Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 85 of 279
Found at i:28119500 original size:28 final size:28
Alignment explanation
Indices: 28119460--28119514 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
28119450 ATTCCAATGA
28119460 TTACGTATTGGAGAAGAACTAAATCTTT
1 TTACGTATTGGAGAAGAACTAAATCTTT
28119488 TTACGTATTGGAGAAGAACTAAATCTT
1 TTACGTATTGGAGAAGAACTAAATCTT
28119515 GCTAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (28 bp):
TTACGTATTGGAGAAGAACTAAATCTTT
Found at i:28120845 original size:26 final size:26
Alignment explanation
Indices: 28120809--28120918 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
28120799 TGATACAAAT
*
28120809 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28120835 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28120861 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
28120887 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28120913 TGATAA
1 TGATAA
28120919 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:28122578 original size:27 final size:27
Alignment explanation
Indices: 28122537--28122676 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 27
28122527 GAGGAAGCGT
*
28122537 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
28122564 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
28122591 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
28122618 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
28122646 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
28122672 TCTGG
1 TCTGG
28122677 CAGCCATGCT
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
26 5 0.05
27 82 0.80
28 15 0.15
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:28122622 original size:54 final size:55
Alignment explanation
Indices: 28122537--28122676 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 55
28122527 GAGGAAGCGT
* * *
28122537 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
28122591 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
28122646 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
28122677 CAGCCATGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 60 0.77
55 18 0.23
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:28138976 original size:30 final size:30
Alignment explanation
Indices: 28138937--28139003 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
28138927 CGTTCAAAAA
* *
28138937 CTTGAGAAGACCCGATATCT-AGTTCAGGAG
1 CTTGGGAAGACCCGATATCTCA-CTCAGGAG
* *
28138967 CTTGGGAAGACTCGATATCTCACTCAGGAT
1 CTTGGGAAGACCCGATATCTCACTCAGGAG
28138997 CTTGGGA
1 CTTGGGA
28139004 TTGAGAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (30 bp):
CTTGGGAAGACCCGATATCTCACTCAGGAG
Found at i:28139050 original size:30 final size:29
Alignment explanation
Indices: 28138950--28139069 Score: 87
Period size: 30 Copynumber: 3.8 Consensus size: 29
28138940 GAGAAGACCC
*
28138950 GATATCTAGTTCAGGAGCTTGGGAAGACTC
1 GATATCTA-TTCAGGAGCTTGGGAAGACTA
* * *
28138980 GATATCTCACTCAGGATCTTGGGATTGAGAAGATAA
1 GATATCT-ATTCAGGAGCTTGGGA---AG-A-CT-A
*
28139016 GATATCTCATTCAGGAGCTTGGGAAGACTT
1 GATATCT-ATTCAGGAGCTTGGGAAGACTA
* *
28139046 GATATCGTGTTCAAGAGCTTGGGA
1 GATATC-TATTCAGGAGCTTGGGA
28139070 TGGAGAAGAC
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
30 40 0.56
31 3 0.04
32 1 0.01
33 4 0.06
34 1 0.01
35 1 0.01
36 22 0.31
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (29 bp):
GATATCTATTCAGGAGCTTGGGAAGACTA
Found at i:28139067 original size:66 final size:66
Alignment explanation
Indices: 28138950--28139108 Score: 178
Period size: 66 Copynumber: 2.4 Consensus size: 66
28138940 GAGAAGACCC
* * *
28138950 GATATCTAGTTCAGGAGCTTGGGAAGACTCGATATCTCACTCAGGATCTTGGGATTGAGAAGATA
1 GATATCTAGTTCAGGAGCTTGGGAAGACTCGATATCTCACTCAAGAGCTTGGGATGGAGAAGATA
28139015 A
66 A
* **
28139016 GATATCTCA-TTCAGGAGCTTGGGAAGACTTGATATCGT-GTTCAAGAGCTTGGGATGGAGAAGA
1 GATATCT-AGTTCAGGAGCTTGGGAAGACTCGATATC-TCACTCAAGAGCTTGGGATGGAGAAGA
***
28139079 CCT
64 TAA
* * *
28139082 GATATCTTGTTTAGGAGTTTGGGAAGA
1 GATATCTAGTTCAGGAGCTTGGGAAGA
28139109 TCCGGTGTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
66 76 0.97
67 2 0.03
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.29
Consensus pattern (66 bp):
GATATCTAGTTCAGGAGCTTGGGAAGACTCGATATCTCACTCAAGAGCTTGGGATGGAGAAGATA
A
Found at i:28140155 original size:64 final size:64
Alignment explanation
Indices: 28140054--28140181 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
28140044 TCTTCAAATC
28140054 TTTCCCTATTCAACTGATAGGCAGCTCTGACCCTTCTTCACTAAAAATCTATTATCTTTCAGTA
1 TTTCCCTATTCAACTGATAGGCAGCTCTGACCCTTCTTCACTAAAAATCTATTATCTTTCAGTA
*
28140118 TTTCCCTATTCAACTGCTAGGCAGCTCTGACCCTTCTTCACTAAAAATCTATTATCTTTCAGTA
1 TTTCCCTATTCAACTGATAGGCAGCTCTGACCCTTCTTCACTAAAAATCTATTATCTTTCAGTA
28140182 CACATCTCGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.26, C:0.27, G:0.09, T:0.38
Consensus pattern (64 bp):
TTTCCCTATTCAACTGATAGGCAGCTCTGACCCTTCTTCACTAAAAATCTATTATCTTTCAGTA
Found at i:28144455 original size:131 final size:131
Alignment explanation
Indices: 28144210--28144457 Score: 329
Period size: 131 Copynumber: 1.9 Consensus size: 131
28144200 AAAACGAAGG
* * *
28144210 CAATACTCGGTGTTTGATAATTCGAGAATCATGCCTTATCGTGCTGGGTTGTGATTTCTCGTTTG
1 CAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAACGTACTGGGTTGTGATTTCTCGTTTG
* * ** * ** *
28144275 TTCAAAACAATCGAATATTCCTTTAGGTTTTTACTCGTGTTTATTAAAAACCTTCCAAAATGAAT
66 TTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTTTATAAAAAACCTTCCAAAATGAAT
28144340 A
131 A
* * * *
28144341 CAATACTCGGTGTTTGATAATTCGGGAATCGTGCCCTAACGTATTGGGTTGTGATTTCTCGTTTT
1 CAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAACGTACTGGGTTGTGATTTCTCGTTTG
28144406 TTCAAAACAATCGAAGATTCCTTCGA-AATTTCACTCACGTTT-TCAAAAAACC
66 TTCAAAACAATCGAAGATTCCTT-GAGAATTTCACTCACGTTTAT-AAAAAACC
28144458 CCTTAAAACG
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
130 1 0.01
131 98 0.98
132 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (131 bp):
CAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAACGTACTGGGTTGTGATTTCTCGTTTG
TTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTTTATAAAAAACCTTCCAAAATGAAT
A
Found at i:28145888 original size:19 final size:18
Alignment explanation
Indices: 28145866--28145925 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
28145856 ATCCCATGCA
28145866 TTTGCATTGCATTGCATC
1 TTTGCATTGCATTGCATC
28145884 -TT---TTGCATTGCATC
1 TTTGCATTGCATTGCATC
*
28145898 TTTTACATTGCATTGCATC
1 -TTTGCATTGCATTGCATC
28145917 ATTTGCATT
1 -TTTGCATT
28145926 AGATTTTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 12 0.34
16 2 0.06
17 2 0.06
19 19 0.54
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.48
Consensus pattern (18 bp):
TTTGCATTGCATTGCATC
Found at i:28145925 original size:14 final size:14
Alignment explanation
Indices: 28145872--28145910 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
28145862 TGCATTTGCA
28145872 TTGCATTGCATCTT
1 TTGCATTGCATCTT
28145886 TTGCATTGCATCTT
1 TTGCATTGCATCTT
*
28145900 TTACATTGCAT
1 TTGCATTGCAT
28145911 TGCATCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.49
Consensus pattern (14 bp):
TTGCATTGCATCTT
Found at i:28149612 original size:64 final size:64
Alignment explanation
Indices: 28149536--28149723 Score: 286
Period size: 64 Copynumber: 2.9 Consensus size: 64
28149526 TCATTCATAA
* * * *
28149536 CACATCTAGTTAGGAGCATTTGATTCATGTCGATTATAACATTCTAATTATTTGAGATAAACAT
1 CACATCTAGTTAGGAACATTTGATTCATGTCGATCATAGCATTCTAATTATTTGACATAAACAT
*
28149600 CACATCTAGTTAGGAACATTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACAT
1 CACATCTAGTTAGGAACATTTGATTCATGTCGATCATAGCATTCTAATTATTTGACATAAACAT
* ** * *
28149664 CACATCTAGTTAGGAACAATTGATTCATGTTAATCATAGCATCCTAATTATTTGGCATAA
1 CACATCTAGTTAGGAACATTTGATTCATGTCGATCATAGCATTCTAATTATTTGACATAA
28149724 GCATAGGCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 113 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGAACATTTGATTCATGTCGATCATAGCATTCTAATTATTTGACATAAACAT
Found at i:28149979 original size:131 final size:131
Alignment explanation
Indices: 28149745--28150271 Score: 806
Period size: 131 Copynumber: 4.0 Consensus size: 131
28149735 TGAAACAGAA
* * **
28149745 TGTAGATCTTATCTCCTTGAAGTTGCAGTGGGGCAAATTGAAGACGACGAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
*
28149810 AGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGATGAAGA
66 AGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGA
28149875 T
131 T
28149876 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
* * * *
28149941 AGTTGCAGTGAAGCAGATTTAAGCTAGTCCTAGCTCCCTAAAATTGTAGTGGAGTAGGCTGAATA
66 AGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGA
28150006 T
131 T
* * * * *
28150007 TGTAGATCTTGTCTCCCTGAAGCTACAGTGGGGCAAATCGAAA-ATGATGAATCTTGGCTTCCTA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATC-AAAGACGACGAATCTTGGCTTCCTG
* *
28150071 AAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGTTCCCTAAAGTTGTAGTGGAGTAGGCCGAAG
65 AAGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAG
28150136 AT
130 AT
* * *
28150138 TGTAGATCTTGTCTCCTTGAAGTTGCAGTGGGGCAAATCGAAGACGACAAATCTTGGCTTCCTGA
1 TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
* * *
28150203 AGTTGTAGTGAAGCAGATTTAAGCCACCA-TCCTAGCTCCCTAATGTTGTAGTGGAGTAGGCTGA
66 AGATGCAGTGAAGCAGATTTAAG-CA--AGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGA
28150267 AGAT
128 AGAT
28150271 T
1 T
28150272 ACAGACCTTG
Statistics
Matches: 358, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
130 2 0.01
131 313 0.87
132 5 0.01
133 37 0.10
134 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (131 bp):
TGTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCAAAGACGACGAATCTTGGCTTCCTGA
AGATGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGA
T
Found at i:28153450 original size:131 final size:131
Alignment explanation
Indices: 28153299--28153542 Score: 364
Period size: 131 Copynumber: 1.9 Consensus size: 131
28153289 GTTTCACAAC
* * *
28153299 TATTAAAAATTCTTTCAAACGAAGGCAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTATC
1 TATTAAAAATCCTTTCAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAAC
*
28153364 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCGTGT
66 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTTTAGGTTTTCACTCGTGT
28153429 T
131 T
* * * *
28153430 TATTAAAAA-CCTTTCAAAACGAATACAATACTTGGTGTTTGATAATTCGGGAATCGTGCCCTAA
1 TATTAAAAATCCTTTC-AAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAA
* ** *
28153494 CGTGTTGGGTTGTGATTTCTCATTTTTTCAAAACAATCGAAGATTCCTT
65 CGTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTT
28153543 CGAAATTTCA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
130 5 0.05
131 95 0.95
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (131 bp):
TATTAAAAATCCTTTCAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAAC
GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTTTAGGTTTTCACTCGTGT
T
Found at i:28153568 original size:131 final size:130
Alignment explanation
Indices: 28153299--28153571 Score: 343
Period size: 131 Copynumber: 2.1 Consensus size: 130
28153289 GTTTCACAAC
* * *
28153299 TATTAAAAATTCTTTCAAACGAAGGCAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTATC
1 TATTAAAAA-CCTTTCAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAAC
* * ** **
28153364 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCGTGT
65 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGT
28153429 T
130 T
* * * *
28153430 TATTAAAAACCTTTCAAAACGAATACAATACTTGGTGTTTGATAATTCGGGAATCGTGCCCTAAC
1 TATTAAAAACCTTTC-AAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAAC
* ** *
28153495 GTGTTGGGTTGTGATTTCTCATTTTTTCAAAACAATCGAAGATTCCTTCGA-AATTTCACTCACG
