Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 68 of 120
Found at i:20229697 original size:15 final size:15
Alignment explanation
Indices: 20229647--20229697 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
20229637 CGGGTTCAGA
* *
20229647 TTTTTTAGGTTCAGG
1 TTTTTTAAGTTCGGG
*
20229662 TTTTTTAAGTTCGAG
1 TTTTTTAAGTTCGGG
*
20229677 TCTTTTTGAGTTCGGG
1 T-TTTTTAAGTTCGGG
20229693 TTTTT
1 TTTTT
20229698 GACTTTTTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.12, C:0.08, G:0.24, T:0.57
Consensus pattern (15 bp):
TTTTTTAAGTTCGGG
Found at i:20235162 original size:103 final size:103
Alignment explanation
Indices: 20235025--20235393 Score: 614
Period size: 103 Copynumber: 3.6 Consensus size: 103
20235015 TTGCATATAA
** * *
20235025 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCAAAGTGCTGATCCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
*
20235090 TAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGTGAGAGGGGGTTGCTAAGTGCTGATTCCCCCG
*
20235128 AGGGGTTGCTAAGTGCTGATTCCCCTAATT-ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AGGGGTTGCTAAGTGCTGATTCCCC-GATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
20235192 TTAAATGTGAGAGGGGGTTGCTAAGTGCTGATTCCCCCG
65 TTAAATGTGAGAGGGGGTTGCTAAGTGCTGATTCCCCCG
* *
20235231 AGGGGTTGCTAAGTGTTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
*
20235296 TAAATTTGAGAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGTGAGAGGGGGTTGCTAAGTGCTGATTCCCCCG
** *
20235334 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
20235394 ATAACGGTTA
Statistics
Matches: 250, Mismatches: 14, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
102 3 0.01
103 244 0.98
104 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.33
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
TAAATGTGAGAGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:20235173 original size:33 final size:33
Alignment explanation
Indices: 20235131--20235385 Score: 122
Period size: 33 Copynumber: 7.5 Consensus size: 33
20235121 TCCCCCGAGG
20235131 GGTTGCTAAGTGCTGATTCCCCTAATT-ATTGGT
1 GGTTGCTAAGTGCTGATTCCCCT-ATTAATTGGT
*
20235164 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAGAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-AAT-T----GGT
**
20235207 GGTTGCTAAGTGCTGATTCCCC---CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
* *
20235234 GGTTGCTAAGTGTTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
*
20235267 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATTTGAGAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-AA-TT----GGT
**
20235310 GGTTGCTAAGTGCTGATTCCCC---CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
** * *
20235337 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
20235370 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
20235386 ATCCACCGAT
Statistics
Matches: 172, Mismatches: 17, Indels: 66
0.67 0.07 0.26
Matches are distributed among these distances:
27 41 0.24
28 4 0.02
30 2 0.01
32 4 0.02
33 53 0.31
34 5 0.03
35 5 0.03
36 2 0.01
37 2 0.01
38 3 0.02
39 3 0.02
42 4 0.02
43 44 0.26
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
Found at i:20239091 original size:51 final size:52
Alignment explanation
Indices: 20239033--20239309 Score: 321
Period size: 51 Copynumber: 5.2 Consensus size: 52
20239023 AGGTTATTTT
* *
20239033 CATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGA-TTCCATTTCTC
1 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCCATTTCTC
* *
20239084 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGA-TTCTATTTCTA
1 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCCATTTCTC
20239135 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAAT-ATTTCCATTTCTC
1 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCCATTTCTC
*
20239186 CATTTTCACTTTCATTTTGAAGAAAACCATAATCA-TTCCAAATGATTTGCCATTTCTC
1 CA---T---TTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTT-CCATTTCTC
* * *
20239244 TATTTTCACTTTTATTTTGAAGAAAACCATCATCA-TTCCAAATGATTTCCCATTTCTC
1 CATTTT--C----ATTTTGGAGAAAACCATAATCATTTCCAAATGATTT-CCATTTCTC
20239302 CATTTTCA
1 CATTTTCA
20239310 CCATTTCTTT
Statistics
Matches: 200, Mismatches: 11, Indels: 29
0.83 0.05 0.12
Matches are distributed among these distances:
50 1 0.00
51 96 0.48
52 4 0.02
54 2 0.01
55 1 0.00
56 9 0.05
57 29 0.14
58 58 0.29
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (52 bp):
CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCCATTTCTC
Found at i:20239261 original size:58 final size:57
Alignment explanation
Indices: 20239137--20239310 Score: 269
Period size: 58 Copynumber: 3.0 Consensus size: 57
20239127 TATTTCTACA
*
20239137 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAAT-ATTTCCATTTCTCCATTTTCAC
1 TTTT-ATTTTGAAGAAAACCATAATCA-TTCCAAATGATTTCCATTTCTCCATTTTCAC
* *
20239195 TTTCATTTTGAAGAAAACCATAATCATTCCAAATGATTTGCCATTTCTCTATTTTCAC
1 TTTTATTTTGAAGAAAACCATAATCATTCCAAATGATTT-CCATTTCTCCATTTTCAC
*
20239253 TTTTATTTTGAAGAAAACCATCATCATTCCAAATGATTTCCCATTTCTCCATTTTCAC
1 TTTTATTTTGAAGAAAACCATAATCATTCCAAATGATTT-CCATTTCTCCATTTTCAC
20239311 CATTTCTTTT
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
56 8 0.07
57 25 0.23
58 74 0.69
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (57 bp):
TTTTATTTTGAAGAAAACCATAATCATTCCAAATGATTTCCATTTCTCCATTTTCAC
Found at i:20240815 original size:32 final size:31
Alignment explanation
Indices: 20240779--20240865 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
20240769 TACTTATTAC
* *
20240779 ATACTGAAACTATAGATTGTGAAATTTCTTAT
1 ATACTGAAACTATAGATTGTGAAATTT-ATAA
* * *
20240811 ATACTAAAACTTTAGATTGAGAAA-TTATAA
1 ATACTGAAACTATAGATTGTGAAATTTATAA
*
20240841 ATTA-TGAAACTATAGATAGTGAAAT
1 A-TACTGAAACTATAGATTGTGAAAT
20240866 CGTGACTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
30 19 0.43
31 4 0.09
32 21 0.48
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (31 bp):
ATACTGAAACTATAGATTGTGAAATTTATAA
Found at i:20247256 original size:63 final size:63
Alignment explanation
Indices: 20247175--20247367 Score: 242
Period size: 63 Copynumber: 3.1 Consensus size: 63
20247165 TAGTTTGGCT
* * * *
20247175 ACAACATTATTGAGTGGCTTGACCACAACGTGCAGCTTGTATGTGATATTCAGTGGCTTGACC
1 ACAACATTATTGAGTGGCTTGACCACAATGTGCAACTTGTCTGCGATATTCAGTGGCTTGACC
* * * *
20247238 ACAACGTTATTGAGTGGCTTGACCACTATGTGCAACTTGTCTACGATATTAAGTGGCTTGACC
1 ACAACATTATTGAGTGGCTTGACCACAATGTGCAACTTGTCTGCGATATTCAGTGGCTTGACC
* * * * * * * *
20247301 ACAACTTTATTTAGTGGTTTGACTACAATGAGCAACTTCTCTGCAATATACAGTGGCTTGACC
1 ACAACATTATTGAGTGGCTTGACCACAATGTGCAACTTGTCTGCGATATTCAGTGGCTTGACC
20247364 ACAA
1 ACAA
20247368 TGTGGAGTGT
Statistics
Matches: 111, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 111 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (63 bp):
ACAACATTATTGAGTGGCTTGACCACAATGTGCAACTTGTCTGCGATATTCAGTGGCTTGACC
Found at i:20250186 original size:644 final size:644
Alignment explanation
Indices: 20248952--20250206 Score: 2126
Period size: 644 Copynumber: 1.9 Consensus size: 644
20248942 AATTGTTAAC
20248952 CATTCTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCCTTTCCT
1 CATTCTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCCTTTCCT
* *
20249017 TTTGTTTTGAATCAACTTACCATCCAAAGCCCCCTTTTTACTCATGATCCACTTTTTACTCCTTT
66 TTTGTTTTGAATCAACTTACAATCCAAAGCCCCCTTTTTACTCATGATCCACTTTTTACTCCCTT
*
20249082 TGTCCCTAAACATACCATCTTTTCACCTTTGACTACCCATGGCCGGTCATAGCACCCCAAAAACC
131 TGTCCCTAAACATACCATCTTTTCACCTTTGACTACACATGGCCGGTCATAGCACCCCAAAAACC
* *
20249147 CTACTTTTCATTTTATTTTTCTAGTTTTTCACTCCTCTCCTCTCTTTACCGTCCACCACCCTTTT
196 CCACTTTTCATTTTATTTTTCTAGTTTTTCACTCCTCTCCTCTCTTTACCGTCCACCACCCTTCT
* * * *
20249212 GCACAAGATTTTCAGCTTTTTCTTCTTTATTTTTCCACCTTTGAAGCCGTATTTCTTCATTCTTC
261 CCACAAGATTTTCAGCTTTTTCTTCTTTATTTTACCACCTTTGAAGCCATATTTCTTCATTCCTC
20249277 TTCCACTCCACCACCACACACGACAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGCA
326 TTCCACTCCACCACCACACACGACAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGCA
* * *
20249342 CTGCCGCCGCACCATTGCCATCGGCCACTGTTGATTTTCACCATTTTTCTTATTTTCTCCTCTTT
391 CAGCCGCCGCACCACTGCCATCGACCACTGTTGATTTTCACCATTTTTCTTATTTTCTCCTCTTT
* *
20249407 CCAAAAATCATCTCCGTAAATTCTTGAATTTGATTTTTAAATATTAAAATATCAAATTTTGTATT
456 CCAAAAATCATCTCCATAAATTCTTGAATTTGATTTTTAAATATTAAAATATCAAATTTCGTATT
* *
20249472 ATTTTATCTAAACTCTTCTATTTTGCGTTTATAGTGTTCAATCCTCCACTTTAATCGGCTTTTCG
521 ATTTTATCTAAACTCTTCTATTTTGCATTTATAGTGTCCAATCCTCCACTTTAATCGGCTTTTCG
20249537 GGATTTATCGT-TGAGCCTTTTTCCTCCGTTTTATCGTAGGTATGAAGGACTACTATTCA
586 GGATTTATCGTCT-AGCCTTTTTCCTCCGTTTTATCGTAGGTATGAAGGACTACTATTCA
* *
20249596 CATTTTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCTTTTCCT
1 CATTCTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCCTTTCCT
20249661 TTTGTTTTGAATCAACTTACAATCCAAAG-CCCCTATTTTACTCATGATCCACTTTTTACTCCCT
66 TTTGTTTTGAATCAACTTACAATCCAAAGCCCCCT-TTTTACTCATGATCCACTTTTTACTCCCT
* * *
20249725 TTGTCTCTAAACATGCCATCTTTTCACCTTTGACTACACATGGCCGGTCCTAGCACCCCAAAAAC
130 TTGTCCCTAAACATACCATCTTTTCACCTTTGACTACACATGGCCGGTCATAGCACCCCAAAAAC
*
20249790 CCCACTTTTCATTTTATTTTTCTAGTTTTTCTCTCCTCTCCTCTCTTTACCGTCCACCACCCTTC
195 CCCACTTTTCATTTTATTTTTCTAGTTTTTCACTCCTCTCCTCTCTTTACCGTCCACCACCCTTC
*
20249855 TCCACAAGTTTTTCAGCTTTTTCTTCTTTATTTTACCACCTTTGAAGCCATATTTCTTCATTCCT
260 TCCACAAGATTTTCAGCTTTTTCTTCTTTATTTTACCACCTTTGAAGCCATATTTCTTCATTCCT
*
20249920 CTTCCACTCCACCACCACACACGGCAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGC
325 CTTCCACTCCACCACCACACACGACAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGC
** *
20249985 ACAGCCGCCGTGCCACCT-CCATCGACCACTGTTGATTTTCACCATTTTTCTTCTTTTCTCCTCT
390 ACAGCCGCCGCACCA-CTGCCATCGACCACTGTTGATTTTCACCATTTTTCTTATTTTCTCCTCT
* *
20250049 TTCCAAAAATCATCTCCATAAATTCTTGAATTTTATTTTTAAATATTAAAATATCAACTTTCGTA
454 TTCCAAAAATCATCTCCATAAATTCTTGAATTTGATTTTTAAATATTAAAATATCAAATTTCGTA
* *
20250114 TTATTTTCTCTAAACTCTTCTATTTTGCATTTATAGTG-CCGACTCCTCCACTTTAATCGAAG-T
519 TTATTTTATCTAAACTCTTCTATTTTGCATTTATAGTGTCC-AATCCTCCACTTTAATCG--GCT
*
20250177 TTT-GGGATTTATTGTCTAGCCTTTTTCCTC
581 TTTCGGGATTTATCGTCTAGCCTTTTTCCTC
20250207 TATTTTGTAA
Statistics
