Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 149 of 160
Found at i:29010483 original size:75 final size:75
Alignment explanation
Indices: 29010358--29010499 Score: 184
Period size: 75 Copynumber: 1.9 Consensus size: 75
29010348 ACAGAAAACA
* *
29010358 CCTTCAATAAATTCTTTCAAAAAATTATAATGAATTAGTAAAGATATTTTT-TGTGGAATAAACA
1 CCTTCAATAAATTCTTTCAAAAAATTATAATGAATTAGTAAAGACATTTTTCTAT--AATAAACA
29010422 CCTTCAGTAATG
64 CCTTCAGTAATG
* *
29010434 CCTTCAATAAATT-TCTTC-AAAAATTATAATGAATTAGTGAATG-CGTTTTTCTATAATAAACA
1 CCTTCAATAAATTCT-TTCAAAAAATTATAATGAATTAGT-AAAGACATTTTTCTATAATAAACA
29010496 CCTT
64 CCTT
29010500 GAATAACCAC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
74 12 0.20
75 26 0.44
76 21 0.36
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (75 bp):
CCTTCAATAAATTCTTTCAAAAAATTATAATGAATTAGTAAAGACATTTTTCTATAATAAACACC
TTCAGTAATG
Found at i:29010782 original size:187 final size:186
Alignment explanation
Indices: 29010430--29010788 Score: 449
Period size: 187 Copynumber: 1.9 Consensus size: 186
29010420 CACCTTCAGT
* * * *
29010430 AATGCCTTCAATAAATTTCTTCAAAAATTATAATGAATTAGTGAATGCGTTTTTCTATAATAAAC
1 AATGCCTTCAATAAATTTCTTCAAAAATTAGAACGAATTAGTGAATGCATTTTTCTAGAATAAAC
* * ** **
29010495 ACCTTGAATAACCACTTAAAATTTTAGTAGTGAAATATTGAAAGCGTTTTCTACTAAAAGATGCA
66 ACATTCAATAACCACTTAAAATTTTAGTAGTGAAATATTGAAAGAATTTTCTACTAAAAGACACA
*
29010560 TTTAATTATCCTAAACAATTTTTAAAAAGAAATTATTGAAGGAGTATAATGCAAAA
131 TTTAATAATCCTAAACAATTTTTAAAAAGAAATTATTGAAGGAGTATAATGCAAAA
* * *
29010616 AATGCCTTCAATAAA-TTCTTTCAAAAGTTAGAACGAATTAGTG-ATGGCATTTTTTTGGAATAA
1 AATGCCTTCAATAAATTTC-TTCAAAAATTAGAACGAATTAGTGAAT-GCATTTTTCTAGAATAA
* * *
29010679 ACGCATTCAATAACC-CTTTTAAAATTTTAGTAGTGCAATATTGAAAGAATTTTCTACTAGAAGA
64 ACACATTCAATAACCAC--TTAAAATTTTAGTAGTGAAATATTGAAAGAATTTTCTACTAAAAGA
* * *
29010743 CACCTTTAATAAT-CTAAAATAATTTTT-ATAAGAAAATTATTGAAGG
127 CACATTTAATAATCCT-AAACAATTTTTAAAAAG-AAATTATTGAAGG
29010789 CGTTTTCTCT
Statistics
Matches: 147, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
185 6 0.04
186 67 0.46
187 74 0.50
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (186 bp):
AATGCCTTCAATAAATTTCTTCAAAAATTAGAACGAATTAGTGAATGCATTTTTCTAGAATAAAC
ACATTCAATAACCACTTAAAATTTTAGTAGTGAAATATTGAAAGAATTTTCTACTAAAAGACACA
TTTAATAATCCTAAACAATTTTTAAAAAGAAATTATTGAAGGAGTATAATGCAAAA
Found at i:29010869 original size:239 final size:238
Alignment explanation
Indices: 29010589--29011086 Score: 622
Period size: 239 Copynumber: 2.1 Consensus size: 238
29010579 TTTTAAAAAG
* ** * *
29010589 AAATTATTGAAGGAGTATAATGCAAAAAATGCCTTCAATAAATTCTTTCAAAAGTTAGAACGAAT
1 AAATTATTGAAGGCGTATAATGCAAAAAACCCCTTCAATAAATTCTTTAAAAAATTAGAACGAAT
** * * ** * **
29010654 TAGTGATGGCATTTTTTTGGAATAAACGCATTCAATAACCCTTTTAAAATTTTAGTAGTGCAATA
66 TAGTGAAAGCATTTTTCTAGAATAAACGCATTCAATAACCCACTTAAAATTTAAACAGTGCAATA
*
29010719 TTGAAAGAATTTTCTACTAGAAGACACCTTTAATAATCTAAAATAA-TTTTTATAAGAAAATTAT
131 TTGAAAGAATTTTCTACTAAAAGACACCTTTAATAATCTAAAATAATTTTTTATAA-AAAATTAT
* *
29010783 TGAAGGCGTTTTCTCTCAAAAAACATCTTTAATAATTATGTACAA-
195 TGAAGGCATTTT-TCTCAAAAAACATCTTCAATAATTATGTA-AAC
* * *
29010828 AAATTATTGAAGGCGTATAATGCAATAAACCCCTTCAATAAATTCTTTAAAAAATTATAATGAAT
1 AAATTATTGAAGGCGTATAATGCAAAAAACCCCTTCAATAAATTCTTTAAAAAATTAGAACGAAT
** *** * *
29010893 TAGTGAAAGTGTTTTTCTAGAATAAACTTTTTCAATAAGCCACTTAAAATTTAAACAGTGGAATA
66 TAGTGAAAGCATTTTTCTAGAATAAACGCATTCAATAACCCACTTAAAATTTAAACAGTGCAATA
* * * * * * *
29010958 TTGAAAGCATTTTTTACTAAAAGACGCCTTTGATAATCTCAAATAATTTTTTTTTAAAAATTATT
131 TTGAAAGAATTTTCTACTAAAAGACACCTTTAATAATCTAAAATAATTTTTTATAAAAAATTATT
* *
29011023 GAAGGCATTTTTTTCAAAAAAGATCTTCAATAATTATGTAAAC
196 GAAGGCATTTTTCTCAAAAAACATCTTCAATAATTATGTAAAC
*
29011066 AAATTATTGTAGGCGTATAAT
1 AAATTATTGAAGGCGTATAAT
29011087 AAAGGAAATT
Statistics
Matches: 220, Mismatches: 37, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
237 2 0.01
238 46 0.21
239 165 0.75
240 7 0.03
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (238 bp):
AAATTATTGAAGGCGTATAATGCAAAAAACCCCTTCAATAAATTCTTTAAAAAATTAGAACGAAT
TAGTGAAAGCATTTTTCTAGAATAAACGCATTCAATAACCCACTTAAAATTTAAACAGTGCAATA
TTGAAAGAATTTTCTACTAAAAGACACCTTTAATAATCTAAAATAATTTTTTATAAAAAATTATT
GAAGGCATTTTTCTCAAAAAACATCTTCAATAATTATGTAAAC
Found at i:29013672 original size:139 final size:140
Alignment explanation
Indices: 29013418--29013674 Score: 338
Period size: 139 Copynumber: 1.8 Consensus size: 140
29013408 ACATTAACAA
* * *
29013418 TTATTGTTCTATTTTAATAGTTTTAATAGTTTCAATACATGATATTAAACTTATCAAAAGTATTG
1 TTATTATTCTATTTTAATAGTTTGAATAGCTTCAATACATGATATTAAACTTATCAAAAGTATTG
* *
29013483 AACTTAATTGCCACGGTTGATATGTATGAAAAAATTATTGTTTATGTCTATTTAGGTAAAAATAC
66 AACTTAATTGCCACGGTTGATATGTATGAAAAAATTATCGTTTATATCTATTTAGGTAAAAATAC
29013548 AATACTGTTG
131 AATACTGTTG
* * * ** *
29013558 TTATTATTCTATTTTAATAGTTTGGATAGCTTCAATACTTGATA-TAAACTTGTC-TGATTAATT
1 TTATTATTCTATTTTAATAGTTTGAATAGCTTCAATACATGATATTAAACTTATCAAAAGT-ATT
* * * * * *
29013621 GAATTTGATTTCTATGGTTGATATGTATGAAAAAGTTATCGTTTATATCTATTT
65 GAACTTAATTGCCACGGTTGATATGTATGAAAAAATTATCGTTTATATCTATTT
29013675 GAGACTATTT
Statistics
Matches: 99, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
138 2 0.02
139 58 0.59
140 39 0.39
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (140 bp):
TTATTATTCTATTTTAATAGTTTGAATAGCTTCAATACATGATATTAAACTTATCAAAAGTATTG
AACTTAATTGCCACGGTTGATATGTATGAAAAAATTATCGTTTATATCTATTTAGGTAAAAATAC
AATACTGTTG
Found at i:29015850 original size:15 final size:15
Alignment explanation
Indices: 29015830--29015862 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29015820 TTAAAAAAAA
29015830 ATTATATTACATTAT
1 ATTATATTACATTAT
*
29015845 ATTATATTATATTAT
1 ATTATATTACATTAT
29015860 ATT
1 ATT
29015863 TTATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATATTACATTAT
Found at i:29015859 original size:10 final size:10
Alignment explanation
Indices: 29015830--29015891 Score: 70
Period size: 10 Copynumber: 5.8 Consensus size: 10
29015820 TTAAAAAAAA
*
29015830 ATTATATTAC
1 ATTATATTAT
29015840 ATTATATTAT
1 ATTATATTAT
29015850 ATTATATTAT
1 ATTATATTAT
*
29015860 ATTTTATATAT
1 ATTATAT-TAT
29015871 ATATATATATAT
1 AT-TATAT-TAT
29015883 ATATATATT
1 AT-TATATT
29015892 TACACACACA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
10 25 0.53
11 6 0.13
12 16 0.34
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTATATTAT
Found at i:29015871 original size:2 final size:2
Alignment explanation
Indices: 29015842--29015890 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
29015832 TATATTACAT
*
29015842 TA TA T- TA TA T- TA TA T- TA TA T- TT 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
29015880 TA TA TA TA TA T
1 TA TA TA TA TA T
29015891 TTACACACAC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:29016165 original size:23 final size:22
Alignment explanation
Indices: 29016134--29016176 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29016124 AAATTTATCG
*
29016134 TAATATTAATTAAATTTAAATAT
1 TAATATTAA-TAAAATTAAATAT
*
29016157 TAATTTTAATAAAATTAAAT
1 TAATATTAATAAAATTAAAT
29016177 TAAAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTAATAAAATTAAATAT
Found at i:29016174 original size:28 final size:28
Alignment explanation
Indices: 29016141--29016200 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
29016131 TCGTAATATT
*
29016141 AATTAAATTTAAAT-ATTAATTTTAATAA
1 AATTAAATTAAAATAATT-ATTTTAATAA
* *
29016169 AATTAAATTAAAATAATTTTTTTATTAA
1 AATTAAATTAAAATAATTATTTTAATAA
29016197 AATT
1 AATT
29016201 TTTTAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTAAATTAAAATAATTATTTTAATAA
Found at i:29017482 original size:45 final size:45
Alignment explanation
Indices: 29017429--29017519 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
29017419 AAATTCTATC
*
29017429 AATATTTTTATTAAAAATATATATTTAATAAATATATCAAAATTT
1 AATATTTTTATTAAAAATATATATTTAATAAATACATCAAAATTT
*
29017474 AATATTTTTATTAAAAATATCTATTTAATAAATACATCAAAATTT
1 AATATTTTTATTAAAAATATATATTTAATAAATACATCAAAATTT
29017519 A
1 A
29017520 TAAAAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (45 bp):
AATATTTTTATTAAAAATATATATTTAATAAATACATCAAAATTT
Found at i:29018989 original size:29 final size:28
Alignment explanation
Indices: 29018924--29018999 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
29018914 CAAATTTAAA
*
29018924 TTATA-ATTAATA-TTTTAAATAATTTT
1 TTATATATTATTATTTTTAAATAATTTT
29018950 TTATATATTATTATTTTTATAATAAATTTT
1 TTATATATTATTATTTTTA-AAT-AATTTT
*
29018980 ATTA-AT-TTATTA-ATTTAAAT
1 -TTATATATTATTATTTTTAAAT
29019000 TTTTTATCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
26 5 0.12
27 9 0.21
28 9 0.21
29 9 0.21
30 8 0.19
31 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTATATATTATTATTTTTAAATAATTTT
Found at i:29020010 original size:13 final size:13
Alignment explanation
Indices: 29019994--29020021 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29019984 CTTTCGATGG
29019994 CTTCTAAACCCAT
1 CTTCTAAACCCAT
29020007 CTTCTAAACCCAT
1 CTTCTAAACCCAT
29020020 CT
1 CT
29020022 ACTGTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (13 bp):
CTTCTAAACCCAT
Found at i:29020220 original size:19 final size:19
Alignment explanation
Indices: 29020196--29020242 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
29020186 GGAGAGTATA
29020196 AAAATCAAATATAAAATTC
1 AAAATCAAATATAAAATTC
29020215 AAAATCAAATATAAAATTC
1 AAAATCAAATATAAAATTC
29020234 AAAATCAAA
1 AAAATCAAA
29020243 AACTACAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATCAAATATAAAATTC
Found at i:29022293 original size:16 final size:16
Alignment explanation
Indices: 29022268--29022307 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29022258 CGATAAATGA
