Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 20 of 190
Found at i:5733185 original size:12 final size:12
Alignment explanation
Indices: 5733170--5733197 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5733160 TAGTTATTGT
5733170 TCTGATGAGTAA
1 TCTGATGAGTAA
5733182 TCTGATGAGTAA
1 TCTGATGAGTAA
5733194 TCTG
1 TCTG
5733198 GTGTTGTGTA
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:0.29, C:0.11, G:0.25, T:0.36
Consensus pattern (12 bp):
TCTGATGAGTAA
Found at i:5736388 original size:43 final size:43
Alignment explanation
Indices: 5736353--5736456 Score: 172
Period size: 43 Copynumber: 2.4 Consensus size: 43
5736343 CAATTTATGT
* *
5736353 TTATCTTCTTCTCTTTTTAAATTCTTTTGTCAACAACCCAAGA
1 TTATCTTCTCCTCTTTTTAAATTATTTTGTCAACAACCCAAGA
*
5736396 TTATCTTCTCCTCTTTTTAAATTATTTTTTCAACAACCCAAGA
1 TTATCTTCTCCTCTTTTTAAATTATTTTGTCAACAACCCAAGA
*
5736439 TTATCTTTTCCTCTTTTT
1 TTATCTTCTCCTCTTTTT
5736457 TAGGTAGATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (43 bp):
TTATCTTCTCCTCTTTTTAAATTATTTTGTCAACAACCCAAGA
Found at i:5738330 original size:17 final size:17
Alignment explanation
Indices: 5738308--5738342 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5738298 AATGATTTTA
5738308 ATATT-AATATAAGTATT
1 ATATTAAATATAA-TATT
5738325 ATATTAAATATAATATT
1 ATATTAAATATAATATT
5738342 A
1 A
5738343 AATCTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
ATATTAAATATAATATT
Found at i:5746459 original size:39 final size:39
Alignment explanation
Indices: 5746405--5746486 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
5746395 CAATGCTTTG
*
5746405 AGACAAAAACTGCTTTCGAGATAAAAGTATTCTTAAGTA
1 AGACAAAAACTGCTTTCGAGATAAAAGTATTCTTAAGCA
* *
5746444 AGACAAAAATTGCTTTCGGGATAAAAGTATTCTTAAGCA
1 AGACAAAAACTGCTTTCGAGATAAAAGTATTCTTAAGCA
5746483 AGAC
1 AGAC
5746487 GTTTTTGAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (39 bp):
AGACAAAAACTGCTTTCGAGATAAAAGTATTCTTAAGCA
Found at i:5750153 original size:30 final size:30
Alignment explanation
Indices: 5750118--5750176 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
5750108 AAAAAACTCT
*
5750118 CAAATTTTTCCCTAAATTTCTCAAAGCTCA
1 CAAATTTCTCCCTAAATTTCTCAAAGCTCA
**
5750148 CAAATTTCTCTTTAAATTTCTCAAAGCTC
1 CAAATTTCTCCCTAAATTTCTCAAAGCTC
5750177 TCTTTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.39
Consensus pattern (30 bp):
CAAATTTCTCCCTAAATTTCTCAAAGCTCA
Found at i:5751946 original size:18 final size:18
Alignment explanation
Indices: 5751923--5751964 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5751913 GTCAGGTACT
*
5751923 TATCCTAGCACTTATATG
1 TATCCTAACACTTATATG
*
5751941 TATCCTAACCCTTATATG
1 TATCCTAACACTTATATG
*
5751959 TTTCCT
1 TATCCT
5751965 TTTCCCAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (18 bp):
TATCCTAACACTTATATG
Found at i:5753054 original size:27 final size:27
Alignment explanation
Indices: 5753016--5753070 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5753006 CTTGCAATAG
*
5753016 CTTTCGGAACCATACATGGCCTCCCTA
1 CTTTCAGAACCATACATGGCCTCCCTA
5753043 CTTTCAGAACCATACATGGCCTCCCTA
1 CTTTCAGAACCATACATGGCCTCCCTA
5753070 C
1 C
5753071 ATTTGGCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.38, G:0.13, T:0.25
Consensus pattern (27 bp):
CTTTCAGAACCATACATGGCCTCCCTA
Found at i:5755748 original size:125 final size:125
Alignment explanation
Indices: 5755526--5755750 Score: 353
Period size: 125 Copynumber: 1.8 Consensus size: 125
5755516 GGCCAAACAT
* *
5755526 GAACTACTGTAGAAAAAGAGCGTCGACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTAACAGTGCATC
* * *
5755591 CTGCTTGAAGCGTTTTTTACATTATGTGTTCAGAAACGTCTTCTCAAAATTATTTTTCAA
66 CTGCTTGAAACGTTTTTCACACTATGTGTTCAGAAACGTCTTCTCAAAATTATTTTTCAA
* * *
5755651 GAACTACTGTAGAAAAATAGTGTCCACTTGGGAGCTTTTTTCT-GTAATTTTGCTAACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTT-TAGTAATTTTGCTAACAGTGCAT
*
5755715 CCTGCTTGAAACGTTTTTCACACTATTTGTTCAGAA
65 CCTGCTTGAAACGTTTTTCACACTATGTGTTCAGAA
5755751 CCTAAACACA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
125 89 0.99
126 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTAACAGTGCATC
CTGCTTGAAACGTTTTTCACACTATGTGTTCAGAAACGTCTTCTCAAAATTATTTTTCAA
Found at i:5755865 original size:34 final size:34
Alignment explanation
Indices: 5755826--5755891 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
5755816 CAATATTATT
*
5755826 TTAAAAAAATTAAACCCTAATTTAATTAATTTTC
1 TTAAAAAAACTAAACCCTAATTTAATTAATTTTC
* *
5755860 TTAAAAACACTAAACCTTAATTTAATTAATTT
1 TTAAAAAAACTAAACCCTAATTTAATTAATTT
5755892 ATTTTAAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (34 bp):
TTAAAAAAACTAAACCCTAATTTAATTAATTTTC
Found at i:5755907 original size:34 final size:33
Alignment explanation
Indices: 5755826--5755917 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 33
5755816 CAATATTATT
* *
5755826 TTAAAAAAATTAAACCCTAATTTAATTAATTTTC
1 TTAAAAACACTAAA-CCTAATTTAATTAATTTTC
5755860 TTAAAAACACTAAACCTTAATTTAATTAATTTAT-
1 TTAAAAACACTAAACC-TAATTTAATTAATTT-TC
* * *
5755894 TTTAAACCCCTAAATCCTAATTTA
1 TTAAAAACACTAAA-CCTAATTTA
5755918 TTTTTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.04
34 45 0.90
35 3 0.06
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (33 bp):
TTAAAAACACTAAACCTAATTTAATTAATTTTC
Found at i:5756027 original size:15 final size:15
Alignment explanation
Indices: 5756003--5756041 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5755993 TTATTTTAAC
* * *
5756003 AAAACTCTAACCCTA
1 AAAACCCTAAACCAA
5756018 AAAACCCTAAACCAA
1 AAAACCCTAAACCAA
5756033 AAAACCCTA
1 AAAACCCTA
5756042 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACCCTAAACCAA
Found at i:5756027 original size:42 final size:42
Alignment explanation
Indices: 5755945--5756023 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
5755935 AATACAGAAC
*
5755945 CCTAAATTATTTTAACAAAACCCTAAACCCTACAAACCTAAG
1 CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACCTAAG
*
5755987 CCTAAATTATTTTAACAAAACTCT-AACCCTAAAAACC
1 CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACC
5756024 CTAAACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 12 0.34
42 23 0.66
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (42 bp):
CCTAAATTATTTTAACAAAACCCTAAACCCTAAAAACCTAAG
Found at i:5759583 original size:41 final size:42
Alignment explanation
Indices: 5759533--5759611 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
5759523 GGGTTTTTAG
5759533 GGTTTGTAGGG-CTAGGGTTTTGTTAAAATAATTTAGGCTTA
1 GGTTTGTAGGGTCTAGGGTTTTGTTAAAATAATTTAGGCTTA
*
5759574 GGTTTGTAGGGTTTAGGGTTTTGTTAAAATAATTTAGG
1 GGTTTGTAGGGTCTAGGGTTTTGTTAAAATAATTTAGG
5759612 GTTTTGGGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 11 0.31
42 25 0.69
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.43
Consensus pattern (42 bp):
GGTTTGTAGGGTCTAGGGTTTTGTTAAAATAATTTAGGCTTA
Found at i:5759731 original size:34 final size:33
Alignment explanation
Indices: 5759638--5759768 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 33
5759628 ATTTTAAAAA
* *
5759638 TAAATTAGGATTTAGTGTTCTTTTCTAAAAATTAAT
1 TAAATTAGGGTTTAGTG-T-TTTT-AAAAAATTAAT
* * ** *
5759674 TAAATTAGAGTTTAGGGGATTTAAATAAATAAAT
1 TAAATTAGGGTTTAGTGTTTTTAAA-AAATTAAT
*
5759708 TAAATTAGGGTTTAGTGTTTTTAAGAAAATTCAT
1 TAAATTAGGGTTTAGTGTTTTTAA-AAAATTAAT
*
5759742 TAAATTAGTGTTTAGT-TTTTTAAAAAA
1 TAAATTAGGGTTTAGTGTTTTTAAAAAA
5759769 AATAATATTA
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
32 4 0.05
33 9 0.11
34 51 0.65
35 1 0.01
36 14 0.18
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.44
Consensus pattern (33 bp):
TAAATTAGGGTTTAGTGTTTTTAAAAAATTAAT
Found at i:5759772 original size:68 final size:71
Alignment explanation
Indices: 5759638--5759778 Score: 157
Period size: 68 Copynumber: 2.0 Consensus size: 71
5759628 ATTTTAAAAA
* *
5759638 TAAATTAGGATTTAGTGTTCTTTTCTAAAAATTAATTAAATTAGAGTTTAGGGGATTTAAATAAA
1 TAAATTAGGATTTAGTGTTCTTTTCAAAAAATTAATTAAATTAGAGTTTAGGGGATTTAAAAAAA
5759703 TAA-AT
66 TAATAT
* * * ***
5759708 TAAATTAGGGTTTAGTG-T-TTTT-AAGAAAATTCATTAAATTAGTGTTTA-GTTTTTTAAAAAA
1 TAAATTAGGATTTAGTGTTCTTTTCAA-AAAATTAATTAAATTAGAGTTTAGGGGATTT-AAAAA
5759769 AATAATAT
64 AATAATAT
5759777 TA
1 TA
5759779 TGTTTAGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
67 5 0.08
68 34 0.57
69 5 0.08
70 16 0.27
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (71 bp):
TAAATTAGGATTTAGTGTTCTTTTCAAAAAATTAATTAAATTAGAGTTTAGGGGATTTAAAAAAA
TAATAT
Found at i:5760010 original size:126 final size:126
Alignment explanation
Indices: 5759825--5760221 Score: 539
Period size: 127 Copynumber: 3.2 Consensus size: 126
5759815 AATAAGGATT
* * * *
5759825 TTTTTTTCTACAATAGTTCTTGAAAAAATAA-TTTGAGAATACGGTTCTGAACAAATAGTGTGAA
1 TTTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
* * * * *
5759889 AAACGCTTCAAGCAGGATGCACTATCAGTAAAATTACTGAAAAAAGCTCTCACATTGACAC
66 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTTGACGC
* * *
5759950 TTTTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGA-GGTTTCTGAATAACTAGTGTCA
1 TTTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGG-TTCTGAACAAATAGTGTCA
* * * *
5760014 AAAACGCTTCAAGAAAGGGTGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC
65 AAAACGCTTCAAG-CAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTTGACGC
* * * *
5760077 TATTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGATGGTTCTGAACAAATACTGTCAA
1 TTTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
* *
5760142 AAACACTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCAAACGTTGACGC
66 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCACACGTTGACGC
*
5760203 TCTTTTTCTACAGTAGTTC
1 TTTTTTTCTACAGTAGTTC
5760222 ATGTTTGGCC
Statistics
Matches: 239, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
125 30 0.13
126 98 0.41
127 109 0.46
128 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTTGACGC
Found at i:5760698 original size:24 final size:23
Alignment explanation
