Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 44 of 255
Found at i:11889774 original size:208 final size:208
Alignment explanation
Indices: 11889514--11890044 Score: 708
Period size: 226 Copynumber: 2.5 Consensus size: 208
11889504 TTTATCCAAG
11889514 CGCCGCTAATACTATGCTTTAACGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGC
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGC
11889579 CAAAATTATGCGTTTTGGTTAAGATATTTTGCT-GCTATTAATATTCTTTAGCGGCGGTTTACCG
66 CAAAATTATGCGTTTTGGTTAAGATATTTTGCTCGCTATTAATATTCTTTAGCGGCGGTTTACCG
11889643 TAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCGTTTTTGTTAAGATATTTTGCGG
131 TAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCG-TTTTGTTAAGATATTTTGCGG
11889708 CGCTAGCTACAAAT
195 CGCTAGCTACAAAT
11889722 CGCCGCTAATACTATGCTTTAACGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGC
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGC
11889787 CAAAATTATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTATTAATATTC
66 CAAAATTATGCGTTTTGGTTAAGATATTTT-----G---CT----------CGCTATTAATATTC
*
11889852 TTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTTT
113 TTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCGTTTT
*
11889917 GTTAAGATATTTTGTGGCGCTAGCTACAAAT
178 GTTAAGATATTTTGCGGCGCTAGCTACAAAT
* * * * * * *
11889948 CGCCGCTAATACTA--CTTTAGCGGCGTTTGACCATATGCGCCACTAGTTCTAGTATAAATCAAG
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCA-C-TAAGCGCCACTAATTCTACTATACATCGAG
* ** * * * *
11890011 ACCAAAACGATGTGTTTCGCTTAAGATAGTTTGC
64 GCCAAAATTATGCGTTTTGGTTAAGATATTTTGC
11890045 GGCGCTTCCA
Statistics
Matches: 286, Mismatches: 16, Indels: 32
0.86 0.05 0.10
Matches are distributed among these distances:
208 95 0.33
213 1 0.00
216 2 0.01
218 1 0.00
221 1 0.00
224 14 0.05
225 1 0.00
226 98 0.34
227 73 0.26
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (208 bp):
CGCCGCTAATACTATGCTTTAACGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGC
CAAAATTATGCGTTTTGGTTAAGATATTTTGCTCGCTATTAATATTCTTTAGCGGCGGTTTACCG
TAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCGTTTTGTTAAGATATTTTGCGGC
GCTAGCTACAAAT
Found at i:11890051 original size:226 final size:224
Alignment explanation
Indices: 11889612--11890161 Score: 719
Period size: 226 Copynumber: 2.4 Consensus size: 224
11889602 ATATTTTGCT
11889612 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
1 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
11889677 AACACTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTT
66 AACACTGCG-TTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTA-GCTTT
* * * ** * *
11889742 AACGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTT
129 AACGGCGTTTCACTAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATGCGTTTCGCTT
*
11889807 AAGATATTTTGCGGCGCTTCTCACAAAGCGCC
194 AAGATAGTTTGCGGCGCTTC-CACAAAGCGCC
11889839 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
1 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
* * *
11889904 AACGCTGCGTTTTGTTAAGATATTTTGTGGCGCTAGCTACAAATCGCCGCTAATACTA-CTTTAG
66 AACACTGCGTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTAGCTTTAA
* * * * *
11889968 CGGCGTTTGACCATATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGATGTGTTTCGCTT
131 CGGCGTTTCA-C-TAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATGCGTTTCGCTT
* *
11890033 AAGATAGTTTGCGGCGCTTCCATAAAGCGTC
194 AAGATAGTTTGCGGCGCTTCCACAAAGCGCC
* * * * * * * * * * *
11890064 GCTATTACTGTACTTTAACGGC-GTTTTCCTATAAACGCCACTAATTCTAAGATACCTCAAGA-C
1 GCTATTAATATTCTTTAGCGGCGGTTTACC-GTAAGCGCCACTAATT-TTATATACATTAAGATC
* * *
11890127 CAAACTCTGCGTTTTGGTTAAGCTATTTTGCGGCG
64 AAAACACTGCGTTTT-GTTAAGATATTTTGCGGCG
11890162 TTTCCAGAAA
Statistics
Matches: 285, Mismatches: 33, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
224 20 0.07
225 56 0.20
226 136 0.48
227 73 0.26
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (224 bp):
GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
AACACTGCGTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTAGCTTTAA
CGGCGTTTCACTAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATGCGTTTCGCTTAA
GATAGTTTGCGGCGCTTCCACAAAGCGCC
Found at i:11890088 original size:114 final size:113
Alignment explanation
Indices: 11889612--11890275 Score: 571
Period size: 113 Copynumber: 5.9 Consensus size: 113
11889602 ATATTTTGCT
* * * * * * *
11889612 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTA-TATACATTAAGATCA
1 GCTATTACTATACTTTAACGGC-GTTTACCATAAGCGCCACTAATTCTAGTATACATCAAGACCA
* * * *
11889676 AAAC-ACTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCC
65 AAACGA-TGCGTTTTGGTTAAGATATTTTGCGGCGCT-TCCACAAAGCGCC
* * * * *
11889726 GCTAATACTATGCTTTAACGGCGTTT--CACTAAGCGCCACTAATTCTACTATACATCGAGGCCA
1 GCTATTACTATACTTTAACGGCGTTTACCA-TAAGCGCCACTAATTCTAGTATACATCAAGACCA
**
11889789 AAATTATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCC
65 AAACGATGCGTTTTGGTTAAGATATTTTGCGGCGCTTC-CACAAAGCGCC
* * * * * * *
11889839 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTA-TATACATTAAGATCA
1 GCTATTACTATACTTTAACGGC-GTTTACCATAAGCGCCACTAATTCTAGTATACATCAAGACCA
* * * * *
11889903 AAACGCTGCGTTTT-GTTAAGATATTTTGTGGCGCTAGCTACAAATCGCC
65 AAACGATGCGTTTTGGTTAAGATATTTTGCGGCGCT-TCCACAAAGCGCC
* * * * *
11889952 GCTAATAC--TACTTTAGCGGCGTTTGACCATATGCGCCACTAGTTCTAGTATAAATCAAGACCA
1 GCTATTACTATACTTTAACGGCGTTT-ACCATAAGCGCCACTAATTCTAGTATACATCAAGACCA
* * * * * *
11890015 AAACGATGTGTTTCGCTTAAGATAGTTTGCGGCGCTTCCATAAAGCGTC
65 AAACGATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCCACAAAGCGCC
* * * *
11890064 GCTATTACTGTACTTTAACGGCGTTTTCCTATAAACGCCACTAATTCTAAG-ATACCTCAAGACC
1 GCTATTACTATACTTTAACGGCGTTTACC-ATAAGCGCCACTAATTCT-AGTATACATCAAGACC
** * * *
11890128 -AAACTCTGCGTTTTGGTTAAGCTATTTTGCGGCGTTTCCAGAAAGCGCC
64 AAAACGATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCCACAAAGCGCC
* * * * * * * *
11890177 GCTATTACTGTCCTTTAATGGCGTTT-CGCGTAAACGCCACTACTTTTAAG-ATACATCAAGACG
1 GCTATTACTATACTTTAACGGCGTTTAC-CATAAGCGCCACTAATTCT-AGTATACATCAAGACC
* * *
11890240 AAAAC-ACAGCGTTTTGGTTAAGAGATTTCGCGGCGC
64 AAAACGA-TGCGTTTTGGTTAAGATATTTTGCGGCGC
11890276 ATTGTGGTAA
Statistics
Matches: 448, Mismatches: 84, Indels: 37
0.79 0.15 0.07
Matches are distributed among these distances:
110 4 0.01
111 30 0.07
112 86 0.19
113 221 0.49
114 87 0.19
115 19 0.04
116 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (113 bp):
GCTATTACTATACTTTAACGGCGTTTACCATAAGCGCCACTAATTCTAGTATACATCAAGACCAA
AACGATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCCACAAAGCGCC
Found at i:11890217 original size:226 final size:225
Alignment explanation
Indices: 11889612--11890244 Score: 650
Period size: 226 Copynumber: 2.8 Consensus size: 225
11889602 ATATTTTGCT
* * * * * * *
11889612 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
1 GCTATTAATATACTTTAACGGCGGTTTACCATAAACGCCACTAATTTAAGATACATCAAGATCAA
*
11889677 AACACTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTT
66 AACACTGCG-TTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACT-TACTTT
* * * * ** * *
11889742 AACGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTT
129 AACGGCGTTTCGCTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTCGCTT
*
11889807 AAGATATTTTGCGGCGCTTCTCACAAAGCGCC
194 AAGATAGTTTGCGGCGCTTCTCACAAAGCGCC
* * * * * * *
11889839 GCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAA
1 GCTATTAATATACTTTAACGGCGGTTTACCATAAACGCCACTAATTTAAGATACATCAAGATCAA
* * *
11889904 AACGCTGCGTTTTGTTAAGATATTTTGTGGCGCTAGCTACAAATCGCCGCTAATAC-TACTTTAG
66 AACACTGCGTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTTACTTTAA
* * * *
11889968 CGGCGTTT-GACCATATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGATGTGTTTCGCT
131 CGGCGTTTCG--C-TAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTCGCT
* *
11890032 TAAGATAGTTTGCGGCGCTTC-CATAAAGCGTC
193 TAAGATAGTTTGCGGCGCTTCTCACAAAGCGCC
* * * *
11890064 GCTATTACTGTACTTTAACGGC-GTTTTCCTATAAACGCCACTAATTCTAAGATACCTCAAGA-C
1 GCTATTAATATACTTTAACGGCGGTTTACC-ATAAACGCCACTAATT-TAAGATACATCAAGATC
* * * ** * * * * *
11890127 CAAACTCTGCGTTTTGGTTAAGCTATTTTGCGGCG-TTTCCAGAAAGCGCCGCTATTACTGTCCT
64 AAAACACTGCGTTTT-GTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACT-TACT
* * * * *
11890191 TTAATGGCGTTTCGCGTAAACGCCACTACTTTTAAG-ATACATCAAGACGAAAAC
127 TTAACGGCGTTTCGC-TAAGCGCCACTAATTCT-AGTATACATCAAGACCAAAAC
11890245 ACAGCGTTTT
Statistics
Matches: 346, Mismatches: 50, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
224 20 0.06
225 73 0.21
226 164 0.47
227 88 0.25
228 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (225 bp):
GCTATTAATATACTTTAACGGCGGTTTACCATAAACGCCACTAATTTAAGATACATCAAGATCAA
AACACTGCGTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTTACTTTAA
CGGCGTTTCGCTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTCGCTTAA
GATAGTTTGCGGCGCTTCTCACAAAGCGCC
Found at i:11890254 original size:338 final size:339
Alignment explanation
Indices: 11889624--11890267 Score: 752
Period size: 338 Copynumber: 1.9 Consensus size: 339
11889614 TATTAATATT
* * * * *
11889624 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACACTGCGTTT
1 CTTTAGCGGCGGTTTACCATAAGCGCCACTAATTCTATATAAATCAAGACCAAAACACTGCGTTT
* * * * *
11889689 TTGTTAAGATATTTTGCGGCGCTAGCTACAAATCGCCGCTAATACTATGCTTTAACGGCGTTTCA
66 TCGTTAAGATAGTTTGCGGCGCTAGCCACAAAGCGCCGCTAATACTATACTTTAACGGCGTTTCA
* ** * * *
11889754 CTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTTTGC
131 CTAAACGCCACTAATTCTAAGATACATCAAGACCAAAACTATGCGTTTTGGTTAAGATATTTTGC
* * *
11889819 GGCGCTTCTCACAAAGCGCCGCTATTAATATTCTTTAGCGGCGGTTTACCGTAAGCGCCACTAAT
196 GGCGCTTCTCACAAAGCGCCGCTATTAATATCCTTTAACGGCGGTTTACCGTAAACGCCACTAAT
* * * * *
11889884 TTTATATACATTAAGATCAAAACGCTGCGTTTT-GTTAAGATATTTTGTGGCGCTAGCTACAAAT
261 TTTAGATACATCAAGATCAAAACACAGCGTTTTGGTTAAGAGATTTTGTGGCGCTAGCTACAAAT
11889948 CGCCGCTAATACTA
326 CGCCGCTAATACTA
* * *
11889962 CTTTAGCGGC-GTTTGACCATATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGA-TGTG
