Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 125 of 126
Found at i:38961515 original size:12 final size:13
Alignment explanation
Indices: 38961493--38961521 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
38961483 TGAGTATAGT
38961493 AAAATATTTTAAA
1 AAAATATTTTAAA
38961506 AAAATA-TTTAAA
1 AAAATATTTTAAA
38961518 AAAA
1 AAAA
38961522 AGAGATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATTTTAAA
Found at i:38961522 original size:13 final size:13
Alignment explanation
Indices: 38961493--38961522 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38961483 TGAGTATAGT
*
38961493 AAAATATTTTAAA
1 AAAATATTTAAAA
38961506 AAAATATTTAAAA
1 AAAATATTTAAAA
38961519 AAAA
1 AAAA
38961523 GAGATATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATATTTAAAA
Found at i:38961656 original size:20 final size:20
Alignment explanation
Indices: 38961633--38961692 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
38961623 AAAAAATTAA
38961633 AAATTAAAAGTATAACTTCT
1 AAATTAAAAGTATAACTTCT
38961653 AAATTGAATAA-TA-AA-----
1 AAATT-AA-AAGTATAACTTCT
38961668 AAATTAAAAGTATAACTTCT
1 AAATTAAAAGTATAACTTCT
38961688 AAATT
1 AAATT
38961693 GAAATATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 18
0.63 0.00 0.37
Matches are distributed among these distances:
13 2 0.06
14 4 0.13
15 7 0.23
20 12 0.39
21 4 0.13
22 2 0.06
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATTAAAAGTATAACTTCT
Found at i:38961671 original size:35 final size:36
Alignment explanation
Indices: 38961631--38961709 Score: 133
Period size: 35 Copynumber: 2.2 Consensus size: 36
38961621 ATAAAAAATT
38961631 AAAAATTAAAAGTATAACTTCTAAATTG-AATAATA
1 AAAAATTAAAAGTATAACTTCTAAATTGAAATAATA
*
38961666 AAAAATTAAAAGTATAACTTCTAAATTGAAATATTA
1 AAAAATTAAAAGTATAACTTCTAAATTGAAATAATA
*
38961702 GAAAATTA
1 AAAAATTA
38961710 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 28 0.68
36 13 0.32
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (36 bp):
AAAAATTAAAAGTATAACTTCTAAATTGAAATAATA
Found at i:38962330 original size:30 final size:30
Alignment explanation
Indices: 38962276--38962335 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
38962266 GCGTTTTAGT
*
38962276 AAAACCGGACCATTCCCATTATTTTTTTTA
1 AAAACCGGACCATTCCCATAATTTTTTTTA
* * *
38962306 AAAAGCGGCCCATTTCCATAATTTTTTTTA
1 AAAACCGGACCATTCCCATAATTTTTTTTA
38962336 GAAATGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (30 bp):
AAAACCGGACCATTCCCATAATTTTTTTTA
Found at i:38964599 original size:24 final size:24
Alignment explanation
Indices: 38964558--38964642 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
38964548 GAAGATGGAA
* * *
38964558 ATGAAGACGAAAATGAGGGTAGAG
1 ATGAAGATGAAGACGAGGGTAGAG
*
38964582 ATGAAGATGAAGACGAGGG-ACTAG
1 ATGAAGATGAAGACGAGGGTA-GAG
* * *
38964606 ATGAAGATGAATAC-AGGGATCGGG
1 ATGAAGATGAAGACGAGGG-TAGAG
*
38964630 GTGAAGATGAAGA
1 ATGAAGATGAAGA
38964643 AGATGAAGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
23 5 0.10
24 43 0.90
ACGTcount: A:0.42, C:0.06, G:0.38, T:0.14
Consensus pattern (24 bp):
ATGAAGATGAAGACGAGGGTAGAG
Found at i:38970082 original size:10 final size:10
Alignment explanation
Indices: 38970067--38970091 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38970057 GGAAATTCCA
38970067 TTAGGTTATT
1 TTAGGTTATT
38970077 TTAGGTTATT
1 TTAGGTTATT
38970087 TTAGG
1 TTAGG
38970092 GTATAGATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (10 bp):
TTAGGTTATT
Found at i:38974073 original size:23 final size:24
Alignment explanation
Indices: 38974034--38974081 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
38974024 TTTATTTGAT
38974034 AATATGTTTTGATATAACAAATTAA
1 AATATGTTTTGATATAA-AAATTAA
*
38974059 AATAT-TTTTGA-ATAAAAGTTAA
1 AATATGTTTTGATATAAAAATTAA
38974081 A
1 A
38974082 GTTGAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 6 0.27
25 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
AATATGTTTTGATATAAAAATTAA
Found at i:38978842 original size:138 final size:137
Alignment explanation
Indices: 38978570--38979674 Score: 1553
Period size: 138 Copynumber: 8.1 Consensus size: 137
38978560 TAGAAAAAAG
* *
38978570 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
38978635 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
66 TATAACTGATTATATTAATAAATTCGGT-AAATATATACAATTAATATTTTGTATGAATCAAATT
38978699 CTATATATT
130 C-ATATATT
* * * * * *
38978708 AATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAATTAATCAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
38978773 TATAACTGATTATATTAATAAATTCGGT-AATATATATAATTAATATTTTTTATGAATCAAATTC
66 TATAACTGATTATATTAATAAATTCGGTAAATATATACAATTAATATTTTGTATGAATCAAATTC
38978837 ATATATT
131 ATATATT
* * * *
38978844 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
38978909 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
66 TATAACTGATTATATTAATAAATTCGGT-AAATATATACAATTAATATTTTGTATGAATCAAATT
38978973 CTATATATT
130 C-ATATATT
* * * * * *
38978982 AATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAATTAATCAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
38979047 TATAACTGATTATATTAATAAATTCGGT-AATATATATAATTAATATTTTTTATGAATCAAATTC
66 TATAACTGATTATATTAATAAATTCGGTAAATATATACAATTAATATTTTGTATGAATCAAATTC
38979111 ATATATT
131 ATATATT
* * * *
38979118 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
38979183 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
66 TATAACTGATTATATTAATAAATTCGGT-AAATATATACAATTAATATTTTGTATGAATCAAATT
38979247 CTATATATT
130 C-ATATATT
* * * * * *
38979256 AATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAATTAATCAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
38979321 TATAACTGATTATATTAATAAATTCGGT-AATATATATAATTAATATTTTTTATGAATCAAATTC
66 TATAACTGATTATATTAATAAATTCGGTAAATATATACAATTAATATTTTGTATGAATCAAATTC
38979385 ATATATT
131 ATATATT
* * *
38979392 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTATTTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
** * * * *
38979457 TATGTCT-ATTTATATTATTAAATTAGGTAAAATATATATAATTAATATTTT-TATGAATCACAT
66 TATAACTGA-TTATATTAATAAATTCGGT-AAATATATACAATTAATATTTTGTATGAATCAAAT
*
38979520 TCAGATATT
129 TCATATATT
* *
38979529 AATTATATTCTTTCCAAAAGAATATTAATTTCTATATCTTTTATATTTTGA-TCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACT-GAAATTAATTA
* * * *
38979593 ATATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTATTATTTTGTATGAATCAAAT
65 ATATAACTGATTATATTAATAAATTCGGT-AAATATATACAATTAATATTTTGTATGAATCAAAT
38979658 TCATATATT
129 TCATATATT
38979667 AATTATAT
1 AATTATAT
38979675 CTATGTTCTC
Statistics
Matches: 854, Mismatches: 98, Indels: 30
0.87 0.10 0.03
Matches are distributed among these distances:
135 1 0.00
136 355 0.42
137 129 0.15
138 369 0.43
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
TATAACTGATTATATTAATAAATTCGGTAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATT
Found at i:38979059 original size:274 final size:274
Alignment explanation
Indices: 38978570--38979674 Score: 1912
Period size: 274 Copynumber: 4.0 Consensus size: 274
38978560 TAGAAAAAAG
* *
38978570 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
38978635 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
66 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
38978700 TATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAA
131 TATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAA
38978765 TTAATCAATATAACTGATTATATTAATAAATTCGGTAATATATATAATTAATATTTTTTATGAAT
196 TTAATCAATATAACTGATTATATTAATAAATTCGGTAATATATATAATTAATATTTTTTATGAAT
38978830 CAAATTCATATATT
261 CAAATTCATATATT
38978844 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
38978909 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
66 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
38978974 TATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAA
131 TATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAA
38979039 TTAATCAATATAACTGATTATATTAATAAATTCGGTAATATATATAATTAATATTTTTTATGAAT
196 TTAATCAATATAACTGATTATATTAATAAATTCGGTAATATATATAATTAATATTTTTTATGAAT
38979104 CAAATTCATATATT
261 CAAATTCATATATT
38979118 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
38979183 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
66 TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
38979248 TATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAA
131 TATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAA
38979313 TTAATCAATATAACTGATTATATTAATAAATTCGGTAATATATATAATTAATATTTTTTATGAAT
196 TTAATCAATATAACTGATTATATTAATAAATTCGGTAATATATATAATTAATATTTTTTATGAAT
38979378 CAAATTCATATATT
261 CAAATTCATATATT
* * *
38979392 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTATTTAA
1 AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
* ** * * * *
38979457 TAT-GTCTATTTATATTATTAAATTAGGTAAAATATATATAATTAATATTTT-TATGAATCACAT
66 TATAAT-TGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
* * * * * *
38979520 -TCAGATATTAATTATATTCTTTCCAAAAGAATATTAATTTCTATATCTTTTATATTTTGA-TCG
130 CT-ATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACT-G
* * * * * * *
38979583 AAATTAATTAATATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTATTATTTTGTA
193 AAATTAATCAATATAACTGATTATATTAATAAATTCGGT--AATATATATAATTAATATTTTTTA
38979648 TGAATCAAATTCATATATT
256 TGAATCAAATTCATATATT
38979667 AATTATAT
1 AATTATAT
38979675 CTATGTTCTC
Statistics
Matches: 801, Mismatches: 25, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
272 2 0.00
273 100 0.12
274 651 0.81
275 48 0.06
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (274 bp):
AATTATATTTTTTTCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGGCCGAAATTAATTAA
TATAATTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
TATATATTAATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTCACTGAAA
TTAATCAATATAACTGATTATATTAATAAATTCGGTAATATATATAATTAATATTTTTTATGAAT
CAAATTCATATATT
Found at i:38981032 original size:14 final size:15
Alignment explanation
Indices: 38981003--38981034 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
38980993 AGGTTTGGGT
38981003 AGAAATATTGAAGGG
1 AGAAATATTGAAGGG
38981018 AGAAATATT-AAGGG
1 AGAAATATTGAAGGG
38981032 AGA
1 AGA
38981035 TTGTAAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (15 bp):
AGAAATATTGAAGGG
Found at i:38982941 original size:12 final size:12
Alignment explanation
Indices: 38982924--38982951 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38982914 TTAACATGTT
38982924 ACCTCATTAAAA
1 ACCTCATTAAAA
38982936 ACCTCATTAAAA
1 ACCTCATTAAAA
38982948 ACCT
1 ACCT
38982952 TACTAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (12 bp):
ACCTCATTAAAA
Found at i:38988246 original size:32 final size:32
Alignment explanation
Indices: 38988074--38988245 Score: 204
Period size: 32 Copynumber: 5.4 Consensus size: 32
38988064 GAATGGCTAC
* * *
38988074 AAGCCATAAGT-ATAGTAATATGATTGGCACA
1 AAGCCATCAGTAATGGTAATATGATCGGCACA
* * * *
38988105 AAGCCATCAGTAGTAGTGATATGATCGACACA
1 AAGCCATCAGTAATGGTAATATGATCGGCACA
* *
38988137 CAA-CCATCAGTAATGGTAATATGATTGACACA
1 -AAGCCATCAGTAATGGTAATATGATCGGCACA
*
38988169 AAGCCATCAGTAATGATAATATGATCGGCACA
1 AAGCCATCAGTAATGGTAATATGATCGGCACA
* *
38988201 AAGCCATCAGTAACGGTAATATTATCGGCACA
1 AAGCCATCAGTAATGGTAATATGATCGGCACA