Indices: 5760642--5760698 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
5760632 AAGAACTTCT
5760642 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAATA
*
5760665 ATTTACTATT-AAAATATTTAAAATA
1 ATTT--TATTAAAAATA-TAAAAATA
5760690 ACTTTTATT
1 A-TTTTATT
5760699 TTATTAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAATA
Found at i:5764129 original size:50 final size:50
Alignment explanation
Indices: 5764075--5764845 Score: 444
Period size: 50 Copynumber: 15.4 Consensus size: 50
5764065 GTGGAGTAGT
* *
5764075 TTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * ** * * * ** * * *
5764125 TTAAAGCTACCACAACGAATCTTACTTCCCTGGCGGTGCAGTGAAACAGG
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * * *
5764175 TTAAAGCTACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * ** * * *** *
5764225 TTAAAGCTACCACAACGAATCTTACTT-CTC-A-AGTGGTGCAGCGGAACAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACA-T--TGCAGTTAAAAAGA
* * * *
5764275 TTAATGCCACAACGGTGAAACTTGCTTCCCTGACA-TGCAGTTAAAAAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * ** * **** * ** * *
5764324 TTAAAGCTACCACAACGAATCTTACTTCTTAAACAGTGCAGTGGAACATA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* *
5764374 TTAATGCCACAACGGCGAATCTTGCTTTCCCGACATTGCAGTTAAAAAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * * ** * * * ** ** *
5764424 CTAAAGCTACCACAAC-AACTCTTACTT-CTCAAGCGGTGCAGTGGAACAGA
1 TTAAAGCCACAACGGCGAA-TCTTGCTTCCCCGA-CATTGCAGTTAAAAAGA
* * *
5764474 TTAATGCCACAACGACGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* ** * * * ** **
5764524 TTAAAGCTACAACAACGAATCTT-ATTCCTCAGGCGA-TGCAGTGGAGCAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCC-CCGAC-ATTGCAGTTAAAAAGA
* * *
5764574 TTAAACCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * ** * * ** * *
5764624 TTAAAGCTACAACAGCGAATCTTATTTCCCTGGCGGTGCAGTGGAACAA-A
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGT-TAAAAAGA
* * * *
5764674 TTAAAGCCACATCAGTGAATCTTGCTTACCCGACATTGCAGTTAAAAAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * * * * * ** ** *
5764724 TTAAAGCTACAACAGCGGATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * * *
5764774 TTAAAGCCACATCGGTGAATCTCGCTTCCCCGATATTGCAGTTAAAAAGA
1 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
*
5764824 TTAAAGCCACAACGGAGAATCT
1 TTAAAGCCACAACGGCGAATCT
5764846 CACTTCCTTA
Statistics
Matches: 511, Mismatches: 193, Indels: 34
0.69 0.26 0.05
Matches are distributed among these distances:
47 1 0.00
48 2 0.00
49 49 0.10
50 442 0.86
51 15 0.03
52 1 0.00
53 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (50 bp):
TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
Found at i:5764218 original size:100 final size:100
Alignment explanation
Indices: 5764042--5764929 Score: 1066
Period size: 100 Copynumber: 8.9 Consensus size: 100
5764032 GAAAATAGGA
* * * ** *
5764042 AATCTTATTTCCTTGGAGGTGCAGTGGAGTAGTTTAAAGCCACATCGGTGAATCTTGCTTCCCCG
1 AATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
*
5764107 ACATTGCAGTTAAAAAGATTAAAGCTACCACAACG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
* * *
5764142 AATCTTACTTCCCTGGCGGTGCAGTGAAACAGGTTAAAGCTACATCGGTGAATCTTGCTTCCCCG
1 AATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* *
5764207 ACATTGTAGTTAAAAAGATTAAAGCTACCACAACG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
* ** * * * * * *
5764242 AATCTTACTTCTCAAGTGGTGCAGCGGAACAGATTAATGCCACAACGGTGAAACTTGCTTCCCTG
1 AATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
*
5764307 ACA-TGCAGTTAAAAAGATTAAAGCTACCACAACG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
* ** * * * * * *
5764341 AATCTTACTT-CTTAAACAGTGCAGTGGAACATATTAATGCCACAACGGCGAATCTTGCTTTCCC
1 AATCTTACTTCCCT-GGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCC
* *
5764405 GACATTGCAGTTAAAAAGACTAAAGCTACCACAAC-
65 GACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
* ** * * **
5764440 AACTCTTACTTCTCAAGCGGTGCAGTGGAACAGATTAATGCCACAACGACGAATCTTGCTTCCCC
1 AA-TCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCC
*
5764505 GACATTGTAGTTAAAAAGATTAAAGCTACAACAACG
65 GACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
* * * *
5764541 AATCTTA-TTCCTCAGGCGATGCAGTGGAGCAGATTAAACCCACATCGGTGAATCTTGCTTCCCC
1 AATCTTACTTCC-CTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCC
*
5764605 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
65 GACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
* * * *
5764641 AATCTTATTTCCCTGGCGGTGCAGTGGAACAAATTAAAGCCACATCAGTGAATCTTGCTTACCCG
1 AATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
*
5764706 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
* *
5764741 GATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCG
1 AATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* * *
5764806 ATATTGCAGTTAAAAAGATTAAAGCCACAACGGA-G
66 ACATTGCAGTTAAAAAGATTAAAGCTACAAC-AACG
* * * * * * * * * * * *
5764841 AATCTCACTTCCTTAGCGGTGTAGTGGCACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCA
1 AATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* * *
5764906 AAATTACAGTTAAATAGATTAAAG
66 ACATTGCAGTTAAAAAGATTAAAG
5764930 TTACGAGTTA
Statistics
Matches: 689, Mismatches: 91, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
99 90 0.13
100 593 0.86
101 6 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (100 bp):
AATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
ACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
Found at i:5768696 original size:29 final size:29
Alignment explanation
Indices: 5768664--5768720 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5768654 GGACGCATTT
*
5768664 TGCAAAAATTGGTCC-TTTCCGGTAAATAA
1 TGCAAAAATTGGCCCATTTCC-GTAAATAA
*
5768693 TGCAGAAATTGGCCCATTTCCGTAAATA
1 TGCAAAAATTGGCCCATTTCCGTAAATA
5768721 TACTTGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (29 bp):
TGCAAAAATTGGCCCATTTCCGTAAATAA
Found at i:5772984 original size:32 final size:33
Alignment explanation
Indices: 5772943--5773014 Score: 130
Period size: 32 Copynumber: 2.2 Consensus size: 33
5772933 GTTTGAGGGT
5772943 TGAGAATTATTCTTAGATGTATAAATAGATGA-
1 TGAGAATTATTCTTAGATGTATAAATAGATGAC
5772975 TGAGAATTATTCTTAGATGTATAAATAGATGAC
1 TGAGAATTATTCTTAGATGTATAAATAGATGAC
5773008 TG-GAATT
1 TGAGAATT
5773015 GATTATAGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 37 0.95
33 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (33 bp):
TGAGAATTATTCTTAGATGTATAAATAGATGAC
Found at i:5774827 original size:40 final size:40
Alignment explanation
Indices: 5774772--5774858 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
5774762 TTTGGTTTTC
5774772 GAAAATTAAAACTCCGAAAAGATTTTTCACTACTAATCAA
1 GAAAATTAAAACTCCGAAAAGATTTTTCACTACTAATCAA
5774812 GAAAATTAAAACTCCGAAAAGATTTTTCACTACTAATCAA
1 GAAAATTAAAACTCCGAAAAGATTTTTCACTACTAATCAA
*
5774852 GTAAATT
1 GAAAATT
5774859 TTTTTGAAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (40 bp):
GAAAATTAAAACTCCGAAAAGATTTTTCACTACTAATCAA
Found at i:5781451 original size:44 final size:46
Alignment explanation
Indices: 5781372--5781458 Score: 151
Period size: 44 Copynumber: 1.9 Consensus size: 46
5781362 CGCTGTAATA
*
5781372 GAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGGATTG
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGATTG
5781418 GAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGGA
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGA
5781459 ATAAAGGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 22 0.55
45 3 0.08
46 15 0.38
ACGTcount: A:0.25, C:0.05, G:0.32, T:0.38
Consensus pattern (46 bp):
GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGATTG
Found at i:5781680 original size:109 final size:112
Alignment explanation
Indices: 5781556--5781800 Score: 273
Period size: 109 Copynumber: 2.3 Consensus size: 112
5781546 GTTATTAAAT
* * * *
5781556 TTTAATAA-GATTATTAATATAAATAATAA-ATAAT-TTAATCATAT-TTTAACATAATTGTTAT
1 TTTAATAATAATTATTAATATAAAT-ATAATATAATAATAAT-ATATATTTAACAAAATTCTTAT
*
5781617 T-AAATAT-AATTTAATAAAAATCATAATATATAATACTATAAAATATAA
64 TCAAATATGAATATAAT-AAAATCATAATATATAATACTATAAAATATAA
* *
5781665 TTTAA-AATAATTATT-AT-TAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTATT
1 TTTAATAATAATTATTAATATAAATATAATATAATAATAATATAT-ATTTAACAAAATTCTTATT
** *
5781727 CTTATATGAATATACTAAAATCATAATATATAATACTATAAAATATAA
65 CAAATATGAATATAATAAAATCATAATATATAATACTATAAAATATAA
5781775 TTTAAT--TAATTATT-AT-TAAATATAAT
1 TTTAATAATAATTATTAATATAAATATAAT
5781801 TTATAATCCA
Statistics
Matches: 118, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
106 4 0.03
107 13 0.11
108 8 0.07
109 46 0.39
110 41 0.35
111 6 0.05
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (112 bp):
TTTAATAATAATTATTAATATAAATATAATATAATAATAATATATATTTAACAAAATTCTTATTC
AAATATGAATATAATAAAATCATAATATATAATACTATAAAATATAA
Found at i:5781690 original size:26 final size:28
Alignment explanation
Indices: 5781657--5781720 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
5781647 TAATACTATA
*
5781657 AAATATAATTTAA-AATAAT-TATTATT
1 AAATATAATTTAATAATAATATATAATT
5781683 AAATATAATTTAATAATAATATATAATT
1 AAATATAATTTAATAATAATATATAATT
* *
5781711 TAATAAAATT
1 AAATATAATT
5781721 CTTATTCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATATAATTTAATAATAATATATAATT
Found at i:5783290 original size:49 final size:49
Alignment explanation
Indices: 5783192--5783295 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 49
5783182 AAAAAAAAAC
* * ** * *
5783192 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCACGAATCAAAAACTCAACACTGTATA
* *
5783241 AAATTAAAATTGAGTTCAATATCACGAATCAAAAACTCAATACTGTATA
1 AAATTAAAATTAAGTTCAATATCACGAATCAAAAACTCAACACTGTATA
5783290 AAATTA
1 AAATTA
5783296 TAGCACATGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCACGAATCAAAAACTCAACACTGTATA
Found at i:5783462 original size:56 final size:56
Alignment explanation
Indices: 5783401--5783517 Score: 216
Period size: 56 Copynumber: 2.1 Consensus size: 56
