Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 99 of 438
Found at i:27932027 original size:19 final size:18
Alignment explanation
Indices: 27932005--27932043 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
27931995 TGAGAATTGA
27932005 CTAAATGGGCCGGAATGGG
1 CTAAATGGGCCGG-ATGGG
*
27932024 CTAAATGGGCCTGATGGG
1 CTAAATGGGCCGGATGGG
27932042 CT
1 CT
27932044 GTTGGGCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (18 bp):
CTAAATGGGCCGGATGGG
Found at i:27932181 original size:29 final size:28
Alignment explanation
Indices: 27932113--27932229 Score: 94
Period size: 29 Copynumber: 4.1 Consensus size: 28
27932103 TGAGCATGAG
*
27932113 TATAATATGATTTGGGCCTAATGGGCCA
1 TATAATATGAATTGGGCCTAATGGGCCA
** * *
27932141 TATGAAGGTGAATTGGGCTTAGTGGGCCA
1 TAT-AATATGAATTGGGCCTAATGGGCCA
*
27932170 TAATAATATGAATTGGGCC-AGATGGGTCA
1 T-ATAATATGAATTGGGCCTA-ATGGGCCA
* * * *
27932199 TTTGAATAAG-ATTGGGCCTAGTGGGCTA
1 TAT-AATATGAATTGGGCCTAATGGGCCA
27932227 TAT
1 TAT
27932230 GCATGTATGT
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
28 20 0.29
29 46 0.68
30 2 0.03
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (28 bp):
TATAATATGAATTGGGCCTAATGGGCCA
Found at i:27937005 original size:40 final size:39
Alignment explanation
Indices: 27936961--27937153 Score: 242
Period size: 39 Copynumber: 4.9 Consensus size: 39
27936951 GTTCAAAACA
* * ** * *
27936961 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
27937001 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
27937041 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* * *
27937080 CCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
27937119 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
27937154 TTCATTCACA
Statistics
Matches: 137, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 97 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:27937072 original size:39 final size:39
Alignment explanation
Indices: 27936991--27937153 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
27936981 TATGGTAACC
* *
27936991 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
27937031 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
27937070 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
27937109 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
27937148 CGCACA
1 CGCACA
27937154 TTCATTCACA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:27942704 original size:40 final size:40
Alignment explanation
Indices: 27942596--27942805 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
27942586 CGGGATTTAA
* * * * *
27942596 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
27942636 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
27942676 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
27942716 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
27942756 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
27942796 CCGGATATAT
1 CCGGATATAT
27942806 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:27950840 original size:40 final size:40
Alignment explanation
Indices: 27950732--27950941 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
27950722 CGGGATTTAA
* * * * *
27950732 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
27950772 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
27950812 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
27950852 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
27950892 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
27950932 CCGGATATAT
1 CCGGATATAT
27950942 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:27961393 original size:39 final size:39
Alignment explanation
Indices: 27961317--27961430 Score: 165
Period size: 39 Copynumber: 2.9 Consensus size: 39
27961307 TATGGTAACC
* * *
27961317 CGCACAAATGCATTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
27961357 CGCACAATTGCCTTCGGGCTTAGCCCGGATGTCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
27961396 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
27961431 TCGAACATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 51 0.76
40 16 0.24
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:27968400 original size:53 final size:53
Alignment explanation
Indices: 27968206--27968412 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 53
27968196 ATTAAGGTTT
* * * * *
27968206 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTT-TTACAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATA-AA-GC
* * * * * * * *
27968260 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAAGC
* * * *
27968315 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAAGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAAGC
* *
27968368 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
27968413 TAAAAAGGAA
Statistics
Matches: 121, Mismatches: 29, Indels: 7
0.77 0.18 0.04
Matches are distributed among these distances:
53 45 0.37
54 37 0.31
55 36 0.30
56 1 0.01
57 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAAGC
Found at i:27971241 original size:39 final size:39
Alignment explanation
Indices: 27971135--27971305 Score: 234
Period size: 39 Copynumber: 4.4 Consensus size: 39
27971125 CCTTGGGACA
* ** * **
27971135 TAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CT
* * * *
27971175 TAACCCGGATATCACAATTTGCACAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
*
27971214 TAGCCCGGATATCATAACTCGCCCAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
27971253 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
27971292 TAGCCCGGATATCA
1 TAGCCCGGATATCA
27971306 CTCGAACATT
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 88 0.77
40 27 0.23
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (39 bp):
TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
Found at i:27974429 original size:20 final size:18
Alignment explanation
Indices: 27974382--27974430 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
27974372 CAAGATAAAC
27974382 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
27974399 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
27974419 ATTAAATTAATA
1 ATTAAATTAATA
27974431 AAATGCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:27974964 original size:2 final size:2
Alignment explanation
Indices: 27974957--27974991 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27974947 TTAAACATTA
27974957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27974992 CATACGGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27975734 original size:23 final size:23
Alignment explanation
Indices: 27975704--27975752 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
27975694 ACAAACATAT
27975704 TTATCATGAAACATACCTCCAAA
1 TTATCATGAAACATACCTCCAAA
27975727 TTATCATGAAACATACCTCCAAA
1 TTATCATGAAACATACCTCCAAA
27975750 TTA
1 TTA
27975753 AGCTTATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.29
Consensus pattern (23 bp):
TTATCATGAAACATACCTCCAAA
Found at i:27981116 original size:36 final size:36
Alignment explanation
Indices: 27981075--27981158 Score: 134
Period size: 36 Copynumber: 2.3 Consensus size: 36
27981065 TACTCTCTAT
*
27981075 TTTGGTGTGTTTCGGATGGA-TGAGCTCTTATGAGCA
1 TTTGGTGTGTTTCGAATGGACT-AGCTCTTATGAGCA
27981111 TTTGGTGTGTTTCGAATGGACTAGCTCTTATGAGCA
1 TTTGGTGTGTTTCGAATGGACTAGCTCTTATGAGCA
*
27981147 TCTGGTGTGTTT
1 TTTGGTGTGTTT
27981159 TGGTAGGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
36 44 0.98
37 1 0.02
ACGTcount: A:0.15, C:0.12, G:0.31, T:0.42
Consensus pattern (36 bp):
TTTGGTGTGTTTCGAATGGACTAGCTCTTATGAGCA
Found at i:27983121 original size:29 final size:29
Alignment explanation
Indices: 27983088--27983184 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 29
27983078 GTACATAGTA
* * *
27983088 CCTGATAAATATAACACCGACACAGAGTG
1 CCTGATAAATGTAACACTGACACAAAGTG
* ** *
27983117 CCTGATAACTGTAACACTGGTACAAAGTA
1 CCTGATAAATGTAACACTGACACAAAGTG
* *
27983146 CTTGATAAATGTAATCACTGACACATAGTG
1 CCTGATAAATGTAA-CACTGACACAAAGTG
27983176 CCTGATAAA
1 CCTGATAAA
27983185 CCCTAATAAC
Statistics
Matches: 53, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
29 34 0.64
30 19 0.36
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (29 bp):
CCTGATAAATGTAACACTGACACAAAGTG
Found at i:27984728 original size:40 final size:40
Alignment explanation
Indices: 27984669--27984794 Score: 171
Period size: 40 Copynumber: 3.1 Consensus size: 40
27984659 CGGAATACAA
* * * *
27984669 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGAACAACTTGCACGAATGCCTTCGGGTATTAGC
* * *
27984709 CTGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATAGAACAACTTGCACGAATGCCTTCGGGTATTAGC
**
27984749 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATAGAACAACTTGCACGAATGCCTTCGGGTATTAGC
27984789 CCGGAT
1 CCGGAT
27984795 GTGGTCACTA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATAGAACAACTTGCACGAATGCCTTCGGGTATTAGC
Found at i:27984809 original size:80 final size:80
Alignment explanation
Indices: 27984669--27984838 Score: 200
Period size: 80 Copynumber: 2.1 Consensus size: 80
27984659 CGGAATACAA
