Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 28 of 100
Found at i:5186056 original size:3 final size:3
Alignment explanation
Indices: 5186043--5186085 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
5186033 TAAATAGCTC
5186043 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5186086 TTTTGTTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5187152 original size:24 final size:24
Alignment explanation
Indices: 5187105--5187185 Score: 103
Period size: 26 Copynumber: 3.4 Consensus size: 24
5187095 ATTATATATA
* *
5187105 TTTTAT-TAAACTTAATTTTT-AT
1 TTTTATATAAATTTTATTTTTAAT
5187127 TTTTATATAAATTTTATTTTTAAT
1 TTTTATATAAATTTTATTTTTAAT
*
5187151 TTATATATATAACTTTTATTTTTAAT
1 TT-T-TATATAAATTTTATTTTTAAT
5187177 TTTTATATA
1 TTTTATATA
5187186 TATGTGAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 6 0.12
23 12 0.23
24 10 0.19
25 2 0.04
26 22 0.42
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATATAAATTTTATTTTTAAT
Found at i:5188640 original size:52 final size:52
Alignment explanation
Indices: 5188555--5188690 Score: 143
Period size: 52 Copynumber: 2.6 Consensus size: 52
5188545 ATAACCATAT
* * * *
5188555 AAACTTGCCCATTAAAAATC-CTTCTCCTCTTAGAATCCCTCT-TCTGTAAGTC
1 AAACTTGCCTATTAAGAATCTCTT-TCTTCTTAGAATCCCTCTCT-TGCAAGTC
* ***
5188607 AAACTTGCCTATTAAGAATCTCTTTCTTTTTAGAATTTTTCTCTTGCAAGTC
1 AAACTTGCCTATTAAGAATCTCTTTCTTCTTAGAATCCCTCTCTTGCAAGTC
*
5188659 AAACTTACCTATTAAGAATCTTCTTTC-TCTTA
1 AAACTTGCCTATTAAGAATC-TCTTTCTTCTTA
5188691 TAATTCTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
52 61 0.86
53 10 0.14
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.41
Consensus pattern (52 bp):
AAACTTGCCTATTAAGAATCTCTTTCTTCTTAGAATCCCTCTCTTGCAAGTC
Found at i:5188710 original size:52 final size:52
Alignment explanation
Indices: 5188602--5188710 Score: 141
Period size: 52 Copynumber: 2.1 Consensus size: 52
5188592 CCTCTTCTGT
* * *
5188602 AAGTCAAACTTGCCTATTAAGAATCTCTTTCTTTTTAGAATTTTTCTCTTGC
1 AAGTCAAACTTACCTATTAAGAATCTCTTTCTTCTTAGAATTTTTCTCTTGA
* *
5188654 AAGTCAAACTTACCTATTAAGAATCTTCTTTC-TCTTATAATTCTTT-TTTTGA
1 AAGTCAAACTTACCTATTAAGAATC-TCTTTCTTCTTAGAATT-TTTCTCTTGA
5188706 AAGTC
1 AAGTC
5188711 TTCTTGTCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
52 41 0.82
53 9 0.18
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (52 bp):
AAGTCAAACTTACCTATTAAGAATCTCTTTCTTCTTAGAATTTTTCTCTTGA
Found at i:5188751 original size:11 final size:11
Alignment explanation
Indices: 5188735--5188776 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5188725 GCAATATCTG
*
5188735 ACAAATCCCAA
1 ACAAATCTCAA
*
5188746 ACAAATCTCTA
1 ACAAATCTCAA
5188757 ACAAATCTCAA
1 ACAAATCTCAA
5188768 ACAAATCTC
1 ACAAATCTC
5188777 TTATGGGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:5188760 original size:22 final size:22
Alignment explanation
Indices: 5188735--5188777 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5188725 GCAATATCTG
5188735 ACAAATCCCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
*
5188757 ACAAATCTCAAACAAATCTCT
1 ACAAATCCCAAACAAATCTCT
5188778 TATGGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:5189033 original size:23 final size:25
Alignment explanation
Indices: 5188994--5189058 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
5188984 GAACTTGTTT
**
5188994 CTTCCCATGTCTCAAACC-AT-GCA
1 CTTCCCACATCTCAAACCTATAGCA
* * *
5189017 CTTCCCACATCTTAAACCTTTAGCT
1 CTTCCCACATCTCAAACCTATAGCA
5189042 CTTCCCACATCTCAAAC
1 CTTCCCACATCTCAAAC
5189059 TTTTAGCTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 15 0.44
24 1 0.03
25 18 0.53
ACGTcount: A:0.26, C:0.40, G:0.05, T:0.29
Consensus pattern (25 bp):
CTTCCCACATCTCAAACCTATAGCA
Found at i:5189142 original size:25 final size:25
Alignment explanation
Indices: 5189017--5189142 Score: 101
Period size: 25 Copynumber: 5.1 Consensus size: 25
5189007 AAACCATGCA
* **
5189017 CTTCCCACATCTTAAACCTTTAGCT
1 CTTCTCACATCTCGAACCTTTAGCT
* * *
5189042 CTTCCCACATCTCAAACTTTTAGCT
1 CTTCTCACATCTCGAACCTTTAGCT
* *
5189067 CTTCT-ACGTCTCGAACCTTCAGCT
1 CTTCTCACATCTCGAACCTTTAGCT
* * * * *
5189091 TTTTTCACATCTTGAATCTTTAACT
1 CTTCTCACATCTCGAACCTTTAGCT
* * *
5189116 CTTCTCACGTTTCGAACCTTCAGCT
1 CTTCTCACATCTCGAACCTTTAGCT
5189141 CT
1 CT
5189143 GATACCACTT
Statistics
Matches: 78, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
24 18 0.23
25 60 0.77
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (25 bp):
CTTCTCACATCTCGAACCTTTAGCT
Found at i:5189758 original size:52 final size:52
Alignment explanation
Indices: 5189672--5189828 Score: 194
Period size: 52 Copynumber: 3.0 Consensus size: 52
5189662 TATAACCATA
* * * * * *
5189672 CAAACTTGCCCATTAAAAATTCT-TCTCCTCTTAGAATTATTCTTCTGTAAGT
1 CAAACTTACCTATTAAGAATTCTCT-TTCTCTTAGAATTCTTCTTCTGCAAGT
*
5189724 CAAACTTACCTATTAAGAA-TCTCTTTCGTTTTAGAATTCTTC-TCTTGCAAGT
1 CAAACTTACCTATTAAGAATTCTCTTTC-TCTTAGAATTCTTCTTC-TGCAAGT
*
5189776 CAAACTTACCTATTAAGAATTCTCTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAATTCTCTTTCTCTTAGAATTCTTCTTCTGCAAGT
5189828 C
1 C
5189829 TTCTTATCCA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
51 7 0.08
52 75 0.82
53 9 0.10
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.42
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATTCTCTTTCTCTTAGAATTCTTCTTCTGCAAGT
Found at i:5193526 original size:23 final size:23
Alignment explanation
Indices: 5193496--5193541 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5193486 ATATAAAGAA
5193496 TTACTTTTATATTTTAATTGCAT
1 TTACTTTTATATTTTAATTGCAT
5193519 TTACTTTTATATTTTAATTGCAT
1 TTACTTTTATATTTTAATTGCAT
5193542 CTCTTCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.61
Consensus pattern (23 bp):
TTACTTTTATATTTTAATTGCAT
Found at i:5194971 original size:7 final size:7
Alignment explanation
Indices: 5194959--5194993 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
5194949 ACAATTAGAA
5194959 AATAAAT
1 AATAAAT
5194966 AATAAAT
1 AATAAAT
5194973 AATAAAT
1 AATAAAT
**
5194980 AGGAAAT
1 AATAAAT
5194987 AATAAAT
1 AATAAAT
5194994 TACAAAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (7 bp):
AATAAAT
Found at i:5195605 original size:26 final size:26
Alignment explanation
Indices: 5195570--5195621 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5195560 TCATGACCCA
5195570 AAAAAAAAAAAAAAATCCTTCTACTC
1 AAAAAAAAAAAAAAATCCTTCTACTC
**
5195596 AAAAAAAAAAAAATTTCCTTCTACTC
1 AAAAAAAAAAAAAAATCCTTCTACTC
5195622 TTATGTATCT
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:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (26 bp):
AAAAAAAAAAAAAAATCCTTCTACTC
Found at i:5195835 original size:42 final size:43
Alignment explanation
Indices: 5195754--5195838 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
5195744 GCAGATACTG
*
5195754 CAGTGATGAAATTTAAATTTTAAATCTATTGGACTAAAAGTTA
1 CAGTGATGAAATTTAAATTTTAAATCTATGGGACTAAAAGTTA
* * *
5195797 CAGTGAT-AAATTTGAATTTT-AATTTATGGGATTAAAAAGTTA
1 CAGTGATGAAATTTAAATTTTAAATCTATGGGACT-AAAAGTTA
5195839 AATGCTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 10 0.27
42 20 0.54
43 7 0.19
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (43 bp):
CAGTGATGAAATTTAAATTTTAAATCTATGGGACTAAAAGTTA
Found at i:5196211 original size:19 final size:19
Alignment explanation
Indices: 5196178--5196220 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5196168 AAGTTTTATA
*
5196178 AAAAATATAATAAAATAATG
1 AAAAATATAAAAAAATAA-G
5196198 AAAAATA-AAAAAAATAAG
1 AAAAATATAAAAAAATAAG
5196216 AAAAA
1 AAAAA
5196221 AGAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAATATAAAAAAATAAG
Found at i:5198657 original size:2 final size:2
Alignment explanation
Indices: 5198652--5198678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5198642 ATTAAATTGA
5198652 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
5198679 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5199053 original size:14 final size:14
Alignment explanation
Indices: 5199034--5199060 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5199024 AAAATAAAAC
5199034 TAAATAATAAATAG
1 TAAATAATAAATAG
5199048 TAAATAATAAATA
1 TAAATAATAAATA
5199061 ACAAAACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
TAAATAATAAATAG
Found at i:5199135 original size:2 final size:2
Alignment explanation
Indices: 5199128--5199178 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5199118 ATTACATGCT
5199128 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5199170 TC TC TC TC T
1 TC TC TC TC T
5199179 TTGTTTAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5202533 original size:21 final size:20
Alignment explanation
Indices: 5202507--5202545 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5202497 CTCCATTAGG
5202507 ATCAATTAGAAACAATCAAGA
1 ATCAATTA-AAACAATCAAGA
*
5202528 ATCAATTAAAAGAATCAA
1 ATCAATTAAAACAATCAA
5202546 AAAAGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (20 bp):
ATCAATTAAAACAATCAAGA
Found at i:5208074 original size:33 final size:30
Alignment explanation
Indices: 5208058--5208122 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
5208048 TTTGTTTAAC
5208058 TTAATTTTTATTTTTATATAAATTTTATTT
1 TTAATTTTTATTTTTATATAAATTTTATTT
**
5208088 TTAATTTTTA--TAGATA-AAACTTTTATTT
1 TTAATTTTTATTTTTATATAAA-TTTTATTT
5208116 TTAATTT
1 TTAATTT
5208123 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.09
28 19 0.59
30 10 0.31
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (30 bp):
TTAATTTTTATTTTTATATAAATTTTATTT
Found at i:5211724 original size:43 final size:43
Alignment explanation
Indices: 5211700--5212028 Score: 129
Period size: 43 Copynumber: 7.6 Consensus size: 43
5211690 AAGTTTCATA
5211700 ACTTTTGAGAA-AT-AATAAAGCTCCTCTAAGCAAAGGTTCAACC
1 ACTTTTGA-AATATAAATAAAGCTCCTCTAAGCAAAGGTTCAA-C
* * * *
5211743 ACTTTTGAAATATAAATAAAGCTCCTCTAAACAGAGGCTCAATA
1 ACTTTTGAAATATAAATAAAGCTCCTCTAAGCAAAGGTTCAA-C