1 CTTTAGCGGCGGTTT-ACCATAAGCGCCACTAATTCTA-TATAAATCAAGACCAAAAC-ACTGCG
* * * * *
11890025 -TTTCGCTTAAGATAGTTTGCGGCGCT-TCCATAAAGCGTCGCTATTACTGTACTTTAACGGCGT
63 TTTTCG-TTAAGATAGTTTGCGGCGCTAGCCACAAAGCGCCGCTAATACTATACTTTAACGGCG-
* * *
11890088 TTTC-CTATAAACGCCACTAATTCTAAGATACCTCAAGACC-AAACTCTGCGTTTTGGTTAAGCT
126 TTTCAC--TAAACGCCACTAATTCTAAGATACATCAAGACCAAAACTATGCGTTTTGGTTAAGAT
* * * * *
11890151 ATTTTGCGGCGTTTC-CAGAAAGCGCCGCTATTACTGTCCTTTAATGGC-GTTT-CGCGTAAACG
189 ATTTTGCGGCGCTTCTCACAAAGCGCCGCTATTAATATCCTTTAACGGCGGTTTAC-CGTAAACG
*
11890213 CCACTACTTTTAAGATACATCAAGA-CGAAAACACAGCGTTTTGGTTAAGAGATTT
253 CCACTAATTTT-AGATACATCAAGATC-AAAACACAGCGTTTTGGTTAAGAGATTT
11890268 CGCGGCGCAT
Statistics
Matches: 254, Mismatches: 41, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
336 1 0.00
337 26 0.10
338 112 0.44
339 87 0.34
340 28 0.11
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (339 bp):
CTTTAGCGGCGGTTTACCATAAGCGCCACTAATTCTATATAAATCAAGACCAAAACACTGCGTTT
TCGTTAAGATAGTTTGCGGCGCTAGCCACAAAGCGCCGCTAATACTATACTTTAACGGCGTTTCA
CTAAACGCCACTAATTCTAAGATACATCAAGACCAAAACTATGCGTTTTGGTTAAGATATTTTGC
GGCGCTTCTCACAAAGCGCCGCTATTAATATCCTTTAACGGCGGTTTACCGTAAACGCCACTAAT
TTTAGATACATCAAGATCAAAACACAGCGTTTTGGTTAAGAGATTTTGTGGCGCTAGCTACAAAT
CGCCGCTAATACTA
Found at i:11890443 original size:12 final size:12
Alignment explanation
Indices: 11890426--11890452 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11890416 TTAGTCCCTA
11890426 ACACATAGGAAC
1 ACACATAGGAAC
11890438 ACACATAGGAAC
1 ACACATAGGAAC
11890450 ACA
1 ACA
11890453 TTTAGTCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.07
Consensus pattern (12 bp):
ACACATAGGAAC
Found at i:11897088 original size:7 final size:7
Alignment explanation
Indices: 11897076--11897169 Score: 71
Period size: 7 Copynumber: 13.4 Consensus size: 7
11897066 GTAATATATA
11897076 TAGGGTT
1 TAGGGTT
11897083 TAGGGTT
1 TAGGGTT
* *
11897090 TAGGATG
1 TAGGGTT
* *
11897097 TATGATT
1 TAGGGTT
*
11897104 CAGGGTT
1 TAGGGTT
*
11897111 TAGGATT
1 TAGGGTT
*
11897118 TAGGGTA
1 TAGGGTT
* *
11897125 TATGATT
1 TAGGGTT
11897132 TAGGGTT
1 TAGGGTT
*
11897139 TAGGGTA
1 TAGGGTT
*
11897146 TAGTGTT
1 TAGGGTT
**
11897153 TAGACTT
1 TAGGGTT
11897160 TAGGGTT
1 TAGGGTT
11897167 TAG
1 TAG
11897170 AGATAAAATT
Statistics
Matches: 64, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.41
Consensus pattern (7 bp):
TAGGGTT
Found at i:11897119 original size:28 final size:28
Alignment explanation
Indices: 11897077--11897142 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
11897067 TAATATATAT
* *
11897077 AGGGTTTAGGGTTTAGGATGTATGATTC
1 AGGGTTTAGGATTTAGGATATATGATTC
* *
11897105 AGGGTTTAGGATTTAGGGTATATGATTT
1 AGGGTTTAGGATTTAGGATATATGATTC
11897133 AGGGTTTAGG
1 AGGGTTTAGG
11897143 GTATAGTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.02, G:0.36, T:0.39
Consensus pattern (28 bp):
AGGGTTTAGGATTTAGGATATATGATTC
Found at i:11903960 original size:23 final size:23
Alignment explanation
Indices: 11903934--11903991 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
11903924 TTTGGTGGCG
11903934 TGTCATACATGTGAATGGTCGCA
1 TGTCATACATGTGAATGGTCGCA
* * *
11903957 TGTCATACATGTGGATGTTCGCG
1 TGTCATACATGTGAATGGTCGCA
11903980 TGT-ATGACATGT
1 TGTCAT-ACATGT
11903992 TAGCAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 2 0.06
23 29 0.94
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (23 bp):
TGTCATACATGTGAATGGTCGCA
Found at i:11907065 original size:20 final size:20
Alignment explanation
Indices: 11907040--11907103 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
11907030 GAAAATGTAA
11907040 ATTTTGAAATTTTTACAAA-T
1 ATTTTGAAATTTTTA-AAATT
*
11907060 ATTTTGAAA-TTTAAAAATT
1 ATTTTGAAATTTTTAAAATT
*
11907079 ATTTTGAATTTTTTAAAATT
1 ATTTTGAAATTTTTAAAATT
11907099 ATTTT
1 ATTTT
11907104 TTTATTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 3 0.08
19 13 0.33
20 23 0.59
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTTGAAATTTTTAAAATT
Found at i:11913730 original size:18 final size:19
Alignment explanation
Indices: 11913709--11913745 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11913699 TTTAAAAAAA
11913709 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
11913727 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
11913746 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:11913746 original size:18 final size:18
Alignment explanation
Indices: 11913709--11913770 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
11913699 TTTAAAAAAA
*
11913709 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAA-TTT
11913727 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
* *
11913745 TAAAAATTATTTTAAAATTT
1 TATAAA-TATTTT-GAATTT
11913765 TA-AAAT
1 TATAAAT
11913771 TTTAAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 16 0.42
19 15 0.39
20 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:11913755 original size:19 final size:19
Alignment explanation
Indices: 11913714--11913769 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
11913704 AAAAATATAA
*
11913714 ATTTTAGAATTTTTATAAAT
1 ATTTTAGAA-TTTTAAAAAT
11913734 ATTTT-GAATTTTAAAAATT
1 ATTTTAGAATTTTAAAAA-T
*
11913753 ATTTTAAAATTTTAAAA
1 ATTTTAGAATTTTAAAA
11913770 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.25
19 9 0.28
20 15 0.47
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
ATTTTAGAATTTTAAAAAT
Found at i:11913764 original size:27 final size:28
Alignment explanation
Indices: 11913712--11913785 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
11913702 AAAAAAATAT
*
11913712 AAATTTTAGAATT-TTTATAAATATTTT-
1 AAATTTTAAAATTATTT-TAAATATTTTA
*
11913739 GAATTTTAAAAATTATTTTAAA-ATTTTA
1 AAATTTT-AAAATTATTTTAAATATTTTA
11913767 AAATTTTAAAATTATTTTA
1 AAATTTTAAAATTATTTTA
11913786 TTTTTTTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 23 0.56
28 15 0.37
29 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AAATTTTAAAATTATTTTAAATATTTTA
Found at i:11913766 original size:8 final size:8
Alignment explanation
Indices: 11913753--11913779 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
11913743 TTTAAAAATT
11913753 ATTTTAAA
1 ATTTTAAA
11913761 ATTTTAAA
1 ATTTTAAA
11913769 ATTTTAAA
1 ATTTTAAA
11913777 ATT
1 ATT
11913780 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTTAAA
Found at i:11913785 original size:19 final size:19
Alignment explanation
Indices: 11913714--11913771 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
11913704 AAAAATATAA
*
11913714 ATTTTAGAATTTTTATAAA-T
1 ATTTTA-AAATTTTA-AAATT
*
11913734 ATTTT-GAATTTTAAAAATT
1 ATTTTAAAATTTT-AAAATT
11913753 ATTTTAAAATTTTAAAATT
1 ATTTTAAAATTTTAAAATT
11913772 TTAAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 8 0.25
19 13 0.41
20 11 0.34
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTTAAAATTTTAAAATT
Found at i:11916227 original size:29 final size:29
Alignment explanation
Indices: 11916194--11916251 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
11916184 CAAGCATCCA
11916194 CGGTACGTAGTTCGGATTGTGTGACTATC
1 CGGTACGTAGTTCGGATTGTGTGACTATC
*
11916223 CGGTACGTAGTTTGGATTGTGTGACTATC
1 CGGTACGTAGTTCGGATTGTGTGACTATC
11916252 TGTGTAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.16, G:0.31, T:0.36
Consensus pattern (29 bp):
CGGTACGTAGTTCGGATTGTGTGACTATC
Found at i:11918914 original size:21 final size:21
Alignment explanation
Indices: 11918874--11918929 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
11918864 GGAGCAGAGA
**
11918874 TATCAATACTTGCT-AAAAGG
1 TATCAATACTTTTTGAAAAGG
11918894 TAT-AGATACTTTTTGAAAAGG
1 TATCA-ATACTTTTTGAAAAGG
11918915 TATCAATACTTTTTG
1 TATCAATACTTTTTG
11918930 TCATTGTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 10 0.32
21 19 0.61
22 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (21 bp):
TATCAATACTTTTTGAAAAGG
Found at i:11919355 original size:32 final size:32
Alignment explanation
Indices: 11919312--11919378 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
11919302 ATTTTAAAAA
*
11919312 TTATATTTAATACAATATAACAATTATTATAT
1 TTATATTTAATACAATAAAACAATTATTATAT
* * * * *
11919344 TTATTTTTAATATAATAAAATATTTATTTTAT
1 TTATATTTAATACAATAAAACAATTATTATAT
11919376 TTA
1 TTA
11919379 CAATAGTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
TTATATTTAATACAATAAAACAATTATTATAT
Found at i:11919647 original size:26 final size:26
Alignment explanation
Indices: 11919607--11919667 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
11919597 GAGCTACTAT
11919607 TATCCAAATGCTAATGAAAGTCTTGA
1 TATCCAAATGCTAATGAAAGTCTTGA
* *
11919633 TATCCAAATGTTAATGAAAGTCTTGT
1 TATCCAAATGCTAATGAAAGTCTTGA
11919659 TATCCAAAT
1 TATCCAAAT
11919668 TCCCTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (26 bp):
TATCCAAATGCTAATGAAAGTCTTGA
Found at i:11923205 original size:69 final size:68
Alignment explanation
Indices: 11923130--11923276 Score: 177
Period size: 68 Copynumber: 2.1 Consensus size: 68
11923120 AGTGAAAATC
* * * *
11923130 AACACATTTGAACAGCTTAATTAATTAAATAAAACCACATAATTGACAGCACATTTGGACAGTGA
1 AACACATTTGAACAGCTTAATTAACT-AATAAAACAACATAAATGACAGCACATTAGGACAGTGA
11923195 ATTT
65 ATTT
* * * * * * *
11923199 AGCACATTTGGATAGCTTTATTGACTAATAAAACAACATAAATGACGGGACATTAGGACAGTGAA
1 AACACATTTGAACAGCTTAATTAACTAATAAAACAACATAAATGACAGCACATTAGGACAGTGAA
11923264 TTT
66 TTT
*
11923267 AACAAATTTG
1 AACACATTTG
11923277 CACAAGCAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
68 45 0.69
69 20 0.31
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (68 bp):
AACACATTTGAACAGCTTAATTAACTAATAAAACAACATAAATGACAGCACATTAGGACAGTGAA
TTT
Found at i:11926473 original size:24 final size:24
Alignment explanation
Indices: 11926420--11926473 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
11926410 AATCAAAAAA
* **
11926420 AGAAAAAGCATTCCAAAATCAATG
1 AGAAAAAGCAATCCAAAAGAAATG
11926444 AGAAAAAGCAATCCAAAAGAAAT-
1 AGAAAAAGCAATCCAAAAGAAATG
11926467 AGAAAAA
1 AGAAAAA