* * * *
27984669 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCTGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTATTAGCCCGGATAGAACGACTAGCAC-AATG
27984733 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAGC
* * * **
27984749 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTATTAGCCCGGAT-AGAACGACTAGCACAATG
* *
27984813 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAGC
*
27984829 TCGGATATAA
1 CCGGATATAA
27984839 TTACTAGCAT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 3 0.04
80 70 0.93
81 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACATGCACGAATGCCTTCGGGTATTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAGC
Found at i:27984817 original size:40 final size:40
Alignment explanation
Indices: 27984685--27984871 Score: 148
Period size: 40 Copynumber: 4.7 Consensus size: 40
27984675 ATAACCACAT
* * * * * *
27984685 GCACGAATGCCTTCGGGTCTTAGCCTGGATAGAACGACTT
1 GCACAAATGCCTTCGGGTATTAGCCCGGATTGAACAACTA
* *
27984725 GCACAAATGCCTTCGGGTATTAGCCCGGATTTAACAACTT
1 GCACAAATGCCTTCGGGTATTAGCCCGGATTGAACAACTA
* **
27984765 GCACGAATGCCTTCGGGTATTAGCCCGGATGTGGTC-ACTA
1 GCACAAATGCCTTCGGGTATTAGCCCGGAT-TGAACAACTA
* * * **
27984805 GCAC-AATGGCCTTCGGGTCTTAACTCGGATAT-AATTACTA
1 GCACAAAT-GCCTTCGGGTATTAGCCCGGAT-TGAACAACTA
* *
27984845 GCATAAATGTCTTCGGG-ACTTAGCCCG
1 GCACAAATGCCTTCGGGTA-TTAGCCCG
27984872 AATATCATTC
Statistics
Matches: 119, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
39 3 0.03
40 111 0.93
41 5 0.04
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTATTAGCCCGGATTGAACAACTA
Found at i:27996505 original size:22 final size:22
Alignment explanation
Indices: 27996480--27996554 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
27996470 AGATAATATA
27996480 CTTATTTTTAATACAAAAGAAT
1 CTTATTTTTAATACAAAAGAAT
*** *
27996502 CTTATTCAAAATAATAATTAAG-AT
1 CTTATTTTTAAT-ACAA--AAGAAT
27996526 ACTTATTTTTAATACAAAAGAAT
1 -CTTATTTTTAATACAAAAGAAT
27996549 CTTATT
1 CTTATT
27996555 CAAAATAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 18 0.45
23 5 0.12
24 5 0.12
25 12 0.30
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.41
Consensus pattern (22 bp):
CTTATTTTTAATACAAAAGAAT
Found at i:27996524 original size:25 final size:25
Alignment explanation
Indices: 27996496--27996570 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
27996486 TTTAATACAA
27996496 AAGAATCTTATTCAAAATAATAATT
1 AAGAATCTTATTCAAAATAATAATT
*** *
27996521 AAG-ATACTTATTTTTAAT-ACAA--
1 AAGAAT-CTTATTCAAAATAATAATT
27996543 AAGAATCTTATTCAAAATAATAATT
1 AAGAATCTTATTCAAAATAATAATT
27996568 AAG
1 AAG
27996571 TAATATAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
22 12 0.32
23 5 0.14
24 5 0.14
25 15 0.41
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (25 bp):
AAGAATCTTATTCAAAATAATAATT
Found at i:27996537 original size:47 final size:47
Alignment explanation
Indices: 27996477--27996570 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
27996467 AATAGATAAT
27996477 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
1 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
27996524 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
1 ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
27996571 TAATATAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (47 bp):
ATACTTATTTTTAATACAAAAGAATCTTATTCAAAATAATAATTAAG
Found at i:27997085 original size:21 final size:21
Alignment explanation
Indices: 27997061--27997116 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
27997051 TTATATTATT
27997061 TATAAAATTTTA-TATATGAAA
1 TATAAAATTTTATTATAT-AAA
27997082 TATAAAATTAATTATTATATAAA
1 TATAAAATT--TTATTATATAAA
27997105 TAATTAAAATTT
1 T-A-TAAAATTT
27997117 ACTATTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 9 0.30
23 8 0.27
24 6 0.20
25 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAAAATTTTATTATATAAA
Found at i:27997726 original size:25 final size:24
Alignment explanation
Indices: 27997685--27997733 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
27997675 TGGAAGAGTT
* *
27997685 TTATTTTATTTTATATTAATATAA
1 TTATTTTATTTAATATTAAAATAA
27997709 TTATTTTCATTTAATATTAAAATAA
1 TTATTTT-ATTTAATATTAAAATAA
27997734 ATATAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTTTATTTAATATTAAAATAA
Found at i:27997769 original size:45 final size:44
Alignment explanation
Indices: 27997720--27997824 Score: 101
Period size: 45 Copynumber: 2.4 Consensus size: 44
27997710 TATTTTCATT
27997720 TAATATTAAAATAAATAT-AAATATTTAATTTTAATTTAATT-TTAA
1 TAATATTAAAATAAATATCAAA-A-TTAATTTTAATTT-ATTCTTAA
** *
27997765 TAATAATT-ATTTACAATTTCAAAATTAATTTTAATTTATTCTTAA
1 TAAT-ATTAAAATA-AATATCAAAATTAATTTTAATTTATTCTTAA
*
27997810 TAAT-TTAAAAAAAAT
1 TAATATTAAAATAAAT
27997825 TGTATAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
43 5 0.10
44 5 0.10
45 28 0.57
46 8 0.16
47 3 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.48
Consensus pattern (44 bp):
TAATATTAAAATAAATATCAAAATTAATTTTAATTTATTCTTAA
Found at i:28001009 original size:17 final size:17
Alignment explanation
Indices: 28000979--28001023 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
28000969 AGATTATTGG
*
28000979 AAGCTTGATCGGGTTGA
1 AAGCTCGATCGGGTTGA
* *
28000996 AAGCTCGATTGGGTTGG
1 AAGCTCGATCGGGTTGA
28001013 AAGCTCG-TCGG
1 AAGCTCGATCGG
28001024 AGATCTATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.27
Consensus pattern (17 bp):
AAGCTCGATCGGGTTGA
Found at i:28001163 original size:20 final size:20
Alignment explanation
Indices: 28001140--28001186 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28001130 AGCTTCGTCC
* *
28001140 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAACTCAGTTG
* *
28001160 AGCTCATTTCAACTCGGTTG
1 AGCTCAATTCAACTCAGTTG
28001180 AGCTCAA
1 AGCTCAA
28001187 CCGAGCTTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (20 bp):
AGCTCAATTCAACTCAGTTG
Found at i:28001445 original size:15 final size:16
Alignment explanation
Indices: 28001425--28001457 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28001415 ATTATATGAA
28001425 TAATTATAT-TTTATT
1 TAATTATATGTTTATT
*
28001440 TAATTATGTGTTTATT
1 TAATTATATGTTTATT
28001456 TA
1 TA
28001458 TTTGTAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TAATTATATGTTTATT
Found at i:28002765 original size:7 final size:8
Alignment explanation
Indices: 28002745--28002775 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
28002735 AAGTATATTA
28002745 AAAAAATC
1 AAAAAATC
28002753 AAAAAAATC
1 -AAAAAATC
28002762 AAAAAATC
1 AAAAAATC
28002770 AAAAAA
1 AAAAAA
28002776 ATTAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATC
Found at i:28002784 original size:17 final size:17
Alignment explanation
Indices: 28002745--28002777 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28002735 AAGTATATTA
28002745 AAAAAATCAAAAAAATC
1 AAAAAATCAAAAAAATC
28002762 AAAAAATCAAAAAAAT
1 AAAAAATCAAAAAAAT
28002778 TAGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAATCAAAAAAATC
Found at i:28002786 original size:10 final size:9
Alignment explanation
Indices: 28002744--28002777 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
28002734 AAAGTATATT
28002744 AAAAAAATC
1 AAAAAAATC
28002753 AAAAAAATC
1 AAAAAAATC
28002762 -AAAAAATC
1 AAAAAAATC
28002770 AAAAAAAT
1 AAAAAAAT
28002778 TAGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:28003687 original size:15 final size:15
Alignment explanation
Indices: 28003651--28003691 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
28003641 AGAAAACAAG
* *
28003651 AAAAGAACA-AGATG
1 AAAAGAAAAGAGATC
28003665 AAAA-AAAAGAGATC
1 AAAAGAAAAGAGATC
28003679 AAAAGAAAAGAGA
1 AAAAGAAAAGAGA
28003692 GGCAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 3 0.13
14 12 0.52
15 8 0.35
ACGTcount: A:0.71, C:0.05, G:0.20, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAGAGATC
Found at i:28003771 original size:19 final size:20
Alignment explanation
Indices: 28003739--28003779 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
28003729 GAATGAAATC
28003739 GAGAGAAGAAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
28003759 GAGAGAA-AAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
28003778 GA
1 GA
28003780 AAGTGAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (20 bp):
GAGAGAAGAAACAAAGAAAA
Found at i:28003822 original size:30 final size:31
Alignment explanation
Indices: 28003765--28003824 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
28003755 AAAAGAGAGA
*
28003765 AAAACAAAGAAAAGAAAGTGAACAAGAAAAC
1 AAAACAAAGAAAAGAAAGTGAAAAAGAAAAC
* * *
28003796 AAAATAAA-AAAAGACATTGAAAAAGAAAA
1 AAAACAAAGAAAAGAAAGTGAAAAAGAAAA
28003825 AGAATGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07
Consensus pattern (31 bp):
AAAACAAAGAAAAGAAAGTGAAAAAGAAAAC
Found at i:28005913 original size:32 final size:32
Alignment explanation
Indices: 28005876--28005939 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28005866 CTCGGTTGAG
28005876 CTCAACTGAGCTTACTTTCTGCTCGTTCTTCA
1 CTCAACTGAGCTTACTTTCTGCTCGTTCTTCA
28005908 CTCAACTGAGCTTACTTTCTGCTCGTTCTTCA
1 CTCAACTGAGCTTACTTTCTGCTCGTTCTTCA