* * * * ** * *
5211787 AC-TTTAAAAAATAAATAAGGCTTCTCTAAATAAAGGCTAAAC
1 ACTTTTGAAATATAAATAAAGCTCCTCTAAGCAAAGGTTCAAC
** ** * * * *
5211829 AAC-TTTGAAA-AGTAAATATGGCTAATTTAAACAGAGGCTC-AC
1 -ACTTTTGAAATA-TAAATAAAGCTCCTCTAAGCAAAGGTTCAAC
* * * ** * * *
5211871 GA-TTGTGAAAAATAAATAAGGCTATTCTAAACATAGGCTCAAC
1 -ACTTTTGAAATATAAATAAAGCTCCTCTAAGCAAAGGTTCAAC
* * * * *
5211914 GACTTTTGAAA-AGTAAATAAGGCTCCTCTCAA-TAGAGGCTCAATG
1 -ACTTTTGAAATA-TAAATAAAGCTCCTCT-AAGCAAAGGTTCAA-C
* * * * * *
5211959 ACTTTTGAAAAATAAATAAAGCACCTCTAAACAAAAGCTCAATG
1 ACTTTTGAAATATAAATAAAGCTCCTCTAAGCAAAGGTTCAA-C
*
5212003 AC-TTTGAAATGTAAATAAAGCTCCTC
1 ACTTTTGAAATATAAATAAAGCTCCTC
5212029 GACAATAATG
Statistics
Matches: 232, Mismatches: 41, Indels: 26
0.78 0.14 0.09
Matches are distributed among these distances:
42 36 0.16
43 100 0.43
44 93 0.40
45 3 0.01
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (43 bp):
ACTTTTGAAATATAAATAAAGCTCCTCTAAGCAAAGGTTCAAC
Found at i:5211771 original size:44 final size:43
Alignment explanation
Indices: 5211700--5212028 Score: 263
Period size: 44 Copynumber: 7.6 Consensus size: 43
5211690 AAGTTTCATA
* * *
5211700 ACTTTTGAGAAAT-AATAAAGCTCCTCTAAGCAAAGGTTCAACC
1 ACTTTTGA-AAATAAATAAAGCTCCTCTAAACAAAGGCTCAACG
* **
5211743 ACTTTTGAAATATAAATAAAGCTCCTCTAAACAGAGGCTCAATA
1 ACTTTTGAAA-ATAAATAAAGCTCCTCTAAACAAAGGCTCAACG
** * * * * *
5211787 ACTTTAAAAAATAAATAAGGCTTCTCTAAATAAAGGCTAAACA
1 ACTTTTGAAAATAAATAAAGCTCCTCTAAACAAAGGCTCAACG
** ** * *
5211830 AC-TTTGAAAAGTAAATATGGCTAATTTAAACAGAGGCTC-ACG
1 ACTTTTGAAAA-TAAATAAAGCTCCTCTAAACAAAGGCTCAACG
* * ** *
5211872 A-TTGTGAAAAATAAATAAGGCTATTCTAAACATAGGCTCAACG
1 ACTTTTG-AAAATAAATAAAGCTCCTCTAAACAAAGGCTCAACG
* * * * *
5211915 ACTTTTGAAAAGTAAATAAGGCTCCTCTCAATAGAGGCTCAATG
1 ACTTTTGAAAA-TAAATAAAGCTCCTCTAAACAAAGGCTCAACG
* * *
5211959 ACTTTTGAAAAATAAATAAAGCACCTCTAAACAAAAGCTCAATG
1 ACTTTTG-AAAATAAATAAAGCTCCTCTAAACAAAGGCTCAACG
*
5212003 AC-TTTGAAATGTAAATAAAGCTCCTC
1 ACTTTTGAAA-ATAAATAAAGCTCCTC
5212029 GACAATAATG
Statistics
Matches: 233, Mismatches: 43, Indels: 20
0.79 0.15 0.07
Matches are distributed among these distances:
42 41 0.18
43 90 0.39
44 98 0.42
45 4 0.02
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (43 bp):
ACTTTTGAAAATAAATAAAGCTCCTCTAAACAAAGGCTCAACG
Found at i:5211865 original size:86 final size:86
Alignment explanation
Indices: 5211703--5212020 Score: 295
Period size: 86 Copynumber: 3.7 Consensus size: 86
5211693 TTTCATAACT
* * * * * * *
5211703 TTTGAGAAAT-AATAAAGCTCCTCTAAGCAAAGGTTCAACCACTTTTGAAATA-TAAATAAAGCT
1 TTTGAAAAATAAATAAGGCTTCTCTAAACAAAGGCTCAACGAC-TTTGAAA-AGTAAATAAGGCT
** *
5211766 CCTCTAAACAGAGGCTCAATAAC
64 AATCTAAACAGAGGCTCAATGAC
* * * * *
5211789 TTTAAAAAATAAATAAGGCTTCTCTAAATAAAGGCTAAACAACTTTGAAAAGTAAATATGGCTAA
1 TTTGAAAAATAAATAAGGCTTCTCTAAACAAAGGCTCAACGACTTTGAAAAGTAAATAAGGCTAA
* *
5211854 TTTAAACAGAGGCTC-ACGA-
66 TCTAAACAGAGGCTCAATGAC
*
5211873 TTGTGAAAAATAAATAAGGCTAT-TCTAAACATAGGCTCAACGACTTTTGAAAAGTAAATAAGGC
1 TT-TGAAAAATAAATAAGGCT-TCTCTAAACAAAGGCTCAACGAC-TTTGAAAAGTAAATAAGGC
** * *
5211937 TCCTCTCAATAGAGGCTCAATGAC
63 TAATCTAAACAGAGGCTCAATGAC
* ** * * *
5211961 TTTTGAAAAATAAATAAAGCACCTCTAAACAAAAGCTCAATGACTTTGAAATGTAAATAA
1 -TTTGAAAAATAAATAAGGCTTCTCTAAACAAAGGCTCAACGACTTTGAAAAGTAAATAA
5212021 AGCTCCTCGA
Statistics
Matches: 188, Mismatches: 35, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
84 2 0.01
85 37 0.20
86 70 0.37
87 43 0.23
88 34 0.18
89 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (86 bp):
TTTGAAAAATAAATAAGGCTTCTCTAAACAAAGGCTCAACGACTTTGAAAAGTAAATAAGGCTAA
TCTAAACAGAGGCTCAATGAC
Found at i:5212277 original size:20 final size:20
Alignment explanation
Indices: 5212252--5212310 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
5212242 CAGGTCCGGG
5212252 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
5212272 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
5212292 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
5212311 GCCCAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:5212364 original size:10 final size:11
Alignment explanation
Indices: 5212349--5212374 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5212339 TTTACCCGTA
5212349 TTTTTTATTTT
1 TTTTTTATTTT
5212360 TTTTTTATTTT
1 TTTTTTATTTT
5212371 TTTT
1 TTTT
5212375 CTCTCTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:5212418 original size:12 final size:14
Alignment explanation
Indices: 5212403--5212439 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5212393 TATTTATTAT
5212403 TATGTAT-TA-ATA
1 TATGTATATATATA
5212415 TATGTATATATATA
1 TATGTATATATATA
*
5212429 TATATATATAT
1 TATGTATATAT
5212440 TTTTTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.32
13 2 0.09
14 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:5213077 original size:20 final size:20
Alignment explanation
Indices: 5213054--5213117 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
5213044 TGCCCAGTTT
*
5213054 CCGGCGAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
5213074 CCGGCAAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
5213094 CCGGCAAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
5213114 CCGG
1 CCGG
5213118 TGAATTTTCG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.41, C:0.31, G:0.23, T:0.05
Consensus pattern (20 bp):
CCGGCAAAGAATCCCAGAAA
Found at i:5213178 original size:20 final size:20
Alignment explanation
Indices: 5213135--5213179 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5213125 TCGGCCAACT
*
5213135 TCCGGCGAAAAAACCCAGAT
1 TCCGGCGAAAAAACCCAGAA
***
5213155 TCCGGCGAAAATTTCCAGAA
1 TCCGGCGAAAAAACCCAGAA
5213175 TCCGG
1 TCCGG
5213180 TGAATCTTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (20 bp):
TCCGGCGAAAAAACCCAGAA
Found at i:5213445 original size:14 final size:15
Alignment explanation
Indices: 5213426--5213467 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
5213416 CCGAGCCGAG
5213426 CCGAGCCGTTCTTC-
1 CCGAGCCGTTCTTCT
5213440 CCGAGCCG--CTTCT
1 CCGAGCCGTTCTTCT
5213453 CCGAGCCGTT-TTCT
1 CCGAGCCGTTCTTCT
5213467 C
1 C
5213468 TTCCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 13 0.52
ACGTcount: A:0.07, C:0.43, G:0.21, T:0.29
Consensus pattern (15 bp):
CCGAGCCGTTCTTCT
Found at i:5213458 original size:13 final size:14
Alignment explanation
Indices: 5213426--5213462 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5213416 CCGAGCCGAG
5213426 CCGAGCCGTTCTTC
1 CCGAGCCGTTCTTC
5213440 CCGAGCCG--CTTC
1 CCGAGCCGTTCTTC
5213452 TCCGAGCCGTT
1 -CCGAGCCGTT
5213463 TTCTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.08, C:0.43, G:0.24, T:0.24
Consensus pattern (14 bp):
CCGAGCCGTTCTTC
Found at i:5213515 original size:1 final size:1
Alignment explanation
Indices: 5213509--5213533 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5213499 CCGCTCCAGG
5213509 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
5213534 ATTTGACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5213742 original size:152 final size:152
Alignment explanation
Indices: 5213564--5214013 Score: 794
Period size: 152 Copynumber: 3.0 Consensus size: 152
5213554 TTGATTTTTT
* * * *
5213564 TTTTCTTTTTTCTTTAATTAATCCGACGACAGAGCCTCTACAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
5213629 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
5213694 TTTCCAATAATTAATTGGATGA
131 TTTCCAATAATTAATTGGATGA
5213716 TTTTGTATTTTT-TTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
1 TTTTGT-TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTG
*
5213780 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATA
65 CATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATA
5213845 ATTTCCAATAATTAATTGGATGA
130 ATTTCCAATAATTAATTGGATGA
*
5213868 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTGC
1 TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
* *
5213933 ATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTACTAAAAGTATTAGAGTCAATTGAGAATAA
66 ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
* *
5213998 TTTCCAACAACTAATT
131 TTTCCAATAATTAATT
5214014 ACTTGGTAAA
Statistics
Matches: 285, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
151 5 0.02
152 275 0.96
153 5 0.02
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (152 bp):
TTTTGTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC
ATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAA
TTTCCAATAATTAATTGGATGA
Found at i:5214367 original size:33 final size:33
Alignment explanation
Indices: 5214321--5214391 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
5214311 TCCCTGCTTC
5214321 ATGCATAAGACATTCTA-AAATGCAATGCATGCT
1 ATGCATAAGACATT-TAGAAATGCAATGCATGCT
5214354 ATGCACTAA-ACATTTAGAAATGCAATGCATGCT
1 ATGCA-TAAGACATTTAGAAATGCAATGCATGCT
5214387 ATGCA
1 ATGCA
5214392 AATGTCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
32 2 0.06
33 31 0.86
34 3 0.08
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (33 bp):
ATGCATAAGACATTTAGAAATGCAATGCATGCT
Found at i:5219133 original size:5 final size:5
Alignment explanation
Indices: 5219123--5219147 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5219113 AATATATGTG
5219123 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
5219148 TTTCTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:5222302 original size:41 final size:41
Alignment explanation
Indices: 5222257--5222338 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
5222247 TAAAAAGAGT
* *
5222257 AAAATGAAGTCTTCAAACCAAAATGTAATGAATTTCTTTTA
1 AAAATCAACTCTTCAAACCAAAATGTAATGAATTTCTTTTA
* *
5222298 AAAATCAACTCTTGAAACCGAAATGTAATGAATTTCTTTTA
1 AAAATCAACTCTTCAAACCAAAATGTAATGAATTTCTTTTA
5222339 TCGTCCAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (41 bp):
AAAATCAACTCTTCAAACCAAAATGTAATGAATTTCTTTTA
Found at i:5224424 original size:23 final size:23
Alignment explanation
