Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004123.1 Hibiscus syriacus cultivar Beakdansim tig00009023_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1596068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:949459 original size:197 final size:198
Alignment explanation
Indices: 948996--949461 Score: 564
Period size: 197 Copynumber: 2.4 Consensus size: 198
948986 AAAATAGATA
* * * ** *
948996 AATTATAATGTAATAGGTAAATTAACAATGTAATCGGTATAAATATACCGATTAATTACAAAACA
1 AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTATTGGAAAATA
* * * *
949061 GGTAAACATAACGTATTGGCATTTGTGAAATTTGTGTCGATACTTATTGTCCAGAATGAATGCTC
66 GGTCAACATAACGTATCGACATTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCTC
949126 AAACGAGGTGCACGCATAAAGTGACAATACATTTATTAAAAGCATCGATCCAAAAAACATCGAAA
131 AAACGAGGTGCACGCATAAAGTGACAATACATTTA-TAAAAGCATCGATCCAAAAAACATCGAAA
949191 CAAT
195 CAAT
* * * *
949195 AATTATGATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACTGTTTTA-TGAGAGAAT
1 AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTATTG-GAAAAT
* * *
949259 AGGTCAACATAATGTATCGACACTTT-TTAAATATGTGTCGATACTT-TTTTCCAGAATGAATGC
65 AGGTCAACATAACGTATCGACA-TTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGC
* ** * * * * ** *
949322 -CCAACGAGGTGCACGCATTTAGTGTCGATACATTTA-AAATTGTATCGATCCCTAAAACATTGA
129 TCAAACGAGGTGCACGCATAAAGTGACAATACATTTATAAA-AGCATCGATCCAAAAAACATCGA
*
949385 AACTGAT
193 AAC-AAT
* * * *
949392 AATTATAATGTAATAGGTAAATTTGCAATGTTACCGGTATAAATAAACCGGTTTATTGGAAAATA
1 AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTATTGGAAAATA
949457 GGTCA
66 GGTCA
949462 CTATAAGCGC
Statistics
Matches: 227, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
195 3 0.01
196 21 0.09
197 93 0.41
198 19 0.08
199 88 0.39
200 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (198 bp):
AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTATTGGAAAATA
GGTCAACATAACGTATCGACATTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCTC
AAACGAGGTGCACGCATAAAGTGACAATACATTTATAAAAGCATCGATCCAAAAAACATCGAAAC
AAT
Found at i:951081 original size:17 final size:17
Alignment explanation
Indices: 951059--951098 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
951049 GGGCCCAATT
951059 CCAAACCAAAACCTAGC
1 CCAAACCAAAACCTAGC
951076 CCAAACCAAAACCTAGC
1 CCAAACCAAAACCTAGC
*
951093 CTAAAC
1 CCAAAC
951099 TAACTGTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.40, G:0.05, T:0.07
Consensus pattern (17 bp):
CCAAACCAAAACCTAGC
Found at i:953587 original size:16 final size:17
Alignment explanation
Indices: 953563--953595 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
953553 CGAGGTGTCA
953563 CATTAACTTTT-CAAAG
1 CATTAACTTTTACAAAG
*
953579 CATTTACTTTTACAAAG
1 CATTAACTTTTACAAAG
953596 TGACTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (17 bp):
CATTAACTTTTACAAAG
Found at i:954085 original size:13 final size:15
Alignment explanation
Indices: 954069--954123 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
954059 ACTTAACATT
954069 TATACCA-AT-TATA
1 TATACCATATATATA
*
954082 TATACTATATATATA
1 TATACCATATATATA
*
954097 TATA-TATATATATA
1 TATACCATATATATA
*
954111 TATA-TATATATAT
1 TATACCATATATAT
954124 TCACATAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 6 0.15
14 25 0.64
15 8 0.21
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
TATACCATATATATA
Found at i:954140 original size:2 final size:2
Alignment explanation
Indices: 954078--954123 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
954068 TTATACCAAT
954078 TA TA TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
954121 TA T
1 TA T
954124 TCACATAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:954939 original size:18 final size:18
Alignment explanation
Indices: 954916--954989 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
954906 GCACTTAAAA
*
954916 TTTGTCCCGAATGACCAC
1 TTTGTCCCGAAGGACCAC
954934 TTTGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
* *
954952 TATGTCTCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
* * * *
954970 TATATCTCGAAGGATCAC
1 TTTGTCCCGAAGGACCAC
954988 TT
1 TT
954990 GTAATCCCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (18 bp):
TTTGTCCCGAAGGACCAC
Found at i:956402 original size:3 final size:3
Alignment explanation
Indices: 956394--956434 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
956384 TTACGGATGG
956394 AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
956435 GAGGAGGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:958933 original size:21 final size:22
Alignment explanation
Indices: 958897--958938 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
958887 GTAATTTTTC
958897 AACTTCCCTCCAAATAAAATTT
1 AACTTCCCTCCAAATAAAATTT
958919 AACTTCCCT-CAAATAAAATT
1 AACTTCCCTCCAAATAAAATT
958939 GAATATTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (22 bp):
AACTTCCCTCCAAATAAAATTT
Found at i:958947 original size:22 final size:22
Alignment explanation
Indices: 958900--958947 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
958890 ATTTTTCAAC
* *
958900 TTCCCTCCAAATAAAATTTAAC
1 TTCCCTCCAAATAAAATTGAAA
958922 TTCCCT-CAAATAAAATTGAATA
1 TTCCCTCCAAATAAAATTGAA-A
958944 TTCC
1 TTCC
958948 TTATTCATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (22 bp):
TTCCCTCCAAATAAAATTGAAA
Found at i:966334 original size:44 final size:44
Alignment explanation
Indices: 966251--966345 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
966241 GTGCATAATA
* *
966251 CATCGATACACTGAATAGTGCATCGATGCATCCCTTTGAATATG
1 CATCGATACACTGAAGAGTGCACCGATGCATCCCTTTGAATATG
*
966295 CATCGATACATCATGAAGA-TGCACCGATGCA-CTCC-TTGAATGTG
1 CATCGATACA-C-TGAAGAGTGCACCGATGCATC-CCTTTGAATATG
966339 CATCGAT
1 CATCGAT
966346 GCACACTGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 26 0.58
45 14 0.31
46 5 0.11
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (44 bp):
CATCGATACACTGAAGAGTGCACCGATGCATCCCTTTGAATATG
Found at i:975594 original size:59 final size:59
Alignment explanation
Indices: 975474--975800 Score: 326
Period size: 59 Copynumber: 5.6 Consensus size: 59
975464 TCGATATGAA
* * * * * **
975474 TTTTAAAGAAATTAAGTCTAATTTTCAGA-GTTT-TTTACATGGTGTTTTCAAATGCTT
1 TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTAACATGATGTTTTCAAAAGAAT
*
975531 TTTTAAAGAAACTAATTCTGATTTTCAGAGGTTTCTTAACATGATGTTTTCAAAAGAAT
1 TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTAACATGATGTTTTCAAAAGAAT
* * * *
975590 TTTTAAACAAACTAGGTCTAATTTTCTA-AGGTTTCTTGACATGATGTTTTCAAAAGAAT
1 TTTTAAAGAAACTAAGTCTGATTTTC-AGAGGTTTCTTAACATGATGTTTTCAAAAGAAT
* * * * * * *
975649 TGTTAAAGAAACTAGGTTTGATTTTCAGAGGTTTCTTGACATGATATTCTCAAATGAA-
1 TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTAACATGATGTTTTCAAAAGAAT
* * ** * * **
975707 TTTTAAAGAAGCTAAGTCTGATTTTCAGAAGTTTCTT-A-ATGAT-TTCCCCACATGTTT
1 TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTAACATGATGTT-TTCAAAAGAAT
**
975764 TTTTAAAGAAGTTAAGTCTGATTTTCAGAGGTTTCTT
1 TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTT
975801 GATGATTACT
Statistics
Matches: 233, Mismatches: 31, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
55 2 0.01
56 11 0.05
57 62 0.27
58 37 0.16
59 120 0.52
60 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.42
Consensus pattern (59 bp):
TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTAACATGATGTTTTCAAAAGAAT
Found at i:979373 original size:138 final size:137
Alignment explanation
Indices: 979073--979398 Score: 365
Period size: 137 Copynumber: 2.4 Consensus size: 137
979063 AGGTTTAATG
* *
979073 CTTAAATTAGGTGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTTGA
1 CTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCGA
* * * *
979138 TCGCATAATTGATTAAAATTAATTAAGATTAATATTAGAGACTCCATTTTAGGCTTAATTTCACA
66 TCGCATAATTGATTAAAATCAAGTAAGAGTAATATTAGAGACTCCATTTTAGGCTTAATTTCAAA
* *
979203 TTTAGTT
131 CTTAGTC
* * *
979210 CTTAAATTAGGAGAATTCTTAATTTGATCCTCGTTTTTGCTCGAGGTTCCAATTTAATTATTCGA
1 CTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCG-
* * * *
979275 ATTC-CATAATTGATTAAAATCGAGT-AGGGTAATGTTTAGAG-CTTCCATTTTAGGTTTAATTT
65 A-TCGCATAATTGATTAAAATCAAGTAAGAGTAAT-ATTAGAGAC-TCCATTTTAGGCTTAATTT
979337 -AAACTTAGTC
127 CAAACTTAGTC
* * * * * * *
979347 CTTTATTCTAAGGA-AATTTTTGATTTGGTCTTCGCTTATGCTAGAGGTTCCA
1 CTTAAAT-T-AGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCA
979399 TTTTGGCTGT
Statistics
Matches: 159, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
137 78 0.49
138 75 0.47
139 6 0.04
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (137 bp):
CTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCGA
TCGCATAATTGATTAAAATCAAGTAAGAGTAATATTAGAGACTCCATTTTAGGCTTAATTTCAAA
CTTAGTC
Found at i:980419 original size:216 final size:218
Alignment explanation
Indices: 979904--980483 Score: 770
Period size: 216 Copynumber: 2.6 Consensus size: 218
979894 AATATGTCCT
*
979904 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGCCTTTCGAG
1 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAG
* * * * * *
979969 CAAGATGATAGGTCTTTTGGGCTATCCATAAGACCTTCGAGCAGGATGTTTTCACATGCTTTTCA
66 CAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTC-
*
980034 AAAAAATGATAAAGCGATTTCCAAAGCATCTCATTTAAATCTTTTCTGAAAATTGTTTTTTAACG
130 AAAAAATGAGAAAGCGATTTCCAAAGCATCTCATTTAAATCTTTTCTGAAAA-----TTTT-A--
*
980099 ATTTCCAAATTTTCTTACTTAGTAAGTCCTTC
187 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTTC
* * * * *
980131 GAGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTTGGGTCATCTATAATCCTTTCGAG
1 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAG
* *
980196 CAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTCA
66 CAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTCA
* **
980261 AAAAATGAGAAAGCGATTTCTAAAGTTTCTCATTTAAATCTTTTCT-AGAAA-TTT-ATTTCCAA
131 AAAAATGAGAAAGCGATTTCCAAAGCATCTCATTTAAATCTTTTCTGA-AAATTTTAATTTCCAA
980323 AGTTTCTTACTTAGTAAGTCCTTC
195 AGTTTCTTACTTAGTAAGTCCTTC
* * *
980347 GGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTCGGGTCATTTATAAGCCTTTCAAG
1 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAG
* * ** * * * * *
980412 TAAGATGATAAGTTCTTTGGGCCATCTGTAAGACCTTCGGGCATGATGTTTTCATATGGTGTTAA
66 CAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTCA
980477 AAAAATG
131 AAAAATG
980484 CTAAAAATGA
Statistics
Matches: 314, Mismatches: 38, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
216 149 0.47
220 3 0.01
225 1 0.00
226 46 0.15
227 115 0.37
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (218 bp):
GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAG
CAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTCA
AAAAATGAGAAAGCGATTTCCAAAGCATCTCATTTAAATCTTTTCTGAAAATTTTAATTTCCAAA
GTTTCTTACTTAGTAAGTCCTTC
Found at i:980509 original size:18 final size:18
Alignment explanation
Indices: 980486--980524 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
