Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 54 of 135
Found at i:14931778 original size:16 final size:16
Alignment explanation
Indices: 14931757--14931787 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14931747 ATAATGTGAA
14931757 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
14931773 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
14931788 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:14932635 original size:26 final size:26
Alignment explanation
Indices: 14932574--14932628 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
14932564 AATTTTAGGC
*
14932574 ACAATTTTGGACACGTTCATGCAGCG
1 ACAATTTTGGACACGTTCATGCAACG
*
14932600 ACAATTTTGGACATGTTCATGCAACG
1 ACAATTTTGGACACGTTCATGCAACG
14932626 ACA
1 ACA
14932629 TTCTTGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (26 bp):
ACAATTTTGGACACGTTCATGCAACG
Found at i:14932703 original size:37 final size:37
Alignment explanation
Indices: 14932662--14932752 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 37
14932652 TTCTTGCGGC
* *
14932662 GACAGTTTTGGGTGCAATCTAAAAGTGCTCATGCGAT
1 GACAGTTTTGGGCGCAATCTAAAAGTGCTCATACGAT
* * * * *
14932699 GACAGTTTTGTGCGCAATCTAGAAGTTCTCATATGGT
1 GACAGTTTTGGGCGCAATCTAAAAGTGCTCATACGAT
*
14932736 GACAGTTTTTGGCGCAA
1 GACAGTTTTGGGCGCAA
14932753 ATTTGGATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (37 bp):
GACAGTTTTGGGCGCAATCTAAAAGTGCTCATACGAT
Found at i:14939177 original size:21 final size:21
Alignment explanation
Indices: 14939153--14939221 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
14939143 GACCATACAA
14939153 TACTAACTTACAAAATGCAAT
1 TACTAACTTACAAAATGCAAT
** * *
14939174 TACTAAAATA-AGATCATACAA-
1 TACTAACTTACA-A-AATGCAAT
14939195 TACTAACTTACAAAATGCAAT
1 TACTAACTTACAAAATGCAAT
14939216 TACTAA
1 TACTAA
14939222 GTATAAAATG
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 6 0.17
21 24 0.67
22 6 0.17
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (21 bp):
TACTAACTTACAAAATGCAAT
Found at i:14939183 original size:42 final size:42
Alignment explanation
Indices: 14939136--14939221 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
14939126 AAAATGAAAG
14939136 AAAATAAGACCATACAATACTAACTTACAAAATGCAATTACT
1 AAAATAAGACCATACAATACTAACTTACAAAATGCAATTACT
*
14939178 AAAATAAGATCATACAATACTAACTTACAAAATGCAATTACT
1 AAAATAAGACCATACAATACTAACTTACAAAATGCAATTACT
14939220 AA
1 AA
14939222 GTATAAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.24
Consensus pattern (42 bp):
AAAATAAGACCATACAATACTAACTTACAAAATGCAATTACT
Found at i:14940663 original size:19 final size:17
Alignment explanation
Indices: 14940639--14940677 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
14940629 CTTTTTCTTT
*
14940639 TTCTCTTGCTTCTTCTCTC
1 TTCTCTT-CTTCCTC-CTC
14940658 TTCTCTTCTTCCTCCTC
1 TTCTCTTCTTCCTCCTC
14940675 TTC
1 TTC
14940678 CTCAACACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 6 0.32
19 7 0.37
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (17 bp):
TTCTCTTCTTCCTCCTC
Found at i:14960071 original size:13 final size:13
Alignment explanation
Indices: 14960053--14960079 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14960043 TATTTAATAA
14960053 AATAATTATAATT
1 AATAATTATAATT
14960066 AATAATTATAATT
1 AATAATTATAATT
14960079 A
1 A
14960080 TATTCAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATTATAATT
Found at i:14979770 original size:123 final size:122
Alignment explanation
Indices: 14979551--14979911 Score: 537
Period size: 123 Copynumber: 2.9 Consensus size: 122
14979541 TATCTTTCCC
* * * *
14979551 TTTTATTTAATATCTAATATTAAAATGGAAATATTCCTTTTGAGAAATATATGAAAGGTTTATTA
1 TTTTATATAATATCTCATATTAAAATGGAAATATT-CTTTAGAGAAATATATGGAAGGTTTATTA
**
14979616 AAATATTATATCCTTCCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCA
65 AAATATTATATCCTTTTCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCA
*
14979674 TTTTATATAATATCTCATATTAAAATGGAAATATTCTATTAGATG-AATATAAGGAAGGTTTATT
1 TTTTATATAATATCTCATATTAAAATGGAAATATTCT-TTAGA-GAAATATATGGAAGGTTTATT
* *
14979738 AAAACATTATATCCTTTTCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCC
64 AAAATATTATATCCTTTTCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCA
* *
14979797 TTTTATATAATATCTCATATTAAAATGAAAATATTCTTTTAAAGAAATATATGGAAGGTTTATTA
1 TTTTATATAATATCTCATATTAAAATGGAAATATTC-TTTAGAGAAATATATGGAAGGTTTATTA
* * *
14979862 AAATATTATAT-CATTTCTGAAAGGATATTAACTTTCATGTTTTTAATATT
65 AAATATTATATCCTTTTC-AAAAGGATATTAACTTCCATGTTTTTAATATT
14979912 TAACGAAATC
Statistics
Matches: 217, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
122 8 0.04
123 207 0.95
124 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (122 bp):
TTTTATATAATATCTCATATTAAAATGGAAATATTCTTTAGAGAAATATATGGAAGGTTTATTAA
AATATTATATCCTTTTCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCA
Found at i:14983851 original size:57 final size:57
Alignment explanation
Indices: 14983755--14983873 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 57
14983745 AAAACATAAA
* *
14983755 TTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTTC-AGTTCTCCATT
1 TTCAATTTCATTTTGGAGAAAACCAAATTCATTTCCAAATG-TTTCTAGTTCTCCATT
* * *
14983812 TTCAATTTCATTTTGGAGAAAACCATAATT-GTTTGCAAATGTTTCTTATTTCTCCATT
1 TTCAATTTCATTTTGGAGAAAACCA-AATTCATTTCCAAATGTTTC-TAGTTCTCCATT
14983870 TTCA
1 TTCA
14983874 CCATTTCTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
56 4 0.07
57 33 0.61
58 17 0.31
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (57 bp):
TTCAATTTCATTTTGGAGAAAACCAAATTCATTTCCAAATGTTTCTAGTTCTCCATT
Found at i:14987326 original size:19 final size:19
Alignment explanation
Indices: 14987287--14987353 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 19
14987277 GGAGCAATAC
14987287 TGATTTGTTTAAAAATCATTT
1 TGATTTG-TT-AAAATCATTT
*
14987308 TGATTTGTTAAAATGATTT
1 TGATTTGTTAAAATCATTT
14987327 TGACTTTGTTAAAATCATTT
1 TGA-TTTGTTAAAATCATTT
*
14987347 TAATTTG
1 TGATTTG
14987354 ATTTTAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 16 0.38
20 19 0.45
21 7 0.17
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.52
Consensus pattern (19 bp):
TGATTTGTTAAAATCATTT
Found at i:14992792 original size:21 final size:20
Alignment explanation
Indices: 14992749--14992792 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
14992739 TGCTATGCGT
*
14992749 GAAATAGAGAGGAAATTATA
1 GAAATAGAGAGGAAATGATA
14992769 GAAATAAGAGAGTGAAATGA-A
1 GAAAT-AGAGAG-GAAATGATA
14992790 GAA
1 GAA
14992793 TGAAGGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (20 bp):
GAAATAGAGAGGAAATGATA
Found at i:14995528 original size:21 final size:22
Alignment explanation
Indices: 14995504--14995556 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
14995494 GTGAAAATTG
14995504 TGATATGTG-TTATGTGATCTA
1 TGATATGTGATTATGTGATCTA
* *
14995525 TGATAAGTGATT-TGTGATGTA
1 TGATATGTGATTATGTGATCTA
14995546 TGATATGTGAT
1 TGATATGTGAT
14995557 GTCATCTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.45
Consensus pattern (22 bp):
TGATATGTGATTATGTGATCTA
Found at i:14996687 original size:37 final size:38
Alignment explanation
Indices: 14996604--14996689 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
14996594 TCTTTAGATA
* *
14996604 TGAAACTATAGATTTTTGAAACTTTAGAAATGTAAAAG
1 TGAAACTATAGATTCTTGAAACTATAGAAATGTAAAAG
* * **
14996642 TGATACTATAGA-TCTTGAAACTATAGAAATGTGATTG
1 TGAAACTATAGATTCTTGAAACTATAGAAATGTAAAAG
14996679 TGAAACTATAG
1 TGAAACTATAG
14996690 GAAATTATAG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 30 0.73
38 11 0.27
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (38 bp):
TGAAACTATAGATTCTTGAAACTATAGAAATGTAAAAG
Found at i:15004224 original size:108 final size:108
Alignment explanation
Indices: 15004035--15004250 Score: 405
Period size: 108 Copynumber: 2.0 Consensus size: 108
15004025 TGCCTACATT
* *
15004035 GCTTTCTGTTCCAATTCCACAAGCAAGTGACATGCTTTACCAAAGACAAGCTGATACGCTGACAT
1 GCTTTCTATTCCAATTCCACAAGCAAGTGACATGCTTTACCAAAGACAAGCTGATACACTGACAT
15004100 CCCAAGCGGGGTTTTGTACGCTGTCCGTAATGCCCATAACGCA
66 CCCAAGCGGGGTTTTGTACGCTGTCCGTAATGCCCATAACGCA
15004143 GCTTTCTATTCCAATTCCACAAGCAAGTGACATGCTTTACCAAAGACAAGCTGATACACTGACAT
1 GCTTTCTATTCCAATTCCACAAGCAAGTGACATGCTTTACCAAAGACAAGCTGATACACTGACAT
*
15004208 CCCAAGCGGGGTTTTGTACGTTGTCCGTAATGCCCATAACGCA
66 CCCAAGCGGGGTTTTGTACGCTGTCCGTAATGCCCATAACGCA
15004251 TCATCAAGTC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (108 bp):
GCTTTCTATTCCAATTCCACAAGCAAGTGACATGCTTTACCAAAGACAAGCTGATACACTGACAT
CCCAAGCGGGGTTTTGTACGCTGTCCGTAATGCCCATAACGCA
Found at i:15014283 original size:45 final size:45
Alignment explanation
Indices: 15014201--15014295 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
15014191 GCCATTATCA
* * * *
15014201 ACATTTCGTAAATTGGGGATTGGTTACATGAAGCCCACTGCAGTG
1 ACATTTCGTAAATTGGGGATTGGTCACATAAAACCCACTACAGTG
* * *
15014246 ACATTTCGTAAGTTGGGGATTGGTCGCATAAAACCCACTATAGTG
1 ACATTTCGTAAATTGGGGATTGGTCACATAAAACCCACTACAGTG
15014291 ACATT
1 ACATT
15014296 GCAACTGGCG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (45 bp):
ACATTTCGTAAATTGGGGATTGGTCACATAAAACCCACTACAGTG
Found at i:15016939 original size:23 final size:22
Alignment explanation
Indices: 15016908--15016951 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
15016898 AAAGAAATAA
*
15016908 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
15016930 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
15016952 GAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:15027919 original size:23 final size:22
Alignment explanation