Matches: 573, Mismatches: 32, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
643 6 0.01
644 560 0.98
645 6 0.01
646 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (644 bp):
CATTCTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCCTTTCCT
TTTGTTTTGAATCAACTTACAATCCAAAGCCCCCTTTTTACTCATGATCCACTTTTTACTCCCTT
TGTCCCTAAACATACCATCTTTTCACCTTTGACTACACATGGCCGGTCATAGCACCCCAAAAACC
CCACTTTTCATTTTATTTTTCTAGTTTTTCACTCCTCTCCTCTCTTTACCGTCCACCACCCTTCT
CCACAAGATTTTCAGCTTTTTCTTCTTTATTTTACCACCTTTGAAGCCATATTTCTTCATTCCTC
TTCCACTCCACCACCACACACGACAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGCA
CAGCCGCCGCACCACTGCCATCGACCACTGTTGATTTTCACCATTTTTCTTATTTTCTCCTCTTT
CCAAAAATCATCTCCATAAATTCTTGAATTTGATTTTTAAATATTAAAATATCAAATTTCGTATT
ATTTTATCTAAACTCTTCTATTTTGCATTTATAGTGTCCAATCCTCCACTTTAATCGGCTTTTCG
GGATTTATCGTCTAGCCTTTTTCCTCCGTTTTATCGTAGGTATGAAGGACTACTATTCA
Found at i:20262952 original size:25 final size:25
Alignment explanation
Indices: 20262924--20262982 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
20262914 AGCTCGTATA
*
20262924 AGCTTATCGATACTCAGCTCGCACG
1 AGCTTACCGATACTCAGCTCGCACG
* **
20262949 AGCTTACCGTTTTTCAGCTCGCACG
1 AGCTTACCGATACTCAGCTCGCACG
20262974 AGCTTACCG
1 AGCTTACCG
20262983 TTTTTTAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.27
Consensus pattern (25 bp):
AGCTTACCGATACTCAGCTCGCACG
Found at i:20262983 original size:25 final size:25
Alignment explanation
Indices: 20262937--20262987 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
20262927 TTATCGATAC
20262937 TCAGCTCGCACGAGCTTACCGTTTT
1 TCAGCTCGCACGAGCTTACCGTTTT
20262962 TCAGCTCGCACGAGCTTACCGTTTT
1 TCAGCTCGCACGAGCTTACCGTTTT
20262987 T
1 T
20262988 TAGCATACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (25 bp):
TCAGCTCGCACGAGCTTACCGTTTT
Found at i:20272683 original size:23 final size:23
Alignment explanation
Indices: 20272628--20272687 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
20272618 ATACCAGTAG
*
20272628 AGTACTCCTG--ACTTGTACTTC
1 AGTACTCCTGTTACTTGAACTTC
* *
20272649 GGTACTCTTGTTACTTGAACTTC
1 AGTACTCCTGTTACTTGAACTTC
*
20272672 AGTGCTCCTGTT-CTTG
1 AGTACTCCTGTTACTTG
20272688 GCACAACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 8 0.26
22 4 0.13
23 19 0.61
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (23 bp):
AGTACTCCTGTTACTTGAACTTC
Found at i:20275330 original size:16 final size:18
Alignment explanation
Indices: 20275299--20275332 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
20275289 CAGCCTCCAT
20275299 GGAGAAAGGAAAGAAAAG
1 GGAGAAAGGAAAGAAAAG
20275317 GGAGAAA-G-AAGAAAAG
1 GGAGAAAGGAAAGAAAAG
20275333 AAAGTAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
GGAGAAAGGAAAGAAAAG
Found at i:20280348 original size:6 final size:6
Alignment explanation
Indices: 20280337--20280366 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
20280327 TTACTAACTT
*
20280337 TTTTTC TTTTTC CTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
20280367 AATTTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:20280372 original size:18 final size:18
Alignment explanation
Indices: 20280337--20280372 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20280327 TTACTAACTT
**
20280337 TTTTTCTTTTTCCTTTTC
1 TTTTTCTTTTTCAATTTC
20280355 TTTTTCTTTTTCAATTTC
1 TTTTTCTTTTTCAATTTC
20280373 AATATATGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCTTTTTCAATTTC
Found at i:20294786 original size:40 final size:40
Alignment explanation
Indices: 20294731--20294810 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
20294721 TTAGAATAAG
20294731 TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
1 TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
20294771 TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
1 TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
20294811 ACCGTTGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (40 bp):
TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
Found at i:20297230 original size:96 final size:93
Alignment explanation
Indices: 20297087--20297258 Score: 308
Period size: 96 Copynumber: 1.8 Consensus size: 93
20297077 CTTATTACCC
*
20297087 AAAAAATATGAAAGTAACAAAAAAAATAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAAAAA
1 AAAAAATATGAAAGTAACAAAAAAAAAAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAAAAA
20297152 GCTCATTAAGTAACAAAAAAATATGTTA
66 GCTCATTAAGTAACAAAAAAATATGTTA
20297180 AAAAAATATGAAAGTAACAAAAAAAACAAAAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAA
1 AAAAAATATGAAAGTAAC--AAAAAA-AAAAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAA
20297245 AAAGCTCATTAAGT
63 AAAGCTCATTAAGT
20297259 GCATCGAAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
93 18 0.24
95 6 0.08
96 51 0.68
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.25
Consensus pattern (93 bp):
AAAAAATATGAAAGTAACAAAAAAAAAAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAAAAA
GCTCATTAAGTAACAAAAAAATATGTTA
Found at i:20299042 original size:16 final size:15
Alignment explanation
Indices: 20299017--20299046 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20299007 ATTAATTTAA
20299017 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
20299032 TTAACCTAAATGCAA
1 TTAA-CTAAATGCAA
20299047 ATGAAATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:20300364 original size:15 final size:15
Alignment explanation
Indices: 20300344--20300372 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20300334 TAGCTAGTTA
20300344 AATTATGCAAAATTT
1 AATTATGCAAAATTT
20300359 AATTATGCAAAATT
1 AATTATGCAAAATT
20300373 CAATGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
AATTATGCAAAATTT
Found at i:20307576 original size:61 final size:61
Alignment explanation
Indices: 20307481--20307598 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 61
20307471 ACATTAATAA
* *
20307481 TAAATTAATAAAATATTATATAGATAAATATTAAATTTAA-TTCCATATCTCATATTAGTAT
1 TAAATTAATAAAATACTATATAGATAAATATTAAATTTAACTT-AATATCTCATATTAGTAT
*
20307542 TAAATTAATAAAATACTATCTAGATAAATATTAAATTTAACTTAATATCTCATATTA
1 TAAATTAATAAAATACTATATAGATAAATATTAAATTTAACTTAATATCTCATATTA
20307599 ATATCTAGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
61 51 0.96
62 2 0.04
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (61 bp):
TAAATTAATAAAATACTATATAGATAAATATTAAATTTAACTTAATATCTCATATTAGTAT
Found at i:20311264 original size:22 final size:22
Alignment explanation
Indices: 20311212--20311276 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
20311202 TATTTGGGAA
* * *
20311212 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
20311234 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
20311256 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
20311277 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:20322018 original size:8 final size:8
Alignment explanation
Indices: 20322005--20322041 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
20321995 TGCTTAAAAA
20322005 TATTAAAT
1 TATTAAAT
20322013 TATTAAAT
1 TATTAAAT
20322021 TATTAAAT
1 TATTAAAT
20322029 TATTAAAT
1 TATTAAAT
20322037 T-TTAA
1 TATTAA
20322042 TAGTATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TATTAAAT
Found at i:20323725 original size:32 final size:31
Alignment explanation
Indices: 20323678--20323748 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 31
20323668 AAATTACTCT
* * *
20323678 TCCCCTAACTTATTACAAGTTGTTATTTTTC
1 TCCCCTAACTCATTACAAGTTATTATTTCTC
20323709 TCCCACTAACTCATTACAAGTTATTATTTCTC
1 TCCC-CTAACTCATTACAAGTTATTATTTCTC
20323741 TCCCCTAA
1 TCCCCTAA
20323749 TGTCGGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 8 0.22
32 28 0.78
ACGTcount: A:0.25, C:0.28, G:0.04, T:0.42
Consensus pattern (31 bp):
TCCCCTAACTCATTACAAGTTATTATTTCTC
Found at i:20328444 original size:40 final size:41
Alignment explanation
Indices: 20328360--20328444 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 41
20328350 AATTATAGAA
* * * *
20328360 TACTGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTAAAAT
*
20328401 TACTGAATATTG-TTATGTGTACT-ACATTGAACTGTAAAAT
1 TACTGAATATTGTTTATGAGTACTGA-ATTGAACTGTAAAAT
20328441 TACT
1 TACT
20328445 AAAGTAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 1 0.03
40 25 0.66
41 12 0.32
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (41 bp):
TACTGAATATTGTTTATGAGTACTGAATTGAACTGTAAAAT
Found at i:20328719 original size:45 final size:45
Alignment explanation
Indices: 20328651--20328751 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
20328641 GCCGACTACT
* * * *
20328651 GTTACTGTTACCGAATTGACACTTTGTATGTTGAATACTGTTACC
1 GTTACTGTTACAGAATTCACACTTTGTATATTGAATACTATTACC
* * *
20328696 GTTACTGTTACAG-ATTCAGCACTTTGTGTATTGAATATTATTACT
1 GTTACTGTTACAGAATTCA-CACTTTGTATATTGAATACTATTACC
*
20328741 GTTCCTGTTAC
1 GTTACTGTTAC
20328752 TGCTACCGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACAGAATTCACACTTTGTATATTGAATACTATTACC
Found at i:20331255 original size:7 final size:7
Alignment explanation
Indices: 20331237--20331272 Score: 63
Period size: 7 Copynumber: 5.0 Consensus size: 7
20331227 ATACAATACA
20331237 ATTTCTCC
1 ATTTC-CC
20331245 ATTTCCC
1 ATTTCCC
20331252 ATTTCCC
1 ATTTCCC
20331259 ATTTCCC
1 ATTTCCC
20331266 ATTTCCC
1 ATTTCCC
20331273 CTCTTCCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 23 0.82
8 5 0.18
ACGTcount: A:0.14, C:0.42, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTCCC
Found at i:20333510 original size:11 final size:11
Alignment explanation
Indices: 20333490--20333597 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
20333480 CAAAAATTAA
20333490 AAAAAGTATTTT
1 AAAAA-TATTTT
20333502 AAAAATATTTT
1 AAAAATATTTT
20333513 --AAA-A--TT
1 AAAAATATTTT
* * *
20333519 AAAAAAAATTA
1 AAAAATATTTT
20333530 AAAAAGTATTTT
1 AAAAA-TATTTT
*
20333542 AAAAAAATTTT
1 AAAAATATTTT
20333553 --AAA-A-TTT
1 AAAAATATTTT
*
20333560 AAAAA-ATTTAA
1 AAAAATATTT-T
20333571 AAAAAGTATTTT
1 AAAAA-TATTTT
*
20333583 AAAAGTATTTT
1 AAAAATATTTT
20333594 AAAA
1 AAAA
20333598 TTAAAAAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 5 0.07
9 11 0.14
10 2 0.03
11 32 0.42
12 17 0.22