Indices: 5224394--5224439 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5224384 ATATAAAGAA
*
5224394 TTACTTTTATATTTTAATTGCAT
1 TTACTTTTATATTTTAATCGCAT
5224417 TTACTTTTATATTTTAATCGCAT
1 TTACTTTTATATTTTAATCGCAT
5224440 CTCTTCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (23 bp):
TTACTTTTATATTTTAATCGCAT
Found at i:5226632 original size:13 final size:13
Alignment explanation
Indices: 5226614--5226663 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
5226604 CTTTTATATA
5226614 AATTTTTATTTTT
1 AATTTTTATTTTT
* *
5226627 AATTTTTATACATAT
1 AATTTTTAT--TTTT
5226642 AATTTTTATTTTT
1 AATTTTTATTTTT
5226655 AATTTTTAT
1 AATTTTTAT
5226664 ATATATGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 20 0.65
15 11 0.35
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTTTTATTTTT
Found at i:5226654 original size:28 final size:29
Alignment explanation
Indices: 5226609--5226669 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
5226599 ATTTACTTTT
5226609 ATATAAATTTTTATTTTTAATTTTTATAC
1 ATATAAATTTTTATTTTTAATTTTTATAC
*
5226638 ATAT-AATTTTTATTTTTAATTTTTATAT
1 ATATAAATTTTTATTTTTAATTTTTATAC
5226666 ATAT
1 ATAT
5226670 GTGAATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
ATATAAATTTTTATTTTTAATTTTTATAC
Found at i:5229690 original size:28 final size:28
Alignment explanation
Indices: 5229604--5229691 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
5229594 TATTTTATTT
* *
5229604 TATTTCTAAAATTTTCACCATTTGGGTC
1 TATTTCTAAAATTTTCACTATTTAGGTC
* * * * *
5229632 TA-TT-TAAAAATTTC-TTTTTATAAGTTT
1 TATTTCTAAAATTTTCACTATT-T-AGGTC
5229659 TATTTCTAAAATTTTCACTATTTAGGTC
1 TATTTCTAAAATTTTCACTATTTAGGTC
5229687 TATTT
1 TATTT
5229692 AGAAAAAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
25 2 0.05
26 10 0.23
27 6 0.14
28 12 0.28
29 10 0.23
30 3 0.07
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.53
Consensus pattern (28 bp):
TATTTCTAAAATTTTCACTATTTAGGTC
Found at i:5231412 original size:43 final size:43
Alignment explanation
Indices: 5231281--5231664 Score: 262
Period size: 44 Copynumber: 9.1 Consensus size: 43
5231271 ACATTAAAAA
* *
5231281 CTCCTCTAAACAAAGGCTTC-ACAACTTTTGAGAAATAAATAAAG
1 CTCCTCTAAACAAAGG-TTCAACAAC-TTTGAAAAATAAATAAGG
* * * * * *
5231325 CTCCTATAAGCAGAGGCTCAACCACTTTTGAAACATAAATAAGG
1 CTCCTCTAAACAAAGGTTCAACAAC-TTTGAAAAATAAATAAGG
* *
5231369 CTCCTCTAAATAGAGGTTCAACAACTTTGAAAAATAAATAAGG
1 CTCCTCTAAACAAAGGTTCAACAACTTTGAAAAATAAATAAGG
* *
5231412 --CCTCT------A--TT-TACAACTTTAAAAAATAAATAAGG
1 CTCCTCTAAACAAAGGTTCAACAACTTTGAAAAATAAATAAGG
* * *
5231444 CTCATTTAAACAAAGGCTT--ACGACTTTGAAAAATAAATAAGG
1 CTCCTCTAAACAAAGG-TTCAACAACTTTGAAAAATAAATAAGG
* * ** ** *
5231486 CTCTTTTAAACAAAGACTCAATGACTTTTGAAAAGTAAATAAGG
1 CTCCTCTAAACAAAGGTTCAACAAC-TTTGAAAAATAAATAAGG
* * * * * *
5231530 CTCCTTTAAATAGAGGCTT-AATAATTTTGAAAAGTAAATAAGG
1 CTCCTCTAAACAAAGG-TTCAACAACTTTGAAAAATAAATAAGG
* * * * * *
5231573 -TCTTCTAAACAGATGCTCAACTACCTTTGAAAAATAAATAAAG
1 CTCCTCTAAACAAAGGTTCAAC-AACTTTGAAAAATAAATAAGG
*
5231616 CTCCTCTAAACAAAGGCTT-AACAACTTTGAAAAGTAAATAAGG
1 CTCCTCTAAACAAAGG-TTCAACAACTTTGAAAAATAAATAAGG
5231659 CTCCTC
1 CTCCTC
5231665 GACAATCATA
Statistics
Matches: 271, Mismatches: 49, Indels: 41
0.75 0.14 0.11
Matches are distributed among these distances:
32 22 0.08
33 2 0.01
34 3 0.01
35 1 0.00
40 1 0.00
41 7 0.03
42 48 0.18
43 84 0.31
44 101 0.37
45 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (43 bp):
CTCCTCTAAACAAAGGTTCAACAACTTTGAAAAATAAATAAGG
Found at i:5231426 original size:32 final size:30
Alignment explanation
Indices: 5231389--5231451 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 30
5231379 TAGAGGTTCA
*
5231389 ACAACTTTGAAAAATAAATAAGGCCTCTATTT
1 ACAACTTTAAAAAATAAATAAGG-CTC-ATTT
5231421 ACAACTTTAAAAAATAAATAAGGCTCATTT
1 ACAACTTTAAAAAATAAATAAGGCTCATTT
5231451 A
1 A
5231452 AACAAAGGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 5 0.17
31 3 0.10
32 22 0.73
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (30 bp):
ACAACTTTAAAAAATAAATAAGGCTCATTT
Found at i:5231483 original size:42 final size:42
Alignment explanation
Indices: 5231419--5231663 Score: 226
Period size: 43 Copynumber: 5.7 Consensus size: 42
5231409 AGGCCTCTAT
* *
5231419 TTACAACTTTAAAAAATAAATAAGGCTCATTTAAACAAAGGC
1 TTACAACTTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGC
* * *
5231461 TTACGACTTTGAAAAATAAATAAGGCTCTTTTAAACAAAGAC
1 TTACAACTTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGC
* * * *
5231503 TCA-ATGACTTTTGAAAAGTAAATAAGGCTCCTTTAAATAGAGGC
1 TTACA--AC-TTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGC
* * * * *
5231547 TTAATAATTTTGAAAAGTAAATAAGG-T-CTTCTAAACAGATGC
1 TT-ACAACTTTGAAAAATAAATAAGGCTCCTT-TAAACAAAGGC
* * * *
5231589 TCAACTACCTTTGAAAAATAAATAAAGCTCCTCTAAACAAAGGC
1 T-TAC-AACTTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGC
*
5231633 TTAACAACTTTGAAAAGTAAATAAGGCTCCT
1 TT-ACAACTTTGAAAAATAAATAAGGCTCCT
5231664 CGACAATCAT
Statistics
Matches: 164, Mismatches: 28, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
41 3 0.02
42 52 0.32
43 60 0.37
44 45 0.27
45 3 0.02
46 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (42 bp):
TTACAACTTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGC
Found at i:5231538 original size:86 final size:87
Alignment explanation
Indices: 5231425--5231661 Score: 302
Period size: 86 Copynumber: 2.7 Consensus size: 87
5231415 CTATTTACAA
* * * *
5231425 CTTTAAAAAATAAATAAGGCTCATTTAAACAAAGGCTT-ACGACTTTGAAAAATAAATAAGGCTC
1 CTTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
*
5231489 TTTTAAACA-AAGACTCAA-TGAC
66 TTCTAAACAGAAG-CTCAACT-AC
* * * * * *
5231511 TTTTGAAAAGTAAATAAGGCTCCTTTAAATAGAGGCTTAATAATTTTGAAAAGTAAATAAGG-TC
1 CTTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
*
5231575 TTCTAAACAGATGCTCAACTAC
66 TTCTAAACAGAAGCTCAACTAC
* *
5231597 CTTTGAAAAATAAATAAAGCTCCTCTAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
1 CTTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
5231662 CTCGACAATC
Statistics
Matches: 127, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
86 103 0.81
87 24 0.19
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (87 bp):
CTTTGAAAAATAAATAAGGCTCCTTTAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
TTCTAAACAGAAGCTCAACTAC
Found at i:5234351 original size:54 final size:55
Alignment explanation
Indices: 5234291--5234402 Score: 183
Period size: 54 Copynumber: 2.1 Consensus size: 55
5234281 TTTGTACAAG
*
5234291 AAAATTGATACTTTCAACTTTTCC-CAAAATGTTTTTTTGAAACTTATTTT-AAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTGAAA-TTATTTTAAAGA
*
5234345 AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTGAAATTTTTTTAAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTGAAATTATTTTAAAGA
5234400 AAA
1 AAA
5234403 TCAAAAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
54 30 0.56
55 24 0.44
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (55 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTGAAATTATTTTAAAGA
Found at i:5234419 original size:17 final size:16
Alignment explanation
Indices: 5234394--5234441 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
5234384 GAAATTTTTT
*
5234394 TAAAGAAAATCAAAAAA
1 TAAATAAAAT-AAAAAA
5234411 TAAATAAAATAAAAAA
1 TAAATAAAATAAAAAA
5234427 TAAAATAAAA-AAAAA
1 T-AAATAAAATAAAAA
5234442 TAAGGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (16 bp):
TAAATAAAATAAAAAA
Found at i:5234427 original size:12 final size:12
Alignment explanation
Indices: 5234399--5234438 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5234389 TTTTTTAAAG
5234399 AAAATCAAAA-AA
1 AAAAT-AAAATAA
*
5234411 TAAATAAAATAA
1 AAAATAAAATAA
5234423 AAAATAAAATAA
1 AAAATAAAATAA
5234435 AAAA
1 AAAA
5234439 AAATAAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:5234456 original size:29 final size:29
Alignment explanation
Indices: 5234394--5234526 Score: 76
Period size: 29 Copynumber: 4.2 Consensus size: 29
5234384 GAAATTTTTT
*
5234394 TAAAGAAAATCAAAAAATAAATAAAATAA
1 TAAATAAAATCAAAAAATAAATAAAATAA
* *
5234423 AAAATAAAAT-AAAAAA-AAATAAGGAATAC
1 TAAATAAAATCAAAAAATAAATAA--AATAA
5234452 TAAATAATTCTAATCTAATAAAAT-AATAATAATAA
1 TAAATAA----AATC-AA-AAAATAAATAA-AATAA
*
5234487 TAATAATAATAATTAAAAAA-ATAATAATAATAA
1 T-A-AATAA-AATCAAAAAATA-AATAA-AATAA
5234520 TAAATAA
1 TAAATAA
5234527 GAAAAAAAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
27 6 0.07
28 6 0.07
29 18 0.22
31 5 0.06
32 5 0.06
33 17 0.20
34 4 0.05
35 7 0.08
36 10 0.12
37 5 0.06
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (29 bp):
TAAATAAAATCAAAAAATAAATAAAATAA
Found at i:5234481 original size:3 final size:3
Alignment explanation
Indices: 5234467--5234522 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
5234457 AATTCTAATC
*
5234467 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TTAA -AA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
5234511 TAA TAA TAA TAA
1 TAA TAA TAA TAA
5234523 ATAAGAAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:5234531 original size:27 final size:27
Alignment explanation
Indices: 5234479--5234534 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
5234469 ATAAAATAAT
*
5234479 AATAATAATAATAATAATAATTAAAAA
1 AATAATAATAATAATAATAATGAAAAA
5234506 AATAATAATAATAATAAATAA-GAAAAA
1 AATAATAATAATAAT-AATAATGAAAAA
5234533 AA
1 AA
5234535 AAAACCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (27 bp):
AATAATAATAATAATAATAATGAAAAA
Found at i:5234535 original size:30 final size:30
Alignment explanation
Indices: 5234471--5234538 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
5234461 CTAATCTAAT
* * *
5234471 AAAATAATAATAATAATAATAATAATAATT
1 AAAAAAATAATAATAATAATAATAAGAATA
*
5234501 AAAAAAATAATAATAATAATAAATAAGAAAA
1 AAAAAAATAATAATAATAAT-AATAAGAATA
5234532 AAAAAAA
1 AAAAAAA
5234539 CCTTTGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (30 bp):
AAAAAAATAATAATAATAATAATAAGAATA