Indices: 15027887--15027930 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
15027877 AAATAAATAA
15027887 AATTAACCCAAATTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
15027909 AATTAAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
15027931 GAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:15030584 original size:22 final size:22
Alignment explanation
Indices: 15030554--15030596 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15030544 CTTACTGTTG
15030554 TCGACGCAATAAAATCTCCTTA
1 TCGACGCAATAAAATCTCCTTA
* *
15030576 TCGATGCAATAGAATCTCCTT
1 TCGACGCAATAAAATCTCCTT
15030597 GTCGGTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (22 bp):
TCGACGCAATAAAATCTCCTTA
Found at i:15033813 original size:13 final size:13
Alignment explanation
Indices: 15033795--15033819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15033785 TTCATTTTAT
15033795 CATTTTTAGCATG
1 CATTTTTAGCATG
15033808 CATTTTTAGCAT
1 CATTTTTAGCAT
15033820 TTTTAAACTT
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:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:15033849 original size:21 final size:21
Alignment explanation
Indices: 15033816--15033855 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15033806 TGCATTTTTA
*
15033816 GCATTTTTAAACTTAGTGACT
1 GCATTTTTAAACTCAGTGACT
15033837 GCATTTTCT-AACTCAGTGA
1 GCATTTT-TAAACTCAGTGA
15033856 TGCTCAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
GCATTTTTAAACTCAGTGACT
Found at i:15049468 original size:21 final size:21
Alignment explanation
Indices: 15049429--15049469 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15049419 ATGTGTTATC
*
15049429 TGATCTATGATAAGTGATTTA
1 TGATCTATGATAAGGGATTTA
* *
15049450 TGATGTATGATATGGGATTT
1 TGATCTATGATAAGGGATTT
15049470 CATCTCATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (21 bp):
TGATCTATGATAAGGGATTTA
Found at i:15054421 original size:50 final size:50
Alignment explanation
Indices: 15054327--15054483 Score: 138
Period size: 50 Copynumber: 3.1 Consensus size: 50
15054317 TGACATCCAT
* * * * *
15054327 TAATTCTCATGATCAGTTAAGTTTGCATCATAAATAATGACATGCTTTAAG
1 TAATTCACATG-TTAGTTAAATTTGCATCATAAATCATGACATGCATTAAG
* * *
15054378 TAACTT-ACATGTTAGTTAAATATGCATCATAAATCCT-ATCATGCATTATG
1 TAA-TTCACATGTTAGTTAAATTTGCATCATAAATCATGA-CATGCATTAAG
* * * * *
15054428 TAATTCCCATGTTATTTAAAGTTTGCATCATTAAATCAAGTCATGCATTTAG
1 TAATTCACATGTTAGTTAAA-TTTGCATCA-TAAATCATGACATGCATTAAG
15054480 TAAT
1 TAAT
15054484 CCATTAGTTC
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
49 3 0.04
50 45 0.54
51 15 0.18
52 21 0.25
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (50 bp):
TAATTCACATGTTAGTTAAATTTGCATCATAAATCATGACATGCATTAAG
Found at i:15078243 original size:18 final size:19
Alignment explanation
Indices: 15078220--15078265 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
15078210 ATCTGCTGCC
15078220 TCTTCTTCCTT-ACATGCA
1 TCTTCTTCCTTCACATGCA
15078238 TCTTCTT-CTTCACATGCA
1 TCTTCTTCCTTCACATGCA
15078256 TCTTCTTCCT
1 TCTTCTTCCT
15078266 CGGTCGCCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.81
19 2 0.08
ACGTcount: A:0.13, C:0.35, G:0.04, T:0.48
Consensus pattern (19 bp):
TCTTCTTCCTTCACATGCA
Found at i:15080642 original size:21 final size:22
Alignment explanation
Indices: 15080611--15080652 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
15080601 ATTCACATGT
15080611 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
15080633 TTTC-TACTCATTCTTCTTTT
1 TTTCTTACTCATGATTCTTTT
15080653 CTTTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.21, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:15085829 original size:27 final size:27
Alignment explanation
Indices: 15085806--15085861 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
15085796 ACTTTGATCT
* *
15085806 TTGATCGTTGACT-TTGACTGTTGACCA
1 TTGACCGTTGA-TATTGACCGTTGACCA
15085833 TTGACCGTTGATATTGACCGTTGACCA
1 TTGACCGTTGATATTGACCGTTGACCA
15085860 TT
1 TT
15085862 AACTTTGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (27 bp):
TTGACCGTTGATATTGACCGTTGACCA
Found at i:15085869 original size:20 final size:20
Alignment explanation
Indices: 15085846--15085898 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
15085836 ACCGTTGATA
15085846 TTGACCGTTGACCATTAACT
1 TTGACCGTTGACCATTAACT
**
15085866 TTGACCGTTGACTGTTAACT
1 TTGACCGTTGACCATTAACT
* *
15085886 TTCATCGTTGACC
1 TTGACCGTTGACC
15085899 GTTGATCGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGACCGTTGACCATTAACT
Found at i:15085923 original size:27 final size:27
Alignment explanation
Indices: 15085866--15085923 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
15085856 ACCATTAACT
* *
15085866 TTGACCGTTGACTGTTAACTTTCATCG
1 TTGACCGTTGACTGTTAACTTTCACCA
* *
15085893 TTGACCGTTGA-TCGTTGACTTTGACCA
1 TTGACCGTTGACT-GTTAACTTTCACCA
15085920 TTGA
1 TTGA
15085924 TTTTTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (27 bp):
TTGACCGTTGACTGTTAACTTTCACCA
Found at i:15087007 original size:3 final size:3
Alignment explanation
Indices: 15086988--15087035 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
15086978 TAGAATATTC
*
15086988 TAT T-T TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15087035 T
1 T
15087036 TTGGATTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15093026 original size:22 final size:22
Alignment explanation
Indices: 15092998--15093063 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
15092988 ACCATGTCAA
* *
15092998 ATTGTTGACCGATCGTTGACCG
1 ATTGTTGACCGACCATTGACCG
15093020 ATTGTTGACCGACCATTGACCG
1 ATTGTTGACCGACCATTGACCG
* *
15093042 ACTGTTGACCGACTATTGACCG
1 ATTGTTGACCGACCATTGACCG
15093064 GCCGTTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (22 bp):
ATTGTTGACCGACCATTGACCG
Found at i:15093054 original size:11 final size:11
Alignment explanation
Indices: 15093000--15093063 Score: 76
Period size: 11 Copynumber: 5.8 Consensus size: 11
15092990 CATGTCAAAT
15093000 TGTTGACCGA-
1 TGTTGACCGAC
*
15093010 TCGTTGACCGAT
1 T-GTTGACCGAC
15093022 TGTTGACCGAC
1 TGTTGACCGAC
**
15093033 CATTGACCGAC
1 TGTTGACCGAC
15093044 TGTTGACCGAC
1 TGTTGACCGAC
*
15093055 TATTGACCG
1 TGTTGACCG
15093064 GCCGTTGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
10 1 0.02
11 44 0.96
12 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (11 bp):
TGTTGACCGAC
Found at i:15093104 original size:13 final size:13
Alignment explanation
Indices: 15093081--15093127 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
15093071 TTTTCGACCG
*
15093081 TTGACCTTTGACT
1 TTGACCGTTGACT
*
15093094 TTGACAGTTGA--
1 TTGACCGTTGACT
*
15093105 TCGACCGTTGACT
1 TTGACCGTTGACT
15093118 TTGACCGTTG
1 TTGACCGTTG
15093128 TTTTTTTCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
11 9 0.33
13 18 0.67
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:15119190 original size:21 final size:21
Alignment explanation
Indices: 15119166--15119222 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
15119156 ATAAGTGTAA
15119166 CATCTACCGAAACTATTTATG
1 CATCTACCGAAACTATTTATG
15119187 CATCTACCGAAACTATTTATG
1 CATCTACCGAAACTATTTATG
* *
15119208 CTTCTACCGATACTA
1 CATCTACCGAAACTA
15119223 AAAACACTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (21 bp):
CATCTACCGAAACTATTTATG
Found at i:15119941 original size:42 final size:42
Alignment explanation
Indices: 15119876--15120024 Score: 192
Period size: 42 Copynumber: 3.5 Consensus size: 42
15119866 TTTGCTTTAT
* * * * *
15119876 CGAGTCATAAGTCTTCCTTTAATCATATTTTCATTCTCATCC
1 CGAGACATGAGTCTGCCTTTAATCATAATCTCATTCTCATCC
* *
15119918 CGAGACATGAGTGTGCTTTTAATCATAATCTCATTCTCATCC
1 CGAGACATGAGTCTGCCTTTAATCATAATCTCATTCTCATCC
* *
15119960 CGAGACATGAGTCTTCCTTTAATTATAATCTCATTCTCATCC
1 CGAGACATGAGTCTGCCTTTAATCATAATCTCATTCTCATCC
*
15120002 CGAGACATG-GATCTTCCTTTAAT
1 CGAGACATGAG-TCTGCCTTTAAT
15120025 ATATCCTCAT
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 1 0.01
42 94 0.99
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (42 bp):
CGAGACATGAGTCTGCCTTTAATCATAATCTCATTCTCATCC
Found at i:15129812 original size:16 final size:17
Alignment explanation
Indices: 15129774--15129813 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
15129764 AACTAACGAG
15129774 TAAAATGCAATGACAAC
1 TAAAATGCAATGACAAC
*
15129791 TAAAATGCAATGATAA-
1 TAAAATGCAATGACAAC
15129807 TAAAATG
1 TAAAATG
15129814 ATATGCATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (17 bp):
TAAAATGCAATGACAAC
Found at i:15171885 original size:18 final size:19
Alignment explanation
Indices: 15171856--15171896 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
15171846 TAATTTAGGT
15171856 TTTTAGTTATTTTCATTTC
1 TTTTAGTTATTTTCATTTC
15171875 TTTTA-TTATTTTCATTTC
1 TTTTAGTTATTTTCATTTC
15171893 TTTT
1 TTTT
15171897 TTTTGTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTAGTTATTTTCATTTC
Found at i:15174386 original size:3 final size:3
Alignment explanation
Indices: 15174380--15174441 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
15174370 ATTAAACATG
15174380 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15174428 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
15174442 TCATTTAACC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:15177853 original size:11 final size:11
Alignment explanation
Indices: 15177837--15177861 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15177827 ATGTGTATGC
15177837 ATTTATTTATT
1 ATTTATTTATT
15177848 ATTTATTTATT
1 ATTTATTTATT
15177859 ATT
1 ATT
