Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 133 of 770
Found at i:38868572 original size:11 final size:11
Alignment explanation
Indices: 38868556--38868581 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38868546 CGAAGCCCAC
38868556 ATCACAATAAT
1 ATCACAATAAT
38868567 ATCACAATAAT
1 ATCACAATAAT
38868578 ATCA
1 ATCA
38868582 TACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:38869294 original size:28 final size:29
Alignment explanation
Indices: 38869257--38869347 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
38869247 AAGTCTACAT
*
38869257 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* * *
38869285 TCATTCATATGACCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
*
38869314 ACATTCATATGGCCCATCTA-GCCCGAATC
1 ACATTCATATGGCCCA-CTAGGCCCAAATC
38869343 A-ATTC
1 ACATTC
38869348 CAAGCCATGT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.45
29 27 0.51
30 2 0.04
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:38872680 original size:40 final size:39
Alignment explanation
Indices: 38872515--38872698 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
38872505 AAATTGAATG
* * *
38872515 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
38872555 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
38872595 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
38872635 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
38872674 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
38872699 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:38872723 original size:80 final size:81
Alignment explanation
Indices: 38872555--38872743 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
38872545 GCTGGAAATT
* * * *
38872555 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
38872620 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
38872636 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
38872699 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
38872715 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
38872744 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:38875813 original size:29 final size:29
Alignment explanation
Indices: 38875774--38875852 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
38875764 CTTAATAATC
*
38875774 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
38875804 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
38875833 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
38875853 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:38879197 original size:22 final size:22
Alignment explanation
Indices: 38879161--38879225 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
38879151 GTAAATACGT
38879161 TTGGCACACAA-CCATAATCAGG
1 TTGGCACA-AAGCCATAATCAGG
* * *
38879183 TTGGCATAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
38879205 TTGGCACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
38879226 AATAATTGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 29 0.85
23 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:38879424 original size:41 final size:41
Alignment explanation
Indices: 38879367--38879487 Score: 197
Period size: 41 Copynumber: 3.0 Consensus size: 41
38879357 TAAAAGCCAC
* *
38879367 CGGTGGATCCACGATCGTTAAGCAACCATGCGATCCTTAAT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAAT
*
38879408 CGGTGGGTCCACGATCGTCAAGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAAT
* *
38879449 CGGTGGATCCACGGTCATCAAGCAACCATGCGATCCTCA
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCA
38879488 GTTTCTTCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21
Consensus pattern (41 bp):
CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAAT
Found at i:38880138 original size:27 final size:27
Alignment explanation
Indices: 38879727--38880142 Score: 265
Period size: 27 Copynumber: 15.4 Consensus size: 27
38879717 TTTCACCCTA
* * * *
38879727 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* ** *
38879754 CAAAGGGTATTTCGGTAATTTTGGAAAC
1 C-AAGGGTATTTTGGTAATTTTACAAAT
* *
38879782 CAATGGTATTTCT-ATAATTTTTA-AAAGT
1 CAAGGGTATTT-TGGTAA-TTTTACAAA-T
* **
38879810 CAAGGGTATTTCT-ATAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
* * * **
38879837 TAGGGGTATTTCT-ATAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
* * *
38879864 CAGGGGTATTTCT-ATAATTTTCCAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
* * *
38879891 TAAGGGTA-TTTCGTAATTTTCCAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
38879917 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
38879944 CGAA-GGTATTTCGGTAATTTTACAAGTT
1 C-AAGGGTATTTTGGTAATTTTACAA-AT
* *
38879972 GAA-GGTATTTTGGTAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * *
38879998 TAAGGGTATTTCGATAATTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
38880025 -TAGAGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTGGTAATTTTACAAAT
* * *
38880052 CAGGGGTATTTTGGTAATATTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
38880079 CAGGGGTATTTTGGTAATTTTTCTAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * ** *
38880106 CGAGGGTATTTTTGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
38880133 CAAGGGTATT
1 CAAGGGTATT
38880143 CAGTAATTCT
Statistics
Matches: 321, Mismatches: 56, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.00
26 26 0.08
27 247 0.77
28 47 0.15
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:38880176 original size:27 final size:26
Alignment explanation
Indices: 38880137--38880214 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 26
38880127 GTAAACCAAG
*
38880137 GGTA-TTCAGTAATTCTATCCTATAGA
1 GGTATTTCAGTAATTCTA-CCTACAGA
*
38880163 GGTATTTCAGTAATTCTACCATACAGG
1 GGTATTTCAGTAATTCTACC-TACAGA
*
38880190 GGTATTTCAGTAATACTAGCCTACA
1 GGTATTTCAGTAATTCTA-CCTACA
38880215 AATTTGAGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.13
27 38 0.83
28 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (26 bp):
GGTATTTCAGTAATTCTACCTACAGA
Found at i:38883537 original size:28 final size:29
Alignment explanation
Indices: 38883489--38883561 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 29
38883479 AAGTCTACGT
* * *
38883489 ACATGCATATGGTCCACTAGGCCC-AATC
1 ACATTCATATGGCCCAATAGGCCCAAATC
*
38883517 TCATTCATATGGCCCAATAGGCCCAAATC
1 ACATTCATATGGCCCAATAGGCCCAAATC
38883546 ACATTCATATGGCCCA
1 ACATTCATATGGCCCA
38883562 TCCAGCCCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 20 0.51
29 19 0.49
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (29 bp):
ACATTCATATGGCCCAATAGGCCCAAATC
Found at i:38887744 original size:28 final size:27
Alignment explanation
Indices: 38887681--38887750 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
38887671 ATAGTGAGTC
38887681 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
38887708 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
38887736 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38887751 GTACAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:38900636 original size:46 final size:46
Alignment explanation
Indices: 38900586--38900761 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
38900576 TGGTTGAGCA
38900586 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
38900632 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
38900677 CATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
38900725 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38900762 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:38900742 original size:93 final size:93
Alignment explanation
Indices: 38900583--38900754 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
38900573 GGATGGTTGA
* * *
38900583 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
38900648 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
38900676 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
38900741 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
38900755 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGCTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:38903379 original size:27 final size:26
Alignment explanation
Indices: 38903331--38903390 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
38903321 GCGAGGCTGC
*
38903331 CAGATATTGTGACGAAGTCACCAAATA
1 CAGATATTGTGACGAAGCCACCAAA-A
* * * *
38903358 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAAAA
38903384 CAGATAT
1 CAGATAT
38903391 ATATATATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAAAA
Found at i:38909179 original size:28 final size:29
Alignment explanation
Indices: 38909112--38909212 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
38909102 ATAGTGAATC
*
38909112 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
38909141 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
38909169 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
38909199 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38909213 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:38913835 original size:2 final size:2
