Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 133 of 316
Found at i:42566486 original size:27 final size:26
Alignment explanation
Indices: 42566448--42566666 Score: 192
Period size: 27 Copynumber: 8.2 Consensus size: 26
42566438 GTAATTCTGT
*
42566448 AAATCGGGGGTACTTTGATAATTTTAC
1 AAATCGAGGGTA-TTTGATAATTTTAC
* * *
42566475 AAGTCGAAGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTATTTGA-TAATTTTAC
* **
42566502 AAATCGAGGGTATTTTAGTAATTTTGT
1 AAATCGAGGGTATTTGA-TAATTTTAC
42566529 AAA-CTGAGGGTATTTCGATAATTTTAC
1 AAATC-GAGGGTATTT-GATAATTTTAC
* *
42566556 AAATTGAGGGTATTTCAATAATTTTAC
1 AAATCGAGGGTATTT-GATAATTTTAC
* * *
42566583 -AATCAATGATATTTTGATAATTTTAC
1 AAATCGAGGGTA-TTTGATAATTTTAC
*
42566609 AAATCGAGGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTATTTGA-TAATTTTAC
* * *
42566636 -AATCAACGGTATTTCGGTAATTTTAC
1 AAATCGAGGGTATTT-GATAATTTTAC
42566662 AAATC
1 AAATC
42566667 AAGGAATTTG
Statistics
Matches: 156, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
26 47 0.30
27 108 0.69
28 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (26 bp):
AAATCGAGGGTATTTGATAATTTTAC
Found at i:42566490 original size:81 final size:81
Alignment explanation
Indices: 42566402--42566584 Score: 208
Period size: 81 Copynumber: 2.3 Consensus size: 81
42566392 ACCCTACAGG
** * * *
42566402 GGTATTTCAATAATTTTGTAAATTGAGGGTAAAACGGTAATTCTGTAAA-TCGGGGGTACTTT-G
1 GGTATTTCAATAATTTTACAAATCGAGGGTAAAACAGTAATTCTGTAAACT-GAGGGTA-TTTCG
*
42566465 ATAATTTTACAAGTCGAA
64 ATAATTTTACAAATCGAA
* **** *
42566483 GGTATTTCAGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTGTAAACTGAGGGTATTTCGAT
1 GGTATTTCAATAATTTTACAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTATTTCGAT
* *
42566548 AATTTTACAAATTGAG
66 AATTTTACAAATCGAA
42566564 GGTATTTCAATAATTTTACAA
1 GGTATTTCAATAATTTTACAA
42566585 TCAATGATAT
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 3 0.04
81 81 0.95
82 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (81 bp):
GGTATTTCAATAATTTTACAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTATTTCGAT
AATTTTACAAATCGAA
Found at i:42566618 original size:53 final size:53
Alignment explanation
Indices: 42566448--42566666 Score: 246
Period size: 53 Copynumber: 4.1 Consensus size: 53
42566438 GTAATTCTGT
* *
42566448 AAATCGGGGGTACTTTGA-TAATTTTACAAGTCGAA-GGTATTTC-AGTAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-TC-AACGGTATTTCGA-TAATTTTAC
* ** * * *
42566502 AAATCGAGGGTATTTTAGTAATTTTGTAAACTGAGGGTATTTCGATAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTACAATC-AACGGTATTTCGATAATTTTAC
* * * * *
42566556 AAATTGAGGGTATTTCAATAATTTTACAATCAATGATATTTTGATAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTACAATCAACGGTATTTCGATAATTTTAC
*
42566609 AAATCGAGGGTATTTCAGTAATTTTACAATCAACGGTATTTCGGTAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTACAATCAACGGTATTTCGATAATTTTAC
42566662 AAATC
1 AAATC
42566667 AAGGAATTTG
Statistics
Matches: 139, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
53 76 0.55
54 62 0.45
55 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (53 bp):
AAATCGAGGGTATTTCAGTAATTTTACAATCAACGGTATTTCGATAATTTTAC
Found at i:42566680 original size:26 final size:25
Alignment explanation
Indices: 42566574--42566686 Score: 100
Period size: 26 Copynumber: 4.3 Consensus size: 25
42566564 GGTATTTCAA
* * *
42566574 TAATTTTACAATCAATGATATTTTGA
1 TAATTTTACAATCAAGGA-ATTTCGG
* * *
42566600 TAATTTTACAAATCGAGGGTATTTCAG
1 TAATTTTAC-AATC-AAGGAATTTCGG
*
42566627 TAATTTTACAATCAACGGTATTTCGG
1 TAATTTTACAATCAA-GGAATTTCGG
*
42566653 TAATTTTACAAATCAAGGAATTTGGG
1 TAATTTTAC-AATCAAGGAATTTCGG
*
42566679 TAGTTTTA
1 TAATTTTA
42566687 TAAACTGGGG
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.01
26 46 0.64
27 23 0.32
28 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.41
Consensus pattern (25 bp):
TAATTTTACAATCAAGGAATTTCGG
Found at i:42566734 original size:26 final size:27
Alignment explanation
Indices: 42566682--42566737 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
42566672 ATTTGGGTAG
*
42566682 TTTTATAAACTGGGGGTACTTTGGTAA
1 TTTTATAAACTGGGGGTACTTTAGTAA
* *
42566709 TTTTAT-AATTGGGGGTATTTTAGTAA
1 TTTTATAAACTGGGGGTACTTTAGTAA
42566735 TTT
1 TTT
42566738 GGTAAACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (27 bp):
TTTTATAAACTGGGGGTACTTTAGTAA
Found at i:42575053 original size:48 final size:48
Alignment explanation
Indices: 42574977--42575334 Score: 200
Period size: 48 Copynumber: 7.6 Consensus size: 48
42574967 GACCACATAT
* * *
42574977 CGATGCCATATCCCAGATATGGTGTTATACGAAGTCTCATATCGATGC
1 CGATGCCATGTCCCAGACATGGTCTTATACGAAGTCTCATATCGATGC
* * * * *
42575025 CGATGCCATGTCCTAGACATGGTCTTATAC-AGGACCTCACATTGATGC
1 CGATGCCATGTCCCAGACATGGTCTTATACGAAG-TCTCATATCGATGC
* * * * ** * *
42575073 CAATGCCATATCCCAGATACGGTCTTACTTGGGA-TCTCATA-CTGATGT
1 CGATGCCATGTCCCAGACATGGTCTTA-TACGAAGTCTCATATC-GATGC
* *
42575121 CGATTCCATGTCCCAGACATGGTCTTATAC-AAG----ATCTCGTAT--
1 CGATGCCATGTCCCAGACATGGTCTTATACGAAGTCTCATATCG-ATGC
* * * * * *
42575163 CGATGCCATGTCCCATACATGGTCTTACACGAAATCACTTAACGATGC
1 CGATGCCATGTCCCAGACATGGTCTTATACGAAGTCTCATATCGATGC
* * * * * * * *
42575211 CGAAGCCATATCCCTGATATGGTCTTATAC-AGGATCACATCTAGATGC
1 CGATGCCATGTCCCAGACATGGTCTTATACGAAG-TCTCATATCGATGC
* * * * * * * *
42575259 GGATGCCATGTCCCAAATATGGTCTTACATG-GGATCTCATTTTGAATGC
1 CGATGCCATGTCCCAGACATGGTCTTATACGAAG-TCTCATATCG-ATGC
*
42575308 CAATGCCATGTCCCAGACATGGTCTTA
1 CGATGCCATGTCCCAGACATGGTCTTA
42575335 CACGGGATCT
Statistics
Matches: 230, Mismatches: 63, Indels: 33
0.71 0.19 0.10
Matches are distributed among these distances:
42 27 0.12
43 5 0.02
44 3 0.01
46 3 0.01
47 7 0.03
48 157 0.68
49 28 0.12
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTATACGAAGTCTCATATCGATGC
Found at i:42575168 original size:96 final size:96
Alignment explanation
Indices: 42574979--42575334 Score: 248
Period size: 96 Copynumber: 3.8 Consensus size: 96
42574969 CCACATATCG
* * *
42574979 ATGCCATATCCCAGATATGGTGTTATACGAAGTCTCATATCGATGCCGATGCCATGTCCTAGACA
1 ATGCCATATCCCAGATACGGTCTTATACGAAGTCTCATATCGATGCCGATGCCATGTCCCAGACA
* *
42575044 TGGTCTTATACAGGACCTCACATTGATGCCA
66 TGGTCTTATACAAGACCTCACATCGATGCCA
** * * *
42575075 ATGCCATATCCCAGATACGGTCTTACTTGGGA-TCTCATA-CTGATGTCGATTCCATGTCCCAGA
1 ATGCCATATCCCAGATACGGTCTTA-TACGAAGTCTCATATC-GATGCCGATGCCATGTCCCAGA
* **
42575138 CATGGTCTTATACAAGATCTCGTATCGATGCC-
64 CATGGTCTTATACAAGACCTCACATCGATGCCA
* * * * * * * * * * * *
42575170 ATG-----TCCCATACATGGTCTTACACGAAATCACTTAACGATGCCGAAGCCATATCCCTGATA
1 ATGCCATATCCCAGATACGGTCTTATACGAAGTCTCATATCGATGCCGATGCCATGTCCCAGACA
* **
42575230 TGGTCTTATACAGGA--TCACATCTAGATGCGG
66 TGGTCTTATACAAGACCTCACATC--GATGCCA
* * * * * * * * *
42575261 ATGCCATGTCCCAAATATGGTCTTACATG-GGATCTCATTTTGAATGCCAATGCCATGTCCCAGA
1 ATGCCATATCCCAGATACGGTCTTATACGAAG-TCTCATATCG-ATGCCGATGCCATGTCCCAGA
42575325 CATGGTCTTA
64 CATGGTCTTA
42575335 CACGGGATCT
Statistics
Matches: 199, Mismatches: 47, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
88 5 0.03
89 2 0.01
90 56 0.28
91 4 0.02
95 4 0.02
96 99 0.50
97 29 0.15
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (96 bp):
ATGCCATATCCCAGATACGGTCTTATACGAAGTCTCATATCGATGCCGATGCCATGTCCCAGACA
TGGTCTTATACAAGACCTCACATCGATGCCA
Found at i:42575209 original size:42 final size:42
Alignment explanation
Indices: 42575121--42575211 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
42575111 ATACTGATGT
* * * *
42575121 CGATTCCATGTCCCAGACATGGTCTTATACAAGATCTCGTAT
1 CGATGCCATGTCCCAGACATGGTCTTACACAAGATCACGTAA
* *
42575163 CGATGCCATGTCCCATACATGGTCTTACACGAA-ATCACTTAA
1 CGATGCCATGTCCCAGACATGGTCTTACAC-AAGATCACGTAA
42575205 CGATGCC
1 CGATGCC
42575212 GAAGCCATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (42 bp):
CGATGCCATGTCCCAGACATGGTCTTACACAAGATCACGTAA
Found at i:42575267 original size:186 final size:186
Alignment explanation
Indices: 42574974--42575334 Score: 458
Period size: 186 Copynumber: 1.9 Consensus size: 186
42574964 TGGGACCACA
* * * * * * * *
42574974 TATCGATGCCATATCCCAGATATGGTGTTATACGAAGTCTCATATCGATGCCGATGCCATGTCCT
1 TATCGATGCCATATCCCAGACATGGTCTTACACGAAATCACATAACGATGCCGAAGCCATATCCT
* *
42575039 AGACATGGTCTTATACAGGACCTCACATTGATGCCAATGCCATATCCCAGATACGGTCTTACTTG
66 AGACATGGTCTTATACAGGA-CTCACATTGATGCCAATGCCATATCCCAAATACGGTCTTACATG
* * *
42575104 GGATCTCATACTG-ATGTCGATTCCATGTCCCAGACATGGTCTTATACAAGATCTCG
130 GGATCTCATACTGAATGCCAATGCCATGTCCCAGACATGGTCTTATACAAGATCTCG
* * *
42575160 TATCGATGCCATGTCCCATACATGGTCTTACACGAAATCACTTAACGATGCCGAAGCCATATCCC
1 TATCGATGCCATATCCCAGACATGGTCTTACACGAAATCACATAACGATGCCGAAGCCATAT-CC
* ** * *
42575225 T-GATATGGTCTTATACAGGA-TCACATCTAGATGCGGATGCCATGTCCCAAATATGGTCTTACA
65 TAGACATGGTCTTATACAGGACTCACAT-T-GATGCCAATGCCATATCCCAAATACGGTCTTACA
**
42575288 TGGGATCTCATTTTGAATGCCAATGCCATGTCCCAGACATGGTCTTA
128 TGGGATCTCATACTGAATGCCAATGCCATGTCCCAGACATGGTCTTA
42575335 CACGGGATCT
Statistics
Matches: 148, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
184 6 0.04
185 1 0.01
186 110 0.74
187 31 0.21
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (186 bp):
TATCGATGCCATATCCCAGACATGGTCTTACACGAAATCACATAACGATGCCGAAGCCATATCCT
AGACATGGTCTTATACAGGACTCACATTGATGCCAATGCCATATCCCAAATACGGTCTTACATGG
GATCTCATACTGAATGCCAATGCCATGTCCCAGACATGGTCTTATACAAGATCTCG
Found at i:42577590 original size:43 final size:43
Alignment explanation
Indices: 42577527--42577658 Score: 112
Period size: 43 Copynumber: 3.1 Consensus size: 43
42577517 ACATAGGATT
* *
42577527 TCGATATGTGTTCTCATGTAAGACCACGTCT-GGAACGTTGGCA
1 TCGATATGTGAT-TCGTGTAAGACCACGTCTAGGAACGTTGGCA
* * *
42577570 TCGATATGTGATTACGTGTAAGACCATGTCTAGG-ACATCGGCA
1 TCGATATGTGATT-CGTGTAAGACCACGTCTAGGAACGTTGGCA
* * * * *
42577613 TTG-TTTTTGATTCGTGTAAGACC-CTGTCTGGGAAAG-TGGCA
1 TCGATATGTGATTCGTGTAAGACCAC-GTCTAGGAACGTTGGCA
42577654 TCGAT
1 TCGAT
42577659 TTATCGATAT
Statistics
Matches: 70, Mismatches: 14, Indels: 11
0.74 0.15 0.12
Matches are distributed among these distances:
41 23 0.33
42 10 0.14
43 35 0.50
44 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
TCGATATGTGATTCGTGTAAGACCACGTCTAGGAACGTTGGCA
Found at i:42577797 original size:92 final size:92
Alignment explanation
Indices: 42577573--42577789 Score: 310
Period size: 92 Copynumber: 2.4 Consensus size: 92
42577563 GTTGGCATCG
** * *
42577573 ATATGTGATTACGTGTAAGACCATGTCTAGGACATCGGCATTGTTTTTGATTCGTGTAAGACCCT
1 ATATGTGATTACGTGTAAGACCATGTCTAGGACATCGGCATCATATTTGATTCATGTAAGACCCT
* *
42577638 GTCTGGGAAAGTGGCATCGATTTATCG
66 GTCTGGGAAAGTGGCATCAATTTATCA
*
42577665 ATATGTGATTACGTCTAAGACCATGT-TCAGGACATCGGCATCATATTTGATTCATGTAAGACCC
1 ATATGTGATTACGTGTAAGACCATGTCT-AGGACATCGGCATCATATTTGATTCATGTAAGACCC
*
42577729 TGTCTGGGACAGTGGCATCAATTTATCA
65 TGTCTGGGAAAGTGGCATCAATTTATCA
* * **
42577757 ATATGTGATTGCATGTAAGACCACCTCTAGGAC
1 ATATGTGATTACGTGTAAGACCATGTCTAGGAC
42577790 GTTGGCATTG
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
91 1 0.01
92 108 0.98
93 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (92 bp):
ATATGTGATTACGTGTAAGACCATGTCTAGGACATCGGCATCATATTTGATTCATGTAAGACCCT
GTCTGGGAAAGTGGCATCAATTTATCA
Found at i:42578541 original size:17 final size:19
Alignment explanation
Indices: 42578519--42578565 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
42578509 CATGTTTACA
42578519 TGGTTGAATA-AATGA-TG
1 TGGTTGAATATAATGATTG
*
42578536 TGGTTG-ATATATTGATTG
1 TGGTTGAATATAATGATTG
42578554 TGGTTGACATAT
1 TGGTTGA-ATAT
42578566 TCGGAAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.12
17 10 0.40
18 8 0.32
20 4 0.16
