Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1549776 original size:16 final size:16
Alignment explanation
Indices: 1549757--1549797 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
1549747 CAGGAAGTTG
1549757 AGTCAAGTTCAAATTA
1 AGTCAAGTTCAAATTA
1549773 AGTCAAGTTCAAATTA
1 AGTCAAGTTCAAATTA
1549789 AGTCAAGTT
1 AGTCAAGTT
1549798 ACGGTGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (16 bp):
AGTCAAGTTCAAATTA
Found at i:1555430 original size:54 final size:54
Alignment explanation
Indices: 1555338--1555867 Score: 499
Period size: 54 Copynumber: 9.8 Consensus size: 54
1555328 TGATTTTTTA
* * * *
1555338 TGTATCGACACTAAGTGTACAACCCAAGGAATTCATAATAAGTTTATGAACAAC
1 TGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
* * * * *
1555392 TGTATTGACAATAAGTGTGTAACCCACGAAATTTATAATAAGTTTATGAACTAC
1 TGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
* * * *
1555446 CGTATC-AGCACTAAGTGTGCAAGCCA-TATATTTCATAATAAGTTTATGAACGAC
1 TGTATCGA-CACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGAC
* * * *
1555500 CGTATCG-CACTAAGTGTGCATCCCACAAAATTCATAATAAGTTTATGAAC-AA
1 TGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
*
1555552 TCGTATC-AGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAATGAC
1 T-GTATCGA-CACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
** * * * *
1555607 CATATCGGCACTAAGTGTGTAACCCACGAAATTCAAAATTAGTTTATGAACGAC
1 TGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
* * * *
1555661 TGTATCGGCACTAAGTGTG-AAGCCCACGTAGTTCATAATAAGTTTATGAACGTC
1 TGTATCGACACTAAGTGTGCAA-CCCACGAAATTCATAATAAGTTTATGAACGAC
* * **
1555715 TATATTGGTACTAAGTGTGCAACCCACTG-AATTCATAATAAGTTTATGAACGAC
1 TGTATCGACACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGAC
** * * *
1555769 CATATC-AGTACTAAGTGTACAACCCAC-AGAATTCATAATAAGGTTTATGAATGA-
1 TGTATCGA-CACTAAGTGTGCAACCCACGA-AATTCATAATAA-GTTTATGAACGAC
* * * *
1555823 TCGTATCGGA-ACTACGTGTGCACCCCATGAAACTT-ATAATGAGTT
1 T-GTATC-GACACTAAGTGTGCAACCCACGAAA-TTCATAATAAGTT
1555868 GAAATCATTA
Statistics
Matches: 397, Mismatches: 58, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
52 1 0.00
53 46 0.12
54 305 0.77
55 41 0.10
56 3 0.01
57 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (54 bp):
TGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
Found at i:1555673 original size:108 final size:108
Alignment explanation
Indices: 1555338--1555867 Score: 554
Period size: 108 Copynumber: 4.9 Consensus size: 108
1555328 TGATTTTTTA
* * * * * * *
1555338 TGTATC-GACACTAAGTGTACAACCCAAGGAATTCATAATAAGTTTATGAACAACTGTATTGACA
1 TGTATCAG-CACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGCA
* * * *
1555402 ATAAGTGTGTAACCCACGAAATTTATAATAAGTTTATGAACTAC
65 CTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
* * * *
1555446 CGTATCAGCACTAAGTGTGCAAGCCA-TATATTTCATAATAAGTTTATGAACGACCGTATC-GCA
1 TGTATCAGCACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCGTATCGGCA
* * *
1555509 CTAAGTGTGCATCCCACAAAATTCATAATAAGTTTATGAAC-AA
65 CTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
* *
1555552 TCGTATCAGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAATGACCATATCGGCA
1 T-GTATCAGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGCA
* * *
1555617 CTAAGTGTGTAACCCACGAAATTCAAAATTAGTTTATGAACGAC
65 CTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
* * * * ** * *
1555661 TGTATCGGCACTAAGTGTG-AAGCCCACGTAGTTCATAATAAGTTTATGAACGTCTATATTGGTA
1 TGTATCAGCACTAAGTGTGCAA-CCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGCA
1555725 CTAAGTGTGCAACCCACTG-AATTCATAATAAGTTTATGAACGAC
65 CTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGAC
** * * * * *
1555769 CATATCAGTACTAAGTGTACAACCCAC-AGAATTCATAATAAGGTTTATGAATGATCGTATCGGA
1 TGTATCAGCACTAAGTGTGCAACCCACGA-AATTCATAATAA-GTTTATGAACGACCGTATCGGC
* * * *
1555833 ACTACGTGTGCACCCCATGAAACTT-ATAATGAGTT
64 ACTAAGTGTGCAACCCACGAAA-TTCATAATAAGTT
1555868 GAAATCATTA
Statistics
Matches: 352, Mismatches: 57, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
106 1 0.00
107 92 0.26
108 210 0.60
109 47 0.13
110 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (108 bp):
TGTATCAGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGCAC
TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGAC
Found at i:1566793 original size:58 final size:58
Alignment explanation
Indices: 1566724--1566840 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
1566714 TTGACTTGAT
*
1566724 CGTTTTTATTTTGGAATCTATTTTAGATTGATTTCTTTTAGGTCAAAAGTTATCCATG
1 CGTTTTTATTTTGGAATCTATTTTAGATTGATTTATTTTAGGTCAAAAGTTATCCATG
1566782 CGTTTTTATTTTGGAATCTATTTTAGATTGATTTATTTTAGGTCAAAAGTTATCCATG
1 CGTTTTTATTTTGGAATCTATTTTAGATTGATTTATTTTAGGTCAAAAGTTATCCATG
1566840 C
1 C
1566841 CCTTCGCTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (58 bp):
CGTTTTTATTTTGGAATCTATTTTAGATTGATTTATTTTAGGTCAAAAGTTATCCATG
Found at i:1567401 original size:16 final size:16
Alignment explanation
Indices: 1567380--1567439 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 16
1567370 GTTAAAATAA
1567380 AAAAAAATAATTAAAT
1 AAAAAAATAATTAAAT
*
1567396 AAAAAAATAATTAAACAAA
1 AAAAAAATAATT--A-AAT
1567415 AGAAAAAATAATTAAAT
1 A-AAAAAATAATTAAAT
*
1567432 AAACAAAT
1 AAAAAAAT
1567440 TAAAGAGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 18 0.49
17 3 0.08
18 2 0.05
19 3 0.08
20 11 0.30
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAAAAATAATTAAAT
Found at i:1567401 original size:20 final size:20
Alignment explanation
Indices: 1567378--1567434 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1567368 TGGTTAAAAT
1567378 AAAAAAAAATAATTAAAT--
1 AAAAAAAAATAATTAAATAA
*
1567396 --AAAAAAATAATTAAACAA
1 AAAAAAAAATAATTAAATAA
*
1567414 AAGAAAAAATAATTAAATAA
1 AAAAAAAAATAATTAAATAA
1567434 A
1 A
1567435 CAAATTAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 15 0.47
20 17 0.53
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAAAAAATAATTAAATAA
Found at i:1568078 original size:19 final size:19
Alignment explanation
Indices: 1568022--1568084 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1568012 CTATTTAAAC
**
1568022 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1568042 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1568062 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1568081 TAAA
1 TAAA
1568085 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1568194 original size:76 final size:75
Alignment explanation
Indices: 1568042--1568205 Score: 222
Period size: 76 Copynumber: 2.2 Consensus size: 75
1568032 AAAAAATAAT
* * * *
1568042 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAATGATA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAAGATAATAATA
1568107 AAATATAAAA
66 AAATATAAAA
*
1568117 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATAA-AAT
1 ATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATAAAAAGATAATAAT
* * *
1568181 ATAATGTTTAAA
65 AAAAT-ATAAAA
*
1568193 ATATTATCCTAAA
1 ATAATATCCTAAA
1568206 TTTGAGTTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 32 0.41
76 46 0.59
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAAGATAATAATA
AAATATAAAA
Found at i:1569939 original size:53 final size:53
Alignment explanation
Indices: 1569858--1569964 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 53
1569848 ATTGTTTGAA
* * *
1569858 TCTGTTGTGTATTTTTCTACACTGTTCGAACCAAATCAGTTTTTTCTGCACTAT
1 TCTGTTGTGAATTTTTCTACACAGTTCGAACCAAATCAATTTTTT-TGCACTAT
* *
1569912 TCTGTT-TGAATTTTTCTGCACAGTTCGAACCAAGTCAATTTTTTTGCACTAT
1 TCTGTTGTGAATTTTTCTACACAGTTCGAACCAAATCAATTTTTTTGCACTAT
1569964 T
1 T
1569965 TTTTCGTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 9 0.19
53 33 0.69
54 6 0.12
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (53 bp):
TCTGTTGTGAATTTTTCTACACAGTTCGAACCAAATCAATTTTTTTGCACTAT
Found at i:1570080 original size:11 final size:10
Alignment explanation
Indices: 1570054--1570101 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
1570044 TAAAGTTCCT
1570054 AAAAAAAT-A
1 AAAAAAATAA
1570063 AAAAAAATAA
1 AAAAAAATAA
1570073 AAACAAAATAA
1 AAA-AAAATAA
*
1570084 AAAATAA-AA
1 AAAAAAATAA
*
1570093 ACAAAAATA
1 AAAAAAATA
1570102 TAACGATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 15 0.45
10 8 0.24
11 10 0.30
ACGTcount: A:0.85, C:0.04, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1570085 original size:18 final size:18
Alignment explanation
Indices: 1570064--1570098 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1570054 AAAAAAATAA
1570064 AAAAAATAAAAACAAAAT
1 AAAAAATAAAAACAAAAT
1570082 AAAAAATAAAAACAAAA
1 AAAAAATAAAAACAAAA
1570099 ATATAACGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.86, C:0.06, G:0.00, T:0.09
Consensus pattern (18 bp):
AAAAAATAAAAACAAAAT
Found at i:1574020 original size:15 final size:15
Alignment explanation
Indices: 1574000--1574033 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1573990 TTCCTCTTGT
*
1574000 TCTTCCTGATGTGCG
1 TCTTCCTCATGTGCG
1574015 TCTTCCTCATGTGCG
1 TCTTCCTCATGTGCG
1574030 TCTT
1 TCTT
1574034 TTTCTGCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.29, G:0.21, T:0.44
Consensus pattern (15 bp):
TCTTCCTCATGTGCG
Found at i:1575808 original size:47 final size:44
Alignment explanation
Indices: 1575736--1575860 Score: 160
Period size: 47 Copynumber: 2.8 Consensus size: 44
1575726 TATAATCATT
*
1575736 TTACCATTTATCCCAAAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCA-TTATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATAC
* * * *
1575781 TTACCATTTAAATTCTATAAGCTCGTAAGCTTATTTTACCCATATAC
1 TTACCA-TT--ATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATAC
*
1575828 TTTCCATTATTCCAAAAGCTCGTAAGCTTATTT
1 TTACCATTATTCCAAAAGCTCGTAAGCTTATTT
1575861 GTATGCTTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 23 0.33
45 9 0.13
46 2 0.03
47 36 0.51
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.38
Consensus pattern (44 bp):
TTACCATTATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:1576009 original size:40 final size:40
Alignment explanation
Indices: 1575965--1576086 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
1575955 ACCGTAGTGC
1575965 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1576005 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1576045 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1576085 TA
1 TA
1576087 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1578879 original size:64 final size:64
Alignment explanation
Indices: 1578754--1578948 Score: 164
Period size: 64 Copynumber: 2.9 Consensus size: 64
1578744 TAAAACATCT
* * * *
1578754 TAAATCCTAATTATAACACTTAAAA-CTATTTAAACTAAAATACCTAAA-A-AATAATATAATAT
1 TAAATCCCAATTAAAATAC-TAAAACCTATTTAAACTAAAATA-C-AAAGATAA-AATAAAATAT
**
1578816 -TC
62 AAA
1578818 TAAATCCCAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCCAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATAAAATAT--A
1578883 AA
63 AA
1578885 TAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 TAA-ATCC-----C--AATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAATA
1578949 TAATGTTTAA
Statistics
Matches: 109, Mismatches: 6, Indels: 21
0.80 0.04 0.15
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 43 0.39
67 3 0.03
68 4 0.04
73 1 0.01
75 15 0.14
76 32 0.29
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (64 bp):
TAAATCCCAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATATAAA
Found at i:1578896 original size:75 final size:76
Alignment explanation
Indices: 1578809--1578973 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
1578799 AAAAAATAAT
*
1578809 ATAATATTCTAAATCCCAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCCCAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1578873 AAAAT-ATAAAA
65 AAAATGATAAAA
* **
1578884 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATCCTAAATCCCAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
1578949 TAATGTTTAAA
66 AAATGATAAAA
*
1578960 ATATTATCCTAAAT
1 ATAATATCCTAAAT
1578974 TTGAGTTTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 31 0.39
76 48 0.61
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATCCCAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:1579761 original size:18 final size:18
Alignment explanation
Indices: 1579738--1579773 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1579728 CAAATTCATT
*
1579738 CTCTTAAACATAAAATCA
1 CTCTTAAACAAAAAATCA
1579756 CTCTTAAACAAAAAATCA
1 CTCTTAAACAAAAAATCA
1579774 TCATGCGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (18 bp):
CTCTTAAACAAAAAATCA
Found at i:1588473 original size:16 final size:16
Alignment explanation
Indices: 1588436--1588473 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
1588426 TCTGCTGGTC
*
1588436 TGATTCAGTAGGAATA
1 TGATTCTGTAGGAATA
1588452 -GATTCTGTAGGAATA
1 TGATTCTGTAGGAATA
1588467 TGATTCT
1 TGATTCT
1588474 CCTCTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (16 bp):
TGATTCTGTAGGAATA
Found at i:1600601 original size:10 final size:11
Alignment explanation
Indices: 1600576--1600600 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1600566 TTTTTTGAAA
1600576 TTTTGGCTTTT
1 TTTTGGCTTTT
1600587 TTTTGGCTTTT
1 TTTTGGCTTTT
1600598 TTT
1 TTT
1600601 GTTTTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (11 bp):
TTTTGGCTTTT
Found at i:1606072 original size:2 final size:2
Alignment explanation
Indices: 1606065--1606092 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1606055 ATGTAACATC
1606065 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
1606093 TTAAACAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1606841 original size:59 final size:59
Alignment explanation
Indices: 1606647--1607042 Score: 600
Period size: 59 Copynumber: 6.8 Consensus size: 59
1606637 TTTCCCATAT
* * * * *
1606647 GGAAATTCATACACTTAGTATGAATCTCTTAACA-GTTTGAACACAAAGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* *
1606705 GGAAATTCATACACTTAGTATGAATTTCTTAAC--TTTTGCATACGAAGTGACCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* * *
1606762 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTTCACACAAAGTGCTCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
1606821 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* *
1606880 GAAAATTCATACACTTAGTATGAATTCCTTAACATTTTTGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
** * * * *
1606939 AAAAATTCATACACTTAGTATGAATTCCTTAACATTTTTGCACATGACGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
*
1606998 GGAAATTCATACACTTAGTATGAATTCCTTAACATTTTTGCACAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
1607043 TTAGTGCCAT
Statistics
Matches: 312, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
57 51 0.16
58 32 0.10
59 229 0.73
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
Found at i:1611321 original size:25 final size:24
Alignment explanation
Indices: 1611293--1611341 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1611283 TGCATGACAT
*
1611293 TGTACATACATGTTTTTATACATCA
1 TGTACATACAT-ATTTTATACATCA
*
1611318 TGTACATATATATTTTATACATCA
1 TGTACATACATATTTTATACATCA
1611342 CCAGGATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (24 bp):
TGTACATACATATTTTATACATCA
Found at i:1611674 original size:40 final size:40
Alignment explanation
Indices: 1611627--1611739 Score: 172
Period size: 40 Copynumber: 2.8 Consensus size: 40
1611617 AAAATACATT
*
1611627 TCGGTGTATATGGTGGGCATGACCTTATGTGTAATACACG
1 TCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACG
* *
1611667 TCGGTGTATATGGTGGGCACGACCTTATGTGTAATGCACT
1 TCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACG
* * *
1611707 TCGGTCTATGTGGTGGGCACAACCTTATGTGTA
1 TCGGTGTATATGGTGGGCACGACCTTATGTGTA
1611740 GCACTACAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (40 bp):
TCGGTGTATATGGTGGGCACGACCTTATGTGTAATACACG
Found at i:1612369 original size:22 final size:22
Alignment explanation
Indices: 1612326--1612370 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1612316 GGCACACTGT
* *
1612326 TTACTGTTCACGGCACTGTTCA
1 TTACTGTTCACAGCACTATTCA
* *
1612348 TTACTGTTCATAGTACTATTCA
1 TTACTGTTCACAGCACTATTCA
1612370 T
1 T
1612371 AAATACATCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (22 bp):
TTACTGTTCACAGCACTATTCA
Found at i:1614314 original size:24 final size:24
Alignment explanation
Indices: 1614287--1614334 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1614277 TGCATGACAT
*
1614287 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATATTTTATACATCA
*
1614311 TGTACATATATATTTTATACATCA
1 TGTACATAGATATTTTATACATCA
1614335 CCAGGAAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (24 bp):
TGTACATAGATATTTTATACATCA
Found at i:1614665 original size:40 final size:40
Alignment explanation
Indices: 1614610--1614730 Score: 197
Period size: 40 Copynumber: 3.0 Consensus size: 40
1614600 GCAGGTTTAA
1614610 AATACACTTTGGTGTATATGGTGGGCACGACCTTATGTGT
1 AATACACTTTGGTGTATATGGTGGGCACGACCTTATGTGT
* *
1614650 AATACACTTCGGTGTATATAGTGGGCACGACCTTATGTGT
1 AATACACTTTGGTGTATATGGTGGGCACGACCTTATGTGT
* * *
1614690 AATGCACTTTAGTGTATATGGTGGGCATGACCTTATGTGT
1 AATACACTTTGGTGTATATGGTGGGCACGACCTTATGTGT
1614730 A
1 A
1614731 GCACTACGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (40 bp):
AATACACTTTGGTGTATATGGTGGGCACGACCTTATGTGT
Found at i:1614831 original size:14 final size:14
Alignment explanation
Indices: 1614792--1614831 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1614782 CTGGGCTATT
1614792 GTTTATTGTTTATG
1 GTTTATTGTTTATG
*
1614806 ATTTA-TGATTTATG
1 GTTTATTG-TTTATG
1614820 GTTTATTGTTTA
1 GTTTATTGTTTA
1614832 ATAAATGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 18 0.82
15 2 0.09
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.62
Consensus pattern (14 bp):
GTTTATTGTTTATG
Found at i:1615350 original size:22 final size:22
Alignment explanation
Indices: 1615322--1615384 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
1615312 ATCGGTGCAC
*
1615322 TGTTCACGGTACTGTTCATTAA
1 TGTTCACAGTACTGTTCATTAA
1615344 TGTTCACAGTACTGTTCATTAA
1 TGTTCACAGTACTGTTCATTAA
* *
1615366 TGTTCATAGTACTATTCAT
1 TGTTCACAGTACTGTTCAT
1615385 AAATACATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.43
Consensus pattern (22 bp):
TGTTCACAGTACTGTTCATTAA
Found at i:1622371 original size:23 final size:24
Alignment explanation
Indices: 1622326--1622371 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1622316 ACTAGGGGTA
* *
1622326 CGTAGAATTTGTCCCGAATGACCG
1 CGTAGAATATGTCCCGAAGGACCG
*
1622350 CGTAGAA-ATGTCCTGAAGGACC
1 CGTAGAATATGTCCCGAAGGACC
1622372 ACATATAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (24 bp):
CGTAGAATATGTCCCGAAGGACCG
Found at i:1622472 original size:21 final size:21
Alignment explanation
Indices: 1622446--1622492 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1622436 AATAAGTGTA
* * *
1622446 CCAAAGTATCATATATATGTT
1 CCAAAGGATCACATATATGTC
*
1622467 CCAAAGGATTACATATATGTC
1 CCAAAGGATCACATATATGTC
1622488 CCAAA
1 CCAAA
1622493 TGACTACGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (21 bp):
CCAAAGGATCACATATATGTC
Found at i:1636279 original size:24 final size:24
Alignment explanation
Indices: 1636252--1636387 Score: 121
Period size: 24 Copynumber: 5.7 Consensus size: 24
1636242 TATATCAAAA
* *
1636252 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAATCAGAATTCAGGTCAAGT
* *
1636276 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAATCAGAATTCAGGTCAAGT
* * * *
1636300 AACAGATCAGAATCCAAGTCAAGT
1 ATCAAATCAGAATTCAGGTCAAGT
* * *
1636324 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAATCAGAATTCAGGTCAAG-T
* * *
1636348 ATCATATCAGAATCCATGTCAAGT
1 ATCAAATCAGAATTCAGGTCAAGT
*
1636372 ATCAGATCAGAATTCA
1 ATCAAATCAGAATTCA
1636388 AATTGAAAAT
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.02
24 92 0.96
25 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAATCAGAATTCAGGTCAAGT
Found at i:1636357 original size:48 final size:47
Alignment explanation
Indices: 1636269--1636384 Score: 153
Period size: 48 Copynumber: 2.4 Consensus size: 47
1636259 CATAATTCAG
*
1636269 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAG-AATCAGGTCAAGTAACAGATCAGAATCCAA
* * * *
1636317 GTCAAGTATCAGATCAGAATCCATGTC-AGATATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAT-CAGGTCAAG-TAACAGATCAGAATCCAA
1636365 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1636385 TCAAATTGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
47 5 0.08
48 56 0.92
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAATCAGGTCAAGTAACAGATCAGAATCCAA
Found at i:1638921 original size:7 final size:7
Alignment explanation
Indices: 1638909--1638945 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
1638899 TGGTCAACGC
1638909 CGGTCAA
1 CGGTCAA
1638916 CGGTCAA
1 CGGTCAA
1638923 CGGGTCAA
1 C-GGTCAA
1638931 CGGTCAA
1 CGGTCAA
1638938 CAGGTCAA
1 C-GGTCAA
1638946 TGGGTCGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.30, C:0.27, G:0.30, T:0.14
Consensus pattern (7 bp):
CGGTCAA
Found at i:1638930 original size:8 final size:8
Alignment explanation
Indices: 1638890--1638951 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
1638880 TCAAAGTTTT
1638890 GGTCAACAG
1 GGTCAAC-G
1638899 TGGTCAACG
1 -GGTCAACG
1638908 CCGGTCAAC-
1 --GGTCAACG
1638917 GGTCAACG
1 GGTCAACG
1638925 GGTCAAC-
1 GGTCAACG
*
1638932 GGTCAACA
1 GGTCAACG
*
1638940 GGTCAATG
1 GGTCAACG
1638948 GGTC
1 GGTC
1638952 GGGCCAACAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
7 14 0.30
8 17 0.37
9 1 0.02
10 14 0.30
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:1638930 original size:15 final size:15
Alignment explanation
Indices: 1638900--1638945 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
1638890 GGTCAACAGT
1638900 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
1638917 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
*
1638932 GGTCAACAGGTCAA
1 GGTCAACGGGTCAA
1638946 TGGGTCGGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 20 0.71
17 8 0.29
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.13
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:1638982 original size:31 final size:31
Alignment explanation
Indices: 1638940--1639004 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1638930 ACGGTCAACA
* * *
1638940 GGTCAATGGGTCGGGCCAACAGGTTGGGTTG
1 GGTCAACGGGTCGGGCCAACAGGTCGGGTCG
* *
1638971 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGCCAACAGGTCGGGTCG
1639002 GGT
1 GGT
1639005 TATAACCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.14, C:0.18, G:0.48, T:0.20
Consensus pattern (31 bp):
GGTCAACGGGTCGGGCCAACAGGTCGGGTCG
Found at i:1638986 original size:13 final size:13
Alignment explanation
