Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 62
Found at i:6475092 original size:2 final size:2
Alignment explanation
Indices: 6475085--6475110 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6475075 TGTGTAAATA
6475085 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6475111 TATGTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6475758 original size:21 final size:21
Alignment explanation
Indices: 6475732--6475774 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6475722 TCAGTAACAA
*
6475732 CACCTCCCCCTCATCCACTTC
1 CACCTCCACCTCATCCACTTC
* *
6475753 CACCTCCACCTTATCCTCTTC
1 CACCTCCACCTCATCCACTTC
6475774 C
1 C
6475775 TGCTCCTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.58, G:0.00, T:0.28
Consensus pattern (21 bp):
CACCTCCACCTCATCCACTTC
Found at i:6479841 original size:20 final size:19
Alignment explanation
Indices: 6479793--6479842 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
6479783 CAACCAATTG
6479793 GTATCGATACCAAGCATCT
1 GTATCGATACCAAGCATCT
* * *
6479812 GATATTGATACCGAGCTTCT
1 G-TATCGATACCAAGCATCT
6479832 AGTATCGATAC
1 -GTATCGATAC
6479843 TAAACCTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (19 bp):
GTATCGATACCAAGCATCT
Found at i:6479970 original size:24 final size:24
Alignment explanation
Indices: 6479919--6479970 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
6479909 ATTTTTAAAG
* * *
6479919 AATTTTTAAGATTATTTTCAATTC
1 AATTTTCAAGATTATATTCAATTA
* *
6479943 AATTTTCAAGTTTATATTCGATTA
1 AATTTTCAAGATTATATTCAATTA
6479967 AATT
1 AATT
6479971 ATTTGAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (24 bp):
AATTTTCAAGATTATATTCAATTA
Found at i:6495201 original size:17 final size:16
Alignment explanation
Indices: 6495170--6495203 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
6495160 CACGTGAGGA
6495170 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
6495186 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
6495203 T
1 T
6495204 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:6498644 original size:27 final size:28
Alignment explanation
Indices: 6498614--6498679 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
6498604 CTTTGATACT
* * *
6498614 TTTGGATATTTGGTTGTTTTTGTTTG-G
1 TTTGGATATTTGGATGTGTTTGTGTGCG
* *
6498641 TTTGGTTATTTGGATGTGTTTGTGTGCT
1 TTTGGATATTTGGATGTGTTTGTGTGCG
6498669 TTTGGATATTT
1 TTTGGATATTT
6498680 TTCCTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.09, C:0.02, G:0.29, T:0.61
Consensus pattern (28 bp):
TTTGGATATTTGGATGTGTTTGTGTGCG
Found at i:6499078 original size:24 final size:23
Alignment explanation
Indices: 6499037--6499081 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
6499027 TTTTAAATAA
*
6499037 ATTTTAAGATTATTTTCGATTTG
1 ATTTTAAGATTATATTCGATTTG
*
6499060 ATTTTCAAGTTTATATTCGATT
1 ATTTT-AAGATTATATTCGATT
6499082 AAATCGTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.56
Consensus pattern (23 bp):
ATTTTAAGATTATATTCGATTTG
Found at i:6500114 original size:22 final size:23
Alignment explanation
Indices: 6500089--6500134 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
6500079 TTTCTTATTG
6500089 TTTTT-ATTTTATT-TCATTCAT
1 TTTTTAATTTTATTATCATTCAT
* *
6500110 TTTTTAATTTTTTTATCTTTCAT
1 TTTTTAATTTTATTATCATTCAT
6500133 TT
1 TT
6500135 ACATTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
23 9 0.43
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTAATTTTATTATCATTCAT
Found at i:6500120 original size:27 final size:29
Alignment explanation
Indices: 6500089--6500143 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
6500079 TTTCTTATTG
*
6500089 TTTTTATTTTATTTCA-TT-CATTTTTTAA
1 TTTTT-TTATATTTCATTTACATTTTTTAA
*
6500117 TTTTTTTATCTTTCATTTACATTTTTT
1 TTTTTTTATATTTCATTTACATTTTTT
6500144 CTTCTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 7 0.30
29 8 0.35
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTTTTTATATTTCATTTACATTTTTTAA
Found at i:6501863 original size:20 final size:20
Alignment explanation
Indices: 6501823--6501864 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6501813 AAAGTAATGA
* * *
6501823 AAGAAATGATTAAATGGAAT
1 AAGAAATGAATAAAAGAAAT
6501843 AAGAAATGAATAAAAGAAAT
1 AAGAAATGAATAAAAGAAAT
6501863 AA
1 AA
6501865 ATTAATGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (20 bp):
AAGAAATGAATAAAAGAAAT
Found at i:6503222 original size:2 final size:2
Alignment explanation
Indices: 6503215--6503246 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6503205 ATATTATAAC
6503215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6503247 AAGATATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6515162 original size:21 final size:21
Alignment explanation
Indices: 6515104--6515185 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 21
6515094 CGCAACTCAG
* *
6515104 TTTCCAAATTCGCATTGCGAA
1 TTTCCAAATTCGCGTTGCGAT
* ** *
6515125 TAT-GTAATTCGCATTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
* *
6515145 TTTCCAGATTCGTGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
6515166 TTTCCAAATTCGCGTTGCGA
1 TTTCCAAATTCGCGTTGCGA
6515186 ATATGTAAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.33
21 32 0.67
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (21 bp):
TTTCCAAATTCGCGTTGCGAT
Found at i:6515874 original size:20 final size:20
Alignment explanation
Indices: 6515811--6515867 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
6515801 GCATTGCGAA
*
6515811 TTTCGCGTTGTGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
6515831 TTTCGCGATGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
6515851 TTTCGCGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
6515868 AAGTTTCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.11, C:0.18, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:6517575 original size:21 final size:21
Alignment explanation
Indices: 6517551--6517590 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6517541 ATGACAATGG
*
6517551 TACTTTACGTGGTGAGGTATC
1 TACTTTACGTGATGAGGTATC
6517572 TACTTTACGTGATGAGGTA
1 TACTTTACGTGATGAGGTA
6517591 GCCGCTCTAC
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:0.23, C:0.12, G:0.28, T:0.38
Consensus pattern (21 bp):
TACTTTACGTGATGAGGTATC
Found at i:6517905 original size:21 final size:20
Alignment explanation
Indices: 6517854--6517905 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
6517844 GACGCACCTG
*
6517854 TCATCATTCAAGAGGCCTCT
1 TCATCATTCAAGAGGCCCCT
* *
6517874 CCTATCGTTCAAGAGGCCCCT
1 TC-ATCATTCAAGAGGCCCCT
*
6517895 ATCATCCTTCA
1 -TCATCATTCA
6517906 TCCCACCGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.23, C:0.35, G:0.13, T:0.29
Consensus pattern (20 bp):
TCATCATTCAAGAGGCCCCT
Found at i:6519400 original size:64 final size:64
Alignment explanation
Indices: 6519317--6519465 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
6519307 AAATTGATGT
* *
6519317 ATTTTTAAAAGTTGATTTGTTTAATTGATGAGAAAATAAGAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGAAAATAAGAATTATTTTTTGCTTGTTTAATTA
* * ***
6519381 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTA
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGAAAATAAGAATTATTTTTTGCTTGTTTAATTA
6519445 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
6519466 GTTTTAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGAAAATAAGAATTATTTTTTGCTTGTTTAATTA
Found at i:6519552 original size:20 final size:20
Alignment explanation
Indices: 6519527--6519609 Score: 112
Period size: 20 Copynumber: 4.2 Consensus size: 20
6519517 GTACACTTTT
*
6519527 GCAACGCGAAAATCAAATTC
1 GCAACGCGAAAGTCAAATTC
6519547 GCAACGCGAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
* *
6519567 GCAACGTGAAAGCCAAATTC
1 GCAACGCGAAAGTCAAATTC
* * *
6519587 ACAACGCGAAAGTTAACTTC
1 GCAACGCGAAAGTCAAATTC
6519607 GCA
1 GCA
6519610 TTGCGATTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (20 bp):
GCAACGCGAAAGTCAAATTC
Found at i:6519721 original size:20 final size:20
Alignment explanation
Indices: 6519669--6519723 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
6519659 AATCGCAACA
*
6519669 CGAATTTGACTTTCACGTTG
1 CGAATTTGACTTTCGCGTTG
*
6519689 CAAATTT-ACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
6519708 CGAATTTGACTTTCGC
1 CGAATTTGACTTTCGC
6519724 AACAATCGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:6519915 original size:18 final size:18
Alignment explanation
Indices: 6519889--6519929 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
6519879 AGGTGAAGCC
*
6519889 GATTGTGATTGAGATTTT
1 GATTTTGATTGAGATTTT
*
6519907 GATTTTGATTGCGATTTT
1 GATTTTGATTGAGATTTT
6519925 GATTT
1 GATTT
6519930 CCTTTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (18 bp):
GATTTTGATTGAGATTTT
Found at i:6522845 original size:16 final size:15
Alignment explanation
Indices: 6522823--6522861 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6522813 GAAATCATTG
6522823 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
6522839 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
6522854 AAAAATTA
1 AAAAATTA
6522862 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:6523050 original size:20 final size:18
Alignment explanation
Indices: 6523004--6523051 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
6522994 CAAAACATTT
6523004 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
6523022 CTATTGCGAAATTAAAATTC
1 GTGTTGCGAAACTAAAA--C
6523042 GTGTTGCGAA
1 GTGTTGCGAA
6523052 TTCGAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 14 0.61
20 9 0.39
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:6523067 original size:20 final size:19
Alignment explanation
Indices: 6523025--6523113 Score: 65
Period size: 20 Copynumber: 4.5 Consensus size: 19
6523015 CTAAAACCTA
*
6523025 TTGCGAAATT-AAAATTCGTG