Found at i:5235030 original size:21 final size:20
Alignment explanation
Indices: 5234994--5235038 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
5234984 AATTTTCCAG
5234994 AAAAAAACTTCAAAATT-CT
1 AAAAAAACTTCAAAATTCCT
*
5235013 AAAAAAATTCTCACAAATTCCT
1 AAAAAAACT-TCA-AAATTCCT
5235035 AAAA
1 AAAA
5235039 CTGTATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 3 0.14
21 5 0.23
22 6 0.27
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAAACTTCAAAATTCCT
Found at i:5235318 original size:24 final size:23
Alignment explanation
Indices: 5235268--5235413 Score: 101
Period size: 24 Copynumber: 6.4 Consensus size: 23
5235258 CCAGCCAAAA
* *
5235268 AAATAAA-AATAGATA-AATAAT
1 AAATAAATAATATATATACTAAT
5235289 AAATAAATAAATATATATACTAAT
1 AAATAAAT-AATATATATACTAAT
* * *
5235313 AGATAAATAATAGATAATAGTTAAT
1 AAATAAATAATATAT-ATA-CTAAT
*
5235338 -AATAAA-AATTTATATACATTAAT
1 AAATAAATAATATATATAC--TAAT
* *
5235361 AGATAAATAATAATATATATTAAT
1 AAATAAATAAT-ATATATACTAAT
*
5235385 AAAT-AATAATA-ATA-GC-AAT
1 AAATAAATAATATATATACTAAT
5235404 AAATAAATAA
1 AAATAAATAA
5235414 GATACAAAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
19 7 0.07
20 5 0.05
21 10 0.10
22 4 0.04
23 28 0.28
24 32 0.32
25 7 0.07
26 6 0.06
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATAAATAATATATATACTAAT
Found at i:5235385 original size:44 final size:45
Alignment explanation
Indices: 5235270--5235395 Score: 123
Period size: 48 Copynumber: 2.7 Consensus size: 45
5235260 AGCCAAAAAA
* *
5235270 ATAAA-AATAGATAAATAATAAATAA-ATAAATATATATACTAATAG
1 ATAAATAATAGAT-AATAGT-AATAATAAAAATATATATACTAATAG
*
5235315 ATAAATAATAGATAATAGTTAATAATAAAAATTTATATACATTAATAG
1 ATAAATAATAGATAATAG-TAATAATAAAAATATATATAC--TAATAG
* *
5235363 ATAAATAATA-ATATATATTAATAAATAATAATA
1 ATAAATAATAGATA-ATAGTAAT-AATAAAAATA
5235396 ATAGCAATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
45 14 0.21
46 20 0.29
47 7 0.10
48 27 0.40
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (45 bp):
ATAAATAATAGATAATAGTAATAATAAAAATATATATACTAATAG
Found at i:5235394 original size:10 final size:10
Alignment explanation
Indices: 5235269--5235409 Score: 76
Period size: 10 Copynumber: 13.9 Consensus size: 10
5235259 CAGCCAAAAA
5235269 AATAAA-AAT
1 AATAAATAAT
5235278 AGATAAATAAT
1 A-ATAAATAAT
5235289 AAATAAATAA-
1 -AATAAATAAT
* *
5235299 ATATATATACT
1 A-ATAAATAAT
*
5235310 AATAGATAAAT
1 AATAAAT-AAT
*
5235321 AATAGATAAT
1 AATAAATAAT
* *
5235331 AGTTAATAAT
1 AATAAATAAT
*
5235341 AA-AAAT-TT
1 AATAAATAAT
*
5235349 ATATACATTAAT
1 A-ATA-AATAAT
5235361 AGATAAATAAT
1 A-ATAAATAAT
* *
5235372 AATATATATT
1 AATAAATAAT
5235382 AATAAATAAT
1 AATAAATAAT
**
5235392 AAT-AATAGC
1 AATAAATAAT
5235401 AATAAATAA
1 AATAAATAA
5235410 ATAAGATACA
Statistics
Matches: 100, Mismatches: 21, Indels: 21
0.70 0.15 0.15
Matches are distributed among these distances:
8 2 0.02
9 13 0.13
10 50 0.50
11 29 0.29
12 6 0.06
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (10 bp):
AATAAATAAT
Found at i:5240484 original size:22 final size:22
Alignment explanation
Indices: 5240459--5240503 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5240449 ATAAATAATA
5240459 AAAAATATAGAAATAAAATATC
1 AAAAATATAGAAATAAAATATC
*
5240481 AAAAATATAGAAATAAAGTATC
1 AAAAATATAGAAATAAAATATC
5240503 A
1 A
5240504 GTTAAATCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (22 bp):
AAAAATATAGAAATAAAATATC
Found at i:5240486 original size:14 final size:13
Alignment explanation
Indices: 5240428--5240487 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
5240418 AAAATATACA
*
5240428 AAAAATAAAATGT
1 AAAAATAAAATAT
5240441 AATAAATAATAA-AT
1 AA-AAATAA-AATAT
*
5240455 AATAA-AAAATAT
1 AAAAATAAAATAT
*
5240467 AGAAATAAAATAT
1 AAAAATAAAATAT
5240480 CAAAAATA
1 -AAAAATA
5240488 TAGAAATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
11 2 0.05
12 7 0.19
13 11 0.30
14 15 0.41
15 2 0.05
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (13 bp):
AAAAATAAAATAT
Found at i:5241049 original size:19 final size:19
Alignment explanation
Indices: 5241027--5241065 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5241017 TTTATTGTGT
*
5241027 ATAAAATATTACTATCACA
1 ATAAAATATTACTAACACA
5241046 ATAAAATATTACTAACACA
1 ATAAAATATTACTAACACA
5241065 A
1 A
5241066 AATGTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAAAATATTACTAACACA
Found at i:5244108 original size:33 final size:30
Alignment explanation
Indices: 5244092--5244156 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
5244082 TTTGTTTAAC
5244092 TTAATTTTTATTTTTATATAAATTTTATTT
1 TTAATTTTTATTTTTATATAAATTTTATTT
** *
5244122 TTAATTTTTA--TAGATATAACTTTTATTT
1 TTAATTTTTATTTTTATATAAATTTTATTT
5244150 TTAATTT
1 TTAATTT
5244157 ATATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 22 0.69
30 10 0.31
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (30 bp):
TTAATTTTTATTTTTATATAAATTTTATTT
Found at i:5244146 original size:28 final size:28
Alignment explanation
Indices: 5244107--5244171 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
5244097 TTTTATTTTT
*
5244107 ATATAAATTTTATTTTTAATTTTTATAG
1 ATATAAATTTTATTTTTAATTTATATAG
* *
5244135 ATATAACTTTTATTTTTAATTTATATAT
1 ATATAAATTTTATTTTTAATTTATATAG
*
5244163 ATATGAATT
1 ATATAAATT
5244172 AAATATAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
ATATAAATTTTATTTTTAATTTATATAG
Found at i:5247846 original size:43 final size:43
Alignment explanation
Indices: 5247735--5248085 Score: 226
Period size: 43 Copynumber: 8.1 Consensus size: 43
5247725 TTTCATAACT
* * * * * * *
5247735 TTTGAGAAAT-AATAAAGCTCCTCTAAGCAAAGGTTCAACCAC
1 TTTGAAAAATAAATAAGGCTTCTCTAAACAGAGGCTCAACAAC
* * * * * *
5247777 TTTTGAAATATAAATAAGACTCCTCTACATAGAGGCTCAATAAC
1 -TTTGAAAAATAAATAAGGCTTCTCTAAACAGAGGCTCAACAAC
* * *
5247821 TTTAAAAAATAAATAAGGCTTCTCTAAACAAAGGCTAAACAAC
1 TTTGAAAAATAAATAAGGCTTCTCTAAACAGAGGCTCAACAAC
* * * *
5247864 TTTGAAAAGTAAATATGGC-TCATTTAAACAGAGGCTC-ACGA-
1 TTTGAAAAATAAATAAGGCTTC-TCTAAACAGAGGCTCAACAAC
* * * *
5247905 TTGTGAAAAATAAATAAAGC-TCTTTTAAACATAGGCTCAACGAC
1 TT-TGAAAAATAAATAAGGCTTC-TCTAAACAGAGGCTCAACAAC
* * * * *
5247949 TTTTGAAAAGTAAATAAGACTTCTCTAAATAGAAGTTCAACAAC
1 -TTTGAAAAATAAATAAGGCTTCTCTAAACAGAGGCTCAACAAC
* ** * * **
5247993 TTTGAAAAGTAAATAAGGCTTCTCTCTATAGAGGCTTAATGAC
1 TTTGAAAAATAAATAAGGCTTCTCTAAACAGAGGCTCAACAAC
* * ** * **
5248036 TTTTGAAAAATTAATAAAGCGCCTCTAAACAAAGGCTCAATGAC
1 -TTTGAAAAATAAATAAGGCTTCTCTAAACAGAGGCTCAACAAC
5248080 TTTGAA
1 TTTGAA
5248086 TTGTAAATAA
Statistics
Matches: 241, Mismatches: 59, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
41 2 0.01
42 35 0.15
43 115 0.48
44 85 0.35
45 4 0.02
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (43 bp):
TTTGAAAAATAAATAAGGCTTCTCTAAACAGAGGCTCAACAAC
Found at i:5266127 original size:16 final size:16
Alignment explanation
Indices: 5266103--5266140 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5266093 ATTTTATTTT
5266103 TATTT-ATTTTTACCA
1 TATTTAATTTTTACCA
* *
5266118 TTTTTAATTTTTTCCA
1 TATTTAATTTTTACCA
5266134 TATTTAA
1 TATTTAA
5266141 AATTACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTAATTTTTACCA
Found at i:5266552 original size:2 final size:2
Alignment explanation
Indices: 5266545--5266574 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5266535 CAACTTCATT
5266545 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
5266575 AAGGATAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5267765 original size:44 final size:43
Alignment explanation
Indices: 5267709--5267852 Score: 159
Period size: 44 Copynumber: 3.3 Consensus size: 43
5267699 TAACTTTCTA
*
5267709 AAAATTTGAAAGGCTTCTTTAAACAGAGCCTTGATCACTTTTTG
1 AAAATTTAAAAGGCTTCTTTAAACAGAG-CTTGATCACTTTTTG
* * *
5267753 AAAATTTAAAAGGCTTCTTTAAACATATGCTCGATAACTTTTT-
1 AAAATTTAAAAGGCTTCTTTAAACAGA-GCTTGATCACTTTTTG
* * *
5267796 AAAATTTAAAAGGATTCTCTAAATAGAAG-TATGA-CAACTTTTTG
1 AAAATTTAAAAGGCTTCTTTAAACAG-AGCT-TGATC-ACTTTTTG
5267840 AAAATTTAAAAGG
1 AAAATTTAAAAGG
5267853 TTCCTCTAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
42 1 0.01
43 32 0.38
44 51 0.60
45 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (43 bp):
AAAATTTAAAAGGCTTCTTTAAACAGAGCTTGATCACTTTTTG
Found at i:5267906 original size:45 final size:44
Alignment explanation
Indices: 5267745--5268235 Score: 210
Period size: 44 Copynumber: 11.1 Consensus size: 44
5267735 AGCCTTGATC
* * * *
5267745 ACTTTTTG-AAAATTTAAAAGGCTTCTT-TAAACATATGCTCGATA
1 ACTTTTTGAAAAATTTAAAAGGCTT-TTCTAAATA-AAGCTCAACA
* *
5267789 ACTTTTT--AAAATTTAAAAGGATTCTCTAAATAGAAG-T-ATGACA
1 ACTTTTTGAAAAATTTAAAAGGCTTTTCTAAATA-AAGCTCA--ACA
*
5267832 ACTTTTTG-AAAATTTAAAAGG-TTCCTCTAAATAAATGCTCAACA
1 ACTTTTTGAAAAATTTAAAAGGCTT-TTCTAAATAAA-GCTCAACA
* * * **
5267876 ACTTATTGAAAAATTTGAAAGGCTTTTCTAAATAGAAACTTGACA
1 ACTTTTTGAAAAATTTAAAAGGCTTTTCTAAATA-AAGCTCAACA
* * * **
5267921 ACTTTTTGAAAAATTTTAAAGACTCATT-TAAGCAAAGGCTCAACA
1 ACTTTTTGAAAAATTTAAAAGGCT-TTTCTAAATAAA-GCTCAACA
* ** * * * * *
5267966 AC-TTTTGAAAATTTTAAAAGGCTCCTCTAAACAGAGTATCGATA
1 ACTTTTTGAAAAATTTAAAAGGCTTTTCTAAATAAAG-CTCAACA
*** * * *
5268010 ACTTTTTGAAAAATTTTGGAGGCTCTTT-TAAGTAGAAGCTCGATA
1 ACTTTTTGAAAAATTTAAAAGGCT-TTTCTAAATA-AAGCTCAACA
* * *
5268055 AC-TTTTG-AGAATTTAAAAGACTTTAT-TAAATAGAGGCTCAACA
1 ACTTTTTGAAAAATTTAAAAGGCTTT-TCTAAATA-AAGCTCAACA
* ** * * **
5268098 AC-TTTTG-AAAATTTAAAAAGCTCCTCTAAGTACAGACTTGACA
1 ACTTTTTGAAAAATTTAAAAGGCTTTTCTAAATAAAG-CTCAACA
* * * * *
5268141 AC-TTTTGAGAATTTTAAAAGG-TTTCTCTAAATAGAGACTCGATA
1 ACTTTTTGAAAAATTTAAAAGGCTTT-TCTAAATAAAG-CTCAACA
* * * *
5268185 GCTTTTTTAAAAAATTTGAAAGG-TTTCTCTAAATAGAGGCTCAACA
1 AC-TTTTTGAAAAATTTAAAAGGCTTT-TCTAAATA-AAGCTCAACA
5268231 ACTTT
1 ACTTT
5268236 AAAATTCTCA
Statistics
Matches: 341, Mismatches: 80, Indels: 51
0.72 0.17 0.11
Matches are distributed among these distances:
42 6 0.02
43 98 0.29
44 103 0.30
45 90 0.26