Indices: 1638965--1639000 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1638955 CCAACAGGTT
*
1638965 GGGTTGGGTCAAC
1 GGGTCGGGTCAAC
1638978 GGGTCGGGTCAAC
1 GGGTCGGGTCAAC
1638991 GGGTCGGGTC
1 GGGTCGGGTC
1639001 GGGTTATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.19, G:0.50, T:0.19
Consensus pattern (13 bp):
GGGTCGGGTCAAC
Found at i:1643677 original size:13 final size:12
Alignment explanation
Indices: 1643647--1643693 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
1643637 GTAAAATACC
1643647 TAAAAATAACTTT
1 TAAAAATAA-TTT
1643660 T-AAAATAATTT
1 TAAAAATAATTT
1643671 TAGAAAATAATTT
1 TA-AAAATAATTT
1643684 TAAAAGATAA
1 TAAAA-ATAA
1643694 AAAGTGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.13
12 10 0.32
13 17 0.55
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (12 bp):
TAAAAATAATTT
Found at i:1645771 original size:2 final size:2
Alignment explanation
Indices: 1645766--1645793 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1645756 ACATATATCC
1645766 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
1645794 GCAACCGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1646758 original size:24 final size:24
Alignment explanation
Indices: 1646713--1646758 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1646703 TGGATTATTT
* *
1646713 TATTATTATTATTGTATGATATGA
1 TATTATTATTATTATATAATATGA
* *
1646737 TATTTTTATTATTATCTAATAT
1 TATTATTATTATTATATAATAT
1646759 AAATTAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (24 bp):
TATTATTATTATTATATAATATGA
Found at i:1648268 original size:25 final size:24
Alignment explanation
Indices: 1648213--1648269 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
1648203 TAAATGTTTT
*
1648213 TTTTTTCTACAACACTTTTAAAAG
1 TTTTTTCTACAACACTTATAAAAG
* *
1648237 TTATTTTCTACTATACTTATAAAAG
1 TT-TTTTCTACAACACTTATAAAAG
1648262 TCTTTTTC
1 T-TTTTTC
1648270 AAAAGTCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 25 0.89
26 1 0.04
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTTTTCTACAACACTTATAAAAG
Found at i:1653049 original size:21 final size:21
Alignment explanation
Indices: 1653025--1653064 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1653015 CGATTTAAAG
1653025 AACTTAAATAGCCAAAACATA
1 AACTTAAATAGCCAAAACATA
* *
1653046 AACTTAAATGGCTAAAACA
1 AACTTAAATAGCCAAAACA
1653065 ACATAAACAA
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:0.55, C:0.17, G:0.07, T:0.20
Consensus pattern (21 bp):
AACTTAAATAGCCAAAACATA
Found at i:1653073 original size:30 final size:28
Alignment explanation
Indices: 1653037--1653143 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 28
1653027 CTTAAATAGC
1653037 CAAAACATAAACTTAAATGGCTAAAACAA
1 CAAAACATAAACTTAAA-GGCTAAAACAA
*
1653066 CATAAACAAAAACTTAAAAGGCTAAAACAA
1 CA-AAACATAAACTT-AAAGGCTAAAACAA
1653096 CAACAACATAAACTTAAAGGACTAAATACAA
1 CAA-AACATAAACTTAAAGG-CTAAA-ACAA
* *
1653127 -AAACCAGAAACTTAAAG
1 CAAAACATAAACTTAAAG
1653144 AACTAAAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
29 21 0.30
30 41 0.59
31 7 0.10
ACGTcount: A:0.60, C:0.18, G:0.07, T:0.15
Consensus pattern (28 bp):
CAAAACATAAACTTAAAGGCTAAAACAA
Found at i:1653137 original size:29 final size:29
Alignment explanation
Indices: 1653038--1653160 Score: 110
Period size: 30 Copynumber: 4.1 Consensus size: 29
1653028 TTAAATAGCC
1653038 AAAACATAAACTTAAATGG-CTAAA-ACAA
1 AAAACATAAACTTAAA-GGACTAAATACAA
*
1653066 CATAAACAAAAACTTAAAAGG-CTAAA-ACAA
1 -A-AAACATAAACTT-AAAGGACTAAATACAA
1653096 CAACAACATAAACTTAAAGGACTAAATACAA
1 -AA-AACATAAACTTAAAGGACTAAATACAA
* * *
1653127 AAACCAGAAACTTAAAGAACTAAAATAGCAA
1 AAAACATAAACTTAAAGGACT-AAATA-CAA
1653158 AAA
1 AAA
1653161 TAAAAATTTA
Statistics
Matches: 82, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
29 23 0.28
30 46 0.56
31 13 0.16
ACGTcount: A:0.62, C:0.16, G:0.07, T:0.15
Consensus pattern (29 bp):
AAAACATAAACTTAAAGGACTAAATACAA
Found at i:1654838 original size:3 final size:3
Alignment explanation
Indices: 1654830--1654875 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
1654820 ATTTAGTTAT
*
1654830 TAA TAA TAA -AA TTAA TAA TAA TAA TAA TAA TTA -AA T-A TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1654873 TAA
1 TAA
1654876 ATATAATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 5 0.14
3 30 0.81
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1654877 original size:12 final size:12
Alignment explanation
Indices: 1654830--1654883 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
1654820 ATTTAGTTAT
1654830 TAATAATAAA-A
1 TAATAATAAATA
1654841 TTAATAAT-AATAA
1 -TAATAATAAAT-A
1654854 TAATAATTAAATA
1 TAATAA-TAAATA
1654867 TAATAATAAATA
1 TAATAATAAATA
1654879 TAATA
1 TAATA
1654884 TTTTTGTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.05
12 24 0.63
13 9 0.24
14 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:1655322 original size:128 final size:129
Alignment explanation
Indices: 1655078--1655323 Score: 304
Period size: 128 Copynumber: 1.9 Consensus size: 129
1655068 GGTCGTCTAA
* * *
1655078 GGGTGACACGACTCCTACGTGATGAGGAGATCTAGTCGGTGGATGACACGGCTCATACGTGATGA
1 GGGTGACACGACTCCTACATGATGAGGAGATCTAGTCGGTGGATGACACGGCTCATACATGAGGA
*
1655143 GGACATAAGACCATCTTTAGGGATGATAACACAGTTCCTACGTGATGAGGACGGTTGTTTATCAG
66 GGACAT-AGACCATCTTTAGGGATGATAACACAGTTCCTACATGATGAGGACGGTTGTTTATCAG
** * * *
1655208 GGGTGACACGTTTCCTACATGATGAGGAGGTCTAGTCGG-GGATGACACGGTTCTTATATATGAG
1 GGGTGACACGACTCCTACATGATGAGGAGATCTAGTCGGTGGATGACACGG--CTCATACATGAG
* * *
1655272 GATGG-CAT-G-CCATCTTTAGGGGTGATAACACGGTTTCTACAT-ATTGAGGACG
64 GA-GGACATAGACCATCTTTAGGGATGATAACACAGTTCCTACATGA-TGAGGACG
1655324 ACGGTTCCTA
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
127 1 0.01
128 37 0.37
129 12 0.12
130 35 0.35
131 13 0.13
132 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (129 bp):
GGGTGACACGACTCCTACATGATGAGGAGATCTAGTCGGTGGATGACACGGCTCATACATGAGGA
GGACATAGACCATCTTTAGGGATGATAACACAGTTCCTACATGATGAGGACGGTTGTTTATCAG
Found at i:1655482 original size:37 final size:36
Alignment explanation
Indices: 1655394--1655500 Score: 133
Period size: 38 Copynumber: 2.9 Consensus size: 36
1655384 AGAGACAAAA
* * *
1655394 CTTTGTTTCAAGGGAAACAAACTCAATGATTTTTTT
1 CTTTGTTTCAAGTGAAACAGACTCAAAGATTTTTTT
1655430 CATTTCGTTTCAAGTGAAACAGACTCAAAGATTTTTTT
1 C-TTT-GTTTCAAGTGAAACAGACTCAAAGATTTTTTT
* * *
1655468 GCTTTGTTTTAAGTGAAATAGACACAAAGATTT
1 -CTTTGTTTCAAGTGAAACAGACTCAAAGATTT
1655501 CTCAAGAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
36 1 0.02
37 28 0.45
38 32 0.52
39 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (36 bp):
CTTTGTTTCAAGTGAAACAGACTCAAAGATTTTTTT
Found at i:1655587 original size:137 final size:137
Alignment explanation
Indices: 1655341--1655862 Score: 429
Period size: 137 Copynumber: 3.8 Consensus size: 137
1655331 CTACATATTC
* * **
1655341 AAGTGAAACAGACTCAAAGATTTCTCAAGAAAGTTATCTTAAGAGAGACAAAACTTTGTTTCAAG
1 AAGTGAAACAGACACAAAGATTTCTCAAGAAAATTATCCCAAGAGAGACAAAACTTTGTTTCAAG
*
1655406 GGAAACAAACTCAATGATTTTTTTCATTTCGTTTCAAGTGAAACAGACTCAAAGATTTTTTTGCT
66 GGAAACAAACTCAAAGATTTTTTTCATTTCGTTTCAAGTGAAACAGACTCAAAGATTTTTTTGCT
1655471 TTGTTTT
131 TTGTTTT
* * *
1655478 AAGTGAAATAGACACAAAGATTTCTCAAGAAAATTTTCCCAAGAGAGCCAAAACTTTGTTTCAAG
1 AAGTGAAACAGACACAAAGATTTCTCAAGAAAATTATCCCAAGAGAGACAAAACTTTGTTTCAAG
* * * ***
1655543 GGAAACATACTCAAAGATTTTTTTCATTTTGTTTTAAGTGAAACAGACTCAAAGATTTCTCAAGA
66 GGAAACAAACTCAAAGATTTTTTTCATTTCGTTTCAAGTGAAACAGACTCAAAGATTT-TTTTG-
*** * *
1655608 AAACTGTCTC
129 -CTTTGTTTT
* ** * * * * **** *
1655618 AA--G--AGAGACA-AAACTTTATTTCAAGGGAAACA-GA-CTCAA-A-AAATTTTCATTTTGTT
1 AAGTGAAACAGACACAAAGATT-TCTCAA--GAAA-ATTATCCCAAGAGAGA-CAAAACTTTGTT
* * * * * * *
1655674 TCAAGTGAAATAGACTCAAAGATTTTTTT-GTTTTGTTTCAAGTGAAATAGACTAAAAGATTTTT
61 TCAAGGGAAACAAACTCAAAGATTTTTTTCATTTCGTTTCAAGTGAAACAGACTCAAAGA---TT
*
1655738 TTTTTG-TTTTTTTT
123 TTTTTGCTTTGTTTT
* * * *
1655752 CAATTGAAACAGACTCAAAGATTTCTCAAGAAAACTATCTCAAGAGAGACAAAACTTTGTTTTC-
1 -AAGTGAAACAGACACAAAGATTTCTCAAGAAAATTATCCCAAGAGAGACAAAACTTTG-TTTCA
* *
1655816 AGGGAAACAGACTCAAAGATTTTTTTTCATTTTGTTTCAAGTGAAAC
64 AGGGAAACAAACTCAAAGA-TTTTTTTCATTTCGTTTCAAGTGAAAC
1655863 CATTTCAAAA
Statistics
Matches: 297, Mismatches: 64, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
134 3 0.01
135 34 0.11
136 46 0.15
137 124 0.42
138 15 0.05
139 34 0.11
140 24 0.08
141 17 0.06
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (137 bp):
AAGTGAAACAGACACAAAGATTTCTCAAGAAAATTATCCCAAGAGAGACAAAACTTTGTTTCAAG
GGAAACAAACTCAAAGATTTTTTTCATTTCGTTTCAAGTGAAACAGACTCAAAGATTTTTTTGCT
TTGTTTT
Found at i:1655599 original size:100 final size:100
Alignment explanation
Indices: 1655436--1655698 Score: 381
Period size: 100 Copynumber: 2.7 Consensus size: 100
1655426 TTTTCATTTC
* *
1655436 GTTTCAAGTGAAACAGACTCAAAGATTTTTTTGC--TTTGTTTTAAGTGAAATAGACACAAAGAT
1 GTTTCAAGGGAAACAGACTCAAAGATTTTTTT-CATTTTGTTTTAAGTGAAATAGACTCAAAGAT
* * *
1655499 TTCTCAAGAAAATTTTCCCAAGAGAGCCAAAACTTT
65 TTCTCAAGAAAACTGTCCCAAGAGAGACAAAACTTT
* *
1655535 GTTTCAAGGGAAACATACTCAAAGATTTTTTTCATTTTGTTTTAAGTGAAACAGACTCAAAGATT
1 GTTTCAAGGGAAACAGACTCAAAGATTTTTTTCATTTTGTTTTAAGTGAAATAGACTCAAAGATT
*
1655600 TCTCAAGAAAACTGTCTCAAGAGAGACAAAACTTT
66 TCTCAAGAAAACTGTCCCAAGAGAGACAAAACTTT
* ** *
1655635 ATTTCAAGGGAAACAGACTCAAA-A-AATTTTCATTTTGTTTCAAGTGAAATAGACTCAAAGATT
1 GTTTCAAGGGAAACAGACTCAAAGATTTTTTTCATTTTGTTTTAAGTGAAATAGACTCAAAGATT
1655698 T
66 T
1655699 TTTTGTTTTG
Statistics
Matches: 148, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
98 37 0.25
99 31 0.21
100 80 0.54
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (100 bp):
GTTTCAAGGGAAACAGACTCAAAGATTTTTTTCATTTTGTTTTAAGTGAAATAGACTCAAAGATT
TCTCAAGAAAACTGTCCCAAGAGAGACAAAACTTT
Found at i:1655714 original size:37 final size:37
Alignment explanation
Indices: 1655636--1655775 Score: 156
Period size: 37 Copynumber: 3.7 Consensus size: 37
1655626 CAAAACTTTA
* ** **
1655636 TTTCAAGGGAAACAGACTCAAA-AAATTTTCATTTTG
1 TTTCAAGTGAAACAGACTCAAAGATTTTTTTGTTTTG
*
1655672 TTTCAAGTGAAATAGACTCAAAGATTTTTTTGTTTTG
1 TTTCAAGTGAAACAGACTCAAAGATTTTTTTGTTTTG
* * *
1655709 TTTCAAGTGAAATAGACTAAAAGATTTTTTTTTTGTTTTT
1 TTTCAAGTGAAACAGACTCAAAGA---TTTTTTTGTTTTG
*
1655749 TTTCAATTGAAACAGACTCAAAGATTT
1 TTTCAAGTGAAACAGACTCAAAGATTT
1655776 CTCAAGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
36 20 0.22
37 36 0.40
40 33 0.37
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTCAAGTGAAACAGACTCAAAGATTTTTTTGTTTTG
Found at i:1655753 original size:40 final size:40
Alignment explanation
Indices: 1655667--1655775 Score: 161
Period size: 40 Copynumber: 2.8 Consensus size: 40
1655657 AAAATTTTCA
1655667 TTTTGTTTCAAGTGAAATAGACTCAAAGA---TTTTTTTG
1 TTTTGTTTCAAGTGAAATAGACTCAAAGATTTTTTTTTTG
*
1655704 TTTTGTTTCAAGTGAAATAGACTAAAAGATTTTTTTTTTG
1 TTTTGTTTCAAGTGAAATAGACTCAAAGATTTTTTTTTTG
* * *
1655744 TTTTTTTTCAATTGAAACAGACTCAAAGATTT
1 TTTTGTTTCAAGTGAAATAGACTCAAAGATTT
1655776 CTCAAGAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
37 28 0.44
40 36 0.56
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (40 bp):
TTTTGTTTCAAGTGAAATAGACTCAAAGATTTTTTTTTTG
Found at i:1655822 original size:175 final size:175
Alignment explanation
Indices: 1655532--1655861 Score: 495
Period size: 175 Copynumber: 1.9 Consensus size: 175
1655522 GAGCCAAAAC
* *
1655532 TTTGTTTCAAGGGAAACATACTCAAAGATTTTTTTCATTTTGTTTTAAGTGAAACAGACTCAAAG
