Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 42 of 322
Found at i:12618053 original size:73 final size:74
Alignment explanation
Indices: 12617960--12618133 Score: 203
Period size: 75 Copynumber: 2.3 Consensus size: 74
12617950 AAAGTTGTTG
* * *
12617960 TATTATATTTTACATCAATAATGTACTCATTTACAATATAAGAAAAAA-ATTAAAAAATAT-TTT
1 TATTATATTGTACATCAATAATATACTCATTTACAATATAAGAAAAAATA-AAAAAAATATATTT
12618023 -TATTGTATTC
65 ATATT-TATTC
* * * * *
12618033 TATTGTATT-TCATATCAATAATATATACTTATTTACAATCTGAGAAAAAATAAAAAAAATATAT
1 TATTATATTGT-ACATCAAT-A-ATATACTCATTTACAATATAAGAAAAAATAAAAAAAATATAT
12618097 TTATATTTATTC
63 TTATATTTATTC
12618109 TATTATATTGTACATCAATAATATA
1 TATTATATTGTACATCAATAATATA
12618134 TCAATATTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
72 1 0.01
73 15 0.18
74 6 0.07
75 34 0.40
76 24 0.28
77 5 0.06
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (74 bp):
TATTATATTGTACATCAATAATATACTCATTTACAATATAAGAAAAAATAAAAAAAATATATTTA
TATTTATTC
Found at i:12618079 original size:75 final size:76
Alignment explanation
Indices: 12617960--12618147 Score: 210
Period size: 76 Copynumber: 2.5 Consensus size: 76
12617950 AAAGTTGTTG
* * * *
12617960 TATTATATTTTACATCAAT-A-ATGTACTCATTTACAATATAAGAAAAAA-ATTAAAAAATAT-T
1 TATTATATTGTACATCAATAATATATACTTATTTACAATATAAGAAAAAATA-AAAAAAATATAT
12618021 TT-TATTGTATTC
65 TTATATT-TATTC
* * * *
12618033 TATTGTATT-TCATATCAATAATATATACTTATTTACAATCTGAGAAAAAATAAAAAAAATATAT
1 TATTATATTGT-ACATCAATAATATATACTTATTTACAATATAAGAAAAAATAAAAAAAATATAT
12618097 TTATATTTATTC
65 TTATATTTATTC
*
12618109 TATTATATTGTACATCAATAATATAT-CAATATTTACAAT
1 TATTATATTGTACATCAATAATATATAC-TTATTTACAAT
12618148 TTACCAAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
72 1 0.01
73 15 0.15
74 1 0.01
75 34 0.35
76 41 0.42
77 5 0.05
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (76 bp):
TATTATATTGTACATCAATAATATATACTTATTTACAATATAAGAAAAAATAAAAAAAATATATT
TATATTTATTC
Found at i:12620865 original size:17 final size:17
Alignment explanation
Indices: 12620845--12620880 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
12620835 GAAGTTATCA
12620845 TGTTTTATT-TTTGTTTT
1 TGTTTTATTCTTT-TTTT
12620862 TGTTTTATTCTTTTTTT
1 TGTTTTATTCTTTTTTT
12620879 TG
1 TG
12620881 AAATTTCGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.06, C:0.03, G:0.11, T:0.81
Consensus pattern (17 bp):
TGTTTTATTCTTTTTTT
Found at i:12629795 original size:11 final size:12
Alignment explanation
Indices: 12629762--12629810 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
12629752 ACACGCAAAC
12629762 AAAAGA-AAA-A
1 AAAAGAGAAAGA
12629772 AAAGAGAGAAAGA
1 AAA-AGAGAAAGA
12629785 AAAAG-GAAAGA
1 AAAAGAGAAAGA
12629796 AAAAGAGAGAAGA
1 AAAAGAGA-AAGA
12629809 AA
1 AA
12629811 TCGCACGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.09
11 14 0.41
12 7 0.21
13 10 0.29
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAGAGAAAGA
Found at i:12629804 original size:25 final size:22
Alignment explanation
Indices: 12629762--12629810 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
12629752 ACACGCAAAC
12629762 AAAAGAAAAAAAAGAGAGAAAGA
1 AAAAGAAAAAAAAGAGAG-AAGA
12629785 AAAAGGAAAGAAAAAGAGAGAAGA
1 AAAA-GAAA-AAAAAGAGAGAAGA
12629809 AA
1 AA
12629811 TCGCACGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.17
24 10 0.42
25 10 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAAGAGAGAAGA
Found at i:12630886 original size:14 final size:14
Alignment explanation
Indices: 12630867--12630894 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12630857 CGAAATAGCC
12630867 TATTTATATATTTT
1 TATTTATATATTTT
12630881 TATTTATATATTTT
1 TATTTATATATTTT
12630895 GATTATACTG
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTATATATTTT
Found at i:12630901 original size:13 final size:14
Alignment explanation
Indices: 12630868--12630898 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12630858 GAAATAGCCT
*
12630868 ATTTATATATTTTT
1 ATTTATATATTTTG
12630882 ATTTATATATTTTG
1 ATTTATATATTTTG
12630896 ATT
1 ATT
12630899 ATACTGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
ATTTATATATTTTG
Found at i:12630933 original size:37 final size:37
Alignment explanation
Indices: 12630892--12630968 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
12630882 ATTTATATAT
* *
12630892 TTTGATTATACTGTTTGAGCAGCCCAATATATTAGAA
1 TTTGATTATACTGTCTGAGCAACCCAATATATTAGAA
12630929 TTTGATTATACTGTCTGAGCAACCCAATATATTAGAA
1 TTTGATTATACTGTCTGAGCAACCCAATATATTAGAA
12630966 TTT
1 TTT
12630969 TATTTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTGATTATACTGTCTGAGCAACCCAATATATTAGAA
Found at i:12631428 original size:17 final size:17
Alignment explanation
Indices: 12631408--12631466 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
12631398 TTAATAGATA
12631408 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
12631425 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
*
12631444 AATTGAAGTGAATGTGAT
1 -ATTGAAGTGAATATGAT
12631462 ATTGA
1 ATTGA
12631467 GATTATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 4 0.12
20 8 0.24
21 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:12631438 original size:37 final size:37
Alignment explanation
Indices: 12631397--12631467 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
12631387 TTAATGAATC
12631397 ATTAATAGATAATTGAAGTGAATATGATATTGAGTTG
1 ATTAATAGATAATTGAAGTGAATATGATATTGAGTTG
*
12631434 ATTAATAGATAATTGAAGTGAATGTGATATTGAG
1 ATTAATAGATAATTGAAGTGAATATGATATTGAG
12631468 ATTATGAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.37
Consensus pattern (37 bp):
ATTAATAGATAATTGAAGTGAATATGATATTGAGTTG
Found at i:12631574 original size:35 final size:35
Alignment explanation
Indices: 12631535--12631612 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
12631525 CGGCTAGTAT
*
12631535 TGGGCGCAAC-TTTCATC-AGTTTATCTGACTAGTGC
1 TGGGCGCAACATTT-ATCGA-TTTATCTGACTAGCGC
* *
12631570 TGGGCAC-ACATTTGTCGATTTATCTGACTAGCGC
1 TGGGCGCAACATTTATCGATTTATCTGACTAGCGC
12631604 TGGGCGCAA
1 TGGGCGCAA
12631613 ATATCGTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
34 25 0.69
35 11 0.31
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (35 bp):
TGGGCGCAACATTTATCGATTTATCTGACTAGCGC
Found at i:12631635 original size:35 final size:35
Alignment explanation
Indices: 12631596--12631718 Score: 111
Period size: 35 Copynumber: 3.4 Consensus size: 35
12631586 GATTTATCTG
*
12631596 ACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCA
1 ACTAGAGCTGGGCGCAAATATCGTTGGTTTATCCA
* * ** *
12631631 ACTAGAGTTGGGCTCACTACTTATATCGTCAGTTTATCCG
1 ACTAGAGCTGGGCGCA--A---ATATCGTTGGTTTATCCA
* * * *
12631671 ACTAGCGCTGAGCGCAACTATCGTTGATTTATCCA
1 ACTAGAGCTGGGCGCAAATATCGTTGGTTTATCCA
12631706 ACTAGAGCTGGGC
1 ACTAGAGCTGGGC
12631719 TCCCTGATTA
Statistics
Matches: 66, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
35 37 0.56
37 1 0.02
38 1 0.02
40 27 0.41
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (35 bp):
ACTAGAGCTGGGCGCAAATATCGTTGGTTTATCCA
Found at i:12631776 original size:74 final size:75
Alignment explanation
Indices: 12631583--12631763 Score: 251
Period size: 75 Copynumber: 2.4 Consensus size: 75
12631573 GCACACATTT
* * * *
12631583 GTCGATTTATCTGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGTTGGGCTCAC
1 GTCGATTTATCCGACTAGCGCTGGGCGCAACTATCGTTGATTTATCCAACTAGAGCTGGGCTCAC
12631648 TACTTATATC
66 TACTTATATC
* *
12631658 GTC-AGTTTATCCGACTAGCGCTGAGCGCAACTATCGTTGATTTATCCAACTAGAGCTGGGCTCC
1 GTCGA-TTTATCCGACTAGCGCTGGGCGCAACTATCGTTGATTTATCCAACTAGAGCTGGGCTCA
12631722 CTGA-TTAT-TC
65 CT-ACTTATATC
* *
12631732 GTCGATATATCCGACTAGCGCTGGGCGTAACT
1 GTCGATTTATCCGACTAGCGCTGGGCGCAACT
12631764 TCCGTCAATT
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
74 30 0.32
75 63 0.67
76 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (75 bp):
GTCGATTTATCCGACTAGCGCTGGGCGCAACTATCGTTGATTTATCCAACTAGAGCTGGGCTCAC
TACTTATATC
Found at i:12635967 original size:21 final size:21
Alignment explanation
Indices: 12635942--12635999 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
12635932 TATAGGGCTC
12635942 ACACGCCCGTGTGGTCTAGGG
1 ACACGCCCGTGTGGTCTAGGG
12635963 ACACGCCCGTGTGGTCTAGGG
1 ACACGCCCGTGTGGTCTAGGG
*
12635984 ACATGCCCGTGTGGTC
1 ACACGCCCGTGTGGTC
12636000 AGGCCGTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (21 bp):
ACACGCCCGTGTGGTCTAGGG
Found at i:12637800 original size:46 final size:46
Alignment explanation
Indices: 12637699--12637786 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
12637689 TGTAACCCGC
* * * *
12637699 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
12637745 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
12637787 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:12639575 original size:46 final size:46
Alignment explanation
Indices: 12639488--12639745 Score: 277
Period size: 46 Copynumber: 5.6 Consensus size: 46
12639478 CGTCTCTCAT
* * * * * *
12639488 CCATGATCTTATTTATCTTCGA-CATGATGCCATAGTGTCTTTCAA
1 CCATGGTCTTATTCATTTTCTATCATGTTGCCATAGTATCTTTCAA
* * * *
12639533 CTATGGTCTTACTCATTTTCTGTCATGTTGCCATTGTATCTTTCAA
1 CCATGGTCTTATTCATTTTCTATCATGTTGCCATAGTATCTTTCAA
* * * * *
12639579 CCATGGTTTTATTCATTTCCCATCATGTTGCCATGGTATCTTTTAA
1 CCATGGTCTTATTCATTTTCTATCATGTTGCCATAGTATCTTTCAA
** * *
12639625 CCATGGTCTTATTCATTTTCTATCACATTGCCTTGGTATCTTTCAA
1 CCATGGTCTTATTCATTTTCTATCATGTTGCCATAGTATCTTTCAA
* * *
12639671 CCATGGTCTTATTCA-TTTCATGTCACGCTGCCATAGTATCTTTCAA
1 CCATGGTCTTATTCATTTTC-TATCATGTTGCCATAGTATCTTTCAA
* *
12639717 CCATGGTCTTATTCATTTCCCATCATGTT
1 CCATGGTCTTATTCATTTTCTATCATGTT
12639746 AATCAAATTT
Statistics
Matches: 175, Mismatches: 35, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
45 19 0.11
46 153 0.87
47 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (46 bp):
CCATGGTCTTATTCATTTTCTATCATGTTGCCATAGTATCTTTCAA
Found at i:12640650 original size:942 final size:939
Alignment explanation
Indices: 12638809--12640687 Score: 3722
Period size: 942 Copynumber: 2.0 Consensus size: 939
12638799 TTAAAATTGG