15177862 CATTAACATT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:15177979 original size:28 final size:28
Alignment explanation
Indices: 15177919--15177977 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
15177909 TCATGAACAA
* *
15177919 TAAACAAACGAACATGAACACATAATTT
1 TAAATAAACGAACATGAACACAAAATTT
15177947 TAAATAAACGAACATGAACA-AAAATTT
1 TAAATAAACGAACATGAACACAAAATTT
15177974 TAAA
1 TAAA
15177978 ATTCTTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.22
Consensus pattern (28 bp):
TAAATAAACGAACATGAACACAAAATTT
Found at i:15179179 original size:14 final size:14
Alignment explanation
Indices: 15179160--15179193 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
15179150 TTGTTATATG
*
15179160 ATCAATTACACAGA
1 ATCAATTACAAAGA
15179174 ATCAATTACAAAGA
1 ATCAATTACAAAGA
*
15179188 AGCAAT
1 ATCAAT
15179194 ACATGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.21
Consensus pattern (14 bp):
ATCAATTACAAAGA
Found at i:15184642 original size:31 final size:31
Alignment explanation
Indices: 15184606--15184669 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
15184596 TAAAAGTAAC
15184606 AAATTCTTAAAAAGGTAACTAAATAATTCTT
1 AAATTCTTAAAAAGGTAACTAAATAATTCTT
15184637 AAATTCTTAAAAAGGTAACTAAATAATTCTT
1 AAATTCTTAAAAAGGTAACTAAATAATTCTT
15184668 AA
1 AA
15184670 CCGAAGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (31 bp):
AAATTCTTAAAAAGGTAACTAAATAATTCTT
Found at i:15192902 original size:81 final size:85
Alignment explanation
Indices: 15192816--15192983 Score: 236
Period size: 81 Copynumber: 2.0 Consensus size: 85
15192806 TAAAATGCTT
* * * *
15192816 TCTCCCTTTCACTTTGAAAGATGAATCGTTCA-TTTTTTTTTT-AGAAAATCATCTTCTTTAGTT
1 TCTCCCTCTCACTTTGAAAGATGAATCATTCATTTTTTTTTTTCAAAAAATCATCTTCTCTAGTT
15192879 T-C-ATTTTTTAATTCAAAC
66 TCCTATTTTTTAATTCAAAC
15192897 TCTCCCTCTCACTTTGAAAGATGAATCATTCATTCTTTTTTTTTTTCAAAAAATCATCTTCTCTA
1 TCTCCCTCTCACTTTGAAAGATGAATCATTCA---TTTTTTTTTTTCAAAAAATCATCTTCTCTA
*
15192962 GTTTCCTTTTTTTTAATTCAAA
63 GTTTCCTATTTTTTAATTCAAA
15192984 TGGAATGTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
81 30 0.40
85 10 0.13
86 20 0.27
87 1 0.01
88 14 0.19
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (85 bp):
TCTCCCTCTCACTTTGAAAGATGAATCATTCATTTTTTTTTTTCAAAAAATCATCTTCTCTAGTT
TCCTATTTTTTAATTCAAAC
Found at i:15194946 original size:18 final size:18
Alignment explanation
Indices: 15194919--15194953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15194909 TTTGTTAACA
*
15194919 GATCGATTAATCGAATTT
1 GATCGATTAATCAAATTT
*
15194937 GATCGGTTAATCAAATT
1 GATCGATTAATCAAATT
15194954 AATTCAGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (18 bp):
GATCGATTAATCAAATTT
Found at i:15195629 original size:16 final size:17
Alignment explanation
Indices: 15195595--15195633 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
15195585 AGCATGAAAA
15195595 CCCAAAACAAAATCAAT
1 CCCAAAACAAAATCAAT
*
15195612 CCCAAAGCAAAA-CAAT
1 CCCAAAACAAAATCAAT
15195628 CCCAAA
1 CCCAAA
15195634 CCACAGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.56, C:0.33, G:0.03, T:0.08
Consensus pattern (17 bp):
CCCAAAACAAAATCAAT
Found at i:15196420 original size:43 final size:43
Alignment explanation
Indices: 15196319--15196437 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 43
15196309 ATCATGCTCT
* **
15196319 CAATCAATCACATACTATCAATATTAGGAAACAGTGTTCCATT
1 CAATCAATCACATACTTTCAATATTAGGAAACAGTGTTCCACA
* *** * *
15196362 CATTTGTTCATATACTTTCAATATTAGGAAATAGTGTTCCACA
1 CAATCAATCACATACTTTCAATATTAGGAAACAGTGTTCCACA
*
15196405 CAATCAATCACATACTTTCAATTTTAGGAAACA
1 CAATCAATCACATACTTTCAATATTAGGAAACA
15196438 ATATTCCTCT
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (43 bp):
CAATCAATCACATACTTTCAATATTAGGAAACAGTGTTCCACA
Found at i:15198575 original size:30 final size:31
Alignment explanation
Indices: 15198509--15198575 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
15198499 TGATATAGAC
* * *
15198509 TAAATTGTAAATATGTGAAAAGTAGTGGGGT
1 TAAATTATAAATATGTCAAAAGTAGAGGGGT
* * *
15198540 CAAATTATAAATAT-TCAAAAGTTGAGTGGT
1 TAAATTATAAATATGTCAAAAGTAGAGGGGT
15198570 TAAATT
1 TAAATT
15198576 GAAAATAGAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (31 bp):
TAAATTATAAATATGTCAAAAGTAGAGGGGT
Found at i:15206114 original size:19 final size:20
Alignment explanation
Indices: 15206086--15206134 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
15206076 TGTACCCTTG
*
15206086 TTTCTCAAATTTTTC-AATT
1 TTTCTTAAATTTTTCTAATT
15206105 TTTCTTAAA-TTTTCTAATT
1 TTTCTTAAATTTTTCTAATT
15206124 TGTT-TTAAATT
1 T-TTCTTAAATT
15206135 AGTCTCAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 18 0.69
20 3 0.12
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTCTTAAATTTTTCTAATT
Found at i:15222137 original size:15 final size:14
Alignment explanation
Indices: 15222112--15222158 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
15222102 GTGGGTGTTG
15222112 AAGAGGAAGAAGAGA
1 AAGA-GAAGAAGAGA
15222127 ACAGAGAAGAAGAAGA
1 A-AGAGAAGAAG-AGA
*
15222143 AAGAGAAGAAAAGA
1 AAGAGAAGAAGAGA
15222157 AA
1 AA
15222159 AGGAAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 5 0.17
15 17 0.59
16 7 0.24
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (14 bp):
AAGAGAAGAAGAGA
Found at i:15222160 original size:15 final size:15
Alignment explanation
Indices: 15222112--15222171 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
15222102 GTGGGTGTTG
*
15222112 AAGAGGAAGAAGAGAA
1 AAGA-GAAGAAAAGAA
*
15222128 CAGAGAAGAAGAAG-A
1 AAGAGAAGAA-AAGAA
15222143 AAGAGAAGAAAAGAA
1 AAGAGAAGAAAAGAA
15222158 AAG-G-A-AAAAGAA
1 AAGAGAAGAAAAGAA
15222170 AA
1 AA
15222172 TGAAGAGGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 9 0.23
13 1 0.03
14 4 0.10
15 20 0.51
16 5 0.13
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAGAAGAAAAGAA
Found at i:15225700 original size:42 final size:42
Alignment explanation
Indices: 15225653--15225746 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
15225643 GGAATGGTGT
*
15225653 AGACTTCTACCGTTACTTGAGACAGTACTATCAATACAAGTG
1 AGACTTCTACCGATACTTGAGACAGTACTATCAATACAAGTG
*
15225695 AGACTTCTACCGATACTTGAGGCAGTACTATCAATACAAGTG
1 AGACTTCTACCGATACTTGAGACAGTACTATCAATACAAGTG
*
15225737 AGGCTTCTAC
1 AGACTTCTAC
15225747 TAAAACATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (42 bp):
AGACTTCTACCGATACTTGAGACAGTACTATCAATACAAGTG
Found at i:15225738 original size:23 final size:23
Alignment explanation
Indices: 15225670--15225740 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 23
15225660 TACCGTTACT
*
15225670 TGAGACAGTACTATCAATACAAG
1 TGAGGCAGTACTATCAATACAAG
* * * * *
15225693 TGA-G-ACTTCTACCGATAC--T
1 TGAGGCAGTACTATCAATACAAG
15225712 TGAGGCAGTACTATCAATACAAG
1 TGAGGCAGTACTATCAATACAAG
15225735 TGAGGC
1 TGAGGC
15225741 TTCTACTAAA
Statistics
Matches: 33, Mismatches: 11, Indels: 8
0.63 0.21 0.15
Matches are distributed among these distances:
19 3 0.09
20 1 0.03
21 20 0.61
23 9 0.27
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (23 bp):
TGAGGCAGTACTATCAATACAAG
Found at i:15230118 original size:471 final size:471
Alignment explanation
Indices: 15229235--15230175 Score: 1641
Period size: 471 Copynumber: 2.0 Consensus size: 471
15229225 TGGATCATTC
15229235 GAAACACACACCCTGTCTCTAAAATACAACATACCATCTGTATCCACTGTAAACCCTGTAGTGGC
1 GAAACACACACCCTGTCTCTAAAATACAACATACCATCTGTATCCACTGTAAACCCTGTAGTGGC
*
15229300 ATCACTTTGTATCTGTCCCTTTTTAGCTATAAGCTTTGGATCATTTCCCTGTAATTCTCGAATCC
66 ATCACTCTGTATCTGTCCCTTTTTAGCTATAAGCTTTGGATCATTTCCCTGTAATTCTCGAATCC
* * * *
15229365 GCTGTAGAAATAACGGTCTCACCCTGAGTTCAGTAGTGACAAAACCATCACTCTCTAGGGACAAA
131 ACTATAGAAATAACGGTCTCACCCTGAGTTCAATAGTGACAAAACCATCACTATCTAGGGACAAA
* *
15229430 CGAGCATTCATTACTCTCAGTGCAAACAATGACTTATGACTCAGGGCATCGACAACAACATTAGC
196 CGAGCATTCATTACTCTCAGTGCAAACAATGAATTACGACTCAGGGCATCGACAACAACATTAGC
* *
15229495 CTTTCCTGGATGATAATCAATCACAAGGTCATAATCCTTTAATAGCTCTAACCATCTGCGCTACT
261 CTTTCCTGGATGATAATCAATCACAAGGTCATAATCCTTTAATAGCTCTAACCATCTACGCTACC
15229560 GCAAATTTAGTTCCCTCTGAGTCATCAGATATTTCAAACTCTTATGATCCGTGAATACATGACAT
326 GCAAATTTAGTTCCCTCTGAGTCATCAGATATTTCAAACTCTTATGATCCGTGAATACATGACAT
* *
15229625 CTTTCACCATATAGATAGTGATGCCAAATCTTCAATGCAAAGACTATTG-TAGCTAATTCCAGAT
391 CTTTCACCATATAGAGAGTGATGCCAAATCTTCAATGCAAAGACTA-TGACAGCTAATTCCAGAT
15229689 CATGAGTTAGATAATTT
455 CATGAGTTAGATAATTT
*
15229706 GAAACACACACCTTGTCTCTAAAATACAACATACCATCTGTATCCACTGTAAACCCTGTAGTGGC
1 GAAACACACACCCTGTCTCTAAAATACAACATACCATCTGTATCCACTGTAAACCCTGTAGTGGC
*
15229771 ATCACTCTGTATTTGTCCCTTTTTAGCTATAAGCTTTGGATCATTTCCCTGTAATTCTCGAATCC
66 ATCACTCTGTATCTGTCCCTTTTTAGCTATAAGCTTTGGATCATTTCCCTGTAATTCTCGAATCC
* * * * *
15229836 ATTATAGAAATAACGGTCTCGCCCTGAGTTTAATAGTGACAAAACCATTACTATTTAGGGACAAA
131 ACTATAGAAATAACGGTCTCACCCTGAGTTCAATAGTGACAAAACCATCACTATCTAGGGACAAA
* * *
15229901 CGAGCATTCATTTCTCTCAGTGCAAACAATGAATTCCGGCTCAGGGCATCGACAACAACATTAGC
196 CGAGCATTCATTACTCTCAGTGCAAACAATGAATTACGACTCAGGGCATCGACAACAACATTAGC
* *
15229966 CTTTCTTGGGTGATAATCAATCACAAGGTCATAATCCTTTAATAGCTCTAACCATCTACGCTACC
261 CTTTCCTGGATGATAATCAATCACAAGGTCATAATCCTTTAATAGCTCTAACCATCTACGCTACC
*
15230031 GTAAATTTAGTTCCCTCTGAGTCATCAGATATTTCAAACTCTTATGATCCGTGAATACATGACAT
326 GCAAATTTAGTTCCCTCTGAGTCATCAGATATTTCAAACTCTTATGATCCGTGAATACATGACAT
15230096 CTTTCACCATATAGAGAGTGATGCCAAATCTTCAATGCAAAGACTATGACAGCTAATTCCAGATC
391 CTTTCACCATATAGAGAGTGATGCCAAATCTTCAATGCAAAGACTATGACAGCTAATTCCAGATC
*
15230161 ATGAGTTGGATAATT
456 ATGAGTTAGATAATT
15230176 CTTTTCATGC
Statistics
Matches: 444, Mismatches: 25, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