29022268 ATGATAATGATGATTT
1 ATGATAATGATGATTT
*
29022284 ATGATGATGATGATTT
1 ATGATAATGATGATTT
*
29022300 ACGATAAT
1 ATGATAAT
29022308 TTTTAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.40
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:29048793 original size:27 final size:27
Alignment explanation
Indices: 29048743--29048794 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
29048733 GATAGTTAAG
**
29048743 AAAATAAATAAATAAATATTTTTAATA
1 AAAATAAATAAATAAATAAATTTAATA
29048770 AAAATAAATAACATAAA-AAATTTAA
1 AAAATAAATAA-ATAAATAAATTTAA
29048795 AATTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAATAAATAAATAAATAAATTTAATA
Found at i:29051586 original size:14 final size:13
Alignment explanation
Indices: 29051569--29051604 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
29051559 TAAATTTTTT
29051569 ATTAAAAATAAATA
1 ATTAAAAATAAA-A
*
29051583 ATTAAAAATTAAA
1 ATTAAAAATAAAA
29051596 ATTAAAAAT
1 ATTAAAAAT
29051605 CGAATTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTAAAAATAAAA
Found at i:29060222 original size:35 final size:37
Alignment explanation
Indices: 29060176--29060248 Score: 123
Period size: 35 Copynumber: 2.0 Consensus size: 37
29060166 TCCATTAACA
29060176 TAGATATGGAATACATA-AGTT-AAACAGAAAACACT
1 TAGATATGGAATACATAGAGTTAAAACAGAAAACACT
29060211 TAGATATGGAATACATAGAGTTACAAACAGAAAACACT
1 TAGATATGGAATACATAGAGTTA-AAACAGAAAACACT
29060249 CTGTGACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 17 0.49
36 4 0.11
38 14 0.40
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (37 bp):
TAGATATGGAATACATAGAGTTAAAACAGAAAACACT
Found at i:29064617 original size:2 final size:2
Alignment explanation
Indices: 29064610--29064634 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29064600 CAATAATACT
29064610 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
29064635 TTATTGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29068100 original size:16 final size:16
Alignment explanation
Indices: 29068081--29068112 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29068071 TGACATTGCA
29068081 AGTAATAATCATTAGG
1 AGTAATAATCATTAGG
29068097 AGTAATAATCATTAGG
1 AGTAATAATCATTAGG
29068113 GGTGAGTAAT
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
AGTAATAATCATTAGG
Found at i:29068344 original size:16 final size:17
Alignment explanation
Indices: 29068294--29068345 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
29068284 TTATTTTTTT
29068294 ATTATAAATAATT-ATTTA
1 ATTATAAAT--TTAATTTA
29068312 ATTATAAATTTAATTTA
1 ATTATAAATTTAATTTA
29068329 A-TA-AAATTTAAATTTA
1 ATTATAAATTT-AATTTA
29068345 A
1 A
29068346 ATATCATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.19
16 11 0.34
17 6 0.19
18 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTATAAATTTAATTTA
Found at i:29071190 original size:47 final size:47
Alignment explanation
Indices: 29071111--29071205 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
29071101 TGGGATTCAG
*
29071111 GACTCCCCCTTAGGTCCGTGATATTTTCTCGCACCCAACCTCGTGAC
1 GACTCCCCCTTAGGTCCGTGACATTTTCTCGCACCCAACCTCGTGAC
*
29071158 GACTCCCCCTTAGGTCCGTGACATTCTT-TCGCACCTAACCTCGTGAC
1 GACTCCCCCTTAGGTCCGTGACATT-TTCTCGCACCCAACCTCGTGAC
29071205 G
1 G
29071206 CCCTCGCCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 43 0.96
48 2 0.04
ACGTcount: A:0.17, C:0.38, G:0.18, T:0.27
Consensus pattern (47 bp):
GACTCCCCCTTAGGTCCGTGACATTTTCTCGCACCCAACCTCGTGAC
Found at i:29071848 original size:376 final size:371
Alignment explanation
Indices: 29071158--29071927 Score: 1308
Period size: 376 Copynumber: 2.1 Consensus size: 371
29071148 ACCTCGTGAC
* ** *
29071158 GACTCCCCCTTAGGTCCGTGACATTCTTTCGCACCTAACCTCGTGACGCCCTCGCCCTCGTCACG
1 GACTCCCCCTTAAGTCCGTGACATTCTCCCGCACCCAACCTCGTGACGCCCTCGCCCTCGTCACG
29071223 GAGGCTGACCACCCTCTCCCTTGAGGTGCTTGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGAT
66 GAGGCTGACCACCCTCTCCCTTGAGGTGCTTGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGAT
*
29071288 ACCACTTGTCACAGGTCGAGACTTAAGCTCCGAACCCGTGCGGCTCCGGGACCCGGACATTCATC
131 ACCACTTGTCACAGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGGACATTCATC
* *
29071353 CTTCCGGCGTCCCGAATCAGCCTGACCGTCATGGTTCACACCCTTGTAAGGTATTGTCCGCTTCA
196 CTTCCGGCGTCCCGAATCAGCCTGACCGCCATGGTTCACACCCTTGTAAGGTATTGTCCGCTCCA
* *
29071418 GCCCCCTTAGCCTCACGATTTTGTCCTACAAAAGGCGTCTCATAAGAGGGAGATGGTGTGAACCC
261 GCCCCCTTAGCCTCACGATTTTGTCCTACAAAAGGCGCCTCATAAGACGGAGATGGTGTGAACCC
*
29071483 TTTTATA-CCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAT
326 TTTTATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAG
*
29071528 GACTCCCCCTTAAGTCCGTGATATTCTCCCGCACCCAACCTCGTGACGCCCTCGCCCTCGTCACG
1 GACTCCCCCTTAAGTCCGTGACATTCTCCCGCACCCAACCTCGTGACGCCCTCGCCCTCGTCACG
29071593 GAGGCTGACCACCCTGCCTGCCTCCCTTGAGGTGCTTGGCGTGGATCGAACGGTTTAGGGCTGGC
66 GAGGCTGACCA--C--CCT--CTCCCTTGAGGTGCTTGGCGTGGATCGAACGGTTTAGGGCTGGC
*
29071658 TCTGATACCACTTGTCACAGGTCGAGACTTAAGCTTCGAACCCGCGCGGCTCCGGGACCCGGACA
125 TCTGATACCACTTGTCACAGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGGACA
* *
29071723 TTCATCCTTCCGGCGTCCCGAATCAGCCTGACCGCCATGGTTTACACCCTTGTGAGGTATTGTCC
190 TTCATCCTTCCGGCGTCCCGAATCAGCCTGACCGCCATGGTTCACACCCTTGTAAGGTATTGTCC
* * *
29071788 GCTCCGGCCCCCTTAGCCTCACGGTTTTGTCCTACAAAAGGTGCCTCATAAGACGGAGATGGTGT
255 GCTCCAGCCCCCTTAGCCTCACGATTTTGTCCTACAAAAGGCGCCTCATAAGACGGAGATGGTGT
*
29071853 GAACCCTTTTATACCCCAGTGACCTTCCTATTATGTTCGATGTGGGATTCAG
320 GAACCCTTTTATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAG
*
29071905 GACTCCCCCTTATGTCCGTGACA
1 GACTCCCCCTTAAGTCCGTGACA
29071928 CAAGGGCTTC
Statistics
Matches: 373, Mismatches: 20, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
370 71 0.19
372 1 0.00
374 3 0.01
376 241 0.65
377 57 0.15
ACGTcount: A:0.18, C:0.33, G:0.24, T:0.25
Consensus pattern (371 bp):
GACTCCCCCTTAAGTCCGTGACATTCTCCCGCACCCAACCTCGTGACGCCCTCGCCCTCGTCACG
GAGGCTGACCACCCTCTCCCTTGAGGTGCTTGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGAT
ACCACTTGTCACAGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGGACATTCATC
CTTCCGGCGTCCCGAATCAGCCTGACCGCCATGGTTCACACCCTTGTAAGGTATTGTCCGCTCCA
GCCCCCTTAGCCTCACGATTTTGTCCTACAAAAGGCGCCTCATAAGACGGAGATGGTGTGAACCC
TTTTATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAG
Found at i:29086322 original size:1 final size:1
Alignment explanation
Indices: 29086318--29086342 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
29086308 AAAAGTTAGG
29086318 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
29086343 ATTAATAGCA
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:29092939 original size:2 final size:2
Alignment explanation
Indices: 29092934--29092960 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29092924 TTTGACAGCC
29092934 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29092961 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29092965 original size:2 final size:2
Alignment explanation
Indices: 29092960--29092988 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29092950 ATATATATAT
29092960 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29092989 AACATCATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29095172 original size:2 final size:2
Alignment explanation
Indices: 29095165--29095190 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29095155 AATCAACCAC
29095165 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29095191 TCTTCTACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29102180 original size:119 final size:119
Alignment explanation
Indices: 29101969--29102206 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
29101959 TACCATCACA
29101969 CATCATGCATTAAGTCCCTTCTCTTACCTCCTAGTGCTGGAAGAACTGCATACGTTATAATATGC
1 CATCATGCATTAAGTCCCTTCTCTTACCTCCTAGTGCTGGAAGAACTGCATACGTTATAATATGC
29102034 AAATAAACAGTTTTATTTACTAAGTAGTATAACTATTGAAATGATCTGATAGAG
66 AAATAAACAGTTTTATTTACTAAGTAGTATAACTATTGAAATGATCTGATAGAG
29102088 CATCATGCATTAAGTCCCTTCTCTTACCTCCTAGTGCTGGAAGAACTGCATACGTTATAATATGC
1 CATCATGCATTAAGTCCCTTCTCTTACCTCCTAGTGCTGGAAGAACTGCATACGTTATAATATGC
29102153 AAATAAACAGTTTTATTTACTAAGTAGTATAACTATTGAAATGATCTGATAGAG
66 AAATAAACAGTTTTATTTACTAAGTAGTATAACTATTGAAATGATCTGATAGAG
29102207 TTTCCATGCA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (119 bp):
CATCATGCATTAAGTCCCTTCTCTTACCTCCTAGTGCTGGAAGAACTGCATACGTTATAATATGC
AAATAAACAGTTTTATTTACTAAGTAGTATAACTATTGAAATGATCTGATAGAG
Found at i:29103194 original size:3 final size:3
Alignment explanation
Indices: 29103186--29103230 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
29103176 TCAACTGGTG
*
29103186 TTA TTA TTA TT- TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29103231 GAATCGAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:29109782 original size:20 final size:20
Alignment explanation
Indices: 29109757--29109796 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29109747 TCATAGGGGA
29109757 ATAATAGTAACTTTTAATGG
1 ATAATAGTAACTTTTAATGG
29109777 ATAATAGTAACTTTTAATGG
1 ATAATAGTAACTTTTAATGG
29109797 TCTAGGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (20 bp):
ATAATAGTAACTTTTAATGG
Found at i:29127250 original size:53 final size:53
Alignment explanation
Indices: 29127170--29127293 Score: 230
Period size: 53 Copynumber: 2.3 Consensus size: 53
29127160 AAAAAGGTGA
* *
29127170 CAGATAAGTCCATCAGGCTCTATTTTACTAGAATGCTCATAGAAATAGTAGGC
1 CAGATAAGTCAATCAGGTTCTATTTTACTAGAATGCTCATAGAAATAGTAGGC
29127223 CAGATAAGTCAATCAGGTTCTATTTTACTAGAATGCTCATAGAAATAGTAGGC
1 CAGATAAGTCAATCAGGTTCTATTTTACTAGAATGCTCATAGAAATAGTAGGC
29127276 CAGATAAGTCAATCAGGT
1 CAGATAAGTCAATCAGGT
