Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000572.1 Hibiscus syriacus cultivar Beakdansim tig00001120_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2399138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1828886 original size:2 final size:2
Alignment explanation
Indices: 1828847--1828873 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1828837 GATGTGTAAG
1828847 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
1828874 CAAAAGTATA
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:1829389 original size:29 final size:30
Alignment explanation
Indices: 1829319--1829377 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1829309 AATTTAAAGC
1829319 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
1829350 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
1829378 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:1829490 original size:20 final size:20
Alignment explanation
Indices: 1829467--1829545 Score: 87
Period size: 20 Copynumber: 4.1 Consensus size: 20
1829457 TTCAAGATTG
* *
1829467 CCCAGGGGGTATAGATTCCC
1 CCCAGGGGGTACAGATACCC
1829487 CCCAGGGGGTACAGATA--C
1 CCCAGGGGGTACAGATACCC
1829505 CCC---GGGTACAGATACCCCC
1 CCCAGGGGGTACAGATA--CCC
1829524 CCCAGGGGGTACAGATACCC
1 CCCAGGGGGTACAGATACCC
1829544 CC
1 CC
1829546 TGCAGGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
15 11 0.22
18 4 0.08
19 4 0.08
20 20 0.40
22 11 0.22
ACGTcount: A:0.23, C:0.37, G:0.28, T:0.13
Consensus pattern (20 bp):
CCCAGGGGGTACAGATACCC
Found at i:1829513 original size:15 final size:15
Alignment explanation
Indices: 1829493--1829522 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1829483 TCCCCCCAGG
1829493 GGGTACAGATACCCC
1 GGGTACAGATACCCC
1829508 GGGTACAGATACCCC
1 GGGTACAGATACCCC
1829523 CCCCAGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:1829663 original size:21 final size:21
Alignment explanation
Indices: 1829637--1829679 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1829627 ATTTGAATAT
*
1829637 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1829658 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1829679 T
1 T
1829680 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1829745 original size:20 final size:22
Alignment explanation
Indices: 1829707--1829746 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1829697 TTTGAGTATA
1829707 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1829729 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1829747 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1830001 original size:34 final size:32
Alignment explanation
Indices: 1829962--1830031 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1829952 TTTTGTAAAG
* *
1829962 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1829996 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1830028 GGGA
1 GGGA
1830032 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1831042 original size:3 final size:3
Alignment explanation
Indices: 1831021--1831064 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1831011 TGAAGAAAGG
* *
1831021 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1831065 TGAGGACGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1832718 original size:29 final size:30
Alignment explanation
Indices: 1832648--1832706 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1832638 AATTTAAGGC
1832648 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
1832679 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
1832707 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:1832821 original size:21 final size:21
Alignment explanation
Indices: 1832796--1832874 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
1832786 TTCAAGATTG
* *
1832796 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
1832817 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
1832835 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
*
1832853 CCTAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
1832874 C
1 C
1832875 TGCAGGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 11 0.22
18 7 0.14
21 31 0.63
ACGTcount: A:0.23, C:0.35, G:0.28, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:1832842 original size:36 final size:36
Alignment explanation
Indices: 1832802--1832873 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1832792 ATTGCCCAGG
* *
1832802 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
*
1832838 GGGTACAGATACCCCCCTAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
1832874 CTGCAGGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:1832843 original size:15 final size:15
Alignment explanation
Indices: 1832823--1832852 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1832813 CCCCCCCAGG
1832823 GGGTACAGATACCCC
1 GGGTACAGATACCCC
1832838 GGGTACAGATACCCC
1 GGGTACAGATACCCC
1832853 CCTAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:1832992 original size:21 final size:21
Alignment explanation
Indices: 1832966--1833008 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1832956 ATTTGAATAT
*
1832966 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1832987 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1833008 T
1 T
1833009 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1833074 original size:20 final size:22
Alignment explanation
Indices: 1833036--1833075 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1833026 TTTGAGTATA
1833036 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1833058 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1833076 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1833329 original size:34 final size:32
Alignment explanation
Indices: 1833290--1833359 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1833280 TTTTGTAAAG
* *
1833290 GGGAAAGGTTATAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
1833324 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
1833356 GGGA
1 GGGA
1833360 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:1841478 original size:83 final size:82
Alignment explanation
Indices: 1841400--1841627 Score: 198
Period size: 83 Copynumber: 2.8 Consensus size: 82
1841390 AAAAAAACAA
* * *
1841400 CGCTAAATTACTACTTTGTTGC-GTGTTTTTTTGAAAAAACAT-AACTATAGATGAACCCTATTG
1 CGCTAAAGTACTACTATGTTGCGGCGTTTTTTT-AAAAAA-ATCAACTATAGATGAACCCTATTG
1841463 CAATATTTATGAAAAATAC
64 CAATATTTATGAAAAATAC
* * *
1841482 TGCTAAAGTACTACTATGTTGCGGCGTTTTTTTAAAAAATTGCCACTATAGATGAACCCTATTAT
1 CGCTAAAGTACTACTATGTTGCGGCGTTTTTTTAAAAAAAT-CAACTATAGATGAACCCTA-T-T
* *
1841547 G-AAGT-TGGTAT-AAAAATGC
63 GCAA-TAT-TTATGAAAAATAC
* * * * * * * *
1841566 CGCTAAAGTACTACTCTATTACGACG-TTTGTTGAAAAAATGCCACCATAGATGAACCCTATT
1 CGCTAAAGTACTACTATGTTGCGGCGTTTTTTTAAAAAAAT-CAACTATAGATGAACCCTATT
1841628 ACGGTGTTTG
Statistics
Matches: 122, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
81 2 0.02
82 26 0.21
83 56 0.46
84 32 0.26
85 6 0.05
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (82 bp):
CGCTAAAGTACTACTATGTTGCGGCGTTTTTTTAAAAAAATCAACTATAGATGAACCCTATTGCA
ATATTTATGAAAAATAC
Found at i:1841641 original size:83 final size:83
Alignment explanation
Indices: 1841443--1841703 Score: 287
Period size: 83 Copynumber: 3.1 Consensus size: 83
1841433 AAAAAACATA
* * * *
1841443 ACTATAGATGAACCCTATTGC-AA-TAT-TTATGAAAAATACTGCTAAAGTACTACTATGTTGCG
1 ACTATAGATGAACCCTATTACGAAGT-TGGTAT-AAAAATGCCGCTAAAGTACTACTATGTTGCG
* * *
1841505 GCGTTTTTTTAAAAAATTGCC
64 ACGTTTGTTGAAAAAA-TGCC
* * * *
1841526 ACTATAGATGAACCCTATTATGAAGTTGGTATAAAAATGCCGCTAAAGTACTACTCTATTACGAC
1 ACTATAGATGAACCCTATTACGAAGTTGGTATAAAAATGCCGCTAAAGTACTACTATGTTGCGAC
1841591 GTTTGTTGAAAAAATGCC
66 GTTTGTTGAAAAAATGCC
* ** * * * *
1841609 ACCATAGATGAACCCTATTACGGTGTTTGTATAAAAACGCCGCTAAAGTATTACTTTGTTGC-AG
1 ACTATAGATGAACCCTATTACGAAGTTGGTATAAAAATGCCGCTAAAGTACTACTATGTTGCGA-
1841673 CGTTTGTTGAAAAAATGCC
65 CGTTTGTTGAAAAAATGCC
*
1841692 ACTATATATGAA
1 ACTATAGATGAA
1841704 TCCTTGTAAC
Statistics
Matches: 151, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
82 1 0.01
83 104 0.69
84 42 0.28
85 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (83 bp):
ACTATAGATGAACCCTATTACGAAGTTGGTATAAAAATGCCGCTAAAGTACTACTATGTTGCGAC
GTTTGTTGAAAAAATGCC
Found at i:1841645 original size:42 final size:42
Alignment explanation
Indices: 1841514--1841645 Score: 119
Period size: 42 Copynumber: 3.1 Consensus size: 42
1841504 GGCGTTTTTT
* *
1841514 TAAAAAATTGCCACTATAGATGAACCCTATTATGAAGTTGGTA
1 TAAAAAA-TGCCACTATAGATGAACCCTATTACGAAGTTTGTA
* * * *
1841557 T-AAAAATGCCGCTAAAG-T-ACTACTCTATTACGACGTTTGT-
1 TAAAAAATGCCACTATAGATGA--ACCCTATTACGAAGTTTGTA
* **
1841597 TGAAAAAATGCCACCATAGATGAACCCTATTACGGTGTTTGTA
1 T-AAAAAATGCCACTATAGATGAACCCTATTACGAAGTTTGTA
1841640 TAAAAA
1 TAAAAA
1841646 CGCCGCTAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
41 24 0.34
42 39 0.56
43 3 0.04
44 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (42 bp):
TAAAAAATGCCACTATAGATGAACCCTATTACGAAGTTTGTA
Found at i:1842456 original size:32 final size:31
Alignment explanation