1 TTGCG-AATTCAAAATT-GAG
6523045 TTGCGAATTCGAAAATTGAG
1 TTGCGAATTC-AAAATTGAG
* * *
6523065 TTGCTACA-ACAAAATTCACG
1 TTGCGA-ATTCAAAATTGA-G
*
6523085 TTGCGAATTCAGAAATCGAG
1 TTGCGAATTCA-AAATTGAG
6523105 TTGCGAATT
1 TTGCGAATT
6523114 TTAAATTCAG
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
19 12 0.22
20 31 0.56
21 12 0.22
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (19 bp):
TTGCGAATTCAAAATTGAG
Found at i:6524621 original size:17 final size:17
Alignment explanation
Indices: 6524599--6524648 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
6524589 AAATTCTTCT
6524599 AACATTCATAGAAATCA
1 AACATTCATAGAAATCA
* *
6524616 AACATTGAT---ACTCA
1 AACATTCATAGAAATCA
*
6524630 AACATTCATAGAAACCA
1 AACATTCATAGAAATCA
6524647 AA
1 AA
6524649 ACATGAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
14 12 0.48
17 13 0.52
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (17 bp):
AACATTCATAGAAATCA
Found at i:6524891 original size:20 final size:20
Alignment explanation
Indices: 6524866--6524903 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6524856 TAATGAACTT
6524866 TTCTCTT-ATATATTATTATG
1 TTCTCTTAATA-ATTATTATG
6524886 TTCTCTTAATAATTATTA
1 TTCTCTTAATAATTATTA
6524904 ATATGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (20 bp):
TTCTCTTAATAATTATTATG
Found at i:6525359 original size:5 final size:5
Alignment explanation
Indices: 6525345--6525380 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
6525335 AAAGGAATGG
*
6525345 ATATA TTATA ATATA ATATA TATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA -ATATA ATATA ATATA
6525381 TATGGATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATATA
Found at i:6525372 original size:16 final size:16
Alignment explanation
Indices: 6525345--6525383 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
6525335 AAAGGAATGG
6525345 ATATAT-TATAATATA
1 ATATATATATAATATA
6525360 ATATATATATAATATA
1 ATATATATATAATATA
6525376 ATATATAT
1 ATATATAT
6525384 GGATAGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATATATATAATATA
Found at i:6542187 original size:2 final size:2
Alignment explanation
Indices: 6542177--6542245 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
6542167 TATATAATTG
*
6542177 AT AT TT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6542218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6542246 TCTTATTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:6542187 original size:15 final size:15
Alignment explanation
Indices: 6542166--6542245 Score: 114
Period size: 14 Copynumber: 5.5 Consensus size: 15
6542156 GAGAATAACA
6542166 ATATATA-ATTGATAT
1 ATATATATATT-ATAT
*
6542181 TTATATATATTATAT
1 ATATATATATTATAT
6542196 ATATATATA-TATAT
1 ATATATATATTATAT
6542210 ATATATATA-TATAT
1 ATATATATATTATAT
6542224 ATATATATA-TATAT
1 ATATATATATTATAT
6542238 ATATATAT
1 ATATATAT
6542246 TCTTATTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
14 41 0.66
15 18 0.29
16 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATATATATATTATAT
Found at i:6546473 original size:23 final size:23
Alignment explanation
Indices: 6546437--6546531 Score: 120
Period size: 23 Copynumber: 4.1 Consensus size: 23
6546427 GGATTCTACA
* *
6546437 TGGTCCTTCAGGACAATTTTATG
1 TGGTCCTTTAGGACAATTCTATG
* *
6546460 TCGTCCTTTGGGACAATTCTATG
1 TGGTCCTTTAGGACAATTCTATG
6546483 TGGTCCTTTAGGACAATTCTATG
1 TGGTCCTTTAGGACAATTCTATG
* *
6546506 TGGTCC-TTCGGAACAAATCTATG
1 TGGTCCTTTAGG-ACAATTCTATG
6546529 TGG
1 TGG
6546532 CACTTCGATG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 4 0.06
23 59 0.94
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (23 bp):
TGGTCCTTTAGGACAATTCTATG
Found at i:6546496 original size:46 final size:46
Alignment explanation
Indices: 6546437--6546531 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 46
6546427 GGATTCTACA
* * * *
6546437 TGGTCCTTCAGGACAATTTTATGTCGTCCTTTGGGACAATTCTATG
1 TGGTCCTTCAGGACAATTCTATGTCGTCCTTCGGAACAAATCTATG
* *
6546483 TGGTCCTTTAGGACAATTCTATGTGGTCCTTCGGAACAAATCTATG
1 TGGTCCTTCAGGACAATTCTATGTCGTCCTTCGGAACAAATCTATG
6546529 TGG
1 TGG
6546532 CACTTCGATG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (46 bp):
TGGTCCTTCAGGACAATTCTATGTCGTCCTTCGGAACAAATCTATG
Found at i:6546537 original size:23 final size:23
Alignment explanation
Indices: 6546495--6546581 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 23
6546485 GTCCTTTAGG
*
6546495 ACAATTCTATGTGGTC-CTTCGGA-
1 ACAAATCTATGTGG-CACTTC-GAT
6546518 ACAAATCTATGTGGCACTTCGAT
1 ACAAATCTATGTGGCACTTCGAT
* * *
6546541 GCATAGTCTATGTGGCACTTCAAT
1 ACA-AATCTATGTGGCACTTCGAT
*
6546565 GCAAATTCTATGTGGCA
1 ACAAA-TCTATGTGGCA
6546582 GTTTCGACTG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
22 3 0.05
23 20 0.36
24 32 0.58
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (23 bp):
ACAAATCTATGTGGCACTTCGAT
Found at i:6546554 original size:24 final size:24
Alignment explanation
Indices: 6546519--6546581 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
6546509 TCCTTCGGAA
*
6546519 CAAA-TCTATGTGGCACTTCGATG
1 CAAAGTCTATGTGGCACTTCAATG
*
6546542 CATAGTCTATGTGGCACTTCAATG
1 CAAAGTCTATGTGGCACTTCAATG
*
6546566 CAAATTCTATGTGGCA
1 CAAAGTCTATGTGGCA
6546582 GTTTCGACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
CAAAGTCTATGTGGCACTTCAATG
Found at i:6551387 original size:39 final size:39
Alignment explanation
Indices: 6551336--6551417 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
6551326 TTAATTAAAG
6551336 AAGTATAATAAAATGTCCAGGTGATCCAACATAACCTTA
1 AAGTATAATAAAATGTCCAGGTGATCCAACATAACCTTA
6551375 AAGTATAATAAAATGTCCAGGTGATCCAACATAACCTTA
1 AAGTATAATAAAATGTCCAGGTGATCCAACATAACCTTA
6551414 AAGT
1 AAGT
6551418 GGCAGCAGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (39 bp):
AAGTATAATAAAATGTCCAGGTGATCCAACATAACCTTA
Found at i:6552319 original size:13 final size:13
Alignment explanation
Indices: 6552301--6552326 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6552291 TTAAGAAAGC
6552301 TTAAAGATGATTA
1 TTAAAGATGATTA
6552314 TTAAAGATGATTA
1 TTAAAGATGATTA
6552327 GAAGCTATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
TTAAAGATGATTA
Found at i:6552911 original size:18 final size:18
Alignment explanation
Indices: 6552884--6552918 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6552874 TACCGAGGTA
*
6552884 GGTACTGAGGTAGGTATC
1 GGTACCGAGGTAGGTATC
6552902 GGTACCGAGGTAGGTAT
1 GGTACCGAGGTAGGTAT
6552919 TGATACCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.40, T:0.26
Consensus pattern (18 bp):
GGTACCGAGGTAGGTATC
Found at i:6552925 original size:18 final size:18
Alignment explanation
Indices: 6552890--6552925 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6552880 GGTAGGTACT
*
6552890 GAGGTAGGTATCGGTACC
1 GAGGTAGGTATCGATACC
*
6552908 GAGGTAGGTATTGATACC
1 GAGGTAGGTATCGATACC
6552926 ATAGAAGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.36, T:0.25
Consensus pattern (18 bp):
GAGGTAGGTATCGATACC
Found at i:6553482 original size:24 final size:24
Alignment explanation
Indices: 6553455--6553504 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
6553445 TTCTATGTGT
* *
6553455 CACTTTGGTGCATAGTCTACATGG
1 CACTTCGGTGCAAAGTCTACATGG
* *
6553479 CACTTCGGTGCAAATTCTACGTGG
1 CACTTCGGTGCAAAGTCTACATGG
6553503 CA
1 CA
6553505 GTTTCAACTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
CACTTCGGTGCAAAGTCTACATGG
Found at i:6562757 original size:32 final size:31
Alignment explanation
Indices: 6562721--6562824 Score: 122
Period size: 31 Copynumber: 3.3 Consensus size: 31
6562711 CGAGAGGAGA
*
6562721 GCCTACCCAAGAAAGTTAT-TCGGGGCCATGGG
1 GCCTACCCAAGAAAG--ATCTCGGGGCCATAGG
*
6562753 GCCTACCCAAGAAAGATCTCGGGGCCGTAGG
1 GCCTACCCAAGAAAGATCTCGGGGCCATAGG
* * *
6562784 GCCTACCCAGGAAAGATCTCGAGGCC-TCGG
1 GCCTACCCAAGAAAGATCTCGGGGCCATAGG
6562814 AGCCTACCCAA
1 -GCCTACCCAA
6562825 CGGTCACCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
30 5 0.08
31 44 0.69
32 15 0.23
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCGGGGCCATAGG
Found at i:6564046 original size:18 final size:18
Alignment explanation
Indices: 6564015--6564103 Score: 133
Period size: 18 Copynumber: 4.9 Consensus size: 18
6564005 GCATAGAATT
*
6564015 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
6564033 TCTCCCGAAAGACCACTG
1 TGTCCCGAAGGACCACTA
6564051 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
6564069 TATCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
6564087 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
6564104 GATAATCCCT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.27, C:0.35, G:0.20, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:6567537 original size:14 final size:14
Alignment explanation
Indices: 6567513--6567568 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
6567503 GGTCAAAGTT
* *
6567513 AATGGGTTGACTCG
1 AATGAGTTGACTCA
*
6567527 AACGAGTTGACTCA
1 AATGAGTTGACTCA
6567541 AATGAGTTGACTCA
1 AATGAGTTGACTCA
6567555 AATGAGTTGACTCA
1 AATGAGTTGACTCA
6567569 GTTCAGGTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (14 bp):
AATGAGTTGACTCA
Found at i:6573068 original size:29 final size:29
Alignment explanation
Indices: 6573035--6573091 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
6573025 TAAAATTGAA
*
6573035 TACTTTAGATACCTATTTTGACCAAAAAG
1 TACTTTAGATACCTATTTTGACAAAAAAG
*
6573064 TACTTTAGATACTTATTTTGACAAAAAA
1 TACTTTAGATACCTATTTTGACAAAAAA
6573092 AAAAGATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (29 bp):
TACTTTAGATACCTATTTTGACAAAAAAG
Found at i:6573573 original size:12 final size:12
Alignment explanation
Indices: 6573556--6573586 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
6573546 CCTTGTCAAC
6573556 CGTCGTCGCATG
1 CGTCGTCGCATG
6573568 CGTCGTCGCATG
1 CGTCGTCGCATG
6573580 CGTCGTC
1 CGTCGTC