*
38988233 AAGCCATTAGTAA
1 AAGCCATCAGTAA
38988246 CATCCCAGTA
Statistics
Matches: 122, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
31 12 0.10
32 108 0.89
33 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAATGGTAATATGATCGGCACA
Found at i:38988285 original size:26 final size:26
Alignment explanation
Indices: 38988255--38988326 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 26
38988245 ACATCCCAGT
*
38988255 AAAGCTACCAGCAATAGTATCACAGC
1 AAAGCTGCCAGCAATAGTATCACAGC
* *
38988281 AAAGCTGCCAGCAACAGTATCGCAGC
1 AAAGCTGCCAGCAATAGTATCACAGC
*
38988307 AAAGCTGCCAGTAATAGTAT
1 AAAGCTGCCAGCAATAGTAT
38988327 ATGTGGCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (26 bp):
AAAGCTGCCAGCAATAGTATCACAGC
Found at i:38988344 original size:27 final size:27
Alignment explanation
Indices: 38988314--38988373 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 27
38988304 AGCAAAGCTG
38988314 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAATAGTGAT-TGTGG-CAGAGCCA
38988341 CCAGTAATAGTGATTGTGGCAGAGCCA
1 CCAGTAATAGTGATTGTGGCAGAGCCA
38988368 CCAGTA
1 CCAGTA
38988374 CAAAACTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.06
27 27 0.87
28 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (27 bp):
CCAGTAATAGTGATTGTGGCAGAGCCA
Found at i:38988591 original size:53 final size:54
Alignment explanation
Indices: 38988521--38988664 Score: 168
Period size: 54 Copynumber: 2.7 Consensus size: 54
38988511 GGGAAAAATA
*
38988521 GTCA-TTTACCCTCCAGGGGCATTAC-GATCATTTTACCCTACA-AGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACAG-TCATTTTACCCTACAGAGGCATTACG
* * * *
38988573 GTCATTTTACCCTACAGGGGAATTACAGTCATTTTACCCTATAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTACAGAGGCATTACG
* * * * *
38988627 GTCATTTTGCCTTACAAGGGCATTACAGTTATTATACC
1 GTCATTTTACCCTACAGGGGCATTACAGTCATTTTACC
38988665 TATTTTAGGG
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 4 0.05
53 33 0.42
54 41 0.53
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (54 bp):
GTCATTTTACCCTACAGGGGCATTACAGTCATTTTACCCTACAGAGGCATTACG
Found at i:38988605 original size:27 final size:27
Alignment explanation
Indices: 38988520--38988664 Score: 152
Period size: 27 Copynumber: 5.4 Consensus size: 27
38988510 GGGGAAAAAT
*
38988520 AGTCA-TTTACCCTCCAGGGGCATTAC
1 AGTCATTTTACCCTACAGGGGCATTAC
*
38988546 -GATCATTTTACCCTACA-AGGCATTAC
1 AG-TCATTTTACCCTACAGGGGCATTAC
* *
38988572 GGTCATTTTACCCTACAGGGGAATTAC
1 AGTCATTTTACCCTACAGGGGCATTAC
* *
38988599 AGTCATTTTACCCTATAGGGGCATTAT
1 AGTCATTTTACCCTACAGGGGCATTAC
* * * *
38988626 GGTCATTTTGCCTTACAAGGGCATTAC
1 AGTCATTTTACCCTACAGGGGCATTAC
* *
38988653 AGTTATTATACC
1 AGTCATTTTACC
38988665 TATTTTAGGG
Statistics
Matches: 97, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
25 1 0.01
26 26 0.27
27 70 0.72
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (27 bp):
AGTCATTTTACCCTACAGGGGCATTAC
Found at i:39005689 original size:3 final size:3
Alignment explanation
Indices: 39005681--39005749 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
39005671 TATTTTTTAG
* * * *
39005681 ATT ATT ATT ATT ATC ATT ATT ATT ACT ATT ATT ACT ATT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
39005729 ATT ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
39005750 TTGTTTTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:39006970 original size:23 final size:23
Alignment explanation
Indices: 39006944--39006992 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
39006934 TCTTCTGCCT
*
39006944 TTTCTATCTTTCTTTTT-CTTTCA
1 TTTCTATC-TTCTTTTTACTTTAA
*
39006967 TTTCTTTCTTCTTTTTACTTTAA
1 TTTCTATCTTCTTTTTACTTTAA
39006990 TTT
1 TTT
39006993 GCATGCCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTCTATCTTCTTTTTACTTTAA
Found at i:39025892 original size:21 final size:18
Alignment explanation
Indices: 39025854--39025899 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 18
39025844 TTTATGCAGT
39025854 AATAGTATTTTAATTTTATA
1 AATA-TATTTTAATTTTA-A
39025874 ACATATATTTTATATTTTAA
1 A-ATATATTTTA-ATTTTAA
39025894 AATATA
1 AATATA
39025900 ATTATCTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AATATATTTTAATTTTAA
Found at i:39029646 original size:24 final size:24
Alignment explanation
Indices: 39029613--39029666 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
39029603 CATCAGAAGA
39029613 GGCACACAAAATGAGAGATATCGTG
1 GGCA-ACAAAATGAGAGATATCGTG
* *
39029638 GGCAACAAAATGTGAGATATTGTG
1 GGCAACAAAATGAGAGATATCGTG
*
39029662 AGCAA
1 GGCAA
39029667 TAAATAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.19
Consensus pattern (24 bp):
GGCAACAAAATGAGAGATATCGTG
Found at i:39032423 original size:31 final size:29
Alignment explanation
Indices: 39032385--39032461 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
39032375 TTAATGGCTC
* * *
39032385 AGTGACTAAAATGTTACAATATGATAACGTA
1 AGTGACTAAAATGTAAC-ATATCA-AACATA
* *
39032416 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACATATCAAACATA
*
39032445 AGTGACTAAAATATAAC
1 AGTGACTAAAATGTAAC
39032462 TTAAGATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.51
30 4 0.10
31 15 0.38
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACATATCAAACATA
Found at i:39039757 original size:24 final size:25
Alignment explanation
Indices: 39039704--39039771 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
39039694 TAACACATTA
39039704 AATAAATA-AAAA-ATATAAAATTTC
1 AATAAATATAAAATATATAAAA-TTC
39039728 AATAAATATAAAATATATAAAA-T-
1 AATAAATATAAAATATATAAAATTC
*
39039751 AATTAAATATTAAATAT-TAAA
1 AA-TAAATATAAAATATATAAA
39039772 TTAAAATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 6 0.15
24 22 0.55
25 4 0.10
26 8 0.20
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAAATATAAAATATATAAAATTC
Found at i:39041322 original size:6 final size:6
Alignment explanation
Indices: 39041311--39041336 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39041301 ATTTTTTAAT
39041311 TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TT
39041337 TTATTTTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:39062633 original size:41 final size:41
Alignment explanation
Indices: 39062574--39062741 Score: 187
Period size: 41 Copynumber: 4.1 Consensus size: 41
39062564 ATACAATTTG
* **
39062574 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCTCAAGG
1 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCACAAAA
* *
39062615 CTTGATACAATACACCGGCACGAAGCCTTCTAGGCACAAAA
1 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCACAAAA
** *
39062656 CCTGATACAATACACTAGCACGAAGCCGGCTAGGCA-AAAA
1 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCACAAAA
* * * * *
39062696 CCCTGATCCAAGACACCGGTACGAAGCC-GACTGGGCTCAAAA
1 -CCTGATACAATACACCGGCACGAAGCCTG-CTAGGCACAAAA
39062738 CCTG
1 CCTG
39062742 CTAGGCTCAA
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 5 0.05
41 98 0.92
42 4 0.04
ACGTcount: A:0.33, C:0.31, G:0.21, T:0.14
Consensus pattern (41 bp):
CCTGATACAATACACCGGCACGAAGCCTGCTAGGCACAAAA
Found at i:39072135 original size:27 final size:27
Alignment explanation
Indices: 39072097--39072149 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
39072087 CTGATGTCGA
39072097 TTGCCATAGAAAAGATACTATTAAGTG
1 TTGCCATAGAAAAGATACTATTAAGTG
* *
39072124 TTGCCATAGAAAATATACTGTTAAGT
1 TTGCCATAGAAAAGATACTATTAAGT
39072150 TATAGGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (27 bp):
TTGCCATAGAAAAGATACTATTAAGTG
Found at i:39080471 original size:17 final size:17
Alignment explanation
Indices: 39080440--39080472 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39080430 GTACTGATTT
39080440 TGACATTCTTATGTCAA
1 TGACATTCTTATGTCAA
39080457 TGACAATTCTT-TGTCA
1 TGAC-ATTCTTATGTCA
39080473 TCAATCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TGACATTCTTATGTCAA
Found at i:39083544 original size:27 final size:25
Alignment explanation
Indices: 39083514--39083565 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
39083504 TTCATTTTTC
*
39083514 ATTTCCCATCTCATATTCATTTCTCAT
1 ATTTCCCATCTCA-ATAC-TTTCTCAT
* *
39083541 ATTTTCCATTTCAATACTTTCTCAT
1 ATTTCCCATCTCAATACTTTCTCAT
39083566 CTCATATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 3 0.14
27 11 0.50
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTCCCATCTCAATACTTTCTCAT
Found at i:39083569 original size:43 final size:43
Alignment explanation
Indices: 39083515--39083599 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
39083505 TCATTTTTCA
39083515 TTTCCCATCTCATATTCATTTCTCATATTT-TCCATTTCAATAC
1 TTTCCCATCTCATATTCATTTCTCATATTTGT-CATTTCAATAC
* *
39083558 TTTCTCATCTCATATTCATTTCTCATCTTTGTCATTTCAATA
1 TTTCCCATCTCATATTCATTTCTCATATTTGTCATTTCAATA
39083600 TCAATAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.01, T:0.51
Consensus pattern (43 bp):
TTTCCCATCTCATATTCATTTCTCATATTTGTCATTTCAATAC
Found at i:39086088 original size:16 final size:16
Alignment explanation
Indices: 39086069--39086099 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39086059 CTCTTAAAGT
39086069 TTATTTTTCTTTTATG
1 TTATTTTTCTTTTATG
39086085 TTATTTTTCTTTTAT
1 TTATTTTTCTTTTAT
39086100 TACTAGTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
TTATTTTTCTTTTATG
Found at i:39094396 original size:16 final size:16
Alignment explanation
Indices: 39094377--39094407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39094367 CTCTTGAAAT
39094377 TTATTTTTCTCTTATG
1 TTATTTTTCTCTTATG
*
39094393 TTATTTTTCTTTTAT
1 TTATTTTTCTCTTAT
39094408 TACTAGTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (16 bp):
TTATTTTTCTCTTATG
Found at i:39098601 original size:138 final size:138
Alignment explanation
Indices: 39098324--39099485 Score: 1794
Period size: 138 Copynumber: 8.4 Consensus size: 138
39098314 TAGAAAAAGG
* * *
39098324 AATTATATTGTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
39098389 TATAATT-TTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
39098453 CATATATT
131 CATATATT
* * *
39098461 AATTATATTCTCTCCAAAAGAATATTAATTTTCATGTCTTTTATAATTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
39098526 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAGTTAGTATTTTGTATCAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
39098591 CATATATT
131 CATATATT
* * **
39098599 AATTATATTCTTTCCAAAATAATATTAATTTCCATGTCTTTTATATATTTTGGA--AAAAAGAAT
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTC-TTT-TATATTTT-GACCGAAATTAAT
* * * * * * *
39098662 TAATATAATTGTTTATATTAATAAACTCGGTAAACTGTATACAATTAAAAGTTTATATGAATCAA
63 TAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAA
* *
39098727 TTTCATAAATT
128 ATTCATATATT
* * *
39098738 AATTATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGAACGAAATTTATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
39098803 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
39098868 CATATATT
131 CATATATT
* * *
39098876 AATTATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGAACGAAATTTATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
39098941 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
39099006 CATATATT
131 CATATATT
* *
39099014 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATGAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