Indices: 1842418--1842494 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1842408 GGAGGCCGTG
* * *
1842418 GGGCCTATCTAAGAACATATCTTAGGGGCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
* *
1842450 GGGCCTACCTGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
1842481 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1842495 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:1849917 original size:19 final size:17
Alignment explanation
Indices: 1849867--1849919 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
1849857 GATAAAATCA
*
1849867 ATTATTAATGTTGTATTTT
1 ATTATT-ATGTT-TATTTG
*
1849886 ATTATTATATTTATATTG
1 ATTATTATGTTTAT-TTG
1849904 ATTATTATTGTTTATT
1 ATTATTA-TGTTTATT
1849920 ATTAACAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.10
18 14 0.48
19 12 0.41
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (17 bp):
ATTATTATGTTTATTTG
Found at i:1850437 original size:14 final size:14
Alignment explanation
Indices: 1850418--1850449 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1850408 GTTAGATTCC
1850418 TTATGAAAATAAAA
1 TTATGAAAATAAAA
*
1850432 TTATGAAAATAAGA
1 TTATGAAAATAAAA
1850446 TTAT
1 TTAT
1850450 TGGGATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (14 bp):
TTATGAAAATAAAA
Found at i:1853010 original size:27 final size:27
Alignment explanation
Indices: 1852980--1853067 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
1852970 TTATATTTTT
1852980 CAAATATTTTTTATTAATTGAATTATG
1 CAAATATTTTTTATTAATTGAATTATG
** * ** * * *
1853007 CAAATATTCATAAGGAACTTTATATTTTT
1 CAAATATTTTTTATTAA-TTGA-ATTATG
1853036 CAAATATTTTTTATTAATTGAATTATG
1 CAAATATTTTTTATTAATTGAATTATG
1853063 CAAAT
1 CAAAT
1853068 TTTGTTCTTA
Statistics
Matches: 43, Mismatches: 16, Indels: 4
0.68 0.25 0.06
Matches are distributed among these distances:
27 21 0.49
28 6 0.14
29 16 0.37
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (27 bp):
CAAATATTTTTTATTAATTGAATTATG
Found at i:1853041 original size:56 final size:56
Alignment explanation
Indices: 1852955--1853067 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
1852945 TTGTCCATAC
1852955 TATTCATAAGGAACTTTATATTTTTCAAATATTTTTTATTAATTGAATTATGCAAA
1 TATTCATAAGGAACTTTATATTTTTCAAATATTTTTTATTAATTGAATTATGCAAA
1853011 TATTCATAAGGAACTTTATATTTTTCAAATATTTTTTATTAATTGAATTATGCAAA
1 TATTCATAAGGAACTTTATATTTTTCAAATATTTTTTATTAATTGAATTATGCAAA
1853067 T
1 T
1853068 TTTGTTCTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (56 bp):
TATTCATAAGGAACTTTATATTTTTCAAATATTTTTTATTAATTGAATTATGCAAA
Found at i:1855123 original size:4 final size:4
Alignment explanation
Indices: 1855116--1855140 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1855106 TATATATATA
1855116 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1855141 TCACCTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1856836 original size:2 final size:2
Alignment explanation
Indices: 1856829--1856871 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1856819 GACTATGTGT
1856829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1856871 T
1 T
1856872 TTAAGTCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1857442 original size:301 final size:302
Alignment explanation
Indices: 1856853--1857442 Score: 1013
Period size: 301 Copynumber: 2.0 Consensus size: 302
1856843 TATATATATA
1856853 TATATATATATATATATATTTAAGTCATTAATAGTTTTAAAATCATTGTAATTAAGTCCTTACCT
1 TATATATATATATATATATTTAAGTCATTAATAGTTTTAAAATCATTGTAATTAAGTCCTTACCT
*
1856918 CTTCTAAAAAATTTTGGTATAATTATTTTTAGGACACTGTCAGTTTTAAAATTAATGGAAATAAC
66 CTTCTAAAAAATTTTGGTATAATTATTTTTAGGACACTATCAGTTTTAAAATTAATGGAAATAAC
*
1856983 TTTGATCCCAAATTTATCTGGTTTAATTATTTTTAAGACCTTTTAATTTTAAAATTAATGAAATT
131 TTTGATCCCAAATTTATCTGGTTTAATTATTTTTAAGACCTTTGAATTTTAAAATTAATGAAATT
*
1857048 AAACTCTTAATCTCTTAATTTTTATACTTTAATTACTTTTTTGACTCTATTTATTTTAAAGTCAA
196 AAACTCTTAATCTCTTAATTTTTATACTTTAATTACTTTTTTGACTCTATTTATTTTAAAATCAA
* *
1857113 ACATCTTTCCCCTCTTAATTCAATCCTGACTCTATGAGTTTT
261 ACAACTTTCCCCTCATAATTCAATCCTGACTCTATGAGTTTT
* * * *
1857155 TATATATAT-TTTTTATTTTTAAGTCATTAATAGTTTTAAAATCATTGTAATTATGTCCTTACCT
1 TATATATATATATATATATTTAAGTCATTAATAGTTTTAAAATCATTGTAATTAAGTCCTTACCT
*
1857219 CTTCTAAAAATTTTTGGTATAATTATTTTTAGGACACTATCAGTTTTAAAATTAATGGAAATAAC
66 CTTCTAAAAAATTTTGGTATAATTATTTTTAGGACACTATCAGTTTTAAAATTAATGGAAATAAC
*
1857284 TTTGATCCCAAATTTATCTGGTTTAATTATTTTTAGGACCTTTGAATTTTAAAATTAATGAAATT
131 TTTGATCCCAAATTTATCTGGTTTAATTATTTTTAAGACCTTTGAATTTTAAAATTAATGAAATT
* * * *
1857349 AAACTCTTTATCTCTTAATTTTTATAGTTTAATTACTTTTTTTACTCTATTTATTTTAAAATTAA
196 AAACTCTTAATCTCTTAATTTTTATACTTTAATTACTTTTTTGACTCTATTTATTTTAAAATCAA
*
1857414 ACAAC-TTCCCCTTCATAATTCGATCCTGA
261 ACAACTTTCCCC-TCATAATTCAATCCTGA
1857443 ATCCGTTCGT
Statistics
Matches: 271, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
300 6 0.02
301 256 0.94
302 9 0.03
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (302 bp):
TATATATATATATATATATTTAAGTCATTAATAGTTTTAAAATCATTGTAATTAAGTCCTTACCT
CTTCTAAAAAATTTTGGTATAATTATTTTTAGGACACTATCAGTTTTAAAATTAATGGAAATAAC
TTTGATCCCAAATTTATCTGGTTTAATTATTTTTAAGACCTTTGAATTTTAAAATTAATGAAATT
AAACTCTTAATCTCTTAATTTTTATACTTTAATTACTTTTTTGACTCTATTTATTTTAAAATCAA
ACAACTTTCCCCTCATAATTCAATCCTGACTCTATGAGTTTT
Found at i:1858355 original size:2 final size:2
Alignment explanation
Indices: 1858350--1858383 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1858340 ATATAAATGG
1858350 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
1858384 TCTTATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1859038 original size:174 final size:171
Alignment explanation
Indices: 1858674--1859026 Score: 607
Period size: 174 Copynumber: 2.0 Consensus size: 171
1858664 AGTGATACGA
1858674 GCTATGTGACATATGAATATGAATTCATATGAAAAGTGACATGAATTACATGAAAATAAACTACA
1 GCTATGTGA-ATATGAATATGAATTCATATGAAAAGTGACATGAATTACATGAAAATAAACTACA
1858739 TGATGATATGCACATGTGATATCAGATATATGTTTACACATACATATGTGACAGAAGAGAAGAAA
65 TGATGATATGCACATGTGATATCAGATATATGTTTACACATACATATGTGACAGAAGAGAAGAAA
1858804 TATGTGATTATATGAAATGTGATAAGAGCTATGTGAAAGAAC
130 TATGTGATTATATGAAATGTGATAAGAGCTATGTGAAAGAAC
1858846 GAGCTATGTGACATATGAATATGAATTCATATGAAAAGTGACATGAATTACATGAAAATAAACTA
1 --GCTATGTGA-ATATGAATATGAATTCATATGAAAAGTGACATGAATTACATGAAAATAAACTA
1858911 CATGATGATATGCACATGTGATATCAGATATATGTTTACACATACATATAGTATGTGACAGAAGA
63 CATGATGATATGCACATGTGATATCAGATATATGTTTACACATAC----A-TATGTGACAGAAGA
1858976 GAAAGAAATATGTGATTATATGAAATGTGATAAAGAGCTATGTGAAAGAAC
123 G-AAGAAATATGTGATTATATGAAATGTGAT-AAGAGCTATGTGAAAGAAC
1859027 CAGTGATATG
Statistics
Matches: 172, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
174 108 0.63
178 1 0.01
179 15 0.09
180 29 0.17
181 19 0.11
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.28
Consensus pattern (171 bp):
GCTATGTGAATATGAATATGAATTCATATGAAAAGTGACATGAATTACATGAAAATAAACTACAT
GATGATATGCACATGTGATATCAGATATATGTTTACACATACATATGTGACAGAAGAGAAGAAAT
ATGTGATTATATGAAATGTGATAAGAGCTATGTGAAAGAAC
Found at i:1859141 original size:21 final size:21
Alignment explanation
Indices: 1859116--1859175 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
1859106 CGAGGGTTAT
*
1859116 AGTGGTCCTTCGAGACAATAC
1 AGTGGTCCTTCGGGACAATAC
* *
1859137 AGTGGTCATTCGGGACAATAT
1 AGTGGTCCTTCGGGACAATAC
*
1859158 AGTGATCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
1859176 ATTTCATATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (21 bp):
AGTGGTCCTTCGGGACAATAC
Found at i:1860004 original size:19 final size:19
Alignment explanation
Indices: 1859980--1860029 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1859970 ATGTTAACGA
1859980 TACTGTTCATAATGTGTTT
1 TACTGTTCATAATGTGTTT
1859999 TACTGTTCATAATGTGTTT
1 TACTGTTCATAATGTGTTT
1860018 TACTGTTCATAA
1 TACTGTTCATAA
1860030 ATACATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (19 bp):
TACTGTTCATAATGTGTTT
Found at i:1870274 original size:24 final size:25
Alignment explanation
Indices: 1870227--1870274 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1870217 AAAAAAGGAA
*
1870227 GAAAAAAGAGAAACAATAACAAAAG
1 GAAAAAAGAGAAACAACAACAAAAG
* *
1870252 GAAAAAAG-GAATCAACAAGAAAA
1 GAAAAAAGAGAAACAACAACAAAA
1870275 AGAGACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.71, C:0.08, G:0.17, T:0.04
Consensus pattern (25 bp):
GAAAAAAGAGAAACAACAACAAAAG
Found at i:1870955 original size:22 final size:22
Alignment explanation
Indices: 1870902--1870955 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1870892 GGTTACCCCA
*
1870902 TCAAACCTTCGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
*
1870924 CCAAACCTTTGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
1870946 TCAAACCTTT
1 TCAAACCTTT
1870956 AACCAAGCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (22 bp):
TCAAACCTTTGAGCATCAAATG
Found at i:1871600 original size:20 final size:20
Alignment explanation
Indices: 1871575--1871620 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1871565 AAGGATACTC
*
1871575 GATTCAAAAGCACTTTTAAA
1 GATTCAAAAGAACTTTTAAA
*
1871595 GATTCAAAAGAACTTTTGAA
1 GATTCAAAAGAACTTTTAAA
1871615 GATTCA
1 GATTCA