28005940 TTTCAATAAA
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:0.16, C:0.31, G:0.12, T:0.41
Consensus pattern (32 bp):
CTCAACTGAGCTTACTTTCTGCTCGTTCTTCA
Found at i:28006171 original size:15 final size:16
Alignment explanation
Indices: 28006151--28006183 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28006141 ATTATATGAA
28006151 TAATTATAT-TTTATT
1 TAATTATATGTTTATT
*
28006166 TAATTATGTGTTTATT
1 TAATTATATGTTTATT
28006182 TA
1 TA
28006184 TTTGTAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TAATTATATGTTTATT
Found at i:28011469 original size:43 final size:42
Alignment explanation
Indices: 28011348--28011504 Score: 144
Period size: 43 Copynumber: 3.6 Consensus size: 42
28011338 ATCTCGTACA
* * *
28011348 ATGCCAACGTCCTAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACTTCC-AGACGTGGTCTTACACGTAAATTAAATA-CG
28011391 ATGCC-ACTGTCCCAGACAG-GGTCTTACACG-AAATTAAATACG
1 ATGCCAACT-T-CCAGAC-GTGGTCTTACACGTAAATTAAATACG
28011433 ATGCCAACATTCCAGACGTGGTCTTACACGTAAATTATAAGT-CG
1 ATGCCAAC-TTCCAGACGTGGTCTTACACGTAAATTA-AA-TACG
* * *
28011477 ATGCCAACGTCCCAGACTTGGTCATACA
1 ATGCCAAC-TTCCAGACGTGGTCTTACA
28011505 GGATAACACA
Statistics
Matches: 97, Mismatches: 7, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
41 1 0.01
42 26 0.27
43 37 0.38
44 32 0.33
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAACTTCCAGACGTGGTCTTACACGTAAATTAAATACG
Found at i:28015777 original size:22 final size:21
Alignment explanation
Indices: 28015752--28015821 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
28015742 GAGTTCATTA
28015752 AATGTTAAATATTAATTATTCC
1 AATGTTAAA-ATTAATTATTCC
* * * *
28015774 AATGGCTAAAATCAGTTCATT-A
1 AAT-GTTAAAATTAATT-ATTCC
*
28015796 AATGTTAGAGATTAATTATTCC
1 AATGTTA-AAATTAATTATTCC
28015818 AATG
1 AATG
28015822 GCTAAAATCT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
21 6 0.17
22 21 0.60
23 8 0.23
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (21 bp):
AATGTTAAAATTAATTATTCC
Found at i:28015810 original size:44 final size:44
Alignment explanation
Indices: 28015743--28015830 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
28015733 AACCCTACAG
*
28015743 AGTTCATTAAATGTTAAATATTAATTATTCCAATGGCTAAAATC
1 AGTTCATTAAATGTTAAAGATTAATTATTCCAATGGCTAAAATC
*
28015787 AGTTCATTAAATGTTAGAGATTAATTATTCCAATGGCTAAAATC
1 AGTTCATTAAATGTTAAAGATTAATTATTCCAATGGCTAAAATC
28015831 TCCAGCAGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (44 bp):
AGTTCATTAAATGTTAAAGATTAATTATTCCAATGGCTAAAATC
Found at i:28023397 original size:5 final size:5
Alignment explanation
Indices: 28023353--28023394 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
28023343 TACGGTTGCA
*
28023353 CACCT CACCT CACCT CACCT CACCT CACCT CACCT CATCT CA
1 CACCT CACCT CACCT CACCT CACCT CACCT CACCT CACCT CA
28023395 TCTTTTTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.21, C:0.57, G:0.00, T:0.21
Consensus pattern (5 bp):
CACCT
Found at i:28026501 original size:20 final size:21
Alignment explanation
Indices: 28026473--28026515 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
28026463 AATTGAAGTG
*
28026473 AATGTGATATTGAG-TTATGA
1 AATGCGATATTGAGATTATGA
28026493 AATGCGATATTGAGATTATGA
1 AATGCGATATTGAGATTATGA
28026514 AA
1 AA
28026516 AGTAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (21 bp):
AATGCGATATTGAGATTATGA
Found at i:28027997 original size:39 final size:39
Alignment explanation
Indices: 28027953--28028028 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
28027943 ATGCAGAGCA
28027953 CATATTAATAATGTTCAAACTATGACATAATTAAAGATT
1 CATATTAATAATGTTCAAACTATGACATAATTAAAGATT
*
28027992 CATATTAATGATGTTCAAACTATGACATAATTAAAGA
1 CATATTAATAATGTTCAAACTATGACATAATTAAAGA
28028029 CACAAACTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (39 bp):
CATATTAATAATGTTCAAACTATGACATAATTAAAGATT
Found at i:28030551 original size:25 final size:25
Alignment explanation
Indices: 28030497--28030551 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
28030487 AATCATTAAA
*
28030497 TTTAATTTAATATTAAGACAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
28030522 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
28030546 TATTAA
1 T-TTAA
28030552 GATAAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:28030722 original size:67 final size:67
Alignment explanation
Indices: 28030589--28030724 Score: 175
Period size: 67 Copynumber: 2.0 Consensus size: 67
28030579 AAATATATTA
* * ** * *
28030589 AAATAATATTATTTTTAGGATACTTAATCTAAAATTAAATTCTTTGATAGAGTCCTAATAGGAGT
1 AAATAATAATATTTTAAAAATACTTAATCTAAAATCAAATTCTTTGATAGAGTCCTAATAGAAGT
28030654 GT
66 GT
* * *
28030656 AAATAATAATATTTTAAAAATACTTAATTTAAAATCAAATTCTTTGGTAGAGT-CTCGATAGAAG
1 AAATAATAATATTTTAAAAATACTTAATCTAAAATCAAATTCTTTGATAGAGTCCT-AATAGAAG
28030720 TGT
65 TGT
28030723 AA
1 AA
28030725 CTCTTTTATT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 2 0.03
67 57 0.97
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (67 bp):
AAATAATAATATTTTAAAAATACTTAATCTAAAATCAAATTCTTTGATAGAGTCCTAATAGAAGT
GT
Found at i:28030975 original size:19 final size:19
Alignment explanation
Indices: 28030951--28030988 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28030941 TCGGTTTTGG
*
28030951 GCCAGGTCTAATTTACTAT
1 GCCAGGCCTAATTTACTAT
28030970 GCCAGGCCTAATTTACTAT
1 GCCAGGCCTAATTTACTAT
28030989 CTTAGGTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (19 bp):
GCCAGGCCTAATTTACTAT
Found at i:28036139 original size:18 final size:18
Alignment explanation
Indices: 28036116--28036150 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
28036106 GGGTTAAGAG
28036116 GTATTACCGGATATATCC
1 GTATTACCGGATATATCC
28036134 GTATTACCGGATATATC
1 GTATTACCGGATATATC
28036151 GAAACATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (18 bp):
GTATTACCGGATATATCC
Found at i:28037927 original size:27 final size:28
Alignment explanation
Indices: 28037871--28037940 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
28037861 AAATTTGTAC
28037871 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
28037899 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
28037926 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28037941 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:28045805 original size:31 final size:28
Alignment explanation
Indices: 28045767--28045840 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
28045757 CATGAAATTG
*
28045767 GCACTAAGTGTGCGGGTTTAAAATTTGTACA
1 GCACTAAGTGTGCGGGTTT--AA-TTATACA
* * *
28045798 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGGGTTTAATTATACA
28045826 GCACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
28045841 ACTCACTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 19 0.50
29 1 0.03
31 18 0.47
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGGGTTTAATTATACA
Found at i:28048689 original size:42 final size:44
Alignment explanation
Indices: 28048643--28048755 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 44
28048633 CCTCTGTTCT
*
28048643 AGACAGGGTCTTACAC-AAAAACA-AA-TACGATGCCAATGTCCC
1 AGACAGGGTCTTACACGAAAAACATAAGT-CGATGCCAACGTCCC
* * *
28048685 AGACATGGTCTTACACGTAAACCATAAGTCGATGCCAACGTCCC
1 AGACAGGGTCTTACACGAAAAACATAAGTCGATGCCAACGTCCC
* *
28048729 AGGC-GTGGTCTTACACGATAACACATA
1 AGACAG-GGTCTTACACGA-AAAACATA
28048756 TCGGATCCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
42 15 0.26
43 5 0.09
44 30 0.53
45 7 0.12
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (44 bp):
AGACAGGGTCTTACACGAAAAACATAAGTCGATGCCAACGTCCC
Found at i:28050534 original size:14 final size:14
Alignment explanation
Indices: 28050515--28050544 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28050505 GATAATGTTA
28050515 GATCAAATAAAACT
1 GATCAAATAAAACT
28050529 GATCAAATAAAACT
1 GATCAAATAAAACT
28050543 GA
1 GA
28050545 ATGTGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (14 bp):
GATCAAATAAAACT
Found at i:28057231 original size:15 final size:15
Alignment explanation
Indices: 28057211--28057245 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
28057201 ACATAATTAA
28057211 AACATGAACTTTATT
1 AACATGAACTTTATT
28057226 AACATGAACTTTATT
1 AACATGAACTTTATT
28057241 AACAT
1 AACAT
28057246 ATGAGTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (15 bp):
AACATGAACTTTATT
Found at i:28057409 original size:31 final size:33
Alignment explanation
Indices: 28057333--28057421 Score: 121
Period size: 31 Copynumber: 2.8 Consensus size: 33
28057323 AAATGCTACT
28057333 CACATAATGCAAGACATAATTTAAA-GATTCAAA
1 CACATAATGCAAGACATAA-TTAAATGATTCAAA
*
28057366 CACATAATGCAAGTCATAATTAAATG-TT-AAA
1 CACATAATGCAAGACATAATTAAATGATTCAAA
* *
28057397 CATATAACGCAAGACATAATTAAAT
1 CACATAATGCAAGACATAATTAAAT
28057422 ATGCAAGCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 25 0.49
32 7 0.14
33 19 0.37
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.26
Consensus pattern (33 bp):
CACATAATGCAAGACATAATTAAATGATTCAAA
Found at i:28066323 original size:50 final size:50
Alignment explanation
Indices: 28066104--28066331 Score: 196
Period size: 50 Copynumber: 4.6 Consensus size: 50