11926474 TATGAATTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.11
Consensus pattern (24 bp):
AGAAAAAGCAATCCAAAAGAAATG
Found at i:11929502 original size:19 final size:19
Alignment explanation
Indices: 11929471--11929513 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
11929461 GGGTATATAA
11929471 TTAA-TTAAATTAT-TTAAT
1 TTAATTTAAATTATATT-AT
*
11929489 TTAATTTAATTTATATTAT
1 TTAATTTAAATTATATTAT
11929508 TTAATT
1 TTAATT
11929514 ATATTGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 16 0.73
20 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTAAATTATATTAT
Found at i:11929509 original size:14 final size:13
Alignment explanation
Indices: 11929471--11929518 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
11929461 GGGTATATAA
*
11929471 TTAATTAAATTAT
1 TTAATTATATTAT
11929484 TTAATT-TA--AT
1 TTAATTATATTAT
11929494 TTAATTTATATTAT
1 TTAA-TTATATTAT
11929508 TTAATTATATT
1 TTAATTATATT
11929519 GTACATTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 6 0.20
11 2 0.07
12 3 0.10
13 13 0.43
14 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:11932071 original size:21 final size:21
Alignment explanation
Indices: 11932046--11932094 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
11932036 GAAGGGTAGT
*
11932046 ACACGGCCGTGTGACAG-AGGC
1 ACACGGCCGAGTGA-AGTAGGC
* *
11932067 ACACGTCCGAGTGAAGTAGGG
1 ACACGGCCGAGTGAAGTAGGC
11932088 ACACGGC
1 ACACGGC
11932095 TGTTTGAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.27, C:0.27, G:0.37, T:0.10
Consensus pattern (21 bp):
ACACGGCCGAGTGAAGTAGGC
Found at i:11932381 original size:60 final size:59
Alignment explanation
Indices: 11932202--11932387 Score: 171
Period size: 60 Copynumber: 3.1 Consensus size: 59
11932192 GCCACAGCCA
* * * *
11932202 TGTGTCCCATAACACACGCCCGTGTTGAATCCCT-A-GGCCCCAAATCAGTCACATGGTCA
1 TGTGTCCCATAACACACGCCCGTGTGGAA-CCCTAATTG-CCCAAATCAGTCACATGGCCG
* * * * ** * * * *
11932261 TGTGTCCCGA-AGCATAGGCTCGTGTGGGAACCCTAATTTTCAAAATTAGTTACATAGCCG
1 TGTGTCCC-ATAACACACGCCCGTGT-GGAACCCTAATTGCCCAAATCAGTCACATGGCCG
*
11932321 TGTGTCCCATAACACACGCCCGTGTGGAAGCCCTAATTGCCCAAATCAGTCACACGGCCG
1 TGTGTCCCATAACACACGCCCGTGTGGAA-CCCTAATTGCCCAAATCAGTCACATGGCCG
11932381 TGTGTCC
1 TGTGTCC
11932388 AATGGACACG
Statistics
Matches: 96, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
59 28 0.29
60 68 0.71
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (59 bp):
TGTGTCCCATAACACACGCCCGTGTGGAACCCTAATTGCCCAAATCAGTCACATGGCCG
Found at i:11939952 original size:47 final size:49
Alignment explanation
Indices: 11939869--11940002 Score: 147
Period size: 46 Copynumber: 2.8 Consensus size: 49
11939859 TGTAACCCGC
* * *
11939869 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTA-CAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTAGCAT
*
11939919 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTAGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTAGCAT
* *
11939962 CCATAAGTGAACTCGGACTCAACTTAACGAGTTCGGATGCC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC
11940003 CAAATATCCC
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
42 3 0.04
43 4 0.06
44 2 0.03
45 2 0.03
46 28 0.40
47 27 0.39
48 2 0.03
49 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTAGCAT
Found at i:11941310 original size:18 final size:18
Alignment explanation
Indices: 11941287--11941329 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
11941277 AAATCAGGAT
11941287 ATTACAGGGTTACAGAGC
1 ATTACAGGGTTACAGAGC
11941305 ATTACAGGGTTACAGAGC
1 ATTACAGGGTTACAGAGC
11941323 ATTACAG
1 ATTACAG
11941330 TGCATAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (18 bp):
ATTACAGGGTTACAGAGC
Found at i:11950124 original size:30 final size:30
Alignment explanation
Indices: 11950078--11950201 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
11950068 TTTTATTATG
*
11950078 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
11950109 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
11950139 CCAATATTTGATGCCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
11950169 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
11950199 CCA
1 CCA
11950202 TAAATATGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 79 0.92
31 7 0.08
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:11950133 original size:15 final size:15
Alignment explanation
Indices: 11950088--11950195 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
11950078 CCAATATCTC
11950088 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
11950103 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
11950118 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
11950133 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
*
11950148 GATGCCCATATCTTT
1 GATACCCATATCTTT
** * *
11950163 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
11950178 GATACCCATATCTTT
1 GATACCCATATCTTT
11950193 GAT
1 GAT
11950196 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:11954817 original size:30 final size:30
Alignment explanation
Indices: 11954771--11954894 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
11954761 TTTTATTATG
*
11954771 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
11954802 CCAATATTTGATACCCATATATTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
11954832 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
11954862 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
11954892 CCA
1 CCA
11954895 TAAATATGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 79 0.92
31 7 0.08
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:11954823 original size:15 final size:15
Alignment explanation
Indices: 11954781--11954888 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
11954771 CCAATATCTC
*
11954781 GATACCCATATCTTT
1 GATACCCATATATTT
**
11954796 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
11954811 GATACCCATATATTT
1 GATACCCATATATTT
**
11954826 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
*
11954841 GATACCCATATCTTT
1 GATACCCATATATTT
** *
11954856 GACTTTCTAT-TATTT
1 GA-TACCCATATATTT
*
11954871 GATACCCATATCTTT
1 GATACCCATATATTT
11954886 GAT
1 GAT
11954889 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 12 0.17
15 45 0.65
16 12 0.17
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATATTT
Found at i:11958059 original size:3 final size:3
Alignment explanation
Indices: 11958051--11958076 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11958041 GGGAAAGAGA
11958051 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
11958077 ATGATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:11958476 original size:22 final size:18
Alignment explanation
Indices: 11958423--11958476 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
11958413 CCCTATTATT
11958423 TTTTATTTTATTAAAAAA
1 TTTTATTTTATTAAAAAA
* *
11958441 TTATATATTTTTAATTTAATAA
1 TT-T-TA-TTTT-ATTAAAAAA
11958463 TTTTATTTTATTAA
1 TTTTATTTTATTAA
11958477 GTTTTAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
18 6 0.21
19 5 0.17
20 4 0.14
21 5 0.17
22 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATTTTATTAAAAAA
Found at i:11959278 original size:27 final size:27
Alignment explanation
Indices: 11959246--11959304 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
11959236 TTTATTAAAG
11959246 TAAAATTTTGAATTTTTTAGTAATTTT
1 TAAAATTTTGAATTTTTTAGTAATTTT
11959273 TAAAATTTTGAATTTTTTAGTAATTTT
1 TAAAATTTTGAATTTTTTAGTAATTTT
11959300 TAAAA
1 TAAAA
11959305 CTTCATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (27 bp):
TAAAATTTTGAATTTTTTAGTAATTTT
Found at i:11960594 original size:41 final size:41
Alignment explanation
Indices: 11960537--11960620 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
11960527 TTAAAACTAT
* *
11960537 ACCAAATTCATCACATCTAAGATTCCAATATGAATAAATAA
1 ACCAAATTCATCACATCTAAGAATCCAAAATGAATAAATAA
*
11960578 ACCAAATTCATCACATCTAATAATCCAAAATGAATAAATAA
1 ACCAAATTCATCACATCTAAGAATCCAAAATGAATAAATAA
11960619 AC
1 AC
11960621 TTCTCTTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (41 bp):
ACCAAATTCATCACATCTAAGAATCCAAAATGAATAAATAA
Found at i:11960914 original size:20 final size:19
Alignment explanation
Indices: 11960882--11960946 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 19
11960872 GACCATTTTT
11960882 TATTTTTATAATTTATATA
1 TATTTTTATAATTTATATA
* *
11960901 TATTTTTCTGAATTTTTATATT
1 TATTTTTAT-AA--TTTATATA
*
11960923 TATATTTAT-ATTT-T-TA
1 TATTTTTATAATTTATATA
11960939 TATTTTTA
1 TATTTTTA
11960947 ATGTGTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
16 8 0.22
17 1 0.03
18 3 0.08
19 8 0.22
20 3 0.08
22 14 0.38
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TATTTTTATAATTTATATA
Found at i:11960938 original size:14 final size:14
Alignment explanation
Indices: 11960912--11960946 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11960902 ATTTTTCTGA
11960912 ATTTTTATATTTAT
1 ATTTTTATATTTAT
* *
11960926 ATTTATATTTTTAT
1 ATTTTTATATTTAT
11960940 ATTTTTA
1 ATTTTTA
11960947 ATGTGTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTTATATTTAT
Found at i:11960943 original size:28 final size:26
Alignment explanation
Indices: 11960876--11960946 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 26
11960866 CGAGATGACC
11960876 ATTTTTTATTTTTATAATTTATATAT
1 ATTTTTTATTTTTATAATTTATATAT
11960902 ATTTTTCTGAATTTTTAT-ATTTATATTTAT
1 ATTTTT-T--ATTTTTATAATTTATA--TAT
11960932 ATTTTTATATTTTTA
1 ATTTTT-TATTTTTA
11960947 ATGTGTATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
26 6 0.15
27 1 0.03
28 14 0.36
29 8 0.21
30 10 0.26
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (26 bp):
ATTTTTTATTTTTATAATTTATATAT
Found at i:11965635 original size:43 final size:43
Alignment explanation
Indices: 11965552--11965656 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
11965542 GATATATCTG
** * ** * *
11965552 AACTTAAACTAAAATAAATTTGGACAGAGTCTACACATGGTTA
1 AACTTAAACTAAAATAAATTTAAACAAAACCCACACATGGTGA
* *