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.43
Consensus pattern (19 bp):
TGGTTGAATATAATGATTG
Found at i:42579412 original size:39 final size:39
Alignment explanation
Indices: 42579358--42579437 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
42579348 CATGAGTATG
42579358 ATTGTGATATCCAGAAAGCTGTGTCTCATCTGGTAATAC
1 ATTGTGATATCCAGAAAGCTGTGTCTCATCTGGTAATAC
42579397 ATTGTGATATCCAGAAAGCTGTGTCTCATCTGGTAATAC
1 ATTGTGATATCCAGAAAGCTGTGTCTCATCTGGTAATAC
42579436 AT
1 AT
42579438 CGTAACCCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (39 bp):
ATTGTGATATCCAGAAAGCTGTGTCTCATCTGGTAATAC
Found at i:42588371 original size:43 final size:42
Alignment explanation
Indices: 42588322--42588438 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 42
42588312 ATGTGTTTTT
*
42588322 GTGTAAGACCACGTCTGGAACATTGGCATCGATATGTGATTAA
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATT-A
* * *
42588365 GTGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATTC
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTA
* *
42588406 GTGTAAGACC-CTGTCTGGGACAGTGGCACCGAT
1 GTGTAAGACCAC-GTCTGGGACATTGGCATCGAT
42588439 TTATCGATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
41 27 0.42
42 9 0.14
43 29 0.45
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTA
Found at i:42588422 original size:41 final size:42
Alignment explanation
Indices: 42588322--42588532 Score: 169
Period size: 41 Copynumber: 4.9 Consensus size: 42
42588312 ATGTGTTTTT
* * *
42588322 GTGTAAGACCAC-GTCTGGAACATTGGCATCGATATGTGATTAA
1 GTGTAAGACC-CTGTCTGGGACATTGGCATCG-TATTTGATTAC
*
42588365 GTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATT-C
1 GTGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTAC
* *
42588406 GTGTAAGACCCTGTCTGGGACAGTGGCACCGATTTATCGATATGTGATTAC
1 GTGTAAGACCCTGTCTGGGACATTGG---C-----ATCG-TATTTGATTAC
* * * * *
42588457 ATGTAAGACCATGTCTGGGACGTCGACATCGTATTTGATT-C
1 GTGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTAC
* * *
42588498 GTGTAAAACCCTGCCTGGGACAGTGGCATCG-ATTT
1 GTGTAAGACCCTGTCTGGGACATTGGCATCGTATTT
42588533 ATCAATATGT
Statistics
Matches: 135, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
40 4 0.03
41 48 0.36
42 16 0.12
43 32 0.24
44 1 0.01
48 1 0.01
49 4 0.03
50 8 0.06
51 21 0.16
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTAC
Found at i:42588423 original size:84 final size:84
Alignment explanation
Indices: 42588322--42588530 Score: 251
Period size: 92 Copynumber: 2.4 Consensus size: 84
42588312 ATGTGTTTTT
* *
42588322 GTGTAAGACCAC-GTCTGGAACATTGGCATCGATATGTGATTA-AGTGTAAGACCATGTCTGGGA
1 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTACA-TGTAAGACCATGTCTGGGA
* *
42588385 CATTGGCATCGTATTTGATTC
64 CATCGACATCGTATTTGATTC
42588406 GTGTAAGACCCTGTCTGGGACAGTGGCACCGATTTATCGATATGTGATTACATGTAAGACCATGT
1 GTGTAAGACCCTGTCTGGGACAGTGG---C-----ATCGATATGTGATTACATGTAAGACCATGT
*
42588471 CTGGGACGTCGACATCGTATTTGATTC
58 CTGGGACATCGACATCGTATTTGATTC
* *
42588498 GTGTAAAACCCTGCCTGGGACAGTGGCATCGAT
1 GTGTAAGACCCTGTCTGGGACAGTGGCATCGAT
42588531 TTATCAATAT
Statistics
Matches: 108, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
83 1 0.01
84 28 0.26
87 1 0.01
89 1 0.01
92 76 0.70
93 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (84 bp):
GTGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATTACATGTAAGACCATGTCTGGGACA
TCGACATCGTATTTGATTC
Found at i:42588475 original size:51 final size:49
Alignment explanation
Indices: 42588392--42588569 Score: 149
Period size: 51 Copynumber: 3.7 Consensus size: 49
42588382 GGACATTGGC
* * *
42588392 ATCG-TATTTGATTCGTGTAAGACCCTGTCTGGGACAGTGGCACCGATTT
1 ATCGATATGTGATTCATGTAAGACCATGTCTGGGACAGTGGCA-CGATTT
*
42588441 ATCGATATGTGATTACATGTAAGACCATGTCTGGGAC-GT----CGA--C
1 ATCGATATGTGATT-CATGTAAGACCATGTCTGGGACAGTGGCACGATTT
* * * * *
42588484 ATCG-TATTTGATTCGTGTAAAACCCTGCCTGGGACAGTGGCATCGATTT
1 ATCGATATGTGATTCATGTAAGACCATGTCTGGGACAGTGGCA-CGATTT
* * *
42588533 ATCAATATGTGATTGCATGTAAGACCACGTCTAGGAC
1 ATCGATATGTGATT-CATGTAAGACCATGTCTGGGAC
42588570 GTTGGCATTG
Statistics
Matches: 99, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
41 18 0.18
42 10 0.10
43 4 0.04
45 3 0.03
47 3 0.03
49 7 0.07
50 18 0.18
51 36 0.36
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (49 bp):
ATCGATATGTGATTCATGTAAGACCATGTCTGGGACAGTGGCACGATTT
Found at i:42588509 original size:92 final size:92
Alignment explanation
Indices: 42588349--42588571 Score: 340
Period size: 92 Copynumber: 2.4 Consensus size: 92
42588339 GAACATTGGC
* * * *
42588349 ATCGATATGTGATTA-AGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTCGTGTAAG
1 ATCGATATGTGATTACA-TGTAAGACCATGTCTGGGACGTCGACATCGTATTTGATTCGTGTAAA
*
42588413 ACCCTGTCTGGGACAGTGGCACCGATTT
65 ACCCTGCCTGGGACAGTGGCACCGATTT
42588441 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACGTCGACATCGTATTTGATTCGTGTAAAA
1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACGTCGACATCGTATTTGATTCGTGTAAAA
*
42588506 CCCTGCCTGGGACAGTGGCATCGATTT
66 CCCTGCCTGGGACAGTGGCACCGATTT
* * * *
42588533 ATCAATATGTGATTGCATGTAAGACCACGTCTAGGACGT
1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACGT
42588572 TGGCATTGTA
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
92 119 0.99
93 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (92 bp):
ATCGATATGTGATTACATGTAAGACCATGTCTGGGACGTCGACATCGTATTTGATTCGTGTAAAA
CCCTGCCTGGGACAGTGGCACCGATTT
Found at i:42589320 original size:17 final size:18
Alignment explanation
Indices: 42589298--42589339 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
42589288 CATGTTTACA
42589298 TGGTTGAGTA-AATGA-TG
1 TGGTTGA-TATAATGATTG
*
42589315 TGGTTGATATATTGATTG
1 TGGTTGATATAATGATTG
42589333 TGGTTGA
1 TGGTTGA
42589340 CATATTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (18 bp):
TGGTTGATATAATGATTG
Found at i:42602192 original size:27 final size:27
Alignment explanation
Indices: 42602145--42602354 Score: 221
Period size: 27 Copynumber: 7.9 Consensus size: 27
42602135 ATTGGTTTAC
* * *
42602145 AAAATTA-CTAAATACCCTCGATTAGA
1 AAAATTACCAAAATACCCTCGATTTGT
* * *
42602171 AAAATTACTAAAATACCCTCGATTAGC
1 AAAATTACCAAAATACCCTCGATTTGT
*
42602198 AAAATTACCAAAATACCCAT-GGTTTGT
1 AAAATTACCAAAATACCC-TCGATTTGT
* * *
42602225 AAAATTACAAAAATACCCCCGATTTGC
1 AAAATTACCAAAATACCCTCGATTTGT
42602252 AAAATTACCAAAATA-CCTCCGATTTGT
1 AAAATTACCAAAATACCCT-CGATTTGT
*
42602279 AAAATTACCAAAATA-CCTCAATTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
** * *
42602305 AAAATTACTGAAATACCCTCAACTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* *
42602332 AAAATTACCAAAGTACCCCCGAT
1 AAAATTACCAAAATACCCTCGAT
42602355 CTACAGAATT
Statistics
Matches: 155, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
26 29 0.19
27 125 0.81
28 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATTTGT
Found at i:42602340 original size:80 final size:77
Alignment explanation
Indices: 42602145--42602367 Score: 234
Period size: 80 Copynumber: 2.8 Consensus size: 77
42602135 ATTGGTTTAC
*
42602145 AAAATTACTAAATACCCTCGATTAGAAAAATTACTAAAATACCCTCGATTAGCAAAATTACCAAA
1 AAAATTACTAAATACCCTCGATT-GAAAAATTACCAAAATACCC-CGATTAGCAAAATTACCAAA
*
42602210 ATACCCATGGTTTGT
64 ATACCCA-GATTTGT
* * * * *
42602225 AAAATTACAAAAATACCCCCGATTTGCAAAATTACCAAAATACCTCCGATTTGTAAAATTACCAA
1 AAAATTAC-TAAATACCCTCGA-TTGAAAAATTACCAAAATACC-CCGATTAGCAAAATTACCAA
42602290 AATACCTCA-ATTTGT
63 AATACC-CAGATTTGT
* * * *
42602305 AAAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGATCTA-CAGAATTACC
1 AAAATTACT-AAATACCCTCGA-TTGAAAAATTACCAAAATA-CCCCGAT-TAGCAAAATTACC
42602368 GTTTTACCTT
Statistics
Matches: 120, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
80 61 0.51
81 54 0.45
82 5 0.04
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (77 bp):
AAAATTACTAAATACCCTCGATTGAAAAATTACCAAAATACCCCGATTAGCAAAATTACCAAAAT
ACCCAGATTTGT
Found at i:42602376 original size:80 final size:81
Alignment explanation
Indices: 42602145--42602404 Score: 208
Period size: 81 Copynumber: 3.2 Consensus size: 81
42602135 ATTGGTTTAC
* * * * *
42602145 AAAATTACT-AAATACCCTCGA-TTAGAAAAATTACTAAAATACCCTCGAT-TAGCAAAATTACC
1 AAAATTACTAAAATACCCCCAACTT-GCAAAATTACCAAAATACCCCCGATCTA-CAAAATTACC
*
42602207 AAAATACC--CATGGTTTGT
64 AAAATACCTTCA--ATTTGT
* * * * * **
42602225 AAAATTACAAAAATACCCCCGATTTGCAAAATTACCAAAATACCTCCGATTTGTAAAATTACCAA
1 AAAATTACTAAAATACCCCCAACTTGCAAAATTACCAAAATACCCCCGATCTACAAAATTACCAA
42602290 AATACC-TCAATTTGT
66 AATACCTTCAATTTGT
* * * * * **
42602305 AAAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGATCTACAGAATTACCGT
1 AAAATTACTAAAATACCCCCAACTTGCAAAATTACCAAAATACCCCCGATCTACAAAATTACCAA
** * **
42602370 TTTACCTTCGATTTAC
66 AATACCTTCAATTTGT
*
42602386 AAAATTATTAAAATACCCC
1 AAAATTACTAAAATACCCC
42602405 TGTAGGGTAG
Statistics
Matches: 144, Mismatches: 31, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
80 68 0.47
81 71 0.49
82 5 0.03
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (81 bp):
AAAATTACTAAAATACCCCCAACTTGCAAAATTACCAAAATACCCCCGATCTACAAAATTACCAA
AATACCTTCAATTTGT
Found at i:42602418 original size:27 final size:27
Alignment explanation
Indices: 42602388--42602446 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
42602378 CGATTTACAA
42602388 AATTATTAAAATACCCCTGTAGGGTAG
1 AATTATTAAAATACCCCTGTAGGGTAG
* *
42602415 AATTATTGAAATACCCCTGTAGTGTAG
1 AATTATTAAAATACCCCTGTAGGGTAG
42602442 AATTA
1 AATTA
42602447 CTGTGATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (27 bp):
AATTATTAAAATACCCCTGTAGGGTAG
Found at i:42603122 original size:6 final size:6
Alignment explanation
Indices: 42603113--42603222 Score: 73
Period size: 6 Copynumber: 17.8 Consensus size: 6
42603103 TTGCATTCAC
* * * *
42603113 ATTCTG ATTCTG ATTTTG -TTACCTG ATACTG ATTCTG ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * *
42603163 ATTCTG ATTCTG ATTTTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTC
1 ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG
*
42603212 ATTTTG ATTCT
1 ATTCTG ATTCT
42603223 AGTTCTAATA
Statistics
Matches: 79, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
5 4 0.05
6 65 0.82
7 7 0.09
8 3 0.04
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:42603148 original size:31 final size:31
Alignment explanation
Indices: 42603113--42603217 Score: 114
Period size: 31 Copynumber: 3.6 Consensus size: 31
42603103 TTGCATTCAC
*
42603113 ATTCTGATTCTGATTTTGTTACCTGA---T-
1 ATTCTGATTCTGATTTTGTCACCTGATTCTG
* *
42603140 A--CTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTTTGTCACCTGATTCTG
* *
42603169 ATTCTGATTTTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTTTGTCACCTGATTCTG
*
42603200 ATTCTGATTCTCATTTTG
1 ATTCTGATTCTGATTTTG
42603218 ATTCTAGTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
25 20 0.31
27 1 0.02
28 1 0.02
29 1 0.02
31 41 0.64
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTTTGTCACCTGATTCTG
Found at i:42603168 original size:19 final size:18
Alignment explanation
Indices: 42603144--42603205 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
42603134 CCTGATACTG
42603144 ATTCTGATTCTGTCACCT
1 ATTCTGATTCTGTCACCT
42603162 AATTCTGATTCTG--A--T
1 -ATTCTGATTCTGTCACCT
42603177 -TT-TGATTCTGTCACCT
1 ATTCTGATTCTGTCACCT
42603193 GATTCTGATTCTG
1 -ATTCTGATTCTG
42603206 ATTCTCATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
12 8 0.22
13 2 0.06
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 2 0.06
19 20 0.56
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (18 bp):
ATTCTGATTCTGTCACCT
Found at i:42603194 original size:25 final size:25
