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 50 of 120
Found at i:13844945 original size:44 final size:44
Alignment explanation
Indices: 13844630--13844949 Score: 126
Period size: 44 Copynumber: 7.3 Consensus size: 44
13844620 CCTGGACAAC
* *
13844630 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAGT
* * * * ** *
13844674 AGTGGAGCAGATCGAAGATGGT-AGATTTTACCTCCCTGTGGTTA-T
1 AGTGGAGTAGATTGAAGAT-GTCAGATCTTATCTCCCT-AAG-CAGT
* * ** **
13844719 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCTCTGGGCAAC
1 AGTGGAGTAGATTGAAG--ATGTCAGATCT-TATC-TCCCTAAGCAGT
* * * *
13844762 ATTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGAAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAGT
* * * * * * **
13844806 AGTGGAGCAGATCGAAGATGACGGATTTTACCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAG-T
* * * * **
13844849 ACAGTGGAGTACATTGAAGCTAGT-A-AT-TCTA-CTTCCTTAGGCAAC
1 --AGTGGAGTAGATTGAAGAT-GTCAGATCT-TATC-TCCCTAAGCAGT
*
13844894 AGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAGT
13844938 AGTGGAGTAGAT
1 AGTGGAGTAGAT
13844950 CAAAGATGGT
Statistics
Matches: 196, Mismatches: 55, Indels: 50
0.65 0.18 0.17
Matches are distributed among these distances:
41 1 0.01
42 5 0.03
43 40 0.20
44 107 0.55
45 39 0.20
46 3 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (44 bp):
AGTGGAGTAGATTGAAGATGTCAGATCTTATCTCCCTAAGCAGT
Found at i:13845059 original size:132 final size:131
Alignment explanation
Indices: 13844521--13845045 Score: 809
Period size: 132 Copynumber: 4.0 Consensus size: 131
13844511 GGTTAAAACT
*
13844521 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTATGGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTA
*
13844586 TAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGG-CAACAGTGGAATAGATTGAAGATTT
13844651 CA
130 CA
* **
13844653 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCCTGTGGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTA
* * *
13844718 TAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAACATTGGAATAGATTGAAGATTT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATTT
13844783 CA
130 CA
* * *
13844785 GATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTA
* * *
13844850 CAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCTTAGGCAACAGTGGAGTAGATTGAAGATTT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATTT
13844915 CA
130 CA
* *
13844917 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACCTCCCTGTGGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTA
* * * * *
13844982 CAATGGAGTACATTGAAGTCAGTAATCCTA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGG-CAACAGTGGAATAGATTGAAGATT
13845046 GTAAGTATTA
Statistics
Matches: 360, Mismatches: 30, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
131 3 0.01
132 355 0.99
133 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (131 bp):
GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGTTA
CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGCAACAGTGGAATAGATTGAAGATTTC
A
Found at i:13845315 original size:19 final size:19
Alignment explanation
Indices: 13845291--13845422 Score: 210
Period size: 19 Copynumber: 6.8 Consensus size: 19
13845281 AATTTTTGAG
13845291 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
13845310 GATATGCAATCCTATATAT
1 GATATGCAATCTTAGATAT
13845329 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
13845348 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
13845369 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
13845388 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
13845407 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
13845423 ATATTTGATT
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 84 0.82
21 19 0.18
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:13845358 original size:59 final size:57
Alignment explanation
Indices: 13845291--13845422 Score: 210
Period size: 59 Copynumber: 2.3 Consensus size: 57
13845281 AATTTTTGAG
* *
13845291 GATATGCAATCTTAGATATGATATGCAATCCTATATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
* *
13845348 GATATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
13845407 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
13845423 ATATTTGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
57 16 0.23
59 53 0.77
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
Found at i:13846662 original size:98 final size:98
Alignment explanation
Indices: 13846493--13846690 Score: 360
Period size: 98 Copynumber: 2.0 Consensus size: 98
13846483 TTTAAAAATC
13846493 GTAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
1 GTAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
*
13846558 CTTAAATCTTGGATAAGCGGATGTTCTTTTAAA
66 CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
* *
13846591 GTAAATGAAATATTTCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
1 GTAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
*
13846656 CTTAAATCTTGGATAAGTGGATGTTCCTTTAAA
66 CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
13846689 GT
1 GT
13846691 TTTATTGTAC
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (98 bp):
GTAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
Found at i:13853388 original size:24 final size:24
Alignment explanation
Indices: 13853326--13853377 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13853316 TTTCTAGAAG
* **
13853326 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGTATTTATTAACATAATAT
13853350 ATTTAGTATTTATTAACATAATAT
1 ATTTAGTATTTATTAACATAATAT
13853374 ATTT
1 ATTT
13853378 GACTTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGTATTTATTAACATAATAT
Found at i:13857772 original size:24 final size:24
Alignment explanation
Indices: 13857738--13857789 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
13857728 TTTCTAGAAG
* **
13857738 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
13857762 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
13857786 ATTT
1 ATTT
13857790 TAATTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:13861874 original size:50 final size:50
Alignment explanation
Indices: 13861759--13862051 Score: 496
Period size: 50 Copynumber: 5.8 Consensus size: 50
13861749 GATAATAACA
* ** *
13861759 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
13861810 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
13861860 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
13861910 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
13861960 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
13862010 TGCCAATGCCATGTCCCAGACGTGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
13862052 TTACCCAAAT
Statistics
Matches: 229, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
50 196 0.86
51 33 0.14
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:13862167 original size:13 final size:13
Alignment explanation
Indices: 13862146--13862176 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13862136 GCTTAGATCA
*
13862146 TCATCAAATAAAT
1 TCATAAAATAAAT
13862159 TCATAAAATAAAT
1 TCATAAAATAAAT
13862172 TCATA
1 TCATA
13862177 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:13863682 original size:3 final size:3
Alignment explanation
Indices: 13863674--13863707 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
13863664 TGCATTAGAC
13863674 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
13863708 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13863807 original size:1 final size:1
Alignment explanation
Indices: 13863803--13863828 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
13863793 GGGGACGAGC
13863803 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
13863829 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13870988 original size:21 final size:20
Alignment explanation
Indices: 13870935--13870990 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
13870925 GCTAAATAAT
*
13870935 TATAAATAGTAATATA-TGA
1 TATAAATAGTAATAAATTGA
* *
13870954 TAAAAATA-TAATAAATTGT
1 TATAAATAGTAATAAATTGA
13870973 TGATAAATAGTAATAAAT
1 T-ATAAATAGTAATAAAT
13870991 GTTTAATAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 6 0.20
21 8 0.27
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
TATAAATAGTAATAAATTGA
Found at i:13870999 original size:21 final size:21
Alignment explanation
Indices: 13870936--13870999 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
13870926 CTAAATAATT
* *
13870936 ATAAATAGTAATATATG-ATA
1 ATAAATAGTAATAAATGTTTA
*
13870956 A-AAATA-TAATAAAT-TGTTG
1 ATAAATAGTAATAAATGT-TTA
13870975 ATAAATAGTAATAAATGTTTA
1 ATAAATAGTAATAAATGTTTA
13870996 ATAA
1 ATAA
13871000 CATAATAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
18 7 0.20
19 7 0.20
20 6 0.17
21 14 0.40
22 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
ATAAATAGTAATAAATGTTTA
Found at i:13883285 original size:13 final size:13
Alignment explanation
Indices: 13883267--13883293 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13883257 CACAAACGGT
13883267 AAAATTTTCACAC
1 AAAATTTTCACAC
13883280 AAAATTTTCACAC
1 AAAATTTTCACAC
13883293 A
