Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 78 of 135
Found at i:23762657 original size:29 final size:30
Alignment explanation
Indices: 23762601--23762702 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
23762591 CAACAAATAA
* ** *
23762601 CCACAAAAGCATTTATACATCATTAGATAG
1 CCACAAAGGCATCCATACATCATAAGATAG
*
23762631 CCACAAAGGCATCCACT-TATC-TAAGATAG
1 CCACAAAGGCATCCA-TACATCATAAGATAG
* * *
23762660 TCACAAAGGCTTCCATACATCATTAGATAG
1 CCACAAAGGCATCCATACATCATAAGATAG
23762690 CCACAAAGGCATC
1 CCACAAAGGCATC
23762703 AACCTGCATT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.02
29 23 0.40
30 33 0.57
31 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (30 bp):
CCACAAAGGCATCCATACATCATAAGATAG
Found at i:23762968 original size:30 final size:30
Alignment explanation
Indices: 23762933--23762999 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
23762923 AAAAAGAGCT
* * *
23762933 CACATATAATAGAATAGCCACAAATTCTTC
1 CACATATAATAGAACAACCACAAAGTCTTC
*
23762963 CACATATAATAGAACAACCATAAAGTCTTC
1 CACATATAATAGAACAACCACAAAGTCTTC
23762993 CACATAT
1 CACATAT
23763000 CGGTAAACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (30 bp):
CACATATAATAGAACAACCACAAAGTCTTC
Found at i:23765312 original size:15 final size:16
Alignment explanation
Indices: 23765273--23765312 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
23765263 TTTTCTGCTT
23765273 TTCTCTTTTTCTTTGC
1 TTCTCTTTTTCTTTGC
23765289 TT-TCTTTTTC-TT-C
1 TTCTCTTTTTCTTTGC
23765302 TTCTCTATTTT
1 TTCTCT-TTTT
23765313 TATATGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 5 0.23
15 12 0.55
16 2 0.09
ACGTcount: A:0.03, C:0.23, G:0.03, T:0.72
Consensus pattern (16 bp):
TTCTCTTTTTCTTTGC
Found at i:23765312 original size:16 final size:16
Alignment explanation
Indices: 23765262--23765313 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
23765252 ATATATATTT
* *
23765262 TTTTTCTGCTTTTCTC
1 TTTTTCTTCTTCTCTC
* *
23765278 TTTTTCTT-TGCTTTC
1 TTTTTCTTCTTCTCTC
*
23765293 TTTTTCTTCTTCTCTA
1 TTTTTCTTCTTCTCTC
23765309 TTTTT
1 TTTTT
23765314 ATATGTGATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTTTCTTCTTCTCTC
Found at i:23765906 original size:17 final size:17
Alignment explanation
Indices: 23765886--23765924 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
23765876 ACTACAACGC
*
23765886 AAATG-AACTAACAAGTA
1 AAATGTAAC-AACAACTA
23765903 AAATGTAACAACAACTA
1 AAATGTAACAACAACTA
23765920 AAATG
1 AAATG
23765925 CAATGACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.59, C:0.13, G:0.10, T:0.18
Consensus pattern (17 bp):
AAATGTAACAACAACTA
Found at i:23781731 original size:27 final size:27
Alignment explanation
Indices: 23781698--23781762 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
23781688 AAGTCAACGA
23781698 TCAAAGTCAA-A-ATCAATGGTCAATGGG
1 TCAAAGTCAACAGATC-A-GGTCAATGGG
* *
23781725 TTAAAGTCAACAGGTCAGGTCAATGGG
1 TCAAAGTCAACAGATCAGGTCAATGGG
23781752 TCAAAGTCAAC
1 TCAAAGTCAAC
23781763 GGGTCGATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 29 0.88
28 2 0.06
29 2 0.06
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (27 bp):
TCAAAGTCAACAGATCAGGTCAATGGG
Found at i:23781766 original size:14 final size:14
Alignment explanation
Indices: 23781716--23781767 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
23781706 AAAATCAATG
* *
23781716 GTCAATGGGTTAAA
1 GTCAACGGGTCAAA
* *
23781730 GTCAACAGGTC-AG
1 GTCAACGGGTCAAA
*
23781743 GTCAATGGGTCAAA
1 GTCAACGGGTCAAA
23781757 GTCAACGGGTC
1 GTCAACGGGTC
23781768 GATCAACGAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (14 bp):
GTCAACGGGTCAAA
Found at i:23781767 original size:27 final size:27
Alignment explanation
Indices: 23781715--23781767 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
23781705 CAAAATCAAT
*
23781715 GGTCAATGGGTTAAAGTCAACAGGTCA
1 GGTCAATGGGTCAAAGTCAACAGGTCA
*
23781742 GGTCAATGGGTCAAAGTCAACGGGTC
1 GGTCAATGGGTCAAAGTCAACAGGTC
23781768 GATCAACGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (27 bp):
GGTCAATGGGTCAAAGTCAACAGGTCA
Found at i:23783773 original size:15 final size:15
Alignment explanation
Indices: 23783755--23783783 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23783745 CCCACAAGTT
23783755 TTATTATTATTATAA
1 TTATTATTATTATAA
23783770 TTATTATTATTATA
1 TTATTATTATTATA
23783784 TTTTTTCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATTATTATAA
Found at i:23803671 original size:81 final size:82
Alignment explanation
Indices: 23803533--23803753 Score: 257
Period size: 81 Copynumber: 2.7 Consensus size: 82
23803523 TAACCAGTAT
* * * * * * *
23803533 ACGATGGTGCTCACACAAGCTGTTGAGAATCTACAACATATGTCGGACCTCAACCATCGATACGG
1 ACGATGCTGCTCACACAAGCTGTTAAGAATCTACAACATATGTAGGATCTTAGCCATCGAGACGG
23803598 TCCAT-TTTATCCACTC
66 TCCATATTTATCCACTC
* * * *
23803614 ACGATGCTACTCACACAAGCTGTCAAGAATCCACAACATATGTAGGATCTTAGCCATC-AGAGGG
1 ACGATGCTGCTCACACAAGCTGTTAAGAATCTACAACATATGTAGGATCTTAGCCATCGAGACGG
23803678 TCCATATTTATCCACTC
66 TCCATATTTATCCACTC
* * ** * * * *
23803695 ATGATTCTGCTCACTTAAGTTGTTAAGAATCTGCAACTTATGCAGGATCTTAGCCATCG
1 ACGATGCTGCTCACACAAGCTGTTAAGAATCTACAACATATGTAGGATCTTAGCCATCG
23803754 GAGAGTCCTT
Statistics
Matches: 116, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
80 9 0.08
81 107 0.92
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (82 bp):
ACGATGCTGCTCACACAAGCTGTTAAGAATCTACAACATATGTAGGATCTTAGCCATCGAGACGG
TCCATATTTATCCACTC
Found at i:23808343 original size:81 final size:81
Alignment explanation
Indices: 23808135--23808351 Score: 215
Period size: 81 Copynumber: 2.7 Consensus size: 81
23808125 AACGTTATAA
* * * * * * *
23808135 GATGCTGCTCACACAAGCTATTGAGAATCCGCAACATATGTCA-GACCTCAGCCATCGATACGGT
1 GATGCTACTCACACAAGCTGTTAAGAATCCGCAACTTATGT-AGGATCTTAGCCATCGAAACGGT
*
23808199 CCATTTTATCCACTCAT
65 CCATTTTATCCACTCAC
* * * ** *
23808216 GATGCTACTCACACAAGCTGTCAATAATCTGCAA-TATATACAGGATCTTAGCCATC-AAAGGGT
1 GATGCTACTCACACAAGCTGTTAAGAATCCGCAACT-TATGTAGGATCTTAGCCATCGAAACGGT
*
23808279 CTATATTTATCCACTCAC
65 CCAT-TTTATCCACTCAC
* * * *
23808297 GATTCTTCTCACACAAGCTGTTAAGAATCCACAACTTATGTTGGATCTTAGCCAT
1 GATGCTACTCACACAAGCTGTTAAGAATCCGCAACTTATGTAGGATCTTAGCCAT
23808352 TAGAGAGTCC
Statistics
Matches: 108, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
80 9 0.08
81 98 0.91
82 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (81 bp):
GATGCTACTCACACAAGCTGTTAAGAATCCGCAACTTATGTAGGATCTTAGCCATCGAAACGGTC
CATTTTATCCACTCAC
Found at i:23814084 original size:21 final size:21
Alignment explanation
Indices: 23814053--23814101 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
23814043 TAACATAGGA
* *
23814053 ATTTTTCATTATTTTTGTTTT
1 ATTTTTCATTACTTTTATTTT
* *
23814074 GTTTTTTATTACTTTTATTTT
1 ATTTTTCATTACTTTTATTTT
23814095 ATTTTTC
1 ATTTTTC
23814102 TTTTTTCGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (21 bp):
ATTTTTCATTACTTTTATTTT
Found at i:23815684 original size:15 final size:16
Alignment explanation
Indices: 23815664--23815696 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23815654 TATTCCATTG
*
23815664 TTTTAT-TTCTTTTAT
1 TTTTATGTTCTTTAAT
23815679 TTTTATGTTCTTTAAT
1 TTTTATGTTCTTTAAT
23815695 TT
1 TT
23815697 AAACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTATGTTCTTTAAT
Found at i:23816115 original size:24 final size:24
Alignment explanation
Indices: 23816069--23816115 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
23816059 AATATATATA
* * *
23816069 TATATGTATAAATTTATATAATAG
1 TATATATATAAATTAATAGAATAG
*
23816093 TATATATATATATTAATAGAATA
1 TATATATATAAATTAATAGAATA
23816116 CTTAAAGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TATATATATAAATTAATAGAATAG
Found at i:23818141 original size:15 final size:16
Alignment explanation
Indices: 23818113--23818142 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23818103 ATAAACTAAA
23818113 TTCCATACTTGATTTC
1 TTCCATACTTGATTTC
23818129 TTCCATA-TTGATTT
1 TTCCATACTTGATTT
23818143 AATTCTTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (16 bp):
TTCCATACTTGATTTC
Found at i:23844586 original size:10 final size:10
Alignment explanation
Indices: 23844571--23844595 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23844561 ATTTCCATTG
23844571 AATATTGTTT
1 AATATTGTTT
23844581 AATATTGTTT
1 AATATTGTTT
23844591 AATAT
1 AATAT
23844596 CCAAATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (10 bp):
AATATTGTTT
Found at i:23844748 original size:20 final size:21
Alignment explanation
Indices: 23844710--23844749 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
23844700 ACTTTCAAAC
23844710 TTTTCTAAAAAATTAATAAAA
1 TTTTCTAAAAAATTAATAAAA
* *
23844731 TTTT-TAAAAAGTTCATAAA
1 TTTTCTAAAAAATTAATAAA
23844750 GTATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (21 bp):
TTTTCTAAAAAATTAATAAAA
Found at i:23848628 original size:6 final size:6
Alignment explanation
Indices: 23848619--23848652 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
23848609 TGGGGTTGGG
* *
23848619 GGGTGA GGGTGA GGGTAA GGGTAA GGGTAA GGGT
1 GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGT
23848653 GAGGCAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.59, T:0.18
Consensus pattern (6 bp):
GGGTAA
Found at i:23848634 original size:12 final size:12
Alignment explanation
Indices: 23848619--23848656 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
23848609 TGGGGTTGGG
*
23848619 GGGTGAGGGTGA
1 GGGTAAGGGTGA
*
23848631 GGGTAAGGGTAA
1 GGGTAAGGGTGA
23848643 GGGTAAGGGTGA
1 GGGTAAGGGTGA
23848655 GG
1 GG
23848657 CAAATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.61, T:0.16
Consensus pattern (12 bp):
GGGTAAGGGTGA
Found at i:23850856 original size:27 final size:27
Alignment explanation