Alignment explanation
Indices: 42603113--42603210 Score: 106
Period size: 25 Copynumber: 3.7 Consensus size: 25
42603103 TTGCATTCAC
* *
42603113 ATTCTGATTCTGATTTTGTTACCTG
1 ATTCTGATTCTGATTCTGTCACCTG
*
42603138 ATACTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTCA-C-----CTG
*
42603169 ATTCTGATTTTGATTCTGTCACCTG
1 ATTCTGATTCTGATTCTGTCACCTG
42603194 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
42603211 CATTTTGATT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
25 37 0.61
26 1 0.02
30 1 0.02
31 22 0.36
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.48
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTCACCTG
Found at i:42610443 original size:43 final size:42
Alignment explanation
Indices: 42610396--42610496 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 42
42610386 ATGCAACTAT
* * *
42610396 CCCAGACAGGGTCTTAAACAAAATCA-TATAGCAATGGCAATG
1 CCCAGACATGGTCTTAAACAAAATCACAATA-CAATGCCAATG
* **
42610438 CCCCAGACATGGTCTTACACGTAATCACAATACAATGCCAATG
1 -CCCAGACATGGTCTTAAACAAAATCACAATACAATGCCAATG
42610481 CCCAGACATGGTCTTA
1 CCCAGACATGGTCTTA
42610497 CATGTAATCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 16 0.31
43 32 0.63
44 3 0.06
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.21
Consensus pattern (42 bp):
CCCAGACATGGTCTTAAACAAAATCACAATACAATGCCAATG
Found at i:42613677 original size:27 final size:27
Alignment explanation
Indices: 42613626--42613677 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
42613616 CATCTCATAT
* *
42613626 TGATTCTGTACTGGGCTTAGGCCCACC
1 TGATTCTGTAATGGGCTTAGACCCACC
42613653 TGATTCTGTTAATGGGC-TAGACCCA
1 TGATTCTG-TAATGGGCTTAGACCCA
42613678 ACTGTTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (27 bp):
TGATTCTGTAATGGGCTTAGACCCACC
Found at i:42619787 original size:10 final size:11
Alignment explanation
Indices: 42619760--42619792 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
42619750 ACCCAACCCA
42619760 TGCATATCATG
1 TGCATATCATG
42619771 TGCATATCATG
1 TGCATATCATG
42619782 -GCATATCATG
1 TGCATATCATG
42619792 T
1 T
42619793 ACAAAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (11 bp):
TGCATATCATG
Found at i:42619860 original size:25 final size:25
Alignment explanation
Indices: 42619832--42619882 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
42619822 ATAACATAAC
* * * *
42619832 CCTAGGGGTATAATGGTCATTTTCA
1 CCTAGGGGCAAAAAGGTCACTTTCA
42619857 CCTAGGGGCAAAAAGGTCACTTTCA
1 CCTAGGGGCAAAAAGGTCACTTTCA
42619882 C
1 C
42619883 ATTATGAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (25 bp):
CCTAGGGGCAAAAAGGTCACTTTCA
Found at i:42626388 original size:10 final size:10
Alignment explanation
Indices: 42626375--42626413 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
42626365 ATATGTGAAT
42626375 ATATCATGGC
1 ATATCATGGC
42626385 ATATCATGTGC
1 ATATCATG-GC
42626396 ATATCATGGC
1 ATATCATGGC
42626406 ATATCATG
1 ATATCATG
42626414 TACAAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:42626401 original size:21 final size:21
Alignment explanation
Indices: 42626375--42626414 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
42626365 ATATGTGAAT
42626375 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
42626396 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
42626415 ACAAAAGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:42633804 original size:26 final size:26
Alignment explanation
Indices: 42633745--42633796 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
42633735 TAAAATTGAT
* *
42633745 AAATGACTGTTATGCCCTATGAGGTA
1 AAATGACTATTATGCCCTATGAGATA
42633771 AAATGACTATTATGCCCTTATGAGAT
1 AAATGACTATTATGCCC-TATGAGAT
42633797 GTATGACTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (26 bp):
AAATGACTATTATGCCCTATGAGATA
Found at i:42635419 original size:44 final size:43
Alignment explanation
Indices: 42635352--42635523 Score: 165
Period size: 43 Copynumber: 4.0 Consensus size: 43
42635342 GCATAGGATT
* * *
42635352 TCGATATGTGATTTCGTGTAAGACCACGTCTAGGACATTGGCA
1 TCGATATTTGATTTCATGTAAGACCACATCTAGGACATTGGCA
* ** * * *
42635395 TCGAT-TTTAGATTTACGTGTAAGACCATGTCTGGGACATCGACA
1 TCGATATTT-GATTT-CATGTAAGACCACATCTAGGACATTGGCA
*
42635439 TC-ATATTTGATTTCATGTAAGACC-CTATCT-GGTACAATGGCA
1 TCGATATTTGATTTCATGTAAGACCAC-ATCTAGG-ACATTGGCA
* *
42635481 TCGATATTTGATTACATGTAAGACCACATCTAGGA-GTTGGCA
1 TCGATATTTGATTTCATGTAAGACCACATCTAGGACATTGGCA
42635523 T
1 T
42635524 TGTACGAGTT
Statistics
Matches: 107, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
41 2 0.02
42 29 0.27
43 43 0.40
44 33 0.31
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (43 bp):
TCGATATTTGATTTCATGTAAGACCACATCTAGGACATTGGCA
Found at i:42636273 original size:23 final size:23
Alignment explanation
Indices: 42636242--42636285 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42636232 TTATGAAACA
* *
42636242 TATGTTTTGGTATGACTTTGGCT
1 TATGATTTGGCATGACTTTGGCT
*
42636265 TATGATTTGGCATGATTTTGG
1 TATGATTTGGCATGACTTTGG
42636286 TATGGATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.07, G:0.27, T:0.50
Consensus pattern (23 bp):
TATGATTTGGCATGACTTTGGCT
Found at i:42642893 original size:301 final size:301
Alignment explanation
Indices: 42642346--42642943 Score: 1124
Period size: 301 Copynumber: 2.0 Consensus size: 301
42642336 TTAGGCTATT
*
42642346 TTCCAAGCCTTTAAGTTACCCTTAATCCTTCACATCTTTATTTCCATAGTACACATTTAATTCAT
1 TTCCAAGCCTTTAACTTACCCTTAATCCTTCACATCTTTATTTCCATAGTACACATTTAATTCAT
*
42642411 GGCCATGACAATTTAGATTGGTCATAAAACATTCATCATGCACATATTTCATAACACCAACCATA
66 GGCCATGACAATGTAGATTGGTCATAAAACATTCATCATGCACATATTTCATAACACCAACCATA
*
42642476 TATGGCCAACAAACATAATCACATCACAAGCATTAGAACATAGCATAGATATATAGGTTCACAAA
131 TATGGCCAACAAACATAATCACATCACAAGCATTAGAACATAGCATAGATAGATAGGTTCACAAA
42642541 CCATAATCAATGTGAGCCACCCTTCATGGCCATATACAAATAACACAATATAGGCCAATACATTT
196 CCATAATCAATGTGAGCCACCCTTCATGGCCATATACAAATAACACAATATAGGCCAATACATTT
*
42642606 GGTTAGTCATGTTAACACATATCATAAGAAAAAAAAATTCC
261 GGCTAGTCATGTTAACACATATCATAAGAAAAAAAAATTCC
*
42642647 TTCCAAGCCTTTAACTTACCCTTAATCCTTTACATCTTTATTTCCATAGTACACATTTAATTCAT
1 TTCCAAGCCTTTAACTTACCCTTAATCCTTCACATCTTTATTTCCATAGTACACATTTAATTCAT
42642712 GGCCATGACAATGTAGATTGGTCATAAAACATTCATCATGCACATATTTCATAACACCAACCATA
66 GGCCATGACAATGTAGATTGGTCATAAAACATTCATCATGCACATATTTCATAACACCAACCATA
* *
42642777 TATGGCCAACAAGCGTAATCACATCACAAGCATTAGAACATAGCATAGATAGATAGGTTCACAAA
131 TATGGCCAACAAACATAATCACATCACAAGCATTAGAACATAGCATAGATAGATAGGTTCACAAA
*
42642842 CCATAATCAATGTGAGCCACCCTTCATGGCCATATACAAATAACTCAATATAGGCCAATACATTT
196 CCATAATCAATGTGAGCCACCCTTCATGGCCATATACAAATAACACAATATAGGCCAATACATTT
42642907 GGCTAGTCATGTTAACACATATCATAAGAAAAAAAAA
261 GGCTAGTCATGTTAACACATATCATAAGAAAAAAAAA
42642944 AACAATTCCT
Statistics
Matches: 289, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
301 289 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (301 bp):
TTCCAAGCCTTTAACTTACCCTTAATCCTTCACATCTTTATTTCCATAGTACACATTTAATTCAT
GGCCATGACAATGTAGATTGGTCATAAAACATTCATCATGCACATATTTCATAACACCAACCATA
TATGGCCAACAAACATAATCACATCACAAGCATTAGAACATAGCATAGATAGATAGGTTCACAAA
CCATAATCAATGTGAGCCACCCTTCATGGCCATATACAAATAACACAATATAGGCCAATACATTT
GGCTAGTCATGTTAACACATATCATAAGAAAAAAAAATTCC
Found at i:42643593 original size:47 final size:47
Alignment explanation
Indices: 42643439--42643579 Score: 264
Period size: 47 Copynumber: 3.0 Consensus size: 47
42643429 ATTAGGTGAG
42643439 TTGGTGACCTATTTTGACTATAATGAAAAATAAAATAAGGAGAAAAA
1 TTGGTGACCTATTTTGACTATAATGAAAAATAAAATAAGGAGAAAAA
42643486 TTGGTGACCTATTTTGACTATAATGAAAAATAAAATAAGGAGAAAAA
1 TTGGTGACCTATTTTGACTATAATGAAAAATAAAATAAGGAGAAAAA
* *
42643533 TTGGTGACCTATTTTGACTAGAATAAAAAATAAAATAAGGAGAAAAA
1 TTGGTGACCTATTTTGACTATAATGAAAAATAAAATAAGGAGAAAAA
42643580 GATATCATCT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 92 1.00
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (47 bp):
TTGGTGACCTATTTTGACTATAATGAAAAATAAAATAAGGAGAAAAA
Found at i:42644502 original size:46 final size:44
Alignment explanation
Indices: 42644411--42644522 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 44
42644401 GTCATTTGTA
42644411 TGCTAGTGTAAGACATGTCTGGGACATACATCAGCCTCGGAATG
1 TGCTAGTGTAAGACATGTCTGGGACATACATCAGCCTCGGAATG
*
42644455 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCAG-CT-GTGAGATG
1 T--GCTAGTGTAAGACATGTCTGGGACATACATCAGCCTCG-GA-ATG
*
42644501 TGTTAGTGTAAGACCATGTCTG
1 TGCTAGTGTAAGA-CATGTCTG
42644523 AGATATGGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
44 13 0.21
45 12 0.20
46 36 0.59
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (44 bp):
TGCTAGTGTAAGACATGTCTGGGACATACATCAGCCTCGGAATG
Found at i:42644619 original size:49 final size:48
Alignment explanation
Indices: 42644553--42644682 Score: 147
Period size: 47 Copynumber: 2.7 Consensus size: 48
42644543 GAGATGAGAA
* *
42644553 CCAGTGTAAGACCATGTCCGGGACATGGAGTCGGCCTCGATCTCGAT-AG
1 CCAGTGTAAGACCATGTCTGGGACATGGAGTCGGACTCGA--TCGATGAG
** * * * *
42644602 TTAGTGTAAGACCATGTCTGGGACTTGGAATC-GACTTGATGGATGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGAGTCGGACTCGATCGATGAG
*
42644649 CCAGTGTAAGACCATGTCTGGGACATGGCGTCGG
1 CCAGTGTAAGACCATGTCTGGGACATGGAGTCGG
42644683 TATTATACCC
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
46 4 0.06
47 29 0.44
48 6 0.09
49 27 0.41
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (48 bp):
CCAGTGTAAGACCATGTCTGGGACATGGAGTCGGACTCGATCGATGAG
Found at i:42644672 original size:96 final size:98
Alignment explanation
Indices: 42644502--42644682 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 98
42644492 TGTGAGATGT
* *
42644502 GTTAGTGTAAGACCATGTCTGAGATATGGCATTGCATTGGAGAGATGAGAACCAGTGTAAGACCA
1 GTTAGTGTAAGACCATGTCTGAGATATGGAATCGCATTGGAGAGATGAG-ACCAGTGTAAGACCA
42644567 TGTCCGGGACATGGAGTCGGCCTCGATCTCGATA
65 TGTCCGGGACATGGAGTCGGCCTCGATCTCGATA
*
42644601 GTTAGTGTAAGACCATGTCTGGGACT-TGGAATCG-ACTT-GATG-GATGAG-CCAGTGTAAGAC
1 GTTAGTGTAAGACCATGTCTGAGA-TATGGAATCGCA-TTGGA-GAGATGAGACCAGTGTAAGAC
* *
42644661 CATGTCTGGGACATGGCGTCGG
63 CATGTCCGGGACATGGAGTCGG
42644683 TATTATACCC
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
96 32 0.43
98 9 0.12
99 32 0.43
100 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (98 bp):
GTTAGTGTAAGACCATGTCTGAGATATGGAATCGCATTGGAGAGATGAGACCAGTGTAAGACCAT
GTCCGGGACATGGAGTCGGCCTCGATCTCGATA
Found at i:42652063 original size:45 final size:44
Alignment explanation
Indices: 42651971--42652073 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 44
42651961 AGGTCATTTG
*
42651971 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGGCTCAGAA
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGGCTCAGAA
*
42652015 TGTGAGCCAGTGTAAGACATGTCTGGG-CATGCAT-TGGCT-ATGAGA
1 TGT--GCCAGTGTAAGACATGTCTGGGACATGCATCAGGCTCA-GA-A
42652060 TGTGCCAGTGTAAG
1 TGTGCCAGTGTAAG
42652074 TCCATTCTAG
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
43 12 0.23
44 9 0.17
45 11 0.21
46 21 0.40
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (44 bp):
TGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGGCTCAGAA
Found at i:42652943 original size:13 final size:13
Alignment explanation
Indices: 42652925--42652949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42652915 GGTAGACACA
42652925 TGGCCGTGTGTCT
1 TGGCCGTGTGTCT
42652938 TGGCCGTGTGTC
1 TGGCCGTGTGTC
42652950 CCCTGCACGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.40, T:0.36
Consensus pattern (13 bp):
TGGCCGTGTGTCT
Found at i:42653497 original size:26 final size:26
Alignment explanation