11965595 AACTTAAACTAGAATAAATTTAAACAAAACCCACATATGGTGA
1 AACTTAAACTAAAATAAATTTAAACAAAACCCACACATGGTGA
* *
11965638 AACTTGAACCAAAATAAAT
1 AACTTAAACTAAAATAAAT
11965657 ATGGAAAGAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (43 bp):
AACTTAAACTAAAATAAATTTAAACAAAACCCACACATGGTGA
Found at i:11968930 original size:16 final size:16
Alignment explanation
Indices: 11968906--11968936 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11968896 TATACTGGTC
11968906 TTGGACCAATGTTGTT
1 TTGGACCAATGTTGTT
*
11968922 TTGGCCCAATGTTGT
1 TTGGACCAATGTTGT
11968937 AACATTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (16 bp):
TTGGACCAATGTTGTT
Found at i:11969068 original size:15 final size:12
Alignment explanation
Indices: 11969039--11969070 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
11969029 AAATTGGTTG
11969039 AATAATTTTTTT
1 AATAATTTTTTT
11969051 AATAATTTTTTT
1 AATAATTTTTTT
11969063 AATAATTT
1 AATAATTT
11969071 ATTAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATAATTTTTTT
Found at i:11969704 original size:27 final size:27
Alignment explanation
Indices: 11969674--11969726 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
11969664 AAATTACAAA
11969674 AAAAAATTCA-AAATAATTTTAAAATTC
1 AAAAAATTCATAAA-AATTTTAAAATTC
* *
11969701 AAAATATTTATAAAAATTTTAAAATT
1 AAAAAATTCATAAAAATTTTAAAATT
11969727 TATATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAAAATTCATAAAAATTTTAAAATTC
Found at i:11969716 original size:19 final size:19
Alignment explanation
Indices: 11969675--11969718 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
11969665 AATTACAAAA
11969675 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
11969694 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
11969712 AAAAATT
1 AAAAATT
11969719 TTAAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:11969740 original size:24 final size:26
Alignment explanation
Indices: 11969674--11969756 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
11969664 AAATTACAAA
* *
11969674 AAAAAATTCAAAATAATTTTAAAATTC
1 AAAATATTTAAAA-AATTTTAAAATTC
11969701 AAAATATTTATAAAAATTTTAAAATT-
1 AAAATATTTA-AAAAATTTTAAAATTC
* * * *
11969727 TATAT-TTTAAAAAATATAAAAATTC
1 AAAATATTTAAAAAATTTTAAAATTC
11969752 TAAAA
1 -AAAA
11969757 AATATATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
24 13 0.29
25 4 0.09
26 5 0.11
27 20 0.44
28 3 0.07
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATATTTAAAAAATTTTAAAATTC
Found at i:11970203 original size:21 final size:20
Alignment explanation
Indices: 11970171--11970209 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11970161 TTTAAAAATT
*
11970171 TTAAAAATTCTATAAAAACA
1 TTAAAAAATCTATAAAAACA
11970191 TTAAAGAAATCTATAAAAA
1 TTAAA-AAATCTATAAAAA
11970210 ATCAGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (20 bp):
TTAAAAAATCTATAAAAACA
Found at i:11970402 original size:21 final size:22
Alignment explanation
Indices: 11970360--11970405 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
11970350 AAATTTTAAT
11970360 TATTTACATAATAATTGATTTTA
1 TATTTACATAATAATT-ATTTTA
11970383 TATTT-CATATATAATT-TTTTA
1 TATTTACATA-ATAATTATTTTA
11970404 TA
1 TA
11970406 AATAATACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.32
22 4 0.18
23 11 0.50
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTACATAATAATTATTTTA
Found at i:11970770 original size:29 final size:30
Alignment explanation
Indices: 11970738--11970796 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
11970728 TCACGTGTAT
*
11970738 AATTAC-ACCAAATTAAAATTCATGTATAC
1 AATTACAACCAAATCAAAATTCATGTATAC
**
11970767 AATTACATATTAAATCAAAATTCATGTATA
1 AATTACA-ACCAAATCAAAATTCATGTATA
11970797 ATTTTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
31 19 0.76
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (30 bp):
AATTACAACCAAATCAAAATTCATGTATAC
Found at i:11971941 original size:22 final size:23
Alignment explanation
Indices: 11971916--11971974 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
11971906 CATAATACTG
*
11971916 AAATGATAGCAAAATAAT-GGAA
1 AAATAATAGCAAAATAATGGGAA
*
11971938 AAATAATAGCAAAATAGTGGGAA
1 AAATAATAGCAAAATAATGGGAA
11971961 AAA-AA-A-CAAAATAA
1 AAATAATAGCAAAATAA
11971975 CAAGGTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 7 0.21
21 1 0.03
22 18 0.55
23 7 0.21
ACGTcount: A:0.64, C:0.05, G:0.15, T:0.15
Consensus pattern (23 bp):
AAATAATAGCAAAATAATGGGAA
Found at i:11972452 original size:9 final size:9
Alignment explanation
Indices: 11972438--11972463 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
11972428 TATTTTTTAG
11972438 ACAATCCTA
1 ACAATCCTA
11972447 ACAATCCTA
1 ACAATCCTA
11972456 ACAATCCT
1 ACAATCCT
11972464 TGTGATCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (9 bp):
ACAATCCTA
Found at i:11972716 original size:17 final size:18
Alignment explanation
Indices: 11972684--11972718 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
11972674 GAAAGCCAAA
*
11972684 AAACTTTATGGTATCGTT
1 AAACTTGATGGTATCGTT
11972702 AAACTTGAT-GTATCGTT
1 AAACTTGATGGTATCGTT
11972719 GCCGTGAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (18 bp):
AAACTTGATGGTATCGTT
Found at i:11988259 original size:51 final size:51
Alignment explanation
Indices: 11988183--11988297 Score: 185
Period size: 51 Copynumber: 2.3 Consensus size: 51
11988173 GCAAGGAGTA
* * *
11988183 GCCGTAGATAGGCCCCTACATTCAGCTGTTTACTCTTTGCATTGTGAAATG
1 GCCGTGGATAGCCCCCTACATTCAGCTGTTTACTCTTCGCATTGTGAAATG
11988234 GCCGTGGATAGCCCCCTACATTCAGCTGTTTACTCTTCGCATTGTGAAATG
1 GCCGTGGATAGCCCCCTACATTCAGCTGTTTACTCTTCGCATTGTGAAATG
* *
11988285 GTCATGGATAGCC
1 GCCGTGGATAGCC
11988298 TCCAATATTG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (51 bp):
GCCGTGGATAGCCCCCTACATTCAGCTGTTTACTCTTCGCATTGTGAAATG
Found at i:11991035 original size:28 final size:28
Alignment explanation
Indices: 11991004--11991066 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
11990994 TTAACTCCTA
11991004 AAAATAATAAAAATTAA-TTTAATTTTTT
1 AAAATAATAAAAATTAATTTTAA-TTTTT
* *
11991032 AAAA-ATTAAAATTTAATTTTAATTTTT
1 AAAATAATAAAAATTAATTTTAATTTTT
11991059 AAAATAAT
1 AAAATAAT
11991067 TTTCTGGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AAAATAATAAAAATTAATTTTAATTTTT
Found at i:11991036 original size:20 final size:21
Alignment explanation
Indices: 11991011--11991051 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
11991001 CTAAAAATAA
11991011 TAAAAATT-AATTTAATTTTT
1 TAAAAATTAAATTTAATTTTT
11991031 TAAAAATTAAAATTTAATTTT
1 TAAAAATT-AAATTTAATTTT
11991052 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAAATTAAATTTAATTTTT
Found at i:11991053 original size:20 final size:19
Alignment explanation
Indices: 11991011--11991051 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 19
11991001 CTAAAAATAA
11991011 TAAAAATTAATTTAATTTTT
1 TAAAAATTAATTTAA-TTTT
11991031 TAAAAATTAAAATTTAATTTT
1 TAAAAATT--AATTTAATTTT
11991052 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAAATTAATTTAATTTT
Found at i:11991472 original size:16 final size:16
Alignment explanation
Indices: 11991451--11991505 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
11991441 GTTTGGTTCA
*
11991451 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
11991467 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
11991483 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
11991499 CTGTAAT
1 CTGTAAT
11991506 CAGTAATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:11991774 original size:61 final size:59
Alignment explanation
Indices: 11991634--11991773 Score: 176
Period size: 61 Copynumber: 2.4 Consensus size: 59
11991624 TTGTTATTAA
* * * * * *
11991634 ATTTTAATAAAATTATTGTTAAATATATTTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATACAATTTAATAAAAAT--AAATAAATAATTTAATAAC
*
11991695 ATTTTAATATAATTATTATTAAATACAATTTAAT-AAAAT-AATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATACAATTTAATAAAAATAAATAAATAATTTAATAAC
11991752 ATTCTTAATATAATTATTATTA
1 ATT-TTAATATAATTATTATTA
11991774 TATGAATTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 18 0.25
58 18 0.25
60 5 0.07
61 30 0.42
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATACAATTTAATAAAAATAAATAAATAATTTAATAAC
Found at i:12005920 original size:11 final size:11
Alignment explanation
Indices: 12005890--12005922 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12005880 TTGATATGTT
12005890 AATGAAGAGAA
1 AATGAAGAGAA
12005901 AAT-AAGAGAA
1 AATGAAGAGAA
*
12005911 AGTGAAGAGAA
1 AATGAAGAGAA
12005922 A
1 A
12005923 TAGTGTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (11 bp):
AATGAAGAGAA
Found at i:12007672 original size:46 final size:46
Alignment explanation
Indices: 12007624--12007873 Score: 308
Period size: 46 Copynumber: 5.5 Consensus size: 46
12007614 GCTCTCTGAT
** * *
12007624 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
12007670 ATGAAACGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
12007716 GGGAAATGAATAAGACCATGGTTGAAAGATACCGTGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
12007762 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * * *
12007808 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATGTC
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
12007854 A--AAGATAAATAAGACCATGG
1 ATGAA-ATGAATAAGACCATGG
12007874 ATGGGAGACA
Statistics
Matches: 177, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
44 2 0.01
45 14 0.08
46 161 0.91
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:12007783 original size:92 final size:92
Alignment explanation
Indices: 12007634--12007846 Score: 345
Period size: 92 Copynumber: 2.3 Consensus size: 92
12007624 ATGAAATGTG
* *
12007634 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAACGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGA
* *
12007699 TACCATGGCAACATGACGGGAAATGAA
66 TACCATGGCAACATGACAGAAAATGAA
*
12007726 TAAGACCATGGTTGAAAGATACCGTGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGA
*
12007791 TACCATGGCAACATGACAGAAAATGAG
66 TACCATGGCAACATGACAGAAAATGAA
* * *
12007818 TAAGACCATAGTTGAAAGACACTATGGCA
1 TAAGACCATGGTTGAAAGATACCATGGCA
12007847 TCATGTCAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 111 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.18
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACAGAAAATGAA
Found at i:12019356 original size:20 final size:18
Alignment explanation
Indices: 12019318--12019361 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
12019308 AAACCCTAAT
12019318 TTTCCC-TTTTCTTTTTC
1 TTTCCCTTTTTCTTTTTC
12019335 TTTCCCTTTTTCCTTCTTTC
1 TTTCCCTTTTT-CTT-TTTC
12019355 TTTCCCT
1 TTTCCCT
12019362 GCTTATTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 3 0.12
20 11 0.46
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCCCTTTTTCTTTTTC
Found at i:12019449 original size:14 final size:15
Alignment explanation
Indices: 12019413--12019449 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
12019403 TTTCTTTTAT
*
12019413 TTATTATAACTATTA
1 TTATTATATCTATTA
12019428 -TATTATATC-ATTA
1 TTATTATATCTATTA
12019441 TTATTATAT
1 TTATTATAT
12019450 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATATCTATTA
Found at i:12030303 original size:14 final size:15
Alignment explanation
Indices: 12030280--12030312 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12030270 AATATTACCC
*
12030280 TTATGGATATTTAT-
1 TTATGAATATTTATA
12030294 TTATGAATATTTATA
1 TTATGAATATTTATA
12030309 TTAT
1 TTAT
12030313 AATGTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (15 bp):
TTATGAATATTTATA
Found at i:12032115 original size:3 final size:3
Alignment explanation
Indices: 12032102--12032171 Score: 61
Period size: 3 Copynumber: 22.7 Consensus size: 3
12032092 TTTTCTTTTG
* ** *
12032102 TAT TTT TAT TAT TAT TGC TAT TAT TGT TAT TAT TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
12032148 TAT TA- TATT TAT ATAA TAT TAT TA
1 TAT TAT TA-T TAT -TAT TAT TAT TA
12032172 ATAGGTACTT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.04
3 44 0.83
4 7 0.13
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:12032905 original size:30 final size:31
Alignment explanation
Indices: 12032871--12032928 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12032861 ATGTAAATAT
12032871 TATGTATATAT-TT-TTAAATACTATATTGTA
1 TATGTATATATATTCTT-AATACTATATTGTA
*
12032901 TATGTATATATATTCTTAGTACTATATT
1 TATGTATATATATTCTTAATACTATATT
12032929 ACGTATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 12 0.48
32 2 0.08
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.53
Consensus pattern (31 bp):
TATGTATATATATTCTTAATACTATATTGTA
Found at i:12045314 original size:73 final size:73
Alignment explanation
Indices: 12045191--12045373 Score: 253
Period size: 73 Copynumber: 2.5 Consensus size: 73
12045181 TTTGTTTGTT
* *
12045191 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAACTGCTG
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATGCT-
12045256 T-TTGTC-AA
65 TCTT-TCAAA
** * *
12045264 AAATCAACTCACGTTGCGGGAGGTGAGTTGAGCCTCTGGGCACGCCGAGGTATTTTCAAATTCTT
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATGCTT
12045329 CTTTCAGAAA
66 CTTTC--AAA
*
12045339 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCT
12045374 TGGCTCGCAT
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
72 3 0.03
73 60 0.62
75 34 0.35
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (73 bp):
AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATGCTT
CTTTCAAA
Found at i:12045491 original size:234 final size:232
Alignment explanation
Indices: 12045098--12046037 Score: 1466
Period size: 234 Copynumber: 4.0 Consensus size: 232
12045088 TCATTTCTGT
12045098 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTCACTT
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTCACTT
* * *
12045163 TCAATTTCTGTTTTTATGTTTGTTTGTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCG
66 TCAATTTCTATTTTTATGTCTGTTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCG
* *
12045228 GGGCACGCTGAGGTATTTTCAACTGCTGTTTGTCAAAAATCAACTCACGTTGCGGGAGGTGAGTT
131 GGGCACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATGTTGCGGGAGGTGAGTT
* *
12045293 GAGCCTCTGGGCACGCCGAGGTATTTTCAAATTCTTC
196 GAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTAC
* *
12045330 TTTCAGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCGCATGTTGAGTCACT
1 TTTCA-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTCACT
12045395 TTCAATTTCTATTTTTATGTCTGTTTTCTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCT
65 TTCAATTTCTATTTTTATGTCTGTTTT-TTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCT
12045460 CGGGGCACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATGTTGCGGGAGGTGAG
129 CGGGGCACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATGTTGCGGGAGGTGAG
12045525 TTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTAC
194 TTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTAC
*
12045564 GTTCAGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTCACT
1 TTTCA-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTCACT
* *
12045629 TTCAATTTCTGTTTTTATGTCTGTTTTTTTTTAAATCAACCCATATTGCGGGAGGTGAGTTGAGC
65 TTCAATTTCTATTTTTATGTCTG---TTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGC
* * * *
12045694 CTTGAGGCACGCTGATGTATTTTCAATTGTTGTTTGTCAAAAATCAACTCATGTTGCGGGAGGTG
127 CTCGGGGCACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATGTTGCGGGAGGTG
12045759 AGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTAC
192 AGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTAC
12045800 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTCACTT
1 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTCACTT
* *
12045865 TTAATTTCTATTTTTATGTCTGTTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGACCCTCG
66 TCAATTTCTATTTTTATGTCTGTTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCG
** * * * * *
12045930 GCTCACGTGCTGAGGTATTTTCAATTTCAATTTCTGTTTGTCAAAAAAACCAACTCATATTGTGA
131 GGGCAC--GCTGAGGTA---T---TTTCAATTGCTGTTTGTC--AAAAATCAACTCATGTTGCGG
* * *
12045995 GAGGTGAGTTGAGCCTCGAGTCACATGTCGAGGTATTTTCAAA
186 GAGGTGAGTTGAGCCTCGGGGCAC--GCCGAGGTATTTTCAAA
12046038 ATCTGTTTTT
Statistics
Matches: 654, Mismatches: 37, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
232 48 0.07
233 81 0.12
234 229 0.35
235 80 0.12
236 140 0.21
237 5 0.01
240 16 0.02
242 39 0.06
244 16 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (232 bp):
TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTCACTT
TCAATTTCTATTTTTATGTCTGTTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCG
GGGCACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATGTTGCGGGAGGTGAGTT
GAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTAC
Found at i:12045504 original size:73 final size:74
Alignment explanation
Indices: 12045425--12045607 Score: 273
Period size: 73 Copynumber: 2.5 Consensus size: 74
12045415 CTGTTTTCTT
*
12045425 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC-AATTGCT
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATT-CT
* *
12045489 -GTT-TGTCAA
65 AGTTCAG-AAA
*
12045498 AAATCAACTCATGTTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTA
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTA
12045563 CGTTCAGAAA
66 -GTTCAGAAA
*
12045573 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCT
12045608 TGGCTCACGT
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
73 57 0.57
74 4 0.04
75 38 0.38
76 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (74 bp):
AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTA
GTTCAGAAA
Found at i:12045752 original size:73 final size:74
Alignment explanation
Indices: 12045661--12045844 Score: 244
Period size: 73 Copynumber: 2.5 Consensus size: 74
12045651 GTTTTTTTTT
* * * * *
12045661 AAATCAACCCATATTGCGGGAGGTGAGTTGAGCCTTGAGGCACGCTGATGTATTTTC-AATTGTT
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTGAGGCACGCCGAGGTATTTTCAAATTCTA
* ***
12045725 GTTTGTCAA
66 CTTTCAAAA
* * *
12045734 AAATCAACTCATGTTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATTCTA
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTGAGGCACGCCGAGGTATTTTCAAATTCTA
12045799 CTTTCAAAA
66 CTTTCAAAA
*
12045808 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTG
12045845 GCTCACGTGT
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
73 51 0.54
74 44 0.46
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (74 bp):
AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTGAGGCACGCCGAGGTATTTTCAAATTCTA
CTTTCAAAA
Found at i:12046187 original size:92 final size:90
Alignment explanation
Indices: 12045973--12046278 Score: 266
Period size: 87 Copynumber: 3.4 Consensus size: 90
12045963 CTGTTTGTCA
* * * *
12045973 AAAAAACCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGAG-TCACATG-TCGAGGTATTTTCA
1 AAAAAA-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GCTAACATGAT-GAGCTACTTTCA
** * *
12046036 AAATCTG-TTTTTCAAATTAT--TTTTC
63 ATTTATGTTTTTTCAATTTATACTTTTC
* * * * * * * **
12046061 AAAAACCAATTGATATTGCAAGAAGTGAATTGAGCCTTGGCTAATGTGATGAGCTACTTTCAATT
1 AAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTAACATGATGAGCTACTTTCAATT
* *
12046126 TCTG-TTTTTCAATTT-TCGCTTTTC
66 TATGTTTTTTCAATTTAT-ACTTTTC
* * * *
12046150 AAAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCA
1 ---AAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTAACATGATGAGCTACTTTCA
*
12046215 ATTTATGTTTTTTCAATTTATATTTTTC
63 ATTTATGTTTTTTCAATTTATACTTTTC
* *
12046243 AAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 AAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCC
12046279 GTGGGTTCAC
Statistics
Matches: 174, Mismatches: 34, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
86 2 0.01
87 55 0.32
88 6 0.03
89 5 0.03
90 34 0.20
92 55 0.32
93 16 0.09
94 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (90 bp):
AAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTAACATGATGAGCTACTTTCAATT
TATGTTTTTTCAATTTATACTTTTC
Found at i:12046229 original size:15 final size:15
Alignment explanation
Indices: 12046209--12046241 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12046199 TGCTGAGGTA
*
12046209 TTTTCAATTTATGTT
1 TTTTCAATTTATATT
12046224 TTTTCAATTTATATT
1 TTTTCAATTTATATT
12046239 TTT
1 TTT
12046242 CAAAGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTCAATTTATATT
Found at i:12048050 original size:22 final size:23
Alignment explanation
Indices: 12048011--12048059 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
12048001 TTTATTTTCG
*
12048011 TTATTTTATTTCATTT-TAAATA
1 TTATTTGATTTCATTTATAAATA
12048033 TTATTTGATTATCATTTATAAATA
1 TTATTTGATT-TCATTTATAAATA
12048057 TTA
1 TTA
12048060 GTGTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.38
23 6 0.25
24 9 0.38
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATTTGATTTCATTTATAAATA
Found at i:12048216 original size:3 final size:3
Alignment explanation
Indices: 12048203--12048278 Score: 64
Period size: 3 Copynumber: 24.7 Consensus size: 3
12048193 TTTTCTTTTG
* ** **
12048203 TAT TTT TAT TAT TAT TGC TAT TAT TAT TGC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
12048251 TATT TAT TA- TATT TAT ATAA TAT TAT TA
1 TA-T TAT TAT TA-T TAT -TAT TAT TAT TA
12048279 ATAGGTACTT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
2 2 0.04
3 48 0.84
4 7 0.12
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:12048429 original size:21 final size:22
Alignment explanation
Indices: 12048405--12048446 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
12048395 TACACTTTGT
* *
12048405 AATACTATTA-TTATATATTTC
1 AATACCATTAGTTATACATTTC
12048426 AATACCATTAGTTATACATTT
1 AATACCATTAGTTATACATTT
12048447 TTGTACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (22 bp):
AATACCATTAGTTATACATTTC
Found at i:12048540 original size:24 final size:22
Alignment explanation
Indices: 12048513--12048570 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
12048503 TAGTGTGTTT
12048513 TATTATATGTATATATACTCTCAA
1 TATTATAT-TAT-TATACTCTCAA
* *
12048537 TATTATATTCTTATACTCTTAA
1 TATTATATTATTATACTCTCAA
**
12048559 TACCATATTATT
1 TATTATATTATT
12048571 CTTATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 19 0.66
23 2 0.07
24 8 0.28
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTATATTATTATACTCTCAA
Found at i:12051679 original size:54 final size:54
Alignment explanation
Indices: 12051607--12051808 Score: 239
Period size: 54 Copynumber: 3.8 Consensus size: 54
12051597 TGGCATTTGG
* * * *
12051607 TAAGACAAGGATACCATGTAAGACCATGCCAAGGCATGGTATTGATAAGTTCTA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTA
* * *
12051661 TAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGA-TTACTA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTA
* * * *
12051715 TAAGGCAAAGG-TCCCGTGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-A
1 TAAGGC-AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTA
* * *
12051768 TAAGGCAAGGATACCACGTAAGACCGTGTCAAGACATGGCA
1 TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCA
12051809 ATGGTAAGTT
Statistics
Matches: 124, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
52 4 0.03
53 33 0.27
54 81 0.65
55 6 0.05
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
TAAGGCAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTA
Found at i:12051832 original size:107 final size:108
Alignment explanation
Indices: 12051623--12051843 Score: 268
Period size: 107 Copynumber: 2.0 Consensus size: 108
12051613 AAGGATACCA
* * *
12051623 TGTAAGACCATGCCAAGGCATGGTATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCAT
1 TGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACCAT
* * * **
12051688 GTCAAGACATGGCATTGATGATTACTATAAGGCAAAGG-TCCCG
66 GTCAAGACATGGCAATGATAATTAC-AAAAGAAAAAGGTTCCCG
* * * *
12051731 TGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCACGTAAGACCGT
1 TGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACCAT
*
12051795 GTCAAGACATGGCAATGGTAAGTTGA-AAAAGAAAAAGGTTCCCG
66 GTCAAGACATGGCAATGATAA-TT-ACAAAAGAAAAAGGTTCCCG
*
12051839 AGTAA
1 TGTAA
12051844 TCCAAAGAGT
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
107 51 0.53
108 44 0.46
109 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.22
Consensus pattern (108 bp):
TGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACCAT
GTCAAGACATGGCAATGATAATTACAAAAGAAAAAGGTTCCCG
Found at i:12057151 original size:47 final size:47
Alignment explanation
Indices: 12057086--12057207 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
12057076 GCATTGGCAC
*
12057086 TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGATAAGGATATCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
12057133 TAAGACAAGGATATCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGATAAGGATATCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
12057180 TAAGATAAGGATATTATGTAAGACCATG
1 TAAGATAAGGATATCATGTAAGACCATG
12057208 CCAAGGCATG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (47 bp):
TAAGATAAGGATATCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:12057312 original size:55 final size:54
Alignment explanation
Indices: 12057195--12057382 Score: 202
Period size: 55 Copynumber: 3.5 Consensus size: 54
12057185 TAAGGATATT
* * * * * *
12057195 ATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGGAATC
1 ATGTAAGACCATGCCAAGACATGGCATGGATGAGTTCTATAAGGCAAAGGTACC
* *
12057249 ATGTAAGACCATGTCAAGACATGGCATGGATGAGTTACTATAAGGCAAAGGTCCC
1 ATGTAAGACCATGCCAAGACATGGCATGGATGAGTT-CTATAAGGCAAAGGTACC
* * * *
12057304 ATGTAAGACCATGCCAAGGCAAGTCATTGG-TGAGTTC-ATAAGAC-AAGGATACC
1 ATGTAAGACCATGCCAAGACATGGCA-TGGATGAGTTCTATAAGGCAAAGG-TACC
* *
12057357 ACGTAAGACCATGTCAAGACATGGCA
1 ATGTAAGACCATGCCAAGACATGGCA
12057383 ATGGTAAGTT
Statistics
Matches: 112, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
52 4 0.04
53 30 0.27
54 33 0.29
55 42 0.38
56 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (54 bp):
ATGTAAGACCATGCCAAGACATGGCATGGATGAGTTCTATAAGGCAAAGGTACC
Found at i:12061918 original size:9 final size:9
Alignment explanation
Indices: 12061891--12061927 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
12061881 TGAGTTTTCG
12061891 AATTCGAAT
1 AATTCGAAT
* *
12061900 AACTCAAAT
1 AATTCGAAT
12061909 AATTCGAAT
1 AATTCGAAT
12061918 AATTCGAAT
1 AATTCGAAT
12061927 A
1 A
12061928 TTAAACATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12062480 original size:17 final size:17
Alignment explanation
Indices: 12062426--12062482 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
12062416 ATTTCTACTA
*
12062426 TTTATATTATTAAATTAAA
1 TTTATATTATTAAATT--G
* *
12062445 TTTCACATT-TTATATTG
1 TTT-ATATTATTAAATTG
12062462 TTTATATTATTAAATTG
1 TTTATATTATTAAATTG
12062479 TTTA
1 TTTA
12062483 GTCATATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 4 0.13
17 14 0.45
19 9 0.29
20 4 0.13
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (17 bp):
TTTATATTATTAAATTG
Found at i:12064586 original size:15 final size:15
Alignment explanation
Indices: 12064562--12064594 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12064552 GAACTGTTTA
12064562 CAAACCTTTCAGGCT
1 CAAACCTTTCAGGCT
*
12064577 CAAACTTTTCAGGCT
1 CAAACCTTTCAGGCT
12064592 CAA
1 CAA
12064595 CCCAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (15 bp):
CAAACCTTTCAGGCT
Found at i:12066137 original size:20 final size:20
Alignment explanation
Indices: 12066112--12066154 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12066102 CTCTCTCACC
* *
12066112 TTTTTTGTTCAAATTTTTAA
1 TTTTTTGTTAAAATTTTAAA
*
12066132 TTTTTTTTTAAAATTTTAAA
1 TTTTTTGTTAAAATTTTAAA
12066152 TTT
1 TTT
12066155 AATTATAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTTGTTAAAATTTTAAA
Found at i:12066148 original size:19 final size:20
Alignment explanation
Indices: 12066112--12066150 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
12066102 CTCTCTCACC
*
12066112 TTTTTTGTTCAAATTTTTAA
1 TTTTTTGTTCAAAATTTTAA
*
12066132 TTTTTT-TTTAAAATTTTAA
1 TTTTTTGTTCAAAATTTTAA
12066151 ATTTAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTTTGTTCAAAATTTTAA
Found at i:12070635 original size:10 final size:10
Alignment explanation
Indices: 12070620--12070677 Score: 75
Period size: 10 Copynumber: 5.9 Consensus size: 10
12070610 AATTTTAGCT
12070620 TTTATCTTTA
1 TTTATCTTTA
12070630 TTTATCTTT-
1 TTTATCTTTA
12070639 TTCTATCTTTA
1 TT-TATCTTTA
*
12070650 ATTATC-TTA
1 TTTATCTTTA
*
12070659 TTTATCTGTA
1 TTTATCTTTA
12070669 TTTATCTTT
1 TTTATCTTT
12070678 TAGAATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 10 0.24
10 30 0.73
11 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:12070674 original size:29 final size:30
Alignment explanation
Indices: 12070621--12070677 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
12070611 ATTTTAGCTT
*
12070621 TTATCTTTATTTATCTTTTTCTATCTTTAA
1 TTATCTTTATTTATCTTATTCTATCTTTAA
12070651 TTATC-TTATTTATCTGTATT-TATCTTT
1 TTATCTTTATTTATCT-TATTCTATCTTT
12070678 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (30 bp):
TTATCTTTATTTATCTTATTCTATCTTTAA
Found at i:12073207 original size:46 final size:46
Alignment explanation
Indices: 12073142--12073373 Score: 306
Period size: 46 Copynumber: 5.0 Consensus size: 46
12073132 TTATCTTTGA
* * * * * *
12073142 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
***
12073188 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * *
12073234 CACGTTGCTATGGTATCTTTCAACCATGGTCTTAGACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
12073280 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
12073326 CA-GATTGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATG-TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
12073372 CA
1 CA
12073374 AATAGCACAC
Statistics
Matches: 168, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
45 5 0.03
46 163 0.97