39099079 TATAATTATTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
39099144 CATATATT
131 CATATATT
*
39099152 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * *
39099217 TAT-ATCTGATTATATTAATAAATTCGGTAAAATATATAAAATTAATATTTTATATCAATGAAAT
66 TATAAT-TGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAAT
39099281 TCATATATT
130 TCATATATT
* * * *
39099290 ACTTATATTCTTTCCAAAA-AATAATAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* ** *
39099354 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGGGTAAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
39099419 CATATATT
131 CATATATT
* *
39099427 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTATTATAGTTTGACCGAAATT
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATT
39099486 GAAAATATAT
Statistics
Matches: 940, Mismatches: 76, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
136 2 0.00
137 198 0.21
138 621 0.66
139 110 0.12
140 7 0.01
141 2 0.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
CATATATT
Found at i:39098924 original size:71 final size:70
Alignment explanation
Indices: 39098847--39099201 Score: 208
Period size: 71 Copynumber: 5.1 Consensus size: 70
39098837 TATACAATTA
39098847 ATATTTTGTATCAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCTATG
1 ATATTTTGTATCAATCAAATTCATATATTAATTATATTCTTTCCAAAA-AATATTAATTTCTATG
39098912 TCTTTT
65 TCTTTT
* * * * * * **
39098918 ATATTTTG----AA-CGAAATTTAT-TAATATAACTGT-TTATATT--AATAAATTCAGTAAAAT
1 ATATTTTGTATCAATC-AAATTCATAT-AT-TAATTATATTCT-TTCCAA-AAAAT-ATTAATTT
* * * *
39098974 ATAT-ACAATTA
60 CTATGTC-TTTT
*
39098985 ATATTTTGTATCAATCAAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATG
1 ATATTTTGTATCAATCAAATTCATATATTAATTATATTCTTTCC-AAAAAATATTAATTTCTATG
39099050 TCTTTT
65 TCTTTT
* * * * * ** *
39099056 ATATTTTG-ACCGAAAT-GAATT-A-ATA-TAATTAT-TTATATT--AATAAATTCAGTAAAATA
1 ATATTTTGTATC--AATCAAATTCATATATTAATTATATTCT-TTCCAA-AAAAT-ATTAATTTC
* * *
39099113 TAT-ACAATTA
61 TATGTC-TTTT
*
39099123 ATATTTTGTATCAATCAAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATG
1 ATATTTTGTATCAATCAAATTCATATATTAATTATATTCTTTCC-AAAAAATATTAATTTCTATG
39099188 TCTTTT
65 TCTTTT
39099194 ATATTTTG
1 ATATTTTG
39099202 ACCGAAATTA
Statistics
Matches: 201, Mismatches: 49, Indels: 68
0.63 0.15 0.21
Matches are distributed among these distances:
65 2 0.01
66 15 0.07
67 58 0.29
68 19 0.09
69 6 0.03
70 19 0.09
71 63 0.31
72 15 0.07
73 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (70 bp):
ATATTTTGTATCAATCAAATTCATATATTAATTATATTCTTTCCAAAAAATATTAATTTCTATGT
CTTTT
Found at i:39099210 original size:67 final size:67
Alignment explanation
Indices: 39099001--39099210 Score: 173
Period size: 67 Copynumber: 3.1 Consensus size: 67
39098991 TGTATCAATC
39099001 AAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGAC
1 AAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGAC
39099066 CG
66 CG
** * * * * ** * * *
39099068 AAATGAAT-TAATATAATTAT-TTATATT--AATAAATTCAGTAAAAT--ATATACAATTAATAT
1 AAATTCATAT-AT-TAATTATATTCT-TTCCAAAAAAAT-ATTAATTTCCATGT-C-TTTTATAT
39099127 TTTGTATCAATC-
60 TTTG-A-C---CG
39099139 AAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGAC
1 AAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGAC
39099204 CG
66 CG
39099206 AAATT
1 AAATT
39099211 AATTAATATA
Statistics
Matches: 103, Mismatches: 22, Indels: 36
0.64 0.14 0.22
Matches are distributed among these distances:
65 3 0.03
66 9 0.09
67 31 0.30
68 10 0.10
69 2 0.02
70 10 0.10
71 26 0.25
72 9 0.09
73 3 0.03
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.45
Consensus pattern (67 bp):
AAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGAC
CG
Found at i:39099220 original size:71 final size:71
Alignment explanation
Indices: 39099001--39099232 Score: 198
Period size: 71 Copynumber: 3.3 Consensus size: 71
39098991 TGTATCAATC
*
39099001 AAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGAC
1 AAATTAATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGAC
39099066 CGAAAT
66 CGAAAT
* * * ** * * *
39099072 GAATTAATATAATTATTTATATTAATAAATT-CAGTAAAATA-T-A--TACA----ATTAATATT
1 AAATTAATAT-ATTAATTATATT-CT---TTCCAAAAAAATATTAATTTCCATGTCTTTTATATT
*
39099128 TTGTATC--AAT
61 TTG-ACCGAAAT
*
39099138 CAAATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGA
1 -AAATTAATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGA
39099203 CCGAAAT
65 CCGAAAT
* *
39099210 TAATTAATATATCTGATTATATT
1 AAATTAATATAT-TAATTATATT
39099233 AATAAATTCG
Statistics
Matches: 119, Mismatches: 23, Indels: 37
0.66 0.13 0.21
Matches are distributed among these distances:
62 2 0.02
63 8 0.07
64 1 0.01
65 2 0.02
66 14 0.12
67 21 0.18
68 2 0.02
70 2 0.02
71 31 0.26
72 23 0.19
73 2 0.02
74 1 0.01
75 8 0.07
76 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (71 bp):
AAATTAATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGAC
CGAAAT
Found at i:39108941 original size:19 final size:19
Alignment explanation
Indices: 39108851--39108941 Score: 76
Period size: 19 Copynumber: 4.8 Consensus size: 19
39108841 GGGTGGTACA
*
39108851 CATACTAGCATATGAAGTG
1 CATACTAGCACATGAAGTG
* **
39108870 CATCCT-GACACACAAAGTG
1 CATACTAG-CACATGAAGTG
* **
39108889 TATACTAGCACAAAAAGTG
1 CATACTAGCACATGAAGTG
* *
39108908 CATCCTAGCATATGAAGTG
1 CATACTAGCACATGAAGTG
*
39108927 CATACTGGCACATGA
1 CATACTAGCACATGA
39108942 GATGCATAGA
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
18 1 0.02
19 53 0.96
20 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (19 bp):
CATACTAGCACATGAAGTG
Found at i:39109080 original size:21 final size:19
Alignment explanation
Indices: 39109048--39109089 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
39109038 ATATGAACCA
39109048 ATTTATTTATCAT-AATCTC
1 ATTTATTTATCATCAAT-TC
39109067 ATTTCATTTCATCATCAATTC
1 ATTT-ATTT-ATCATCAATTC
39109088 AT
1 AT
39109090 GTATGTCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 9 0.45
22 3 0.15
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATTTATCATCAATTC
Found at i:39110053 original size:22 final size:22
Alignment explanation
Indices: 39110008--39110056 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
39109998 ATACACGTTA
* *
39110008 GAAATAAGTCGGGACTAAATTT
1 GAAAAAAGTCGGGACTAAAATT
39110030 GAAAAAAGTCGGGAC-AAACATT
1 GAAAAAAGTCGGGACTAAA-ATT
39110052 GAAAA
1 GAAAA
39110057 TTTTCAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.18
Consensus pattern (22 bp):
GAAAAAAGTCGGGACTAAAATT
Found at i:39111533 original size:25 final size:25
Alignment explanation
Indices: 39111494--39111551 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
39111484 TCTTGTACAC
* *
39111494 GTATGCTCATACGAGCTATGAATTA
1 GTATGCTCATACGAGCGATAAATTA
*
39111519 GTATGCTCACT-CGAGCGGTAAATTA
1 GTATGCTCA-TACGAGCGATAAATTA
39111544 GTATGCTC
1 GTATGCTC
39111552 TCATGAGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (25 bp):
GTATGCTCATACGAGCGATAAATTA
Found at i:39111564 original size:25 final size:26
Alignment explanation
Indices: 39111514--39111579 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
39111504 ACGAGCTATG
*
39111514 AATTAGTATGCTCAC-TCGAGCGGTA
1 AATTAGTATGCTCTCATCGAGCGGTA
**
39111539 AATTAGTATGCTCTCAT-GAGTTGTA
1 AATTAGTATGCTCTCATCGAGCGGTA
**
39111564 AATCGGTATGCTCTCA
1 AATTAGTATGCTCTCA
39111580 CAAGCTGTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 34 0.97
26 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (26 bp):
AATTAGTATGCTCTCATCGAGCGGTA
Found at i:39113497 original size:39 final size:39
Alignment explanation
Indices: 39113454--39113557 Score: 208
Period size: 39 Copynumber: 2.7 Consensus size: 39
39113444 CAATGGAAGA
39113454 TGGATTGGATAAATAGATGTCCAAGTGAAACCTCTAAGG
1 TGGATTGGATAAATAGATGTCCAAGTGAAACCTCTAAGG
39113493 TGGATTGGATAAATAGATGTCCAAGTGAAACCTCTAAGG
1 TGGATTGGATAAATAGATGTCCAAGTGAAACCTCTAAGG
39113532 TGGATTGGATAAATAGATGTCCAAGT
1 TGGATTGGATAAATAGATGTCCAAGT
39113558 TTGAAGAACT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.27
Consensus pattern (39 bp):
TGGATTGGATAAATAGATGTCCAAGTGAAACCTCTAAGG
Found at i:39122449 original size:23 final size:23
Alignment explanation
Indices: 39122377--39122440 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
39122367 TTGGACAAAA
*
39122377 GTGTAAAGCAGGGTCACACGCCC
1 GTGTAAAGCAGGGTCACACGACC
*
39122400 GTGTAAAGTAGGGTCACACGACC
1 GTGTAAAGCAGGGTCACACGACC
*
39122423 GTGTAAACCAGGGTCACA
1 GTGTAAAGCAGGGTCACA
39122441 TGGTCGTGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.25, G:0.30, T:0.16
Consensus pattern (23 bp):
GTGTAAAGCAGGGTCACACGACC
Found at i:39123672 original size:22 final size:22
Alignment explanation
Indices: 39123587--39123672 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 22
39123577 GCTTTAACAG
*
39123587 TAGGCACCGGAGTGCGAATCAA
1 TAGGCACCGGAGTGCAAATCAA
**
39123609 TAGATACCGGAGTGCAAATCAA
1 TAGGCACCGGAGTGCAAATCAA
* ** *
39123631 TCGGCACCATAGTGCGAATCAA
1 TAGGCACCGGAGTGCAAATCAA
* *
39123653 TAGGCACCGTAGTGAAAATC
1 TAGGCACCGGAGTGCAAATC
39123673 TCGTAAAAGT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (22 bp):
TAGGCACCGGAGTGCAAATCAA
Found at i:39125979 original size:36 final size:36
Alignment explanation
Indices: 39125939--39126059 Score: 131
Period size: 37 Copynumber: 3.4 Consensus size: 36
39125929 CAGTGACATA
39125939 CTTAACATGCGAATCAGAATCAGAAATAATGA-CATG
1 CTTAACATGCGAATCAGAATCAG-AATAATGAGCATG
* * * *
39125975 CTTAACATGCGAGTCAAAATTAGATTAAT-AGCATG
1 CTTAACATGCGAATCAGAATCAGAATAATGAGCATG
* *
39126010 ATTAACATGCGAATCAGAATATCAGAAT-ATTAGCATG
1 CTTAACATGCGAATCAG-A-ATCAGAATAATGAGCATG
*
39126047 TTTAACATGCGAA
1 CTTAACATGCGAA
39126060 CTAGAACATC
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
34 1 0.01
35 23 0.32
36 23 0.32
37 24 0.34
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
CTTAACATGCGAATCAGAATCAGAATAATGAGCATG
Found at i:39130020 original size:19 final size:19
Alignment explanation
Indices: 39129996--39130042 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
39129986 TGTTATCTTA
* *
39129996 TTTAATCTTTCTTTTATTT
1 TTTAATCTTGCTTTTATTG
39130015 TTTAATCTTGCTTTTATTG
1 TTTAATCTTGCTTTTATTG
39130034 TTTAATCTT
1 TTTAATCTT
39130043 AGGGTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.68
Consensus pattern (19 bp):
TTTAATCTTGCTTTTATTG
Found at i:39132364 original size:18 final size:18
Alignment explanation
Indices: 39132337--39132376 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
39132327 CCTTCGAAAC
39132337 TGTCGATGCAATCAAATG
1 TGTCGATGCAATCAAATG
*
39132355 TGTCGGTGCAATCAAATG
1 TGTCGATGCAATCAAATG
39132373 TGTC
1 TGTC
39132377 AACACAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (18 bp):
TGTCGATGCAATCAAATG
Found at i:39137767 original size:21 final size:21
Alignment explanation
Indices: 39137743--39137784 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
39137733 CAAAAGCAGA
* *
39137743 AGTTGTTGCAGAAGAGGAAGT
1 AGTTGCTGAAGAAGAGGAAGT
39137764 AGTTGCTGAAGAAGAGGAAGT
1 AGTTGCTGAAGAAGAGGAAGT
39137785 TTCTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.38, T:0.21
Consensus pattern (21 bp):
AGTTGCTGAAGAAGAGGAAGT
Found at i:39138264 original size:17 final size:17
Alignment explanation
Indices: 39138239--39138275 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
