Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 46 of 51
Found at i:11417634 original size:36 final size:37
Alignment explanation
Indices: 11417594--11417747 Score: 182
Period size: 36 Copynumber: 4.4 Consensus size: 37
11417584 ACATTTAAAA
*
11417594 ATATATAGTTTTTGAAA-ATATTTTGAAAATATATAT
1 ATATATAGTTTTTGAAATATTTTTTGAAAATATATAT
**
11417630 ATATATA-TTTTT-AAA-ACGTTTTGAAAATATATAT
1 ATATATAGTTTTTGAAATATTTTTTGAAAATATATAT
*
11417664 A-ATATAG-TTTAGAAATATTTTTTCGAAAATATATAT
1 ATATATAGTTTTTGAAATATTTTTT-GAAAATATATAT
*
11417700 A-ATGTAGTTTTTGAAAGTATTTTTTGAAAATATATA-
1 ATATATAGTTTTTGAAA-TATTTTTTGAAAATATATAT
11417736 ATAT-TAGTTTTT
1 ATATATAGTTTTT
11417748 TATATTATAT
Statistics
Matches: 104, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
33 8 0.08
34 24 0.23
35 10 0.10
36 34 0.33
37 20 0.19
38 8 0.08
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (37 bp):
ATATATAGTTTTTGAAATATTTTTTGAAAATATATAT
Found at i:11417762 original size:17 final size:18
Alignment explanation
Indices: 11417730--11417767 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
11417720 TTTTTGAAAA
11417730 TATATAATATTAGTTTTT
1 TATATAATATTAGTTTTT
*
11417748 TATATTATA-TAGTTTTT
1 TATATAATATTAGTTTTT
11417765 TAT
1 TAT
11417768 TTACATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TATATAATATTAGTTTTT
Found at i:11417770 original size:21 final size:19
Alignment explanation
Indices: 11417746--11417790 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
11417736 ATATTAGTTT
*
11417746 TTTATATTATATAGTTTTTTA
1 TTTATATTATAT--TTATTTA
*
11417767 TTTACATTATATTTATTTA
1 TTTATATTATATTTATTTA
11417786 TTTAT
1 TTTAT
11417791 TTGTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATATTATATTTATTTA
Found at i:11419170 original size:22 final size:22
Alignment explanation
Indices: 11419127--11419171 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11419117 CTCTTTTAAA
* * **
11419127 TATTTAATTTTTTTCCTGATTT
1 TATTTAATGTTTTTACACATTT
11419149 TATTTAATGTTTTTACACATTT
1 TATTTAATGTTTTTACACATTT
11419171 T
1 T
11419172 TTAAAAATCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.64
Consensus pattern (22 bp):
TATTTAATGTTTTTACACATTT
Found at i:11419983 original size:20 final size:20
Alignment explanation
Indices: 11419944--11419983 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11419934 TGTTTGAACT
*
11419944 TTATAATTTTATTATAATTG
1 TTATAATTTTAATATAATTG
* *
11419964 TTATTATTTTAATATTATTG
1 TTATAATTTTAATATAATTG
11419984 AAGTATTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTATAATTTTAATATAATTG
Found at i:11426607 original size:17 final size:17
Alignment explanation
Indices: 11426585--11426617 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11426575 TTATGTTATA
11426585 AAGTCATAACGTATTAG
1 AAGTCATAACGTATTAG
11426602 AAGTCATAACGTATTA
1 AAGTCATAACGTATTA
11426618 TAAATTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
AAGTCATAACGTATTAG
Found at i:11432217 original size:15 final size:15
Alignment explanation
Indices: 11432170--11432229 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
11432160 ATTAAATTCA
*
11432170 GGTTACTTTCTGTTC
1 GGTTACTTTCGGTTC
* * *
11432185 AGGTTATTTTTGGGTC
1 -GGTTACTTTCGGTTC
*
11432201 GGTTGCTTTCGGTTC
1 GGTTACTTTCGGTTC
*
11432216 GGTTATTTTCGGTT
1 GGTTACTTTCGGTT
11432230 ATGGTTATTT
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
15 23 0.68
16 11 0.32
ACGTcount: A:0.07, C:0.13, G:0.28, T:0.52
Consensus pattern (15 bp):
GGTTACTTTCGGTTC
Found at i:11432237 original size:16 final size:15
Alignment explanation
Indices: 11432170--11432245 Score: 62
Period size: 16 Copynumber: 4.9 Consensus size: 15
11432160 ATTAAATTCA
* *
11432170 GGTTACTTTCTGTTC
1 GGTTATTTTCGGTTC
* *
11432185 AGGTTATTTTTGGGTC
1 -GGTTATTTTCGGTTC
**
11432201 GGTTGCTTTCGGTTC
1 GGTTATTTTCGGTTC
*
11432216 GGTTATTTTCGGTTAT
1 GGTTATTTTCGGTT-C
*
11432232 GGTTATTTTTGGTT
1 GGTTATTTTCGGTT
11432246 TGGCTAAAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
15 23 0.49
16 24 0.51
ACGTcount: A:0.08, C:0.11, G:0.28, T:0.54
Consensus pattern (15 bp):
GGTTATTTTCGGTTC
Found at i:11433591 original size:3 final size:3
Alignment explanation
Indices: 11433576--11433613 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
11433566 TCCGAGATTA
*
11433576 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11433614 ATATATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:11433778 original size:14 final size:14
Alignment explanation
Indices: 11433759--11433785 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11433749 TTGAGTAACT
11433759 TGTGTTGTGTTATG
1 TGTGTTGTGTTATG
11433773 TGTGTTGTGTTAT
1 TGTGTTGTGTTAT
11433786 TTCTTAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (14 bp):
TGTGTTGTGTTATG
Found at i:11433904 original size:21 final size:21
Alignment explanation
Indices: 11433816--11433910 Score: 88
Period size: 21 Copynumber: 4.4 Consensus size: 21
11433806 GGTTAAGACC
11433816 TTTCGATGAAAGGACTTAATC-
1 TTTC-ATGAAAGGACTTAATCT
*
11433837 TTTCAATTAAAGGACTT-ATCCT
1 TTTC-ATGAAAGGACTTAAT-CT
* *
11433859 TTTGATGAAAAGTG-CTTAACCT
1 TTTCATG-AAAG-GACTTAATCT
*
11433881 TTTCATGAAAGGATTTAATCT
1 TTTCATGAAAGGACTTAATCT
11433902 TTTCATGAA
1 TTTCATGAA
11433911 GAGAATTGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.05
21 37 0.62
22 18 0.30
23 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.39
Consensus pattern (21 bp):
TTTCATGAAAGGACTTAATCT
Found at i:11434130 original size:111 final size:112
Alignment explanation
Indices: 11433936--11434172 Score: 433
Period size: 111 Copynumber: 2.1 Consensus size: 112
11433926 AGTATGATTG
*
11433936 AATGGATGCAACTTTAAACCAAAAATTAAGTCCATTCATCAAGTGACATGACTTATTATTATTTA
1 AATGGATGCAACTTTAAACCAAAAATTAAGTCCATTCATCAAGTAACATGACTTATTATTATTTA
11434001 GCTATAAATAGAATCAATTCATTCAATAAA-TTTCCAACAATCCCCC
66 GCTATAAATAGAATCAATTCATTCAATAAATTTTCCAACAATCCCCC
11434047 AATGGATGCAACTTTAAACCAAAAATTAAGTCCATTCATCAAGTAACATGACTTATTATTATTTA
1 AATGGATGCAACTTTAAACCAAAAATTAAGTCCATTCATCAAGTAACATGACTTATTATTATTTA
11434112 GCTATAAATAGAATCAATTCATTCAATAAATTTTCCAACAATCCCCC
66 GCTATAAATAGAATCAATTCATTCAATAAATTTTCCAACAATCCCCC
*
11434159 ACATGAATG-AACTT
1 A-ATGGATGCAACTT
11434173 GGTGGTTCAA
Statistics
Matches: 122, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
111 94 0.77
112 22 0.18
113 6 0.05
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (112 bp):
AATGGATGCAACTTTAAACCAAAAATTAAGTCCATTCATCAAGTAACATGACTTATTATTATTTA
GCTATAAATAGAATCAATTCATTCAATAAATTTTCCAACAATCCCCC
Found at i:11436984 original size:22 final size:23
Alignment explanation
Indices: 11436959--11437014 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 23
11436949 GGACTTATCA
*
11436959 TTTTGATGAAAAGTG-TTTAACC
1 TTTTCATGAAAAGTGATTTAACC
*
11436981 TTTTCATG-AAA-TGATTTAATC
1 TTTTCATGAAAAGTGATTTAACC
11437002 TTTTCATGAAAAG
1 TTTTCATGAAAAG
11437015 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 17 0.59
22 10 0.34
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (23 bp):
TTTTCATGAAAAGTGATTTAACC
Found at i:11437927 original size:346 final size:342
Alignment explanation
Indices: 11437008--11438043 Score: 1968
Period size: 341 Copynumber: 3.0 Consensus size: 342
11436998 AATCTTTTCA
* * * *
11437008 TGAAAAGAATTGTTGAATAAGTATGATTAAATGAATGCAACTTTAAACCAAAAATTAAATCCATT
1 TGAAGAGAATTATTGAATAAATATGATTAAATGAATGCAACTTTAAACCAAAAATTAAGTCCATT
11437073 CATCAAGTGGCATGACTTATTATTAATTAGCTATAAATAACATCAATTCATTCAATAATTTTTCC
66 CATCAAGTGGCATGACTTATTATTAATTAGCTATAAATAACATCAATTCATTCAATAATTTTTCC
11437138 AAACACATTTGCAAGGCTTCAAAATCAGGCAACCATCCCAAACTAGGCAAAAAGATTTAACATCT
131 AAACACATTTGCAAGGCTTCAAAATCAGGCAACCATCCCAAACTAGGCAAAAAGATTTAACATCT
11437203 GCCGATATAACAAGATGAAGGTTCCAAAAAGAAAACCATCTAGGATCCTCCACACCACCTCGTAA
196 GCCGATATAACAAGATGAAGGTTCCAAAAAGAAAACCATCTAGGATCCTCCACACCACCTCGTAA
11437268 TGGCAGAACAAGTGGTTGACCGACTCACACTCCTTTCTACATAGCACATAAAGACTAGAATCCAG
261 TGGCAGAACAAGTGGTTGACCGACTCACACTCCTTTCTACATAGCACATAAAGACTAGAATCCAG
11437333 ATTAGTAAACGCTCCGTT
326 ATTAGT-AACGCTCCGTT
11437351 TGAAGAGAATTATTGAATAAATATGATTAAATGAATGCAACTTTAAACCAAAAATTAAGTCCATT
1 TGAAGAGAATTATTGAATAAATATGATTAAATGAATGCAACTTTAAACCAAAAATTAAGTCCATT
11437416 CATCAAGTGGCATGACTTATTATTAATTAGC--TAAATAACATCAATTCATTCAATAATTTTTCC
66 CATCAAGTGGCATGACTTATTATTAATTAGCTATAAATAACATCAATTCATTCAATAATTTTTCC
11437479 AAACACATTTGCAAGGCTTCAAAATCAGGCAACCATCCCAAACTAGGCAAAAAGATTTAACATCT
131 AAACACATTTGCAAGGCTTCAAAATCAGGCAACCATCCCAAACTAGGCAAAAAGATTTAACATCT
11437544 GCCGATATAACAAGATGAAGGTTCCAAAAAGAAAACCATCTAGATCAGATCCTCCACACCACCTC
196 GCCGATATAACAAGATGAAGGTTCCAAAAAGAAAACCATCTAG----GATCCTCCACACCACCTC
11437609 GTAATGGCAGAACAAGTGGTTGACCGACTCACACTCCTTTCTACATAGCACATAAAGACTAGAAT
257 GTAATGGCAGAACAAGTGGTTGACCGACTCACACTCCTTTCTACATAGCACATAAAGACTAGAAT
11437674 CCAGATTAGTAACGCTCCGTT
322 CCAGATTAGTAACGCTCCGTT
11437695 TGAAGAGAATTATTGAATAAATATGATTAAATGAATGCAACTTTAAACCAAAAATTAAGTCCATT
1 TGAAGAGAATTATTGAATAAATATGATTAAATGAATGCAACTTTAAACCAAAAATTAAGTCCATT
11437760 CATCAAGTGGCATGACTTATTATTAATTAGCTATAAATAACATCAATTCATTCAATAATTTTTCC
66 CATCAAGTGGCATGACTTATTATTAATTAGCTATAAATAACATCAATTCATTCAATAATTTTTCC
11437825 AAACACATTTGCAAGGCTTCAAAATCAGGCAACCATCCCAAACTAGGCAAAAAGATTTAACATCT
131 AAACACATTTGCAAGGCTTCAAAATCAGGCAACCATCCCAAACTAGGCAAAAAGATTTAACATCT
*
11437890 GCCGATATAACAAGATGAAGGGTCCAAAAAGAAAACCATCTAGGATCCTCCACACCACCTCGTAA
196 GCCGATATAACAAGATGAAGGTTCCAAAAAGAAAACCATCTAGGATCCTCCACACCACCTCGTAA
11437955 TGGCAGAACAAGTGGTTGACCGACTCACACTCCTTTCTACATAGCACATAAAGACTAGAATCCAG
261 TGGCAGAACAAGTGGTTGACCGACTCACACTCCTTTCTACATAGCACATAAAGACTAGAATCCAG
11438020 ATTAGTAACGCTCCGTT
326 ATTAGTAACGCTCCGTT
11438037 TGAAGAG
1 TGAAGAG
11438044 TTCCGCTAGA
Statistics
Matches: 682, Mismatches: 5, Indels: 13
0.97 0.01 0.02
Matches are distributed among these distances:
341 140 0.21
342 111 0.16
343 92 0.13
344 107 0.16
345 93 0.14
346 139 0.20
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (342 bp):
