period size: 21 Copynumber: 3.9 Consensus size: 21
3240142 CAGATTGCCT
3240152 AGGGGGTACAGATTCCCCCCC
1 AGGGGGTACAGATTCCCCCCC
3240173 AGGGGGTACAGATT-CCCCCC
1 AGGGGGTACAGATTCCCCCCC
* * *
3240193 AGGGGGAATAGATTTCCCCCC
1 AGGGGGTACAGATTCCCCCCC
3240214 AGGGGGTATC-GATTCCCC
1 AGGGGGTA-CAGATTCCCC
3240232 GGGAACAGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 18 0.35
21 34 0.65
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (21 bp):
AGGGGGTACAGATTCCCCCCC
Done.