1 TTTGTTTCAAGGGAAACAGACTAAAAGATTTTTTTCATTTTGTTTTAAGTGAAACAGACTCAAAG
*
1655597 ATTTCTCAAGAAAACTGTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAGACTCAAA-A-A
66 ATTTCTCAAGAAAACTATCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAGACTCAAAGATA
1655660 ATTTTCATTTTGTTTCAAGTGAAATAGACTCAAAGATTTTTTTGT
131 ATTTTCATTTTGTTTCAAGTGAAATAGACTCAAAGATTTTTTTGT
* * ** * *
1655705 TTTGTTTCAAGTGAAATAGACTAAAAGATTTTTTTTTTGTTTTTTTTCAATTGAAACAGACTCAA
1 TTTGTTTCAAGGGAAACAGACTAAAAGATTTTTTTCAT-TTTGTTTT-AAGTGAAACAGACTCAA
*
1655770 AGATTTCTCAAGAAAACTATCTCAAGAGAGACAAAACTTTGTTTTC-AGGGAAACAGACTCAAAG
64 AGATTTCTCAAGAAAACTATCTCAAGAGAGACAAAACTTT-ATTTCAAGGGAAACAGACTCAAAG
**
1655834 ATTTTTTTTCATTTTGTTTCAAGTGAAA
128 A-TAATTTTCATTTTGTTTCAAGTGAAA
1655862 CCATTTCAAA
Statistics
Matches: 139, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
173 32 0.23
174 7 0.05
175 72 0.52
176 5 0.04
178 23 0.17
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (175 bp):
TTTGTTTCAAGGGAAACAGACTAAAAGATTTTTTTCATTTTGTTTTAAGTGAAACAGACTCAAAG
ATTTCTCAAGAAAACTATCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAGACTCAAAGATA
ATTTTCATTTTGTTTCAAGTGAAATAGACTCAAAGATTTTTTTGT
Found at i:1655992 original size:37 final size:36
Alignment explanation
Indices: 1655868--1655990 Score: 149
Period size: 37 Copynumber: 3.4 Consensus size: 36
1655858 GAAACCATTT
** *
1655868 CAAAATTTGTTTTAAAGAACAAATGTCTCAAGTGAGA
1 CAAAATTTGTTTTAGCGAA-AATTGTCTCAAGTGAGA
** * *
1655905 TGAAATTTGTTTT-GCGAGAAATTTTCTCAAGCGAGA
1 CAAAATTTGTTTTAGCGA-AAATTGTCTCAAGTGAGA
1655941 CAAAATTTGTTTTTAGCGAAAATTGTCTCAAGTGAGA
1 CAAAATTTG-TTTTAGCGAAAATTGTCTCAAGTGAGA
1655978 CAAAATTTGTTTT
1 CAAAATTTGTTTT
1655991 TAAGAAAGCA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
36 27 0.38
37 41 0.57
38 4 0.06
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (36 bp):
CAAAATTTGTTTTAGCGAAAATTGTCTCAAGTGAGA
Found at i:1656006 original size:37 final size:37
Alignment explanation
Indices: 1655868--1656011 Score: 127
Period size: 37 Copynumber: 3.9 Consensus size: 37
1655858 GAAACCATTT
*
1655868 CAAAATTTG-TTTTAAAGAACAAAT-GTCTCAAGTGAGA
1 CAAAATTTGTTTTTAGAG-A-AAATGGTCTCAAGTGAGA
** ** ** *
1655905 TGAAATTTGTTTTGCGAG-AAATTTTCTCAAGCGAGA
1 CAAAATTTGTTTTTAGAGAAAATGGTCTCAAGTGAGA
* *
1655941 CAAAATTTGTTTTTAGCGAAAATTGTCTCAAGTGAGA
1 CAAAATTTGTTTTTAGAGAAAATGGTCTCAAGTGAGA
1655978 CAAAATTTGTTTTTA-AGAAAGCA-GGTCTCAAGTG
1 CAAAATTTGTTTTTAGAGAAA--ATGGTCTCAAGTG
1656012 TGACGACCCT
Statistics
Matches: 86, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
35 4 0.05
36 28 0.33
37 48 0.56
38 6 0.07
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (37 bp):
CAAAATTTGTTTTTAGAGAAAATGGTCTCAAGTGAGA
Found at i:1657259 original size:14 final size:13
Alignment explanation
Indices: 1657240--1657371 Score: 76
Period size: 14 Copynumber: 9.7 Consensus size: 13
1657230 ATTTTCTTTG
1657240 TTTTTCTTTTGTTC
1 TTTTTCTTTT-TTC
*
1657254 TTTTTC--TTTGC
1 TTTTTCTTTTTTC
1657265 TTTTTCTCTGTTTCTC
1 TTTTTCT-T-TTT-TC
*
1657281 TGTTTCTTTTTTC
1 TTTTTCTTTTTTC
*
1657294 TTTTCTCTTTGTT-
1 TTTT-TCTTTTTTC
*
1657307 TTTTTCTTTTCTC
1 TTTTTCTTTTTTC
1657320 TTCTTT-TTTTTCTC
1 TT-TTTCTTTTT-TC
*
1657334 TTTGCTCTTTGTTT-
1 TTT-TTCTTT-TTTC
*
1657348 TTTTCCTTTTCTTC
1 TTTTTCTTTT-TTC
1657362 TTTTCTCTTT
1 TTTT-TCTTT
1657372 GTTTTGATTG
Statistics
Matches: 91, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
11 8 0.09
12 9 0.10
13 22 0.24
14 31 0.34
15 12 0.13
16 9 0.10
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:1657295 original size:40 final size:38
Alignment explanation
Indices: 1657241--1657367 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 38
1657231 TTTTCTTTGT
1657241 TTTTCTTTTGTTCTTTT-TCTTTGCTTTTTCTCTGTTTCTC
1 TTTTCTTTT-TTCTTTTCTCTTTG-TTTTTCTCT-TTTCTC
*
1657281 TGTTTCTTTTTTCTTTTCTCTTTGTTTTTTTCTTTTCTC
1 T-TTTCTTTTTTCTTTTCTCTTTGTTTTTCTCTTTTCTC
*
1657320 TTCTT-TTTTTTCTCTTTGCTCTTTGTTTTTTTCCTTTTCTTC
1 TT-TTCTTTTTTCT-TTT-CTCTTTGTTTTTCT-CTTTTC-TC
1657362 TTTTCT
1 TTTTCT
1657368 CTTTGTTTTG
Statistics
Matches: 78, Mismatches: 1, Indels: 14
0.84 0.01 0.15
Matches are distributed among these distances:
38 9 0.12
39 12 0.15
40 30 0.38
41 22 0.28
42 5 0.06
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.75
Consensus pattern (38 bp):
TTTTCTTTTTTCTTTTCTCTTTGTTTTTCTCTTTTCTC
Found at i:1657311 original size:19 final size:19
Alignment explanation
Indices: 1657246--1657364 Score: 118
Period size: 19 Copynumber: 5.9 Consensus size: 19
1657236 TTTGTTTTTC
*
1657246 TTTTGTTCTTTT-TCTTTG
1 TTTTTTTCTTTTCTCTTTG
*
1657264 CTTTTTCTCTGTTTCTCTGTT-
1 -TTTTTTTCT-TTTCTCT-TTG
1657285 TCTTTTTTCTTTTCTCTTTG
1 T-TTTTTTCTTTTCTCTTTG
1657305 TTTTTTTCTTTTCTCTTCT-
1 TTTTTTTCTTTTCTCTT-TG
1657324 TTTTTTTCTCTTTGCTCTTTG
1 TTTTTTTCT-TTT-CTCTTTG
1657345 TTTTTTTCCTTTTCTTCTTT
1 TTTTTTT-CTTTTC-TCTTT
1657365 TCTCTTTGTT
Statistics
Matches: 86, Mismatches: 3, Indels: 20
0.79 0.03 0.18
Matches are distributed among these distances:
19 34 0.40
20 18 0.21
21 30 0.35
22 4 0.05
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTTTTCTTTTCTCTTTG
Found at i:1657329 original size:21 final size:19
Alignment explanation
Indices: 1657240--1657365 Score: 110
Period size: 21 Copynumber: 6.2 Consensus size: 19
1657230 ATTTTCTTTG
1657240 TTTTTCTTTTGTTCTTTT-TC
1 TTTTT-TTTT-TTCTTTTCTC
* *
1657260 TTTGCTTTTTCTCTGTTTCTC
1 TTT-TTTTTTTTCT-TTTCTC
*
1657281 TGTTTCTTTTTTCTTTTCTC
1 T-TTTTTTTTTTCTTTTCTC
*
1657301 TTTGTTTTTTTCTTTTCTC
1 TTTTTTTTTTTCTTTTCTC
*
1657320 TTCTTTTTTTTCTCTTTGCTC
1 TT-TTTTTTTT-TCTTTTCTC
*
1657341 TTTGTTTTTTTCCTTTTCTTC
1 TTT-TTTTTTTTCTTTTC-TC
1657362 TTTT
1 TTTT
1657366 CTCTTTGTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
19 21 0.24
20 31 0.36
21 33 0.38
22 2 0.02
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTTTTTTTTCTTTTCTC
Found at i:1660998 original size:30 final size:29
Alignment explanation
Indices: 1660963--1661103 Score: 124
Period size: 29 Copynumber: 4.8 Consensus size: 29
1660953 TTAAATAGCC
*
1660963 AAAACATAAACTTAAAGGGCTAAAACAGT
1 AAAACATAAACTTAAAGGACTAAAACAGT
*
1660992 ATAAACAAAAACTTAAAAGG-CTAAAACAGT
1 A-AAACATAAACTT-AAAGGACTAAAACAGT
* * *
1661022 AATAATATAAACTTAAAGGACT-AATCAGA
1 AA-AACATAAACTTAAAGGACTAAAACAGT
* * * *
1661051 AAAATAGAAACTTAAAGGACTAAAATAGA
1 AAAACATAAACTTAAAGGACTAAAACAGT
* * * *
1661080 AAAATAGAAATTTAAGGGACTAAA
1 AAAACATAAACTTAAAGGACTAAA
1661104 TAGAAAAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
28 18 0.19
29 41 0.42
30 33 0.34
31 5 0.05
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (29 bp):
AAAACATAAACTTAAAGGACTAAAACAGT
Found at i:1661094 original size:29 final size:28
Alignment explanation
Indices: 1661025--1661121 Score: 124
Period size: 28 Copynumber: 3.4 Consensus size: 28
1661015 AAACAGTAAT
*
1661025 AATATAAACTTAAAGGACT-AATCAGAAA
1 AATAGAAACTTAAAGGACTAAAT-AGAAA
1661053 AATAGAAACTTAAAGGACTAAAATAGAAA
1 AATAGAAACTTAAAGGACT-AAATAGAAA
* *
1661082 AATAGAAATTTAAGGGACTAAATAGAAAAA
1 AATAGAAACTTAAAGGACTAAATAG--AAA
1661112 AATAGAAACT
1 AATAGAAACT
1661122 CAGAGGGCTG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
28 24 0.39
29 22 0.36
30 15 0.25
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (28 bp):
AATAGAAACTTAAAGGACTAAATAGAAA
Found at i:1661136 original size:30 final size:30
Alignment explanation
Indices: 1661050--1661136 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
1661040 GACTAATCAG
* *
1661050 AAAAATAGAAACTTAAAGGACTAAAATAG--
1 AAAAATAGAAACTCAAGGGACT-AAATAGAA
* *
1661079 AAAAATAGAAATTTAAGGGACTAAATAGAA
1 AAAAATAGAAACTCAAGGGACTAAATAGAA
*
1661109 AAAAATAGAAACTCAGAGGG-CTGAATAG
1 AAAAATAGAAACTCA-AGGGACTAAATAG
1661137 TAATTTCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 6 0.12
29 20 0.40
30 20 0.40
31 4 0.08
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.17
Consensus pattern (30 bp):
AAAAATAGAAACTCAAGGGACTAAATAGAA
Found at i:1662757 original size:12 final size:13
Alignment explanation
Indices: 1662734--1662764 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1662724 ATTAATAATA
1662734 ATAATAATTAAAT
1 ATAATAATTAAAT
1662747 ATAATAA-TAAAT
1 ATAATAATTAAAT
1662759 ATAATA
1 ATAATA
1662765 TTTTTGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAATTAAAT
Found at i:1664121 original size:16 final size:16
Alignment explanation
Indices: 1664097--1664135 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1664087 CCATTCCCCT
* * *
1664097 CATATATCAACATATA
1 CATACATCAACACAAA
1664113 CATACATCAACACAAA
1 CATACATCAACACAAA
1664129 CATACAT
1 CATACAT
1664136 GATACATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (16 bp):
CATACATCAACACAAA
Found at i:1664468 original size:37 final size:36
Alignment explanation
Indices: 1664412--1664503 Score: 114
Period size: 37 Copynumber: 2.6 Consensus size: 36
1664402 CCTTGAGATT
* *
1664412 ATTT-TCTTAAAATAAATTTTGTCTCGCTTAAGACA
1 ATTTATCTAAAAACAAATTTTGTCTCGCTTAAGACA
* *
1664447 GTTTTATCTAAAAACAAATTTTGTCTCGCTTGAGACA
1 -ATTTATCTAAAAACAAATTTTGTCTCGCTTAAGACA
* *
1664484 ATTTCTCTCAAAACAAATTT
1 ATTTATCTAAAAACAAATTT
1664504 CATCTTGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 20 0.42
37 28 0.58
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (36 bp):
ATTTATCTAAAAACAAATTTTGTCTCGCTTAAGACA
Found at i:1664682 original size:36 final size:35
Alignment explanation
Indices: 1664638--1664764 Score: 93
Period size: 36 Copynumber: 3.7 Consensus size: 35
1664628 TTTAATCCAA
*
1664638 TCTCTGAGATCGTTTCCCTTGAAACGAATTTTGTC
1 TCTCTGAGATAGTTTCCCTTGAAACGAATTTTGTC
** * ****
1664673 TCTCTTGAGACGGTTTCTCTTGAAAC--A-CCCATC
1 TCTC-TGAGATAGTTTCCCTTGAAACGAATTTTGTC
* *
1664706 T-TC-GAGATAGTTTCCCTTGAAAAGAATTTTGTG
1 TCTCTGAGATAGTTTCCCTTGAAACGAATTTTGTC
**
1664739 TCTCTTGAGATAGTTTCTATTGAAAC
1 TCTC-TGAGATAGTTTCCCTTGAAAC
1664765 ATCATCTTTG
Statistics
Matches: 66, Mismatches: 19, Indels: 13
0.67 0.19 0.13
Matches are distributed among these distances:
30 16 0.24
32 3 0.05
33 5 0.08
34 3 0.05
35 4 0.06
36 35 0.53
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (35 bp):
TCTCTGAGATAGTTTCCCTTGAAACGAATTTTGTC
Found at i:1664725 original size:66 final size:65
Alignment explanation
Indices: 1664643--1664793 Score: 194
Period size: 66 Copynumber: 2.3 Consensus size: 65
1664633 TCCAATCTCT
* * *
1664643 GAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACGGTTTCTCTTGAAACACCCATCTT
1 GAGATAGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAACA-CCATCTT
1664708 C
65 C
* * * * *
1664709 GAGATAGTTTCCCTTGAAAAGAATTTTGTGTCTCTTGAGATAGTTTCTATTGAAACATCATCTTT
1 GAGATAGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAACACCATCTTC
* * *
1664774 GAGTTTGTTTCTCTTGAAAC
1 GAGATAGTTTCCCTTGAAAC
1664794 ACAAAATCTT
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 22 0.30
66 51 0.70
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (65 bp):
GAGATAGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAACACCATCTTC
Found at i:1664783 original size:29 final size:29
Alignment explanation
Indices: 1664743--1664825 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 29
1664733 TTTGTGTCTC
*
1664743 TTGAG-ATAGTTTCTATTGAAACATC-ATCT
1 TTGAGTAT-GTTTCTCTTGAAACA-CAATCT
*
1664772 TTGAGTTTGTTTCTCTTGAAACACAAAATCT
1 TTGAGTATGTTTCTCTTGAAACAC--AATCT
*
1664803 TTGAGTATGTTTCCCTTGAAACA
1 TTGAGTATGTTTCTCTTGAAACA