TGAAGAGAATTATTGAATAAATATGATTAAATGAATGCAACTTTAAACCAAAAATTAAGTCCATT
CATCAAGTGGCATGACTTATTATTAATTAGCTATAAATAACATCAATTCATTCAATAATTTTTCC
AAACACATTTGCAAGGCTTCAAAATCAGGCAACCATCCCAAACTAGGCAAAAAGATTTAACATCT
GCCGATATAACAAGATGAAGGTTCCAAAAAGAAAACCATCTAGGATCCTCCACACCACCTCGTAA
TGGCAGAACAAGTGGTTGACCGACTCACACTCCTTTCTACATAGCACATAAAGACTAGAATCCAG
ATTAGTAACGCTCCGTT
Found at i:11439897 original size:2 final size:2
Alignment explanation
Indices: 11439890--11439921 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11439880 ACAATAAACG
11439890 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
11439922 CATGTAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11441022 original size:20 final size:20
Alignment explanation
Indices: 11440993--11441162 Score: 88
Period size: 20 Copynumber: 7.6 Consensus size: 20
11440983 TTCATTTATG
*
11440993 GCATCCTTTCATGCCTTAAT
1 GCATCATTTCATGCCTTAAT
*
11441013 GCATCATTTCATGCATTTCATTTAT
1 GCATCATTTCATGC----C-TTAAT
*
11441038 GGCATCATTTCATGTCTTAAT
1 -GCATCATTTCATGCCTTAAT
*
11441059 GCATCATTTCATGCATTTCATTTAT
1 GCATCATTTCATGC----C-TTAAT
*
11441084 GGCATCCTTTCATGCCTTAAT
1 -GCATCATTTCATGCCTTAAT
* * *
11441105 GCATCCTTTCATTCATTTCTTTTAT
1 GCATCATTTCATGC----C-TTAAT
*
11441130 GGCATCCTTTCATGCCTTAAT
1 -GCATCATTTCATGCCTTAAT
*
11441151 GCATTATTTCAT
1 GCATCATTTCAT
11441163 ACATATAATG
Statistics
Matches: 118, Mismatches: 14, Indels: 36
0.70 0.08 0.21
Matches are distributed among these distances:
20 49 0.42
21 12 0.10
22 3 0.03
24 3 0.03
25 12 0.10
26 39 0.33
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (20 bp):
GCATCATTTCATGCCTTAAT
Found at i:11441028 original size:12 final size:12
Alignment explanation
Indices: 11441011--11441098 Score: 62
Period size: 12 Copynumber: 7.3 Consensus size: 12
11441001 TCATGCCTTA
11441011 ATGCATCATTTC
1 ATGCATCATTTC
11441023 ATGCATTTCATTT-
1 ATGCA--TCATTTC
11441036 ATGGCATCATTTC
1 AT-GCATCATTTC
*
11441049 ATG--TC--TTA
1 ATGCATCATTTC
11441057 ATGCATCATTTC
1 ATGCATCATTTC
11441069 ATGCATTTCATTT-
1 ATGCA--TCATTTC
*
11441082 ATGGCATCCTTTC
1 AT-GCATCATTTC
11441095 ATGC
1 ATGC
11441099 CTTAATGCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
8 5 0.08
10 4 0.07
12 26 0.43
13 8 0.13
14 18 0.30
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (12 bp):
ATGCATCATTTC
Found at i:11441044 original size:26 final size:25
Alignment explanation
Indices: 11440981--11441144 Score: 124
Period size: 20 Copynumber: 7.0 Consensus size: 25
11440971 TTATTTGTTA
11440981 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTC-TTTATGGCATCCTTTCATGC
* *
11441007 ----CTTAAT-GCATCATTTCATGC
1 ATTTCTTTATGGCATCCTTTCATGC
*
11441027 ATTTCATTTATGGCATCATTTCATG-
1 ATTTC-TTTATGGCATCCTTTCATGC
* *
11441052 ---TCTTAAT-GCATCATTTCATGC
1 ATTTCTTTATGGCATCCTTTCATGC
11441073 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTC-TTTATGGCATCCTTTCATGC
* *
11441099 ----CTTAAT-GCATCCTTTCATTC
1 ATTTCTTTATGGCATCCTTTCATGC
11441119 ATTTCTTTTATGGCATCCTTTCATGC
1 ATTTC-TTTATGGCATCCTTTCATGC
11441145 CTTAATGCAT
Statistics
Matches: 110, Mismatches: 10, Indels: 36
0.71 0.06 0.23
Matches are distributed among these distances:
20 39 0.35
21 12 0.11
22 4 0.04
24 4 0.04
25 12 0.11
26 39 0.35
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (25 bp):
ATTTCTTTATGGCATCCTTTCATGC
Found at i:11441049 original size:46 final size:46
Alignment explanation
Indices: 11440981--11441162 Score: 310
Period size: 46 Copynumber: 4.0 Consensus size: 46
11440971 TTATTTGTTA
11440981 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
11441027 ATTTCATTTATGGCATCATTTCATGTCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
11441073 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATTC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
11441119 ATTTCTTTTATGGCATCCTTTCATGCCTTAATGCATTATTTCAT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCAT
11441163 ACATATAATG
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 127 1.00
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:11446250 original size:161 final size:163
Alignment explanation
Indices: 11445985--11446298 Score: 598
Period size: 161 Copynumber: 1.9 Consensus size: 163
11445975 GGAGCAGGGG
11445985 GAGGTTAAAATTGAGTCAGTATGGCGTCAAGGGATTGCATGAAAGTTCCAAACTCAGGCACCAAA
1 GAGGTTAAAATTGAGTCAGTATGGCGTCAAGGGATTGCATGAAAGTTCCAAACTCAGGCACCAAA
11446050 ATCCCCTGATGTGCAGGTGCACTAGAATTTTCAAAGGGAAGAGGCT-TTCACTA-TAGCCTCAT-
66 ATCCCCTGATGTGCAGGTGCACTAGAATTTTCAAAGGGAAGAGGCTGTTCACTATTAGCCTCATA
11446112 ACTTACACTAACCAGTTCCTTCTTTCTGTCTCCC
131 ACTTACACT-ACCAGTTCCTTCTTTCTGTCTCCC
11446146 GAGGTTAAAATTGAGTCAGTATGGCGTCAAGGGATTGCATGAAAGTTCCAAACTCAGGCACCAAA
1 GAGGTTAAAATTGAGTCAGTATGGCGTCAAGGGATTGCATGAAAGTTCCAAACTCAGGCACCAAA
11446211 ATCCCCTGATGTGCAGGTGCACTAGAATTTTCAAAGGGAAGAGGCTGTTCACTATTAGCCTCATA
66 ATCCCCTGATGTGCAGGTGCACTAGAATTTTCAAAGGGAAGAGGCTGTTCACTATTAGCCTCATA
11446276 ACTTACACTACCAGTTCCTTCTT
131 ACTTACACTACCAGTTCCTTCTT
11446299 GCATCTCTTG
Statistics
Matches: 150, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
161 111 0.74
162 7 0.05
163 23 0.15
164 9 0.06
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (163 bp):
GAGGTTAAAATTGAGTCAGTATGGCGTCAAGGGATTGCATGAAAGTTCCAAACTCAGGCACCAAA
ATCCCCTGATGTGCAGGTGCACTAGAATTTTCAAAGGGAAGAGGCTGTTCACTATTAGCCTCATA
ACTTACACTACCAGTTCCTTCTTTCTGTCTCCC
Found at i:11447148 original size:46 final size:46
Alignment explanation
Indices: 11447095--11447274 Score: 254
Period size: 46 Copynumber: 3.9 Consensus size: 46
11447085 TTATTTGTTA
*
11447095 ATTTCATTTATGACA-CCATTTCATGCCTTAATGCAACCTTTCATGC
1 ATTTCATTTATGACATCC-TTTCATGCCTTAATGCATCCTTTCATGC
* * *
11447141 ATTTCATTTATGGCATCCTTTCATGCCTTAACGCATCATTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
11447187 ATTTCATTTATGATATCCTTTCATGCCTTAGTGCATCCTTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
11447233 ATTTCATTTATGTCATCATTTCATGTCTTAATGCATCTTTTC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTC
11447275 CATACATATA
Statistics
Matches: 118, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
46 116 0.98
47 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.44
Consensus pattern (46 bp):
ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:11447164 original size:26 final size:26
Alignment explanation
Indices: 11447131--11447257 Score: 91
Period size: 26 Copynumber: 5.3 Consensus size: 26
11447121 CTTAATGCAA
11447131 CCTTTCATGCATTTCATTTATGGCAT
1 CCTTTCATGCATTTCATTTATGGCAT
**
11447157 CCTTTCATGC----C--TTAACGCAT
1 CCTTTCATGCATTTCATTTATGGCAT
* **
11447177 CATTTCATGCATTTCATTTATGATAT
1 CCTTTCATGCATTTCATTTATGGCAT
11447203 CCTTTCATGC----C--TTA-GTGCAT
1 CCTTTCATGCATTTCATTTATG-GCAT
*
11447223 CCTTTCATGCATTTCATTTATGTCAT
1 CCTTTCATGCATTTCATTTATGGCAT
*
11447249 CATTTCATG
1 CCTTTCATG
11447258 TCTTAATGCA
Statistics
Matches: 75, Mismatches: 12, Indels: 28
0.65 0.10 0.24
Matches are distributed among these distances:
19 1 0.01
20 31 0.41
22 2 0.03
24 2 0.03
26 38 0.51
27 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.45
Consensus pattern (26 bp):
CCTTTCATGCATTTCATTTATGGCAT
Found at i:11449476 original size:17 final size:18
Alignment explanation
Indices: 11449454--11449488 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11449444 TTCTATCTTT
11449454 ACTGG-AAAAGCCTGTGC
1 ACTGGAAAAAGCCTGTGC
11449471 ACTGGAAAAAGCCTGTGC
1 ACTGGAAAAAGCCTGTGC
11449489 TCGGAGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (18 bp):
ACTGGAAAAAGCCTGTGC
Found at i:11449979 original size:18 final size:19
Alignment explanation
Indices: 11449956--11450000 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
11449946 GCTTGAGATA
*
11449956 ACCTAAAGA-AAATAAAAT
1 ACCTAAAGAGAAATAAAAC
11449974 ACCTAAA-AGAAATAAAAC
1 ACCTAAAGAGAAATAAAAC
11449992 ACCTAAAGA
1 ACCTAAAGA
11450001 TAATCATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.64, C:0.16, G:0.07, T:0.13
Consensus pattern (19 bp):
ACCTAAAGAGAAATAAAAC
Found at i:11451466 original size:2 final size:2
Alignment explanation
Indices: 11451459--11451496 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
11451449 CGATTCAAGG
*
11451459 CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11451497 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:11453423 original size:46 final size:46
Alignment explanation
Indices: 11453356--11453466 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
11453346 TAATGGTCGT
* * *
11453356 TGCCTTAACGCATCATTTCATGCATTTCATTTATGAT-ATCCTTTCA
1 TGCCTTAATGCATCCTTTCATGCATTTCATTTATG-TCATCATTTCA
*
11453402 TGCCTTAGTGCATCCTTTCATGCATTTCATTTATGTCATCATTTCA
1 TGCCTTAATGCATCCTTTCATGCATTTCATTTATGTCATCATTTCA
11453448 TGCCTTAATGCATCCTTTC
1 TGCCTTAATGCATCCTTTC
11453467 CATACATATA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 1 0.02
46 58 0.98
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (46 bp):
TGCCTTAATGCATCCTTTCATGCATTTCATTTATGTCATCATTTCA
Found at i:11453466 original size:20 final size:20
Alignment explanation
Indices: 11453393--11453466 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
11453383 CATTTATGAT
*
11453393 ATCCTTTCATGCCTTAGTGC
1 ATCCTTTCATGCCTTAATGC
*
11453413 ATCCTTTCATGCATTTCATTTATGTC
1 ATCCTTTCATGC----C-TTAATG-C
*
11453439 ATCATTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
11453459 ATCCTTTC
1 ATCCTTTC
11453467 CATACATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
20 20 0.47
21 5 0.12
22 1 0.02
24 1 0.02
25 4 0.09
26 12 0.28
ACGTcount: A:0.19, C:0.27, G:0.09, T:0.45
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:11456172 original size:18 final size:19
Alignment explanation
Indices: 11456149--11456193 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
11456139 GCTTGAGATA
*
11456149 ACCTAAAGA-AAATAAAAT
1 ACCTAAAGAGAAATAAAAC
11456167 ACCTAAA-AGAAATAAAAC
1 ACCTAAAGAGAAATAAAAC
11456185 ACCTAAAGA
1 ACCTAAAGA
11456194 TAATCATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.64, C:0.16, G:0.07, T:0.13
Consensus pattern (19 bp):