5783391 ACAAACCACA
* *
5783401 TTTTTCTTTAAAGAATTTTTAGAAGCACTTTCAATCATAATAACAATGAATATTTG
1 TTTTTCTTTAAACAATTTTTACAAGCACTTTCAATCATAATAACAATGAATATTTG
5783457 TTTTTCTTTAAACAATTTTTACAAGCACTTTCAATCATAATAACAATGAATATTTG
1 TTTTTCTTTAAACAATTTTTACAAGCACTTTCAATCATAATAACAATGAATATTTG
5783513 TTTTT
1 TTTTT
5783518 TAATCAAGTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (56 bp):
TTTTTCTTTAAACAATTTTTACAAGCACTTTCAATCATAATAACAATGAATATTTG
Found at i:5784037 original size:25 final size:25
Alignment explanation
Indices: 5784003--5784064 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
5783993 CAATTTACTG
5784003 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAATACCTCTT
5784028 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAATACCTCTT
5784053 GAAATT-CAACTA
1 G-AATTGCAACTA
5784065 GAGCTTCAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 32 0.89
26 4 0.11
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (25 bp):
GAATTGCAACTATAAAATACCTCTT
Found at i:5790355 original size:18 final size:18
Alignment explanation
Indices: 5790332--5790368 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5790322 ATCAGTTCAT
*
5790332 TCTTCTGTTAGTTAGTTA
1 TCTTCTATTAGTTAGTTA
5790350 TCTTCTATTAGTTAGTTA
1 TCTTCTATTAGTTAGTTA
5790368 T
1 T
5790369 TCTCTTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.57
Consensus pattern (18 bp):
TCTTCTATTAGTTAGTTA
Found at i:5790380 original size:22 final size:22
Alignment explanation
Indices: 5790338--5790380 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5790328 TCATTCTTCT
*
5790338 GTTAGTTAGTTATCTTCTATTA
1 GTTAGTTAGTTATCTTATATTA
*
5790360 GTTAGTTA-TTCTCTTGATATT
1 GTTAGTTAGTTATCTT-ATATT
5790381 GTAATTAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.56
Consensus pattern (22 bp):
GTTAGTTAGTTATCTTATATTA
Found at i:5791861 original size:21 final size:23
Alignment explanation
Indices: 5791819--5791862 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
5791809 CCCAACTAGT
*
5791819 TTTAGTTATATTTTTGTCATTTA
1 TTTAGTTATATTTTTGTAATTTA
*
5791842 TTTA-TTA-ATTTTTTTAATTTA
1 TTTAGTTATATTTTTGTAATTTA
5791863 ATCATTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTAGTTATATTTTTGTAATTTA
Found at i:5802122 original size:25 final size:25
Alignment explanation
Indices: 5802094--5802147 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
5802084 AGCTCTGGAT
* *
5802094 AGCCATATATCGAGAAGTTCAAGCG
1 AGCCATATATCGAGAAGCTCAAGAG
*
5802119 AGCC--ATATCGAGAAGCTCTAGAG
1 AGCCATATATCGAGAAGCTCAAGAG
5802142 AGCCAT
1 AGCCAT
5802148 TAATCAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 20 0.83
25 4 0.17
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (25 bp):
AGCCATATATCGAGAAGCTCAAGAG
Found at i:5802130 original size:23 final size:23
Alignment explanation
Indices: 5802100--5802147 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5802090 GGATAGCCAT
* *
5802100 ATATCGAGAAGTTCAAGCGAGCC
1 ATATCGAGAAGCTCAAGAGAGCC
*
5802123 ATATCGAGAAGCTCTAGAGAGCC
1 ATATCGAGAAGCTCAAGAGAGCC
5802146 AT
1 AT
5802148 TAATCAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (23 bp):
ATATCGAGAAGCTCAAGAGAGCC
Found at i:5804625 original size:28 final size:28
Alignment explanation
Indices: 5804523--5804617 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 28
5804513 ACGGCCGTGC
* *
5804523 CCCCTGTTTTT-AAGATTTTATAGCTTTG
1 CCCCTCTTTTTCAA-ATTTTATAGTTTTG
* *
5804551 CCCCTCTTTTTCAAATTTTACAATTTTG
1 CCCCTCTTTTTCAAATTTTATAGTTTTG
** *
5804579 CCATTATTTTTCAAATTTTATAGTTTTG
1 CCCCTCTTTTTCAAATTTTATAGTTTTG
5804607 CCCCTCTTTTT
1 CCCCTCTTTTT
5804618 TATATTTTGC
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 52 0.96
29 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (28 bp):
CCCCTCTTTTTCAAATTTTATAGTTTTG
Found at i:5804633 original size:28 final size:28
Alignment explanation
Indices: 5804547--5804665 Score: 132
Period size: 28 Copynumber: 4.2 Consensus size: 28
5804537 ATTTTATAGC
5804547 TTTGCCCCTCTTTTTCAAATTTTACAAT
1 TTTGCCCCTCTTTTTCAAATTTTACAAT
** * * *
5804575 TTTGCCATTATTTTTCAAATTTTATAGT
1 TTTGCCCCTCTTTTTCAAATTTTACAAT
* * *
5804603 TTTGCCCCTCTTTTTTATATTTTGCAAT
1 TTTGCCCCTCTTTTTCAAATTTTACAAT
*
5804631 TTTGCCCAT-TTCTTTACAAATTTTACAAT
1 TTTGCCCCTCTT-TTT-CAAATTTTACAAT
5804660 TTTGCC
1 TTTGCC
5804666 TAGAATTTTA
Statistics
Matches: 72, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
27 2 0.03
28 54 0.75
29 16 0.22
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (28 bp):
TTTGCCCCTCTTTTTCAAATTTTACAAT
Found at i:5804654 original size:57 final size:56
Alignment explanation
Indices: 5804537--5804665 Score: 170
Period size: 56 Copynumber: 2.3 Consensus size: 56
5804527 TGTTTTTAAG
* *
5804537 ATTTTATAGCTTTGCCCCTCTTTTTCAAATTTTACAATTTTGCCATTATTTTTCAA
1 ATTTTATAGTTTTGCCCCTCTTTTTCAAATTTTACAATTTTGCCATTATTTTACAA
* * *
5804593 ATTTTATAGTTTTGCCCCTCTTTTTTATATTTTGCAATTTTGCCCATT-TCTTTACAA
1 ATTTTATAGTTTTGCCCCTCTTTTTCAAATTTTACAATTTTG-CCATTAT-TTTACAA
* *
5804650 ATTTTACAATTTTGCC
1 ATTTTATAGTTTTGCC
5804666 TAGAATTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
56 39 0.61
57 25 0.39
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (56 bp):
ATTTTATAGTTTTGCCCCTCTTTTTCAAATTTTACAATTTTGCCATTATTTTACAA
Found at i:5812029 original size:9 final size:9
Alignment explanation
Indices: 5811985--5812219 Score: 73
Period size: 10 Copynumber: 24.6 Consensus size: 9
5811975 GCATGTGACG
*
5811985 AAAAATGAT
1 AAAAATTAT
*
5811994 AAAAA-AAT
1 AAAAATTAT
*
5812002 AAAAACTAAT
1 AAAAA-TTAT
*
5812012 AAAATTTAT
1 AAAAATTAT
*
5812021 ACAAATTAT
1 AAAAATTAT
5812030 AAAAATTATT
1 AAAAATTA-T
***
5812040 AAGTTTTAAT
1 AAAAATT-AT
*
5812050 AAAAAATATTT
1 -AAAAAT-TAT
*
5812061 AAAAGTTATT
1 AAAAATTA-T
*
5812071 AAAAATTAGAA
1 AAAAATT--AT
*
5812082 AAAAATTGT
1 AAAAATTAT
*
5812091 AAAAAATTGT
1 -AAAAATTAT
**
5812101 AAACTTTTAT
1 AAA-AATTAT
*
5812111 AAAAATAAT
1 AAAAATTAT
5812120 AAAAATTAT
1 AAAAATTAT
5812129 -AAAATATAT
1 AAAAAT-TAT
* *
5812138 AGAAATATAAA
1 A-AAA-ATTAT
5812149 AAAAATTAT
1 AAAAATTAT
*
5812158 -AAAATTTT
1 AAAAATTAT
* *
5812166 ATAAAGTCAT
1 A-AAAATTAT
5812176 AAGAAAATTAT
1 -A-AAAATTAT
5812187 AAAAA-TAT
1 AAAAATTAT
**
5812195 AAAAAAAAT
1 AAAAATTAT
5812204 ATAAAATTCAT
1 A-AAAATT-AT
5812215 AAAAA
1 AAAAA
5812220 AAAAATTATC
Statistics
Matches: 165, Mismatches: 40, Indels: 41
0.67 0.16 0.17
Matches are distributed among these distances:
8 27 0.16
9 50 0.30
10 57 0.35
11 27 0.16
12 4 0.02
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5812122 original size:29 final size:29
Alignment explanation
Indices: 5812090--5812170 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
5812080 AAAAAAATTG
*
5812090 TAAAAAATTGTAAACTTTTATAAAA-ATAA
1 TAAAAAATTATAAA-TTTTATAAAATATAA
* *
5812119 T-AAAAATTATAAAATATATAGAAATATAA
1 TAAAAAATTATAAATTTTATA-AAATATAA
5812148 -AAAAAATTATAAAATTTTATAAA
1 TAAAAAATTAT-AAATTTTATAAA
5812171 GTCATAAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 5 0.12
28 14 0.33
29 16 0.37
30 8 0.19
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (29 bp):
TAAAAAATTATAAATTTTATAAAATATAA
Found at i:5812134 original size:17 final size:18
Alignment explanation
Indices: 5812107--5812219 Score: 70
Period size: 18 Copynumber: 6.0 Consensus size: 18
5812097 TTGTAAACTT
5812107 TTATAAAA-ATAATAAAAA
1 TTATAAAATAT-ATAAAAA
*
5812125 TTATAAAATATATAGAAA
1 TTATAAAATATATAAAAA
* * *
5812143 TATAAAAAAAATTATAAAATT
1 T-TATAAAATA-TATAAAA-A
*
5812164 TTATAAAGTCATA-AGAAAA
1 TTATAAAAT-ATATA-AAAA
*
5812183 TTATAAAAATATAAAAAAA
1 TTAT-AAAATATATAAAAA
*
5812202 ATATAAAAT-TCATAAAAA
1 TTATAAAATAT-ATAAAAA
5812220 AAAAATTATC
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.01
18 26 0.35
19 24 0.32
20 21 0.28
21 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (18 bp):
TTATAAAATATATAAAAA
Found at i:5812216 original size:20 final size:20
Alignment explanation
Indices: 5812172--5812222 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5812162 TTTTATAAAG
* *
5812172 TCATAAGAAAATTATAAAAA
1 TCATAAAAAAAATATAAAAA
*
5812192 T-ATAAAAAAAATATAAAAT
1 TCATAAAAAAAATATAAAAA
5812211 TCATAAAAAAAA
1 TCATAAAAAAAA
5812223 AATTATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
TCATAAAAAAAATATAAAAA
Found at i:5812585 original size:17 final size:17
Alignment explanation
Indices: 5812560--5812620 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
5812550 TTATTTTTTT
5812560 TTATAATATTTTTTACAA
1 TTAT-ATATTTTTTACAA
* *
5812578 TTTTATA-TTTTTACTA
1 TTATATATTTTTTACAA
*
5812594 TTATA-ATTTTTTATTAA
1 TTATATATTTTTTA-CAA
5812611 -TATATATTTT
1 TTATATATTTT
5812621 ATAATTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 1 0.03
16 22 0.63
17 9 0.26
18 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATATTTTTTACAA
Found at i:5812604 original size:31 final size:30
Alignment explanation
Indices: 5812547--5812604 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
5812537 CCTCTACTTG
** *
5812547 ATTTTATTTTTTTTTATAATATTTTTTACA
1 ATTTTATTTTTTACTATAATAATTTTTACA
*
5812577 ATTTTATATTTTTACTATTATAATTTTT
1 ATTTTAT-TTTTTACTATAATAATTTTT
5812605 TATTAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 7 0.30
31 16 0.70
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (30 bp):
ATTTTATTTTTTACTATAATAATTTTTACA
Found at i:5815513 original size:262 final size:265
Alignment explanation
Indices: 5815042--5815653 Score: 776
Period size: 262 Copynumber: 2.3 Consensus size: 265
5815032 GTTACATTAG
* * * ** * *
5815042 GTTGTGTCACAAGTCAATCGGGCATCAATTTAGTTAGAGAAACTGT--AAAAATGTCCTTTTGAA
1 GTTGTGTCACAAGTCAACCGGGCAACAAATCGGTTAG-GAAAAT-TACAAAAATATCCTTTTGAA
* * * *
5815105 TTTAAAATAATTTATATT-TTTCGAAGGTACTTTAGTTTTTTTTTTTTAAAAAAAACTAATAAAA
64 TTTAAAATAATTTATATTATTTCGAAGGCACTATAGTTCTTTTTATTT-AAAAAAACTAATAAAA
* * *
5815169 ATATGCACATAGTGAGATTTGATCTCATGCTAATTGCATTAGAAAAACTTTAAATTTACCCTTCA
128 ATATGCACATAGTGAGATTTGAGCTCATGCTAATTGCATTAAAAAAACTTTAAATTTACCATTCA
*