29127294 ATTTTCTTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 69 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (53 bp):
CAGATAAGTCAATCAGGTTCTATTTTACTAGAATGCTCATAGAAATAGTAGGC
Found at i:29130194 original size:37 final size:36
Alignment explanation
Indices: 29130123--29130208 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
29130113 AAAAAATTAA
*
29130123 AAATT-AATTCAAAAAAATAATTTTTTATTTAATTC
1 AAATTAAATTCAAAAAAATAATTTTTTATTCAATTC
**
29130158 AAATTAAATTCAAAAATTTTAATTTTTTATTCAATTC
1 AAATTAAATTCAAAAA-AATAATTTTTTATTCAATTC
*
29130195 AATTTAAATTCAAA
1 AAATTAAATTCAAA
29130209 TATTAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 5 0.11
36 10 0.22
37 30 0.67
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (36 bp):
AAATTAAATTCAAAAAAATAATTTTTTATTCAATTC
Found at i:29131400 original size:19 final size:18
Alignment explanation
Indices: 29131377--29131426 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
29131367 AAAATTAATA
29131377 AATAAATAAAAATTTGTAT
1 AATAAATAAAAATTTGT-T
* *
29131396 GATAAATAATAATTTGTT
1 AATAAATAAAAATTTGTT
29131414 AATAAAATAAAAA
1 AAT-AAATAAAAA
29131427 ATAACAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
AATAAATAAAAATTTGTT
Found at i:29132975 original size:21 final size:21
Alignment explanation
Indices: 29132931--29132972 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29132921 TCCAAAATTT
*
29132931 TTATATCAAAAGTTACAAAAA
1 TTATATCAAAAGTAACAAAAA
29132952 TTATATCAAAAGTAATCAAAA
1 TTATATCAAAAGTAA-CAAAA
29132973 TTACCAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (21 bp):
TTATATCAAAAGTAACAAAAA
Found at i:29132993 original size:21 final size:22
Alignment explanation
Indices: 29132969--29133013 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
29132959 AAAAGTAATC
*
29132969 AAAA-TTACCAAACTTAAAATA
1 AAAAGTTACCAAAATTAAAATA
* *
29132990 AAAAGTTATCAAAATTAAATTA
1 AAAAGTTACCAAAATTAAAATA
29133012 AA
1 AA
29133014 GATTGTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAGTTACCAAAATTAAAATA
Found at i:29133002 original size:22 final size:21
Alignment explanation
Indices: 29132969--29133027 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 21
29132959 AAAAGTAATC
*
29132969 AAAATTACCAAACTTAAAATA
1 AAAATTACCAAAATTAAAATA
* *
29132990 AAAAGTTATCAAAATTAAATTA
1 AAAA-TTACCAAAATTAAAATA
* **
29133012 AAGATTGTCAAAATTA
1 AAAATTACCAAAATTA
29133028 TATCAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAATTACCAAAATTAAAATA
Found at i:29133040 original size:12 final size:11
Alignment explanation
Indices: 29132931--29133070 Score: 50
Period size: 10 Copynumber: 13.4 Consensus size: 11
29132921 TCCAAAATTT
29132931 TTATATCAAAA
1 TTATATCAAAA
*
29132942 GT-TA-CAAAAA
1 TTATATC-AAAA
29132952 TTATATCAAAA
1 TTATATCAAAA
*
29132963 GTA-ATCAAAA
1 TTATATCAAAA
* *
29132973 -T-TACCAAAC
1 TTATATCAAAA
* *
29132982 TTAAAATAAAAA
1 TT-ATATCAAAA
*
29132994 GT-TATCAAAA
1 TTATATCAAAA
* *
29133004 TTAAATTAAAGA
1 TTATATCAAA-A
*
29133016 -T-TGTCAAAA
1 TTATATCAAAA
29133025 TTATATCAATAA
1 TTATATCAA-AA
29133037 TTAT-T-AAAA
1 TTATATCAAAA
* *
29133046 TTATTTTAAAA
1 TTATATCAAAA
*
29133057 TT-TACCAAAA
1 TTATATCAAAA
29133067 TTAT
1 TTAT
29133071 GTCGAATGTT
Statistics
Matches: 92, Mismatches: 22, Indels: 30
0.64 0.15 0.21
Matches are distributed among these distances:
9 14 0.15
10 37 0.40
11 28 0.30
12 13 0.14
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.34
Consensus pattern (11 bp):
TTATATCAAAA
Found at i:29133324 original size:10 final size:10
Alignment explanation
Indices: 29133284--29133333 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
29133274 ATCAAATTTT
29133284 ATTATATCAA
1 ATTATATCAA
*
29133294 A-TATTAACAA
1 ATTA-TATCAA
*
29133304 ATTAT-TAAA
1 ATTATATCAA
29133313 ATTATATCAA
1 ATTATATCAA
*
29133323 ATTTTATCAA
1 ATTATATCAA
29133333 A
1 A
29133334 ATTAAATTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 9 0.28
10 21 0.66
11 2 0.06
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTATATCAA
Found at i:29133452 original size:21 final size:20
Alignment explanation
Indices: 29133422--29133508 Score: 75
Period size: 21 Copynumber: 4.2 Consensus size: 20
29133412 TATCAAAATT
* *
29133422 ATTATATCAAATGTTATTATA
1 ATTATTTCAAA-GTTATTAAA
* **
29133443 ATTATTTCAAAGGTACCAAA
1 ATTATTTCAAAGTTATTAAA
* *
29133463 ATTAATTCAATGGTTATTAAA
1 ATTATTTCAA-AGTTATTAAA
*
29133484 ATTATTTCAAAGATTATTATA
1 ATTATTTCAAAG-TTATTAAA
29133505 ATTA
1 ATTA
29133509 AATTAAAAAC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 15 0.29
21 36 0.71
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (20 bp):
ATTATTTCAAAGTTATTAAA
Found at i:29143652 original size:27 final size:30
Alignment explanation
Indices: 29143587--29143662 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
29143577 CAAACAAGAG
* *
29143587 ATTAAGAATTTATTTAAGTGTAAATTAAAA
1 ATTAAAAATTTATTTAAATGTAAATTAAAA
29143617 ATTAAAAATTTATTTAAATGT-AA-T-AAA
1 ATTAAAAATTTATTTAAATGTAAATTAAAA
*
29143644 A-TATAAAATTTATCTAAAT
1 ATTA-AAAATTTATTTAAAT
29143663 AACTCGATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 2 0.05
27 18 0.43
28 1 0.02
29 2 0.05
30 19 0.45
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (30 bp):
ATTAAAAATTTATTTAAATGTAAATTAAAA
Found at i:29145124 original size:23 final size:24
Alignment explanation
Indices: 29145093--29145139 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
29145083 AAGGCGGTTT
29145093 CAGAGAAT-GTCTTGATTGAGGAAG
1 CAGAGAATGGT-TTGATTGAGGAAG
*
29145117 CAGA-AATGGTTTGTTTGAGGAAG
1 CAGAGAATGGTTTGATTGAGGAAG
29145140 GTGGTTATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.32, C:0.06, G:0.34, T:0.28
Consensus pattern (24 bp):
CAGAGAATGGTTTGATTGAGGAAG
Found at i:29157720 original size:111 final size:111
Alignment explanation
Indices: 29157502--29157723 Score: 374
Period size: 112 Copynumber: 2.0 Consensus size: 111
29157492 GCACTAAATA
*
29157502 AGAGCGTTGACAAAGTATCCTTGTGGGCCTACAATGAAAGGAATTGTGTATAGCTAACGTTAGTC
1 AGAGCGTTGACAAAGTATCCTTGTGGGCCTACAATGAAAGGAATTGAGTATAGCTAACGTTAGTC
*
29157567 TTTTAAGTGTTATTATTCTCAAGCCTGTTTTAGCCACTGGCAATGC
66 TTTTAAGTGTTATTATTCTCAAGCCTGTTTTAGCCACCGGCAATGC
* * *
29157613 AGAGCTGTTGACAAAGTATCCTTGTGGGCCTACAATGAAAGGGATTGAGTATAGCTAATGTTTGT
1 AGAGC-GTTGACAAAGTATCCTTGTGGGCCTACAATGAAAGGAATTGAGTATAGCTAACGTTAGT
*
29157678 C-TTTAAGTGTTATTATTCTTAAGCCTGTTTTAGCCACCGGCAATGC
65 CTTTTAAGTGTTATTATTCTCAAGCCTGTTTTAGCCACCGGCAATGC
29157724 TTAAGTTGCA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
111 48 0.46
112 56 0.54
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (111 bp):
AGAGCGTTGACAAAGTATCCTTGTGGGCCTACAATGAAAGGAATTGAGTATAGCTAACGTTAGTC
TTTTAAGTGTTATTATTCTCAAGCCTGTTTTAGCCACCGGCAATGC
Found at i:29164161 original size:17 final size:16
Alignment explanation
Indices: 29164137--29164190 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
29164127 GCTTCGATGT
29164137 ATTTGATTAAAACTGG
1 ATTTGATTAAAACTGG
* *
29164153 ATGTTGATTAAATAATGT
1 AT-TTGATTAAA-ACTGG
29164171 ATTTGATTAAAACTGG
1 ATTTGATTAAAACTGG
29164187 ATTT
1 ATTT
29164191 CAAAGAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.28
17 18 0.56
18 5 0.16
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.43
Consensus pattern (16 bp):
ATTTGATTAAAACTGG
Found at i:29183299 original size:35 final size:36
Alignment explanation
Indices: 29183232--29183304 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
29183222 GGATTGAATA
29183232 AGGAGCTGCGCGGTAGTTACAAAATGAGAATTTGAG
1 AGGAGCTGCGCGGTAGTTACAAAATGAGAATTTGAG
*
29183268 AGGAGCTGGGCGGTAGTTAC-AAATGAGAATTTGAG
1 AGGAGCTGCGCGGTAGTTACAAAATGAGAATTTGAG
29183303 AG
1 AG
29183305 AATATAGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 17 0.47
36 19 0.53
ACGTcount: A:0.33, C:0.10, G:0.36, T:0.22
Consensus pattern (36 bp):
AGGAGCTGCGCGGTAGTTACAAAATGAGAATTTGAG
Found at i:29193524 original size:32 final size:32
Alignment explanation
Indices: 29193483--29193555 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
29193473 CCCGATCTTG
* *
29193483 AACAGAACCCATTCGACGTTTGCAGTAGCTTC
1 AACAGAACCCATTCGACGTTTGCAGCAGCTTA
*
29193515 AACAGAACCCATTCGACTTTTGCAGCAGCTTA
1 AACAGAACCCATTCGACGTTTGCAGCAGCTTA
29193547 AACAGAACC
1 AACAGAACC
29193556 TGAACCCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (32 bp):
AACAGAACCCATTCGACGTTTGCAGCAGCTTA
Found at i:29193575 original size:38 final size:36
Alignment explanation
Indices: 29193487--29193596 Score: 120
Period size: 38 Copynumber: 3.1 Consensus size: 36
29193477 ATCTTGAACA
* *
29193487 GAACCCATTCGACGTTTGCAGTAGCTT--C-AA-CA
1 GAACCCATTCGACGTTTGCAGCAGCTTAACAAACCT
*
29193519 GAACCCATTCGACTTTTGCAGCAGCTTAAACAGAACCT
1 GAACCCATTCGACGTTTGCAGCAGCTT-AACA-AACCT
*
29193557 GAACCCATTCGACGTTTGCAGCAACTTCAACAAAACCT
1 GAACCCATTCGACGTTTGCAGCAGCTT-AAC-AAACCT
29193595 GA
1 GA
29193597 TCTTGAACAG
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
32 25 0.38
35 1 0.02
37 2 0.03
38 36 0.55
39 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (36 bp):
GAACCCATTCGACGTTTGCAGCAGCTTAACAAACCT
Found at i:29193681 original size:32 final size:32
Alignment explanation
Indices: 29193640--29193707 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
29193630 TGCTCGTTCC
29193640 ACCCATTCGACGTTTGCAGCAGCTTCAACAGA
1 ACCCATTCGACGTTTGCAGCAGCTTCAACAGA
* *
29193672 ACCCATTCGACGTTTGCAGTAGCTTTAACAGA
1 ACCCATTCGACGTTTGCAGCAGCTTCAACAGA
29193704 ACCC
1 ACCC
29193708 GATCTTGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (32 bp):
ACCCATTCGACGTTTGCAGCAGCTTCAACAGA
Found at i:29193730 original size:113 final size:116
Alignment explanation
Indices: 29193521--29193771 Score: 391
Period size: 113 Copynumber: 2.2 Consensus size: 116