Indices: 23850820--23850876 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
23850810 TTTTCTTAAG
*
23850820 AAATCAAAACCAAATTTTTATTAAAGCC
1 AAATCAAAACCAAAATTTT-TTAAAGCC
*
23850848 AAATC-AAACCAAAATTTTTTAAAGTC
1 AAATCAAAACCAAAATTTTTTAAAGCC
23850874 AAA
1 AAA
23850877 ATTTACATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 10 0.37
27 12 0.44
28 5 0.19
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (27 bp):
AAATCAAAACCAAAATTTTTTAAAGCC
Found at i:23868761 original size:27 final size:27
Alignment explanation
Indices: 23868671--23868874 Score: 128
Period size: 27 Copynumber: 7.3 Consensus size: 27
23868661 CTGAATGAAC
*
23868671 AGAAGCCTTTGTGGCAATCCCTGAATA
1 AGAAGCCTTTGTGGCAATCTCTGAATA
* * * *
23868698 GGAAGCCTTTCGTGGTGAGT-TCTAAATGA
1 AGAAGCCTTT-GTGG-CAATCTCTGAAT-A
*
23868727 AGGGAAGCCTTTGTGGCAATCCCTGAATA
1 A--GAAGCCTTTGTGGCAATCTCTGAATA
* * *
23868756 AGAAGCCTTTGTGGTGAGT-TCTAAATAAA
1 AGAAGCCTTTGTGG-CAATCTCTGAAT--A
*
23868785 AGGAAGCCTTTGTGGCAATCTATGAATA
1 A-GAAGCCTTTGTGGCAATCTCTGAATA
* * * * *
23868813 GGAAGCCTTTGTGACGACCTATGAA-A
1 AGAAGCCTTTGTGGCAATCTCTGAATA
* * *
23868839 GGAAGCCTTTGTGGAAATCTTTGAA-A
1 AGAAGCCTTTGTGGCAATCTCTGAATA
23868865 AGAAAGCCTT
1 AG-AAGCCTT
23868875 CATGGAGAAC
Statistics
Matches: 137, Mismatches: 28, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
26 23 0.17
27 55 0.40
28 12 0.09
29 11 0.08
30 27 0.20
31 9 0.07
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (27 bp):
AGAAGCCTTTGTGGCAATCTCTGAATA
Found at i:23868797 original size:57 final size:57
Alignment explanation
Indices: 23868672--23868825 Score: 254
Period size: 57 Copynumber: 2.7 Consensus size: 57
23868662 TGAATGAACA
* *
23868672 GAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTTCGTGGTGAGTTCTAAATGAAGG
1 GAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTT-GTGGTGAGTTCTAAATAAAAG
*
23868730 GAAGCCTTTGTGGCAATCCCTGAATAAGAAGCCTTTGTGGTGAGTTCTAAATAAAAG
1 GAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTTGTGGTGAGTTCTAAATAAAAG
**
23868787 GAAGCCTTTGTGGCAATCTATGAATAGGAAGCCTTTGTG
1 GAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTTGTG
23868826 ACGACCTATG
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
57 55 0.61
58 35 0.39
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (57 bp):
GAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTTGTGGTGAGTTCTAAATAAAAG
Found at i:23869579 original size:3 final size:3
Alignment explanation
Indices: 23869566--23869606 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
23869556 CCAAAATCAA
*
23869566 AAT AGT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
23869607 ATTATTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:23869592 original size:16 final size:16
Alignment explanation
Indices: 23869571--23869602 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23869561 ATCAAAATAG
23869571 TAATAATAATAATAAA
1 TAATAATAATAATAAA
23869587 TAATAATAATAATAAA
1 TAATAATAATAATAAA
23869603 ATAAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATAATAATAATAAA
Found at i:23869593 original size:19 final size:19
Alignment explanation
Indices: 23869565--23869601 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
23869555 TCCAAAATCA
*
23869565 AAATAGTAATAATAATAAT
1 AAATAATAATAATAATAAT
23869584 AAATAATAATAATAATAA
1 AAATAATAATAATAATAA
23869602 AATAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AAATAATAATAATAATAAT
Found at i:23870690 original size:11 final size:12
Alignment explanation
Indices: 23870674--23870705 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
23870664 CAGTTAATGC
23870674 TCGGTCAACGA-
1 TCGGTCAACGAG
23870685 TCGGTCAAC-AG
1 TCGGTCAACGAG
23870696 TCGGTCAACG
1 TCGGTCAACG
23870706 GCTGGTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 18 0.95
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (12 bp):
TCGGTCAACGAG
Found at i:23876297 original size:27 final size:27
Alignment explanation
Indices: 23876257--23876328 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
23876247 GAGTTCGAAA
23876257 TGAA-AGGAAGCCTTTGTGGCA-ATCCT
1 TGAATAGGAAGCCTTTGTGG-AGATCCT
* *
23876283 TGAATAGGAAGCCTTTATGGAGATCTT
1 TGAATAGGAAGCCTTTGTGGAGATCCT
23876310 TGAATAGGAAGCCTTTGTG
1 TGAATAGGAAGCCTTTGTG
23876329 ACGACCTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 5 0.12
27 36 0.88
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
TGAATAGGAAGCCTTTGTGGAGATCCT
Found at i:23883320 original size:50 final size:50
Alignment explanation
Indices: 23883261--23883360 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
23883251 ATACTAAACA
* * *
23883261 TACACAATTCTTACAACAGACAGTGTTCCTATGGCGCGTACACTATGCCC
1 TACACAATTCTTACAACAGACAGTGTTCCTATGACGCCTACACTACGCCC
*
23883311 TACACAATTCTTACGACAGACAGTGTTCCTATGACGCCTACACTACGCCC
1 TACACAATTCTTACAACAGACAGTGTTCCTATGACGCCTACACTACGCCC
23883361 ATTCATACGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (50 bp):
TACACAATTCTTACAACAGACAGTGTTCCTATGACGCCTACACTACGCCC
Found at i:23886422 original size:57 final size:57
Alignment explanation
Indices: 23886361--23886471 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
23886351 AAATTGTTCG
* * *
23886361 TATTGATGATAAATTGAGTCATAAA-GCTGTCCAAAATAAGGTTATTCAAGCTGTTTA
1 TATTGACGATAAACTGAGTCA-AAATACTGTCCAAAATAAGGTTATTCAAGCTGTTTA
* * * *
23886418 TATTGACGTTTAACTGAGTCAAAATACTGTCCAAATTAAGGTTATTCATGCTGT
1 TATTGACGATAAACTGAGTCAAAATACTGTCCAAAATAAGGTTATTCAAGCTGT
23886472 CTATTTGGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
56 3 0.07
57 43 0.93
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (57 bp):
TATTGACGATAAACTGAGTCAAAATACTGTCCAAAATAAGGTTATTCAAGCTGTTTA
Found at i:23886506 original size:57 final size:57
Alignment explanation
Indices: 23886375--23886498 Score: 146
Period size: 57 Copynumber: 2.2 Consensus size: 57
23886365 GATGATAAAT
* *
23886375 TGAGTCATAAAGCTGTCCAAAATAAGGTTATTCAAGCTGTTTATATTGACGTTTAAC
1 TGAGTCATAAAGCTGTCCAAAATAAGGTTATTCAAGCTGTCTATATTGACATTTAAC
* * * *
23886432 TGAGTCA-AAATACTGTCCAAATTAAGGTTATTCATGCTGTCTAT-TTGGATATATTAA-
1 TGAGTCATAAA-GCTGTCCAAAATAAGGTTATTCAAGCTGTCTATATT-GACAT-TTAAC
23886489 TGAGTCATAA
1 TGAGTCATAA
23886499 GGTTGTCCTG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
56 5 0.09
57 46 0.81
58 6 0.11
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (57 bp):
TGAGTCATAAAGCTGTCCAAAATAAGGTTATTCAAGCTGTCTATATTGACATTTAAC
Found at i:23891710 original size:18 final size:18
Alignment explanation
Indices: 23891676--23891713 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
23891666 TAAATTTTCG
*
23891676 AATTCGAATAGCGCGAAT
1 AATTCGAATAACGCGAAT
23891694 AATTCGAATAAAC-CGAAT
1 AATTCGAAT-AACGCGAAT
23891712 AA
1 AA
23891714 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (18 bp):
AATTCGAATAACGCGAAT
Found at i:23892295 original size:23 final size:22
Alignment explanation
Indices: 23892269--23892314 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
23892259 AGGTAAGAAA
* *
23892269 GTTAATTTTTTCTTGAAATACAT
1 GTTAATTTTAT-TTGAAAAACAT
*
23892292 GTTAGTTTTATTTGAAAAACAT
1 GTTAATTTTATTTGAAAAACAT
23892314 G
1 G
23892315 AAATATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (22 bp):
GTTAATTTTATTTGAAAAACAT
Found at i:23897689 original size:5 final size:5
Alignment explanation
Indices: 23897678--23897721 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
23897668 TAAACATCCT
* * *
23897678 CACCC TACCC TACCC TACCC CACCC CACCC CACCC CACCC CACC
1 CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACC
23897722 TTTTCTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.20, C:0.73, G:0.00, T:0.07
Consensus pattern (5 bp):
CACCC
Found at i:23899197 original size:2 final size:2
Alignment explanation
Indices: 23899160--23899186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23899150 CCTTCTCTTT
23899160 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
23899187 TTTCTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:23901283 original size:26 final size:26
Alignment explanation
Indices: 23901254--23901305 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
23901244 GGATTTTATT
*
23901254 CTTGTAGACTAAGAAACTAAAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
*
23901280 CTTGTAGAATAAGAAACTATAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
23901306 GGAAACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (26 bp):
CTTGTAGAATAAGAAACTAAAATTAA
Found at i:23904468 original size:2 final size:2
Alignment explanation
Indices: 23904461--23904509 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
23904451 ATCATTTATC
* * *
23904461 AT AT AT AT AT AT AT AT AT TT A- AT AT A- AT AT AT CT A- AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23904500 AT AT AT AT AT
1 AT AT AT AT AT
23904510 TACAAGATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23913233 original size:45 final size:44
Alignment explanation
Indices: 23913165--23913698 Score: 489
Period size: 45 Copynumber: 11.9 Consensus size: 44
23913155 GGTGTTGTAA
* * * *
23913165 CTTCAACCTGCCCTCTGAATTAGGCGTAAAAGATTGGATGATGG
1 CTTCAATCTGCCCTTTGGATTAGGGGTAAAAGATTGGATGATGG
* * *
23913209 CTTCAATCCGCTCCTTTGGATTAGGGGTAAAAGATTAGATGATGA
1 CTTCAATCTGC-CCTTTGGATTAGGGGTAAAAGATTGGATGATGG
* * * * * * *
23913254 CTTCAACCTGCCCCTCTGAACTAGGGGTAAAAGGTTAGATGGTGG
1 CTTCAATCTG-CCCTTTGGATTAGGGGTAAAAGATTGGATGATGG
* * *
23913299 CTTCAA-CTTGCCCCTTTAGATTAAGGGTAAAAGGTTGGATGATGG
1 CTTCAATC-TG-CCCTTTGGATTAGGGGTAAAAGATTGGATGATGG
* *
23913344 CTTCAATCTACCCTTCTGGATTAGGGGTAAAAGATTGGATGATTG
1 CTTCAATCTGCCCTT-TGGATTAGGGGTAAAAGATTGGATGATGG
* * * *
23913389 CTTCAATCTGTCGCTCTGGATTAGAGGTAAAAGACTGGATGATGG
1 CTTCAATCTG-CCCTTTGGATTAGGGGTAAAAGATTGGATGATGG
* * *