Alignment explanation
Indices: 38913828--38913867 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
38913818 ACTAGCACAG
38913828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38913868 GTGGCGAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38915249 original size:191 final size:191
Alignment explanation
Indices: 38914925--38915314 Score: 762
Period size: 191 Copynumber: 2.0 Consensus size: 191
38914915 ATTAGAGTTT
*
38914925 AAAACCAACACCAACTCTTGCCGTCCCAACATAGTAAAATAATCAACCTTTGCATGCCAAGGGAT
1 AAAACCAACACCAACTCTTGCCATCCCAACATAGTAAAATAATCAACCTTTGCATGCCAAGGGAT
38914990 TCGAACCAAAGTCCTCTCACATGCCAACTCACGCCACCACTATTAGGCCATCAACTCATTTGTGT
66 TCGAACCAAAGTCCTCTCACATGCCAACTCACGCCACCACTATTAGGCCATCAACTCATTTGTGT
*
38915055 CATAAATCCAACACATTAAACTTTAAAGTGCACCTACTTGCTTCTAGATTTATTGAAAAGA
131 CATAAATCCAACACATTAAACTTTAAAGCGCACCTACTTGCTTCTAGATTTATTGAAAAGA
38915116 AAAACCAACACCAACTCTTGCCATCCCAACATAGTAAAATAATCAACCTTTGCATGCCAAGGGAT
1 AAAACCAACACCAACTCTTGCCATCCCAACATAGTAAAATAATCAACCTTTGCATGCCAAGGGAT
38915181 TCGAACCAAAGTCCTCTCACATGCCAACTCACGCCACCACTATTAGGCCATCAACTCATTTGTGT
66 TCGAACCAAAGTCCTCTCACATGCCAACTCACGCCACCACTATTAGGCCATCAACTCATTTGTGT
38915246 CATAAATCCAACACATTAAACTTTAAAGCGCACCTACTTGCTTCTAGATTTATTGAAAAGA
131 CATAAATCCAACACATTAAACTTTAAAGCGCACCTACTTGCTTCTAGATTTATTGAAAAGA
38915307 AAAACCAA
1 AAAACCAA
38915315 AATATATTGC
Statistics
Matches: 197, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 197 1.00
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.24
Consensus pattern (191 bp):
AAAACCAACACCAACTCTTGCCATCCCAACATAGTAAAATAATCAACCTTTGCATGCCAAGGGAT
TCGAACCAAAGTCCTCTCACATGCCAACTCACGCCACCACTATTAGGCCATCAACTCATTTGTGT
CATAAATCCAACACATTAAACTTTAAAGCGCACCTACTTGCTTCTAGATTTATTGAAAAGA
Found at i:38917675 original size:29 final size:29
Alignment explanation
Indices: 38917643--38917729 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
38917633 GGCCTAACAA
*
38917643 GCCATATAAATGTGATTTGGGCCTAATTG
1 GCCATATAAATGTGATTTGGGCCTAATGG
* * *
38917672 GCCATATACAGGTGATTTGGGCCAAATGG
1 GCCATATAAATGTGATTTGGGCCTAATGG
* * *
38917701 GCCATATGAATATGA-TTGGGCTTAATGG
1 GCCATATAAATGTGATTTGGGCCTAATGG
38917729 G
1 G
38917730 TCAGATACAG
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 12 0.25
29 36 0.75
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (29 bp):
GCCATATAAATGTGATTTGGGCCTAATGG
Found at i:38926154 original size:28 final size:28
Alignment explanation
Indices: 38926089--38926189 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
38926079 ATAGTGAATC
*
38926089 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
38926118 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
38926146 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
38926176 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38926190 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:38932809 original size:20 final size:20
Alignment explanation
Indices: 38932784--38932850 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
38932774 GATATGCTAT
*
38932784 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
38932804 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
38932824 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
38932844 ACATGAT
1 ACATGAT
38932851 GTATTCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:38932943 original size:25 final size:24
Alignment explanation
Indices: 38932902--38932982 Score: 110
Period size: 24 Copynumber: 3.3 Consensus size: 24
38932892 GGAAGTGCAG
38932902 AAGGGCTTATGCCCCAGTTTATTGAA
1 AAGGGCTT-TGCCCCAGTTTATT-AA
*
38932928 AAGGGCTTTGCCCCAGTTTATCAA
1 AAGGGCTTTGCCCCAGTTTATTAA
*
38932952 AAGGGTTTTGCCCCAG-TTATTAA
1 AAGGGCTTTGCCCCAGTTTATTAA
38932975 AAGAGGCT
1 AAG-GGCT
38932983 AGGCCTCCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.18
24 20 0.40
25 13 0.26
26 8 0.16
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (24 bp):
AAGGGCTTTGCCCCAGTTTATTAA
Found at i:38933229 original size:31 final size:31
Alignment explanation
Indices: 38933192--38933255 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
38933182 CCATTAAACG
38933192 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* *
38933223 AAAGGCTTCGGCCCAGTATTATGCAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
38933254 AA
1 AA
38933256 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:38935664 original size:40 final size:40
Alignment explanation
Indices: 38935579--38935729 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
38935569 AATTGAATGA
* * *
38935579 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
38935619 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
38935660 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
38935699 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
38935730 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:38935743 original size:40 final size:40
Alignment explanation
Indices: 38935616--38935745 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
38935606 ATGCTGGAAA
* * * *
38935616 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
38935656 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
38935696 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
38935736 TTATATCCGG
1 TTATATCCGG
38935746 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:38940983 original size:30 final size:30
Alignment explanation
Indices: 38940947--38941047 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
38940937 GACAAGATTG
* * *
38940947 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
38940977 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
38941005 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
38941034 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38941048 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:38941059 original size:29 final size:28
Alignment explanation
Indices: 38940976--38941051 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
38940966 AAAATTGTAC
* *
38940976 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
38941004 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
38941033 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
38941052 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:38947158 original size:20 final size:20
Alignment explanation
Indices: 38947149--38947199 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
38947139 TTGATATTAT
38947149 ATGCACATGATATGTATAAA
1 ATGCACATGATATGTATAAA
*
38947169 ATGCACATGATATGTATGAA
1 ATGCACATGATATGTATAAA
38947189 ATGCACATGAT
1 ATGCACATGAT
38947200 GTATTCATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (20 bp):
ATGCACATGATATGTATAAA
Found at i:38948126 original size:143 final size:143
Alignment explanation
Indices: 38947918--38948212 Score: 563
Period size: 143 Copynumber: 2.1 Consensus size: 143
38947908 TGAGTTAAAT
*
38947918 TTCGGCCATGCATGTTGTTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
* *
38947983 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCCTTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAAATTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
38948048 GTGTGCATGAGTA
131 GTGTGCATGAGTA
38948061 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
38948126 GAGTGAGTTCGAATGTTTAACAAAAAGGAAAATTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAAATTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
38948191 GTGTGCATGAGTA
131 GTGTGCATGAGTA
38948204 TTCGGCCAT
1 TTCGGCCAT
38948213 ATGGGGTATA
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 149 1.00
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (143 bp):
TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
GAGTGAGTTCGAATGTTTAACAAAAAGGAAAATTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
GTGTGCATGAGTA
Found at i:38948728 original size:29 final size:29
Alignment explanation
Indices: 38948695--38948826 Score: 156
Period size: 29 Copynumber: 4.6 Consensus size: 29
38948685 GTGACGAGAT
*
38948695 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
38948724 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
38948753 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
** * **
38948782 TAACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
38948811 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
38948827 AGCTCGAAGG
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:38950313 original size:25 final size:24
Alignment explanation
Indices: 38950285--38950354 Score: 106
Period size: 24 Copynumber: 2.9 Consensus size: 24
38950275 ACAGCTTATG
38950285 CCCCAGTTTATTGAAAAGGGCTTTA
1 CCCCAGTTTATT-AAAAGGGCTTTA
*
38950310 CCCCAGTTTATCAAAAGGGCTTTA
1 CCCCAGTTTATTAAAAGGGCTTTA
38950334 CCCCAG-TTATTAAAAGAGGCT
1 CCCCAGTTTATTAAAAG-GGCT
38950355 AGGCCTCCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
23 9 0.21
24 22 0.52
25 11 0.26