1871621 TGTTGGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (20 bp):
GATTCAAAAGAACTTTTAAA
Found at i:1872126 original size:105 final size:106
Alignment explanation
Indices: 1871931--1872146 Score: 344
Period size: 105 Copynumber: 2.0 Consensus size: 106
1871921 ATATCGTGCC
* * *
1871931 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGTTGGTTGTCAACAAACCATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATCGCTGGTTGTCAACAAACAATTTCCC
* * *
1871996 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
1872037 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATCGCTGGTTGTCAACAAACAATTTCCC
* * *
1872101 AGTTCCAGAACCAATTTCAACTTCACGGCGGAGGATATTGG
66 AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
1872142 ACTCG
1 ACTCG
1872147 GAAGGGGTCA
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
105 63 0.62
106 38 0.38
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATCGCTGGTTGTCAACAAACAATTTCCC
AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1873200 original size:2 final size:2
Alignment explanation
Indices: 1873188--1873221 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1873178 TTAATATAAA
1873188 AT AT A- AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1873222 GTAATATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1873210 original size:19 final size:19
Alignment explanation
Indices: 1873170--1873221 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1873160 TTCGTCCCAT
1873170 TATAATATT-TAATATAAAA
1 TATAATATTAT-ATATAAAA
*
1873189 TATAATA-TATATAT-ATA
1 TATAATATTATATATAAAA
1873206 TATATATATTATATAT
1 TATA-ATATTATATAT
1873222 GTAATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 8 0.28
19 15 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATAATATTATATATAAAA
Found at i:1873218 original size:17 final size:16
Alignment explanation
Indices: 1873188--1873234 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
1873178 TTAATATAAA
1873188 ATATAATATA-TATAT
1 ATATAATATATTATAT
1873203 ATATATATATATTATAT
1 ATATA-ATATATTATAT
*
1873220 ATGTAATATTATTAT
1 ATATAATA-TATTAT
1873235 TTTTATTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 5 0.18
16 8 0.29
17 15 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATAATATATTATAT
Found at i:1877019 original size:24 final size:24
Alignment explanation
Indices: 1876992--1877050 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
1876982 GAAAGTCAAC
1876992 GGTCAACGGTCAACGATCGGGTCG
1 GGTCAACGGTCAACGATCGGGTCG
*
1877016 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTCAACGATCGGGTCG
*
1877040 GGCCAACGGTC
1 GGTCAACGGTC
1877051 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.39, T:0.15
Consensus pattern (24 bp):
GGTCAACGGTCAACGATCGGGTCG
Found at i:1877021 original size:17 final size:17
Alignment explanation
Indices: 1876999--1877075 Score: 52
Period size: 17 Copynumber: 4.3 Consensus size: 17
1876989 AACGGTCAAC
1876999 GGTCAACGATCGGGTCG
1 GGTCAACGATCGGGTCG
1877016 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAAC-G---A---TCGGGTCG
* *
1877040 GGCCAACGGTCGGGTCG
1 GGTCAACGATCGGGTCG
1877057 GGTC-A-GA-CGGGTCG
1 GGTCAACGATCGGGTCG
1877071 GGTCA
1 GGTCA
1877076 GACCGGTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
14 11 0.23
15 1 0.02
16 1 0.02
17 18 0.38
18 1 0.02
21 1 0.02
23 1 0.02
24 14 0.29
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (17 bp):
GGTCAACGATCGGGTCG
Found at i:1877069 original size:14 final size:14
Alignment explanation
Indices: 1877050--1877083 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1877040 GGCCAACGGT
1877050 CGGGTCGGGTCAGA
1 CGGGTCGGGTCAGA
1877064 CGGGTCGGGTCAGA
1 CGGGTCGGGTCAGA
*
1877078 CCGGTC
1 CGGGTC
1877084 AAACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.26, G:0.47, T:0.15
Consensus pattern (14 bp):
CGGGTCGGGTCAGA
Found at i:1877083 original size:9 final size:9
Alignment explanation
Indices: 1877071--1877120 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
1877061 AGACGGGTCG
*
1877071 GGTCAGACC
1 GGTCAAACC
1877080 GGTCAAACC
1 GGTCAAACC
1877089 GGTCAAACC
1 GGTCAAACC
*
1877098 GGTTCAAAACT
1 GG-TC-AAACC
*
1877109 GTTCAAACC
1 GGTCAAACC
1877118 GGT
1 GGT
1877121 TTTCCAGCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 25 0.74
10 4 0.12
11 5 0.15
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1883959 original size:7 final size:7
Alignment explanation
Indices: 1883941--1883985 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
1883931 GTCAAAGAAA
1883941 GTCAACG
1 GTCAACG
* *
1883948 ATCAACA
1 GTCAACG
1883955 GTCAACG
1 GTCAACG
1883962 GTCAACG
1 GTCAACG
1883969 GTCAACG
1 GTCAACG
1883976 GTCAACG
1 GTCAACG
1883983 GTC
1 GTC
1883986 GGGTCGGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1884000 original size:17 final size:17
Alignment explanation
Indices: 1883978--1884010 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1883968 GGTCAACGGT
1883978 CAACGGTCGGGTCGGGC
1 CAACGGTCGGGTCGGGC
1883995 CAACGGTCGGGTCGGG
1 CAACGGTCGGGTCGGG
1884011 TCGGGTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.27, G:0.48, T:0.12
Consensus pattern (17 bp):
CAACGGTCGGGTCGGGC
Found at i:1884010 original size:22 final size:22
Alignment explanation
Indices: 1883982--1884034 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1883972 AACGGTCAAC
*
1883982 GGTCGGGTCGGGCCAACGGTCG
1 GGTCGGGTCGGGCCAACAGTCG
*
1884004 GGTCGGGTCGGGTCAACAGTCG
1 GGTCGGGTCGGGCCAACAGTCG
1884026 GGTCGGGTC
1 GGTCGGGTC
1884035 AGACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.09, C:0.25, G:0.49, T:0.17
Consensus pattern (22 bp):
GGTCGGGTCGGGCCAACAGTCG
Found at i:1884043 original size:14 final size:14
Alignment explanation
Indices: 1884024--1884057 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1884014 GGTCAACAGT
1884024 CGGGTCGGGTCAGA
1 CGGGTCGGGTCAGA
1884038 CGGGTCGGGTCAGA
1 CGGGTCGGGTCAGA
*
1884052 CCGGTC
1 CGGGTC
1884058 AAACCGGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.26, G:0.47, T:0.15
Consensus pattern (14 bp):
CGGGTCGGGTCAGA
Found at i:1884057 original size:9 final size:9
Alignment explanation
Indices: 1884045--1884104 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
1884035 AGACGGGTCG
*
1884045 GGTCAGACC
1 GGTCAAACC
1884054 GGTCAAACC
1 GGTCAAACC
*
1884063 GGTCCAGACC
1 GGT-CAAACC
1884073 GGTCAAACC
1 GGTCAAACC
*
1884082 GGTTCAAAACT
1 GG-TC-AAACC
1884093 GGTCAAACC
1 GGTCAAACC
1884102 GGT
1 GGT
1884105 TTTCCAGCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.58
10 12 0.28
11 6 0.14
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1884072 original size:19 final size:19
Alignment explanation
Indices: 1884048--1884104 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1884038 CGGGTCGGGT
1884048 CAGACCGGTCAAACCGGTC
1 CAGACCGGTCAAACCGGTC
1884067 CAGACCGGTCAAACCGGTTC
1 CAGACCGGTCAAACCGG-TC
* * *
1884087 AAAACTGGTCAAACCGGT
1 CAGACCGGTCAAACCGGT
1884105 TTTCCAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.14
Consensus pattern (19 bp):
CAGACCGGTCAAACCGGTC
Found at i:1884098 original size:20 final size:20
Alignment explanation
Indices: 1884051--1884105 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1884041 GTCGGGTCAG
* *
1884051 ACCGGTCAAACCGG-TCCAG
1 ACCGGTCAAACCGGTTCAAA
1884070 ACCGGTCAAACCGGTTCAAA
1 ACCGGTCAAACCGGTTCAAA
*
1884090 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
1884106 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTCAAA
Found at i:1889903 original size:590 final size:591
Alignment explanation
Indices: 1888610--1890385 Score: 3473
Period size: 590 Copynumber: 3.0 Consensus size: 591
1888600 CCGTGTTGGA
1888610 TTTAATTGGTAATCTAGTTACAGTCATATGAAAATGAAACATGTATGAAACTTATGCTAGGTTAG
1 TTTAATTGGTAATCTAGTTACAGTCATATGAAAATGAAACATGTATGAAACTTATGCTAGGTTAG
*
1888675 TCTCAGATTGAGAATCATTTCACTGCAACAACTCTTCAGGTGTTGGTGATCGTCCAGTTTTACAA
66 TCTCAGATTGAGAATCATTTCACTGCAACAACTCTTCAGGTGTTGATGATCGTCCAGTTTTACAA
1888740 ATTATTTGTCCCTCTTTAAAGTGTTGGCCTTGGTTCTCATCTAGTTTTTGTGATGTGCAGGGAAA
131 ATTATTTGTCCCTCTTTAAAGTGTTGGCCTTGGTTCTCATCTAGTTTTTGTGATGTGCAGGGAAA
1888805 TCAACTCTTACTGATTCTCTTGTTGCTGCTGCTGGAATTATTGCACAAGAAGTTGCCGGTGATGT
196 TCAACTCTTACTGATTCTCTTGTTGCTGCTGCTGGAATTATTGCACAAGAAGTTGCCGGTGATGT
1888870 TCGTATGACAGATACCCGTGCTGATGAGGCCGAGCGCGGTATCACAATCAAGTCTACCGGTATCT
261 TCGTATGACAGATACCCGTGCTGATGAGGCCGAGCGCGGTATCACAATCAAGTCTACCGGTATCT
*
1888935 CTCTGTATTATGAAATGTCTGATGACTCTTTGAAGAGCTACAAAGGAGAGAGAAAAGGAAATGAG
326 CTCTGTATTATGATATGTCTGATGACTCTTTGAAGAGCTACAAAGGAGAGAGAAAAGGAAAT-AG
1889000 TACCTGATCAATCTTATCGATTCCCCTGGTCACGTTGACTTTTCATCTGAGGTCACAGCTGCTCT
390 TACCTGATCAATCTTATCGATTCCCCTGGTCACGTTGACTTTTCATCTGAGGTCACAGCTGCTCT
1889065 TCGTATTACTGATGGCGCCCTTGTTGTTGTTGACTGTATTGAAGGTGTCTGTGTGCAAACAGAGA
455 TCGTATTACTGATGGCGCCCTTGTTGTTGTTGACTGTATTGAAGGTGTCTGTGTGCAAACAGAGA
1889130 CTGTCCTCCGTCAGGCTCTCGGTGAAAGAATCAGGCCTGTATTGACTGTTAACAAGATGGACAGG
520 CTGTCCTCCGTCAGGCTCTCGGTGAAAGAATCAGGCCTGTATTGACTGTTAACAAGATGGACAGG
1889195 TGCTTCC
585 TGCTTCC
1889202 TTTAATTGGTAATCTAGTTACAGTCATATGAAAATGAAACATGTATGAAACTTATGCTAGGTTAG