Indices: 42653468--42653520 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
42653458 CTCGGAAGTG
42653468 ATTATATGCATGTGGTTAAGTATGGT
1 ATTATATGCATGTGGTTAAGTATGGT
42653494 ATTATATGCATGTGGTTAAGTATGGT
1 ATTATATGCATGTGGTTAAGTATGGT
42653520 A
1 A
42653521 ATGCCTCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (26 bp):
ATTATATGCATGTGGTTAAGTATGGT
Found at i:42654817 original size:48 final size:50
Alignment explanation
Indices: 42654749--42655018 Score: 179
Period size: 50 Copynumber: 5.5 Consensus size: 50
42654739 GCACCGACGC
* * * *
42654749 CATGTCCTAGACCTGATCTTACACTGGTTCACA-C-ATCAAAGT-C-GATGT
1 CATGTCCTAGACATGGTCTTACACTAGATCACATCTATC--AGTGCTGATGT
* *
42654797 CATGTCCTAGACATGGTCTTACACTAGATCTCATCTATCGGTGCTGATGT
1 CATGTCCTAGACATGGTCTTACACTAGATCACATCTATCAGTGCTGATGT
* * * * *
42654847 CATGTCCCAGACATGGTCTTACA-T---TGA-ATCATATCA-AGCCGATGC
1 CATGTCCTAGACATGGTCTTACACTAGATCACATC-TATCAGTGCTGATGT
* * * * * * *
42654892 CATATCCCAGACATGGTCCTACACTAGCTCTCATATATCGAG-GCTGATGC
1 CATGTCCTAGACATGGTCTTACACTAGATCACATCTATC-AGTGCTGATGT
* * * * *
42654942 CATGTACC-AGACATGGTCTTACACTAGCTCTCCTATATCGAG-GCTGATGC
1 CATGT-CCTAGACATGGTCTTACACTAGATCACATCTATC-AGTGCTGATGT
*
42654992 CATGTCCTAGACATGATCTTACACTAG
1 CATGTCCTAGACATGGTCTTACACTAG
42655019 CCCTCATATA
Statistics
Matches: 185, Mismatches: 23, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
45 30 0.16
46 6 0.03
48 30 0.16
49 10 0.05
50 107 0.58
51 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (50 bp):
CATGTCCTAGACATGGTCTTACACTAGATCACATCTATCAGTGCTGATGT
Found at i:42654859 original size:50 final size:50
Alignment explanation
Indices: 42654792--42655030 Score: 265
Period size: 50 Copynumber: 4.9 Consensus size: 50
42654782 CATCAAAGTC
* * *
42654792 GATGTCATGTCCTAGACATGGTCTTACACTAGATCTCATCTATCG-GTGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGATCTCATATATCGAG-GCT
* * * * *
42654842 GATGTCATGTCCCAGACATGGTCTTACA-TTGA-ATC--ATATC-AAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGATCTCATATATCGAGGCT
* * *
42654887 GATGCCATATCCCAGACATGGTCCTACACTAGCTCTCATATATCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGATCTCATATATCGAGGCT
* * *
42654937 GATGCCATGTACCAGACATGGTCTTACACTAGCTCTCCTATATCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGATCTCATATATCGAGGCT
* * **
42654987 GATGCCATGTCCTAGACATGATCTTACACTAGCCCTCATATATC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGATCTCATATATC
42655031 CCTAGCATCA
Statistics
Matches: 160, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
45 27 0.17
46 6 0.04
47 2 0.01
48 2 0.01
49 8 0.05
50 115 0.72
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (50 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGATCTCATATATCGAGGCT
Found at i:42654915 original size:95 final size:95
Alignment explanation
Indices: 42654791--42654964 Score: 260
Period size: 95 Copynumber: 1.8 Consensus size: 95
42654781 ACATCAAAGT
* * * * * * *
42654791 CGATGTCATGTCCTAGACATGGTCTTACACTAGATCTCATCTATCG-GTGCTGATGTCATGTCCC
1 CGATGCCATATCCCAGACATGGTCCTACACTAGATCTCATATATCGAG-GCTGATGCCATGTACC
42654855 AGACATGGTCTTACATTGAATCATATCAAGC
65 AGACATGGTCTTACATTGAATCATATCAAGC
*
42654886 CGATGCCATATCCCAGACATGGTCCTACACTAGCTCTCATATATCGAGGCTGATGCCATGTACCA
1 CGATGCCATATCCCAGACATGGTCCTACACTAGATCTCATATATCGAGGCTGATGCCATGTACCA
42654951 GACATGGTCTTACA
66 GACATGGTCTTACA
42654965 CTAGCTCTCC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
95 69 0.99
96 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (95 bp):
CGATGCCATATCCCAGACATGGTCCTACACTAGATCTCATATATCGAGGCTGATGCCATGTACCA
GACATGGTCTTACATTGAATCATATCAAGC
Found at i:42657730 original size:15 final size:15
Alignment explanation
Indices: 42657695--42657739 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
42657685 CAAAGATAAC
*
42657695 AAGAAAACCAAG-TA
1 AAGAAATCCAAGATA
42657709 AAGAAATCCAAGATA
1 AAGAAATCCAAGATA
*
42657724 GAGAAATCCCAAGATA
1 AAGAAAT-CCAAGATA
42657740 CGATACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 8 0.30
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAAGATA
Found at i:42660331 original size:54 final size:53
Alignment explanation
Indices: 42660247--42660357 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 53
42660237 AGGAAGTGTC
* *
42660247 CTGGTGGCTATGCCATAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATACCATAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTT
* * *
42660301 CTGGTGGCTCTACCATAATTATCTGTTCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATACCATAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
42660354 CTGG
1 CTGG
42660358 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
53 12 0.23
54 40 0.77
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.39
Consensus pattern (53 bp):
CTGGTGGCTATACCATAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
Found at i:42660354 original size:26 final size:26
Alignment explanation
Indices: 42660247--42660357 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 26
42660237 AGGAAGTGTC
* * *
42660247 CTGGTGGCTATGCCATAATTATCTGAT
1 CTGGTGGCTCTGCCA-CATTATCTGTT
42660274 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
* *
42660301 CTGGTGGCTCTACCATAATTATCTGTT
1 CTGGTGGCTCTGCCA-CATTATCTGTT
* *
42660328 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
42660354 CTGG
1 CTGG
42660358 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 16 0.22
27 55 0.75
28 2 0.03
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.39
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:42664513 original size:95 final size:94
Alignment explanation
Indices: 42664402--42664579 Score: 261
Period size: 95 Copynumber: 1.9 Consensus size: 94
42664392 GTATACCGAG
* * * *
42664402 GCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCTCGTCTA-TAGGTGCCGATGTCATGTC
1 GCCGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATACTA-G-GCCGATGCCATG-C
42664466 CCAA-ACATGGTCTTACACTGACTCATATCAA
63 CCAAGACATGGTCTTACACTGACTCATATCAA
*
42664497 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCTAGGCCGATGCCATGCCC
1 GCCGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATA-CTAGGCCGATGCCATGCCC
42664562 AAGACATGGTCTTACACT
65 AAGACATGGTCTTACACT
42664580 AGCCCACATA
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
94 5 0.07
95 67 0.89
96 1 0.01
97 2 0.03
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (94 bp):
GCCGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATACTAGGCCGATGCCATGCCCA
AGACATGGTCTTACACTGACTCATATCAA
Found at i:42664581 original size:50 final size:50
Alignment explanation
Indices: 42664355--42664593 Score: 251
Period size: 50 Copynumber: 4.9 Consensus size: 50
42664345 CATTAAAGTT
* * * * * *
42664355 GATGCCATGTCCCAGGCATGCTCTTACACTAACTCTCGTATACCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCTAGGCC
* * * *
42664405 GATGCCATATCCCAGACATGGTCTTACACTGGCTCTCGTCTA--TAGGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCTA-G-GCC
* * * *
42664455 GATGTCATGTCCCAAACATGGTCTTACACT-G-ACTC--ATATC-AAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCTAGGCC
42664500 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCTAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCTAGGCC
* *
42664550 GATGCCATG-CCCAAGACATGGTCTTACACTAGCCCACATATATC
1 GATGCCATGTCCC-AGACATGGTCTTACACTAGCTCTCATATATC
42664594 CCTAGCATCA
Statistics
Matches: 160, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
45 31 0.19
46 3 0.02
47 4 0.03
48 4 0.03
49 10 0.06
50 108 0.68
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (50 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATATCTAGGCC
Found at i:42671066 original size:51 final size:51
Alignment explanation
Indices: 42670980--42671086 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 51
42670970 AAGTTAACAA
**
42670980 TAGAAACCACGATTTTAAAAAAGATTGTACTTGAAGGTTTTAAACTATTGT
1 TAGAAACCACGATTTTAAAAAAGAGAGTACTTGAAGGTTTTAAACTATTGT
* * *
42671031 TAGAAACCATGATTTTATAAAAGAGAGTA-TATGAAGGTTTTAAACTTTTGT
1 TAGAAACCACGATTTTAAAAAAGAGAGTACT-TGAAGGTTTTAAACTATTGT
42671082 TAGAA
1 TAGAA
42671087 TAGGTTCGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
50 1 0.02
51 49 0.98
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (51 bp):
TAGAAACCACGATTTTAAAAAAGAGAGTACTTGAAGGTTTTAAACTATTGT
Found at i:42678529 original size:13 final size:13
Alignment explanation
Indices: 42678507--42678540 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
42678497 AGAAAAATAG
42678507 AAAAATAAAAAA-
1 AAAAATAAAAAAT
*
42678519 AATAATAAAAAAT
1 AAAAATAAAAAAT
42678532 AAAAATAAA
1 AAAAATAAA
42678541 GATGAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:42681857 original size:21 final size:21
Alignment explanation
Indices: 42681833--42681909 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
42681823 TTGCACTTTC
*
42681833 GTAGATTCTTCCGATTCCCAA
1 GTAGCTTCTTCCGATTCCCAA
*
42681854 GTAGCTTCTTCCAATTCCCAA
1 GTAGCTTCTTCCGATTCCCAA
*
42681875 GTAG--TCTTCTGATTCCCAA
1 GTAGCTTCTTCCGATTCCCAA
42681894 GTAGCTTCTTCC-ATTC
1 GTAGCTTCTTCCGATTC
42681910 TGTGACGTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.35
20 4 0.08
21 28 0.57
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (21 bp):
GTAGCTTCTTCCGATTCCCAA
Found at i:42685847 original size:47 final size:47
Alignment explanation
Indices: 42685786--42686220 Score: 677
Period size: 47 Copynumber: 9.4 Consensus size: 47
42685776 CAGCCAAGAC
42685786 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
42685833 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
42685880 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
42685927 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
42685974 AGTGTATATATGTCATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
42686021 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTCAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
42686068 AGTGTATA-ATGTGA-CAGG---GATGGCCGATGTGATG--TGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
42686108 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
42686155 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
42686202 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
42686221 TCCCGAAGGG
Statistics
Matches: 356, Mismatches: 25, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
40 13 0.04
41 6 0.02
42 18 0.05
45 18 0.05
46 6 0.02
47 295 0.83
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:42686395 original size:37 final size:37
Alignment explanation
Indices: 42686339--42686417 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
42686329 CCGAGCTCTA
* *
42686339 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
42686376 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
42686413 AAGAC
1 AAGAC
42686418 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:42690482 original size:40 final size:40
Alignment explanation
Indices: 42690425--42690629 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
42690415 TCGAATGATG
* * * *
42690425 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
* *
42690465 TCCGGACTAAGAT-CCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
**
42690505 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
42690545 ACCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
* * * **
42690585 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
42690625 TCCGG
1 TCCGG
42690630 TTAAATTCCG
Statistics
Matches: 141, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
39 4 0.03
40 129 0.91
41 8 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:42690558 original size:80 final size:82