ACCTAAAGAGAAATAAAAC
Found at i:11457301 original size:16 final size:15
Alignment explanation
Indices: 11457267--11457314 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
11457257 TTTTTTATTT
11457267 TTTTTGAATGTTTCTTC
1 TTTTT-AAT-TTTCTTC
*
11457284 TTTTTTATTTTCTCTC
1 TTTTTAATTTTCT-TC
11457300 TTTTTAA-TTTCTTC
1 TTTTTAATTTTCTTC
11457314 T
1 T
11457315 GTTGTTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 3 0.11
15 10 0.36
16 10 0.36
17 5 0.18
ACGTcount: A:0.10, C:0.15, G:0.04, T:0.71
Consensus pattern (15 bp):
TTTTTAATTTTCTTC
Found at i:11457689 original size:2 final size:2
Alignment explanation
Indices: 11457676--11457712 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11457666 TTCAAGGCAA
*
11457676 AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
11457713 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:11459643 original size:46 final size:46
Alignment explanation
Indices: 11459576--11459686 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
11459566 TAATGGTCTT
* * *
11459576 TGCCTTAACGCATCATTTCATGCATTTCATTTATGAT-ATCCTTTCA
1 TGCCTTAATGCATCCTTTCATGCATTTCATTTATG-TCATCATTTCA
*
11459622 TGCCTTAGTGCATCCTTTCATGCATTTCATTTATGTCATCATTTCA
1 TGCCTTAATGCATCCTTTCATGCATTTCATTTATGTCATCATTTCA
11459668 TGCCTTAATGCATCCTTTC
1 TGCCTTAATGCATCCTTTC
11459687 CATACATATA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 1 0.02
46 58 0.98
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (46 bp):
TGCCTTAATGCATCCTTTCATGCATTTCATTTATGTCATCATTTCA
Found at i:11459686 original size:20 final size:20
Alignment explanation
Indices: 11459613--11459686 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
11459603 CATTTATGAT
*
11459613 ATCCTTTCATGCCTTAGTGC
1 ATCCTTTCATGCCTTAATGC
*
11459633 ATCCTTTCATGCATTTCATTTATGTC
1 ATCCTTTCATGC----C-TTAATG-C
*
11459659 ATCATTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
11459679 ATCCTTTC
1 ATCCTTTC
11459687 CATACATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
20 20 0.47
21 5 0.12
22 1 0.02
24 1 0.02
25 4 0.09
26 12 0.28
ACGTcount: A:0.19, C:0.27, G:0.09, T:0.45
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:11462399 original size:18 final size:19
Alignment explanation
Indices: 11462376--11462420 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
11462366 GCTTGAGATA
*
11462376 ACCTAAAGA-AAATAAAAT
1 ACCTAAAGAGAAATAAAAC
11462394 ACCTAAA-AGAAATAAAAC
1 ACCTAAAGAGAAATAAAAC
11462412 ACCTAAAGA
1 ACCTAAAGA
11462421 TAATCATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.64, C:0.16, G:0.07, T:0.13
Consensus pattern (19 bp):
ACCTAAAGAGAAATAAAAC
Found at i:11463532 original size:15 final size:14
Alignment explanation
Indices: 11463507--11463543 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
11463497 TTTTTGAATG
*
11463507 TTTCTTCTTTTTAT
1 TTTCTTCTTTTTAA
11463521 TTTCTCTCTTTTTAA
1 TTTCT-TCTTTTTAA
11463536 TTTCTTCT
1 TTTCTTCT
11463544 GTTGTTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTCTTCTTTTTAA
Found at i:11463909 original size:2 final size:2
Alignment explanation
Indices: 11463902--11463931 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11463892 CGATTCAAGG
11463902 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11463932 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:11465916 original size:3 final size:3
Alignment explanation
Indices: 11465908--11465932 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11465898 TTCAGACTAC
11465908 TGT TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT T
11465933 CTCTTCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:11466636 original size:38 final size:38
Alignment explanation
Indices: 11466558--11466636 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
11466548 GCCGGTATAT
* **
11466558 ATTTAAATTAAATATATAAATATTATATATATTTGTTA
1 ATTTAAATTAAATATATAAATATTATATATATATAATA
* *
11466596 ATTTAAATTAAATTTATTAATATTATATATATATAATA
1 ATTTAAATTAAATATATAAATATTATATATATATAATA
11466634 ATT
1 ATT
11466637 ATTTTTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (38 bp):
ATTTAAATTAAATATATAAATATTATATATATATAATA
Found at i:11466740 original size:30 final size:29
Alignment explanation
Indices: 11466706--11466782 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
11466696 CCCTTCCCCA
11466706 TCCCCGTTACCGTTTAACATAAACAATTTT
1 TCCCCGTT-CCGTTTAACATAAACAATTTT
* * **
11466736 TCCCCGTCCCCGTTTAGCATAAACGGTTTT
1 TCCCCGT-TCCGTTTAACATAAACAATTTT
*
11466766 TCCACGTCTCCGTTTAA
1 TCCCCGT-TCCGTTTAA
11466783 TTCGGTTTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.22, C:0.31, G:0.12, T:0.35
Consensus pattern (29 bp):
TCCCCGTTCCGTTTAACATAAACAATTTT
Found at i:11467225 original size:15 final size:15
Alignment explanation
Indices: 11467188--11467225 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
11467178 GACCTGACAG
*
11467188 AGTCAACCCGGACTT
1 AGTCAACTCGGACTT
11467203 AGTCAACTCGGACTT
1 AGTCAACTCGGACTT
*
11467218 AGTTAACT
1 AGTCAACT
11467226 TGTTGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (15 bp):
AGTCAACTCGGACTT
Found at i:11469636 original size:35 final size:35
Alignment explanation
Indices: 11469551--11469641 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 35
11469541 GTTCAGCTTT
* *
11469551 GATCAAGCTCGTAATTCCTTATATAGGTTCAACACT
1 GATCAA-CTTGTAATTCCTTATATAGGTTCAACACC
* **
11469587 GATCGAC-TGCTAATTCCTTATATAGGTTCAGTACC
1 GATCAACTTG-TAATTCCTTATATAGGTTCAACACC
11469622 GATCAACTTGTAATTCCTTA
1 GATCAACTTGTAATTCCTTA
11469642 CGGACTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
34 1 0.02
35 39 0.83
36 7 0.15
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (35 bp):
GATCAACTTGTAATTCCTTATATAGGTTCAACACC
Found at i:11475013 original size:99 final size:99
Alignment explanation
Indices: 11474842--11475037 Score: 347
Period size: 99 Copynumber: 2.0 Consensus size: 99
11474832 AGGGAAATGT
*
11474842 ATAACAGTGTTCGGTTGGAGGGTATTACTATGGTTTTAAAATATGTTTTAAACTACAGACATTTT
1 ATAACAGTGTTCGGTTGGAGGGTATTACTATGGTTTTAAAATATGTTTTAAACTACAAACATTTT
11474907 TAAAGGATTTATATATGTTAGTCTATCGTTTTCC
66 TAAAGGATTTATATATGTTAGTCTATCGTTTTCC
* *
11474941 ATAACGGTGTTCGGTTGGAGGGTATTACTATGGTTTTGAAATATGTTTTAAACTACAAACATTTT
1 ATAACAGTGTTCGGTTGGAGGGTATTACTATGGTTTTAAAATATGTTTTAAACTACAAACATTTT
* *
11475006 TAAAGGATTTATATATGTTAGTTTATGGTTTT
66 TAAAGGATTTATATATGTTAGTCTATCGTTTT
11475038 AAAATATGTT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.43
Consensus pattern (99 bp):
ATAACAGTGTTCGGTTGGAGGGTATTACTATGGTTTTAAAATATGTTTTAAACTACAAACATTTT
TAAAGGATTTATATATGTTAGTCTATCGTTTTCC
Found at i:11475043 original size:60 final size:60
Alignment explanation
Indices: 11474969--11475087 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
11474959 AGGGTATTAC
*
11474969 TATGGTTTTGAAATATGTTTTAAACTACAAACATTTTTAAAGGATTTATATATGTTAGTT
1 TATGGTTTTAAAATATGTTTTAAACTACAAACATTTTTAAAGGATTTATATATGTTAGTT
11475029 TATGGTTTTAAAATATGTTTTAAACTACAAACATTTTTAAAGGATTTATATATGTTAGT
1 TATGGTTTTAAAATATGTTTTAAACTACAAACATTTTTAAAGGATTTATATATGTTAGT
11475088 CTATTTTGTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (60 bp):
TATGGTTTTAAAATATGTTTTAAACTACAAACATTTTTAAAGGATTTATATATGTTAGTT
Found at i:11476772 original size:17 final size:17
Alignment explanation
Indices: 11476750--11476791 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
11476740 TCTTGAGATA
**
11476750 ACCTAAAAAAATAAAGT
1 ACCTAAAAAAATAAAAC
11476767 ACCT-AAAAAATAAAAC
1 ACCTAAAAAAATAAAAC
11476783 ACCTAAAAA
1 ACCTAAAAA
11476792 TAATCCTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.67, C:0.17, G:0.02, T:0.14
Consensus pattern (17 bp):
ACCTAAAAAAATAAAAC
Found at i:11486672 original size:25 final size:26
Alignment explanation
Indices: 11486644--11486715 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 26
11486634 ATAAATACAT
11486644 GGCACTTTCGAGTGCAAAT-CTATGA
1 GGCACTTTCGAGTGCAAATACTATGA
* *
11486669 GGCACTTTCAAGTGCATACATGACTATGT
1 GGCACTTTCGAGTGCA-A-AT-ACTATGA
*
11486698 GGAACTTTCGAGTG-AAAT
1 GGCACTTTCGAGTGCAAAT
11486716 TATATATGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 15 0.38
26 3 0.08
27 3 0.08
28 1 0.03
29 17 0.44
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (26 bp):
GGCACTTTCGAGTGCAAATACTATGA
Found at i:11488922 original size:27 final size:28
Alignment explanation
Indices: 11488874--11488938 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
11488864 GAAAGGACTG
*
11488874 AAATACCCCTAAACTATAAAATAATC-A
1 AAATACCCCTAAACTATAAAATAACCTA
* * *
11488901 AAATACCCCTAAAGTGTGAAATAACCTA
1 AAATACCCCTAAACTATAAAATAACCTA
11488929 AAATATCCCC
1 AAATA-CCCC
11488939 AAGCCCTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 22 0.69
28 6 0.19
29 4 0.12
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.22
Consensus pattern (28 bp):
AAATACCCCTAAACTATAAAATAACCTA
Found at i:11492143 original size:17 final size:17
Alignment explanation
Indices: 11492121--11492153 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11492111 TACGGTCTGA
11492121 AGAAAGTATTCA-AAGAG
1 AGAAAG-ATTCAGAAGAG
11492138 AGAAAGATTCAGAAGA
1 AGAAAGATTCAGAAGA
11492154 TTGAATTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.55, C:0.06, G:0.24, T:0.15
Consensus pattern (17 bp):
AGAAAGATTCAGAAGAG
Found at i:11493829 original size:9 final size:9
Alignment explanation
Indices: 11493815--11493839 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11493805 CATGTCATTT
11493815 ATTTCAATC
1 ATTTCAATC
11493824 ATTTCAATC
1 ATTTCAATC
11493833 ATTTCAA
1 ATTTCAA
11493840 ACAATTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTTCAATC
Found at i:11508183 original size:6 final size:6
Alignment explanation
Indices: 11508172--11508198 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11508162 GTAGAGACTT
11508172 GTTAGA GTTAGA GTTAGA GTTAGA GTT
1 GTTAGA GTTAGA GTTAGA GTTAGA GTT
11508199 CATAGAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (6 bp):
GTTAGA
Found at i:11517056 original size:14 final size:14