1 TTTAATTGGTAATCTAGTTACAGTCATATGAAAATGAAACATGTATGAAACTTATGCTAGGTTAG
*
1889267 TCTCAGATTGAGAATCATTTCACTGCAACAACTCTTCAGGTGTTGATGATCTTCCAGTTTTACAA
66 TCTCAGATTGAGAATCATTTCACTGCAACAACTCTTCAGGTGTTGATGATCGTCCAGTTTTACAA
1889332 ATTATTTGTCCCTCTTTAAAGTGTTGGCCTTGGTTCTCATCTAGTTTTTGTGATGTGCAGGGAAA
131 ATTATTTGTCCCTCTTTAAAGTGTTGGCCTTGGTTCTCATCTAGTTTTTGTGATGTGCAGGGAAA
1889397 TCAACTCTTACTGATTCTCTTGTTGCTGCTGCTGGAATTATTGCACAAGAAGTTGCCGGTGATGT
196 TCAACTCTTACTGATTCTCTTGTTGCTGCTGCTGGAATTATTGCACAAGAAGTTGCCGGTGATGT
*
1889462 TCGTATGACAGATACCCGTGCTGATGAGGCTGAGCGCGGTATCACAATCAAGTCTACCGGTATCT
261 TCGTATGACAGATACCCGTGCTGATGAGGCCGAGCGCGGTATCACAATCAAGTCTACCGGTATCT
1889527 CTCTGTATTATGATATGTCTGATGACTCTTTGAAGAGCTACAAAGGAGAGAGAAAAGGAAAT-GT
326 CTCTGTATTATGATATGTCTGATGACTCTTTGAAGAGCTACAAAGGAGAGAGAAAAGGAAATAGT
1889591 ACCTGATCAATCTTATCGATTCCCCTGGTCACGTTGACTTTTCATCTGAGGTCACAGCTGCTCTT
391 ACCTGATCAATCTTATCGATTCCCCTGGTCACGTTGACTTTTCATCTGAGGTCACAGCTGCTCTT
1889656 CGTATTACTGATGGCGCCCTTGTTGTTGTTGACTGTATTGAAGGTGTCTGTGTGCAAACAGAGAC
456 CGTATTACTGATGGCGCCCTTGTTGTTGTTGACTGTATTGAAGGTGTCTGTGTGCAAACAGAGAC
1889721 TGTCCTCCGTCAGGCTCTCGGTGAAAGAATCAGGCCTGTATTGACTGTTAACAAGATGGACAGGT
521 TGTCCTCCGTCAGGCTCTCGGTGAAAGAATCAGGCCTGTATTGACTGTTAACAAGATGGACAGGT
1889786 GCTTCC
586 GCTTCC
1889792 TTTAATTGGTAATCTAGTTACAGTCATATGAAAATGAAACATGTATGAAACTTATGCTAGGTTAG
1 TTTAATTGGTAATCTAGTTACAGTCATATGAAAATGAAACATGTATGAAACTTATGCTAGGTTAG
1889857 TCTCAGATTGAGAATCATTTCACTGCAACAACTCTTCAGGTGTTGATGATCGTCCAGTTTTACAA
66 TCTCAGATTGAGAATCATTTCACTGCAACAACTCTTCAGGTGTTGATGATCGTCCAGTTTTACAA
1889922 ATTATTTGTCCCTCTTTAAAGTGTTGGCCTTGGTTCTCATCTAGTTTTTGTGATGTGCAGGGAAA
131 ATTATTTGTCCCTCTTTAAAGTGTTGGCCTTGGTTCTCATCTAGTTTTTGTGATGTGCAGGGAAA
1889987 TCAACTCTTACTGATTCTCTTGTTGCTGCTGCTGGAATTATTGCACAAGAAGTTGCCGGTGATGT
196 TCAACTCTTACTGATTCTCTTGTTGCTGCTGCTGGAATTATTGCACAAGAAGTTGCCGGTGATGT
1890052 TCGTATGACAGATACCCGTGCTGATGAGGCCGAGCGCGGTATCACAATCAAGTCTACCGGTATCT
261 TCGTATGACAGATACCCGTGCTGATGAGGCCGAGCGCGGTATCACAATCAAGTCTACCGGTATCT
1890117 CTCTGTATTATGATATGTCTGATGACTCTTTGAAGAGCTACAAAGGAGAGAGAAAAGGAAATGAG
326 CTCTGTATTATGATATGTCTGATGACTCTTTGAAGAGCTACAAAGGAGAGAGAAAAGGAAAT-AG
1890182 TACCTGATCAATCTTATCGATTCCCCTGGTCACGTTGACTTTTCATCTGAGGTCACAGCTGCTCT
390 TACCTGATCAATCTTATCGATTCCCCTGGTCACGTTGACTTTTCATCTGAGGTCACAGCTGCTCT
*
1890247 TCGTATTACTGATGGTGCCCTTGTTGTTGTTGACTGTATTGAAGGTGTCTGTGTGCAAACAGAGA
455 TCGTATTACTGATGGCGCCCTTGTTGTTGTTGACTGTATTGAAGGTGTCTGTGTGCAAACAGAGA
*
1890312 CTATCCTCCGTCAGGCTCTCGGTGAAAGAATCAGGCCTGTATTGACTGTTAACAAGATGGACAGG
520 CTGTCCTCCGTCAGGCTCTCGGTGAAAGAATCAGGCCTGTATTGACTGTTAACAAGATGGACAGG
1890377 TGCTTCC
585 TGCTTCC
1890384 TT
1 TT
1890386 GAACTCCAGG
Statistics
Matches: 1174, Mismatches: 8, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
590 588 0.50
592 586 0.50
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (591 bp):
TTTAATTGGTAATCTAGTTACAGTCATATGAAAATGAAACATGTATGAAACTTATGCTAGGTTAG
TCTCAGATTGAGAATCATTTCACTGCAACAACTCTTCAGGTGTTGATGATCGTCCAGTTTTACAA
ATTATTTGTCCCTCTTTAAAGTGTTGGCCTTGGTTCTCATCTAGTTTTTGTGATGTGCAGGGAAA
TCAACTCTTACTGATTCTCTTGTTGCTGCTGCTGGAATTATTGCACAAGAAGTTGCCGGTGATGT
TCGTATGACAGATACCCGTGCTGATGAGGCCGAGCGCGGTATCACAATCAAGTCTACCGGTATCT
CTCTGTATTATGATATGTCTGATGACTCTTTGAAGAGCTACAAAGGAGAGAGAAAAGGAAATAGT
ACCTGATCAATCTTATCGATTCCCCTGGTCACGTTGACTTTTCATCTGAGGTCACAGCTGCTCTT
CGTATTACTGATGGCGCCCTTGTTGTTGTTGACTGTATTGAAGGTGTCTGTGTGCAAACAGAGAC
TGTCCTCCGTCAGGCTCTCGGTGAAAGAATCAGGCCTGTATTGACTGTTAACAAGATGGACAGGT
GCTTCC
Found at i:1898916 original size:34 final size:34
Alignment explanation
Indices: 1898873--1898974 Score: 127
Period size: 34 Copynumber: 3.0 Consensus size: 34
1898863 AAAATCTTCA
*
1898873 AGACATTTTACAGTCGACTCCTCAACAACAAAAT
1 AGACATTTTACAGCCGACTCCTCAACAACAAAAT
* **
1898907 AGACATTTTACAGGCGACGACTCAACAACAAGAA-
1 AGACATTTTACAGCCGACTCCTCAACAACAA-AAT
*
1898941 AGACATTTTACAGGCCG-CTCCTCTACAACAAAAT
1 AGACATTTTACA-GCCGACTCCTCAACAACAAAAT
1898975 GTAAGGCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
33 2 0.03
34 51 0.88
35 5 0.09
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (34 bp):
AGACATTTTACAGCCGACTCCTCAACAACAAAAT
Found at i:1904665 original size:2 final size:2
Alignment explanation
Indices: 1904660--1904698 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1904650 ACAAAAACAA
1904660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1904699 AAAATAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1910158 original size:15 final size:16
Alignment explanation
Indices: 1910138--1910179 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1910128 ATTATCGACC
1910138 TTAAATATA-ATATAA
1 TTAAATATATATATAA
*
1910153 TTAAATAATATATATGA
1 TTAAAT-ATATATATAA
1910170 -TAAATATATA
1 TTAAATATATA
1910180 ATTTAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 11 0.46
16 8 0.33
17 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TTAAATATATATATAA
Found at i:1919412 original size:30 final size:30
Alignment explanation
Indices: 1919376--1919450 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
1919366 AACCTCCACT
1919376 CCTTCCATTTTCAACTTAGCGAGCTCATAA
1 CCTTCCATTTTCAACTTAGCGAGCTCATAA
1919406 CCTTCCATTTTCAACTTAGCGAGCTCATAA
1 CCTTCCATTTTCAACTTAGCGAGCTCATAA
1919436 CCTTCCATTTTCAAC
1 CCTTCCATTTTCAAC
1919451 CATCGACTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.25, C:0.32, G:0.08, T:0.35
Consensus pattern (30 bp):
CCTTCCATTTTCAACTTAGCGAGCTCATAA
Found at i:1921737 original size:147 final size:147
Alignment explanation
Indices: 1921460--1921753 Score: 417
Period size: 147 Copynumber: 2.0 Consensus size: 147
1921450 AAATAAATTA
* * *
1921460 ATAAACACTATGCCTCAAACTTCACGTTAATCTACAGCTGCTGAAATCAACAACAGTCCAGAAAA
1 ATAAAAACTATGCCTCAAACTTCACGATAATCTACAGCTGCTGAAATCAACAACAGTCCACAAAA
* * * * * *
1921525 AGAAATTATGATTTAAGATTACAGTTTCTCTACCAAAACCAAGCAAAAGACACAGAGACGGCAAC
66 AGAAATTACGATTTAAGATCACAATTTCTCTACCAAAACCAAACAAAAGACACAAAGACGCCAAC
*
1921590 GGATAATATAGCAAAAT
131 GGATAATATAGAAAAAT
* * * *
1921607 ATAAAAACTATGCCTCAATCTTCATGATAATTTACAGCTGCTGAAATTAACAACAGTCCACAAAA
1 ATAAAAACTATGCCTCAAACTTCACGATAATCTACAGCTGCTGAAATCAACAACAGTCCACAAAA
* * * * *
1921672 AGAATTTACGCTTTGAGATCACAATTTCTCTATCAAAACCAAACAAAAGACACAAAGATGCCAAC
66 AGAAATTACGATTTAAGATCACAATTTCTCTACCAAAACCAAACAAAAGACACAAAGACGCCAAC
1921737 GGATAATATAGAAAAAT
131 GGATAATATAGAAAAAT
1921754 TACAAGAACC
Statistics
Matches: 128, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
147 128 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (147 bp):
ATAAAAACTATGCCTCAAACTTCACGATAATCTACAGCTGCTGAAATCAACAACAGTCCACAAAA
AGAAATTACGATTTAAGATCACAATTTCTCTACCAAAACCAAACAAAAGACACAAAGACGCCAAC
GGATAATATAGAAAAAT
Found at i:1926202 original size:31 final size:31
Alignment explanation
Indices: 1926167--1926243 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
1926157 CAATAAGAAA
* * * *
1926167 AATGATCATTTTGTAACAATTTGATAAGTTT
1 AATGATCATTTTATAACAATTCGATAAATAT
*
1926198 AATGA-CAATTTTATAATAATTCGATAAATAT
1 AATGATC-ATTTTATAACAATTCGATAAATAT
*
1926229 AATGAT-AATTTATAA
1 AATGATCATTTTATAA
1926244 TAGTTGAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 9 0.24
31 29 0.76
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (31 bp):
AATGATCATTTTATAACAATTCGATAAATAT
Found at i:1947970 original size:19 final size:21
Alignment explanation
Indices: 1947936--1947974 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
1947926 TTCTCTCATA
1947936 TTTTTCATTCTTATCTCATTC
1 TTTTTCATTCTTATCTCATTC
1947957 TTTTTCA-T-TTATCTCATT
1 TTTTTCATTCTTATCTCATT
1947975 TTTGCTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTCATTCTTATCTCATTC
Found at i:1949667 original size:37 final size:37
Alignment explanation
Indices: 1949578--1949681 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
1949568 CTTTTCGTCC
* *
1949578 TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* *
1949615 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
1949652 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
1949682 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:1950142 original size:22 final size:22
Alignment explanation
Indices: 1950101--1950142 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1950091 TATATATATA
*
1950101 TTATTATATTTTATTTATTTAT
1 TTATTATATTTTATTCATTTAT
1950123 TTATTATAATTTT-TTCATTT
1 TTATTAT-ATTTTATTCATTT
1950143 TTCTTTGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTATATTTTATTCATTTAT
Found at i:1950184 original size:2 final size:2
Alignment explanation
Indices: 1950177--1950203 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1950167 TTCCTATTAT
1950177 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1950204 TATTTTTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1950243 original size:14 final size:16
Alignment explanation
Indices: 1950203--1950247 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1950193 TATATATATA
1950203 TTATTTTTATCTATGT
1 TTATTTTTATCTATGT
1950219 TTACTTATTTAT-TATGT
1 TTA-TT-TTTATCTATGT
1950236 TT-TTTTTA-CTAT
1 TTATTTTTATCTAT
1950248 ATTTTCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 7 0.27
15 2 0.08
16 3 0.12