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
CCCCAGTTTATTAAAAGGGCTTTA
Found at i:38950601 original size:31 final size:31
Alignment explanation
Indices: 38950564--38950655 Score: 103
Period size: 38 Copynumber: 2.7 Consensus size: 31
38950554 CCGTTAAACG
38950564 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
38950595 AAAGGCTTCGGCCCAGTGTTATGCAATATGAAATATGA
1 AAAGGCTTCGGCCCA--G---T--AATATGAAATATGA
*
38950633 AAAGGCTTTGGCCCAGTAGATAT
1 AAAGGCTTCGGCCCAGTA-ATAT
38950656 CGAGATTGGT
Statistics
Matches: 52, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
31 16 0.31
32 4 0.08
33 2 0.04
36 2 0.04
38 28 0.54
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:38960475 original size:12 final size:12
Alignment explanation
Indices: 38960443--38960475 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
38960433 TAGTTAGAAA
*
38960443 AAGAAATTATTG
1 AAGAAATTGTTG
38960455 AAGAAATTGTTG
1 AAGAAATTGTTG
38960467 AAGAAATTG
1 AAGAAATTG
38960476 GGTAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (12 bp):
AAGAAATTGTTG
Found at i:38963335 original size:40 final size:40
Alignment explanation
Indices: 38963281--38963358 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
38963271 CGGATGTAAC
38963281 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
38963321 AACCTGCACGAATGCCTTCGGGACTTAACCCGGTTATA
1 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATA
38963359 TTTTTTTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (40 bp):
AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:38973805 original size:39 final size:40
Alignment explanation
Indices: 38973627--38973809 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
38973617 CCGCACCAAG
* * * * * * * *
38973627 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * *
38973667 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT
*
38973707 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * * *
38973747 GCCTTCGGGTCTTAACCCGGATATAATTTC-AGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* *
38973786 GTCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
38973810 CATTCAATTT
Statistics
Matches: 122, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 31 0.25
40 89 0.73
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
Found at i:38981792 original size:40 final size:40
Alignment explanation
Indices: 38981718--38981863 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
38981708 CCGCACCAAG
* * * * * *
38981718 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
38981758 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
38981798 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
38981838 GCCTTCGGGTCTTAACCCGGATATAA
1 GCCTTCGGGTCTTAGCCCGGATATAA
38981864 TTTTCAGCAT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:38981878 original size:40 final size:40
Alignment explanation
Indices: 38981750--38981901 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
38981740 ATCACGATTT
* * * * *
38981750 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
38981790 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
* * **
38981830 GCACAATTGCCTTCGGGTCTTAACCCGGATATA-ATTTTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACT-A
* * *
38981870 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
38981902 CATTCAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
39 4 0.04
40 91 0.94
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
Found at i:38983762 original size:44 final size:45
Alignment explanation
Indices: 38983667--38983788 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 45
38983657 GTAATCAAAC
* * *
38983667 ATCGATGCCAGTGTCCCAGACAGGGTCTTACA--CAAAATTAGAT
1 ATCGATGCCAATGTCCTAGACATGGTCTTACATGCAAAATTAGAT
*
38983710 AT-GATGCCAATGTCCTAAACATGGTCTTACATGCAAAA-TAGA-
1 ATCGATGCCAATGTCCTAGACATGGTCTTACATGCAAAATTAGAT
* * * *
38983752 AGTCGATGCCAACGTCATAGACGTGATCTTACATGCA
1 A-TCGATGCCAATGTCCTAGACATGGTCTTACATGCA
38983789 GAACAAATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 26 0.39
43 7 0.11
44 33 0.50
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (45 bp):
ATCGATGCCAATGTCCTAGACATGGTCTTACATGCAAAATTAGAT
Found at i:38987161 original size:42 final size:42
Alignment explanation
Indices: 38987107--38987264 Score: 160
Period size: 42 Copynumber: 3.7 Consensus size: 42
38987097 AACATATACA
* * *
38987107 ATGCCAACGTCCTAGA-GTGGTCTTACATGTAATCAAACATCG
1 ATGCCAATGTCCTAGACATGGTCTTACATGAAATCAAA-ATCG
* * * *
38987149 ATGCCACTGTCCTAGACAGGGTCTTACACGAAATC-AGATACG
1 ATGCCAATGTCCTAGACATGGTCTTACATGAAATCAAAAT-CG
* *
38987191 ATGCCAATGTCCCAAACATGGTCTTACATGCAAAAT-AAAAGTCG
1 ATGCCAATGTCCTAGACATGGTCTTACATG--AAATCAAAA-TCG
*
38987235 ATGCCAATGTCATAGACATGGTCTTACATG
1 ATGCCAATGTCCTAGACATGGTCTTACATG
38987265 TAGAACAAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
41 2 0.02
42 42 0.45
43 14 0.15
44 35 0.37
45 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCTAGACATGGTCTTACATGAAATCAAAATCG
Found at i:38997954 original size:43 final size:42
Alignment explanation
Indices: 38997899--38998011 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
38997889 AACATATACA
* * *
38997899 ATGCCAAC-GTCCCAGA-AGTGGTCTTATATGTAATCAAACATCG
1 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAACA-CG
* *
38997942 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATGAAATACG
1 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAACACG
* * *
38997984 ATGCCAATGTCCCAGACATGGTGTTACA
1 ATGCCACTGTCCCAGACAGGGTCTTACA
38998012 TGCAAAACAG
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 29 0.48
43 29 0.48
44 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAACACG
Found at i:38997997 original size:42 final size:42
Alignment explanation
Indices: 38997894--38998011 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 42
38997884 TAGAGAACAT
* * * * *
38997894 ATACAATGCCAACGTCCCAGA-AGTGGTCTTATATGTAATCAA
1 ATACGATGCCAATGTCCCAGACAG-GGTCTTACACGAAATCAA
* * *
38997936 ACATCGATGCCACTGTCCCAGACAGGGTCTTACACGAAATGAA
1 ATA-CGATGCCAATGTCCCAGACAGGGTCTTACACGAAATCAA
* *
38997979 ATACGATGCCAATGTCCCAGACATGGTGTTACA
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACA
38998012 TGCAAAACAG
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
42 29 0.47
43 31 0.50
44 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACAGGGTCTTACACGAAATCAA
Found at i:39002990 original size:40 final size:40
Alignment explanation
Indices: 39002863--39002992 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
39002853 ATGCTGGAAA
* *
39002863 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
39002903 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
39002943 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
39002983 TTATATCCGG
1 TTATATCCGG
39002993 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:39009053 original size:39 final size:40
Alignment explanation
Indices: 39008976--39009225 Score: 395
Period size: 40 Copynumber: 6.3 Consensus size: 40
39008966 AAACCAAGTA
* * *
39008976 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
39009015 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39009054 CCTTCGGGACTTAGCCCGGATATAGTAAC-CGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39009093 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39009133 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39009173 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39009213 CCTTC-GGACTTAG
1 CCTTCGGGACTTAG
39009226 AATTCAAACA
Statistics
Matches: 199, Mismatches: 7, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
38 4 0.02
39 88 0.44
40 107 0.54
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39011173 original size:24 final size:24
Alignment explanation
Indices: 39011141--39011187 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
39011131 GTGGATCCTT
39011141 TCAAGTTCAGGGGGTAAAAGCAAA
1 TCAAGTTCAGGGGGTAAAAGCAAA
39011165 TCAAGTTCAGGGGGTAAAAGCAA
1 TCAAGTTCAGGGGGTAAAAGCAA
39011188 CCTATAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.30, T:0.17
Consensus pattern (24 bp):
TCAAGTTCAGGGGGTAAAAGCAAA
Found at i:39016733 original size:28 final size:27
Alignment explanation
Indices: 39016668--39016752 Score: 120
Period size: 27 Copynumber: 3.1 Consensus size: 27
39016658 TGGAAGCATC
*
39016668 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
39016695 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
*
39016723 CTGGTGGCTCTGTCACATTATCTGT-T
1 CTGGTGGCTCTGCCACATTATCTGTAT
39016749 CTGG
1 CTGG
39016753 CAGTCATGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 5 0.09
27 32 0.59
28 17 0.31
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:39024316 original size:28 final size:26
Alignment explanation
Indices: 39024285--39024348 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
39024275 AATTACTTGA
**
39024285 ATACCCCTATGTATGGAAAATTACTGTT
1 ATACCCCTA-G-ATGGAAAATTACCATT
* *
39024313 ATACCCCTAGGTGTAAAATTACCATT