65 GTGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTT-GAGAATTTCACTCACG
28153559 TT
129 TT
28153561 T-TCTAAAAACC
1 TAT-TAAAAACC
28153572 CTTGAAAATG
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
130 6 0.05
131 115 0.94
132 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (130 bp):
TATTAAAAACCTTTCAAACGAAGACAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTAACG
TGCTAAGTTGTGATTTCTCATTTGTTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTT
Found at i:28153608 original size:131 final size:131
Alignment explanation
Indices: 28153315--28153666 Score: 323
Period size: 131 Copynumber: 2.7 Consensus size: 131
28153305 AAATTCTTTC
* * * * * * * **
28153315 AAACGAAGGCAATACTCGGTGTTTGATAATTCGAGAATCATGCCCTATCGTGCTAAGTTGTGATT
1 AAACGAAGACAATACTTGATGCTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGTGATT
* * ** ** *
28153380 TCTCATTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCGTGTTTATTAAAAACCTTTC
66 TCTCATTTGTTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTTTATTAAAAACCCTTC
28153445 A
131 A
* * * * * *
28153446 AAACGAATACAATACTTGGTGTTTGATAATTCGGGAATCGTGCCCTAACGTGTTGGGTTGTGATT
1 AAACGAAGACAATACTTGATGCTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGTGATT
*
28153511 TCTCATTTTTTCAAAACAATCGAAGATTCCTTCGA-AATTTCACTCACGTTT-TCTAAAAACCCT
66 TCTCATTTGTTCAAAACAATCGAAGATTCCTT-GAGAATTTCACTCACGTTTAT-TAAAAACCCT
*
28153574 TGA
129 TCA
* * * * * * ***
28153577 AAATGAAGGCGATA-TTCGATGCTTGGCAATTCGAGGAATAGTACCCTATCGTGCTGGGTTACAA
1 AAACGAAGACAATACTT-GATGCTTGACAATTCG-GGAATCGTGCCCTATCGTGCTGGGTTGTGA
* * *
28153641 TTTCCCGTTTGTTCAAAATAATCGAA
64 TTTCTCATTTGTTCAAAACAATCGAA
28153667 TATCTCTTCA
Statistics
Matches: 180, Mismatches: 37, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
130 3 0.02
131 131 0.73
132 46 0.26
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (131 bp):
AAACGAAGACAATACTTGATGCTTGACAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGTGATT
TCTCATTTGTTCAAAACAATCGAAGATTCCTTGAGAATTTCACTCACGTTTATTAAAAACCCTTC
A
Found at i:28156036 original size:23 final size:24
Alignment explanation
Indices: 28156004--28156069 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
28155994 AATTAATCTA
*
28156004 AATATAACTTAAAATCTAAATT-T
1 AATAAAACTTAAAATCTAAATTCT
* *
28156027 ACTAATACTTAAAAAATCT-AATTCT
1 AATAAAACTT--AAAATCTAAATTCT
28156052 AATAAAACTTAAAATCTA
1 AATAAAACTTAAAATCTA
28156070 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 14 0.41
24 4 0.12
25 16 0.47
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (24 bp):
AATAAAACTTAAAATCTAAATTCT
Found at i:28156046 original size:25 final size:25
Alignment explanation
Indices: 28155991--28156065 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
28155981 CGGGTCACTG
*
28155991 AAAAAT-TAA-TCTAAATATAACTT-
1 AAAAATCTAATTCT-AATAAAACTTA
* *
28156014 -AAAATCTAAATT-TACTAATACTTA
1 AAAAATCT-AATTCTAATAAAACTTA
28156038 AAAAATCTAATTCTAATAAAACTTA
1 AAAAATCTAATTCTAATAAAACTTA
28156063 AAA
1 AAA
28156066 TCTATTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 5 0.12
23 8 0.20
24 7 0.17
25 21 0.51
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAATCTAATTCTAATAAAACTTA
Found at i:28160386 original size:5 final size:5
Alignment explanation
Indices: 28160378--28160444 Score: 75
Period size: 5 Copynumber: 13.0 Consensus size: 5
28160368 TAACTAATTT
*
28160378 AATAA AATAA AATAA AATAA AATAA ATTGAA AAT-A AATAAA AATAA AA-ATA
1 AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA AAT-AA AATAA AATA-A
28160429 AATAAA AATAA AATAA
1 AAT-AA AATAA AATAA
28160445 TGTATTCCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
4 5 0.09
5 36 0.67
6 12 0.22
7 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:28160398 original size:15 final size:16
Alignment explanation
Indices: 28160378--28160444 Score: 79
Period size: 16 Copynumber: 4.3 Consensus size: 16
28160368 TAACTAATTT
28160378 AATAAAAT-AAAATAA
1 AATAAAATAAAAATAA
*
28160393 AATAAAAT-AAATTGAA
1 AATAAAATAAAAAT-AA
28160409 AAT-AAATAAAAATAA
1 AATAAAATAAAAATAA
28160424 AA-ATAAATAAAAATAA
1 AATA-AAATAAAAATAA
28160440 AATAA
1 AATAA
28160445 TGTATTCCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
15 20 0.44
16 24 0.53
17 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (16 bp):
AATAAAATAAAAATAA
Found at i:28163804 original size:16 final size:16
Alignment explanation
Indices: 28163785--28163836 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
28163775 TTATTAGGTA
28163785 ATGGGTTTATTTGGGT
1 ATGGGTTTATTTGGGT
*
28163801 ATGGGTTAATTGTGGGT
1 ATGGGTTTATT-TGGGT
28163818 AATGTGG-TTAGTTTGGGT
1 -ATG-GGTTTA-TTTGGGT
28163836 A
1 A
28163837 GGTAAGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 10 0.33
17 6 0.20
18 10 0.33
19 4 0.13
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.44
Consensus pattern (16 bp):
ATGGGTTTATTTGGGT
Found at i:28170849 original size:36 final size:36
Alignment explanation
Indices: 28170802--28170873 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
28170792 GCCTATCCGC
28170802 AGTTGCTCAAATAAATAAAGTAAGTTCTTAAGTAAT
1 AGTTGCTCAAATAAATAAAGTAAGTTCTTAAGTAAT
*
28170838 AGTTGCTCAAATAAATAAAGTATGTTCTTAAGTAAT
1 AGTTGCTCAAATAAATAAAGTAAGTTCTTAAGTAAT
28170874 TGAGTTTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (36 bp):
AGTTGCTCAAATAAATAAAGTAAGTTCTTAAGTAAT
Found at i:28171972 original size:47 final size:47
Alignment explanation
Indices: 28171918--28172813 Score: 1668
Period size: 47 Copynumber: 19.1 Consensus size: 47
28171908 TTAGGATTTT
** * *
28171918 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28171965 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172012 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172059 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172106 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172153 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172200 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172247 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172294 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172341 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172388 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172435 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172482 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172529 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172576 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172623 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
28172670 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
* *
28172717 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
* * * * * *
28172764 ATGTGATGAACGTGGAAC-TGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGAGATAAGGCCGAATGGCCA
28172811 ATG
1 ATG
28172814 CGAAACGTGT
Statistics
Matches: 836, Mismatches: 12, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
47 832 1.00
48 4 0.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
Found at i:28172840 original size:46 final size:46
Alignment explanation
Indices: 28172787--28172877 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
28172777 GGAACTGTAT
* *
28172787 ATATGTGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
28172833 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
28172878 TGTATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:28174359 original size:100 final size:101
Alignment explanation
Indices: 28174211--28174402 Score: 305
Period size: 100 Copynumber: 1.9 Consensus size: 101
28174201 ATGCCAAATT
* * *
28174211 TAACTTATGTAATACATATATTGTTCGAATCAACCCATAACACATACTTTGATAAAA-TACCTTT
1 TAACTTATGTAATACATACATTATTCAAATCAACCCATAACACATACTTTGATAAAATTACCTTT
*
28174275 TTACCCCTAACTTTTCACTTATTTACAAATTGGTCC
66 TTACCCCTAACTATTCACTTATTTACAAATTGGTCC
* * * *
28174311 TAACTTATTTAATACATACATTATTCAAATCGAGCCATAACACATACTTTGGTAAAATTACCTTT
1 TAACTTATGTAATACATACATTATTCAAATCAACCCATAACACATACTTTGATAAAATTACCTTT
28174376 TTACCCCTAACTATTCACTTATTTACA
66 TTACCCCTAACTATTCACTTATTTACA
28174403 CTTTAGTCCC
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 50 0.60
101 33 0.40
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (101 bp):
TAACTTATGTAATACATACATTATTCAAATCAACCCATAACACATACTTTGATAAAATTACCTTT
TTACCCCTAACTATTCACTTATTTACAAATTGGTCC
Found at i:28177586 original size:34 final size:34
Alignment explanation
Indices: 28177533--28177601 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
28177523 CCTCTCAAAG
*
28177533 TCTGCAAAACAGTTATCAAGTGTTCAACATGCTC
1 TCTGCAAAACAGTTATCAAGTGTTCAACATACTC
* * *
28177567 TCTGCAAAATAGTTCTCAAGTGTTCAGCATACTC
1 TCTGCAAAACAGTTATCAAGTGTTCAACATACTC
28177601 T
1 T
28177602 GCCTTATCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (34 bp):
TCTGCAAAACAGTTATCAAGTGTTCAACATACTC
Found at i:28179533 original size:38 final size:38
Alignment explanation
Indices: 28179481--28179561 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
28179471 GACCCATCGA
*
28179481 GGCCTATAATGGCCTAAGTCTATGAAAACGCACGTGGT
1 GGCCTATAACGGCCTAAGTCTATGAAAACGCACGTGGT
* *
28179519 GGCCTATAACGGCCTAAGTTTATGAAAAGGCACGTGGT
1 GGCCTATAACGGCCTAAGTCTATGAAAACGCACGTGGT
28179557 GGCCT
1 GGCCT
28179562 CTTCAGCCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.23
Consensus pattern (38 bp):
GGCCTATAACGGCCTAAGTCTATGAAAACGCACGTGGT
Found at i:28187668 original size:27 final size:27
Alignment explanation
Indices: 28187632--28187727 Score: 129
Period size: 27 Copynumber: 3.6 Consensus size: 27
28187622 GGGTTATAAA
* *
28187632 ATTATTGAAATACCCCTGTAGGGTAGG
1 ATTATCGAAATACCCCTATAGGGTAGG
* *
28187659 ATTATCGAAATACCCTTATAGAGTAGG
1 ATTATCGAAATACCCCTATAGGGTAGG
*
28187686 ATTATCGAAATACCCCTATATGGTAGG
1 ATTATCGAAATACCCCTATAGGGTAGG
* *
28187713 ATTACCAAAATACCC
1 ATTATCGAAATACCC
28187728 TTGTAGGCTA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (27 bp):
ATTATCGAAATACCCCTATAGGGTAGG
Found at i:28187790 original size:26 final size:26
Alignment explanation
Indices: 28187725--28187797 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
28187715 TACCAAAATA
* *
28187725 CCCTTGTAGGCTAAAATGACCATTTTG
1 CCCTTATAGG-TAAAATGACTATTTTG
* *
28187752 TCC-TAAAGAGTAAAATGACTATTTTG
1 CCCTTATAG-GTAAAATGACTATTTTG
28187778 CCCTTATAGGT-AAATGACTA
1 CCCTTATAGGTAAAATGACTA
28187798 ACTTGGGCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 9 0.24
26 22 0.58
27 7 0.18
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (26 bp):
CCCTTATAGGTAAAATGACTATTTTG
Found at i:28198168 original size:29 final size:29
Alignment explanation
Indices: 28198127--28198203 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
28198117 AAACATATTC
* * *
28198127 ATATGGCCCATTAGGCCCAAATCGCCTCT
1 ATATGGCCTATTAGGCCCAAATCACATCT
*
28198156 ATATGGCCTATTAGGCCCAAATCACATTT
1 ATATGGCCTATTAGGCCCAAATCACATCT
*
28198185 ATATGGCCTGTTAGGCCCA
1 ATATGGCCTATTAGGCCCA
28198204 GTAACATTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (29 bp):
ATATGGCCTATTAGGCCCAAATCACATCT
Found at i:28199050 original size:59 final size:59
Alignment explanation
Indices: 28198978--28199100 Score: 219
Period size: 59 Copynumber: 2.1 Consensus size: 59
28198968 ACTTAGTATG
* **
28198978 GTGAATAAGGTTTATTTGGTACAGATTAAAGAAGAAGAGTAGAAGAAGAAATCGGCTAA
1 GTGAATAAGGTTTATTTGGTACAGACTAAAGAAGAAGAGTAGAAGAAGAAATCAACTAA
28199037 GTGAATAAGGTTTATTTGGTACAGACTAAAGAAGAAGAGTAGAAGAAGAAATCAACTAA
1 GTGAATAAGGTTTATTTGGTACAGACTAAAGAAGAAGAGTAGAAGAAGAAATCAACTAA
28199096 GTGAA
1 GTGAA
28199101 ATAAAGAAAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.23
Consensus pattern (59 bp):
GTGAATAAGGTTTATTTGGTACAGACTAAAGAAGAAGAGTAGAAGAAGAAATCAACTAA
Found at i:28200827 original size:51 final size:51
Alignment explanation
Indices: 28200748--28200883 Score: 177