5815234 ACCAAAGCTTTATTTTGTTATTTTAATACATTTTTATTTTAGTATCTATACTATTATTTAAAC-C
193 ACCAAAACTTTATTTTGTTATTTTAATACATTTTTATTTTAGTATCTATACTATTATTTAAACTC
*
5815298 CTTACCAA
258 CTGACCAA
5815306 GTTGGTGTCACAAGTCAACCGGGCAACAAATCGGTTAGGAAAATTACAAAAATATCCTTTTGAAT
1 GTT-GTGTCACAAGTCAACCGGGCAACAAATCGGTTAGGAAAATTACAAAAATATCCTTTTGAAT
* *
5815371 TTAAAATAAGTCATATTATTT-G-AGAGCACTATAG-TCTTTTTATTT-AAAAAACTAATAAAAA
65 TTAAAATAATTTATATTATTTCGAAG-GCACTATAGTTCTTTTTATTTAAAAAAACTAATAAAAA
* * * * *
5815432 TATGCATATGGTGGGATTTGAGCTCAT-ATCAATTGCA-TAAACAAAACTTTAAATTTATCATTC
129 TATGCACATAGTGAGATTTGAGCTCATGCT-AATTGCATTAAA-AAAACTTTAAATTTACCATTC
5815495 AACCAAAACTTTATTTTGTTATTTTAATACATTTTTATTTTAGTATCTATACTATTATTTAAACT
192 AACCAAAACTTTATTTTGTTATTTTAATACATTTTTATTTTAGTATCTATACTATTATTTAAACT
**
5815560 CCTGACTGA
257 CCTGACCAA
* ** * * * * * *
5815569 GTTGTATCATGAGTCAACCAGACACCAACTCGGTTAGAAAAATTACAAAAATATCATTTTGAATT
1 GTTGTGTCACAAGTCAACCGGGCAACAAATCGGTTAGGAAAATTACAAAAATATCCTTTTGAATT
*
5815634 TCAAATAATTTATATTATTT
66 TAAAATAATTTATATTATTT
5815654 AAGGATATCT
Statistics
Matches: 303, Mismatches: 37, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
261 4 0.01
262 198 0.65
263 10 0.03
264 19 0.06
265 69 0.23
266 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (265 bp):
GTTGTGTCACAAGTCAACCGGGCAACAAATCGGTTAGGAAAATTACAAAAATATCCTTTTGAATT
TAAAATAATTTATATTATTTCGAAGGCACTATAGTTCTTTTTATTTAAAAAAACTAATAAAAATA
TGCACATAGTGAGATTTGAGCTCATGCTAATTGCATTAAAAAAACTTTAAATTTACCATTCAACC
AAAACTTTATTTTGTTATTTTAATACATTTTTATTTTAGTATCTATACTATTATTTAAACTCCTG
ACCAA
Found at i:5816577 original size:2 final size:2
Alignment explanation
Indices: 5816570--5816614 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5816560 TTAACTTCTC
5816570 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5816612 AT A
1 AT A
5816615 AAGAAAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5821911 original size:22 final size:22
Alignment explanation
Indices: 5821886--5821970 Score: 107
Period size: 22 Copynumber: 3.9 Consensus size: 22
5821876 AAACGGTTGA
**
5821886 TCTCATGTTTAACGTACTAAGC
1 TCTCATGGCTAACGTACTAAGC
** * *
5821908 TCTCATGTTTAACGAACTAAAC
1 TCTCATGGCTAACGTACTAAGC
*
5821930 CCTCATGGCTAACGTACTAAGC
1 TCTCATGGCTAACGTACTAAGC
5821952 TCTCATGGCTAACGTACTA
1 TCTCATGGCTAACGTACTA
5821971 GAAAGGAACT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (22 bp):
TCTCATGGCTAACGTACTAAGC
Found at i:5823023 original size:3 final size:3
Alignment explanation
Indices: 5823017--5823077 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
5823007 GGCGACAACA
5823017 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5823065 AAG AAG AAG AAG A
1 AAG AAG AAG AAG A
5823078 CATTGTTTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5829630 original size:25 final size:24
Alignment explanation
Indices: 5829576--5829638 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
5829566 TTCAAAAAAA
5829576 AAAATATTTATATTAAAAAATATC
1 AAAATATTTATATTAAAAAATATC
* *
5829600 ATAAATATTT-TATTAAATATAATTTT
1 A-AAATATTTATATTAAA-A-AATATC
5829626 AAAAT-TTTATATT
1 AAAATATTTATATT
5829639 TTGAGTTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
24 11 0.33
25 17 0.52
26 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATTTATATTAAAAAATATC
Found at i:5833282 original size:21 final size:21
Alignment explanation
Indices: 5833256--5833295 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5833246 ATAAATAATA
5833256 TAATGGTTTTG-CGTTTTAACT
1 TAATGGTTTTGAC-TTTTAACT
5833277 TAATGGTTTTGACTTTTAA
1 TAATGGTTTTGACTTTTAA
5833296 ATTTAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (21 bp):
TAATGGTTTTGACTTTTAACT
Found at i:5835088 original size:3 final size:3
Alignment explanation
Indices: 5835082--5835113 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5835072 TGAAGAAGGT
*
5835082 GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5835114 CATTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5836927 original size:10 final size:10
Alignment explanation
Indices: 5836912--5836983 Score: 81
Period size: 10 Copynumber: 6.8 Consensus size: 10
5836902 GAGAAGAAAG
5836912 AAAGAAAGAA
1 AAAGAAAGAA
5836922 AAAGAAAGAA
1 AAAGAAAGAA
*
5836932 AAGGAAAGGAGAA
1 AAAG-AA--AGAA
5836945 GAAAGAAAGAA
1 -AAAGAAAGAA
*
5836956 AAAGAAAGGA
1 AAAGAAAGAA
*
5836966 GAAGAAAGAA
1 AAAGAAAGAA
5836976 AAAGAAAG
1 AAAGAAAG
5836984 GAGAAGAAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
10 37 0.71
11 6 0.12
13 6 0.12
14 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:5836946 original size:20 final size:20
Alignment explanation
Indices: 5836902--5837018 Score: 105
Period size: 20 Copynumber: 5.6 Consensus size: 20
5836892 AGAGGGACAA
5836902 GAGAAGAAAG--AAAGAAAG
1 GAGAAGAAAGAAAAAGAAAG
* * *
5836920 AAAAAGAAAGAAAAGGAAAGG
1 GAGAAGAAAGAAAAAGAAA-G
5836941 AGAAGAAAGAAAGAAAAAGAAAG
1 -G-AG-AAGAAAGAAAAAGAAAG
5836964 GAGAAGAAAGAAAAAGAAAG
1 GAGAAGAAAGAAAAAGAAAG
5836984 GAGAAG-AAGAAGAAGAGGAAAG
1 GAGAAGAAAGAA-AA-A-GAAAG
*
5837006 GAAGAAAAAAGAA
1 G-AGAAGAAAGAA
5837019 GTACAGGTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
18 8 0.10
19 5 0.06
20 31 0.38
21 4 0.05
22 7 0.09
23 6 0.07
24 20 0.25
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
GAGAAGAAAGAAAAAGAAAG
Found at i:5836949 original size:24 final size:24
Alignment explanation
Indices: 5836918--5837018 Score: 117
Period size: 24 Copynumber: 4.5 Consensus size: 24
5836908 AAAGAAAGAA
5836918 AGAA-AAAGAAAGAAAAGGAAAGG
1 AGAAGAAAGAAAGAAAAGGAAAGG
*
5836941 AGAAGAAAGAAAGAAAAAGAAAGG
1 AGAAGAAAGAAAGAAAAGGAAAGG
5836965 AGAAGAAAG--A-AAAA-GAAAGG
1 AGAAGAAAGAAAGAAAAGGAAAGG
*
5836985 AGAAG-AAG-AAGAAGAGGAAAGG
1 AGAAGAAAGAAAGAAAAGGAAAGG
*
5837007 AAGAAAAAAGAA
1 -AGAAGAAAGAA
5837019 GTACAGGTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
19 3 0.04
20 12 0.18
21 7 0.10
22 7 0.10
23 8 0.12
24 30 0.44
25 1 0.01
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (24 bp):
AGAAGAAAGAAAGAAAAGGAAAGG
Found at i:5836990 original size:10 final size:10
Alignment explanation
Indices: 5836902--5836991 Score: 63
Period size: 10 Copynumber: 9.8 Consensus size: 10
5836892 AGAGGGACAA
5836902 GAGAAGAAA-
1 GAGAAGAAAG
5836911 GA-AAGAAAG
1 GAGAAGAAAG
* *
5836920 AAAAAGAAA-
1 GAGAAGAAAG
*
5836929 GAAAAGGAAAG
1 GAGAA-GAAAG
5836940 GAGAAGAAA-
1 GAGAAGAAAG
5836949 GA-AAG-AA-
1 GAGAAGAAAG
5836956 -A-AAGAAAG
1 GAGAAGAAAG
5836964 GAGAAGAAAG
1 GAGAAGAAAG
* *
5836974 AAAAAGAAAG
1 GAGAAGAAAG
5836984 GAGAAGAA
1 GAGAAGAA
5836992 GAAGAAGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
6 4 0.06
7 4 0.06
8 9 0.14
9 10 0.15
10 35 0.53
11 4 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAGAAGAAAG
Found at i:5838297 original size:2 final size:2
Alignment explanation
Indices: 5838290--5838316 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5838280 TCTAAATTGA
5838290 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5838317 CTACTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5838988 original size:40 final size:40
Alignment explanation
Indices: 5838933--5839153 Score: 379
Period size: 40 Copynumber: 5.5 Consensus size: 40
5838923 AGGCTTGTGC
5838933 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
5838973 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* * *
5839013 ATAACAGGCTTAATGCCGGTGAAATATTCAGATTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* *
5839053 CTAGCAGGCTTAATGTCAGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
5839093 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
5839133 CTAGCAGGCTTCATGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
5839154 TACGGAATCA
Statistics
Matches: 169, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 169 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
Found at i:5844755 original size:40 final size:40
Alignment explanation
Indices: 5844700--5844880 Score: 326
Period size: 40 Copynumber: 4.5 Consensus size: 40
5844690 AGGCTTGTGC
5844700 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
5844740 CTAGCAGGCTTAATGCCGGTGAAATATTCAGATTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
5844780 CTAGCAGGCTTAATGCCAGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
5844820 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
5844860 CTAGCAGGCTTCATGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
5844881 TACGGAATCA
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 135 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
Found at i:5846433 original size:12 final size:12
Alignment explanation
Indices: 5846412--5846446 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
5846402 AGATCATGAT
*
5846412 CCCGAACCAGAG
1 CCCGAGCCAGAG
5846424 CCCGAGCCAGAG
1 CCCGAGCCAGAG
5846436 CCCGAGCCAGA
1 CCCGAGCCAGA
5846447 TCCCAAGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.43, G:0.29, T:0.00
Consensus pattern (12 bp):
CCCGAGCCAGAG
Found at i:5850132 original size:3 final size:3
Alignment explanation
Indices: 5850126--5850164 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
5850116 ACCACCACCA
* *
5850126 CCT CCT CCT CCT CTT CCT CCT CTT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
5850165 TCTTCTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
CCT
Found at i:5851171 original size:23 final size:24
Alignment explanation
Indices: 5851132--5851177 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
5851122 ATTATATATT
5851132 AAATATATATTTTTATTTTTAATC
1 AAATATATATTTTTATTTTTAATC
5851156 AAATATAT-TTTTTATTTTTAAT
1 AAATATATATTTTTATTTTTAAT
5851178 TTAGATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
AAATATATATTTTTATTTTTAATC
Found at i:5853232 original size:3 final size:3
Alignment explanation
Indices: 5853224--5853316 Score: 71
Period size: 3 Copynumber: 30.0 Consensus size: 3
5853214 TTTAGCACTT
* * * *
5853224 TTA TTA TTA TTA TTA TTTC TTCA TTA TT- TTA ATG TTA TTA TCTT TTA