23913434 CTTCAATCTGCCCTTCTGAATTAGGGGTAAAAGATTGGATGCTGA
1 CTTCAATCTGCCCTT-TGGATTAGGGGTAAAAGATTGGATGATGG
* * * * * * *
23913479 CTTCAACCTGCCTTTCTAGATTAGGAGTAAAAGGTTGGATGGTGA
1 CTTCAATCTGCCCTT-TGGATTAGGGGTAAAAGATTGGATGATGG
* *
23913524 CTTCAACCTGCCTCTTTGGATTAGGGGTAAAAGGTTGGATGATGG
1 CTTCAATCTGCC-CTTTGGATTAGGGGTAAAAGATTGGATGATGG
* * * * ** *
23913569 CTTCAACTTTGCCCTCTAGA-TATGGGTAAAAGATTAAATGACT-T
1 CTTCAA-TCTGCCCTTTGGATTAGGGGTAAAAGATTGGATGA-TGG
* * *
23913613 CTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGACTGGATGACGG
1 CTTCAATCTG-CCCTTTGGATTAGGGGTAAAAGATTGGATGATGG
* ** *
23913658 CTTCAATTTGCCCCTTTGGATTAATGGTAAAAGATTAGATG
1 CTTCAATCTG-CCCTTTGGATTAGGGGTAAAAGATTGGATG
23913699 GTGATGTAAC
Statistics
Matches: 402, Mismatches: 75, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
43 3 0.01
44 49 0.12
45 339 0.84
46 11 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCCCTTTGGATTAGGGGTAAAAGATTGGATGATGG
Found at i:23924698 original size:22 final size:21
Alignment explanation
Indices: 23924673--23924714 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23924663 TCATATATAA
23924673 AACAAAAATAAAAATGCAAAGC
1 AACAAAAAT-AAAATGCAAAGC
* *
23924695 AACATATATAAAATGCAAAG
1 AACAAAAATAAAATGCAAAG
23924715 GATAACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.64, C:0.12, G:0.10, T:0.14
Consensus pattern (21 bp):
AACAAAAATAAAATGCAAAGC
Found at i:23926149 original size:16 final size:16
Alignment explanation
Indices: 23926130--23926172 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
23926120 TTATTTTATT
23926130 TTTGTTTTTGTTCAAG
1 TTTGTTTTTGTTCAAG
** **
23926146 TTTGTTTTACTTCTTG
1 TTTGTTTTTGTTCAAG
23926162 TTTGTTTTTGT
1 TTTGTTTTTGT
23926173 AGAATAAGTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.07, C:0.07, G:0.16, T:0.70
Consensus pattern (16 bp):
TTTGTTTTTGTTCAAG
Found at i:23927479 original size:10 final size:10
Alignment explanation
Indices: 23927464--23927490 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
23927454 CCTTGTTCAT
23927464 ATATAAAAAA
1 ATATAAAAAA
23927474 ATATAAAAAA
1 ATATAAAAAA
23927484 ATATAAA
1 ATATAAA
23927491 TGAAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
ATATAAAAAA
Found at i:23929055 original size:21 final size:24
Alignment explanation
Indices: 23929002--23929062 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
23928992 ATATATGCTT
* *
23929002 ATAAACTACCGATACATTAGTACC
1 ATAAACTACCGATACATTAGCACA
*
23929026 ATGAACTACCGATAC-TT-GCA-A
1 ATAAACTACCGATACATTAGCACA
*
23929047 ATAAACTACCAATACA
1 ATAAACTACCGATACA
23929063 ATTAAAGCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 13 0.42
22 2 0.06
23 2 0.06
24 14 0.45
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (24 bp):
ATAAACTACCGATACATTAGCACA
Found at i:23938391 original size:16 final size:16
Alignment explanation
Indices: 23938367--23938398 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23938357 TCCTTACAAA
*
23938367 TTTATTCATTTAACAT
1 TTTAGTCATTTAACAT
23938383 TTTAGTCATTTAACAT
1 TTTAGTCATTTAACAT
23938399 AAAAATCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCATTTAACAT
Found at i:23942339 original size:22 final size:21
Alignment explanation
Indices: 23942311--23942375 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
23942301 CCCTCCTCCC
23942311 TCTCTTCCATTTTCTCTCTTT
1 TCTCTTCCATTTTCTCTCTTT
*
23942332 TCTTCTT-C-TTTTCCTTTCCTTT
1 TC-TCTTCCATTTT-CTCT-CTTT
* *
23942354 TCTCATCCATTTTCTCCCTTT
1 TCTCTTCCATTTTCTCTCTTT
23942375 T
1 T
23942376 TGCTAGCCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 13 0.37
23 4 0.11
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.62
Consensus pattern (21 bp):
TCTCTTCCATTTTCTCTCTTT
Found at i:23945545 original size:27 final size:26
Alignment explanation
Indices: 23945499--23945551 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
23945489 TAAATAAATA
*
23945499 TGGACTTTATTTATGCTTTGGCTTTTG
1 TGGACTTTATTTAT-CTTTGGATTTTG
23945526 TGGACTTTATTGTTAT-TTTGGATTTT
1 TGGACTTTA-T-TTATCTTTGGATTTT
23945552 ATTTTCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 18 0.78
28 1 0.04
29 4 0.17
ACGTcount: A:0.13, C:0.08, G:0.21, T:0.58
Consensus pattern (26 bp):
TGGACTTTATTTATCTTTGGATTTTG
Found at i:23947446 original size:27 final size:27
Alignment explanation
Indices: 23947395--23947462 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
23947385 ACTCGACCCG
* *
23947395 TTGACCTGAGTTGACCGATTAGACCAA
1 TTGACCAGAGTTGACCAATTAGACCAA
* *
23947422 TTGACCCGAGTTGACCAATCT-GACCCA
1 TTGACCAGAGTTGACCAAT-TAGACCAA
*
23947449 TTAACCAGAGTTGA
1 TTGACCAGAGTTGA
23947463 TCTACCCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
TTGACCAGAGTTGACCAATTAGACCAA
Found at i:23947474 original size:27 final size:28
Alignment explanation
Indices: 23947444--23947520 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 28
23947434 GACCAATCTG
*
23947444 ACCCATT-AACCAGAGTTGATCTACCCA
1 ACCCATTGAACCAGAGTTGATCGACCCA
* * *
23947471 ACCCGTTGAACC-TAGTTGATCGACCCG
1 ACCCATTGAACCAGAGTTGATCGACCCA
23947498 ACCCATTGAACCAG-GTTGATCGA
1 ACCCATTGAACCAGAGTTGATCGA
23947521 TCTGTCCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
27 38 0.90
28 4 0.10
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
ACCCATTGAACCAGAGTTGATCGACCCA
Found at i:23947506 original size:81 final size:80
Alignment explanation
Indices: 23947390--23947611 Score: 212
Period size: 81 Copynumber: 2.8 Consensus size: 80
23947380 CGATAACTCG
***
23947390 ACCCGTTGACCTGAGTTGACCGATTAGACCAATTGACCCGAGTTGACCAATCTGACCCATTAACC
1 ACCCGTTGACCT-AGTTGACCGACCCGACCAATTGACCCGAGTTGACCAATCTGACCCATTAACC
* *
23947455 AGAGTTGATCTACCCA
65 AGAGTTGATCAACACA
* * * * * * * *
23947471 ACCCGTTGAACCTAGTTGATCGACCCGACCCATTGAACC-AGGTTGATCGATCTGTCCCGTTGAC
1 ACCCGTTG-ACCTAGTTGACCGACCCGACCAATTGACCCGA-GTTGACCAATCTGACCCATTAAC
* *
23947535 CCGAGTTGATCAACATA
64 CAGAGTTGATCAACACA
* * * * * * *
23947552 ACCTGTTGATCGAGTTGACCGACCCGACCTACTGACCCGAGTTGACCAACCCGACCCATT
1 ACCCGTTGACCTAGTTGACCGACCCGACCAATTGACCCGAGTTGACCAATCTGACCCATT
23947612 GACTCGAGTT
Statistics
Matches: 110, Mismatches: 28, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
80 39 0.35
81 67 0.61
82 4 0.04
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.23
Consensus pattern (80 bp):
ACCCGTTGACCTAGTTGACCGACCCGACCAATTGACCCGAGTTGACCAATCTGACCCATTAACCA
GAGTTGATCAACACA
Found at i:23947533 original size:27 final size:27
Alignment explanation
Indices: 23947457--23947545 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
23947447 CATTAACCAG
* *
23947457 AGTTGATCTACCCAACCCGTTGAACCT
1 AGTTGATCGACCCGACCCGTTGAACCT
*
23947484 AGTTGATCGACCCGACCCATTGAACC-
1 AGTTGATCGACCCGACCCGTTGAACCT
* * * * *
23947510 AGGTTGATCGATCTGTCCCGTTGACCCG
1 A-GTTGATCGACCCGACCCGTTGAACCT
23947538 AGTTGATC
1 AGTTGATC
23947546 AACATAACCT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 50 0.96
28 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (27 bp):
AGTTGATCGACCCGACCCGTTGAACCT
Found at i:23947642 original size:27 final size:27
Alignment explanation
Indices: 23947557--23947642 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
23947547 ACATAACCTG
*
23947557 TTGA-TCGAGTTGACCGACCCGACCTA
1 TTGACTCGAGTTGACCGACCCGACCCA
* * *
23947583 CTGACCCGAGTTGACCAACCCGACCCA
1 TTGACTCGAGTTGACCGACCCGACCCA
* *
23947610 TTGACTCGAGTTAACTGACCCGACCCA
1 TTGACTCGAGTTGACCGACCCGACCCA
23947637 TTGACT
1 TTGACT
23947643 TTAACTTTGG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 3 0.06
27 47 0.94
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (27 bp):
TTGACTCGAGTTGACCGACCCGACCCA
Found at i:23947647 original size:23 final size:24
Alignment explanation
Indices: 23947600--23947648 Score: 64
Period size: 27 Copynumber: 2.0 Consensus size: 24
23947590 GAGTTGACCA
23947600 ACCCGACCCATTGACTCGAGTTAACTG
1 ACCCGACCCATTGACT---GTTAACTG
23947627 ACCCGACCCATTGACT-TTAACT
1 ACCCGACCCATTGACTGTTAACT
23947649 TTGGCCTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.27
27 16 0.73
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (24 bp):
ACCCGACCCATTGACTGTTAACTG
Found at i:23948296 original size:9 final size:9
Alignment explanation
Indices: 23948282--23948307 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
23948272 TTTCTTGTTT
23948282 TCAAGAAAA
1 TCAAGAAAA
23948291 TCAAGAAAA
1 TCAAGAAAA
23948300 TCAAGAAA
1 TCAAGAAA
23948308 CCAAATCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
TCAAGAAAA
Found at i:23949281 original size:13 final size:13
Alignment explanation
Indices: 23949263--23949287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23949253 TTTTGAGCTT
23949263 ACAAATCTATTTA
1 ACAAATCTATTTA
23949276 ACAAATCTATTT
1 ACAAATCTATTT
23949288 TGTTTTCCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
ACAAATCTATTTA
Found at i:23960326 original size:17 final size:18
Alignment explanation
Indices: 23960306--23960339 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23960296 ATAAAAGTTT
23960306 TGATTTT-TAAAAAATAG
1 TGATTTTCTAAAAAATAG
*
23960323 TGATTTTCTATAAAATA
1 TGATTTTCTAAAAAATA
23960340 AAAGAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (18 bp):
TGATTTTCTAAAAAATAG
Found at i:23960460 original size:147 final size:144
Alignment explanation
Indices: 23960277--23960607 Score: 418
Period size: 147 Copynumber: 2.3 Consensus size: 144
23960267 AGTTTTGATT
*
23960277 TTTTTTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAAAAATAGTG-ATTTTCTATAAAATAA
1 TTTTTTAACT-ATTTCGAAATAAAAGTTTTGATTTTTAAAAAATAGTGAATTTTCTATAAAA-AA
* * *
23960341 AAGAAAGTTTAGATTTTTTAAAAAT-AAAAATATGTTTTTTAGTCATTCTAAAGAAAAA-TTTAA
64 AAGAAAGCTTAGA-TTTTTAAAAATAAAAAATCTG-TTTTTAGGCATTCTAAA-AAAAAGTTTAA
**
23960404 TTTTTTAAACAATTTTTTGA