1 A
13883294 TATAAATTAA
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:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:13888597 original size:104 final size:105
Alignment explanation
Indices: 13888469--13888675 Score: 258
Period size: 104 Copynumber: 2.0 Consensus size: 105
13888459 TGTAGGGTTC
* * * **
13888469 ACACGGGCAAAGGACACGGTCGTGTGT-CTAGGCTGTGTAACTCACTGTTTGTGAC-TTAGGACC
1 ACACGGGCAAAGGACACGGCCGTGTGTCCT-GGCCGTGTAACTCACTGTTTATG-CTTTAAAACC
* **
13888532 ACACGGACGAGCACATGGGCGTGTGTCCAGGCCGTGTGAGTT
64 ACACGGACAAGCACATGGGAATGTGTCCAGGCCGTGTGAGTT
*
13888574 ACACGGGC-AAGGACACGGCCGTGTGTCCTGGCCGTGTAACTCTCTGTTTATGCTTTAAAACCAC
1 ACACGGGCAAAGGACACGGCCGTGTGTCCTGGCCGTGTAACTCACTGTTTATGCTTTAAAACCAC
* ** *
13888638 ATGGGTAAGGACATGGGAATGTGTCCAGGCCGTGTGAG
66 ACGGACAAGCACATGGGAATGTGTCCAGGCCGTGTGAG
13888676 CCATATCGGC
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
103 1 0.01
104 76 0.87
105 10 0.11
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (105 bp):
ACACGGGCAAAGGACACGGCCGTGTGTCCTGGCCGTGTAACTCACTGTTTATGCTTTAAAACCAC
ACGGACAAGCACATGGGAATGTGTCCAGGCCGTGTGAGTT
Found at i:13888687 original size:104 final size:104
Alignment explanation
Indices: 13888468--13888714 Score: 257
Period size: 104 Copynumber: 2.4 Consensus size: 104
13888458 GTGTAGGGTT
* * * **
13888468 CACACGGGCAAAGGACACGGTCGTGTGT-CTAGGCTGTGTAACTCACTGTTTGTGACTTAGGACC
1 CACACGGGC-AAGGACACGGACGTGTGTCCT-GGCCGTGTAACTCACTGTTTATGACTTAAAACC
* ** *
13888532 ACACGGACGAGCACATGGGCGTGTGTCCAGGCCGTGTGAGT
64 ACACGGACAAGCACATGGGAATGTGTCCAGGCCGTGTGAGC
* * *
13888573 TACACGGGCAAGGACACGGCCGTGTGTCCTGGCCGTGTAACTCTCTGTTTATG-CTTTAAAACCA
1 CACACGGGCAAGGACACGGACGTGTGTCCTGGCCGTGTAACTCACTGTTTATGAC-TTAAAACCA
* ** *
13888637 CATGGGTAAGGACATGGGAATGTGTCCAGGCCGTGTGAGC
65 CACGGACAAGCACATGGGAATGTGTCCAGGCCGTGTGAGC
* * * *
13888677 CATATC-GGCAAGGACATGGATGTGTGTCCAGGCCGTGT
1 CACA-CGGGCAAGGACACGGACGTGTGTCCTGGCCGTGT
13888715 GGCGTATAAA
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
103 1 0.01
104 106 0.90
105 11 0.09
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (104 bp):
CACACGGGCAAGGACACGGACGTGTGTCCTGGCCGTGTAACTCACTGTTTATGACTTAAAACCAC
ACGGACAAGCACATGGGAATGTGTCCAGGCCGTGTGAGC
Found at i:13892539 original size:20 final size:21
Alignment explanation
Indices: 13892504--13892542 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
13892494 CGTTTCATAT
*
13892504 ATAATATCACATTCAATTTTC
1 ATAATAGCACATTCAATTTTC
13892525 ATAATAGCA-ATTCAATTT
1 ATAATAGCACATTCAATTT
13892543 AACATCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (21 bp):
ATAATAGCACATTCAATTTTC
Found at i:13893993 original size:26 final size:26
Alignment explanation
Indices: 13893964--13894015 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
13893954 ATTTATTTTA
*
13893964 TTTAATTTCT-TTTTAAAAATTAAAAT
1 TTTAATTTATGTTTT-AAAATTAAAAT
* *
13893990 TTTATTTTATGTTTTCAAATTAAAAT
1 TTTAATTTATGTTTTAAAATTAAAAT
13894016 CAACTCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTAATTTATGTTTTAAAATTAAAAT
Found at i:13894504 original size:15 final size:15
Alignment explanation
Indices: 13894484--13894515 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
13894474 ATAAACAAGT
13894484 ACAATTTGACAATTC
1 ACAATTTGACAATTC
13894499 ACAATTTGACAATTC
1 ACAATTTGACAATTC
13894514 AC
1 AC
13894516 TTTAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (15 bp):
ACAATTTGACAATTC
Found at i:13899814 original size:19 final size:18
Alignment explanation
Indices: 13899754--13899859 Score: 67
Period size: 19 Copynumber: 5.8 Consensus size: 18
13899744 TTTTAGGACA
*
13899754 TTTTTAAAATT-TTAACT
1 TTTTTAAAATTATTAAAT
*
13899771 TTATTTATATATTATTTAGAAT
1 TT-TTTA-AAATTA-TTA-AAT
13899793 TTTTTAAAATTATTATAAT
1 TTTTTAAAATTATTA-AAT
*
13899812 TTTTTAAAAATA-TAAAT
1 TTTTTAAAATTATTAAAT
* * *
13899829 ATTATAAATATT-TTTAA-
1 TTTTTAAA-ATTATTAAAT
*
13899846 TTTTAAAAATTATT
1 TTTTTAAAATTATT
13899860 TAGAACCTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
16 3 0.04
17 18 0.26
18 11 0.16
19 21 0.30
20 5 0.07
21 7 0.10
22 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (18 bp):
TTTTTAAAATTATTAAAT
Found at i:13907525 original size:2 final size:2
Alignment explanation
Indices: 13907518--13907542 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13907508 CACATAGGTT
13907518 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
13907543 ATCTGTCCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:13920997 original size:14 final size:14
Alignment explanation
Indices: 13920972--13921011 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
13920962 ATTTAATAAA
* *
13920972 TAAAAATAAAAATC
1 TAAAACTAAAAGTC
13920986 TTAAAACTAAAAGTC
1 -TAAAACTAAAAGTC
13921001 TAAAACTAAAA
1 TAAAACTAAAA
13921012 CACACGTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAAACTAAAAGTC
Found at i:13925393 original size:41 final size:41
Alignment explanation
Indices: 13925348--13925435 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
13925338 ATAATCACTC
* *
13925348 TTTACACCTTCCACAATATGTACCACCATATTGTCCAACCA
1 TTTACACCTTCCACAATATATACCACCATATTATCCAACCA
** *
13925389 TTTACACCTTCCACGGTGTATACCACCATATTATCCAACCA
1 TTTACACCTTCCACAATATATACCACCATATTATCCAACCA
13925430 TTTACA
1 TTTACA
13925436 AGTCAATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.31
Consensus pattern (41 bp):
TTTACACCTTCCACAATATATACCACCATATTATCCAACCA
Found at i:13932341 original size:19 final size:19
Alignment explanation
Indices: 13932310--13932347 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
13932300 TATAATTCCA
*
13932310 AAAATATGAAAAAGTAAAT
1 AAAATATGAAAAAGAAAAT
13932329 AAAATAT-ATAAAAGAAAAT
1 AAAATATGA-AAAAGAAAAT
13932348 GAAAGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AAAATATGAAAAAGAAAAT
Found at i:13932775 original size:23 final size:23
Alignment explanation
Indices: 13932749--13932797 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
13932739 TTACTTCGTT
*
13932749 CTTCTACTGTTTTTCGTGGGTAC
1 CTTCTACTGTTCTTCGTGGGTAC
*
13932772 CTTCTGCTGTTCTTCGTGGGTAC
1 CTTCTACTGTTCTTCGTGGGTAC
13932795 CTT
1 CTT
13932798 GAGGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.06, C:0.24, G:0.22, T:0.47
Consensus pattern (23 bp):
CTTCTACTGTTCTTCGTGGGTAC
Found at i:13941834 original size:132 final size:132
Alignment explanation
Indices: 13941592--13942145 Score: 837
Period size: 132 Copynumber: 4.2 Consensus size: 132
13941582 CTGCAACTGC
* * * *
13941592 AGGGAGATAAGA-CTTACAATCTTCAACCTATTCCACTGCTGACC-AGGG-AGATAGGATTACTG
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTG-CCTAGGGAAG-TAGAATTACTG
* * * *
13941654 ACTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTAC
63 GCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAC
13941719 TGCTT
128 TGCTT
* *
13941724 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTGGCT
* * * * *
13941789 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCAATCTTCAATCTGCTCTAGTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
13941854 TT
131 TT
* * *
13941856 AGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTG-CTCAGAGAAGTAGAATTATTGGC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCT-AGGGAAGTAGAATTACTGGC
* *
13941920 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATTCGTCATCTTCGATCTGCTCCACTACTG
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
13941985 CTT
130 CTT
* * *
13941988 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGTAAGTAGAATTATTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTGGCT
13942053 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
13942118 TT
131 TT
13942120 AGGGAGATAAGATCTGAAATCTTCAA
1 AGGGAGATAAGATCTGAAATCTTCAA
13942146 CCTTCTCCGC
Statistics
Matches: 386, Mismatches: 31, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
131 4 0.01
132 376 0.97
133 6 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:13942142 original size:44 final size:44
Alignment explanation
Indices: 13942094--13942409 Score: 114
Period size: 44 Copynumber: 7.2 Consensus size: 44
13942084 AAAATCCGCC
*
13942094 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
* * * * * * * * **
13942138 ATCTTCAACCTTCTCCGCTGCTGCTCAGGAAGACAAG-GCTTGGT
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATC-TGAA
** * * * **
13942182 GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATCCGCC
1 ATCTTCAATCTGC-T-CCACTACTGCTTAGG-GAGATAAGATCTGAA
* *
13942226 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACA
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA-A
* * * * * * * **
13942270 ACCTTCAACCTTCTCCGCTGCTGCTTAGGGAGACAAG-GCTTGGT
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATC-TGAA
** * * **
13942314 GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGAT-TCGCC
1 ATCTTCAATCTGC-T-CCACTACTGCTTAGG-GAGATAAGATCT-GAA
* * *
13942358 GTCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACA
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA-A
13942402 ATCTTCAA
1 ATCTTCAA
13942410 CCTTCTCTGC
Statistics
Matches: 188, Mismatches: 63, Indels: 42
0.64 0.22 0.14
Matches are distributed among these distances:
42 12 0.06
43 11 0.06
44 147 0.78
45 10 0.05
46 8 0.04
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (44 bp):
ATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
Found at i:13942223 original size:132 final size:132
Alignment explanation
Indices: 13942087--13942508 Score: 720
Period size: 132 Copynumber: 3.2 Consensus size: 132
13942077 GGGAGGTAAA
*
13942087 ATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA-AATCTTCAACCTTC
1 ATCCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACAATCTTCAACCTTC
13942151 TCCGCTGCTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGAT
65 TCCGCTGCTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGAT
13942216 AAG
130 AAG
*
13942219 ATCCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAACCTTCAACCTTCT
1 ATCCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCT
* *
13942284 CCGCTGCTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATA
66 CCGCTGCTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATA
13942349 AG
131 AG
* *
13942351 ATTCGCCGTCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCT
1 ATCCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCT
* * *
13942416 CTGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGTTTCCCACTATCTTGGAAAGATA
66 CCGCTGCTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATA
13942481 AG
131 AG
* * *
13942483 ATTCGCTGTCTTCAATCTGCTCCACT
1 ATCCGCCGTCTTCGATCTGCTCCACT
13942509 GTCAATACAG
Statistics
Matches: 276, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
131 1 0.00
132 275 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (132 bp):
ATCCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCT
CCGCTGCTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATA
AG
Found at i:13942233 original size:264 final size:264
Alignment explanation
Indices: 13941699--13942508 Score: 892
Period size: 264 Copynumber: 3.1 Consensus size: 264
13941689 AAATCCACCA
* *
13941699 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT
* *
13941764 GCCTAGGGAAGTAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGC
66 GCCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGC
* * * * * * *
13941829 AATCTTCAATCTGCTCTAGTACTGCTTAGGGAGATAAGATCTGAAATCTTTAATCTAT-TCCACT
131 CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAACCT-TCTCCGCT
* * ** * * * ** * *
13941893 GTTGCTCAGAGAAGTAGAA---TTATTGGCTTCAATGTAC-T-CCACTATAACCACAGG-GAGGT
195 GCTGCTCAG-GAAG-ACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT---C-TTGGAAAGAT
* * *
13941952 AAAATTCGTCA
254 AAGATTCGCCG
13941963 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT
* * *
13942028 GCCCAGGTAAGTAGAATTATTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGC
66 GCCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGC
13942093 CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAACCTTCTCCGCTG
131 CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAACCTTCTCCGCTG
*
13942158 CTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATCC
196 CTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC
13942223 GCCG
261 GCCG
* * *
13942227 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACAACCTTCAACCT-TCTCCGCTG
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA-AATCTTCAATCTAT-TCCACTG
* * ** ** ** * * * ** * * *
13942290 CTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT---C-TTGGAAAGATAAG
64 TTGCCTAGGGA-AGTAGAATTACTGGCTTCAATGTAC-T-CCACTATAACCACAGG-GAGGTAAA
* * *
13942351 ATTCGCCGTCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACAATCTTCAACCTTC
125 ATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA-AATCTTCAACCTTC
* * *
13942415 TCTGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGTTTCCCACTATCTTGGAAAGAT
189 TCCGCTGCTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGAT
*
13942480 AAGATTCGCTG
254 AAGATTCGCCG
*
13942491 TCTTCAATCTGCTCCACT
1 TCTTCGATCTGCTCCACT
13942509 GTCAATACAG
Statistics
Matches: 473, Mismatches: 59, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
262 3 0.01
263 12 0.03
264 413 0.87
265 29 0.06
266 2 0.00
267 14 0.03
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (264 bp):
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT
GCCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGC
CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAACCTTCTCCGCTG
CTGCTCAGGAAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC
GCCG
Found at i:13943782 original size:6 final size:6
Alignment explanation
Indices: 13943782--13943822 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
13943772 TTTTTTGTTT
*
13943782 TTTTTG TTTTTG TTTTTG TTTTTG -TTTTG TTTTTT TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
13943823 AATCTGAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:13943822 original size:23 final size:21
Alignment explanation
Indices: 13943772--13943822 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 21
13943762 TTCACTTTCA
13943772 TTTTTTGTTTTTTTTGTTTTT
1 TTTTTTGTTTTTTTTGTTTTT
*
13943793 GTTTTTGTTTTTGTTTTGTTTTT
1 TTTTTTG-TTTT-TTTTGTTTTT
13943816 TTTTTTG
1 TTTTTTG
13943823 AATCTGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 6 0.23
22 4 0.15
23 16 0.62
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (21 bp):
TTTTTTGTTTTTTTTGTTTTT
Found at i:13951091 original size:19 final size:19
Alignment explanation
Indices: 13951067--13951177 Score: 186
Period size: 19 Copynumber: 5.8 Consensus size: 19
13951057 AATCATATAT
13951067 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
13951086 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
*
13951105 TCTGAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
13951124 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
13951143 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
13951162 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
13951178 CTCAAAAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 84 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:13951118 original size:38 final size:37
Alignment explanation
Indices: 13951044--13951177 Score: 169
Period size: 38 Copynumber: 3.4 Consensus size: 37
13951034 AAATTAAATC
*
13951044 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCT-AGATTGCATATCATA
*
13951086 TCTAAGATTATATATCATATCTGAGATTGCATATCATA
1 TCTAAGATTACATATCATATCT-AGATTGCATATCATA
*
13951124 TCTAAGATTGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATATCTA-GATTGCATATCATA
*
13951162 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
13951178 CTCAAAAATT
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
37 1 0.01
38 68 0.79
39 3 0.03
41 4 0.05
42 10 0.12
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (37 bp):
TCTAAGATTACATATCATATCTAGATTGCATATCATA
Found at i:13951383 original size:20 final size:19
Alignment explanation
Indices: 13951360--13951399 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
13951350 ACATCGATAC
* *
13951360 AAATTGATACTATTCAAAAT
1 AAATTGAAACAATT-AAAAT
13951380 AAATTGAAACAATTAAAAT
1 AAATTGAAACAATTAAAAT
13951399 A
1 A
13951400 TATCAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATTGAAACAATTAAAAT
Found at i:13966039 original size:8 final size:8
Alignment explanation
Indices: 13966026--13966057 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
13966016 ATTGGTATTC
13966026 AATATTAT
1 AATATTAT
13966034 AATATTAT
1 AATATTAT
13966042 AATATTAT
1 AATATTAT
13966050 AATATTAT
1 AATATTAT
13966058 TGCCCTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AATATTAT
Found at i:13969278 original size:181 final size:181
Alignment explanation
Indices: 13968969--13969327 Score: 583
Period size: 181 Copynumber: 2.0 Consensus size: 181
13968959 GAGGTTTGTA
* * * * *
13968969 TTAGGGTCAATGAGTAGGTCGAGTAGTTGAATTTATTTTTGCAATTTAGTATTAGAATGAGTCTG
1 TTAGGGTCAATGACTAGGTCGAGCAGTTGAAATTATTTTTGCAATTTAGTATTAGAATGAGCCTA
* * * *
13969034 TTGGTTCAGTGGTTGAATGAGTGTTCGTCTATCATTGGGTCTTGGGTTTGAGTCCTTATGTGTGT
66 CTGGTTCAGTGGTTGAATGAGTGTTAGTCTATCATTAGGTCTCGGGTTTGAGTCCTTATGTGTGT
13969099 TATTTTAGTTTTGGTTGAAGTCTAGTTTTGTTTTAAAGATTAATTATTAAG
131 TATTTTAGTTTTGGTTGAAGTCTAGTTTTGTTTTAAAGATTAATTATTAAG
* *
13969150 TTAGTGTCAATGACTAGGTCGAGCAGTTGAAATTATTTTTGCAATTTAGTTTTAGAATGAGCCTA
1 TTAGGGTCAATGACTAGGTCGAGCAGTTGAAATTATTTTTGCAATTTAGTATTAGAATGAGCCTA
*
13969215 CTGGTTCGGTGGTTGAATGAGTGTTAGTCTATCATTAGGTCTCGGGTTTGAGTCCTTATGTGTGT
66 CTGGTTCAGTGGTTGAATGAGTGTTAGTCTATCATTAGGTCTCGGGTTTGAGTCCTTATGTGTGT
* * *
13969280 TATTTTAGTTTTGGTTTAAGTTTAGTTTTGTTTTAAAGGTTAATTATT
131 TATTTTAGTTTTGGTTGAAGTCTAGTTTTGTTTTAAAGATTAATTATT
13969328 TATTTACTTT
Statistics
Matches: 163, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
181 163 1.00
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.45
Consensus pattern (181 bp):
TTAGGGTCAATGACTAGGTCGAGCAGTTGAAATTATTTTTGCAATTTAGTATTAGAATGAGCCTA
CTGGTTCAGTGGTTGAATGAGTGTTAGTCTATCATTAGGTCTCGGGTTTGAGTCCTTATGTGTGT
TATTTTAGTTTTGGTTGAAGTCTAGTTTTGTTTTAAAGATTAATTATTAAG
Found at i:13969305 original size:17 final size:17
Alignment explanation
Indices: 13969283--13969315 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13969273 TGTGTGTTAT