1 TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA TTA T-TA TTA
* * * *
5853271 TTA TTA TGA TTA TTA ATA TTA TGA TTA TTAA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
5853317 GTTTTATTTG
Statistics
Matches: 69, Mismatches: 16, Indels: 10
0.73 0.17 0.11
Matches are distributed among these distances:
2 2 0.03
3 58 0.84
4 9 0.13
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:5856706 original size:17 final size:19
Alignment explanation
Indices: 5856678--5856715 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5856668 CTAAAAAGTT
5856678 TTTAGTTTTGGGCT-AGGG
1 TTTAGTTTTGGGCTGAGGG
5856696 TTTAG-TTTGGGCTGAGGG
1 TTTAGTTTTGGGCTGAGGG
5856714 TT
1 TT
5856716 AATTTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.11, C:0.05, G:0.39, T:0.45
Consensus pattern (19 bp):
TTTAGTTTTGGGCTGAGGG
Found at i:5856722 original size:18 final size:17
Alignment explanation
Indices: 5856683--5856722 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
5856673 AAGTTTTTAG
*
5856683 TTTTGGGCTAGGGTTTA
1 TTTTGGGCTAGGGTTAA
*
5856700 GTTTGGGCTGAGGGTTAA
1 TTTTGGGCT-AGGGTTAA
5856718 TTTTG
1 TTTTG
5856723 TATTTGGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.12, C:0.05, G:0.38, T:0.45
Consensus pattern (17 bp):
TTTTGGGCTAGGGTTAA
Found at i:5859804 original size:26 final size:27
Alignment explanation
Indices: 5859766--5859816 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
5859756 CATGGCACAT
*
5859766 AAAAAATAAAAAAAAATATTTTTAACA
1 AAAAAATAAAAAAAAACATTTTTAACA
*
5859793 AAAAAAT-TAAAAAAACATTTTTAA
1 AAAAAATAAAAAAAAACATTTTTAA
5859817 ATTTACTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAAATAAAAAAAAACATTTTTAACA
Found at i:5860292 original size:29 final size:28
Alignment explanation
Indices: 5860243--5860338 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 28
5860233 AAAAAAATAT
*
5860243 AAATTACATTTTAACCCCTAACTTTTCTA
1 AAATTACATATTAA-CCCTAACTTTTCTA
* *
5860272 AAATTACATATTGACCACTAACTTTTTTA
1 AAATTACATATTAACC-CTAACTTTTCTA
*
5860301 AAATTACATTTTAACCCTAAACTTTTCCTA
1 AAATTACATATTAACCCT-AACTTTT-CTA
5860331 AAATTACA
1 AAATTACA
5860339 ATTTGACCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.07
29 44 0.76
30 10 0.17
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.40
Consensus pattern (28 bp):
AAATTACATATTAACCCTAACTTTTCTA
Found at i:5860358 original size:58 final size:58
Alignment explanation
Indices: 5860243--5860358 Score: 148
Period size: 58 Copynumber: 2.0 Consensus size: 58
5860233 AAAAAAATAT
***
5860243 AAATTACATTTTAACCCCTAACTTTTCTAAAATTACATATTGACCACTAACTTTTTTA
1 AAATTACATTTTAACCCCTAACTTTTCTAAAATTACATATTGACCACTAAAAGTTTTA
*
5860301 AAATTACATTTTAA-CCCTAAACTTTTCCTAAAATTACA-ATTTGACC-TTAAAAGTTTTA
1 AAATTACATTTTAACCCCT-AACTTTT-CTAAAATTACATA-TTGACCACTAAAAGTTTTA
5860359 CACCCTTTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
57 4 0.08
58 30 0.59
59 17 0.33
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (58 bp):
AAATTACATTTTAACCCCTAACTTTTCTAAAATTACATATTGACCACTAAAAGTTTTA
Found at i:5860675 original size:11 final size:11
Alignment explanation
Indices: 5860659--5860695 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
5860649 AATTGACACG
5860659 AAAGAGAAGAA
1 AAAGAGAAGAA
5860670 AAAGAG-AGAA
1 AAAGAGAAGAA
5860680 AGAAGAGAAGAA
1 A-AAGAGAAGAA
5860692 AAAG
1 AAAG
5860696 GGAAATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.21
11 14 0.58
12 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAGAGAAGAA
Found at i:5860820 original size:20 final size:20
Alignment explanation
Indices: 5860801--5860839 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5860791 AGGGCCGAAG
5860801 GAAAAAA-AGAAAGAAAGAA
1 GAAAAAAGAGAAAGAAAGAA
5860820 GAAAAAAGAGAAAGAAAGAA
1 GAAAAAAGAGAAAGAAAGAA
5860840 AAATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAGAAAGAAAGAA
Found at i:5861318 original size:16 final size:16
Alignment explanation
Indices: 5861278--5861329 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
5861268 CCCAATTTGC
5861278 AAGA-AAAAGGAAAAA
1 AAGAGAAAAGGAAAAA
*
5861293 AA-AGTGAAA-GAAAAA
1 AAGAG-AAAAGGAAAAA
5861308 TAAGAGAAAAGGAAAAA
1 -AAGAGAAAAGGAAAAA
5861325 AAGAG
1 AAGAG
5861330 CCCGAGTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 1 0.03
15 8 0.27
16 13 0.43
17 8 0.27
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (16 bp):
AAGAGAAAAGGAAAAA
Found at i:5861662 original size:21 final size:21
Alignment explanation
Indices: 5861623--5861662 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5861613 AAATTGATTT
*
5861623 ATCAAAATTTACTTGTAAATC
1 ATCAAAATTTAATTGTAAATC
*
5861644 ATCAAAATTTAATTTTAAA
1 ATCAAAATTTAATTGTAAA
5861663 ATATATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (21 bp):
ATCAAAATTTAATTGTAAATC
Found at i:5872421 original size:50 final size:50
Alignment explanation
Indices: 5872366--5872552 Score: 196
Period size: 50 Copynumber: 3.7 Consensus size: 50
5872356 ATCATTCGAA
*
5872366 ACACGTAGTAGCCCT-CACATAGTACTACACACGTGATCAAACTTTTCGAT
1 ACACGTAGTAG-CCTGCACATAGTACTACACACGTGATCAAACTTTCCGAT
* * * * *
5872416 TCACGTAGTAGCCTGCACATAGTACTACTCACATGATCGAAGCTATCCGAT
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGATC-AAACTTTCCGAT
* * * * * *** * *
5872467 ACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTTTCATTCCGGT
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTCCGAT
*
5872517 ACACGTAGTAGCCTACACATAGTACTACACACGTGA
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGA
5872553 CCATCACTTT
Statistics
Matches: 110, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
49 3 0.03
50 68 0.62
51 39 0.35
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
ACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTCCGAT
Found at i:5872489 original size:51 final size:50
Alignment explanation
Indices: 5872366--5872497 Score: 158
Period size: 51 Copynumber: 2.6 Consensus size: 50
5872356 ATCATTCGAA
* * * *
5872366 ACACGTAGTAGCCCT-CACATAGTACTACACACGTGATCAAACTTTTCGAT
1 ACACATAGTAG-CCTGCACATAGTACTACACACATGATCAAACTATCCGAT
* * * *
5872416 TCACGTAGTAGCCTGCACATAGTACTACTCACATGATCGAAGCTATCCGAT
1 ACACATAGTAGCCTGCACATAGTACTACACACATGATC-AAACTATCCGAT
*
5872467 ACGCATAGTAGCCTGCACATAGTACTACACA
1 ACACATAGTAGCCTGCACATAGTACTACACA
5872498 TGCGACCTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 3 0.04
50 31 0.44
51 36 0.51
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
ACACATAGTAGCCTGCACATAGTACTACACACATGATCAAACTATCCGAT
Found at i:5878611 original size:23 final size:25
Alignment explanation
Indices: 5878581--5878630 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
5878571 AAATTTAATA
5878581 ATAAAATAAT-ACTAAA-AATATTT
1 ATAAAATAATAACTAAATAATATTT
* *
5878604 ATAAAATATTAATTAAATAATATTT
1 ATAAAATAATAACTAAATAATATTT
5878629 AT
1 AT
5878631 CTAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 5 0.22
25 9 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAAAATAATAACTAAATAATATTT
Found at i:5880565 original size:51 final size:50
Alignment explanation
Indices: 5880436--5880680 Score: 226
Period size: 50 Copynumber: 4.9 Consensus size: 50
5880426 TTATCATTCG
* * *
5880436 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AACTTTCCA
1 ATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAA-TATCCA
* * *
5880486 ATTCACATAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCTA
1 ATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TAATATCCA
* * * * *
5880537 ACACACGTAGTAGCCTGGACATAGTACTACACACGTGATCGA-AGCTATCCG
1 ATACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATA-ATATCCA
* * * * * * ** *
5880588 GTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTTTCGT-TTCA
1 ATACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATAATATCCA
* *
5880638 ATACACGTAGTAGCCTACACATAGTACTACACATGTGACCATA
1 ATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATA
5880681 TGTAAGCATT
Statistics
Matches: 155, Mismatches: 34, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
49 1 0.01
50 76 0.49
51 74 0.48
52 4 0.03
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
ATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAATATCCA
Found at i:5880575 original size:101 final size:101
Alignment explanation
Indices: 5880438--5880675 Score: 307
Period size: 101 Copynumber: 2.4 Consensus size: 101
5880428 ATCATTCGAT
* * *
5880438 ACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAACTTTCCAATTCACATAGTAGCCT
1 ACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCCAATACACATAGTAGCCT
*
5880502 GCACATAGTACTACACACGTGACCATTAATATCTAAC
66 GCACATAGTACTACACACGCGACCATTAATATC-AAC
** * ** *
5880539 ACACGTAGTAGCCTGGACATAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAGTAGCCT
1 ACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCCAATACACATAGTAGCCT
* * ** * *
5880604 GCACATAGTACTACACATGCGACCTTTCGTTTCAAT
66 GCACATAGTACTACACACGCGACCATTAATATCAAC
*
5880640 ACACGTAGTAGCCTACACATAGTACTACACATGTGA
1 ACACGTAGTAGCCTACACATAGTACTACACACGTGA
5880676 CCATATGTAA
Statistics
Matches: 118, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
101 71 0.60
102 47 0.40
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (101 bp):
ACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCCAATACACATAGTAGCCT
GCACATAGTACTACACACGCGACCATTAATATCAAC
Found at i:5884075 original size:19 final size:19
Alignment explanation
Indices: 5884051--5884088 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5884041 CCGTGGAGAT
5884051 TGGGAAATAAAGGATTCAA
1 TGGGAAATAAAGGATTCAA
5884070 TGGGAAATAAAGGATTCAA
1 TGGGAAATAAAGGATTCAA
5884089 AATTAGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.21
Consensus pattern (19 bp):
TGGGAAATAAAGGATTCAA
Found at i:5886631 original size:75 final size:75
Alignment explanation
Indices: 5886349--5887405 Score: 1155
Period size: 75 Copynumber: 14.0 Consensus size: 75
5886339 TCGTCTTTGA
** *
5886349 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACATTGAGGTATTTTCAAGT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATT
5886414 TCTATTTTTC
66 TCTATTTTTC
* * * *
5886424 AAAAAATAAACTCATAATCTGAGAAGTGAGTTGAGCCTCAGGTCGCACGCTAAGGTATTTTCAAT
1 -AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAAT
*
5886489 TTCTGTTGTTTTTC
65 TTC---TATTTTTC
* * * * * * *
5886503 AAAAATGAACTTATAATCCGAGAGGTGAGTTGAGCCTCAGGTCACATGCTGAGGTATTTTTAATT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATT
** *
5886568 TCTGCTTATC
66 TCTATTTTTC
* * ***
5886578 AAAAATTAACTCATAATCCGAGAAGTCAGTTGAGCCTCGGGTCGCATATTGAGGTATTTTCAATT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATT
5886643 TCTATTTTTC
66 TCTATTTTTC
* * * * * *
5886653 AAAAATCAACTTATAATCCGAGAGGTGAGTCGAGCCTTGGGTTGCACACTGAGGTATTTTCAATT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATT
*
5886718 TCTGTTTTTC
66 TCTATTTTTC
* * * * * *
5886728 AAAAATCAACCCATAATCCGAGAAAATGAGTTGGGCCTCGGGGCGCGCGCTGAGGTATTCTCAAT
1 AAAAATCAACTCATAATCCGAG-AAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAAT
* *
5886793 TTTTGTTTTTC
65 TTCTATTTTTC
* * * * *
5886804 AAAAATCAATTCATAATCCTAAAAGTGAGTTGAGCCTTGGGTCGCACGCTAAGGTATTTTCAATT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATT
5886869 TCTATTTTTC
66 TCTATTTTTC
* * * *
5886879 AAAAATCAATTCATAATTCGAGAAGATGAGTGGAGCCTCGGGTCG-AGCACTGAGGTATTTTCAA
1 AAAAATCAACTCATAATCCGAGAAG-TGAGTTGAGCCTCGGGTCGCA-CGCTGAGGTATTTTCAA
*
5886943 TTTTTATTTTTC
64 TTTCTATTTTTC
* * * * *
5886955 AAAAATCAACTCATAATCTGAGAAGTGAGTTGAGTCTCAGGTCACACGCTGATGTATTTTTCAAT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTCAAT
*
5887020 TTATATTTTTC
65 TTCTATTTTTC
* * * * *
5887031 AAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCGAGTCGCGCGCTGAGGTATCTTCAATT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATT
5887096 TCTATTTTTC
66 TCTATTTTTC
* * * * * * *
5887106 AAAGATCAACTCATAATTCGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTTCAAT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTCAAT
5887171 TTCTATTTTTC
65 TTCTATTTTTC
* * * * * * * * * *
5887182 AAAAATAAACTCAAAATCTGAGAGGTGAGTTGAGCCTTGAGTCACATGCCGAGGTATTTTTTAAT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTCAAT
5887247 TTCTATTTTTC
65 TTCTATTTTTC
* ** * * * * *
5887258 AAAAATCAACTTATAATCTAAGAGGTGAGTTGAGCCACAGGTCGCGCGCTAAGGTATTTT-ATAT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCA-AT
*
5887322 TTCTGTTTTTC
65 TTCTATTTTTC
* * * * ** * *
5887333 AAAGATCAACTCATAATTCGAGAGGTGAGTTGAGCCTCGGGTCGTACGCCAAGGTGTTTTCAAGT
1 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATT
*
5887398 TCTGTTTT
66 TCTATTTT
5887406 AAAATAAAAA
Statistics
Matches: 828, Mismatches: 142, Indels: 23
0.83 0.14 0.02
Matches are distributed among these distances:
74 1 0.00
75 383 0.46
76 378 0.46
78 59 0.07
79 7 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (75 bp):
AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATT
TCTATTTTTC
Found at i:5886832 original size:151 final size:150
Alignment explanation
Indices: 5886349--5887405 Score: 1125
Period size: 151 Copynumber: 7.0 Consensus size: 150
5886339 TCGTCTTTGA
* * * ** *
5886349 AAAAATCAACTCATAATCCGAGAAGTGAGTTGAGCCTCGGGTCGCACATTGAGGTATTTTCAAGT
1 AAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTATTTTCAATT
* * * * *
5886414 TCTATTTTTCAAAAAATAAACTCATAATCTGAGAAGTGAGTTGAGCCTCAGGTCGCACGCTAAGG
66 TCTATTTTTC-AAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
*
5886479 TATTTTCAATTTCTGTTGTTTTTC
130 TATTTTCAATTTC---TATTTTTC
* * * *
5886503 AAAAATGAACTT-ATAATCCGAGAGGTGAGTTGAGCCTCAGGTCACATGCTGAGGTATTTTTAAT
1 AAAAATCAA-TTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTATTTTCAAT
** * * * * ***
5886567 TTCTGCTTATCAAAAATTAACTCATAATCCGAGAAGTCAGTTGAGCCTCGGGTCGCATATTGAGG
65 TTCTATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
5886632 TATTTTCAATTTCTATTTTTC
130 TATTTTCAATTTCTATTTTTC
* ** * *
5886653 AAAAATCAACTT-ATAATCCGAGAGGTGAGTCGAGCCTTGGGTTGCACACTGAGGTATTTTCAAT
1 AAAAATCAA-TTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTATTTTCAAT
* * ** * * *
5886717 TTCTGTTTTTCAAAAATCAACCCATAATCCGAGAAAATGAGTTGGGCCTCGGGGCGCGCGCTGAG
65 TTCTATTTTTCAAAAATCAACTCATAATCCGAG-AGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
* * *
5886782 GTATTCTCAATTTTTGTTTTTC
129 GTATTTTCAATTTCTATTTTTC
* * * ** *
5886804 AAAAATCAATTCATAATCCTAAAAGTGAGTTGAGCCTTGGGTCGCACGCTAAGGTATTTTCAATT
1 AAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTATTTTCAATT
* * * * *
5886869 TCTATTTTTCAAAAATCAATTCATAATTCGAGAAGATGAGTGGAGCCTCGGGTCG-AGCACTGAG
66 TCTATTTTTCAAAAATCAACTCATAATCCGAG-AGGTGAGTTGAGCCTCGGGTCGCA-CGCTGAG
*
5886933 GTATTTTCAATTTTTATTTTTC
129 GTATTTTCAATTTCTATTTTTC
* * * * * *
5886955 AAAAATCAACTCATAATCTGAGAAGTGAGTTGAGTCTCAGGTCACACGCTGATGTATTTTTCAAT
1 AAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTA-TTTTCAAT
* * * *
5887020 TTATATTTTTCAAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCGAGTCGCGCGCTGAGG
65 TTCTATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
*
5887085 TATCTTCAATTTCTATTTTTC
130 TATTTTCAATTTCTATTTTTC
* * * * * *
5887106 AAAGATCAACTCATAATTCGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGTATTTTTCAAT
1 AAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTA-TTTTCAAT
* * * * * * * *
5887171 TTCTATTTTTCAAAAATAAACTCAAAATCTGAGAGGTGAGTTGAGCCTTGAGTCACATGCCGAGG
65 TTCTATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGG
*
5887236 TATTTTTTAATTTCTATTTTTC
130 TA-TTTTCAATTTCTATTTTTC
** * * *
5887258 AAAAATCAACTT-ATAATCTAAGAGGTGAGTTGAGCCACAGGTCGCGCGCTAAGGTATTTT-ATA
1 AAAAATCAA-TTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTATTTTCA-A
* * * * **
5887321 TTTCTGTTTTTCAAAGATCAACTCATAATTCGAGAGGTGAGTTGAGCCTCGGGTCGTACGCCAAG
64 TTTCTATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
* * *
5887386 GTGTTTTCAAGTTCTGTTTT
129 GTATTTTCAATTTCTATTTT
5887406 AAAATAAAAA
Statistics
Matches: 763, Mismatches: 131, Indels: 22
0.83 0.14 0.02
Matches are distributed among these distances:
150 108 0.14
151 435 0.57
152 99 0.13
153 60 0.08
154 60 0.08
155 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (150 bp):
AAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCGCACGCTGAGGTATTTTCAATT
TCTATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
ATTTTCAATTTCTATTTTTC
Found at i:5887798 original size:28 final size:30
Alignment explanation
Indices: 5887709--5887832 Score: 157
Period size: 29 Copynumber: 4.3 Consensus size: 30
5887699 AAGAAAATAT
*
5887709 AAATTACATTTTGACACC-CAACTTTCCTA
1 AAATTACATTTTGACACCTAAACTTTCCTA
* * *
5887738 AAATTACATTTTGACACTTCAACTTCCCTA
1 AAATTACATTTTGACACCTAAACTTTCCTA
*
5887768 AAATTAGATTTTGAC-CCT-AACTTTCCTA
1 AAATTACATTTTGACACCTAAACTTTCCTA
* *
5887796 AAATTACATTTTGAC-CTTAAATTTTCCTA
1 AAATTACATTTTGACACCTAAACTTTCCTA
5887825 AAATTACA
1 AAATTACA
5887833 CATTAACCCC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
28 25 0.29
29 36 0.42
30 24 0.28
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (30 bp):
AAATTACATTTTGACACCTAAACTTTCCTA
Found at i:5887799 original size:58 final size:58
Alignment explanation
Indices: 5887709--5887832 Score: 187
Period size: 58 Copynumber: 2.1 Consensus size: 58
5887699 AAGAAAATAT
*
5887709 AAATTACATTTTGACACCCAACTTTCCTAAAATTACATTTTGACACTTCAACTTCCCTA
1 AAATTACATTTTGACACCCAACTTTCCTAAAATTACATTTTGAC-CTTAAACTTCCCTA
* * * *
5887768 AAATTAGATTTTGAC-CCTAACTTTCCTAAAATTACATTTTGACCTTAAATTTTCCTA
1 AAATTACATTTTGACACCCAACTTTCCTAAAATTACATTTTGACCTTAAACTTCCCTA
5887825 AAATTACA
1 AAATTACA
5887833 CATTAACCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 18 0.31
58 27 0.46
59 14 0.24
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (58 bp):
AAATTACATTTTGACACCCAACTTTCCTAAAATTACATTTTGACCTTAAACTTCCCTA
Found at i:5888068 original size:27 final size:26
Alignment explanation
Indices: 5888038--5888092 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
5888028 AGCACCAAAC
5888038 AAAGAAAAATG-AAAAATGAAAAAAGAA
1 AAAGAAAAA-GCAAAAATGAAAAAA-AA
* *
5888065 AAAGACAAAGCAAAAATTAAAAAAAA
1 AAAGAAAAAGCAAAAATGAAAAAAAA
5888091 AA
1 AA
5888093 CAGCCAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (26 bp):
AAAGAAAAAGCAAAAATGAAAAAAAA
Found at i:5888200 original size:11 final size:11
Alignment explanation
Indices: 5888184--5888219 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
5888174 AATCGGCACG
5888184 AAAGAGAAGAA
1 AAAGAGAAGAA
5888195 AAAGAG-AGAA
1 AAAGAGAAGAA
5888205 AGAAGAGAAGAA
1 A-AAGAGAAGAA
5888217 AAA
1 AAA
5888220 AGGAAAGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.22
11 13 0.57
12 5 0.22
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAGAGAAGAA
Found at i:5888210 original size:22 final size:20
Alignment explanation
Indices: 5888185--5888226 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
5888175 ATCGGCACGA
5888185 AAGAGAAGAAAAAGAGAGAAAG
1 AAGAGAAGAAAAA-AG-GAAAG
5888207 AAGAGAAGAAAAAAGGAAAG
1 AAGAGAAGAAAAAAGGAAAG
5888227 GAGAAAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AAGAGAAGAAAAAAGGAAAG
Found at i:5888351 original size:4 final size:4
Alignment explanation
Indices: 5888333--5888398 Score: 63
Period size: 4 Copynumber: 17.5 Consensus size: 4
5888323 AAGGAAAAAG
5888333 AGAA AGAAA ACGAA AG-A A-AA AGAA AGAA AGAA AG-A AGAA AGAA AG--
1 AGAA AG-AA A-GAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
5888378 AGAA AGAA AG-A AGAA AAAA AG
1 AGAA AGAA AGAA AGAA AGAA AG
5888399 TAATAAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
2 2 0.04
3 10 0.19
4 33 0.63
5 6 0.12
6 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:5888381 original size:25 final size:24
Alignment explanation
Indices: 5888326--5888398 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
5888316 AGGGTTGAAG
*
5888326 GAAAAAG--AGAAAGAAAACGAAA
1 GAAAAAGAAAGAAAGAAAAAGAAA
5888348 GAAAAAGAAAGAAAGAAAGAAGAAA
1 GAAAAAGAAAGAAAGAAA-AAGAAA
* *
5888373 GAAAGAGAAAGAAAGAAGAAAAAAA
1 GAAAAAGAAAGAAAGAA-AAAGAAA
5888398 G
1 G
5888399 TAATAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