980476 AAAAAATGCT
980486 AAAAATG-AGAAGTACAAA
1 AAAAATGAAGAAGT-CAAA
980504 AAAAATGAAAGAAGTCAAA
1 AAAAATG-AAGAAGTCAAA
980523 AA
1 AA
980525 GAAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.69, C:0.05, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAATGAAGAAGTCAAA
Found at i:981232 original size:17 final size:14
Alignment explanation
Indices: 981210--981249 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
981200 ACTATTTAAA
981210 TATTATTATTATGT
1 TATTATTATTATGT
981224 TATTATTATTATGT
1 TATTATTATTATGT
981238 TATTATTATTAT
1 TATTATTATTAT
981250 ACAAACTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TATTATTATTATGT
Found at i:983643 original size:17 final size:14
Alignment explanation
Indices: 983621--983660 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
983611 ACTATTTAAA
983621 TATTATTATTATGT
1 TATTATTATTATGT
983635 TATTATTATTATGT
1 TATTATTATTATGT
983649 TATTATTATTAT
1 TATTATTATTAT
983661 ACAAACTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TATTATTATTATGT
Found at i:985834 original size:137 final size:137
Alignment explanation
Indices: 985562--985834 Score: 347
Period size: 137 Copynumber: 2.0 Consensus size: 137
985552 AGGTTTAATG
* * *
985562 CTTAAATTAGGTGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTTGA
1 CTTAAATTAGGAGAATTCTTAATTTGATCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCGA
* * * *
985627 TCGCATAATTGATTAAAATTAATTAAGATTAATATTAGAGACTCCATCTTAGGCTTAATTTCACA
66 TCGCATAATTGATTAAAATCAAGTAAGAGTAATATTAGAGACTCCATCTTAGGCTTAATTTCAAA
*
985692 TTTAGTT
131 CTTAGTT
* *
985699 CTTAAATTAGGAGAATTCTTAATTTGATCCTCGTTTTTGCTCGAGGTTCCAATTTAATTATTCGA
1 CTTAAATTAGGAGAATTCTTAATTTGATCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCG-
* * * * *
985764 ATTC-CATAATTGATTAAAATCGAGTATG-GTAATGTTTAGAG-CTTCCATTTTAGGTTTAATTT
65 A-TCGCATAATTGATTAAAATCAAGTAAGAGTAAT-ATTAGAGAC-TCCATCTTAGGCTTAATTT
985826 -AAACTTAGT
127 CAAACTTAGT
985835 CCTTTATTCT
Statistics
Matches: 117, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
137 71 0.61
138 44 0.38
139 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (137 bp):
CTTAAATTAGGAGAATTCTTAATTTGATCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCGA
TCGCATAATTGATTAAAATCAAGTAAGAGTAATATTAGAGACTCCATCTTAGGCTTAATTTCAAA
CTTAGTT
Found at i:986911 original size:216 final size:220
Alignment explanation
Indices: 986396--986957 Score: 772
Period size: 216 Copynumber: 2.5 Consensus size: 220
986386 AATATGTCCT
*
986396 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGCCTTTCGAG
1 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAG
* * * * ** *
986461 CAAGATGACAAGTCTTTTGGGCTATCCATAAGACCTTCGAGCAGGATGTTTTCACATTCTTTTCA
66 CAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTCA
*
986526 AAAAAATGATAAAGCGATTTCCAAAGCATCTCATTTAAATCTTTTCTGAAAATTGTTTTTTAACG
131 AAAAAATGAGAAAGCGATTTCCAAAGCATCTCATTTAAATCTTTTCTGAAAA----TTTTT-A--
986591 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTTC
189 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTTC
* * * * * *
986623 GAGTCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCATTTGGGTCATCTATAATCCTTTCGAG
1 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAG
* *
986688 CAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTC-
66 CAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTCA
* ** *
986752 AAAAAATGAGAAAGCGATTTCTAAAGTTTCTCATTTAAATCTTTTCT-ATAA-TTTT-ATTTCCA
131 AAAAAATGAGAAAGCGATTTCCAAAGCATCTCATTTAAATCTTTTCTGAAAATTTTTAATTTCCA
986814 AAGTTTCTTACTTAGTAAGTCCTTC
196 AAGTTTCTTACTTAGTAAGTCCTTC
* *
986839 GGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTTTCAAG
1 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAG
* * * ** *
986904 TAAGATGATGAGTTCTTTGGGCCATCTGTAAGACCTTCGGGCATGATGTTTTCA
66 CAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
986958 TATGGTGTTA
Statistics
Matches: 298, Mismatches: 37, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
216 135 0.45
220 4 0.01
225 3 0.01
226 43 0.14
227 113 0.38
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (220 bp):
GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAG
CAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATCTTCA
AAAAAATGAGAAAGCGATTTCCAAAGCATCTCATTTAAATCTTTTCTGAAAATTTTTAATTTCCA
AAGTTTCTTACTTAGTAAGTCCTTC
Found at i:987017 original size:18 final size:18
Alignment explanation
Indices: 986996--987034 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
986986 AAAAAATGCT
986996 AAAAATG-AGAAGTACAAA
1 AAAAATGAAGAAGT-CAAA
987014 AAAAATGAAAGAAGTCAAA
1 AAAAATG-AAGAAGTCAAA
987033 AA
1 AA
987035 GGAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.69, C:0.05, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAATGAAGAAGTCAAA
Found at i:987742 original size:17 final size:14
Alignment explanation
Indices: 987720--987759 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
987710 ACTATTTAAA
987720 TATTATTATTATGT
1 TATTATTATTATGT
987734 TATTATTATTATGT
1 TATTATTATTATGT
987748 TATTATTATTAT
1 TATTATTATTAT
987760 ACAAACTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TATTATTATTATGT
Found at i:989953 original size:138 final size:137
Alignment explanation
Indices: 989653--989978 Score: 365
Period size: 137 Copynumber: 2.4 Consensus size: 137
989643 AGGTTTAATG
* *
989653 CTTAAATTAGGTGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTTGA
1 CTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCGA
* * * *
989718 TCGCATAATTGATTAAAATTAATTAAGATTAATATTAGAGACTCCATTTTAGGCTTAATTTCACA
66 TCGCATAATTGATTAAAATCAAGTAAGAGTAATATTAGAGACTCCATTTTAGGCTTAATTTCAAA
* *
989783 TTTAGTT
131 CTTAGTC
* * *
989790 CTTAAATTAGGAGAATTCTTAATTTGATCCTCGTTTTTGCTCGAGGTTCCAATTTAATTATTCGA
1 CTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCG-
* * * *
989855 ATTC-CATAATTGATTAAAATCGAGT-AGGGTAATGTTTAGAG-CTTCCATTTTAGGTTTAATTT
65 A-TCGCATAATTGATTAAAATCAAGTAAGAGTAAT-ATTAGAGAC-TCCATTTTAGGCTTAATTT
989917 -AAACTTAGTC
127 CAAACTTAGTC
* * * * * * *
989927 CTTTATTCTAAGGA-AATTTTTGATTTGGTCTTCGCTTATGCTAGAGGTTCCA
1 CTTAAAT-T-AGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCA
989979 TTTTGGCTGT
Statistics
Matches: 159, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
137 78 0.49
138 75 0.47
139 6 0.04
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (137 bp):
CTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTATTCGA
TCGCATAATTGATTAAAATCAAGTAAGAGTAATATTAGAGACTCCATTTTAGGCTTAATTTCAAA
CTTAGTC
Found at i:994867 original size:60 final size:58
Alignment explanation
Indices: 994775--994889 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 58
994765 TCTTTAAGGA
*
994775 AAATAATTCTTGTATTTTTTAATTTAGTGGACATTTTAATTTTACAAATAAATTAGGC
1 AAATAATTATTGTATTTTTTAATTTAGTGGACATTTTAATTTTACAAATAAATTAGGC
994833 AAATAATTATTGTATTTTTTTTAATTTAGTGGACATTTTAATTTTACAAATAAATTA
1 AAATAATTATTGTA--TTTTTTAATTTAGTGGACATTTTAATTTTACAAATAAATTA
994890 AGAGATTATA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
58 13 0.24
60 41 0.76
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (58 bp):
AAATAATTATTGTATTTTTTAATTTAGTGGACATTTTAATTTTACAAATAAATTAGGC
Found at i:997747 original size:15 final size:15
Alignment explanation
Indices: 997692--997769 Score: 59
Period size: 15 Copynumber: 5.2 Consensus size: 15
997682 TCAAACCGAT
* *
997692 CCAAACCGAGTCAAT
1 CCAAACTGAGTCAAC
*
997707 CCAAA-TAGTGTCAAC
1 CCAAACT-GAGTCAAC
* * *
997722 TCGAACAGAGTCAAC
1 CCAAACTGAGTCAAC
*
997737 CCAAATTGAGTCAAC
1 CCAAACTGAGTCAAC
* *
997752 TCAAACTAAGTCAAC
1 CCAAACTGAGTCAAC
997767 CCA
1 CCA
997770 TTAACTTTAA
Statistics
Matches: 46, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.17
Consensus pattern (15 bp):
CCAAACTGAGTCAAC
Found at i:997764 original size:30 final size:30
Alignment explanation
Indices: 997693--997769 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
997683 CAAACCGATC
* * *
997693 CAAACCGAGTCAATCCAAATAGTGTCAACT
1 CAAACAGAGTCAACCCAAATAGAGTCAACT
* *
997723 CGAACAGAGTCAACCCAAATTGAGTCAACT
1 CAAACAGAGTCAACCCAAATAGAGTCAACT
997753 CAAACTA-AGTCAACCCA
1 CAAAC-AGAGTCAACCCA
997770 TTAACTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 39 0.98
31 1 0.03
ACGTcount: A:0.42, C:0.29, G:0.13, T:0.17
Consensus pattern (30 bp):
CAAACAGAGTCAACCCAAATAGAGTCAACT
Found at i:997798 original size:22 final size:22
Alignment explanation
Indices: 997768--997811 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
997758 TAAGTCAACC
997768 CATTAACTTTAACTTTGACCAA
1 CATTAACTTTAACTTTGACCAA
* *
997790 CATTGACTTTGACTTTGACCAA
1 CATTAACTTTAACTTTGACCAA
997812 AAAGTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (22 bp):
CATTAACTTTAACTTTGACCAA
Found at i:998756 original size:20 final size:20
Alignment explanation
Indices: 998731--998768 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
998721 TTTGTTTCAC
998731 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
998751 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
998769 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:998995 original size:34 final size:33
Alignment explanation
Indices: 998932--998996 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
998922 AATATTTATA
** *
998932 TATATTTTTTTAAAAATTTAAATTCATAAAATT
1 TATATTTTTTTAAAAATGAAAAATCATAAAATT
998965 TATATTTTTTTACAAAACTGAAAAAT-ATAAAA
1 TATATTTTTTTA-AAAA-TGAAAAATCATAAAA
998997 AGGTTTAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 12 0.44
34 10 0.37
35 5 0.19
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (33 bp):
TATATTTTTTTAAAAATGAAAAATCATAAAATT
Found at i:1000989 original size:17 final size:16
Alignment explanation
Indices: 1000961--1001005 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1000951 AAATGTAATT
* *
1000961 ATAAAAATAAAAGGTG
1 ATAAAAACAAAAAGTG
1000977 ATAAAAACAAAAAGTG
1 ATAAAAACAAAAAGTG
1000993 ATAAAAACAAAAA
1 ATAAAAACAAAAA
1001006 TGTTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (16 bp):
ATAAAAACAAAAAGTG
Found at i:1003876 original size:16 final size:16
Alignment explanation
Indices: 1003855--1003888 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1003845 ATTTGAACTT
*
1003855 AAGAAATTTAAATATG
1 AAGAAACTTAAATATG
*
1003871 AAGAAACTTAAATTTG
1 AAGAAACTTAAATATG
1003887 AA
1 AA
1003889 AACGCTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (16 bp):
AAGAAACTTAAATATG
Found at i:1003905 original size:2 final size:2
Alignment explanation
Indices: 1003898--1003926 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1003888 AAACGCTTGA
1003898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1003927 AATTAAGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1005440 original size:40 final size:40
Alignment explanation
Indices: 1005371--1005450 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1005361 AATTCCCAGG
* * * *
1005371 AAAAAGGAAACACACACAAACCTATGATTGCTTATCTGTC
1 AAAAAAGAAACACACACAAACCCACGATTGCTCATCTGTC
* *