29193511 CTTCAACAGA
* *
29193521 ACCCATTCGACTTTTGCAGCAGCTTAAACAGAACCTGAACCCATTCGACGTTTGCAGCAACTTCA
1 ACCCATTCGACGTTTGCAGCAGCTT--ACA-AACCAGAACCCATTCGACGTTTGCAGCAACTTCA
*
29193586 ACAAAACCTGATCTTGAACAGAACCCGATCCCTCAATGAAGCCCTGCTCGTTCC
63 ACAAAACCCGATCTTGAACAGAACCCGATCCCTCAATGAAGCCCTGCTCGTTCC
* * *
29193640 ACCCATTCGACGTTTGCAGCAGCTT-C-AA-CAGAACCCATTCGACGTTTGCAGTAGCTTTAACA
1 ACCCATTCGACGTTTGCAGCAGCTTACAAACCAGAACCCATTCGACGTTTGCAGCAACTTCAACA
*
29193702 GAACCCGATCTTGAACAGAACCCGATCCCTCAATGAAGCCCTGCTCGTTCC
66 AAACCCGATCTTGAACAGAACCCGATCCCTCAATGAAGCCCTGCTCGTTCC
29193753 ACCCATTCGACGTTTGCAG
1 ACCCATTCGACGTTTGCAG
29193772 TAGCACCCAT
Statistics
Matches: 125, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
113 98 0.78
114 2 0.02
116 1 0.01
119 24 0.19
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (116 bp):
ACCCATTCGACGTTTGCAGCAGCTTACAAACCAGAACCCATTCGACGTTTGCAGCAACTTCAACA
AAACCCGATCTTGAACAGAACCCGATCCCTCAATGAAGCCCTGCTCGTTCC
Found at i:29193852 original size:86 final size:87
Alignment explanation
Indices: 29193715--29193901 Score: 304
Period size: 86 Copynumber: 2.2 Consensus size: 87
29193705 CCCGATCTTG
*
29193715 AACAGAACCCGATCCCTCAATGAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGCACCC
1 AACAGAACCCGATCCCTCAAAGAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGCACCC
29193780 ATTCGACGTTTGCAGCAGCTTC
66 ATTCGACGTTTGCAGCAGCTTC
* *
29193802 AACAGAACTCGATCCCTCAAAGAAG-CCTGCTCGTTTCACCCATTCGACGTTTGCAGTAGCACCC
1 AACAGAACCCGATCCCTCAAAGAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGCACCC
* *
29193866 ATTCGACGTTTGCAGTAGCTTG
66 ATTCGACGTTTGCAGCAGCTTC
* *
29193888 TACACAACCCGATC
1 AACAGAACCCGATC
29193902 TTGAACAGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 69 0.75
87 23 0.25
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.24
Consensus pattern (87 bp):
AACAGAACCCGATCCCTCAAAGAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGCACCC
ATTCGACGTTTGCAGCAGCTTC
Found at i:29193868 original size:23 final size:23
Alignment explanation
Indices: 29193838--29193884 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
29193828 CTGCTCGTTT
29193838 CACCCATTCGACGTTTGCAGTAG
1 CACCCATTCGACGTTTGCAGTAG
29193861 CACCCATTCGACGTTTGCAGTAG
1 CACCCATTCGACGTTTGCAGTAG
29193884 C
1 C
29193885 TTGTACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (23 bp):
CACCCATTCGACGTTTGCAGTAG
Found at i:29194136 original size:25 final size:25
Alignment explanation
Indices: 29194108--29194161 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
29194098 GTTTAAATAA
* *
29194108 GAATGCCTTAATTAAATACCTTTAT
1 GAATGCCTAAATTAAATACCCTTAT
29194133 GAATGCCTAAATTAAATACCCTTAT
1 GAATGCCTAAATTAAATACCCTTAT
29194158 GAAT
1 GAAT
29194162 ATTGTGGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (25 bp):
GAATGCCTAAATTAAATACCCTTAT
Found at i:29197669 original size:12 final size:12
Alignment explanation
Indices: 29197648--29197685 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
29197638 TGTTGGTTTG
29197648 TTGT-AACTTAT
1 TTGTGAACTTAT
29197659 TTGTGAACTTAT
1 TTGTGAACTTAT
29197671 TTGTGAACTTAT
1 TTGTGAACTTAT
29197683 TTG
1 TTG
29197686 CTTGGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (12 bp):
TTGTGAACTTAT
Found at i:29197832 original size:3 final size:3
Alignment explanation
Indices: 29197826--29197884 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
29197816 ATTATTATTA
* * * *
29197826 TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTA TTG TTG TTA TTA TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
29197874 TTG TTG TTG TT
1 TTG TTG TTG TT
29197885 ATCTTGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.07, C:0.00, G:0.25, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:29197838 original size:9 final size:9
Alignment explanation
Indices: 29197810--29197886 Score: 91
Period size: 9 Copynumber: 8.6 Consensus size: 9
29197800 TGTTGTGTAA
*
29197810 GTTATTATT
1 GTTATTGTT
* *
29197819 ATTATTATT
1 GTTATTGTT
*
29197828 GTTGTTGTT
1 GTTATTGTT
*
29197837 GTTGTTGTT
1 GTTATTGTT
29197846 GTTATTGTT
1 GTTATTGTT
29197855 GTTATTGTT
1 GTTATTGTT
*
29197864 GTTATTATT
1 GTTATTGTT
*
29197873 GTTGTTGTT
1 GTTATTGTT
29197882 GTTAT
1 GTTAT
29197887 CTTGAAAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.13, C:0.00, G:0.21, T:0.66
Consensus pattern (9 bp):
GTTATTGTT
Found at i:29198015 original size:23 final size:24
Alignment explanation
Indices: 29197959--29198017 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
29197949 CTCGAGCTCG
*
29197959 AATAATCGA-ATTTTTTTTAGTAT
1 AATAATCGAGCTTTTTTTTAGTAT
*
29197982 AAAAATCGAGCTTTTTTTTA-TAT
1 AATAATCGAGCTTTTTTTTAGTAT
*
29198005 ATTAATCGAGCTT
1 AATAATCGAGCTT
29198018 AATAGAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.47
Consensus pattern (24 bp):
AATAATCGAGCTTTTTTTTAGTAT
Found at i:29202542 original size:3 final size:3
Alignment explanation
Indices: 29202531--29202577 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
29202521 CTCATGATGA
* * * *
29202531 TCT TGT TCT TCT TCT TCT TCT TCG TCC TCT TCT TCG TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
29202578 AATAGCAAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.34, G:0.06, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:29202551 original size:12 final size:12
Alignment explanation
Indices: 29202531--29202577 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
29202521 CTCATGATGA
* *
29202531 TCTTGTTCTTCT
1 TCTTCTTCTTCG
29202543 TCTTCTTCTTCG
1 TCTTCTTCTTCG
*
29202555 TCCTCTTCTTCG
1 TCTTCTTCTTCG
29202567 TCTTCTTCTTC
1 TCTTCTTCTTC
29202578 AATAGCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.34, G:0.06, T:0.60
Consensus pattern (12 bp):
TCTTCTTCTTCG
Found at i:29207776 original size:63 final size:63
Alignment explanation
Indices: 29207677--29207796 Score: 222
Period size: 63 Copynumber: 1.9 Consensus size: 63
29207667 AAACTATTAG
*
29207677 TTCACAACAATAGAATATCGATATTAAGATATTTGTATAATAACTCTTAAAATTTTGTTTTCC
1 TTCACAACAATAGAATATCAATATTAAGATATTTGTATAATAACTCTTAAAATTTTGTTTTCC
*
29207740 TTCACAACAATTGAATATCAATATTAAGATATTTGTATAATAACTCTTAAAATTTTG
1 TTCACAACAATAGAATATCAATATTAAGATATTTGTATAATAACTCTTAAAATTTTG
29207797 CAAAGTAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (63 bp):
TTCACAACAATAGAATATCAATATTAAGATATTTGTATAATAACTCTTAAAATTTTGTTTTCC
Found at i:29211453 original size:2 final size:2
Alignment explanation
Indices: 29211446--29211471 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29211436 AGTACACCAT
29211446 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
29211472 AAGGATCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29211767 original size:22 final size:22
Alignment explanation
Indices: 29211733--29211774 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29211723 TATCAAAATT
*
29211733 ATAAATATGTTATTTTTTTAAA
1 ATAAAAATGTTATTTTTTTAAA
*
29211755 ATAAAAATTTTATTTTTTTA
1 ATAAAAATGTTATTTTTTTA
29211775 CTAACTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATAAAAATGTTATTTTTTTAAA
Found at i:29212181 original size:22 final size:22
Alignment explanation
Indices: 29212156--29212199 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29212146 AGTTTTTTCA
*
29212156 TTTATTTATCATGA-TAGATTTT
1 TTTATTTAGCAT-ATTAGATTTT
29212178 TTTATTTAGCATATTAGATTTT
1 TTTATTTAGCATATTAGATTTT
29212200 GACAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (22 bp):
TTTATTTAGCATATTAGATTTT
Found at i:29214209 original size:42 final size:42
Alignment explanation
Indices: 29214148--29214230 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
29214138 TCGTGTTTCT
** * *
29214148 TTTGGAGTCAGAGCGGAGATTGTAGAGATAGGTAAATTGTAC
1 TTTGGAGTCAGAGAAGAGATAGTAGAGATAGATAAATTGTAC
29214190 TTTGGAGTCAGAGAAGAGATAGTAGAGATAGATAAATTGTA
1 TTTGGAGTCAGAGAAGAGATAGTAGAGATAGATAAATTGTA
29214231 TTTTCTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.28
Consensus pattern (42 bp):
TTTGGAGTCAGAGAAGAGATAGTAGAGATAGATAAATTGTAC
Found at i:29219054 original size:8 final size:8
Alignment explanation
Indices: 29219043--29219078 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
29219033 CTTTGTCAGT
29219043 TTGTCCTC
1 TTGTCCTC
29219051 TTGTCCTC
1 TTGTCCTC
*
29219059 TTGTTCTC
1 TTGTCCTC
*
29219067 TAGTCCTC
1 TTGTCCTC
29219075 TTGT
1 TTGT
29219079 AGATCTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.03, C:0.31, G:0.14, T:0.53
Consensus pattern (8 bp):
TTGTCCTC
Found at i:29219613 original size:62 final size:63
Alignment explanation
Indices: 29219515--29219640 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 63
29219505 GTATTATAAT
29219515 AATAATAAAAAAAGGATCAACTTATGTAGTATAAAATTAAAAAAATTTTACACATTTTTTTAA
1 AATAATAAAAAAAGGATCAACTTATGTAGTATAAAATTAAAAAAATTTTACACATTTTTTTAA
29219578 AATAA-AAAAAAAGGATCAACTTATGTAGTATAAAATTAAAAAAATTTTACACATTTTTTTAA
1 AATAATAAAAAAAGGATCAACTTATGTAGTATAAAATTAAAAAAATTTTACACATTTTTTTAA
29219640 A
1 A
29219641 CATTGATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 58 0.92
63 5 0.08
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (63 bp):
AATAATAAAAAAAGGATCAACTTATGTAGTATAAAATTAAAAAAATTTTACACATTTTTTTAA
Found at i:29222704 original size:30 final size:30
Alignment explanation
Indices: 29222669--29222778 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 30
29222659 TCAACATTCC
*
29222669 AAACCATAAAATTGAAACCCTAAACCCT-A
1 AAACCATAAAATCGAAACCCTAAACCCTCA
* *
29222698 CAAACCATAAAATCAAAATCCTAAACCCTCA
1 -AAACCATAAAATCGAAACCCTAAACCCTCA
* * *
29222729 AAACCCTAAAATCGAAACCTTAAACACTCA
1 AAACCATAAAATCGAAACCCTAAACCCTCA
* *
29222759 AAACCTTAAAAT-TAAACCCT
1 AAACCATAAAATCGAAACCCT
29222779 TCAAAAGCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 6 0.09