Period size: 51 Copynumber: 2.7 Consensus size: 51
28200738 CCCGATGACT
* *
28200748 TGCACATAGTACCACCCTTGTAATCAAAGCTATCTTCTTTACA-A-AGTGGCC
1 TGCACATAGTACCACACTTGTGATCAAAGCTATC-T-TTTACACATAGTGGCC
* *
28200799 TTCACATAGTACCACACTTGTGACCAAAGCTATCTTTTACACATAGTGGCC
1 TGCACATAGTACCACACTTGTGATCAAAGCTATCTTTTACACATAGTGGCC
* * *
28200850 TGCACTTAGTACCACACATGTGATCGAAGCTATC
1 TGCACATAGTACCACACTTGTGATCAAAGCTATC
28200884 GGGTATGCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 6 0.08
50 2 0.03
51 66 0.89
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
TGCACATAGTACCACACTTGTGATCAAAGCTATCTTTTACACATAGTGGCC
Found at i:28200895 original size:51 final size:49
Alignment explanation
Indices: 28200787--28200974 Score: 171
Period size: 51 Copynumber: 3.8 Consensus size: 49
28200777 CTATCTTCTT
* * * * **
28200787 TACAAAGTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTT
1 TACATAGTGGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCTGG
* * *
28200836 TACACATAGTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGG
1 T--ACATAGTGGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCTGG
* * * * * *
28200887 TATGCATAGTAGCCTGCACTTAGAACTACACATGCGACCTAA-CCATCTGG
1 TA--CATAGTGGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCTGG
* *
28200937 TACATGAGTGGCCTGCACTTAGTACTACACACGTGACC
1 TACAT-AGTGGCCTGCACTTAGTACCACACATGTGACC
28200975 TAAAACCATT
Statistics
Matches: 113, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
48 3 0.03
49 30 0.27
50 8 0.07
51 72 0.64
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (49 bp):
TACATAGTGGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCTGG
Found at i:28200964 original size:49 final size:49
Alignment explanation
Indices: 28200839--28200977 Score: 163
Period size: 49 Copynumber: 2.8 Consensus size: 49
28200829 TATCTTTTAC
* * * *
28200839 ACATAGTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGGT
1 ACATAGTGGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGGT
* * * *
28200888 ATGCATAGTAGCCTGCACTTAGAACTACACATGCGACCTAA-CCATCTGGT
1 A--CATAGTGGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGGT
*
28200938 ACATGAGTGGCCTGCACTTAGTACTACACACGTGACCTAA
1 ACAT-AGTGGCCTGCACTTAGTACTACACATGTGACCTAA
28200978 AACCATTTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
48 3 0.04
49 32 0.43
50 8 0.11
51 32 0.43
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (49 bp):
ACATAGTGGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGGT
Found at i:28204783 original size:42 final size:42
Alignment explanation
Indices: 28204684--28204819 Score: 116
Period size: 43 Copynumber: 3.2 Consensus size: 42
28204674 AGACATTGTA
* * * *
28204684 TAAGACCATGTTTGGGACACAGGCCTC--TATTGAGATTTACGTA
1 TAAGACCATGTCTGGGACAGAGGCATCGATATT--GATTT-CGTG
* **
28204727 TAAGATCATGTCTGGGACATCGGCATCG-TATCTGATTTCGTG
1 TAAGACCATGTCTGGGACAGAGGCATCGATAT-TGATTTCGTG
* * *
28204769 TAAGACCCTGTCTGGGACAGAGGCATCGATATTGAGTTACATG
1 TAAGACCATGTCTGGGACAGAGGCATCGATATTGA-TTTCGTG
28204812 TAAGACCA
1 TAAGACCA
28204820 CGTCCGAGAT
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
42 30 0.39
43 42 0.55
44 3 0.04
45 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACAGAGGCATCGATATTGATTTCGTG
Found at i:28211153 original size:26 final size:26
Alignment explanation
Indices: 28211124--28211176 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
28211114 TCAAACATGC
28211124 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
28211150 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
28211176 A
1 A
28211177 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:28212697 original size:26 final size:26
Alignment explanation
Indices: 28212661--28212770 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
28212651 CATGAAATTC
28212661 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28212687 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28212713 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
28212739 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28212765 TTATCA
1 TTATCA
28212771 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28224087 original size:15 final size:15
Alignment explanation
Indices: 28224067--28224123 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 15
28224057 TTTTCTTGCC
*
28224067 TCTCTTTTCTTTTGA
1 TCTCTTTTCTTTTCA
28224082 TCTCTTTTTGCTTTTCA
1 TCTC-TTTT-CTTTTCA
28224099 TCT-TTTTCTTTTC-
1 TCTCTTTTCTTTTCA
*
28224112 TC-ATTTTCTTTT
1 TCTCTTTTCTTTT
28224124 TACAAGAGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 11 0.29
14 6 0.16
15 8 0.21
16 4 0.11
17 9 0.24
ACGTcount: A:0.05, C:0.21, G:0.04, T:0.70
Consensus pattern (15 bp):
TCTCTTTTCTTTTCA
Found at i:28224095 original size:17 final size:16
Alignment explanation
Indices: 28224066--28224111 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
28224056 CTTTTCTTGC
*
28224066 CTCTCTTTTCTTTTGAT
1 CTCT-TTTTCTTTTCAT
28224083 CTCTTTTTGCTTTTCA-
1 CTCTTTTT-CTTTTCAT
28224099 -TCTTTTTCTTTTC
1 CTCTTTTTCTTTTC
28224112 TCATTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 4 0.15
17 10 0.37
ACGTcount: A:0.04, C:0.24, G:0.04, T:0.67
Consensus pattern (16 bp):
CTCTTTTTCTTTTCAT
Found at i:28224612 original size:27 final size:27
Alignment explanation
Indices: 28224582--28224741 Score: 257
Period size: 27 Copynumber: 5.9 Consensus size: 27
28224572 AGTATTTTAG
*
28224582 TAATTCTACCCTACAGGGATATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
28224609 TAATTCTACCCTACAGGGGTATTGCAA
1 TAATTCTACCCTACAGGGGTATTTCGA
*
28224636 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
*
28224663 TAATTCTACCCTACAAGGGTATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
28224690 TAATTCTACCCTACAGGGGTATTTTGG
1 TAATTCTACCCTACAGGGGTATTTCGA
28224717 TAATTCTACCCTACAGGGGTATTTC
1 TAATTCTACCCTACAGGGGTATTTC
28224742 AGTAATTTTG
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCGA
Found at i:28224763 original size:27 final size:27
Alignment explanation
Indices: 28224733--28224971 Score: 128
Period size: 27 Copynumber: 8.9 Consensus size: 27
28224723 TACCCTACAG
**
28224733 GGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
*** * * ** *
28224760 GGGTAAAACGGTAATTCTGTAAATCAA
1 GGGTATTTCAGTAATTTTACAAATCGA
* *
28224787 GGGTACTTT-GGTAATTTTACAAGTCGA
1 GGGTA-TTTCAGTAATTTTACAAATCGA
* **
28224814 GGGTATTTCAATAATTTTACAGGTCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
* *
28224841 GGGTATTTTAGTAATTTCACAAATC-A
1 GGGTATTTCAGTAATTTTACAAATCGA
** *
28224867 GGGGTATTTTGGTAATTTTACAAA-CTAA
1 -GGGTATTTCAGTAATTTTACAAATC-GA
* *
28224895 GGGTATTT-TGATAATTTTACAAA-CCA
1 GGGTATTTCAG-TAATTTTACAAATCGA
** ** * *
28224921 GGGGTATTTTGGTAATTTTGTAAACCAA
1 -GGGTATTTCAGTAATTTTACAAATCGA
**
28224949 GGGTATTTTGGTAATTTTACAAA
1 GGGTATTTCAGTAATTTTACAAA
28224972 CCAGGGGTAT
Statistics
Matches: 171, Mismatches: 32, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
26 7 0.04
27 160 0.94
28 4 0.02
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACAAATCGA
Found at i:28224829 original size:54 final size:52
Alignment explanation
Indices: 28224649--28225165 Score: 272
Period size: 54 Copynumber: 9.4 Consensus size: 52
28224639 TTCTACCCTA
* * ** * * * **
28224649 CAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCT
1 CAGGGGTATTTTGGTAATTTTACAAT-CAAGGGTATTTTGGTAATTTTACAAT
* ** * **
28224702 ACAGGGGTATTTTGGTAATTCTACCCTACAGGGGTATTTCAGTAATTTTGTA-AAT
1 -CAGGGGTATTTTGGTAATTTTACAAT-CAAGGGTATTTTGGTAA-TTT-TACAAT
**** *
28224757 C-GAGGGTAAAACGGTAATTCTGTA-AATCAAGGGTACTTTGGTAATTTTACAAGT
1 CAG-GGGTATTTTGGTAATT-T-TACAATCAAGGGTATTTTGGTAATTTTACAA-T
*** * * * *
28224811 C-GAGGGTATTTCAATAATTTTACAGGTCGAGGGTATTTTAGTAATTTCACAAAT
1 CAG-GGGTATTTTGGTAATTTTACA-ATCAAGGGTATTTTGGTAATTTTAC-AAT
* * *
28224865 CAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTTGATAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAATC-AAGGGTATTTTGGTAATTTTAC-AAT
* *
28224919 CAGGGGTATTTTGGTAATTTTGTA-AACCAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAA-TTT-TACAATCAAGGGTATTTTGGTAATTTTAC-AAT
* * *
28224973 CAGGGGTATTTTGGAAATTTTGTAAACCAAGGGTAAACAAAGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAA-TTT-T--A-CAA---T---C-AAGGGTATTTTGGTAATTTTAC-AAT
* * *
28225038 CAGGGGTATTTTGGAAATTTTGTA-AACCAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAA-TTT-TACAATCAAGGGTATTTTGGTAATTTTAC-AAT
* * * * * * *
28225092 CAGTGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTGATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTA-CAATCAAGGGTATTTTGGTAATTTTAC-AAT
28225146 CAGGGGTATTTTGGTAATTT
1 CAGGGGTATTTTGGTAATTT
28225166 GGTAAACTAA
Statistics
Matches: 384, Mismatches: 52, Indels: 54
0.78 0.11 0.11
Matches are distributed among these distances:
52 6 0.02
53 12 0.03
54 291 0.76
55 14 0.04
56 7 0.02
58 2 0.01
61 2 0.01
63 1 0.00
64 1 0.00
65 48 0.12
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (52 bp):
CAGGGGTATTTTGGTAATTTTACAATCAAGGGTATTTTGGTAATTTTACAAT
Found at i:28224972 original size:27 final size:27
Alignment explanation
Indices: 28224784--28225165 Score: 325
Period size: 27 Copynumber: 13.7 Consensus size: 27
28224774 TTCTGTAAAT
* **
28224784 CAAGGGTACTTTGGTAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *** ***
28224811 CGAGGGTATTTCAATAATTTTACAGGT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * * *
28224838 CGAGGGTATTTTAGTAATTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
*
28224865 CAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
28224892 TAAGGGTATTTTGATAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* **
28224919 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
28224946 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * **
28224973 CAGGGGTATTTTGGAAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* **
28225000 CAAGGGTAAACAAAGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGT------A---TTTTGG--TAATTTTACAAAC
* * **
28225038 CAGGGGTATTTTGGAAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
28225065 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
28225092 C-AGTGGTATTTTGGTGATTTTATAAAC
1 CAAG-GGTATTTTGGTAATTTTACAAAC
* *
28225119 CAAGGGTATTTTAGTGATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
*
28225146 CAGGGGTATTTTGGTAATTT
1 CAAGGGTATTTTGGTAATTT
28225166 GGTAAACTAA
Statistics
Matches: 286, Mismatches: 56, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
26 2 0.01
27 258 0.90
28 2 0.01
29 3 0.01
32 1 0.00
33 1 0.00
36 3 0.01
38 16 0.06
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:28225016 original size:65 final size:65
Alignment explanation
Indices: 28224940--28225072 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 65
28224930 TGGTAATTTT
* *
28224940 GTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGG
1 GTAAACAAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGG
28225005 GTAAACAAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGG
1 GTAAACAAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGG
28225070 GTA
1 GTA
28225073 TTTTGGTAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (65 bp):
GTAAACAAAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGG
Found at i:28225104 original size:119 final size:119
Alignment explanation
Indices: 28224888--28225126 Score: 408
Period size: 119 Copynumber: 2.0 Consensus size: 119
28224878 GTAATTTTAC
* *
28224888 AAACTAAGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGT
1 AAACAAAGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGGGT
*
28224953 ATTTTGGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGGGT
66 ATTTTGGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTATAAACCAAGGGT
28225007 AAACAAAGGGTATTTT-AGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGGG
1 AAACAAAGGGTATTTTGA-TAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGGG
* **
28225071 TATTTTGGTAATTTTACAAACCAGTGGTATTTTGGTGATTTTATAAACCAAGGGT
65 TATTTTGGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTATAAACCAAGGGT
28225126 A
1 A
28225127 TTTTAGTGAT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
118 1 0.01
119 112 0.99
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (119 bp):
AAACAAAGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGGGT
ATTTTGGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTATAAACCAAGGGT
Found at i:28225129 original size:173 final size:173
Alignment explanation
Indices: 28224840--28225172 Score: 540
Period size: 173 Copynumber: 1.9 Consensus size: 173
28224830 TTACAGGTCG
* * *
28224840 AGGGTATTTTAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTTG
1 AGGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGAAATTTTACAAACCAAGGGTATTTTG
* *
28224905 ATAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACA
66 ATAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
*
28224970 AACCAGGGGTATTTTGGAAATTTTGTAAACCAAGGGTAAACAA
131 AACCAGGGGTATTTTGGAAATTTGGTAAACCAAGGGTAAACAA
* **
28225013 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGTAAACCAAGGGTATTTTG
1 AGGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGAAATTTTACAAACCAAGGGTATTTTG
* * * *
28225078 GTAATTTTACAAACCAGTGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTGATTTTACA
66 ATAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
*
28225143 AACCAGGGGTATTTTGGTAATTTGGTAAAC
131 AACCAGGGGTATTTTGGAAATTTGGTAAAC
28225173 TAAAGTATTC
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
173 146 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (173 bp):
AGGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGAAATTTTACAAACCAAGGGTATTTTG
ATAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTTTACA
AACCAGGGGTATTTTGGAAATTTGGTAAACCAAGGGTAAACAA
Found at i:28226653 original size:66 final size:65
Alignment explanation
Indices: 28226517--28226667 Score: 173
Period size: 66 Copynumber: 2.3 Consensus size: 65
28226507 TGACTTGGGT
* *
28226517 CACACGGCCAAACACACGCCCGTGTGCTAGGCCATGCCAAATCTGTAGGGCATACTGACTTATAC
1 CACACGGCCAATCACACGCCCGTGTGCTAGACCATGCCAAATCTGTAGGGCATACTGACTTATAC
* * * *
28226582 AACACGGCCAAGTCACACGCCCGTGTGCTAGACCATGTGCC-AAT-TAG-GGGGTATACTGGCTT
1 CACACGGCCAA-TCACACGCCCGTGTGCTAGACCA--TGCCAAATCT-GTAGGGCATACTGACTT
*
28226644 GTAC
62 ATAC
*
28226648 CACACGGCCGATCACACGCC
1 CACACGGCCAATCACACGCC
28226668 TCACTACAGG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
65 19 0.26
66 46 0.63
67 4 0.05
68 4 0.05
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (65 bp):
CACACGGCCAATCACACGCCCGTGTGCTAGACCATGCCAAATCTGTAGGGCATACTGACTTATAC
Found at i:28226853 original size:41 final size:41
Alignment explanation
Indices: 28226808--28227028 Score: 300
Period size: 41 Copynumber: 5.4 Consensus size: 41
28226798 CGTTTTTTAC
*
28226808 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
* * * **
28226849 TAAAACGCCGGTAAAAAACAGAGAATTAGCGGCGCTTTCTA
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
* * * *
28226890 TAAAACGACGCTAAAAA-TAGGGCATTAGCGGTGCTTTCGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
* * *
28226930 TAAAATGCCGCTAAAAACCAGAGCATTAGCGTCGCTTTGGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
* *
28226971 TAAAACGCCGCTAAAAACCAGAGCATTAGCGACGCTTTTGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
28227012 TAAAACGCCGCTAAAAA
1 TAAAACGCCGCTAAAAA
28227029 TCCCATAACC
Statistics
Matches: 155, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 32 0.21
41 123 0.79
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (41 bp):
TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGG
Found at i:28226952 original size:81 final size:82
Alignment explanation
Indices: 28226808--28227028 Score: 300
Period size: 81 Copynumber: 2.7 Consensus size: 82
28226798 CGTTTTTTAC
*
28226808 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGGTAAAAAACAGAGA
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAACAGAGA
*
28226873 ATTAGCGGCGCTTTCTA
66 ATTAGCGGCGCTTTCGA
* * * * * * * *
28226890 TAAAACGACGCTAAAAA-TAGGGCATTAGCGGTGCTTTCGGTAAAATGCCGCTAAAAACCAGAGC
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAACAGAGA
* * *
28226954 ATTAGCGTCGCTTTGGG
66 ATTAGCGGCGCTTTCGA
* *
28226971 TAAAACGCCGCTAAAAACCAGAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAAA
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAA
28227029 TCCCATAACC
Statistics
Matches: 118, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
81 68 0.58
82 50 0.42
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (82 bp):
TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAACAGAGA
ATTAGCGGCGCTTTCGA
Found at i:28226959 original size:122 final size:122
Alignment explanation
Indices: 28226808--28227029 Score: 347
Period size: 122 Copynumber: 1.8 Consensus size: 122
28226798 CGTTTTTTAC
*
28226808 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGGTAAAAAACAGAGA
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAACAGAGA
*
28226873 ATTAGCGGCGCTTTCT-ATAAAACGACGCTAAAAATAGGGCATTAGCGGTGCTTTCGG
66 ATTAGCGACGCTTT-TGATAAAACGACGCTAAAAATAGGGCATTAGCGGTGCTTTCGG
* * * * *
28226930 TAAAATGCCGCTAAAAACCAGAGCATTAGCGTCGCTTTGGGTAAAACGCCGCTAAAAACCAGAGC
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAACAGAGA
* *
28226995 ATTAGCGACGCTTTTGGTAAAACGCCGCTAAAAAT
66 ATTAGCGACGCTTTTGATAAAACGACGCTAAAAAT
28227030 CCCATAACCC
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 1 0.01
122 89 0.99
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (122 bp):
TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAAACAGAGA
ATTAGCGACGCTTTTGATAAAACGACGCTAAAAATAGGGCATTAGCGGTGCTTTCGG
Found at i:28227208 original size:14 final size:14
Alignment explanation
Indices: 28227186--28227225 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28227176 TTAATTATCA
* *
28227186 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
28227200 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
*
28227214 ATATGGTTTAAG
1 TTATGGTTTAAG
28227226 CAGGTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:28228111 original size:15 final size:15
Alignment explanation
Indices: 28228091--28228122 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28228081 TTTAATTTAG
*
28228091 AAGATAAATGTATAT
1 AAGATAAATATATAT
28228106 AAGATAAATATATAT
1 AAGATAAATATATAT
28228121 AA
1 AA
28228123 AATATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:28228161 original size:24 final size:24
Alignment explanation
Indices: 28228094--28228161 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
28228084 AATTTAGAAG
* *
28228094 ATAAATGTATATAAGATAAATATAT
1 ATAAATATATATATGA-AAATATAT
* *
28228119 ATAAA-ATATTATTTTAAAATATAT
1 ATAAATATA-TATATGAAAATATAT
28228143 ATAAATATATATATGAAAA
1 ATAAATATATATATGAAAA
28228162 AGTGGTTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
ATAAATATATATATGAAAATATAT
Found at i:28229733 original size:18 final size:17
Alignment explanation
Indices: 28229712--28229754 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
28229702 ATCTTAATGA
28229712 TGATGATGATGTTGATAC
1 TGATGATGATGTTGAT-C
*
28229730 TGATGTTGATGTTGATC
1 TGATGATGATGTTGATC
28229747 TCGATGAT
1 T-GATGAT
28229755 TATACCCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (17 bp):
TGATGATGATGTTGATC
Found at i:28231718 original size:133 final size:133
Alignment explanation
Indices: 28231543--28231794 Score: 459
Period size: 133 Copynumber: 1.9 Consensus size: 133
28231533 TGGTGATTCC
28231543 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
1 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
* *
28231608 TGGACTTAGATTGATTTAAGAGTTTAATGCTGTCTTGTTGCTTACATTTTATATAATAAAATTGT
66 TGGACATAGATTGATTTAAGAGTTTAATGCTGTCTTGTTGCTCACATTTTATATAATAAAATTGT
28231673 TAT
131 TAT
28231676 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
1 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
* * *
28231741 TGGACATAGATTTATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATAT
66 TGGACATAGATTGATTTAAGAGTTTAATGCTGTCTTGTTGCTCACATTTTATAT
28231795 TGTTGAATTC
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 114 1.00
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.52
Consensus pattern (133 bp):
ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
TGGACATAGATTGATTTAAGAGTTTAATGCTGTCTTGTTGCTCACATTTTATATAATAAAATTGT
TAT
Found at i:28233892 original size:21 final size:21
Alignment explanation
Indices: 28233863--28233902 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28233853 GTTTTTATAT
*
28233863 TTTGGTTCAACTTAAGTATTA
1 TTTGATTCAACTTAAGTATTA
28233884 TTTGATTCAACTTAAGTAT
1 TTTGATTCAACTTAAGTAT
28233903 GAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTGATTCAACTTAAGTATTA
Found at i:28234354 original size:21 final size:21
Alignment explanation
Indices: 28234325--28234364 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28234315 GTTTTTATAT
*
28234325 TTTGGTTCAACTTAAGTATTA
1 TTTGATTCAACTTAAGTATTA
28234346 TTTGATTCAACTTAAGTAT
1 TTTGATTCAACTTAAGTAT
28234365 GAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTGATTCAACTTAAGTATTA
Found at i:28234376 original size:462 final size:462
Alignment explanation
Indices: 28233480--28234456 Score: 1864
Period size: 462 Copynumber: 2.1 Consensus size: 462
28233470 TTCTCCCCAA
*
28233480 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATATAGGCTGGAAACCTGACGGGTTGCCTTAT
1 CCTTATTTTAAATGTTTTAAAGATTCAAAG--TATATAGGCTGGAAACCTGACGGGTTGCCTTAT
28233545 ATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAA
64 ATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAA
28233610 AAATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTC
129 AAATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTC
* **
28233675 ACCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTTATATTATTATATTCAAATTACTATT
194 ACCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTACCATATTCAAATTACTATT
28233740 TTGTTATATTAAACATGTTTGATTTTAATATTTATTATTTTTAAATGTCTTTAAAATTTATAACT
259 TTGTTATATTAAACATGTTTGATTTTAATATTTATTATTTTTAAATGTCTTTAAAATTTATAACT
28233805 AATTTTTATCAAAATAGTATTATTAATTATTATTTGAAGTATGAATAAGTTTTTATATTTTGGTT
324 AATTTTTATCAAAATAGTATTATTAATTATTATTTGAAGTATGAATAAGTTTTTATATTTTGGTT
28233870 CAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCTTGC
389 CAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCTTGC
28233935 TTGTCCATT
454 TTGTCCATT
*
28233944 CCTTATTTTAAATGTTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGTGTTGCCTTATAT
1 CCTTATTTTAAATGTTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
*
28234009 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAATGCCACGTATGATGAATCTTAAAAA
66 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
28234074 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCAC
131 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCAC
* *
28234139 CAATTTACTTCTAAAAATTAAGCTACGATTCTTTCTTGATATTACCATATTCAAATTACTATTTT
196 CAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTACCATATTCAAATTACTATTTT
28234204 GTTATATTAAACATGTTTGATTTTAATATTTATTATTTTTAAATGTCTTTAAAATTTATAACTAA
261 GTTATATTAAACATGTTTGATTTTAATATTTATTATTTTTAAATGTCTTTAAAATTTATAACTAA
28234269 TTTTTATCAAAATAGTATTATTAATTATTATTTGAAGTATGAATAAGTTTTTATATTTTGGTTCA
326 TTTTTATCAAAATAGTATTATTAATTATTATTTGAAGTATGAATAAGTTTTTATATTTTGGTTCA
28234334 ACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCTTGCTT
391 ACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCTTGCTT
28234399 GTCCATT
456 GTCCATT
28234406 CCTTATTTTAAATGTTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGAC
1 CCTTATTTTAAATGTTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGAC
28234457 CTTATAGTAT
Statistics
Matches: 505, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
462 476 0.94
464 29 0.06
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (462 bp):
CCTTATTTTAAATGTTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCAC
CAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTACCATATTCAAATTACTATTTT
GTTATATTAAACATGTTTGATTTTAATATTTATTATTTTTAAATGTCTTTAAAATTTATAACTAA
TTTTTATCAAAATAGTATTATTAATTATTATTTGAAGTATGAATAAGTTTTTATATTTTGGTTCA
ACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCTTGCTT
GTCCATT
Found at i:28241020 original size:43 final size:43
Alignment explanation
Indices: 28240973--28241256 Score: 288
Period size: 43 Copynumber: 6.6 Consensus size: 43
28240963 CTGGGCAAAT
* *
28240973 TAGCGGCGTTTTTTAAAAAAGCGCTGCTAAAAGTATAGGTCTA
1 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTA
* *
28241016 TAGCGGCATTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTA
1 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTA
*
28241059 TAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTA
1 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTA
* * * * *
28241102 TAGCGGCGTTTTTTATAAAAGTGCCGCTAAAGGTCCTA-GTCTT
1 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTAC-AGGTCTA
* * * * * *
28241145 TAGCGGCACTTTTATAAAAAA-CGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGC-GTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTA
* * * * * * * * *
28241188 TGGCGGCCTTTTTT-TAAGAGCGCCGTTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTA
28241230 TAGCGGCGCTTTTTTAAAAAA-CGCCGC
1 TAGCGGCG-TTTTTTAAAAAAGCGCCGC
28241257 GAACTTTTGT
Statistics
Matches: 210, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.01
42 33 0.16
43 160 0.76
44 14 0.07
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (43 bp):
TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCTA
Found at i:28241122 original size:86 final size:85
Alignment explanation
Indices: 28240972--28241256 Score: 331
Period size: 86 Copynumber: 3.3 Consensus size: 85
28240962 TCTGGGCAAA
* * *
28240972 TTAGCGGCGTTTTTTAAAAAAGCGCTGCTAAAAGTATAGGTCTATAGCGGCATTTTTTACAAAAG
1 TTAGCGGCGTTTTTTAAAAAA-CGCCGCTAAAAGTACAGGTCTATAGCGGCATTTTTTATAAAAG
* *
28241037 CGCCGCTAAAAGTACAGGTCT
65 CGCCGCTAAAGGTCCAGGTCT
* * *
28241058 ATAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTATAAAAG
1 TTAGCGGCGTTTTTTA-AAAAACGCCGCTAAAAGTACAGGTCTATAGCGGCATTTTTTATAAAAG
*
28241123 TGCCGCTAAAGGTCCTA-GTCT
65 CGCCGCTAAAGGTCC-AGGTCT
* * * * * * * * *
28241144 TTAGCGGCACTTTTATAAAAAACGCCGCTAAAGGTCCTGGTCTTTGGCGGCCTTTTTT-TAAGAG
1 TTAGCGGC-GTTTTTTAAAAAACGCCGCTAAAAGTACAGGTCTATAGCGGCATTTTTTATAAAAG
* *
28241208 CGCCGTTAAAGGTCCTGGTCT
65 CGCCGCTAAAGGTCCAGGTCT
28241229 TTAGCGGCGCTTTTTTAAAAAACGCCGC
1 TTAGCGGCG-TTTTTTAAAAAACGCCGC
28241257 GAACTTTTGT
Statistics
Matches: 169, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
85 47 0.28
86 111 0.66
87 11 0.07
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (85 bp):
TTAGCGGCGTTTTTTAAAAAACGCCGCTAAAAGTACAGGTCTATAGCGGCATTTTTTATAAAAGC
GCCGCTAAAGGTCCAGGTCT
Found at i:28241149 original size:129 final size:128
Alignment explanation
Indices: 28240973--28241256 Score: 322
Period size: 129 Copynumber: 2.2 Consensus size: 128
28240963 CTGGGCAAAT
* * *
28240973 TAGCGGCGTTTTTTAAAAAAGCGCTGCTAAAAGTATAGGTCTATAGCGGCA-TTTTTTACAAAAG
1 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTATAGGTCTATAGCGGCACTTTTATA-AAAAA
*
28241037 CGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTA
65 CGCCGCTAAAAGTACAGGTCTATAGCGGCCTTTTTT-CAAAAGCGCCGCTAAAAGTACAGGTCTA
* * * * *
28241102 TAGCGGCGTTTTTTATAAAAGTGCCGCTAAAGGTCCTA-GTCTTTAGCGGCACTTTTATAAAAAA
1 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGT-ATAGGTCTATAGCGGCACTTTTATAAAAAA
* * * * * * * * * * * *
28241166 CGCCGCTAAAGGTCCTGGTCTTTGGCGGCCTTTTTTTAAGAGCGCCGTTAAAGGTCCTGGTCTT
65 CGCCGCTAAAAGTACAGGTCTATAGCGGCCTTTTTTCAAAAGCGCCGCTAAAAGTACAGGTCTA
28241230 TAGCGGCGCTTTTTTAAAAAA-CGCCGC
1 TAGCGGCG-TTTTTTAAAAAAGCGCCGC
28241257 GAACTTTTGT
Statistics
Matches: 129, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
128 34 0.26
129 87 0.67
130 8 0.06
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (128 bp):
TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTATAGGTCTATAGCGGCACTTTTATAAAAAAC
GCCGCTAAAAGTACAGGTCTATAGCGGCCTTTTTTCAAAAGCGCCGCTAAAAGTACAGGTCTA
Found at i:28242449 original size:28 final size:29
Alignment explanation
Indices: 28242418--28242474 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
28242408 TATCCGAAAT
*
28242418 CCTGATAT-CATGGCTCGAAGCCAAATCA
1 CCTGATATGCATGCCTCGAAGCCAAATCA
*
28242446 CCTGATATGCTTGCCTCGAAGCCAAATCA
1 CCTGATATGCATGCCTCGAAGCCAAATCA
28242475 GTATCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (29 bp):
CCTGATATGCATGCCTCGAAGCCAAATCA
Found at i:28257143 original size:50 final size:51
Alignment explanation
Indices: 28257029--28257222 Score: 284
Period size: 51 Copynumber: 3.8 Consensus size: 51
28257019 TGAACCTTAG
* * *
28257029 GAATAAAATAACTTTGGACACGAGTGTGGTACTATGTGGAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
*
28257080 GAATATAATAGCTTTGGACACAAGTGTGGTACTATGT-AAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * *
28257130 GAATAAAATAGCTTTGGATACAAGTTTGGTACTGTGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* *
28257181 GAATAAAATATCTTTGG-CTACAAGGGTGGTACTATGTGAAGG
1 GAATAAAATAGCTTTGGAC-ACAAGTGTGGTACTATGTGAAGG
28257223 TCGCCGTGTA
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
50 45 0.35
51 83 0.65
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:28257175 original size:101 final size:102
Alignment explanation
Indices: 28257029--28257222 Score: 284
Period size: 101 Copynumber: 1.9 Consensus size: 102
28257019 TGAACCTTAG
* * *
28257029 GAATAAAATAACTTTGGACACGAGTGTGGTACTATGTGGAGGCCACTTTGTGAATATAATAGCTT
1 GAATAAAATAACTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTT
*
28257094 TGGAC-ACAAGTGTGGTACTATGT-AAGGCCACTTTGT
66 TGG-CTACAAGGGTGGTACTATGTGAAGGCCACTTTGT
* * * * *
28257130 GAATAAAATAGCTTTGGATACAAGTTTGGTACTGTGTGAAGGCCACTTTGTGAATAAAATATCTT
1 GAATAAAATAACTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTT
28257195 TGGCTACAAGGGTGGTACTATGTGAAGG
66 TGGCTACAAGGGTGGTACTATGTGAAGG
28257223 TCGCCGTGTA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 1 0.01
101 77 0.94
102 4 0.05
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.31
Consensus pattern (102 bp):
GAATAAAATAACTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAAAATAGCTT
TGGCTACAAGGGTGGTACTATGTGAAGGCCACTTTGT
Found at i:28258768 original size:34 final size:34
Alignment explanation
Indices: 28258730--28258797 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
28258720 TTCGGTGTTG
28258730 AACACGGGTAAGGGGTGTTACAAGAAGGAAGTTT
1 AACACGGGTAAGGGGTGTTACAAGAAGGAAGTTT
*
28258764 AACACGGGTAAGGGGTGTTATAAGAAGGAAGTTT
1 AACACGGGTAAGGGGTGTTACAAGAAGGAAGTTT
28258798 GATTTGGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.22
Consensus pattern (34 bp):
AACACGGGTAAGGGGTGTTACAAGAAGGAAGTTT
Found at i:28260942 original size:19 final size:19
Alignment explanation
Indices: 28260875--28260948 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 19
28260865 TAAGTTAAAT
28260875 TAAAAAATATTAATTACTA
1 TAAAAAATATTAATTACTA
* *
28260894 TATACAATATTAATTTACATAA
1 TAAAAAATATTAA-TTAC-T-A
*
28260916 TTTAAAAAATAATAATTACTA
1 --TAAAAAATATTAATTACTA
28260937 TAAAAAAGTATT
1 TAAAAAA-TATT
28260949 GGTACAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
19 18 0.42
20 7 0.16
21 2 0.05
22 2 0.05
23 4 0.09
24 10 0.23
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (19 bp):
TAAAAAATATTAATTACTA
Found at i:28263334 original size:48 final size:48
Alignment explanation
Indices: 28263263--28263464 Score: 143
Period size: 48 Copynumber: 4.3 Consensus size: 48
28263253 GACTATATAA
* ** *
28263263 CGATGCCATATCCTAGATTTGGTCTTATACAAAG-TCTCATATCGGTGC
1 CGATGCCATATCCCAGACGTGGTCTTATACAAAGATCACATAT-GGTGC
* * * *
28263311 CGATGCCATATCCCAGACGTGGTCTTATA-TAGGACCTCATA---T--
1 CGATGCCATATCCCAGACGTGGTCTTATACAAAGATCACATATGGTGC
* * * * * *
28263353 CGATGCCATGTCCCAGACATGGTCTTATACGAA-ATCACTTAATGATAC
1 CGATGCCATATCCCAGACGTGGTCTTATACAAAGATCACAT-ATGGTGC
* * * *
28263401 CGAAGCCATATCCCTGATGTGGTCTTATAC-ATGATCACATATTGGTGC
1 CGATGCCATATCCCAGACGTGGTCTTATACAAAGATCACATA-TGGTGC
*
28263449 CGATGCCATGTCCCAG
1 CGATGCCATATCCCAG
28263465 GCATGGTATT
Statistics
Matches: 119, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
42 31 0.26
43 2 0.02
44 1 0.01
46 1 0.01
47 4 0.03
48 80 0.67
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (48 bp):
CGATGCCATATCCCAGACGTGGTCTTATACAAAGATCACATATGGTGC
Found at i:28263409 original size:90 final size:89
Alignment explanation
Indices: 28263223--28263429 Score: 213
Period size: 90 Copynumber: 2.3 Consensus size: 89
28263213 TAGAGTGCCA
* * * * * **
28263223 AAGCCATGTCCTAGACATGGTCTTACATAGGACTATATAACGATGCCATATCCTAGATTTGGTCT
1 AAGCCATATCCCAGACGTGGTCTTATATAGGACTATAT-ACGATGCCATATCCCAGACATGGTCT
* * *
28263288 TATACAAAGTCTCATATCGGTGCCG
65 TATACAAAGTCACATATCGATACCG
* *
28263313 ATGCCATATCCCAGACGTGGTCTTATATAGGACCTCATAT-CGATGCCATGTCCCAGACATGGTC
1 AAGCCATATCCCAGACGTGGTCTTATATAGGA-CT-ATATACGATGCCATATCCCAGACATGGTC
*
28263377 TTATACGAAA-TCACTTAAT-GATACCG
64 TTATAC-AAAGTCACAT-ATCGATACCG
* *
28263403 AAGCCATATCCCTGATGTGGTCTTATA
1 AAGCCATATCCCAGACGTGGTCTTATA
28263430 CATGATCACA
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
90 86 0.89
91 7 0.07
92 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (89 bp):
AAGCCATATCCCAGACGTGGTCTTATATAGGACTATATACGATGCCATATCCCAGACATGGTCTT
ATACAAAGTCACATATCGATACCG
Found at i:28263566 original size:49 final size:48
Alignment explanation
Indices: 28263436--28263575 Score: 163
Period size: 48 Copynumber: 2.9 Consensus size: 48
28263426 TATACATGAT
* * *
28263436 CACATATTGGTGCCGATGCCATGTCCCAGGCATGGTATTACACTAGCA
1 CACATATCGATGCCGATGCCATGTCCCAGACATGGTATTACACTAGCA
* ** * * *
28263484 CACATATCTACACCGATACCATGTCCCAAACATGGTATTACACTAGCT
1 CACATATCGATGCCGATGCCATGTCCCAGACATGGTATTACACTAGCA
* * *
28263532 CTCATCTCGGATGCCGATGCCATGTCCCAGACATGGTCTTACAC
1 CACATATC-GATGCCGATGCCATGTCCCAGACATGGTATTACAC
28263576 GGGATCTCAT
Statistics
Matches: 74, Mismatches: 17, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
48 45 0.61
49 29 0.39
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (48 bp):
CACATATCGATGCCGATGCCATGTCCCAGACATGGTATTACACTAGCA
Found at i:28266249 original size:23 final size:23
Alignment explanation
Indices: 28266219--28266289 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
28266209 CACAAAGACA
28266219 ATCATTAGAATCAGAATTATAAC
1 ATCATTAGAATCAGAATTATAAC
*
28266242 ATCATTAGAAT-A-AA-GA-AAC
1 ATCATTAGAATCAGAATTATAAC
28266261 AATCATTAGAATCAGAATTATAAC
1 -ATCATTAGAATCAGAATTATAAC
28266285 ATCAT
1 ATCAT
28266290 ATGCATTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.07
20 12 0.29
21 3 0.07
22 3 0.07
23 17 0.41
24 3 0.07
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (23 bp):
ATCATTAGAATCAGAATTATAAC
Found at i:28270775 original size:43 final size:43
Alignment explanation
Indices: 28270627--28270783 Score: 124
Period size: 43 Copynumber: 3.7 Consensus size: 43
28270617 TGTGTTATCG
* * **
28270627 TGTAAGACAAAGTCTGGAACGTTGGCATCAAT-TTGTGATTTATG
1 TGTAAGACAACGTCTGGGACGTTGGCATCAATATT-TGA-TTACA
* * * * * * *
28270671 TGTAAGACCATGTCTGGGACATTGGCAT-TATATATAATTTCA
1 TGTAAGACAACGTCTGGGACGTTGGCATCAATATTTGATTACA
* * *
28270713 CGTAAGAC-CCAGTCTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACAAC-GTCTGGGAC-GTTGGCATCAATATTTGATTACA
28270756 TGTAAGACAACGTCTGGGACGTTGGCAT
