Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 93 of 349
Found at i:28700206 original size:28 final size:29
Alignment explanation
Indices: 28700174--28700228 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
28700164 ACAGGCGACC
*
28700174 ACACGGGAGTGT-CTAGGCTGTGTGAAGG
1 ACACGGGAGTGTGCTAGGCCGTGTGAAGG
* *
28700202 ACACGGGCGTGTGCTTGGCCGTGTGAA
1 ACACGGGAGTGTGCTAGGCCGTGTGAA
28700229 AACCCTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.18, C:0.18, G:0.42, T:0.22
Consensus pattern (29 bp):
ACACGGGAGTGTGCTAGGCCGTGTGAAGG
Found at i:28701712 original size:36 final size:36
Alignment explanation
Indices: 28701665--28701736 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
28701655 TCTCCTGAGT
*
28701665 ACAAAACATGAAATAACCGGATTAAGAGCACCAAAA
1 ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA
*
28701701 ACAAAACATGAAATAACCGGATTAAAAGTACCAAAA
1 ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA
28701737 TCCACAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.12
Consensus pattern (36 bp):
ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA
Found at i:28707218 original size:28 final size:29
Alignment explanation
Indices: 28707186--28707240 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
28707176 ACAGGCGACC
*
28707186 ACACGGGAGTGT-CTAGGCTGTGTGAAGG
1 ACACGGGAGTGTGCTAGGCCGTGTGAAGG
* *
28707214 ACACGGGCGTGTGCTTGGCCGTGTGAA
1 ACACGGGAGTGTGCTAGGCCGTGTGAA
28707241 AACCCCTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.18, C:0.18, G:0.42, T:0.22
Consensus pattern (29 bp):
ACACGGGAGTGTGCTAGGCCGTGTGAAGG
Found at i:28717084 original size:13 final size:13
Alignment explanation
Indices: 28717066--28717092 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28717056 TTCTTTTTAT
28717066 AAATATTGATATC
1 AAATATTGATATC
28717079 AAATATTGATATC
1 AAATATTGATATC
28717092 A
1 A
28717093 CTCTATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATATTGATATC
Found at i:28720211 original size:23 final size:23
Alignment explanation
Indices: 28720185--28720230 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28720175 AAAATTAAAA
28720185 CAAAATTTTCATCTTGCTCACAT
1 CAAAATTTTCATCTTGCTCACAT
28720208 CAAAATTTTCATCTTGCTCACAT
1 CAAAATTTTCATCTTGCTCACAT
28720231 TAAGATTCAA
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:0.04, T:0.39
Consensus pattern (23 bp):
CAAAATTTTCATCTTGCTCACAT
Found at i:28723261 original size:21 final size:21
Alignment explanation
Indices: 28723223--28723272 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
28723213 GAGAACTAAT
*
28723223 TTTTATTATATAACATTTTCA
1 TTTTATTATATAACATTTTAA
*
28723244 TTTT-TTATATAATGATTTTAA
1 TTTTATTATATAA-CATTTTAA
28723265 TTTATATT
1 TTT-TATT
28723273 TTTTTATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.33
21 13 0.54
22 1 0.04
23 2 0.08
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTATTATATAACATTTTAA
Found at i:28723465 original size:25 final size:25
Alignment explanation
Indices: 28723437--28723490 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
28723427 CTTATATCAA
28723437 ATATTT-TAATTATTATTTTCA-TATT
1 ATATTTATAATTA-TATTTT-ATTATT
*
28723462 ATATTTATATTTATATTTTATTATT
1 ATATTTATAATTATATTTTATTATT
28723487 ATAT
1 ATAT
28723491 CGAAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 1 0.04
25 20 0.77
26 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
ATATTTATAATTATATTTTATTATT
Found at i:28724137 original size:2 final size:2
Alignment explanation
Indices: 28724132--28724181 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
28724122 CTATATATAC
28724132 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28724174 AG AG AG AG
1 AG AG AG AG
28724182 CGCAAGCGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28732866 original size:28 final size:28
Alignment explanation
Indices: 28732822--28733091 Score: 156
Period size: 28 Copynumber: 9.6 Consensus size: 28
28732812 GACCATATAA
28732822 ATGGCACTTAGTGTGCGAAGTATCGAGG
1 ATGGCACTTAGTGTGCGAAGTATCGAGG
* * * *
28732850 ATGGTACTTAGTCTGCGATA-CATTC-AGA
1 ATGGCACTTAGTGTGCGA-AGTA-TCGAGG
* *
28732878 ATGGCACTTAGTATGCGAAGTATTG-GG
1 ATGGCACTTAGTGTGCGAAGTATCGAGG
* *
28732905 AATGGAACTTAGTGTGCAAAGTATCGAGG
1 -ATGGCACTTAGTGTGCGAAGTATCGAGG
* * **
28732934 ATGGCACTTGGTGTGCGATA-CATTC-AAA
1 ATGGCACTTAGTGTGCGA-AGTA-TCGAGG
* * * * *
28732962 ATGGTATTTAGTGTGCAAAGTATTGAGA
1 ATGGCACTTAGTGTGCGAAGTATCGAGG
* * * *
28732990 ATGACATTTAATGTGTGAAGTATCGAGG
1 ATGGCACTTAGTGTGCGAAGTATCGAGG
* * ** * **
28733018 ATGACACTTAGTGTACGAAACATCTAAA
1 ATGGCACTTAGTGTGCGAAGTATCGAGG
* * *
28733046 ATGGCACTTAGTGTACGAGGTATTG-GG
1 ATGGCACTTAGTGTGCGAAGTATCGAGG
*
28733073 TATGGCACCTAGTGTGCGA
1 -ATGGCACTTAGTGTGCGA
28733092 GACATTGAAT
Statistics
Matches: 179, Mismatches: 52, Indels: 22
0.71 0.21 0.09
Matches are distributed among these distances:
27 5 0.03
28 166 0.93
29 8 0.04
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAGTATCGAGG
Found at i:28732965 original size:84 final size:84
Alignment explanation
Indices: 28732821--28733091 Score: 312
Period size: 84 Copynumber: 3.2 Consensus size: 84
28732811 CGACCATATA
* * * *
28732821 AATGGCACTTAGTGTGCGAAGTATCGAGGATGGTACTTAGTCTGCGATACATTCAGAATGGCACT
1 AATGGAACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGATACATTCAAAATGGCACT
*
28732886 TAGTATGCGAAGTATTGGG
66 TAGTGTGCGAAGTATTGGG
* * * *
28732905 AATGGAACTTAGTGTGCAAAGTATCGAGGATGGCACTTGGTGTGCGATACATTCAAAATGGTATT
1 AATGGAACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGATACATTCAAAATGGCACT
* *
28732970 TAGTGTGCAAAGTATTGAG
66 TAGTGTGCGAAGTATTGGG
* * * * * *
28732989 AAT-GACATTTAATGTGTGAAGTATCGAGGATGACACTTAGTGTACGAAACA-TCTAAAATGGCA
1 AATGGA-ACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGATACATTC-AAAATGGCA
* *
28733052 CTTAGTGTACGAGGTATTGGG
64 CTTAGTGTGCGAAGTATTGGG
* * *
28733073 TATGGCACCTAGTGTGCGA
1 AATGGAACTTAGTGTGCGA
28733092 GACATTGAAT
Statistics
Matches: 153, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
83 4 0.03
84 148 0.97
85 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (84 bp):
AATGGAACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGATACATTCAAAATGGCACT
TAGTGTGCGAAGTATTGGG
Found at i:28733181 original size:32 final size:32
Alignment explanation
Indices: 28733144--28733205 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
28733134 TGAGATTGGC
*
28733144 ACAAGATGGTACAGGTATGTATGAAAATTCGT
1 ACAAGATGGTACAGGTATGTACGAAAATTCGT
28733176 ACAAGATGGTACAGGTATGTACGAAAATTC
1 ACAAGATGGTACAGGTATGTACGAAAATTC
28733206 AATTGAGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (32 bp):
ACAAGATGGTACAGGTATGTACGAAAATTCGT
Found at i:28736267 original size:24 final size:25
Alignment explanation
Indices: 28736231--28736330 Score: 71
Period size: 24 Copynumber: 4.1 Consensus size: 25
28736221 TTCCAAGCCA
**
28736231 AATAACATAAAGCTCATGT-GAGCTT
1 AATAACAGGAAGCTCAT-TCGAGCTT
* * *
28736256 -GTAACGGGAAGCTTATTCGAGCTT
1 AATAACAGGAAGCTCATTCGAGCTT
**
28736280 AATAACAGGAAGCTCATAAGAGCTT
1 AATAACAGGAAGCTCATTCGAGCTT
* * * *
28736305 AA-ATCAGAAAACTCATGCGAGCTT
1 AATAACAGGAAGCTCATTCGAGCTT
28736329 AA
1 AA
28736331 CGGGTGTAAC
Statistics
Matches: 58, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
23 1 0.02
24 36 0.62
25 21 0.36
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (25 bp):
AATAACAGGAAGCTCATTCGAGCTT
Found at i:28737001 original size:29 final size:29
Alignment explanation
Indices: 28736962--28737018 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
28736952 CAGGGGACAC
*
28736962 ACAGCCGTGTACTTGACTATGTGTCACAG
1 ACAGCCATGTACTTGACTATGTGTCACAG
*
28736991 ACAGCCATGTACTTGACTGTGTGTCACA
1 ACAGCCATGTACTTGACTATGTGTCACA
28737019 CATGGCTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (29 bp):
ACAGCCATGTACTTGACTATGTGTCACAG
Found at i:28738196 original size:18 final size:18
Alignment explanation
Indices: 28738173--28738230 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
28738163 AGCCCATTTG
28738173 AGTAACAGTAATCAGTGC
1 AGTAACAGTAATCAGTGC
* *
28738191 AGTAACCA-TGATCAATGC
1 AGTAA-CAGTAATCAGTGC
28738209 AGTAACAGTAATCAGTGC
1 AGTAACAGTAATCAGTGC
28738227 AGTA
1 AGTA
28738231 TGCAAGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.06
18 30 0.88
19 2 0.06
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (18 bp):
AGTAACAGTAATCAGTGC
Found at i:28738518 original size:23 final size:23
Alignment explanation
Indices: 28738492--28738538 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
28738482 CCATGCAATA
28738492 CAACATA-ATATTATACATGG-ATG
1 CAACATACATA-TA-ACATGGCATG
28738515 CAACATACATATAACATGGCATG
1 CAACATACATATAACATGGCATG
28738538 C
1 C
28738539 TCAAATATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 13 0.59
24 3 0.14
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.26
Consensus pattern (23 bp):
CAACATACATATAACATGGCATG
Found at i:28738622 original size:27 final size:27
Alignment explanation
Indices: 28738600--28738662 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
28738590 GCGTATTACA
* *
28738600 GTCATTTTAGCCTATAGGGGTATTTCG
1 GTCATTTTACCCAATAGGGGTATTTCG
* *
28738627 GTCATTCTACCCAATGGGGGTATTTCG
1 GTCATTTTACCCAATAGGGGTATTTCG
28738654 GTCATTTTA
1 GTCATTTTA
28738663 TCATATAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCAATAGGGGTATTTCG
Found at i:28740608 original size:12 final size:13
Alignment explanation
Indices: 28740591--28740622 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28740581 ATAGCACATT
28740591 TCAAAAC-ATGCA
1 TCAAAACTATGCA
28740603 TCAAAACTATGCA
1 TCAAAACTATGCA
28740616 -CAAAACT
1 TCAAAACT
28740623 TACCATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (13 bp):
TCAAAACTATGCA
Found at i:28741225 original size:86 final size:85
Alignment explanation
Indices: 28741072--28741231 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 85
28741062 GACAAGTACA
* ** * * * *
28741072 ATGCCGACGTCCTAGATGTGGTCTTACATGTAATTCAGTATCGATGCCTCTGTCCCAGACAGGGT
1 ATGCCGACGTCCCAGACATGGTCTTACATGTAATTCAGAATCGATGCCACTGTCCCAAACACGGT
28741137 CTTATACGAAAACAGATACG
66 CTTATACGAAAACAGATACG
* *
28741157 ATGCCGATGTCCCAGACATGGTCTTACATGTAAATTTCA-AATCGATGCCAGTGTCCCAAACACG
1 ATGCCGACGTCCCAGACATGGTCTTACATGT-AA-TTCAGAATCGATGCCACTGTCCCAAACACG
28741221 GTCTTATACGA
64 GTCTTATACGA
28741232 TAATTTAGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 27 0.42
86 33 0.52
87 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (85 bp):
ATGCCGACGTCCCAGACATGGTCTTACATGTAATTCAGAATCGATGCCACTGTCCCAAACACGGT
CTTATACGAAAACAGATACG
Found at i:28747284 original size:44 final size:44
Alignment explanation
Indices: 28747078--28747332 Score: 282
Period size: 44 Copynumber: 5.6 Consensus size: 44
28747068 TATGTGAGCC
* **
28747078 AGTGTAAGACATGTCTGGGACATGCATCGG-TCACATTATGAAATGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCT-A-A-GA-GATGTGCT
* * * *
28747125 AGTGTAAGACATGTTTAGGACATGCATTGGCATTAAGACGA-GAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGC--TAAGA-GATGTGCT
* * *
28747171 AGTGTAAGACATGTCTGGGACATGCATCGACCT-CGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCG-GCTAAGAGATGT--GCT
28747217 AGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGATGTGCT
* *
28747261 AGTGTAAGACATGTCTGGAACATGCATCGGCTAAGAGTTGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGATGTGCT
*
28747305 AGTGTAAGACATATCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