6573587 AGGTCACCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.35, G:0.32, T:0.26
Consensus pattern (12 bp):
CGTCGTCGCATG
Found at i:6574693 original size:135 final size:134
Alignment explanation
Indices: 6574438--6574683 Score: 341
Period size: 135 Copynumber: 1.8 Consensus size: 134
6574428 ATTGCTAATT
* * * * *
6574438 TTTTATTTTATTGCCCTTTAACCGTTGTTATTTATTTATTTATTTATTGTTTCTAATATTCACTT
1 TTTTATTTTATTGCACTCTAACCATAGTTATTTATTTATTTATTTATTGTTTCTAATATTCACAT
* * *
6574503 CGACCTTGTGGTGACCTGGTCAGGGGCATGATCCACATTATTATGGCTCAGACTCTTCTAACTAA
66 CGAACTTGTGGTGACCCGATCAGGGGCATGATCCACATTATTATGGCTCAGACTCTTCTAACTAA
6574568 TGAC
131 TGAC
* *
6574572 TTTTATTTTATTGCACTCTAACCATAGTTTATTTATTTATTTATTTATTGTTTTTAATATTTGA-
1 TTTTATTTTATTGCACTCTAACCATAG-TTATTTATTTATTTATTTATTGTTTCTAATA-TTCAC
** * *
6574636 ATCGAACTTGTGGTGACCCGATTTGGTGTATGATCCACATTATTATGG
64 ATCGAACTTGTGGTGACCCGATCAGGGGCATGATCCACATTATTATGG
6574684 TTTGGACTCT
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
134 23 0.24
135 70 0.73
136 3 0.03
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (134 bp):
TTTTATTTTATTGCACTCTAACCATAGTTATTTATTTATTTATTTATTGTTTCTAATATTCACAT
CGAACTTGTGGTGACCCGATCAGGGGCATGATCCACATTATTATGGCTCAGACTCTTCTAACTAA
TGAC
Found at i:6574908 original size:16 final size:15
Alignment explanation
Indices: 6574887--6574958 Score: 69
Period size: 16 Copynumber: 4.8 Consensus size: 15
6574877 TAACTACTAA
6574887 CATTTTAATTTTATTG
1 CATTTTAATTTTA-TG
6574903 CATTTT-A-TTTATG
1 CATTTTAATTTTATG
*
6574916 C-TATTTAACTTTATG
1 CAT-TTTAATTTTATG
*
6574931 CACTTTTAAATTTATG
1 CA-TTTTAATTTTATG
*
6574947 CATTTTTATTTT
1 CATTTTAATTTT
6574959 CTTTATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 1 0.02
13 6 0.12
14 5 0.10
15 16 0.33
16 19 0.40
17 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.60
Consensus pattern (15 bp):
CATTTTAATTTTATG
Found at i:6574922 original size:29 final size:29
Alignment explanation
Indices: 6574890--6574951 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
6574880 CTACTAACAT
*
6574890 TTTAATTTTATTGCA-TTTT-ATTTATGCTA
1 TTTAACTTTA-TGCACTTTTAATTTATGC-A
6574919 TTTAACTTTATGCACTTTTAAATTTATGCA
1 TTTAACTTTATGCACTTTT-AATTTATGCA
6574949 TTT
1 TTT
6574952 TTATTTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.14
29 13 0.45
30 4 0.14
31 8 0.28
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.58
Consensus pattern (29 bp):
TTTAACTTTATGCACTTTTAATTTATGCA
Found at i:6578887 original size:13 final size:12
Alignment explanation
Indices: 6578843--6578880 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
6578833 GCGAGGATAG
6578843 AAAAAAGAGAATA
1 AAAAAAGAGAA-A
*
6578856 AATAAAGAGAAA
1 AAAAAAGAGAAA
6578868 AAAAAA-AGAAA
1 AAAAAAGAGAAA
6578879 AA
1 AA
6578881 GAGAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 7 0.30
12 6 0.26
13 10 0.43
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:6580060 original size:44 final size:44
Alignment explanation
Indices: 6579994--6580080 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
6579984 TCAATGATGG
* *
6579994 ATCCAGAAATGATAAATGTTGGGGGAATTTTGAAGGCCCATATT
1 ATCCAGAAATGATAAATGTTGGGGCAATTTTGAAGACCCATATT
* * *
6580038 ATCCAGAAATGATAAATTTTGGGGCATTTTTTAAGACCCATAT
1 ATCCAGAAATGATAAATGTTGGGGCAATTTTGAAGACCCATAT
6580081 CTTTCAGGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (44 bp):
ATCCAGAAATGATAAATGTTGGGGCAATTTTGAAGACCCATATT
Found at i:6581619 original size:37 final size:36
Alignment explanation
Indices: 6581560--6581799 Score: 186
Period size: 36 Copynumber: 6.7 Consensus size: 36
6581550 GTTTGTCGCC
* * *
6581560 TTTGAGATTGTTTCTCTCGAAACTTAGTTTCGTCTCG
1 TTTGAGATAGTTTCTCTTGAAAC-AAGTTTCGTCTCG
* ** * *
6581597 TTTGAGATAGTTTTTCTTGAAACAAAATT-GATATCA
1 TTTGAGATAGTTTCTCTTGAAACAAGTTTCG-TCTCG
* *
6581633 CTTGAGATTA-TTTCTCTTGAAACAAAGTTTCATCTCG
1 TTTGAGA-TAGTTTCTCTTGAAAC-AAGTTTCGTCTCG
** *
6581670 TTTGAGATAGTTT-TCTTGAAACAAAATT-GATCTCA
1 TTTGAGATAGTTTCTCTTGAAACAAGTTTCG-TCTCG
* *
6581705 CTTGAGATTA-TTTCTCTTGAAACAACTTT-GTCTCG
1 TTTGAGA-TAGTTTCTCTTGAAACAAGTTTCGTCTCG
* * * * *
6581740 CTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCG
1 TTTGAGATAGTTTCTCTTGAAACAAGTTTCGTCTCG
* *
6581776 CTTGAGATAATTTCTCTTGAAACA
1 TTTGAGATAGTTTCTCTTGAAACA
6581800 CAAATCTTTT
Statistics
Matches: 166, Mismatches: 27, Indels: 21
0.78 0.13 0.10
Matches are distributed among these distances:
34 1 0.01
35 47 0.28
36 80 0.48
37 38 0.23
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTGAGATAGTTTCTCTTGAAACAAGTTTCGTCTCG
Found at i:6581651 original size:36 final size:36
Alignment explanation
Indices: 6581592--6581804 Score: 220
Period size: 36 Copynumber: 5.9 Consensus size: 36
6581582 CTTAGTTTCG
* *
6581592 TCTCGTTTGAGA-TAGTTTTTCTTGAAACAAAATTGA
1 TCTCGCTTGAGATTA-TTTCTCTTGAAACAAAATTGA
* * * *
6581628 TATCACTTGAGATTATTTCTCTTGAAACAAAGTTTCA
1 TCTCGCTTGAGATTATTTCTCTTGAAACAAA-ATTGA
*
6581665 TCTCGTTTGAGA-TAGTTT-TCTTGAAACAAAATTGA
1 TCTCGCTTGAGATTA-TTTCTCTTGAAACAAAATTGA
* **
6581700 TCTCACTTGAGATTATTTCTCTTGAAACAACTTTG-
1 TCTCGCTTGAGATTATTTCTCTTGAAACAAAATTGA
** *
6581735 TCTCGCTTGAGACAATTTCTCTTGAAACAAATTTTG-
1 TCTCGCTTGAGATTATTTCTCTTGAAACAAA-ATTGA
*
6581771 TCTCGCTTGAGATAATTTCTCTTGAAACACAAAT
1 TCTCGCTTGAGATTATTTCTCTTGAAACA-AAAT
6581805 CTTTTAGATT
Statistics
Matches: 149, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
35 43 0.29
36 87 0.58
37 19 0.13
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (36 bp):
TCTCGCTTGAGATTATTTCTCTTGAAACAAAATTGA
Found at i:6581717 original size:72 final size:72
Alignment explanation
Indices: 6581561--6581799 Score: 313
Period size: 72 Copynumber: 3.3 Consensus size: 72
6581551 TTTGTCGCCT
* * **
6581561 TTGAGATTGTTTCTCTCGAAACTTAGTTTCGTCTCGTTTGAGATAGTTTTTCTTGAAACAAAATT
1 TTGAGATTATTTCTCTTGAAACAAAGTTTCGTCTCGTTTGAGATAG-TTTTCTTGAAACAAAATT
*
6581626 GATATCAC
65 GATCTCAC
*
6581634 TTGAGATTATTTCTCTTGAAACAAAGTTTCATCTCGTTTGAGATAGTTTTCTTGAAACAAAATTG
1 TTGAGATTATTTCTCTTGAAACAAAGTTTCGTCTCGTTTGAGATAGTTTTCTTGAAACAAAATTG
6581699 ATCTCAC
66 ATCTCAC
* * * * *
6581706 TTGAGATTATTTCTCTTGAAAC-AACTTT-GTCTCGCTTGAGACAATTTCTCTTGAAACAAATTT
1 TTGAGATTATTTCTCTTGAAACAAAGTTTCGTCTCGTTTGAGATAGTTT-TCTTGAAACAAA-AT
*
6581769 TG-TCTCGC
64 TGATCTCAC
*
6581777 TTGAGATAATTTCTCTTGAAACA
1 TTGAGATTATTTCTCTTGAAACA
6581800 CAAATCTTTT
Statistics
Matches: 149, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
70 15 0.10
71 43 0.29
72 50 0.34
73 41 0.28
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (72 bp):
TTGAGATTATTTCTCTTGAAACAAAGTTTCGTCTCGTTTGAGATAGTTTTCTTGAAACAAAATTG
ATCTCAC
Found at i:6582428 original size:65 final size:64
Alignment explanation
Indices: 6582306--6582514 Score: 229
Period size: 65 Copynumber: 3.2 Consensus size: 64
6582296 TTGATCTCAC
* * * * *
6582306 TTGAGATTATTTTTCTCAAAACAAATTTTATCTTACTAGAGACAGACTTCTTTAAGACACAAACA
1 TTGAGATTGTTTTTCTCAAAA-AAAATTTATCTCACTAGAGACAGTCTTCCTTAAGACACAAA-A
6582371 T
64 T
* *
6582372 TTGAGATTGTTTTTCTCAAAAAAAAATTATCTCACTTGAGACAGTCTTCCTTAAGACACAAATAT
1 TTGAGATTGTTTTTCTCAAAAAAAATTTATCTCACTAGAGACAGTCTTCCTTAAGACACAAA-AT
* * * * * * * *
6582437 TTGAGATTGTTCTTCTTAAAAAAAATTTGTCTCGCTAGAGACAATTTTCCCTCAAAACACAAAAT
1 TTGAGATTGTTTTTCTCAAAAAAAATTTATCTCACTAGAGACAGTCTT-CCTTAAGACACAAAAT
*
6582502 TTGGAAATTGTTT
1 TT-GAGATTGTTT
6582515 CACTTAAAAC
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
65 81 0.67
66 40 0.33
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (64 bp):
TTGAGATTGTTTTTCTCAAAAAAAATTTATCTCACTAGAGACAGTCTTCCTTAAGACACAAAAT
Found at i:6582603 original size:67 final size:67
Alignment explanation
Indices: 6582532--6582866 Score: 445
Period size: 67 Copynumber: 5.0 Consensus size: 67
6582522 AACAAAATTG
* * * *
6582532 ATAAACCTTTGATATTTTTTCTCTTAAAACAAAATTTTGTCTCGCTTGAGACATTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAA
6582597 AC
66 AC
* * * * *
6582599 ATAAACTTTTGAGGTTGTTTCTCTCAAAACAAAGTTTTGTTTCGCTTGAGATAATTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAA
*
6582664 AT
66 AC
* * * * *
6582666 ATAAACCTTTCATATTGTTTCTCTCGAAACAAAGTTTTGTCTCACTTGAGACATATTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAA
6582731 AC
66 AC
* * * *
6582733 ATAAACTTTTGAGATTGTTTCTCTCAAAACGAAGTTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAA
6582798 AC
66 AC
* * ** *
6582800 ATAAACCTTTAAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACATTTTTTCCTTGA
1 ATAAACCTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTGAGACATTTTCT-CTTGA
6582865 AA
65 AA
6582867 TGCAAATTTT
Statistics
Matches: 228, Mismatches: 39, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
67 221 0.97
68 7 0.03
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (67 bp):
ATAAACCTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAA
AC
Found at i:6582878 original size:134 final size:134
Alignment explanation
Indices: 6582532--6582866 Score: 490
Period size: 134 Copynumber: 2.5 Consensus size: 134
6582522 AACAAAATTG
* * ** *
6582532 ATAAACCTTTGATATTTTTTCTCTTAAAACAAAATTTTGTCTCGCTTGAGACATTTTCTCTTGAA
1 ATAAACCTTTAATATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAA
* * * *
6582597 ACATAAACTTTTGAGGTTGTTTCTCTCAAAACAAAGTTTTGTTTCGCTTGAGATAATTTCTCTTG
66 ACATAAACTTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTAAGACAATTTCTCTTG
*
6582662 AAAT
131 AAAC
* * *
6582666 ATAAACCTTTCATATTGTTTCTCTCGAAACAAAGTTTTGTCTCACTTGAGACATATTCTCTTGAA
1 ATAAACCTTTAATATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAA
* *
6582731 ACATAAACTTTTGAGATTGTTTCTCTCAAAACGAAGTTTTGTCTCGCTTAAGACAGTTTCTCTTG
66 ACATAAACTTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTAAGACAATTTCTCTTG
6582796 AAAC
131 AAAC
* ** *
6582800 ATAAACCTTTAAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACATTTTTTCCTTGA
1 ATAAACCTTTAATATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACATTTTCT-CTTGA