1664826 AAGTTTTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.02
29 19 0.41
30 1 0.02
31 25 0.54
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (29 bp):
TTGAGTATGTTTCTCTTGAAACACAATCT
Found at i:1665102 original size:131 final size:131
Alignment explanation
Indices: 1664864--1665106 Score: 351
Period size: 131 Copynumber: 1.9 Consensus size: 131
1664854 CTTGAAACAA
* * * ** *
1664864 ATCCCTAAAGTTGGTATGCCGTCCTCATCGCGTAGGAACCATGTCATCCCCCGACCAGACCTCCT
1 ATCCCTAAAGATGGCATGCCATCCTCATCAAGTAGGAACCATGTCATCCACCGACCAGACCTCCT
* * * * *
1664929 CATCAAGTAGGAGCGGTGTCACCCCTAGATAACCTATTGTCCTCATCATGTAGAAACTGTGTTAT
66 CATCAAGTAAGAGCCGTGTCACCCATAGATAACCAATCGTCCTCATCATGTAGAAACTGTGTTAT
1664994 C
131 C
* * *
1664995 ATCCCTAAAGATGGCATGTCATCCTCATCAATTAGGAACCGTGTCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGGCATGCCATCCTCATCAAGTAGGAACCATGTCATCCACCGACCAGACCTCCT
*
1665060 CATCGAGTAAGAGCCGTGTCACCCATAGATAACCAATCGTCCTCATC
66 CATCAAGTAAGAGCCGTGTCACCCATAGATAACCAATCGTCCTCATC
1665107 GCATAGGAAC
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
131 97 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGCATGCCATCCTCATCAAGTAGGAACCATGTCATCCACCGACCAGACCTCCT
CATCAAGTAAGAGCCGTGTCACCCATAGATAACCAATCGTCCTCATCATGTAGAAACTGTGTTAT
C
Found at i:1665223 original size:3 final size:3
Alignment explanation
Indices: 1665217--1665261 Score: 72
Period size: 3 Copynumber: 14.3 Consensus size: 3
1665207 TTCCCAACAA
1665217 TAT TAT TAAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT T-AT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1665262 TACATTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1667581 original size:23 final size:23
Alignment explanation
Indices: 1667555--1667609 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
1667545 AAATCACCAA
1667555 TTTTTCAAATAA-AGTCATAATTGT
1 TTTTTCAAATAATA-T-ATAATTGT
* *
1667579 TTTTTAAAATAATATTTAATTG-
1 TTTTTCAAATAATATATAATTGT
1667601 TTTTTCAAA
1 TTTTTCAAA
1667610 AAAATGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.30
23 6 0.22
24 12 0.44
25 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (23 bp):
TTTTTCAAATAATATATAATTGT
Found at i:1669829 original size:19 final size:19
Alignment explanation
Indices: 1669793--1669840 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1669783 TAGTTTTGAA
1669793 ATATATTTTAAAAGAATAT
1 ATATATTTTAAAAGAATAT
*
1669812 ATATAGTTTTAGAA-AATAT
1 ATATA-TTTTAAAAGAATAT
*
1669831 ATATAATTTA
1 ATATATTTTA
1669841 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 15 0.58
20 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATATTTTAAAAGAATAT
Found at i:1669875 original size:81 final size:80
Alignment explanation
Indices: 1669747--1669924 Score: 211
Period size: 81 Copynumber: 2.2 Consensus size: 80
1669737 TATGGTTTTT
* * *
1669747 AATATATATATATATATATATTGTTTTGAAAACATATAGTTTTGAAATATA-TTTTAAAAGAATA
1 AATATATATATATATATATATTATATTGAAAACATATAGTTTTGAAATATACATTTAAAA-AATA
1669811 TATATAGTTTTA-GAA
65 TATATAGTTTTATGAA
* * * *
1669826 AATATATATA-ATTTATATATATATATTGAAAGCATATATAGTTTTGAAATATACATTTGATAAA
1 AATATATATATATATATATAT-TATATTGAAA--ACATATAGTTTTGAAATATACATTTAAAAAA
*
1669890 TATATATGGTTTTATTGAA
63 TATATATAGTTTTA-TGAA
1669909 AATATATAT-TATATAT
1 AATATATATATATATAT
1669925 TTCGAATAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
78 9 0.11
79 18 0.22
81 34 0.41
82 5 0.06
83 17 0.20
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (80 bp):
AATATATATATATATATATATTATATTGAAAACATATAGTTTTGAAATATACATTTAAAAAATAT
ATATAGTTTTATGAA
Found at i:1669948 original size:3 final size:3
Alignment explanation
Indices: 1669935--1669985 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
1669925 TTCGAATAAC
*
1669935 TTA TTA TTTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1669981 TTA TT
1 TTA TT
1669986 TCATTTTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1674119 original size:33 final size:33
Alignment explanation
Indices: 1674076--1674220 Score: 245
Period size: 33 Copynumber: 4.4 Consensus size: 33
1674066 AGAATAATAA
* *
1674076 CATTTTCAACACATCTAATTTGAATATATTTCC
1 CATTTGCAACACATCTCATTTGAATATATTTCC
1674109 CATTTGCAACACATCTCATTTGAATATATTTCC
1 CATTTGCAACACATCTCATTTGAATATATTTCC
* *
1674142 CATTTGCAACACATCTTATTTGAATACATTTCC
1 CATTTGCAACACATCTCATTTGAATATATTTCC
*
1674175 CATTTGAAACACATCTCATTTGAATATATTTCC
1 CATTTGCAACACATCTCATTTGAATATATTTCC
1674208 CATTTGCAACACA
1 CATTTGCAACACA
1674221 AATATTTCAA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 104 1.00
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (33 bp):
CATTTGCAACACATCTCATTTGAATATATTTCC
Found at i:1674130 original size:16 final size:15
Alignment explanation
Indices: 1674109--1674198 Score: 63
Period size: 16 Copynumber: 5.5 Consensus size: 15
1674099 ATATATTTCC
1674109 CATTTGCAACACATCT
1 CATTTG-AACACATCT
* * *
1674125 CATTTGAATATATTTCC
1 CATTTGAACACA--TCT
1674142 CATTTGCAACACATCT
1 CATTTG-AACACATCT
* * *
1674158 TATTTGAATACATTTCC
1 CATTTGAACACA--TCT
1674175 CATTTGAAACACATCT
1 CATTTG-AACACATCT
1674191 CATTTGAA
1 CATTTGAA
1674199 TATATTTCCC
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
15 11 0.20
16 21 0.38
17 15 0.27
18 9 0.16
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (15 bp):
CATTTGAACACATCT
Found at i:1676412 original size:49 final size:46
Alignment explanation
Indices: 1676305--1676414 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 46
1676295 TTCATTTGGG
* * *
1676305 CATCCTTTCATACCCATTATGTATTATTTACATTTTTCCTTTATGA
1 CATCCTTTCATACCAATTATGTATTATGTACATTTTTCCTATATGA
** * *
1676351 CATCAATACATACCAATTATGTATTGATGTACATTTTATATCTATATGA
1 CATCCTTTCATACCAATTATGTATT-ATGTACATTTT-T-CCTATATGA
1676400 CATCCTTTCATACCA
1 CATCCTTTCATACCA
1676415 CATATGCACC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
46 21 0.41
47 10 0.20
48 1 0.02
49 19 0.37
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (46 bp):
CATCCTTTCATACCAATTATGTATTATGTACATTTTTCCTATATGA
Found at i:1676621 original size:81 final size:81
Alignment explanation
Indices: 1676481--1676828 Score: 418
Period size: 81 Copynumber: 4.3 Consensus size: 81
1676471 ACATTTAATT
* * * * *
1676481 TTCATCTAACTT-GCATGATTGATACTTTTTTGC-CAAATGCACAACTAGGCCAATTATCTTCTA
1 TTCATCTAA-TTGGCATAATTGACACCTTTCTGCTCAAATGCACAACTAGGCC-ATTATCTTTTA
* * *
1676544 CTCAGCTGTCCTTAACCG
64 CTCAACAGTCTTTAACCG
* *
1676562 TTCATCTAATTGACATAATTGACACCTTTCTGCT-AAATGTACAACTAGGCCATTAATCTTTTAC
1 TTCATCTAATTGGCATAATTGACACCTTTCTGCTCAAATGCACAACTAGGCCATT-ATCTTTTAC
*
1676626 TCAACAGTTTTTAACCG
65 TCAACAGTCTTTAACCG
* * * * *
1676643 TTCATCTAACTGGCATAATTGACACCTTCCT-TTCAAATGCACAGCTAGGCCATTATTTTTTACT
1 TTCATCTAATTGGCATAATTGACACCTTTCTGCTCAAATGCACAACTAGGCCATTATCTTTTACT
* *
1676707 CAACGGTCTTTAACCA
66 CAACAGTCTTTAACCG
* * * *
1676723 TTCATCTAATTGCCATAATTGACACCTTTCTG-TCAAATGCGCAGCTAGGCCATTAATATTTTAC
1 TTCATCTAATTGGCATAATTGACACCTTTCTGCTCAAATGCACAACTAGGCCATT-ATCTTTTAC
1676787 TCAACAGTCTTTAACCG
65 TCAACAGTCTTTAACCG
*
1676804 TTCATCTAACTGGCATAATTGACAC
1 TTCATCTAATTGGCATAATTGACAC
1676829 ACACAACTAG
Statistics
Matches: 231, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
80 77 0.33
81 154 0.67
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (81 bp):
TTCATCTAATTGGCATAATTGACACCTTTCTGCTCAAATGCACAACTAGGCCATTATCTTTTACT
CAACAGTCTTTAACCG
Found at i:1676876 original size:68 final size:68
Alignment explanation
Indices: 1676767--1676896 Score: 233
Period size: 68 Copynumber: 1.9 Consensus size: 68
1676757 AAATGCGCAG
1676767 CTAGGCCATTAATATTTTACTCAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACACA
1 CTAGGCCATTAATATTTTACTCAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACACA
1676832 CAA
66 CAA
* * *
1676835 CTAGGTCATTAATATTTTACTCAACGGTCTTTAACCGTTCATCTAGCTGGCATAATTGACAC
1 CTAGGCCATTAATATTTTACTCAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACAC
1676897 TTTTCTGTCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (68 bp):
CTAGGCCATTAATATTTTACTCAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACACA
CAA
Found at i:1676970 original size:81 final size:81
Alignment explanation
Indices: 1676830--1677003 Score: 276
Period size: 81 Copynumber: 2.1 Consensus size: 81
1676820 AATTGACACA
* * ** *
1676830 CACAACTAGGTCATTAATATTTTACTCAACGGTCTTTAACCGTTCATCTAGCTGGCATAATTGAC
1 CACAGCTAGGCCATTAATATTTTACTCAACAATCTTTAACCGTTCATCTAACTGGCATAATTGAC
*
1676895 ACTTTTCTGTCAAATG
66 ACCTTTCTGTCAAATG
*
1676911 CACAGCTAGGCCATTAATCTTTTACTCAACAATCTTTAACCGTTCATCTAACTGGCATAATTGAC
1 CACAGCTAGGCCATTAATATTTTACTCAACAATCTTTAACCGTTCATCTAACTGGCATAATTGAC
1676976 ACCTTTCTGTCAAATG
66 ACCTTTCTGTCAAATG
*
1676992 CACAGTTAGGCC
1 CACAGCTAGGCC
1677004 TCAAAGGCAC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (81 bp):
CACAGCTAGGCCATTAATATTTTACTCAACAATCTTTAACCGTTCATCTAACTGGCATAATTGAC
ACCTTTCTGTCAAATG
Found at i:1677088 original size:230 final size:231
Alignment explanation
Indices: 1676562--1677152 Score: 687
Period size: 230 Copynumber: 2.6 Consensus size: 231
1676552 TCCTTAACCG
* * *
1676562 TTCATCTAATTGACATAATTGACACCTTTCTGCTAAATGTACAACTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
* * * *
1676627 CAACAGTTTTTAACCGTTCATCTAACTGGCATAATTGACACCTTCCTTTCAAATGCACAGCTAGG
66 CAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG
* ** *
1676692 CCATTATTTTTTACTCAACGGTCTTTAACCATTCATCTAATTGCCATAATTGACACCTTTCTGTC
131 CCATTATCTTTTACTCAACAATCTTTAACCATTCATCTAACTGCCATAATTGACACCTTTCTGTC
* * ***
1676757 AAATGCGCAGCTAGGCCATTAATATTTTACTCAACA
196 AAATGCACAGCTAGGCCATCAATATGGCACTCAACA
* * * * * * * * * * *
1676793 GTC-TTTAACCGTTCATCTAACTGGCA--TAAT-TGACACA--CACAACTAGGTCATTAATATTT
1 TTCATCTAACTG-ACA--TAATTGACACCT-TTCTGCCAAATGCACAACTAGGCCATTAATCTTT
* *
1676852 TACTCAACGGTCTTTAACCGTTCATCTAGCTGGCATAATTGACACTTTTCTGTCAAATGCACAGC
62 TACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGC
* *
1676917 TAGGCCATTAATCTTTTACTCAACAATCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
127 TAGGCCATT-ATCTTTTACTCAACAATCTTTAACCATTCATCTAACTGCCATAATTGACACCTTT
* * *
1676982 CTGTCAAATGCACAGTTAGGCC-TCAA-A-GGCACTTAGCA
191 CTGTCAAATGCACAGCTAGGCCATCAATATGGCACTCAACA
* * * *
1677020 TTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTAC
1 -TTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTAC
** * *
1677085 TCAACGGTCTTTAACTATTCATCTAACTGTCATAATTGACACCTTTCTGTCAAATGCACAGTTAG
65 TCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAG
1677150 GCC
130 GCC
1677153 TCAAAGGTAC
Statistics
Matches: 294, Mismatches: 54, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
226 7 0.02
227 7 0.02
228 10 0.03
229 96 0.33
230 157 0.53
231 9 0.03
232 1 0.00
233 7 0.02
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (231 bp):
TTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
CAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGG
CCATTATCTTTTACTCAACAATCTTTAACCATTCATCTAACTGCCATAATTGACACCTTTCTGTC
AAATGCACAGCTAGGCCATCAATATGGCACTCAACA
Found at i:1677189 original size:298 final size:294
Alignment explanation
Indices: 1676555--1677367 Score: 922
Period size: 298 Copynumber: 2.7 Consensus size: 294
1676545 TCAGCTGTCC
*
1676555 TTAACCGTTCATCTAATTGACATAATTGACACCTTTCTGCTAAATGTACAACTAGGCCATTAATC
1 TTAACCGTTCATCTAATTG-CATAATTGACACCTTTCTGC-AAATGCACAACTAGGCCATTAATC
* * *
1676620 TTTTACTCAACAGTTTTTAACCGTTCATCTAACTGGCATAATTGACACCTTCCTTTCAAATGCAC