13 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:20333536 original size:40 final size:41
Alignment explanation
Indices: 20333463--20333613 Score: 218
Period size: 40 Copynumber: 3.7 Consensus size: 41
20333453 ACCAAAAATT
20333463 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATTAAAAAAAGTATTTTAAAAA
20333507 TATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
* * * *
20333547 AATTTTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
20333588 TATTTTAAAATT-AAAAAAA-TAAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAA
20333614 TAAAAATATT
Statistics
Matches: 100, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
39 7 0.07
40 43 0.43
41 35 0.35
42 3 0.03
43 6 0.06
44 6 0.06
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:20333564 original size:30 final size:29
Alignment explanation
Indices: 20333523--20333586 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
20333513 AAAATTAAAA
*
20333523 AAAATTAAAAAAGTATTTTAAAAAA-ATTTT
1 AAAATTAAAAAA--ATTTAAAAAAAGATTTT
*
20333553 AAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAATTAAAAAAATTTAAAAAAAG-ATTTT
20333583 AAAA
1 AAAA
20333587 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.33
30 20 0.67
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTAAAAAAATTTAAAAAAAGATTTT
Found at i:20333573 original size:10 final size:10
Alignment explanation
Indices: 20333513--20333575 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
20333503 AAAATATTTT
20333513 AAAA-TTAAA
1 AAAATTTAAA
*
20333522 AAAAATTAAA
1 AAAATTTAAA
20333532 AAAGTATTTTAAA
1 AAA--A-TTTAAA
*
20333545 AAAATTT--T
1 AAAATTTAAA
20333553 AAAATTT-AA
1 AAAATTTAAA
20333562 AAAATTTAAA
1 AAAATTTAAA
20333572 AAAA
1 AAAA
20333576 GTATTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 7 0.16
9 11 0.24
10 17 0.38
11 1 0.02
12 1 0.02
13 8 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:20335477 original size:9 final size:9
Alignment explanation
Indices: 20335465--20335562 Score: 52
Period size: 10 Copynumber: 10.0 Consensus size: 9
20335455 CAAAAAATCA
20335465 TTAAAAATT
1 TTAAAAATT
*
20335474 TTAAAACTTAT
1 TTAAAA-AT-T
20335485 TTAAAAATT
1 TTAAAAATT
* *
20335494 TATAGAATTT
1 T-TAAAAATT
20335504 TGTAAAAATT
1 T-TAAAAATT
* *
20335514 CTAAAAATA
1 TTAAAAATT
* *
20335523 ATAATAATT
1 TTAAAAATT
*
20335532 TTGAATGAATT
1 TT-AA-AAATT
20335543 ATTAAAAATT
1 -TTAAAAATT
20335553 TTACAAAATT
1 TTA-AAAATT
20335563 ACAAAAAAAC
Statistics
Matches: 67, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
9 25 0.37
10 27 0.40
11 13 0.19
12 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (9 bp):
TTAAAAATT
Found at i:20335623 original size:32 final size:31
Alignment explanation
Indices: 20335542--20335624 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
20335532 TTGAATGAAT
20335542 TATTAAAAATT-TTACAAAATTACAAAAAAAC
1 TATTAAAAATTATTA-AAAATTACAAAAAAAC
* *
20335573 TATTCAATAA-TAGT-AAAATTACAAAAAGAAAC
1 TATT-AAAAATTATTAAAAATTAC-AAAA-AAAC
20335605 TA-TAAAAATTATTAAAAATT
1 TATTAAAAATTATTAAAAATT
20335625 GAAAAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
30 12 0.29
31 13 0.31
32 17 0.40
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (31 bp):
TATTAAAAATTATTAAAAATTACAAAAAAAC
Found at i:20336422 original size:17 final size:17
Alignment explanation
Indices: 20336374--20336412 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
20336364 GAAAGAAGAT
* *
20336374 ATTTCGTTTAAGTTTTA
1 ATTTTGTTTAATTTTTA
20336391 ATTTTGTTTAATTTTTA
1 ATTTTGTTTAATTTTTA
20336408 ATTTT
1 ATTTT
20336413 TTATGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (17 bp):
ATTTTGTTTAATTTTTA
Found at i:20337762 original size:140 final size:140
Alignment explanation
Indices: 20337551--20337839 Score: 443
Period size: 140 Copynumber: 2.1 Consensus size: 140
20337541 AATCATAAGA
** * *
20337551 CGACACTTTTGGGGTGACACTTTCCTAAGTGTTGGGATAAACTTGCCGACATATGCTTTGGTCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAAACTTGCCGACATACGCTTTGGCCAA
** * * *
20337616 GTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAATAGTTGGCTTTGTTC
66 CCCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTGTGTCC
*
20337681 GACACTATGC
131 AACACTATGC
* * * *
20337691 CGATACTTTTGGGCCGACACTTTCCTAAGTGTTGGTATAGATTTGCCGACATACGCTTTGGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAAACTTGCCGACATACGCTTTGGCCAA
20337756 CCCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTGTGTCC
66 CCCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTGTGTCC
20337821 AACACTATGC
131 AACACTATGC
*
20337831 TGACACTTT
1 CGACACTTT
20337840 CCTAAGTGTT
Statistics
Matches: 133, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
140 133 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (140 bp):
CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAAACTTGCCGACATACGCTTTGGCCAA
CCCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTGTGTCC
AACACTATGC
Found at i:20342103 original size:120 final size:122
Alignment explanation
Indices: 20341970--20342190 Score: 392
Period size: 120 Copynumber: 1.8 Consensus size: 122
20341960 AGTGGGGGGA
20341970 ATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTCATTAAATTATATAT-T
1 ATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTCATTAAATTATATATAT
* *
20342034 TTTAA-TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATATTATTATAT
66 TTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATATTATTATAT
* *
20342090 ATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTTTATATAT
1 ATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTCATTAAATTATATATAT
20342155 TTTAATTAAAATATATTTAATAATAATTATGTTAAA
66 TTTAATTAAAATATATTTAATAATAATTATGTTAAA
20342191 GTATCATTAA
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
120 61 0.64
121 6 0.06
122 28 0.29
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (122 bp):
ATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTCATTAAATTATATATAT
TTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATATTATTATAT
Found at i:20342424 original size:16 final size:16
Alignment explanation
Indices: 20342403--20342461 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
20342393 TTAAATTGCT
20342403 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
20342419 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
20342435 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
20342451 ATTACGCCTCT
1 ATTACGCCTCT
20342462 GTAACAACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.20, C:0.37, G:0.05, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:20349398 original size:125 final size:123
Alignment explanation
Indices: 20349208--20349521 Score: 520
Period size: 125 Copynumber: 2.5 Consensus size: 123
20349198 CGAGTTGATG
** *
20349208 TTTCTGAGTAAATAGTATAAAATCGCTTTTAGTAAGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAG-CAGATGCTATTTGAGAAGAATTTGTGAAATCG
*
20349273 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTTTTGACT
65 CGGCCTCGTAGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAAT-AATTTTTTTTGACT
*
20349333 TTTCTTACCAAATAGTATAAAATCGCTTTTAGCATGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAGCA-GATGCTATTTGAGAAGAATTTGTGAAATCG
* *
20349398 CGGCCTCGTAGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTTTTACT
65 CGGCCTCGTAGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTGACT
*
20349457 TTTCTGACCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAGCAG-ATGCTATTTGAGAAGAATTTGTGAAATCG
20349522 NNNNNNNNNN
Statistics
Matches: 178, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
123 1 0.01
124 74 0.42
125 103 0.58
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (123 bp):
TTTCTGACCAAATAGTATAAAATCGCTTTTAGCAGATGCTATTTGAGAAGAATTTGTGAAATCGC
GGCCTCGTAGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTGACT
Found at i:20352478 original size:114 final size:114
Alignment explanation
Indices: 20352273--20352656 Score: 574
Period size: 114 Copynumber: 3.4 Consensus size: 114
20352263 NNNNNNNNNN
* * *
20352273 ACAAAGCGCCGCAAAAAATCTTAACCGAAACGCATCATTTTGGGTTGAGGTATATTAGAATTAGT
1 ACAAAGCGCCGCAAAAAATCTTAACCAAAACGCATCGTTTTGGGTTGAGGTATTTTAGAATTAGT
* ** *
20352338 GGCGCTTACGGATAAATGCCATTAAAGCACACCATTAGCAGCGCATTAT
66 GGCGCTTAAGGATAAATGCCGCTAAAGCACACCATTAGCGGCGCATTAT
* * *
20352387 TCAAAGCGCCGCAAAAAATCTTAACCAAAACGCATCGTTTTGGGTTGAGGTATTTTATATTTAGT
1 ACAAAGCGCCGCAAAAAATCTTAACCAAAACGCATCGTTTTGGGTTGAGGTATTTTAGAATTAGT
*
20352452 GGCGCTTAAGGATAAATGCCGCTAAAGCACACCATTAGCGGCACATTAT
66 GGCGCTTAAGGATAAATGCCGCTAAAGCACACCATTAGCGGCGCATTAT
* *
20352501 ACAAAGCGCCGCAAAAAATCATAACCAAAACGCATCGTTTTTGGTTGAGGTATTTTTAGAATTAG
1 ACAAAGCGCCGCAAAAAATCTTAACCAAAACGCATCGTTTTGGGTTGAGGTA-TTTTAGAATTAG
* * * *
20352566 TGGCGC-TATAGTA-AAACGCCGCTAAAGTACATCATTAGCGGCGCATTAT
65 TGGCGCTTA-AGGATAAATGCCGCTAAAGCACACCATTAGCGGCGCATTAT
20352615 ACAAAGCGCCGCAAACAAATCTTAACCAAAACGCATCGTTTT
1 ACAAAGCGCCGCAAA-AAATCTTAACCAAAACGCATCGTTTT
20352657 AAACCGAAAC
Statistics
Matches: 245, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
114 201 0.82
115 44 0.18
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (114 bp):
ACAAAGCGCCGCAAAAAATCTTAACCAAAACGCATCGTTTTGGGTTGAGGTATTTTAGAATTAGT
GGCGCTTAAGGATAAATGCCGCTAAAGCACACCATTAGCGGCGCATTAT
Found at i:20353136 original size:21 final size:21
Alignment explanation
Indices: 20353072--20353136 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
20353062 GGGCCATGGT
*
20353072 TTAAGGGTT-GGGGTTTAATG
1 TTAAGGGTTAGGGGTTTAAGG
*
20353092 -TATAGGTGTTACGGG-TTAATGG
1 TTA-AGG-GTTAGGGGTTTAA-GG
*
20353114 TTAAGGGTTAGGGGTTTAGGG
1 TTAAGGGTTAGGGGTTTAAGG
20353135 TT
1 TT
20353137 TATAGTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 18 0.51
22 10 0.29
23 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.40, T:0.38
Consensus pattern (21 bp):
TTAAGGGTTAGGGGTTTAAGG
Found at i:20353948 original size:22 final size:20
Alignment explanation
Indices: 20353914--20353961 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
20353904 AGTAGGTATT
* * *
20353914 TAAAAATTGATATGAATTATG
1 TAAAAATTAATATAAAAT-TG
20353935 TAAAAATTAAATATAAAATTG
1 TAAAAATT-AATATAAAATTG