28747333 AGCACGGATA
Statistics
Matches: 179, Mismatches: 21, Indels: 19
0.82 0.10 0.09
Matches are distributed among these distances:
43 2 0.01
44 73 0.41
45 3 0.02
46 67 0.37
47 31 0.17
48 1 0.01
49 1 0.01
50 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGATGTGCT
Found at i:28747284 original size:90 final size:90
Alignment explanation
Indices: 28747073--28747332 Score: 287
Period size: 90 Copynumber: 2.9 Consensus size: 90
28747063 GCTATTATGT
* * * * *
28747073 GAGCCAGTGTAAGACATGTCTGGGACATGCATCG-GTCACATTATGAAATGCTAGTGTAAGACAT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGCCTC-GA-GATGTAA-GCTAGTGTAAGACAT
* * *
28747137 GTTTAGGACATGCATTGGCATTAAGACGA
63 GTCTGGGACATGCATCGGCA-TAAGACGA
*
28747166 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGTAAGCCAGTGTAAGACATGT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCG-CCTCGAGATGTAAGCTAGTGTAAGACATGT
28747231 CTGGGACATGCATCGGC-TAAGA-GA
65 CTGGGACATGCATCGGCATAAGACGA
* * * * * *
28747255 TGTGCTAGTGTAAGACATGTCTGGAACATGCATCGGCTAAGAGTTGT--GCTAGTGTAAGACATA
1 -GAGCTAGTGTAAGACATGTCTGGGACATGCATCGCCT-CGAGATGTAAGCTAGTGTAAGACATG
28747318 TCTGGGACATGCATC
64 TCTGGGACATGCATC
28747333 AGCACGGATA
Statistics
Matches: 147, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
88 29 0.20
89 4 0.03
90 43 0.29
92 30 0.20
93 38 0.26
94 1 0.01
95 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (90 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGCCTCGAGATGTAAGCTAGTGTAAGACATGTC
TGGGACATGCATCGGCATAAGACGA
Found at i:28747357 original size:136 final size:139
Alignment explanation
Indices: 28747069--28747362 Score: 365
Period size: 136 Copynumber: 2.1 Consensus size: 139
28747059 CATTGCTATT
*
28747069 ATGT-GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGTCACATTATGAAATGCTAGTGTAAG
1 ATGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGTCACATGATGAAATGCTAGTGTAAG
* * *
28747133 ACATGTTTAGGACATGCATTGGCATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGACATGCAT
66 ACATGTCTAGGACATGCATCGGCA-TAAGACGAGAGCTAGTGTAAGACATATCTGGGACATGCAT
*
28747198 CGACCTCGAG
130 CGACCACGAG
**
28747208 ATGTA-AGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTA-A-GA-GATGTGCTAGTGTAA
1 ATGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGTC-ACATGATGAAATGCTAGTGTAA
* *
28747268 GACATGTCT-GGAACATGCATCGGC-TAAGA-GTTGTGCTAGTGTAAGACATATCTGGGACATGC
65 GACATGTCTAGG-ACATGCATCGGCATAAGACG-AGAGCTAGTGTAAGACATATCTGGGACATGC
* *
28747330 ATC-AGCACGGAT
128 ATCGACCAC-GAG
28747342 ATGTGAGAGCCAGTGTAAGAC
1 ATGT-AGAGCCAGTGTAAGAC
28747363 CATATCTAGG
Statistics
Matches: 137, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
133 4 0.03
134 42 0.31
135 3 0.02
136 46 0.34
137 1 0.01
138 2 0.01
139 39 0.28
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (139 bp):
ATGTAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGTCACATGATGAAATGCTAGTGTAAG
ACATGTCTAGGACATGCATCGGCATAAGACGAGAGCTAGTGTAAGACATATCTGGGACATGCATC
GACCACGAG
Found at i:28754415 original size:27 final size:27
Alignment explanation
Indices: 28754385--28754589 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
28754375 ATATTAAGTC
* *
28754385 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
28754412 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
28754440 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
28754467 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
28754494 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
28754521 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
28754548 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
28754575 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28754590 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.83
28 26 0.17
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28754524 original size:54 final size:54
Alignment explanation
Indices: 28754385--28754588 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
28754375 ATATTAAGTC
* * * **
28754385 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
28754440 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
28754494 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
28754548 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
28754589 TGTACAATTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:28754554 original size:81 final size:81
Alignment explanation
Indices: 28754439--28754588 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
28754429 ATAATCAAAC
* * * * * *
28754439 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
28754504 GTGCATCATTTTCATT
66 GTGCATCATTTTCATT
* *
28754520 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
28754585 GTGC
66 GTGC
28754589 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTTCATT
Found at i:28758860 original size:16 final size:16
Alignment explanation
Indices: 28758841--28758872 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28758831 AATTATTTTA
28758841 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
28758857 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
28758873 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:28759228 original size:50 final size:50
Alignment explanation
Indices: 28759053--28759393 Score: 312
Period size: 50 Copynumber: 6.8 Consensus size: 50
28759043 ACCGAAGCTC
*
28759053 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* ** * * * * ** *
28759103 TCTAGTACATGTAGTAGCCTGCACTTAGTATTGCACACGTGATCGAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAA
* * *
28759155 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGAGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * * * *
28759204 TTTGGTACACGTAGTAGCCTGCACTTAGTACTACTCACAT--GACTTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTA--CACATGCGACCTATCAA
* ** * * ** *
28759254 TCTGATACATGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAA
* * * *
28759306 -CAGGTACGCATAGTAGCCTACACATAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
*
28759355 TCTGGTACACATAGTAGTCTGCACTTAGTACTACACATG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATG
28759394 TGACTCACAA
Statistics
Matches: 225, Mismatches: 56, Indels: 20
0.75 0.19 0.07
Matches are distributed among these distances:
48 4 0.02
49 6 0.03
50 138 0.61
51 68 0.30
52 9 0.04
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
Found at i:28759312 original size:101 final size:100
Alignment explanation
Indices: 28759163--28759396 Score: 240
Period size: 101 Copynumber: 2.3 Consensus size: 100
28759153 AACGGGTACG
* * ** * ** * *
28759163 CATAGTAGCCTGCACTTAGTACTACACATGAGA-CCTA-TCAATTTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAA-CAGGTACACATAGTAGCCTAC
* * *
28759226 ACTTAGTACTACTCACAT-GACTTAACCATCTGATACA
65 ACATAGTACTA--CACATCGACCTAACAATCTGATACA
** *
28759263 TGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAACAGGTACGCATAGTAGCCTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAACAGGTACACATAGTAGCCTACA
* *
28759328 CATAGTACTACACATGCGACCTATCAATCTGGTACA
66 CATAGTACTACACAT-CGACCTAACAATCTGATACA
* *
28759364 CATAGTAGTCTGCACTTAGTACTACACATGTGA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGA
28759397 CTCACAAAGG
Statistics
Matches: 109, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
99 5 0.05
100 29 0.27
101 72 0.66
102 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (100 bp):
CATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAACAGGTACACATAGTAGCCTACA
CATAGTACTACACATCGACCTAACAATCTGATACA
Found at i:28759398 original size:151 final size:151
Alignment explanation
Indices: 28759053--28759398 Score: 514
Period size: 151 Copynumber: 2.3 Consensus size: 151
28759043 ACCGAAGCTC
* * * *
28759053 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACATGTAGT
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACTTAACAATCTAGTACATGTAGT
* * * * * *
28759118 AGCCTGCACTTAGTATTGCACACGTGATCGAAGTTAACGGGTACGCATAGTAGCCTGCACTTAGT
66 AGCCTGCACTTAGTACTACACACGTGATCAAAGTTAACAGGTACGCATAGTAGCCTACACATAGT
28759183 ACTACACATGAGACCTATCAA
131 ACTACACATGAGACCTATCAA
* * * ** *
28759204 TTTGGTACACGTAGTAGCCTGCACTTAGTACTACTCACATGACTTAACCATCT-GATACATGTAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACTTAACAATCTAG-TACATGTAG
28759268 TAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAACAGGTACGCATAGTAGCCTACACATAG
65 TAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAACAGGTACGCATAGTAGCCTACACATAG
*
28759333 TACTACACATGCGACCTATCAA
130 TACTACACATGAGACCTATCAA
*
28759355 TCTGGTACACATAGTAGTCTGCACTTAGTACTACACATGTGACT
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACT
28759399 CACAAAGGAT
Statistics
Matches: 171, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
150 1 0.01
151 170 0.99
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (151 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACTTAACAATCTAGTACATGTAGT
AGCCTGCACTTAGTACTACACACGTGATCAAAGTTAACAGGTACGCATAGTAGCCTACACATAGT
ACTACACATGAGACCTATCAA
Found at i:28762202 original size:40 final size:40
Alignment explanation
Indices: 28761927--28762188 Score: 349
Period size: 40 Copynumber: 6.7 Consensus size: 40
28761917 TTGAATGATG
* * * *
28761927 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28761967 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
28762007 TCCGGGCTAAG-CCCGAAGGCA-TT-TGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28762044 TCCGGACTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28762083 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28762123 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28762164 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28762189 AACGAGTAGC
Statistics
Matches: 199, Mismatches: 15, Indels: 16
0.87 0.07 0.07
Matches are distributed among these distances:
37 31 0.16
38 4 0.02
39 33 0.17
40 121 0.61
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28769626 original size:40 final size:39
Alignment explanation
Indices: 28769542--28769804 Score: 291
Period size: 40 Copynumber: 6.6 Consensus size: 39
28769532 TTGAATGATG
* * * *
28769542 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28769582 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
28769622 TCCGGGCTAAGCCCGAAGACATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
28769661 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
28769701 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
* * *
28769741 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGCTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
28769782 -CCGGGCT--GTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
28769805 AATGAGTAGC
Statistics
Matches: 195, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
38 15 0.08
39 34 0.17
40 136 0.70
41 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28769766 original size:80 final size:80
Alignment explanation
Indices: 28769542--28769804 Score: 340
Period size: 80 Copynumber: 3.3 Consensus size: 80
28769532 TTGAATGATG
* * * *
28769542 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGATCCGAAGGCATT
*
28769606 TGTGCGAGATACTAAT
65 TGTGCGAGATACTAAA
* *
28769622 TCCGGGCTAAG-CCCGAAGACATTTGTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
*
28769686 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* ** *