17 9 0.35
18 5 0.19
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (16 bp):
TTATTTTTATCTATGT
Found at i:1950268 original size:2 final size:2
Alignment explanation
Indices: 1950261--1950293 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1950251 TTCCTAACAT
1950261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1950294 TTCTTACTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1950427 original size:23 final size:21
Alignment explanation
Indices: 1950398--1950451 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
1950388 CTATTTAGTA
1950398 TTTTATTATATTATACATACAT
1 TTTTATTAT-TTATACATACAT
* *
1950420 TTTATATT-TTTATATATATAT
1 TTT-TATTATTTATACATACAT
1950441 TTTTATTATTT
1 TTTTATTATTT
1950452 TATTTATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 16 0.57
22 4 0.14
23 4 0.14
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTATTTATACATACAT
Found at i:1950452 original size:9 final size:10
Alignment explanation
Indices: 1950438--1950487 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
1950428 TTTATATATA
1950438 TATTTTTA-T
1 TATTTTTATT
1950447 TA-TTTTATT
1 TATTTTTATT
1950456 TATACTATTTATT
1 TAT--T-TTTATT
1950469 TATTTTTATT
1 TATTTTTATT
1950479 ATATTTTTA
1 -TATTTTTA
1950488 GTTTCTTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 5 0.14
9 5 0.14
10 6 0.17
11 9 0.26
12 1 0.03
13 9 0.26
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1950455 original size:14 final size:14
Alignment explanation
Indices: 1950421--1950487 Score: 66
Period size: 14 Copynumber: 4.8 Consensus size: 14
1950411 TACATACATT
1950421 TTATATTTTTA-TA
1 TTATATTTTTATTA
1950434 TATATATTTTTATTA
1 T-TATATTTTTATTA
* * *
1950449 TTTTATTTATACTA
1 TTATATTTTTATTA
*
1950463 TT-TATTTATTTTTA
1 TTATATTT-TTATTA
1950477 TTATATTTTTA
1 TTATATTTTTA
1950488 GTTTCTTTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
13 6 0.14
14 29 0.67
15 8 0.19
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATATTTTTATTA
Found at i:1950467 original size:43 final size:42
Alignment explanation
Indices: 1950398--1950487 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
1950388 CTATTTAGTA
1950398 TTTTATTATATTATACATACATTTTATATT-TTTATATATATAT
1 TTTTATTATATTATACATACATTTTAT-TTATTTATAT-TATAT
* ** *
1950441 TTTTATTATTTTATTTATAC-TATTTATTTATTTTTATTATAT
1 TTTTATTATATTATACATACAT-TTTATTTATTTATATTATAT
1950483 TTTTA
1 TTTTA
1950488 GTTTCTTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 13 0.32
43 28 0.68
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (42 bp):
TTTTATTATATTATACATACATTTTATTTATTTATATTATAT
Found at i:1950602 original size:20 final size:19
Alignment explanation
Indices: 1950575--1950630 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1950565 TTTTATCTTC
1950575 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
1950594 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
1950614 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
1950631 ATTATTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:1954946 original size:24 final size:23
Alignment explanation
Indices: 1954918--1954973 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1954908 AAAGGACAAA
*
1954918 AACAAAAAAGAAGAAAAAAAAAGG
1 AACAAAAAACAA-AAAAAAAAAGG
* *
1954942 AACAAAAATCAAAAAGAAAAAGG
1 AACAAAAAACAAAAAAAAAAAGG
*
1954965 GACAAAAAA
1 AACAAAAAA
1954974 ACACATGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (23 bp):
AACAAAAAACAAAAAAAAAAAGG
Found at i:1958203 original size:106 final size:106
Alignment explanation
Indices: 1957033--1958202 Score: 1815
Period size: 106 Copynumber: 11.0 Consensus size: 106
1957023 ATATCGTGCC
* * * *
1957033 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGA-CGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
*
1957097 CAAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1957139 ACTCTAGACAACACAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1957204 AATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1957245 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1957310 AATTTCAGAGCCAATCTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
1957351 ACTCAAGACAACACAAATTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1957416 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1957457 ACTCCAGACAACGTAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1957522 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATACTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1957563 ACTCGAGACAACGCAAGTTCAATTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1957628 AATTTTAGAGCCAATTTTAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1957669 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1957734 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1957775 ACTCCAAACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1957840 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1957881 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1957946 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1957987 ACTCGAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1958052 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
1958093 ACTCGAGGCAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1958158 GATTCCATAGCCAATTTCAACTTCAC-GAC-AGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGG
1958199 ACTC
1 ACTC
1958203 GGAACAATGC
Statistics
Matches: 985, Mismatches: 76, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
105 1 0.00
106 982 1.00
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1959042 original size:37 final size:37
Alignment explanation
Indices: 1958952--1959048 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
1958942 CTTTTTCGTC
*
1958952 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1958989 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** *
1959026 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
1959049 GATATGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1959495 original size:15 final size:14
Alignment explanation
Indices: 1959475--1959521 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1959465 TATATATATA
1959475 TATTTAATTATATTT
1 TATTTAATT-TATTT
1959490 TATTT-ATTTA-TT
1 TATTTAATTTATTT
*
1959502 TATTATAATTTTTTT
1 TATT-TAATTTATTT
1959517 TATTT
1 TATTT
1959522 TTCTTTGCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 6 0.21
13 3 0.11
14 8 0.29
15 11 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTAATTTATTT
Found at i:1959512 original size:23 final size:23
Alignment explanation
Indices: 1959475--1959521 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1959465 TATATATATA
1959475 TATTTAATTATATTTTATTTATT
1 TATTTAATTATATTTTATTTATT
*
1959498 TATTT-ATTATAATTTTTTTTATT
1 TATTTAATTAT-ATTTTATTTATT
1959521 T
1 T
1959522 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTAATTATATTTTATTTATT
Found at i:1959539 original size:5 final size:5
Alignment explanation
Indices: 1959531--1959578 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
1959521 TTTCTTTGCG
* *
1959531 TTATA TTATA TTATT TTCTA TTATTA TTATA -TATA -TATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTAT
1959579 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 8 0.22
5 24 0.65
6 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1959557 original size:13 final size:13
Alignment explanation
Indices: 1959539--1959584 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
1959529 CGTTATATTA
*
1959539 TATTATTTTCTAT
1 TATTATTTTATAT
*
1959552 TATTATTATATA-
1 TATTATTTTATAT
*
1959564 TA-TATATTATAT
1 TATTATTTTATAT
1959576 TATTATTTT
1 TATTATTTT
1959585 TTATCTATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
11 7 0.27
12 4 0.15
13 15 0.58
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATTTTATAT
Found at i:1959560 original size:21 final size:24
Alignment explanation
Indices: 1959531--1959582 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1959521 TTTCTTTGCG
* *
1959531 TTATATTATATTATTTTCTATTATTA
1 TTATA-TATA-TATATTATATTATTA
1959557 TTATATATATATATTATATTATTA
1 TTATATATATATATTATATTATTA
1959581 TT
1 TT
1959583 TTTTATCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.62
25 4 0.17
26 5 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATATATATATATTATATTATTA
Found at i:1959843 original size:22 final size:20
Alignment explanation
Indices: 1959715--1959850 Score: 64
Period size: 21 Copynumber: 6.4 Consensus size: 20
1959705 ATATTATATG
*
1959715 TATATTTATT-TTTCATTTA
1 TATATTTATTATTTTATTTA
* *
1959734 TTTATTATTATTATTACTATTTA
1 TATA-T-TTATTATT-TTATTTA
* **
1959757 GTAT-TTTATTATATTATACA
1 -TATATTTATTATTTTATTTA
*
1959777 TACATTT-TTATAATTATATATATA
1 TATATTTATTAT--TT-TAT-T-TA
1959801 TATATTTATTATTTTATTTA
1 TATATTTATTATTTTATTTA
1959821 TACTATTTATTTATTTTCA-TTA
1 TA-TATTTA-TTATTTT-ATTTA
*
1959843 TATTTTTA
1 TATATTTA
1959851 GTTTCTTTGC
Statistics
Matches: 88, Mismatches: 14, Indels: 28
0.68 0.11 0.22
Matches are distributed among these distances:
19 9 0.10
20 12 0.14
21 25 0.28
22 21 0.24
23 8 0.09
24 9 0.10
25 4 0.05