1 ATACCCCTAGATGGAAAATTACCATT
39024339 ATACCCCTAG
1 ATACCCCTAG
39024349 GGTTACTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.69
27 1 0.03
28 9 0.28
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (26 bp):
ATACCCCTAGATGGAAAATTACCATT
Found at i:39024493 original size:27 final size:26
Alignment explanation
Indices: 39024453--39024564 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
39024443 AGGAAGCGTC
*
39024453 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
39024480 CTGGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACAT-TATCTGA-T
*
39024507 CTGGTGGCTCTGCCATGATTATCTGTAT
1 CTGGTGGCTCTGCCA-CATTATCTG-AT
* ** *
39024535 CTGGTGACTCTATCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
39024561 CTGG
1 CTGG
39024565 CAGTCATGCT
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
26 8 0.11
27 49 0.67
28 15 0.21
29 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:39024557 original size:54 final size:54
Alignment explanation
Indices: 39024453--39024564 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
39024443 AGGAAGCGTC
* *
39024453 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTATT
* ** * *
39024507 CTGGTGGCTCTGCCATGATTATCTGTATCTGGTGACTCTATCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTACCACATATATCTATT
39024561 CTGG
1 CTGG
39024565 CAGTCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTATT
Found at i:39028150 original size:28 final size:28
Alignment explanation
Indices: 39028110--39028206 Score: 122
Period size: 28 Copynumber: 3.5 Consensus size: 28
39028100 AGCTATGGAC
*
39028110 GGCACTTAGTGTGCAAGATATCGAGTGT
1 GGCACTTAGTGTGCGAGATATCGAGTGT
* * *
39028138 GGCACTTAGTGTGTGAGATACCAAGTGT
1 GGCACTTAGTGTGCGAGATATCGAGTGT
* * * *
39028166 GGCCCTTAGTGTGCGAGATATTGAATAT
1 GGCACTTAGTGTGCGAGATATCGAGTGT
39028194 GGCACTTAGTGTG
1 GGCACTTAGTGTG
39028207 TGAGGCATTG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAGATATCGAGTGT
Found at i:39029615 original size:22 final size:20
Alignment explanation
Indices: 39029585--39029628 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
39029575 AATTTATGTG
*
39029585 AATGAATGCTTTATGCTTGATA
1 AATGAATGCTATATG-TTG-TA
*
39029607 AATGTATGCTATATGTTGTA
1 AATGAATGCTATATGTTGTA
39029627 AA
1 AA
39029629 ATGATCGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (20 bp):
AATGAATGCTATATGTTGTA
Found at i:39032425 original size:56 final size:56
Alignment explanation
Indices: 39032358--39032468 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
39032348 TCTTACATGT
*
39032358 AATCACATATCGATGCCAACATACTAGACGTGGTCTTACTCGCACACATATATCGG
1 AATCACATATCGATGCCAACATACTAAACGTGGTCTTACTCGCACACATATATCGG
*
39032414 AATCACATATCGATGCCAACATATTAAACGTGGTCTTACTCGCACACATATATCG
1 AATCACATATCGATGCCAACATACTAAACGTGGTCTTACTCGCACACATATATCG
39032469 ATGCCATGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (56 bp):
AATCACATATCGATGCCAACATACTAAACGTGGTCTTACTCGCACACATATATCGG
Found at i:39034982 original size:47 final size:46
Alignment explanation
Indices: 39034913--39035036 Score: 139
Period size: 45 Copynumber: 2.7 Consensus size: 46
39034903 ATATTTGAGT
* * *
39034913 TCCGAGCTTGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGGC
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTGATGATGCGAA-T--GC
* *
39034959 ATCCGAGCTCGTTGAGTTGAGTCCGAATTCACTTATGATGCGAATGC
1 -TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTGATGATGCGAATGC
39035006 T-CGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
39035037 TATGGGCGGG
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
45 29 0.43
46 1 0.01
47 29 0.43
48 2 0.03
49 5 0.07
50 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTGATGATGCGAATGC
Found at i:39039439 original size:46 final size:46
Alignment explanation
Indices: 39039391--39039572 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
39039381 GCTCTCTGAT
* * *
39039391 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
39039437 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAGCCTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
39039483 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
39039529 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
39039573 TTAAAGATAA
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 120 0.99
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:39039553 original size:92 final size:92
Alignment explanation
Indices: 39039386--39039557 Score: 265
Period size: 92 Copynumber: 1.9 Consensus size: 92
39039376 AGTGTGCTCT
* ** * * *
39039386 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGATATGAAATGTGTAAG
1 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAG
*
39039451 ACCATGGTTGAAAGATACCATGACAGC
66 ACCATAGTTGAAAGATACCATGACAGC
39039478 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAA
1 CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAA
39039542 GACCATAGTTGAAAGA
65 GACCATAGTTGAAAGA
39039558 CACTATGGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 1 0.01
92 71 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (92 bp):
CTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAG
ACCATAGTTGAAAGATACCATGACAGC
Found at i:39052105 original size:2 final size:2
Alignment explanation
Indices: 39052098--39052126 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39052088 ACACGGCCGA
39052098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39052127 ACATCATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39053322 original size:5 final size:5
Alignment explanation
Indices: 39053306--39053342 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
39053296 AGAGTTTTTT
*
39053306 GGCCC GGGCCC GGCCC GGCCC AGCCC GGCCC GGCCC G
1 GGCCC -GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC G
39053343 AATTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.03, C:0.57, G:0.41, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:39053383 original size:15 final size:16
Alignment explanation
Indices: 39053360--39053397 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
39053350 TATTAATATA
*
39053360 TTTATTTATTTT-ATT
1 TTTAATTATTTTAATT
39053375 TTTAATTATTTTAAATT
1 TTTAATTATTTT-AATT
39053392 TTTAAT
1 TTTAAT
39053398 ATAACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTATTTTAATT
Found at i:39053483 original size:22 final size:21
Alignment explanation
Indices: 39053447--39053502 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
39053437 TTAAGAATTG
* *
39053447 TTTTAGTA-TTATTTTTATTT
1 TTTTAATATTTATTTTTATGT
39053467 ATTTTAATATTTATTTTTATGT
1 -TTTTAATATTTATTTTTATGT
*
39053489 TTTTAA-ATATATTT
1 TTTTAATATTTATTT
39053503 GATTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 13 0.42
22 11 0.35
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTAATATTTATTTTTATGT
Found at i:39062494 original size:20 final size:19
Alignment explanation
Indices: 39062471--39062530 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 19
39062461 TAAACATGGT
39062471 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
39062490 CATGTATGATATGCACATG-
1 -ATGTATGATATGCACATGA
39062509 A--TATGATATGCACATG-
1 ATGTATGATATGCACATGA
39062525 ATGTAT
1 ATGTAT
39062531 TTATAAATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
16 16 0.42
18 4 0.11
20 18 0.47
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (19 bp):
ATGTATGATATGCACATGA
Found at i:39062515 original size:16 final size:16
Alignment explanation
Indices: 39062475--39062526 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
39062465 CATGGTATGT
*
39062475 ATGATATGCACATG-AC
1 ATGATATG-ATATGCAC
39062491 ATG-TATGATATGCAC
1 ATGATATGATATGCAC
39062506 ATGATATGATATGCAC
1 ATGATATGATATGCAC
39062522 ATGAT
1 ATGAT
39062527 GTATTTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
14 4 0.12
15 9 0.27
16 20 0.61
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGATATGATATGCAC
Found at i:39062603 original size:24 final size:24
Alignment explanation
Indices: 39062576--39062743 Score: 214
Period size: 24 Copynumber: 7.0 Consensus size: 24
39062566 GAGGAAGTGC
*
39062576 AAAAGGGCTTATGCCTCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
39062600 AAAAAGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
39062624 AAAAGGGGTTATGCCCTAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
*
39062648 AACAA-GGCTTATGCCCCAGTTATC
1 AA-AAGGGCTTATGCCCCAGTTATT
39062672 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
39062696 AAAAGGGCTTTTGCACCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
39062720 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39062744 ATGATAAAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.02
24 109 0.88
25 13 0.10
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:39068957 original size:70 final size:71
Alignment explanation
Indices: 39068806--39068968 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
39068796 GAGATGTATC