1 TGTAAGACAACGTCTGGGACGTTGGCAT
28270784 TGTAGGAGCT
Statistics
Matches: 87, Mismatches: 20, Indels: 13
0.73 0.17 0.11
Matches are distributed among these distances:
42 25 0.29
43 36 0.41
44 26 0.30
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACAACGTCTGGGACGTTGGCATCAATATTTGATTACA
Found at i:28271965 original size:18 final size:16
Alignment explanation
Indices: 28271933--28271971 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
28271923 TTAGTAAATG
28271933 AATAATAAAATGTTAT
1 AATAATAAAATGTTAT
*
28271949 TATAATAATATATGTTAT
1 AATAATAA-A-ATGTTAT
28271967 AATAA
1 AATAA
28271972 AATTCATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
AATAATAAAATGTTAT
Found at i:28273594 original size:9 final size:9
Alignment explanation
Indices: 28273581--28273618 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
28273571 TGTAACTGAG
28273581 CTTTCAACT
1 CTTTCAACT
*
28273590 TTTTCAACT
1 CTTTCAACT
28273599 CTTTCAACT
1 CTTTCAACT
28273608 CTTTCAACT
1 CTTTCAACT
28273617 CT
1 CT
28273619 GTCAGAGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.47
Consensus pattern (9 bp):
CTTTCAACT
Found at i:28274047 original size:15 final size:15
Alignment explanation
Indices: 28274027--28274061 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
28274017 CTTTGTCAAC
28274027 AGACAAACTCTTATT
1 AGACAAACTCTTATT
28274042 AGACAAACTCTTATT
1 AGACAAACTCTTATT
28274057 AGACA
1 AGACA
28274062 CCATATTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (15 bp):
AGACAAACTCTTATT
Found at i:28278757 original size:179 final size:175
Alignment explanation
Indices: 28278452--28278770 Score: 414
Period size: 179 Copynumber: 1.8 Consensus size: 175
28278442 TGCATCCTCC
* * *
28278452 AATCTTCAATCTTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCTGCTCTTT
1 AATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCTACTCTCT
* * *
28278517 TGCTACCTCAGAGAGATAAAGTCAGTGGCTAAAATTTGTTCCATTGCCAATACATGGAGATAAGA
66 TGCTACCTCAGAGAAATAAAGTCAGTGGCTAAAATCTGCTCCATTGCCAATACATGGAGATAAGA
28278582 TTCACCATCTATGAAGATCTCTCCACTGTAATCTCAGGGAGATAA
131 TTCACCATCTATGAAGATCTCTCCACTGTAATCTCAGGGAGATAA
*
28278627 AATCTTCAAT-TCTCAGTCTGCTTCCTTGCTATCTCAGGAAGATAAGACTCATTCTTCAA-C-CT
1 AATCTTCAATCT-TCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT-A-----CAATCGCT
* * * *
28278689 ACTCTCTTGCTACCTCAGAGAAAT-AAGGCTGGTGGCTAAACTCTGC-CTCATTGCCGATACATG
59 ACTCTCTTGCTACCTCAGAGAAATAAAGTC-AGTGGCTAAAATCTGCTC-CATTGCCAATACATG
*
28278752 GAGATAAGGTTCACCATCT
122 GAGATAAGATTCACCATCT
28278771 GCGATTTGTT
Statistics
Matches: 123, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
174 1 0.01
175 45 0.37
176 1 0.01
178 5 0.04
179 67 0.54
180 1 0.01
181 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (175 bp):
AATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCTACTCTCT
TGCTACCTCAGAGAAATAAAGTCAGTGGCTAAAATCTGCTCCATTGCCAATACATGGAGATAAGA
TTCACCATCTATGAAGATCTCTCCACTGTAATCTCAGGGAGATAA
Found at i:28279127 original size:177 final size:177
Alignment explanation
Indices: 28278883--28279260 Score: 557
Period size: 177 Copynumber: 2.1 Consensus size: 177
28278873 GTTGAGAGAA
*
28278883 ATAAGATCTTCCACAT-TT-AGTCTGCTTCCTTGCTACCTCAAGAAGATAAGACTACAATTGCCA
1 ATAAGATCTT-CA-ATCTTCAGTCTGCTTCCTTGCCACCTCAAGAAGATAAGACTACAATTGCCA
* *
28278946 ACCTGCTCTCTTACTACCTTAGAGAGATAAGGTCAATAGCTAAAATCTGCTCCATTGCCGATACA
64 ACCTGCTCTCTTACTAACTCAGAGAGATAAGGTCAATAGCTAAAATCTGCTCCATTGCCGATACA
28279011 TGGAGATAAGATTCGCCATCCTCGATCCGCTCCACTACTGCTTAGGGAG
129 TGGAGATAAGATTCGCCATCCTCGATCCGCTCCACTACTGCTTAGGGAG
* *
28279060 ATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCCACCTCAGGAAGATAAGACTATC-ATCT-TCA
1 ATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCCACCTCAAGAAGATAAGACTA-CAAT-TGCCA
* * * * *
28279123 ACCTGCTCTCTTGCTAACTCAGAGAGATAAGGTCAGTGGTTAAAATCTGCTCCATTGCTGATACA
64 ACCTGCTCTCTTACTAACTCAGAGAGATAAGGTCAATAGCTAAAATCTGCTCCATTGCCGATACA
* * * *
28279188 TGGAGATAAGATTTGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAG
129 TGGAGATAAGATTCGCCATCCTCGATCCGCTCCACTACTGCTTAGGGAG
28279237 ATAAGATCTTTCAATCTTCAGTCT
1 ATAAGATC-TTCAATCTTCAGTCT
28279261 ACTCCACTGT
Statistics
Matches: 182, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
175 2 0.01
176 4 0.02
177 159 0.87
178 17 0.09
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (177 bp):
ATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCCACCTCAAGAAGATAAGACTACAATTGCCAAC
CTGCTCTCTTACTAACTCAGAGAGATAAGGTCAATAGCTAAAATCTGCTCCATTGCCGATACATG
GAGATAAGATTCGCCATCCTCGATCCGCTCCACTACTGCTTAGGGAG
Found at i:28279136 original size:44 final size:45
Alignment explanation
Indices: 28279057--28279153 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 45
28279047 ACTGCTTAGG
** *
28279057 GAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCCACCTCAG-
1 GAGATAAGATCTTCAATCTTCAACCTGCTTCCTTGCCAACTCAGA
*
28279101 GAAGATAAGA-CTATC-ATCTTCAACCTGC-TCTCTTGCTAACTCAGA
1 G-AGATAAGATCT-TCAATCTTCAACCTGCTTC-CTTGCCAACTCAGA
28279146 GAGATAAG
1 GAGATAAG
28279154 GTCAGTGGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
43 2 0.04
44 32 0.71
45 11 0.24
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (45 bp):
GAGATAAGATCTTCAATCTTCAACCTGCTTCCTTGCCAACTCAGA
Found at i:28279713 original size:64 final size:64
Alignment explanation
Indices: 28279557--28279793 Score: 307
Period size: 62 Copynumber: 3.9 Consensus size: 64
28279547 TTCATGTATC
* * *
28279557 ATGCTTATGCCAACTAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGA--TG
1 ATGCTGATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTG
* * *
28279619 ATGCTGATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAGTGCTCCTAACTAAATGTG
1 ATGCTGATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTG
* * *
28279683 ATGCTTATGTCAAATAATTAGGATGC-----T----ATGAATCAAATGCTTCTAACTAGATGTA
1 ATGCTGATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTG
*
28279738 ATGCTGATATCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAAC
1 ATGCTGATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAAC
28279794 ATGTTATGAA
Statistics
Matches: 150, Mismatches: 14, Indels: 20
0.82 0.08 0.11
Matches are distributed among these distances:
55 48 0.32
59 1 0.01
60 1 0.01
62 54 0.36
64 46 0.31
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (64 bp):
ATGCTGATGTCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTG
Found at i:28279776 original size:55 final size:55
Alignment explanation
Indices: 28279655--28279773 Score: 177
Period size: 55 Copynumber: 2.2 Consensus size: 55
28279645 TATGATCGAA
* * * *
28279655 ATGAATCAAGTGCTCCTAACTAAATGTGATGCTTATGTCAAATAATTAGGATGCT
1 ATGAATCAAATGCTCCTAACTAAATGTAATGCTGATATCAAATAATTAGGATGCT
* *
28279710 ATGAATCAAATGCTTCTAACTAGATGTAATGCTGATATCAAATAATTAGGATGCT
1 ATGAATCAAATGCTCCTAACTAAATGTAATGCTGATATCAAATAATTAGGATGCT
28279765 ATG-ATCAAA
1 ATGAATCAAA
28279774 ATGAATCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 6 0.10
55 52 0.90
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (55 bp):
ATGAATCAAATGCTCCTAACTAAATGTAATGCTGATATCAAATAATTAGGATGCT
Found at i:28279854 original size:15 final size:14
Alignment explanation
Indices: 28279827--28279853 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28279817 CAAAAATGAA
28279827 AATGATCTTTTTTG
1 AATGATCTTTTTTG
28279841 AATGATCTTTTTT
1 AATGATCTTTTTT
28279854 TTTTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59
Consensus pattern (14 bp):
AATGATCTTTTTTG
Found at i:28290962 original size:40 final size:40
Alignment explanation
Indices: 28290918--28291172 Score: 231
Period size: 40 Copynumber: 6.1 Consensus size: 40
28290908 AGTTTCGTTC
* * *
28290918 ATAGCCGAAGCTATCTCAAATCGCACACTAAGTGTCATAT
1 ATAGCCGAAGCTATGTCGAATCGCACACTAAGTGCCATAT
* * * *
28290958 ATAGCTGAAGCTATCTCGATCTCGCACACTAAGTGTCATAT
1 ATAGCCGAAGCTATGTCGA-ATCGCACACTAAGTGCCATAT
* * *
28290999 ATAGCTGAAGCTATGTCGAATCTCACATTAAGTGCCATATAAGTGTCATAT
1 ATAGCCGAAGCTATGTCGAATCGCAC----A----C---TAAGTGCCATAT
*
28291050 ATAGCTGAAGCTATGTCGAATCGCACACTAAGTGCCATAT
1 ATAGCCGAAGCTATGTCGAATCGCACACTAAGTGCCATAT
* * *
28291090 ATAGCCGAAGGTATGTCGAATCGCACACTAAGAGCCATGT
1 ATAGCCGAAGCTATGTCGAATCGCACACTAAGTGCCATAT
** * * *
28291130 ATAATCGAAGCTTTGTTGAATCGCACACTAAGTGCCACAT
1 ATAGCCGAAGCTATGTCGAATCGCACACTAAGTGCCATAT
28291170 ATA
1 ATA
28291173 TATATGATTT
Statistics
Matches: 183, Mismatches: 20, Indels: 24
0.81 0.09 0.11
Matches are distributed among these distances:
40 104 0.57
41 38 0.21
43 1 0.01
44 1 0.01
47 1 0.01
48 1 0.01
51 37 0.20
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (40 bp):
ATAGCCGAAGCTATGTCGAATCGCACACTAAGTGCCATAT
Found at i:28291047 original size:51 final size:51
Alignment explanation
Indices: 28290987--28291090 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
28290977 TCTCGCACAC
* *
28290987 TAAGTGTCATATATAGCTGAAGCTATGTCGAATCTCACATTAAGTGCCATA
1 TAAGTGTCATATATAGCTGAAGCTATGTCGAATCGCACACTAAGTGCCATA
28291038 TAAGTGTCATATATAGCTGAAGCTATGTCGAATCGCACACTAAGTGCCATA
1 TAAGTGTCATATATAGCTGAAGCTATGTCGAATCGCACACTAAGTGCCATA
28291089 TA
1 TA
28291091 TAGCCGAAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (51 bp):
TAAGTGTCATATATAGCTGAAGCTATGTCGAATCGCACACTAAGTGCCATA
Found at i:28291105 original size:91 final size:92
Alignment explanation
Indices: 28290946--28291127 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 92
28290936 AATCGCACAC
* * *
28290946 TAAGTGTCATATATAGCTGAAGCTATCTCGATCTCGCACACTAAGTGTCATATATAGCTGAAGCT
1 TAAGTGTCATATATAGCTGAAGCTATCTCGATATCGCACACTAAGTGCCATATATAGCCGAAGCT
* * *
28291011 ATGTCGAATCTCACATTAAGTGCCATA
66 ATGTCGAATCGCACACTAAGAGCCATA
* *
28291038 TAAGTGTCATATATAGCTGAAGCTATGTCGA-ATCGCACACTAAGTGCCATATATAGCCGAAGGT
1 TAAGTGTCATATATAGCTGAAGCTATCTCGATATCGCACACTAAGTGCCATATATAGCCGAAGCT
28291102 ATGTCGAATCGCACACTAAGAGCCAT
66 ATGTCGAATCGCACACTAAGAGCCAT
28291128 GTATAATCGA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 52 0.63
92 30 0.37
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (92 bp):
TAAGTGTCATATATAGCTGAAGCTATCTCGATATCGCACACTAAGTGCCATATATAGCCGAAGCT
ATGTCGAATCGCACACTAAGAGCCATA
Found at i:28297610 original size:30 final size:30
Alignment explanation
Indices: 28297576--28297632 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
28297566 TAACGTGCTT
28297576 TAATGATTCAGATTTATTTTTAAGATCTAA
1 TAATGATTCAGATTTATTTTTAAGATCTAA
* *
28297606 TAATGATTCTGGTTTATTTTTAAGATC
1 TAATGATTCAGATTTATTTTTAAGATC
28297633 CATTGGATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (30 bp):
TAATGATTCAGATTTATTTTTAAGATCTAA
Found at i:28302474 original size:254 final size:254
Alignment explanation
Indices: 28302015--28302539 Score: 704
Period size: 254 Copynumber: 2.1 Consensus size: 254
28302005 CATTTTACTT
* * *
28302015 TTATACGATTTGAAATAGGCTCTAAGTCCCTATACTTTTTAGACATTTGAAAATTATCCCTACTA
1 TTATACTATTTGAAATAGGCTCTAAGTCCCTATACTTTTCAGACATTTGAAAATTAGCCCTACTA
*
28302080 CTACATTATATAATATTATATCATATCATATCATATAGTATATAATATATTGATAGTTTTTATAT
66 CTA-ATTATATAATATTATATCATATCA-ATCATATA-TATATAATATATTAATAGTTTTTATAT
* * *
28302145 ATGCATCAATGATTAAATATTATAATATCATGTAATTCTATATCTTTTATTGTAATCTATAATAT
128 ATGCATCAATGATTAAACATTATAATATCATGTAATCCTATATCTTTTATTATAATCTATAATAT
28302210 AATAATAGTTATATATAATAGA-AGTAAATTATATATTAATTATTA-ATTATTAATGTTTATTA
193 AATAATAGTTATATATAATA-ATAGTAAATTATATATTAATTATTATA-TATTAATGTTTATTA
* * * * *
28302272 TTATACTATTTGAAATATGCTCTAAGTTCCTATACTTTTCATAGATTTGAAAGTTAGCCCT-CTT
1 TTATACTATTTGAAATAGGCTCTAAGTCCCTATACTTTTCAGACATTTGAAAATTAGCCCTAC-T
*
28302336 ACT-ATTATATAATGTTATATCATATC-AT-ATAT-TATATAATATATTAATAGTTTATATATAT
65 ACTAATTATATAATATTATATCATATCAATCATATATATATAATATATTAATAG-TT-T-T-TAT
* * * * *
28302397 ATATGCATTAATTATTAAACATTATAATATCATGTACTCCTATATTTTTTATTATAATTTATAAT
126 ATATGCATCAATGATTAAACATTATAATATCATGTAATCCTATATCTTTTATTATAATCTATAAT