6582865 AA
65 AA
6582867 TGCAAATTTT
Statistics
Matches: 179, Mismatches: 21, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
134 172 0.96
135 7 0.04
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (134 bp):
ATAAACCTTTAATATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACATTTTCTCTTGAA
ACATAAACTTTTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTAAGACAATTTCTCTTG
AAAC
Found at i:6583309 original size:139 final size:139
Alignment explanation
Indices: 6583059--6583697 Score: 803
Period size: 139 Copynumber: 4.6 Consensus size: 139
6583049 TTGGCAACCA
* * * * *
6583059 ACCAGATCTCCTCAACGCGTAGGAGCAATGTCACCCTCAAACAATCAAACTTCTTCATCACGTAG
1 ACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACGTAG
* * * * *
6583124 AAATCGTGTTGTCTCTAAAGTATCCCTAAAGACGGCTAGACGTCCTCATCATGTAGGAACAATGT
66 GAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGT
*
6583189 CATCCACCG
131 CGTCCACCG
* * * *
6583198 ACCAGATCTCCTCAACACGTAGGAGCAGTGTCATCCTCAGACGATCAGACTTCCTCATTACATAG
1 ACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACGTAG
* * *
6583263 GAACCGTGTTATCTCCAAATTATCCCTAAAGACGGCTAGATGTCCTCATCACATAGGAACAATGT
66 GAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGT
*
6583328 CGTACACCG
131 CGTCCACCG
* * ** * * *
6583337 ACCAAATCTACTCAACGCGTAGGAGCAACGTCATCCTCAGATAACCAGACTTTCTCATCACGTAG
1 ACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACGTAG
* *
6583402 GAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACATCCTTATCACGTAGGAACAATGT
66 GAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGT
6583467 CGTCCACCG
131 CGTCCACCG
* * * * *
6583476 ACCAGATCTCCTCAACGTGTAGGAGCAGCGTCATCCTCAGGCAATCAGATTTCCTCATCGCGTAG
1 ACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACGTAG
* * * *
6583541 GAACCGTGTTGTCTCCAATTTATCCCTAAAGACAGCTAGACGTCCTCAAT-ACGTAGGAATAACG
66 GAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTC-ATCACGTAGGAACAATG
*
6583605 TCGTCTACCG
130 TCGTCCACCG
* * * * ** ** * * * *
6583615 ACCAAATCTCTTCAACGAGAAAAAATAGTGTCATCCTTAGACAATCAGACTTCCTCAACGCTTAG
1 ACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACGTAG
*
6583680 GAACCATGTTGTCTCCAA
66 GAACCGTGTTGTCTCCAA
6583698 CATCATCTCC
Statistics
Matches: 431, Mismatches: 68, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
139 429 1.00
140 2 0.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (139 bp):
ACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACGTAG
GAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGT
CGTCCACCG
Found at i:6585007 original size:137 final size:134
Alignment explanation
Indices: 6584826--6585100 Score: 388
Period size: 137 Copynumber: 2.0 Consensus size: 134
6584816 AATTGTTAAT
* ** *
6584826 TTTTATTTTATTGCACTTTAACTGTTTTTATTTATTTATATATTTATTGTTTCTAATATTCGATT
1 TTTTATTTTATTGCACTCTAACCATTTTTATTTATTTATATATTTATTGTTTCTAATATTCGAAT
* * * * *
6584891 CGACCTTGTGGTGACCCGATCCAGGGTATGATCTACATTATTATGGTTCAGACTTTACTAACTAC
66 CGACATTGTGGTGACCCGATCCAAGGTATGATCCACATTATTATGGTTCAGACTCTACTAACCAC
*
6584956 TGAC
131 TAAC
* * *
6584960 TTTTATTTTTTTGCACTCTAACCATTGTTTATTTATTTATTTTTATTTATTGTTTCTAATATTTG
1 TTTTATTTTATTGCACTCTAACCATT-TTTATTTATTTA--TATATTTATTGTTTCTAATATTCG
* *
6585025 AATCGACATTGTGGTGACCCGATCCAAGGTATGATCCACATTATTATGGTTCGGACTCTGCTAAC
63 AATCGACATTGTGGTGACCCGATCCAAGGTATGATCCACATTATTATGGTTCAGACTCTACTAAC
6585090 CACTAAC
128 CACTAAC
6585097 TTTT
1 TTTT
6585101 TTATATATTT
Statistics
Matches: 123, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
134 22 0.18
135 12 0.10
137 89 0.72
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (134 bp):
TTTTATTTTATTGCACTCTAACCATTTTTATTTATTTATATATTTATTGTTTCTAATATTCGAAT
CGACATTGTGGTGACCCGATCCAAGGTATGATCCACATTATTATGGTTCAGACTCTACTAACCAC
TAAC
Found at i:6587826 original size:2 final size:2
Alignment explanation
Indices: 6587814--6587843 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6587804 TTTATTAAAC
6587814 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6587844 GTCAATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6597297 original size:2 final size:2
Alignment explanation
Indices: 6597290--6597359 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
6597280 TTATGAATTG
6597290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6597332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6597360 GACTTAGGAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6598497 original size:29 final size:28
Alignment explanation
Indices: 6598435--6598500 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
6598425 GAATTAATAT
* *
6598435 AACAATACAAGCTTATAAATTATATAAA
1 AACAATAAAAGCTTATAAATTACATAAA
* *
6598463 ATACAATAAAAGCTTATACATTTACATGAA
1 A-ACAATAAAAGCTTATA-AATTACATAAA
6598493 AACAATAA
1 AACAATAA
6598501 CTCATGATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 22 0.69
30 9 0.28
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (28 bp):
AACAATAAAAGCTTATAAATTACATAAA
Found at i:6604407 original size:2 final size:2
Alignment explanation
Indices: 6604400--6604476 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
6604390 TGCATTATTG
6604400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6604442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6604477 CATCCCTTCA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6604512 original size:25 final size:24
Alignment explanation
Indices: 6604470--6604517 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6604460 TATATATATA
*
6604470 TATATATCATCCCTTCATATCACT
1 TATATATCATCCATTCATATCACT
*
6604494 TATATATCATTCATATCATATCAC
1 TATATATCATCCAT-TCATATCAC
6604518 ATTACATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATATCATCCATTCATATCACT
Found at i:6604669 original size:29 final size:29
Alignment explanation
Indices: 6604620--6604680 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
6604610 AGTCCATTAT
* *
6604620 TCTTTTACTCAACAGTGTTTAACCTTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
6604649 TCTTTTACTCAATAGTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
6604678 TCT
1 TCT
6604681 AACTAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.46
Consensus pattern (29 bp):
TCTTTTACTCAACAGTATTTAACCGTTCA
Found at i:6604732 original size:110 final size:110
Alignment explanation
Indices: 6604570--6604846 Score: 353
Period size: 110 Copynumber: 2.5 Consensus size: 110
6604560 GCTTTTCACT
* * * * * * *
6604570 TAACTTGCATATTTGACACTTTTCTGTCAAATGCACATCTAGTCCATTATTCTTTTACTCAACAG
1 TAACTAGCATAATTAACACATTTCAGTCAATTGCACAACTAGTCCATTATTCTTTTACTCAACAG
* *
6604635 TGTTTAACCTTTCATCTTTTACTCAA-TAGTATTTAACCGTTCATC
66 TGTTTAACCTTTCATCTTTTACTCAACT-GTATTTAACCATTCAGC
* *
6604680 TAACTAGTATAATTAACACCTTTCAGTCAATTGCACAACTAGTCCATTATTCTTTTACTCAACAG
1 TAACTAGCATAATTAACACATTTCAGTCAATTGCACAACTAGTCCATTATTCTTTTACTCAACAG
* *
6604745 TGTTTAACCTTTTATCTTTTACTCAACTGTATTTAATCATTCAGC
66 TGTTTAACCTTTCATCTTTTACTCAACTGTATTTAACCATTCAGC
* * **
6604790 TAACTGGCATAATTTACACATTT-ATGTCAATTGCACAGTTAAG-CCATTATTCTTTTA
1 TAACTAGCATAATTAACACATTTCA-GTCAATTGCACAACT-AGTCCATTATTCTTTTA
6604847 TTTTAGAGCA
Statistics
Matches: 146, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
109 1 0.01
110 142 0.97
111 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (110 bp):
TAACTAGCATAATTAACACATTTCAGTCAATTGCACAACTAGTCCATTATTCTTTTACTCAACAG
TGTTTAACCTTTCATCTTTTACTCAACTGTATTTAACCATTCAGC
Found at i:6605211 original size:79 final size:79
Alignment explanation
Indices: 6605098--6605413 Score: 472
Period size: 79 Copynumber: 4.0 Consensus size: 79
6605088 CAATTATAGC
* * * * *
6605098 ATTCTTTTAGGTTGAT-AGTGCACACATATGCATTTCAACTTTGGCATCCTGTCATGCTAATAAT
1 ATTCTTTTATGTTGATGA-TGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAAT
6605162 GCACCCATATGCATT
65 GCACCCATATGCATT
* * * * * * *
6605177 ATTCTTTTATGCTGATAATGTACCCATGTACATTTCAACTATGACATCATTTCATGCCAATAATG
1 ATTCTTTTATGTTGATGATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATG
6605242 CACCCATATGCATT
66 CACCCATATGCATT
* *
6605256 ATTCTTTTATGTTGATGATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATACCAATAATG
1 ATTCTTTTATGTTGATGATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATG
6605321 CACCCATATGCATT
66 CACCCATATGCATT
* *
6605335 ATTCTTTTATGTTGATGATGCACTCATATGTATTTCAACTATGGCATCCTTTCATGCCAATAATG
1 ATTCTTTTATGTTGATGATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATG
6605400 CACCCATATGCATT
66 CACCCATATGCATT
6605414 TCAGCTATTA
Statistics
Matches: 212, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
79 211 1.00
80 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (79 bp):
ATTCTTTTATGTTGATGATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATG
CACCCATATGCATT
Found at i:6605416 original size:45 final size:45
Alignment explanation
Indices: 6605352--6605447 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
6605342 TATGTTGATG
* * * *
6605352 ATGCACTCATATGTATTTCAACTATGGCATCCTTTCATGCCAATA
1 ATGCACCCATATGCATTTCAACTATGACATCATTTCATGCCAATA
* *
6605397 ATGCACCCATATGCATTTCAGCTATTACATCATTTCATGCCAATA
1 ATGCACCCATATGCATTTCAACTATGACATCATTTCATGCCAATA
6605442 ATGCAC
1 ATGCAC
6605448 ATACAGTGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.33
Consensus pattern (45 bp):
ATGCACCCATATGCATTTCAACTATGACATCATTTCATGCCAATA
Found at i:6606005 original size:94 final size:95
Alignment explanation
Indices: 6605888--6606110 Score: 288
Period size: 95 Copynumber: 2.4 Consensus size: 95
6605878 TGGTTCTTCA
* *
6605888 GTATCGATACTCC-TACCATGGTATCGATACTACTATACTATGGTACCGATACCCCC-TGCGGTA
1 GTATCGATAC-CCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCTTCCGGTA
**
6605951 TCGATACCAATTTTAGACTCGATGTTACCTG
65 TCGATACCAAAATTAGACTCGATGTTACCTG
* * * *
6605982 GTATCGATACCCTTTCCATGGTATCGATACTACCATACTCTTGTATCGATACCCCCTTCCGGTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCTTCCGGTAT
** * *
6606047 CGATACCAAAATTAGGTTCGATGTTGCTTG
66 CGATACCAAAATTAGACTCGATGTTACCTG
* * *
6606077 GTATCAATATCCTTACCAGGGTATCGATACTACC
1 GTATCGATACCCTTACCATGGTATCGATACTACC
6606111 TTGTCGGTAT
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
93 2 0.02
94 48 0.43
95 61 0.55
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCTTCCGGTAT
CGATACCAAAATTAGACTCGATGTTACCTG
Found at i:6614350 original size:18 final size:18
Alignment explanation
Indices: 6614329--6614391 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
6614319 TTCGTCCCGT
6614329 AGGACCACTATGTCCTGA
1 AGGACCACTATGTCCTGA
* *
6614347 AGGACCATTGTATATGTCCTGT
1 AGGACCA----CTATGTCCTGA
*
6614369 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCTGA
6614387 AGGAC
1 AGGAC
6614392 TACTCCTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 20 0.56
22 16 0.44
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (18 bp):
AGGACCACTATGTCCTGA
Found at i:6615992 original size:19 final size:19
Alignment explanation
Indices: 6615968--6616015 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
6615958 TATTATAGGG
**
6615968 ATGCATCGATGCATGACTT
1 ATGCATCGATGCATGACCA
*
6615987 ATGCATCGATGCATTACCA
1 ATGCATCGATGCATGACCA
6616006 ATGCATCGAT
1 ATGCATCGAT
6616016 ACACCTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCATGACCA
Found at i:6617406 original size:19 final size:19
Alignment explanation
Indices: 6617382--6617433 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
6617372 TATACATGAG
6617382 ATATGTGTTACATGTCATC
1 ATATGTGTTACATGTCATC
*
6617401 ATATGTGTTACATGTTATC
1 ATATGTGTTACATGTCATC
6617420 ATATGTGTTACATG
1 ATATGTGTTACATG
6617434 ATCTACGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (19 bp):
ATATGTGTTACATGTCATC
Found at i:6617695 original size:24 final size:24
Alignment explanation
Indices: 6617660--6617716 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
6617650 CATCCGAGAC
*
6617660 ATTTATATGTGGCACTTTAGTGCA
1 ATTTATACGTGGCACTTTAGTGCA
* * * *
6617684 ATTTCTACGTGGTATTTTGGTGCA
1 ATTTATACGTGGCACTTTAGTGCA
6617708 ATTTATACG
1 ATTTATACG
6617717 AGCTGTGGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (24 bp):
ATTTATACGTGGCACTTTAGTGCA
Found at i:6618475 original size:25 final size:25
Alignment explanation
Indices: 6618438--6618486 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
6618428 CACGAATCCA
* **
6618438 TTAAAAAATAAATTTTTAAAAAAAT
1 TTAAAAAAAAAATTTAAAAAAAAAT
6618463 TTAAAAAAAAAATTTAAAAAAAAA
1 TTAAAAAAAAAATTTAAAAAAAAA
6618487 AATCAAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
TTAAAAAAAAAATTTAAAAAAAAAT
Found at i:6618489 original size:14 final size:13
Alignment explanation
Indices: 6618455--6618487 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
6618445 ATAAATTTTT
6618455 AAAAAAATTTAAA
1 AAAAAAATTTAAA
6618468 AAAAAAATTTAAA
1 AAAAAAATTTAAA
6618481 AAAAAAA
1 AAAAAAA
6618488 ATCAAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAATTTAAA
Found at i:6621390 original size:17 final size:18
Alignment explanation
Indices: 6621357--6621390 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6621347 CCGTTACTAG
6621357 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
6621375 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
6621391 GATCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:6622907 original size:15 final size:15
Alignment explanation
Indices: 6622887--6622923 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
6622877 TCCACGTGTT
6622887 TTCTTCTTCTCCCCC
1 TTCTTCTTCTCCCCC
*
6622902 TTCTTCTTCTCCCCT
1 TTCTTCTTCTCCCCC
6622917 TTCTTCT
1 TTCTTCT
6622924 CTTTCTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (15 bp):
TTCTTCTTCTCCCCC
Found at i:6626748 original size:32 final size:31
Alignment explanation
Indices: 6626707--6626779 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
6626697 TAGTTTAACT
* *
6626707 GAAATCAACCCAAACCGAAAGGAATCTGAACC
1 GAAAGCAACCCAAACCGAAAGGAA-CCGAACC
** * *
6626739 GAAAGCAACCTGAACCGAAAGTAACCGAATC
1 GAAAGCAACCCAAACCGAAAGGAACCGAACC
6626770 GAAAGCAACC
1 GAAAGCAACC
6626780 TGAACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 15 0.43
32 20 0.57
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (31 bp):
GAAAGCAACCCAAACCGAAAGGAACCGAACC
Found at i:6626774 original size:15 final size:16
Alignment explanation
Indices: 6626719--6626785 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
6626709 AATCAACCCA
* *
6626719 AACCGAAAGGAATCTG
1 AACCGAAAGCAACCTG
6626735 AACCGAAAGCAACCTG
1 AACCGAAAGCAACCTG
*
6626751 AACCGAAAGTAACC-G
1 AACCGAAAGCAACCTG
*
6626766 AATCGAAAGCAACCTG
1 AACCGAAAGCAACCTG
6626782 AACC
1 AACC
6626786 AAAAATCAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.30
16 31 0.70
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.09
Consensus pattern (16 bp):
AACCGAAAGCAACCTG
Found at i:6626776 original size:31 final size:32
Alignment explanation
Indices: 6626719--6626785 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
6626709 AATCAACCCA
*
6626719 AACCGAAAGGAATCTGAACCGAAAGCAACCTG
1 AACCGAAAGGAATCCGAACCGAAAGCAACCTG
* *
6626751 AACCGAAAGTAA-CCGAATCGAAAGCAACCTG
1 AACCGAAAGGAATCCGAACCGAAAGCAACCTG
6626782 AACC
1 AACC
6626786 AAAAATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.09
Consensus pattern (32 bp):
AACCGAAAGGAATCCGAACCGAAAGCAACCTG
Found at i:6634380 original size:40 final size:40
Alignment explanation
Indices: 6634324--6634422 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 40
6634314 ATAGGAGTCA
* * *
6634324 AATATTGCACAATAGTGCTGAGGTCAAGCCTTGCTTACCT
1 AATAATGCACCATAGTGCTGAGGTCAAGCCTTGCTCACCT
* * * *
6634364 AATAATGCTCTATAGTGTTGAGGTCGAGCCTTGCTCACCT
1 AATAATGCACCATAGTGCTGAGGTCAAGCCTTGCTCACCT
6634404 AATAATGCACCATAGTGCT
1 AATAATGCACCATAGTGCT
6634423 TTGTACCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (40 bp):
AATAATGCACCATAGTGCTGAGGTCAAGCCTTGCTCACCT
Found at i:6636975 original size:29 final size:32
Alignment explanation
Indices: 6636896--6636975 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 32
6636886 CATAATTTTT
*
6636896 AAAA-TTATATTTTAGTC-CTTAAACTTTTCC
1 AAAATTTATATTTTTGTCACTTAAACTTTTCC
* * *
6636926 AAAGTTTATA-CTTTGACCACTT-AAC-TTT-C
1 AAAATTTATATTTTTG-TCACTTAAACTTTTCC
6636955 AAAATTTATATTTTTGTCACT
1 AAAATTTATATTTTTGTCACT
6636976 ATCCAAATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
29 14 0.36
30 13 0.33
31 9 0.23
32 3 0.08
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46
Consensus pattern (32 bp):
AAAATTTATATTTTTGTCACTTAAACTTTTCC
Found at i:6639907 original size:63 final size:63
Alignment explanation
Indices: 6639805--6639941 Score: 247
Period size: 63 Copynumber: 2.2 Consensus size: 63
6639795 TAGATTTTGT
* *
6639805 TGAACCAGTTGAAGAGAAGACCAACCCTAATCCAGCCCCTGAACAACCACCAGATCTCAACAC
1 TGAACCAGTTAAAGAGAAGACCAACCCTAATCCAACCCCTGAACAACCACCAGATCTCAACAC
*
6639868 TGAACTAGTTAAAGAGAAGACCAACCCTAATCCAACCCCTGAACAACCACCAGATCTCAACAC
1 TGAACCAGTTAAAGAGAAGACCAACCCTAATCCAACCCCTGAACAACCACCAGATCTCAACAC
6639931 TGAACCAGTTA
1 TGAACCAGTTA
6639942 TTGACCATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.39, C:0.33, G:0.13, T:0.15
Consensus pattern (63 bp):
TGAACCAGTTAAAGAGAAGACCAACCCTAATCCAACCCCTGAACAACCACCAGATCTCAACAC
Found at i:6643499 original size:45 final size:46
Alignment explanation
Indices: 6643431--6643558 Score: 161
Period size: 45 Copynumber: 2.8 Consensus size: 46
6643421 AGCCTAAACA
* * *
6643431 GAAA-CAACTCGAATTAACTCAAAAATCTAAAGGTTGATCTGAACC
1 GAAACCAACCCGAATTGACCCAAAAATCTAAAGGTTGATCTGAACC
* *
6643476 -AAACCAACCTGAATTGACCCAAAAATCTAAAGGTTGATTTGAACC
1 GAAACCAACCCGAATTGACCCAAAAATCTAAAGGTTGATCTGAACC
** * *
6643521 GAAACCAACCCGAATTGACCTGAAAACCTAAAGCTTGA
1 GAAACCAACCCGAATTGACCCAAAAATCTAAAGGTTGA
6643559 CCCGAATTGA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
44 3 0.04
45 36 0.51
46 32 0.45
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (46 bp):
GAAACCAACCCGAATTGACCCAAAAATCTAAAGGTTGATCTGAACC
Found at i:6643571 original size:46 final size:46
Alignment explanation
Indices: 6643431--6643574 Score: 121
Period size: 46 Copynumber: 3.2 Consensus size: 46
6643421 AGCCTAAACA
* * * * * * *
6643431 GAAA-CAACTCGAATTAACTCAAAAATCTAAAGGTTGATCTGAACC
1 GAAACCAACCCGAATTGACCCAAAAACCTAAAGCTTGACCCGAACC
* * * ***
6643476 -AAACCAACCTGAATTGACCCAAAAATCTAAAGGTTGATTTGAACC
1 GAAACCAACCCGAATTGACCCAAAAACCTAAAGCTTGACCCGAACC
** **
6643521 GAAACCAACCCGAATTGACCTGAAAACCTAAAGCTTGACCCGAATT
1 GAAACCAACCCGAATTGACCCAAAAACCTAAAGCTTGACCCGAACC
6643567 GAAACCAA
1 GAAACCAA
6643575 TCGATTCGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
44 3 0.04
45 36 0.44
46 43 0.52
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (46 bp):
GAAACCAACCCGAATTGACCCAAAAACCTAAAGCTTGACCCGAACC
Found at i:6644860 original size:36 final size:35
Alignment explanation
Indices: 6644819--6644932 Score: 155
Period size: 34 Copynumber: 3.3 Consensus size: 35
6644809 TTTTTAATAC
6644819 TAATATC-TAATACTAAAATATTAAAAACTATATATA
1 TAATATCAT-ATACTAAAATATTAAAAACTATAT-TA
*
6644855 TAATATCATATACTAAAATATTAAAAATTAT-TTA
1 TAATATCATATACTAAAATATTAAAAACTATATTA
6644889 CT-ATATCATATACTAAAATATTAAAAACTAGTATT-
1 -TAATATCATATACTAAAATATTAAAAACTA-TATTA
6644924 TAATATCAT
1 TAATATCAT
6644933 TTTAAAAAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
34 30 0.42
35 10 0.14
36 30 0.42
37 1 0.01
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.39
Consensus pattern (35 bp):
TAATATCATATACTAAAATATTAAAAACTATATTA
Found at i:6644980 original size:41 final size:40
Alignment explanation
Indices: 6644934--6645019 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 40
6644924 TAATATCATT
* *
6644934 TTAAAAAATTATATACTAAAGTCCA-TCATATAATATGTACA
1 TTAAAAAA-TATATACTAAAATACACT-ATATAATATGTACA