Alignment explanation
Indices: 42690425--42690610 Score: 281
Period size: 80 Copynumber: 2.3 Consensus size: 82
42690415 TCGAATGATG
*
42690425 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATT
42690489 GGTGCGAGTTACTA-AA
66 GGTGCGAGTTACTATAA
* * * *
42690505 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATT
*
42690569 TGTGCGAGTTACTATAA
66 GGTGCGAGTTACTATAA
*
42690586 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42690611 AACGAGTAGC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
80 87 0.91
81 9 0.09
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATT
GGTGCGAGTTACTATAA
Found at i:42694306 original size:47 final size:44
Alignment explanation
Indices: 42694191--42694313 Score: 133
Period size: 47 Copynumber: 2.7 Consensus size: 44
42694181 CCACTTGTGT
*
42694191 GAGCTAGTGTAAGACATGTCTGGGACATGGATCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGATCAG-C-CATTATGA
* *
42694237 GAGCCAGTGTAAGACCAAGTCTGGGACATGGCATCAG-CATTGA-GA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATGG-ATCAGCCATT-ATGA
42694282 CGAGTGCTAGTGTAAGACATGTCTGGGACATG
1 -GA--GCTAGTGTAAGACATGTCTGGGACATG
42694314 CTTCAGCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
45 6 0.09
46 16 0.24
47 29 0.44
48 15 0.23
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.22
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGGATCAGCCATTATGA
Found at i:42694342 original size:46 final size:46
Alignment explanation
Indices: 42694191--42694363 Score: 161
Period size: 46 Copynumber: 3.7 Consensus size: 46
42694181 CCACTTGTGT
* * * * *
42694191 GAGCTAGTGTAAGACATGTCTGGGACATGGATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GATGA
* * * *
42694237 GAGCCAGTGTAAGACCAAGTCTGGGACATGGCATCAGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGATGA
* * *
42694285 GTGCTAGTGTAAGACATGTCTGGGACATGCTTCAGCCTCGAGATGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATG-A
* **
42694332 -AGCCAGTGTAAGACATGTTTAAGACATGCATC
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATC
42694364 GGCTGCGAGA
Statistics
Matches: 101, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
46 52 0.51
47 27 0.27
48 21 0.21
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATGA
Found at i:42700161 original size:13 final size:13
Alignment explanation
Indices: 42700143--42700177 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
42700133 CCTAGCACAC
42700143 GGGCGTGTGGCAG
1 GGGCGTGTGGCAG
42700156 GGGCGTGTGGCAG
1 GGGCGTGTGGCAG
*
42700169 GGTCGTGTG
1 GGGCGTGTG
42700178 TGCAAGTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.14, G:0.60, T:0.20
Consensus pattern (13 bp):
GGGCGTGTGGCAG
Found at i:42705775 original size:79 final size:80
Alignment explanation
Indices: 42705633--42705815 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
42705623 TACTCGTTCA
* *
42705633 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
42705698 TTAGTAAC-TCGCACC
66 ATAGTAACTTAGCA-C
* **
42705713 AATGCCTTCGGG-CTTAGCCTGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
42705775 ATATGGTCACTTAGCAC
64 ATATAGTAACTTAGCAC
*
42705792 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
42705816 CATTCTTCGA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 4 0.05
79 58 0.66
80 26 0.30
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:42705815 original size:40 final size:40
Alignment explanation
Indices: 42705612--42705815 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
42705602 CGGAATTTAA
** *
42705612 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42705652 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42705692 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42705731 CTGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42705771 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42705811 CCGGA
1 CCGGA
42705816 CATTCTTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42708458 original size:27 final size:26
Alignment explanation
Indices: 42708410--42708469 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
42708400 GCGAGGCTGC
* *
42708410 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCA-AAA
* * *
42708437 CAGATATTGTGGCTAGGCCACCAAAA
1 CAGATATTGTGACGAAGCCACCAAAA
42708463 CAGATAT
1 CAGATAT
42708470 ATATATGGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAAAA
Found at i:42708512 original size:69 final size:67
Alignment explanation
Indices: 42708437--42708576 Score: 172
Period size: 67 Copynumber: 2.1 Consensus size: 67
42708427 TCACCAGATA
* * * *
42708437 CAGATATTGTGGCTAGGCCACCAAAACAGATATATATATGGCGAAGCCACCAGATTGCAGCGAGG
1 CAGATATTGTGACGAAGCCACCAAAACAG--ATATATATGGCGAAGCCACCAGATTGCAGCGAAG
*
42708502 CTGC
64 CAGC
* * * * *
42708506 CAGATATTGTGACGAAGTCACTAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAAGCA
1 CAGATATTGTGACGAAGCCACCAAAACAGATATATATGGCGAAGCCACCAGATTGCAGCGAAGCA
42708571 GC
66 GC
42708573 CAGA
1 CAGA
42708577 ACGCTTCCTC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
67 38 0.62
69 23 0.38
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAAAACAGATATATATGGCGAAGCCACCAGATTGCAGCGAAGCA
GC
Found at i:42712630 original size:69 final size:69
Alignment explanation
Indices: 42712519--42712657 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
42712509 ATCCACCTCC
42712519 TTAACCCTCAACTGATGATACCCAGATTAAAGGTCAATCTTGGAAAGTACTGAAGCTCCTCTAAG
1 TTAACCCTCAACTGATGATACCCAGATTAAAGGTCAATCTTGGAAAGTACTGAAGCTCCTCTAAG
42712584 TTGG
66 TTGG
42712588 TTAACCCTCAACTGATGATACCCAGATTAAAGGTCAATCTTGGAAAGTACTGAAGCTCCTCTAAG
1 TTAACCCTCAACTGATGATACCCAGATTAAAGGTCAATCTTGGAAAGTACTGAAGCTCCTCTAAG
42712653 TTGG
66 TTGG
42712657 T
1 T
42712658 CAAATAAATC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (69 bp):
TTAACCCTCAACTGATGATACCCAGATTAAAGGTCAATCTTGGAAAGTACTGAAGCTCCTCTAAG
TTGG
Found at i:42715447 original size:39 final size:39
Alignment explanation
Indices: 42715350--42715611 Score: 311
Period size: 39 Copynumber: 6.6 Consensus size: 39
42715340 TTGAATGATG
*
42715350 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
42715388 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
*
42715429 TCCGGGCTAAGCCGGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
42715468 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
42715507 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
42715546 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT
* * *
42715585 AACCGGGATATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
42715612 AACGAGGAGC
Statistics
Matches: 200, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
39 130 0.65
40 58 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:42715633 original size:79 final size:79
Alignment explanation
Indices: 42715402--42715644 Score: 255
Period size: 78 Copynumber: 3.1 Consensus size: 79
42715392 GGACTAAGAT
* * * **
42715402 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCGGAAGGCATTTGTGCGAGAT-ACTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGATAAGCCCGAAGGCATTTGAACGAG-TGACTA
* *
42715466 ATTCCGGGCTAAG-C
65 AATCCGGGTTAAGTC
* * ** *
42715480 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGATAAGCCCGAAGGCATTTGAACGAGTGACTAA
42715545 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
*
42715559 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGATATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGATAAG-CCCGAAGGCATTTGAACGAGTGA-
* * *
42715621 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAGTC
42715638 CCGAAGG
1 CCGAAGG
42715645 TACGTGATTT
Statistics
Matches: 147, Mismatches: 12, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
77 1 0.01
78 75 0.51
79 46 0.31
80 25 0.17
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGATAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAGTC
Found at i:42719408 original size:27 final size:26
Alignment explanation
Indices: 42719360--42719411 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42719350 GCAAGGCTGC
*
42719360 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
42719386 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
42719412 TTGCAGCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42722898 original size:22 final size:22
Alignment explanation
Indices: 42722873--42722915 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
42722863 AATTCCATTC
42722873 AATACTTTAATTT-AGACAATTA
1 AATA-TTTAATTTCAGACAATTA
* *
42722895 AATATTTCATTTCATACAATT
1 AATATTTAATTTCAGACAATT
42722916 TTATCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (22 bp):
AATATTTAATTTCAGACAATTA
Found at i:42725090 original size:42 final size:42
Alignment explanation
Indices: 42724929--42725092 Score: 161
Period size: 42 Copynumber: 3.9 Consensus size: 42
42724919 TACCATACCA
* * * *
42724929 ATGCCATATCCCAGATATAGTCTTACA-TAGGATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTCATATCG
* * * *
42724971 ATGCCAATAGCCCAGCTACGGTTTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
* * * * *
42725014 ATGTCATATTCCATATATGGTCTTATACGAAGTCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
*
42725056 ATGCCATATCCCATATATGGTCTTACAC-ATAGTCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGA-AGTCTCA
42725093 GTAACCCTAA
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
41 1 0.01
42 66 0.67
43 30 0.30
44 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:42728685 original size:39 final size:39
Alignment explanation
Indices: 42728632--42728793 Score: 236
Period size: 39 Copynumber: 4.2 Consensus size: 39
42728622 GGACTTTAGC
* * * * *
42728632 CCGGACATATTTCCAGCACGTAGCGTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
* *
42728671 CCGAATATAATTCCAGCACATAGCCTACGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
* *
42728710 CCGGATATATTTCCAGCA-ATAGCCTGCGAACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42728748 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42728787 CCGGATA
1 CCGGATA
42728794 CACATCAAAT
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 35 0.32
39 74 0.68
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:42728765 original size:77 final size:78
Alignment explanation
Indices: 42728632--42728793 Score: 254
Period size: 77 Copynumber: 2.1 Consensus size: 78
42728622 GGACTTTAGC
* * * * *
42728632 CCGGACATATTTCCAGCACGTAGCGTGCGGACCTTAAGTCCGAATATAATTCCAGCACATAGCCT
1 CCGGATATATTTCCAGCACATAGCCTGCGAACCCTAAGTCCGAATATAATTCCAGCACATAGCCT
42728697 ACGGACCCTAAGT
66 ACGGACCCTAAGT
*
42728710 CCGGATATATTTCCAGCA-ATAGCCTGCGAACCCTAAGTCCGGATATAATTCCAGCACATAGCCT
1 CCGGATATATTTCCAGCACATAGCCTGCGAACCCTAAGTCCGAATATAATTCCAGCACATAGCCT
*
42728774 GCGGACCCTAAGT
66 ACGGACCCTAAGT
42728787 CCGGATA
1 CCGGATA
42728794 CACATCAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 60 0.78
78 17 0.22
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (78 bp):
CCGGATATATTTCCAGCACATAGCCTGCGAACCCTAAGTCCGAATATAATTCCAGCACATAGCCT
ACGGACCCTAAGT
Found at i:42730807 original size:18 final size:18
Alignment explanation
Indices: 42730784--42730821 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42730774 AGAAGAAAGA
42730784 TGAGCATTCTTTAAATTT
1 TGAGCATTCTTTAAATTT
42730802 TGAGCATTCTTTAAATTT
1 TGAGCATTCTTTAAATTT
42730820 TG
1 TG
42730822 TTTTCTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (18 bp):
TGAGCATTCTTTAAATTT
Found at i:42733722 original size:47 final size:47
Alignment explanation
Indices: 42733652--42733875 Score: 203
Period size: 46 Copynumber: 4.8 Consensus size: 47