39138229 GATAAGTATA
* *
39138239 CATTGTCATTGCATTTT
1 CATTATCATTACATTTT
39138256 CATTATCATTACATTTT
1 CATTATCATTACATTTT
39138273 CAT
1 CAT
39138276 GTCAGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (17 bp):
CATTATCATTACATTTT
Found at i:39142139 original size:35 final size:35
Alignment explanation
Indices: 39142100--39142224 Score: 126
Period size: 35 Copynumber: 3.6 Consensus size: 35
39142090 ATTGTTATTT
**
39142100 TGATTCGCATGTTAAACATGTTATTATTCTAATTA
1 TGATTCGCATGTTAAACATGCCATTATTCTAATTA
* * * *
39142135 TGATTCGCGTGTTAAGCATGCCATTTTTCTGATTA
1 TGATTCGCATGTTAAACATGCCATTATTCTAATTA
* * * * *
39142170 TGATTTGCATGTTAAGCATGCCATTATACTTATTT
1 TGATTCGCATGTTAAACATGCCATTATTCTAATTA
*
39142205 TGATTTGCATG-TAAAGCATG
1 TGATTCGCATGTTAAA-CATG
39142225 TCACTATGTT
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
34 3 0.04
35 73 0.96
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (35 bp):
TGATTCGCATGTTAAACATGCCATTATTCTAATTA
Found at i:39142246 original size:35 final size:35
Alignment explanation
Indices: 39142172--39142266 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 35
39142162 TCTGATTATG
* * * *
39142172 ATTTGCATGTTAAGCATGCCATTATACTTATTTTG
1 ATTTGCATGTAAAGCATGCCACTATACTTATTCTA
* *
39142207 ATTTGCATGTAAAGCATGTCACTAT-GTTGATTCTA
1 ATTTGCATGTAAAGCATGCCACTATACTT-ATTCTA
*
39142242 ATTTGAATGTAAAGCATGCCTACTA
1 ATTTGCATGTAAAGCATGCC-ACTA
39142267 AAAATTTTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 2 0.04
35 44 0.88
36 4 0.08
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (35 bp):
ATTTGCATGTAAAGCATGCCACTATACTTATTCTA
Found at i:39142444 original size:31 final size:31
Alignment explanation
Indices: 39142363--39142444 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
39142353 ATATTAGTAA
* *
39142363 GTCATCATTGTCGGGCAACTCGAGGTGGCAG
1 GTCATTATTGTCGGGCAACCCGAGGTGGCAG
* * ** *
39142394 GTCATTGTTGCCGAACAACCCGAGGTGGCGG
1 GTCATTATTGTCGGGCAACCCGAGGTGGCAG
39142425 GTCATTATTGTCGGGCAACC
1 GTCATTATTGTCGGGCAACC
39142445 TAGGATGACT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (31 bp):
GTCATTATTGTCGGGCAACCCGAGGTGGCAG
Found at i:39149368 original size:5 final size:5
Alignment explanation
Indices: 39149360--39149388 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
39149350 TTCTTTTATT
39149360 ATATA ATATA ATATA ATAT- ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
39149389 TAACTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:39157991 original size:11 final size:11
Alignment explanation
Indices: 39157975--39158008 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39157965 TGTCCCCAAG
39157975 TTGAATTAATT
1 TTGAATTAATT
*
39157986 TTGAATTCATT
1 TTGAATTAATT
39157997 TATGAATTAATT
1 T-TGAATTAATT
39158009 CACTTGTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (11 bp):
TTGAATTAATT
Found at i:39158820 original size:10 final size:9
Alignment explanation
Indices: 39158807--39158846 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
39158797 ATTAATTTTG
39158807 ATTAAATTAA
1 ATTAAATT-A
39158817 ATTAAATTA
1 ATTAAATTA
*
39158826 ATCAAATTA
1 ATTAAATTA
39158835 ATTAAAATTA
1 ATT-AAATTA
39158845 AT
1 AT
39158847 ATAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 11 0.41
10 16 0.59
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTAAATTA
Found at i:39158834 original size:19 final size:19
Alignment explanation
Indices: 39158810--39158846 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
39158800 AATTTTGATT
39158810 AAATTAAATT-AAATTAATC
1 AAATT-AATTAAAATTAATC
39158829 AAATTAATTAAAATTAAT
1 AAATTAATTAAAATTAAT
39158847 ATAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTAATTAAAATTAATC
Found at i:39175029 original size:18 final size:19
Alignment explanation
Indices: 39174992--39175029 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
39174982 AGAAAGAAAA
*
39174992 TTTTAAATTTTTTATTGAT
1 TTTTAAATTTTTTATAGAT
39175011 TTTTAAATTTTTT-TAGAT
1 TTTTAAATTTTTTATAGAT
39175029 T
1 T
39175030 ATGACATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTAAATTTTTTATAGAT
Found at i:39183000 original size:15 final size:16
Alignment explanation
Indices: 39182980--39183012 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39182970 ATCAAGGCTC
39182980 AAAAAGAAGCAG-AGA
1 AAAAAGAAGCAGAAGA
*
39182995 AAAAAGAGGCAGAAGA
1 AAAAAGAAGCAGAAGA
39183011 AA
1 AA
39183013 GAAAAAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.67, C:0.06, G:0.27, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGCAGAAGA
Found at i:39187336 original size:40 final size:41
Alignment explanation
Indices: 39187273--39187351 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
39187263 TATGAAAGTG
*
39187273 ATTAGACGTGATGTTTCATTATGTTTGTTATATGAGTCATAA
1 ATTAGACGTGATG-TTCACTATGTTTGTTATATGAGTCATAA
* * *
39187315 ATTAGATGTGATG-TCACTATGTTTTTTATATTAGTCA
1 ATTAGACGTGATGTTCACTATGTTTGTTATATGAGTCA
39187352 AAAAAGTAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 21 0.64
42 12 0.36
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.47
Consensus pattern (41 bp):
ATTAGACGTGATGTTCACTATGTTTGTTATATGAGTCATAA
Found at i:39187919 original size:14 final size:14
Alignment explanation
Indices: 39187900--39187930 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39187890 ACTTCTGATA
39187900 TCCCAACCTTGAAT
1 TCCCAACCTTGAAT
39187914 TCCCAACCTTGAAT
1 TCCCAACCTTGAAT
39187928 TCC
1 TCC
39187931 AATTCTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.39, G:0.06, T:0.29
Consensus pattern (14 bp):
TCCCAACCTTGAAT
Found at i:39190890 original size:22 final size:22
Alignment explanation
Indices: 39190865--39190907 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39190855 CTCCTAAACA
*
39190865 TGTCCTC-AAGATCACGTGACCT
1 TGTCCTCGAAGA-CAAGTGACCT
39190887 TGTCCTCGAAGACAAGTGACC
1 TGTCCTCGAAGACAAGTGACC
39190908 AACATAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (22 bp):
TGTCCTCGAAGACAAGTGACCT
Found at i:39207659 original size:46 final size:46
Alignment explanation
Indices: 39207600--39207697 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 46
39207590 AGCTCGTCAA
* *
39207600 CCCTTCATATTTGAAATAAC-AGCATCGATATTACATTTCAGCTTGC
1 CCCTACATATTTGAAATAACTA-CATCGACATTACATTTCAGCTTGC
** * *
39207646 CCCTACATATTTGAAATCGCTACATCGACATTACATTTTAGCTTGT
1 CCCTACATATTTGAAATAACTACATCGACATTACATTTCAGCTTGC
39207692 CCCTAC
1 CCCTAC
39207698 GTAGATTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.35
Consensus pattern (46 bp):
CCCTACATATTTGAAATAACTACATCGACATTACATTTCAGCTTGC
Found at i:39210469 original size:9 final size:9
Alignment explanation
Indices: 39210455--39210490 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
39210445 CATGCAAATT
39210455 AGAAAAGAA
1 AGAAAAGAA
39210464 AGAAAAGGAA
1 AGAAAA-GAA
39210474 AG-AAAGAA
1 AGAAAAGAA
39210482 AGAAAAGAA
1 AGAAAAGAA
39210491 GGAGAGAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 5 0.20
9 15 0.60
10 5 0.20
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (9 bp):
AGAAAAGAA
Found at i:39210498 original size:13 final size:13
Alignment explanation
Indices: 39210455--39210490 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
39210445 CATGCAAATT
39210455 AGAAAAGAAAGAAA
1 AGAAAAGAAAG-AA
*
39210469 AGGAAAGAAAGAA
1 AGAAAAGAAAGAA
39210482 AGAAAAGAA
1 AGAAAAGAA
39210491 GGAGAGAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:39211208 original size:25 final size:25
Alignment explanation
Indices: 39211160--39211208 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
39211150 CATAATTGAA
* * *
39211160 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
39211185 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
39211209 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:39211631 original size:25 final size:25
Alignment explanation
Indices: 39211603--39211660 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
39211593 GTTATTGATT
**
39211603 TTGAAATGGCTAAGATGAGAAAATA
1 TTGAAATGGAAAAGATGAGAAAATA
39211628 TTGAAATGGAAAAGATGAGAAAATA
1 TTGAAATGGAAAAGATGAGAAAATA
39211653 TTGAAATG
1 TTGAAATG
39211661 AATTCAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.50, C:0.02, G:0.24, T:0.24
Consensus pattern (25 bp):
TTGAAATGGAAAAGATGAGAAAATA
Found at i:39215713 original size:113 final size:113
Alignment explanation
Indices: 39215546--39215814 Score: 262
Period size: 113 Copynumber: 2.4 Consensus size: 113
39215536 TTCTATGCTT
* *
39215546 CTTTCATTTCTTTAGAGGCGCTTTTAA-AAAAACGCCGCAATAGAACATGATTTAGCGGCGCAAC
1 CTTTCATTTCTTTAGTGGCGC-TTTAATAAAAACGCCGCAATAGAACAGGATTTAGCGGCGC-AC
* * * * *
39215610 AT--AGAAAATGCCGCAAAATAATTTGAGCTAA-ACGGCTTTGTTTTTTTTC
64 ATGCAG-AAACGCCGCAAAATAATTTCAG-TAATACGACTTCGTTTTATTTC
* * ** * **
39215659 CTTTTATTTCTTTAGTGGCGCTTTAATAAAATCGCCGCAATAG-ATGGGCCTTTAGCGGCGCTTA
1 CTTTCATTTCTTTAGTGGCGCTTTAATAAAAACGCCGCAATAGAACAGG-ATTTAGCGGCGCACA
*
39215723 TGCAGAAACGCCGCAAAATAATTTCAGTAATATGACTTCGTTTTATTTC
65 TGCAGAAACGCCGCAAAATAATTTCAGTAATACGACTTCGTTTTATTTC
* * * *
39215772 CATTTGATTTCTTTTGTGGCAC-TTACTAACAAACGCCGCAATA
1 C-TTTCATTTCTTTAGTGGCGCTTTAATAA-AAACGCCGCAATA
39215815 TAATGCTTAT
Statistics
Matches: 129, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
112 12 0.09
113 86 0.67
114 31 0.24
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (113 bp):
CTTTCATTTCTTTAGTGGCGCTTTAATAAAAACGCCGCAATAGAACAGGATTTAGCGGCGCACAT
GCAGAAACGCCGCAAAATAATTTCAGTAATACGACTTCGTTTTATTTC
Found at i:39216249 original size:7 final size:7
Alignment explanation
Indices: 39216239--39216292 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
39216229 TAGGTTTAGT
*
39216239 GTTTTGG
1 GTTTGGG
*
39216246 GTTTAGG
1 GTTTGGG
*
39216253 GTTTGGAA
1 GTTTGG-G
39216261 GTTTGGG
1 GTTTGGG
**
39216268 GTTTAAG
1 GTTTGGG
39216275 GTTTGGG
1 GTTTGGG
39216282 GTTTGGG
1 GTTTGGG
39216289 GTTT
1 GTTT
39216293 AGGCCACTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
7 32 0.84
8 6 0.16
ACGTcount: A:0.09, C:0.00, G:0.44, T:0.46
Consensus pattern (7 bp):
GTTTGGG
Found at i:39216269 original size:22 final size:21
Alignment explanation
Indices: 39216239--39216295 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
39216229 TAGGTTTAGT
*
39216239 GTTTTGGGTTTAGGGTTTGGAA
1 GTTTGGGGTTTAGGGTTTGG-A
* *
39216261 GTTTGGGGTTTAAGGTTTGGG
1 GTTTGGGGTTTAGGGTTTGGA
39216282 GTTTGGGGTTTAGG
1 GTTTGGGGTTTAGG
39216296 CCACTTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.11, C:0.00, G:0.46, T:0.44
Consensus pattern (21 bp):
GTTTGGGGTTTAGGGTTTGGA
Found at i:39216417 original size:137 final size:137
Alignment explanation
Indices: 39216276--39216562 Score: 574
Period size: 137 Copynumber: 2.1 Consensus size: 137
39216266 GGGTTTAAGG
39216276 TTTGGGGTTTGGGGTTTAGGCCACTTTAGTCATGTTAAGAGGTTAGTGTTCAAGGCTTATAAGAG
1 TTTGGGGTTTGGGGTTTAGGCCACTTTAGTCATGTTAAGAGGTTAGTGTTCAAGGCTTATAAGAG
39216341 GTTAGTGTTTTAGGGCTTGATGCTTGTGGTTTACGGTTTGCAGTTTATAATTTAAGGTTTACAAT
66 GTTAGTGTTTTAGGGCTTGATGCTTGTGGTTTACGGTTTGCAGTTTATAATTTAAGGTTTACAAT
39216406 GCATGGT
131 GCATGGT
39216413 TTTGGGGTTTGGGGTTTAGGCCACTTTAGTCATGTTAAGAGGTTAGTGTTCAAGGCTTATAAGAG
1 TTTGGGGTTTGGGGTTTAGGCCACTTTAGTCATGTTAAGAGGTTAGTGTTCAAGGCTTATAAGAG
39216478 GTTAGTGTTTTAGGGCTTGATGCTTGTGGTTTACGGTTTGCAGTTTATAATTTAAGGTTTACAAT