28769701 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCAAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT-CCGAAGGCATT
*
28769765 TGTGCGAGCTACTATAA
65 TGTGCGAGATACTA-AA
28769782 -CCGGGCT--GTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28769805 AATGAGTAGC
Statistics
Matches: 163, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
78 16 0.10
79 64 0.39
80 81 0.50
81 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:28771776 original size:46 final size:46
Alignment explanation
Indices: 28771726--28771898 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
28771716 TGGTTGAGCA
* *
28771726 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
28771772 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
28771819 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
28771865 TCTGAGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28771899 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 60 0.58
47 29 0.28
48 3 0.03
50 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:28771882 original size:93 final size:93
Alignment explanation
Indices: 28771723--28771893 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
28771713 GGATGGTTGA
* *
28771723 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
28771788 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
28771816 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
*
28771881 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
28771894 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:28772160 original size:19 final size:20
Alignment explanation
Indices: 28772123--28772160 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28772113 ATAAGGTGGT
28772123 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28772143 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28772161 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28774738 original size:48 final size:48
Alignment explanation
Indices: 28774667--28774847 Score: 218
Period size: 48 Copynumber: 3.8 Consensus size: 48
28774657 TAGTAGAGTC
* * * * **
28774667 CCAATGTCATATCCCAAATATGGTCTTATATGGGACCATTTATCGATG
1 CCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATATCGATG
* * * *
28774715 CCAATGCCATGTCCCAGACATGGTATTACATGGGATCACATAACGATG
1 CCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATATCGATG
*
28774763 CCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACATATCGATG
1 CCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATATCGATG
** * * *
28774811 CTGATGCCATATCCCAAATATGGTCTTATAAGGGATC
1 CCAATGCCATATCCCAAACATGGTCTTACATGGGATC
28774848 TCATCAACCC
Statistics
Matches: 114, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 114 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (48 bp):
CCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATATCGATG
Found at i:28791328 original size:16 final size:16
Alignment explanation
Indices: 28791307--28791338 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28791297 TGTCGACAAC
*
28791307 CAACTTTTTAGCTTTT
1 CAACTTTTCAGCTTTT
28791323 CAACTTTTCAGCTTTT
1 CAACTTTTCAGCTTTT
28791339 GCTGTTTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (16 bp):
CAACTTTTCAGCTTTT
Found at i:28800616 original size:56 final size:56
Alignment explanation
Indices: 28800550--28800674 Score: 169
Period size: 56 Copynumber: 2.2 Consensus size: 56
28800540 GCTATATGCG
* **
28800550 TGCGAGTAAGACCATATTTAATACGTTGGCATCGATATGTGATTTTGATAAATGTA
1 TGCGAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCGATAAATGTA
* ** * *
28800606 TGCGAGTAAGACCACGTTTAATTTGTTGGCATCGATATGTGATTCCGATATATGTG
1 TGCGAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCGATAAATGTA
*
28800662 TGTGAGTAAGACC
1 TGCGAGTAAGACC
28800675 CTGTTTGGGA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (56 bp):
TGCGAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCGATAAATGTA
Found at i:28805579 original size:7 final size:7
Alignment explanation
Indices: 28805564--28805594 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28805554 ACCTCATTTG
28805564 ATCCCTC
1 ATCCCTC
*
28805571 ATCCATC
1 ATCCCTC
28805578 ATCCCTC
1 ATCCCTC
28805585 ATCCCTC
1 ATCCCTC
28805592 ATC
1 ATC
28805595 TTCCATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCCCTC
Found at i:28806533 original size:7 final size:7
Alignment explanation
Indices: 28806521--28806545 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28806511 TTCATTCATC
28806521 AATTACT
1 AATTACT
28806528 AATTACT
1 AATTACT
28806535 AATTACT
1 AATTACT
28806542 AATT
1 AATT
28806546 CATCAACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTACT
Found at i:28811611 original size:15 final size:14
Alignment explanation
Indices: 28811591--28811633 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
28811581 TCATACGGGT
28811591 TAATAAATAAAATAA
1 TAATAAA-AAAATAA
28811606 TAATAAAAATATATAA
1 TAATAAAAA-A-ATAA
28811622 T-ATAAAAAAATA
1 TAATAAAAAAATA
28811634 GGCAATAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 3 0.12
15 15 0.58
16 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TAATAAAAAAATAA
Found at i:28811623 original size:13 final size:13
Alignment explanation
Indices: 28811591--28811633 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
28811581 TCATACGGGT
28811591 TAATAA-ATAAAA
1 TAATAATATAAAA
28811603 TAATAATA-AAAA
1 TAATAATATAAAA
28811615 TATATAATATAAAA
1 TA-ATAATATAAAA
*
28811629 AAATA
1 TAATA
28811634 GGCAATAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 12 0.44
13 10 0.37
14 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATAATATAAAA
Found at i:28816320 original size:56 final size:56
Alignment explanation
Indices: 28816227--28816455 Score: 273
Period size: 56 Copynumber: 4.1 Consensus size: 56
28816217 CATGACATAG
* * * * *
28816227 GATTCCAATATGTGATGTGTGAGTAAGACCATGTTTAATACGTTGCCATCGATATGT
1 GATTCCGATATATG-TGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGT
* *
28816284 GATTCCGATATATGTGTGCAAGTAAGACCACATTTAATACGTTGGCATCGATATGT
1 GATTCCGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGT
* *
28816340 GATTCCGGTATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATTGATATGT
1 GATTCCGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGT
** * * * **
28816396 GATTTTGATTTATGTGTTCGAGTAAGACC-CTGTCTAGGACAG-TGGCATCGATATGT
1 GATTCCGATATATGTGTGCGAGTAAGACCAC-GTTTAATAC-GTTGGCATCGATATGT
28816452 GATT
1 GATT
28816456 ACATGTAAGA
Statistics
Matches: 150, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
55 1 0.01
56 136 0.91
57 13 0.09
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.34
Consensus pattern (56 bp):
GATTCCGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGT
Found at i:28823668 original size:7 final size:7
Alignment explanation
Indices: 28823656--28823680 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28823646 TTCATTCATC
28823656 AATTACT
1 AATTACT
28823663 AATTACT
1 AATTACT
28823670 AATTACT
1 AATTACT
28823677 AATT
1 AATT
28823681 CATCAACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTACT
Found at i:28828931 original size:17 final size:17
Alignment explanation
Indices: 28828899--28828945 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
28828889 CCATTACAGT
*
28828899 AACAGTAAACAATGCAGC
1 AACAGT-AACAGTGCAGC
*
28828917 AACAGTAACAGTGCAGT
1 AACAGTAACAGTGCAGC
*
28828934 AACAATAACAGT
1 AACAGTAACAGT
28828946 TCAGATATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (17 bp):
AACAGTAACAGTGCAGC
Found at i:28831059 original size:17 final size:17
Alignment explanation
Indices: 28831037--28831081 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
28831027 TTTACCCATA
*
28831037 TGGGGCCCACGAGCTCG
1 TGGGGCCCACAAGCTCG
28831054 TGGGGCCCACAAGCTCG
1 TGGGGCCCACAAGCTCG
28831071 TGGGGCCCACA
1 TGGGGCCCACA
28831082 TAGCCCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.16, C:0.36, G:0.38, T:0.11
Consensus pattern (17 bp):
TGGGGCCCACAAGCTCG
Found at i:28837699 original size:44 final size:44
Alignment explanation
Indices: 28837649--28837737 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
28837639 AAGTATCTTC
28837649 AATCTTATCTCATTATAAAACAAATTTTAGATCAAGTCTAAACA
1 AATCTTATCTCATTATAAAACAAATTTTAGATCAAGTCTAAACA
*
28837693 AATCTTATCTCATTATAAAACCAATTTTAGATCAAGTCTAAACA
1 AATCTTATCTCATTATAAAACAAATTTTAGATCAAGTCTAAACA
28837737 A
1 A
28837738 TCATTGAAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (44 bp):
AATCTTATCTCATTATAAAACAAATTTTAGATCAAGTCTAAACA
Found at i:28837738 original size:21 final size:22
Alignment explanation
Indices: 28837666--28837737 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
28837656 TCTCATTATA
28837666 AAACAAATTTTAGATCAAGTCT
1 AAACAAATTTTAGATCAAGTCT
* ** * *
28837688 AAACAAATCTTATCTC-ATTAT
1 AAACAAATTTTAGATCAAGTCT
*
28837709 AAAACCAATTTTAGATCAAGTCT
1 -AAACAAATTTTAGATCAAGTCT
28837732 AAACAA
1 AAACAA
28837738 TCATTGAAGT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
21 3 0.08
22 30 0.83
23 3 0.08
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (22 bp):
AAACAAATTTTAGATCAAGTCT
Found at i:28841050 original size:22 final size:24
Alignment explanation
Indices: 28841008--28841053 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
28840998 CAATACAAAA
*
28841008 TTTTTAATTTTTCCTTTTAATTTC
1 TTTTTAATTTTTCATTTTAATTTC
28841032 TTTTTAA-TTTT-ATTTTAATTTC
1 TTTTTAATTTTTCATTTTAATTTC
28841054 ACTAATCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 4 0.19
24 7 0.33
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTTAATTTTTCATTTTAATTTC
Found at i:28841537 original size:24 final size:24
Alignment explanation
Indices: 28841491--28841537 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
28841481 AATTATCAAT
* *
28841491 TTGAGTTTTAAATATTGATGGGTA
1 TTGAGTTTTAAATATTAAAGGGTA
*
28841515 TTGAGTTTTAAATTTTAAAGGGT
1 TTGAGTTTTAAATATTAAAGGGT
28841538 TTATGCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (24 bp):
TTGAGTTTTAAATATTAAAGGGTA
Found at i:28847279 original size:18 final size:18
Alignment explanation
Indices: 28847239--28847279 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28847229 AATAAATTAT
*
28847239 AAAAATTATTTAAAAATA
1 AAAAATTATTTAAAAAGA
28847257 AAAAATTA-TTAAAAAGA
1 AAAAATTATTTAAAAAGA
28847274 ATAAAA
1 A-AAAA
28847280 CATGGCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATTATTTAAAAAGA
Found at i:28848160 original size:30 final size:30
Alignment explanation
Indices: 28848126--28848185 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
28848116 ACTTATCAAG
28848126 CAAATATCTCTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
* *
28848156 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
28848186 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:28848959 original size:13 final size:14
Alignment explanation
Indices: 28848931--28848964 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28848921 AATTAACACG
28848931 AAATAGTTTATTTT
1 AAATAGTTTATTTT
28848945 AAATAGTTT-TTTT
1 AAATAGTTTATTTT
28848958 AAA-AGTT
1 AAATAGTT
28848965 ACCAATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 7 0.35
14 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (14 bp):
AAATAGTTTATTTT
Found at i:28863099 original size:49 final size:49
Alignment explanation
Indices: 28863042--28863162 Score: 145
Period size: 49 Copynumber: 2.4 Consensus size: 49
28863032 GTGGTGTGTT
* *