39068806 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39068871 AGGACA
66 AGGACA
39068877 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
39068941 CGGACA
66 AGGACA
39068947 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39068969 AGACAAATCG
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39076529 original size:70 final size:71
Alignment explanation
Indices: 39076379--39076541 Score: 319
Period size: 70 Copynumber: 2.3 Consensus size: 71
39076369 GAGATGTATC
39076379 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39076444 AGGACA
66 AGGACA
39076450 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39076514 AGGACA
66 AGGACA
39076520 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39076542 AGACAAATCG
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 52 0.57
71 40 0.43
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39082742 original size:29 final size:29
Alignment explanation
Indices: 39082709--39082811 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
39082699 GTGACGAGAT
39082709 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
39082738 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** *
39082767 TAGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
39082796 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
39082812 AGCTCGGAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:39084420 original size:20 final size:20
Alignment explanation
Indices: 39084397--39084435 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39084387 TAAACATGGT
39084397 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
39084417 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
39084436 TGTATTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:39084622 original size:25 final size:24
Alignment explanation
Indices: 39084486--39084631 Score: 204
Period size: 24 Copynumber: 6.0 Consensus size: 24
39084476 GAGGAAGTGC
*
39084486 AAAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
39084510 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
39084534 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
39084558 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
39084582 AAAAGGGCTTTTGGCCCCCAGTTATT
1 AAAAGGGCTTAT-G-CCCCAGTTATT
*
39084608 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39084632 ATGATAAAGC
Statistics
Matches: 112, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
24 83 0.74
25 10 0.09
26 16 0.14
27 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:39090958 original size:16 final size:16
Alignment explanation
Indices: 39090937--39090973 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
39090927 TTATTTATCA
39090937 GATATTTCATTAATCC
1 GATATTTCATTAATCC
39090953 GATATTTCATTAATCC
1 GATATTTCATTAATCC
39090969 GATAT
1 GATAT
39090974 CTTTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.43
Consensus pattern (16 bp):
GATATTTCATTAATCC
Found at i:39095126 original size:18 final size:19
Alignment explanation
Indices: 39095088--39095126 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
39095078 TGGTTCAAGC
*
39095088 TTTCAATCTCATATCTCAA
1 TTTCAATCTCACATCTCAA
*
39095107 TTTCAAT-TCACATTTCAA
1 TTTCAATCTCACATCTCAA
39095125 TT
1 TT
39095127 CTTAATTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCACATCTCAA
Found at i:39097358 original size:40 final size:40
Alignment explanation
Indices: 39097240--39097445 Score: 195
Period size: 40 Copynumber: 5.2 Consensus size: 40
39097230 AATGATACCT
*
39097240 GGGCTAAGTCCCGAAGGCATTTATGCTAGTGAAT-ATATCC
1 GGGCTAAGACCCGAAGGCATTTATGCTAGTG-ATCATATCC
* * *
39097280 GAGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCC
1 GGGCTAAGACCCGAAGGCATTTATGCTAGTGATCATATCC
** *
39097320 GGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TCATATCC
1 GGGCTAAGACCCGAAGGCATTTATGCTAG-TGATCATATCC
* * * * *
39097360 GGGCTAAGACCTGAAGGCATTTGTGCAAGAT-ACCAAATCC
1 GGGCTAAGACCCGAAGGCATTTATGCTAG-TGATCATATCC
* * * * * *
39097400 GGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC
1 GGGCTAAGACCCGAAGGCATTTATGCTAGTGATCATATCC
39097440 -GGCTAA
1 GGGCTAA
39097446 ATTCCGAAGA
Statistics
Matches: 139, Mismatches: 23, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
39 8 0.06
40 129 0.93
41 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGACCCGAAGGCATTTATGCTAGTGATCATATCC
Found at i:39098980 original size:45 final size:45
Alignment explanation
Indices: 39098876--39099014 Score: 190
Period size: 45 Copynumber: 3.1 Consensus size: 45
39098866 TAACAGTACG
*
39098876 GTAACAATATCCGACACACAAAGTGCCGAATCGGTAACCTGTAACA
1 GTAACAATATTCGACACACAAAGTGCCGAATCGGTAA-CTGTAACA
* *
39098922 GTAACAATATTCGACACACAGAGTGCTGAATCGGTAA-TGGTAACA
1 GTAACAATATTCGACACACAAAGTGCCGAATCGGTAACT-GTAACA
* * * *
39098967 GTAACAATATTCGACACACAAAGTGTCGAATTGGTAACAGTAGCA
1 GTAACAATATTCGACACACAAAGTGCCGAATCGGTAACTGTAACA
39099012 GTA
1 GTA
39099015 GCGGTAACAG
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
44 1 0.01
45 47 0.57
46 34 0.41
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (45 bp):
GTAACAATATTCGACACACAAAGTGCCGAATCGGTAACTGTAACA
Found at i:39099002 original size:39 final size:41
Alignment explanation
Indices: 39098876--39099008 Score: 112
Period size: 46 Copynumber: 3.1 Consensus size: 41
39098866 TAACAGTACG
* *
39098876 GTAACAATATCCGACACACAAAGTGCCGAATCGGTAACCT-GTAACA
1 GTAACAATATTCGACACACAAAGTGCTGAA---GT-A--TGGTAACA
*
39098922 GTAACAATATTCGACACACAGAGTGCTGAATCGGTAATGGTAACA
1 GTAACAATATTCGACACACAAAGTGCTGAA---GT-ATGGTAACA
39098967 GTAACAATATTCGACACACAAAGTG-TCGAA-T-TGGTAACA
1 GTAACAATATTCGACACACAAAGTGCT-GAAGTATGGTAACA
39099006 GTA
1 GTA
39099009 GCAGTAGCGG
Statistics
Matches: 81, Mismatches: 4, Indels: 11
0.84 0.04 0.11
Matches are distributed among these distances:
39 11 0.14
41 1 0.01
44 2 0.02
45 33 0.41
46 34 0.42
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (41 bp):
GTAACAATATTCGACACACAAAGTGCTGAAGTATGGTAACA
Found at i:39099748 original size:18 final size:17
Alignment explanation
Indices: 39099649--39099757 Score: 56
Period size: 16 Copynumber: 6.7 Consensus size: 17
39099639 ACTAATATCT
*
39099649 TTTCAA-TCAATATACA
1 TTTCAATTCAATTTACA
* *
39099665 TTTCAAAT-AA-TCACA
1 TTTCAATTCAATTTACA
*
39099680 -TTCAATTCAATTT-GA
1 TTTCAATTCAATTTACA
* *
39099695 -TTCAATTCCAA-TCACT
1 TTTCAATT-CAATTTACA
39099711 TTTCCAA-TCAATTTACA
1 TTT-CAATTCAATTTACA
*
39099728 TTTTAATTTCAATTT-CAA
1 TTTCAA-TTCAATTTAC-A
39099746 TTTCAATTCAAT
1 TTTCAATTCAAT
39099758 AACAATTCAC
Statistics
Matches: 70, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
14 6 0.09
15 14 0.20
16 17 0.24
17 17 0.24
18 16 0.23
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTCAATTCAATTTACA
Found at i:39105284 original size:40 final size:40
Alignment explanation
Indices: 39105239--39105406 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39105229 CGGAATACAA
39105239 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
39105279 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
39105319 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
39105359 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
39105399 CCGGATAT
1 CCGGATAT
39105407 CATTCAATTG
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.03
40 100 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:39113330 original size:40 final size:40
Alignment explanation
Indices: 39113285--39113452 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39113275 CGGAATACAA
39113285 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
39113325 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
39113365 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
39113405 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
39113445 CCGGATAT
1 CCGGATAT
39113453 CATTCAATTG
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.03
40 100 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:39118699 original size:40 final size:40
Alignment explanation
Indices: 39118644--39118834 Score: 287
Period size: 40 Copynumber: 4.8 Consensus size: 40
39118634 CGGATGATAA
39118644 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
39118684 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* * *
39118724 CCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* *
39118764 CC-GGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T
* * *
39118803 CAGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
39118835 AGCTATATCC
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
38 1 0.01
39 31 0.23
40 105 0.77
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:39118810 original size:79 final size:80
Alignment explanation
Indices: 39118640--39118827 Score: 290
Period size: 79 Copynumber: 2.4 Consensus size: 80
39118630 TATTCGGATG
* * *
39118640 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCA
*
39118705 TTTGTGCGAGTTACT
66 TTGGTGCGAGTTACT
*
39118720 A-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACCAAATCC-GGCTAAGTCCCGAAGGC