126 -TTTTTAAACAAAATTTTGA
* * * * * * * *
23960424 TTTTTTCAACTATTTCGAAATAAAAGTTTGGGTTTTTTAGTAAACTTGTGAATTTTTTTTATAAA
1 TTTTTT-AACTATTTCGAAATAAAAGTTT-TGATTTTTA-AAAAATAGTGAATTTTCTATAAAAA
*
23960489 AAAGAAAGCTTAGATTTTTAAAAATAAAAAATCTGTTTTTAGGCATTTTAAAAAAAAGTTTAATT
63 AAAGAAAGCTTAGATTTTTAAAAATAAAAAATCTGTTTTTAGGCATTCTAAAAAAAAGTTTAATT
23960554 TTTAAACAAAATTTT-A
128 TTTAAACAAAATTTTGA
23960570 TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAA
1 TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAA
23960608 GTAAAGTAAT
Statistics
Matches: 160, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
144 7 0.04
145 22 0.14
146 7 0.04
147 44 0.28
148 41 0.26
149 29 0.18
150 10 0.06
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (144 bp):
TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAAAAATAGTGAATTTTCTATAAAAAAAA
GAAAGCTTAGATTTTTAAAAATAAAAAATCTGTTTTTAGGCATTCTAAAAAAAAGTTTAATTTTT
AAACAAAATTTTGA
Found at i:23960572 original size:18 final size:19
Alignment explanation
Indices: 23960534--23960577 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
23960524 TTTTTAGGCA
23960534 TTTTAAAAAAAAGTTTAAT
1 TTTTAAAAAAAAGTTTAAT
* * *
23960553 TTTTAAACAAAATTTTATT
1 TTTTAAAAAAAAGTTTAAT
23960572 TTTTAA
1 TTTTAA
23960578 CTATTTCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTAAAAAAAAGTTTAAT
Found at i:23973648 original size:246 final size:246
Alignment explanation
Indices: 23973193--23973679 Score: 825
Period size: 246 Copynumber: 2.0 Consensus size: 246
23973183 TGGCAAAGAG
23973193 AAACAAATAAGAAAACAAAGAAACAAACCTTACAAGATCAAGATGTTTGCCAATTAAGCACAAAT
1 AAACAAATAAGAAAACAAAGAAACAAACCTTACAAGATCAAGATGTTTGCCAATTAAGCACAAAT
* * * *
23973258 ACAACGAAGAACACTTGAGTTAAATGAATACAATGAGAGCTCACAAGTGTTTACAAGAAAAGATA
66 ACAAAGAAGAAAACTTGAGTTAAATGAATACAATGAAAGCTCACAAGTGTTTACAAGAAAAAATA
* *
23973323 TGAAAGAATTAAGCTCTAAGTTATTTTTATTGATCTTTAAGCTTTGCACATTGCTCTTCATGTTG
131 TGAAAAAATTAAGCTCTAAGTTATTTTTATTGATCTTTAAGCTTTGCACATTGCTCTACATGTTG
23973388 ATAGACCTTTGGAAGATAGTATTTATACCCTCTAATTGATTTCCAACCATT
196 ATAGACCTTTGGAAGATAGTATTTATACCCTCTAATTGATTTCCAACCATT
* * *
23973439 AAACAAATAAGAAAACAAAGAAACAAATCTTATAAGATCAAGATGTTTGTCAATTAAGCACAAAT
1 AAACAAATAAGAAAACAAAGAAACAAACCTTACAAGATCAAGATGTTTGCCAATTAAGCACAAAT
*
23973504 ACAAAGAAGAAAACTTGA-TCTAAATGAATACAATTAAAGCTCACAAGTGTTTACAAGAAAAAAT
66 ACAAAGAAGAAAACTTGAGT-TAAATGAATACAATGAAAGCTCACAAGTGTTTACAAGAAAAAAT
*
23973568 ATGAAAAAAATTAAGCTCTAGGTTATTTTTATTGATCTTTAAGCTTTGCACATTGCTCTACATGT
130 ATG-AAAAAATTAAGCTCTAAGTTATTTTTATTGATCTTTAAGCTTTGCACATTGCTCTACATGT
* *
23973633 TGCTAGACC-TTGGAAGATGGTATTTATACCCTCTAATTGATTTCCAA
194 TGATAGACCTTTGGAAGATAGTATTTATACCCTCTAATTGATTTCCAA
23973680 ACGTTATGGT
Statistics
Matches: 226, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
245 1 0.00
246 159 0.70
247 66 0.29
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (246 bp):
AAACAAATAAGAAAACAAAGAAACAAACCTTACAAGATCAAGATGTTTGCCAATTAAGCACAAAT
ACAAAGAAGAAAACTTGAGTTAAATGAATACAATGAAAGCTCACAAGTGTTTACAAGAAAAAATA
TGAAAAAATTAAGCTCTAAGTTATTTTTATTGATCTTTAAGCTTTGCACATTGCTCTACATGTTG
ATAGACCTTTGGAAGATAGTATTTATACCCTCTAATTGATTTCCAACCATT
Found at i:23973894 original size:21 final size:21
Alignment explanation
Indices: 23973849--23973895 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
23973839 CTAGTAGAAG
***
23973849 GTATCAATACTTTTTGAATCT
1 GTATCAATACTTTTTGAAAAA
*
23973870 GTATCTATACTTTTTGAAAAA
1 GTATCAATACTTTTTGAAAAA
23973891 GTATC
1 GTATC
23973896 GATAGTCTTT
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:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (21 bp):
GTATCAATACTTTTTGAAAAA
Found at i:23976650 original size:21 final size:21
Alignment explanation
Indices: 23976569--23976650 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
23976559 TACGTGGTAC
*
23976569 AAGGTATTGATACTTTTTGAA
1 AAGGTATCGATACTTTTTGAA
*
23976590 GCA-GTATCGATACTTTTTGTAA
1 -AAGGTATCGATACTTTTTG-AA
** *
23976612 AAGGTATAAATACATTTTGAA
1 AAGGTATCGATACTTTTTGAA
*
23976633 AAGGTATCGATAGTTTTT
1 AAGGTATCGATACTTTTT
23976651 TGTCATTGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
21 32 0.67
22 16 0.33
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (21 bp):
AAGGTATCGATACTTTTTGAA
Found at i:23979599 original size:22 final size:22
Alignment explanation
Indices: 23979574--23979616 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
23979564 AAAATATTTC
*
23979574 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
23979596 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
23979617 TTCTTTAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:23981838 original size:225 final size:225
Alignment explanation
Indices: 23981447--23981896 Score: 882
Period size: 225 Copynumber: 2.0 Consensus size: 225
23981437 TGTGCCACTT
23981447 TTCAGTGAGTTAAATCCAGGAATTAGAAGGCCAGATATTGAGGCACCCTAATTTGGGTTGAAACC
1 TTCAGTGAGTTAAATCCAGGAATTAGAAGGCCAGATATTGAGGCACCCTAATTTGGGTTGAAACC
23981512 AGTGATGTTTCAAATGCTACAAATGGTGGGTTAATTCAGTGGTATGCCCATGAAAGATTCACATC
66 AGTGATGTTTCAAATGCTACAAATGGTGGGTTAATTCAGTGGTATGCCCATGAAAGATTCACATC
23981577 TCCACCTTCGATTGTTTATGGAGGTGAGTGATTCATTCAAGATAGCCGATGTGACTGAAGACGCA
131 TCCACCTTCGATTGTTTATGGAGGTGAGTGATTCATTCAAGATAGCCGATGTGACTGAAGACGCA
23981642 CTGAGATTGAAGTTGTTTCCATACTCGTTG
196 CTGAGATTGAAGTTGTTTCCATACTCGTTG
23981672 TTCAGTGAGTTAAATCCAGGAATTAGAAGGCCAGATATTGAGGCACCCTAATTTGGGTTGAAACC
1 TTCAGTGAGTTAAATCCAGGAATTAGAAGGCCAGATATTGAGGCACCCTAATTTGGGTTGAAACC
23981737 AGTGATGTTTCAAATGCTACAAATGGTGGGTTAATTCAGTGGTATGCCCATGAAAGATTCACATC
66 AGTGATGTTTCAAATGCTACAAATGGTGGGTTAATTCAGTGGTATGCCCATGAAAGATTCACATC
*
23981802 TCCACCTTCGATTGTTTATGGAGGTGAGTGATTCATTCAAGATAGCCGATGTGACTGAAGACGTA
131 TCCACCTTCGATTGTTTATGGAGGTGAGTGATTCATTCAAGATAGCCGATGTGACTGAAGACGCA
*
23981867 CTGAGGTTGAAGTTGTTTCCATACTCGTTG
196 CTGAGATTGAAGTTGTTTCCATACTCGTTG
23981897 CAAGATCGAG
Statistics
Matches: 223, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
225 223 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (225 bp):
TTCAGTGAGTTAAATCCAGGAATTAGAAGGCCAGATATTGAGGCACCCTAATTTGGGTTGAAACC
AGTGATGTTTCAAATGCTACAAATGGTGGGTTAATTCAGTGGTATGCCCATGAAAGATTCACATC
TCCACCTTCGATTGTTTATGGAGGTGAGTGATTCATTCAAGATAGCCGATGTGACTGAAGACGCA
CTGAGATTGAAGTTGTTTCCATACTCGTTG
Found at i:24002205 original size:24 final size:24
Alignment explanation
Indices: 24002172--24002226 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
24002162 GACTAATAAG
*
24002172 AGTTTGACTGAAA-AAAAAAAGCAA
1 AGTTTAACTGAAACAAAAAAA-CAA
* *
24002196 AGTTTAACTGAAACAAATAAACAG
1 AGTTTAACTGAAACAAAAAAACAA
24002220 AGTTTAA
1 AGTTTAA
24002227 TTGGAAGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.22
Consensus pattern (24 bp):
AGTTTAACTGAAACAAAAAAACAA
Found at i:24004171 original size:24 final size:24
Alignment explanation
Indices: 24004114--24004173 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
24004104 TAGACTAATA
* * *
24004114 AGAGTTTGACTGAAATAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
24004138 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
24004162 AGAGTTTAATTG
1 AGAGTTTAATTG
24004174 GAAGATTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:24006537 original size:43 final size:43
Alignment explanation
Indices: 24006486--24006573 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
24006476 TCGATACCTA
* * * * *
24006486 GTAAAAGGTATCGATTCTTTTTGAAACGGTATTGATACTTTTT
1 GTAAAAGGTATAGATACTTTCTGAAAAGGTATCGATACTTTTT
*
24006529 GTAAAAGGTATAGATACTTTCTGAAAATGTATCGATACTTTTT
1 GTAAAAGGTATAGATACTTTCTGAAAAGGTATCGATACTTTTT
24006572 GT
1 GT
24006574 CATTGTTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (43 bp):
GTAAAAGGTATAGATACTTTCTGAAAAGGTATCGATACTTTTT
Found at i:24006538 original size:22 final size:22
Alignment explanation
Indices: 24006486--24006573 Score: 108
Period size: 21 Copynumber: 4.1 Consensus size: 22
24006476 TCGATACCTA
*
24006486 GTAAAAGGTATCGATTCTTTTT
1 GTAAAAGGTATCGATACTTTTT
* *
24006508 G-AAACGGTATTGATACTTTTT
1 GTAAAAGGTATCGATACTTTTT
* *
24006529 GTAAAAGGTATAGATACTTTCT
1 GTAAAAGGTATCGATACTTTTT
*
24006551 G-AAAATGTATCGATACTTTTT
1 GTAAAAGGTATCGATACTTTTT
24006572 GT
1 GT
24006574 CATTGTTTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 36 0.65
22 19 0.35
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (22 bp):
GTAAAAGGTATCGATACTTTTT
Found at i:24020950 original size:23 final size:21
Alignment explanation
Indices: 24020930--24020970 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24020920 TATAAGTTAA
*
24020930 TACATATATATATGTATAGTT
1 TACAGATATATATGTATAGTT
*
24020951 TATAGATATATATGTATAGT
1 TACAGATATATATGTATAGT
24020971 AACAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (21 bp):
TACAGATATATATGTATAGTT
Found at i:24027113 original size:2 final size:2
Alignment explanation
Indices: 24027106--24027148 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
24027096 TGTCATTAAG
24027106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24027148 T
1 T
24027149 GAATTAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24028217 original size:36 final size:36
Alignment explanation
Indices: 24028170--24028305 Score: 164
Period size: 36 Copynumber: 3.8 Consensus size: 36
24028160 GGTAACAGGC
*
24028170 ATGACTTTTGGGTCAACAGGGAGTAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* * * * *
24028206 ATGACCGTTGGGTCAATAGGGAATAAAATGGGAATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* * * *
24028242 ATGACCTTTGTGTTAACAGAGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* *
24028278 ATGATCTTTGGGTCAACAGGGCGTAAAA
1 ATGACCTTTGGGTCAACAGGGAGTAAAA
24028306 CGAATAACAA
Statistics
Matches: 80, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