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (20 bp):
TATATTTATTATTTTATTTA
Found at i:1959962 original size:20 final size:19
Alignment explanation
Indices: 1959935--1959991 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1959925 TTTTATCTTC
1959935 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
1959954 ATTTCATTTTTTTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
1959975 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
1959992 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:1960424 original size:27 final size:27
Alignment explanation
Indices: 1960372--1960424 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1960362 CAATGACATG
* * * *
1960372 GCTAAATTGTTTTTTTTTAAAGTTCAT
1 GCTAAATTGGTTTTCTTAAAAATTCAT
1960399 GCTAAATTGGTTTTCTTAAAAATTCA
1 GCTAAATTGGTTTTCTTAAAAATTCA
1960425 ACGGCATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.49
Consensus pattern (27 bp):
GCTAAATTGGTTTTCTTAAAAATTCAT
Found at i:1960505 original size:7 final size:7
Alignment explanation
Indices: 1960471--1960520 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
1960461 TTAAATATAA
*
1960471 AAAAATA
1 AAAAATT
1960478 AAAAATT
1 AAAAATT
* *
1960485 AAATATA
1 AAAAATT
1960492 AAAAATT
1 AAAAATT
1960499 AAAAATT
1 AAAAATT
*
1960506 AAATGATT
1 AAA-AATT
1960514 AAAAATT
1 AAAAATT
1960521 TAAATAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (7 bp):
AAAAATT
Found at i:1960508 original size:15 final size:15
Alignment explanation
Indices: 1960470--1960520 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
1960460 TTTAAATATA
*
1960470 AAAAAATAAAAAATT
1 AAAAATTAAAAAATT
*
1960485 AAATA-TAAAAAATT
1 AAAAATTAAAAAATT
**
1960499 AAAAATTAAATGATT
1 AAAAATTAAAAAATT
1960514 AAAAATT
1 AAAAATT
1960521 TAAATAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAAATTAAAAAATT
Found at i:1960525 original size:21 final size:21
Alignment explanation
Indices: 1960461--1960520 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
1960451 ATTTTAAATT
*
1960461 TTAAATATAAAAAAATAAAAAA
1 TTAAATAT-AAAAAATTAAAAA
1960483 TTAAATATAAAAAATTAAAAA
1 TTAAATATAAAAAATTAAAAA
*
1960504 TTAAATGATTAAAAATT
1 TTAAAT-ATAAAAAATT
1960521 TAAATAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
TTAAATATAAAAAATTAAAAA
Found at i:1971418 original size:2 final size:2
Alignment explanation
Indices: 1971411--1971453 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1971401 AAGAAAAATA
*
1971411 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT -T 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
1971452 AT
1 AT
1971454 GTTGATTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1972714 original size:38 final size:38
Alignment explanation
Indices: 1972672--1972753 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
1972662 ATATAAATGT
* * *
1972672 TATAAATACTTATAAAATAAAA-AAACCTATTTGAAGTA
1 TATAAAAAATTATAAAATAAAAGAAA-ATATTTGAAGTA
*
1972710 TATAAAAAATTATAAATTAAAAGGAAAATATTTGAAGTA
1 TATAAAAAATTATAAAATAAAA-GAAAATATTTGAAGTA
*
1972749 GATAA
1 TATAA
1972754 TGGGGTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 19 0.51
39 15 0.41
40 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (38 bp):
TATAAAAAATTATAAAATAAAAGAAAATATTTGAAGTA
Found at i:1985456 original size:279 final size:281
Alignment explanation
Indices: 1984930--1985493 Score: 1114
Period size: 279 Copynumber: 2.0 Consensus size: 281
1984920 AGTTACAACT
1984930 AATCTGTTCTAAAAGCAGGTTATTTGGGCTGAATGTTGAAGATGAAGTGCTGAGGAACTGGGCTG
1 AATCTGTTCTAAAAGCAGGTTATTTGGGCTGAATGTTGAAGATGAAGTGCTGAGGAACTGGGCTG
1984995 ATTTGATAAGATGCTCGGTTGGTGCCTTCCCTGCTGAGCACCTTGGCTTACCTCTAGGAGCTAAG
66 ATTTGATAAGATGCTCGGTTGGTGCCTTCCCTGCTGAGCACCTTGGCTTACCTCTAGGAGCTAAG
1985060 AGGAATTCTGCATCTCTGCGGGATCCTGTGATCCGGAAATTCTATGACAAGTTGGCAGGTGGAAA
131 AGGAATTCTGCATCTCTGCGGGATCCTGTGATCCGGAAATTCTATGACAAGTTGGCAGGTGGAAA
1985125 GCAGCGACTTTGTCCATGGCGGGTAGATTGGTGTTATTGAAATCGGTTCTATCAGCCTTGCCAAT
196 GCAGCGACTTTGTCCATGGCGGGTAGATTGGTGTTATTGAAATCGGTTCTATCAGCCTTGCCAAT
1985190 TTATTATCTCTCGATCTTTAG
261 TTATTATCTCTCGATCTTTAG
1985211 AATCTGTTCTAAAAGCAGGTT-TTT-GGCTGAATGTTGAAGATGAAGTGCTGAGGAACTGGGCTG
1 AATCTGTTCTAAAAGCAGGTTATTTGGGCTGAATGTTGAAGATGAAGTGCTGAGGAACTGGGCTG
1985274 ATTTGATAAGATGCTCGGTTGGTGCCTTCCCTGCTGAGCACCTTGGCTTACCTCTAGGAGCTAAG
66 ATTTGATAAGATGCTCGGTTGGTGCCTTCCCTGCTGAGCACCTTGGCTTACCTCTAGGAGCTAAG
1985339 AGGAATTCTGCATCTCTGCGGGATCCTGTGATCCGGAAATTCTATGACAAGTTGGCAGGTGGAAA
131 AGGAATTCTGCATCTCTGCGGGATCCTGTGATCCGGAAATTCTATGACAAGTTGGCAGGTGGAAA
1985404 GCAGCGACTTTGTCCATGGCGGGTAGATTGGTGTTATTGAAATCGGTTCTATCAGCCTTGCCAAT
196 GCAGCGACTTTGTCCATGGCGGGTAGATTGGTGTTATTGAAATCGGTTCTATCAGCCTTGCCAAT
1985469 TTATTATCTCTCGATCTTTAG
261 TTATTATCTCTCGATCTTTAG
1985490 AATC
1 AATC
1985494 CCTATGGAGG
Statistics
Matches: 283, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
279 259 0.92
280 3 0.01
281 21 0.07
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (281 bp):
AATCTGTTCTAAAAGCAGGTTATTTGGGCTGAATGTTGAAGATGAAGTGCTGAGGAACTGGGCTG
ATTTGATAAGATGCTCGGTTGGTGCCTTCCCTGCTGAGCACCTTGGCTTACCTCTAGGAGCTAAG
AGGAATTCTGCATCTCTGCGGGATCCTGTGATCCGGAAATTCTATGACAAGTTGGCAGGTGGAAA
GCAGCGACTTTGTCCATGGCGGGTAGATTGGTGTTATTGAAATCGGTTCTATCAGCCTTGCCAAT
TTATTATCTCTCGATCTTTAG
Found at i:1996870 original size:17 final size:18
Alignment explanation
Indices: 1996832--1996892 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
1996822 AAGTATACGT
*
1996832 TAATATAATATTCAAAAGTA
1 TAATAT-ATATT-AAAATTA
1996852 TAATAT-TATTAAAATTA
1 TAATATATATTAAAATTA
* *
1996869 TATTATATATTAAATATTT
1 TAATATATATTAAA-ATTA
1996888 TAATA
1 TAATA
1996893 ATTCTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 11 0.31
18 11 0.31
19 7 0.20
20 6 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TAATATATATTAAAATTA
Found at i:1998020 original size:12 final size:12
Alignment explanation
Indices: 1998003--1998037 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1997993 AATATGAGTA
1998003 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1998015 TTTTCTTTTTTT
1 TTTTCTTTTTTT
* *
1998027 GTTTGTTTTTT
1 TTTTCTTTTTT
1998038 GGGGTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:1998907 original size:13 final size:13
Alignment explanation
Indices: 1998889--1998916 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1998879 TTTAGTTGTA
1998889 ATTTTATTATTTT
1 ATTTTATTATTTT
1998902 ATTTTATTATTTT
1 ATTTTATTATTTT
1998915 AT
1 AT
1998917 ATTTTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTTATTATTTT
Found at i:2000214 original size:14 final size:14
Alignment explanation
Indices: 2000195--2000228 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2000185 AGACTAAGAT
*
2000195 AAGAAAATAGAGAG
1 AAGAAAATAGAAAG
2000209 AAGAAAATAGAAAG
1 AAGAAAATAGAAAG
2000223 AA-AAAA
1 AAGAAAA
2000229 GGAGAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (14 bp):
AAGAAAATAGAAAG
Found at i:2006959 original size:2 final size:2
Alignment explanation
Indices: 2006952--2006981 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2006942 ATACATTTAA
2006952 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2006982 GGAAGCTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2021638 original size:29 final size:29
Alignment explanation
Indices: 2021596--2021663 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
2021586 TTAATGGAAC
2021596 CATTCAGCGCTGAATGTTGAACGGTTTAA
1 CATTCAGCGCTGAATGTTGAACGGTTTAA
2021625 CATTCAGCGCTGAATGTTGAACGGTTTAA
1 CATTCAGCGCTGAATGTTGAACGGTTTAA
2021654 CATTCAGCGC
1 CATTCAGCGC
2021664 GTTTGTTTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (29 bp):
CATTCAGCGCTGAATGTTGAACGGTTTAA
Found at i:2021753 original size:27 final size:27
Alignment explanation
Indices: 2021715--2021780 Score: 116
Period size: 27 Copynumber: 2.4 Consensus size: 27
2021705 AAAACAATGT
2021715 TGAATGATTCAGCACAGATA-TACATTC
1 TGAATGATTCAGCACAGA-AGTACATTC
2021742 TGAATGATTCAGCACAGAAGTACATTC
1 TGAATGATTCAGCACAGAAGTACATTC
2021769 TGAATGATTCAG
1 TGAATGATTCAG
2021781 AGTCAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (27 bp):
TGAATGATTCAGCACAGAAGTACATTC
Found at i:2021871 original size:15 final size:16
Alignment explanation
Indices: 2021833--2021873 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2021823 CCAGAGCCTC
*
2021833 TGAATCATTCAGCATT
1 TGAATCATTCAGAATT
2021849 TGAATCATTCAGAATT
1 TGAATCATTCAGAATT
2021865 T-AATCATTC
1 TGAATCATTC
2021874 TGAAGTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGAATT
Found at i:2026581 original size:23 final size:23
Alignment explanation
Indices: 2026534--2026582 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2026524 AATAACATAT
**
2026534 TAGGTAGCGCTTAGATAATGTAA
1 TAGGTAGCGCTTAGATAATAAAA
*
2026557 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTAGATAATAAAA
2026580 TAG
1 TAG
2026583 ACATTTAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (23 bp):
TAGGTAGCGCTTAGATAATAAAA
Found at i:2026644 original size:87 final size:87
Alignment explanation
Indices: 2026498--2026659 Score: 279
Period size: 87 Copynumber: 1.9 Consensus size: 87
2026488 ATATTATATT
* *