28066094 CTGATATGCA
* ** * *
28066104 TAGTAGCCTGCACTTTGTACTACACTTGCGAC-CAACAAT-TCGGTATACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACTCAACAGTAT-GGTACACG
* * * * **
28066153 TAGTAGCATGCACTTAGTACTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CTCAACAGTATGGTACACG
* * * * *
28066203 TAGTATCCTGCACTTAGTACTACACACGTGA-TCGA-AGTCATTGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACTCAACAGT-A-TG-GTACACG
* * * *
28066254 TAGTAGTCTGCACTTAGTACTACACATGCGACTTAATAGTATGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACTCAACAGTATGGTACACG
28066304 TAGTAGCCTGCACTTAGTACTACACACG
1 TAGTAGCCTGCACTTAGTACTACACACG
28066332 TGTATTCACA
Statistics
Matches: 142, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
47 1 0.01
48 3 0.02
49 26 0.18
50 68 0.48
51 38 0.27
52 3 0.02
53 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACTCAACAGTATGGTACACG
Found at i:28068146 original size:25 final size:27
Alignment explanation
Indices: 28068109--28068161 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28068099 TCAAACATGC
28068109 ATTTAGGTCAATTTAACC-CTAGGGGT
1 ATTTAGGTCAATTTAACCACTAGGGGT
* *
28068135 ATTTCGGT-AATTTATCCACTAGGGGT
1 ATTTAGGTCAATTTAACCACTAGGGGT
28068161 A
1 A
28068162 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACCACTAGGGGT
Found at i:28069679 original size:26 final size:26
Alignment explanation
Indices: 28069648--28069755 Score: 164
Period size: 26 Copynumber: 4.2 Consensus size: 26
28069638 TGAAATGCCC
*
28069648 ATCATGAAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
28069674 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
* *
28069700 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
28069726 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
28069752 ATCA
1 ATCA
28069756 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
25 4 0.05
26 68 0.91
27 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:28082116 original size:10 final size:10
Alignment explanation
Indices: 28082101--28082126 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28082091 GTTAGGGATA
28082101 AATTTCCATG
1 AATTTCCATG
28082111 AATTTCCATG
1 AATTTCCATG
28082121 AATTTC
1 AATTTC
28082127 ATTTTTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (10 bp):
AATTTCCATG
Found at i:28083976 original size:40 final size:40
Alignment explanation
Indices: 28083932--28084027 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
28083922 TGCGAGTACC
* *
28083932 TGTCAACTTGTGTGAGCAACCATTGTTGTTATGTCCTGAT
1 TGTCAACTTGTGTGAGCAACCAGTGTTGTTACGTCCTGAT
* * *
28083972 TGTCAGCTTGTGTGAGCAGCCCGTGTTGTTACGTCCTGAT
1 TGTCAACTTGTGTGAGCAACCAGTGTTGTTACGTCCTGAT
28084012 TGTCAACTTGTGTGAG
1 TGTCAACTTGTGTGAG
28084028 TAGGCCCGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (40 bp):
TGTCAACTTGTGTGAGCAACCAGTGTTGTTACGTCCTGAT
Found at i:28087007 original size:40 final size:40
Alignment explanation
Indices: 28086962--28087163 Score: 191
Period size: 40 Copynumber: 5.2 Consensus size: 40
28086952 CGGAATACAA
*
28086962 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * *
28087002 CCGG--ATAA--AGTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* *
28087038 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* ** * *
28087078 CCGGATGTAGTCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTTGCACGAA-TGCCTTCGGGTCTTAGC
** ** * *
28087118 CCGGATATAATTA-TTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTT-GCACGAATGCCTTCGGGTCTTAGC
28087158 CCGGAT
1 CCGGAT
28087164 CATTCAATTG
Statistics
Matches: 133, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
36 28 0.21
38 7 0.05
39 3 0.02
40 93 0.70
41 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:28087148 original size:80 final size:76
Alignment explanation
Indices: 28086962--28087163 Score: 217
Period size: 80 Copynumber: 2.6 Consensus size: 76
28086952 CGGAATACAA
* * *
28086962 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAAAGTTGCACAAATGCCTT
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAGTTGCACAAATGCCTT
*
28087027 CGGGTATTAGC
66 CGGGTATTAAC
* * ** *
28087038 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTCACTAGCACAATTG
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAGT---T-GCACAAATG
*
28087103 CCTTCGGGTCTTAAC
62 CCTTCGGGTATTAAC
** * * *
28087118 CCGGATATAATTA-TTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTT-GCACAAATGCCTTCGGGTCTTAGCCCGGAT
28087164 CATTCAATTG
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
76 46 0.43
79 3 0.03
80 57 0.54
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (76 bp):
CCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAGTTGCACAAATGCCTT
CGGGTATTAAC
Found at i:28091776 original size:40 final size:40
Alignment explanation
Indices: 28091739--28091924 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
28091729 GCTACTCGTT
*
28091739 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
28091779 CAGATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28091819 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28091859 CGAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28091900 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28091925 CATCATTCGA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28096455 original size:30 final size:29
Alignment explanation
Indices: 28096361--28096462 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
28096351 TATAGTGAAT
* * *
28096361 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
28096390 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
28096418 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
28096448 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28096463 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:28104297 original size:30 final size:29
Alignment explanation
Indices: 28104203--28104304 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
28104193 TATAGTGAAT
* * *
28104203 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
28104232 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
28104260 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
28104290 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28104305 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:28112145 original size:30 final size:29
Alignment explanation
Indices: 28112051--28112152 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
28112041 TATAGTGAAT
* * *
28112051 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
28112080 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
28112108 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
28112138 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28112153 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:28115410 original size:32 final size:32
Alignment explanation
Indices: 28115374--28115444 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 32
28115364 TACTTAATTG
* *
28115374 AAATATTTTAAAATTTTAGTTG-CTCTTTTTGT
1 AAATATTTTAAAA-ATTAGATGTCTCTTTTTGT
28115406 AAATA--TTAAAAATTAGATGTCTCTTTTTGT
1 AAATATTTTAAAAATTAGATGTCTCTTTTTGT
28115436 AAATATTTT
1 AAATATTTT
28115445 TAAAGGTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 6 0.18
30 21 0.62
32 7 0.21
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (32 bp):
AAATATTTTAAAAATTAGATGTCTCTTTTTGT
Found at i:28115534 original size:16 final size:15
Alignment explanation
Indices: 28115507--28115540 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
28115497 ATAACTAGTA
*
28115507 TATAATTATATTTAT
1 TATAATTATATTAAT
28115522 TATAATATATATTAAT
1 TATAAT-TATATTAAT
28115538 TAT
1 TAT
28115541 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:28116146 original size:2 final size:2
Alignment explanation
Indices: 28116139--28116165 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28116129 GCATACGTAT
28116139 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 T
28116166 CATTAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28117533 original size:47 final size:45
Alignment explanation
Indices: 28117473--28117597 Score: 142
Period size: 45 Copynumber: 2.7 Consensus size: 45
28117463 AATGCTGATG
* *
28117473 TCCCAGACATGGTCTTACACGTAACCATATATAAATCAATGCCAACA
1 TCCCAGACGTGGTCTTACTCG-AA-CATATATAAATCAATGCCAACA
* * * * * *
28117520 TCCCAGACGTGGTCTTACTTGAAAAAACATATATCGATGCCAACA
1 TCCCAGACGTGGTCTTACTCGAACATATATAAATCAATGCCAACA
28117565 TCCCAGACGTGGTCTTACTCGAAAACATATATA
1 TCCCAGACGTGGTCTTACTCG--AACATATATA
28117598 TTGAAATCTT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
45 37 0.58
46 2 0.03
47 25 0.39
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.25
Consensus pattern (45 bp):
TCCCAGACGTGGTCTTACTCGAACATATATAAATCAATGCCAACA
Found at i:28117574 original size:45 final size:45
Alignment explanation
Indices: 28117511--28117598 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
28117501 ATATAAATCA
*
28117511 ATGCCAACATCCCAGACGTGGTCTTACTTGAAAAAACATATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACTCGAAAAAACATATATCG
* *
28117556 ATGCCAACATCCCAGACGTGGTCTTACTCGAAAACATATATAT
1 ATGCCAACATCCCAGACGTGGTCTTACTCGAAAAAACATATAT