20353956 TAAAAA
1 TAAAAA
20353962 GATGGGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
TAAAAATTAATATAAAATTG
Found at i:20354611 original size:190 final size:190
Alignment explanation
Indices: 20354273--20354651 Score: 598
Period size: 190 Copynumber: 2.0 Consensus size: 190
20354263 TGTAAATCCC
* ** *
20354273 TAGACCTTTCACCTTTTCAACGACGATTTCCCCTCTTCTCGGTCGAATATCGCTTCTCGTCTGGG
1 TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGG
* *
20354338 CTGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTTAACTCCGTATATGGCTGTTCATTT
66 CTGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTTAACTACGTATATGGCTATTCATTT
* *
20354403 TTATGTTCGATTTTTTCTTTCTGTAATGCCCACTTTGTTTTTCCTTTCTCTTTAAATTCA
131 TTATGTTCGATTTTTTCTTTCTCTAATGCCCACTTTGTTTTTCCTTTCGCTTTAAATTCA
* *
20354463 TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTTTCGATCGAATATTGCTTCTCGTCTGGG
1 TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGG
* *
20354528 CTGACTGGTAAAAATCTTTCCAAATCCCTAATTTCTTCGTTGAA-TACGTATATGGCTATTCATT
66 CTGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTT-AACTACGTATATGGCTATTCATT
* * * *
20354592 TTTCTGTTTGATTTTTTCTTTCTCTAATGCTCGCTTTGTTTTTCCTTTCGCTTTAAATTC
130 TTTATGTTCGATTTTTTCTTTCTCTAATGCCCACTTTGTTTTTCCTTTCGCTTTAAATTC
20354652 TGTGTTGCTT
Statistics
Matches: 172, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
190 170 0.99
191 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (190 bp):
TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGG
CTGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTTAACTACGTATATGGCTATTCATTT
TTATGTTCGATTTTTTCTTTCTCTAATGCCCACTTTGTTTTTCCTTTCGCTTTAAATTCA
Found at i:20362319 original size:31 final size:30
Alignment explanation
Indices: 20362284--20362343 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
20362274 GGAGGTGGGA
*
20362284 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* *
20362315 TGGGAGGGAGTAAAAATTTTAGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
20362344 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:20362656 original size:9 final size:9
Alignment explanation
Indices: 20362642--20362669 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20362632 AGTTGATTCA
20362642 AATAACTCG
1 AATAACTCG
20362651 AATAACTCG
1 AATAACTCG
20362660 AATAACTCG
1 AATAACTCG
20362669 A
1 A
20362670 TTCGTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (9 bp):
AATAACTCG
Found at i:20364134 original size:13 final size:12
Alignment explanation
Indices: 20364114--20364145 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
20364104 TCACCAACTT
20364114 ATATGTTAGTCC
1 ATATGTTAGTCC
20364126 ATGATGTTAGTCC
1 AT-ATGTTAGTCC
20364139 ATATGTT
1 ATATGTT
20364146 CAAAATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (12 bp):
ATATGTTAGTCC
Found at i:20365493 original size:70 final size:71
Alignment explanation
Indices: 20365344--20365543 Score: 201
Period size: 70 Copynumber: 2.8 Consensus size: 71
20365334 CCTTAGACGT
* * * * *
20365344 GTCTATTCCAACCTTTTAAAGGTTGTCTTAGACGGGTCTATCCTAACCTTTTTAAATGTTGTTTT
1 GTCTATCCCAACCTTTTTAAGGTTGTATTAGAC-GGACTATCCTAACCTTTTTAAAGGTTGTTTT
*
20365409 AGATAAG
65 AGACAAG
* * * *
20365416 GTATATCCCAACCTTTTTAAGGTTGTATTAGA-TGACTATCTTGACCTTTTTAAAGGTTGCTTTT
1 GTCTATCCCAACCTTTTTAAGGTTGTATTAGACGGACTATCCTAACCTTTTTAAAGGTTG-TTTT
20365480 -GACAAG
65 AGACAAG
* * * *
20365486 GTCTATCCCAACTTTTTTAGGGTTGCT-TTAGACGGGTCTATTCC-AACCTTTTTTAAGG
1 GTCTATCCCAACCTTTTTAAGGTTG-TATTAGAC-GGACTA-TCCTAACCTTTTTAAAGG
20365544 GTTACCTTAG
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
70 54 0.51
71 5 0.05
72 44 0.42
73 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.41
Consensus pattern (71 bp):
GTCTATCCCAACCTTTTTAAGGTTGTATTAGACGGACTATCCTAACCTTTTTAAAGGTTGTTTTA
GACAAG
Found at i:20365538 original size:35 final size:34
Alignment explanation
Indices: 20365336--20365543 Score: 136
Period size: 36 Copynumber: 5.9 Consensus size: 34
20365326 AAAAATTACC
* *
20365336 TTAGACGTGTCTATTCCAACCTTTTAAAGGTTGT
1 TTAGACGGGTCTATTCCAACCTTTTTAAGGTTGT
*
20365370 CTTAGACGGGTCTA-TCCTAACCTTTTTAAATGTTGTT
1 -TTAGACGGGTCTATTCC-AACCTTTTT-AAGGTTG-T
** * *
20365407 TTAGATAAGGTATATCCCAACCTTTTTAAGGTTGT
1 TTAGA-CGGGTCTATTCCAACCTTTTTAAGGTTGT
* * **
20365442 ATTAGA--TGACTA-TCTTGACCTTTTTAAAGGTTGCT
1 -TTAGACGGGTCTATTC-CAACCTTTTT-AAGGTTG-T
* * * * *
20365477 TTTGACAAGGTCTATCCCAACTTTTTTAGGGTTGCT
1 TTAGAC-GGGTCTATTCCAACCTTTTTAAGGTTG-T
20365513 TTAGACGGGTCTATTCCAACCTTTTTTAAGG
1 TTAGACGGGTCTATTCCAACC-TTTTTAAGG
20365544 GTTACCTTAG
Statistics
Matches: 132, Mismatches: 27, Indels: 27
0.71 0.15 0.15
Matches are distributed among these distances:
32 1 0.01
33 11 0.08
34 14 0.11
35 34 0.26
36 43 0.33
37 26 0.20
38 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (34 bp):
TTAGACGGGTCTATTCCAACCTTTTTAAGGTTGT
Found at i:20365554 original size:37 final size:35
Alignment explanation
Indices: 20365485--20365555 Score: 97
Period size: 37 Copynumber: 2.0 Consensus size: 35
20365475 CTTTTGACAA
* *
20365485 GGTCTATCCCAACTTTTTTAGGGTTGCTTTAGACG
1 GGTCTATCCCAACTTTTTTAGGGTTACCTTAGACG
*
20365520 GGTCTATTCCAACCTTTTTTAAGGGTTACCTTAGAC
1 GGTCTATCCCAA-CTTTTTT-AGGGTTACCTTAGAC
20365556 AATGTCTAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 11 0.35
36 7 0.23
37 13 0.42
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (35 bp):
GGTCTATCCCAACTTTTTTAGGGTTACCTTAGACG
Found at i:20367041 original size:47 final size:47
Alignment explanation
Indices: 20366987--20367081 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
20366977 TTTTTATTTT
20366987 TTATAGATGACAATCTTAGTTTTGGAGAAGTGTCATCAATGGAAATC
1 TTATAGATGACAATCTTAGTTTTGGAGAAGTGTCATCAATGGAAATC
* * * * **
20367034 TTATAGATGGCAGTCTTATTTTTGGAGAAGTGTCGTCGGTGGAAATC
1 TTATAGATGACAATCTTAGTTTTGGAGAAGTGTCATCAATGGAAATC
20367081 T
1 T
20367082 CAAGTTGCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (47 bp):
TTATAGATGACAATCTTAGTTTTGGAGAAGTGTCATCAATGGAAATC
Found at i:20371717 original size:19 final size:20
Alignment explanation
Indices: 20371668--20371717 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
20371658 TTAATAAAAA
*
20371668 TTATAAAAAAATCAAAATAAT
1 TTAT-AAAAATTCAAAATAAT
*
20371689 TT-TTAAAATTCAAAAT-AT
1 TTATAAAAATTCAAAATAAT
20371707 TTATAAAAATT
1 TTATAAAAATT
20371718 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 1 0.04
21 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TTATAAAAATTCAAAATAAT
Found at i:20375192 original size:4 final size:4
Alignment explanation
Indices: 20375177--20375228 Score: 95
Period size: 4 Copynumber: 13.0 Consensus size: 4
20375167 TTCAAAACAC
*
20375177 CATA CGTA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
20375225 CATA
1 CATA
20375229 AAAAAACTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:20386274 original size:15 final size:15
Alignment explanation
Indices: 20386254--20386306 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
20386244 GTAAGATATA
20386254 ATTTTTTCTTATCGT
1 ATTTTTTCTTATCGT
* *
20386269 ATTTTTAT-TCATACAT
1 ATTTTT-TCTTAT-CGT
20386285 AATTTTTTCTTATCGT
1 -ATTTTTTCTTATCGT
20386301 ATTTTT
1 ATTTTT
20386307 ATTCATACCG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 15 0.50
16 6 0.20
17 9 0.30
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (15 bp):
ATTTTTTCTTATCGT
Found at i:20386292 original size:32 final size:32
Alignment explanation
Indices: 20386251--20386314 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
20386241 ACTGTAAGAT
20386251 ATAATTTTTTCTTATCGTATTTTTATTCATAC
1 ATAATTTTTTCTTATCGTATTTTTATTCATAC
20386283 ATAATTTTTTCTTATCGTATTTTTATTCATAC
1 ATAATTTTTTCTTATCGTATTTTTATTCATAC
20386315 CGTCTGGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (32 bp):
ATAATTTTTTCTTATCGTATTTTTATTCATAC
Found at i:20392774 original size:45 final size:45
Alignment explanation
Indices: 20392704--20392876 Score: 149
Period size: 45 Copynumber: 3.8 Consensus size: 45
20392694 TCGGCTTGAA
* *
20392704 GAAAATGAATAAGACTATAGTTGAAAGACACTATGGCACTATA-C
1 GAAAATGAATAAGACCATAGATGAAAGACACTATGGCACTATATC
* * * * *
20392748 TGGAACTGAATAAGTCCATAGATGAAAGAAACTATGGCATTATATC
1 -GAAAATGAATAAGACCATAGATGAAAGACACTATGGCACTATATC
* *
20392794 GAAAATGAGTAAGACCATA-ACTGAAAGACGCTATGGCA-TA-AT-
1 GAAAATGAATAAGACCATAGA-TGAAAGACACTATGGCACTATATC
* * * *
20392836 GATTATAATGAGTAAGACCATAGCTAAAAGACATTATGGCA
1 GA--A-AATGAATAAGACCATAGATGAAAGACACTATGGCA
20392877 TCACAATTCT
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 4 0.04
45 96 0.91
46 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (45 bp):
GAAAATGAATAAGACCATAGATGAAAGACACTATGGCACTATATC
Found at i:20392857 original size:90 final size:90
Alignment explanation
Indices: 20392758--20393008 Score: 220
Period size: 90 Copynumber: 2.8 Consensus size: 90
20392748 TGGAACTGAA
* * * * *
20392758 TAAGTCCATAGATGAAAGAAACTATGGCATTA-TA-TCGAAAATGAGTAAGACCATAACTGAAAG
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAATTC--AAACGAGTAAGACCATAACTGAAAG
* * *
20392821 ACGCTATGGCATAATGATTATAATGAG
64 ACGCTATGACATAATGACTATAACGAG
* * * * *
20392848 TAAGACCATAGCTAAAAGACATTATGGCATCACAATTCTAACGAGTAAGACCATAGCTGAAAGAC
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAATTCAAACGAGTAAGACCATAACTGAAAGAC
* * *
20392913 GTTATGACATCATGACTGTAACGAG
66 GCTATGACATAATGACTATAACGAG
* * * *** * * *
20392938 TAAGGCCATAGCTAGAAGACGTTATGTCATCATAATTCTAACGAGTAAGACCATAGA-TGAAAGA
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAATTCAAACGAGTAAGACCATA-ACTGAAAGA
*
20393002 TGCTATG
65 CGCTATG
20393009 GTATCATGAA
Statistics
Matches: 134, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
90 131 0.98
91 1 0.01
92 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (90 bp):
TAAGACCATAGATAAAAGAAACTATGGCATCACAATTCAAACGAGTAAGACCATAACTGAAAGAC
GCTATGACATAATGACTATAACGAG
Found at i:20392877 original size:45 final size:45
Alignment explanation
Indices: 20392800--20393036 Score: 242
Period size: 45 Copynumber: 5.3 Consensus size: 45
20392790 TATCGAAAAT
* * * * * * *
20392800 GAGTAAGACCATAACTGAAAGACGCTATGGCATAATGATTATAAT
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