2026498 ATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTAGATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATAAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGTA
2026563 GCGCTTATATAATAAAATAGAC
66 GCGCTTATATAATAAAATAGAC
* * *
2026585 ATTTAACCGGAAATATTATAAAGTACAATAATAAATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATAAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGTA
2026650 GCGCTTATAT
66 GCGCTTATAT
2026660 TGACCTATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (87 bp):
ATTTAACCGGAAATATTATAAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAATAGGTA
GCGCTTATATAATAAAATAGAC
Found at i:2027079 original size:196 final size:197
Alignment explanation
Indices: 2026681--2027128 Score: 509
Period size: 196 Copynumber: 2.3 Consensus size: 197
2026671 CTCATAAAAA
* * * * * *
2026681 CGGTAAATTTAAACCGGTTACATTATAAATTGAACTATTACATTATAAATATCGGTTTCGATGTT
1 CGGTATATTTCAACCGGTTACATTGTAAATTTAACTATTACATTATAATTATCGATTTCGATGTT
* * *
2026746 TTCAGGATCAATACAATTTTAAATGTATCGACACTTTATGCGTGCAACTCGTTTATGCTTTATTT
66 TTCAGGATCAATACAATTTTAAATGTATCGACACTTTATGCGTACAACTCGTTTATGCATCATTT
* * * * *
2026811 TGGAAAAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATTTGCTAATTA
131 TGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACATATTTGCTAATGA
2026876 AC
196 AC
* * *
2026878 CGGTATATGTT-AACCGGTTACATTGTAAATTTACCTTTTACATAATAATTATCGATTTCGATG-
1 CGGTATAT-TTCAACCGGTTACATTGTAAATTTAACTATTACATTATAATTATCGATTTCGATGT
* * *
2026941 TTT-AGAGATCGATAC-TTTTTAAAATGTATCGACACTTTATGCGTACACCTCG-TT-TGCCATC
65 TTTCAG-GATCAATACAATTTT-AAATGTATCGACACTTTATGCGTACAACTCGTTTATG-CATC
* * *
2027002 A-TTT-GAAAAAATGTATCGACACAAATTAAACAAAGTGTCGATACTTTATGTTGACATATTCT-
127 ATTTTGGAAAAAA-GTATCGACACAAATTAAA-AAAGTGTCGATACATAATGTAGACATATT-TG
*
2027064 CTCATGAACC
189 CTAATGAA-C
* * * *
2027074 CGGTATATTTCTACCGGTTACATTGGAAATTTATCTATTACATTATATTTATCGA
1 CGGTATATTTCAACCGGTTACATTGTAAATTTAACTATTACATTATAATTATCGA
2027129 CACAAAATCT
Statistics
Matches: 213, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
193 7 0.03
194 21 0.10
195 43 0.20
196 88 0.41
197 52 0.24
198 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (197 bp):
CGGTATATTTCAACCGGTTACATTGTAAATTTAACTATTACATTATAATTATCGATTTCGATGTT
TTCAGGATCAATACAATTTTAAATGTATCGACACTTTATGCGTACAACTCGTTTATGCATCATTT
TGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACATATTTGCTAATGA
AC
Found at i:2027211 original size:106 final size:107
Alignment explanation
Indices: 2027035--2027227 Score: 255
Period size: 106 Copynumber: 1.8 Consensus size: 107
2027025 AATTAAACAA
* * * * *
2027035 AGTGTCGATACTTTATGTTGACATATTCTCTCATGAACCCGGTATATTTCTACCGGTTACATTGG
1 AGTGTCGATACTTTATGTTAACATATTCTATAATGAACACGGTATATGTCTACCGGTTACATTGG
2027100 AAATTTA-TCTATTACATTATATTTATCGACACAAAATCTAAT
66 AAATTTACT-TATTACATTATATTTATCGACACAAAATCTAAT
* * * * * *
2027142 AGTGTCGATACTTTATGTTAACATGTTTTATAATTAA-ACGGTATATGTGTACTGGTTACATTGT
1 AGTGTCGATACTTTATGTTAACATATTCTATAATGAACACGGTATATGTCTACCGGTTACATTGG
*
2027206 CAATTTACTTATTACATTATAT
66 AAATTTACTTATTACATTATAT
2027228 CATTTGTCAT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
106 41 0.56
107 32 0.44
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (107 bp):
AGTGTCGATACTTTATGTTAACATATTCTATAATGAACACGGTATATGTCTACCGGTTACATTGG
AAATTTACTTATTACATTATATTTATCGACACAAAATCTAAT
Found at i:2028292 original size:37 final size:37
Alignment explanation
Indices: 2028242--2028318 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
2028232 GCCATGATGA
2028242 ACAAATCGCCTATTTCAGTTGTCACCGATTGGGATCG
1 ACAAATCGCCTATTTCAGTTGTCACCGATTGGGATCG
2028279 ACAAATCGCCTATTTCAGTTGTCACCGATTGGGATCG
1 ACAAATCGCCTATTTCAGTTGTCACCGATTGGGATCG
2028316 ACA
1 ACA
2028319 CTTATTTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (37 bp):
ACAAATCGCCTATTTCAGTTGTCACCGATTGGGATCG
Found at i:2030899 original size:182 final size:181
Alignment explanation
Indices: 2030254--2030901 Score: 863
Period size: 182 Copynumber: 3.6 Consensus size: 181
2030244 ATTAAAGTAC
* * * *
2030254 CGACACTTTCAACATAAT-CGGTAGCGCTTTATCGGTTTTGTCATTTCGATACCGGTTTTATCAT
1 CGACACTTTCAATAT-ATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCAT
* * ** *
2030318 ATTTTTACCTATTATATTGTTATGGATCGATACACTTTCT-TAAAGTATCGACAC-TTTAGGCGC
65 ATTATTACCTGTTATATTACTATGGATCGATACA-TTTTTATAAAGTATCGACACTTTTAGGCGC
* * *
2030381 TATAATTTCTTCTATTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
129 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * ** *** *
2030434 CGACACTTTAAATATATCCGGTATCTTTTTACCGGTTTTATCATTTCGAGACATATTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCATA
* * *
2030499 TTATTACCGGATATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTCAGGCGCT
66 TTATTACCTGTTATATTACTATGGATCGATACATTTTTATAAAGTATCGACACTTTT-AGGCGCT
*
2030564 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATATTTATATTAATTTAT
130 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
** * * *
2030616 CGACACTTTCAATATATCCGGTAGCTTTTTAACGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCATA
* *
2030681 TTAATACATGTTATATTACTATGGATCGATACATTTTTATAAAGTATCGACACCTTTTAGGCGCT
66 TTATTACCTGTTATATTACTATGGATCGATACATTTTTATAAAGTATCGACA-CTTTTAGGCGCT
* * *
2030746 ATAACTTCTTTTCTTTTAAATTACAAAAGGGTCGACACTTATATTAATTTAT
130 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
** * *
2030798 CGACACTTTCAATATATCTAGTAGCGCTTTACCGGTTTTATCATAAT-GACACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCAT-TTCGAGACCGGTTTTATCAT
* *
2030862 ATTTTTACCTGTTATATTGCTATGGATCGATACATTTTTA
65 ATTATTACCTGTTATATTACTATGGATCGATACATTTTTA
2030902 ATTTGTATCG
Statistics
Matches: 412, Mismatches: 50, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
179 6 0.01
180 91 0.22
181 3 0.01
182 306 0.74
183 6 0.01
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (181 bp):
CGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCATA
TTATTACCTGTTATATTACTATGGATCGATACATTTTTATAAAGTATCGACACTTTTAGGCGCTA
TAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
Found at i:2035292 original size:2 final size:2
Alignment explanation
Indices: 2035285--2035337 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2035275 TTATAAAATA
2035285 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
*
2035327 AT AT AT TT AT A
1 AT AT AT AT AT A
2035338 AGTGGCATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2036281 original size:2 final size:2
Alignment explanation
Indices: 2036274--2036300 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2036264 CTACATAATA
2036274 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
2036301 AAGGTTTTAT
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:2040619 original size:33 final size:33
Alignment explanation
Indices: 2040573--2040650 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
2040563 GTATTGTGGC
2040573 CTGC-GTTATGTTCAGGAGCATCATCACTAGAA
1 CTGCTGTTATGTTCAGGAGCATCATCACTAGAA
2040605 CTGCTGTTATGTTCAGGAGCATCATCACTAGAA
1 CTGCTGTTATGTTCAGGAGCATCATCACTAGAA
2040638 CTGCTGTTATGTT
1 CTGCTGTTATGTT
2040651 TTTCTCAGGC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 4 0.09
33 41 0.91
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (33 bp):
CTGCTGTTATGTTCAGGAGCATCATCACTAGAA
Found at i:2052382 original size:12 final size:12
Alignment explanation
Indices: 2052365--2052394 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2052355 AAGTGTCTAA
2052365 TAATAATAAAAT
1 TAATAATAAAAT
2052377 TAATAATAAAAT
1 TAATAATAAAAT
2052389 TAATAA
1 TAATAA
2052395 AAATAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATAATAAAAT
Found at i:2052404 original size:12 final size:12
Alignment explanation
Indices: 2052363--2052404 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
2052353 TAAAGTGTCT
2052363 AATAATAATAAA
1 AATAATAATAAA
*
2052375 ATTAATAAT-AA
1 AATAATAATAAA
2052386 AAT--TAATAAA
1 AATAATAATAAA
2052396 AATAATAAT
1 AATAATAAT
2052405 TTTTTCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 4 0.16
10 5 0.20
11 4 0.16
12 12 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:2053181 original size:24 final size:25
Alignment explanation
Indices: 2053142--2053192 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
2053132 GAACTCCAAA
2053142 AAATTAAAATCAACAT-ATTTCTAT
1 AAATTAAAATCAACATAATTTCTAT
**
2053166 AAATTAAAATTTACATAAATTTCTAT
1 AAATTAAAATCAACAT-AATTTCTAT
2053192 A
1 A
2053193 TTAATAATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
26 9 0.39
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATTAAAATCAACATAATTTCTAT
Found at i:2069584 original size:4 final size:4
Alignment explanation
Indices: 2069575--2069600 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2069565 CAATGCATAT
2069575 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
2069601 TATTTCATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:2073921 original size:128 final size:128
Alignment explanation
Indices: 2073693--2074321 Score: 1134
Period size: 128 Copynumber: 4.9 Consensus size: 128
2073683 TAATCGGAGT