28863042 AGTGTAAGACCTGTTTGGGACACGGCATCGACAC-CGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACACGGCATCGAC-CTCGATAGATGAAAGCC
* * * * * *
28863091 AGTGTAAGACCTGTCTAGGACATGGCATTGGCCTCGCTATATGAAAGCC
1 AGTGTAAGACCTGTCTGGGACACGGCATCGACCTCGATAGATGAAAGCC
28863140 AGTGTAAGACCATGTCTGGGACA
1 AGTGTAAGACC-TGTCTGGGACA
28863163 TAGCGTCAGC
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.82
50 10 0.16
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.21
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACACGGCATCGACCTCGATAGATGAAAGCC
Found at i:28867068 original size:12 final size:13
Alignment explanation
Indices: 28867034--28867073 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
28867024 TTTTTTTAAG
28867034 TAGTTTATTGATA
1 TAGTTTATTGATA
28867047 TAGTCATTATT-ATA
1 TAGT--TTATTGATA
28867061 TAGTTTATTGATA
1 TAGTTTATTGATA
28867074 AAAATAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 7 0.29
15 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (13 bp):
TAGTTTATTGATA
Found at i:28871312 original size:22 final size:18
Alignment explanation
Indices: 28871269--28871317 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
28871259 CCCGAAAAGG
28871269 TGATTGATTACCAGTTGA
1 TGATTGATTACCAGTTGA
*
28871287 TGATTGATTACCAGTTGG
1 TGATTGATTACCAGTTGA
28871305 TGATTGATTACCA
1 TGATTGATTACCA
28871318 ACGAAGGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (18 bp):
TGATTGATTACCAGTTGA
Found at i:28874076 original size:48 final size:47
Alignment explanation
Indices: 28873967--28874181 Score: 188
Period size: 46 Copynumber: 4.6 Consensus size: 47
28873957 TGATATATGT
* * *
28873967 GCTAGTGTAAGACATGTTTGGAACATGCATCAGCC--ACA-ACATTAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTTA-AGATATTA-A
* *
28874013 GCCAGTGTAAGACATGTCTAGGACATGCATCAGCCTTAAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTTAAGATA-TTAA
* * * * *
28874061 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCATTGAGATGA--GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTTAAGAT-ATTAA
* * *** *
28874107 GCTAGTGTAAGACATGTCTGGGACATGCATCGGGCTCGCGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTTAAGATAT-TAA
* *
28874155 GCTAGTGTAAGACCTGTTTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
28874182 GCGTCAACTT
Statistics
Matches: 141, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
45 1 0.01
46 69 0.49
47 1 0.01
48 66 0.47
49 4 0.03
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTTAAGATATTAA
Found at i:28874119 original size:94 final size:94
Alignment explanation
Indices: 28873967--28874181 Score: 270
Period size: 94 Copynumber: 2.3 Consensus size: 94
28873957 TGATATATGT
* *
28873967 GCTAGTGTAAGACATGTTTGGAACATGCATCAGCCACAACATTAGAGCCAGTGTAAGACATGTCT
1 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCACAACATGAGAGCCAGTGTAAGACATGTCT
* **
28874032 AGGACATGCATCAGCCTTAAGATATTTAA
66 AGGACATGCATCAGCCTCAAGATATACAA
* ** * *
28874061 GCTAGTGTAAGACATGTTTGGGACATGCATC-GGCATTGAGATGAGAGCTAGTGTAAGACATGTC
1 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCA-CAACATGAGAGCCAGTGTAAGACATGTC
* * * **
28874125 TGGGACATGCATCGGGCTCGCGATATACAA
65 TAGGACATGCATCAGCCTCAAGATATACAA
*
28874155 GCTAGTGTAAGACCTGTTTGGGACATG
1 GCTAGTGTAAGACATGTTTGGGACATG
28874182 GCGTCAACTT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
93 3 0.03
94 101 0.97
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCACAACATGAGAGCCAGTGTAAGACATGTCT
AGGACATGCATCAGCCTCAAGATATACAA
Found at i:28874270 original size:49 final size:49
Alignment explanation
Indices: 28874099--28874323 Score: 151
Period size: 49 Copynumber: 4.7 Consensus size: 49
28874089 ATCGGCATTG
* * * *** **
28874099 AGATGAGAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGGCTCGCG
1 AGATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCAACCTCGAT
* * * * *
28874147 ATAT-ACAAGCTAGTGTAAGACCTGTTTGGGACATGGCGTCAA-CTTG-T
1 AGATGA-AAGCTAGTGTAAGACCTATCTGGGACATGGCATCAACCTCGAT
* * * * *
28874194 -GGTG--TGTTAGTGTAAGACCTTTTTGGGACATGGCATCAACAC-CGAT
1 AGATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCAAC-CTCGAT
* * *
28874240 AGATGAGAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGCT
1 AGATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCAACCTCGAT
* * *
28874289 ATATGAAAGCCAGTGTAAGACCATGTCTGGGACAT
1 AGATGAAAGCTAGTGTAAGACC-TATCTGGGACAT
28874324 AGCACCGACA
Statistics
Matches: 139, Mismatches: 27, Indels: 20
0.75 0.15 0.11
Matches are distributed among these distances:
44 31 0.22
45 1 0.01
46 3 0.02
47 4 0.03
48 32 0.23
49 57 0.41
50 11 0.08
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (49 bp):
AGATGAAAGCTAGTGTAAGACCTATCTGGGACATGGCATCAACCTCGAT
Found at i:28883888 original size:37 final size:37
Alignment explanation
Indices: 28883838--28883912 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
28883828 TAGAGTTGTA
**
28883838 GAGAGAACTAATCGAACTCTTTTGAACATGGTTCGGT
1 GAGAGAACTAATCGAACTCTTTTGAACACAGTTCGGT
28883875 GAGAGAACTAATCGAACTCTTTTGAACACAGTTCGGT
1 GAGAGAACTAATCGAACTCTTTTGAACACAGTTCGGT
28883912 G
1 G
28883913 CATGCTAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (37 bp):
GAGAGAACTAATCGAACTCTTTTGAACACAGTTCGGT
Found at i:28887838 original size:10 final size:10
Alignment explanation
Indices: 28887823--28887861 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28887813 TATTTCTCTC
*
28887823 AAAAAAAGTA
1 AAAAAAAATA
28887833 AAAAAAAATA
1 AAAAAAAATA
*
28887843 AAAAAATATA
1 AAAAAAAATA
28887853 AAAATAAAA
1 AAAA-AAAA
28887862 CAATAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 22 0.88
11 3 0.12
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:28887845 original size:8 final size:8
Alignment explanation
Indices: 28887834--28887870 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
28887824 AAAAAAGTAA
28887834 AAAAAAAT
1 AAAAAAAT
28887842 AAAAAAAT
1 AAAAAAAT
*
28887850 ATAAAAAT
1 AAAAAAAT
*
28887858 AAAACAAT
1 AAAAAAAT
28887866 AAAAA
1 AAAAA
28887871 TATTATGTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:28887871 original size:22 final size:20
Alignment explanation
Indices: 28887822--28887873 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
28887812 ATATTTCTCT
*
28887822 CAAAAAAA-GTAAAAAAAAA
1 CAAAAAAATATAAAAAAAAA
*
28887841 TAAAAAAATATAAAAATAAAA
1 CAAAAAAATATAAAAA-AAAA
28887862 CAATAAAAATAT
1 CAA-AAAAATAT
28887874 TATGTGCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.26
20 6 0.22
21 6 0.22
22 8 0.30
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (20 bp):
CAAAAAAATATAAAAAAAAA
Found at i:28890290 original size:20 final size:20
Alignment explanation
Indices: 28890253--28890291 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28890243 AAAAGGCTCT
***
28890253 TTGACCTTTAACTTTAACGG
1 TTGACCTTTAAAGGTAACGG
28890273 TTGACCTTTAAAGGTAACG
1 TTGACCTTTAAAGGTAACG
28890292 ACACTTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
TTGACCTTTAAAGGTAACGG
Found at i:28890452 original size:11 final size:11
Alignment explanation
Indices: 28890438--28890634 Score: 77
Period size: 11 Copynumber: 18.9 Consensus size: 11
28890428 TATAGAAAAG
*
28890438 TATTTAAAATT
1 TATTAAAAATT
*
28890449 TATTAAAAAAT
1 TATTAAAAATT
28890460 TATTAAAAATT
1 TATTAAAAATT
** *
28890471 TAGAAAAAAAT
1 TATTAAAAATT
28890482 TATTAAAAA-T
1 TATTAAAAATT
* *
28890492 TATTAAAAGTA
1 TATTAAAAATT
28890503 TA-TAAAAA--
1 TATTAAAAATT
*
28890511 TATTAAAAATA
1 TATTAAAAATT
* *
28890522 TA-GAAAAA-A
1 TATTAAAAATT
28890531 TA-TAAAAA-T
1 TATTAAAAATT
*
28890540 CATT-AAAATT
1 TATTAAAAATT
*
28890550 TA-TAAAAA-G
1 TATTAAAAATT
*
28890559 AATATATAAAA-T
1 TAT-TA-AAAATT
28890571 T-TTAAAAA-T
1 TATTAAAAATT
*
28890580 CATT-AAAATT
1 TATTAAAAATT
28890590 TA-TAAAAATAT
1 TATTAAAAAT-T
28890601 ATATATATAAAATT
1 -TAT-TA-AAAATT
*
28890615 T-TTTAAAATT
1 TATTAAAAATT
*
28890625 TATAAAAAAT
1 TATTAAAAAT
28890635 ATAAAAAATA
Statistics
Matches: 142, Mismatches: 25, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
8 2 0.01
9 31 0.22
10 44 0.31
11 49 0.35
12 7 0.05
13 1 0.01
14 3 0.02
15 5 0.04
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (11 bp):
TATTAAAAATT
Found at i:28890583 original size:40 final size:43
Alignment explanation
Indices: 28890533--28890616 Score: 138
Period size: 40 Copynumber: 2.0 Consensus size: 43
28890523 AGAAAAAATA
28890533 TAAAAATCATTAAAATTTAT-AAAA-AGA-ATATATAAAATTT
1 TAAAAATCATTAAAATTTATAAAAATAGATATATATAAAATTT
*
28890573 TAAAAATCATTAAAATTTATAAAAATATATATATATAAAATTT
1 TAAAAATCATTAAAATTTATAAAAATAGATATATATAAAATTT
28890616 T
1 T
28890617 TTAAAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 20 0.50
41 4 0.10
42 2 0.05
43 14 0.35
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (43 bp):
TAAAAATCATTAAAATTTATAAAAATAGATATATATAAAATTT
Found at i:28890603 original size:10 final size:10
Alignment explanation
Indices: 28890418--28890659 Score: 99
Period size: 10 Copynumber: 25.1 Consensus size: 10
28890408 TATGTTAATT
*
28890418 TATAAAAAAA
1 TATATAAAAA
* *
28890428 TATAGAAAAG
1 TATATAAAAA
*
28890438 TAT-TTAAAA
1 TATATAAAAA
*
28890447 TTTATTAAAAA
1 TATA-TAAAAA
28890458 -ATTATTAAAAA
1 TA-TA-TAAAAA
* *
28890469 TTTAGAAAAA
1 TATATAAAAA
*
28890479 AATTATTAAAAA
1 TA-TA-TAAAAA
*
28890491 T-TATTAAAAG
1 TATA-TAAAAA
28890501 TATATAAAAA
1 TATATAAAAA
28890511 TAT-TAAAAA
1 TATATAAAAA
*
28890520 TATAGAAAAA
1 TATATAAAAA
28890530 -ATATAAAAA
1 TATATAAAAA
28890539 TCAT-T-AAAA
1 T-ATATAAAAA
*
28890548 TTTATAAAAA
1 TATATAAAAA
*
28890558 GAATATATAAAA
1 -TATATA-AAAA
*
28890570 T-TTTAAAAA
1 TATATAAAAA
28890579 TCAT-T-AAAA
1 T-ATATAAAAA
*
28890588 TTTATAAAAA
1 TATATAAAAA
28890598 TATAT----A
1 TATATAAAAA
28890604 TATAT-AAAA
1 TATATAAAAA
* * *
28890613 TTTTTTAAAA
1 TATATAAAAA
*
28890623 TTTATAAAAA
1 TATATAAAAA
28890633 -ATATAAAAA
1 TATATAAAAA
28890642 -ATAT-AAAA
1 TATATAAAAA
28890650 TATA-AAAAA
1 TATATAAAAA
28890659 T
1 T
28890660 GTTATGAAAT
Statistics
Matches: 178, Mismatches: 30, Indels: 49
0.69 0.12 0.19
Matches are distributed among these distances:
6 6 0.03
8 6 0.03
9 63 0.35
10 67 0.38
11 27 0.15
12 9 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (10 bp):
TATATAAAAA
Found at i:28890637 original size:9 final size:9
Alignment explanation
Indices: 28890625--28890659 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28890615 TTTTAAAATT
28890625 TATAAAAAA
1 TATAAAAAA
28890634 TATAAAAAA
1 TATAAAAAA
28890643 TAT--AAAA
1 TATAAAAAA
28890650 TATAAAAAA
1 TATAAAAAA
28890659 T
1 T
28890660 GTTATGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.29
9 17 0.71
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
TATAAAAAA
Found at i:28890638 original size:44 final size:43
Alignment explanation
Indices: 28890533--28890656 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 43
28890523 AGAAAAAATA
* * *
28890533 TAAAAATCATT--AAAATTTATAAAA-AGAATATATAAAATTT
1 TAAAAATCATTAAAAAATATAAAAAATATAATATATAAAATTT
**
28890573 TAAAAATCATTAAAATTTAT-AAAAATATATATATATAAAATTTT
1 TAAAAATCATTAAAAAATATAAAAAATATA-ATATATAAAA-TTT
* * *
28890617 TTAAAAT-TTATAAAAAATATAAAAAATATAAAATATAAAA
1 TAAAAATCAT-TAAAAAATATAAAAAATATAATATATAAAA
28890657 AATGTTATGA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
40 11 0.16
41 4 0.06
42 6 0.09
43 11 0.16
44 26 0.39
45 9 0.13
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (43 bp):
TAAAAATCATTAAAAAATATAAAAAATATAATATATAAAATTT