46 43 0.13
47 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (44 bp):
ACTTTTTGAAAAATTTAAAAGGCTTTTCTAAATAAAGCTCAACA
Found at i:5267992 original size:134 final size:131
Alignment explanation
Indices: 5267829--5268126 Score: 325
Period size: 134 Copynumber: 2.2 Consensus size: 131
5267819 TAGAAGTATG
* * *
5267829 ACAACTTTTTGAAAATTTAAAAGGTTCCTCTAAATAAA-TGCTCAACAACTTATTGAAAAA-TTT
1 ACAAC-TTTTGAAAATTTAAAAGGCTCCTCTAAACAAAGT-ATCAACAACTTATTGAAAAATTTT
* * *
5267892 GAAAGGCT-TTTCTAAATAGAAACTTGACAACTTTTTGAAAAATTTTAAAGACTCAT-TTAAGCA
64 G-AAGGCTCTTT-TAAATAGAAACTCGACAAC-TTTTG-AAAATTTAAAAGACT-ATATTAAACA
5267955 AAGGCTCA
124 AAGGCTCA
* * * *
5267963 ACAACTTTTGAAAATTTTAAAAGGCTCCTCTAAACAGAGTATCGATAACTTTTTGAAAAATTTTG
1 ACAACTTTTGAAAA-TTTAAAAGGCTCCTCTAAACAAAGTATCAACAACTTATTGAAAAATTTTG
* * * * * * * *
5268028 GAGGCTCTTTTAAGTAGAAGCTCGATAACTTTTGAGAATTTAAAAGACTTTATTAAATAGAGGCT
65 AAGGCTCTTTTAAATAGAAACTCGACAACTTTTGAAAATTTAAAAGACTATATTAAACAAAGGCT
5268093 CA
130 CA
*
5268095 ACAACTTTTGAAAATTTAAAAAGCTCCTCTAA
1 ACAACTTTTGAAAATTTAAAAGGCTCCTCTAA
5268127 GTACAGACTT
Statistics
Matches: 140, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
131 18 0.13
132 39 0.28
133 14 0.10
134 61 0.44
135 8 0.06
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (131 bp):
ACAACTTTTGAAAATTTAAAAGGCTCCTCTAAACAAAGTATCAACAACTTATTGAAAAATTTTGA
AGGCTCTTTTAAATAGAAACTCGACAACTTTTGAAAATTTAAAAGACTATATTAAACAAAGGCTC
A
Found at i:5267995 original size:89 final size:85
Alignment explanation
Indices: 5267700--5268175 Score: 289
Period size: 89 Copynumber: 5.4 Consensus size: 85
5267690 GAGGCTAAAT
* * * * **
5267700 AACTTTCTAAAAATTTGAAAGGCTTCTTTAAACAGAGCCTTGATC-ACTTTTTGAAAATTTAAAA
1 AACTTT-TGAAAATTTAAAAGGCTTCTCTAAATAGA-AATTGA-CAACTTTTTGAAAATTTAAAA
* * *
5267764 GGCTTCTTTAAACATATGCTCGAT
63 GGC-TCTTTAAACAAATGCTCAAC
* * *
5267788 AACTTTTTAAAATTTAAAAGGATTCTCTAAATAGAAGTATGACAACTTTTTGAAAATTTAAAAGG
1 AACTTTTGAAAATTTAAAAGGCTTCTCTAAATAGAAAT-TGACAACTTTTTGAAAATTTAAAAGG
* * *
5267853 TTCCTCTAAATAAATGCTCAAC
65 CT-CTTTAAACAAATGCTCAAC
* * *
5267875 AACTTATTGAAAAATTTGAAAGGCTTTTCTAAATAGAAACTTGACAACTTTTTGAAAAATTTTAA
1 AACTT-TTG-AAAATTTAAAAGGCTTCTCTAAATAGAAA-TTGACAACTTTTTG-AAAATTTAAA
* * *
5267940 AGACTCATTTAAGCAAAGGCTCAAC
62 AGGCTC-TTTAAACAAATGCTCAAC
* * * * * ***
5267965 AACTTTTGAAAATTTTAAAAGGCTCCTCTAAACAGAGTATCGATAACTTTTTGAAAAATTTTGGA
1 AACTTTTGAAAA-TTTAAAAGGCTTCTCTAAATAGA-AATTGACAACTTTTTG-AAAATTTAAAA
** * *
5268030 GGCTCTTTTAAGTAGAA-GCTCGAT
63 GGCTC-TTTAAACA-AATGCTCAAC
* * * ** ** *
5268054 AACTTTTGAGAATTTAAAAGACTT-TATTAAATAGAGGCTCAACAAC-TTTTGAAAATTTAAAAA
1 AACTTTTGAAAATTTAAAAGGCTTCT-CTAAATAGA-AATTGACAACTTTTTGAAAATTTAAAAG
* * **
5268117 GCTCCTCTAAGTACAGA--CTTGAC
64 GCT-CTTTAA--ACAAATGCTCAAC
* *
5268140 AACTTTTGAGAATTTTAAAAGGTTTCTCTAAATAGA
1 AACTTTTGA-AAATTTAAAAGGCTTCTCTAAATAGA
5268176 GACTCGATAG
Statistics
Matches: 308, Mismatches: 63, Indels: 35
0.76 0.16 0.09
Matches are distributed among these distances:
86 31 0.10
87 94 0.31
88 38 0.12
89 110 0.36
90 35 0.11
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (85 bp):
AACTTTTGAAAATTTAAAAGGCTTCTCTAAATAGAAATTGACAACTTTTTGAAAATTTAAAAGGC
TCTTTAAACAAATGCTCAAC
Found at i:5271210 original size:31 final size:29
Alignment explanation
Indices: 5271167--5271241 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
5271157 TTCATAATCT
* *
5271167 TGTCTTTTCTTTCTTTCTTT-AT-ATTTA
1 TGTCTTTTCTTTCTTTCTTTCTTGATATA
*
5271194 TGTTTTTTCTTTCTTTCTTTCTTGATATA
1 TGTCTTTTCTTTCTTTCTTTCTTGATATA
5271223 TGTCTTTTCTTTCTTTCTT
1 TGTCTTTTCTTTCTTTCTT
5271242 CATATAGGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.45
28 1 0.02
29 22 0.52
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.71
Consensus pattern (29 bp):
TGTCTTTTCTTTCTTTCTTTCTTGATATA
Found at i:5271234 original size:29 final size:27
Alignment explanation
Indices: 5271167--5271247 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 27
5271157 TTCATAATCT
*
5271167 TGTCTTTTCTTTCTTTCTTTATATTTA
1 TGTCTTTTCTTTCTTTCTTTATATATA
* *
5271194 TGTTTTTTCTTTCTTTCTTTCTTGATATA
1 TGTCTTTTCTTTCTTTCTTT-AT-ATATA
*
5271223 TGTCTTTTCTTTCTTTCTTCATATA
1 TGTCTTTTCTTTCTTTCTTTATATA
5271248 GGATGCATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 22 0.48
28 2 0.04
29 22 0.48
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (27 bp):
TGTCTTTTCTTTCTTTCTTTATATATA
Found at i:5285370 original size:11 final size:11
Alignment explanation
Indices: 5285354--5285378 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5285344 AATCATCAAA
5285354 AAAAAAAAATG
1 AAAAAAAAATG
5285365 AAAAAAAAATG
1 AAAAAAAAATG
5285376 AAA
1 AAA
5285379 GAATGAAGCT
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:5286262 original size:36 final size:34
Alignment explanation
Indices: 5286221--5286312 Score: 114
Period size: 37 Copynumber: 2.6 Consensus size: 34
5286211 AGCATTTTTG
*
5286221 GAAAAGACATTTGCATTTCATGTA-CATCTTTTTAA
1 GAAAAGACATTTGCATTTCATG-AGCATC-ATTTAA
*
5286256 GAAAAAGACATTTTGCATCTCATGAGCATCATTTAA
1 G-AAAAGACA-TTTGCATTTCATGAGCATCATTTAA
*
5286292 GAAAAGACATATGCATTTCAT
1 GAAAAGACATTTGCATTTCAT
5286313 TTGCCTCATA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
34 10 0.20
35 9 0.18
36 15 0.30
37 16 0.32
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (34 bp):
GAAAAGACATTTGCATTTCATGAGCATCATTTAA
Found at i:5286820 original size:4 final size:4
Alignment explanation
Indices: 5286806--5286912 Score: 63
Period size: 4 Copynumber: 26.0 Consensus size: 4
5286796 TTTTTATTTG
* * * * *
5286806 TATT TATTT TATT TACTAA TATT TATT TA-T TATT TATC TGTT AATT TTTT
1 TATT TA-TT TATT TA-T-T TATT TATT TATT TATT TATT TATT TATT TATT
* * * * * *
5286856 TATT TATC TATT AATA TATT TATT TATT CATT TATT AACTT TTTT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT
*
5286905 TATC TATT
1 TATT TATT
5286913 AATATATATT
Statistics
Matches: 74, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
3 3 0.04
4 61 0.82
5 8 0.11
6 2 0.03
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (4 bp):
TATT
Found at i:5286860 original size:20 final size:20
Alignment explanation
Indices: 5286807--5286940 Score: 103
Period size: 21 Copynumber: 6.4 Consensus size: 20
5286797 TTTTATTTGT
*
5286807 ATTTATTTTATTTA-CTAATA
1 ATTT-TTTTATTTATCTATTA
* *
5286827 TTTATTTATTATTTATCTGTTA
1 ATT-TTT-TTATTTATCTATTA
5286849 ATTTTTTTATTTATCTATTAA
1 ATTTTTTTATTTATCTATT-A
* *
5286870 TATATTTATTTATTCATTTATTA
1 -AT-TTT-TTTATTTATCTATTA
5286893 ACTTTTTTTATTTATCTATTA
1 A-TTTTTTTATTTATCTATTA
* *
5286914 ATATATATT-TTTATCTATT-
1 AT-TTTTTTATTTATCTATTA
5286933 ATTTTTTT
1 ATTTTTTT
5286941 TCTTTTTTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.04
19 2 0.02
20 27 0.29
21 30 0.33
22 12 0.13
23 5 0.05
24 12 0.13
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (20 bp):
ATTTTTTTATTTATCTATTA
Found at i:5286954 original size:49 final size:45
Alignment explanation
Indices: 5286812--5286927 Score: 143
Period size: 45 Copynumber: 2.7 Consensus size: 45
5286802 TTTGTATTTA
* * * * *
5286812 TTTTATTTA-CTAAT-ATTTATTTA-TTATTTATCTGTTAA-TTT
1 TTTTATTTATCTATTAATATATTTATTTATTCATTTATTAACTTT
5286853 TTTTATTTATCTATTAATATATTTATTTATTCATTTATTAACTTT
1 TTTTATTTATCTATTAATATATTTATTTATTCATTTATTAACTTT
5286898 TTTTATTTATCTATTAATATATATT-TTTAT
1 TTTTATTTATCTATTAATATAT-TTATTTAT
5286928 CTATTATTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
41 9 0.14
42 4 0.06
43 8 0.12
44 12 0.18
45 30 0.46
46 2 0.03
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (45 bp):
TTTTATTTATCTATTAATATATTTATTTATTCATTTATTAACTTT
Found at i:5287703 original size:3 final size:3
Alignment explanation
Indices: 5287695--5287726 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5287685 CGTTAAGGTT
5287695 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5287727 CCTTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5287737 original size:18 final size:18
Alignment explanation
Indices: 5287698--5287753 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
5287688 TAAGGTTTTA
* *
5287698 TTATTATTATT-ATTATT
1 TTATTATTATTCCTTAAT
5287715 ATTATTATTATTCCTTAAT
1 -TTATTATTATTCCTTAAT
*
5287734 TTATCATTATTCCTTAAT
1 TTATTATTATTCCTTAAT
5287752 TT
1 TT
5287754 TAATTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 30 0.88
19 4 0.12
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATTATTCCTTAAT
Found at i:5287938 original size:63 final size:62
Alignment explanation
Indices: 5287821--5288059 Score: 185
Period size: 60 Copynumber: 3.9 Consensus size: 62
5287811 ATAAAAATTC
* *
5287821 CAAAAAAAATAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGGTA
1 CAAAAAAAATAATATTTTTAGGGAAAAGTTAAAAGTATCAATTTCTCTTAAAAATAAAGGTA
* *
5287883 CAAAAAATATATAATATTTTTAGGG-AAAGTTAAAAGTATCAATTTC-CTTTCAAAATAAA-ATA
1 CAAAAAA-A-ATAATATTTTTAGGGAAAAGTTAAAAGTATCAATTTCTC-TTAAAAATAAAGGTA
***** * * * **
5287945 TTTCTAAAA-AATA-TTTT-GGGAAAAAAGTTAAAAGTACCAATTTTTCTTAACAATAAAAATTA
1 CAAAAAAAATAATATTTTTAGGG--AAAAGTTAAAAGTATCAATTTCTCTTAAAAAT-AAAGGTA
* * * *
5288007 -TAAAAAAAT-AT-TTTTGAAGGAAAAGTTGAAAGTATCAATTT-TCTT-AAAATAAA
1 CAAAAAAAATAATATTTTTAGGGAAAAGTTAAAAGTATCAATTTCTCTTAAAAATAAA
5288060 AACTTCCAAA
Statistics
Matches: 143, Mismatches: 22, Indels: 29
0.74 0.11 0.15
Matches are distributed among these distances:
57 6 0.04
58 8 0.06
59 8 0.06
60 45 0.31
61 15 0.10
62 16 0.11
63 30 0.21
64 15 0.10
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (62 bp):
CAAAAAAAATAATATTTTTAGGGAAAAGTTAAAAGTATCAATTTCTCTTAAAAATAAAGGTA
Found at i:5289326 original size:72 final size:72
Alignment explanation
Indices: 5289209--5289422 Score: 401
Period size: 72 Copynumber: 3.0 Consensus size: 72
5289199 GCATAAAAAA
* *
5289209 CATTTGCCTGAAAGATTGTCTTTAACAACAAGCTTTTCATGGACTCCACAGAACAACTAGTTTTC
1 CATTTGCCTAAAAGATTGTCTTCAACAACAAGCTTTTCATGGACTCCACAGAACAACTAGTTTTC
5289274 TCTTCAT
66 TCTTCAT