2073693 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2073758 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2073821 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
2073886 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
2073949 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
2074013 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGAACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
2074077 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCACATTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2074142 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2074205 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
2074270 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2074322 AATCAGGTAA
Statistics
Matches: 476, Mismatches: 23, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
127 1 0.00
128 474 1.00
129 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:2074783 original size:33 final size:34
Alignment explanation
Indices: 2074723--2074821 Score: 128
Period size: 33 Copynumber: 2.9 Consensus size: 34
2074713 AATTTAATGT
*
2074723 TAAATTTCGAATACTATAATTTATATTTTAAATA
1 TAAATTTCGAATAATATAATTTATATTTTAAATA
* * * * *
2074757 TAAATTT-GAATAATATTATTTTTATTTTTATTT
1 TAAATTTCGAATAATATAATTTATATTTTAAATA
*
2074790 TAAATTTCGAATAATATAATTTGTATTTTAAA
1 TAAATTTCGAATAATATAATTTATATTTTAAA
2074822 AACATTTATC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.50
34 27 0.50
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (34 bp):
TAAATTTCGAATAATATAATTTATATTTTAAATA
Found at i:2075429 original size:21 final size:21
Alignment explanation
Indices: 2075341--2075434 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
2075331 TATGGTATAA
*
2075341 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
2075362 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
2075383 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
2075404 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
2075425 AACCCTGCGG
1 AACCCTGCGG
2075435 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:2077266 original size:34 final size:32
Alignment explanation
Indices: 2077215--2077289 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
2077205 AATTCTCAAT
* *
2077215 AAATAATAATTATATAAATGTTATTTTAATA-AAA
1 AAATAATAATTACATAAA---TATATTAATATAAA
*
2077249 AAATAATATTTACATAAATATATTAATATAAA
1 AAATAATAATTACATAAATATATTAATATAAA
2077281 AAATAATAA
1 AAATAATAA
2077290 CTATTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 9 0.25
32 11 0.31
34 16 0.44
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (32 bp):
AAATAATAATTACATAAATATATTAATATAAA
Found at i:2077315 original size:35 final size:34
Alignment explanation
Indices: 2077245--2077322 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
2077235 TTATTTTAAT
* * * *
2077245 AAAAAAATAATATTTACATAAATATATTAATATA
1 AAAAAAATAATATTTACAAAAAAATACTAACATA
2077279 AAAAATAATAACTATTTA-AAAAAAATACTAACATA
1 AAAAA-AATAA-TATTTACAAAAAAATACTAACATA
2077314 AAAATAAAT
1 AAAA-AAAT
2077323 TTCTTACCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 5 0.14
35 25 0.68
36 7 0.19
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (34 bp):
AAAAAAATAATATTTACAAAAAAATACTAACATA
Found at i:2083500 original size:30 final size:29
Alignment explanation
Indices: 2083466--2083529 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2083456 AACAATATCT
2083466 TAATTCATAAAGAATTAAAACAAAATGTAA
1 TAATTCAT-AAGAATTAAAACAAAATGTAA
* *
2083496 TAATTGATTAGAATTAAAACAAAATGTAA
1 TAATTCATAAGAATTAAAACAAAATGTAA
2083525 TAATT
1 TAATT
2083530 GATTATGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (29 bp):
TAATTCATAAGAATTAAAACAAAATGTAA
Found at i:2083509 original size:29 final size:29
Alignment explanation
Indices: 2083476--2083534 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2083466 TAATTCATAA
2083476 AGAATTAAAACAAAATGTAATAATTGATT
1 AGAATTAAAACAAAATGTAATAATTGATT
2083505 AGAATTAAAACAAAATGTAATAATTGATT
1 AGAATTAAAACAAAATGTAATAATTGATT
2083534 A
1 A
2083535 TGTATGTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (29 bp):
AGAATTAAAACAAAATGTAATAATTGATT
Found at i:2088710 original size:35 final size:35
Alignment explanation
Indices: 2088637--2088730 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
2088627 AAAAATTCAA
* * * * *
2088637 GAGCTCGATTGAAACTCGAGACTCTAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGA-ACTCAAACTCGAATTT
*
2088673 GAGTTCGATTCAAGCTCGAACTCAAACTCGAATTT
1 GAGCTCGATTCAAGCTCGAACTCAAACTCGAATTT
2088708 GAGCTCGATTCAAGCTCGAACTC
1 GAGCTCGATTCAAGCTCGAACTC
2088731 GATTCAAGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 35 0.69
36 16 0.31
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (35 bp):
GAGCTCGATTCAAGCTCGAACTCAAACTCGAATTT
Found at i:2088733 original size:17 final size:17
Alignment explanation
Indices: 2088711--2088749 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2088701 CGAATTTGAG
2088711 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
2088728 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
2088745 CTCGA
1 CTCGA
2088750 ACCTACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:2092279 original size:7 final size:7
Alignment explanation
Indices: 2092263--2092321 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
2092253 GCGCATAATT
2092263 TAAA-CC
1 TAAACCC
2092269 TAAACCC
1 TAAACCC
2092276 TAAACCC
1 TAAACCC
*
2092283 T-AACACA
1 TAAAC-CC
2092290 TAAACCC
1 TAAACCC
2092297 TAAACCC
1 TAAACCC
*
2092304 TAAACTC
1 TAAACCC
*
2092311 TAAACCT
1 TAAACCC
2092318 TAAA
1 TAAA
2092322 TCATATCACA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
6 7 0.16
7 35 0.78
8 3 0.07
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:2092295 original size:21 final size:21
Alignment explanation
Indices: 2092269--2092399 Score: 122
Period size: 21 Copynumber: 6.2 Consensus size: 21
2092259 AATTTAAACC
2092269 TAAACCCTAAACCCTAACACA
1 TAAACCCTAAACCCTAACACA
*
2092290 TAAACCCTAAACCCTAA-ACTC
1 TAAACCCTAAACCCTAACAC-A
* * * *
2092311 TAAACCTTAAATCATATCACA
1 TAAACCCTAAACCCTAACACA
** *
2092332 TAAAATCTAAACTCTAACACA
1 TAAACCCTAAACCCTAACACA
2092353 TAAACCCTAAACCCTAA-ACTA
1 TAAACCCTAAACCCTAACAC-A
* * * *
2092374 TAAACCTTAAATCATATCACA
1 TAAACCCTAAACCCTAACACA
2092395 TAAAC
1 TAAAC
2092400 TACAAACCAT
Statistics
Matches: 86, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
20 4 0.05
21 78 0.91
22 4 0.05
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCCTAAACCCTAACACA
Found at i:2092407 original size:49 final size:49
Alignment explanation
Indices: 2092353--2092463 Score: 170
Period size: 49 Copynumber: 2.3 Consensus size: 49
2092343 CTCTAACACA
2092353 TAAACCCTAAACCCTAAACTATAAACCTTAAATCATATCACATAAACTAC
1 TAAACCCTAAACCCTAAACTATAAACCTTAAATCATATCACATAAACT-C
* * *
2092403 -AAACCATAAACCCTAAACTCTAAATCTTAAATCATATCACATAAACTC
1 TAAACCCTAAACCCTAAACTATAAACCTTAAATCATATCACATAAACTC
*
2092451 TAAATCCTAAACC
1 TAAACCCTAAACC
2092464 TTATAACATA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
48 1 0.02
49 54 0.98
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (49 bp):
TAAACCCTAAACCCTAAACTATAAACCTTAAATCATATCACATAAACTC
Found at i:2092426 original size:63 final size:63
Alignment explanation
Indices: 2092275--2092398 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
2092265 AACCTAAACC
* *
2092275 CTAAACCCTAACACATAAACCCTAAACCCTAAACTCTAAACCTTAAATCATATCACATAAAAT
1 CTAAACTCTAACACATAAACCCTAAACCCTAAACTATAAACCTTAAATCATATCACATAAAAT
2092338 CTAAACTCTAACACATAAACCCTAAACCCTAAACTATAAACCTTAAATCATATCACATAAA
1 CTAAACTCTAACACATAAACCCTAAACCCTAAACTATAAACCTTAAATCATATCACATAAA
2092399 CTACAAACCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (63 bp):
CTAAACTCTAACACATAAACCCTAAACCCTAAACTATAAACCTTAAATCATATCACATAAAAT
Found at i:2092472 original size:28 final size:28
Alignment explanation
Indices: 2092403--2092474 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
2092393 CATAAACTAC
* *
2092403 AAACCATA-AACCCTAAACTCTAAATCTT
1 AAACCATATAA-CATAAACTCTAAATCCT
* *
2092431 AAATCATATCACATAAACTCTAAATCCT
1 AAACCATATAACATAAACTCTAAATCCT
*
2092459 AAACCTTATAACATAA
1 AAACCATATAACATAA
2092475 TTAGACGGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 35 0.97
29 1 0.03
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (28 bp):
AAACCATATAACATAAACTCTAAATCCT
Found at i:2092868 original size:14 final size:14
Alignment explanation
Indices: 2092851--2092891 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2092841 TTTATTAATC
2092851 AATAATGTATTTTT
1 AATAATGTATTTTT
2092865 AAT-ATG--TTTTT
1 AATAATGTATTTTT
*
2092876 AATAATGTAATTTT
1 AATAATGTATTTTT
2092890 AA
1 AA
2092892 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 8 0.35
12 3 0.13
13 3 0.13
14 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:2093009 original size:12 final size:11
Alignment explanation
Indices: 2092982--2093015 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2092972 TCGTTAAGAA
2092982 CTCGAGTCGAG
1 CTCGAGTCGAG
*
2092993 TTCGAGTTCGAG
1 CTCGAG-TCGAG
2093005 CTCGAGTCGAG
1 CTCGAGTCGAG
2093016 TCCATTCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (11 bp):
CTCGAGTCGAG
Done.