470 2 0.00
471 442 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (471 bp):
GAAACACACACCCTGTCTCTAAAATACAACATACCATCTGTATCCACTGTAAACCCTGTAGTGGC
ATCACTCTGTATCTGTCCCTTTTTAGCTATAAGCTTTGGATCATTTCCCTGTAATTCTCGAATCC
ACTATAGAAATAACGGTCTCACCCTGAGTTCAATAGTGACAAAACCATCACTATCTAGGGACAAA
CGAGCATTCATTACTCTCAGTGCAAACAATGAATTACGACTCAGGGCATCGACAACAACATTAGC
CTTTCCTGGATGATAATCAATCACAAGGTCATAATCCTTTAATAGCTCTAACCATCTACGCTACC
GCAAATTTAGTTCCCTCTGAGTCATCAGATATTTCAAACTCTTATGATCCGTGAATACATGACAT
CTTTCACCATATAGAGAGTGATGCCAAATCTTCAATGCAAAGACTATGACAGCTAATTCCAGATC
ATGAGTTAGATAATTT
Found at i:15233483 original size:21 final size:21
Alignment explanation
Indices: 15233459--15233510 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
15233449 TGAGGCAATA
15233459 CTACCGATACAAGT-AAGACTT
1 CTACCGATACAAGTCAAG-CTT
* * * *
15233480 CTACCAAAACATGTCATGCTT
1 CTACCGATACAAGTCAAGCTT
15233501 CTACCGATAC
1 CTACCGATAC
15233511 TAAAAACTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.25
Consensus pattern (21 bp):
CTACCGATACAAGTCAAGCTT
Found at i:15240650 original size:37 final size:38
Alignment explanation
Indices: 15240550--15240652 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
15240540 GACCTCGAGT
* **
15240550 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGAGC
** ** * *
15240591 CGATGAGGTACTGGGTACCACTTTGCTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
15240628 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
15240653 TTGCTTCGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 20 0.42
38 13 0.27
41 15 0.31
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
Found at i:15246020 original size:25 final size:23
Alignment explanation
Indices: 15245971--15246024 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
15245961 ATATGTATAT
*
15245971 GAAATAAAAGAATAAAGAAGAAA
1 GAAACAAAAGAATAAAGAAGAAA
*
15245994 GAAACAAAAGAAATAAAAGAAGGAA
1 GAAACAAAAG-AAT-AAAGAAGAAA
15246019 GAAACA
1 GAAACA
15246025 GAGAGCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 9 0.33
24 3 0.11
25 15 0.56
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.06
Consensus pattern (23 bp):
GAAACAAAAGAATAAAGAAGAAA
Found at i:15246916 original size:37 final size:38
Alignment explanation
Indices: 15246816--15246918 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
15246806 GACCTCGAGT
* **
15246816 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGAGC
** ** * *
15246857 CGATGAGGTACTGGGTACCACTTTGCTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
15246894 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
15246919 TTGCTTCGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 20 0.42
38 13 0.27
41 15 0.31
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
Found at i:15278127 original size:17 final size:17
Alignment explanation
Indices: 15278080--15278117 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
15278070 TTTTCTCTAG
*
15278080 TTGTCATTACATTTTAA
1 TTGTCACTACATTTTAA
*
15278097 TTGTCACTGCATTTTAA
1 TTGTCACTACATTTTAA
15278114 TTGT
1 TTGT
15278118 TCTCACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.53
Consensus pattern (17 bp):
TTGTCACTACATTTTAA
Found at i:15285235 original size:14 final size:15
Alignment explanation
Indices: 15285218--15285248 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
15285208 TAAATGTAGA
15285218 AATTTAAA-TGCAAG
1 AATTTAAAGTGCAAG
15285232 AATTTAAAGTGCAAG
1 AATTTAAAGTGCAAG
15285247 AA
1 AA
15285249 AATAAATTAC
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:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (15 bp):
AATTTAAAGTGCAAG
Found at i:15285270 original size:44 final size:44
Alignment explanation
Indices: 15285187--15285270 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
15285177 ATAAGTGTTG
** **
15285187 GAATTTACGGTGCAAGAAAAGTAAATGTAGAAATTTAAATGCAA
1 GAATTTAAAGTGCAAGAAAAGTAAATGTAGAAAAGTAAATGCAA
15285231 GAATTTAAAGTGCAAGAAAA-TAAAT-TACGAGAAAGTAAAT
1 GAATTTAAAGTGCAAGAAAAGTAAATGTA-GA-AAAGTAAAT
15285271 TGGTAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
42 2 0.06
43 7 0.21
44 25 0.74
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (44 bp):
GAATTTAAAGTGCAAGAAAAGTAAATGTAGAAAAGTAAATGCAA
Found at i:15299614 original size:18 final size:18
Alignment explanation
Indices: 15299568--15299615 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
15299558 CCAACGGAGA
*
15299568 AGAAATGTAAGCGCAAAT
1 AGAAATGTAAGCGCAAAG
* ** *
15299586 ATAAAAATAAGCGCAAGG
1 AGAAATGTAAGCGCAAAG
15299604 AGAAATGTAAGC
1 AGAAATGTAAGC
15299616 CACATCTTCG
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.15
Consensus pattern (18 bp):
AGAAATGTAAGCGCAAAG
Found at i:15305106 original size:17 final size:19
Alignment explanation
Indices: 15305086--15305120 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
15305076 CAAATGTTTC
15305086 CCATTTCT-TC-ATTTTTT
1 CCATTTCTATCAATTTTTT
15305103 CCATTTCTATCAATTTTT
1 CCATTTCTATCAATTTTT
15305121 ATTCATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (19 bp):
CCATTTCTATCAATTTTTT
Found at i:15310105 original size:10 final size:10
Alignment explanation
Indices: 15310090--15310114 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15310080 CTCCACAGTT
15310090 GTTTTCAAAA
1 GTTTTCAAAA
15310100 GTTTTCAAAA
1 GTTTTCAAAA
15310110 GTTTT
1 GTTTT
15310115 GGGGTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (10 bp):
GTTTTCAAAA
Found at i:15311815 original size:30 final size:31
Alignment explanation
Indices: 15311752--15311821 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
15311742 CTAAATTATG
15311752 ATTTTAGTGAAACTTAAGGATCAAATTCGAA
1 ATTTTAGTGAAACTTAAGGATCAAATTCGAA
* * *
15311783 ATTTTA-TGAAATTTAAGG-TCTAATTTGTAA
1 ATTTTAGTGAAACTTAAGGATCAAATTCG-AA
15311813 A-TTTAGTGA
1 ATTTTAGTGA
15311822 TGTTAAGGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 11 0.32
30 17 0.50
31 6 0.18
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.40
Consensus pattern (31 bp):
ATTTTAGTGAAACTTAAGGATCAAATTCGAA
Found at i:15315005 original size:21 final size:21
Alignment explanation
Indices: 15314981--15315020 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15314971 CTATGATCAG
* *
15314981 AACTACCGATACTTCAGAATT
1 AACTACCAATACTACAGAATT
15315002 AACTACCAATACTACAGAA
1 AACTACCAATACTACAGAA
15315021 GTCAGAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23
Consensus pattern (21 bp):
AACTACCAATACTACAGAATT
Found at i:15315662 original size:25 final size:25
Alignment explanation
Indices: 15315629--15315796 Score: 95
Period size: 25 Copynumber: 6.6 Consensus size: 25
15315619 AATAAATTAT
*
15315629 CGCTCTTACAAGCCAGACCGAATAA
1 CGCTCTTACAAGCCAGACAGAATAA
* * *
15315654 CGCTATTACGAGCCAGACAGAATAT
1 CGCTCTTACAAGCCAGACAGAATAA
* * * *
15315679 CGCTCTTTCAAGCTAGATAGAATAT
1 CGCTCTTACAAGCCAGACAGAATAA
* * **
15315704 CGCTCTTTCGAGCCAGAATCTA-AAGTGT
1 CGCTCTTACAAGCCAG-A-C-AGAA-TAA
** * * *
15315732 TTCTCTTACGAGCCAAATAGAATAA
1 CGCTCTTACAAGCCAGACAGAATAA
* * * *
15315757 TGCTCTTACGAGCCAGACAAAATAT
1 CGCTCTTACAAGCCAGACAGAATAA
*
15315782 CGCTCTTACGAGCCA
1 CGCTCTTACAAGCCA
15315797 AAATCCAAGT
Statistics
Matches: 112, Mismatches: 26, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
25 91 0.81
26 3 0.03
27 3 0.03
28 15 0.13
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (25 bp):
CGCTCTTACAAGCCAGACAGAATAA
Found at i:15315680 original size:50 final size:49
Alignment explanation
Indices: 15315626--15315796 Score: 162
Period size: 50 Copynumber: 3.4 Consensus size: 49
15315616 CCAAATAAAT
** *
15315626 TATCGCTCTTACAAGCCAGACCGAATAACGCTATTACGAGCCAGACAGAA
1 TATCGCTCTTACAAGCCAGATAGAATAACGCTCTTACGAGCCAGACA-AA
* * * *
15315676 TATCGCTCTTTCAAGCTAGATAGAATATCGCTCTTTCGAGCCAGAATCTAAA
1 TATCGCTCTTACAAGCCAGATAGAATAACGCTCTTACGAGCCAG-A-C-AAA
* ** * * *
15315728 GTGTTTCTCTTACGAGCCAAATAGAATAATGCTCTTACGAGCCAGACAAAA
1 -TATCGCTCTTACAAGCCAGATAGAATAACGCTCTTACGAGCCAGAC-AAA
*
15315779 TATCGCTCTTACGAGCCA
1 TATCGCTCTTACAAGCCA
15315797 AAATCCAAGT
Statistics
Matches: 96, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
50 52 0.54
51 5 0.05
52 4 0.04
53 35 0.36
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (49 bp):
TATCGCTCTTACAAGCCAGATAGAATAACGCTCTTACGAGCCAGACAAA
Found at i:15325004 original size:11 final size:11
Alignment explanation
Indices: 15324985--15325015 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
15324975 CAATATTTAT
15324985 TTCTTTTTTTC
1 TTCTTTTTTTC
15324996 -TCTTTTTTTC
1 TTCTTTTTTTC
15325006 TTCTTTTTTT
1 TTCTTTTTTT
15325016 GTGAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:15329892 original size:17 final size:17
Alignment explanation
Indices: 15329845--15329882 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
15329835 TTTTCTCTAT
*
15329845 TTGTCATTACATTTTAA
1 TTGTCACTACATTTTAA
15329862 TTGTCACTACATTTTAA
1 TTGTCACTACATTTTAA
15329879 TTGT
1 TTGT
15329883 TCTCACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.53
Consensus pattern (17 bp):
TTGTCACTACATTTTAA
Found at i:15333844 original size:15 final size:15
Alignment explanation
Indices: 15333815--15333864 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
15333805 AGTGACAGTG
**
15333815 TTCTCAGCAGATTCT
1 TTCTCAGCATTTTCT
15333830 TTCTCAGCATTTTCT
1 TTCTCAGCATTTTCT
* * *
15333845 TCCTTAACATTTTCT
1 TTCTCAGCATTTTCT
15333860 TTCTC
1 TTCTC
15333865 GTCCTTCTCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.16, C:0.28, G:0.06, T:0.50
Consensus pattern (15 bp):
TTCTCAGCATTTTCT