22 7 0.16
24 9 0.20
25 27 0.61
26 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.25, T:0.00
Consensus pattern (24 bp):
GAAAAAGAAAGAAAGAAAAAGAAA
Found at i:5893478 original size:23 final size:25
Alignment explanation
Indices: 5893446--5893491 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
5893436 TCATGTGAAA
5893446 ATATACTCATTCAGCTT-TAATTTC
1 ATATACTCATTCAGCTTCTAATTTC
5893470 ATAT-CTCATTCAGCTTCTAATT
1 ATATACTCATTCAGCTTCTAATT
5893492 CAACTTCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (25 bp):
ATATACTCATTCAGCTTCTAATTTC
Found at i:5893808 original size:2 final size:2
Alignment explanation
Indices: 5893801--5893858 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
5893791 TCCTCCGAAC
5893801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5893843 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5893859 CAATCTACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5894250 original size:46 final size:46
Alignment explanation
Indices: 5894171--5894355 Score: 280
Period size: 46 Copynumber: 4.0 Consensus size: 46
5894161 ACAAGGCTAT
* * * *
5894171 AACTTAGTATGATTTTCTTCACGGAAATACCATACGTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
5894217 AACTCAGTGTGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
5894263 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
5894309 AACTCAGTATGGTTTTCTTCACTGAAATACCATACTTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
5894355 A
1 A
5894356 CTTTTCCATG
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:5898710 original size:19 final size:19
Alignment explanation
Indices: 5898671--5898711 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5898661 TTAAGAATAA
* * *
5898671 TAATATTAATAATGACGAT
1 TAATAATAATAATAACAAT
5898690 TAATAATAATAATAACAAT
1 TAATAATAATAATAACAAT
5898709 TAA
1 TAA
5898712 CAATTTAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
TAATAATAATAATAACAAT
Found at i:5900440 original size:9 final size:9
Alignment explanation
Indices: 5900426--5900482 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
5900416 TTTGGTTAAA
5900426 AATTACCCG
1 AATTACCCG
5900435 AATTACCCG
1 AATTACCCG
*
5900444 AATTAACCG
1 AATTACCCG
5900453 AATTA-CCG
1 AATTACCCG
*
5900461 AAAAATACCCG
1 --AATTACCCG
*
5900472 AATTATCCG
1 AATTACCCG
5900481 AA
1 AA
5900483 ATTTTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 3 0.07
9 31 0.76
10 4 0.10
11 3 0.07
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:5903154 original size:22 final size:22
Alignment explanation
Indices: 5903122--5903168 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5903112 ACGTAACATA
*
5903122 TAATAAAAATGATAAAAATTTT
1 TAATAAAAATGATAAAAATTAT
*
5903144 TAATAAGAATGATAAAAATTAT
1 TAATAAAAATGATAAAAATTAT
5903166 TAA
1 TAA
5903169 ATTTTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (22 bp):
TAATAAAAATGATAAAAATTAT
Found at i:5903189 original size:8 final size:8
Alignment explanation
Indices: 5903176--5903223 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 8
5903166 TAAATTTTAA
5903176 TAAAAATAT
1 TAAAAA-AT
5903185 TAAAAAA-
1 TAAAAAAT
5903192 TAAAAAA-
1 TAAAAAAT
5903199 TAAAAACAT
1 TAAAAA-AT
5903208 TAAAAAAT
1 TAAAAAAT
5903216 TATAAAAA
1 TA-AAAAA
5903224 AATTAGTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 13 0.36
8 6 0.17
9 17 0.47
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (8 bp):
TAAAAAAT
Found at i:5903195 original size:16 final size:15
Alignment explanation
Indices: 5903174--5903223 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 15
5903164 ATTAAATTTT
5903174 AATAAAAATATTAAAA
1 AATAAAAA-ATTAAAA
5903190 AATAAAAAA-TAAAA
1 AATAAAAAATTAAAA
5903204 ACATTAAAAAATTATAAA
1 A-A-TAAAAAATTA-AAA
5903222 AA
1 AA
5903224 AATTAGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.20
15 2 0.07
16 15 0.50
17 3 0.10
18 4 0.13
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (15 bp):
AATAAAAAATTAAAA
Found at i:5903199 original size:29 final size:29
Alignment explanation
Indices: 5903124--5903199 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
5903114 GTAACATATA
* *
5903124 ATAAAAATGATAAAAATTTTTAATAAGAATG
1 ATAAAAA--ATAAAAAATTTTAATAAAAATG
* **
5903155 ATAAAAATTATTAAATTTTAATAAAAAT-
1 ATAAAAAATAAAAAATTTTAATAAAAATG
5903183 ATTAAAAAATAAAAAAT
1 A-TAAAAAATAAAAAAT
5903200 AAAAACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.78
31 7 0.19
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (29 bp):
ATAAAAAATAAAAAATTTTAATAAAAATG
Found at i:5903204 original size:23 final size:23
Alignment explanation
Indices: 5903174--5903238 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
5903164 ATTAAATTTT
5903174 AATAAAAATATTAAAAAATAAAA
1 AATAAAAATATTAAAAAATAAAA
* * *
5903197 AATAAAAACATTAAAAAATTATA
1 AATAAAAATATTAAAAAATAAAA
*
5903220 AA-AAAATTAGTTAAAAAAT
1 AATAAAAATA-TTAAAAAAT
5903239 TATGAATTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
AATAAAAATATTAAAAAATAAAA
Found at i:5903238 original size:12 final size:11
Alignment explanation
Indices: 5903206--5903241 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5903196 AAATAAAAAC
5903206 ATTAAAAAATT
1 ATTAAAAAATT
*
5903217 ATAAAAAAATT
1 ATTAAAAAATT
5903228 AGTTAAAAAATT
1 A-TTAAAAAATT
5903240 AT
1 AT
5903242 GAATTCTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:5912786 original size:5 final size:5
Alignment explanation
Indices: 5912776--5912801 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5912766 TATTATTATA
5912776 TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT T
5912802 TTTAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:5922239 original size:3 final size:3
Alignment explanation
Indices: 5922231--5922268 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5922221 CGACGGCAGT
5922231 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5922269 CATTGTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5923734 original size:115 final size:114
Alignment explanation
Indices: 5923480--5923843 Score: 575
Period size: 115 Copynumber: 3.2 Consensus size: 114
5923470 TAAGCCCAAC
* * * * *
5923480 GAGCTTTTGGGGATTTAGCGGCGTTCTTAAGAAAGCACCGCTAATGCTCAGGACTTTAGTGGCGT
1 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGT
5923545 TTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
66 TTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
* * *
5923594 GAGCTTTCGTGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGTTCAGGGCTTTAGCGGCGT
1 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGT
*
5923659 TTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAATGACGCCGTTTTCT
66 TTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCT
* *
5923709 GAGCTTTTGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCG
1 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC-TTTAGCGGCG
* *
5923774 TTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCCGTTTTCT
65 TTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
* *
5923824 GATCTTTCGAGGATTTAGCG
1 GAGCTTTCGGGGATTTAGCG
5923844 CCGCTTTAAT
Statistics
Matches: 228, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
114 74 0.32
115 127 0.56
116 27 0.12
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (114 bp):
GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGT
TTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
Found at i:5923912 original size:99 final size:98
Alignment explanation
Indices: 5923742--5923942 Score: 314
Period size: 99 Copynumber: 2.0 Consensus size: 98
5923732 TTTATAAGAA
* *
5923742 AGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCC
1 AGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAGCC
*
5923807 CAACGACGCCGTTTTCTGATCTTTCGAGGATTT
66 CAACGACGCCGTTTTCTGAGCTTTCGAGGATTT
* *
5923840 AGCGCCGCTTTAATGCTCATGGC-TTTAGCGGCGTTTTTGGGAAAGCGCTACAAAAAAACCTAAG
1 AGCGCCGC--TAATGCTCAGGGCTTTTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAG
* *
5923904 CTCAACGACGCCGTTTTCTGAGCTTTCGGGGATTT
64 CCCAACGACGCCGTTTTCTGAGCTTTCGAGGATTT
5923939 AGCG
1 AGCG
5923943 GCGTTTTTAA
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
98 8 0.09
99 74 0.79
100 12 0.13
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (98 bp):
AGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAGCC
CAACGACGCCGTTTTCTGAGCTTTCGAGGATTT
Found at i:5924239 original size:36 final size:37
Alignment explanation
Indices: 5924199--5924281 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 37
5924189 GTGTTACCAT
* *
5924199 TTTAAGGTTT-ATGGATTATGGGTTTAGGGGTTAT-GG
1 TTTAAGGTTTAAAGG-TTATGGGTTAAGGGGTTATGGG
* *
5924235 TTTAAGGTTTAAAGGTTATGTGTTAAGGGTTTATGGG
1 TTTAAGGTTTAAAGGTTATGGGTTAAGGGGTTATGGG
*
5924272 TTTAGGGTTT
1 TTTAAGGTTT
5924282 TAGGGTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 26 0.65
37 14 0.35
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (37 bp):
TTTAAGGTTTAAAGGTTATGGGTTAAGGGGTTATGGG
Found at i:5924245 original size:21 final size:22
Alignment explanation
Indices: 5924199--5924273 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
5924189 GTGTTACCAT
* *
5924199 TTTAAGGTTTATG-GATTATGGG
1 TTTAAGGGTTATGTG-TTAAGGG
*
5924221 TTTAGGGGTTATG-GTTTAA-GG
1 TTTAAGGGTTATGTG-TTAAGGG
*
5924242 TTTAAAGGTTATGTGTTAAGGG
1 TTTAAGGGTTATGTGTTAAGGG
*
5924264 TTTATGGGTT
1 TTTAAGGGTT
5924274 TAGGGTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.40
22 26 0.60
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (22 bp):
TTTAAGGGTTATGTGTTAAGGG
Found at i:5924268 original size:15 final size:15
Alignment explanation
Indices: 5924200--5924281 Score: 62
Period size: 15 Copynumber: 5.7 Consensus size: 15
5924190 TGTTACCATT
*
5924200 TTAA-GGTTTATGGA
1 TTAAGGGTTTATGGG
* *
5924214 TTATGGGTTTAGGGG
1 TTAAGGGTTTATGGG
* * *
5924229 TT-ATGGTTTAAGGT
1 TTAAGGGTTTATGGG
* *
5924243 TTAAAGG-TTATGTG
1 TTAAGGGTTTATGGG
5924257 TTAAGGGTTTATGGG
1 TTAAGGGTTTATGGG
*
5924272 TTTAGGGTTT
1 TTAAGGGTTT