28117599 TGAAATCTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (45 bp):
ATGCCAACATCCCAGACGTGGTCTTACTCGAAAAAACATATATCG
Found at i:28128903 original size:37 final size:37
Alignment explanation
Indices: 28128853--28128943 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
28128843 TTATTACGAA
*
28128853 GTCTTACCCGGACATAATCTCCATACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
28128890 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
28128927 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
28128944 TTTCCAAGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 46 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:28129038 original size:48 final size:48
Alignment explanation
Indices: 28128983--28129086 Score: 181
Period size: 48 Copynumber: 2.2 Consensus size: 48
28128973 TGTTACAACA
28128983 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
* * *
28129031 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGT
1 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
28129079 TTCACATT
1 TTCACATT
28129087 CATCACATCG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.33
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
Found at i:28129132 original size:49 final size:49
Alignment explanation
Indices: 28129078--28129362 Score: 479
Period size: 49 Copynumber: 5.9 Consensus size: 49
28129068 CACACATATG
28129078 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
* *
28129127 CTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
28129174 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
28129223 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
* *
28129272 CTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
28129319 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
28129363 CATCTCCTAC
Statistics
Matches: 222, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
47 88 0.40
49 134 0.60
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.34
Consensus pattern (49 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
Found at i:28129196 original size:96 final size:96
Alignment explanation
Indices: 28129078--28129364 Score: 488
Period size: 96 Copynumber: 3.0 Consensus size: 96
28129068 CACACATATG
*
28129078 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
* *
28129143 TCGGCCATTAGGCCTTATCACATATATACTC
66 TTGGCCATTAGGCCTTATCACATATATACAC
*
28129174 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
28129239 TTGGCCATTAGGCCTTATCACATATATATACAC
66 TTGGCCATTAGGCCTTATCAC--ATATATACAC
* *
28129272 CTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTCTTTCACATTCATCACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
28129335 TTGGCCATTAGGCCTTATCACATATATACA
66 TTGGCCATTAGGCCTTATCACATATATACA
28129365 TCTCCTACAT
Statistics
Matches: 182, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
94 9 0.05
96 129 0.71
98 44 0.24
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (96 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TTGGCCATTAGGCCTTATCACATATATACAC
Found at i:28129235 original size:145 final size:145
Alignment explanation
Indices: 28129078--28129362 Score: 561
Period size: 145 Copynumber: 2.0 Consensus size: 145
28129068 CACACATATG
28129078 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
28129143 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
66 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
28129208 CACATATATATACAC
131 CACATATATATACAC
*
28129223 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
28129288 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
66 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
28129353 CACATATATA
131 CACATATATA
28129363 CATCTCCTAC
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 139 1.00
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.34
Consensus pattern (145 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
CACATATATATACAC
Found at i:28133030 original size:40 final size:40
Alignment explanation
Indices: 28132981--28133240 Score: 255
Period size: 40 Copynumber: 6.5 Consensus size: 40
28132971 CCAGCATGAT
*
28132981 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28133021 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
28133061 TGCTCTTCGGAATTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
28133101 TGCTCTTCGGAACTTAG--CGGATATAACCACAAGCAC-AA
1 TGCTCTTCGGGACTTAGCCCGGATA-CATCACTAGCACGAA
* * * * * *
28133139 TTGC-CTTCGGGTCTTAACCCGGGTATAACAACTCA-CACAAA
1 -TGCTCTTCGGGACTTAGCCCGGATACATC-ACT-AGCACGAA
* * **
28133180 TGC-CTTCGGGTCTTAGCCCGGATATATTCACTAGCATAAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
28133220 TGC-CTTCGGGACTTAGCCCGG
1 TGCTCTTCGGGACTTAGCCCGG
28133241 GTATCATTCA
Statistics
Matches: 190, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
38 18 0.09
39 15 0.08
40 153 0.81
41 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:28135192 original size:37 final size:37
Alignment explanation
Indices: 28135142--28135232 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
28135132 TTATTACGAA
28135142 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
28135179 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
28135216 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
28135233 TTTCCAAGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:28135327 original size:48 final size:48
Alignment explanation
Indices: 28135272--28135375 Score: 181
Period size: 48 Copynumber: 2.2 Consensus size: 48
28135262 TGTTACAACA
28135272 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
* * *
28135320 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGT
1 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
28135368 TTCACATT
1 TTCACATT
28135376 CATCACATCG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.33
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
Found at i:28135475 original size:47 final size:47
Alignment explanation
Indices: 28135367--28135650 Score: 471
Period size: 47 Copynumber: 6.0 Consensus size: 47
28135357 CACACATATG
28135367 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACAC
* *
28135416 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
28135463 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACAC
28135512 TTTCACATTCATCACAT-GGCCATTAGGCCTTATCACATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
28135558 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
28135605 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
28135651 TCTCCTACAT
Statistics
Matches: 222, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
46 26 0.12
47 115 0.52
48 19 0.09
49 62 0.28
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
Found at i:28135582 original size:142 final size:144
Alignment explanation
Indices: 28135367--28135648 Score: 541
Period size: 142 Copynumber: 2.0 Consensus size: 144
28135357 CACACATATG
28135367 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATACACCTTCACATTCATCACA
28135432 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
65 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
28135497 CACATATATATACAC
130 CACATATATATACAC
28135512 TTTCACATTCATCACAT-GGCCATTAGGCCTTATCAC-ATATATACACCTTCACATTCATCACAT
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACCTTCACATTCATCACAT
28135575 CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTATC
66 CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTATC
28135640 ACATATATA
131 ACATATATA
28135649 CATCTCCTAC
Statistics
Matches: 137, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
142 101 0.74
144 19 0.14
145 17 0.12
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (144 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACCTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTATC
ACATATATATACAC
Found at i:28139447 original size:39 final size:40
Alignment explanation
Indices: 28139377--28139560 Score: 275
Period size: 40 Copynumber: 4.7 Consensus size: 40
28139367 CCAACCCAAT
* * ** *
28139377 TGCCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
28139417 TGCCTTC-GGACTTAACCCGGAAATAGCAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
28139456 TGCCTTCGGG-CTTAA-CCGGAAATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
28139494 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCATGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
28139534 TGCCTTCGGGACTTAACCCGGATATAA
1 TGCCTTCGGGACTTAACCCGGAAATAA
28139561 TCCTCAATTG
Statistics
Matches: 132, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
38 32 0.24
39 43 0.33
40 57 0.43
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.18
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
Found at i:28139535 original size:78 final size:79
Alignment explanation
Indices: 28139377--28139560 Score: 273
Period size: 78 Copynumber: 2.3 Consensus size: 79
28139367 CCAACCCAAT
* * **
28139377 TGCCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAATGCCTTCGGACTTAACCCGGAAATA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACAAATGCCTTCGGACTTAACCCGGAAATA