5289281 CATTTGCCTAAAAGATTGTCTTCAACAACAAGCTTTTCATGGACTCCACAGAACAACTAGTTTTC
1 CATTTGCCTAAAAGATTGTCTTCAACAACAAGCTTTTCATGGACTCCACAGAACAACTAGTTTTC
5289346 TCTTCAT
66 TCTTCAT
*
5289353 CATTTGCCTAAAAGATTGTCTTCAACAATAAGCTTTTCATGGACTCCACAGAACAACTAGTTTTC
1 CATTTGCCTAAAAGATTGTCTTCAACAACAAGCTTTTCATGGACTCCACAGAACAACTAGTTTTC
5289418 TCTTC
66 TCTTC
5289423 GTCTGTATTA
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 139 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (72 bp):
CATTTGCCTAAAAGATTGTCTTCAACAACAAGCTTTTCATGGACTCCACAGAACAACTAGTTTTC
TCTTCAT
Found at i:5298762 original size:15 final size:14
Alignment explanation
Indices: 5298735--5298829 Score: 59
Period size: 14 Copynumber: 6.1 Consensus size: 14
5298725 CTATGCTTAA
5298735 AAATAAAAAAAAAG
1 AAATAAAAAAAAAG
5298749 AAATAAAAAGAAAAG
1 AAATAAAAA-AAAAG
5298764 AAA-AATTGAAAAATGAAG
1 AAATAA---AAAAA--AAG
5298782 AAATAAAAAAAATAAAG
1 AAAT--AAAAAA-AAAG
*
5298799 AAAAAATAAAATAAAG
1 AAATAA-AAAA-AAAG
5298815 AAA-AAATAAAAAAG
1 AAATAAA-AAAAAAG
5298829 A
1 A
5298830 TGACTCAAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 24
0.73 0.01 0.26
Matches are distributed among these distances:
14 17 0.25
15 15 0.22
16 14 0.21
17 9 0.13
18 10 0.15
19 1 0.01
21 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (14 bp):
AAATAAAAAAAAAG
Found at i:5298783 original size:33 final size:35
Alignment explanation
Indices: 5298733--5298827 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 35
5298723 TACTATGCTT
*
5298733 AAAAATAAAA-AAA-AAGAAATAAAAAGA-AAAGA
1 AAAAATAAAATAAAGAAGAAATAAAAAAATAAAGA
* * *
5298765 AAAATTGAAA-AATGAAGAAATAAAAAAAATAAAGA
1 AAAAATAAAATAAAGAAGAAAT-AAAAAAATAAAGA
*
5298800 AAAAATAAAATAAAGAAAAAATAAAAAA
1 AAAAATAAAATAAAGAAGAAATAAAAAA
5298828 GATGACTCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
32 10 0.20
33 7 0.14
34 6 0.12
35 19 0.37
36 9 0.18
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (35 bp):
AAAAATAAAATAAAGAAGAAATAAAAAAATAAAGA
Found at i:5298804 original size:36 final size:34
Alignment explanation
Indices: 5298733--5298827 Score: 99
Period size: 36 Copynumber: 2.8 Consensus size: 34
5298723 TACTATGCTT
*
5298733 AAAAATAAAA-AAA-AAGAAAT-AAAAAGAAAAG
1 AAAAATAAAATAAAGAAGAAATAAAAAAAAAAAG
* *
5298764 AAAAATTGAAA-AATGAAGAAATAAAAAAAATAAAG
1 AAAAA-TAAAATAAAGAAGAAATAAAAAAAA-AAAG
*
5298799 AAAAAATAAAATAAAGAAAAAATAAAAAA
1 -AAAAATAAAATAAAGAAGAAATAAAAAA
5298828 GATGACTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
31 5 0.10
32 6 0.12
33 7 0.13
34 6 0.12
35 8 0.15
36 20 0.38
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (34 bp):
AAAAATAAAATAAAGAAGAAATAAAAAAAAAAAG
Found at i:5298818 original size:16 final size:16
Alignment explanation
Indices: 5298733--5298825 Score: 82
Period size: 16 Copynumber: 5.6 Consensus size: 16
5298723 TACTATGCTT
5298733 AAAAATAAAA-AAA-A
1 AAAAATAAAATAAAGA
* *
5298747 AGAAATAAAAAGAAAAGA
1 AAAAAT-AAAA-TAAAGA
* *
5298765 AAAATTGAAAAATGAAGA
1 AAAAAT--AAAATAAAGA
*
5298783 AATAAAAAAAATAAAGA
1 AA-AAATAAAATAAAGA
5298800 AAAAATAAAATAAAGA
1 AAAAATAAAATAAAGA
5298816 AAAAATAAAA
1 AAAAATAAAA
5298826 AAGATGACTC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
14 5 0.08
15 4 0.06
16 23 0.36
17 14 0.22
18 11 0.17
19 7 0.11
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAAATAAAATAAAGA
Found at i:5300020 original size:40 final size:41
Alignment explanation
Indices: 5299958--5300038 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
5299948 GCTTTATTTA
*
5299958 TTTTTTTCAAAGTCATTAAGCCTTTGA-TTAGAGGAGCTTTG
1 TTTTTTTCAAAGTCATTAAGCCTCT-ACTTAGAGGAGCTTTG
* *
5299999 TTTTTTTC-AAGTCGTTGAGCCTCTACTTAGAGGAGCTTTG
1 TTTTTTTCAAAGTCATTAAGCCTCTACTTAGAGGAGCTTTG
5300039 ATCAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 1 0.03
40 27 0.75
41 8 0.22
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (41 bp):
TTTTTTTCAAAGTCATTAAGCCTCTACTTAGAGGAGCTTTG
Found at i:5300065 original size:5 final size:5
Alignment explanation
Indices: 5300055--5300116 Score: 60
Period size: 5 Copynumber: 12.8 Consensus size: 5
5300045 ATTTTAACCA
* *
5300055 AAAAC AAAAC --AAC AAAA- AAAAGC AAAAC AAAAC AAAAC AAAAT AAAAA
1 AAAAC AAAAC AAAAC AAAAC AAAA-C AAAAC AAAAC AAAAC AAAAC AAAAC
5300103 AAAAGC AAAA- AAAA
1 AAAA-C AAAAC AAAA
5300117 AAGTGTCAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
3 3 0.06
4 8 0.16
5 30 0.61
6 8 0.16
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.02
Consensus pattern (5 bp):
AAAAC
Found at i:5300083 original size:15 final size:15
Alignment explanation
Indices: 5300065--5300118 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
5300055 AAAACAAAAC
5300065 AACAAAAAAAAGCAA
1 AACAAAAAAAAGCAA
5300080 AACAAAACAAAA-CAA
1 AACAAAA-AAAAGCAA
*
5300095 AATAAAAAAAAAGCAA
1 AA-CAAAAAAAAGCAA
5300111 AA-AAAAAA
1 AACAAAAAA
5300119 GTGTCAAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
14 6 0.17
15 16 0.46
16 13 0.37
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.02
Consensus pattern (15 bp):
AACAAAAAAAAGCAA
Found at i:5300277 original size:3 final size:3
Alignment explanation
Indices: 5300269--5300396 Score: 75
Period size: 3 Copynumber: 39.7 Consensus size: 3
5300259 ATTTGCATTT
*
5300269 TTA TTA TTA TTT TTA TTTA TTA TTA TTA TTTA TTTA TT- TATA TTA TTTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA -TTA TTA T-TA TTA -TTA
*
5300318 TTA TTTA TCTA TTCA TATA TTTA TTA AT- TTA TTA TT- TT- TTA TTTA
1 TTA -TTA T-TA TT-A T-TA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* *
5300363 TCTA TTA ATA TTA TTT TTA TCTA TTA TTA TTA TT
1 T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
5300397 TTTCTTTTTT
Statistics
Matches: 102, Mismatches: 8, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
2 6 0.06
3 60 0.59
4 34 0.33
5 2 0.02
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5300289 original size:4 final size:4
Alignment explanation
Indices: 5300280--5300378 Score: 84
Period size: 4 Copynumber: 25.8 Consensus size: 4
5300270 TATTATTATT
5300280 TTTA TTTA -TTA -TTA -TTA TTTA TTTA TTTA TATTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
* * * * * *
5300325 TCTA TTCA TATA TTTA TTAA TTTA -TTA TTT- TTTA TTTA TCTA TTAA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5300371 TATTA TTT
1 T-TTA TTT
5300379 TTATCTATTA
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
3 18 0.23
4 52 0.68
5 7 0.09
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:5300315 original size:30 final size:31
Alignment explanation
Indices: 5300281--5300397 Score: 127
Period size: 30 Copynumber: 3.9 Consensus size: 31
5300271 ATTATTATTT
5300281 TTATTTATTA-TTATTATTTATTTATTTATA
1 TTATTTATTATTTATTATTTATTTATTTATA
* *
5300311 TTATTTATTATTTATCTATTCATATATTTAT-
1 TTATTTATTATTTAT-TATTTATTTATTTATA
* * * *
5300342 TAATTTATTATTTTTTATTTATCTATTAATA
1 TTATTTATTATTTATTATTTATTTATTTATA
*
5300373 TTATTT-TTATCTATTA-TTA-TTATTT
1 TTATTTATTATTTATTATTTATTTATTT
5300398 TTCTTTTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
28 4 0.06
29 3 0.04
30 30 0.42
31 22 0.31
32 13 0.18
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (31 bp):
TTATTTATTATTTATTATTTATTTATTTATA
Found at i:5301318 original size:64 final size:62
Alignment explanation
Indices: 5301239--5301358 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 62
5301229 TAAAAATTTC
* *
5301239 AAAAAAAATAATATTTTTAGGGAAAAGTTAAAAGCATCAATTTTCCTTAAAAATAAAGTTACA
1 AAAAAAAATAATATTTTTAAGG-AAAGTTAAAAGCATCAATTTCCCTTAAAAATAAAGTTACA
* * *
5301302 AAAAAAATATAATATTTTTAAGGAAAGTTGAAAGTATCAATTTCCCTTCAAAATAAA
1 AAAAAAA-ATAATATTTTTAAGGAAAGTTAAAAGCATCAATTTCCCTTAAAAATAAA
5301359 AGATTTCTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 37 0.73
64 14 0.27
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (62 bp):
AAAAAAAATAATATTTTTAAGGAAAGTTAAAAGCATCAATTTCCCTTAAAAATAAAGTTACA
Found at i:5301415 original size:60 final size:60
Alignment explanation
Indices: 5301217--5301479 Score: 225
Period size: 60 Copynumber: 4.3 Consensus size: 60
5301207 TTTTTTAATT
* * * * *
5301217 ATTTTCC-TAAAATAAAAATT-TCAAAAAAAATAATATTTTTAGGGAAAAGTTAAAAGCATCA
1 ATTTTCCTTAAAATAAAAATTAT-AAAAAAAAT-AT-TTTTGAAGAAAAAGTTGAAAGTATCA
* * * *
5301278 ATTTTCCTTAAAA-ATAAAGTTACAAAAAAAATATAATATTTTTAAG-GAAAGTTGAAAGTATCA
1 ATTTTCCTTAAAATA-AAAATTA-TAAAAAAA-AT-AT-TTTTGAAGAAAAAGTTGAAAGTATCA
* ** * * *
5301341 ATTTCCCTTCAAAATAAAAGATT-TCTAAAAAATA-TTTTGGAGAAAAAGTTGGAAGTACCA
1 ATTTTCCTT-AAAATAAAA-ATTATAAAAAAAATATTTTTGAAGAAAAAGTTGAAAGTATCA
* *
5301401 ATTTTTCTTAAAAATAAAAATTATAAAAAAAATATTTTTGAAGGAAAAGTT-AAAGTATCA
1 ATTTTCCTT-AAAATAAAAATTATAAAAAAAATATTTTTGAAGAAAAAGTTGAAAGTATCA
5301461 ATTTTCCTTAAAATAAAAA
1 ATTTTCCTTAAAATAAAAA
5301480 CTTCCAAATG
Statistics
Matches: 165, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
59 19 0.12
60 54 0.33
61 23 0.14
62 12 0.07
63 34 0.21
64 20 0.12
65 3 0.02
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.33
Consensus pattern (60 bp):
ATTTTCCTTAAAATAAAAATTATAAAAAAAATATTTTTGAAGAAAAAGTTGAAAGTATCA
Found at i:5302211 original size:27 final size:28
Alignment explanation
Indices: 5302159--5302213 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
5302149 GGTGATATCC
*
5302159 GAGTATCAAAGTTTGAATTGTATTTTTT
1 GAGTATCAAAGTTTGAATTGCATTTTTT
* *
5302187 GAGTGTCAAA-TTTGAATTGCCTTTTTT
1 GAGTATCAAAGTTTGAATTGCATTTTTT
5302214 CGATGGCGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (28 bp):
GAGTATCAAAGTTTGAATTGCATTTTTT
Found at i:5302450 original size:75 final size:75
Alignment explanation
Indices: 5302187--5302450 Score: 332
Period size: 75 Copynumber: 3.5 Consensus size: 75
5302177 TGTATTTTTT
* * * ** *
5302187 GAGTGTCAAA-TTTGAATTGCCTTTTTTCGATGGCGATATCTGAAGTCATTTTCATATTCTCGGT
1 GAGTGTCAAAGTTTGAATTGCATTTTTTCAATGACGATATCCAAAGTCATTTGCATATTCTCGGT
*
5302251 GGTGATATCC
66 GGTGATATTC
* * * * *
5302261 AAGTGTCAAAGTTTGAATTGCATTTTTTCAATGGCGATATCCGAAGTCATTTGTATATTCTCGAT