42733642 CAGCCACATT
* * *
42733652 ATGAGAGCCAATGTAATACCATGTCTGGGACATGGAATCGGCATTGAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAA
* * * * *
42733700 ACGAGAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTCGAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTTGAA
*
42733746 ATGTA-AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGC-T-ACA
1 ATG-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGA-A
* ** * *
42733790 A-GATGTGTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAC
1 ATGA-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAA
* *
42733837 ATGTGAGCCAGTGTAAGACCATGTCCGGGACATGGCATC
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
42733876 AGCATTATAC
Statistics
Matches: 141, Mismatches: 25, Indels: 21
0.75 0.13 0.11
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 11 0.08
45 15 0.11
46 48 0.34
47 48 0.34
48 16 0.11
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (47 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAA
Found at i:42733846 original size:91 final size:92
Alignment explanation
Indices: 42733708--42733878 Score: 249
Period size: 91 Copynumber: 1.9 Consensus size: 92
42733698 AAACGAGAGC
* * *
42733708 TAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATGTAAGCCAGTGTAAGA-CATGTCTG
1 TAGTGTAAGACATGTCTAGGACATGCATCGGACTCGACATGTAAGCCAGTGTAAGACCATGTCCG
42733772 GGACAT-GCATCAGCTACAAGATGTGT
66 GGACATGGCATCAGCTACAAGATGTGT
* * *
42733798 TAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGACATGTGAGCCAGTGTAAGACCATGTC
1 TAGTGTAAGA-CATGTCTAGGACAT-GCATCGGACTCGACATGTAAGCCAGTGTAAGACCATGTC
42733862 CGGGACATGGCATCAGC
64 CGGGACATGGCATCAGC
42733879 ATTATACCCC
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
90 10 0.14
91 35 0.49
92 18 0.25
93 8 0.11
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (92 bp):
TAGTGTAAGACATGTCTAGGACATGCATCGGACTCGACATGTAAGCCAGTGTAAGACCATGTCCG
GGACATGGCATCAGCTACAAGATGTGT
Found at i:42736138 original size:42 final size:42
Alignment explanation
Indices: 42736088--42736214 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
42736078 CTTCATTTTC
** * *
42736088 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
* *
42736131 T-GATGCCATAACCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
42736172 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
42736213 TC
1 TC
42736215 TTACTGATGC
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 10 0.14
42 62 0.84
43 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:42736241 original size:46 final size:47
Alignment explanation
Indices: 42736173--42736292 Score: 143
Period size: 47 Copynumber: 2.6 Consensus size: 47
42736163 ATTCATATAT
* * * **
42736173 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTTAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
* * * * *
42736219 TGATGCCATATCTCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
42736266 CGATGCCATATCCCAGATATGGTCTTA
1 CGATGCCATATCCCAGATATGGTCTTA
42736293 TACGGAAATC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
46 25 0.41
47 36 0.59
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
Found at i:42736349 original size:31 final size:31
Alignment explanation
Indices: 42736314--42736462 Score: 192
Period size: 31 Copynumber: 4.8 Consensus size: 31
42736304 CTTGTCACTT
*
42736314 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * *
42736345 GTAGCCGGAGATACCATTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
42736376 GTAGCCGGAA-CTACCACATTTCATTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
**
42736407 GTAGTAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
42736438 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
42736463 TGTCATTTGT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
30 3 0.03
31 94 0.95
32 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:42736548 original size:50 final size:51
Alignment explanation
Indices: 42736438--42736566 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
42736428 CACTGATCAG
* * * *
42736438 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAACT
*
42736489 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAACT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAACT
*
42736539 GTAGGCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
42736567 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 43 0.61
51 27 0.39
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAACT
Found at i:42739501 original size:47 final size:47
Alignment explanation
Indices: 42739438--42739554 Score: 157
Period size: 47 Copynumber: 2.5 Consensus size: 47
42739428 ATCCGATGCG
*
42739438 TGTCCCAGACACGTCTTACACTGGATA-TCATCATCGAGGCCGACG-CA
1 TGTCCCAGACATGTCTTACACTGG-TACTCATC-TCGAGGCCGACGCCA
* * * *
42739485 TGTCCCAAACATGTCTTACACTGGTACTCATCTCTATGCCGATGCCA
1 TGTCCCAGACATGTCTTACACTGGTACTCATCTCGAGGCCGACGCCA
42739532 TGTCCCAGACATGTCTTACACTG
1 TGTCCCAGACATGTCTTACACTG
42739555 ACACACAAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 11 0.18
47 51 0.82
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (47 bp):
TGTCCCAGACATGTCTTACACTGGTACTCATCTCGAGGCCGACGCCA
Found at i:42739544 original size:138 final size:141
Alignment explanation
Indices: 42739298--42739553 Score: 335
Period size: 141 Copynumber: 1.8 Consensus size: 141
42739288 CGATGCCATA
* * *
42739298 TCCCAGACATGGTCTTACACTAGCTAGTATCATCGAGGCCAATGCCATGTCCCAAACATGGTCTT
1 TCCCAGACATCGTCTTACACTAGATAGTATCATCGAGGCCAACGCCATGTCCCAAACATGGTCTT
* * *
42739363 ATACTAGCTCTCGTATATACGTGCTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTT
66 ACACTAGCTCTCATATATAC-TGCCGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTT
42739428 ATCCGATGCGTG
130 ATCCGATGCGTG
* *
42739440 TCCCAGACA-CGTCTTACACTGGATA-TCATCATCGAGGCCGACG-CATGTCCCAAACAT-GTCT
1 TCCCAGACATCGTCTTACACTAGATAGT-ATCATCGAGGCCAACGCCATGTCCCAAACATGGTCT
* * *
42739501 TACACT-GGTACTCATCTCTA-TGCCGATGCCATGTCCCAGACATGTCTTACACT
65 TACACTAGCT-CTCATATATACTGCCGATG-CATGTCCCAGACATGTCTTACACT
42739554 GACACACAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
137 7 0.07
138 26 0.26
139 16 0.16
140 15 0.15
141 27 0.27
142 9 0.09
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (141 bp):
TCCCAGACATCGTCTTACACTAGATAGTATCATCGAGGCCAACGCCATGTCCCAAACATGGTCTT
ACACTAGCTCTCATATATACTGCCGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTA
TCCGATGCGTG
Found at i:42753702 original size:38 final size:38
Alignment explanation
Indices: 42753651--42753729 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
42753641 GCGTGTGGTA
42753651 CCACACGGGTAGTCCACACGAACGTGTGGGAATTTGGG
1 CCACACGGGTAGTCCACACGAACGTGTGGGAATTTGGG
* *
42753689 CCACACGGGTAGTCTACACGGACGTGTGGGAATTTGGG
1 CCACACGGGTAGTCCACACGAACGTGTGGGAATTTGGG
42753727 CCA
1 CCA
42753730 GGCCATGTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.24, G:0.34, T:0.19
Consensus pattern (38 bp):
CCACACGGGTAGTCCACACGAACGTGTGGGAATTTGGG
Found at i:42754576 original size:42 final size:42
Alignment explanation
Indices: 42754464--42754612 Score: 165
Period size: 42 Copynumber: 3.5 Consensus size: 42
42754454 TACCAAAGCC
* *
42754464 ATATCCCAGATATGGTCTCACATG-GGATCTCATATCGATGCCA
1 ATATCCCAGATATGGTCTTACATGAAG-TCTCATATCGATG-CA
* * * *
42754507 ATAGCCCAGTTATGGTCTGACACGAAGTCTCATATCGATGCA
1 ATATCCCAGATATGGTCTTACATGAAGTCTCATATCGATGCA
* ** * * *
42754549 AGATCGTAGATATGGTCTTACATGAAGTCTCATATAGATTCC
1 ATATCCCAGATATGGTCTTACATGAAGTCTCATATCGATGCA
42754591 ATATCCCAGATATGGTCTTACA
1 ATATCCCAGATATGGTCTTACA
42754613 CATAATCTTA
Statistics
Matches: 87, Mismatches: 18, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
42 53 0.61
43 33 0.38
44 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (42 bp):
ATATCCCAGATATGGTCTTACATGAAGTCTCATATCGATGCA
Found at i:42762683 original size:27 final size:26
Alignment explanation
Indices: 42762653--42762829 Score: 167
Period size: 27 Copynumber: 6.5 Consensus size: 26
42762643 AAATTGTGCG
*
42762653 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTA
* *
42762680 GCACTAAGTGTGCGAAATGAATATG-A
1 GCACTAAGTGTGCG-ATTGACTATGTA
* **
42762706 TGCACTAAGTGTGCGAATTGACCATGCG
1 -GCACTAAGTGTGCG-ATTGACTATGTA
42762734 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTA
* * *
42762762 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTA
* *
42762789 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGA-TTGACTATGTA
*
42762816 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
42762830 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTA
Found at i:42762772 original size:82 final size:81
Alignment explanation
Indices: 42762649--42762808 Score: 232
Period size: 82 Copynumber: 2.0 Consensus size: 81
42762639 GATTAAATTG
* * *
42762649 TGCGGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTA
1 TGCGGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTA
42762713 AGTGTGCGAATTGACCA
65 AGTGTGCGAATTGACCA
** *
42762730 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTA
1 TGCGGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTA
*
42762795 AGTGTGCGAGTTGA
65 AGTGTGCGAATTGA
42762809 TTATATAGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
81 22 0.31
82 48 0.69
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
TGCGGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAA
GTGTGCGAATTGACCA
Found at i:42762820 original size:82 final size:81
Alignment explanation
Indices: 42762653--42762829 Score: 212
Period size: 82 Copynumber: 2.2 Consensus size: 81
42762643 AAATTGTGCG
* * *
42762653 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
* *
42762718 GCGAATTGACCATGCG
66 GCGAATTGACCATACA
** *
42762734 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAGT
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGT
* ** *
42762798 GTGCGAGTTGATTATATA
64 GTGCGAATTGACCATACA
*
42762816 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
42762830 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.22
82 63 0.78
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATACA
Found at i:42769096 original size:17 final size:17
Alignment explanation
Indices: 42769076--42769108 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42769066 TAGATTAATG
*
42769076 ATACATATAGATAATAC
1 ATACATAAAGATAATAC
42769093 ATACATAAAGATAATA
1 ATACATAAAGATAATA
42769109 ATATATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (17 bp):
ATACATAAAGATAATAC
Found at i:42769191 original size:25 final size:24
Alignment explanation
Indices: 42769163--42769224 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
42769153 GGATCCTTAA
42769163 AGAAACAAAT-TATATAAGTAAATTT
1 AGAAA-AAATATATATAA-TAAATTT
*
42769188 AGAAGAAAATATATATAATAGATTT
1 AGAA-AAAATATATATAATAAATTT
*
42769213 AAAAAGAAATAT
1 AGAAA-AAATAT
42769225 TTGCATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 1 0.03
25 23 0.72
26 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (24 bp):
AGAAAAAATATATATAATAAATTT
Found at i:42769219 original size:26 final size:25
Alignment explanation
Indices: 42769169--42769221 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
42769159 TTAAAGAAAC
*
42769169 AAATTATATAAGTAAATTTAGAAGA
1 AAATTATATAAGTAAATTTAAAAGA
*
42769194 AAATATATATAA-TAGATTTAAAAAGA
1 AAAT-TATATAAGTAAATTT-AAAAGA
42769220 AA
1 AA
42769222 TATTTGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (25 bp):
AAATTATATAAGTAAATTTAAAAGA
Found at i:42771246 original size:175 final size:174
Alignment explanation
Indices: 42770936--42771297 Score: 419
Period size: 175 Copynumber: 2.1 Consensus size: 174