Alignment explanation
Indices: 11517037--11517070 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11517027 CTACCCCTCA
11517037 TCTTCTCCACCTTT
1 TCTTCTCCACCTTT
**
11517051 TCTTCTTTACCTTT
1 TCTTCTCCACCTTT
11517065 TCTTCT
1 TCTTCT
11517071 TTCTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (14 bp):
TCTTCTCCACCTTT
Found at i:11517071 original size:14 final size:14
Alignment explanation
Indices: 11517045--11517072 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11517035 CATCTTCTCC
11517045 ACCTTTTCTTCTTT
1 ACCTTTTCTTCTTT
11517059 ACCTTTTCTTCTTT
1 ACCTTTTCTTCTTT
11517073 CTATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
ACCTTTTCTTCTTT
Found at i:11523802 original size:37 final size:37
Alignment explanation
Indices: 11523746--11523817 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
11523736 GTTCAACCTG
* *
11523746 AGCCTTTAATCGCTTATCTGAACTCTGTAGCCTCTAT
1 AGCCTTTAATCGATCATCTGAACTCTGTAGCCTCTAT
* *
11523783 AGCCTTTAATTGATCATCTGATCTCTGTAGCCTCT
1 AGCCTTTAATCGATCATCTGAACTCTGTAGCCTCT
11523818 TGGTTTCACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (37 bp):
AGCCTTTAATCGATCATCTGAACTCTGTAGCCTCTAT
Found at i:11537740 original size:6 final size:6
Alignment explanation
Indices: 11537729--11537767 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
11537719 ATCCAAAAAC
*
11537729 TCACAA TCACAA TCACCA TCACAA TCACAA TCACAA TCA
1 TCACAA TCACAA TCACAA TCACAA TCACAA TCACAA TCA
11537768 TCGTCTCTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (6 bp):
TCACAA
Found at i:11547739 original size:15 final size:14
Alignment explanation
Indices: 11547709--11547738 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11547699 ATCAATTAAC
*
11547709 AAGCAAAATAAAAA
1 AAGCAAAAAAAAAA
11547723 AAGCAAAAAAAAAA
1 AAGCAAAAAAAAAA
11547737 AA
1 AA
11547739 ATGTTGGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.03
Consensus pattern (14 bp):
AAGCAAAAAAAAAA
Found at i:11551958 original size:213 final size:215
Alignment explanation
Indices: 11551516--11552016 Score: 778
Period size: 213 Copynumber: 2.3 Consensus size: 215
11551506 ATTTTATGAA
* * *
11551516 AAATACAAATTTAAGAACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGAACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
11551581 ACAACATGCATTGATGAAGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATATAA
66 ACAACA-GCATTGATGAAGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATATAA
*
11551646 AAAAAAGTATTAAATTATACCCATTTAAAAAGTTATGGGTCAATTAAAAATATAAATAAGTAATA
130 AAAAAAGTATTAAATTATA-CCATTTAAAAAGTTATGGCTCAATTAAAAATATAAATAAGTAATA
11551711 AGTATGGGTCAATTTCAGATGC
194 AGTATGGGTCAATTTCAGATGC
*
11551733 AAATATAATTTTAAGAACTAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAA
1 AAATATAATTTTAAGAACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* * **
11551798 GCAAACA-CATTGATGAGGGATCAAATTGAAATAATTTTAAATTGTGAAGGTT-AAATT-A-ATA
66 AC-AACAGCATTGATGAAGGATCAAATCAAAATAATTTTAAATTGTG-AGGTTGAAATTAATATA
*
11551859 CAAAAAAGTATTAAATTATA-CATTTAAAAAGTTATGGCTCAATTAAAAAATATAAATAAGTAAT
129 AAAAAAAGTATTAAATTATACCATTTAAAAAGTTATGGCTCAATT-AAAAATATAAATAAGTAAT
* *
11551923 AAGTATGGGTCAATTTCATATGT
193 AAGTATGGGTCAATTTCAGATGC
* * * *
11551946 AAATATAATTTTAAGGACTAAATTAAACAAATATGAAATTATAAATAAAAATTTAAATAAACTAA
1 AAATATAATTTTAAGAACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
11552011 ACAACA
66 ACAACA
11552017 TAAAGGATCA
Statistics
Matches: 263, Mismatches: 18, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
212 27 0.10
213 101 0.38
214 22 0.08
215 1 0.00
216 41 0.16
217 67 0.25
218 4 0.02
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (215 bp):
AAATATAATTTTAAGAACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACAGCATTGATGAAGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATATAAA
AAAAAGTATTAAATTATACCATTTAAAAAGTTATGGCTCAATTAAAAATATAAATAAGTAATAAG
TATGGGTCAATTTCAGATGC
Found at i:11552126 original size:2 final size:2
Alignment explanation
Indices: 11552115--11552251 Score: 90
Period size: 2 Copynumber: 69.0 Consensus size: 2
11552105 TTGAAACAAC
* *
11552115 TA TA -A TA TA TA TA TA TA TA TA -A TA TA AA CTA TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
11552157 TA TA AA CTA TA TA TA T- TG TA TA TA TA AA CTA TA TA -A TT TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
11552199 TT TA TA T- TA TA TA TA TA TA -A AA CTA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
*
11552239 TA AA CTA TA TA TA
1 TA TA -TA TA TA TA
11552252 CCATGTATAA
Statistics
Matches: 106, Mismatches: 16, Indels: 26
0.72 0.11 0.18
Matches are distributed among these distances:
1 7 0.07
2 93 0.88
3 6 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:11552139 original size:11 final size:11
Alignment explanation
Indices: 11552115--11552251 Score: 74
Period size: 11 Copynumber: 12.4 Consensus size: 11
11552105 TTGAAACAAC
11552115 TATAATATATA
1 TATAATATATA
11552126 TAT-ATATATAA
1 TATAATATAT-A
11552137 TATAA-ACTATA
1 TATAATA-TATA
*
11552148 TAGT-TTATATA
1 TA-TAATATATA
11552159 TA-AACTATATA
1 TATAA-TATATA
**
11552170 TATTGTATATA
1 TATAATATATA
11552181 TA-AACTATATA
1 TATAA-TATATA
* *
11552192 -ATTTATATTTA
1 TA-TAATATATA
*
11552203 TATTATATATA
1 TATAATATATA
*
11552214 TATAAAACTATA
1 TATAATA-TATA
11552226 TAT-ATATTATA
1 TATAATA-TATA
11552237 TATAA-ACTATA
1 TATAATA-TATA
11552248 TATA
1 TATA
11552252 CCATGTATAA
Statistics
Matches: 98, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
10 7 0.07
11 75 0.77
12 16 0.16
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (11 bp):
TATAATATATA
Found at i:11552147 original size:22 final size:20
Alignment explanation
Indices: 11552122--11552308 Score: 147
Period size: 20 Copynumber: 9.1 Consensus size: 20
11552112 AACTATAATA
11552122 TATATATATATATAATATAAAC
1 TATATATAT-TAT-ATATAAAC
11552144 TATATAGT-TTATATATAAAC
1 TATATA-TATTATATATAAAC
11552164 TATATATATTGTATATATAAAC
1 TATATATA-T-TATATATAAAC
**
11552186 TATATA-ATT-TATATTTA-
1 TATATATATTATATATAAAC
11552203 TAT-TATA-TATATATAAAAC
1 TATATATATTATATAT-AAAC
11552222 TATATATATATTATATATAAAC
1 --TATATATATTATATATAAAC
** *
11552244 TATATATACCATGTATAAAC
1 TATATATATTATATATAAAC
11552264 TATAATATAAGTTTATATATAAAC
1 TAT-ATAT-A--TTATATATAAAC
*
11552288 TAT-TGA-ACTATATATAAAC
1 TATAT-ATATTATATATAAAC
11552307 TA
1 TA
11552309 CTTAGTTTAT
Statistics
Matches: 137, Mismatches: 11, Indels: 37
0.74 0.06 0.20
Matches are distributed among these distances:
16 3 0.02
17 9 0.07
18 7 0.05
19 15 0.11
20 35 0.26
21 13 0.09
22 34 0.25
23 9 0.07
24 12 0.09
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (20 bp):
TATATATATTATATATAAAC
Found at i:11552304 original size:43 final size:42
Alignment explanation
Indices: 11552124--11552308 Score: 169
Period size: 42 Copynumber: 4.5 Consensus size: 42
11552114 CTATAATATA
*
11552124 TATATATA-TATAATATAAACTATATA-GT-TTATATATAAAC
1 TATATATACTAT-ATATAAACTATATATATATTATATATAAAC
* * *
11552164 TATATATATTGTATATATAAACTATATA-AT-TTATATTTATA-
1 TATATATA--CTATATATAAACTATATATATATTATATATAAAC
11552205 T-TATATA-TATATA-AAACTATATATATATTATATATAAAC
1 TATATATACTATATATAAACTATATATATATTATATATAAAC
* *
11552244 TATATATACCATGTATAAACTATA-ATATAAGTTTATATATAAAC
1 TATATATACTATATATAAACTATATATAT-A--TTATATATAAAC
11552288 TAT-TGA-ACTATATATAAACTA
1 TATAT-ATACTATATATAAACTA
11552309 CTTAGTTTAT
Statistics
Matches: 123, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
36 10 0.08
37 8 0.07
38 9 0.07
39 1 0.01
40 20 0.16
41 9 0.07
42 33 0.27
43 17 0.14
44 16 0.13
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (42 bp):
TATATATACTATATATAAACTATATATATATTATATATAAAC
Found at i:11552353 original size:29 final size:28
Alignment explanation
Indices: 11552317--11552371 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
11552307 TACTTAGTTT
*
11552317 ATTAATATAAATTATA-AAGTTTATATGA
1 ATTAATATAAACTATACAA-TTTATATGA
*
11552345 ATTATATATGAACTATACAATTTATAT
1 ATTA-ATATAAACTATACAATTTATAT
11552372 TTATATTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 17 0.74
30 2 0.09
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (28 bp):
ATTAATATAAACTATACAATTTATATGA
Found at i:11552395 original size:9 final size:10
Alignment explanation
Indices: 11552338--11552414 Score: 50
Period size: 11 Copynumber: 7.4 Consensus size: 10
11552328 TTATAAAGTT
11552338 TATATGAATTA
1 TATAT-AATTA
*
11552349 TATATGAACTA
1 TATAT-AATTA
* *
11552360 TACA-ATTTA
1 TATATAATTA
*
11552369 TATTTATATTA
1 TATATA-ATTA
*
11552380 TGTATAATTA
1 TATATAATTA
11552390 TA-ATAATATA
1 TATATAAT-TA
11552400 TATATAAATTA
1 TATAT-AATTA
11552411 TATA
1 TATA
11552415 GTTTATTAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
9 10 0.20
10 10 0.20
11 28 0.55
12 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (10 bp):
TATATAATTA
Found at i:11554641 original size:2 final size:2
Alignment explanation
Indices: 11554634--11554665 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11554624 ATCACAAAGC
11554634 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
11554666 GGGTTATCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11557956 original size:33 final size:34
Alignment explanation
Indices: 11557877--11557956 Score: 117
Period size: 35 Copynumber: 2.4 Consensus size: 34
11557867 TCAAAATTCC
*
11557877 AAAACACTTTAATTACATTCTAAACCCTAAATTTT
1 AAAATACTTTAATTACATTCTAAACCCTAAA-TTT
*
11557912 AAAATACTTTAATTATATTCTAAACCCTAAA-TT
1 AAAATACTTTAATTACATTCTAAACCCTAAATTT
*
11557945 AAAATATTTTAA
1 AAAATACTTTAA
11557957 AATTTGGGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
33 13 0.31
35 29 0.69
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAATACTTTAATTACATTCTAAACCCTAAATTT
Found at i:11558015 original size:35 final size:34
Alignment explanation
Indices: 11557939--11558016 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
11557929 TTCTAAACCC
*
11557939 TAAATTAAAATATTTTAAAATTTGGGGTTTAAAA
1 TAAATTGAAATATTTTAAAATTTGGGGTTTAAAA
* * *