66 GTTAGTGTTTTAGGGCTTGATGCTTGTGGTTTACGGTTTGCAGTTTATAATTTAAGGTTTACAAT
39216543 GCATGGT
131 GCATGGT
39216550 TTTGGGGTTTGGG
1 TTTGGGGTTTGGG
39216563 CAATTTAAGG
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 150 1.00
ACGTcount: A:0.20, C:0.08, G:0.31, T:0.41
Consensus pattern (137 bp):
TTTGGGGTTTGGGGTTTAGGCCACTTTAGTCATGTTAAGAGGTTAGTGTTCAAGGCTTATAAGAG
GTTAGTGTTTTAGGGCTTGATGCTTGTGGTTTACGGTTTGCAGTTTATAATTTAAGGTTTACAAT
GCATGGT
Found at i:39217012 original size:70 final size:70
Alignment explanation
Indices: 39216929--39217059 Score: 244
Period size: 70 Copynumber: 1.9 Consensus size: 70
39216919 AAATTTTAAC
39216929 AATTGAAAATAATAAATCTGTATAAAATTTTTAAATAATATTATTAATAATAATAATAATGGCCT
1 AATTGAAAATAATAAATCTGTATAAAATTTTTAAATAATATTATTAATAATAATAATAATGGCCT
39216994 AATAT
66 AATAT
* *
39216999 AATTGAAAATAATAAATCTGTATTAAATTTTTAAATAATATTATTAATAATATTAATAATG
1 AATTGAAAATAATAAATCTGTATAAAATTTTTAAATAATATTATTAATAATAATAATAATG
39217060 TCATAATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.40
Consensus pattern (70 bp):
AATTGAAAATAATAAATCTGTATAAAATTTTTAAATAATATTATTAATAATAATAATAATGGCCT
AATAT
Found at i:39218567 original size:16 final size:18
Alignment explanation
Indices: 39218527--39218574 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
39218517 GTATTGCACC
*
39218527 TTTTGAATGTTAAGCTATG
1 TTTTGAATGTTAAACTA-G
39218546 TTTTGAATGTTAAAC-A-
1 TTTTGAATGTTAAACTAG
39218562 TTTTGAATGTTAA
1 TTTTGAATGTTAA
39218575 GAAGATGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 13 0.46
18 1 0.04
19 14 0.50
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (18 bp):
TTTTGAATGTTAAACTAG
Found at i:39218688 original size:25 final size:26
Alignment explanation
Indices: 39218660--39218711 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39218650 AAAATGTTGC
*
39218660 ACAGTTAAAC-ATAAACTGAACAAAA
1 ACAGTTAAACTAAAAACTGAACAAAA
* *
39218685 ACAGTTTAGCTAAAAACTGAACAAAA
1 ACAGTTAAACTAAAAACTGAACAAAA
39218711 A
1 A
39218712 TCCAGCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.58, C:0.15, G:0.10, T:0.17
Consensus pattern (26 bp):
ACAGTTAAACTAAAAACTGAACAAAA
Found at i:39218994 original size:21 final size:21
Alignment explanation
Indices: 39218970--39219042 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
39218960 GTTTTGGGAC
*
39218970 TATTTATTTATATTTTCAGCG
1 TATTTATTTATATTTTCAGCA
* *
39218991 TATTTAATATTATTGATATT-A-TA
1 TATTT-AT-TTA-T-ATTTTCAGCA
39219014 TTATTTATTTATATTTTCAGCA
1 -TATTTATTTATATTTTCAGCA
39219036 TATTTAT
1 TATTTAT
39219043 ATAAACATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
20 4 0.10
21 14 0.35
22 6 0.15
23 5 0.12
24 7 0.17
25 4 0.10
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTTATTTATATTTTCAGCA
Found at i:39219849 original size:9 final size:9
Alignment explanation
Indices: 39219835--39220248 Score: 190
Period size: 9 Copynumber: 48.4 Consensus size: 9
39219825 ACTATCACAT
39219835 CTTACATAA
1 CTTACATAA
*
39219844 CTTACATAG
1 CTTACATAA
*
39219853 CTTA-ATTA
1 CTTACATAA
*
39219861 --TACTTAA
1 CTTACATAA
39219868 CTTACATAA
1 CTTACATAA
*
39219877 CTTACATTA
1 CTTACATAA
*
39219886 --TACACAA
1 CTTACATAA
39219893 CTTACATAA
1 CTTACATAA
*
39219902 CTTTCATTATACA
1 C-TT-A-CATA-A
*
39219915 CATACATAA
1 CTTACATAA
39219924 CTTACATATA
1 CTTACATA-A
* *
39219934 -ATACACAA
1 CTTACATAA
*
39219942 CATACATAA
1 CTTACATAA
39219951 CTTACATAA
1 CTTACATAA
* *
39219960 TTTTCAT-A
1 CTTACATAA
*
39219968 -GTACATAA
1 CTTACATAA
39219976 CTTACATAA
1 CTTACATAA
*
39219985 --TA-TTGAA
1 CTTACAT-AA
39219992 CTTACATAA
1 CTTACATAA
* *
39220001 TTTTCATAA
1 CTTACATAA
39220010 --TACATAA
1 CTTACATAA
* *
39220017 GTTACTTAA
1 CTTACATAA
* *
39220026 TTTTCATAA
1 CTTACATAA
* *
39220035 --TAAAAAA
1 CTTACATAA
39220042 CTTACATAA
1 CTTACATAA
39220051 CTTACATAA
1 CTTACATAA
* *
39220060 TTTTCATAA
1 CTTACATAA
39220069 CTTACATAA
1 CTTACATAA
39220078 CTT--AT-A
1 CTTACATAA
* *
39220084 CAGTACACAA
1 C-TTACATAA
39220094 CTTACATAA
1 CTTACATAA
* *
39220103 TTTTCATAA
1 CTTACATAA
39220112 --TACATAA
1 CTTACATAA
39220119 CTTACATAA
1 CTTACATAA
39220128 -TTGATCATAA
1 CTT-A-CATAA
**
39220138 --TACAGCA
1 CTTACATAA
39220145 CTTACATAA
1 CTTACATAA
*
39220154 -TT-CACAA
1 CTTACATAA
39220161 CTTACATAA
1 CTTACATAA
*
39220170 -TATTCATAA
1 CT-TACATAA
39220179 --TACATAA
1 CTTACATAA
39220186 CTTACATAA
1 CTTACATAA
* *
39220195 TTTTCATAA
1 CTTACATAA
*
39220204 --TAAATAA
1 CTTACATAA
39220211 CTTACATAA
1 CTTACATAA
39220220 --TACATAA
1 CTTACATAA
39220227 CTTACATAA
1 CTTACATAA
*
39220236 CTTACATAG
1 CTTACATAA
39220245 CTTA
1 CTTA
39220249 ATTATACTTA
Statistics
Matches: 303, Mismatches: 62, Indels: 80
0.68 0.14 0.18
Matches are distributed among these distances:
6 5 0.02
7 59 0.19
8 13 0.04
9 204 0.67
10 14 0.05
11 2 0.01
12 4 0.01
13 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (9 bp):
CTTACATAA
Found at i:39219894 original size:25 final size:25
Alignment explanation
Indices: 39219837--39220153 Score: 216
Period size: 25 Copynumber: 12.6 Consensus size: 25
39219827 TATCACATCT
* * *
39219837 TACATAACTTACATAGCTTA-ATTA
1 TACACAACTTACATAACTTACATAA
** *
39219861 TACTTAACTTACATAACTTACATTA
1 TACACAACTTACATAACTTACATAA
* *
39219886 TACACAACTTACATAACTTTCATTA
1 TACACAACTTACATAACTTACATAA
39219911 TACAC-A--TACATAACTTACATATAA
1 TACACAACTTACATAACTTAC--ATAA
*
39219935 TACACAACATACATAACTTACATAA
1 TACACAACTTACATAACTTACATAA
*** *
39219960 TTTTCATA-GTACATAACTTACATAA
1 TACACA-ACTTACATAACTTACATAA
*** * *
39219985 TATTGAACTTACATAATTTTCATAA
1 TACACAACTTACATAACTTACATAA
* * * * *
39220010 TACATAAGTTACTTAATTTTCATAA
1 TACACAACTTACATAACTTACATAA
* *
39220035 TAAAAAACTTACATAACTTACATAA
1 TACACAACTTACATAACTTACATAA
* * * * *
39220060 TTTTCATAACTTACATAACTTATACAG
1 --TACACAACTTACATAACTTACATAA
* *
39220087 TACACAACTTACATAATTTTCATAA
1 TACACAACTTACATAACTTACATAA
*
39220112 TACATAACTTACATAA-TTGATCATAA
1 TACACAACTTACATAACTT-A-CATAA
39220138 TACAGC-ACTTACATAA
1 TACA-CAACTTACATAA
39220154 TTCACAACTT
Statistics
Matches: 237, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
22 11 0.05
24 30 0.13
25 145 0.61
26 20 0.08
27 31 0.13
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (25 bp):
TACACAACTTACATAACTTACATAA
Found at i:39219896 original size:49 final size:50
Alignment explanation
Indices: 39219812--39220258 Score: 156
Period size: 50 Copynumber: 9.1 Consensus size: 50
39219802 TAAAAACATA
* * * *
39219812 ACTTAA-TTACATGACTATCACATCT-TACATAACTTACATAGCTTAATTAT
1 ACTTAACTTACATAACT-T-ACATATATACACAACTTACATAACTTAATTAT
*
39219862 ACTTAACTTACATAACTTACAT-TATACACAACTTACATAACTTTCATTAT
1 ACTTAACTTACATAACTTACATATATACACAACTTACATAAC-TTAATTAT
* * *
39219912 AC---ACATACATAACTTACATATAATACACAACATACATAACTTACATAAT
1 ACTTAACTTACATAACTTACATAT-ATACACAACTTACATAACTTA-ATTAT
* * *** * * *
39219961 -TTTCATA-GTACATAACTTACATA-ATATTGAACTTACATAATTTTCATAAT
1 ACTT-A-ACTTACATAACTTACATATATACACAACTTACATAA-CTTAATTAT
* * * * * * * *
39220011 ACATAAGTTACTTAATTTTCATA-ATAAAAAACTTACATAACTTACATAATTT
1 ACTTAACTTACATAACTTACATATATACACAACTTACATAACTTA-AT--TAT
* * * * * *
39220063 TCATAACTTACATAACTT--ATACAGTACACAACTTACATAATTTTCATAAT
1 ACTTAACTTACATAACTTACATATA-TACACAACTTACATAA-CTTAATTAT
* * *
39220113 ACATAACTTACATAA-TTGATCATA-ATACAGC-ACTTACATAA-TTCA-CA-
1 ACTTAACTTACATAACTT-A-CATATATACA-CAACTTACATAACTTAATTAT
* * * * *
39220160 ACTT-ACATA-AT-A-TT-CATA-ATACATAACTTACATAATTTTCATAAT
1 ACTTAACTTACATAACTTACATATATACACAACTTACATAA-CTTAATTAT
** * *
39220205 AAATAACTTACATAA--TACATA-ACTTACATAACTTACATAGCTTAATTAT
1 ACTTAACTTACATAACTTACATATA--TACACAACTTACATAACTTAATTAT
39220254 ACTTA
1 ACTTA
39220259 TTCTTAAATC
Statistics
Matches: 307, Mismatches: 54, Indels: 73
0.71 0.12 0.17
Matches are distributed among these distances:
41 19 0.06
43 4 0.01
44 4 0.01
45 4 0.01
46 8 0.03
47 22 0.07
48 11 0.04
49 58 0.19
50 96 0.31
51 27 0.09
52 48 0.16
53 6 0.02
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (50 bp):
ACTTAACTTACATAACTTACATATATACACAACTTACATAACTTAATTAT
Found at i:39219995 original size:41 final size:41
Alignment explanation
Indices: 39219949--39220026 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
39219939 CAACATACAT
*
39219949 AACTTACATAATTTTCATAGTACATAACTTACATAATATTG
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTG
* *
39219990 AACTTACATAATTTTCATAATACATAAGTTACTTAAT
1 AACTTACATAATTTTCATAATACATAACTTACATAAT
39220027 TTTCATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (41 bp):
AACTTACATAATTTTCATAATACATAACTTACATAATATTG
Found at i:39220077 original size:43 final size:41
Alignment explanation
Indices: 39220030--39220120 Score: 103
Period size: 43 Copynumber: 2.2 Consensus size: 41
39220020 ACTTAATTTT
* *
39220030 CATAA-TAAAAAACTTACATAACTTACATAATTTTCATAACTTA
1 CATAACTAAAAAA-GTACACAACTTACATAATTTTCATAA--TA
* * *
39220073 CATAACTTATACAGTACACAACTTACATAATTTTCATAATA
1 CATAACTAAAAAAGTACACAACTTACATAATTTTCATAATA
39220114 CATAACT
1 CATAACT
39220121 TACATAATTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 9 0.21
43 29 0.69
44 4 0.10
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (41 bp):
CATAACTAAAAAAGTACACAACTTACATAATTTTCATAATA
Found at i:39220115 original size:16 final size:16
Alignment explanation
Indices: 39219870--39220235 Score: 151
Period size: 16 Copynumber: 22.0 Consensus size: 16
39219860 ATACTTAACT
*
39219870 TACATAACTTACATTA
1 TACATAACTTACATAA
*
39219886 TACACAACTTACATAA
1 TACATAACTTACATAA
* * *
39219902 CTTTCATTA--TACA-CA
1 --TACATAACTTACATAA
39219917 TACATAACTTACATATAA
1 TACATAACTTAC--ATAA
* *
39219935 TACACAACATACATAA
1 TACATAACTTACATAA
* * *
39219951 CTTACATAATTTTCATAG
1 --TACATAACTTACATAA
39219969 TACATAACTTACATAA
1 TACATAACTTACATAA
*
39219985 TA-TTGAACTTACATAA
1 TACAT-AACTTACATAA
*
39220001 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
* * *
39220017 GTTACTTAATTTTCATAA
1 --TACATAACTTACATAA
* *
39220035 TAAAAAACTTACATAA
1 TACATAACTTACATAA
* *
39220051 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
* * *
39220069 CTTACATAACTTATACAG
1 --TACATAACTTACATAA
*
39220087 TACACAACTTACATAA
1 TACATAACTTACATAA
*
39220103 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
39220119 CTTACATAA-TTGATCATAA
1 --TACATAACTT-A-CATAA
**
39220138 TACAGCACTTACATAA
1 TACATAACTTACATAA
* *
39220154 TTCACAACTTACATAA
1 TACATAACTTACATAA
39220170 TATTCATAA--TACATAA
1 TA--CATAACTTACATAA
* *
39220186 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
*
39220204 TAAATAACTTACATAA
1 TACATAACTTACATAA
39220220 TACATAACTTACATAA
1 TACATAACTTACATAA
39220236 CTTACATAGC
Statistics
Matches: 261, Mismatches: 60, Indels: 58
0.69 0.16 0.15
Matches are distributed among these distances:
13 5 0.02
15 5 0.02
16 157 0.60
17 8 0.03
18 80 0.31
19 6 0.02
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:39220177 original size:25 final size:25
Alignment explanation
Indices: 39220149--39220243 Score: 122
Period size: 25 Copynumber: 3.8 Consensus size: 25
39220139 ACAGCACTTA
* *
39220149 CATAATTCACAACTTACATAATATT
1 CATAATACATAACTTACATAATATT
*
39220174 CATAATACATAACTTACATAATTTT
1 CATAATACATAACTTACATAATATT
*
39220199 CATAATAAATAACTTACATAATA--
1 CATAATACATAACTTACATAATATT
39220222 CATAACTTACATAACTTACATA
1 CATAA--TACATAACTTACATA