* *
6644975 TT-AAAAATATATACTAAAATAGACTTTATAATATGTACA
1 TTAAAAAATATATACTAAAATACACTATATAATATGTACA
6645014 TTAAAA
1 TTAAAA
6645020 CCATATGCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
39 28 0.72
40 9 0.23
41 2 0.05
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (40 bp):
TTAAAAAATATATACTAAAATACACTATATAATATGTACA
Found at i:6652810 original size:95 final size:95
Alignment explanation
Indices: 6652644--6652865 Score: 284
Period size: 95 Copynumber: 2.3 Consensus size: 95
6652634 CGACGAGGTC
* * * * **
6652644 GTATCGATACCATGGTAAGGGTATCAATACCAAGCAACATCGAATTTAAAATTGGTATCGATACC
1 GTATCAATACCATGGTAAGGGTATCGATACTAAGCAACATCAAACCTAAAATTGGTATCGATACC
* *
6652709 AGAAAGGGGTATCGGTACCATAGTATAGTA
66 AGAAAGGGGTATCGGTACCATAATATAGAA
* * *
6652739 GTATCAATACCATGGTAAGGGTATCGATACTAGGCAACTTCAAACCTAAAATTGGTATCGATGCC
1 GTATCAATACCATGGTAAGGGTATCGATACTAAGCAACATCAAACCTAAAATTGGTATCGATACC
**
6652804 TTAAAGGGGTATCGGTACCATAATATAGAA
66 AGAAAGGGGTATCGGTACCATAATATAGAA
* * *
6652834 GTATCAGTACCAGGGT-AGTAGTATCGATACTA
1 GTATCAATACCATGGTAAG-GGTATCGATACTA
6652866 TTGAGCTTGG
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 2 0.02
95 108 0.98
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (95 bp):
GTATCAATACCATGGTAAGGGTATCGATACTAAGCAACATCAAACCTAAAATTGGTATCGATACC
AGAAAGGGGTATCGGTACCATAATATAGAA
Found at i:6653243 original size:58 final size:58
Alignment explanation
Indices: 6653166--6653316 Score: 266
Period size: 58 Copynumber: 2.6 Consensus size: 58
6653156 TGTGCAAAAT
* *
6653166 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTTTGTGCAAAAAGA
1 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCAAAAAGA
6653224 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCAAAAAGA
1 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCAAAAAGA
* *
6653282 TAAGAAATTCATACTAAGGGTAAGAATTTTCGTAT
1 TAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
6653317 GGGAAATATA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 89 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (58 bp):
TAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCAAAAAGA
Found at i:6654482 original size:68 final size:68
Alignment explanation
Indices: 6653531--6654464 Score: 1485
Period size: 68 Copynumber: 13.8 Consensus size: 68
6653521 AAAAGATTAA
* * * *
6653531 AGGCCTAACTATGCATTTGACAGAAAGGTGTTATGTATGCCATTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6653596 TTG
66 TTG
* * * *
6653599 AGGCCTAACTCTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAAATGACAGGCTAAGTGTCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6653664 TTG
66 TTG
* * * * *
6653667 AGGCCTAACTGTGCATTTGACAAAAATGTATCATTTATG-CAGTTAAATGAAAGGCTAAGAGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6653731 TTG
66 TTG
6653734 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6653799 TTG
66 TTG
*
6653802 AGGCCTAACTGTGCATTTGACAGAAAGGTTTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6653867 TTG
66 TTG
* * * * *
6653870 AGGCCTAACTGTTCATTTGACAGAAATGTGTCATTTTTTCCAGTTAGATGAAAGGCTAAATGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6653935 TTG
66 TTG
* * *
6653938 AGGCCTAACTGTGCATTTGACAGAAAGGTGTTATTTATGCCAGTTAGATAAAAGGCTAAGTGTCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6654003 TTG
66 TTG
* * * * *
6654006 AGGCCTAACTGTTCATTTAATAGAAATGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6654071 TTG
66 TTG
* * *
6654074 AGGCCTAACTGTGCATTTGACAGAAAGGTGGCATTTATGCCAGCTAGATGAAAGGCTAAATGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6654139 TTG
66 TTG
6654142 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6654207 TTG
66 TTG
** * * *
6654210 AGGCCTAACTGCACATTTAACAGAAATGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6654275 TTG
66 TTG
*
6654278 AGGCCTAACTGTGCATTTGACAGAAAGGTTTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6654343 TTG
66 TTG
* *
6654346 AGGCCTAACTTTGCATTTGACAG-AAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6654410 TTG
66 TTG
* * *
6654413 AGGCCTAGCTGTGCATTTGACAGAAAGTTGTCAATTATGCCAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
6654465 CAGTTAAGTA
Statistics
Matches: 792, Mismatches: 72, Indels: 4
0.91 0.08 0.00
Matches are distributed among these distances:
67 124 0.16
68 668 0.84
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:6654550 original size:81 final size:80
Alignment explanation
Indices: 6654414--6654651 Score: 341
Period size: 81 Copynumber: 2.9 Consensus size: 80
6654404 GTGCCTTTGA
6654414 GGCCTAGCTGTGCATTTGACAGAAAGTTGTCAATTATGCCAGTTAGATGAACAGTTAAGTACCAT
1 GGCCTAGCTGTGCATTTGACAGAAAG-TGTCAATTATGCCAGTTAGATGAACAGTTAAGTACCAT
6654479 TGAGTAAAATAATAAT
65 TGAGTAAAATAATAAT
* * * *
6654495 GGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAGCAGTTAAGTGCCGT
1 GGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAACAGTTAAGTACCAT
6654560 TGAGTAAAATAATAAT
65 TGAGTAAAATAATAAT
* * * * ** **
6654576 GGCCTAGCTGTGCATTTAACATAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAACACTGT
1 GGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAACAGTTAAGTACCAT
6654641 TGAGTAAAATA
65 TGAGTAAAATA
6654652 TGAATAGTTA
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
81 140 0.99
82 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (80 bp):
GGCCTAGCTGTGCATTTGACAGAAAGTGTCAATTATGCCAGTTAGATGAACAGTTAAGTACCATT
GAGTAAAATAATAAT
Found at i:6655541 original size:19 final size:19
Alignment explanation
Indices: 6655519--6655561 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
6655509 AATTTTACGG
6655519 GTTTTCAAATGATAACTAA
1 GTTTTCAAATGATAACTAA
6655538 GTTTTCAAATGATAACTAA
1 GTTTTCAAATGATAACTAA
6655557 GTTTT
1 GTTTT
6655562 ATAAAGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (19 bp):
GTTTTCAAATGATAACTAA
Found at i:6661592 original size:3 final size:3
Alignment explanation
Indices: 6661573--6661619 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
6661563 GTGATTCCCA
* *
6661573 CTT CTTT CTT TTT CTT CTT CTT -TT CTT CTT CTT CTT CCTC CTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT
6661619 C
1 C
6661620 CTTTGAAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:6661599 original size:17 final size:16
Alignment explanation
Indices: 6661573--6661619 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
6661563 GTGATTCCCA
*
6661573 CTTCTTTCTTTTTCTT
1 CTTCTTTCTTCTTCTT
6661589 CTTCTTTTCTTCTTCTT
1 CTTC-TTTCTTCTTCTT
* *
6661606 CTTCCTCCTTCTTC
1 CTTCTTTCTTCTTC
6661620 CTTTGAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTCTTTCTTCTTCTT
Found at i:6667229 original size:18 final size:20
Alignment explanation
Indices: 6667201--6667237 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6667191 TACCCCCATG
6667201 ATTAGTTTTTTAA-AATTTT
1 ATTAGTTTTTTAATAATTTT
6667220 ATTA-TTTTTTAATAATTT
1 ATTAGTTTTTTAATAATTT
6667238 CACTAGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
ATTAGTTTTTTAATAATTTT
Found at i:6669085 original size:108 final size:109
Alignment explanation
Indices: 6668887--6669087 Score: 235
Period size: 108 Copynumber: 1.9 Consensus size: 109
6668877 GGTAGTTTCT
* * * * ** ** *
6668887 GTTTAAAGCTTATGGGGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTGATTTGTTA
1 GTTTAAAGCTGATGGAGCCTTAGAAACCCGACGATAACAAAATAGGTTAATTACTAAAAATATTA
* ** * ** *
6668952 TCAATATTATCAATATATTAGGTAGCACCTAAAATGTAAGCAAA
66 TCAACACAATCAACATAACAAGTAGCACCTAAAATGTAAGCAAA
6668996 GTTT-AAGCTGATGGAGCCTTAGAAACCCGACGATAACAAAATAGGTTAATTACTAAAAATATTA
1 GTTTAAAGCTGATGGAGCCTTAGAAACCCGACGATAACAAAATAGGTTAATTACTAAAAATATTA
6669060 TCAACCACAAT-AACATAACAAGTAGCAC
66 TCAA-CACAATCAACATAACAAGTAGCAC
6669088 TTATTTAATG
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
108 68 0.91
109 7 0.09
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (109 bp):
GTTTAAAGCTGATGGAGCCTTAGAAACCCGACGATAACAAAATAGGTTAATTACTAAAAATATTA
TCAACACAATCAACATAACAAGTAGCACCTAAAATGTAAGCAAA
Found at i:6669094 original size:226 final size:225
Alignment explanation
Indices: 6668651--6669197 Score: 771
Period size: 226 Copynumber: 2.4 Consensus size: 225
6668641 AATAACATAA
* * *
6668651 AGGTAGCGCCTT-TTTAAAAC-TGAT-GGGTCTTATAAATTTGATGATAACAAAATAGGTTAATT
1 AGGTAGCG-CTTGTTT-AAACTTGATGGGGCCTTAGAAA-TTGACGATAACAAAATAGGTTAATT
* ** *
6668713 ACTTGATTTGTTATCAATATTATCAACATATTAGGTAGCGTCTAAAATGTTACCAAAGTTTAAGC
63 ACTTGATTTGTTATCAATATTATCAATATATTAGGTAGCACCTAAAATGTAACCAAAGTTTAAGC
* * ** *
6668778 TGATGAAGCCTTAGAAATCCGACGATAACAAAAAAGGATAGTTACTCGAAACATTATCAACCATA
128 TGATGAAGCCTTAGAAACCCGACGATAACAAAAAAGGATAATTACTAAAAACATTATCAACCACA
***
6668843 ATAACATAACAAGTAGTGGTTATTTAATGTAAT
193 ATAACATAACAAGTAGCACTTATTTAATGTAAT
**
6668876 AGGTAG-TTTCTGTTTAAAGCTT-ATGGGGCCTTAGAAATCTGACGATAACAAAATAGGTTAATT
1 AGGTAGCGCT-TGTTTAAA-CTTGATGGGGCCTTAGAAAT-TGACGATAACAAAATAGGTTAATT
*
6668939 ACTTGATTTGTTATCAATATTATCAATATATTAGGTAGCACCTAAAATGTAAGCAAAGTTTAAGC
63 ACTTGATTTGTTATCAATATTATCAATATATTAGGTAGCACCTAAAATGTAACCAAAGTTTAAGC
* * * *
6669004 TGATGGAGCCTTAGAAACCCGACGATAACAAAATAGGTTAATTACTAAAAATATTATCAACCACA
128 TGATGAAGCCTTAGAAACCCGACGATAACAAAAAAGGATAATTACTAAAAACATTATCAACCACA
*
6669069 ATAACATAACAAGTAGCACTTATTTAATGTCAT
193 ATAACATAACAAGTAGCACTTATTTAATGTAAT
*
6669102 AGGTAGCGCTTGTTTAAATTTGATGGGGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTAC
1 AGGTAGCGCTTGTTTAAACTTGATGGGGCCTTAGAAATT-GACGATAACAAAATAGGTTAATTAC
*
6669167 TTGATTTGTTTTCAATATTATCAATATATTA
65 TTGATTTGTTATCAATATTATCAATATATTA
6669198 CCATGTGCAT
Statistics
Matches: 286, Mismatches: 27, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
223 1 0.00
224 4 0.01
225 16 0.06
226 264 0.92
227 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (225 bp):
AGGTAGCGCTTGTTTAAACTTGATGGGGCCTTAGAAATTGACGATAACAAAATAGGTTAATTACT
TGATTTGTTATCAATATTATCAATATATTAGGTAGCACCTAAAATGTAACCAAAGTTTAAGCTGA