12638809 TCAAATTGCTATTTAAGACCTCATTAATATTCCAAAACAATTTCATACTAAAAACTTCTAGAATA
1 TCAAATTGCTATTTAAGACCTCATTAATATTCCAAAACAATTTCATACTAAAAACTTCTAGAATA
12638874 CAAGTTTTGCAACTTATTCGATTTAGTCCCTACTTTCAATTTAAGCACTTTAGGCATAGAATTTC
66 CAAGTTTTGCAACTTATTCGATTTAGTCCCTACTTTCAATTTAAGCACTTTAGGCATAGAATTTC
12638939 ATCACGAAATTTTCACACAATCATGCAATCATATCATAAACCTCAAAATAATTATTTTATAATTA
131 ATCACGAAATTTTCACACAATCATGCAATCATATCATAAACCTCAAAATAATTATTTTATAATTA
12639004 TTTCTATCTCAAATTTATGGTCACGAAACCACTATTCCGATTAAGCCCTAATTCGACATATCACA
196 TTTCTATCTCAAATTTATGGTCACGAAACCACTATTCCGATTAAGCCCTAATTCGACATATCACA
12639069 CTTTAGTTTAATAATAGTCTCAACTTACATAATTTCCTTGTATCAACATATCAAAGATAATCATA
261 CTTTAGTTTAATAATAGTCTCAACTTACATAATTTCCTTGTATCAACATATCAAAGATAATCATA
12639134 TATGTACATGTCACGAAACATATTATTCTCTTACCGTTTCTTCATAAGCATATATCATTCATTTC
326 TATGTACATGTCACGAAACATATTATTCTCTTACCGTTTCTTCATAAGCATATATCATTCATTTC
12639199 GTTATACAATATTTCATGCACCATCATTTCCATATATCTTATGTATATTTATTTCGATAATAGTT
391 GTTATACAATATTTCATGCACCATCATTTCCATATATCTTATGTATATTTATTTCGATAATAGTT
12639264 CATATTAAACTTAACATAAATTAAATTTCATGTACCTATACTTATTTCATTTATCTATCTTCTTA
456 CATATTAAACTTAACATAAATTAAATTTCATGTACCTATACTTATTTCATTTATCTATCTTCTTA
12639329 ATTATTTCATACAACTATTTTGTACATATATTTCCATATGACCAATTCTTGTAAACATTTCACAC
521 ATTATTTCATACAACTATTTTGTACATATATTTCCATATGACCAATTCTTGTAAACATTTCACAC
12639394 AACCATTTTGTATAACCAATTCATATAACTATTCGTCATCTGGTACATATTACCTGAATATTAGT
586 AACCATTTTGTATAACCAATTCATATAACTATTCGTCATCTGGTACATATTACCTGAATATTAGT
12639459 TGTTCAATAGATGTCTTGGCGTCTCTCATCCATGATCTTATTTATCTTCGACATGATGCCATAGT
651 TGTTCAATAGATGTCTTGGCGTCTCTCATCCATGATCTTATTTATCTTCGACATGATGCCATAGT
12639524 GTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATTGTATCTTTCAACCATGGTTTT
716 GTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATTGTATCTTTCAACCATGGTTTT
12639589 ATTCATTTCCCATCATGTTGCCATGGTATCTTTTAACCATGGTCTTATTCATTTTCTATCACATT
781 ATTCATTTCCCATCATGTTGCCATGGTATCTTTTAACCATGGTCTTATTCATTTTCTATCACATT
12639654 GCCTTGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATAGTATCTTTCAACC
846 GCCTTGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATAGTATCTTTCAACC
12639719 ATGGTCTTATTCATTTCCCATCATGTTAA
911 ATGGTCTTATTCATTTCCCATCATGTTAA
*
12639748 TCAAATTTCTATTTAAGACCTCCTCATTAATATTCCAAAACAATTTCATACTAAAAACTTCTAGA
1 TCAAATTGCTATTTAAGA---CCTCATTAATATTCCAAAACAATTTCATACTAAAAACTTCTAGA
12639813 ATACAAGTTTTGCAACTTATTCGATTTAGTCCCTACTTTCAATTTAAGCACTTTAGGCATAGAAT
63 ATACAAGTTTTGCAACTTATTCGATTTAGTCCCTACTTTCAATTTAAGCACTTTAGGCATAGAAT
12639878 TTCATCACGAAATTTTCACACAATCATGCAATCATATCATAAACCTCAAAATAATTATTTTATAA
128 TTCATCACGAAATTTTCACACAATCATGCAATCATATCATAAACCTCAAAATAATTATTTTATAA
12639943 TTATTTCTATCTCAAATTTATGGTCACGAAACCACTATTCCGATTAAGCCCTAATTCGACATATC
193 TTATTTCTATCTCAAATTTATGGTCACGAAACCACTATTCCGATTAAGCCCTAATTCGACATATC
12640008 ACACTTTAGTTTAATAATAGTCTCAACTTACATAATTTCCTTGTATCAACATATCAAAGATAATC
258 ACACTTTAGTTTAATAATAGTCTCAACTTACATAATTTCCTTGTATCAACATATCAAAGATAATC
12640073 ATATATGTACATGTCACGAAACATATTATTCTCTTACCGTTTCTTCATAAGCATATATCATTCAT
323 ATATATGTACATGTCACGAAACATATTATTCTCTTACCGTTTCTTCATAAGCATATATCATTCAT
12640138 TTCGTTATACAATATTTCATGCACCATCATTTCCATATATCTTATGTATATTTATTTCGATAATA
388 TTCGTTATACAATATTTCATGCACCATCATTTCCATATATCTTATGTATATTTATTTCGATAATA
12640203 GTTCATATTAAACTTAACATAAATTAAATTTCATGTACCTATACTTATTTCATTTATCTATCTTC
453 GTTCATATTAAACTTAACATAAATTAAATTTCATGTACCTATACTTATTTCATTTATCTATCTTC
12640268 TTAATTATTTCATACAACTATTTTGTACATATATTTCCATATGACCAATTCTTGTAAACATTTCA
518 TTAATTATTTCATACAACTATTTTGTACATATATTTCCATATGACCAATTCTTGTAAACATTTCA
12640333 CACAACCATTTTGTATAACCAATTCATATAACTATTCGTCATCTGGTACATATTACCTGAATATT
583 CACAACCATTTTGTATAACCAATTCATATAACTATTCGTCATCTGGTACATATTACCTGAATATT
12640398 AGTTGTTCAATAGATGTCTTGGCGTCTCTCATCCATGATCTTATTTATCTTCGACATGATGCCAT
648 AGTTGTTCAATAGATGTCTTGGCGTCTCTCATCCATGATCTTATTTATCTTCGACATGATGCCAT
12640463 AGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATTGTATCTTTCAACCATGGT
713 AGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATTGTATCTTTCAACCATGGT
12640528 TTTATTCATTTCCCATCATGTTGCCATGGTATCTTTTAACCATGGTCTTATTCATTTTCTATCAC
778 TTTATTCATTTCCCATCATGTTGCCATGGTATCTTTTAACCATGGTCTTATTCATTTTCTATCAC
12640593 ATTGCCTTGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATAGTATCTTTCA
843 ATTGCCTTGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATAGTATCTTTCA
12640658 ACCATGGTCTTATTCATTTCCCATCATGTT
908 ACCATGGTCTTATTCATTTCCCATCATGTT
12640688 TCCATGGTAT
Statistics
Matches: 936, Mismatches: 1, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
939 17 0.02
942 919 0.98
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (939 bp):
TCAAATTGCTATTTAAGACCTCATTAATATTCCAAAACAATTTCATACTAAAAACTTCTAGAATA
CAAGTTTTGCAACTTATTCGATTTAGTCCCTACTTTCAATTTAAGCACTTTAGGCATAGAATTTC
ATCACGAAATTTTCACACAATCATGCAATCATATCATAAACCTCAAAATAATTATTTTATAATTA
TTTCTATCTCAAATTTATGGTCACGAAACCACTATTCCGATTAAGCCCTAATTCGACATATCACA
CTTTAGTTTAATAATAGTCTCAACTTACATAATTTCCTTGTATCAACATATCAAAGATAATCATA
TATGTACATGTCACGAAACATATTATTCTCTTACCGTTTCTTCATAAGCATATATCATTCATTTC
GTTATACAATATTTCATGCACCATCATTTCCATATATCTTATGTATATTTATTTCGATAATAGTT
CATATTAAACTTAACATAAATTAAATTTCATGTACCTATACTTATTTCATTTATCTATCTTCTTA
ATTATTTCATACAACTATTTTGTACATATATTTCCATATGACCAATTCTTGTAAACATTTCACAC
AACCATTTTGTATAACCAATTCATATAACTATTCGTCATCTGGTACATATTACCTGAATATTAGT
TGTTCAATAGATGTCTTGGCGTCTCTCATCCATGATCTTATTTATCTTCGACATGATGCCATAGT
GTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATTGTATCTTTCAACCATGGTTTT
ATTCATTTCCCATCATGTTGCCATGGTATCTTTTAACCATGGTCTTATTCATTTTCTATCACATT
GCCTTGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATAGTATCTTTCAACC
ATGGTCTTATTCATTTCCCATCATGTTAA
Found at i:12640715 original size:138 final size:138
Alignment explanation
Indices: 12640457--12640771 Score: 445
Period size: 138 Copynumber: 2.3 Consensus size: 138
12640447 TTCGACATGA
* * * * * *
12640457 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATTGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGCTGCCATAGTATCTTTCAA
* * * **
12640521 CCATGGTTTTATTCATTTCCCATCATGTTGCCATGGTATCTTTTAACCATGGTCTTATTCATTTT
65 CCATGGTCTTATTCATTTCCCATCATGTTGCCATGGTATCTTTCAACCATAGTCTTACACA-TTT
12640586 C-TATCACAT
129 CATATCACAT
* *
12640595 TGCCTTGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATAGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGCTGCCATAGTATCTTTCAAC
*
12640660 CATGGTCTTATTCATTTCCCATCATGTTTCCATGGTATCTTTCAACCATAGTCTTACACATTTCA
66 CATGGTCTTATTCATTTCCCATCATGTTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCA
**
12640725 TATCATGT
131 TATCACAT
*
12640733 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
12640772 TTTAGAAAGC
Statistics
Matches: 156, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
137 8 0.05
138 148 0.95
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (138 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGCTGCCATAGTATCTTTCAAC
CATGGTCTTATTCATTTCCCATCATGTTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCA
TATCACAT
Found at i:12640762 original size:46 final size:46
Alignment explanation
Indices: 12640452--12640771 Score: 374
Period size: 46 Copynumber: 7.0 Consensus size: 46
12640442 TTATCTTCGA
* * * * * *
12640452 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATAT
* * **
12640498 CATGTTGCCATTGTATCTTTCAACCATGGTTTTATTCATTTCCCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
*
12640544 CATGTTGCCATGGTATCTTTTAACCATGGTCTTATTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATAT
** * *
12640590 CACATTGCCTTGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* * * **
12640636 CACGCTGCCATAGTATCTTTCAACCATGGTCTTATTCATTTCCCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* * **
12640682 CATGTTTCCATGGTATCTTTCAACCATAGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
**
12640728 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
12640772 TTTAGAAAGC
Statistics
Matches: 236, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
45 8 0.03
46 224 0.95
47 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
Found at i:12643759 original size:3 final size:3
Alignment explanation
Indices: 12643751--12643775 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12643741 AAAACTTATT
12643751 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
12643776 CACGTTGGTT
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:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:12643856 original size:11 final size:11
Alignment explanation
Indices: 12643840--12643881 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
12643830 TATACTAAAT
12643840 AATTAATAATA
1 AATTAATAATA
12643851 AATTAATAATA
1 AATTAATAATA
12643862 GAA-TAATAATA
1 -AATTAATAATA
*
12643873 AAATAATAA
1 AATTAATAA
12643882 AATATCTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.07
11 25 0.86
12 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AATTAATAATA
Found at i:12643920 original size:24 final size:24
Alignment explanation
Indices: 12643868--12643917 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12643858 AATAGAATAA
*
12643868 TAATAAAATAATAAAATATCTCAT
1 TAATAAAATAATAAAATATCTAAT
**
12643892 TAATAAAATAAT-ATTTATCTAAT
1 TAATAAAATAATAAAATATCTAAT
12643915 TAA
1 TAA
12643918 ATAGTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
TAATAAAATAATAAAATATCTAAT
Found at i:12646938 original size:30 final size:30
Alignment explanation
Indices: 12646904--12646966 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
12646894 ACTTATTTTA
*
12646904 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAGAGACAT
12646934 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAGAGACAT
12646964 TTG
1 TTG
12646967 CTTATTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAGAGACAT
Found at i:12647336 original size:36 final size:36
Alignment explanation
Indices: 12647296--12647373 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
12647286 AGATTTTTCT
* *
12647296 TAAATATTATCACAAAATAATTTTAAATATTATCAC
1 TAAATATTATCACAAAATAATTCTAAATATTACCAC
* *
12647332 TAAATATTATTACTAAATAATTCTAAATATTACCAC
1 TAAATATTATCACAAAATAATTCTAAATATTACCAC