1 GAGTGTCAAAGTTTGAATTGCATTTTTTCAATGACGATATCCAAAGTCATTTGCATATTCTCGGT
5302326 GGTGATATTC
66 GGTGATATTC
* * *
5302336 GAGTGTCAAGGTTTGAATTGCATTTTCTCAGTGACGATATCCAAAGTCATTTGCATATTCTCGGT
1 GAGTGTCAAAGTTTGAATTGCATTTTTTCAATGACGATATCCAAAGTCATTTGCATATTCTCGGT
*
5302401 GGTGATATTT
66 GGTGATATTC
* * ** *
5302411 GAGTGTTAAAGCTTGAATTATATTTTTTCAATGATGATAT
1 GAGTGTCAAAGTTTGAATTGCATTTTTTCAATGACGATAT
5302451 ACGAGTCTTT
Statistics
Matches: 164, Mismatches: 25, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 9 0.05
75 155 0.95
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (75 bp):
GAGTGTCAAAGTTTGAATTGCATTTTTTCAATGACGATATCCAAAGTCATTTGCATATTCTCGGT
GGTGATATTC
Found at i:5302636 original size:99 final size:99
Alignment explanation
Indices: 5302366--5302619 Score: 332
Period size: 99 Copynumber: 2.6 Consensus size: 99
5302356 CATTTTCTCA
*
5302366 GTGACGATATCCAAAGTCATTTGCATATTCTCGGTGGTGATATTTGAGTGTTAAAGCTTGAATTA
1 GTGACGATATCCAAAGTCATTTGCATATTCTCGGTGGTGATATTTGAGTGTTAAAACTTGAATTA
* * * *
5302431 TATTTTTTCAATGATGATATACGAGTCTTTTTTG
66 CATTTTCTCAATGATAATATACGAGTCTTTTTCG
* * ** **
5302465 GTGGCAATATCTGAAGTCATTTGCATATTCTCGGTGGTGATATCCGAGTGTTAAAACTTGAATTA
1 GTGACGATATCCAAAGTCATTTGCATATTCTCGGTGGTGATATTTGAGTGTTAAAACTTGAATTA
5302530 CATTTTCTCAATGATAATAT-CTGAGT-TTCTTTCG
66 CATTTTCTCAATGATAATATAC-GAGTCTT-TTTCG
* ** * *
5302564 GTGACGGTATCCAAAGTCATTTATATTTTCTCGATGGTGATATTTGAGTGTTAAAA
1 GTGACGATATCCAAAGTCATTTGCATATTCTCGGTGGTGATATTTGAGTGTTAAAA
5302620 AATCATTTGC
Statistics
Matches: 131, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
98 3 0.02
99 128 0.98
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.41
Consensus pattern (99 bp):
GTGACGATATCCAAAGTCATTTGCATATTCTCGGTGGTGATATTTGAGTGTTAAAACTTGAATTA
CATTTTCTCAATGATAATATACGAGTCTTTTTCG
Found at i:5302796 original size:49 final size:49
Alignment explanation
Indices: 5302736--5302967 Score: 274
Period size: 49 Copynumber: 4.8 Consensus size: 49
5302726 TCAATAGTTT
* * *
5302736 AATTTTAAAGTTATTAAGCCTCTGCTTAGAGGAGCTTTTCCAAGATGAG
1 AATTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTCCAAGATGAG
* * * *
5302785 AATTTTGAAGTTGTTGAGGCTCTGCTTAGAGGAGCTTTTTCAAGATGA-
1 AATTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTCCAAGATGAG
* * * * *
5302833 AATTTTAAAGTTATTGAGCCTCTACTTATATGAGCTTTTTCAAAAT--G
1 AATTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTCCAAGATGAG
* *
5302880 AATTTTAAAGGTGTTGAGCCTCTACTTAGAGGAGCTTTCCCAAGATGATG
1 AATTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTCCAAGATGA-G
* * *
5302930 AATTTT-AAGTTGTTGAGCCTTTAATTAAAGGAGCTTTT
1 AATTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTT
5302968 TAAATTTAAA
Statistics
Matches: 155, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
47 39 0.25
48 39 0.25
49 70 0.45
50 7 0.05
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (49 bp):
AATTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGCTTTTCCAAGATGAG
Found at i:5302853 original size:97 final size:96
Alignment explanation
Indices: 5302736--5302967 Score: 279
Period size: 97 Copynumber: 2.4 Consensus size: 96
5302726 TCAATAGTTT
* * * * * *
5302736 AATTTTAAAGTTATTAAGCCTCTGCTTAGAGGAGCTTTTCCAAGATGAGAATTTTGAAGTTGTTG
1 AATTTTAAAGTTATTGAGCCTCTACTTAAAGGAGCTTTTCCAAAAT--GAATTTTAAAGGTGTTG
* * **
5302801 AGGCTCTGCTTAGAGGAGCTTTTTCAAGATGA-
64 AGCCTCTACTTAGAGGAGCTTTCCCAAGATGAG
* * *
5302833 AATTTTAAAGTTATTGAGCCTCTACTTATATGAGCTTTTTCAAAATGAATTTTAAAGGTGTTGAG
1 AATTTTAAAGTTATTGAGCCTCTACTTAAAGGAGCTTTTCCAAAATGAATTTTAAAGGTGTTGAG
5302898 CCTCTACTTAGAGGAGCTTTCCCAAGATGATG
66 CCTCTACTTAGAGGAGCTTTCCCAAGATGA-G
* * *
5302930 AATTTT-AAGTTGTTGAGCCTTTAATTAAAGGAGCTTTT
1 AATTTTAAAGTTATTGAGCCTCTACTTAAAGGAGCTTTT
5302968 TAAATTTAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
95 43 0.37
96 27 0.23
97 46 0.40
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (96 bp):
AATTTTAAAGTTATTGAGCCTCTACTTAAAGGAGCTTTTCCAAAATGAATTTTAAAGGTGTTGAG
CCTCTACTTAGAGGAGCTTTCCCAAGATGAG
Found at i:5303121 original size:17 final size:15
Alignment explanation
Indices: 5303091--5303126 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
5303081 GTAAACACCA
5303091 TTTTATTATTATTAT
1 TTTTATTATTATTAT
5303106 TTTTATGTATTTATTAT
1 TTTTAT-TA-TTATTAT
5303123 TTTT
1 TTTT
5303127 TTCTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 2 0.11
17 11 0.58
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTATTATTATTAT
Found at i:5303135 original size:15 final size:16
Alignment explanation
Indices: 5303099--5303147 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
5303089 CATTTTATTA
* *
5303099 TTATTATTTTTATGTAT
1 TTATTATTTTT-TCTCT
5303116 TTATTATTTTTT-TCT
1 TTATTATTTTTTCTCT
5303131 TTATT-TTTTTTCTCT
1 TTATTATTTTTTCTCT
5303146 TT
1 TT
5303148 TCCTTTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 6 0.20
15 12 0.40
16 1 0.03
17 11 0.37
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTATTTTTTCTCT
Found at i:5303166 original size:6 final size:6
Alignment explanation
Indices: 5303124--5303174 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
5303114 ATTTATTATT
* * *
5303124 TTTTTC TTTATTT TTTTTC TCTTTTC CTTTTC TTTTTC TTTTTT TTTTTC
1 TTTTTC TTT-TTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
5303174 T
1 T
5303175 GGTAGCGGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:5304397 original size:19 final size:19
Alignment explanation
Indices: 5304373--5304419 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
5304363 TCTTTTCTTT
*
5304373 TAATAAAAATAAAATTAAC
1 TAATAAAAATAAAAATAAC
* *
5304392 TAAT-AAATTAAAAATAAG
1 TAATAAAAATAAAAATAAC
5304410 TAATAAAAAT
1 TAATAAAAAT
5304420 GAGAAAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
TAATAAAAATAAAAATAAC
Found at i:5304884 original size:16 final size:18
Alignment explanation
Indices: 5304849--5304886 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5304839 TTTTTTGAAT
5304849 AAAAAATGAAACATTAAA
1 AAAAAATGAAACATTAAA
5304867 AAAAAAT-AAA-ATTTAAA
1 AAAAAATGAAACA-TTAAA
5304884 AAA
1 AAA
5304887 TAATTTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.05
17 11 0.58
18 7 0.37
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAATGAAACATTAAA
Found at i:5309602 original size:23 final size:22
Alignment explanation
Indices: 5309576--5309641 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
5309566 TATATATTTT
*
5309576 TATTCTTATTTTTTATCTATTAA
1 TATT-TTATTATTTATCTATTAA
* **
5309599 TATTTTTATTATTTATCTGTTTT
1 TA-TTTTATTATTTATCTATTAA
5309622 TATTTTATTATTTATCTATT
1 TATTTTATTATTTATCTATT
5309642 TCTTTTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 17 0.46
23 18 0.49
24 2 0.05
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTATTATTTATCTATTAA
Found at i:5309603 original size:45 final size:45
Alignment explanation
Indices: 5309528--5309641 Score: 110
Period size: 45 Copynumber: 2.5 Consensus size: 45
5309518 CCTAATTGGC
*
5309528 TTTTATTTT-TATTTTTAT-TATTTATCTATTTATTA-ATATATATAT
1 TTTTATTTTAT-TTTTTATCTA-TTATATATTT-TTATATATATATAT
* * *
5309573 TTTTATTCTTATTTTTTATCTATTA-ATATTTTTATTATTTATCTGT
1 TTTTATT-TTATTTTTTATCTATTATATATTTTTA-TATATATATAT
*
5309619 TTTTATTTTATTATTTATCTATT
1 TTTTATTTTATTTTTTATCTATT
5309642 TCTTTTATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
44 3 0.05
45 27 0.46
46 26 0.44
47 3 0.05
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (45 bp):
TTTTATTTTATTTTTTATCTATTATATATTTTTATATATATATAT
Found at i:5309627 original size:6 final size:6
Alignment explanation
Indices: 5309528--5309588 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
5309518 CCTAATTGGC
** * *
5309528 TTTTAT TTTTAT TTTTAT TATTTAT CTATTTAT TAATAT ATATAT TTTTAT
1 TTTTAT TTTTAT TTTTAT T-TTTAT -T-TTTAT TTTTAT TTTTAT TTTTAT
*
5309579 TCTTAT TTTT
1 TTTTAT TTTT
5309589 TATCTATTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
6 32 0.71
7 6 0.13
8 7 0.16
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTAT
Found at i:5309651 original size:17 final size:17
Alignment explanation
Indices: 5309528--5309699 Score: 67
Period size: 17 Copynumber: 10.2 Consensus size: 17
5309518 CCTAATTGGC
5309528 TTTTATTT-T-TATTT-
1 TTTTATTTATCTATTTA
5309542 TTATTATTTATCTATTTA
1 TT-TTATTTATCTATTTA
* * * *
5309560 TTAATATATATATTTTTA
1 TT-TTATTTATCTATTTA
*
5309578 TTCTTATTTTTTATCTATTAA
1 TT-TTA---TTTATCTATTTA
*
5309599 TATT-TTTAT-TATTTA
1 TTTTATTTATCTATTTA
* *
5309614 -TCTGTTT-T-TATTT-
1 TTTTATTTATCTATTTA
* *
5309627 TATTATTTATCTATTTC
1 TTTTATTTATCTATTTA
*
5309644 TTTTATTTATCTAATTA
1 TTTTATTTATCTATTTA
*
5309661 TTTTTTGTTATCTA-TTA
1 TTTTAT-TTATCTATTTA
* * *
5309678 ATATATTTATCTTTTTTA
1 TTTTATTTATC-TATTTA
5309696 TTTT
1 TTTT
5309700 GATTAATTTT
Statistics
Matches: 116, Mismatches: 27, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
14 13 0.11
15 15 0.13
16 16 0.14
17 31 0.27
18 30 0.26
20 2 0.02
21 9 0.08
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (17 bp):
TTTTATTTATCTATTTA
Found at i:5309653 original size:62 final size:62
Alignment explanation
Indices: 5309537--5309656 Score: 156
Period size: 62 Copynumber: 1.9 Consensus size: 62
5309527 CTTTTATTTT
*
5309537 TATTTTTATTATTTATCTATTTATTAATATATATATTTTTATTCTTATTTTTTATCTATTAA
1 TATTTTTATTATTTATCTATTTATTAATATATATATTTTTATTCTTATTATTTATCTATTAA
* * *
5309599 TATTTTTATTATTTATCTGTTT-TTATTTTAT-TATTTATCTATTTCTT-TTATTTATCTA
1 TATTTTTATTATTTATCTATTTATTAATATATATATTT-T-TA-TTCTTATTATTTATCTA
5309657 ATTATTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
60 5 0.10
61 8 0.16
62 33 0.65
63 5 0.10
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (62 bp):
TATTTTTATTATTTATCTATTTATTAATATATATATTTTTATTCTTATTATTTATCTATTAA
Found at i:5310147 original size:17 final size:19
Alignment explanation
Indices: 5310104--5310142 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5310094 TTGTTTAGAG
*
5310104 AGAAGGGAGAGAAAAGAAA
1 AGAAGAGAGAGAAAAGAAA