TGAAGCCTTAGAAACCCGACGATAACAAAAAAGGATAATTACTAAAAACATTATCAACCACAATA
ACATAACAAGTAGCACTTATTTAATGTAAT
Found at i:6669589 original size:76 final size:75
Alignment explanation
Indices: 6669499--6669662 Score: 231
Period size: 76 Copynumber: 2.2 Consensus size: 75
6669489 TAAACTCAAG
*
6669499 TTTAGGATAATATTTTAAACATTATA-TTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATATTATTTT-AACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
*
6669563 TTTTAATTAAGT
64 TTTTAATTAAGA
* * * *
6669575 TTTAGGATATTATTTTTATATTTTATTTTTATCTTTTTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATATTATTTTAACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
*
6669640 TTAATTAGGA
66 TTAATTAAGA
*
6669650 TTTAGAATATTAT
1 TTTAGGATATTAT
6669663 ATTATTATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 36 0.46
76 43 0.54
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTAGGATATTATTTTAACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGA
Found at i:6669604 original size:14 final size:14
Alignment explanation
Indices: 6669584--6669617 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
6669574 TTTTAGGATA
6669584 TTATTTTTAT-ATT
1 TTATTTTTATCATT
*
6669597 TTATTTTTATCTTT
1 TTATTTTTATCATT
6669611 TTATTTT
1 TTATTTT
6669618 AGTTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTTATCATT
Found at i:6669643 original size:75 final size:78
Alignment explanation
Indices: 6669520--6669684 Score: 239
Period size: 76 Copynumber: 2.1 Consensus size: 78
6669510 ATTTTAAACA
* *
6669520 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATAT
1 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
6669585 TAT-TT-TTATATT
66 TATATTATTAT-TT
* *
6669597 TTAT-TTTTATCTTTTTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAATAT
1 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
6669660 TATATTATTATTT
66 TATATTATTATTT
6669673 TTAGGTATTTTA
1 TTA--TATTTTA
6669685 GTTTAAATAG
Statistics
Matches: 79, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
75 30 0.38
76 35 0.44
77 8 0.10
78 1 0.01
79 5 0.06
ACGTcount: A:0.28, C:0.01, G:0.10, T:0.61
Consensus pattern (78 bp):
TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
TATATTATTATTT
Found at i:6670334 original size:17 final size:18
Alignment explanation
Indices: 6670307--6670353 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
6670297 AATCTCTTTA
6670307 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
*
6670326 A-TTTTTATTTAATTCTT
1 ATTTTTTATTTAATTATT
6670343 ATTTTTTATTT
1 ATTTTTTATTT
6670354 CCCTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.54
18 11 0.42
19 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:6677828 original size:76 final size:75
Alignment explanation
Indices: 6677747--6677894 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
6677737 TAAACTCAAA
6677747 TTTAGGATAATATTTTAAACATTATA-TTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
6677811 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * *
6677823 TTTAGGATATTATTTTTATATTTTATTTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
6677888 TTAATTA
66 TTAATTA
6677895 GATTTAGAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 23 0.34
76 44 0.66
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:6677852 original size:14 final size:14
Alignment explanation
Indices: 6677833--6677865 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
6677823 TTTAGGATAT
6677833 TATTTTTATATTT-
1 TATTTTTATATTTG
*
6677846 TATTTTTATCTTTG
1 TATTTTTATATTTG
6677860 TATTTT
1 TATTTT
6677866 AGTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (14 bp):
TATTTTTATATTTG
Found at i:6677922 original size:75 final size:77
Alignment explanation
Indices: 6677768--6677931 Score: 246
Period size: 76 Copynumber: 2.1 Consensus size: 77
6677758 ATTTTAAACA
* *
6677768 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATAT
1 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
6677833 TATTTTTATATT
66 TATTTTTATATT
6677845 TTAT-TTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATT-AGATTTAGAATAT
1 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
6677907 TATATTATTAT-TT
66 TAT-TT-TTATATT
6677920 TTAGGTATTTTA
1 TTA--TATTTTA
6677932 GTTTAAATAG
Statistics
Matches: 80, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
74 14 0.17
75 23 0.29
76 33 0.41
77 5 0.06
78 5 0.06
ACGTcount: A:0.28, C:0.01, G:0.10, T:0.60
Consensus pattern (77 bp):
TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
TATTTTTATATT
Found at i:6678578 original size:16 final size:17
Alignment explanation
Indices: 6678554--6678599 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
6678544 AATCTCTTTA
*
6678554 ATTTGTTTATTTAATT-
1 ATTTTTTTATTTAATTC
6678570 ATTTTTTTATTTAATTC
1 ATTTTTTTATTTAATTC
*
6678587 TTATTTTTTATTT
1 AT-TTTTTTATTT
6678600 TAACCACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 10 0.38
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTTTATTTAATTC
Found at i:6678653 original size:16 final size:16
Alignment explanation
Indices: 6678632--6678662 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6678622 TCCCCCTTTT
6678632 ATATTTATTACTATTA
1 ATATTTATTACTATTA
*
6678648 ATATTTATTATTATT
1 ATATTTATTACTATT
6678663 TTCTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTATTACTATTA
Found at i:6679287 original size:32 final size:32
Alignment explanation
Indices: 6679250--6679313 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
6679240 TAATCGGTTT
6679250 GGGTATCGATACTTTGTACATGTGTATCGATA
1 GGGTATCGATACTTTGTACATGTGTATCGATA
6679282 GGGTATCGATACTTTGTACATGTGTATCGATA
1 GGGTATCGATACTTTGTACATGTGTATCGATA
6679314 CATATAGCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (32 bp):
GGGTATCGATACTTTGTACATGTGTATCGATA
Found at i:6679676 original size:200 final size:198
Alignment explanation
Indices: 6679284--6679897 Score: 763
Period size: 199 Copynumber: 3.1 Consensus size: 198
6679274 TATCGATAGG
* * * *
6679284 GTATCGATACTTTGTACATGTGTATCGATACATAT-AGCGTGCAAATTG-TTGAGAAGCATATTG
1 GTATCGATACTTTGTACATGTGTATCGATACTTTTGA-CATGCAAATTGTTTGAGAAGCATACTG
* * * * * ** * * *
6679347 GACTAAAAGTACCAATACCTATATATAAAGTATCGATACTTGGTATATACACCTATTATCATTAA
65 AAATAAAAGTATCGATACATATATA-AAAGTATCGATACTTTATGTTTACGCCTATTATCATT-A
* * * * * *
6679412 AACCGATAAACTTTTACCCTTTACATTATTAATTTACCTATTACTTTATAGTAATAGG-TTTCAA
128 AACCGGTAGA-TTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTTC-A
6679476 AATTCCAA
191 AATTCCAA
*
6679484 GTATCGATACTTTGTACATGTGTATCGATGCTTTTGACATGCAAATTGTTTGAGAAGCATACTGA
1 GTATCGATACTTTGTACATGTGTATCGATACTTTTGACATGCAAATTGTTTGAGAAGCATACTGA
* *
6679549 AATAAAAGTATCGATACATATATTAAAAGTGTCGATACTTTATGTTTATGCCTATTATCATTAAA
66 AATAAAAGTATCGATACATATA-TAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAA
* * *
6679614 TCGGTCGATTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTTCAAAGT
130 CCGGTAGATTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTTCAAATT
6679679 CCAA
195 CCAA
* * *
6679683 GTATCGATAC-TTGTTATATGTGTATCGATACTTTTTG-CTTGCAAATTGTTTGAGATGCATACT
1 GTATCGATACTTTG-TACATGTGTATCGATAC-TTTTGACATGCAAATTGTTTGAGAAGCATACT
* *
6679746 -AGAATAACAGTATCGATACATATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCTTT
64 GA-AATAAAAGTATCGATACATATATAA-AAGTATCGATACTTTATGTTTACGCCTATTATCATT
* * * *
6679810 AAACCGGTAGATTGTTACCGTTTACATTGTAAATTTACCTATTAATTTAAAGTAATATGTTTTGA
127 AAACCGGTAGATT-TTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTTCA
*
6679875 AATTCAAA
191 AATTCCAA
6679883 GTATCGATACTTTGT
1 GTATCGATACTTTGT
6679898 TGCGGGAAAA
Statistics
Matches: 362, Mismatches: 42, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
198 7 0.02
199 165 0.46
200 122 0.34
201 66 0.18
202 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (198 bp):
GTATCGATACTTTGTACATGTGTATCGATACTTTTGACATGCAAATTGTTTGAGAAGCATACTGA
AATAAAAGTATCGATACATATATAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAAC
CGGTAGATTTTACCATTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTTCAAATTC
CAA
Found at i:6681858 original size:6 final size:6
Alignment explanation
Indices: 6681841--6681877 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
6681831 ATAGTGGAGC
* *
6681841 TCAAAT TGAAAT TTAAAT TCAAAT TCAAAT TCAAAT T
1 TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT T
6681878 GAAAATTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (6 bp):
TCAAAT
Found at i:6687989 original size:192 final size:191
Alignment explanation
Indices: 6687623--6688179 Score: 598
Period size: 192 Copynumber: 2.8 Consensus size: 191
6687613 TATCTTTGTG
* * * * **
6687623 TAAGGTATCGATACTTTCGAAACGTTTTCATTTTTTCATTTCTTTTCAATTCCTAAAGTATTGAT
1 TAAGGTATCGATACTTTTGAGACG---TC-TTTATTCATTTCTTTTCAATTCCTACAGTACCGAT
* * *
6687688 ACTATGGTACATATACTTATAAAAGTATCGATACTATCAACATATCCAATAGCGCTTTACCGGTT
62 ACTTTGGTACATATACTTATAAAAGTATCGATACTATCAACAT-T-CGATAGCTCTTTACCGGTT
* * * *
6687753 TTTTCAGATTGAAATTGGTTTTTTCAGATTTCAACATGTTATATTGTCATGTATTC-ATACATGT
125 TTGTCAAATTGAAATTGGTTTTGTCAAATTTCAACATGTTATATTGTCATGTA-TCGATACATGT
6687817 GTC
189 GTC
* * *
6687820 TAAGGTATCGATACTTTAT-AGGCG-CTATTATTCAATTCTTTTCAATTCCTACAGTACCGACAC
1 TAAGGTATCGATACTTT-TGAGACGTCT-TTATTCATTTCTTTTCAATTCCTACAGTACCGATAC
* * * * * *
6687883 TTTGGTACACATACTTATAAAAGTATCGGTACTGTCAAGACTTCGATATCTCTTTACCGATTTTG
64 TTTGGTACATATACTTATAAAAGTATCGATACTATCAACA-TTCGATAGCTCTTTACCGGTTTTG
* *
6687948 TCAAATTGAAATTGGTTTTGTCAAATTTCAACATGTTATATTGTCATGTATCGATACGTGTGTG
128 TCAAATTGAAATTGGTTTTGTCAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTC
* * *
6688012 TAAGGTATCGATACTTTTGAGACGTTTTCCTTTTTTCATTTCTTTTAAATTCCTACAATACCGAT
1 TAAGGTATCGATACTTTTGAGACG---T-CTTTATTCATTTCTTTTCAATTCCTACAGTACCGAT
* * * * * *
6688077 ACTTTGGTACATATACTTATAAATGTATCAATACAAATTTCAATAATTCAGGTAGCTCTTTACTG