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:12080144 original size:16 final size:16
Alignment explanation
Indices: 12080123--12080193 Score: 76
Period size: 16 Copynumber: 4.5 Consensus size: 16
12080113 CAACCCAATT
12080123 TTTATTTGTATTTTTA-
1 TTTATTT-TATTTTTAC
12080139 TTTATTTTATTTTT-C
1 TTTATTTTATTTTTAC
* *
12080154 TTAATTTT-TATTTTAT
1 TTTATTTTAT-TTTTAC
*
12080170 TTTATTTTATTATTAC
1 TTTATTTTATTTTTAC
12080186 TTTATTTT
1 TTTATTTT
12080194 GTTTGGATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.02
15 18 0.39
16 26 0.57
17 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTTTTAC
Found at i:12080146 original size:21 final size:22
Alignment explanation
Indices: 12080122--12080198 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 22
12080112 GCAACCCAAT
12080122 TTTTATTTGTATTTTTA-TTTA
1 TTTTATTTGTATTTTTACTTTA
* *
12080143 TTTTATTTTTCTTAATTTTTATTTTA
1 TTTTA--TTT-GT-ATTTTTACTTTA
*
12080169 TTTTATTT-TATTATTACTTTA
1 TTTTATTTGTATTTTTACTTTA
*
12080190 TTTTGTTTG
1 TTTTATTTG
12080199 GATGTTGATA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 22 0.48
22 1 0.02
23 3 0.07
24 4 0.09
25 7 0.15
26 9 0.20
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTATTTGTATTTTTACTTTA
Found at i:12080149 original size:5 final size:5
Alignment explanation
Indices: 12080122--12080193 Score: 67
Period size: 5 Copynumber: 13.8 Consensus size: 5
12080112 GCAACCCAAT
*
12080122 TTTTA TTTGTA TTTT- TATTTA TTTTA TTTT- TCTTAA TTTTTA TTTTA
1 TTTTA TTT-TA TTTTA T-TTTA TTTTA TTTTA T-TTTA -TTTTA TTTTA
*
12080169 TTTTA TTTTA TTATTA CTTTA TTTT
1 TTTTA TTTTA TT-TTA TTTTA TTTT
12080194 GTTTGGATGT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 40 0.71
6 13 0.23
7 1 0.02
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:12080520 original size:3 final size:3
Alignment explanation
Indices: 12080512--12080554 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
12080502 TTGCTGCCCA
12080512 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12080555 TAAGAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12081197 original size:99 final size:99
Alignment explanation
Indices: 12081035--12081218 Score: 269
Period size: 99 Copynumber: 1.9 Consensus size: 99
12081025 ATAATTTTTT
* * * *
12081035 TTAGGAATATGTCGGGCTGAGTAATCAAGGTGGGGTGTTTGGCTGTCATCTCTCTTCGTGTCAAA
1 TTAGGAATATGTCGGGCTGAGTAACCAAGGCGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAA
* *
12081100 AGGTTTAATATGTTCTTAAGAAAAATATAATAAA
66 AGGTTCAATATATTCTTAAGAAAAATATAATAAA
* * **
12081134 TTAGGAGTATGTTGGGCTGAGTAACCGGGGCGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAA
1 TTAGGAATATGTCGGGCTGAGTAACCAAGGCGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAA
*
12081199 AGGTTCAATGTATTCTTAAG
66 AGGTTCAATATATTCTTAAG
12081219 CAATAATAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 74 1.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (99 bp):
TTAGGAATATGTCGGGCTGAGTAACCAAGGCGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAA
AGGTTCAATATATTCTTAAGAAAAATATAATAAA
Found at i:12081260 original size:19 final size:18
Alignment explanation
Indices: 12081236--12081286 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
12081226 AATAATGATT
12081236 AAAATAAAAACAAAA-AGGA
1 AAAATAAAAA-AAAATA-GA
12081255 AAAATAGAAAAAAAATAGA
1 AAAATA-AAAAAAAATAGA
*
12081274 AAAAGAAAAAAAA
1 AAAATAAAAAAAA
12081287 GTGATGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.24
19 17 0.59
20 5 0.17
ACGTcount: A:0.82, C:0.02, G:0.10, T:0.06
Consensus pattern (18 bp):
AAAATAAAAAAAAATAGA
Found at i:12081940 original size:10 final size:10
Alignment explanation
Indices: 12081915--12081964 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
12081905 AATTTTAGCT
*
12081915 TTTATCTTTTT
1 TTTATC-TTTA
12081926 TTTATCTTTA
1 TTTATCTTTA
*
12081936 ATTATCTTTA
1 TTTATCTTTA
12081946 TTTAT-TTGTA
1 TTTATCTT-TA
12081956 TTTATCTTT
1 TTTATCTTT
12081965 TAGAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 2 0.06
10 24 0.71
11 8 0.24
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:12086604 original size:20 final size:20
Alignment explanation
Indices: 12086581--12086627 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12086571 TCTCCCACGT
12086581 CCGTGTGACTT-TCCACACAC
1 CCGTGTGACTTAT-CACACAC
* *
12086601 CCGTGTAACTTATCACACGC
1 CCGTGTGACTTATCACACAC
12086621 CCGTGTG
1 CCGTGTG
12086628 GCACAGCCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (20 bp):
CCGTGTGACTTATCACACAC
Found at i:12091878 original size:29 final size:29
Alignment explanation
Indices: 12091817--12091887 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
12091807 TTATTTAAAT
12091817 TAAATTTTAAAAAATATAAAAATAAAAAAAC
1 TAAATTTT-AAAAATAT-AAAATAAAAAAAC
* * *
12091848 TAATTTCTTAAAAATAT-AAATACAAAGAC
1 TAAATT-TTAAAAATATAAAATAAAAAAAC
12091877 TAAATTTTAAA
1 TAAATTTTAAA
12091888 TTCATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 5 0.14
29 15 0.43
31 13 0.37
32 2 0.06
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (29 bp):
TAAATTTTAAAAATATAAAATAAAAAAAC
Found at i:12095528 original size:28 final size:28
Alignment explanation
Indices: 12095488--12095545 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
12095478 CTTAGAGAAT
12095488 AATAAATATAAAAGGAAAATATGAGCAC
1 AATAAATATAAAAGGAAAATATGAGCAC
12095516 AATAAATATAAAAGGAAAATATGAGCAC
1 AATAAATATAAAAGGAAAATATGAGCAC
12095544 AA
1 AA
12095546 CACAAATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.17
Consensus pattern (28 bp):
AATAAATATAAAAGGAAAATATGAGCAC
Found at i:12097814 original size:15 final size:15
Alignment explanation
Indices: 12097794--12097823 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12097784 TTGTATGGGC
*
12097794 TTAGGTTATTGGGTA
1 TTAGGTAATTGGGTA
12097809 TTAGGTAATTGGGTA
1 TTAGGTAATTGGGTA
12097824 AGCAGATGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (15 bp):
TTAGGTAATTGGGTA
Found at i:12098419 original size:15 final size:15
Alignment explanation
Indices: 12098395--12098427 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12098385 GAACTTTTGA
12098395 CAAACCTTTCAGGCT
1 CAAACCTTTCAGGCT
*
12098410 CAAACTTTTCAGGCT
1 CAAACCTTTCAGGCT
12098425 CAA
1 CAA
12098428 CCCAATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (15 bp):
CAAACCTTTCAGGCT
Found at i:12099988 original size:14 final size:13
Alignment explanation
Indices: 12099966--12100007 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
12099956 CAAAGGCATG
12099966 TTTAAGTATTTAT
1 TTTAAGTATTTAT
12099979 TTTGAAGTA-TTAT
1 TTT-AAGTATTTAT
12099992 ATTTAAGTATTTAT
1 -TTTAAGTATTTAT
12100006 TT
1 TT
12100008 GATTTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (13 bp):
TTTAAGTATTTAT
Found at i:12101334 original size:18 final size:19
Alignment explanation
Indices: 12101294--12101340 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
12101284 TTTCCCGAGA
* *
12101294 ATTTTAATATGCTTCTAGC
1 ATTTTAATATCCTTCAAGC
*
12101313 ATTTTAA-ATCCTTCAAGG
1 ATTTTAATATCCTTCAAGC
12101331 ATTTTAATAT
1 ATTTTAATAT
12101341 AAACTTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (19 bp):
ATTTTAATATCCTTCAAGC
Found at i:12106796 original size:40 final size:40
Alignment explanation
Indices: 12106741--12106820 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
12106731 AATCACGTAA
* * *
12106741 CTTGCGTTCGTGATTTAAGATCTCGATAGTCTTGCTATCT
1 CTTGCATTCGCGATTTAAGATCTCGATAGTCTTGCGATCT
12106781 CTTGCATTCGCGATTTAAGATCTCGATAGTCTTGCGATCT
1 CTTGCATTCGCGATTTAAGATCTCGATAGTCTTGCGATCT
12106821 AGAAAAGCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.40
Consensus pattern (40 bp):
CTTGCATTCGCGATTTAAGATCTCGATAGTCTTGCGATCT
Found at i:12108113 original size:9 final size:9
Alignment explanation
Indices: 12108099--12108124 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12108089 GTTATTTGAA
12108099 TCGAGTTAT
1 TCGAGTTAT
12108108 TCGAGTTAT
1 TCGAGTTAT
12108117 TCGAGTTA
1 TCGAGTTA
12108125 ATCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12113383 original size:16 final size:17
Alignment explanation
Indices: 12113362--12113393 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12113352 ATTTAGTTTT
12113362 TGTTTCTCT-TTCTCTC
1 TGTTTCTCTGTTCTCTC
12113378 TGTTTCTCTGTTCTCT
1 TGTTTCTCTGTTCTCT
12113394 GTCTCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.28, G:0.09, T:0.62
Consensus pattern (17 bp):
TGTTTCTCTGTTCTCTC
Found at i:12114223 original size:15 final size:15
Alignment explanation
Indices: 12114199--12114231 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12114189 GAACTGTTGA
12114199 CAAACCTTTCAGGCT
1 CAAACCTTTCAGGCT
*
12114214 CAAACTTTTCAGGCT
1 CAAACCTTTCAGGCT
12114229 CAA
1 CAA
12114232 CCCAATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (15 bp):
CAAACCTTTCAGGCT
Found at i:12118580 original size:19 final size:18
Alignment explanation
Indices: 12118545--12118580 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12118535 GAAGCAAGCA
*
12118545 ATGATTGAAGAAATCAGG
1 ATGATTGAAAAAATCAGG
12118563 ATGATTGAAAAGAATCAG
1 ATGATTGAAAA-AATCAG
12118581 ACCTGGAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (18 bp):
ATGATTGAAAAAATCAGG
Found at i:12120764 original size:14 final size:14
Alignment explanation
Indices: 12120745--12120771 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12120735 CAAAGGCATG
12120745 TTTAAATATTTATA
1 TTTAAATATTTATA
12120759 TTTAAATATTTAT
1 TTTAAATATTTAT
12120772 TTGACTTTAG
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAAATATTTATA
Found at i:12122454 original size:16 final size:15
Alignment explanation
Indices: 12122433--12122504 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 15
12122423 CAAAGATTGG
12122433 GAACAACTCTTATTTA
1 GAACAACT-TTATTTA
*
12122449 GAACAATTGTTATGTTCA
1 GAACAACT-TTAT-TT-A
* * *
12122467 TAACAACTATAGTTTG
1 GAACAACTTTA-TTTA
12122483 GAACAACTTCTATTTA
1 GAACAACTT-TATTTA
12122499 GAACAA
1 GAACAA
12122505 TTATGTTTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