5310123 AGAAGAGAGAGAAAAGAAA
1 AGAAGAGAGAGAAAAGAAA
5310142 A
1 A
5310143 AGAGAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
AGAAGAGAGAGAAAAGAAA
Found at i:5314282 original size:26 final size:28
Alignment explanation
Indices: 5314253--5314314 Score: 101
Period size: 26 Copynumber: 2.2 Consensus size: 28
5314243 ACAAATGGAG
5314253 TAAGAAAATTCTCACTGATTT-AAAAA-
1 TAAGAAAATTCTCACTGATTTGAAAAAC
5314279 TAAGAAAATTCTCACTGATTTGAAAAAC
1 TAAGAAAATTCTCACTGATTTGAAAAAC
5314307 TGAAGAAA
1 T-AAGAAA
5314315 GCTTAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 21 0.64
27 5 0.15
28 1 0.03
29 6 0.18
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.27
Consensus pattern (28 bp):
TAAGAAAATTCTCACTGATTTGAAAAAC
Found at i:5316975 original size:27 final size:27
Alignment explanation
Indices: 5316936--5317009 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
5316926 TGAAAGGTGA
**
5316936 AAAAAAAAGAAAAAAAATGGTGAAGGTG
1 AAAAAAAAGAAAAAAAATGG-GAAAATG
5316964 -AAAAAAAGAAAAAAAA-GGGAAAATG
1 AAAAAAAAGAAAAAAAATGGGAAAATG
5316989 AAAAAAAAAGAGAAAAAAATG
1 -AAAAAAAAGA-AAAAAAATG
5317010 AAAGAGGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.12
26 2 0.05
27 25 0.62
28 7 0.17
29 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (27 bp):
AAAAAAAAGAAAAAAAATGGGAAAATG
Found at i:5316986 original size:18 final size:19
Alignment explanation
Indices: 5316965--5317006 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5316955 GTGAAGGTGA
5316965 AAAAAAG-AAAAAAAAG-G
1 AAAAAAGAAAAAAAAAGAG
* *
5316982 GAAAATGAAAAAAAAAGAG
1 AAAAAAGAAAAAAAAAGAG
5317001 AAAAAA
1 AAAAAA
5317007 ATGAAAGAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
17 5 0.26
18 9 0.47
19 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAAAAAAAGAG
Found at i:5317012 original size:27 final size:26
Alignment explanation
Indices: 5316925--5317021 Score: 86
Period size: 27 Copynumber: 3.5 Consensus size: 26
5316915 ATCAACATGG
*
5316925 ATGAAAGGTGAAAAAAAAAGAAAAAAA
1 ATGAAAAG-GAAAAAAAAAGAAAAAAA
** **
5316952 ATGGTGAAGGTGAAAAAAAGAAAAAAA
1 AT-GAAAAGGAAAAAAAAAGAAAAAAA
* *
5316979 AGGGAAAATGAAAAAAAAAGAGAAAAAA
1 A-TGAAAAGGAAAAAAAAAGA-AAAAAA
5317007 ATGAAAGAGGAAAAA
1 ATGAAA-AGGAAAAA
5317022 GGAAGACTCA
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
27 36 0.68
28 17 0.32
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (26 bp):
ATGAAAAGGAAAAAAAAAGAAAAAAA
Found at i:5318192 original size:22 final size:23
Alignment explanation
Indices: 5318167--5318225 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
5318157 GAATATTTTG
*
5318167 ATGAGAATTTTTGAGAACTC-AA
1 ATGAGAATCTTTGAGAACTCAAA
**
5318189 ATGAGAATCTTTGA-ATTTCAAA
1 ATGAGAATCTTTGAGAACTCAAA
5318211 ATGAGAATCTTTGAG
1 ATGAGAATCTTTGAG
5318226 GAGTGAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (23 bp):
ATGAGAATCTTTGAGAACTCAAA
Found at i:5318868 original size:42 final size:41
Alignment explanation
Indices: 5318788--5319205 Score: 340
Period size: 41 Copynumber: 10.1 Consensus size: 41
5318778 ATGATTATTA
* *
5318788 AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAA
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5318829 AGGAGCAATTTATTTTTCAAAGTCGTGGTTGCCTTTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGG-TGCCTCTGTTTAG
*
5318871 AGGAGCAATTTA-TTTTCTAAAGTCGTGGTTGCCTCTATTTAG
1 AGGAGCAATTTATTTTTC-AAAGTCGTGG-TGCCTCTGTTTAG
* * *
5318913 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * ** *
5318954 AGGATC-ATTTATTTTT-GAAGTCATGGTGCTTCTACTTAA
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *** * * * *
5318993 AGAATTTATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAA
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * **
5319034 ATGAGCCATTTATTTTTCAAAGTCGTTGAGCCTCTAATTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * * * *
5319075 AGAAGCCATTTATCTTTCAAAGTCGTTGAGCCTTTGATTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * *
5319116 GGGAGCCATTTA-TTTTCAAGGTCGTGGAGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*** * * **
5319156 AGGAGGTTTGTTTATTTTTTCAAAGTCGTAGAGCCTCTACTTAG
1 AGGA-G-CAATTTA-TTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5319200 AGGAGC
1 AGGAGC
5319206 TTTGATAAAG
Statistics
Matches: 313, Mismatches: 55, Indels: 17
0.81 0.14 0.04
Matches are distributed among these distances:
39 19 0.06
40 45 0.14
41 145 0.46
42 70 0.22
43 6 0.02
44 28 0.09
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (41 bp):
AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:5319430 original size:6 final size:6
Alignment explanation
Indices: 5319419--5319449 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5319409 TCCAATTGGC
*
5319419 TTTTAT TTTTAT TTTCAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
5319450 ATTCGTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:5319553 original size:20 final size:21
Alignment explanation
Indices: 5319477--5319555 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 21
5319467 TATATATTTT
5319477 TTTATTCTTATTTTTTTATCTA-
1 TTTATT-TTA-TTTTTTATCTAC
*
5319499 TTAATATTTTTATTATTTATCTAC
1 TT--TA-TTTTATTTTTTATCTAC
5319523 TTTTATTTTATTTTTTATCTA-
1 -TTTATTTTATTTTTTATCTAC
*
5319544 TTTCTTTTATTT
1 TTTATTTTATTT
5319556 ATCTAATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
20 11 0.22
22 17 0.35
23 12 0.24
24 5 0.10
25 4 0.08
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTATTTTATTTTTTATCTAC
Found at i:5319558 original size:17 final size:17
Alignment explanation
Indices: 5319511--5319602 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
5319501 AATATTTTTA
5319511 TTATTTATCTACTTTTATT
1 TTATTTATCTA--TTTATT
*
5319530 TTATTTTTTATCTATTTCTT
1 TTA---TTTATCTATTTATT
*
5319550 TTATTTATCTAATTATT
1 TTATTTATCTATTTATT
* *
5319567 TTTTGTTATCTA-TTAAT
1 TTAT-TTATCTATTTATT
* * *
5319584 ATATTTATTTTTTTATT
1 TTATTTATCTATTTATT
5319601 TT
1 TT
5319603 GATTAATTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
16 5 0.09
17 26 0.46
18 7 0.12
19 3 0.05
20 8 0.14
22 8 0.14
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.71
Consensus pattern (17 bp):
TTATTTATCTATTTATT
Found at i:5319588 original size:22 final size:21
Alignment explanation
Indices: 5319542--5319594 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
5319532 ATTTTTTATC
*
5319542 TATTTCTTTTATTTATCTAAT
1 TATTTCTTTTATCTATCTAAT
*
5319563 TATTTTTTGTTATCTAT-TAAT
1 TATTTCTT-TTATCTATCTAAT
*
5319584 ATATTTATTTT
1 -TATTTCTTTT
5319595 TTTATTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTTCTTTTATCTATCTAAT
Found at i:5319596 original size:59 final size:60
Alignment explanation
Indices: 5319461--5319599 Score: 143
Period size: 59 Copynumber: 2.4 Consensus size: 60
5319451 TTCGTCTATT
*
5319461 TATTAATATA--TATTTTTTTATTCTTATTTTTTTATCTATTAATATTTTTATTATTTATC
1 TATTAATATATTTATTTTTTTA-TCTTATTTTTTTATCTATTAATATTTTTATTAGTTATC
* *
5319520 TACTT-TTAT-TTTA-TTTTTTATC-TATTTCTTTTATTTATCTAAT-TATTTT-TT-GTTATC
1 TA-TTAATATATTTATTTTTTTATCTTATTT-TTTTATCTAT-TAATAT-TTTTATTAGTTATC
5319577 TATTAATATATTTATTTTTTTAT
1 TATTAATATATTTATTTTTTTAT
5319600 TTTGATTAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
56 2 0.03
57 15 0.22
58 18 0.27
59 28 0.42
60 4 0.06
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (60 bp):
TATTAATATATTTATTTTTTTATCTTATTTTTTTATCTATTAATATTTTTATTAGTTATC
Found at i:5320029 original size:19 final size:18
Alignment explanation
Indices: 5320003--5320050 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
5319993 AGAATTGTTT
5320003 AGAGAGAAGGGAGAGAAA
1 AGAGAGAAGGGAGAGAAA
* *
5320021 AGAAGAGAAGAGAGAGAAT
1 AG-AGAGAAGGGAGAGAAA
5320040 AG-GAGAAGGGA
1 AGAGAGAAGGGA
5320051 ATTCTGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 2 0.08
19 16 0.62
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (18 bp):
AGAGAGAAGGGAGAGAAA
Found at i:5320331 original size:14 final size:13
Alignment explanation
Indices: 5320306--5320352 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
5320296 AGATTTTCGA
5320306 TATTTTTTTAATT
1 TATTTTTTTAATT
5320319 TATTTTATTTAATT
1 TATTTT-TTTAATT
*
5320333 TATTTGTTTTACTT
1 TATTT-TTTTAATT
5320347 T-TTTTT
1 TATTTTT
5320353 ATTTTATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 2 0.06
13 9 0.29
14 19 0.61
15 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (13 bp):
TATTTTTTTAATT
Found at i:5320357 original size:9 final size:9
Alignment explanation
Indices: 5320306--5320357 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
5320296 AGATTTTCGA
5320306 TATTTTTTT
1 TATTTTTTT
* *
5320315 AATTTATTT
1 TATTTTTTT
**
5320324 TATTTAATT
1 TATTTTTTT
*
5320333 TATTTGTTT
1 TATTTTTTT
5320342 TACTTTTTTT
1 TA-TTTTTTT
5320352 TATTTT
1 TATTTT
5320358 ATCAAAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
9 27 0.77
10 8 0.23
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (9 bp):
TATTTTTTT
Found at i:5320825 original size:50 final size:51
Alignment explanation
Indices: 5320730--5320825 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 51
5320720 TCTTTCCAAG
*
5320730 AAAAAAAAATAATTTCTAAATAGGCCCAAATGGTGGAAATTTTAGAAATTC
1 AAAAAAAAATAATTTCTAAATAGGCCCAAATGGTGGAAATATTAGAAATTC
* * *
5320781 AAAAAAAAA-AATTTTTAATTTGGCCCAAATGGTGG-AATAATTAGA
1 AAAAAAAAATAATTTCTAAATAGGCCCAAATGGTGGAAAT-ATTAGA
5320826 TTTATTTTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 3 0.08
50 28 0.70
51 9 0.22
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (51 bp):
AAAAAAAAATAATTTCTAAATAGGCCCAAATGGTGGAAATATTAGAAATTC
Found at i:5326951 original size:11 final size:11
Alignment explanation
Indices: 5326935--5326973 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
5326925 TTATTTATTG
5326935 ATAAATTAATA
1 ATAAATTAATA
*
5326946 ATAAATTAATT
1 ATAAATTAATA
*
5326957 ATAAATTTATA
1 ATAAATTAATA
5326968 ATAAAT
1 ATAAAT
5326974 ATTTAGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAAATTAATA
Done.