* * *
28302462 ATAATAATAGTTATATATGATAATAGTACATTATATATTAATTATTATATATTATTGTTTATTA
191 ATAATAATAGTTATATATAATAATAGTAAATTATATATTAATTATTATATATTAATGTTTATTA
*
28302526 TTATATTATATTGA
1 TTATACTAT-TTGA
28302540 TTATTGAATA
Statistics
Matches: 238, Mismatches: 22, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
250 17 0.07
251 2 0.01
252 5 0.02
253 4 0.02
254 125 0.53
255 27 0.11
256 1 0.00
257 57 0.24
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.47
Consensus pattern (254 bp):
TTATACTATTTGAAATAGGCTCTAAGTCCCTATACTTTTCAGACATTTGAAAATTAGCCCTACTA
CTAATTATATAATATTATATCATATCAATCATATATATATAATATATTAATAGTTTTTATATATG
CATCAATGATTAAACATTATAATATCATGTAATCCTATATCTTTTATTATAATCTATAATATAAT
AATAGTTATATATAATAATAGTAAATTATATATTAATTATTATATATTAATGTTTATTA
Found at i:28302484 original size:16 final size:17
Alignment explanation
Indices: 28302455--28302488 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28302445 TTATTATAAT
28302455 TTATAATATAATAATAG
1 TTATAATATAATAATAG
*
28302472 TTAT-ATATGATAATAG
1 TTATAATATAATAATAG
28302488 T
1 T
28302489 ACATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
TTATAATATAATAATAG
Found at i:28302527 original size:20 final size:20
Alignment explanation
Indices: 28302502--28302544 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
28302492 TTATATATTA
*
28302502 ATTATTATA-TATTATTGTTT
1 ATTATTATATTA-TATTGATT
28302522 ATTATTATATTATATTGATT
1 ATTATTATATTATATTGATT
28302542 ATT
1 ATT
28302545 GAATAACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTATTATATTATATTGATT
Found at i:28303617 original size:249 final size:243
Alignment explanation
Indices: 28303143--28303664 Score: 629
Period size: 249 Copynumber: 2.1 Consensus size: 243
28303133 TTCATATAGT
*
28303143 ATATAATATATTAATAGTTTATATATATACGCATCAATGATTAAACATTATAATATAATGTAATA
1 ATATAATATATTAATAGTTTATA-A-ATATGCATCAATGATTAAACATTATAATATAATGTAATA
* * * * *
28303208 TTACATCTTTTATTACATTCTATAATATAATAGTAGTACATTATATATATTAGTTATTATAAAAA
64 TTACATCTTTTATTACAATCTATAATATAATAATAGTACATTATAAATAGTAGTCATTATAAAAA
* * *
28303273 AATATAATATATTATTTTTTATTATTATATGGGTTGAAATATACTCAAGTCCCTATAATTTTTGT
129 AATATAATATATTATTTTTTATTATCATATGAGTTGAAATATACTCAAGTCCCTATAATTTTCGT
* * *
28303338 ACATTTGAAAGTTAATCCTCCTATTATATTACATAATGCTATATCATATC
194 AAATTTGAAAGTTAATCCTCCTACTATATTACATAATGATATATCATATC
* * *
28303388 ATATAATATGTTAATAGTTTATAAATATGCATCAATGATTAAACATTATAATATCATGTAATGTT
1 ATATAATATATTAATAGTTTATAAATATGCATCAATGATTAAACATTATAATATAATGTAATATT
* * * **
28303453 ATATTTTTTAATTATAATCTATAATATAATAATA-TTTA-TATAAATAGTAGTGCATTATATATT
66 ACATCTTTT-ATTACAATCTATAATATAATAATAGTACATTATAAATAGTAGT-CATTATA-A--
* * * * * *
28303516 ACATATTATTACATATATT-TTTTTTATTATCCTACT-AGTTGAAATATGCTCTAAGTCCTTATT
126 A-AAAATA-TA-ATATATTATTTTTTATTATCATA-TGAGTTGAAATATACTC-AAGTCCCTATA
* * *
28303579 ATTTTCGTAAATTTGAAAGTTAGTCCTCTTACTATATTATATAATGATATATCATATC
186 ATTTTCGTAAATTTGAAAGTTAATCCTCCTACTATATTACATAATGATATATCATATC
* *
28303637 ATATAATTTATTAATAGTTTATATATAT
1 ATATAATATATTAATAGTTTATAAATAT
28303665 ACATGCATCA
Statistics
Matches: 235, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
242 11 0.05
243 53 0.23
244 23 0.10
245 22 0.09
246 1 0.00
247 4 0.02
248 28 0.12
249 93 0.40
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (243 bp):
ATATAATATATTAATAGTTTATAAATATGCATCAATGATTAAACATTATAATATAATGTAATATT
ACATCTTTTATTACAATCTATAATATAATAATAGTACATTATAAATAGTAGTCATTATAAAAAAA
TATAATATATTATTTTTTATTATCATATGAGTTGAAATATACTCAAGTCCCTATAATTTTCGTAA
ATTTGAAAGTTAATCCTCCTACTATATTACATAATGATATATCATATC
Found at i:28305440 original size:29 final size:28
Alignment explanation
Indices: 28305399--28305454 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
28305389 CCGAAGTACT
*
28305399 GATATCATGGCCCAAAGTCAAATCAGTC
1 GATATCATGGCCCAAAGCCAAATCAGTC
*
28305427 GATATGCATGGCCCAATGCCAAATCAGT
1 GATAT-CATGGCCCAAAGCCAAATCAGT
28305455 ATAACTCGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (28 bp):
GATATCATGGCCCAAAGCCAAATCAGTC
Found at i:28307074 original size:12 final size:12
Alignment explanation
Indices: 28307057--28307082 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28307047 GTGTTCTTTA
28307057 TTTTATTTTATT
1 TTTTATTTTATT
28307069 TTTTATTTTATT
1 TTTTATTTTATT
28307081 TT
1 TT
28307083 CACAAATTGG
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:28311336 original size:5 final size:5
Alignment explanation
Indices: 28311326--28311353 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28311316 TTACGTGTTC
28311326 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
28311354 CACAGTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:28314723 original size:13 final size:13
Alignment explanation
Indices: 28314705--28314729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28314695 TATGTGATAT
28314705 GTGTGAAAATTTC
1 GTGTGAAAATTTC
28314718 GTGTGAAAATTT
1 GTGTGAAAATTT
28314730 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:28315920 original size:44 final size:42
Alignment explanation
Indices: 28315845--28316006 Score: 139
Period size: 42 Copynumber: 3.8 Consensus size: 42
28315835 CCGATATGTA
* ** *
28315845 ATTTCGTGTGAGACCACATCTGGGACGTTGGCATCGATTTGAG
1 ATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATTT-AG
* *
28315888 ATTTACGTGTAAGACCATGTCTGAGACATTGGCATCG-TATATG
1 ATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGATTTA-G
* * * * *
28315931 ATTTCGTGTAAGACCTTGTTTGGGATAGTGGCATCGATATTTG
1 ATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT-TTAG
* * * *
28315974 ATTACATGTAAGA-CTTGTCTGGGACGTTGGCAT
1 ATTTCGTGTAAGACCATGTCTGGGACATTGGCAT
28316007 TGTACAAGCT
Statistics
Matches: 96, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
42 44 0.46
43 24 0.25
44 28 0.29
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.34
Consensus pattern (42 bp):
ATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATTTAG
Found at i:28321182 original size:25 final size:25
Alignment explanation
Indices: 28321154--28321204 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28321144 AGTTTTAGAA
28321154 AATGAGATATCGGGACCTCGTTTCT
1 AATGAGATATCGGGACCTCGTTTCT
28321179 AATGAGATATCGGGACCTCGTTTCT
1 AATGAGATATCGGGACCTCGTTTCT
28321204 A
1 A
28321205 TAAACTGAGC
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:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (25 bp):
AATGAGATATCGGGACCTCGTTTCT
Found at i:28322495 original size:29 final size:29
Alignment explanation
Indices: 28322296--28322484 Score: 247
Period size: 29 Copynumber: 6.5 Consensus size: 29
28322286 GCATCGATTA
* ** * *
28322296 ATGAAAAGGGATAGTTTCGACTATCGACT
1 ATGAAAAGGGATGGTGACGACCATCAACT
*
28322325 ATGAAAAGGGATGGTGACGACCATCAAAT
1 ATGAAAAGGGATGGTGACGACCATCAACT
28322354 ATGAAAAGGGATGGTGACGACCATC-ACAT
1 ATGAAAAGGGATGGTGACGACCATCAAC-T
* *
28322383 AAGAAAAGGGATGGTGATGACCATCAACT
1 ATGAAAAGGGATGGTGACGACCATCAACT
* *
28322412 TTGAAAAGGGATGGTGACCACCATCGAA-T
1 ATGAAAAGGGATGGTGACGACCATC-AACT
*
28322441 GTGAAAAGGGATGGTGACGACCATCAACT
1 ATGAAAAGGGATGGTGACGACCATCAACT
28322470 ATGAAAAGGGATGGT
1 ATGAAAAGGGATGGT
28322485 TTCGACTATC
Statistics
Matches: 140, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.02
29 133 0.95
30 4 0.03
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.20
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACGACCATCAACT
Found at i:28324324 original size:40 final size:40
Alignment explanation
Indices: 28324253--28324328 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
28324243 TAGTGCCACA
***
28324253 TATAGCCGAAGCTATTCTAATTTGCAAACTAAGTGCTATT
1 TATAGCCGAAGCTATTCTAAAACGCAAACTAAGTGCTATT
*
28324293 TATAGCCGAAGCTA-TCTCAAAACGCACACTAAGTGC
1 TATAGCCGAAGCTATTCT-AAAACGCAAACTAAGTGC
28324329 CAAACATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.10
40 28 0.90
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (40 bp):
TATAGCCGAAGCTATTCTAAAACGCAAACTAAGTGCTATT
Found at i:28332128 original size:53 final size:53
Alignment explanation
Indices: 28331945--28332151 Score: 209
Period size: 53 Copynumber: 3.8 Consensus size: 53
28331935 ATTAGGGTTT
* * * *
28331945 AAGGATACCAAGTAAGACAATGCCAAGGCATGGCATTGGTAAGTT-ATACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCAT--AAGGC
* * * * * * * *
28331999 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGAC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
28332054 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
28332107 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
28332152 TAAAAAGGAA
Statistics
Matches: 122, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
53 45 0.37
54 36 0.30
55 39 0.32
57 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:28339539 original size:55 final size:54
Alignment explanation
Indices: 28339404--28339541 Score: 141
Period size: 55 Copynumber: 2.5 Consensus size: 54
28339394 GTTTAAGGAT
* * * * *
28339404 ACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAGGAA
1 ACCATGTAAGACCATGCCAAGGCATGGCATTGATAACTACTACAAGGCAAAGAA
* * * * * * *
28339458 ATCATGTTAGGCCATGTCAAGACATGGCATTGATAAACTACTATAAGGCAAAGAT
1 ACCATGTAAGACCATGCCAAGGCATGGCATTGAT-AACTACTACAAGGCAAAGAA
* *
28339513 CCCATGTAAGACCCTGCCAAGGCATGGCA
1 ACCATGTAAGACCATGCCAAGGCATGGCA
28339542 ATGGTGAATT
Statistics
Matches: 64, Mismatches: 19, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
54 27 0.42
55 37 0.58
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (54 bp):
ACCATGTAAGACCATGCCAAGGCATGGCATTGATAACTACTACAAGGCAAAGAA
Found at i:28343056 original size:29 final size:29
Alignment explanation
Indices: 28343023--28343112 Score: 146
Period size: 29 Copynumber: 3.1 Consensus size: 29
28343013 TGAGCATGAC
*
28343023 TATAAATGTGAATTGGGCCTGATGGGCCA
1 TATAAATGTGAATTGGGCCTAATGGGCCA
* *
28343052 TATAAATGTGATTTGGGCCTAATGGGTCA
1 TATAAATGTGAATTGGGCCTAATGGGCCA
28343081 TATAAATGTG-ATTGGGCCTAATGGGCCA
1 TATAAATGTGAATTGGGCCTAATGGGCCA
28343109 TATA
1 TATA
28343113 CAGGTATATG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 20 0.36
29 36 0.64
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (29 bp):
TATAAATGTGAATTGGGCCTAATGGGCCA
Found at i:28347016 original size:29 final size:29
Alignment explanation
Indices: 28346982--28347057 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
28346972 TGAGCATGAC
* *
28346982 TATAAATGTGAATTGGGCCGGATGATCCA
1 TATAAATGTGAATTGGGCCGAATGAGCCA
* *
28347011 TATAAATGT-AATTTGGGCCTAATGGGCCA
1 TATAAATGTGAA-TTGGGCCGAATGAGCCA
28347040 TATAAATGTG-ATTGGGCC
1 TATAAATGTGAATTGGGCC
28347058 TAGTAGGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.22
29 32 0.78
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (29 bp):
TATAAATGTGAATTGGGCCGAATGAGCCA
Found at i:28347066 original size:28 final size:29
Alignment explanation
Indices: 28347008--28347071 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
28346998 GCCGGATGAT
*
28347008 CCATATAAATGTAATTTGGGCCTAATGGG
1 CCATATAAATGTAATTTGGGCCTAATAGG
* *
28347037 CCATATAAATGTGA-TTGGGCCTAGTAGG
1 CCATATAAATGTAATTTGGGCCTAATAGG
28347065 CCATATA
1 CCATATA
28347072 CAGGTATGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (29 bp):
CCATATAAATGTAATTTGGGCCTAATAGG
Found at i:28352601 original size:40 final size:40
Alignment explanation
Indices: 28352530--28352605 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
28352520 TAGTGACACA
* *
28352530 TATAGCCGAAGCTATTCTAATTCGCAAACTAAGTGCTATT
1 TATAGCCGAAGCTATTCGAATACGCAAACTAAGTGCTATT
*
28352570 TATAGCCGAAGCTATCTCGAA-ACGCACACTAAGTGC
1 TATAGCCGAAGCTAT-TCGAATACGCAAACTAAGTGC
28352606 CAAACATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (40 bp):
TATAGCCGAAGCTATTCGAATACGCAAACTAAGTGCTATT
Found at i:28364218 original size:22 final size:21
Alignment explanation