13969283 TTTAGTTTTGGTTTAAG
1 TTTAGTTTTGGTTTAAG
*
13969300 TTTAGTTTTGTTTTAA
1 TTTAGTTTTGGTTTAA
13969316 AGGTTAATTA
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:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (17 bp):
TTTAGTTTTGGTTTAAG
Found at i:13970171 original size:20 final size:21
Alignment explanation
Indices: 13970146--13970195 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
13970136 GTGCAGCTTG
13970146 CACACAGGCT-TGTAGACCAC
1 CACACAGGCTGTGTAGACCAC
*
13970166 CACACAGG-TGTGTAGACCTC
1 CACACAGGCTGTGTAGACCAC
13970186 CACAC-GGCTG
1 CACACAGGCTG
13970196 GAGCACATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.26, C:0.34, G:0.24, T:0.16
Consensus pattern (21 bp):
CACACAGGCTGTGTAGACCAC
Found at i:13972070 original size:19 final size:18
Alignment explanation
Indices: 13972046--13972083 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13972036 AAGGTAATTT
*
13972046 ATTTTTTTAAATGTGTTTA
1 ATTTTTTT-AATATGTTTA
13972065 ATTTTTTTAATATGTTTA
1 ATTTTTTTAATATGTTTA
13972083 A
1 A
13972084 CGATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (18 bp):
ATTTTTTTAATATGTTTA
Found at i:13979550 original size:58 final size:58
Alignment explanation
Indices: 13979456--13979635 Score: 186
Period size: 58 Copynumber: 3.1 Consensus size: 58
13979446 AAAAAAAAGG
** * *
13979456 AAAAAGTTTAGGCCTTAATGTGAGAACAATTACCAAGTTCACG-GACTAATTTGGATAA
1 AAAAAGTTTAGGCCCCAATGTGAGAACAATTGCCAAGTTCA-GAGACTAACTTGGATAA
* * *
13979514 AAAAAGTTTAGGCCCCAATTTGAGAACAATTGCCAAGTTTAGAGCCTAACTTGGATAA
1 AAAAAGTTTAGGCCCCAATGTGAGAACAATTGCCAAGTTCAGAGACTAACTTGGATAA
* * * * * *
13979572 AAGAAAGTTTAAGCTCCAATGTGAGAA-AACTTGTCAAGTTCA-AAATGTAACTTGGACAA
1 AA-AAAGTTTAGGCCCCAATGTGAGAACAA-TTGCCAAGTTCAGAGA-CTAACTTGGATAA
13979631 AAAAA
1 AAAAA
13979636 TATGTTTAGG
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
57 1 0.01
58 57 0.56
59 44 0.43
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (58 bp):
AAAAAGTTTAGGCCCCAATGTGAGAACAATTGCCAAGTTCAGAGACTAACTTGGATAA
Found at i:13980919 original size:31 final size:31
Alignment explanation
Indices: 13980879--13980946 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
13980869 TTGGTACAAT
13980879 TATACATATGAAACTTTAATTATAATTCAAA
1 TATACATATGAAACTTTAATTATAATTCAAA
* * * * *
13980910 TATATATATGAAACTTTTATTTTGATTCAAT
1 TATACATATGAAACTTTAATTATAATTCAAA
13980941 TATACA
1 TATACA
13980947 CGTTTGAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (31 bp):
TATACATATGAAACTTTAATTATAATTCAAA
Found at i:13995327 original size:25 final size:27
Alignment explanation
Indices: 13995276--13995327 Score: 90
Period size: 25 Copynumber: 2.0 Consensus size: 27
13995266 AACATATTTT
13995276 TTCATAAATTTTACTAGGGGTAAAATC
1 TTCATAAATTTTACTAGGGGTAAAATC
13995303 TTCAT-AATTTTACTA-GGGTAAAATC
1 TTCATAAATTTTACTAGGGGTAAAATC
13995328 GGGATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 10 0.40
26 10 0.40
27 5 0.20
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (27 bp):
TTCATAAATTTTACTAGGGGTAAAATC
Found at i:13995334 original size:25 final size:26
Alignment explanation
Indices: 13995282--13995334 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
13995272 TTTTTTCATA
**
13995282 AATTTTACTAGGGGTAAAATCTTCAT
1 AATTTTACTAGGGGTAAAATCGGCAT
*
13995308 AATTTTACTA-GGGTAAAATCGGGAT
1 AATTTTACTAGGGGTAAAATCGGCAT
13995333 AA
1 AA
13995335 GAAAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (26 bp):
AATTTTACTAGGGGTAAAATCGGCAT
Found at i:13996729 original size:16 final size:16
Alignment explanation
Indices: 13996708--13996738 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13996698 TTGGATTGAA
*
13996708 AAAATTATTTAATTAG
1 AAAATTAATTAATTAG
13996724 AAAATTAATTAATTA
1 AAAATTAATTAATTA
13996739 AATTTATTTT
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AAAATTAATTAATTAG
Found at i:14004193 original size:17 final size:16
Alignment explanation
Indices: 14004159--14004216 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
14004149 ATTTTAATAG
*
14004159 ATTTAATATTAGATTTA
1 ATTTAATATT-TATTTA
14004176 ATTTAATATTTATCTTA
1 ATTTAATATTTAT-TTA
*
14004193 A--TAGTATTT-TATTA
1 ATTTAATATTTAT-TTA
14004207 ATTTAATATT
1 ATTTAATATT
14004217 AAAGTGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 8 0.24
17 14 0.41
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTAATATTTATTTA
Found at i:14004313 original size:62 final size:59
Alignment explanation
Indices: 14004229--14004344 Score: 169
Period size: 62 Copynumber: 1.9 Consensus size: 59
14004219 AGTGATTATA
* * *
14004229 TTAATATTAAATTGAATTTAATATTTATCTTGTAGATAAATTTTCTATTAATTTAATAAGAT
1 TTAATATTAAATTGAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAGAT
*
14004291 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAAT
1 TTAATATTAAATTGAATCTAATATTTATCTTGATAAATATTATATTAATTTAAT
14004345 TTTAGAGTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 21 0.42
60 1 0.02
61 1 0.02
62 27 0.54
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTGAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGAT
Found at i:14034745 original size:43 final size:43
Alignment explanation
Indices: 14034695--14034812 Score: 136
Period size: 43 Copynumber: 2.7 Consensus size: 43
14034685 AGGACTCCGA
* *
14034695 TATGTGTTTTCGTGTAAGACCACGTCTGGGACA-TCGGCATC-G
1 TATGTGTTTACGTGTAAGACCACGTCTGGGACAGT-GACATCAG
14034737 -ACCTGTGTTTACGTGTAAGACC-CTGTCTGGGACAGTGACATCAG
1 TA--TGTGTTTACGTGTAAGACCAC-GTCTGGGACAGTGACATCAG
* *
14034781 TATGTGATTACATGTAAGACCACGTCTGGGAC
1 TATGTGTTTACGTGTAAGACCACGTCTGGGAC
14034813 GTTGGCATTG
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
41 1 0.02
42 1 0.02
43 59 0.91
44 3 0.05
45 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (43 bp):
TATGTGTTTACGTGTAAGACCACGTCTGGGACAGTGACATCAG
Found at i:14037108 original size:5 final size:5
Alignment explanation
Indices: 14037094--14037134 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
14037084 TACTAAGGGG
* *
14037094 TCTTT ACTTT TCTTT TCTTT TGTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
14037135 AGGATACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:14040071 original size:22 final size:22
Alignment explanation
Indices: 14040031--14040077 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
14040021 TGTTGCCATG
* *
14040031 TTTTTTTGTTGTCTCACTACCA
1 TTTTGTTGTTGTCTAACTACCA
* *
14040053 TTTTGTTGTTGTTTAACTATCA
1 TTTTGTTGTTGTCTAACTACCA
14040075 TTT
1 TTT
14040078 CACTATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.60
Consensus pattern (22 bp):
TTTTGTTGTTGTCTAACTACCA
Found at i:14040107 original size:33 final size:33
Alignment explanation
Indices: 14040052--14040119 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
14040042 TCTCACTACC
** *
14040052 ATTTTGTTGTTGTTTAACTATCATTTCACTATT
1 ATTTTGTTGTCATTTAACTATCACTTCACTATT
* *
14040085 ATTTTGTTGTCATTTCATTATCACTTCACTATT
1 ATTTTGTTGTCATTTAACTATCACTTCACTATT
14040118 AT
1 AT
14040120 ATTGCTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (33 bp):
ATTTTGTTGTCATTTAACTATCACTTCACTATT
Found at i:14040199 original size:52 final size:53
Alignment explanation
Indices: 14040138--14040247 Score: 204
Period size: 52 Copynumber: 2.1 Consensus size: 53
14040128 TATTATTTTT
14040138 GTTTATTGTTTGGATATTGTATAACTCTTGTTGTATTGTTAATTTTTCTACTA
1 GTTTATTGTTTGGATATTGTATAACTCTTGTTGTATTGTTAATTTTTCTACTA
14040191 GTTT-TTGTTTGGATATTGTATAACTCTTGTTGTATTGTTAATTTTTCTACTA
1 GTTTATTGTTTGGATATTGTATAACTCTTGTTGTATTGTTAATTTTTCTACTA
*
14040243 CTTTA
1 GTTTA
14040248 GAGACATTTG
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 51 0.93
53 4 0.07
ACGTcount: A:0.20, C:0.08, G:0.15, T:0.57
Consensus pattern (53 bp):
GTTTATTGTTTGGATATTGTATAACTCTTGTTGTATTGTTAATTTTTCTACTA
Found at i:14044627 original size:4 final size:4
Alignment explanation
Indices: 14044618--14044670 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
14044608 ACCTGATGCA
14044618 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
14044666 ACAT A
1 ACAT A
14044671 TAAATTACTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:14045349 original size:20 final size:21
Alignment explanation
Indices: 14045312--14045350 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
14045302 ATACTTTTAT
14045312 AATAATATTTATTATTTTAAA
1 AATAATATTTATTATTTTAAA
14045333 AATAAT-TTTAATT-TTTTA
1 AATAATATTT-ATTATTTTA
14045351 TTGAGTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATAATATTTATTATTTTAAA
Found at i:14047860 original size:12 final size:13
Alignment explanation
Indices: 14047828--14047864 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
14047818 AAATTATCAA
14047828 ACCCAACCCAATT
1 ACCCAACCCAATT
14047841 ACCCAACCCAATT
1 ACCCAACCCAATT
14047854 A-CCAACCCAAT
1 ACCCAACCCAAT
14047865 AAAACTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.41, C:0.46, G:0.00, T:0.14
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:14047894 original size:51 final size:52
Alignment explanation
Indices: 14047833--14047953 Score: 221
Period size: 51 Copynumber: 2.4 Consensus size: 52
14047823 ATCAAACCCA