Found at i:24030502 original size:108 final size:108
Alignment explanation
Indices: 24030367--24030597 Score: 428
Period size: 108 Copynumber: 2.1 Consensus size: 108
24030357 ATGAACACTT
*
24030367 AAAAAGCCTT-AAAATAACTTATTTTTTAACAAATTTTTGAAGTTTGAAGGATTTCTATCGATAC
1 AAAAAG-CTTCAAAATAACTTATTTTTTAACAAATTTTTGAAGTCTGAAGGATTTCTATCGATAC
24030431 TTAGTAGGACAAGTATCGGTAGAACTCTAGGTGGAAAGACCTTA
65 TTAGTAGGACAAGTATCGGTAGAACTCTAGGTGGAAAGACCTTA
24030475 AAAAAGCTTCAAAATAACTTATTTTTTAACAAATTTTTGAAGTCTGAAGGATTTCTATCGATACT
1 AAAAAGCTTCAAAATAACTTATTTTTTAACAAATTTTTGAAGTCTGAAGGATTTCTATCGATACT
*
24030540 TAGTAGGACAAGTATTGGTAGAACTCTAGGTGGAAAGACCTTA
66 TAGTAGGACAAGTATCGGTAGAACTCTAGGTGGAAAGACCTTA
24030583 AAAAAGCTTCAAAAT
1 AAAAAGCTTCAAAAT
24030598 TCTATCGGTA
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
107 3 0.03
108 117 0.98
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (108 bp):
AAAAAGCTTCAAAATAACTTATTTTTTAACAAATTTTTGAAGTCTGAAGGATTTCTATCGATACT
TAGTAGGACAAGTATCGGTAGAACTCTAGGTGGAAAGACCTTA
Found at i:24030663 original size:21 final size:21
Alignment explanation
Indices: 24030617--24030670 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
24030607 AGAACTAGGT
* * *
24030617 CTTCTACCGATACAACTCTAG
1 CTTCTACCAATACAACCCTAA
*
24030638 GTTCTACCAATACAACCCTAA
1 CTTCTACCAATACAACCCTAA
*
24030659 CTTCTATCAATA
1 CTTCTACCAATA
24030671 GAACATACTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.30
Consensus pattern (21 bp):
CTTCTACCAATACAACCCTAA
Found at i:24033158 original size:78 final size:78
Alignment explanation
Indices: 24033029--24033186 Score: 262
Period size: 78 Copynumber: 2.0 Consensus size: 78
24033019 ACGTTGATCC
24033029 TAACTTACTTTCTTTTTATGCACTTGTCGTGCTCGCCCCACTTCCATTGCCACCGCCAATACAAA
1 TAACTTACTTTCTTTTTATGCACTTGTCGTGCTCGCCCCACTTCCATTGCCACCGCCAATACAAA
*
24033094 AAGAACATGATAG
66 AAGAACAGGATAG
* ** *
24033107 TAACTTACTTTCTTTTTATGCACTTGTCGTGCTTGCCCTGCTTCCATTGCCACCGCCAGTACAAA
1 TAACTTACTTTCTTTTTATGCACTTGTCGTGCTCGCCCCACTTCCATTGCCACCGCCAATACAAA
*
24033172 AAGACCAGGATAG
66 AAGAACAGGATAG
24033185 TA
1 TA
24033187 GCCAATAAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (78 bp):
TAACTTACTTTCTTTTTATGCACTTGTCGTGCTCGCCCCACTTCCATTGCCACCGCCAATACAAA
AAGAACAGGATAG
Found at i:24036728 original size:18 final size:18
Alignment explanation
Indices: 24036690--24036728 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24036680 TTAATGTAAT
*
24036690 TTATTTTATTTTTAATCG
1 TTATTTTATTTTTAATAG
24036708 TTATTTTATCTTTTAA-AG
1 TTATTTTAT-TTTTAATAG
24036726 TTA
1 TTA
24036729 ACGTAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (18 bp):
TTATTTTATTTTTAATAG
Found at i:24050725 original size:19 final size:19
Alignment explanation
Indices: 24050697--24050752 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
24050687 CCAGTACAGT
* *
24050697 ATATTTCTCTAACGGGCCA
1 ATATTGCTCTAACGAGCCA
*
24050716 ATATTGCTCTCACGAGCCA
1 ATATTGCTCTAACGAGCCA
* *
24050735 GTA-TGCTCAAACGAGCCA
1 ATATTGCTCTAACGAGCCA
24050753 GTATGCTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (19 bp):
ATATTGCTCTAACGAGCCA
Found at i:24057121 original size:18 final size:18
Alignment explanation
Indices: 24057087--24057142 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
24057077 CAGTATATTA
24057087 CTCTCACGAGCCAGTATCG
1 CTCTCACGAGCCAGTAT-G
24057106 CTCTCACGAG-CAGTATG
1 CTCTCACGAGCCAGTATG
** *
24057123 CTCAAACGAGTCAGTATG
1 CTCTCACGAGCCAGTATG
24057141 CT
1 CT
24057143 ATTCCTTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 9 0.26
18 15 0.44
19 10 0.29
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.23
Consensus pattern (18 bp):
CTCTCACGAGCCAGTATG
Found at i:24060411 original size:27 final size:27
Alignment explanation
Indices: 24060298--24060402 Score: 156
Period size: 27 Copynumber: 3.9 Consensus size: 27
24060288 TACAGAAATG
* *
24060298 TAGCTCATTCGAGCCTAGAACAGAGTT
1 TAGCTCATTCGAGCCCATAACAGAGTT
*
24060325 TAGCTCATTCGAACCCATAACAGAGTT
1 TAGCTCATTCGAGCCCATAACAGAGTT
* * *
24060352 TAGCTCATTCAAGCCCAAAATAGAGTT
1 TAGCTCATTCGAGCCCATAACAGAGTT
24060379 TAGCTCATTCGAGCCCATAACAGA
1 TAGCTCATTCGAGCCCATAACAGA
24060403 ATAACGCTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (27 bp):
TAGCTCATTCGAGCCCATAACAGAGTT
Found at i:24067396 original size:27 final size:27
Alignment explanation
Indices: 24067363--24067516 Score: 193
Period size: 27 Copynumber: 5.7 Consensus size: 27
24067353 ATAAGAATGT
* *
24067363 AGCTCATTCGAGCCCAAAATAGAGTTT
1 AGCTCATTCGAGCCCAGAATAGAGTTC
* * *
24067390 AGTTCATTTGAGCCTAGAATAGAGTTC
1 AGCTCATTCGAGCCCAGAATAGAGTTC
* *
24067417 AGCTCATTTC-AGCCCAGAACAGAGTTT
1 AGCTCA-TTCGAGCCCAGAATAGAGTTC
*
24067444 AGCTCATTTGAGCCCAGAATAGAGTTC
1 AGCTCATTCGAGCCCAGAATAGAGTTC
* * *
24067471 AGCTCATTTGAGCCTAGAACAGAGTTC
1 AGCTCATTCGAGCCCAGAATAGAGTTC
24067498 AGCTCATTCGAGCCCAGAA
1 AGCTCATTCGAGCCCAGAA
24067517 CAGAATAACG
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.02
27 104 0.96
28 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (27 bp):
AGCTCATTCGAGCCCAGAATAGAGTTC
Found at i:24067422 original size:54 final size:54
Alignment explanation
Indices: 24067363--24067516 Score: 220
Period size: 54 Copynumber: 2.9 Consensus size: 54
24067353 ATAAGAATGT
* * * *
24067363 AGCTCATTCGAGCCCAAAATAGAGTTTAGTTCATTTGAGCCTAGAATAGAGTTC
1 AGCTCATTCGAGCCCAGAACAGAGTTTAGCTCATTTGAGCCCAGAATAGAGTTC
24067417 AGCTCATTTC-AGCCCAGAACAGAGTTTAGCTCATTTGAGCCCAGAATAGAGTTC
1 AGCTCA-TTCGAGCCCAGAACAGAGTTTAGCTCATTTGAGCCCAGAATAGAGTTC
* * * *
24067471 AGCTCATTTGAGCCTAGAACAGAGTTCAGCTCATTCGAGCCCAGAA
1 AGCTCATTCGAGCCCAGAACAGAGTTTAGCTCATTTGAGCCCAGAA
24067517 CAGAATAACG
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
53 2 0.02
54 85 0.94
55 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (54 bp):
AGCTCATTCGAGCCCAGAACAGAGTTTAGCTCATTTGAGCCCAGAATAGAGTTC
Found at i:24067466 original size:81 final size:81
Alignment explanation
Indices: 24067362--24067520 Score: 257
Period size: 81 Copynumber: 2.0 Consensus size: 81
24067352 TATAAGAATG
* * *
24067362 TAGCTCATTCGAGCCCAAAATAGAGTTTAGTTCATTTGAGCCTAGAATAGAGTTCAGCTCATTTC
1 TAGCTCATTCGAGCCCAAAATAGAGTTCAGCTCATTTGAGCCTAGAACAGAGTTCAGCTCA-TTC
24067427 -AGCCCAGAACAGAGTT
65 GAGCCCAGAACAGAGTT
* *
24067443 TAGCTCATTTGAGCCCAGAATAGAGTTCAGCTCATTTGAGCCTAGAACAGAGTTCAGCTCATTCG
1 TAGCTCATTCGAGCCCAAAATAGAGTTCAGCTCATTTGAGCCTAGAACAGAGTTCAGCTCATTCG
24067508 AGCCCAGAACAGA
66 AGCCCAGAACAGA
24067521 ATAACGCTCT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
80 3 0.04
81 69 0.96
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (81 bp):
TAGCTCATTCGAGCCCAAAATAGAGTTCAGCTCATTTGAGCCTAGAACAGAGTTCAGCTCATTCG
AGCCCAGAACAGAGTT
Found at i:24069542 original size:24 final size:24
Alignment explanation
Indices: 24069515--24069568 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
24069505 TGAAAATGGG
24069515 GAGTTTTA-GTATAAATAAAACGGT
1 GAGTTTTATGT-TAAATAAAACGGT
* *
24069539 GAGTTTTATGTTAAATGAAAGGGT
1 GAGTTTTATGTTAAATAAAACGGT
24069563 GAGTTT
1 GAGTTT
24069569 CATTCTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (24 bp):
GAGTTTTATGTTAAATAAAACGGT
Found at i:24078958 original size:37 final size:37
Alignment explanation
Indices: 24078887--24078963 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
24078877 TTACTACTAA
* ***
24078887 TGTCGTTGCATGAGCACTTCTAGATTGTGTCCAAAAC
1 TGTCGTCGCATGAGCACTTCTAGATTGCACCCAAAAC
24078924 TGTCGTCGCATGAGCACTT-TCAGATTGCACCCAAAAC
1 TGTCGTCGCATGAGCACTTCT-AGATTGCACCCAAAAC
24078961 TGT
1 TGT
24078964 TACCGCAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (37 bp):
TGTCGTCGCATGAGCACTTCTAGATTGCACCCAAAAC
Found at i:24081361 original size:36 final size:36
Alignment explanation
Indices: 24081312--24081388 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
24081302 ATATAATCAG
* *
24081312 TCACATGGTATGAAAAACATACCCACATATTTACTA
1 TCACATGGCATGAAAAACATACCCACATATTCACTA
* * * * *
24081348 TCACATGGCATGAATAACTTGCCCTCATATTCACTT
1 TCACATGGCATGAAAAACATACCCACATATTCACTA
24081384 TCACA
1 TCACA
24081389 ACAGTCATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (36 bp):
TCACATGGCATGAAAAACATACCCACATATTCACTA
Found at i:24090904 original size:19 final size:20
Alignment explanation
Indices: 24090868--24090905 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
24090858 GTGGAGATAG
*
24090868 AGAAAGGAAAAGAGGGACAA
1 AGAAAGGAAAAGAAGGACAA
*
24090888 AGAAA-GAAAGGAAGGACA
1 AGAAAGGAAAAGAAGGACA
24090906 TGATATCGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.61, C:0.05, G:0.34, T:0.00
Consensus pattern (20 bp):
AGAAAGGAAAAGAAGGACAA
Found at i:24091393 original size:17 final size:17
Alignment explanation
Indices: 24091339--24091398 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
24091329 TGTTAGAAAT
24091339 CATTGTCA-TCACA-TTC
1 CATTGTCACT-ACATTTC
*
24091355 TCATTGTCACTACATTTG
1 -CATTGTCACTACATTTC
*
24091373 CATTGTCACTGCATTTC
1 CATTGTCACTACATTTC
24091390 CATTTGTCA
1 CA-TTGTCA
24091399 TTGTAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 28 0.76
18 9 0.24
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.42
Consensus pattern (17 bp):
CATTGTCACTACATTTC
Found at i:24096573 original size:392 final size:392
Alignment explanation
Indices: 24095849--24096631 Score: 1332
Period size: 392 Copynumber: 2.0 Consensus size: 392
24095839 AGAAGATATT
* *
24095849 TATTCAACGACCTTGCCCTTCCTCCGGTTATCCACAGCCGTACTTGTCTCTTGATCTAAATGTTA
1 TATTCAACGACCTTGCCCTTCCCCCGATTATCCACAGCCGTACTTGTCTCTTGATCTAAATGTTA
* * *
24095914 GAGTATGCTCAAAGACCAATCATGAGATTATTGTAATCACATACTCATTTTACCCTGTTTATTAA
66 GAGTATGCCCAAAGACCAATCATGAGATGATTGTAATCACATACTCATTTTACCCTGTTTAGTAA
* *
24095979 TAAAAGACATTGCCATTGTTATTTCAGTTTCTTTTTCTGTGTATTTAAATAAAATGATTTATAAT