Indices: 28364189--28364232 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
28364179 ATCTATAGTT
28364189 ACTCTTTCCCACTTCCACACC
1 ACTCTTTCCCACTTCCACACC
28364210 ANCTCTTTCCCACTTCCACACC
1 A-CTCTTTCCCACTTCCACACC
28364232 A
1 A
28364233 AAATTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.20, C:0.50, G:0.00, T:0.27
Consensus pattern (21 bp):
ACTCTTTCCCACTTCCACACC
Found at i:28367119 original size:20 final size:21
Alignment explanation
Indices: 28367094--28367152 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
28367084 AATGCAAAAA
*
28367094 AATAACATACGT-GTATGCAG
1 AATAACATACGTAGAATGCAG
* *
28367114 AATAACATGCTTAGAATGCAG
1 AATAACATACGTAGAATGCAG
* *
28367135 AATAACATGCTTAGAATG
1 AATAACATACGTAGAATG
28367153 AATCATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 10 0.29
21 25 0.71
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (21 bp):
AATAACATACGTAGAATGCAG
Found at i:28367134 original size:21 final size:21
Alignment explanation
Indices: 28367108--28367152 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
28367098 ACATACGTGT
28367108 ATGCAGAATAACATGCTTAGA
1 ATGCAGAATAACATGCTTAGA
28367129 ATGCAGAATAACATGCTTAGA
1 ATGCAGAATAACATGCTTAGA
28367150 ATG
1 ATG
28367153 AATCATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.24
Consensus pattern (21 bp):
ATGCAGAATAACATGCTTAGA
Found at i:28375520 original size:43 final size:43
Alignment explanation
Indices: 28375453--28375620 Score: 198
Period size: 43 Copynumber: 3.9 Consensus size: 43
28375443 AAAGCTCATA
* * * *
28375453 CAATGCC-ATATCCCAGATATGGTCTTACATGTTACCACAAAT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAAAT
* * * * *
28375495 CGATGCCACTGTCCCAGACAGGGTCTTACACGAAATCACAACA-
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAA-AT
*
28375538 CAATGCCAATGTCCCAGACATGATCTTACATGTAATCAC-AAT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAAAT
*
28375580 ACAATGCCAATGTCCCAGACATGGTTTTACATGTAATCACA
1 -CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
28375621 TCTCGATAAC
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 95 0.91
44 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.24
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAAAT
Found at i:28380132 original size:55 final size:53
Alignment explanation
Indices: 28380045--28380299 Score: 247
Period size: 55 Copynumber: 4.8 Consensus size: 53
28380035 ATTAGGGTTT
* * *
28380045 AAGGATACCATGTAAGACCATGCCAAGGCATGGTAATTGGTATGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGG-AATTGGTA-AGTTTCTAAGGC
* * *
28380100 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTT--TCTAAGGC
** * *
28380155 AAAGG-T-CCTATGTAAGACCATGTCAAGATGTGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACC-ATGTAAGACCATGTCAAGACATGGAATTGGTAAGTTTC-TAAGGC
* *
28380208 GAGGATACCATGTAAGACCATGTCGAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGG-AATTGGTAAGTTTCTAAGGC
* * *
28380257 AAGGATACCATGTAAGACCATGACAAGTCATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAG
28380300 GCACCTGTGT
Statistics
Matches: 169, Mismatches: 21, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
48 2 0.01
49 36 0.21
52 6 0.04
53 37 0.22
54 15 0.09
55 69 0.41
56 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.24
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTTTCTAAGGC
Found at i:28383415 original size:93 final size:93
Alignment explanation
Indices: 28383303--28383473 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
28383293 GCCCCTAAGT
* * *
28383303 GAACTCGGACTCAATTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28383368 CGAGTTTGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
28383396 GAACTCTGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28383461 CGAGTTCGGATGC
66 CGAGTTCGGATGC
28383474 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:28383470 original size:46 final size:46
Alignment explanation
Indices: 28383298--28383470 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
28383288 AACCCGCCCC
* * * *
28383298 TAAGTGAACTCGGACTCAATTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
28383344 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
28383392 TCA-CGAACTCTGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
28383437 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28383471 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 58 0.57
47 27 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:28383930 original size:30 final size:30
Alignment explanation
Indices: 28383896--28383955 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28383886 ATTTAATACG
28383896 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
28383926 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
28383956 GGATCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:28390713 original size:40 final size:40
Alignment explanation
Indices: 28390639--28390777 Score: 185
Period size: 40 Copynumber: 3.5 Consensus size: 40
28390629 AAGTATCTTT
* *
28390639 GGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTC
* **
28390678 GGGTCTTAGCCCGGATATAGTCACTAGCATGAATGCCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
*
28390718 GGGACTTAGCCAGGATATAGTCACTAGCACAAATGCCTTC
1 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
28390758 GGGACTTAGCCCAGG-TATAG
1 GGGACTTAGCCC-GGATATAG
28390778 CAGTGCAAAG
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 7 0.08
40 77 0.89
41 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (40 bp):
GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
Found at i:28395105 original size:37 final size:37
Alignment explanation
Indices: 28395055--28395128 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
28395045 ATCTGATAAG
28395055 TAGGTTTGTAAATATTATATTTAATATTTATGAGTTA
1 TAGGTTTGTAAATATTATATTTAATATTTATGAGTTA
28395092 TAGGTTTGTAAATATTATATTTAATATTTATGAGTTA
1 TAGGTTTGTAAATATTATATTTAATATTTATGAGTTA
28395129 ATTGTGAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (37 bp):
TAGGTTTGTAAATATTATATTTAATATTTATGAGTTA
Found at i:28397480 original size:39 final size:39
Alignment explanation
Indices: 28397436--28397548 Score: 190
Period size: 39 Copynumber: 2.9 Consensus size: 39
28397426 ATGCAAGACA
*
28397436 CTGGAAATGAATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
28397475 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
28397514 CGGGAAATGTATCCGGGTTAAAGTCCCGCAGGCTT
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTT
28397549 TGTATTGGTA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.22, C:0.26, G:0.31, T:0.21
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:28403223 original size:40 final size:40
Alignment explanation
Indices: 28403145--28403360 Score: 276
Period size: 40 Copynumber: 5.3 Consensus size: 40
28403135 ACCCAAGTAT
* *
28403145 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
28403184 CTTCGGGCCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
28403224 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
28403264 CTTCGAGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
28403307 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
28403347 CTTCGGGACTTAGC
1 CTTCGGGACTTAGC
28403361 TCGAATATCA
Statistics
Matches: 154, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 12 0.08
40 106 0.69
41 1 0.01
43 35 0.23
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:28403341 original size:83 final size:80
Alignment explanation
Indices: 28403145--28403360 Score: 283
Period size: 83 Copynumber: 2.7 Consensus size: 80
28403135 ACCCAAGTAT
* * * *
28403145 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGCCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
28403209 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* * * *
28403224 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGCCTTCGAGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
28403288 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
28403307 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGC
28403361 TCGAATATCA
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
79 13 0.11
80 47 0.40
83 58 0.49
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:28413291 original size:55 final size:54
Alignment explanation
Indices: 28413204--28413412 Score: 266
Period size: 55 Copynumber: 3.9 Consensus size: 54
28413194 ATTAGGGTTT
* * * *
28413204 AAGGATACCATGTAAGACCATGCCGAGGCATGGCAATTGGTAAGGTTTGTAAGGA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAA-GTTTATAAGGA
*
28413259 AAGGATACCATGTAAGA-CAGTGTCAAGACATGG-AATTGTTAAGTTACTATAAGGAA
1 AAGGATACCATGTAAGACCA-TGTCAAGACATGGCAATTGGTAAGTT--TATAAGG-A
* * *
28413315 AAGG-TCCCATGTAAGACCATGTCAAGACATGGC-ATTGGTGAGTTCATAAGGA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTATAAGGA
28413367 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTT
28413413 CAAAAGGATA
Statistics
Matches: 134, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
52 5 0.04
53 45 0.34
54 11 0.08
55 66 0.49
56 7 0.05
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTATAAGGA
Found at i:28413410 original size:108 final size:110
Alignment explanation
Indices: 28413211--28413411 Score: 293
Period size: 108 Copynumber: 1.8 Consensus size: 110
28413201 TTTAAGGATA
* * **
28413211 CCATGTAAGACCATGCCGAGGCATGGCAATTGGTAAGGTTTGTAAGGAAAGGATACCATGTAAGA
1 CCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTTCATAAGGAAAGGATACCATGTAAGA
*
28413276 CAGTGTCAAGACATGGAATTGTTAAGTTACTATAAGGAAAAGGTC
66 CAGTGTCAAGACATGGAATTGGTAAGTTACTATAAGGAAAAGGTC
* *
28413321 CCATGTAAGACCATGTCAAGACATGGC-ATTGGTGA-GTTCATAAGGAAAGGATACCATGTAAGA
1 CCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTTCATAAGGAAAGGATACCATGTAAGA
28413384 CCA-TGTCAAGACATGGCAA-TGGTAAGTT
66 -CAGTGTCAAGACATGG-AATTGGTAAGTT
28413412 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
108 47 0.57
109 11 0.13
110 24 0.29
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTTCATAAGGAAAGGATACCATGTAAGA
CAGTGTCAAGACATGGAATTGGTAAGTTACTATAAGGAAAAGGTC
Found at i:28418249 original size:40 final size:40
Alignment explanation
Indices: 28418194--28418371 Score: 263
Period size: 40 Copynumber: 4.5 Consensus size: 40
28418184 CGGATGATAA
* *
28418194 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
28418234 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28418274 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28418314 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
28418354 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28418372 TACTCGGTTT
Statistics
Matches: 128, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
39 17 0.13
40 110 0.86
41 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28422402 original size:33 final size:33
Alignment explanation
Indices: 28422355--28422452 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 33
28422345 CTGACTGCAT
* *
28422355 ACTGTACTAATTCTGTAATGGGCTTAGGCCC-C
1 ACTGTACTAATTCTGAAATGGGCTCAGGCCCAC
*
28422387 ACTGATACTATTTCTGAAATGGGCTCAGGCCCAC
1 ACTG-TACTAATTCTGAAATGGGCTCAGGCCCAC
** * *
28422421 ACTGTTTTTGATTCTGAAATGGGCTAAGGCCC
1 ACTG-TACTAATTCTGAAATGGGCTCAGGCCC
28422453 TAACCGAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 4 0.07
33 24 0.44
34 27 0.49
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (33 bp):
ACTGTACTAATTCTGAAATGGGCTCAGGCCCAC
Found at i:28428970 original size:16 final size:17
Alignment explanation
Indices: 28428944--28428982 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
28428934 AATGAGCAAG
*
28428944 GAAAGAAAGAAGGAAAAA
1 GAAA-AAAGAAAGAAAAA
28428962 -AAAAAAGAAAGAAAAA
1 GAAAAAAGAAAGAAAAA
28428978 GAAAA
1 GAAAA
28428983 GGGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAGAAAAA
Done.