1005411 AAAAAAGAAACACAGACACACCCACGATTGCTCATCTGTC
1 AAAAAAGAAACACACACAAACCCACGATTGCTCATCTGTC
1005451 TGTTAAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.19
Consensus pattern (40 bp):
AAAAAAGAAACACACACAAACCCACGATTGCTCATCTGTC
Found at i:1010226 original size:19 final size:20
Alignment explanation
Indices: 1010198--1010236 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1010188 TTTAGGAAAA
*
1010198 ATCGG-TTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
1010217 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
1010237 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:1010296 original size:12 final size:12
Alignment explanation
Indices: 1010281--1010326 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1010271 CGGTTTTTTT
*
1010281 ACCGGATAAAAA
1 ACCGGTTAAAAA
1010293 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1010308 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1010320 ACCGGTT
1 ACCGGTT
1010327 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1010308 original size:15 final size:13
Alignment explanation
Indices: 1010287--1010327 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1010277 TTTTACCGGA
1010287 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1010300 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1010314 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1010327 T
1 T
1010328 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1012645 original size:21 final size:21
Alignment explanation
Indices: 1012621--1012660 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1012611 TTTATTTTAT
1012621 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1012642 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1012661 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1012708 original size:33 final size:33
Alignment explanation
Indices: 1012655--1012753 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1012645 TTTGTTTCAA
1012655 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1012687 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1012720 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1012753 T
1 T
1012754 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1013015 original size:21 final size:21
Alignment explanation
Indices: 1012989--1013045 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1012979 TGGAGCGTGG
*
1012989 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
1013010 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
1013031 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
1013046 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:1013236 original size:15 final size:15
Alignment explanation
Indices: 1013211--1013266 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1013201 ATCTGGAATA
*
1013211 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1013226 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1013241 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1013258 TTAAAACCG
1 TTAAAACCG
1013267 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1013275 original size:21 final size:18
Alignment explanation
Indices: 1013230--1013263 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1013220 GTTTTTTTAT
1013230 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1013247 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1013264 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1013383 original size:15 final size:17
Alignment explanation
Indices: 1013357--1013388 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1013347 TTCTATGGAA
1013357 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1013373 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1013389 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1024577 original size:23 final size:24
Alignment explanation
Indices: 1024523--1024588 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
1024513 AAAAAATTAA
*
1024523 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAGCTCGAGACTC
* **
1024547 GAGCTCGATTGAAGCTCGATTCT-
1 GAGCTCGATTAAAGCTCGAGACTC
*
1024570 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTAAAGCTCGA
1024589 AATTGCCCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (24 bp):
GAGCTCGATTAAAGCTCGAGACTC
Found at i:1025658 original size:22 final size:22
Alignment explanation
Indices: 1025617--1025683 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1025607 GCTGTATAAA
1025617 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1025640 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1025662 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1025684 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1027385 original size:21 final size:21
Alignment explanation
Indices: 1027361--1027405 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1027351 TCTTGTTCGT
* *
1027361 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1027382 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1027403 TTG
1 TTG
1027406 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1030509 original size:22 final size:22
Alignment explanation
Indices: 1030468--1030534 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1030458 CTCGTATAAA
1030468 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1030491 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1030513 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1030535 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1032248 original size:20 final size:21
Alignment explanation
Indices: 1032219--1032262 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1032209 TCTTGTTCGT
*
1032219 TTGAAGGGGTATCG-TTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1032239 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1032260 TTG
1 TTG
1032263 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1033476 original size:10 final size:10
Alignment explanation
Indices: 1033461--1033520 Score: 75
Period size: 10 Copynumber: 5.6 Consensus size: 10
1033451 ATAAATGAAT
1033461 GAACATAAAC
1 GAACATAAAC
1033471 GAACATAAAC
1 GAACATAAAC
1033481 GAACATAAAC
1 GAACATAAAC
1033491 GAACGAATATAAAC
1 GAAC----ATAAAC
*
1033505 GAACATAACC
1 GAACATAAAC
1033515 GAACAT
1 GAACAT
1033521 TCACGAACGT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 35 0.78
14 10 0.22
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1033486 original size:34 final size:34
Alignment explanation
Indices: 1033448--1033542 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 34
1033438 GATTGGCTTA
* *
1033448 AACATAAATGAATGAACATAAACGAACATAAACG
1 AACATAAACGAACGAACATAAACGAACATAAACG
* *
1033482 AACATAAACGAACGAATATAAACGAACATAACCG
1 AACATAAACGAACGAACATAAACGAACATAAACG
** *
1033516 AACATTCACGAACGTAA-ATGAACGAAC
1 AACATAAACGAACG-AACATAAACGAAC
1033543 GAGACCTATG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
34 51 0.96
35 2 0.04
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.14
Consensus pattern (34 bp):
AACATAAACGAACGAACATAAACGAACATAAACG
Found at i:1033495 original size:24 final size:24
Alignment explanation
Indices: 1033468--1033518 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1033458 AATGAACATA
1033468 AACGAACATAAACGAACATAAACG
1 AACGAACATAAACGAACATAAACG
* *
1033492 AACGAATATAAACGAACATAACCG
1 AACGAACATAAACGAACATAAACG
1033516 AAC
1 AAC
1033519 ATTCACGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.10
Consensus pattern (24 bp):
AACGAACATAAACGAACATAAACG
Found at i:1033497 original size:14 final size:14
Alignment explanation
Indices: 1033478--1033508 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1033468 AACGAACATA
1033478 AACGAACATAAACG
1 AACGAACATAAACG
*
1033492 AACGAATATAAACG
1 AACGAACATAAACG
1033506 AAC
1 AAC
1033509 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1033748 original size:31 final size:31
Alignment explanation
Indices: 1033705--1033773 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
1033695 ACTACGTATT
* *
1033705 CAACAATCACTTTAATTTCGTTTTAGCCATC
1 CAACTATCACTTTAATTTCGTTTTAACCATC
*
1033736 CAACTATCACTTTAATTTCGTTTTAATCATC
1 CAACTATCACTTTAATTTCGTTTTAACCATC
1033767 CAACTAT
1 CAACTAT
1033774 TTTTTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (31 bp):
CAACTATCACTTTAATTTCGTTTTAACCATC
Found at i:1041693 original size:23 final size:23
Alignment explanation
Indices: 1041667--1041722 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
1041657 ATTGTAAAGT
1041667 TTTATTTAATTATAGACTTTTTA
1 TTTATTTAATTATAGACTTTTTA
** ** *
1041690 TTTATTTTGTTATTTATTTTTTA
1 TTTATTTAATTATAGACTTTTTA
1041713 -TTATTTAATT
1 TTTATTTAATT
1041723 GTTCGAATTA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTATTTAATTATAGACTTTTTA
Found at i:1041704 original size:12 final size:11
Alignment explanation
Indices: 1041684--1041718 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
1041674 AATTATAGAC
1041684 TTTTTATTTAT
1 TTTTTATTTAT
1041695 TTTGTTATTTAT
1 TTT-TTATTTAT
1041707 TTTTTA-TTAT
1 TTTTTATTTAT
1041717 TT
1 TT
1041719 AATTGTTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.26
11 6 0.26
12 11 0.48
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:1043996 original size:35 final size:35
Alignment explanation
Indices: 1043950--1044025 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
1043940 AAAACAGTCC
* *
1043950 TCAATTTCATTCTAAACCC-GAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCTAAATTT-CAAAATAAT
1043985 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
1044020 TCAATT
1 TCAATT
1044026 AAATTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
Found at i:1044575 original size:130 final size:130
Alignment explanation
Indices: 1044422--1044669 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
1044412 TATTTATATA
* * ** *
1044422 ATCAATTTGGTCCTACATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTA
* *
1044487 TTAGCACATGATCATGACACGTGTTATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTTATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1044552 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTA
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTA
* *
1044617 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTTATTGGTGACACATGTCACCACCTAATTA
1044670 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTA
TTAACACATGATCATGACACATGTTATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1044700 original size:130 final size:128
Alignment explanation
Indices: 1044438--1044697 Score: 299
Period size: 130 Copynumber: 2.0 Consensus size: 128
1044428 TTGGTCCTAC
* ** * *
1044438 ATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCATG
1 ATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTATTAACACATGATCATG
* *** * * * ***
1044503 ACACGTGTTATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCTAA
66 ACACATGTTATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAA--TAGAAATAA
1044568 ATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTATTAACACATGATCATG
1 ATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTATTAACACATGATCATG
* * *
1044633 ATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAA-AGAAATA
66 ACACATGTTATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAATAGAAATA
1044696 A
128 A
1044697 A
1 A
1044698 ATTTGGGTCT
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
129 5 0.05
130 93 0.85
132 6 0.06
133 5 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (128 bp):
ATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTATTAACACATGATCATG
ACACATGTTATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAATAGAAATAA
Found at i:1045025 original size:28 final size:27
Alignment explanation
Indices: 1044994--1045056 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1044984 AGTTGATACA
*
1044994 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1045022 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1045050 ATATTTT
1 ATATTTT
1045057 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1045153 original size:15 final size:16
Alignment explanation
Indices: 1045129--1045165 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1045119 TTTAATTTCT
1045129 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
1045143 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
1045159 TGATTCA
1 T-ATTCA
1045166 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:1052188 original size:62 final size:62
Alignment explanation
Indices: 1052091--1052215 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
1052081 ATTTTTATTT
1052091 TTTTACAAATTCTAAATTTAATCCTAATCTTGCTTATAGGGAAGGAAAAGAAAGTGGAGTGC
1 TTTTACAAATTCTAAATTTAATCCTAATCTTGCTTATAGGGAAGGAAAAGAAAGTGGAGTGC
1052153 TTTTACAAATTCTAAATTTAATCCTAATCTTGCTTATAGGGAAGGAAAAGAAAGTGGAGTGC
1 TTTTACAAATTCTAAATTTAATCCTAATCTTGCTTATAGGGAAGGAAAAGAAAGTGGAGTGC
1052215 T
1 T
1052216 ACTAGTGAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (62 bp):
TTTTACAAATTCTAAATTTAATCCTAATCTTGCTTATAGGGAAGGAAAAGAAAGTGGAGTGC
Found at i:1054065 original size:23 final size:23
Alignment explanation
Indices: 1054025--1054069 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1054015 CCCCATGTTG
**
1054025 CTGCTGCCCATGCCTCACCCATA
1 CTGCTGCCCACACCTCACCCATA
*
1054048 CTGCTGCCCACACTTCACCCAT
1 CTGCTGCCCACACCTCACCCAT
1054070 CACTCCACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.49, G:0.11, T:0.22
Consensus pattern (23 bp):
CTGCTGCCCACACCTCACCCATA
Found at i:1055953 original size:22 final size:22
Alignment explanation
Indices: 1055925--1055982 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
1055915 CTACGGCAAC
1055925 ATCCGTCCTCATCTCCGACGAA
1 ATCCGTCCTCATCTCCGACGAA
*
1055947 ATTCGTCGC-CATCTCCGACGAA
1 ATCCGTC-CTCATCTCCGACGAA
1055969 ATCCGT-CT-ATCTCC
1 ATCCGTCCTCATCTCC
1055983 ATCTCTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 7 0.22
22 24 0.75
23 1 0.03
ACGTcount: A:0.21, C:0.40, G:0.14, T:0.26
Consensus pattern (22 bp):
ATCCGTCCTCATCTCCGACGAA
Found at i:1056188 original size:16 final size:16
Alignment explanation
Indices: 1056167--1056198 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1056157 AGATTGCTTA
1056167 GTAAATTCATTCGGTT
1 GTAAATTCATTCGGTT
1056183 GTAAATTCATTCGGTT
1 GTAAATTCATTCGGTT
1056199 ACTGCCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (16 bp):
GTAAATTCATTCGGTT
Found at i:1058554 original size:21 final size:20
Alignment explanation
Indices: 1058488--1058560 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
1058478 CCTGTCATCG
* * *
1058488 TTCAAGAGGCCTCTCCTATTG
1 TTCAAGAGGCCCCTCCCA-TA
** *
1058509 TTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCCCCTCCCAT-A
1058530 TTCAAGAGGCCCCTCCCACTA
1 TTCAAGAGGCCCCTCCCA-TA
1058551 TTCAAGAGGC
1 TTCAAGAGGC
1058561 TCTTGTCATC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (20 bp):
TTCAAGAGGCCCCTCCCATA
Found at i:1058570 original size:42 final size:42
Alignment explanation
Indices: 1058478--1058580 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 42
1058468 GACCGATTCA
* * * * *
1058478 CCTGTCATCGTTCAAGAGGCCTCTCCTATTGTTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCCCCTCCCACTATTCAAGAGGCC
* * *
1058520 CCTATCATCCTTCAAGAGGCCCCTCCCACTATTCAAGAGGCT
1 CCTGTCATCATTCAAGAGGCCCCTCCCACTATTCAAGAGGCC
* *
1058562 CTTGTCATCATTAAAGAGG
1 CCTGTCATCATTCAAGAGG
1058581 TCTCTTTCAC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.27
Consensus pattern (42 bp):
CCTGTCATCATTCAAGAGGCCCCTCCCACTATTCAAGAGGCC
Found at i:1058599 original size:21 final size:21
Alignment explanation
Indices: 1058550--1058600 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1058540 CCCTCCCACT
*
1058550 ATTCAAGAGGCTCTTGTCATC
1 ATTCAAGAGGCTCTTGTCACC
*
1058571 ATTAAAGAGGTCTCTT-TCACC
1 ATTCAAGAGG-CTCTTGTCACC
*
1058592 GTTCAAGAG
1 ATTCAAGAG
1058601 CCCGATTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (21 bp):
ATTCAAGAGGCTCTTGTCACC
Found at i:1060080 original size:20 final size:20
Alignment explanation
Indices: 1060019--1060082 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1060009 TTTTCTTAAC
* **
1060019 GCGAAAATCAAATTCGCAAA
1 GCGAAAGTCAAATTCGCATT
*
1060039 GCGAAAGTTAAATTCG-ATTT
1 GCGAAAGTCAAATTCGCA-TT
*
1060059 GCGAAAGTCAAATTCGCGTT
1 GCGAAAGTCAAATTCGCATT
1060079 GCGA
1 GCGA
1060083 TTTCGCGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.97
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCATT
Found at i:1060127 original size:29 final size:29
Alignment explanation
Indices: 1060093--1060149 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1060083 TTTCGCGTTT
*
1060093 CGAATTTGACTTTCGCAATAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
1060122 CGAATTTGACTTTCGCAACAATCGCAAC
1 CGAATTTGACTTTCGCAACAATCGCAAC
1060150 AAAAAATCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAACG
Found at i:1063567 original size:20 final size:19
Alignment explanation
Indices: 1063523--1063651 Score: 75
Period size: 20 Copynumber: 6.5 Consensus size: 19
1063513 CAAAACATTT
*
1063523 GTGTTGCGAAACTAAAA-C
1 GTGTTGCGAAATTAAAATC
*
1063541 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
1063561 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
** *
1063581 GAATTGCGAAAATAAAATTC
1 GTGTTGCGAAATTAAAA-TC
* *
1063601 GCGTTGTG-AATTCAGAAATC
1 GTGTTGCGAAATT-A-AAATC
* * *
1063621 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
1063641 AGTGTTGCGAA
1 -GTGTTGCGAA
1063652 TTTGGAAATC
Statistics
Matches: 85, Mismatches: 16, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
18 15 0.18
19 11 0.13
20 36 0.42
21 23 0.27
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:1063597 original size:40 final size:40
Alignment explanation
Indices: 1063544--1063662 Score: 141
Period size: 40 Copynumber: 3.0 Consensus size: 40
1063534 CTAAAACCTG
1063544 TTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAA
1 TTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAA
* * * *
1063584 TTGCGAAAATAAAATTCGCGTTGTGAATTC-AGAAATCGAG
1 TTGCGAAATTAAAATTCGTGTTGCGAATTCGA-AAATCGAA
* * * *
1063624 TTGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAATCG
1 TTGCGAAATTAAAATTC-GTGTTGCGAATTCGAAAATCG
1063663 CAACGCGAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.02
40 48 0.74
41 16 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (40 bp):
TTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAA
Found at i:1063683 original size:21 final size:21
Alignment explanation
Indices: 1063647--1063695 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1063637 ATTCAGTGTT
*
1063647 GCGAATTT-GGAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
*
1063667 GCGAATTTAGAAAATCGCAAT
1 GCGAATTTAGAAAATCGCAAC
1063688 GCG-ATTTA
1 GCGAATTTA
1063696 CTTATTCACG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:1065804 original size:32 final size:32
Alignment explanation
Indices: 1065768--1065829 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1065758 TCTTACCTGT
* *
1065768 ACTAACTAATTTCTTTTCTTTTGCTTGTGTAC
1 ACTAACTAATTTCCTCTCTTTTGCTTGTGTAC
** *
1065800 ACTAACTTTTTTCCTCTCTTTTGTTTGTGT
1 ACTAACTAATTTCCTCTCTTTTGCTTGTGT
1065830 CGTTTTTCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.56
Consensus pattern (32 bp):
ACTAACTAATTTCCTCTCTTTTGCTTGTGTAC
Found at i:1067555 original size:10 final size:11
Alignment explanation
Indices: 1067541--1067638 Score: 55
Period size: 10 Copynumber: 8.9 Consensus size: 11
1067531 AAAGCAATGA
1067541 AAAAACAAAGG
1 AAAAACAAAGG
1067552 AAAAACAAAGG
1 AAAAACAAAGG
* *
1067563 AAAATAGAGAAAAG
1 -AAA-A-ACAAAGG
1067577 AAAAACAAA-G
1 AAAAACAAAGG
*
1067587 -ACAA-AAA-G
1 AAAAACAAAGG
1067595 AAAAACAAA-G
1 AAAAACAAAGG
*
1067605 AAAAGCAAAGAG
1 AAAAACAAAG-G
1067617 AAAGAAACAAA-G
1 -AA-AAACAAAGG
*
1067629 AAAAAAAAAG
1 AAAAACAAAG
1067639 CAAAGAAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
8 4 0.06
9 6 0.09
10 19 0.28
11 17 0.25
12 6 0.09
13 6 0.09
14 11 0.16
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.01
Consensus pattern (11 bp):
AAAAACAAAGG
Found at i:1067599 original size:24 final size:24
Alignment explanation
Indices: 1067551--1067660 Score: 65
Period size: 25 Copynumber: 4.7 Consensus size: 24
1067541 AAAAACAAAG
*
1067551 GAAAAACAAAGGA-AAATAGAGAAAA
1 GAAAAACAAA-GACAAAAAGA-AAAA
1067576 GAAAAACAAAGACAAAAAGAAAAA
1 GAAAAACAAAGACAAAAAGAAAAA
* * *
1067600 CAAAGA-AAAG-C--AAAGAGAAA
1 GAAAAACAAAGACAAAAAGAAAAA
*
1067620 G--AAACAAAGA-AAAAAAAAGCAAA
1 GAAAAACAAAGACAAAAAGAA--AAA
1067643 GAAAACAACAAAGACAAA
1 G-AAA-AACAAAGACAAA
1067661 GCAAAGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 8 0.12
21 4 0.06
22 1 0.02
23 8 0.12
24 10 0.15
25 16 0.25
26 1 0.02
27 8 0.12
28 3 0.05
ACGTcount: A:0.75, C:0.09, G:0.15, T:0.01
Consensus pattern (24 bp):
GAAAAACAAAGACAAAAAGAAAAA
Found at i:1067629 original size:34 final size:33
Alignment explanation
Indices: 1067521--1067672 Score: 108
Period size: 34 Copynumber: 4.3 Consensus size: 33
1067511 CAAACAAAAT
* * *
1067521 AAAGAGAAAAAAAGCAATGAAAAAACAAAGGAAAAAC
1 AAAGAAAAAAAAAGAAAAG-AAAAACAAA-G--AAAC
* * *
1067558 AAAGGAAAATAGAGAAAAGAAAAACAAAGACAA-
1 AAAGAAAAAAAAAGAAAAGAAAAACAAAGA-AAC
* * *
1067591 AAAGAAAAACAAAGAAAAGCAAAGAGAAAGAAAC
1 AAAGAAAAAAAAAGAAAAG-AAAAACAAAGAAAC
*
1067625 AAAGAAAAAAAAAGCAAAGAAAACAACAAAGACAAAGC
1 AAAGAAAAAAAAAGAAAAG-AAA-AACAAAG--AAA-C
1067663 AAAGAAAAAA
1 AAAGAAAAAA
1067673 GATGACAAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
33 19 0.21
34 31 0.34
35 6 0.07
36 9 0.10
37 16 0.17
38 11 0.12
ACGTcount: A:0.74, C:0.09, G:0.16, T:0.01
Consensus pattern (33 bp):
AAAGAAAAAAAAAGAAAAGAAAAACAAAGAAAC
Found at i:1067636 original size:43 final size:42
Alignment explanation
Indices: 1067511--1067636 Score: 103
Period size: 43 Copynumber: 2.8 Consensus size: 42
1067501 TGTGAAGATC