62 ACTTTGGTACATATACTTATAAAAGTATCGATAC---TATCAA-CATTC-GATAGCTCTTTACCG
* * *
6688142 GTTTTGTCAAATTAAAATCGATTTTGTCAAATTTCAAC
122 GTTTTGTCAAATTGAAATTGGTTTTGTCAAATTTCAAC
6688180 CGGTTTTTTT
Statistics
Matches: 302, Mismatches: 43, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
191 3 0.01
192 95 0.31
193 67 0.22
194 1 0.00
196 59 0.20
197 22 0.07
199 8 0.03
200 47 0.16
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (191 bp):
TAAGGTATCGATACTTTTGAGACGTCTTTATTCATTTCTTTTCAATTCCTACAGTACCGATACTT
TGGTACATATACTTATAAAAGTATCGATACTATCAACATTCGATAGCTCTTTACCGGTTTTGTCA
AATTGAAATTGGTTTTGTCAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTC
Found at i:6688186 original size:20 final size:20
Alignment explanation
Indices: 6688141--6688214 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
6688131 GCTCTTTACT
**
6688141 GGTTTTGTCAAATTAAAATC
1 GGTTTTGTCAAATTTCAATC
* *
6688161 GATTTTGTCAAATTTCAACC
1 GGTTTTGTCAAATTTCAATC
**
6688181 GGTTTT-TTTAATTTCTAATC
1 GGTTTTGTCAAATTTC-AATC
*
6688201 GGTTTAGTCAAATT
1 GGTTTTGTCAAATT
6688215 CGTTACTTGT
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
19 7 0.17
20 29 0.71
21 5 0.12
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (20 bp):
GGTTTTGTCAAATTTCAATC
Found at i:6689155 original size:2 final size:2
Alignment explanation
Indices: 6689150--6689228 Score: 57
Period size: 2 Copynumber: 43.5 Consensus size: 2
6689140 TAATGGTGTG
* *
6689150 TA TA TA TA T- TA TA CA TA TA -A TA TA -A TA -A TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
6689188 T- TA TA CA TA TA -A AA TA -A TA -A TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6689226 TA T
1 TA T
6689229 TTTAATTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
1 8 0.13
2 52 0.87
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6689186 original size:32 final size:30
Alignment explanation
Indices: 6689148--6689228 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
6689138 ATTAATGGTG
*
6689148 TGTATATATATTATACATATAATATAATAA
1 TGTATATATATTATACATATAAAATAATAA
6689178 TGTATATATATTATACATATAAAATAATAA
1 TGTATATATATTATACATATAAAATAATAA
*
6689208 TGTATATATATATATATATAT
1 TGTATATATAT-TATACATAT
6689229 TTTAATTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 40 0.83
31 8 0.17
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (30 bp):
TGTATATATATTATACATATAAAATAATAA
Found at i:6689596 original size:46 final size:46
Alignment explanation
Indices: 6689545--6689732 Score: 331
Period size: 46 Copynumber: 4.1 Consensus size: 46
6689535 TAATAAAATA
*
6689545 TTATAATATATATTTCTAAATAATTTTGAGTGATTATAAGGTATAT
1 TTATAATATATATTTCTAAATAATTTCGAGTGATTATAAGGTATAT
6689591 TTATAATATATATTTCTAAATAATTTCGAGTGATTATAAGGTATAT
1 TTATAATATATATTTCTAAATAATTTCGAGTGATTATAAGGTATAT
*
6689637 TTATAATATATATTTCTAAATAATTTCGAGTGATTATAAGTTATAT
1 TTATAATATATATTTCTAAATAATTTCGAGTGATTATAAGGTATAT
* * *
6689683 TTATAATATATATTTCTAAATAATTTTGAGTAATTATAAAGTATAT
1 TTATAATATATATTTCTAAATAATTTCGAGTGATTATAAGGTATAT
6689729 TTAT
1 TTAT
6689733 CTTATAAAAG
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 136 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (46 bp):
TTATAATATATATTTCTAAATAATTTCGAGTGATTATAAGGTATAT
Found at i:6690183 original size:19 final size:19
Alignment explanation
Indices: 6690161--6690197 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6690151 AATAAGGTTC
6690161 TTTTATTAAGATTAAATTA
1 TTTTATTAAGATTAAATTA
6690180 TTTTATTAAGATTAAATT
1 TTTTATTAAGATTAAATT
6690198 CATGTCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTATTAAGATTAAATTA
Found at i:6693948 original size:32 final size:32
Alignment explanation
Indices: 6693911--6694041 Score: 199
Period size: 32 Copynumber: 4.0 Consensus size: 32
6693901 TTTTAGGTTA
* *
6693911 CAACCATATTTTAGGTTGAAATTTGTTTAGTG
1 CAACCATATTTTAGGTTGGAACTTGTTTAGTG
6693943 CAACCATATTTTAGGTTGGAACTTGTTTTAGGTTG
1 CAACCATATTTTAGGTTGGAACTTG-TTTA-G-TG
* *
6693978 GAACCATATTTTAGTTTGGAACTTGTTTAGTG
1 CAACCATATTTTAGGTTGGAACTTGTTTAGTG
6694010 CAACCATATTTTAGGTTGGAACTTGTTTAGTG
1 CAACCATATTTTAGGTTGGAACTTGTTTAGTG
6694042 TTGTATATTT
Statistics
Matches: 90, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
32 55 0.61
33 5 0.06
34 5 0.06
35 25 0.28
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (32 bp):
CAACCATATTTTAGGTTGGAACTTGTTTAGTG
Found at i:6693973 original size:17 final size:17
Alignment explanation
Indices: 6693951--6694037 Score: 81
Period size: 17 Copynumber: 5.2 Consensus size: 17
6693941 TGCAACCATA
6693951 TTTTAGGTTGGAACTTG
1 TTTTAGGTTGGAACTTG
* *
6693968 TTTTAGGTTGGAACCATA
1 TTTTAGGTTGGAA-CTTG
*
6693986 TTTTAGTTTGGAACTTG
1 TTTTAGGTTGGAACTTG
* * *
6694003 -TTTA-G-TGCAACCATA
1 TTTTAGGTTGGAA-CTTG
6694018 TTTTAGGTTGGAACTTG
1 TTTTAGGTTGGAACTTG
6694035 TTT
1 TTT
6694038 AGTGTTGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
14 4 0.08
15 2 0.04
16 8 0.15
17 21 0.40
18 18 0.34
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.46
Consensus pattern (17 bp):
TTTTAGGTTGGAACTTG
Found at i:6693983 original size:67 final size:67
Alignment explanation
Indices: 6693897--6694037 Score: 237
Period size: 67 Copynumber: 2.1 Consensus size: 67
6693887 TAGGAACCTG
*
6693897 CTTGTTTTAGGTTACAACCATATTTTAGGTTGAAATTTGTTTAGTGCAACCATATTTTAGGTTGG
1 CTTGTTTTAGGTTACAACCATATTTTAGGTTGAAACTTGTTTAGTGCAACCATATTTTAGGTTGG
6693962 AA
66 AA
** * *
6693964 CTTGTTTTAGGTTGGAACCATATTTTAGTTTGGAACTTGTTTAGTGCAACCATATTTTAGGTTGG
1 CTTGTTTTAGGTTACAACCATATTTTAGGTTGAAACTTGTTTAGTGCAACCATATTTTAGGTTGG
6694029 AA
66 AA
6694031 CTTGTTT
1 CTTGTTT
6694038 AGTGTTGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.45
Consensus pattern (67 bp):
CTTGTTTTAGGTTACAACCATATTTTAGGTTGAAACTTGTTTAGTGCAACCATATTTTAGGTTGG
AA
Found at i:6694400 original size:40 final size:39
Alignment explanation
Indices: 6694307--6694538 Score: 146
Period size: 40 Copynumber: 5.8 Consensus size: 39
6694297 AATATGAAAG
* * * * *
6694307 TGGTGATATATTGTACAGGATACACACCCAACTAT-AGCA
1 TGGTGATGTATTGTACGGGGTACACACCTAAATATAAG-A
* * *
6694346 AGATGATGTATTGTACGGGGTACACATCTAAATATGAAGA
1 TGGTGATGTATTGTACGGGGTACACACCTAAATAT-AAGA
* * * *
6694386 TGGTGATGTATTGTACAGGATACACACCCAACTATAAGGA
1 TGGTGATGTATTGTACGGGGTACACACCTAAATATAA-GA
* * *** * *
6694426 AGTTGATGTATCAAATGGGGTACACATCTAAATATTAA-A
1 TGGTGATGTATTGTACGGGGTACACACCTAAATA-TAAGA
* * * * *
6694465 GTGATGATGTATTGTACGAGATACACACCCAATTATAAGCAA
1 -TGGTGATGTATTGTACGGGGTACACACCTAAATATAAG--A
* *
6694507 T-GTGATGTATCGTACGGTGTACACACCTAAAT
1 TGGTGATGTATTGTACGGGGTACACACCTAAAT
6694539 TTATAAGTAT
Statistics
Matches: 141, Mismatches: 44, Indels: 15
0.70 0.22 0.08
Matches are distributed among these distances:
39 33 0.23
40 101 0.72
41 6 0.04
42 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (39 bp):
TGGTGATGTATTGTACGGGGTACACACCTAAATATAAGA
Found at i:6694473 original size:80 final size:80
Alignment explanation
Indices: 6694295--6694546 Score: 298
Period size: 80 Copynumber: 3.2 Consensus size: 80
6694285 CTAGAATTTT
* * * **
6694295 TAAATATGAAAGTGGTGATATATTGTACAGGATACACACCCAACTAT-AGCAAGATGATGTATTG
1 TAAATATTAAAGTGGTGATGTATTGTACAGGATACACACCCAACTATAAGCAAGTTGATGTATCA
*
6694359 TACGGGGTACACATC
66 AACGGGGTACACATC
* *
6694374 TAAATA-TGAAGATGGTGATGTATTGTACAGGATACACACCCAACTATAAGGAAGTTGATGTATC
1 TAAATATTAAAG-TGGTGATGTATTGTACAGGATACACACCCAACTATAAGCAAGTTGATGTATC
*
6694438 AAATGGGGTACACATC
65 AAACGGGGTACACATC
* *
6694454 TAAATATTAAAGTGATGATGTATTGTAC-GAGATACACACCCAATTATAAGCAA-TGTGATGTAT
1 TAAATATTAAAGTGGTGATGTATTGTACAG-GATACACACCCAACTATAAGCAAGT-TGATGTAT
** * *
6694517 CGTACGGTGTACACACC
64 CAAACGGGGTACACATC
6694534 TAAAT-TTATAAGT
1 TAAATATTA-AAGT
6694547 ATCAAAATAT
Statistics
Matches: 149, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
78 3 0.02
79 45 0.30
80 97 0.65
81 4 0.03
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (80 bp):
TAAATATTAAAGTGGTGATGTATTGTACAGGATACACACCCAACTATAAGCAAGTTGATGTATCA
AACGGGGTACACATC
Found at i:6698096 original size:20 final size:20
Alignment explanation
Indices: 6698071--6698133 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
6698061 AATGAATCGG
6698071 CTGAAAATCGGTAGAACCGA
1 CTGAAAATCGGTAGAACCGA
*
6698091 CTGAAAATCGATAGAACCGA
1 CTGAAAATCGGTAGAACCGA
* *
6698111 TTGAAAACCGGTTGAGAACCGA
1 CTGAAAATCGG-T-AGAACCGA
6698133 C
1 C
6698134 AAAACTGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 27 0.75
21 1 0.03
22 8 0.22
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.16
Consensus pattern (20 bp):
CTGAAAATCGGTAGAACCGA
Found at i:6698457 original size:12 final size:11
Alignment explanation
Indices: 6698430--6698470 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
6698420 TCGAGACTCG
*
6698430 AGCTCGATTGA
1 AGCTCGATTCA
*
6698441 AGCTCGATTTTA
1 AGCTCGA-TTCA
6698453 AGCTCGATTCA
1 AGCTCGATTCA
6698464 AGCTCGA
1 AGCTCGA
6698471 ATCTTAGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:6703054 original size:20 final size:21
Alignment explanation
Indices: 6703029--6703121 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
6703019 TTTTCCCAAT
*
6703029 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
6703049 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
6703070 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
6703090 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
6703111 TCGCAATGCGA
1 TCGCAATGCGA
6703122 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:6703074 original size:41 final size:41
Alignment explanation
Indices: 6703029--6703121 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
6703019 TTTTCCCAAT
6703029 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
6703070 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
6703111 TCGCAATGCGA
1 TCGCAATGCGA
6703122 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Done.