30 61 0.90
31 1 0.01
ACGTcount: A:0.51, C:0.29, G:0.02, T:0.18
Consensus pattern (30 bp):
AAACCATAAAATCGAAACCCTAAACCCTCA
Found at i:29222724 original size:51 final size:51
Alignment explanation
Indices: 29222624--29222724 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
29222614 CTTCAAATCC
* * * * *
29222624 TAAAATCGAAATCCTAAATCCTTCAAACCCTAAAATCAACATTCCAAACCA
1 TAAAATCGAAACCCTAAACCCTACAAACCATAAAATCAACAATCCAAACCA
*
29222675 TAAAATTGAAACCCTAAACCCTACAAACCATAAAATCAA-AATCCTAAACC
1 TAAAATCGAAACCCTAAACCCTACAAACCATAAAATCAACAATCC-AAACC
29222725 CTCAAAACCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 4 0.09
51 39 0.91
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.20
Consensus pattern (51 bp):
TAAAATCGAAACCCTAAACCCTACAAACCATAAAATCAACAATCCAAACCA
Found at i:29222764 original size:16 final size:16
Alignment explanation
Indices: 29222710--29222768 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
29222700 AACCATAAAA
*
29222710 TCAAAATCC-TAAACCC
1 TCAAAA-CCTTAAACAC
*
29222726 TCAAAACCCTAAA-A-
1 TCAAAACCTTAAACAC
*
29222740 TCGAAACCTTAAACAC
1 TCAAAACCTTAAACAC
29222756 TCAAAACCTTAAA
1 TCAAAACCTTAAA
29222769 ATTAAACCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 11 0.31
15 3 0.08
16 22 0.61
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.19
Consensus pattern (16 bp):
TCAAAACCTTAAACAC
Found at i:29222773 original size:22 final size:23
Alignment explanation
Indices: 29222748--29222797 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
29222738 AATCGAAACC
29222748 TTAAACAC-TCAAAACCTTAAAA
1 TTAAACACTTCAAAACCTTAAAA
* *
29222770 TTAAACCCTTCAAAAGCTTAAAA
1 TTAAACACTTCAAAACCTTAAAA
29222793 TTAAA
1 TTAAA
29222798 ATCCTAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.26
Consensus pattern (23 bp):
TTAAACACTTCAAAACCTTAAAA
Found at i:29222875 original size:21 final size:21
Alignment explanation
Indices: 29222851--29222910 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
29222841 TCAAAATCCT
29222851 AAACCCCAAACCTTAAAAATA
1 AAACCCCAAACCTTAAAAATA
* *
29222872 AAACCTCAAATCC-TAAAATTA
1 AAACCCCAAA-CCTTAAAAATA
*
29222893 AAACCCTAAAACCTTAAA
1 AAACCC-CAAACCTTAAA
29222911 CCCTCTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 23 0.72
22 9 0.28
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCCAAACCTTAAAAATA
Found at i:29222954 original size:21 final size:22
Alignment explanation
Indices: 29222930--29222976 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
29222920 CCTTAAAATC
* *
29222930 AAAACCCCAAACCC-AAACCTT
1 AAAACCCAAAACCCTAAACCCT
*
29222951 AAAA-TCAAAACCCTAAACCCT
1 AAAACCCAAAACCCTAAACCCT
29222972 AAAAC
1 AAAAC
29222977 TAAAACCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.53, C:0.36, G:0.00, T:0.11
Consensus pattern (22 bp):
AAAACCCAAAACCCTAAACCCT
Found at i:29222961 original size:14 final size:14
Alignment explanation
Indices: 29222699--29222967 Score: 94
Period size: 14 Copynumber: 18.7 Consensus size: 14
29222689 TAAACCCTAC
*
29222699 AAACCATAAAATCA
1 AAACCTTAAAATCA
*
29222713 AAATCC-TAAACCCTCA
1 AAA-CCTTAAA--ATCA
* *
29222729 AAACCCTAAAATCG
1 AAACCTTAAAATCA
29222743 AAACCTTAAACACTCA
1 AAACCTTAAA-A-TCA
*
29222759 AAACCTTAAAATTA
1 AAACCTTAAAATCA
* *
29222773 AACCCTTCAAAAGCTTA
1 AAACCTT-AAAA--TCA
29222790 AAA--TTAAAATCCTA
1 AAACCTTAAAAT-C-A
29222804 AAA-CTCTAAAATCA
1 AAACCT-TAAAATCA
* *
29222818 AAACC-T-AAACCC
1 AAACCTTAAAATCA
29222830 AAACCTTAAAATCA
1 AAACCTTAAAATCA
** *
29222844 AAATCC-TAAACCCC
1 AAA-CCTTAAAATCA
29222858 AAACCTTAAAAAT-A
1 AAACCTT-AAAATCA
*
29222872 AAACC-TCAAATCCTA
1 AAACCTTAAAAT-C-A
*
29222887 AAA--TTAAAACCCTA
1 AAACCTTAAAA-TC-A
* *
29222901 AAACCTTAAACCCTCT
1 AAACCTTAAA--ATCA
29222917 AAACCTTAAAATCA
1 AAACCTTAAAATCA
** * *
29222931 AAACC-CCAAACCC
1 AAACCTTAAAATCA
29222944 AAACCTTAAAATCA
1 AAACCTTAAAATCA
*
29222958 AAACCCTAAA
1 AAACCTTAAA
29222968 CCCTAAAACT
Statistics
Matches: 190, Mismatches: 36, Indels: 58
0.67 0.13 0.20
Matches are distributed among these distances:
12 14 0.07
13 14 0.07
14 89 0.47
15 24 0.13
16 43 0.23
17 6 0.03
ACGTcount: A:0.52, C:0.28, G:0.01, T:0.19
Consensus pattern (14 bp):
AAACCTTAAAATCA
Found at i:29222981 original size:21 final size:20
Alignment explanation
Indices: 29222938--29223017 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 20
29222928 TCAAAACCCC
*
29222938 AAACCC-AAACCTTAAAATCA
1 AAACCCTAAACCCTAAAAT-A
29222958 AAACCCTAAACCCTAAAACTA
1 AAACCCTAAACCCTAAAA-TA
* *
29222979 AAA-CCTCAAATCCTAAAATTG
1 AAACCCT-AAACCCTAAAA-TA
29223000 AAACCCTATAACCCTAAA
1 AAACCCTA-AACCCTAAA
29223018 CCTTCTAAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 9 0.18
21 29 0.58
22 12 0.24
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.17
Consensus pattern (20 bp):
AAACCCTAAACCCTAAAATA
Found at i:29222981 original size:27 final size:28
Alignment explanation
Indices: 29222800--29222974 Score: 173
Period size: 27 Copynumber: 6.2 Consensus size: 28
29222790 AAATTAAAAT
*
29222800 CCTAAAACTCTAAAATCAAAA-CCTAAAC
1 CCTAAACCT-TAAAATCAAAACCCTAAAC
*
29222828 CC-AAACCTTAAAATCAAAATCCTAAAC
1 CCTAAACCTTAAAATCAAAACCCTAAAC
* *
29222855 CCCAAACCTTAAAAAT-AAAA-CCTCAAAT
1 CCTAAACCTT-AAAATCAAAACCCT-AAAC
* * *
29222883 CCTAAA-ATTAAAACCCTAAAACCTTAAACC
1 CCTAAACCTTAAAA-TC-AAAACCCTAAA-C
*
29222913 CTCTAAACCTTAAAATCAAAACCCCAAAC
1 C-CTAAACCTTAAAATCAAAACCCTAAAC
29222942 CC-AAACCTTAAAATCAAAACCCTAAAC
1 CCTAAACCTTAAAATCAAAACCCTAAAC
29222969 CCTAAA
1 CCTAAA
29222975 ACTAAAACCT
Statistics
Matches: 123, Mismatches: 12, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
26 15 0.12
27 45 0.37
28 25 0.20
29 14 0.11
30 12 0.10
31 6 0.05
32 6 0.05
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (28 bp):
CCTAAACCTTAAAATCAAAACCCTAAAC
Found at i:29223049 original size:107 final size:109
Alignment explanation
Indices: 29222804--29223050 Score: 329
Period size: 107 Copynumber: 2.2 Consensus size: 109
29222794 TAAAATCCTA
* *
29222804 AAACTCTAAAATCAAAACCTAAACCCAAACCTTAAAATCAAAATCCTAAACCCCAAACCTTAAAA
1 AAACCCTAAAATCAAAACCTAAACCCAAACCTTAAAATCAAAACCCTAAA--CC--ACCTTAAAA
*
29222869 ATAAAACCTCAAATCCTAAAATTAAAACCCTAAAACCTTAAACCCTCT
62 ATAAAACCTCAAATCCTAAAATTAAAACCCTAAAACCCTAAACCCTCT
* * *
29222917 AAACCTTAAAATCAAAACCCCAAACCCAAACCTTAAAATCAAAACCCTAAA-C-CC-TAAAACTA
1 AAACCCTAAAATCAAAA-CCTAAACCCAAACCTTAAAATCAAAACCCTAAACCACCTTAAAAATA
* * *
29222979 AAACCTCAAATCCTAAAATTGAAACCCTATAACCCTAAACCTTCT
65 AAACCTCAAATCCTAAAATTAAAACCCTAAAACCCTAAACCCTCT
*
29223024 AAACCCTGAAATCAAAACCTTAAACCC
1 AAACCCTAAAATCAAAACC-TAAACCC
29223051 TCTAAATCCT
Statistics
Matches: 120, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
106 2 0.02
107 69 0.57
108 2 0.02
111 1 0.01
113 15 0.12
114 31 0.26
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.19
Consensus pattern (109 bp):
AAACCCTAAAATCAAAACCTAAACCCAAACCTTAAAATCAAAACCCTAAACCACCTTAAAAATAA
AACCTCAAATCCTAAAATTAAAACCCTAAAACCCTAAACCCTCT
Found at i:29234961 original size:35 final size:36
Alignment explanation
Indices: 29234879--29234963 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
29234869 CTGGTCACAT
* * * * * *
29234879 TTATTCTTTAACTCATAGTTTAATCTTAGTCATTTT
1 TTATTTTTTGACTCATAGTTCAATCTCAATCATTTA
*
29234915 TTATTTTTTGACTCATTGTTCAATCTCAATCA-TTA
1 TTATTTTTTGACTCATAGTTCAATCTCAATCATTTA
29234950 TTATTTTTTGACTC
1 TTATTTTTTGACTC
29234964 GCGATATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 16 0.38
36 26 0.62
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (36 bp):
TTATTTTTTGACTCATAGTTCAATCTCAATCATTTA
Found at i:29235149 original size:70 final size:70
Alignment explanation
Indices: 29235036--29235169 Score: 162
Period size: 70 Copynumber: 1.9 Consensus size: 70
29235026 CTCTAACTCG
* * * *
29235036 TAGTTCAATCCTGGTTGTCATTATACTCTGACTCACGATTTAATCTTGGTTATTTTTATTTTTTG
1 TAGTTCAATCCTAGTTGTCATTATACTCTGACTCACGATTTAATCATAGTCATTTTTATTTTTTG
29235101 ATTCA
66 ATTCA
** * * * *
29235106 TAGTTCAATCCTAGTTGTTGTTATTCTTTGACTCATGGA-TTAATCATAGTCGTTTTTATTTTTT
1 TAGTTCAATCCTAGTTGTCATTATACTCTGACTCA-CGATTTAATCATAGTCATTTTTATTTTTT
29235170 TGACTCGCGG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
70 51 0.96
71 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.13, T:0.51
Consensus pattern (70 bp):
TAGTTCAATCCTAGTTGTCATTATACTCTGACTCACGATTTAATCATAGTCATTTTTATTTTTTG
ATTCA
Found at i:29235165 original size:35 final size:35
Alignment explanation
Indices: 29234842--29235175 Score: 106
Period size: 35 Copynumber: 9.5 Consensus size: 35
29234832 GTACCTAATC
* * * * **
29234842 TTTTATTTTTTGACTCACAGCTCAATCCTGGTCAC
1 TTTTATTTTTTGACTCATAGTTCAATCATAGTCGT
* * * * * *
29234877 ATTTATTCTTTAACTCATAGTTTAATCTTAGTCATT
1 TTTTATTTTTTGACTCATAGTTCAATCATAGTC-GT
* * *
29234913 TTTTATTTTTTGACTCATTGTTCAATC-TCAATCAT
1 TTTTATTTTTTGACTCATAGTTCAATCAT-AGTCGT
* ** *
29234948 TATTATTTTTTGACTCGCGATA--T-AATCCCAGTTGT
1 TTTTATTTTTTGACT--C-ATAGTTCAATCATAGTCGT
* * * * *
29234983 TGTTATTCTTTGACTTATAATTCAAT-ATCGATCGT
1 TTTTATTTTTTGACTCATAGTTCAATCATAG-TCGT
* * * * * *
29235018 TTTTATTTCTCTAACTCGTAGTTCAATCCTGGTTGT
1 TTTTATTT-TTTGACTCATAGTTCAATCATAGTCGT
** ** * * * * * **
29235054 CATTATACTCTGACTCA-CGATTTAATCTTGGTTAT
1 TTTTATTTTTTGACTCATAG-TTCAATCATAGTCGT
* * *
29235089 TTTTATTTTTTGATTCATAGTTCAATCCTAGTTGT
1 TTTTATTTTTTGACTCATAGTTCAATCATAGTCGT
* * *
29235124 TGTTATTCTTTGACTCATGGATT-AATCATAGTCGT
1 TTTTATTTTTTGACTCATAG-TTCAATCATAGTCGT
29235159 TTTTATTTTTTTGACTC
1 TTTTA-TTTTTTGACTC
29235176 GCGGTTCAAT
Statistics
Matches: 214, Mismatches: 69, Indels: 31
0.68 0.22 0.10
Matches are distributed among these distances:
32 3 0.01
34 3 0.01
35 144 0.67
36 59 0.28
37 3 0.01