*
28139442 GCAACCAGCACGAA
66 ACAACCAGCACGAA
*
28139456 TGCCTTCGGG-CTTAA-CCGGAAATAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAAT
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACAAATGCCTTC-GGACTTAACCCGGAAAT
*
28139519 AACAACCAGCATGAA
65 AACAACCAGCACGAA
*
28139534 TGCCTTCGGGACTTAACCCGGATATAA
1 TGCCTTCGGGACTTAACCCGGAAATAA
28139561 TCCTCAATTG
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
77 27 0.29
78 43 0.46
79 15 0.16
80 9 0.10
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.18
Consensus pattern (79 bp):
TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACAAATGCCTTCGGACTTAACCCGGAAATA
ACAACCAGCACGAA
Found at i:28147486 original size:39 final size:40
Alignment explanation
Indices: 28147372--28147557 Score: 284
Period size: 40 Copynumber: 4.7 Consensus size: 40
28147362 CCAACCCAAT
* * * ** *
28147372 TGCCTTCAGGATTTAGCCCGGATGTAACAACCAGCACAAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
28147412 TGCCTTCGGGACTTAACCCGGAAATAGCAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
28147452 TGCCTTCGGGACTTAACCC-GAAATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
28147491 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCATGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
28147531 TGCCTTCGGGACTTAACCCGGATATAA
1 TGCCTTCGGGACTTAACCCGGAAATAA
28147558 TCCTCAATTG
Statistics
Matches: 135, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 38 0.28
40 97 0.72
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.18
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
Found at i:28147532 original size:79 final size:79
Alignment explanation
Indices: 28147396--28147550 Score: 283
Period size: 79 Copynumber: 2.0 Consensus size: 79
28147386 AGCCCGGATG
*
28147396 TAACAACCAGCACAAATGCCTTCGGGACTTAACCCGGAAATAGCAACCAGCACGAATGCCTTCGG
1 TAACAACCAGCACAAATGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGCCTTCGG
28147461 GACTTAACCCGAAA
66 GACTTAACCCGAAA
* *
28147475 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAATAACAACCAGCATGAATGCCTTCGG
1 TAACAACCAGCACAAATGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGCCTTCGG
28147540 GACTTAACCCG
66 GACTTAACCCG
28147551 GATATAATCC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.16
Consensus pattern (79 bp):
TAACAACCAGCACAAATGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATGCCTTCGG
GACTTAACCCGAAA
Found at i:28152013 original size:17 final size:19
Alignment explanation
Indices: 28151976--28152014 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
28151966 TTTCTCCTAA
*
28151976 ATTTCAATTTTATTTAATT
1 ATTTCAATTTTATTGAATT
28151995 ATTT-AATTTT-TTGAATT
1 ATTTCAATTTTATTGAATT
28152012 ATT
1 ATT
28152015 AATATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
ATTTCAATTTTATTGAATT
Found at i:28163774 original size:40 final size:39
Alignment explanation
Indices: 28163729--28163858 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
28163719 CGGAACATAA
28163729 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
28163769 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
28163809 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
28163849 CCGGATATAA
1 CCGGATATAA
28163859 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:28163873 original size:40 final size:40
Alignment explanation
Indices: 28163745--28163896 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
28163735 ATAACCATGT
* * *
28163745 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
28163785 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
28163825 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
28163865 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
28163897 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:28163879 original size:80 final size:80
Alignment explanation
Indices: 28163745--28163894 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
28163735 ATAACCATGT
*
28163745 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
28163809 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
28163825 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
28163888 CCCGGAT
64 CCCGGAT
28163895 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:28167101 original size:23 final size:23
Alignment explanation
Indices: 28167069--28167119 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
28167059 CATGTGAACC
* *
28167069 AATGACAATGACACTTCGGTGCA
1 AATGAAAATGACACTTCAGTGCA
* *
28167092 AATGAAAATGGCACTTTAGTGCA
1 AATGAAAATGACACTTCAGTGCA
28167115 AATGA
1 AATGA
28167120 TAGTGGCCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (23 bp):
AATGAAAATGACACTTCAGTGCA
Found at i:28168197 original size:17 final size:17
Alignment explanation
Indices: 28168175--28168225 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
28168165 TAGGGTTATG
28168175 GAGCATTACCGAACATA
1 GAGCATTACCGAACATA
28168192 GAGCATTACCGAACATA
1 GAGCATTACCGAACATA
*
28168209 GAGCATTACCAAACATA
1 GAGCATTACCGAACATA
28168226 TTATACAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (17 bp):
GAGCATTACCGAACATA
Found at i:28182692 original size:43 final size:43
Alignment explanation
Indices: 28182644--28182778 Score: 152
Period size: 43 Copynumber: 3.2 Consensus size: 43
28182634 GATTTTGTGG
*
28182644 AAGACCATGTCTAGGACTTTGGCATCGATATGAGATTACGTGT
1 AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACGTGT
28182687 AAGACCATGTCTAGGACATTGGCATCG-TAT-ATGATTA-GTGT
1 AAGACCATGTCTAGGACATTGGCATCGATATGA-GATTACGTGT
* ** * ** *
28182728 AAGATCC-TGTCTGGGACAGAGGCATCGATATGTGAAAACATGT
1 AAGA-CCATGTCTAGGACATTGGCATCGATATGAGATTACGTGT
28182771 AAGACCAT
1 AAGACCAT
28182779 ATCCGAGATA
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
41 26 0.33
42 18 0.23
43 34 0.44
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (43 bp):
AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACGTGT
Found at i:28184321 original size:48 final size:48
Alignment explanation
Indices: 28184266--28184369 Score: 181
Period size: 48 Copynumber: 2.2 Consensus size: 48
28184256 AAAACAGGGA
* *
28184266 AAAATAAAACGGAGTAAGCATTACATTCTTAATAAGTTCATATGACGG
1 AAAATAAAACGGAGTAAGCATTACATGCTTAATAAGTTCATATAACGG
28184314 AAAATAAAACGGAGTAAGCATTACATGCTTAATAAGTTCATATAACGG
1 AAAATAAAACGGAGTAAGCATTACATGCTTAATAAGTTCATATAACGG
*
28184362 AAACTAAA
1 AAAATAAA
28184370 CTTACCAATC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (48 bp):
AAAATAAAACGGAGTAAGCATTACATGCTTAATAAGTTCATATAACGG
Found at i:28185428 original size:20 final size:20
Alignment explanation
Indices: 28185399--28185443 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28185389 AGCACATGTA
* *
28185399 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
28185419 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
28185439 TTCAT
1 TTCAT
28185444 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:28187859 original size:39 final size:39
Alignment explanation
Indices: 28187793--28187921 Score: 170
Period size: 39 Copynumber: 3.3 Consensus size: 39
28187783 GGTAAACTAT
28187793 TGTACTGAATAATTGATAGTTACTGAATAACTAAATTAC
1 TGTACTGAATAATTGATAGTTACTGAATAACTAAATTAC
* * * * *
28187832 TGTATTGAATAATTGATAATTATTGAATTACTAAACTAC
1 TGTACTGAATAATTGATAGTTACTGAATAACTAAATTAC
* * *
28187871 TGCACTGAAT-ATCTGATAGTTACTGAATGACTAAATTAT
1 TGTACTGAATAAT-TGATAGTTACTGAATAACTAAATTAC
28187910 TGTACTGAATAA
1 TGTACTGAATAA
28187922 CTAATTGTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
38 2 0.03
39 72 0.96
40 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (39 bp):
TGTACTGAATAATTGATAGTTACTGAATAACTAAATTAC
Found at i:28187932 original size:39 final size:39
Alignment explanation
Indices: 28187785--28187934 Score: 165
Period size: 39 Copynumber: 3.8 Consensus size: 39
28187775 TTAATAGGGG
* *
28187785 TAAACTATTGTACTGAATAATTGATAGTTACTGAATAAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * * * * *
28187824 TAAATTACTGTATTGAATAATTGATAATTATTGAATTAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * *
28187863 TAAACTACTGCACTGAATATCTGATAGTTACTGAATGAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * * *
28187902 TAAATTATTGTACTGAATAACTAATTGTTACTG
1 TAAACTACTGTACTGAATAACTGATAGTTACTG
28187935 GTTAAATATG
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (39 bp):
TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
Found at i:28188564 original size:23 final size:23
Alignment explanation
Indices: 28188537--28188582 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28188527 GGACTATCCG
28188537 AACAGGTCCCGATTCGATTCTAA
1 AACAGGTCCCGATTCGATTCTAA
28188560 AACAGGTCCCGATTCGATTCTAA
1 AACAGGTCCCGATTCGATTCTAA
28188583 CGTGTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (23 bp):
AACAGGTCCCGATTCGATTCTAA
Found at i:28192800 original size:41 final size:41
Alignment explanation
Indices: 28192753--28192835 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
28192743 CTGAATAGAT
*
28192753 AATTTAGTTAGGGCTAACTTATTCTATAACAATGTCTTTGC
1 AATTTAGTCAGGGCTAACTTATTCTATAACAATGTCTTTGC
* *
28192794 AATTTAGTCAGGGTTAACTTCTTCTATAACAATGTCTTTGC
1 AATTTAGTCAGGGCTAACTTATTCTATAACAATGTCTTTGC