* *
20392845 GAGTAAGACCATAGCTAAAAGACATTATGGCATCACAATTCTAAC
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
* * * * *
20392890 GAGTAAGACCATAGCTGAAAGACGTTATGACATCATGACTGTAAC
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
* * *
20392935 GAGTAAGGCCATAGCTAGAAGACGTTATGTCATCATAATTCTAAC
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
* * * * * *
20392980 GAGTAAGACCATAGATGAAAGATGCTATGGTATCATGAA-TCAAAC
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCAT-AATTCTAAC
*
20393025 GAATAAGACCAT
1 GAGTAAGACCAT
20393037 GGTTGGAAGA
Statistics
Matches: 158, Mismatches: 33, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
45 156 0.99
46 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (45 bp):
GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
Found at i:20393015 original size:90 final size:90
Alignment explanation
Indices: 20392800--20393036 Score: 298
Period size: 90 Copynumber: 2.6 Consensus size: 90
20392790 TATCGAAAAT
* * *
20392800 GAGTAAGACCATA-ACTGAAAGACGCTATGGCATAATGATTATAATGAGTAAGACCATAGCTAAA
1 GAGTAAGACCATAGA-TGAAAGACGCTATGGCATCATGACTATAACGAGTAAGACCATAGCTAAA
20392864 AGACATTATGGCATCACAATTCTAAC
65 AGACATTATGGCATCACAATTCTAAC
* * * * * *
20392890 GAGTAAGACCATAGCTGAAAGACGTTATGACATCATGACTGTAACGAGTAAGGCCATAGCTAGAA
1 GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGACTATAACGAGTAAGACCATAGCTAAAA
* * *
20392955 GACGTTATGTCATCATAATTCTAAC
66 GACATTATGGCATCACAATTCTAAC
* * * *
20392980 GAGTAAGACCATAGATGAAAGATGCTATGGTATCATGAATCA-AACGAATAAGACCAT
1 GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGACT-ATAACGAGTAAGACCAT
20393037 GGTTGGAAGA
Statistics
Matches: 124, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
90 124 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (90 bp):
GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGACTATAACGAGTAAGACCATAGCTAAAA
GACATTATGGCATCACAATTCTAAC
Found at i:20399794 original size:4 final size:4
Alignment explanation
Indices: 20399787--20399812 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
20399777 AAATGCATGC
20399787 ATGA ATGA ATGA ATGA ATGA ATGA AT
1 ATGA ATGA ATGA ATGA ATGA ATGA AT
20399813 TGCCATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (4 bp):
ATGA
Found at i:20411868 original size:46 final size:46
Alignment explanation
Indices: 20411761--20411975 Score: 265
Period size: 45 Copynumber: 4.7 Consensus size: 46
20411751 TGAATCAAAG
* * *
20411761 AAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGGAAAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTG-AAAAT
* *
20411808 GAATAAGACCATGGTTGAAAGACACTATGGCAACACGA-TGAAAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTG-AAAAT
* * * * * *
20411854 GAATAAGACCATGGTAGAAAGACATTATGGCATCAAGA-AGAGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTGAAAAT
* *
20411899 AAATAAGACCATGGTTGAAAGACACTATGGCATCAAGACT-AGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTGAAAAT
*
20411944 AAATAAGACCATGGTTGAAAGACACCATGGCA
1 AAATAAGACCATGGTTGAAAGACACTATGGCA
20411976 CACTTTGATC
Statistics
Matches: 153, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
45 75 0.49
46 42 0.27
47 36 0.24
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (46 bp):
AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTGAAAAT
Found at i:20413765 original size:12 final size:12
Alignment explanation
Indices: 20413748--20413777 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20413738 TCAGGCAGTT
20413748 ACACGGCCTAGC
1 ACACGGCCTAGC
*
20413760 ACACGGCCTGGC
1 ACACGGCCTAGC
20413772 ACACGG
1 ACACGG
20413778 GCGTGTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:20420325 original size:22 final size:22
Alignment explanation
Indices: 20420297--20420372 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
20420287 ATTCATTTAA
20420297 TAGTACGTTAGCCATGAGAGCT
1 TAGTACGTTAGCCATGAGAGCT
* *
20420319 TAGTACGTTAGCCATGAGGGTT
1 TAGTACGTTAGCCATGAGAGCT
* **
20420341 TAGTTCGTTAAACATGAGAGCT
1 TAGTACGTTAGCCATGAGAGCT
20420363 TAGTACGTTA
1 TAGTACGTTA
20420373 AACATGAAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (22 bp):
TAGTACGTTAGCCATGAGAGCT
Found at i:20421349 original size:16 final size:16
Alignment explanation
Indices: 20421316--20421345 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20421306 GATTTTCTGA
20421316 TTGTTTTTTCTTTTCT
1 TTGTTTTTTCTTTTCT
20421332 TTGTTTTTT-TTTTC
1 TTGTTTTTTCTTTTC
20421346 CTTTTTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (16 bp):
TTGTTTTTTCTTTTCT
Found at i:20429509 original size:31 final size:32
Alignment explanation
Indices: 20429448--20429512 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
20429438 TTTTAATCTC
20429448 AAAGTTAAAAACAATGGGAGCTAAAAGCAAAT
1 AAAGTTAAAAACAATGGGAGCTAAAAGCAAAT
*
20429480 AAAGTTAAAAACAGTGGGAGCT-AAAGCAAAT
1 AAAGTTAAAAACAATGGGAGCTAAAAGCAAAT
20429511 AA
1 AA
20429513 TTCCTTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.15
Consensus pattern (32 bp):
AAAGTTAAAAACAATGGGAGCTAAAAGCAAAT
Found at i:20431716 original size:23 final size:23
Alignment explanation
Indices: 20431671--20431717 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
20431661 TCAGAGTAAT
**
20431671 TTAATCTCTATCAATTTTGAGAG
1 TTAATCTCTATCAATTTCAAGAG
20431694 TTAATCTCTATCAATTTCAAGAG
1 TTAATCTCTATCAATTTCAAGAG
20431717 T
1 T
20431718 GAGAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (23 bp):
TTAATCTCTATCAATTTCAAGAG
Found at i:20431910 original size:51 final size:51
Alignment explanation
Indices: 20431808--20431926 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
20431798 GCCCTCAAAG
* * *
20431808 TTTACATATTCTGTCAATTTGGTCTTGATTTAACAAATTTAGCCAATAACA
1 TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGCCAATAACA
* * * **
20431859 TTTACACATTTTATCAATTTGGTCCTGATTTAATATATTTAGCTTGA-AACA
1 TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGC-CAATAACA
20431910 TTTACACATTCTATCAA
1 TTTACACATTCTATCAA
20431927 CATTTACACA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 57 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (51 bp):
TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGCCAATAACA
Found at i:20445960 original size:27 final size:27
Alignment explanation
Indices: 20445919--20446040 Score: 133
Period size: 27 Copynumber: 4.5 Consensus size: 27
20445909 ACACGCTAGA
*
20445919 AAAAGAAAGCCTTTGTGCTGATCTATC
1 AAAAGAAAGCCTTTGTGCTGATCTATG
* *
20445946 AAAAGAAAGCTTTTGTGGTGATCTATG
1 AAAAGAAAGCCTTTGTGCTGATCTATG
* *
20445973 AAAA-AGAAGCATTTATGGCT-ATCTATG
1 AAAAGA-AAGCCTTTGT-GCTGATCTATG
*
20446000 AAAAGAAAGCCTTTGTGGC-AATCTATG
1 AAAAGAAAGCCTTTGT-GCTGATCTATG
*
20446027 AAAAGAATGCCTTT
1 AAAAGAAAGCCTTT
20446041 ATGGTGCACT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
26 1 0.01
27 78 0.95
28 3 0.04
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (27 bp):
AAAAGAAAGCCTTTGTGCTGATCTATG
Found at i:20446004 original size:54 final size:55
Alignment explanation
Indices: 20445917--20446044 Score: 163
Period size: 54 Copynumber: 2.3 Consensus size: 55
20445907 GAACACGCTA
* * **
20445917 GAAAAAGAAAGCCTTTGT-GCTGATCTATCAAAAGAAAGCTTTTGTGGTGATCTAT
1 GAAAAAG-AAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTTGTGGCAATCTAT
* *
20445972 GAAAAAGAAGCATTTATGGCT-ATCTATGAAAAGAAAGCCTTTGTGGCAATCTAT
1 GAAAAAGAAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTTGTGGCAATCTAT
20446026 G-AAAAGAATGCCTTTATGG
1 GAAAAAGAA-GCCTTTATGG
20446045 TGCACTCTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
53 7 0.11
54 47 0.73
55 10 0.16
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (55 bp):
GAAAAAGAAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTTGTGGCAATCTAT
Found at i:20449935 original size:40 final size:39
Alignment explanation
Indices: 20449877--20449999 Score: 156
Period size: 40 Copynumber: 3.1 Consensus size: 39
20449867 AGCTCGCATG
* * *
20449877 GGGAGCTTTCACTAATACACATCTTATCCCTAAGCTTACA
1 GGGAGC-TTCACTGATACACAACTTATCCATAAGCTTACA
* * *
20449917 GGAGAGCTTCACTGATACACAGCTTATCTATAAGCTCACA
1 GG-GAGCTTCACTGATACACAACTTATCCATAAGCTTACA
*
20449957 TGGGAGTTTCACTGATACACAACTTATCCATAAGCTTACA
1 -GGGAGCTTCACTGATACACAACTTATCCATAAGCTTACA
20449997 GGG
1 GGG
20450000 GAAATTTTCC
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 3 0.04
40 63 0.88
41 6 0.08
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (39 bp):
GGGAGCTTCACTGATACACAACTTATCCATAAGCTTACA
Found at i:20450014 original size:40 final size:39
Alignment explanation
Indices: 20449891--20450019 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 39
20449881 GCTTTCACTA
* * * **
20449891 ATACACATCTTATCCCTAAGCTTACAGGAG-AGCTTCACTG
1 ATACACAACTTATCCATAAGCTTACAGGGGAATTTTC-C-G
* * * * *
20449931 ATACACAGCTTATCTATAAGCTCACATGGG-AGTTTCACTG
1 ATACACAACTTATCCATAAGCTTACAGGGGAATTTTC-C-G
20449971 ATACACAACTTATCCATAAGCTTACAGGGGAAATTTTCCG
1 ATACACAACTTATCCATAAGCTTACAGGGG-AATTTTCCG
20450011 ATACACAAC
1 ATACACAAC
20450020 GTATAAAATC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
40 69 0.92
41 1 0.01
42 5 0.07
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (39 bp):
ATACACAACTTATCCATAAGCTTACAGGGGAATTTTCCG
Found at i:20450014 original size:80 final size:82
Alignment explanation
Indices: 20449867--20450017 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 82
20449857 CTATCACTTC
* * * ** *
20449867 AGCTCGCATGGGGAGCTTTCACTAATACACATCTTATCCCTAAGCTTACAGGAGAGCTTCACTGA
1 AGCTCACATGGGGAGCTTTCACTAATACACAACTTATCCATAAGCTTACAGGAGAAATTCACCGA
20449932 TACACAGCTTATCTATA
66 TACACAGCTTATCTATA
* * **
20449949 AGCTCACAT-GGGAG-TTTCACTGATACACAACTTATCCATAAGCTTACAGGGGAAATTTTCCGA
1 AGCTCACATGGGGAGCTTTCACTAATACACAACTTATCCATAAGCTTACAGGAGAAATTCACCGA
20450012 TACACA
66 TACACA
20450018 ACGTATAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 46 0.78
81 5 0.08
82 8 0.14
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (82 bp):
AGCTCACATGGGGAGCTTTCACTAATACACAACTTATCCATAAGCTTACAGGAGAAATTCACCGA
TACACAGCTTATCTATA
Found at i:20455668 original size:50 final size:50
Alignment explanation
Indices: 20455481--20455722 Score: 170
Period size: 50 Copynumber: 4.7 Consensus size: 50
20455471 GATAATAACA