14047833 ACCCAATTACCCAACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
14047884 ACCCAATTACCCAA-CCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
14047935 ACCCAATTA-CCAACCCAAT
1 ACCCAATTACCCAACCCAAT
14047954 AAAAATAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
50 11 0.16
51 57 0.84
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (52 bp):
ACCCAATTACCCAACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:14047903 original size:12 final size:12
Alignment explanation
Indices: 14047886--14047911 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14047876 TAAAGTCTAC
14047886 CCAATTACCCAA
1 CCAATTACCCAA
14047898 CCAATTACCCAA
1 CCAATTACCCAA
14047910 CC
1 CC
14047912 CAATAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (12 bp):
CCAATTACCCAA
Found at i:14047952 original size:38 final size:39
Alignment explanation
Indices: 14047898--14047973 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 39
14047888 AATTACCCAA
*
14047898 CCAATTACCCAACCCAATAAAACTAAAACTAAAGTCTAC
1 CCAATTACCCAACCCAATAAAAATAAAACTAAAGTCTAC
14047937 CCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCTA
1 CCAATTACCCAACCCAATAAAAATAAAACTAAAGTCTA
14047974 ACTCTTAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (39 bp):
CCAATTACCCAACCCAATAAAAATAAAACTAAAGTCTAC
Found at i:14048134 original size:37 final size:37
Alignment explanation
Indices: 14048107--14048181 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
14048097 TGTTAATTTT
* *
14048107 AAGAATTATATAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATATAATATTTTTAATTATGTAGTAATTCA
* * *
14048144 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATATAATATTTTTAATTATGTAGTAATTCA
14048181 A
1 A
14048182 TTCGGGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.45
Consensus pattern (37 bp):
AAGAATTATATAATATTTTTAATTATGTAGTAATTCA
Found at i:14048216 original size:9 final size:9
Alignment explanation
Indices: 14048204--14048229 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
14048194 GGGTAATTCA
14048204 GTTAATTTG
1 GTTAATTTG
14048213 GTTAATTTG
1 GTTAATTTG
14048222 GTTAATTT
1 GTTAATTT
14048230 TTAACCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (9 bp):
GTTAATTTG
Found at i:14048487 original size:20 final size:20
Alignment explanation
Indices: 14048462--14048500 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14048452 TTAGGAATAG
14048462 TGGGGTCAAGTCATGAACAA
1 TGGGGTCAAGTCATGAACAA
* *
14048482 TGGGGTCATGTCGTGAACA
1 TGGGGTCAAGTCATGAACA
14048501 GTAATAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.23
Consensus pattern (20 bp):
TGGGGTCAAGTCATGAACAA
Found at i:14048724 original size:9 final size:9
Alignment explanation
Indices: 14048710--14048735 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
14048700 TTTTTTGTAT
14048710 AATGTTTTA
1 AATGTTTTA
14048719 AATGTTTTA
1 AATGTTTTA
14048728 AATGTTTT
1 AATGTTTT
14048736 GTTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (9 bp):
AATGTTTTA
Found at i:14053080 original size:15 final size:15
Alignment explanation
Indices: 14053060--14053090 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14053050 GTTATGTAAG
14053060 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
14053075 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
14053090 T
1 T
14053091 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:14056864 original size:19 final size:19
Alignment explanation
Indices: 14056840--14056879 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
14056830 ACGAAAGTTC
*
14056840 ATGCAAGAAAGCACATAAA
1 ATGCAAGAAAACACATAAA
14056859 ATGCAAGAAAACACATAAA
1 ATGCAAGAAAACACATAAA
14056878 AT
1 AT
14056880 AAAGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.15, G:0.12, T:0.12
Consensus pattern (19 bp):
ATGCAAGAAAACACATAAA
Found at i:14056888 original size:19 final size:19
Alignment explanation
Indices: 14056844--14056887 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
14056834 AAGTTCATGC
* *
14056844 AAGAAAGCACATAAAATGC
1 AAGAAAACACATAAAATGA
14056863 AAGAAAACACATAAAAT-A
1 AAGAAAACACATAAAATGA
14056881 AAGAAAA
1 AAGAAAA
14056888 ATAGTATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.09
Consensus pattern (19 bp):
AAGAAAACACATAAAATGA
Found at i:14068306 original size:30 final size:30
Alignment explanation
Indices: 14068271--14068329 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
14068261 TATTTTATTG
*
14068271 TTAATTTTGTTATTATTTTAAAGGCATTTA
1 TTAATTTTGTTATTATTTTAAAGACATTTA
*
14068301 TTAATTTTGTTATTATTTTAGAGACATTT
1 TTAATTTTGTTATTATTTTAAAGACATTT
14068330 GCTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTA
Found at i:14069185 original size:14 final size:15
Alignment explanation
Indices: 14069164--14069198 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
14069154 GTCTTCTAAG
14069164 ATAAATAAATGTTTT
1 ATAAATAAATGTTTT
*
14069179 A-AAATAACTGTTTT
1 ATAAATAAATGTTTT
14069193 ATAAAT
1 ATAAAT
14069199 TCTGATAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (15 bp):
ATAAATAAATGTTTT
Found at i:14081178 original size:20 final size:20
Alignment explanation
Indices: 14081140--14081181 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14081130 ACTTCGACAT
*
14081140 CTCTGTTTGCATTTTGGTGC
1 CTCTGTTTGCATTTCGGTGC
14081160 CTCTGTTTGC-TCTTCGGTGC
1 CTCTGTTTGCAT-TTCGGTGC
14081180 CT
1 CT
14081182 TCAATTGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.02, C:0.26, G:0.24, T:0.48
Consensus pattern (20 bp):
CTCTGTTTGCATTTCGGTGC
Found at i:14084878 original size:6 final size:6
Alignment explanation
Indices: 14084867--14084918 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
14084857 AGGTTTCCAA
* * * *
14084867 AAATGG AAATGG AAATGG AAATGG AAATGA AAATGA AAATGA AAATGT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
14084915 AAAT
1 AAAT
14084919 AACTCATTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (6 bp):
AAATGG
Found at i:14085134 original size:26 final size:26
Alignment explanation
Indices: 14085067--14085139 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
14085057 TATTTTCTCG
*
14085067 AAATTTTACTAGGGGAAAAATCATCA
1 AAATTTTACTAGGGGTAAAATCATCA
* * * *
14085093 AAATTTTACCAAGGGTAAAATCGTTA
1 AAATTTTACTAGGGGTAAAATCATCA
* *
14085119 GAATTTTACTGGGGGTAAAAT
1 AAATTTTACTAGGGGTAAAAT
14085140 AGGGATAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (26 bp):
AAATTTTACTAGGGGTAAAATCATCA
Found at i:14091838 original size:43 final size:43
Alignment explanation
Indices: 14091790--14091904 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
14091780 ATGTATTTTT
* * *
14091790 GTGTAAGACCACGCCTGGGACGTTGGCATCGATTTGTGTTTAC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTAC
* * *
14091833 GTGTAAGACCATGTCTTGGACATTGGCATCGATATGTGATTAC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTAC
* *
14091876 ATGTGAGACCACGTCTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
14091905 TGTACGAGCC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTAC
Found at i:14101435 original size:16 final size:17
Alignment explanation
Indices: 14101404--14101437 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
14101394 ATAAAACTAC
14101404 TTAATAATGATATTAAAA
1 TTAATAAT-ATATTAAAA
14101422 TTAATAAT-TATTAAAA
1 TTAATAATATATTAAAA
14101438 CTAAGGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TTAATAATATATTAAAA
Found at i:14102898 original size:28 final size:28
Alignment explanation
Indices: 14102839--14102898 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
14102829 GTCTTGACGG
* * *
14102839 ACTTACCTCGTATTTACTGTCCCGACGG
1 ACTTACCTCGTATTTACTATCCCAACGA
* * *
14102867 ACTTACCTCGTGTTTACTATCTCAATGA
1 ACTTACCTCGTATTTACTATCCCAACGA
14102895 ACTT
1 ACTT
14102899 TATCTCTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (28 bp):
ACTTACCTCGTATTTACTATCCCAACGA
Found at i:14103244 original size:51 final size:51
Alignment explanation
Indices: 14103147--14103319 Score: 157
Period size: 51 Copynumber: 3.4 Consensus size: 51
14103137 TGGTCCATGT
* * * ** * *
14103147 TGCCATAGCATCTTTCATCCATTGTCTTACGTTATGTACCTCATACCAGAC
1 TGCCATAACATCTTTCATCTATGGTCTTACGCAATATACCTTATACCAGAC
* * * *
14103198 TGCCATAACCTCTTTCATCTATGGTCTTACGCCATATATCTTATACCAGAT
1 TGCCATAACATCTTTCATCTATGGTCTTACGCAATATACCTTATACCAGAC
* * * * * * * *
14103249 TGTCATAGCCTATTTAATATATGGTCTTACACAATATACCTTATACTAGAC
1 TGCCATAACATCTTTCATCTATGGTCTTACGCAATATACCTTATACCAGAC
* *
14103300 TACCATAACATGTTTCATCT
1 TGCCATAACATCTTTCATCT
14103320 CTACTCTTAT
Statistics
Matches: 95, Mismatches: 27, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 95 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (51 bp):
TGCCATAACATCTTTCATCTATGGTCTTACGCAATATACCTTATACCAGAC
Found at i:14107109 original size:16 final size:18
Alignment explanation
Indices: 14107074--14107115 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
14107064 AAAAGTAAAC
14107074 AAAATCAAAATAAGAACCG
1 AAAA-CAAAATAAGAACCG
14107093 AAAACAAAAT-A-AACCG
1 AAAACAAAATAAGAACCG
14107109 AAAACAA
1 AAAACAA
14107116 GAAATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.52
17 1 0.04
18 6 0.26
19 4 0.17