Found at i:15339580 original size:29 final size:29
Alignment explanation
Indices: 15339548--15339951 Score: 261
Period size: 30 Copynumber: 13.6 Consensus size: 29
15339538 TATTTTATTA
* * *
15339548 AAAAATATATTTTCACCCCCAAACTTTCC
1 AAAAATACATTTTAACCCCTAAACTTTCC
* * *
15339577 AAAAATTTAGA-TTTGATCCCTAAACTTTCC
1 AAAAA--TACATTTTAACCCCTAAACTTTCC
* *
15339607 AAAAATTCAGATTTTAA-CCTTAAACTTTCC
1 AAAAA-T-ACATTTTAACCCCTAAACTTTCC
* **
15339637 AAAATTTTGGA-TTTAACCTCC-AAAC-TTCTC
1 AAAA--ATACATTTTAACC-CCTAAACTTTC-C
* * *
15339667 AAAAACTTCATTTTGACCCC-AAACTTCTCT
1 AAAAA-TACATTTTAACCCCTAAACTT-TCC
* * *
15339697 AAAATTATATTTTGACCCCTAAACTTCTCC
1 AAAAATACATTTTAACCCCTAAACTT-TCC
* * *
15339727 AAAAATATATTTTGACCCCTAAACTTCTCT
1 AAAAATACATTTTAACCCCTAAACTT-TCC
* * *
15339757 AAAATTACATTTTAA-CCTTAAAATTTTCC
1 AAAAATACATTTTAACCCCT-AAACTTTCC
*
15339786 AAAATTACATTTTAACCCCTAAAC-TTCTC
1 AAAAATACATTTTAACCCCTAAACTTTC-C
* *
15339815 TAAAATCACATTTTAACCCCTAAACCTTCC
1 AAAAAT-ACATTTTAACCCCTAAACTTTCC
* **
15339845 CAAAATCACATTTTAA-CCCTAAACTTCTTT
1 AAAAAT-ACATTTTAACCCCTAAACTT-TCC
*
15339875 AAAATTACATTTTAA-CCCTAAACTTTCC
1 AAAAATACATTTTAACCCCTAAACTTTCC
* *
15339903 TAAAATTACATTTTTACCCCTAAACTTTTCC
1 -AAAAATACATTTTAACCCCTAAAC-TTTCC
* *
15339934 AAAATTACATTTTTACCC
1 AAAAATACATTTTAACCC
15339952 AAATTCTCTG
Statistics
Matches: 313, Mismatches: 39, Indels: 45
0.79 0.10 0.11
Matches are distributed among these distances:
28 4 0.01
29 105 0.34
30 185 0.59
31 19 0.06
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAATACATTTTAACCCCTAAACTTTCC
Found at i:15339722 original size:89 final size:88
Alignment explanation
Indices: 15339594--15339973 Score: 296
Period size: 89 Copynumber: 4.3 Consensus size: 88
15339584 TAGATTTGAT
* * * *
15339594 CCCTAAACTT-TCCAAAAATTCAGATTTTAACCTTAAACTT-TCCAAAATTTTGGA-TTTAACCT
1 CCCTAAACTTCT-CTAAAATT-ACATTTTACCCCTAAACTTCTCCAAAATTTT--ATTTTAACC-
*
15339656 CC-AAACTTCTCAAAAACTTCATTTTGA
61 CCTAAACTTCTCAAAAACTTCATTTTAA
* * * * *
15339683 CCCCAAACTTCTCTAAAATTATATTTTGACCCCTAAACTTCTCCAAAAATATATTTTGACCCCTA
1 CCCTAAACTTCTCTAAAATTACATTTT-ACCCCTAAACTTCTCCAAAATTTTATTTTAACCCCTA
*
15339748 AACTTCTCTAAAA-TTACATTTTAA
65 AACTTCTCAAAAACTT-CATTTTAA
* * * * * ***
15339772 CCTTAAAATTTTCCAAAATTACATTTTAACCCCTAAACTTCTCTAAAATCACATTTTAACCCCTA
1 CCCTAAACTTCTCTAAAATTACATTTT-ACCCCTAAACTTCTCCAAAATTTTATTTTAACCCCTA
* * *
15339837 AACCTTCCCAAAATC-ACATTTTAA
65 AA-CTTCTCAAAAACTTCATTTTAA
* * ** *
15339861 CCCTAAACTTCTTTAAAATTACATTTTAACCCTAAACTT-TCCTAAAATTACATTTTTACCCCTA
1 CCCTAAACTTCTCTAAAATTACATTTTACCCCTAAACTTCTCC-AAAATTTTATTTTAACCCCTA
* * *
15339925 AACTTTTCCAAAA-TTACATTTTTA
65 AACTTCTCAAAAACTT-CATTTTAA
*
15339949 CCC-AAA-TTCTCTGAAACTT-CATTTT
1 CCCTAAACTTCTCT-AAAATTACATTTT
15339974 TGACCCCATT
Statistics
Matches: 236, Mismatches: 43, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
86 11 0.05
87 17 0.07
88 53 0.22
89 137 0.58
90 18 0.08
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.37
Consensus pattern (88 bp):
CCCTAAACTTCTCTAAAATTACATTTTACCCCTAAACTTCTCCAAAATTTTATTTTAACCCCTAA
ACTTCTCAAAAACTTCATTTTAA
Found at i:15339938 original size:30 final size:30
Alignment explanation
Indices: 15339658--15339951 Score: 305
Period size: 30 Copynumber: 9.9 Consensus size: 30
15339648 TTTAACCTCC
* *
15339658 AAACTTCTCAAAAACTT-CATTTTGACCCC-
1 AAACTTCTCCAAAA-TTACATTTTTACCCCT
* * *
15339687 AAACTTCTCTAAAATTATATTTTGACCCCT
1 AAACTTCTCCAAAATTACATTTTTACCCCT
* * *
15339717 AAACTTCTCCAAAAATATATTTTGACCCCT
1 AAACTTCTCCAAAATTACATTTTTACCCCT
* * *
15339747 AAACTTCTCTAAAATTACA-TTTTAACCTT
1 AAACTTCTCCAAAATTACATTTTTACCCCT
* * *
15339776 AAAATTTTCCAAAATTACATTTTAACCCCT
1 AAACTTCTCCAAAATTACATTTTTACCCCT
* * *
15339806 AAACTTCTCTAAAATCACATTTTAACCCCT
1 AAACTTCTCCAAAATTACATTTTTACCCCT
* *
15339836 AAACCTTC-CCAAAATCACA-TTTTAACCCT
1 AAA-CTTCTCCAAAATTACATTTTTACCCCT
** *
15339865 AAACTTCTTTAAAATTACA-TTTTAACCCT
1 AAACTTCTCCAAAATTACATTTTTACCCCT
15339894 AAACTT-TCCTAAAATTACATTTTTACCCCT
1 AAACTTCTCC-AAAATTACATTTTTACCCCT
*
15339924 AAACTTTTCCAAAATTACATTTTTACCC
1 AAACTTCTCCAAAATTACATTTTTACCC
15339952 AAATTCTCTG
Statistics
Matches: 228, Mismatches: 29, Indels: 15
0.84 0.11 0.06
Matches are distributed among these distances:
28 7 0.03
29 91 0.40
30 123 0.54
31 7 0.03
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.36
Consensus pattern (30 bp):
AAACTTCTCCAAAATTACATTTTTACCCCT
Found at i:15339938 original size:59 final size:58
Alignment explanation
Indices: 15339556--15339951 Score: 311
Period size: 59 Copynumber: 6.7 Consensus size: 58
15339546 TAAAAAATAT
* * * * * * *
15339556 ATTTTCACCCCCAAACTTTCCAAAAATTTAGATTTGATCCCTAAACTTTCCAAAAATT-C
1 ATTTTTACCCCTAAACTTTTCTAAAA-TTACATTTTAACCCTAAACTTTCC-AAAATTAC
* * * * ** * *
15339615 AGATTTTAACCTTAAAC-TTTCCAAAATTTTGGA-TTTAACCTCCAAACTTCTCAAAAACTT-C
1 A-TTTTTACCCCTAAACTTTTCTAAAA--TTACATTTTAACC-CTAAACTT-TCCAAAA-TTAC
* * * * * *
15339676 ATTTTGACCCC-AAACTTCTCTAAAATTATATTTTGACCCCTAAACTTCTCCAAAAATAT
1 ATTTTTACCCCTAAACTTTTCTAAAATTACATTTT-AACCCTAAACTT-TCCAAAATTAC
* * * *
15339735 ATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCTTAAAATTTTCCAAAATTAC
1 ATTTTTACCCCTAAACTTTTCTAAAATTACATTTTAACCCT-AAACTTTCCAAAATTAC
* * * * *
15339794 ATTTTAACCCCTAAACTTCTCTAAAATCACATTTTAACCCCTAAACCTTCCCAAAATCAC
1 ATTTTTACCCCTAAACTTTTCTAAAATTACATTTTAA-CCCTAAA-CTTTCCAAAATTAC
*
15339854 A-TTTTAACCCTAAACTTCTT-TAAAATTACATTTTAACCCTAAACTTTCCTAAAATTAC
1 ATTTTTACCCCTAAACTT-TTCTAAAATTACATTTTAACCCTAAACTTTCC-AAAATTAC
* *
15339912 ATTTTTACCCCTAAACTTTTCCAAAATTACATTTTTACCC
1 ATTTTTACCCCTAAACTTTTCTAAAATTACATTTTAACCC
15339952 AAATTCTCTG
Statistics
Matches: 274, Mismatches: 46, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
57 5 0.02
58 21 0.08
59 157 0.57
60 85 0.31
61 6 0.02
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (58 bp):
ATTTTTACCCCTAAACTTTTCTAAAATTACATTTTAACCCTAAACTTTCCAAAATTAC
Found at i:15346317 original size:58 final size:58
Alignment explanation
Indices: 15346254--15346599 Score: 293
Period size: 58 Copynumber: 6.0 Consensus size: 58
15346244 GTTTGGGGTC
* * *
15346254 AAAATGTGATTTTTGGAAAGTTTGAGATAAAAATATGATTTTTGGAAG-TTCAGGGGCA
1 AAAATGTGATTTTTGGAAAGTTTGAGGTAAAAATGTGATTTTTGGAAGTTTGA-GGGCA
* *
15346312 AAAATGTGATATTT-GAGAAGTTTGAGATAAAAATAG-GATTTTTGGAAGTTTGAGGGCA
1 AAAATGTGATTTTTGGA-AAGTTTGAGGTAAAAAT-GTGATTTTTGGAAGTTTGAGGGCA
* * * *
15346370 AAAATGTGTTTTTTGG-AAGATCGAGGGTAAAAATGTGATTTTTGGAAGTTTGAGGGTA
1 AAAATGTGATTTTTGGAAAGTTTGA-GGTAAAAATGTGATTTTTGGAAGTTTGAGGGCA
* * * * *
15346428 AAAA-GTAATTTTT-GAGAAGTTCGGGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGGTA
1 AAAATGTGATTTTTGGA-AAGTT-TGAGGTAAAAATGTGATTTTTG-GAAGTTTGAGGGCA
* ** * *
15346487 AAAATGTGATTTTTGG-AAGTTCATG-GGCAAAAATGT-ATTTTTGGAAGTTCAAAGG-T
1 AAAATGTGATTTTTGGAAAGTT--TGAGGTAAAAATGTGATTTTTGGAAGTTTGAGGGCA
* * * *
15346543 AAAATGTGA-TTTTGGAAAAGTTCGAGGGTCAAAATGTAATTTTAGAGAAGTTT-AGGG
1 AAAATGTGATTTTTGG-AAAGTTTGA-GGTAAAAATGTGATTTTTG-GAAGTTTGAGGG
15346600 GTCAAAATAT
Statistics
Matches: 240, Mismatches: 29, Indels: 38
0.78 0.09 0.12
Matches are distributed among these distances:
55 7 0.03
56 10 0.04
57 39 0.16
58 130 0.54
59 44 0.18
60 9 0.04
61 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
AAAATGTGATTTTTGGAAAGTTTGAGGTAAAAATGTGATTTTTGGAAGTTTGAGGGCA
Found at i:15346564 original size:116 final size:115
Alignment explanation
Indices: 15346225--15346615 Score: 386
Period size: 116 Copynumber: 3.4 Consensus size: 115
15346215 AAATGAAGTC
* * *
15346225 AAAAATGAATTTTCGA-AGAGTTTG-GGGTCAAAATGTGATTTTTGGAAAGTT--TGAGATAAAA
1 AAAAATGAATTTTTGAGA-AGTTTGAGGGTAAAAATGTGATTTTTGG-AAGTTCATG-GGTAAAA
* * * * * *
15346286 ATATGATTTTTGGAAGTTCAGGGGCAAAAATGTGATATTTGAGAAGTT-TGAGAT
63 ATGTGATTTTTGGAAGTTCAAGGG-TAAAATGTGAT-TTTGAGAAGTTCGGGGGT
* * * *
15346340 AAAAATAGGATTTTTG-GAAGTTTGAGGGCAAAAATGTGTTTTTTGGAAGATCGA-GGGTAAAAA
1 AAAAAT-GAATTTTTGAGAAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTC-ATGGGTAAAAA
** * *
15346403 TGTGATTTTTGGAAGTTTGAGGGTAAAAAGTAATTTTTGAGAAGTTCGGGGGT
64 TGTGATTTTTGGAAGTTCAAGGGTAAAATGTGA-TTTTGAGAAGTTCGGGGGT
*
15346456 AAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTCATGGGCAAAAAT
1 AAAAATG-AATTTTTGAGAAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTCATGGGTAAAAAT
* * *
15346521 GT-ATTTTTGGAAGTTCAAAGGTAAAATGTGATTTTGGAAAAGTTCGAGGGT
65 GTGATTTTTGGAAGTTCAAGGGTAAAATGTGATTTT-GAGAAGTTCGGGGGT
* * * *
15346572 CAAAATGTAATTTTAGAGAAGTTT-AGGGGTCAAAATATGATTTT
1 AAAAATG-AATTTTTGAGAAGTTTGA-GGGTAAAAATGTGATTTT
15346616 CAAAGAAAAC
Statistics
Matches: 230, Mismatches: 33, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
115 40 0.17
116 145 0.63
117 45 0.20
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (115 bp):
AAAAATGAATTTTTGAGAAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTCATGGGTAAAAATG
TGATTTTTGGAAGTTCAAGGGTAAAATGTGATTTTGAGAAGTTCGGGGGT
Found at i:15346602 original size:30 final size:30
Alignment explanation
Indices: 15346225--15346607 Score: 223
Period size: 29 Copynumber: 13.2 Consensus size: 30
15346215 AAATGAAGTC
*
15346225 AAAAATG-AATTTTCGA-AGAGTTT-GGGGT
1 AAAAATGTAATTTTTGAGA-AGTTTAGGGGT
* * * *
15346253 CAAAATGTGATTTTTG-GAAAGTTT-GAGAT
1 AAAAATGTAATTTTTGAG-AAGTTTAGGGGT
* * * *
15346282 AAAAATATGATTTTTG-GAAGTTCAGGGGC
1 AAAAATGTAATTTTTGAGAAGTTTAGGGGT
* * * *
15346311 AAAAATGTGATATTTGAGAAGTTT-GAGAT
1 AAAAATGTAATTTTTGAGAAGTTTAGGGGT
* *
15346340 AAAAATAG-GATTTTTG-GAAGTTT-GAGGGC
1 AAAAAT-GTAATTTTTGAGAAGTTTAG-GGGT
** * *
15346369 AAAAATGTGTTTTTTG-GAAG-ATCGAGGGT
1 AAAAATGTAATTTTTGAGAAGTTTAG-GGGT