Found at i:28890641 original size:19 final size:19
Alignment explanation
Indices: 28890443--28890679 Score: 102
Period size: 19 Copynumber: 12.2 Consensus size: 19
28890433 AAAAGTATTT
28890443 AAAATTTATTAAAAAATTATTA
1 AAAATTTA-TAAAAAA-TA-TA
*
28890465 AAAATTTAGAAAAAAATTATTA
1 AAAATTTA-TAAAAAA-TA-TA
*
28890487 AAAA-TTATTAAAAGTATATA
1 AAAATTTA-TAAAA-AATATA
*
28890507 AAAA--TATTAAAAATATA
1 AAAATTTATAAAAAATATA
** *
28890524 GAAAAAATAT-AAAAATCATT
1 -AAAATTTATAAAAAAT-ATA
28890544 AAAATTTATAAAAAGAATATA
1 AAAATTTAT-AAAA-AATATA
*
28890565 TAAAATTT-T-AAAAATCATT
1 -AAAATTTATAAAAAAT-ATA
28890584 AAAATTTAT-AAAAATAT-
1 AAAATTTATAAAAAATATA
* * ** * *
28890601 -ATATATATAAAATTTTTT
1 AAAATTTATAAAAAATATA
28890619 AAAATTTATAAAAAATATA
1 AAAATTTATAAAAAATATA
* *
28890638 AAAA-ATATAAAATATA-A
1 AAAATTTATAAAAAATATA
28890655 AAAATGTTATGAAATAAATA-A
1 AAAAT-TTAT-AAA-AAATATA
28890676 AAAA
1 AAAA
28890680 GAAACTAAAA
Statistics
Matches: 170, Mismatches: 27, Indels: 37
0.73 0.12 0.16
Matches are distributed among these distances:
16 6 0.04
17 15 0.09
18 30 0.18
19 46 0.27
20 14 0.08
21 24 0.14
22 35 0.21
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATTTATAAAAAATATA
Found at i:28895259 original size:33 final size:34
Alignment explanation
Indices: 28895216--28895281 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
28895206 CCCACACTAT
* *
28895216 TACTGTATAGGGCTAAGGCCCAGACTG-TACTGA
1 TACTGAATAGGGCCAAGGCCCAGACTGTTACTGA
* *
28895249 TACTGAATAGGGCCCAGGCCCATACTGTTACTG
1 TACTGAATAGGGCCAAGGCCCAGACTGTTACTG
28895282 CATTCATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (34 bp):
TACTGAATAGGGCCAAGGCCCAGACTGTTACTGA
Found at i:28895901 original size:342 final size:343
Alignment explanation
Indices: 28895240--28895921 Score: 1132
Period size: 342 Copynumber: 2.0 Consensus size: 343
28895230 AAGGCCCAGA
* *
28895240 CTGTACTGATACTGAATAGGGCCCAGGCCCATACTGTTACTGCATTCATTGTTTACTATTTGACT
1 CTGTACTGATACTGAATAGGGCCCAGGCCCAGACTGTTACTGCATGCATTGTTTACTATTTGACT
28895305 AGTAAGGGATTACACACTGAGTTTTCACAAACTCACCCTTTCTTTTAACTGTACAGGTAATCCTC
66 AGTAAGGGATTACACACTGAGTTTTCACAAACTCACCCTTTCTTTTAACTGTACAGGTAATCCTC
* * * * *
28895370 ATCCTTAGACGGTTTGGAGCCGCGAGGGACTCAGAGGTGGCCACACGATTGCTGATGTTCTACTT
131 AGCCTTAGACGGTTTAGAGCCACGAGGGACTCAGAGGTGGCCAAACAATTGCTGATGTTCTACTT
*
28895435 TTGACTTTAATTACTCAAAATTCATATTAGATTTTTGGTTATTTAATAAGACCATTTGAGGTTTT
196 TTGACTTTAATTACTCAAAATTCATATTAGATTTTTGGTTATGTAATAAGACCATTTGAGGTTTT
* *
28895500 TAACTTTTATTTAGGCTTTGATTTCTTACCTTAAGCTGCTAGACTAGGAATATACGAGTTTTCAA
261 TAACTTCTATTTAGGCTTTGATTTCTTACCTTAAGCTGCTAGACTAGGAATAGACGAGTTTTCAA
*
28895565 ACCAATTACTGTTTTAAG
326 ACCAATTACTATTTTAAG
*
28895583 CTGTACTGATACTGAATAGGGCCCAGG-CCAGACTGTTACTGCATGCATTGTTTACTGTTTGACT
1 CTGTACTGATACTGAATAGGGCCCAGGCCCAGACTGTTACTGCATGCATTGTTTACTATTTGACT
* * *
28895647 AGTAGGGGATTACACACTGAGTTTTCGCAAACTCACCCTTTCTTTTAACTGTACATGTAATCCTC
66 AGTAAGGGATTACACACTGAGTTTTCACAAACTCACCCTTTCTTTTAACTGTACAGGTAATCCTC
* * *
28895712 AGCCTTTGACGGTTTAGAGTCACGAGGGACTCGGAGGTGGCCAAACAATTGCTGATGTTCTACTT
131 AGCCTTAGACGGTTTAGAGCCACGAGGGACTCAGAGGTGGCCAAACAATTGCTGATGTTCTACTT
* * * * *
28895777 TTGATTTTAATTACTCAAATTTCATATTTGATTTTTTGTTATGTAATAAGGCCATTTGAGGTTTT
196 TTGACTTTAATTACTCAAAATTCATATTAGATTTTTGGTTATGTAATAAGACCATTTGAGGTTTT
* *
28895842 TAACTTCTATTTGGGCTTTGATTTCTTACCTTAAGCTGCTAGATTAGGAATAGACGAGTTTTCAA
261 TAACTTCTATTTAGGCTTTGATTTCTTACCTTAAGCTGCTAGACTAGGAATAGACGAGTTTTCAA
28895907 ACCAATTACTATTTT
326 ACCAATTACTATTTT
28895922 CAAAAACATA
Statistics
Matches: 314, Mismatches: 25, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
342 287 0.91
343 27 0.09
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (343 bp):
CTGTACTGATACTGAATAGGGCCCAGGCCCAGACTGTTACTGCATGCATTGTTTACTATTTGACT
AGTAAGGGATTACACACTGAGTTTTCACAAACTCACCCTTTCTTTTAACTGTACAGGTAATCCTC
AGCCTTAGACGGTTTAGAGCCACGAGGGACTCAGAGGTGGCCAAACAATTGCTGATGTTCTACTT
TTGACTTTAATTACTCAAAATTCATATTAGATTTTTGGTTATGTAATAAGACCATTTGAGGTTTT
TAACTTCTATTTAGGCTTTGATTTCTTACCTTAAGCTGCTAGACTAGGAATAGACGAGTTTTCAA
ACCAATTACTATTTTAAG
Found at i:28898381 original size:66 final size:65
Alignment explanation
Indices: 28898301--28898463 Score: 179
Period size: 66 Copynumber: 2.5 Consensus size: 65
28898291 CTTGTGTCAT
* * *
28898301 ACGGCCAAGGACACGCCCGTGTGCTAGGCCGTGTGAAAACTTGA-GAGTATACTAACTTATGCAA
1 ACGGCCAAGCACACGCCCGTGTGCTAGGCCGTGT-AAAACTTAAGGAGTATACTAACTTATACAA
28898365 C
65 C
* * * * * *
28898366 ACGGCCAAGTCACACGCCTGTGTGCTAGGCCGTGTACAATTTAAGGGGTATACTAACTTCTACCA
1 ACGGCCAAG-CACACGCCCGTGTGCTAGGCCGTGTAAAACTTAAGGAGTATACTAACTTATACAA
28898431 C
65 C
*
28898432 ACGGCC-AGCCACACGCCCATGTG-TGAGGCCGT
1 ACGGCCAAG-CACACGCCCGTGTGCT-AGGCCGT
28898464 CTGGAGCAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
64 1 0.01
65 36 0.43
66 46 0.55
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (65 bp):
ACGGCCAAGCACACGCCCGTGTGCTAGGCCGTGTAAAACTTAAGGAGTATACTAACTTATACAAC
Found at i:28899498 original size:23 final size:23
Alignment explanation
Indices: 28899465--28899580 Score: 132
Period size: 23 Copynumber: 5.1 Consensus size: 23
28899455 TAAGCTGATG
*
28899465 AACAGTAAGCTCTATTGAGCTGA
1 AACAGTAAGCTCTATCGAGCTGA
*
28899488 AACGGTAAGCTCTATCGAGCTG-
1 AACAGTAAGCTCTATCGAGCTGA
28899510 AACAGTAAGCTCATAT-GAGCTGA
1 AACAGTAAGCTC-TATCGAGCTGA
**
28899533 AATGGTAAGCTCTATCGAGCT-A
1 AACAGTAAGCTCTATCGAGCTGA
* *
28899555 AATAGTAAGCTC-ATGCAAGCTGA
1 AACAGTAAGCTCTAT-CGAGCTGA
28899578 AAC
1 AAC
28899581 GATAATTCCA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.03
22 37 0.46
23 41 0.51
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (23 bp):
AACAGTAAGCTCTATCGAGCTGA
Found at i:28899514 original size:45 final size:45
Alignment explanation
Indices: 28899463--28899568 Score: 169
Period size: 45 Copynumber: 2.4 Consensus size: 45
28899453 CCTAAGCTGA
28899463 TGAACAGTAAGCTC-TATTGAGCTGAAACGGTAAGCTCTATCGAGC
1 TGAACAGTAAGCTCATA-TGAGCTGAAACGGTAAGCTCTATCGAGC
*
28899508 TGAACAGTAAGCTCATATGAGCTGAAATGGTAAGCTCTATCGAGC
1 TGAACAGTAAGCTCATATGAGCTGAAACGGTAAGCTCTATCGAGC
* *
28899553 TAAATAGTAAGCTCAT
1 TGAACAGTAAGCTCAT
28899569 GCAAGCTGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 55 0.96
46 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (45 bp):
TGAACAGTAAGCTCATATGAGCTGAAACGGTAAGCTCTATCGAGC
Found at i:28899576 original size:45 final size:45
Alignment explanation
Indices: 28899465--28899581 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 45
28899455 TAAGCTGATG
** *
28899465 AACAGTAAGCTC-TATTGAGCTGAAACGGTAAGCTCTATCGAGCTG
1 AACAGTAAGCTCATA-CAAGCTGAAACGGTAAGCTCTATCGAGCTA
** *
28899510 AACAGTAAGCTCATATGAGCTGAAATGGTAAGCTCTATCGAGCTA
1 AACAGTAAGCTCATACAAGCTGAAACGGTAAGCTCTATCGAGCTA
* *
28899555 AATAGTAAGCTCATGCAAGCTGAAACG
1 AACAGTAAGCTCATACAAGCTGAAACG
28899582 ATAATTCCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
45 62 0.97
46 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
AACAGTAAGCTCATACAAGCTGAAACGGTAAGCTCTATCGAGCTA
Found at i:28899823 original size:18 final size:19
Alignment explanation
Indices: 28899783--28899823 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28899773 ATTCATACTT
* *
28899783 CAAGTATTTCAATTATATA
1 CAAGCATTTCAATAATATA
28899802 CAAGCATTTCAATAAT-TA
1 CAAGCATTTCAATAATATA
28899820 CAAG
1 CAAG
28899824 TATAGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (19 bp):
CAAGCATTTCAATAATATA
Found at i:28906155 original size:39 final size:39
Alignment explanation
Indices: 28906112--28906191 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
28906102 ATCCTTTCAT
28906112 GAATATTTGGTAATAGCCCGCTAAGCCTAGAAAACTATG
1 GAATATTTGGTAATAGCCCGCTAAGCCTAGAAAACTATG
*
28906151 GAATATTTGGTAATAGCCTGCTAAGCCTAGAAAACTATG
1 GAATATTTGGTAATAGCCCGCTAAGCCTAGAAAACTATG
28906190 GA
1 GA
28906192 CTTCCATACG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (39 bp):
GAATATTTGGTAATAGCCCGCTAAGCCTAGAAAACTATG
Found at i:28910735 original size:21 final size:21
Alignment explanation
Indices: 28910694--28910735 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28910684 AAGAAAGGAA
* **
28910694 ATAATAAAAGAAATACTAAGG
1 ATAATAAAAGAAAAAAAAAGG
28910715 ATAATAAAAGAAAAAAAAAGG
1 ATAATAAAAGAAAAAAAAAGG
28910736 GGTTATTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (21 bp):
ATAATAAAAGAAAAAAAAAGG
Found at i:28912244 original size:28 final size:28
Alignment explanation
Indices: 28912177--28912297 Score: 170
Period size: 28 Copynumber: 4.3 Consensus size: 28
28912167 GAGATTGGAG
* * * * *
28912177 CTAAGTGTGCGGGTTTAAATTGTACAACA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
28912206 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
28912234 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
28912262 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
28912290 CTGAGTGT
1 CTAAGTGT
28912298 ACGGACTTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 69 0.82
29 15 0.18
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:28917200 original size:23 final size:23
Alignment explanation
Indices: 28917140--28917269 Score: 117
Period size: 23 Copynumber: 5.7 Consensus size: 23
28917130 GTTACATTTT
* *
28917140 GAGCTGAAACAGAAAGCTC-TATT
1 GAGCTGAAACAGTAAGCTCATA-C
*
28917163 GAGCT-AAACAATAAGCTCATAC
1 GAGCTGAAACAGTAAGCTCATAC
*
28917185 GAGCTGAAACGGTAAGCTC-TATC
1 GAGCTGAAACAGTAAGCTCATA-C
* *
28917208 AAGCTG-AACAATAAGCTCATAC
1 GAGCTGAAACAGTAAGCTCATAC
* *
28917230 CAGCTGAAACAGTAAGCTCCA-AT
1 GAGCTGAAACAGTAAGCT-CATAC
28917253 GAGCTGAAAACAGTAAG
1 GAGCTG-AAACAGTAAG
28917270 ATTTTTTGAG
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
22 34 0.39
23 42 0.48
24 12 0.14
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (23 bp):
GAGCTGAAACAGTAAGCTCATAC
Found at i:28917204 original size:45 final size:45
Alignment explanation
Indices: 28917140--28917257 Score: 164
Period size: 45 Copynumber: 2.6 Consensus size: 45
28917130 GTTACATTTT
*
28917140 GAGCTGAAACAGAAAGCTCTATTGAGCTAAACAATAAGCTCATAC
1 GAGCTGAAACAGTAAGCTCTATTGAGCTAAACAATAAGCTCATAC
* ** *
28917185 GAGCTGAAACGGTAAGCTCTATCAAGCTGAACAATAAGCTCATAC
1 GAGCTGAAACAGTAAGCTCTATTGAGCTAAACAATAAGCTCATAC
* * *
28917230 CAGCTGAAACAGTAAGCTCCAATGAGCT
1 GAGCTGAAACAGTAAGCTCTATTGAGCT
28917258 GAAAACAGTA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (45 bp):
GAGCTGAAACAGTAAGCTCTATTGAGCTAAACAATAAGCTCATAC
Found at i:28925630 original size:27 final size:27
Alignment explanation
Indices: 28925296--28925629 Score: 508
Period size: 27 Copynumber: 12.4 Consensus size: 27
28925286 TGGATAAGTT
* *
28925296 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
28925323 GTAGAATTA-TCGAAATACCCCTGTAGG
1 GTAGAATTACT-GAAATACCCCTGTAGG
* *
28925350 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
28925377 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28925404 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28925431 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28925458 GTAGAATTACTGAAATACCCCTTTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
28925485 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28925512 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28925539 GTAGAATTACTGAAATACCCTTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28925566 GTAGAATTACTGAAATACCTCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* * * * *
28925593 ATAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28925620 GTAAAATTAC