39220244 GCTTAATTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 5 0.08
25 57 0.92
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (25 bp):
CATAATACATAACTTACATAATATT
Found at i:39220188 original size:92 final size:93
Alignment explanation
Indices: 39220050--39220220 Score: 258
Period size: 92 Copynumber: 1.8 Consensus size: 93
39220040 AACTTACATA
* * *
39220050 ACTTACATAATTTTCATAACTTACATAACTTATACAGTACACAACTTACATAATTTTCATAATAC
1 ACTTACATAA-TTTCACAACTTACATAAATTATACAGTACACAACTTACATAATTTTCATAATAA
39220115 ATAACTTACATAATTGATCATAATACAGC
65 ATAACTTACATAATTGATCATAATACAGC
*
39220144 ACTTACATAA-TTCACAACTTACATAATATTCATA-A-TACATAACTTACATAATTTTCATAATA
1 ACTTACATAATTTCACAACTTACATAA-ATT-ATACAGTACACAACTTACATAATTTTCATAATA
39220206 AATAACTTACATAAT
64 AATAACTTACATAAT
39220221 ACATAACTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
92 55 0.77
93 3 0.04
94 13 0.18
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (93 bp):
ACTTACATAATTTCACAACTTACATAAATTATACAGTACACAACTTACATAATTTTCATAATAAA
TAACTTACATAATTGATCATAATACAGC
Found at i:39222837 original size:14 final size:15
Alignment explanation
Indices: 39222818--39222846 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39222808 GGCACATTAC
39222818 TTGGTATTCT-TTTT
1 TTGGTATTCTGTTTT
39222832 TTGGTATTCTGTTTT
1 TTGGTATTCTGTTTT
39222847 GGCACAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (15 bp):
TTGGTATTCTGTTTT
Found at i:39222845 original size:39 final size:38
Alignment explanation
Indices: 39222774--39222852 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 38
39222764 GACTTTGTGG
39222774 ATTACTTGGTATTCTGTTTTGGTAGGATTGTTTTGGCAC
1 ATTACTTGGTATTCTGTTTTGGTA-GATTGTTTTGGCAC
* *
39222813 ATTACTTGGTATTCTTTTTTTGGTA-TTCTGTTTTGGCAC
1 ATTACTTGGTATTC-TGTTTTGGTAGAT-TGTTTTGGCAC
39222852 A
1 A
39222853 GTTTCTTCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 1 0.03
39 26 0.72
40 9 0.25
ACGTcount: A:0.15, C:0.11, G:0.22, T:0.52
Consensus pattern (38 bp):
ATTACTTGGTATTCTGTTTTGGTAGATTGTTTTGGCAC
Found at i:39224247 original size:9 final size:9
Alignment explanation
Indices: 39224233--39224646 Score: 190
Period size: 9 Copynumber: 48.4 Consensus size: 9
39224223 ACTATCACAT
39224233 CTTACATAA
1 CTTACATAA
*
39224242 CTTACATAG
1 CTTACATAA
*
39224251 CTTA-ATTA
1 CTTACATAA
*
39224259 --TACTTAA
1 CTTACATAA
39224266 CTTACATAA
1 CTTACATAA
*
39224275 CTTACATTA
1 CTTACATAA
*
39224284 --TACACAA
1 CTTACATAA
39224291 CTTACATAA
1 CTTACATAA
*
39224300 CTTTCATTATACA
1 C-TT-A-CATA-A
*
39224313 CATACATAA
1 CTTACATAA
39224322 CTTACATATA
1 CTTACATA-A
* *
39224332 -ATACACAA
1 CTTACATAA
*
39224340 CATACATAA
1 CTTACATAA
39224349 CTTACATAA
1 CTTACATAA
* *
39224358 TTTTCAT-A
1 CTTACATAA
*
39224366 -GTACATAA
1 CTTACATAA
39224374 CTTACATAA
1 CTTACATAA
*
39224383 --TA-TTGAA
1 CTTACAT-AA
39224390 CTTACATAA
1 CTTACATAA
* *
39224399 TTTTCATAA
1 CTTACATAA
39224408 --TACATAA
1 CTTACATAA
* *
39224415 GTTACTTAA
1 CTTACATAA
* *
39224424 TTTTCATAA
1 CTTACATAA
* *
39224433 --TAAAAAA
1 CTTACATAA
39224440 CTTACATAA
1 CTTACATAA
39224449 CTTACATAA
1 CTTACATAA
* *
39224458 TTTTCATAA
1 CTTACATAA
39224467 CTTACATAA
1 CTTACATAA
39224476 CTT--AT-A
1 CTTACATAA
* *
39224482 CAGTACACAA
1 C-TTACATAA
39224492 CTTACATAA
1 CTTACATAA
* *
39224501 TTTTCATAA
1 CTTACATAA
39224510 --TACATAA
1 CTTACATAA
39224517 CTTACATAA
1 CTTACATAA
39224526 -TTGATCATAA
1 CTT-A-CATAA
**
39224536 --TACAGCA
1 CTTACATAA
39224543 CTTACATAA
1 CTTACATAA
*
39224552 -TT-CACAA
1 CTTACATAA
39224559 CTTACATAA
1 CTTACATAA
*
39224568 -TATTCATAA
1 CT-TACATAA
39224577 --TACATAA
1 CTTACATAA
39224584 CTTACATAA
1 CTTACATAA
* *
39224593 TTTTCATAA
1 CTTACATAA
*
39224602 --TAAATAA
1 CTTACATAA
39224609 CTTACATAA
1 CTTACATAA
39224618 --TACATAA
1 CTTACATAA
39224625 CTTACATAA
1 CTTACATAA
*
39224634 CTTACATAG
1 CTTACATAA
39224643 CTTA
1 CTTA
39224647 ATTATACTTA
Statistics
Matches: 303, Mismatches: 62, Indels: 80
0.68 0.14 0.18
Matches are distributed among these distances:
6 5 0.02
7 59 0.19
8 13 0.04
9 204 0.67
10 14 0.05
11 2 0.01
12 4 0.01
13 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (9 bp):
CTTACATAA
Found at i:39224292 original size:25 final size:25
Alignment explanation
Indices: 39224235--39224551 Score: 216
Period size: 25 Copynumber: 12.6 Consensus size: 25
39224225 TATCACATCT
* * *
39224235 TACATAACTTACATAGCTTA-ATTA
1 TACACAACTTACATAACTTACATAA
** *
39224259 TACTTAACTTACATAACTTACATTA
1 TACACAACTTACATAACTTACATAA
* *
39224284 TACACAACTTACATAACTTTCATTA
1 TACACAACTTACATAACTTACATAA
39224309 TACAC-A--TACATAACTTACATATAA
1 TACACAACTTACATAACTTAC--ATAA
*
39224333 TACACAACATACATAACTTACATAA
1 TACACAACTTACATAACTTACATAA
*** *
39224358 TTTTCATA-GTACATAACTTACATAA
1 TACACA-ACTTACATAACTTACATAA
*** * *
39224383 TATTGAACTTACATAATTTTCATAA
1 TACACAACTTACATAACTTACATAA
* * * * *
39224408 TACATAAGTTACTTAATTTTCATAA
1 TACACAACTTACATAACTTACATAA
* *
39224433 TAAAAAACTTACATAACTTACATAA
1 TACACAACTTACATAACTTACATAA
* * * * *
39224458 TTTTCATAACTTACATAACTTATACAG
1 --TACACAACTTACATAACTTACATAA
* *
39224485 TACACAACTTACATAATTTTCATAA
1 TACACAACTTACATAACTTACATAA
*
39224510 TACATAACTTACATAA-TTGATCATAA
1 TACACAACTTACATAACTT-A-CATAA
39224536 TACAGC-ACTTACATAA
1 TACA-CAACTTACATAA
39224552 TTCACAACTT
Statistics
Matches: 237, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
22 11 0.05
24 30 0.13
25 145 0.61
26 20 0.08
27 31 0.13
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (25 bp):
TACACAACTTACATAACTTACATAA
Found at i:39224294 original size:49 final size:50
Alignment explanation
Indices: 39224210--39224656 Score: 156
Period size: 50 Copynumber: 9.1 Consensus size: 50
39224200 TAAAAACATA
* * * *
39224210 ACTTAA-TTACATGACTATCACATCT-TACATAACTTACATAGCTTAATTAT
1 ACTTAACTTACATAACT-T-ACATATATACACAACTTACATAACTTAATTAT
*
39224260 ACTTAACTTACATAACTTACAT-TATACACAACTTACATAACTTTCATTAT
1 ACTTAACTTACATAACTTACATATATACACAACTTACATAAC-TTAATTAT
* * *
39224310 AC---ACATACATAACTTACATATAATACACAACATACATAACTTACATAAT
1 ACTTAACTTACATAACTTACATAT-ATACACAACTTACATAACTTA-ATTAT
* * *** * * *
39224359 -TTTCATA-GTACATAACTTACATA-ATATTGAACTTACATAATTTTCATAAT
1 ACTT-A-ACTTACATAACTTACATATATACACAACTTACATAA-CTTAATTAT
* * * * * * * *
39224409 ACATAAGTTACTTAATTTTCATA-ATAAAAAACTTACATAACTTACATAATTT
1 ACTTAACTTACATAACTTACATATATACACAACTTACATAACTTA-AT--TAT
* * * * * *
39224461 TCATAACTTACATAACTT--ATACAGTACACAACTTACATAATTTTCATAAT
1 ACTTAACTTACATAACTTACATATA-TACACAACTTACATAA-CTTAATTAT
* * *
39224511 ACATAACTTACATAA-TTGATCATA-ATACAGC-ACTTACATAA-TTCA-CA-
1 ACTTAACTTACATAACTT-A-CATATATACA-CAACTTACATAACTTAATTAT
* * * * *
39224558 ACTT-ACATA-AT-A-TT-CATA-ATACATAACTTACATAATTTTCATAAT
1 ACTTAACTTACATAACTTACATATATACACAACTTACATAA-CTTAATTAT
** * *
39224603 AAATAACTTACATAA--TACATA-ACTTACATAACTTACATAGCTTAATTAT
1 ACTTAACTTACATAACTTACATATA--TACACAACTTACATAACTTAATTAT
39224652 ACTTA
1 ACTTA
39224657 TTCTTAAATC
Statistics
Matches: 307, Mismatches: 54, Indels: 73
0.71 0.12 0.17
Matches are distributed among these distances:
41 19 0.06
43 4 0.01
44 4 0.01
45 4 0.01
46 8 0.03
47 22 0.07
48 11 0.04
49 58 0.19
50 96 0.31
51 27 0.09
52 48 0.16
53 6 0.02
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (50 bp):
ACTTAACTTACATAACTTACATATATACACAACTTACATAACTTAATTAT
Found at i:39224393 original size:41 final size:41
Alignment explanation
Indices: 39224347--39224424 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
39224337 CAACATACAT
*
39224347 AACTTACATAATTTTCATAGTACATAACTTACATAATATTG
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTG
* *
39224388 AACTTACATAATTTTCATAATACATAAGTTACTTAAT
1 AACTTACATAATTTTCATAATACATAACTTACATAAT
39224425 TTTCATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (41 bp):
AACTTACATAATTTTCATAATACATAACTTACATAATATTG
Found at i:39224475 original size:43 final size:41
Alignment explanation
Indices: 39224428--39224518 Score: 103
Period size: 43 Copynumber: 2.2 Consensus size: 41
39224418 ACTTAATTTT
* *
39224428 CATAA-TAAAAAACTTACATAACTTACATAATTTTCATAACTTA
1 CATAACTAAAAAA-GTACACAACTTACATAATTTTCATAA--TA
* * *
39224471 CATAACTTATACAGTACACAACTTACATAATTTTCATAATA
1 CATAACTAAAAAAGTACACAACTTACATAATTTTCATAATA
39224512 CATAACT
1 CATAACT
39224519 TACATAATTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 9 0.21
43 29 0.69
44 4 0.10
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (41 bp):
CATAACTAAAAAAGTACACAACTTACATAATTTTCATAATA
Found at i:39224513 original size:16 final size:16
Alignment explanation
Indices: 39224268--39224633 Score: 151
Period size: 16 Copynumber: 22.0 Consensus size: 16
39224258 ATACTTAACT
*
39224268 TACATAACTTACATTA
1 TACATAACTTACATAA
*
39224284 TACACAACTTACATAA
1 TACATAACTTACATAA
* * *
39224300 CTTTCATTA--TACA-CA
1 --TACATAACTTACATAA
39224315 TACATAACTTACATATAA
1 TACATAACTTAC--ATAA
* *
39224333 TACACAACATACATAA
1 TACATAACTTACATAA
* * *
39224349 CTTACATAATTTTCATAG
1 --TACATAACTTACATAA
39224367 TACATAACTTACATAA
1 TACATAACTTACATAA
*
39224383 TA-TTGAACTTACATAA
1 TACAT-AACTTACATAA
*
39224399 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
* * *
39224415 GTTACTTAATTTTCATAA
1 --TACATAACTTACATAA
* *
39224433 TAAAAAACTTACATAA
1 TACATAACTTACATAA
* *
39224449 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
* * *
39224467 CTTACATAACTTATACAG
1 --TACATAACTTACATAA
*
39224485 TACACAACTTACATAA
1 TACATAACTTACATAA
*
39224501 TTTTCATAA--TACATAA
1 --TACATAACTTACATAA
39224517 CTTACATAA-TTGATCATAA
1 --TACATAACTT-A-CATAA
**
39224536 TACAGCACTTACATAA
1 TACATAACTTACATAA
* *
39224552 TTCACAACTTACATAA
1 TACATAACTTACATAA
39224568 TATTCATAA--TACATAA
1 TA--CATAACTTACATAA
* *
39224584 CTTACATAATTTTCATAA
1 --TACATAACTTACATAA
*
39224602 TAAATAACTTACATAA
1 TACATAACTTACATAA
39224618 TACATAACTTACATAA
1 TACATAACTTACATAA
39224634 CTTACATAGC
Statistics
Matches: 261, Mismatches: 60, Indels: 58
0.69 0.16 0.15
Matches are distributed among these distances:
13 5 0.02
15 5 0.02
16 157 0.60
17 8 0.03
18 80 0.31
19 6 0.02
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:39224575 original size:25 final size:25
Alignment explanation
Indices: 39224547--39224641 Score: 122
Period size: 25 Copynumber: 3.8 Consensus size: 25
39224537 ACAGCACTTA
* *
39224547 CATAATTCACAACTTACATAATATT
1 CATAATACATAACTTACATAATATT
*
39224572 CATAATACATAACTTACATAATTTT
1 CATAATACATAACTTACATAATATT
*
39224597 CATAATAAATAACTTACATAATA--
1 CATAATACATAACTTACATAATATT
39224620 CATAACTTACATAACTTACATA
1 CATAA--TACATAACTTACATA
39224642 GCTTAATTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 5 0.08
25 57 0.92
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (25 bp):
CATAATACATAACTTACATAATATT
Found at i:39224586 original size:92 final size:93
Alignment explanation
Indices: 39224448--39224618 Score: 258
Period size: 92 Copynumber: 1.8 Consensus size: 93
39224438 AACTTACATA
* * *
39224448 ACTTACATAATTTTCATAACTTACATAACTTATACAGTACACAACTTACATAATTTTCATAATAC
1 ACTTACATAA-TTTCACAACTTACATAAATTATACAGTACACAACTTACATAATTTTCATAATAA
39224513 ATAACTTACATAATTGATCATAATACAGC
65 ATAACTTACATAATTGATCATAATACAGC
*
39224542 ACTTACATAA-TTCACAACTTACATAATATTCATA-A-TACATAACTTACATAATTTTCATAATA
1 ACTTACATAATTTCACAACTTACATAA-ATT-ATACAGTACACAACTTACATAATTTTCATAATA
39224604 AATAACTTACATAAT
64 AATAACTTACATAAT