ACGTcount: A:0.69, C:0.17, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAACAAAATAAGAACCG
Found at i:14110914 original size:33 final size:33
Alignment explanation
Indices: 14110877--14111009 Score: 91
Period size: 33 Copynumber: 4.2 Consensus size: 33
14110867 CATGATAGAT
14110877 AGATAACCACAAGGGCGTCCAAGCACATACACA
1 AGATAACCACAAGGGCGTCCAAGCACATACACA
* * * *
14110910 AGATAGCCA-TAGAGGCGTCCATGCAGATA-A-A
1 AGATAACCACAAG-GGCGTCCAAGCACATACACA
* * * *
14110941 TAGATAGCCACAAAGGCATCC-A-CATA-ACATC-
1 -AGATAACCACAAGGGCGTCCAAGCACATACA-CA
* * *
14110972 ATATAACCACAAGGGTGTCCAATCACATACACA
1 AGATAACCACAAGGGCGTCCAAGCACATACACA
14111005 AGATA
1 AGATA
14111010 GTTATAGAGG
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
29 1 0.01
30 19 0.26
31 2 0.03
32 22 0.30
33 30 0.41
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.15
Consensus pattern (33 bp):
AGATAACCACAAGGGCGTCCAAGCACATACACA
Found at i:14112046 original size:21 final size:21
Alignment explanation
Indices: 14112007--14112046 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
14111997 ATGCAACCTT
*
14112007 TATTTAACTTAATCAAAGTAC
1 TATTTAACTTAACCAAAGTAC
* *
14112028 TATTTAACTTCACCCAAGT
1 TATTTAACTTAACCAAAGT
14112047 CTTCTTTGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (21 bp):
TATTTAACTTAACCAAAGTAC
Found at i:14114893 original size:2 final size:2
Alignment explanation
Indices: 14114886--14114916 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14114876 TACCAAATGC
14114886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14114917 GGAATACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14115846 original size:54 final size:54
Alignment explanation
Indices: 14115770--14115885 Score: 146
Period size: 54 Copynumber: 2.1 Consensus size: 54
14115760 ACATGACCTG
* * * *
14115770 GGACATGGCCGTGTGATCCAAGTCAGTGAGTTGCACGGGC-AGAGACACGGGCTA
1 GGACACGGCCATGTGATCCAAGTCAGTGAGTTACACGAGCAAG-GACACGGGCTA
* *
14115824 GGACACGGCCATGTG-TCTCAAGTTAGTGAGTTACACGAGCAAGGACACGGGCTG
1 GGACACGGCCATGTGATC-CAAGTCAGTGAGTTACACGAGCAAGGACACGGGCTA
14115878 GGACACGG
1 GGACACGG
14115886 GCTGGGATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
53 2 0.04
54 50 0.93
55 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.36, T:0.16
Consensus pattern (54 bp):
GGACACGGCCATGTGATCCAAGTCAGTGAGTTACACGAGCAAGGACACGGGCTA
Found at i:14115881 original size:12 final size:12
Alignment explanation
Indices: 14115866--14115892 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
14115856 ACACGAGCAA
14115866 GGACACGGGCTG
1 GGACACGGGCTG
14115878 GGACACGGGCTG
1 GGACACGGGCTG
14115890 GGA
1 GGA
14115893 TATGGCTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.52, T:0.07
Consensus pattern (12 bp):
GGACACGGGCTG
Found at i:14118405 original size:6 final size:6
Alignment explanation
Indices: 14118394--14118419 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
14118384 CTATTTTAGT
14118394 GGCATA GGCATA GGCATA GGCATA GG
1 GGCATA GGCATA GGCATA GGCATA GG
14118420 GAGAGCAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (6 bp):
GGCATA
Found at i:14123180 original size:16 final size:16
Alignment explanation
Indices: 14123137--14123184 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
14123127 CACGGTTATG
14123137 CCACACG-TCCGTGTGC
1 CCACACGCT-CGTGTGC
* *
14123153 CCATACGTTCGTGTGC
1 CCACACGCTCGTGTGC
*
14123169 CCACATGCTCGTGTGC
1 CCACACGCTCGTGTGC
14123185 TAGGCCGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 26 0.96
17 1 0.04
ACGTcount: A:0.12, C:0.38, G:0.25, T:0.25
Consensus pattern (16 bp):
CCACACGCTCGTGTGC
Found at i:14128509 original size:25 final size:25
Alignment explanation
Indices: 14128446--14128588 Score: 101
Period size: 25 Copynumber: 5.8 Consensus size: 25
14128436 TCCTGTACAT
14128446 GTATGCTCA-ACGAGCTGT-GAATTG
1 GTATGCTCACACGAGCTGTAG-ATTG
* * *
14128470 GTATGCGCACTCGAGTTGTAGATTG
1 GTATGCTCACACGAGCTGTAGATTG
* * *
14128495 GTATGCTCTCACGAGCTGTAAATTA
1 GTATGCTCACACGAGCTGTAGATTG
* ** * *
14128520 GTATGCTCACATGAATTATAGATCG
1 GTATGCTCACACGAGCTGTAGATTG
** * **
14128545 GTATGCTCTGACGAGCTGTAAATCA
1 GTATGCTCACACGAGCTGTAGATTG
* *
14128570 GTATGCTTACACGATCTGT
1 GTATGCTCACACGAGCTGT
14128589 GGGTCGGAAC
Statistics
Matches: 88, Mismatches: 29, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
24 8 0.09
25 79 0.90
26 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAGATTG
Found at i:14128524 original size:50 final size:50
Alignment explanation
Indices: 14128446--14128575 Score: 156
Period size: 50 Copynumber: 2.6 Consensus size: 50
14128436 TCCTGTACAT
* * * * *
14128446 GTATGCTC-AACGAGCTGTGAATTGGTATGCGCAC-TCGAGTTGTAGATTG
1 GTATGCTCTAACGAGCTGTAAATTAGTATGCGCACAT-GAATTATAGATCG
* *
14128495 GTATGCTCTCACGAGCTGTAAATTAGTATGCTCACATGAATTATAGATCG
1 GTATGCTCTAACGAGCTGTAAATTAGTATGCGCACATGAATTATAGATCG
* *
14128545 GTATGCTCTGACGAGCTGTAAATCAGTATGC
1 GTATGCTCTAACGAGCTGTAAATTAGTATGC
14128576 TTACACGATC
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
49 8 0.11
50 61 0.87
51 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (50 bp):
GTATGCTCTAACGAGCTGTAAATTAGTATGCGCACATGAATTATAGATCG
Found at i:14132716 original size:20 final size:20
Alignment explanation
Indices: 14132691--14132756 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
14132681 GGTCACACGT
*
14132691 CCCCTGTTTATACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* * * *
14132711 CCCCTGATTGCACATAC-GTG
1 CCCCTGTTTGTAC-TTCGGTA
14132731 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
14132751 CCCCTG
1 CCCCTG
14132757 AATGCATTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.14, C:0.35, G:0.18, T:0.33
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:14132746 original size:40 final size:39
Alignment explanation
Indices: 14132687--14132762 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 39
14132677 CAGAGGTCAC
*
14132687 ACGTCCCCTGTTTATACTTCGGTACCCCTGATTGCACAT
1 ACGTCCCCTGTTTATACTTCGGTACCCCTGAATGCACAT
*
14132726 ACGTGCCCCTGTTTGTACTTCGGTACCCCTGAATGCA
1 ACGT-CCCCTGTTTATACTTCGGTACCCCTGAATGCA
14132763 TTTATGTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.17, C:0.33, G:0.18, T:0.32
Consensus pattern (39 bp):
ACGTCCCCTGTTTATACTTCGGTACCCCTGAATGCACAT
Found at i:14134018 original size:26 final size:29
Alignment explanation
Indices: 14133989--14134042 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 29
14133979 TTAGGGACAG
*
14133989 TATGTGTAT-GTAT-GATTGAT-TTATGA
1 TATGTGTATAGTATAGAATGATATTATGA
*
14134015 TATGTTTATAGTATAGAATGATATTATG
1 TATGTGTATAGTATAGAATGATATTATG
14134043 TTTAGATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 4 0.17
28 6 0.26
29 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (29 bp):
TATGTGTATAGTATAGAATGATATTATGA
Found at i:14139937 original size:52 final size:52
Alignment explanation
Indices: 14139857--14139962 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
14139847 TTACATAACT
14139857 TAGTAAGATCATAGTATTACATTAAATTTAACACAATTAGATACAATCCATG
1 TAGTAAGATCATAGTATTACATTAAATTTAACACAATTAGATACAATCCATG
*
14139909 TAGTAAGATCATAGTATTACATTCAATTTAACACAATTAGATACAATCCATG
1 TAGTAAGATCATAGTATTACATTAAATTTAACACAATTAGATACAATCCATG
14139961 TA
1 TA
14139963 CTACTAGCCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (52 bp):
TAGTAAGATCATAGTATTACATTAAATTTAACACAATTAGATACAATCCATG
Found at i:14140032 original size:28 final size:28
Alignment explanation
Indices: 14139992--14140045 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
14139982 CTAGAGTATA
14139992 AACAACACACGTAAATGCGTTCAGGGGT
1 AACAACACACGTAAATGCGTTCAGGGGT
*
14140020 AACAACACACGTAAATGTGTTCAGGG
1 AACAACACACGTAAATGCGTTCAGGG
14140046 ATACCGAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (28 bp):
AACAACACACGTAAATGCGTTCAGGGGT
Found at i:14143597 original size:2 final size:2
Alignment explanation
Indices: 14143590--14143649 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
14143580 CGTAAAACGC
14143590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14143632 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
14143650 CTAATTCAAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14152368 original size:23 final size:23
Alignment explanation
Indices: 14152326--14152370 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
14152316 ATTGGGATTC
*
14152326 AAAAAAACTCAAGTATCAAATTT
1 AAAAAAACTCAAGTACCAAATTT
* *
14152349 AAAAAAACTTAGGTACCAAATT
1 AAAAAAACTCAAGTACCAAATT
14152371 GGGTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.24
Consensus pattern (23 bp):
AAAAAAACTCAAGTACCAAATTT
Found at i:14164399 original size:2 final size:2
Alignment explanation
Indices: 14164392--14164429 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
14164382 ATTTAATTAT
*
14164392 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
14164430 AGCATAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:14164872 original size:18 final size:18
Alignment explanation
Indices: 14164817--14164876 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
14164807 TGGTGAATTA
*
14164817 TATTATTATGGCGAACTG
1 TATTAATATGGCGAACTG
* * * *
14164835 TGTTAATCTGG-TATCTG