64 TTTTACTCAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
* * * * * *
1676685 AGCTAGGCCATTATTTTTTACTCAACGGTC-TTTAACCA-TTCATCTAATTGCCATAATTGACAC
129 AGTTAGG-C-----------CTCAAAGG-CACTT-AGCATTTCATCTAACTGGCATAATTGACAC
* *
1676748 CTTTCTGT-CAAATGCGCAGCTAGGCCATTAATATTTTACTCAACAGTCTTTAACCGTTCATCTA
180 CTTTCT-TCCAAATGCACAGCTAGGCCATTAATATTTTACTCAACAGTCTTTAACCATTCATCTA
** *
1676812 ACTGGCATAATTGACACACACAACTAGGTCATTAATATTTTACTCAACGGTCT
244 ACTGGCATAATTGACACACACAACTA-GTCA-TAATAAGTTACTCAAAGGTCT
* * * *
1676865 TTAACCGTTCATCTAGCTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTAGGCCATTAATC
1 TTAACCGTTCATCTA-ATTGCATAATTGACACCTTTCTG-CAAATGCACAACTAGGCCATTAATC
*
1676930 TTTTACTCAACAATCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
64 TTTTACTCAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
1676995 AGTTAGGCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATG
129 AGTTAGGCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATG
* * * * *
1677060 CACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACTATTCATCTAACTGTCATAATTGAC
194 CACAGCTAGGCCATTAATATTTTACTCAACAGTCTTTAACCATTCATCTAACTGGCATAATTGAC
***
1677125 AC-C-TTTCT-GTCA-AATGCACAGTTAGGCCTCAAAGGTAC-
259 ACACACAACTAGTCATAAT--A-AGTTA---CTCAAAGGT-CT
* * * *
1677163 TTAGCCTTTCCTCTAATTAGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATC
1 TTAACCGTTCATCTAATT-GCATAATTGACACCTTTCTG-CAAATGCACAACTAGGCCATTAATC
* * * * * *
1677228 TATTACTCAACGGTGTTTAGCAGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCAC
64 TTTTACTCAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
* * * *
1677293 AATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACAGGCATAATTGACACCTTTCTGCCAAATG
129 AGTTAGGCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATG
1677358 CACAGCTAGG
194 CACAGCTAGG
1677368 ACGTGTATAT
Statistics
Matches: 442, Mismatches: 48, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
292 3 0.01
294 5 0.01
295 3 0.01
296 2 0.00
297 7 0.02
298 295 0.67
299 1 0.00
309 1 0.00
310 122 0.28
311 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (294 bp):
TTAACCGTTCATCTAATTGCATAATTGACACCTTTCTGCAAATGCACAACTAGGCCATTAATCTT
TTACTCAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAG
TTAGGCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCA
CAGCTAGGCCATTAATATTTTACTCAACAGTCTTTAACCATTCATCTAACTGGCATAATTGACAC
ACACAACTAGTCATAATAAGTTACTCAAAGGTCT
Found at i:1677277 original size:149 final size:147
Alignment explanation
Indices: 1676723--1677367 Score: 766
Period size: 149 Copynumber: 4.3 Consensus size: 147
1676713 TCTTTAACCA
* * * * *
1676723 TTCATCTAATTGCCATAATTGACACCTTTCTGTCAAATGCGCAGCTAGGCCATTAATATTTTACT
1 TTCATCTAATAG-CATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* * *** *
1676788 CAACAGTCTTTAACCGTTCATCTAACTGGCATAATTGACACACACAACTAGGTCATTAAT--A-T
65 CAACGGTCTTTAACAGTTCATCTAACT-GCATAATTGACAC-C-TTTCT--GTCA--AATGCACA
* * * * *
1676850 TTTA---CTCAACGGTC-TTTAACCG
123 GTTAGGCCTCAAAGG-CACTTAGCCT
* * * * *
1676872 TTCATCTAGCTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTA-ATAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
** *
1676937 CAACAATCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGG
65 CAACGGTCTTTAACAGTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACAGTTAGG
*
1677002 CCTCAAAGGCACTTAGCAT
129 CCTCAAAGGCACTTAGCCT
* *
1677021 TTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTACT
1 TTCATCTAA-TAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
1677086 CAACGGTCTTTAACTA-TTCATCTAACTGTCATAATTGACACCTTTCTGTCAAATGCACAGTTAG
65 CAACGGTCTTTAAC-AGTTCATCTAACTG-CATAATTGACACCTTTCTGTCAAATGCACAGTTAG
*
1677150 GCCTCAAAGGTACTTAGCCT
128 GCCTCAAAGGCACTTAGCCT
* * *
1677170 TTCCTCTAATTAGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATCTATTACT
1 TTCATCTAA-TAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* * *
1677235 CAACGGTGTTTAGCAGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAATTAGG
65 CAACGGTCTTTAACAGTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACAGTTAGG
1677300 CCTCAAAGGCACTTAGCCT
129 CCTCAAAGGCACTTAGCCT
*
1677319 TTCATCTAACAGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGG
1 TTCATCTAATA-GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGG
1677368 ACGTGTATAT
Statistics
Matches: 443, Mismatches: 39, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
143 3 0.01
145 5 0.01
146 3 0.01
147 2 0.00
148 5 0.01
149 422 0.95
150 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (147 bp):
TTCATCTAATAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTC
AACGGTCTTTAACAGTTCATCTAACTGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
TCAAAGGCACTTAGCCT
Found at i:1677686 original size:55 final size:55
Alignment explanation
Indices: 1677572--1677825 Score: 311
Period size: 55 Copynumber: 4.6 Consensus size: 55
1677562 TTCCTATACG
* * * *
1677572 AAAATTAATACCCTTAGTATGTATTTCTTAG-TTTGCACACATAA-TGCCCATATG
1 AAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACA-AAGTGCCCATATC
* * *
1677626 GAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCATACATAA-TGCTCATATC
1 AAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACA-AAGTGCCCATATC
* * * *
1677681 AAAATTCATTCACTTAGTATGAATTTCTTATTTTTGCATACAAAGTGCCCATACC
1 AAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATATC
* *
1677736 AAAATTCATACACTTAGTTTGAATTTCTTATTTTTGCACACAAAGTG-CCATA-C
1 AAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATATC
*
1677789 TGAAATTCATACACTTAGTATGAATTTCTTAAGTTTT
1 -AAAATTCATACACTTAGTATGAATTTCTT-AGTTTT
1677826 CTTTTTTTTC
Statistics
Matches: 178, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 61 0.34
55 116 0.65
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (55 bp):
AAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATATC
Found at i:1677700 original size:109 final size:108
Alignment explanation
Indices: 1677567--1677824 Score: 315
Period size: 109 Copynumber: 2.4 Consensus size: 108
1677557 TATATTTCCT
* * * * ***
1677567 ATACGAAAATTAATACCCTTAGTATGTATTTCTTAGTTTGCACACATAA-TGCCCATATGGAAAT
1 ATACTAAAATTCATACACTTAGTATGAATTTCTTAGTTTGCACACA-AAGTGCCCATACCAAAAT
*
1677631 TCATACACTTAGTATGAATTTCTTAGTTTTGCATACATAA-TGCTC
65 TCATACACTTAGTATGAATTTCTTAGTTTTGCACACA-AAGTGC-C
* * *
1677676 ATA-TCAAAATTCATTCACTTAGTATGAATTTCTTATTTTTGCATACAAAGTGCCCATACCAAAA
1 ATACT-AAAATTCATACACTTAGTATGAATTTCTTA-GTTTGCACACAAAGTGCCCATACCAAAA
* *
1677740 TTCATACACTTAGTTTGAATTTCTTATTTTTGCACACAAAGTGCC
64 TTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCC
*
1677785 ATACTGAAATTCATACACTTAGTATGAATTTCTTAAGTTT
1 ATACTAAAATTCATACACTTAGTATGAATTTCTT-AGTTT
1677825 TCTTTTTTTT
Statistics
Matches: 127, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
109 67 0.53
110 60 0.47
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (108 bp):
ATACTAAAATTCATACACTTAGTATGAATTTCTTAGTTTGCACACAAAGTGCCCATACCAAAATT
CATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCC
Found at i:1682123 original size:49 final size:46
Alignment explanation
Indices: 1682015--1682134 Score: 141
Period size: 49 Copynumber: 2.5 Consensus size: 46
1682005 TTTTCATTTG
* * *
1682015 GACATCCTTTCATACCCATTATGTATTGTTTACATTTTTCCTTTAT
1 GACATCCTTTCATACCAATTATGCATTGTTTACATTTTTCCTATAT
* * * *
1682061 AACATCCATTCATATCAATTATGCATTGTTGTACATTTTATATCTATAT
1 GACATCCTTTCATACCAATTATGCATTGTT-TACATTTT-T-CCTATAT
*
1682110 GACATCCTTTCATACCACTTATGCA
1 GACATCCTTTCATACCAATTATGCA
1682135 CCGTTTATAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
46 25 0.42
47 8 0.13
48 1 0.02
49 26 0.43
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.44
Consensus pattern (46 bp):
GACATCCTTTCATACCAATTATGCATTGTTTACATTTTTCCTATAT
Found at i:1682296 original size:81 final size:80
Alignment explanation
Indices: 1682193--1682801 Score: 443
Period size: 81 Copynumber: 7.5 Consensus size: 80
1682183 ACACTTACAT
* * * * *
1682193 TTCATCTAACTTGCATGATTGACACTTTTCTGCCAAATGCACAGCTATGCCATTTATCTTTTACT
1 TTCATCTAAC-TGCATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
* * *
1682258 AAACGATCTTTAACCA
65 CAACGGTCTTTAACCG
* *
1682274 TTCATCTAACTGACATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAATATTTTACT
1 TTCATCTAACTG-CATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
* **
1682339 CAACGGTTTTACTCAATGGTCTTTAAC
65 CAACGGTCTT--T-AA----C----CG
* * *
1682366 CATTCATCTAATTGGCATAATTGACACATTTCTGTCAAATGCACATCTAGGCCATTAATCTTTTA
1 --TTCATCTAACT-GCATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTA
* *
1682431 CTCAATGGTCTTTAACTG
63 CTCAACGGTCTTTAACCG
* * * *
1682449 TTCATCTAACTCGCATAATTAACACTTTTCTGCGAAATGCACAACTAGGCCATTAATATTTTACT
1 TTCATCTAACT-GCATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
* *
1682514 CAATGGCCTTTAACCG
65 CAACGGTCTTTAACCG
* * * *
1682530 TTCATCTAATTGCATAATTGA-AGCCTTTCTGTCAAATGCACAACTAAGCCATTAATCTTTTACT
1 TTCATCTAACTGCATAATTGACA-CATTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
*
1682594 CAACAGTCTTTAACCG
65 CAACGGTCTTTAACCG
* * * ** * * ****
1682610 TTCACCCAACTGGCATAATTAACACATTTCTATCAAATGCACAATTAGGCC-TCAA--AGGCACT
1 TTCATCTAACT-GCATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
* * * *
1682672 -TA--GCCTTTCATC-
65 CAACGGTCTTTAACCG
* * * * * *
1682684 -T-AACT---TGCATAATTGACACCTTTCTGCCAATTGCACAACTAAGCCATTTATCATTTACTC
1 TTCATCTAACTGCATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACTC
* *
1682744 AACTGTCTTTAACTG
66 AACGGTCTTTAACCG
* * * *
1682759 TTCATCTAACTGGCATAATTAATACCTTTCTGTCAAATGCACA
1 TTCATCTAACT-GCATAATTGACACATTTCTGCCAAATGCACA
1682802 GTTAAGCCTC
Statistics
Matches: 418, Mismatches: 79, Indels: 62
0.75 0.14 0.11
Matches are distributed among these distances:
68 32 0.08
69 3 0.01
71 4 0.01
72 3 0.01
73 1 0.00
74 6 0.01
75 7 0.02
76 1 0.00
77 4 0.01
78 3 0.01
79 1 0.00
80 72 0.17
81 204 0.49
82 1 0.00
83 1 0.00
84 2 0.00
87 1 0.00
88 1 0.00
91 2 0.00
92 1 0.00
94 67 0.16
95 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (80 bp):
TTCATCTAACTGCATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACTC
AACGGTCTTTAACCG
Found at i:1682416 original size:94 final size:91
Alignment explanation
Indices: 1682250--1682516 Score: 304
Period size: 94 Copynumber: 3.0 Consensus size: 91
1682240 TGCCATTTAT
* * * *
1682250 CTTTTACTAAACGATCTTTAACCATTCATCTAACTGACATAATTGACACATTTCTGCCAAATGCA
1 CTTTTACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACACATTTCTG-CAAATGCA
*
1682315 CAGCTAGGCCATTAATATTTTACTCAA
65 CAACTAGGCCATTAATATTTTACTCAA
*
1682342 CGGTTTTACTCAATGGTCTTTAACCATTCATCTAATTGGCATAATTGACACATTTCTGTCAAATG
1 C--TTTTACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACACATTTCTG-CAAATG
*
1682407 CACATCTAGGCCA-T--TA----A-T---
63 CACAACTAGGCCATTAATATTTTACTCAA
** * * *
1682425 CTTTTACTCAATGGTCTTTAACTGTTCATCTAACTCGCATAATTAACACTTTTCTGCGAAATGCA
1 CTTTTACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACACATTTCTGC-AAATGCA
1682490 CAACTAGGCCATTAATATTTTACTCAA
65 CAACTAGGCCATTAATATTTTACTCAA
1682517 TGGCCTTTAA
Statistics
Matches: 147, Mismatches: 14, Indels: 28
0.78 0.07 0.15
Matches are distributed among these distances:
80 1 0.01
81 66 0.45
82 1 0.01
83 1 0.01
84 2 0.01
86 1 0.01
87 1 0.01
88 1 0.01
89 1 0.01
91 2 0.01
92 1 0.01
93 1 0.01
94 68 0.46
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (91 bp):
CTTTTACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACACATTTCTGCAAATGCAC
AACTAGGCCATTAATATTTTACTCAA