39224619 ACATAACTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
92 55 0.77
93 3 0.04
94 13 0.18
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (93 bp):
ACTTACATAATTTCACAACTTACATAAATTATACAGTACACAACTTACATAATTTTCATAATAAA
TAACTTACATAATTGATCATAATACAGC
Found at i:39229457 original size:21 final size:21
Alignment explanation
Indices: 39229431--39229477 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39229421 AACTTAAAGC
* *
39229431 AGAGGCGACAGTGAGGGAAGT
1 AGAGGCGACAGCGAGAGAAGT
*
39229452 AGAGGCTACAGCGAGAGAAGT
1 AGAGGCGACAGCGAGAGAAGT
39229473 AGAGG
1 AGAGG
39229478 TTCAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.45, T:0.09
Consensus pattern (21 bp):
AGAGGCGACAGCGAGAGAAGT
Found at i:39229940 original size:44 final size:43
Alignment explanation
Indices: 39229892--39230146 Score: 216
Period size: 42 Copynumber: 6.0 Consensus size: 43
39229882 ATTCTATAGA
**
39229892 GGCGTTTGTGGAAAAAATTGCCGCTAAAGAACATGACCTTTAGC
1 GGCGTTTGTGG-AAAAAGCGCCGCTAAAGAACATGACCTTTAGC
* * * * *
39229936 GGCGTTTATGGAAAAAAACACCGCTAAAGAACATTACTTTTAGC
1 GGCGTTTGTGG-AAAAAGCGCCGCTAAAGAACATGACCTTTAGC
* ** **
39229980 GGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTCTTTAGC
1 GGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCTTTAGC
* * *
39230023 GGCGTTTGTTGG--TATGCGCCGCTAAAGAACATTACCTTTAGC
1 GGCGTTTG-TGGAAAAAGCGCCGCTAAAGAACATGACCTTTAGC
* ** *
39230065 GGCGTTTCT-GAGGAAGCGCCGCTAAAGAACATGACCTTTTGC
1 GGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCTTTAGC
* * * * *
39230107 AGTGTTTTTTTG---AAGCGCTGCTAAAGAACATGACCTTTAG
1 GGCG-TTTGTGGAAAAAGCGCCGCTAAAGAACATGACCTTTAG
39230147 TAGCGTTTAT
Statistics
Matches: 173, Mismatches: 33, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
40 1 0.01
41 27 0.16
42 58 0.34
43 35 0.20
44 52 0.30
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
GGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCTTTAGC
Found at i:39230813 original size:29 final size:29
Alignment explanation
Indices: 39230757--39230835 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
39230747 GAAACATATG
* * *
39230757 TAGAGTTGCACCAAAGTGCATTAACAGAA
1 TAGAGGTGCACCGAAGTGCAATAACAGAA
**
39230786 TAGAGGTGCACCGAAGTGCAATGTCAGAA
1 TAGAGGTGCACCGAAGTGCAATAACAGAA
*
39230815 TAAAGG-GCACCAGAA-TGCAAT
1 TAGAGGTGCACC-GAAGTGCAAT
39230836 CGGAACAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 11 0.26
29 32 0.74
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (29 bp):
TAGAGGTGCACCGAAGTGCAATAACAGAA
Found at i:39234625 original size:6 final size:6
Alignment explanation
Indices: 39234610--39234639 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39234600 GAAACTAGCT
39234610 AAAG-A AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
39234640 GCCACATTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:39235559 original size:43 final size:44
Alignment explanation
Indices: 39235454--39235561 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
39235444 TGTGTTGTCG
* * *
39235454 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTTACG
1 TGTAAGACCATGTCTGGGACGTTGACATCGACTTGTGATTTACA
* *
39235498 TGTAAGACCCTGTTTGGGACAG-TGACATCGA-TATGTGA-TTACA
1 TGTAAGACCATGTCTGGGAC-GTTGACATCGACT-TGTGATTTACA
39235541 TGTAAGACCATGTCTGGGACG
1 TGTAAGACCATGTCTGGGACG
39235562 ATGGCATTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
42 1 0.02
43 23 0.42
44 30 0.55
45 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACGTTGACATCGACTTGTGATTTACA
Found at i:39240148 original size:50 final size:50
Alignment explanation
Indices: 39240044--39240231 Score: 250
Period size: 50 Copynumber: 3.6 Consensus size: 50
39240034 GGGAATGAGA
* *
39240044 TCCCATGTAAGACCATGTATGGGACATGGCATTGACATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACA-C--CGAG---ATGAGAGG
* *
39240100 TCCCATGTAAAACCATGTCTGAGACATGGCATTGACACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATGAGAGG
* *
39240150 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATGAGAGG
**
39240200 TCCCCCGTAAGACCATGTCTGGGACATGGCAT
1 TCCCATGTAAGACCATGTCTGGGACATGGCAT
39240232 GGGCGCCAAC
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
50 83 0.69
53 3 0.02
55 1 0.01
56 34 0.28
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATGAGAGG
Found at i:39240246 original size:50 final size:50
Alignment explanation
Indices: 39240092--39240286 Score: 239
Period size: 50 Copynumber: 3.9 Consensus size: 50
39240082 CATTGAGATT
* * *
39240092 ATGAGAGGTCCCATGTAAAACCATGTCTGAGACATGGCATTGACACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
*
39240142 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * * *
39240192 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCGCCAAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * *
39240242 ATGAGAACT-CCAGTGTAAGACCATATCTGGGATATGACATTGGCA
1 ATGAGAGGTCCCA-TGTAAGACCATGTCTGGGACATGGCATTGGCA
39240287 GTACAGAAAA
Statistics
Matches: 124, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
49 2 0.02
50 122 0.98
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:39240246 original size:100 final size:103
Alignment explanation
Indices: 39240044--39240283 Score: 254
Period size: 100 Copynumber: 2.3 Consensus size: 103
39240034 GGGAATGAGA
* * *
39240044 TCCCATGTAAGACCATGTATGGGACATGGCATTGACATCATTGAGATTATGAGAGGTCCCATGTA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCA-CGAG--TATGAGAGGTCCCACGTA
* * * **
39240109 AAACCATGTCTGAGACATGGCATTGACACCGAGATGAGAGG
63 AAACCATGTCTGAGACATGGCATGGACACCAACATGAGAAC
* * * *
39240150 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGAG-ATGAGAGGTCCCCCGTAAGA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCACGAGTATGAGAGGTCCCACGTAAAA
* * *
39240212 CCATGTCTGGGACATGGCATGGGCGCCAACATGAGAAC
66 CCATGTCTGAGACATGGCATGGACACCAACATGAGAAC
* * *
39240250 T-CCAGTGTAAGACCATATCTGGGATATGACATTG
1 TCCCA-TGTAAGACCATGTCTGGGACATGGCATTG
39240284 GCAGTACAGA
Statistics
Matches: 114, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
99 3 0.03
100 73 0.64
103 3 0.03
105 1 0.01
106 34 0.30
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (103 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCACGAGTATGAGAGGTCCCACGTAAAA
CCATGTCTGAGACATGGCATGGACACCAACATGAGAAC
Found at i:39240552 original size:12 final size:12
Alignment explanation
Indices: 39240535--39240573 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39240525 ATGAGTTATT
39240535 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
39240547 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
39240559 TAAGTGAGTAAG
1 TAAGTAAGCAAG
39240571 TAA
1 TAA
39240574 AGAAGTGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:39240561 original size:20 final size:20
Alignment explanation
Indices: 39240536--39240579 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39240526 TGAGTTATTT
39240536 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
** *
39240556 AAGTAAGTGAGTAAGTAAAG
1 AAGTAAGCAAGTAAGTAAAC
39240576 AAGT
1 AAGT
39240580 GAGTAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.25, T:0.18
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:39246304 original size:43 final size:44
Alignment explanation
Indices: 39246197--39246304 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 44
39246187 TATGTGTTGT
* *
39246197 CATGTAAGACCACATTTGGGACGTTGGCATCGACTTGTGATTTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTTA
*
39246241 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTGA-TTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGATTTA
39246284 CATGTAAGACCACGTCTGGGA
1 CATGTAAGACCACGTCTGGGA
39246305 TGATGGCGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
43 23 0.41
44 32 0.57
45 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTTA
Found at i:39252885 original size:27 final size:27
Alignment explanation
Indices: 39252855--39253119 Score: 186
Period size: 27 Copynumber: 9.9 Consensus size: 27
39252845 AGCAAATATC
* * *
39252855 GAAATACCCTTGCAGGGTAAAATTATT
1 GAAATACCCTCGAAGGGTAAAATTACT
39252882 GAAATA-CCTCGAAGGGTAAAATTACT
1 GAAATACCCTCGAAGGGTAAAATTACT
* *
39252908 AAAATACCCTCGAAGGGTAAAATTACC
1 GAAATACCCTCGAAGGGTAAAATTACT
* * *
39252935 AAAATACCC-CTAATGGGTAAAATTACC
1 GAAATACCCTCGAA-GGGTAAAATTACT
* *
39252962 AAAATACCCTCGATA-TGTAAAATTACT
1 GAAATACCCTCGA-AGGGTAAAATTACT
* *
39252989 GAAATACCC-CCATTA-GGTTAAATTACT
1 GAAATACCCTCGA--AGGGTAAAATTACT
*** *
39253016 GAAATACTCCTATTA-GGTAAAATTACC
1 GAAATAC-CCTCGAAGGGTAAAATTACT
* * *
39253043 AAAATACCCTTGATA-GGTAAAATTACA
1 GAAATACCCTCGA-AGGGTAAAATTACT
* * * *
39253070 AAAATACTCTCGATGGGTAAAATTACC
1 GAAATACCCTCGAAGGGTAAAATTACT
* *
39253097 AAAATACCCT-TATAGGGTAAAAT
1 GAAATACCCTCGA-AGGGTAAAAT
39253120 GACCGTGATG
Statistics
Matches: 198, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
26 31 0.16
27 162 0.82
28 4 0.02
29 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (27 bp):
GAAATACCCTCGAAGGGTAAAATTACT
Found at i:39252970 original size:54 final size:54
Alignment explanation
Indices: 39252856--39253119 Score: 239
Period size: 54 Copynumber: 4.9 Consensus size: 54
39252846 GCAAATATCG
* * *** * *
39252856 AAATACCCTTGCAGGGTAAAATTATTGAAATACCTCGAA-GGGTAAAATTACTA
1 AAATACCCTCGAAGGGTAAAATTACCAAAATACCCCTAATGGGTAAAATTACTA
*
39252909 AAATACCCTCGAAGGGTAAAATTACCAAAATACCCCTAATGGGTAAAATTACCA
1 AAATACCCTCGAAGGGTAAAATTACCAAAATACCCCTAATGGGTAAAATTACTA
* ** * * * * *
39252963 AAATACCCTCGATA-TGTAAAATTACTGAAATACCCCCATTAGGTTAAATTACTG
1 AAATACCCTCGA-AGGGTAAAATTACCAAAATACCCCTAATGGGTAAAATTACTA
*** * * * *
39253017 AAATACTCCTATTA-GGTAAAATTACCAAAATACCCTTGATAGGTAAAATTACAA
1 AAATAC-CCTCGAAGGGTAAAATTACCAAAATACCCCTAATGGGTAAAATTACTA
* * *
39253071 AAATACTCTCGATGGGTAAAATTACCAAAATA-CCCTTATAGGGTAAAAT
1 AAATACCCTCGAAGGGTAAAATTACCAAAATACCCCTAAT-GGGTAAAAT
39253120 GACCGTGATG
Statistics
Matches: 168, Mismatches: 38, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
53 39 0.23
54 125 0.74
55 4 0.02
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (54 bp):
AAATACCCTCGAAGGGTAAAATTACCAAAATACCCCTAATGGGTAAAATTACTA
Found at i:39253012 original size:81 final size:80
Alignment explanation
Indices: 39252869--39253119 Score: 267
Period size: 81 Copynumber: 3.1 Consensus size: 80
39252859 TACCCTTGCA
***
39252869 GGGTAAAATTATTGAAATA-CCTCGA-AGGGTAAAATTACTAAAATACCCTCGA-AGGGTAAAAT
1 GGGTAAAATTACCAAAATACCCTCGATA-GGTAAAATTACTAAAATACCC-CGATA-GGTAAAAT
39252931 TACCAAAATACCCCTAAT
63 TACCAAAATACCCCTAAT
* * * *
39252949 GGGTAAAATTACCAAAATACCCTCGATATGTAAAATTACTGAAATACCCCCATTAGGTTAAATTA
1 GGGTAAAATTACCAAAATACCCTCGATAGGTAAAATTACTAAAATACCCCGA-TAGGTAAAATTA
** * *
39253014 CTGAAATACTCCTATT
65 CCAAAATACCCCTAAT
* * * * *
39253030 AGGTAAAATTACCAAAATACCCTTGATAGGTAAAATTACAAAAATACTCTCGATGGGTAAAATTA
1 GGGTAAAATTACCAAAATACCCTCGATAGGTAAAATTACTAAAATAC-CCCGATAGGTAAAATTA
*
39253095 CCAAAATA-CCCTTAT
65 CCAAAATACCCCTAAT
39253110 AGGGTAAAAT
1 -GGGTAAAAT
39253120 GACCGTGATG
Statistics
Matches: 139, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
80 22 0.16
81 112 0.81
82 5 0.04
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (80 bp):
GGGTAAAATTACCAAAATACCCTCGATAGGTAAAATTACTAAAATACCCCGATAGGTAAAATTAC
CAAAATACCCCTAAT
Found at i:39253330 original size:24 final size:24
Alignment explanation