1 GTAGAATTAC
28925630 CATTTTGCCC
Statistics
Matches: 282, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
27 282 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (27 bp):
GTAGAATTACTGAAATACCCCTGTAGG
Found at i:28925653 original size:27 final size:27
Alignment explanation
Indices: 28925631--28925693 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
28925621 TAAAATTACC
28925631 ATTTTGCCCCTAGGGTGTTAAATGACT
1 ATTTTGCCCCTAGGGTGTTAAATGACT
28925658 ATTTTGCCCCTAGGGTGTTAAATGACT
1 ATTTTGCCCCTAGGGTGTTAAATGACT
28925685 ATTTTGCCC
1 ATTTTGCCC
28925694 ATCGTGCGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (27 bp):
ATTTTGCCCCTAGGGTGTTAAATGACT
Found at i:28925754 original size:20 final size:20
Alignment explanation
Indices: 28925729--28925766 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28925719 TGATGATTGG
*
28925729 GTTAGTTAACGTGGATTTAT
1 GTTAGTTAACGTGAATTTAT
*
28925749 GTTAGTTATCGTGAATTT
1 GTTAGTTAACGTGAATTT
28925767 GTAAGTCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.47
Consensus pattern (20 bp):
GTTAGTTAACGTGAATTTAT
Found at i:28926395 original size:31 final size:32
Alignment explanation
Indices: 28926357--28926418 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
28926347 CTCGCTGCAA
* *
28926357 TCTGGTGGCTTCGCCAC-ATATATATATCTGT
1 TCTGGTGGCCTAGCCACAATATATATATCTGT
*
28926388 TCTGGTGGCCTAGCCACAATATCTATATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
28926419 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:28930858 original size:134 final size:134
Alignment explanation
Indices: 28930611--28930861 Score: 421
Period size: 134 Copynumber: 1.9 Consensus size: 134
28930601 TGGATAAGTT
*
28930611 GTAGAATTACTGAAATACCCCTGTAGGGAAGAATTACTGAAATACCCCTGTAGGGTAGAATTATT
1 GTAGAATTACTGAAATACCCCTGTAGGGAAGAATTACTGAAATACCCCTGTAGGGTAGAATTACT
*
28930676 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTATTGAAATACCCCT
66 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTATTGAAATACCCCT
28930741 GCAG
131 GCAG
* *
28930745 GTAGAATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGTAGGGTAGAATTACT
1 GTAGAATTACTGAAATACCCCTGTAGGGAAGAATTACTGAAATACCCCTGTAGGGTAGAATTACT
* * ** *
28930810 GAAATACCCTTGTAGGGTAGAATTACTGAAATACCTTTGTAGGATAGAATTA
66 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTA
28930862 CCGAGATACC
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 108 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (134 bp):
GTAGAATTACTGAAATACCCCTGTAGGGAAGAATTACTGAAATACCCCTGTAGGGTAGAATTACT
GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGATAGAATTATTGAAATACCCCT
GCAG
Found at i:28930890 original size:27 final size:27
Alignment explanation
Indices: 28930611--28930889 Score: 407
Period size: 27 Copynumber: 10.4 Consensus size: 27
28930601 TGGATAAGTT
28930611 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28930638 GAAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28930665 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* *
28930692 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* *
28930719 GTAGAATTATTGAAATACCCCTGCA-G
1 GTAGAATTACTGAAATACCCCTGTAGG
28930745 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28930772 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28930799 GTAGAATTACTGAAATACCCTTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
**
28930826 GTAGAATTACTGAAATACCTTTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* * * * *
28930853 ATAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28930880 GTAAAATTAC
1 GTAGAATTAC
28930890 CATTTTGCCC
Statistics
Matches: 228, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
26 24 0.11
27 204 0.89
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (27 bp):
GTAGAATTACTGAAATACCCCTGTAGG
Found at i:28937087 original size:27 final size:27
Alignment explanation
Indices: 28937020--28937269 Score: 333
Period size: 27 Copynumber: 9.3 Consensus size: 27
28937010 TGGATAAGTT
* *
28937020 GTAGAATTACCGAAATACCCCTATA-G
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28937046 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* *
28937073 GTAGAATTACTGAAATGCTCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28937100 GTAGAATTACTGAAATACCCCTATAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* *
28937127 TTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28937154 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
28937181 GTAGAATTACTCAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* *
28937208 GTAGAATTACCGACATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* * *
28937235 GTAGAATTA-TCGAGATACCCTTGTGGG
1 GTAGAATTACT-GAAATACCCCTGTAGG
*
28937262 GTAAAATT
1 GTAGAATT
28937270 CCCATTTTGC
Statistics
Matches: 199, Mismatches: 23, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
26 24 0.12
27 175 0.88
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
GTAGAATTACTGAAATACCCCTGTAGG
Found at i:28937154 original size:81 final size:80
Alignment explanation
Indices: 28937020--28937269 Score: 367
Period size: 81 Copynumber: 3.1 Consensus size: 80
28937010 TGGATAAGTT
*
28937020 GTAGAATTACCGAAATACCCCTATAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACTG
1 GTAGAATTACTGAAATACCCCTATAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACTG
* *
28937085 AAATGCTCCTGTAGG
66 AAATACCCCTGTAGG
*
28937100 GTAGAATTACTGAAATACCCCTATAGGTTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATT
1 GTAGAATTACTGAAATACCCCTATAGG-TAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
28937165 GAAATACCCCTGTAGG
65 GAAATACCCCTGTAGG
* * *
28937181 GTAGAATTACTCAAATACCCCTGTAGGGTAGAATTACCGACATACCCCTGTAGGGTAGAATTA-T
1 GTAGAATTACTGAAATACCCCTATA-GGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * *
28937245 CGAGATACCCTTGTGGG
65 -GAAATACCCCTGTAGG
*
28937262 GTAAAATT
1 GTAGAATT
28937270 CCCATTTTGC
Statistics
Matches: 156, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
80 27 0.17
81 127 0.81
82 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (80 bp):
GTAGAATTACTGAAATACCCCTATAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACTG
AAATACCCCTGTAGG
Found at i:28937985 original size:27 final size:26
Alignment explanation
Indices: 28937947--28938006 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
28937937 CCACATATAT
* *
28937947 ATATTTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
28937973 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
28938000 ATATCTG
1 ATATCTG
28938007 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:28949369 original size:43 final size:43
Alignment explanation
Indices: 28949305--28949628 Score: 488
Period size: 43 Copynumber: 7.5 Consensus size: 43
28949295 AAGTTTGGTT
*
28949305 TAATGTAA-TGGCACTAAGTGTGCGATATAATTATAGCTTCGGC
1 TAAT-TAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
28949348 TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
1 TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
*
28949391 TAATTAATTGGGACTAAGTGTGCGATACAATTATAGCTTCGGC
1 TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
** **
28949434 TAATTAATTGGCACTAAGTGTGTAATACAATTATAGCTTCTAC
1 TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
* * *
28949477 TAATTAATTGGCACTAAGTGTGCAATATAATTATAGCTTCGGT
1 TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
*
28949520 TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGT
1 TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
* * * *
28949563 TAATTAATTGGCACTAAGTGTGCGAAACCATTATAACTTCGGT
1 TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
* *
28949606 TAATTAATTAGCACTAAATGTGC
1 TAATTAATTGGCACTAAGTGTGC
28949629 AAGTTTATTG
Statistics
Matches: 261, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
42 3 0.01
43 258 0.99
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (43 bp):
TAATTAATTGGCACTAAGTGTGCGATACAATTATAGCTTCGGC
Found at i:28954185 original size:43 final size:43
Alignment explanation
Indices: 28954137--28954586 Score: 549
Period size: 43 Copynumber: 10.5 Consensus size: 43
28954127 CACATATTGG
* *** * *
28954137 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACACAT
1 AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGT
* *
28954180 AATCACATATCGATGTCAACATCCCAGACGTGGTTTTACACGT
1 AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGT
28954223 GAA-CACATATCGATGCC-ACTATCCCAGACAG-GGTCTTACACGT
1 -AATCACATATCGATGCCAAC-ATCCCAGAC-GTGGTCTTACACGT
* *
28954266 AATCACATATCGATGCCAACGTCCCAGACGTAGTCTTACACG-
1 AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGT
* * *
28954308 AGAACACATATCGATGCC-ACTATCCTAGACAG-GGTCTTACACAT
1 A-ATCACATATCGATGCCAAC-ATCCCAGAC-GTGGTCTTACACGT
*
28954352 AATCACATATCGATGGCAACATCCCAGACGTGGTCTTACACGT
1 AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGT
** *
28954395 AATCACATATCGATGCCAATGTCCTAGACGTGGTCTTACACGT
1 AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGT
*
28954438 AATCACATATCGATGCCAACATCCCAGATGTGGTCTTACACG-
1 AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGT
* * * *
28954480 AGAACACATATCAATGCC-ACTGTCCTAGACAG-GGTCTTACACGT
1 A-ATCACATATCGATGCCAAC-ATCCCAGAC-GTGGTCTTACACGT
*
28954524 AATCACATATCGATGCCAACATCCCAGACGTGATCTTACACGT
1 AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGT
28954567 AATCACATATCGATGCCAAC
1 AATCACATATCGATGCCAAC
28954587 TCAAAAATGT
Statistics
Matches: 350, Mismatches: 39, Indels: 36
0.82 0.09 0.08
Matches are distributed among these distances:
42 13 0.04
43 324 0.93
44 13 0.04
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGT
Found at i:28954187 original size:56 final size:55
Alignment explanation
Indices: 28954072--28954191 Score: 145
Period size: 56 Copynumber: 2.1 Consensus size: 55
28954062 ACTCTTAAAT
* * *
28954072 ACATATCGGAATCACATATCGATGCTAACATATTAAACGTGGATTTACTTGCACAC
1 ACATATCGGAATCACATATCGATGCCAACATATTAAACGTGGATTTAC-TACAAAC
* *
28954128 ACATATTGGAATCACATATCGATGCCAACGTATTAAACGTGG-TCTTAC-ACATAATC
1 ACATATCGGAATCACATATCGATGCCAACATATTAAACGTGGAT-TTACTACA-AA-C
28954184 ACATATCG
1 ACATATCG
28954192 ATGTCAACAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
54 2 0.04
55 2 0.04
56 51 0.93
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (55 bp):
ACATATCGGAATCACATATCGATGCCAACATATTAAACGTGGATTTACTACAAAC
Found at i:28954291 original size:86 final size:86
Alignment explanation
Indices: 28954168--28954584 Score: 642
Period size: 86 Copynumber: 4.8 Consensus size: 86
28954158 TATTAAACGT
* * *
28954168 GGTCTTACACATAATCACATATCGATGTCAACATCCCAGACGTGGTTTTACACGTGAACACATAT
1 GGTCTTACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGTGAACACATAT
*
28954233 CGATGCCACTATCCCAGACAG
66 CGATGCCACTATCCTAGACAG
* * *
28954254 GGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACGTAGTCTTACACGAGAACACATAT
1 GGTCTTACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGTGAACACATAT
28954319 CGATGCCACTATCCTAGACAG
66 CGATGCCACTATCCTAGACAG
* *
28954340 GGTCTTACACATAATCACATATCGATGGCAACATCCCAGACGTGGTCTTACACGT-AATCACATA
1 GGTCTTACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGTGAA-CACATA
* *
28954404 TCGATGCCAATGTCCTAGAC-G
65 TCGATGCCACTATCCTAGACAG
* *
28954425 TGGTCTTACACGTAATCACATATCGATGCCAACATCCCAGATGTGGTCTTACACGAGAACACATA
1 -GGTCTTACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGTGAACACATA
* *
28954490 TCAATGCCACTGTCCTAGACAG