*
15346398 AAAAATGTGATTTTTG-GAAGTTT-GAGGGT
1 AAAAATGTAATTTTTGAGAAGTTTAG-GGGT
**
15346427 AAAAA-GTAATTTTTGAGAAGTTCGGGGGT
1 AAAAATGTAATTTTTGAGAAGTTTAGGGGT
15346456 AAAAATGTAATTTTTGAGAAGTTT-GAGGGT
1 AAAAATGTAATTTTTGAGAAGTTTAG-GGGT
* * * *
15346486 AAAAATGTGATTTTTG-GAAGTTCATGGGC
1 AAAAATGTAATTTTTGAGAAGTTTAGGGGT
* **
15346515 AAAAATGT-ATTTTTG-GAAGTTCAAAGGT
1 AAAAATGTAATTTTTGAGAAGTTTAGGGGT
* * * *
15346543 -AAAATGTGATTTTGGAAAAG-TTCGAGGGT
1 AAAAATGTAATTTTTGAGAAGTTTAG-GGGT
* *
15346572 CAAAATGTAATTTTAGAGAAGTTTAGGGGT
1 AAAAATGTAATTTTTGAGAAGTTTAGGGGT
*
15346602 CAAAAT
1 AAAAAT
15346608 ATGATTTTCA
Statistics
Matches: 289, Mismatches: 46, Indels: 38
0.77 0.12 0.10
Matches are distributed among these distances:
27 7 0.02
28 54 0.19
29 152 0.53
30 73 0.25
31 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAAATGTAATTTTTGAGAAGTTTAGGGGT
Found at i:15347244 original size:20 final size:20
Alignment explanation
Indices: 15347219--15347261 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
15347209 TAGTGACCAG
* *
15347219 CCATCGCCGTCTGCCGTCAA
1 CCATCGCCATCCGCCGTCAA
*
15347239 CCATCGTCATCCGCCGTCAA
1 CCATCGCCATCCGCCGTCAA
15347259 CCA
1 CCA
15347262 CCGTCGTCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.16, T:0.19
Consensus pattern (20 bp):
CCATCGCCATCCGCCGTCAA
Found at i:15347266 original size:20 final size:20
Alignment explanation
Indices: 15347231--15347274 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
15347221 ATCGCCGTCT
*
15347231 GCCGTCAACCATCGTCATCC
1 GCCGTCAACCACCGTCATCC
*
15347251 GCCGTCAACCACCGTCGTCC
1 GCCGTCAACCACCGTCATCC
15347271 GCCG
1 GCCG
15347275 CCGTACACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.48, G:0.20, T:0.16
Consensus pattern (20 bp):
GCCGTCAACCACCGTCATCC
Found at i:15348247 original size:6 final size:6
Alignment explanation
Indices: 15348236--15348325 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
15348226 TTTTTTTTAA
* * * *
15348236 TTAAAT TTAAAT TT-AAT TTAAA- ATAAAT TTAAAC TCAAA- ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
15348281 TTAAAT TGATAAAT TTAAAC TTAAA- AT-AAT TTAAATT TTAAAT TT
1 TTAAAT T--TAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TT
15348326 TAAAATTGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.21
6 38 0.58
7 6 0.09
8 6 0.09
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:15348250 original size:16 final size:16
Alignment explanation
Indices: 15348243--15348314 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 16
15348233 TAATTAAATT
15348243 TAAATTTAATTTAAAA
1 TAAATTTAATTTAAAA
* *
15348259 TAAATTTAAACTCAAAA
1 TAAATTT-AATTTAAAA
* *
15348276 TAAATTTAAATT--GA
1 TAAATTTAATTTAAAA
*
15348290 TAAATTTAAACTTAAAA
1 TAAATTT-AATTTAAAA
15348307 T-AATTTAA
1 TAAATTTAA
15348315 ATTTTAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
14 8 0.18
15 6 0.13
16 15 0.33
17 16 0.36
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:15348275 original size:17 final size:16
Alignment explanation
Indices: 15348243--15348315 Score: 71
Period size: 16 Copynumber: 4.6 Consensus size: 16
15348233 TAATTAAATT
**
15348243 TAAATTTAATTTAAAA
1 TAAATTTAAACTAAAA
15348259 TAAATTTAAACTCAAAA
1 TAAATTTAAACT-AAAA
**
15348276 TAAATTTAAA-T-TGA
1 TAAATTTAAACTAAAA
15348290 TAAATTTAAACTTAAAA
1 TAAATTTAAAC-TAAAA
15348307 T-AATTTAAA
1 TAAATTTAAA
15348316 TTTTAAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 11 0.23
16 20 0.43
17 16 0.34
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (16 bp):
TAAATTTAAACTAAAA
Found at i:15348296 original size:31 final size:29
Alignment explanation
Indices: 15348249--15348325 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 29
15348239 AATTTAAATT
15348249 TAATTTAAA--ATAAATTTAAACTCAAAA
1 TAATTTAAATTATAAATTTAAACTCAAAA
*
15348276 TAAATTTAAATTGATAAATTTAAACTTAAAA
1 T-AATTTAAATT-ATAAATTTAAACTCAAAA
*
15348307 TAATTTAAATTTTAAATTT
1 TAATTTAAATTATAAATTT
15348326 TAAAATTGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
27 1 0.02
28 8 0.18
29 7 0.16
30 10 0.23
31 18 0.41
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
TAATTTAAATTATAAATTTAAACTCAAAA
Found at i:15350125 original size:21 final size:20
Alignment explanation
Indices: 15350101--15350162 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
15350091 CTACCGTTAG
15350101 AACTGAGACTTCTATCGATAC
1 AACTG-GACTTCTATCGATAC
* *
15350122 AACTCTGG-GTTCTACCGATAC
1 AA--CTGGACTTCTATCGATAC
*
15350143 AATCCGGACTTCTATCGATA
1 AA-CTGGACTTCTATCGATA
15350163 GAACAGACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 1 0.03
23 3 0.09
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (20 bp):
AACTGGACTTCTATCGATAC
Found at i:15356675 original size:23 final size:22
Alignment explanation
Indices: 15356645--15356706 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 22
15356635 ATAATAAAAT
*
15356645 AAAATAAAACTAAAACTAAA-TAA
1 AAAATAAAA-TAAAAATAAACT-A
15356668 AAAATAAAAATAAAAATAAACTA
1 AAAAT-AAAATAAAAATAAACTA
15356691 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
15356707 GAAAAACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 11 0.31
23 20 0.56
24 5 0.14
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAATAAAATAAAAATAAACTA
Found at i:15356688 original size:28 final size:30
Alignment explanation
Indices: 15356635--15356744 Score: 113
Period size: 28 Copynumber: 3.6 Consensus size: 30
15356625 AAAATAGTGC
*
15356635 ATAATAAAAT-AAAATAAAACTAAAACTAA
1 ATAATAAAATAAAAATAAAAATAAAACTAA
15356664 ATAA-AAAATAAAAATAAAAAT-AAACTAA
1 ATAATAAAATAAAAATAAAAATAAAACTAA
*
15356692 A-AATAAAATAAAAATGAAAAACAAAA-TGAAA
1 ATAATAAAATAAAAAT-AAAAATAAAACT--AA
15356723 ATGAAGCTAAAATAAAAATAAA
1 AT-AA--TAAAATAAAAATAAA
15356745 TGTACTAATT
Statistics
Matches: 69, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
27 2 0.03
28 24 0.35
29 20 0.29
30 3 0.04
31 3 0.04
33 2 0.03
34 3 0.04
35 12 0.17
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.17
Consensus pattern (30 bp):
ATAATAAAATAAAAATAAAAATAAAACTAA
Found at i:15356705 original size:6 final size:6
Alignment explanation
Indices: 15356640--15356744 Score: 78
Period size: 6 Copynumber: 18.3 Consensus size: 6
15356630 AGTGCATAAT
* * *
15356640 AAAAT- AAAATA AAACTA AAACTA AATA-A AAAATA AAAATA AAAAT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * * **
15356685 AAACTA AAAAT- AAAATA AAAATGA AAAA-C AAAATG AAAATG AAGCT-
1 AAAATA AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA
15356731 AAAATA AAAATA AA
1 AAAATA AAAATA AA
15356745 TGTACTAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
5 25 0.31
6 51 0.63
7 5 0.06
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:15356711 original size:12 final size:11
Alignment explanation
Indices: 15356637--15356744 Score: 96
Period size: 11 Copynumber: 9.5 Consensus size: 11
15356627 AATAGTGCAT
15356637 AATAAAAT-AA
1 AATAAAATAAA
15356647 AATAAAACTAAA
1 AATAAAA-TAAA
*
15356659 ACT-AAATAAAA
1 AATAAAAT-AAA
15356670 AATAAAAATAAA
1 AAT-AAAATAAA
*
15356682 AATAAACTAAA
1 AATAAAATAAA
15356693 AATAAAATAAA
1 AATAAAATAAA
15356704 AATGAAAA-ACAA
1 AAT-AAAATA-AA
*
15356716 AATGAAAATGAA
1 AAT-AAAATAAA
**
15356728 GCTAAAATAAA
1 AATAAAATAAA
15356739 AATAAA
1 AATAAA
15356745 TGTACTAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
10 8 0.10
11 41 0.51
12 27 0.34
13 4 0.05
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.17
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:15356767 original size:11 final size:11
Alignment explanation
Indices: 15356751--15356787 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15356741 TAAATGTACT
*
15356751 AATTTTTTTTC
1 AATTTTTTTTG
15356762 AA--TTTTTTG
1 AATTTTTTTTG
15356771 AATTTTTTTTG
1 AATTTTTTTTG
15356782 AATTTT
1 AATTTT
15356788 CTAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:15358924 original size:19 final size:19
Alignment explanation
Indices: 15358902--15358946 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
15358892 TTATATTAGG
15358902 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
15358921 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
15358940 ATTTAAT
1 ATTTAAT
15358947 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:15361929 original size:25 final size:23
Alignment explanation
Indices: 15361901--15361946 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
15361891 GTTAGATCCA
15361901 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
15361926 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
15361947 TCCTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:15362026 original size:3 final size:3
Alignment explanation
Indices: 15362018--15362051 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
15362008 TATAAACAAT
*
15362018 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
15362052 CAAATAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:15362714 original size:28 final size:30
Alignment explanation
Indices: 15362666--15362728 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
15362656 TTAATAAAAA
*
15362666 AAAATTATATTTTATTCTTTAAAAA-TA-T
1 AAAATTATATTTTAATCTTTAAAAATTATT
*
15362694 AAAATTTTA-TTTAATCATTTAAAAATTATT
1 AAAATTATATTTTAATC-TTTAAAAATTATT
15362724 AAAAT
1 AAAAT
15362729 AGTGATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.20
28 16 0.53
29 2 0.07
30 6 0.20
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
AAAATTATATTTTAATCTTTAAAAATTATT
Found at i:15364300 original size:30 final size:29
Alignment explanation