16 27 0.63
17 8 0.19
18 8 0.19
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (15 bp):
GAACAACTTTATTTA
Found at i:12123140 original size:24 final size:23
Alignment explanation
Indices: 12123101--12123167 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
12123091 CACCAAACTT
12123101 TTCTCCTCTTTT-CTCTCCTTACTC
1 TTCTCCT-TTTTCCTCTCCTT-CTC
*
12123125 TTCTCCTTTTTCCTCTCCCTTTTC
1 TTCTCCTTTTTCCTCT-CCTTCTC
* *
12123149 TTCT-CTCTTTCCTTTCCTT
1 TTCTCCTTTTTCCTCTCCTT
12123168 TTGTTTCGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.11
23 13 0.34
24 17 0.45
25 4 0.11
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.58
Consensus pattern (23 bp):
TTCTCCTTTTTCCTCTCCTTCTC
Found at i:12125595 original size:47 final size:47
Alignment explanation
Indices: 12125526--12125843 Score: 325
Period size: 47 Copynumber: 6.6 Consensus size: 47
12125516 TTCGGAGAAA
* * *
12125526 TGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGG
1 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCGG
*
12125573 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAG
1 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCGG
* ** * * * *
12125620 TGTGATATGTGATTTTCGTATAAGACCATAGCTGGGCTATGGCTTTGGAG
1 TGTGATATGTGCTACT-GTATAAGACCATATCTGGGATATGGC-ATCG-G
* * *
12125670 AAATGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGG
1 ---TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCGG
*
12125720 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAG
1 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCGG
* * * ** * *
12125767 TGTGATATGTGAT-CCGTGTAAGACCATGGCTGGGCTATGGCCTCGG
1 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCGG
**
12125813 TATGTGATATGTGACTA-TGTGCAAGACCATA
1 --TGTGATATGTG-CTACTGTATAAGACCATA
12125844 GTTTTACTAT
Statistics
Matches: 225, Mismatches: 36, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
46 26 0.12
47 111 0.49
48 35 0.16
49 13 0.06
50 2 0.01
51 2 0.01
52 23 0.10
53 13 0.06
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (47 bp):
TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCGG
Found at i:12125695 original size:100 final size:99
Alignment explanation
Indices: 12125573--12125761 Score: 288
Period size: 100 Copynumber: 1.9 Consensus size: 99
12125563 ATGGCATCGG
* * **
12125573 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATGTGATTTTCG
1 TGTGATATGTGCTACCGTATAAGACCATATCCGGGATATGGCATCAGTGTGATATGTGATACT-G
*
12125638 TATAAGACCATAGCTGGGCTATGGCTTTGGAGAAA
65 TATAAGACCATAGCTGGGATATGGCTTTGGAGAAA
* * *
12125673 TGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
1 TGTGATATGTGCTACCGTATAAGACCATATCCGGGATATGGCATCAGTGTGATATGTGATACTGT
*
12125738 ATAAGACCATATCTGGGATATGGC
66 ATAAGACCATAGCTGGGATATGGC
12125762 ATCAGTGTGA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 24 0.30
100 56 0.70
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (99 bp):
TGTGATATGTGCTACCGTATAAGACCATATCCGGGATATGGCATCAGTGTGATATGTGATACTGT
ATAAGACCATAGCTGGGATATGGCTTTGGAGAAA
Found at i:12125740 original size:147 final size:147
Alignment explanation
Indices: 12125464--12125812 Score: 605
Period size: 147 Copynumber: 2.4 Consensus size: 147
12125454 TGGTTGGACC
* * *
12125464 ATGGCAGCA-TGTGAAATGTGATTTCCGTATAAGACCATAGCTGGGCTACGGCTTCGGAGAAATG
1 ATGGCATCAGTGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATG
12125528 TGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGTAT
66 TGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGTAT
12125593 AAGACCATATCTGGGAT
131 AAGACCATATCTGGGAT
* *
12125610 ATGGCATCAGTGTGATATGTGATTTTCGTATAAGACCATAGCTGGGCTATGGCTTTGGAGAAATG
1 ATGGCATCAGTGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATG
12125675 TGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGTAT
66 TGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGTAT
12125740 AAGACCATATCTGGGAT
131 AAGACCATATCTGGGAT
* * *
12125757 ATGGCATCAGTGTGATATGTGA--TCCGTGTAAGACCATGGCTGGGCTATGGCCTCGG
1 ATGGCATCAGTGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGG
12125813 TATGTGATAT
Statistics
Matches: 192, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
145 29 0.15
146 8 0.04
147 155 0.81
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (147 bp):
ATGGCATCAGTGTGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATG
TGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGTAT
AAGACCATATCTGGGAT
Found at i:12126211 original size:24 final size:22
Alignment explanation
Indices: 12126168--12126211 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
12126158 ATAAATTGCG
* *
12126168 AAAATTGAGTTAAGGGCTGAAT
1 AAAATTGAGTTAAAGCCTGAAT
12126190 AAAATATGAGATTAAAGCCTGA
1 AAAAT-TGAG-TTAAAGCCTGA
12126212 TGAGTCTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 4 0.22
24 9 0.50
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (22 bp):
AAAATTGAGTTAAAGCCTGAAT
Found at i:12128236 original size:21 final size:21
Alignment explanation
Indices: 12128176--12128236 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
12128166 TCTACAAATC
* *
12128176 TGGTAGCTTGTCCACATATTTT
1 TGGTAGCTTGTCTACA-ATTAT
* * *
12128198 TGGTAGTTTATCTGCAATTAT
1 TGGTAGCTTGTCTACAATTAT
*
12128219 TGGTGGCTTGTCTACAAT
1 TGGTAGCTTGTCTACAAT
12128237 ATGGTGTGTA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.44
Consensus pattern (21 bp):
TGGTAGCTTGTCTACAATTAT
Found at i:12141663 original size:15 final size:15
Alignment explanation
Indices: 12141643--12141684 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
12141633 ATGAACTTCC
12141643 CCAAAATAATAAAAT
1 CCAAAATAATAAAAT
12141658 CCAAAATAATAAAAAT
1 CCAAAATAAT-AAAAT
*
12141674 -AAAAATAATAA
1 CCAAAATAATAA
12141685 TTATATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 2 0.08
15 18 0.72
16 5 0.20
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
CCAAAATAATAAAAT
Found at i:12144135 original size:39 final size:39
Alignment explanation
Indices: 12144078--12144216 Score: 147
Period size: 39 Copynumber: 3.6 Consensus size: 39
12144068 ATGGTTTTAT
12144078 AAGTTGTGTATCAGCAAAGCTCCTCCATGAGCTAAGGAG
1 AAGTTGTGTATCAGCAAAGCTCCTCCATGAGCTAAGGAG
* * * *
12144117 AAGTTGTGTATCAACAAAGCTCC-CCTTGAGCTTATGGAT
1 AAGTTGTGTATCAGCAAAGCTCCTCCATGAGC-TAAGGAG
* * * *
12144156 AAATTGTGTATCAGCAAAGCT-TTCTATGAGCTAAGGAC
1 AAGTTGTGTATCAGCAAAGCTCCTCCATGAGCTAAGGAG
** * *
12144194 AAGCCGTGTATTAGCAAATCTCC
1 AAGTTGTGTATCAGCAAAGCTCC
12144217 CTTGTGAGCT
Statistics
Matches: 80, Mismatches: 17, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
38 28 0.35
39 52 0.65
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (39 bp):
AAGTTGTGTATCAGCAAAGCTCCTCCATGAGCTAAGGAG
Found at i:12144217 original size:77 final size:79
Alignment explanation
Indices: 12144076--12144244 Score: 216
Period size: 78 Copynumber: 2.2 Consensus size: 79
12144066 GAATGGTTTT
* **
12144076 ATAAGTTGTGTATCAGCAAAGCTCCTCCATGAGCTAAGGAGAAGTTGTGTATCAACAAAGCTCCC
1 ATAAGTTGTGTATCAGCAAAGCTCCTCCATGAGCTAAGGACAAGCCGTGTATCAACAAAGCTCCC
*
12144141 CT-TGAGCTTATGG
66 CTGTGAGCTTATGA
* * * * * *
12144154 ATAAATTGTGTATCAGCAAAGCT-TTCTATGAGCTAAGGACAAGCCGTGTATTAGCAAATCTCCC
1 ATAAGTTGTGTATCAGCAAAGCTCCTCCATGAGCTAAGGACAAGCCGTGTATCAACAAAGCTCCC
*
12144218 TTGTGAGCTTATGA
66 CTGTGAGCTTATGA
*
12144232 ATAAGCTGTGTAT
1 ATAAGTTGTGTAT
12144245 TAACAAACTT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
77 34 0.44
78 43 0.56
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (79 bp):
ATAAGTTGTGTATCAGCAAAGCTCCTCCATGAGCTAAGGACAAGCCGTGTATCAACAAAGCTCCC
CTGTGAGCTTATGA
Found at i:12144304 original size:40 final size:40
Alignment explanation
Indices: 12144076--12144305 Score: 177
Period size: 40 Copynumber: 5.8 Consensus size: 40
12144066 GAATGGTTTT
* * *
12144076 ATAAGTTGTGTATCAGCAAAGCTCCTCCATGAGC-TAAGG
1 ATAAGCTGTGTATCAGCAAAGCTCCTCCGTGAGCTTATGG
* * * *
12144115 AGAAGTTGTGTATCAACAAAGCTCC-CCTTGAGCTTATGG
1 ATAAGCTGTGTATCAGCAAAGCTCCTCCGTGAGCTTATGG
** * ** *
12144154 ATAAATTGTGTATCAGCAAAGCT-TTCTATGAGC-TAAGG
1 ATAAGCTGTGTATCAGCAAAGCTCCTCCGTGAGCTTATGG
* * * * * *
12144192 ACAAGCCGTGTATTAGCAAATCTCC-CTTGTGAGCTTATGA
1 ATAAGCTGTGTATCAGCAAAGCTCCTC-CGTGAGCTTATGG
* * *
12144232 ATAAGCTGTGTATTAACAAA-CTTCC-CCTGTGAGCTTATGA
1 ATAAGCTGTGTATCAGCAAAGC-TCCTCC-GTGAGCTTATGG
*
12144272 ATAAGCTGTGTATCAGCAAAGCTCCTACGTGAGC
1 ATAAGCTGTGTATCAGCAAAGCTCCTCCGTGAGC
12144306 AAATGATAAA
Statistics
Matches: 154, Mismatches: 28, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
38 29 0.19
39 60 0.39
40 63 0.41
41 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (40 bp):
ATAAGCTGTGTATCAGCAAAGCTCCTCCGTGAGCTTATGG
Found at i:12147959 original size:27 final size:27
Alignment explanation
Indices: 12147929--12147982 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
12147919 AACAAAGCTG
*
12147929 CCAGTAACAGTATATGTGGCAAAGCCA
1 CCAGAAACAGTATATGTGGCAAAGCCA
* *
12147956 CCAGAAATAGTATATGTGGCGAAGCCA
1 CCAGAAACAGTATATGTGGCAAAGCCA
12147983 TCGGTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (27 bp):
CCAGAAACAGTATATGTGGCAAAGCCA
Found at i:12149972 original size:40 final size:40
Alignment explanation
Indices: 12149868--12150132 Score: 338
Period size: 40 Copynumber: 6.7 Consensus size: 40
12149858 GCTCCTCGTT
* * ** *
12149868 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
12149908 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* *
12149947 CAAATGCCTTCGGAACTTAATCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
**
12149987 CGTATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
12150027 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* * * * *
12150067 CAAATGCCTTCGGAACTTAATCCGGATATATTC-ACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCA
*
12150108 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
12150133 CAGCATTCAA
Statistics
Matches: 201, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.17
40 157 0.78
41 9 0.04
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
Done.