Found at i:1682489 original size:175 final size:160
Alignment explanation
Indices: 1682345--1682801 Score: 494
Period size: 149 Copynumber: 2.9 Consensus size: 160
1682335 TACTCAACGG
*
1682345 TTTTACTCAATGGTCTTTAACCATTCATCTAATTGGCATAATTGACACATTTCTGTCAAATGCAC
1 TTTTACTCAATGGCCTTTAACCATTCATCTAATT-GCATAATTGACACATTTCTGTCAAATGCAC
* * * * *
1682410 ATCTAGGCCATTAATCTTTTACTCAATGGTCTTTAACTGTTCATCTAACTCGCATAATTAACACT
65 AACTAAGCCATTAATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACT-GCATAATTAACACA
*
1682475 TTTCTGCGAAATGCACAACTAGGCCATTAATA
129 TTTCTGCCAAATGCACAACTAGGCCATTAATA
* *
1682507 TTTTACTCAATGGCCTTTAACCGTTCATCTAATTGCATAATTGA-AGCCTTTCTGTCAAATGCAC
1 TTTTACTCAATGGCCTTTAACCATTCATCTAATTGCATAATTGACA-CATTTCTGTCAAATGCAC
* * *
1682571 AACTAAGCCATTAATCTTTTACTCAACAGTCTTTAACCGTTCACCCAACTGGCATAATTAACACA
65 AACTAAGCCATTAATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACT-GCATAATTAACACA
** *
1682636 TTTCTATCAAATGCACAATTAGG-C-------
129 TTTCTGCCAAATGCACAACTAGGCCATTAATA
* * * * * *
1682660 -----CTCAAAGGCAC-TTAGCCTTTCATCTAACTTGCATAATTGACACCTTTCTGCCAATTGCA
1 TTTTACTCAATGGC-CTTTAACCATTCATCTAA-TTGCATAATTGACACATTTCTGTCAAATGCA
* * * * *
1682719 CAACTAAGCCATTTATCATTTACTCAACTGTCTTTAACTGTTCATCTAACTGGCATAATTAATAC
64 CAACTAAGCCATTAATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACT-GCATAATTAACAC
* *
1682784 CTTTCTGTCAAATGCACA
128 ATTTCTGCCAAATGCACA
1682802 GTTAAGCCTC
Statistics
Matches: 261, Mismatches: 30, Indels: 21
0.84 0.10 0.07
Matches are distributed among these distances:
148 22 0.08
149 102 0.39
150 1 0.00
160 2 0.01
161 102 0.39
162 32 0.12
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (160 bp):
TTTTACTCAATGGCCTTTAACCATTCATCTAATTGCATAATTGACACATTTCTGTCAAATGCACA
ACTAAGCCATTAATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGCATAATTAACACATT
TCTGCCAAATGCACAACTAGGCCATTAATA
Found at i:1682719 original size:68 final size:68
Alignment explanation
Indices: 1682617--1682870 Score: 211
Period size: 68 Copynumber: 3.5 Consensus size: 68
1682607 CCGTTCACCC
* * *
1682617 AACTGGCATAATTAACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAGCCTTTCA
1 AACTGGCATAATTAACACCTTTCTGTCAAATGCACAATTAAGCCTCAAAGGCACTTAGCCTTTCA
1682682 TCT
66 TCT
* * * * * * **
1682685 AACTTGCATAATTGACACCTTTCTGCCAATTGCACAACTAAGCCATTTATCATTTACTCAACTGT
1 AACTGGCATAATTAACACCTTTCTGTCAAATGCACAATTAAGCC-----TCA--AAGGC-A----
***
1682750 CTTTAACTGTTCATCT
54 CTTAGCCT-TTCATCT
* *
1682766 AACTGGCATAATTAATACCTTTCTGTCAAATGCACAGTTAAGCCTCAAAGGCACTTAGCCTTTCA
1 AACTGGCATAATTAACACCTTTCTGTCAAATGCACAATTAAGCCTCAAAGGCACTTAGCCTTTCA
1682831 TCT
66 TCT
* * *
1682834 AACTGGCATAATTGACACCTTTTTTTCCAAATGCACA
1 AACTGGCATAATTAACACCTTTCTGT-CAAATGCACA
1682871 GCTAGACCAT
Statistics
Matches: 141, Mismatches: 31, Indels: 27
0.71 0.16 0.14
Matches are distributed among these distances:
68 65 0.46
69 15 0.11
73 4 0.03
74 2 0.01
75 2 0.01
76 4 0.03
80 5 0.04
81 44 0.31
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (68 bp):
AACTGGCATAATTAACACCTTTCTGTCAAATGCACAATTAAGCCTCAAAGGCACTTAGCCTTTCA
TCT
Found at i:1682811 original size:149 final size:149
Alignment explanation
Indices: 1682530--1683190 Score: 896
Period size: 149 Copynumber: 4.4 Consensus size: 149
1682520 CCTTTAACCG
* * * *
1682530 TTCATCTAA-TTGCATAATTGA-AGCCTTTCTGTCAAATGCACAACTAAGCCATTAATCTTTTAC
1 TTCATCTAACTGGCATAATTGACA-CCTTTCTGCCAAATGCACAGCTAAGCCATTTATCTTTTAC
* * * *
1682593 TCAACAGTCTTTAACCGTTCACCCAACTGGCATAATTAACACATTTCTATCAAATGCACAATTAG
65 TCAACTGTCTTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGCACAATTAG
1682658 GCCTCAAAGGCACTTAGCCT
130 GCCTCAAAGGCACTTAGCCT
* * * *
1682678 TTCATCTAACTTGCATAATTGACACCTTTCTGCCAATTGCACAACTAAGCCATTTATCATTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAAGCCATTTATCTTTTACT
* * * * *
1682743 CAACTGTCTTTAACTGTTCATCTAACTGGCATAATTAATACCTTTCTGTCAAATGCACAGTTAAG
66 CAACTGTCTTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGCACAATTAGG
1682808 CCTCAAAGGCACTTAGCCT
131 CCTCAAAGGCACTTAGCCT
* *
1682827 TTCATCTAACTGGCATAATTGACACCTTTTTTTCCAAATGCACAGCT-AGACCATTTATCTTTTA
1 TTCATCTAACTGGCATAATTGACACC-TTTCTGCCAAATGCACAGCTAAG-CCATTTATCTTTTA
* * *
1682891 CTCAACTGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAATTA
64 CTCAACTGTCTTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGCACAATTA
*
1682956 GGCCTCAAAGGCACTTAGTCT
129 GGCCTCAAAGGCACTTAGCCT
* * * *
1682977 TTCATCTAACTAGCATAATTGACACCTTTCTACTAAATGCACAGCTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAAGCCATTTATCTTTTACT
* * ** * * * * *
1683042 TAACGGTCTTTAACAATTCATCTAACTGGCACAATTGACACCATTCTATCAAATGCATAGTTAGG
66 CAACTGTCTTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGCACAATTAGG
*
1683107 CCTCAAAGGCACTTAGTCT
131 CCTCAAAGGCACTTAGCCT
* * * * *
1683126 TTCATCTAACTGGTATGATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATGTATTTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAAGCCATTTATCTTTTACT
1683191 TAGACCAGTT
Statistics
Matches: 460, Mismatches: 48, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
148 9 0.02
149 316 0.69
150 135 0.29
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (149 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAAGCCATTTATCTTTTACT
CAACTGTCTTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGCACAATTAGG
CCTCAAAGGCACTTAGCCT
Found at i:1682960 original size:299 final size:299
Alignment explanation
Indices: 1682530--1683190 Score: 918
Period size: 299 Copynumber: 2.2 Consensus size: 299
1682520 CCTTTAACCG
* * * * *
1682530 TTCATCTAA-TTGCATAATTGA-AGCCTTTCTGT-CAAATGCACAACTA-AGCCATTAATCTTTT
1 TTCATCTAACTGGCATAATTGACA-CCTTTTTTTCCAAATGCACAGCTAGA-CCATTTATCTTTT
*
1682591 ACTCAACAGTCTTTAACCGTTCACCCAACTGGCATAATTAACACATTTCTATCAAATGCACAATT
64 ACTCAACAGTCTTTAACCGTTCACCCAACTGGCATAATTAACACATTTATATCAAATGCACAATT
* * *
1682656 AGGCCTCAAAGGCACTTAGCCTTTCATCTAACTTGCATAATTGACACCTTTCTGCCAATTGCACA
129 AGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGCACA
* ** * * *
1682721 ACTAAGCCATTTATCATTTACTCAACTGTCTTTAACTGTTCATCTAACTGGCATAATTAATACCT
194 ACTAAGCCATTTATCATTTACTCAACGGTCTTTAACAATTCATCTAACTGGCACAATTAACACCA
*
1682786 TTCTGTCAAATGCACAGTTAAGCCTCAAAGGCACTTAGCCT
259 TTCTATCAAATGCACAGTTAAGCCTCAAAGGCACTTAGCCT
1682827 TTCATCTAACTGGCATAATTGACACCTTTTTTTCCAAATGCACAGCTAGACCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTTTTTCCAAATGCACAGCTAGACCATTTATCTTTTAC
* * * * * *
1682892 TCAACTGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAATTAG
66 TCAACAGTCTTTAACCGTTCACCCAACTGGCATAATTAACACATTTATATCAAATGCACAATTAG
* * *
1682957 GCCTCAAAGGCACTTAGTCTTTCATCTAACTAGCATAATTGACACCTTTCTACTAAATGCACAGC
131 GCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGCACAAC
* * * *
1683022 TAGGCCATTTATCTTTTACTTAACGGTCTTTAACAATTCATCTAACTGGCACAATTGACACCATT
196 TAAGCCATTTATCATTTACTCAACGGTCTTTAACAATTCATCTAACTGGCACAATTAACACCATT
* * *
1683087 CTATCAAATGCATAGTTAGGCCTCAAAGGCACTTAGTCT
261 CTATCAAATGCACAGTTAAGCCTCAAAGGCACTTAGCCT
* * * * * * *
1683126 TTCATCTAACTGGTATGATTGACACC-TTTCTGCCAAATGCACAGCTAGGCCATGTATTTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTTTTTCCAAATGCACAGCTAGACCATTTATCTTTTAC
1683190 T
66 T
1683191 TAGACCAGTT
Statistics
Matches: 321, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
297 9 0.03
298 52 0.16
299 259 0.81
300 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (299 bp):
TTCATCTAACTGGCATAATTGACACCTTTTTTTCCAAATGCACAGCTAGACCATTTATCTTTTAC
TCAACAGTCTTTAACCGTTCACCCAACTGGCATAATTAACACATTTATATCAAATGCACAATTAG
GCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGCACAAC
TAAGCCATTTATCATTTACTCAACGGTCTTTAACAATTCATCTAACTGGCACAATTAACACCATT
CTATCAAATGCACAGTTAAGCCTCAAAGGCACTTAGCCT
Found at i:1683015 original size:68 final size:69
Alignment explanation
Indices: 1682909--1683176 Score: 229
Period size: 68 Copynumber: 3.8 Consensus size: 69
1682899 TCTTTAACCG
* * *
1682909 TTCATCTAACTGGCATAATTGACACCTTTAT-GTCAAATGCACAATTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAATTGACACCTTTCTACTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
1682973 GTCT
66 GTCT
* * * *****
1682977 TTCATCTAACTAGCATAATTGACACCTTTCTACT-AAATGCACAGCTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTCTACTCAAATGCACAGTTAGGCC--TCA-AAGGCAC
1683041 TTAACGGTCTTT
63 TT-A--GTC--T
* * *
1683053 AACAATTCATCTAACTGGCACAATTGACACCATTCTA-TCAAATGCATAGTTAGGCCTCAAAGGC
1 -----TTCATCTAACTGGCATAATTGACACCTTTCTACTCAAATGCACAGTTAGGCCTCAAAGGC
1683117 ACTTAGTCT
61 ACTTAGTCT
* * * *
1683126 TTCATCTAACTGGTATGATTGACACCTTTCTGC-CAAATGCACAGCTAGGCC
1 TTCATCTAACTGGCATAATTGACACCTTTCTACTCAAATGCACAGTTAGGCC
1683177 ATGTATTTTT
Statistics
Matches: 155, Mismatches: 29, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
68 87 0.56
69 1 0.01
70 2 0.01
71 4 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 3 0.02
76 1 0.01
77 1 0.01
78 4 0.03
79 2 0.01
80 1 0.01
81 44 0.28
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (69 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTACTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
GTCT
Found at i:1683507 original size:55 final size:55
Alignment explanation
Indices: 1683390--1683647 Score: 322
Period size: 55 Copynumber: 4.7 Consensus size: 55
1683380 TATTTCCTAT
* * * * * * *
1683390 ACGAAAATCAATACCCTTAGTATGTATTTCTT-GGTTTGCATATATAGTGCCCAT-
1 ACGAAATTC-ATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATA
* *
1683444 ACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTACCCATA
1 ACG-AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATA
*
1683500 ACGAAATTCATACACTTAGTATGAATTTCTTATTTTTGCACACAAAGTGCCCATA
1 ACGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATA
* * * *
1683555 CCGAAATTCATACACTTAGTATGAAATTCTTATTTTTACACACAAAGTGCCCATA
1 ACGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATA
* * *
1683610 CCAAAATTCATACACTTGGTATGAATTTCTTAAGTTTT
1 ACGAAATTCATACACTTAGTATGAATTTCTT-AGTTTT
1683648 CTTTTTTCCA
Statistics
Matches: 183, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
54 23 0.13
55 152 0.83
56 8 0.04
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (55 bp):
ACGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATA
Found at i:1686732 original size:15 final size:15
Alignment explanation
Indices: 1686714--1686776 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
1686704 ATATATCTAG
* *
1686714 ATAACATATATCCGA
1 ATAACACATATCCAA
*
1686729 ATAATACATATCCAA
1 ATAACACATATCCAA
1686744 ATAACACA-A-CCAA
1 ATAACACATATCCAA
*
1686757 ATAACTACATATACAA
1 ATAAC-ACATATCCAA
1686773 ATAA
1 ATAA
1686777 TCCGAATGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.22
14 4 0.10
15 20 0.50
16 7 0.17
ACGTcount: A:0.56, C:0.21, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAACACATATCCAA
Found at i:1693300 original size:12 final size:12
Alignment explanation
Indices: 1693279--1693319 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
1693269 TACAAATACT
1693279 TAACTCTTCACC
1 TAACTCTTCACC
*
1693291 TAATTCTTCACC
1 TAACTCTTCACC
1693303 TAACTCTTCACC
1 TAACTCTTCACC
1693315 TAACT
1 TAACT
1693320 AAATTGATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (12 bp):
TAACTCTTCACC
Found at i:1697970 original size:11 final size:12
Alignment explanation
Indices: 1697954--1697984 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1697944 ATATACAAAT
1697954 ACCTAACTC-TC
1 ACCTAACTCTTC