131 TAAAAGACATTGCCATTGTTATTTCAGTTTCTTTTTCTGTATATTTAAATAAAATAATTTATAAT
*
24096044 AATGTCCTGAGGATAATATGATTATTCTTAAAAGGTCCTTAGTCAAGTATTATTGTAGACGTGGA
196 AATGTCCTGAGAATAATATGATTATTCTTAAAAGGTCCTTAGTCAAGTATTATTGTAGACGTGGA
24096109 CAACAATAATGCATTGAGACTAATATGTAGTTGATTGATGACAAAGTGTTGTCATTGACATAGGG
261 CAACAATAATGCATTGAGACTAATATGTAGTTGATTGATGACAAAGTGTTGTCATTGACATAGGG
**
24096174 ATGTCAAAATCAATACATGAGTATATGCTAGAGAACGAAATATTGGACTGACTCGCTATGAGTAT
326 ATGTCAAAATCAATACATGAGTATATGCTAGAGAACGAAATATCAGACTGACTCGCTATGAGTAT
24096239 GC
391 GC
* * *
24096241 TATTCAACGACCTTGCTCTTCCCCCGATTATCGACAGTCGTACTTGTCTCTTGATCTAAATGTTA
1 TATTCAACGACCTTGCCCTTCCCCCGATTATCCACAGCCGTACTTGTCTCTTGATCTAAATGTTA
* *
24096306 GAGTATGCCCAAAGACCAATCATGAGATGATTGTAATCACATAGTCATTTTACCTTGTTTAGTAA
66 GAGTATGCCCAAAGACCAATCATGAGATGATTGTAATCACATACTCATTTTACCCTGTTTAGTAA
* *
24096371 TAAAAGACATTGTCATTGTTATTTCAGTTTCTTTTTCTGTATATTTAAATAAACTAATTTATAAT
131 TAAAAGACATTGCCATTGTTATTTCAGTTTCTTTTTCTGTATATTTAAATAAAATAATTTATAAT
* **
24096436 AATGTCCTGAGAATAATATGATTATTCTTAAAAGGTCCTTAGTCAAGTATTATTGTGGGGGTGGA
196 AATGTCCTGAGAATAATATGATTATTCTTAAAAGGTCCTTAGTCAAGTATTATTGTAGACGTGGA
*
24096501 CAACAATAATGCATTGAGACTAATATGTAGTTGATTGATGCCAAAGTGTTGTCATTGACATAGGG
261 CAACAATAATGCATTGAGACTAATATGTAGTTGATTGATGACAAAGTGTTGTCATTGACATAGGG
* * * * *
24096566 ATGTCAAAATCAATACATGAGTATCTGTTAGTGAGCGACATATCAGACTGACTCGCTATGAGTAT
326 ATGTCAAAATCAATACATGAGTATATGCTAGAGAACGAAATATCAGACTGACTCGCTATGAGTAT
24096631 G
391 G
24096632 TTTTTTGGAT
Statistics
Matches: 365, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
392 365 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (392 bp):
TATTCAACGACCTTGCCCTTCCCCCGATTATCCACAGCCGTACTTGTCTCTTGATCTAAATGTTA
GAGTATGCCCAAAGACCAATCATGAGATGATTGTAATCACATACTCATTTTACCCTGTTTAGTAA
TAAAAGACATTGCCATTGTTATTTCAGTTTCTTTTTCTGTATATTTAAATAAAATAATTTATAAT
AATGTCCTGAGAATAATATGATTATTCTTAAAAGGTCCTTAGTCAAGTATTATTGTAGACGTGGA
CAACAATAATGCATTGAGACTAATATGTAGTTGATTGATGACAAAGTGTTGTCATTGACATAGGG
ATGTCAAAATCAATACATGAGTATATGCTAGAGAACGAAATATCAGACTGACTCGCTATGAGTAT
GC
Found at i:24097529 original size:106 final size:106
Alignment explanation
Indices: 24097408--24097610 Score: 343
Period size: 106 Copynumber: 1.9 Consensus size: 106
24097398 TTTATTGAAA
* *
24097408 ATAATTTAACGTAATTATAATTATTAATTTTAATGATTTCGTTAAATATTAAAACATGGAAGTTA
1 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAACATGGAAGATA
24097473 ATATCCTTTTGGAAAGGATATAATATTTTAATAAACATTCC
66 ATATCCTTTTGGAAAGGATATAATATTTTAATAAACATTCC
* * *
24097514 ATAATTTAATGTAATTATAATTATTAATTATAATGATTTTGTTAAATATTAAAACGTGGAAGATA
1 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAACATGGAAGATA
* *
24097579 ATATCCTTTTGGAATGGATATAATGTTTTAAT
66 ATATCCTTTTGGAAAGGATATAATATTTTAAT
24097611 GAACCTTCTA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 90 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (106 bp):
ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAACATGGAAGATA
ATATCCTTTTGGAAAGGATATAATATTTTAATAAACATTCC
Found at i:24097697 original size:123 final size:122
Alignment explanation
Indices: 24097558--24097800 Score: 344
Period size: 123 Copynumber: 2.0 Consensus size: 122
24097548 GATTTTGTTA
* * * *
24097558 AATATTAAAACGTGGAAGATAATATCCTTTTGGAATGGATATAATGTTTTAATGAACCTTCTATA
1 AATATTAAAACATGGAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATA
* * * * *
24097623 TATTTCTCTAAGGGA-GTATTTCCATTTTAATATGAGATATTATATAAAATGAAATTG
66 TACTTCTCTAA-AGATATATTTCCATTTTAATATGAGATATTAAATAAAAGGAAATTG
* *
24097680 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAATCTTCCAT
1 AATATT-AAAACATGGAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* *
24097745 ATACTTCTCTAAAGATATATTTTCATTTTAATATGAGATGTTAAATAAAAGGAAAT
65 ATACTTCTCTAAAGATATATTTCCATTTTAATATGAGATATTAAATAAAAGGAAAT
24097801 ACAACAGAAT
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
122 8 0.08
123 98 0.92
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (122 bp):
AATATTAAAACATGGAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATA
TACTTCTCTAAAGATATATTTCCATTTTAATATGAGATATTAAATAAAAGGAAATTG
Found at i:24101006 original size:12 final size:12
Alignment explanation
Indices: 24100976--24101007 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
24100966 TTATTGTCTC
*
24100976 TGCAACCCTTGA
1 TGCAACTCTTGA
24100988 TGCAACTCTTGA
1 TGCAACTCTTGA
24101000 TGCAACTC
1 TGCAACTC
24101008 AAGAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (12 bp):
TGCAACTCTTGA
Found at i:24105600 original size:17 final size:17
Alignment explanation
Indices: 24105580--24105639 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
24105570 ATTGTCACCA
*
24105580 CATTTCCCTTGTCATTG
1 CATTTCCATTGTCATTG
** *
24105597 CATTTTTATTGTCACTG
1 CATTTCCATTGTCATTG
* *
24105614 CATCTACATTGTCATTG
1 CATTTCCATTGTCATTG
24105631 CATTTCCAT
1 CATTTCCAT
24105640 ATATCATTGT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.10, T:0.47
Consensus pattern (17 bp):
CATTTCCATTGTCATTG
Found at i:24121693 original size:40 final size:41
Alignment explanation
Indices: 24121631--24121777 Score: 140
Period size: 40 Copynumber: 3.7 Consensus size: 41
24121621 CATCGACTCA
*
24121631 TAGCTTGCTAAGCCATAACTTGAATTTTA-ACACCGGCTTG
1 TAGCTTGCTAAGCCATAGCTTGAATTTTATACACCGGCTTG
* * * * *
24121671 TAGCTTACTAAGTCGTAGCTTGAA-TTTATTCACCGGTTTG
1 TAGCTTGCTAAGCCATAGCTTGAATTTTATACACCGGCTTG
* * * **
24121711 TAGCCTGCTAAGCCAAAGCTTGAA-TTTATTCACCGGCTCA
1 TAGCTTGCTAAGCCATAGCTTGAATTTTATACACCGGCTTG
* *
24121751 TAACCTGCTAAGCCGA-AGCTTGAATTT
1 TAGCTTGCTAAGCC-ATAGCTTGAATTT
24121778 ATTCATCGAC
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
39 4 0.04
40 82 0.92
41 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (41 bp):
TAGCTTGCTAAGCCATAGCTTGAATTTTATACACCGGCTTG
Found at i:24121762 original size:80 final size:80
Alignment explanation
Indices: 24121618--24121858 Score: 252
Period size: 80 Copynumber: 3.0 Consensus size: 80
24121608 TTACTAATCA
* * * * * ** * *
24121618 ATTCATCGACTCATAGCTTGCTAAGCCATAA-CTTGAATTT-TAACACCGGCTTGTAGCTTACTA
1 ATTCACCGACTCGTAGCCTGCTAAACCA-AAGCTTGAATTTAT-TCACCGGCTCATAACCTACTA
*
24121681 AGTCGTAGCTTGAATTT
64 AGTCGAAGCTTGAATTT
** * * *
24121698 ATTCACCGGTTTGTAGCCTGCTAAGCCAAAGCTTGAATTTATTCACCGGCTCATAACCTGCTAAG
1 ATTCACCGACTCGTAGCCTGCTAAACCAAAGCTTGAATTTATTCACCGGCTCATAACCTACTAAG
*
24121763 CCGAAGCTTGAATTT
66 TCGAAGCTTGAATTT
* *** *
24121778 ATTCATCGACTCGTAGCCTGCTAAATTGAAGCTTGAATTTATTCACCGGCTCATAGCCTACTAAG
1 ATTCACCGACTCGTAGCCTGCTAAACCAAAGCTTGAATTTATTCACCGGCTCATAACCTACTAAG
*
24121843 TCGAAGCTTAAATTT
66 TCGAAGCTTGAATTT
24121858 A
1 A
24121859 GTTTCAAAGC
Statistics
Matches: 133, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
79 2 0.02
80 130 0.98
81 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (80 bp):
ATTCACCGACTCGTAGCCTGCTAAACCAAAGCTTGAATTTATTCACCGGCTCATAACCTACTAAG
TCGAAGCTTGAATTT
Found at i:24121778 original size:40 final size:40
Alignment explanation
Indices: 24121678--24121858 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
24121668 TTGTAGCTTA
* * **
24121678 CTAAGTCGTAGCTTGAATTTATTCACCGGTTTGTAGCCTG
1 CTAAGTCGAAGCTTGAATTTATTCACCGGCTCATAGCCTG
* * *
24121718 CTAAGCCAAAGCTTGAATTTATTCACCGGCTCATAACCTG
1 CTAAGTCGAAGCTTGAATTTATTCACCGGCTCATAGCCTG
* * * *
24121758 CTAAGCCGAAGCTTGAATTTATTCATCGACTCGTAGCCTG
1 CTAAGTCGAAGCTTGAATTTATTCACCGGCTCATAGCCTG
* * *
24121798 CTAAATTGAAGCTTGAATTTATTCACCGGCTCATAGCCTA
1 CTAAGTCGAAGCTTGAATTTATTCACCGGCTCATAGCCTG
*
24121838 CTAAGTCGAAGCTTAAATTTA
1 CTAAGTCGAAGCTTGAATTTA
24121859 GTTTCAAAGC
Statistics
Matches: 119, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 119 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (40 bp):
CTAAGTCGAAGCTTGAATTTATTCACCGGCTCATAGCCTG
Found at i:24123973 original size:22 final size:23
Alignment explanation
Indices: 24123924--24123967 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24123914 TATATGTCTA
*
24123924 AATTTCTTTTATATATACATATC
1 AATTTCTTTTATAAATACATATC
*
24123947 AATTTCTTTTA-AAATATATAT
1 AATTTCTTTTATAAATACATAT
24123968 GTATTTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTTCTTTTATAAATACATATC
Found at i:24137455 original size:13 final size:13
Alignment explanation
Indices: 24137437--24137463 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24137427 ACTATTCTAC
24137437 TGTAAATAGTAAA
1 TGTAAATAGTAAA
24137450 TGTAAATAGTAAA
1 TGTAAATAGTAAA
24137463 T
1 T
24137464 TCAAGTTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTAAATAGTAAA
Found at i:24144452 original size:22 final size:21
Alignment explanation
Indices: 24144396--24144463 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
24144386 ACATTCAAAC
*
24144396 AATAGCAACAAAATATTAACAA
1 AATAGCAACAAAATA-TAGCAA
* ** *
24144418 TATAATAATAAAATGATAGCAA
1 AATAGCAACAAAAT-ATAGCAA
24144440 AATAGCAACAAAATAATAGCAA
1 AATAGCAACAAAAT-ATAGCAA
24144462 AA
1 AA
24144464 CAACTACAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.19
Consensus pattern (21 bp):
AATAGCAACAAAATATAGCAA
Found at i:24144462 original size:11 final size:11
Alignment explanation
Indices: 24144402--24144463 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
24144392 AAACAATAGC
*
24144402 AACAAAATATT
1 AACAAAATAAT
*
24144413 AACAATATAAT
1 AACAAAATAAT
* *
24144424 AATAAAATGAT
1 AACAAAATAAT
* **
24144435 AGCAAAATAGC
1 AACAAAATAAT
24144446 AACAAAATAAT
1 AACAAAATAAT
*
24144457 AGCAAAA
1 AACAAAA
24144464 CAACTACAAA
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (11 bp):
AACAAAATAAT
Found at i:24144472 original size:22 final size:22
Alignment explanation
Indices: 24144427--24144474 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
24144417 ATATAATAAT
* * *
24144427 AAAATGATAGCAAAATAGCAAC