* * *
1067511 CAAACAAAATAAAGAGAAAAAAAGCAATGAAAAAACAAAGGAAAAA
1 CAAAGAAAA-AAAGAGAAAGAAA-CAAAG-AAAAA-AAAGGAAAAA
* * *
1067557 CAAAGGAAAATAGAGAAAAGAAAAACAAAG-ACAAAAA-GAAAAA
1 CAAAGAAAAAAAGAG-AAAG--AAACAAAGAAAAAAAAGGAAAAA
1067600 CAAAGAAAAGCAAAGAGAAAGAAACAAAGAAAAAAAA
1 CAAAGAAAA--AAAGAGAAAGAAACAAAGAAAAAAAA
1067637 AGCAAAGAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
42 8 0.12
43 20 0.31
44 7 0.11
45 13 0.20
46 10 0.15
47 4 0.06
48 3 0.05
ACGTcount: A:0.75, C:0.08, G:0.15, T:0.02
Consensus pattern (42 bp):
CAAAGAAAAAAAGAGAAAGAAACAAAGAAAAAAAAGGAAAAA
Found at i:1067664 original size:52 final size:50
Alignment explanation
Indices: 1067521--1067670 Score: 167
Period size: 52 Copynumber: 2.9 Consensus size: 50
1067511 CAAACAAAAT
* * * *
1067521 AAAGAGAAAAAAAGCAATGAAAAAACAAAGGAAAAACAAAGGAAAATAGAGA
1 AAAGAAAAAAAAAGCAAAGAAAAAACAAA-GAAAAGCAAA-GAAAATAGAAA
* * *
1067573 AAAGAAAAACAAAGACAAAAAGAAAAACAAAGAAAAGCAAAGAGAA-AGAAA
1 AAAGAAAAAAAAAG-CAAAGA-AAAAACAAAGAAAAGCAAAGAAAATAGAAA
1067624 CAAAGAAAAAAAAAGCAAAGAAAACAACAAAGACAAAGCAAAGAAAA
1 -AAAGAAAAAAAAAGCAAAGAAAA-AACAAAGA-AAAGCAAAGAAAA
1067671 AAGATGACAA
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
50 3 0.04
51 17 0.20
52 41 0.49
53 13 0.16
54 9 0.11
ACGTcount: A:0.74, C:0.09, G:0.16, T:0.01
Consensus pattern (50 bp):
AAAGAAAAAAAAAGCAAAGAAAAAACAAAGAAAAGCAAAGAAAATAGAAA
Found at i:1069447 original size:31 final size:31
Alignment explanation
Indices: 1069377--1069447 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1069367 AGTTTCTCTA
*
1069377 GAAACACAAAATCTTTGAGTCTGTATCTATT
1 GAAACAAAAAATCTTTGAGTCTGTATCTATT
* *
1069408 AAAACAAAACAATCTTTGAGT-TGTTTC-ATTT
1 GAAACAAAA-AATCTTTGAGTCTGTATCTA-TT
1069439 GAAACAAAA
1 GAAACAAAA
1069448 TTTTGTCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 1 0.03
31 22 0.65
32 11 0.32
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (31 bp):
GAAACAAAAAATCTTTGAGTCTGTATCTATT
Found at i:1069493 original size:30 final size:29
Alignment explanation
Indices: 1069459--1069522 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
1069449 TTTGTCTCTC
1069459 TTGAGACAGTTTCTCTTAACAAAATCATCT
1 TTGAGACAGTTTCTCTTAA-AAAATCATCT
* * * * *
1069489 TTGAGTCTGTTTCTTTTGAAACATCATCT
1 TTGAGACAGTTTCTCTTAAAAAATCATCT
1069518 TTGAG
1 TTGAG
1069523 TAGGTTTCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (29 bp):
TTGAGACAGTTTCTCTTAAAAAATCATCT
Found at i:1069515 original size:29 final size:29
Alignment explanation
Indices: 1069467--1069539 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
1069457 TCTTGAGACA
* * **
1069467 GTTTCTCTTAACAAAATCATCTTTGAGTCT
1 GTTTCTCTTGA-AACATCATCTTTGAGTAG
*
1069497 GTTTCTTTTGAAACATCATCTTTGAGTAG
1 GTTTCTCTTGAAACATCATCTTTGAGTAG
1069526 GTTTCTCTTGAAAC
1 GTTTCTCTTGAAAC
1069540 CATTATCAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (29 bp):
GTTTCTCTTGAAACATCATCTTTGAGTAG
Found at i:1069827 original size:134 final size:134
Alignment explanation
Indices: 1069586--1069956 Score: 494
Period size: 134 Copynumber: 2.8 Consensus size: 134
1069576 GTGGAGCTGT
* * * * ** *
1069586 GTTATCATCCTTCCTAAAGACGACCATAACTCTTCATCACGTATGAGCCGTGTCATCCCCATACT
1 GTTATCAACCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACC
* * *
1069651 AGATCTCCTCATCGCGTAGGAGCCGTGTCACCCCTAGCTAACCA-ACCGTCCTCATTACGTAGGA
66 AGATCTCCTCATCGCGTAGGAGCCGTGTCACCCCTAGATAACCAGA-CGTCCTCATCACGTAAGA
*
1069715 ACTGA
130 ACCGA
* * *
1069720 GTTATCAACTTTCCTAAATATGACCAGAACTCTTCATCACGTATGAGTTGTGTCATCCCCCGACC
1 GTTATCAACCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACC
* *
1069785 AGATCTCCTCATCGCGTAGGAGCCG-GATCACCCCTAGATAACCAGATGTCCTCATCGCGTAAGA
66 AGATCTCCTCATCGCGTAGGAGCCGTG-TCACCCCTAGATAACCAGACGTCCTCATCACGTAAGA
*
1069849 ACCGG
130 ACCGA
* * *
1069854 GTTATCACCCTTCCTAAAGATGTCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCTCGACC
1 GTTATCAACCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACC
* * * *
1069919 AGATTTCCTCATCACGTAGGAACCGTGTCACCCTTAGA
66 AGATCTCCTCATCGCGTAGGAGCCGTGTCACCCCTAGA
1069957 CGACCAGAAC
Statistics
Matches: 207, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
133 1 0.00
134 204 0.99
135 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (134 bp):
GTTATCAACCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACC
AGATCTCCTCATCGCGTAGGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAAGAA
CCGA
Found at i:1069988 original size:43 final size:40
Alignment explanation
Indices: 1069877--1069989 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
1069867 CTAAAGATGT
*
1069877 CCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCTCGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCTCGA
** * * *
1069917 CCAGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCC-T---CGA
*
1069960 CCAGAACTCTTCATCGCGTATGAGCCGTGT
1 CCAGAACTCTTCATCACGTATGAGCCGTGT
1069990 TGTCCCCAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
39 3 0.05
40 27 0.47
43 27 0.47
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCTCGA
Found at i:1070362 original size:23 final size:23
Alignment explanation
Indices: 1070335--1070379 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1070325 CCCCATGTTG
1070335 CTGCTGCCCATGCCTCACCCATA
1 CTGCTGCCCATGCCTCACCCATA
* *
1070358 CTGCTTCCCATGCTTCACCCAT
1 CTGCTGCCCATGCCTCACCCAT
1070380 CACTCCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.47, G:0.11, T:0.27
Consensus pattern (23 bp):
CTGCTGCCCATGCCTCACCCATA
Found at i:1072085 original size:19 final size:19
Alignment explanation
Indices: 1072058--1072114 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
1072048 GAACGCAATA
*
1072058 AGTGTATCGATTCATAGGC
1 AGTGCATCGATTCATAGGC
1072077 AGTGCATCGATACATCATAGGC
1 AGTGCATCGAT---TCATAGGC
*
1072099 AGTGCATCGATACATA
1 AGTGCATCGATTCATA
1072115 AGGACCAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 14 0.42
22 19 0.58
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
AGTGCATCGATTCATAGGC
Found at i:1072097 original size:22 final size:22
Alignment explanation
Indices: 1072069--1072113 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1072059 GTGTATCGAT
1072069 TCATAGGCAGTGCATCGATACA
1 TCATAGGCAGTGCATCGATACA
1072091 TCATAGGCAGTGCATCGATACA
1 TCATAGGCAGTGCATCGATACA
1072113 T
1 T
1072114 AAGGACCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
TCATAGGCAGTGCATCGATACA
Found at i:1072519 original size:59 final size:59
Alignment explanation
Indices: 1072443--1073054 Score: 621
Period size: 59 Copynumber: 10.4 Consensus size: 59
1072433 TGGCATTATA
*
1072443 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
*
1072502 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * *
1072561 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTTCATATGGAGCACTGAG
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * * * * * *
1072620 TGTGCTAAAGTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAGG-GCACT-ATA
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATAT-GGAGCACTGA-G
* * *
1072679 TGTCCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * **
1072738 TGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTTCATATGGAGCGTTGAG
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * *
1072797 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAA
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * * * * * * *
1072856 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCTAGATAGG-GCAAT-ATA
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATAT-GGAGCACTGA-G
* * * * * **
1072915 TGTGCTAAAATGGTAAGGGAATCATACTAATGGTAT-GGATTCTTGCATA-GG-GCACTTCG
1 TGTGCTAAAATGGTAAGGAAATCATACTGA--GTATATGAAT-TTCCATATGGAGCACTGAG
* * * * *
1072974 TGTGCTAAAATGAG-GAGGAAATCATATTAAGTATATG-ATATTCCAAATAGAGCACTGAG
1 TGTGCTAAAATG-GTAAGGAAATCATACTGAGTATATGAAT-TTCCATATGGAGCACTGAG
* * **
1073033 AGTGCTAATATTATAAGGAAAT
1 TGTGCTAAAATGGTAAGGAAAT
1073055 TATATGAATT
Statistics
Matches: 461, Mismatches: 77, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
57 10 0.02
58 6 0.01
59 430 0.93
60 8 0.02
61 7 0.02
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.30
Consensus pattern (59 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
Found at i:1072593 original size:31 final size:31
Alignment explanation
Indices: 1072496--1072594 Score: 80
Period size: 31 Copynumber: 3.3 Consensus size: 31
1072486 CATATGGAGC
*
1072496 ACTGAGTGTGCTAAAATGGTAAGGAAATCAT
1 ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
* * * *** * *
1072527 ACTGAGTGT-ATGAATTTCCATATGG-AGC--
1 ACTGAGTGTGCTAAAATGGTA-AGGGAATCAT
1072555 ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
1 ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
1072586 ACTGAGTGT
1 ACTGAGTGT
1072595 ATGGATTTTC
Statistics
Matches: 46, Mismatches: 17, Indels: 10
0.63 0.23 0.14
Matches are distributed among these distances:
28 12 0.26
29 7 0.15
30 7 0.15
31 20 0.43
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.28
Consensus pattern (31 bp):
ACTGAGTGTGCTAAAATGGTAAGGGAATCAT
Found at i:1072852 original size:236 final size:236
Alignment explanation
Indices: 1072434--1072940 Score: 888
Period size: 236 Copynumber: 2.1 Consensus size: 236
1072424 ATTACCAAAT
* *
1072434 GGCATTATATGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACT
1 GGCAATATATGTGCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCACT
1072499 GAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGT
66 GAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGT
* *
1072564 GCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTTCATATGGAGCACTGAGTGTGCTAAA
131 GCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAATGTGCTAAA
1072629 GTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAG
196 GTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAG
* *
1072670 GGCACTATATGTCCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCACT
1 GGCAATATATGTGCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCACT
* * **
1072735 GAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTTCATATGGAGCGTTGAGTGT
66 GAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGT
1072800 GCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAATGTGCTAAA
131 GCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAATGTGCTAAA
* *
1072865 GTGATAAGGAAATCATATTGAATATATGGATTTCTAGATAG
196 GTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAG
* *
1072906 GGCAATATATGTGCTAAAATGGTAAGGGAATCATA
1 GGCAATATATGTGCTAAAATGATAAGGAAATCATA
1072941 CTAATGGTAT
Statistics
Matches: 256, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
236 256 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (236 bp):
GGCAATATATGTGCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCACT
GAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGT
GCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAATGTGCTAAA
GTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAG
Found at i:1072979 original size:236 final size:238
Alignment explanation
Indices: 1072434--1073040 Score: 883
Period size: 236 Copynumber: 2.6 Consensus size: 238
1072424 ATTACCAAAT
* *
1072434 GGCATTATATGTGCTAAAATGATAAGGAAATCATACTGA--GTATATGAATTTCCATATGGAGCA
1 GGCAATATATGTGCTAAAATGATAAGGAAATCATACTAATGGTATATGAATTTCCATATGGAGCA
*
1072497 CTGAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGT
66 CTGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCACTGAGT
* *
1072562 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTTCATATGGAGCACTGAGTGTGCTA
131 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAATGTGCTA
1072627 AAGTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAG
196 AAGTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAG
* *
1072670 GGCACTATATGTCCTAAAATGATAAGGAAATC--A-TAATGAGTATATGAATTTCCATATGGAGC
1 GGCAATATATGTGCTAAAATGATAAGGAAATCATACTAATG-GTATATGAATTTCCATATGGAGC
* **
1072732 ACTGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTTCATATGGAGCGTTGAG
65 ACTGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCACTGAG
1072797 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAATGTGCT
130 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAATGTGCT
* *
1072862 AAAGTGATAAGGAAATCATATTGAATATATGGATTTCTAGATAG
195 AAAGTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAG
* * * * *
1072906 GGCAATATATGTGCTAAAATGGTAAGGGAATCATACTAATGGTAT-GGATTCTTGCATA-GG-GC
1 GGCAATATATGTGCTAAAATGATAAGGAAATCATACTAATGGTATATGAAT-TTCCATATGGAGC
** * * * * *
1072968 ACTTCGTGTGCTAAAATGAG-GAGGAAATCATATTAAGTATATG-ATATTCCAAATAGAGCACTG
65 ACTGAGTGTGCTAAAATG-GTAAGGAAATCATATTGAGTGTATGAAT-TTCCATATGGAGCACTG
*
1073031 AGAGTGCTAA
128 AGTGTGCTAA
1073041 TATTATAAGG
Statistics
Matches: 333, Mismatches: 29, Indels: 18
0.88 0.08 0.05
Matches are distributed among these distances:
233 2 0.01
234 1 0.00
235 2 0.01
236 306 0.92
237 6 0.02
238 11 0.03
239 5 0.02
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.30
Consensus pattern (238 bp):
GGCAATATATGTGCTAAAATGATAAGGAAATCATACTAATGGTATATGAATTTCCATATGGAGCA
CTGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCACTGAGT
GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAATGTGCTA
AAGTGATAAGGAAAGCATATTGAATATATGGATTTCCAGATAG
Found at i:1073199 original size:44 final size:44
Alignment explanation
Indices: 1073136--1073355 Score: 305
Period size: 44 Copynumber: 5.0 Consensus size: 44
1073126 TCAGTGATGT
*
1073136 AAATTATAGTAAGTATATTGATAACATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
*
1073180 AAATTATAGTAAGTATATTGATAAAATAAGCTTATGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
* * * ** *
1073224 AAGTTATAGTAAGTAGATTTATAGCATGAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
*
1073268 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
* * * * * *
1073312 GAATAATGGTAAGTATATTGGTAAAATAAGCTAAAGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
1073356 TATTAAATGG
Statistics
Matches: 155, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 155 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
Found at i:1075382 original size:13 final size:13
Alignment explanation
Indices: 1075366--1075393 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1075356 TGATATCAGA
1075366 AATGGTTATGATT
1 AATGGTTATGATT
1075379 AATGGTTATGATT
1 AATGGTTATGATT
1075392 AA
1 AA
1075394 GATGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (13 bp):
AATGGTTATGATT
Found at i:1078802 original size:59 final size:59
Alignment explanation
Indices: 1078736--1079352 Score: 642
Period size: 59 Copynumber: 10.5 Consensus size: 59
1078726 TGGCATTATA
1078736 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* *
1078795 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * * * *
1078854 TGTGCTAAAATGGTAAGGGACTCATACTGAGTGTATGGATTTTCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * * *
1078913 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAT-G-GCACT-ATA
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCC--ATATGGAGCACTGA-G
* *
1078972 TGTCCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * *
1079031 TGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCGCTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * * *
1079090 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
* * * * * * *
1079149 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGG-GCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATAT-GGAGCACTGA-G
* * * * * **
1079208 TGTGCTAAAATGGTAAGGTAAA-CATACTAATGGTAT-GGATTCTTGCATA-GG-GCACTTCG
1 TGTGCTAAAATGATAAGG-AAATCATACTGA--GTATATGAAT-TTCCATATGGAGCACTGAG
** * * * *
1079267 TGTGCTAAAATGAGGAGGAAATCATATTAAGTATATG-ATATTCCAGATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAAT-TTCCATATGGAGCACTGAG
* * * *
1079326 AGTGCTAATATTATAAGGAAATTATAC
1 TGTGCTAAAATGATAAGGAAATCATAC
1079353 GAATTGTACA
Statistics
Matches: 473, Mismatches: 68, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
57 14 0.03
58 9 0.02
59 427 0.90
60 11 0.02
61 12 0.03
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCACTGAG
Found at i:1079145 original size:236 final size:236
Alignment explanation
Indices: 1078725--1079233 Score: 912
Period size: 236 Copynumber: 2.2 Consensus size: 236
1078715 TGATTACCAA
*
1078725 ATGGCATTATATGTGCTAAAATGATAAGGAAATCATACTGAGTATATGAATTTCCATATGGAGCA
1 ATGGCATTATATGTGCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCA
1078790 CTGAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGT
66 CTGAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGT
* *
1078855 GTGCTAAAATGGTAAGGGACTCATACTGAGTGTATGGATTTTCATATGGAGCACTGAGTGTGCTA
131 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCTA
1078920 AAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGAT
196 AAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGAT
* *
1078961 ATGGCACTATATGTCCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCA
1 ATGGCATTATATGTGCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCA
* *
1079026 CTGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCGCTGAGT
66 CTGAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGT
*
1079091 GTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCTA
131 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCTA
1079156 AAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGAT
196 AAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGAT
* *
1079197 AGGGCATTATATGTGCTAAAATGGTAAGGTAAA-CATA
1 ATGGCATTATATGTGCTAAAATGATAAGG-AAATCATA
1079234 CTAATGGTAT
Statistics
Matches: 260, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
236 257 0.99
237 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (236 bp):
ATGGCATTATATGTGCTAAAATGATAAGGAAATCATAATGAGTATATGAATTTCCATATGGAGCA
CTGAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGT
GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCTA
AAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGAT
Found at i:1079272 original size:236 final size:237
Alignment explanation
Indices: 1078727--1079333 Score: 892
Period size: 236 Copynumber: 2.6 Consensus size: 237
1078717 ATTACCAAAT
*
1078727 GGCATTATATGTGCTAAAATGATAAGGAAATCATACTGA--GTATATGAATTTCCATATGGAGCA
1 GGCATTATATGTGCTAAAATGATAAGGAAA-CATACTAATGGTATATGAATTTCCATATGGAGCA
*
1078790 CTGAGTGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAGT
65 CTGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCACTGAGT
* *
1078855 GTGCTAAAATGGTAAGGGACTCATACTGAGTGTATGGATTTTCATATGGAGCACTGAGTGTGCTA
130 GTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCTA
*
1078920 AAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAT
195 AAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAG
* *
1078963 GGCACTATATGTCCTAAAATGATAAGG-AA-AT-CATAATGAGTATATGAATTTCCATATGGAGC
1 GGCATTATATGTGCTAAAATGATAAGGAAACATAC-TAATG-GTATATGAATTTCCATATGGAGC
*
1079025 ACTGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCGCTGAG
64 ACTGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCACTGAG
*
1079090 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCT
129 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCT
1079155 AAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAG
194 AAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAG
* * * *
1079199 GGCATTATATGTGCTAAAATGGTAAGGTAAACATACTAATGGTAT-GGATTCTTGCATA-GG-GC
1 GGCATTATATGTGCTAAAATGATAAGG-AAACATACTAATGGTATATGAAT-TTCCATATGGAGC
** * * * * *
1079261 ACTTCGTGTGCTAAAATGAG-GAGGAAATCATATTAAGTATATG-ATATTCCAGATAGAGCACTG
64 ACTGAGTGTGCTAAAATG-GTAAGGAAATCATATTGAGTGTATGAAT-TTCCATATGGAGCACTG
*
1079324 AGAGTGCTAA
127 AGTGTGCTAA
1079334 TATTATAAGG
Statistics
Matches: 336, Mismatches: 24, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
232 1 0.00
233 4 0.01
235 4 0.01
236 301 0.90
237 6 0.02
238 12 0.04
239 7 0.02
240 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (237 bp):
GGCATTATATGTGCTAAAATGATAAGGAAACATACTAATGGTATATGAATTTCCATATGGAGCAC
TGAGTGTGCTAAAATGGTAAGGAAATCATATTGAGTGTATGAATTTCCATATGGAGCACTGAGTG
TGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCTAA
AGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAG
Found at i:1079492 original size:44 final size:44
Alignment explanation
Indices: 1079429--1079692 Score: 348
Period size: 44 Copynumber: 6.0 Consensus size: 44
1079419 TCAGTGATGT
* *
1079429 AAATTATAGTAAGTATATTGACAACATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
*
1079473 AAATTATAGTAAGTATATTGATAACATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
* * ** *
1079517 AAGTTATAGTAAGTAGATTGATAGCATGAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
* *
1079561 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGTTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
* * * *
1079605 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
* * * * * *
1079649 GAATAATGGTAAGTATATTGGTAAAATAAGCATATGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
1079693 GATTAAATGG
Statistics
Matches: 202, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 202 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
Found at i:1081255 original size:16 final size:17
Alignment explanation
Indices: 1081224--1081258 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1081214 TATATTAACA
*
1081224 TATATACGTAAATAAGT
1 TATATACATAAATAAGT
1081241 TATATACAT-AATAAGT
1 TATATACATAAATAAGT
1081257 TA
1 TA
1081259 CAAAGCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (17 bp):
TATATACATAAATAAGT
Found at i:1081291 original size:2 final size:2
Alignment explanation
Indices: 1081284--1081359 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1081274 GGAAGCAACC
1081284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1081326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1081360 TACCATAAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1081840 original size:16 final size:16