11557973 TATAATTGAATTATTTTGAAATTTGGGGTTTATAA
1 TA-AATTGAAATATTTTAAAATTTGGGGTTTAAAA
11558008 TGAAATTGA
1 T-AAATTGA
11558017 GGATTGTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.05
35 35 0.92
36 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (34 bp):
TAAATTGAAATATTTTAAAATTTGGGGTTTAAAA
Found at i:11566914 original size:26 final size:26
Alignment explanation
Indices: 11566884--11566969 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 26
11566874 TATTGTACTG
* *
11566884 TAATGTAATGTAGGATTTAATGTTTC
1 TAATGTAATGTACGAGTTAATGTTTC
* *
11566910 TAATGTAATGTACAAGTTAATGTTTT
1 TAATGTAATGTACGAGTTAATGTTTC
* * *
11566936 TTATGTAATGTATGAGTTAATGCTTC
1 TAATGTAATGTACGAGTTAATGTTTC
*
11566962 AAATGTAA
1 TAATGTAA
11566970 AATTTAGTAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (26 bp):
TAATGTAATGTACGAGTTAATGTTTC
Found at i:11567883 original size:24 final size:24
Alignment explanation
Indices: 11567833--11567906 Score: 98
Period size: 25 Copynumber: 3.1 Consensus size: 24
11567823 AATTAAATCT
11567833 AATTATTTAAATTT-ATGA-TGTA
1 AATTATTTAAATTTAATGATTGTA
11567855 AATTATTTAAATTTAATGATTGTA
1 AATTATTTAAATTTAATGATTGTA
* * *
11567879 AATTATGTAAAATTTATTAATTGTA
1 AATTAT-TTAAATTTAATGATTGTA
11567904 AAT
1 AAT
11567907 GATCATATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 14 0.30
23 4 0.09
24 10 0.22
25 18 0.39
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (24 bp):
AATTATTTAAATTTAATGATTGTA
Found at i:11571548 original size:21 final size:21
Alignment explanation
Indices: 11571522--11571569 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
11571512 TTGAGTAACA
11571522 CATTTT-CATACATTGCATTTG
1 CATTTTACAT-CATTGCATTTG
* *
11571543 CATTTTACATCTTTGCATTTT
1 CATTTTACATCATTGCATTTG
11571564 CATTTT
1 CATTTT
11571570 GCATTTGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (21 bp):
CATTTTACATCATTGCATTTG
Found at i:11571576 original size:6 final size:7
Alignment explanation
Indices: 11571534--11571575 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
11571524 TTTTCATACA
11571534 TTGCA-T
1 TTGCATT
11571540 TTGCATT
1 TTGCATT
*
11571547 TTACATCT
1 TTGCAT-T
11571555 TTGCATT
1 TTGCATT
11571562 TT-CATT
1 TTGCATT
11571568 TTGCATT
1 TTGCATT
11571575 T
1 T
11571576 GTTGTTTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 11 0.35
7 14 0.45
8 6 0.19
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.57
Consensus pattern (7 bp):
TTGCATT
Found at i:11574486 original size:2 final size:2
Alignment explanation
Indices: 11574474--11574529 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
11574464 TTCCTTTCAA
*
11574474 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11574516 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
11574530 CCCTTGTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11579292 original size:18 final size:18
Alignment explanation
Indices: 11579269--11579306 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11579259 TAAAGCAAAG
*
11579269 AATTGTCTCACTTGAGAC
1 AATTGTCTCACTTGAAAC
*
11579287 AATTGTTTCACTTGAAAC
1 AATTGTCTCACTTGAAAC
11579305 AA
1 AA
11579307 GAAATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (18 bp):
AATTGTCTCACTTGAAAC
Found at i:11579347 original size:39 final size:37
Alignment explanation
Indices: 11579224--11579345 Score: 111
Period size: 37 Copynumber: 3.2 Consensus size: 37
11579214 GTTTCACTCG
* *
11579224 AAACAAAAATTTATCTCACTCAAGATAGTTTTTCCTA
1 AAACAAAAATTTATCTCACTCAAGATAATTTTTCTTA
* * ** * *
11579261 AAGCAAAGAA-TTGTCTCACTTGAGACAATTGTTTCACTTG
1 AAACAAA-AATTTATCTCACTCAAGATAATT-TTT--CTTA
11579301 AAACAAGAAATTTTATCTCACTCAAGATAATTTTTCTTA
1 AAACAA-AAA-TTTATCTCACTCAAGATAATTTTTCTTA
11579340 AAACAA
1 AAACAA
11579346 GATTTGTCTC
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
37 21 0.33
38 5 0.08
39 9 0.14
40 9 0.14
41 4 0.06
42 16 0.25
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (37 bp):
AAACAAAAATTTATCTCACTCAAGATAATTTTTCTTA
Found at i:11579586 original size:112 final size:113
Alignment explanation
Indices: 11579401--11579866 Score: 476
Period size: 123 Copynumber: 4.0 Consensus size: 113
11579391 TCACTCGATG
* * * **
11579401 GATCAACATTTCCA-AAAGAAGTTCATAATGAGAAGAACTCATTTGAAGAAAAAGAAGAAGTTCA
1 GATCAACATTTACAGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
* * ** *
11579465 TACTGAGAAGAACTTGTTCAACCTTTTGCTCGAAT-TCATCAC-TCGATG
65 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCT-ATCACAGAGATA
*
11579513 GATCAGCATTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
1 GATCAACATTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
*
11579578 AATGAGAAGAACTTGTTCAACCTTTTG-TATGACTCTATCACAGAAGGAGATA
66 AATGAGAAGAACTTGTTCAACCTTTTGCT-CGACTCTATCAC---A-GAGATA
* * * *
11579630 GATCAGTATCAACTTTTCCAGAGAAAGTTTATAATGAGAAGGACTTATCTGAAGAGGAAGAAGAA
1 GATCA--A-C-A--TTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAA
11579695 GTTCATAATGAGAA-AAGCTTGTTCAACCTTTTGCAT-GACTCTATCACAGAAAGAGATA
60 GTTCATAATGAGAAGAA-CTTGTTCAACCTTTTGC-TCGACTCTATCAC----AGAGATA
** * * *
11579753 GATCAACATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAG
1 GATCAACATTTACA----GAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAG
*
11579818 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGA
61 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGA
11579867 AGGAGATAGA
Statistics
Matches: 300, Mismatches: 29, Indels: 44
0.80 0.08 0.12
Matches are distributed among these distances:
111 1 0.00
112 90 0.30
113 3 0.01
117 11 0.04
118 3 0.01
119 1 0.00
120 2 0.01
121 7 0.02
122 78 0.26
123 101 0.34
124 2 0.01
125 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (113 bp):
GATCAACATTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAGATA
Found at i:11579848 original size:122 final size:122
Alignment explanation
Indices: 11579528--11579917 Score: 597
Period size: 123 Copynumber: 3.2 Consensus size: 122
11579518 GCATTTACAG
11579528 AGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * *
11579592 GTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAGATCAGTATCAACTTTTCC
66 GTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCC
* * * *
11579649 AGAGAAAGTTTATAATGAGAAGGACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA-AAGC
1 AGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA-C
* *
11579713 TTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCC
64 TTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCC
* *
11579772 AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTT
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* *
11579837 GTTCAACCTTTTGC-TCGACTCTATCGCAGAAGGAGATAGATCAGCATCAATATTTCC
66 GTTCAACCTTTTGCAT-GACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCC
*
11579894 AGAAGGAGTTCATAACGAGAAGAA
1 AGAA-GAGTTCATAATGAGAAGAA
11579918 GAAGTTCATA
Statistics
Matches: 243, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
121 4 0.02
122 111 0.46
123 128 0.53
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (122 bp):
AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCC
Found at i:11580580 original size:2 final size:2
Alignment explanation
Indices: 11580571--11580605 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
11580561 ACAACAACAA
11580571 AT AT -T 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
11580606 TACATGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11581875 original size:61 final size:61
Alignment explanation
Indices: 11581810--11581947 Score: 142
Period size: 61 Copynumber: 2.2 Consensus size: 61
11581800 AATTATAATT
** *
11581810 TATATAAAATATA-ACATGCATCTATACTTAAAATATA-TACTTAAT-TATGTAT--ATATATA
1 TATATAAAATATATACATGCATAAATA-TAAAAATATAGTA-TT-ATGTATGTATGAATATATA
* *
11581869 TATATATATATATATATATGCATAAATATAAAAATATATGTATTATGTATGTATGAATATATA
1 TATATA-AAATATATACATGCATAAATATAAAAATATA-GTATTATGTATGTATGAATATATA
11581932 TATATAAAATTATATA
1 TATATAAAA-TATATA
11581948 AATTCTAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
59 6 0.09
60 17 0.26
61 19 0.29
62 4 0.06
63 19 0.29
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (61 bp):
TATATAAAATATATACATGCATAAATATAAAAATATAGTATTATGTATGTATGAATATATA
Found at i:11581947 original size:2 final size:2
Alignment explanation
Indices: 11581859--11581937 Score: 63
Period size: 2 Copynumber: 40.0 Consensus size: 2
11581849 CTTAATTATG
* * * *
11581859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG CA TA AA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
11581901 AA TA TA TG TA T- TA TG TA TG TA TGA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
11581938 AAATTATATA
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
1 2 0.03
2 57 0.95
3 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:11591262 original size:29 final size:29
Alignment explanation
Indices: 11591229--11591288 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
11591219 TCTGGACCGT
* *
11591229 TACCTATGTCTTTT-GGGAGATATGAAAGG
1 TACCTATGT-TTTTCGGAACATATGAAAGG
*
11591258 TACCTATGTTTTTCGGAACATATGATAGG
1 TACCTATGTTTTTCGGAACATATGAAAGG
11591287 TA
1 TA
11591289 TCGGGATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (29 bp):
TACCTATGTTTTTCGGAACATATGAAAGG
Found at i:11593708 original size:211 final size:212
Alignment explanation
Indices: 11593454--11593876 Score: 807
Period size: 212 Copynumber: 2.0 Consensus size: 212
11593444 TGCTAGCATG
11593454 CAAATGTTAATTTTGGAGTGAAAGAGAACGCTAATTATTTCATACGGATGGGAAATTATAGTG-T
1 CAAATGTTAATTTTGGAGTGAAAGAGAACGCTAATTATTTCATACGGATGGGAAATTATAGTGTT
11593518 AAAGATCTCCATCGTTTGAAATAGAGTATAGGGGATAGATATTATCAGGAAATTGTATTATGTAT
66 AAAGATCTCCATCGTTTGAAATAGAGTATAGGGGATAGATATTATCAGGAAATTGTATTATGTAT
11593583 TAGTAAGATTAAAGGTTTGATAATTTGAGTAAATGGAGGATGAGTTATTTTTAATGGAAAGAATA
131 TAGTAAGATTAAAGGTTTGATAATTTGAGTAAATGGAGGATGAGTTATTTTTAATGGAAAGAATA
11593648 TATATGAAGAGTTTGGCAA
196 TATATG-A-AGTTTGGCAA
11593667 CAAATG-TAATTTTGGAGTG-AAGAGAACGCTAATTATTTCATACGGATGGGAAATTATAGTGTT