* * ** *
20455481 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTT-AT-T-GTAC
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCG--G
* * * * * *
20455530 TACCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATATCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTT-TCATCTCGG
* * * * *
20455580 TGCCCATGCCATGTTCTAGACATGGTCTTAC-GGAGGACCTTTCATCTCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATG-GGACCTTTCATCTCGG
* * * * *
20455630 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTTAATGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTTTCAT---C-T--CGG
20455686 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
20455723 TCTCATTCCC
Statistics
Matches: 154, Mismatches: 26, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
48 3 0.02
49 35 0.23
50 73 0.47
51 4 0.03
52 1 0.01
53 1 0.01
54 1 0.01
56 36 0.23
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCGG
Found at i:20455697 original size:56 final size:54
Alignment explanation
Indices: 20455630--20455738 Score: 164
Period size: 56 Copynumber: 2.0 Consensus size: 54
20455620 TTCATCTCGG
20455630 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTTAATGA
1 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGA--TCTCATAACCTTAATGA
* * **
20455686 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCATTCCCTTAATG
1 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGATCTCATAACCTTAATG
20455739 TCATGACATT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 14 0.29
56 35 0.71
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (54 bp):
TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGATCTCATAACCTTAATGA
Found at i:20463872 original size:3 final size:3
Alignment explanation
Indices: 20463866--20463917 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
20463856 ACTGCTGCTC
20463866 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20463914 TTA T
1 TTA T
20463918 ATCTTTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20470739 original size:44 final size:45
Alignment explanation
Indices: 20470630--20470785 Score: 154
Period size: 45 Copynumber: 3.5 Consensus size: 45
20470620 ACTCGATGCG
* * ** * *
20470630 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACTTA-CTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGGTCAGCTTCA
* * * * *
20470675 ATCCGCTCCACTACAACTTCAGGGAGATAGGATT-TTCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTCAGCTTCA
* * *
20470719 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTCAGCTTCA
*
20470764 ATCTGCCCCACTGCAACTTCAG
1 ATCTGCTCCACTGCAACTTCAG
20470786 TTGGGATAAG
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
43 1 0.01
44 35 0.39
45 54 0.60
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTCAGCTTCA
Found at i:20470782 original size:45 final size:43
Alignment explanation
Indices: 20470630--20470978 Score: 183
Period size: 44 Copynumber: 8.0 Consensus size: 43
20470620 ACTCGATGCG
* * * *
20470630 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACTTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-CTCACTTCA
* * * * *
20470675 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTTTCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTC-ACTTCA
* * *
20470719 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-CTCA-CTTCA
* * *
20470764 ATCTGCCCCACTGCAACTTCAGTTGG-GATAAGACCTGCTTACTT-A
1 ATCTGCTCCACTGCAACTTCAG--GGAGATAAGA--TTCTCACTTCA
* * * * * * * * *
20470809 GTCTTCTCCACTGTAACTTTAGGGAAATAAGA-CCTGACGT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCACTTCA
* ** * * * * *
20470850 GTCCACTCTACTGCAACTTCAGAGAGATAAGATCCATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-TCACTTCA
* * * *
20470894 ATTCT-CTCCACTACAACTTCAGGGAGATAGGATTATTGACTTCA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-CTCACTTCA
* *
20470938 ATTTGCTCCACTACAA-TCTCAGGGAGATAAGATT-T-ACTTCA
1 ATCTGCTCCACTGCAACT-TCAGGGAGATAAGATTCTCACTTCA
20470979 CCGACCTGTT
Statistics
Matches: 235, Mismatches: 54, Indels: 34
0.73 0.17 0.11
Matches are distributed among these distances:
41 36 0.15
42 3 0.01
43 10 0.04
44 98 0.42
45 73 0.31
46 10 0.04
47 4 0.02
48 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCACTTCA
Found at i:20481615 original size:16 final size:16
Alignment explanation
Indices: 20481591--20481639 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
20481581 TTCGCTGTAT
20481591 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
20481607 TGGATTAGAGGCGTAA
1 TGGAATAGAGGCGTAA
20481623 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
20481639 T
1 T
20481640 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:20481670 original size:45 final size:44
Alignment explanation
Indices: 20481619--20481708 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
20481609 GATTAGAGGC
20481619 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGC-AATC-ATGTGTTTGGTTGAAT
*
20481664 GTAATGGAATAGAGGCGTAATAGCAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGCAATCATGTGTTTGGTTGAAT
20481708 G
1 G
20481709 GAATAGAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.42
45 24 0.56
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGCAATCATGTGTTTGGTTGAAT
Found at i:20481723 original size:39 final size:42
Alignment explanation
Indices: 20481619--20481727 Score: 136
Period size: 45 Copynumber: 2.6 Consensus size: 42
20481609 GATTAGAGGC
20481619 GTAATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGC-AATCAATTGTTTGGTT--AT
*
20481664 GTAATGGAATAGAGGCGTAATAGCAATC-TTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGCAATCAAT-TGTTTGGTTAT
*
20481704 G-AATGGAATAGAGGTGTAATAGCA
1 GTAATGGAATAGAGGCGTAATAGCA
20481728 TAATGGAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
39 22 0.36
40 2 0.03
43 2 0.03
44 11 0.18
45 24 0.39
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.30
Consensus pattern (42 bp):
GTAATGGAATAGAGGCGTAATAGCAATCAATTGTTTGGTTAT
Found at i:20481920 original size:22 final size:22
Alignment explanation
Indices: 20481892--20481997 Score: 140
Period size: 22 Copynumber: 4.8 Consensus size: 22
20481882 TTTATTGTTC
*
20481892 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
20481914 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
20481936 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
20481958 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
20481980 AAACATGAGAGCTTAGTA
1 AAACATGAGAGCTTAGTA
20481998 TATTATAATT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:20482179 original size:38 final size:37
Alignment explanation
Indices: 20482136--20482342 Score: 127
Period size: 38 Copynumber: 5.3 Consensus size: 37
20482126 TAAAAATATC
* *
20482136 TAATTTAATAAAATTCTTAATATTAAATATTCTTATA
1 TAATTTAATAAAATTCTTAATATTAAATATTATAATA
*
20482173 TGAATTTAATAAAA-TCATAATA-TATAATACTATATAATA
1 T-AATTTAATAAAATTCTTAATATTA-AATA-T-TATAATA
* * * ** *
20482212 TAATTTAACATAATTATTATTAAATATAATTTAATAAAAAAATA
1 TAATTT-A-ATAA-AATTCTT--A-AT-ATTAAATATTATAATA
* *
20482256 TAATTTAATAAAATTCTTAATATTAAATATTCTTATA
1 TAATTTAATAAAATTCTTAATATTAAATATTATAATA
*
20482293 TGAATTTAATAAAA-TCATAATA-TATAATACTATATAATA
1 T-AATTTAATAAAATTCTTAATATTA-AATA-T-TATAATA
20482332 TAGA-TTAATAA
1 TA-ATTTAATAA
20482343 TGTAGATACT
Statistics
Matches: 131, Mismatches: 21, Indels: 35
0.70 0.11 0.19
Matches are distributed among these distances:
36 4 0.03
37 34 0.26
38 41 0.31
39 15 0.11
40 4 0.03
41 6 0.05
42 6 0.05
43 1 0.01
44 12 0.09
45 2 0.02
46 5 0.04
47 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (37 bp):
TAATTTAATAAAATTCTTAATATTAAATATTATAATA
Found at i:20482186 original size:56 final size:55
Alignment explanation
Indices: 20482115--20482306 Score: 190
Period size: 56 Copynumber: 3.3 Consensus size: 55
20482105 TTATTATTAA
*
20482115 ATATAATTTAATAAAAATATCTAATTTAATAAAATTCTTAATATTAAATATTCTT
1 ATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTT
* * * * *
20482170 ATATGAATTTAATAAAATCATAATATATAATACTATATAATATAAT-TTAACA-TAATTATTATT
1 ATAT-AATTTAAT--AA--A-AATATATAAT-TTA-ATAA-A-ATTCTTAATATTAAATATTCTT
*
20482233 AAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATATTAAATATTCTT
1 --ATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTT
20482290 ATATGAATTTAATAAAA
1 ATAT-AATTTAATAAAA
20482307 TCATAATATA
Statistics
Matches: 110, Mismatches: 12, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
55 10 0.09
56 26 0.24
57 13 0.12
58 4 0.04
59 9 0.08
60 2 0.02
61 9 0.08
62 4 0.04
63 13 0.12
64 14 0.13
65 6 0.05
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (55 bp):
ATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTT
Found at i:20482221 original size:120 final size:120
Alignment explanation
Indices: 20482003--20482333 Score: 572
Period size: 120 Copynumber: 2.8 Consensus size: 120
20481993 TAGTATATTA
* * * * * *
20482003 TAATTAAAATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAAT
1 TAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAAT
* *
20482068 CATAATATATGATACTATAAAATATAATTTAACATAATTATTATTAAATATAATT
66 CATAATATATAATACTATATAATATAATTTAACATAATTATTATTAAATATAATT
*
20482123 TAATAAAAATATCTAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAAT
1 TAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAAT
20482188 CATAATATATAATACTATATAATATAATTTAACATAATTATTATTAAATATAATT
66 CATAATATATAATACTATATAATATAATTTAACATAATTATTATTAAATATAATT
*
20482243 TAATAAAAAAATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAAT
1 TAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAAT
20482308 CATAATATATAATACTATATAATATA
66 CATAATATATAATACTATATAATATA
20482334 GATTAATAAT
Statistics
Matches: 200, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 200 1.00
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (120 bp):
TAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAAT
CATAATATATAATACTATATAATATAATTTAACATAATTATTATTAAATATAATT
Found at i:20482256 original size:18 final size:18
Alignment explanation
Indices: 20482233--20482268 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20482223 AATTATTATT
20482233 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