28192835 A
1 A
28192836 TAATCTGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (41 bp):
AATTTAGTCAGGGCTAACTTATTCTATAACAATGTCTTTGC
Found at i:28195486 original size:21 final size:22
Alignment explanation
Indices: 28195460--28195503 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28195450 TTTATTCATG
28195460 TTTCATTTACACATAC-TCACA
1 TTTCATTTACACATACATCACA
* *
28195481 TTTCATTTCCATATACATCACA
1 TTTCATTTACACATACATCACA
28195503 T
1 T
28195504 AACATTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTCATTTACACATACATCACA
Found at i:28195763 original size:42 final size:43
Alignment explanation
Indices: 28195684--28195824 Score: 162
Period size: 42 Copynumber: 3.3 Consensus size: 43
28195674 TCCCTGATGT
* * * *
28195684 GGTCTTACATGTAATCAAATATTGATGCCATTGTCCCAGACAG
1 GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAGACAG
* *
28195727 GGTCTTACACGAAATCATATA-CGATGCCAATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAGACAG
* *
28195769 GGTCTTACACGTAAATCACAA-ATCAATGCCAATGTCCCAAAC-G
1 GGTCTTACACG-AAATCA-AATATCGATGCCAATGTCCCAGACAG
28195812 TGGTCTTACACGA
1 -GGTCTTACACGA
28195825 TAACACATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.35
43 26 0.31
44 29 0.35
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAGACAG
Found at i:28195817 original size:86 final size:85
Alignment explanation
Indices: 28195665--28195824 Score: 198
Period size: 86 Copynumber: 1.9 Consensus size: 85
28195655 AGCTCGTATA
* ** * ** * *
28195665 ATGCCAACGTCCCTGATGTGGTCTTACATGTAATCAAATATTGATGCCATTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCAATGCCAATGTCCCAAACAGGGT
28195730 CTTACACGAAATCATATACG
66 CTTACACGAAATCATATACG
*
28195750 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACAA-ATCAATGCCAATGTCCCAAAC-GT
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATCA-AATATCAATGCCAATGTCCCAAACAG-
28195813 GGTCTTACACGA
63 GGTCTTACACGA
28195825 TAACACATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 27 0.43
86 34 0.54
87 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (85 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCAATGCCAATGTCCCAAACAGGGT
CTTACACGAAATCATATACG
Found at i:28195848 original size:44 final size:44
Alignment explanation
Indices: 28195683--28195823 Score: 146
Period size: 44 Copynumber: 3.3 Consensus size: 44
28195673 GTCCCTGATG
* ** * *
28195683 TGGTCTTACATGT-AATCA-AATATTGATGCCATTGTCCCAGACA
1 TGGTCTTACACGTAAATCACAA-ATCAATGCCAATGTCCCAAACA
* * * * *
28195726 GGGTCTTACACG-AAATCATATA-CGATGCCAATGTCCCAGACA
1 TGGTCTTACACGTAAATCACAAATCAATGCCAATGTCCCAAACA
*
28195768 TGGTCTTACACGTAAATCACAAATCAATGCCAATGTCCCAAACG
1 TGGTCTTACACGTAAATCACAAATCAATGCCAATGTCCCAAACA
28195812 TGGTCTTACACG
1 TGGTCTTACACG
28195824 ATAACACATA
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
42 29 0.35
43 24 0.29
44 30 0.36
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (44 bp):
TGGTCTTACACGTAAATCACAAATCAATGCCAATGTCCCAAACA
Found at i:28204539 original size:18 final size:18
Alignment explanation
Indices: 28204516--28204553 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28204506 AAGGTAAGAG
28204516 TTGAAGAGAATTGCCTTT
1 TTGAAGAGAATTGCCTTT
28204534 TTGAAGAGAATTGCCTTT
1 TTGAAGAGAATTGCCTTT
28204552 TT
1 TT
28204554 CTTTTCACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (18 bp):
TTGAAGAGAATTGCCTTT
Found at i:28207596 original size:40 final size:40
Alignment explanation
Indices: 28207537--28207704 Score: 250
Period size: 40 Copynumber: 4.2 Consensus size: 40
28207527 CGGATGATAA
* * *
28207537 CCGGGCAAAGTCCCGAAGGCATTTGTGCGAGTGACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28207577 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28207617 CCGGGCTAAGTCCCGGAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28207657 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
28207697 CC-GGCTAA
1 CCGGGCTAA
28207705 ATTCTGAAGG
Statistics
Matches: 117, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 8 0.07
40 109 0.93
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28219071 original size:29 final size:28
Alignment explanation
Indices: 28219038--28219110 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
28219028 CCTTCGAGCT
28219038 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATAT-TTTCCAGCA
*
28219067 TGCACACTTAGTGCCATATTTTCCAGCA
1 CGCACACTTAGTGCCATATTTTCCAGCA
28219095 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28219111 ATCTCGTCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 24 0.57
29 18 0.43
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATTTTCCAGCA
Found at i:28219099 original size:28 final size:29
Alignment explanation
Indices: 28218980--28219110 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 29
28218970 TACTCGATTT
** * *
28218980 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
28219009 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
28219038 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
28219067 TGCACACTTAGTGCCATAT-TTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
28219095 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28219111 ATCTCGTCAC
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
28 26 0.31
29 59 0.69
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:28225498 original size:23 final size:22
Alignment explanation
Indices: 28225462--28225504 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
28225452 TAACATCCAT
* *
28225462 GCCAAAACATACCATAACATGA
1 GCCAAAACAAACCAAAACATGA
28225484 GCCATAAACAAACCAAAACAT
1 GCCA-AAACAAACCAAAACAT
28225505 ATGGTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.53, C:0.28, G:0.07, T:0.12
Consensus pattern (22 bp):
GCCAAAACAAACCAAAACATGA
Found at i:28226321 original size:42 final size:43
Alignment explanation
Indices: 28226240--28226321 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
28226230 TATTACATGT
*
28226240 AATCAAATATCGATGACACTGTCCCAGACAGGGTCTTACACAA
1 AATCAAATATCGATGACAATGTCCCAGACAGGGTCTTACACAA
* * *
28226283 AATCAAATAT-GATGCCAATGTCTCAGACATGGTCTTACA
1 AATCAAATATCGATGACAATGTCCCAGACAGGGTCTTACA
28226322 AGTAAATCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 25 0.71
43 10 0.29
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (43 bp):
AATCAAATATCGATGACAATGTCCCAGACAGGGTCTTACACAA
Found at i:28226329 original size:43 final size:43
Alignment explanation
Indices: 28226227--28226365 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 43
28226217 ATCTTAGATG
* * * *
28226227 TGGTATTACATGT-AATCAAATATCGATGACACTGTCCCAGACA
1 TGGTCTTACAAGTAAATCAAATAT-GATGCCAATGTCCCAGACA
* *
28226270 GGGTCTTACACA--AAATCAAATATGATGCCAATGTCTCAGACA
1 TGGTCTTACA-AGTAAATCAAATATGATGCCAATGTCCCAGACA
** **
28226312 TGGTCTTACAAGTAAATCATAAGT-TGATGCCAACCTCCCAGATG
1 TGGTCTTACAAGTAAATCA-AA-TATGATGCCAATGTCCCAGACA
28226356 TGGTCTTACA
1 TGGTCTTACA
28226366 CGATAACACA
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 25 0.32
43 24 0.31
44 27 0.35
45 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (43 bp):
TGGTCTTACAAGTAAATCAAATATGATGCCAATGTCCCAGACA
Found at i:28229954 original size:48 final size:47
Alignment explanation
Indices: 28229882--28230068 Score: 178
Period size: 48 Copynumber: 3.9 Consensus size: 47
28229872 CATTTGAGTG
* * *
28229882 ATATGTGTGCTAGTGTAAGACCATGTTTGGAACATGGCATTGGCCAC
1 ATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCAC
* * ****
28229929 ATTATGTGAGCCAGTATAAGACCATGTTTAGG-ACATGGTATCGGTGTTG
1 A-TATGTGAGCCAGTGTAAGACCATGTTT-GGAACATGGCATCGG-CCAC
* * * * *
28229978 ATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCAC
1 ATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCAC
* * *
28230025 AATATGAGAGCCATTGTAAGACCATGTTTGGATCATGGCATCGG
1 -ATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGG
28230069 TATTGAGACG
Statistics
Matches: 108, Mismatches: 27, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
47 3 0.03
48 102 0.94
49 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (47 bp):
ATATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCAC
Found at i:28230045 original size:96 final size:96
Alignment explanation
Indices: 28229880--28230163 Score: 322
Period size: 96 Copynumber: 3.0 Consensus size: 96
28229870 GACATTTGAG
* * * * * * * *
28229880 TGATATGTGTGCTAGTGTAAGACCATGTTTGGAACATGGCATTGGCCACATTATGTGAGCCAGTA
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCACAATATGAGAGCCAGTG
* *
28229945 TAAGACCATGTTTAGGACATGGTATCGGTGT
66 TAAGACCATGTTTAGGACATGGCATCGGTAT
* *
28229976 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCACAATATGAGAGCCATTG
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCACAATATGAGAGCCAGTG
28230041 TAAGACCATGTTT-GGATCATGGCATCGGTAT
66 TAAGACCATGTTTAGGA-CATGGCATCGGTAT
* * * * * * **
28230072 TGAGACGAGAGCTAGTGTAAGGCCATGTCTGGGACATGG-GATCGGCCTCGACGTGTA-AGCCAG
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCG-TCGGCCACAATATG-AGAGCCAG
* *
28230135 TGTAAGACCATGTCTAGGACGTGGCATCG
64 TGTAAGACCATGTTTAGGACATGGCATCG
28230164 ATAATTTACT
Statistics
Matches: 161, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
95 4 0.02