1 AAAATAATAGCAAAACAACAAC
*
24144449 AAAATAATAGCAAAACAACTAC
1 AAAATAATAGCAAAACAACAAC
24144471 AAAA
1 AAAA
24144475 AAAAAAAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.65, C:0.15, G:0.08, T:0.12
Consensus pattern (22 bp):
AAAATAATAGCAAAACAACAAC
Found at i:24145049 original size:14 final size:14
Alignment explanation
Indices: 24145032--24145072 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
24145022 AACACAATAC
24145032 TCAATCTTCAATTT
1 TCAATCTTCAATTT
*
24145046 TCAATCTTCAAATT
1 TCAATCTTCAATTT
24145060 TCAAATC-TCAATT
1 TC-AATCTTCAATT
24145073 CTGAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (14 bp):
TCAATCTTCAATTT
Found at i:24151436 original size:26 final size:25
Alignment explanation
Indices: 24151402--24151487 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 25
24151392 CAGTAATTTA
*
24151402 GCTCATACGAGCCCAGTCAAGATATC
1 GCTCTTACGAG-CCAGTCAAGATATC
* *
24151428 GCTCTTACGAGCCAATACAATATATC
1 GCTCTTACGAGCCAGT-CAAGATATC
**
24151454 GCTCTTACGAGCCAGTTTAGTATATC
1 GCTCTTACGAGCCAGTCAAG-ATATC
24151480 GCTCTTAC
1 GCTCTTAC
24151488 AAGCTAGTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
25 5 0.10
26 46 0.90
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (25 bp):
GCTCTTACGAGCCAGTCAAGATATC
Found at i:24151496 original size:26 final size:26
Alignment explanation
Indices: 24151423--24151505 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
24151413 CCCAGTCAAG
* * * *
24151423 ATATCGCTCTTACGAGCCAATACAAT
1 ATATCGCTCTTACAAGCCAGTTCAGT
* *
24151449 ATATCGCTCTTACGAGCCAGTTTAGT
1 ATATCGCTCTTACAAGCCAGTTCAGT
*
24151475 ATATCGCTCTTACAAGCTAGTTCAGT
1 ATATCGCTCTTACAAGCCAGTTCAGT
24151501 ATATC
1 ATATC
24151506 TTCCATCTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (26 bp):
ATATCGCTCTTACAAGCCAGTTCAGT
Found at i:24166312 original size:26 final size:26
Alignment explanation
Indices: 24166270--24166404 Score: 137
Period size: 26 Copynumber: 5.2 Consensus size: 26
24166260 CCTAGTCAGG
* *
24166270 ATATCGCT-TCTACGAGCTAGTACAAT
1 ATATCGCTCT-TACGAGCCAGTTCAAT
* * *
24166296 ATATTGCTCTTATGAGCCAGTTCAGT
1 ATATCGCTCTTACGAGCCAGTTCAAT
* *
24166322 ATGTCGCTCTTACGATCCAGTTCAAT
1 ATATCGCTCTTACGAGCCAGTTCAAT
* * *
24166348 ATATCGCTCTTACGAGTCAGTTTAGT
1 ATATCGCTCTTACGAGCCAGTTCAAT
* * *
24166374 ATATCACTCTTACGAGCCAATTCAGT
1 ATATCGCTCTTACGAGCCAGTTCAAT
24166400 ATATC
1 ATATC
24166405 TTCAGAGTCT
Statistics
Matches: 89, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 88 0.99
27 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (26 bp):
ATATCGCTCTTACGAGCCAGTTCAAT
Found at i:24166329 original size:52 final size:52
Alignment explanation
Indices: 24166247--24166392 Score: 161
Period size: 52 Copynumber: 2.8 Consensus size: 52
24166237 TTCAGTAATT
* * *
24166247 TTGCTCATATGAGCCTAG-TCAGGATATCGCT-TCTACGAGCTAGTACAATATA
1 TTGCTCTTATGAGCC-AGTTCAGTATATCGCTCT-TACGAGCCAGTACAATATA
* * *
24166299 TTGCTCTTATGAGCCAGTTCAGTATGTCGCTCTTACGATCCAGTTCAATATA
1 TTGCTCTTATGAGCCAGTTCAGTATATCGCTCTTACGAGCCAGTACAATATA
* * * * *
24166351 TCGCTCTTACGAGTCAGTTTAGTATATCACTCTTACGAGCCA
1 TTGCTCTTATGAGCCAGTTCAGTATATCGCTCTTACGAGCCA
24166393 ATTCAGTATA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
51 2 0.03
52 76 0.96
53 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCTCTTATGAGCCAGTTCAGTATATCGCTCTTACGAGCCAGTACAATATA
Found at i:24167399 original size:30 final size:31
Alignment explanation
Indices: 24167349--24167410 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
24167339 TTATGTCTTT
24167349 TACGATTTAATCCTTTTTCACTTAATAACTA
1 TACGATTTAATCCTTTTTCACTTAATAACTA
24167380 TACGATTTAATCC-TTTTCACTTAATAACTA
1 TACGATTTAATCCTTTTTCACTTAATAACTA
24167410 T
1 T
24167411 CCAAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.45
Consensus pattern (31 bp):
TACGATTTAATCCTTTTTCACTTAATAACTA
Found at i:24170393 original size:19 final size:21
Alignment explanation
Indices: 24170355--24170398 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
24170345 TGGCCAAGGG
*
24170355 CACGGGCATGTGTGGTTTGATA
1 CACGGGCA-GTGTGGTTTGAGA
24170377 CACGGGCA-TGT-GTTTGAGA
1 CACGGGCAGTGTGGTTTGAGA
24170396 CAC
1 CAC
24170399 AAGATCATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
22 8 0.38
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.27
Consensus pattern (21 bp):
CACGGGCAGTGTGGTTTGAGA
Found at i:24172411 original size:60 final size:59
Alignment explanation
Indices: 24172166--24172443 Score: 310
Period size: 61 Copynumber: 4.7 Consensus size: 59
24172156 GAGAATTCGA
* * * *
24172166 GGTTAAAATAT-AGTTTTGGAAAAGTTTAAGGGTAAAAATGTAATTTTGGTAAAGTTTAG
1 GGTTAAAATATGA-TTTTAGAGAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
* * * * *
24172225 GGTTGAAATGTGATTTTAGAGAAGTTTAA-GGTTAAAATGTGATTTTGGGAAGGTTTAG
1 GGTTAAAATATGATTTTAGAGAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
* * ** *
24172283 GGTCAAAATATGATTTTGGAGAAGTTTGGGGGTTAAAATGTAATTTTGGAAAAGTTTTTGG
1 GGTTAAAATATGATTTTAGAGAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAG--TTTAG
* * *
24172344 GGTTAAAATGTGATTTT-GAGAAAGTTTAAGGGTTAAAATATAATTTTGAAAAAGTTTAAG
1 GGTTAAAATATGATTTTAGAG-AAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTT-AG
* **
24172404 GGTTAAAATATAATTTTAGAGAAGTTTGGGGGTTAAAATG
1 GGTTAAAATATGATTTTAGAGAAGTTTAAGGGTTAAAATG
24172444 GGATTTTAAA
Statistics
Matches: 182, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
58 48 0.26
59 47 0.26
60 36 0.20
61 51 0.28
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.37
Consensus pattern (59 bp):
GGTTAAAATATGATTTTAGAGAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
Found at i:24172451 original size:30 final size:28
Alignment explanation
Indices: 24172187--24172450 Score: 215
Period size: 30 Copynumber: 8.9 Consensus size: 28
24172177 AGTTTTGGAA
* *
24172187 AAGTTTAAGGGTAAAAATGTAATTTTG-G
1 AAGTTT-AGGGTTAAAATGTGATTTTGAG
*
24172215 TAAAGTTTAGGGTTGAAATGTGATTTTAGAG
1 --AAGTTTAGGGTTAAAATGTGATTTT-GAG
* *
24172246 AAGTTTAAGGTTAAAATGTGATTTTGGG
1 AAGTTTAGGGTTAAAATGTGATTTTGAG
* *
24172274 AAGGTTTAGGGTCAAAATATGATTTTGGAG
1 AA-GTTTAGGGTTAAAATGTGATTTT-GAG
* * *
24172304 AAGTTTGGGGGTTAAAATGTAATTTTGGAA
1 AAGTTT-AGGGTTAAAATGTGATTTT-GAG
*
24172334 AAGTTTTTGGGGTTAAAATGTGATTTTGAG
1 AAG--TTTAGGGTTAAAATGTGATTTTGAG
* * *
24172364 AAAGTTTAAGGGTTAAAATATAATTTTGAAA
1 -AAGTTT-AGGGTTAAAATGTGATTTTG-AG
* *
24172395 AAGTTTAAGGGTTAAAATATAATTTTAGAG
1 AAGTTT-AGGGTTAAAATGTGATTTT-GAG
* *
24172425 AAGTTTGGGGGTTAAAATGGGATTTT
1 AAGTTT-AGGGTTAAAATGTGATTTT
24172451 AAATAAAATA
Statistics
Matches: 196, Mismatches: 27, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.02
29 66 0.34
30 99 0.51
31 24 0.12
32 3 0.02
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (28 bp):
AAGTTTAGGGTTAAAATGTGATTTTGAG
Found at i:24174919 original size:39 final size:39
Alignment explanation
Indices: 24174869--24175379 Score: 401
Period size: 39 Copynumber: 13.1 Consensus size: 39
24174859 TTGTAATTTG
*
24174869 CCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
* *
24174908 CCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTAC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
* * * * *
24174947 CCCAGGCTCGGGGTAAAAGATCGGATGGTTGTAATCTGC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
** *
24174986 CCCAGGCTCAAGGTAAAAGATTGGTTGATGTTGATCTGC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
* * *
24175025 CCGAGGCTCGGGGTAAAAGA-TCG--GATGGCTGCAATTTGC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGG-TG--ATCTGC
* * *
24175064 CCCAGGCTCGAGGTAAGAGATTGGCTT-ATAGTGATCTGC
1 CCCAGGCTCGGGGTAAAAGATTGG-TTGATGGTGATCTGC
* * * * * **
24175103 CCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
* ** * * *
24175142 CCCAGGCTCGGGGTAAGAGATTGACTGACGATGATTTGC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
* *
24175181 CCCAGGCTTGGGGTAAAAGATTGG--G-TGGCTGCAATCTGT
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGG-TG--ATCTGC
* * * *
24175220 CCCGGGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
* * * * * * * * *
24175259 CCTAGGCTTGAGGTAAAAGATCGGATGGTTGCGATCTAC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
* ** *
24175298 CCCAAGCTCGACGTAAGAGATTGGTTGATGGTGATCTGC
1 CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
* * * *
24175337 CCTAGGCT-GAGGGTAAAAGATCGGATAACT-GTGATCTGC
1 CCCAGGCTCG-GGGTAAAAGATTGGTTGA-TGGTGATCTGC
24175376 CCCA
1 CCCA
24175380 TGATTAAGGA
Statistics
Matches: 363, Mismatches: 93, Indels: 32
0.74 0.19 0.07
Matches are distributed among these distances:
36 5 0.01
37 5 0.01
38 4 0.01
39 336 0.93
40 3 0.01
41 4 0.01
42 6 0.02
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (39 bp):
CCCAGGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGC
Found at i:24174984 original size:78 final size:78
Alignment explanation
Indices: 24174869--24175362 Score: 587
Period size: 78 Copynumber: 6.3 Consensus size: 78
24174859 TTGTAATTTG
* * * * * ** *
24174869 CCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATTGGTT
1 CCCAGGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGTT
*
24174934 GATGGTGATCTAC
66 GATGGTGATCTGC
* * *
24174947 CCCAGGCTCGGGGTAAAAGATCGGATGGTTGTAATCTGCCCCAGGCTCAAGGTAAAAGATTGGTT
1 CCCAGGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGTT
*
24175012 GATGTTGATCTGC
66 GATGGTGATCTGC
* * *
24175025 CCGAGGCTCGGGGTAAAAGATCGGATGGCTGCAATTTGCCCCAGGCTCGAGGTAAGAGATTGGCT
1 CCCAGGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGG-T
*
24175090 T-ATAGTGATCTGC
65 TGATGGTGATCTGC
* * **
24175103 CCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACT
1 CCCAGGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGTT
* * *
24175168 GACGATGATTTGC
66 GATGGTGATCTGC
* * * * * * * *