Alignment explanation
Indices: 1081815--1081845 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1081805 CTCTCTTCAC
1081815 TCATTCTCTTTCTTTT
1 TCATTCTCTTTCTTTT
*
1081831 TCATTTTCTTTCTTT
1 TCATTCTCTTTCTTT
1081846 CATATAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (16 bp):
TCATTCTCTTTCTTTT
Found at i:1082995 original size:3 final size:3
Alignment explanation
Indices: 1082987--1083019 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1082977 TATATAATTA
*
1082987 AAT AAT AAT AAT ATT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1083020 TTAAAAGACG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1083346 original size:111 final size:111
Alignment explanation
Indices: 1083176--1083525 Score: 565
Period size: 111 Copynumber: 3.2 Consensus size: 111
1083166 GCTGTCACTC
* * * *
1083176 AGGGAATATCAGATCTGGGGATGTTGGTTTATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
1083241 GGGAATATCAAATCTTGAAAAAGAGGGATCTGTTCCGCTTCCTCTG
66 GGGAATATCAAATCTTGAAAAAGAGGGATCTGTTCCGCTTCCTCTG
* *
1083287 AGGGAATATCAGATCTGGGAAAATTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCACCCA
1 AGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * * *
1083352 GAGAATATCAAATCTTGAAAGAGAGAGATTTGTTCCGCTTCCTCTG
66 GGGAATATCAAATCTTGAAAAAGAGGGATCTGTTCCGCTTCCTCTG
* * * *
1083398 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCGGGGTAGATTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
*
1083463 GGGAATATCAAATCTTGAAAAAGAGGGATCTGTTCCGCTTTCTCTG
66 GGGAATATCAAATCTTGAAAAAGAGGGATCTGTTCCGCTTCCTCTG
1083509 AGGGAATATCAGATCTG
1 AGGGAATATCAGATCTG
1083526 AATTTGCTTC
Statistics
Matches: 218, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 218 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (111 bp):
AGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
GGGAATATCAAATCTTGAAAAAGAGGGATCTGTTCCGCTTCCTCTG
Found at i:1083576 original size:37 final size:37
Alignment explanation
Indices: 1083526--1083599 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1083516 ATCAGATCTG
**
1083526 AATTTGCTTCACTACTCTTTTGTGAAGGCTTAAGATT
1 AATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
*
1083563 AATTTGCTTCACTACTCTTCGGTGAAGGCTTTAGATT
1 AATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
1083600 GCCCGTTGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (37 bp):
AATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
Found at i:1084055 original size:43 final size:43
Alignment explanation
Indices: 1083998--1084109 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 43
1083988 CGATTCCCTT
* *
1083998 CGTCGTGAAATTGAAATCTTGGATGGGTGGGCACGATATCCTC
1 CGTCGTGGAGTTGAAATCTTGGATGGGTGGGCACGATATCCTC
** * *
1084041 CGTCGTGGAGTTGAAAT-TGTGGATCCGTTGGTACGATATCCTC
1 CGTCGTGGAGTTGAAATCT-TGGATGGGTGGGCACGATATCCTC
*
1084084 CGTCGTGGAGTTGAAATCGTGGATGG
1 CGTCGTGGAGTTGAAATCTTGGATGG
1084110 CCCCTTCGTC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
42 1 0.02
43 57 0.98
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCTTGGATGGGTGGGCACGATATCCTC
Found at i:1084335 original size:335 final size:335
Alignment explanation
Indices: 1083705--1084557 Score: 1341
Period size: 335 Copynumber: 2.5 Consensus size: 335
1083695 CTATTCTCTT
* * * * *
1083705 CGTCGTGAAGTTAAAATCCGTGGATCCATGGGTACAATATCCTCCGTCGTGGAGTTGAAATCGTG
1 CGTCGTGGAGTTGAAAT-CGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTG
* *
1083770 GATGGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTGCGTCGTGAAGTTAAAATCCA
65 GATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTAAAATCCA
* * * * * * *
1083835 AGCTTATGATGTTTCGGGTCCAATATCCTTTGCCGTGAAGTTGATATTGACTCTGAAACTGGAAA
130 AGCTTGTGCTATTTCGAGTCCAATATCCTTCGCCTTGAAGTTGAAATTGACTCTGAAACTGGAAA
* *
1083900 ATTTATTGACATACACTCCTTCTTCGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTA
195 ATTTATTGACAGACACTCCTTCTTCGAGTTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTA
* * * * *
1083965 TAGATGGATGTTGCTTGTGTGTACGATTCCCTTCGTCGTGAAATTGAAATCTTGGATGGGTGGGC
260 GAGATGAATGTTGCTTGTGTGTACCATTCCCTTCGTCGTGAAATTGAAACCGTGGATGGGTGGGC
1084030 ACGATATCCTC
325 ACGATATCCTC
*
1084041 CGTCGTGGAGTTGAAATTGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
1 CGTCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
* *
1084106 ATGGCCCCTTCGTCGTGAAGTTGAACTTTGACTTGAATATCCTTCGTCGTGAAGTTAAAATCCAA
66 ATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTAAAATCCAA
* * *
1084171 GCTTGTGCTATTTCGAGTCCAATATCCTTCGCCTTGAAGTTAAAATTGGCTCTGAAACTGGAAAG
131 GCTTGTGCTATTTCGAGTCCAATATCCTTCGCCTTGAAGTTGAAATTGACTCTGAAACTGGAAAA
* *
1084236 TTTATTGACAGACACTCCTTCTTTGAGTTGGATATCATTCTTCGTGAAGTTGAAATCCAATCTAG
196 TTTATTGACAGACACTCCTTCTTCGAGTTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAG
* * *
1084301 AGATGAATGTTGCTTGTGTGTACCATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCA
261 AGATGAATGTTGCTTGTGTGTACCATTCCCTTCGTCGTGAAATTGAAACCGTGGATGGGTGGGCA
1084366 CGATATCCTC
326 CGATATCCTC
*
1084376 CGTCGTGGAGTTGAAATCGTGGATCTGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
1 CGTCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
* *
1084441 ATGGCCCC-TCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGCCGTGAAGTTGAAATCCAA
66 ATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTAAAATCCAA
* *
1084505 GCTTGTGCTATTTTGAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGACTCT
131 GCTTGTGCTATTTCGAGTCCAATATCCTTCGCCT-TGAAGTTGAAATTGACTCT
1084558 AAAAGCTGCA
Statistics
Matches: 474, Mismatches: 42, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
333 1 0.00
334 99 0.21
335 359 0.76
336 15 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (335 bp):
CGTCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
ATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTAAAATCCAA
GCTTGTGCTATTTCGAGTCCAATATCCTTCGCCTTGAAGTTGAAATTGACTCTGAAACTGGAAAA
TTTATTGACAGACACTCCTTCTTCGAGTTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAG
AGATGAATGTTGCTTGTGTGTACCATTCCCTTCGTCGTGAAATTGAAACCGTGGATGGGTGGGCA
CGATATCCTC
Found at i:1084381 original size:43 final size:43
Alignment explanation
Indices: 1084328--1084443 Score: 178
Period size: 43 Copynumber: 2.7 Consensus size: 43
1084318 GTGTACCATT
* * *
1084328 TCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATA
1 TCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGGGCACGATA
* * *
1084371 TCCTCCGTCGTGGAGTTGAAATCGTGGATCTGTTGGTACGATA
1 TCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGGGCACGATA
1084414 TCCTCCGTCGTGGAGTTGAAATCGTGGATG
1 TCCTCCGTCGTGGAGTTGAAATCGTGGATG
1084444 GCCCCTCGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (43 bp):
TCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGGGCACGATA
Found at i:1084792 original size:32 final size:32
Alignment explanation
Indices: 1084718--1084779 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1084708 TTGCATCATG
* *
1084718 ATGTTGAATCCCCAAATATGCCCCAATATTCA
1 ATGTTGAATCTCCAAATATGCCCCAACATTCA
*
1084750 ATATTGAATCTCCAAATATGCCCCAACATT
1 ATGTTGAATCTCCAAATATGCCCCAACATT
1084780 TGTTGTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATGCCCCAACATTCA
Found at i:1085836 original size:7 final size:7
Alignment explanation
Indices: 1085824--1085869 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
1085814 TATCGTCCCT
1085824 TTTTTTC
1 TTTTTTC
1085831 TTTTTTC
1 TTTTTTC
1085838 TTTTTTTC
1 -TTTTTTC
*
1085846 TCTTTT-
1 TTTTTTC
*
1085852 TTTTCTC
1 TTTTTTC
1085859 TTTTTTC
1 TTTTTTC
1085866 TTTT
1 TTTT
1085870 CTTTAATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 4 0.12
7 22 0.67
8 7 0.21
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:1085843 original size:9 final size:9
Alignment explanation
Indices: 1085823--1085869 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
1085813 TTATCGTCCC
1085823 TTTTTTTC-
1 TTTTTTTCT
1085831 -TTTTTTCT
1 TTTTTTTCT
1085839 TTTTTTCTCT
1 TTTTTT-TCT
1085849 TTTTTTTCT
1 TTTTTTTCT
*
1085858 CTTTTTTCT
1 TTTTTTTCT
1085867 TTT
1 TTT
1085870 CTTTAATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 7 0.21
9 18 0.53
10 9 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1085854 original size:11 final size:11
Alignment explanation
Indices: 1085838--1085864 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1085828 TTCTTTTTTC
1085838 TTTTTTTCTCT
1 TTTTTTTCTCT
1085849 TTTTTTTCTCT
1 TTTTTTTCTCT
1085860 TTTTT
1 TTTTT
1085865 CTTTTCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:1085860 original size:21 final size:20
Alignment explanation
Indices: 1085831--1085905 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
1085821 CCTTTTTTTC
1085831 TTTTTTCTTTTTTTCTC-TT
1 TTTTTTCTTTTTTTCTCTTT
1085850 TTTTTTCTCTTTTTTCT-TTT
1 TTTTTTCT-TTTTTTCTCTTT
* *
1085870 CTTTAATTTCTTTTTTGCTCTATG
1 -TTT--TTTCTTTTTTTCTCT-TT
1085894 TTTTTTCTTTTT
1 TTTTTTCTTTTT
1085906 GTTATGATTG
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 8 0.17
20 10 0.21
21 12 0.26
22 7 0.15
23 9 0.19
24 1 0.02
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTTCTTTTTTTCTCTTT
Found at i:1085883 original size:28 final size:28
Alignment explanation
Indices: 1085824--1085883 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1085814 TATCGTCCCT
* ** *
1085824 TTTTTTCTTTTTTCTTTTTTTCTCTTTT
1 TTTTCTCTTTTTTCTTTTTTTCAATTTC
1085852 TTTTCTCTTTTTTCTTTTCTTT-AATTTC
1 TTTTCTCTTTTTTCTTTT-TTTCAATTTC
1085880 TTTT
1 TTTT
1085884 TTGCTCTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTTCTCTTTTTTCTTTTTTTCAATTTC
Found at i:1091870 original size:16 final size:17
Alignment explanation
Indices: 1091839--1091873 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1091829 TATATTAACA
*
1091839 TATATACGTAAATAAGT
1 TATATACATAAATAAGT
1091856 TATATACAT-AATAAGT
1 TATATACATAAATAAGT
1091872 TA
1 TA
1091874 CAAAGCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (17 bp):
TATATACATAAATAAGT
Found at i:1091907 original size:2 final size:2
Alignment explanation
Indices: 1091900--1091944 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1091890 GAAGCAAACC
1091900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1091942 AT A
1 AT A
1091945 CCATAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1092462 original size:21 final size:21
Alignment explanation
Indices: 1092436--1092902 Score: 369
Period size: 21 Copynumber: 22.1 Consensus size: 21
1092426 TCACAACACA
1092436 AACTTCGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
*
1092457 AACTTCGACTATCGCAATGCA
1 AACTTCGACTATCGCAATGCG
*
1092478 AACTTGGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
*
1092499 AA-TAT-GTA-AATCGCAATGCG
1 AACT-TCG-ACTATCGCAATGCG
*
1092519 ATA-GTCGACTATCGCAATGCG
1 A-ACTTCGACTATCGCAATGCG
* **
1092540 AACTTGGACTATCGCAACACG
1 AACTTCGACTATCGCAATGCG
1092561 AACTTCGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
* *
1092582 AACTTGCGAACT-TGGACTAT-CG
1 AACTT-CG-ACTATCG-CAATGCG
* *