1 CAAATGTTAATTTTGGAGTGAAAGAGAACGCTAATTATTTCATACGGATGGGAAATTATAGTGTT
11593730 AAAGATCTCCATCGTTTGAAATAGAGTATAGGGGATAGATATTATCAGGAAATTGTATTATGTAT
66 AAAGATCTCCATCGTTTGAAATAGAGTATAGGGGATAGATATTATCAGGAAATTGTATTATGTAT
11593795 TAGTAAGATTAAAGGTTTGATAATTTGAGTAAATGGAGGATGAGTTATTTTTAATGGAAAGAATA
131 TAGTAAGATTAAAGGTTTGATAATTTGAGTAAATGGAGGATGAGTTATTTTTAATGGAAAGAATA
11593860 TATATGAAGTTTGGCAA
196 TATATGAAGTTTGGCAA
11593877 AGGTTTAGGT
Statistics
Matches: 209, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
210 10 0.05
211 43 0.21
212 150 0.72
213 6 0.03
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.34
Consensus pattern (212 bp):
CAAATGTTAATTTTGGAGTGAAAGAGAACGCTAATTATTTCATACGGATGGGAAATTATAGTGTT
AAAGATCTCCATCGTTTGAAATAGAGTATAGGGGATAGATATTATCAGGAAATTGTATTATGTAT
TAGTAAGATTAAAGGTTTGATAATTTGAGTAAATGGAGGATGAGTTATTTTTAATGGAAAGAATA
TATATGAAGTTTGGCAA
Found at i:11596500 original size:29 final size:30
Alignment explanation
Indices: 11596448--11596507 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
11596438 TGGACAATAT
** *
11596448 TACCTATGTTCTTTGGGAGATATGAATAGG
1 TACCTATGTTCTTTCAGACATATGAATAGG
*
11596478 TACCTATGTTC-TTCAGACATATGGATAGG
1 TACCTATGTTCTTTCAGACATATGAATAGG
11596507 T
1 T
11596508 CCTTCGGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (30 bp):
TACCTATGTTCTTTCAGACATATGAATAGG
Found at i:11598469 original size:30 final size:30
Alignment explanation
Indices: 11598435--11598527 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
11598425 CAAATATAAA
11598435 CAGGACGGGGAACAAAGTCCCATGAAGAAT
1 CAGGACGGGGAACAAAGTCCCATGAAGAAT
*
11598465 CAGGATGGGGAACAAAGTCCCATGAAGAAT
1 CAGGACGGGGAACAAAGTCCCATGAAGAAT
**
11598495 CAGGACATGGAACAAAGTCCCATGCAA-AAT
1 CAGGACGGGGAACAAAGTCCCATG-AAGAAT
11598525 CAG
1 CAG
11598528 AAATGGATCA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
30 56 0.97
31 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (30 bp):
CAGGACGGGGAACAAAGTCCCATGAAGAAT
Found at i:11599158 original size:20 final size:20
Alignment explanation
Indices: 11599113--11599169 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
11599103 AGTCAACAGG
**
11599113 TCAAAGTCAACGGTCAGTGA
1 TCAAAGTCAACGGTCAACGA
* *
11599133 TTAAAGTCAGCGGTCAACGA
1 TCAAAGTCAACGGTCAACGA
* *
11599153 TCAAAGTAAATGGTCAA
1 TCAAAGTCAACGGTCAA
11599170 TGGTCGGGTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (20 bp):
TCAAAGTCAACGGTCAACGA
Found at i:11604028 original size:20 final size:21
Alignment explanation
Indices: 11603982--11604021 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11603972 TAATTTTCAA
*
11603982 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
11604003 ACATTGTTGCACCTAATTT
1 ACATTGTTGCACCTAATTT
11604022 GGCATTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:11604512 original size:37 final size:37
Alignment explanation
Indices: 11604462--11604534 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
11604452 GCTTGTGTAA
11604462 CTACATATTTTGCCTCAGTTGTGGACGTAGCCACAAG
1 CTACATATTTTGCCTCAGTTGTGGACGTAGCCACAAG
11604499 CTACATATTTTGCCTCAGTTGTGGACGTAGCCACAA
1 CTACATATTTTGCCTCAGTTGTGGACGTAGCCACAA
11604535 CTGACTGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (37 bp):
CTACATATTTTGCCTCAGTTGTGGACGTAGCCACAAG
Found at i:11608694 original size:21 final size:21
Alignment explanation
Indices: 11608664--11608711 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
11608654 TAATTTTCAA
*
11608664 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
11608685 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
*
11608706 GCATTG
1 ACATTG
11608712 CAATATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:11619638 original size:43 final size:42
Alignment explanation
Indices: 11619591--11619702 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 42
11619581 CAACATATAT
* * * * *
11619591 CGGCGTTTTCTGAACAGACGCCGCAATAGGATTTGTTATTTAG
1 CGGCGTTTTCAGAA-AAACGCCGCAATAGGAGTTGATATTTAA
*
11619634 CGGCGTTTGTCAGAAAAACGCCGCAATAGGAGTTGATGTTTAA
1 CGGCGTTT-TCAGAAAAACGCCGCAATAGGAGTTGATATTTAA
*
11619677 CGGCGTTTTTTC-TAAAAACGCCGCAA
1 CGGCG--TTTTCAGAAAAACGCCGCAA
11619703 ATGGTTTTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 49 0.83
44 7 0.12
45 3 0.05
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (42 bp):
CGGCGTTTTCAGAAAAACGCCGCAATAGGAGTTGATATTTAA
Found at i:11619724 original size:43 final size:44
Alignment explanation
Indices: 11619677--11619787 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 44
11619667 TGATGTTTAA
* *
11619677 CGGCGTTTTTTCTAAAAACGCCGCAAAT-GGTTTTGAGATGTAG
1 CGGCGTTTTTACTAAAAACGCCGCAAATAAGTTTTGAGATGTAG
* * * *
11619720 CGGCG-TTTTACTTAAAACCGCCGC-AATAAGTTTTGATATTTTG
1 CGGCGTTTTTAC-TAAAAACGCCGCAAATAAGTTTTGAGATGTAG
* * *
11619763 CGACGTTTTTCCCAAAAACGCCGCA
1 CGGCGTTTTTACTAAAAACGCCGCA
11619788 GTAAGTTATG
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
42 8 0.15
43 41 0.76
44 5 0.09
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (44 bp):
CGGCGTTTTTACTAAAAACGCCGCAAATAAGTTTTGAGATGTAG
Found at i:11619897 original size:44 final size:42
Alignment explanation
Indices: 11619848--11619960 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 42
11619838 TTGAGAATTA
11619848 GCGGCGTTTCTAGTGCAAAAACGCCGCTAAATGCATAGTATATT
1 GCGGCGTTTCTAGTGC--AAACGCCGCTAAATGCATAGTATATT
** *
11619892 GCGGCG-TT-T-GT--AAACGCCGCTAAATGTTTGGTATATT
1 GCGGCGTTTCTAGTGCAAACGCCGCTAAATGCATAGTATATT
*
11619929 GCGGCATTTCTAGTTTGCAAACGCCGCTAAAT
1 GCGGCGTTTCTAG--TGCAAACGCCGCTAAAT
11619961 AACACAAGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
37 28 0.48
38 2 0.03
39 1 0.02
40 1 0.02
41 2 0.03
42 2 0.03
43 2 0.03
44 20 0.34
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (42 bp):
GCGGCGTTTCTAGTGCAAACGCCGCTAAATGCATAGTATATT
Found at i:11623840 original size:42 final size:41
Alignment explanation
Indices: 11623772--11623907 Score: 150
Period size: 42 Copynumber: 3.3 Consensus size: 41
11623762 TTTATACAAA
* * *
11623772 AAACGCCGCTAATTTACCACTCTATTGCGGCATTTTTGGTAT
1 AAACGCCGCTAAATTA-CACTATATTGCGGCATTTTTGCTAT
* * *
11623814 AAACTCCGCTAAATTAACACTATATTGCGGCGTTTTAGCTA-
1 AAACGCCGCTAAATT-ACACTATATTGCGGCATTTTTGCTAT
* *
11623855 AAACGCCGCTACATGT-CTACTATATTGCGGCATTTTTACTAT
1 AAACGCCGCTAAAT-TAC-ACTATATTGCGGCATTTTTGCTAT
11623897 AAACGCCGCTA
1 AAACGCCGCTA
11623908 TTGTTTAACC
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
40 1 0.01
41 32 0.41
42 45 0.57
43 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (41 bp):
AAACGCCGCTAAATTACACTATATTGCGGCATTTTTGCTAT
Found at i:11625095 original size:32 final size:31
Alignment explanation
Indices: 11625040--11625121 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
11625030 TTGTAACAGC
**
11625040 TATGCATTATCTAAATGTGACACTGACACTCT-
1 TATGCATTATCTAAATGCAACACT-A-ACTCTA
*
11625072 TGTGCATTATCTAAATGCAACACTAACTCTA
1 TATGCATTATCTAAATGCAACACTAACTCTA
*
11625103 GTATGCATCATCTAAATGC
1 -TATGCATTATCTAAATGC
11625122 CACATTGAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
30 5 0.12
31 1 0.02
32 37 0.86
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (31 bp):
TATGCATTATCTAAATGCAACACTAACTCTA
Found at i:11627306 original size:21 final size:21
Alignment explanation
Indices: 11627282--11627375 Score: 102
Period size: 21 Copynumber: 4.4 Consensus size: 21
11627272 TATCGAAGTG
11627282 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
*
11627303 CCACATAGATT-TACACCAAAGTG-
1 CCACATA-ATTGT-C-CCGAAG-GA
* *
11627326 CCACATATTTGTCCCGAATGA
1 CCACATAATTGTCCCGAAGGA
*
11627347 CCACATAATTATCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
11627368 CCACATAA
1 CCACATAA
11627376 AACCCTCGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 38 0.63
22 7 0.12
23 13 0.22
24 1 0.02
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:11630561 original size:3 final size:3
Alignment explanation
Indices: 11630553--11630605 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
11630543 CGAGTTGTTT
* *
11630553 TTA TTA TTA TTA TTA TCT- TTA TTTA TTA TTA TTA CTA ATA TTA TT-
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
11630598 TTA TTA TT
1 TTA TTA TT
11630606 TTTCAAGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
2 3 0.07
3 36 0.84
4 4 0.09
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11630594 original size:19 final size:18
Alignment explanation
Indices: 11630554--11630604 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
11630544 GAGTTGTTTT
*
11630554 TATTATTATTATTATCTT
1 TATTATTATTATTATCTA
11630572 TATTTATTATTATTA-CTAA
1 TA-TTATTATTATTATCT-A
11630591 TATTATT-TTATTAT
1 TATTATTATTATTAT
11630605 TTTTCAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 14 0.48
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATTATTATCTA
Found at i:11630596 original size:22 final size:23
Alignment explanation
Indices: 11630551--11630605 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
11630541 TCCGAGTTGT
* *
11630551 TTTTATTATTATTATTATCTTTA
1 TTTTATTATTATTATAATCATTA
11630574 -TTTATTATTATTACTAAT-ATTA
1 TTTTATTATTATTA-TAATCATTA
11630596 TTTTATTATT
1 TTTTATTATT
11630606 TTTCAAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTATTATTATAATCATTA
Found at i:11631288 original size:12 final size:12
Alignment explanation
Indices: 11631271--11631304 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11631261 GATTCGAAAG
11631271 AAAAAATAGAAC
1 AAAAAATAGAAC
*
11631283 AAAAAATAAAAC
1 AAAAAATAGAAC
11631295 AAAAAA-AGAA
1 AAAAAATAGAA
11631305 ATAAAAAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 3 0.15
12 17 0.85
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAAATAGAAC
Found at i:11635238 original size:24 final size:24
Alignment explanation
Indices: 11635178--11635241 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
11635168 AAAAGGCAAT
11635178 TATTTTTCAAAATTTTTTATTAAA
1 TATTTTTCAAAATTTTTTATTAAA
* *
11635202 CATTTTTCAAAATTCTTTTAATT-GA
1 TATTTTTCAAAATT-TTTT-ATTAAA
11635227 TATTTTTC-AAATTTT
1 TATTTTTCAAAATTTT