1697965 ACCTAACTCTTC
1 ACCTAACTCTTC
1697977 ACCTAACT
1 ACCTAACT
1697985 AAATTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:1699631 original size:2 final size:2
Alignment explanation
Indices: 1699624--1699656 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1699614 ATAGTTATTA
1699624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1699657 TCAATTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1699868 original size:20 final size:20
Alignment explanation
Indices: 1699840--1699877 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1699830 TAAGGAGGAT
1699840 GAACAAAAATTATAGGGGGC
1 GAACAAAAATTATAGGGGGC
* *
1699860 GAACTAAAATTCTAGGGG
1 GAACAAAAATTATAGGGG
1699878 CAAAACATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (20 bp):
GAACAAAAATTATAGGGGGC
Found at i:1711444 original size:5 final size:5
Alignment explanation
Indices: 1711434--1711471 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
1711424 CACGGTCAAC
*
1711434 GGTCG GGTCG GGTCG GGTCG GGTC- AGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1711472 AGACCGGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.03, C:0.21, G:0.55, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1711464 original size:14 final size:14
Alignment explanation
Indices: 1711434--1711473 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1711424 CACGGTCAAC
*
1711434 GGTCGGGTCGGGTCG
1 GGTCGGGTC-AGTCG
1711449 GGTCGGGTCAGTCG
1 GGTCGGGTCAGTCG
1711463 GGTCGGGTCAG
1 GGTCGGGTCAG
1711474 ACCGGTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.05, C:0.20, G:0.55, T:0.20
Consensus pattern (14 bp):
GGTCGGGTCAGTCG
Found at i:1718666 original size:19 final size:19
Alignment explanation
Indices: 1718644--1718681 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1718634 TCGGGTCGGG
1718644 TCGGGTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
*
1718663 TCGGTTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
1718682 CCGGTCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (19 bp):
TCGGGTCAGACCGGTCAAA
Found at i:1718684 original size:28 final size:28
Alignment explanation
Indices: 1718647--1718714 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
1718637 GGTCGGGTCG
* *
1718647 GGTCAGACCGGTC-AAATCGGTTCAGACC
1 GGTCAAACCGGTCGAAATCGG-TCAAACC
1718675 GGTCAAACCGGTCGAAATCGGTCAAACC
1 GGTCAAACCGGTCGAAATCGGTCAAACC
*
1718703 GATCAGAACCGG
1 GGTCA-AACCGG
1718715 CGTCCAGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.63
29 13 0.37
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.15
Consensus pattern (28 bp):
GGTCAAACCGGTCGAAATCGGTCAAACC
Found at i:1718686 original size:19 final size:19
Alignment explanation
Indices: 1718649--1718686 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1718639 TCGGGTCGGG
*
1718649 TCAGACCGGTCAAATCGGT
1 TCAGACCGGTCAAACCGGT
1718668 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1718687 CGAAATCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1718696 original size:10 final size:9
Alignment explanation
Indices: 1718647--1718714 Score: 64
Period size: 9 Copynumber: 7.2 Consensus size: 9
1718637 GGTCGGGTCG
*
1718647 GGTCAGACC
1 GGTCAAACC
*
1718656 GGTCAAATC
1 GGTCAAACC
*
1718665 GGTTCAGACC
1 GG-TCAAACC
1718675 GGTCAAACC
1 GGTCAAACC
*
1718684 GGTCGAAATC
1 GGTC-AAACC
1718694 GGTCAAACC
1 GGTCAAACC
*
1718703 GATCAGAACC
1 GGTCA-AACC
1718713 GG
1 GG
1718715 CGTCCAGCCC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
9 27 0.57
10 20 0.43
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1722698 original size:16 final size:17
Alignment explanation
Indices: 1722674--1722708 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1722664 GTAAAAAAAA
1722674 TTATAA-TTTTTTTATT
1 TTATAATTTTTTTTATT
*
1722690 TTATGATTTTTTTTATT
1 TTATAATTTTTTTTATT
1722707 TT
1 TT
1722709 TTGTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (17 bp):
TTATAATTTTTTTTATT
Found at i:1727218 original size:31 final size:31
Alignment explanation
Indices: 1727180--1727240 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1727170 CCGAAGGACC
*
1727180 AGTCCATA-GATCCCGAAGAACCTAGGTAAAT
1 AGTCCATATG-TCCCGAAGAACATAGGTAAAT
1727211 AGTCCATATGTCCCGAAGAACATAGGTAAA
1 AGTCCATATGTCCCGAAGAACATAGGTAAA
1727241 CAATATCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (31 bp):
AGTCCATATGTCCCGAAGAACATAGGTAAAT
Found at i:1727466 original size:19 final size:19
Alignment explanation
Indices: 1727427--1727466 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1727417 TATTAATGGG
** *
1727427 ATGCATCGATGCATTACTT
1 ATGCATCGATGCACGAATT
1727446 ATGCATCGATGCACGAATT
1 ATGCATCGATGCACGAATT
1727465 AT
1 AT
1727467 ATTCGATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (19 bp):
ATGCATCGATGCACGAATT
Found at i:1727496 original size:64 final size:64
Alignment explanation
Indices: 1727382--1727503 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
1727372 TATTACTGGG
* * *
1727382 ATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGGATGCATCGATGCATTACTT
1 ATGCATCGATGCACGAATTACATTCGATGTTTCATTATTAAAGAGATGCATCGATGCATTACTT
* *
1727446 ATGCATCGATGCACGAATTATATTCGATGTATTTATT-TTAAA-AGAGTGCATCGATGCA
1 ATGCATCGATGCACGAATTACATTCGATGT-TTCATTATTAAAGAGA-TGCATCGATGCA
1727504 CTTCCTGTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.04
64 44 0.86
65 5 0.10
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACGAATTACATTCGATGTTTCATTATTAAAGAGATGCATCGATGCATTACTT
Found at i:1727515 original size:64 final size:64
Alignment explanation
Indices: 1727382--1727519 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
1727372 TATTACTGGG
* * * *
1727382 ATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGGATGCATCGATGCATTACTT
1 ATGCATCGATGCACGAATTACATTCGATGTTTCATTATTAAAGAGATGCATCGATGCATTACCT
* *
1727446 ATGCATCGATGCACGAATTATATTCGATGTATTTATT-TTAAA-AGAGTGCATCGATGCACTT-C
1 ATGCATCGATGCACGAATTACATTCGATGT-TTCATTATTAAAGAGA-TGCATCGATGCA-TTAC
1727508 CT
63 CT
*
1727510 GTGCATCGAT
1 ATGCATCGAT
1727520 ACACCTTCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 2 0.03
64 55 0.86
65 7 0.11
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACGAATTACATTCGATGTTTCATTATTAAAGAGATGCATCGATGCATTACCT
Found at i:1728487 original size:17 final size:18
Alignment explanation
Indices: 1728465--1728499 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1728455 AGAATACCAA
1728465 AAAT-GGTATCGGTACTG
1 AAATGGGTATCGGTACTG
1728482 AAATGGGTATCGGTACTG
1 AAATGGGTATCGGTACTG
1728500 TGGGTAGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (18 bp):
AAATGGGTATCGGTACTG
Found at i:1728924 original size:28 final size:28
Alignment explanation
Indices: 1728893--1728949 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1728883 TGTGATATAC
* * *
1728893 TATGTAAATATTTTCTACGTGAAAATGT
1 TATGTAAATATGTGCTAAGTGAAAATGT
* *
1728921 TATGTGAATATGTGCTAAGTGAATATGT
1 TATGTAAATATGTGCTAAGTGAAAATGT
1728949 T
1 T
1728950 CTATGGAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.42
Consensus pattern (28 bp):
TATGTAAATATGTGCTAAGTGAAAATGT
Found at i:1729152 original size:23 final size:23
Alignment explanation
Indices: 1729126--1729235 Score: 89
Period size: 23 Copynumber: 4.7 Consensus size: 23
1729116 GGTTCTAAGC
1729126 GGTCCTTCGGGACAAATCTATGT
1 GGTCCTTCGGGACAAATCTATGT
* * * * **
1729149 GGTCATTCGGAAGAATTCTACAT
1 GGTCCTTCGGGACAAATCTATGT
* * *
1729172 GGTCTTTCGGGATAAATTCTATGC
1 GGTCCTTCGGGACAAA-TCTATGT
1729196 GGTCCTTCGGGGA-AAATCTATGT
1 GGTCCTTC-GGGACAAATCTATGT
*
1729219 GG-CACTTCGGTACAAAT
1 GGTC-CTTCGGGACAAAT
1729236 TCTACGCGGT
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
22 4 0.06
23 45 0.67
24 14 0.21
25 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (23 bp):
GGTCCTTCGGGACAAATCTATGT
Found at i:1731831 original size:20 final size:19
Alignment explanation
Indices: 1731808--1731846 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1731798 CTTAATTCCA
1731808 TTTTCACCATCTTCTTCATC
1 TTTTCACCATCTT-TTCATC
* *
1731828 TTTTTATCATCTTTTCATC
1 TTTTCACCATCTTTTCATC
1731847 CAAAATTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTCACCATCTTTTCATC
Found at i:1732198 original size:21 final size:21
Alignment explanation
Indices: 1732174--1732216 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1732164 TCTCTATCAA
1732174 TATTGAGAAATAGAACCAATG
1 TATTGAGAAATAGAACCAATG
* **
1732195 TATTGAGTAATTTAACCAATG
1 TATTGAGAAATAGAACCAATG
1732216 T
1 T
1732217 GGTGATGGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (21 bp):
TATTGAGAAATAGAACCAATG
Found at i:1743354 original size:14 final size:15
Alignment explanation
Indices: 1743335--1743363 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1743325 ATATGCTTAT
1743335 TTTATCAG-ATATTC
1 TTTATCAGAATATTC
1743349 TTTATCAGAATATTC
1 TTTATCAGAATATTC
1743364 ATGAGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (15 bp):
TTTATCAGAATATTC
Found at i:1745529 original size:65 final size:64
Alignment explanation
Indices: 1745409--1745639 Score: 195
Period size: 65 Copynumber: 3.6 Consensus size: 64
1745399 TTTTTCATAG
* * *
1745409 TGATGCACCGATGCACCA-ATTCATGCATCGATGCAC-CATGAAATAAATTTG-AACATCGAATG
1 TGATGCATCGATGCA-CATATT-ATGCATCGATGCACTCA-G-GAT-ATTTTGAAACATCGAATG
1745471 CATT
61 CATT
* *
1745475 TCATGCATCGATGCACATATTATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACATATTATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
1745539 T
64 T
* * *** * * * *
1745540 TGATGTATCAATGCACCA-GCCATACATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CATATTATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
* *
1745604 TGATGCATTGATGCAC-TCTTAGTGCATCGATGCACT
1 TGATGCATCGATGCACATATTA-TGCATCGATGCACT
1745640 AAGGGTCCAA
Statistics
Matches: 133, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
62 2 0.02
63 4 0.03
64 42 0.32
65 63 0.47
66 22 0.17
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (64 bp):
TGATGCATCGATGCACATATTATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:1745619 original size:17 final size:19
Alignment explanation
Indices: 1745591--1745639 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1745581 TATTTTGAAA
1745591 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
* *
1745609 CATTGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
1745628 CATCGATGCACT
1 CATCGATGCACT
1745640 AAGGGTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1748732 original size:2 final size:2
Alignment explanation
Indices: 1748720--1748778 Score: 68
Period size: 2 Copynumber: 30.0 Consensus size: 2
1748710 TTAATACATC
* *
1748720 TA TA CA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1748761 TGA TA TA -A GA TA TA TA TA
1 T-A TA TA TA TA TA TA TA TA
1748779 ATAAAAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1752969 original size:23 final size:23
Alignment explanation
Indices: 1752894--1752974 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
1752884 ACACCTAACA
*
1752894 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
*
1752916 GTGCATCGAT--ACACCATGAA-
1 GTGCATCGATGCACACCTTGAAT
* * *
1752936 GTTTCACCGATGCACGCCTTGAAT
1 G-TGCATCGATGCACACCTTGAAT
1752960 GTGCATCGATGCACA
1 GTGCATCGATGCACA
1752975 AGGTCATGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
20 2 0.04
21 13 0.29
22 10 0.22
23 19 0.42
24 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Done.