Indices: 15364262--15364507 Score: 125
Period size: 30 Copynumber: 8.3 Consensus size: 29
15364252 GTAAAATGAT
15364262 AATTTTTGGAGAATTCGGGGTCAAAAATGG
1 AATTTTTGGA-AATTCGGGGTCAAAAATGG
*
15364292 ATTTTTTGGAAATTCGAGGGT--AAAATGG
1 AATTTTTGGAAATTCG-GGGTCAAAAATGG
** *
15364320 TAATTTTTGGAAAGTTCCAGGTCAAAGATGG
1 -AATTTTTGGAAA-TTCGGGGTCAAAAATGG
* **
15364351 AATTTATGGAAATTCGGAGGGT-AAAAATTA
1 AATTTTTGGAAATTC-G-GGGTCAAAAATGG
* ** *
15364381 AATTTTTGGAAGTTTAAGGG-C-AAAATGT
1 AATTTTTGGAA-ATTCGGGGTCAAAAATGG
* * *
15364409 AATTTTTGTAAAGTTTAGGGG-CAAAAATGT
1 AATTTTTGGAAA--TTCGGGGTCAAAAATGG
* * *
15364439 AA-TTTTAGAAAGTTTGGGGGTC-AAAATGT
1 AATTTTTGGAAA--TTCGGGGTCAAAAATGG
* *
15364468 AATTTTTAGAAAGTTTAGGGGTCAAAATAT-G
1 AATTTTTGGAAA--TTCGGGGTCAAAA-ATGG
15364499 -ATTTTTGGA
1 AATTTTTGGA
15364508 TAGTTCAAGG
Statistics
Matches: 174, Mismatches: 26, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
28 22 0.13
29 57 0.33
30 79 0.45
31 14 0.08
32 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
AATTTTTGGAAATTCGGGGTCAAAAATGG
Found at i:15364314 original size:59 final size:60
Alignment explanation
Indices: 15364250--15364391 Score: 182
Period size: 59 Copynumber: 2.4 Consensus size: 60
15364240 GGATACCCAG
** * *
15364250 GGGTAAAATGATAATTTTTGGAGAA-TTCGGGGTCAAAAATGGATTTTTTGGAAATTC-GA
1 GGGTAAAATGATAATTTTTGGA-AAGTTCCAGGTCAAAAATGGAATTTATGGAAATTCGGA
* *
15364309 GGGTAAAATGGTAATTTTTGGAAAGTTCCAGGTCAAAGATGGAATTTATGGAAATTCGGA
1 GGGTAAAATGATAATTTTTGGAAAGTTCCAGGTCAAAAATGGAATTTATGGAAATTCGGA
*
15364369 GGGTAAAAATTA-AATTTTTGGAA
1 GGGT-AAAATGATAATTTTTGGAA
15364392 GTTTAAGGGC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.03
59 48 0.67
60 17 0.24
61 5 0.07
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (60 bp):
GGGTAAAATGATAATTTTTGGAAAGTTCCAGGTCAAAAATGGAATTTATGGAAATTCGGA
Found at i:15364415 original size:29 final size:29
Alignment explanation
Indices: 15364381--15364505 Score: 155
Period size: 30 Copynumber: 4.3 Consensus size: 29
15364371 GTAAAAATTA
* *
15364381 AATTTTTGGAAGTTTAAGGG-CAAAATGT
1 AATTTTTGAAAGTTTAGGGGTCAAAATGT
15364409 AATTTTTGTAAAGTTTAGGGG-CAAAAATGT
1 AATTTTTG-AAAGTTTAGGGGTC-AAAATGT
* *
15364439 AATTTTAGAAAGTTTGGGGGTCAAAATGT
1 AATTTTTGAAAGTTTAGGGGTCAAAATGT
*
15364468 AATTTTTAGAAAGTTTAGGGGTCAAAATAT
1 AATTTTT-GAAAGTTTAGGGGTCAAAATGT
*
15364498 GATTTTTG
1 AATTTTTG
15364506 GATAGTTCAA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
28 8 0.09
29 36 0.42
30 41 0.48
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
AATTTTTGAAAGTTTAGGGGTCAAAATGT
Found at i:15366276 original size:17 final size:15
Alignment explanation
Indices: 15366256--15366305 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 15
15366246 GTTTAAAACC
15366256 ATTTCAAATTTAACTAA
1 ATTT-AAATTTAAC-AA
15366273 ATTTAAATTTAAAACAA
1 ATTTAAATTT--AACAA
15366290 ATTTAAATTTAA-AA
1 ATTTAAATTTAACAA
15366304 AT
1 AT
15366306 AAATTTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.13
15 2 0.06
16 6 0.19
17 16 0.52
18 3 0.10
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAATTTAACAA
Found at i:15376302 original size:30 final size:28
Alignment explanation
Indices: 15376254--15376541 Score: 256
Period size: 30 Copynumber: 9.8 Consensus size: 28
15376244 GGATACTCGA
15376254 GGGT-AAAATGATAATTTTTGGAGAATTTG
1 GGGTAAAAATG-TAATTTTTGGA-AATTTG
* * *
15376283 GGGTCAAAAATGAAATTTTTGGCAATTCGGG
1 GGGT-AAAAATGTAATTTTTGGAAATT--TG
* *
15376314 GGGTAAAAATGTAATTTTTGGAAGTTCG
1 GGGTAAAAATGTAATTTTTGGAAATTTG
* *
15376342 GGGGAAAAATGTAATTTTTAGAAATTTAAG
1 GGGTAAAAATGTAATTTTTGGAAATTT--G
* *
15376372 GGGT-AAAATGTAATTTTTTGAAGTTTAG
1 GGGTAAAAATGTAATTTTTGGAAATTT-G
*
15376400 GGGTAAAAATGTAATTTTTGTAAAGTTTG
1 GGGTAAAAATGTAATTTTTGGAAA-TTTG
* *
15376429 AGGGCAAAAATGTAATTTTTAGAAAGTTTG
1 -GGGTAAAAATGTAATTTTTGGAAA-TTTG
*
15376459 AGGGTTAAAATGTAATTTTTGGAAAGTTTGG
1 -GGGTAAAAATGTAATTTTTGGAAA-TTT-G
* *
15376490 GGGTCAAAATGTAATTTTTAGAAAGTTTG
1 GGGTAAAAATGTAATTTTTGGAAA-TTTG
* * *
15376519 AGGATCAAAATATAATTTTTGGA
1 -GGGTAAAAATGTAATTTTTGGA
15376542 TAGTTAGGGA
Statistics
Matches: 220, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
28 30 0.14
29 46 0.21
30 132 0.60
31 12 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTTGGAAATTTG
Found at i:15377619 original size:3 final size:3
Alignment explanation
Indices: 15377611--15377671 Score: 54
Period size: 3 Copynumber: 19.7 Consensus size: 3
15377601 ACTTTCTTTT
* *
15377611 TTA TTA TTA ATA TTAA TTA TTA TTA TTA ATA -TA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
15377657 -TA GTTA TTA CTTA TT
1 TTA -TTA TTA -TTA TT
15377672 TAAAATGACA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
2 4 0.08
3 34 0.69
4 11 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:15378364 original size:11 final size:11
Alignment explanation
Indices: 15378350--15378423 Score: 67
Period size: 11 Copynumber: 6.5 Consensus size: 11
15378340 CAAATTTAAC
15378350 TAAAATAAATT
1 TAAAATAAATT
* *
15378361 TAAATTTAAAAAT
1 TAAA-AT-AAATT
*
15378374 AAAAATAAATT
1 TAAAATAAATT
15378385 TAAAATAAATT
1 TAAAATAAATT
**
15378396 TAAAACCAATT
1 TAAAATAAATT
* *
15378407 TAAACTTAATT
1 TAAAATAAATT
15378418 TAAAAT
1 TAAAAT
15378424 TAAAATTTGA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
11 40 0.82
12 2 0.04
13 7 0.14
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:15378374 original size:18 final size:17
Alignment explanation
Indices: 15378350--15378399 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 17
15378340 CAAATTTAAC
15378350 TAAAATAAATTTAAATT
1 TAAAATAAATTTAAATT
**
15378367 TAAAAATAAAAATAAATT
1 T-AAAATAAATTTAAATT
15378385 TAAAATAAATTTAAA
1 TAAAATAAATTTAAA
15378400 ACCAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATAAATTTAAATT
Found at i:15378426 original size:11 final size:11
Alignment explanation
Indices: 15378313--15378426 Score: 61
Period size: 11 Copynumber: 10.2 Consensus size: 11
15378303 TGGACTTTCA
*
15378313 AATTTAATATT
1 AATTTAAAATT
*
15378324 AAGTTTAAAACT
1 AA-TTTAAAATT
*
15378336 -ATTTCAAATTT
1 AATTT-AAAATT
* *
15378347 AA-CTAAAATA
1 AATTTAAAATT
*
15378357 AATTTAAATTT
1 AATTTAAAATT
* * *
15378368 AAAAATAAAAATA
1 --AATTTAAAATT
*
15378381 AATTTAAAATA
1 AATTTAAAATT
**
15378392 AATTTAAAACC
1 AATTTAAAATT
*
15378403 AATTTAAACTT
1 AATTTAAAATT
15378414 AATTTAAAATT
1 AATTTAAAATT
15378425 AA
1 AA
15378427 AATTTGATCC
Statistics
Matches: 75, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
10 9 0.12
11 51 0.68
12 8 0.11
13 7 0.09
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:15380458 original size:78 final size:78
Alignment explanation
Indices: 15380329--15380487 Score: 318
Period size: 78 Copynumber: 2.0 Consensus size: 78
15380319 ACTTTATGTA
15380329 AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
1 AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
15380394 TAATAACAAAAAC
66 TAATAACAAAAAC
15380407 AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
1 AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
15380472 TAATAACAAAAAC
66 TAATAACAAAAAC
15380485 AAT
1 AAT
15380488 GAATGAATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (78 bp):
AATCTTAGATAAATAAGAATGCAAAGTTCTAGCCTAACTTATAACCTAAGATTCATATGTATGAA
TAATAACAAAAAC
Found at i:15381939 original size:29 final size:28
Alignment explanation
Indices: 15381905--15382089 Score: 210
Period size: 29 Copynumber: 6.5 Consensus size: 28
15381895 AGGTTATAGT
* *
15381905 AAAATTGTAATATTTTGAAAAATAGTGGG
1 AAAATTGTAA-AATTTGAAAAATAGTGGC
*
15381934 AAAATTGTAAAATTTGGAAAATAGTGGC
1 AAAATTGTAAAATTTGAAAAATAGTGGC
*
15381962 AAAACTGTAAAATTTGGAAAACA-AGTGGC
1 AAAATTGTAAAATTT-GAAAA-ATAGTGGC
* * *
15381991 AAAACTGTAAAATCTAGAAAACTAGTGGC
1 AAAATTGTAAAAT-TTGAAAAATAGTGGC
* * *
15382020 AAAATTCTAAAATCTAAAAAATAGTGGC
1 AAAATTGTAAAATTTGAAAAATAGTGGC
*
15382048 AAAATTGTAAAATTTGAAAAACCAGTGGC
1 AAAATTGTAAAATTTGAAAAA-TAGTGGC
*
15382077 AAAACTGTAAAAT
1 AAAATTGTAAAAT
15382090 AATTGCAGTT
Statistics
Matches: 133, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
28 58 0.44
29 73 0.55
30 2 0.02
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (28 bp):
AAAATTGTAAAATTTGAAAAATAGTGGC
Found at i:15381982 original size:57 final size:57
Alignment explanation
Indices: 15381918--15382089 Score: 222
Period size: 57 Copynumber: 3.0 Consensus size: 57
15381908 ATTGTAATAT
*
15381918 TTTGAAAAATAGTGGGAAAATTGTAAAATTTGGAAAA-TAGTGGCAAAACTGTAAAA
1 TTTGAAAAATAGTGGCAAAATTGTAAAATTTGGAAAACTAGTGGCAAAACTGTAAAA
* * * * *
15381974 TTTGGAAAACA-AGTGGCAAAACTGTAAAATCTAGAAAACTAGTGGCAAAATTCTAAAA
1 TTT-GAAAA-ATAGTGGCAAAATTGTAAAATTTGGAAAACTAGTGGCAAAACTGTAAAA
* * * *
15382032 TCTAAAAAATAGTGGCAAAATTGTAAAATTTGAAAAACCAGTGGCAAAACTGTAAAA
1 TTTGAAAAATAGTGGCAAAATTGTAAAATTTGGAAAACTAGTGGCAAAACTGTAAAA
15382089 T
1 T
15382090 AATTGCAGTT
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
56 4 0.04
57 73 0.75
58 20 0.21
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (57 bp):
TTTGAAAAATAGTGGCAAAATTGTAAAATTTGGAAAACTAGTGGCAAAACTGTAAAA
Found at i:15382057 original size:86 final size:86
Alignment explanation
Indices: 15381921--15382089 Score: 257
Period size: 86 Copynumber: 2.0 Consensus size: 86
15381911 GTAATATTTT
* * * ** *
15381921 GAAAAATAGTGGGAAAATTGTAAAATTTGGAAAATAGTGGCAAAACTGTAAAATTTGGAAAACAA
1 GAAAAATAGTGGCAAAATTCTAAAATCTAAAAAATAGTGGCAAAACTGTAAAATTTGAAAAACAA
15381986 GTGGCAAAACTGTAAAATCTA
66 GTGGCAAAACTGTAAAATCTA
* * *
15382007 GAAAACTAGTGGCAAAATTCTAAAATCTAAAAAATAGTGGCAAAATTGTAAAATTTGAAAAACCA
1 GAAAAATAGTGGCAAAATTCTAAAATCTAAAAAATAGTGGCAAAACTGTAAAATTTGAAAAACAA