Indices: 39253298--39253353 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
39253288 CCTTATGTTA
39253298 TGTATGACTGATTTGTT-TGTGATT
1 TGTATGACTGATTT-TTCTGTGATT
*
39253322 TTTATGACTGATTTTTCTGTGATT
1 TGTATGACTGATTTTTCTGTGATT
39253346 TGTATGAC
1 TGTATGAC
39253354 CAATTCTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.18, C:0.07, G:0.21, T:0.54
Consensus pattern (24 bp):
TGTATGACTGATTTTTCTGTGATT
Found at i:39253492 original size:27 final size:27
Alignment explanation
Indices: 39253441--39253492 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
39253431 GGTGGCTCTA
**
39253441 CCACAATCACTGTTACTAGTGGCTTGG
1 CCACAATCACTGTTACTAGCAGCTTGG
39253468 CCACATAT-ACTGTTACTAGCAGCTT
1 CCACA-ATCACTGTTACTAGCAGCTT
39253493 TGCTGCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (27 bp):
CCACAATCACTGTTACTAGCAGCTTGG
Found at i:39253539 original size:26 final size:26
Alignment explanation
Indices: 39253486--39253539 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
39253476 ACTGTTACTA
* * *
39253486 GCAGCTTTGCTGCGATACTATTGCTG
1 GCAGATTTGCTGCGATACTACTGATG
* *
39253512 GCAGATTTTCTGCGATGCTACTGATG
1 GCAGATTTGCTGCGATACTACTGATG
39253538 GC
1 GC
39253540 TGTGTGCTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (26 bp):
GCAGATTTGCTGCGATACTACTGATG
Found at i:39253568 original size:32 final size:32
Alignment explanation
Indices: 39253527--39253611 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
39253517 TTTTCTGCGA
**
39253527 TGCTACTGATGGCTGTGTGCTGATCATATCAC
1 TGCTACTGATGGCTGTGTGCCAATCATATCAC
* *
39253559 TGCTACTGATGGCTTTGTGCCAATCATATTAC
1 TGCTACTGATGGCTGTGTGCCAATCATATCAC
*
39253591 TG-TACTTATGGCT-TGTAGCCA
1 TGCTACTGATGGCTGTGT-GCCA
39253612 TTCTGTTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
30 3 0.06
31 14 0.30
32 30 0.64
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (32 bp):
TGCTACTGATGGCTGTGTGCCAATCATATCAC
Found at i:39253621 original size:22 final size:21
Alignment explanation
Indices: 39253596--39253660 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
39253586 ATTACTGTAC
39253596 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
** * *
39253618 TTATAACTTATAGCTATCCTGT
1 TTATGGCTT-TAGCCATTCTGT
*
39253640 TTACGGCTCTTAGCCATTCTG
1 TTATGGCT-TTAGCCATTCTG
39253661 ATTACTGGTA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:39258402 original size:32 final size:32
Alignment explanation
Indices: 39258364--39258459 Score: 192
Period size: 32 Copynumber: 3.0 Consensus size: 32
39258354 TTAAAAGTCG
39258364 TCATCTCCTAATCTAGCAGTTTAAAATATTCA
1 TCATCTCCTAATCTAGCAGTTTAAAATATTCA
39258396 TCATCTCCTAATCTAGCAGTTTAAAATATTCA
1 TCATCTCCTAATCTAGCAGTTTAAAATATTCA
39258428 TCATCTCCTAATCTAGCAGTTTAAAATATTCA
1 TCATCTCCTAATCTAGCAGTTTAAAATATTCA
39258460 AGGAAAAACC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (32 bp):
TCATCTCCTAATCTAGCAGTTTAAAATATTCA
Found at i:39259175 original size:27 final size:27
Alignment explanation
Indices: 39259154--39259430 Score: 262
Period size: 27 Copynumber: 10.3 Consensus size: 27
39259144 GGGGTATAAT
*
39259154 AGTCATTTTACCCTAT-GAGGGTATTTC
1 AGTCATTTTACCCT-TCGAGGGTAATTC
*
39259181 AGTCCTTTTACCCTTCGAGGGTAATTC
1 AGTCATTTTACCCTTCGAGGGTAATTC
39259208 -GATCATTTTACCCTTCGAGGGTAATTC
1 AG-TCATTTTACCCTTCGAGGGTAATTC
* * *
39259235 AGTTATTTTACCCTTCGGGGGTATTTC
1 AGTCATTTTACCCTTCGAGGGTAATTC
* *
39259262 AATCATTTTACCCTTCGGGGGTAATT-
1 AGTCATTTTACCCTTCGAGGGTAATTC
* *
39259288 TGATCATTTTACCCTTCGGGGGTAATTC
1 AG-TCATTTTACCCTTCGAGGGTAATTC
* * *
39259316 GGTCATTTTACCTTTTGAGGGTAATT-
1 AGTCATTTTACCCTTCGAGGGTAATTC
* *
39259342 TGATCATTTTACCTTTCG-GGGTAATT-
1 AG-TCATTTTACCCTTCGAGGGTAATTC
*
39259368 AGGTTATTTTACCCTTC-AGGGGTAATTC
1 A-GTCATTTTACCCTTCGA-GGGTAATTC
* * * * *
39259396 AATTATTTTTCCTTTCAAGGGTAATTC
1 AGTCATTTTACCCTTCGAGGGTAATTC
*
39259423 GGTCATTT
1 AGTCATTT
39259431 GCCCATGATT
Statistics
Matches: 213, Mismatches: 26, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
26 23 0.11
27 186 0.87
28 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (27 bp):
AGTCATTTTACCCTTCGAGGGTAATTC
Found at i:39259284 original size:81 final size:80
Alignment explanation
Indices: 39259158--39259404 Score: 293
Period size: 81 Copynumber: 3.1 Consensus size: 80
39259148 TATAATAGTC
* * * *
39259158 ATTTTACCCTATGAGGGTATTTCAGTCCTTTTACCCTTCGAGGGTAATTCGATCATTTTACCCTT
1 ATTTTACCCT-TGAGGGTATTTCAATCATTTTACCCTTCGGGGGTAATTAGATCATTTTACCCTT
39259223 CGAGGGTAATTCAGTT
65 CGAGGGTAATTCAGTT
* *
39259239 ATTTTACCCTTCGGGGGTATTTCAATCATTTTACCCTTCGGGGGTAATTTGATCATTTTACCCTT
1 ATTTTACCCTT-GAGGGTATTTCAATCATTTTACCCTTCGGGGGTAATTAGATCATTTTACCCTT
* * *
39259304 CGGGGGTAATTCGGTC
65 CGAGGGTAATTCAGTT
* * * * *
39259320 ATTTTACCTTTTGAGGGTAATTT-GATCATTTTACCTTTC-GGGGTAATTAGGTTATTTTACCCT
1 ATTTTACC-CTTGAGGGT-ATTTCAATCATTTTACCCTTCGGGGGTAATTAGATCATTTTACCCT
*
39259383 TC-AGGGGTAATTCAATT
64 TCGA-GGGTAATTCAGTT
39259400 ATTTT
1 ATTTT
39259405 TCCTTTCAAG
Statistics
Matches: 143, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
80 39 0.27
81 98 0.69
82 6 0.04
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (80 bp):
ATTTTACCCTTGAGGGTATTTCAATCATTTTACCCTTCGGGGGTAATTAGATCATTTTACCCTTC
GAGGGTAATTCAGTT
Found at i:39265832 original size:32 final size:32
Alignment explanation
Indices: 39265793--39265861 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
39265783 ATTATTTAAA
*
39265793 ATTCATCATCTCCTAATCTAATAGTTTAAAAT
1 ATTCATCATCTCCTAATCTAACAGTTTAAAAT
*
39265825 ATTCATCATCTCCTAATCTAGCAGTTTAAAAT
1 ATTCATCATCTCCTAATCTAACAGTTTAAAAT
39265857 ATTCA
1 ATTCA
39265862 AGGAAAAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.39
Consensus pattern (32 bp):
ATTCATCATCTCCTAATCTAACAGTTTAAAAT
Found at i:39266168 original size:33 final size:30
Alignment explanation
Indices: 39266102--39266206 Score: 106
Period size: 30 Copynumber: 3.4 Consensus size: 30
39266092 ATACAATATG
* *
39266102 CAGTAACAGTCTG-GGCCCTTAGCCCTATT-
1 CAGTAACAGTGTGTGGGCCTTAGCCC-ATTA
* *
39266131 CAGTAGCAGTATAGTGTGGGCCTTAGTCCATTA
1 CAGTAACAG--T-GTGTGGGCCTTAGCCCATTA
*
39266164 CAGTAACAGTGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGTGGGCCTTAGCCCATTA
*
39266194 CAATAACAGTGTG
1 CAGTAACAGTGTG
39266207 GGTCGTATCC
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
29 8 0.13
30 30 0.48
31 2 0.03
32 5 0.08
33 18 0.29
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (30 bp):
CAGTAACAGTGTGTGGGCCTTAGCCCATTA
Found at i:39266176 original size:28 final size:28
Alignment explanation
Indices: 39266143--39266229 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 28
39266133 GTAGCAGTAT
* * *
39266143 AGTGTGGGCCTTAGTCCATTACAGTAAC
1 AGTGTGGGCCTTAGCCCAATACAATAAC
39266171 AGTGTGTGGGCCTTAGCCCAATACAATAAC
1 A--GTGTGGGCCTTAGCCCAATACAATAAC
* * * *
39266201 AGTGTGGGTCGTATCCCAATACAGTAAC
1 AGTGTGGGCCTTAGCCCAATACAATAAC
39266229 A
1 A
39266230 ATGCAATGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 25 0.50
30 25 0.50
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAATAAC
Found at i:39266645 original size:27 final size:27
Alignment explanation
Indices: 39266615--39266781 Score: 214
Period size: 27 Copynumber: 6.2 Consensus size: 27
39266605 TGTTTTGGTT
*
39266615 ATTTTACCCTTCGGGGGTAATT-AGATC
1 ATTTTACCCTTCAGGGGTAATTCAG-TC
*
39266642 ATTTTACCCTTCAAGGGTAATTCAGTC
1 ATTTTACCCTTCAGGGGTAATTCAGTC
*
39266669 ATTTTACCTTTC-GAGGGTAATTC-GATC
1 ATTTTACCCTTCAG-GGGTAATTCAG-TC
*
39266696 ATTTTACCCTTTAGGGGTAATTCAGTC
1 ATTTTACCCTTCAGGGGTAATTCAGTC
39266723 ATTTTACCCTTCAGGGGTAATTCAGTC
1 ATTTTACCCTTCAGGGGTAATTCAGTC
** **
39266750 ATTTTACCCTTCAAAGGTAATTTGGTC
1 ATTTTACCCTTCAGGGGTAATTCAGTC
39266777 ATTTT
1 ATTTT
39266782 CCCATGATTC
Statistics
Matches: 124, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
26 1 0.01
27 119 0.96
28 4 0.03
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTTCAGGGGTAATTCAGTC
Found at i:39266700 original size:81 final size:81
Alignment explanation
Indices: 39266615--39266781 Score: 246
Period size: 81 Copynumber: 2.1 Consensus size: 81
39266605 TGTTTTGGTT
* *
39266615 ATTTTACCCTTCGGGGGTAATT-AGATCATTTTACCCTTCAAGGGTAATTCAGTCATTTTACCTT
1 ATTTTACCCTTCAGGGGTAATTCAG-TCATTTTACCCTTCAAGGGTAATTCAGTCATTTTACCCT
* *
39266679 TCGAGGGTAATTCGATC
65 TCAAAGGTAATTCGATC
* *
39266696 ATTTTACCCTTTAGGGGTAATTCAGTCATTTTACCCTTCAGGGGTAATTCAGTCATTTTACCCTT
1 ATTTTACCCTTCAGGGGTAATTCAGTCATTTTACCCTTCAAGGGTAATTCAGTCATTTTACCCTT
* *
39266761 CAAAGGTAATTTGGTC
66 CAAAGGTAATTCGATC
39266777 ATTTT
1 ATTTT
39266782 CCCATGATTC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 75 0.97
82 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (81 bp):
ATTTTACCCTTCAGGGGTAATTCAGTCATTTTACCCTTCAAGGGTAATTCAGTCATTTTACCCTT
CAAAGGTAATTCGATC
Found at i:39272353 original size:247 final size:247
Alignment explanation
Indices: 39271906--39272400 Score: 828
Period size: 247 Copynumber: 2.0 Consensus size: 247
39271896 TTTCTTGATT
* * *
39271906 CTTGAAATCGTTCCAAACAACAAGATTGGGCCAAGATTCAGTTTCTTGATTTTCTTGAAAACAAG
1 CTTGAAATCGCTCCAAACAACAAAATTGAGCCAAGATTCAGTTTCTTGATTTTCTTGAAAACAAG
39271971 AAAGTGAATCTTGATTTTCTCTTTCTTTCATGTACGCATCTAAGGCCTTGCTAACAAACTCCTAA
66 AAAGTGAATCTTGATTTTCTCTTTCTTTCATGTACGCATCTAAGGCCTTGCTAACAAACTCCTAA
* *
39272036 ATGATCCCATTTAGTTTGGAACGCATTTGTCGGGCCTTTGATCTTGTTATTGGGCCTTGTGGTAA
131 ATGATCCCATTTAGTTTGGAACGCATTTGTCGGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAA
* *
39272101 TTTGAGCCCATCACGTTCTTGGGCTTGGGTTGGGCTTTTGTGACTCGTATCA
196 TTTGAGCCCATCACGTTCTTGAGCTTGGGTTGGGCCTTTGTGACTCGTATCA
** *
39272153 CTTGAAATCGCTCCAAACAGTAAAATTGAGCCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAG
1 CTTGAAATCGCTCCAAACAACAAAATTGAGCCAAGATTCAGTTTCTTGATTTTCTTGAAAACAAG
* * *
39272218 AAAGTGAATCTTGATTTTCTCTTTCTTTCGTGTACGCCTCTAAGGCCTTGCTAACAAATTCCTAA
66 AAAGTGAATCTTGATTTTCTCTTTCTTTCATGTACGCATCTAAGGCCTTGCTAACAAACTCCTAA
* * * * *
39272283 ATGGTCCCATTTAGTTTGGAACGCATTTTTCTGGCCTTTGACCTCGTTATTGGGCCTTTTGGTGA
131 ATGATCCCATTTAGTTTGGAACGCATTTGTCGGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAA
39272348 TTTGAGCCCATCACGTTCTTGAGCTTGGGTTGGGCCTTTGTGACTCGTATCA
196 TTTGAGCCCATCACGTTCTTGAGCTTGGGTTGGGCCTTTGTGACTCGTATCA
39272400 C
1 C
39272401 ATTCCATAAC
Statistics
Matches: 230, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
247 230 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (247 bp):
CTTGAAATCGCTCCAAACAACAAAATTGAGCCAAGATTCAGTTTCTTGATTTTCTTGAAAACAAG
AAAGTGAATCTTGATTTTCTCTTTCTTTCATGTACGCATCTAAGGCCTTGCTAACAAACTCCTAA
ATGATCCCATTTAGTTTGGAACGCATTTGTCGGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAA
TTTGAGCCCATCACGTTCTTGAGCTTGGGTTGGGCCTTTGTGACTCGTATCA
Found at i:39275545 original size:10 final size:10
Alignment explanation
Indices: 39275519--39275586 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
39275509 TTTCATGTGG
*
39275519 TTCAGCTCAC
1 TTCAGCTCAA
*
39275529 TTGAGCTCAA
1 TTCAGCTCAA
*
39275539 GTCAGCTC-A
1 TTCAGCTCAA
*
39275548 TTCGAGTTCAA
1 TTC-AGCTCAA
*
39275559 GTCAGCTC-A
1 TTCAGCTCAA
39275568 TTCGAGCTCAA
1 TTC-AGCTCAA
39275579 TTCAGCTC
1 TTCAGCTC
39275587 GTTATTTTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
9 6 0.13
10 32 0.71
11 7 0.16
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (10 bp):
TTCAGCTCAA
Done.