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACCAAATCCGGGCTAAGTCCCGAAGGC
39118783 ATTGGTGCGAGTTACT
65 ATTGGTGCGAGTTACT
* *
39118799 ATAACAGGGCTATGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
39118828 AGCGAGTAGC
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
79 57 0.58
80 41 0.42
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCA
TTGGTGCGAGTTACT
Found at i:39118845 original size:79 final size:78
Alignment explanation
Indices: 39118640--39118860 Score: 284
Period size: 79 Copynumber: 2.8 Consensus size: 78
39118630 TATTCGGATG
39118640 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA-TCC-GGCTAAGTCCCGAAGGCA
*
39118705 TTTGTGCGAGTTACT
64 TTGGTGCGAGTTACT
* * *
39118720 A-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACCAAATCCGGCTAAGTCCCGAAGGCA
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAATCCGGCTAAGTCCCGAAGGCA
39118784 TTGGTGCGAGTTACT
64 TTGGTGCGAGTTACT
* * * * * *
39118799 ATAACAGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGGTTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTA-ATCCGGCTAAGTCCCGAAGG
39118861 TACGTGATTT
Statistics
Matches: 123, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
78 4 0.03
79 78 0.63
80 38 0.31
81 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCCGGCTAAGTCCCGAAGGCATT
GGTGCGAGTTACT
Found at i:39121542 original size:40 final size:40
Alignment explanation
Indices: 39121487--39121654 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 40
39121477 TGAATGATAC
* *
39121487 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
39121527 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
39121567 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
39121607 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
39121647 CC-GGCTAA
1 CCGGGCTAA
39121655 ATTTCGAAGA
Statistics
Matches: 106, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 6 0.06
40 98 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:39123084 original size:40 final size:40
Alignment explanation
Indices: 39123029--39123208 Score: 263
Period size: 40 Copynumber: 4.5 Consensus size: 40
39123019 GGGTGTTACA
*
39123029 CCGAAGGCAGTTGTGCGAGTTACCAAATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTC
* *
39123069 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTC
*
39123109 CCGAAGGCATTTGTGCGAGTTACCAAATCCTGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTC
* * * *
39123149 CCGAAGGCATTGGTGCGAGTTACTATAA-CCGGGCTATGTT
1 CCGAAGGCATTTGTGCGAGTTACCA-AATCCGGGCTAAGTC
*
39123189 CCGAAGGCATTTGAGCGAGT
1 CCGAAGGCATTTGTGCGAGT
39123209 AGCTATATCT
Statistics
Matches: 126, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
40 124 0.98
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTC
Found at i:39128281 original size:28 final size:28
Alignment explanation
Indices: 39128249--39128347 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
39128239 TGCATAAGCC
*
39128249 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
39128277 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
39128305 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
39128334 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39128348 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:39135950 original size:28 final size:28
Alignment explanation
Indices: 39135918--39136016 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
39135908 TGCATAAGCC
*
39135918 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
39135946 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
39135974 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
39136003 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39136017 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:39141989 original size:49 final size:49
Alignment explanation
Indices: 39141928--39142279 Score: 563
Period size: 49 Copynumber: 7.3 Consensus size: 49
39141918 ATGTATGAGA
39141928 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39141977 TATATATATGTGATAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
39142026 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39142075 TATATATATGTGATAAGGCCTAATGGCCGATGTGAAGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39142124 CATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-G
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * *
39142171 TGTATATATGTGATAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * *
39142220 --TATATACGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
39142267 TATA-A-ATGTGATA
1 TATATATATGTGATA
39142280 TGTTCCGAAG
Statistics
Matches: 285, Mismatches: 14, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
47 90 0.32
48 7 0.02
49 188 0.66
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (49 bp):
TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:39155799 original size:34 final size:34
Alignment explanation
Indices: 39155756--39155822 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
39155746 TTATTAGTCA
39155756 TTTGAAGTATAAGGAACGGAATGTATTTGAGGAG
1 TTTGAAGTATAAGGAACGGAATGTATTTGAGGAG
39155790 TTTGAAGTATAAGGAACGGAATGTATTTGAGGA
1 TTTGAAGTATAAGGAACGGAATGTATTTGAGGA
39155823 TTGTTTGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.30
Consensus pattern (34 bp):
TTTGAAGTATAAGGAACGGAATGTATTTGAGGAG
Found at i:39156551 original size:21 final size:21
Alignment explanation
Indices: 39156525--39156565 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39156515 CTTGCAAAGA
*
39156525 AAAAAAAATTCTTCTCGTCGG
1 AAAAAAAATTCCTCTCGTCGG
*
39156546 AAAAAAATTTCCTCTCGTCG
1 AAAAAAAATTCCTCTCGTCG
39156566 AATTAGATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAAAAAATTCCTCTCGTCGG
Found at i:39157364 original size:13 final size:13
Alignment explanation
Indices: 39157346--39157370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39157336 TCAAAGAAAC
39157346 ATTGTTGTCAAAA
1 ATTGTTGTCAAAA
39157359 ATTGTTGTCAAA
1 ATTGTTGTCAAA
39157371 CGGTCAAAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
ATTGTTGTCAAAA
Found at i:39162394 original size:2 final size:2
Alignment explanation
Indices: 39162387--39162430 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
39162377 AATGTCATAC
*
39162387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
39162430 A
1 A
39162431 CAATTCACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39164820 original size:17 final size:17
Alignment explanation
Indices: 39164798--39164922 Score: 70
Period size: 17 Copynumber: 7.5 Consensus size: 17
39164788 TATCAAGATA
*
39164798 AATATTAGATTAAATTT
1 AATATTAAATTAAATTT
39164815 AATATTAAATTAAA-TT
1 AATATTAAATTAAATTT
39164831 AA-ATT-AA-TAGAATATT
1 AATATTAAATTA-AAT-TT
* * * *
39164847 TATA-TACA--AGA-TA
1 AATATTAAATTAAATTT
*
39164860 AAAATTAAATTAAATTT
1 AATATTAAATTAAATTT
*
39164877 AATAATAAGA-TAATCACTTT
1 AATATTAA-ATTAA--A-TTT
39164897 AATATTAAATTAAATTT
1 AATATTAAATTAAATTT
39164914 AATATTAAA
1 AATATTAAA
39164923 CCTATTAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 28
0.66 0.11 0.23
Matches are distributed among these distances:
13 5 0.06
14 7 0.09
15 4 0.05
16 11 0.14
17 37 0.46
18 2 0.02
19 2 0.02
20 13 0.16
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.40
Consensus pattern (17 bp):
AATATTAAATTAAATTT
Found at i:39168607 original size:9 final size:9
Alignment explanation
Indices: 39168591--39168624 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39168581 TTTATTAATA
39168591 AATTAATTT
1 AATTAATTT
*
39168600 AGTTAATTT
1 AATTAATTT
*
39168609 AAATAATTT
1 AATTAATTT
39168618 AATTAAT
1 AATTAAT
39168625 ACATTAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
AATTAATTT
Found at i:39168617 original size:18 final size:19
Alignment explanation
Indices: 39168589--39168624 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39168579 TATTTATTAA
*
39168589 TAAATTAATTTAGTTAATT
1 TAAATTAATTTAATTAATT
39168608 TAAA-TAATTTAATTAAT
1 TAAATTAATTTAATTAAT
39168625 ACATTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TAAATTAATTTAATTAATT
Found at i:39171298 original size:37 final size:37
Alignment explanation
Indices: 39171248--39171332 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
39171238 GGAATATGTT
*
39171248 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
39171285 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
39171322 CCGGGTAAGAC
1 CCGGGTAAGAC
39171333 TTCTTTTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:39173429 original size:29 final size:29
Alignment explanation
Indices: 39173387--39173492 Score: 194
Period size: 29 Copynumber: 3.7 Consensus size: 29
39173377 GCGAATGATT
39173387 GAGGCACTATGTGTGCGAGATCAGTAATC
1 GAGGCACTATGTGTGCGAGATCAGTAATC
39173416 GAGGCACTATGTGTGCGAGATCAGTAATC
1 GAGGCACTATGTGTGCGAGATCAGTAATC
*
39173445 GAGGCACTATGTGTGCGAGATCAGTAATT
1 GAGGCACTATGTGTGCGAGATCAGTAATC
*
39173474 GAGGCACTGTGTGTGCGAG
1 GAGGCACTATGTGTGCGAG