12647368 TAAATA
1 TAAATA
12647374 ATTCAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (36 bp):
TAAATATTATCACAAAATAATTCTAAATATTACCAC
Found at i:12647337 original size:13 final size:13
Alignment explanation
Indices: 12647319--12647373 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
12647309 AAAATAATTT
12647319 TAAATATTATCAC
1 TAAATATTATCAC
*
12647332 TAAATATTATTAC
1 TAAATATTATCAC
*
12647345 TAAATA--AT-TC
1 TAAATATTATCAC
*
12647355 TAAATATTACCAC
1 TAAATATTATCAC
12647368 TAAATA
1 TAAATA
12647374 ATTCAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 7 0.20
11 2 0.06
12 1 0.03
13 25 0.71
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:12647357 original size:23 final size:23
Alignment explanation
Indices: 12647331--12647382 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
12647321 AATATTATCA
**
12647331 CTAAATATTATTACTAAATAATT
1 CTAAATATTACCACTAAATAATT
12647354 CTAAATATTACCACTAAATAATT
1 CTAAATATTACCACTAAATAATT
*
12647377 CAAAAT
1 CTAAAT
12647383 TTAAAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTACCACTAAATAATT
Found at i:12653491 original size:18 final size:18
Alignment explanation
Indices: 12653464--12653514 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
12653454 GTTTATAGAT
*
12653464 ATCCTTGGACTTACAGCA
1 ATCCTAGGACTTACAGCA
* * *
12653482 ATCCTCGGACTTGCAGCG
1 ATCCTAGGACTTACAGCA
12653500 ATCCTAGGACTTACA
1 ATCCTAGGACTTACA
12653515 TCGCTCATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (18 bp):
ATCCTAGGACTTACAGCA
Found at i:12657919 original size:47 final size:47
Alignment explanation
Indices: 12657845--12657939 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
12657835 TGCCCACATA
*
12657845 ACCACTGTCAACTAGGGCCCCAATTATGCTCCATCTTTTGACAGCAT
1 ACCACTGTCAACTAGGGCCCCAATTATGCTCAATCTTTTGACAGCAT
* * *
12657892 ACCACTGTTAACTAGGGCCCCAGTTATGCTCAATCTTTTGATAGCAT
1 ACCACTGTCAACTAGGGCCCCAATTATGCTCAATCTTTTGACAGCAT
12657939 A
1 A
12657940 ACCTTTGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (47 bp):
ACCACTGTCAACTAGGGCCCCAATTATGCTCAATCTTTTGACAGCAT
Found at i:12670090 original size:4 final size:4
Alignment explanation
Indices: 12670081--12670134 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
12670071 CTTATTACTA
* * **
12670081 TTAT TTAT TTAT TTAT CTAT TTAT TTAT TTAC TTGC TTAT TT-T TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
*
12670128 ATAT TTA
1 TTAT TTA
12670135 AAAACAAGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:12670309 original size:13 final size:13
Alignment explanation
Indices: 12670291--12670316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12670281 GCATCTTGCA
12670291 TTTTTATTTTTAT
1 TTTTTATTTTTAT
12670304 TTTTTATTTTTAT
1 TTTTTATTTTTAT
12670317 CACTTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:12673448 original size:29 final size:30
Alignment explanation
Indices: 12673375--12673449 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
12673365 TGGTTAACAC
* *
12673375 ATCCCTTTTCATAAATCGGTAACCGAAGTT
1 ATCCCTTTTCATAATTCGATAACCGAAGTT
* *
12673405 ATCCCTTTTCATAATTCGATAGCCGAGGTT
1 ATCCCTTTTCATAATTCGATAACCGAAGTT
12673435 -TCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
12673450 TGATGGTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATAACCGAAGTT
Found at i:12673472 original size:29 final size:30
Alignment explanation
Indices: 12673435--12673510 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
12673425 AGCCGAGGTT
12673435 TCCCTTTTCATAATTTGATGGTCATCACCA
1 TCCCTTTTCATAATTTGATGGTCATCACCA
* *
12673465 TCCC-TTTCATAAATCGATGGTCATCACCA
1 TCCCTTTTCATAATTTGATGGTCATCACCA
12673494 TCCCTTTTTCATAATTT
1 TCCC-TTTTCATAATTT
12673511 ATAGCCGAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.68
30 4 0.10
31 9 0.22
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.41
Consensus pattern (30 bp):
TCCCTTTTCATAATTTGATGGTCATCACCA
Found at i:12673621 original size:30 final size:30
Alignment explanation
Indices: 12673582--12673659 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
12673572 ATAGTCGAAG
* **
12673582 CCATTCCTTTTCATAATTTGATGGTCGTCA
1 CCATCCCTTTTCATAATTCAATGGTCGTCA
*
12673612 CCATCCCTTTTCATTATTCAATGGTCGTCA
1 CCATCCCTTTTCATAATTCAATGGTCGTCA
* *
12673642 CCAACCATTTTCATAATT
1 CCATCCCTTTTCATAATT
12673660 GATAACCAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.23, C:0.27, G:0.09, T:0.41
Consensus pattern (30 bp):
CCATCCCTTTTCATAATTCAATGGTCGTCA
Found at i:12676046 original size:13 final size:15
Alignment explanation
Indices: 12676021--12676057 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
12676011 ATTGACAACA
12676021 TAATAATTAAAT-ATT
1 TAATAA-TAAATAATT
12676036 TAA-AATAAATAATT
1 TAATAATAAATAATT
12676050 TAATAATA
1 TAATAATA
12676058 TTTTCTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAAATAATT
Found at i:12676057 original size:24 final size:24
Alignment explanation
Indices: 12675990--12676060 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
12675980 TTTGAGTATA
*
12675990 TAAACATAAAAAATTAATAATATT
1 TAAACATAAATAATTAATAATATT
*
12676014 GACAACAT-AATAATT-A-AATATT
1 TA-AACATAAATAATTAATAATATT
12676036 TAAA-ATAAATAATTTAATAATATT
1 TAAACATAAATAA-TTAATAATATT
12676060 T
1 T
12676061 TCTTATCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.05
21 7 0.18
22 9 0.23
23 2 0.05
24 14 0.36
25 5 0.13
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (24 bp):
TAAACATAAATAATTAATAATATT
Found at i:12679099 original size:468 final size:468
Alignment explanation
Indices: 12678223--12679161 Score: 1878
Period size: 468 Copynumber: 2.0 Consensus size: 468
12678213 ATGGGTCTCA
12678223 TGGATGGTTCTGATTGTGAATGTTGGGACCCCAGGGAGCTTTGCTGCATGTATACGCCACGGACA
1 TGGATGGTTCTGATTGTGAATGTTGGGACCCCAGGGAGCTTTGCTGCATGTATACGCCACGGACA
12678288 TCCCTCACTTGCACATTTGGCAGTAAAACGAGTCTTATCAGATTTGATGGTCTGCATTTCAAAGT
66 TCCCTCACTTGCACATTTGGCAGTAAAACGAGTCTTATCAGATTTGATGGTCTGCATTTCAAAGT
12678353 GAAGAGCAATAGCCGCATCTCTCAATGCCCTACGACAGCTTTTGACATCCGGGAACTCTTGCCCA
131 GAAGAGCAATAGCCGCATCTCTCAATGCCCTACGACAGCTTTTGACATCCGGGAACTCTTGCCCA
12678418 ACAGCCAATTCGTAAGTTGGATTTGAATTCCGAACCTGAAGGACAGGAGGAAGACTAACTACAAT
196 ACAGCCAATTCGTAAGTTGGATTTGAATTCCGAACCTGAAGGACAGGAGGAAGACTAACTACAAT
12678483 CTGGGAGTGCTGCAAATCTCGGGCAGGATCAATTCCCATCTCCTGGCTGTCGTCCACGGCCAATG
261 CTGGGAGTGCTGCAAATCTCGGGCAGGATCAATTCCCATCTCCTGGCTGTCGTCCACGGCCAATG
12678548 CCAGACTATCATCAAGCTCTTGGTTTTCTGAAACGGTCAATTCATTATGCTCTGATAAAGCTAAC
326 CCAGACTATCATCAAGCTCTTGGTTTTCTGAAACGGTCAATTCATTATGCTCTGATAAAGCTAAC
12678613 TCATTGTCACCATGGTCTGGTTTTCGATCATTAGCTAACTCATTATCATGCCCATAACTGTGGCC
391 TCATTGTCACCATGGTCTGGTTTTCGATCATTAGCTAACTCATTATCATGCCCATAACTGTGGCC
12678678 AACATCCTCTTCT
456 AACATCCTCTTCT
12678691 TGGATGGTTCTGATTGTGAATGTTGGGACCCCAGGGAGCTTTGCTGCATGTATACGCCACGGACA
1 TGGATGGTTCTGATTGTGAATGTTGGGACCCCAGGGAGCTTTGCTGCATGTATACGCCACGGACA
12678756 TCCCTCACTTGCACATTTGGCAGTAAAACGAGTCTTATCAGATTTGATGGTCTGCATTTCAAAGT
66 TCCCTCACTTGCACATTTGGCAGTAAAACGAGTCTTATCAGATTTGATGGTCTGCATTTCAAAGT
12678821 GAAGAGCAATAGCCGCATCTCTCAATGCCCTACGACAGCTTTTGACATCCGGGAACTCTTGCCCA
131 GAAGAGCAATAGCCGCATCTCTCAATGCCCTACGACAGCTTTTGACATCCGGGAACTCTTGCCCA
12678886 ACAGCCAATTCGTAAGTTGGATTTGAATTCCGAACCTGAAGGACAGGAGGAAGACTAACTACAAT
196 ACAGCCAATTCGTAAGTTGGATTTGAATTCCGAACCTGAAGGACAGGAGGAAGACTAACTACAAT
12678951 CTGGGAGTGCTGCAAATCTCGGGCAGGATCAATTCCCATCTCCTGGCTGTCGTCCACGGCCAATG
261 CTGGGAGTGCTGCAAATCTCGGGCAGGATCAATTCCCATCTCCTGGCTGTCGTCCACGGCCAATG
12679016 CCAGACTATCATCAAGCTCTTGGTTTTCTGAAACGGTCAATTCATTATGCTCTGATAAAGCTAAC
326 CCAGACTATCATCAAGCTCTTGGTTTTCTGAAACGGTCAATTCATTATGCTCTGATAAAGCTAAC
12679081 TCATTGTCACCATGGTCTGGTTTTCGATCATTAGCTAACTCATTATCATGCCCATAACTGTGGCC
391 TCATTGTCACCATGGTCTGGTTTTCGATCATTAGCTAACTCATTATCATGCCCATAACTGTGGCC
12679146 AACATCCTCTTCT
456 AACATCCTCTTCT
12679159 TGG
1 TGG
12679162 TCATGCCTCT
Statistics
Matches: 471, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
468 471 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (468 bp):
TGGATGGTTCTGATTGTGAATGTTGGGACCCCAGGGAGCTTTGCTGCATGTATACGCCACGGACA
TCCCTCACTTGCACATTTGGCAGTAAAACGAGTCTTATCAGATTTGATGGTCTGCATTTCAAAGT
GAAGAGCAATAGCCGCATCTCTCAATGCCCTACGACAGCTTTTGACATCCGGGAACTCTTGCCCA
ACAGCCAATTCGTAAGTTGGATTTGAATTCCGAACCTGAAGGACAGGAGGAAGACTAACTACAAT
CTGGGAGTGCTGCAAATCTCGGGCAGGATCAATTCCCATCTCCTGGCTGTCGTCCACGGCCAATG
CCAGACTATCATCAAGCTCTTGGTTTTCTGAAACGGTCAATTCATTATGCTCTGATAAAGCTAAC
TCATTGTCACCATGGTCTGGTTTTCGATCATTAGCTAACTCATTATCATGCCCATAACTGTGGCC
AACATCCTCTTCT
Found at i:12681698 original size:11 final size:11
Alignment explanation
Indices: 12681684--12681708 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12681674 TTTTAAAAAA
12681684 ATTATTAAATT
1 ATTATTAAATT
12681695 ATTATTAAATT
1 ATTATTAAATT
12681706 ATT
1 ATT
12681709 TAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:12681718 original size:14 final size:14
Alignment explanation
Indices: 12681701--12681727 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12681691 AATTATTATT
12681701 AAATTATTTAAAAA
1 AAATTATTTAAAAA
12681715 AAATTATTTAAAA
1 AAATTATTTAAAA
12681728 TCTTTAATGG
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATTATTTAAAAA
Found at i:12696609 original size:27 final size:29
Alignment explanation
Indices: 12696573--12696643 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 29
12696563 AAATTAATTT
12696573 ATAATAAAATTATAATTTAA-CTTCT-AA
1 ATAATAAAATTATAATTTAATCTTCTAAA
* * *
12696600 AT-ATGAAAATAATTATTTAATCTTTTAAA
1 ATAAT-AAAATTATAATTTAATCTTCTAAA
12696629 ATAATAAAATTATAA
1 ATAATAAAATTATAA
12696644 AATCATACCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.06
27 15 0.43
28 4 0.11
29 12 0.34
30 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
ATAATAAAATTATAATTTAATCTTCTAAA
Found at i:12697501 original size:20 final size:21
Alignment explanation
Indices: 12697465--12697508 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
12697455 AATTACAAAT
12697465 AATTTAAGAAATAAAAATAAA
1 AATTTAAGAAATAAAAATAAA
*
12697486 AATTTAA-AACTAAAAATAAA
1 AATTTAAGAAATAAAAATAAA