38 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (35 bp):
TTTTATTTTTTGACTCATAGTTCAATCATAGTCGT
Found at i:29235456 original size:32 final size:33
Alignment explanation
Indices: 29235405--29235494 Score: 85
Period size: 35 Copynumber: 2.7 Consensus size: 33
29235395 TGGTCATTTT
* *
29235405 TTTTTCTGACTTACGGTTTAATC-ATA-ATTGTTA
1 TTTTT-TGACTCACAGTTTAATCTA-ACATTGTTA
29235438 TTTTTTGACTCACAGTTTAATCTAAGCCATTGTTA
1 TTTTTTGACTCACAGTTTAATCTAA--CATTGTTA
* * *
29235473 TTCTCTAACTCACAGTTTAATC
1 TTTTTTGACTCACAGTTTAATC
29235495 CCAGTCGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
32 16 0.33
33 6 0.12
35 26 0.54
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.47
Consensus pattern (33 bp):
TTTTTTGACTCACAGTTTAATCTAACATTGTTA
Found at i:29235470 original size:35 final size:35
Alignment explanation
Indices: 29235431--29235518 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
29235421 TTTAATCATA
*
29235431 ATTGTTATTTTTTGACTCACAGTTTAATCTAAGCC
1 ATTGTTATTTTTTGACTCACAGTTTAATCCAAGCC
* * * * *
29235466 ATTGTTATTCTCTAACTCACAGTTTAATCCCAGTC
1 ATTGTTATTTTTTGACTCACAGTTTAATCCAAGCC
* *
29235501 GTTTTTATTTTTTGACTC
1 ATTGTTATTTTTTGACTC
29235519 GCGATTCAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (35 bp):
ATTGTTATTTTTTGACTCACAGTTTAATCCAAGCC
Found at i:29235613 original size:35 final size:35
Alignment explanation
Indices: 29235574--29235651 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
29235564 TCAGTTATCA
* **
29235574 TTATTCTCTGACTTGCAATTTAATCTTGGTTGTTT
1 TTATTCTCTGACTCGCAATTTAATCACGGTTGTTT
* *
29235609 TTATTTTCTGACTCGCAGTTTAATCACGGTTGTTT
1 TTATTCTCTGACTCGCAATTTAATCACGGTTGTTT
29235644 TATATTCT
1 T-TATTCT
29235652 GTCATAGTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 31 0.86
36 5 0.14
ACGTcount: A:0.18, C:0.15, G:0.14, T:0.53
Consensus pattern (35 bp):
TTATTCTCTGACTCGCAATTTAATCACGGTTGTTT
Found at i:29235645 original size:104 final size:102
Alignment explanation
Indices: 29235501--29235723 Score: 238
Period size: 102 Copynumber: 2.2 Consensus size: 102
29235491 AATCCCAGTC
* * * * *
29235501 GTTTTTATTTTTTGACTCGCGATTCAATCCCGATCTTTTTATTTTCTGACTTATGGTTCAATCTC
1 GTTTTTATTTTTTGACTCGCGATTCAATCACGATCTTTTTATATTCTG--TCATAGTTCAAAC-C
* * *
29235566 AG-TTATCATTATTCTCTGACTTGCAATTTAATCTT-GGTT
63 AGATTATCATTATTCTCTGACTCGCAATTTAAT-TTCGATA
* * * *
29235605 GTTTTTATTTTCTGACTCGC-AGTTTAATCACGGT-TGTTTTATATTCTGTCATAGTTCAAACCT
1 GTTTTTATTTTTTGACTCGCGA-TTCAATCACGATCT-TTTTATATTCTGTCATAGTTCAAACCA
* *
29235668 GATTGTCATTATTCTCTGACTCGCGATTTAATTTCGATA
64 GATTATCATTATTCTCTGACTCGCAATTTAATTTCGATA
29235707 GTTTTTATTTTTTGACT
1 GTTTTTATTTTTTGACT
29235724 TTTGGTTCAA
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
101 4 0.04
102 55 0.55
103 2 0.02
104 39 0.39
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (102 bp):
GTTTTTATTTTTTGACTCGCGATTCAATCACGATCTTTTTATATTCTGTCATAGTTCAAACCAGA
TTATCATTATTCTCTGACTCGCAATTTAATTTCGATA
Found at i:29235761 original size:20 final size:20
Alignment explanation
Indices: 29235732--29235771 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29235722 CTTTTGGTTC
*
29235732 AATCTTGATCGTCTTTATTT
1 AATCTCGATCGTCTTTATTT
29235752 AATCTCGATCGTCTTTATTT
1 AATCTCGATCGTCTTTATTT
29235772 TTTGACTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (20 bp):
AATCTCGATCGTCTTTATTT
Found at i:29237378 original size:3 final size:3
Alignment explanation
Indices: 29237370--29237427 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
29237360 TTGTTATTTT
29237370 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29237418 ATA ATA ATA A
1 ATA ATA ATA A
29237428 CGATGATGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29237974 original size:7 final size:7
Alignment explanation
Indices: 29237950--29237989 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
29237940 TTTTAAATTG
29237950 AAACCCT
1 AAACCCT
*
29237957 AAAACCT
1 AAACCCT
29237964 AAACCCT
1 AAACCCT
29237971 AAACCCTTT
1 AAACCC--T
29237980 AAACCCT
1 AAACCCT
29237987 AAA
1 AAA
29237990 ATCAAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 22 0.76
9 7 0.24
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:29238043 original size:28 final size:27
Alignment explanation
Indices: 29237978--29238051 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
29237968 CCTAAACCCT
*
29237978 TTAAACCCTAAAATCAAAATTCTAAAC
1 TTAAACCTTAAAATCAAAATTCTAAAC
* *
29238005 TCCAAATCTTAAAATCAAAA-TCATAAACC
1 T-TAAACCTTAAAATCAAAATTC-TAAA-C
29238034 TTAAACCTTAAAA-CAAAA
1 TTAAACCTTAAAATCAAAA
29238052 ACCCTAAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 8 0.21
28 29 0.74
29 2 0.05
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (27 bp):
TTAAACCTTAAAATCAAAATTCTAAAC
Found at i:29238112 original size:38 final size:39
Alignment explanation
Indices: 29238056--29238131 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 39
29238046 ACAAAAACCC
* *
29238056 TAAATCCTAAAATTGAAACCCTAAAACCT-TAAACCTTT
1 TAAACCCTAAAATCGAAACCCTAAAACCTCTAAACCTTT
*
29238094 TAAACCCTAAAATCGAAACCTTAAAACCTCTAAACCTT
1 TAAACCCTAAAATCGAAACCCTAAAACCTCTAAACCTT
29238132 AAAAAACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (39 bp):
TAAACCCTAAAATCGAAACCCTAAAACCTCTAAACCTTT
Found at i:29238113 original size:30 final size:30
Alignment explanation
Indices: 29238079--29238135 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29238069 TGAAACCCTA
*
29238079 AAACCTT-AAACCTTTTAAACCCTAAAATCG
1 AAACCTTAAAACC-TCTAAACCCTAAAATCG
*
29238109 AAACCTTAAAACCTCTAAACCTTAAAA
1 AAACCTTAAAACCTCTAAACCCTAAAA
29238136 AACTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25
Consensus pattern (30 bp):
AAACCTTAAAACCTCTAAACCCTAAAATCG
Found at i:29238122 original size:8 final size:8
Alignment explanation
Indices: 29238029--29238229 Score: 63
Period size: 8 Copynumber: 26.2 Consensus size: 8
29238019 TCAAAATCAT
29238029 AAACCTT-
1 AAACCTTA
29238036 AAACCTTA
1 AAACCTTA
*
29238044 AAA-C-AA
1 AAACCTTA
*
29238050 AAACCCTA
1 AAACCTTA
*
29238058 AATCC-TA
1 AAACCTTA
*
29238065 AAA--TTG
1 AAACCTTA
*
29238071 AAACCCTA
1 AAACCTTA
29238079 AAACCTT-
1 AAACCTTA
*
29238086 AAACCTTTT
1 AAACC-TTA
*
29238095 AAACCCTA
1 AAACCTTA
**
29238103 AAA--TCG
1 AAACCTTA
29238109 AAACCTTA
1 AAACCTTA
29238117 AAACCTCT-
1 AAACCT-TA
29238125 AAACCTTAA
1 AAACCTT-A
*
29238134 AAAAC-TA
1 AAACCTTA
**
29238141 AAAATTCTA
1 AAACCT-TA
*
29238150 AAATCTT-
1 AAACCTTA
*
29238157 AAACCTTC
1 AAACCTTA
29238165 AAA--TTA
1 AAACCTTA
29238171 AAACCTTA
1 AAACCTTA
* *
29238179 AAATCTCA
1 AAACCTTA
*
29238187 AAA-CTCA
1 AAACCTTA
**
29238194 AAAAATTAA
1 AAACCTT-A
*
29238203 AAACTTTTA
1 AAAC-CTTA
29238212 AAACCTTA
1 AAACCTTA
29238220 AAACCTTA
1 AAACCTTA
29238228 AA
1 AA
29238230 CCCAATACCA
Statistics
Matches: 145, Mismatches: 28, Indels: 41
0.68 0.13 0.19
Matches are distributed among these distances:
6 16 0.11
7 37 0.26
8 65 0.45
9 25 0.17
10 2 0.01
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.25
Consensus pattern (8 bp):
AAACCTTA
Found at i:29238142 original size:38 final size:38
Alignment explanation
Indices: 29238062--29238143 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
29238052 ACCCTAAATC
* * **
29238062 CTAAAATTGAAACCCTAAAACCTTAAACCTTTTAAACC
1 CTAAAATCGAAACCCTAAAACCTTAAACCTTTAAAAAA
*
29238100 CTAAAATCGAAACCTTAAAACCTCTAAACC-TTAAAAAA
1 CTAAAATCGAAACCCTAAAACCT-TAAACCTTTAAAAAA
29238138 CTAAAA
1 CTAAAA
29238144 ATTCTAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 32 0.84
39 6 0.16
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.23
Consensus pattern (38 bp):
CTAAAATCGAAACCCTAAAACCTTAAACCTTTAAAAAA
Found at i:29238159 original size:62 final size:62
Alignment explanation
Indices: 29238093--29238311 Score: 153
Period size: 62 Copynumber: 3.6 Consensus size: 62
29238083 CTTAAACCTT
* * * *
29238093 TTAAACCCTAAAATCGAAACCTTAAAACCTCTAAACCTTAAAAAACTAAAAA-TTCTAAAATC
1 TTAAACCCTAAAATCAAAACCTTAAAACCTC-AAAACTCAAAAAACTAAAAACTTCTAAAACC
* * * * * *
29238155 TTAAACCTTCAAATTAAAACCTTAAAATCTCAAAACTCAAAAAATTAAAAACTTTTAAAACC
1 TTAAACCCTAAAATCAAAACCTTAAAACCTCAAAACTCAAAAAACTAAAAACTTCTAAAACC
* ** * * * * * *
29238217 TTAAAACCTTAAACCCAATACCAT-AAACCTCCAAAACCCTAAAATCT-AAAAC--CTAAAACT
1 TT-AAACCCTAAAATCAAAACCTTAAAACCT-CAAAACTCAAAAAACTAAAAACTTCTAAAACC
*** *
29238277 TTAAATTTTAAAATTCAAAACC-TAAAACCCCAAAA
1 TTAAACCCTAAAA-TCAAAACCTTAAAACCTCAAAA
29238312 TTGGTACGCA
Statistics
Matches: 123, Mismatches: 29, Indels: 13
0.75 0.18 0.08
Matches are distributed among these distances:
59 14 0.11
60 19 0.15
61 17 0.14
62 46 0.37
63 27 0.22
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.24
Consensus pattern (62 bp):
TTAAACCCTAAAATCAAAACCTTAAAACCTCAAAACTCAAAAAACTAAAAACTTCTAAAACC
Found at i:29240505 original size:63 final size:63
Alignment explanation
Indices: 29240425--29240574 Score: 176
Period size: 63 Copynumber: 2.4 Consensus size: 63
29240415 TGGTGCCACT
* * *
29240425 CCCCGGCGTTCCTTTCCCTGTATTCACATGTACTCCACCGTTTCCAACATTCACAGAAGTACC
1 CCCCGGCTTTCCCTTCCCTGTATTCACATGTACTACACCGTTTCCAACATTCACAGAAGTACC
* * * * * * *
29240488 CCCCGGCTTTCCCTTCCCAGTGTTTACATTTACTACGCCTTTTCCAACATTCACAGAAGTGCC
1 CCCCGGCTTTCCCTTCCCTGTATTCACATGTACTACACCGTTTCCAACATTCACAGAAGTACC
* *
29240551 CCCAGG-TTTCCCTTTTCCTGTATT
1 CCCCGGCTTTCCC-TTCCCTGTATT
29240575 GACGTTTGCA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
62 6 0.08
63 66 0.92
ACGTcount: A:0.18, C:0.37, G:0.13, T:0.33
Consensus pattern (63 bp):
CCCCGGCTTTCCCTTCCCTGTATTCACATGTACTACACCGTTTCCAACATTCACAGAAGTACC
Found at i:29244504 original size:2 final size:2
Alignment explanation
Indices: 29244497--29244525 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29244487 GATTGTTGCT