20482251 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
20482269 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAATTTAATAAAA
Found at i:20491764 original size:16 final size:17
Alignment explanation
Indices: 20491726--20491764 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20491716 AAAAAATTAT
*
20491726 AAATAAAATATTCAAAA
1 AAATAAAACATTCAAAA
*
20491743 ATATAAAACATT-AAAA
1 AAATAAAACATTCAAAA
20491759 AAATAA
1 AAATAA
20491765 TCAATCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAACATTCAAAA
Found at i:20496542 original size:42 final size:43
Alignment explanation
Indices: 20496444--20496544 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 43
20496434 TTGATATTTT
* * *
20496444 TAGTAATAATTATATATCATATTATTATTTTATGTATTAGTGA
1 TAGTAATAATTATATATCATATTAATATATTATGTATTAGTAA
*
20496487 TACTAATACATTATA-AT-ATATTAATATATTATGTATTCA-TAA
1 TAGTAATA-ATTATATATCATATTAATATATTATGTATT-AGTAA
*
20496529 TAGTTATATATTATAT
1 TAGTAATA-ATTATAT
20496545 TACTTAATAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
42 32 0.67
43 10 0.21
44 6 0.12
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (43 bp):
TAGTAATAATTATATATCATATTAATATATTATGTATTAGTAA
Found at i:20496545 original size:22 final size:22
Alignment explanation
Indices: 20496510--20496568 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
20496500 TAATATATTA
20496510 ATATATTATGTATT-CATAATAGTT
1 ATATATTA--TATTACATAATAG-T
*
20496534 ATATATTATATTACTTAATAGT
1 ATATATTATATTACATAATAGT
*
20496556 ATATATTCTATTA
1 ATATATTATATTA
20496569 TTCTATTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 17 0.53
23 7 0.22
24 8 0.25
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
ATATATTATATTACATAATAGT
Found at i:20497073 original size:16 final size:16
Alignment explanation
Indices: 20497063--20497093 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20497053 ATTGGGCTTG
20497063 AATATTTTTGGGCTCC
1 AATATTTTTGGGCTCC
*
20497079 AATTTTTTTGGGCTC
1 AATATTTTTGGGCTC
20497094 AAAATTTGTT
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:0.16, C:0.16, G:0.19, T:0.48
Consensus pattern (16 bp):
AATATTTTTGGGCTCC
Found at i:20498765 original size:17 final size:17
Alignment explanation
Indices: 20498743--20498775 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20498733 AATAAAAAGC
20498743 TATAAAATTTTTAATAT
1 TATAAAATTTTTAATAT
*
20498760 TATAAACTTTTTAATA
1 TATAAAATTTTTAATA
20498776 AAAATTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAAATTTTTAATAT
Found at i:20499204 original size:11 final size:11
Alignment explanation
Indices: 20499185--20499254 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 11
20499175 TATCGAAACC
*
20499185 ATAACAACAAA
1 ATAATAACAAA
* *
20499196 ATAAAAACAAT
1 ATAATAACAAA
**
20499207 ATAATAGTAAA
1 ATAATAACAAA
20499218 ATAATAACAAA
1 ATAATAACAAA
* * **
20499229 ACAACAATGAA
1 ATAATAACAAA
20499240 ATAATAACAAA
1 ATAATAACAAA
20499251 ATAA
1 ATAA
20499255 CAACGAAAAA
Statistics
Matches: 43, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (11 bp):
ATAATAACAAA
Found at i:20499210 original size:22 final size:22
Alignment explanation
Indices: 20499185--20499263 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
20499175 TATCGAAACC
* *
20499185 ATAACAACAAAATAAAAACAAT
1 ATAACAACAAAATAATAACAAA
* **
20499207 ATAATAGTAAAATAATAACAAA
1 ATAACAACAAAATAATAACAAA
* **
20499229 ACAACAATGAAATAATAACAAA
1 ATAACAACAAAATAATAACAAA
20499251 ATAACAACGAAAA
1 ATAACAAC-AAAA
20499264 AGTTAATTCG
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 41 0.93
23 3 0.07
ACGTcount: A:0.70, C:0.11, G:0.04, T:0.15
Consensus pattern (22 bp):
ATAACAACAAAATAATAACAAA
Found at i:20499707 original size:35 final size:31
Alignment explanation
Indices: 20499627--20499695 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
20499617 TTCCTTCGCA
*
20499627 CAAACAGCATGACAGAAACTAACAAAGCAAG
1 CAAACAGCATGACAGAAACCAACAAAGCAAG
20499658 CAAACAGCATGACAGAAACCAACAAAGCAAG
1 CAAACAGCATGACAGAAACCAACAAAGCAAG
20499689 CAAACAG
1 CAAACAG
20499696 GCAACTGGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.55, C:0.25, G:0.16, T:0.04
Consensus pattern (31 bp):
CAAACAGCATGACAGAAACCAACAAAGCAAG
Found at i:20501496 original size:70 final size:67
Alignment explanation
Indices: 20501377--20501506 Score: 179
Period size: 70 Copynumber: 1.9 Consensus size: 67
20501367 AACAATATAA
* **
20501377 TGGTTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAATAAAGTAGTTTTGCCTTTTAACTT
1 TGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAATAAAGTAGTTTTGCCTTTTAACTT
20501442 AC
66 AC
***
20501444 TGGTTTTGACTTTTAACTTTAAAAAAGATAAACATTTATCAAAATGGCGTAGTTTTGCCTTTT
1 TGGTTTTGACTTTTAAC-TT-AAAAAG-TAAACATTTATCAAAATAAAGTAGTTTTGCCTTTT
20501507 CTTATTCGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
67 16 0.30
68 2 0.04
69 4 0.07
70 32 0.59
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (67 bp):
TGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAATAAAGTAGTTTTGCCTTTTAACTT
AC
Found at i:20506332 original size:26 final size:26
Alignment explanation
Indices: 20506303--20506357 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
20506293 TTTCAGTAAA
20506303 GAACAATCATCAAAACTGTTTCCATT
1 GAACAATCATCAAAACTGTTTCCATT
20506329 GAACAATCATCAAAACTGTTTCCATT
1 GAACAATCATCAAAACTGTTTCCATT
20506355 GAA
1 GAA
20506358 ATCTGAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (26 bp):
GAACAATCATCAAAACTGTTTCCATT
Found at i:20512695 original size:20 final size:19
Alignment explanation
Indices: 20512653--20512695 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20512643 ATTGAACTTG
*
20512653 AAAATTGGACCTAAGATCC
1 AAAATTGGACCTAAGACCC
*
20512672 AAAATTGGACCTGAGAACCC
1 AAAATTGGACCTAAG-ACCC
20512692 AAAA
1 AAAA
20512696 CCAAGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATTGGACCTAAGACCC
Found at i:20513081 original size:61 final size:58
Alignment explanation
Indices: 20513015--20513147 Score: 185
Period size: 61 Copynumber: 2.2 Consensus size: 58
20513005 TCCAAAAATA
* * * *
20513015 ATATTATTTTAATAGTTTTAATATTAAATTAAATTTAATATTTATCTTGTATATAAGTATT
1 ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTG-ATA-AA-TATT
* *
20513076 CTATTAATTTAATAGATTTAATATAAAATTTAATCTAATATTTATCTTGATAAATATT
1 ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTGATAAATATT
20513134 ATATTAATTTAATA
1 ATATTAATTTAATA
20513148 TTAAAGTGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 17 0.26
59 2 0.03
60 3 0.05
61 43 0.66
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTGATAAATATT
Found at i:20513586 original size:25 final size:26
Alignment explanation
Indices: 20513545--20513596 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
20513535 AAAAAATTAA
* *
20513545 CTTTGGTTTTCTTAAA-CTTATTTTC
1 CTTTGGTTTTCTCAAACCTGATTTTC
20513570 CTTTGTGTTTT-TCAAACCTGATTTTC
1 CTTTG-GTTTTCTCAAACCTGATTTTC
20513596 C
1 C
20513597 AACAGCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.56
Consensus pattern (26 bp):
CTTTGGTTTTCTCAAACCTGATTTTC
Found at i:20524581 original size:22 final size:22
Alignment explanation
Indices: 20524556--20524599 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20524546 ATTGCACTCA
*
20524556 AATT-ATTAATATATTGAATTTT
1 AATTAATT-ATATAATGAATTTT
*
20524578 AATTAATTTTATAATGAATTTT
1 AATTAATTATATAATGAATTTT
20524600 CATAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTAATTATATAATGAATTTT
Found at i:20524607 original size:22 final size:22
Alignment explanation
Indices: 20524565--20524609 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20524555 AAATTATTAA
* *
20524565 TATATTGAATTTTAATTAATTT
1 TATAATGAATTTTAATAAATTT
*
20524587 TATAATGAATTTTCATAAATTT
1 TATAATGAATTTTAATAAATTT
20524609 T
1 T
20524610 GATTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TATAATGAATTTTAATAAATTT
Found at i:20527750 original size:45 final size:45
Alignment explanation
Indices: 20527699--20527784 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
20527689 TGTGAACCGA
* * *
20527699 ACATCATAAATTAGTAAGGTGGTTGCTATGTGCTGATTCCATCGG
1 ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCATCGG
** *
20527744 ACATCATTGATTAATAAGGTGGTTACTGTGTGCTGAATCCA
1 ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCA
20527785 CCGAGTATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCATCGG
Found at i:20537123 original size:45 final size:45
Alignment explanation
Indices: 20537059--20537147 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
20537049 AACAGATACT
* * *
20537059 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
20537104 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
20537148 TTGGTTCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:20537216 original size:51 final size:50
Alignment explanation
Indices: 20537158--20537344 Score: 187
Period size: 51 Copynumber: 3.7 Consensus size: 50
20537148 TTGGTTCACA
* * *
20537158 CAGTAGCCTGCACATAGTAATACACATGTGACCATTACCATTCGATACACG
1 CAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGGTACACG
* * * * * *
20537209 CAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGCA
1 CAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATTCGGTACACG
* * * * * * *
20537260 TAGTACCCTACACATAGTACTACAGATGCGACC-TATCATTCCGGTACACG
1 CAGTAGCCTGCACATAGTACTACACACGTGACCATACCATT-CGGTACACG
*
20537310 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CAGTAGCCTGCACATAGTACTACACACGTGACCAT
20537345 CATTTTCACT
Statistics
Matches: 106, Mismatches: 27, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
49 3 0.03
50 36 0.34
51 65 0.61
52 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (50 bp):
CAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGGTACACG
Found at i:20539504 original size:24 final size:26
Alignment explanation
Indices: 20539462--20539514 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
20539452 TTCTCCTAAA
*
20539462 TTTCAAATTTATTGCATTATTTAAT-T
1 TTTCAAATTTATTGAATTA-TTAATAT
20539488 TTTC-AATTTATT-AATTATTAATAT
1 TTTCAAATTTATTGAATTATTAATAT
20539512 TTT
1 TTT
20539515 ATGAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 8 0.32