15382072 GTGGCAAAACTGTAAAAT
66 GTGGCAAAACTGTAAAAT
15382090 AATTGCAGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 74 1.00
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (86 bp):
GAAAAATAGTGGCAAAATTCTAAAATCTAAAAAATAGTGGCAAAACTGTAAAATTTGAAAAACAA
GTGGCAAAACTGTAAAATCTA
Found at i:15387246 original size:33 final size:33
Alignment explanation
Indices: 15387209--15387294 Score: 163
Period size: 33 Copynumber: 2.6 Consensus size: 33
15387199 GTTGGTTGGA
15387209 TAGCTCTTATGAGCATACTGTTTACTGATTGAT
1 TAGCTCTTATGAGCATACTGTTTACTGATTGAT
*
15387242 TAGCTCTTATGAGTATACTGTTTACTGATTGAT
1 TAGCTCTTATGAGCATACTGTTTACTGATTGAT
15387275 TAGCTCTTATGAGCATACTG
1 TAGCTCTTATGAGCATACTG
15387295 CGAATTTACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (33 bp):
TAGCTCTTATGAGCATACTGTTTACTGATTGAT
Found at i:15391097 original size:37 final size:36
Alignment explanation
Indices: 15391047--15391172 Score: 161
Period size: 37 Copynumber: 3.5 Consensus size: 36
15391037 AAAGGCTTGC
*
15391047 TAGGCACATAGCCCGATTACATTCG-CACGAGGCCTG
1 TAGGCACATAGCCCGATTACA-TCGACACGAAGCCTG
*
15391083 TTAGGCACATAGCCCGATTACA-CTGACATGAAGCC--
1 -TAGGCACATAGCCCGATTACATC-GACACGAAGCCTG
*
15391118 TAGGCACATAGCTCGATTACATCGACACGAAGCCTGG
1 TAGGCACATAGCCCGATTACATCGACACGAAGCCT-G
15391155 TAGGCACATAGCCCGATT
1 TAGGCACATAGCCCGATT
15391173 CCTTTCAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
34 30 0.38
35 2 0.03
36 1 0.01
37 45 0.58
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (36 bp):
TAGGCACATAGCCCGATTACATCGACACGAAGCCTG
Found at i:15408513 original size:37 final size:37
Alignment explanation
Indices: 15408466--15408558 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
15408456 GAAAGGCCTA
* * * *
15408466 CTAGGAACATAGCCTGATTACACCGGCATGAATACTG
1 CTAGGCACATAGCCTGATTACACCGACATGAAGACAG
* * *
15408503 CTAGGCACATAGCCCGGTTACACCGACATGAAGCCAG
1 CTAGGCACATAGCCTGATTACACCGACATGAAGACAG
15408540 CTAGGCACATAGCCTGATT
1 CTAGGCACATAGCCTGATT
15408559 CCTTTCATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (37 bp):
CTAGGCACATAGCCTGATTACACCGACATGAAGACAG
Found at i:15431251 original size:13 final size:13
Alignment explanation
Indices: 15431233--15431257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15431223 TAAGTATGAA
15431233 ATGCTAAAAATGT
1 ATGCTAAAAATGT
15431246 ATGCTAAAAATG
1 ATGCTAAAAATG
15431258 ATACAAAATG
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (13 bp):
ATGCTAAAAATGT
Found at i:15433813 original size:12 final size:13
Alignment explanation
Indices: 15433789--15433837 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
15433779 GCTACAAATG
*
15433789 CTTC-TTCTTTTT
1 CTTCTTTCTCTTT
15433801 CTT-TTTCTCTTT
1 CTTCTTTCTCTTT
15433813 CTTCTTCTCTCTTCT
1 CTTCTT-TCTCTT-T
15433828 CTTCTTTCTC
1 CTTCTTTCTC
15433838 AACTTCCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 13 0.41
13 2 0.06
14 10 0.31
15 7 0.22
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
CTTCTTTCTCTTT
Found at i:15451661 original size:28 final size:30
Alignment explanation
Indices: 15451614--15451672 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
15451604 GAATTTTTTG
*
15451614 TAAAATTTAGTTGTTAA-TTTTGTAAATAT
1 TAAAATTTAGCTGTTAATTTTTGTAAATAT
*
15451643 TAAAA-TTAGCTGTTTATTTTTGTAAATAT
1 TAAAATTTAGCTGTTAATTTTTGTAAATAT
15451672 T
1 T
15451673 TTTAAAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.53
Consensus pattern (30 bp):
TAAAATTTAGCTGTTAATTTTTGTAAATAT
Found at i:15453459 original size:21 final size:21
Alignment explanation
Indices: 15453432--15453479 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
15453422 AGCAAGCTGA
15453432 AGAAGAAGAAGAAGAAGACCC
1 AGAAGAAGAAGAAGAAGACCC
* *
15453453 TGAAGAAGAAGAAGAAGATCC
1 AGAAGAAGAAGAAGAAGACCC
15453474 AGAAGA
1 AGAAGA
15453480 GGATGCTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.29, T:0.04
Consensus pattern (21 bp):
AGAAGAAGAAGAAGAAGACCC
Found at i:15457823 original size:14 final size:15
Alignment explanation
Indices: 15457786--15457826 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
15457776 TTTGGAACGG
15457786 GAAAAGTAAATGCTAA
1 GAAAA-TAAATGCTAA
15457802 -AAACATAAATGC-AA
1 GAAA-ATAAATGCTAA
15457816 GAAAATAAATG
1 GAAAATAAATG
15457827 GTAAACAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 9 0.39
15 13 0.57
16 1 0.04
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (15 bp):
GAAAATAAATGCTAA
Found at i:15471499 original size:37 final size:37
Alignment explanation
Indices: 15471458--15471542 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
15471448 TACTAGGAAT
* *
15471458 ATAGCCTGATTACACCGGCATGAATACTGCTAGGCAC
1 ATAGCCTGATTACACCGACATGAAGACTGCTAGGCAC
* * * *
15471495 ATAGCCCGGTTACACCGACATGAAGCCTTCTAGGCAC
1 ATAGCCTGATTACACCGACATGAAGACTGCTAGGCAC
15471532 ATAGCCTGATT
1 ATAGCCTGATT
15471543 CCTTTCATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (37 bp):
ATAGCCTGATTACACCGACATGAAGACTGCTAGGCAC
Found at i:15479748 original size:15 final size:15
Alignment explanation
Indices: 15479728--15479761 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
15479718 CAAAAGACAA
*
15479728 AAAATCACCTGAAAT
1 AAAATCACATGAAAT
*
15479743 AAAATCACATGCAAT
1 AAAATCACATGAAAT
15479758 AAAA
1 AAAA
15479762 GGAAAAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAATCACATGAAAT
Found at i:15484048 original size:196 final size:193
Alignment explanation
Indices: 15483617--15484063 Score: 477
Period size: 194 Copynumber: 2.3 Consensus size: 193
15483607 ATCAGTACCA
* * * * * *
15483617 GATGCTACTCACACGAGCTATCAAGGACTTGCAAACATATGCAGTACCCTAGCCATCGATATGAT
1 GATGCTACTCACACGAGCTATCAAGAACTCG-TAACATATGCGGTACCTTAGCCATCGATACGAT
* * * *
15483682 GTCTGTCTGTAAACTGTCCCCTAACGATGCTGGCTCACACAAGCTATCGTGAATATGCATTTAAG
65 ATCTGTCTATAAACTGTCCCCTAACGATGCTGGCTCACACAAGCTATCGAGAATATGCACTTAAG
* * * * * * *
15483747 CATAAATCCTAGCCATCGTAGGGCTTGTAATCCATTTAGGATTCATATCTCTTTTTTGACTCAC
130 CATAAATCCCAACCATCATAGGGCCTGTAATCCATTTAGGATTCATATATCTTTCTCGACTCAC
* * * * * * *
15483811 GATG-TCGCTCACACGAGCTAACGAGTACTCATAAAATATGCGGTACCTTAGCCATCGATACGGT
1 GATGCT-ACTCACACGAGCTATCAAGAACTCGTAACATATGCGGTACCTTAGCCATCGATACGAT
* * ** *
15483875 ATCTGTGC-ATATAACTGTTTCCCTAATGATGCT-GCTCACATGAGCTGTCGAGAATATGCACTT
65 ATCTGT-CTATA-AACTG-TCCCCTAACGATGCTGGCTCACACAAGCTATCGAGAATATGCACTT
* * * * *
15483938 ATGCATAGATCCCAACCATCATAGGGCCTGTAGTCCATTCTTGGATTCATTTATCATTTCTCGAC
127 AAGCATAAATCCCAACCATCATAGGGCCTGTAATCCATT-TAGGATTCATATATC-TTTCTCGAC
15484003 TCAC
190 TCAC
* * *
15484007 GATGCTACTGACACGAGTTATCAAGAACTCGTAACATATGCGGTACCTCAGCCATCG
1 GATGCTACTCACACGAGCTATCAAGAACTCGTAACATATGCGGTACCTTAGCCATCG
15484064 CGTCGGTATC
Statistics
Matches: 204, Mismatches: 42, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
193 35 0.17
194 86 0.42
195 25 0.12
196 57 0.28
197 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (193 bp):
GATGCTACTCACACGAGCTATCAAGAACTCGTAACATATGCGGTACCTTAGCCATCGATACGATA
TCTGTCTATAAACTGTCCCCTAACGATGCTGGCTCACACAAGCTATCGAGAATATGCACTTAAGC
ATAAATCCCAACCATCATAGGGCCTGTAATCCATTTAGGATTCATATATCTTTCTCGACTCAC
Found at i:15494244 original size:25 final size:25
Alignment explanation
Indices: 15494209--15494272 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
15494199 GTGACATCTT
15494209 TGGCTGCAAATCTGGATCAAACTTG
1 TGGCTGCAAATCTGGATCAAACTTG
*
15494234 TGGCTGTAAATCTGGATCAAACTTG
1 TGGCTGCAAATCTGGATCAAACTTG
* *
15494259 TGGCCGCAATTCTG
1 TGGCTGCAAATCTG
15494273 ATTCCTTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (25 bp):
TGGCTGCAAATCTGGATCAAACTTG
Found at i:15496399 original size:17 final size:17
Alignment explanation
Indices: 15496335--15496402 Score: 52
Period size: 17 Copynumber: 4.0 Consensus size: 17
15496325 AATATTAATG
15496335 GAAATGCAACT-ACAA-T
1 GAAATGCAA-TGACAATT
** *
15496351 GCAAATGCGTTGACAAAT
1 G-AAATGCAATGACAATT
*
15496369 AAAATGCAGA-GACAATT
1 GAAATGCA-ATGACAATT
15496386 GAAATGCAATGACAATT
1 GAAATGCAATGACAATT
15496403 ATATGAAATG
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 3 0.08
17 36 0.90
18 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (17 bp):
GAAATGCAATGACAATT
Found at i:15496831 original size:12 final size:13
Alignment explanation
Indices: 15496807--15496855 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
15496797 GCTACAAATG
*
15496807 CTTC-TTCTTTTT
1 CTTCTTTCTCTTT
15496819 CTT-TTTCTCTTT
1 CTTCTTTCTCTTT
15496831 CTTCTTCTCTCTTCT
1 CTTCTT-TCTCTT-T
15496846 CTTCTTTCTC
1 CTTCTTTCTC
15496856 AACTTCCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 13 0.41
13 2 0.06
14 10 0.31
15 7 0.22
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
CTTCTTTCTCTTT
Found at i:15514858 original size:28 final size:30
Alignment explanation
Indices: 15514811--15514869 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
15514801 GAATTTTTTG
*
15514811 TAAAATTTAGTTGTTAA-TTTTGTAAATAT
1 TAAAATTTAGCTGTTAATTTTTGTAAATAT
*
15514840 TAAAA-TTAGCTGTTTATTTTTGTAAATAT
1 TAAAATTTAGCTGTTAATTTTTGTAAATAT
15514869 T
1 T
15514870 TTTAAAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.53
Consensus pattern (30 bp):
TAAAATTTAGCTGTTAATTTTTGTAAATAT
Found at i:15514910 original size:18 final size:18
Alignment explanation
Indices: 15514884--15514920 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15514874 AAACAGCTAA
*
15514884 AAATAATTTTTTTTATTT
1 AAATAATTTATTTTATTT
*
15514902 AAATTATTTATTTTATTT
1 AAATAATTTATTTTATTT
15514920 A
1 A
15514921 TTTTTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AAATAATTTATTTTATTT
Done.