12697506 AAT
1 AAT
12697509 AAAAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (21 bp):
AATTTAAGAAATAAAAATAAA
Found at i:12697512 original size:5 final size:6
Alignment explanation
Indices: 12697473--12697513 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
12697463 ATAATTTAAG
*
12697473 AAATAA AAATAA AAATTTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
12697514 AACATATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:12697514 original size:20 final size:20
Alignment explanation
Indices: 12697476--12697514 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12697466 ATTTAAGAAA
**
12697476 TAAAAATAAAAATTTAAAAC
1 TAAAAATAAAAATAAAAAAC
12697496 TAAAAATAAAAATAAAAAA
1 TAAAAATAAAAATAAAAAA
12697515 ACATATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:12697580 original size:9 final size:9
Alignment explanation
Indices: 12697535--12697591 Score: 71
Period size: 9 Copynumber: 6.3 Consensus size: 9
12697525 TATACAAATG
12697535 ATTCGGTTA
1 ATTCGGTTA
12697544 ATTCGAG-TA
1 ATTCG-GTTA
12697553 ATTCGGTTA
1 ATTCGGTTA
**
12697562 ATTCAATTA
1 ATTCGGTTA
12697571 ATTCGGTTA
1 ATTCGGTTA
*
12697580 ATTCAGTTA
1 ATTCGGTTA
12697589 ATT
1 ATT
12697592 TTATACTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
8 1 0.02
9 39 0.95
10 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (9 bp):
ATTCGGTTA
Found at i:12697589 original size:18 final size:18
Alignment explanation
Indices: 12697535--12697591 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
12697525 TATACAAATG
12697535 ATTCGGTTAATTCGAG-TA
1 ATTCGGTTAATTC-AGTTA
*
12697553 ATTCGGTTAATTCAATTA
1 ATTCGGTTAATTCAGTTA
12697571 ATTCGGTTAATTCAGTTA
1 ATTCGGTTAATTCAGTTA
12697589 ATT
1 ATT
12697592 TTATACTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 1 0.03
18 35 0.97
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (18 bp):
ATTCGGTTAATTCAGTTA
Found at i:12705289 original size:27 final size:25
Alignment explanation
Indices: 12705237--12705294 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
12705227 GTTCTTATCC
*
12705237 TTTTTTTTTGTTTTTTTTTGTTTTGGG
1 TTTTTTTCTGTTTTTTTTTG-TTT-GG
12705264 TTTTTTTCTGTTCATTTTTTTG-TTGG
1 TTTTTTTCTGTT--TTTTTTTGTTTGG
12705290 TTTTT
1 TTTTT
12705295 AACATAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.25
27 13 0.46
29 8 0.29
ACGTcount: A:0.02, C:0.03, G:0.16, T:0.79
Consensus pattern (25 bp):
TTTTTTTCTGTTTTTTTTTGTTTGG
Found at i:12709291 original size:16 final size:16
Alignment explanation
Indices: 12709266--12709304 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12709256 ATAACATAAA
12709266 ATTTTA-ATAATATAT
1 ATTTTATATAATATAT
12709281 ATTTTATATAATATAT
1 ATTTTATATAATATAT
*
12709297 ATTATATA
1 ATTTTATA
12709305 CAATGGAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTATATAATATAT
Found at i:12714423 original size:19 final size:21
Alignment explanation
Indices: 12714399--12714439 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
12714389 CACTAATAAA
12714399 AAGATAAAGA-A-AACAAAAT
1 AAGATAAAGAGATAACAAAAT
12714418 AAGATAAAGAGATAACAAAAT
1 AAGATAAAGAGATAACAAAAT
12714439 A
1 A
12714440 TAAAAATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 1 0.05
21 9 0.45
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.12
Consensus pattern (21 bp):
AAGATAAAGAGATAACAAAAT
Found at i:12715491 original size:74 final size:74
Alignment explanation
Indices: 12715407--12715554 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
12715397 ATTATCCAAA
12715407 AATAATATTGTGCAACTGAAGTCAACCTTAAAATTTATAGCTATTTTCTGGTAGTTTTTCATAGA
1 AATAATATTGTGCAACTGAAGTCAACCTTAAAATTTATAGCTATTTTCTGGTAGTTTTTCATAGA
12715472 TACAAAATG
66 TACAAAATG
12715481 AATAATATTGTGCAACTGAAGTCAACCTTAAAATTTATAGCTATTTTCTGGTAGTTTTTCATAGA
1 AATAATATTGTGCAACTGAAGTCAACCTTAAAATTTATAGCTATTTTCTGGTAGTTTTTCATAGA
12715546 TACAAAATG
66 TACAAAATG
12715555 GAAAAAGAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (74 bp):
AATAATATTGTGCAACTGAAGTCAACCTTAAAATTTATAGCTATTTTCTGGTAGTTTTTCATAGA
TACAAAATG
Found at i:12717858 original size:3 final size:3
Alignment explanation
Indices: 12717845--12717876 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12717835 TATTTATGTT
12717845 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12717877 AGTAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12718864 original size:44 final size:44
Alignment explanation
Indices: 12718764--12718855 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
12718754 TGTTCAGGGA
*
12718764 TACTTCGACCTT-GAGTCGATGAGGCACCATAAGTGTCGTATTGT
1 TACTTCGA-CTTCGAGTCGATGAGGCACCATAAGTGTCGTACTGT
* **
12718808 TACTTCGACTTCGAGTCGATGAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACTTCGAGTCGATGAGGCACCATAAGTGTCGTACTGT
12718852 TACT
1 TACT
12718856 GTTGCTTCGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 3 0.07
44 40 0.93
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (44 bp):
TACTTCGACTTCGAGTCGATGAGGCACCATAAGTGTCGTACTGT
Found at i:12726329 original size:38 final size:38
Alignment explanation
Indices: 12726278--12726354 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
12726268 TTTGGTTTAC
12726278 ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
1 ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
*
12726316 ATAGAAAATGGGGAATCTACCGGAAACAAACATTAATG
1 ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
12726354 A
1 A
12726355 GAGACTTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (38 bp):
ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
Found at i:12729608 original size:47 final size:47
Alignment explanation
Indices: 12729539--12729633 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
12729529 AACAGATAGT
* *
12729539 AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGATATTAGCAA
1 AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGAGATCAGCAA
12729586 AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGAGATCAGCAA
1 AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGAGATCAGCAA
12729633 A
1 A
12729634 TGTTTTAGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (47 bp):
AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGAGATCAGCAA
Found at i:12730949 original size:13 final size:13
Alignment explanation
Indices: 12730931--12730970 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
12730921 TAATCATATA
12730931 ATAAATTATTAAT
1 ATAAATTATTAAT
12730944 ATAAATTATT-A-
1 ATAAATTATTAAT
12730955 ATAAATTATTTAAT
1 ATAAATTA-TTAAT
12730969 AT
1 AT
12730971 TTAGATCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.33
12 3 0.12
13 11 0.46
14 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAAATTATTAAT
Found at i:12732013 original size:21 final size:21
Alignment explanation
Indices: 12731961--12732034 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
12731951 TATTTTAAAT
*
12731961 AAAAATAAAATATTACAATTAA
1 AAAAATAAAA-ATTAAAATTAA
*
12731983 AAAAATTAAAAATTAAAATTCA
1 AAAAA-TAAAAATTAAAATTAA
*
12732005 AAAAATAAAAA-TAAATTTTAA
1 AAAAATAAAAATTAAA-ATTAA
*
12732026 AAATATAAA
1 AAAAATAAA
12732035 TTTTTTTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.09
21 17 0.38
22 19 0.42
23 5 0.11
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATAAAAATTAAAATTAA
Found at i:12732422 original size:35 final size:34
Alignment explanation
Indices: 12732356--12732422 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
12732346 ATATTTTTAA
** * *
12732356 ATTTTTTGAATTTTAAAGTGTTTTTATTTTTTTC
1 ATTTTTTGAATTTTAAAAAGTTTTAAATTTTTTC
*
12732390 ATTTTTTTATATTTTAAAAAGTTTTAAATTTTT
1 ATTTTTTGA-ATTTTAAAAAGTTTTAAATTTTT
12732423 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 8 0.30
35 19 0.70
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (34 bp):
ATTTTTTGAATTTTAAAAAGTTTTAAATTTTTTC
Found at i:12732446 original size:25 final size:24
Alignment explanation
Indices: 12732392--12732450 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
12732382 TTTTTTTCAT
* *
12732392 TTTTTTATATTTTAAAAAGTTTTAA
1 TTTTTT-TATTTTAAAAAATTATAA
*
12732417 -ATTTTTATTTTAAAAAATTGATAA
1 TTTTTTTATTTTAAAAAATT-ATAA
12732441 TTTTTTTATT
1 TTTTTTTATT
12732451 CTCTTTAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 13 0.46
24 7 0.25
25 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (24 bp):
TTTTTTTATTTTAAAAAATTATAA
Found at i:12732891 original size:57 final size:57
Alignment explanation
Indices: 12732818--12732934 Score: 198
Period size: 57 Copynumber: 2.1 Consensus size: 57
12732808 ATCTACATGA
* * *
12732818 TTTGGGGTGGAATATGCGAATATGCGTTATTTTTGAATAGAGCAGAACCTTCTTTTC
1 TTTGGGGTAGAATATGCGAATATGCGTTATTCTTGAAGAGAGCAGAACCTTCTTTTC
*
12732875 TTTGGGGTAGAGTATGCGAATATGCGTTATTCTTGAAGAGAGCAGAACCTTCTTTTC
1 TTTGGGGTAGAATATGCGAATATGCGTTATTCTTGAAGAGAGCAGAACCTTCTTTTC
12732932 TTT
1 TTT
12732935 CTTTTATGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (57 bp):
TTTGGGGTAGAATATGCGAATATGCGTTATTCTTGAAGAGAGCAGAACCTTCTTTTC
Found at i:12736183 original size:13 final size:13
Alignment explanation
Indices: 12736162--12736225 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
12736152 TTTTAAACCA
12736162 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
* *
12736175 ACTTCTCAAAATT
1 ACTTTTCAAAAGT
* * * *
12736188 ATTTTTCCACAGC
1 ACTTTTCAAAAGT
*
12736201 ACTTTTTAAAAGT
1 ACTTTTCAAAAGT
*
12736214 ACTTCTCAAAAG
1 ACTTTTCAAAAG
12736226 CAATGCTAAA
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:12737579 original size:21 final size:21
Alignment explanation
Indices: 12737553--12737593 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12737543 TTGTGTTCCT
*
12737553 CTGCCTCTCTCGCTGCTGCCG
1 CTGCCTCCCTCGCTGCTGCCG
*
12737574 CTGCCTCCCTCTCTGCTGCC
1 CTGCCTCCCTCGCTGCTGCC
12737594 TCCATTCTAA
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:0.00, C:0.51, G:0.20, T:0.29
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTGCCG
Found at i:12737760 original size:43 final size:43
Alignment explanation
Indices: 12737655--12737816 Score: 243
Period size: 43 Copynumber: 3.7 Consensus size: 43