1092604 CAA-TGCGAATATGTAAATCGCAATGCG
1 -AACTTCG---A-CT--ATCGCAATGCG
*
1092631 ATA-GTCGACTATCGCAATGCG
1 A-ACTTCGACTATCGCAATGCG
* *
1092652 AACTTGGACTATCGCAACGCG
1 AACTTCGACTATCGCAATGCG
1092673 AACTTCGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
1092694 AACTTCGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
*
1092715 AACTTTGACTATCGCAATGC-
1 AACTTCGACTATCGCAATGCG
* * *
1092735 AAATAT-GTA-AATCGCAACGCG
1 AACT-TCG-ACTATCGCAATGCG
1092756 AACTTCGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
*
1092777 AACTTGGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
* *
1092798 AA-TAT-GTA-AATCGCAATGTG
1 AACT-TCG-ACTATCGCAATGCG
* *
1092818 ATA-GTCGACTATCGCAATGCA
1 A-ACTTCGACTATCGCAATGCG
*
1092839 AACTTGGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
*
1092860 AA-TAT-GTA-AATCGCAATGCG
1 AACT-TCG-ACTATCGCAATGCG
*
1092880 ATA-GTCGACTATCGCAATGCG
1 A-ACTTCGACTATCGCAATGCG
1092901 AA
1 AA
1092903 TATGTAAATC
Statistics
Matches: 363, Mismatches: 48, Indels: 71
0.75 0.10 0.15
Matches are distributed among these distances:
20 66 0.18
21 267 0.74
22 7 0.02
23 10 0.03
24 2 0.01
26 4 0.01
27 7 0.02
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
AACTTCGACTATCGCAATGCG
Found at i:1092514 original size:62 final size:64
Alignment explanation
Indices: 1092436--1092902 Score: 402
Period size: 62 Copynumber: 7.4 Consensus size: 64
1092426 TCACAACACA
* *
1092436 AACTTCG-ACTATCGCAATGCGAACTTCGACTATCGCAATGCAAACTTGGACTATCGCAATGCG
1 AACTTCGTACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCG
* * * **
1092499 AA-TAT-GTA-AATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAACAC
1 AACT-TCGTACTATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGC
1092560 G
64 G
* *
1092561 AACTTCG-ACTATCGCAATGCGAACTTGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AATC
1 AACTTCGTACTAT--C---GC-AA--TGCGAACTTGGACTATCGCAATGCGAACT-TGGACTATC
1092623 GCAATGCG
57 GCAATGCG
* * *
1092631 ATA-GTCG-ACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCG
1 A-ACTTCGTACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCG
* * * * *
1092694 AACTTCG-ACTATCGCAATGCGAACTTTGACTATCGCAATGC-AAATATGTA-AATCGCAACGCG
1 AACTTCGTACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACTATCGCAATGCG
* * *
1092756 AACTTCG-ACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATGTG
1 AACTTCGTACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACTATCGCAATGCG
* * * *
1092818 ATA-GTCG-ACTATCGCAATGCAAACTTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATGC
1 A-ACTTCGTACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACTATCGCAATGC
1092879 G
64 G
*
1092880 ATA-GTCG-ACTATCGCAATGCGAA
1 A-ACTTCGTACTATCGCAATGCGAA
1092903 TATGTAAATC
Statistics
Matches: 349, Mismatches: 32, Indels: 47
0.82 0.07 0.11
Matches are distributed among these distances:
62 230 0.66
63 62 0.18
64 2 0.01
65 3 0.01
68 3 0.01
69 2 0.01
70 20 0.06
71 27 0.08
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (64 bp):
AACTTCGTACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCG
Found at i:1092675 original size:112 final size:109
Alignment explanation
Indices: 1092436--1092799 Score: 468
Period size: 104 Copynumber: 3.4 Consensus size: 109
1092426 TCACAACACA
* *
1092436 AACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGC--A---AACTTGGACTATCGCAAT
1 AACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTAACTTGGACTATCGCAAT
1092496 GCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCG
66 GCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCG
*
1092540 AACTTGGACTATCGCAACACGAACTTCGACTATCGCAATGCGAACTTGCGAACTTGGACTATCGC
1 AACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTT---AACTTGGACTATCGC
1092605 AATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCG
63 AATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCG
1092652 AACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTT--C---GACTATCGCAAT
1 AACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTAACTTGGACTATCGCAAT
* * * * *
1092712 GCGAACTTTG-ACTATCGCAATGCAAATA-T-GTA-AATCGCAACGCG
66 GCGAA-TATGTA-AATCGCAATGC-GATAGTCG-ACTATCGCAATGCG
* * *
1092756 AACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA
1 AACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAA
1092800 TATGTAAATC
Statistics
Matches: 236, Mismatches: 12, Indels: 24
0.87 0.04 0.09
Matches are distributed among these distances:
104 108 0.46
105 15 0.06
106 4 0.02
107 1 0.00
112 108 0.46
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (109 bp):
AACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTAACTTGGACTATCGCAAT
GCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCG
Found at i:1092941 original size:21 final size:21
Alignment explanation
Indices: 1092911--1093064 Score: 199
Period size: 21 Copynumber: 7.4 Consensus size: 21
1092901 AATATGTAAA
*
1092911 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
1092932 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
1092953 TCGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
1092973 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
* *
1092994 TCGCATTGCGGTAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
1093015 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
1093036 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
1093057 TCGCATTG
1 TCGCATTG
1093065 AGATTTATTC
Statistics
Matches: 117, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
20 16 0.14
21 100 0.85
22 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:1092947 original size:62 final size:62
Alignment explanation
Indices: 1092586--1092902 Score: 480
Period size: 62 Copynumber: 5.1 Consensus size: 62
1092576 AATGCGAACT
1092586 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
1 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
* * *
1092648 TGCGAACTTGGACTATCGCAACGCGAACT-TCG-ACTATCGCAATGCGA-ACTTCGACTATCGCA
1 TGCGAACTTGGACTATCGCAATGCGAA-TAT-GTA-AATCGCAATGCGATA-GTCGACTATCGCA
1092710 A
62 A
* * * *
1092711 TGCGAACTTTGACTATCGCAATGCAAATATGTAAATCGCAACGCGA-ACTTCGACTATCGCAA
1 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATA-GTCGACTATCGCAA
*
1092773 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGTGATAGTCGACTATCGCAA
1 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
*
1092835 TGCAAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
1 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
1092897 TGCGAA
1 TGCGAA
1092903 TATGTAAATC
Statistics
Matches: 232, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
62 178 0.77
63 54 0.23
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (62 bp):
TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAA
Found at i:1092957 original size:62 final size:61
Alignment explanation
Indices: 1092891--1093064 Score: 194
Period size: 62 Copynumber: 2.8 Consensus size: 61
1092881 TAGTCGACTA
* *
1092891 TCGCAATGCGAATATGT-AAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCG-ATA-GTCAAATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
* * *
1092953 TCGCATTGCGATAGTCGACTATCGCATTGCGAT-TTAC-ATA-TTCGCATTGCGGTAGTCCAAGT
1 TCGCATTGCGATAGTC-A-AATCGCATTGCGATAGT-CGA-AGTTCGCATTGCGATAGTCCAAGT
*
1093015 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCGAAGTTCGCATTG
1 TCGCATTGCGATAGTC-AA-ATCGCATTGCGATAGTCGAAGTTCGCATTG
1093065 AGATTTATTC
Statistics
Matches: 95, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
60 2 0.02
61 3 0.03
62 65 0.68
63 25 0.26
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (61 bp):
TCGCATTGCGATAGTCAAATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
Found at i:1092964 original size:83 final size:83
Alignment explanation
Indices: 1092870--1093053 Score: 266
Period size: 83 Copynumber: 2.2 Consensus size: 83
1092860 AATATGTAAA
* *
1092870 TCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGACTATCGCAATGCG-AT-T-TACATATTCGCAATGCGATAGTCCAAGT
1092932 TCGCATTGCGATAGTCCAAGT
63 TCGCATTGCGATAGTCCAAGT
* * *
1092953 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGGTAGTCCAAGTTCG
1 TCGCATTGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCG
*
1093018 CATTGCGATAGTCGAAGT
66 CATTGCGATAGTCCAAGT
1093036 TCGCATTGCGATAGTCGA
1 TCGCATTGCGATAGTCGA
1093054 AGTTCGCATT
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
80 2 0.02
81 2 0.02
82 3 0.03
83 85 0.92
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (83 bp):
TCGCATTGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCG
CATTGCGATAGTCCAAGT
Found at i:1093085 original size:42 final size:41
Alignment explanation
Indices: 1092917--1093093 Score: 171
Period size: 42 Copynumber: 4.2 Consensus size: 41
1092907 TAAATCGCAA
*
1092917 TGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAATTC-CAT
* * * *
1092959 TGCGATAGTCG-ACTATCGCATTGCGAT-TTACATATTCGCAT
1 TGCGATAGTCGAAGT-TCGCATTGCGATAGTCCAAATTC-CAT
* * * *
1093000 TGCGGTAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAATTC-CAT
* *
1093042 TGCGATAGTCGAAGTTCGCATTGAGATTTATTCCAAATT-CAT
1 TGCGATAGTCGAAGTTCGCATTGCGA--TAGTCCAAATTCCAT
*
1093084 TGTGATAGTC
1 TGCGATAGTC
1093094 CAAAATCGCA
Statistics
Matches: 110, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
41 33 0.30
42 69 0.63
44 8 0.07
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (41 bp):
TGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAATTCCAT
Found at i:1093382 original size:21 final size:21
Alignment explanation
Indices: 1093358--1093495 Score: 149
Period size: 21 Copynumber: 6.6 Consensus size: 21
1093348 TTTGGAATAA
*
1093358 ATCGCAACGCGAACTTTGACT
1 ATCGCAATGCGAACTTTGACT
*
1093379 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTTGACT
*
1093400 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTTGACT
*
1093421 ATCGCAATGCGAA-TATAT-A-A
1 ATCGCAATGCGAACT-T-TGACT
*
1093441 ATCGCAATGCGATA-GTTGACT
1 ATCGCAATGCGA-ACTTTGACT
* *
1093462 ATCACAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTTGACT
*
1093483 ATCGCATTGCGAA
1 ATCGCAATGCGAA
1093496 TACGATTTAC
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.01
20 16 0.16
21 82 0.83
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGCAATGCGAACTTTGACT
Found at i:1093452 original size:62 final size:62
Alignment explanation
Indices: 1093379--1093497 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
1093369 AACTTTGACT
*
1093379 ATCGCAATGCGA-ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATATAA
1 ATCGCAATGCGATACTT-GACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATATAA
* *
1093441 ATCGCAATGCGATAGTTGACTATCACAATGCGAACTTGGACTATCGCATTGCGAATA
1 ATCGCAATGCGATACTTGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATA
1093498 CGATTTACGT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
62 50 0.94
63 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (62 bp):
ATCGCAATGCGATACTTGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATATAA
Done.