42770926 GTTTTCTCAA
* * * *
42770936 GGAGATAAGATCTACAATCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACGATTGTCAA
1 GGAGATAAGATCTTCAATCAGTCTACTTCCTTGCTACCTCAGAAAGATAAGACTACAATTGTCAA
* * * *
42771001 TCTACTCTCTTGCTTCCTCAAAAAGATAAAGCTAGTGGCTAAAATCTGCTCCATTGTCGATATAT
66 CCTACTCTCTTGCTACCTCAAAAAGATAAAGCCAGTGGCTAAAATCTGCTCCATTGTCGATACAT
* ** * *
42771066 GGAGATACGATTCGCC-TCTTTCGATCTGCTCCACTACTGCTTTG
131 GGAGATAAGATTAACCATC-TTCAATCTGCTCCACTACTGCTTAG
* *
42771110 GGAGATAAGATCTTCAATCTTCAGTCTACTTTCTTGCTACTTCAGAAAGATAAGACT-CAATCT-
1 GGAGATAAGATCTTCAA---TCAGTCTACTTCCTTGCTACCTCAGAAAGATAAGACTACAAT-TG
** * * * * * *
42771173 TCAACCTGTTCTTTTTCTACCTCAGAGAGATAAGGCCAGTGG-TAAATTCTGCTCCATTGTCGAT
62 TCAACCTACTCTCTTGCTACCTCAAAAAGATAAAGCCAGTGGCTAAAATCTGCTCCATTGTCGAT
*
42771237 ACATGGAGATAAGATTAACCATCTTCAATCTGCTCCCCTACTGCTTAG
127 ACATGGAGATAAGATTAACCATCTTCAATCTGCTCCACTACTGCTTAG
*
42771285 GGATATAA-ATCTT
1 GGAGATAAGATCTT
42771298 GGGGCTTAAA
Statistics
Matches: 158, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
174 21 0.13
175 66 0.42
176 37 0.23
177 34 0.22
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (174 bp):
GGAGATAAGATCTTCAATCAGTCTACTTCCTTGCTACCTCAGAAAGATAAGACTACAATTGTCAA
CCTACTCTCTTGCTACCTCAAAAAGATAAAGCCAGTGGCTAAAATCTGCTCCATTGTCGATACAT
GGAGATAAGATTAACCATCTTCAATCTGCTCCACTACTGCTTAG
Found at i:42771651 original size:89 final size:88
Alignment explanation
Indices: 42771215--42771651 Score: 299
Period size: 89 Copynumber: 4.9 Consensus size: 88
42771205 AGGCCAGTGG
* * *
42771215 TAAATTCTGCTCCATTGTCGATACATGGAGATAAGATTAACCATC-TTCAATCTGCTCCCCTACT
1 TAAA-TCTGCTCCATTCT-GATACATGGAGATAAGATTCACC-TCTTTCAATCTGCTCCGCTACT
*
42771279 GCTTAGGGATATAA-ATCTTGGGGCT
63 GCTTAGGGAGATAAGATCTTGGGGCT
* * * * * * *
42771304 TAAATTTGCTCTATTGTCGATACATGGAGATAGGATTCGCCTCTTTCGATCTTCTCCGCTACTGC
1 TAAATCTGCTCCATTCT-GATACATGGAGATAAGATTCACCTCTTTCAATCTGCTCCGCTACTGC
* ****
42771369 TTAGGGAGGTAAGATCTTCAATCT
65 TTAGGGAGATAAGATCTTGGGGCT
* * * * * *
42771393 TCAGTCTACTTCC-TTGCT-ACCT-CA-GGAAGATAAGACTCA-TTC-TTCAACCTGCTCTCTTG
1 TAAATCTGC-TCCATT-CTGA--TACATGG-AGATAAGATTCACCTCTTTCAATCTGCTC-C--G
* * *
42771452 CTAC--CTCAGAGAGATAAG-GC-TGGTGGCT
58 CTACTGCTTAGGGAGATAAGATCTTGG-GGCT
* * * ** * * **
42771480 TAAATCTACTCCATTGCTGATACATAGAGATAAGATTCGCCAT-TTTTTATCTGCTCCACTGCAA
1 TAAATCTGCTCCATT-CTGATACATGGAGATAAGATTCACC-TCTTTCAATCTGCTCCGCTACTG
*
42771544 CTTCAGGGAAATAA-ATCTTGGGGCT
64 CTT-AGGGAGATAAGATCTTGGGGCT
*
42771569 TAAATCTGCTCCATTACTGATACATGGAGATAAGATTCACCTCTTTCGATCTGCTCCGCTACTGC
1 TAAATCTGCTCCATT-CTGATACATGGAGATAAGATTCACCTCTTTCAATCTGCTCCGCTACTGC
42771634 TTAGGGAGATAAGATCTT
65 TTAGGGAGATAAGATCTT
42771652 TAACATCCAG
Statistics
Matches: 262, Mismatches: 61, Indels: 50
0.70 0.16 0.13
Matches are distributed among these distances:
86 8 0.03
87 38 0.15
88 92 0.35
89 112 0.43
90 12 0.05
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (88 bp):
TAAATCTGCTCCATTCTGATACATGGAGATAAGATTCACCTCTTTCAATCTGCTCCGCTACTGCT
TAGGGAGATAAGATCTTGGGGCT
Found at i:42771672 original size:265 final size:264
Alignment explanation
Indices: 42771037--42771818 Score: 998
Period size: 263 Copynumber: 3.0 Consensus size: 264
42771027 TAAAGCTAGT
* * * *
42771037 GGCTAAAATCTGCTCCATTGTCGATATATGGAGATACGATTCGCCTCTTTCGATCTGCTCCACTA
1 GGCTTAAATCTGCTCCATTGTCGATACATGGAGATAAGATTCGCCTCTTTCGATCTGCTCCGCTA
* * * *
42771102 CTGCTTTGGGAGATAAGATCTTCAATCTTCAGTCTACTTTCTTGCTACTTCAGAAAGATAAGACT
66 CTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACT
* * * * ** *
42771167 CAATCTTCAACCTGTTCTTTTTCTACCTCAGAGAGATAAGGCCAGTGG--TAAATTCTGCTCCAT
131 CATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAA-TCTACTCCAT
* * * ** *
42771230 TG-TCGATACATGGAGATAAGATTAACCATCTTCAATCTGCTCCCCTACTGCTTAGGGATATAAA
195 TGCT-GATACATGGAGATAAGATTAGCCATCTTCAATCTGCTCCACTGCAACTTAGGGAAATAAA
42771294 TCTTGG
259 TCTTGG
* * * *
42771300 GGCTTAAATTTGCTCTATTGTCGATACATGGAGATAGGATTCGCCTCTTTCGATCTTCTCCGCTA
1 GGCTTAAATCTGCTCCATTGTCGATACATGGAGATAAGATTCGCCTCTTTCGATCTGCTCCGCTA
*
42771365 CTGCTTAGGGAGGTAAGATCTTCAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACT
66 CTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACT
42771430 CATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCATT
131 CATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCATT
* * * **
42771495 GCTGATACATAGAGATAAGATTCGCCATTTTTTATCTGCTCCACTGCAACTTCAGGGAAATAAAT
196 GCTGATACATGGAGATAAGATTAGCCATCTTCAATCTGCTCCACTGCAACTT-AGGGAAATAAAT
42771560 CTTGG
260 CTTGG
* *
42771565 GGCTTAAATCTGCTCCATT-ACTGATACATGGAGATAAGATTCACCTCTTTCGATCTGCTCCGCT
1 GGCTTAAATCTGCTCCATTGTC-GATACATGGAGATAAGATTCGCCTCTTTCGATCTGCTCCGCT
* * *
42771629 ACTGCTTAGGGAGATAAGATCTTTAA-CATCCAGTCTGCTTCCTTGCTACCTCA-G--G--AAG-
65 ACTGCTTAGGGAGATAAGATCTTCAATC-TTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGA
* * * *
42771687 ---ATTCTTCAACCTACTCTCTTGTTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCCACTCTA
129 CTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCA
* * * * *
42771749 TTGCTGATACATGGAGATAAGATTTGTCATCTTCGATCTGCTCCATTGCAACTTTAGGGAGATAA
194 TTGCTGATACATGGAGATAAGATTAGCCATCTTCAATCTGCTCCACTGCAAC-TTAGGGAAATAA
42771814 GATCT
258 -ATCT
42771819 GATTTCACCA
Statistics
Matches: 459, Mismatches: 52, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
256 112 0.24
257 6 0.01
260 3 0.01
262 1 0.00
263 160 0.35
264 53 0.12
265 124 0.27
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (264 bp):
GGCTTAAATCTGCTCCATTGTCGATACATGGAGATAAGATTCGCCTCTTTCGATCTGCTCCGCTA
CTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACT
CATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTACTCCATT
GCTGATACATGGAGATAAGATTAGCCATCTTCAATCTGCTCCACTGCAACTTAGGGAAATAAATC
TTGG
Found at i:42779387 original size:39 final size:39
Alignment explanation
Indices: 42779329--42779545 Score: 303
Period size: 39 Copynumber: 5.5 Consensus size: 39
42779319 TAATGGAGAA
*
42779329 TTATATCTGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
42779368 TTATATCTGGGCTATGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
42779407 TTATATCCGGGCTAAGT-CCGAAGGCATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
42779445 TTATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
42779484 TTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
42779523 TTATATCTGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
42779546 CATGCTTTGT
Statistics
Matches: 164, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
38 36 0.22
39 106 0.65
40 22 0.13
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:42779447 original size:77 final size:78
Alignment explanation
Indices: 42779329--42779545 Score: 312
Period size: 77 Copynumber: 2.8 Consensus size: 78
42779319 TAATGGAGAA
* *
42779329 TTATATCTGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCTGGGCTATGTCCCGAAGGC
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCTGGGCTAAGTCCCGAAGGC
42779394 ATTCGTGCTGGTG
66 ATTCGTGCTGGTG
* * *
42779407 TTATATCCGGGCTAAGT-CCGAAGGCATTCGTGCTAGTGTTATATCCGGGTTAAGTCCCGAAGGC
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCTGGGCTAAGTCCCGAAGGC
*
42779471 ATTTGTGCTGGTG
66 ATTCGTGCTGGTG
* * *
42779484 TTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTATTATATCTGGGCTTAAAGTCCCG
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTGTTATATCTGGGC-T-AAGTCCCG
42779546 CATGCTTTGT
Statistics
Matches: 123, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
77 68 0.55
78 39 0.32
79 8 0.07
80 8 0.07
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (78 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCTGGGCTAAGTCCCGAAGGC
ATTCGTGCTGGTG
Found at i:42785880 original size:39 final size:39
Alignment explanation
Indices: 42785826--42786083 Score: 412
Period size: 39 Copynumber: 6.6 Consensus size: 39
42785816 TAATGGAGAA
42785826 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
42785865 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
42785904 TTATATCCGGGCTACGTCCCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
42785943 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGT-
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
42785981 TTATATCCAGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
42786020 TTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
42786059 TTATATCCGGGCTTAAAGTCCCGAA
1 TTATATCCGGGC-T-AAGTCCCGAA
42786084 TGCTTTGTGG
Statistics
Matches: 204, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
38 37 0.18
39 144 0.71
40 23 0.11
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:42788458 original size:100 final size:100
Alignment explanation
Indices: 42788266--42788458 Score: 212
Period size: 100 Copynumber: 1.9 Consensus size: 100
42788256 TTATAGAGAA
*
42788266 TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAAAATGCAAGATCAAATTTAACATCA
1 TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAAAATGCAAGATCAAATATAACATCA
* * *
42788331 CCTAAGTACTTACTCATATGGCTGAATATACAAAT
66 CATAAGTACATACTCATATGGCCGAATATACAAAT
* *** * * * *
42788366 TCAAATATAATATCACTTTTGTGCATACCT-TCATGGTCAAATATTCAAGATTC-AATATAACGT
1 TCAAAGATAATATCACAAATGTGCATACCTAT-ATGGCCAAAAATGCAAGA-TCAAATATAACAT
* *
42788429 CACATATGTACATAC-CTATGTGGCCGAATA
64 CACATAAGTACATACTC-ATATGGCCGAATA
42788459 AATACAAGAT
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
99 2 0.03
100 72 0.95
101 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30
Consensus pattern (100 bp):
TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAAAATGCAAGATCAAATATAACATCA
CATAAGTACATACTCATATGGCCGAATATACAAAT
Found at i:42789218 original size:9 final size:9
Alignment explanation
Indices: 42789204--42789232 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
42789194 CATACTAGTC
42789204 CATTTATTT
1 CATTTATTT
42789213 CATTTATTT
1 CATTTATTT
42789222 CATTTATTT
1 CATTTATTT
42789231 CA
1 CA
42789233 CATTTTAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (9 bp):
CATTTATTT
Found at i:42789619 original size:23 final size:22
Alignment explanation
Indices: 42789593--42789646 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42789583 TTAATTTATG
*
42789593 TTATAATATATAC-ATATTATTA
1 TTATAATATA-ACTATAATATTA
* *
42789615 CTTATATTATAACTTTAATATTA
1 -TTATAATATAACTATAATATTA
42789638 TTATAATAT
1 TTATAATAT
42789647 TATTTCCACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATAATATAACTATAATATTA
Found at i:42800385 original size:131 final size:131
Alignment explanation
Indices: 42800216--42800571 Score: 439
Period size: 131 Copynumber: 2.7 Consensus size: 131
42800206 TGTTCAATCG
* * ** * * * * *
42800216 TTTTGAGCAAATGAGAAATCACAACCCAACACGATAGGGCACTATT-CTCAAATTGTCAAACACC
1 TTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTG-CAAACATC
* * * * *
42800280 GAATATTGCCTTCGTTTTAAATAATTTTTAGAAGATATGAATGAAATTTTGAAG-GGATACTCGA
65 GAATCTTGTCTTCGTTTTAAAGAATTTTTAAAAGAAATGAATGAAATTTTGAAGTGG-TACTCGA
42800344 TTA
129 TTA
* *
42800347 TTTTGAGCAAACGCGAAATTGCAACCCAACATGTTAGGGCACGATTCCGCGAATTGCTAAATATC
1 TTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGC-AAACATC
* * * *
42800412 GAATCTTGTCTCCGTTTTCAAGAA-TTTTAAAAGAAATGAGTGAAATTTTGAAGTGGTATTCGAT
65 GAATCTTGTCTTCGTTTTAAAGAATTTTTAAAAGAAATGAATGAAATTTTGAAGTGGTACTCGAT
42800476 TA
130 TA
* *
42800478 TTTTGAGCAAACACGAAATTGCAATCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATC
1 TTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTG-CAAACATC
* *
42800543 GAATCTCGTCTTCGTTTTGAAGAATTTTT
65 GAATCTTGTCTTCGTTTTAAAGAATTTTT
42800572 GAATGAATGA