24175181 CCCAGGCTTGGGGTAAAAGATTGGGTGGCTGCAATCTGTCCCGGGCTCGGGGTAAGAGATTGGCT
1 CCCAGGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGTT
*
24175246 AATGGTGATCTGC
66 GATGGTGATCTGC
* * * * * * *
24175259 CCTAGGCTTGAGGTAAAAGATCGGATGGTTGCGATCTACCCCAAGCTCGACGTAAGAGATTGGTT
1 CCCAGGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGTT
24175324 GATGGTGATCTGC
66 GATGGTGATCTGC
*
24175337 CCTAGGCT-GAGGGTAAAAGATCGGAT
1 CCCAGGCTCG-GGGTAAAAGATCGGAT
24175363 AACTGTGATC
Statistics
Matches: 356, Mismatches: 57, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
77 2 0.01
78 352 0.99
79 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (78 bp):
CCCAGGCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGTT
GATGGTGATCTGC
Found at i:24190335 original size:7 final size:7
Alignment explanation
Indices: 24190320--24190357 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
24190310 GAAAAAAGTG
*
24190320 AACGATC
1 AACGGTC
24190327 AACGGTC
1 AACGGTC
*
24190334 AATGGTC
1 AACGGTC
24190341 AAC-GTC
1 AACGGTC
24190347 AACGGTC
1 AACGGTC
24190354 AACG
1 AACG
24190358 ATTCGAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (7 bp):
AACGGTC
Found at i:24204465 original size:43 final size:43
Alignment explanation
Indices: 24204412--24204585 Score: 152
Period size: 43 Copynumber: 4.0 Consensus size: 43
24204402 CTGTTAATGT
* *
24204412 TAACGACGTTTTTGGGAAAAACACCATTAAAGACCATGTTCTA
1 TAACGACGTTTGTGGGAAAAACACCACTAAAGACCATGTTCTA
* * *
24204455 TAACGACGTTTGTGTGAAAAACACCCCTAAAGACCATGTTCTT
1 TAACGACGTTTGTGGGAAAAACACCACTAAAGACCATGTTCTA
* * * ** * * *
24204498 TAGCGGA-ATTTATAAGAAAAATACCGCTAAAGACCATGTTCTT
1 TAAC-GACGTTTGTGGGAAAAACACCACTAAAGACCATGTTCTA
** * * * **
24204541 TAGTGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCATGTTCTA
1 TAACGACGTTTGTGGGAAAAACACCACTAAAGACCATGTTCTA
24204584 TA
1 TA
24204586 GCGGCATTTT
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 1 0.01
43 103 0.97
44 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (43 bp):
TAACGACGTTTGTGGGAAAAACACCACTAAAGACCATGTTCTA
Found at i:24204604 original size:86 final size:86
Alignment explanation
Indices: 24204439--24204604 Score: 206
Period size: 86 Copynumber: 1.9 Consensus size: 86
24204429 AAAACACCAT
* *
24204439 TAAAGACCATGTTCTATAACGACGTTTGTGTGAAAAACACCCCTAAAGACCATGTTCTTTAGCGG
1 TAAAGACCATGTTCTATAACGACGTTTGTGGGAAAAACACCCCTAAAGACCATGTTCTATAGCGG
*
24204504 AATTTATAAGAAAAATACCGC
66 AATTTATAACAAAAATACCGC
* ** * * * **
24204525 TAAAGACCATGTTCTTTAGTGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCATGTTCTATAGCGG
1 TAAAGACCATGTTCTATAACGACGTTTGTGGGAAAAACACCCCTAAAGACCATGTTCTATAGCGG
* * *
24204590 CATTTTTCACAAAAA
66 AATTTATAACAAAAA
24204605 CGTCGTGACT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (86 bp):
TAAAGACCATGTTCTATAACGACGTTTGTGGGAAAAACACCCCTAAAGACCATGTTCTATAGCGG
AATTTATAACAAAAATACCGC
Found at i:24209494 original size:20 final size:20
Alignment explanation
Indices: 24209428--24209515 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
24209418 GGCATTGAGA
* *
24209428 TGCATATAAGGGCATAAAAG
1 TGCATACAAGGGCATCAAAG
* *
24209448 TGCATA-TAGCGGCATCAAAA
1 TGCATACAAG-GGCATCAAAG
*
24209468 TGCATACAAGAGCATCAAAG
1 TGCATACAAGGGCATCAAAG
* *
24209488 TGCATAC-AGCGGCACCGAAG
1 TGCATACAAG-GGCATCAAAG
24209508 TGCATACA
1 TGCATACA
24209516 GGGTTAACAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.07
20 49 0.89
21 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (20 bp):
TGCATACAAGGGCATCAAAG
Found at i:24209512 original size:40 final size:40
Alignment explanation
Indices: 24209427--24209515 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
24209417 GGGCATTGAG
* * * *
24209427 ATGCATATAAGGGCATAAAAGTGCATATAGCGGCATCAAA
1 ATGCATACAAGAGCATAAAAGTGCATACAGCGGCACCAAA
* *
24209467 ATGCATACAAGAGCATCAAAGTGCATACAGCGGCACCGAA
1 ATGCATACAAGAGCATAAAAGTGCATACAGCGGCACCAAA
*
24209507 GTGCATACA
1 ATGCATACA
24209516 GGGTTAACAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (40 bp):
ATGCATACAAGAGCATAAAAGTGCATACAGCGGCACCAAA
Found at i:24209516 original size:20 final size:20
Alignment explanation
Indices: 24209438--24209516 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
24209428 TGCATATAAG
* *
24209438 GGCATAAAAGTGCATATAGC
1 GGCATCAAAGTGCATACAGC
*
24209458 GGCATCAAAATGCATACAAG-
1 GGCATCAAAGTGCATAC-AGC
*
24209478 AGCATCAAAGTGCATACAGC
1 GGCATCAAAGTGCATACAGC
* *
24209498 GGCACCGAAGTGCATACAG
1 GGCATCAAAGTGCATACAG
24209517 GGTTAACAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.04
20 45 0.92
21 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (20 bp):
GGCATCAAAGTGCATACAGC
Found at i:24214115 original size:18 final size:20
Alignment explanation
Indices: 24214064--24214121 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
24214054 AATTTTATAT
*
24214064 ATTTTTAAAATATAAATTTTGA
1 ATTTTTAAAA-AT-TATTTTGA
*
24214086 ATTTTTATAAA-TATTTTGA
1 ATTTTTAAAAATTATTTTGA
24214105 A-TTTTAAAAATTATTTT
1 ATTTTTAAAAATTATTTT
24214122 ATTTTTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.25
19 14 0.44
21 1 0.03
22 9 0.28
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTTAAAAATTATTTTGA
Found at i:24218752 original size:16 final size:16
Alignment explanation
Indices: 24218673--24218807 Score: 64
Period size: 15 Copynumber: 9.1 Consensus size: 16
24218663 ATATATTAAT
24218673 TTATATTTTAATAATAA
1 TTATA-TTTAATAATAA
24218690 TTATA-TTAA-AA-AA
1 TTATATTTAATAATAA
* *
24218703 -TATTATTAAATTATATA
1 TTA-TATTTAATAATA-A
*
24218720 TTAT-TTT-ATTA-AA
1 TTATATTTAATAATAA
24218733 TTATATTTAATAATAA
1 TTATATTTAATAATAA
* *
24218749 TTAT-GTTAAAATATAA
1 TTATATTTAATA-ATAA
*
24218765 TTA-AATTAAT--TAA
1 TTATATTTAATAATAA
* *
24218778 -TAT-TTTTATTA-AA
1 TTATATTTAATAATAA
24218791 TTATATTTAATAATAA
1 TTATATTTAATAATAA
24218807 T
1 T
24218808 CATTAAAATT
Statistics
Matches: 89, Mismatches: 12, Indels: 35
0.65 0.09 0.26
Matches are distributed among these distances:
12 8 0.09
13 14 0.16
14 12 0.13
15 23 0.26
16 23 0.26
17 7 0.08
18 2 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (16 bp):
TTATATTTAATAATAA
Found at i:24218758 original size:26 final size:26
Alignment explanation
Indices: 24218726--24218807 Score: 74
Period size: 32 Copynumber: 2.9 Consensus size: 26
24218716 TATATTATTT
24218726 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTTAATAATAATTA
* * * *
24218752 TGTTAAAATATAATTAAATTAATTAATATTTT
1 TATT-AAAT-T-A-T-ATTTAA-TAATAATTA
24218784 TATTAAATTATATTTAATAATAAT
1 TATTAAATTATATTTAATAATAAT
24218808 CATTAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
26 9 0.21
27 9 0.21
28 2 0.05
29 2 0.05
30 2 0.05
31 9 0.21
32 10 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (26 bp):
TATTAAATTATATTTAATAATAATTA
Found at i:24218802 original size:58 final size:58
Alignment explanation
Indices: 24218666--24218807 Score: 198
Period size: 58 Copynumber: 2.4 Consensus size: 58
24218656 TTAGATTATA
* * *
24218666 TATTAATTTATATTTTAATAATAATTATATTAAAAAATATTATTAAATTATATATTATTT
1 TATTAAATTATA-TTTAATAATAATTATATT-AAAAATATAATTAAATTATATAATATTT
*
24218726 TATTAAATTATATTTAATAATAATTATGTT-AAAATATAATTAAATTA-ATTAATATTTT
1 TATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAATTATA-TAATA-TTT
24218784 TATTAAATTATATTTAATAATAAT
1 TATTAAATTATATTTAATAATAAT
24218808 CATTAAAATT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
56 1 0.01
57 20 0.26
58 27 0.36
59 17 0.22
60 11 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (58 bp):
TATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAATTATATAATATTT
Found at i:24218998 original size:16 final size:16
Alignment explanation
Indices: 24218977--24219048 Score: 101
Period size: 16 Copynumber: 4.5 Consensus size: 16
24218967 TGAATTACTG
24218977 ATTACAG-TCCTATTCC
1 ATTACAGCT-CTATTCC
*
24218993 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
*
24219009 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
*
24219025 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
24219041 ATTACAGC
1 ATTACAGC
24219049 GAACCAAACG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
16 49 0.98
17 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:24220037 original size:24 final size:24
Alignment explanation
Indices: 24219969--24220040 Score: 63
Period size: 26 Copynumber: 2.9 Consensus size: 24
24219959 TTTTAATAAA
* * *
24219969 TAAAAAATTTAAAATAATTATATAT
1 TAAAAAAATTAAAA-AAATATTTAT
* * *
24219994 TAAAATAAAATAATATAAATATTTTT
1 TAAAA-AAATTAA-AAAAATATTTAT
24220020 TAAAAAAATTAAAAAAATATT
1 TAAAAAAATTAAAAAAATATT
24220041 ATGGGTAAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
24 8 0.22
25 11 0.30
26 17 0.46
27 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAAAAATTAAAAAAATATTTAT
Found at i:24222234 original size:21 final size:21
Alignment explanation
Indices: 24222203--24222258 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
24222193 CAGTAGTAGA
*
24222203 CTTCTACCGATACTTGTGATG
1 CTTCTACCGATACTTGTCATG
* * *
24222224 GTTCTAGCGATACATGTCATG
1 CTTCTACCGATACTTGTCATG
24222245 CTTCTACCGATACT
1 CTTCTACCGATACT
24222259 AAAAACTCCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (21 bp):
CTTCTACCGATACTTGTCATG
Found at i:24224522 original size:45 final size:45
Alignment explanation
Indices: 24224450--24224547 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 45
24224440 CACTTGGACA
* *
24224450 GCACATCGCTAGCCAAATCGGAGGTGGTTCAACCCTCGGTTGCAT
1 GCACATCGCTAGCCAAATCGGAAGTGGTTCAACCCTCGATTGCAT
* *
24224495 GCACATTGCTAGCCAAATTGGAAGTGGTTCAACCCTCGATTGCAT
1 GCACATCGCTAGCCAAATCGGAAGTGGTTCAACCCTCGATTGCAT
24224540 GCACATCG
1 GCACATCG
24224548 AGTCACTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (45 bp):
GCACATCGCTAGCCAAATCGGAAGTGGTTCAACCCTCGATTGCAT
Done.