12737645 ATTTGCTNGG
* * * *
12737655 AAAGCGCCGCTAAAGGTCAAGGCTTTTAGCAGCATTTTTTGGGG
1 AAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGC-GTTTGTGGGA
*
12737699 AAAGCGCCGCTAAAGGTCAAGACTTTTAGCGGCGTTTGTGGGA
1 AAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGA
*
12737742 AAAGCACCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGA
1 AAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGA
* *
12737785 AAAGCGCCGCTAAAGATTAAGGCTTTTAGCGG
1 AAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGG
12737817 TGCTTTTTTT
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 77 0.71
44 31 0.29
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGA
Found at i:12737929 original size:31 final size:31
Alignment explanation
Indices: 12737894--12737976 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
12737884 CTTCCTGCAT
* * *
12737894 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATACAACCAAAAACAACAAATATAACA
* * *
12737925 TAAAATACAGCCAAAAACAGCAAATTTAACA
1 TAAAATACAACCAAAAACAACAAATATAACA
12737956 TAAAAAATACAACCAAAAACA
1 T--AAAATACAACCAAAAACA
12737977 TTAATTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 26 0.60
33 17 0.40
ACGTcount: A:0.63, C:0.19, G:0.02, T:0.16
Consensus pattern (31 bp):
TAAAATACAACCAAAAACAACAAATATAACA
Found at i:12738245 original size:21 final size:21
Alignment explanation
Indices: 12738221--12738266 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12738211 GCTCGTGCCT
*
12738221 CTGCCTCTCTCGCTGCAGCCG
1 CTGCCTCCCTCGCTGCAGCCG
* * *
12738242 CTGCCTCCCTCTCTGCTGCCT
1 CTGCCTCCCTCGCTGCAGCCG
12738263 CTGC
1 CTGC
12738267 TCTAAGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.50, G:0.20, T:0.28
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCAGCCG
Found at i:12743861 original size:9 final size:9
Alignment explanation
Indices: 12743847--12743968 Score: 118
Period size: 9 Copynumber: 12.9 Consensus size: 9
12743837 ATGTATTAGT
12743847 TAAGTTATG
1 TAAGTTATG
12743856 TAAGTTGTTATG
1 TAA---GTTATG
*
12743868 TACGTTATG
1 TAAGTTATG
*
12743877 TGAGTTATG
1 TAAGTTATG
*
12743886 TAAATTATG
1 TAAGTTATG
12743895 TAAGTTATG
1 TAAGTTATG
*
12743904 TAAATTATG
1 TAAGTTATG
12743913 TAAGTTGTTATG
1 TAA---GTTATG
*
12743925 TAAATTATG
1 TAAGTTATG
*
12743934 TAAGTTATA
1 TAAGTTATG
*
12743943 TGAGTTATG
1 TAAGTTATG
12743952 TAAGTTATG
1 TAAGTTATG
*
12743961 TAATTTAT
1 TAAGTTAT
12743969 TGAAGTAATG
Statistics
Matches: 92, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
9 76 0.83
12 16 0.17
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:12743923 original size:57 final size:57
Alignment explanation
Indices: 12743851--12743968 Score: 173
Period size: 57 Copynumber: 2.1 Consensus size: 57
12743841 ATTAGTTAAG
** * *
12743851 TTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATGTAAA
1 TTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATGTAAA
* * *
12743908 TTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATGTAAT
1 TTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATGTAAA
12743965 TTAT
1 TTAT
12743969 TGAAGTAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.47
Consensus pattern (57 bp):
TTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATGTAAA
Found at i:12748227 original size:25 final size:25
Alignment explanation
Indices: 12748195--12748253 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
12748185 AGCGGAGAGC
12748195 GACGGCGAAGGGACGCAGAAGAGAT
1 GACGGCGAAGGGACGCAGAAGAGAT
12748220 GACGGCGAAGGGACGCAGAAGAGAT
1 GACGGCGAAGGGACGCAGAAGAGAT
12748245 GACGGCGAA
1 GACGGCGAA
12748254 CAACGATGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.44, T:0.03
Consensus pattern (25 bp):
GACGGCGAAGGGACGCAGAAGAGAT
Found at i:12748799 original size:158 final size:156
Alignment explanation
Indices: 12748503--12748877 Score: 381
Period size: 158 Copynumber: 2.4 Consensus size: 156
12748493 ATCTTTGAAG
* *
12748503 AAAACGACGCCG-TTCCTGTTAAGCACTA-A-TGTTTTTTGCGGCGTTTATT-TAAAAAACGCCG
1 AAAACGACGCCGTTTTC-GTTAA--ACTATACTGTATTTTGCGGCGTTT-TTAT-AAAAACGCCG
* * *
12748564 CTAATCCCTATATACTCAACTAAAACGACGACGTGTACTATAAACTTGAATTATTTTGCGGCGTT
61 CAAATCCCTATATACTCAACTAAAACGACGACGTGTACCATAAACTTGAATTATGTTGCGGCGTT
* *
12748629 TTTGAAAGCGCCACTAATACCCGTAT--ATACT
126 TTTAAAAACGCCACTAATACCC-TATCAAT-CT
* *
12748660 AAAACGGCGCCGTTTTCGTTAAACTA-ATCTGTATTTTGTGGCGTTTTCTATAAAAACGCCGCAA
1 AAAACGACGCCGTTTTCGTTAAACTATA-CTGTATTTTGCGGCGTTTT-TATAAAAACGCCGCAA
* * * * * *
12748724 ATCCCCTATATATTGAACTAAAACGACGACGCT-T-CCAGTACACTTTACTTCTGTTGCGGCGTT
64 AT-CCCTATATACTCAACTAAAACGACGACG-TGTACCA-TAAACTTGAATTATGTTGCGGCGTT
* *
12748787 TTTAAAAACGCCACTAGTACTCTATCAATCT
126 TTTAAAAACGCCACTAATACCCTATCAATCT
* * * *
12748818 AAAACGACGCCGTTTTCTTTCAACTATACTGTTTTTTGCGGCGTTTTTTTAAAAAACGCC
1 AAAACGACGCCGTTTTCGTTAAACTATACTGTATTTTGCGGCGTTTTTAT-AAAAACGCC
12748878 ACTAATCTCT
Statistics
Matches: 183, Mismatches: 23, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
155 5 0.03
156 1 0.01
157 53 0.29
158 120 0.66
159 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (156 bp):
AAAACGACGCCGTTTTCGTTAAACTATACTGTATTTTGCGGCGTTTTTATAAAAACGCCGCAAAT
CCCTATATACTCAACTAAAACGACGACGTGTACCATAAACTTGAATTATGTTGCGGCGTTTTTAA
AAACGCCACTAATACCCTATCAATCT
Found at i:12749872 original size:14 final size:14
Alignment explanation
Indices: 12749852--12749896 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
12749842 TCCTACACCT
12749852 TAAACCCTAAACTA
1 TAAACCCTAAACTA
* *
12749866 TATACCCTAAACCA
1 TAAACCCTAAACTA
12749880 TAAACCCTAAACTA
1 TAAACCCTAAACTA
12749894 TAA
1 TAA
12749897 TGATAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:12750181 original size:7 final size:7
Alignment explanation
Indices: 12750169--12750274 Score: 88
Period size: 7 Copynumber: 15.1 Consensus size: 7
12750159 AAAAATGCCA
12750169 CTAAACC
1 CTAAACC
12750176 CTAAACC
1 CTAAACC
*
12750183 CTAAACT
1 CTAAACC
12750190 CTAAACC
1 CTAAACC
*
12750197 CTTAACC
1 CTAAACC
* *
12750204 ATTAACC
1 CTAAACC
*
12750211 CCAAACC
1 CTAAACC
*
12750218 CTTACACC
1 C-TAAACC
* *
12750226 TTAAACT
1 CTAAACC
12750233 CT-AACC
1 CTAAACC
*
12750239 CTAACCC
1 CTAAACC
12750246 CTAAACC
1 CTAAACC
*
12750253 CTAAATC
1 CTAAACC
* *
12750260 ATAATCC
1 CTAAACC
12750267 CTAAACC
1 CTAAACC
12750274 C
1 C
12750275 ATAATTCATC
Statistics
Matches: 75, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
6 5 0.07
7 66 0.88
8 4 0.05
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:12750329 original size:14 final size:14
Alignment explanation
Indices: 12750312--12750409 Score: 61
Period size: 14 Copynumber: 6.7 Consensus size: 14
12750302 AGTTAACTCC
*
12750312 TAAACCTTAAACCT
1 TAAACCATAAACCT
* *
12750326 TAAACCATATATCT
1 TAAACCATAAACCT
* *
12750340 TAAACTATAGTTAACTCA
1 TAAACCATA---AAC-CT
* *
12750358 TAAACCTTAAACCC
1 TAAACCATAAACCT
* *
12750372 TAAACCATATATCT
1 TAAACCATAAACCT
*
12750386 TAAACCATAAACCA
1 TAAACCATAAACCT
*
12750400 TAAACTATAA
1 TAAACCATAA
12750410 TGATAATTAA
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
14 50 0.81
15 3 0.05
17 1 0.02
18 8 0.13
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.29
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:12750341 original size:21 final size:21
Alignment explanation
Indices: 12750317--12750401 Score: 82
Period size: 21 Copynumber: 3.9 Consensus size: 21
12750307 ACTCCTAAAC
12750317 CTTAAACCTTAAACCATATAT
1 CTTAAACCTTAAACCATATAT
* *
12750338 CTTAAA-CTATAGTTAACTCATAAAC
1 CTTAAACCT-TA---AAC-CATATAT
*
12750363 CTTAAACCCTAAACCATATAT
1 CTTAAACCTTAAACCATATAT
*
12750384 CTTAAACCATAAACCATA
1 CTTAAACCTTAAACCATA
12750402 AACTATAATG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.04
21 30 0.58
22 3 0.06
24 3 0.06
25 13 0.25
26 1 0.02
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.29
Consensus pattern (21 bp):
CTTAAACCTTAAACCATATAT
Found at i:12750354 original size:46 final size:46
Alignment explanation
Indices: 12750301--12750390 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
12750291 CTTCAAATAC
* *
12750301 TAGTTAACTCCTAAACCTTAAACCTTAAACCATATATCTTAAACTA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACTA
12750347 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAAC
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAAC
12750391 CATAAACCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.31
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACTA
Found at i:12750409 original size:7 final size:7
Alignment explanation
Indices: 12750356--12750409 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
12750346 ATAGTTAACT
12750356 CATAAAC
1 CATAAAC
*
12750363 CTTAAAC
1 CATAAAC
*
12750370 CCTAAAC
1 CATAAAC
* *
12750377 CATATAT
1 CATAAAC
*
12750384 CTTAAAC
1 CATAAAC
12750391 CATAAAC
1 CATAAAC
12750398 CATAAAC
1 CATAAAC
*
12750405 TATAA
1 CATAA
12750410 TGATAATTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (7 bp):
CATAAAC
Found at i:12750708 original size:40 final size:39
Alignment explanation
Indices: 12750566--12750731 Score: 181
Period size: 40 Copynumber: 4.1 Consensus size: 39
12750556 GTTATATGAC
* *
12750566 TTTTAGCGGCGTTTTTACAAAA-GCGCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTATAAAACGC-CGCTATTGCTCT-GT
* *
12750606 TTTTAGCGGCGTTTTTATAAAAGCGCTGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTTATAAAA-CGCCGCTATTGCTCTGT
* * *
12750646 TTTTTGCGGCATTTTTACTAAAACGCCCCTATTGCTCTGT
1 TTTTAGCGGCGTTTTTA-TAAAACGCCGCTATTGCTCTGT
* * *
12750686 TTTTAGTGGCGTTTTTGGTAAAACGCCGCTATTGCTATGT
1 TTTTAGCGGCGTTTTT-ATAAAACGCCGCTATTGCTCTGT
12750726 GTTTTA
1 -TTTTA
12750732 CAATTTTTGC
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
40 85 0.79
41 21 0.19
42 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (39 bp):
TTTTAGCGGCGTTTTTATAAAACGCCGCTATTGCTCTGT
Found at i:12750771 original size:12 final size:12
Alignment explanation
Indices: 12750754--12750780 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12750744 CGTTTTATCA
12750754 AAAAACGCCGCT
1 AAAAACGCCGCT
12750766 AAAAACGCCGCT
1 AAAAACGCCGCT
12750778 AAA