5924282 TAGGGTTTAA
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
14 23 0.45
15 28 0.55
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (15 bp):
TTAAGGGTTTATGGG
Found at i:5924281 original size:7 final size:7
Alignment explanation
Indices: 5924199--5924311 Score: 59
Period size: 7 Copynumber: 15.7 Consensus size: 7
5924189 GTGTTACCAT
*
5924199 TTTAAGG
1 TTTAGGG
*
5924206 TTTATGG
1 TTTAGGG
*
5924213 ATTATGGG
1 TTTA-GGG
5924221 TTTAGGG
1 TTTAGGG
* *
5924228 GTTATGG
1 TTTAGGG
*
5924235 TTTAAGG
1 TTTAGGG
*
5924242 TTTAAAGG
1 TTT-AGGG
*
5924250 -TTATGTG
1 TTTA-GGG
*
5924257 TTAAGGG
1 TTTAGGG
5924264 TTTATGGG
1 TTTA-GGG
5924272 TTTAGGG
1 TTTAGGG
5924279 TTTTAGGG
1 -TTTAGGG
*
5924287 TTTA-AG
1 TTTAGGG
**
5924293 TTTATAG
1 TTTAGGG
5924300 TTTAGGG
1 TTTAGGG
5924307 TTTAG
1 TTTAG
5924312 ATTAACTAGT
Statistics
Matches: 83, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
6 6 0.07
7 52 0.63
8 25 0.30
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:5924287 original size:15 final size:15
Alignment explanation
Indices: 5924199--5924310 Score: 58
Period size: 15 Copynumber: 7.7 Consensus size: 15
5924189 GTGTTACCAT
*
5924199 TTTAAGGTTTAT-GG
1 TTTAGGGTTTATGGG
*
5924213 ATTATGGGTTTA-GGG
1 TTTA-GGGTTTATGGG
* * *
5924228 GTTATGGTTTA-AGG
1 TTTAGGGTTTATGGG
* *
5924242 TTTAAAGG-TTATGTG
1 TTT-AGGGTTTATGGG
*
5924257 TTAAGGGTTTATGGG
1 TTTAGGGTTTATGGG
5924272 TTTAGGGTTT-TAGGG
1 TTTAGGGTTTAT-GGG
* *
5924287 TTTA-AGTTTAT-AG
1 TTTAGGGTTTATGGG
5924300 TTTAGGGTTTA
1 TTTAGGGTTTA
5924311 GATTAACTAG
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
13 5 0.07
14 29 0.39
15 40 0.54
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (15 bp):
TTTAGGGTTTATGGG
Found at i:5924458 original size:7 final size:7
Alignment explanation
Indices: 5924448--5924502 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
5924438 GATTTAAGGT
5924448 TTAGGGG
1 TTAGGGG
*
5924455 TTAGTGG
1 TTAGGGG
5924462 TTAGGGG
1 TTAGGGG
5924469 TTAGGGG
1 TTAGGGG
* *
5924476 TTAAGAG
1 TTAGGGG
*
5924483 TTAGGGAT
1 TTAGGG-G
*
5924491 TTAAGGG
1 TTAGGGG
5924498 TTAGG
1 TTAGG
5924503 ACTTAAGGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:5924512 original size:22 final size:22
Alignment explanation
Indices: 5924473--5924520 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
5924463 TAGGGGTTAG
* * *
5924473 GGGTTAAGAGTTAGGGATTTAA
1 GGGTTAAGACTTAAGGATTCAA
*
5924495 GGGTTAGGACTTAAGGATTCAA
1 GGGTTAAGACTTAAGGATTCAA
5924517 GGGT
1 GGGT
5924521 CGGGTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.29
Consensus pattern (22 bp):
GGGTTAAGACTTAAGGATTCAA
Found at i:5924846 original size:19 final size:18
Alignment explanation
Indices: 5924817--5924870 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
5924807 GGACCAAATT
*
5924817 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAATTAAA
* *
5924835 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAATTAAA
5924854 ATAAAAACACTAAAATT
1 ATAAAAA-A-TAAAATT
5924871 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:5924925 original size:47 final size:48
Alignment explanation
Indices: 5924855--5924953 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 48
5924845 AAAAATGAAA
* *
5924855 TAAAAACACTAAAATTTTTAATTTTATCTAATTTTTATATATATTACT
1 TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
5924903 TAAAAA-ACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
5924950 TAAA
1 TAAA
5924954 CAAAACTATG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 43 0.88
48 6 0.12
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (48 bp):
TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
Found at i:5925308 original size:16 final size:15
Alignment explanation
Indices: 5925287--5925325 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
5925277 ACGCTGTGGT
5925287 TTTATTCCCCTCCAAA
1 TTTATTCCCCTCC-AA
*
5925303 TTTATTCCCCTTCAA
1 TTTATTCCCCTCCAA
5925318 TTT-TTCCC
1 TTTATTCCC
5925326 ATACCCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 5 0.23
16 12 0.55
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTATTCCCCTCCAA
Found at i:5925658 original size:18 final size:18
Alignment explanation
Indices: 5925635--5925669 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5925625 ATTATTTTTA
5925635 TTCTTTCTACTTTTCTTT
1 TTCTTTCTACTTTTCTTT
* *
5925653 TTCTTTTTTCTTTTCTT
1 TTCTTTCTACTTTTCTT
5925670 GGTAGTTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (18 bp):
TTCTTTCTACTTTTCTTT
Found at i:5929908 original size:70 final size:70
Alignment explanation
Indices: 5929783--5929913 Score: 169
Period size: 70 Copynumber: 1.9 Consensus size: 70
5929773 TTTATCAAAA
* * * *
5929783 GCGCTGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGTAAAAGCACCGCTAAAGATCATGTTGA
1 GCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAGCACCGCAAAAGAACATGTTGA
5929848 GTAAG
66 GTAAG
*
5929853 GCGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTT-T-ATCACAAA-CGCCGCAAAAGAACATG
1 GCGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTTGTGAT-A-AAAGCACCGCAAAAGAACATG
5929914 ATTTTTAGCG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
69 1 0.02
70 46 0.87
71 6 0.11
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (70 bp):
GCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAGCACCGCAAAAGAACATGTTGA
GTAAG
Found at i:5929921 original size:43 final size:43
Alignment explanation
Indices: 5929854--5929950 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
5929844 TTGAGTAAGG
* * * * *
5929854 CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTATCACAAA
1 CGCCGCAAAAGAACATGTTCTTTAGCGACGCTTTAAACACAAA
5929897 CGCCGCAAAAGAACATGATT-TTTAGCGACGCTTTAAACACAAA
1 CGCCGCAAAAGAACATG-TTCTTTAGCGACGCTTTAAACACAAA
5929940 CGCCGCAAAAG
1 CGCCGCAAAAG
5929951 TTAGTGACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 46 0.96
44 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (43 bp):
CGCCGCAAAAGAACATGTTCTTTAGCGACGCTTTAAACACAAA
Found at i:5930057 original size:22 final size:23
Alignment explanation
Indices: 5930022--5930064 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5930012 TAGCGGCGCT
* *
5930022 AAAAAGCGCTGCTAAAGGCCTAA
1 AAAAAGCGCCGCTAAAAGCCTAA
5930045 AAAAAG-GCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
5930065 GTTTTGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (23 bp):
AAAAAGCGCCGCTAAAAGCCTAA
Found at i:5930274 original size:13 final size:13
Alignment explanation
Indices: 5930247--5930289 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5930237 ATAATTAATT
*
5930247 TATAA-AAATTAA
1 TATAATAAAATAA
*
5930259 TATATTAAAATAA
1 TATAATAAAATAA
5930272 TATAATAAAAT-A
1 TATAATAAAATAA
5930284 TATAAT
1 TATAAT
5930290 TTTAATCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAATAAAATAA
Found at i:5932454 original size:63 final size:63
Alignment explanation
Indices: 5932385--5932523 Score: 154
Period size: 63 Copynumber: 2.2 Consensus size: 63
5932375 CAGAGGGGCG
* * *
5932385 TGTGTCCAGGCCGTGTCACTCACCAAGTTCGTATTAGAGGCACACGGACAAGACACACCGGCA
1 TGTGTCCAAGCCGTGTCACTCACCAAGTTCATATTAGAGACACACGGACAAGACACACCGGCA
* * ** * * * * **
5932448 TGTGTCCAAGCCATGTGACTCACTGAGTTTATATTTGAGACACACGGGCAAGGCACATGGGCA
1 TGTGTCCAAGCCGTGTCACTCACCAAGTTCATATTAGAGACACACGGACAAGACACACCGGCA
5932511 TGTG-CCAAGCCGT
1 TGTGTCCAAGCCGT
5932524 ATAGGCGTGT
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
62 8 0.13
63 54 0.87
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.21
Consensus pattern (63 bp):
TGTGTCCAAGCCGTGTCACTCACCAAGTTCATATTAGAGACACACGGACAAGACACACCGGCA
Found at i:5935336 original size:16 final size:17
Alignment explanation
Indices: 5935315--5935354 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
5935305 TTCTATATGG
5935315 ATTTTACT-TATATTTT
1 ATTTTACTATATATTTT
5935331 ATTTTACTACTATATTTT
1 ATTTTACTA-TATATTTT
5935349 ATTTTA
1 ATTTTA
5935355 ACAAAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTACTATATATTTT
Found at i:5935558 original size:24 final size:23
Alignment explanation
Indices: 5935531--5935575 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5935521 ATCATTGGGC
5935531 TGTTTCAAAATTTTACCGTTGGTA
1 TGTTT-AAAATTTTACCGTTGGTA
* *
5935555 TGTTTGAATTTTTACCGTTGG
1 TGTTTAAAATTTTACCGTTGG
5935576 AAAAATTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (23 bp):
TGTTTAAAATTTTACCGTTGGTA
Found at i:5937121 original size:19 final size:18
Alignment explanation
Indices: 5937065--5937123 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
5937055 TTTAATTGCT
5937065 ATTTTAACCCCTTTAGTTA
1 ATTTTAA-CCCTTTAGTTA
* * *
5937084 ATTTTAA-TCTATAATTTA
1 ATTTTAACCCT-TTAGTTA
5937102 ACTTTTAACCCTTTAGTTA
1 A-TTTTAACCCTTTAGTTA
5937121 ATT
1 ATT
5937124 GCTATTGTCC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
17 2 0.06
18 8 0.26
19 19 0.61
20 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTTAACCCTTTAGTTA
Found at i:5939206 original size:21 final size:21
Alignment explanation
Indices: 5939180--5939219 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5939170 TTTTCTAAAA
*
5939180 TTAAAA-GTCAAAACTATTAAG
1 TTAAAACG-CAAAACAATTAAG
5939201 TTAAAACGCAAAACAATTA
1 TTAAAACGCAAAACAATTA
5939220 TATTATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (21 bp):
TTAAAACGCAAAACAATTAAG
Found at i:5941446 original size:63 final size:63
Alignment explanation
Indices: 5941365--5941493 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
5941355 TTTATCTTAT
5941365 AATTTAGAGTTTTATTGATTCGTTAACCTAGAATTTCTTTATCTTGAACTTTTAATTGATCAG
1 AATTTAGAGTTTTATTGATTCGTTAACCTAGAATTTCTTTATCTTGAACTTTTAATTGATCAG
5941428 AATTTAGAGTTTTATTGATTCGTTAACCTAGAATTTCTTTATCTTGAACTTTTAATTGATCAG
1 AATTTAGAGTTTTATTGATTCGTTAACCTAGAATTTCTTTATCTTGAACTTTTAATTGATCAG
5941491 AAT
1 AAT
5941494 ATTGTAATTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.47
Consensus pattern (63 bp):
AATTTAGAGTTTTATTGATTCGTTAACCTAGAATTTCTTTATCTTGAACTTTTAATTGATCAG
Done.