65 TCGATGCCACTATCCTAGACAG
*
28954512 GGTCTTACACGTAATCACATATCGATGCCAACATCCCAGACGTGATCTTACACGT-AATCACATA
1 GGTCTTACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGTGAA-CACATA
28954576 TCGATGCCA
65 TCGATGCCA
28954585 ACTCAAAAAT
Statistics
Matches: 302, Mismatches: 24, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
85 5 0.02
86 294 0.97
87 3 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (86 bp):
GGTCTTACACGTAATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGTGAACACATAT
CGATGCCACTATCCTAGACAG
Found at i:28959995 original size:29 final size:28
Alignment explanation
Indices: 28959927--28959995 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
28959917 TTTGTGATAG
*
28959927 AGGCATTTCCTTTCAGAGGTTCGCCACAT
1 AGGCA-TTCCTTTCAGAGGTTCGCCACAA
* **
28959956 AGGC-TTACCTTTCATGAGTTTTTCCACAA
1 AGGCATT-CCTTTCA-GAGGTTCGCCACAA
28959985 AGGCATTCCTT
1 AGGCATTCCTT
28959996 AACATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 2 0.06
28 7 0.21
29 22 0.67
30 2 0.06
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (28 bp):
AGGCATTCCTTTCAGAGGTTCGCCACAA
Found at i:28960027 original size:60 final size:60
Alignment explanation
Indices: 28959947--28960142 Score: 172
Period size: 60 Copynumber: 3.3 Consensus size: 60
28959937 TTTCAGAGGT
* *
28959947 TCGCCACATAGGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTC-TGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTAC
** * * *
28960008 TCGCCA-AAAGGCTTTCCTTTCTAGAGTTTTTCCGTAAAGGCATTTCTT-TCA--AAGGT--
1 TCGCCACAAAGGCTTTCCTTTCT-GAGTTTTTCCACAAAGGCATTCCTTAACATTCA-GTAC
* * * *
28960064 TCGCAACATAGG-TTTACCTTTTGTTGAGTTTTTCCACAAAGGCGTTCCTTAACATTCAGTAC
1 TCGCCACAAAGGCTTT-CC-TTT-CTGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTAC
* *
28960126 TTGCCACAAAGGTTTTC
1 TCGCCACAAAGGCTTTC
28960143 TTGTCCAGAG
Statistics
Matches: 104, Mismatches: 19, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
56 8 0.08
57 7 0.07
58 26 0.25
59 6 0.06
60 37 0.36
61 7 0.07
62 10 0.10
63 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (60 bp):
TCGCCACAAAGGCTTTCCTTTCTGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTAC
Found at i:28960092 original size:118 final size:119
Alignment explanation
Indices: 28959892--28960263 Score: 428
Period size: 118 Copynumber: 3.1 Consensus size: 119
28959882 TCAGAGATAA
* * ** *
28959892 CCACAAAGGCTTTCGTGTCTAGA-TTTTTGTGATAGAGGCATTTCCTTTCAGAGGTTCGCCACAT
1 CCACAAAGGCTTTCCTTTCTAGAGTTTTTACG-TAGAGGCATTTCCTTTCAAAGGTTCGCCACAT
28959956 AGGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCG
65 AGGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCG
* * *
28960011 CCA-AAAGGCTTTCCTTTCTAGAGTTTTTCCGTAAAGGCATTT-CTTTCAAAGGTTCGCAACATA
1 CCACAAAGGCTTTCCTTTCTAGAGTTTTTACGTAGAGGCATTTCCTTTCAAAGGTTCGCCACATA
* ** * *
28960074 GGTTTACCTTTTGTTGAGTTTTTCCACAAAGGCGTTCCTTAACATTCAGTACTTG
66 GGCTTACC-TTTCATGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCG
* * * * ** * * *
28960129 CCACAAAGG-TTTTCTTGTCCAGAGTTTTAACATAGAGTAATTTCCTTTCATAGGTTTGCCACGT
1 CCACAAAGGCTTTCCTT-TCTAGAGTTTTTACGTAGAGGCATTTCCTTTCAAAGGTTCGCCACAT
* * * * * *
28960193 AGGCTTACCTTTCATAAGTTTTACCGCAAAGGCATTCCTTAAAATTTAGTACTCA
65 AGGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCG
*
28960248 CTACAAAGGCTTTCCT
1 CCACAAAGGCTTTCCT
28960264 ATCCAATGTT
Statistics
Matches: 210, Mismatches: 37, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
117 26 0.12
118 78 0.37
119 77 0.37
120 29 0.14
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (119 bp):
CCACAAAGGCTTTCCTTTCTAGAGTTTTTACGTAGAGGCATTTCCTTTCAAAGGTTCGCCACATA
GGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCG
Found at i:28960224 original size:119 final size:118
Alignment explanation
Indices: 28959931--28960268 Score: 392
Period size: 119 Copynumber: 2.8 Consensus size: 118
28959921 TGATAGAGGC
*
28959931 ATTTCCTTTCAGAGGTTCGCCACATAGGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTT
1 ATTTCCTTTCAAAGGTTCGCCACATAGGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTT
* ** * *
28959996 AACATTCAGTACTCGCCAAAAGGCTTTCCTTTCTAGAGTTTTTCCGTAAAGGC
66 AACATTCAGTACTCGCCAAAAGGCTTTCCTTTCCAGAGTTTTAACATAAAGGA
* * ** *
28960049 ATTT-CTTTCAAAGGTTCGCAACATAGGTTTACCTTTTGTTGAGTTTTTCCACAAAGGCGTTCCT
1 ATTTCCTTTCAAAGGTTCGCCACATAGGCTTACC-TTTCATGAGTTTTTCCACAAAGGCATTCCT
* * * *
28960113 TAACATTCAGTACTTGCCACAAAGG-TTTTCTTGTCCAGAGTTTTAACATAGAGTA
65 TAACATTCAGTACTCGCCA-AAAGGCTTTCCTT-TCCAGAGTTTTAACATAAAGGA
* * * * * *
28960168 ATTTCCTTTCATAGGTTTGCCACGTAGGCTTACCTTTCATAAGTTTTACCGCAAAGGCATTCCTT
1 ATTTCCTTTCAAAGGTTCGCCACATAGGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTT
* * * * *
28960233 AAAATTTAGTACTCACTACAAAGGCTTTCCTATCCA
66 AACATTCAGTACTCGCCA-AAAGGCTTTCCTTTCCA
28960269 ATGTTTGCCA
Statistics
Matches: 182, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
117 26 0.14
118 55 0.30
119 72 0.40
120 29 0.16
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (118 bp):
ATTTCCTTTCAAAGGTTCGCCACATAGGCTTACCTTTCATGAGTTTTTCCACAAAGGCATTCCTT
AACATTCAGTACTCGCCAAAAGGCTTTCCTTTCCAGAGTTTTAACATAAAGGA
Found at i:28964213 original size:16 final size:16
Alignment explanation
Indices: 28964192--28964258 Score: 89
Period size: 16 Copynumber: 4.2 Consensus size: 16
28964182 TGAATTACTA
28964192 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
** *
28964208 ATTACAATTTTATTCC
1 ATTACAGCTCTATTCC
*
28964224 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
*
28964240 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
28964256 ATT
1 ATT
28964259 CCAGTGAACC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:28968038 original size:30 final size:30
Alignment explanation
Indices: 28968004--28968060 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
28967994 TTCCCGAGCC
28968004 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
28968034 TAGGGGCAAAATTGTAATTTTGCAAAA
1 TAGGGGCAAAAGTGTAAATATGCAAAA
28968061 TTTTGAGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:28968879 original size:64 final size:64
Alignment explanation
Indices: 28968799--28968982 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
28968789 AGACATTATG
* * *
28968799 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
** * * * *
28968863 ATGTAGCTAGGTCGCATACGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28968928 AA
63 AA
* * *
28968930 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
28968983 CGAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 24 0.25
66 20 0.21
67 33 0.34
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28971853 original size:27 final size:27
Alignment explanation
Indices: 28971825--28971994 Score: 170
Period size: 27 Copynumber: 6.3 Consensus size: 27
28971815 CAAAATAGTC
* * *
28971825 ATTTTACCCTACAAGGGTATGTCGATC
1 ATTTTACACTACAAGGGTATTTCGATA
28971852 ATTTTACACTACAAGGGTATTTC-AGTA
1 ATTTTACACTACAAGGGTATTTCGA-TA
*
28971879 ATTTTACACTACAAGGGTATTTTGATA
1 ATTTTACACTACAAGGGTATTTCGATA
* *
28971906 ATTTTACA-AATCGAGGGTATTTCGATA
1 ATTTTACACTA-CAAGGGTATTTCGATA
* *
28971933 ATTTTACAAATAGAA-GGTATTTC-AGTA
1 ATTTTAC-ACTACAAGGGTATTTCGA-TA
* *
28971960 ATTTTACAAATA-GAGGGTATTTCGATA
1 ATTTTAC-ACTACAAGGGTATTTCGATA
28971987 ATTTTACA
1 ATTTTACA
28971995 AATCGAGGGT
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.04
27 114 0.92
28 4 0.03
29 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGATA
Found at i:28971883 original size:54 final size:54
Alignment explanation
Indices: 28971825--28972193 Score: 203
Period size: 54 Copynumber: 6.9 Consensus size: 54
28971815 CAAAATAGTC
* * *
28971825 ATTTTACCCTACAAGGGTATGTCGATCATTTTAC-ACTACAAGGGTATTTC-AGTA
1 ATTTTACACTACAAGGGTATGTCGATAATTTTACAAAT-CAAGGGTATTTCGA-TA
* * *
28971879 ATTTTACACTACAAGGGTATTTTGATAATTTTACAAATCGAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATGTCGATAATTTTACAAATCAAGGGTATTTCGATA
* * *
28971933 ATTTTACAAATAGAA-GGTATTTC-AGTAATTTTACAAAT-AGAGGGTATTTCGATA
1 ATTTTAC-ACTACAAGGGTATGTCGA-TAATTTTACAAATCA-AGGGTATTTCGATA
* * * * *
28971987 ATTTTACA-AATCGAGGGTATTTC-AGTATTTTTACAAATTAAGGGTATTTC-AGTA
1 ATTTTACACTA-CAAGGGTATGTCGA-TAATTTTACAAATCAAGGGTATTTCGA-TA
* * * * * ***
28972041 ATTTCACAAT-CGAGGGTATTTTGAT-ATTTTACAAATTGTGGGTATTTC-AGTA
1 ATTTTACACTACAAGGGTATGTCGATAATTTTACAAATCAAGGGTATTTCGA-TA
* * * * * *
28972093 ATTTTACA-AATCGAGGGT-TTTC-AGTAATTTTAC-AATCGAGGGCATTTCGGTA
1 ATTTTACACTA-CAAGGGTATGTCGA-TAATTTTACAAATCAAGGGTATTTCGATA
* * ** * * *
28972145 GTTTTACA-AATCGGGGGTATTTCAATAATTTTACAAATCGAGGGTATTT
1 ATTTTACACTA-CAAGGGTATGTCGATAATTTTACAAATCAAGGGTATTT
28972194 TATTAATTTC
Statistics
Matches: 266, Mismatches: 30, Indels: 38
0.80 0.09 0.11
Matches are distributed among these distances:
51 1 0.00
52 66 0.25
53 43 0.16
54 147 0.55
55 9 0.03
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (54 bp):
ATTTTACACTACAAGGGTATGTCGATAATTTTACAAATCAAGGGTATTTCGATA
Found at i:28971952 original size:81 final size:79
Alignment explanation
Indices: 28971865--28972202 Score: 430
Period size: 81 Copynumber: 4.2 Consensus size: 79
28971855 TTACACTACA
* * *
28971865 AGGGTATTTCAGTAATTTTACACTACAAGGGTATTTTGATAATTTTACAAATCGAGGGTATTTCG
1 AGGGTATTTCAGTAATTTTACAAT-CGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTC-
28971930 ATAATTTTACAAATAG
64 ATAATTTTACAAATAG
* *
28971946 AAGGTATTTCAGTAATTTTACAAATAGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
1 AGGGTATTTCAGTAATTTTAC-AATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
*
28972011 GTATTTTTACAAATTA-
65 -TAATTTTACAAA-TAG
* * * *
28972027 AGGGTATTTCAGTAATTTCACAATCGAGGGTATTTTGAT-ATTTTACAAATTGTGGGTATTTCAG
1 AGGGTATTTCAGTAATTTTACAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA-
*
28972091 TAATTTTACAAATCG
65 TAATTTTACAAATAG
* * * *
28972106 AGGGT-TTTCAGTAATTTTACAATCGAGGGCATTTCGGTAGTTTTACAAATCGGGGGTATTTCAA
1 AGGGTATTTCAGTAATTTTACAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTC-A
*
28972170 TAATTTTACAAATCG
65 TAATTTTACAAATAG
* *
28972185 AGGGTATTTTATTAATTT
1 AGGGTATTTCAGTAATTT
28972203 CTCTTCATTA
Statistics
Matches: 227, Mismatches: 23, Indels: 15
0.86 0.09 0.06
Matches are distributed among these distances:
78 30 0.13
79 79 0.35
80 28 0.12
81 86 0.38
82 4 0.02
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (79 bp):
AGGGTATTTCAGTAATTTTACAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAT
AATTTTACAAATAG
Found at i:28971995 original size:27 final size:26
Alignment explanation
Indices: 28971865--28972202 Score: 353
Period size: 27 Copynumber: 12.7 Consensus size: 26
28971855 TTACACTACA
* *
28971865 AGGGTATTTCAGTAATTTTAC-ACTACA
1 AGGGTATTTCA-TAATTTTACAAAT-CG
*
28971892 AGGGTATTTTGATAATTTTACAAATCG
1 AGGGTA-TTTCATAATTTTACAAATCG
*
28971919 AGGGTATTTCGATAATTTTACAAATAG
1 AGGGTATTTC-ATAATTTTACAAATCG
* *
28971946 AAGGTATTTCAGTAATTTTACAAATAG
1 AGGGTATTTCA-TAATTTTACAAATCG
28971973 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTC-ATAATTTTACAAATCG
* **
28972000 AGGGTATTTCAGTATTTTTACAAATTA
1 AGGGTATTTCA-TAATTTTACAAATCG
*
28972027 AGGGTATTTCAGTAATTTCAC-AATCG
1 AGGGTATTTCA-TAATTTTACAAATCG
* *
28972053 AGGGTATTTTGAT-ATTTTACAAATTG
1 AGGGTA-TTTCATAATTTTACAAATCG
*
28972079 TGGGTATTTCAGTAATTTTACAAATCG
1 AGGGTATTTCA-TAATTTTACAAATCG
28972106 AGGGT-TTTCAGTAATTTTAC-AATCG
1 AGGGTATTTCA-TAATTTTACAAATCG
* * *
28972131 AGGGCATTTCGGTAGTTTTACAAATCG
1 AGGGTATTTC-ATAATTTTACAAATCG
*