1 AAA
12750781 GCCCTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAAACGCCGCT
Found at i:12756201 original size:41 final size:41
Alignment explanation
Indices: 12756149--12756231 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
12756139 TCACTGTATT
12756149 AAAGTACGTATGAATTGATGCACTTTTGCAAAATCATTGCA
1 AAAGTACGTATGAATTGATGCACTTTTGCAAAATCATTGCA
*
12756190 AAAGTATGTATGAATTGATGCACTTTTGCAAAATCATTGCA
1 AAAGTACGTATGAATTGATGCACTTTTGCAAAATCATTGCA
12756231 A
1 A
12756232 GTGCAAATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (41 bp):
AAAGTACGTATGAATTGATGCACTTTTGCAAAATCATTGCA
Found at i:12757774 original size:24 final size:25
Alignment explanation
Indices: 12757729--12757776 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
12757719 TAAATAAAAA
*
12757729 ATTTAAAATATAATAAATCAAATAC
1 ATTTAAAATATAATAAAACAAATAC
*
12757754 ATTTAAAA-ATATTAAAACAAATA
1 ATTTAAAATATAATAAAACAAATA
12757777 TTAAAACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (25 bp):
ATTTAAAATATAATAAAACAAATAC
Found at i:12757775 original size:12 final size:12
Alignment explanation
Indices: 12757760--12757785 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12757750 ATACATTTAA
12757760 AAATATTAAAAC
1 AAATATTAAAAC
12757772 AAATATTAAAAC
1 AAATATTAAAAC
12757784 AA
1 AA
12757786 GAAACAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:12757874 original size:28 final size:29
Alignment explanation
Indices: 12757843--12757901 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
12757833 TTGAAAATAT
** *
12757843 AATAAAAAGTAGTTAT-ATTAAAATTAAA
1 AATAAAAAGTAAATATAATTAAAAATAAA
*
12757871 AATAAAATGTAAATATAATTAAAAATAAA
1 AATAAAAAGTAAATATAATTAAAAATAAA
12757900 AA
1 AA
12757902 AATATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (29 bp):
AATAAAAAGTAAATATAATTAAAAATAAA
Found at i:12759660 original size:43 final size:43
Alignment explanation
Indices: 12759544--12759670 Score: 109
Period size: 43 Copynumber: 2.9 Consensus size: 43
12759534 ATTGTTTCTG
* **
12759544 TTTATCCGATGATGCACTATGCGTGCTAATATA-ATTGCTTCGGC
1 TTTATCCGATGATGCACTATGCGTGC-AGTATACATT-CTTCGAA
* ** *
12759588 TTGT-TCAG-TGATGCACTATGTATACCAGTATACATTCTTC-AA
1 TT-TATCCGATGATGCACTATGCGT-GCAGTATACATTCTTCGAA
*
12759630 TTTATCCGATGATGCACTATGCGTGTCAGTATACTTTCTTC
1 TTTATCCGATGATGCACTATGCGTG-CAGTATACATTCTTC
12759671 TGATTATTAG
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
41 1 0.02
42 5 0.08
43 49 0.75
44 9 0.14
45 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (43 bp):
TTTATCCGATGATGCACTATGCGTGCAGTATACATTCTTCGAA
Found at i:12760192 original size:30 final size:30
Alignment explanation
Indices: 12760135--12760199 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
12760125 AATAGTCTAT
*
12760135 ATTTTTATAATTTTTAAAAGATTAAATAAA
1 ATTTTTATAATTTTTAAAAGATAAAATAAA
* * *
12760165 ATTTTTATTA-TTTTAAAAGGTCAAAATACA
1 ATTTTTATAATTTTTAAAAGAT-AAAATAAA
12760195 ATTTT
1 ATTTT
12760200 ACTATTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAGATAAAATAAA
Found at i:12760222 original size:22 final size:21
Alignment explanation
Indices: 12760194--12760254 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
12760184 GTCAAAATAC
*
12760194 AATTTTACTATTACTAATTTAA
1 AATTTTACTATTA-TAAATTAA
12760216 AATTTTA-TAAATTATAAATTAA
1 AATTTTACT--ATTATAAATTAA
* *
12760238 AAATTTACTATTTTAAA
1 AATTTTACTATTATAAA
12760255 GAAGTCTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 8 0.24
22 20 0.61
23 5 0.15
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTTACTATTATAAATTAA
Found at i:12762703 original size:16 final size:16
Alignment explanation
Indices: 12762679--12762720 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
12762669 TTTGGTTCGC
* *
12762679 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
12762695 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
12762711 TGTAATGGAA
1 TGTAATGGAA
12762721 AAGCTGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:12762986 original size:18 final size:17
Alignment explanation
Indices: 12762965--12762999 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12762955 TTATTATTAA
*
12762965 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12762983 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12763000 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12763007 original size:79 final size:79
Alignment explanation
Indices: 12762924--12763162 Score: 210
Period size: 79 Copynumber: 3.1 Consensus size: 79
12762914 TTATTATCAA
12762924 TAATAAATCATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
1 TAATAAATCATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
12762989 TTTAATAAAATTCT
66 TTTAATAAAATTCT
* * * * **** * * *
12763003 TAATAATTAGCA-TAAAT-TTGTTTTGGTA-AATTATTATT--GT-TATTGTT-ATTTAAAT-TT
1 TAATAA--ATCATTTAATCATATTTAAACATAATTATTATTAAATATATT-TTAATTAAAATATA
* * *
12763060 TAA--TAAGATTAATATCAA
63 TAATTTAATA-AAAT-TC-T
* *
12763078 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
1 TAATAAATCATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
12763143 TTTAATAAAATTCT
66 TTTAATAAAATTCT
12763157 TAATAA
1 TAATAA
12763163 TTAATATTCT
Statistics
Matches: 114, Mismatches: 30, Indels: 32
0.65 0.17 0.18
Matches are distributed among these distances:
72 4 0.04
73 5 0.04
74 10 0.09
75 22 0.19
76 13 0.11
78 12 0.11
79 28 0.25
80 10 0.09
81 6 0.05
82 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (79 bp):
TAATAAATCATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
TTTAATAAAATTCT
Found at i:12763136 original size:16 final size:16
Alignment explanation
Indices: 12763099--12763140 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12763089 TTAATCATAT
*
12763099 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
12763115 TT-AAATATATTATAA
1 TTAAAATATATTATAA
12763130 TTAAAATATAT
1 TTAAAATATAT
12763141 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:12763139 original size:154 final size:156
Alignment explanation
Indices: 12762852--12763165 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 156
12762842 TAGAATACCC
12762852 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
* *
12762917 TTATCAATAATAAATCATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
12762982 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAATAA
* *
12763009 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
12763072 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
12763137 ATATAATTTAATAAAATTCTTAATAA
131 ATATAATTTAATAAAATTCTTAATAA
12763163 TTA
1 TTA
12763166 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
154 92 0.60
155 1 0.01
157 60 0.39
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAA
Found at i:12763147 original size:14 final size:15
Alignment explanation
Indices: 12763108--12763149 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12763098 TTTAAACATA
*
12763108 ATTATTATTAAATAT
1 ATTATAATTAAATAT
12763123 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
12763137 A-TATAATTTAATA
1 ATTATAATTAAATA
12763150 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:12763268 original size:18 final size:17
Alignment explanation
Indices: 12763229--12763260 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12763219 TTTTAAATAA
12763229 TTAATATTAAATATATT
1 TTAATATTAAATATATT
12763246 TTAAT-TTAAATATAT
1 TTAATATTAAATATAT
12763261 GATTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATTAAATATATT
Found at i:12776512 original size:43 final size:43
Alignment explanation
Indices: 12776458--12776616 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
12776448 AGCTCGTACA
*
12776458 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
* * * *
12776501 ATGCCATTGTCCCAGACAG-GGTCTTACACGAAATGATATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAATCAAATATCG
* * *
12776543 ATGCCAATGTCCTAGACATGGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGT-AATC-AAATATCG
* ** *
12776587 ATGCCAACGTCTTAGACGTGCTCTTACACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG
12776617 ATAACACATA
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 28 0.29
43 37 0.39
44 30 0.32
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
Found at i:12784489 original size:18 final size:18
Alignment explanation
Indices: 12784450--12784493 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
12784440 TCAAATAAAT
* **
12784450 TATTAAAAAAATTTAAAA
1 TATTTAAAAAATAAAAAA
12784468 -ATTTAAAAAATAAAAAA
1 TATTTAAAAAATAAAAAA
12784485 TATTTAAAA
1 TATTTAAAA
12784494 TATATAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TATTTAAAAAATAAAAAA
Found at i:12784821 original size:5 final size:5
Alignment explanation
Indices: 12784811--12784854 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
12784801 GAAAATTAAG
12784811 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
12784855 TTATTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:12795506 original size:13 final size:14
Alignment explanation
Indices: 12795490--12795518 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12795480 ATCAACCATT
12795490 AAAAATCTAG-AAA
1 AAAAATCTAGTAAA
12795503 AAAAATCTAGTAAA
1 AAAAATCTAGTAAA
12795517 AA
1 AA
12795519 CTTGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAATCTAGTAAA
Found at i:12795817 original size:22 final size:22
Alignment explanation
Indices: 12795792--12795834 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12795782 TCTCCCTATT
12795792 TTGCTACCATTTTACTATTATG
1 TTGCTACCATTTTACTATTATG
** *
12795814 TTGCTATTATTTTATTATTAT
1 TTGCTACCATTTTACTATTAT
12795835 TGTTTTGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTACTATTATG
Found at i:12795900 original size:30 final size:30
Alignment explanation
Indices: 12795864--12795925 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
12795854 ACTTAATTTA
12795864 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
12795894 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
12795924 TT
1 TT
12795926 ACTTGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:12801037 original size:26 final size:26