29244497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29244526 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29245606 original size:40 final size:41
Alignment explanation
Indices: 29245548--29245642 Score: 147
Period size: 40 Copynumber: 2.3 Consensus size: 41
29245538 ATAAAAAAAA
* *
29245548 AAAAAAAACTTAATTTAATGAGCTGAGTTTGTTTTATTAG-T
1 AAAAAAAA-TAAAATTAATGAGCTGAGTTTGTTTTATTAGTT
29245589 AAAAAAAATAAAATTAATGAGCTGAGTTTGTTTTATTAGTT
1 AAAAAAAATAAAATTAATGAGCTGAGTTTGTTTTATTAGTT
*
29245630 AAAAAAAAAAAAA
1 AAAAAAAATAAAA
29245643 GACCTAAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 29 0.58
41 21 0.42
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.35
Consensus pattern (41 bp):
AAAAAAAATAAAATTAATGAGCTGAGTTTGTTTTATTAGTT
Found at i:29245788 original size:55 final size:55
Alignment explanation
Indices: 29245704--29245812 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
29245694 TCTTTAGTGG
29245704 AAAGAGTATTGTATAATAAATATGATTCGTTTTGCTTTTATTATTACTTAATTTA
1 AAAGAGTATTGTATAATAAATATGATTCGTTTTGCTTTTATTATTACTTAATTTA
29245759 AAAGAGTATTGTATAATAAATATGATTCGTTTTGCTTTTATTATTACTTAATTT
1 AAAGAGTATTGTATAATAAATATGATTCGTTTTGCTTTTATTATTACTTAATTT
29245813 TAAGTAATCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.50
Consensus pattern (55 bp):
AAAGAGTATTGTATAATAAATATGATTCGTTTTGCTTTTATTATTACTTAATTTA
Found at i:29247181 original size:2 final size:2
Alignment explanation
Indices: 29247174--29247222 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
29247164 GCTATTATTG
29247174 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
29247216 TC TC TC T
1 TC TC TC T
29247223 TTCTATTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29255298 original size:2 final size:2
Alignment explanation
Indices: 29255285--29255319 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29255275 GTCTGCTGCA
*
29255285 TC TC TA TC 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 TC TC TC TC T
29255320 TTATTTCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29262702 original size:21 final size:22
Alignment explanation
Indices: 29262673--29262729 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
29262663 ATTGATAAAG
*
29262673 TTTTAAAATTTTAATTTTAATAA
1 TTTT-AAATTTAAATTTTAATAA
*
29262696 -TTTAAATTTAAATTTTCATAA
1 TTTTAAATTTAAATTTTAATAA
*
29262717 TTTTAAATATAAA
1 TTTTAAATTTAAA
29262730 AATTATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAATTTAAATTTTAATAA
Found at i:29262703 original size:15 final size:14
Alignment explanation
Indices: 29262668--29262723 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
29262658 GATTTATTGA
29262668 TAAAGTTTTAAAATT
1 TAAA-TTTTAAAATT
*
29262683 TTAATTTTAATAATT
1 TAAATTTTAA-AATT
*
29262698 TAAA-TTTAAATTT
1 TAAATTTTAAAATT
29262711 TCATAATTTTAAA
1 T-A-AATTTTAAA
29262724 TATAAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 4 0.12
14 12 0.35
15 12 0.35
16 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (14 bp):
TAAATTTTAAAATT
Found at i:29262729 original size:22 final size:21
Alignment explanation
Indices: 29262685--29262729 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
29262675 TTAAAATTTT
*
29262685 AATTTTAATAATTTAAATTTA
1 AATTTTAATAATTTAAATATA
*
29262706 AATTTTCATAATTTTAAATATA
1 AATTTTAATAA-TTTAAATATA
29262728 AA
1 AA
29262730 AATTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTTAATAATTTAAATATA
Found at i:29271474 original size:337 final size:338
Alignment explanation
Indices: 29270859--29271534 Score: 1160
Period size: 337 Copynumber: 2.0 Consensus size: 338
29270849 GGGGGGGGGG
29270859 GGGAGAAAAGAGATTTCAATTTGGTTTTTTCTTAGAATATGTTCATTGTAAAATCAATTAGGTTT
1 GGGAGAAAAGAGATTTCAATTTGGTTTTTTCTTAGAATATGTTCATTGTAAAATCAATTAGGTTT
* * *
29270924 CAATACTTGAAAGGGGCGTTTGGTTCAAGAGAATCTACAAATTTTCTTCGAAAATCTTGATGGTA
66 CAATAATTGAAAGGGGCATTTGGTTCAAGAGAACCTACAAATTTTCTTCGAAAATCTTGATGGTA
* * *
29270989 GTTATTAGATTTTCATGTTTGATTTTAGGTAATTCGACTACAGGAGAAAGTGACAGATTCTCAAT
131 GTTATTAGATTTTCATGTTTGATTCTAGGTAATCCGACTACAGAAGAAAGTGACAGATTCTCAAT
29271054 AATACCCAAAATCTCAGAATCATAACTCACATATTCTTGTGGTATTTTAGGATTTTGGAAGGGAA
196 AATACCCAAAATCTCAGAATCATAACTCACATATTCTTGTGGTATTTTAGGATTTTGGAAGGGAA
* * *
29271119 AGTTGTATTATTTTTAAATTTGATTTGAA-CAAAAAATTTTAAAATAGTCATTATTCTTTTGAAA
261 AGTTGTATTATTTTTAAATTTGATTTGAATAAAAAAAATTGAAAATAGTCATTATTCTTTTGAAA
29271183 AGCATGTTTCGAA
326 AGCATGTTTCGAA
29271196 GGGAGAAAAGAGATTTCAATTTGGTTTTTTCTTAGAATATGTTCATTGTAAAATCAATTAGGTTT
1 GGGAGAAAAGAGATTTCAATTTGGTTTTTTCTTAGAATATGTTCATTGTAAAATCAATTAGGTTT
* *
29271261 CATTAATTGAAGGGGGCATTTGGTTCAAGAGAACCTACAAATTTTCTTCGAAAATCTTGATGGTA
66 CAATAATTGAAAGGGGCATTTGGTTCAAGAGAACCTACAAATTTTCTTCGAAAATCTTGATGGTA
*
29271326 GTTATTAGATTTTCATGTTTGATTCTAGGTAATCCGATTAC-GAAAGAAAGTGACAGATTCTCAA
131 GTTATTAGATTTTCATGTTTGATTCTAGGTAATCCGACTACAG-AAGAAAGTGACAGATTCTCAA
* * *
29271390 TAATACCTAAAATTTTAGAATCATAAACTCACATATTCTTGTGGTATTTTAGGA-TTTGGAAGGG
195 TAATACCCAAAATCTCAGAATCAT-AACTCACATATTCTTGTGGTATTTTAGGATTTTGGAAGGG
*
29271454 AAAGTTGTATTATTTTTAAATTTGATTTGAATAAAAAAAATTGAAAATAGTCGTTATTCTTTTGA
259 AAAGTTGTATTATTTTTAAATTTGATTTGAATAAAAAAAATTGAAAATAGTCATTATTCTTTTGA
*
29271519 AAAGCATGTTTTGAA
324 AAAGCATGTTTCGAA
29271534 G
1 G
29271535 TGATAACAAT
Statistics
Matches: 319, Mismatches: 17, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
336 1 0.00
337 245 0.77
338 73 0.23
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (338 bp):
GGGAGAAAAGAGATTTCAATTTGGTTTTTTCTTAGAATATGTTCATTGTAAAATCAATTAGGTTT
CAATAATTGAAAGGGGCATTTGGTTCAAGAGAACCTACAAATTTTCTTCGAAAATCTTGATGGTA
GTTATTAGATTTTCATGTTTGATTCTAGGTAATCCGACTACAGAAGAAAGTGACAGATTCTCAAT
AATACCCAAAATCTCAGAATCATAACTCACATATTCTTGTGGTATTTTAGGATTTTGGAAGGGAA
AGTTGTATTATTTTTAAATTTGATTTGAATAAAAAAAATTGAAAATAGTCATTATTCTTTTGAAA
AGCATGTTTCGAA
Found at i:29280571 original size:12 final size:12
Alignment explanation
Indices: 29280556--29280611 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
29280546 CTTTTTTTTT
29280556 AATAAGTAA-AAC
1 AATAA-TAATAAC
*
29280568 AATAATAATAAT
1 AATAATAATAAC
29280580 AATAATAATAAC
1 AATAATAATAAC
*
29280592 AGTAATAAT-AC
1 AATAATAATAAC
29280603 AATAATAAT
1 AATAATAAT
29280612 TGGGCCAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
11 13 0.33
12 26 0.67
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:29280574 original size:3 final size:3
Alignment explanation
Indices: 29280555--29280611 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
29280545 CCTTTTTTTT
* * *
29280555 TAA TAA GTAA -AA CAA TAA TAA TAA TAA TAA TAA TAA CAG TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
29280600 T-A CAA TAA TAA T
1 TAA TAA TAA TAA T
29280612 TGGGCCAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:29281137 original size:65 final size:64
Alignment explanation
Indices: 29280978--29281223 Score: 205
Period size: 65 Copynumber: 3.8 Consensus size: 64
29280968 CGTAGGTCAA
* * * * * *
29280978 AAAAATAAATTAATCTGGACTGAGTCGAGATCAAAATAAAG-GACCT-AGATTGAACCGCAAGTC
1 AAAAATAAAATGATCTGGA-TTAATCGAGATCAAAAT-GAGTGA-CTGAGATTGAACCGCGAGTC
29281041 T-
63 TC
* * * * *
29281042 GAAAATAAAATGATCTGGACTGAATCGAGATCGAAACGAGTGACTGAGATTGAATCGGCGAGTC-
1 AAAAATAAAATGATCTGGA-TTAATCGAGATCAAAATGAGTGACTGAGATTGAA-CCGCGAGTCT
29281106 C
64 C
* * * * *
29281107 AAAAATAAAATGATCTAGATTAAGCTGAGATAAAAAATAAGTGA-TCGAGATTGAACCGCGGGTC
1 AAAAATAAAATGATCTGGATTAATC-GAGAT-CAAAATGAGTGACT-GAGATTGAACCGCGAGTC
*
29281171 TG
63 TC
* *
29281173 AAAAATAAAATGATCTGGATTGAATCGAGATCTAAATGAGTGACTGGGATT
1 AAAAATAAAATGATCTGGATT-AATCGAGATCAAAATGAGTGACTGAGATT
29281224 AAACTACTGT
Statistics
Matches: 146, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
63 4 0.03
64 45 0.31
65 51 0.35
66 43 0.29
67 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (64 bp):
AAAAATAAAATGATCTGGATTAATCGAGATCAAAATGAGTGACTGAGATTGAACCGCGAGTCTC
Found at i:29281203 original size:66 final size:64
Alignment explanation
Indices: 29280978--29281216 Score: 225
Period size: 64 Copynumber: 3.7 Consensus size: 64
29280968 CGTAGGTCAA
* * * * *
29280978 AAAAATAAATTAATCTGGACTGAGTCGAGATCAAAATAAAG-GACCTAGATTGAACCGCAAGTCT
1 AAAAATAAAATGATCTGGACTGAATCGAGATCAAAAT-AAGTGA-CGAGATTGAACCGCGAGTCT
29281042 G
64 G
* ** *
29281043 -AAAATAAAATGATCTGGACTGAATCGAGATCGAAACGAGTGACTGAGATTGAATCGGCGAGTC-
1 AAAAATAAAATGATCTGGACTGAATCGAGATCAAAATAAGTGAC-GAGATTGAA-CCGCGAGTCT
*
29281106 C
64 G
* * * * *
29281107 AAAAATAAAATGATCTAGA-TTAAGCTGAGATAAAAAATAAGTGATCGAGATTGAACCGCGGGTC
1 AAAAATAAAATGATCTGGACTGAATC-GAGAT-CAAAATAAGTGA-CGAGATTGAACCGCGAGTC
29281171 TG
63 TG
* * *
29281173 AAAAATAAAATGATCTGGATTGAATCGAGATCTAAATGAGTGAC
1 AAAAATAAAATGATCTGGACTGAATCGAGATCAAAATAAGTGAC
29281217 TGGGATTAAA
Statistics
Matches: 139, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
63 3 0.02
64 46 0.33
65 45 0.32
66 40 0.29
67 5 0.04
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (64 bp):
AAAAATAAAATGATCTGGACTGAATCGAGATCAAAATAAGTGACGAGATTGAACCGCGAGTCTG
Found at i:29281473 original size:65 final size:65
Alignment explanation
Indices: 29281271--29281551 Score: 201
Period size: 65 Copynumber: 4.3 Consensus size: 65
29281261 AGCCTGAAAT
* * * * * * **
29281271 ATAAAATGATCTAGACTGAGCCAAGATCGAAACT-AATGA-TCAGGATTGAATTACGGGT-TCAA
1 ATAAAATGATCTGGATTGAGCCAAGATC-AAAATGAGTGATTGA-GATTGAACTACAAGTCT-AA
29281333 AAA
63 AAA
** * * * * * * *
29281336 ATAAAATGATCTGGATTGAATCGAGATAAAAAAATGAGTGATCGGGATTAAACTACAAGTTTGAA
1 ATAAAATGATCTGGATTGAGCCAAGAT--CAAAATGAGTGATTGAGATTGAACTACAAGTCTAAA
29281401 AA
64 AA
* * **
29281403 ATAAAATGATTTGGATTGAGCCAAGATCAAAATGAGTGATTGAGATTGAACCACGGGTCTAAAAA
1 ATAAAATGATCTGGATTGAGCCAAGATCAAAATGAGTGATTGAGATTGAACTACAAGTCTAAAAA