39173493 TTTTTCAACA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (29 bp):
GAGGCACTATGTGTGCGAGATCAGTAATC
Found at i:39174074 original size:40 final size:41
Alignment explanation
Indices: 39173976--39174074 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
39173966 TTCGAATGGT
* ** * *
39173976 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTTACTAA
1 ATCCGGGCTATGTCCCGAAGGCAATTGTGCGAAGTAACTAA
39174017 ATCCGGGCTAAT-TCCCGAAGGCAATTGTGCGAA-TAACTATA
1 ATCCGGGCT-ATGTCCCGAAGGCAATTGTGCGAAGTAACTA-A
39174058 A-CCGGGCTATGTCCCGA
1 ATCCGGGCTATGTCCCGA
39174075 GGACAATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 2 0.04
40 18 0.36
41 29 0.58
42 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.25
Consensus pattern (41 bp):
ATCCGGGCTATGTCCCGAAGGCAATTGTGCGAAGTAACTAA
Found at i:39177016 original size:37 final size:37
Alignment explanation
Indices: 39176966--39177050 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
39176956 GGAATATGTT
*
39176966 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
39177003 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
39177040 CCGGGTAAGAC
1 CCGGGTAAGAC
39177051 TTCTTTTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:39179401 original size:13 final size:13
Alignment explanation
Indices: 39179385--39179409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39179375 CAAGAATTGC
39179385 ACACAAGTGCCAT
1 ACACAAGTGCCAT
39179398 ACACAAGTGCCA
1 ACACAAGTGCCA
39179410 ACTATATTCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.16, T:0.12
Consensus pattern (13 bp):
ACACAAGTGCCAT
Found at i:39180862 original size:28 final size:29
Alignment explanation
Indices: 39180813--39180868 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
39180803 TATAGGGGTT
39180813 TTCACACAGCCAAGCACACGCCCGTGTCC
1 TTCACACAGCCAAGCACACGCCCGTGTCC
* * *
39180842 TTCACACGGCCTAG-ACACGCCTGTGTC
1 TTCACACAGCCAAGCACACGCCCGTGTC
39180869 TAAAAACTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.21, C:0.41, G:0.20, T:0.18
Consensus pattern (29 bp):
TTCACACAGCCAAGCACACGCCCGTGTCC
Found at i:39182744 original size:16 final size:16
Alignment explanation
Indices: 39182723--39182754 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39182713 ACATTACCCA
39182723 AGCCTAGCCGAATGTT
1 AGCCTAGCCGAATGTT
39182739 AGCCTAGCCGAATGTT
1 AGCCTAGCCGAATGTT
39182755 CTTTCCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (16 bp):
AGCCTAGCCGAATGTT
Found at i:39197730 original size:6 final size:6
Alignment explanation
Indices: 39197702--39197781 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
39197692 TAAACCTAAT
* * *
39197702 ATTAAA AGTAAA AATATAG ATTAAA ATTAAA ATT-AA ATTCAAA ATTAAA
1 ATTAAA ATTAAA ATTA-AA ATTAAA ATTAAA ATTAAA ATT-AAA ATTAAA
* * * *
39197751 ATTAAA AATAAA AATAAA ACTAAA AGTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA A
39197782 ATTTTAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
5 5 0.08
6 49 0.78
7 9 0.14
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.26
Consensus pattern (6 bp):
ATTAAA
Found at i:39199483 original size:49 final size:47
Alignment explanation
Indices: 39199332--39199534 Score: 192
Period size: 49 Copynumber: 4.2 Consensus size: 47
39199322 TATGTGTCAA
** * * * * *
39199332 TGTAAGACCTGCCTGGGAGACGGCATTGACATAGATAAGTGAGAGCCAG
1 TGTAAGACCTATCTGGGACATGGCATCGACTTAGAT--GTAAGAGCCAG
* ** * *
39199381 TGTAAGACCTGTCTGGGACATGGCATCGACACAGATAAGTGAGAGCCAA
1 TGTAAGACCTATCTGGGACATGGCATCGACTTAGAT--GTAAGAGCCAG
* * *
39199430 TGTAAGACCTATCTGGGACATGGCATCAGCCTT-GATGTACGTAAGTCAG
1 TGTAAGACCTATCTGGGACATGGCATC-GACTTAGATGTAAG--AGCCAG
*
39199479 TGTAAGACCTGTCTGGGACATGGCATCGACTTAGATGTAAGAGCCAG
1 TGTAAGACCTATCTGGGACATGGCATCGACTTAGATGTAAGAGCCAG
39199526 TGTAAGACC
1 TGTAAGACC
39199535 ATGTTTGAAA
Statistics
Matches: 132, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
47 17 0.13
48 4 0.03
49 109 0.83
50 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.22
Consensus pattern (47 bp):
TGTAAGACCTATCTGGGACATGGCATCGACTTAGATGTAAGAGCCAG
Found at i:39203578 original size:27 final size:28
Alignment explanation
Indices: 39203548--39203617 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
39203538 ATAATAAGTC
*
39203548 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
39203575 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
39203603 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39203618 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:39211498 original size:27 final size:28
Alignment explanation
Indices: 39211468--39211537 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
39211458 ATAATAAGTC
*
39211468 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
39211495 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
39211523 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39211538 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:39219149 original size:14 final size:11
Alignment explanation
Indices: 39219119--39219149 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
39219109 CATGTAAATG
39219119 ACATAATAACC
1 ACATAATAACC
39219130 ACATAATAACC
1 ACATAATAACC
39219141 ACATAATAA
1 ACATAATAA
39219150 GGCTAAACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (11 bp):
ACATAATAACC
Found at i:39221795 original size:24 final size:24
Alignment explanation
Indices: 39221758--39221808 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
39221748 ATAGGCTATG
*
39221758 ACAGGTGCACGAGCCTCGGGTCTA
1 ACAGGTGCACGAGCCTCGAGTCTA
* *
39221782 ACAGGTGTATGAGCCTCGAGTCTA
1 ACAGGTGCACGAGCCTCGAGTCTA
39221806 ACA
1 ACA
39221809 ATTGTATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (24 bp):
ACAGGTGCACGAGCCTCGAGTCTA
Found at i:39221814 original size:24 final size:24
Alignment explanation
Indices: 39221768--39221815 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39221758 ACAGGTGCAC
* *
39221768 GAGCCTCGGGTCTAACAGGTGTAT
1 GAGCCTCGAGTCTAACAAGTGTAT
*
39221792 GAGCCTCGAGTCTAACAATTGTAT
1 GAGCCTCGAGTCTAACAAGTGTAT
39221816 CTTTTGTTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (24 bp):
GAGCCTCGAGTCTAACAAGTGTAT
Found at i:39226979 original size:142 final size:142
Alignment explanation
Indices: 39226718--39226999 Score: 363
Period size: 142 Copynumber: 2.0 Consensus size: 142
39226708 TGGGTGATAT
* * **
39226718 GTGTGTCAGTGTAATACCTGTCTGGGACACGGCATCGACACAGCTAAGTGCGAGCCAGTGTAAGA
1 GTGTGTCAGTGTAAGACCTGTCTGGGACACGGCATCGACACAGATAAGTAAGAGCCAGTGTAAGA
* * **
39226783 CTAGTCTAGAACATGGTATCGGCCTCAAGATATGCAAGCTAGTGTAAGGTCTGTCTGGGACATGG
66 CTAGTCTAGAACATGGCATCGACCTCAAGATATGCAAGCTAGTGTAAGACCTGTCTGGGACATGG
*
39226848 CATCGGCTTAAG
131 CATCGACTTAAG
* * * * *
39226860 GTGTGTTAGTGTAAGACCTGTTTGGGACATGGCATTGACACAGATAAGTAAGAGCCCGTGTAAGA
1 GTGTGTCAGTGTAAGACCTGTCTGGGACACGGCATCGACACAGATAAGTAAGAGCCAGTGTAAGA
* * *
39226925 CCT-GTCTAGGACATGGCATCGACCTCGATG-TATGTAAG-TCAGTGTAAGACCTGTCTGGGACA
66 -CTAGTCTAGAACATGGCATCGACCTC-AAGATATGCAAGCT-AGTGTAAGACCTGTCTGGGACA
39226987 TGGCATCGACTTA
128 TGGCATCGACTTA
39227000 GATGTGAGAG
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
141 1 0.01
142 115 0.96
143 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (142 bp):
GTGTGTCAGTGTAAGACCTGTCTGGGACACGGCATCGACACAGATAAGTAAGAGCCAGTGTAAGA
CTAGTCTAGAACATGGCATCGACCTCAAGATATGCAAGCTAGTGTAAGACCTGTCTGGGACATGG
CATCGACTTAAG
Found at i:39227004 original size:49 final size:48
Alignment explanation
Indices: 39226823--39227001 Score: 161
Period size: 49 Copynumber: 3.8 Consensus size: 48
39226813 TATGCAAGCT
** * * *
39226823 AGTGTAAGGTCTGTCTGGGACATGGCATCGGCTTA-AG-GTGT--GTT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGAGTATGTAAGTC
* * ** * *
39226867 AGTGTAAGACCTGTTTGGGACATGGCATTGACACAGA-TAAGTAAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGAGTATGT-A-AGTC
* * * *
39226916 CGTGTAAGACCTGTCTAGGACATGGCATCGACCTCGATGTATGTAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGA-GTATGTAAGTC
39226965 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGA
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGA
39227002 TGTGAGAGCT
Statistics
Matches: 103, Mismatches: 24, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
44 28 0.27
45 3 0.03
49 67 0.65
50 1 0.01
51 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGAGTATGTAAGTC
Found at i:39230597 original size:30 final size:30
Alignment explanation
Indices: 39230553--39230636 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
39230543 GAACTTCCAC
*
39230553 AAGGGCTGGGCACATGCCCGTGTGAGCCAT
1 AAGGGCTGGCCACATGCCCGTGTGAGCCAT
* *
39230583 AAGGGTTGGCCACATGCCCGTGTGAGCCAC
1 AAGGGCTGGCCACATGCCCGTGTGAGCCAT
* *
39230613 ACA-GGCTGGCCATACGCCCGTGTG
1 A-AGGGCTGGCCACATGCCCGTGTG
39230637 CCAGCCCGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 46 0.98
31 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.35, T:0.17
Consensus pattern (30 bp):
AAGGGCTGGCCACATGCCCGTGTGAGCCAT