Alignment explanation
Indices: 12801008--12801078 Score: 142
Period size: 26 Copynumber: 2.7 Consensus size: 26
12800998 AATAGACTCA
12801008 TAATTCTATTTCTACTATTAATCATT
1 TAATTCTATTTCTACTATTAATCATT
12801034 TAATTCTATTTCTACTATTAATCATT
1 TAATTCTATTTCTACTATTAATCATT
12801060 TAATTCTATTTCTACTATT
1 TAATTCTATTTCTACTATT
12801079 TTTTGTGATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (26 bp):
TAATTCTATTTCTACTATTAATCATT
Found at i:12801909 original size:93 final size:93
Alignment explanation
Indices: 12801782--12801952 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
12801772 CCCATAAGCG
*
12801782 AACTCAGACTCAACTCAATGAGCTCGAGCTTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGCTCGAGCTTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
12801847 GAGTTCGAATGCCTAGTTACATCTCACA
66 GAGTTCGAATGCCTAGTTACATCTCACA
* * *
12801875 AACTCGGACTCAACTCAACGAGTTCG-GGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCAGACTCAACTCAACGAGCTCGAGCT-TTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
12801939 CGAGTTCGGATGCC
65 CGAGTTCGAATGCC
12801953 CAAATATCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (93 bp):
AACTCAGACTCAACTCAACGAGCTCGAGCTTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGAATGCCTAGTTACATCTCACA
Found at i:12801947 original size:46 final size:47
Alignment explanation
Indices: 12801773--12801946 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 47
12801763 TGTAACCCGC
* * * *
12801773 CCATAAGCGAACTCAGACTCAACTCAATGAGCTCGAGCT-TTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAGCTGTTCGCAT
*
12801819 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG-A-G-CT-GTTCGCAT
* *
12801869 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCG-GGTGTTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGAGCTGTTCGCAT
12801912 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
12801947 GATGCCCAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 5 0.05
43 6 0.06
44 1 0.01
46 57 0.53
47 27 0.25
48 1 0.01
49 2 0.02
50 5 0.05
51 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAGCTGTTCGCAT
Found at i:12815667 original size:53 final size:53
Alignment explanation
Indices: 12815553--12815672 Score: 132
Period size: 53 Copynumber: 2.3 Consensus size: 53
12815543 CCTAGCTCAT
* * * ** *
12815553 AAGGAGCATGCAGAATGAGACATATCACAAATCTCACAAAAACCCATGTTTTT
1 AAGGAGCACGCAGAATGAAACATATCACAAAACTCACAAAAACCCATACTTTC
** * * *
12815606 AAATAGCACGCAGAGTGAAACTTATCACAAAACTCACAAAAGCCCATACTTTC
1 AAGGAGCACGCAGAATGAAACATATCACAAAACTCACAAAAACCCATACTTTC
*
12815659 GAGGAGCACGCAGA
1 AAGGAGCACGCAGA
12815673 CTGAGGCTCA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (53 bp):
AAGGAGCACGCAGAATGAAACATATCACAAAACTCACAAAAACCCATACTTTC
Found at i:12819848 original size:16 final size:16
Alignment explanation
Indices: 12819827--12819895 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
12819817 TTTGGTTCGC
12819827 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
12819843 TGTATTTGATTAGAGG
1 TGTATTGGATTAGAGG
12819859 TGTATTAGGATTAGAGG
1 TGTATT-GGATTAGAGG
12819876 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12819892 TGTA
1 TGTA
12819896 ATAGCTAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 35 0.70
17 15 0.30
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:12819871 original size:33 final size:32
Alignment explanation
Indices: 12819827--12819895 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
12819817 TTTGGTTCGC
*
12819827 TGTATTGGATTAGAGGTGTATTTGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
12819859 TGTATTAGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
12819892 TGTA
1 TGTA
12819896 ATAGCTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:12820152 original size:18 final size:19
Alignment explanation
Indices: 12820131--12820167 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12820121 TTATTATTAA
12820131 ATAT-ATTT-TAATTAAAAT
1 ATATAATTTATAA-TAAAAT
12820149 ATATAATTTATAATAAAAT
1 ATATAATTTATAATAAAAT
12820168 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 10 0.59
20 3 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATTTATAATAAAAT
Found at i:12820275 original size:59 final size:58
Alignment explanation
Indices: 12820209--12820394 Score: 157
Period size: 59 Copynumber: 3.1 Consensus size: 58
12820199 CTCAAATCAT
* *
12820209 AATATATGATACTATAAAATATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTT-AAATAATTATTATTAAATATATTTTAATAAA
* * * * *
12820268 AATATATGAT-TTAATAAAATTCTTAATATTAAAT-ATTCTTATATGAAT-T-TTCTAA-AATCA
1 AATATATGATACT-ATAAAA-T-ATAAT-TTAAATAATTATTAT-TAAATATATTTTAATAA--A
* **
12820328 TAATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAAGTTAATAAA
1 -AATATATGATACTATAAAATATAATTTAA-ATAATTATTATTAAATATATTTTAATAAA
12820388 AATATAT
1 AATATAT
12820395 AATTTATCAT
Statistics
Matches: 98, Mismatches: 15, Indels: 28
0.70 0.11 0.20
Matches are distributed among these distances:
58 6 0.06
59 38 0.39
60 19 0.19
61 30 0.31
62 5 0.05
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (58 bp):
AATATATGATACTATAAAATATAATTTAAATAATTATTATTAAATATATTTTAATAAA
Found at i:12820332 original size:120 final size:120
Alignment explanation
Indices: 12820111--12820400 Score: 456
Period size: 120 Copynumber: 2.4 Consensus size: 120
12820101 TTAATCATAT
12820111 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTATAATAAAATTCTTAATA
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAA-TT-TAATAAAATTCTTAATA
* * *
12820176 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
64 ATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
12820233 TTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
12820297 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
** *
12820353 TTTAACATAATTATTATTAAATATAAGTTAATAAAAATATATAATTTA
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTA
12820401 TCATCATACT
Statistics
Matches: 154, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
119 2 0.01
120 109 0.71
121 2 0.01
122 39 0.25
123 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:12824632 original size:16 final size:16
Alignment explanation
Indices: 12824608--12824656 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
12824598 AACCATACCA
12824608 AAATATTCAAAGTTTC
1 AAATATTCAAAGTTTC
*
12824624 AAATCTTCAAA---TC
1 AAATATTCAAAGTTTC
*
12824637 AAATATTCGAAGTTTC
1 AAATATTCAAAGTTTC
12824653 AAAT
1 AAAT
12824657 CTTGAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 11 0.41
16 16 0.59
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (16 bp):
AAATATTCAAAGTTTC
Found at i:12824643 original size:29 final size:29
Alignment explanation
Indices: 12824608--12824669 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
12824598 AACCATACCA
12824608 AAATATTCAAAGTTTCAAATCTTCAAATC
1 AAATATTCAAAGTTTCAAATCTTCAAATC
* * *
12824637 AAATATTCGAAGTTTCAAATCTTGAATTC
1 AAATATTCAAAGTTTCAAATCTTCAAATC
12824666 AAAT
1 AAAT
12824670 TTTATATTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (29 bp):
AAATATTCAAAGTTTCAAATCTTCAAATC
Found at i:12833560 original size:43 final size:43
Alignment explanation
Indices: 12833499--12833587 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
12833489 CTTGCTCGAC
**
12833499 TCACCGGCATTAAGCCTGCTAGGCACGAAGACCCAAATACACA
1 TCACCGGCACAAAGCCTGCTAGGCACGAAGACCCAAATACACA
* *
12833542 TCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACAAAGCCTGCTAGGCACGAAGACCCAAATACACA
12833585 TCA
1 TCA
12833588 TCGAGTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.34, G:0.20, T:0.12
Consensus pattern (43 bp):
TCACCGGCACAAAGCCTGCTAGGCACGAAGACCCAAATACACA
Found at i:12835222 original size:38 final size:38
Alignment explanation
Indices: 12835136--12835276 Score: 169
Period size: 38 Copynumber: 3.7 Consensus size: 38
12835126 AAACCCGAAC
* *
12835136 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGAT
1 ATAATACCAGCACGAAGCCTGCGGGA-TTT-AACTCAGAT
* *
12835176 ATAATACCAGCACTAGGCCTGCGGGATTTAA-TCTAGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACTC-AGAT
*
12835214 ATAATACCAGCACGAAGCCTGCGGGATTTAACTCGGAT
1 ATAATACCAGCACGAAGCCTGCGGGATTTAACTCAGAT
* *
12835252 ATAATTCCAGCA-TATAGCCTGCGGG
1 ATAATACCAGCACGA-AGCCTGCGGG
12835277 TCTTTAAGCC
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
37 3 0.03
38 59 0.66
39 5 0.06
40 22 0.25
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (38 bp):
ATAATACCAGCACGAAGCCTGCGGGATTTAACTCAGAT
Found at i:12838483 original size:18 final size:18
Alignment explanation
Indices: 12838460--12838521 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 18
12838450 ATGAACTGTA
12838460 AGCTCACCAAAATGTGCG
1 AGCTCACCAAAATGTGCG
12838478 AGCTCACC-AAATGTGCG
1 AGCTCACCAAAATGTGCG
* * *
12838495 CA-CTTACCAAGAT-TGCT
1 -AGCTCACCAAAATGTGCG
12838512 AGCTCACCAA
1 AGCTCACCAA
12838522 CACTACGAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.03
17 24 0.65
18 12 0.32
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19
Consensus pattern (18 bp):
AGCTCACCAAAATGTGCG
Found at i:12840711 original size:13 final size:13
Alignment explanation
Indices: 12840693--12840717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12840683 AACATGGATT
12840693 CAAACAAACTATG
1 CAAACAAACTATG
12840706 CAAACAAACTAT
1 CAAACAAACTAT
12840718 TTAATCAAAG
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:0.56, C:0.24, G:0.04, T:0.16
Consensus pattern (13 bp):
CAAACAAACTATG
Found at i:12841498 original size:34 final size:34
Alignment explanation
Indices: 12841455--12841524 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
12841445 GACACATACA
12841455 ATGTAAACAATCAAATTAAAAAGAACTATCATTT
1 ATGTAAACAATCAAATTAAAAAGAACTATCATTT
12841489 ATGTAAACAATCAAATTAAAAAGAACTATCATTT
1 ATGTAAACAATCAAATTAAAAAGAACTATCATTT
12841523 AT
1 AT
12841525 TGTACCTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (34 bp):
ATGTAAACAATCAAATTAAAAAGAACTATCATTT
Found at i:12844160 original size:23 final size:23
Alignment explanation
Indices: 12844122--12844176 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