28972158 GGGGTATTTCAATAATTTTACAAATCG
1 AGGGTATTTC-ATAATTTTACAAATCG
*
28972185 AGGGTATTTTATTAATTT
1 AGGGTATTTCA-TAATTT
28972203 CTCTTCATTA
Statistics
Matches: 265, Mismatches: 32, Indels: 28
0.82 0.10 0.09
Matches are distributed among these distances:
25 19 0.07
26 53 0.20
27 186 0.70
28 7 0.03
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (26 bp):
AGGGTATTTCATAATTTTACAAATCG
Found at i:28974900 original size:11 final size:11
Alignment explanation
Indices: 28974884--28974911 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28974874 GCCAAAGCCC
28974884 ATATCACAATA
1 ATATCACAATA
28974895 ATATCACAATA
1 ATATCACAATA
28974906 ATATCA
1 ATATCA
28974912 TACATGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATCACAATA
Found at i:28975427 original size:27 final size:27
Alignment explanation
Indices: 28975397--28975485 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
28975387 TATGTCAGTC
28975397 ATTTTACACTACAAGGGTATTTTGGTA
1 ATTTTACACTACAAGGGTATTTTGGTA
* *
28975424 ATTTTACACTATAAGGGTATTTTGATA
1 ATTTTACACTACAAGGGTATTTTGGTA
* * * *
28975451 ATTTTACA-AATCGAGGGTGTTTCGGTA
1 ATTTTACACTA-CAAGGGTATTTTGGTA
28975478 ATTTTACA
1 ATTTTACA
28975486 AATTGAGGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 1 0.02
27 52 0.98
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTTGGTA
Found at i:28975486 original size:27 final size:27
Alignment explanation
Indices: 28975410--28975801 Score: 400
Period size: 27 Copynumber: 14.7 Consensus size: 27
28975400 TTACACTACA
* * *
28975410 AGGGTATTTTGGTAATTTTACACTAT-A
1 AGGGTATTTCGGTAATTTTACA-AATCG
* *
28975437 AGGGTATTTTGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
28975464 AGGGTGTTTCGGTAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
28975491 AGGGTATTTCGATAATTTTATAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* **
28975518 AGGGTATTTCGATAATTACACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
** *
28975545 AGGGTATTTCGAAAATTTTACAAATCA
1 AGGGTATTTCGGTAATTTTACAAATCG
*
28975572 AGGGTATTTCAGTAATTTTAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
28975598 AGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* ** *
28975625 GGGGTATTTCAATAATTTTACAAATCT
1 AGGGTATTTCGGTAATTTTACAAATCG
* ** * *
28975652 AGGGTTTTTCATTGATTTCAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
28975678 AGGGTATTTTGGTAATTTTACAAATCT
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
28975705 AGGGTATTTCAGTAATTTCAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
28975731 AGGATATGTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * **
28975758 AGAGTTTTTTAGTAA-TTT-CATAATCG
1 AGGGTATTTCGGTAATTTTACA-AATCG
28975784 AGGGTATTTCGGTAATTT
1 AGGGTATTTCGGTAATTT
28975802 CTCTTTATTA
Statistics
Matches: 301, Mismatches: 58, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
25 2 0.01
26 85 0.28
27 214 0.71
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAATCG
Found at i:28975616 original size:53 final size:54
Alignment explanation
Indices: 28975410--28975801 Score: 406
Period size: 53 Copynumber: 7.3 Consensus size: 54
28975400 TTACACTACA
* * * *
28975410 AGGGTATTTTGGTAATTTTACACTAT-AAGGGTATTTTGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACA-AATCGAGGGTATTTCGATAATTTTACAAATCG
* * * *
28975464 AGGGTGTTTCGGTAATTTTACAAATTGAGGGTATTTCGATAATTTTATAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCG
* ** * *
28975518 AGGGTATTTCGATAATTACACAAATCGAGGGTATTTCGAAAATTTTACAAATCA
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCG
* *
28975572 AGGGTATTTCAGTAATTTTAC-AATCGAGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCG
* ** * * * *
28975625 GGGGTATTTCAATAATTTTACAAATCTAGGGTTTTTC-ATTGATTTCAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCGA-TAATTTTACAAATCG
* * *
28975678 AGGGTATTTTGGTAATTTTACAAATCTAGGGTATTTC-AGTAATTTCAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCGA-TAATTTTACAAATCG
* * * **
28975731 AGGATATGTCGGTAATTTTACAAATCGAGAGT-TTTTTAGTAA-TTT-CATAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCGA-TAATTTTACA-AATCG
28975784 AGGGTATTTCGGTAATTT
1 AGGGTATTTCGGTAATTT
28975802 CTCTTTATTA
Statistics
Matches: 286, Mismatches: 46, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.00
52 5 0.02
53 154 0.54
54 126 0.44
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (54 bp):
AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCG
Found at i:28975642 original size:80 final size:80
Alignment explanation
Indices: 28975408--28975793 Score: 379
Period size: 80 Copynumber: 4.8 Consensus size: 80
28975398 TTTTACACTA
** * * *
28975408 CAAGGGTATTTTGGTAATTTTACACTAT-AAGGGTATTTTGATAATTTTACAAATCGAGGGTGTT
1 CAAGGGTATTTCAGTAATTTTACA--ATCGAGGGTATTTTGGTAATTTTACAAATCGAGGGTATT
**
28975472 TCGGTAATTTTACAAAT
64 TCAATAATTTTACAAAT
** * * * * **
28975489 TGAGGGTATTTC-GATAATTTTATAAATTGAGGGTATTTCGATAATTACACAAATCGAGGGTATT
1 CAAGGGTATTTCAG-TAATTTTA-CAATCGAGGGTATTTTGGTAATTTTACAAATCGAGGGTATT
28975553 TCGAA-AATTTTACAAAT
64 TC-AATAATTTTACAAAT
* *
28975570 CAAGGGTATTTCAGTAATTTTACAATCGAGGGTATTTCGGTAATTTTACAAATCGGGGGTATTTC
1 CAAGGGTATTTCAGTAATTTTACAATCGAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTC
28975635 AATAATTTTACAAAT
66 AATAATTTTACAAAT
* * * * * *
28975650 CTAGGGTTTTTCATTGATTTCACAATCGAGGGTATTTTGGTAATTTTACAAATCTAGGGTATTTC
1 CAAGGGTATTTCAGTAATTTTACAATCGAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTC
* *
28975715 AGTAATTTCAC-AAT
66 AATAATTTTACAAAT
* * * * * * *
28975729 CGAGGATATGTCGGTAATTTTACAAATCGAGAGTTTTTTAGTAA-TTT-CATAATCGAGGGTATT
1 CAAGGGTATTTCAGTAATTTTAC-AATCGAGGGTATTTTGGTAATTTTACA-AATCGAGGGTATT
28975792 TC
64 TC
28975794 GGTAATTTCT
Statistics
Matches: 256, Mismatches: 41, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
78 2 0.01
79 37 0.14
80 135 0.53
81 80 0.31
82 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (80 bp):
CAAGGGTATTTCAGTAATTTTACAATCGAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTC
AATAATTTTACAAAT
Found at i:28976154 original size:28 final size:28
Alignment explanation
Indices: 28976100--28976205 Score: 122
Period size: 28 Copynumber: 3.8 Consensus size: 28
28976090 GTCCACACTT
* * * *
28976100 ATTCATTTGGCCCCTTTAGGCCGAATCTC
1 ATTCATATGG-CCCATTAGGCCCAATCAC
* * * *
28976129 GTTCACATTGCCCATCAGGCCCAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
*
28976157 TTTCATATGGCCCATTAGGCCCAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
28976185 ATTCATATGGCCCATTAGGCC
1 ATTCATATGGCCCATTAGGCC
28976206 TAACTACTTC
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
28 58 0.91
29 6 0.09
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (28 bp):
ATTCATATGGCCCATTAGGCCCAATCAC
Found at i:28982843 original size:29 final size:29
Alignment explanation
Indices: 28982810--28982893 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
28982800 TTATATTCAC
28982810 ATGG-CCTATAAGGCCCAAATCACATTTTG
1 ATGGCCCT-TAAGGCCCAAATCACATTTTG
* *
28982839 ATGGCCCTTTAGGTCCAAATCACATTTAT-
1 ATGGCCCTTAAGGCCCAAATCACATTT-TG
* * *
28982868 ATGACCCTTTAGACCCAAATCACATT
1 ATGGCCCTTAAGGCCCAAATCACATT
28982894 ATATTCATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (29 bp):
ATGGCCCTTAAGGCCCAAATCACATTTTG
Found at i:28983140 original size:8 final size:8
Alignment explanation
Indices: 28983108--28983143 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
28983098 TGTAGCCAAA
28983108 CTTTT-GG
1 CTTTTCGG
28983115 CTTTTCGG
1 CTTTTCGG
*
28983123 CATTTCGG
1 CTTTTCGG
28983131 CTTTTCGG
1 CTTTTCGG
28983139 CTTTT
1 CTTTT
28983144 GCCGATCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.03, C:0.22, G:0.22, T:0.53
Consensus pattern (8 bp):
CTTTTCGG
Found at i:28986120 original size:24 final size:27
Alignment explanation
Indices: 28986088--28986139 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
28986078 AGTTCATGCA
28986088 ATATTAAAGC-ATTTAA-ATAC-AACT
1 ATATTAAAGCTATTTAACATACGAACT
28986112 ATATTAAAGCTTATTTAACATACGAACT
1 ATATTAAAGC-TATTTAACATACGAACT
28986140 TACTTCGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.42
26 6 0.25
27 4 0.17
28 4 0.17
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (27 bp):
ATATTAAAGCTATTTAACATACGAACT
Found at i:28989748 original size:41 final size:41
Alignment explanation
Indices: 28989649--28989806 Score: 131
Period size: 41 Copynumber: 3.8 Consensus size: 41
28989639 ATGTGTTCTT
** * * **
28989649 GTGTAAGACCACATCTTGGACATTGGCATCGATATGTGATTAT
1 GTGTAAGACCATGTCTGGGACA-TGGCATTG-TATGTGATTGC
*
28989692 GTGTAAGACCATGTCTGGGACATCGGCATTGTATTTGATT-C
1 GTGTAAGACCATGTCTGGGACAT-GGCATTGTATGTGATTGC
* * * *
28989733 GTGTAAGACCTTGTCTAGGACA-GTCATCGATATGTGATTGC
1 GTGTAAGACCATGTCTGGGACATGGCATTG-TATGTGATTGC
* * *
28989774 ATGTAAGACCATATCTGGGACGTTGGCATTGTA
1 GTGTAAGACCATGTCTGGGAC-ATGGCATTGTA
28989807 CGATATACGT
Statistics
Matches: 92, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
39 5 0.05
40 8 0.09
41 38 0.41
42 11 0.12
43 30 0.33
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (41 bp):
GTGTAAGACCATGTCTGGGACATGGCATTGTATGTGATTGC
Found at i:28999566 original size:39 final size:40
Alignment explanation
Indices: 28999521--28999688 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
28999511 CGGGGTTTAG
* * *
28999521 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
28999560 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
28999600 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
28999640 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
28999681 CCGGATAT
1 CCGGATAT
28999689 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:28999671 original size:41 final size:40
Alignment explanation
Indices: 28999544--28999688 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
28999534 CTCGCACAAG
* * * * *
28999544 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
28999584 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
28999624 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
28999665 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
28999689 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:29000918 original size:38 final size:38
Alignment explanation
Indices: 29000876--29000951 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
29000866 CAAGAACTCC
29000876 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
29000914 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
29000952 AAAGGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:29004333 original size:30 final size:30
Alignment explanation
Indices: 29004299--29004363 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
29004289 CCCAAAGGCT
*
29004299 GTGTCCTCTACACGGCTGGGACACACGGCC
1 GTGTCCTCTACACAGCTGGGACACACGGCC
*
29004329 GTGTCCTCTCCACAGCTGGGACACACGGCC
1 GTGTCCTCTACACAGCTGGGACACACGGCC
29004359 GTGTC
1 GTGTC
29004364 TCTGCCCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.15, C:0.37, G:0.29, T:0.18
Consensus pattern (30 bp):
GTGTCCTCTACACAGCTGGGACACACGGCC
Found at i:29004792 original size:22 final size:21
Alignment explanation
Indices: 29004767--29004811 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
29004757 AATTTCATCC
*
29004767 ATCACACTCATTATCACAAAAA
1 ATCACAATCATTATC-CAAAAA
* *
29004789 ATCACAATCCTTATCGAAAAA
1 ATCACAATCATTATCCAAAAA
29004810 AT
1 AT
29004812 ACCTTTAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
ATCACAATCATTATCCAAAAA
Done.