Found at i:39231837 original size:17 final size:17
Alignment explanation
Indices: 39231810--39231842 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39231800 TTAGGCTCCA
39231810 AAGTCTTACCACTTTTGT
1 AAGTCTTACCA-TTTTGT
39231828 AAGT-TTACCATTTTG
1 AAGTCTTACCATTTTG
39231843 CAATGCTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
AAGTCTTACCATTTTGT
Found at i:39234137 original size:41 final size:41
Alignment explanation
Indices: 39234090--39234209 Score: 118
Period size: 41 Copynumber: 3.2 Consensus size: 41
39234080 CATCTTCTTT
39234090 TTTTTCATTCTTCTTCCCATTTCCTTCCAACCTTCTCTCTC
1 TTTTTCATTCTTCTTCCCATTTCCTTCCAACCTTCTCTCTC
* * * *
39234131 TTTTTCA---TTC-TCACA--T-C-T-GAAGCATCT-TCT-
1 TTTTTCATTCTTCTTCCCATTTCCTTCCAACCTTCTCTCTC
*
39234161 TTTTTCATTCTTCTTCCCATTTCCTTCCAACCTTCTCCCTC
1 TTTTTCATTCTTCTTCCCATTTCCTTCCAACCTTCTCTCTC
39234202 TTTTTCAT
1 TTTTTCAT
39234210 GCTTTTATCC
Statistics
Matches: 59, Mismatches: 9, Indels: 22
0.66 0.10 0.24
Matches are distributed among these distances:
30 7 0.12
31 3 0.05
32 6 0.10
33 4 0.07
34 5 0.08
35 1 0.02
36 1 0.02
37 5 0.08
38 4 0.07
39 6 0.10
40 2 0.03
41 15 0.25
ACGTcount: A:0.12, C:0.35, G:0.02, T:0.51
Consensus pattern (41 bp):
TTTTTCATTCTTCTTCCCATTTCCTTCCAACCTTCTCTCTC
Found at i:39234203 original size:71 final size:72
Alignment explanation
Indices: 39234047--39234209 Score: 265
Period size: 71 Copynumber: 2.3 Consensus size: 72
39234037 TCAACTTTAC
* * **
39234047 CCTTCTCCCTTTTTTTTATTCTCATGTCTGAAGCATCTTCTTTTTTTTCATTCTTCTTCCCATTT
1 CCTTCTCCCTCTTTTTCATTCTCACATCTGAAGCATCTTC-TTTTTTTCATTCTTCTTCCCATTT
39234112 CCTTCCAA
65 CCTTCCAA
*
39234120 CCTTCTCTCTCTTTTTCATTCTCACATCTGAAGCATCTTC-TTTTTTCATTCTTCTTCCCATTTC
1 CCTTCTCCCTCTTTTTCATTCTCACATCTGAAGCATCTTCTTTTTTTCATTCTTCTTCCCATTTC
39234184 CTTCCAA
66 CTTCCAA
39234191 CCTTCTCCCTCTTTTTCAT
1 CCTTCTCCCTCTTTTTCAT
39234210 GCTTTTATCC
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 49 0.58
73 35 0.42
ACGTcount: A:0.12, C:0.33, G:0.03, T:0.52
Consensus pattern (72 bp):
CCTTCTCCCTCTTTTTCATTCTCACATCTGAAGCATCTTCTTTTTTTCATTCTTCTTCCCATTTC
CTTCCAA
Found at i:39236670 original size:44 final size:44
Alignment explanation
Indices: 39236607--39236691 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
39236597 AATAAGTCTG
39236607 TTTTTCAGTCAGTTTGGTATT-GGCATTAAAAACTTACTGAACTA
1 TTTTTCAGTCAGTTTGGTATTCGG-ATTAAAAACTTACTGAACTA
* *
39236651 TTTTTCAGTCAGTTTGGTATTCTGATTAAAAACTTATTGAA
1 TTTTTCAGTCAGTTTGGTATTCGGATTAAAAACTTACTGAA
39236692 TTAACCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (44 bp):
TTTTTCAGTCAGTTTGGTATTCGGATTAAAAACTTACTGAACTA
Found at i:39237332 original size:33 final size:33
Alignment explanation
Indices: 39237295--39237361 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
39237285 AACTCTTGTT
*
39237295 TCCATCATGTATGTTTGAACTCGATCAAATTGG
1 TCCATCATGGATGTTTGAACTCGATCAAATTGG
* * *
39237328 TCCATCATGGATGTTTGGATTTGATCAAATTGG
1 TCCATCATGGATGTTTGAACTCGATCAAATTGG
39237361 T
1 T
39237362 TGGTTTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (33 bp):
TCCATCATGGATGTTTGAACTCGATCAAATTGG
Found at i:39237850 original size:15 final size:15
Alignment explanation
Indices: 39237830--39237860 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39237820 ATAAAAAATG
39237830 TTATTAAATAATATT
1 TTATTAAATAATATT
*
39237845 TTATTAAATTATATT
1 TTATTAAATAATATT
39237860 T
1 T
39237861 AATAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTAAATAATATT
Found at i:39237853 original size:25 final size:26
Alignment explanation
Indices: 39237809--39237878 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
39237799 TTTAATTCAT
*
39237809 ATAATAATTATATAAAAAATGT-TATTAA
1 ATAATAATTATAT--TAAAT-TATATTAA
* *
39237837 ATAAT-ATTTTATTAAATTATATTTA
1 ATAATAATTATATTAAATTATATTAA
39237862 ATAATAATTATATTAAA
1 ATAATAATTATATTAAA
39237879 ATATGGTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 1 0.03
25 14 0.39
26 10 0.28
27 6 0.17
28 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (26 bp):
ATAATAATTATATTAAATTATATTAA
Found at i:39238080 original size:16 final size:16
Alignment explanation
Indices: 39238059--39238113 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
39238049 TGAATTACTG
*
39238059 ATTACAACTCTGTTCA
1 ATTACAACTCTATTCA
* *
39238075 ATTACAGCCCTATTCA
1 ATTACAACTCTATTCA
* *
39238091 AATACAACTCTATTCC
1 ATTACAACTCTATTCA
39238107 ATTACAA
1 ATTACAA
39238114 TAAACCAAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (16 bp):
ATTACAACTCTATTCA
Found at i:39239443 original size:17 final size:19
Alignment explanation
Indices: 39239421--39239468 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
39239411 AATTCATGTC
39239421 TAAAATTACT-AATT-AAG
1 TAAAATTACTCAATTCAAG
*
39239438 TAAAATTCACTCATTTCAAG
1 TAAAATT-ACTCAATTCAAG
*
39239458 TATAATTACTC
1 TAAAATTACTC
39239469 GAGTAAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 3 0.12
19 7 0.27
20 9 0.35
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (19 bp):
TAAAATTACTCAATTCAAG
Found at i:39242572 original size:14 final size:14
Alignment explanation
Indices: 39242553--39242591 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
39242543 AAAAACTTTA
* *
39242553 TATGCATATGTGTG
1 TATGCAGATGTATG
39242567 TATGCAGATGTATG
1 TATGCAGATGTATG
39242581 TATGCAGATGT
1 TATGCAGATGT
39242592 CCCAATTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (14 bp):
TATGCAGATGTATG
Found at i:39245913 original size:37 final size:36
Alignment explanation
Indices: 39245863--39245949 Score: 129
Period size: 37 Copynumber: 2.3 Consensus size: 36
39245853 TACGAAGTCT
* *
39245863 TACCCGGACATAATCTCTACATGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
39245899 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
39245936 TCACCCGGAACATA
1 T-ACCCGG-ACATA
39245950 TTTCCAAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 1 0.02
37 40 0.87
38 5 0.11
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:39246049 original size:49 final size:49
Alignment explanation
Indices: 39245985--39246143 Score: 264
Period size: 49 Copynumber: 3.2 Consensus size: 49
39245975 CACATGTTAC
*
39245985 ATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCACATATAT
1 ATACATTTTCACATTCATCGCATCGGCCATTAGGCCTCATCACATATAT
* *
39246034 ATACATTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATAC
1 ATACATTTTCACATTCATCGCATCGGCCATTAGGCCTCATCACATATAT
* * *
39246083 ATATATTTTCACATTCATCACATCGACCATTAGGCCTCATCACATATAT
1 ATACATTTTCACATTCATCGCATCGGCCATTAGGCCTCATCACATATAT
39246132 ATACATTTTCAC
1 ATACATTTTCAC
39246144 GAATCTTGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 101 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.34
Consensus pattern (49 bp):
ATACATTTTCACATTCATCGCATCGGCCATTAGGCCTCATCACATATAT
Found at i:39250725 original size:46 final size:46
Alignment explanation
Indices: 39250644--39250852 Score: 180
Period size: 46 Copynumber: 4.5 Consensus size: 46
39250634 AAGTCAATGC
* **
39250644 CATGTCCCAGACATGGTCTTACACTGG--CACATCTCGTAGCTAATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCGTAGCCGATG
* *
39250689 CATGTCCCAAACATGTCTTACACTGGCT-TACATCTCG-AGGTCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCGTA-GCCGATG
* * * *
39250735 CTTG-CCTTAGACATGTCTTACACTAGCTCTCGTCTCAGT-GCCGATG
1 CATGTCC-CAGACATGTCTTACACTGGCTCTCATCTC-GTAGCCGATG
* * * *
39250781 CCATGTCCCAAACATGGTTTTACACTGGCTCTCATAAT-GTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGTAGCCGATG
39250829 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
39250853 AGCACACAAA
Statistics
Matches: 131, Mismatches: 20, Indels: 25
0.74 0.11 0.14
Matches are distributed among these distances:
44 12 0.09
45 16 0.12
46 52 0.40
47 25 0.19
48 25 0.19
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGTAGCCGATG
Found at i:39250805 original size:48 final size:46
Alignment explanation
Indices: 39250745--39250855 Score: 127
Period size: 48 Copynumber: 2.4 Consensus size: 46
39250735 CTTGCCTTAG
* *
39250745 ACATGTCTTACACTAGCTCTCGT-CTCAGT-GCCGATGCCATGTCCCAA
1 ACATGTCTTACACTAGCTCTCATAAT--GTGGCCGATG-CATGTCCCAA
* * *
39250792 ACATGGTTTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAG
1 ACAT-GTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAA
39250839 ACATGTCTTACACTAGC
1 ACATGTCTTACACTAGC
39250856 ACACAAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
46 11 0.20
47 19 0.35
48 23 0.43
49 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (46 bp):
ACATGTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAA
Found at i:39254103 original size:24 final size:24
Alignment explanation
Indices: 39254055--39254103 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
39254045 TTAACATCCT
**
39254055 TTTGTAACAACCTTGTCATTAGAG
1 TTTGTAACAACCTTGTCACCAGAG
*
39254079 TTTGTAACAACCTTGTCACCGGAG
1 TTTGTAACAACCTTGTCACCAGAG
39254103 T
1 T
39254104 GGCTATCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (24 bp):
TTTGTAACAACCTTGTCACCAGAG
Done.