12844112 TTGAATTGAA
12844122 GATTTGAA-A-CTTCGAATATTT
1 GATTTGAAGATCTTCGAATATTT
*
12844143 TATTTGAAGATCTTCGAATATTT
1 GATTTGAAGATCTTCGAATATTT
*
12844166 GAATTGAAGAT
1 GATTTGAAGAT
12844177 TTGAAACTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 7 0.24
22 1 0.03
23 21 0.72
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (23 bp):
GATTTGAAGATCTTCGAATATTT
Found at i:12844601 original size:16 final size:17
Alignment explanation
Indices: 12844563--12844603 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
12844553 AAACATTAAA
*
12844563 ATAATATATAAAATTAT
1 ATAATATATAAAATAAT
12844580 -TAA-ATATTAAAATAAT
1 ATAATATA-TAAAATAAT
12844596 ATAATATA
1 ATAATATA
12844604 AATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 3 0.15
16 11 0.55
17 3 0.15
18 3 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATATATAAAATAAT
Found at i:12844979 original size:21 final size:21
Alignment explanation
Indices: 12844964--12845002 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
12844954 TTTTTATTTA
12844964 TCAAAATTACATTTTTTTAAC
1 TCAAAATTACATTTTTTTAAC
12844985 TCAAAATT--ATTTTTTTAA
1 TCAAAATTACATTTTTTTAA
12845003 TGTACCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
TCAAAATTACATTTTTTTAAC
Found at i:12846323 original size:31 final size:32
Alignment explanation
Indices: 12846285--12846359 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 32
12846275 GTATAATAGG
* *
12846285 CCCACATGCCCA-TGTGGCTTGCCTATGTTGA
1 CCCACATGCCCAGTATGGCTTGCCCATGTTGA
*
12846316 CCCACATG-CCAGTATGGCTTGCCCATGTTGG
1 CCCACATGCCCAGTATGGCTTGCCCATGTTGA
*
12846347 CCCACACGCCCAG
1 CCCACATGCCCAG
12846360 ATTGGCCTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 3 0.08
31 31 0.82
32 4 0.11
ACGTcount: A:0.17, C:0.37, G:0.23, T:0.23
Consensus pattern (32 bp):
CCCACATGCCCAGTATGGCTTGCCCATGTTGA
Found at i:12848263 original size:44 final size:44
Alignment explanation
Indices: 12848213--12848305 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
12848203 GAAATATAGA
* **
12848213 ATAGGAAAGGTAAGATAGGTGGAAAACGATTATAAAATTTGAAG
1 ATAGGAAAGGTAAGATAAGTGGAAAACGACCATAAAATTTGAAG
* *
12848257 ATAGGAATGGTAAGATAAGTGGAAAACGACCATGAAATTTGAAG
1 ATAGGAAAGGTAAGATAAGTGGAAAACGACCATAAAATTTGAAG
12848301 ATAGG
1 ATAGG
12848306 CGGATTTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.46, C:0.04, G:0.28, T:0.22
Consensus pattern (44 bp):
ATAGGAAAGGTAAGATAAGTGGAAAACGACCATAAAATTTGAAG
Found at i:12848405 original size:65 final size:66
Alignment explanation
Indices: 12848246--12848466 Score: 256
Period size: 66 Copynumber: 3.3 Consensus size: 66
12848236 AAACGATTAT
*
12848246 AAAATTTGAAGATAGGAATGGTAAGATA-AGTGGAAAACGACCATG--AAATTTGAAGATAGGCG
1 AAAATTTG-A-ATAGGAATGGTAAGATAGA-TGGAAAAAGA--ATGTAAAATTTGAAGATAGGCG
*
12848308 GATTTC
61 GATTTG
* * *
12848314 AAAATTTGATTAGGGATGGTAAGATAGATGGAAAAAGAATGTAAAATTTAAAGATA-GCAGG-TT
1 AAAATTTGAATAGGAATGGTAAGATAGATGGAAAAAGAATGTAAAATTTGAAGATAGGC-GGATT
12848377 TG
65 TG
* * *
12848379 AAAATTTGAATAGGAATGGTAAGATAGGT-GAAAAATGACTATAAAATTTGAAGATAGGCGGATT
1 AAAATTTGAATAGGAATGGTAAGATAGATGGAAAAA-GAATGTAAAATTTGAAGATAGGCGGATT
12848443 TG
65 TG
*
12848445 AAAATTTGAATAGGGATGGTAA
1 AAAATTTGAATAGGAATGGTAA
12848467 AATGACTAAG
Statistics
Matches: 134, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
64 9 0.07
65 50 0.37
66 65 0.49
67 2 0.01
68 8 0.06
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (66 bp):
AAAATTTGAATAGGAATGGTAAGATAGATGGAAAAAGAATGTAAAATTTGAAGATAGGCGGATTT
G
Found at i:12855531 original size:23 final size:23
Alignment explanation
Indices: 12855469--12855534 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
12855459 ATTTTAATAG
*
12855469 ATTTAATATTAAATTTAATTTGAT
1 ATTTAATATTAAA-GTAATTTGAT
* * * *
12855493 ACTT-ATATTGATAGTATTTTGTT
1 ATTTAATATT-AAAGTAATTTGAT
12855516 ATTTAATATTAAAGTAATT
1 ATTTAATATTAAAGTAATT
12855535 ATCTTAATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (23 bp):
ATTTAATATTAAAGTAATTTGAT
Found at i:12864562 original size:871 final size:870
Alignment explanation
Indices: 12862880--12864623 Score: 3434
Period size: 871 Copynumber: 2.0 Consensus size: 870
12862870 GCAATTTTAA
12862880 GGTACCTAAAGATATGTTTGAAAGAAGGGACCTATGAGCCCACTTGATGTAGGATAATTACTATA
1 GGTACCTAAAGATATGTTTGAAAGAAGGGACCTATGAGCCCACTTGATGTAGGATAATTACTATA
12862945 TGAATGAGTTTGGAGCGTCAGACGTAGTCAAATGAAAGGTTTCTCTACAACGCTGAAAGTAAACA
66 TGAATGAGTTTGGAGCGTCAGACGTAGTCAAATGAAAGGTTTCTCTACAACGCTGAAAGTAAACA
12863010 CCAAGGAATGGTATCTCTCCCTTCTACAAGGATCTATTCATAATTTCTCGCAACTGGGACAAATG
131 CCAAGGAATGGTATCTCTCCCTTCTACAAGGATCTATTCATAATTTCTCGCAACTGGGACAAATG
12863075 TTCTTGGGTAGGTTCAAGGCCTATCGAGCAATCATGAACGCACTCATGAGGTTAATGTCAGTAAA
196 TTCTTGGGTAGGTTCAAGGCCTATCGAGCAATCATGAACGCACTCATGAGGTTAATGTCAGTAAA
12863140 GTAGTGGGAGGGTGAGTCCCTTCAAGACTACAAAAAAGGTCCTATGTGGCTACATTCAACACAAA
261 GTAGTGGGAGGGTGAGTCCCTTCAAGACTACAAAAAAGGTCCTATGTGGCTACATTCAACACAAA
12863205 AAACCTAGAAGACTAGTGGGCGATACACGCCTTCATTATGGAAGTGTAGAATGTCCACATGCAGT
326 AAACCTAGAAGACTAGTGGGCGATACACGCCTTCATTATGGAAGTGTAGAATGTCCACATGCAGT
12863270 ATTTATTCACAAACAATAGATTGCAGAGCCTAGCCGACCTATACGAGTGAGCCTATAAGTTCCTA
391 ATTTATTCACAAACAATAGATTGCAGAGCCTAGCCGACCTATACGAGTGAGCCTATAAGTTCCTA
12863335 AAGGCAAAAGAAATTAAGAGAACGTCGTAGGTCAATTTTCAAAGAGATGATCGACAACCCAAGAG
456 AAGGCAAAAGAAATTAAGAGAACGTCGTAGGTCAATTTTCAAAGAGATGATCGACAACCCAAGAG
12863400 TAGAGCGGGATAGCATAGTAGGTAATCTCCCATCAATCAATCCCTACGAGTCAAGATCGACAGAC
521 TAGAGCGGGATAGCATAGTAGGTAATCTCCCATCAATCAATCCCTACGAGTCAAGATCGACAGAC
* *
12863465 TACACAAGACCTTAGCCCAATGTGACACACTTAGAAACCCGCAAAGGCCCTAGTAGGAATACACA
586 TACACAAGACCTTAGCCCAATGTGACACACTTAGAAACCCGCAAAGGCCCCAGTAAGAATACACA
12863530 AGGCATAATCCTCCCCAGGGCAGGTTTGAGGCTTACACCTCGCTGAATGCCACGCGAGCCTACAT
651 AGGCATAATCCTCCCCAGGGCAGGTTTGAGGCTTACACCTCGCTGAATGCCACGCGAGCCTACAT
12863595 CCTTAACCTAGTAAAGAGCCTGGGCATCCTTCTTAAACCAACTCCGATGTGGAGTATTAGTAGAA
716 CCTTAACCTAGTAAAGAGCCTGGGCATCCTTCTTAAACCAACTCCGATGTGGAGTATTAGTAGAA
12863660 AGACGAAATCCAGGAACCGATGTGCCTTACACGATGATATAGGGCATAAGATGAAAGACTATTTT
781 AGACGAAATCCAGGAACCGATGTGCCTTACACGATGATATA-GGCATAAGATGAAAGACTATTTT
12863725 ACATTAAAGGACGCCATAAAAGAAGC
845 ACATTAAAGGACGCCATAAAAGAAGC
12863751 GGTACCTAAAGATATGTTTGAAAGAAGGGACCTATGAGCCCACTTGATGTAGGATAATTACTATA
1 GGTACCTAAAGATATGTTTGAAAGAAGGGACCTATGAGCCCACTTGATGTAGGATAATTACTATA
12863816 TGAATGAGTTTGGAGCGTCAGACGTAGTCAAATGAAAGGTTTCTCTACAACGCTGAAAGTAAACA
66 TGAATGAGTTTGGAGCGTCAGACGTAGTCAAATGAAAGGTTTCTCTACAACGCTGAAAGTAAACA
12863881 CCAAGGAATGGTATCTCTCCCTTCTACAAGGATCTATTCATAATTTCTCGCAACTGGGACAAATG
131 CCAAGGAATGGTATCTCTCCCTTCTACAAGGATCTATTCATAATTTCTCGCAACTGGGACAAATG
*
12863946 TTCTTGGGTAGGTTCAAGGCCTATCGAGCAATCATGAACGCATTCATGAGGTTAATGTCAGTAAA
196 TTCTTGGGTAGGTTCAAGGCCTATCGAGCAATCATGAACGCACTCATGAGGTTAATGTCAGTAAA
12864011 GTAGTGGGAGGGTGAGTCCCTTCAAGACTACAAAAAAGGTCCTATGTGGCTACATTCAACACAAA
261 GTAGTGGGAGGGTGAGTCCCTTCAAGACTACAAAAAAGGTCCTATGTGGCTACATTCAACACAAA
12864076 AAACCTAGAAGACTAGTGGGCGATACACGCCTTCATTATGGAAGTGTAGAATGTCCACATGCAGT
326 AAACCTAGAAGACTAGTGGGCGATACACGCCTTCATTATGGAAGTGTAGAATGTCCACATGCAGT
12864141 ATTTATTCACAAACAATAGATTGCAGAGCCTAGCCGACCTATACGAGTGAGCCTATAAGTTCCTA
391 ATTTATTCACAAACAATAGATTGCAGAGCCTAGCCGACCTATACGAGTGAGCCTATAAGTTCCTA
12864206 AAGGCAAAAGAAATTAAGAGAACGTCGTAGGTCAATTTTCAAAGAGATGATCGACAACCCAAGAG
456 AAGGCAAAAGAAATTAAGAGAACGTCGTAGGTCAATTTTCAAAGAGATGATCGACAACCCAAGAG
12864271 TAGAGCGGGATAGCATAGTAGGTAATCTCCCATCAATCAATCCCTACGAGTCAAGATCGACAGAC
521 TAGAGCGGGATAGCATAGTAGGTAATCTCCCATCAATCAATCCCTACGAGTCAAGATCGACAGAC
12864336 TACACAAGACCTTAGCCCAATGTGACACACTTAGAAACCCGCAAAGGCCCCAGTAAGAATACACA
586 TACACAAGACCTTAGCCCAATGTGACACACTTAGAAACCCGCAAAGGCCCCAGTAAGAATACACA
*
12864401 AGGCATAATCCTCCTCAGGGCAGGTTTGAGGCTTACACCTCGCTGAATGCCACGCGAGCCTACAT
651 AGGCATAATCCTCCCCAGGGCAGGTTTGAGGCTTACACCTCGCTGAATGCCACGCGAGCCTACAT
12864466 CCTTAACCTAGTAAAGAGCCTGGGCATCCTTCTTAAACCAACTCCGATGTGGAGTATTAGTAGAA
716 CCTTAACCTAGTAAAGAGCCTGGGCATCCTTCTTAAACCAACTCCGATGTGGAGTATTAGTAGAA
*
12864531 AGACGAAATCCAGGAACCGATGTGCCTTACACGATGATATAGGCATAAGATGAGAGACTATTTTA
781 AGACGAAATCCAGGAACCGATGTGCCTTACACGATGATATAGGCATAAGATGAAAGACTATTTTA
12864596 CATTAAAGGACGCCATAAAAGAAGC
846 CATTAAAGGACGCCATAAAAGAAGC
12864621 GGT
1 GGT
12864624 TCGGAATGGC
Statistics
Matches: 868, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
870 51 0.06
871 817 0.94
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (870 bp):
GGTACCTAAAGATATGTTTGAAAGAAGGGACCTATGAGCCCACTTGATGTAGGATAATTACTATA
TGAATGAGTTTGGAGCGTCAGACGTAGTCAAATGAAAGGTTTCTCTACAACGCTGAAAGTAAACA
CCAAGGAATGGTATCTCTCCCTTCTACAAGGATCTATTCATAATTTCTCGCAACTGGGACAAATG
TTCTTGGGTAGGTTCAAGGCCTATCGAGCAATCATGAACGCACTCATGAGGTTAATGTCAGTAAA
GTAGTGGGAGGGTGAGTCCCTTCAAGACTACAAAAAAGGTCCTATGTGGCTACATTCAACACAAA
AAACCTAGAAGACTAGTGGGCGATACACGCCTTCATTATGGAAGTGTAGAATGTCCACATGCAGT
ATTTATTCACAAACAATAGATTGCAGAGCCTAGCCGACCTATACGAGTGAGCCTATAAGTTCCTA
AAGGCAAAAGAAATTAAGAGAACGTCGTAGGTCAATTTTCAAAGAGATGATCGACAACCCAAGAG
TAGAGCGGGATAGCATAGTAGGTAATCTCCCATCAATCAATCCCTACGAGTCAAGATCGACAGAC
TACACAAGACCTTAGCCCAATGTGACACACTTAGAAACCCGCAAAGGCCCCAGTAAGAATACACA
AGGCATAATCCTCCCCAGGGCAGGTTTGAGGCTTACACCTCGCTGAATGCCACGCGAGCCTACAT
CCTTAACCTAGTAAAGAGCCTGGGCATCCTTCTTAAACCAACTCCGATGTGGAGTATTAGTAGAA
AGACGAAATCCAGGAACCGATGTGCCTTACACGATGATATAGGCATAAGATGAAAGACTATTTTA
CATTAAAGGACGCCATAAAAGAAGC
Found at i:12865637 original size:5 final size:5
Alignment explanation
Indices: 12865627--12865661 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
12865617 TAGGAAGATA
12865627 TTATT TTATT TTCATT TTA-T TTATT TTATT TTATT
1 TTATT TTATT TT-ATT TTATT TTATT TTATT TTATT
12865662 AAATTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:12865659 original size:14 final size:15
Alignment explanation
Indices: 12865631--12865661 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12865621 AAGATATTAT
12865631 TTTATTTTCATTTTA
1 TTTATTTTCATTTTA
12865646 TTTATTTT-ATTTTA
1 TTTATTTTCATTTTA
12865660 TT
1 TT
12865662 AAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTCATTTTA
Done.