96 153 0.95
97 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (96 bp):
TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCACAATATGAGAGCCAGTG
TAAGACCATGTTTAGGACATGGCATCGGTAT
Found at i:28231827 original size:44 final size:42
Alignment explanation
Indices: 28231735--28231837 Score: 109
Period size: 44 Copynumber: 2.4 Consensus size: 42
28231725 TCTCAGACAA
*
28231735 GGTCTTACACAAAATCAAATACGATGCCAATGTCCCAAACAT
1 GGTCTTACACAAAATCAAATACGATGCCAACGTCCCAAACAT
** * * *
28231777 CATCTTACACATAAATCTCAAAT-CGATGCCAACGTCCTATACGT
1 GGTCTTACACA-AAA--TCAAATACGATGCCAACGTCCCAAACAT
*
28231821 GGTCTTACACGAAATCA
1 GGTCTTACACAAAATCA
28231838 CATATCAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
41 3 0.06
42 9 0.18
43 6 0.12
44 25 0.51
45 6 0.12
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (42 bp):
GGTCTTACACAAAATCAAATACGATGCCAACGTCCCAAACAT
Found at i:28235196 original size:48 final size:49
Alignment explanation
Indices: 28234973--28235183 Score: 238
Period size: 48 Copynumber: 4.4 Consensus size: 49
28234963 GATATGTGCA
* *
28234973 CCAGTGTAAGACCATGTCTGGGACATGGCGTCGACCA-CGATATG-AGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCG-GCATCGATATGTAGAG
* * *
28235021 CCAGTGTAAGACCATGTTTGGAACATGGCATCAGCA---ATATTGTGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATA-TGT-AGAG
* * *
28235069 CCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGATATGT-GTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGTAGAG
* * * *
28235117 CTAGTGTAAGACCATGTCTGGGACATAGCATCGGCCTCGACATGTA-AG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGTAGAG
28235165 CCAGTGTAAGACCATGTCT
1 CCAGTGTAAGACCATGTCT
28235184 AGAACGTGGC
Statistics
Matches: 138, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
45 3 0.02
46 2 0.01
47 2 0.01
48 125 0.91
50 3 0.02
51 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (49 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGTAGAG
Found at i:28238048 original size:5 final size:5
Alignment explanation
Indices: 28238038--28238100 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
28238028 TCACTCCTTC
* * *
28238038 CTCAA CTCAA CTCGAA CTCGA CTCGAA CTCGA CTCGAA CTCGA CTCGAA
1 CTCAA CTCAA CTC-AA CTCAA CTC-AA CTCAA CTC-AA CTCAA CTC-AA
*
28238087 CTCGA CTCAA CTCA
1 CTCAA CTCAA CTCA
28238101 GTCCCACATT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
5 29 0.63
6 17 0.37
ACGTcount: A:0.30, C:0.38, G:0.13, T:0.19
Consensus pattern (5 bp):
CTCAA
Found at i:28238061 original size:11 final size:11
Alignment explanation
Indices: 28238041--28238099 Score: 102
Period size: 11 Copynumber: 5.5 Consensus size: 11
28238031 CTCCTTCCTC
*
28238041 AACTCAACTCG
1 AACTCGACTCG
28238052 AACTCGACTCG
1 AACTCGACTCG
28238063 AACTCGACTCG
1 AACTCGACTCG
28238074 AACTCGACTCG
1 AACTCGACTCG
28238085 AACTCGACTC-
1 AACTCGACTCG
28238095 AACTC
1 AACTC
28238100 AGTCCCACAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
10 5 0.11
11 42 0.89
ACGTcount: A:0.31, C:0.37, G:0.14, T:0.19
Consensus pattern (11 bp):
AACTCGACTCG
Found at i:28239193 original size:108 final size:108
Alignment explanation
Indices: 28239001--28239325 Score: 443
Period size: 108 Copynumber: 3.0 Consensus size: 108
28238991 AAATAAGAAA
* * * *
28239001 TTGCCAAATGCTAGAGCAAGCTGAGAAAATAAATTTTGAAGCTTTCTTTCATGTTAGTTTGAACC
1 TTGCCAAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAACTTTCATTCATGTTAGTTTGAACC
* *
28239066 ATCATCCATAATTATATTGAATTAAGTTTTGCATCAATTTTGT
66 ATCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTGT
* * * * * * *
28239109 TTTCCAAATGCTAGGGCAAGCTGAGCCAATAACTCTTGAAACTTTCGTTCTTATTAGTTTGAACC
1 TTGCCAAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAACTTTCATTCATGTTAGTTTGAACC
* *
28239174 GTCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTGC
66 ATCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTGT
* * * * *
28239217 TTGCCAAATACTAGAGCTAGCTGGGCAAATAACTTTTGAATCTTTCATTCGTGTTAGTTTGAACC
1 TTGCCAAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAACTTTCATTCATGTTAGTTTGAACC
* * *
28239282 ATCCTCCTTAATTACATTGAGTTAAGTTTTGCATCAATGTTGT
66 ATCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTGT
28239325 T
1 T
28239326 AATAAGTTCC
Statistics
Matches: 187, Mismatches: 30, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
108 187 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (108 bp):
TTGCCAAATGCTAGAGCAAGCTGAGCAAATAACTTTTGAAACTTTCATTCATGTTAGTTTGAACC
ATCATCCTTAATTATATTGAATTAAGTTTTGCATCAATGTTGT
Found at i:28243922 original size:20 final size:21
Alignment explanation
Indices: 28243897--28243939 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
28243887 AAAGTAGCAT
* *
28243897 TAAGAACTGGAGTGC-AATAA
1 TAAGAACTGAAGTACGAATAA
28243917 TAAGAACTGAAGTACGAATAA
1 TAAGAACTGAAGTACGAATAA
28243938 TA
1 TA
28243940 GTAAGCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (21 bp):
TAAGAACTGAAGTACGAATAA
Found at i:28249886 original size:11 final size:11
Alignment explanation
Indices: 28249870--28249899 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
28249860 GATAGAAATA
28249870 ATTATTTTATG
1 ATTATTTTATG
28249881 ATTATTTTATG
1 ATTATTTTATG
28249892 ATTATTTT
1 ATTATTTT
28249900 GAGGTCTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
ATTATTTTATG
Found at i:28252327 original size:83 final size:83
Alignment explanation
Indices: 28252188--28252352 Score: 285
Period size: 83 Copynumber: 2.0 Consensus size: 83
28252178 TTTAAATAGG
*
28252188 TTATGTTGCATGCTATGAAACATGTTTGAGTAAATGAGTGTTTGAGGGTAGCAATTGGCTTGGAA
1 TTATGTTGCATGCTATGAAACATGTTTGAGTAAATGAGTGGTTGAGGGTAGCAATTGGCTTGGAA
*
28252253 ATTATCCTCTAAAATGTC
66 ATTAGCCTCTAAAATGTC
* *
28252271 TTATGTTGCATGCTATGAAACATGTTTGATTAAATGAGTGGTTGAGGGTGGCAATTGGCTTGGAA
1 TTATGTTGCATGCTATGAAACATGTTTGAGTAAATGAGTGGTTGAGGGTAGCAATTGGCTTGGAA
*
28252336 ATTGGCCTCTAAAATGT
66 ATTAGCCTCTAAAATGT
28252353 TCACACGAGC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (83 bp):
TTATGTTGCATGCTATGAAACATGTTTGAGTAAATGAGTGGTTGAGGGTAGCAATTGGCTTGGAA
ATTAGCCTCTAAAATGTC
Found at i:28255706 original size:53 final size:53
Alignment explanation
Indices: 28255529--28255735 Score: 198
Period size: 53 Copynumber: 3.8 Consensus size: 53
28255519 ATTAGGGTTT
* * * * *
28255529 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * * *
28255583 AAGGAAATCATGTAAGACCATGTCTAGACATGACATTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * * *
28255638 AAAGATCCCATGTAAGACCATGCCAAGGCATAGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
28255691 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
28255736 TGAAAAGGAA
Statistics
Matches: 118, Mismatches: 33, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 45 0.38
54 36 0.31
55 37 0.31
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:28257633 original size:7 final size:7
Alignment explanation
Indices: 28257623--28257654 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
28257613 AATAGAAAAA
*
28257623 AGAGGAG
1 AGAGAAG
28257630 AGAGAAG
1 AGAGAAG
28257637 AGAGAAG
1 AGAGAAG
28257644 AGAGAAG
1 AGAGAAG
28257651 AGAG
1 AGAG
28257655 GTGCAATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (7 bp):
AGAGAAG
Found at i:28259497 original size:43 final size:43
Alignment explanation
Indices: 28259449--28259541 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
28259439 ATTCTAGAAA
28259449 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
* *
28259492 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
28259535 TATTTTC
1 TATTTTC
28259542 CCAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (43 bp):
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:28260683 original size:15 final size:15
Alignment explanation
Indices: 28260663--28260692 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28260653 GTCTCCATTT
28260663 ACTAAGGAACAATTA
1 ACTAAGGAACAATTA
28260678 ACTAAGGAACAATTA
1 ACTAAGGAACAATTA
28260693 GAGCATCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (15 bp):
ACTAAGGAACAATTA
Found at i:28266778 original size:68 final size:68
Alignment explanation
Indices: 28266669--28266805 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
28266659 CCGATTTGCA
28266669 ACGTTGGGAAAGATTTTCACTACCAATTTGCATAAGAACGATTTACCTACATATTGCATCATTCT
1 ACGTTGGGAAAGATTTTCACTACCAATTTGCATAAGAACGATTTACCTACATATTGCATCATTCT
28266734 ACT
66 ACT
28266737 ACGTTGGGAAAGATTTTCACTACCAATTTGCATAAGAACGATTTACCTACATATTGCATCATTCT
1 ACGTTGGGAAAGATTTTCACTACCAATTTGCATAAGAACGATTTACCTACATATTGCATCATTCT
28266802 ACT
66 ACT
28266805 A
1 A
28266806 TCTGTGCAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (68 bp):
ACGTTGGGAAAGATTTTCACTACCAATTTGCATAAGAACGATTTACCTACATATTGCATCATTCT
ACT
Found at i:28276269 original size:16 final size:16
Alignment explanation
Indices: 28276228--28276272 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
28276218 GTAAATTCTA
* *
28276228 AAATCCCCAACTTGTC
1 AAATCCCCAAATAGTC
*
28276244 AAATTCCCCAAATAGTG
1 AAA-TCCCCAAATAGTC
28276261 AAATCCCCAAAT
1 AAATCCCCAAAT
28276273 CCAAAACCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (16 bp):
AAATCCCCAAATAGTC
Done.