11635242 GAAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 18 0.51
25 12 0.34
26 3 0.09
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTTTTCAAAATTTTTTATTAAA
Found at i:11637491 original size:137 final size:136
Alignment explanation
Indices: 11637230--11637884 Score: 695
Period size: 137 Copynumber: 4.8 Consensus size: 136
11637220 TAAACCATCA
* * * * *
11637230 AAGTACAGCTAGATGTCCTCAACATAAAGGAACAATGTCATCCACCGACCAGATCTCCTCAACAC
1 AAGTACAGCTAGAAGTCCTCAACACAAAGGAACAATGTCGTTCACCGACCAGATCTCCTCAACGC
* * * * * * * *
11637295 AAAGGAGTAGTGTCATCTTTAGACAACCAGACTTCCTCAATATGAAGTAACTATATTGTCTCCAA
66 AAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGGAACT-TGTTGTCTCCAA
11637360 ATTATCC
130 ATTATCC
* * * * * * * *
11637367 AAGTACGGCTAGAAGTCCTCAACACGAAGGAATAATATCGTCCACCGACCATATCTTCTCAATGC
1 AAGTACAGCTAGAAGTCCTCAACACAAAGGAACAATGTCGTTCACCGACCAGATCTCCTCAACGC
* * *
11637432 AAAGGAGCATTTTCATCCTCATACAATCAGACTTCCTCAACACGAAGGAACTGTGTTGTCTCCAA
66 AAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGGAACT-TGTTGTCTCCAA
11637497 ATTATCC
130 ATTATCC
** * * *
11637504 AAGTACAGCTAGATA-TCCTCAACATGAAGGAACAATGTCGTTCATCTACCATATCTCCTCAACG
1 AAGTACAGCTAGA-AGTCCTCAACACAAAGGAACAATGTCGTTCACCGACCAGATCTCCTCAACG
* ** *
11637568 CAAAGAAGCAGTGTCATCCTCAGACAAGT-AGACTTCCTCAACACGAAGAGGCCTTGTTTTCTCC
65 CAAAGGAGCAGTGTCATCCTCAGACAA-TCAGACTTCCTCAACACGAAG-GAACTTGTTGTCTCC
11637632 AAATTATCC
128 AAATTATCC
* * * ** * *
11637641 AA-AAAAGTTAGACTTCCTCAACACAAAGGAACAATGTCGTTTACCGATCAGATCTCCTCAACGC
1 AAGTACAGCTAGAAGTCCTCAACACAAAGGAACAATGTCGTTCACCGACCAGATCTCCTCAACGC
* * * *
11637705 AAATGAGCAGTGTCATCCTTAGACAATCAGACTTCCTCAAAACGAAGAAACCTTGTTGTCTCCAA
66 AAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGGAA-CTTGTTGTCTCCAA
11637770 ATTATCC
130 ATTATCC
* * * ** ** * * * * * *
11637777 AAATGCATCTAGACTTCCTCAATGCTAAGAAACAATGTTGTTTACCAACCAGATCTCCTCAATGC
1 AAGTACAGCTAGAAGTCCTCAACACAAAGGAACAATGTCGTTCACCGACCAGATCTCCTCAACGC
* * *
11637842 GAGGGAGCAATGTCATCCTCAGACAATCAGACTTCCTCAACAC
66 AAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACAC
11637885 AAATGAACCA
Statistics
Matches: 434, Mismatches: 77, Indels: 14
0.83 0.15 0.03
Matches are distributed among these distances:
135 1 0.00
136 113 0.26
137 315 0.73
138 5 0.01
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (136 bp):
AAGTACAGCTAGAAGTCCTCAACACAAAGGAACAATGTCGTTCACCGACCAGATCTCCTCAACGC
AAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGGAACTTGTTGTCTCCAAA
TTATCC
Found at i:11637813 original size:273 final size:273
Alignment explanation
Indices: 11637228--11637884 Score: 698
Period size: 273 Copynumber: 2.4 Consensus size: 273
11637218 ATTAAACCAT
* * * * * *
11637228 CAAAGTACAGCTAGATGTCCTCAACATAAAGGAACAATGTCATCCACCGACCAGATCTCCTCAAC
1 CAAA-TACAGCTAGATATCCTCAACATGAAGAAACAATGTCGTTCACCAACCAGATCTCCTCAAC
* * * * * * * * * * * *
11637293 ACAAAGGAGTAGTGTCATCTTTAGACAACCAGACTTCCTCAATATGAAGTA--ACTATATTGTCT
65 GCAAAGAAGCAATGTCATCCTCAGACAATCAGACTTCCTCAACACGAAG-AGGCCT-TGTTTTCT
* ** * ** * * *
11637356 CCAAATTATCCAAGTACGGCTAGAAGTCCTCAACACGAAGGAATAATATCGTCCACCGACCATAT
128 CCAAATTATCCAA-AAAAGTTAGACTTCCTCAACACAAAGGAACAATATCGTCCACCGACCAGAT
* * * * * * *
11637421 CTTCTCAATGCAAAGGAGCATTTTCATCCTCATACAATCAGACTTCCTCAACACGAAGGAACTGT
192 CTCCTCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAAAACGAAGAAACTGT
11637486 GTTGTCTCCAAATTATC
257 GTTGTCTCCAAATTATC
* * * * *
11637503 CAAGTACAGCTAGATATCCTCAACATGAAGGAACAATGTCGTTCATCTACCATATCTCCTCAACG
1 CAAATACAGCTAGATATCCTCAACATGAAGAAACAATGTCGTTCACCAACCAGATCTCCTCAACG
*
11637568 CAAAGAAGCAGTGTCATCCTCAGACAAGT-AGACTTCCTCAACACGAAGAGGCCTTGTTTTCTCC
66 CAAAGAAGCAATGTCATCCTCAGACAA-TCAGACTTCCTCAACACGAAGAGGCCTTGTTTTCTCC
* ** *
11637632 AAATTATCCAAAAAAGTTAGACTTCCTCAACACAAAGGAACAATGTCGTTTACCGATCAGATCTC
130 AAATTATCCAAAAAAGTTAGACTTCCTCAACACAAAGGAACAATATCGTCCACCGACCAGATCTC
* *
11637697 CTCAACGCAAATGAGCAGTGTCATCCTTAGACAATCAGACTTCCTCAAAACGAAGAAACCT-TGT
195 CTCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAAAACGAAGAAA-CTGTGT
11637761 TGTCTCCAAATTATC
259 TGTCTCCAAATTATC
* * * *
11637776 CAAATGCATCTAGACT-TCCTC-A-ATGCTAAGAAACAATGTTGTTTACCAACCAGATCTCCTCA
1 CAAATACAGCTAGA-TATCCTCAACATG--AAGAAACAATGTCGTTCACCAACCAGATCTCCTCA
* * * *
11637838 ATGCGAGGGAGCAATGTCATCCTCAGACAATCAGACTTCCTCAACAC
63 ACGCAAAGAAGCAATGTCATCCTCAGACAATCAGACTTCCTCAACAC
11637885 AAATGAACCA
Statistics
Matches: 319, Mismatches: 55, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
271 3 0.01
272 2 0.01
273 194 0.61
274 115 0.36
275 5 0.02
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (273 bp):
CAAATACAGCTAGATATCCTCAACATGAAGAAACAATGTCGTTCACCAACCAGATCTCCTCAACG
CAAAGAAGCAATGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGAGGCCTTGTTTTCTCCA
AATTATCCAAAAAAGTTAGACTTCCTCAACACAAAGGAACAATATCGTCCACCGACCAGATCTCC
TCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAAAACGAAGAAACTGTGTTG
TCTCCAAATTATC
Found at i:11638456 original size:3 final size:3
Alignment explanation
Indices: 11638448--11638503 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
11638438 GACTGAGTTG
* * * *
11638448 TTA TTA TTA TTA TCA TTA TTTA TTA TTA TTA CTA ATA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
11638494 TTA TTT TTA T
1 TTA TTA TTA T
11638504 GTTACAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11639032 original size:22 final size:23
Alignment explanation
Indices: 11639007--11639054 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
11638997 CTAAATCTAG
* * *
11639007 ACCAATCCCGAAAAATTC-GGGA
1 ACCAATACCAAAAAAATCAGGGA
11639029 ACC-ATACCAAAAAAATCAGGGA
1 ACCAATACCAAAAAAATCAGGGA
11639051 ACCA
1 ACCA
11639055 TCATTGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.48, C:0.27, G:0.15, T:0.10
Consensus pattern (23 bp):
ACCAATACCAAAAAAATCAGGGA
Found at i:11642707 original size:178 final size:182
Alignment explanation
Indices: 11642408--11642767 Score: 692
Period size: 178 Copynumber: 2.0 Consensus size: 182
11642398 GAGATTGAGA
11642408 GAGATATTCCGAAGATATTAAGGGCTTGTTTCAATTCTCCCGTTTGAATTGAGTCATCGCTTCAG
1 GAGATATTCCGAAGATATTAAGGGCTTGTTTCAATTCTCCCGTTTGAATTGAGTCATCGCTTCAG
11642473 CTCTCGGCTTATGAAAAATTTAGCTAAGCATGACAAAAGTCATACTTAGCATATTTAAAAACAAG
66 CTCTCGGCTTATGAAAAATTTAGCTAAGCATGACAAAAGTCATACTTAGCATATTTAAAAACAAG
11642538 TTG-AAAT-AAAGT-AAAAAC-AAAAACTTGAAAAGTCAAATAAAAGAGAAC
131 TTGAAAATAAAAGTAAAAAACAAAAAACTTGAAAAGTCAAATAAAAGAGAAC
11642586 GAGATATTCCGAAGATATTAAGGGCTTGTTTCAATTCTCCCGTTTGAATTGAGTCATCGCTTCAG
1 GAGATATTCCGAAGATATTAAGGGCTTGTTTCAATTCTCCCGTTTGAATTGAGTCATCGCTTCAG
11642651 CTCTCGGCTTATGAAAAATTTAGCTAAGCATGACAAAAGTCATACTTAGCATATTTAAAAACAAG
66 CTCTCGGCTTATGAAAAATTTAGCTAAGCATGACAAAAGTCATACTTAGCATATTTAAAAACAAG
11642716 TTGAAAATAAAAGTAAAAAACAAAAAACTTGAAAAGTCAAATAAAAGAGAAC
131 TTGAAAATAAAAGTAAAAAACAAAAAACTTGAAAAGTCAAATAAAAGAGAAC
11642768 TTTTATAAAA
Statistics
Matches: 178, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
178 133 0.75
179 4 0.02
180 5 0.03
181 6 0.03
182 30 0.17
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (182 bp):
GAGATATTCCGAAGATATTAAGGGCTTGTTTCAATTCTCCCGTTTGAATTGAGTCATCGCTTCAG
CTCTCGGCTTATGAAAAATTTAGCTAAGCATGACAAAAGTCATACTTAGCATATTTAAAAACAAG
TTGAAAATAAAAGTAAAAAACAAAAAACTTGAAAAGTCAAATAAAAGAGAAC
Found at i:11653139 original size:20 final size:20
Alignment explanation
Indices: 11653125--11653181 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
11653115 CCAACCCGGT
11653125 CTGAATCAAGTCAACCCGAC
1 CTGAATCAAGTCAACCCGAC
* *
11653145 CTGAATCGAGTCAACTCGAC
1 CTGAATCAAGTCAACCCGAC
* * *
11653165 CTAAACCGAGTCAACCC
1 CTGAATCAAGTCAACCC
11653182 AACATGACCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.35, G:0.16, T:0.16
Consensus pattern (20 bp):
CTGAATCAAGTCAACCCGAC
Found at i:11653252 original size:22 final size:23
Alignment explanation
Indices: 11653227--11653269 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
11653217 ATTTGATCGA
*
11653227 TCTGATCGTTAACT-TTGACTGG
1 TCTGACCGTTAACTGTTGACTGG
*
11653249 TCTGACCGTTGACTGTTGACT
1 TCTGACCGTTAACTGTTGACT
11653270 TTGACAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (23 bp):
TCTGACCGTTAACTGTTGACTGG
Found at i:11659373 original size:21 final size:21
Alignment explanation
Indices: 11659347--11659387 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11659337 AATCTCAAAT
11659347 CCTAAACCCTAAACTTTAAAC
1 CCTAAACCCTAAACTTTAAAC
* * *
11659368 CCTAAATCCTCAAGTTTAAA
1 CCTAAACCCTAAACTTTAAA
11659388 TTATAAATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.27
Consensus pattern (21 bp):
CCTAAACCCTAAACTTTAAAC
Found at i:11670052 original size:29 final size:29
Alignment explanation
Indices: 11670004--11670069 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
11669994 AAATGAATTA
*
11670004 TTATTTTTAACAACAGTTAATAATGTT-TAT
1 TTATTTTTAACAACAATTAA-AAT-TTATAT
*
11670034 TTATTTTTAATAA-AATTAAAATTTAATAT
1 TTATTTTTAACAACAATTAAAATTT-ATAT
11670063 TTATTTT
1 TTATTTT
11670070 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 2 0.06
28 3 0.09
29 15 0.47
30 12 0.38
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (29 bp):
TTATTTTTAACAACAATTAAAATTTATAT
Found at i:11676498 original size:33 final size:34
Alignment explanation
Indices: 11676423--11676487 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
11676413 CAAAATAAAC
*
11676423 CAAAATACATTAACAAAAAGTCCAACAAATTTAA
1 CAAAATAAATTAACAAAAAGTCCAACAAATTTAA
11676457 CAAAATAAATTAA-AATAAA-TCCAACCAAATT
1 CAAAATAAATTAACAA-AAAGTCCAA-CAAATT
11676488 AATGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.22
Consensus pattern (34 bp):
CAAAATAAATTAACAAAAAGTCCAACAAATTTAA
Found at i:11679337 original size:17 final size:19
Alignment explanation
Indices: 11679317--11679355 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
11679307 TTATATCATC
11679317 AATAAATAAA-TATA-AAA
1 AATAAATAAACTATATAAA
11679334 AATAAATAAACTATATAAA
1 AATAAATAAACTATATAAA
11679353 AAT
1 AAT
11679356 TTGAAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.50