25 8 0.32
26 4 0.16
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCAAATTTATTGAATTATTAATAT
Found at i:20539513 original size:25 final size:26
Alignment explanation
Indices: 20539462--20539514 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
20539452 TTCTCCTAAA
* *
20539462 TTTCAAATTTATTGCATTATTTAATT
1 TTTCAAATTTATTGAATTATTAAATT
20539488 TTTC-AATTTATT-AATTATTAATATT
1 TTTCAAATTTATTGAATTATTAA-ATT
20539513 TT
1 TT
20539515 ATGAAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 13 0.54
26 4 0.17
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCAAATTTATTGAATTATTAAATT
Found at i:20544946 original size:28 final size:27
Alignment explanation
Indices: 20544905--20544969 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
20544895 AATACGAAAG
* *
20544905 AAAAGAAATTATATATTAAA-ATAAATTT
1 AAAATAAATAATATA-TAAATA-AAATTT
20544933 AAAATAAATAATATATAAATGAAAATTT
1 AAAATAAATAATATATAAAT-AAAATTT
*
20544961 GAAATAAAT
1 AAAATAAAT
20544970 TGAAAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.12
28 27 0.84
29 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAATAAATAATATATAAATAAAATTT
Found at i:20545295 original size:3 final size:3
Alignment explanation
Indices: 20545287--20545346 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
20545277 AACTAATATA
* * * * * *
20545287 AAT AAT AAT ACT AAT AGT TAT AAT AAC ATT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20545335 AAT GAA- AAT AAT
1 AAT -AAT AAT AAT
20545347 TGAGTAATTA
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20545324 original size:15 final size:15
Alignment explanation
Indices: 20545287--20545337 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
20545277 AACTAATATA
20545287 AATAATAAT-ACTAAT
1 AATAATAATAAC-AAT
* * *
20545302 AGTTATAATAACATT
1 AATAATAATAACAAT
20545317 AATAATAATAACAAT
1 AATAATAATAACAAT
20545332 AATAAT
1 AATAAT
20545338 GAAAATAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 27 0.93
16 2 0.07
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:20545996 original size:5 final size:6
Alignment explanation
Indices: 20545984--20546008 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20545974 AAAACCAAAC
20545984 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
20546009 GATGAAACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:20549587 original size:23 final size:23
Alignment explanation
Indices: 20549538--20549591 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
20549528 CTCATCCGCT
* * **
20549538 ACACACCAACTCCGACCGTTCTT
1 ACACACCAACTCCGACCATCCCA
20549561 ACACACCAACTCCGACCATCCCA
1 ACACACCAACTCCGACCATCCCA
20549584 ACACACCA
1 ACACACCA
20549592 TGTGGGGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.48, G:0.06, T:0.13
Consensus pattern (23 bp):
ACACACCAACTCCGACCATCCCA
Found at i:20550616 original size:22 final size:22
Alignment explanation
Indices: 20550602--20550644 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20550592 AAGAATAAAT
*
20550602 CAATTGAAACAAAAGCAAAGAC
1 CAATTGAAACAAAAGCAAAAAC
*
20550624 CAATTGAAACAAAAGCCAAAA
1 CAATTGAAACAAAAGCAAAAA
20550645 TTCAAGAAAA
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:0.60, C:0.19, G:0.12, T:0.09
Consensus pattern (22 bp):
CAATTGAAACAAAAGCAAAAAC
Found at i:20550826 original size:11 final size:11
Alignment explanation
Indices: 20550812--20550841 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20550802 CAAAAATAAA
20550812 ATCCCAACCAT
1 ATCCCAACCAT
20550823 ATCCCAACCAT
1 ATCCCAACCAT
*
20550834 ATCTCAAC
1 ATCCCAAC
20550842 TATTCCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (11 bp):
ATCCCAACCAT
Found at i:20551879 original size:64 final size:65
Alignment explanation
Indices: 20551796--20551924 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 65
20551786 GAAAATGGTG
* * *
20551796 AAATGAGAAACATTTGGAAATGATTATGGTTTTCTCTGAAATGAAAATGAAAATGAAAATGGAAA
1 AAATGAGAAACATTTGGAAATGAATATGGTTTTCTCTAAAATAAAAATGAAAATGAAAATGGAAA
* * * *
20551861 AAATG-GAATCATTTGGAAATGAATGTGGTTTTCTCTAAAATAAAAATGGAAATGGAAATGGAAA
1 AAATGAGAAACATTTGGAAATGAATATGGTTTTCTCTAAAATAAAAATGAAAATGAAAATGGAAA
20551925 TGGAATGGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
64 52 0.91
65 5 0.09
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.28
Consensus pattern (65 bp):
AAATGAGAAACATTTGGAAATGAATATGGTTTTCTCTAAAATAAAAATGAAAATGAAAATGGAAA
Found at i:20551933 original size:11 final size:11
Alignment explanation
Indices: 20551905--20551940 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
20551895 CTAAAATAAA
20551905 AATGGAAATGG
1 AATGGAAATGG
20551916 AAATGGAAATGG
1 -AATGGAAATGG
20551928 AATGGAAATGG
1 AATGGAAATGG
20551939 AA
1 AA
20551941 ATGAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (11 bp):
AATGGAAATGG
Found at i:20551933 original size:17 final size:18
Alignment explanation
Indices: 20551904--20551949 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
20551894 TCTAAAATAA
20551904 AAATGGAAATGGAAATGG
1 AAATGGAAATGGAAATGG
20551922 AAATGG-AATGGAAATGG
1 AAATGGAAATGGAAATGG
*
20551939 AAATGAAAATG
1 AAATGGAAATG
20551950 ACTTGGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.30, T:0.17
Consensus pattern (18 bp):
AAATGGAAATGGAAATGG
Found at i:20551950 original size:6 final size:6
Alignment explanation
Indices: 20551904--20551949 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
20551894 TCTAAAATAA
*
20551904 AAATGG AAATGG AAATGG AAATGG -AATGG AAATGG AAATGA AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
20551950 ACTTGGAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.52, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:20551960 original size:23 final size:23
Alignment explanation
Indices: 20551905--20551949 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
20551895 CTAAAATAAA
*
20551905 AATGGAAATGGAAATGGAAATGG
1 AATGGAAATGGAAATGAAAATGG
20551928 AATGGAAATGGAAATGAAAATG
1 AATGGAAATGGAAATGAAAATG
20551950 ACTTGGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.18
Consensus pattern (23 bp):
AATGGAAATGGAAATGAAAATGG
Found at i:20556503 original size:41 final size:41
Alignment explanation
Indices: 20556452--20556534 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
20556442 ATGGGAGTTC
* *
20556452 TCATATCGGTGGCC-ACGCCATGTCCCAGACATGGTCTTACA
1 TCATATCGGT-GCCAACACCATGTCCCAGACATGATCTTACA
*
20556493 TCATCTCGGTGCCAACACCATGTCCCAGACATGATCTTACA
1 TCATATCGGTGCCAACACCATGTCCCAGACATGATCTTACA
20556534 T
1 T
20556535 GAGACCTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 3 0.08
41 35 0.92
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (41 bp):
TCATATCGGTGCCAACACCATGTCCCAGACATGATCTTACA
Found at i:20563557 original size:50 final size:51
Alignment explanation
Indices: 20563494--20563622 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 51
20563484 TTGTACTGCA
* * *
20563494 AATGCCATATCCCAGATATGGTCTTACATGGGAG-TTCTCATATCGGTGTCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGAGACTCTCATATCGGTG-CC
* *
20563545 -ATGCCATGTCCCAGACATGGTCTT--ATGGGAGACCTCTCATCTCGTTGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGAGA-CTCTCATATCGGTGCC
*
20563594 AACGCCATGTCCCAGACATGGTCTTACAT
1 AATGCCATGTCCCAGACATGGTCTTACAT
20563623 CATCTCGGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
48 7 0.10
49 2 0.03
50 56 0.84
52 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (51 bp):
AATGCCATGTCCCAGACATGGTCTTACATGGGAGACTCTCATATCGGTGCC
Found at i:20563626 original size:41 final size:41
Alignment explanation
Indices: 20563581--20563663 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
20563571 GGGAGACCTC
* *
20563581 TCATCTCGTTGCCAACGCCATGTCCCAGACATGGTCTTACA
1 TCATCTCGGTGCCAACACCATGTCCCAGACATGGTCTTACA
*
20563622 TCATCTCGGTGGCAACACCATGTCCCAGACATGGTCTTACA
1 TCATCTCGGTGCCAACACCATGTCCCAGACATGGTCTTACA
20563663 T
1 T
20563664 GGGACCTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.27
Consensus pattern (41 bp):
TCATCTCGGTGCCAACACCATGTCCCAGACATGGTCTTACA
Found at i:20563720 original size:97 final size:97
Alignment explanation
Indices: 20563590--20563816 Score: 436
Period size: 97 Copynumber: 2.3 Consensus size: 97
20563580 CTCATCTCGT
*
20563590 TGCCAACGCCATGTCCCAGACATGGTCTTACATCATCTCGGTGGCAACACCATGTCCCAGACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATCATCTCGGTGGCAACACCATGTCCCAGACATG
*
20563655 GTCTTACATGGGACCTTTCAGAATCTCAATGA
66 GTCTTACATGGGACCTTTCAAAATCTCAATGA
20563687 TGCCAATGCCATGTCCCAGACATGGTCTTACATCATCTCGGTGGCAACACCATGTCCCAGACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATCATCTCGGTGGCAACACCATGTCCCAGACATG
20563752 GTCTTACATGGGACCTTTCAAAATCTCAATGA
66 GTCTTACATGGGACCTTTCAAAATCTCAATGA
20563784 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
20563817 AGGATCTCTT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 128 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (97 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATCATCTCGGTGGCAACACCATGTCCCAGACATG
GTCTTACATGGGACCTTTCAAAATCTCAATGA
Found at i:20564854 original size:19 final size:19
Alignment explanation
Indices: 20564814--20564855 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20564804 AAACATTAGA
*
20564814 AAAAATATATAAAAAATGT
1 AAAAATATATAAAAAATAT
20564833 AAAAATATA-AAAAAATTAT
1 AAAAATATATAAAAAA-TAT
20564852 AAAA
1 AAAA
20564856 TGCATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAATATATAAAAAATAT
Found at i:20565084 original size:12 final size:10
Alignment explanation
Indices: 20565051--20565076 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20565041 TTTTACAAAT
20565051 TTTATATTTC
1 TTTATATTTC
20565061 TTTATATTTC
1 TTTATATTTC
20565071 TTTATA
1 TTTATA
20565077 ATTTTCTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATTTC
Found at i:20567288 original size:16 final size:16
Alignment explanation
Indices: 20567264--20567297 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20567254 CTAAGTGAAA
20567264 AAAAATTATAAATTAT
1 AAAAATTATAAATTAT
*
20567280 AAAATTTATAAATTAT
1 AAAAATTATAAATTAT
20567296 AA
1 AA
20567298 TATATAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATTATAAATTAT
Done.