1 TATTAATATGGCGAACTG
14164852 TATTAATATGGCGAACTG
1 TATTAATATGGCGAACTG
14164870 TATTAAT
1 TATTAAT
14164877 TTGCCAAACC
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (18 bp):
TATTAATATGGCGAACTG
Found at i:14167569 original size:43 final size:43
Alignment explanation
Indices: 14167506--14167588 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
14167496 TTACTTTACC
14167506 ACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTATTTTTT
1 ACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTATTTTTT
*
14167549 ACTTAAACTCTGATTCGTGTAGGTTATTTTAATATTATTT
1 ACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTATTT
14167589 GATCTACAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (43 bp):
ACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTATTTTTT
Found at i:14169523 original size:44 final size:44
Alignment explanation
Indices: 14169457--14169547 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
14169447 AACTCTGTTT
*
14169457 TTAGTTTACCACTTAAATTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTACCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
*
14169501 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTACCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
14169545 TTA
1 TTA
14169548 TTTGACCTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (44 bp):
TTAGTTTACCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
Found at i:14170989 original size:2 final size:2
Alignment explanation
Indices: 14170978--14171019 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
14170968 TGTCCTTTGT
14170978 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14171019 T
1 T
14171020 TAAATTTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14171257 original size:21 final size:20
Alignment explanation
Indices: 14171223--14171262 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
14171213 TTTTTTCAAT
*
14171223 TTTTAAAATTAAAAAAAAAC
1 TTTTAAAATAAAAAAAAAAC
14171243 TTTTAAAAGTAAAAAAAAAA
1 TTTTAAAA-TAAAAAAAAAA
14171263 AAGGTAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
TTTTAAAATAAAAAAAAAAC
Found at i:14171258 original size:19 final size:20
Alignment explanation
Indices: 14171223--14171261 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
14171213 TTTTTTCAAT
*
14171223 TTTTAAAATTAAAAAAAAAC
1 TTTTAAAAGTAAAAAAAAAC
14171243 TTTTAAAAGTAAAAAAAAA
1 TTTTAAAAGTAAAAAAAAA
14171262 AAAGGTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
TTTTAAAAGTAAAAAAAAAC
Found at i:14172575 original size:46 final size:47
Alignment explanation
Indices: 14172475--14172585 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 47
14172465 GTGGTTTAAC
* *
14172475 CACATATTTGTTCTAGCAACTTGACTGCAAATATAGTGGCTTGACCA
1 CACATATCTGTTCTGGCAACTTGACTGCAAATATAGTGGCTTGACCA
* *
14172522 CACATATCTGTTCTGGCAGCTTGACTGC-AATATAGTGGCTTGACTA
1 CACATATCTGTTCTGGCAACTTGACTGCAAATATAGTGGCTTGACCA
* *
14172568 CATATATCTGATCTGGCA
1 CACATATCTGTTCTGGCA
14172586 TTTTAACTGC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 33 0.57
47 25 0.43
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (47 bp):
CACATATCTGTTCTGGCAACTTGACTGCAAATATAGTGGCTTGACCA
Found at i:14179749 original size:5 final size:5
Alignment explanation
Indices: 14179729--14179762 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
14179719 ATTTGATGTA
* *
14179729 TTTAT TTAAA TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
14179763 ATGTATGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:14180897 original size:14 final size:15
Alignment explanation
Indices: 14180874--14180902 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14180864 TATTTAGATG
14180874 TTTTGATTATTAAAT
1 TTTTGATTATTAAAT
14180889 TTTTG-TTATTAAAT
1 TTTTGATTATTAAAT
14180903 ATTCTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTTGATTATTAAAT
Found at i:14184515 original size:395 final size:395
Alignment explanation
Indices: 14183785--14184972 Score: 2241
Period size: 395 Copynumber: 3.0 Consensus size: 395
14183775 TTGCTTATAA
* *
14183785 TATTGCTATTGAAATAATAAAATAAAATGAGGATCCTGAGTCTAAATCTATTGAGGAATGTAAAA
1 TATTGCTATAGAAATAATAAAAGAAAATGAGGATCCTGAGTCTAAATCTATTGAGGAATGTAAAA
*
14183850 ATAGAAAAGATTGGCAAAAATGGAAAGATGCAATTCAAGCATAATTGAATTCACTTTCTAAACGT
66 ATAGAAAAGATTGGCAAAAATGGAAAGATGCAATTCAAGCAGAATTGAATTCACTTTCTAAACGT
*
14183915 GAAGTTTTTGGACCTGTAGTCCAAACACCTAAAGGTGTAAAGCCAATAGGATATAAATGAGTATT
131 GAAGTTTTTGGACCTGTAGTCCAAACACCTAAAGGTGTAAAGCCAGTAGGATATAAATGAGTATT
*
14183980 TGTATGAAAATGAAATGAAATTGATGAAGTCGTAAGATATAAAGCTTGATTTGTAGCACAAGGAT
196 TGTATGAAAATGAAATGAAATTGATGAAGTCGTAAGATATAAAGCTCGATTTGTAGCACAAGGAT
14184045 TTTCACAAAGGCCTGGCATTGATTATGAATAGACATATTTTCCTGTGGTGGATGCAATCACGTTT
261 TTTCACAAAGGCCTGGCATTGATTATGAATAGACATATTTTCCTGTGGTGGATGCAATCACGTTT
*
14184110 AGATATCTTATTAGTATGGCAGTACGTAAAAAGCTTGGCATGCATCTAATGGATGTTGTTACATC
326 AGATATCTTATTAGTATGGCAGTAAGTAAAAAGCTTGGCATGCATCTAATGGATGTTGTTACATC
14184175 CTATT
391 CTATT
*
14184180 TATTGCTATAGAAATAATAAAAGAAAATGAGGATCCTGGGTCTAAATCTATTGAGGAATGTAAAA
1 TATTGCTATAGAAATAATAAAAGAAAATGAGGATCCTGAGTCTAAATCTATTGAGGAATGTAAAA
14184245 ATAGAAAAGATTGGCAAAAATGGAAAGATGCAATTCAAGCAGAATTGAATTCACTTTCTAAACGT
66 ATAGAAAAGATTGGCAAAAATGGAAAGATGCAATTCAAGCAGAATTGAATTCACTTTCTAAACGT
*
14184310 GAAGTTTTTGGACTTGTAGTCCAAACACCTAAAGGTGTAAAGCCAGTAGGATATAAATGAGTATT
131 GAAGTTTTTGGACCTGTAGTCCAAACACCTAAAGGTGTAAAGCCAGTAGGATATAAATGAGTATT
14184375 TGTATGAAAATGAAATGAAATTGATGAAGTCGTAAGATATAAAGCTCGATTTGTAGCACAAGGAT
196 TGTATGAAAATGAAATGAAATTGATGAAGTCGTAAGATATAAAGCTCGATTTGTAGCACAAGGAT
14184440 TTTCACAAAGGCCTGGCATTGATTATGAATAGACATATTTTCCTGTGGTGGATGCAATCACGTTT
261 TTTCACAAAGGCCTGGCATTGATTATGAATAGACATATTTTCCTGTGGTGGATGCAATCACGTTT
*
14184505 AGATATCTTATTAGTATGGCAGTATGTAAAAAGCTTGGCATGCATCTAATGGATGTTGTTACATC
326 AGATATCTTATTAGTATGGCAGTAAGTAAAAAGCTTGGCATGCATCTAATGGATGTTGTTACATC
14184570 CTATT
391 CTATT
14184575 TATTGCTATAGAAATAATAAAAGAAAATGAGGATCCTGAGTCTAAATCTATTGAGGAATGTAAAA
1 TATTGCTATAGAAATAATAAAAGAAAATGAGGATCCTGAGTCTAAATCTATTGAGGAATGTAAAA
* * *
14184640 ATAGAAAAGATTGGCAAAAATGGAAAGATGGAGTTCAAGCAGAATTGAATTCACTTTCTAAACCT
66 ATAGAAAAGATTGGCAAAAATGGAAAGATGCAATTCAAGCAGAATTGAATTCACTTTCTAAACGT
14184705 GAAGTTTTTGGACCTGTAGTCCAAACACCTAAAGGTGTAAAGCCAGTAGGATATAAATGAGTATT
131 GAAGTTTTTGGACCTGTAGTCCAAACACCTAAAGGTGTAAAGCCAGTAGGATATAAATGAGTATT
14184770 TGTATGAAAATGAAATGAAATTGATGAAGTCGTAAGATATAAAGCTCGATTTGTAGCACAAGGAT
196 TGTATGAAAATGAAATGAAATTGATGAAGTCGTAAGATATAAAGCTCGATTTGTAGCACAAGGAT
*
14184835 TTTCACAAAGGCCTGGCATTGATTATGAATAGACATATTTTCATGTGGTGGATGCAATCACGTTT
261 TTTCACAAAGGCCTGGCATTGATTATGAATAGACATATTTTCCTGTGGTGGATGCAATCACGTTT
* *
14184900 AGATATCTTATTAGTATGGCAATAAGTAAAAAGCTTGACATGCATCTAATGGATGTTGTTACATC
326 AGATATCTTATTAGTATGGCAGTAAGTAAAAAGCTTGGCATGCATCTAATGGATGTTGTTACATC
14184965 CTATT
391 CTATT
14184970 TAT
1 TAT
14184973 ATGGTACACT
Statistics
Matches: 776, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
395 776 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (395 bp):
TATTGCTATAGAAATAATAAAAGAAAATGAGGATCCTGAGTCTAAATCTATTGAGGAATGTAAAA
ATAGAAAAGATTGGCAAAAATGGAAAGATGCAATTCAAGCAGAATTGAATTCACTTTCTAAACGT
GAAGTTTTTGGACCTGTAGTCCAAACACCTAAAGGTGTAAAGCCAGTAGGATATAAATGAGTATT
TGTATGAAAATGAAATGAAATTGATGAAGTCGTAAGATATAAAGCTCGATTTGTAGCACAAGGAT
TTTCACAAAGGCCTGGCATTGATTATGAATAGACATATTTTCCTGTGGTGGATGCAATCACGTTT
AGATATCTTATTAGTATGGCAGTAAGTAAAAAGCTTGGCATGCATCTAATGGATGTTGTTACATC
CTATT
Found at i:14185758 original size:52 final size:52
Alignment explanation
Indices: 14185680--14185789 Score: 220
Period size: 52 Copynumber: 2.1 Consensus size: 52
14185670 ATCTCAGAGG
14185680 GACTATTGATATGGGGTTATTTTATTGAAATGATTCAAAATCCCTATTAGTT
1 GACTATTGATATGGGGTTATTTTATTGAAATGATTCAAAATCCCTATTAGTT
14185732 GACTATTGATATGGGGTTATTTTATTGAAATGATTCAAAATCCCTATTAGTT
1 GACTATTGATATGGGGTTATTTTATTGAAATGATTCAAAATCCCTATTAGTT
14185784 GACTAT
1 GACTAT
14185790 GTTGATGTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (52 bp):
GACTATTGATATGGGGTTATTTTATTGAAATGATTCAAAATCCCTATTAGTT
Found at i:14200139 original size:19 final size:19
Alignment explanation
Indices: 14200115--14200155 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
14200105 GTCTTATAAG
14200115 AATACTTTAAGTATTCTAA
1 AATACTTTAAGTATTCTAA
14200134 AATACTTTAAGTATTCTAA
1 AATACTTTAAGTATTCTAA
14200153 AAT
1 AAT
14200156 GGGAGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (19 bp):
AATACTTTAAGTATTCTAA
Found at i:14200582 original size:40 final size:40
Alignment explanation
Indices: 14200538--14200624 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
14200528 GGCATGTCCA
* * * *
14200538 CATTACTAGTAGCTTCTTTGCATTACTAGCAATTTATCTG
1 CATTACTAGCAGCTTATCTGCACTACTAGCAATTTATCTG
* *
14200578 CATTACTAGCAGCTTATCTGCACTACTGGCAGTTTATCTG
1 CATTACTAGCAGCTTATCTGCACTACTAGCAATTTATCTG
14200618 CATTACT
1 CATTACT
14200625 GGTGACTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (40 bp):
CATTACTAGCAGCTTATCTGCACTACTAGCAATTTATCTG
Found at i:14200626 original size:20 final size:20
Alignment explanation
Indices: 14200556--14200624 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