* * *** * * * *
29281468 ATAAAATGATCTAGACTGAGTTGAGATCGAAATGAGTGATCT-AAATTGATCTACAAGTCAAAAA
1 ATAAAATGATCTGGATTGAGCCAAGATCAAAATGAGTGAT-TGAGATTGAACTACAAGTCTAAAA
29281532 A
65 A
*
29281533 ATAAAATGATTTGGATTGA
1 ATAAAATGATCTGGATTGA
29281552 ACAAGATTAG
Statistics
Matches: 165, Mismatches: 45, Indels: 12
0.74 0.20 0.05
Matches are distributed among these distances:
65 117 0.71
66 5 0.03
67 42 0.25
68 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (65 bp):
ATAAAATGATCTGGATTGAGCCAAGATCAAAATGAGTGATTGAGATTGAACTACAAGTCTAAAAA
Found at i:29281494 original size:132 final size:130
Alignment explanation
Indices: 29281264--29281551 Score: 303
Period size: 132 Copynumber: 2.2 Consensus size: 130
29281254 AATCGAGAGC
* * * * * **
29281264 CTGAAATATAAAATGATCTAGACTGAGCCAAGATCGAAACTAATGATCAGGATTGAATTACGGGT
1 CTGAAAAATAAAATGATTTGGATTGAGCCAAGATCGAAAATAATGATCAGGATTGAACCACGGGT
* * **
29281329 TCAAAAAATAAAATGATCTGGATTGAATCGAGATAAAAAAATGAGTGATCGGGATTAAACTACAA
66 TCAAAAAATAAAATGATCTAGACTGAATCGAGAT--AAAAATGAGTGATCGAAATTAAACTACAA
29281394 GT
129 GT
* * *
29281396 TTGAAAAATAAAATGATTTGGATTGAGCCAAGATC-AAAATGAGTGAT-TGAGATTGAACCACGG
1 CTGAAAAATAAAATGATTTGGATTGAGCCAAGATCGAAAAT-AATGATCAG-GATTGAACCACGG
* * ** * * *
29281459 G-TCTAAAAAATAAAATGATCTAGACTGAGTTGAGATCGAAATGAGTGATCTAAATTGATCTACA
64 GTTC-AAAAAATAAAATGATCTAGACTGAATCGAGATAAAAATGAGTGATCGAAATTAAACTACA
29281523 AGT
128 AGT
**
29281526 CAAAAAAATAAAATGATTTGGATTGA
1 CTGAAAAATAAAATGATTTGGATTGA
29281552 ACAAGATTAG
Statistics
Matches: 129, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
130 47 0.36
131 7 0.05
132 75 0.58
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (130 bp):
CTGAAAAATAAAATGATTTGGATTGAGCCAAGATCGAAAATAATGATCAGGATTGAACCACGGGT
TCAAAAAATAAAATGATCTAGACTGAATCGAGATAAAAATGAGTGATCGAAATTAAACTACAAGT
Found at i:29287498 original size:16 final size:16
Alignment explanation
Indices: 29287456--29287500 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
29287446 CATATGCAAG
*
29287456 TGAATAAC-AAATATA
1 TGAATAACTAAATAAA
*
29287471 TG-A-AACTGAATAAA
1 TGAATAACTAAATAAA
29287485 TGAATAACTAAATAAA
1 TGAATAACTAAATAAA
29287501 ATATAAGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
13 3 0.12
14 8 0.33
15 3 0.12
16 10 0.42
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (16 bp):
TGAATAACTAAATAAA
Found at i:29288404 original size:3 final size:3
Alignment explanation
Indices: 29288396--29288421 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29288386 TTAGTATATC
29288396 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
29288422 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29288536 original size:21 final size:20
Alignment explanation
Indices: 29288495--29288593 Score: 78
Period size: 21 Copynumber: 4.9 Consensus size: 20
29288485 AAAAGAATCT
* * *
29288495 AAATAAAAATAGAACAAATA
1 AAATAAATATAAAATAAATA
*
29288515 AAATGAAATAGAAAATAAATA
1 AAAT-AAATATAAAATAAATA
* * *
29288536 AGA-AAATTTAGAA-AAATA
1 AAATAAATATAAAATAAATA
29288554 AAATAAATATAAATATAAATAAA
1 AAATAAATATAAA-ATAAAT--A
29288577 AAATAAA-ATAAAATAAA
1 AAATAAATATAAAATAAA
29288594 ACCTGCGATC
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.11
19 14 0.23
20 5 0.08
21 23 0.37
22 5 0.08
23 8 0.13
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (20 bp):
AAATAAATATAAAATAAATA
Found at i:29288539 original size:12 final size:11
Alignment explanation
Indices: 29288514--29288593 Score: 54
Period size: 12 Copynumber: 6.7 Consensus size: 11
29288504 TAGAACAAAT
*
29288514 AAAATGAAATAG
1 AAAAT-AAATAA
29288526 AAAATAAATAA
1 AAAATAAATAA
*
29288537 GAAAATTTAGAAAAA
1 -AAAA--TA-AATAA
29288552 TAAAATAAATATA
1 -AAAATAAATA-A
*
29288565 AATATAAATAA
1 AAAATAAATAA
*
29288576 AAAATAAA-AT
1 AAAATAAATAA
29288586 AAAATAAA
1 AAAATAAA
29288594 ACCTGCGATC
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
10 9 0.16
11 13 0.23
12 21 0.38
13 3 0.05
14 2 0.04
15 8 0.14
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:29288557 original size:39 final size:39
Alignment explanation
Indices: 29288504--29288580 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
29288494 TAAATAAAAA
29288504 TAGAACAAATAAAATGAAATAGAAA-ATAAATAAGAAAATT
1 TAGAACAAATAAAAT-AAATAGAAATATAAATAA-AAAATT
*
29288544 TAGAA-AAATAAAATAAATATAAATATAAATAAAAAAT
1 TAGAACAAATAAAATAAATAGAAATATAAATAAAAAAT
29288581 AAAATAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 13 0.37
39 17 0.49
40 5 0.14
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (39 bp):
TAGAACAAATAAAATAAATAGAAATATAAATAAAAAATT
Found at i:29288565 original size:6 final size:5
Alignment explanation
Indices: 29288548--29288594 Score: 58
Period size: 5 Copynumber: 8.8 Consensus size: 5
29288538 AAAATTTAGA
*
29288548 AAAAT AAAAT AAATAT AAATAT AAATAA AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAA-AT AAA-AT AAA-AT AAAAT AAAAT AAAAT AAAA
29288595 CCTGCGATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 23 0.59
6 16 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:29288591 original size:17 final size:17
Alignment explanation
Indices: 29288548--29288594 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
29288538 AAAATTTAGA
*
29288548 AAAATAAAAT-AAATAT
1 AAAATAAAATAAAAAAT
29288564 -AAATATAAATAAAAAAT
1 AAAATA-AAATAAAAAAT
29288581 AAAATAAAATAAAA
1 AAAATAAAATAAAA
29288595 CCTGCGATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 13 0.48
18 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAAAATAAAAAAT
Found at i:29290060 original size:63 final size:63
Alignment explanation
Indices: 29289775--29290066 Score: 213
Period size: 63 Copynumber: 4.7 Consensus size: 63
29289765 TGAAAAACGT
* * *
29289775 CTTAAATAAATT-T-TTTAAAAAAAATGAAATAGATTATTTAAGGTCTTTTT-GTTAAAAAATAC
1 CTTAAAT-AATTCTCTTT-AAAAAAATGAAATGGATTATTTAAGGTGTTTTTCGTTGAAAAATAC
* * * * * * * *
29289837 CTTAAATAATTCACTTTAAAAAAATGAAGGTAGATTGTTTAAGATATTTTTTGTT-AAAAATAT
1 CTTAAATAATTCTCTTTAAAAAAATGAA-ATGGATTATTTAAGGTGTTTTTCGTTGAAAAATAC
* * ** * **
29289900 CTTAAATAA-TCTCCTTTAAAAAAATG-AAGGGATTATTTAAGGCGTTTTTCAATGAGAAACGC
1 CTTAAATAATTCT-CTTTAAAAAAATGAAATGGATTATTTAAGGTGTTTTTCGTTGAAAAATAC
* * **** * * *
29289962 CTTAAATAATCCTC-TTATATTTTTTACAA-GAGATTACTTAAGGTGTTTTTCGTTGAAAAATGC
1 CTTAAATAATTCTCTTTAAAAAAATGA-AATG-GATTATTTAAGGTGTTTTTCGTTGAAAAATAC
* *
29290025 CGTAAAGAATTCTCTTTAAAAAAATGAAATGGATTATTTAAG
1 CTTAAATAATTCTCTTTAAAAAAATGAAATGGATTATTTAAG
29290067 ACGTTTTTGA
Statistics
Matches: 174, Mismatches: 44, Indels: 23
0.72 0.18 0.10
Matches are distributed among these distances:
61 25 0.14
62 36 0.21
63 103 0.59
64 10 0.06
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (63 bp):
CTTAAATAATTCTCTTTAAAAAAATGAAATGGATTATTTAAGGTGTTTTTCGTTGAAAAATAC
Found at i:29306632 original size:21 final size:23
Alignment explanation
Indices: 29306591--29306633 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
29306581 TTATGATCAA
29306591 ATAAAGTAATATAATTATTGAAT
1 ATAAAGTAATATAATTATTGAAT
*
29306614 ATAAA-TATTATAATT-TTGAA
1 ATAAAGTAATATAATTATTGAA
29306634 CAAATTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
ATAAAGTAATATAATTATTGAAT
Found at i:29307732 original size:6 final size:7
Alignment explanation
Indices: 29307715--29307739 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29307705 TTTTGAACTT
29307715 TTTTTAA
1 TTTTTAA
29307722 TTTTTAA
1 TTTTTAA
29307729 TTTTTAA
1 TTTTTAA
29307736 TTTT
1 TTTT
29307740 GTTATAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:29316419 original size:24 final size:24
Alignment explanation
Indices: 29316390--29316437 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
29316380 ATTTTTTATT
*
29316390 AATTTTTT-ATCATAATTATAATA
1 AATTTTTTAATAATAATTATAATA
29316413 AATTTTTTAATAATAATTATAATA
1 AATTTTTTAATAATAATTATAATA
29316437 A
1 A
29316438 TATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTTTTTAATAATAATTATAATA
Found at i:29316434 original size:21 final size:22
Alignment explanation
Indices: 29316385--29316434 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
29316375 CATAAATTTT
* *
29316385 TTATTAATTTTTTATCATAATTA
1 TTATAAATTTTTTA-CATAATAA
*
29316408 TAATAAATTTTTTA-ATAATAA
1 TTATAAATTTTTTACATAATAA
29316429 TTATAA
1 TTATAA
29316435 TAATATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.48
23 12 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATAAATTTTTTACATAATAA
Found at i:29327868 original size:32 final size:33
Alignment explanation
Indices: 29327827--29327891 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
29327817 TTCTTCCATT
29327827 GTTGGATGATAAATCATTT-AATACTTAGAAGC
1 GTTGGATGATAAATCATTTAAATACTTAGAAGC
*
29327859 GTTGGATGATGAATCATTTAAATACTTAGAAGC
1 GTTGGATGATAAATCATTTAAATACTTAGAAGC
29327892 TGCATGTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (33 bp):
GTTGGATGATAAATCATTTAAATACTTAGAAGC
Found at i:29334862 original size:5 final size:5
Alignment explanation
Indices: 29334852--29334890 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
29334842 TGTTTGTAGT
29334852 TTATA TTATA TTATA TTATA TTATA TATATA TATATA TT
1 TTATA TTATA TTATA TTATA TTATA T-TATA T-TATA TT
29334891 TCATCATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 22 0.67
6 11 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:29362230 original size:11 final size:11
Alignment explanation
Indices: 29362214--29362256 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
29362204 TTATATAATT
29362214 AAAAAGAAAAA
1 AAAAAGAAAAA
*
29362225 AAAAAGAAAAG
1 AAAAAGAAAAA
* *
29362236 GAAAAGCAAAA
1 AAAAAGAAAAA
*
29362247 GAAAAGAAAA
1 AAAAAGAAAA
29362257 TAATAGTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Done.