Statistics
Matches: 193, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
131 155 0.80
132 38 0.20
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (131 bp):
TTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCAAACATCG
AATCTTGTCTTCGTTTTAAAGAATTTTTAAAAGAAATGAATGAAATTTTGAAGTGGTACTCGATT
A
Found at i:42801034 original size:27 final size:27
Alignment explanation
Indices: 42801004--42801057 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
42800994 ACAAATTTAT
*
42801004 ATAGAAAATA-AGAATATAATTCTTGAA
1 ATAGAAAATATAGAATACAATT-TTGAA
* *
42801031 ATAGATATTATAGAATACAATTTTGAA
1 ATAGAAAATATAGAATACAATTTTGAA
42801058 TTAAGTCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.33
Consensus pattern (27 bp):
ATAGAAAATATAGAATACAATTTTGAA
Found at i:42801508 original size:14 final size:14
Alignment explanation
Indices: 42801467--42801509 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
42801457 AAGGGAAAAC
42801467 ATATGTATAAAATA
1 ATATGTATAAAATA
* *
42801481 ATATAT-TATTAATA
1 ATATGTATA-AAATA
42801495 ATATGTATAAAATA
1 ATATGTATAAAATA
42801509 A
1 A
42801510 AATGAACCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
ATATGTATAAAATA
Found at i:42801606 original size:10 final size:10
Alignment explanation
Indices: 42801593--42801625 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
42801583 AAATAAATGA
42801593 ATAGATATAT
1 ATAGATATAT
*
42801603 ATAGTTATAT
1 ATAGATATAT
42801613 ATAGATATAT
1 ATAGATATAT
42801623 ATA
1 ATA
42801626 TACATGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (10 bp):
ATAGATATAT
Found at i:42807300 original size:28 final size:29
Alignment explanation
Indices: 42807268--42807353 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 29
42807258 TACCTGTATC
*
42807268 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAAGCCCAAATCACATTCATA
* * *
42807296 TGGCCCATTAGGCCCAAATGACATTTATA
1 TGGCCCATTAAGCCCAAATCACATTCATA
* * * *
42807325 TGGCCCGTT-AGACCGAGTCACATTCATA
1 TGGCCCATTAAGCCCAAATCACATTCATA
42807353 T
1 T
42807354 TCATGCTCAC
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 28 0.61
29 18 0.39
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAAGCCCAAATCACATTCATA
Found at i:42807470 original size:19 final size:18
Alignment explanation
Indices: 42807421--42807456 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42807411 TGGGACCAAC
*
42807421 AGCCCATCGGGCCCATTT
1 AGCCCATCAGGCCCATTT
42807439 AGCCCATCAGGCCCATTT
1 AGCCCATCAGGCCCATTT
42807457 CGGCCCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.22
Consensus pattern (18 bp):
AGCCCATCAGGCCCATTT
Found at i:42807594 original size:16 final size:16
Alignment explanation
Indices: 42807573--42807615 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
42807563 GTAGCCAAAC
42807573 TTTCGGCTTTT-TGGCA
1 TTTCGGCTTTTCT-GCA
42807589 TTTCGGCTTTTCTGCA
1 TTTCGGCTTTTCTGCA
42807605 TTTCGGCTTTT
1 TTTCGGCTTTT
42807616 GCCGATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.05, C:0.21, G:0.21, T:0.53
Consensus pattern (16 bp):
TTTCGGCTTTTCTGCA
Found at i:42807783 original size:8 final size:8
Alignment explanation
Indices: 42807770--42807803 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
42807760 CTAAATAAAA
42807770 TTCGGGAT
1 TTCGGGAT
42807778 TTCGGGAT
1 TTCGGGAT
*
42807786 TTCAGGAT
1 TTCGGGAT
*
42807794 TTCGAGAT
1 TTCGGGAT
42807802 TT
1 TT
42807804 TTGGATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.41
Consensus pattern (8 bp):
TTCGGGAT
Found at i:42807809 original size:16 final size:16
Alignment explanation
Indices: 42807774--42807822 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
42807764 ATAAAATTCG
* **
42807774 GGATTTCGGGATTTCA
1 GGATTTCGAGATTTTT
42807790 GGATTTCGAGATTTTT
1 GGATTTCGAGATTTTT
*
42807806 GGATTTTGAGATTTTT
1 GGATTTCGAGATTTTT
42807822 G
1 G
42807823 AGGCGTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.18, C:0.06, G:0.29, T:0.47
Consensus pattern (16 bp):
GGATTTCGAGATTTTT
Found at i:42810424 original size:39 final size:39
Alignment explanation
Indices: 42810220--42810442 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
42810210 TTGAATGCTG
* * * * *
42810220 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
** *
42810260 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
42810300 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* * *
42810340 TCCGGCTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
42810380 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
42810419 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42810443 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 22, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
39 38 0.25
40 106 0.68
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:42810462 original size:79 final size:80
Alignment explanation
Indices: 42810294--42810477 Score: 187
Period size: 79 Copynumber: 2.3 Consensus size: 80
42810284 TGTGCGAGAT
* * * *
42810294 ACTAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGCTTAAGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGCTTAAGTCCCGAAG
** *
42810359 GCATTCGTGCGAGTT
66 GCATTCGAACGAGTG
* * * * *
42810374 ATTAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGC-TATGTCCCGAA
1 ACTAAATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACC-GGCTTAAGTCCCGAA
*
42810437 GGCATTTGAACGAG-G
65 GGCATTCGAACGAGTG
* *
42810452 AGCTATATCC-GGTTAAATCCCGAAGG
1 A-CTAAATCCGGGTTAAGTCCCGAAGG
42810478 TACGTGATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
78 15 0.18
79 45 0.53
80 25 0.29
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
ACTAAATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGCTTAAGTCCCGAAG
GCATTCGAACGAGTG
Found at i:42818263 original size:39 final size:39
Alignment explanation
Indices: 42818059--42818281 Score: 198
Period size: 40 Copynumber: 5.6 Consensus size: 39
42818049 TTGAATGCTG
* * * * *
42818059 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
** *
42818099 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* * *
42818139 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATGCTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* * *
42818179 TCCGGCTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
42818219 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
42818258 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42818282 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 24, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
39 38 0.25
40 104 0.68
41 10 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:42822670 original size:37 final size:37
Alignment explanation
Indices: 42822612--42822788 Score: 291
Period size: 37 Copynumber: 4.8 Consensus size: 37
42822602 CGAATAGTCC
* *
42822612 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
42822649 CCACACGTAGTCATCGAGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
42822686 CCACACATAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
**
42822723 CCACACGTAGTCATCGGGTCTTACCTAGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
42822760 GCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
42822789 ATATATTTCC
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 129 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
Found at i:42822979 original size:48 final size:48
Alignment explanation
Indices: 42822914--42823351 Score: 687
Period size: 48 Copynumber: 9.1 Consensus size: 48
42822904 GGTCATTCGG
* * * *
42822914 CCACAATATACACATCTCCTACATATTTCACACTAGCCATTCGGCTTTA
1 CCAC-ATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
* * *
42822963 CCACGTATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTA
1 CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
* * *
42823011 CCACGTATACATATCCCATACATATTTCACATTAGCCATTCAGCTTTA
1 CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
* * * *
42823059 CCACATATACACATCCCATACATATTTCACATTAGCCATTCGGTTTTA
1 CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
*
42823107 CCACATATACACATCTCATACATATTTCACATTAGCCATTCCGCTTTA
1 CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
*
42823155 CCACATATACACATCTCATACATATTTCACATTAGCCATTCCGCTTTA
1 CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
*
42823203 CCACACATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
1 CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
* *
42823251 CCATACATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
1 CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
*
42823299 CCACATATACATATCTCATACATATTTCACATTAGTCATTCCGCTTTA
1 CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
42823347 CCACA
1 CCACA
42823352 CACATATATA
Statistics
Matches: 370, Mismatches: 19, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
48 366 0.99
49 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.33
Consensus pattern (48 bp):
CCACATATACATATCTCATACATATTTCACATTAGCCATTCCGCTTTA
Found at i:42828761 original size:29 final size:29
Alignment explanation
Indices: 42828722--42828798 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
42828712 AATTATATTC
*
42828722 ATATGACCCATTTGGCCCAAATCACATGT
1 ATATGGCCCATTTGGCCCAAATCACATGT
* *
42828751 ATATGGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCCATTTGGCCCAAATCACATGT
42828780 ATATGGCCC-TTTAGGCCCA
1 ATATGGCCCATTT-GGCCCA
42828799 GTCACATTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 2 0.05
29 41 0.95
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATTTGGCCCAAATCACATGT
Found at i:42832918 original size:13 final size:13
Alignment explanation
Indices: 42832900--42832924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42832890 ACACACAAAG
42832900 TGTTAAAAATATT
1 TGTTAAAAATATT
42832913 TGTTAAAAATAT
1 TGTTAAAAATAT
42832925 ATACAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TGTTAAAAATATT
Found at i:42833335 original size:17 final size:17
Alignment explanation
Indices: 42833315--42833347 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42833305 TAGATTAATG
*
42833315 ATACATATAGATAATAC
1 ATACATAAAGATAATAC
42833332 ATACATAAAGATAATA
1 ATACATAAAGATAATA
42833348 ATATATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (17 bp):
ATACATAAAGATAATAC
Found at i:42833580 original size:23 final size:23
Alignment explanation
Indices: 42833544--42833590 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
42833534 TATAAAAAGT
* *
42833544 ATTTGAACATAATATCATACAAA
1 ATTTGAAAACAATATCATACAAA
*
42833567 ATTTGAAAACAATATCATATAAA
1 ATTTGAAAACAATATCATACAAA
42833590 A
1 A
42833591 GGAAATTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (23 bp):
ATTTGAAAACAATATCATACAAA
Found at i:42842287 original size:31 final size:31
Alignment explanation
Indices: 42842251--42842313 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
42842241 CTCATAAGTT
42842251 AGTATACTTGTCCATGATACAAATGAAATTA
1 AGTATACTTGTCCATGATACAAATGAAATTA
*
42842282 AGTATATTTGTCCATGATACAAATGAAATTA
1 AGTATACTTGTCCATGATACAAATGAAATTA
42842313 A
1 A
42842314 CCATAAGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (31 bp):
AGTATACTTGTCCATGATACAAATGAAATTA
Found at i:42845645 original size:17 final size:17
Alignment explanation
Indices: 42845623--42845657 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42845613 GAGAATAAGT
42845623 AAGATACAACACATCAA
1 AAGATACAACACATCAA
42845640 AAGATACAACACATCAA
1 AAGATACAACACATCAA
42845657 A
1 A
42845658 TCACAGACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.11
Consensus pattern (17 bp):
AAGATACAACACATCAA
Done.