14200546 GTAGCTTCTT
*
14200556 TGCATTACTAGCAATTTATC
1 TGCATTACTAGCAGTTTATC
*
14200576 TGCATTACTAGCAGCTTATC
1 TGCATTACTAGCAGTTTATC
* *
14200596 TGCACTACTGGCAGTTTATC
1 TGCATTACTAGCAGTTTATC
14200616 TGCATTACT
1 TGCATTACT
14200625 GGTGACTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (20 bp):
TGCATTACTAGCAGTTTATC
Found at i:14200641 original size:20 final size:20
Alignment explanation
Indices: 14200618--14200679 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
14200608 AGTTTATCTG
*
14200618 CATTACTGGTGACTTGACCA
1 CATTACTGGTGACTTGTCCA
* **
14200638 CATTACTAGT-AGCTTGTCTG
1 CATTACTGGTGA-CTTGTCCA
14200658 CATTACTGGTGACTTGTCCA
1 CATTACTGGTGACTTGTCCA
14200678 CA
1 CA
14200680 AATAGGAGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (20 bp):
CATTACTGGTGACTTGTCCA
Found at i:14205024 original size:44 final size:46
Alignment explanation
Indices: 14204963--14205069 Score: 134
Period size: 45 Copynumber: 2.4 Consensus size: 46
14204953 TCTCATTTTC
*
14204963 ATTTCCA-TT-TCCATTTT-GAGAAAACCATATTCATTT-TCAAATG
1 ATTTCCATTTCTCCATTTTGGAGAAAACCATAATCATTTCT-AAATG
* *
14205006 ATTT-CATTTCTCCATTTTGGAGAAAGCCATAATCATTTCTGAATG
1 ATTTCCATTTCTCCATTTTGGAGAAAACCATAATCATTTCTAAATG
*
14205051 GTTTCCATTTCTCCATTTT
1 ATTTCCATTTCTCCATTTT
14205070 TATTCATTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
42 2 0.04
43 6 0.11
44 8 0.15
45 24 0.44
46 15 0.27
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (46 bp):
ATTTCCATTTCTCCATTTTGGAGAAAACCATAATCATTTCTAAATG
Found at i:14209268 original size:9 final size:9
Alignment explanation
Indices: 14209254--14209283 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
14209244 GTAGTGATTC
*
14209254 AATTCGGTT
1 AATTCGGGT
14209263 AATTCGGGT
1 AATTCGGGT
14209272 AATTCGGGT
1 AATTCGGGT
14209281 AAT
1 AAT
14209284 ATATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (9 bp):
AATTCGGGT
Found at i:14211450 original size:29 final size:30
Alignment explanation
Indices: 14211417--14211478 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
14211407 TTCAAACAAA
*
14211417 TATGCATTGTTATATATGA-ACTTTGATTT
1 TATGCATTGTTATATATGAGACTTTCATTT
* * *
14211446 TATGCGTTTTTATATATGAGATTTTCATTT
1 TATGCATTGTTATATATGAGACTTTCATTT
14211476 TAT
1 TAT
14211479 TCAATTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (30 bp):
TATGCATTGTTATATATGAGACTTTCATTT
Found at i:14222832 original size:8 final size:9
Alignment explanation
Indices: 14222814--14222846 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
14222804 ATTAAAGAAA
14222814 AAATAAAAT
1 AAATAAAAT
14222823 AAAT-AAAT
1 AAATAAAAT
14222831 -AATAAAAT
1 AAATAAAAT
14222839 AAATAAAA
1 AAATAAAA
14222847 ACAATGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.14
8 8 0.36
9 11 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:14222834 original size:16 final size:16
Alignment explanation
Indices: 14222815--14222845 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
14222805 TTAAAGAAAA
14222815 AATAAAATAAATAAAT
1 AATAAAATAAATAAAT
14222831 AATAAAATAAATAAA
1 AATAAAATAAATAAA
14222846 AACAATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAAAATAAATAAAT
Found at i:14222856 original size:21 final size:20
Alignment explanation
Indices: 14222813--14222862 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
14222803 AATTAAAGAA
*
14222813 AAAATAAAATAAATAAATAAT
1 AAAAT-AAATAAAAAAATAAT
*
14222834 AAAATAAATAAAAACAATGAT
1 AAAATAAATAAAAA-AATAAT
14222855 AACAATAA
1 AA-AATAA
14222863 TAGTTCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 12 0.48
22 5 0.20
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATAAATAAAAAAATAAT
Found at i:14223142 original size:18 final size:18
Alignment explanation
Indices: 14223111--14223145 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14223101 TGAAAAAAAA
**
14223111 AAATAAATGTATAAATAT
1 AAATAAATAAATAAATAT
14223129 AAATAAATAAATAAATA
1 AAATAAATAAATAAATA
14223146 CAAAGAAAAA
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:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATAAATAAATAAATAT
Found at i:14228410 original size:43 final size:43
Alignment explanation
Indices: 14228344--14228514 Score: 172
Period size: 43 Copynumber: 4.0 Consensus size: 43
14228334 GACTCGTACA
* * *
14228344 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
* *
14228387 ATGCC-ACTGTCCCAGACAG-GGTCTTACAC-AAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAACACATATCG
* ** ** * *
14228428 ATGCCAATGTCTTAGATATGGTCTTACACGTAAACACA-AGTTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATA-TCG
14228471 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
14228514 A
1 A
14228515 AATCCTATGT
Statistics
Matches: 101, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
41 24 0.24
42 16 0.16
43 59 0.58
44 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
Found at i:14231124 original size:34 final size:34
Alignment explanation
Indices: 14231086--14231152 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
14231076 TCAAAATAGA
*
14231086 TCAATACGATAAC-AATCAATATGCTTATAACAAT
1 TCAATACAATAACAAAT-AATATGCTTATAACAAT
* *
14231120 TCAATATAATAGCAAATAATATGCTTATAACAA
1 TCAATACAATAACAAATAATATGCTTATAACAA
14231153 ATTGATTCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (34 bp):
TCAATACAATAACAAATAATATGCTTATAACAAT
Found at i:14237442 original size:21 final size:21
Alignment explanation
Indices: 14237398--14237442 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
14237388 TTATTTGATT
* *
14237398 ATATTTATTAATTTAAATTGA
1 ATATTTATTAATTCAAAATGA
14237419 ATATTTATTAATATCAAAAT-A
1 ATATTTATTAAT-TCAAAATGA
14237440 ATA
1 ATA
14237443 ATAACATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
ATATTTATTAATTCAAAATGA
Found at i:14240739 original size:24 final size:24
Alignment explanation
Indices: 14240712--14240767 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
14240702 CATTTAATAA
* *
14240712 AATAAAAGTTGTTTTTA-ATATTTT
1 AATAAAAATTATTTTTATAT-TTTT
14240736 AATAATAAATTATTTTTATATTTTT
1 AATAA-AAATTATTTTTATATTTTT
14240761 AATAAAA
1 AATAAAA
14240768 TAGAAGTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.25
25 19 0.68
26 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
AATAAAAATTATTTTTATATTTTT
Found at i:14243594 original size:127 final size:126
Alignment explanation
Indices: 14243311--14243702 Score: 581
Period size: 126 Copynumber: 3.1 Consensus size: 126
14243301 AAACAAGAAA
* *
14243311 TACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCAT-AATTTTTGCTGACAGTGCATCCTG
1 TACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCATCAA-TTTTGCTGACAGTGCATCCTG
*
14243375 CTTGAAGGATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAAC
65 CTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAAC
* * * *
14243437 TACTGTAGAAAAAAAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGTTGACAGTGCATCTTAC
1 TACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTGC
14243502 TTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTTCAGGAAC
66 TTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTA-TTTTTTCAGGAAC
* *
14243564 TACTATAGAAAAAGAGCGTCCATATGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTGC
1 TACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTGC
* * * * * * * *
14243629 TTGAAGCGTTTTTGACATTATCTT-TTTAGAATCGTCTTCTCAAAATTAGTTTTCCTGAAAC
66 TTGAAGCATTTTTGACACTAT-TTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAAC
*
14243690 AACTGTAGAAAAA
1 TACTGTAGAAAAA
14243703 AATAAAATCC
Statistics
Matches: 240, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
126 123 0.51
127 115 0.48
128 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (126 bp):
TACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTGC
TTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAAC
Found at i:14243826 original size:33 final size:33
Alignment explanation
Indices: 14243781--14243886 Score: 110
Period size: 34 Copynumber: 3.2 Consensus size: 33
14243771 ACTGAACCCC
* **
14243781 AATTTAATTTAATTTCTTAAAAACTGT-AAACCTT
1 AATTTAA-TTAATTTTTTAAAAACCCTAAAACC-T
*
14243815 AATTTAATTAATTTATTTAAAACCCCTAAAACCT
1 AATTTAATTAATTT-TTTAAAAACCCTAAAACCT
*
14243849 AATTTAATTAATTTTTTAAAAAACACT-AAA-CT
1 AATTTAATTAATTTTTT-AAAAACCCTAAAACCT
14243881 AATTTA
1 AATTTA
14243887 TTTTTTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
32 8 0.13
33 13 0.21
34 37 0.59
35 5 0.08
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (33 bp):
AATTTAATTAATTTTTTAAAAACCCTAAAACCT
Found at i:14243948 original size:41 final size:40
Alignment explanation
Indices: 14243899--14243991 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 40
14243889 TTTTAAAATT
*
14243899 CCTAAACCCTAACCCTAAATGATTTTAACAAAACCCTACC
1 CCTAAACCCTAACCCTAAATGATTTTAACAAAACCCTAAC
* *
14243939 CCTACAACCCTAACCCTAATTTATTTTAACAAAACCCTAAC
1 CCTA-AACCCTAACCCTAAATGATTTTAACAAAACCCTAAC
*
14243980 TCTAAACCCTAA
1 CCTAAACCCTAA
14243992 AAACCCTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 12 0.25
41 36 0.75
ACGTcount: A:0.40, C:0.34, G:0.01, T:0.25
Consensus pattern (40 bp):
CCTAAACCCTAACCCTAAATGATTTTAACAAAACCCTAAC
Done.