18 4 0.20
19 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAATAAACTATATAAA
Found at i:11679830 original size:20 final size:20
Alignment explanation
Indices: 11679807--11679845 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11679797 TCAATACTTA
*
11679807 AATTAAAGTTGCTAAAGTTT
1 AATTAAAGTTACTAAAGTTT
11679827 AATTAAAGTTACTAAAGTT
1 AATTAAAGTTACTAAAGTT
11679846 CAATGCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (20 bp):
AATTAAAGTTACTAAAGTTT
Found at i:11680421 original size:18 final size:19
Alignment explanation
Indices: 11680376--11680435 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
11680366 TAGACATGAG
11680376 TTCTCTCATATTTTCTTCTC
1 TTCT-TCATATTTTCTTCTC
* *
11680396 TTCATTCAT-TTTTCTTGTT
1 TTC-TTCATATTTTCTTCTC
*
11680415 TTCTTCATCTTTTCCTTCTC
1 TTCTTCATATTTT-CTTCTC
11680435 T
1 T
11680436 ATTCTTTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.15
19 15 0.45
20 12 0.36
21 1 0.03
ACGTcount: A:0.08, C:0.27, G:0.02, T:0.63
Consensus pattern (19 bp):
TTCTTCATATTTTCTTCTC
Found at i:11681246 original size:24 final size:22
Alignment explanation
Indices: 11681197--11681238 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11681187 CCAGAATGTC
11681197 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
11681218 CAGGAGGGAACCGATTCCCCC
1 AAGGAGGGAACCGATACCCCC
11681239 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:11682124 original size:96 final size:96
Alignment explanation
Indices: 11681947--11682126 Score: 324
Period size: 96 Copynumber: 1.9 Consensus size: 96
11681937 GTCGAAGGTC
*
11681947 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
11682012 TTGATCCTTGGCATATGTACTTAAGGAATGA
66 TTGATCCCTAGCATATGTACTTAAGGAATGA
11682043 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
11682108 TTGATCCCTAGTATATGTA
66 TTGATCCCTAGCATATGTA
11682127 TATGATTCTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (96 bp):
TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTACTTAAGGAATGA
Found at i:11682215 original size:47 final size:47
Alignment explanation
Indices: 11682163--11682282 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
11682153 TCTTATGGAC
11682163 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCA
* *
11682210 ATTATTATATGGCACTACGGTACAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCA
* *
11682257 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
11682283 ATATGAGCTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 19 0.28
47 49 0.72
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCA
Found at i:11682283 original size:23 final size:23
Alignment explanation
Indices: 11682163--11682287 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
11682153 TCTTATGGAC
*
11682163 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
11682187 ATTCTACGCGACACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
11682210 ATTATTATATGGCACTACGGTACA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
11682234 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
11682257 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
11682280 ATTATATG
1 ATTATATG
11682288 AGCTGTGGTG
Statistics
Matches: 77, Mismatches: 23, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
23 58 0.75
24 19 0.25
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:11687068 original size:23 final size:22
Alignment explanation
Indices: 11687020--11687068 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
11687010 CCAGAATGTC
11687020 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
11687041 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
11687064 AAGGA
1 AAGGA
11687069 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:11687983 original size:103 final size:103
Alignment explanation
Indices: 11687758--11687975 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
11687748 GTCGAGGGTC
*
11687758 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
* *
11687823 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
11687861 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
*
11687926 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
11687964 TATGTGGTCCTT
1 TATGTGGTCCTT
11687976 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:11688082 original size:23 final size:23
Alignment explanation
Indices: 11687982--11688083 Score: 123
Period size: 23 Copynumber: 4.3 Consensus size: 23
11687972 CCTTATGGAC
* *
11687982 ATTATTATATGGCACTACGATGCA
1 ATTA-TATGTGGCACTACGGTGCA
*
11688006 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
11688030 ATTCTACGTGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
11688053 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
11688076 ATTATATG
1 ATTATATG
11688084 AGCTGTGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
23 44 0.63
24 26 0.37
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:11697300 original size:256 final size:260
Alignment explanation
Indices: 11696980--11697497 Score: 992
Period size: 256 Copynumber: 2.0 Consensus size: 260
11696970 TCATGAAAAA
11696980 TTATTTAGGAAAATAGGGTGAATTCAACGGTGATTTGTAATGTCATTGACAAATGAGGGTGAATT
1 TTATTTAGGAAAATAGGGTGAATTCAACGGTGATTTGTAATGTCATTGACAAATGAGGGTGAATT
11697045 TGCTCCATTTTTTTTAATTTTAGAATCAAATTGTAAAAAATAAAAGTGTAGGGACTAAAAT-AAA
66 TGCTCCATTTTTTTT-ATTTTAGAATCAAATTGTAAAAAATAAAAGTGTAGGGACTAAAATAAAA
11697109 TTTTCTAAAATTATCTTGAAGTGAA-TTATTTTCGGACTCCTTCCCTAAACTTATTGCTTCATTT
130 TTTTCTAAAATTATCTTGAAGTGAATTTATTTTCGGACTCCTTCCCTAAACTTATTGCTTCATTT
11697173 TA-T-TATAGTCAACTTTTTATAAAGAAAAC-ATTTTAGTCCATGTACTTTTAAATTTATTTCAA
195 TATTATATAGTCAACTTTTTATAAAGAAAACAATTTTAGTCCATGTACTTTTAAATTTATTTCAA
11697235 T
260 T
11697236 TTATTTAGGAAAATAGGGTGAATTCAACGGTGATTTGTAATGTCATTGACAAATGAGGGTGAATT
1 TTATTTAGGAAAATAGGGTGAATTCAACGGTGATTTGTAATGTCATTGACAAATGAGGGTGAATT
11697301 TGCTCCATTTTTTTTATTTTAGAATCAAATTGTAAAAAATAAAAGTGTAGGGACTAAAATAAAAT
66 TGCTCCATTTTTTTTATTTTAGAATCAAATTGTAAAAAATAAAAGTGTAGGGACTAAAATAAAAT
11697366 TTTCTAAAATTATCTTGAAGTGAATTTATTTTCGGACTCCTTCCCTAAACTTATTGCTTCATTTT
131 TTTCTAAAATTATCTTGAAGTGAATTTATTTTCGGACTCCTTCCCTAAACTTATTGCTTCATTTT
11697431 ATTATATAGTCAACTTTTTATAAAGAAAACAATTTTAGTCCATGTACTTTTAAATTTATTTCAAT
196 ATTATATAGTCAACTTTTTATAAAGAAAACAATTTTAGTCCATGTACTTTTAAATTTATTTCAAT
11697496 TT
1 TT
11697498 TAGTCATGCA
Statistics
Matches: 257, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
255 45 0.18
256 108 0.42
257 41 0.16
258 1 0.00
259 26 0.10
260 36 0.14
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (260 bp):
TTATTTAGGAAAATAGGGTGAATTCAACGGTGATTTGTAATGTCATTGACAAATGAGGGTGAATT
TGCTCCATTTTTTTTATTTTAGAATCAAATTGTAAAAAATAAAAGTGTAGGGACTAAAATAAAAT
TTTCTAAAATTATCTTGAAGTGAATTTATTTTCGGACTCCTTCCCTAAACTTATTGCTTCATTTT
ATTATATAGTCAACTTTTTATAAAGAAAACAATTTTAGTCCATGTACTTTTAAATTTATTTCAAT
Found at i:11698929 original size:18 final size:18
Alignment explanation
Indices: 11698906--11698968 Score: 117
Period size: 18 Copynumber: 3.5 Consensus size: 18
11698896 TGAGAATGAG
*
11698906 ATCTTCTTCAGAATATTT
1 ATCTTCTTAAGAATATTT
11698924 ATCTTCTTAAGAATATTT
1 ATCTTCTTAAGAATATTT
11698942 ATCTTCTTAAGAATATTT
1 ATCTTCTTAAGAATATTT
11698960 ATCTTCTTA
1 ATCTTCTTA
11698969 TTTCCCTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (18 bp):
ATCTTCTTAAGAATATTT
Found at i:11700914 original size:64 final size:64
Alignment explanation
Indices: 11700707--11700915 Score: 219
Period size: 64 Copynumber: 3.2 Consensus size: 64
11700697 ATTTTTAGAG
* ** *
11700707 TGATGCACCGATGCACCAAGACATGCATCGATGCAC-CATGAATAAATTGAAA-ATCGAATTCAT
1 TGATGCACCGATGCACC-AGCCATGCATCGATGCACTC-TGAATATTTTGAAACATCGAATGCAT
11700770 T
64 T
* * * *
11700771 TCATGCACCGATGCA-CATACTATGCATCGATGCACTCAGAAT-TTTATGAAAACATCGAATGCA
1 TGATGCACCGATGCACCA-GCCATGCATCGATGCACTCTGAATATTT-TG-AAACATCGAATGCA
11700834 TT
63 TT
* ** * *
11700836 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCAAATGCACT
1 TGATGCACCGATGCACCAGCCATGCATCGATGCACTCTGAATATTTTGAAACATCGAATGCATT
*
11700900 TGATGCATCGATGCAC
1 TGATGCACCGATGCAC
11700916 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
62 2 0.02
63 21 0.17
64 48 0.40
65 45 0.37
66 5 0.04
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (64 bp):
TGATGCACCGATGCACCAGCCATGCATCGATGCACTCTGAATATTTTGAAACATCGAATGCATT
Found at i:11707870 original size:21 final size:21
Alignment explanation
Indices: 11707828--11707871 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11707818 ACCCCGGGAG
*
11707828 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
11707849 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
11707870 CT
1 CT
11707872 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:11708435 original size:2 final size:2
Alignment explanation
Indices: 11708428--11708459 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11708418 CAGCTTAAGC
11708428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11708460 CTTATAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11709131 original size:64 final size:64
Alignment explanation
Indices: 11708931--11709139 Score: 228
Period size: 64 Copynumber: 3.2 Consensus size: 64
11708921 TTTTTCAGAG
** * *
11708931 TGATGCACCGATGCACCAAGCCATGCATCGATGCAC-CATGAATAAATT-GAACATCAAATGCAT
1 TGATGCACCGATGCACCAA-CCATGCATCGATGCACTC-TGAATATTTTAAAACATCGAATGCAT
11708994 T
64 T
* * * *
11708995 TCATGCACCGATGCA-TATACTATGCATCGATGCACTCAGAAT-TTTATGAAAACATCGAATGCA
1 TGATGCACCGATGCACCA-ACCATGCATCGATGCACTCTGAATATTT-T-AAAACATCGAATGCA
11709058 TT
63 TT
* ** *
11709060 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTAAAACATCGAATGCACT
1 TGATGCACCGATGCACCAACCATGCATCGATGCACTCTGAATATTTTAAAACATCGAATGCATT
*
11709124 TGATGCATCGATGCAC
1 TGATGCACCGATGCAC
11709140 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 21 0.17
64 48 0.39
65 48 0.39
66 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (64 bp):
TGATGCACCGATGCACCAACCATGCATCGATGCACTCTGAATATTTTAAAACATCGAATGCATT
Done.